Query 039446
Match_columns 146
No_of_seqs 29 out of 31
Neff 2.2
Searched_HMMs 46136
Date Fri Mar 29 09:42:56 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/039446.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/039446hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05553 DUF761: Cotton fibre 99.3 4.4E-13 9.5E-18 85.1 1.6 34 106-140 1-34 (38)
2 TIGR00340 zpr1_rel ZPR1-relate 44.8 21 0.00046 28.3 2.6 39 105-143 114-152 (163)
3 KOG4617 Uncharacterized conser 40.6 22 0.00049 30.8 2.3 90 17-120 108-205 (249)
4 cd08786 CARD_RIP2_CARD3 Caspas 32.7 18 0.00038 27.2 0.4 18 8-25 65-82 (87)
5 PF04967 HTH_10: HTH DNA bindi 31.8 35 0.00076 22.7 1.7 27 13-41 25-51 (53)
6 TIGR00310 ZPR1_znf ZPR1 zinc f 26.3 64 0.0014 26.2 2.6 38 106-143 118-155 (192)
7 PF03367 zf-ZPR1: ZPR1 zinc-fi 22.0 67 0.0015 25.1 1.9 39 106-144 121-159 (161)
8 smart00709 Zpr1 Duplicated dom 21.7 90 0.002 24.6 2.6 38 107-144 121-158 (160)
9 PF11485 DUF3211: Protein of u 21.3 1.1E+02 0.0024 24.1 3.0 21 109-129 111-131 (136)
10 TIGR01827 gatC_rel Asp-tRNA(As 20.3 1.1E+02 0.0023 21.5 2.5 17 110-126 2-18 (73)
No 1
>PF05553 DUF761: Cotton fibre expressed protein; InterPro: IPR008480 This family consists of several plant proteins of unknown function. Three of the sequences from Gossypium hirsutum (Upland cotton) in this family are described as G. hirsutum fibre expressed proteins []. The remaining sequences, found in Arabidopsis thaliana, are uncharacterised.
Probab=99.33 E-value=4.4e-13 Score=85.08 Aligned_cols=34 Identities=56% Similarity=0.830 Sum_probs=30.8
Q ss_pred CCcchhHHHHHHHHHHHHHHhHhhhhccceeeecC
Q 039446 106 GDDDIDRRAEIFITNFRRQLLYERQVSLELRYRRG 140 (146)
Q Consensus 106 ~d~dID~rAe~FIanFr~QlklqRQ~SLqLrY~~~ 140 (146)
++++||++||+||++||+||+||||.|+ .+|+++
T Consensus 1 ~~~evd~rAe~FI~~f~~qlrlqr~~S~-~ry~em 34 (38)
T PF05553_consen 1 SDDEVDRRAEEFIAKFREQLRLQRQESL-QRYQEM 34 (38)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHH
Confidence 3679999999999999999999999999 688764
No 2
>TIGR00340 zpr1_rel ZPR1-related zinc finger protein. A model ZPR1_znf (TIGR00310) has been created to describe the domain shared by this protein and ZPR1.
Probab=44.75 E-value=21 Score=28.29 Aligned_cols=39 Identities=26% Similarity=0.362 Sum_probs=33.6
Q ss_pred CCCcchhHHHHHHHHHHHHHHhHhhhhccceeeecCCCC
Q 039446 105 DGDDDIDRRAEIFITNFRRQLLYERQVSLELRYRRGNSF 143 (146)
Q Consensus 105 ~~d~dID~rAe~FIanFr~QlklqRQ~SLqLrY~~~NSf 143 (146)
+.+++..+++++||++.++-+.-++...|-|.=..||||
T Consensus 114 ~~~~e~~~k~~~~l~kL~~~~~g~~pfTlIldDP~GNS~ 152 (163)
T TIGR00340 114 DEDDEAVKKCEEILKRIREVIEGKFKFTLIIEDPFGNSF 152 (163)
T ss_pred ccCHHHHHHHHHHHHHHHHHHhCCCCeEEEEECCCCCee
Confidence 345567799999999999988888899998888899998
No 3
>KOG4617 consensus Uncharacterized conserved protein [Function unknown]
Probab=40.61 E-value=22 Score=30.79 Aligned_cols=90 Identities=23% Similarity=0.269 Sum_probs=62.0
Q ss_pred hhhhhccccCccc-------hhhHHHHHHHHHHHhhhccccchhhhhhhhhcccccCcccccccCCCCcceeeccCCCCC
Q 039446 17 LNKQMGKHQSRSL-------MQGHLKKAVKKLHMILSRIKLSKWNLASICRAGFSQSRRSLSFNDRLGLQYCIVDRDPDE 89 (146)
Q Consensus 17 ~~~~mg~~~~~~s-------lLg~Lr~AVkKv~flL~sf~~~~W~lasi~~~~ss~s~RrlSFndrpgL~~~i~~~esd~ 89 (146)
+..||-+++-+|+ -||.|--||.++..|- +| +....+-.++- |+ --.||++-|+ |+|.+-
T Consensus 108 ~~~q~~~~~y~w~nC~~~y~~lt~l~~~~~~~~~l~-n~--~~~~~~~~~~~------~~---~a~pg~~~c~-DvE~~m 174 (249)
T KOG4617|consen 108 LQDQMNRTRYNWSNCCQRYVKLTNLLIAVGVVVLLP-NF--TFYITAVVVTK------RR---EANPGLLNCQ-DVELDM 174 (249)
T ss_pred hHHHHHHHHHHHHHHHHHHhhhhHHHHHhhhhhhcc-ch--hhhhhhhheee------ee---ecCCCccccc-chhhcc
Confidence 3347777777773 5788889999998888 44 44444444332 22 4579999999 678888
Q ss_pred CCcchhheeeccccCCCC-cchhHHHHHHHHH
Q 039446 90 GSSVRVLQRTKSCAYDGD-DDIDRRAEIFITN 120 (146)
Q Consensus 90 ~s~~r~~~R~~s~~~~~d-~dID~rAe~FIan 120 (146)
.++....++.-.|+..++ +-|--++ +||++
T Consensus 175 n~T~~Lwt~~~~ct~~~~~d~i~~~~-~~i~~ 205 (249)
T KOG4617|consen 175 NSTSTLWTAAVLCTSTEDPDAISART-EKIAN 205 (249)
T ss_pred chHHHHHHHHHhccCCCCcchhhHHH-HHHHH
Confidence 888888888888776544 4454454 46655
No 4
>cd08786 CARD_RIP2_CARD3 Caspase activation and recruitment domain of Receptor Interacting Protein 2. Caspase activation and recruitment domain (CARD) of Receptor Interacting Protein 2 (RIP2/RIPK2/RICK/CARDIAK/CARD3). RIP kinases serve as essential sensors of cellular stress. Vertebrates contain several types containing a homologous N-terminal kinase domain and varying C-terminal domains. RIP2 harbors a C-terminal CARD domain and functions as an effector kinase downstream of the pattern recognition receptors from the Nod-like (NLR)-family, NOD1 and NOD2, which recognizes bacterial peptidoglycans released upon infection. This cascade is implicated in inflammatory immune responses and the clearance of intracellular pathogens. RIP2 associates with NOD1 and NOD2 via CARD-CARD interactions. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein
Probab=32.66 E-value=18 Score=27.21 Aligned_cols=18 Identities=39% Similarity=0.490 Sum_probs=15.0
Q ss_pred ccchhhhhhhhhhhcccc
Q 039446 8 ASNIITSLHLNKQMGKHQ 25 (146)
Q Consensus 8 ~~~~~~~~~~~~~mg~~~ 25 (146)
+--+||-|+-|||||-+.
T Consensus 65 ~qivV~~l~~nk~~~l~~ 82 (87)
T cd08786 65 ARVVVQKLKDNKQMGLQP 82 (87)
T ss_pred HHHHHHHhhccccCCCCC
Confidence 345789999999999876
No 5
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=31.79 E-value=35 Score=22.68 Aligned_cols=27 Identities=33% Similarity=0.506 Sum_probs=21.6
Q ss_pred hhhhhhhhhccccCccchhhHHHHHHHHH
Q 039446 13 TSLHLNKQMGKHQSRSLMQGHLKKAVKKL 41 (146)
Q Consensus 13 ~~~~~~~~mg~~~~~~slLg~Lr~AVkKv 41 (146)
|.--|.+.+|--+ ..+.-+||+|.+||
T Consensus 25 tl~elA~~lgis~--st~~~~LRrae~kl 51 (53)
T PF04967_consen 25 TLEELAEELGISK--STVSEHLRRAERKL 51 (53)
T ss_pred CHHHHHHHhCCCH--HHHHHHHHHHHHHH
Confidence 3445677888776 78999999999997
No 6
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=26.34 E-value=64 Score=26.21 Aligned_cols=38 Identities=18% Similarity=0.364 Sum_probs=32.5
Q ss_pred CCcchhHHHHHHHHHHHHHHhHhhhhccceeeecCCCC
Q 039446 106 GDDDIDRRAEIFITNFRRQLLYERQVSLELRYRRGNSF 143 (146)
Q Consensus 106 ~d~dID~rAe~FIanFr~QlklqRQ~SLqLrY~~~NSf 143 (146)
.+++..+++++||++.++-+.-++...|-|.=..||||
T Consensus 118 ~~~e~~~k~~~~i~kL~~~~~g~~pfTlIidDP~GNS~ 155 (192)
T TIGR00310 118 EDEETKKRAEEILERLKEAIEGKEKFTVILEDPLGGSY 155 (192)
T ss_pred cCHHHHHHHHHHHHHHHHHHhCCCCEEEEEECCCCCee
Confidence 34556689999999999998888888888888889998
No 7
>PF03367 zf-ZPR1: ZPR1 zinc-finger domain; InterPro: IPR004457 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents ZPR1-type zinc finger domains. An orthologous protein found once in each of the completed archaeal genomes corresponds to a zinc finger-containing domain repeated as the N-terminal and C-terminal halves of the mouse protein ZPR1. ZPR1 is an experimentally proven zinc-binding protein that binds the tyrosine kinase domain of the epidermal growth factor receptor (EGFR); binding is inhibited by EGF stimulation and tyrosine phosphorylation, and activation by EGF is followed by some redistribution of ZPR1 to the nucleus. By analogy, other proteins with the ZPR1 zinc finger domain may be regulatory proteins that sense protein phosphorylation state and/or participate in signal transduction (see also IPR004470 from INTERPRO). Deficiencies in ZPR1 may contribute to neurodegenerative disorders. ZPR1 appears to be down-regulated in patients with spinal muscular atrophy (SMA), a disease characterised by degeneration of the alpha-motor neurons in the spinal cord that can arise from mutations affecting the expression of Survival Motor Neurons (SMN) []. ZPR1 interacts with complexes formed by SMN [], and may act as a modifier that effects the severity of SMA. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2QKD_A.
Probab=21.96 E-value=67 Score=25.12 Aligned_cols=39 Identities=26% Similarity=0.335 Sum_probs=30.2
Q ss_pred CCcchhHHHHHHHHHHHHHHhHhhhhccceeeecCCCCC
Q 039446 106 GDDDIDRRAEIFITNFRRQLLYERQVSLELRYRRGNSFD 144 (146)
Q Consensus 106 ~d~dID~rAe~FIanFr~QlklqRQ~SLqLrY~~~NSf~ 144 (146)
.+++-..++++||++.++-+..++...|-|.=..||||=
T Consensus 121 ~~~e~~~~~~~~i~~L~~~~~g~~pfTlIidDP~GnS~I 159 (161)
T PF03367_consen 121 DDPEEKEKIEEFIEKLDELIEGKRPFTLIIDDPSGNSFI 159 (161)
T ss_dssp H-HHHHHHHHHHHHHHHHHHCTSS-EEEEEEETTS--EE
T ss_pred CCHHHHHHHHHHHHHHHHHHcCCCCEEEEEECCCCccee
Confidence 456677889999999999999899999988888999983
No 8
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=21.74 E-value=90 Score=24.56 Aligned_cols=38 Identities=18% Similarity=0.322 Sum_probs=31.5
Q ss_pred CcchhHHHHHHHHHHHHHHhHhhhhccceeeecCCCCC
Q 039446 107 DDDIDRRAEIFITNFRRQLLYERQVSLELRYRRGNSFD 144 (146)
Q Consensus 107 d~dID~rAe~FIanFr~QlklqRQ~SLqLrY~~~NSf~ 144 (146)
+++-..++++||++.++-+.-++...|-|.=..||||=
T Consensus 121 ~~e~~~k~~~~~~~L~~~~~g~~~fTliidDP~GnS~I 158 (160)
T smart00709 121 DPETKEKIDEFLEKLKELIEGKEPFTLILDDPAGNSYI 158 (160)
T ss_pred CHHHHHHHHHHHHHHHHHHcCCCCEEEEEECCCCceec
Confidence 45566899999999999888888888888878889984
No 9
>PF11485 DUF3211: Protein of unknown function (DUF3211); InterPro: IPR021578 This archaeal family of proteins has no known function. ; PDB: 2EJX_A.
Probab=21.34 E-value=1.1e+02 Score=24.10 Aligned_cols=21 Identities=29% Similarity=0.371 Sum_probs=19.3
Q ss_pred chhHHHHHHHHHHHHHHhHhh
Q 039446 109 DIDRRAEIFITNFRRQLLYER 129 (146)
Q Consensus 109 dID~rAe~FIanFr~QlklqR 129 (146)
-|+++-+.|.++|-+-++|||
T Consensus 111 ~i~~~i~~f~~~ldE~IRlER 131 (136)
T PF11485_consen 111 FISKWIEKFKKNLDEEIRLER 131 (136)
T ss_dssp HHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhhhhHHHHHHh
Confidence 578899999999999999998
No 10
>TIGR01827 gatC_rel Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase, subunit C, putative. This model represents a family small family related to GatC, the third subunit of an enzyme for completing the charging of tRNA(Gln) by amidating the Glu-tRNA(Gln). The few known archaea that contain a member of this family appear to produce Asn-tRNA(Asn) by an analogous amidotransferase reaction. This protein is proposed to substitute for GatC in the charging of both tRNAs.
Probab=20.34 E-value=1.1e+02 Score=21.49 Aligned_cols=17 Identities=29% Similarity=0.411 Sum_probs=15.8
Q ss_pred hhHHHHHHHHHHHHHHh
Q 039446 110 IDRRAEIFITNFRRQLL 126 (146)
Q Consensus 110 ID~rAe~FIanFr~Qlk 126 (146)
|.+.||+-..+|-+||.
T Consensus 2 ~~~~~~~~~~~~~e~L~ 18 (73)
T TIGR01827 2 ILKEAEEILEEFSERLE 18 (73)
T ss_pred hHHHHHHHHHHHHHHHH
Confidence 78999999999999986
Done!