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
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
//