Align D-serine/D-alanine/glycine transporter (characterized)
to candidate PP_0927 PP_0927 aromatic amino acid transport protein
Query= SwissProt::P0AAE0 (470 letters) >FitnessBrowser__Putida:PP_0927 Length = 453 Score = 348 bits (893), Expect = e-100 Identities = 183/459 (39%), Positives = 277/459 (60%), Gaps = 9/459 (1%) Query: 11 DQAPAEQSLRRNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFMLFFV 70 DQ+ E+ L+R L NRHIQLIA+GGAIGTGLF+G +TI LAGPS++ Y I G M F + Sbjct: 3 DQSTPER-LQRGLKNRHIQLIALGGAIGTGLFLGIAQTIQLAGPSVLLGYAIAGLMAFLI 61 Query: 71 MRAMGELLLSNLEYKSFSDFASDLLGPWAGYFTGWTYWFCWVVTGMADVVAITAYAQFWF 130 MR +GE+++ SFS FA +AG+ +GW YW +V+ GMA++ A+ Y Q+W+ Sbjct: 62 MRQLGEMVVEEPVAGSFSHFAHQYWSEFAGFVSGWNYWVVYVLVGMAELTAVGIYVQYWW 121 Query: 131 PDLSDWVASLAVIVLLLTLNLATVKMFGEMEFWFAMIKIVAIVSLIVVGLVMVAMHFQSP 190 PD W + V++ +NL VK++GEMEFWFA++K+VAIVS+I G ++ P Sbjct: 122 PDFPTWATAAIFFVVINLINLTQVKVYGEMEFWFALVKVVAIVSMIGFGAWLLGSGHGGP 181 Query: 191 TGVEASFAHLWNDGGWFPKGLSGFFAGFQIAVFAFVGIELVGTTAAETKDPEKSLPRAIN 250 +AS A+LW GG+FP G++G + +F+F G+ELVG TAAE +P +S+P+A N Sbjct: 182 ---DASVANLWQYGGFFPNGVTGLVMALAVIMFSFGGLELVGITAAEADNPRESIPKATN 238 Query: 251 SIPIRIIMFYVFALIVIMSVTPWSSVVPEKSPFVELFVLVGLPAAASVINFVVLTSAASS 310 + RI++FY+ AL V++S+ PW VV SPFV +F + A+++N VVLT+A S Sbjct: 239 QVVYRILIFYIGALAVLLSLYPWQKVVQGGSPFVMIFHELDSDLVATILNIVVLTAALSV 298 Query: 311 ANSGVFSTSRMLFGLAQEGVAPKAFAKLSKRAVPAKGLTFSCICLLGGVVMLYVNPSVIG 370 NS V++ SRMLFGLA +G AP+ K+S+ VP L S V++ Y+ P G Sbjct: 299 YNSCVYANSRMLFGLASQGDAPRQLLKVSRSGVPLTALAVSAFATGLCVLINYLMPG--G 356 Query: 371 AFTMITTVSAILFMFVWTIILCSYLVYRKQRPHLHEKSIYKMPLGKLMCWVCMAFFVFVV 430 AF ++ ++ + W I ++L +RK + YK L ++C+AF V ++ Sbjct: 357 AFGLLMALAVSALVINWASISITHLKFRKAKLAAGITPFYKSLGHPLTNYLCLAFIVLIL 416 Query: 431 VLLTLEDDTRQALLVTPLWFIALGLGWLFIGKKRAAELR 469 V++ L R ++++ P W L W+ K+A + + Sbjct: 417 VVMYLTPPIRISVMLIPAWIAVL---WVAFKLKKARQAK 452 Lambda K H 0.329 0.141 0.440 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: 588 Number of extensions: 29 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: 470 Length of database: 453 Length adjustment: 33 Effective length of query: 437 Effective length of database: 420 Effective search space: 183540 Effective search space used: 183540 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