Alignments for a candidate for iorA in Desulfuromusa kysingii DSM 7343

GapMind for catabolism of small carbon sources

Alignments for a candidate for iorA in Desulfuromusa kysingii DSM 7343

Align indolepyruvate ferredoxin oxidoreductase (subunit 2/2) (EC 1.2.7.8) (characterized)
to candidate WP_092347349.1 BLU87_RS09500 indolepyruvate oxidoreductase

Query= BRENDA::O07835
         (647 letters)



>NCBI__GCF_900107645.1:WP_092347349.1
          Length = 608

 Score =  372 bits (955), Expect = e-107
 Identities = 244/631 (38%), Positives = 351/631 (55%), Gaps = 45/631 (7%)

Query: 18  LLLGNHAIARGALEANIAVFAAYPGTPSSELTDTMAAVAKKA--GVYMEYSTNEKVAFET 75
           LL+GN AI +G +EA   V AAYPGTPS+E+   +    ++A   +++E+S NEK+AFE 
Sbjct: 7   LLMGNEAIGQGLIEAGCQVAAAYPGTPSTEILQAVIDRQEQAVEPLHIEWSVNEKIAFEV 66

Query: 76  ALAAAWSGLRAMTAMKHVGLNVAADSFLSSVGMGVEGGFVIMVADDPSMWSSQNEQDTRV 135
           ALAA+++G R++  MK VGLNVAAD F+ +  +G++GG + +VADDP   SSQNEQDTR+
Sbjct: 67  ALAASYTGKRSVAVMKQVGLNVAADPFMRTAYIGIKGGMLTIVADDPGPHSSQNEQDTRL 126

Query: 136 YAKFANVPVLEPSSPHEAKEMTKYAFELSEKFKHFVILRTTTRSSHARGDVVLGELPEEI 195
           +   A VPVL+PSSP EAK M + AFELSEK++  ++LR TTR  H+R +V L E P E+
Sbjct: 127 FCLQARVPVLDPSSPAEAKAMIQPAFELSEKYETNIVLRPTTRICHSRQNVSL-EKPIEL 185

Query: 196 KTGKRKFGKFKKDPTRFVDVPAHARKFHPLILEKIEKIREELNNCPFNWIEGKEDAKVGI 255
           K    +   F+ +PTR+   PA   + H  +   +E+I  E    P      +   +   
Sbjct: 186 K----RQADFEPNPTRWAATPAFLPQLHRNLNRHLEEIALEPAWQPRLLSGNESQPRTAF 241

Query: 256 IAPGLSYAYVKEALAWLGVE-DVKILKLGTPFPVPYGLLGKFFDGLEKVLIVEELEPVVE 314
           IA G++Y+ + + L  LG++  + + ++  P+P+            ++VLI+EE  PV+E
Sbjct: 242 IASGIAYSNLVDLLEELGLDHTIDLYQVLMPYPLNPDFCKLMQKKYDRVLILEETYPVIE 301

Query: 315 EQVKTWAYDKGLRIPIHGKDLVPRVYEMTTRRAVEAIAKFLGLETPINFAEIDEKYEKVS 374
            Q+   A+   +     G   VPR  E+T     +A+A FL L  P          EK +
Sbjct: 302 LQL---AHPGAVGKQTGG---VPREGELTPDVIHQALADFLQLAPPA---------EKPA 346

Query: 375 QIVPPRPPSLCPACPHRNSFFAIRKAAGPKAIYPSDIGCYTLGVLPPLRTVDTTVAMGAS 434
                R PSLCP C HR +F+ I+K   PK I+PSDIGCYTLG+   L  V T   MGA 
Sbjct: 347 ARRGQR-PSLCPGCSHRTAFYTIKKCF-PKGIFPSDIGCYTLGM--NLGAVHTVHCMGAC 402

Query: 435 IGIGHGLSIAMNGSLAEEEHKEGKEKQIIVATIGDSTFYHTGLPALANAIYNRSNVLIVV 494
           I  G G   A          ++  +   IV TIGDSTF+H G+PAL NA+  ++ +++V+
Sbjct: 403 ISQGAGFYQAY--------QQDDGQFPTIVVTIGDSTFFHAGIPALINAVIQQTRMIVVI 454

Query: 495 LDNLVTAMTGDQPNPGTG-QTPHGMGKRIPIEDVAKAMGADFVAVVDPYDIKATYETIKK 553
           LDN   AMTG QP P  G    +   K I IE + KA G +F+   +PYD +     +K+
Sbjct: 455 LDNATAAMTGGQPVPHMGVAAGNKPTKAIAIEPLVKASGVEFLETCNPYDHERFEALLKQ 514

Query: 554 A-----LEVEGVSVVVSRQVCALYKIGQMRRRGMKWPIYHVVEDKCTGCKICINAYGCPA 608
           A         GV+V+++R  C +       R+  K      ++D C GC+ C +A+ CPA
Sbjct: 515 ADSYIRSPEGGVAVLIARHGCIM---DPATRKAQK-SFTVTIQDNCIGCEKCTSAFECPA 570

Query: 609 IYWDPETKKAKVDPTMCWGCGGCAQVCPFDA 639
           +  D     A VD   C GCG C  VCP  A
Sbjct: 571 LSMDRTRNIAVVDQDRCIGCGTCIPVCPVAA 601


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: 935
Number of extensions: 51
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: 608
Length adjustment: 38
Effective length of query: 609
Effective length of database: 570
Effective search space:   347130
Effective search space used:   347130
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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