GapMind for catabolism of small carbon sources

 

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

Align Dehydrocarnitine CoA-transferase and acetoacetate CoA-transferase, subunit B (characterized)
to candidate CA265_RS06310 CA265_RS06310 succinyl-CoA--3-ketoacid-CoA transferase

Query= reanno::pseudo6_N2E2:Pf6N2E2_2112
         (221 letters)



>FitnessBrowser__Pedo557:CA265_RS06310
          Length = 219

 Score =  288 bits (737), Expect = 6e-83
 Identities = 143/215 (66%), Positives = 176/215 (81%), Gaps = 1/215 (0%)

Query: 4   SREQMAQRVAREMQDGYYVNLGIGIPTLVANYIPEGMEVMLQSENGLLGMGAFPTEAEVD 63
           S+E++AQR+A+E++DGYYVNLGIGIPTLVANYIP+G+ V+LQSENGLLGMG FP E E D
Sbjct: 3   SKEEIAQRIAKEIKDGYYVNLGIGIPTLVANYIPKGINVVLQSENGLLGMGPFPFEGEED 62

Query: 64  ADMINAGKQTVTARIGASIFSSAESFAMIRGGHIDLTVLGAFEVDVEGNIASWMIPGKLV 123
           AD+INAGKQT+T   G+SIF SA SF MIR   +DLT+LGA EV   G+IA+W IPGK+V
Sbjct: 63  ADLINAGKQTITTLPGSSIFDSAMSFGMIRAQKVDLTILGAMEVSENGDIANWKIPGKMV 122

Query: 124 KGMGGAMDLVAGAENIIVTMTHASKDGESKLLPRCSLPLTGAGCIKRVLTDLAYLEI-QD 182
           KGMGGAMDLVA A+NIIV M H +K GESKLLP+C+LPLTG  CIK+++T+LA L+I  +
Sbjct: 123 KGMGGAMDLVASAKNIIVAMQHINKAGESKLLPKCTLPLTGVKCIKKIVTELAVLDILPE 182

Query: 183 GAFILKERAPGVSVEEIVAKTAGKLIVPDHVPEMQ 217
           G F L ERAPGVS+E I   TAG+LI+   +PEM+
Sbjct: 183 GGFKLLERAPGVSIEFIQQSTAGRLIIEGDIPEMR 217


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: 227
Number of extensions: 8
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: 221
Length of database: 219
Length adjustment: 22
Effective length of query: 199
Effective length of database: 197
Effective search space:    39203
Effective search space used:    39203
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: 45 (21.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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