Alignments for a candidate for hcrA in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for hcrA in Dinoroseobacter shibae DFL-12

Align 4-hydroxybenzoyl-CoA reductase subunit alpha; 4-HBCR subunit alpha; EC 1.3.7.9 (characterized)
to candidate 3609273 Dshi_2659 aldehyde oxidase and xanthine dehydrogenase molybdopterin binding (RefSeq)

Query= SwissProt::O33819
         (769 letters)



>FitnessBrowser__Dino:3609273
          Length = 791

 Score =  302 bits (774), Expect = 4e-86
 Identities = 251/804 (31%), Positives = 375/804 (46%), Gaps = 56/804 (6%)

Query: 5   LPQHGTVGVRTPLVDGVEKVTGKAKYTADIAAPDALVGRILRSPHAHARILAIDTSAAEA 64
           +P+ G +G  +   + V  +TG+ +YT DI   +      LRS  AH +I  IDT+AAE 
Sbjct: 1   MPKDGGIGASSKRREDVRFLTGRGRYTDDINLNNQTYAYFLRSEVAHGKINGIDTAAAEG 60

Query: 65  LEGVIAVCTGAETPVPFGV-----------LPIAENEYP-LARDKVRYRGDPVAAVAAID 112
           ++GVI V T  +     GV            P+ E ++P LA  KVR+ GDP+A V A  
Sbjct: 61  MDGVIRVFTAKDFEGVGGVPCGWQVTDIHGQPMKEPKHPVLAEGKVRHVGDPIAVVVAES 120

Query: 113 EVTAEKALALIKVDYEVLPAYMTPKAAMKAGAIALHDDKPNNILRE---VHAEFGDVAAA 169
              A  A   I++D E LPA M  KAA+  GA  +HDD  +N+  E   V      V  A
Sbjct: 121 LEQARDAAEAIELDIEELPAVMDMKAALAEGATKVHDDLDDNLCYEWGFVEENRAAVDEA 180

Query: 170 FAEADLIREKTYTFAEVNHVHMELNATLAEYDPVRDMLTLNTTTQVPYYVHLKVAA-CLQ 228
              A  +     T   +    ME    + +Y P     TL TT+Q P+ + L + A  L 
Sbjct: 181 IKNAHHVTTLELTNNRLVANPMEPRVAVGDYHPGTQDYTLYTTSQNPHVIRLLMGAFVLG 240

Query: 229 MDSARIRVIKPFLGGGFGARTEGLHFEIIAGLLARKAKGTVRLLQTREETFIAHRGRPWT 288
           +   ++RV+ P +GGGFG++      E      + +    V+   +R E F++       
Sbjct: 241 IPEHKLRVVAPDVGGGFGSKIYHYAEEAFVTFASGQIGRPVKWTSSRSEAFVSDAHGRDH 300

Query: 289 EVKMKIGLKKDGKIAALALEATQAGGAYAGY---GIITILYTGALMHGLYHIPAIKHDAW 345
             K+++ L ++ K  AL  +     GAY       I T L+ G L+ G Y  P I  +  
Sbjct: 301 VTKIELALDENHKFTALRCDTYANMGAYLSTFAPSIPTWLH-GTLLAGNYTTPLIYTNVK 359

Query: 346 RVYTNTPPCGAMRGHGTVDTRAAFEALLTEMGEELGIDSLKIRQINMLP--QIPYVTMYA 403
            V+T T P  A RG G  +     E ++ +   ELG+D  ++R+IN +   Q PY T  A
Sbjct: 360 AVFTTTTPVDAYRGAGRPEATFQLERVVDKAARELGVDPAELRRINFIKPEQFPYDTPVA 419

Query: 404 QRVMSYGVPECLEKVKAASGWE--ERKGKLPKGRGL--GIALSHFVSGTS-TPKHWTGEP 458
               +      LEK    +G +  E +    K RG   G  L+HF+      P +  G+ 
Sbjct: 420 VTYDTGNYHATLEKGLEMAGADTFEARAAESKARGKLRGFGLAHFIEACGIAPSNLVGQL 479

Query: 459 HATVNL------KLDFDGGITLLTGAADIGQGSNTMASQVAAEVLGVRLSRIRVISADSA 512
            A   L      +++  G I+++TG+   GQG  T   QV AE+LG+  + I ++  D+A
Sbjct: 480 GARAGLYESATVRVNATGSISVMTGSHSHGQGHETAFPQVVAEMLGIDENMIEIVHGDTA 539

Query: 513 LTPKDNGSYSSRVTFMVGNASISAAEELKGVLVKAAAKKLDAREEDIEVIDEMFMVSGSQ 572
            TP   G+Y SR   + G+A + A E++     K AA  L+A E DIE+ D  F V+G+ 
Sbjct: 540 NTPMGMGTYGSRSIAVGGSAMVRATEKIINKAKKIAAHLLEAAEGDIELKDGAFTVAGT- 598

Query: 573 DPGLSFQEVVKAAMVDSGTITVKGTYTCPTEFQGDKKIRGSAIGATMGFCY--AAQVVEA 630
           D  +++ +V  AA V          +  P E   +  +  +A      F Y   A + E 
Sbjct: 599 DKSVAWGDVTLAAYV---------PHNYPLE-DIEPGLEETAFYDPSNFTYPSGAYICEV 648

Query: 631 SVDEITGKVTAHKVWVAVDVGKALNPLAVEGQTQGGVWMGMGQALSEETVYD-NGRMVHG 689
            VD  TGKV       A D G  +NP+ VEGQ  GGV  G+GQAL E   YD +G+++ G
Sbjct: 649 EVDPDTGKVDVLAFTAADDFGNVINPMIVEGQVHGGVAQGIGQALLENCSYDADGQLLSG 708

Query: 690 NILDYRVPTIVESPDIEVIIVESMDP--NGPFGAKEASEGMLAGFLPAIHEAVYEAV--- 744
           + +DY +P   + P  EV     + P  + P G K   E    G  PA+  AV +A+   
Sbjct: 709 SYMDYTMPRADDLPMFEV-DHSCITPCTHNPLGVKGCGEAGAIGSPPAVVNAVIDALHRA 767

Query: 745 ---GVRATDFPLSPDRITELLDAK 765
               V   D PL+P R+   +  K
Sbjct: 768 GQTHVTHIDMPLTPSRVWAAIHGK 791


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: 1382
Number of extensions: 73
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: 791
Length adjustment: 41
Effective length of query: 728
Effective length of database: 750
Effective search space:   546000
Effective search space used:   546000
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)
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