Align PTS system, fructose subfamily, IIC subunit, component of Fructose Enzyme II complex (IIAFru - IIBFru - IICFru) (based on homology) (characterized)
to candidate 17988 b3949 predicted enzyme IIC component of PTS (NCBI)
Query= TCDB::D2RXA8 (392 letters) >FitnessBrowser__Keio:17988 Length = 359 Score = 243 bits (621), Expect = 5e-69 Identities = 136/351 (38%), Positives = 204/351 (58%), Gaps = 23/351 (6%) Query: 13 LLSVKEDLMTGVSFMIPFVTIGGIFLALAFMVAELPGTAGSTETVFEETGSLAWYLAQIG 72 L + ++ LMTGVS MIPFV GGI LA++ M L G + V + L IG Sbjct: 8 LKNTRQHLMTGVSHMIPFVVSGGILLAVSVM---LYGKGAVPDAVADPNLKK---LFDIG 61 Query: 73 DLGLTIMIPVLGGYIAYAVADKPGLAPGFILSWVIQQEAVIEAAGLVIGFEADGAVAGFL 132 GLT+M+P L YI Y++A++ LAP I +WV + AGF Sbjct: 62 VAGLTLMVPFLAAYIGYSIAERSALAPCAIGAWV-----------------GNSFGAGFF 104 Query: 133 GAIVAGLLAGYVARWMKGWSVPSVVSQMMPILVIPVFTTLLLAPVVILGLGVPIAIVDDA 192 GA++AG++ G V ++K V V+ +MPI +IP+ TL+ A +++ GLG P+ + ++ Sbjct: 105 GALIAGIIGGIVVHYLKKIPVHKVLRSVMPIFIIPIVGTLITAGIMMWGLGEPVGALTNS 164 Query: 193 LTSALEGMQGSNALLLGAILGGMMAVDMGGPINKVAYVFGTVLVADQIFAPMAAVMIGGM 252 LT L+GMQ + ++L I+G M+A DMGGP+NKVAY F + VA ++ +A +G Sbjct: 165 LTQWLQGMQQGSIVMLAVIMGLMLAFDMGGPVNKVAYAFMLICVAQGVYTVVAIAAVGIC 224 Query: 253 VPPLGLALSNFIAPQKYAAEMYENAKAAVPLGLAFITEGAIPYAAADPLRVIPSAVLGSA 312 +PPLG+ L+ I + ++AE E KAA+ +G +TEGAIP+AAADPLRVIPS ++GS Sbjct: 225 IPPLGMGLATLIGRKNFSAEERETGKAALVMGCVGVTEGAIPFAAADPLRVIPSIMVGSV 284 Query: 313 TAGAAALWLGVTMPAPHGGIFVVFLSSSALLFLACIALGTIVTATVATLIK 363 A +G A GG+ V+ + L ++A +A+G +VTA ++K Sbjct: 285 CGAVTAALVGAQCYAGWGGLIVLPVVEGKLGYIAAVAVGAVVTAVCVNVLK 335 Lambda K H 0.322 0.138 0.402 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: 429 Number of extensions: 26 Number of successful extensions: 3 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: 392 Length of database: 359 Length adjustment: 30 Effective length of query: 362 Effective length of database: 329 Effective search space: 119098 Effective search space used: 119098 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 50 (23.9 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