Align lysine-specific permease (characterized)
to candidate 1937132 b3795 predicted transporter (NCBI)
Query= CharProtDB::CH_003129 (489 letters) >FitnessBrowser__Keio:1937132 Length = 461 Score = 306 bits (785), Expect = 8e-88 Identities = 175/464 (37%), Positives = 268/464 (57%), Gaps = 27/464 (5%) Query: 11 PGLRRELKARHLTMIAIGGSIGTGLFVASGATISQAGPGGALLSYMLIGLMVYFLMTSLG 70 P L+R L+ARH+ +IA+GG+IG GLF+ + +T+ AGP LL+Y++ GL V+F+M S+G Sbjct: 6 PELQRGLEARHIELIALGGTIGVGLFMGAASTLKWAGPS-VLLAYIIAGLFVFFIMRSMG 64 Query: 71 ELAAYMPVSGSFATYGQNYVEEGFGFALGWNYWYNWAVTIAVDLVAAQLVMSWWFPDTPG 130 E+ PV+GSFA Y Y+ FG+ W+YW+ W ++ A + + +WFP+ Sbjct: 65 EMLFLEPVTGSFAVYAHRYMSPFFGYLTAWSYWFMWMAVGISEITAIGVYVQFWFPEMAQ 124 Query: 131 WIWSALFLGVIFLLNYISVRGFGEAEYWFSLIKVTTVIVFIIVGV-LMIIGIFKGAQPAG 189 WI + + + ++ L N +VR +GE E+WF++IKVTT+IV I++G+ ++ G G Q G Sbjct: 125 WIPALIAVALVALANLAAVRLYGEIEFWFAMIKVTTIIVMIVIGLGVIFFGFGNGGQSIG 184 Query: 190 WSNWTIGEAPFAGGFAAMIGVAMIVGFSFQGTELIGIAAGESEDPAKNIPRAVRQVFWRI 249 +SN T FAGG+ + IV S+QG ELIGI AGE+++P + AV +V WRI Sbjct: 185 FSNLTEHGGFFAGGWKGFLTALCIVVASYQGVELIGITAGEAKNPQVTLRSAVGKVLWRI 244 Query: 250 LLFYVFAILIISLIIPYTDPSLLRNDVKDISVSPFTLVFQHAGLLSAAAVMNAVILTAVL 309 L+FYV AI +I I P+ N++ + SPF L F G+ +AA ++N V+LTA L Sbjct: 245 LIFYVGAIFVIVTIFPW-------NEIGS-NGSPFVLTFAKIGITAAAGIINFVVLTAAL 296 Query: 310 SAGNSGMYASTRMLYTLACDGKAPRIFAKLSRGGVP--RNALYATTVIAGLCFLTSMFGN 367 S NSGMY+ RMLY LA + + P AK+SR GVP A+ ++ G C + Sbjct: 297 SGCNSGMYSCGRMLYALAKNRQLPAAMAKVSRHGVPVAGVAVSIAILLIGSCLNYIIPNP 356 Query: 368 QTVYLWLLNTSGMTGFIAWLGIAISHYRFRRGYVLQGHDINDLPYRSGFFPLG--PIFAF 425 Q V++++ + S + G + W I IS RFRR + I P+RS FP AF Sbjct: 357 QRVFVYVYSASVLPGMVPWFVILISQLRFRRAHKAA---IASHPFRSILFPWANYVTMAF 413 Query: 426 ILCLIITLGQNYEAFLKDTIDWGGVAATYIGIPLFLIIWFGYKL 469 ++C++I + N + + + ++GI L + YK+ Sbjct: 414 LICVLIGMYFNEDTRM----------SLFVGIIFMLAVTAIYKV 447 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: 743 Number of extensions: 56 Number of successful extensions: 5 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: 461 Length adjustment: 33 Effective length of query: 456 Effective length of database: 428 Effective search space: 195168 Effective search space used: 195168 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