Align L-malate/citrate:H+ symporter (electroneutral) (characterized)
to candidate GFF3854 Psest_3924 Na+/citrate symporter
Query= TCDB::P94363 (450 letters) >FitnessBrowser__psRCH2:GFF3854 Length = 437 Score = 251 bits (642), Expect = 2e-71 Identities = 142/421 (33%), Positives = 239/421 (56%), Gaps = 17/421 (4%) Query: 36 IPLPVYALLFILITVFVMHHDVKSDILTSIAVMAFFGFTFAQIGKSIPIVRS-IGGPAIL 94 +PLP++A+ +++ ++ + + ++ ++ VM G G +PI+R+ +GG AI+ Sbjct: 27 LPLPLFAIALLVMAAAIVTDTLPTGMIGALLVMMLLGELLGFAGDRLPIIRTYLGGGAIM 86 Query: 95 ATFIPSAVVYYHLLPNDIVKSTTEFTENSNFLYLFIAGIVVGSILGMKRETLVKAFMKIF 154 A F +++VY+ LP + F + FL +IA ++ GSILGM + LVK + Sbjct: 87 ALFGAASMVYFGWLPAAVADDVASFMKGGGFLDFYIAALITGSILGMDAKVLVKVGSRYA 146 Query: 155 IPLIVGSVTAAIVGLAVGTLLGLGFQHTLLYIVIPIMAGGVGEGAIPLSIGYSDIMPISQ 214 +PL+ + AA+ +AVG LLG Q ++ I +PIM GG+G GA+P+S Y ++ Sbjct: 147 LPLLCSVLFAALFAMAVGALLGFSPQDAVVVIAMPIMGGGMGAGAVPMSQIYEQLLGQPA 206 Query: 215 GEAFALVLPSIMLGSLCAIILAGLLNRIGKKKPEWTGNGK----VDRSEEESPALEESQS 270 ++++P++ LG++ AII+AGLLN +G + P TGNG+ VD S++E P Sbjct: 207 SYYISILVPALALGNVFAIIIAGLLNGLGNRYPSLTGNGQMMPGVDVSDKEGP------- 259 Query: 271 GQQMFNLSLFASGGILAVSLYLVGMLAHDFFGFPAPVAMLLLAVLIKLFRLVPASIENGA 330 L G + A+S ++ G + F M++L L+K+ LVP SI + A Sbjct: 260 ----ITLPALGIGLVAALSFFIAGQILGKFVPLHPYALMIVLVALLKVSNLVPESINDAA 315 Query: 331 FGVSRFFSTAVTYPLLFAIGVSMTPWDKLVAAFNLSNIITILSVVVTMMAVGFFTGKWLN 390 RF + T+ LLF IGV+ T +++ A +L+ ++ + +VV G+ + Sbjct: 316 SQWFRFVARNWTFALLFGIGVAFTDLGQVLDAISLTYVLIVFAVVAGAAFGAGLVGRLVG 375 Query: 391 MYPIETAI-INACHSGQGGTGDVAILSAAERLELMPFAQVSTRIGGAITVSLTLLLLHQF 449 YPIE+AI C + GGTGDVA+LSAA R+ LMPFAQ+S+R+GGA+ + ++ +++ F Sbjct: 376 FYPIESAITAGLCMANMGGTGDVAVLSAARRMSLMPFAQISSRLGGALILLISSVVVPLF 435 Query: 450 Y 450 + Sbjct: 436 F 436 Lambda K H 0.326 0.141 0.412 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: 623 Number of extensions: 37 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: 450 Length of database: 437 Length adjustment: 32 Effective length of query: 418 Effective length of database: 405 Effective search space: 169290 Effective search space used: 169290 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 (21.6 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