Align Amino-acid permease RocE (characterized)
to candidate PP_0660 PP_0660 S-methyl-L-methionine transporter
Query= SwissProt::P39137 (467 letters) >FitnessBrowser__Putida:PP_0660 Length = 479 Score = 469 bits (1206), Expect = e-136 Identities = 218/465 (46%), Positives = 327/465 (70%), Gaps = 1/465 (0%) Query: 3 TNQDNGNQLQRTMKSRHLFMISLGGVIGTGFFLGTGFTINQAGPLGAVLSYLVGGFIMFL 62 T + + ++ M++RH+ M++LGGVIGTG FL +G+T+NQAGPLGAV++Y++G +++L Sbjct: 8 TRNASAHTFKQDMQTRHIVMLALGGVIGTGLFLTSGYTVNQAGPLGAVIAYILGAIMVYL 67 Query: 63 TMLCLGELAVAFPVSGSFQTYATKFISPAFGFAFGWLYWLGWAVTCAIEFLSAGQLMQRW 122 M+CLGELAV P GSF +YAT+++ P G+ W+YWL W V EF +AG LM RW Sbjct: 68 VMMCLGELAVHMPEVGSFSSYATRYLGPGTGYMVAWMYWLTWTVAIGSEFTAAGILMVRW 127 Query: 123 FPHIDVWIWCLVFAALMFILNAITTKAFAESEFWFSGIKILIILLFIILGGAAMFGLIDL 182 FP VW+W +F A +FI N I+ ++FAE+EFW S +K+L ++ F+++GG A+ G ++ Sbjct: 128 FPDTPVWMWSALFGAAVFISNIISVRSFAETEFWLSLVKVLAVIAFLVVGGGAILGGFEI 187 Query: 183 KGGEQAPFLTHFYEDGLFPNGIKAMLITMITVNFAFQGTELIGVAAGESEDPEKTIPRSI 242 + A L +F +GLFP G ++ +T++ V FAF GTELIG+AAGE++DPEK +P++I Sbjct: 188 QQAHSAG-LGNFTREGLFPTGFWSIAMTLLAVAFAFSGTELIGIAAGETKDPEKNVPKAI 246 Query: 243 KQTVWRTLVFFVLSIIVIAGMIPWKQAGVVESPFVAVFEQIGIPYAADIMNFVILIALLS 302 + TV R +FF+ +I V+A ++P +QAGV+ESPFV VF IGIPYAADIMNFVI+ ALLS Sbjct: 247 RTTVLRLALFFIGTIFVLATLLPREQAGVIESPFVMVFAMIGIPYAADIMNFVIITALLS 306 Query: 303 VANSGLYASTRILYAMANEGQAFKALGKTNQRGVPMYSLIVTMAVACLSLLTKFAQAETV 362 ANSGLYA++R+L+ ++++G + ++RG P +++++MA SLL+ +T+ Sbjct: 307 AANSGLYAASRMLWTLSDQGNMPRRYATLSRRGTPFNAIVLSMAGGMASLLSSVFAPDTI 366 Query: 363 YMVLLSLAGMSAQVGWITISLSQIMFRRKYIREGGKIEDLKFKTPLYPVLPLIGLTLNTV 422 Y+ L+S++G++ V WI+I+ SQI FRR YI GGK+EDLKF+ YP +PL + + Sbjct: 367 YLALVSISGLAVVVVWISIAASQIAFRRHYIASGGKLEDLKFRVRGYPFVPLGAIFCCVL 426 Query: 423 VLISLAFDPEQRIALYCGVPFMIICYIIYHVVIKKRQQANRQLEL 467 + +AFDP QR+ALY G+PF+ CY+ Y + K R + LE+ Sbjct: 427 ACVGIAFDPAQRVALYFGLPFIAWCYLAYWLTCKYRSRRTAPLEI 471 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: 595 Number of extensions: 21 Number of successful extensions: 2 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: 479 Length adjustment: 33 Effective length of query: 434 Effective length of database: 446 Effective search space: 193564 Effective search space used: 193564 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