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 WP_023434295.1 N177_RS20200 high-affinity branched-chain amino acid ABC transporter permease LivM
Query= TCDB::P21628 (417 letters) >NCBI__GCF_000496075.1:WP_023434295.1 Length = 441 Score = 409 bits (1051), Expect = e-119 Identities = 218/419 (52%), Positives = 294/419 (70%), Gaps = 8/419 (1%) Query: 2 SQSLKRALFSALLVILVSYPILGLKLRTV--GIKLEVLGADAQTLWTIAAAALAMFVWQL 59 ++ +K A +SAL+ + ++ PI+GL+ T G+ L D + A + + + Sbjct: 12 AELVKDAAYSALIALALAAPIIGLQTVTARGGLGLNARWDDVFLIVLAVFAGRLLLNFTI 71 Query: 60 FRDRIPLKLGRGVGYKVNGSGL-KNFLSLPSTQRWAVLALVVVAFVWPFFASRGAVDIAT 118 +R + +G+ + G ++ +L LA+ ++ PF + R +D++ Sbjct: 72 WRHQGARPIGQKWFQRAGGRPFARHGHTLSKIIGPLALAVALLLPALPF-SDRYVMDLSI 130 Query: 119 LILIYVMLGIGLNIVVGLAGLLDLGYVGFYAVGAYTYALLAEYAGFGFWTALPIAGMMAA 178 ++L Y+MLG GLNIVVGLAGLLDLGYV FYA+GAY++ALLA + GFW LP+AG++AA Sbjct: 131 MVLTYIMLGWGLNIVVGLAGLLDLGYVAFYAIGAYSFALLATHFDLGFWICLPLAGILAA 190 Query: 179 LFGFLLGFPVLRLRGDYLAIVTLGFGEIIRILLRNMTEITGGPNGIGSIPKPTLFGLTFE 238 +G +LGFPVLRLRGDYLAIVTL FGEIIR++L N E TGGPNGI IP PTLFGL F Sbjct: 191 FWGVILGFPVLRLRGDYLAIVTLAFGEIIRVVLLNWYEFTGGPNGILGIPDPTLFGLEFA 250 Query: 239 RRAPEGMQTFHEFFGIAYNTNYKVILLYVVALLLVLLALFVINRLMRMPIGRAWEALRED 298 RR G TFHEFFG++Y++ +K+I LY + L L L+ FV RL R+P+GRAWEALRED Sbjct: 251 RR---GDNTFHEFFGLSYSSMHKIIFLYYIILCLALITNFVTLRLRRLPVGRAWEALRED 307 Query: 299 EVACRALGLNPTIVKLSAFTIGASFAGFAGSFFAARQGLVTPESFTFIESAMILAIVVLG 358 E+ACR+LG+N T KL+AF IGA F GFAGSFFA RQG ++PESFTFIESA+ILAIVVLG Sbjct: 308 EIACRSLGINTTNTKLTAFAIGAMFGGFAGSFFATRQGFISPESFTFIESALILAIVVLG 367 Query: 359 GMGSQLGVILAAVVMV-LLQEMRGFNEYRMLIFGLTMIVMMIWRPQGLLPMQRPHLELK 416 G+GSQ+GV++AA+VM+ + R F +YRMLIFGL M+ +M+WRP+GL+ + P + LK Sbjct: 368 GLGSQVGVVIAAIVMMGGFEYFREFEQYRMLIFGLAMVFIMVWRPRGLISTRSPSVILK 426 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: 592 Number of extensions: 33 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: 441 Length adjustment: 32 Effective length of query: 385 Effective length of database: 409 Effective search space: 157465 Effective search space used: 157465 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 24 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