Query 041172
Match_columns 141
No_of_seqs 53 out of 55
Neff 2.8
Searched_HMMs 46136
Date Fri Mar 29 04:26:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041172.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041172hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05678 VQ: VQ motif; InterP 99.3 1.2E-12 2.7E-17 79.5 3.3 30 29-58 1-30 (31)
2 PF06252 DUF1018: Protein of u 57.1 7.3 0.00016 28.4 1.7 19 39-57 2-20 (119)
3 cd04751 Commd3 COMM_Domain con 42.5 27 0.00059 25.0 2.7 18 33-50 66-83 (95)
4 cd04750 Commd2 COMM_Domain con 35.5 37 0.0008 26.5 2.6 19 33-51 138-156 (166)
5 cd06407 PB1_NLP A PB1 domain i 33.9 35 0.00075 24.1 2.0 32 24-55 2-34 (82)
6 KOG0952 DNA/RNA helicase MER3/ 33.1 33 0.00072 35.4 2.5 15 20-35 160-174 (1230)
7 PF07541 EIF_2_alpha: Eukaryot 29.5 47 0.001 24.5 2.2 19 20-38 90-108 (114)
8 PF00567 TUDOR: Tudor domain; 27.5 1.3E+02 0.0028 19.7 3.9 32 22-53 5-40 (121)
9 PF14178 YppF: YppF-like prote 21.0 70 0.0015 22.3 1.7 21 37-57 36-56 (60)
10 PF03103 DUF243: Domain of unk 20.8 75 0.0016 23.7 1.9 23 13-35 21-43 (97)
No 1
>PF05678 VQ: VQ motif; InterPro: IPR008889 This short motif is found in a variety of plant proteins. These proteins vary greatly in length and are mostly composed of low complexity regions. They all conserve a short motif FXhVQChTG, where X is any amino acid and h is a hydrophobic amino acid. The function of this motif is uncertain, however one protein in this family has been found to bind the SigA sigma factor Q9LDH1 from SWISSPROT. It would seem plausible that this motif is needed for this activity and that this whole family might be involved in modulating plastid sigma factors.
Probab=99.32 E-value=1.2e-12 Score=79.53 Aligned_cols=30 Identities=50% Similarity=0.627 Sum_probs=27.6
Q ss_pred EecCceEEeechhhHHHHHHHHhCCCCCcc
Q 041172 29 YISSPVKFETCASKFRALVQELTGKDSDAD 58 (141)
Q Consensus 29 yI~np~~VkT~As~FRalVQeLTGkds~~~ 58 (141)
|+.+|++|+||+++||+|||+|||+++.++
T Consensus 1 ~~~~p~vi~~d~~~Fr~lVQ~LTG~~~~~~ 30 (31)
T PF05678_consen 1 YRSPPTVIHTDPSNFRALVQRLTGAPSAPA 30 (31)
T ss_pred CCCCCEEEEeCHHHHHHHHHHhHCcCCCCC
Confidence 577999999999999999999999999763
No 2
>PF06252 DUF1018: Protein of unknown function (DUF1018); InterPro: IPR009363 This family consists of several bacterial and phage proteins, related to Gp16 of phage Mu, of unknown function.
Probab=57.08 E-value=7.3 Score=28.37 Aligned_cols=19 Identities=42% Similarity=0.616 Sum_probs=16.7
Q ss_pred chhhHHHHHHHHhCCCCCc
Q 041172 39 CASKFRALVQELTGKDSDA 57 (141)
Q Consensus 39 ~As~FRalVQeLTGkds~~ 57 (141)
|...+|++++++||++|..
T Consensus 2 ddd~YR~~L~~~~Gk~S~k 20 (119)
T PF06252_consen 2 DDDTYRALLQRVTGKSSSK 20 (119)
T ss_pred CHHHHHHHHHHHhChhhHH
Confidence 4578999999999999965
No 3
>cd04751 Commd3 COMM_Domain containing protein 3. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=42.46 E-value=27 Score=24.98 Aligned_cols=18 Identities=22% Similarity=0.484 Sum_probs=15.9
Q ss_pred ceEEeechhhHHHHHHHH
Q 041172 33 PVKFETCASKFRALVQEL 50 (141)
Q Consensus 33 p~~VkT~As~FRalVQeL 50 (141)
+.-+.+|+++|+.||++|
T Consensus 66 ~i~f~c~~e~L~~Li~~L 83 (95)
T cd04751 66 DINFTCTLEQLQDLVNKL 83 (95)
T ss_pred eEEEEeCHHHHHHHHHHH
Confidence 556779999999999998
No 4
>cd04750 Commd2 COMM_Domain containing protein 2. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=35.52 E-value=37 Score=26.51 Aligned_cols=19 Identities=21% Similarity=0.193 Sum_probs=17.4
Q ss_pred ceEEeechhhHHHHHHHHh
Q 041172 33 PVKFETCASKFRALVQELT 51 (141)
Q Consensus 33 p~~VkT~As~FRalVQeLT 51 (141)
+..++||+++||-|.|||-
T Consensus 138 ~~~l~td~~~l~~l~~eLe 156 (166)
T cd04750 138 THLLQTDPANLVHLTQTLE 156 (166)
T ss_pred ceEEEeCHHHHHHHHHHHH
Confidence 6788999999999999995
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=33.87 E-value=35 Score=24.07 Aligned_cols=32 Identities=25% Similarity=0.324 Sum_probs=23.7
Q ss_pred ccEEEEecCceEEeec-hhhHHHHHHHHhCCCC
Q 041172 24 DVKVVYISSPVKFETC-ASKFRALVQELTGKDS 55 (141)
Q Consensus 24 ~iKVvyI~np~~VkT~-As~FRalVQeLTGkds 55 (141)
.||++|-..-.+++-. ..+|+.|.+++..+=.
T Consensus 2 ~vK~~~~~d~~r~~l~~~~~~~~L~~~i~~r~~ 34 (82)
T cd06407 2 RVKATYGEEKIRFRLPPSWGFTELKQEIAKRFK 34 (82)
T ss_pred EEEEEeCCeEEEEEcCCCCCHHHHHHHHHHHhC
Confidence 4899998877777744 4489999988876543
No 6
>KOG0952 consensus DNA/RNA helicase MER3/SLH1, DEAD-box superfamily [RNA processing and modification]
Probab=33.09 E-value=33 Score=35.40 Aligned_cols=15 Identities=53% Similarity=0.924 Sum_probs=12.3
Q ss_pred CCCCccEEEEecCceE
Q 041172 20 RCKKDVKVVYISSPVK 35 (141)
Q Consensus 20 ~~k~~iKVvyI~np~~ 35 (141)
-.|...||||| .||+
T Consensus 160 i~k~~fKiVYI-aPmK 174 (1230)
T KOG0952|consen 160 IAKDDFKIVYI-APMK 174 (1230)
T ss_pred cccCCceEEEE-echH
Confidence 46789999999 5975
No 7
>PF07541 EIF_2_alpha: Eukaryotic translation initiation factor 2 alpha subunit; InterPro: IPR011488 In Eukaryota and Archaea, translation initiation factor 2 (eIF2/aIF2), which contains three subunits (alpha, beta and gamma), is pivotal for binding of charged initiator tRNA to the small ribosomal subunit. This entry represents the alpha subunit of both eukaryota and archaeal translation initiator factor 2.; GO: 0003723 RNA binding, 0003743 translation initiation factor activity, 0005850 eukaryotic translation initiation factor 2 complex; PDB: 2QN6_B 3CW2_C 2AHO_B 3QSY_B 3V11_B 2QMU_B 1YZ7_A 1YZ6_A 3AEV_A 1KL9_A ....
Probab=29.46 E-value=47 Score=24.51 Aligned_cols=19 Identities=26% Similarity=0.151 Sum_probs=15.6
Q ss_pred CCCCccEEEEecCceEEee
Q 041172 20 RCKKDVKVVYISSPVKFET 38 (141)
Q Consensus 20 ~~k~~iKVvyI~np~~VkT 38 (141)
...-+|+|.||+.|.|+-|
T Consensus 90 ~~~~~v~I~~igaP~Y~i~ 108 (114)
T PF07541_consen 90 TEDVPVKIKLIGAPRYRIT 108 (114)
T ss_dssp CTTCCEEEEEECTTEEEEE
T ss_pred CCCCeEEEEEECCCeEEEE
Confidence 3556899999999999764
No 8
>PF00567 TUDOR: Tudor domain; InterPro: IPR008191 There are multiple copies of this domain in the Drosophila melanogaster tudor protein and it has been identified in several RNA-binding proteins []. Although the function of this domain is unknown, in Drosophila melanogaster the tudor protein is required during oogenesis for the formation of primordial germ cells and for normal abdominal segmentation [].; PDB: 3NTI_A 3NTK_B 3NTH_A 2DIQ_A 3FDR_A 3PNW_O 3S6W_A 3PMT_A 2WAC_A 2O4X_A ....
Probab=27.46 E-value=1.3e+02 Score=19.71 Aligned_cols=32 Identities=22% Similarity=0.336 Sum_probs=24.8
Q ss_pred CCccEEEEecCceEEee----chhhHHHHHHHHhCC
Q 041172 22 KKDVKVVYISSPVKFET----CASKFRALVQELTGK 53 (141)
Q Consensus 22 k~~iKVvyI~np~~VkT----~As~FRalVQeLTGk 53 (141)
.-.++|++|.+|..+-. ....+..|.++|...
T Consensus 5 ~~~v~It~v~~~~~~~v~~~~~~~~~~~l~~~l~~~ 40 (121)
T PF00567_consen 5 TFEVYITHVDSPGEFYVQPDSADKAYEKLQEELQDY 40 (121)
T ss_dssp EEEEEEEEECTTSEEEEEECCCHHHHHHHHHHHHHH
T ss_pred EEEEEEEEEecCCEEEEEEcCCHHHHHHHHHHHHHH
Confidence 45789999999976653 578889998888643
No 9
>PF14178 YppF: YppF-like protein
Probab=20.99 E-value=70 Score=22.34 Aligned_cols=21 Identities=29% Similarity=0.493 Sum_probs=16.5
Q ss_pred eechhhHHHHHHHHhCCCCCc
Q 041172 37 ETCASKFRALVQELTGKDSDA 57 (141)
Q Consensus 37 kT~As~FRalVQeLTGkds~~ 57 (141)
+.+..+||.||+||--+-+..
T Consensus 36 ei~i~eYR~lvreLE~~GA~~ 56 (60)
T PF14178_consen 36 EISINEYRNLVRELEANGAVS 56 (60)
T ss_pred cccHHHHHHHHHHHHHhCCCC
Confidence 357899999999997665554
No 10
>PF03103 DUF243: Domain of unknown function (DUF243); InterPro: IPR004145 This domain is only found in fly proteins. It is found associated with YLP motifs (IPR004019 from INTERPRO) in some proteins.
Probab=20.84 E-value=75 Score=23.73 Aligned_cols=23 Identities=22% Similarity=0.345 Sum_probs=18.3
Q ss_pred cccccccCCCCccEEEEecCceE
Q 041172 13 KHNNYYKRCKKDVKVVYISSPVK 35 (141)
Q Consensus 13 ~~~~~~k~~k~~iKVvyI~np~~ 35 (141)
..+...+..++..|||+|-.|.-
T Consensus 21 ~~~~~~~~~~K~yrVvFIKaP~~ 43 (97)
T PF03103_consen 21 AAHQLAGPPQKHYRVVFIKAPEN 43 (97)
T ss_pred chhhhcccCCCCcEEEEEECCCC
Confidence 34556778899999999998854
Done!