Align Amino-acid permease RocE (characterized)
to candidate AO353_05930 AO353_05930 amino acid permease
Query= SwissProt::P39137 (467 letters) >FitnessBrowser__pseudo3_N2E3:AO353_05930 Length = 470 Score = 320 bits (821), Expect = 5e-92 Identities = 170/457 (37%), Positives = 271/457 (59%), Gaps = 13/457 (2%) Query: 3 TNQDNGNQLQRTMKSRHLFMISLGGVIGTGFFLGTGFTINQAGPLGAVLSYLVGGFIMFL 62 +N+++G L+R + S + MI++GG IGTG F+G+ + I AGP +LSY +G I L Sbjct: 11 SNREHG--LRRQLTSGQMSMIAIGGAIGTGLFMGSAYAIGYAGP-SVLLSYAIGAVITLL 67 Query: 63 TMLCLGELAVAFPVSGSFQTYATKFISPAFGFAFGWLYWLGWAVTCAIEFLSAGQLMQRW 122 M CL E+ VA SGSF YA +ISP GF + YW + E + M+ W Sbjct: 68 LMGCLAEMTVAHSTSGSFGAYAEFYISPLAGFLVRYAYWAAIVLAVGTEVTAVAMYMKYW 127 Query: 123 FPHIDVWIWCLVFAALMFILNAITTKAFAESEFWFSGIKILIILLFIILGGAAMFGLIDL 182 F ++ WIW + F++++ +LNAI+ K F E+WFS IKI I+ FIIL +FG + Sbjct: 128 FANVPEWIWIVSFSSILIVLNAISVKTFGTFEYWFSTIKIGAIVGFIILAVYVVFGSGNP 187 Query: 183 KGGEQAPFLTHFYED--GLFPNGIKAMLITMITVNFAFQGTELIGVAAGESEDPEKTIPR 240 + G H Y G FPNG++ M + +I F++ E+I VAAGE+EDPE+ + + Sbjct: 188 EYG------VHHYTSHGGFFPNGLQGMWVAVIVSIFSYLSVEMIAVAAGEAEDPERAVKK 241 Query: 241 SIKQTVWRTLVFFVLSIIVIAGMIPWKQAGVVESPFVAVFEQIGIPYAADIMNFVILIAL 300 + + T+ R +VF++L++ ++ ++PW QAG +SPFV V + IGIP A +MNFVILIA Sbjct: 242 AFRATIVRLVVFYLLTLALMLAIVPWVQAGHAQSPFVTVMQTIGIPGATGVMNFVILIAA 301 Query: 301 LSVANSGLYASTRILYAMANEGQAFKALGKTNQRGVPMYSLIVTMAVACLSLLTKFAQAE 360 LS NS LY +TR++++++ G A KA+G ++ G+P+ +L+++ + L+ L E Sbjct: 302 LSAMNSQLYITTRMMFSLSRGGYAPKAMGALSKSGIPLNALLLSSSGIALATLLNVMYPE 361 Query: 361 TVYMVLLSLAGMSAQVGWITISLSQIMFRRKYIREGGKIEDLKFKTPLYPVLPLIGLTLN 420 + + ++++++ A W I L+ FRR + R G + L F+ L+P L+GL L Sbjct: 362 SSFTLMMAISMFGAIFTWFMIFLTHYCFRRYHQRHGER--KLSFRMRLFPYTTLLGLVLM 419 Query: 421 TVVLISLAFDPEQRIALYCGVPFMIICYIIYHVVIKK 457 V+I+ F ++ L GVPF++I ++Y V +K Sbjct: 420 GAVMITTYFTEAFKMTLVFGVPFLLILSLVYGVFFRK 456 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: 538 Number of extensions: 21 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: 470 Length adjustment: 33 Effective length of query: 434 Effective length of database: 437 Effective search space: 189658 Effective search space used: 189658 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