Align ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate PP_0618 PP_0618 Branched-chain amino acid ABC transporter, permease protein
Query= TCDB::Q8DQI0 (292 letters) >FitnessBrowser__Putida:PP_0618 Length = 286 Score = 160 bits (405), Expect = 3e-44 Identities = 94/295 (31%), Positives = 168/295 (56%), Gaps = 20/295 (6%) Query: 1 MNLMLQQLVNGLILGSVYALLALGYTMVYGIIKLINFAHGDIYMMGAFIGYFLINSFQMN 60 ++L L QL+NGL LG +Y L+A+G T+++G++ +NFAHG +++GA++ Y + + N Sbjct: 2 LDLYLFQLLNGLGLGMIYFLIAVGLTIIFGLLNFVNFAHGAFFLLGAYLCYTAV-AVTGN 60 Query: 61 FFVALIVAMLATAILGVVIEFLAYRPLRHSTRIAVLITAIGVSFLLEYGMVYL---VGAN 117 F++AL++A L A L +E L + + H ++ +G++ +++ V + VG N Sbjct: 61 FWLALLIAPLVVAALAWAVERLLIKRIYHLPHTFQILVTLGIALIIQEASVLIWGPVGKN 120 Query: 118 TRAFPQAIQTVRYDLGPISLTNVQLMILGISLILMILLQVIVQKTKMGKAMRAVSVDSDA 177 A P ++ V LG +L ++G + ++ I L +++++T+ G +RA S ++ Sbjct: 121 I-AVPPELRGVLI-LGDFIYPYYRLFLIGFAALIGIGLWLLLERTRFGALVRAGSESTET 178 Query: 178 AQLMGINVNRTISFTFALGSALAGAAGVLIALYYNSLEPLMGVTPGLK------SFVAAV 231 L+G N+ R S TFALG LAG AGVL A PL G P + +FV V Sbjct: 179 VSLLGTNIFRLFSLTFALGVGLAGVAGVLFA-------PLRGAQPFVGPEILGIAFVVVV 231 Query: 232 LGGIGIIPGAALGGFVIGLLETFATAFGMSDFRDAIVYGILLLILIVRPAGILGK 286 +GG+G GA +GG ++G++++ T+ ++YG + +++VRP G+ G+ Sbjct: 232 IGGMGSFGGALVGGLLVGVVQSMMTSL-WPQGASLMIYGAMAAVILVRPYGLFGR 285 Lambda K H 0.330 0.146 0.407 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: 246 Number of extensions: 12 Number of successful extensions: 4 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: 292 Length of database: 286 Length adjustment: 26 Effective length of query: 266 Effective length of database: 260 Effective search space: 69160 Effective search space used: 69160 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 48 (23.1 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