Align Amino-acid permease RocE (characterized)
to candidate PfGW456L13_3211 Arginine permease RocE
Query= SwissProt::P39137 (467 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3211 Length = 474 Score = 540 bits (1392), Expect = e-158 Identities = 250/463 (53%), Positives = 349/463 (75%), Gaps = 5/463 (1%) Query: 1 MNTNQDN-----GNQLQRTMKSRHLFMISLGGVIGTGFFLGTGFTINQAGPLGAVLSYLV 55 MN N D G QL R +KSRH+FM+SLGGVIGTG F+G+G TINQ GP+GA+L+YLV Sbjct: 1 MNENTDRSTDHKGIQLTRALKSRHIFMLSLGGVIGTGLFMGSGVTINQGGPVGAILAYLV 60 Query: 56 GGFIMFLTMLCLGELAVAFPVSGSFQTYATKFISPAFGFAFGWLYWLGWAVTCAIEFLSA 115 GF+M+L M+CLGEL+V PVSGSFQT+ATK+I PA GF GW+YW+ WA T +EF +A Sbjct: 61 AGFLMYLVMVCLGELSVQMPVSGSFQTHATKYIGPATGFMIGWVYWMSWATTVGLEFTAA 120 Query: 116 GQLMQRWFPHIDVWIWCLVFAALMFILNAITTKAFAESEFWFSGIKILIILLFIILGGAA 175 G LM RWFP + +W W +F ++F +NA+ T+AF E+E+WFSGIK+ IL FI++G Sbjct: 121 GMLMTRWFPEVPIWYWSALFVVVLFGINAMATRAFGEAEYWFSGIKVAAILGFIVVGVLV 180 Query: 176 MFGLIDLKGGEQAPFLTHFYEDGLFPNGIKAMLITMITVNFAFQGTELIGVAAGESEDPE 235 +FG++ L G AP T+ D LFPNG+ A+ M+TV +AFQG E++GVAAGE++ PE Sbjct: 181 IFGVMPLSSGAPAPMATNLIGDSLFPNGLSAVFAVMMTVVYAFQGCEIMGVAAGETDQPE 240 Query: 236 KTIPRSIKQTVWRTLVFFVLSIIVIAGMIPWKQAGVVESPFVAVFEQIGIPYAADIMNFV 295 K+IPR+++ V+R L+F+VL+IIV++ ++PW+QAG++ESPFV VF+ +GIPYAAD+MNFV Sbjct: 241 KSIPRAVRNVVFRVLIFYVLAIIVLSAIVPWQQAGLMESPFVQVFDMVGIPYAADLMNFV 300 Query: 296 ILIALLSVANSGLYASTRILYAMANEGQAFKALGKTNQRGVPMYSLIVTMAVACLSLLTK 355 IL A+LSV NSGLYASTRIL+AM+ G A K+L ++RGVP+ +L +T+ A +SL+T Sbjct: 301 ILTAILSVGNSGLYASTRILWAMSKTGMAPKSLSPLSKRGVPLRALSITLCFALVSLMTS 360 Query: 356 FAQAETVYMVLLSLAGMSAQVGWITISLSQIMFRRKYIREGGKIEDLKFKTPLYPVLPLI 415 F A+T++MVL++++GMS V WI I+L+Q FR+ Y+R+GGK+ DLK++ P +PVLPL+ Sbjct: 361 FVAADTLFMVLMAVSGMSGTVTWIVIALAQYKFRKAYLRDGGKLRDLKYRAPWFPVLPLM 420 Query: 416 GLTLNTVVLISLAFDPEQRIALYCGVPFMIICYIIYHVVIKKR 458 +TL + + LA D QR +LY G F+ +CY Y ++ +KR Sbjct: 421 CITLCCSLFVFLALDETQRPSLYWGFGFIALCYGAYFLIHRKR 463 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: 642 Number of extensions: 28 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: 474 Length adjustment: 33 Effective length of query: 434 Effective length of database: 441 Effective search space: 191394 Effective search space used: 191394 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