Align Glucose/galactose porter (characterized)
to candidate Ga0059261_3850 Ga0059261_3850 Fucose permease
Query= TCDB::P0C105 (412 letters) >FitnessBrowser__Korea:Ga0059261_3850 Length = 423 Score = 250 bits (638), Expect = 6e-71 Identities = 152/386 (39%), Positives = 212/386 (54%), Gaps = 8/386 (2%) Query: 24 ALTSLTLLFFMWGFITCLNDILIPHLKNVFQLNYTQSMLIQFCFFGAYFIVSLPAGQLVK 83 A ++ LFF WGF+ ND LI +++VF+L++T+++L FF A+ VSLPA L+ Sbjct: 11 AFAAVAALFFAWGFVCANNDPLIAAVRHVFRLSWTEALLTHIVFFFAFATVSLPAAALLA 70 Query: 84 RISYKRGIVVGLIVAAIGCALFIPAASYRVYALFLGALFVLASGVTILQVAANPYVTILG 143 R R I++ L GC + + + LG LF+LA+GV LQVAANP LG Sbjct: 71 RAGATRTILIALGSMLAGCLVIQAVRWVPAFGVVLGGLFLLAAGVATLQVAANPLAAALG 130 Query: 144 KPETAASRLTLTQAFNSLGTTVAPVFGAVLILSA-----ATDATVNAEADAVRFPYLLLA 198 P RLTL + NSLG FGA +L+ A A+ A A + +L++ Sbjct: 131 PPGQRHFRLTLAHSLNSLGMVCGAHFGAQFLLAEVNLTPAMPASRVAGAPTIAHAFLVIG 190 Query: 199 -LAFTVLAIIFAILKPPDVQEDEPALSDKKEGSAWQYRHLVLGAIGIFVYVGAEVSVGSF 257 L F + + A+ + + PA G A + R + GA I +YVGAEVS+GS Sbjct: 191 GLTFGLALLTLAVRRTIERAAPAPAPGGGL-GDALRSRWAIAGAAAIGLYVGAEVSIGSV 249 Query: 258 LVNFLSDPTVAGLSETDAAHHVA-YFWGGAMVGRFIGSAAMRYIDDGKALAFNAFVAIIL 316 L+ FLS P GL A +VA +WGGA+ GRF+GS A+R+I + LA A A L Sbjct: 250 LIPFLSSPDTLGLPAAVAGAYVANLYWGGALAGRFLGSWALRFIPAARLLALFAGSAAAL 309 Query: 317 LFITVATTGHIAMWSVLAIGLFNSIMFPTIFSLALHGLGSHTSQGSGILCLAIVGGAIVP 376 + G A W VLAIGLFNSI+FPT+F L L G + SG+LC+AI GA++P Sbjct: 310 CLAALVLPGPAAAWCVLAIGLFNSILFPTVFGLTLERSGVSEAATSGLLCVAIGAGAVLP 369 Query: 377 LIQGALADAIGIHLAFLMPIICYAYI 402 + G +AD G+ F++P+I Y YI Sbjct: 370 FLVGRIADLAGLGWTFVIPMIGYVYI 395 Lambda K H 0.328 0.141 0.420 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: 543 Number of extensions: 26 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: 412 Length of database: 423 Length adjustment: 32 Effective length of query: 380 Effective length of database: 391 Effective search space: 148580 Effective search space used: 148580 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: 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