Query 027709
Match_columns 220
No_of_seqs 140 out of 205
Neff 2.6
Searched_HMMs 46136
Date Fri Mar 29 14:00:20 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027709.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027709hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1561 CCAAT-binding factor, 100.0 5E-44 1.1E-48 320.7 9.8 118 66-190 126-248 (307)
2 smart00521 CBF CCAAT-Binding t 100.0 1.7E-38 3.8E-43 231.2 5.9 62 123-184 1-62 (62)
3 PF02045 CBFB_NFYA: CCAAT-bind 100.0 5.5E-36 1.2E-40 215.8 4.4 57 125-181 1-58 (58)
4 COG5224 HAP2 CCAAT-binding fac 99.8 4.5E-21 9.7E-26 168.4 3.4 66 124-191 157-222 (248)
5 PF06203 CCT: CCT motif; Inte 77.3 3.2 7E-05 29.0 3.1 28 158-186 18-45 (45)
6 KOG1561 CCAAT-binding factor, 72.6 0.95 2.1E-05 42.0 -0.6 47 138-189 14-60 (307)
7 PF15046 DUF4532: Protein of u 40.8 84 0.0018 29.5 6.1 49 124-183 131-196 (279)
8 PF04615 Utp14: Utp14 protein; 15.1 1E+02 0.0023 31.0 2.0 44 132-175 231-293 (735)
9 KOG4823 Uncharacterized conser 15.0 74 0.0016 30.4 0.9 21 160-180 141-171 (328)
10 PF02162 XYPPX: XYPPX repeat ( 14.5 1.4E+02 0.003 17.1 1.5 12 89-100 2-13 (15)
No 1
>KOG1561 consensus CCAAT-binding factor, subunit B (HAP2) [Transcription]
Probab=100.00 E-value=5e-44 Score=320.67 Aligned_cols=118 Identities=50% Similarity=0.823 Sum_probs=101.8
Q ss_pred cCcccccc-cCCCCCCCcccccccCCCCCCCCCCCCCCc--cchhhhhcccc-CCCCCCCCCCC-CceeechhhhHHHHH
Q 027709 66 AGHAMAPA-AYPYPDPYYRSIFAPYDAQPYPPQPYGGQP--MVHLQLMGIQQ-AGVPLPTDAVE-EPVFVNAKQYHGILR 140 (220)
Q Consensus 66 ~g~s~a~~-~yPY~Dpyygg~~aaYg~q~~~~~~y~~q~--m~~~q~~G~~~-~r~plp~~~~e-ePvyVNaKQY~rIlR 140 (220)
..|..+++ .+||.+|||+|+++.++ . |++++ .+++|+.||.+ .++|||.++.| |||||||||||+|||
T Consensus 126 ~~~~~~~~s~~~~~~p~~~g~~~~~~--~-----y~~~~~~~~~~q~~g~~~~~r~pLP~~~~e~ePl~VNaKQY~~Ilr 198 (307)
T KOG1561|consen 126 SMSPANNTSGNPITSPHYRGVLDMSG--A-----YSGQPTNTASTQYSGPVPHDRTPLPQTDSETEPLYVNAKQYHRILR 198 (307)
T ss_pred ccccccccccCCCCCCcccceecccc--c-----ccCCCCccccccccCCCCcCcccCCccccCCCceeEcHHHHHHHHH
Confidence 34544544 47899999999999543 2 33333 35778999988 99999999877 999999999999999
Q ss_pred HHHHHHHHHhhhhhhhcCCCcccchhhHHHhhccCCCCCcccccccchhh
Q 027709 141 RRQSRAKAESENKVLKSRKPYLHESRHLHALRRARGCGGRFLNSKKNENQ 190 (220)
Q Consensus 141 RRq~RaklE~~~kl~k~rkpYLHESRH~HAm~R~RG~gGRFL~~k~~~~~ 190 (220)
||++|||||+++||+|.||||||||||+|||||+||+||||||+||.+.+
T Consensus 199 RRq~RaKlEa~~klik~RkpYLHESRH~HAmkR~RG~GGRFln~k~~~~~ 248 (307)
T KOG1561|consen 199 RRQARAKLEATTKLIKARKPYLHESRHLHAMKRARGEGGRFLNTKEYHDD 248 (307)
T ss_pred HHHHHhhhhhcccchhhcCccccchhhHHHhhcccCCCCCCCchhhhhhh
Confidence 99999999999999999999999999999999999999999999996654
No 2
>smart00521 CBF CCAAT-Binding transcription Factor.
Probab=100.00 E-value=1.7e-38 Score=231.21 Aligned_cols=62 Identities=76% Similarity=1.183 Sum_probs=60.1
Q ss_pred CCCCceeechhhhHHHHHHHHHHHHHHhhhhhhhcCCCcccchhhHHHhhccCCCCCccccc
Q 027709 123 AVEEPVFVNAKQYHGILRRRQSRAKAESENKVLKSRKPYLHESRHLHALRRARGCGGRFLNS 184 (220)
Q Consensus 123 ~~eePvyVNaKQY~rIlRRRq~RaklE~~~kl~k~rkpYLHESRH~HAm~R~RG~gGRFL~~ 184 (220)
++|+|||||||||++|||||++|||+|+++||++.||||||||||+|||+|+||+||||||+
T Consensus 1 ~~~~piyVNaKQy~~IlrRR~~Rak~e~~~kl~~~rkpYlhESRH~HAm~R~Rg~gGRFl~~ 62 (62)
T smart00521 1 AEEEPVYVNAKQYHRILRRRQARAKLEAQGKLPKERKPYLHESRHLHAMRRPRGSGGRFLNT 62 (62)
T ss_pred CCCcceeEcHHHHHHHHHHHHHHHHHHHhcchhhccCCcccchhHHHHHccCcCCCCCCCCC
Confidence 36899999999999999999999999999999999999999999999999999999999985
No 3
>PF02045 CBFB_NFYA: CCAAT-binding transcription factor (CBF-B/NF-YA) subunit B; InterPro: IPR001289 The CCAAT-binding factor (CBFB/NF-YA) is a mammalian transcription factor that binds to a CCAAT motif in the promoters of a wide variety of genes, including type I collagen and albumin []. The factor is a heteromeric complex of A and B subunits, both of which are required for DNA-binding []. The subunits can interact in the absence of DNA-binding, conserved regions in each being important in mediating this interaction. The B subunit contains a region of similarity with the yeast protein HAP2 []. For the B subunit it has been suggested that the N-terminal portion of the conserved region is involved in subunit interaction and the C-terminal region involved in DNA-binding [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=100.00 E-value=5.5e-36 Score=215.77 Aligned_cols=57 Identities=75% Similarity=1.184 Sum_probs=56.2
Q ss_pred CCceeechhhhHHHHHHHHHHHHHHhhhhh-hhcCCCcccchhhHHHhhccCCCCCcc
Q 027709 125 EEPVFVNAKQYHGILRRRQSRAKAESENKV-LKSRKPYLHESRHLHALRRARGCGGRF 181 (220)
Q Consensus 125 eePvyVNaKQY~rIlRRRq~RaklE~~~kl-~k~rkpYLHESRH~HAm~R~RG~gGRF 181 (220)
|+|||||||||++|||||++|||||+++|+ ++.||||||||||+|||+|+||+||||
T Consensus 1 ~~piyVNaKQY~rIlrRR~~Rakle~~~k~~~~~rk~YlheSRH~HA~~R~Rg~gGRF 58 (58)
T PF02045_consen 1 EEPIYVNAKQYHRILRRRQARAKLEAEGKLSPKKRKPYLHESRHKHAMRRPRGPGGRF 58 (58)
T ss_pred CCCeeECHHHHHHHHHHHHHHHHHHHhCCcchhhhHHHHHHHHHHHHHcCccCCCCCC
Confidence 689999999999999999999999999999 999999999999999999999999999
No 4
>COG5224 HAP2 CCAAT-binding factor, subunit B [Transcription]
Probab=99.82 E-value=4.5e-21 Score=168.38 Aligned_cols=66 Identities=39% Similarity=0.508 Sum_probs=60.4
Q ss_pred CCCceeechhhhHHHHHHHHHHHHHHhhhhhhhcCCCcccchhhHHHhhccCCCCCcccccccchhhh
Q 027709 124 VEEPVFVNAKQYHGILRRRQSRAKAESENKVLKSRKPYLHESRHLHALRRARGCGGRFLNSKKNENQQ 191 (220)
Q Consensus 124 ~eePvyVNaKQY~rIlRRRq~RaklE~~~kl~k~rkpYLHESRH~HAm~R~RG~gGRFL~~k~~~~~~ 191 (220)
.++|.|||+|||++|++||-+|++||.. |.-.|..|||||||+|||+|+|+++||||++.+.+.-+
T Consensus 157 sfqp~Yvnakq~n~i~kr~~~r~~ld~~--~~~~r~~ylHesrhkham~r~r~ptgrfLtasEi~~ln 222 (248)
T COG5224 157 SFQPDYVNAKQGNEISKRPGLRVYLDDS--VSAGRAFYLHESRHKHAMLRVRDPTGRFLTASEIDPLN 222 (248)
T ss_pred ccCcchhhhhhhhHHhcchhHHHHHHHH--hhhhhhhccccchhhhhhhcccCCCcceecHHhhhhhh
Confidence 4789999999999999999999999985 55677779999999999999999999999999988664
No 5
>PF06203 CCT: CCT motif; InterPro: IPR010402 The CCT (CONSTANS, CO-like, and TOC1) domain is a highly conserved basic module of ~43 amino acids, which is found near the C terminus of plant proteins often involved in light signal transduction. The CCT domain is found in association with other domains, such as the B-box zinc finger, the GATA-type zinc finger, the ZIM motif or the response regulatory domain. The CCT domain contains a putative nuclear localisation signal within the second half of the CCT motif and has been shown to be involved in nuclear localization and probably also has a role in protein-protein interaction [].; GO: 0005515 protein binding
Probab=77.31 E-value=3.2 Score=29.01 Aligned_cols=28 Identities=36% Similarity=0.392 Sum_probs=23.1
Q ss_pred CCCcccchhhHHHhhccCCCCCccccccc
Q 027709 158 RKPYLHESRHLHALRRARGCGGRFLNSKK 186 (220)
Q Consensus 158 rkpYLHESRH~HAm~R~RG~gGRFL~~k~ 186 (220)
-|.-.+++|..=|..|+|-. |||+..++
T Consensus 18 ~kkirY~~Rk~~A~~R~Rvk-GRFvk~~e 45 (45)
T PF06203_consen 18 EKKIRYESRKAVADKRPRVK-GRFVKKSE 45 (45)
T ss_pred cccCCcchHHHHHhhCCccC-CcccCCCC
Confidence 34677899999999999975 99987653
No 6
>KOG1561 consensus CCAAT-binding factor, subunit B (HAP2) [Transcription]
Probab=72.60 E-value=0.95 Score=42.00 Aligned_cols=47 Identities=49% Similarity=0.841 Sum_probs=36.9
Q ss_pred HHHHHHHHHHHHhhhhhhhcCCCcccchhhHHHhhccCCCCCcccccccchh
Q 027709 138 ILRRRQSRAKAESENKVLKSRKPYLHESRHLHALRRARGCGGRFLNSKKNEN 189 (220)
Q Consensus 138 IlRRRq~RaklE~~~kl~k~rkpYLHESRH~HAm~R~RG~gGRFL~~k~~~~ 189 (220)
+++++..+++.+.. -.....+|+++|+.+.|.+ +.+++|++..+.+.
T Consensus 14 ~~~~~~~~q~~~~~-~~~~~~~p~~~~s~~~~q~----~~s~~~~s~~g~~~ 60 (307)
T KOG1561|consen 14 ILKRREARQKPEER-GVQTTKKPYLHESGHKHQM----GPGGRFLSADGVSK 60 (307)
T ss_pred cccccccccccccc-ccccccccccCcccccccc----cccccccCcccccc
Confidence 77777777776654 4567899999999999999 88999998444433
No 7
>PF15046 DUF4532: Protein of unknown function (DUF4532)
Probab=40.78 E-value=84 Score=29.50 Aligned_cols=49 Identities=33% Similarity=0.506 Sum_probs=32.7
Q ss_pred CCCceeechhhhHHHHHHHHH------HHHHHhhhhh-----------hhcCCCcccchhhHHHhhccCCCCCcccc
Q 027709 124 VEEPVFVNAKQYHGILRRRQS------RAKAESENKV-----------LKSRKPYLHESRHLHALRRARGCGGRFLN 183 (220)
Q Consensus 124 ~eePvyVNaKQY~rIlRRRq~------RaklE~~~kl-----------~k~rkpYLHESRH~HAm~R~RG~gGRFL~ 183 (220)
.+.||||++++=+.++.|=.+ |.|+.+|.|+ ++.=|+|-|-| .||||-.
T Consensus 131 ~~~pif~D~~rK~qvI~rt~KELkE~~kLKLRSe~RvPPlD~~GNIlPP~nFkky~h~s-----------aggr~~p 196 (279)
T PF15046_consen 131 SCTPIFVDPNRKNQVILRTVKELKEFEKLKLRSEARVPPLDAQGNILPPENFKKYRHIS-----------AGGRFEP 196 (279)
T ss_pred hcccceechhhhhHHHHHHHHHHhhhHhhhhhhhccCCCcCCCCCCcCchhhccccccc-----------CCceecC
Confidence 468999999999888877544 3344445443 34556774444 4999943
No 8
>PF04615 Utp14: Utp14 protein; InterPro: IPR006709 A large ribonuclear protein complex is required for the processing of the small-ribosomal-subunit rRNA - the small-subunit (SSU) processome [, ]. This preribosomal complex contains the U3 snoRNA and at least 40 proteins, which have the following properties: They are nucleolar. They are able to coimmunoprecipitate with the U3 snoRNA and Mpp10 (a protein specific to the SSU processome). They are required for 18S rRNA biogenesis. There appears to be a linkage between polymerase I transcription and the formation of the SSU processome; as some, but not all, of the SSU processome components are required for pre-rRNA transcription initiation. These SSU processome components have been termed t-Utps. They form a pre-complex with pre-18S rRNA in the absence of snoRNA U3 and other SSU processome components. It has been proposed that the t-Utp complex proteins are both rDNA and rRNA binding proteins that are involved in the initiation of pre18S rRNA transcription. Initially binding to rDNA then associating with the 5' end of the nascent pre18S rRNA. The t-Utpcomplex forms the nucleus around which the rest of the SSU processome components, including snoRNA U3, assemble []. From electron microscopy the SSU processome may correspond to the terminal knobs visualized at the 5' ends of nascent 18S rRNA. This entry contains Utp14, a large ribonuclear protein associated with snoRNA U3 [].; GO: 0006364 rRNA processing, 0032040 small-subunit processome
Probab=15.14 E-value=1e+02 Score=30.98 Aligned_cols=44 Identities=25% Similarity=0.395 Sum_probs=28.3
Q ss_pred hhhhHHHHHHHHHHHHHHh-------------------hhhhhhcCCCcccchhhHHHhhccC
Q 027709 132 AKQYHGILRRRQSRAKAES-------------------ENKVLKSRKPYLHESRHLHALRRAR 175 (220)
Q Consensus 132 aKQY~rIlRRRq~RaklE~-------------------~~kl~k~rkpYLHESRH~HAm~R~R 175 (220)
-|.||||+|+...|+.+.. +.+-++.|-.--|-+.-++|.+-.|
T Consensus 231 SK~yhri~kk~k~k~~~k~~e~l~~~dpe~a~e~~e~~e~~Ra~ERmtlkHkn~sKWAK~~~~ 293 (735)
T PF04615_consen 231 SKTYHRILKKEKEKEQEKEFEELEESDPEAAEEELEKLEKKRAEERMTLKHKNTSKWAKSMLR 293 (735)
T ss_pred hhHHHHHHHHHHHHhhcchHHHHhhcChhhhHHHHHHHHHHHHHHHhhccccccCHHHHHHHH
Confidence 3669999999988843211 1112345666677777778777666
No 9
>KOG4823 consensus Uncharacterized conserved protein [Function unknown]
Probab=14.96 E-value=74 Score=30.43 Aligned_cols=21 Identities=43% Similarity=0.537 Sum_probs=15.5
Q ss_pred CcccchhhHHH----------hhccCCCCCc
Q 027709 160 PYLHESRHLHA----------LRRARGCGGR 180 (220)
Q Consensus 160 pYLHESRH~HA----------m~R~RG~gGR 180 (220)
--|||+||+|+ .+|.|-+.|+
T Consensus 141 ~~lhenRdkht~r~~~ssVlr~r~lri~eg~ 171 (328)
T KOG4823|consen 141 VVLHENRDKHTQRITESSVLRKRRLRISEGE 171 (328)
T ss_pred hhhhhccchhhhhhhHHHHhhhhcccCCcCC
Confidence 44899999999 4556666665
No 10
>PF02162 XYPPX: XYPPX repeat (two copies); InterPro: IPR006031 This repeat is found in a wide variety of proteins and generally consists of the motif XYPPX where X can be any amino acid. The family includes annexin VII ANX7_DICDI, the carboxy tail of certain rhodopsins OPSD_LOLSU. This family also includes plaque matrix proteins, however this motif is embedded in a ten residue repeat in FP1_MYTED. The molecular function of this repeat is unknown. It is also not clear is all the members of this family share a common evolutionary ancestor due to its short length and biased amino acid composition.
Probab=14.49 E-value=1.4e+02 Score=17.12 Aligned_cols=12 Identities=58% Similarity=1.076 Sum_probs=6.8
Q ss_pred CCCCCCCCCCCC
Q 027709 89 YDAQPYPPQPYG 100 (220)
Q Consensus 89 Yg~q~~~~~~y~ 100 (220)
|-+|.|+||.|.
T Consensus 2 ~ppqG~pPQ~~P 13 (15)
T PF02162_consen 2 YPPQGYPPQGYP 13 (15)
T ss_pred CCCcCCCCCCCC
Confidence 445666666554
Done!