Alignments for a candidate for iorA in Desulfobacter vibrioformis DSM 8776

GapMind for catabolism of small carbon sources

Alignments for a candidate for iorA in Desulfobacter vibrioformis DSM 8776

Align indolepyruvate ferredoxin oxidoreductase (subunit 2/2) (EC 1.2.7.8) (characterized)
to candidate WP_035235383.1 Q366_RS00625 indolepyruvate oxidoreductase

Query= BRENDA::O07835
         (647 letters)



>NCBI__GCF_000745975.1:WP_035235383.1
          Length = 604

 Score =  361 bits (927), Expect = e-104
 Identities = 227/630 (36%), Positives = 351/630 (55%), Gaps = 46/630 (7%)

Query: 18  LLLGNHAIARGALEANIAVFAAYPGTPSSELTDTMAAVAKKAG--VYMEYSTNEKVAFET 75
           L+LGN A+A G L+    +  AYPGTPSSE+   + ++ K+    ++ +++ NEKVAFET
Sbjct: 6   LILGNEALAYGLLKNGCQMACAYPGTPSSEILSAVVSLKKEMDLDIHAQWAVNEKVAFET 65

Query: 76  ALAAAWSGLRAMTAMKHVGLNVAADSFLSSVGMGVEGGFVIMVADDPSMWSSQNEQDTRV 135
           A A A +GLR   AMK VGLNVAAD  +SSV +GV+GGF+++ ADDP   SSQ EQD+R+
Sbjct: 66  AYAGAQAGLRTAVAMKQVGLNVAADPLMSSVYLGVKGGFLVISADDPGPHSSQTEQDSRL 125

Query: 136 YAKFANVPVLEPSSPHEAKEMTKYAFELSEKFKHFVILRTTTRSSHARGDVVLGELPEEI 195
            A  A +PVL+P SP +A E+   AFELSE F+  V+LR TTR  H+R  + +    E+I
Sbjct: 126 MAVMAKLPVLDPDSPGQAAELAGIAFELSEAFEIPVMLRPTTRVCHSRQSMDV----EKI 181

Query: 196 KTGKRKFGKFKKDPTRFVDVPAHARKFHPLILEKIEKIREELNNCPFNWIEGKEDAKVGI 255
           +  +R+   F K+P R+   P    + H  +  K+ KI +     P       +     I
Sbjct: 182 EMTRRE-AAFDKNPGRWAATPKFRLQLHKELEAKLTKIADYEPTRPRLVSGTAKGCGQAI 240

Query: 256 IAPGLSYAYVKEALAWLGVEDVKILKLGTPFPVPYGLLGKFFDGLEKVLIVEELEPVVEE 315
           +  G++ A  ++ +    + D+ + ++  PFP+    + +  +  +++L++EE   V+E 
Sbjct: 241 VVAGVAAANARDIIKERSL-DIPVYQVVQPFPLHKEFI-RQMNAYDEILVLEETWGVIEM 298

Query: 316 QVKTWAYDKGLRIPIHGKDLVPRVYEMTTRRAVEAIAKFLGLETPINFAEIDEKYEKVSQ 375
           Q+     DK  R+       +  V E+      E I  F G         +D +  +++ 
Sbjct: 299 QLA----DKN-RVKGKNTGFISPVGELLPENVEERICAFAG---------VDYQAPQIT- 343

Query: 376 IVPPRPPSLCPACPHRNSFFAIRKAAGPKAIYPSDIGCYTLGVLPPLRTVDTTVAMGASI 435
           ++P R P+LC  CPHR SF+AI+KAA PK I+ SDIGCYTLG    L  VDT   MGA I
Sbjct: 344 MLPGRRPTLCAGCPHRASFYAIKKAA-PKGIFTSDIGCYTLGC--NLGAVDTVTCMGAGI 400

Query: 436 GIGHGLSIAMNGSLAEEEHKEGKEKQIIVATIGDSTFYHTGLPALANAIYNRSNVLIVVL 495
               G +IA         + + +++  + +TIGDSTF+H+G+P L   +  +   ++V+L
Sbjct: 401 SQAAGFTIA---------YAKNEKQPPVFSTIGDSTFFHSGIPGLIETVTKKIPFVLVIL 451

Query: 496 DNLVTAMTGDQPNPGTGQTPHGMG-KRIPIEDVAKAMGADFVAVVDPYDIKATYETIKKA 554
           DN  TAMTG QP P +G+   G     + I  + K  G +F+ + DPYD+ A  + +K+A
Sbjct: 452 DNRTTAMTGHQPTPASGRDASGDSCIAVNIPAIVKGCGVNFIKIADPYDLPAFIDILKEA 511

Query: 555 ---LEVEGVSVVVSRQVCALYKIGQMRRRGMKWPIYHVV--EDKCTGCKICINAYGCPAI 609
               +  G +VV++   C L     M R  +K     V+  +D C GC  C++ + CPA+
Sbjct: 512 KAYCKENGPAVVIAEHPCLL----DMDRAELKASFKKVIVNKDICDGCGYCVSHFECPAL 567

Query: 610 YWDPETKKAKVDPTMCWGCGGCAQVCPFDA 639
             + +T++  +DP +C GC  C+ VCP DA
Sbjct: 568 GLNNDTEQVCIDPGLCTGCAVCSFVCPKDA 597


Lambda     K      H
   0.319    0.136    0.412 

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: 945
Number of extensions: 44
Number of successful extensions: 9
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: 647
Length of database: 604
Length adjustment: 38
Effective length of query: 609
Effective length of database: 566
Effective search space:   344694
Effective search space used:   344694
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 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