Align Aspartate-proton symporter; L-aspartate transporter (characterized)
to candidate GFF2803 PS417_14300 aspartate:proton symporter
Query= SwissProt::O07002 (520 letters) >FitnessBrowser__WCS417:GFF2803 Length = 539 Score = 664 bits (1713), Expect = 0.0 Identities = 304/512 (59%), Positives = 406/512 (79%), Gaps = 1/512 (0%) Query: 1 MSKQGNFQKSMSLFDLILIGMGAIFGSAWLFAVSNVASKAGPSGAFSWILGGAIILLIGL 60 MS QG F+K +SL DL IG+GAIFGS WLFA S+V++ AGP+G SW++GG +LL+G+ Sbjct: 1 MSAQGKFKKQLSLMDLTFIGLGAIFGSGWLFAASHVSAIAGPAGIISWLIGGFAVLLLGI 60 Query: 61 VYAELGAALPRTGGIIRYPVYSHGHLVGYLISFVTIVAYTSLISIEVTAVRQYVAYWFPG 120 VY ELGAALPR GG++RYPVYSHG L+GYL+ F+T++A++SL++IEV A RQY A WFP Sbjct: 61 VYCELGAALPRAGGVVRYPVYSHGPLLGYLMGFITLIAFSSLVAIEVVASRQYAAAWFPE 120 Query: 121 LTIKGSDSPTISGWILQFALLCLFFLLNYWSVKTFAKANFIISIFKYIVPITIIIVLIFH 180 LT GS PT GW++QFALLCLFF+LNY SVKTFA AN ++S+FK+IVP+ +I VL Sbjct: 121 LTKAGSSDPTTLGWLVQFALLCLFFVLNYRSVKTFAIANNLVSVFKFIVPLLVIGVLFTF 180 Query: 181 FQPENLSVQGFAPFGFTGIQAAISTGGVMFAYLGLHPIVSVAGEVQNPKRNIPIALIICI 240 F+P N VQGFAPFG +GI+ A+S GGV+FAYLGL PI+SVA EV+NP+R IPIALI+ + Sbjct: 181 FKPANFQVQGFAPFGLSGIEMAVSAGGVIFAYLGLTPIISVASEVKNPQRTIPIALILSV 240 Query: 241 IVSTIIYTVLQVTFIGAIPTETLKHGWPAIGREFSLPFKDIAVMLGLGWLATLVILDAIL 300 ++ST IY +LQ F+G +PTE L +GW I +E +LP++DIA+ LG+GWLA LV+ DA++ Sbjct: 241 LLSTAIYVLLQTAFLGGVPTEMLANGWAGISKELALPYRDIALALGVGWLAYLVVADAVI 300 Query: 301 SPGGNGNIFMNTTSRLVYAWARNGTLFGIFSKVNKDTGTPRASLWLSFALSIFWTLPFPS 360 SP G GNI+MN T R+VY WA+ GT F IF+++++ +G PR +LWL+FALS+FWTLPFPS Sbjct: 301 SPSGCGNIYMNATPRVVYGWAQTGTFFKIFTRIDEKSGIPRPALWLTFALSVFWTLPFPS 360 Query: 361 WNALVNVCSVALILSYAIAPISSAALRVNAKDLNRPFYLKGMSIIGPLSFIFTAFIVYWS 420 W AL+NV S ALILSYA+AP++ AALR NA + RPF +KGM+++GPLSFI A IVYWS Sbjct: 361 WEALINVVSAALILSYAVAPVTVAALRRNAPQMARPFRVKGMAVLGPLSFIIAALIVYWS 420 Query: 421 GWKTVSWLLGSQLVMFLIYLCFSKYTPKEDVSLAQQLKSAWWLIGFYIMMLIFSYIGSFG 480 GW TVSWLLG Q++MF++YL +++ P +++ QQ++S+ WLIGFY + ++ S +GSFG Sbjct: 421 GWNTVSWLLGLQILMFVVYLLCARWVPTAHLNIKQQVRSSAWLIGFYAVTILLSKLGSFG 480 Query: 481 HGLGIISNPVDLILVAIGSLAIYYWAKYTGLP 512 G+G+I +P+D I+VA +L IYYW TG+P Sbjct: 481 -GIGVIGHPLDTIVVAACALGIYYWGAATGVP 511 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: 992 Number of extensions: 50 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: 539 Length adjustment: 35 Effective length of query: 485 Effective length of database: 504 Effective search space: 244440 Effective search space used: 244440 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 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