Align Aspartate-proton symporter; L-aspartate transporter (characterized)
to candidate PfGW456L13_3582 Aspartate-proton symporter
Query= SwissProt::O07002 (520 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3582 Length = 548 Score = 673 bits (1736), Expect = 0.0 Identities = 301/512 (58%), Positives = 410/512 (80%), Gaps = 1/512 (0%) Query: 1 MSKQGNFQKSMSLFDLILIGMGAIFGSAWLFAVSNVASKAGPSGAFSWILGGAIILLIGL 60 MS QG F+K +SL DL IG+GAIFGS WLFA S+V++ AGP+G FSW+LGG +LL+G+ Sbjct: 1 MSGQGKFKKQLSLIDLTFIGLGAIFGSGWLFAASHVSAIAGPAGIFSWLLGGFAVLLLGI 60 Query: 61 VYAELGAALPRTGGIIRYPVYSHGHLVGYLISFVTIVAYTSLISIEVTAVRQYVAYWFPG 120 VY ELGAALPR GG++RYPVYSHG L+GYL+ F+T++A++SL++IEV A RQY A WFP Sbjct: 61 VYCELGAALPRAGGVVRYPVYSHGPLLGYLMGFITLIAFSSLVAIEVVAARQYAAAWFPA 120 Query: 121 LTIKGSDSPTISGWILQFALLCLFFLLNYWSVKTFAKANFIISIFKYIVPITIIIVLIFH 180 LT GS +PT GW++QF LLCLFF+LNY+SVKTFAKAN +IS+FK+IVP+ +I VL Sbjct: 121 LTQAGSSNPTAIGWLVQFGLLCLFFMLNYYSVKTFAKANNLISMFKFIVPLLVIGVLFTF 180 Query: 181 FQPENLSVQGFAPFGFTGIQAAISTGGVMFAYLGLHPIVSVAGEVQNPKRNIPIALIICI 240 F+PEN QGF PFG +G++ A+S GG++FAYLGL PI+SVA EV+NP+R IPIALI+ + Sbjct: 181 FKPENFQSQGFMPFGLSGVEMAVSAGGIIFAYLGLTPIISVASEVKNPQRTIPIALILSV 240 Query: 241 IVSTIIYTVLQVTFIGAIPTETLKHGWPAIGREFSLPFKDIAVMLGLGWLATLVILDAIL 300 ++ST IY +LQV F+G +PTE L +GW + +E +LP++DIA+ LG+GWLA LV+ DA++ Sbjct: 241 LLSTAIYVLLQVAFLGGVPTEMLANGWAGVAKELALPYRDIALALGVGWLAYLVVADAVI 300 Query: 301 SPGGNGNIFMNTTSRLVYAWARNGTLFGIFSKVNKDTGTPRASLWLSFALSIFWTLPFPS 360 SP G GNI+MN T R++Y WA+ GT F +F+++++ +G PR +LWL+FALS+FWTLPFPS Sbjct: 301 SPSGCGNIYMNATPRVIYGWAQTGTFFKVFTRIDEKSGIPRPALWLTFALSVFWTLPFPS 360 Query: 361 WNALVNVCSVALILSYAIAPISSAALRVNAKDLNRPFYLKGMSIIGPLSFIFTAFIVYWS 420 W AL+NV S AL+LSYA+AP+S AALR NA D+ RPF +K M ++GP+SFI A IVYWS Sbjct: 361 WEALINVVSAALVLSYAVAPVSVAALRRNAPDMPRPFKVKRMGVLGPVSFIIAALIVYWS 420 Query: 421 GWKTVSWLLGSQLVMFLIYLCFSKYTPKEDVSLAQQLKSAWWLIGFYIMMLIFSYIGSFG 480 GW TVSWLLG Q++MF++YL ++ P + +SLAQQ++S+ WLIGFY + ++ S++GSFG Sbjct: 421 GWSTVSWLLGLQILMFVVYLLCGRFVPTQHLSLAQQVRSSAWLIGFYAVTIVLSWLGSFG 480 Query: 481 HGLGIISNPVDLILVAIGSLAIYYWAKYTGLP 512 G+G++++P D ++VA ++ IYYW TG+P Sbjct: 481 -GMGVLTHPFDTVVVAACAMGIYYWGAATGVP 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: 1043 Number of extensions: 47 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: 548 Length adjustment: 35 Effective length of query: 485 Effective length of database: 513 Effective search space: 248805 Effective search space used: 248805 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