Query 032940
Match_columns 130
No_of_seqs 113 out of 220
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 07:50:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032940.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032940hhsearch_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 1.9E-53 4.2E-58 344.9 11.2 117 10-126 1-119 (243)
2 KOG3237 Uncharacterized conser 100.0 1.2E-52 2.6E-57 342.4 9.0 124 1-124 1-126 (250)
3 COG5223 Uncharacterized conser 100.0 3.5E-38 7.5E-43 254.4 6.4 125 1-125 1-126 (240)
4 PF10241 KxDL: Uncharacterized 56.8 16 0.00035 25.5 3.4 24 40-63 65-88 (88)
5 PF04998 RNA_pol_Rpb1_5: RNA p 45.4 6.7 0.00015 30.5 -0.1 34 59-107 3-36 (277)
6 cd07605 I-BAR_IMD Inverse (I)- 34.8 53 0.0011 26.9 3.6 31 32-62 119-149 (223)
7 PF02202 Tachykinin: Tachykini 31.2 8.2 0.00018 18.3 -1.0 6 59-64 3-8 (11)
8 TIGR02390 RNA_pol_rpoA1 DNA-di 22.5 37 0.0008 32.8 0.7 35 58-107 786-820 (868)
9 COG4549 Uncharacterized protei 19.5 39 0.00084 27.4 0.2 10 58-67 108-117 (178)
10 PF14746 WASH-7_C: WASH comple 16.7 69 0.0015 25.5 1.0 31 99-129 57-88 (170)
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=1.9e-53 Score=344.94 Aligned_cols=117 Identities=50% Similarity=0.743 Sum_probs=113.2
Q ss_pred cccccccCCchhhhhcccccccccHHHHHHHHHHHHHHHHHHHHHHHhhCCCchhhhhhhccccC-Cccccccc-cCCCC
Q 032940 10 RRAHKERAQPQSRKKFGLLEKHKDYVVRAKAYRKKEETIRRLKEKAAFRNPDEFYLKMIKTKIVD-GVHRLESE-ANKYT 87 (130)
Q Consensus 10 rr~HrER~Qp~~R~~lGlLEKkKDY~~RA~dy~~K~~~lk~Lk~KA~~rNpDEFyf~M~~~k~~~-Gvh~~~~~-~~~~t 87 (130)
||+|+|||||++|++||||||||||++||+|||+|+++|+.|++||++||||||||+|+|+++.+ |+|+..++ ++.+|
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 HHHHHHhhhhcHHHHHHHHHHHHhhHHHHHhhhhhcccc
Q 032940 88 QEELILMKTQDIGYILQKLQSERNGRDKRNKIYIWTKSY 126 (130)
Q Consensus 88 ~e~~kl~kTQDl~Yv~~~~~~e~kKiekL~~~~~~~~~~ 126 (130)
+|+++||+|||++||+++++++.+|||+|++.++++.+.
T Consensus 81 ~e~~~llkTQD~~Yv~~~~~~e~kKIekL~~~l~~~~~~ 119 (243)
T PF03998_consen 81 KEQVKLLKTQDLNYVRTKRQIERKKIEKLQSELHLLDGK 119 (243)
T ss_pred HHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHhhhhhhcc
Confidence 999999999999999999999999999999999888754
No 2
>KOG3237 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=1.2e-52 Score=342.44 Aligned_cols=124 Identities=48% Similarity=0.697 Sum_probs=122.2
Q ss_pred CCccccccc--cccccccCCchhhhhcccccccccHHHHHHHHHHHHHHHHHHHHHHHhhCCCchhhhhhhccccCCccc
Q 032940 1 MSSRRNAIP--RRAHKERAQPQSRKKFGLLEKHKDYVVRAKAYRKKEETIRRLKEKAAFRNPDEFYLKMIKTKIVDGVHR 78 (130)
Q Consensus 1 MSSlrna~k--rr~HrER~Qp~~R~~lGlLEKkKDY~~RA~dy~~K~~~lk~Lk~KA~~rNpDEFyf~M~~~k~~~Gvh~ 78 (130)
||||+||++ +++|||||||.+|++||+|||||||++||.|||+||++|+.|+++|+++|||||||+|+|+++.||+|+
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 899999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccCCCCHHHHHHhhhhcHHHHHHHHHHHHhhHHHHHhhhhhcc
Q 032940 79 LESEANKYTQEELILMKTQDIGYILQKLQSERNGRDKRNKIYIWTK 124 (130)
Q Consensus 79 ~~~~~~~~t~e~~kl~kTQDl~Yv~~~~~~e~kKiekL~~~~~~~~ 124 (130)
+..+.+++|+|||+||+|||++||.+++++|++|||+|.+.|++++
T Consensus 81 ~k~e~~e~t~eqlklmktQDi~YV~~kr~~ErkKIerlka~L~~~~ 126 (250)
T KOG3237|consen 81 EKDEVDEPTMEQLKLMKTQDIGYVRMKRQRERKKIERLKAQLHCVD 126 (250)
T ss_pred cccccccCCHHHHHHHhhhhHHHHHHHHHHHHHHHHHHhccccccc
Confidence 9988899999999999999999999999999999999999999887
No 3
>COG5223 Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=3.5e-38 Score=254.39 Aligned_cols=125 Identities=35% Similarity=0.470 Sum_probs=117.7
Q ss_pred CCc-cccccccccccccCCchhhhhcccccccccHHHHHHHHHHHHHHHHHHHHHHHhhCCCchhhhhhhccccCCcccc
Q 032940 1 MSS-RRNAIPRRAHKERAQPQSRKKFGLLEKHKDYVVRAKAYRKKEETIRRLKEKAAFRNPDEFYLKMIKTKIVDGVHRL 79 (130)
Q Consensus 1 MSS-lrna~krr~HrER~Qp~~R~~lGlLEKkKDY~~RA~dy~~K~~~lk~Lk~KA~~rNpDEFyf~M~~~k~~~Gvh~~ 79 (130)
||+ |.++-+|++|+||+||.+|++||+|||+|||++||.|||+|+.+|+.||++|..||||||||+|.+.++.+||.++
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 6666689999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccCCCCHHHHHHhhhhcHHHHHHHHHHHHhhHHHHHhhhhhccc
Q 032940 80 ESEANKYTQEELILMKTQDIGYILQKLQSERNGRDKRNKIYIWTKS 125 (130)
Q Consensus 80 ~~~~~~~t~e~~kl~kTQDl~Yv~~~~~~e~kKiekL~~~~~~~~~ 125 (130)
.++.+.+++|++++++|||.+|+++.++.|..+++.+...+.|-.|
T Consensus 81 ~ReDe~~~md~~KmlktqD~~~~R~~r~lEr~k~~~~~~qi~f~es 126 (240)
T COG5223 81 YREDEPTIMDLAKMLKTQDNEIQRCRRKLERYKPMPCGTQIKFEES 126 (240)
T ss_pred eccccchHHHHHHHHHhhhhHHHHHHHHHHHhCCcchhceeeeecc
Confidence 9888899999999999999999999999999999999888777654
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=56.84 E-value=16 Score=25.48 Aligned_cols=24 Identities=33% Similarity=0.393 Sum_probs=19.8
Q ss_pred HHHHHHHHHHHHHHHHHhhCCCch
Q 032940 40 AYRKKEETIRRLKEKAAFRNPDEF 63 (130)
Q Consensus 40 dy~~K~~~lk~Lk~KA~~rNpDEF 63 (130)
|-.--..+|..|+.++....|+||
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
>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=45.37 E-value=6.7 Score=30.52 Aligned_cols=34 Identities=26% Similarity=0.674 Sum_probs=25.4
Q ss_pred CCCchhhhhhhccccCCccccccccCCCCHHHHHHhhhhcHHHHHHHHH
Q 032940 59 NPDEFYLKMIKTKIVDGVHRLESEANKYTQEELILMKTQDIGYILQKLQ 107 (130)
Q Consensus 59 NpDEFyf~M~~~k~~~Gvh~~~~~~~~~t~e~~kl~kTQDl~Yv~~~~~ 107 (130)
||-||||+.+.+| .|.- + --+||-|-+|+.-++.
T Consensus 3 ~~~e~f~~~~~~R--~gl~--d-----------ta~kTa~sGyl~R~lv 36 (277)
T PF04998_consen 3 TPTEYFFHCMGGR--EGLI--D-----------TAVKTADSGYLQRRLV 36 (277)
T ss_dssp THHHHHHHHHHHH--HHHH--H-----------HHHCHHHHHHHHHHHH
T ss_pred CHHHHHHHHhccc--cccc--c-----------cceeeeccccchhhhh
Confidence 7899999999988 4521 0 1289999999976654
No 6
>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=34.82 E-value=53 Score=26.88 Aligned_cols=31 Identities=16% Similarity=0.365 Sum_probs=26.3
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHhhCCCc
Q 032940 32 KDYVVRAKAYRKKEETIRRLKEKAAFRNPDE 62 (130)
Q Consensus 32 KDY~~RA~dy~~K~~~lk~Lk~KA~~rNpDE 62 (130)
++|+.+..++.+.+..++.|+.|+...||+.
T Consensus 119 ~E~K~~~~~l~K~~sel~Kl~KKs~~~~~~k 149 (223)
T cd07605 119 KEYKQKREDLDKARSELKKLQKKSQKSGTGK 149 (223)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHcccCCCc
Confidence 5778888899999999999999998766653
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=31.23 E-value=8.2 Score=18.28 Aligned_cols=6 Identities=67% Similarity=1.641 Sum_probs=4.7
Q ss_pred CCCchh
Q 032940 59 NPDEFY 64 (130)
Q Consensus 59 NpDEFy 64 (130)
+||.||
T Consensus 3 ~pd~F~ 8 (11)
T PF02202_consen 3 KPDQFY 8 (11)
T ss_dssp CHHHHC
T ss_pred Ccccce
Confidence 688887
No 8
>TIGR02390 RNA_pol_rpoA1 DNA-directed RNA polymerase subunit A'. This family consists of the archaeal A' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein.
Probab=22.49 E-value=37 Score=32.83 Aligned_cols=35 Identities=23% Similarity=0.587 Sum_probs=23.4
Q ss_pred hCCCchhhhhhhccccCCccccccccCCCCHHHHHHhhhhcHHHHHHHHH
Q 032940 58 RNPDEFYLKMIKTKIVDGVHRLESEANKYTQEELILMKTQDIGYILQKLQ 107 (130)
Q Consensus 58 rNpDEFyf~M~~~k~~~Gvh~~~~~~~~~t~e~~kl~kTQDl~Yv~~~~~ 107 (130)
-||.||||+.+..| +|.- + | -+||-|-+|+.-+..
T Consensus 786 L~p~EfFfH~m~gR--eGLi---D-----T-----AvKTa~sGYLqRrLv 820 (868)
T TIGR02390 786 LDPTEYFFHAAGGR--EGLV---D-----T-----AVRTSQSGYMQRRLI 820 (868)
T ss_pred CCHHHHHHHHhhhc--cccc---c-----c-----cccccccchhHHHHH
Confidence 48999999998887 5521 0 1 157777888765543
No 9
>COG4549 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=19.48 E-value=39 Score=27.37 Aligned_cols=10 Identities=50% Similarity=0.893 Sum_probs=7.6
Q ss_pred hCCCchhhhh
Q 032940 58 RNPDEFYLKM 67 (130)
Q Consensus 58 rNpDEFyf~M 67 (130)
.||||||=.-
T Consensus 108 nlPde~YD~f 117 (178)
T COG4549 108 NLPDEFYDEF 117 (178)
T ss_pred CCchhhccce
Confidence 5999999443
No 10
>PF14746 WASH-7_C: WASH complex subunit 7, C-terminal
Probab=16.70 E-value=69 Score=25.51 Aligned_cols=31 Identities=13% Similarity=0.160 Sum_probs=23.6
Q ss_pred HHHHHHHHHHHHhhHHHHHhhhhhcc-ccccc
Q 032940 99 IGYILQKLQSERNGRDKRNKIYIWTK-SYIAC 129 (130)
Q Consensus 99 l~Yv~~~~~~e~kKiekL~~~~~~~~-~~~~~ 129 (130)
++||.++.+...+=..+=+..++||+ ||.++
T Consensus 57 ln~ve~~i~~Kekl~Kk~k~~~~ftDDGFa~G 88 (170)
T PF14746_consen 57 LNYVEYMIQCKEKLFKKNKEGASFTDDGFAMG 88 (170)
T ss_pred HHHHHHHHHhHHHHHhcCCCCCeeecccHHHH
Confidence 67999998887776666666788888 87654
Done!