Align Branched-chain amino acid ABC transporter,substrate-binding periplasmic component (characterized, see rationale)
to candidate BPHYT_RS01885 BPHYT_RS01885 branched-chain amino acid ABC transporter substrate-binding protein
Query= uniprot:G8ALJ3 (366 letters) >FitnessBrowser__BFirm:BPHYT_RS01885 Length = 381 Score = 221 bits (564), Expect = 2e-62 Identities = 131/372 (35%), Positives = 204/372 (54%), Gaps = 11/372 (2%) Query: 1 MNYKLSLLVAVAATAM------TASVAKADIAVATAGPITGQYATFGEQMKKGIEQAVAD 54 MN K+ L+ ++A AM T++ A + + P+TG A G+ + G AV + Sbjct: 1 MNIKIQKLLPISAAAMLFATLATSAAADTVVKIGHVAPLTGGIAHLGKDNENGARLAVEE 60 Query: 55 INAAGGVLGQK---LKLEVGDDACDPKQAVAVANQLAKAGVKFVAGHFCSGSSIPASQVY 111 INA G +G + L+L+ DDA DP+ A VA +L V V GH SG+SIPAS++Y Sbjct: 61 INAKGLTIGGQKITLQLDAQDDAADPRTATQVAQKLVDDKVVAVVGHLNSGTSIPASKIY 120 Query: 112 AEEGVLQISPASTNPKLTEQNLKNVFRVCGRDDQQGQIAGKYLLENYKGKNVAILHDKSA 171 ++ G++QISP++TNP T+Q K +RV D QQG Y + K K+VAI+ D +A Sbjct: 121 SDAGIVQISPSATNPAYTQQGFKTTYRVVATDAQQGPALANYAAKGLKVKSVAIVDDSTA 180 Query: 172 YGKGLADETQKALNAGGQKEKIYEAYTAGEKDYSALVSKLKQEAVDVVYVGGYHTEAGLL 231 YG+GLA+E +K + G ++A D+ A+++K+K E D + GG G Sbjct: 181 YGQGLANEFEKTAKSLGLNVMSHDATNDKAVDFRAILTKIKGENPDAIMYGGMDATGGPF 240 Query: 232 ARQMKDQGLNAPIVSGDALVTNEYWAITGPAGENTMMT-FGPDPREMPEAKEAVEKFRKA 290 A+Q K GL A +++GD + T++ + G A +N + + G +M + K++K Sbjct: 241 AKQAKQLGLRAKVLAGDGVCTDKLADLAGDATDNIVCSEAGMALEKMAGGSAFLAKYQKR 300 Query: 291 GYEP-EGYTLYTYAALQIWAEAAKQANSTDSAKIADVLRKNSYNTVIGKIGFDAKGDVTS 349 +P + Y +TY A+ I +A K+ANSTD AKI + Y VIG+ FD+KGD+ Sbjct: 301 FGQPIQIYAPFTYDAVYIIVDAMKRANSTDPAKILAAMPSTDYKGVIGETTFDSKGDLQH 360 Query: 350 PAYVWYRWNNGQ 361 Y + +G+ Sbjct: 361 GVISLYNYKSGK 372 Lambda K H 0.312 0.129 0.366 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: 397 Number of extensions: 20 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: 366 Length of database: 381 Length adjustment: 30 Effective length of query: 336 Effective length of database: 351 Effective search space: 117936 Effective search space used: 117936 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 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