Query 034684
Match_columns 87
No_of_seqs 21 out of 23
Neff 2.3
Searched_HMMs 46136
Date Fri Mar 29 05:25:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034684.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034684hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0782 Predicted diacylglycer 50.6 9.1 0.0002 35.1 1.5 26 11-37 609-634 (1004)
2 PF13227 DUF4035: Protein of u 38.2 33 0.00072 21.6 2.3 39 10-58 5-43 (53)
3 PF14216 DUF4326: Domain of un 29.5 46 0.001 22.0 2.0 30 9-38 19-48 (86)
4 PF13465 zf-H2C2_2: Zinc-finge 27.4 21 0.00045 18.4 0.0 10 21-30 9-18 (26)
5 PF06747 CHCH: CHCH domain; I 25.6 42 0.0009 17.7 1.0 15 52-66 4-18 (35)
6 PF01029 NusB: NusB family; I 22.4 1.2E+02 0.0026 19.8 2.9 30 31-60 61-90 (134)
7 smart00571 DDT domain in diffe 22.4 1.3E+02 0.0028 18.4 2.9 33 33-65 30-62 (63)
8 COG1948 MUS81 ERCC4-type nucle 19.7 96 0.0021 24.6 2.4 28 32-69 74-102 (254)
9 PHA01474 nonstructural protein 19.5 55 0.0012 20.7 0.8 13 50-62 13-25 (52)
10 KOG4304 Transcriptional repres 19.4 19 0.00042 27.9 -1.5 28 19-46 40-67 (250)
No 1
>KOG0782 consensus Predicted diacylglycerol kinase [Signal transduction mechanisms]
Probab=50.65 E-value=9.1 Score=35.14 Aligned_cols=26 Identities=38% Similarity=0.838 Sum_probs=21.2
Q ss_pred CCCCCCCCCCcCCCCcCccchhHHHHH
Q 034684 11 ESPWGTPEGEHRQPKAHRCNDRAEDVI 37 (87)
Q Consensus 11 ~s~~g~~~~~~~~~rphRCNDR~eDvl 37 (87)
.-|||.| |||-.++|-||+|=.-.||
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=38.25 E-value=33 Score=21.61 Aligned_cols=39 Identities=31% Similarity=0.512 Sum_probs=31.7
Q ss_pred CCCCCCCCCCCcCCCCcCccchhHHHHHHHHhhCCCCcccCchHHHHHH
Q 034684 10 RESPWGTPEGEHRQPKAHRCNDRAEDVIQACFEGNPFKTVPGPFKLFWQ 58 (87)
Q Consensus 10 r~s~~g~~~~~~~~~rphRCNDR~eDvlqa~fegn~~~tvp~~fkLfwr 58 (87)
|+||.|. ||=|=|...+..|.+...+-+.-..-|-+||.
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 67778999999999998888866667777874
No 3
>PF14216 DUF4326: Domain of unknown function (DUF4326)
Probab=29.53 E-value=46 Score=21.97 Aligned_cols=30 Identities=17% Similarity=0.313 Sum_probs=15.8
Q ss_pred CCCCCCCCCCCCcCCCCcCccchhHHHHHH
Q 034684 9 RRESPWGTPEGEHRQPKAHRCNDRAEDVIQ 38 (87)
Q Consensus 9 ~r~s~~g~~~~~~~~~rphRCNDR~eDvlq 38 (87)
-|.|+||+|-.-....-.-.|-+++.+.|.
T Consensus 19 gR~s~wGNPf~~~~~~~R~~~v~~yr~~l~ 48 (86)
T PF14216_consen 19 GRPSKWGNPFRVGEDGDREEAVEKYREWLW 48 (86)
T ss_pred CCCCcCCCCCcCCCCCCHHHHHHHHHHHHH
Confidence 368999999544432222334444444443
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=27.42 E-value=21 Score=18.38 Aligned_cols=10 Identities=30% Similarity=0.630 Sum_probs=8.6
Q ss_pred cCCCCcCccc
Q 034684 21 HRQPKAHRCN 30 (87)
Q Consensus 21 ~~~~rphRCN 30 (87)
|.+.|||.|+
T Consensus 9 H~~~k~~~C~ 18 (26)
T PF13465_consen 9 HTGEKPYKCP 18 (26)
T ss_dssp HSSSSSEEES
T ss_pred cCCCCCCCCC
Confidence 7788999986
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=25.61 E-value=42 Score=17.71 Aligned_cols=15 Identities=13% Similarity=0.488 Sum_probs=11.8
Q ss_pred hHHHHHHHHhcCCCC
Q 034684 52 PFKLFWQCMRSKPGE 66 (87)
Q Consensus 52 ~fkLfwrCmRSk~Ge 66 (87)
.++.++.|+++..++
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
>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=22.43 E-value=1.2e+02 Score=19.76 Aligned_cols=30 Identities=10% Similarity=0.242 Sum_probs=25.1
Q ss_pred hhHHHHHHHHhhCCCCcccCchHHHHHHHH
Q 034684 31 DRAEDVIQACFEGNPFKTVPGPFKLFWQCM 60 (87)
Q Consensus 31 DR~eDvlqa~fegn~~~tvp~~fkLfwrCm 60 (87)
+.+..+|+.+..++++..++...+...+.+
T Consensus 61 ~~ld~~i~~~~~~~~~~rl~~~~~~iLrla 90 (134)
T PF01029_consen 61 EELDALISKLLKNWPLERLPPVDRAILRLA 90 (134)
T ss_dssp HHHHHHHHHTSTSSTGGGSGHHHHHHHHHH
T ss_pred HHHHHHHHHHhccCCccccCHHHHHHHHHH
Confidence 567889999888999999998888877765
No 7
>smart00571 DDT domain in different transcription and chromosome remodeling factors.
Probab=22.36 E-value=1.3e+02 Score=18.35 Aligned_cols=33 Identities=15% Similarity=0.110 Sum_probs=20.7
Q ss_pred HHHHHHHHhhCCCCcccCchHHHHHHHHhcCCC
Q 034684 33 AEDVIQACFEGNPFKTVPGPFKLFWQCMRSKPG 65 (87)
Q Consensus 33 ~eDvlqa~fegn~~~tvp~~fkLfwrCmRSk~G 65 (87)
++|+++|+-+-++..-+-.....+.+++...+|
T Consensus 30 l~~f~~Al~~~~~~~ll~ei~~~LL~~i~~d~~ 62 (63)
T smart00571 30 LEDFIAALKCRDQNGLLTEVHVVLLRAILKDEG 62 (63)
T ss_pred HHHHHHHHhcCCcchHHHHHHHHHHHHHHhCCC
Confidence 788888877665554444445556666666555
No 8
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=19.69 E-value=96 Score=24.62 Aligned_cols=28 Identities=32% Similarity=0.508 Sum_probs=22.3
Q ss_pred hHHHHHHHHhhCCCCcccCchHHHHHHHHhcC-CCCCCC
Q 034684 32 RAEDVIQACFEGNPFKTVPGPFKLFWQCMRSK-PGEEPT 69 (87)
Q Consensus 32 R~eDvlqa~fegn~~~tvp~~fkLfwrCmRSk-~GeEP~ 69 (87)
+..|+++|+++| +||=||-|=+ .|..|+
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 7899998865 555553
No 9
>PHA01474 nonstructural protein
Probab=19.49 E-value=55 Score=20.73 Aligned_cols=13 Identities=38% Similarity=0.935 Sum_probs=10.3
Q ss_pred CchHHHHHHHHhc
Q 034684 50 PGPFKLFWQCMRS 62 (87)
Q Consensus 50 p~~fkLfwrCmRS 62 (87)
...|.-||.|+|-
T Consensus 13 ysrfssfwscari 25 (52)
T PHA01474 13 YSRFSSFWSCARI 25 (52)
T ss_pred ehhhhhhhhhhhe
Confidence 3468899999984
No 10
>KOG4304 consensus Transcriptional repressors of the hairy/E(spl) family (contains HLH) [Transcription]
Probab=19.42 E-value=19 Score=27.89 Aligned_cols=28 Identities=21% Similarity=0.475 Sum_probs=24.3
Q ss_pred CCcCCCCcCccchhHHHHHHHHhhCCCC
Q 034684 19 GEHRQPKAHRCNDRAEDVIQACFEGNPF 46 (87)
Q Consensus 19 ~~~~~~rphRCNDR~eDvlqa~fegn~~ 46 (87)
|-+|+.|=++|=|.|.|+|..++..+.-
T Consensus 40 EKkRRaRIN~~L~eLK~Li~e~~~~~~~ 67 (250)
T KOG4304|consen 40 EKKRRARINRCLDELKDLIPEALKKDGQ 67 (250)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhcch
Confidence 5678889999999999999999988743
Done!