Align lysine-specific permease (characterized)
to candidate PfGW456L13_3211 Arginine permease RocE
Query= CharProtDB::CH_003129 (489 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3211 Length = 474 Score = 396 bits (1018), Expect = e-115 Identities = 193/438 (44%), Positives = 287/438 (65%), Gaps = 10/438 (2%) Query: 13 LRRELKARHLTMIAIGGSIGTGLFVASGATISQAGPGGALLSYMLIGLMVYFLMTSLGEL 72 L R LK+RH+ M+++GG IGTGLF+ SG TI+Q GP GA+L+Y++ G ++Y +M LGEL Sbjct: 16 LTRALKSRHIFMLSLGGVIGTGLFMGSGVTINQGGPVGAILAYLVAGFLMYLVMVCLGEL 75 Query: 73 AAYMPVSGSFATYGQNYVEEGFGFALGWNYWYNWAVTIAVDLVAAQLVMSWWFPDTPGWI 132 + MPVSGSF T+ Y+ GF +GW YW +WA T+ ++ AA ++M+ WFP+ P W Sbjct: 76 SVQMPVSGSFQTHATKYIGPATGFMIGWVYWMSWATTVGLEFTAAGMLMTRWFPEVPIWY 135 Query: 133 WSALFLGVIFLLNYISVRGFGEAEYWFSLIKVTTVIVFIIVGVLMIIGI--FKGAQPAGW 190 WSALF+ V+F +N ++ R FGEAEYWFS IKV ++ FI+VGVL+I G+ PA Sbjct: 136 WSALFVVVLFGINAMATRAFGEAEYWFSGIKVAAILGFIVVGVLVIFGVMPLSSGAPAPM 195 Query: 191 SNWTIGEAPFAGGFAAMIGVAMIVGFSFQGTELIGIAAGESEDPAKNIPRAVRQVFWRIL 250 + IG++ F G +A+ V M V ++FQG E++G+AAGE++ P K+IPRAVR V +R+L Sbjct: 196 ATNLIGDSLFPNGLSAVFAVMMTVVYAFQGCEIMGVAAGETDQPEKSIPRAVRNVVFRVL 255 Query: 251 LFYVFAILIISLIIPYTDPSLLRNDVKDISVSPFTLVFQHAGLLSAAAVMNAVILTAVLS 310 +FYV AI+++S I+P+ L+ SPF VF G+ AA +MN VILTA+LS Sbjct: 256 IFYVLAIIVLSAIVPWQQAGLME--------SPFVQVFDMVGIPYAADLMNFVILTAILS 307 Query: 311 AGNSGMYASTRMLYTLACDGKAPRIFAKLSRGGVPRNALYATTVIAGLCFLTSMFGNQTV 370 GNSG+YASTR+L+ ++ G AP+ + LS+ GVP AL T A + +TS T+ Sbjct: 308 VGNSGLYASTRILWAMSKTGMAPKSLSPLSKRGVPLRALSITLCFALVSLMTSFVAADTL 367 Query: 371 YLWLLNTSGMTGFIAWLGIAISHYRFRRGYVLQGHDINDLPYRSGFFPLGPIFAFILCLI 430 ++ L+ SGM+G + W+ IA++ Y+FR+ Y+ G + DL YR+ +FP+ P+ LC Sbjct: 368 FMVLMAVSGMSGTVTWIVIALAQYKFRKAYLRDGGKLRDLKYRAPWFPVLPLMCITLCCS 427 Query: 431 ITLGQNYEAFLKDTIDWG 448 + + + + ++ WG Sbjct: 428 LFVFLALDETQRPSLYWG 445 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: 786 Number of extensions: 48 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: 474 Length adjustment: 34 Effective length of query: 455 Effective length of database: 440 Effective search space: 200200 Effective search space used: 200200 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