Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate BPHYT_RS04435 BPHYT_RS04435 ABC transporter
Query= uniprot:Q1MCU1 (463 letters) >FitnessBrowser__BFirm:BPHYT_RS04435 Length = 646 Score = 154 bits (390), Expect = 6e-42 Identities = 113/369 (30%), Positives = 186/369 (50%), Gaps = 67/369 (18%) Query: 110 IALIALLLYPMVVVAIKGPQGSLTYVDNFGIQILIYVMLAWGLNIVVGLAGLLDLGYVAF 169 +ALIAL ++P++ G+ Y+ I+IY +L +GL+IVVG G + LG+ Sbjct: 11 LALIALAVFPVL-------SGNPYYIHLLET-IMIYAILLFGLDIVVGYTGQVSLGHAGL 62 Query: 170 YAVGAYSYALLSSYFGLSFWVLLPLSGIFAALWGVILGFPVLRLRGDYLAIVTLAFGEII 229 + VGAY+ +L G+ F V PL+ + A +G IL P LR+ G YLA+VTLAFG I+ Sbjct: 63 FGVGAYTAGVLFFKLGMPFIVTAPLAILITAAFGAILALPALRVSGPYLAMVTLAFGTIL 122 Query: 230 RLVLINWTDVTKGTFGISSIPKATLFGIPFDATAGGFAKLFHLPISSAYYKIFLFYLILA 289 ++++ +T G G+ IPK +L G P + ++ ++L+ A Sbjct: 123 QILINEMDFLTNGPMGV-KIPKPSLAGRPMN-------------------EVEYYWLVAA 162 Query: 290 LCMLTAYVTIRLRRMPIGRAWEALREDEIACRSLGINTVTTKLTAFATGAMFAGFAGSFF 349 L + + V R+ R +GRA+EALR+ IA +G++ K+ AF A FAG AG + Sbjct: 163 LLVASLIVVHRVLRSHLGRAFEALRDSPIASDCMGVSVYRYKVYAFVISAGFAGLAGCLY 222 Query: 350 AARQGFVSPESFVFLESAVILAIVVLGG----MGSLTGIAI------------------- 386 + + ++SP ++ F + + L +++GG G+L G AI Sbjct: 223 SYSEQYISPNTYNFELTILFLLAIIMGGRKTRTGALLGSAIIVLLPKLLDDIDMFRTVAS 282 Query: 387 --AAIVMVG-GTELLREMSFLKLIFGPDF-------------TPELYRMLIFGLAMVVVM 430 AA+V++G G L R++S + + P T +R+ IFGL +++V+ Sbjct: 283 VLAAVVVIGAGVALARKVSTPRKVAIPVLGTAGLAAFSYRIETLADWRLTIFGLMILLVV 342 Query: 431 LFKPRGFVG 439 + G VG Sbjct: 343 YYLQDGVVG 351 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: 698 Number of extensions: 44 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: 463 Length of database: 646 Length adjustment: 36 Effective length of query: 427 Effective length of database: 610 Effective search space: 260470 Effective search space used: 260470 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: 52 (24.6 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