HorA Server Transitive Detail

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


Query <-- 0.715 --> Intermediate <-- 1.354 --> Hit

SVM
score
SVM
score

The query (542d3.pdb) is transitively linked to the hit (d1hkqa_) through the intermediate protein (d1ri7a1) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1ri7a1 Putative transcriptional regulator PH1519"​Winged helix"​ DNA-​binding domainDNA/​RNA-​binding 3-​helical bundleAll α
Hit d1hkqa_ Replication protein A,​ repA"​Winged helix"​ DNA-​binding domainDNA/​RNA-​binding 3-​helical bundleAll α

Supporting Alignments

Query <-- 0.715 --> Intermediate
DALI alignment (Z-score: 3.0 Raw score:159.80) query 1 pDYPVLDAILELYVDRD-TGADAIVAA-gYDRELVVKTLRMVDTAEykrrqyppgtkisa 58 :::::::::::::::: ::::::::: ::::::::::::::::: d1ri7a1 1 -LDEIDKKIIKILQNDGkAPLREISKItgLAESTIHERIRKLRESG-----------vik 48 query 59 KGFGkdrrlpitnrwregh 77 :::: d1ri7a1 49 KFTA-------iidpealg 60 FAST alignment (Normalized score: 4.52 Raw score:307.00) query 1 PDYPVLDAILELYVDR-DTGADAIVA-AGYDRELVVKTLRMVDTAEYKRRQYPPGTKISA 58 ::::::::::::::: ::::::::: ::::::::::::::::: d1ri7a1 1 -LDEIDKKIIKILQNDGKAPLREISKITGLAESTIHERIRKLRE---------------- 43 query 59 KGFGKDRRLPITNRWREGH----------------- 77 d1ri7a1 44 -------------------SGVIKKFTAIIDPEALG 60 TMalign alignment (TM-score: 0.42 Raw score:32.51) query 1 PDYPVLDAILELYVDRD--TGADAIVAAGYDR-ELVVKTLRM-VDTAE--YKRRQYPPGT 54 :: :::::::::: ::: ::::::::::::: ::::::::: : ::: : d1ri7a1 1 LD-EIDKKIIKIL-QNDGKAPLREISKITGLAESTIHERIRKLR-ESGVI--K------- 48 query 55 KISAKGFGKDRR--------LPITNRWREGH 77 :: :: d1ri7a1 49 ------KF--TAIIDPEALG----------- 60 HHsearch alignment (Probability: 0.05 E-value:0.06) query 4 PVLDAILELYVDRD--TGADAIVAA-GYDRELVVKTLRMVDTA 43 :::::::::::::: ::::::::: ::::::::::::::::: d1ri7a1 2 DEIDKKIIKILQNDGKAPLREISKITGLAESTIHERIRKLRES 44
Intermediate <-- 1.354 --> Hit
DALI alignment (Z-score: 2.9 Raw score:165.50) d1ri7a1 1 -----------LDEIDKKIIKILQND------------GKAPLREISKITGL----AEST 33 ::::::::::::::: :::::::::::::: :::: d1hkqa_ 1 qsnkliesshtLTLNEKRLVLCAASLidsrkplpkdgyLTIRADTFAEVFGIdvkhAYAA 60 d1ri7a1 34 IHERIRKLRES--------------GVIKK------------------------ftaiid 55 ::::::::::: ::::: d1hkqa_ 61 LDDAATKLFNRdirryvkgkvvermRWVFHvkyregqgcvelgfsptiiphltmlhkeft 120 d1ri7a1 56 pealg 60 d1hkqa_ 121 syqlk 125 FAST alignment (Normalized score: 3.55 Raw score:307.30) d1ri7a1 1 -----------LDEIDKKIIKILQND--------------GKAPLREISKITGLAESTIH 35 ::::::::::::: :::::::::::::::::::: d1hkqa_ 1 QSNKLIESSHTLTLNEKRLVLCAA--SLIDSRKPLPKDGYLTIRADTFAEVFGIDVKHAY 58 d1ri7a1 36 ERIRKLRES-------------------GVIKKFTAIIDPEALG---------------- 60 :::::::: :::: d1hkqa_ 59 AALDDAAT-KLFNRDIRRYVKGKVVERMRWVF------------HVKYREGQGCVELGFS 105 d1ri7a1 61 -------------------- 61 d1hkqa_ 106 PTIIPHLTMLHKEFTSYQLK 125 TMalign alignment (TM-score: 0.55 Raw score:33.12) d1ri7a1 1 -----------LDEIDKKIIKILQND------------GKAPLREISKIT-GL--AE-ST 33 ::::::::::::::: :::::::::::: :: :: :: d1hkqa_ 1 QSNKLIESSHTLTLNEKRLVLCAASLIDSRKPLPKDGYLTIRADTFAEVFGIDVKHAYAA 60 d1ri7a1 34 IHERIRKLRESG--------------VIKK-------------FT----AI--------- 53 ::::::::: :: :::: :: : d1hkqa_ 61 LDDAATKLF-NRDIRRYVKGKVVERMRWVFHVKYREGQGCVELGFSPTI-IPHLTMLHKE 118 d1ri7a1 54 -------IDPEALG 60 d1hkqa_ 119 FTSYQLK------- 125 HHsearch alignment (Probability: 0.07 E-value:0.02) d1ri7a1 17 KAPLREISKITGLAESTIHERIRKLRE 43 ::::::::::::::::::::::::::: d1hkqa_ 40 TIRADTFAEVFGIDVKHAYAALDDAAT 66