Align PTS system, fructose subfamily, IIC subunit, component of Fructose Enzyme II complex (IIAFru - IIBFru - IICFru) (based on homology) (characterized)
to candidate WP_000701472.1 HK29_RS06445 PTS transporter subunit EIIA
Query= TCDB::D2RXA8 (392 letters) >NCBI__GCF_000382825.1:WP_000701472.1 Length = 650 Score = 259 bits (663), Expect = 1e-73 Identities = 149/351 (42%), Positives = 212/351 (60%), Gaps = 16/351 (4%) Query: 20 LMTGVSFMIPFVTIGGIFLALAFMVAELPGTAGSTETVFEETGS---LAWYLAQIGDLGL 76 LM+GVS M+PFV GGI +ALAF++ G G + GS LA +IG Sbjct: 295 LMSGVSQMLPFVIGGGIMIALAFLI---DGAFGVPQDSLGNLGSYHELASMFMKIGGAAF 351 Query: 77 TIMIPVLGGYIAYAVADKPGLAPGFILSWVIQQEAVIEAAGLVIGFEADGAVAG----FL 132 +M+PV GY+AY++A+KPGL GF+ + ++ G EA +AG FL Sbjct: 352 GLMLPVFAGYVAYSIAEKPGLVAGFVAGAIAKEGFAFGKIPYAAGGEATSTLAGVSSGFL 411 Query: 133 GAIVAGLLAGYVARWMKGW-SVPSVVSQMMPILVIPVFTTLLLAPVVILGLGVPIAIVDD 191 GA+V G +AG + +K + VP + IL++P+ T+L V+L + +P+A ++ Sbjct: 412 GALVGGFIAGALVLAIKKYVKVPRSLEGAKSILLLPLLGTILTG-FVMLAVNIPMAAINT 470 Query: 192 ALTSALEGMQGSNALLLGAILGGMMAVDMGGPINKVAYVFGTVLVADQIFA----PMAAV 247 A+ L G+ G +A+LLG +LGGMMAVDMGGP+NK AYVFGT +A + + MAAV Sbjct: 471 AMNDFLGGLGGGSAVLLGIVLGGMMAVDMGGPVNKAAYVFGTGTLAATVSSGGSVAMAAV 530 Query: 248 MIGGMVPPLGLALSNFIAPQKYAAEMYENAKAAVPLGLAFITEGAIPYAAADPLRVIPSA 307 M GGMVPPL + ++ + K+ E + + +GL+FITEGAIP+ AADP R IPS Sbjct: 531 MAGGMVPPLAIFVATLLFKDKFTKEERNSGLTNIIMGLSFITEGAIPFGAADPARAIPSF 590 Query: 308 VLGSATAGAAALWLGVTMPAPHGGIFVVFLSSSALLFLACIALGTIVTATV 358 +LGSA AG G+ + APHGGIFV+ L+S+ALL+L + +G IV+ V Sbjct: 591 ILGSAVAGGLVGLAGIKLMAPHGGIFVIALTSNALLYLVFVLIGAIVSGVV 641 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: 717 Number of extensions: 44 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 392 Length of database: 650 Length adjustment: 34 Effective length of query: 358 Effective length of database: 616 Effective search space: 220528 Effective search space used: 220528 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 24 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