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_4628 Branched-chain amino acid transport system permease protein LivM (TC 3.A.1.4.1)
Query= TCDB::P21628 (417 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4628 Length = 358 Score = 125 bits (313), Expect = 3e-33 Identities = 99/339 (29%), Positives = 152/339 (44%), Gaps = 49/339 (14%) Query: 92 RWAVLALVVVAFVWPFFASRGAVDIATLILIYVM--LGIGLNIVVGLAGLLDLGYVGFYA 149 R A+ L+ VAFV + A LI +M +G+N++VG G + LG F A Sbjct: 26 RIAIALLLAVAFVAVPMLASDYFFRAILIPFVIMSLAALGVNVLVGYCGQISLGSGAFMA 85 Query: 150 VGAY-TYALLAEYAGFGFWTALPIAGMMAALFGFLLGFPVLRLRGDYLAIVTLG---FGE 205 VGAY Y G AL + G+ A FG L G P LR++G YLA+ TL F + Sbjct: 86 VGAYGAYNFFVRLPGLPLIPALILGGLCATFFGILFGLPSLRVKGLYLAVATLAAQFFSD 145 Query: 206 IIRILLRNMTEITGGPNGIGSIPKPTLFGLTFERRAPEGMQTFHEFFGIAYNTNYKVILL 265 + + +R T T P+G S+ +FG+ E + Sbjct: 146 WMFLRIRWFTLDT--PSGSVSVSNLQVFGMPIESATSK---------------------- 181 Query: 266 YVVALLLVLLALFVINRLMRMPIGRAWEALREDEVACRALGLNPTIVKLSAFTIGASFAG 325 Y+ L ++++ + L+R IGR W A+R+ +VA +G+ P KLSAF + + G Sbjct: 182 YLFCLAILVVMALMAKNLVRGAIGREWMAIRDMDVAASVIGIRPMYAKLSAFAVSSFIIG 241 Query: 326 FAGSFFA-ARQGLVTPESFTFIESAMILAIVVLGGMGSQLGVILAAVVMVLLQ------- 377 AG +A G P +F+ S +L +V++GGMGS +G A +V+L Sbjct: 242 VAGGLWAFVYLGAWEPGAFSVDMSFRLLFMVIIGGMGSIMGSFFGAAFIVVLPIALNQFL 301 Query: 378 -----------EMRGFNEYRMLIFGLTMIVMMIWRPQGL 405 G + ++IFG ++ +I P GL Sbjct: 302 PLFLGLFGISISTAGVSHAELMIFGGLIVWFLIVEPHGL 340 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: 405 Number of extensions: 30 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