|  | SWISS-MODEL Homology Modelling Report

## Model Building Report

This document lists the results for the homology modelling project "Untitled Project" submitted to SWISS-MODEL workspace on March 29, 2023, 4:10 a.m..The submitted primary amino acid sequence is given in Table T1.

If you use any results in your research, please cite the relevant publications:

- Waterhouse, A., Bertoni, M., Bienert, S., Studer, G., Tauriello, G., Gumienny, R., Heer, F.T., de Beer, T.A.P., Rempfer, C., Bordoli, L., Lepore, R., Schwede, T. SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res. 46(W1), W296-W303 (2018).
- Bienert, S., Waterhouse, A., de Beer, T.A.P., Tauriello, G., Studer, G., Bordoli, L., Schwede, T. The SWISS-MODEL Repository - new features and functionality. Nucleic Acids Res. 45, D313-D319 (2017).
- Studer, G., Tauriello, G., Bienert, S., Biasini, M., Johner, N., Schwede, T. ProMod3 - A versatile homology modelling toolbox. PLOS Comp. Biol. 17(1), e1008667 (2021).
- Studer, G., Rempfer, C., Waterhouse, A.M., Gumienny, G., Haas, J., Schwede, T. QMEANDisCo - distance constraints applied on model quality estimation. Bioinformatics 36, 1765-1771 (2020).
- Bertoni, M., Kiefer, F., Biasini, M., Bordoli, L., Schwede, T. Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology. Scientific Reports 7 (2017).

## Results

The SWISS-MODEL template library (SMTL version 2023-03-23, PDB release 2023-03-17) was searched with for evolutionary related structures matching the target sequence in Table T1. For details on the template search, see Materials and Methods. Overall 515 templates were found (Table T2).

## Models

The following models were built (see Materials and Methods "Model Building"):

### Model #01 | File | Built with | Oligo-State | Ligands | GMQE | QMEANDisCo Global
--- | --- | --- | --- | --- | --- | ---
| PDB | ProMod3 3.2.1 | monomer | 1 x MO: MOLYBDENUM ATOM; | 0.79 | 0.80 ± 0.05

Template | Seq Identity | Oligo-state | QSQE | Found by | Method | Resolution | Seq Similarity | Range | Coverage | Description
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
7b04.1.B | 57.58 | monomer | 0.00 | HHblits | X-ray | 2.97Å | 0.48 | 28 - 1144 | 1.00 | Nitrite oxidoreductase subunit A

### Included Ligands

Ligand | Description
--- | ---
1 x MO | MOLYBDENUM ATOM

### Excluded ligands

Ligand Name.Number | Reason for Exclusion | Description
--- | --- | ---
CA.10 | Binding site not conserved. | CALCIUM ION
CA.11 | Binding site not conserved. | CALCIUM ION
F3S.4 | Binding site not conserved. | FE3-S4 CLUSTER
HEM.9 | Binding site not conserved. | PROTOPORPHYRIN IX CONTAINING FE
MD1.5 | Binding site not conserved. | PHOSPHORIC ACID 4-(2-AMINO-4-OXO-3,4,5,6,-TETRAHYDRO-PTERIDIN-6-YL)-2-HYDROXY-3,4-DIMERCAPTO-BUT-3-EN-YL ESTER GUANYLATE ESTER
MD1.6 | Binding site not conserved. | PHOSPHORIC ACID 4-(2-AMINO-4-OXO-3,4,5,6,-TETRAHYDRO-PTERIDIN-6-YL)-2-HYDROXY-3,4-DIMERCAPTO-BUT-3-EN-YL ESTER GUANYLATE ESTER
SF4.1 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.2 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.3 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.8 | Binding site not conserved. | IRON/SULFUR CLUSTER

    Target    MFLSRRQFLKVSVGTVAAVAVADKVLALTALQPVIEVGNPLGDYPDRSWERVYHDQYRYDSSFTWVCSPNDTHACRVRAF
    7b04.1.B  MKLTRRAFLQVAGATGATLTLAKNAMAFRLLKPAVVVDNPLDTYPDRRWESVYRDQYQYDRTFTYCCSPNDTHACRIRAF

    Target    VRNGVVMRVEQNYDHQTYEDLYGNRGTFAHNPRMCLKGFTFHRRVYGPYRLKGPLMRKGWKQWMDDNAPELTAETKRKYK
    7b04.1.B  VRNNVMMRVEQNYDHQNYSDLYGNKATRNWNPRMCLKGYTFHRRVYGPYRLRYPLIRKGWKRWADDGFPELTPENKTKYM

    Target    FDSRFLDDMLRVSWDTAFTYAAKAMITIATRY-SGEAGARRLREQGYAPEMIEMMKGAGTRCFKHRAGMPVLGIIGKMGN
    7b04.1.B  FDNRGNDELLRASWDEAFTYASKGIIHITKKYSGPEGAQK-LIDQGYPKEMVDRMQGAGTRTFKGRGGMGLLGVIGKYGM

    Target    TRMNGGINALLDTWIRKVSPDQAQGGRYWSNYTWHGDQNPAHPFWSGVQGSDIDLSDMRFSKLNTSWGKNFVENKMPEAH
    7b04.1.B  YRFNNC-LAIVDAHNRGVGPDQALGGRNWSNYTWHGDQAPGHPFSHGLQTSDVDMNDVRFSKLLIQTGKNLIENKMPEAH

    Target    WKLECIERGARVVVITPEYNPTAYRADYWMPLRPESDGALFLGAMKIIIDENMHDIDFLKSFTDAPILVRTDTLQYLDPR
    7b04.1.B  WVTEVMERGGKIVVITPEYSPSAQKADYWIPIRNNTDTALFLGITKILIDNKWYDADYVKKFTDFPLLIRTDTLKRVSPK

    Target    DVIADYKFPDFSKSYSGRIQSLKPEQIQRLGGMMVWDLNKKQVVPLHREQVGWHYTNSGIDAALTGTYRVKLLNGREIDA
    7b04.1.B  DIIPNYKLQDISDGPSYHIQGLKDEQREIIGDFVVWDAKSKGPKAITRDDVGETLVKKGIDPVLEGSFKLKTIDGKEIEV

    Target    MPIWQMYMVHFQDYDLDTVHQITRTPKDLIVRWARDSGTIKPAAIHNGEGTCHYFHQTANARGAAMVLIITGNVGKFGTG
    7b04.1.B  MTLLEMYKIHLRDYDIDSVVSMTNSPKDLIERLAKDIATIKPVAIHYGEGVNHYFHATLMNRSYYLPVMLTGNVGYFGSG

    Target    QHTWAGNYKAGTWTATPWSGAGLSVHTGEDPFNITLDPNAHGKEIKTRSYYYGEEVGYWNHGDTALIVNTPKYGRKVFTG
    7b04.1.B  SHTWAGNYKAGNFQASKWSGPGFYGWVAEDVFKPNLDPYASAKDLNIKGRALDEEVAYWNHSERPLIVNTPKYGRKVFTG

    Target    KTHMPTPSKFRWVVNVNVVNNAKHHYDMVRNVDPNIECLITQDIEMTSDINHADIAFAANSWMEFTYPEMTVTVSNPWVQ
    7b04.1.B  KTHMPSPTKVLWFTNVNLINNAKHVYQMLKNVNPNIEQIMSTDIEITGSIEYADFAFPANSWVEFQEFEITNSCSNPFIQ

    Target    IWK-GGIRPLYDTRNDLDTFAGVAAKLSDMTGDKRMRDYFAMVYQNRVDVYVQRMLDASSTFYGYSADVMLKSE---KGW
    7b04.1.B  IWGKTGITPVYESKDDVKILAGMASKLGELLRDKRFEDNWKFAIEGRASVYINRLLDGSTTMKGYTCEDILNGKYGEPGV

    Target    MV-MVRTYPRHPFWEETNESKPMWTRSGRYENYRIEPEAIEYGENFISHREGPEATPYLPNAIFTTNPYVRPDDYGIPIT
    7b04.1.B  AMLLFRTYPRHPFWEQVHESLPFYTPTGRLQAYNDEPEIIEYGENFIVHREGPEATPYLPNAIVSTNPYIRPDDYGIPEN

    Target    AQHHDDKTVRNIKLSWHEIKRHSNPLWEKGYQFYCVTPKTRHRVHSQWSVNDWVQIYESNFGDPYRMDKRTPGVGEHQIH
    7b04.1.B  AEYWEDRTVRNIKKSWEETKKTKNFLWEKGYHFYCVTPKSRHTVHSQWAVTDWNFIWNNNFGDPYRMDKRMPGVGEHQIH

    Target    INPQAAKDRGINDGDYVYVDGNPVDRPYRGWKPSDPYYKVARLMIRAKYNPAYPYHVTMAKHAPFVATAKSVKGHETRPD
    7b04.1.B  IHPQAARDLGIEDGDYVYVDANPADRPYEGWKPNDSFYKVSRLMLRAKYNPAYPYNCTMMKHSAWISSDKTVQAHETRP-

    Target    GRAIAIDTGYQSNFRYGAQQSFTRNWLMPMHQTDSLPGKHAVAWKFKWGYQVDHHAINTVPKECLIRITKAEDGGIGARG
    7b04.1.B  DGRALSPSGYQSSFRYGSQQSITRDWSMPMHQLDSLFHKAKIGMKFIFGFEADNHCINTVPKETLVKITKAENGGMGGKG

    Target    PWEPVRTGFTPGQENEFMIKWLKGEHIKIKV
    7b04.1.B  VWDPVKTGYTAGNENDFMKKFLNGELIKVD-

### Model #03 | File | Built with | Oligo-State | Ligands | GMQE | QMEANDisCo Global
--- | --- | --- | --- | --- | --- | ---
| PDB | ProMod3 3.2.1 | monomer | 1 x 6MO: MOLYBDENUM(VI) ION; | 0.40 | 0.49 ± 0.05

Template | Seq Identity | Oligo-state | QSQE | Found by | Method | Resolution | Seq Similarity | Range | Coverage | Description
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
3ir5.1.A | 20.97 | monomer | 0.00 | HHblits | X-ray | 2.30Å | 0.31 | 2 - 1111 | 0.81 | Respiratory nitrate reductase 1 alpha chain

### Included Ligands

Ligand | Description
--- | ---
1 x 6MO | MOLYBDENUM(VI) ION

### Excluded ligands

Ligand Name.Number | Reason for Exclusion | Description
--- | --- | ---
AGA.5 | Binding site not conserved. | (1S)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PENTANOYLOXY)METHYL]ETHYL OCTANOATE
F3S.9 | Binding site not conserved. | FE3-S4 CLUSTER
HEM.10 | Binding site not conserved. | PROTOPORPHYRIN IX CONTAINING FE
HEM.11 | Binding site not conserved. | PROTOPORPHYRIN IX CONTAINING FE
MD1.1 | Binding site not conserved. | PHOSPHORIC ACID 4-(2-AMINO-4-OXO-3,4,5,6,-TETRAHYDRO-PTERIDIN-6-YL)-2-HYDROXY-3,4-DIMERCAPTO-BUT-3-EN-YL ESTER GUANYLATE ESTER
MD1.2 | Binding site not conserved. | PHOSPHORIC ACID 4-(2-AMINO-4-OXO-3,4,5,6,-TETRAHYDRO-PTERIDIN-6-YL)-2-HYDROXY-3,4-DIMERCAPTO-BUT-3-EN-YL ESTER GUANYLATE ESTER
SF4.4 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.6 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.7 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.8 | Binding site not conserved. | IRON/SULFUR CLUSTER

    Target    MFLSRRQFLKVSVGTVAAVAVADKVLALTALQPVIEVGNPLGDYPDRSWERVYHDQYRYDSSFTWVCSPNDTHACRVRAF
    3ir5.1.A  -FLDRFRYFKQKGETFADGH--------GQL-----------LNTNRDWEDGYRQRWQHDKIVRSTCGVNCTGSCSWKIY

    Target    VRNGVVMRVEQNYDHQTYEDLYGNRGTFAHNPRMCLKGFTFHRRVYGPYRLKGPLMRKGWK-QWMDDNA----P-----E
    3ir5.1.A  VKNGLVTWETQQTDYPRT-----RPDLPNHEPRGCPRGASYSWYLYSANRLKYPMMRKRLMKMWREAKALHSDPVEAWAS

    Target    -LTAETKRKYKFDSRFLDDMLRVSWDTAFTYAAKAMITIATRYSGEAGARRLREQGYAPEMIEMMKGAGTRCF-KHRAGM
    3ir5.1.A  IIEDADKAKSFKQARGRGGFVRSSWQEVNELIAASNVYTIKNYGPDRVAGF--------------SPIPAMSMVSYASGA

    Target    PVLGIIGKMGNTRMNGGINALLDTWIRKVSPDQAQGGRYWSNYTWHGDQNPAHPFWSGVQGSDIDLSDMRFSKLNTSWGK
    3ir5.1.A  RYLS---LIGGT--------------------------CLSFYDWYCDLPPASPQTWGEQTDVPESADWYNSSYIIAWGS

    Target    NFVENKMPEAHWKLECIERGARVVVITPEYNPTAYRADYWMPLRPESDGALFLGAMKIIIDENM------HDIDFLKSFT
    3ir5.1.A  NVPQTRTPDAHFFTEVRYKGTKTVAVTPDYAEIAKLCDLWLAPKQGTDAAMALAMGHVMLREFHLDNPSQYFTDYVRRYT

    Target    DAPILVRTD-------TLQYLDPRDVIADYKFPDFSKSYSGRIQSLKPEQIQRLGGMMVWDLNKKQVVPLHREQV-----
    3ir5.1.A  DMPMLVMLEERDGYYAAGRMLRAADLVDALGQEN-----------------NPEWKTVAFNT-NGEMVAPNGSIGFRWGE

    Target    --GWHYT----------------------------------------NSGIDAALTG---TYRVKLLNGREIDAMPIWQM
    3ir5.1.A  KGKWNLEQRDGKTGEETELQLSLLGSQDEIAEVGFPYFGGDGTEHFNKVELENVLLHKLPVKRLQLADGSTALVTTVYDL

    Target    YM------------------VHFQDYDLDTVHQITRTPKDLIVRWARDSGTI-----KPAAIHNGEGTCHYFHQTANARG
    3ir5.1.A  TLANYGLERGLNDVNCATSYDDVKAYTPAWAEQITGVSRSQIIRIAREFADNADKTHGRSMIIVGAGLNHWYHLDMNYRG

    Target    AAMVLIITGNVGKFGTGQHTWAGNYKAGTWTATPWSGAGLSV----HT---GEDPF--------------N-ITLDPNAH
    3ir5.1.A  LINMLIFCGCVGQSGGGWAHYVGQEKLRPQ--TGWQPLAFALDWQRPARHMNSTSYFYNHSSQWRYETVTAEELLSPMAD

    Target    GKEIKTR---SYYYGEEVGYWNHG----DTALI---------VNTPKY-GRKVFTGKT--------HMPTPSKFRWVVNV
    3ir5.1.A  KSRYTGHLIDFNVRAERMGWLPSAPQLGTNPLTIAGEAEKAGMNPVDYTVKSLKEGSIRFAAEQPENGKNHPRNLFIWRS

    Target    NVVNNAKHHYD-MV------------------------------RNVDPNIECLITQDIEMTSDINHADIAFAANSWMEF
    3ir5.1.A  NLLGSSGKGHEFMLKYLLGTEHGIQGKDLGQQGGVKPEEVDWQDNGLEGKLDLVVTLDFRLSSTCLYSDIILPTATWYEK

    Target    TYPEMTVTVSNPWVQIWKGGIRPLYDTRNDLDTFAGVAAKLSDMTGD----K--------------------RMRDYFAM
    3ir5.1.A  DDM--NTSDMHPFIHPLSAAVDPAWEAKSDWEIYKAIAKKFSEVCVGHLGKETDIVTLPIQHDSAAELAQPLDVKDWKKG

    Target    V------------------YQNR---------------------------VDVYVQR-----------------------
    3ir5.1.A  ECDLIPGKTAPHIMVVERDYPATYERFTSIGPLMEKIGNGGKGIAWNTQSEMDLLRKLNYTKAEGPAKGQPMLNTAIDAA

    Target    --MLDASSTFYGY----SADVMLKS------------EKGWMVMVR--------------------TYPRHPFWEETNES
    3ir5.1.A  EMILTLAPETNGQVAVKAWAALSEFTGRDHTHLALNKEDEKIRFRDIQAQPRKIISSPTWSGLEDEHVSYNAGYTNVHEL

    Target    KPMWTRSGRYENYRIEPEAIEYGENFISHREGPEATPYLPNAIFTTNPYVRPDDYGIPITAQHHDDKTVRNIKLSWHEIK
    3ir5.1.A  IPWRTLSGRQQLYQDHQWMRDFGESLLVYRPPIDTRSV-----------------------------------KEVIGQ-

    Target    RHSNPLWEKGYQFYCVTPKTRHRVHSQWSVNDWVQIYESNFGDPYRMDKRTPGVGEHQIHINPQAAKDRGINDGDYVYVD
    3ir5.1.A  ---KSNGNQEKALNFLTPHQKWGIHSTYSDNLLMLTLG---------------RGGPVVWLSEADAKDLGIADNDWIEVF

    Target    GNPVDRPYRGWKPSDPYYKVARLMIRAKYNPAYPYHVTMAKHAPFVATAKSVKGHETRPDGRAIAIDTGYQSNFRYGAQQ
    3ir5.1.A  NS-----------------NGALTARAVVSQRVPAGMTMMYHAQERIVNL--------P--GSE------ITQQRGGIHN

    Target    SFTRNWLMPMHQTDSLPGKHAVAWKFKWGYQVDHHAINTVPKECLIRITKAEDGGIGARGPWEPVRTGFTPGQENEFMIK
    3ir5.1.A  SVTRITPKPTHMIGGYAHLA---------YGFNYYGTVGSNRDEFVVVRKMKNIDWL-----------------------

    Target    WLKGEHIKIKV
    3ir5.1.A  -----------

### Model #02 | File | Built with | Oligo-State | Ligands | GMQE | QMEANDisCo Global
--- | --- | --- | --- | --- | --- | ---
| PDB | ProMod3 3.2.1 | monomer (matching prediction) | None | 0.37 | 0.48 ± 0.05

Template | Seq Identity | Oligo-state | QSQE | Found by | Method | Resolution | Seq Similarity | Range | Coverage | Description
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
1r27.4.A | 20.78 | homo-dimer | 0.25 | HHblits | X-ray | 2.00Å | 0.31 | 47 - 1111 | 0.81 | Respiratory nitrate reductase 1 alpha chain

### Excluded ligands

Ligand Name.Number | Reason for Exclusion | Description
--- | --- | ---
F3S.5 | Binding site not conserved. | FE3-S4 CLUSTER
F3S.13 | Binding site not conserved. | FE3-S4 CLUSTER
F3S.21 | Binding site not conserved. | FE3-S4 CLUSTER
F3S.29 | Binding site not conserved. | FE3-S4 CLUSTER
MGD.3 | Binding site not conserved. | 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
MGD.4 | Binding site not conserved. | 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
MGD.11 | Binding site not conserved. | 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
MGD.12 | Binding site not conserved. | 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
MGD.19 | Binding site not conserved. | 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
MGD.20 | Binding site not conserved. | 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
MGD.27 | Binding site not conserved. | 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
MGD.28 | Binding site not conserved. | 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
MO.1 | Not in contact with model. | MOLYBDENUM ATOM
MO.9 | Binding site not conserved. | MOLYBDENUM ATOM
MO.17 | Binding site not conserved. | MOLYBDENUM ATOM
MO.25 | Binding site not conserved. | MOLYBDENUM ATOM
SF4.2 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.6 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.7 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.8 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.10 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.14 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.15 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.16 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.18 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.22 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.23 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.24 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.26 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.30 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.31 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.32 | Binding site not conserved. | IRON/SULFUR CLUSTER

    Target    MFLSRRQFLKVSVGTVAAVAVADKVLALTALQPVIEVGNPLGDYPDRSWERVYHDQYRYDSSFTWVCSPNDTHACRVRAF
    1r27.4.A  -FLDRFRYFKQKGETFADGHG--------QL-----------LNTNRDWEDGYRQRWQHDKIVRSTHGVNCTGSCSWKIY

    Target    VRNGVVMRVEQNYDHQTYEDLYGNRGTFAHNPRMCLKGFTFHRRVYGPYRLKGPLMRKGWK-QWMDDN----APEL----
    1r27.4.A  VKNGLVTWETQQTDYPRT-----RPDLPNHEPRGCPRGASYSWYLYSANRLKYPMMRKRLMKMWREAKALHSDPVEAWAS

    Target    --TAETKRKYKFDSRFLDDMLRVSWDTAFTYAAKAMITIATRYSGEAGARRLREQGYAPEMIEMMKGAGTRCF-KHRAGM
    1r27.4.A  IIEDADKAKSFKQARGRGGFVRSSWQEVNELIAASNVYTIKNYGPDRVAGFS--------------PIPAMSMVSYASGA

    Target    PVLGIIGKMGNTRMNGGINALLDTWIRKVSPDQAQGGRYWSNYTWHGDQNPAHPFWSGVQGSDIDLSDMRFSKLNTSWGK
    1r27.4.A  RYL---SLIGGT--------------------------CLSFYDWYCDLPPASPQTWGEQTDVPESADWYNSSYIIAWGS

    Target    NFVENKMPEAHWKLECIERGARVVVITPEYNPTAYRADYWMPLRPESDGALFLGAMKIIIDENM------HDIDFLKSFT
    1r27.4.A  NVPQTRTPDAHFFTEVRYKGTKTVAVTPDYAEIAKLCDLWLAPKQGTDAAMALAMGHVMLREFHLDNPSQYFTDYVRRYT

    Target    DAPILVRTDT-------LQYLDPRDVIADYKFPDFSKSYSGRIQSLKPEQIQRLGGMMVWDLNKKQVVPLHREQV-----
    1r27.4.A  DMPMLVMLEERDGYYAAGRMLRAADLVDALGQEN-----------------NPEWKTVAFNT-NGEMVAPNGSIGFRWGE

    Target    --GWHYTN----------------SGI-------D-------------AALT-------GTYRVKLLNGREIDAMPIWQM
    1r27.4.A  KGKWNLEQRDGKTGEETELQLSLLGSQDEIAEVGFPYFGGDGTEHFNKVELENVLLHKLPVKRLQLADGSTALVTTVYDL

    Target    YM------------------VHFQDYDLDTVHQITRTPKDLIVRWARDSGTI-----KPAAIHNGEGTCHYFHQTANARG
    1r27.4.A  TLANYGLERGLNDVNCATSYDDVKAYTPAWAEQITGVSRSQIIRIAREFADNADKTHGRSMIIVGAGLNHWYHLDMNYRG

    Target    AAMVLIITGNVGKFGTGQHTWAGNYKA-GTWTATPWSGAGLSV----HT---GEDPF--------------N-ITLDPNA
    1r27.4.A  LINMLIFCGCVGQSGGGWAHYVGQEKLRPQT---GWQPLAFALDWQRPARHMNSTSYFYNHSSQWRYETVTAEELLSPMA

    Target    HGKEIKTR---SYYYGEEVGYWNH----GDTALI---------VNTPKYG-RKVFTGKT--------HMPTPSKFRWVVN
    1r27.4.A  DKSRYTGHLIDFNVRAERMGWLPSAPQLGTNPLTIAGEAEKAGMNPVDYTVKSLKEGSIRFAAEQPENGKNHPRNLFIWR

    Target    VNVVNNAKHHYD-MV------------------------------RNVDPNIECLITQDIEMTSDINHADIAFAANSWME
    1r27.4.A  SNLLGSSGKGHEFMLKYLLGTEHGIQGKDLGQQGGVKPEEVDWQDNGLEGKLDLVVTLDFRLSSTCLYSDIILPTATWYE

    Target    FTYPEMTVTVSNPWVQIWKGGIRPLYDTRNDLDTFAGVAAKLSDMTGD----K--------------------RMRDYFA
    1r27.4.A  KDDM--NTSDMHPFIHPLSAAVDPAWEAKSDWEIYKAIAKKFSEVCVGHLGKETDIVTLPIQHDSAAELAQPLDVKDWKK

    Target    MV------------------YQN---------------------------RVDVYVQR----------------------
    1r27.4.A  GECDLIPGKTAPHIMVVERDYPATYERFTSIGPLMEKIGNGGKGIAWNTQSEMDLLRKLNYTKAEGPAKGQPMLNTAIDA

    Target    ---MLDASSTFYGY----SADVMLKSE------------KGWMVMV--------------------RTYPRHPFWEETNE
    1r27.4.A  AEMILTLAPETNGQVAVKAWAALSEFTGRDHTHLALNKEDEKIRFRDIQAQPRKIISSPTWSGLEDEHVSYNAGYTNVHE

    Target    SKPMWTRSGRYENYRIEPEAIEYGENFISHREGPEATPYLPNAIFTTNPYVRPDDYGIPITAQHHDDKTVRNIKLSWHEI
    1r27.4.A  LIPWRTLSGRQQLYQDHQWMRDFGESLLVYRPPIDTRSV-------------KEVIG-----------------------

    Target    KRHSNPLWEKGYQFYCVTPKTRHRVHSQWSVNDWVQIYESNFGDPYRMDKRTPGVGEHQIHINPQAAKDRGINDGDYVYV
    1r27.4.A  ---QKSNGNQEKALNFLTPHQKWGIHSTYSDNLLMLTLG---------------RGGPVVWLSEADAKDLGIADNDWIEV

    Target    DGNPVDRPYRGWKPSDPYYKVARLMIRAKYNPAYPYHVTMAKHAPFVATAKSVKGHETRPDGRAIAIDTGYQSNFRYGAQ
    1r27.4.A  FNS-----------------NGALTARAVVSQRVPAGMTMMYHAQERIVNL--------P--------GSEITQQRGGIH

    Target    QSFTRNWLMPMHQTDSLPGKHAVAWKFKWGYQVDHHAINTVPKECLIRITKAEDGGIGARGPWEPVRTGFTPGQENEFMI
    1r27.4.A  NSVTRITPKPTHMIGGYAHLA---------YGFNYYGTVGSNRDEFVVVRKMKNIDWL----------------------

    Target    KWLKGEHIKIKV
    1r27.4.A  ------------

### Model #04 | File | Built with | Oligo-State | Ligands | GMQE | QMEANDisCo Global
--- | --- | --- | --- | --- | --- | ---
| PDB | ProMod3 3.2.1 | monomer | None | 0.32 | 0.48 ± 0.05

Template | Seq Identity | Oligo-state | QSQE | Found by | Method | Resolution | Seq Similarity | Range | Coverage | Description
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
6sdv.1.A | 20.13 | monomer | 0.00 | HHblits | X-ray | 1.90Å | 0.30 | 42 - 747 | 0.53 | Formate dehydrogenase, alpha subunit, selenocysteine-containing,Formate dehydrogenase, alpha subunit, selenocysteine-containing,W-formate dehydrogenase - alpha subunit

### Excluded ligands

Ligand Name.Number | Reason for Exclusion | Description
--- | --- | ---
GOL.6 | Not biologically relevant. | GLYCEROL
GOL.7 | Not biologically relevant. | GLYCEROL
GOL.8 | Not biologically relevant. | GLYCEROL
GOL.9 | Not biologically relevant. | GLYCEROL
GOL.10 | Not biologically relevant. | GLYCEROL
GOL.11 | Not biologically relevant. | GLYCEROL
GOL.12 | Not biologically relevant. | GLYCEROL
GOL.13 | Not biologically relevant. | GLYCEROL
GOL.14 | Not biologically relevant. | GLYCEROL
GOL.15 | Not biologically relevant. | GLYCEROL
H2S.5 | Binding site not conserved. | HYDROSULFURIC ACID
MGD.1 | Binding site not conserved. | 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
MGD.2 | Binding site not conserved. | 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
NO3.16 | Not biologically relevant. | NITRATE ION
NO3.17 | Not biologically relevant. | NITRATE ION
PEG.18 | Not biologically relevant. | DI(HYDROXYETHYL)ETHER
SF4.3 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.19 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.20 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.21 | Binding site not conserved. | IRON/SULFUR CLUSTER
W.4 | Not in contact with model. | TUNGSTEN ION

    Target    MFLSRRQFLKVSVGTVAAVAVADKVLALTALQPVIEVGNPLGDYPDRSWERVYHDQYRYDSSFTWVCSPNDTHACRVRAF
    6sdv.1.A  MTVTRRHFLKLSAGAAVAGAFTGLGLSL---APTVA---RAEL--QK---------LQWAKQTTSICC-YCAVGCGLIVH

    Target    VR---NGVVMRVEQNYDHQTYEDLYGNRGTFAHNPRMCLKGFTFHRRVYGPYRLKGPLMRKGWKQWMDDNAPELTAETKR
    6sdv.1.A  TAKDGQGRAVNVEGDPDHPI------------NEGSLCPKGASIFQLGENDQRGTQPLYRAPFS----------------

    Target    KYKFDSRFLDDMLRVSWDTAFTYAAKAMITIATRYSGEAGARRLREQGYAPEMIEMMKGAGTRCFKHRAGMPVLGIIGKM
    6sdv.1.A  ---------DTWKPVTWDFALTEIAKRIKKTRDASFTEKNAAGDLV--NRTEAIASFGSAAM------------------

    Target    GNTRMNGGINALLDTWIRKVSPD-QAQGGRYWSNYTWHGDQNPAHPFWSGVQGSDIDLSDMRFSKLNTSWGKNFVENKMP
    6sdv.1.A  -----DNEECWAYGNILRSLGLVYIEHQARIU-----HSPTVPALAESFGRGAMTNHWNDLANSDCILIMGSNAAENHPI

    Target    EAHWKLECIERGARVVVITPEYNPTAYRADYWMPLRPESDGALFLGAMKIIIDENMHDIDFLKSFTDAPILVRTDTLQYL
    6sdv.1.A  AFKWVLRAKDKGATLIHVDPRFTRTSARCDVYAPIRSGADIPFLGGLIKYILDNKLYFTDYVREYTNASLIVGEKFSF--

    Target    DPRDVIADYKFPDFSKSYSGRIQSLKPEQIQRLGGMMVWDLNKKQVVPLHREQVGWHYTNSGIDAALTGTYRVKLLNGRE
    6sdv.1.A  --KDG----LFSGYD----A--------------ANKKYDKSM----------WAFELDA-------NG---VPKRDPAL

    Target    IDAMPIWQMYMVHFQDYDLDTVHQITRTPKDLIVRWARDSGTI----KPAAIHNGEGTCHYFHQTANARGAAMVLIITGN
    6sdv.1.A  KHPRCVINLLKKHYERYNLDKVAAITGTSKEQLQQVYKAYAATGKPDKAGTIMYAMGWTQHSVGVQNIRAMAMIQLLLGN

    Target    VGKFGTGQHTWAGNYK-AGTWTATPWSGAGLSVHTGEDPFNIT-------LDPNAHGKEIKTRSYYYGEEVGYW------
    6sdv.1.A  IGVAGGGVNALRGESNVQGSTDQ----GLLAHIWPGYNPVPNSKAATLELYNAATPQSKDPMSVNWWQNRPKYVASYLKA

    Target    --NHGDT---ALIVN---T-----PKYGRKVFTGKTHMPTPSKFRWVVNVNVVNNAKHHYDMVRNVDPNIECLITQDIEM
    6sdv.1.A  LYPDEEPAAAYDYLPRIDAGRKLTDYFWLNIFE--KMDKGEFKGLFAWGMNPACGGANA-NKNRKAMGKLEWLVNVNLFE

    Target    TSDINH--------AD-----IAFAANSWMEFTYPEMTVTVSNPWVQIWKGGIRPLYDTRNDLDTFAGVAAKLSDMTGDK
    6sdv.1.A  NETSSFWKGPGMNPAEIGTEVFFLPCCVSIEKEGS---VANSGRWMQWRYRGPKPYAETKPDGDIMLDMFKKVRE-----

    Target    RMRDYFAMVYQNRVDVYVQRMLDASSTFYGYSADVMLKSEKGWMVMVRTYPRHPFWEETNESKPMWTRSGRYENYRIEPE
    6sdv.1.A  --------------------------------------------------------------------------------

    Target    AIEYGENFISHREGPEATPYLPNAIFTTNPYVRPDDYGIPITAQHHDDKTVRNIKLSWHEIKRHSNPLWEKGYQFYCVTP
    6sdv.1.A  --------------------------------------------------------------------------------

    Target    KTRHRVHSQWSVNDWVQIYESNFGDPYRMDKRTPGVGEHQIHINPQAAKDRGINDGDYVYVDGNPVDRPYRGWKPSDPYY
    6sdv.1.A  --------------------------------------------------------------------------------

    Target    KVARLMIRAKYNPAYPYHVTMAKHAPFVATAKSVKGHETRPDGRAIAIDTGYQSNFRYGAQQSFTRNWLMPMHQTDSLPG
    6sdv.1.A  --------------------------------------------------------------------------------

    Target    KHAVAWKFKWGYQVDHHAINTVPKECLIRITKAEDGGIGARGPWEPVRTGFTPGQENEFMIKWLKGEHIKIKV
    6sdv.1.A  -------------------------------------------------------------------------

### Model #05 | File | Built with | Oligo-State | Ligands | GMQE | QMEANDisCo Global
--- | --- | --- | --- | --- | --- | ---
| PDB | ProMod3 3.2.1 | monomer (matching prediction) | 1 x MO: MOLYBDENUM ATOM; | 0.21 | 0.44 ± 0.05

Template | Seq Identity | Oligo-state | QSQE | Found by | Method | Resolution | Seq Similarity | Range | Coverage | Description
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
1r27.4.A | 27.20 | homo-dimer | 0.07 | BLAST | X-ray | 2.00Å | 0.34 | 47 - 639 | 0.47 | Respiratory nitrate reductase 1 alpha chain

### Included Ligands

Ligand | Description
--- | ---
1 x MO | MOLYBDENUM ATOM

### Excluded ligands

Ligand Name.Number | Reason for Exclusion | Description
--- | --- | ---
F3S.5 | Binding site not conserved. | FE3-S4 CLUSTER
F3S.13 | Binding site not conserved. | FE3-S4 CLUSTER
F3S.21 | Binding site not conserved. | FE3-S4 CLUSTER
F3S.29 | Binding site not conserved. | FE3-S4 CLUSTER
MGD.3 | Binding site not conserved. | 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
MGD.4 | Binding site not conserved. | 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
MGD.11 | Binding site not conserved. | 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
MGD.12 | Binding site not conserved. | 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
MGD.19 | Binding site not conserved. | 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
MGD.20 | Binding site not conserved. | 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
MGD.27 | Binding site not conserved. | 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
MGD.28 | Binding site not conserved. | 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
MO.9 | Binding site not conserved. | MOLYBDENUM ATOM
MO.17 | Binding site not conserved. | MOLYBDENUM ATOM
MO.25 | Binding site not conserved. | MOLYBDENUM ATOM
SF4.2 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.6 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.7 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.8 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.10 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.14 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.15 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.16 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.18 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.22 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.23 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.24 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.26 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.30 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.31 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.32 | Binding site not conserved. | IRON/SULFUR CLUSTER

    Target    MFLSRRQFLKVSVGTVAAVAVADKVLALTALQPVIEVGNPLGDYPDRSWERVYHDQYRYDSSFTWVCSPNDTHACRVRAF
    1r27.4.A  ---------------------------------------------NRDWEDGYRQRWQHDKIVRSTHGVNCTGSCSWKIY

    Target    VRNGVVMRVEQNYDH-QTYEDLYGNRGTFAHNPRMCLKGFTFHRRVYGPYRLKGPLMRKGW-KQWMDDNA---------P
    1r27.4.A  VKNGLVTWETQQTDYPRTRPDLPN------HEPRGCPRGASYSWYLYSANRLKYPMMRKRLMKMWREAKALHSDPVEAWA

    Target    ELTAETKRKYKF-DSRFLDDMLRVSWDTAFTYAAKAMITIATRYSGEAGARRLREQGYAPEMIEMMKGAGTRCFKHRAGM
    1r27.4.A  SIIEDADKAKSFKQARGRGGFVRSSWQEVNELIAASNVYTIKNYGPD------RVAGFSP-------------------I

    Target    PVLGIIGKMGNTRMNGGINALLDTWIRKVSPDQAQGGRYWSNYTWHGDQNPAHPFWSGVQGSDIDLSDMRFSKLNTSWGK
    1r27.4.A  PAMSMVSYASGARYLSLI-----------------GGTCLSFYDWYCDLPPASPQTWGEQTDVPESADWYNSSYIIAWGS

    Target    NFVENKMPEAHWKLECIERGARVVVITPEYNPTAYRADYWMPLRPESDGALFLGAMKIIIDENMHD------IDFLKSFT
    1r27.4.A  NVPQTRTPDAHFFTEVRYKGTKTVAVTPDYAEIAKLCDLWLAPKQGTDAAMALAMGHVMLREFHLDNPSQYFTDYVRRYT

    Target    DAPILVRTD----------TLQYLDPRDVIADYKFPDFSK---SYSGRIQSLKPEQIQRLGGMMVWDLNKK---------
    1r27.4.A  DMPMLVMLEERDGYYAAGRMLRAADLVDALGQENNPEWKTVAFNTNGEMVAPNGSIGFRWGEKGKWNLEQRDGKTGEETE

    Target    -QVVPLHRE----QVGW---------HYTNSGIDAALTGTYRVKLLNGREIDAMPIWQMYMVHFQDYDLDT---------
    1r27.4.A  LQLSLLGSQDEIAEVGFPYFGGDGTEHFNKVELENVLLHKLPVKRLQLADGSTALVTTVYDLTLANYGLERGLNDVNCAT

    Target    ------------VHQITRTPKDLIVRWARD-----SGTIKPAAIHNGEGTCHYFHQTANARGAAMVLIITGNVGKFGTGQ
    1r27.4.A  SYDDVKAYTPAWAEQITGVSRSQIIRIAREFADNADKTHGRSMIIVGAGLNHWYHLDMNYRGLINMLIFCGCVGQSGGGW

    Target    HTWAGNYKAGTWTATPWSGAGLSVHTGEDPFNITLDPNAHGKEIKTRSYYYGEEVGYWNHGDTALIVNTPKYGRKVFTGK
    1r27.4.A  AHYVGQEK-------------LRPQTGWQPLAFALDWQRPARHMNSTSYFYNHSSQWRYETVTAEELLSPMADKSRYTG-

    Target    THMPTPSKFRWVVNVNVVNNAKHHYDMVRNVDPNIECLITQDIEMTSDINHADIAFAANSWMEFTYPEMTVTVSNPWVQI
    1r27.4.A  --------------------------------------------------------------------------------

    Target    WKGGIRPLYDTRNDLDTFAGVAAKLSDMTGDKRMRDYFAMVYQNRVDVYVQRMLDASSTFYGYSADVMLKSEKGWMVMVR
    1r27.4.A  --------------------------------------------------------------------------------

    Target    TYPRHPFWEETNESKPMWTRSGRYENYRIEPEAIEYGENFISHREGPEATPYLPNAIFTTNPYVRPDDYGIPITAQHHDD
    1r27.4.A  --------------------------------------------------------------------------------

    Target    KTVRNIKLSWHEIKRHSNPLWEKGYQFYCVTPKTRHRVHSQWSVNDWVQIYESNFGDPYRMDKRTPGVGEHQIHINPQAA
    1r27.4.A  --------------------------------------------------------------------------------

    Target    KDRGINDGDYVYVDGNPVDRPYRGWKPSDPYYKVARLMIRAKYNPAYPYHVTMAKHAPFVATAKSVKGHETRPDGRAIAI
    1r27.4.A  --------------------------------------------------------------------------------

    Target    DTGYQSNFRYGAQQSFTRNWLMPMHQTDSLPGKHAVAWKFKWGYQVDHHAINTVPKECLIRITKAEDGGIGARGPWEPVR
    1r27.4.A  --------------------------------------------------------------------------------

    Target    TGFTPGQENEFMIKWLKGEHIKIKV
    1r27.4.A  -------------------------

## Materials and Methods

## Template Search

Template search with has been performed against the SWISS-MODEL template library (SMTL, last update: 2023-03-23, last included PDB release: 2023-03-17).

## Template Selection

For each identified template, the template's quality has been predicted from features of the target-template alignment. The templates with the highest quality have then been selected for model building.

## Model Building

Models are built based on the target-template alignment using ProMod3 (Studer et al.). Coordinates which are conserved between the target and the template are copied from the template to the model. Insertions and deletions are remodelled using a fragment library. Side chains are then rebuilt. Finally, the geometry of the resulting model is regularized by using a force field.

## Model Quality Estimation

The global and per-residue model quality has been assessed using the QMEAN scoring function (Studer et al.).

## Ligand Modelling

Ligands present in the template structure are transferred by homology to the model when the following criteria are met: (a) The ligands are annotated as biologically relevant in the template library, (b) the ligand is in contact with the model, (c) the ligand is not clashing with the protein, (d) the residues in contact with the ligand are conserved between the target and the template. If any of these four criteria is not satisfied, a certain ligand will not be included in the model. The model summary includes information on why and which ligand has not been included.

## Oligomeric State Conservation

The quaternary structure annotation of the template is used to model the target sequence in its oligomeric form. The method (Bertoni et al.) is based on a supervised machine learning algorithm, Support Vector Machines (SVM), which combines interface conservation, structural clustering, and other template features to provide a quaternary structure quality estimate (QSQE). The QSQE score is a number between 0 and 1, reflecting the expected accuracy of the interchain contacts for a model built based a given alignment and template. Higher numbers indicate higher reliability. This complements the GMQE score which estimates the accuracy of the tertiary structure of the resulting model.

## References

- BLAST
  Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., Madden, T.L. BLAST+: architecture and applications. BMC Bioinformatics 10, 421-430 (2009).
- HHblits
  Steinegger, M., Meier, M., Mirdita, M., Vöhringer, H., Haunsberger, S. J., Söding, J. HH-suite3 for fast remote homology detection and deep protein annotation. BMC Bioinformatics 20, 473 (2019).

## Table T1:

Primary amino acid sequence for which templates were searched and models were built.

MFLSRRQFLKVSVGTVAAVAVADKVLALTALQPVIEVGNPLGDYPDRSWERVYHDQYRYDSSFTWVCSPNDTHACRVRAFVRNGVVMRVEQNYDHQTYED
LYGNRGTFAHNPRMCLKGFTFHRRVYGPYRLKGPLMRKGWKQWMDDNAPELTAETKRKYKFDSRFLDDMLRVSWDTAFTYAAKAMITIATRYSGEAGARR
LREQGYAPEMIEMMKGAGTRCFKHRAGMPVLGIIGKMGNTRMNGGINALLDTWIRKVSPDQAQGGRYWSNYTWHGDQNPAHPFWSGVQGSDIDLSDMRFS
KLNTSWGKNFVENKMPEAHWKLECIERGARVVVITPEYNPTAYRADYWMPLRPESDGALFLGAMKIIIDENMHDIDFLKSFTDAPILVRTDTLQYLDPRD
VIADYKFPDFSKSYSGRIQSLKPEQIQRLGGMMVWDLNKKQVVPLHREQVGWHYTNSGIDAALTGTYRVKLLNGREIDAMPIWQMYMVHFQDYDLDTVHQ
ITRTPKDLIVRWARDSGTIKPAAIHNGEGTCHYFHQTANARGAAMVLIITGNVGKFGTGQHTWAGNYKAGTWTATPWSGAGLSVHTGEDPFNITLDPNAH
GKEIKTRSYYYGEEVGYWNHGDTALIVNTPKYGRKVFTGKTHMPTPSKFRWVVNVNVVNNAKHHYDMVRNVDPNIECLITQDIEMTSDINHADIAFAANS
WMEFTYPEMTVTVSNPWVQIWKGGIRPLYDTRNDLDTFAGVAAKLSDMTGDKRMRDYFAMVYQNRVDVYVQRMLDASSTFYGYSADVMLKSEKGWMVMVR
TYPRHPFWEETNESKPMWTRSGRYENYRIEPEAIEYGENFISHREGPEATPYLPNAIFTTNPYVRPDDYGIPITAQHHDDKTVRNIKLSWHEIKRHSNPL
WEKGYQFYCVTPKTRHRVHSQWSVNDWVQIYESNFGDPYRMDKRTPGVGEHQIHINPQAAKDRGINDGDYVYVDGNPVDRPYRGWKPSDPYYKVARLMIR
AKYNPAYPYHVTMAKHAPFVATAKSVKGHETRPDGRAIAIDTGYQSNFRYGAQQSFTRNWLMPMHQTDSLPGKHAVAWKFKWGYQVDHHAINTVPKECLI
RITKAEDGGIGARGPWEPVRTGFTPGQENEFMIKWLKGEHIKIKV

## Table T2:

Template | Seq Identity | Oligo-state | QSQE | Found by | Method | Resolution | Seq Similarity | Coverage | Description
--- | --- | --- | --- | --- | --- | --- | --- | --- | ---
7b04.1.B | 57.58 | monomer | - | HHblits | X-ray | 2.97Å | 0.48 | 1.00 | Nitrite oxidoreductase subunit A
7b04.1.B | 58.37 | monomer | - | BLAST | X-ray | 2.97Å | 0.49 | 1.00 | Nitrite oxidoreductase subunit A
7b04.2.B | 58.37 | monomer | - | BLAST | X-ray | 2.97Å | 0.49 | 1.00 | Nitrite oxidoreductase subunit A
7b04.2.B | 57.58 | monomer | - | HHblits | X-ray | 2.97Å | 0.48 | 1.00 | Nitrite oxidoreductase subunit A
1r27.4.A | 20.78 | homo-dimer | 0.25 | HHblits | X-ray | 2.00Å | 0.31 | 0.81 | Respiratory nitrate reductase 1 alpha chain
3ir5.1.A | 20.97 | monomer | - | HHblits | X-ray | 2.30Å | 0.31 | 0.81 | Respiratory nitrate reductase 1 alpha chain
3egw.1.A | 20.85 | homo-dimer | 0.17 | HHblits | X-ray | 1.90Å | 0.31 | 0.78 | Respiratory nitrate reductase 1 alpha chain
3ir7.1.A | 20.86 | monomer | - | HHblits | X-ray | 2.50Å | 0.31 | 0.81 | Respiratory nitrate reductase 1 alpha chain
1q16.1.A | 20.78 | monomer | - | HHblits | X-ray | 1.90Å | 0.31 | 0.81 | Respiratory nitrate reductase 1 alpha chain
3ir6.1.A | 20.85 | monomer | - | HHblits | X-ray | 2.80Å | 0.31 | 0.80 | Respiratory nitrate reductase 1 alpha chain
2vpz.1.A | 20.23 | monomer | - | HHblits | X-ray | 2.40Å | 0.30 | 0.61 | THIOSULFATE REDUCTASE
2vpx.1.D | 20.23 | monomer | - | HHblits | X-ray | 3.10Å | 0.30 | 0.61 | THIOSULFATE REDUCTASE
2e7z.1.A | 19.55 | monomer | - | HHblits | X-ray | 1.26Å | 0.30 | 0.58 | Acetylene hydratase Ahy
6sdv.1.A | 20.13 | monomer | - | HHblits | X-ray | 1.90Å | 0.30 | 0.53 | Formate dehydrogenase, alpha subunit, selenocysteine-containing,Formate dehydrogenase, alpha subunit, selenocysteine-containing,W-formate dehydrogenase - alpha subunit
8bqg.1.A | 19.54 | monomer | - | HHblits | X-ray | 1.95Å | 0.30 | 0.50 | Formate dehydrogenase, alpha subunit, selenocysteine-containing
1r27.4.A | 27.20 | homo-dimer | 0.07 | BLAST | X-ray | 2.00Å | 0.34 | 0.47 | Respiratory nitrate reductase 1 alpha chain
3ir5.1.A | 27.39 | monomer | - | BLAST | X-ray | 2.30Å | 0.34 | 0.47 | Respiratory nitrate reductase 1 alpha chain
3ir7.1.A | 27.20 | monomer | - | BLAST | X-ray | 2.50Å | 0.34 | 0.47 | Respiratory nitrate reductase 1 alpha chain
3egw.1.A | 27.02 | homo-dimer | 0.07 | BLAST | X-ray | 1.90Å | 0.34 | 0.47 | Respiratory nitrate reductase 1 alpha chain
1q16.1.A | 27.20 | monomer | - | BLAST | X-ray | 1.90Å | 0.34 | 0.47 | Respiratory nitrate reductase 1 alpha chain
3ir6.1.A | 27.20 | monomer | - | BLAST | X-ray | 2.80Å | 0.34 | 0.47 | Respiratory nitrate reductase 1 alpha chain
6q8o.1.C | 14.74 | monomer | - | HHblits | X-ray | 3.61Å | 0.26 | 0.44 | NADH-quinone oxidoreductase subunit 3
6ziy.1.C | 14.74 | monomer | - | HHblits | EM | NA | 0.26 | 0.44 | NADH-quinone oxidoreductase subunit 3
6zjl.1.C | 14.74 | monomer | - | HHblits | EM | NA | 0.26 | 0.44 | NADH-quinone oxidoreductase subunit 3
6zjn.1.C | 14.74 | monomer | - | HHblits | EM | NA | 0.26 | 0.44 | NADH-quinone oxidoreductase subunit 3
3m9s.1.C | 14.74 | monomer | - | HHblits | X-ray | 4.50Å | 0.26 | 0.44 | NADH-quinone oxidoreductase subunit 3
6zjy.1.C | 14.74 | monomer | - | HHblits | EM | NA | 0.26 | 0.44 | NADH-quinone oxidoreductase subunit 3
2fug.2.C | 14.74 | monomer | - | HHblits | X-ray | 3.30Å | 0.26 | 0.44 | NADH-quinone oxidoreductase chain 3
6zk9.1.C | 11.75 | monomer | - | HHblits | EM | NA | 0.25 | 0.33 | NADH:ubiquinone oxidoreductase core subunit S1
7zd6.1.4 | 11.75 | monomer | - | HHblits | EM | NA | 0.25 | 0.33 | NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
6qcf.1.C | 11.78 | monomer | - | HHblits | EM | NA | 0.25 | 0.33 | NADH:ubiquinone oxidoreductase core subunit S1
7qsd.1.G | 11.75 | monomer | - | HHblits | EM | NA | 0.25 | 0.33 | NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
6qc5.1.C | 11.78 | monomer | - | HHblits | EM | NA | 0.25 | 0.33 | NADH:ubiquinone oxidoreductase core subunit S1
5o31.1.8 | 12.01 | monomer | - | HHblits | EM | 4.13Å | 0.25 | 0.33 | NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
7dgr.10.A | 12.01 | monomer | - | HHblits | EM | NA | 0.25 | 0.33 | NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
6sdr.1.A | 26.60 | monomer | - | BLAST | X-ray | 2.10Å | 0.35 | 0.08 | Formate dehydrogenase, alpha subunit, selenocysteine-containing
8bqg.1.A | 26.60 | monomer | - | BLAST | X-ray | 1.95Å | 0.35 | 0.08 | Formate dehydrogenase, alpha subunit, selenocysteine-containing
6sdv.1.A | 26.60 | monomer | - | BLAST | X-ray | 1.90Å | 0.35 | 0.08 | Formate dehydrogenase, alpha subunit, selenocysteine-containing,Formate dehydrogenase, alpha subunit, selenocysteine-containing,W-formate dehydrogenase - alpha subunit
2vpx.1.D | 32.20 | monomer | - | BLAST | X-ray | 3.10Å | 0.40 | 0.05 | THIOSULFATE REDUCTASE
2e7z.1.A | 37.93 | monomer | - | BLAST | X-ray | 1.26Å | 0.41 | 0.05 | Acetylene hydratase Ahy
2vpz.1.A | 32.20 | monomer | - | BLAST | X-ray | 2.40Å | 0.40 | 0.05 | THIOSULFATE REDUCTASE
1m2j.1.A | 24.53 | monomer | - | HHblits | X-ray | 1.70Å | 0.32 | 0.05 | Silent Information Regulator 2
3k35.1.A | 20.37 | monomer | - | HHblits | X-ray | 2.00Å | 0.30 | 0.05 | NAD-dependent deacetylase sirtuin-6
1ici.1.A | 23.64 | monomer | - | HHblits | X-ray | 2.10Å | 0.31 | 0.05 | TRANSCRIPTIONAL REGULATORY PROTEIN, SIR2 FAMILY
1m2h.1.A | 24.53 | monomer | - | HHblits | X-ray | 1.80Å | 0.32 | 0.05 | Silent Information Regulator 2
4twi.1.A | 24.07 | monomer | - | HHblits | X-ray | 1.79Å | 0.32 | 0.05 | NAD-dependent protein deacylase 1
1m2k.1.A | 24.53 | monomer | - | HHblits | X-ray | 1.47Å | 0.32 | 0.05 | Silent Information Regulator 2
1m2g.1.A | 24.53 | monomer | - | HHblits | X-ray | 1.70Å | 0.32 | 0.05 | Silent Information Regulator 2
6xvg.3.A | 20.37 | monomer | - | HHblits | X-ray | 2.10Å | 0.30 | 0.05 | NAD-dependent protein deacetylase sirtuin-6
3riy.2.A | 20.00 | monomer | - | HHblits | X-ray | 1.55Å | 0.29 | 0.05 | NAD-dependent deacetylase sirtuin-5

The table above shows the top 50 filtered templates. A further 346 templates were found which were considered to be less suitable for modelling than the filtered list.
1aa6.1.A, 1be3.1.E, 1bgy.1.P, 1cz4.1.A, 1cz5.1.A, 1dms.1.A, 1e18.1.A, 1e5v.2.A, 1e60.1.A, 1eu1.1.A, 1fdo.1.A, 1g8j.1.A, 1g8k.1.A, 1h0h.1.A, 1jeo.1.A, 1kb9.1.E, 1kqf.1.A, 1l0l.1.E, 1l0n.1.E, 1m2n.1.A, 1m2n.1.B, 1m3s.1.A, 1m3s.1.B, 1ma3.1.A, 1ntk.1.E, 1ntm.1.E, 1ogy.1.A, 1q16.1.A, 1q90.1.E, 1r27.4.A, 1s5p.1.A, 1s7g.1.A, 1s7g.1.B, 1s7g.1.C, 1s7g.1.D, 1s7g.1.E, 1sqb.1.E, 1sqp.1.P, 1sqq.1.P, 1sqv.1.E, 1tk9.1.A, 1tmo.1.A, 1vf5.1.D, 1vf5.1.L, 1vim.1.A, 1vim.1.D, 1viv.1.A, 1wlf.1.A, 1x94.1.A, 1x94.1.B, 1yc5.1.A, 1zrt.1.C, 1zrt.1.F, 2b4y.1.A, 2b4y.3.A, 2d2c.1.D, 2d2c.1.L, 2e75.1.D, 2e76.1.D, 2e7z.1.A, 2fyn.1.C, 2fyn.2.C, 2fyu.1.E, 2h2i.1.A, 2h4h.1.A, 2h59.1.B, 2i2w.1.A, 2i2w.2.B, 2iv2.1.A, 2ivf.1.A, 2ki8.1.A, 2nya.1.A, 2nyr.1.A, 2nyr.1.B, 2pjh.1.B, 2pq4.1.B, 2qjk.1.C, 2qjp.1.C, 2qjy.3.F, 2v3v.1.A, 2v45.1.A, 2vpx.1.D, 2vpz.1.A, 2x3y.1.A, 2xbl.1.A, 2ybb.1.b, 3cf4.1.B, 3cwb.1.E, 3egw.1.A, 3etn.1.A, 3fxa.1.A, 3h1h.1.E, 3h1h.1.O, 3h1i.1.E, 3hu2.1.A, 3ir5.1.A, 3ir6.1.A, 3ir7.1.A, 3jr3.1.A, 3jwp.1.A, 3l75.1.E, 3l75.1.O, 3o27.1.A, 3o27.1.B, 3o5a.1.A, 3pki.1.A, 3qc8.1.A, 3qq7.1.A, 3qq8.1.A, 3qwz.1.A, 3sho.1.A, 3sho.1.C, 3tiw.1.A, 3tiw.2.A, 3u31.1.A, 3zg6.1.A, 4aay.1.A, 4bv2.3.A, 4dmr.1.A, 4g1c.1.A, 4g1c.2.A, 4ga5.1.A, 4ga6.1.A, 4h44.1.D, 4hda.1.A, 4hda.2.A, 4kdi.1.A, 4kdi.2.A, 4kdl.1.A, 4ogq.1.L, 4pv1.1.L, 4rv0.1.A, 4twj.1.A, 4u3f.1.E, 4utn.1.A, 4utn.2.A, 4v4c.1.A, 4ydd.1.A, 5b6c.1.A, 5bwl.1.A, 5cuo.1.A, 5cup.1.A, 5e7o.1.A, 5e7p.1.A, 5epp.1.A, 5g4f.1.A, 5g4f.1.B, 5g4f.1.C, 5g4f.1.D, 5g4f.1.E, 5g4f.1.F, 5g4g.1.A, 5glf.1.A, 5glf.2.A, 5glf.3.A, 5glf.4.A, 5gpn.24.A, 5kkz.1.C, 5kli.1.C, 5klv.1.P, 5ltz.1.A, 5lu6.1.A, 5lu7.1.A, 5mf6.1.A, 5nqd.1.A, 5o31.1.8, 5oj7.1.A, 5ojn.1.A, 5okd.1.E, 5t5i.1.B, 5t5i.1.D, 5x16.1.A, 5x4l.1.A, 5x4l.2.A, 5xhs.1.A, 5xtb.1.L, 5xte.1.C, 5y2f.1.A, 6aco.1.A, 6acp.1.A, 6btm.1.B, 6cz7.1.A, 6enx.1.A, 6eo0.1.A, 6eqs.3.A, 6f0k.1.B, 6fky.1.A, 6fky.2.A, 6flg.1.A, 6g72.1.G, 6gcs.1.A, 6giq.1.E, 6hd3.1.A, 6hu9.1.E, 6ljk.1.A, 6ljm.1.A, 6lod.1.B, 6nhg.1.E, 6nin.1.C, 6qc5.1.C, 6qcf.1.C, 6rfq.1.A, 6rfs.1.A, 6rqf.1.D, 6rqf.1.L, 6rxj.1.A, 6rxm.1.A, 6rxm.2.A, 6rxm.3.A, 6rxm.4.A, 6rxm.5.A, 6rxm.6.A, 6rxo.1.A, 6rxo.2.A, 6rxp.2.A, 6rxq.4.A, 6rxs.1.A, 6s6y.1.B, 6sdr.1.A, 6sdv.1.A, 6t0b.1.E, 6t0b.1.O, 6t15.1.E, 6t15.1.O, 6tg9.1.A, 6x89.1.H, 6xkt.1.E, 6xkz.1.F, 6yj4.1.G, 6ymx.1.Q, 6ymx.1.Z, 6zk9.1.C, 6zr2.1.G, 7a23.1.O, 7ak5.1.G, 7ak6.1.G, 7aqr.1.F, 7ar7.1.G, 7ar8.1.G, 7arc.1.F, 7b04.1.B, 7b04.2.B, 7bkb.1.F, 7bkb.1.J, 7bkb.1.L, 7cl0.1.A, 7dbo.1.A, 7dbo.2.A, 7dg7.1.A, 7dg9.1.A, 7dgr.10.A, 7dgr.60.A, 7dgs.50.A, 7dgs.60.A, 7di0.1.A, 7di0.2.A, 7di0.3.A, 7di1.1.A, 7du6.1.A, 7du7.1.A, 7dvc.1.A, 7dvc.5.A, 7dvf.1.A, 7dvh.1.A, 7dvh.2.A, 7dvh.4.A, 7dww.1.A, 7dww.2.A, 7dxr.1.A, 7dxr.1.B, 7dxr.2.B, 7dxs.1.A, 7dxs.1.B, 7dxs.2.A, 7dxs.2.B, 7dxt.1.A, 7dxu.1.A, 7dxu.1.B, 7dxu.2.B, 7dxv.1.A, 7dxv.1.B, 7dxw.1.A, 7dxx.1.A, 7dxx.1.B, 7dxy.1.A, 7dxz.1.A, 7dxz.2.A, 7dxz.2.B, 7dxz.3.A, 7dyc.1.A, 7dyc.2.A, 7dyc.3.A, 7e1v.1.P, 7e5z.1.A, 7en5.1.A, 7en6.1.A, 7en6.1.B, 7en6.1.C, 7en6.1.D, 7jrg.1.E, 7l5i.1.A, 7l5s.1.A, 7nz1.1.E, 7p61.1.C, 7p63.1.C, 7q5y.1.A, 7qrm.1.D, 7qsd.1.G, 7qv7.1.L, 7qv7.1.O, 7r0w.1.L, 7r0w.1.Q, 7rja.1.H, 7rjb.1.I, 7t2r.1.A, 7t30.1.A, 7tce.2.F, 7tgh.58.A, 7tlj.1.C, 7tz6.1.E, 7tz6.1.P, 7v2c.1.L, 7vw6.1.A, 7vxu.1.L, 7wbb.1.A, 7wbb.1.B, 7wbb.1.C, 7wbb.1.D, 7wbb.1.E, 7wbb.1.G, 7z0t.1.G, 7zd6.1.4, 7zm7.1.I, 7zxy.1.D, 7zxy.1.L, 8asi.1.A, 8asi.1.E, 8asj.1.E, 8b9z.1.G, 8ba0.1.G, 8bel.1.B, 8bel.1.I, 8bpx.51.A, 8bqg.1.A, 8e73.55.A, 8e9g.1.G