Align ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate AO356_29015 AO356_29015 ABC transporter permease
Query= TCDB::Q8DQI0 (292 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_29015 Length = 293 Score = 149 bits (377), Expect = 6e-41 Identities = 90/299 (30%), Positives = 164/299 (54%), Gaps = 13/299 (4%) Query: 1 MNLMLQQLVNGLILGSVYALLALGYTMVYGIIKLINFAHGDIYMMGAFIGYFLINSFQMN 60 MN L+ L+ GL+ G++Y+L+A+G+ ++Y + NFA G + + A + + + ++ Sbjct: 1 MNFFLETLIGGLLAGTLYSLVAIGFVLIYKASGVFNFAQGAMLLFAA-LTFVSLREQGLS 59 Query: 61 FFVALIVAMLATAILGVVIEFLAYRPLRHSTRIAVLITAIGVSFLLEYGMVYLVGANTRA 120 F +AL++ +L + ++IE L RPL + ++I + + +G+SF++E L+GA RA Sbjct: 60 FALALLLTVLVMVVGALLIERLVLRPLVNRSQITLFMATLGLSFIIEGLAQGLMGAQVRA 119 Query: 121 FPQAIQTVRYDLGPISLTNVQLMILGISLILMILLQVIVQKTKMGKAMRAVSVDSDAAQL 180 I+ V +G I ++ L+ G+S + + +L ++ KT++G A+RAV+ D+ AA Sbjct: 120 LDLGIEDVPLFVGEIMISQFDLIAAGVSALTVAVLALLFNKTRIGVALRAVADDTRAALS 179 Query: 181 MGINVNRTISFTFALGSALAGAAGVLIALYYNSLEPLMGVTPGLKSFVAAVLGGIGIIPG 240 +GIN+NR +A+ + AG+L L V LK+ ++GG I G Sbjct: 180 LGINLNRIWQIVWAVAGVVGLVAGLLWGARQGVQFSLSLVV--LKALPVLIIGGFTSIGG 237 Query: 241 AALGGFVIGLLETFATAF-------GMSDFRDAIVYGILLLILIVRPAGILGKNVKEKV 292 A +GG ++G E A A+ G++ + Y + L+ L +RPAG+ G + E+V Sbjct: 238 AIVGGLIVGAAENLAEAYIGPLIGGGITPW---FAYFLALIFLYIRPAGLFGDRIIERV 293 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: 216 Number of extensions: 12 Number of successful extensions: 3 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: 293 Length adjustment: 26 Effective length of query: 266 Effective length of database: 267 Effective search space: 71022 Effective search space used: 71022 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