|  | SWISS-MODEL Homology Modelling Report

## Model Building Report

This document lists the results for the homology modelling project "13_July_SF_Bin2_scaffold_9994_c1_2-2545_1" submitted to SWISS-MODEL workspace on March 29, 2023, 7:37 p.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 428 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 | None | 0.86 | 0.83 ± 0.05

Template | Seq Identity | Oligo-state | QSQE | Found by | Method | Resolution | Seq Similarity | Range | Coverage | Description
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
7b04.1.B | 65.28 | monomer | 0.00 | HHblits | X-ray | 2.97Å | 0.51 | 1 - 845 | 1.00 | Nitrite oxidoreductase subunit A

### 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
MO.7 | Binding site not conserved. | MOLYBDENUM ATOM
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    IMDGKNLVENKLTDSHWFIECMERGAKIVVIAPEYGPPSTKADYWIPIRPQTDAALWLGITRLMIEKKWYDETFVKGFTD
    7b04.1.B  IQTGKNLIENKMPEAHWVTEVMERGGKIVVITPEYSPSAQKADYWIPIRNNTDTALFLGITKILIDNKWYDADYVKKFTD

    Target    FPLLVRTDTLQRLRAHEVFPQYKTSLSADGPSMKIQGLSAEQHAKLGDFVVWDGKTNAPAAITRDDVGATITKKGIDPVL
    7b04.1.B  FPLLIRTDTLKRVSPKDIIPNYKLQDISDGPSYHIQGLKDEQREIIGDFVVWDAKSKGPKAITRDDVGETLVKKGIDPVL

    Target    AGSFKVKLVDGKEVEVATLWTLYQDHLKDYDLDTVVEITQAPKEMIEQLAQDIATMKPVAIHQGEGINHWFHATEMNRAA
    7b04.1.B  EGSFKLKTIDGKEIEVMTLLEMYKIHLRDYDIDSVVSMTNSPKDLIERLAKDIATIKPVAIHYGEGVNHYFHATLMNRSY

    Target    YLPLMLTGNIGRPGAGCQTWAGNYKAALFQGSPWTGPGFKGWVAEDPFDINLNPKAHGKEIHAHAYTKDEEPAYWNHGDL
    7b04.1.B  YLPVMLTGNVGYFGSGSHTWAGNYKAGNFQASKWSGPGFYGWVAEDVFKPNLDPYASAKDLNIKGRALDEEVAYWNHSER

    Target    ALIVDTPKFGRKNFTGKTHMPTPTKALIFNNVNLINNAKWAYGMIKNVNPNVEMIVSMDIQMTASIEYADLALPANSWLE
    7b04.1.B  PLIVNTPKYGRKVFTGKTHMPSPTKVLWFTNVNLINNAKHVYQMLKNVNPNIEQIMSTDIEITGSIEYADFAFPANSWVE

    Target    FEGLEITASCSNPFLQIWK-GGIPPVFDSRDDLDILAGIANALADVTGEKRFRDYFAFAAADKRGIYIQRLLDTCTTTAG
    7b04.1.B  FQEFEITNSCSNPFIQIWGKTGITPVYESKDDVKILAGMASKLGELLRDKRFEDNWKFAIEGRASVYINRLLDGSTTMKG

    Target    YKLADIMAGKYGPPGGCLLNFRTYPRIPFYEQVHDSEPFHTDTGRMHAYADVPEAIEYGENFIVHREGPEATPYLPNVIV
    7b04.1.B  YTCEDILNGKYGEPGVAMLLFRTYPRHPFWEQVHESLPFYTPTGRLQAYNDEPEIIEYGENFIVHREGPEATPYLPNAIV

    Target    SSNPHIRPEDYGIAADAEHWDDRTIRNIKMPWSKVKETKNFLWEKGFQFYCLTPKTRHRVHSGWSNVDWHMLMDSNFGDP
    7b04.1.B  STNPYIRPDDYGIPENAEYWEDRTVRNIKKSWEETKKTKNFLWEKGYHFYCVTPKSRHTVHSQWAVTDWNFIWNNNFGDP

    Target    YRLDKRAPCVGEHQLHINPQAARDLNINDGDYVYVDANPADRPYLGAKPDDPFYRVSRCMLRVTYNRAYPYNIVMMKHAP
    7b04.1.B  YRMDKRMPGVGEHQIHIHPQAARDLGIEDGDYVYVDANPADRPYEGWKPNDSFYKVSRLMLRAKYNPAYPYNCTMMKHSA

    Target    FIATEKSVKAHETRPDGRALSANTGYQANLRYGSQQSVTRNWHMPMHQTDTLFHKSKVFMGFIFGGEADNHAVNTVPKET
    7b04.1.B  WISSDKTVQAHETRPDGRALSP-SGYQSSFRYGSQQSITRDWSMPMHQLDSLFHKAKIGMKFIFGFEADNHCINTVPKET

    Target    LVRVTKAEDGGMGGKGIWQPATTGFSPDNESDFMKKYLAGELTKVKT
    7b04.1.B  LVKITKAENGGMGGKGVWDPVKTGYTAGNENDFMKKFLNGELIKVD-

### Model #02 | File | Built with | Oligo-State | Ligands | GMQE | QMEANDisCo Global
--- | --- | --- | --- | --- | --- | ---
| PDB | ProMod3 3.2.1 | monomer (matching prediction) | None | 0.45 | 0.50 ± 0.05

Template | Seq Identity | Oligo-state | QSQE | Found by | Method | Resolution | Seq Similarity | Range | Coverage | Description
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
1r27.4.A | 22.77 | homo-dimer | - | HHblits | X-ray | 2.00Å | 0.32 | 1 - 812 | 0.82 | 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 | Binding site not conserved. | 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    IMDGKNLVENKLTDSHWFIECMERGAKIVVIAPEYGPPSTKADYWIPIRPQTDAALWLGITRLMIEKKW------YDETF
    1r27.4.A  IAWGSNVPQTRTPDAHFFTEVRYKGTKTVAVTPDYAEIAKLCDLWLAPKQGTDAAMALAMGHVMLREFHLDNPSQYFTDY

    Target    VKGFTDFPLLVRTDT-------LQRLRAHEVFPQYKTSLSADGPSMKIQGLSAEQHAKLGDFVVWDGKTNAPAAITRDDV
    1r27.4.A  VRRYTDMPMLVMLEERDGYYAAGRMLRAADLVDALG-----------------QENNPEWKTVAFNT-NGEMVAPNGS-I

    Target    GA------TITK------------------KGID--------------------PVLA-------GSFKVKLVDGKEVEV
    1r27.4.A  GFRWGEKGKWNLEQRDGKTGEETELQLSLLGSQDEIAEVGFPYFGGDGTEHFNKVELENVLLHKLPVKRLQLADGSTALV

    Target    ATLWTLYQ------------------DHLKDYDLDTVVEITQAPKEMIEQLAQDIATM-----KPVAIHQGEGINHWFHA
    1r27.4.A  TTVYDLTLANYGLERGLNDVNCATSYDDVKAYTPAWAEQITGVSRSQIIRIAREFADNADKTHGRSMIIVGAGLNHWYHL

    Target    TEMNRAAYLPLMLTGNIGRPGAGCQTWAGNYKAALFQG-------SPWTGPGF------------KGWVAEDPFDIN-LN
    1r27.4.A  DMNYRGLINMLIFCGCVGQSGGGWAHYVGQEKLRPQTGWQPLAFALDWQRPARHMNSTSYFYNHSSQWRYETVTAEELLS

    Target    PKAHGKEIHA-------HAYTKDEEPAYWNHGDLALIV---------DTPKFG-RKNFTGK--------THMPTPTKALI
    1r27.4.A  PMADKSRYTGHLIDFNVRAERMGWLPSAPQLGTNPLTIAGEAEKAGMNPVDYTVKSLKEGSIRFAAEQPENGKNHPRNLF

    Target    FNNVNLINNAKWAYG-M------------------------------IKNVNPNVEMIVSMDIQMTASIEYADLALPANS
    1r27.4.A  IWRSNLLGSSGKGHEFMLKYLLGTEHGIQGKDLGQQGGVKPEEVDWQDNGLEGKLDLVVTLDFRLSSTCLYSDIILPTAT

    Target    WLEFEGLEITASCSNPFLQIWKGGIPPVFDSRDDLDILAGIANALADVTGEK------------------------RFRD
    1r27.4.A  WYEKDDMNT--SDMHPFIHPLSAAVDPAWEAKSDWEIYKAIAKKFSEVCVGHLGKETDIVTLPIQHDSAAELAQPLDVKD

    Target    YFA---------------------------FAAA------------------DKRGIYIQRL------------------
    1r27.4.A  WKKGECDLIPGKTAPHIMVVERDYPATYERFTSIGPLMEKIGNGGKGIAWNTQSEMDLLRKLNYTKAEGPAKGQPMLNTA

    Target    -------LDTCTTTAGY----KLADIMAGKY-G-------PPGGCLLNF---------------------RTYPRIPFYE
    1r27.4.A  IDAAEMILTLAPETNGQVAVKAWAALSEFTGRDHTHLALNKEDE-KIRFRDIQAQPRKIISSPTWSGLEDEHVSYNAGYT

    Target    QVHDSEPFHTDTGRMHAYADVPEAIEYGENFIVHREGPEATPYLPNVIVSSNPHIRPEDYGIAADAEHWDDRTIRNIKMP
    1r27.4.A  NVHELIPWRTLSGRQQLYQDHQWMRDFGESLLVYRPPIDTRSVK-------------EVIG-------------------

    Target    WSKVKETKNFLWEKGFQFYCLTPKTRHRVHSGWSNVDWHMLMDSNFGDPYRLDKRAPCVGEHQLHINPQAARDLNINDGD
    1r27.4.A  ------QK-SNGNQEKALNFLTPHQKWGIHSTYSDNLLMLTLG---------------RGGPVVWLSEADAKDLGIADND

    Target    YVYVDANPADRPYLGAKPDDPFYRVSRCMLRVTYNRAYPYNIVMMKHAPFIATEKSVKAHETRPDGRALSANTGYQANLR
    1r27.4.A  WIEVFNSN-----------------GALTARAVVSQRVPAGMTMMYHAQE----RIVNLPG--------SEITQ----QR

    Target    YGSQQSVTRNWHMPMHQTDTLFHKSKVFMGFIFGGEADNHAVNTVPKETLVRVTKAEDGGMGGKGIWQPATTGFSPDNES
    1r27.4.A  GGIHNSVTRITPKPTHMIGGYAHLAYG-----F----NYYGTVGSNRDEFVVVRKMKNIDWL------------------

    Target    DFMKKYLAGELTKVKT
    1r27.4.A  ----------------

### Model #03 | File | Built with | Oligo-State | Ligands | GMQE | QMEANDisCo Global
--- | --- | --- | --- | --- | --- | ---
| PDB | ProMod3 3.2.1 | monomer | None | 0.11 | 0.32 ± 0.05

Template | Seq Identity | Oligo-state | QSQE | Found by | Method | Resolution | Seq Similarity | Range | Coverage | Description
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
2fug.2.C | 17.10 | monomer | 0.00 | HHblits | X-ray | 3.30Å | 0.27 | 367 - 722 | 0.23 | NADH-quinone oxidoreductase chain 3

### Excluded ligands

Ligand Name.Number | Reason for Exclusion | Description
--- | --- | ---
FES.2 | Binding site not conserved. | FE2/S2 (INORGANIC) CLUSTER
FES.6 | Binding site not conserved. | FE2/S2 (INORGANIC) CLUSTER
FMN.10 | Binding site not conserved. | FLAVIN MONONUCLEOTIDE
SF4.1 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.3 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.4 | Binding site not conserved. | IRON/SULFUR CLUSTER
SF4.5 | 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
SF4.9 | Binding site not conserved. | IRON/SULFUR CLUSTER

    Target    IMDGKNLVENKLTDSHWFIECMERGAKIVVIAPEYGPPSTKADYWIPIRPQTDAALWLGITRLMIEKKWYDETFVKGFTD
    2fug.2.C  --------------------------------------------------------------------------------

    Target    FPLLVRTDTLQRLRAHEVFPQYKTSLSADGPSMKIQGLSAEQHAKLGDFVVWDGKTNAPAAITRDDVGATITKKGIDPVL
    2fug.2.C  --------------------------------------------------------------------------------

    Target    AGSFKVKLVDGKEVEVATLWTLYQDHLKDYDLDTVVEITQAPKEMIEQLAQDIATMKPVAIHQGEGINHWFHATEMNRAA
    2fug.2.C  --------------------------------------------------------------------------------

    Target    YLPLMLTGNIGRPGAGCQTWAGNYKAALFQGSPWTGPGFKGWVAEDPFDINLNPKAHGKEIHAHAYTKDEEPAYWNHGDL
    2fug.2.C  --------------------------------------------------------------------------------

    Target    ALIVDTPKFGRKNFTGKTHMPTPTKALIFNNVNLINNAKWAYGMIKNVNPNVEMIVSMDIQMTASI-EYADLALPANSWL
    2fug.2.C  ----------------------------------------------EALKGKRFVVMHLSHLHPLAERYAHVVLPAPTFY

    Target    EFEGLEITASCSNPFLQIWKGGIPPVFDSRDDLDILAGIANALADVTGEKRFRDYFAFAAADKRGIYIQRLLDTCTTTAG
    2fug.2.C  EKRGHL---VNLEGRVLPLSPAPIENGEAEGALQVLALLAEALGVRPP------F---R-------LHLEA---------

    Target    YKLADIMAGKYGPPGGCLLNFRTYPRIPFYEQVHDSEPFHTDTGRMHAYADVPEAIEYGENFIVHREGPEATPYLPNVIV
    2fug.2.C  --QKALK----------------------------ARKVPEAMGRLSFRLKELR---------------------P----

    Target    SSNPHIRPEDYGIAADAEHWDDRTIRNIKMPWSKVKETKNFLWEKGFQFYCLTPKTRHRVHSGWSNVDWHMLMDSNFGDP
    2fug.2.C  ------------------------------------------KERKGAFYLRPTMWKA-----HQAVGKAQE--------

    Target    YRLDKRAPCVGEHQLHINPQAARDLNINDGDYVYVDANPADRPYLGAKPDDPFYRVSRCMLRVTYNRAYPYNIVMMKHAP
    2fug.2.C  ---------AARAELWAHPETARAEALPEGAQVAVETPF-----------------GRVEARVVHREDVPKGHLYLSALG

    Target    FIATEKSVKAHETRPDGRALSANTGYQANLRYGSQQSVTRNWHMPMHQTDTLFHKSKVFMGFIFGGEADNHAVNTVPKET
    2fug.2.C  PAAG----------------------------------------------------------------------------

    Target    LVRVTKAEDGGMGGKGIWQPATTGFSPDNESDFMKKYLAGELTKVKT
    2fug.2.C  -----------------------------------------------

## 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.

IMDGKNLVENKLTDSHWFIECMERGAKIVVIAPEYGPPSTKADYWIPIRPQTDAALWLGITRLMIEKKWYDETFVKGFTDFPLLVRTDTLQRLRAHEVFP
QYKTSLSADGPSMKIQGLSAEQHAKLGDFVVWDGKTNAPAAITRDDVGATITKKGIDPVLAGSFKVKLVDGKEVEVATLWTLYQDHLKDYDLDTVVEITQ
APKEMIEQLAQDIATMKPVAIHQGEGINHWFHATEMNRAAYLPLMLTGNIGRPGAGCQTWAGNYKAALFQGSPWTGPGFKGWVAEDPFDINLNPKAHGKE
IHAHAYTKDEEPAYWNHGDLALIVDTPKFGRKNFTGKTHMPTPTKALIFNNVNLINNAKWAYGMIKNVNPNVEMIVSMDIQMTASIEYADLALPANSWLE
FEGLEITASCSNPFLQIWKGGIPPVFDSRDDLDILAGIANALADVTGEKRFRDYFAFAAADKRGIYIQRLLDTCTTTAGYKLADIMAGKYGPPGGCLLNF
RTYPRIPFYEQVHDSEPFHTDTGRMHAYADVPEAIEYGENFIVHREGPEATPYLPNVIVSSNPHIRPEDYGIAADAEHWDDRTIRNIKMPWSKVKETKNF
LWEKGFQFYCLTPKTRHRVHSGWSNVDWHMLMDSNFGDPYRLDKRAPCVGEHQLHINPQAARDLNINDGDYVYVDANPADRPYLGAKPDDPFYRVSRCML
RVTYNRAYPYNIVMMKHAPFIATEKSVKAHETRPDGRALSANTGYQANLRYGSQQSVTRNWHMPMHQTDTLFHKSKVFMGFIFGGEADNHAVNTVPKETL
VRVTKAEDGGMGGKGIWQPATTGFSPDNESDFMKKYLAGELTKVKT

## Table T2:

Template | Seq Identity | Oligo-state | QSQE | Found by | Method | Resolution | Seq Similarity | Coverage | Description
--- | --- | --- | --- | --- | --- | --- | --- | --- | ---
7b04.1.B | 65.28 | monomer | - | HHblits | X-ray | 2.97Å | 0.51 | 1.00 | Nitrite oxidoreductase subunit A
7b04.1.B | 65.48 | monomer | - | BLAST | X-ray | 2.97Å | 0.51 | 1.00 | Nitrite oxidoreductase subunit A
7b04.2.B | 65.48 | monomer | - | BLAST | X-ray | 2.97Å | 0.51 | 1.00 | Nitrite oxidoreductase subunit A
7b04.2.B | 65.28 | monomer | - | HHblits | X-ray | 2.97Å | 0.51 | 1.00 | Nitrite oxidoreductase subunit A
1r27.4.A | 22.77 | homo-dimer | - | HHblits | X-ray | 2.00Å | 0.32 | 0.82 | Respiratory nitrate reductase 1 alpha chain
3egw.1.A | 22.35 | homo-dimer | 0.08 | HHblits | X-ray | 1.90Å | 0.32 | 0.81 | Respiratory nitrate reductase 1 alpha chain
3ir5.1.A | 22.25 | monomer | - | HHblits | X-ray | 2.30Å | 0.32 | 0.82 | Respiratory nitrate reductase 1 alpha chain
1q16.1.A | 22.25 | monomer | - | HHblits | X-ray | 1.90Å | 0.32 | 0.82 | Respiratory nitrate reductase 1 alpha chain
3ir7.1.A | 22.66 | monomer | - | HHblits | X-ray | 2.50Å | 0.32 | 0.82 | Respiratory nitrate reductase 1 alpha chain
3ir6.1.A | 22.53 | monomer | - | HHblits | X-ray | 2.80Å | 0.32 | 0.81 | Respiratory nitrate reductase 1 alpha chain
1e60.1.A | 19.42 | monomer | - | HHblits | X-ray | 2.00Å | 0.29 | 0.61 | Dimethyl sulfoxide/trimethylamine N-oxide reductase
1e18.1.A | 19.61 | monomer | - | HHblits | X-ray | 2.00Å | 0.29 | 0.61 | DMSO REDUCTASE.
1e5v.2.A | 19.42 | monomer | - | HHblits | X-ray | 2.40Å | 0.29 | 0.61 | Dimethyl sulfoxide/trimethylamine N-oxide reductase
4dmr.1.A | 18.87 | monomer | - | HHblits | X-ray | 1.90Å | 0.29 | 0.61 | DMSO REDUCTASE
1dms.1.A | 18.13 | monomer | - | HHblits | X-ray | 1.88Å | 0.29 | 0.61 | DMSO REDUCTASE
3ir6.1.A | 28.63 | monomer | - | BLAST | X-ray | 2.80Å | 0.35 | 0.31 | Respiratory nitrate reductase 1 alpha chain
3ir5.1.A | 28.63 | monomer | - | BLAST | X-ray | 2.30Å | 0.35 | 0.31 | Respiratory nitrate reductase 1 alpha chain
1r27.4.A | 28.63 | monomer | - | BLAST | X-ray | 2.00Å | 0.35 | 0.31 | Respiratory nitrate reductase 1 alpha chain
3ir7.1.A | 28.63 | monomer | - | BLAST | X-ray | 2.50Å | 0.35 | 0.31 | Respiratory nitrate reductase 1 alpha chain
1q16.1.A | 28.63 | monomer | - | BLAST | X-ray | 1.90Å | 0.35 | 0.31 | Respiratory nitrate reductase 1 alpha chain
3egw.1.A | 28.63 | monomer | - | BLAST | X-ray | 1.90Å | 0.35 | 0.31 | Respiratory nitrate reductase 1 alpha chain
6ziy.1.C | 17.10 | monomer | - | HHblits | EM | NA | 0.27 | 0.23 | NADH-quinone oxidoreductase subunit 3
6q8o.1.C | 17.10 | monomer | - | HHblits | X-ray | 3.61Å | 0.27 | 0.23 | NADH-quinone oxidoreductase subunit 3
6zjl.1.C | 17.10 | monomer | - | HHblits | EM | NA | 0.27 | 0.23 | NADH-quinone oxidoreductase subunit 3
3m9s.1.C | 17.10 | monomer | - | HHblits | X-ray | 4.50Å | 0.27 | 0.23 | NADH-quinone oxidoreductase subunit 3
6zjn.1.C | 17.10 | monomer | - | HHblits | EM | NA | 0.27 | 0.23 | NADH-quinone oxidoreductase subunit 3
6zjy.1.C | 17.10 | monomer | - | HHblits | EM | NA | 0.27 | 0.23 | NADH-quinone oxidoreductase subunit 3
2fug.2.C | 17.10 | monomer | - | HHblits | X-ray | 3.30Å | 0.27 | 0.23 | NADH-quinone oxidoreductase chain 3
6zk9.1.C | 14.04 | monomer | - | HHblits | EM | NA | 0.26 | 0.20 | NADH:ubiquinone oxidoreductase core subunit S1
7zd6.1.4 | 14.62 | monomer | - | HHblits | EM | NA | 0.26 | 0.20 | NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
5xtb.1.L | 12.64 | monomer | - | HHblits | EM | NA | 0.26 | 0.21 | NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
7dgr.10.A | 14.04 | monomer | - | HHblits | EM | NA | 0.26 | 0.20 | NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
5o31.1.8 | 14.04 | monomer | - | HHblits | EM | 4.13Å | 0.26 | 0.20 | NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
3ir5.1.A | 12.96 | monomer | - | HHblits | X-ray | 2.30Å | 0.25 | 0.06 | Respiratory nitrate reductase 1 alpha chain
6ljm.1.A | 13.64 | monomer | - | HHblits | X-ray | 1.78Å | 0.28 | 0.05 | NAD-dependent protein deacylase sirtuin-5, mitochondrial
3ir6.1.A | 12.96 | monomer | - | HHblits | X-ray | 2.80Å | 0.25 | 0.06 | Respiratory nitrate reductase 1 alpha chain
1r27.4.A | 12.96 | monomer | - | HHblits | X-ray | 2.00Å | 0.25 | 0.06 | Respiratory nitrate reductase 1 alpha chain
3ir7.1.A | 13.21 | monomer | - | HHblits | X-ray | 2.50Å | 0.25 | 0.06 | Respiratory nitrate reductase 1 alpha chain
1q16.1.A | 12.96 | monomer | - | HHblits | X-ray | 1.90Å | 0.25 | 0.06 | Respiratory nitrate reductase 1 alpha chain
3egw.1.A | 12.96 | monomer | - | HHblits | X-ray | 1.90Å | 0.25 | 0.06 | Respiratory nitrate reductase 1 alpha chain
1dms.1.A | 18.37 | monomer | - | HHblits | X-ray | 1.88Å | 0.29 | 0.06 | DMSO REDUCTASE
1e5v.2.A | 20.83 | monomer | - | HHblits | X-ray | 2.40Å | 0.30 | 0.06 | Dimethyl sulfoxide/trimethylamine N-oxide reductase
4dmr.1.A | 20.83 | monomer | - | HHblits | X-ray | 1.90Å | 0.30 | 0.06 | DMSO REDUCTASE
1e60.1.A | 20.83 | monomer | - | HHblits | X-ray | 2.00Å | 0.30 | 0.06 | Dimethyl sulfoxide/trimethylamine N-oxide reductase
1e18.1.A | 20.83 | monomer | - | HHblits | X-ray | 2.00Å | 0.30 | 0.06 | DMSO REDUCTASE.
1e60.1.A | 12.73 | monomer | - | HHblits | X-ray | 2.00Å | 0.29 | 0.07 | Dimethyl sulfoxide/trimethylamine N-oxide reductase
4dmr.1.A | 13.21 | monomer | - | HHblits | X-ray | 1.90Å | 0.30 | 0.06 | DMSO REDUCTASE
1dms.1.A | 13.21 | monomer | - | HHblits | X-ray | 1.88Å | 0.29 | 0.06 | DMSO REDUCTASE
1e18.1.A | 12.73 | monomer | - | HHblits | X-ray | 2.00Å | 0.29 | 0.07 | DMSO REDUCTASE.
1e5v.2.A | 12.73 | monomer | - | HHblits | X-ray | 2.40Å | 0.29 | 0.07 | Dimethyl sulfoxide/trimethylamine N-oxide reductase

The table above shows the top 50 filtered templates. A further 254 templates were found which were considered to be less suitable for modelling than the filtered list.
1aa6.1.A, 1cz4.1.A, 1cz5.1.A, 1eu1.1.A, 1fdo.1.A, 1g8j.1.A, 1g8k.1.A, 1h0h.1.A, 1ici.1.A, 1j75.1.A, 1jeo.1.A, 1kqf.1.A, 1m2g.1.A, 1m2h.1.A, 1m2j.1.A, 1m2k.1.A, 1m2n.1.A, 1m2n.1.B, 1ogy.1.A, 1pnq.1.A, 1pnq.2.A, 1q16.1.A, 1r27.4.A, 1tmo.1.A, 1wlf.1.A, 1x94.1.A, 1x94.1.B, 1yc5.1.A, 2b4y.1.A, 2b4y.3.A, 2e7z.1.A, 2h2i.1.A, 2h4h.1.A, 2h59.1.B, 2heo.1.A, 2heo.1.B, 2i2w.1.A, 2i2w.2.B, 2iv2.1.A, 2ivf.1.A, 2ki8.1.A, 2kz3.1.A, 2l1p.1.A, 2lnb.1.A, 2nya.1.A, 2nyr.1.A, 2nyr.1.B, 2o3f.1.A, 2pjh.1.B, 2v3v.1.A, 2v45.1.A, 2vpx.1.D, 2vpz.1.A, 2x3y.1.A, 2xvc.1.A, 3egw.1.A, 3eua.1.A, 3fxa.1.A, 3hu2.1.A, 3ir5.1.A, 3ir6.1.A, 3ir7.1.A, 3iwf.1.A, 3jr3.1.A, 3jwp.1.A, 3nzl.1.A, 3o27.1.A, 3o27.1.B, 3o5a.1.A, 3qc8.1.A, 3qq7.1.A, 3qq8.1.A, 3qwz.1.A, 3riy.2.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, 4g1c.1.A, 4g1c.2.A, 4ga5.1.A, 4ga6.1.A, 4hda.1.A, 4hda.2.A, 4ivn.1.A, 4kdi.1.A, 4kdi.2.A, 4kdl.1.A, 4rv0.1.A, 4s1w.1.A, 4s1w.1.B, 4twi.1.A, 4utn.1.A, 4utn.2.A, 4v4c.1.A, 4ydd.1.A, 5b6c.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, 5lu5.1.A, 5lu6.1.A, 5lu7.1.A, 5nqd.1.A, 5o31.1.8, 5t5i.1.B, 5t5i.1.D, 5x4l.1.A, 5x4l.2.A, 5xtb.1.L, 6aco.1.A, 6acp.1.A, 6btm.1.B, 6cz7.1.A, 6enx.1.A, 6eo0.1.A, 6eqs.3.A, 6f0k.1.B, 6g72.1.G, 6gcs.1.A, 6hd3.1.A, 6ljk.1.A, 6lod.1.B, 6qc5.1.C, 6qcf.1.C, 6rfq.1.A, 6rfs.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, 6tg9.1.A, 6x89.1.H, 6yj4.1.G, 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, 7dbo.1.A, 7dbo.2.A, 7dg7.1.A, 7dg9.1.A, 7dgr.10.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, 7e5z.1.A, 7en5.1.A, 7en6.1.A, 7en6.1.B, 7en6.1.C, 7en6.1.D, 7l5i.1.A, 7l5s.1.A, 7nz1.1.E, 7p61.1.C, 7p63.1.C, 7q5y.1.A, 7qsd.1.G, 7qv7.1.L, 7qv7.1.O, 7t2r.1.A, 7t30.1.A, 7tgh.58.A, 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, 8b9z.1.G, 8ba0.1.G, 8bqg.1.A, 8e73.55.A, 8e9g.1.G