Align L-fucose-proton symporter; 6-deoxy-L-galactose permease; L-fucose permease (characterized)
to candidate BWI76_RS23685 BWI76_RS23685 MFS transporter
Query= SwissProt::P11551 (438 letters) >FitnessBrowser__Koxy:BWI76_RS23685 Length = 444 Score = 298 bits (763), Expect = 2e-85 Identities = 166/407 (40%), Positives = 240/407 (58%), Gaps = 6/407 (1%) Query: 26 IPFALLCSLFFLWAVANNLNDILLPQFQQAFTLTNFQAGLIQSAFYFGYFIIPIPAGILM 85 + F L+C LF LW +A NLNDIL+ QF++ F LT+ Q L+QS F+ GYF + +PA L+ Sbjct: 31 LQFLLVCCLFALWGMAGNLNDILIAQFKKGFDLTDTQTALVQSIFFLGYFFVALPAAALI 90 Query: 86 KKLSYKAGIITGLFLYALGAALFWPAAEIMNYTLFLVGLFIIAAGLGCLETAANPFVTVL 145 K+ SYKA II GL LYALG LF PAA+IM Y FL L +IA GL LET+AN + ++L Sbjct: 91 KRYSYKAAIIIGLCLYALGCFLFVPAAQIMTYGAFLACLGVIACGLSFLETSANTYSSLL 150 Query: 146 GPESSGHFRLNLAQTFNSFGAIIAVVFGQSLIL-SNVPHQSQDVLDKMSPEQLSAYKHSL 204 GP S R+N +Q FNS G I V+ GQ ++ N P S + L M A +H + Sbjct: 151 GPIQSSTQRINFSQIFNSLGVISGVLIGQVMVFGENDP--SHEQLLAMPAAAADAARHQM 208 Query: 205 VLSVQTPYMIIVAIVLLVALLIMLTKFPALQS--DNHSDAKQGSFSASLSRLARIRHWRW 262 V V PY+II ++++++AL+ + KFP+ + S ++L RL I +R Sbjct: 209 VGQVVGPYLIIGSVLVVLALVFVFIKFPSCKGTPSQQQQIPTESMGSTLKRLFAIPRFRL 268 Query: 263 AVLAQFCYVGAQTACWSYLIRYAVEEIPGMTAGFAANYLTGTMVCFFIGRFTGTWLISRF 322 +L+QF YVGAQ WS+ IR+ G + A +L ++V + +G+ TWL++R Sbjct: 269 GILSQFLYVGAQVGVWSFTIRFVQLVQQGTSEHSATYWLLASLVIYAVGKTVATWLMNRL 328 Query: 323 APHKVLAAYALIAMALCLISAFAGGHVGLIALTLCSAFMSIQYPTIFSLGIKNLGQDTKY 382 P +L +AL A L LI+ F+ + + AL L S M+ +PT F L IK +G+DT+ Sbjct: 329 NPALLLGTFALAATVLLLIAVFSSSMLAVYALILVSFCMAPCWPTNFGLVIKGMGKDTQT 388 Query: 383 GSSFIVMTIIGGGIVTPVMGFVSDA-AGNIPTAELIPALCFAVIFIF 428 S +VM+IIGG ++ VMG +SD GN+ A + P LCF + + Sbjct: 389 AGSIVVMSIIGGAVIPLVMGIISDMNGGNMQIAFIAPLLCFVYVAFY 435 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: 481 Number of extensions: 24 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 438 Length of database: 444 Length adjustment: 32 Effective length of query: 406 Effective length of database: 412 Effective search space: 167272 Effective search space used: 167272 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