Align High-affinity branched-chain amino acid ABC transporter permease LivM (characterized, see rationale)
to candidate HSERO_RS08280 HSERO_RS08280 leucine/isoleucine/valine transporter permease subunit
Query= uniprot:A0A159ZYE0 (418 letters) >FitnessBrowser__HerbieS:HSERO_RS08280 Length = 408 Score = 508 bits (1308), Expect = e-148 Identities = 270/421 (64%), Positives = 319/421 (75%), Gaps = 20/421 (4%) Query: 1 MTRHLKSALFSALLVWAVAYPVLGLKLTIVG--INLEVHGTSPAILATIAVCSLLMFLRV 58 M K+A+ +AL+ + P+LG++L + G + L H T P ++A +AV Sbjct: 1 MPETFKNAVTAALVTAVLTIPLLGMQLQLEGYRVVLNTHWT-PVLVAVLAV--------F 51 Query: 59 LFSTQISAMWKSSPG--LPVIPAKASNFLTLPTTQRWIVLALIVGALVWPFFGSRGAVDI 116 LF + +SS G LP +P P QR V+ L++ ALVWPFFGSRG VD+ Sbjct: 52 LFQLAKPVLSRSSAGIKLPALPRMQ------PRQQRAAVMILLMAALVWPFFGSRGYVDV 105 Query: 117 ATLILIYVMLGLGLNIVVGLAGLLDLGYVGFYAVGAYSYALLSHYFGLSFWICLPIAGMM 176 TL LIYV+LGLGLNIVVG AGLLDLGYVGFYAVGAY+YAL + YFGL+FW C+P+A Sbjct: 106 MTLALIYVVLGLGLNIVVGFAGLLDLGYVGFYAVGAYTYALCNQYFGLTFWECVPLAAAA 165 Query: 177 AATFGFLLGFPVLRLRGDYLAIVTLGFGEIIRLFLRNLTDITGGPNGISNIEKPTFFGLT 236 +A FGFLLGFPVLRLRGDYLAIVTLGFGEIIRL L N+T ITGGP+G+S I KPT FGL Sbjct: 166 SALFGFLLGFPVLRLRGDYLAIVTLGFGEIIRLLLNNMTSITGGPDGVSGIPKPTVFGLV 225 Query: 237 FERK-AAEGLQTFHEYFGLEYNSINKVIFLYLVALLLALAALFVINRLLRMPIGRAWEAL 295 R EG TFH+ FGL Y + VIFLY +ALL+ L FV +RLLRMP+GRAWEAL Sbjct: 226 MARNPVTEGGTTFHQLFGLSYQGGHMVIFLYFLALLMVLFTYFVTSRLLRMPMGRAWEAL 285 Query: 296 REDEIACRALGLNPTVIKLSAFTLGAAFAGFAGSFFAARQGLVTPESFTFIESAIILAIV 355 REDEIACR+LG+NPT +KLSAFTLGAAFAG AGSFFAARQGLVTPESFTFIESA+ILAIV Sbjct: 286 REDEIACRSLGINPTKVKLSAFTLGAAFAGLAGSFFAARQGLVTPESFTFIESALILAIV 345 Query: 356 VLGGMGSQLGVILAAIVMILLPEMMREFSEYRMLMFGALMVLMMIWRPQGLLPMQRPHME 415 VLGGMGSQLGVILAAI++ +LPE+ R F+EYRML+FG +MVLMM+WRPQGLLP RPH+E Sbjct: 346 VLGGMGSQLGVILAAILLTVLPELARSFAEYRMLIFGLVMVLMMMWRPQGLLPATRPHVE 405 Query: 416 L 416 L Sbjct: 406 L 406 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: 642 Number of extensions: 28 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: 408 Length adjustment: 31 Effective length of query: 387 Effective length of database: 377 Effective search space: 145899 Effective search space used: 145899 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: 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