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 HSERO_RS08280 HSERO_RS08280 leucine/isoleucine/valine transporter permease subunit
Query= TCDB::P21628 (417 letters) >FitnessBrowser__HerbieS:HSERO_RS08280 Length = 408 Score = 496 bits (1278), Expect = e-145 Identities = 259/418 (61%), Positives = 319/418 (76%), Gaps = 15/418 (3%) Query: 1 MSQSLKRALFSALLVILVSYPILGLKLRTVGIKLEVLGADAQTLWT-IAAAALAMFVWQL 59 M ++ K A+ +AL+ +++ P+LG++L+ G ++ + T WT + A LA+F++QL Sbjct: 1 MPETFKNAVTAALVTAVLTIPLLGMQLQLEGYRVVL-----NTHWTPVLVAVLAVFLFQL 55 Query: 60 FRDRIPLKLGRGVGYKVNGSGLKNFLSLPSTQRWAVLALVVVAFVWPFFASRGAVDIATL 119 + P+ G K+ P QR AV+ L++ A VWPFF SRG VD+ TL Sbjct: 56 AK---PVLSRSSAGIKLPALPRMQ----PRQQRAAVMILLMAALVWPFFGSRGYVDVMTL 108 Query: 120 ILIYVMLGIGLNIVVGLAGLLDLGYVGFYAVGAYTYALLAEYAGFGFWTALPIAGMMAAL 179 LIYV+LG+GLNIVVG AGLLDLGYVGFYAVGAYTYAL +Y G FW +P+A +AL Sbjct: 109 ALIYVVLGLGLNIVVGFAGLLDLGYVGFYAVGAYTYALCNQYFGLTFWECVPLAAAASAL 168 Query: 180 FGFLLGFPVLRLRGDYLAIVTLGFGEIIRILLRNMTEITGGPNGIGSIPKPTLFGLTFER 239 FGFLLGFPVLRLRGDYLAIVTLGFGEIIR+LL NMT ITGGP+G+ IPKPT+FGL R Sbjct: 169 FGFLLGFPVLRLRGDYLAIVTLGFGEIIRLLLNNMTSITGGPDGVSGIPKPTVFGLVMAR 228 Query: 240 R-APEGMQTFHEFFGIAYNTNYKVILLYVVALLLVLLALFVINRLMRMPIGRAWEALRED 298 EG TFH+ FG++Y + VI LY +ALL+VL FV +RL+RMP+GRAWEALRED Sbjct: 229 NPVTEGGTTFHQLFGLSYQGGHMVIFLYFLALLMVLFTYFVTSRLLRMPMGRAWEALRED 288 Query: 299 EVACRALGLNPTIVKLSAFTIGASFAGFAGSFFAARQGLVTPESFTFIESAMILAIVVLG 358 E+ACR+LG+NPT VKLSAFT+GA+FAG AGSFFAARQGLVTPESFTFIESA+ILAIVVLG Sbjct: 289 EIACRSLGINPTKVKLSAFTLGAAFAGLAGSFFAARQGLVTPESFTFIESALILAIVVLG 348 Query: 359 GMGSQLGVILAAVVMVLLQEM-RGFNEYRMLIFGLTMIVMMIWRPQGLLPMQRPHLEL 415 GMGSQLGVILAA+++ +L E+ R F EYRMLIFGL M++MM+WRPQGLLP RPH+EL Sbjct: 349 GMGSQLGVILAAILLTVLPELARSFAEYRMLIFGLVMVLMMMWRPQGLLPATRPHVEL 406 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: 613 Number of extensions: 36 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: 417 Length of database: 408 Length adjustment: 31 Effective length of query: 386 Effective length of database: 377 Effective search space: 145522 Effective search space used: 145522 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