Align lysine-specific permease (characterized)
to candidate 14398 b0260 putative amino acid/amine transport protein (VIMSS)
Query= CharProtDB::CH_003129 (489 letters) >FitnessBrowser__Keio:14398 Length = 467 Score = 337 bits (864), Expect = 5e-97 Identities = 181/469 (38%), Positives = 267/469 (56%), Gaps = 21/469 (4%) Query: 4 ETKTTEAPGLRRELKARHLTMIAIGGSIGTGLFVASGATISQAGPGGALLSYMLIGLMVY 63 +T AP L+R +K RHL M+++GG IGTGLF +G IS G G LL+Y++ L+V+ Sbjct: 2 QTTQQNAP-LKRTMKTRHLIMLSLGGVIGTGLFFNTGYIISTTGAAGTLLAYLIGALVVW 60 Query: 64 FLMTSLGELAAYMPVSGSFATYGQNYVEEGFGFALGWNYWYNWAVTIAVDLVAAQLVMSW 123 +M LGEL+ MP +G+F Y Y+ G+ + W YW W V + AA M + Sbjct: 61 LVMQCLGELSVAMPETGAFHVYAARYLGPATGYTVAWLYWLTWTVALGSSFTAAGFCMQY 120 Query: 124 WFPDTPGWIWSALFLGVIFLLNYISVRGFGEAEYWFSLIKVTTVIVFIIVGVLMIIGIF- 182 WFP P W+W +F +IF LN IS R F E E+WFSL+KV T+I FII+G I G Sbjct: 121 WFPQVPVWVWCVVFCAIIFGLNVISTRFFAEGEFWFSLVKVVTIIAFIILGGAAIFGFIP 180 Query: 183 --KGAQPAGWSNWTIGEAPFAGGFAAMIGVAMIVGFSFQGTELIGIAAGESEDPAKNIPR 240 G+ G SN T E F G ++ + V F+F GTELIGIAAGE+E+P K IP Sbjct: 181 MQDGSPAPGLSNIT-AEGWFPHGGLPILMTMVAVNFAFSGTELIGIAAGETENPRKVIPV 239 Query: 241 AVRQVFWRILLFYVFAILIISLIIPYTDPSLLRNDVKDISVSPFTLVFQHAGLLSAAAVM 300 A+R R+++F++ + +++ +IP + SPF LVF+ G+ AA + Sbjct: 240 AIRTTIARLIIFFIGTVFVLAALIPMQQVG--------VEKSPFVLVFEKVGIPYAADIF 291 Query: 301 NAVILTAVLSAGNSGMYASTRMLYTLACDGKAPRIFAKLSRGGVPRNALYATTVIAGLCF 360 N VILTA+LSA NSG+YAS RML++L+ + P FA++++ GVP AL + + L Sbjct: 292 NFVILTAILSAANSGLYASGRMLWSLSNERTLPACFARVTKNGVPLTALSVSMLGGVLAL 351 Query: 361 LTSMFGNQTVYLWLLNTSGMTGFIAWLGIAISHYRFRRGYVLQGHDINDLPYRSGFFPLG 420 +S+ TV++ L SG WL I SH+ FRR ++ QG +++L YR+ ++PL Sbjct: 352 FSSVVAPDTVFVALSAISGFAVVAVWLSICASHFVFRRRHLQQGKALSELHYRAPWYPLV 411 Query: 421 PIFAFILCLIITLGQNYEAFLKDTIDWGGVAATYIGIPLFLIIWFGYKL 469 P+ F+LCL+ +G ++ + A + G+P + + Y L Sbjct: 412 PVLGFVLCLVACVGLAFDPAQR--------IALWCGLPFVALCYGAYFL 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: 721 Number of extensions: 31 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: 467 Length adjustment: 34 Effective length of query: 455 Effective length of database: 433 Effective search space: 197015 Effective search space used: 197015 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 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