Reference:
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
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
Comments and suggestions to: grishin@chop.swmed.edu
Query:542d3.pdb
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL
Click the hit # to scoll down to alignments.
| HIT # |
SCOPid | PROTEIN | SCOP SUPERFAMILY | SCOP FOLD | SCOP CLASS |
Z-score | Raw score |
|---|---|---|---|---|---|---|---|
| SCOP domains with score worse than the threshold (Z-score ≤ 5.0) | |||||||
| 1 | d1uhsa_ | Homeodomain-only protein, Hop | Homeodomain-like | DNA/RNA-binding 3-helical bundle | All α | 3.50 | 178.30 |
| 2 | d1sfua_ | 34L | "Winged helix" DNA-binding domain | DNA/RNA-binding 3-helical bundle | All α | 3.30 | 163.90 |
| 3 | d1je8a_ | Nitrate/nitrite response regulator (NarL) | C-terminal effector domain of the bipartite response regulators | DNA/RNA-binding 3-helical bundle | All α | 3.20 | 153.30 |
| 4 | d1mija_ | Homeo-prospero domain of Prospero protein | Homeodomain-like | DNA/RNA-binding 3-helical bundle | All α | 3.00 | 204.30 |
| 5 | d1sfxa_ | Hypothetical protein AF2008 | "Winged helix" DNA-binding domain | DNA/RNA-binding 3-helical bundle | All α | 3.00 | 170.00 |
| 6 | d1ri7a1 | Putative transcriptional regulator PH1519 | "Winged helix" DNA-binding domain | DNA/RNA-binding 3-helical bundle | All α | 3.00 | 159.80 |
| 7 | d1a9xa1 | Carbamoyl phosphate synthetase, large subunit connection domain | Carbamoyl phosphate synthetase, large subunit connection domain | Carbamoyl phosphate synthetase, large subunit connection domain | All α | 2.90 | 187.80 |
| 8 | d1fjla_ | Paired protein | Homeodomain-like | DNA/RNA-binding 3-helical bundle | All α | 2.80 | 142.00 |
| 9 | d1u5ta2 | Vacuolar sorting protein SNF8 | (Winged helix( DNA-binding domain | DNA/RNA-binding 3-helical bundle | All α | 2.70 | 142.40 |
| 10 | d1lvaa3 | C-terminal fragment of elongation factor SelB | "Winged helix" DNA-binding domain | DNA/RNA-binding 3-helical bundle | All α | 2.60 | 134.90 |
| 11 | d1hcra_ | HIN recombinase (DNA-binding domain) | Homeodomain-like | DNA/RNA-binding 3-helical bundle | All α | 2.40 | 121.00 |
| 12 | d1t56a1 | Ethr repressor | Homeodomain-like | DNA/RNA-binding 3-helical bundle | All α | 2.30 | 139.90 |
| 13 | d1mkma1 | Transcriptional regulator IclR, N-terminal domain | "Winged helix" DNA-binding domain | DNA/RNA-binding 3-helical bundle | All α | 2.30 | 125.50 |
| 14 | d1a1va2 | HCV helicase domain | P-loop containing nucleoside triphosphate hydrolases | P-loop containing nucleoside triphosphate hydrolases | α/β | 2.20 | 181.80 |
| 15 | d1jw2a_ | Hemolysin expression modulating protein HHA | Hemolysin expression modulating protein HHA | Open three-helical up-and-down bundle | All α | 2.10 | 128.20 |
| 16 | d1n1ca_ | TorA specific chaperone TorD | TorD-like (Pfam 06192) | TorD-like (Pfam 06192) | All α | 2.10 | 118.30 |
query 1 -------PDYPVLDAILELYVDRD-----tGADAIVA-aGYDRELVVKTLRMVDTAEYKR 47
::::::::::::::::: ::::::: :::::::::::::::::::::
d1uhsa_ 1 gsegaatMTEDQVEILEYNFNKVNkhpdptTLCLIAAeaGLTEEQTQKWFKQRLAEWRRS 60
query 48 RQYppgtkisakgfgkdrrlpitnrwregh 77
:::
d1uhsa_ 61 EGL------------------psecrsvtd 72
query 1 ---pDYPVLDAILELyVDRD-----TGADAIVAA-GYDRELVVKTLRMVDTAEykrrqyp 51
::::::::::: :::: ::::::::: ::::::::::::::::::
d1sfua_ 1 ctvnDAEIFSLVKKE-VLSLntndyTTAISLSNRlKINKKKINQQLYKLQKED--tvkmv 57
query 52 pgtkisakGFGKdrrlpitnrwregh 77
::::
d1sfua_ 58 psnppkwfKNYN-------------c 70
query 1 ----pdypvlDAILELYvDRDTGADAIVAA-GYDRELVVKTLRMVDTAEykrrqyppgtk 55
::::::: :::::::::::: ::::::::::::::::::
d1je8a_ 1 rdvnqltpreRDILKLI-AQGLPNKMIARRlDITESTVKVHVKHMLKKM----klksrve 55
query 56 isAKGFGKDRrlpitnrwregh 77
::::::::
d1je8a_ 56 aaVWVHQERI-----------f 66
query 1 ---PDYPVLDAILELyVDRD--tGADAIVAAG-------yDRELVVKTLRMVDTA-EYKR 47
:::::::::::: :::: ::::::::: ::::::::::::::: ::::
d1mija_ 1 sstLTPMHLRKAKLM-FFWVrypSSAVLKMYFpdikfnknNTAQLVKWFSNFREFyYIQM 59
query 48 RQY--------PPGT------------kISAKG-fGKDRR-------------------- 66
::: :::: ::::: :::::
d1mija_ 60 EKYarqavtesELYRvlnlhynrnnhieVPQNFrfVVESTlreffraiqggkdteqswkk 119
query 67 lPITN---------rwregh 77
::::
d1mija_ 120 sIYKIisrmddpvpeyfksp 139
query 1 ----------------pdYPVLDAILELYVD-RDTGADAIVAA-GYDRELVVKTLRMVDT 42
::::::::::::: ::::::::::: ::::::::::::::::
d1sfxa_ 1 hmsnplgelvkaleklsfKPSDVRIYSLLLErGGMRVSEIARElDLSARFVRDRLKVLLK 60
query 43 AE------------------------yKRRQY--PPGTkisakgfgkdrrlpitnrwreg 76
:: ::::: ::::
d1sfxa_ 61 RGfvrreivekgwvgyiysaekpekvlKEFKSsiLGEI------------eriekmftdg 108
query 77 h 77
d1sfxa_ 109 s 109
query 1 pDYPVLDAILELYVDRD-TGADAIVAA-gYDRELVVKTLRMVDTAEykrrqyppgtkisa 58
:::::::::::::::: ::::::::: :::::::::::::::::
d1ri7a1 1 -LDEIDKKIIKILQNDGkAPLREISKItgLAESTIHERIRKLRESG-----------vik 48
query 59 KGFGkdrrlpitnrwregh 77
::::
d1ri7a1 49 KFTA-------iidpealg 60
query 1 ----------------------------pDYPVLDAILELYVdRDTGADAIVAAG-YDRE 31
::::::::::::: :::::::::::: ::::
d1a9xa1 1 evgatgfdpkvslddpealtkirrelkdaGADRIWYIADAFR-AGLSVDGVFNLTnIDRW 59
query 32 LVVKTLRMVDTA-EYKR--------------------------RQYPPGT---------- 54
:::::::::::: :::: :::::::
d1a9xa1 60 FLVQIEELVRLEeKVAEvgitglnadflrqlkrkgfadarlakLAGVREAeirklrdqyd 119
query 55 -----------kisakgfgkdrrlpitnrwregh 77
d1a9xa1 120 lhpvykrvdtcaaefatdtaymystyeeeceanp 153
query 1 ------PDYPvlDAILELYVDRD--------tGADAIVAA-GYDRELVVKTLRMVDTAEY 45
:::: ::::::::::: :::::::: :::::::::::::::::::
d1fjla_ 1 kqrrsrTTFS--ASQLDELERAFertqypdiyTREELAQRtNLTEARIQVWFQNRRARLR 58
query 46 KRRQYPPgtkisakgfgkdrrlpitnrwregh 77
:::::::
d1fjla_ 59 KQHTSVS------------------------- 65
query 1 pdYPVLDAILELY-vdRDTGADAIVAA-GYDRELVVKTLRMVDTAE--ykrrqyppgtki 56
::::::::::: ::::::::::: ::::::::::::::::::
d1u5ta2 1 -lTSDQTKILEICsilGYSSISLLKANlGWEAVRSKSALDEMVANGllwidyqggaealy 59
query 57 saKGFGKdrrlpitnrwregh 77
:::::
d1u5ta2 60 wdPSWIT------------rq 68
query 1 ---pDYPVLDAILELYVDR---DTGADAIVAA-GYDRELVVKTLRMVDTAEykrrqyppg 53
::::::::::::::: :::::::::: ::::::::::::::::::
d1lvaa3 1 fsetQKKLLKDLEDKYRVSrwqPPSFKEVAGSfNLDPSELEELLHYLVREG--------- 51
query 54 tkisakgfgkdrrlpitnrwregh 77
d1lvaa3 52 -----------vlvkindefywhr 64
query 1 -----PDYPVLDAILELYVdRDTGADAIVAaGYDRElvVKTLRMVDtaeykrrqyppgtk 55
:::::::::::::: :::::::::: ::::: ::::::::
d1hcra_ 1 grpraINKHEQEQISRLLE-KGHPRQQLAI-IFGIG-vSTLYRYFP-------------- 43
query 56 isakgfgkdrrLPITNRwregh 77
::::::
d1hcra_ 44 ----------aSSIKKR---mn 52
query 1 pDYPVLDAILELYVDRD-------tGADAIVA------aGYDR--ELVVKTLRMVDTAEY 45
:::::::::::::::: ::::::: :::: :::::::::::::::
d1t56a1 1 -GDDRELAILATAENLLedrpladiSVDDLAKgagisrpTFYFyfPSKEAVLLTLLDRVV 59
query 46 KRRQY--PPGTkisakgfgkdrrlpitnrwregh 77
::::: ::::
d1t56a1 60 NQADMalQTLA--------------------enp 73
query 1 --PDYPvLDAILE--lyvdrDTGADAIVAA-GYDRELVVKTLRMVDTAE----------- 44
:::: :::::: :::::::::: ::::::::::::::::::
d1mkma1 1 mnTLKK-AFEILDfivknpgDVSVSEIAEKfNMSVSNAYKYMVVLEEKGfvlrkkdkryv 59
query 45 -yKRRQY--PPGTkisakgfgkdrrlpitnrwregh 77
::::: ::::
d1mkma1 60 pgYKLIEygSFVL--------------------rrf 75
query 1 ------------------------------------------------------------ 1
d1a1va2 1 pgsvtvphpnieevalsttgeipfygkaiplevikggrhlifchskkkcdelaaklvalg 60
query 1 ------------------------------------------------------------ 1
d1a1va2 61 inavayyrgldvsviptsgdvvvvatdalftgdfdsvidcntxvtqtvdfsldptftiet 120
query 1 ----------------------------------pdyPVLDAILELYVDR--------dt 18
:::::::::::::
d1a1va2 121 ttlpqdavsrtqrrgrtgrgkpgiyrfvapgerpsgmFDSSVLCECYDAGxawyeltpae 180
query 19 GADAIVAAG------ydrELVVKTLRMVDTAEykRRQYPP----gTKISA-KGFG--KDR 65
::::::::: :::::::::::::: :::::: ::::: :::: :::
d1a1va2 181 TTVRLRAYMntpglpvcqDHLEFWEGVFTGLT--HIDAHFlsqtkQSGENfPYLVayQAT 238
query 66 R---------------------------------------------lPITN--RWREgh 77
: :::: ::::
d1a1va2 239 VcaraqapppswdqmwkclirlkptlhgptpllyrlgavqnevtlthPITKyiMTCM-s 296
query 1 ------PDYPVLDAILE-lyVDRD-TGADAIVAAG--yDRELVVKTLRMVDTA-EYKRrq 49
::::::::::: :::: :::::::::: ::::::::::::::: ::::
d1jw2a_ 1 msekplTKTDYLMRLRRcqtIDTLeRVIEKNKYELsdnELAVFYSAADHRLAElTMNK-- 58
query 50 yppgtkisakgfgkdrrlPITNRWregh 77
::::::
d1jw2a_ 59 ----------lydkipssVWKFIR---- 72
query 1 ------------------------------------------------------------ 1
d1n1ca_ 1 vdinparalvyqllsslfarevdeqrlkeltseaaqqfweqlsleanftqsvdkirstln 60
query 1 ------------------------------------------------------------ 1
d1n1ca_ 61 gikddeallelaadycglflvgtsaspyaslylllfgeqhqqmseflhqsklqvqshfpe 120
query 1 ----PDYP-------------------vldaiLELYvdrdTGADAIVAAG---yDRELVV 34
:::: :::: :::::::::: ::::::
d1n1ca_ 121 padhLAVMlaymahlcchsensvqlsflqtcvNSWL---aKFINHLTQCNkngfYSAVAT 177
query 35 KTLRMVDTAEYKRRQY-PPGTkisakgfgkdrrlpitnrwregh 77
:::::::::::::::: ::::
d1n1ca_ 178 LTLAWVKQDIAQLEPAvAIIS----------------------l 199