Align lysine-specific permease (characterized)
to candidate WP_084936496.1 HA51_RS20955 S-methylmethionine permease
Query= CharProtDB::CH_003129 (489 letters) >NCBI__GCF_002095475.1:WP_084936496.1 Length = 469 Score = 336 bits (862), Expect = 9e-97 Identities = 182/466 (39%), Positives = 262/466 (56%), Gaps = 22/466 (4%) Query: 6 KTTEAPGLRRELKARHLTMIAIGGSIGTGLFVASGATISQAGPGGALLSYMLIGLMVYFL 65 +T +R +K RHL M+++GG IGTGLF +G IS G G LL+Y++ L+V+ + Sbjct: 5 ETPSQDNFKRTMKVRHLVMLSLGGVIGTGLFFNTGYIISTTGAAGTLLAYLIGALVVWLV 64 Query: 66 MTSLGELAAYMPVSGSFATYGQNYVEEGFGFALGWNYWYNWAVTIAVDLVAAQLVMSWWF 125 M LGELA MP +G+F Y Y+ G+ + W YW W V + L AA M +WF Sbjct: 65 MVCLGELAVAMPETGAFHVYAARYLSPATGYTVAWLYWLTWTVALGSSLTAAGFCMQYWF 124 Query: 126 PDTPGWIWSALFLGVIFLLNYISVRGFGEAEYWFSLIKVTTVIVFIIVGVLMIIGIF--- 182 P TP W+W +F I+LLN +S R F E E+WFS+IKV T+I FII+G + G Sbjct: 125 PTTPVWLWCLVFCIAIYLLNIVSTRFFAEGEFWFSIIKVVTIIAFIILGAGAMFGFIPMK 184 Query: 183 KGAQPAGWSNWTI-GEAPFAGGFAAMIGVAMIVGFSFQGTELIGIAAGESEDPAKNIPRA 241 G+ G SN T G P G ++ + V F+F GTELIGIAAGE+E P K +P A Sbjct: 185 DGSAAPGLSNLTASGWLPH--GTLPILMTMVAVNFAFSGTELIGIAAGETEQPQKALPLA 242 Query: 242 VRQVFWRILLFYVFAILIISLIIPYTDPSLLRNDVKDISVSPFTLVFQHAGLLSAAAVMN 301 +R R+++F++ + +++ +IP +++ SPF LVF+ G+ AA + N Sbjct: 243 IRTTVARLIIFFIGTVFVLAALIPMDQAGIVK--------SPFVLVFEKIGIPYAADIFN 294 Query: 302 AVILTAVLSAGNSGMYASTRMLYTLACDGKAPRIFAKLSRGGVPRNALYATTVIAGLCFL 361 VILTA+LSA NSG+YAS RML++LA + PR FA+++ GVP AL + + L Sbjct: 295 FVILTAILSAANSGLYASGRMLWSLANENTLPRCFARVNHRGVPVLALTISMLGGLLALF 354 Query: 362 TSMFGNQTVYLWLLNTSGMTGFIAWLGIAISHYRFRRGYVLQGHDINDLPYRSGFFPLGP 421 +S+ TV++ L SG WL I SHY FRR ++ G + L YR+ +PL P Sbjct: 355 SSVIAPDTVFVALSAISGFAVVAVWLSICASHYVFRRRHLQAGGTLQQLAYRAPLYPLTP 414 Query: 422 IFAFILCLIITLGQNYEAFLKDTIDWGGVAATYIGIPLFLIIWFGY 467 I F+LCL+ +G ++ + A + GIP L + Y Sbjct: 415 ILGFLLCLLACVGLAFDPSQR--------IALWCGIPFVLFCYAAY 452 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: 722 Number of extensions: 32 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: 469 Length adjustment: 34 Effective length of query: 455 Effective length of database: 435 Effective search space: 197925 Effective search space used: 197925 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: 51 (24.3 bits)
This GapMind analysis is from Sep 24 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