Align lysine-specific permease (characterized)
to candidate PP_0660 PP_0660 S-methyl-L-methionine transporter
Query= CharProtDB::CH_003129 (489 letters) >FitnessBrowser__Putida:PP_0660 Length = 479 Score = 369 bits (946), Expect = e-106 Identities = 191/467 (40%), Positives = 281/467 (60%), Gaps = 19/467 (4%) Query: 5 TKTTEAPGLRRELKARHLTMIAIGGSIGTGLFVASGATISQAGPGGALLSYMLIGLMVYF 64 T+ A +++++ RH+ M+A+GG IGTGLF+ SG T++QAGP GA+++Y+L +MVY Sbjct: 8 TRNASAHTFKQDMQTRHIVMLALGGVIGTGLFLTSGYTVNQAGPLGAVIAYILGAIMVYL 67 Query: 65 LMTSLGELAAYMPVSGSFATYGQNYVEEGFGFALGWNYWYNWAVTIAVDLVAAQLVMSWW 124 +M LGELA +MP GSF++Y Y+ G G+ + W YW W V I + AA ++M W Sbjct: 68 VMMCLGELAVHMPEVGSFSSYATRYLGPGTGYMVAWMYWLTWTVAIGSEFTAAGILMVRW 127 Query: 125 FPDTPGWIWSALFLGVIFLLNYISVRGFGEAEYWFSLIKVTTVIVFIIVGVLMIIGIF-- 182 FPDTP W+WSALF +F+ N ISVR F E E+W SL+KV VI F++VG I+G F Sbjct: 128 FPDTPVWMWSALFGAAVFISNIISVRSFAETEFWLSLVKVLAVIAFLVVGGGAILGGFEI 187 Query: 183 KGAQPAGWSNWTIGEAPFAGGFAAMIGVAMIVGFSFQGTELIGIAAGESEDPAKNIPRAV 242 + A AG N+T E F GF ++ + V F+F GTELIGIAAGE++DP KN+P+A+ Sbjct: 188 QQAHSAGLGNFT-REGLFPTGFWSIAMTLLAVAFAFSGTELIGIAAGETKDPEKNVPKAI 246 Query: 243 RQVFWRILLFYVFAILIISLIIPYTDPSLLRNDVKDISVSPFTLVFQHAGLLSAAAVMNA 302 R R+ LF++ I +++ ++P ++ SPF +VF G+ AA +MN Sbjct: 247 RTTVLRLALFFIGTIFVLATLLPREQAGVIE--------SPFVMVFAMIGIPYAADIMNF 298 Query: 303 VILTAVLSAGNSGMYASTRMLYTLACDGKAPRIFAKLSRGGVPRNALYATTVIAGLCFLT 362 VI+TA+LSA NSG+YA++RML+TL+ G PR +A LSR G P NA+ + L+ Sbjct: 299 VIITALLSAANSGLYAASRMLWTLSDQGNMPRRYATLSRRGTPFNAIVLSMAGGMASLLS 358 Query: 363 SMFGNQTVYLWLLNTSGMTGFIAWLGIAISHYRFRRGYVLQGHDINDLPYRSGFFPLGPI 422 S+F T+YL L++ SG+ + W+ IA S FRR Y+ G + DL +R +P P+ Sbjct: 359 SVFAPDTIYLALVSISGLAVVVVWISIAASQIAFRRHYIASGGKLEDLKFRVRGYPFVPL 418 Query: 423 FAFILCLIITLGQNYEAFLKDTIDWGGVAATYIGIPLFLIIWFGYKL 469 A C++ +G ++ + A Y G+P + Y L Sbjct: 419 GAIFCCVLACVGIAFDPAQR--------VALYFGLPFIAWCYLAYWL 457 Lambda K H 0.327 0.142 0.451 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: 757 Number of extensions: 35 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: 489 Length of database: 479 Length adjustment: 34 Effective length of query: 455 Effective length of database: 445 Effective search space: 202475 Effective search space used: 202475 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 (21.7 bits) S2: 52 (24.6 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