GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hcl in Tistlia consotensis USBA 355

Align Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized)
to candidate WP_085124880.1 B9O00_RS21930 AMP-binding protein

Query= SwissProt::Q8GQN9
         (527 letters)



>NCBI__GCF_900177295.1:WP_085124880.1
          Length = 518

 Score =  207 bits (526), Expect = 1e-57
 Identities = 161/512 (31%), Positives = 245/512 (47%), Gaps = 22/512 (4%)

Query: 27  DLIGRNLLAGRGGKTVYIDDAGSYTYDELALRVNRCGSALRTTLGLQPKDRVLVCVLDGI 86
           +L+ R   A +G +  + D   + TY +L     R    L   LG+QP + V + + + +
Sbjct: 12  ELLERQATA-QGERIAFRDARSAVTYADLEAVTGRLAGHL-ADLGVQPGESVAIFLPNSV 69

Query: 87  DFPTTFLGAIKGGVVPIAINTLLTESDYEYMLTDSAARVAVVSQELLPLFAPMLGKVP-T 145
           ++  + L  ++ G V + I+   T  +  Y L D+  R  V + E + L   + G+VP  
Sbjct: 70  EWVESCLAVVRAGGVAVPISYDATAGEVAYRLADAGCRAVVTTDERVALLDGLRGEVPEA 129

Query: 146 LEHLVVAGGA-------GEDSLAALLATGSEQFEAAPTRPDDHCFWLYSSGSTGAPKGTV 198
           +  ++V  G        G    A L A         P   D   F LY+SG+TG  KG +
Sbjct: 130 IAPILVERGPERAAETPGGLRFAELAAREPASAPRDPRDIDVPAFILYTSGTTGRAKGVL 189

Query: 199 -HIHSDLIHTAELYARPILGIREGDVVFSAAKLFFAYGLGNGLIFPLAVGATAVLMAERP 257
             +H  L  TA  +A P+ G+   D V S   LF +Y L   ++  LAVGA+  LM +  
Sbjct: 190 LTVHGMLWVTAACWA-PLAGLARDDTVLSPLPLFHSYALNLSVLSILAVGASEYLMEKYS 248

Query: 258 TPAAVFERLRRHQPDIFYGVPTLYASML-ANPDCPKEGELRLRACTSAGEALPEDVGRRW 316
           T  AV   L+      F GVPT++   L A    P      LR C SAG  +P  + R +
Sbjct: 249 TGEAV-RLLQSGAYSFFPGVPTMFHYFLQATQQQPGLRFPALRVCVSAGAIMPATLNREF 307

Query: 317 QARFGVDILDGIGSTEMLHIFLSNRAGDVHY-GTSGKPVPGYRLRLIDE-DGAEITTAGV 374
           + RFGV +LDG G TE   +   N  G     G+ G  +PG  +R++D   GAE+  AG 
Sbjct: 308 EERFGVPLLDGYGITETSTMVTMNPLGAERVPGSCGPALPGLEVRIVDPLSGAEVP-AGA 366

Query: 375 AGELQISGPSSAVMYWNNPEKTAATFMGEWTRSGDKYLVNDEGYYVYAGRSDDMLKVSGI 434
            GEL + GP+  + Y + P +TAA     W  +GD    +  G+    GR  +++   G 
Sbjct: 367 EGELIVRGPNVMLGYHDKPAETAAALRDGWYHTGDLAKRDAAGFITITGRLKELIIRGGQ 426

Query: 435 YVSPIEVESALIAHEAVLEAAVVGWEDEDHLIKPKAFIVLKPGYGAG-EALRTDLKAHVK 493
            ++P E+E  +   E VL+ AVVG   E     P  F+V +P      EA    L AH +
Sbjct: 427 NIAPAEIEEVVNLWEEVLDCAVVGMAHEHLGEVPALFVVAQPERAVDVEA----LLAHCR 482

Query: 494 NLLAPYKYPRWIEFVDDLPKTATGKIQRFKLR 525
             L+ YK P  +  V+++P+T +GKI RF+L+
Sbjct: 483 TYLSAYKVPALVRLVEEIPRTGSGKIIRFRLK 514


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: 699
Number of extensions: 38
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: 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 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