GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuC in Dyadobacter tibetensis Y620-1

Align Methylglutaconyl-CoA hydratase, mitochondrial; AU-specific RNA-binding enoyl-CoA hydratase; AU-binding enoyl-CoA hydratase; muAUH; Itaconyl-CoA hydratase; EC 4.2.1.18; EC 4.2.1.56 (characterized)
to candidate WP_025763018.1 X939_RS0109475 enoyl-CoA hydratase

Query= SwissProt::Q9JLZ3
         (314 letters)



>NCBI__GCF_000566685.1:WP_025763018.1
          Length = 259

 Score =  130 bits (328), Expect = 3e-35
 Identities = 82/261 (31%), Positives = 138/261 (52%), Gaps = 5/261 (1%)

Query: 55  RHLEEENR-GIVVLGINRAYGKNALSKNLLKMLSKAVDALKSDKKVRTIIIRSEVPGIFC 113
           +HL  +N+ GIV + +NR +  +AL+K L+K ++ A++   SD++VR +++ +E    FC
Sbjct: 3   QHLNFQNKEGIVRISLNRPHVHHALNKELIKEITLAIEVAASDEEVRAVLLTAEGDTAFC 62

Query: 114 AGADLKERAKMHSSEVGPFVSKIRSVINDIANLPVPTIAAIDGLALGGGLELALACDIRV 173
           +GADLK+                  +I  I +LP P +  ++GLA+G G  LAL+CD+ V
Sbjct: 63  SGADLKDTLDSKIDVDQTLREYYNPMIMAIRSLPKPVVCRLNGLAVGAGASLALSCDMVV 122

Query: 174 AASSAKMGLVETKLAIIPGGGGTQRLPRAIGMSLAKELIFSARVLDGQEAKAVGLISHVL 233
           A  SA +  +  ++ ++P  G T  LPR +G + A  L  + + +  +EA+ +G+I+H +
Sbjct: 123 ATESAYLAFMFVQIGLMPDAGATFILPRLVGSARAFALASTGQRVTAREAQHIGMIAHAV 182

Query: 234 EQNQEGDAAYRKALDLAREFLPQGPVAMRVAKLAINQGMEVDLVTGLAIEEACYAQTIST 293
             + E D+   K L   R    Q   AM   K  +NQ     L   L +E     Q   T
Sbjct: 183 PAS-ELDSTVEKLLLYYRHAPTQAIAAM---KQVLNQSQHSSLEQMLDLERIHQHQLSKT 238

Query: 294 KDRLEGLLAFKEKRPPRYKGE 314
            D   G+ +F +K+ P Y+G+
Sbjct: 239 TDAKNGISSFLQKKKPDYQGK 259


Lambda     K      H
   0.318    0.135    0.377 

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: 153
Number of extensions: 9
Number of successful extensions: 2
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: 314
Length of database: 259
Length adjustment: 26
Effective length of query: 288
Effective length of database: 233
Effective search space:    67104
Effective search space used:    67104
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: 47 (22.7 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