Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate Echvi_1022 Echvi_1022 ABC-type spermidine/putrescine transport systems, ATPase components
Query= uniprot:D8IUY7 (241 letters) >FitnessBrowser__Cola:Echvi_1022 Length = 345 Score = 96.7 bits (239), Expect = 5e-25 Identities = 70/215 (32%), Positives = 111/215 (51%), Gaps = 9/215 (4%) Query: 20 AVKGIDLEVNEGELVTLIGANGAGKTTTLKAITGTLPASRVEGHIEYLGQPL-KGKKSFE 78 AVK I +E+ EG + ++G NG+GKTT LK I G + G I + GQ + GK + Sbjct: 20 AVKDIHMEIEEGSVQAIVGENGSGKTTLLKLIAGLEHPDK--GEIVFSGQTIVNGKSALP 77 Query: 79 LVKDKLAMVPEGRGVFTRMSIQENLLMGAYT-SDDKGQIAADIDKWFAVFPRLKERAAQM 137 + ++ ++ + +F +M++ EN+ + S + QIA D L++ + Sbjct: 78 ANQREVGVIFQEYALFPQMTLLENVREALHQESRNARQIAMDS----LALAGLEDSFSAY 133 Query: 138 AGTLSGGEQQMLAMARALMSHPKLLLLDEPSMGLSPIMVEKIFEVIRN-VSAQGITILLV 196 LS G++Q A+ARAL S PKLLLLD+P L +I E IR+ V A GIT ++ Sbjct: 134 PHQLSSGQRQRAALARALASRPKLLLLDDPFRSLDTRFKNEISEDIRDIVKATGITAIVA 193 Query: 197 EQNAKLALEAAHRGYVMESGLITMQGQAQQMLDDP 231 +AK AL A ++ G++ G ++ P Sbjct: 194 SHHAKDALSLADSIAILHKGILQQVGTPVEIYKKP 228 Lambda K H 0.317 0.134 0.365 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: 203 Number of extensions: 15 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: 241 Length of database: 345 Length adjustment: 26 Effective length of query: 215 Effective length of database: 319 Effective search space: 68585 Effective search space used: 68585 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: 41 (21.6 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