GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braG in Bacillus altitudinis 41KF2b

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 WP_007501258.1 BA79_RS10715 phosphate ABC transporter ATP-binding protein

Query= TCDB::P21630
         (233 letters)



>NCBI__GCF_000691145.1:WP_007501258.1
          Length = 270

 Score =  107 bits (268), Expect = 2e-28
 Identities = 75/236 (31%), Positives = 126/236 (53%), Gaps = 14/236 (5%)

Query: 1   MLSFDKVSTYYGKIQALHDVSVEVKKGEIVTLIGANGAGKSTLLMTLCGS----PQAAS- 55
           +L    +S YYG+ +A++ +S E++K  I  LIG +G GKST L ++       P A S 
Sbjct: 23  ILQVQDLSIYYGEKRAVNQISFEIEKNAITALIGPSGCGKSTFLRSINRMNDLIPGARSE 82

Query: 56  GSIRYEGEELVGLPSSTI-MRKSIAVVPEGRRVFSRLTVEENLAMGGFFTDKDDYQVQMD 114
           G+I YEG  ++    + + +R+ I +V +    F + ++  N+     +  +    V  D
Sbjct: 83  GAIMYEGLNILDDRINVVNLRREIGMVFQKPNPFPK-SIYNNITHALKYAGEKRKSVLDD 141

Query: 115 KVLE------LFPRLKERYEQRAGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPII 168
            V E      L+  +K+R  + A ++SGG+QQ L I R L  KP +LLLDEP+  L PI 
Sbjct: 142 AVEESLTKAALWDEVKDRLHRSALSLSGGQQQRLCIARTLAMKPSVLLLDEPASALDPIS 201

Query: 169 IQQIFEIIEQLRREGVTVFLVEQNANQALKLADRAYVLENGRIVMHDTGAALLTNP 224
             +I E++ +L+ +  ++ +V  N  QAL+++D      NG +V +D    + T P
Sbjct: 202 NAKIEELLSELKHD-YSIVIVTHNMQQALRVSDHTAFFLNGDLVEYDATERIFTRP 256


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: 133
Number of extensions: 7
Number of successful extensions: 3
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: 270
Length adjustment: 24
Effective length of query: 209
Effective length of database: 246
Effective search space:    51414
Effective search space used:    51414
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 24 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