Query 030803
Match_columns 171
No_of_seqs 175 out of 496
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 04:48:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030803.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030803hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02309 AUX_IAA: AUX/IAA fami 100.0 7.6E-42 1.7E-46 282.6 0.2 149 2-170 1-152 (215)
2 cd06398 PB1_Joka2 The PB1 doma 45.5 35 0.00076 25.3 3.7 36 129-164 2-40 (91)
3 cd06404 PB1_aPKC PB1 domain is 45.4 39 0.00085 25.2 4.0 32 130-163 3-34 (83)
4 PF00564 PB1: PB1 domain; Int 42.0 33 0.00071 23.4 3.0 35 129-164 3-37 (84)
5 cd06407 PB1_NLP A PB1 domain i 37.4 54 0.0012 23.7 3.6 33 129-163 2-34 (82)
6 cd06396 PB1_NBR1 The PB1 domai 35.5 70 0.0015 23.6 4.0 34 130-163 3-36 (81)
7 cd06402 PB1_p62 The PB1 domain 32.2 78 0.0017 23.5 3.8 36 128-163 1-41 (87)
8 PF11576 DUF3236: Protein of u 31.9 17 0.00037 29.9 0.3 9 10-18 101-109 (154)
9 PF12426 DUF3674: RNA dependen 29.8 26 0.00057 23.0 0.8 14 155-168 7-21 (41)
10 PRK14763 coenzyme PQQ biosynth 24.5 24 0.00052 21.1 -0.1 8 6-13 7-14 (26)
11 smart00666 PB1 PB1 domain. Pho 23.3 1.6E+02 0.0034 20.0 3.9 33 130-164 4-36 (81)
12 cd06403 PB1_Par6 The PB1 domai 20.3 1.3E+02 0.0029 22.3 3.1 32 130-163 3-36 (80)
No 1
>PF02309 AUX_IAA: AUX/IAA family; InterPro: IPR003311 The Aux/IAA family of genes are key regulators of auxin-modified gene expression []. The plant hormone auxin (indole-3-acetic acid, IAA) regulates diverse cellular and developmental responses in plants, including cell division, expansion, differentiation and patterning of embryo responses []. Auxin can regulate the gene expression of several families, including GH3 and SAUR, as well as Aux/IAA itself. The Aux/IAA proteins act as repressors of auxin-induced gene expression, possibly through modulating the activity of DNA-binding auxin response factors (ARFs) (IPR010525 from INTERPRO). Aux/IAA and ARF are thought to interact through C-terminal protein-protein interaction domains found in both Aux/IAA and ARF. Recent evidence suggests that Aux/IAA proteins can also mediate light responses []. Some members of the AUX/IAA family are longer and contain an N-terminal DNA binding domain [] and may have an early function in the establishment of vascular and body patterns in embryonic and post-embryonic development in some plants.; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2P1N_F 2P1Q_C 2P1O_C.
Probab=100.00 E-value=7.6e-42 Score=282.55 Aligned_cols=149 Identities=46% Similarity=0.725 Sum_probs=6.0
Q ss_pred CCccccccccCCCCCCCCCCCCCCCCCCCCccccCccCCCCCCCcchhhhhhcccCcCCCCCc-cccccccCCCCC-cCC
Q 030803 2 INFEATELRLGLPGGNGGSSEGGGGGGGGEKAKNNNINGMKRGFADTVVDLKLNLSTKESGGI-DVIEKTKGKSAS-ATG 79 (171)
Q Consensus 2 lnl~~TELRLGLPG~~~~~~~~~~~~~~~~~~~~~~~~~~KRgfset~vdl~l~l~~~~~~~~-~~~~~~~~~~~~-~~~ 79 (171)
||||+|||||||||+.++. ............++||+|+++ +|............. .......+.... ...
T Consensus 1 ln~~~TELrLGLPG~~~~~-------~~~~~~~~~~~~~~kR~F~~a-id~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 (215)
T PF02309_consen 1 LNLKATELRLGLPGSESPD-------ASSSSSSKKSSSGNKRGFSEA-IDSSSSNSQSSSSSSSDSSSSSSSSSTSSSSS 72 (215)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred CCchhhhhcccCCCCCCCC-------cccccccccccCcccccchhh-hhhcccccccccccccccCccccccccccccc
Confidence 8999999999999987531 000011112347889999998 877652111000000 000000000000 000
Q ss_pred CCCC-CCCCCcCCCCCCCccchhhhhhhhhcccccccccccCCCCCCCcceEEEeecCcccceeeccccccCHHHHHHHH
Q 030803 80 ATDL-SKPPAKSQVVGWPPVRSFRKNIMAVQKDNEEGDNKASSSSSSNVAFVKVSMDGAPYLRKVDLKLYKSYQELSDAL 158 (171)
Q Consensus 80 ~~~~-~~p~~k~qvVGWPPVrs~RkN~~~~~~~~~~~~~~~~~~~~~~~~yVKVsMDG~pigRKVDL~~y~sY~~L~~~L 158 (171)
..+. ..|.+++|+|||||||+||||++.... .....+||||+|||+||||||||++|+||++|+.+|
T Consensus 73 ~~~~~~~p~~~~~~vgwpp~~s~r~n~~~~~~------------~~~~~~~vKV~mdG~~igRkVDL~~~~sY~~L~~~L 140 (215)
T PF02309_consen 73 DSSSSSPPASKAQVVGWPPVRSFRKNSLSEKQ------------SSSSRSYVKVNMDGVPIGRKVDLSAYSSYEELSSAL 140 (215)
T ss_dssp -------------BTTBS----S---------------------------------------------------------
T ss_pred ccccCCCCcccccccCCCcccccccccccccc------------cccCCceeEEEecCcccceecCHHHhhCHHHHHHHH
Confidence 1122 234478999999999999999887211 112379999999999999999999999999999999
Q ss_pred HHhhcccccccc
Q 030803 159 GKMFSSFTIGTY 170 (171)
Q Consensus 159 e~MF~~f~ig~~ 170 (171)
++||.+|+|++|
T Consensus 141 ~~MF~~~~i~~~ 152 (215)
T PF02309_consen 141 EKMFSCFSIEQC 152 (215)
T ss_dssp ------------
T ss_pred HHhcCCCCcccc
Confidence 999999998855
No 2
>cd06398 PB1_Joka2 The PB1 domain is present in the Nicotiana plumbaginifolia Joka2 protein which interacts with sulfur stress inducible UP9 protein. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module
Probab=45.51 E-value=35 Score=25.26 Aligned_cols=36 Identities=22% Similarity=0.250 Sum_probs=28.2
Q ss_pred eEEEeecCcccceeeccc---cccCHHHHHHHHHHhhcc
Q 030803 129 FVKVSMDGAPYLRKVDLK---LYKSYQELSDALGKMFSS 164 (171)
Q Consensus 129 yVKVsMDG~pigRKVDL~---~y~sY~~L~~~Le~MF~~ 164 (171)
=|||+.+|.-+==++++. ..-+|++|...+.+.|+-
T Consensus 2 ~vKv~y~~~~rRf~l~~~~~~~d~~~~~L~~kI~~~f~l 40 (91)
T cd06398 2 VVKVKYGGTLRRFTFPVAENQLDLNMDGLREKVEELFSL 40 (91)
T ss_pred EEEEEeCCEEEEEEeccccccCCCCHHHHHHHHHHHhCC
Confidence 489999998544455553 467999999999999973
No 3
>cd06404 PB1_aPKC PB1 domain is an essential modular domain of the atypical protein kinase C (aPKC) which in complex with Par6 and Par3 proteins is crucial for establishment of apical-basal polarity of animal cells. PB1 domain is a modular domain mediating specific protein-protein interaction which play roles in many critical cell processes. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi,
Probab=45.37 E-value=39 Score=25.15 Aligned_cols=32 Identities=25% Similarity=0.375 Sum_probs=27.4
Q ss_pred EEEeecCcccceeeccccccCHHHHHHHHHHhhc
Q 030803 130 VKVSMDGAPYLRKVDLKLYKSYQELSDALGKMFS 163 (171)
Q Consensus 130 VKVsMDG~pigRKVDL~~y~sY~~L~~~Le~MF~ 163 (171)
||+.-.|--+---+|. .-+|++|.+.+.+||.
T Consensus 3 ~K~~y~gdi~it~~d~--~~s~e~L~~~v~~~c~ 34 (83)
T cd06404 3 VKAAYNGDIMITSIDP--SISLEELCNEVRDMCR 34 (83)
T ss_pred EEEEecCcEEEEEcCC--CcCHHHHHHHHHHHhC
Confidence 7899999766666666 7789999999999998
No 4
>PF00564 PB1: PB1 domain; InterPro: IPR000270 The Phox and Bem1p domain, is present in many eukaryotic cytoplasmic signalling proteins. The domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate.; GO: 0005515 protein binding; PDB: 1IPG_A 1IP9_A 2KFK_A 1WMH_A 1VD2_A 1WI0_A 1OEY_C 1PQS_A 1Q1O_A 1TZ1_A ....
Probab=41.96 E-value=33 Score=23.42 Aligned_cols=35 Identities=23% Similarity=0.251 Sum_probs=28.8
Q ss_pred eEEEeecCcccceeeccccccCHHHHHHHHHHhhcc
Q 030803 129 FVKVSMDGAPYLRKVDLKLYKSYQELSDALGKMFSS 164 (171)
Q Consensus 129 yVKVsMDG~pigRKVDL~~y~sY~~L~~~Le~MF~~ 164 (171)
=|||+.+|.-+. -+.+..--+|.+|...+.+.|..
T Consensus 3 ~vK~~~~~~~~~-~~~~~~~~s~~~L~~~i~~~~~~ 37 (84)
T PF00564_consen 3 RVKVRYGGDIRR-IISLPSDVSFDDLRSKIREKFGL 37 (84)
T ss_dssp EEEEEETTEEEE-EEEECSTSHHHHHHHHHHHHHTT
T ss_pred EEEEEECCeeEE-EEEcCCCCCHHHHHHHHHHHhCC
Confidence 489999997544 47777777999999999999985
No 5
>cd06407 PB1_NLP A PB1 domain is present in NIN like proteins (NLP), a key enzyme in a process of establishment of symbiosis betweeen legumes and nitrogen fixing bacteria (Rhizobium). The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes like osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-inte
Probab=37.45 E-value=54 Score=23.70 Aligned_cols=33 Identities=21% Similarity=0.274 Sum_probs=25.7
Q ss_pred eEEEeecCcccceeeccccccCHHHHHHHHHHhhc
Q 030803 129 FVKVSMDGAPYLRKVDLKLYKSYQELSDALGKMFS 163 (171)
Q Consensus 129 yVKVsMDG~pigRKVDL~~y~sY~~L~~~Le~MF~ 163 (171)
=|||...|--+ -+-|..--+|++|...+.++|.
T Consensus 2 ~vK~~~~~d~~--r~~l~~~~~~~~L~~~i~~r~~ 34 (82)
T cd06407 2 RVKATYGEEKI--RFRLPPSWGFTELKQEIAKRFK 34 (82)
T ss_pred EEEEEeCCeEE--EEEcCCCCCHHHHHHHHHHHhC
Confidence 38999988733 3444445599999999999997
No 6
>cd06396 PB1_NBR1 The PB1 domain is an essential part of NBR1 protein, next to BRCA1, a scaffold protein mediating specific protein-protein interaction with both titin protein kinase and with another scaffold protein p62. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The NBR1 protein contains a type I PB1 domain.
Probab=35.51 E-value=70 Score=23.55 Aligned_cols=34 Identities=15% Similarity=0.172 Sum_probs=30.3
Q ss_pred EEEeecCcccceeeccccccCHHHHHHHHHHhhc
Q 030803 130 VKVSMDGAPYLRKVDLKLYKSYQELSDALGKMFS 163 (171)
Q Consensus 130 VKVsMDG~pigRKVDL~~y~sY~~L~~~Le~MF~ 163 (171)
|||+..|--+-=+++-...-+|.+|...+.++|+
T Consensus 3 vKaty~~d~~rf~~~~~~~~~~~~L~~ev~~rf~ 36 (81)
T cd06396 3 LKVTYNGESQSFLVSDSENTTWASVEAMVKVSFG 36 (81)
T ss_pred EEEEECCeEEEEEecCCCCCCHHHHHHHHHHHhC
Confidence 8999999877778887778899999999999998
No 7
>cd06402 PB1_p62 The PB1 domain is an essential part of p62 scaffold protein (alias sequestosome 1,SQSTM) involved in cell signaling, receptor internalization, and protein turnover. The PB1 domain is a modular domain mediating specific protein-protein interaction which play roles in many critical cell processes. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants.
Probab=32.19 E-value=78 Score=23.50 Aligned_cols=36 Identities=22% Similarity=0.396 Sum_probs=27.7
Q ss_pred ceEEEeecC---cccceeecc--ccccCHHHHHHHHHHhhc
Q 030803 128 AFVKVSMDG---APYLRKVDL--KLYKSYQELSDALGKMFS 163 (171)
Q Consensus 128 ~yVKVsMDG---~pigRKVDL--~~y~sY~~L~~~Le~MF~ 163 (171)
+.||.+..| .+=.|.+=| ....+|++|...+.++|.
T Consensus 1 ~~vkayl~~~~~~~EIRRf~l~~~~~~s~~~L~~~V~~~f~ 41 (87)
T cd06402 1 LTVKAYLLGKDANAEIRRFAIDEDVSTSYEYLVEKVAAVFP 41 (87)
T ss_pred CeEEEeecCCCCccceEEEEecCCCCcCHHHHHHHHHHHcc
Confidence 468888877 455565544 666799999999999996
No 8
>PF11576 DUF3236: Protein of unknown function (DUF3236); InterPro: IPR012019 This family of proteins with unknown function appears to be restricted to Methanobacteria. ; PDB: 3BRC_B.
Probab=31.85 E-value=17 Score=29.90 Aligned_cols=9 Identities=56% Similarity=1.202 Sum_probs=6.1
Q ss_pred ccCCCCCCC
Q 030803 10 RLGLPGGNG 18 (171)
Q Consensus 10 RLGLPG~~~ 18 (171)
|||.||+++
T Consensus 101 RLGvPGSGS 109 (154)
T PF11576_consen 101 RLGVPGSGS 109 (154)
T ss_dssp E-SSTTS-E
T ss_pred cccCCCCcc
Confidence 999999863
No 9
>PF12426 DUF3674: RNA dependent RNA polymerase; InterPro: IPR024378 This domain is found in the RNA-directed RNA polymerase. It is located towards the N terminus and is approximately 40 amino acids in length. There is a conserved MFNLKF sequence motif. There are two completely conserved residues (E and P) that may be functionally important.
Probab=29.83 E-value=26 Score=23.01 Aligned_cols=14 Identities=50% Similarity=0.835 Sum_probs=10.4
Q ss_pred HHHHHHhhc-ccccc
Q 030803 155 SDALGKMFS-SFTIG 168 (171)
Q Consensus 155 ~~~Le~MF~-~f~ig 168 (171)
..+||.||+ .|-||
T Consensus 7 R~aLEAMFNLKFhi~ 21 (41)
T PF12426_consen 7 RSALEAMFNLKFHIG 21 (41)
T ss_pred HHHHHHHhceeeeeC
Confidence 578999998 45554
No 10
>PRK14763 coenzyme PQQ biosynthesis protein A; Provisional
Probab=24.46 E-value=24 Score=21.08 Aligned_cols=8 Identities=63% Similarity=1.107 Sum_probs=6.6
Q ss_pred ccccccCC
Q 030803 6 ATELRLGL 13 (171)
Q Consensus 6 ~TELRLGL 13 (171)
.||||||+
T Consensus 7 ~~d~R~Gf 14 (26)
T PRK14763 7 ATEMRFGF 14 (26)
T ss_pred eeeeeeee
Confidence 58999986
No 11
>smart00666 PB1 PB1 domain. Phox and Bem1p domain, present in many eukaryotic cytoplasmic signalling proteins. The domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate.
Probab=23.32 E-value=1.6e+02 Score=20.01 Aligned_cols=33 Identities=24% Similarity=0.397 Sum_probs=27.5
Q ss_pred EEEeecCcccceeeccccccCHHHHHHHHHHhhcc
Q 030803 130 VKVSMDGAPYLRKVDLKLYKSYQELSDALGKMFSS 164 (171)
Q Consensus 130 VKVsMDG~pigRKVDL~~y~sY~~L~~~Le~MF~~ 164 (171)
|||.-.| --|-+-+..--+|.+|...+.+.|..
T Consensus 4 vK~~~~~--~~~~~~~~~~~s~~dL~~~i~~~~~~ 36 (81)
T smart00666 4 VKLRYGG--ETRRLSVPRDISFEDLRSKVAKRFGL 36 (81)
T ss_pred EEEEECC--EEEEEEECCCCCHHHHHHHHHHHhCC
Confidence 7888855 46777777788999999999999974
No 12
>cd06403 PB1_Par6 The PB1 domain is an essential part of Par6 protein which in complex with Par3 and aPKC proteins is crucial for establishment of apical-basal polarity of animal cells. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants. The
Probab=20.29 E-value=1.3e+02 Score=22.32 Aligned_cols=32 Identities=19% Similarity=0.376 Sum_probs=22.8
Q ss_pred EEEeecCccccee--eccccccCHHHHHHHHHHhhc
Q 030803 130 VKVSMDGAPYLRK--VDLKLYKSYQELSDALGKMFS 163 (171)
Q Consensus 130 VKVsMDG~pigRK--VDL~~y~sY~~L~~~Le~MF~ 163 (171)
||.+.|.. -|. +|-....+|+++..-|+.||.
T Consensus 3 VKSkfdaE--fRRFsl~r~~~~~f~ef~~ll~~lH~ 36 (80)
T cd06403 3 VKSKFDAE--FRRFSLDRNKPGKFEDFYKLLEHLHH 36 (80)
T ss_pred eecccCCe--EEEEEeccccCcCHHHHHHHHHHHhC
Confidence 56666654 243 444456999999999999995
Done!