Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate RR42_RS14415 RR42_RS14415 leucine/isoleucine/valine transporter permease subunit
Query= uniprot:Q1MCU1 (463 letters) >FitnessBrowser__Cup4G11:RR42_RS14415 Length = 424 Score = 325 bits (832), Expect = 2e-93 Identities = 175/306 (57%), Positives = 215/306 (70%), Gaps = 18/306 (5%) Query: 143 LIYVMLAWGLNIVVGLAGLLDLGYVAFYAVGAYSYALLSSYFGLSFWVLLPLSGIFAALW 202 LIYV+L GLNIVVG AGLLDLGYV FYAVG Y+YALL+ YFGL+FW LP++ +AL+ Sbjct: 126 LIYVILGLGLNIVVGYAGLLDLGYVGFYAVGGYTYALLNQYFGLTFWECLPIAAGMSALF 185 Query: 203 GVILGFPVLRLRGDYLAIVTLAFGEIIRLVLINWTDVTKGTFGISSIPKATLFGIPFDAT 262 G +LGFPVLRLRGDYLAIVTL FGEIIRL+L N T +T G G+S IPK T+FGI + Sbjct: 186 GFVLGFPVLRLRGDYLAIVTLGFGEIIRLLLNNLTSLTGGPDGVSGIPKPTVFGIEMARS 245 Query: 263 AG-----GFAKLFHLPISSAYYKIFLFYLILALCMLTAYVTIRLRRMPIGRAWEALREDE 317 A F +L S + IFL+ L L L T +VT RL RMP+GRAWEALREDE Sbjct: 246 ASVEGVKTFHELLGWDYSGEHMVIFLYLLALLLVGFTLFVTSRLIRMPMGRAWEALREDE 305 Query: 318 IACRSLGINTVTTKLTAFATGAMFAGFAGSFFAARQGFVSPESFVFLESAVILAIVVLGG 377 IACRSLG+N KL+AF GA FAG G+FFAARQG V+PESF F+ESA+ILA+VVLGG Sbjct: 306 IACRSLGLNPTRIKLSAFTLGAAFAGLGGAFFAARQGLVNPESFTFIESALILAVVVLGG 365 Query: 378 MGSLTGIAIAAIVMVGGTELLREMSFLKLIFGPDFTPELYRMLIFGLAMVVVMLFKPRGF 437 MGS G+ +AAI++ E+ R + YRMLIFGL MV++M+++P+G Sbjct: 366 MGSQLGVILAAILLTALPEMARGFA-------------EYRMLIFGLVMVLMMMWRPQGL 412 Query: 438 VGSREP 443 + + P Sbjct: 413 LPASRP 418 Lambda K H 0.330 0.145 0.432 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: 625 Number of extensions: 38 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: 463 Length of database: 424 Length adjustment: 32 Effective length of query: 431 Effective length of database: 392 Effective search space: 168952 Effective search space used: 168952 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