Align High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate GFF4157 HP15_4097 inner-membrane translocator
Query= TCDB::P21628 (417 letters) >FitnessBrowser__Marino:GFF4157 Length = 347 Score = 164 bits (415), Expect = 4e-45 Identities = 108/332 (32%), Positives = 161/332 (48%), Gaps = 39/332 (11%) Query: 90 TQRWAVLALVVVAFVWPFFASRGAVDIATLILIYVMLGIGLNIVVGLAGLLDLGYVGFYA 149 TQ+ + +++ V+PF + + L+ I V+ GLNI+ G GL+ LG GF Sbjct: 21 TQKLWLGFFLLILLVFPFVVDSYLLYLGCLVGIAVISTTGLNILTGFTGLISLGQAGFMG 80 Query: 150 VGAYTYALLAEYAGFGFWTALPIAGMMAALFGFLLGFPVLRLRGDYLAIVTLGFGEIIRI 209 VGAYT A L+ F L +AG+MAA G L+G P LR++G YLAI TL + Sbjct: 81 VGAYTVAWLSINTALPFPVTLVLAGLMAAAVGILVGLPSLRVKGLYLAIATLAASVFLHF 140 Query: 210 LLRNMTEITGGPNGIGSIPKPTLFGLTFERRAPEGMQTFHEFFGIAYNTNYKVILLYVVA 269 + +TGG G+ S+ LFGLTF+ ++Y + Sbjct: 141 IFAEWESVTGGMGGL-SLEPAHLFGLTFQ----------------------SDFMMYFII 177 Query: 270 LLLVLLALFVINRLMRMPIGRAWEALREDEVACRALGLNPTIVKLSAFTIGASFAGFAGS 329 + L +L + + R IGRA+ A+R+ +++ LG+N KL +F + + +AG AG Sbjct: 178 VPLAVLMVLAARNVFRTRIGRAFIAIRDRDISAEILGINLLRYKLMSFALSSFYAGIAGG 237 Query: 330 FFAARQGLVTPESFTFIESAMILAIVVLGGMGSQLGVILAAVVMVLLQEMRG-------- 381 FA +VTPESF S LA V++GGMG+ LG IL A M L+ E Sbjct: 238 LFAYFYRVVTPESFPLSMSIFYLAAVIVGGMGNLLGGILGAAFMTLVPEALKLLTAALTP 297 Query: 382 --------FNEYRMLIFGLTMIVMMIWRPQGL 405 + +IFG ++ +I+ P GL Sbjct: 298 FYPNAPVFMSPMLEIIFGALIVGFLIFEPHGL 329 Lambda K H 0.330 0.146 0.439 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: 428 Number of extensions: 33 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: 417 Length of database: 347 Length adjustment: 30 Effective length of query: 387 Effective length of database: 317 Effective search space: 122679 Effective search space used: 122679 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 50 (23.9 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