Align Glucose/galactose transporter (characterized, see rationale)
to candidate Ga0059261_3850 Ga0059261_3850 Fucose permease
Query= uniprot:A0KXM0 (423 letters) >FitnessBrowser__Korea:Ga0059261_3850 Length = 423 Score = 255 bits (651), Expect = 2e-72 Identities = 150/400 (37%), Positives = 217/400 (54%), Gaps = 6/400 (1%) Query: 23 RFALVSLTSLFFMWGFITCLNDILIPHLKAVFSLNYTQAMLIQFCFFGAYFLVSIPAGQL 82 R A ++ +LFF WGF+ ND LI ++ VF L++T+A+L FF A+ VS+PA L Sbjct: 9 RAAFAAVAALFFAWGFVCANNDPLIAAVRHVFRLSWTEALLTHIVFFFAFATVSLPAAAL 68 Query: 83 VKRLGYQKGIVTGLVIASIGCGLFYPAASFATYGLFLGALFVLASGITILQVAANPYVNA 142 + R G + I+ L GC + +G+ LG LF+LA+G+ LQVAANP A Sbjct: 69 LARAGATRTILIALGSMLAGCLVIQAVRWVPAFGVVLGGLFLLAAGVATLQVAANPLAAA 128 Query: 143 LGSSETASSRLNLTQAFNALGTTVAPFFGSILILSVAASVSSELAQANAEAEVVKLPYLL 202 LG RL L + N+LG FG+ +L+ + A A A + +L+ Sbjct: 129 LGPPGQRHFRLTLAHSLNSLGMVCGAHFGAQFLLAEVNLTPAMPASRVAGAPTIAHAFLV 188 Query: 203 LAAALAVLAIIFAKLDLPVIREHSQAAAEEVQTHLGKTSALQSMHLVLGAVGIFVYVGAE 262 + LA++ +R + AA G AL+S + GA I +YVGAE Sbjct: 189 IGGLTFGLALLTL-----AVRRTIERAAPAPAPGGGLGDALRSRWAIAGAAAIGLYVGAE 243 Query: 263 VSIGSFLVNFLGEAHIVGMPEEQAAHYIA-YYWGGAMVGRFIGSAVMQKIPAGTVLAFNA 321 VSIGS L+ FL +G+P A Y+A YWGGA+ GRF+GS ++ IPA +LA A Sbjct: 244 VSIGSVLIPFLSSPDTLGLPAAVAGAYVANLYWGGALAGRFLGSWALRFIPAARLLALFA 303 Query: 322 FMAALLVLVAMTTSGSVAMWAILGVGLFNSIMFPTIFSLALRDLGPHTSQGSGILCLAIV 381 AA L L A+ G A W +L +GLFNSI+FPT+F L L G + SG+LC+AI Sbjct: 304 GSAAALCLAALVLPGPAAAWCVLAIGLFNSILFPTVFGLTLERSGVSEAATSGLLCVAIG 363 Query: 382 GGAIVPLLQGVLADNLGIQLAFILPVVCYGFILFYGAKGS 421 GA++P L G +AD G+ F++P++ Y +IL + + + Sbjct: 364 AGAVLPFLVGRIADLAGLGWTFVIPMIGYVYILGFAFRAA 403 Lambda K H 0.326 0.138 0.402 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: 477 Number of extensions: 22 Number of successful extensions: 4 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: 423 Length of database: 423 Length adjustment: 32 Effective length of query: 391 Effective length of database: 391 Effective search space: 152881 Effective search space used: 152881 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