Alignments for a candidate for hcrA in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for hcrA in Phaeobacter inhibens BS107

Align 4-hydroxybenzoyl-CoA reductase subunit alpha; 4-HBCR subunit alpha; EC 1.3.7.9 (characterized)
to candidate GFF2054 PGA1_c20870 molybdenum hydroxylase family protein, large subunit

Query= SwissProt::O33819
         (769 letters)



>FitnessBrowser__Phaeo:GFF2054
          Length = 787

 Score =  286 bits (731), Expect = 4e-81
 Identities = 241/798 (30%), Positives = 368/798 (46%), Gaps = 61/798 (7%)

Query: 5   LPQHGTVGVRTPLVDGVEKVTGKAKYTADIAAPDALVGRILRSPHAHARILAIDTSAAEA 64
           +P+   +G      + V  +TG   YT DI          LRS  AH R+ ++DTS A A
Sbjct: 1   MPKDSGIGASPKRREDVRFLTGTGNYTDDINMRGQAYVHFLRSDVAHGRLTSVDTSDAAA 60

Query: 65  LEGVIAVCTGAETPVPFGVLP------------IAENEYP-LARDKVRYRGDPVAAVAAI 111
           + GV+ + TGA+     G LP            + E  +P LA+ KVR+ GDP+AAV A 
Sbjct: 61  MPGVVRIFTGADFE-GVGGLPCGWQVTDRHGEVMQEPAHPVLAQGKVRHVGDPIAAVVAE 119

Query: 112 DEVTAEKALALIKVDYEVLPAYMTPKAAMKAGAIALHDDKPNNILRE---VHAEFGDVAA 168
               A  A   I +D E LPA +  K A+K GA  +HDD  +N+  +   V    G V  
Sbjct: 120 TPEQARDAAEAIVLDIEDLPAVINMKEAVKDGATKVHDDLTSNLCYDWGFVEENRGAVDK 179

Query: 169 AFAEADLIREKTYTFAEVNHVHMELNATLAEYDPVRDMLTLNTTTQVPYYVHLKVAA-CL 227
           A  +A  +         +    ME    + +++      TL TT+Q P+ + L + A  L
Sbjct: 180 AIKDAAHVTTLELVNNRLVANPMEPRVAVGDFNRATGDSTLYTTSQNPHVIRLLMGAFVL 239

Query: 228 QMDSARIRVIKPFLGGGFGARTEGLHFEIIAGLLARKAKGTVRLLQTREETFIAHRGRPW 287
            +   ++RV+ P +GGGFG++      E      A+     V+   +R E F++      
Sbjct: 240 GIPEHKLRVVAPDVGGGFGSKIFHYAEEAFCTFAAKALNRAVKWTSSRSEAFMSDAHGRD 299

Query: 288 TEVKMKIGLKKDGKIAALALEATQAGGAYAGY---GIITILYTGALMHGLYHIPAIKHDA 344
              K+++ L  D    AL  E     GAY       + T L+ G LM G Y  P I  + 
Sbjct: 300 HVTKIELALDADNNFTALRTETYANMGAYLSTFAPSVPTWLH-GTLMAGNYKTPLIYVNV 358

Query: 345 WRVYTNTPPCGAMRGHGTVDTRAAFEALLTEMGEELGIDSLKIRQINMLPQIPYVTMYAQ 404
             V+TNT    A RG G  +     E ++ +   ELG+D + +R+ N + + PY T  A 
Sbjct: 359 KAVFTNTVAVDAYRGAGRPEATYQLERVIDKAARELGVDPIALRRQNFITEFPYATPVAV 418

Query: 405 RVMS---YGVPECLEKVKAASGWEER------KGKLPKGRGLGIALSHFVSGTSTPKHWT 455
              +       + LE++   SG++ R      KGKL   RGLG+       G + P +  
Sbjct: 419 EYDTGDYVATMDKLEEIADLSGFDARRAASKAKGKL---RGLGVNCYIEACGIA-PSNLV 474

Query: 456 GEPHATVNL------KLDFDGGITLLTGAADIGQGSNTMASQVAAEVLGVRLSRIRVISA 509
           G+  A   L      +++  GGI ++TG+   GQG  T   QV A+++G+    + +   
Sbjct: 475 GQLGARAGLYESATVRVNATGGIVVMTGSHSHGQGHETSFPQVIADMIGIPEDMVEIEHG 534

Query: 510 DSALTPKDNGSYSSRVTFMVGNASISAAEELKGVLVKAAAKKLDAREEDIEVIDEMFMVS 569
           D+   P   G+Y SR   + G+A + A E++     K AA  L+A + DIE+ D  F V+
Sbjct: 535 DTDKAPMGMGTYGSRSLAVGGSAMVRATEKIIAKAKKIAAHILEASDADIELKDGQFTVA 594

Query: 570 GSQDPGLSFQEVVKAAMVDSGTITVKGTYTCPTEFQGDKKIRGSAIGATMGFCY--AAQV 627
           G+ D  L++ +V  AA V          +  P E   +  +  +A      F Y   A  
Sbjct: 595 GT-DKSLAWGDVTLAAYV---------PHNYPLE-DIEPGLEETAFYDPANFTYPSGAYA 643

Query: 628 VEASVDEITGKVTAHKVWVAVDVGKALNPLAVEGQTQGGVWMGMGQALSEETVY-DNGRM 686
            E  VD  TGKVT  +   A D G  +NP+ V+GQ  GG+  G+GQAL E  VY D+G++
Sbjct: 644 CEVEVDPDTGKVTIERFAAADDFGNIVNPMIVDGQVHGGIGQGIGQALLEGCVYDDDGQL 703

Query: 687 VHGNILDYRVPTIVESPDIEV-IIVESMDPNGPFGAKEASEGMLAGFLPAIHEAVYEAV- 744
           +  + +DY +P   + P  +V    ++   + P G K   E    G  PA+  AV +A+ 
Sbjct: 704 LSASFMDYAMPRADDLPFYKVDHSCQTPCTHNPLGVKGCGEAGAIGTPPAVVNAVVDALQ 763

Query: 745 ----GVRATDFPLSPDRI 758
                V   D PLSP R+
Sbjct: 764 SAGKDVTHIDMPLSPARV 781


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: 1351
Number of extensions: 55
Number of successful extensions: 8
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: 787
Length adjustment: 41
Effective length of query: 728
Effective length of database: 746
Effective search space:   543088
Effective search space used:   543088
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 17 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)
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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