GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ctfA in Pseudomonas simiae WCS417

Align Butyrate--acetoacetate CoA-transferase subunit A; Short=Coat A; EC 2.8.3.9 (characterized, see rationale)
to candidate GFF2064 PS417_10525 succinyl-CoA:3-ketoacid-CoA transferase

Query= uniprot:P33752
         (218 letters)



>FitnessBrowser__WCS417:GFF2064
          Length = 232

 Score =  171 bits (432), Expect = 1e-47
 Identities = 83/213 (38%), Positives = 129/213 (60%)

Query: 2   NSKIIRFENLRSFFKDGMTIMIGGFLNCGTPTKLIDFLVNLNIKNLTIISNDTCYPNTGI 61
           + ++  +E   +  +DGMT++ GGF  CG P  LI  +     ++LT++SN+      G+
Sbjct: 5   DKRVASYEEALAGLEDGMTVLSGGFGLCGIPENLIAEIKRKGTRDLTVVSNNCGVDGFGL 64

Query: 62  GKLISNNQVKKLIASYIGSNPDTGKKLFNNELEVELSPQGTLVERIRAGGSGLGGVLTKT 121
           G L+   Q+ K+IASY+G N    K+L + E+EV L+PQGTL E++RAGG+G+    T T
Sbjct: 65  GVLLEEKQISKVIASYVGENALFEKQLLSGEIEVVLTPQGTLAEKMRAGGAGIPAFFTAT 124

Query: 122 GLGTLIEKGKKKISINGTEYLLELPLTADVALIKGSIVDEAGNTFYKGTTKNFNPYMAMA 181
           G+GT + +GK+    NG  YL+E  +T D A++KG   D  GN  Y+ T +NFNP  A A
Sbjct: 125 GVGTPVAEGKETREFNGRPYLMEESITGDFAIVKGWKADHFGNVIYRHTAQNFNPLAATA 184

Query: 182 AKTVIVEAENLVSCEKLEKEKAMTPGVLINYIV 214
            K  +VE E +V   +L+  +  TPG+ ++ I+
Sbjct: 185 GKITVVEVEEIVEPGELDPAQIHTPGIYVDRII 217


Lambda     K      H
   0.315    0.136    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: 136
Number of extensions: 4
Number of successful extensions: 1
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: 218
Length of database: 232
Length adjustment: 22
Effective length of query: 196
Effective length of database: 210
Effective search space:    41160
Effective search space used:    41160
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: 42 (22.0 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