GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Phaeobacter inhibens BS107

Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate GFF2642 PGA1_c26820 probable enoyl-CoA hydratase PaaG

Query= reanno::BFirm:BPHYT_RS17335
         (258 letters)



>FitnessBrowser__Phaeo:GFF2642
          Length = 261

 Score =  146 bits (369), Expect = 4e-40
 Identities = 90/258 (34%), Positives = 139/258 (53%), Gaps = 6/258 (2%)

Query: 4   ENILVETRGRVGLVTLNRPKALNALNDALMDELGAALREFDADDAIGAIVVTGSEKAFAA 63
           E +LVE  G    +TLNRP  LN+  + +   L AAL E   D    A+++TG+ + F A
Sbjct: 3   ETLLVEDHGTWVEITLNRPDRLNSFTEEMHHALRAAL-EAARDGGARAVLLTGAGRGFCA 61

Query: 64  GADIGMMSTYTYMDVYKGDYITRNW-----ETVRSIRKPIIAAVAGFALGGGCELAMMCD 118
           G D+G              +  R +       +R++  P+I AV G A G G  LA+ CD
Sbjct: 62  GQDLGDRDPRKMDGPPDLGHTVRTFYAPLVNLIRALDFPVICAVNGVAAGAGANLALACD 121

Query: 119 IIFAADTAKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERAGLVS 178
           ++ AA++AKF Q   K+G++P  GG+  LPR + +A+A  L LTA  + A +AE  GL+ 
Sbjct: 122 VVLAAESAKFIQSFSKVGLIPDTGGSWHLPRLLGEARAKGLALTAEPLPAKKAEDWGLIW 181

Query: 179 RVIPAASLVDEAIAAAATIAEFPSPAVMMVKESVNRAYETTLAEGVHFERRLFHSLFATE 238
           + +P   L+ EA A A   A  P+  + + K+++  A  TTL++ +  E     +   + 
Sbjct: 182 KAVPDEELMAEARAMAEKFANGPTLGLGLTKQTIQAAAVTTLSDQLEIEADAMKTCGESA 241

Query: 239 DQKEGMAAFVEKRKPVFK 256
           D  EG+A+F+EKR P FK
Sbjct: 242 DYAEGVASFLEKRVPAFK 259


Lambda     K      H
   0.321    0.134    0.380 

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: 140
Number of extensions: 9
Number of successful extensions: 3
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: 258
Length of database: 261
Length adjustment: 24
Effective length of query: 234
Effective length of database: 237
Effective search space:    55458
Effective search space used:    55458
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