GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gloB in Shewanella amazonensis SB2B

Align palmitoyl-CoA hydrolase (EC 3.1.2.2) (characterized)
to candidate 6935785 Sama_0003 carboxylesterase (RefSeq)

Query= BRENDA::P33018
         (278 letters)



>FitnessBrowser__SB2B:6935785
          Length = 281

 Score =  343 bits (880), Expect = 2e-99
 Identities = 163/280 (58%), Positives = 208/280 (74%), Gaps = 4/280 (1%)

Query: 1   MEMLEEHRCFEGWQQRWRHDSSTLNCPMTFSIFLPPPRDHTPPPVLYWLSGLTCNDENFT 60
           +E++  +R F+GW +++ H SS+L+C M F+IFLPP  +    PVLYWLSGLTC+DENF 
Sbjct: 3   LELVSANRSFDGWHKQYSHQSSSLDCKMRFAIFLPPQAETQSVPVLYWLSGLTCSDENFM 62

Query: 61  TKAGAQRVAAELGIVLVMPDTSPRGEKVAND-DG-YDLGQGAGFYLNATQPPWATHYRMY 118
            KAGAQR+AA LG+ +V  DTSPRGE VA+D DG +D G GAGFYLNAT+ PW  HYRMY
Sbjct: 63  QKAGAQRLAATLGLAIVAMDTSPRGEGVADDPDGAWDFGLGAGFYLNATEAPWNKHYRMY 122

Query: 119 DYLRDELPALVQSQFNVSDRCAISGHSMGGHGALIMALKNPGKYTSVSAFAPIVNPCSVP 178
           DY+  ELP L+++ F VS + +I+GHSMGGHGAL +ALKNPG+Y SVSAF+PI NP   P
Sbjct: 123 DYVVKELPKLIETNFPVSSKRSIAGHSMGGHGALTIALKNPGRYASVSAFSPICNPSQSP 182

Query: 179 WGIKAFSSYLGEDKNAWLEWDSCALMYASNAQDAIPTLIDQGDNDQFLADQLQPAVLAEA 238
           WG KAF +YLG+D+ +W E+DSC L+      + IP L+DQGD D FL  +L P  L  A
Sbjct: 183 WGQKAFGNYLGKDRESWREYDSCELI--GRGAEPIPMLVDQGDADSFLEAELMPQRLQHA 240

Query: 239 ARQKAWPMTLRIQPGYDHSYYFIASFIEDHLRFHAQYLLK 278
           A    +P+ LR+QPGYDHSYYFIASFI++HL FH  +L +
Sbjct: 241 ADNADFPLNLRMQPGYDHSYYFIASFIDEHLEFHHHWLTR 280


Lambda     K      H
   0.320    0.136    0.441 

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: 292
Number of extensions: 9
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: 278
Length of database: 281
Length adjustment: 26
Effective length of query: 252
Effective length of database: 255
Effective search space:    64260
Effective search space used:    64260
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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