GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hcl in Ruegeria conchae TW15

Align Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized)
to candidate WP_010442785.1 G7G_RS0117685 AMP-binding protein

Query= SwissProt::Q8GQN9
         (527 letters)



>NCBI__GCF_000192475.1:WP_010442785.1
          Length = 508

 Score =  169 bits (427), Expect = 3e-46
 Identities = 153/527 (29%), Positives = 243/527 (46%), Gaps = 62/527 (11%)

Query: 18  IPERYNAADDLIGRNLLAGRGGKTVYID----DAGSYTYDELALRVNRCGSALRTTLGLQ 73
           IP+R N A     R  L+    +   +D    D    T+ +L   V+    AL   +  +
Sbjct: 18  IPDRLNMA-----RQCLSQPSEQVAILDLTASDPREVTFGDLGEMVDGIARALINDV--R 70

Query: 74  PKDRVLVCVLDGIDFPTTFLGAIKGGVVPI---------AINTLLTESDYEYMLTDSAAR 124
           P DRV V +          L   K G + +         A+++ + ++  +++LTDS   
Sbjct: 71  PGDRVGVLLSQSPGCAAAHLAIWKIGAISVPLFKLFKHDALSSRVGDAGLKFVLTDSEG- 129

Query: 125 VAVVSQELLPLFAPMLGKVPTLEHLVVAGGAGEDSLAALLATGSEQFEAAPTRPDDHCFW 184
            A+V     P+ A  +G+                               A T P++    
Sbjct: 130 AALVGDLAKPVLADQIGQE------------------------GPPVPFADTSPEEPAVL 165

Query: 185 LYSSGSTGAPKGTVHIHSDLIHTAELYARPILGIREGDVVFSAAKLFFAYGLGNGLIFPL 244
           +Y+SG+TG+PKG +H H  L       +     +R+GD +++ A   +  GL + L+  L
Sbjct: 166 IYTSGTTGSPKGALHGHRVLTGHLPGVSISHNHLRQGDCLWTPADWAWIGGLFDVLMPGL 225

Query: 245 AVGATAVLMA-ERPTPAAVFERLRRHQPDIFYGVPTLYASMLANPDCPKEGELRLRACTS 303
           A+G   V    ++ TP A  + + R      +  PT    ML   D    G   LR+  S
Sbjct: 226 ALGVPIVAARLDKFTPEACADLVMRGGVRNVFFPPTALR-MLKAADQTIPG---LRSVAS 281

Query: 304 AGEALPEDVGRRWQARFGVDILDGIGSTEMLHIFLSNRAGD--VHYGTSGKPVPGYRLRL 361
            GE L  ++    +  FG+ I +  G TE  ++ +S+ A D   H G  GKPVPG+ + +
Sbjct: 282 GGEPLGVEMLAWGKKAFGLTINEFYGQTEC-NMVVSSCAEDFPAHPGCIGKPVPGHEVAV 340

Query: 362 IDEDGAEITTAGVAGELQISGPSSAVM--YWNNPEKTAATFMGEWTRSGDKYLVNDEGYY 419
           ID DG      G   ++ I   S+++M  YWN P+ T   F G+W  +GD+ +   + Y 
Sbjct: 341 IDGDGRPTNEEG---DVAIRRGSASMMLEYWNRPDATTEKFRGDWLITGDRGVWEGD-YL 396

Query: 420 VYAGRSDDMLKVSGIYVSPIEVESALIAHEAVLEAAVVGWEDEDHLIKPKAFIVLKPGYG 479
            + GR DD++  +G  + P E+E  L+ H AV    VVG  D       KA++VLKPG  
Sbjct: 397 RFVGRDDDVITSAGYRIGPAEIEDCLLTHPAVATVGVVGKPDPLRTEIVKAYVVLKPG-- 454

Query: 480 AGEALRTDLKAHVKNLLAPYKYPRWIEFVDDLPKTATGKIQRFKLRS 526
             EA   +L+  VK+ LA Y YPR + F+D+LP T TGK+ R +L++
Sbjct: 455 -AEAAEQELQDWVKDRLAQYSYPREVAFLDELPMTVTGKVIRKELKA 500


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: 702
Number of extensions: 47
Number of successful extensions: 6
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: 508
Length adjustment: 35
Effective length of query: 492
Effective length of database: 473
Effective search space:   232716
Effective search space used:   232716
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 24 2021. 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