GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hcl in Rhizobium etli CFN 42

Align Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized)
to candidate WP_011426974.1 RHE_RS19290 AMP-binding protein

Query= SwissProt::Q8GQN9
         (527 letters)



>NCBI__GCF_000092045.1:WP_011426974.1
          Length = 550

 Score =  206 bits (523), Expect = 2e-57
 Identities = 161/524 (30%), Positives = 252/524 (48%), Gaps = 22/524 (4%)

Query: 17  KIPERYNAADDLIGRNLL---AGRGGKTVYID------DAGSYTYDELALRVNRCGSALR 67
           +IPE +N     IGR +    A R  + V ++      D  S TY EL+   +   +AL 
Sbjct: 19  RIPEDFN-----IGRAVSDEWAARDPERVCLEHFSPNGDHLSLTYGELSAASSMFANAL- 72

Query: 68  TTLGLQPKDRVLVCVLDGIDFPTTFLGAIKGGVVPIAINTLLTESDYEYMLTDSAARVAV 127
            +LG++  DRV + V    +     +   K G + + +  L      EY L  S A   +
Sbjct: 73  ASLGIKRGDRVALLVPQSFETVIAHVAIYKIGAIALPLALLFGVEALEYRLRISGAAAII 132

Query: 128 VSQELLPLFAPMLGKVPTLEHLV-VAGGAGEDSLAALLATGSEQFEAAPTRPDDHCFWLY 186
            +   L     +  ++P L H++ V+  A   S A L+A+ +  FE   T PDD    ++
Sbjct: 133 TNDFGLDRVRQIRDRLPELRHVISVSDAADALSFADLIASHASVFEGEKTTPDDAALMIF 192

Query: 187 SSGSTGAPKGTVHIHSDLI-HTAELYARPILGIREGDVVFSAAKLFFAYGLGNGLIFPLA 245
           +SG+TG PKG +H H  L  H   +        + GD V++ +   +A GL N L+  L 
Sbjct: 193 TSGTTGPPKGALHGHRVLPGHIPGMQFAHEGFPKVGDKVWTPSDWAWAGGLLNALLPSLL 252

Query: 246 VGATAVLM-AERPTPAAVFERLRRHQPDIFYGVPTLYASMLANPDCPKEGELRLRACTSA 304
           +G   V   A++      +  +   +    +  PT    M +  D   + +L LR   SA
Sbjct: 253 LGVPVVSSPAQKFDADTAYRIMAEMKVRNAFIPPTALRLMRSVSDPRSKYDLVLRTVGSA 312

Query: 305 GEALPEDVGRRWQARFGVDILDGIGSTEMLHIFLSNRA-GDVHYGTSGKPVPGYRLRLID 363
           GEAL  +     +   G+ + +  G TE   +  S+ A G    G  G+ VPG+R+ ++ 
Sbjct: 313 GEALGRETYDWARRTLGITVNEFYGQTECNFVLSSSAAFGVTKAGAIGRAVPGHRVAIVS 372

Query: 364 EDGAEITTAGVAGELQISGPSSAVM--YWNNPEKTAATFMGEWTRSGDKYLVNDEGYYVY 421
           E G E+  AG +G++ I+ P   +   YWN+   T   F+  W  +GD    +++GY  +
Sbjct: 373 EAGDELP-AGESGQIAIASPDPVMFLGYWNDAAATERKFLHGWLLTGDIGRQDEDGYVTF 431

Query: 422 AGRSDDMLKVSGIYVSPIEVESALIAHEAVLEAAVVGWEDEDHLIKPKAFIVLKPGYGAG 481
            GR DD++  SG  + P E+E  L  H AV  AA VG  D       KA+IVL PG+   
Sbjct: 432 EGRDDDVITSSGYRIGPAEIEDCLTGHPAVQLAAAVGKPDVVRTEIVKAYIVLSPGHSPS 491

Query: 482 EALRTDLKAHVKNLLAPYKYPRWIEFVDDLPKTATGKIQRFKLR 525
           EAL  +++  VK  L+ ++YPR +EFV+ LP T TGK+ R  LR
Sbjct: 492 EALAAEIREWVKMRLSMHEYPREVEFVESLPLTTTGKVIRRLLR 535


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: 717
Number of extensions: 36
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: 550
Length adjustment: 35
Effective length of query: 492
Effective length of database: 515
Effective search space:   253380
Effective search space used:   253380
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