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 <-- 0.752 --> Hit

SVM
scoreSVM
score

The query (T592_B.pdb B) is transitively linked to the hit (d1hf2a2) 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 d1hf2a2 Cell-​division inhibitor MinC,​ N-​terminal domainCell-​division inhibitor MinC,​ N-​terminal domainCell-​division inhibitor MinC,​ N-​terminal domainα/β

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 <-- 0.752 --> Hit

DALI alignment (Z-score: 3.4   Raw score:228.10)

d1t6t1_        1 prnlsewikelKKASreAVILVEGkndkkalskfsiknvidlsgKRYADVVDMLEGK---     57
                            ::::  :::::::                    :::::::::::::   
d1hf2a2        1 -----mvdfkmTKEG--LVLLIKD---------------yqnleEVLNAISARITQMggf     38

d1t6t1_       58 ---wEKVILLF-DLDThGERINQKMKELLSSQGFLVDENFR--NFLKkwniihieei    108
                     ::::::: :::: ::::::::::::::::::::::::  ::::          
d1hf2a2       39 fakgDRISLMIeNHNK-HSQDIPRIVSHLRNLGLEVSQILVgkVQSR-----ttves     89

FAST alignment (Normalized score: 2.81   Raw score:275.60)

d1t6t1_        1 PRNLSEWIKELKKASRE---------AVILVEGKNDKKALSKFSIKNVIDLSG----KRY     47
                                           :::::                          :::
d1hf2a2        1 -----------------MVDFKMTKEGLVLL----------------------IKDYQNL     21

d1t6t1_       48 ADVVDMLEGKW---------------EKVILLFDL--DTHGERINQKMKELLSSQGFLVD     90
                 ::::::                    :::::::    :::::::::::::::::::::: 
d1hf2a2       22 EEVLNA-----ISARITQMGGFFAKGDRISLMI--ENHNKHSQDIPRIVSHLRNLGLEV-     73

d1t6t1_       91 ENFRNFLKKWNIIHIEEI----------------    108
                                                   
d1hf2a2       74 ------------------SQILVGKVQSRTTVES     89

TMalign alignment (TM-score: 0.44   Raw score:47.02)

d1t6t1_        1 -----PRNLSEWIKELKKASREAVILVEGK----NDKKALSKFSIKNVIDLS-GKRYADV     50
                                :::::  ::::::::                    ::  ::::::
d1hf2a2        1 MVDFK----------MTKEG--LVLLIKDYQNLE----------------EVL-NAISAR     31

d1t6t1_       51 VDMLEGKW---EKVILLF-DLDTHGERINQKMKELLSSQGFLVDENFR---NFLKK----     99
                 ::::::::   ::::::: ::: :::::::::::::::::::::::::    ::::    
d1hf2a2       32 ITQMGGFFAKGDRISLMIENHN-KHSQDIPRIVSHLRNLGLEVSQILVGKV-QSRTTVES     89

d1t6t1_      100 WNIIHIEEI    108
                          
d1hf2a2       90 ---------     90

HHsearch alignment (Probability: 0.02   E-value:0.09)

d1t6t1_       16 REAVILVEGKNDKKALSKFSIKNVIDLSGKRYADVVDMLEGKWEKVILLFDLDTHGERIN     75
                 ::::::::::::::::::: ::::::        ::::::::::::::::::::::::::
d1hf2a2        9 EGLVLLIKDYQNLEEVLNA-ISARIT--------QMGGFFAKGDRISLMIENHNKHSQDI     59

d1t6t1_       76 QKMKELLSSQGFLVDENF     93
                 ::::::::::::::::::
d1hf2a2       60 PRIVSHLRNLGLEVSQIL     77