Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate WP_232502519.1 LFE_RS09120 ATP-binding cassette domain-containing protein
Query= TCDB::Q8DQH8 (254 letters) >NCBI__GCF_000284315.1:WP_232502519.1 Length = 588 Score = 110 bits (274), Expect = 9e-29 Identities = 76/244 (31%), Positives = 123/244 (50%), Gaps = 25/244 (10%) Query: 4 LEVKQLTKHFGGLTAVGDVTLELNEGELVGLIGPNGAGKTTLFNLLTGVYEPSEGTVTLD 63 +EV+ L ++F AV ++T + +GE+ GL+G NGAGKTT F +L G+ EP+ G + Sbjct: 342 IEVENLDRYFDSFKAVNNLTFHVKKGEVFGLLGANGAGKTTTFRMLAGLLEPTAGKL--- 398 Query: 64 GHLLNGKSPYKIASLG---LGRTFQNIRLFKDLTVLDNVLIAFGNHHKQHVFTSFLRLPA 120 ++ G+ K+A+ +G Q L+ LTV N+ +F S A Sbjct: 399 --IVAGEDVRKVAAQARGKIGYMAQKFSLYSQLTVFQNL-----------IFYS----SA 441 Query: 121 FYKSEKELKAKALELLKIFDLDGDAETLAKNLSYGQQRRLEIVRALATEPKILFLDEPAA 180 + S K K + L F+L+ + L G ++RL + AL EP ILFLDEP + Sbjct: 442 YGLSGTLQKEKIQDSLNFFELEPYKNVSSGILPLGFRQRLALSCALIHEPSILFLDEPTS 501 Query: 181 GMNPQETAELTELIRRIKDEFKITIMLIEHDMNLVMEVTERIYVLEYGRLIAQGTPDEIK 240 G++P E +I + +++++ H M E +R+ ++ G L+A G+P EIK Sbjct: 502 GVDPNARREFWHIINALA-TVGVSVLVTTHFME-EAEYCDRLLIMAQGALLAMGSPAEIK 559 Query: 241 TNKR 244 R Sbjct: 560 EKTR 563 Score = 102 bits (254), Expect = 2e-26 Identities = 75/242 (30%), Positives = 125/242 (51%), Gaps = 22/242 (9%) Query: 3 LLEVKQLTKHF----GGLTAVGDVTLELNEGELVGLIGPNGAGKTTLFNLLTGVYEPSEG 58 L+ V +LTK F G +TA+ ++ L +G + GLIGP+GAGKTTL LL+G+ P G Sbjct: 10 LITVNELTKTFPSPRGIVTALDKISFSLKKGSITGLIGPDGAGKTTLMRLLSGLLWPDGG 69 Query: 59 TVTLDGHLLNGKSPYKIASLGLGRTFQNIRLFKDLTVLDNVLIAFGNHHKQHVFTSFLRL 118 + + G+ K+P + LG Q L++DL+V +N+ ++ + + Sbjct: 70 DIRIMGN-DPSKAPLSVQG-SLGYMPQKFGLYEDLSVQENL----------DLYANLQGV 117 Query: 119 PAFYKSEKELKAKALELLKIFDLDGDAETLAKNLSYGQQRRLEIVRALATEPKILFLDEP 178 P KEL A LL + L + LA LS G +++L + +L +P IL LDEP Sbjct: 118 PK--DRRKELYA---PLLSMTGLSPFQKRLAGQLSGGMKQKLGVACSLVHQPPILLLDEP 172 Query: 179 AAGMNPQETAELTELIRRIKDEFKITIMLIEHDMNLVMEVTERIYVLEYGRLIAQGTPDE 238 G++P EL E++R++ E T+ + ++ E + I +L G+++ G P+ Sbjct: 173 TVGVDPVSRRELWEILRKLVSESGATLFVSTSYLD-EAERCDEILILYNGKVLGSGPPES 231 Query: 239 IK 240 + Sbjct: 232 FR 233 Lambda K H 0.319 0.139 0.385 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: 342 Number of extensions: 18 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 254 Length of database: 588 Length adjustment: 30 Effective length of query: 224 Effective length of database: 558 Effective search space: 124992 Effective search space used: 124992 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. 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