Align PTS system glucose-specific EIICBA component; EIICBA-Glc; EII-Glc; EIICBA-Glc 1; EC 2.7.1.199 (characterized)
to candidate 5210198 Shew_2641 PTS system, glucose-like IIB subunint (RefSeq)
Query= SwissProt::Q57071 (675 letters) >FitnessBrowser__PV4:5210198 Length = 490 Score = 318 bits (816), Expect = 3e-91 Identities = 181/499 (36%), Positives = 281/499 (56%), Gaps = 33/499 (6%) Query: 3 KKFFGQLQRIGKALMLPVAILPAAGLLLALGNAFQGDALQSLMPFIKAEGFQNVAKMMEG 62 +++F QR+ +AL+LP+AILPAAG+++ L + +PFI A+ +A +M Sbjct: 21 RQWFKFAQRLSQALLLPIAILPAAGVMIGLAT--------NPIPFISAD----LATLMWT 68 Query: 63 AGGIIFDNLAIIFALGVAIGLASGDGVAAIAAFVGFIVLNKTMGMFLGVTPEKAADAATG 122 G ++F + ++FA+ +AIG G+AA +A G+ G+F A Sbjct: 69 VGNLVFSMMPMLFAVTIAIGFCRDQGIAAFSAVFGY-------GVFFSSLSALAKIYHLP 121 Query: 123 FANVLGIPTLQTGVFGGIIIGALAAWCYNKFYNISLPSYLGFFAGKRFVPIMMATCSFIL 182 +LG T+ TG+ GG+++GA I LP+ FF G+R P++M + +L Sbjct: 122 TEMILGQATIDTGIAGGMMVGAFTCLVVKHSERIRLPAVFSFFEGRRSAPLLMLPMAILL 181 Query: 183 AFPMAIIWPSIQGGLNAFSEGLLASNTGLAVFLFGFIKRLLIPFGLHHIFHAPFWFEFGS 242 A+ ++WP + + S + A ++G ++RLLIP GLHHI++APF+ E G Sbjct: 182 AYLFLLLWPLLSNWIEQISNWAVYQEPASAFAVYGMVERLLIPLGLHHIWNAPFYLEMGQ 241 Query: 243 YKNAAGQIIHGDQRIFIEQIRDNVPLTAGKFMQGEFPVMMFGLPAAALAIYQTAKKENKK 302 Y N GD+ + E R + G + + M+GLPAAALAI++ A K + Sbjct: 242 YFN-------GDEWVRGEVARYLAGDPQAGNLAGGYLIKMWGLPAAALAIWRCADKHERN 294 Query: 303 VVAGLMLSGALTSFLTGITEPLEFSFLFVAPLLFFIHAVLDGLSFLILYLLDLHLGYTFS 362 VAG+MLS A +LTG+TEP+EF+F+FVAPLLF +HA++ G+++ + LD+H FS Sbjct: 295 RVAGIMLSAATACWLTGVTEPIEFAFMFVAPLLFILHALMTGIAYAVTISLDIHHSVVFS 354 Query: 363 GGFIDFFLLGILPNKTQWWLVIPVGLVYAAIYYIIFRFLIVKFNFKTPGREDKEVKSSNV 422 G +DF LL +W+L++ G + A IYY++FR I+ FN KTPGR E S Sbjct: 355 HGLVDFSLLLGQSRNVEWFLIL--GPLTAVIYYLVFRGAILAFNLKTPGR--MEAGSGQR 410 Query: 423 AASELPFKVLDAMGGKANIKHLDACITRLRVEVNDKAKVDVQELKDLGASGVLEVGNNMQ 482 A ++ A+GG+ NI L AC+TRLR+ V VD +L LGA GV+ VGN +Q Sbjct: 411 AGL---ISMITALGGQDNINELTACLTRLRISVKHAELVDKAQLNKLGAKGVVLVGNGVQ 467 Query: 483 AIFGPKSDQIKHDMQQIMD 501 ++G K++ I+ +Q+ +D Sbjct: 468 LVYGTKAESIRRLLQRYLD 486 Lambda K H 0.324 0.143 0.421 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: 759 Number of extensions: 40 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: 675 Length of database: 490 Length adjustment: 36 Effective length of query: 639 Effective length of database: 454 Effective search space: 290106 Effective search space used: 290106 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 53 (25.0 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