Query 030677
Match_columns 173
No_of_seqs 142 out of 205
Neff 2.9
Searched_HMMs 46136
Date Fri Mar 29 02:56:13 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030677.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030677hhsearch_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 1.4E-29 3.1E-34 221.1 7.1 96 59-159 127-225 (307)
2 smart00521 CBF CCAAT-Binding t 99.9 5.2E-24 1.1E-28 151.0 3.7 45 115-159 1-45 (62)
3 PF02045 CBFB_NFYA: CCAAT-bind 99.9 2.7E-23 5.9E-28 145.7 2.8 43 117-159 1-44 (58)
4 COG5224 HAP2 CCAAT-binding fac 98.7 4.7E-09 1E-13 90.4 1.2 43 116-160 157-199 (248)
5 PF12984 DUF3868: Domain of un 36.0 22 0.00047 27.2 1.4 37 118-157 79-115 (115)
6 PF04615 Utp14: Utp14 protein; 25.6 39 0.00085 32.8 1.5 16 124-139 231-246 (735)
7 KOG3088 Secretory carrier memb 24.8 2.2E+02 0.0048 26.3 6.0 32 105-137 44-75 (313)
8 COG4172 ABC-type uncharacteriz 24.5 44 0.00095 32.6 1.6 43 115-157 385-427 (534)
9 PHA03175 UL43 envelope protein 17.7 96 0.0021 29.5 2.3 20 119-138 71-90 (413)
10 cd08049 TAF8 TATA Binding Prot 17.0 1.1E+02 0.0024 20.5 1.9 32 117-148 18-49 (54)
No 1
>KOG1561 consensus CCAAT-binding factor, subunit B (HAP2) [Transcription]
Probab=99.96 E-value=1.4e-29 Score=221.13 Aligned_cols=96 Identities=38% Similarity=0.545 Sum_probs=79.2
Q ss_pred CcccccC-CCCCCCCCcccccccCCCCCCCCCCCCCCCcccccccCCCC-CCCCCCCCCCC-CceEecchhhHHHHHHHH
Q 030677 59 GHAMAPA-AYPYPDPYYRSIFAPYDAQPYPPQPYGGQPMVHLQLMGIQQ-AGVPLPTDAVE-EPVFVNAKQYHGILRRRQ 135 (173)
Q Consensus 59 ghsma~~-~yPY~DpyyGg~~aaY~~q~~~~~~yg~q~m~hpq~~Gm~~-~rvpLP~~~~e-ePiyVNaKQY~rILrRRq 135 (173)
.|..+++ .+|+.+|+|+|++..++ +|.+++.. .+++|++|+.+ .|+|||.++.| |||||||||||||||||+
T Consensus 127 ~~~~~~~s~~~~~~p~~~g~~~~~~--~y~~~~~~---~~~~q~~g~~~~~r~pLP~~~~e~ePl~VNaKQY~~IlrRRq 201 (307)
T KOG1561|consen 127 MSPANNTSGNPITSPHYRGVLDMSG--AYSGQPTN---TASTQYSGPVPHDRTPLPQTDSETEPLYVNAKQYHRILRRRQ 201 (307)
T ss_pred cccccccccCCCCCCcccceecccc--cccCCCCc---cccccccCCCCcCcccCCccccCCCceeEcHHHHHHHHHHHH
Confidence 4444444 47899999999999544 22222332 25778999988 99999998877 999999999999999999
Q ss_pred HHHHHHhhccccccccccchhhcc
Q 030677 136 SRAKAESENKVLKSRKACHKLQVL 159 (173)
Q Consensus 136 ~RaKlE~~~kl~k~RKpYlhe~~~ 159 (173)
+|||||+++||+|+|||||||+-|
T Consensus 202 ~RaKlEa~~klik~RkpYLHESRH 225 (307)
T KOG1561|consen 202 ARAKLEATTKLIKARKPYLHESRH 225 (307)
T ss_pred HHhhhhhcccchhhcCccccchhh
Confidence 999999999999999999999865
No 2
>smart00521 CBF CCAAT-Binding transcription Factor.
Probab=99.89 E-value=5.2e-24 Score=150.96 Aligned_cols=45 Identities=58% Similarity=0.740 Sum_probs=42.7
Q ss_pred CCCCceEecchhhHHHHHHHHHHHHHHhhccccccccccchhhcc
Q 030677 115 AVEEPVFVNAKQYHGILRRRQSRAKAESENKVLKSRKACHKLQVL 159 (173)
Q Consensus 115 ~~eePiyVNaKQY~rILrRRq~RaKlE~~~kl~k~RKpYlhe~~~ 159 (173)
++|+||||||||||+|||||++|||+|+++|++|.|||||||+=|
T Consensus 1 ~~~~piyVNaKQy~~IlrRR~~Rak~e~~~kl~~~rkpYlhESRH 45 (62)
T smart00521 1 AEEEPVYVNAKQYHRILRRRQARAKLEAQGKLPKERKPYLHESRH 45 (62)
T ss_pred CCCcceeEcHHHHHHHHHHHHHHHHHHHhcchhhccCCcccchhH
Confidence 368999999999999999999999999999999999999999865
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=99.87 E-value=2.7e-23 Score=145.66 Aligned_cols=43 Identities=58% Similarity=0.782 Sum_probs=41.4
Q ss_pred CCceEecchhhHHHHHHHHHHHHHHhhccc-cccccccchhhcc
Q 030677 117 EEPVFVNAKQYHGILRRRQSRAKAESENKV-LKSRKACHKLQVL 159 (173)
Q Consensus 117 eePiyVNaKQY~rILrRRq~RaKlE~~~kl-~k~RKpYlhe~~~ 159 (173)
|||||||||||++|||||++|||+|+++|+ +|.|||||||+-|
T Consensus 1 ~~piyVNaKQY~rIlrRR~~Rakle~~~k~~~~~rk~YlheSRH 44 (58)
T PF02045_consen 1 EEPIYVNAKQYHRILRRRQARAKLEAEGKLSPKKRKPYLHESRH 44 (58)
T ss_pred CCCeeECHHHHHHHHHHHHHHHHHHHhCCcchhhhHHHHHHHHH
Confidence 699999999999999999999999999999 9999999999865
No 4
>COG5224 HAP2 CCAAT-binding factor, subunit B [Transcription]
Probab=98.69 E-value=4.7e-09 Score=90.44 Aligned_cols=43 Identities=23% Similarity=0.142 Sum_probs=36.7
Q ss_pred CCCceEecchhhHHHHHHHHHHHHHHhhccccccccccchhhccC
Q 030677 116 VEEPVFVNAKQYHGILRRRQSRAKAESENKVLKSRKACHKLQVLC 160 (173)
Q Consensus 116 ~eePiyVNaKQY~rILrRRq~RaKlE~~~kl~k~RKpYlhe~~~~ 160 (173)
.+.|.|||||||++|+|||-+|++|+..-+. .|.-||||.+|-
T Consensus 157 sfqp~Yvnakq~n~i~kr~~~r~~ld~~~~~--~r~~ylHesrhk 199 (248)
T COG5224 157 SFQPDYVNAKQGNEISKRPGLRVYLDDSVSA--GRAFYLHESRHK 199 (248)
T ss_pred ccCcchhhhhhhhHHhcchhHHHHHHHHhhh--hhhhccccchhh
Confidence 3689999999999999999999999886664 444599999874
No 5
>PF12984 DUF3868: Domain of unknown function, B. Theta Gene description (DUF3868); InterPro: IPR024480 This domain of unknown function is found in a number of bacterial proteins. The function of the proteins is not known, but the Bacteroides thetaiotaomicron gene appears to be upregulated in the presence of host or other bacterial species compared to pure culture [, ].
Probab=36.04 E-value=22 Score=27.22 Aligned_cols=37 Identities=14% Similarity=0.158 Sum_probs=26.4
Q ss_pred CceEecchhhHHHHHHHHHHHHHHhhccccccccccchhh
Q 030677 118 EPVFVNAKQYHGILRRRQSRAKAESENKVLKSRKACHKLQ 157 (173)
Q Consensus 118 ePiyVNaKQY~rILrRRq~RaKlE~~~kl~k~RKpYlhe~ 157 (173)
-||.||-++=+...+|+.+..+.+++. ...++||-||
T Consensus 79 P~V~I~Gr~r~~~y~R~~al~~~~~~~---~~~~~~~~~~ 115 (115)
T PF12984_consen 79 PPVVINGRNRYKVYQRNLALMSKKEEA---SYAYPYLVEK 115 (115)
T ss_pred CCEEEechHHHHHHHHHHHhccCcchh---cccCceeecC
Confidence 389999999888888888766554433 3456776553
No 6
>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=25.57 E-value=39 Score=32.83 Aligned_cols=16 Identities=31% Similarity=0.767 Sum_probs=12.2
Q ss_pred chhhHHHHHHHHHHHH
Q 030677 124 AKQYHGILRRRQSRAK 139 (173)
Q Consensus 124 aKQY~rILrRRq~RaK 139 (173)
-|.||||+|++..|..
T Consensus 231 SK~yhri~kk~k~k~~ 246 (735)
T PF04615_consen 231 SKTYHRILKKEKEKEQ 246 (735)
T ss_pred hhHHHHHHHHHHHHhh
Confidence 4788999888877743
No 7
>KOG3088 consensus Secretory carrier membrane protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=24.82 E-value=2.2e+02 Score=26.32 Aligned_cols=32 Identities=19% Similarity=0.221 Sum_probs=16.0
Q ss_pred CCCCCCCCCCCCCCceEecchhhHHHHHHHHHH
Q 030677 105 QQAGVPLPTDAVEEPVFVNAKQYHGILRRRQSR 137 (173)
Q Consensus 105 ~~~rvpLP~~~~eePiyVNaKQY~rILrRRq~R 137 (173)
.++.+..|+|.. ...=...+.=.+=|.|||+.
T Consensus 44 ~~~tv~~P~~~~-~~~a~~~~~kq~eL~~rqeE 75 (313)
T KOG3088|consen 44 QGPTVDIPLDSP-STQAKDLAKKQAELLKKQEE 75 (313)
T ss_pred CCCccccCCCCC-cchhhHHHHHHHHHHHHHHH
Confidence 456677777632 22233333344555666553
No 8
>COG4172 ABC-type uncharacterized transport system, duplicated ATPase component [General function prediction only]
Probab=24.49 E-value=44 Score=32.61 Aligned_cols=43 Identities=14% Similarity=0.047 Sum_probs=37.7
Q ss_pred CCCCceEecchhhHHHHHHHHHHHHHHhhccccccccccchhh
Q 030677 115 AVEEPVFVNAKQYHGILRRRQSRAKAESENKVLKSRKACHKLQ 157 (173)
Q Consensus 115 ~~eePiyVNaKQY~rILrRRq~RaKlE~~~kl~k~RKpYlhe~ 157 (173)
..+|.+.|+-++-.+-=|....++.+++-+--+..|-.|=||-
T Consensus 385 II~EGL~vh~~~ls~~eR~~rv~~aL~EVGLDp~~r~RYPhEF 427 (534)
T COG4172 385 IIEEGLRVHEPKLSAAERDQRVIEALEEVGLDPATRNRYPHEF 427 (534)
T ss_pred HhhhhhhhcCCCCCHHHHHHHHHHHHHHcCCChhHhhcCCccc
Confidence 4569999999999999899889999998888888999999983
No 9
>PHA03175 UL43 envelope protein; Provisional
Probab=17.73 E-value=96 Score=29.53 Aligned_cols=20 Identities=45% Similarity=0.512 Sum_probs=16.0
Q ss_pred ceEecchhhHHHHHHHHHHH
Q 030677 119 PVFVNAKQYHGILRRRQSRA 138 (173)
Q Consensus 119 PiyVNaKQY~rILrRRq~Ra 138 (173)
-+--.+.|+++|+||||+-.
T Consensus 71 ~~~~~~~~~~~~~~~~~~~~ 90 (413)
T PHA03175 71 GTAARAAQFDEILRRRQSGL 90 (413)
T ss_pred cchhhhcchhhHHHhhhhhh
Confidence 44567889999999999754
No 10
>cd08049 TAF8 TATA Binding Protein (TBP) Associated Factor 8. The TATA Binding Protein (TBP) Associated Factor 8 (TAF8) is one of several TAFs that bind TBP, and is involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and the assembly of the preinitiation complex. The TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs' functions, such as serving as activator-binding sites, involvement in the core-promo
Probab=17.03 E-value=1.1e+02 Score=20.52 Aligned_cols=32 Identities=16% Similarity=0.292 Sum_probs=23.7
Q ss_pred CCceEecchhhHHHHHHHHHHHHHHhhccccc
Q 030677 117 EEPVFVNAKQYHGILRRRQSRAKAESENKVLK 148 (173)
Q Consensus 117 eePiyVNaKQY~rILrRRq~RaKlE~~~kl~k 148 (173)
.-|+|.....=...+|.|.++.+...|..|.|
T Consensus 18 ~Tp~~~~~~~d~~~~r~~~~~~~r~~e~aL~~ 49 (54)
T cd08049 18 RTPTYSERETDPKKLREELASQRRLAEKALLR 49 (54)
T ss_pred cCCCCCCCccCHHHHHHHHHHHHHHHHHHHHH
Confidence 45777777777788888888888877776654
Done!