Align high affinity cationic amino acid transporter 1 (characterized)
to candidate CA265_RS15000 CA265_RS15000 amino acid permease
Query= CharProtDB::CH_091324 (622 letters) >FitnessBrowser__Pedo557:CA265_RS15000 Length = 491 Score = 226 bits (577), Expect = 1e-63 Identities = 135/410 (32%), Positives = 222/410 (54%), Gaps = 20/410 (4%) Query: 28 LSRCLNTYDLVALGVGSTLGAGVYVLAGAVARENAGPAIVISFLIAALASVLAGLCYGEF 87 L R L+ LVALGVG+ +GAG++V A A +NAGP++ I F+IAA+ LAGLCY E Sbjct: 23 LKRTLSAGALVALGVGAIIGAGLFVRTAAAAAQNAGPSVTIGFIIAAIGCALAGLCYAEL 82 Query: 88 GARVPKTGSAYLYSYVTVGELWAFITGWNLILSYIIGTSSVARAWSATFDELIGKPIG-- 145 + +P +GSAY Y+Y T+GEL A++ GW+L+L Y +G ++V AWS ++L+ + + Sbjct: 83 SSSIPISGSAYTYTYATMGELMAWVIGWDLVLEYAVGAATVGIAWSEYLNKLLVEVLHTS 142 Query: 146 ----EFSRQHMALNAPGVLAQTPDIFAVIIIIILTGLLTLGVKESAMVNK--IFTCINVL 199 E+ + G + ++ A+ I+ +L+ LL G ESA VN + T + ++ Sbjct: 143 PIPYEWCHSPFQSHPDGTVNGIMNLPALFIVGLLSLLLIKGTSESAFVNGLIVITKVGIV 202 Query: 200 VLCFIVVSGFVKGSIKNWQLTEKNFSCNNNDTNVKYGEGGFMPFGFSGVLSGAATCFYAF 259 +L ++ GF+ S + + ++ + +G GF GV+ A T F+AF Sbjct: 203 ILIIVLGWGFINESNHHPYIPAATTYVDHAGISHSFG-------GFWGVIGAAGTVFFAF 255 Query: 260 VGFDCIATTGEEVKNPQKAIPVGIVASLLICFIAYFGVSAALTLMMP---YFCLDIDSPL 316 +GFD ++T +E KNP+ A+P+GI+ SL +C + Y + LT + P + ++ + Sbjct: 256 IGFDAVSTAAQETKNPKTAMPIGILGSLAVCTVLYILFAHVLTGIAPVEFFRTKGGEASV 315 Query: 317 PGAFKH--QGWEEAKYAVAIGSLCALSTSLLGSMFPMPRVIYAMAEDGLLFKFLAKINNR 374 A G+ V + L S+ +L + RV Y+M++DGLL K + ++ + Sbjct: 316 VAAISEYMTGYSWLSKLVTVAILAGFSSVILVMLLGQSRVFYSMSKDGLLPKMFSDLHPK 375 Query: 375 TKTPVIATVTSGAIAAVMAFLFELKDLVDLMSIGTLLAYSLVAACVLVLR 424 KTP A + I + A + D+ SIGTL A+ LV V++LR Sbjct: 376 FKTPYKANLVILIIVGLFAAFIPGDVVGDMTSIGTLFAFMLVCVAVIILR 425 Score = 60.8 bits (146), Expect = 1e-13 Identities = 48/142 (33%), Positives = 73/142 (51%), Gaps = 19/142 (13%) Query: 455 SESQTGFLPVAEKFSLKSILSPKNVEPSKFSGLIVNISAGLLAALIITVCIVAVLGREAL 514 S S+ G LP + S L PK P K + L++ I GL AA I V+G + Sbjct: 358 SMSKDGLLP-----KMFSDLHPKFKTPYK-ANLVILIIVGLFAAFIPG----DVVG-DMT 406 Query: 515 AEGTLWAVFVMTGSVLLCMLVTGIIWRQPESKTKLSFKVPFVPVLPVLSIFVNIYLMMQL 574 + GTL+A +L+C+ V II R+ + FK P+VP++P+L + +++ L Sbjct: 407 SIGTLFAF------MLVCVAV--IILRKTDPDLPRQFKTPWVPLIPILGVVACGLMILGL 458 Query: 575 DQGTWVRFAVWMLIGFTIYFGY 596 W+R W+ +GF IYFGY Sbjct: 459 GWTNWLRLFGWLALGFIIYFGY 480 Lambda K H 0.324 0.138 0.417 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: 729 Number of extensions: 36 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 622 Length of database: 491 Length adjustment: 36 Effective length of query: 586 Effective length of database: 455 Effective search space: 266630 Effective search space used: 266630 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 53 (25.0 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