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: T0542_Ad2+3.pdb
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL


Query <-- 1.905 --> Intermediate <-- 0.877 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1miob_) through the intermediate protein (d1vl2a1) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1vl2a1 Argininosuccinate synthetase,​ N-​terminal domainAdenine nucleotide alpha hydrolases-​likeAdenine nucleotide alpha hydrolase-​likeα/β
Hit d1miob_ Nitrogenase iron-​molybdenum protein,​ beta chain​(​Helical backbone​(​ metal receptorChelatase-​likeα/β

Supporting Alignments

Query <-- 1.905 --> Intermediate
DALI alignment (Z-score: 12.5 Raw score:953.20) query 1 dadeevysalvvglrayvakngFRSVLIGLSGGIDSALVAAIACDALGaqNVYGVSMPSK 60 :::::::::::::::::::::::::: :::::::::: d1vl2a1 1 ----------------------KEKVVLAYSGGLDTSVILKWLCEKGF--DVIAYVANVG 36 query 61 ySSDHsKGDAAELARRTGL-NFRTVSIEPMFDAY-MASLG-------ltGLAEENLQSRL 111 :::: ::::::::::::: :::::::::::::: ::::: ::::::::::: d1vl2a1 37 -QKDD-FVAIKEKALKTGAsKVYVEDLRREFVTDyIFTALlgnamyegrYLLGTAIARPL 94 query 112 RGTTLMAISNQEGH-IVLAPGNKselavGYST-lyGDSV--------gAYGPIK----DV 157 :::::::::::::: :::::::: :::: :::: :::::: :: d1vl2a1 95 IAKRQVEIAEKEGAqYVAHGATG-----KGNDqvrFELTyaalnpnlkVISPWKdpefLA 149 query 158 YK-TSIFRLAEWRnraaaergqtPPIPeasitkpdypvldailelyvdrdtgadaivaag 216 :: :::::::::: :::: d1vl2a1 150 KFkTDLINYAMEK----------GIPI--------------------------------- 166 query 217 ydrelvvktlrmvdtaeykrrqyppgtkisakgfgkdrrlpitnrwregh 266 d1vl2a1 167 -------------------------------------------------- 167 FAST alignment (Normalized score: 7.91 Raw score:1662.00) query 1 DADEEVYSALVVGLRAYVAKNGF-RSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPS 59 :::::::::::::::::::::: ::: ::::::::: d1vl2a1 1 -----------------------KEKVVLAYSGGLDTSVILKWLCE-KGF-DVIAYVANV 35 query 60 KYSSDHSKGDAAELARRTG-LNFRTVSIEPMFD-AYMA---SLGLTGL-------AEENL 107 :::: ::::::::::::: ::::::::::::: :::: :::: ::::: d1vl2a1 36 -GQKD-DFVAIKEKALKTGASKVYVEDLRREFVTDYIFTALLGNA---MYEGRYLLGTAI 90 query 108 QSRLRGTTLMAISNQEG-HIVLAPGNKSELAVGYSTLY------GDSVG---------AY 151 ::::::::::::::::: :::::::::: :::: :: d1vl2a1 91 ARPLIAKRQVEIAEKEGAQYVAHGATGK----------GNDQVRFELT-YAALNPNLKVI 139 query 152 GPIKDVY----------KTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVLDAILEL 201 :: :::::::::: d1vl2a1 140 SP-----WKDPEFLAKFKTDLINYAME--------------------------------- 161 query 202 YVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNR 261 d1vl2a1 162 ------------------------------------------------------------ 162 query 262 WREGH----- 266 d1vl2a1 162 -----KGIPI 166 TMalign alignment (TM-score: 0.47 Raw score:124.53) query 1 DADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSK 60 :::::::::::::::::::::::::: :::::::::: d1vl2a1 1 ----------------------KEKVVLAYSGGLDTSVILKWLCEKGF--DVIAYVANVG 36 query 61 YSSDHSKGDAAELARRTGL-NFRTVSIEPMFDAY-MASLG---LT----GLAEENLQSRL 111 :::: ::::::::::::: :::::::::::::: ::::: :: ::::::::::: d1vl2a1 37 -QKDD-FVAIKEKALKTGASKVYVEDLRREFVTDYIFTALLGNAMYEGRYLLGTAIARPL 94 query 112 RGTTLMAISNQEGH-IVLAPGNKSELAVGYSTLYGDS-VG--------AYGPIK-D--VY 158 :::::::::::::: :::::::: : :::::::: :: :::::: : :: d1vl2a1 95 IAKRQVEIAEKEGAQYVAHGATG--K---GNDQVRFELTYAALNPNLKVISPWKDPEFLA 149 query 159 KTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVLDAILELYVDRDTGADAIVAAGYD 218 :::::::::::: : : ::: d1vl2a1 150 -KFKTDLINYAME-K------G-IPI---------------------------------- 166 query 219 RELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH 266 d1vl2a1 167 ------------------------------------------------ 167 HHsearch alignment (Probability: 0.97 E-value:0.00) query 24 RSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSKYSSDHSKGDAAELARRTGL-NFR 82 ::::::::::::::::::::::: ::: ::::::: ::::::::::::::::::: ::: d1vl2a1 2 EKVVLAYSGGLDTSVILKWLCEK-GFD-VIAYVAN--VGQKDDFVAIKEKALKTGASKVY 57 query 83 TVSIEPMFDAYMASLGLTGLA--------EENLQSRLRGTTLMAISNQEGHIVLAPG--- 131 ::::::::::::::::::::: :::::::::::::::::::::::::::: d1vl2a1 58 VEDLRREFVTDYIFTALLGNAMYEGRYLLGTAIARPLIAKRQVEIAEKEGAQYVAHGATG 117 query 132 ---NKSELAVGYSTLYGDSVGAYGP-----IKDVYKTSIFRLAEWRNRAA 173 :::::::::::::::::: ::: :::::::::::::::::::: d1vl2a1 118 KGNDQVRFELTYAALNPNLKV-ISPWKDPEFLAKFKTDLINYAMEKGIPI 166
Intermediate <-- 0.877 --> Hit
DALI alignment (Z-score: 5.0 Raw score:485.50) d1vl2a1 1 ------------------------------------------------------------ 1 d1miob_ 1 ldatpkeiverkalrinpaktcqpvgamyaalgihnclphshgsqgccsyhrtvlsrhfk 60 d1vl2a1 1 ------------------------------------------------------------ 1 d1miob_ 61 epamastssftegasvfgggsniktavknifslynpdiiavhttclsetlgddlptyisq 120 d1vl2a1 1 ------------------------------------------------------------ 1 d1miob_ 121 medagsipegklvihtntpsyvgshvtgfanmvqgivnylsentgakngkinvipgfvgp 180 d1vl2a1 1 ------------------------------------------------------------ 1 d1miob_ 181 admreikrlfeamdipyimfpdtsgvldgpttgeykmypeggtkiedlkdtgnsdltlsl 240 d1vl2a1 1 ------------------------------------------------------------ 1 d1miob_ 241 gsyasdlgaktlekkckvpfktlrtpigvsatdefimalseatgkevpasieeergqlid 300 d1vl2a1 1 ----------KEKVVLAYSGGlDTSVILKWLCEKGFDV-IAYVANvgqkddFVAIKEKAL 49 ::::::::::: :::::::::::::::: :::::: ::::::::: d1miob_ 301 lmidaqqylqGKKVALLGDPD-EIIALSKFIIELGAIPkYVVTGT-----pGMKFQKEID 354 d1vl2a1 50 KTG------aSKVYVEdlrrefvtdyiftallgnamyegryllgtaiarplIAKRQVEIA 103 ::: :::::: ::::::::: d1miob_ 355 AMLaeagiegSKVKVE----------------------------------gDFFDVHQWI 380 d1vl2a1 104 EKEGAQYVAHgatgkgndQVRFElTYAALNPnLKVISP---------wkdPEFL--AKFK 152 :::::::::: ::::: ::::::: :::::: :::: :::: d1miob_ 381 KNEGVDLLIS--------NTYGK-FIAREEN-IPFVRFgfpimdryghyyNPKVgyKGAI 430 d1vl2a1 153 -------------tdlinyamekgipi 166 d1miob_ 431 rlveeitnvildkierecteedfevvr 457 FAST alignment (Normalized score: 1.77 Raw score:486.30) d1vl2a1 1 K-----------------------------------EKVVLAYSG--------------- 10 :::::: d1miob_ 1 -LDATPKEIVERKALRINPAKTCQPVGAMYAALGIHNCLPHS---HGSQGCCSYHRTVLS 56 d1vl2a1 11 -----------------------GLDTSVILKWLCE-KGF-DVIAYVA---NVGQKDDFV 42 ::::::::::::: ::: :::::: ::::::::: d1miob_ 57 RHFKEPAMASTSSFTEGASVFGGGSNIKTAVKNIFSLYNPDIIAVHT-TCLSETLGDDLP 115 d1vl2a1 43 AIKEKALKTGA---------SKVYVEDLRREFVTDYIFTALLGNAMYEGRYLLGTAI-AR 92 :::::::: :::::::::: :: d1miob_ 116 TYISQMED---AGSIPEGKLVIHTNTPSYV---------------------------GSH 145 d1vl2a1 93 PLIAKRQVEIAEKEGAQYVAHGATGKGNDQVRFELTYAALNPNLKVISPWKDPEFLAKFK 152 ::::::::::::: d1miob_ 146 VTGFANMVQGIVN----------------------------------------------- 158 d1vl2a1 153 TDLINYAMEKGIPI---------------------------------------------- 166 d1miob_ 159 --------------YLSENTGAKNGKINVIPGFVGPADMREIKRLFEAMDIPYIMFPDTS 204 d1vl2a1 167 ------------------------------------------------------------ 167 d1miob_ 205 GVLDGPTTGEYKMYPEGGTKIEDLKDTGNSDLTLSLGSYASDLGAKTLEKKCKVPFKTLR 264 d1vl2a1 167 ------------------------------------------------------------ 167 d1miob_ 265 TPIGVSATDEFIMALSEATGKEVPASIEEERGQLIDLMIDAQQYLQGKKVALLGDPDEII 324 d1vl2a1 167 ------------------------------------------------------------ 167 d1miob_ 325 ALSKFIIELGAIPKYVVTGTPGMKFQKEIDAMLAEAGIEGSKVKVEGDFFDVHQWIKNEG 384 d1vl2a1 167 ------------------------------------------------------------ 167 d1miob_ 385 VDLLISNTYGKFIAREENIPFVRFGFPIMDRYGHYYNPKVGYKGAIRLVEEITNVILDKI 444 d1vl2a1 167 ------------- 167 d1miob_ 445 ERECTEEDFEVVR 457 TMalign alignment (TM-score: 0.47 Raw score:78.67) d1vl2a1 1 ------------------------------------------------------------ 1 d1miob_ 1 LDATPKEIVERKALRINPAKTCQPVGAMYAALGIHNCLPHSHGSQGCCSYHRTVLSRHFK 60 d1vl2a1 1 ------------------------------------------------------------ 1 d1miob_ 61 EPAMASTSSFTEGASVFGGGSNIKTAVKNIFSLYNPDIIAVHTTCLSETLGDDLPTYISQ 120 d1vl2a1 1 ------------------------------------------------------------ 1 d1miob_ 121 MEDAGSIPEGKLVIHTNTPSYVGSHVTGFANMVQGIVNYLSENTGAKNGKINVIPGFVGP 180 d1vl2a1 1 ------------------------------------------------------------ 1 d1miob_ 181 ADMREIKRLFEAMDIPYIMFPDTSGVLDGPTTGEYKMYPEGGTKIEDLKDTGNSDLTLSL 240 d1vl2a1 1 ------------------------------------------------------------ 1 d1miob_ 241 GSYASDLGAKTLEKKCKVPFKTLRTPIGVSATDEFIMALSEATGKEVPASIEEERGQLID 300 d1vl2a1 1 ----------KEKVVLAYSGGLDTSVILKWLCEKGFDVIAYVANVGQKDDFVAIKEKALK 50 ::::::::::: :::::::::::::::::::::: : ::: :::::::: d1miob_ 301 LMIDAQQYLQGKKVALLGDPD-EIIALSKFIIELGAIPKYVVTG--T-PGM-KFQKEIDA 355 d1vl2a1 51 TGA---S--KVYVEDLRREFVTDYIFTALLGNAMYEGRYLLGTAIARPLIAKRQVEIAEK 105 ::: : ::::::: ::::::::::: d1miob_ 356 MLAEAGIEGSKVKVEG---------------------------------DFFDVHQWIKN 382 d1vl2a1 106 EGAQYVAHGATGKGNDQVRFELTYAALNPNLKVISPW--------K--DPEFLAKFKTD- 154 :::::::: ::::: :::::: :::::::: : :::::::: : d1miob_ 383 EGVDLLIS--------NTYGK-FIAREE-NIPFVRFGFPIMDRYGHYY-NPKVGYKG-AI 430 d1vl2a1 155 ---------------------------LINYAMEKGIPI 166 d1miob_ 431 RLVEEITNVILDKIERECTEEDFEVVR------------ 457 HHsearch alignment (Probability: 0.44 E-value:0.01) d1vl2a1 17 ILKWLCE-KGFDVIAYVANVGQKDDFVAIKEKALKTGASKVYVEDLRREFVTDYIFTALL 75 ::::::: :::::::::::::::::::::::::::::::::::: ::::::::::::: d1miob_ 248 GAKTLEKKCKVPFKTLRTPIGVSATDEFIMALSEATGKEVPASI---EEERGQLIDLMID 304 d1vl2a1 76 GNAMYEGRYLLGTAIARPLIAKRQVEIAEKEGAQYVAHGATGK 118 :::::::::::: ::::::::::::::::::::::::::::: d1miob_ 305 AQQYLQGKKVAL--LGDPDEIIALSKFIIELGAIPKYVVTGTP 345