Align D-mannitol and D-mannose transporter (MFS superfamily) (characterized)
to candidate BWI76_RS23685 BWI76_RS23685 MFS transporter
Query= reanno::SB2B:6936374 (413 letters) >FitnessBrowser__Koxy:BWI76_RS23685 Length = 444 Score = 226 bits (577), Expect = 8e-64 Identities = 141/414 (34%), Positives = 216/414 (52%), Gaps = 40/414 (9%) Query: 23 LLFGAMTSLFFIWGFITALNDILIPHLKGIFDLSYTQAMLVQFCFFGAYFLVSPLAGVLI 82 L F + LF +WG LNDILI K FDL+ TQ LVQ FF YF V+ A LI Sbjct: 31 LQFLLVCCLFALWGMAGNLNDILIAQFKKGFDLTDTQTALVQSIFFLGYFFVALPAAALI 90 Query: 83 ARIGYLRGIIFGLSTMATGCLLFYPASSLEQYALFLLALFVLASGITILQVSANPFVARL 142 R Y II GL A GC LF PA+ + Y FL L V+A G++ L+ SAN + + L Sbjct: 91 KRYSYKAAIIIGLCLYALGCFLFVPAAQIMTYGAFLACLGVIACGLSFLETSANTYSSLL 150 Query: 143 GPERTAASRLNLAQALNSLGHTLGPLFGSLLIFGAAAGTHE------------------- 183 GP +++ R+N +Q NSLG G L G +++FG +HE Sbjct: 151 GPIQSSTQRINFSQIFNSLGVISGVLIGQVMVFGENDPSHEQLLAMPAAAADAARHQMVG 210 Query: 184 AVQLPYLLLAAVIGIIAVGFIFLG----GKVKHADMGVDHRHKGSLLSH----KRLLLGA 235 V PYL++ +V+ ++A+ F+F+ + GS L R LG Sbjct: 211 QVVGPYLIIGSVLVVLALVFVFIKFPSCKGTPSQQQQIPTESMGSTLKRLFAIPRFRLGI 270 Query: 236 LAIFLYVGAEVSIGSFLVNYFAEPSIGGLDEKSAAELVSWYWGGA-----MIGRFAGAAL 290 L+ FLYVGA+V + SF + + L ++ +E + YW A +G+ L Sbjct: 271 LSQFLYVGAQVGVWSFTIRFVQ------LVQQGTSEHSATYWLLASLVIYAVGKTVATWL 324 Query: 291 TRRFNPAMVLAANAVFANLLLMLTIVSSGELALVAVLAVGFFNSIMFPTIFTLAIEGLGE 350 R NPA++L A+ A +LL++ + SS LA+ A++ V F + +PT F L I+G+G+ Sbjct: 325 MNRLNPALLLGTFALAATVLLLIAVFSSSMLAVYALILVSFCMAPCWPTNFGLVIKGMGK 384 Query: 351 LTSRGSGLLCQAIVGGALLPVIQGVVADNVG--VQLSFIVPTFCYFYICWYAFF 402 T ++ +I+GGA++P++ G+++D G +Q++FI P C+ Y+ +Y F+ Sbjct: 385 DTQTAGSIVVMSIIGGAVIPLVMGIISDMNGGNMQIAFIAPLLCFVYVAFYGFW 438 Lambda K H 0.329 0.142 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: 427 Number of extensions: 15 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: 413 Length of database: 444 Length adjustment: 32 Effective length of query: 381 Effective length of database: 412 Effective search space: 156972 Effective search space used: 156972 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