Align D-mannitol and D-mannose transporter (MFS superfamily) (characterized)
to candidate N515DRAFT_0592 N515DRAFT_0592 glucose/galactose transporter
Query= reanno::SB2B:6936374 (413 letters) >FitnessBrowser__Dyella79:N515DRAFT_0592 Length = 430 Score = 181 bits (459), Expect = 4e-50 Identities = 136/398 (34%), Positives = 199/398 (50%), Gaps = 35/398 (8%) Query: 31 LFFIWGFITALNDILIPHLKGIFDLSYTQAMLVQFCFFGAYFLVSPLAGVLIARIGYLRG 90 LFFI+GF+T LN LI +K F L A LV F+ +YF ++ + ++ R G +G Sbjct: 27 LFFIFGFVTWLNGPLITFVKLAFSLDDVNAFLVPMVFYCSYFFLALPSSAVLKRTGMKKG 86 Query: 91 IIFGLSTMATGCLLFYPASSLEQYALFLLALFVLASGITILQVSANPFVARLGPERTAAS 150 + GL MA G +LF S+ Y L LFV+ +G+ +LQ ++NP+++ LGP +AA Sbjct: 87 MALGLFVMAIGAVLFGQFVSMRVYGGALAGLFVIGAGLALLQTASNPYISILGPIDSAAQ 146 Query: 151 RLNLAQALNSLGHTLGP-LFGSLLIFG--------AAAGTHEA-----------VQLPYL 190 R+ N + L P +FG L++ G AA T EA V +PYL Sbjct: 147 RIAFMGICNKVAGALAPFVFGWLVLSGIDTFDQQVKAAPTPEAREALLNTFAAKVHMPYL 206 Query: 191 LLAAVIGIIAVGF-------IFLGGKVKHADMGVDHRHKGSLLSHKRLLLGALAIFLYVG 243 +A ++ ++AV I G A++G KG+LLS L LG L +FLYVG Sbjct: 207 AMAGLLVLLAVWVLRSPLPEIKPSGANSEAEIG---HAKGNLLSFPHLWLGVLCLFLYVG 263 Query: 244 AEVSIGSFLVNYFAEPSIGGLDEKSAAELVSWYWGGAMIGRFAGAALTRR-FNPAMVLAA 302 EV G + Y GL + S+ ++G AG L + + LA Sbjct: 264 VEVMAGDAIGTYGQGL---GLPLDATKHFTSFTLFAMLLGYLAGLVLIPKIISQQSYLAV 320 Query: 303 NAVFANLLLMLTIVSSGELALVAVLAVGFFNSIMFPTIFTLAIEGLGELTSRGSGLLCQA 362 +AV + ++G ++ V A+GF N++M+P IF LAI+GLG T GS LL A Sbjct: 321 SAVLGVAFTVGAWATTGYTSVGFVAALGFANAMMWPAIFPLAIKGLGRWTEAGSALLIMA 380 Query: 363 IVGGALLPVIQGVVADNVGVQLSF-IVPTFCYFYICWY 399 IVGGAL+P + + QL F ++ CY YI +Y Sbjct: 381 IVGGALVPQAFVHLKQHYDFQLVFMLLMVPCYLYILFY 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: 468 Number of extensions: 31 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: 430 Length adjustment: 32 Effective length of query: 381 Effective length of database: 398 Effective search space: 151638 Effective search space used: 151638 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