Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate 6938983 Sama_3081 ABC transporter, ATP-binding protein, putative (RefSeq)
Query= TCDB::Q8DQH8 (254 letters) >FitnessBrowser__SB2B:6938983 Length = 270 Score = 132 bits (331), Expect = 1e-35 Identities = 80/254 (31%), Positives = 131/254 (51%), Gaps = 17/254 (6%) Query: 3 LLEVKQLTKHFGGLTAVGDVTLELNEGELVGLIGPNGAGKTTLFNLLTGVYEPSEGTVTL 62 L+EV+ L G D++L + +G++ ++GP+G GKTTL L+ G P G V Sbjct: 8 LVEVRNLGFSRGERVIYEDISLSIPKGKVTAIMGPSGIGKTTLLKLIAGQLVPDHGEVLF 67 Query: 63 DGHLLNGKSPYKIASLG--LGRTFQNIRLFKDLTVLDNVLIAFGNHHKQHVFTSFLRLPA 120 DG ++ S ++ L + FQ+ LF D+ V DN+ A H Sbjct: 68 DGVNIHDISRSELFELRKRMSMLFQSGALFTDMNVFDNIAFALREHSGL----------- 116 Query: 121 FYKSEKELKAKALELLKIFDLDGDAETLAKNLSYGQQRRLEIVRALATEPKILFLDEPAA 180 E ++ L L+ L G A + LS G QRR+ + RA+A EP+++ DEP A Sbjct: 117 ---DEAIIRRIVLMKLEAVGLRGAAMLMPSELSGGMQRRVALARAIALEPEMVMYDEPFA 173 Query: 181 GMNPQETAELTELIRRIKDEFKITIMLIEHDMNLVMEVTERIYVLEYGRLIAQGTPDEIK 240 G +P L +LIR + D +T +++ HD+ V+ + + +YV+ R+IAQGTP ++K Sbjct: 174 GQDPISMGVLVKLIRELSDALNLTSVVVSHDVGEVLGIADYVYVIAEKRIIAQGTPAQLK 233 Query: 241 TNKRV-IEAYLGGE 253 ++ + ++GGE Sbjct: 234 SSHDPRLRQFIGGE 247 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: 166 Number of extensions: 10 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: 270 Length adjustment: 25 Effective length of query: 229 Effective length of database: 245 Effective search space: 56105 Effective search space used: 56105 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