Query 040903
Match_columns 357
No_of_seqs 57 out of 59
Neff 2.5
Searched_HMMs 46136
Date Fri Mar 29 12:56:48 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040903.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040903hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1832 HIV-1 Vpr-binding prot 57.9 8.9 0.00019 43.9 3.2 10 126-135 1328-1337(1516)
2 PF03356 Pox_LP_H2: Viral late 34.3 19 0.00041 34.0 1.0 47 109-175 64-112 (189)
3 PHA03072 putative viral membra 31.6 22 0.00049 33.6 1.0 47 109-175 64-112 (190)
4 KOG3431 Apoptosis-related prot 22.1 60 0.0013 29.2 1.9 9 160-168 111-119 (129)
5 PHA03201 uracil DNA glycosylas 21.9 4.3E+02 0.0094 26.8 7.9 53 91-154 67-121 (318)
6 PF08346 AntA: AntA/AntB antir 21.4 28 0.0006 27.7 -0.3 10 329-338 55-64 (71)
7 PHA00008 J DNA packaging prote 21.0 40 0.00086 23.0 0.4 7 339-345 17-23 (26)
8 PF04726 Microvir_J: Microviru 19.1 39 0.00085 22.7 0.1 6 340-345 17-22 (24)
9 COG2344 AT-rich DNA-binding pr 19.1 47 0.001 31.9 0.7 42 124-175 22-63 (211)
10 PF03066 Nucleoplasmin: Nucleo 18.9 38 0.00083 30.1 0.0 8 258-265 92-99 (149)
No 1
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=57.85 E-value=8.9 Score=43.86 Aligned_cols=10 Identities=40% Similarity=0.690 Sum_probs=5.2
Q ss_pred HHhhcccccc
Q 040903 126 RIHNNRNKHK 135 (357)
Q Consensus 126 rih~~rk~~k 135 (357)
.+|..|-|++
T Consensus 1328 dvh~~r~k~p 1337 (1516)
T KOG1832|consen 1328 DVHTRRVKHP 1337 (1516)
T ss_pred hhcccccccc
Confidence 4555555544
No 2
>PF03356 Pox_LP_H2: Viral late protein H2; InterPro: IPR005023 This entry represents the late protein H2 found in Vaccinia and other poxviruses. This protein is a highly conserved viral membrane protein found in all sequenced poxviruses, containing an N-terminal transmembrane domain and four conserved cysteines thought to be involved in the formation of intramolecular disulphide bonds []. H2 has been shown to be necessary for entry into the host cell and virus-induced cell-cell fusion, but is not required for virus morphogenesis or the attachment of virus particles to cells. It is part of an entry-fusion complex composed of eight viral membrane proteins [].
Probab=34.32 E-value=19 Score=34.02 Aligned_cols=47 Identities=28% Similarity=0.707 Sum_probs=32.9
Q ss_pred cCcCCCCchHHHHHHHHHHhhccccccCCcchhHHhhhhhhhhhHHHHhhhccccccee--ccCCCCCc
Q 040903 109 PKANSCKSWQSVMEEIERIHNNRNKHKNKRPSWAESIGLKKEVMQFLTCLKNIRFDFRC--FGAFPRAD 175 (357)
Q Consensus 109 ~kk~~~k~w~svmeEierih~~rk~~k~~~~~W~e~lGikkd~m~FL~~Lr~~Rf~~rC--FGsfp~a~ 175 (357)
+=|+.-++|..++++=-+|...|-+.+ ++| +-|+ |.|+| ||+|-.++
T Consensus 64 RIKn~v~sWrpLV~~Kt~iEsdrGr~~--------~~~-r~d~-----------f~F~CvDFG~yf~pv 112 (189)
T PF03356_consen 64 RIKNNVKSWRPLVESKTKIESDRGRLL--------ALG-RDDL-----------FEFNCVDFGSYFLPV 112 (189)
T ss_pred HHHHhhhhhhHHHHHHHHHHhhhhhHh--------hcC-cccc-----------eEEEeeeccceeeEE
Confidence 334667899999998888877776655 444 3332 67788 79986665
No 3
>PHA03072 putative viral membrane protein; Provisional
Probab=31.63 E-value=22 Score=33.56 Aligned_cols=47 Identities=26% Similarity=0.673 Sum_probs=32.6
Q ss_pred cCcCCCCchHHHHHHHHHHhhccccccCCcchhHHhhhhhhhhhHHHHhhhccccccee--ccCCCCCc
Q 040903 109 PKANSCKSWQSVMEEIERIHNNRNKHKNKRPSWAESIGLKKEVMQFLTCLKNIRFDFRC--FGAFPRAD 175 (357)
Q Consensus 109 ~kk~~~k~w~svmeEierih~~rk~~k~~~~~W~e~lGikkd~m~FL~~Lr~~Rf~~rC--FGsfp~a~ 175 (357)
+=|+.-++|..++++=-+|...|-+.+ +++ +-|+ |.|+| ||+|-.++
T Consensus 64 RIKn~i~sWrpLV~~KT~iEsdrGr~~--------~~~-r~d~-----------f~F~CvDFG~yf~pv 112 (190)
T PHA03072 64 RIKNNVKSWRPLVESKTKLESDRGRLL--------AAG-RDDL-----------FEFNCVDFGSYFLPV 112 (190)
T ss_pred HHHHhhhhhhHHHHHHHHHHhhhhhHh--------hcC-Cccc-----------eEEEeeeccceeeEE
Confidence 334667899999998888877776655 444 3332 66788 79886665
No 4
>KOG3431 consensus Apoptosis-related protein/predicted DNA-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=22.08 E-value=60 Score=29.22 Aligned_cols=9 Identities=44% Similarity=0.910 Sum_probs=7.0
Q ss_pred cccccceec
Q 040903 160 NIRFDFRCF 168 (357)
Q Consensus 160 ~~Rf~~rCF 168 (357)
.|.||=|-|
T Consensus 111 kV~f~RRr~ 119 (129)
T KOG3431|consen 111 KVKFDRRRF 119 (129)
T ss_pred eeeeecccc
Confidence 477888887
No 5
>PHA03201 uracil DNA glycosylase; Provisional
Probab=21.88 E-value=4.3e+02 Score=26.84 Aligned_cols=53 Identities=9% Similarity=0.137 Sum_probs=29.0
Q ss_pred CCCCCCCceeeeccceeccCcCCCCchHHHHHHHHHHhhccccccCCcchhHHhhh--hhhhhhHH
Q 040903 91 IAEPTSPKVTCAGQIKVRPKANSCKSWQSVMEEIERIHNNRNKHKNKRPSWAESIG--LKKEVMQF 154 (357)
Q Consensus 91 ~~EPtSPKVTC~GQIkvr~kk~~~k~w~svmeEierih~~rk~~k~~~~~W~e~lG--ikkd~m~F 154 (357)
..-++.+...|.|-+-+.--....-.|..+..... ..++|.+.|. ++++.+..
T Consensus 67 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----------i~~~W~~~L~~e~~k~y~~~ 121 (318)
T PHA03201 67 TFSSSAPPRPPLGLDDAPAATPPPLDWTEFRRRFL-----------VGDAWRPLLEPELANPLTAR 121 (318)
T ss_pred ccCCCCCCCCccccccccccccCCcchHHHHHhcc-----------CCHHHHHHHHHHhccHHHHH
Confidence 34455566677665443333334446876654431 3457999986 55554443
No 6
>PF08346 AntA: AntA/AntB antirepressor; InterPro: IPR013557 In Escherichia coli the two proteins AntA and AntB have 62% amino acid identities near their N termini. AntA appears to be encoded by a truncated and divergent copy of AntB. The two proteins are homologous to putative antirepressors found in numerous bacteriophages, such as the hypothetical antirepressor protein encoded by the gene LO142 of the Bacteriophage 933W.
Probab=21.43 E-value=28 Score=27.72 Aligned_cols=10 Identities=50% Similarity=0.870 Sum_probs=8.0
Q ss_pred eecccccccc
Q 040903 329 YKISSDVAKE 338 (357)
Q Consensus 329 ~klS~DIAKE 338 (357)
|.||+|+|||
T Consensus 55 Y~LTLdmAKe 64 (71)
T PF08346_consen 55 YHLTLDMAKE 64 (71)
T ss_pred EEEeHHHHHH
Confidence 6788888887
No 7
>PHA00008 J DNA packaging protein
Probab=21.00 E-value=40 Score=23.05 Aligned_cols=7 Identities=43% Similarity=1.032 Sum_probs=4.1
Q ss_pred eeeecCC
Q 040903 339 TWIVDGM 345 (357)
Q Consensus 339 TWvVGG~ 345 (357)
-|+|||.
T Consensus 17 LWYVGGt 23 (26)
T PHA00008 17 LWYVGGT 23 (26)
T ss_pred EEEeccE
Confidence 3666664
No 8
>PF04726 Microvir_J: Microvirus J protein; InterPro: IPR006815 This small protein is involved in DNA packaging, interacting with DNA via its hydrophobic C terminus. In bacteriophage phi-X174, J is present in 60 copies, and forms an S-shaped polypeptide chain without any secondary structure. It is thought to interact with DNA through simple charge interactions [].; GO: 0003677 DNA binding, 0019073 viral DNA genome packaging, 0019028 viral capsid; PDB: 1M06_J 1GFF_3 1RB8_J 2BPA_3.
Probab=19.08 E-value=39 Score=22.70 Aligned_cols=6 Identities=50% Similarity=1.276 Sum_probs=1.7
Q ss_pred eeecCC
Q 040903 340 WIVDGM 345 (357)
Q Consensus 340 WvVGG~ 345 (357)
|+|||.
T Consensus 17 wyvgg~ 22 (24)
T PF04726_consen 17 WYVGGT 22 (24)
T ss_dssp --SSS-
T ss_pred EEecce
Confidence 555554
No 9
>COG2344 AT-rich DNA-binding protein [General function prediction only]
Probab=19.07 E-value=47 Score=31.92 Aligned_cols=42 Identities=26% Similarity=0.532 Sum_probs=29.1
Q ss_pred HHHHhhccccccCCcchhHHhhhhhhhhhHHHHhhhcccccceeccCCCCCc
Q 040903 124 IERIHNNRNKHKNKRPSWAESIGLKKEVMQFLTCLKNIRFDFRCFGAFPRAD 175 (357)
Q Consensus 124 ierih~~rk~~k~~~~~W~e~lGikkd~m~FL~~Lr~~Rf~~rCFGsfp~a~ 175 (357)
.|++|...+.+- ++-.-.+++||.-. -||=||.|||.|-...
T Consensus 22 le~l~a~~v~rv-sS~els~~~~vdsa---------tIRrDfSYFG~lGkrG 63 (211)
T COG2344 22 LERLHASGVERV-SSKELSEALGVDSA---------TIRRDFSYFGELGKRG 63 (211)
T ss_pred HHHHHHcCCcee-cHHHHHHHhCCCHH---------HHhhhhHHHHhcCCCC
Confidence 567777777633 22236678887653 4899999999995554
No 10
>PF03066 Nucleoplasmin: Nucleoplasmin; InterPro: IPR004301 The nucleophosmin/nucleoplasmin family of chaperones includes nucleophosmin, nucleoplasmin and nucleoplasmin-like proteins. They function as nuclear chaperones which are needed for the proper assembly of nucleosomes and the attainment of proper higher order chromatin structures [].; GO: 0003676 nucleic acid binding; PDB: 2P1B_E 1XB9_I 1XE0_C 1NLQ_A 2VTX_E 1K5J_D 1EJY_N 1EE5_B 3T30_J.
Probab=18.86 E-value=38 Score=30.06 Aligned_cols=8 Identities=38% Similarity=1.099 Sum_probs=5.4
Q ss_pred hhcccCcc
Q 040903 258 MRCRSAPA 265 (357)
Q Consensus 258 MRCRSAPA 265 (357)
.+|-|.|.
T Consensus 92 L~~GsGPV 99 (149)
T PF03066_consen 92 LKCGSGPV 99 (149)
T ss_dssp EEESSS-E
T ss_pred EEecCCCE
Confidence 37999995
Done!