Align D-cellobiose transporter (MFS superfamily) (characterized)
to candidate 1937170 b3876 predited transporter (NCBI)
Query= reanno::SB2B:6937231 (444 letters) >FitnessBrowser__Keio:1937170 Length = 467 Score = 210 bits (534), Expect = 9e-59 Identities = 142/446 (31%), Positives = 226/446 (50%), Gaps = 12/446 (2%) Query: 2 LSVREKIAYGLGDTASNIVFQTVMLFLTFFYTDIFGISAAYVGTMFLAVRIMDAVTDPLM 61 L++REKIAYG+GD SN++ L+L FYTD G+ A Y G +FL + A TD L Sbjct: 11 LNLREKIAYGMGDVGSNLMLCIGTLYLLKFYTDELGMPAYYGGIIFLVAKFFTAFTDMLT 70 Query: 62 GYLADRTNTRW--GRYRPYLLWFAFPFAAISVLAFTTPDLSESGKEWYAFATYALLMLAY 119 G+L D G++RP++L+ A P A I+ L F K A A + + L+Y Sbjct: 71 GFLLDSRKNIGPKGKFRPFILYAAVPAALIATLQFIATTFCLPVKTTIATALFMMFGLSY 130 Query: 120 TAINIPYCALGAALTTNPAERVSVQSYRFVFAMLGGVMVSALTLPLVDFFGQGDKAKGYQ 179 + +N Y A+ A+T NP ER + +YR A +G ++ + +PL F D GY Sbjct: 131 SLMNCSYGAMIPAITKNPNERAQLAAYRQGGATIGLLICTVAFIPLQSLFS--DSTVGYA 188 Query: 180 LTILAMSIVGTVMFLLCFIGTKER--DFSSDDNSGNFKAASKALWANDQWRVLSAAAIFL 237 L SI G + +LC+ G KE D + + + + A++ N VL A + Sbjct: 189 CAALMFSIGGFIFMMLCYRGVKEHYVDTTPTGHKASILKSFCAIFRNPPLLVLCIANLCT 248 Query: 238 LTGLVLKSTLAIYYVKYFLGREDMISV--FVTSGVVGNIFGVALAKKLADKMCKVKAYIR 295 L +K + +YY +Y L +++S F + G + + GV L K + Y+ Sbjct: 249 LAAFNIKLAIQVYYTQYVLNDINLLSWMGFFSMGCI--LIGVLLVPLTVKCFGKKQVYLA 306 Query: 296 LQLIAAALCMAAWFVPADQYVLALVFYIAWNFTINMGTPLLWAKMADTVDYGQFKTGVRT 355 ++ A + +F ++ + + +A+ T + + L WA + DTVDYG++KTG+R Sbjct: 307 GMVLWAVGDILNYFWGSNSFTFVMFSCVAFFGTAFVNS-LNWALVPDTVDYGEWKTGIRA 365 Query: 356 TGLVYSSVIFFIKLGLAIGGALGGWLLAAYGYQPDVAQTEETRAGILLCFTLYP-ALASI 414 G VY+ FF K+ A+ G L G +L GY P++AQ++ T G+ ++P ALA I Sbjct: 366 EGSVYTGYTFFRKISAALAGFLPGIMLTQIGYVPNIAQSDATLQGLRQLIFIWPCALAII 425 Query: 415 AVAFVMRHYTLDSQRVAEISVSLQQK 440 A + YTL+ +R A I + Q+ Sbjct: 426 AALTMGFFYTLNEKRFALIIEEINQR 451 Lambda K H 0.327 0.139 0.421 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: 23 Number of successful extensions: 5 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: 444 Length of database: 467 Length adjustment: 33 Effective length of query: 411 Effective length of database: 434 Effective search space: 178374 Effective search space used: 178374 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