GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Echinicola vietnamensis KMM 6221, DSM 17526

Align 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized)
to candidate Echvi_0343 Echvi_0343 Enoyl-CoA hydratase/carnithine racemase

Query= CharProtDB::CH_091794
         (261 letters)



>FitnessBrowser__Cola:Echvi_0343
          Length = 258

 Score =  125 bits (314), Expect = 9e-34
 Identities = 85/256 (33%), Positives = 133/256 (51%), Gaps = 6/256 (2%)

Query: 5   NVILEKEGKVAVVTINRPKALNALNSDTLKEMDYVIGEIENDSEVLAVILTGAGEKSFVA 64
           +V  E++G++  V ++RP+  NALN+  +  +   +   E    V  VI+   G K F +
Sbjct: 4   HVKFEQKGRIGYVILSRPEKRNALNAAMVSGLQAALDRCEAIETVKVVIIKAEG-KVFCS 62

Query: 65  GADISEMKEM--NTIEGRKFGILG-NKVFRRLELLEKPVIAAVNGFALGGGCEIAMSCDI 121
           GAD+ +++ M  NT +       G  K+F RL    K VIA V G AL GGC +   CD 
Sbjct: 63  GADLQDIERMQDNTFDENLADSEGLKKLFLRLYTFPKVVIAQVQGHALAGGCGLVSVCDF 122

Query: 122 RIASSNARFGQPEVGLGITPGFGGTQRLSRLVGMGMAKQLIFTAQNIKADEALRIGLVNK 181
             A   A+ G  EV +G  P       L R +G G AK+L+ T + + A  A  IGL+ +
Sbjct: 123 AYAVPTAKLGYTEVRIGFVPAM-VLVFLVRKLGEGKAKELLLTGELLVAPAAKEIGLIQE 181

Query: 182 VVEPSELMNTAKEIANKIVS-NAPVAVKLSKQAINRGMQCDIDTALAFESEAFGECFSTE 240
           V EP+ L    +EIA +++S N+  ++ L+K+ I       ++ AL + +    +   TE
Sbjct: 182 VFEPAALDGAVQEIAERLISQNSGESMALTKKMIAAVQDLPLEEALEYAARMNAKARETE 241

Query: 241 DQKDAMTAFIEKRKIE 256
           D K  + AF+ K+KIE
Sbjct: 242 DCKRGIAAFLGKKKIE 257


Lambda     K      H
   0.317    0.134    0.365 

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: 163
Number of extensions: 8
Number of successful extensions: 4
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: 261
Length of database: 258
Length adjustment: 24
Effective length of query: 237
Effective length of database: 234
Effective search space:    55458
Effective search space used:    55458
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: 41 (21.6 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