GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaF in Shewanella amazonensis SB2B

Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate 6937208 Sama_1378 enoyl-CoA hydratase (RefSeq)

Query= BRENDA::P76082
         (255 letters)



>FitnessBrowser__SB2B:6937208
          Length = 257

 Score =  159 bits (403), Expect = 4e-44
 Identities = 99/258 (38%), Positives = 145/258 (56%), Gaps = 4/258 (1%)

Query: 1   MSELIVSRQQRVLLLTLNRPAARNALNNALLMQLVNELEAAATDTSISVCVITGNA-RFF 59
           M+ LI   +    +LT++ P A N      L +L  ++     +  I   V+TG   +FF
Sbjct: 1   MAFLIERIEGNTAILTISNPPA-NTWTRESLNELKEKVLELNDNNEIYALVLTGEGEKFF 59

Query: 60  AAGADLNEMAEKDL--AATLNDTRPQLWARLQAFNKPLIAAVNGYALGAGCELALLCDVV 117
           +AGADL   A+ D   AAT+     + +  L AF    IAA+NGYA+G G E+AL CD+ 
Sbjct: 60  SAGADLKLFADGDKGNAATMAKAFGEAFETLSAFRGVSIAAINGYAMGGGLEVALACDIR 119

Query: 118 VAGENARFGLPEITLGIMPGAGGTQRLIRSVGKSLASKMVLSGESITAQQAQQAGLVSDV 177
           +A   A   LPE T+G++P AGGTQ L   VG+  A +M+L GE I A +A   GLV +V
Sbjct: 120 IAEIQAVMALPEATVGLLPCAGGTQNLTALVGEGWAKRMILCGERIDATKALNLGLVEEV 179

Query: 178 FPSDLTLEYALQLASKMARHSPLALQAAKQALRQSQEVALQAGLAQERQLFTLLAATEDR 237
                +L  A+ LA+K+A+ SP A+   K+ ++  + +     L  ER+LF  L  TED+
Sbjct: 180 VEKGESLSAAIALAAKVAKQSPSAVAVCKKLIQSGRNMPRTQALPLERELFVGLFDTEDQ 239

Query: 238 HEGISAFLQKRTPDFKGR 255
            EG++AFL+KR   +K R
Sbjct: 240 AEGVNAFLEKRAAQWKNR 257


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: 131
Number of extensions: 3
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: 255
Length of database: 257
Length adjustment: 24
Effective length of query: 231
Effective length of database: 233
Effective search space:    53823
Effective search space used:    53823
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