Alignments for a candidate for iorA in Desulfacinum hydrothermale DSM 13146

GapMind for catabolism of small carbon sources

Alignments for a candidate for iorA in Desulfacinum hydrothermale DSM 13146

Align Indolepyruvate oxidoreductase subunit IorA; IOR; Indolepyruvate ferredoxin oxidoreductase subunit alpha; EC 1.2.7.8 (characterized)
to candidate WP_084056817.1 B9A12_RS05180 indolepyruvate ferredoxin oxidoreductase subunit alpha

Query= SwissProt::P80910
         (618 letters)



>NCBI__GCF_900176285.1:WP_084056817.1
          Length = 621

 Score =  549 bits (1414), Expect = e-160
 Identities = 292/628 (46%), Positives = 413/628 (65%), Gaps = 26/628 (4%)

Query: 3   LDDILDAGRGDRLFLLGNEAAVRAAIESGVGVASTYPGTPSSEIGNVLSKIAKRAGIYFE 62
           + ++L   +G +  LLGNEA +R A+E+ V   + YPGTPSSEI +  +++   AG+  E
Sbjct: 1   MHELLSPEKGGKRLLLGNEAIIRGALEANVRFVAAYPGTPSSEIIDGFARLGHEAGVEVE 60

Query: 63  FSINEKVALEVAAAAAASGVRSFTFMKHVGLNVASDSFMSVAYTGVRAGMVVLSADDPSM 122
           +S+NEKV++E A AAA SGVRS   MKHVGLNVA+D+FM++AY GV+AGMV+++ADDPS+
Sbjct: 61  YSVNEKVSVESACAAAISGVRSLCSMKHVGLNVAADAFMTLAYVGVKAGMVIVTADDPSL 120

Query: 123 FSSQNEQDNRHYARLAWVPLLEPSNPQEILEYMNHAFELSEEYRIPVLLRTTTRVSHMRG 182
            SSQNEQDNR YA++A VP+LEP+ PQE  + +  A+E+SE +RIP LLRTTTRV+H RG
Sbjct: 121 HSSQNEQDNRFYAKMAHVPMLEPATPQEAKDMVQPAYEISERFRIPCLLRTTTRVNHCRG 180

Query: 183 VVEAGERRAEPVKGFFRKNPEQFVPVPATARVMRRELVEKMKKLKRVADTSELNRVLNED 242
           VVE G+  +  V+G F+++P   V VP   R +R +L+EK K+L+ V+++S  NRV   +
Sbjct: 181 VVELGDLPSGSVQGDFQRDPFNLVVVPMVGRKLRLQLLEKEKQLQEVSESSPFNRV---E 237

Query: 243 SESDLGIIASGGAFNYVYDALQTLGLD--VPVLKLGFTYPFPAGLVAEFLSGLEGVLVVE 300
                GI+ SG +  +V DA++ LG+   V VL LG T P P  L+ +FL  ++ V+VVE
Sbjct: 238 GSGRWGIVTSGVSVLHVRDAVRELGIQDKVSVLSLGMTSPIPERLIGDFLQNVDRVMVVE 297

Query: 301 EVDSVMEKEVLAVATSEGLDVGVHGKLDGTLPEIYEYSEDIVRRAISGLTGIKSHEKG-I 359
           E+D  +E+ V  VA   G  + + GK    +P+ +E     V++A+     +       +
Sbjct: 298 ELDPYLEEAVRNVAQKMGRSLTIAGKGPAGIPQAFELDSLKVQKALGRFFDVPVQAPAPL 357

Query: 360 EAP-ELPERPPALCPGCPHRAMYYSVRRAASELGIEGEDLIFPTDIGCYTLGIEPPYSAA 418
            AP +LP RPP LCPGCPHRA +YS+++      I GED ++PTDIGCYTLG+ PP   A
Sbjct: 358 SAPQDLPARPPNLCPGCPHRATFYSIKK------IFGEDAVYPTDIGCYTLGLLPPLQMA 411

Query: 419 DYLLSMGSSVGTACGFSAATSQRIVSFIGDSTFFHAGIPPLINAVHNRQRFVLVILDNRT 478
           D+L+ MGSSV TA GFS    + +V+FIGDSTFFH+G+  L+NAV + +  +LVI+DN T
Sbjct: 412 DFLICMGSSVSTAGGFSRVLDRPVVAFIGDSTFFHSGMTGLVNAVTHDRNILLVIMDNGT 471

Query: 479 TAMTGGQPHPGLPVDGMGEEAPAISIEDITRACGVEFVETVNPMNIRRSS---ETIRRAL 535
           TAMTG QPHPG+ +   G + P + +E + R CGV+ V  VNP+N++++    E I+  L
Sbjct: 472 TAMTGHQPHPGVSITPGGRKEPKVDVEQVVRGCGVQRVTVVNPLNVKKTQAALEEIKEDL 531

Query: 536 QHESVAVVISRYPCMLSEGAVRGRPVRV---DEEKCDLCLECLNELACPAIV-EEDGR-- 589
           +   V+V+ISR PC L E    G   RV     + CDLC +CL++L CPA V E DG   
Sbjct: 532 KEGGVSVLISRSPCPLFERRALGIKQRVVFQVTDACDLCRDCLSQLGCPAFVWERDGAGG 591

Query: 590 --VFIDPLYCRGCTICLQICPAGAIKPE 615
             V I+   C GC +C Q+C   A+KP+
Sbjct: 592 QCVRINETLCNGCAVCAQLC--DAVKPK 617


Lambda     K      H
   0.319    0.137    0.398 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 938
Number of extensions: 37
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 618
Length of database: 621
Length adjustment: 37
Effective length of query: 581
Effective length of database: 584
Effective search space:   339304
Effective search space used:   339304
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources