Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate 5210736 Shew_3164 ABC transporter-related protein (RefSeq)
Query= uniprot:D8IUY7 (241 letters) >FitnessBrowser__PV4:5210736 Length = 241 Score = 105 bits (263), Expect = 6e-28 Identities = 72/240 (30%), Positives = 129/240 (53%), Gaps = 15/240 (6%) Query: 5 ILKVQQLSVAYGGIQAVKGIDLEVNEGELVTLIGANGAGKTTTLKAITGTLPASRVEGHI 64 ++K+ L +G Q +KGID + GE+V++IG +G+GK+T L+ I L +G I Sbjct: 1 MIKISNLHKYFGDNQVLKGIDESIARGEVVSVIGPSGSGKSTFLRCIN--LLEQPTQGEI 58 Query: 65 EYLGQPLKGKKS-FELVKDKLAMVPEGRGVFTRMSIQENLLMGAYTSDDKGQIAADIDKW 123 GQ + + + ++ K+ MV + +F ++Q+N+ + Q AD + Sbjct: 59 VIDGQSITAPDACIDKLRQKVGMVFQNFNLFPHKTVQQNITLAPVKLGLMTQAEADSEAM 118 Query: 124 FAVFP-RLKERAAQMAGTLSGGEQQMLAMARALMSHPKLLLLDEPSMGLSPIMVEKIFEV 182 + L ++A+ +LSGG++Q +A+ARAL P+L+L DEP+ L P MV + +V Sbjct: 119 RLLDQVGLSDKASAYPASLSGGQKQRVAIARALAMKPELMLFDEPTSALDPEMVGDVLDV 178 Query: 183 IRNVSAQGITILLVEQNAKLALEAAHR------GYVMESGL-ITMQGQAQQMLDDPRVKA 235 ++ ++ G+T+++V A + + R GYV+ES + + GQ Q +PR +A Sbjct: 179 MKQLAQAGMTMVIVTHEMGFAKDVSDRVIFMDGGYVVESNVPALLFGQPQ----EPRTQA 234 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: 129 Number of extensions: 6 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: 241 Length adjustment: 23 Effective length of query: 218 Effective length of database: 218 Effective search space: 47524 Effective search space used: 47524 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: 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