Align lysine-specific permease (characterized)
to candidate Pf6N2E2_4959 S-methylmethionine permease
Query= CharProtDB::CH_003129 (489 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4959 Length = 476 Score = 379 bits (974), Expect = e-110 Identities = 198/480 (41%), Positives = 290/480 (60%), Gaps = 19/480 (3%) Query: 2 VSETKTTEAPGLRRELKARHLTMIAIGGSIGTGLFVASGATISQAGPGGALLSYMLIGLM 61 + E + G ++E++ RH+ M+A+GG IGTGLF+ SG T++QAGP GA+++Y++ LM Sbjct: 3 IKEQQLNTRAGFKQEMQTRHIVMLALGGVIGTGLFLTSGYTVNQAGPMGAVIAYIIGALM 62 Query: 62 VYFLMTSLGELAAYMPVSGSFATYGQNYVEEGFGFALGWNYWYNWAVTIAVDLVAAQLVM 121 VY +M LGELA MP +GSF+TY ++ G G+ + W YW W V I + AA ++M Sbjct: 63 VYMVMMCLGELAVQMPETGSFSTYATRFLGPGTGYTVAWLYWLTWTVAIGSEFTAAGILM 122 Query: 122 SWWFPDTPGWIWSALFLGVIFLLNYISVRGFGEAEYWFSLIKVTTVIVFIIVGVLMIIGI 181 S WFPDTP WIWSALF GV+FL N ISVR F E E+W SLIKV TV+VF+++G I+G+ Sbjct: 123 SRWFPDTPVWIWSALFAGVVFLSNVISVRLFAETEFWLSLIKVLTVVVFLLIGGGAILGL 182 Query: 182 FK--GAQPAGWSNWTIGEAPFAGGFAAMIGVAMIVGFSFQGTELIGIAAGESEDPAKNIP 239 A G SN+T E F GF + + V F+F GTELIGIAAGE++DP +N+P Sbjct: 183 LNIDQAHSIGLSNFT-REGLFPTGFMPIAMTLLAVSFAFSGTELIGIAAGETKDPQRNVP 241 Query: 240 RAVRQVFWRILLFYVFAILIISLIIPYTDPSLLRNDVKDISVSPFTLVFQHAGLLSAAAV 299 RA+R R+ +F+V I +++ ++P L+ SPF VF + G+ +A + Sbjct: 242 RAIRTTVLRLAVFFVGTIFVLATLLPREQAGLVE--------SPFVTVFTYIGIPYSADI 293 Query: 300 MNAVILTAVLSAGNSGMYASTRMLYTLACDGKAPRIFAKLSRGGVPRNALYATTVIAGLC 359 MN VI++A+LSA NSG+YA++RML+TL+ G P+ F+ L+R G P NA+ + Sbjct: 294 MNFVIISALLSAANSGLYAASRMLWTLSDQGHLPKQFSALTRMGTPLNAIIVSMAGGAAS 353 Query: 360 FLTSMFGNQTVYLWLLNTSGMTGFIAWLGIAISHYRFRRGYVLQGHDINDLPYRSGFFPL 419 L+S+F T+YL L++ SG+ + W+ IA S FRR YV G DI L +R +P Sbjct: 354 LLSSVFAADTIYLALVSISGLAVVVVWMSIAASQIAFRRHYVANGGDIRKLKFRVRGYPW 413 Query: 420 GPIFAFILCLIITLGQNYEAFLKDTIDWGGVAATYIGIPLFLIIWFGYKLIKGTHFVRYS 479 P+ A + C + +G ++ + A Y G+P +F Y + + + R S Sbjct: 414 VPLGALVCCSLACIGIAFDPEQR--------VALYFGLPFIAWCYFVYYITRKSRERRLS 465 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: 736 Number of extensions: 46 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: 476 Length adjustment: 34 Effective length of query: 455 Effective length of database: 442 Effective search space: 201110 Effective search space used: 201110 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