GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Paraburkholderia bryophila 376MFSha3.1

Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate H281DRAFT_01200 H281DRAFT_01200 short chain enoyl-CoA hydratase (EC 4.2.1.17)

Query= BRENDA::Q9I5I4
         (272 letters)



>FitnessBrowser__Burk376:H281DRAFT_01200
          Length = 278

 Score =  307 bits (786), Expect = 2e-88
 Identities = 162/254 (63%), Positives = 188/254 (74%), Gaps = 1/254 (0%)

Query: 18  KLTVEKHGHTALITINHPPANTWDRDSLIGLRQLIEHLNRDDDIYALVVTGQGPKFFSAG 77
           +L     G  A +T+  PPAN +  D L+ L+Q +E LN +  + A+V+TG+GPKFFSAG
Sbjct: 3   ELDYAHEGAVAQLTLKRPPANAFTPDGLLQLQQTVERLNGETRVRAIVITGEGPKFFSAG 62

Query: 78  ADLNMFADGDKARAREMARRFGEAFEALRDFRGVSIAAINGYAMGGGLECALACDIRIAE 137
           ADLN FADG++  AR  A RFG AFEAL++ R V IAAING+AMGGGLECALACDIRIAE
Sbjct: 63  ADLNAFADGNREVARVAAARFGAAFEALQNARPVVIAAINGFAMGGGLECALACDIRIAE 122

Query: 138 RQAQMALPEAAVGLLPCAGGTQALPWLVGEGWAKRMILCNERVDAETALRIGLVEQVVDS 197
           + A MALPE AVGLLPC  GTQ LPWLVGEGWAKRMIL  ERVDA TALRIGLVE+VV+ 
Sbjct: 123 QHAVMALPETAVGLLPCGCGTQTLPWLVGEGWAKRMILTGERVDAATALRIGLVEEVVEK 182

Query: 198 GEARGAALLLAAKVARQSPVAIRTIKPLIQGARERAP-NTWLPEERERFVDLFDAQDTRE 256
           G AR AAL +AA+VA  SP A+   K LI   R   P +  L  ERERFVDLFD  D RE
Sbjct: 183 GAAREAALSMAARVATLSPQAVGFSKTLIHQGRNGVPRSAALALERERFVDLFDGADQRE 242

Query: 257 GVNAFLEKRDPKWR 270
           GVNAFLEKR P+W+
Sbjct: 243 GVNAFLEKRTPRWQ 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: 243
Number of extensions: 8
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: 272
Length of database: 278
Length adjustment: 25
Effective length of query: 247
Effective length of database: 253
Effective search space:    62491
Effective search space used:    62491
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