Align Proline-specific permease (ProY) (characterized)
to candidate PP_0927 PP_0927 aromatic amino acid transport protein
Query= TCDB::P37460 (456 letters) >FitnessBrowser__Putida:PP_0927 Length = 453 Score = 380 bits (975), Expect = e-110 Identities = 195/444 (43%), Positives = 275/444 (61%), Gaps = 3/444 (0%) Query: 6 KLKRGLSTRHIRFMALGSAIGTGLFYGSADAIKMAGPSVLLAYIIGGVAAYIIMRALGEM 65 +L+RGL RHI+ +ALG AIGTGLF G A I++AGPSVLL Y I G+ A++IMR LGEM Sbjct: 9 RLQRGLKNRHIQLIALGGAIGTGLFLGIAQTIQLAGPSVLLGYAIAGLMAFLIMRQLGEM 68 Query: 66 SVHNPAASSFSRYAQENLGPLAGYITGWTYCFEILIVAIADVTAFGIYMGVWFPAVPHWI 125 V P A SFS +A + AG+++GW Y ++V +A++TA GIY+ W+P P W Sbjct: 69 VVEEPVAGSFSHFAHQYWSEFAGFVSGWNYWVVYVLVGMAELTAVGIYVQYWWPDFPTWA 128 Query: 126 WVLSVVLIICAINLMSVKVFGELEFWFSFFKVATIIIMIVAGIGIIVWGIGNGGQPTGIH 185 ++I INL VKV+GE+EFWF+ KV I+ MI G G + G G+GG + Sbjct: 129 TAAIFFVVINLINLTQVKVYGEMEFWFALVKVVAIVSMI--GFGAWLLGSGHGGPDASVA 186 Query: 186 NLWSNGGFFSNGWLGMIMSLQMVMFAYGGIEIIGITAGEAKDPEKSIPRAINSVPMRILV 245 NLW GGFF NG G++M+L ++MF++GG+E++GITA EA +P +SIP+A N V RIL+ Sbjct: 187 NLWQYGGFFPNGVTGLVMALAVIMFSFGGLELVGITAAEADNPRESIPKATNQVVYRILI 246 Query: 246 FYVGTLFVIMSIYPWNQVGTNGSPFVLTFQHMGITFAASILNFVVLTASLSAINSDVFGV 305 FY+G L V++S+YPW +V GSPFV+ F + A+ILN VVLTA+LS NS V+ Sbjct: 247 FYIGALAVLLSLYPWQKVVQGGSPFVMIFHELDSDLVATILNIVVLTAALSVYNSCVYAN 306 Query: 306 GRMLHGMAEQGSAPKVFAKTSRRGIPWVTVLVMTIALLFAVYLNYIMPENVFLVIASLAT 365 RML G+A QG AP+ K SR G+P + V A V +NY+MP F ++ +LA Sbjct: 307 SRMLFGLASQGDAPRQLLKVSRSGVPLTALAVSAFATGLCVLINYLMPGGAFGLLMALAV 366 Query: 366 FATVWVWIMILLSQIAFRRRLPPEEVKALKFKVPGGVVTTIAGLIFLVFIIALIGYHPDT 425 A V W I ++ + FR+ + +K G +T L F+V I+ ++ P Sbjct: 367 SALVINWASISITHLKFRKAKLAAGITPF-YKSLGHPLTNYLCLAFIVLILVVMYLTPPI 425 Query: 426 RISLYVGFAWIVLLLIGWIFKRRR 449 RIS+ + AWI +L + + K+ R Sbjct: 426 RISVMLIPAWIAVLWVAFKLKKAR 449 Lambda K H 0.329 0.143 0.449 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: 575 Number of extensions: 31 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: 456 Length of database: 453 Length adjustment: 33 Effective length of query: 423 Effective length of database: 420 Effective search space: 177660 Effective search space used: 177660 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 (21.8 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