Align lysine-specific permease (characterized)
to candidate PP_3727 PP_3727 Amino-acid permease RocE
Query= CharProtDB::CH_003129 (489 letters) >FitnessBrowser__Putida:PP_3727 Length = 468 Score = 397 bits (1019), Expect = e-115 Identities = 196/446 (43%), Positives = 288/446 (64%), Gaps = 10/446 (2%) Query: 5 TKTTEAPGLRRELKARHLTMIAIGGSIGTGLFVASGATISQAGPGGALLSYMLIGLMVYF 64 T + E L R LK+RH+ M+++GG IGTGLF+ SG TI+Q GP GA+L+Y++ GL++Y Sbjct: 2 TDSVEKIQLTRALKSRHIFMLSLGGVIGTGLFMGSGVTINQGGPVGAILAYLVAGLLMYL 61 Query: 65 LMTSLGELAAYMPVSGSFATYGQNYVEEGFGFALGWNYWYNWAVTIAVDLVAAQLVMSWW 124 +M LGEL+ MPVSGSF + Y+ GF +GW YW +WA T+ ++ AA ++M+ W Sbjct: 62 VMVCLGELSVQMPVSGSFQAHATKYIGPATGFMIGWVYWMSWATTVGLEFTAAGMLMTRW 121 Query: 125 FPDTPGWIWSALFLGVIFLLNYISVRGFGEAEYWFSLIKVTTVIVFIIVGVLMIIGI--F 182 FP+ P W WSALF+ V+F LN ++ R FGEAEYWFS IKV T++ FI++G+L+I G Sbjct: 122 FPEVPIWYWSALFVVVLFGLNALATRAFGEAEYWFSGIKVATILGFIVIGLLVIFGAIPL 181 Query: 183 KGAQPAGWSNWTIGEAPFAGGFAAMIGVAMIVGFSFQGTELIGIAAGESEDPAKNIPRAV 242 PA N +GE+ F G +A+ V M V ++FQG E++G+AAGE+E P K+IPRAV Sbjct: 182 SSGAPAPMLNNLVGESLFPHGLSAVFAVMMTVVYAFQGCEIMGVAAGETEHPEKSIPRAV 241 Query: 243 RQVFWRILLFYVFAILIISLIIPYTDPSLLRNDVKDISVSPFTLVFQHAGLLSAAAVMNA 302 R V +R+L+FYV AI ++S I+P+ L+ SPF VF G+ AA +MN Sbjct: 242 RNVVFRVLIFYVLAIAVLSAIVPHEQAGLME--------SPFVQVFDMVGIPYAADLMNF 293 Query: 303 VILTAVLSAGNSGMYASTRMLYTLACDGKAPRIFAKLSRGGVPRNALYATTVIAGLCFLT 362 VILTA+LS GNSG+YASTR+L+ ++ G AP+ + LS+ GVP AL T A + +T Sbjct: 294 VILTAILSVGNSGLYASTRILWAMSKTGMAPKSLSPLSKRGVPLRALSITLCFALISLMT 353 Query: 363 SMFGNQTVYLWLLNTSGMTGFIAWLGIAISHYRFRRGYVLQGHDINDLPYRSGFFPLGPI 422 S T+++ L+ SGM+G + W+ IA++ YRFR+ ++ G + DL Y++ +PL P+ Sbjct: 354 SFVAADTLFMVLMAVSGMSGTVTWIVIALAQYRFRKAWLRDGGQLQDLKYKAPLYPLVPL 413 Query: 423 FAFILCLIITLGQNYEAFLKDTIDWG 448 LC + + + + ++ WG Sbjct: 414 LCITLCSSLFVFLALDETQRPSLYWG 439 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: 768 Number of extensions: 38 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: 468 Length adjustment: 34 Effective length of query: 455 Effective length of database: 434 Effective search space: 197470 Effective search space used: 197470 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