Align D-mannitol and D-mannose transporter (MFS superfamily) (characterized)
to candidate 5208608 Shew_1119 glucose/galactose transporter (RefSeq)
Query= reanno::SB2B:6936374 (413 letters) >FitnessBrowser__PV4:5208608 Length = 418 Score = 169 bits (427), Expect = 2e-46 Identities = 131/413 (31%), Positives = 204/413 (49%), Gaps = 48/413 (11%) Query: 28 MTSLFFIWGFITALNDILIPHLKGIFDLSYTQAMLVQFCFFGAYFLVSPLAGVLIARIGY 87 + LFFI GF T LN L+P+LK I L+ QA L+ F F+ A + + +I ++GY Sbjct: 4 VAGLFFILGFATWLNGSLMPYLKQILQLTPLQASLILFSFYIAVTFTALPSAWVIRKVGY 63 Query: 88 LRGIIFGLSTMATGCLLFYPASSLEQYALFLLALFVLASGITILQVSANPFVARLGPERT 147 G+ G+ M LLF PA+ + +ALFL A V+ +G T+LQ + NP+V R+GPE + Sbjct: 64 KTGMAMGMGIMMIAGLLFIPAAKTQVFALFLFAQLVMGTGQTLLQTAVNPYVVRIGPEES 123 Query: 148 AASRLNLAQALNSLGHTLGPLFGSLLI---FGAAAGTH----------EAVQLPYLLLAA 194 AA+R+++ LN + PL + LI F G + PYL +A Sbjct: 124 AAARVSVMGILNKGAGVIAPLVFTALILDSFKDRVGVELTQAQIDEMANGLVFPYLGMAI 183 Query: 195 VIGIIAVGFIFLGGKVKHADM----GVDHRHKGS------LLSHKRLLLGALAIFLYVGA 244 IG++A+ VK + + D + +G+ LSH L LG +A+F YV Sbjct: 184 FIGVLAL-------LVKKSPLPELENEDEQEEGTKGHTREALSHPNLALGVVALFFYVAV 236 Query: 245 EV----SIGSFLVNYFAEPSIGGLDEKSAAELVSWYWGGAM-IGRF--------AGAALT 291 EV +IG+F ++ E + G + + +V Y G + I RF A L Sbjct: 237 EVIAGDTIGTFALSLGVE-NYGVMTSYTMICMVIGYSLGILTIPRFISQPKALMISAILG 295 Query: 292 RRFNPAMVLAANAVFANLLLMLTIVSSGEL--ALVAVLAVGFFNSIMFPTIFTLAIEGLG 349 ++ N +A +L L L+ + +G N+I++P ++ LA+ G+G Sbjct: 296 LMLTLGILFGDNESYAIANALLVPFGGAMLPDTLLMIAFLGLANAIVWPAVWPLALSGMG 355 Query: 350 ELTSRGSGLLCQAIVGGALLPVIQGVV--ADNVGVQLSFIVPTFCYFYICWYA 400 +LTS GS LL I GGA P+ G+ A ++G Q ++V CY +I +YA Sbjct: 356 KLTSTGSALLVMGIAGGAFGPLFWGLTSSATSLGQQGGYMVMLPCYLFILFYA 408 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: 453 Number of extensions: 29 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: 418 Length adjustment: 31 Effective length of query: 382 Effective length of database: 387 Effective search space: 147834 Effective search space used: 147834 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