GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hpcD in Marinobacter adhaerens HP15

Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate GFF929 HP15_908 enoyl-CoA hydratase/isomerase

Query= BRENDA::A4YI89
         (259 letters)



>FitnessBrowser__Marino:GFF929
          Length = 259

 Score =  160 bits (406), Expect = 2e-44
 Identities = 98/258 (37%), Positives = 145/258 (56%), Gaps = 3/258 (1%)

Query: 4   ETIETKKEGNLFWITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKGKAF-C 62
           + I+ +K G++  +T+N P   N      L  L   V +   D +I  +++TG+G+ F  
Sbjct: 3   DLIQLEKRGHIAVLTINNPPA-NTWTKDSLIALTNIVKELNEDRDIFALVMTGQGEKFYS 61

Query: 63  AGADITQFNQLTPAEAWKFSKKGREIMDKIEALSKPTIAMINGYALGGGLELALACDIRI 122
           AGAD+  F     A A +  +   E    ++     +IA +NGYA+GGGLE A+ACDIRI
Sbjct: 62  AGADLKTFADGDKARANEMGQLFGEAFSTLQRFRGVSIAAVNGYAMGGGLECAMACDIRI 121

Query: 123 AAEEAQLGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLVNRVV 182
           A E AQ+ LPE  +G+ P  GGTQ L  ++G+G A  M++ G+R+    A + GLV  VV
Sbjct: 122 AEEHAQMALPEAGVGLLPCAGGTQNLPWLVGEGWAKRMILCGERVKADTALRIGLVEEVV 181

Query: 183 PLANLEQETRKLAEKIAKKSPISLALIKEVVNRGLDSPLL-SGLALESVGWGVVFSTEDK 241
           P      +  +LAE   ++SP S A  K +V    D      G  +E   +  +FSTED+
Sbjct: 182 PSGQGLDKALELAEMACQQSPSSTARCKTLVMSARDGRSHDDGWRMERELFVELFSTEDQ 241

Query: 242 KEGVSAFLEKREPTFKGK 259
           KEGV+AFLEKR+P +K +
Sbjct: 242 KEGVNAFLEKRKPEWKNR 259


Lambda     K      H
   0.315    0.135    0.382 

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: 139
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: 259
Length of database: 259
Length adjustment: 24
Effective length of query: 235
Effective length of database: 235
Effective search space:    55225
Effective search space used:    55225
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: 42 (22.0 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