GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Keio:14809 b0679 fused N-acetyl glucosamine
           specific PTS enzyme: IIC, IIB , and IIA components
           (NCBI)
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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