Align Na(+)-malate symporter; Sodium-dependent malate transporter (characterized)
to candidate AO353_24495 AO353_24495 malate permease
Query= SwissProt::O05256 (448 letters) >FitnessBrowser__pseudo3_N2E3:AO353_24495 Length = 447 Score = 527 bits (1357), Expect = e-154 Identities = 250/424 (58%), Positives = 332/424 (78%), Gaps = 1/424 (0%) Query: 24 QKIWSWEIGVIPLPLYTVLAVIIILAAYYNELPANMLGGFAIIMILGVFLGDIGQRIPIL 83 + + +EIGVIPLP++ +AVI+ L+A+ LP NM+GG A+IM +G+F G +G R+PIL Sbjct: 23 RSLCGYEIGVIPLPIFLGIAVIVYLSAHLGFLPNNMIGGLAVIMTMGMFFGQLGSRLPIL 82 Query: 84 KDIGGPAILSLFVPSFLVFYNVLNSTSLDAVTNLMKTSNFLYFYIACLVVGSILGMNRIV 143 K+IGG AIL L +PS LVFY ++DA LMK +NFLYF IA LVVGSILGM+R + Sbjct: 83 KEIGGGAILCLMLPSILVFYGFFGPATIDATKMLMKEANFLYFVIASLVVGSILGMSRFI 142 Query: 144 LIQGFIRMFVPLVAGTIAAVAAGILVGFIFGYSAYDSFFFVVVPIIAGGIGEGILPLSIA 203 LIQG +RMF+PL+ GT+AAVA+G++VG + GYS Y +FFF++VPII GGIGEGILPLS+A Sbjct: 143 LIQGMMRMFIPLLVGTLAAVASGLIVGKLVGYSFYHTFFFIIVPIIGGGIGEGILPLSLA 202 Query: 204 YSQILGSSADVFVSQLVPAAIIGNVFAIICAALMKKLGDKRPDLNGNGRLVKSKKANEIF 263 YS ILG + D++V++LVPAA++GN+ AIICA + +L KRP LNG G L+++K N+ F Sbjct: 203 YSAILGGTPDIYVAKLVPAAVVGNIAAIICAGYLARLALKRPHLNGEGSLIRAKDENDKF 262 Query: 264 NQKEAE-AKIDFKLMGAGVLLACTFFIFGGLLEKFIFIPGAILMIISAAAVKYANILPKK 322 +E + IDF+++GAG+L+ C FF+ GGLLEK + +PG +LMI++A KY +LP+K Sbjct: 263 QAREDNGSTIDFRVIGAGILVICAFFVLGGLLEKILGVPGPVLMILAAVLFKYIRVLPEK 322 Query: 323 MEEGAYQLYKFISSSFTWPLMVGLGILFIPLDDVASVISIPFVIICISVVIAMIGSGYFV 382 +E+G YK ISS+F WP+M+GLG+L++PLD V V SI +V++C+SVV +M +G+F+ Sbjct: 323 LEKGTNAFYKLISSAFIWPVMIGLGMLYVPLDSVVKVFSISYVLVCVSVVASMAIAGFFI 382 Query: 383 GKLMNMYPVESAIVTCCHSGLGGTGDVAILSASGRMGLMPFAQISTRLGGAGTVICATVL 442 G LM MYP+ESAIVTCCHSGLGGTGDVAILSAS RM LMPFAQISTRLGGA TVI A++L Sbjct: 383 GNLMKMYPIESAIVTCCHSGLGGTGDVAILSASNRMSLMPFAQISTRLGGASTVIIASIL 442 Query: 443 LRFF 446 LR F Sbjct: 443 LRIF 446 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: 875 Number of extensions: 47 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: 447 Length adjustment: 33 Effective length of query: 415 Effective length of database: 414 Effective search space: 171810 Effective search space used: 171810 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