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: T592_B.pdb B
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL


Query <-- 0.610 --> Intermediate <-- 1.570 --> Hit

SVM
score
SVM
score

The query (T592_B.pdb B) is transitively linked to the hit (d1vdda_) through the intermediate protein (d1t6t1_) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1t6t1_ Hypothetical protein aq 2086Toprim domain (Pfam 01751)Toprim domain (Pfam 01751)α/β
Hit d1vdda_ Recombination protein RecRRecombination protein RecRRecombination protein RecRmulti

Supporting Alignments

Query <-- 0.610 --> Intermediate
DALI alignment (Z-score: 4.8 Raw score:306.10) query 1 npneayrhymkklsyetDIADLSIDikkgyEGIIVVDvRDAEaYKECH----IPTAISIP 56 :::::::: ::::::: :::: ::::: :::::::: d1t6t1_ 1 -----------prnlseWIKELKKA----sREAVILV-EGKN-DKKALskfsIKNVIDLS 43 query 57 gnKINEdTTKRLSKEK-VIITYCWGPA--CNGATKAAAKFAQLGFRVKE------liggi 107 :::: ::::::::: :::::::::: :::::::::::::::::::: d1t6t1_ 44 gkRYAD-VVDMLEGKWeKVILLFDLDThgERINQKMKELLSSQGFLVDEnfrnflkkwni 102 query 108 EYWRkengevegtlgakadlfwnmkkesle 137 :::: d1t6t1_ 103 IHIE------------------------ei 108 FAST alignment (Normalized score: 4.56 Raw score:554.40) query 1 NPNEAYRHYMKKLSYET------DIADLSIDIKKGYEGIIVVDVRDAEAYKECH------ 48 ::::::::: ::::::: ::::::: d1t6t1_ 1 -----------------PRNLSEWIKELKKAS----REAVILV-EGKNDKK---ALSKFS 35 query 49 IPTAISIPGNKI-----NEDTTKRLSKE--KVIITYCWGPA---CNGATKAAAKFAQLGF 98 :::::: ::::::: ::: :::::::::: :::::::::::::::: d1t6t1_ 36 IKNVID------LSGKRYADVVDM-LEGKWEKVILLFDLD-THGERINQKMKELLSSQGF 87 query 99 RVKELIGGIEYWRKENGEVEGTLGAKADLFWNMKKESLE------------------ 137 ::: d1t6t1_ 88 LVD------------------------------------ENFRNFLKKWNIIHIEEI 108 TMalign alignment (TM-score: 0.48 Raw score:65.09) query 1 --NPNEAYRHYMKKLSYETDIA-DLS-IDIKKGYEGIIVVDVRDAEAYKECHI--P---- 50 :: ::: ::: :::::::::: : :: ::: : d1t6t1_ 1 PR------------------NLSEWIKELK-KASREAVILV-E----GK-NDKKALSKFS 35 query 51 -T-AISIPGNKINEDTTKRL--SKEKVIITYCWGPA--CNGATKAAAKFAQLGFRVKE-- 102 : :::::::::: :::::: ::: :::::::::: :::::::::::::::::::: d1t6t1_ 36 IKNVIDLSGKRYA-DVVDMLEGKWE-KVILLFDLDTHGERINQKMKELLSSQGFLVDENF 93 query 103 LI-GG---IEYWRKENGEVEGTLGAKADLFWNMKKESLE 137 :: :: :::::: : d1t6t1_ 94 RNFLKKWNIIHIEE--I---------------------- 108 HHsearch alignment (Probability: 0.05 E-value:0.04) query 49 IPTAISIPGNKINEDTTKRLSKEKVIITYCWGPACNGATKAAA----KFAQLGFRV 100 ::::::::::::::::::::::::::::::::: :::::::: ::::::::: d1t6t1_ 36 IKNVIDLSGKRYADVVDMLEGKWEKVILLFDLD--THGERINQKMKELLSSQGFLV 89
Intermediate <-- 1.570 --> Hit
DALI alignment (Z-score: 7.8 Raw score:440.90) d1t6t1_ 1 ------------------------------------------------------------ 1 d1vdda_ 1 mkyppslvslirelsrlpgigpksaqrlafhlfeqpredierlasalleakrdlhvcpic 60 d1t6t1_ 1 ---prnlsewikelkkaSREAVILVEGKNDKKALSK-FSIK-NVIDLS------------ 43 ::::::::::::::::::: :::: :::::: d1vdda_ 61 fnitdaekcdvcadpsrDQRTICVVEEPGDVIALERsGEYRgLYHVLHgvlspmngvgpd 120 d1t6t1_ 44 GKRYADVVDMLEGKwEKVILLFDLDTHGERINQKMKELLSSQGFLVDEnfRNFLkkWNII 103 :::::::::::::: ::::::::::::::::::::::::::::::::: :::: :::: d1vdda_ 121 KLHIKPLLPRVGQG-MEVILATGTTVEGDATALYLQRLLEPLGAAISR--IAYG--VPVG 175 d1t6t1_ 104 -------------------hieei 108 d1vdda_ 176 gsleytdevtlgraltgrqtvskp 199 FAST alignment (Normalized score: 5.69 Raw score:834.30) d1t6t1_ 1 PRNLSEWIKELKKA---------------------------------------------- 14 d1vdda_ 1 --------------MKYPPSLVSLIRELSRLPGIGPKSAQRLAFHLFEQPREDIERLASA 46 d1t6t1_ 15 -------------------------------SREAVILVEGKNDKKALSKFSIK-----N 38 :::::::::::::::::::: : d1vdda_ 47 LLEAKRDLHVCPICFNITDAEKCDVCADPSRDQRTICVVEEPGDVIALERS---GEYRGL 103 d1t6t1_ 39 VIDLSG---------------KRYADVVDMLEGKWEKVILLFDLDTHGERINQKMKELLS 83 ::: ::::::::::::: ::::::::::::::::::::::::: d1vdda_ 104 YHV---LHGVLSPMNGVGPDKLHIKPLLPRVGQG-MEVILATGTTVEGDATALYLQRLLE 159 d1t6t1_ 84 SQGFLVDENFRNFLKKWNIIHIEEI--------------------------------- 108 ::::::: d1vdda_ 160 PLGAAIS------------------RIAYGVPVGGSLEYTDEVTLGRALTGRQTVSKP 199 TMalign alignment (TM-score: 0.62 Raw score:67.01) d1t6t1_ 1 ------------------------------------------------------------ 1 d1vdda_ 1 MKYPPSLVSLIRELSRLPGIGPKSAQRLAFHLFEQPREDIERLASALLEAKRDLHVCPIC 60 d1t6t1_ 1 ----------------PRNLSEWIKELKKASR-EAVILVEGKNDKKALSKFS-IK-NVID 41 :: ::::::::::::::::::: :: :::: d1vdda_ 61 FNITDAEKCDVCADPS--------------RDQRTICVVEEPGDVIALERSGEYRGLYHV 106 d1t6t1_ 42 LS-------------GKRYADVVDMLEGKWEKVILLFDLDTHGERINQKMKELLSSQGFL 88 :: :: :::::::::: ::::::::::::::::::::::::::::::: d1vdda_ 107 LHGVLSPMNGVGPDKLH-IKPLLPRVGQ-GMEVILATGTTVEGDATALYLQRLLEPLGAA 164 d1t6t1_ 89 VDENFRNFLKKWNI-------------------------IHIEEI 108 ::: : : ::::: d1vdda_ 165 ISR--I-A-YGVPVGGSLEYTDEVTLGRALTGRQTVSKP------ 199 HHsearch alignment (Probability: 0.96 E-value:0.00) d1t6t1_ 14 ASREAVILVEGKNDKKALSKFS-IKNVIDLSGKRYAD------------VVDMLEGKWEK 60 :::::::::::::::::::::: :::::::::::::: ::::::::::: d1vdda_ 77 RDQRTICVVEEPGDVIALERSGEYRGLYHVLHGVLSPMNGVGPDKLHIKPLLPRVGQGME 136 d1t6t1_ 61 VILLFDLDTHGERINQKMKELLSSQGFLVD 90 :::::::::::::::::::::::::::::: d1vdda_ 137 VILATGTTVEGDATALYLQRLLEPLGAAIS 166