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 ferredoxin oxidoreductase (subunit 2/2) (EC 1.2.7.8) (characterized)
to candidate WP_028314756.1 G491_RS0111840 indolepyruvate ferredoxin oxidoreductase

Query= BRENDA::O07835
         (647 letters)



>NCBI__GCF_000429905.1:WP_028314756.1
          Length = 644

 Score =  404 bits (1038), Expect = e-117
 Identities = 254/649 (39%), Positives = 355/649 (54%), Gaps = 40/649 (6%)

Query: 12  KPGERVLLLGNHAIARGALEANIAVFAAYPGTPSSELTDTMAAVAKKAGVYMEYSTNEKV 71
           K GE+VL +GN AIARGALEA ++V A YPGTPSSE+ + +A V+K+A +Y+E+S NEK+
Sbjct: 8   KKGEKVLFMGNQAIARGALEAGVSVAAGYPGTPSSEIIENLADVSKEANMYVEWSANEKI 67

Query: 72  AFETALAAAWSGLRAMTAMKHVGLNVAADSFLSSVGMGVEGGFVIMVADDPSMWSSQNEQ 131
           A E A AA+++GLR+M  MK  G+NVA+D  L  V  G  GG V++  DDP   SS NE 
Sbjct: 68  AVEVAAAASFAGLRSMCTMKQNGVNVASDFLLHLVLSGTRGGMVLVPCDDPGALSSINEG 127

Query: 132 DTRVYAKFANVPVLEPSSPHEAKEMTKYAFELSEKFKHFVILRTTTRSSHARGDVVLGEL 191
           + R +AK   +P+LE     EAK+M K+AFELSE+  + V+ R+ TR SHA G V LGE+
Sbjct: 128 EARHFAKLLEIPLLEAGDFQEAKDMLKWAFELSEEIHNLVMFRSVTRLSHASGSVELGEI 187

Query: 192 PEEIKTGKRKFGKFKKDPTRFVDVPAHARKFHPLILEKIEKIREELNNCPFNWIEGKEDA 251
           P      K     F  DP     V A     H L  +K++K  E     PFN   G E+ 
Sbjct: 188 PHTEPQAKFVNNGFILDPLEGPIVSAPVGYKHGLQQDKLKKAEELFEESPFNTYVGPENP 247

Query: 252 KVGIIAPGLSYAYVKEALAWLGVED-VKILKLGTPFPVPYGLLGKFFDGLEKVLIVEELE 310
           ++ +I    +  Y +EA+     +D V +LKLGT FP+P  L+ K     +KVL+VEE+ 
Sbjct: 248 EILLITSSGATLYSREAIHLCNAKDKVGLLKLGTTFPLPSKLIAKHLKTTDKVLVVEEVL 307

Query: 311 PVVEEQVKTWAYDKGLRI---PIHGK--DLVPRVYEMTTRRAVEAIAKFLGLETPINFAE 365
           P +EE +K  A +    +     +GK    +P   E+       A+A  LG      ++ 
Sbjct: 308 PFMEENLKVLAQELAPEVGQKTFYGKRSGNIPMTGELNPDLVATALATLLG----DAYSP 363

Query: 366 IDEKYE-KVSQIV----PPRPPSLCPACPHRNSFFAIRK---AAGPKAIYPSDIGCYTLG 417
            D++Y+ K +Q V    P R  + CP CPHR SF++I     A   +     DIGCY++ 
Sbjct: 364 QDQEYQTKAAQQVFFNAPVRDLTFCPGCPHRASFWSIHNVLAADNREGFVCGDIGCYSMA 423

Query: 418 VLPP-LRTVDTTVAMGASIGIGHGLSIAMNGSLAEEEHKEGKEKQIIVATIGDSTFYHTG 476
            LP    T+ T  AMG+  G+  G        L           Q +V+  GDSTF+H+G
Sbjct: 424 FLPSGFSTLKTLHAMGSGTGVASGFGKLGQFGL----------DQPVVSVCGDSTFFHSG 473

Query: 477 LPALANAIYNRSNVLIVVLDNLVTAMTGDQPNPGTGQTPHG-MGKRIPIEDVAKAMGADF 535
           +PAL NAI+++S++ +V+LDN  T MTG Q +PG      G     + I  + +A+GA  
Sbjct: 474 IPALVNAIHHKSDITMVILDNSGTGMTGFQSHPGLPVDAQGNESPALDIPTICRALGAT- 532

Query: 536 VAVVDPYDIKATYETIKKALEVEGVSVVVSRQVCALYKIGQMRRRGMKWPIYHVVEDKCT 595
           V V DP+    T +T  K LE  G  V+V RQ+CAL       ++G K     V ED C 
Sbjct: 533 VEVCDPFYPYKTQQTFHKLLEAPGAKVLVLRQICAL----SPEKKGKKQFEMSVDEDVCL 588

Query: 596 G--C---KICINAYGCPAIYWDPETKKAKVDPTMCWGCGGCAQVCPFDA 639
           G  C   K+C   + CP + WD E K A +D  +C GCG CA +CP  A
Sbjct: 589 GENCGCNKLCTRVFRCPGLRWDEEKKVATIDEVICAGCGMCAAICPSGA 637


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: 1016
Number of extensions: 45
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: 647
Length of database: 644
Length adjustment: 38
Effective length of query: 609
Effective length of database: 606
Effective search space:   369054
Effective search space used:   369054
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