Align D-mannitol and D-mannose transporter (MFS superfamily) (characterized)
to candidate 6936095 Sama_0292 glucose/galactose transporter (RefSeq)
Query= reanno::SB2B:6936374 (413 letters) >FitnessBrowser__SB2B:6936095 Length = 389 Score = 520 bits (1340), Expect = e-152 Identities = 266/373 (71%), Positives = 304/373 (81%), Gaps = 1/373 (0%) Query: 28 MTSLFFIWGFITALNDILIPHLKGIFDLSYTQAMLVQFCFFGAYFLVSPLAGVLIARIGY 87 MT+LFFIWGFITALNDILIPHLK F+LSYTQAMLVQFCFFGAYF+VSP AG LI +IGY Sbjct: 1 MTTLFFIWGFITALNDILIPHLKAAFELSYTQAMLVQFCFFGAYFIVSPFAGKLIEKIGY 60 Query: 88 LRGIIFGLSTMATGCLLFYPASSLEQYALFLLALFVLASGITILQVSANPFVARLGPERT 147 +RGI+ GL TMATGCLLFYPA+ + YALFLL LFVLASGITILQVSANP+VA LG ERT Sbjct: 61 IRGIVTGLCTMATGCLLFYPAAEVSVYALFLLGLFVLASGITILQVSANPYVAILGAERT 120 Query: 148 AASRLNLAQALNSLGHTLGPLFGSLLIFGAAAGTHEAVQLPYLLLAAVIGIIAVGFIFLG 207 AASRL+LAQA+NSLGHTL PLFG+ LIFGAA+ H AVQLPYL+LA + + AVGF+FL Sbjct: 121 AASRLSLAQAINSLGHTLAPLFGAALIFGAASNAH-AVQLPYLILAGAVLLTAVGFVFLK 179 Query: 208 GKVKHADMGVDHRHKGSLLSHKRLLLGALAIFLYVGAEVSIGSFLVNYFAEPSIGGLDEK 267 D H S+ HK L+LGALAIFLYVGAEVS+GSFLVNYF+E I L E+ Sbjct: 180 LPTLQTDHETQVSHSDSIWQHKHLVLGALAIFLYVGAEVSVGSFLVNYFSESHIAALSEQ 239 Query: 268 SAAELVSWYWGGAMIGRFAGAALTRRFNPAMVLAANAVFANLLLMLTIVSSGELALVAVL 327 A+ +VS+YWGGAM+GRF G+ALTR P VLA NA+ A LLL+LT+ SSG LA+ +VL Sbjct: 240 EASRMVSYYWGGAMVGRFVGSALTRILQPTYVLATNALMAILLLVLTMNSSGALAMWSVL 299 Query: 328 AVGFFNSIMFPTIFTLAIEGLGELTSRGSGLLCQAIVGGALLPVIQGVVADNVGVQLSFI 387 AVGFFNSIMFPTIFTLAI GLG LTSRGSGLLCQAIVGGA+LP++QGVVAD+ VQ SF+ Sbjct: 300 AVGFFNSIMFPTIFTLAIRGLGPLTSRGSGLLCQAIVGGAILPLLQGVVADSSSVQFSFV 359 Query: 388 VPTFCYFYICWYA 400 +P Y YI WYA Sbjct: 360 IPMVAYLYIGWYA 372 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: 517 Number of extensions: 16 Number of successful extensions: 2 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: 389 Length adjustment: 31 Effective length of query: 382 Effective length of database: 358 Effective search space: 136756 Effective search space used: 136756 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