Align ABC transporter related (characterized, see rationale)
to candidate HSERO_RS21250 HSERO_RS21250 amino acid ABC transporter ATP-binding protein
Query= uniprot:B2TBJ9 (263 letters) >FitnessBrowser__HerbieS:HSERO_RS21250 Length = 244 Score = 244 bits (623), Expect = 1e-69 Identities = 131/250 (52%), Positives = 178/250 (71%), Gaps = 11/250 (4%) Query: 9 LSVKNIHKSFGDHHVLKGISLDAHQGDVISILGASGSGKSTFLRCLNLLETPDDGSVSLA 68 +++ N+ K FGD+ VLKGISLD G+VI+I+G SGSGKST LRC+N LE+ D+G++S+A Sbjct: 4 IAIDNVKKRFGDNEVLKGISLDVEPGEVIAIIGKSGSGKSTLLRCINGLESIDEGNISVA 63 Query: 69 GEELKMKRRGDGKLQPSDRRQVDRVRSQLGMVFQNFNLWSHMTVLENLIEGPMRVQKRSR 128 G +L G +L+ + +R ++GM+FQ FNL+ H++V N++ PM V+ S Sbjct: 64 GAKL-----GASELE------LRNLRLKVGMIFQQFNLFPHLSVGRNVMIAPMIVKGVSE 112 Query: 129 AESVEEAEALLAKVGLAEKRGHYPAHLSGGQQQRVAIARALAMHPKVMLFDEPTSALDPE 188 AE+++ A+A L KVGL K YP LSGGQQQRVAIARAL+M P+ +L DE TSALDPE Sbjct: 113 AEAMKTAKANLEKVGLGHKFDAYPDQLSGGQQQRVAIARALSMSPQALLCDEITSALDPE 172 Query: 189 LVGEVLRVMRSLAEEGRTMLVVTHEMGFARHVSNRVMFLHQGQVEADGTPDEVFVECKSD 248 LV EVL VMR LA+EG T+L+VTHEM FAR V NR++F+HQG+V G P+E+F K+ Sbjct: 173 LVNEVLTVMRGLAKEGMTLLMVTHEMRFAREVCNRLVFMHQGKVHEIGPPEELFGNPKTP 232 Query: 249 RFRQFVSSHQ 258 +QF+ Q Sbjct: 233 ELQQFIGMTQ 242 Lambda K H 0.318 0.133 0.377 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: 178 Number of extensions: 4 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: 263 Length of database: 244 Length adjustment: 24 Effective length of query: 239 Effective length of database: 220 Effective search space: 52580 Effective search space used: 52580 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