Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate 209488 DVU0549 high-affinity branched-chain amino acid ABC transporter, permease protein
Query= uniprot:Q1MCU1 (463 letters) >MicrobesOnline__882:209488 Length = 407 Score = 317 bits (811), Expect = 6e-91 Identities = 177/326 (54%), Positives = 222/326 (68%), Gaps = 29/326 (8%) Query: 116 LLYPMVVVAIKGPQGSLTYVDNFGIQILIYVMLAWGLNIVVGLAGLLDLGYVAFYAVGAY 175 LL +VV A+ P TY N I L+YVML GLNIVVGL+G L LGYVAFYAVGAY Sbjct: 93 LLAVLVVFAVL-PMLVSTYQTNIMISALLYVMLGLGLNIVVGLSGQLVLGYVAFYAVGAY 151 Query: 176 SYALLSSYFGLSFWVLLPLSGIFAALWGVILGFPVLRLRGDYLAIVTLAFGEIIRLVLIN 235 +YALL++ FGL FW +LP+ G AA++G++LGFPVLRL+GDYLAIVTL FGEI+RLVL N Sbjct: 152 AYALLNADFGLGFWTVLPIGGALAAVFGILLGFPVLRLKGDYLAIVTLGFGEIVRLVLEN 211 Query: 236 WTDVTKGTFGISSIPKATLFGIPFDATAGGFAKLFHLPISSAYYKIFLFYLILALCMLTA 295 W VT+G GIS I + LFG+ L +S A +++YLILA + T Sbjct: 212 WGSVTRGPSGISKIARPGLFGM-------------ELSVSEA--TTYIYYLILAAVIFTI 256 Query: 296 YVTIRLRRMPIGRAWEALREDEIACRSLGINTVTTKLTAFATGAMFAGFAGSFFAARQGF 355 + RL+ IGRAW+ALREDEIAC ++GI+ TTKLTAFA GA +AGFAG FAA+ F Sbjct: 257 FAVGRLKDSRIGRAWQALREDEIACEAMGIDLTTTKLTAFALGACWAGFAGVIFAAKTTF 316 Query: 356 VSPESFVFLESAVILAIVVLGGMGSLTGIAIAAIVMVGGTELLREMSFLKLIFGPDFTPE 415 ++P SF FLESA+ILA+VVLGGMGS G+ + A+V++ E LR S Sbjct: 317 INPASFTFLESAMILAMVVLGGMGSTLGVVLGALVLILLPEYLRAFS------------- 363 Query: 416 LYRMLIFGLAMVVVMLFKPRGFVGSR 441 YRMLIFG AMV++M+F+P+G V R Sbjct: 364 EYRMLIFGAAMVLMMVFRPQGLVSCR 389 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: 594 Number of extensions: 26 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 463 Length of database: 407 Length adjustment: 32 Effective length of query: 431 Effective length of database: 375 Effective search space: 161625 Effective search space used: 161625 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