GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuA in Limnohabitans curvus MWH-C5

Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate WP_108358862.1 B9Z44_RS01325 acyl-CoA dehydrogenase

Query= reanno::psRCH2:GFF1051
         (387 letters)



>NCBI__GCF_003063475.1:WP_108358862.1
          Length = 387

 Score =  251 bits (642), Expect = 2e-71
 Identities = 140/382 (36%), Positives = 213/382 (55%), Gaps = 8/382 (2%)

Query: 12  ETIDMLREQVQAFVAAEIAPRAEAIDQENLFPADMWRKFGEMGLLGVTVSEEYGGAGLGY 71
           E+ D+L   +Q F+   + P    +++ +  PAD+     EMGL G+++ EE+GG GL  
Sbjct: 6   ESFDLLLPTLQRFIQERLVPAENYLEEHDEVPADIVEDMKEMGLFGLSIPEEFGGIGLSM 65

Query: 72  LAHVVAMEEISRGSASVALSYGAHSNLCVNQINRNGNPEQKARYLPKLISGEHVGALAMS 131
              V    EI R S +    +G +  +    I  +G PEQKA  LPK+ SGE + + A++
Sbjct: 66  SQEVQVAYEIGRTSLAFRSVFGTNVGIGSQGILMDGTPEQKANILPKVASGELIMSFALT 125

Query: 132 EPNAGSDVVSMKLRAEKRGDRYVLNGSKTWITNGPDANTYVIYAKTDLDKGAHGITAFIV 191
           EP+AGSD  S+K RA+  GD YVLNG+K +ITN P A  + + A+T    GA G+++FIV
Sbjct: 126 EPDAGSDAASLKTRADLDGDHYVLNGTKRYITNAPRAGAFTLMARTG-GPGAGGVSSFIV 184

Query: 192 ERDWKGFSRGNKFDKLGMRGSNTCELFFDDVEVPQENVLGAENG-GVKVLMSGLDYERVV 250
             D  G   G    K+G RG+ TC++  ++V VP  N++G   G G K  M  LD  R+ 
Sbjct: 185 PSDLPGIKLGKTDKKMGQRGTKTCDVILENVRVPAANIIGGVPGQGFKTAMKVLDRGRLH 244

Query: 251 LAGGPTGIMQSCLDVVVPYIHDRKQFGQSIGEFQFIQGKVADMYTQLNASRAYLYAVAQA 310
           ++    G+    ++    Y  DRKQFG++IGEFQ IQ  +AD   +L A  + +  VAQ 
Sbjct: 245 ISAVSCGMAHRIIEEATAYARDRKQFGKAIGEFQLIQAMLADSQAELLAGWSLVQDVAQR 304

Query: 311 CDRGETTRKD------AAGVILYTAENATQMALQAIQILGGNGYINEFPTGRLLRDAKLY 364
            D       D       +   L+  E   ++A + +Q+ GG GYINE+P  R  RD +L 
Sbjct: 305 FDGKPAHVSDPDVSMRVSCAKLFCTEMVGRVADRGVQVHGGAGYINEYPVERFYRDVRLL 364

Query: 365 EIGAGTSEIRRMLIGRELFNES 386
            +  GT++I++++IGREL  ++
Sbjct: 365 RLYEGTTQIQQLIIGRELLRQA 386


Lambda     K      H
   0.318    0.135    0.391 

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: 389
Number of extensions: 16
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: 387
Length of database: 387
Length adjustment: 30
Effective length of query: 357
Effective length of database: 357
Effective search space:   127449
Effective search space used:   127449
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: 50 (23.9 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