Query 031143
Match_columns 165
No_of_seqs 116 out of 229
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 09:51:17 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031143.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031143hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3237 Uncharacterized conser 100.0 1.6E-65 3.4E-70 431.7 11.2 164 1-164 1-172 (250)
2 PF03998 Utp11: Utp11 protein; 100.0 6.4E-65 1.4E-69 428.4 12.2 154 10-163 1-162 (243)
3 COG5223 Uncharacterized conser 100.0 2.1E-47 4.5E-52 317.3 5.3 159 1-162 1-164 (240)
4 PF10241 KxDL: Uncharacterized 50.1 23 0.0005 25.7 3.4 24 40-63 65-88 (88)
5 cd07605 I-BAR_IMD Inverse (I)- 36.2 46 0.001 28.3 3.6 32 32-63 119-150 (223)
6 PF04998 RNA_pol_Rpb1_5: RNA p 30.0 14 0.00029 30.1 -0.6 33 59-106 3-35 (277)
7 PF02202 Tachykinin: Tachykini 22.8 13 0.00028 18.1 -1.2 6 59-64 3-8 (11)
8 PF10443 RNA12: RNA12 protein; 17.0 1.7E+02 0.0037 27.6 3.7 38 86-124 392-429 (431)
9 COG4549 Uncharacterized protei 14.9 57 0.0012 27.3 0.1 10 58-67 108-117 (178)
10 PF05370 DUF749: Domain of unk 14.6 17 0.00037 27.2 -2.7 41 100-141 20-61 (87)
No 1
>KOG3237 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=1.6e-65 Score=431.69 Aligned_cols=164 Identities=45% Similarity=0.631 Sum_probs=158.5
Q ss_pred CCccccccc--cccccccCCcchhhccccccccccHHHHHHHHhHHHHHHHHHHHHHHhhCCCchhhhhhhhhhcCCccc
Q 031143 1 MSSRRNAIP--RRAHKERAQPQSRKKFGLLEKHKDYVVRAKAYRKKEETIRRLKEKAAFRNPDEFYLKMIKTKIVDGVHR 78 (165)
Q Consensus 1 Msslrna~k--rr~HrER~QP~~R~~lGlLEKkKDY~~RA~dy~~K~~~lk~Lr~KA~~rNpDEFyf~M~~sk~~~Gvh~ 78 (165)
||||+||++ +++|||||||.+|++||+|||||||++||.|||+|+++|+.||++|+++|||||||+|+|+++.+|+|+
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 899999999 899999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccCCCCHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHhhhcccC--CCCCCCeeEEeeCccccc-cCC---CCCChhh
Q 031143 79 LESEANKYTQEELILMKTQDIGYILQKLQSERNKIEKLTTMLHSLD--SNLSSRHVYYAEDRFMLS-KLP---FFSEGNN 152 (165)
Q Consensus 79 ~~~~~~~~t~e~~kl~ktQDl~Yv~~~~~~e~kKiekL~~~L~~~~--~~~~nkH~vFvd~~~e~~-~~~---fdT~~el 152 (165)
+..+.+++|.|||+||+|||++||.+++++|++|||+|.++||+++ .+.+|+||+||||.+|++ |+| |+|++||
T Consensus 81 ~k~e~~e~t~eqlklmktQDi~YV~~kr~~ErkKIerlka~L~~~~~~~~~s~kH~~F~d~~~ea~~Fdp~~~f~tt~el 160 (250)
T KOG3237|consen 81 EKDEVDEPTMEQLKLMKTQDIGYVRMKRQRERKKIERLKAQLHCVDRNKGESNKHTKFVDDREEAKSFDPAKFFQTTLEL 160 (250)
T ss_pred cccccccCCHHHHHHHhhhhHHHHHHHHHHHHHHHHHHhcccccccccccccCceeEEeccHHHHhccChHHHhcccHHH
Confidence 9988889999999999999999999999999999999999999999 577899999999999998 555 9999999
Q ss_pred HhhHhhhhhhhc
Q 031143 153 ILDLLAILYMEN 164 (165)
Q Consensus 153 l~R~~n~~~~~~ 164 (165)
++|+|||+.-|.
T Consensus 161 v~R~~nr~~kee 172 (250)
T KOG3237|consen 161 VGRSENRLKKEE 172 (250)
T ss_pred hhhhhhhhhHHH
Confidence 999999997653
No 2
>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=6.4e-65 Score=428.36 Aligned_cols=154 Identities=45% Similarity=0.671 Sum_probs=146.1
Q ss_pred cccccccCCcchhhccccccccccHHHHHHHHhHHHHHHHHHHHHHHhhCCCchhhhhhhhhhcC-Cccccccc-cCCCC
Q 031143 10 RRAHKERAQPQSRKKFGLLEKHKDYVVRAKAYRKKEETIRRLKEKAAFRNPDEFYLKMIKTKIVD-GVHRLESE-ANKYT 87 (165)
Q Consensus 10 rr~HrER~QP~~R~~lGlLEKkKDY~~RA~dy~~K~~~lk~Lr~KA~~rNpDEFyf~M~~sk~~~-Gvh~~~~~-~~~~t 87 (165)
||+|||||||++|++||||||||||++||+|||+|+++|+.|++||++||||||||+|||+++.+ |+|+...+ ++.+|
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 99998887 78899
Q ss_pred HHHHHHhhhhhHHHHHHHHHHHHHHHHHHHhhhcccCCCCC--CCeeEEeeCccccccCC----CCCChhhHhhHhhhhh
Q 031143 88 QEELILMKTQDIGYILQKLQSERNKIEKLTTMLHSLDSNLS--SRHVYYAEDRFMLSKLP----FFSEGNNILDLLAILY 161 (165)
Q Consensus 88 ~e~~kl~ktQDl~Yv~~~~~~e~kKiekL~~~L~~~~~~~~--nkH~vFvd~~~e~~~~~----fdT~~ell~R~~n~~~ 161 (165)
.++++||+|||++||+++++++.+||++|+++||+++.... |+|||||||++|++.|+ |||+|+++++.+|+|.
T Consensus 81 ~e~~~llkTQD~~Yv~~~~~~e~kKIekL~~~l~~~~~~~~~~~kh~vFvD~~~e~~~f~~~~~~~t~~e~~~~~~nr~~ 160 (243)
T PF03998_consen 81 KEQVKLLKTQDLNYVRTKRQIERKKIEKLQSELHLLDGKSSGKNKHIVFVDSEEEAKEFDPAEYFDTDPELLDRRENRPK 160 (243)
T ss_pred HHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHhhhhhhcccCCCCCceEEecCchHHHhccHHHhhccchhhhcccccccc
Confidence 99999999999999999999999999999999999985443 69999999999999555 9999999999999977
Q ss_pred hh
Q 031143 162 ME 163 (165)
Q Consensus 162 ~~ 163 (165)
++
T Consensus 161 ~~ 162 (243)
T PF03998_consen 161 KD 162 (243)
T ss_pred HH
Confidence 65
No 3
>COG5223 Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=2.1e-47 Score=317.29 Aligned_cols=159 Identities=33% Similarity=0.424 Sum_probs=150.0
Q ss_pred CCc-cccccccccccccCCcchhhccccccccccHHHHHHHHhHHHHHHHHHHHHHHhhCCCchhhhhhhhhhcCCcccc
Q 031143 1 MSS-RRNAIPRRAHKERAQPQSRKKFGLLEKHKDYVVRAKAYRKKEETIRRLKEKAAFRNPDEFYLKMIKTKIVDGVHRL 79 (165)
Q Consensus 1 Mss-lrna~krr~HrER~QP~~R~~lGlLEKkKDY~~RA~dy~~K~~~lk~Lr~KA~~rNpDEFyf~M~~sk~~~Gvh~~ 79 (165)
||+ |.++-+|++||||+||.+|++||+|||||||++||.|||+|+.+|+.||++|..||||||||+|.+.++.+|+..+
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 775 5555588999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred ccccCCCCHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHhhhcccCCCCCCCeeEEeeCccccc-cCC---CCCChhhHhh
Q 031143 80 ESEANKYTQEELILMKTQDIGYILQKLQSERNKIEKLTTMLHSLDSNLSSRHVYYAEDRFMLS-KLP---FFSEGNNILD 155 (165)
Q Consensus 80 ~~~~~~~t~e~~kl~ktQDl~Yv~~~~~~e~kKiekL~~~L~~~~~~~~nkH~vFvd~~~e~~-~~~---fdT~~ell~R 155 (165)
.++++.++.|++++++|||.+|+++.++.|+.+++.+..++++ ..++.|++|||+..+++ |.| |.|+.|||+|
T Consensus 81 ~ReDe~~~md~~KmlktqD~~~~R~~r~lEr~k~~~~~~qi~f---~es~~htifvD~r~~~kef~peeFf~tt~elV~r 157 (240)
T COG5223 81 YREDEPTIMDLAKMLKTQDNEIQRCRRKLERYKPMPCGTQIKF---EESSLHTIFVDMRFGQKEFIPEEFFRTTEELVVR 157 (240)
T ss_pred eccccchHHHHHHHHHhhhhHHHHHHHHHHHhCCcchhceeee---eccccchhhhhhhhhhhhcCHHHHHHHHHHHHHH
Confidence 8888899999999999999999999999999999999999999 46789999999999998 666 9999999999
Q ss_pred Hhhhhhh
Q 031143 156 LLAILYM 162 (165)
Q Consensus 156 ~~n~~~~ 162 (165)
+.||++=
T Consensus 158 ~enrl~k 164 (240)
T COG5223 158 RENRLEK 164 (240)
T ss_pred HHHHHHH
Confidence 9999874
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=50.13 E-value=23 Score=25.68 Aligned_cols=24 Identities=33% Similarity=0.393 Sum_probs=20.0
Q ss_pred HHhHHHHHHHHHHHHHHhhCCCch
Q 031143 40 AYRKKEETIRRLKEKAAFRNPDEF 63 (165)
Q Consensus 40 dy~~K~~~lk~Lr~KA~~rNpDEF 63 (165)
|-.--..+|..|+.++....|+||
T Consensus 65 DLd~i~krir~lk~kl~~~yP~~y 88 (88)
T PF10241_consen 65 DLDYIFKRIRSLKAKLAKQYPEEY 88 (88)
T ss_pred HHHHHHHHHHHHHHHHHHhCCCcC
Confidence 344456789999999999999998
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=36.19 E-value=46 Score=28.29 Aligned_cols=32 Identities=16% Similarity=0.406 Sum_probs=27.2
Q ss_pred ccHHHHHHHHhHHHHHHHHHHHHHHhhCCCch
Q 031143 32 KDYVVRAKAYRKKEETIRRLKEKAAFRNPDEF 63 (165)
Q Consensus 32 KDY~~RA~dy~~K~~~lk~Lr~KA~~rNpDEF 63 (165)
++|+.++.++.+.+..+++|++|+.-.||+.+
T Consensus 119 ~E~K~~~~~l~K~~sel~Kl~KKs~~~~~~k~ 150 (223)
T cd07605 119 KEYKQKREDLDKARSELKKLQKKSQKSGTGKY 150 (223)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHcccCCCcc
Confidence 57888888999999999999999998777643
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=29.97 E-value=14 Score=30.15 Aligned_cols=33 Identities=27% Similarity=0.687 Sum_probs=24.5
Q ss_pred CCCchhhhhhhhhhcCCccccccccCCCCHHHHHHhhhhhHHHHHHHH
Q 031143 59 NPDEFYLKMIKTKIVDGVHRLESEANKYTQEELILMKTQDIGYILQKL 106 (165)
Q Consensus 59 NpDEFyf~M~~sk~~~Gvh~~~~~~~~~t~e~~kl~ktQDl~Yv~~~~ 106 (165)
||-||||+.+.+| .|.- + --+||-|-+|+.-++
T Consensus 3 ~~~e~f~~~~~~R--~gl~---d----------ta~kTa~sGyl~R~l 35 (277)
T PF04998_consen 3 TPTEYFFHCMGGR--EGLI---D----------TAVKTADSGYLQRRL 35 (277)
T ss_dssp THHHHHHHHHHHH--HHHH---H----------HHHCHHHHHHHHHHH
T ss_pred CHHHHHHHHhccc--cccc---c----------cceeeeccccchhhh
Confidence 7899999999888 4421 1 127999999997554
No 7
>PF02202 Tachykinin: Tachykinin family; InterPro: IPR002040 This family includes peptides, which belong to the tachykinin family. Tachykinins [, , ] are a group of biologically active peptides which excite neurons, evoke behavioral responses, are potent vasodilatators and contract (directly or indirectly) many smooth muscles. Tachykinins, like most other active peptides, are synthesized as larger protein precursors that are enzymatically converted to their mature forms. Tachykinins are from ten to twelve residues long.; GO: 0007217 tachykinin receptor signaling pathway, 0007268 synaptic transmission; PDB: 1MYU_A 1N6T_A 2GFR_A.
Probab=22.77 E-value=13 Score=18.06 Aligned_cols=6 Identities=67% Similarity=1.641 Sum_probs=4.6
Q ss_pred CCCchh
Q 031143 59 NPDEFY 64 (165)
Q Consensus 59 NpDEFy 64 (165)
+||.||
T Consensus 3 ~pd~F~ 8 (11)
T PF02202_consen 3 KPDQFY 8 (11)
T ss_dssp CHHHHC
T ss_pred Ccccce
Confidence 578887
No 8
>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=17.02 E-value=1.7e+02 Score=27.59 Aligned_cols=38 Identities=24% Similarity=0.440 Sum_probs=31.8
Q ss_pred CCHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHhhhcccC
Q 031143 86 YTQEELILMKTQDIGYILQKLQSERNKIEKLTTMLHSLD 124 (165)
Q Consensus 86 ~t~e~~kl~ktQDl~Yv~~~~~~e~kKiekL~~~L~~~~ 124 (165)
|..|. .+-...|+.|+......|.++|.+++.+|..+.
T Consensus 392 L~~D~-~l~~~~d~~~~~~li~~e~~~I~k~E~EL~~L~ 429 (431)
T PF10443_consen 392 LVNDK-VLSARMDLAYLKKLIKIENKKIKKYEEELRKLG 429 (431)
T ss_pred HhhCH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 44443 456789999999999999999999999998764
No 9
>COG4549 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=14.94 E-value=57 Score=27.31 Aligned_cols=10 Identities=50% Similarity=0.893 Sum_probs=7.8
Q ss_pred hCCCchhhhh
Q 031143 58 RNPDEFYLKM 67 (165)
Q Consensus 58 rNpDEFyf~M 67 (165)
.||||||=+-
T Consensus 108 nlPde~YD~f 117 (178)
T COG4549 108 NLPDEFYDEF 117 (178)
T ss_pred CCchhhccce
Confidence 5999999544
No 10
>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=14.60 E-value=17 Score=27.22 Aligned_cols=41 Identities=12% Similarity=0.253 Sum_probs=20.6
Q ss_pred HHHHHHHHHHHHHHHHHHhhhcccC-CCCCCCeeEEeeCcccc
Q 031143 100 GYILQKLQSERNKIEKLTTMLHSLD-SNLSSRHVYYAEDRFML 141 (165)
Q Consensus 100 ~Yv~~~~~~e~kKiekL~~~L~~~~-~~~~nkH~vFvd~~~e~ 141 (165)
.||+++...|.+++..=. .+..+. .+..+-|++|+|+....
T Consensus 20 ~fv~~kA~~ekreL~~dd-~vAIlnI~gTtSy~v~FLd~~~~i 61 (87)
T PF05370_consen 20 DFVKVKAAIEKRELKDDD-EVAILNIQGTTSYQVFFLDSYNSI 61 (87)
T ss_dssp -STHHHHCTTT---SS---EEEEEE-TTTT-EEEEE-S---S-
T ss_pred hHhhhhhhhccccCCCCC-cEEEEEecCCceEEEEEEcCCCCH
Confidence 789999999988663322 333333 46677899999985544
Done!