GapMind for catabolism of small carbon sources

 

Alignments for a candidate for treV in Pseudomonas simiae WCS417

Align TreV, component of Trehalose porter (characterized)
to candidate GFF2490 PS417_12700 ABC transporter ATP-binding protein

Query= TCDB::Q97ZC0
         (324 letters)



>FitnessBrowser__WCS417:GFF2490
          Length = 367

 Score =  242 bits (617), Expect = 1e-68
 Identities = 120/235 (51%), Positives = 169/235 (71%)

Query: 17  VINGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKIIADGADITDKPPEKRNV 76
           +I GI  ++   EF V +GPSG GKSTLL+++AG+E++ +G I  DG DIT+  P KR++
Sbjct: 18  IIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSEGTIELDGRDITEVTPAKRDL 77

Query: 77  AMVFQNYALYPNMSVRDNIAFPLKMRGMKKEEIIERVEKAAKLLGISEILDKKVTQISGG 136
           AMVFQ YALYP+MSVR N++F L + G+ K+ +  +V +AA++L +  +L++K  Q+SGG
Sbjct: 78  AMVFQTYALYPHMSVRKNMSFALDLAGVDKKLVESKVSEAARILELGPLLERKPKQLSGG 137

Query: 137 QQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELKRIQKELKGTFIYVTHDQKEA 196
           Q+QRVA+ RAIVRNP  FL DEPLSNLDA +R   R EL R+ KEL+ T IYVTHDQ EA
Sbjct: 138 QRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELARLHKELQATMIYVTHDQVEA 197

Query: 197 LSLADRIAILHKGKFEQVSDPKTLYEYPKTKWVAQFVGEFPMNFLPGELMKEKAQ 251
           ++LAD++ +L+ G+ EQV  P  LY  P   +VA F+G   M FL G++ + ++Q
Sbjct: 198 MTLADKVVVLNSGRIEQVGSPLELYHQPANLFVAGFLGTPKMGFLKGKVTRVESQ 252


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: 276
Number of extensions: 8
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: 367
Length adjustment: 29
Effective length of query: 295
Effective length of database: 338
Effective search space:    99710
Effective search space used:    99710
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