Align D-mannitol and D-mannose transporter (MFS superfamily) (characterized)
to candidate Ga0059261_2650 Ga0059261_2650 glucose/galactose transporter
Query= reanno::SB2B:6936374 (413 letters) >FitnessBrowser__Korea:Ga0059261_2650 Length = 425 Score = 315 bits (808), Expect = 1e-90 Identities = 177/410 (43%), Positives = 252/410 (61%), Gaps = 24/410 (5%) Query: 14 AAPAQSHQQLLFGAMTSLFFIWGFITALNDILIPHLKGIFDLSYTQAMLVQFCFFGAYFL 73 AAPA + + SLFF+WGFIT +N+ L+PHL+ +FDL YT+ L++ +F AYF+ Sbjct: 12 AAPAPESYRRALALLASLFFMWGFITVINNTLLPHLRSVFDLDYTRTTLIESVWFIAYFV 71 Query: 74 VSPLAGVLIARIGYLRGIIFGLSTMATGCLLFYPASSLEQYALFLLALFVLASGITILQV 133 S + LI RIGY R ++ GL MA G A+S+ Y + L LFV+ASGIT+LQV Sbjct: 72 ASIPSARLIERIGYQRSLVAGLLVMAAGSAGMMLAASIPSYGVTLAMLFVIASGITLLQV 131 Query: 134 SANPFVARLGPERTAASRLNLAQALNSLGHTLGPLFGSLLIFG-AAAGTHEA-------- 184 +ANP+VA +G TA+SRLNL QA+NS G L P FG+ LI G + GT EA Sbjct: 132 AANPYVAVVGRPETASSRLNLVQAMNSAGTMLAPAFGAWLILGRSKGGTSEAGTVLTQAE 191 Query: 185 -------VQLPYLLLAAVIGIIAVGFI-----FLGGKVKHADMGVDHRHKGSLLSHKRLL 232 V LPY L+A + ++A+ +G + + + R SL H+ L+ Sbjct: 192 RFADAQSVILPYGLVAVALVMLALVIACFPLPAMGAATRR--LAKEERRNHSLWKHRNLV 249 Query: 233 LGALAIFLYVGAEVSIGSFLVNYFAEPSIGGLDEKSAAELVSWYWGGAMIGRFAGAALTR 292 G AIF+Y+ AE+ + + VN+ ++P I L + A +++ WGG M GRFAG+AL + Sbjct: 250 FGVPAIFIYLIAEIGVANLFVNFVSQPDIANLTHEQAGHYLTFLWGGMMAGRFAGSALMQ 309 Query: 293 RFNPAMVLAANAVFANLLLMLTIVSSGELALVAVLAVGFFNSIMFPTIFTLAIEGLGELT 352 RF+ A VLA A+ A ++++ ++G A+ A++ VGFF+SIMFPTIFTL I GLG LT Sbjct: 310 RFDAAHVLAVFAIGAFAVMLVATFATGPTAMWALILVGFFHSIMFPTIFTLGIRGLGPLT 369 Query: 353 SRGSGLLCQAIVGGALLPVIQGVVADNVGVQLSFIVPTFCYFYICWYAFF 402 GSGLL AI GGAL+ ++QG +AD G+QLSF++ C Y+ +YA + Sbjct: 370 EEGSGLLIMAIAGGALV-IVQGWLADQWGLQLSFLLTAACEVYVLFYALW 418 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: 443 Number of extensions: 18 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: 425 Length adjustment: 32 Effective length of query: 381 Effective length of database: 393 Effective search space: 149733 Effective search space used: 149733 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