Align Glucose/galactose porter (characterized)
to candidate Ga0059261_0767 Ga0059261_0767 glucose/galactose transporter
Query= TCDB::P0C105 (412 letters) >FitnessBrowser__Korea:Ga0059261_0767 Length = 434 Score = 376 bits (965), Expect = e-109 Identities = 202/389 (51%), Positives = 258/389 (66%), Gaps = 13/389 (3%) Query: 31 LFFMWGFITCLNDILIPHLKNVFQLNYTQSMLIQFCFFGAYFIVSLPAGQLVKRISYKRG 90 LFF++G IT LND++IP LK +F LNYTQ+ML+QFCFF AY ++ +P +LVK++ Y RG Sbjct: 33 LFFIFGGITSLNDVIIPKLKELFTLNYTQAMLVQFCFFTAYLVIGIPGAKLVKKLGYMRG 92 Query: 91 IVVGLIVAAIGCALFIPAASYRVYALFLGALFVLASGVTILQVAANPYVTILGKPETAAS 150 V GL+ +GC LFIPA+ Y Y +FL ALFVLASGV I+QV ANP +++LGKPETA S Sbjct: 93 AVAGLLTMMVGCLLFIPASQYATYGVFLFALFVLASGVVIVQVVANPLISLLGKPETAHS 152 Query: 151 RLTLTQAFNSLGTTVAPVFGAVLILSAATDATVN------------AEADAVRFPYLLLA 198 RLT QAFNSLGTTV P+ G++LIL + T + AE+ A+ YL +A Sbjct: 153 RLTFAQAFNSLGTTVFPIVGSILILGSLATVTADQLSGPALEAYRVAESKAIMHGYLGIA 212 Query: 199 LAFTVLAIIFAILKPPDVQEDEPALSDKKEGSAWQYRHLVLGAIGIFVYVGAEVSVGSFL 258 A V+A + + + E A + GA+ IF+YVGAEVS+GS + Sbjct: 213 AALAVVAGVVWLFRNRLKGERHQASAGLAGLDLLGRPRFGFGALCIFLYVGAEVSIGSLI 272 Query: 259 VNFLSDPTVAGLSETDAAHHVAYFWGGAMVGRFIGSAAMRYIDDGKALAFNAFVAIILLF 318 VN+L P V GL E A + ++WGGAMVGRFIGS MR I GK LAF A A+ L+ Sbjct: 273 VNYLMQPGVMGLQEQAAGKLIGFYWGGAMVGRFIGSGLMRVISPGKLLAFVAVGAVALIL 332 Query: 319 ITVATTGHIAMWSVLAIGLFNSIMFPTIFSLALHGLGSHTSQGSGILCLAIVGGAIVPLI 378 I+ TTGH+A +S+LAIGL NSIMFPTIFSLA LG + GSGI+ +AI GGA+VPL Sbjct: 333 ISTNTTGHVAGYSLLAIGLMNSIMFPTIFSLASEKLGGRAADGSGIINIAIFGGAVVPLA 392 Query: 379 QGALADAIG-IHLAFLMPIICYAYIAFYG 406 GALADA G + LA ++P ICYA IA +G Sbjct: 393 TGALADATGSLGLALILPAICYAIIAGFG 421 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: 600 Number of extensions: 36 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: 412 Length of database: 434 Length adjustment: 32 Effective length of query: 380 Effective length of database: 402 Effective search space: 152760 Effective search space used: 152760 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