Align Branched-chain amino acid ABC transporter,substrate-binding periplasmic component (characterized, see rationale)
to candidate BWI76_RS07260 BWI76_RS07260 branched chain amino acid ABC transporter substrate-binding protein
Query= uniprot:G8ALJ3 (366 letters) >FitnessBrowser__Koxy:BWI76_RS07260 Length = 385 Score = 205 bits (521), Expect = 2e-57 Identities = 115/362 (31%), Positives = 199/362 (54%), Gaps = 5/362 (1%) Query: 6 SLLVAVAATAMTASVAKADIAVATAGPITGQYATFGEQMKKGIEQAVADINAAGGVLGQK 65 ++L++ A++ S A + + AGP+TG A G+ ++ G + A+ DIN +G K Sbjct: 12 AILLSGFASSAAWSAASETVIIGLAGPLTGPSARIGKDLENGAQLAIDDINKQHPTIGGK 71 Query: 66 ---LKLEVGDDACDPKQAVAVANQLAKAGVKFVAGHFCSGSSIPASQVYAEEGVLQISPA 122 KL+ DD DP+ AVAVA +L +GV V GH+ +G+SIPA++VY + G+ Q++P Sbjct: 72 AVTFKLQSEDDQSDPRTAVAVAQRLVDSGVAGVVGHWNTGTSIPAARVYHDAGIAQVAPV 131 Query: 123 STNPKLTEQNLKNVFRVCGRDDQQGQIAGKYLLENYKGKNVAILHDKSAYGKGLADETQK 182 +T T+Q FRV G DD GQ AG+Y ++ K K +A++ D++A+G+GLADE K Sbjct: 132 ATGHAYTKQGFDTSFRVMGHDDDGGQFAGQYAVQTLKAKRIAVIDDRTAFGQGLADEFIK 191 Query: 183 ALNAGGQKEKIYEAYTAGEKDYSALVSKLKQEAVDVVYVGGYHTEAGLLARQMKDQGLNA 242 +L G + D+SA+++ ++ + D+++ GG ++A LAR++K G+NA Sbjct: 192 SLEVQGINIVDRQYVDDKTVDFSAVLTAIRSKNADLIFFGGVDSQAAPLARRIKQLGMNA 251 Query: 243 PIVSGDALVTNEYWAITGPAGENTMMTFGPDPREMPEAKEAVEKFRKAGYEP--EGYTLY 300 ++ V+ + + G+ + P E +A E+ ++ Y E + + Sbjct: 252 TLMGAGGFVSQTFLQLAQKEGDGVVALEPGLPVERMPGGKAFEQAYQSRYHTHIELHAPF 311 Query: 301 TYAALQIWAEAAKQANSTDSAKIADVLRKNSYNTVIGKIGFDAKGDVTSPAYVWYRWNNG 360 Y A ++ A ++A+S D A LR +Y V G+I FD +G++ SP + Y+ G Sbjct: 312 AYDATRVLVAAMEKADSVDPADYLPALRAINYAGVTGQIAFDKEGNLKSPTFTVYKVVEG 371 Query: 361 QY 362 ++ Sbjct: 372 KW 373 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: 350 Number of extensions: 16 Number of successful extensions: 4 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: 385 Length adjustment: 30 Effective length of query: 336 Effective length of database: 355 Effective search space: 119280 Effective search space used: 119280 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