Align L-fucose-proton symporter; 6-deoxy-L-galactose permease; L-fucose permease (characterized)
to candidate N515DRAFT_1222 N515DRAFT_1222 MFS transporter, FHS family, L-fucose permease
Query= SwissProt::P11551 (438 letters) >FitnessBrowser__Dyella79:N515DRAFT_1222 Length = 422 Score = 379 bits (974), Expect = e-110 Identities = 201/408 (49%), Positives = 266/408 (65%), Gaps = 5/408 (1%) Query: 26 IPFALLCSLFFLWAVANNLNDILLPQFQQAFTLTNFQAGLIQSAFYFGYFIIPIPAGILM 85 +P AL+ SLFFLW VANNLND+L+PQF++AF L +FQAGL+QSAFY GYF++ +PAGI M Sbjct: 14 LPLALIVSLFFLWGVANNLNDVLIPQFKKAFVLNDFQAGLVQSAFYLGYFLVAMPAGIYM 73 Query: 86 KKLSYKAGIITGLFLYALGAALFWPAAEIMNYTLFLVGLFIIAAGLGCLETAANPFVTVL 145 ++ YK+ ++ GL LY LGA LFWPAA+ Y FL LF+IA+GL LET+ANPFVT+L Sbjct: 74 RRFGYKSAVVFGLALYGLGALLFWPAAQQGTYGFFLFALFVIASGLAFLETSANPFVTLL 133 Query: 146 GPESSGHFRLNLAQTFNSFGAIIAVVFGQSLILSNVPHQSQDVLDKMSPEQLSAYKHSLV 205 GP S RLNLAQ FN G+I ++ GQ I S V H + + L +S + +A+ Sbjct: 134 GPRESAARRLNLAQAFNPLGSITGILIGQHFIFSGVEH-TPEQLAALSAAERAAFVAHET 192 Query: 206 LSVQTPYMIIVAIVLLVALLIMLTKFPALQSDNHSDAKQGSFSASLSRLARIRHWRWAVL 265 +VQ PY+ I +VL LLI+LT+FPA+ + + +L+RL R + + Sbjct: 193 AAVQLPYLAIGLVVLAWGLLILLTRFPAVHAVEEGAVPRD--HGALARLLGDRRFLATLA 250 Query: 266 AQFCYVGAQTACWSYLIRYAVEEIPGMTAGFAANYLTGTMVCFFIGRFTGTWLISRFAPH 325 AQF YVGAQ WSYLIRY +PG A AANY+ ++ CF GRF G+ L+ AP Sbjct: 251 AQFFYVGAQVGVWSYLIRYVQATMPGTPAKLAANYMLVSLACFMAGRFAGSALMRYVAPR 310 Query: 326 KVLAAYALIAMALCLISAFAGGHVGLIALTLCSAFMSIQYPTIFSLGIKNLGQD-TKYGS 384 ++LA +A + +AL + + G G AL CS FMS+ YPTIF+LG++ G D K GS Sbjct: 311 RLLALFAAVNVALTVFAVAVPGVAGACALVACSFFMSVMYPTIFALGVEGRGDDERKLGS 370 Query: 385 SFIVMTIIGGGIVTPVMGFVSDAAGNIPTAELIPALCFAVIFIFARFR 432 + +VMTIIGG ++T MG VSDAAG I A L+PA F VI +FAR R Sbjct: 371 ALLVMTIIGGAVLTAAMGAVSDAAG-ISRAMLVPAASFVVILLFARLR 417 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: 453 Number of extensions: 20 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: 438 Length of database: 422 Length adjustment: 32 Effective length of query: 406 Effective length of database: 390 Effective search space: 158340 Effective search space used: 158340 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