Align D-mannitol and D-mannose transporter (MFS superfamily) (characterized)
to candidate Pf6N2E2_1003 Fucose permease
Query= reanno::SB2B:6936374 (413 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1003 Length = 460 Score = 224 bits (572), Expect = 3e-63 Identities = 135/389 (34%), Positives = 206/389 (52%), Gaps = 9/389 (2%) Query: 19 SHQQLLFGAMTSLFFIWGFITALNDILIPHLKGIFDLSYTQAMLVQFCFFGAYFLVSPLA 78 S +L F +TSLFF+WG L D+L H + +S Q+ LVQ +FGAYF+++ Sbjct: 59 SSTRLAFIFVTSLFFMWGLSHGLLDVLNKHFQDTLHISRGQSGLVQTAYFGAYFIIALPV 118 Query: 79 GVLIARIGYLRGIIFGLSTMATGCLLFYPASSLEQYALFLLALFVLASGITILQVSANPF 138 G+ + R GY GI+ GL+ A G LLF PAS + + FL+ALFVLA G+ L+ +AN + Sbjct: 119 GLFMERFGYKAGILAGLALFAIGALLFIPASMVGTFMPFLVALFVLACGLGCLETAANLY 178 Query: 139 VARLGPERTAASRLNLAQALNSLGHTLGPLFGSLLIFGAA----AGTHEAVQLPYLLLAA 194 A LG + RL AQ+ N LG +GP+ G + F + V + Y LA Sbjct: 179 AAALGDPAKSEQRLTFAQSFNGLGAFIGPVIGGAVFFAPPIEFNGNRVDLVSVTYAALAI 238 Query: 195 VIGIIAVGFIFLG----GKVKHADMGVDHRHKGSLLSHKRLLLGALAIFLYVGAEVSIGS 250 ++ ++ V F + K +D+ + + SL +A F VGA V IG+ Sbjct: 239 IVMLMFVAFARIQLPEIRNEKSSDVLLPSAGEVSLWKKSNFTGALVAQFCNVGAYVGIGA 298 Query: 251 FLVNYFAEPSIGGLDEKSAAELVSWYWGGAMIGRFAGAALTRRFNPAMVLAANAVFANLL 310 F +NY A G+ + A+ L+S M+GRFAG + R +L N++ + +L Sbjct: 299 FFINY-AIDHWQGISAQKASYLLSLGMLAYMVGRFAGTWVMRYVPARSLLILNSLVSMVL 357 Query: 311 LMLTIVSSGELALVAVLAVGFFNSIMFPTIFTLAIEGLGELTSRGSGLLCQAIVGGALLP 370 ++ I +++ AV A+ F S+M+PTIF + I GLG T + L +VGGA +P Sbjct: 358 CIVAIAGFERISIFAVAAIYLFMSVMYPTIFAMGIRGLGTQTKKAGSCLVMTLVGGAFVP 417 Query: 371 VIQGVVADNVGVQLSFIVPTFCYFYICWY 399 ++ G +AD+ G+ +F VP C+ I WY Sbjct: 418 LLMGALADHFGIAAAFYVPLACFAAIAWY 446 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: 469 Number of extensions: 22 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: 460 Length adjustment: 32 Effective length of query: 381 Effective length of database: 428 Effective search space: 163068 Effective search space used: 163068 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