GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaI in Sphingomonas koreensis DSMZ 15582

Align 3-oxoadipate CoA-transferase subunit A; EC 2.8.3.6 (characterized)
to candidate Ga0059261_0265 Ga0059261_0265 3-oxoacid CoA-transferase, A subunit

Query= CharProtDB::CH_021928
         (231 letters)



>FitnessBrowser__Korea:Ga0059261_0265
          Length = 235

 Score =  200 bits (509), Expect = 2e-56
 Identities = 105/217 (48%), Positives = 143/217 (65%), Gaps = 3/217 (1%)

Query: 2   INKTYESIASAVEGIT-DGSTIMVGGFGTAGMPSELIDGLIATGARDLTIISNNAGNGEI 60
           + K Y S  +A+EG+  DG TI  GGFG  G+P  LID + A+G RD+TI SNNAG    
Sbjct: 1   MKKLYPSAEAALEGLLHDGITICAGGFGLCGIPERLIDAIQASGVRDMTIASNNAGIDNE 60

Query: 61  GLAALLMAGSVRKVVCSFPRQSDSYVFDELYRAGKIELEVVPQGNLAERIAAAGSGIGAF 120
           GL  LL +  VRK++ S+  ++    F+  Y AG++E+E  PQG LAER  A G+GI  F
Sbjct: 61  GLGKLLRSRQVRKMISSYVGENKE--FERQYLAGELEVEFCPQGTLAERCRAGGAGIPGF 118

Query: 121 FSPTGYGTLLAEGKETREIDGRMYVLEMPLHADFALIKAHKGDRWGNLTYRKAARNFGPI 180
           ++ TG GT +AEGKET+  DG+ Y+LE  + AD A+IK  K D  GNL +RK ARNF   
Sbjct: 119 YTKTGVGTKVAEGKETKVFDGQEYILERGIRADLAIIKGWKADEAGNLIFRKTARNFNQP 178

Query: 181 MAMAAKTAIAQVDQVVELGELDPEHIITPGIFVQRVV 217
           MA AA   +A+V++VV +G LDP+ I  PGI+V+R++
Sbjct: 179 MATAANICVAEVEEVVPVGSLDPDAIHLPGIYVKRMI 215


Lambda     K      H
   0.318    0.135    0.381 

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: 124
Number of extensions: 7
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: 231
Length of database: 235
Length adjustment: 23
Effective length of query: 208
Effective length of database: 212
Effective search space:    44096
Effective search space used:    44096
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 (21.7 bits)
S2: 46 (22.3 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