Align High-affinity branched-chain amino acid ABC transporter permease LivM (characterized, see rationale)
to candidate PP_4865 PP_4865 High-affinity branched-chain amino acid transport system permease protein BraE
Query= uniprot:A0A159ZYE0 (418 letters) >FitnessBrowser__Putida:PP_4865 Length = 435 Score = 402 bits (1033), Expect = e-116 Identities = 203/327 (62%), Positives = 249/327 (76%), Gaps = 1/327 (0%) Query: 92 RWIVLALIVGALVWPFFGSRGAVDIATLILIYVMLGLGLNIVVGLAGLLDLGYVGFYAVG 151 R+I+ ALIV A+V+P F ++ + + L LIYV+LGLGLNIVVGLAGLLDLGYV FYA+G Sbjct: 106 RYIIPALIVIAIVFPIFANKYLLTVVILGLIYVLLGLGLNIVVGLAGLLDLGYVAFYAIG 165 Query: 152 AYSYALLSHYFGLSFWICLPIAGMMAATFGFLLGFPVLRLRGDYLAIVTLGFGEIIRLFL 211 AY AL Y GL FW LP+A + AA G +LGFPVLR+ GDYLAIVTLGFGEIIRL L Sbjct: 166 AYGLALGYQYLGLGFWSVLPLAAIAAALAGCILGFPVLRMHGDYLAIVTLGFGEIIRLVL 225 Query: 212 RNLTDITGGPNGISNIEKPTFFGLTFERKAAEGLQTFHEYFGLEYNSINKVIFLYLVALL 271 N TGGPNG+ PTFFGL F R+A +G HE+FG EYN+ K +F+Y V + Sbjct: 226 NNWLSFTGGPNGMP-APSPTFFGLEFGRRAKDGGVPIHEFFGFEYNASLKFVFIYAVLFM 284 Query: 272 LALAALFVINRLLRMPIGRAWEALREDEIACRALGLNPTVIKLSAFTLGAAFAGFAGSFF 331 + LA L++ +RL RMP+GRAWEALREDEIACR++GLN ++KLSAFTLGA+ AG AG FF Sbjct: 285 VVLAVLYIKHRLTRMPVGRAWEALREDEIACRSMGLNHVLVKLSAFTLGASTAGLAGVFF 344 Query: 332 AARQGLVTPESFTFIESAIILAIVVLGGMGSQLGVILAAIVMILLPEMMREFSEYRMLMF 391 A QG V P SFTF ESA+ILAIVVLGGMGS +GV++AA V+ + PE++R FSEYR+L+F Sbjct: 345 ATYQGFVNPSSFTFFESALILAIVVLGGMGSTVGVVIAAFVLTVAPELLRSFSEYRVLLF 404 Query: 392 GALMVLMMIWRPQGLLPMQRPHMELRK 418 G LMVLMMIWRP+GL+ + R + RK Sbjct: 405 GVLMVLMMIWRPRGLIRISRTGVTPRK 431 Lambda K H 0.331 0.145 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: 663 Number of extensions: 37 Number of successful extensions: 2 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: 418 Length of database: 435 Length adjustment: 32 Effective length of query: 386 Effective length of database: 403 Effective search space: 155558 Effective search space used: 155558 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 (21.9 bits) S2: 51 (24.3 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