Align alpha-ketoglutarate permease (MHS family) (characterized)
to candidate N515DRAFT_0974 N515DRAFT_0974 MFS transporter, MHS family, proline/betaine transporter
Query= reanno::pseudo5_N2C3_1:AO356_17790 (439 letters) >FitnessBrowser__Dyella79:N515DRAFT_0974 Length = 433 Score = 194 bits (494), Expect = 3e-54 Identities = 125/406 (30%), Positives = 199/406 (49%), Gaps = 14/406 (3%) Query: 27 SIFSGSVGNMVEWYDWYVYAAFSLYFAKVFFPKGDTTAQLLNTAAIFAVGFLMRPIGGWL 86 S+ ++ +VEWYD+ +Y F+ ++VFF G+++ LL T A FA+ + MRP+G + Sbjct: 14 SMAVAALSTVVEWYDFTLYLYFATVLSRVFFGGGESS--LLATLAGFAISYAMRPLGAVV 71 Query: 87 MGLYADRAGRKRALMASVYLMCFGSLIIALSPSYETIGVGAPILLVFARLLQGLSVGGEY 146 G DR GR+R L+ S+ LM L AL PS+ G A LL+ R SVGGEY Sbjct: 72 FGHIGDRIGRRRTLLLSMMLMTLAMLATALLPSHAVAGPAAGALLLLLRCFMAFSVGGEY 131 Query: 147 GTSATYLSEMATKERRGFFSSFQYVTLISGQLIALGVLIVLQQFLTTEQLYAWGWRIPFA 206 YL E A K+RRG +S G L+A+GV + ++T QL +WGWRIPF Sbjct: 132 TGVVAYLLEGARKDRRGLITSLASAASEIGALLAVGVSALTVSAMSTAQLDSWGWRIPFF 191 Query: 207 IGALCAVVALYLRRGMEETESFTKKEKS---KESAM-RTLLRHPKELMTVVGLTMGGTLA 262 +GA A R MEE+ F ++ + +S + L H L ++ G++ Sbjct: 192 VGAALAGCVWIARSTMEESPDFVRQVEQHTVPDSPLGHMLANHRPALFRTFAISALGSIT 251 Query: 263 FYTYTTYMQKYLVNTVGMSISDSTTISAATLFLFMCLQPVIGGLSDKIGRRPILIAFGIL 322 +Y TY+ +L ++ ++ S +S + + P+ G LSD++GRRP+L+ + Sbjct: 252 YYVGITYVPAFLSSSGILAEERSLWLSTLAAVAVILVTPLAGALSDRVGRRPVLVWLAVA 311 Query: 323 GTLFTVPILTTLHTIQTWWGAFFLIMAALIIVSGYTSINAVVKAELFPTEIRALGVGLPY 382 L + + + A I+ A + G +++ A AE FP E R G+ L Sbjct: 312 SVLLPLAMFQLMARAMELNIALGAIVLA-CLAGGVSAVGAPATAEQFPGEGRLSGLALGV 370 Query: 383 ALTVSIFGGTAEYIA-LWFKSIGMETGYYWYVTACIAVSLLVYITM 427 + +IFGG ++A L K G W+ + L+ + + Sbjct: 371 TMATAIFGGLTPFLAELLIKMTG------WHAVPGAMIGLVAIVVL 410 Lambda K H 0.326 0.138 0.416 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: 477 Number of extensions: 21 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: 439 Length of database: 433 Length adjustment: 32 Effective length of query: 407 Effective length of database: 401 Effective search space: 163207 Effective search space used: 163207 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 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