GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dch in Herbaspirillum seropedicae SmR1

Align cyclohexa-1,5-dienecarbonyl-CoA hydratase monomer (EC 4.2.1.100) (characterized)
to candidate HSERO_RS19405 HSERO_RS19405 enoyl-CoA hydratase

Query= metacyc::MONOMER-18320
         (256 letters)



>FitnessBrowser__HerbieS:HSERO_RS19405
          Length = 258

 Score =  132 bits (331), Expect = 9e-36
 Identities = 85/261 (32%), Positives = 130/261 (49%), Gaps = 12/261 (4%)

Query: 1   MGFNTILFEKKDKVATITLNVPNS-NWLTIPMMKEINEALMDVKKDPTIQLLVFDHAGDK 59
           M +  I  E  +KV  I L+ P + N L+  +M E+ EAL+       I  ++     +K
Sbjct: 1   MSYENIQVETHEKVGLIRLHRPKALNALSDGLMTELGEALLAFDAQEEIGCIIIT-GSEK 59

Query: 60  AFCDGVDVADHVPEKVDEMIDLFHGMF-----RNMAAMDVTSVCLVNGRSLGGGCELMAF 114
           AF  G D++        + +D+F G F       +  +    +  V G +LGGGCEL   
Sbjct: 60  AFAAGADISAMAGY---DYMDVFKGEFITRNWETLRRIRKPVIAAVAGYALGGGCELAMM 116

Query: 115 CDIVIASEKAKIGQPEINLAVFPPVAAAW-FPKIMGLKKAMELILTGKIISAKEAEAIGL 173
           CD +IA++ AK GQPEI L + P        P+ +   KAM+L LTG+++ A+EAE  GL
Sbjct: 117 CDFIIAADNAKFGQPEIKLGIVPGAGGTQRLPRAVSKAKAMDLALTGRMMDAEEAERAGL 176

Query: 174 VNVVLPVEGFREAAQKFMADFTSKSRPVAMWARRAIMAGLNLDFLQALKASEIIYMQGCM 233
           V+ ++  +   E A           R VAM  + ++         + +K    ++   C 
Sbjct: 177 VSRIVAADKLLEEAMAAAIIIAEMPRQVAMMVKDSVNRAYETTLSEGMKYERALF-YSCF 235

Query: 234 ATEDANEGLASFLEKRKPVFK 254
           ATED  EG+ +FLEKR+PVFK
Sbjct: 236 ATEDQKEGMKAFLEKRQPVFK 256


Lambda     K      H
   0.322    0.136    0.401 

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: 157
Number of extensions: 8
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: 256
Length of database: 258
Length adjustment: 24
Effective length of query: 232
Effective length of database: 234
Effective search space:    54288
Effective search space used:    54288
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