Align L-malate/citrate:H+ symporter (electroneutral) (characterized)
to candidate AO353_24495 AO353_24495 malate permease
Query= TCDB::P94363 (450 letters) >FitnessBrowser__pseudo3_N2E3:AO353_24495 Length = 447 Score = 331 bits (848), Expect = 3e-95 Identities = 161/418 (38%), Positives = 259/418 (61%) Query: 32 KVGIIPLPVYALLFILITVFVMHHDVKSDILTSIAVMAFFGFTFAQIGKSIPIVRSIGGP 91 ++G+IPLP++ + +++ + + ++++ +AV+ G F Q+G +PI++ IGG Sbjct: 29 EIGVIPLPIFLGIAVIVYLSAHLGFLPNNMIGGLAVIMTMGMFFGQLGSRLPILKEIGGG 88 Query: 92 AILATFIPSAVVYYHLLPNDIVKSTTEFTENSNFLYLFIAGIVVGSILGMKRETLVKAFM 151 AIL +PS +V+Y + +T + +NFLY IA +VVGSILGM R L++ M Sbjct: 89 AILCLMLPSILVFYGFFGPATIDATKMLMKEANFLYFVIASLVVGSILGMSRFILIQGMM 148 Query: 152 KIFIPLIVGSVTAAIVGLAVGTLLGLGFQHTLLYIVIPIMAGGVGEGAIPLSIGYSDIMP 211 ++FIPL+VG++ A GL VG L+G F HT +I++PI+ GG+GEG +PLS+ YS I+ Sbjct: 149 RMFIPLLVGTLAAVASGLIVGKLVGYSFYHTFFFIIVPIIGGGIGEGILPLSLAYSAILG 208 Query: 212 ISQGEAFALVLPSIMLGSLCAIILAGLLNRIGKKKPEWTGNGKVDRSEEESPALEESQSG 271 + A ++P+ ++G++ AII AG L R+ K+P G G + R+++E+ + + Sbjct: 209 GTPDIYVAKLVPAAVVGNIAAIICAGYLARLALKRPHLNGEGSLIRAKDENDKFQAREDN 268 Query: 272 QQMFNLSLFASGGILAVSLYLVGMLAHDFFGFPAPVAMLLLAVLIKLFRLVPASIENGAF 331 + + +G ++ + +++G L G P PV M+L AVL K R++P +E G Sbjct: 269 GSTIDFRVIGAGILVICAFFVLGGLLEKILGVPGPVLMILAAVLFKYIRVLPEKLEKGTN 328 Query: 332 GVSRFFSTAVTYPLLFAIGVSMTPWDKLVAAFNLSNIITILSVVVTMMAVGFFTGKWLNM 391 + S+A +P++ +G+ P D +V F++S ++ +SVV +M GFF G + M Sbjct: 329 AFYKLISSAFIWPVMIGLGMLYVPLDSVVKVFSISYVLVCVSVVASMAIAGFFIGNLMKM 388 Query: 392 YPIETAIINACHSGQGGTGDVAILSAAERLELMPFAQVSTRIGGAITVSLTLLLLHQF 449 YPIE+AI+ CHSG GGTGDVAILSA+ R+ LMPFAQ+STR+GGA TV + +LL F Sbjct: 389 YPIESAIVTCCHSGLGGTGDVAILSASNRMSLMPFAQISTRLGGASTVIIASILLRIF 446 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: 601 Number of extensions: 26 Number of successful extensions: 1 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: 447 Length adjustment: 33 Effective length of query: 417 Effective length of database: 414 Effective search space: 172638 Effective search space used: 172638 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