Align L-fucose-proton symporter; 6-deoxy-L-galactose permease; L-fucose permease (characterized)
to candidate Ga0059261_2650 Ga0059261_2650 glucose/galactose transporter
Query= SwissProt::P11551 (438 letters) >FitnessBrowser__Korea:Ga0059261_2650 Length = 425 Score = 214 bits (545), Expect = 4e-60 Identities = 139/415 (33%), Positives = 224/415 (53%), Gaps = 10/415 (2%) Query: 23 SYIIPFALLCSLFFLWAVANNLNDILLPQFQQAFTLTNFQAGLIQSAFYFGYFIIPIPAG 82 SY ALL SLFF+W +N+ LLP + F L + LI+S ++ YF+ IP+ Sbjct: 18 SYRRALALLASLFFMWGFITVINNTLLPHLRSVFDLDYTRTTLIESVWFIAYFVASIPSA 77 Query: 83 ILMKKLSYKAGIITGLFLYALGAALFWPAAEIMNYTLFLVGLFIIAAGLGCLETAANPFV 142 L++++ Y+ ++ GL + A G+A AA I +Y + L LF+IA+G+ L+ AANP+V Sbjct: 78 RLIERIGYQRSLVAGLLVMAAGSAGMMLAASIPSYGVTLAMLFVIASGITLLQVAANPYV 137 Query: 143 TVLGPESSGHFRLNLAQTFNSFGAIIAVVFGQSLILSNVPHQSQDVLDKMSPEQLSAYKH 202 V+G + RLNL Q NS G ++A FG LIL + + ++ + A Sbjct: 138 AVVGRPETASSRLNLVQAMNSAGTMLAPAFGAWLILGRSKGGTSEAGTVLTQAERFADAQ 197 Query: 203 SLVLSVQTPYMIIVAIVLLVALLIMLTKFPALQSDNHSDAKQGSFSASLSRLARIRHWRW 262 S++L PY ++ ++++AL+I PA+ + AK+ + S L + R+ + Sbjct: 198 SVIL----PYGLVAVALVMLALVIACFPLPAMGAATRRLAKEERRNHS---LWKHRNLVF 250 Query: 263 AVLAQFCYVGAQTACWSYLIRYAVE-EIPGMTAGFAANYLTGTMVCFFIGRFTGTWLISR 321 V A F Y+ A+ + + + + +I +T A +YLT GRF G+ L+ R Sbjct: 251 GVPAIFIYLIAEIGVANLFVNFVSQPDIANLTHEQAGHYLTFLWGGMMAGRFAGSALMQR 310 Query: 322 FAPHKVLAAYALIAMALCLISAFAGGHVGLIALTLCSAFMSIQYPTIFSLGIKNLGQDTK 381 F VLA +A+ A A+ L++ FA G + AL L F SI +PTIF+LGI+ LG T+ Sbjct: 311 FDAAHVLAVFAIGAFAVMLVATFATGPTAMWALILVGFFHSIMFPTIFTLGIRGLGPLTE 370 Query: 382 YGSSFIVMTIIGGGIVTPVMGFVSDAAGNIPTAELIPALCFAVIFIFARFRSQTA 436 GS ++M I GG +V V G+++D G + + L+ A C + +A + S+TA Sbjct: 371 EGSGLLIMAIAGGALVI-VQGWLADQWG-LQLSFLLTAACEVYVLFYALWGSRTA 423 Lambda K H 0.329 0.140 0.425 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: 424 Number of extensions: 25 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: 438 Length of database: 425 Length adjustment: 32 Effective length of query: 406 Effective length of database: 393 Effective search space: 159558 Effective search space used: 159558 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 (21.8 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