Align ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate Synpcc7942_2494 Synpcc7942_2494 putative branched-chain amino acid ABC transporter, permease protein
Query= TCDB::Q8DQH9 (318 letters) >FitnessBrowser__SynE:Synpcc7942_2494 Length = 307 Score = 155 bits (391), Expect = 2e-42 Identities = 104/289 (35%), Positives = 159/289 (55%), Gaps = 29/289 (10%) Query: 35 YVQILQQIGINIILAVGLNLIVGFSGQFSLGHAGFMAIGAYAAAIIGSK----SPTY--G 88 ++ + +G + L+V L L+ +GQ SL F A+G Y AAI+ +K SP Y G Sbjct: 10 FLLVSMLLGATLGLSVYLPLM---AGQLSLASPAFYALGGYLAAILSTKGLTASPEYSVG 66 Query: 89 AFFGAMLVGALLSGAVALLVGIPTLRLKGDYLAVATLGVSEIIRIFIINGGSLTNGAAGI 148 A M + A+ + +A LVG P LRL+G YLA+AT+ + EI+R+ +N S+T GA GI Sbjct: 67 ALLLEMGLAAIAAAVLAFLVGYPVLRLRGIYLAIATIALVEIVRVVALNL-SITGGAVGI 125 Query: 149 LGIPNFTTWQMVYFFV-----VITTIATLNFLRSPIGRSTLSVREDEIAAESVGVNTTKI 203 GIP + + Y ++ +I A + G ++REDE+AA ++ VNTT+ Sbjct: 126 FGIPQPFSSAVGYLWIALPLLLIAVAACWRLQQVRTGLVLAAIREDELAASAIAVNTTRY 185 Query: 204 KIIAFVFGAITASIAGSLQAGFIGSVVPKDYTFINSINVLIIVVFGGLGSITGAIVSAIV 263 K++AFV GA+ AS+ G++ A F+ + P+ TF SI L V+ GG S G ++ +V Sbjct: 186 KVLAFVLGAVLASLVGAVSAHFLNTWNPRQGTFDASITFLAFVLIGGSRSAFGPVLGGMV 245 Query: 264 LGILNMLLQDVASV--------------RMIIYALALVLVMIFRPGGLL 298 L L LL+ + SV R++I+ L LVL I+ P GL+ Sbjct: 246 LTALPELLRAIGSVPGLWPGLSRLLQDGRLLIFGLLLVLGSIYFPQGLI 294 Lambda K H 0.327 0.143 0.403 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: 224 Number of extensions: 15 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: 318 Length of database: 307 Length adjustment: 27 Effective length of query: 291 Effective length of database: 280 Effective search space: 81480 Effective search space used: 81480 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 (21.6 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