GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Btheta:350222 BT0694 ABC transporter,
           ATP-binding protein (NCBI ptt file)
          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 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