GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ptsG-crr in Escherichia coli BW25113

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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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