Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate GFF3249 Psest_3312 ABC-type (unclassified) transport system, ATPase component
Query= TCDB::Q8DQH8 (254 letters) >FitnessBrowser__psRCH2:GFF3249 Length = 241 Score = 146 bits (368), Expect = 4e-40 Identities = 86/258 (33%), Positives = 147/258 (56%), Gaps = 25/258 (9%) Query: 1 MALLEVKQLTKHFGGLTAVGDVTLELNEGELVGLIGPNGAGKTTLFNLLTGVYEPSEGTV 60 MA+L+ + L K + V DV+L + G++VGL+GPNGAGKTT F ++ G+ +G V Sbjct: 1 MAVLKAQHLAKSYKSRQVVRDVSLSIESGQIVGLLGPNGAGKTTCFYMIVGLVNADQGRV 60 Query: 61 TLDGHLLNGKSPYKIASLGLGRTFQNIRLFKDLTVLDNVLIAFGNHHKQHVFTSFLRLPA 120 +D + + + A G+G Q +F+ L+V DN++ A Sbjct: 61 LIDQNDVTHLPMHGRARAGIGYLPQEASIFRKLSVADNIM-------------------A 101 Query: 121 FYKSEKEL----KAKALE-LLKIFDLDGDAETLAKNLSYGQQRRLEIVRALATEPKILFL 175 ++ K+L + +ALE LL+ F ++ ++L +LS G++RR+EI RALAT PK + L Sbjct: 102 ILETRKDLDRSGRQQALEGLLQEFHINHIRDSLGMSLSGGERRRVEIARALATAPKFILL 161 Query: 176 DEPAAGMNPQETAELTELIRRIKDEFKITIMLIEHDMNLVMEVTERIYVLEYGRLIAQGT 235 DEP AG++P ++ ++I +K + I +++ +H++ +++ E Y++ G+LIA+G Sbjct: 162 DEPFAGVDPISVGDIKQIIHHLKAK-GIGVLITDHNVRETLDICETAYIVNDGQLIAEGD 220 Query: 236 PDEIKTNKRVIEAYLGGE 253 I +N+ V E YLG E Sbjct: 221 AQTILSNQLVKEVYLGHE 238 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: 151 Number of extensions: 8 Number of successful extensions: 3 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: 241 Length adjustment: 24 Effective length of query: 230 Effective length of database: 217 Effective search space: 49910 Effective search space used: 49910 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: 46 (22.3 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