Align D-mannitol and D-mannose transporter (MFS superfamily) (characterized)
to candidate 350805 BT1277 L-fucose permease (NCBI ptt file)
Query= reanno::SB2B:6936374 (413 letters) >FitnessBrowser__Btheta:350805 Length = 438 Score = 191 bits (485), Expect = 4e-53 Identities = 133/418 (31%), Positives = 197/418 (47%), Gaps = 47/418 (11%) Query: 25 FGAMTSLFFIWGFITALNDILIPHLKGIFDLSYTQAMLVQFCFFGAYFLVSPLAGVLIAR 84 F +TS F +WGF + + ++ IF +S T LVQ F+G YF ++ A + I + Sbjct: 20 FILITSCFALWGFANDITNPMVKAFSKIFRMSATDGALVQVAFYGGYFAMAFPAAMFIRK 79 Query: 85 IGYLRGIIFGLSTMATGCLLFYPASSLEQYALFLLALFVLASGITILQVSANPFVARLGP 144 Y G++ GL A G LF+PA +Y FL+A F+L G++ L+ S NP++ +G Sbjct: 80 FSYKAGVLLGLGLYAFGAFLFFPAKMTGEYYPFLIAYFILTCGLSFLETSCNPYILSMGT 139 Query: 145 ERTAASRLNLAQALNSLGHTLGPLFGSLLIFGA--AAGTHEAVQL--------------- 187 E TA RLNLAQ+ N +G LG I GT E L Sbjct: 140 EETATRRLNLAQSFNPMGSLLGMYVAMQFIQAKLHPMGTDERALLNDSEFQAIKESDLAV 199 Query: 188 ---PYLLLAAVIGIIAVGFIFLGGKVKHADMGVDHRHK-------GSLLSHKRLLLGALA 237 PYL +IG++ + + L VK G D HK + + R G +A Sbjct: 200 LIAPYL----IIGLVILAMLLLIRFVKMPKNG-DQNHKIDFFPTLKRIFTQTRYREGVIA 254 Query: 238 IFLYVGAEVSIGSFLVNY----FAEPSIGGLDEKSAAELVSWYWGGAM----IGRFAGAA 289 F YVG ++ +F++ Y F P G+DEKSA L Y AM I RF Sbjct: 255 QFFYVGVQIMCWTFIIQYGTRLFMSPEY-GMDEKSAEVLSQQYNIVAMVIFCISRFICTF 313 Query: 290 LTRRFNPAMVLAANAVFANLLLMLTIVSSGELALVAVLAVGFFNSIMFPTIFTLAIEGLG 349 + R N +L A+F + + TI L ++AV S+MFPTI+ +A++G+G Sbjct: 314 ILRYLNAGKLLMILAIFGGIFTLGTIFLQNIFGLYCLVAVSACMSLMFPTIYGIALKGMG 373 Query: 350 ELTSRGSGLLCQAIVGGALLPVIQGVVAD------NVGVQLSFIVPTFCYFYICWYAF 401 + G+ L AI+GG++LP +Q + D V +SFI+P C+ I Y + Sbjct: 374 DDAKFGAAGLIMAILGGSVLPPLQASIIDMKEIASMPAVNVSFILPLTCFLVIIGYGY 431 Lambda K H 0.329 0.142 0.425 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: 457 Number of extensions: 28 Number of successful extensions: 4 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: 413 Length of database: 438 Length adjustment: 32 Effective length of query: 381 Effective length of database: 406 Effective search space: 154686 Effective search space used: 154686 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