Align lysine-specific permease (characterized)
to candidate PP_0927 PP_0927 aromatic amino acid transport protein
Query= CharProtDB::CH_003129 (489 letters) >FitnessBrowser__Putida:PP_0927 Length = 453 Score = 265 bits (678), Expect = 2e-75 Identities = 150/395 (37%), Positives = 223/395 (56%), Gaps = 16/395 (4%) Query: 13 LRRELKARHLTMIAIGGSIGTGLFVASGATISQAGPGGALLSYMLIGLMVYFLMTSLGEL 72 L+R LK RH+ +IA+GG+IGTGLF+ TI AGP LL Y + GLM + +M LGE+ Sbjct: 10 LQRGLKNRHIQLIALGGAIGTGLFLGIAQTIQLAGPS-VLLGYAIAGLMAFLIMRQLGEM 68 Query: 73 AAYMPVSGSFATYGQNYVEEGFGFALGWNYWYNWAVTIAVDLVAAQLVMSWWFPDTPGWI 132 PV+GSF+ + Y E GF GWNYW + + +L A + + +W+PD P W Sbjct: 69 VVEEPVAGSFSHFAHQYWSEFAGFVSGWNYWVVYVLVGMAELTAVGIYVQYWWPDFPTWA 128 Query: 133 WSALFLGVIFLLNYISVRGFGEAEYWFSLIKVTTVIVFIIVGVLMIIGIFKGAQPAGWSN 192 +A+F VI L+N V+ +GE E+WF+L+KV ++ I G ++G G A +N Sbjct: 129 TAAIFFVVINLINLTQVKVYGEMEFWFALVKVVAIVSMIGFGA-WLLGSGHGGPDASVAN 187 Query: 193 -WTIGEAPFAGGFAAMIGVAMIVGFSFQGTELIGIAAGESEDPAKNIPRAVRQVFWRILL 251 W G F G ++ ++ FSF G EL+GI A E+++P ++IP+A QV +RIL+ Sbjct: 188 LWQYG-GFFPNGVTGLVMALAVIMFSFGGLELVGITAAEADNPRESIPKATNQVVYRILI 246 Query: 252 FYVFAILIISLIIPYTDPSLLRNDVKDISVSPFTLVFQHAGLLSAAAVMNAVILTAVLSA 311 FY+ A+ ++ + P+ +++ SPF ++F A ++N V+LTA LS Sbjct: 247 FYIGALAVLLSLYPW--QKVVQGG------SPFVMIFHELDSDLVATILNIVVLTAALSV 298 Query: 312 GNSGMYASTRMLYTLACDGKAPRIFAKLSRGGVPRNALYATTVIAGLCFLTS--MFGNQT 369 NS +YA++RML+ LA G APR K+SR GVP AL + GLC L + M G Sbjct: 299 YNSCVYANSRMLFGLASQGDAPRQLLKVSRSGVPLTALAVSAFATGLCVLINYLMPGGAF 358 Query: 370 VYLWLLNTSGMTGFIAWLGIAISHYRFRRGYVLQG 404 L L S + I W I+I+H +FR+ + G Sbjct: 359 GLLMALAVSALV--INWASISITHLKFRKAKLAAG 391 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: 660 Number of extensions: 47 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: 453 Length adjustment: 33 Effective length of query: 456 Effective length of database: 420 Effective search space: 191520 Effective search space used: 191520 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