Align Branched-chain amino acid ABC transporter,substrate-binding periplasmic component (characterized, see rationale)
to candidate BPHYT_RS31715 BPHYT_RS31715 branched-chain amino acid ABC transporter substrate-binding protein
Query= uniprot:G8ALJ3 (366 letters) >FitnessBrowser__BFirm:BPHYT_RS31715 Length = 380 Score = 229 bits (583), Expect = 1e-64 Identities = 136/366 (37%), Positives = 196/366 (53%), Gaps = 8/366 (2%) Query: 4 KLSLLVAVAATAMTASVAKADIAV---ATAGPITGQYATFGEQMKKGIEQAVADINAAGG 60 K VA + A A+ A DI V +A P TG A G++ + G AV D+N G Sbjct: 6 KHGFAVAALSAACNAAFAADDITVIKIGSAAPTTGAIANLGKENENGARLAVEDVNRRGL 65 Query: 61 VL-GQKLKLEVG--DDACDPKQAVAVANQLAKAGVKFVAGHFCSGSSIPASQVYAEEGVL 117 V+ G+K+KLE+ DD DP+Q VA +L GV V GH SG SI AS++Y + +L Sbjct: 66 VINGKKIKLELDAVDDQADPRQGTQVAQRLVDDGVVAVVGHLNSGVSIAASRIYHDAQIL 125 Query: 118 QISPASTNPKLTEQNLKNVFRVCGRDDQQGQIAGKYLLENYKGKNVAILHDKSAYGKGLA 177 QISP STNPK T+Q +R+ D QQ + Y LE K K VAI+ D +AYG+GLA Sbjct: 126 QISPDSTNPKFTQQGFNTTYRLVATDAQQSPVLAHYALETLKAKKVAIVDDSTAYGQGLA 185 Query: 178 DETQKALNAGGQKEKIYEAYTAGEKDYSALVSKLKQEAVDVVYVGGYHTEAGLLARQMKD 237 D+ A+ +GG EA D+ +++K+K ++ DV++ GG AG +Q+ Sbjct: 186 DQFSSAVKSGGATVVAREATNDKTIDFKGVITKIKGQSPDVIFYGGMDATAGPFIKQVAQ 245 Query: 238 QGLNAPIVSGDALVTNEYWAITGPAGENTMMTFGPDPREMPEAKEAVEK--FRKAGYEPE 295 GLNA ++ GD ++E A+ GPA + + + P +A A EK ++ G + Sbjct: 246 LGLNAKVLGGDGTCSDEVIALAGPAVDRLVCSIAGLPLSRMKAGPAFEKEYQQRFGMPVQ 305 Query: 296 GYTLYTYAALQIWAEAAKQANSTDSAKIADVLRKNSYNTVIGKIGFDAKGDVTSPAYVWY 355 Y Y Y A+ + +A K++ STD AKI Y + G+I FD KGDV SP Y Sbjct: 306 IYAPYAYDAVMVIVDAMKKSGSTDHAKILAAASATDYQGLTGQIQFDDKGDVRSPRLTLY 365 Query: 356 RWNNGQ 361 + +G+ Sbjct: 366 GYKDGK 371 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: 333 Number of extensions: 18 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: 380 Length adjustment: 30 Effective length of query: 336 Effective length of database: 350 Effective search space: 117600 Effective search space used: 117600 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