Align D-mannitol and D-mannose transporter (MFS superfamily) (characterized)
to candidate Ga0059261_3850 Ga0059261_3850 Fucose permease
Query= reanno::SB2B:6936374 (413 letters) >FitnessBrowser__Korea:Ga0059261_3850 Length = 423 Score = 236 bits (601), Expect = 1e-66 Identities = 154/397 (38%), Positives = 208/397 (52%), Gaps = 24/397 (6%) Query: 25 FGAMTSLFFIWGFITALNDILIPHLKGIFDLSYTQAMLVQFCFFGAYFLVSPLAGVLIAR 84 F A+ +LFF WGF+ A ND LI ++ +F LS+T+A+L FF A+ VS A L+AR Sbjct: 12 FAAVAALFFAWGFVCANNDPLIAAVRHVFRLSWTEALLTHIVFFFAFATVSLPAAALLAR 71 Query: 85 IGYLRGIIFGLSTMATGCLLFYPASSLEQYALFLLALFVLASGITILQVSANPFVARLGP 144 G R I+ L +M GCL+ + + + L LF+LA+G+ LQV+ANP A LGP Sbjct: 72 AGATRTILIALGSMLAGCLVIQAVRWVPAFGVVLGGLFLLAAGVATLQVAANPLAAALGP 131 Query: 145 ERTAASRLNLAQALNSLGHTLGPLFGSLLIFGAAAGTHEAVQLPYLLLAAVIG--IIAVG 202 RL LA +LNSLG G FG+ + E P + + V G IA Sbjct: 132 PGQRHFRLTLAHSLNSLGMVCGAHFGAQFLLA------EVNLTPAMPASRVAGAPTIAHA 185 Query: 203 FIFLGGKV---------------KHADMGVDHRHKGSLLSHKRLLLGALAIFLYVGAEVS 247 F+ +GG + A G L + + GA AI LYVGAEVS Sbjct: 186 FLVIGGLTFGLALLTLAVRRTIERAAPAPAPGGGLGDALRSRWAIAGAAAIGLYVGAEVS 245 Query: 248 IGSFLVNYFAEPSIGGLDEKSA-AELVSWYWGGAMIGRFAGAALTRRFNPAMVLAANAVF 306 IGS L+ + + P GL A A + + YWGGA+ GRF G+ R A +LA A Sbjct: 246 IGSVLIPFLSSPDTLGLPAAVAGAYVANLYWGGALAGRFLGSWALRFIPAARLLALFAGS 305 Query: 307 ANLLLMLTIVSSGELALVAVLAVGFFNSIMFPTIFTLAIEGLGELTSRGSGLLCQAIVGG 366 A L + +V G A VLA+G FNSI+FPT+F L +E G + SGLLC AI G Sbjct: 306 AAALCLAALVLPGPAAAWCVLAIGLFNSILFPTVFGLTLERSGVSEAATSGLLCVAIGAG 365 Query: 367 ALLPVIQGVVADNVGVQLSFIVPTFCYFYICWYAFFA 403 A+LP + G +AD G+ +F++P Y YI +AF A Sbjct: 366 AVLPFLVGRIADLAGLGWTFVIPMIGYVYILGFAFRA 402 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: 460 Number of extensions: 20 Number of successful extensions: 3 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: 423 Length adjustment: 32 Effective length of query: 381 Effective length of database: 391 Effective search space: 148971 Effective search space used: 148971 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: 50 (23.9 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