GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hcl in Methylocapsa aurea KYG

Align Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized)
to candidate WP_036258835.1 DL86_RS04845 malonyl-CoA synthase

Query= SwissProt::Q8GQN9
         (527 letters)



>NCBI__GCF_000746085.1:WP_036258835.1
          Length = 507

 Score =  197 bits (502), Expect = 6e-55
 Identities = 149/480 (31%), Positives = 226/480 (47%), Gaps = 16/480 (3%)

Query: 50  YTYDELALRVNRCGSALRTTLGLQPKDRVLVCVLDGIDFPTTFLGAIKGGVVPIAINTLL 109
           ++Y +      R  +AL + LG++P DRV   V         +LGA++ G + + +N   
Sbjct: 30  FSYGDAVAASARSAAAL-SALGVKPGDRVAAQVEKSAAAVMLYLGAVRAGAIFLPLNPAY 88

Query: 110 TESDYEYMLTDSAARVAVVSQELLPLFAPMLGKV--PTLEHLVVAGGAGEDSLAALLATG 167
           T ++  Y L+D+   V +   +     A ++ K   P LE L   G  G  S A L AT 
Sbjct: 89  TLAEIAYFLSDAEPAVVICDPDRRGELASLVAKAGAPLLETL---GADGRGSFADLCATQ 145

Query: 168 SEQFEAAPTRPDDHCFWLYSSGSTGAPKGTVHIHSDLIHTAELYARPILGIREGDVVFSA 227
           S  F  A   PDD    LY+SG+TG  KG +  H++L   A             DV+  A
Sbjct: 146 SGDFSDAARGPDDLAAILYTSGTTGRSKGAMLTHANLASNAATLVEA-WRFTPADVLLHA 204

Query: 228 AKLFFAYGLGNGLIFPLAVGATAVLMAERPTPAAVFERLRRHQPDIFYGVPTLYASMLAN 287
             ++  +GL   +   L      + +A       +       Q     GVPT Y  +L  
Sbjct: 205 LPIYHTHGLFVAINTILFSAGRILFLARFDADECL---ALMPQASAMMGVPTFYTRLLRR 261

Query: 288 PDCPKEGELRLRACTSAGEALPEDVGRRWQARFGVDILDGIGSTEMLHIFLSNRAGDVHY 347
           PD  +     +R   S    L  +  R W  R G  IL+  G TE   I  +   G+   
Sbjct: 262 PDVLRRASAHMRLFISGSAPLLAETHREWVERTGHAILERYGMTETNMIASNPYDGERIA 321

Query: 348 GTSGKPVPGYRLRLID-EDGAEITTAGVAGELQISGPSSAVMYWNNPEKTAATFMGE-WT 405
           GT G P+PG  +R+ D E GA++    + G +++ GP+    YW NPEKTAA F  + + 
Sbjct: 322 GTVGPPLPGVAVRIADPETGADLGRDKI-GVIEVKGPNVFKGYWRNPEKTAAEFRADGFF 380

Query: 406 RSGDKYLVNDEGYYVYAGRSDDMLKVSGIYVSPIEVESALIAHEAVLEAAVVGWEDEDHL 465
            +GD   ++  GY    GR+ D++   G  V P EVE+ + A   V+E+AVVG   ED  
Sbjct: 381 ITGDLGKIDANGYVHIIGRAKDLIITGGFNVYPKEVEAEIDAIAGVVESAVVGLPHEDFG 440

Query: 466 IKPKAFIVLKPGYGAGEALRTDLKAHVKNLLAPYKYPRWIEFVDDLPKTATGKIQRFKLR 525
               A +V  PG G  EA    +++ ++N LA +K P+ + FV++LP+ A GK+Q+  LR
Sbjct: 441 EGIAAIVVRTPGSGLDEA---GVRSALENRLAKFKLPKRVIFVEELPRNAMGKVQKNALR 497


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: 700
Number of extensions: 39
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: 507
Length adjustment: 35
Effective length of query: 492
Effective length of database: 472
Effective search space:   232224
Effective search space used:   232224
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