GapMind for catabolism of small carbon sources

 

Aligments for a candidate for ech in Shewanella loihica PV-4

Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate 5209192 Shew_1670 enoyl-CoA hydratase (RefSeq)

Query= BRENDA::Q9I5I4
         (272 letters)



>lcl|FitnessBrowser__PV4:5209192 Shew_1670 enoyl-CoA hydratase
           (RefSeq)
          Length = 257

 Score =  324 bits (830), Expect = 1e-93
 Identities = 166/247 (67%), Positives = 187/247 (75%)

Query: 25  GHTALITINHPPANTWDRDSLIGLRQLIEHLNRDDDIYALVVTGQGPKFFSAGADLNMFA 84
           GHTA++T+N+PPANTW  DSL  L+Q +  LN + +IYALV+TG+G KFFSAGADL +FA
Sbjct: 10  GHTAVLTMNNPPANTWTADSLALLKQKVTELNANKEIYALVLTGEGEKFFSAGADLKLFA 69

Query: 85  DGDKARAREMARRFGEAFEALRDFRGVSIAAINGYAMGGGLECALACDIRIAERQAQMAL 144
           DGDK  A  MA+ FGEAFEAL  FRGVSIAAINGYAMGGGLE ALACDIRIAE QA MAL
Sbjct: 70  DGDKGNAATMAKHFGEAFEALSGFRGVSIAAINGYAMGGGLEVALACDIRIAEAQAVMAL 129

Query: 145 PEAAVGLLPCAGGTQALPWLVGEGWAKRMILCNERVDAETALRIGLVEQVVDSGEARGAA 204
           PEA VGLLPCAGGTQ L  +VGEGWAKRMILC ERV A+ AL IGL+E+VVD G A   A
Sbjct: 130 PEATVGLLPCAGGTQNLTAMVGEGWAKRMILCGERVGADKALSIGLIEEVVDKGAALDTA 189

Query: 205 LLLAAKVARQSPVAIRTIKPLIQGARERAPNTWLPEERERFVDLFDAQDTREGVNAFLEK 264
           + LA KVA QSP ++   K LIQ  R       LP ERE FV LFD +D  EGVNAFLEK
Sbjct: 190 MALAEKVANQSPSSVTVCKQLIQSGRAMPRTQALPLERELFVGLFDTEDQAEGVNAFLEK 249

Query: 265 RDPKWRN 271
           R   W+N
Sbjct: 250 RKANWKN 256


Lambda     K      H
   0.321    0.136    0.412 

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: 238
Number of extensions: 5
Number of successful extensions: 1
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: 272
Length of database: 257
Length adjustment: 25
Effective length of query: 247
Effective length of database: 232
Effective search space:    57304
Effective search space used:    57304
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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