Align Glucose/galactose porter (characterized)
to candidate BWI76_RS23685 BWI76_RS23685 MFS transporter
Query= TCDB::P0C105 (412 letters) >FitnessBrowser__Koxy:BWI76_RS23685 Length = 444 Score = 233 bits (594), Expect = 8e-66 Identities = 134/404 (33%), Positives = 215/404 (53%), Gaps = 34/404 (8%) Query: 31 LFFMWGFITCLNDILIPHLKNVFQLNYTQSMLIQFCFFGAYFIVSLPAGQLVKRISYKRG 90 LF +WG LNDILI K F L TQ+ L+Q FF YF V+LPA L+KR SYK Sbjct: 39 LFALWGMAGNLNDILIAQFKKGFDLTDTQTALVQSIFFLGYFFVALPAAALIKRYSYKAA 98 Query: 91 IVVGLIVAAIGCALFIPAASYRVYALFLGALFVLASGVTILQVAANPYVTILGKPETAAS 150 I++GL + A+GC LF+PAA Y FL L V+A G++ L+ +AN Y ++LG +++ Sbjct: 99 IIIGLCLYALGCFLFVPAAQIMTYGAFLACLGVIACGLSFLETSANTYSSLLGPIQSSTQ 158 Query: 151 RLTLTQAFNSLGTTVAPVFGAVLIL--------------SAATDATVNAEADAVRFPYLL 196 R+ +Q FNSLG + G V++ +AA DA + V PYL+ Sbjct: 159 RINFSQIFNSLGVISGVLIGQVMVFGENDPSHEQLLAMPAAAADAARHQMVGQVVGPYLI 218 Query: 197 LALAFTVLAIIFAILKPPDVQ---EDEPALSDKKEGSAWQYRHLV----LGAIGIFVYVG 249 + VLA++F +K P + + + + GS + + LG + F+YVG Sbjct: 219 IGSVLVVLALVFVFIKFPSCKGTPSQQQQIPTESMGSTLKRLFAIPRFRLGILSQFLYVG 278 Query: 250 AEVSVGSFLVNFLSDPTVAGLSETDAAHHVAYFWGGA-----MVGRFIGSAAMRYIDDGK 304 A+V V SF + F+ L + + H A +W A VG+ + + M ++ Sbjct: 279 AQVGVWSFTIRFVQ------LVQQGTSEHSATYWLLASLVIYAVGKTVATWLMNRLNPAL 332 Query: 305 ALAFNAFVAIILLFITVATTGHIAMWSVLAIGLFNSIMFPTIFSLALHGLGSHTSQGSGI 364 L A A +LL I V ++ +A+++++ + + +PT F L + G+G T I Sbjct: 333 LLGTFALAATVLLLIAVFSSSMLAVYALILVSFCMAPCWPTNFGLVIKGMGKDTQTAGSI 392 Query: 365 LCLAIVGGAIVPLIQGALADAIG--IHLAFLMPIICYAYIAFYG 406 + ++I+GGA++PL+ G ++D G + +AF+ P++C+ Y+AFYG Sbjct: 393 VVMSIIGGAVIPLVMGIISDMNGGNMQIAFIAPLLCFVYVAFYG 436 Lambda K H 0.328 0.141 0.420 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: 563 Number of extensions: 29 Number of successful extensions: 6 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: 412 Length of database: 444 Length adjustment: 32 Effective length of query: 380 Effective length of database: 412 Effective search space: 156560 Effective search space used: 156560 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 (21.7 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