HorA Server Result

References:
H. Cheng, BH. Kim, and N. Grishin (2008). Discrimination between distant homologs and structural analogs: lessons from manually constructed, reliable datasets. J. Mol. Biol. 377(4): 1265-1278 link
BH. Kim, H. Cheng, and N. Grishin (2009). HorA web server to infer homology between proteins using sequence and structural similarity. Nucleic Acids Res. 37(Web Server issue):W532-8 link
Comments and suggestions to: grishin@chop.swmed.edu


Title:
mbp1 (HTH example)
Query:
1bm8 a
Dna-Binding Domain Of Mbp1
Mode:
Database search, accurate
Database:
SCOP1.69 less than 40% identity from ASTRAL
 
Scores:
dali   daliZ   gdtts   tmscore   rmsd   AHM   LBcontactA   LBcontactB   LHM   identity   blosum   compass   pearson  
Searches:
DALI   FAST   TMalign   HHsearch
Multiple sequence alignment
HHsearch hidden markov model

Mouse: rotate:Left; translate:Ctrl+Right; zoom:Middle

Downloads: 
PDB file 
PyMOL

Databases: 
PDB
SCOP
CATH
NCBI


Summary of Hits

Hits are found by three methods: Combined Score, SVM model and HHsearch. Hits are ordered by the combined score (Comb score). The combined scores is a similarity measure from sequence and structural similarities. A higher combined score (Comb score) indicates a higher probablity that the hit is homologous to the query.

top hits.
  
SVM score above .


Click the hit # to scroll down to alignments.   Download tab-delimited summary table.
Hit
#
SCOP Id Pro​tein Name SCOP​ Superfamily SCOP​ Fold SCOP
Class
Comb score SVM score HH prob DALI Z FAST SN TM​score
Domains with score better than the threshold ( Comb score > 2.0 OR SVM score > 0.6 OR HH prob > 0.9 )
1 d1bm8a_ DNA-​binding domain of Mlu1-​box binding protein MBP1 DNA-​binding domain of Mlu1-​box binding protein MBP1 DNA-​binding domain of Mlu1-​box binding protein MBP1 α+β 36.65 -0.164 1.00 24.7 26.7 1.00
2 d1l8ra_ Retinal determination protein Dachshund Putative DNA-​binding domain Putative DNA-​binding domain All α 5.124 -1.038 0.01 5.3 4.6 0.51
3 d1sbxa_ Ski oncogene Putative DNA-​binding domain Putative DNA-​binding domain All α 4.448 -0.588 0.01 4.3 4.4 0.48
4 d1a79a2 Tetrameric tRNA splicing endonuclease,​ N-​terminal domain tRNA-​intron endonuclease N-​terminal domain-​like MutS N-​terminal domain-​like α+β 2.799 -0.112 0.01 3.0 4.0 0.40
5 d1tnsa_ mu transposase,​ DNA-​binding domain Putative DNA-​binding domain Putative DNA-​binding domain All α 2.467 -1.624 0.03 2.3 3.0 0.38
6 d1kafa_ DNA-​binding C-​terminal domain of the transcription factor MotA DNA-​binding C-​terminal domain of the transcription factor MotA DNA-​binding C-​terminal domain of the transcription factor MotA α+β 2.147 -1.135 0.01 3.5 3.7 0.48
SCOP domains with score worse than the threshold
7 d1qpma_ mu transposase,​ DNA-​binding domain Putative DNA-​binding domain Putative DNA-​binding domain All α 1.95 -0.573 0.03 2.2 2.2 0.39
8 d1umwa2 Serine/​threonine-​protein kinase plk C-​terminal domain Polo-​box domain Polo-​box domain α+β 1.95 -1.287 0.01 2.8 2.8 0.37
9 d1r11a3 Dimeric tRNA splicing endonuclease,​ domains 1 and 3 tRNA-​intron endonuclease N-​terminal domain-​like MutS N-​terminal domain-​like α+β 1.86 -1.339 0.00 2.6 3.2 0.37
10 d1jg5a_ GTP cyclohydrolase I feedback regulatory protein,​ GFRP GTP cyclohydrolase I feedback regulatory protein,​ GFRP GTP cyclohydrolase I feedback regulatory protein,​ GFRP α+β 1.77 -1.284 0.01 1.8 2.5 0.41
11 d1jrma_ Hypothetical protein MTH637 YggU-​like YggU-​like α+β 1.71 -0.944 0.01 1.2 1.4 0.41
12 d1d1ra_ YciH eIF1-​like eIF1-​like α+β 1.71 -1.552 0.01 2.1 2.9 0.46
13 d1qjta_ Eps15 EF-​hand EF Hand-​like All α 1.69 -0.944 0.01 1.8 2.8 0.38
14 d1r0va3 Dimeric tRNA splicing endonuclease,​ domains 1 and 3 tRNA-​intron endonuclease N-​terminal domain-​like MutS N-​terminal domain-​like α+β 1.68 -1.022 0.01 1.8 3.1 0.38
15 d1xpaa1 DNA repair factor XPA DNA-​ and RPA-​binding domain,​ C-​terminal subdomain Putative DNA-​binding domain Putative DNA-​binding domain All α 1.63 -1.221 0.01 1.5 2.6 0.37
16 d1h3fa2 Tyrosyl-​tRNA synthetase (TyrRS),​ C-​terminal domain Alpha-​L RNA-​binding motif Alpha-​L RNA-​binding motif α+β 1.61 -0.501 0.02 1.1 1.9 0.37


Alignments and Scores

hit structures.    
residues per line.
   
all residues in one line.


hit structures. 
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1: d1bm8a_ DNA-​binding domain of Mlu1-​box binding protein MBP1 (hh: 1.000)

SCOP Superfamily: DNA-​binding domain of Mlu1-​box binding protein MBP1  |  SCOP Fold: DNA-​binding domain of Mlu1-​box binding protein MBP1  |  SCOP Class: Alpha and beta proteins (a+b)

Consensus: 1.00  Contact: 1144
Modified z-scores:
dali:1.00 daliz:1.00 gdtts:1.00 tmscore:1.00 rmsd:0.10 AHM:0.06 LBcontacta:1.00 LBcontactb:1.00 LHM:0.03
id:1.00 blosum:1.00 compass:1.00 pearson:1.00
Scaled scores:
dali:1.00 daliz:1.00 gdtts:1.00 tmscore:1.00 rmsd:1.00 AHM:1.00 LBcontacta:1.00 LBcontactb:1.00 LHM:1.00
id:1.00 blosum:1.00 compass:1.00 pearson:1.00

hit structure      alignment
DALI alignment (Z-score: 24.7 Raw score:1052.50)
1bm8 a         1 QIYSARYSGVDVYEFIHSTGSIMKRKKDDWVNATHILKAANFAKAKRTRILEKEVLKETH     60
d1bm8a_        1 QIYSARYSGVDVYEFIHSTGSIMKRKKDDWVNATHILKAANFAKAKRTRILEKEVLKETH     60

1bm8 a        61 EKVQGGFGKYQGTWVPLNIAKQLAEKFSVYDQLKPLFDF     99
d1bm8a_       61 EKVQGGFGKYQGTWVPLNIAKQLAEKFSVYDQLKPLFDF     99


hit structure      alignment
FAST alignment (Normalized score: 26.71 Raw score:2645.00)
1bm8 a         1 QIYSARYSGVDVYEFIHSTGSIMKRKKDDWVNATHILKAANFAKAKRTRILEKEVLKETH     60
d1bm8a_        1 QIYSARYSGVDVYEFIHSTGSIMKRKKDDWVNATHILKAANFAKAKRTRILEKEVLKETH     60

1bm8 a        61 EKVQGGFGKYQGTWVPLNIAKQLAEKFSVYDQLKPLFDF     99
d1bm8a_       61 EKVQGGFGKYQGTWVPLNIAKQLAEKFSVYDQLKPLFDF     99


hit structure      alignment
TMalign alignment (TM-score: 1.00 Raw score:99.00)
1bm8 a         1 QIYSARYSGVDVYEFIHSTGSIMKRKKDDWVNATHILKAANFAKAKRTRILEKEVLKETH     60
d1bm8a_        1 QIYSARYSGVDVYEFIHSTGSIMKRKKDDWVNATHILKAANFAKAKRTRILEKEVLKETH     60

1bm8 a        61 EKVQGGFGKYQGTWVPLNIAKQLAEKFSVYDQLKPLFDF     99
d1bm8a_       61 EKVQGGFGKYQGTWVPLNIAKQLAEKFSVYDQLKPLFDF     99


hit structure      alignment
HHsearch alignment (Probability: 1.00 E-value:0.00)
DALI match       ************************************************************
1bm8 a         1 QIYSARYSGVDVYEFIHSTGSIMKRKKDDWVNATHILKAANFAKAKRTRILEKEVLKETH     60
d1bm8a_        1 QIYSARYSGVDVYEFIHSTGSIMKRKKDDWVNATHILKAANFAKAKRTRILEKEVLKETH     60

DALI match       ***************************************
1bm8 a        61 EKVQGGFGKYQGTWVPLNIAKQLAEKFSVYDQLKPLFDF     99
d1bm8a_       61 EKVQGGFGKYQGTWVPLNIAKQLAEKFSVYDQLKPLFDF     99



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2: d1l8ra_ Retinal determination protein Dachshund (cs: 5.124)

SCOP Superfamily: Putative DNA-​binding domain  |  SCOP Fold: Putative DNA-​binding domain  |  SCOP Class: All alpha proteins

Consensus: 0.56  Contact: 536
Modified z-scores:
dali:1.00 daliz:0.99 gdtts:0.98 tmscore:1.00 rmsd:0.35 AHM:0.43 LBcontacta:0.97 LBcontactb:0.98 LHM:0.14
id:0.41 blosum:0.05 compass:0.40 pearson:0.89
Scaled scores:
dali:0.69 daliz:0.40 gdtts:0.51 tmscore:0.51 rmsd:0.73 AHM:0.62 LBcontacta:0.42 LBcontactb:0.71 LHM:0.40
id:-0.04 blosum:0.00 compass:0.08 pearson:0.11

hit structure      alignment
DALI alignment (Z-score: 5.3 Raw score:297.00)
1bm8 a         1 qiysarysgVDVYEFIHstGSIMKRK--KDDWVNATHILKAANFA-kAKRTRILeKEVL-     56
d1l8ra_        1 -----gsqnNECKMVDLrgAKVASFTveGCELICLPQAFDLFLKHlvGGLHTVY-TKLKr     54

1bm8 a        57 -KETHEKVQG--GFGK----------yQGTWVPLNIAKQLAEKFSvydqlkplfdf     99
d1l8ra_       55 lEITPVVCNVeqVRILrglgaiqpgvnRCKLISRKDFETLYNDCT---------na    101


hit structure      alignment
FAST alignment (Normalized score: 4.57 Raw score:457.40)
1bm8 a         1 QIYSARYSG----VDVYEFIHS--TGSIMKRK---KDDWVNATHILKAAN------FAKA     45
d1l8ra_        1 ---------GSQNNECKMVD--LRGAKVASF-TVEGCELICLPQAFDL--FLKHLVGGLH     46

1bm8 a        46 KRTRILEKEVLKETHEKVQGGFGKY------------------QGTWVPLNIAKQLAEKF     87
d1l8ra_       47 TVYTKLKR--LEITPVVCN------VEQVRILRGLGAIQPGVNRCKLISRKDFETLYND-     97

1bm8 a        88 SVYDQLKPLFDF----     99
d1l8ra_       98 ------------CTNA    101


hit structure      alignment
TMalign alignment (TM-score: 0.51 Raw score:50.47)
1bm8 a         1 ---QIYSARYSGVDVYEF--IHSTGSIMKRK--KDDWVNATHILKA-ANF--AKAKRTRI     50
d1l8ra_        1 GSQ-------NNECKMVDLRGA---KVASFTVEGCELICLPQAFDLFLKHLV--GGL-HT     47

1bm8 a        51 LEKEVL--KETHEKVQG--GF--G---KY-----QGTWVPLNIAKQLAEKFS--VYDQLK     94
d1l8ra_       48 VYTKLKRLEITPVVCNVEQVRILRGLGAIQPGVNRCKLISRKDFETLYNDCTNA------    101

1bm8 a        95 PLFDF     99
d1l8ra_      102 -----    102


hit structure      alignment
HHsearch alignment (Probability: 0.01 E-value:0.93)
DALI match                           
1bm8 a         1 QIYSARYSGVDVYEFIHSTG     20
d1l8ra_        6 ECKMVDLRGAKVASFTVEGC     25



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3: d1sbxa_ Ski oncogene (cs: 4.448)

SCOP Superfamily: Putative DNA-​binding domain  |  SCOP Fold: Putative DNA-​binding domain  |  SCOP Class: All alpha proteins

Consensus: 0.55  Contact: 528
Modified z-scores:
dali:1.00 daliz:0.99 gdtts:0.98 tmscore:0.99 rmsd:0.36 AHM:0.43 LBcontacta:0.96 LBcontactb:0.97 LHM:0.13
id:0.90 blosum:0.15 compass:0.31 pearson:0.83
Scaled scores:
dali:0.69 daliz:0.38 gdtts:0.49 tmscore:0.49 rmsd:0.74 AHM:0.61 LBcontacta:0.40 LBcontactb:0.66 LHM:0.43
id:0.05 blosum:0.05 compass:0.07 pearson:0.09

hit structure      alignment
DALI alignment (Z-score: 4.3 Raw score:264.20)
1bm8 a         1 ---qiysarySGVDVYEFihstGSIMKRKK--DDWVNATHILKA-ANFAkaKRTRILeKE     54
d1sbxa_        1 gshmfmpsdrSTERCETV-legETISCFVVggEKRLCLPQILNSvLRDF--SLQQIN-AV     56

1bm8 a        55 VL--KETHEKVQG--GFGK----------yqGTWVPLNIAKQLAEKFSvydqlkplfdf     99
d1sbxa_       57 CDelHIYCSRCTAdqLEILkvmgilpfsapsCGLITKTDAERLCNALL---------yg    106


hit structure      alignment
FAST alignment (Normalized score: 4.44 Raw score:455.00)
1bm8 a         1 QIYSARYSG-----------VDVYEFIHS--TGSIMKRK---KDDWVNATHILKA---AN     41
d1sbxa_        1 ---------GSHMFMPSDRSTERCETV--LEGETISCF-VVGGEKRLCLPQILN-SVLRD     47

1bm8 a        42 FAKAKRTRILEKEVLKETHEKVQGGFGKY---------------------QGTWVPLNIA     80
d1sbxa_       48 FSLQQINAVCDE--LHIYCS---------RCTADQLEILKVMGILPFSAPSCGLITKTDA     96

1bm8 a        81 KQLAEKFSVYDQLKPLFDF----     99
d1sbxa_       97 ERLCNA-------------LLYG    106


hit structure      alignment
TMalign alignment (TM-score: 0.48 Raw score:47.49)
1bm8 a         1 ----------QIYSARYSGVDVYEFIH--STGSIMKRKK--DDWVNATHILKAANFAKAK     46
d1sbxa_        1 GSHMFMPSDR--------STERCETVLEG--ETISCFVVGGEKRLCLPQILNSVLRD-FS     49

1bm8 a        47 RTRILEKEVL--KETHEKVQG--GF--G---KY-----QGTWVPLNIAKQLAEKFSV-YD     91
d1sbxa_       50 L-QQINAVCDELHIYCSRCTADQLEILKVMGILPFSAPSCGLITKTDAERLCNALLYG--    106

1bm8 a        92 QLKPLFDF     99
d1sbxa_      107 --------    107


hit structure      alignment
HHsearch alignment (Probability: 0.01 E-value:0.78)
DALI match                   
1bm8 a         9 GVDVYEFIHSTG     20
d1sbxa_       21 GETISCFVVGGE     32



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4: d1a79a2 Tetrameric tRNA splicing endonuclease,​ N-​terminal domain (cs: 2.799)

SCOP Superfamily: tRNA-​intron endonuclease N-​terminal domain-​like  |  SCOP Fold: MutS N-​terminal domain-​like  |  SCOP Class: Alpha and beta proteins (a+b)

Consensus: 0.64  Contact: 293
Modified z-scores:
dali:0.98 daliz:0.97 gdtts:0.93 tmscore:0.97 rmsd:0.35 AHM:0.38 LBcontacta:0.89 LBcontactb:0.94 LHM:0.16
id:0.85 blosum:0.38 compass:0.66 pearson:0.95
Scaled scores:
dali:0.70 daliz:0.43 gdtts:0.50 tmscore:0.45 rmsd:0.74 AHM:0.63 LBcontacta:0.42 LBcontactb:0.70 LHM:0.37
id:0.06 blosum:0.07 compass:0.14 pearson:0.22

hit structure      alignment
DALI alignment (Z-score: 3.0 Raw score:178.60)
1bm8 a         1 qiysarysgvdvyefihstgsiMKRKkdDWVNathilkaanfakakRTRILEkEVLK-ET     59
d1a79a2        1 ------------------kitgLLDG--DRVI------------vfDKNGIS-KLSArHY     27

1bm8 a        60 HEKVQggfgkyQGTWVPLNIAKQLAEKF-----------sVYDQLKPLFDF--     99
d1a79a2       28 GNVEG------NFLSLSLVEALYLINLGwlevkykdnkplSFEELYEYARNve     74


hit structure      alignment
FAST alignment (Normalized score: 3.95 Raw score:338.20)
1bm8 a         1 QIYSARYSGVDVYEFIHSTGS---IMKRKKDDWVNATHILKAANFAKAK--RTRILEKEV     55
d1a79a2        1 ---------------------KITGLLD--GDRVI--------------VFDKNGIS-KL     22

1bm8 a        56 LKE-THEKVQGGFGKY-QGTWVPLNIAKQLAEKFS--------------VYDQLKPLFDF     99
d1a79a2       23 SARHYGNVE-------GNFLSLSLVEALYLIN---LGWLEVKYKDNKPLSFEELYEYAR-     71

1bm8 a       100 ---    100
d1a79a2       72 NVE     74


hit structure      alignment
TMalign alignment (TM-score: 0.40 Raw score:39.41)
1bm8 a         1 --QIYSARYSGVDVYEFIHSTGSIMKRKKDDWVNATHILKAANFAKAKRTRILEKEVLKE     58
d1a79a2        1 KI--------------------TGLLDG--DRVI-VF--D-----KN-GISKLSAR--HY     27

1bm8 a        59 THEKVQGGFGKYQGTWVPLNIAKQLAEKFSVY-------DQLK--PLF-DF-----     99
d1a79a2       28 GNVEGN-------FLSLSLVEALYLINLGWLEVKYKDNK-PLSFEE-LYEYARNVE     74


hit structure      alignment
HHsearch alignment (Probability: 0.01 E-value:0.19)
DALI match                     
1bm8 a        75 VPLNIAKQLAEKFS     88
d1a79a2       61 LSFEELYEYARNVE     74



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5: d1tnsa_ mu transposase,​ DNA-​binding domain (cs: 2.467)

SCOP Superfamily: Putative DNA-​binding domain  |  SCOP Fold: Putative DNA-​binding domain  |  SCOP Class: All alpha proteins

Consensus: 0.42  Contact: 273
Modified z-scores:
dali:0.95 daliz:0.88 gdtts:0.95 tmscore:0.97 rmsd:0.31 AHM:0.30 LBcontacta:0.78 LBcontactb:0.80 LHM:0.11
id:0.68 blosum:0.44 compass:0.30 pearson:0.65
Scaled scores:
dali:0.63 daliz:0.29 gdtts:0.51 tmscore:0.43 rmsd:0.73 AHM:0.67 LBcontacta:0.31 LBcontactb:0.47 LHM:0.41
id:0.00 blosum:0.06 compass:0.04 pearson:0.04

hit structure      alignment
DALI alignment (Z-score: 2.3 Raw score:156.60)
1bm8 a         1 qiysarysgvdvyefihstgsimkrkkDDWVNATHILKAA---nFAKAKRTRILEKEVLk     57
d1tnsa_        1 ---------------------------MELWVSPKELANLpglpKTSAGVIYVAKKQGW-     32

1bm8 a        58 etHEKVQGGFG-kyQGTWVpLNIA-kQLAEkfSVYDQLKPL-----fdf     99
d1tnsa_       33 --QNRTRAGVKggkAIEYN-ANSLpvEAKA--ALLLRQGEIetslgyfe     76


hit structure      alignment
FAST alignment (Normalized score: 3.02 Raw score:261.70)
1bm8 a         1 QIYSARYSGVDVYEFIHSTGSIMKRKKDDWVNATHILKAAN------FAKAKRTRILEKE     54
d1tnsa_        1 --------------------------MELWV-SPKELA---NLPGLPKTSAGVIYVAKK-     29

1bm8 a        55 VL-KETHEKVQGGFGKY----QGTWVPLNIAKQLAEKF---SVYDQLKPLFDF-------     99
d1tnsa_       30 --QGWQNRTRAG-----VKGGKAIEYNANS--------LPVEAKAALLLRQG-EIETSLG     73

1bm8 a       100 ---    100
d1tnsa_       74 YFE     76


hit structure      alignment
TMalign alignment (TM-score: 0.38 Raw score:37.27)
1bm8 a         1 QIYSARYSGVDVYEFIHSTGSIMKRKKDDWVNATHILKAAN----FAKAKRTRILEKEVL     56
d1tnsa_        1 ---------------------------MELWVSPKELA-NLPGLPK---TSAGVIYV-AK     28

1bm8 a        57 --KETHEKVQGGFG--KYQGTWVPLNIAKQ-LAEKFSVYDQLKPL---FDF----     99
d1tnsa_       29 KQGWQNRTR-AGVKGG--KAIEYNANSLPVEAKA--ALLLRQGEIETS--LGYFE     76


hit structure      alignment
HHsearch alignment (Probability: 0.03 E-value:0.04)
DALI match       ........... ...............  .......
1bm8 a        30 WVNATHILKAANFAKAKRTRILEKEVLKETHEKVQG     65
d1tnsa_        4 WVSPKELANLPGLPKTSAGVIYVAKKQGWQNRTRAG     39



hit structures. 
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6: d1kafa_ DNA-​binding C-​terminal domain of the transcription factor MotA (cs: 2.147)

SCOP Superfamily: DNA-​binding C-​terminal domain of the transcription factor MotA  |  SCOP Fold: DNA-​binding C-​terminal domain of the transcription factor MotA  |  SCOP Class: Alpha and beta proteins (a+b)

Consensus: 0.51  Contact: 316
Modified z-scores:
dali:0.95 daliz:0.94 gdtts:0.90 tmscore:0.93 rmsd:0.29 AHM:0.30 LBcontacta:0.96 LBcontactb:0.93 LHM:0.15
id:0.51 blosum:0.31 compass:0.65 pearson:0.83
Scaled scores:
dali:0.76 daliz:0.48 gdtts:0.55 tmscore:0.53 rmsd:0.78 AHM:0.70 LBcontacta:0.59 LBcontactb:0.78 LHM:0.42
id:-0.01 blosum:0.03 compass:0.05 pearson:0.13

hit structure      alignment
DALI alignment (Z-score: 3.5 Raw score:225.20)
1bm8 a         1 --------------------------QIYSARysgvDVYEFIHST-----GSIMKRKkDD     29
d1kafa_        1 meitsdmeedkdlmlklldkngfvlkKVEIYR----SNYLAILEKrtngiRNFEINN-NG     55

1bm8 a        30 WVNAthilkaanfakakRTRILEkEVLKETHEKVQGgfgkyQGTWVPLN--IAKQLAEkf     87
d1kafa_       56 NMRI--------fgykmMEHHIQ-KFTDIGMSCKIA-kngnVYLDIKRSaeNIEAVIT--    103

1bm8 a        88 svydqlkplfdf     99
d1kafa_      104 -------vasel    108


hit structure      alignment
FAST alignment (Normalized score: 3.69 Raw score:381.80)
1bm8 a         1 --------------------------QIYSARYSG-VDVYEFIHS-----TGSIMKRKKD     28
d1kafa_        1 MEITSDMEEDKDLMLKLLDKNGFVLKKVEI-----YRSNYLAILEKRTNGIRNFEINNN-     54

1bm8 a        29 DWVNATHILKAANFAKAK------RTRILEKEVLKETHEKVQGGFGKYQ-------GTWV     75
d1kafa_       55 GNMR--------------IFGYKMMEHHI-QKFTDIGMSCK--------IAKNGNVYLDI     91

1bm8 a        76 PL---NIAKQLAEKFSVYDQLKPLFDF----     99
d1kafa_       92 K-RSAENIEAVITV-------------ASEL    108


hit structure      alignment
TMalign alignment (TM-score: 0.48 Raw score:47.77)
1bm8 a         1 --------------------------QIYSARYSGVDVYEFIH-ST----GSIMKRKKDD     29
d1kafa_        1 MEITSDMEEDKDLMLKLLDKNGFVLKKVEIYR----SNYLAILEKRTNGIRNFEINNNG-     55

1bm8 a        30 WVNATHILK-AANFAKAKRTRILEKEVLKETHEKVQG-GFGKYQGTWVPL--NIAKQLAE     85
d1kafa_       56 NMRIFG--YK----MMEHHIQKFT-DI--G-MSCKIAK-NGN-VYLDIKRSAENIEAVIT    103

1bm8 a        86 KFSV-YDQLKPLFDF     99
d1kafa_      104 VASEL----------    108


hit structure      alignment
HHsearch alignment (Probability: 0.01 E-value:0.22)
DALI match                  
1bm8 a        14 EFIHSTGSIMK     24
d1kafa_       48 NFEINNNGNMR     58



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7: d1qpma_ mu transposase,​ DNA-​binding domain (svm: -0.573)

SCOP Superfamily: Putative DNA-​binding domain  |  SCOP Fold: Putative DNA-​binding domain  |  SCOP Class: All alpha proteins

Consensus: 0.35  Contact: 227
Modified z-scores:
dali:0.92 daliz:0.82 gdtts:0.92 tmscore:0.95 rmsd:0.36 AHM:0.34 LBcontacta:0.82 LBcontactb:0.92 LHM:0.11
id:0.98 blosum:0.77 compass:0.66 pearson:0.92
Scaled scores:
dali:0.63 daliz:0.27 gdtts:0.46 tmscore:0.40 rmsd:0.72 AHM:0.66 LBcontacta:0.37 LBcontactb:0.67 LHM:0.44
id:0.13 blosum:0.13 compass:0.10 pearson:0.17

hit structure      alignment
DALI alignment (Z-score: 2.2 Raw score:144.50)
1bm8 a         1 qiysarysgvdvyefihstgsimkrkKDDWVNaTHILKAA-NFAK-AKRTRILEKEvlKE     58
d1qpma_        1 --------------------------KSIWCSpQEIMAADgMPGSvAGVHYRANVQ--GW     32

1bm8 a        59 THEKVqGGFGkyqGTWVPLNI-akQLAEkfSVYDQLKPlfdf     99
d1qpma_       33 TKRKKeGVKG-gkAVEYDVMSmptKERE--QVIAHLGL--st     69


hit structure      alignment
FAST alignment (Normalized score: 2.18 Raw score:180.50)
1bm8 a         1 QIYSARYSGVDVYEFIHSTGSIMKRKKDDWVNATHILKAANFAKA------KRTRILEKE     54
d1qpma_        1 --------------------------KSIWCSPQEIMA-------ADGMPGSVAGV-HYR     26

1bm8 a        55 VL--KETHEKVQGGFGKY-------QGTWVPLNIAKQLAEKF----SVYDQLKPLFDF--     99
d1qpma_       27 ANVQGWTKRK--------KEGVKGGKAVEYDVM---------SMPTKEREQVIAHL--GL     67

1bm8 a       100 --    100
d1qpma_       68 ST     69


hit structure      alignment
TMalign alignment (TM-score: 0.39 Raw score:38.14)
1bm8 a         1 QIYSARYSGVDVYEFIHSTGSIMKRKKDDWVNAT-HILKAAN--FAKAKRTRILEKEVL-     56
d1qpma_        1 --------------------------KS-IWCSPQEIM-AADGMPG--SVAGVH-YRANV     29

1bm8 a        57 KETHEKVQGGFGK--YQGTWVPLNIAK-QLAEKFSVYDQLK--PLFDF     99
d1qpma_       30 QGWTKRKKEGVKGGK-AVEYDVMSMPTKEREQ---VIAHLGLST----     69


hit structure      alignment
HHsearch alignment (Probability: 0.03 E-value:0.10)
DALI match       *** *******..............  ******* *    ...             ....
1bm8 a        30 WVNATHILKAANFAKAKRTRILEKEVLKETHEKVQG----GFGKYQGTWVPLNIAKQLAE     85
d1qpma_        4 WCSPQEIMAADGMPGSVAGVHYRANVQGWTKRKKEGVKGGKAVEYDVMSMPTKEREQVIA     63

DALI match           
1bm8 a        86 KFSV     89
d1qpma_       64 HLGL     67



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8: d1umwa2 Serine/​threonine-​protein kinase plk C-​terminal domain (svm: -1.287)

SCOP Superfamily: Polo-​box domain  |  SCOP Fold: Polo-​box domain  |  SCOP Class: Alpha and beta proteins (a+b)

Consensus: 0.34  Contact: 300
Modified z-scores:
dali:0.94 daliz:0.93 gdtts:0.93 tmscore:0.94 rmsd:0.31 AHM:0.39 LBcontacta:0.92 LBcontactb:0.90 LHM:0.21
id:0.66 blosum:0.28 compass:0.60 pearson:0.87
Scaled scores:
dali:0.73 daliz:0.47 gdtts:0.61 tmscore:0.52 rmsd:0.74 AHM:0.56 LBcontacta:0.60 LBcontactb:0.82 LHM:0.26
id:0.03 blosum:0.04 compass:0.14 pearson:0.17

hit structure      alignment
DALI alignment (Z-score: 2.8 Raw score:198.80)
1bm8 a         1 --------------------QIYSARysgVDVYEFIHS--TGSIMKRKKDDWVNatHILK     38
d1umwa2        1 egdelarlpylrtwfrtrsaIILHLS---NGSVQINFFqdHTKLILCPLMAAVT--YIDE     55

1bm8 a        39 aanfakakrtrilekevlkethekvqggfgkyqGTWVPLNIakqlaeKFSV-YDQLKPLF     97
d1umwa2       56 ------------------------------krdFRTYRLSL-leeygCCKElASRLRYAR     84

1bm8 a        98 DF--------     99
d1umwa2       85 TMvdkllssr     94


hit structure      alignment
FAST alignment (Normalized score: 2.77 Raw score:267.70)
1bm8 a         1 --------------------QIYSARYSGVDVYEFI-HST-GSIMKRKKDDWVNATHILK     38
d1umwa2        1 EGDELARLPYLRTWFRTRSAIILH---LSNGSVQINFFQDHTKLILCPLMAAVT------     51

1bm8 a        39 AANFAKAKRTRILEKEVLKETHEKVQGGFGKYQ-------GTWVPLNIAKQLAEKFSV--     89
d1umwa2       52 ---------------------------------YIDEKRDFRTYRLSLLEE-------YG     71

1bm8 a        90 -YDQLKPLFDF--------------     99
d1umwa2       72 CCKELASRL--RYARTMVDKLLSSR     94


hit structure      alignment
TMalign alignment (TM-score: 0.37 Raw score:36.89)
1bm8 a         1 ---------QI-YSARYSGVDVYEFIHSTGSIMKRKKDDWVNATHILKAANFA-------     43
d1umwa2        1 EGDELARLPYLRTWFRT-RSAIILHLSNGSVQINFFQDHTKLI-LC-PLM-AAVTYIDEK     56

1bm8 a        44 ------KAKRTRILE-KEVLKETHEKV-QG-GFGKYQ-----GTWVPLNIAKQLAEKFSV     89
d1umwa2       57 RDFRTY--RL-SLLEEY-GCCKELASRLRYARTMVDKLLSSR------------------     94

1bm8 a        90 YDQLKPLFDF     99
d1umwa2       95 ----------     95


hit structure      alignment
HHsearch alignment (Probability: 0.01 E-value:0.24)
DALI match                   
1bm8 a        20 GSIMKRKKDDWV     31
d1umwa2       19 SAIILHLSNGSV     30



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9: d1r11a3 Dimeric tRNA splicing endonuclease,​ domains 1 and 3 (svm: -1.339)

SCOP Superfamily: tRNA-​intron endonuclease N-​terminal domain-​like  |  SCOP Fold: MutS N-​terminal domain-​like  |  SCOP Class: Alpha and beta proteins (a+b)

Consensus: 0.59  Contact: 226
Modified z-scores:
dali:0.95 daliz:0.94 gdtts:0.92 tmscore:0.95 rmsd:0.33 AHM:0.48 LBcontacta:0.73 LBcontactb:0.84 LHM:0.16
id:0.70 blosum:0.37 compass:0.66 pearson:0.74
Scaled scores:
dali:0.73 daliz:0.44 gdtts:0.57 tmscore:0.47 rmsd:0.74 AHM:0.56 LBcontacta:0.35 LBcontactb:0.61 LHM:0.31
id:0.02 blosum:0.06 compass:0.03 pearson:0.12

hit structure      alignment
DALI alignment (Z-score: 2.6 Raw score:143.80)
1bm8 a         1 qiysarysgvdvyefihstgsimkrkkDDWVNAThilkaanfakakrtriLEKEvLKETH     60
d1r11a3        1 --------------------------gGDFAVVK---------------aKKSLeRRGFG     19

1bm8 a        61 EKVQggfgkyQGTWVPLNIAKQLAEKF----sVYDQLKPLFDF--     99
d1r11a3       20 VKRG------DKIYLHPLEVVYLQIKGiesfgELEDVLSWAESrm     58


hit structure      alignment
FAST alignment (Normalized score: 3.19 Raw score:241.70)
1bm8 a         1 QIYSARYSGVDVYEFIHSTGSIMKRKKDDWVNATHILKAANFAKAKRTRILE----KEVL     56
d1r11a3        1 --------------------------GGDFAV--------------------VKAKKSLE     14

1bm8 a        57 KE-THEKVQGGFGKY--QGTWVPLNIAKQLAEKFS-------VYDQLKPLFDF---     99
d1r11a3       15 RRGFGVK--------RGDKIYLHPLEVVYLQI---KGIESFGELEDVLSWAE-SRM     58


hit structure      alignment
TMalign alignment (TM-score: 0.37 Raw score:37.00)
1bm8 a         1 QIYSARYSGVDVYEFIHSTGSIMKRKKDDWVNATHILKAANFAKAKRTRILEKEVLKETH     60
d1r11a3        1 ------------G-----------G---DFAV-VK-----------AKKSLERR--GF-G     19

1bm8 a        61 EKVQGGFGKYQGTWVPLNIAKQLAEKFS-VYDQLKPLF-DF-----     99
d1r11a3       20 VKRG------DKIYLHPLEVVYLQIKGIESFGELED-VLSWAESRM     58


hit structure      alignment
HHsearch alignment (Probability: 0.00 E-value:0.43)
DALI match              
1bm8 a        67 FGKYQGT     73
d1r11a3       35 YLQIKGI     41



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10: d1jg5a_ GTP cyclohydrolase I feedback regulatory protein,​ GFRP (svm: -1.284)

SCOP Superfamily: GTP cyclohydrolase I feedback regulatory protein,​ GFRP  |  SCOP Fold: GTP cyclohydrolase I feedback regulatory protein,​ GFRP  |  SCOP Class: Alpha and beta proteins (a+b)

Consensus: 0.48  Contact: 172
Modified z-scores:
dali:0.77 daliz:0.76 gdtts:0.82 tmscore:0.80 rmsd:0.35 AHM:0.34 LBcontacta:0.65 LBcontactb:0.66 LHM:0.15
id:0.55 blosum:0.56 compass:0.61 pearson:0.75
Scaled scores:
dali:0.68 daliz:0.36 gdtts:0.54 tmscore:0.38 rmsd:0.74 AHM:0.65 LBcontacta:0.40 LBcontactb:0.53 LHM:0.38
id:0.01 blosum:0.08 compass:0.06 pearson:0.15

hit structure      alignment
DALI alignment (Z-score: 1.8 Raw score:151.50)
1bm8 a         1 qiysarysgvdvyefihsTGSIMKRKK---ddwVNAThilkaanfakakRTRILeKEVLk     57
d1jg5a_        1 ------------------PYLLISTQIrmevgpTMVG--------dehsDPELM-QQLG-     32

1bm8 a        58 etheKVQGG--fgkyQGTW-VPLNIAKQLAEKFSVYdqLKPL-----------fdf     99
d1jg5a_       33 ---aSKRRVlgnnfyEYYVnDPPRIVLDKLECRGFR--VLSMtgvgqtlvwclhke     83


hit structure      alignment
FAST alignment (Normalized score: 2.48 Raw score:224.70)
1bm8 a         1 QIYSARYSGVDVYEFIHST--GSIMKRKKD----DWVNATHILKAANFAKAK------RT     48
d1jg5a_        1 -------------------PYLLISTQI--RMEVGPTM--------------VGDEHSDP     25

1bm8 a        49 RILEKEVLK-ETHEKVQGGFGK---YQGTW--VPLNIAKQLAEKFSVYDQLKPLFDF---     99
d1jg5a_       26 ELMQ-----QLGASK-RRVL--GNNFYEYYVNDPPRIVLDKLECRG-----------FRV     66

1bm8 a       100 -----------------    100
d1jg5a_       67 LSMTGVGQTLVWCLHKE     83


hit structure      alignment
TMalign alignment (TM-score: 0.41 Raw score:41.05)
1bm8 a         1 QIYSARYSGVDVYEFIHSTGSIMKRKKDD--W-VNATH--ILKAANFAKAKRTRILEKEV     55
d1jg5a_        1 -----------------PY-LLISTQIRMEVGPTMVGDEH--S----DP-ELMQQL---G     32

1bm8 a        56 LKETHEKVQGG---FGKYQGTW-VPLNIAKQLAEKFSVYDQLKPL--------F-----D     98
d1jg5a_       33 A-----SKRRVLGNNFY-EYYVNDPPRIVLDKLECRGFR--VLSMTGVGQTLVWCLHKE-     83

1bm8 a        99 F     99
d1jg5a_       84 -     84


hit structure      alignment
HHsearch alignment (Probability: 0.01 E-value:0.40)
DALI match                
1bm8 a        13 YEFIHSTGS     21
d1jg5a_       44 YEYYVNDPP     52



hit structures. 
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11: d1jrma_ Hypothetical protein MTH637 (svm: -0.944)

SCOP Superfamily: YggU-​like  |  SCOP Fold: YggU-​like  |  SCOP Class: Alpha and beta proteins (a+b)

Consensus: 0.17  Contact: 246
Modified z-scores:
dali:0.85 daliz:0.71 gdtts:0.78 tmscore:0.85 rmsd:0.51 AHM:0.49 LBcontacta:0.76 LBcontactb:0.77 LHM:0.13
id:0.89 blosum:0.77 compass:0.67 pearson:0.90
Scaled scores:
dali:0.64 daliz:0.24 gdtts:0.39 tmscore:0.33 rmsd:0.63 AHM:0.56 LBcontacta:0.38 LBcontactb:0.53 LHM:0.42
id:0.07 blosum:0.15 compass:0.17 pearson:0.20

hit structure      alignment
DALI alignment (Z-score: 1.2 Raw score:168.30)
1bm8 a         1 qiysarysgvdvyefihstgsiMKRKkDDWVN--------athiLKAA-------NFAKA     45
d1jrma_        1 ---------------vitmdclREVG-DDLLVnievspasgkfgIPSYnewrkriEVKIH     44

1bm8 a        46 ----------krtriLEKEVLkETHEKVQGGFGkyQGTWV---PLNIAKQLAEK-FSVYD     91
d1jrma_       45 sppqkgkanreiikeFSETFG-RDVEIVSGQKSrqKTIRIqgmGRDLFLKLVSEkFGLEI    103

1bm8 a        92 Qlkplfdf     99
d1jrma_      104 P-------    104


hit structure      alignment
FAST alignment (Normalized score: 1.44 Raw score:146.30)
1bm8 a         1 QIYSARYSGVDVYEFIHSTG-----SIMKRKKD-DWVNATHILKAAN-------------     41
d1jrma_        1 --------------------VITMDCLREV---GDDLL---------VNIEVSPASGKFG     28

1bm8 a        42 -------------------FAKAKRTRILEKEVL-KETHEKVQGGFGKYQGTW-------     74
d1jrma_       29 IPSYNEWRKRIEVKIHSPPQKGKANREIIK-EFSETFGRDVE-----------IVSGQKS     76

1bm8 a        75 ---------VPLNIAKQLAEKFSVYDQLKPLFDF-------     99
d1jrma_       77 RQKTIRIQGMGRDLFLKLVSE-------------KFGLEIP    104


hit structure      alignment
TMalign alignment (TM-score: 0.41 Raw score:40.48)
1bm8 a         1 QIYSARYSGVDVYEFIHSTGSIMKRKKDD---WVN-A---T-----HIL----------K     38
d1jrma_        1 VI-----------TM------DCLR--EVGDDLLVNIEVSPASGKFGIPSYNEWRKRIEV     41

1bm8 a        39 AANFA--K---AK--RT-RILEK--EVLKETHEKVQGGF--G-KYQGTW--VPLNIAKQL     83
d1jrma_       42 --KIHSPPQKGKANREIIKEFSETFGRD---V-EIV-SGQKSRQKTIRIQGMGRDLFLKL     94

1bm8 a        84 A-EKFSVYDQLKPLFDF     99
d1jrma_       95 VSE--KFGL--E--IP-    104


hit structure      alignment
HHsearch alignment (Probability: 0.01 E-value:0.71)
DALI match                            
1bm8 a         9 GVDVYEFIHSTGSIMKRKKDD     29
d1jrma_        3 TMDCLREVGDDLLVNIEVSPA     23



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12: d1d1ra_ YciH (svm: -1.552)

SCOP Superfamily: eIF1-​like  |  SCOP Fold: eIF1-​like  |  SCOP Class: Alpha and beta proteins (a+b)

Consensus: 0.39  Contact: 230
Modified z-scores:
dali:0.86 daliz:0.77 gdtts:0.87 tmscore:0.89 rmsd:0.37 AHM:0.35 LBcontacta:0.83 LBcontactb:0.82 LHM:0.11
id:0.80 blosum:0.58 compass:0.50 pearson:0.85
Scaled scores:
dali:0.64 daliz:0.30 gdtts:0.50 tmscore:0.42 rmsd:0.74 AHM:0.66 LBcontacta:0.39 LBcontactb:0.56 LHM:0.50
id:0.05 blosum:0.09 compass:0.11 pearson:0.15

hit structure      alignment
DALI alignment (Z-score: 2.1 Raw score:157.00)
1bm8 a         1 qiysarysgvdvyefihstgsIMKRKK----DDWVNATHilkaaNFAKAKRTRILEkEVL     56
d1d1ra_        1 --------------kgdgvvrIQRQTSgrkgKGVCLITG----vDLDDAELTKLAA-ELK     41

1bm8 a        57 K---ETHEKVQggfgkyqGTWVPLNIaKQLAEKFS---vydQLKPlfdf     99
d1d1ra_       42 KkcgCGGAVKD------gVIEIQGDKrDLLKSLLEakgmkvKLAG-gle     83


hit structure      alignment
FAST alignment (Normalized score: 2.94 Raw score:266.30)
1bm8 a         1 QIYSARYSGVDVYEFIHST-----GSIMKR-----KKDDWVNATHILK-AANFAKAKRTR     49
d1d1ra_        1 -------------------KGDGVVRIQR-QTSGRKGKGVCLI-----TGVDLDDAELTK     35

1bm8 a        50 ILEKEVLKE-------THEKVQGGFGKYQ---GTWV---PLNIAKQLAEKFSVYDQLKPL     96
d1d1ra_       36 LAAE-----LKKKCGCGGAV---------KDGVIEIQGDKRDLLKSLLEAKG--------     73

1bm8 a        97 FDF----------     99
d1d1ra_       74 ---MKVKLAGGLE     83


hit structure      alignment
TMalign alignment (TM-score: 0.46 Raw score:45.29)
1bm8 a         1 ----QIYSARYSGVDVYEFIHST-GSIMKRKK-----DDWVNATHILKAANFAKAKRTRI     50
d1d1ra_        1 KGDG------------------VV-RIQRQTSGRKGKG-VCLI-TG-V--DLDDAELTKL     36

1bm8 a        51 LEKEVL-KETHEKVQGGFGKYQGTW-V-PLNIAKQLAEKF-SVYDQLKPLFDF--     99
d1d1ra_       37 AA-ELKKKCGCGGAV--KDG-VIEIQGDKRDLLKSLLEAKGMKV--KL-A-GGLE     83


hit structure      alignment
HHsearch alignment (Probability: 0.01 E-value:0.08)
DALI match       ...        
1bm8 a        62 KVQGGFGKYQG     72
d1d1ra_       49 AVKDGVIEIQG     59



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13: d1qjta_ Eps15 (svm: -0.944)

SCOP Superfamily: EF-​hand  |  SCOP Fold: EF Hand-​like  |  SCOP Class: All alpha proteins

Consensus: 0.35  Contact: 218
Modified z-scores:
dali:0.81 daliz:0.80 gdtts:0.88 tmscore:0.89 rmsd:0.28 AHM:0.28 LBcontacta:0.57 LBcontactb:0.62 LHM:0.16
id:0.65 blosum:0.37 compass:0.60 pearson:0.88
Scaled scores:
dali:0.63 daliz:0.35 gdtts:0.55 tmscore:0.45 rmsd:0.77 AHM:0.70 LBcontacta:0.25 LBcontactb:0.31 LHM:0.37
id:0.01 blosum:0.04 compass:0.15 pearson:0.20

hit structure      alignment
DALI alignment (Z-score: 1.8 Raw score:160.70)
1bm8 a         1 qiysarysgvdvyefihstgsIMKRK-KDDW--vNATHILKAANFAKAKRTRILEkEVLK     57
d1qjta_        1 ---lsltqlssgnpvyekyyrQVEAGnTGRVlalDAAAFLKKSGLPDLILGKIWD-LADT     56

1bm8 a        58 ETHEkvqggfgkyqgtWVPLNIAKQLAEKFS-------------vydqlkplfdf     99
d1qjta_       57 DGKG------------VLSKQEFFVALRLVAcaqnglevslsslslavppprfhd     99


hit structure      alignment
FAST alignment (Normalized score: 2.81 Raw score:277.70)
1bm8 a         1 QIYSARYSGVDVYEFIHSTGSI-------------------MKRKKDDWVNATHILKA--     39
d1qjta_        1 ----------------------LSLTQLSSGNPVYEKYYRQVEAGNTGRVLALDAAAFLK     38

1bm8 a        40 -ANFAKAKRTRILEKEVLKETHEKVQGGFGKYQG------TWVPLNIAKQLAEKFSVYDQ     92
d1qjta_       39 KSGLPDLILGKIWDL-------------------ADTDGKGVLSKQEFFVALRL------     73

1bm8 a        93 LKPLFDF--------------------------     99
d1qjta_       74 -------VACAQNGLEVSLSSLSLAVPPPRFHD     99


hit structure      alignment
TMalign alignment (TM-score: 0.38 Raw score:38.04)
1bm8 a         1 ---------------QIYSARYSGVDVYEF--IHSTGSIMKR-KKDDW-V-NATHILKAA     40
d1qjta_        1 LSLTQLSSGNPVYEK--------------YYR------QVEAGNTGRVLALDAAAFLKKS     40

1bm8 a        41 NFAKAKRTRILEKEVLK-ET--HEKVQGGFGKYQGTWVPLNIAKQLAEKF----------     87
d1qjta_       41 GL---PDLILG-KIWDLADTDGKG------------VLSKQEFFVALRLVACAQNGLEVS     84

1bm8 a        88 ----------SVYDQLKPLFDF     99
d1qjta_       85 LSSLSLAVPPPRF-HD------     99


hit structure      alignment
HHsearch alignment (Probability: 0.01 E-value:0.17)
DALI match                    
1bm8 a        27 KDDWVNATHILKA     39
d1qjta_       58 GKGVLSKQEFFVA     70



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14: d1r0va3 Dimeric tRNA splicing endonuclease,​ domains 1 and 3 (svm: -1.022)

SCOP Superfamily: tRNA-​intron endonuclease N-​terminal domain-​like  |  SCOP Fold: MutS N-​terminal domain-​like  |  SCOP Class: Alpha and beta proteins (a+b)

Consensus: 0.41  Contact: 259
Modified z-scores:
dali:0.93 daliz:0.91 gdtts:0.94 tmscore:0.95 rmsd:0.30 AHM:0.31 LBcontacta:0.91 LBcontactb:0.88 LHM:0.20
id:0.85 blosum:0.55 compass:0.67 pearson:0.88
Scaled scores:
dali:0.70 daliz:0.39 gdtts:0.57 tmscore:0.48 rmsd:0.76 AHM:0.64 LBcontacta:0.51 LBcontactb:0.70 LHM:0.26
id:0.07 blosum:0.10 compass:0.03 pearson:0.19

hit structure      alignment
DALI alignment (Z-score: 1.8 Raw score:136.20)
1bm8 a         1 qiysarysgvdvyefihstgsIMKRKkdDWVNathilkaanfakakrTRIL-EKEVlket     59
d1r0va3        1 ----------geqkeelpeiaGVLSD--EYVI------------tkqTEIFsRYFY----     32

1bm8 a        60 HEKVQggfgkyQGTWVPLNIAKQLAEKF---svydQLKPLFDF------     99
d1r0va3       33 GSEKG------DLVTLSLIESLYLLDLGklnllnaDREELVKRarever     75


hit structure      alignment
FAST alignment (Normalized score: 3.09 Raw score:266.20)
1bm8 a         1 QIYSARYSGVDVYEFIHSTGS-----------IMKRKKDDWVNATHILKAANFAKAK--R     47
d1r0va3        1 ---------------------GEQKEELPEIAGVLS--DEYVI--------------TKQ     23

1bm8 a        48 TRILEKEVLKE--THEKVQGGFGKYQ---GTWVPLNIAKQLAEKFS---------VYDQL     93
d1r0va3       24 TEIFSR-----YFYGSE---------KGDLVTLSLIESLYLLD---LGKLNLLNADREEL     66

1bm8 a        94 KPLFDF----     99
d1r0va3       67 VKRAR-EVER     75


hit structure      alignment
TMalign alignment (TM-score: 0.38 Raw score:37.70)
1bm8 a         1 ----------QIYSARYSGVDVYEFIHSTGSIMKRKKDDWVNATHILKAANFAKAKRTRI     50
d1r0va3        1 GEQKEELPEI-------------------AGVLS-D--EYVI-TK--------Q--TE--     25

1bm8 a        51 L--EKEVLKETHEKVQGGFGKYQGTWVPLNIAKQLAEKFS-VY--DQLKPLF-DF-----     99
d1r0va3       26 IFSRY--F-Y-GSEKG------DLVTLSLIESLYLLDLGKLNLLN-ADREELVKRAREVE     74

1bm8 a       100 -    100
d1r0va3       75 R     75


hit structure      alignment
HHsearch alignment (Probability: 0.01 E-value:0.36)
DALI match                    
1bm8 a        77 LNIAKQLAEKFSV     89
d1r0va3        8 PEIAGVLSDEYVI     20



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15: d1xpaa1 DNA repair factor XPA DNA-​ and RPA-​binding domain,​ C-​terminal subdomain (svm: -1.221)

SCOP Superfamily: Putative DNA-​binding domain  |  SCOP Fold: Putative DNA-​binding domain  |  SCOP Class: All alpha proteins

Consensus: 0.51  Contact: 309
Modified z-scores:
dali:0.88 daliz:0.77 gdtts:0.90 tmscore:0.93 rmsd:0.40 AHM:0.38 LBcontacta:0.84 LBcontactb:0.90 LHM:0.19
id:0.31 blosum:0.13 compass:0.37 pearson:0.70
Scaled scores:
dali:0.64 daliz:0.25 gdtts:0.47 tmscore:0.39 rmsd:0.68 AHM:0.61 LBcontacta:0.40 LBcontactb:0.64 LHM:0.20
id:-0.05 blosum:-0.01 compass:0.07 pearson:0.09

hit structure      alignment
DALI alignment (Z-score: 1.5 Raw score:142.50)
1bm8 a         1 qiysarysgvdvyefihstgsimkrkkDDWVNATHILKAAnfakakrtrilEKEVL----     56
d1xpaa1        1 -------------------------dkHKLITKTEAKQEY--------llkDCDLEkrep     27

1bm8 a        57 KETHEKVQGGFGKY--qGTWVPLNIAKQLAEKFSVYDQ-----lkplfdf     99
d1xpaa1       28 PLKFIVKKNPHHSQwgdMKLYLKLQIVKRSLEVWGSQEaleeakevrqen     77


hit structure      alignment
FAST alignment (Normalized score: 2.57 Raw score:224.60)
1bm8 a         1 QIYSARYSGVDVYEFIHSTGSIMKRKK--DDWVNATHILKAANFAKAKRTRI--LEKEVL     56
d1xpaa1        1 ---------------------------DKHKLITKTEAKQEY----------LLKDCDLE     23

1bm8 a        57 ----KETHEKVQGGFGK---------YQGTWVPLNIAKQLAEKFSVYDQLKPLFDF----     99
d1xpaa1       24 KREPPLKFIV-------KKNPHHSQWGDMKLYLKLQIVKRSLE-------------VWGS     63

1bm8 a       100 --------------    100
d1xpaa1       64 QEALEEAKEVRQEN     77


hit structure      alignment
TMalign alignment (TM-score: 0.37 Raw score:36.56)
1bm8 a         1 QIYSARYSGVDVYEFIHSTGSIMK-RKKDDWVNATHILKA-ANFAKAKRTRI-LEKEVLK     57
d1xpaa1        1 -----------------------DK---HKLITKTEAKQEYL-L----K-DCDLEKRE-P     27

1bm8 a        58 -ETHEKVQGGF---GKY--QGTWVPLNIAKQLAEKFSVYDQ-LK---------PLFDF     99
d1xpaa1       28 PLKFI-V-KKNPHHSQWGDM-KLYLKLQIVKRSLEVWGSQEALEEAKEVRQEN-----     77


hit structure      alignment
HHsearch alignment (Probability: 0.01 E-value:0.11)
DALI match                  
1bm8 a         3 YSARYSGVDVY     13
d1xpaa1       38 HHSQWGDMKLY     48



hit structures. 
top
16: d1h3fa2 Tyrosyl-​tRNA synthetase (TyrRS),​ C-​terminal domain (svm: -0.501)

SCOP Superfamily: Alpha-​L RNA-​binding motif  |  SCOP Fold: Alpha-​L RNA-​binding motif  |  SCOP Class: Alpha and beta proteins (a+b)

Consensus: 0.42  Contact: 123
Modified z-scores:
dali:0.65 daliz:0.71 gdtts:0.60 tmscore:0.61 rmsd:0.35 AHM:0.34 LBcontacta:0.67 LBcontactb:0.73 LHM:0.15
id:0.68 blosum:0.84 compass:0.74 pearson:0.85
Scaled scores:
dali:0.71 daliz:0.38 gdtts:0.43 tmscore:0.27 rmsd:0.65 AHM:0.57 LBcontacta:0.51 LBcontactb:0.76 LHM:0.46
id:0.05 blosum:0.16 compass:0.21 pearson:0.27

hit structure      alignment
DALI alignment (Z-score: 1.1 Raw score:150.90)
1bm8 a         1 qiysarysgvdvyefihstgsiMKRKkdDWVNATHILK-AANFAK-AKRTRILEKEvlke     58
d1h3fa2        1 -----------eeipevtipasELKE--GRIWVARLFTlAGLTPSnAEARRLIQNR----     43

1bm8 a        59 thekvqggfgkyqGTWVPlniakQLAE---kFSVYdqLKPLfdf     99
d1h3fa2       44 -glrldgevltdpMLQVD-lsrpRILQrgkdRFVR--VRLS--d     81


hit structure      alignment
FAST alignment (Normalized score: 1.88 Raw score:168.40)
1bm8 a         1 QIYSARYSGVDVYEFIHSTGSIMKRKK--------------DDWVNATHILKAAN--FAK     44
d1h3fa2        1 ---------------------------EEIPEVTIPASELKEGRIWVARLFTLAGLTPSN     33

1bm8 a        45 AKRTRILEKEVLKETHEKVQGGFGKYQ-------------GTWVPLNIAKQLAE------     85
d1h3fa2       34 AEARRLIQN------------------RGLRLDGEVLTDPMLQV----------DLSRPR     65

1bm8 a        86 --------KFSVYDQLKPLFDF----     99
d1h3fa2       66 ILQRGKDRFVRV----------RLSD     81


hit structure      alignment
TMalign alignment (TM-score: 0.37 Raw score:36.68)
1bm8 a         1 -------QIYSARYSGVDVYEFIHSTGSIMKRKKDDWVNATHILKA-ANFAK-AKRTRIL     51
d1h3fa2        1 EEIPEVTIP----------AS--------ELKE--GRIWVARLFTLAGLTPSNAEARRLI     40

1bm8 a        52 E-K-------EVLKETHEKVQGGFGKYQGTWVPLNIAKQLAEK-----FSVYDQLKPLFD     98
d1h3fa2       41 QNRGLRLDGEVLTD--P-M----------LQVDLSRPRIL--QRGKDRFV-R--VR--LS     80

1bm8 a        99 F     99
d1h3fa2       81 D     81


hit structure      alignment
HHsearch alignment (Probability: 0.02 E-value:0.08)
DALI match       . **********....  ..**********          
1bm8 a        27 KDDWVNATHILKAANF--AKAKRTRILEKEVLKETHEKVQ     64
d1h3fa2       14 KEGRIWVARLFTLAGLTPSNAEARRLIQNRGLRLDGEVLT     53