Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate H281DRAFT_01586 H281DRAFT_01586 amino acid/amide ABC transporter ATP-binding protein 1, HAAT family
Query= TCDB::Q8DQH8 (254 letters) >FitnessBrowser__Burk376:H281DRAFT_01586 Length = 269 Score = 186 bits (472), Expect = 4e-52 Identities = 106/251 (42%), Positives = 146/251 (58%), Gaps = 7/251 (2%) Query: 1 MALLEVKQLTKHFGGLTAVGDVTLELNEGELVGLIGPNGAGKTTLFNLLTGVYEPSEGTV 60 M+LL V L K FGGL AV DV+ L G+L+ L+GPNGAGK+T FN++ G PS G++ Sbjct: 1 MSLLHVSGLCKSFGGLKAVDDVSFTLEAGQLLALLGPNGAGKSTCFNMVNGQLSPSSGSI 60 Query: 61 TLDGHLLNGKSPYKIASLGLGRTFQNIRLFKDLTVLDNVLIAFGNHHKQHVFTSFLRLPA 120 DGH L G P I LG+GRTFQ F +TVL+NV +A + ++ F + + Sbjct: 61 RFDGHELVGMRPRDIWRLGVGRTFQIAATFNSMTVLENVQMALVSRERK-TFGVWKPAAS 119 Query: 121 FYKSEKELKAKALELLKIFDLDGDAETLAKNLSYGQQRRLEIVRALATEPKILFLDEPAA 180 Y E A LL+ + DA L+YG +R+E+ ALA PK+L +DEP A Sbjct: 120 RYADE------AFALLEQVGMAADANRACGVLAYGDVKRVELAIALANRPKLLLMDEPTA 173 Query: 181 GMNPQETAELTELIRRIKDEFKITIMLIEHDMNLVMEVTERIYVLEYGRLIAQGTPDEIK 240 GM P+E EL L +R+ E KI ++ EH M++V +R+ VL G+LIA+G D I+ Sbjct: 174 GMAPKERNELMALTKRLVTEQKIGVLFTEHSMDVVFAYADRMIVLARGKLIAEGDGDTIR 233 Query: 241 TNKRVIEAYLG 251 + RV E Y G Sbjct: 234 NDPRVQEVYFG 244 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: 171 Number of extensions: 5 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: 254 Length of database: 269 Length adjustment: 25 Effective length of query: 229 Effective length of database: 244 Effective search space: 55876 Effective search space used: 55876 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: 47 (22.7 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