GapMind for catabolism of small carbon sources

 

Alignments for a candidate for treV in Phaeobacter inhibens BS107

Align TreV, component of Trehalose porter (characterized)
to candidate GFF1645 PGA1_c16680 sugar ABC transporter, ATP-binding protein

Query= TCDB::Q97ZC0
         (324 letters)



>FitnessBrowser__Phaeo:GFF1645
          Length = 355

 Score =  244 bits (624), Expect = 2e-69
 Identities = 137/298 (45%), Positives = 186/298 (62%), Gaps = 22/298 (7%)

Query: 3   VELIDIVKKYGKNIVINGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKIIAD 62
           +EL D+ K+YG   V+  I   I+ GEF V++GPSG GKSTLL+++AG+E +  G    D
Sbjct: 4   IELRDVAKRYGAVEVLRDINLDIQDGEFIVLVGPSGCGKSTLLRMIAGLEPITSGDFEID 63

Query: 63  GADITDKPPEKRNVAMVFQNYALYPNMSVRDNIAFPLKMRGMKKEEIIERVEKAAKLLGI 122
           G  + D  P  R++AMVFQ+YALYP+M V  N+ F +++R    EE   RV +AA+ LG+
Sbjct: 64  GQRMNDVRPRDRDIAMVFQSYALYPHMDVARNMGFSMEIRKDPAEERRSRVARAAETLGL 123

Query: 123 SEILDKKVTQISGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELKRIQKEL 182
           S ++D+    +SGGQ+QRVA+ RAI+R+P  FL DEPLSNLDA +R   R E+ R+ K+L
Sbjct: 124 SSLVDRLPKALSGGQRQRVAMGRAIIRDPRAFLFDEPLSNLDAALRVEMRLEIARLHKQL 183

Query: 183 KGTFIYVTHDQKEALSLADRIAILHKGKFEQVSDPKTLYEYPKTKWVAQFVGEFPMNFLP 242
             T IYVTHDQ EAL+LADRI +L+ G  +QV  P  LYE P  K+VAQF+G   MN LP
Sbjct: 184 GATMIYVTHDQVEALTLADRIVVLNGGDIQQVGSPLELYERPANKFVAQFIGSPTMNILP 243

Query: 243 ------------GELM-------KEKAQEIGFRPEW---VEVGKGNLSCMVESVEASG 278
                       G ++          A E+G RPE    VE G+G+L  + + VE  G
Sbjct: 244 VSGAASGVMATNGMMLTLDHMHDTAAAVELGIRPEHLDVVEPGEGHLIAVADVVERLG 301


Lambda     K      H
   0.318    0.137    0.385 

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: 269
Number of extensions: 10
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: 324
Length of database: 355
Length adjustment: 28
Effective length of query: 296
Effective length of database: 327
Effective search space:    96792
Effective search space used:    96792
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: 49 (23.5 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