Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate BPHYT_RS01885 BPHYT_RS01885 branched-chain amino acid ABC transporter substrate-binding protein
Query= SwissProt::P21175 (373 letters) >FitnessBrowser__BFirm:BPHYT_RS01885 Length = 381 Score = 211 bits (538), Expect = 2e-59 Identities = 121/363 (33%), Positives = 196/363 (53%), Gaps = 5/363 (1%) Query: 6 QRLSRLFAAMAIAGFASYSMAADTI-KIALAGPVTGPVAQYGDMQRAGALMAIEQINKAG 64 Q+L + AA + + S AADT+ KI P+TG +A G GA +A+E+IN G Sbjct: 6 QKLLPISAAAMLFATLATSAAADTVVKIGHVAPLTGGIAHLGKDNENGARLAVEEINAKG 65 Query: 65 GVNGAQ---LEGVIYDDACDPKQAVAVANKVVNDGVKFVVGHVCSSSTQPATDIYEDEGV 121 G Q L+ DDA DP+ A VA K+V+D V VVGH+ S ++ PA+ IY D G+ Sbjct: 66 LTIGGQKITLQLDAQDDAADPRTATQVAQKLVDDKVVAVVGHLNSGTSIPASKIYSDAGI 125 Query: 122 LMITPSATAPEITSRGYKLIFRTIGLDNMQGPVAGKFIAERYKDKTIAVLHDKQQYGEGI 181 + I+PSAT P T +G+K +R + D QGP + A+ K K++A++ D YG+G+ Sbjct: 126 VQISPSATNPAYTQQGFKTTYRVVATDAQQGPALANYAAKGLKVKSVAIVDDSTAYGQGL 185 Query: 182 ATEVKKTVEDAGIKVAVFEGLNAGDKDFNALISKLKKAGVQFVYFGGYHPEMGLLLRQAK 241 A E +KT + G+ V + N DF A+++K+K + +GG G +QAK Sbjct: 186 ANEFEKTAKSLGLNVMSHDATNDKAVDFRAILTKIKGENPDAIMYGGMDATGGPFAKQAK 245 Query: 242 QAGLDARFMGPEGVGNSEITAIAGDASEGMLAT-LPRAFEQDPKNKALIDAFKAKNQDPS 300 Q GL A+ + +GV ++ +AGDA++ ++ + A E+ A + ++ + P Sbjct: 246 QLGLRAKVLAGDGVCTDKLADLAGDATDNIVCSEAGMALEKMAGGSAFLAKYQKRFGQPI 305 Query: 301 GIFVLPAYSAVTVIAKGIEKAGEADPEKVAEALRANTFETPTGNLGFDEKGDLKNFDFTV 360 I+ Y AV +I +++A DP K+ A+ + ++ G FD KGDL++ ++ Sbjct: 306 QIYAPFTYDAVYIIVDAMKRANSTDPAKILAAMPSTDYKGVIGETTFDSKGDLQHGVISL 365 Query: 361 YEW 363 Y + Sbjct: 366 YNY 368 Lambda K H 0.316 0.133 0.377 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: 393 Number of extensions: 17 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: 373 Length of database: 381 Length adjustment: 30 Effective length of query: 343 Effective length of database: 351 Effective search space: 120393 Effective search space used: 120393 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 (21.6 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