GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Shewanella amazonensis SB2B

Align Enoyl-CoA hydratase AFT3-1; AF-toxin biosynthesis protein 3-1; EC 4.2.1.17 (characterized)
to candidate 6938954 Sama_3052 enoyl-CoA hydratase/isomerase family protein (RefSeq)

Query= SwissProt::Q96VB3
         (296 letters)



>FitnessBrowser__SB2B:6938954
          Length = 246

 Score =  103 bits (256), Expect = 5e-27
 Identities = 74/245 (30%), Positives = 115/245 (46%), Gaps = 9/245 (3%)

Query: 21  DADGIAVIVLARSQSRNALTLPMLTDMVQLLSAMDADDSVKCIVFTGEGPFFCSGVDLTE 80
           D DG+ VI   R + RNAL L M   + + L   ++D+ ++  + TGE   F SG D+ +
Sbjct: 8   DLDGVRVISFNRPEKRNALDLDMYRQLTEYLMQGESDNDIRAFLLTGEANCFTSGNDVAD 67

Query: 81  GF--GEIGKTRDTHRDAGGKLALAIHNCRKPTIAAINGTAVGVGITMTLPMSIRIAAKTA 138
                E+G      R         +   RKP +AA++G+AVG+G T+ L   +  A  +A
Sbjct: 68  FLQNSELGPNHPAVR-----FLYCLLELRKPLVAAVSGSAVGIGTTLLLHCDLVYADNSA 122

Query: 139 KISFPFVRRGIVADAASSFYLPRLIGYGRALHLFTTGALYPAESGLLHGLFSETVNAASS 198
           K   PFV   +V +A +S  LP L+GY +A  L      + AE+ L   L +  + +   
Sbjct: 123 KFQLPFVNLALVPEAGASILLPELVGYQKAAELLLLAEPFDAETALSLKLIN-ALCSKEE 181

Query: 199 TLPRALEVARDIAVNASQVGVYLTRDLVYRSPRSPEQAHLLESAALYTRYQSRDFEEGVQ 258
               AL+ AR +A    Q  +  TR L+       +    LE  A   R +S + +   Q
Sbjct: 182 LQQTALDKARKLASQPPQ-ALQQTRQLMRPHKHRVQHQMHLELEAFGERLKSDEAKARFQ 240

Query: 259 SFLEK 263
           +FL K
Sbjct: 241 AFLTK 245


Lambda     K      H
   0.321    0.136    0.394 

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: 142
Number of extensions: 5
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: 296
Length of database: 246
Length adjustment: 25
Effective length of query: 271
Effective length of database: 221
Effective search space:    59891
Effective search space used:    59891
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 (21.9 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