Query 031592
Match_columns 157
No_of_seqs 110 out of 228
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 02:39:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031592.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031592hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03998 Utp11: Utp11 protein; 100.0 6.8E-61 1.5E-65 400.7 12.8 138 10-147 1-142 (243)
2 KOG3237 Uncharacterized conser 100.0 7E-60 1.5E-64 394.5 11.1 145 1-145 1-149 (250)
3 COG5223 Uncharacterized conser 100.0 2.4E-43 5.2E-48 290.8 6.4 142 1-145 1-143 (240)
4 PF10241 KxDL: Uncharacterized 51.5 21 0.00047 25.6 3.3 24 40-63 65-88 (88)
5 cd07605 I-BAR_IMD Inverse (I)- 35.5 48 0.001 27.9 3.5 31 32-62 119-149 (223)
6 PF04998 RNA_pol_Rpb1_5: RNA p 26.1 18 0.00039 29.2 -0.5 34 59-107 3-36 (277)
7 PF10258 RNA_GG_bind: PHAX RNA 26.0 90 0.002 22.7 3.2 69 26-94 9-79 (87)
8 PF05370 DUF749: Domain of unk 20.0 12 0.00026 27.8 -2.4 43 100-143 20-63 (87)
9 PF10443 RNA12: RNA12 protein; 18.4 1.4E+02 0.003 27.9 3.5 33 92-124 397-429 (431)
10 COG4549 Uncharacterized protei 18.4 42 0.00091 27.9 0.1 11 58-68 108-118 (178)
No 1
>PF03998 Utp11: Utp11 protein; InterPro: IPR007144 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 Utp11, a large ribonuclear protein that associates with snoRNA U3 [].; GO: 0006364 rRNA processing, 0032040 small-subunit processome
Probab=100.00 E-value=6.8e-61 Score=400.74 Aligned_cols=138 Identities=54% Similarity=0.808 Sum_probs=132.1
Q ss_pred cccccccCCcchhhccccccccccHHHHHHHHhHHHHHHHHHHHHHHhhCCCchhhhhhhccccC-CcccccCc-CCCCC
Q 031592 10 RRAHKERAQPQSRKKFGLLEKHKDYVIRAKAYHKKEESIRRLKEKAAFRNPDEFYFKMIKTKTVD-GVHRLEGE-ANKYT 87 (157)
Q Consensus 10 rr~HrER~Qp~~R~~lGlLEKkKDY~~RA~dy~~K~~~lk~Lr~KA~~rNpDEFyf~M~~sk~~~-G~h~~~~~-~~~~t 87 (157)
||+|||||||++|++||||||||||++||+|||+|+++|+.|++||++||||||||+|||+++.+ |+|+...+ ++.+|
T Consensus 1 rr~HrERsQP~~R~~lGlLEKkKDY~lRA~dy~~K~~~Lk~Lr~KA~~RNpDEFyf~M~~sk~~~~G~h~~~~~~~~~~~ 80 (243)
T PF03998_consen 1 RRNHRERSQPASRKKLGLLEKKKDYKLRAKDYHKKEAKLKRLREKAANRNPDEFYFGMINSKTDDDGVHVEKREENEELS 80 (243)
T ss_pred CCcccccCChHHhhhcCcccccccHHHHHHHHHHHHHHHHHHHHHHHHhCCChhhHHHHhcccCCCCeeccCccccccCC
Confidence 68999999999999999999999999999999999999999999999999999999999999999 99999887 78999
Q ss_pred HHHHHHhhhhhHHHHHHHHHHHHHHHHHHHhhhccCCCCCC--CCeEEEecCHHHHHhhhhh
Q 031592 88 QEELMLMKTQDIGYVLQKLQSERNKIEKLTTMLHSLDNNPS--SRHVYFAEDRFVLSKLSFL 147 (157)
Q Consensus 88 ~e~~kl~ktQDl~Yv~~~~~~e~kKIekL~~~L~~~~~~~~--nkH~vFvd~~~e~~~f~~~ 147 (157)
+++++||+|||++||+++++++.+||++|+++||++++... |+|||||||++|+++|...
T Consensus 81 ~e~~~llkTQD~~Yv~~~~~~e~kKIekL~~~l~~~~~~~~~~~kh~vFvD~~~e~~~f~~~ 142 (243)
T PF03998_consen 81 KEQVKLLKTQDLNYVRTKRQIERKKIEKLQSELHLLDGKSSGKNKHIVFVDSEEEAKEFDPA 142 (243)
T ss_pred HHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHhhhhhhcccCCCCCceEEecCchHHHhccHH
Confidence 99999999999999999999999999999999999986544 5999999999999999743
No 2
>KOG3237 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=7e-60 Score=394.45 Aligned_cols=145 Identities=50% Similarity=0.775 Sum_probs=142.2
Q ss_pred Cccchhccc--cccccccCCcchhhccccccccccHHHHHHHHhHHHHHHHHHHHHHHhhCCCchhhhhhhccccCCccc
Q 031592 1 MSSLRNALP--RRAHKERAQPQSRKKFGLLEKHKDYVIRAKAYHKKEESIRRLKEKAAFRNPDEFYFKMIKTKTVDGVHR 78 (157)
Q Consensus 1 MSslrna~k--rr~HrER~Qp~~R~~lGlLEKkKDY~~RA~dy~~K~~~lk~Lr~KA~~rNpDEFyf~M~~sk~~~G~h~ 78 (157)
||||+||++ |++|||||||.+|++||+|||||||++||.|||+|+.+|+.||++|+++|||||||+|+|+++.+|+|+
T Consensus 1 mss~~~a~ks~rk~HRERsQP~~Rrk~G~LEKkKDY~~RA~dy~kKq~tLK~LrekA~eKNpDEfyh~M~~~K~~dG~hi 80 (250)
T KOG3237|consen 1 MSSFVNASKSRRKVHRERSQPEARRKYGFLEKKKDYKKRAQDYHKKQDTLKKLREKALEKNPDEFYHKMHNSKTKDGRHI 80 (250)
T ss_pred CcchhhcchhhhhHHHhhcChhHHHhhhhHHhhhHHHHHHHHHHHHHHHHHHHHHHHHhcChHHHHHHHhhccccCCccc
Confidence 999999999 999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCcCCCCCHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHhhhccCC--CCCCCCeEEEecCHHHHHhhh
Q 031592 79 LEGEANKYTQEELMLMKTQDIGYVLQKLQSERNKIEKLTTMLHSLD--NNPSSRHVYFAEDRFVLSKLS 145 (157)
Q Consensus 79 ~~~~~~~~t~e~~kl~ktQDl~Yv~~~~~~e~kKIekL~~~L~~~~--~~~~nkH~vFvd~~~e~~~f~ 145 (157)
...+.+++|+|||+||+|||++||.+++++|++|||+|.++||+++ .+.+|+||+||||.+|+++|.
T Consensus 81 ~k~e~~e~t~eqlklmktQDi~YV~~kr~~ErkKIerlka~L~~~~~~~~~s~kH~~F~d~~~ea~~Fd 149 (250)
T KOG3237|consen 81 EKDEVDEPTMEQLKLMKTQDIGYVRMKRQRERKKIERLKAQLHCVDRNKGESNKHTKFVDDREEAKSFD 149 (250)
T ss_pred cccccccCCHHHHHHHhhhhHHHHHHHHHHHHHHHHHHhcccccccccccccCceeEEeccHHHHhccC
Confidence 9988889999999999999999999999999999999999999999 678899999999999999997
No 3
>COG5223 Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=2.4e-43 Score=290.82 Aligned_cols=142 Identities=37% Similarity=0.501 Sum_probs=134.9
Q ss_pred Ccc-chhccccccccccCCcchhhccccccccccHHHHHHHHhHHHHHHHHHHHHHHhhCCCchhhhhhhccccCCcccc
Q 031592 1 MSS-LRNALPRRAHKERAQPQSRKKFGLLEKHKDYVIRAKAYHKKEESIRRLKEKAAFRNPDEFYFKMIKTKTVDGVHRL 79 (157)
Q Consensus 1 MSs-lrna~krr~HrER~Qp~~R~~lGlLEKkKDY~~RA~dy~~K~~~lk~Lr~KA~~rNpDEFyf~M~~sk~~~G~h~~ 79 (157)
||+ |.++-+|++||||+||.+|++||+|||||||++||.|||+|+.+|+.||++|+.||||||||+|.+.++.+|+.++
T Consensus 1 Ms~~f~~v~qrK~hrERtQp~~RrkyG~LEK~KDyvkRaqd~~~kq~~lk~lrEka~ernpdEyyh~mhs~Ktd~gv~~~ 80 (240)
T COG5223 1 MSLGFTKVPQRKVHRERTQPKDRRKYGKLEKKKDYVKRAQDINKKQDELKKLREKARERNPDEYYHGMHSVKTDGGVSSI 80 (240)
T ss_pred CCcccccchHhhhHHHhcCcchhhhhhhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhcChHHHHHHhhhhcccCCccce
Confidence 786 5555579999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCcCCCCCHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHhhhccCCCCCCCCeEEEecCHHHHHhhh
Q 031592 80 EGEANKYTQEELMLMKTQDIGYVLQKLQSERNKIEKLTTMLHSLDNNPSSRHVYFAEDRFVLSKLS 145 (157)
Q Consensus 80 ~~~~~~~t~e~~kl~ktQDl~Yv~~~~~~e~kKIekL~~~L~~~~~~~~nkH~vFvd~~~e~~~f~ 145 (157)
.++++++++|++++++|||.+|+++.++.|+.+++.+..+++| ..++.||+|||+..+++.|.
T Consensus 81 ~ReDe~~~md~~KmlktqD~~~~R~~r~lEr~k~~~~~~qi~f---~es~~htifvD~r~~~kef~ 143 (240)
T COG5223 81 YREDEPTIMDLAKMLKTQDNEIQRCRRKLERYKPMPCGTQIKF---EESSLHTIFVDMRFGQKEFI 143 (240)
T ss_pred eccccchHHHHHHHHHhhhhHHHHHHHHHHHhCCcchhceeee---eccccchhhhhhhhhhhhcC
Confidence 8888899999999999999999999999999999999999999 46789999999999999996
No 4
>PF10241 KxDL: Uncharacterized conserved protein; InterPro: IPR019371 This entry represents a conserved region of 80 residues which defines a family of short proteins. There is a characteristic KxDL motif towards the C terminus. The function is unknown.
Probab=51.48 E-value=21 Score=25.62 Aligned_cols=24 Identities=33% Similarity=0.403 Sum_probs=19.9
Q ss_pred HHhHHHHHHHHHHHHHHhhCCCch
Q 031592 40 AYHKKEESIRRLKEKAAFRNPDEF 63 (157)
Q Consensus 40 dy~~K~~~lk~Lr~KA~~rNpDEF 63 (157)
|-..-..+|..|+.++....|+||
T Consensus 65 DLd~i~krir~lk~kl~~~yP~~y 88 (88)
T PF10241_consen 65 DLDYIFKRIRSLKAKLAKQYPEEY 88 (88)
T ss_pred HHHHHHHHHHHHHHHHHHhCCCcC
Confidence 334456789999999999999998
No 5
>cd07605 I-BAR_IMD Inverse (I)-BAR, also known as the IRSp53/MIM homology Domain (IMD), a dimerization module that binds and bends membranes. Inverse (I)-BAR (or IMD) is a member of the Bin/Amphiphysin/Rvs (BAR) domain family. It is a dimerization and lipid-binding module that bends membranes and induces membrane protrusions in the opposite direction compared to classical BAR and F-BAR domains, which produce membrane invaginations. IMD domains are found in Insulin Receptor tyrosine kinase Substrate p53 (IRSp53), Missing in Metastasis (MIM), and Brain-specific Angiogenesis Inhibitor 1-Associated Protein 2-like (BAIAP2L) proteins. These are multi-domain proteins that act as scaffolding proteins and transducers of a variety of signaling pathways that link membrane dynamics and the underlying actin cytoskeleton. Most members contain an N-terminal IMD, an SH3 domain, and a WASP homology 2 (WH2) actin-binding motif at the C-terminus, exccept for MIM which does not carry an SH3 domain. Some me
Probab=35.48 E-value=48 Score=27.94 Aligned_cols=31 Identities=16% Similarity=0.371 Sum_probs=26.5
Q ss_pred ccHHHHHHHHhHHHHHHHHHHHHHHhhCCCc
Q 031592 32 KDYVIRAKAYHKKEESIRRLKEKAAFRNPDE 62 (157)
Q Consensus 32 KDY~~RA~dy~~K~~~lk~Lr~KA~~rNpDE 62 (157)
++|+.+..++.+.+..++.|+.|+.-.||+.
T Consensus 119 ~E~K~~~~~l~K~~sel~Kl~KKs~~~~~~k 149 (223)
T cd07605 119 KEYKQKREDLDKARSELKKLQKKSQKSGTGK 149 (223)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHcccCCCc
Confidence 5788888899999999999999998777653
No 6
>PF04998 RNA_pol_Rpb1_5: RNA polymerase Rpb1, domain 5; InterPro: IPR007081 RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). This domain, domain 5, represents the discontinuous cleft domain that is required to form the central cleft or channel where the DNA is bound [, ].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 1ZYR_D 1SMY_D 2A68_N 2O5J_D 3AOH_N 2O5I_D 2CW0_N 2A6H_N 2A69_D 3EQL_D ....
Probab=26.06 E-value=18 Score=29.15 Aligned_cols=34 Identities=29% Similarity=0.679 Sum_probs=23.9
Q ss_pred CCCchhhhhhhccccCCcccccCcCCCCCHHHHHHhhhhhHHHHHHHHH
Q 031592 59 NPDEFYFKMIKTKTVDGVHRLEGEANKYTQEELMLMKTQDIGYVLQKLQ 107 (157)
Q Consensus 59 NpDEFyf~M~~sk~~~G~h~~~~~~~~~t~e~~kl~ktQDl~Yv~~~~~ 107 (157)
||-||||+.+.+|. |. + +. -+||-|-+||.-++.
T Consensus 3 ~~~e~f~~~~~~R~--gl-~-dt-----------a~kTa~sGyl~R~lv 36 (277)
T PF04998_consen 3 TPTEYFFHCMGGRE--GL-I-DT-----------AVKTADSGYLQRRLV 36 (277)
T ss_dssp THHHHHHHHHHHHH--HH-H-HH-----------HHCHHHHHHHHHHHH
T ss_pred CHHHHHHHHhcccc--cc-c-cc-----------ceeeeccccchhhhh
Confidence 78999999987653 31 1 11 179999999976553
No 7
>PF10258 RNA_GG_bind: PHAX RNA-binding domain; InterPro: IPR019385 The phosphorylated adaptor for RNA export (PHAX) protein transports U3 snoRNA from the nucleus after transcription []. This entry represents the highly conserved U3 snoRNA-binding domain of PHAX, which is characterised by having two pairs of adjacent glycines with the sequence motif GGx12GG.; PDB: 2XC7_A 2W4S_B.
Probab=25.99 E-value=90 Score=22.72 Aligned_cols=69 Identities=19% Similarity=0.133 Sum_probs=48.6
Q ss_pred ccccccccHHHHHHHHhHHHHHHHHHHHH-HHhhCCCchhhhhhhccccCCccccc-CcCCCCCHHHHHHh
Q 031592 26 GLLEKHKDYVIRAKAYHKKEESIRRLKEK-AAFRNPDEFYFKMIKTKTVDGVHRLE-GEANKYTQEELMLM 94 (157)
Q Consensus 26 GlLEKkKDY~~RA~dy~~K~~~lk~Lr~K-A~~rNpDEFyf~M~~sk~~~G~h~~~-~~~~~~t~e~~kl~ 94 (157)
.|-|++.|...|+=..-=.+..+..+.+- +-+.|..-+.-.-...+|.+||-... ...+..|+++.+.+
T Consensus 9 ~L~E~k~~li~rvV~~lG~~~~~~l~~et~~Ie~~GG~~~~dG~RrRTpGGVF~~LlK~~~~i~~e~~k~I 79 (87)
T PF10258_consen 9 RLKEPKKDLIERVVKRLGVEKALELLNETMKIEKNGGMMTADGSRRRTPGGVFFNLLKNDDDISPEDKKEI 79 (87)
T ss_dssp HCT-TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHCT-EE-TTSSCE-SHHHHHHHHHHHTTSS-HHHHHHH
T ss_pred HhCCCCHHHHHHHHHHHCHHHHHHHHHHHHHHHHcCCeEeecCccCcCCCcchhHhhccCccCCHHHHHHH
Confidence 57799999999999999999999988874 45778887777777778888887542 22356788887643
No 8
>PF05370 DUF749: Domain of unknown function (DUF749); InterPro: IPR008032 This is a family of unknown function found in archaebacterial proteins. The family has been solved via structural genomics techniques and comprises of segregated helical and anti-parallel beta sheet regions. It is a putative metal-binding protein. ; PDB: 1IQS_A 1IQO_A.
Probab=19.99 E-value=12 Score=27.77 Aligned_cols=43 Identities=16% Similarity=0.287 Sum_probs=21.7
Q ss_pred HHHHHHHHHHHHHHHHHHhhhccCC-CCCCCCeEEEecCHHHHHh
Q 031592 100 GYVLQKLQSERNKIEKLTTMLHSLD-NNPSSRHVYFAEDRFVLSK 143 (157)
Q Consensus 100 ~Yv~~~~~~e~kKIekL~~~L~~~~-~~~~nkH~vFvd~~~e~~~ 143 (157)
.||+.+...|.+++..=. .+.++. .+..+-|++|+|+...++.
T Consensus 20 ~fv~~kA~~ekreL~~dd-~vAIlnI~gTtSy~v~FLd~~~~iee 63 (87)
T PF05370_consen 20 DFVKVKAAIEKRELKDDD-EVAILNIQGTTSYQVFFLDSYNSIEE 63 (87)
T ss_dssp -STHHHHCTTT---SS---EEEEEE-TTTT-EEEEE-S---S-HH
T ss_pred hHhhhhhhhccccCCCCC-cEEEEEecCCceEEEEEEcCCCCHHH
Confidence 789999999988763322 344443 4567889999998655444
No 9
>PF10443 RNA12: RNA12 protein; InterPro: IPR018850 Mitochondrial escape protein 2 (also known as RNA12) plays a role in maintaining the mitochondrial genome and in controlling mtDNA escape [, ]. It is also involved in the regulation of mtDNA nucleotide structure and number []. Additionally, this protein have a dispensable role in the early maturation of pre-rRNA [].
Probab=18.38 E-value=1.4e+02 Score=27.90 Aligned_cols=33 Identities=27% Similarity=0.434 Sum_probs=29.3
Q ss_pred HHhhhhhHHHHHHHHHHHHHHHHHHHhhhccCC
Q 031592 92 MLMKTQDIGYVLQKLQSERNKIEKLTTMLHSLD 124 (157)
Q Consensus 92 kl~ktQDl~Yv~~~~~~e~kKIekL~~~L~~~~ 124 (157)
.+-.+.|+.|+......|.++|.+++.+|..++
T Consensus 397 ~l~~~~d~~~~~~li~~e~~~I~k~E~EL~~L~ 429 (431)
T PF10443_consen 397 VLSARMDLAYLKKLIKIENKKIKKYEEELRKLG 429 (431)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 355788999999999999999999999998764
No 10
>COG4549 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=18.37 E-value=42 Score=27.86 Aligned_cols=11 Identities=45% Similarity=0.890 Sum_probs=8.4
Q ss_pred hCCCchhhhhh
Q 031592 58 RNPDEFYFKMI 68 (157)
Q Consensus 58 rNpDEFyf~M~ 68 (157)
.||||||-+-+
T Consensus 108 nlPde~YD~fv 118 (178)
T COG4549 108 NLPDEFYDEFV 118 (178)
T ss_pred CCchhhccceE
Confidence 59999995544
Done!