GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaI in Pedobacter sp. GW460-11-11-14-LB5

Align 3-oxoadipate CoA-transferase subunit A; EC 2.8.3.6 (characterized)
to candidate CA265_RS06305 CA265_RS06305 succinyl-CoA--3-ketoacid-CoA transferase

Query= CharProtDB::CH_021928
         (231 letters)



>FitnessBrowser__Pedo557:CA265_RS06305
          Length = 234

 Score =  202 bits (515), Expect = 3e-57
 Identities = 99/216 (45%), Positives = 144/216 (66%), Gaps = 2/216 (0%)

Query: 1   MINKTYESIASAVEGITDGSTIMVGGFGTAGMPSELIDGLIATGARDLTIISNNAGNGEI 60
           MINK       A++ I+DG T+M+GGFG  G+P   I  L+    ++LT ISNNAG  + 
Sbjct: 1   MINKVVSGAEEAIKDISDGVTLMLGGFGLCGIPENCIKALVNKQVKNLTCISNNAGVDDF 60

Query: 61  GLAALLMAGSVRKVVCSFPRQSDSYVFDELYRAGKIELEVVPQGNLAERIAAAGSGIGAF 120
           G+  +L    V+K++ S+  ++    F+    +G++E++++PQG LA R  AAG G+ A 
Sbjct: 61  GIGLMLKQRQVKKMISSYVGENAE--FERQLLSGELEVDLIPQGTLATRCLAAGYGMPAI 118

Query: 121 FSPTGYGTLLAEGKETREIDGRMYVLEMPLHADFALIKAHKGDRWGNLTYRKAARNFGPI 180
           F+P G GT +AEGKE R  DG+ Y++E    ADFA++KA KGD  GNL +R  +RNF P+
Sbjct: 119 FTPAGVGTEVAEGKEIRNFDGKDYLMEYAFDADFAIVKAWKGDTAGNLIFRSTSRNFNPV 178

Query: 181 MAMAAKTAIAQVDQVVELGELDPEHIITPGIFVQRV 216
           MAMA K  IA+V+++VE GELDP++I TPGI+V R+
Sbjct: 179 MAMAGKITIAEVEELVEAGELDPDYIHTPGIYVHRI 214


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: 152
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: 234
Length adjustment: 23
Effective length of query: 208
Effective length of database: 211
Effective search space:    43888
Effective search space used:    43888
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