Query 003233
Match_columns 837
No_of_seqs 12 out of 14
Neff 1.8
Searched_HMMs 46136
Date Thu Mar 28 19:35:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/003233.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/003233hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF10470 AKAP7_RIRII_bdg: PKA- 19.4 91 0.002 27.4 2.3 41 120-171 2-45 (61)
2 PF13007 LZ_Tnp_IS66: Transpos 7.9 2.2E+02 0.0049 23.5 1.4 21 812-832 2-22 (78)
3 PF10446 DUF2457: Protein of u 7.3 1.7E+02 0.0037 33.6 0.5 34 710-748 20-53 (458)
4 PF03533 SPO11_like: SPO11 hom 5.4 3.6E+02 0.0079 22.6 1.3 23 710-732 3-25 (43)
5 PF12537 DUF3735: Protein of u 4.9 2E+02 0.0043 24.7 -0.6 8 804-811 22-29 (72)
6 cd04757 Commd9 COMM_Domain con 4.6 3.7E+02 0.008 25.6 1.0 32 779-820 75-106 (108)
7 PF07440 Caerin_1: Caerin 1 pr 4.3 2.2E+02 0.0049 21.3 -0.5 21 804-824 1-21 (24)
8 PTZ00227 variable surface prot 3.7 4.7E+02 0.01 29.8 1.1 20 807-826 348-367 (418)
9 PF02075 RuvC: Crossover junct 3.1 5.5E+02 0.012 24.4 0.7 17 816-832 101-117 (149)
10 PF00633 HHH: Helix-hairpin-he 2.7 6.4E+02 0.014 18.9 0.6 13 806-818 16-28 (30)
No 1
>PF10470 AKAP7_RIRII_bdg: PKA-RI-RII subunit binding domain of A-kinase anchor protein; InterPro: IPR019511 This entry represents the RI-RII subunit-binding domain found at the C-terminal of the cyclic AMP-dependent protein kinase A (PKA) anchor protein, AKAP7. This protein anchors PKA, for its role in regulating PKA-mediated gene transcription in both somatic cells and oocytes, by binding to its regulatory subunits, RI and RII, hence being known as a dual-specific AKAP []. The 25 crucial amino acids of RII-binding domains in general form structurally conserved amphipathic helices with unrelated sequences; hydrophobic amino acid residues form the backbone of the interaction and hydrogen bond- and salt-bridge-forming amino acid residues increase the affinity of the interaction []. The nuclear localisation signal-containing domain is found at the N terminus.
Probab=19.39 E-value=91 Score=27.42 Aligned_cols=41 Identities=37% Similarity=0.454 Sum_probs=33.5
Q ss_pred CCCcHHHHHhhhhcccCCchhhhhhhhccccchhhhhhhHHhh---hcCcccccc
Q 003233 120 GDNDDAERQRATLENTGSDEAEETKIVSNAVDETKDQVSKETA---ENGASSTVE 171 (837)
Q Consensus 120 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~ 171 (837)
+..|||+-+|+. ..||-|||-..-.|++.||- .+|.+|+|-
T Consensus 2 ~epDdaeL~~lS-----------KrlVenAVlkAvQQy~eEtq~k~~~~~gs~~k 45 (61)
T PF10470_consen 2 SEPDDAELVRLS-----------KRLVENAVLKAVQQYLEETQNKEQPGDGSPVK 45 (61)
T ss_pred CChhHHHHHHHH-----------HHHHHHHHHHHHHHHHHHHHhhccCCCCCCcc
Confidence 456788888764 57999999999999999998 788887764
No 2
>PF13007 LZ_Tnp_IS66: Transposase C of IS166 homeodomain; InterPro: IPR024463 This entry represents a leucine-zipper-like, or homeodomain-like, region of the transposase TnpC from insertion element IS66 [].
Probab=7.93 E-value=2.2e+02 Score=23.53 Aligned_cols=21 Identities=19% Similarity=0.419 Sum_probs=18.0
Q ss_pred hhhhhHHhhhhhhcCCCCCCC
Q 003233 812 KVKHSISKVKKAITGKSSHPK 832 (837)
Q Consensus 812 KVKhsiaKVKKai~GK~~h~K 832 (837)
.++++|+.+++.+.|++|=..
T Consensus 2 ~L~~~l~~l~r~~FG~kSEk~ 22 (78)
T PF13007_consen 2 QLKEQLALLKRQLFGRKSEKL 22 (78)
T ss_pred hHHHHHHHHHHHHhccccccc
Confidence 468999999999999998653
No 3
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=7.33 E-value=1.7e+02 Score=33.60 Aligned_cols=34 Identities=24% Similarity=0.355 Sum_probs=26.6
Q ss_pred ccccccccccchhhhhhHhHhhhhhhhcCCCCcCCcchh
Q 003233 710 LMDSATASLTDPLQSSRIETTKVAEQVGEGGEPKGRTEE 748 (837)
Q Consensus 710 ~~~sa~~SL~D~mQ~S~rEt~~~a~~~ge~~e~~~~tE~ 748 (837)
+.+..++.|.|.|.. | .+-+.||++-++++..|+
T Consensus 20 ~~~~~KlTi~DtlkK---E--~~IRkLgeEaEEEA~~EE 53 (458)
T PF10446_consen 20 TDYKRKLTINDTLKK---E--NAIRKLGEEAEEEAEEEE 53 (458)
T ss_pred ccccccccHHHHHHH---H--HHHhhhhHHHHHHHhhcc
Confidence 556788999999864 3 345889999999888886
No 4
>PF03533 SPO11_like: SPO11 homologue; InterPro: IPR004084 Spo11 is a meiosis-specific protein in yeast that covalently binds to DNA double-strand breaks (DSBs) during the early stages of meiosis []. These DSBs initiate homologous recombination, which is required for chromosomal segregation and generation of genetic diversity during meiosis. Mouse and human homologues of Spo11 have been cloned and characterised. The proteins are 82% identical and share ~25% identity with other family members. Mouse Spo11 has been localised to chromosome 2H4, and human SPO11 to chromosome 20q13.2-q13.3, a region amplified in some breast and ovarian tumours []. Similarity between SPO11 and archaebacterial TOP6A proteins points to evolutionary specialisation of a DNA-cleavage function for meiotic recombination []. Note that the yeast SPO11 protein shares far less similarity to other SPO11 proteins than the human and mouse homologues do to each other.; GO: 0003677 DNA binding, 0007131 reciprocal meiotic recombination
Probab=5.44 E-value=3.6e+02 Score=22.58 Aligned_cols=23 Identities=17% Similarity=0.075 Sum_probs=18.4
Q ss_pred ccccccccccchhhhhhHhHhhh
Q 003233 710 LMDSATASLTDPLQSSRIETTKV 732 (837)
Q Consensus 710 ~~~sa~~SL~D~mQ~S~rEt~~~ 732 (837)
.+|++.+|+|+.|-|-+---+++
T Consensus 3 APmGPeASFf~vLdrHRasLlaa 25 (43)
T PF03533_consen 3 APMGPEASFFEVLDRHRASLLAA 25 (43)
T ss_pred CCCCcchHHHHHHHHHHHHHHHH
Confidence 58999999999999876554444
No 5
>PF12537 DUF3735: Protein of unknown function (DUF3735); InterPro: IPR022535 This conserved domain is found in a subunit of a voltage dependent anion channel required for acidification and functions of the Golgi apparatus; it may function in counter-ion conductance. It belongs to the Golgi pH regulator (1.A.38 from TC) family
Probab=4.88 E-value=2e+02 Score=24.74 Aligned_cols=8 Identities=63% Similarity=1.012 Sum_probs=6.5
Q ss_pred cccccccc
Q 003233 804 NILSGVGS 811 (837)
Q Consensus 804 niLSGVGS 811 (837)
.||||+|+
T Consensus 22 AiLSG~ga 29 (72)
T PF12537_consen 22 AILSGFGA 29 (72)
T ss_pred HHHhhhhH
Confidence 57899886
No 6
>cd04757 Commd9 COMM_Domain containing protein 9. 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=4.62 E-value=3.7e+02 Score=25.64 Aligned_cols=32 Identities=22% Similarity=0.575 Sum_probs=25.7
Q ss_pred CCCCceeeecccchhhhhhhccccccccccccchhhhhHHhh
Q 003233 779 SSDAPVTIEAKRDAVDVKVAHKKSHNILSGVGSKVKHSISKV 820 (837)
Q Consensus 779 ~~da~v~vea~rd~v~~k~~~kKshniLSGVGSKVKhsiaKV 820 (837)
.+-.+|.+|-+++++ +++|+|.| |++.||++|
T Consensus 75 ~~~~~v~~ELsKe~l---------~tml~~L~-~i~~QL~~v 106 (108)
T cd04757 75 PPLSTLTMELSKETL---------DTMLDGLG-RIRDQLSAV 106 (108)
T ss_pred CCcceEEEEcCHHHH---------HHHHHHHH-HHHHHHHHH
Confidence 445689999988884 57889998 789999887
No 7
>PF07440 Caerin_1: Caerin 1 protein; InterPro: IPR010000 This family consists of several caerin 1 proteins from Litoria species, Australian tree frogs. The caerin 1 peptides are among the most powerful of the broad-spectrum antibiotic amphibian peptides []. These peptides are excreted from amphibian skin, and can interact with and disrupt bacterial membranes, leading to the permeabilisation of the cell membrane. Caerin 1.1 forms a helix-bend-helix sturcture, where both helices are required for activity, as well as the bend region for flexibility.; GO: 0005576 extracellular region
Probab=4.28 E-value=2.2e+02 Score=21.34 Aligned_cols=21 Identities=33% Similarity=0.482 Sum_probs=16.6
Q ss_pred cccccccchhhhhHHhhhhhh
Q 003233 804 NILSGVGSKVKHSISKVKKAI 824 (837)
Q Consensus 804 niLSGVGSKVKhsiaKVKKai 824 (837)
|+||-+||-.||-|-.|--.|
T Consensus 1 gl~~vlgsvakhvlphvvpvi 21 (24)
T PF07440_consen 1 GLFSVLGSVAKHVLPHVVPVI 21 (24)
T ss_pred ChHHHHHHHHHHhccccchhh
Confidence 578889999999887776555
No 8
>PTZ00227 variable surface protein Vir14; Provisional
Probab=3.74 E-value=4.7e+02 Score=29.78 Aligned_cols=20 Identities=35% Similarity=0.536 Sum_probs=17.4
Q ss_pred ccccchhhhhHHhhhhhhcC
Q 003233 807 SGVGSKVKHSISKVKKAITG 826 (837)
Q Consensus 807 SGVGSKVKhsiaKVKKai~G 826 (837)
+-|||-.||.++|+||-|-+
T Consensus 348 t~~~~~~~~~~~~~~~~~~~ 367 (418)
T PTZ00227 348 TPLGKSFKHTRAKVRKRIRP 367 (418)
T ss_pred CccchhhHHhHHHHhhhCCC
Confidence 56899999999999998843
No 9
>PF02075 RuvC: Crossover junction endodeoxyribonuclease RuvC; InterPro: IPR002176 The Escherichia coli ruvC gene is involved in DNA repair and in the late step of RecE and RecF pathway recombination []. RuvC protein (3.1.22.4 from EC) cleaves cruciform junctions, which are formed by the extrusion of inverted repeat sequences from a super-coiled plasmid and which are structurally analogous to Holliday junctions, by introducing nicks into strands with the same polarity. The nicks leave a 5'terminal phosphate and a 3'terminal hydroxyl group which are ligated by E. coli or Bacteriophage T4 DNA ligases. Analysis of the cleavage sites suggests that DNA topology rather than a particular sequence determines the cleavage site. RuvC protein also cleaves Holliday junctions that are formed between gapped circular and linear duplex DNA by the function of RecA protein. The active form of RuvC protein is a dimer. This is mechanistically suited for an endonuclease involved in swapping DNA strands at the crossover junctions. It is inferred that RuvC protein is an endonuclease that resolves Holliday structures in vivo []. RucC is a small protein of about 20 kD. It requires and binds a magnesium ion. The structure of E. coli ruvC is a 3-layer alpha-beta sandwich containing a 5-stranded beta-sheet sandwiched between 5 alpha-helices [].; GO: 0004520 endodeoxyribonuclease activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 1HJR_A.
Probab=3.07 E-value=5.5e+02 Score=24.41 Aligned_cols=17 Identities=47% Similarity=0.599 Sum_probs=11.5
Q ss_pred hHHhhhhhhcCCCCCCC
Q 003233 816 SISKVKKAITGKSSHPK 832 (837)
Q Consensus 816 siaKVKKai~GK~~h~K 832 (837)
+=..|||+|||+....|
T Consensus 101 ~P~~vKk~vtG~G~A~K 117 (149)
T PF02075_consen 101 TPSEVKKAVTGNGRASK 117 (149)
T ss_dssp EHHHHHHHHTSSTT--H
T ss_pred CHHHHHHHhhCCCccCH
Confidence 44679999999876544
No 10
>PF00633 HHH: Helix-hairpin-helix motif; InterPro: IPR000445 The HhH motif is an around 20 amino acids domain present in prokaryotic and eukaryotic non-sequence-specific DNA binding proteins [, , ]. The HhH motif is similar to, but distinct from, the HtH motif. Both of these motifs have two helices connected by a short turn. In the HtH motif the second helix binds to DNA with the helix in the major groove. This allows the contact between specific base and residues throughout the protein. In the HhH motif the second helix does not protrude from the surface of the protein and therefore cannot lie in the major groove of the DNA. Crystallographic studies suggest that the interaction of the HhH domain with DNA is mediated by amino acids located in the strongly conserved loop (L-P-G-V) and at the N-terminal end of the second helix []. This interaction could involve the formation of hydrogen bonds between protein backbone nitrogens and DNA phosphate groups []. The structural difference between the HtH and HhH domains is reflected at the functional level: whereas the HtH domain, found primarily in gene regulatory proteins, binds DNA in a sequence specific manner, the HhH domain is rather found in proteins involved in enzymatic activities and binds DNA with no sequence specificity []. The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain [].; GO: 0003677 DNA binding; PDB: 3C1Z_A 3C23_A 3C1Y_A 3C21_A 1Z00_A 2A1J_B 1KEA_A 1VRL_A 1RRQ_A 3G0Q_A ....
Probab=2.72 E-value=6.4e+02 Score=18.90 Aligned_cols=13 Identities=38% Similarity=0.721 Sum_probs=8.6
Q ss_pred cccccchhhhhHH
Q 003233 806 LSGVGSKVKHSIS 818 (837)
Q Consensus 806 LSGVGSKVKhsia 818 (837)
|.|||.|.-+.|.
T Consensus 16 lpGIG~~tA~~I~ 28 (30)
T PF00633_consen 16 LPGIGPKTANAIL 28 (30)
T ss_dssp STT-SHHHHHHHH
T ss_pred CCCcCHHHHHHHH
Confidence 6788888776653
Done!