GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hcl in Rhizobium leguminosarum bv. trifolii WSM1325

Align Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized)
to candidate WP_012755263.1 RLEG_RS23870 AMP-binding protein

Query= SwissProt::Q8GQN9
         (527 letters)



>NCBI__GCF_000023185.1:WP_012755263.1
          Length = 528

 Score =  179 bits (454), Expect = 2e-49
 Identities = 147/484 (30%), Positives = 222/484 (45%), Gaps = 22/484 (4%)

Query: 51  TYDELALRVNRCGSALRTTLGLQPKD-RVLVCVLDGIDFPTTFLGAIKGGVVPIAINTLL 109
           +Y EL  R+ RC   L   LG +    RV +   + +D         + G + + +N  L
Sbjct: 45  SYAELDTRIARCAGLLSDVLGARRDGGRVALLARNSLDSIVLAFACQRAGAIYVPLNWRL 104

Query: 110 TESDYEYMLTDSAARVAVVSQELLPLFAPMLGKVPTLEHLVVAGGAGEDSLAALLATGSE 169
             ++   +L D A  + V  +E     A + G  P +  +  A G      A   A    
Sbjct: 105 NAAELRPILADCAPVLLVHDEEFAATVASLAGADPEMAVISTADGP-----AGFAARIEA 159

Query: 170 QFEAAPTRPDDH--CFWLYSSGSTGAPKGTVHIHSDLIHTAELYARPILG-IREGDVVFS 226
              AAP   D    C  LY+SG+TG PKG V    +    A  ++  ++G I  G V   
Sbjct: 160 SLPAAPVSADADGACVLLYTSGTTGQPKGVVITRRNAFFAAFNFS--VVGEIGPGSVALC 217

Query: 227 AAKLFFAYGLGNGLIFPLAVGATAVLMAERPTPAAVFERLRRHQPDI--FYGVPTLYASM 284
               F   GL       L +G T V+ ++R TPA     L   Q  +  ++ VP +  ++
Sbjct: 218 DLPFFHTIGLIAVARTTLMLGGTLVV-SDRFTPARTLAALADRQRAVTHYFAVPQIALAL 276

Query: 285 LANPDCPKEGELRLRACTSAGEALPEDVGRRWQARFGVDILDGIGSTE---MLHIFLSNR 341
             +P         L A    G  L + +   +    GV +++G G +E   +LH+ +  R
Sbjct: 277 RNDPVYSAAALAGLHALFVGGAPLTQALIESYLDD-GVALVNGYGMSEAGTVLHVPIDRR 335

Query: 342 AGDVHYGTSGKPVPGYRLRLIDEDGAEITTAGVAGELQISGPSSAVMYWNNPEKTAATFM 401
           A   + G+ G P P   +R++ EDG E+   G  GEL + GP+    YWN P++TAA F 
Sbjct: 336 AVQDNPGSVGLPAPLLDIRIVGEDGREVDD-GETGELWLRGPAVTPGYWNKPQETAAAFT 394

Query: 402 GEWTRSGDKYLVNDEGYYVYAGRSDDMLKVSGIYVSPIEVESALIAHEAVLEAAVVGWED 461
             W R+GD       G+Y    R  DM    G  V P EVE+AL +H A+L+AAVVG  D
Sbjct: 395 EGWYRTGDLGRREANGFYHIVDRLKDMYISGGENVYPAEVEAALASHPAILDAAVVGIPD 454

Query: 462 EDHLIKPKAFIVLKPGYGAGEALRTDLKAHVKNLLAPYKYPRWIEFVDDLPKTATGKIQR 521
                   A++VL+PG     A   ++  H    LA +K P  I FV+ +P+TA+GK+Q+
Sbjct: 455 IRWGECGLAYVVLRPG---AVATGDEIAGHCAARLAAFKRPARILFVEAIPRTASGKVQK 511

Query: 522 FKLR 525
           + LR
Sbjct: 512 YVLR 515


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: 712
Number of extensions: 34
Number of successful extensions: 4
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: 528
Length adjustment: 35
Effective length of query: 492
Effective length of database: 493
Effective search space:   242556
Effective search space used:   242556
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

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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:

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:

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:

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:

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