Align Amino-acid permease RocE (characterized)
to candidate PP_3727 PP_3727 Amino-acid permease RocE
Query= SwissProt::P39137 (467 letters) >FitnessBrowser__Putida:PP_3727 Length = 468 Score = 529 bits (1362), Expect = e-155 Identities = 243/452 (53%), Positives = 343/452 (75%) Query: 10 QLQRTMKSRHLFMISLGGVIGTGFFLGTGFTINQAGPLGAVLSYLVGGFIMFLTMLCLGE 69 QL R +KSRH+FM+SLGGVIGTG F+G+G TINQ GP+GA+L+YLV G +M+L M+CLGE Sbjct: 9 QLTRALKSRHIFMLSLGGVIGTGLFMGSGVTINQGGPVGAILAYLVAGLLMYLVMVCLGE 68 Query: 70 LAVAFPVSGSFQTYATKFISPAFGFAFGWLYWLGWAVTCAIEFLSAGQLMQRWFPHIDVW 129 L+V PVSGSFQ +ATK+I PA GF GW+YW+ WA T +EF +AG LM RWFP + +W Sbjct: 69 LSVQMPVSGSFQAHATKYIGPATGFMIGWVYWMSWATTVGLEFTAAGMLMTRWFPEVPIW 128 Query: 130 IWCLVFAALMFILNAITTKAFAESEFWFSGIKILIILLFIILGGAAMFGLIDLKGGEQAP 189 W +F ++F LNA+ T+AF E+E+WFSGIK+ IL FI++G +FG I L G AP Sbjct: 129 YWSALFVVVLFGLNALATRAFGEAEYWFSGIKVATILGFIVIGLLVIFGAIPLSSGAPAP 188 Query: 190 FLTHFYEDGLFPNGIKAMLITMITVNFAFQGTELIGVAAGESEDPEKTIPRSIKQTVWRT 249 L + + LFP+G+ A+ M+TV +AFQG E++GVAAGE+E PEK+IPR+++ V+R Sbjct: 189 MLNNLVGESLFPHGLSAVFAVMMTVVYAFQGCEIMGVAAGETEHPEKSIPRAVRNVVFRV 248 Query: 250 LVFFVLSIIVIAGMIPWKQAGVVESPFVAVFEQIGIPYAADIMNFVILIALLSVANSGLY 309 L+F+VL+I V++ ++P +QAG++ESPFV VF+ +GIPYAAD+MNFVIL A+LSV NSGLY Sbjct: 249 LIFYVLAIAVLSAIVPHEQAGLMESPFVQVFDMVGIPYAADLMNFVILTAILSVGNSGLY 308 Query: 310 ASTRILYAMANEGQAFKALGKTNQRGVPMYSLIVTMAVACLSLLTKFAQAETVYMVLLSL 369 ASTRIL+AM+ G A K+L ++RGVP+ +L +T+ A +SL+T F A+T++MVL+++ Sbjct: 309 ASTRILWAMSKTGMAPKSLSPLSKRGVPLRALSITLCFALISLMTSFVAADTLFMVLMAV 368 Query: 370 AGMSAQVGWITISLSQIMFRRKYIREGGKIEDLKFKTPLYPVLPLIGLTLNTVVLISLAF 429 +GMS V WI I+L+Q FR+ ++R+GG+++DLK+K PLYP++PL+ +TL + + + LA Sbjct: 369 SGMSGTVTWIVIALAQYRFRKAWLRDGGQLQDLKYKAPLYPLVPLLCITLCSSLFVFLAL 428 Query: 430 DPEQRIALYCGVPFMIICYIIYHVVIKKRQQA 461 D QR +LY G F+ +CY Y V ++RQ A Sbjct: 429 DETQRPSLYWGFGFIALCYAAYFFVNRRRQGA 460 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: 661 Number of extensions: 26 Number of successful extensions: 1 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