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.
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:
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