Align Fructose import permease protein FrcC (characterized)
to candidate N515DRAFT_2415 N515DRAFT_2415 simple sugar transport system permease protein
Query= SwissProt::Q9F9B1 (360 letters) >FitnessBrowser__Dyella79:N515DRAFT_2415 Length = 337 Score = 135 bits (340), Expect = 2e-36 Identities = 98/320 (30%), Positives = 159/320 (49%), Gaps = 20/320 (6%) Query: 48 AAVPLIVLVLSLIAF----GVILGGKFFSAFTMTLILQQVAIVGIVGAAQTLVILTAGID 103 A VPL+V ++ +A GV+ G + L++ A + IV T VIL GID Sbjct: 23 AQVPLLVTLVLFVAMAGAGGVLYHGFLTPQVFLNLLIDN-AFLCIVAVGMTFVILAGGID 81 Query: 104 LSVGAIMVLSSVIMGQFTFRYGFPPALSVICGLGVGALCGYINGTLVARMKLPPFIVTLG 163 LSVGA++ S+V++ + R+G+PP ++ L VG G G L+ R +L PF+VTL Sbjct: 82 LSVGAVVAFSTVLLAELVQRHGWPPLAAIALVLAVGTGFGAGMGVLIQRFRLQPFVVTLA 141 Query: 164 MWQIVLASNFLYSANETIRAQDISANASILQFFGQNFRI---GNAVFTYGVVVMVLLVCL 220 + L S + Q A+ + N R+ G ++ + G +V + +V Sbjct: 142 GMFLARGVATLISVDSIDIDQPWLASVA-------NLRLPLGGGSMLSVGALVALAVVAA 194 Query: 221 LWYVLNRTAWGRYVYAVGDDPEAAKLAGVNVTRMLISIYTLSGLICALAG--WALIGRIG 278 + +++GR VYA+G +A+L G+ V ++ +Y LSG ALAG + L G Sbjct: 195 GALLAGASSFGRTVYAIGGSESSARLMGLPVDATVVRVYALSGFCAALAGVVYTLYMLSG 254 Query: 279 SVSPTAGQFANIESITAVVIGGISLFGGRGSIMGMLFGALIVGVFSLGLRLMG-TDPQWT 337 G +++I AVVIGG L GG G ++G L G L++G+ + G WT Sbjct: 255 YSQHALG--LELDAIAAVVIGGTVLAGGSGYVLGTLLGVLVLGLIQTLIVFDGELSSWWT 312 Query: 338 YLLIGLLIIIAVAIDQWIRK 357 ++IG L++ + + R+ Sbjct: 313 RIVIGALLLAFCLLQRLFRR 332 Lambda K H 0.327 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: 372 Number of extensions: 25 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: 360 Length of database: 337 Length adjustment: 29 Effective length of query: 331 Effective length of database: 308 Effective search space: 101948 Effective search space used: 101948 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: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. 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