Align PTS system, fructose subfamily, IIC subunit, component of Fructose Enzyme II complex (IIAFru - IIBFru - IICFru) (based on homology) (characterized)
to candidate 14863 b0731 fused 2-O-a-mannosyl-D-glycerate specific PTS enzymes: IIA component/IIB component/IIC component (NCBI)
Query= TCDB::D2RXA8 (392 letters) >FitnessBrowser__Keio:14863 Length = 658 Score = 213 bits (541), Expect = 2e-59 Identities = 129/325 (39%), Positives = 188/325 (57%), Gaps = 25/325 (7%) Query: 16 VKEDLMTGVSFMIPFVTIGGIFLALAFMVAELPGTAGSTETVFEETGSLAWYLAQIGD-- 73 +K+ L++G+SF +P + GG LA+A +++++ G + +F E S W ++G Sbjct: 306 LKQALLSGISFAVPLIVAGGTVLAVAVLLSQIFGL----QDLFNEENSWLWMYRKLGGGL 361 Query: 74 LGLTIMIPVLGGYIAYAVADKPGLAPGFILSWVIQQEAVIEAAGLVIGFEADGAVAGFLG 133 LG+ +M+PVL Y AY++ADKP LAPGF AAGL A+ +GFLG Sbjct: 362 LGI-LMVPVLAAYTAYSLADKPALAPGF-------------AAGLA----ANMIGSGFLG 403 Query: 134 AIVAGLLAGYVARWMKGW-SVPSVVSQMMPILVIPVFTTLLLAPVVILGLGVPIAIVDDA 192 A+V GL+AGY+ RW+K + S + + + PV TL +++ +G P+A ++++ Sbjct: 404 AVVGGLIAGYLMRWVKNHLRLSSKFNGFLTFYLYPVLGTLGAGSLMLFVVGEPVAWINNS 463 Query: 193 LTSALEGMQGSNALLLGAILGGMMAVDMGGPINKVAYVFGTVLVADQIFAPMAAVMIGGM 252 LT+ L G+ GSNALLLGAILG M + D+GGP+NK AY F +A+ ++ P A M Sbjct: 464 LTAWLNGLSGSNALLLGAILGFMCSFDLGGPVNKAAYAFCLGAMANGVYGPYAIFASVKM 523 Query: 253 VPPLGLALSNFIAPQKYAAEMYENAKAAVPLGLAFITEGAIPYAAADPLRVIPSAVLGSA 312 V + S +AP+ + E K+ LGLA ITEGAIP A DPLRVI S VLGS Sbjct: 524 VSAFTVTASTMLAPRLFKEFEIETGKSTWLLGLAGITEGAIPMAIEDPLRVIGSFVLGSM 583 Query: 313 TAGAAALWLGVTMPAPHGGIFVVFL 337 GA + + + P GIF +FL Sbjct: 584 VTGAIVGAMNIGLSTPGAGIFSLFL 608 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: 631 Number of extensions: 30 Number of successful extensions: 5 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: 658 Length adjustment: 34 Effective length of query: 358 Effective length of database: 624 Effective search space: 223392 Effective search space used: 223392 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: 52 (24.6 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