Align High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate 3610344 Dshi_3725 inner-membrane translocator (RefSeq)
Query= TCDB::P21627 (307 letters) >FitnessBrowser__Dino:3610344 Length = 294 Score = 139 bits (349), Expect = 1e-37 Identities = 94/308 (30%), Positives = 162/308 (52%), Gaps = 25/308 (8%) Query: 1 MPEIYHYL--QQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSY----IAF 54 M E H++ Q++NGL +G + L+A+G T+++G++ +IN +HGE Y +G+Y +A Sbjct: 1 MAEYLHFVLAPQMLNGLALGVSVILVALGLTIIFGLLDVINMSHGEFYAVGAYGALALAA 60 Query: 55 IAITLLAMMGLDSVPLMMLAAFAASIIVTSAFGYSIERVAYRPLRGGNRLIP-LISAIGM 113 + +M + VPLMM+ IVT Y I RV G +R + L+ G+ Sbjct: 61 FGVNYWVLMAM--VPLMMIPLG----IVTER--YLIRRV----YDGADRHVSTLLLTFGL 108 Query: 114 SIFLQNAVMLSQDSKEKAIPTLLPGNFVFGESSMNGVVISYMQILIFVVTFLVMFGLTLF 173 + ++ + + T P N + G + + G+ I ++ + ++ V+ + Sbjct: 109 GLIAEDVLKIIFGPN-----TQRPENPLPGATDLMGIFIPTYRLFLIAISAAVILAVAFV 163 Query: 174 ISRSRLGRACRACAEDLKMTNLLGINSNNIIALTFVIGAALAAVAAVLLGMQYGVINPGI 233 + R+RLG RA + D M LG+ + + F G ALA +A VLL Y V P + Sbjct: 164 VYRTRLGAIVRAASFDRNMAASLGVRVGWVYSGAFAFGVALAGLAGVLLAPIYSVF-PTM 222 Query: 234 GFLAGIKAFTAAVLGGIGSIPGAMLGGLLLGVAEAFGADVFGDQYKDVVAFGLLILVLLF 293 G + AFT ++GG+GSI GA++ G++L +A + V + + + FG+++LVL+F Sbjct: 223 GRDFILIAFTVVIVGGMGSIWGAVVAGIVLTQIQAISSLVISPVWSEPIVFGVMVLVLMF 282 Query: 294 RPTGILGR 301 RP G+ GR Sbjct: 283 RPQGLFGR 290 Lambda K H 0.328 0.145 0.413 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: 296 Number of extensions: 14 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: 307 Length of database: 294 Length adjustment: 27 Effective length of query: 280 Effective length of database: 267 Effective search space: 74760 Effective search space used: 74760 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 (21.7 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