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 8502039 DvMF_2752 inner-membrane translocator (RefSeq)
Query= TCDB::P21628 (417 letters) >FitnessBrowser__Miya:8502039 Length = 330 Score = 214 bits (545), Expect = 3e-60 Identities = 131/325 (40%), Positives = 186/325 (57%), Gaps = 27/325 (8%) Query: 85 LSLPSTQRWAVLALVVVAFVWPFFASRGAVDIATLILIYVMLGIGLNIVVGLAGLLDLGY 144 +++ T +A +A+VV V P D+ I +Y +L + LNI++G AGL +G+ Sbjct: 1 MTVSRTTSYAGIAVVVA--VLPLLLDPYWTDVFVSIGLYSVLALSLNIILGQAGLFHMGH 58 Query: 145 VGFYAVGAYTYALLAEYAGFGFWTALPIAGMMAALFGFLLGFPVLRLRGDYLAIVTLGFG 204 FYAVGAY A+ G A+P AG+ AALF ++ P++ LRGDYL IVT+G Sbjct: 59 AAFYAVGAYVTAIANTMWGVPVLWAMPFAGLAAALFAMVVARPIIHLRGDYLLIVTIGIV 118 Query: 205 EIIRI-LLRNMTEITGGPNGIGSIPKPTLFGLTFERRAPEGMQTFHEFFGIAYNTNYKVI 263 EI+RI L+ N+ +TGG NGI I +P LFG F IA K + Sbjct: 119 EIVRIALINNVFGLTGGANGIFGISRPMLFG-----------------FKIA-----KPV 156 Query: 264 LLYVVALLLVLLALFVINRLMRMPIGRAWEALREDEVACRALGLNPTIVKLSAFTIGASF 323 Y + V ++ + RL GRA ++ED+ A G+N KL AF +GA + Sbjct: 157 HFYYLVWAYVACSILLFRRLENSRFGRALNYIKEDDTAAEGSGVNIASYKLWAFVLGAFW 216 Query: 324 AGFAGSFFAARQGLVTPESFTFIESAMILAIVVLGGMGSQLGVILAAVVMVLLQEM-RGF 382 AG G+ +AA+ +++PESF+F ES ++ AIV+LGG GS GV+L A +++ L E R F Sbjct: 217 AGMTGTIYAAKMTIISPESFSFWESVVLFAIVILGG-GSNRGVLLGAFLLIGLPEFFREF 275 Query: 383 NEYRMLIFGLTMIVMMIWRPQGLLP 407 RML FGL M+VMMI+RPQG+LP Sbjct: 276 ASARMLAFGLAMVVMMIFRPQGMLP 300 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: 436 Number of extensions: 25 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: 330 Length adjustment: 30 Effective length of query: 387 Effective length of database: 300 Effective search space: 116100 Effective search space used: 116100 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: 49 (23.5 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