Align Branched-chain amino acid ABC transporter,substrate-binding periplasmic component (characterized, see rationale)
to candidate WP_013418499.1 RVAN_RS04095 branched-chain amino acid ABC transporter substrate-binding protein
Query= uniprot:G8ALJ3 (366 letters) >NCBI__GCF_000166055.1:WP_013418499.1 Length = 366 Score = 426 bits (1096), Expect = e-124 Identities = 207/344 (60%), Positives = 260/344 (75%), Gaps = 1/344 (0%) Query: 24 DIAVATAGPITGQYATFGEQMKKGIEQAVADINAAGGVLGQKLKLEVGDDACDPKQAVAV 83 DI++A AGP+TG+ ATFG Q K G E AVADINA GGVLG++LKLE+GDD CDPKQA AV Sbjct: 23 DISIAIAGPMTGKEATFGAQFKAGGEAAVADINAKGGVLGKQLKLEMGDDQCDPKQARAV 82 Query: 84 ANQLAKAGVKFVAGHFCSGSSIPASQVYAEEGVLQISPASTNPKLTEQNLKN-VFRVCGR 142 A QL+ +GV FVAGHFCS SSIPAS VY E+G++QISP STNPKLT++ + +R+CGR Sbjct: 83 AEQLSSSGVAFVAGHFCSSSSIPASSVYNEQGIVQISPGSTNPKLTDERPGDFTYRMCGR 142 Query: 143 DDQQGQIAGKYLLENYKGKNVAILHDKSAYGKGLADETQKALNAGGQKEKIYEAYTAGEK 202 DDQQG +AG YL + + K +AILHDK+AYG+GLADET+KALNA G++E YEA T GEK Sbjct: 143 DDQQGGVAGAYLAKEFADKKIAILHDKTAYGQGLADETKKALNAAGKQEVFYEAITPGEK 202 Query: 203 DYSALVSKLKQEAVDVVYVGGYHTEAGLLARQMKDQGLNAPIVSGDALVTNEYWAITGPA 262 DY+A+V+KLKQ VDVVY+GGYHTE GL+ RQM+ QG+ +V GDALV+ E +I G Sbjct: 203 DYTAVVTKLKQNGVDVVYLGGYHTEGGLIIRQMRAQGMKTILVGGDALVSTELGSIAGDD 262 Query: 263 GENTMMTFGPDPREMPEAKEAVEKFRKAGYEPEGYTLYTYAALQIWAEAAKQANSTDSAK 322 E TMMTF PDPR+ P AKE VE K G PEGY +YTYAA+Q WA+AA++A S + K Sbjct: 263 VEGTMMTFSPDPRKNPAAKEVVEALEKKGINPEGYVVYTYAAIQTWAQAAEKAGSIEGDK 322 Query: 323 IADVLRKNSYNTVIGKIGFDAKGDVTSPAYVWYRWNNGQYAQVK 366 + ++ ++T +GK FDAKGD P+YV+YRW Y Q++ Sbjct: 323 VVVAMKDLEFDTALGKFKFDAKGDPNLPSYVFYRWGKKNYEQIQ 366 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: 472 Number of extensions: 21 Number of successful extensions: 2 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: 366 Length adjustment: 30 Effective length of query: 336 Effective length of database: 336 Effective search space: 112896 Effective search space used: 112896 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: 49 (23.5 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