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

GapMind for catabolism of small carbon sources

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

Align Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized)
to candidate Ac3H11_3090 Benzoate-CoA ligase (EC 6.2.1.25)

Query= SwissProt::Q8GQN9
         (527 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_3090
          Length = 518

 Score =  545 bits (1405), Expect = e-159
 Identities = 289/515 (56%), Positives = 352/515 (68%), Gaps = 13/515 (2%)

Query: 17  KIPERYNAADDLIGRNLLAGRGGKTVYIDDAGSYTYDELALRVNRCGSALRTTLGLQPKD 76
           ++PE +N A+ L   N    RG +  YIDD  + +Y  L  R  R  + L    G++ ++
Sbjct: 3   RLPEHFNFAEHLFALN--RARGDRMAYIDDHETLSYGALEDRARRLAAVLAAA-GVRREE 59

Query: 77  RVLVCVLDGIDFPTTFLGAIKGGVVPIAINTLLTESDYEYMLTDSAARVAVVSQELLPLF 136
           RVL+ +LD  D+P  FLG +  GV+P+A+NTLL   DY YML+ + AR  +VS  LLP+ 
Sbjct: 60  RVLLLMLDTCDWPVAFLGCLYAGVLPVAVNTLLKPEDYAYMLSHARARAVLVSGALLPVL 119

Query: 137 APMLGKVPTLEHLVVAGG------AGEDSLAALLATGSEQFEAAPTRPDDHCFWLYSSGS 190
              + + P    L V         AG   + A +A        A T PD   FWLYSSGS
Sbjct: 120 NDAMERQPHEVALQVVSQPQGPLPAGAVDMRAAIAAAVPLAAPAATGPDAPGFWLYSSGS 179

Query: 191 TGAPKGTVHIHSDLIHTAELYARPILGIREGDVVFSAAKLFFAYGLGNGLIFPLAVGATA 250
           TG PKGTVH H +L  TAELY +P+LG+ E D  FSAAKL+FAYGLGN L FPL+VGAT 
Sbjct: 180 TGKPKGTVHTHGNLWWTAELYGKPVLGLTEQDRCFSAAKLYFAYGLGNSLTFPLSVGATV 239

Query: 251 VLMAERPTPAAVFERLRRHQPDIFYGVPTLYASMLANPDCPKEGELRLRACTSAGEALPE 310
           VLMAERPTP A FER  RHQP +F+G PT +A MLA+P  P    + LR C+SAGEALP 
Sbjct: 240 VLMAERPTPDATFERWTRHQPTVFFGAPTGFAGMLASPRLPPRSAVSLRMCSSAGEALPA 299

Query: 311 DVGRRWQARFGVDILDGIGSTEMLHIFLSNRAGDVHYGTSGKPVPGYRLRLIDEDGAEIT 370
           ++ +R++A FG DI+DGIGSTEMLHIFLSNR GDV YGT+GKPVPGY + L  EDG E+ 
Sbjct: 300 EIAQRFKAHFGCDIIDGIGSTEMLHIFLSNRPGDVRYGTTGKPVPGYEVSLRGEDGREVP 359

Query: 371 TAGVAGELQISGPSSAVMYWNNPEKTAATFMGEWTRSGDKYLVNDEGYYVYAGRSDDMLK 430
             G  G+L I GPS+A++YWNN EKT  TF G WT+SGDKY+ + EGYY YAGRSDDMLK
Sbjct: 360 D-GEIGDLYIQGPSAALLYWNNREKTRETFQGAWTKSGDKYVRDAEGYYTYAGRSDDMLK 418

Query: 431 VSGIYVSPIEVESALIAHEAVLEAAVVGWEDEDHLIKPKAFIVLKPGYGAGEALRTDLKA 490
           VSGIYVSP EVE+ L+ H+AVLEAAV+G +D D L K KAF+VLK G     A   DLKA
Sbjct: 419 VSGIYVSPFEVEATLMQHQAVLEAAVIGAQDADGLTKTKAFVVLKDGQ---TATPDDLKA 475

Query: 491 HVKNLLAPYKYPRWIEFVDDLPKTATGKIQRFKLR 525
            VK  LAPYKYPR IEFV +LPKTATGKIQRF+LR
Sbjct: 476 FVKERLAPYKYPRLIEFVPELPKTATGKIQRFRLR 510


Lambda     K      H
   0.319    0.138    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: 823
Number of extensions: 32
Number of successful extensions: 5
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: 527
Length of database: 518
Length adjustment: 35
Effective length of query: 492
Effective length of database: 483
Effective search space:   237636
Effective search space used:   237636
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: 52 (24.6 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