Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate 17517 b3456 leucine/isoleucine/valine transporter subunit (NCBI)
Query= uniprot:Q1MCU1 (463 letters) >FitnessBrowser__Keio:17517 Length = 425 Score = 320 bits (819), Expect = 7e-92 Identities = 176/343 (51%), Positives = 230/343 (67%), Gaps = 18/343 (5%) Query: 115 LLLYPMVVVAIKGPQGSLTYVDNFGIQILIYVMLAWGLNIVVGLAGLLDLGYVAFYAVGA 174 L L ++V+A+ P + +IY++L GLN+VVGL+GLL LGY FYA+GA Sbjct: 91 LFLVALLVLAVAWPFMVSRGTVDIATLTMIYIILGLGLNVVVGLSGLLVLGYGGFYAIGA 150 Query: 175 YSYALLSSYFGLSFWVLLPLSGIFAALWGVILGFPVLRLRGDYLAIVTLAFGEIIRLVLI 234 Y++ALL+ Y+GL FW LP++G+ AA G +LGFPVLRLRGDYLAIVTL FGEI+R++L+ Sbjct: 151 YTFALLNHYYGLGFWTCLPIAGLMAAAAGFLLGFPVLRLRGDYLAIVTLGFGEIVRILLL 210 Query: 235 NWTDVTKGTFGISSIPKATLFGIPFDATA--GG---FAKLFHLPISSAYYKIFLFYLILA 289 N T++T G GIS IPK TLFG+ F TA GG F+ F L + IFL+ + L Sbjct: 211 NNTEITGGPNGISQIPKPTLFGLEFSRTAREGGWDTFSNFFGLKYDPSDRVIFLYLVALL 270 Query: 290 LCMLTAYVTIRLRRMPIGRAWEALREDEIACRSLGINTVTTKLTAFATGAMFAGFAGSFF 349 L +L+ +V RL RMP+GRAWEALREDEIACRSLG++ KLTAF A FAGFAG+ F Sbjct: 271 LVVLSLFVINRLLRMPLGRAWEALREDEIACRSLGLSPRRIKLTAFTISAAFAGFAGTLF 330 Query: 350 AARQGFVSPESFVFLESAVILAIVVLGGMGSLTGIAIAAIVMVGGTELLREMSFLKLIFG 409 AARQGFVSPESF F ESA +LAIVVLGGMGS + +AAI++V EL+R+ + Sbjct: 331 AARQGFVSPESFTFAESAFVLAIVVLGGMGSQFAVILAAILLVVSRELMRDFN------- 383 Query: 410 PDFTPELYRMLIFGLAMVVVMLFKPRGFVGSREPTAFLRERKA 452 Y ML+ G MV++M+++P+G + P L+ A Sbjct: 384 ------EYSMLMLGGLMVLMMIWRPQGLLPMTRPQLKLKNGAA 420 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: 570 Number of extensions: 25 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: 425 Length adjustment: 32 Effective length of query: 431 Effective length of database: 393 Effective search space: 169383 Effective search space used: 169383 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