GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braG in Shewanella loihica PV-4

Align High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate 5210884 Shew_3310 ABC transporter-related protein (RefSeq)

Query= TCDB::P21630
         (233 letters)



>FitnessBrowser__PV4:5210884
          Length = 243

 Score =  134 bits (338), Expect = 1e-36
 Identities = 78/236 (33%), Positives = 131/236 (55%), Gaps = 6/236 (2%)

Query: 1   MLSFDKVSTYYGKIQALHDVSVEVKKGEIVTLIGANGAGKSTLLMTLCGSPQAASGSIRY 60
           +L  + ++  Y     + DVS+ VK G+IV L+G NGAGK+T    + G  Q+  G I  
Sbjct: 5   ILKAENLAKSYKSRAVVQDVSLTVKTGQIVGLLGPNGAGKTTTFYMVVGLVQSDKGRIFI 64

Query: 61  EGEELVGLPSSTIMRKSIAVVPEGRRVFSRLTVEENLAMGGFFT----DKDDYQVQMDKV 116
           + ++L   P     RK I  +P+   +F +L+V +N+ M    T    + D  + +++ +
Sbjct: 65  DDDDLTLDPMHLRARKGIGYLPQEASIFRKLSVRDNI-MAVLQTRSDLNNDGREEELEHL 123

Query: 117 LELFPRLKERYEQRAGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFEII 176
           LE F  +    +     +SGGE++ + I RAL + PK +LLDEP  G+ PI +  I +II
Sbjct: 124 LEEF-HITHIRDSHGMALSGGERRRVEIARALAANPKFILLDEPFAGVDPISVIDIKKII 182

Query: 177 EQLRREGVTVFLVEQNANQALKLADRAYVLENGRIVMHDTGAALLTNPKVRDAYLG 232
           EQL+  G+ V + + N  + L + ++AY++ +G ++   T A +L N +VR  YLG
Sbjct: 183 EQLKNRGLGVLITDHNVRETLDVCEKAYIVSHGNLIAEGTPAEILDNQQVRAVYLG 238


Lambda     K      H
   0.318    0.136    0.374 

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: 115
Number of extensions: 9
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: 233
Length of database: 243
Length adjustment: 23
Effective length of query: 210
Effective length of database: 220
Effective search space:    46200
Effective search space used:    46200
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: 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