Query 027001
Match_columns 229
No_of_seqs 30 out of 32
Neff 2.5
Searched_HMMs 46136
Date Fri Mar 29 03:34:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027001.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027001hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG4043 Preprotein translocase 99.7 1.7E-18 3.6E-23 138.7 3.8 65 130-194 2-75 (111)
2 cd06555 ASCH_PF0470_like ASC-1 99.7 5E-18 1.1E-22 134.1 4.7 64 131-194 1-77 (109)
3 PF04266 ASCH: ASCH domain; I 98.5 2E-07 4.4E-12 68.6 4.4 72 133-205 1-89 (105)
4 cd06541 ASCH ASC-1 homology or 98.3 8.6E-07 1.9E-11 67.8 4.6 53 133-185 2-66 (105)
5 cd06552 ASCH_yqfb_like ASC-1 h 94.4 0.047 1E-06 40.4 3.4 66 136-202 5-84 (100)
6 PF12961 DUF3850: Domain of Un 81.9 0.94 2E-05 34.5 1.8 45 132-177 2-61 (72)
7 cd06554 ASCH_ASC-1_like ASC-1 68.9 2.9 6.4E-05 33.6 1.5 27 133-159 4-30 (113)
8 PF07527 Hairy_orange: Hairy O 44.8 21 0.00046 23.6 2.2 28 4-40 7-34 (43)
9 PF12917 HD_2: HD containing h 25.5 36 0.00078 30.8 1.2 20 135-154 112-132 (215)
10 PRK04980 hypothetical protein; 22.0 1.5E+02 0.0032 23.9 4.0 31 133-163 5-35 (102)
11 TIGR03337 phnR transcriptional 20.1 80 0.0017 26.0 2.1 20 69-88 1-20 (231)
No 1
>COG4043 Preprotein translocase subunit Sec61beta [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.73 E-value=1.7e-18 Score=138.69 Aligned_cols=65 Identities=17% Similarity=0.089 Sum_probs=62.0
Q ss_pred hhhcccchhhHHhhhcccceeeeccccccccccC---------CeEEEEEeeeeeccchhhhhhhhcccccccc
Q 027001 130 EFELHVQEPFFSFIKDGLETVEGRCTISDYNRCG---------LCLVVYELNFHNYVFFFLGSFHIIFDSVKYC 194 (229)
Q Consensus 130 ~~EmhVQEp~fslik~GkKtVEGRLa~eky~rIk---------~cL~v~V~~Vr~Y~SF~e~~~~~~~d~vk~~ 194 (229)
.|+|+|||+||++||+|+||||||+|+.++++|| ..|+|+|.+||.|.||++|+..|+++||.|-
T Consensus 2 ~~~mgL~eeylE~IK~GkK~iEvRl~d~krr~ik~GD~IiF~~~~l~v~V~~vr~Y~tF~~mlreepiE~v~p~ 75 (111)
T COG4043 2 VHRMGLREEYLELIKAGKKKIEVRLADPKRRQIKPGDKIIFNGDKLKVEVIDVRVYDTFEEMLREEPIENVLPD 75 (111)
T ss_pred ceeechHHHHHHHHHcccceEEEEecCHhhcCCCCCCEEEEcCCeeEEEEEEEeehhHHHHHHHhcChhhhCCC
Confidence 4899999999999999999999999999999998 4899999999999999999999999999874
No 2
>cd06555 ASCH_PF0470_like ASC-1 homology domain, subfamily similar to Pyrococcus furiosus Pf0470. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation.
Probab=99.72 E-value=5e-18 Score=134.13 Aligned_cols=64 Identities=22% Similarity=0.155 Sum_probs=60.8
Q ss_pred hhcccchhhHHhhhcccceeeeccccccccccC-------------CeEEEEEeeeeeccchhhhhhhhcccccccc
Q 027001 131 FELHVQEPFFSFIKDGLETVEGRCTISDYNRCG-------------LCLVVYELNFHNYVFFFLGSFHIIFDSVKYC 194 (229)
Q Consensus 131 ~EmhVQEp~fslik~GkKtVEGRLa~eky~rIk-------------~cL~v~V~~Vr~Y~SF~e~~~~~~~d~vk~~ 194 (229)
+||||+++||++|++|+||||+||+|++|++|+ +++.|+|++|++|+||++|+.+++++++.|-
T Consensus 1 h~m~l~~~~F~~I~~G~KtiEiRlnD~kr~~ikvGD~I~f~~~~~~~~l~v~V~~i~~Y~sF~~ll~~e~~~~~~~~ 77 (109)
T cd06555 1 HEMGLEEEPFELIKSGKKTIEIRLNDEKRQQIKVGDKILFNDLDTGQQLLVKVVDIRKYDSFRELLEEEGLEKVGPG 77 (109)
T ss_pred CccccChHHHHHHHcCCCEEEEEecccchhcCCCCCEEEEEEcCCCcEEEEEEEEEEecCCHHHHHHhcCHhhcCCC
Confidence 589999999999999999999999999999998 3799999999999999999999999999875
No 3
>PF04266 ASCH: ASCH domain; InterPro: IPR007374 The ASCH domain adopts a beta-barrel fold similar to that of the PUA domain (IPR002478 from INTERPRO). It is thought to function as an RNA-binding domain during coactivation, RNA-processing and possibly during prokaryotic translation regulation [].; PDB: 1TE7_A 2Z0T_C 1WK2_A 2DP9_A 1T62_A 3S9X_A 2E5O_A 1XNE_A 3IUW_B 1S04_A.
Probab=98.46 E-value=2e-07 Score=68.56 Aligned_cols=72 Identities=17% Similarity=0.054 Sum_probs=53.5
Q ss_pred cccchhhHHhhhcccceeeeccccccccccC--------------CeEEEEEeeeeeccchhhhhhhhccc---cccccc
Q 027001 133 LHVQEPFFSFIKDGLETVEGRCTISDYNRCG--------------LCLVVYELNFHNYVFFFLGSFHIIFD---SVKYCF 195 (229)
Q Consensus 133 mhVQEp~fslik~GkKtVEGRLa~eky~rIk--------------~cL~v~V~~Vr~Y~SF~e~~~~~~~d---~vk~~~ 195 (229)
|+++++|+++|.+|+||+|.|+.+.++.+++ ....++|.+|+.| +|.++..+.+.. ++..+.
T Consensus 1 Lsi~~~~~~~Il~G~Kt~e~R~~~~~~~~~~g~~~iv~~~~~~~~~~~~v~v~~V~~~-~~~e~~~~~a~~eg~s~e~~~ 79 (105)
T PF04266_consen 1 LSIKPEYAELILSGKKTAEIRLWDEKLPKIRGDLVIVFNTDPDGKPVGIVEVTEVEVY-PFSELTEEHARLEGESLEEWR 79 (105)
T ss_dssp EEECHHHHHHHHTTSSCEEEECSTTTCCTTTTCEEEEETETTTTEEEEEEEEEEEEEE-EHHHHHHHHHHHHCC-HHHHH
T ss_pred CEechHHHHHHHCCCcEEEEEcccceeccCCCCEEEEEEEecCCcEEEEEEEEEEEEe-hhhhCCHHHHhHhccCHHHHH
Confidence 5789999999999999999999999988873 2467799999999 999986554432 444444
Q ss_pred ccchhHHHHH
Q 027001 196 ADQQGIYEWL 205 (229)
Q Consensus 196 ~~~~~~~~~~ 205 (229)
+.-..+|.-.
T Consensus 80 ~~~~~~y~~~ 89 (105)
T PF04266_consen 80 EEHRDIYPRE 89 (105)
T ss_dssp HHHHHHCHHH
T ss_pred HHHHHHcccc
Confidence 4444444433
No 4
>cd06541 ASCH ASC-1 homology or ASCH domain, a small beta-barrel domain found in all three kingdoms of life. ASCH resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation. The domain has been named after the ASC-1 protein, the activating signal cointegrator 1 or thyroid hormone receptor interactor protein 4 (TRIP4). ASC-1 is conserved in many eukaryotes and has been suggested to participate in a protein complex that interacts with RNA. It has been shown that ASC-1 mediates the interaction between various transciption factors and the basal transcriptional machinery.
Probab=98.30 E-value=8.6e-07 Score=67.78 Aligned_cols=53 Identities=11% Similarity=-0.092 Sum_probs=45.5
Q ss_pred cccchhhHHhhhcccceeeeccccccccccC--------C----eEEEEEeeeeeccchhhhhhh
Q 027001 133 LHVQEPFFSFIKDGLETVEGRCTISDYNRCG--------L----CLVVYELNFHNYVFFFLGSFH 185 (229)
Q Consensus 133 mhVQEp~fslik~GkKtVEGRLa~eky~rIk--------~----cL~v~V~~Vr~Y~SF~e~~~~ 185 (229)
+++.+++|++|.+|+||+|.|+++++++.++ . .+.++|.+|+.|++|.++..+
T Consensus 2 l~~~~~~~~lI~~G~Ktat~r~~~~~~~~~k~Gd~~i~~~~~~~~~~i~v~~V~~~~~f~~~~~e 66 (105)
T cd06541 2 LMFGDRYGQLVVSGRKTIEIRSLDIYEQLPKAGDYLIILDGQQPLAIAEVVKVEIMPMVNELSEE 66 (105)
T ss_pred ceechHHHHHHHCCCCEEEEEcchhcccCCCCCCEEEEecCCCcEEEEEEEEEEEEECHHHccHH
Confidence 5788999999999999999999999877776 3 589999999999999554433
No 5
>cd06552 ASCH_yqfb_like ASC-1 homology domain, subfamily similar to Escherichia coli Yqfb. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation.
Probab=94.45 E-value=0.047 Score=40.41 Aligned_cols=66 Identities=15% Similarity=-0.098 Sum_probs=43.6
Q ss_pred chhhHHhhhcccceeeeccccccccccCC----------eEEEEEeeeeeccchhhhh----hhhcccccccccccchhH
Q 027001 136 QEPFFSFIKDGLETVEGRCTISDYNRCGL----------CLVVYELNFHNYVFFFLGS----FHIIFDSVKYCFADQQGI 201 (229)
Q Consensus 136 QEp~fslik~GkKtVEGRLa~eky~rIk~----------cL~v~V~~Vr~Y~SF~e~~----~~~~~d~vk~~~~~~~~~ 201 (229)
-..++.+|.+|+||++-|......-+.+. ...++|.+|+. .+|.++. .++||.++.-..++-+.+
T Consensus 5 ~~~~~~~I~sG~Kt~t~R~~~~~~~~~Gd~~~~~~~~~~~~~~~v~~V~~-~~~~~l~~~~A~~eG~~s~~~~~~~l~~~ 83 (100)
T cd06552 5 FERYEEAILSGKKTATIRDGGESHLKPGDVVEVHTGERIFGEAEITSVEE-KTLGELTDEDARQEGFPSLEELKEALKEI 83 (100)
T ss_pred hHHHHHHHHcCCCEEEEeCCCccCCCCCCEEEEEECCEEEEEEEEEEEEE-EEhhhCCHHHHHhcCCccHHHHHHHHHHH
Confidence 35789999999999999996554444442 45567888877 7787754 345665554444444443
Q ss_pred H
Q 027001 202 Y 202 (229)
Q Consensus 202 ~ 202 (229)
|
T Consensus 84 Y 84 (100)
T cd06552 84 Y 84 (100)
T ss_pred c
Confidence 3
No 6
>PF12961 DUF3850: Domain of Unknown Function with PDB structure (DUF3850)
Probab=81.94 E-value=0.94 Score=34.50 Aligned_cols=45 Identities=22% Similarity=0.294 Sum_probs=34.2
Q ss_pred hcccchhhHHhhhcccceeeeccccccccccC---------------CeEEEEEeeeeecc
Q 027001 132 ELHVQEPFFSFIKDGLETVEGRCTISDYNRCG---------------LCLVVYELNFHNYV 177 (229)
Q Consensus 132 EmhVQEp~fslik~GkKtVEGRLa~eky~rIk---------------~cL~v~V~~Vr~Y~ 177 (229)
|+-++..||+.+.+|.||-|-|..|-+|+ ++ +.+.++|..|--|.
T Consensus 2 ~LKi~p~yF~~V~~G~KtfEiRkNDRdf~-VGD~L~L~E~~~~~YTGr~~~~~Ityi~~~~ 61 (72)
T PF12961_consen 2 ELKILPEYFEAVLSGRKTFEIRKNDRDFQ-VGDILVLREWDNGEYTGREIEAEITYITDYE 61 (72)
T ss_pred ceeecHHHHHHHHCCCceEEEEecCCCCC-CCCEEEEEEecCCCccccEEEEEEEEEeecC
Confidence 56788999999999999999999997664 22 45666666665443
No 7
>cd06554 ASCH_ASC-1_like ASC-1 homology domain, ASC-1-like subfamily. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation. The domain has been named after the ASC-1 protein, the activating signal cointegrator 1 or thyroid hormone receptor interactor protein 4 (TRIP4). ASC-1 is conserved in many eukaryotes and has been suggested to participate in a protein complex that interacts with RNA. It has been shown that ASC-1 mediates the interaction between various transciption factors and the basal transcriptional machinery.
Probab=68.86 E-value=2.9 Score=33.57 Aligned_cols=27 Identities=33% Similarity=0.748 Sum_probs=23.1
Q ss_pred cccchhhHHhhhcccceeeeccccccc
Q 027001 133 LHVQEPFFSFIKDGLETVEGRCTISDY 159 (229)
Q Consensus 133 mhVQEp~fslik~GkKtVEGRLa~eky 159 (229)
+-+..||=++|-.|.|+||+|--.-+|
T Consensus 4 lsi~qPwa~li~~g~K~~E~R~w~t~~ 30 (113)
T cd06554 4 LSIHQPWASLIVRGIKRIEGRSWATNY 30 (113)
T ss_pred eEEeCcHHHHHHcCCCceecccCCCCc
Confidence 456789999999999999999776665
No 8
>PF07527 Hairy_orange: Hairy Orange; InterPro: IPR003650 This domain confers specificity among members of the Hairy/E(SPL) family. HES-2 (hairy and enhancer of split 2) is a transcription factor, and the hairy protein is a pair-rule protein that regulates embryonic segmentation and adult bristle patterning. These proteins are transcriptional repressors of genes that require the BHLH protein for their transcription.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DB7_A.
Probab=44.82 E-value=21 Score=23.63 Aligned_cols=28 Identities=25% Similarity=0.643 Sum_probs=18.5
Q ss_pred HHHHHHHHHHHHhhcccccccCcCCCCCHHHHhhhhc
Q 027001 4 LKDCMEELLKFTLSSHIDETLDFDLGISSKFCTNLLQ 40 (229)
Q Consensus 4 L~dcleELvkFtL~Shv~~t~~fdL~LS~~FCs~LL~ 40 (229)
.++|+.|..||. +++. ++.++++.+|+.
T Consensus 7 y~~C~~Ev~~fL--~~~~-------~~~~~~~~rLl~ 34 (43)
T PF07527_consen 7 YSECLNEVSRFL--SSVE-------GVDPGVRARLLS 34 (43)
T ss_dssp HHHHHHHHHHHH--HHTS----------THHHHHHHH
T ss_pred HHHHHHHHHHHH--hcCC-------CCChHHHHHHHH
Confidence 468999999998 3443 124477777763
No 9
>PF12917 HD_2: HD containing hydrolase-like enzyme ; PDB: 3MZO_B.
Probab=25.53 E-value=36 Score=30.78 Aligned_cols=20 Identities=35% Similarity=0.601 Sum_probs=15.0
Q ss_pred cchhhHHhhhcccc-eeeecc
Q 027001 135 VQEPFFSFIKDGLE-TVEGRC 154 (229)
Q Consensus 135 VQEp~fslik~GkK-tVEGRL 154 (229)
.|+.|...+++||. |+|||+
T Consensus 112 ~q~~Y~~~l~E~KDdt~EG~I 132 (215)
T PF12917_consen 112 FQEAYRRRLKEGKDDTLEGQI 132 (215)
T ss_dssp GHHHHHHHHS---SSSHHHHH
T ss_pred HHHHHHHHhhcCCcccHHHHH
Confidence 68999999999995 999995
No 10
>PRK04980 hypothetical protein; Provisional
Probab=22.00 E-value=1.5e+02 Score=23.90 Aligned_cols=31 Identities=23% Similarity=0.129 Sum_probs=22.4
Q ss_pred cccchhhHHhhhcccceeeeccccccccccC
Q 027001 133 LHVQEPFFSFIKDGLETVEGRCTISDYNRCG 163 (229)
Q Consensus 133 mhVQEp~fslik~GkKtVEGRLa~eky~rIk 163 (229)
+-.-+.|-.+|-+|+||+-.|-..+..-+.+
T Consensus 5 itF~~r~~~~ILsGkKTiTiRd~se~~~~~G 35 (102)
T PRK04980 5 ITFFERFEADILAGRKTITIRDESESHFKPG 35 (102)
T ss_pred eeEHHHHHHHHHcCCceEEeeCCcccCCCCC
Confidence 3445677789999999999998655444433
No 11
>TIGR03337 phnR transcriptional regulator protein. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Salmonella, Vibrio Aeromonas hydrophila, Hahella chejuensis and Psychromonas ingrahamii.
Probab=20.12 E-value=80 Score=26.00 Aligned_cols=20 Identities=25% Similarity=0.391 Sum_probs=18.6
Q ss_pred HHHHHHHHHHHhhhhcCCcc
Q 027001 69 PLYKRLALALCRSVNCGAFC 88 (229)
Q Consensus 69 PLykrLA~aL~rci~sg~fc 88 (229)
|||..++..|.+.|.+|.+.
T Consensus 1 p~y~qi~~~l~~~I~~g~~~ 20 (231)
T TIGR03337 1 PQYLYIKDHLSYQIRAGALL 20 (231)
T ss_pred CHHHHHHHHHHHHHHcCCCC
Confidence 79999999999999999874
Done!