SEA-PHAGES | Function for subcluster A11 phage Gilberta (37505-37777 rev): Thioredoxin, NrdH-like glutaredoxin or glutaredoxin?

Link to this post \| posted 08 May, 2022 02:08
fbaliraine	There is a "mixed bag" with many hits to NrdH-like glutaredoxin and glutaredoxin in phagesDB, with a few hits to Thioredoxin for this Gilberta sequence MRTMFAPITIYTQPRCAPCDALKKRLEKEGIAFDAVDITKNEEAYAYVTGVLKAAATPIIVTDTHDPIIGDRPAELEELIEYYTTSETGVZ However, the PDB HHPred shows more than 22 hits to Thioredoxin with alignments of 78-93% and probability of 99%, versus less than 5 hits to NrdH-like glutaredoxin with alignments ranging from 81-85% and probability of 99%, besides hits to glutaredoxin, all three of which are options currently provided in the Official Functions list. Should we go for, “Thioredoxin” or use “NrdH-like glutaredoxin” or the general term "glutaredoxin"? In the “Cluster EB/ED glutaredoxin” forum post of 06 May, 2019, the use of “NrdH-like glutaredoxin” was considered appropriate for “HHPRED hit with >98% prob and >98% coverage to 4FIW_A which is the published crystal structure of NrdH from E coli.” See details of hits below: HHPred PDB hits to Thioredoxin (6MOS_A, 93.4% alignment, 99.14% probability; 7ASW_A, 91.2% alignment, 98.91% probability; 3ZIT_B, 84.62% alignment, 99.47% probability; d1nhoa_, 85.71 alighment, 99.23% probability; d1f9ma_, d1ti3a_, d1r26a1, & d1ep7a_, 86.81 alignment, 99.2% probability; d4oo4a_, 85.71 alignment, 99.18% probability; d4j56e1 & d1thxa_, 85.71 % alignment, 99.13% probability; 3KP8_A, 84.61% alignment, 99.12% probability; d1nw2a_, 84.61% alignment, 99.02% probability; d1iloa_ c, 78.02% alignment, 99.1% probability; d3diea1, 83.52% alignment, 99.1% probability; 7B02_A, 86.81% alignment, 99.1% probability; 3HZ4_A & 7RGV_A, 90.1% alignment, 99.1% probability; 7BZK_B, 6ZYW_P, 6I1C_B, & 6Q6T_A, 89.01% alignment, 99.0% probability; 1THX_A, 87.91% alignment, 99.02% probability). HHPred hits to NrdH-like glutaredoxin in (d1r7ha_, 81.32% alignment, 99.49% probability; d1h75a_, 83.52% alignment, 99.46 probability; 1R7H_A, 81.32% alignment, 99.11% probability; 4K8M_A, 84.61% alignment, 98.99% probability). Thanks! Edited 08 May, 2022 02:16

Link to this post | posted 08 May, 2022 02:08

There is a "mixed bag" with many hits to NrdH-like glutaredoxin and glutaredoxin in phagesDB, with a few hits to Thioredoxin for this Gilberta sequence MRTMFAPITIYTQPRCAPCDALKKRLEKEGIAFDAVDITKNEEAYAYVTGVLKAAATPIIVTDTHDPIIGDRPAELEELIEYYTTSETGVZ
However, the PDB HHPred shows more than 22 hits to Thioredoxin with alignments of 78-93% and probability of 99%, versus less than 5 hits to NrdH-like glutaredoxin with alignments ranging from 81-85% and probability of 99%, besides hits to glutaredoxin, all three of which are options currently provided in the Official Functions list. Should we go for, “Thioredoxin” or use “NrdH-like glutaredoxin” or the general term "glutaredoxin"?

In the “Cluster EB/ED glutaredoxin” forum post of 06 May, 2019, the use of “NrdH-like glutaredoxin” was considered appropriate for “HHPRED hit with >98% prob and >98% coverage to 4FIW_A which is the published crystal structure of NrdH from E coli.” See details of hits below:
HHPred PDB hits to Thioredoxin (6MOS_A, 93.4% alignment, 99.14% probability; 7ASW_A, 91.2% alignment, 98.91% probability; 3ZIT_B, 84.62% alignment, 99.47% probability; d1nhoa_, 85.71 alighment, 99.23% probability; d1f9ma_, d1ti3a_, d1r26a1, & d1ep7a_, 86.81 alignment, 99.2% probability; d4oo4a_, 85.71 alignment, 99.18% probability; d4j56e1 & d1thxa_, 85.71 % alignment, 99.13% probability; 3KP8_A, 84.61% alignment, 99.12% probability; d1nw2a_, 84.61% alignment, 99.02% probability; d1iloa_ c, 78.02% alignment, 99.1% probability; d3diea1, 83.52% alignment, 99.1% probability; 7B02_A, 86.81% alignment, 99.1% probability; 3HZ4_A & 7RGV_A, 90.1% alignment, 99.1% probability; 7BZK_B, 6ZYW_P, 6I1C_B, & 6Q6T_A, 89.01% alignment, 99.0% probability; 1THX_A, 87.91% alignment, 99.02% probability).

HHPred hits to NrdH-like glutaredoxin in (d1r7ha_, 81.32% alignment, 99.49% probability; d1h75a_, 83.52% alignment, 99.46 probability; 1R7H_A, 81.32% alignment, 99.11% probability; 4K8M_A, 84.61% alignment, 98.99% probability).
Thanks!

Edited 08 May, 2022 02:16

Link to this post \| posted 08 May, 2022 17:39
cdshaffer	Trying to determine substrate specificity to that level is tricky. If you are lucky there might be some comments in the published papers on those crystals you listed and they could indicate which specific amino acid side chains are involved in binding the substrate. If you go to the PDB database and look up each crystal by name you will get a link to the primary publication. However, another suitable annotation would be to use a less specific term to imply that the exact substrate is undetermined. The generic approved term here is oxidoreductase. I don't have these memorized, I used QuickGo to look up terms and see what the scientists that think hard about how terms are related to one another and publish that in the Gene Ontology say about these terms. For example, here is the link to the page on the "Thioredoxin". If you look at the ancestor chart and following the black "is a" arrows you can see that Thioredoxin "is a" peroxidase activity which "is a" oxidoreductase activity, acting on… which "is a" oxidoreductase activity. And a quick search you can see that oxidoreductase is on the approved terms list. So I would say the best annotation given the results you have shown in "oxidoreductase" and any higher level of specificity would require both a deep dive and at least some good luck.

Link to this post | posted 08 May, 2022 17:39

cdshaffer

Trying to determine substrate specificity to that level is tricky. If you are lucky there might be some comments in the published papers on those crystals you listed and they could indicate which specific amino acid side chains are involved in binding the substrate. If you go to the PDB database and look up each crystal by name you will get a link to the primary publication.

However, another suitable annotation would be to use a less specific term to imply that the exact substrate is undetermined. The generic approved term here is oxidoreductase. I don't have these memorized, I used QuickGo to look up terms and see what the scientists that think hard about how terms are related to one another and publish that in the Gene Ontology say about these terms. For example, here is the link to the page on the "Thioredoxin". If you look at the ancestor chart and following the black "is a" arrows you can see that Thioredoxin "is a" peroxidase activity which "is a" oxidoreductase activity, acting on… which "is a" oxidoreductase activity. And a quick search you can see that oxidoreductase is on the approved terms list.

So I would say the best annotation given the results you have shown in "oxidoreductase" and any higher level of specificity would require both a deep dive and at least some good luck.

Link to this post \| posted 09 May, 2022 19:05
fbaliraine	Thanks. I’ve looked at the “Thioredoxin” link that you’ve kindly provided, but there is something noteworthy in HHPred. In PDB, the reference sequence phage Onyinye gene78 for “oxidoreductase” is almost thrice as long 792 bp vs 273 bp of Gilberta) and mostly hits “Polyketide oxygenase PgaE,” chain A, with ref Sequence in pfam hitting the "FAD folding domain" but I do not see any hits in Gilberta to any "FAD folding domain." Instead, in PDB Gilberta hits the "Molecule" THIOREDOXIN chains A & B, with the pfam ref hitting “Glutaredoxin or Glutaredoxin-like NRDH-redoxin, THIOREDOXIN; OXIDOREDUCTASE, GLUTAREDOXIN.” On the other hand, the ref sequence for Thioredoxin, phage Cjw1 gp 37 (246 bp) has a comparable length to Gilberta’s 273 bp and they both have several hits the molecule Thioredoxin chain A, but not the “Polyketide oxygenase PgaE,” or “FAD domain”. Edited 09 May, 2022 19:08

Link to this post | posted 09 May, 2022 19:05

fbaliraine

Thanks. I’ve looked at the “Thioredoxin” link that you’ve kindly provided, but there is something noteworthy in HHPred.

In PDB, the reference sequence phage Onyinye gene78 for “oxidoreductase” is almost thrice as long 792 bp vs 273 bp of Gilberta) and mostly hits “Polyketide oxygenase PgaE,” chain A, with ref Sequence in pfam hitting the "FAD folding domain" but I do not see any hits in Gilberta to any "FAD folding domain." Instead, in PDB Gilberta hits the "Molecule" THIOREDOXIN chains A & B, with the pfam ref hitting “Glutaredoxin or Glutaredoxin-like NRDH-redoxin, THIOREDOXIN; OXIDOREDUCTASE, GLUTAREDOXIN.” On the other hand, the ref sequence for Thioredoxin, phage Cjw1 gp 37 (246 bp) has a comparable length to Gilberta’s 273 bp and they both have several hits the molecule Thioredoxin chain A, but not the “Polyketide oxygenase PgaE,” or “FAD domain”.

Edited 09 May, 2022 19:08

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Function for subcluster A11 phage Gilberta (37505-37777 rev): Thioredoxin, NrdH-like glutaredoxin or glutaredoxin?