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_036831855.1 N784_RS02455 ABC transporter ATP-binding protein
Query= TCDB::Q8DQH8 (254 letters) >NCBI__GCF_000775615.1:WP_036831855.1 Length = 507 Score = 129 bits (323), Expect = 2e-34 Identities = 78/241 (32%), Positives = 130/241 (53%), Gaps = 13/241 (5%) Query: 3 LLEVKQLTKHFGGLTAVGDVTLELNEGELVGLIGPNGAGKTTLFNLLTGVYEPSEGTVTL 62 ++E+ + K F G+ A +V L++ GE+ L+G NGAGK+TL N+L G+Y+P +G + + Sbjct: 4 VIEMLNIRKEFPGIVANNNVNLQVKPGEIHALLGENGAGKSTLMNVLFGLYQPEQGEIKV 63 Query: 63 DGHLLNGKSPYKIASLGLGRTFQNIRLFKDLTVLDNVLIAFGNHHKQHVFTSFLRLPAFY 122 G +N +P LG+G Q+ L TV +N+++ K V + Sbjct: 64 KGETVNITNPNVANELGIGMVHQHFMLVDTFTVTENIILGMEPTKKGTVNVA-------- 115 Query: 123 KSEKELKAKALELLKIFDLDGDAETLAKNLSYGQQRRLEIVRALATEPKILFLDEPAAGM 182 K+EKE+K E+ + + L D +++S G Q+R+EI++ L IL DEP A + Sbjct: 116 KAEKEVK----EISERYGLKVDPSAKIQDISVGMQQRVEILKTLYRGADILIFDEPTAVL 171 Query: 183 NPQETAELTELIRRIKDEFKITIMLIEHDMNLVMEVTERIYVLEYGRLIAQGTPDEIKTN 242 PQE +EL +++ + E K +I+LI H + +MEV +R V+ G I + TN Sbjct: 172 TPQEISELMDIMGTLVKEGK-SIILITHKLKEIMEVCDRCTVIRKGEGIGTVNVADTSTN 230 Query: 243 K 243 + Sbjct: 231 E 231 Score = 80.5 bits (197), Expect = 6e-20 Identities = 59/227 (25%), Positives = 113/227 (49%), Gaps = 13/227 (5%) Query: 16 LTAVGDVTLELNEGELVGLIGPNGAGKTTLFNLLTGVYEPSEGTVTLDGHLLNGKSPYKI 75 + V + L++ GE+VG+ G +G G++ L + G+ G++TL+G + SP K+ Sbjct: 270 INMVKGLNLQVRAGEIVGIAGVDGNGQSELIEAIAGLRNVESGSITLNGKEITNLSPRKV 329 Query: 76 ASLGLGRTFQN---IRLFKDLTVLDNVLIAFGNHHKQHVFTSFLRLPAFYKSEKELKAKA 132 G+ Q+ L D + +N+++ + + + LR YK KA Sbjct: 330 TESGVAHIPQDRHKYGLVLDFPIGENMVLQ-TYYQQPYSKKGVLRYKEIYK-------KA 381 Query: 133 LELLKIFDLDGDAE-TLAKNLSYGQQRRLEIVRALATEPKILFLDEPAAGMNPQETAELT 191 L++ FD+ E TLA++LS G Q++ I R L P +L +P G++ + Sbjct: 382 KSLIEEFDVRTPNEYTLARSLSGGNQQKAIIGRELDRSPDLLIAAQPTRGLDVGAIEFIH 441 Query: 192 ELIRRIKDEFKITIMLIEHDMNLVMEVTERIYVLEYGRLIAQGTPDE 238 + + +D K ++L+ +++ +M V++RI V+ G+++A P E Sbjct: 442 QRLIEARDSGK-AVLLLSFELDEIMNVSDRIAVMFDGQVVANVLPHE 487 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: 311 Number of extensions: 15 Number of successful extensions: 6 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: 507 Length adjustment: 29 Effective length of query: 225 Effective length of database: 478 Effective search space: 107550 Effective search space used: 107550 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: 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