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 Ac3H11_1694 Branched-chain amino acid transport system permease protein LivM (TC 3.A.1.4.1)
Query= TCDB::P21628 (417 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1694 Length = 358 Score = 263 bits (671), Expect = 8e-75 Identities = 157/346 (45%), Positives = 211/346 (60%), Gaps = 46/346 (13%) Query: 96 LALVVVAFVWPFFASRGAVDIATLILIYVMLGIGLNIVVGLAGLLDLGYVGFYAVGAYTY 155 +AL+V+ + F + V IA L L+YV+L +GLNIVVG AGLLDLGYV FYAVGAY + Sbjct: 13 VALLVLPLILQSFGNAW-VRIADLALLYVLLALGLNIVVGYAGLLDLGYVAFYAVGAYLF 71 Query: 156 ALLAE------YAGFG----------FWTALPIAGMMAALFGFLLGFPVLRLRGDYLAIV 199 AL+A +A F W +P+A ++AA FG +LG P L+LRGDYLAIV Sbjct: 72 ALMASPHLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLKLRGDYLAIV 131 Query: 200 TLGFGEIIRILLRNM---TEITGGPNGIGSIPKPTLFGLTFERRAPEGMQTFHEFFGIAY 256 TLGFGEIIRI L N+ +T GP G+G I +FGL +R E FG Sbjct: 132 TLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRL--------EVFGFDI 183 Query: 257 NTNYKVILLYVVALLLVLLALFVINRLMRMPIGRAWEALREDEVACRALGLNPTIVKLSA 316 N+ V L Y + L+LV++++ + RL IGRAW A+REDE+A +A+G+N +KL A Sbjct: 184 NS---VTLYYYLFLVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLLA 240 Query: 317 FTIGASFAGFAGSFFAARQGLVTPESFTFIESAMILAIVVLGGMGSQLGVILAAVVMVLL 376 F +GASF G +G+ F A QG V+PESF+ +ES MI+A+VVLGG+G GVIL AV++ L Sbjct: 241 FGMGASFGGVSGAMFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVLLSAL 300 Query: 377 QEMRGFNE---------------YRMLIFGLTMIVMMIWRPQGLLP 407 E+ + R L+ L MI++M+ RP+GL P Sbjct: 301 PEVLRYVAGPLQAMTDGRLDSAILRQLLIALAMIIIMLLRPRGLWP 346 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: 458 Number of extensions: 23 Number of successful extensions: 5 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: 358 Length adjustment: 30 Effective length of query: 387 Effective length of database: 328 Effective search space: 126936 Effective search space used: 126936 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