Align L-fucose-proton symporter; 6-deoxy-L-galactose permease; L-fucose permease (characterized)
to candidate AO353_25100 AO353_25100 glucose transporter
Query= SwissProt::P11551 (438 letters) >FitnessBrowser__pseudo3_N2E3:AO353_25100 Length = 425 Score = 197 bits (500), Expect = 7e-55 Identities = 132/401 (32%), Positives = 200/401 (49%), Gaps = 17/401 (4%) Query: 33 SLFFLWAVANNLNDILLPQFQQAFTLTNFQAGLIQSAFYFGYFIIPIPAGILMKKLSYKA 92 SLFF+ +LND+L+P+ + F+L+ +A L+QS+F+F YFI IPAG+L+ ++ Y Sbjct: 28 SLFFILGSITSLNDVLVPKLKHLFSLSYTEAMLVQSSFFFAYFIFAIPAGLLISRIGYMR 87 Query: 93 GIITGLFLYALGAALFWPAAEIMNYTLFLVGLFIIAAGLGCLETAANPFVTVLGPESSGH 152 + GL L A G LF PA + + FL LF++A G+ ++ ANP +++LG ++ Sbjct: 88 AAVLGLLLMAGGCLLFIPATQSALFPAFLGALFVLAIGVTTVQVVANPLLSLLGTAATAP 147 Query: 153 FRLNLAQTFNSFGAIIAVVFGQSLILSNVPHQSQDVLDKMSPEQLSAYKHSLVLSVQTPY 212 RL L FNS G +A G LIL ++ L SP +L+++ + Y Sbjct: 148 SRLTLGHAFNSLGTTVAPYLGAILILGSLNAVDTSAL---SPAELTSFLSQEASVISNTY 204 Query: 213 MIIVAIVLLVALLIMLTKFPALQSDNHSDAKQGSFSASLSRLARIRHWRWAVLAQFCYVG 272 I + +VAL++ L K LQ + + +L + R + + F YVG Sbjct: 205 ASITLFICMVALIVWL-KRNELQPSTRPERLNPLAALNLLKQPR---FALGTASIFLYVG 260 Query: 273 AQTACWS----YLIRYAVEEIPGMTAG-FAANYLTGTMVCFFIGRFTGTWLISRFAPHKV 327 A+ S YL+ +P AG A Y G +V GRF G+ L+ FAP K+ Sbjct: 261 AEVTIGSLITDYLMLPTTLALPAEAAGKHVAFYWGGALV----GRFIGSALMRTFAPGKL 316 Query: 328 LAAYALIAMALCLISAFAGGHVGLIALTLCSAFMSIQYPTIFSLGIKNLGQDTKYGSSFI 387 LA A + L ISA G V +L F SI +PTIF+L LG GS Sbjct: 317 LAFAATAVIVLLTISATTQGVVAGWSLLAVGLFNSIMFPTIFTLATAGLGHRAAEGSGLF 376 Query: 388 VMTIIGGGIVTPVMGFVSDAAGNIPTAELIPALCFAVIFIF 428 I+GG + P+ G+ +D + + A +PA C+A I I+ Sbjct: 377 CCAIVGGAFIPPLTGYAADLS-TLAMALSVPATCYACIAIY 416 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: 423 Number of extensions: 22 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