Query 023986
Match_columns 274
No_of_seqs 117 out of 134
Neff 3.0
Searched_HMMs 46136
Date Fri Mar 29 08:06:16 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023986.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023986hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00612 IQ: IQ calmodulin-bin 96.4 0.0027 6E-08 37.7 2.1 20 111-130 1-20 (21)
2 smart00015 IQ Short calmodulin 95.8 0.0077 1.7E-07 37.3 2.2 21 110-130 2-22 (26)
3 PF08763 Ca_chan_IQ: Voltage g 65.3 5.3 0.00011 27.7 2.0 19 112-130 10-28 (35)
4 KOG0377 Protein serine/threoni 53.5 8.3 0.00018 39.9 1.9 22 111-132 17-38 (631)
5 KOG4427 E3 ubiquitin protein l 39.2 17 0.00037 39.8 1.7 24 109-132 28-51 (1096)
6 KOG0942 E3 ubiquitin protein l 38.0 17 0.00036 40.1 1.4 22 109-130 27-48 (1001)
7 PF00727 IL4: Interleukin 4 Th 29.0 59 0.0013 27.7 3.0 27 98-124 30-59 (117)
8 PF10792 DUF2605: Protein of u 26.6 2.8 6E-05 34.8 -5.1 24 246-269 26-49 (98)
9 COG4382 Mu-like prophage prote 24.1 1E+02 0.0022 28.0 3.7 65 146-221 76-140 (170)
10 PF06839 zf-GRF: GRF zinc fing 20.2 45 0.00098 22.9 0.6 10 225-234 35-44 (45)
No 1
>PF00612 IQ: IQ calmodulin-binding motif; InterPro: IPR000048 The IQ motif is an extremely basic unit of about 23 amino acids, whose conserved core usually fits the consensus A-x(3)-I-Q-x(2)-F-R-x(4)-K-K. The IQ motif, which can be present in one or more copies, serves as a binding site for different EF-hand proteins including the essential and regulatory myosin light chains, calmodulin (CaM), and CaM-like proteins [, ].Many IQ motifs are protein kinase C (PKC) phosphorylation sites [, ]. Resolution of the 3D structure of scallop myosin has shown that the IQ motif forms a basic amphipathic helix []. Some proteins known to contain an IQ motif are listed below: A number of conventional and unconventional myosins. Neuromodulin (GAP-43). This protein is associated with nerve growth. It is a major component of the motile "growth cones" that form the tips of elongating axons. Neurogranin (NG/p17). Acts as a "third messenger" substrate of protein kinase C-mediated molecular cascades during synaptic development and remodeling. Sperm surface protein Sp17. Ras GTPase-activating-like protein IQGAP1. IQGAP1 contains 4 IQ motifs. This entry covers the entire IQ motif.; GO: 0005515 protein binding; PDB: 2DFS_A 2IX7_C 1OE9_A 1W7J_A 1W7I_A 1KQM_A 1KK7_A 1WDC_A 1DFL_A 1B7T_A ....
Probab=96.37 E-value=0.0027 Score=37.74 Aligned_cols=20 Identities=25% Similarity=0.451 Sum_probs=17.9
Q ss_pred HHHHHHHHHhhhhhhhhhcc
Q 023986 111 DAAATKLQKVYKSYRTRRNL 130 (274)
Q Consensus 111 ~~AA~~iQKvYRgYRTRR~L 130 (274)
..||++||+.||||..|+++
T Consensus 1 ~~aai~iQ~~~R~~~~Rk~~ 20 (21)
T PF00612_consen 1 RKAAIIIQSYWRGYLARKRY 20 (21)
T ss_dssp HHHHHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHHHhc
Confidence 37999999999999999874
No 2
>smart00015 IQ Short calmodulin-binding motif containing conserved Ile and Gln residues. Calmodulin-binding motif.
Probab=95.79 E-value=0.0077 Score=37.27 Aligned_cols=21 Identities=29% Similarity=0.506 Sum_probs=19.3
Q ss_pred HHHHHHHHHHhhhhhhhhhcc
Q 023986 110 LDAAATKLQKVYKSYRTRRNL 130 (274)
Q Consensus 110 ~~~AA~~iQKvYRgYRTRR~L 130 (274)
...||++||..||||..|+..
T Consensus 2 ~~~aa~~IQa~~Rg~~~r~~y 22 (26)
T smart00015 2 LTRAAIIIQAAWRGYLARKRY 22 (26)
T ss_pred HHHHHHHHHHHHHHHHHHHhh
Confidence 568999999999999999986
No 3
>PF08763 Ca_chan_IQ: Voltage gated calcium channel IQ domain; InterPro: IPR014873 Ca2+ ions are unique in that they not only carry charge but they are also the most widely used of diffusible second messengers. Voltage-dependent Ca2+ channels (VDCC) are a family of molecules that allow cells to couple electrical activity to intracellular Ca2+ signalling. The opening and closing of these channels by depolarizing stimuli, such as action potentials, allows Ca2+ ions to enter neurons down a steep electrochemical gradient, producing transient intracellular Ca2+ signals. Many of the processes that occur in neurons, including transmitter release, gene transcription and metabolism are controlled by Ca2+ influx occurring simultaneously at different cellular locales. The pore is formed by the alpha-1 subunit which incorporates the conduction pore, the voltage sensor and gating apparatus, and the known sites of channel regulation by second messengers, drugs, and toxins []. The activity of this pore is modulated by 4 tightly-coupled subunits: an intracellular beta subunit; a transmembrane gamma subunit; and a disulphide-linked complex of alpha-2 and delta subunits, which are proteolytically cleaved from the same gene product. Properties of the protein including gating voltage-dependence, G protein modulation and kinase susceptibility can be influenced by these subunits. Voltage-gated calcium channels are classified as T, L, N, P, Q and R, and are distinguished by their sensitivity to pharmacological blocks, single-channel conductance kinetics, and voltage-dependence. On the basis of their voltage activation properties, the voltage-gated calcium classes can be further divided into two broad groups: the low (T-type) and high (L, N, P, Q and R-type) threshold-activated channels. The voltage-gated calcium channel alpha 1 subunit contains an IQ domain, named for its isoleucine-glutamine (IQ) motif, which interacts with hydrophobic pockets of Ca2+/calmodulin []. The interaction regulates two self-regulatory calcium dependent feedback mechanisms, calcium dependent inactivation (CDI), and calcium-dependent facilitation (CDF). ; PDB: 3OXQ_F 2F3Z_B 3G43_E 2F3Y_B 2BE6_D 3DVM_B 3BXK_D 2VAY_B 3DVK_B 3BXL_B ....
Probab=65.30 E-value=5.3 Score=27.73 Aligned_cols=19 Identities=16% Similarity=0.438 Sum_probs=17.0
Q ss_pred HHHHHHHHhhhhhhhhhcc
Q 023986 112 AAATKLQKVYKSYRTRRNL 130 (274)
Q Consensus 112 ~AA~~iQKvYRgYRTRR~L 130 (274)
=||..||..||.++.||+-
T Consensus 10 YAt~lI~dyfr~~K~rk~~ 28 (35)
T PF08763_consen 10 YATLLIQDYFRQFKKRKEQ 28 (35)
T ss_dssp HHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 4899999999999999864
No 4
>KOG0377 consensus Protein serine/threonine phosphatase RDGC/PPEF, contains STphosphatase and EF-hand domains [Signal transduction mechanisms]
Probab=53.53 E-value=8.3 Score=39.94 Aligned_cols=22 Identities=32% Similarity=0.371 Sum_probs=19.2
Q ss_pred HHHHHHHHHhhhhhhhhhccCC
Q 023986 111 DAAATKLQKVYKSYRTRRNLAD 132 (274)
Q Consensus 111 ~~AA~~iQKvYRgYRTRR~Lad 132 (274)
-+||..|||-||+|..|+++.-
T Consensus 17 ikaAilIQkWYRr~~ARle~rr 38 (631)
T KOG0377|consen 17 IKAAILIQKWYRRYEARLEARR 38 (631)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 4799999999999999987753
No 5
>KOG4427 consensus E3 ubiquitin protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=39.18 E-value=17 Score=39.84 Aligned_cols=24 Identities=33% Similarity=0.398 Sum_probs=21.1
Q ss_pred hHHHHHHHHHHhhhhhhhhhccCC
Q 023986 109 ELDAAATKLQKVYKSYRTRRNLAD 132 (274)
Q Consensus 109 e~~~AA~~iQKvYRgYRTRR~Lad 132 (274)
..++||..||++.|||=+|+.+++
T Consensus 28 rr~~aa~~iq~~lrsyl~Rkk~~~ 51 (1096)
T KOG4427|consen 28 RREAAALFIQRVLRSYLVRKKAQI 51 (1096)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 367899999999999999988764
No 6
>KOG0942 consensus E3 ubiquitin protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=37.96 E-value=17 Score=40.14 Aligned_cols=22 Identities=27% Similarity=0.552 Sum_probs=19.3
Q ss_pred hHHHHHHHHHHhhhhhhhhhcc
Q 023986 109 ELDAAATKLQKVYKSYRTRRNL 130 (274)
Q Consensus 109 e~~~AA~~iQKvYRgYRTRR~L 130 (274)
.++.+|++||+-.||||.|++-
T Consensus 27 k~e~~av~vQs~~Rg~~~r~~~ 48 (1001)
T KOG0942|consen 27 KQEKNAVKVQSFWRGFRVRHNQ 48 (1001)
T ss_pred HHhccchHHHHHHHHHHHHHHH
Confidence 4678999999999999999764
No 7
>PF00727 IL4: Interleukin 4 This family is a subset of the SCOP family; InterPro: IPR002354 Cytokines are protein messengers that carry information from cell to cell []. Interleukin is one such molecule, and participates in several B-cell activation processes: e.g., it enhances production and secretion of IgG1 and IgE []; it induces expression of class II major histocompatability complex (MHC) molecules on resting B-cells; and it regulates expression of the low affinity Fc receptor for IgE on lymphocytes and monocytes. Interleukin-4 (IL4) has a compact, globular fold (similar to other cytokines), stabilised by 3 disulphide bonds []. One half of the structure is dominated by a 4 alpha-helix bundle with a left-handed twist []. The helices are anti-parallel, with 2 overhand connections, which fall into a 2-stranded anti-parallel beta-sheet [].; GO: 0005136 interleukin-4 receptor binding, 0008083 growth factor activity, 0006955 immune response, 0005576 extracellular region; PDB: 1HIK_A 1HZI_A 1ITI_A 2INT_A 1RCB_A 1CYL_A 3QB7_A 1BBN_A 2B8Z_A 1ITM_A ....
Probab=29.05 E-value=59 Score=27.73 Aligned_cols=27 Identities=33% Similarity=0.504 Sum_probs=22.3
Q ss_pred CccccCCCCCchHH---HHHHHHHHhhhhh
Q 023986 98 PVVFHSPRPVSELD---AAATKLQKVYKSY 124 (274)
Q Consensus 98 ~~~~~sp~~~~e~~---~AA~~iQKvYRgY 124 (274)
|.+|..|+..+|.+ +||+.+|.+|..+
T Consensus 30 ~Dvfa~~KnttekEllCrAatvLr~~y~~h 59 (117)
T PF00727_consen 30 ADVFAAPKNTTEKELLCRAATVLRQFYSHH 59 (117)
T ss_dssp E-GGGSSSSSSHHHHHHHHHHHHHHHHHHH
T ss_pred hHHhccCCCCCcchhhhHHHHHHHHHHhcc
Confidence 46899998888876 8999999999865
No 8
>PF10792 DUF2605: Protein of unknown function (DUF2605); InterPro: IPR019728 This entry represents a protein conserved in Cyanobacteria. The function is not known.
Probab=26.65 E-value=2.8 Score=34.76 Aligned_cols=24 Identities=21% Similarity=0.347 Sum_probs=20.2
Q ss_pred ChHHHhhhhhhccCcccccCeEEE
Q 023986 246 PRNVLQRQCIKYLGPVSFAPMHLI 269 (274)
Q Consensus 246 PR~kLe~e~I~YL~peER~~Yev~ 269 (274)
.|+-|+.+.|.+|+++|++.-+..
T Consensus 26 s~~LLe~e~~~fls~~eQ~~Ll~R 49 (98)
T PF10792_consen 26 SRELLETEPISFLSPEEQSDLLER 49 (98)
T ss_pred HHHHHhcCCcccCCHHHHHHHHHH
Confidence 688999999999999998865443
No 9
>COG4382 Mu-like prophage protein gp16 [Function unknown]
Probab=24.12 E-value=1e+02 Score=27.98 Aligned_cols=65 Identities=22% Similarity=0.075 Sum_probs=46.5
Q ss_pred HHhhhcCCCCCcCCCCCchhHHHHHHHHHHHHHHhcCCCChhHHHhHHHHHHHHHhcCCCccccccHHHHHHHhhc
Q 023986 146 DFAALKRSSVSFFNIEKPETALSRWARARTRAAKVGKGLSKDENAQKLALQHWLEAIDPRHRYGHNLHFYYDIWSD 221 (274)
Q Consensus 146 d~A~l~r~siSff~~~k~etA~srW~Ra~t~AakvGkGlskd~kAqkl~lq~WLE~IDprHRYG~NL~~Yy~~W~~ 221 (274)
..|-++...-..|..+.++||.++|.+-.+.++..+-|+..-. |++. |++ ++|..|--|++.|..
T Consensus 76 iRa~wkqm~k~Gf~~dp~~talns~~~~~~~e~~~~vg~~~wq---------~~~~-~a~-~f~kdlve~lkr~~l 140 (170)
T COG4382 76 IRAGWKQMAKGGFHGDPHLTALNSAAMLDKVEALLTVGGKHWQ---------YAHA-MAR-MFGKDLVEYLKRTQL 140 (170)
T ss_pred HHhhhhhhccCCCCCChHHHHHHHHHHHHHHHHHhhhhhhhHH---------HHHh-hHH-HHHHHHHHHhhHHHH
Confidence 3455666666788888999999999999999998887763221 2222 344 777777777777764
No 10
>PF06839 zf-GRF: GRF zinc finger; InterPro: IPR010666 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 presumed zinc-binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to IPR000380 from INTERPRO. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=20.18 E-value=45 Score=22.94 Aligned_cols=10 Identities=40% Similarity=0.737 Sum_probs=7.5
Q ss_pred CCCCceeeec
Q 023986 225 TQPFFYWLDV 234 (274)
Q Consensus 225 ~q~FFyWLD~ 234 (274)
+=+||.|.|.
T Consensus 35 ~C~fF~W~De 44 (45)
T PF06839_consen 35 GCNFFQWEDE 44 (45)
T ss_pred CcCCEEeccC
Confidence 3479999884
Done!