Align Aspartate-proton symporter; L-aspartate transporter (characterized)
to candidate PP_1259 PP_1259 Aspartate-proton symporter
Query= SwissProt::O07002 (520 letters) >FitnessBrowser__Putida:PP_1259 Length = 537 Score = 665 bits (1717), Expect = 0.0 Identities = 302/508 (59%), Positives = 405/508 (79%), Gaps = 1/508 (0%) Query: 5 GNFQKSMSLFDLILIGMGAIFGSAWLFAVSNVASKAGPSGAFSWILGGAIILLIGLVYAE 64 G F+K +SL DL IG+GAIFGS WLFA S+V++ AGP+G SW LGG +LL+G+VY E Sbjct: 3 GKFKKQLSLLDLTFIGLGAIFGSGWLFAASHVSAIAGPAGILSWFLGGFAVLLLGIVYCE 62 Query: 65 LGAALPRTGGIIRYPVYSHGHLVGYLISFVTIVAYTSLISIEVTAVRQYVAYWFPGLTIK 124 LGAALPR GG++RYPVYSHG L+GYL+ F+T++A++SLI+IEV A RQY A WFPGLT Sbjct: 63 LGAALPRAGGVVRYPVYSHGPLLGYLMGFITLIAFSSLIAIEVVASRQYAAAWFPGLTKA 122 Query: 125 GSDSPTISGWILQFALLCLFFLLNYWSVKTFAKANFIISIFKYIVPITIIIVLIFHFQPE 184 GS PT+ GW++QFALL LFF LNY SVKTFAKAN ++S+FK+IVP+ +I VL F+PE Sbjct: 123 GSSDPTVLGWLVQFALLGLFFFLNYRSVKTFAKANNLVSVFKFIVPLLVIGVLFTFFKPE 182 Query: 185 NLSVQGFAPFGFTGIQAAISTGGVMFAYLGLHPIVSVAGEVQNPKRNIPIALIICIIVST 244 N VQGFAPFG +G++ A+S GG++FAYLGL PI+SVA EV+NP+R IPIALI+ +++ST Sbjct: 183 NFEVQGFAPFGLSGVEMAVSAGGIIFAYLGLTPIISVASEVKNPQRTIPIALILSVLLST 242 Query: 245 IIYTVLQVTFIGAIPTETLKHGWPAIGREFSLPFKDIAVMLGLGWLATLVILDAILSPGG 304 IY +LQ+ F+G++PTE L +GW ++ +E +LP++DIA+ LG+GWLA LV+ DA++SP G Sbjct: 243 AIYALLQLAFLGSVPTEMLANGWASVTKELALPYRDIALALGVGWLAYLVVADAVISPSG 302 Query: 305 NGNIFMNTTSRLVYAWARNGTLFGIFSKVNKDTGTPRASLWLSFALSIFWTLPFPSWNAL 364 GNI+MN T R++Y WA+ GT F F++++ ++G PR +LWL+F LS+FWTLPFPSW AL Sbjct: 303 CGNIYMNATPRVIYGWAQTGTFFKYFTRIDAESGIPRPALWLTFGLSVFWTLPFPSWEAL 362 Query: 365 VNVCSVALILSYAIAPISSAALRVNAKDLNRPFYLKGMSIIGPLSFIFTAFIVYWSGWKT 424 +NV S AL+LSYA+AP+S AALR NA + RPF +KGM+++GPLSFI A IVYWSGW T Sbjct: 363 INVVSAALVLSYAVAPVSVAALRRNAPHMPRPFRVKGMTVLGPLSFIIAALIVYWSGWNT 422 Query: 425 VSWLLGSQLVMFLIYLCFSKYTPKEDVSLAQQLKSAWWLIGFYIMMLIFSYIGSFGHGLG 484 VSWLL Q+VMF++YL S++ P + +SL QQ++S+ WLIGFY + ++ S++GSFG GLG Sbjct: 423 VSWLLALQIVMFVLYLLCSRFVPTQHLSLGQQVRSSAWLIGFYALTILLSWLGSFG-GLG 481 Query: 485 IISNPVDLILVAIGSLAIYYWAKYTGLP 512 +I +P D ++VA +L IYYW TG+P Sbjct: 482 VIGHPFDTVVVAACALGIYYWGAATGVP 509 Lambda K H 0.328 0.143 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: 1022 Number of extensions: 44 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: 520 Length of database: 537 Length adjustment: 35 Effective length of query: 485 Effective length of database: 502 Effective search space: 243470 Effective search space used: 243470 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 Apr 09 2024. 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