Align Amino-acid permease RocE (characterized)
to candidate BWI76_RS19685 BWI76_RS19685 lysine transporter
Query= SwissProt::P39137 (467 letters) >FitnessBrowser__Koxy:BWI76_RS19685 Length = 489 Score = 376 bits (966), Expect = e-109 Identities = 187/457 (40%), Positives = 285/457 (62%), Gaps = 18/457 (3%) Query: 11 LQRTMKSRHLFMISLGGVIGTGFFLGTGFTINQAGPLGAVLSYLVGGFIMFLTMLCLGEL 70 L+R +K+RHL MI++GG IGTG F+ +G TI+QAGP GA+LSY++ G +++ M LGEL Sbjct: 13 LRRELKARHLTMIAIGGSIGTGLFVASGATISQAGPGGALLSYILIGLMVYFLMTSLGEL 72 Query: 71 AVAFPVSGSFQTYATKFISPAFGFAFGWLYWLGWAVTCAIEFLSAGQLMQRWFPHIDVWI 130 A PVSGSF TY ++ FGFA GW YW WAVT A++ ++A +M WFP W+ Sbjct: 73 AAFMPVSGSFATYGQNYVEEGFGFALGWNYWYNWAVTIAVDLVAAQLVMTYWFPDAPGWV 132 Query: 131 WCLVFAALMFILNAITTKAFAESEFWFSGIKILIILLFIILGGAAMFGLIDLKGGEQAPF 190 W +F +MF+LN I+ K F E+E+WFS IK+ +++FII+G +FG+ KG + A + Sbjct: 133 WSALFLGIMFLLNWISVKGFGEAEYWFSLIKVATVIIFIIVGVMMIFGI--FKGAQPAGW 190 Query: 191 LTHFYEDGLFPNGIKAMLITMITVNFAFQGTELIGVAAGESEDPEKTIPRSIKQTVWRTL 250 +D F G AM+ + V F+FQGTELIG+AAGESE+PEK IPR+++Q WR L Sbjct: 191 SNWVIDDAPFAGGFAAMIGVAMIVGFSFQGTELIGIAAGESENPEKNIPRAVRQVFWRIL 250 Query: 251 VFFVLSIIVIAGMIPWKQAGVVE--------SPFVAVFEQIGIPYAADIMNFVILIALLS 302 +F+V +I++I+ +IP+ ++ SPF VF+ G+ AA IMN VIL A+LS Sbjct: 251 LFYVFAILIISLIIPYTDPSLLRNDVKDISVSPFTLVFQHAGLLSAAAIMNAVILTAVLS 310 Query: 303 VANSGLYASTRILYAMANEGQAFKALGKTNQRGVPMYSLIVTMAVACLSLLTKFAQAETV 362 NSG+YASTR+LY +A +G+A + K ++ GVP +L T +A L L+ +TV Sbjct: 311 AGNSGMYASTRMLYTLACDGKAPRIFSKLSKGGVPRNALYATTVIAGLCFLSSMFGNQTV 370 Query: 363 YMVLLSLAGMSAQVGWITISLSQIMFRRKYIREGGKIEDLKFKTPLYPVLPLIGLTLNTV 422 Y+ LL+ +GM+ + W+ I++S FRR Y+ +G + DL +++ +P+ P+ L + Sbjct: 371 YLWLLNTSGMTGFIAWLGIAISHYRFRRGYVLQGNDLNDLPYRSGFFPLGPIFAFVLCLI 430 Query: 423 VLISLAFDPEQR--------IALYCGVPFMIICYIIY 451 + + ++ + A Y G+P ++ + Y Sbjct: 431 ITLGQNYEAFLKDTIDWGGVAATYIGIPLFLVIWFGY 467 Lambda K H 0.329 0.142 0.438 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: 676 Number of extensions: 35 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: 467 Length of database: 489 Length adjustment: 34 Effective length of query: 433 Effective length of database: 455 Effective search space: 197015 Effective search space used: 197015 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