Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate GFF1300 PS417_06605 leucine/isoleucine/valine transporter permease subunit
Query= uniprot:Q1MCU1 (463 letters) >FitnessBrowser__WCS417:GFF1300 Length = 417 Score = 357 bits (915), Expect = e-103 Identities = 215/440 (48%), Positives = 279/440 (63%), Gaps = 37/440 (8%) Query: 20 LTEALFAAVLSFGMFVLYVGLKTDQNISNELIIVQRWGLLAIFVAVAAIGRFAMVVFIRP 79 L A F+A+L + + +GLK + L + + +A+ ++ F V+F + Sbjct: 5 LKSAFFSALLVWAVAFPVLGLKLSI-VGINLEVHGTGPVTLTIIALCSVLMFLRVLFTQ- 62 Query: 80 NIDRRKLSKAREGELDISTEKSFF------HRHFLKIALIALLLYPMVVVAIKGPQGSLT 133 L K+ G L +S + S F R+ + +IA L++P G +G++ Sbjct: 63 --QVGALFKSNRGPL-VSPKVSQFLTLPRTQRYIIIALIIAALIWPFF-----GSRGAV- 113 Query: 134 YVDNFGIQILIYVMLAWGLNIVVGLAGLLDLGYVAFYAVGAYSYALLSSYFGLSFWVLLP 193 + ILIYV+L GLNIVVGLAGLLDLGYV FYAVGAY+YALLS Y G SFW+ LP Sbjct: 114 ---DIATLILIYVLLGLGLNIVVGLAGLLDLGYVGFYAVGAYTYALLSHYLGWSFWICLP 170 Query: 194 LSGIFAALWGVILGFPVLRLRGDYLAIVTLAFGEIIRLVLINWTDVTKGTFGISSIPKAT 253 L+G+ AA +G +LGFPVLRLRGDYLAIVTL FGEIIRL L N TD+T G GISSIPK T Sbjct: 171 LAGMAAATFGFLLGFPVLRLRGDYLAIVTLGFGEIIRLFLRNLTDITGGPNGISSIPKPT 230 Query: 254 LFGIPFDATAGGFAKLFH----LPISSAYYKIFLFYLILALCMLTAYVTIRLRRMPIGRA 309 FG+ FD TA + FH + + +FL+ + L L + +V RL RMPIGRA Sbjct: 231 FFGLSFDRTAAEGMQTFHEYFGIDYNPVSKVVFLYLVALLLALAALFVINRLLRMPIGRA 290 Query: 310 WEALREDEIACRSLGINTVTTKLTAFATGAMFAGFAGSFFAARQGFVSPESFVFLESAVI 369 WEALREDEIACR+LG+N KL+AF GA FAGFAGSFFAARQG V+PESF F+ESA+I Sbjct: 291 WEALREDEIACRALGLNPTIIKLSAFTLGAAFAGFAGSFFAARQGLVTPESFTFIESAII 350 Query: 370 LAIVVLGGMGSLTGIAIAAIVMVGGTELLREMSFLKLIFGPDFTPELYRMLIFGLAMVVV 429 LAIVVLGGMGS G+ +AAIVM+ E++RE S YRML+FG MV++ Sbjct: 351 LAIVVLGGMGSQLGVILAAIVMILLPEMMREFS-------------EYRMLMFGAMMVLM 397 Query: 430 MLFKPRGFVGSREPTAFLRE 449 M+++P+G + + P LR+ Sbjct: 398 MIWRPQGLLPMQRPHMELRK 417 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: 624 Number of extensions: 36 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: 417 Length adjustment: 32 Effective length of query: 431 Effective length of database: 385 Effective search space: 165935 Effective search space used: 165935 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