Alignments for a candidate for iorA in Desulfovibrio vulgaris Miyazaki F

GapMind for catabolism of small carbon sources

Alignments for a candidate for iorA in Desulfovibrio vulgaris Miyazaki F

Align Indolepyruvate oxidoreductase subunit IorA; IOR; Indolepyruvate ferredoxin oxidoreductase subunit alpha; EC 1.2.7.8 (characterized)
to candidate 8499845 DvMF_0610 indolepyruvate ferredoxin oxidoreductase, alpha subunit (RefSeq)

Query= SwissProt::P80910
         (618 letters)



>FitnessBrowser__Miya:8499845
          Length = 629

 Score =  476 bits (1224), Expect = e-138
 Identities = 263/602 (43%), Positives = 360/602 (59%), Gaps = 17/602 (2%)

Query: 12  GDRLFLLGNEAAVRAAIESGVGVASTYPGTPSSEIGNVLSKIAKRAGIYFEFSINEKVAL 71
           G R  LLGNEA VR A+E+GV + + YPGTPSSE+ +   +I        E+S+NEKVA+
Sbjct: 26  GARRLLLGNEAIVRGALEAGVNLVACYPGTPSSEVPDTFRRIGGGGRYRLEYSVNEKVAM 85

Query: 72  EVAAAAAASGVRSFTFMKHVGLNVASDSFMSVAYTGVRAGMVVLSADDPSMFSSQNEQDN 131
           EV A AA +G  +   MKHVG+NVA+D  +++ YTG+  G+++LSADDP   +SQNEQDN
Sbjct: 86  EVGAGAALAGALTLVTMKHVGVNVAADPLLTMTYTGLPGGLLLLSADDPGCHASQNEQDN 145

Query: 132 RHYARLAWVPLLEPSNPQEILEYMNHAFELSEEYRIPVLLRTTTRVSHMRGVVEAGERRA 191
           R YAR A +P  EP+  QE  +    A  L+ E   PVLLRTTTRV+H+RG VE G    
Sbjct: 146 RTYARFAGMPCFEPATAQEAKDMTRDALLLARELEQPVLLRTTTRVNHLRGAVEFGPLGQ 205

Query: 192 EPVKGFFRKNPEQFVPVPATARVMRRELVEKMKKLKRVADTSELNRVLNEDSESDLGIIA 251
                 F +NP +FVPVPA ARV   ELV+ +   +  A+ S  N V     E   G+IA
Sbjct: 206 PAPIVPFERNPRRFVPVPAVARVRHAELVKHLGMAREKAEHSPWNTV---RGEGRFGVIA 262

Query: 252 SGGAFNYVYDALQTLGLD--VPVLKLGFTYPFPAGLVAEFLSGLEGVLVVEEVDSVMEKE 309
           SG +  Y+ DAL   G D  V VL LG T+P P  L+ +FLS  + VLV+EE++ ++E +
Sbjct: 263 SGISRAYLSDALHETGWDDRVKVLDLGMTWPLPEALLTDFLSQCDAVLVLEELEPLLEND 322

Query: 310 VLAVATSEGLDVGVHGKLDGTLPEIYEYSEDIVRRAISGLTGIKSHEKGIEAPE--LPER 367
           V A+     L V V GK  G L    EYS   V +A++ L G  +       PE  LP R
Sbjct: 323 VRALVQRNNLPVAVSGK-GGALTIYGEYSTQTVTQALADLLGETARLPIACDPETALPVR 381

Query: 368 PPALCPGCPHRAMYYSVRRAASELGIEGEDLIFPTDIGCYTLGIEPPYSAADYLLSMGSS 427
           PP LCPGC HRA+YY+VR+      + G+D ++ +DIGCYTLG+ PP   AD+L  MGSS
Sbjct: 382 PPNLCPGCSHRALYYAVRK------VFGDDAVYSSDIGCYTLGLLPPLRMADFLFCMGSS 435

Query: 428 VGTACGFSAATSQRIVSFIGDSTFFHAGIPPLINAVHNRQRFVLVILDNRTTAMTGGQPH 487
           V +  GF+ A+ +  ++FIGDSTFFH+GI  L+NAV N+   ++V+LDN TTAMTG QP+
Sbjct: 436 VSSGSGFATASGKPTLAFIGDSTFFHSGITGLVNAVFNKHDLIVVVLDNGTTAMTGHQPN 495

Query: 488 PGLPVDGMGEEAPAISIEDITRACGVEFVETVNPMNIRRSSETIRRALQHESVAVVISRY 547
           PG+  + +G     + IE + R CGV  V  V P N++ + + +    +   V V+I+  
Sbjct: 496 PGVVQEVLGNACVHLDIEAVVRGCGVADVVKVRPFNVKSTMKALAEMKERSGVRVIIAEE 555

Query: 548 PCMLSEGAVRGRP---VRVDEEKCDLCLECLNELACPAIVEEDGRVFIDPLYCRGCTICL 604
           PC+L       +P   V    E+     +CL  LACPA   +D  + +D   C GC +CL
Sbjct: 556 PCVLYARRTLKKPRNQVAYVAEQGPSVADCLEHLACPAFFRDDTGIHVDENLCGGCMVCL 615

Query: 605 QI 606
           Q+
Sbjct: 616 QV 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: 950
Number of extensions: 43
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: 629
Length adjustment: 37
Effective length of query: 581
Effective length of database: 592
Effective search space:   343952
Effective search space used:   343952
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: 54 (25.4 bits)

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

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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