Align ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate 3607448 Dshi_0861 inner-membrane translocator (RefSeq)
Query= TCDB::Q8DQI0 (292 letters) >FitnessBrowser__Dino:3607448 Length = 305 Score = 140 bits (352), Expect = 5e-38 Identities = 94/308 (30%), Positives = 159/308 (51%), Gaps = 30/308 (9%) Query: 3 LMLQQLVNGLILGSVYALLALGYTMVYGIIKLINFAHGDIYMMGAFIGYFLINSFQMNFF 62 L+++Q++NGL G + L+A G T+V+G++ LIN AHG +YM+GAF + + +F Sbjct: 5 LLIEQVLNGLQFGVMLFLMAAGLTLVFGVMGLINLAHGSLYMVGAFAAAAVAGA-TGSFV 63 Query: 63 VALIVAMLATAILGVVIEFLAYRPLRHSTRIAVLITAIGVSFLLEYGMVYLVGANTRAFP 122 + L A+ A A G +IE R L + ++ + + G ++ G +FP Sbjct: 64 LGLAAALAAAAAAGALIEVTIIRRLYARDHLDQVLATFALILIFSEGTRWIFG----SFP 119 Query: 123 QAIQTVRYDLGPISL------TNVQLMILGISLILMILLQVIVQKTKMGKAMRAVSVDSD 176 ++ GP++L +L I+GI L + L ++ KT++G +RA D + Sbjct: 120 LFLEVPAALSGPVTLPFGIEYPAYRLAIIGIGLAIAAALFWLIAKTRIGVQIRAGEADRE 179 Query: 177 AAQLMGINVNRTISFTFALGSALAGAAGVLIALYYNSLEPLMGVTPGLKSFVAAVLGGIG 236 +G++++R + FALG+ALAG AG L+ S++ MG + +FV V+GGIG Sbjct: 180 MIAALGVDIDRLYTLVFALGAALAGLAGALVGA-LQSVQVGMGEPVLILAFVVIVIGGIG 238 Query: 237 IIPGAALGGFVIGLLET-----------------FATAFGMSDFRDAIVYGILLLILIVR 279 I GA +G ++GL +T ATA G S +Y ++ +LI R Sbjct: 239 SIKGAFVGALLLGLTDTLGRTLLPVAFGTVLEPSMATAVG-SALASMAIYILMAGVLIFR 297 Query: 280 PAGILGKN 287 P+G+ G++ Sbjct: 298 PSGLFGQS 305 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: 213 Number of extensions: 12 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: 305 Length adjustment: 27 Effective length of query: 265 Effective length of database: 278 Effective search space: 73670 Effective search space used: 73670 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