Align inositol transporter 4 (characterized)
to candidate N515DRAFT_0382 N515DRAFT_0382 MFS transporter, sugar porter (SP) family
Query= CharProtDB::CH_091598 (582 letters) >FitnessBrowser__Dyella79:N515DRAFT_0382 Length = 472 Score = 186 bits (471), Expect = 2e-51 Identities = 122/360 (33%), Positives = 193/360 (53%), Gaps = 29/360 (8%) Query: 24 TPYIMRLALSAGIGGLLFGYDTGVISGALLFIKEDFDEVDKKTWLQSTIVSMAVAGAIVG 83 T ++ +A +A +GG LFG+DT VI+GA+ ++ F L + + AV+ A++G Sbjct: 14 TARVVLIAAAAALGGFLFGFDTAVINGAVDAVRGSFG-------LGAGRIGFAVSCALLG 66 Query: 84 AAVGGW----INDKFGRRMSILIADVLFLIGAIVMAFAPAPWVIIVGRIFVGFGVGMASM 139 +A+G W + D++GR ++ +A VL I A+ W +++ R+ G GVG+AS+ Sbjct: 67 SALGAWYAGPLADRWGRVRTMQVAAVLLAISALGSGLVAGVWDLVLWRLVGGIGVGVASV 126 Query: 140 TSPLYISEASPARIRGALVSTNGLLITGGQFFSYLINLAFVHTPG-----------TWRW 188 +P YI+E SPAR+RG L S L I G F + L + T G WRW Sbjct: 127 IAPTYIAEVSPARVRGRLGSLQQLAIVLGIFAALLSDAWLAGTAGGASQKLWLGLEAWRW 186 Query: 189 MLGVAGVPAIVQFVLMLSLPESPRWLYRKDRIAESRAILERIYPADEVEAEMEALKLSVE 248 M VA VPA++ L+L +PESPR L K R+ E++ +L ++ + A L + Sbjct: 187 MFLVAVVPALIYGSLVLGVPESPRHLVAKGRMDEAKQVLRQVLDLQDEHALQHKLGDIAQ 246 Query: 249 AEKADEAIIGDSFSAKLKGAFGNPVVRRGLAAGITVQVAQQFVGINTVMYYSPSIVQFAG 308 + +++ + G PVV GI + V QQFVGIN + YYS ++ G Sbjct: 247 SLRSEYRPGLRDLRGSMAGLL--PVV----WVGILLSVFQQFVGINVIFYYSSTLWHSVG 300 Query: 309 YASNKTAMALSLITSGLNALGSIVSMMFVDRYGRRKLMIISMFGIIACLIILATVFSQAA 368 + S A ++S++TS +N L ++V++ VDR GR+ L+ I G+ L ++A FSQAA Sbjct: 301 F-SESDAFSISVVTSVVNVLVTLVAIALVDRIGRKPLLAIGSAGMTVTLGLMAWCFSQAA 359 Score = 73.2 bits (178), Expect = 2e-17 Identities = 35/104 (33%), Positives = 63/104 (60%), Gaps = 1/104 (0%) Query: 453 PSKFGFLAIVFLGLYIVVYAPGMGTVPWIVNSEIYPLRYRGLGGGIAAVSNWVSNLIVSE 512 P+ +G +A+V Y+V + G + W++ E++P R R + +AA + WV+N I++ Sbjct: 368 PAPWGMVALVAANAYVVFFGLSWGPMVWVLLGEMFPNRIRAIALAVAAAAQWVANFIITS 427 Query: 513 SFLSLTHALGSSGTFLLFAGFSTIGLFFIWLLVPETKGLQFEEV 556 SF +L+ LG S + ++A F+ + L F+ V ETKG++ EE+ Sbjct: 428 SFPALSE-LGLSFAYGVYAFFALVSLVFVVKAVRETKGMELEEM 470 Lambda K H 0.324 0.139 0.422 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: 653 Number of extensions: 41 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 582 Length of database: 472 Length adjustment: 35 Effective length of query: 547 Effective length of database: 437 Effective search space: 239039 Effective search space used: 239039 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 (21.6 bits) S2: 52 (24.6 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