GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaF in Shewanella loihica PV-4

Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate 5210229 Shew_2672 carnitinyl-CoA dehydratase (RefSeq)

Query= BRENDA::P76082
         (255 letters)



>FitnessBrowser__PV4:5210229
          Length = 261

 Score =  148 bits (373), Expect = 1e-40
 Identities = 99/264 (37%), Positives = 158/264 (59%), Gaps = 12/264 (4%)

Query: 1   MSE-LIVSRQQRVLLLTLNRPAARNALNNALLMQLVNELEAAATDTSISVCVITG-NARF 58
           MSE L V+R   +L + L+RP A NA++     ++     A   D  + V +ITG  ARF
Sbjct: 1   MSESLHVTRNGSILEIVLDRPKA-NAIDAKTSYEMGEVFLAFRDDPELRVAIITGAGARF 59

Query: 59  FAAGADLNEMAEKDLAATLNDTRPQLWARLQAF---NKPLIAAVNGYALGAGCELALLCD 115
           F+AG DL   AE +  A   D  P  +A L      +KP+IAAVNGYA G G ELAL  D
Sbjct: 60  FSAGWDLKAAAEGE--APDADFGPGGFAGLTELFDLDKPVIAAVNGYAFGGGFELALAAD 117

Query: 116 VVVAGENARFGLPEITLGIMPGAGGTQRLIRSVGKSLASKMVLSGESITAQQAQQAGLVS 175
           ++V  +NA F LPE  LGI+P +GG  RL + +   + ++++++G S+ AQ+A + G+V+
Sbjct: 118 LIVCADNASFALPEAKLGIVPDSGGMLRLPKLLPAPIVNELMMTGRSMDAQEALRWGVVN 177

Query: 176 DVFPSDLTLEYALQLASKMARHSPLALQAAKQALRQSQEVALQAGLAQER----QLFTLL 231
            V   +  +E A +LA+++++ +PLAL A K+  R++ E++++ G A  R    + +  +
Sbjct: 178 RVVEQEALMETARELANEISQSAPLALAAIKEIYRETGELSVEQGYAHIRGGQLKHYPSV 237

Query: 232 AATEDRHEGISAFLQKRTPDFKGR 255
             +ED  EG +AF +KR P ++G+
Sbjct: 238 LHSEDALEGPAAFAEKRDPVWQGK 261


Lambda     K      H
   0.318    0.130    0.356 

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: 115
Number of extensions: 6
Number of successful extensions: 3
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: 255
Length of database: 261
Length adjustment: 24
Effective length of query: 231
Effective length of database: 237
Effective search space:    54747
Effective search space used:    54747
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 (21.8 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 17 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