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 AO353_13350 AO353_13350 branched-chain amino acid ABC transporter permease
Query= TCDB::P21628 (417 letters) >FitnessBrowser__pseudo3_N2E3:AO353_13350 Length = 432 Score = 407 bits (1047), Expect = e-118 Identities = 215/414 (51%), Positives = 284/414 (68%), Gaps = 12/414 (2%) Query: 1 MSQSLKRALFSALLVILVSYPILGLKLRTVGIKLEVLGADAQTLWTIAAAALAMFVWQLF 60 + +SL + + L+ ++V PI+G+ L L+ + W + A + LF Sbjct: 11 VKKSLIDTVLAGLIALIVFGPIVGVVLEGYSYNLQ----PTRVAWMVGAVMIGRLALSLF 66 Query: 61 RDRIPLKLGRGVG--YKVNGSGLKNFL-SLPSTQRWAVLALVVVAFVWPFFASRGAVDIA 117 G V +++ GSG+ S R+ + AL+V+A V+P FA + + + Sbjct: 67 MQTAK---GEKVQQRFEIVGSGVHVLAPDFKSRLRFIIPALIVIAIVFPVFADKYLLTVV 123 Query: 118 TLILIYVMLGIGLNIVVGLAGLLDLGYVGFYAVGAYTYALLAEYAGFGFWTALPIAGMMA 177 L LIYV+LG+GLNIVVGLAGLLDLGYV FYA+GAY AL Y G GFWT LP++ +MA Sbjct: 124 ILGLIYVLLGLGLNIVVGLAGLLDLGYVAFYAIGAYGLALGYHYLGLGFWTVLPLSALMA 183 Query: 178 ALFGFLLGFPVLRLRGDYLAIVTLGFGEIIRILLRNMTEITGGPNGIGSIPKPTLFGLTF 237 AL G +LGFPVLR+ GDYLAIVTLGFGEIIR++L N TGGPNG+ +P P+ FG+ F Sbjct: 184 ALAGCILGFPVLRMHGDYLAIVTLGFGEIIRLILTNWLSFTGGPNGM-PVPSPSFFGIEF 242 Query: 238 ERRAPEGMQTFHEFFGIAYNTNYKVILLYVVALLLVLLALFVINRLMRMPIGRAWEALRE 297 R A +G FHEFFG YN N K + +Y V L+V+L L++ +RL RMP+GRAWEALRE Sbjct: 243 TRVAKDGGIPFHEFFGTEYNPNIKFMFIYAVLFLVVMLVLYIKHRLTRMPVGRAWEALRE 302 Query: 298 DEVACRALGLNPTIVKLSAFTIGASFAGFAGSFFAARQGLVTPESFTFIESAMILAIVVL 357 DE+ACRA+GLN +VKLSAFT+GAS AG AG FFA+ QG V P SFTF ESA+ILAIVVL Sbjct: 303 DEIACRAMGLNHVLVKLSAFTLGASTAGLAGVFFASYQGFVNPTSFTFFESALILAIVVL 362 Query: 358 GGMGSQLGVILAAVVMVLLQE-MRGFNEYRMLIFGLTMIVMMIWRPQGLLPMQR 410 GGMGS +GV++AA V+ + E +RGF EYR+L+FG+ M++MMIW+P+GL+ + R Sbjct: 363 GGMGSTVGVVIAAFVLTVAPELLRGFAEYRVLLFGILMVLMMIWKPRGLIRISR 416 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: 603 Number of extensions: 37 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: 432 Length adjustment: 32 Effective length of query: 385 Effective length of database: 400 Effective search space: 154000 Effective search space used: 154000 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: 51 (24.3 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