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_4985 Branched-chain amino acid transport system permease protein LivM (TC 3.A.1.4.1)
Query= TCDB::P21628 (417 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4985 Length = 345 Score = 158 bits (399), Expect = 3e-43 Identities = 116/332 (34%), Positives = 170/332 (51%), Gaps = 41/332 (12%) Query: 94 AVLALVVVAFVWPFFASRGAVDIATLILIYVMLGIGLNIVVGLAGLLDLGYVGFYAVGAY 153 AV A ++V F PF AS + +A L+ I V GLNI+ G GL+ LG F +GAY Sbjct: 27 AVGAALLVLF--PFMASDYWLYLACLVSINVASATGLNILTGYTGLVSLGQAAFMGLGAY 84 Query: 154 TYALLAEYAGFGFWTALPIAGMMAALFGFLLGFPVLRLRGDYLAIVTLGFGEIIRILLRN 213 T A+L G F L G +A L G ++G P LR++G YLAI T+ I + N Sbjct: 85 TVAVLETKVGTPFVLNLLAGGFVAMLGGIVVGIPSLRVKGLYLAIATIAASFIAHFIFAN 144 Query: 214 MTEITGGPNGIGSIPKPTLFGLTFERRAPEGMQTFHEFFGIAYNTNYKVILLYVVALLLV 273 + TGG G+ S+P LFG+ A +T++++ L V +L+ Sbjct: 145 W-KFTGGTGGL-SVPPAKLFGM-------------------ALDTSFRLYWLIVPVTILM 183 Query: 274 LLALFVINRLMRMPIGRAWEALREDEVACRALGLNPTIVKLSAFTIGASFAGFAGSFFAA 333 LL L R +GRA+ A+R+ +++ LG+ KL +F + + +AG AG +A Sbjct: 184 LLG---AANLFRTRVGRAFIAIRDRDISAEVLGIPLLRYKLLSFGLSSFYAGVAGGLWAY 240 Query: 334 RQGLVTPESFTFIESAMILAIVVLGGMGSQLGVILAAVVMVLLQE--------MRGFNE- 384 +VTPESF + S LA +++GGMGS LG IL AV M ++ E M G +E Sbjct: 241 FFRVVTPESFPLLMSIFFLAAIIVGGMGSILGGILGAVFMTMVPELLKLVVDLMPGGSEL 300 Query: 385 ------YRMLIFGLTMIVMMIWRPQGLLPMQR 410 R +IFGL +I +++ P GL + R Sbjct: 301 TVLLSPVRTVIFGLLIIGFLVFEPHGLAEVWR 332 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: 419 Number of extensions: 26 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 417 Length of database: 345 Length adjustment: 30 Effective length of query: 387 Effective length of database: 315 Effective search space: 121905 Effective search space used: 121905 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