Align Amino-acid permease RocE (characterized)
to candidate GFF4621 PS417_23645 amino acid permease
Query= SwissProt::P39137 (467 letters) >FitnessBrowser__WCS417:GFF4621 Length = 468 Score = 317 bits (813), Expect = 4e-91 Identities = 163/447 (36%), Positives = 261/447 (58%), Gaps = 7/447 (1%) Query: 11 LQRTMKSRHLFMISLGGVIGTGFFLGTGFTINQAGPLGAVLSYLVGGFIMFLTMLCLGEL 70 L+R + S + MI++GG IGTG F+G+ + I AGP ++SY +G I L M CL E+ Sbjct: 18 LRRQLTSGQMSMIAIGGAIGTGLFMGSAYAIGYAGP-SVLVSYAIGALITLLLMGCLAEM 76 Query: 71 AVAFPVSGSFQTYATKFISPAFGFAFGWLYWLGWAVTCAIEFLSAGQLMQRWFPHIDVWI 130 VA SGSF YA +ISP GF + YW + E + M+ WF ++ W+ Sbjct: 77 TVAHSTSGSFGAYAEFYISPLAGFLVRYAYWAAIVLAVGAEVTAVAMYMKYWFANVPEWV 136 Query: 131 WCLVFAALMFILNAITTKAFAESEFWFSGIKILIILLFIILGGAAMFGLIDLKGGEQAPF 190 W + F++++ +LNAI+ K F E+WFS IKI I+ FIIL +FG G Q Sbjct: 137 WIVSFSSVLILLNAISVKTFGNFEYWFSTIKISAIVGFIILAVYVVFG----SGNPQYGV 192 Query: 191 LTHFYEDGLFPNGIKAMLITMITVNFAFQGTELIGVAAGESEDPEKTIPRSIKQTVWRTL 250 + DG FP+G+ M I +I F++ E+I VAAGE+ DPE+ + ++ + T+ R + Sbjct: 193 QNYTAHDGFFPHGLSGMWIAVIVSIFSYLSVEMIAVAAGEAADPEQAVKKAFRATIVRLV 252 Query: 251 VFFVLSIIVIAGMIPWKQAGVVESPFVAVFEQIGIPYAADIMNFVILIALLSVANSGLYA 310 VF++L++ ++ ++PW QAG +SPFV V + IGIP A +MNFVILIA LS NS LY Sbjct: 253 VFYLLTLALMLAIVPWNQAGQAQSPFVTVMQTIGIPGATGVMNFVILIAALSAMNSQLYI 312 Query: 311 STRILYAMANEGQAFKALGKTNQRGVPMYSLIVTMAVACLSLLTKFAQAETVYMVLLSLA 370 +TR++++++ G A K++G ++ G+P+ +L+++ + L+ L E+ + ++++++ Sbjct: 313 TTRMMFSLSRAGFAPKSMGALSKNGIPLNALLLSSSGIALATLLNVVYPESSFTLMMAIS 372 Query: 371 GMSAQVGWITISLSQIMFRRKYIREGGKIEDLKFKTPLYPVLPLIGLTLNTVVLISLAFD 430 A W I L+ + FRR R GG L F+ L+P L+GL L V+++ F Sbjct: 373 MFGAIFTWFMIFLTHLFFRRYRKRHGG--PTLSFQLRLFPYSTLLGLVLMGAVMVTTYFT 430 Query: 431 PEQRIALYCGVPFMIICYIIYHVVIKK 457 ++ L GVPF++I +Y+ +K Sbjct: 431 EAFKMTLVFGVPFLLILSAVYYGFFRK 457 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: 536 Number of extensions: 22 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: 468 Length adjustment: 33 Effective length of query: 434 Effective length of database: 435 Effective search space: 188790 Effective search space used: 188790 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