GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livG in Bacteroides thetaiotaomicron VPI-5482

Align High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized)
to candidate 350222 BT0694 ABC transporter, ATP-binding protein (NCBI ptt file)

Query= TCDB::P0A9S7
         (255 letters)



>FitnessBrowser__Btheta:350222
          Length = 224

 Score = 90.5 bits (223), Expect = 3e-23
 Identities = 65/200 (32%), Positives = 104/200 (52%), Gaps = 25/200 (12%)

Query: 19  LAVNNVNLELYPQEIVSLIGPNGAGKTTVFNCLTGFYKPTGGTILLRDQHLEGLP----- 73
           +A+N+VNLE+   E V+++GP+G GK+T+ N L     PT G+  L  + + GL      
Sbjct: 19  VALNHVNLEVKEGEFVAIMGPSGCGKSTLLNILGLLDNPTEGSYRLLGEEVAGLKEKERT 78

Query: 74  GQQIARMGVVRTFQHVRLFREMTVIENL-LVAQHQQLKTGLFSGLLKTPSFRRAQSEALD 132
           G +  ++G V  FQ   L  E+ V EN+ L   +  +K+          S RR   E + 
Sbjct: 79  GVRKGKLGFV--FQSFNLIDELNVFENVELPLTYLGIKS----------SERRRMVEDI- 125

Query: 133 RAATWLERIGLLEHANRQASNLAYGDQRRLEIARCMVTQPEILMLDEPAAGLNPKETKEL 192
                L+R+ +   A      L+ G Q+R+ IAR +VT P++++ DEP   L+ K   E+
Sbjct: 126 -----LKRMNISHRAKHFPQQLSGGQQQRVAIARAVVTNPKLILADEPTGNLDSKNGAEV 180

Query: 193 DELIAELRNHHNTTILLIEH 212
             L+ EL N   TTI+++ H
Sbjct: 181 MNLLTEL-NKEGTTIIMVTH 199


Lambda     K      H
   0.320    0.137    0.395 

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: 133
Number of extensions: 6
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: 255
Length of database: 224
Length adjustment: 23
Effective length of query: 232
Effective length of database: 201
Effective search space:    46632
Effective search space used:    46632
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 46 (22.3 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