Align Leucine/isoleucine/valine ABC transporter,permease component (characterized, see rationale)
to candidate RR42_RS14415 RR42_RS14415 leucine/isoleucine/valine transporter permease subunit
Query= uniprot:G8ALI9 (505 letters) >FitnessBrowser__Cup4G11:RR42_RS14415 Length = 424 Score = 388 bits (996), Expect = e-112 Identities = 219/459 (47%), Positives = 280/459 (61%), Gaps = 57/459 (12%) Query: 18 LKEAAMTAFVALLLTIPLVGLRTVDRPTGLGLETRWNEVAAAVGLVFLGRLGLCLIREGH 77 LK A + A + +LTIP++GL+ + LE W V AVG VFL +L L + Sbjct: 21 LKNAIVAAVMTAILTIPVLGLQLKLDGYKVVLEPHWQPVWLAVGAVFLFQLFKPLFQR-- 78 Query: 78 AVTVLVLAAAATAAGFFIAMPTEALRVILIAGGAVIAIRAVLAIRTGRSKLSQAERDKRM 137 ATA I +P+ + Sbjct: 79 ----------ATAG---IKVPS-------------------------------------L 88 Query: 138 DHIAAQVQHASRWLGPIAVVVALAFPFTPLADRQLLDIGILLLTYIMLGWGLNIVVGLAG 197 + A Q WL + V L FPF + R +D+ L L Y++LG GLNIVVG AG Sbjct: 89 PALGATQQRKVIWL---LLAVGLVFPF--FSSRGAVDVATLALIYVILGLGLNIVVGYAG 143 Query: 198 LLDLGYVAFYAVGAYSYALLAHYFGFSFWVCLPLAGFLAAMSGVLLGFPVLRLRGDYFAI 257 LLDLGYV FYAVG Y+YALL YFG +FW CLP+A ++A+ G +LGFPVLRLRGDY AI Sbjct: 144 LLDLGYVGFYAVGGYTYALLNQYFGLTFWECLPIAAGMSALFGFVLGFPVLRLRGDYLAI 203 Query: 258 VTLGFGEIIRIILINWYQFTGGPNGISGIPRPSFFGIADFTRTPAEGTAAFHEMFGLEFS 317 VTLGFGEIIR++L N TGGP+G+SGIP+P+ FGI EG FHE+ G ++S Sbjct: 204 VTLGFGEIIRLLLNNLTSLTGGPDGVSGIPKPTVFGIEMARSASVEGVKTFHELLGWDYS 263 Query: 318 PLHRIIFLYYLILVLALVVNLFTMRVRKLPLGRAWEALREDDIACASLGINRTNMKLAAF 377 H +IFLY L L+L T R+ ++P+GRAWEALRED+IAC SLG+N T +KL+AF Sbjct: 264 GEHMVIFLYLLALLLVGFTLFVTSRLIRMPMGRAWEALREDEIACRSLGLNPTRIKLSAF 323 Query: 378 AIAAMFGGFAGSFFATRQGFISPESFTFIESAIILAIVVLGGMGSQIGVVVAAFLVIGLP 437 + A F G G+FFA RQG ++PESFTFIESA+ILA+VVLGGMGSQ+GV++AA L+ LP Sbjct: 324 TLGAAFAGLGGAFFAARQGLVNPESFTFIESALILAVVVLGGMGSQLGVILAAILLTALP 383 Query: 438 EAFRELADYRMLAFGMGMVLIMLWRPRGLLAHRDPTILL 476 E R A+YRML FG+ MVL+M+WRP+GLL P + L Sbjct: 384 EMARGFAEYRMLIFGLVMVLMMMWRPQGLLPASRPHVEL 422 Lambda K H 0.329 0.144 0.438 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: 661 Number of extensions: 34 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: 2 Length of query: 505 Length of database: 424 Length adjustment: 33 Effective length of query: 472 Effective length of database: 391 Effective search space: 184552 Effective search space used: 184552 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 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