Query 034327
Match_columns 98
No_of_seqs 22 out of 24
Neff 2.2
Searched_HMMs 46136
Date Fri Mar 29 12:16:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034327.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034327hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0782 Predicted diacylglycer 44.8 13 0.00027 34.9 1.5 26 11-37 609-634 (1004)
2 PF13227 DUF4035: Protein of u 35.9 38 0.00083 21.8 2.3 39 10-58 5-43 (53)
3 PF14216 DUF4326: Domain of un 25.6 59 0.0013 21.9 2.0 29 9-37 19-47 (86)
4 PF13465 zf-H2C2_2: Zinc-finge 22.1 29 0.00062 18.2 -0.1 10 21-30 9-18 (26)
5 PF06747 CHCH: CHCH domain; I 21.3 56 0.0012 17.5 1.0 15 52-66 4-18 (35)
6 smart00571 DDT domain in diffe 20.4 1.5E+02 0.0031 18.4 2.9 33 33-65 30-62 (63)
7 COG1948 MUS81 ERCC4-type nucle 18.4 1.1E+02 0.0023 24.8 2.4 28 32-69 74-102 (254)
8 PF01029 NusB: NusB family; I 18.2 1.6E+02 0.0034 19.5 2.8 31 31-61 61-91 (134)
9 PF10078 DUF2316: Uncharacteri 17.6 2.3E+02 0.005 19.6 3.6 34 45-79 49-82 (89)
10 PF04056 Ssl1: Ssl1-like; Int 17.5 82 0.0018 24.1 1.5 17 32-48 24-40 (193)
No 1
>KOG0782 consensus Predicted diacylglycerol kinase [Signal transduction mechanisms]
Probab=44.83 E-value=13 Score=34.87 Aligned_cols=26 Identities=38% Similarity=0.838 Sum_probs=21.2
Q ss_pred CCCCCCCCCCCCCCCcCccchhHHHHH
Q 034327 11 ESPWGTPEGEHRQPKAHRCNDRAEDVI 37 (98)
Q Consensus 11 ~s~~g~~~~~~~~~rpHRCNDR~eDvl 37 (98)
.-|||.| |||-.++|-||+|=.-.||
T Consensus 609 TmPWG~p-gdhhDfePqrhdDGyvEVi 634 (1004)
T KOG0782|consen 609 TMPWGEP-GDHHDFEPQRHDDGYVEVI 634 (1004)
T ss_pred ccCCCCC-CccccCCccccCCceEEEE
Confidence 4699999 7888999999999765544
No 2
>PF13227 DUF4035: Protein of unknown function (DUF4035)
Probab=35.93 E-value=38 Score=21.77 Aligned_cols=39 Identities=31% Similarity=0.512 Sum_probs=31.8
Q ss_pred CCCCCCCCCCCCCCCCcCccchhHHHHHHHHhcCCCCcccCchHHHHHH
Q 034327 10 RESPWGTPEGEHRQPKAHRCNDRAEDVIQACFEGNPFKTVPGPFKLFWQ 58 (98)
Q Consensus 10 r~s~~g~~~~~~~~~rpHRCNDR~eDvlqa~fegnp~~tvp~~fkLfwr 58 (98)
|+||.|. ||=|=|...+..|.+...+-+.-..-|-+||.
T Consensus 5 r~~P~G~----------~R~D~~~Aqia~A~~n~qg~k~~l~D~mp~w~ 43 (53)
T PF13227_consen 5 REQPFGD----------WRGDYRAAQIAAAMINSQGKKPKLSDFMPFWG 43 (53)
T ss_pred ccCCcch----------HHHHHHHHHHHHHHHcCCCCCCcHHHHHhhcC
Confidence 6788876 67788999999999999998866677777874
No 3
>PF14216 DUF4326: Domain of unknown function (DUF4326)
Probab=25.59 E-value=59 Score=21.85 Aligned_cols=29 Identities=17% Similarity=0.354 Sum_probs=15.4
Q ss_pred CCCCCCCCCCCCCCCCCcCccchhHHHHH
Q 034327 9 RRESPWGTPEGEHRQPKAHRCNDRAEDVI 37 (98)
Q Consensus 9 ~r~s~~g~~~~~~~~~rpHRCNDR~eDvl 37 (98)
-|.|+||+|-.-....-.-.|-+++.+.+
T Consensus 19 gR~s~wGNPf~~~~~~~R~~~v~~yr~~l 47 (86)
T PF14216_consen 19 GRPSKWGNPFRVGEDGDREEAVEKYREWL 47 (86)
T ss_pred CCCCcCCCCCcCCCCCCHHHHHHHHHHHH
Confidence 36899999955443222223444444444
No 4
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=22.07 E-value=29 Score=18.16 Aligned_cols=10 Identities=30% Similarity=0.630 Sum_probs=8.4
Q ss_pred CCCCCcCccc
Q 034327 21 HRQPKAHRCN 30 (98)
Q Consensus 21 ~~~~rpHRCN 30 (98)
|.+.|||.|+
T Consensus 9 H~~~k~~~C~ 18 (26)
T PF13465_consen 9 HTGEKPYKCP 18 (26)
T ss_dssp HSSSSSEEES
T ss_pred cCCCCCCCCC
Confidence 6788999986
No 5
>PF06747 CHCH: CHCH domain; InterPro: IPR010625 A conserved motif was identified in the LOC118487 protein was called the CHCH motif. Alignment of this protein with related members showed the presence of three subgroups of proteins, which are called the S (Small), N (N-terminal extended) and C (C-terminal extended) subgroups. All three sub-groups of proteins have in common that they contain a predicted conserved [coiled coil 1]-[helix 1]-[coiled coil 2]-[helix 2] domain (CHCH domain). Within each helix of the CHCH domain, there are two cysteines present in a C-X9-C motif. The N-group contains an additional double helix domain, and each helix contains the C-X9-C motif. This family contains a number of characterised proteins: Cox19 protein - a nuclear gene of Saccharomyces cerevisiae, codes for an 11 kDa protein (Cox19p) required for expression of cytochrome oxidase. Because cox19 mutants are able to synthesise the mitochondrial and nuclear gene products of cytochrome oxidase, Cox19p probably functions post-translationally during assembly of the enzyme. Cox19p is present in the cytoplasm and mitochondria, where it exists as a soluble intermembrane protein. This dual location is similar to what was previously reported for Cox17p, a low molecular weight copper protein thought to be required for maturation of the CuA centre of subunit 2 of cytochrome oxidase. Cox19p have four conserved potential metal ligands, these are three cysteines and one histidine. Mrp10 - belongs to the class of yeast mitochondrial ribosomal proteins that are essential for translation []. Eukaryotic NADH-ubiquinone oxidoreductase 19 kDa (NDUFA8) subunit []. The CHCH domain was previously called DUF657 []. ; PDB: 2ZXT_A 3A3C_A 2L0Y_A 2K3J_A.
Probab=21.34 E-value=56 Score=17.51 Aligned_cols=15 Identities=13% Similarity=0.488 Sum_probs=11.7
Q ss_pred hHHHHHHHHhcCCCC
Q 034327 52 PFKLFWQCMRSKPGE 66 (98)
Q Consensus 52 ~fkLfwrCmRSk~Ge 66 (98)
.++.++.|+++..++
T Consensus 4 e~~~~~~Cl~~n~~~ 18 (35)
T PF06747_consen 4 EMKAYLACLKENNFD 18 (35)
T ss_dssp HHHHHHHHHHCH-SS
T ss_pred HHHHHHHHHHHCCCc
Confidence 478899999998874
No 6
>smart00571 DDT domain in different transcription and chromosome remodeling factors.
Probab=20.45 E-value=1.5e+02 Score=18.44 Aligned_cols=33 Identities=15% Similarity=0.110 Sum_probs=20.6
Q ss_pred HHHHHHHHhcCCCCcccCchHHHHHHHHhcCCC
Q 034327 33 AEDVIQACFEGNPFKTVPGPFKLFWQCMRSKPG 65 (98)
Q Consensus 33 ~eDvlqa~fegnp~~tvp~~fkLfwrCmRSk~G 65 (98)
++|+++|+-+-++..-+-.....+.+++...+|
T Consensus 30 l~~f~~Al~~~~~~~ll~ei~~~LL~~i~~d~~ 62 (63)
T smart00571 30 LEDFIAALKCRDQNGLLTEVHVVLLRAILKDEG 62 (63)
T ss_pred HHHHHHHHhcCCcchHHHHHHHHHHHHHHhCCC
Confidence 788888877665554444445556666665555
No 7
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=18.38 E-value=1.1e+02 Score=24.83 Aligned_cols=28 Identities=32% Similarity=0.508 Sum_probs=22.8
Q ss_pred hHHHHHHHHhcCCCCcccCchHHHHHHHHhcC-CCCCCC
Q 034327 32 RAEDVIQACFEGNPFKTVPGPFKLFWQCMRSK-PGEEPT 69 (98)
Q Consensus 32 R~eDvlqa~fegnp~~tvp~~fkLfwrCmRSk-~GeEP~ 69 (98)
+..|+++|+++| +||=||-|=+ .|..|+
T Consensus 74 s~~Dfv~Si~dg----------RlfeQ~~rL~~~y~rpv 102 (254)
T COG1948 74 SISDFVSSIIDG----------RLFEQAKRLKKSYERPV 102 (254)
T ss_pred cHHHHHHHHhcc----------hHHHHHHHHHhcCCccE
Confidence 688999999988 8899998865 666554
No 8
>PF01029 NusB: NusB family; InterPro: IPR006027 This domain is found in a number of functionally different proteins: NusB a prokaryotic transcription factor involved in antitermination TIM44, the mitochondrial inner membrane translocase subunit RsmB, the 16S rRNA m5C967 methyltransferase NusB is a prokaryotic transcription factor involved in antitermination processes, during which it interacts with the boxA portion of the mRNA nut site. Previous studies have shown that NusB exhibits an all-helical fold, and that the protein from Escherichia coli forms monomers, while Mycobacterium tuberculosis NusB is a dimer. The functional significance of NusB dimerization is unknown. An N-terminal arginine-rich sequence is the probable RNA binding site, exhibiting aromatic residues as potential stacking partners for the RNA bases. The RNA binding region is hidden in the subunit interface of dimeric NusB proteins, such as NusB from M. tuberculosis, suggesting that such dimers have to undergo a considerable conformational change or dissociate for engagement with RNA. In certain organisms, dimerization may be employed to package NusB in an inactive form until recruitment into antitermination complexes [, ]. The antitermination proteins of E. coli are recruited in the replication cycle of Bacteriophage lambda, where they play an important role in switching from the lysogenic to the lytic cycle.; GO: 0003723 RNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1SQG_A 1SQF_A 3IMQ_A 3D3C_C 3D3B_A 1EY1_A 1EYV_A 1TZV_A 1TZT_B 1TZX_B ....
Probab=18.22 E-value=1.6e+02 Score=19.55 Aligned_cols=31 Identities=10% Similarity=0.208 Sum_probs=25.5
Q ss_pred hhHHHHHHHHhcCCCCcccCchHHHHHHHHh
Q 034327 31 DRAEDVIQACFEGNPFKTVPGPFKLFWQCMR 61 (98)
Q Consensus 31 DR~eDvlqa~fegnp~~tvp~~fkLfwrCmR 61 (98)
+.++.+|+.+..++++..+++..+...+++=
T Consensus 61 ~~ld~~i~~~~~~~~~~rl~~~~~~iLrla~ 91 (134)
T PF01029_consen 61 EELDALISKLLKNWPLERLPPVDRAILRLAI 91 (134)
T ss_dssp HHHHHHHHHTSTSSTGGGSGHHHHHHHHHHH
T ss_pred HHHHHHHHHHhccCCccccCHHHHHHHHHHH
Confidence 5678899998889999999988888877653
No 9
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=17.60 E-value=2.3e+02 Score=19.60 Aligned_cols=34 Identities=29% Similarity=0.479 Sum_probs=24.1
Q ss_pred CCcccCchHHHHHHHHhcCCCCCCCCcccccCCCC
Q 034327 45 PFKTVPGPFKLFWQCMRSKPGEEPTEPFTYLQLDP 79 (98)
Q Consensus 45 p~~tvp~~fkLfwrCmRSk~GeEP~dpY~~L~l~p 79 (98)
+....+=-+|-..-=+=.+.|.||. ||++|.=++
T Consensus 49 ~~~~~vW~lRdyL~~~i~~~G~eP~-PfS~L~g~~ 82 (89)
T PF10078_consen 49 PFPEDVWILRDYLNDKIKEQGKEPV-PFSALKGDP 82 (89)
T ss_pred CCcccchHHHHHHHHHHHHcCCCCC-CeeeeCCCc
Confidence 3334444566677777788999995 899997665
No 10
>PF04056 Ssl1: Ssl1-like; InterPro: IPR007198 Ssl1-like proteins are 40 kDa subunits of the transcription factor II H complex. This domain is often found associated with the C2H2 type Zn-finger (IPR007087 from INTERPRO).; GO: 0008270 zinc ion binding, 0006281 DNA repair, 0006355 regulation of transcription, DNA-dependent
Probab=17.46 E-value=82 Score=24.08 Aligned_cols=17 Identities=24% Similarity=0.581 Sum_probs=14.2
Q ss_pred hHHHHHHHHhcCCCCcc
Q 034327 32 RAEDVIQACFEGNPFKT 48 (98)
Q Consensus 32 R~eDvlqa~fegnp~~t 48 (98)
-++++++.||+-||...
T Consensus 24 ~l~~Fv~eff~qNPiSq 40 (193)
T PF04056_consen 24 ALEEFVREFFDQNPISQ 40 (193)
T ss_pred HHHHHHHHHHhcCChhh
Confidence 45889999999999854
Done!