Align High-affinity branched-chain amino acid ABC transporter permease LivM (characterized, see rationale)
to candidate RR42_RS14415 RR42_RS14415 leucine/isoleucine/valine transporter permease subunit
Query= uniprot:A0A159ZYE0 (418 letters) >FitnessBrowser__Cup4G11:RR42_RS14415 Length = 424 Score = 501 bits (1289), Expect = e-146 Identities = 262/413 (63%), Positives = 314/413 (76%), Gaps = 12/413 (2%) Query: 5 LKSALFSALLVWAVAYPVLGLKLTIVGINLEVHGTSPAILATIAVCSLLMFLRVLFSTQI 64 LK+A+ +A++ + PVLGL+L + G + + + + L + LF Sbjct: 21 LKNAIVAAVMTAILTIPVLGLQLKLDGYKVVLEPHWQPVWLAVGAVFLFQLFKPLFQRAT 80 Query: 65 SAMWKSSPGLPVIPAKASNFLTLPTTQRWIVLALIVGALVWPFFGSRGAVDIATLILIYV 124 + + P LP + A T QR ++ L+ LV+PFF SRGAVD+ATL LIYV Sbjct: 81 AGI--KVPSLPALGA---------TQQRKVIWLLLAVGLVFPFFSSRGAVDVATLALIYV 129 Query: 125 MLGLGLNIVVGLAGLLDLGYVGFYAVGAYSYALLSHYFGLSFWICLPIAGMMAATFGFLL 184 +LGLGLNIVVG AGLLDLGYVGFYAVG Y+YALL+ YFGL+FW CLPIA M+A FGF+L Sbjct: 130 ILGLGLNIVVGYAGLLDLGYVGFYAVGGYTYALLNQYFGLTFWECLPIAAGMSALFGFVL 189 Query: 185 GFPVLRLRGDYLAIVTLGFGEIIRLFLRNLTDITGGPNGISNIEKPTFFGLTFERKAA-E 243 GFPVLRLRGDYLAIVTLGFGEIIRL L NLT +TGGP+G+S I KPT FG+ R A+ E Sbjct: 190 GFPVLRLRGDYLAIVTLGFGEIIRLLLNNLTSLTGGPDGVSGIPKPTVFGIEMARSASVE 249 Query: 244 GLQTFHEYFGLEYNSINKVIFLYLVALLLALAALFVINRLLRMPIGRAWEALREDEIACR 303 G++TFHE G +Y+ + VIFLYL+ALLL LFV +RL+RMP+GRAWEALREDEIACR Sbjct: 250 GVKTFHELLGWDYSGEHMVIFLYLLALLLVGFTLFVTSRLIRMPMGRAWEALREDEIACR 309 Query: 304 ALGLNPTVIKLSAFTLGAAFAGFAGSFFAARQGLVTPESFTFIESAIILAIVVLGGMGSQ 363 +LGLNPT IKLSAFTLGAAFAG G+FFAARQGLV PESFTFIESA+ILA+VVLGGMGSQ Sbjct: 310 SLGLNPTRIKLSAFTLGAAFAGLGGAFFAARQGLVNPESFTFIESALILAVVVLGGMGSQ 369 Query: 364 LGVILAAIVMILLPEMMREFSEYRMLMFGALMVLMMIWRPQGLLPMQRPHMEL 416 LGVILAAI++ LPEM R F+EYRML+FG +MVLMM+WRPQGLLP RPH+EL Sbjct: 370 LGVILAAILLTALPEMARGFAEYRMLIFGLVMVLMMMWRPQGLLPASRPHVEL 422 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: 689 Number of extensions: 37 Number of successful extensions: 3 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: 424 Length adjustment: 32 Effective length of query: 386 Effective length of database: 392 Effective search space: 151312 Effective search space used: 151312 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