Align lysine-specific permease (characterized)
to candidate PP_1059 PP_1059 Uncharacterized amino acid permease YtnA
Query= CharProtDB::CH_003129 (489 letters) >FitnessBrowser__Putida:PP_1059 Length = 472 Score = 308 bits (788), Expect = 3e-88 Identities = 170/460 (36%), Positives = 266/460 (57%), Gaps = 23/460 (5%) Query: 6 KTTEAPGLRRELKARHLTMIAIGGSIGTGLFVASGATISQAGPGGALLSYMLIGLMVYFL 65 + TE L+REL RH+ ++A+G IG GLF+ S I AGP +LSY++ GL + + Sbjct: 11 QATEGGPLKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPA-IMLSYIIGGLAILVI 69 Query: 66 MTSLGELAAYMPVSGSFATYGQNYVEEGFGFALGWNYWYNWAVTIAVDLVAAQLVMSWWF 125 M +LGE+A + PV+GSF+ Y Q+Y+ GF GWNYW+ W VT ++ A + M WF Sbjct: 70 MRALGEMAVHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAIYMGIWF 129 Query: 126 PDTPGWIWSALFLGVIFLLNYISVRGFGEAEYWFSLIKVTTVIVFIIVGV-LMIIGIFKG 184 PD P WIW+ LG + +N ++V+ FGE E+WF+LIK+ T+I ++ G+ ++ G Sbjct: 130 PDVPRWIWALAALGSMGAVNLVAVKAFGEFEFWFALIKIVTIIAMVLGGIGIIAFGFGND 189 Query: 185 AQPAGWSN-WTIGEAPFAGGFAAMIGVAMIVGFSFQGTELIGIAAGESEDPAKNIPRAVR 243 G SN W+ G G ++ + M++ F++ G E+IG+ AGE+ +P K IP+A+ Sbjct: 190 GVAVGISNLWSNGGFMPNGVTGVLMSLQMVM-FAYLGVEMIGLTAGEARNPQKTIPQAIG 248 Query: 244 QVFWRILLFYVFAILIISLIIPYTDPSLLRNDVKDISVSPFTLVFQHAGLLSAAAVMNAV 303 VFWRILLFYV A+ +I I P+ N++ SPF + F+ G+ +AA ++N V Sbjct: 249 SVFWRILLFYVGALFVILSIYPW-------NEIGS-QGSPFVMTFERLGIKTAAGIINFV 300 Query: 304 ILTAVLSAGNSGMYASTRMLYTLACDGKAPRIFAKLSRGGVPRNALYATTVIAGLCFLTS 363 ++TA LS+ N G++++ RMLY+LA +G+AP FA+ S+ GVPRNAL + L L + Sbjct: 301 VITAALSSCNGGIFSTGRMLYSLAQNGQAPAAFARTSKNGVPRNALLLSIGALLLGVLAN 360 Query: 364 MFGNQTVYLWLLNTSGMTGFIAWLGIAISHYRFRRGYVLQGHDINDLPYRSGFFPLGPIF 423 + V++W+ + + W+ I ++ +FR G L + L YR +PL Sbjct: 361 YLVPEKVFVWVTSIATFGAIWTWVMILLAQLKFRAG--LTTAERKALKYRMWLWPLSSYL 418 Query: 424 AFILCLIITLGQNYEAFLKDTIDWGGVAATYIGIPLFLII 463 A +++ A+ +DT A YIG P FL++ Sbjct: 419 ALAFLVLVV---GLMAYFEDT-----RVALYIG-PAFLVL 449 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: 735 Number of extensions: 40 Number of successful extensions: 4 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: 472 Length adjustment: 34 Effective length of query: 455 Effective length of database: 438 Effective search space: 199290 Effective search space used: 199290 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