GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Duganella sacchari Sac-22

Align isovalerate--CoA ligase (EC 6.2.1.1) (characterized)
to candidate WP_072781751.1 BUA36_RS04545 fatty-acid--CoA ligase

Query= metacyc::MONOMER-20124
         (573 letters)



>NCBI__GCF_900143065.1:WP_072781751.1
          Length = 543

 Score =  184 bits (468), Expect = 6e-51
 Identities = 153/508 (30%), Positives = 249/508 (49%), Gaps = 22/508 (4%)

Query: 67  RYTWAQTHHRCLKLASALTTHLGISPGDVVATFSYNLPEIYELHFAVPMAGGILCTLNAR 126
           RYT+     R  +LA AL   LG+  G+ VAT ++N     E ++AV  +G +L T+N R
Sbjct: 40  RYTFRDCAQRAKQLAKALQA-LGLQMGERVATLAWNGYRHLEAYYAVSGSGAVLHTINPR 98

Query: 127 NDSAMVSTLLAHSEAKLIFVEPQLLETARAALDLLAQKDIKPPTLVLLTDSESFTSSSYD 186
                ++ +  H+E + +  +   L    A       K +K   L+   D     ++  +
Sbjct: 99  LHPEQLAYICNHAEDQYLLFDFCFLPLVEAIAPHC--KTVKGFVLLGAADRMPAQTNIPN 156

Query: 187 H--YNHLLANGSDDFEIRRPKNEWDPISINYTSGTTARPKAVVYSHRGAYLNSIATVLLH 244
              Y  LLA  S D+      +E    ++ YTSGTT  PK  +YSHR   L++ A+ L +
Sbjct: 157 LLCYEDLLAAQSPDYTWPT-FDEHAAATLCYTSGTTGNPKGALYSHRSTVLHAYASALPN 215

Query: 245 GMGTTS--VYLWSVPMFHCNGWCFPWGAAAQGATNICIRK-VSPKAIFDNIHLHKVTHFG 301
            +  +S    +  VPMFH N W  P+     GA  +     +  K++++ +   KVT   
Sbjct: 216 VLNVSSRDSVMPVVPMFHVNAWGLPYSVPLSGAKMVFPGPALDGKSVYELMEQEKVTFSA 275

Query: 302 AAPTV-LNMIVNSPEGNLHTPLPHKVEVMTGGSPPPPKVIARMEEMGFQVNHIYGLTETC 360
             PTV L +I  + +  L     H+  V+ G + PP  +   ++E   QV H +G+TE  
Sbjct: 276 GVPTVWLGLINYAMQHQLKFSTFHRT-VIGGSACPPAMMNTLIDEFDVQVIHGWGMTEMS 334

Query: 361 --GPAANCVCKPEWDALQPEERYALKARQGLNHLAMEEMDVRDPVTMESVRADGATIGEV 418
             G     + K   +  +  +R  L+ +QG + +   +M + D +  E +  DG T G +
Sbjct: 335 PLGTTGGLLSK-HLELPKAAQRQILQ-KQG-HAIYGVDMKIVDELG-EELPWDGVTSGSL 390

Query: 419 MFRGNTVMSGYFKDLKATEEAFEGGWFRSGDLGVKHEDGYIQLKDRKKDVVISGGENIST 478
           + +G  +++ YFK      +  E GWF +GD+     DG++Q+ DR KDV+ SGGE I T
Sbjct: 391 LVKGPWIIASYFKGEGG--DVLEDGWFPTGDVATIDADGFMQITDRAKDVIKSGGEWIGT 448

Query: 479 VEVETVLYSHEAVLEAAVVARPDKLWGETPCAFVTLKEGFDNDVSADQIIKFCRDRLPHY 538
           +++E +  SH AV++AA +      W E P   V  K G   +VS +Q++     ++  +
Sbjct: 449 IDLENIAMSHPAVMQAACIGVFHPKWDERPLLVVVRKPG--QEVSREQLLAHFDGKVAKW 506

Query: 539 MAPKTVVF-EELPKTSTGKIQKYILKEK 565
             P  VVF + LP   TGKIQK  L+E+
Sbjct: 507 WLPDDVVFADALPVGGTGKIQKNKLREQ 534


Lambda     K      H
   0.318    0.133    0.408 

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: 777
Number of extensions: 52
Number of successful extensions: 7
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: 573
Length of database: 543
Length adjustment: 36
Effective length of query: 537
Effective length of database: 507
Effective search space:   272259
Effective search space used:   272259
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 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