Align Major myo-inositol transporter, IolT1, of 456 aas (characterized)
to candidate CA265_RS01275 CA265_RS01275 hypothetical protein
Query= TCDB::E1WAV3 (456 letters) >FitnessBrowser__Pedo557:CA265_RS01275 Length = 462 Score = 279 bits (714), Expect = 1e-79 Identities = 156/446 (34%), Positives = 258/446 (57%), Gaps = 21/446 (4%) Query: 1 MGGILFGYDTAVISGAIGSLTSYFHLSPAETGWAVSCVVVGCVIGSFSAGYLSKRFGRKK 60 +GG LFG+D AV+SG I L S + LS A+ G VSC ++GC++G +GYLS + GR+K Sbjct: 19 LGGFLFGFDMAVVSGIIEPLKSQYGLSSAQEGLFVSCALLGCIVGVSFSGYLSDKVGRRK 78 Query: 61 SLMVSALLFTISAVGTSLSYTFTHFVIYRIIGGLAVGLAATVSPMYMSEVSPKNMRGRAL 120 L ++A+LF +SAVG + S + + +R++ G+ VG+A+ VSP+Y+SEV+P RGR + Sbjct: 79 VLFLAAILFLVSAVGFAFSVAYPVLIFFRVLAGMGVGVASNVSPLYISEVAPSQKRGRLV 138 Query: 121 SMQQFAIVFGQILIFYVN----YKIASIAADT------WL-IELGWRYMFAAGIIPCILF 169 Q AI G IL Y++ + A++ A WL +E WR MF G++P F Sbjct: 139 VFYQLAITIG-ILAAYISNLFLQRYATVHAGAGEGILHWLFVENVWRGMFIVGVVPAAAF 197 Query: 170 CILVFLIPESPRWMMMIGREEETLKILTKISNEEHARHLLADIKTSLQNDQLNAHQKLNY 229 C+L+ ++PESPRW++ GR EE L L KI+ E R L IK + + + +++L Sbjct: 198 CLLLLIVPESPRWLVQYGRNEEALNTLIKINGAETGRLELDSIK-EMASQKSGGYKELMR 256 Query: 230 RDGNVRFILILGCMIAMLQQVTGVNVMMYYAPIVLKDVTGSAQEALFQTIWIGVIQLIGS 289 + +L L ++ L Q +G+N +++Y P +LK +ALF + +G ++ + Sbjct: 257 LP--LSKLLALATILTALSQFSGINGVIFYGPTILKSAGIVTSDALFYQVILGSANVLFT 314 Query: 290 IIGAMIMDKMGRLSLMRKGTIGSIIGLLLTSWALYSQATGYFALFGMLFFMIFYALSWGV 349 I +D GR L G++ + L LT + TG+F LF ++ F++F+A S G Sbjct: 315 FIAISKVDTWGRRPLYIIGSLCAAGALALTGFCFLMDITGWFMLFSIILFLLFFAFSLGP 374 Query: 350 GAWVLISEIFPNRMRSQGMSISVGFMWMANFLVSQFFPMINENPYLLSHFHGAFPMWIFA 409 +V+ +EIFP +R +S+ + MW+++++V+ FP++ + + + F +IF+ Sbjct: 375 LKFVISTEIFPTHIRGTALSMCIMTMWVSDWVVNMLFPIMRDGLGIATTF------FIFS 428 Query: 410 ICCIFSYFFICRYLPETKGISLEKME 435 CI S+ + + L ETKG SLE++E Sbjct: 429 FFCILSFLYAKKKLFETKGKSLEEIE 454 Lambda K H 0.329 0.141 0.436 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: 636 Number of extensions: 35 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: 456 Length of database: 462 Length adjustment: 33 Effective length of query: 423 Effective length of database: 429 Effective search space: 181467 Effective search space used: 181467 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 (21.8 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