Align ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate 3610344 Dshi_3725 inner-membrane translocator (RefSeq)
Query= TCDB::Q8DQI0 (292 letters) >FitnessBrowser__Dino:3610344 Length = 294 Score = 149 bits (376), Expect = 7e-41 Identities = 91/286 (31%), Positives = 163/286 (56%), Gaps = 5/286 (1%) Query: 3 LMLQQLVNGLILGSVYALLALGYTMVYGIIKLINFAHGDIYMMGAFIGYFLINSFQMNFF 62 ++ Q++NGL LG L+ALG T+++G++ +IN +HG+ Y +GA+ G + +F +N++ Sbjct: 8 VLAPQMLNGLALGVSVILVALGLTIIFGLLDVINMSHGEFYAVGAY-GALALAAFGVNYW 66 Query: 63 VALIVAMLATAILGVVIE-FLAYRPLRHSTR-IAVLITAIGVSFLLEYGMVYLVGANTRA 120 V + + L LG+V E +L R + R ++ L+ G+ + E + + G NT+ Sbjct: 67 VLMAMVPLMMIPLGIVTERYLIRRVYDGADRHVSTLLLTFGLGLIAEDVLKIIFGPNTQR 126 Query: 121 FPQAIQTVRYDLGPISLTNVQLMILGISLILMILLQVIVQKTKMGKAMRAVSVDSDAAQL 180 P+ DL I + +L ++ IS +++ + +V +T++G +RA S D + A Sbjct: 127 -PENPLPGATDLMGIFIPTYRLFLIAISAAVILAVAFVVYRTRLGAIVRAASFDRNMAAS 185 Query: 181 MGINVNRTISFTFALGSALAGAAGVLIALYYNSLEPLMGVTPGLKSFVAAVLGGIGIIPG 240 +G+ V S FA G ALAG AGVL+A Y S+ P MG L +F ++GG+G I G Sbjct: 186 LGVRVGWVYSGAFAFGVALAGLAGVLLAPIY-SVFPTMGRDFILIAFTVVIVGGMGSIWG 244 Query: 241 AALGGFVIGLLETFATAFGMSDFRDAIVYGILLLILIVRPAGILGK 286 A + G V+ ++ ++ + + IV+G+++L+L+ RP G+ G+ Sbjct: 245 AVVAGIVLTQIQAISSLVISPVWSEPIVFGVMVLVLMFRPQGLFGR 290 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: 218 Number of extensions: 11 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: 292 Length of database: 294 Length adjustment: 26 Effective length of query: 266 Effective length of database: 268 Effective search space: 71288 Effective search space used: 71288 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