Example for requesting to return TOPITS results in STRIP format

Threading based on PHD predictions of secondary structure and accessibility

Bold face: keywords "prediction-based threading", and "return topits strip"

Effect: alignments with possible remote homologues (<25% sequence identity) are returned additionally in STRIP format


Threading based on your prediction of secondary structure and accessibility

Bold face: keyword "prediction-based threading"

Effect: alignments with possible remote homologues (<25% sequence identity) are returned

NOTE : only the output specific for this option is given!





TOPITS (threading) results in STRIP format:			
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~			

________________________________________________________________________________

==================================================  MAXHOM-STRIP  =====================================================
 test sequence    : /home/phd/tmp/dev/work/t-retTopits-all-15007.dsspIn
 list name        : /home/phd/ut/topits/mat/x2.list
 last name was    : /data/dssp/1xxa.dssp_!_A
 seq_length       :     24
 alignments       :   38
 sort-mode        : ZSCORE
 weights 1        : NO
 weights 2        : NO
 smin             : -1.00
 smax             :  2.00
 maplow           :  0.00
 maphigh          :  0.00
 epsilon          :  0.00
 gamma            :  0.00
 gap_open         : 2
 gap_elongation   : 0.2
 INDEL in sec-struc of SEQ 1: YES
 INDEL in sec-struc of SEQ 2: NO
 NBEST alignments   :    1
 secondary structure alignment: NO
=================================================== SUMMARY ===========================================================
 IAL    VAL   LEN IDEL NDEL  ZSCORE   %IDEN  STRHOM  LEN2   RMS SIGMA NAME
   1   18.37   24    0    0    1.46    0.21    0.75   180 -1.00 0.000 1ytb_A                                   TATA-BOX BINDING PROTEIN (YTBP) COMPLEXED WITH DNA
   2   17.37   24    1    1    1.28    0.21    0.83   457 -1.00 0.000 2yhx                                     YEAST HEXOKINASE B (E.C.2.7.1.1) COMPLEX WITH
   3   17.28   23    1    1    1.26    0.17    0.96   185 -1.00 0.000 1xnb                                     XYLANASE (ENDO-1,4-BETA-XYLANASE) (E.C.3.2.1.8)
   4   16.67   24    2    1    1.15    0.17    0.79   421 -1.00 0.000 1ysc                                     SERINE CARBOXYPEPTIDASE (CPY, CPD-Y, OR PROTEINASE C)
   5   16.10   23    1    1    1.05    0.13    0.91   122 -1.00 0.000 1whi                                     MOL_ID: 1;
   6   16.02   24    0    0    1.03    0.13    0.83   220 -1.00 0.000 1xxa_A                                   MOL_ID: 1;
   7   15.95   23    0    0    1.02    0.26    0.70    87 -1.00 0.000 1wkt                                     MOL_ID: 1;
   8   15.95   23    4    2    1.02    0.30    0.87   301 -1.00 0.000 1xso_A                                   CU, ZN SUPEROXIDE DISMUTASE (E.C.1.15.1.1)
   9   15.95   23    4    2    1.02    0.30    0.87   301 -1.00 0.000 1xso_A                                   CU, ZN SUPEROXIDE DISMUTASE (E.C.1.15.1.1)
  10   15.92   24    4    1    1.01    0.21    0.75   218 -1.00 0.000 1yal                                     MOL_ID: 1;
  11   15.83   20    0    0    1.00    0.20    1.00   410 -1.00 0.000 1wht_B                                   SERINE CARBOXYPEPTIDASE II (E.C.3.4.16.1) COMPLEXED WITH
  12   15.62   23    0    0    0.96    0.17    0.87    93 -1.00 0.000 1wit                                     MOL_ID: 1;
  13   15.18   24    0    0    0.88    0.13    0.75   220 -1.00 0.000 1xxa_A                                   MOL_ID: 1;
  14   15.18   24    0    0    0.88    0.13    0.75   220 -1.00 0.000 1xxa_A                                   MOL_ID: 1;
  15   14.13   19    4    1    0.69    0.21    0.74   320 -1.00 0.000 1xyz_A                                   MOL_ID: 1;
  16   14.05   24   21    1    0.67    0.21    0.88   410 -1.00 0.000 1wht_B                                   SERINE CARBOXYPEPTIDASE II (E.C.3.4.16.1) COMPLEXED WITH
  17   13.58   19    3    1    0.59    0.32    0.77   345 -1.00 0.000 1xaa                                     MOL_ID: 1;
  18   12.10   23    4    1    0.32    0.35    0.52   386 -1.00 0.000 1xis                                     XYLOSE ISOMERASE (E.C.5.3.1.5) COMPLEX WITH MN*CL2
  19    9.80   23    0    0   -0.10    0.17    0.48   108 -1.00 0.000 1ycc                                     CYTOCHROME C (ISOZYME 1) (REDUCED)
  20    9.65   22    2    1   -0.13    0.18    0.58   343 -1.00 0.000 9wga_A                                   WHEAT GERM AGGLUTININ (ISOLECTIN 2)
  21    8.28   22    2    1   -0.37    0.18    0.54   343 -1.00 0.000 9wga_A                                   WHEAT GERM AGGLUTININ (ISOLECTIN 2)
  22    8.28   23    0    0   -0.37    0.22    0.26   360 -1.00 0.000 1wdc_C                                   MOL_ID: 1;
  23    8.28   23    0    0   -0.37    0.22    0.26   360 -1.00 0.000 1wdc_B                                   MOL_ID: 1;
  24    8.28   23    0    0   -0.37    0.22    0.26   360 -1.00 0.000 1wdc_A                                   MOL_ID: 1;
  25    6.67   24   16    2   -0.67    0.17    0.58   360 -1.00 0.000 1wdc_A                                   MOL_ID: 1;
  26    6.67   24   16    2   -0.67    0.17    0.58   360 -1.00 0.000 1wdc_C                                   MOL_ID: 1;
  27    6.67   24   16    2   -0.67    0.17    0.58   360 -1.00 0.000 1wdc_B                                   MOL_ID: 1;
  28    6.47   19    4    1   -0.70    0.16    0.48    32 -1.00 0.000 1zfd                                     MOL_ID: 1;
  29    4.25    6    0    0   -1.11    0.33    0.33   128 -1.00 0.000 1yrn_A                                   MOL_ID: 1;
  30    4.25    6    0    0   -1.11    0.33    0.33   128 -1.00 0.000 1yrn_B                                   MOL_ID: 1;
  31    4.03    5    0    0   -1.15    0.20    0.60   128 -1.00 0.000 1yrn_A                                   MOL_ID: 1;
  32    4.03    5    0    0   -1.15    0.20    0.60   128 -1.00 0.000 1yrn_B                                   MOL_ID: 1;
  33    3.72    4    0    0   -1.20    0.25    0.75   101 -1.00 0.000 3wrp                                     $TRP APOREPRESSOR
  34    3.10    3    0    0   -1.32    0.33    1.00   360 -1.00 0.000 1wdc_A                                   MOL_ID: 1;
  35    3.10    3    0    0   -1.32    0.33    1.00   360 -1.00 0.000 1wdc_B                                   MOL_ID: 1;
  36    3.10    3    0    0   -1.32    0.33    1.00   360 -1.00 0.000 1wdc_C                                   MOL_ID: 1;
  37    2.52    3    0    0   -1.42    0.00    0.67    37 -1.00 0.000 1wfb_A                                   ANTIFREEZE PROTEIN ISOFORM HPLC6 (-180 DEGREES C)
  38    0.70    1    0    0   -1.75    0.00    1.00   220 -1.00 0.000 1xxa_A                                   MOL_ID: 1;
==================================== ALIGNMENTS ===================================
   1 -  24               ....:....1....:....2....:....3....:....4....:....5
      t-re               KGPAVGIDLGTTYSCVGVFQHGKV
                         LLLEEEEELLLLEEEEEEEELLLE
                         OOOBBBBBBBBBBBBBBBBOOOOB
                         LLLEEEEEELLLEEEEEEELLLLE
                            AV             F  GK
   1. 1ytb_A       18.37 RFAAVIMRIREPKTTALIFASGKM
                         LLLLEEEEELLLLEEEEELLLLEE
                          G    I  G     V     G
   2. 2yhx         17.37 AGSFLAIVMGGGDLEVILIsaGRQ
                         LEEEEEEEELLLEEEEEEEEELLE
                          G        T    VG
   3. 1xnb         17.28 SGGNYSVNwnTGNFVVGKGWTTG
                         LLLEEEEEELLLEEEEEEEELLL
                             V            VF  G
   4. 1ysc         16.67 ITDEVAGEVkkHFTYLRVFNGGHM
                         LLLLEEEEELLLEEEEEELLLLLL
                                        V V   G
   5. 1whi         16.10 QESRLKVADNSGAREVLVIklGG
                         LLLEEEELELLLEEEEEEEELLL
                              G   G             V
   6. 1xxa_A       16.02 AEGILGTIAGDDTIFTTPANGFTV
                         LLLEEEEEELLLEEEEEELLLLLH
                             VGI         G    GK
   7. 1wkt         15.95 WNTCVGIGANVHWMVTGGSTDGK
                         LLLLEELLLLLLEEEELLLLLLL
                            AV    G     V  F  G V
   8. 1xso_A       15.95  VKAVCVLAGsdVKGVVHFeeGAV
                          LEEEEEEELLLLEEEEEEELLLE
                            AV    G     V  F  G V
   9. 1xso_A       15.95  VKAVCVLAGsdVKGVVHFeeGAV
                          LEEEEEEELLLLEEEEEEELLLE
                         K    G  L      VG
  10. 1yal         15.92 KSGVfgTKLDHAVTAVGYGTSDGK
                         LLLEELLLLLEEEEEEEEEEELLE
                                D G   S     Q
  11. 1wht_B       15.83    YITVDEGAGRSLFYLLQEAP
                            EEEEELLLLEEEEEEEELLL
                               I  G T      F
  12. 1wit         15.62 ASRKIKIKAGFTHNLEVDFIGAP
                         LLLEEEELLLELLEEEEEEELLL
                              G   G             V
  13. 1xxa_A       15.18 AEGILGTIAGDDTIFTTPANGFTV
                         HHLEEEEEELLLEEEEEELLLLLH
                              G   G             V
  14. 1xxa_A       15.18 AEGILGTIAGDDTIFTTPANGFTV
                         HHLEEEEEELLLEEEEEELLLLLH
                          G  V      T       Q
  15. 1xyz_A       14.13 IGVIVSF....TEIDIRIPQSEN
                         LLLEEEE....EEEEEEEELLLL
                          G       G T S         V
  16. 1wht_B       14.05 AGLRIWVFSGDttSWYPWYDDQEV
                         LLLEEEEEEELLEEEEEEEELLEE
                           P      GT    V    HG
  17. 1xaa         13.58  LPSASLGRGTP...VFEPVHGS
                          LEEEEEELLLL...EEEELLLL
                          G    IDLG  Y     F  G
  18. 1xis         12.10 AGKLFHIDlgIKYDQDLRFGAGD
                         LLLELLLEELLLLLLLELLLLLL
                             VG  L            G
  19. 1ycc          9.80 GPHKVGPNLHGIFGRHSGQAEGY
                         LLLLLLLLLLLLLLLELLLLLLL
                              G        C    Q G
  20. 9wga_A        9.65 GAGCQGGPCRADIKCGS..QSGGK
                         LLLLLELLLLLLLELEL..LLLLE
                              G        C    Q G
  21. 9wga_A        8.28 GAGCQGGPCRADIKCGS..QSGGK
                         LLLLLELLLLLLLELEH..HHLLE
                          G      LG    C G
  22. 1wdc_C        8.28 DGAVDAFKLGDVCRCLGINPRNE
                         LLLEEHHHHHHHHHHLLLLLLHH
                          G      LG    C G
  23. 1wdc_B        8.28 DGAVDAFKLGDVCRCLGINPRNE
                         LLLEEHHHHHHHHHHLLLLLLHH
                          G      LG    C G
  24. 1wdc_A        8.28 DGAVDAFKLGDVCRCLGINPRNE
                         LLLEEHHHHHHHHHHLLLLLLHH
                               I  G           GK
  25. 1wdc_A        6.67 ETKKLNIemGDNFnkEAPVEGGKF
                         LLLLEEHHLLLLLLHHLLEELLEE
                               I  G           GK
  26. 1wdc_C        6.67 ETKKLNIemGDNFnkEAPVEGGKF
                         LLLLEEHHLLLLLLHHLLEELLEE
                               I  G           GK
  27. 1wdc_B        6.67 ETKKLNIemGDNFnkEAPVEGGKF
                         LLLLEEHHLLLLLLHHLLEELLEE
                           P           C   F
  28. 1zfd          6.47 DRP....YSCDHPGCDKAFVRNH
                         LLL....ELLLLLLLLLLELLLH
                                          VF
  29. 1yrn_A        4.25                  VFRRKQ
                                          HHHHLL
                                          VF
  30. 1yrn_B        4.25                  VFRRKQ
                                          HHHHLL
                          G
  31. 1yrn_A        4.03 SGEPL
                         LLLLL
                          G
  32. 1yrn_B        4.03 SGEPL
                         LLLLL
                                            Q
  33. 3wrp          3.72                    QNDL
                                            LLLL
                         K
  34. 1wdc_A        3.10 KPL
                         LLL
                         K
  35. 1wdc_B        3.10 KPL
                         LLL
                         K
  36. 1wdc_C        3.10 KPL
                         LLL

  37. 1wfb_A        2.52                     TAR
                                             HLL

  38. 1xxa_A        0.70 R
                         L
 14    10     0
//