GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braG in Phaeobacter inhibens BS107

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 GFF3203 PGA1_c32560 high-affinity branched-chain amino acid transport ATP-binding protein

Query= TCDB::P21630
         (233 letters)



>FitnessBrowser__Phaeo:GFF3203
          Length = 278

 Score =  191 bits (484), Expect = 2e-53
 Identities = 107/241 (44%), Positives = 145/241 (60%), Gaps = 9/241 (3%)

Query: 1   MLSFDKVSTYYGK-IQALHDVSVEVKKGEIVTLIGANGAGKSTLLMTLCG-----SPQAA 54
           +L  + +   Y   I  L  VS++V KG I  L+G NGAGK+T L  +         +  
Sbjct: 15  LLEVNNIEVIYNHVILVLKGVSLKVPKGGITALLGGNGAGKTTTLKAVSNLLHSERGEVT 74

Query: 55  SGSIRYEGEELVGLPSSTIMRKSIAVVPEGRRVFSRLTVEENLAMGGFFTDKDDYQVQMD 114
            GSI Y GE +     + +++K +  V EGR  F  LTVEENL  G +     +  +Q D
Sbjct: 75  KGSISYRGERIQDRDPAELVKKGVIQVMEGRHCFEHLTVEENLLTGAYTRSDGNANIQRD 134

Query: 115 --KVLELFPRLKERYEQRAGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQI 172
              V   FPRLKER   +AG  SGGEQQM+A+GRALMS+P+ +LLDEPS+GLAP +++QI
Sbjct: 135 LEMVYSYFPRLKERRRSQAGYTSGGEQQMVAMGRALMSRPETILLDEPSMGLAPQLVEQI 194

Query: 173 FEIIEQL-RREGVTVFLVEQNANQALKLADRAYVLENGRIVMHDTGAALLTNPKVRDAYL 231
           FEI++ +   EGVT  L EQN N AL+ +   Y+LE+GR+VM    A L  NP V++ YL
Sbjct: 195 FEIVKSINENEGVTFLLAEQNTNVALRYSHYGYILESGRVVMDGPAAELRENPDVKEFYL 254

Query: 232 G 232
           G
Sbjct: 255 G 255


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: 177
Number of extensions: 8
Number of successful extensions: 4
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: 278
Length adjustment: 24
Effective length of query: 209
Effective length of database: 254
Effective search space:    53086
Effective search space used:    53086
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: 47 (22.7 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