Align Na(+)-malate symporter; Sodium-dependent malate transporter (characterized)
to candidate GFF3854 Psest_3924 Na+/citrate symporter
Query= SwissProt::O05256 (448 letters) >FitnessBrowser__psRCH2:GFF3854 Length = 437 Score = 303 bits (775), Expect = 9e-87 Identities = 160/415 (38%), Positives = 255/415 (61%), Gaps = 8/415 (1%) Query: 34 IPLPLYTVLAVIIILAAYYNELPANMLGGFAIIMILGVFLGDIGQRIPILKD-IGGPAIL 92 +PLPL+ + +++ A + LP M+G ++M+LG LG G R+PI++ +GG AI+ Sbjct: 27 LPLPLFAIALLVMAAAIVTDTLPTGMIGALLVMMLLGELLGFAGDRLPIIRTYLGGGAIM 86 Query: 93 SLFVPSFLVFYNVLNSTSLDAVTNLMKTSNFLYFYIACLVVGSILGMNRIVLIQGFIRMF 152 +LF + +V++ L + D V + MK FL FYIA L+ GSILGM+ VL++ R Sbjct: 87 ALFGAASMVYFGWLPAAVADDVASFMKGGGFLDFYIAALITGSILGMDAKVLVKVGSRYA 146 Query: 153 VPLVAGTIAAVAAGILVGFIFGYSAYDSFFFVVVPIIAGGIGEGILPLSIAYSQILGSSA 212 +PL+ + A + VG + G+S D+ + +PI+ GG+G G +P+S Y Q+LG A Sbjct: 147 LPLLCSVLFAALFAMAVGALLGFSPQDAVVVIAMPIMGGGMGAGAVPMSQIYEQLLGQPA 206 Query: 213 DVFVSQLVPAAIIGNVFAIICAALMKKLGDKRPDLNGNGRLVKSKKANEIFNQKEAEAKI 272 ++S LVPA +GNVFAII A L+ LG++ P L GNG+++ + + E I Sbjct: 207 SYYISILVPALALGNVFAIIIAGLLNGLGNRYPSLTGNGQMMPG------VDVSDKEGPI 260 Query: 273 DFKLMGAGVLLACTFFIFGGLLEKFIFIPGAILMIISAAAVKYANILPKKMEEGAYQLYK 332 +G G++ A +FFI G +L KF+ + LMI+ A +K +N++P+ + + A Q ++ Sbjct: 261 TLPALGIGLVAALSFFIAGQILGKFVPLHPYALMIVLVALLKVSNLVPESINDAASQWFR 320 Query: 333 FISSSFTWPLMVGLGILFIPLDDVASVISIPFVIICISVVIAMIGSGYFVGKLMNMYPVE 392 F++ ++T+ L+ G+G+ F L V IS+ +V+I +VV VG+L+ YP+E Sbjct: 321 FVARNWTFALLFGIGVAFTDLGQVLDAISLTYVLIVFAVVAGAAFGAGLVGRLVGFYPIE 380 Query: 393 SAIVT-CCHSGLGGTGDVAILSASGRMGLMPFAQISTRLGGAGTVICATVLLRFF 446 SAI C + +GGTGDVA+LSA+ RM LMPFAQIS+RLGGA ++ ++V++ F Sbjct: 381 SAITAGLCMANMGGTGDVAVLSAARRMSLMPFAQISSRLGGALILLISSVVVPLF 435 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: 681 Number of extensions: 45 Number of successful extensions: 5 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: 437 Length adjustment: 32 Effective length of query: 416 Effective length of database: 405 Effective search space: 168480 Effective search space used: 168480 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 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