Query 034184
Match_columns 102
No_of_seqs 15 out of 17
Neff 1.9
Searched_HMMs 46136
Date Fri Mar 29 10:42:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034184.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034184hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd02988 Phd_like_VIAF Phosduci 23.6 24 0.00053 26.1 -0.2 9 52-60 1-9 (192)
2 KOG3170 Conserved phosducin-li 16.5 45 0.00098 27.4 -0.1 14 48-61 4-17 (240)
3 PF06880 DUF1262: Protein of u 13.6 93 0.002 22.6 0.9 13 79-91 62-74 (104)
4 PF13101 DUF3945: Protein of u 9.6 2.3E+02 0.005 17.5 1.6 33 33-69 13-45 (59)
5 PF02251 PA28_alpha: Proteasom 9.5 1.2E+02 0.0027 19.6 0.4 20 63-87 45-64 (64)
6 PF03089 RAG2: Recombination a 8.8 2.3E+02 0.0051 24.3 1.8 21 35-55 239-259 (337)
7 KOG2944 Glyoxalase [Carbohydra 8.6 1.1E+02 0.0025 23.9 -0.1 24 2-25 109-133 (170)
8 PF08366 LLGL: LLGL2; InterPr 8.4 1.2E+02 0.0026 21.5 -0.0 44 18-64 43-87 (105)
9 PF09961 DUF2195: Uncharacteri 8.0 2.7E+02 0.0059 20.6 1.7 38 16-53 23-60 (121)
10 PHA01745 hypothetical protein 7.7 1.1E+02 0.0025 25.8 -0.4 18 76-93 70-87 (306)
No 1
>cd02988 Phd_like_VIAF Phosducin (Phd)-like family, Viral inhibitor of apoptosis (IAP)-associated factor (VIAF) subfamily; VIAF is a Phd-like protein that functions in caspase activation during apoptosis. It was identified as an IAP binding protein through a screen of a human B-cell library using a prototype IAP. VIAF lacks a consensus IAP binding motif and while it does not function as an IAP antagonist, it still plays a regulatory role in the complete activation of caspases. VIAF itself is a substrate for IAP-mediated ubiquitination, suggesting that it may be a target of IAPs in the prevention of cell death. The similarity of VIAF to Phd points to a potential role distinct from apoptosis regulation. Phd functions as a cytosolic regulator of G protein by specifically binding to G protein betagamma (Gbg)-subunits. The C-terminal domain of Phd adopts a thioredoxin fold, but it does not contain a CXXC motif. Phd interacts with G protein beta mostly through the N-terminal helical domain.
Probab=23.59 E-value=24 Score=26.10 Aligned_cols=9 Identities=44% Similarity=0.896 Sum_probs=6.7
Q ss_pred CCCCcchhh
Q 034184 52 GEWSDIQAT 60 (102)
Q Consensus 52 ~EW~d~q~t 60 (102)
|||+|||..
T Consensus 1 tew~di~r~ 9 (192)
T cd02988 1 TEWNDILRK 9 (192)
T ss_pred CchhHHHHH
Confidence 688888753
No 2
>KOG3170 consensus Conserved phosducin-like protein [Signal transduction mechanisms]
Probab=16.49 E-value=45 Score=27.38 Aligned_cols=14 Identities=36% Similarity=0.643 Sum_probs=11.5
Q ss_pred cCCCCCCCcchhhh
Q 034184 48 PIGDGEWSDIQATE 61 (102)
Q Consensus 48 pvgd~EW~d~q~tE 61 (102)
|..|+||+||+-.-
T Consensus 4 ~~~dtewnDIlRkk 17 (240)
T KOG3170|consen 4 ESEDTEWNDILRKK 17 (240)
T ss_pred cccccchHHHHHhc
Confidence 67899999998654
No 3
>PF06880 DUF1262: Protein of unknown function (DUF1262); InterPro: IPR010683 This family represents a conserved region within a number of proteins of unknown function that seem to be specific to Arabidopsis thaliana. Note that some family members contain more than one copy of this region.
Probab=13.62 E-value=93 Score=22.56 Aligned_cols=13 Identities=31% Similarity=0.697 Sum_probs=10.8
Q ss_pred ccccccCCCCCCC
Q 034184 79 LDIPVVSPPVNNH 91 (102)
Q Consensus 79 LDIpVvs~P~~~~ 91 (102)
+=|||..||.+.+
T Consensus 62 ~FIPVl~QPLSSn 74 (104)
T PF06880_consen 62 VFIPVLNQPLSSN 74 (104)
T ss_pred EEEEcCCCcCcCC
Confidence 5599999998765
No 4
>PF13101 DUF3945: Protein of unknown function (DUF3945)
Probab=9.59 E-value=2.3e+02 Score=17.53 Aligned_cols=33 Identities=21% Similarity=0.408 Sum_probs=24.9
Q ss_pred CCceeEeeccccccccCCCCCCCcchhhhhhhhhccc
Q 034184 33 GASVVHMTVDQVNLQPIGDGEWSDIQATEARIADVRE 69 (102)
Q Consensus 33 ~e~vV~m~~d~v~i~pvgd~EW~d~q~tEa~isDVRE 69 (102)
.+.++.|..+.+-|+ .+|.+.+-|+...++.++
T Consensus 13 Tn~l~~~~~~~i~ip----~~i~g~~Ls~~q~~~L~~ 45 (59)
T PF13101_consen 13 TNELVYMPVDKIRIP----DKIKGVELSPEQKEDLRE 45 (59)
T ss_pred cCceEEecccccccc----ceecCccCCHHHHHHHHC
Confidence 455688888888877 778888888777777664
No 5
>PF02251 PA28_alpha: Proteasome activator pa28 alpha subunit; InterPro: IPR003185 PA28 activator complex (also known as 11S regulator of 20S proteasome) is a ring shaped hexameric structure of alternating alpha (PA28alpha) and beta (PA28beta) subunits. The catalytic properties of PA28alpha and PA28beta-activated proteosome are similar [, ]. This entry represents the alpha subunit. The activator complex binds to the 20S proteasome and stimulates peptidase activity in and ATP-independent manner.; GO: 0008537 proteasome activator complex; PDB: 1AVO_K.
Probab=9.54 E-value=1.2e+02 Score=19.58 Aligned_cols=20 Identities=30% Similarity=0.793 Sum_probs=3.2
Q ss_pred hhhhccccccCCCCCcccccccCCC
Q 034184 63 RIADVREVAPETEGSSLDIPVVSPP 87 (102)
Q Consensus 63 ~isDVREv~~E~e~sSLDIpVvs~P 87 (102)
.++|..+|-++ |||||=.||
T Consensus 45 n~~dls~i~~~-----lnIPiPdP~ 64 (64)
T PF02251_consen 45 NLSDLSSIHAP-----LNIPIPDPP 64 (64)
T ss_dssp --S-GGGS-----------------
T ss_pred ccccHHhhcCc-----CCCCCCCCC
Confidence 45566666543 999985543
No 6
>PF03089 RAG2: Recombination activating protein 2; InterPro: IPR004321 The variable portion of the genes encoding immunoglobulins and T cell receptors are assembled from component V, D, and J DNA segments by a site-specific recombination reaction termed V(D)J recombination. V(D)J recombination is targeted to specific sites on the chromosome by recombination signal sequences (RSSs) that flank antigen receptor gene segments. The RSS consists of a conserved heptamer (consensus, 5'-CACAGTG-3') and nonamer (consensus, 5'-ACAAAAACC-3') separated by a spacer of either 12 or 23 bp. Efficient recombination occurs between a 12-RSS and a 23-RSS, a restriction known as the 12/23 rule. V(D)J recombination can be divided into two phases, DNA cleavage and DNA joining. DNA cleavage requires two lymphocyte-specific factors, the products of the recombination activating genes, RAG1 and RAG2, which together recognise the RSSs and create double strand breaks at the RSS-coding segment junctions []. RAG-mediated DNA cleavage occurs in a synaptic complex termed the paired complex, which is constituted from two distinct RSS-RAG complexes, a 12-SC and a 23-SC (where SC stands for signal complex). The DNA cleavage reaction involves two distinct enzymatic steps, initial nicking that creates a 3'-OH between a coding segment and its RSS, followed by hairpin formation in which the newly created 3'-OH attacks a phosphodiester bond on the opposite DNA strand. This generates a blunt, 5' phosphorylated signal end containing all of the RSS elements, and a covalently sealed hairpin coding end. The second phase of V(D)J recombination, in which broken DNA fragments are processed and joined, is less well characterised. Signal ends are typically joined precisely to form a signal joint, whereas joining of the coding ends requires the hairpin structure to be opened and typically involves nucleotide addition and deletion before formation of the coding joint. The factors involved in these processes include ubiquitously expressed proteins involved in the repair of DNA double strand breaks by nonhomologous end joining, terminal deoxynucleotidyl transferase, and Artemis protein. In addition to their critical roles in RSS recognition and DNA cleavage, the RAG proteins may perform two distinct types of functions in the postcleavage phase of V(D)J. A structural function has been inferred from the finding that, after DNA cleavage in vitro, the DNA ends remain associated with the RAG proteins in a "four end" complex known as the cleaved signal complex. After release of the coding ends in vitro, and after coding joint formation in vivo, the RAG proteins remain in a stable signal end complex (SEC) containing the two signal ends. These postcleavage complexes may serve as essential scaffolds for the second phase of the reaction, with the RAG proteins acting to organise the DNA processing and joining events. The second type of RAG protein-mediated postcleavage activity is the catalysis of phosphodiester bond hydrolysis and strand transfer reactions. The RAG proteins are capable of opening hairpin coding ends in vitro. The RAG proteins also show 3' flap endonuclease activity that may contribute to coding end processing/joining and can utilise the 3' OH group on the signal ends to attack hairpin coding ends (forming hybrid or open/shut joints) or virtually any DNA duplex (forming a transposition product).; GO: 0003677 DNA binding, 0006310 DNA recombination, 0005634 nucleus
Probab=8.75 E-value=2.3e+02 Score=24.35 Aligned_cols=21 Identities=19% Similarity=0.474 Sum_probs=19.1
Q ss_pred ceeEeeccccccccCCCCCCC
Q 034184 35 SVVHMTVDQVNLQPIGDGEWS 55 (102)
Q Consensus 35 ~vV~m~~d~v~i~pvgd~EW~ 55 (102)
+.|-|++++++|.|..-.+|.
T Consensus 239 ~~V~Ldd~~I~ie~~E~P~Wt 259 (337)
T PF03089_consen 239 NTVSLDDDGIHIEEREPPEWT 259 (337)
T ss_pred eEEEEeCCceEeccCCCCCCC
Confidence 458899999999999999996
No 7
>KOG2944 consensus Glyoxalase [Carbohydrate transport and metabolism]
Probab=8.59 E-value=1.1e+02 Score=23.91 Aligned_cols=24 Identities=17% Similarity=0.389 Sum_probs=20.0
Q ss_pred CCCCC-CCCCcCCCccccccccccc
Q 034184 2 DNSLP-QTKDVDLSDENVDKACLSV 25 (102)
Q Consensus 2 ~~s~p-~tKhvD~sd~nVDKAClS~ 25 (102)
+|+.| .--|+=.+=+||++||-+.
T Consensus 109 gN~~prGfgHIci~V~di~sac~~l 133 (170)
T KOG2944|consen 109 GNKEPRGFGHICIEVDDINSACERL 133 (170)
T ss_pred CCCCCCccceEEEEeCCHHHHHHHH
Confidence 57777 7789999999999999754
No 8
>PF08366 LLGL: LLGL2; InterPro: IPR013577 This domain is found in lethal giant larvae homologue 2 (LLGL2) proteins and syntaxin-binding proteins like tomosyn []. It has been identified in eukaryotes and tends to be found together with WD repeats (IPR001680 from INTERPRO).
Probab=8.41 E-value=1.2e+02 Score=21.48 Aligned_cols=44 Identities=20% Similarity=0.428 Sum_probs=30.8
Q ss_pred cccccccccccccCCCCceeEeeccccccccCCCCCCC-cchhhhhhh
Q 034184 18 VDKACLSVSRAVPEPGASVVHMTVDQVNLQPIGDGEWS-DIQATEARI 64 (102)
Q Consensus 18 VDKAClS~sr~vpv~~e~vV~m~~d~v~i~pvgd~EW~-d~q~tEa~i 64 (102)
=|+-|+++.+. ....+.+|+-.=+|.-++-+..|. ++|...|.+
T Consensus 43 gdr~~vTV~~g---~~~~~ldf~s~VIDF~~i~~~~~~~e~~~P~alv 87 (105)
T PF08366_consen 43 GDRHCVTVMQG---KTHVVLDFTSRVIDFFTICESPWPNEFQDPYALV 87 (105)
T ss_pred CCCceEEEEeC---CEEEEEEcCCceEEEEEEcCCCCccccCCCcEEE
Confidence 46789998872 122347788888899999999887 566655443
No 9
>PF09961 DUF2195: Uncharacterized protein conserved in bacteria (DUF2195); InterPro: IPR018696 This family of various bacterial proteins has no known function.
Probab=8.03 E-value=2.7e+02 Score=20.62 Aligned_cols=38 Identities=21% Similarity=0.342 Sum_probs=29.5
Q ss_pred cccccccccccccccCCCCceeEeeccccccccCCCCC
Q 034184 16 ENVDKACLSVSRAVPEPGASVVHMTVDQVNLQPIGDGE 53 (102)
Q Consensus 16 ~nVDKAClS~sr~vpv~~e~vV~m~~d~v~i~pvgd~E 53 (102)
+|==-||+.+.-.-|-..++.|++.-+=---+|||+=.
T Consensus 23 ~N~LaaCv~~~~~~~~~~~n~v~l~~~~~l~~siG~CG 60 (121)
T PF09961_consen 23 DNALAACVDVKPGQPQTADNQVSLKATFSLRRSIGECG 60 (121)
T ss_pred eCcHHHHhcCcccCccccCCeEEEEEEEEEecccCccc
Confidence 45556999999988988999988876655567898754
No 10
>PHA01745 hypothetical protein
Probab=7.65 E-value=1.1e+02 Score=25.84 Aligned_cols=18 Identities=33% Similarity=0.405 Sum_probs=13.7
Q ss_pred CCcccccccCCCCCCCCC
Q 034184 76 GSSLDIPVVSPPVNNHHE 93 (102)
Q Consensus 76 ~sSLDIpVvs~P~~~~h~ 93 (102)
=-|||||...-|+...++
T Consensus 70 y~SLDiP~~~dp~d~kNf 87 (306)
T PHA01745 70 FFSLDIPSIFEPLSRKNF 87 (306)
T ss_pred eeecCCCCcCCChhhhhH
Confidence 569999998778775443
Done!