Alignments for a candidate for hcrA in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for hcrA in Acidovorax sp. GW101-3H11

Align 4-hydroxybenzoyl-CoA reductase subunit alpha; 4-HBCR subunit alpha; EC 1.3.7.9 (characterized)
to candidate Ac3H11_3591 Carbon-monoxide dehydrogenase form II, large subunit (EC 1.2.99.2)

Query= SwissProt::O33819
         (769 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_3591
          Length = 795

 Score =  281 bits (718), Expect = 1e-79
 Identities = 240/790 (30%), Positives = 367/790 (46%), Gaps = 65/790 (8%)

Query: 24  VTGKAKYTADIAAPDALVGRILRSPHAHARILAIDTSAAEALEGVIAVCTGAETP----- 78
           +TG  +YT D+          +RSPHAHA I +I+TSAA+A  GV+ V  GA+       
Sbjct: 25  LTGAGQYTDDVVLAAQCHAVFVRSPHAHAGINSINTSAAKAAPGVLGVFVGADVAADNIN 84

Query: 79  -VPFGVL-------PIAENEYP-LARDKVRYRGDPVAAVAAIDEVTAEKALALIKVDYEV 129
            +P G L       P+ E  +P LA+ KVRY GD VA V A     A  A  L++VDY+V
Sbjct: 85  GLPCGWLITSTNGEPMKEPPHPILAQGKVRYVGDHVAMVVAQTLQQARDAAELVEVDYDV 144

Query: 130 LPAYMTPKAAMKAGAIA---LHDDKPNN-ILREVHAEFGDVAAAFAEADLIREKTYTFAE 185
           LPA +    A  AGA+A   LHD  P+N   +    + G V AAFA A  + +       
Sbjct: 145 LPAVVNVADAA-AGAVAGAALHDIAPDNHCFKWAIGDKGAVDAAFAGAAHVTQLDLINNR 203

Query: 186 VNHVHMELNATLAEYDPVRDMLTLNTTTQVPYYVHLKVAACLQ-MDSARIRVIKPFLGGG 244
           +    ME  A +  Y    D  TL  + Q P+   L + A +  +   ++RVI P +GGG
Sbjct: 204 LIPNAMEPRAAIGSYSRANDEYTLYVSNQNPHVERLLMTAFVMGLPEHKVRVIAPDVGGG 263

Query: 245 FGARTEGLHFEIIAGLLARKAKGTVRLLQTREETFIAH-RGRPWTEVKMKIGLKKDGKIA 303
           FG++      ++     A+K    ++ +  R E+F++   GR       ++ + KDGK  
Sbjct: 264 FGSKIYLYAEDVCLTWAAKKLNRNIKWVADRSESFLSDAHGRDHIS-HAEMAMDKDGKFL 322

Query: 304 ALALEATQAGGAYAGY---GIITILYTGALMHGLYHIPAI--KHDAWRVYTNTPPCGAMR 358
           A+ +      GAY       + TILY   L+ G Y  P +  + D+W  +TNT P  A R
Sbjct: 323 AMRVHTHANLGAYLSTFASAVPTILYA-TLLAGQYTTPQVYVEVDSW--FTNTAPVDAYR 379

Query: 359 GHGTVDTRAAFEALLTEMGEELGIDSLKIRQINMLPQIPYVTMYAQRVMSYGVPECL--- 415
           G G  +     E L+T    ELG+   +IR+ N +   PY T  A +        C+   
Sbjct: 380 GAGRPEATYLLERLVTRCAWELGLSQDEIRKRNFITSFPYQTPVALQYDIGDYHACMTQA 439

Query: 416 EKVKAASGWEERKGKLP-KGRGLGIALSHFVSGTS-TPKHWTGEPHATVNL------KLD 467
           +++   +G+  RK     KG   GI  S ++      P +  G   A   L      ++ 
Sbjct: 440 QQLADVAGFAARKAASEAKGFKRGIGYSSYIEACGIAPSNIAGALGARAGLFECGEVRVH 499

Query: 468 FDGGITLLTGAADIGQGSNTMASQVAAEVLGVRLSRIRVISADSALTPKDNGSYSSRVTF 527
             G +T+ TG+   GQG  T  +QV A  LG+ +  + ++  D+   P   G+Y SR   
Sbjct: 500 PTGSVTVFTGSHSHGQGHETTFAQVVAARLGIPVENVDIVHGDTGRVPFGMGTYGSRSIS 559

Query: 528 MVGNASISAAEELKGVLVKAAAKKLDAREEDIEVIDEMFMVSGSQDPGLSFQEVVKAAMV 587
           + G A + A ++++    K AA  ++A + DI+     F V G+ D  + F +V   A V
Sbjct: 560 VGGAAIMKALDKIEAKAKKIAAHLMEASDADIDFSGGEFTVRGT-DKKIPFGQVALTAYV 618

Query: 588 DSGTITVKGTYTCPTEFQGDKKIRG---SAIGATMGFCYAA--QVVEASVDEITGKVTAH 642
                        P  +  DK   G   +A      F + A   + E  +D  TG     
Sbjct: 619 -------------PHNYPLDKLEPGLNETAFYDPTNFTFPAGTYICEVEIDPATGSTRVD 665

Query: 643 KVWVAVDVGKALNPLAVEGQTQGGVWMGMGQALSEETVYD--NGRMVHGNILDYRVPTIV 700
           K     D G  +NP+ VEGQ  GG+  G+GQA+ E  VYD   G+++ G+ +DY +P   
Sbjct: 666 KFTAVDDFGTIINPMIVEGQVHGGLVQGIGQAVLENCVYDRETGQLLTGSFMDYAMPRAD 725

Query: 701 ESPDIEVIIVESMDPNGPFGAKEASEGMLAGFLPAIHEAVYEA---VGVRATDFPLSPDR 757
           + P+ ++  V +   + P G K   E    G  PA+  AV +A   +GV+  D P SP R
Sbjct: 726 DFPEFKLGHVCTPCTHNPLGTKGCGEAGAIGSPPAVINAVLDALRPLGVKDFDMPASPHR 785

Query: 758 ITELLDAKEA 767
           + E + + +A
Sbjct: 786 VWEAIQSAKA 795


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: 1329
Number of extensions: 61
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: 795
Length adjustment: 41
Effective length of query: 728
Effective length of database: 754
Effective search space:   548912
Effective search space used:   548912
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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Protein sequences (fasta format)
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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