Alignments for a candidate for hcrA in Sedimenticola selenatireducens DSM 17993

GapMind for catabolism of small carbon sources

Alignments for a candidate for hcrA in Sedimenticola selenatireducens DSM 17993

Align 4-hydroxybenzoyl-CoA reductase subunit alpha; 4-HBCR subunit alpha; EC 1.3.7.9 (characterized)
to candidate WP_029133526.1 A3GO_RS0111500 4-hydroxybenzoyl-CoA reductase subunit alpha

Query= SwissProt::O33819
         (769 letters)



>NCBI__GCF_000428045.1:WP_029133526.1
          Length = 770

 Score = 1175 bits (3040), Expect = 0.0
 Identities = 579/771 (75%), Positives = 668/771 (86%), Gaps = 3/771 (0%)

Query: 1   MSPKLPQ--HGTVGVRTPLVDGVEKVTGKAKYTADIAAPDALVGRILRSPHAHARILAID 58
           M+  LP+   G VGVRTPLVDG++KVTGKA+YTADI   DAL GRILRSP AH RIL+ID
Sbjct: 1   MNAPLPRLTKGPVGVRTPLVDGIDKVTGKARYTADIPRVDALAGRILRSPIAHGRILSID 60

Query: 59  TSAAEALEGVIAVCTGAETPVPFGVLPIAENEYPLARDKVRYRGDPVAAVAAIDEVTAEK 118
           TSAAEALEGVIA+CTG +  VPFGVLPIAENE+PLARDKVRYRG+PVAAVAAIDE TAE+
Sbjct: 61  TSAAEALEGVIAICTGDDCKVPFGVLPIAENEFPLARDKVRYRGEPVAAVAAIDEATAEQ 120

Query: 119 ALALIKVDYEVLPAYMTPKAAMKAGAIALHDDKPNNILREVHAEFGDVAAAFAEADLIRE 178
           A+ALIKV+YE L AY   + AM  GA  +HDDKPNN+LR+VH EFGDV A FA ADLI+E
Sbjct: 121 AMALIKVEYEPLKAYTEARKAMAEGAEVIHDDKPNNVLRKVHQEFGDVDAGFARADLIQE 180

Query: 179 KTYTFAEVNHVHMELNATLAEYDPVRDMLTLNTTTQVPYYVHLKVAACLQMDSARIRVIK 238
           +TY FAEVNHVH+ELNATLAEYDP R+ LTLNTTTQVPYYVHLKVA CL+MD +R+RVIK
Sbjct: 181 RTYRFAEVNHVHIELNATLAEYDPEREWLTLNTTTQVPYYVHLKVAHCLEMDESRVRVIK 240

Query: 239 PFLGGGFGARTEGLHFEIIAGLLARKAKGTVRLLQTREETFIAHRGRPWTEVKMKIGLKK 298
           PFLGGGFGARTE LHFEIIA LLARKA+GTVRL QTREETFIAHRGRP TE+K+++G+ +
Sbjct: 241 PFLGGGFGARTEALHFEIIAALLARKARGTVRLTQTREETFIAHRGRPDTEIKIRMGMTR 300

Query: 299 DGKIAALALEATQAGGAYAGYGIITILYTGALMHGLYHIPAIKHDAWRVYTNTPPCGAMR 358
           DG+I A+  E  Q GGAYAGYGIITILYTGALMHG+Y++PAI+HD WRVYTNTPPCGAMR
Sbjct: 301 DGRITAVHNEVIQRGGAYAGYGIITILYTGALMHGIYNLPAIRHDGWRVYTNTPPCGAMR 360

Query: 359 GHGTVDTRAAFEALLTEMGEELGIDSLKIRQINMLPQIPYVTMYAQRVMSYGVPECLEKV 418
           GHGTVD RAAFEAL+ EM E+L +D  ++R +N+L Q P  T+YAQ+V+SYG+PECL+KV
Sbjct: 361 GHGTVDPRAAFEALMNEMAEQLALDPFQVRHVNLL-QAPCTTLYAQKVLSYGLPECLDKV 419

Query: 419 KAASGWEERKGKLPKGRGLGIALSHFVSGTSTPKHWTGEPHATVNLKLDFDGGITLLTGA 478
             ASGW ER+G+LPKGRGLG+A SHFVSGTSTPKHWTGEPHATVNLKLDFDGGIT+LTGA
Sbjct: 420 LKASGWAERRGQLPKGRGLGMACSHFVSGTSTPKHWTGEPHATVNLKLDFDGGITILTGA 479

Query: 479 ADIGQGSNTMASQVAAEVLGVRLSRIRVISADSALTPKDNGSYSSRVTFMVGNASISAAE 538
           ADIGQGSNTM +QV  EVLGV + R+RVISADSALTPKDNGSYSSRVT MVGNA+  AAE
Sbjct: 480 ADIGQGSNTMVTQVVGEVLGVEMGRLRVISADSALTPKDNGSYSSRVTLMVGNAAKHAAE 539

Query: 539 ELKGVLVKAAAKKLDAREEDIEVIDEMFMVSGSQDPGLSFQEVVKAAMVDSGTITVKGTY 598
           +L+ +L++AAA+KL+     IE   E F +SG  D  L F E V+AAMVDSGT+TVKGT+
Sbjct: 540 QLRDILIEAAARKLEVAPNRIECGHECFRISGEADKTLDFAETVRAAMVDSGTVTVKGTF 599

Query: 599 TCPTEFQGDKKIRGSAIGATMGFCYAAQVVEASVDEITGKVTAHKVWVAVDVGKALNPLA 658
           TCP EFQGDK+IRGSAIGATMGFCYAAQVVEASVDE+TGKVTAHKVWVAVDVG+ALNPLA
Sbjct: 600 TCPPEFQGDKQIRGSAIGATMGFCYAAQVVEASVDEVTGKVTAHKVWVAVDVGRALNPLA 659

Query: 659 VEGQTQGGVWMGMGQALSEETVYDNGRMVHGNILDYRVPTIVESPDIEVIIVESMDPNGP 718
           VEGQ QGGVWMGMGQ +SEET +D  RM+HGN+LDYRVPTIVESPDIEV IVES+DPNGP
Sbjct: 660 VEGQIQGGVWMGMGQTVSEETRFDRERMIHGNLLDYRVPTIVESPDIEVHIVESIDPNGP 719

Query: 719 FGAKEASEGMLAGFLPAIHEAVYEAVGVRATDFPLSPDRITELLDAKEAAA 769
           FGAKEASEGMLAGFLPA+ +AV++A G+R    PL+P+R+++ L+A+E A+
Sbjct: 720 FGAKEASEGMLAGFLPALMDAVHDATGLRPDALPLTPERMSDWLEAQENAS 770


Lambda     K      H
   0.317    0.134    0.386 

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: 1661
Number of extensions: 59
Number of successful extensions: 2
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: 769
Length of database: 770
Length adjustment: 41
Effective length of query: 728
Effective length of database: 729
Effective search space:   530712
Effective search space used:   530712
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 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)
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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