Query 034460
Match_columns 94
No_of_seqs 109 out of 327
Neff 4.2
Searched_HMMs 46136
Date Fri Mar 29 03:06:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034460.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034460hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3399 Predicted Yippee-type 100.0 1.4E-38 3.1E-43 225.4 -3.3 80 3-82 40-119 (122)
2 PF03226 Yippee-Mis18: Yippee 99.9 2.1E-24 4.5E-29 143.1 3.9 64 4-71 26-93 (96)
3 PF11648 RIG-I_C-RD: C-termina 81.6 1.6 3.4E-05 30.5 2.7 40 9-48 35-74 (123)
4 PF08600 Rsm1: Rsm1-like; Int 56.6 12 0.00026 24.8 2.5 21 34-54 19-40 (91)
5 PF03811 Zn_Tnp_IS1: InsA N-te 51.2 8.4 0.00018 21.9 0.9 27 33-59 4-31 (36)
6 COG3791 Uncharacterized conser 45.8 9.2 0.0002 26.7 0.6 24 28-51 63-86 (133)
7 PF10246 MRP-S35: Mitochondria 45.6 16 0.00035 25.7 1.8 51 9-64 11-67 (104)
8 PF10058 DUF2296: Predicted in 45.2 7.2 0.00016 23.9 0.0 35 9-48 2-36 (54)
9 PF14976 FAM72: FAM72 protein 44.0 20 0.00043 26.7 2.2 25 28-52 65-89 (150)
10 PF01641 SelR: SelR domain; I 43.6 14 0.00031 26.3 1.4 26 28-54 81-106 (124)
11 TIGR00357 methionine-R-sulfoxi 36.9 18 0.00038 26.2 1.0 23 28-51 84-106 (134)
12 PF14803 Nudix_N_2: Nudix N-te 35.6 14 0.0003 20.8 0.2 14 36-49 2-15 (34)
13 PF04828 GFA: Glutathione-depe 34.7 23 0.00049 21.6 1.1 20 28-47 42-61 (92)
14 PRK04016 DNA-directed RNA poly 34.6 9.7 0.00021 24.4 -0.6 18 33-50 3-20 (62)
15 PF02945 Endonuclease_7: Recom 33.2 6.3 0.00014 26.0 -1.7 16 32-47 50-65 (81)
16 PRK05508 methionine sulfoxide 31.9 24 0.00052 25.2 1.0 18 32-49 77-94 (119)
17 PF13248 zf-ribbon_3: zinc-rib 31.1 15 0.00032 19.0 -0.2 13 32-44 14-26 (26)
18 PRK05417 glutathione-dependent 30.7 36 0.00077 25.8 1.8 39 30-73 89-128 (191)
19 COG1644 RPB10 DNA-directed RNA 30.6 13 0.00028 24.1 -0.5 18 33-50 3-20 (63)
20 PF01194 RNA_pol_N: RNA polyme 29.8 8.9 0.00019 24.4 -1.4 20 33-52 3-22 (60)
21 PRK00222 methionine sulfoxide 29.7 27 0.00058 25.6 1.0 19 33-51 91-109 (142)
22 PF10083 DUF2321: Uncharacteri 28.7 12 0.00026 28.0 -1.0 26 22-47 56-81 (158)
23 TIGR02820 formald_GSH S-(hydro 27.2 44 0.00096 25.2 1.8 21 27-48 83-103 (182)
24 PF13240 zinc_ribbon_2: zinc-r 27.1 19 0.00042 18.4 -0.1 11 34-44 13-23 (23)
25 PLN00032 DNA-directed RNA poly 25.8 17 0.00037 23.9 -0.6 17 33-49 3-19 (71)
26 PF10955 DUF2757: Protein of u 23.2 41 0.00089 22.2 0.8 11 36-46 6-16 (76)
27 PF09814 HECT_2: HECT-like Ubi 22.6 41 0.00088 26.2 0.8 13 33-45 192-204 (354)
28 PHA02565 49 recombination endo 21.6 23 0.0005 26.5 -0.7 20 26-47 49-68 (157)
29 PF02150 RNA_POL_M_15KD: RNA p 21.5 40 0.00086 18.7 0.4 10 35-44 2-11 (35)
30 PF07154 DUF1392: Protein of u 21.5 97 0.0021 23.1 2.6 35 2-36 83-118 (150)
31 KOG3497 DNA-directed RNA polym 21.2 47 0.001 21.7 0.8 19 32-50 2-20 (69)
No 1
>KOG3399 consensus Predicted Yippee-type zinc-binding protein [General function prediction only]
Probab=100.00 E-value=1.4e-38 Score=225.41 Aligned_cols=80 Identities=54% Similarity=0.830 Sum_probs=77.8
Q ss_pred cccccccccccccCcCCccceEeeeeceEEeeeeeeecCCceeeeeeeecccccCcccceEEEEecceeCCCCCcceeee
Q 034460 3 TIDHLSLTDSVNVSVGEKEERLMMTGMHTVADIFCVGCGSIVGWKYETAHEKSQKYKEGKSVLERFKVSGPDGSNYWVSH 82 (94)
Q Consensus 3 t~~~~lf~~vvNv~~g~~e~r~m~TG~H~V~DI~C~~C~~~lGWkY~~A~e~sQKYKEGKfILE~~~i~~~~g~~~~~~~ 82 (94)
+|+||||++|+||+.|+.|+|.|+||+|+|+||+|..|++.|||||+.|||+||||||||||||+++|.+++|.+.|..+
T Consensus 40 ~G~AyLf~~vvNv~~ge~e~R~mlTG~h~V~di~C~~C~~~~GWkYe~a~e~sQkyKEGk~ilE~~~i~~~~g~~~~~~~ 119 (122)
T KOG3399|consen 40 TGRAYLFNRVVNVIIGETEQRVMLTGLHTVADIFCVLCGTGLGWKYEHAYEKSQKYKEGKFILELAEIFKPEGWDLEVGA 119 (122)
T ss_pred CCcchhhhhhhhheechHHHHHHHHhHHhhcchhhhhcCCCcceeeeeccCchhhhcCcchHHHHHHhcCCCCchhhcCC
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999998844
No 2
>PF03226 Yippee-Mis18: Yippee zinc-binding/DNA-binding /Mis18, centromere assembly; InterPro: IPR004910 This entry represents the Yippee-like (YPEL) family of putative zinc-binding proteins which is highly conserved among eukaryotes. The first protein in this family to be characterised, the Yippee protein from Drosophila, was identified by yeast interaction trap screen as a protein that physically interacts with moth hemolin []. It was subsequently found to be a member of a highly conserved family of proteins found in diverse eukaryotes including plants, animals and fungi []. Mammals contain five members of this family, YPEL1 to YPEL5, while other organisms tend to contain only two or three members. The mammalian proteins all appear to localise in the nucleus. YPEL1-4 are located in an unknown structure located on or close to the mitotic apparatus in the mitotic phase, whereas in the interphase they are located in the nuclei and nucleoli. In contrast, YPEL5 is localised to the centrosome and nucleus during interphase and at the mitotic spindle during mitosis, suggesting a function distinct from that of YPEL1-4. The localisation of the YPEL proteins suggests a novel, thopugh still unknown, function involved in cell division.
Probab=99.90 E-value=2.1e-24 Score=143.07 Aligned_cols=64 Identities=53% Similarity=0.900 Sum_probs=60.7
Q ss_pred ccccccccccccCcCCccceEeeeec----eEEeeeeeeecCCceeeeeeeecccccCcccceEEEEeccee
Q 034460 4 IDHLSLTDSVNVSVGEKEERLMMTGM----HTVADIFCVGCGSIVGWKYETAHEKSQKYKEGKSVLERFKVS 71 (94)
Q Consensus 4 ~~~~lf~~vvNv~~g~~e~r~m~TG~----H~V~DI~C~~C~~~lGWkY~~A~e~sQKYKEGKfILE~~~i~ 71 (94)
+++|||+ ||..+++++|.|+||. |+|+||+|++|++.|||||++|+++ |+||||+||||++.|.
T Consensus 26 ~~a~l~~---~v~~~~~~~~~~~t~~~~~~~~~~~l~C~~C~~~lGwkY~~a~~~-~~~k~g~file~~~i~ 93 (96)
T PF03226_consen 26 GKAYLFN---NVSNGVPVDRELMTGETGGDHTVRDLFCSGCNTILGWKYESAPEE-QKYKEGKFILEKASIS 93 (96)
T ss_pred ccEEEEe---eeeecccccceEEEeeCCCCEEEEEeEcccCChhHCcEEEEcCHh-HhhhCCEEEEEhhHEE
Confidence 5899998 8888888999999999 9999999999999999999999999 9999999999999885
No 3
>PF11648 RIG-I_C-RD: C-terminal domain of RIG-I; InterPro: IPR021673 This family of proteins represents the regulatory domain RD of RIG-I, a protein which initiates a signalling cascade that provides essential antiviral protection for the host. The RD domain binds viral RNA, activating the RIG-I ATPase by RNA-dependent dimerisation. The structure of RD contains a zinc-binding domain and is thought to confer ligand specificity []. ; GO: 0016817 hydrolase activity, acting on acid anhydrides; PDB: 2RQB_A 3GA3_A 2W4R_D 3EQT_A 2RQA_A 2RMJ_A 3NCU_A 2QFD_C 2QFB_D 3TMI_A ....
Probab=81.61 E-value=1.6 Score=30.52 Aligned_cols=40 Identities=18% Similarity=0.190 Sum_probs=30.7
Q ss_pred cccccccCcCCccceEeeeeceEEeeeeeeecCCceeeee
Q 034460 9 LTDSVNVSVGEKEERLMMTGMHTVADIFCVGCGSIVGWKY 48 (94)
Q Consensus 9 f~~vvNv~~g~~e~r~m~TG~H~V~DI~C~~C~~~lGWkY 48 (94)
|...+.+...|++.....-+-+....|+|..|+..+|-.+
T Consensus 35 F~~~~~~~~~~~~~~~~~~d~~~~~~I~C~~C~~~wG~~m 74 (123)
T PF11648_consen 35 FWERYIVRPHPKPLQKSFGDWEPNGKIHCKNCGQDWGIMM 74 (123)
T ss_dssp HHCTEEEEECSSCTSEEESSSEEEEEEEETSTSBEEEEEE
T ss_pred ceeeEEeccCCccccceecceEeCCEEEcCCCChHhhhhe
Confidence 4466677777766444455788999999999999999755
No 4
>PF08600 Rsm1: Rsm1-like; InterPro: IPR013909 This entry contains Nuclear-interacting partner of ALK (NIPA) and NIPA like proteins, as well as mRNA export factor Rsm1, all of which contain a C3HC-type zinc finger. The domain represented in this entry is found C-terminal to the zinc-finger like domain IPR012935 from INTERPRO. Rsm1 is involved in mRNA export from the nucleus []. NIPA is an essential component of an SCF-type E3 ligase complex, SCF(NIPA), a complex that controls mitotic entry by mediating ubiquitination and subsequent degradation of cyclin B1 (CCNB1). Its cell-cycle-dependent phosphorylation regulates the assembly of the SCF(NIPA) complex, restricting CCNB1 ubiquitination activity to interphase. Its inactivation results in nuclear accumulation of CCNB1 in interphase and premature mitotic entry [].
Probab=56.60 E-value=12 Score=24.75 Aligned_cols=21 Identities=19% Similarity=0.564 Sum_probs=16.2
Q ss_pred eeeeeecCCcee-eeeeeeccc
Q 034460 34 DIFCVGCGSIVG-WKYETAHEK 54 (94)
Q Consensus 34 DI~C~~C~~~lG-WkY~~A~e~ 54 (94)
-+.|..|...|| |.|-.....
T Consensus 19 ~~~C~~C~Rr~GLW~f~~~~ss 40 (91)
T PF08600_consen 19 LLSCSYCFRRLGLWMFKSKESS 40 (91)
T ss_pred eEEccccCcEeeeeecccCccC
Confidence 578999999999 877554443
No 5
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=51.19 E-value=8.4 Score=21.92 Aligned_cols=27 Identities=26% Similarity=0.432 Sum_probs=21.8
Q ss_pred eeeeeeecCCce-eeeeeeecccccCcc
Q 034460 33 ADIFCVGCGSIV-GWKYETAHEKSQKYK 59 (94)
Q Consensus 33 ~DI~C~~C~~~l-GWkY~~A~e~sQKYK 59 (94)
-+|+|..|++.- --|+-+.-.-.|+|.
T Consensus 4 i~v~CP~C~s~~~v~k~G~~~~G~qryr 31 (36)
T PF03811_consen 4 IDVHCPRCQSTEGVKKNGKSPSGHQRYR 31 (36)
T ss_pred EeeeCCCCCCCCcceeCCCCCCCCEeEe
Confidence 378999999988 777777777777774
No 6
>COG3791 Uncharacterized conserved protein [Function unknown]
Probab=45.81 E-value=9.2 Score=26.70 Aligned_cols=24 Identities=25% Similarity=0.517 Sum_probs=17.9
Q ss_pred eceEEeeeeeeecCCceeeeeeee
Q 034460 28 GMHTVADIFCVGCGSIVGWKYETA 51 (94)
Q Consensus 28 G~H~V~DI~C~~C~~~lGWkY~~A 51 (94)
+.+.+.-.||..|+++|-|+....
T Consensus 63 ~s~~~~r~FC~~CGs~l~~~~~~~ 86 (133)
T COG3791 63 SSGSAGRGFCPTCGSPLFWRGPDE 86 (133)
T ss_pred ecCCCCCeecccCCCceEEecCCC
Confidence 344555569999999999977543
No 7
>PF10246 MRP-S35: Mitochondrial ribosomal protein MRP-S35; InterPro: IPR019375 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This is a family of short mitochondrial ribosomal proteins, less than 200 amino acids long. MRP-S35 was proposed as a more appropriate name to this group of proteins [].
Probab=45.56 E-value=16 Score=25.67 Aligned_cols=51 Identities=27% Similarity=0.405 Sum_probs=32.4
Q ss_pred cccccccCcCCccceEeeeec--eEEeeeeeeecCCceeeeee----eecccccCcccceEE
Q 034460 9 LTDSVNVSVGEKEERLMMTGM--HTVADIFCVGCGSIVGWKYE----TAHEKSQKYKEGKSV 64 (94)
Q Consensus 9 f~~vvNv~~g~~e~r~m~TG~--H~V~DI~C~~C~~~lGWkY~----~A~e~sQKYKEGKfI 64 (94)
+.+--=+..|++++|. ++|. |.|.|- =---+|||+- +.-..+++|..|-=+
T Consensus 11 LR~S~fi~lG~~~gk~-V~G~I~hvv~dd----LYIDfG~KFhcVc~rp~~~~~~y~~G~rV 67 (104)
T PF10246_consen 11 LRNSPFIQLGDPEGKI-VIGKIFHVVDDD----LYIDFGGKFHCVCKRPAVNGEKYVRGSRV 67 (104)
T ss_pred hcCChhhhcCCccCCE-EEEEEEEEecCc----eEEEeCCceeEEEecccccccccccCCEE
Confidence 3333345689988876 6777 888762 2234688764 233467889998644
No 8
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=45.19 E-value=7.2 Score=23.92 Aligned_cols=35 Identities=20% Similarity=0.317 Sum_probs=26.4
Q ss_pred cccccccCcCCccceEeeeeceEEeeeeeeecCCceeeee
Q 034460 9 LTDSVNVSVGEKEERLMMTGMHTVADIFCVGCGSIVGWKY 48 (94)
Q Consensus 9 f~~vvNv~~g~~e~r~m~TG~H~V~DI~C~~C~~~lGWkY 48 (94)
|++++.+..|..+ |+...--.+.|..|.+.=|---
T Consensus 2 ~Dki~d~L~G~d~-----~~~~~r~aLIC~~C~~hNGla~ 36 (54)
T PF10058_consen 2 FDKILDVLLGDDP-----TSPSNRYALICSKCFSHNGLAP 36 (54)
T ss_pred hHHHHHHHhCCCC-----ccccCceeEECcccchhhcccc
Confidence 6788889998877 4444445567999999998743
No 9
>PF14976 FAM72: FAM72 protein
Probab=44.04 E-value=20 Score=26.67 Aligned_cols=25 Identities=36% Similarity=0.777 Sum_probs=20.7
Q ss_pred eceEEeeeeeeecCCceeeeeeeec
Q 034460 28 GMHTVADIFCVGCGSIVGWKYETAH 52 (94)
Q Consensus 28 G~H~V~DI~C~~C~~~lGWkY~~A~ 52 (94)
-.=.++|+-|..|+..+|+.....-
T Consensus 65 C~C~~~d~aC~~CGn~vGYhV~~PC 89 (150)
T PF14976_consen 65 CKCKIQDIACLGCGNIVGYHVVVPC 89 (150)
T ss_pred CceEeeeeeeecCCCeeeeEEEEEc
Confidence 3458999999999999999876554
No 10
>PF01641 SelR: SelR domain; InterPro: IPR002579 Peptide methionine sulphoxide reductase (Msr) reverses the inactivation of many proteins due to the oxidation of critical methionine residues by reducing methionine sulphoxide, Met(O), to methionine []. It is present in most living organisms, and the cognate structural gene belongs to the so-called minimum gene set [, ]. The domains: MsrA and MsrB, reduce different epimeric forms of methionine sulphoxide. This group represents MsrB, the crystal structure of which has been determined to 1.8A []. The overall structure shows no resemblance to the structures of MsrA (IPR002569 from INTERPRO) from other organisms; though the active sites show approximate mirror symmetry. In each case, conserved amino acid motifs mediate the stereo-specific recognition and reduction of the substrate. Unlike the MsrA domain, the MsrB domain activates the cysteine or selenocysteine nucleophile through a unique Cys-Arg-Asp/Glu catalytic triad. The collapse of the reaction intermediate most likely results in the formation of a sulphenic or selenenic acid moiety. Regeneration of the active site occurs through a series of thiol-disulphide exchange steps involving another active site Cys residue and thioredoxin. In a number of pathogenic bacteria, including Neisseria gonorrhoeae, the MsrA and MsrB domains are fused; the MsrA being N-terminal to MsrB. This arrangement is reversed in Treponema pallidum. In N. gonorrhoeae and Neisseria meningitidis, a thioredoxin domain is fused to the N terminus. This may function to reduce the active sites of the downstream MsrA and MsrB domains. ; GO: 0008113 peptide-methionine-(S)-S-oxide reductase activity, 0055114 oxidation-reduction process; PDB: 1L1D_A 3E0O_D 2KZN_A 3HCG_B 3HCH_A 2L1U_A 3MAO_A 2K8D_A 3HCJ_A 3HCI_A ....
Probab=43.57 E-value=14 Score=26.30 Aligned_cols=26 Identities=27% Similarity=0.675 Sum_probs=19.7
Q ss_pred eceEEeeeeeeecCCceeeeeeeeccc
Q 034460 28 GMHTVADIFCVGCGSIVGWKYETAHEK 54 (94)
Q Consensus 28 G~H~V~DI~C~~C~~~lGWkY~~A~e~ 54 (94)
|+.. ..|.|..|+..||--......+
T Consensus 81 g~~R-~Ev~C~~Cg~HLGHVF~DGp~~ 106 (124)
T PF01641_consen 81 GMVR-TEVRCARCGSHLGHVFDDGPPP 106 (124)
T ss_dssp SSEE-EEEEETTTCCEEEEEESTSSTT
T ss_pred CceE-EEEEecCCCCccccEeCCCCCC
Confidence 4443 4689999999999987766654
No 11
>TIGR00357 methionine-R-sulfoxide reductase. This model describes a domain found in PilB, a protein important for pilin expression, N-terminal to a domain coextensive to with the known peptide methionine sulfoxide reductase (MsrA), a protein repair enzyme, of E. coli. Among the early completed genomes, this module is found if and only if MsrA is also found, whether N-terminal to MsrA (as for Helicobacter pylori), C-terminal (as for Treponema pallidum), or in a separate polypeptide. Although the function of this region is not clear, an auxiliary function to MsrA is suggested.
Probab=36.92 E-value=18 Score=26.24 Aligned_cols=23 Identities=22% Similarity=0.671 Sum_probs=17.7
Q ss_pred eceEEeeeeeeecCCceeeeeeee
Q 034460 28 GMHTVADIFCVGCGSIVGWKYETA 51 (94)
Q Consensus 28 G~H~V~DI~C~~C~~~lGWkY~~A 51 (94)
|+.. ..|.|..|+..||--+...
T Consensus 84 gm~R-tEv~C~~Cg~HLGHVF~DG 106 (134)
T TIGR00357 84 GMIR-TEVRCRNCDAHLGHVFDDG 106 (134)
T ss_pred CcEE-EEEEecCCCCccCcccCCC
Confidence 5544 4699999999999866543
No 12
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=35.61 E-value=14 Score=20.79 Aligned_cols=14 Identities=29% Similarity=0.774 Sum_probs=6.9
Q ss_pred eeeecCCceeeeee
Q 034460 36 FCVGCGSIVGWKYE 49 (94)
Q Consensus 36 ~C~~C~~~lGWkY~ 49 (94)
||..|+..|-++..
T Consensus 2 fC~~CG~~l~~~ip 15 (34)
T PF14803_consen 2 FCPQCGGPLERRIP 15 (34)
T ss_dssp B-TTT--B-EEE--
T ss_pred ccccccChhhhhcC
Confidence 79999999988765
No 13
>PF04828 GFA: Glutathione-dependent formaldehyde-activating enzyme; InterPro: IPR006913 The GFA family consists mainly of glutathione-dependent formaldehyde-activating enzymes, but also includes centromere protein V and a fission yeast protein described as uncharacterised lyase. Glutathione-dependent formaldehyde-activating enzyme catalyse the condensation of formaldehyde and glutathione to S-hydroxymethylglutathione. All known members of this family contain 5 strongly conserved cysteine residues.; GO: 0016846 carbon-sulfur lyase activity, 0008152 metabolic process; PDB: 3FAC_B 1XA8_A 1X6M_B.
Probab=34.72 E-value=23 Score=21.60 Aligned_cols=20 Identities=30% Similarity=0.444 Sum_probs=13.5
Q ss_pred eceEEeeeeeeecCCceeee
Q 034460 28 GMHTVADIFCVGCGSIVGWK 47 (94)
Q Consensus 28 G~H~V~DI~C~~C~~~lGWk 47 (94)
....+.-.||..|++.|.+.
T Consensus 42 s~~~~~r~FC~~CGs~l~~~ 61 (92)
T PF04828_consen 42 SGKGVERYFCPTCGSPLFSE 61 (92)
T ss_dssp TTSSCEEEEETTT--EEEEE
T ss_pred CCCcCcCcccCCCCCeeecc
Confidence 34455568999999999975
No 14
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=34.55 E-value=9.7 Score=24.44 Aligned_cols=18 Identities=28% Similarity=0.746 Sum_probs=15.5
Q ss_pred eeeeeeecCCceeeeeee
Q 034460 33 ADIFCVGCGSIVGWKYET 50 (94)
Q Consensus 33 ~DI~C~~C~~~lGWkY~~ 50 (94)
-+|.|-+|+..+|=+|++
T Consensus 3 iPvRCFTCGkvi~~~we~ 20 (62)
T PRK04016 3 IPVRCFTCGKVIAEKWEE 20 (62)
T ss_pred CCeEecCCCCChHHHHHH
Confidence 468999999999988765
No 15
>PF02945 Endonuclease_7: Recombination endonuclease VII; InterPro: IPR004211 This family of proteins which includes Bacteriophage T4 endonuclease VII, Mycobacteriophage D29 gene 59, and other as yet uncharacterised proteins. The T4 endonuclease VII (Endo VII) recognises a broad spectrum of DNA substrates ranging from branched DNAs to single base mismatches. The structure of this enzyme has been resolved and it was found that the monomers form an elongated, intertwined molecular dimer that exibits extreme domain swapping. Two pairs of antiparallel helices which form a novel 'four-helix cross' motif are the major dimerisation elements [].; PDB: 3GOX_A 3FC3_A 1EN7_B 1E7L_B 2QNF_A 2QNC_A 1E7D_A.
Probab=33.19 E-value=6.3 Score=25.99 Aligned_cols=16 Identities=25% Similarity=0.696 Sum_probs=14.8
Q ss_pred EeeeeeeecCCceeee
Q 034460 32 VADIFCVGCGSIVGWK 47 (94)
Q Consensus 32 V~DI~C~~C~~~lGWk 47 (94)
||-+-|..|+..+|+-
T Consensus 50 vRGlLC~~CN~~lG~~ 65 (81)
T PF02945_consen 50 VRGLLCRSCNTALGKV 65 (81)
T ss_dssp EEEEEEHHHHHHHHHC
T ss_pred chhhhhhHHhhhhccc
Confidence 9999999999999974
No 16
>PRK05508 methionine sulfoxide reductase B; Provisional
Probab=31.94 E-value=24 Score=25.17 Aligned_cols=18 Identities=33% Similarity=0.894 Sum_probs=15.0
Q ss_pred EeeeeeeecCCceeeeee
Q 034460 32 VADIFCVGCGSIVGWKYE 49 (94)
Q Consensus 32 V~DI~C~~C~~~lGWkY~ 49 (94)
=..|.|..|+..||--+.
T Consensus 77 RtEv~C~~C~~HLGHVF~ 94 (119)
T PRK05508 77 RTEIVCANCGGHLGHVFE 94 (119)
T ss_pred EEEEEeCCCCCccCcccC
Confidence 356999999999998654
No 17
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=31.12 E-value=15 Score=19.04 Aligned_cols=13 Identities=31% Similarity=0.807 Sum_probs=9.2
Q ss_pred EeeeeeeecCCce
Q 034460 32 VADIFCVGCGSIV 44 (94)
Q Consensus 32 V~DI~C~~C~~~l 44 (94)
..+-||..|++.|
T Consensus 14 ~~~~fC~~CG~~L 26 (26)
T PF13248_consen 14 PDAKFCPNCGAKL 26 (26)
T ss_pred cccccChhhCCCC
Confidence 3456888888765
No 18
>PRK05417 glutathione-dependent formaldehyde-activating enzyme; Provisional
Probab=30.68 E-value=36 Score=25.79 Aligned_cols=39 Identities=18% Similarity=0.188 Sum_probs=24.8
Q ss_pred eEEeeeeeeecCCceeeeeeee-cccccCcccceEEEEecceeCC
Q 034460 30 HTVADIFCVGCGSIVGWKYETA-HEKSQKYKEGKSVLERFKVSGP 73 (94)
Q Consensus 30 H~V~DI~C~~C~~~lGWkY~~A-~e~sQKYKEGKfILE~~~i~~~ 73 (94)
..+.--||..|++.|-++.+.. +. -.|..+|=...+-++
T Consensus 89 ~~i~R~FC~~CGS~L~~~~e~~~~~-----~pgl~fV~~gllDd~ 128 (191)
T PRK05417 89 ATIQRHACKECGVHMYGRIENKDHP-----FYGLDFVHTELSQEQ 128 (191)
T ss_pred CCeEeeeCCCCCCccccccccccCC-----CCCeEEEehhhcCCC
Confidence 3455569999999998877622 11 137777766655444
No 19
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=30.63 E-value=13 Score=24.09 Aligned_cols=18 Identities=33% Similarity=0.951 Sum_probs=15.2
Q ss_pred eeeeeeecCCceeeeeee
Q 034460 33 ADIFCVGCGSIVGWKYET 50 (94)
Q Consensus 33 ~DI~C~~C~~~lGWkY~~ 50 (94)
-+|.|-+|+.++|=+|+.
T Consensus 3 iPiRCFsCGkvi~~~w~~ 20 (63)
T COG1644 3 IPVRCFSCGKVIGHKWEE 20 (63)
T ss_pred CceEeecCCCCHHHHHHH
Confidence 478999999999988753
No 20
>PF01194 RNA_pol_N: RNA polymerases N / 8 kDa subunit; InterPro: IPR000268 In eukaryotes, there are three different forms of DNA-dependent RNA polymerases (2.7.7.6 from EC) transcribing different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. In archaebacteria, there is generally a single form of RNA polymerase which also consists of an oligomeric assemblage of 10 to 13 polypeptides. Archaebacterial subunit N (gene rpoN) [] is a small protein of about 8 kDa, it is evolutionary related [] to a 8.3 kDa component shared by all three forms of eukaryotic RNA polymerases (gene RPB10 in yeast and POLR2J in mammals) as well as to African swine fever virus (ASFV) protein CP80R []. There is a conserved region which is located at the N-terminal extremity of these polymerase subunits; this region contains two cysteines that binds a zinc ion [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_N 3HKZ_N 1EF4_A 3H0G_V 2Y0S_N 2R92_J 3M4O_J 3S2D_J 1R9S_J 1Y1W_J ....
Probab=29.79 E-value=8.9 Score=24.43 Aligned_cols=20 Identities=30% Similarity=0.717 Sum_probs=14.6
Q ss_pred eeeeeeecCCceeeeeeeec
Q 034460 33 ADIFCVGCGSIVGWKYETAH 52 (94)
Q Consensus 33 ~DI~C~~C~~~lGWkY~~A~ 52 (94)
-+|.|-+|+.++|=+|++=-
T Consensus 3 iPVRCFTCGkvi~~~~e~y~ 22 (60)
T PF01194_consen 3 IPVRCFTCGKVIGNKWEEYL 22 (60)
T ss_dssp -SSS-STTTSBTCGHHHHHH
T ss_pred CceecCCCCCChhHhHHHHH
Confidence 36889999999998876533
No 21
>PRK00222 methionine sulfoxide reductase B; Provisional
Probab=29.68 E-value=27 Score=25.56 Aligned_cols=19 Identities=21% Similarity=0.663 Sum_probs=15.9
Q ss_pred eeeeeeecCCceeeeeeee
Q 034460 33 ADIFCVGCGSIVGWKYETA 51 (94)
Q Consensus 33 ~DI~C~~C~~~lGWkY~~A 51 (94)
..|.|..|+.+||-.+...
T Consensus 91 tEv~C~~Cg~HLGHVF~DG 109 (142)
T PRK00222 91 TEVRCANCDSHLGHVFPDG 109 (142)
T ss_pred EEEEeCCCCCccCcccCCC
Confidence 4689999999999977654
No 22
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=28.71 E-value=12 Score=27.97 Aligned_cols=26 Identities=31% Similarity=0.624 Sum_probs=21.3
Q ss_pred ceEeeeeceEEeeeeeeecCCceeee
Q 034460 22 ERLMMTGMHTVADIFCVGCGSIVGWK 47 (94)
Q Consensus 22 ~r~m~TG~H~V~DI~C~~C~~~lGWk 47 (94)
+-.+.-|.|.-.+-||..|+.+.=|.
T Consensus 56 ~gv~~~g~~~~~PsYC~~CGkpyPWt 81 (158)
T PF10083_consen 56 EGVFGLGGHYEAPSYCHNCGKPYPWT 81 (158)
T ss_pred CCeeeeCCCCCCChhHHhCCCCCchH
Confidence 34555677888999999999999995
No 23
>TIGR02820 formald_GSH S-(hydroxymethyl)glutathione synthase. The formation of S-(hydroxymethyl)glutathione synthase from glutathione and formaldehyde occurs naturally, but this enzyme speeds its formation in some species as part of a pathway of formaldehyde detoxification.
Probab=27.16 E-value=44 Score=25.16 Aligned_cols=21 Identities=19% Similarity=0.379 Sum_probs=14.2
Q ss_pred eeceEEeeeeeeecCCceeeee
Q 034460 27 TGMHTVADIFCVGCGSIVGWKY 48 (94)
Q Consensus 27 TG~H~V~DI~C~~C~~~lGWkY 48 (94)
.|.+. .--||..|++.|-++.
T Consensus 83 ss~~~-~R~FC~~CGS~L~~~~ 103 (182)
T TIGR02820 83 ASATI-QRHACKGCGTHMYGRI 103 (182)
T ss_pred CCCCE-EeecCCCCCCcccccc
Confidence 34443 4449999999995543
No 24
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=27.08 E-value=19 Score=18.40 Aligned_cols=11 Identities=36% Similarity=1.014 Sum_probs=7.8
Q ss_pred eeeeeecCCce
Q 034460 34 DIFCVGCGSIV 44 (94)
Q Consensus 34 DI~C~~C~~~l 44 (94)
..||..|++.|
T Consensus 13 ~~fC~~CG~~l 23 (23)
T PF13240_consen 13 AKFCPNCGTPL 23 (23)
T ss_pred CcchhhhCCcC
Confidence 34788888764
No 25
>PLN00032 DNA-directed RNA polymerase; Provisional
Probab=25.80 E-value=17 Score=23.92 Aligned_cols=17 Identities=29% Similarity=0.907 Sum_probs=15.0
Q ss_pred eeeeeeecCCceeeeee
Q 034460 33 ADIFCVGCGSIVGWKYE 49 (94)
Q Consensus 33 ~DI~C~~C~~~lGWkY~ 49 (94)
-+|.|-+|+.++|=+|+
T Consensus 3 iPVRCFTCGkvig~~we 19 (71)
T PLN00032 3 IPVRCFTCGKVIGNKWD 19 (71)
T ss_pred CceeecCCCCCcHHHHH
Confidence 37899999999998887
No 26
>PF10955 DUF2757: Protein of unknown function (DUF2757); InterPro: IPR020115 This entry contains proteins with no known function.
Probab=23.17 E-value=41 Score=22.25 Aligned_cols=11 Identities=36% Similarity=1.117 Sum_probs=10.0
Q ss_pred eeeecCCceee
Q 034460 36 FCVGCGSIVGW 46 (94)
Q Consensus 36 ~C~~C~~~lGW 46 (94)
+|+.|+..+|=
T Consensus 6 ~CRHCg~~IG~ 16 (76)
T PF10955_consen 6 YCRHCGTKIGT 16 (76)
T ss_pred EecCCCCEEEE
Confidence 69999999995
No 27
>PF09814 HECT_2: HECT-like Ubiquitin-conjugating enzyme (E2)-binding; InterPro: IPR019193 This entry consists of E3 ubiquitin-protein ligases which accept ubiquitin from specific E2 ubiquitin-conjugating enzymes, and transfer it to substrates, generally promoting their degradation by the proteasome [].
Probab=22.56 E-value=41 Score=26.23 Aligned_cols=13 Identities=31% Similarity=0.639 Sum_probs=11.6
Q ss_pred eeeeeeecCCcee
Q 034460 33 ADIFCVGCGSIVG 45 (94)
Q Consensus 33 ~DI~C~~C~~~lG 45 (94)
.-+.|..|+..||
T Consensus 192 ~~v~C~~C~~~LG 204 (354)
T PF09814_consen 192 RIVRCKRCSSQLG 204 (354)
T ss_pred cEEEeCCCCceeC
Confidence 4588999999999
No 28
>PHA02565 49 recombination endonuclease VII; Provisional
Probab=21.63 E-value=23 Score=26.46 Aligned_cols=20 Identities=25% Similarity=0.539 Sum_probs=17.2
Q ss_pred eeeceEEeeeeeeecCCceeee
Q 034460 26 MTGMHTVADIFCVGCGSIVGWK 47 (94)
Q Consensus 26 ~TG~H~V~DI~C~~C~~~lGWk 47 (94)
.||. ||-+-|..|+..+|+-
T Consensus 49 ~TG~--VRGLLC~~CN~~lG~~ 68 (157)
T PHA02565 49 NAGR--VRGLLCNLCNALEGQM 68 (157)
T ss_pred cccc--ccccCchhhhhhhhhh
Confidence 4665 9999999999999984
No 29
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=21.50 E-value=40 Score=18.75 Aligned_cols=10 Identities=40% Similarity=1.235 Sum_probs=7.8
Q ss_pred eeeeecCCce
Q 034460 35 IFCVGCGSIV 44 (94)
Q Consensus 35 I~C~~C~~~l 44 (94)
+||..|+..|
T Consensus 2 ~FCp~C~nlL 11 (35)
T PF02150_consen 2 RFCPECGNLL 11 (35)
T ss_dssp -BETTTTSBE
T ss_pred eeCCCCCccc
Confidence 4899999877
No 30
>PF07154 DUF1392: Protein of unknown function (DUF1392); InterPro: IPR009824 This family consists of several hypothetical cyanobacterial proteins of around 150 residues in length, which seem to be specific to Anabaena species. The function of this family is unknown.
Probab=21.48 E-value=97 Score=23.10 Aligned_cols=35 Identities=14% Similarity=0.302 Sum_probs=29.4
Q ss_pred ccccccccccccccCc-CCccceEeeeeceEEeeee
Q 034460 2 LTIDHLSLTDSVNVSV-GEKEERLMMTGMHTVADIF 36 (94)
Q Consensus 2 ~t~~~~lf~~vvNv~~-g~~e~r~m~TG~H~V~DI~ 36 (94)
|..|||-.-.+|++.+ ++...+.|+-|.-.|.+-+
T Consensus 83 v~kp~F~LGd~V~~~f~~~~pkqRlIlGv~lv~~~W 118 (150)
T PF07154_consen 83 VQKPAFRLGDRVEFRFYSDGPKQRLILGVFLVNNSW 118 (150)
T ss_pred ccCCceecCCEEEEEecCCCCceEEEEEEEEecCce
Confidence 5679999999999999 6888888999988887644
No 31
>KOG3497 consensus DNA-directed RNA polymerase, subunit RPB10 [Transcription]
Probab=21.24 E-value=47 Score=21.68 Aligned_cols=19 Identities=42% Similarity=0.914 Sum_probs=15.7
Q ss_pred EeeeeeeecCCceeeeeee
Q 034460 32 VADIFCVGCGSIVGWKYET 50 (94)
Q Consensus 32 V~DI~C~~C~~~lGWkY~~ 50 (94)
+-+|.|-+|+..+|=|.+.
T Consensus 2 IiPiRCFtCGKvig~KWe~ 20 (69)
T KOG3497|consen 2 IIPIRCFTCGKVIGDKWET 20 (69)
T ss_pred eeeeEeeeccccccccHHH
Confidence 4579999999999987653
Done!