Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate Echvi_1022 Echvi_1022 ABC-type spermidine/putrescine transport systems, ATPase components
Query= TCDB::Q8DQH7 (236 letters) >FitnessBrowser__Cola:Echvi_1022 Length = 345 Score = 112 bits (280), Expect = 9e-30 Identities = 81/238 (34%), Positives = 127/238 (53%), Gaps = 29/238 (12%) Query: 1 MSVLKVENLSVHYGMIQ--AVRDVSFEVNEGEVVSLIGANGAGKTTILRTLSGLVRPSSG 58 MS+L++ +S + + AV+D+ E+ EG V +++G NG+GKTT+L+ ++GL P G Sbjct: 1 MSLLQLHGISKKFPQTKQFAVKDIHMEIEEGSVQAIVGENGSGKTTLLKLIAGLEHPDKG 60 Query: 59 KIEFLGQEI----QKMPAQKIVAGGLSQVPEGRHVFPGLTVMENLEMGAFLKKNREENQ- 113 +I F GQ I +PA + G + Q +FP +T++EN+ A +++R Q Sbjct: 61 EIVFSGQTIVNGKSALPANQREVGVIFQ---EYALFPQMTLLENVR-EALHQESRNARQI 116 Query: 114 -------ANLKKVFSRFPRLEERKNQDAATLSGGEQQMLAMGRALMSTPKLLLLDEPSMG 166 A L+ FS +P LS G++Q A+ RAL S PKLLLLD+P Sbjct: 117 AMDSLALAGLEDSFSAYPH----------QLSSGQRQRAALARALASRPKLLLLDDPFRS 166 Query: 167 LAPIFIQEIFDIIQDIQK-QGTTVLLIEQNANKALAISDRGYVLETGKIVLSGTGKEL 223 L F EI + I+DI K G T ++ +A AL+++D +L G + GT E+ Sbjct: 167 LDTRFKNEISEDIRDIVKATGITAIVASHHAKDALSLADSIAILHKGILQQVGTPVEI 224 Lambda K H 0.315 0.134 0.358 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: 172 Number of extensions: 12 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: 236 Length of database: 345 Length adjustment: 26 Effective length of query: 210 Effective length of database: 319 Effective search space: 66990 Effective search space used: 66990 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 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