GapMind for catabolism of small carbon sources

 

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

Align Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate CA265_RS04200 CA265_RS04200 phosphonate ABC transporter ATP-binding protein

Query= uniprot:A0A165KQ08
         (355 letters)



>FitnessBrowser__Pedo557:CA265_RS04200
          Length = 226

 Score =  138 bits (348), Expect = 1e-37
 Identities = 88/210 (41%), Positives = 118/210 (56%), Gaps = 8/210 (3%)

Query: 16  KGDKSVEVLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEPTEGEIRIGGKNVVGM 75
           KG K+  VLR V   +  GEF+ ++GPSG GKSTLLNII  L+EPT G     G+NV  +
Sbjct: 14  KGIKNY-VLRLVTTSIKQGEFVSIMGPSGAGKSTLLNIIGMLEEPTYGSYEFLGENVTSL 72

Query: 76  PPRDR------DIAMVFQSYALYPTLSVADNIGFALEMRKMPKPERQKRIDEVAAMLQIS 129
             R R       I  VFQ+Y L   ++V +NI   L  +K+   ER  RI ++     I 
Sbjct: 73  NERKRIELYRNHIGFVFQAYHLIDEMTVYENIEAPLLYKKVGSAERASRIADLLDRFNIV 132

Query: 130 HLLDRRPSQLSGGQRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEMRAEIKRLHQASG 189
              D  P+QLSGGQ+Q V + RALA QP + L DEP  NL +    E+    K+L+Q  G
Sbjct: 133 AKKDLFPNQLSGGQQQLVGIARALAAQPSIILADEPTGNLQSAQADEIMTLFKKLNQEDG 192

Query: 190 ITSVYVTHDQVEAMTLGSRIAVMKGGVVQQ 219
           IT + VTH +  A   G+RI  +  GVV++
Sbjct: 193 ITIIQVTHSEKNAQ-YGNRILHIADGVVKE 221


Lambda     K      H
   0.318    0.135    0.388 

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: 169
Number of extensions: 8
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 355
Length of database: 226
Length adjustment: 26
Effective length of query: 329
Effective length of database: 200
Effective search space:    65800
Effective search space used:    65800
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: 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