Align D-galacturonate transporter (MFS superfamily) (characterized)
to candidate 17200 b3127 predicted (D)-galactarate transporter (NCBI)
Query= reanno::WCS417:GFF828 (454 letters) >FitnessBrowser__Keio:17200 Length = 444 Score = 582 bits (1500), Expect = e-171 Identities = 270/434 (62%), Positives = 349/434 (80%) Query: 5 KPTHVRYLILLMLFLVTTINYADRATIAIAGSSLQKDLGIDAVTLGYIFSAFGWAYVAGQ 64 K H RYLILL++F+VT +NYADRAT++IAG+ + K+L + AV++GYIFSAFGWAY+ Q Sbjct: 11 KGVHTRYLILLIIFIVTAVNYADRATLSIAGTEVAKELQLSAVSMGYIFSAFGWAYLLMQ 70 Query: 65 IPGGWLLDRFGSKKVYALSIFTWSLFTVLQGYVGEFGVSTAVVALFMLRFMVGLAEAPSF 124 IPGGWLLD+FGSKKVY S+F WSLFT LQG+V F ++ A +++F +RFM+G +EAPSF Sbjct: 71 IPGGWLLDKFGSKKVYTYSLFFWSLFTFLQGFVDMFPLAWAGISMFFMRFMLGFSEAPSF 130 Query: 125 PGNARIVAAWFPTAERGTASAIFNSAQYFATVLFAPLMGWIVYSFGWQHVFIVMGVIGII 184 P NARIVAAWFPT ERGTASAIFNSAQYF+ LF+PL+GW+ +++GW+HVF VMGVIG + Sbjct: 131 PANARIVAAWFPTKERGTASAIFNSAQYFSLALFSPLLGWLTFAWGWEHVFTVMGVIGFV 190 Query: 185 FSLIWLKVIHSPRQHPMINEAEFNHIAANGAMVDMDQDKGKGKKTDGPKWDYIRQLLTNR 244 + +W+K+IH+P HP ++ E I+ NGA+VDMD K GPK YI+QLL+NR Sbjct: 191 LTALWIKLIHNPTDHPRMSAEELKFISENGAVVDMDHKKPGSAAASGPKLHYIKQLLSNR 250 Query: 245 MMLGVYLGQYCINGITYFFLTWFPVYLVQDRGMTILKAGFIASLPAICGFIGGVLGGVIS 304 MMLGV+ GQY IN IT+FFLTWFP+YLVQ++GM+ILK G +AS+PA+CGF GGVLGGV S Sbjct: 251 MMLGVFFGQYFINTITWFFLTWFPIYLVQEKGMSILKVGLVASIPALCGFAGGVLGGVFS 310 Query: 305 DYLLRKGHSLTFARKAPIIGGLLISSSIVACNYVDIEWMVVGFMALAFFGKGVGALGWAV 364 DYL+++G SLT ARK PI+ G+L++S+I+ CNY + +VV MALAFFGKG GALGW V Sbjct: 311 DYLIKRGLSLTLARKLPIVLGMLLASTIILCNYTNNTTLVVMLMALAFFGKGFGALGWPV 370 Query: 365 VSDTSPKQIAGLSGGLFNTFGNLASITTPIVIGYIISTTGSFKWALVFVGANALVAVFSY 424 +SDT+PK+I GL GG+FN FGN+ASI TP+VIGY++S SF ALVFVG +AL+A+ Y Sbjct: 371 ISDTAPKEIVGLCGGVFNVFGNVASIVTPLVIGYLVSELHSFNAALVFVGCSALMAMVCY 430 Query: 425 LVIVGPIKRVVLKE 438 L +VG IKR+ L++ Sbjct: 431 LFVVGDIKRMELQK 444 Lambda K H 0.327 0.142 0.444 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: 787 Number of extensions: 34 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: 454 Length of database: 444 Length adjustment: 33 Effective length of query: 421 Effective length of database: 411 Effective search space: 173031 Effective search space used: 173031 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 (21.7 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