Alignments for a candidate for iorA in Desulfatibacillum aliphaticivorans DSM 15576

GapMind for catabolism of small carbon sources

Alignments for a candidate for iorA in Desulfatibacillum aliphaticivorans DSM 15576

Align Indolepyruvate oxidoreductase subunit IorA; IOR; Indolepyruvate ferredoxin oxidoreductase subunit alpha; EC 1.2.7.8 (characterized)
to candidate WP_028316789.1 G491_RS0127265 indolepyruvate ferredoxin oxidoreductase subunit alpha

Query= SwissProt::P80910
         (618 letters)



>NCBI__GCF_000429905.1:WP_028316789.1
          Length = 617

 Score =  541 bits (1393), Expect = e-158
 Identities = 278/613 (45%), Positives = 401/613 (65%), Gaps = 18/613 (2%)

Query: 12  GDRLFLLGNEAAVRAAIESGVGVASTYPGTPSSEIGNVLSKIAKRAGIYFEFSINEKVAL 71
           G  + +LGNEA  R A+E+GV  A+TYPGTPSSE+     +++K + +YFE+S NEKVAL
Sbjct: 10  GKEMLVLGNEAIARGAVEAGVACATTYPGTPSSELSLAFFQMSKESDLYFEYSTNEKVAL 69

Query: 72  EVAAAAAASGVRSFTFMKHVGLNVASDSFMSVAYTGVRAGMVVLSADDPSMFSSQNEQDN 131
           EVAAAAA +G+RS   MKHVG+NVA+D+ M++AY GV+AGMV+L+ADDP MFSSQNEQDN
Sbjct: 70  EVAAAAANAGIRSMCVMKHVGVNVAADALMTLAYIGVKAGMVLLTADDPFMFSSQNEQDN 129

Query: 132 RHYARLAWVPLLEPSNPQEILEYMNHAFELSEEYRIPVLLRTTTRVSHMRGVVEAGERRA 191
           R+Y ++A + +LEPS+  E      +AFELSE+   PV+LRTTTR++H  G +  GE   
Sbjct: 130 RYYGKMAGLCVLEPSSLPEAKAMATYAFELSEKLGEPVILRTTTRINHSTGAITLGELVK 189

Query: 192 EPVKGFFRKNPEQFVPVPATARVMRRELVEKMKKLKRVADTSELNRVLNEDSESDLGIIA 251
             +KG F K+P   V +PA +R +   L++++ + +++ D ++ N V     E   GI+ 
Sbjct: 190 PNIKGSFTKDPFNLVAIPAVSRRLHTRLLQRLAEAEKITDQTDFNYV---QGEGAWGIVC 246

Query: 252 SGGAFNYVYDALQTLGL--DVPVLKLGFTYPFPAGLVAEFLSGLEGVLVVEEVDSVMEKE 309
           +G ++NYV DAL  LG+   V +L++GF+ P P   V EFL G E +LV EE +  ME+ 
Sbjct: 247 NGVSYNYVCDALNDLGVADKVSILRIGFSNPMPVAKVTEFLKGKEKILVAEEGEPFMEEA 306

Query: 310 VLAVATSEGLDVGVHGKLDGTLPEIYEYSEDIVRRAISGLTGIKSHEKG----IEAPELP 365
           + ++A   G  + + GK         E+    VR+AI+G  G+           + PE+P
Sbjct: 307 MRSMAQEVGCTIPIKGKGPELFSREGEFDPAGVRKAIAGFFGVDLAPAASLDLSDLPEIP 366

Query: 366 ERPPALCPGCPHRAMYYSVRRAASELGIEGEDLIFPTDIGCYTLGIEPPYSAADYLLSMG 425
            RPP LC GC HRA++Y V++AA ++     +++ PTDIGCYTLG+ PP S+AD+L+ MG
Sbjct: 367 ARPPNLCAGCTHRAVFYEVKKAAEDM-----EIMHPTDIGCYTLGVLPPLSSADFLICMG 421

Query: 426 SSVGTACGFSAATSQRIVSFIGDSTFFHAGIPPLINAVHNRQRFVLVILDNRTTAMTGGQ 485
           SS+ T CGFS    Q++V++IGDSTFFH+G+P LINAVHN     +VILDN TTAMTG Q
Sbjct: 422 SSISTGCGFSKFIDQKVVTYIGDSTFFHSGVPGLINAVHNNHNVTMVILDNGTTAMTGHQ 481

Query: 486 PHPGLPVDGMGEEA-PAISIEDITRACGVEFVETVNPMNIRRSSETIRRALQHESVAVVI 544
           P+PG+  D MG+E    ISIE++ +  GVE V  + P  +++S + I+ AL ++ V+V+I
Sbjct: 482 PNPGVDRDAMGQEGYNRISIENVVKGLGVESVTVIKPYKVQKSVDAIKEALAYQGVSVII 541

Query: 545 SRYPCMLSEGAVR---GRPVRVDEEKCDLCLECLNELACPAIVEEDGRVFIDPLYCRGCT 601
           ++  C L   A++    +P R+D EKC     C++ L CPA+  E+ +V I+   C GC 
Sbjct: 542 AQELCPLYAKALKRPAKKPFRIDMEKCKDHRLCVDALGCPAMYVENNKVAINAEQCIGCA 601

Query: 602 ICLQICPAGAIKP 614
           +C Q+CP  AI P
Sbjct: 602 VCAQVCPEHAIVP 614


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: 907
Number of extensions: 47
Number of successful extensions: 7
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: 617
Length adjustment: 37
Effective length of query: 581
Effective length of database: 580
Effective search space:   336980
Effective search space used:   336980
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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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