GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Shewanella halifaxensis HAW-EB4

Align Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized)
to candidate WP_012275357.1 SHAL_RS01130 crotonobetainyl-CoA hydratase

Query= SwissProt::Q0AVM1
         (260 letters)



>NCBI__GCF_000019185.1:WP_012275357.1
          Length = 261

 Score =  143 bits (360), Expect = 4e-39
 Identities = 89/254 (35%), Positives = 139/254 (54%), Gaps = 6/254 (2%)

Query: 4   ENIILEKEEKLAVLYINRPKAMNALNKDTLLEIKDAVTAVNDDPAVELLIITGSGDKSFV 63
           E++ + +   +  + ++RPKA NA++  T  E+ +   A  +DP + + IITG+G++ F 
Sbjct: 3   ESLHVTRNGAILEITLDRPKA-NAIDAKTSFEMGEVFLAFREDPELRVAIITGAGERFFS 61

Query: 64  AGADIAFMQNLSAMEAREFGALGQKVFRLIEAMEKPVIAAVNGFALGGGCELAMCCDFRI 123
           AG D+       A +A +FG  G      I  ++KPVIAAVNG+A GGG ELA+  D  I
Sbjct: 62  AGWDLKAAAEGEAPDA-DFGPGGFAGLTEIFDLDKPVIAAVNGYAFGGGFELALAADMII 120

Query: 124 AASNAKFGQPEVGLGITPGFGGTQRLPRLVGPGMAKQLLYTADVINADEAFRIGLVNKVV 183
            + NA F  PE  LGI P  GG  RLP+L+ P +  +L+ T   + A+EA R G+VN+VV
Sbjct: 121 CSENASFALPEAKLGIVPDSGGMLRLPKLLPPAIVNELMMTGRGMGAEEALRWGVVNRVV 180

Query: 184 QPEELLPEVKKIAGRILSKGQLAVRLSKAAANEGMQTDIDRA-MSIEADA---FGLCFAT 239
           + ++L+   +++A +I     LA+   K    E  +  ++     I A     +     +
Sbjct: 181 ESDKLMDSARELAQQIAQGAPLAIAAIKEIYRETSELSVEEGYRHIRAGGLKNYPSVLRS 240

Query: 240 QDQKEGMTAFLEKR 253
           +D  EG  AF EKR
Sbjct: 241 EDALEGPLAFSEKR 254


Lambda     K      H
   0.319    0.136    0.378 

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: 182
Number of extensions: 13
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: 260
Length of database: 261
Length adjustment: 25
Effective length of query: 235
Effective length of database: 236
Effective search space:    55460
Effective search space used:    55460
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 24 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