Query psy5840
Match_columns 132
No_of_seqs 104 out of 196
Neff 4.2
Searched_HMMs 46136
Date Fri Aug 16 19:24:56 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5840.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5840hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03066 Nucleoplasmin: Nucleo 100.0 5.7E-40 1.2E-44 251.0 8.8 82 1-84 32-114 (149)
2 PF06524 NOA36: NOA36 protein; 72.6 1.8 3.9E-05 37.3 1.1 6 30-35 209-214 (314)
3 PF03066 Nucleoplasmin: Nucleo 66.4 1.9 4.1E-05 33.2 0.0 17 55-71 74-90 (149)
4 PTZ00415 transmission-blocking 52.9 6.5 0.00014 41.7 1.1 12 5-16 28-39 (2849)
5 KOG4264|consensus 39.4 14 0.0003 34.8 1.0 23 66-88 54-76 (694)
6 PF05475 Chlam_vir: Chlamydia 32.4 61 0.0013 27.4 3.5 31 35-73 204-237 (264)
7 PF04889 Cwf_Cwc_15: Cwf15/Cwc 32.3 28 0.0006 28.9 1.6 14 98-111 142-155 (244)
8 TIGR00986 3a0801s05tom22 mitoc 25.6 36 0.00078 26.7 1.1 28 83-110 27-54 (145)
9 KOG0772|consensus 25.2 35 0.00076 32.2 1.1 8 56-63 90-97 (641)
10 cd02859 AMPKbeta_GBD_like AMP- 24.9 64 0.0014 21.6 2.1 19 56-74 2-20 (79)
11 KOG3214|consensus 24.1 27 0.00059 26.2 0.1 14 91-104 94-107 (109)
12 KOG0682|consensus 21.9 40 0.00086 31.2 0.8 12 64-75 188-199 (500)
13 KOG2140|consensus 21.5 43 0.00094 31.9 0.9 13 91-103 427-439 (739)
14 cd06265 RNase_A_canonical Cano 21.3 1.2E+02 0.0027 22.1 3.1 43 30-73 73-115 (115)
15 PF02724 CDC45: CDC45-like pro 21.3 46 0.001 30.9 1.1 16 56-71 74-89 (622)
16 KOG0699|consensus 20.4 39 0.00085 30.9 0.4 18 89-106 296-313 (542)
17 PF03153 TFIIA: Transcription 20.3 58 0.0013 27.6 1.4 10 122-131 350-359 (375)
No 1
>PF03066 Nucleoplasmin: Nucleoplasmin; InterPro: IPR004301 The nucleophosmin/nucleoplasmin family of chaperones includes nucleophosmin, nucleoplasmin and nucleoplasmin-like proteins. They function as nuclear chaperones which are needed for the proper assembly of nucleosomes and the attainment of proper higher order chromatin structures [].; GO: 0003676 nucleic acid binding; PDB: 2P1B_E 1XB9_I 1XE0_C 1NLQ_A 2VTX_E 1K5J_D 1EJY_N 1EE5_B 3T30_J.
Probab=100.00 E-value=5.7e-40 Score=250.97 Aligned_cols=82 Identities=44% Similarity=0.631 Sum_probs=70.9
Q ss_pred CeeeeeecCCCCCCCceEEEEEEecccCC-CeeeEEEEeecCcccceeccCccCCCCCeEEEEEecccceEeeeceeeee
Q psy5840 1 MFLFQAVIGANAKEGEVHVVEVEAMGFRA-DIKLPIVVLKAAGVNNHAPLDLLFPDPPVTFKLVKGSGPIYLFGNHSVGT 79 (132)
Q Consensus 1 L~Lr~vcLGa~AK~dE~nvVEvea~~~~~-~ikv~IAtLk~s~~~p~v~Ldl~f~~pPVtF~L~~GSGPVhIsGqhlv~~ 79 (132)
|+|||||||++|| +|+|||||++|||++ ++++||||||+| ++||++|+++|++|||||||++|||||||||||++++
T Consensus 32 L~L~~v~Lga~AK-dE~~vVe~e~~~~eg~~~kv~lAtLk~s-~~~~vsL~~~~~~ppVtf~L~~GsGPVhisG~~~~~~ 109 (149)
T PF03066_consen 32 LSLRQVCLGAGAK-DELNVVEVEAMNYEGKPIKVPLATLKMS-VQPMVSLDGFEITPPVTFRLKCGSGPVHISGQHLVAM 109 (149)
T ss_dssp EEEEEEEE-TTS--SSEEEEEEEEEBTTSCEEEEEEEEEBTT-TBSEEEEEEEEESSSEEEEEEESSS-EEEEEEEEEE-
T ss_pred EEEEEeecCCCcc-CceeEEEEEeccCCCCeeEEEEEEecCC-ccceEEcCCcccCCCEEEEEEecCCCEEeeCcccccc
Confidence 7899999999999 799999999999998 799999999999 9999999999989999999999999999999999998
Q ss_pred cCCCC
Q psy5840 80 GEPMG 84 (132)
Q Consensus 80 ~e~~e 84 (132)
+++.+
T Consensus 110 ~~d~~ 114 (149)
T PF03066_consen 110 EEDEE 114 (149)
T ss_dssp -----
T ss_pred ccccc
Confidence 87654
No 2
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=72.59 E-value=1.8 Score=37.34 Aligned_cols=6 Identities=33% Similarity=0.373 Sum_probs=2.5
Q ss_pred CeeeEE
Q psy5840 30 DIKLPI 35 (132)
Q Consensus 30 ~ikv~I 35 (132)
+++.|=
T Consensus 209 ~~PCPK 214 (314)
T PF06524_consen 209 PIPCPK 214 (314)
T ss_pred CCCCCC
Confidence 344443
No 3
>PF03066 Nucleoplasmin: Nucleoplasmin; InterPro: IPR004301 The nucleophosmin/nucleoplasmin family of chaperones includes nucleophosmin, nucleoplasmin and nucleoplasmin-like proteins. They function as nuclear chaperones which are needed for the proper assembly of nucleosomes and the attainment of proper higher order chromatin structures [].; GO: 0003676 nucleic acid binding; PDB: 2P1B_E 1XB9_I 1XE0_C 1NLQ_A 2VTX_E 1K5J_D 1EJY_N 1EE5_B 3T30_J.
Probab=66.41 E-value=1.9 Score=33.17 Aligned_cols=17 Identities=18% Similarity=0.327 Sum_probs=10.1
Q ss_pred CCCeEEEEEecccceEe
Q psy5840 55 DPPVTFKLVKGSGPIYL 71 (132)
Q Consensus 55 ~pPVtF~L~~GSGPVhI 71 (132)
.|.|.+-+..-..||.+
T Consensus 74 ~~~vsL~~~~~~ppVtf 90 (149)
T PF03066_consen 74 QPMVSLDGFEITPPVTF 90 (149)
T ss_dssp BSEEEEEEEEESSSEEE
T ss_pred cceEEcCCcccCCCEEE
Confidence 45566655444667765
No 4
>PTZ00415 transmission-blocking target antigen s230; Provisional
Probab=52.88 E-value=6.5 Score=41.70 Aligned_cols=12 Identities=33% Similarity=0.548 Sum_probs=6.9
Q ss_pred eeecCCCCCCCc
Q psy5840 5 QAVIGANAKEGE 16 (132)
Q Consensus 5 ~vcLGa~AK~dE 16 (132)
+|-.|.+.++|+
T Consensus 28 ~~~~~~~~~~~~ 39 (2849)
T PTZ00415 28 NAIIGNGICDDE 39 (2849)
T ss_pred ceeecCCcccch
Confidence 455666666544
No 5
>KOG4264|consensus
Probab=39.35 E-value=14 Score=34.84 Aligned_cols=23 Identities=26% Similarity=0.413 Sum_probs=9.8
Q ss_pred ccceEeeeceeeeecCCCCCCCC
Q psy5840 66 SGPIYLFGNHSVGTGEPMGEDDD 88 (132)
Q Consensus 66 SGPVhIsGqhlv~~~e~~ee~dd 88 (132)
.|-.|++-+..-.-.+..|+|||
T Consensus 54 tgalHlrrvesa~~~e~~Ed~de 76 (694)
T KOG4264|consen 54 TGALHLRRVESAKPAESVEDDDE 76 (694)
T ss_pred cCccchhcccccCcccccccccc
Confidence 34556655443332222334444
No 6
>PF05475 Chlam_vir: Chlamydia virulence protein PGP3-D; InterPro: IPR008444 This family consists of Chlamydia virulence proteins which are thought to be required for the growth of these bacteria in mammalian cells []. Humans mount a humoral and mucosal immune response to plasmid protein pGP3 from Chlamydia trachomatis infections [, ]. This immune response to pGP3 in humans and animal models of chlamydia-induced disease has potential uses in diagnostic assays and protective immunisation strategies [].
Probab=32.37 E-value=61 Score=27.39 Aligned_cols=31 Identities=35% Similarity=0.629 Sum_probs=22.6
Q ss_pred EEEeecCcccceeccCccCCCCCeEEEEEec---ccceEeee
Q psy5840 35 IVVLKAAGVNNHAPLDLLFPDPPVTFKLVKG---SGPIYLFG 73 (132)
Q Consensus 35 IAtLk~s~~~p~v~Ldl~f~~pPVtF~L~~G---SGPVhIsG 73 (132)
+|+||.+ +... + ..||||.|+.| ||-|.+..
T Consensus 204 ~cSLrt~-v~Ns---g----~~PvtfSLRvGGmeSGVVWVNA 237 (264)
T PF05475_consen 204 VCSLRTC-VTNS---G----TTPVTFSLRVGGMESGVVWVNA 237 (264)
T ss_pred eeeeEEE-eecC---C----CCceEEEEEecccccceEEEEc
Confidence 7888876 3322 2 46999999988 89888754
No 7
>PF04889 Cwf_Cwc_15: Cwf15/Cwc15 cell cycle control protein; InterPro: IPR006973 This family represents Cwf15/Cwc15 (from Schizosaccharomyces pombe and Saccharomyces cerevisiae respectively) and their homologues. The function of these proteins is unknown, but they form part of the spliceosome and are thus thought to be involved in mRNA splicing [].; GO: 0000398 nuclear mRNA splicing, via spliceosome, 0005681 spliceosomal complex
Probab=32.33 E-value=28 Score=28.91 Aligned_cols=14 Identities=21% Similarity=0.567 Sum_probs=6.7
Q ss_pred ccccchhhHhhhhc
Q psy5840 98 EEEVDESEILSKNL 111 (132)
Q Consensus 98 ~ee~~e~~~~~~~~ 111 (132)
++++||.+.|-+.|
T Consensus 142 ~ddeDd~~~Ll~EL 155 (244)
T PF04889_consen 142 DDDEDDTAALLREL 155 (244)
T ss_pred cccchHHHHHHHHH
Confidence 34445555554443
No 8
>TIGR00986 3a0801s05tom22 mitochondrial import receptor subunit Tom22. translocase (Tom) import receptor, five proteins of the Tom channel complex, five proteins of the inner membrane translocase (Tim) and three "motor" proteins. This family is specific for the Tom22 proteins.
Probab=25.61 E-value=36 Score=26.70 Aligned_cols=28 Identities=25% Similarity=0.093 Sum_probs=13.1
Q ss_pred CCCCCCcccccccccccccchhhHhhhh
Q psy5840 83 MGEDDDEESIDEDFSEEEVDESEILSKN 110 (132)
Q Consensus 83 ~ee~dd~e~eee~~~~ee~~e~~~~~~~ 110 (132)
.++|.|-+++++.+++.++.|.|-+...
T Consensus 27 ~~~~td~~se~~~d~~~~~~e~ETl~ER 54 (145)
T TIGR00986 27 DEDFTDVDSEDSVDSDFESLEEETFTDR 54 (145)
T ss_pred ccccccccccccccccccccccCcHHHH
Confidence 3455554444443344444455555443
No 9
>KOG0772|consensus
Probab=25.17 E-value=35 Score=32.22 Aligned_cols=8 Identities=25% Similarity=0.397 Sum_probs=3.3
Q ss_pred CCeEEEEE
Q psy5840 56 PPVTFKLV 63 (132)
Q Consensus 56 pPVtF~L~ 63 (132)
|++++..+
T Consensus 90 ~~~~ss~~ 97 (641)
T KOG0772|consen 90 PRVSSSIN 97 (641)
T ss_pred CCCccccc
Confidence 34444443
No 10
>cd02859 AMPKbeta_GBD_like AMP-activated protein kinase (AMPK) beta subunit glycogen binding domain (GBD). AMPK is a metabolic stress sensing protein that senses AMP/ATP and has recently been found to act as a glycogen sensor as well. The protein functions as a alpha-beta-gamma heterotrimer. This domain is the glycogen binding domain of the beta subunit.
Probab=24.86 E-value=64 Score=21.60 Aligned_cols=19 Identities=32% Similarity=0.586 Sum_probs=16.6
Q ss_pred CCeEEEEEecccceEeeec
Q psy5840 56 PPVTFKLVKGSGPIYLFGN 74 (132)
Q Consensus 56 pPVtF~L~~GSGPVhIsGq 74 (132)
.||+|+...+...|.|.|.
T Consensus 2 ~~v~f~~~~~a~~V~v~G~ 20 (79)
T cd02859 2 VPTTFVWPGGGKEVYVTGS 20 (79)
T ss_pred eEEEEEEcCCCcEEEEEEE
Confidence 4899999988889999995
No 11
>KOG3214|consensus
Probab=24.05 E-value=27 Score=26.20 Aligned_cols=14 Identities=43% Similarity=0.499 Sum_probs=7.5
Q ss_pred cccccccccccchh
Q psy5840 91 SIDEDFSEEEVDES 104 (132)
Q Consensus 91 ~eee~~~~ee~~e~ 104 (132)
++|++++|||+||+
T Consensus 94 d~e~~s~eee~ded 107 (109)
T KOG3214|consen 94 DEEEESEEEEDDED 107 (109)
T ss_pred cccccCchhhcccc
Confidence 45555555555543
No 12
>KOG0682|consensus
Probab=21.93 E-value=40 Score=31.19 Aligned_cols=12 Identities=33% Similarity=0.595 Sum_probs=10.3
Q ss_pred ecccceEeeece
Q psy5840 64 KGSGPIYLFGNH 75 (132)
Q Consensus 64 ~GSGPVhIsGqh 75 (132)
+|+|||||+|-+
T Consensus 188 AG~g~VHl~gG~ 199 (500)
T KOG0682|consen 188 AGGGVVHLVGGV 199 (500)
T ss_pred cCCceeEecccH
Confidence 699999999854
No 13
>KOG2140|consensus
Probab=21.48 E-value=43 Score=31.94 Aligned_cols=13 Identities=46% Similarity=0.406 Sum_probs=6.0
Q ss_pred cccccccccccch
Q psy5840 91 SIDEDFSEEEVDE 103 (132)
Q Consensus 91 ~eee~~~~ee~~e 103 (132)
+|+|++++||++|
T Consensus 427 ~eee~e~~ee~~e 439 (739)
T KOG2140|consen 427 DEEEDESVEEDEE 439 (739)
T ss_pred ccccccccccccc
Confidence 4444444444444
No 14
>cd06265 RNase_A_canonical Canonical RNase A family includes all vertebrate homologues to the bovine pancreatic ribonuclease A (RNase A) that contain the catalytic site, necessary for RNase activity. In the human genome 8 RNases , refered to as "canonical" RNases, have been identified, pancreatic RNase (RNase 1), Eosinophil Derived Neurotoxin (SEDN/RNASE 2), Eosinophil Cationic Protein (ECP/RNase 3), RNase 4, Angiogenin (RNase 5), RNase 6 or k6, the skin derived RNase (RNase 7) and RNase 8. The eight human genes are all located in a cluster on chromosome 14. Canonical RNase A enzymes have special biological activities; for example, some stimulate the development of vascular endothelial cells, dendritic cells, and neurons, are cytotoxic/anti-tumoral and/or anti-pathogenic. RNase A is involved in endonucleolytic cleavage of 3'-phosphomononucleotides and 3'-phosphooligonucleotides ending in C-P or U-P with 2',3'-cyclic phosphate intermediates. The catalytic mechanism is a transphosphoryla
Probab=21.30 E-value=1.2e+02 Score=22.08 Aligned_cols=43 Identities=9% Similarity=0.013 Sum_probs=25.9
Q ss_pred CeeeEEEEeecCcccceeccCccCCCCCeEEEEEecccceEeee
Q psy5840 30 DIKLPIVVLKAAGVNNHAPLDLLFPDPPVTFKLVKGSGPIYLFG 73 (132)
Q Consensus 30 ~ikv~IAtLk~s~~~p~v~Ldl~f~~pPVtF~L~~GSGPVhIsG 73 (132)
+.++|.|.|+.+...|.+.-...-..-.|.+.- .|.-|||+-|
T Consensus 73 ~~~iT~C~lt~g~~~p~C~Y~~~~~~k~i~VaC-~~~~PVH~d~ 115 (115)
T cd06265 73 PFPVTDCNLTGGSRYPNCRYRGTPSTRKIVVAC-ENGVPVHLDG 115 (115)
T ss_pred ccEeEEEEeCCCCCCCCCceeeecccceEEEEc-CCCcccccCC
Confidence 689999999986456665544222222344333 3456999754
No 15
>PF02724 CDC45: CDC45-like protein; InterPro: IPR003874 CDC45 is an essential gene required for initiation of DNA replication in Saccharomyces cerevisiae (cell division control protein 45), forming a complex with MCM5/CDC46. Homologs of CDC45 have been identified in human [], mouse and the smut fungus, Melampsora spp., (tsd2 protein) among others.; GO: 0006270 DNA-dependent DNA replication initiation
Probab=21.26 E-value=46 Score=30.92 Aligned_cols=16 Identities=25% Similarity=0.347 Sum_probs=10.6
Q ss_pred CCeEEEEEecccceEe
Q psy5840 56 PPVTFKLVKGSGPIYL 71 (132)
Q Consensus 56 pPVtF~L~~GSGPVhI 71 (132)
+.++|.+.-+.-|.||
T Consensus 74 ~~~~iyViDshRP~~L 89 (622)
T PF02724_consen 74 EDVTIYVIDSHRPWNL 89 (622)
T ss_pred CceEEEEEeCCCCccH
Confidence 4667776666667665
No 16
>KOG0699|consensus
Probab=20.38 E-value=39 Score=30.95 Aligned_cols=18 Identities=22% Similarity=0.507 Sum_probs=7.6
Q ss_pred cccccccccccccchhhH
Q psy5840 89 EESIDEDFSEEEVDESEI 106 (132)
Q Consensus 89 ~e~eee~~~~ee~~e~~~ 106 (132)
||+.+++.++||.+|...
T Consensus 296 Ded~e~e~ddEE~~e~~m 313 (542)
T KOG0699|consen 296 DEDAEDEQDDEEMVEGSM 313 (542)
T ss_pred ccccccccchhhhhhhcc
Confidence 333344444444444443
No 17
>PF03153 TFIIA: Transcription factor IIA, alpha/beta subunit; InterPro: IPR004855 Transcription factor IIA (TFIIA) is one of several factors that form part of a transcription pre-initiation complex along with RNA polymerase II, the TATA-box-binding protein (TBP) and TBP-associated factors, on the TATA-box sequence upstream of the initiation start site. After initiation, some components of the pre-initiation complex (including TFIIA) remain attached and re-initiate a subsequent round of transcription. TFIIA binds to TBP to stabilise TBP binding to the TATA element. TFIIA also inhibits the cytokine HMGB1 (high mobility group 1 protein) binding to TBP [], and can dissociate HMGB1 already bound to TBP/TATA-box. Human and Drosophila TFIIA have three subunits: two large subunits, LN/alpha and LC/beta, derived from the same gene, and a small subunit, S/gamma. Yeast TFIIA has two subunits: a large TOA1 subunit that shows sequence similarity to the N-terminal of LN/alpha and the C-terminal of LC/beta, and a small subunit, TOA2 that is highly homologous with S/gamma. The conserved regions of the large and small subunits of TFIIA combine to form two domains: a four-helix bundle (helical domain) composed of two helices from each of the N-terminal regions of TOA1 and TOA2 in yeast; and a beta-barrel (beta-barrel domain) composed of beta-sheets from the C-terminal regions of TOA1 and TOA2 []. This entry represents the precursor that yields both the alpha and beta subunits of TFIIA. The TFIIA heterotrimer is an essential general transcription initiation factor for the expression of genes transcribed by RNA polymerase II []. ; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005672 transcription factor TFIIA complex; PDB: 1NVP_B 1YTF_B 1RM1_C 1NH2_B.
Probab=20.26 E-value=58 Score=27.59 Aligned_cols=10 Identities=30% Similarity=0.414 Sum_probs=6.5
Q ss_pred eeeeeeeeee
Q psy5840 122 LSFKVGIECL 131 (132)
Q Consensus 122 ~~~~~~~~~~ 131 (132)
..||-||-|+
T Consensus 350 ~~lk~g~~~~ 359 (375)
T PF03153_consen 350 CTLKDGIMHI 359 (375)
T ss_dssp EEEEEEEEEE
T ss_pred EEeeeeEEEE
Confidence 4577777664
Done!