Align PTS system glucose-specific EIICBA component; EIICBA-Glc; EII-Glc; EIICBA-Glc 1; EC 2.7.1.199 (characterized)
to candidate 14809 b0679 fused N-acetyl glucosamine specific PTS enzyme: IIC, IIB , and IIA components (NCBI)
Query= SwissProt::Q57071 (675 letters) >FitnessBrowser__Keio:14809 Length = 648 Score = 472 bits (1214), Expect = e-137 Identities = 270/662 (40%), Positives = 394/662 (59%), Gaps = 58/662 (8%) Query: 7 GQLQRIGKALMLPVAILPAAGLLLALGNAFQGDALQSLMPFIKAEGFQNVAKMMEGAGGI 66 G QR+G+AL LP+A+LP A LLL G Q D L NVA + + AGG Sbjct: 5 GFFQRLGRALQLPIAVLPVAALLLRFG---QPDLL-------------NVAFIAQ-AGGA 47 Query: 67 IFDNLAIIFALGVAIGLASGD-GVAAIAAFVGFIVLNKTMGMFLGVTPEKAADAATGFAN 125 IFDNLA+IFA+GVA + G AA+A VG+ VL K M + + PE Sbjct: 48 IFDNLALIFAIGVASSWSKDSAGAAALAGAVGYFVLTKAM---VTINPE----------- 93 Query: 126 VLGIPTLQTGVFGGIIIGALAAWCYNKFYNISLPSYLGFFAGKRFVPIMMATCSFILAFP 185 + GV GII G + YN++ +I LP +L FF GKRFVPI +LA Sbjct: 94 ------INMGVLAGIITGLVGGAAYNRWSDIKLPDFLSFFGGKRFVPIATGFFCLVLAAI 147 Query: 186 MAIIWPSIQGGLNAFSEGLLASNTGLAVFLFGFIKRLLIPFGLHHIFHAPFWFEFGSYKN 245 +WP +Q ++A E ++++ L +FGFI RLLIP GLH + + WF+ G + N Sbjct: 148 FGYVWPPVQHAIHAGGEWIVSAGA-LGSGIFGFINRLLIPTGLHQVLNTIAWFQIGEFTN 206 Query: 246 AAGQIIHGDQRIFIEQIRDNVPLTAGKFMQGEFPVMMFGLPAAALAIYQTAKKENKKVVA 305 AAG + HGD F TAG FM G FP+MMFGLP AALA+Y A KE + +V Sbjct: 207 AAGTVFHGDINRFYAGDG-----TAGMFMSGFFPIMMFGLPGAALAMYFAAPKERRPMVG 261 Query: 306 GLMLSGALTSFLTGITEPLEFSFLFVAPLLFFIHAVLDGLSFLILYLLDLHLGYTFSGGF 365 G++LS A+T+FLTG+TEPLEF F+F+APLL+ +HA+L G+S + LL +H G++FS G Sbjct: 262 GMLLSVAVTAFLTGVTEPLEFLFMFLAPLLYLLHALLTGISLFVATLLGIHAGFSFSAGA 321 Query: 366 IDFFLLGILPNKTQ-WWLVIPVGLVYAAIYYIIFRFLIVKFNFKTPGREDKEVK------ 418 ID+ L+ LP +Q W+++ +G+++ AIY+++F +I FN KTPGREDKE + Sbjct: 322 IDYALMYNLPAASQNVWMLLVMGVIFFAIYFVVFSLVIRMFNLKTPGREDKEDEIVTEEA 381 Query: 419 --SSNVAASELPFKVLDAMGGKANIKHLDACITRLRVEVNDKAKVDVQELKDLGASGVLE 476 ++ ++L + A+GG N+K +DACITRLR+ V D A+V+ K LGASGV++ Sbjct: 382 NSNTEEGLTQLATNYIAAVGGTDNLKAIDACITRLRLTVADSARVNDTMCKRLGASGVVK 441 Query: 477 VG-NNMQAIFGPKSDQIKHDMQQIMDGKITSPEETTVTEEGDKETAEIAAAGGGV----V 531 + +Q I G K++ I M++++ + T A+ A V + Sbjct: 442 LNKQTIQVIVGAKAESIGDAMKKVVARGPVAAASAEATPATAAPVAKPQAVPNAVSIAEL 501 Query: 532 YAPIKGEVVDISEVPDKVFSEKMMGDGIAIKPETGEVVAPFDGVVKMVFPTKHAIGLESK 591 +PI G+VV + +VPD+ F+ K +GDG+A+KP VV+P G + +F T HA LE++ Sbjct: 502 VSPITGDVVALDQVPDEAFASKAVGDGVAVKPTDKIVVSPAAGTIVKIFNTNHAFCLETE 561 Query: 592 DGIELLIHFGLETVKLEGKGFDILVKENDNIVLGQPLMKVDLDYIKEHADSTITPIVVTN 651 G E+++H G++TV LEGKGF LV+E + GQP++++DLDY+ +A S I+P+V +N Sbjct: 562 KGAEIVVHMGIDTVALEGKGFKRLVEEGAQVSAGQPILEMDLDYLNANARSMISPVVCSN 621 Query: 652 LN 653 ++ Sbjct: 622 ID 623 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: 1112 Number of extensions: 55 Number of successful extensions: 8 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: 648 Length adjustment: 38 Effective length of query: 637 Effective length of database: 610 Effective search space: 388570 Effective search space used: 388570 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: 54 (25.4 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