GapMind for catabolism of small carbon sources

 

Aligments for a candidate for treV in Phaeobacter inhibens BS107

Align TreV, component of Trehalose porter (characterized)
to candidate GFF1302 PGA1_c13180 ABC transporter, ATP binding protein

Query= TCDB::Q97ZC0
         (324 letters)



>lcl|FitnessBrowser__Phaeo:GFF1302 PGA1_c13180 ABC transporter, ATP
           binding protein
          Length = 334

 Score =  250 bits (638), Expect = 4e-71
 Identities = 130/263 (49%), Positives = 175/263 (66%), Gaps = 1/263 (0%)

Query: 3   VELIDIVKKYGKNIVINGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKIIAD 62
           ++L  + K +G   VI  +   IE GEF V +GPSG GKSTLL+++AG+E +  G I  D
Sbjct: 4   IKLESVTKNFGPVEVIPPLDLTIEDGEFTVFVGPSGCGKSTLLRLIAGLEDITSGTIRID 63

Query: 63  GADITDKPPEKRNVAMVFQNYALYPNMSVRDNIAFPLKMRGMKKEEIIERVEKAAKLLGI 122
           G D T+ PP KR +AMVFQ+YALYP+MSVR NIAFP+KM G+  +E   R++ AA  L +
Sbjct: 64  GEDATNIPPAKRGLAMVFQSYALYPHMSVRKNIAFPMKMAGIPADEQKRRIDNAAAALNL 123

Query: 123 SEILDKKVTQISGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELKRIQKEL 182
           ++ LD++  Q+SGGQ+QRVA+ RAIVR P+ FL DEPLSNLDA +R   R E+  + K L
Sbjct: 124 TDYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVGMRLEISELHKRL 183

Query: 183 KGTFIYVTHDQKEALSLADRIAILHKGKFEQVSDPKTLYEYPKTKWVAQFVGEFPMNFLP 242
             T IYVTHDQ EA+++AD+I +L  G  EQV  P  LY  P+  +VA F+G   MN L 
Sbjct: 184 ATTMIYVTHDQVEAMTMADKIVVLQAGVIEQVGSPMELYRAPRNVFVAGFIGSPKMNLLT 243

Query: 243 G-ELMKEKAQEIGFRPEWVEVGK 264
           G +  +  A  IG RPE + + +
Sbjct: 244 GPQAAQHNAATIGIRPEHLSISE 266


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: 247
Number of extensions: 5
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: 334
Length adjustment: 28
Effective length of query: 296
Effective length of database: 306
Effective search space:    90576
Effective search space used:    90576
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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