Align Na(+)-malate symporter; Sodium-dependent malate transporter (characterized)
to candidate PfGW456L13_3595 Citrate-sodium symport
Query= SwissProt::O05256 (448 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3595 Length = 448 Score = 530 bits (1365), Expect = e-155 Identities = 250/424 (58%), Positives = 333/424 (78%), Gaps = 1/424 (0%) Query: 24 QKIWSWEIGVIPLPLYTVLAVIIILAAYYNELPANMLGGFAIIMILGVFLGDIGQRIPIL 83 + + ++EIGVIPLP++ +AVI+ L+A+ LP NM+GG A+IM +GVF G +G R+PIL Sbjct: 24 RSLCAYEIGVIPLPIFLGIAVIVYLSAHLGFLPKNMIGGLAVIMTMGVFFGQMGSRLPIL 83 Query: 84 KDIGGPAILSLFVPSFLVFYNVLNSTSLDAVTNLMKTSNFLYFYIACLVVGSILGMNRIV 143 K+IGG AIL L +PS LVFY ++DA LMK +NFLYF IA LVVGSILGM+R + Sbjct: 84 KEIGGGAILCLMLPSILVFYGFFGPATIDATKMLMKEANFLYFVIASLVVGSILGMSRFI 143 Query: 144 LIQGFIRMFVPLVAGTIAAVAAGILVGFIFGYSAYDSFFFVVVPIIAGGIGEGILPLSIA 203 L+QG +RMF+PL+ GT+AAVA+G++VG + GYS + +FFF++VPII GGIGEGILPLS+A Sbjct: 144 LVQGMLRMFIPLLVGTLAAVASGLIVGKLVGYSFHHTFFFIIVPIIGGGIGEGILPLSLA 203 Query: 204 YSQILGSSADVFVSQLVPAAIIGNVFAIICAALMKKLGDKRPDLNGNGRLVKSKKANEIF 263 YS ILG + D++V+QL PAA++GN+ AIICA + +L KRP +NG G L+++K N+ F Sbjct: 204 YSAILGGTPDIYVAQLAPAAVVGNIVAIICAGYLARLALKRPTINGEGSLIRAKDENDQF 263 Query: 264 NQKEAEAKI-DFKLMGAGVLLACTFFIFGGLLEKFIFIPGAILMIISAAAVKYANILPKK 322 KE I DF++MGAGVL+ C FF+ GGLLEK + IPG ++MI++A KY +LP+K Sbjct: 264 LVKEDTGTIVDFRVMGAGVLVICAFFVLGGLLEKVVGIPGPVMMILAAVLFKYLRVLPEK 323 Query: 323 MEEGAYQLYKFISSSFTWPLMVGLGILFIPLDDVASVISIPFVIICISVVIAMIGSGYFV 382 +E+GA YK +SS+F WP+M+GLG+L++PLD V V S+ +V++C+SVV++M +G+F+ Sbjct: 324 LEKGANSFYKLVSSAFIWPVMIGLGMLYVPLDSVVKVFSVGYVLVCVSVVVSMTVAGFFI 383 Query: 383 GKLMNMYPVESAIVTCCHSGLGGTGDVAILSASGRMGLMPFAQISTRLGGAGTVICATVL 442 G LM MYP+ESAIVTCCHSGLGGTGDVAILSAS RM LMPFAQISTR+GGA TVI AT+L Sbjct: 384 GNLMKMYPIESAIVTCCHSGLGGTGDVAILSASNRMSLMPFAQISTRIGGASTVILATIL 443 Query: 443 LRFF 446 LR F Sbjct: 444 LRLF 447 Lambda K H 0.328 0.145 0.427 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: 876 Number of extensions: 43 Number of successful extensions: 2 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: 448 Length of database: 448 Length adjustment: 33 Effective length of query: 415 Effective length of database: 415 Effective search space: 172225 Effective search space used: 172225 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: 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