Align PTS system glucose-specific EIICBA component; EIICBA-Glc; EII-Glc; EIICBA-Glc 1; EC 2.7.1.199 (characterized)
to candidate GFF4494 PS417_23000 PTS N-acetyl-D-glucosamine transporter
Query= SwissProt::Q57071 (675 letters) >FitnessBrowser__WCS417:GFF4494 Length = 568 Score = 373 bits (957), Expect = e-107 Identities = 227/540 (42%), Positives = 315/540 (58%), Gaps = 58/540 (10%) Query: 1 MWKKFFGQLQRIGKALMLPVAILPAAGLLLALGNAFQGDALQSLMPFIKAEGFQNVAKMM 60 M++ F LQR+G+ALMLP+AILP AGLLL LG+ D L N+A +M Sbjct: 1 MYQHFIEGLQRLGRALMLPIAILPIAGLLLRLGDT---DLL-------------NIA-VM 43 Query: 61 EGAGGIIFDNLAIIFALGVAIGLA-SGDGVAAIAAFVGFIVLNKTMGMFLGVTPEKAADA 119 AG IF NLA+IFA+G+A+G A +G A +A +G++V+ T+ K D Sbjct: 44 HDAGQAIFANLALIFAIGIAVGFARDNNGTAGLAGAIGYLVMVSTL---------KVMDT 94 Query: 120 ATGFANVLGIPTLQTGVFGGIIIGALAAWCYNKFYNISLPSYLGFFAGKRFVPIMMATCS 179 + + G+ GI G +A YN+F +I LP YL FF G+RFVPI+ + Sbjct: 95 S-----------INMGMLAGIASGLMAGGLYNRFKDIKLPEYLAFFGGRRFVPIVTGFSA 143 Query: 180 FILAFPMAIIWPSIQGGLNAFSEGLLASNTGLAVFLFGFIKRLLIPFGLHHIFHAPFWFE 239 L +IWP IQ G+N+F L+ S + L F+FG RLLI GLHHI + WF Sbjct: 144 VGLGVIFGLIWPPIQHGINSFGVLLMESGS-LGAFVFGVFNRLLIVTGLHHILNNMAWFV 202 Query: 240 FGSYKN-AAGQIIHGD-QRIFIEQIRDNVPLTAGKFMQGEFPVMMFGLPAAALAIYQTAK 297 FGS+ + G ++ GD R F + G+FM G FPVM+FGLPAA LA+Y+ A Sbjct: 203 FGSFTDPVTGAVVTGDLTRYFAGDPK------GGQFMTGMFPVMLFGLPAACLAMYRNAL 256 Query: 298 KENKKVVAGLMLSGALTSFLTGITEPLEFSFLFVAPLLFFIHAVLDGLSFLILYLLDLHL 357 E +KV+ G+ LS ALTSFLTG+TEP+EF+F+F+AP L+ IHAVL GLS + +L++HL Sbjct: 257 PERRKVMGGIFLSMALTSFLTGVTEPIEFAFMFLAPFLYLIHAVLTGLSMAVTNMLNIHL 316 Query: 358 GYTFSGGFIDFFLLGILPNKTQWWLVIPVGLVYAAIYYIIFRFLIVKFNFKTPGREDKE- 416 G+TFSGGFID +LG T WLV PVGL YA IYY +F + I FN KTPGRED + Sbjct: 317 GFTFSGGFID-MVLG-WGKSTNGWLVFPVGLAYALIYYSVFNYCIRHFNLKTPGREDTQV 374 Query: 417 VKSSNVAASELPFKVLDAMGGKANIKHLDACITRLRVEVNDKAKVDVQELKDLGASGVLE 476 V++ ++ ++ + A+GG N+ + AC TRLR+++ D+ K ELK LGA V+ Sbjct: 375 VQAEAMSDNQRATAYIQALGGAQNLLSVGACTTRLRLDMVDRNKAVDAELKALGAMAVVR 434 Query: 477 VGN--NMQAIFGPKSDQIKHDMQQIMDG------KITSPEETTVTEEGDKETAEIAAAGG 528 GN ++Q + GP +D I +++ M G + +P E V + + A GG Sbjct: 435 PGNGGSLQVVVGPMADSIADEIRLAMPGFVAAAPVVVAPVEKPVAVNVQEAEKWLNALGG 494 Score = 41.2 bits (95), Expect = 1e-07 Identities = 22/73 (30%), Positives = 45/73 (61%), Gaps = 2/73 (2%) Query: 430 KVLDAMGGKANIKHLDA-CITRLRVEVNDKAKVDVQELKDLGASGVLEVGNNM-QAIFGP 487 K L+A+GG+ N++ L+A +TRLRVE+ D + + +L LG GV ++ + + + G Sbjct: 487 KWLNALGGRGNVRQLEAVAMTRLRVELGDDSGLSEADLTALGCQGVSQLESGVWHLLIGD 546 Query: 488 KSDQIKHDMQQIM 500 K+ + +++++ Sbjct: 547 KATGLGEALERLV 559 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: 979 Number of extensions: 52 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 675 Length of database: 568 Length adjustment: 37 Effective length of query: 638 Effective length of database: 531 Effective search space: 338778 Effective search space used: 338778 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