Query 537021.9.peg.880_1
Match_columns 43
No_of_seqs 1 out of 3
Neff 1.0
Searched_HMMs 39220
Date Wed May 25 02:53:13 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i peg_880.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 pfam02943 FeThRed_B Ferredoxin 58.7 4.3 0.00011 22.5 1.0 12 22-33 74-85 (105)
2 pfam06520 consensus 47.0 17 0.00044 19.2 2.6 22 21-42 32-53 (186)
3 TIGR02387 rpoC1_cyan DNA-direc 46.3 14 0.00035 19.7 2.0 28 12-39 50-78 (625)
4 TIGR02386 rpoC_TIGR DNA-direct 44.5 7.6 0.00019 21.1 0.4 17 17-33 44-61 (1552)
5 PRK10030 putative peptidoglyca 34.2 33 0.00085 17.7 2.4 20 21-40 46-65 (199)
6 cd00153 RalGDS_RA This CD repr 27.7 34 0.00086 17.7 1.5 15 7-21 17-31 (87)
7 PRK11470 hypothetical protein; 24.1 62 0.0016 16.3 2.3 24 19-42 30-53 (200)
8 COG4802 FtrB Ferredoxin-thiore 23.2 37 0.00094 17.5 1.0 12 21-32 78-89 (110)
9 COG5610 Predicted hydrolase (H 20.2 43 0.0011 17.1 0.8 15 15-29 168-182 (635)
10 TIGR01130 ER_PDI_fam protein d 17.8 34 0.00087 17.6 -0.1 4 24-27 29-33 (522)
No 1
>pfam02943 FeThRed_B Ferredoxin thioredoxin reductase catalytic beta chain.
Probab=58.67 E-value=4.3 Score=22.46 Aligned_cols=12 Identities=50% Similarity=1.309 Sum_probs=9.6
Q ss_pred CCEEEEEEEEEE
Q ss_conf 450440144488
Q 537021.9.peg.8 22 KKWCHCGIFFQV 33 (43)
Q Consensus 22 kkwchcgiffqv 33 (43)
++-||||+|..-
T Consensus 74 ~~~ChC~Lfvt~ 85 (105)
T pfam02943 74 RKECHCGLFLTP 85 (105)
T ss_pred CCCEEEEEEECC
T ss_conf 173348867667
No 2
>pfam06520 consensus
Probab=46.96 E-value=17 Score=19.25 Aligned_cols=22 Identities=23% Similarity=0.422 Sum_probs=17.7
Q ss_pred CCCEEEEEEEEEEECCEEEEEE
Q ss_conf 7450440144488336378850
Q 537021.9.peg.8 21 NKKWCHCGIFFQVVGNGFLLLN 42 (43)
Q Consensus 21 nkkwchcgiffqvvgngfllln 42 (43)
+..|-||||++..-|..++++.
T Consensus 32 ~S~~SHvGIIv~~~g~~~~V~E 53 (186)
T pfam06520 32 RCWYNHVGIIIGHNGKDYLVAE 53 (186)
T ss_pred CCCCCCEEEEEEECCCEEEEEE
T ss_conf 8987624899987796689998
No 3
>TIGR02387 rpoC1_cyan DNA-directed RNA polymerase, gamma subunit; InterPro: IPR012755 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 kD, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. The RNA polymerase gamma subunit, encoded by the rpoC1 gene, is found in cyanobacteria and corresponds to the N-terminal region the beta' subunit, encoded by rpoC, in other bacteria. The equivalent subunit in plastids and chloroplasts is designated beta', while the product of the rpoC2 gene is designated beta''.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006350 transcription.
Probab=46.32 E-value=14 Score=19.75 Aligned_cols=28 Identities=32% Similarity=0.829 Sum_probs=20.7
Q ss_pred EEEECCCCCCCCE-EEEEEEEEEECCEEE
Q ss_conf 7873146897450-440144488336378
Q 537021.9.peg.8 12 LLYSQEMTPNKKW-CHCGIFFQVVGNGFL 39 (43)
Q Consensus 12 llysqemtpnkkw-chcgiffqvvgngfl 39 (43)
|.-..-..|.|.| ||||-+-.|--.|..
T Consensus 50 lfCe~ifGPskdWeC~CGkykrvrhrGiv 78 (625)
T TIGR02387 50 LFCEKIFGPSKDWECYCGKYKRVRHRGIV 78 (625)
T ss_pred EEEHHCCCCCCCCCCCCCCEEEEEECCEE
T ss_conf 00010137886641104640155422126
No 4
>TIGR02386 rpoC_TIGR DNA-directed RNA polymerase, beta' subunit; InterPro: IPR012754 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 kD, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This entry represents the beta-prime subunit, RpoC, found in most bacteria. It excludes some, mainly cyanobacterial, species where RpoC is replaced by two homologous proteins that include an additional domain. One arm of the "claw" is predominantly formed by this subunit, the other being predominantly formed by the beta subunit. The active site of the enzyme is defined by three invariant aspartate residues within the beta-prime subunit .; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006350 transcription.
Probab=44.53 E-value=7.6 Score=21.14 Aligned_cols=17 Identities=41% Similarity=1.093 Sum_probs=11.8
Q ss_pred CCCCCCCE-EEEEEEEEE
Q ss_conf 46897450-440144488
Q 537021.9.peg.8 17 EMTPNKKW-CHCGIFFQV 33 (43)
Q Consensus 17 emtpnkkw-chcgiffqv 33 (43)
=.-|.|.| |+||-|=.+
T Consensus 44 IFGPtKDwEC~CGKYK~~ 61 (1552)
T TIGR02386 44 IFGPTKDWECYCGKYKKV 61 (1552)
T ss_pred CCCCCCCCEECCCCCCCC
T ss_conf 558887623056753223
No 5
>PRK10030 putative peptidoglycan peptidase; Provisional
Probab=34.16 E-value=33 Score=17.70 Aligned_cols=20 Identities=10% Similarity=0.434 Sum_probs=15.2
Q ss_pred CCCEEEEEEEEEEECCEEEE
Q ss_conf 74504401444883363788
Q 537021.9.peg.8 21 NKKWCHCGIFFQVVGNGFLL 40 (43)
Q Consensus 21 nkkwchcgiffqvvgngfll 40 (43)
+..|-||||.+..-|+-+.+
T Consensus 46 ~S~~SHvGIi~~~~~~~~V~ 65 (199)
T PRK10030 46 HSDYSHTGMIVKRNKKPYVF 65 (199)
T ss_pred CCCCCCEEEEEEECCCEEEE
T ss_conf 89976068999888967999
No 6
>cd00153 RalGDS_RA This CD represents the C-terminal Ras-associating (RA) domain of three closely related guanine-nucleotide exchange factors (GEF's), Ral guanine nucleotide dissociation stimulator (RalGDS), RalGDS-like (RGL), and RalGDS-like factor (RLF). The RalGDS proteins are downstream effectors of the Ras-related protein Ral, providing a mechanism for Ral activation by extracellular signals. The RA domain is structurally similar to ubiquitin and exists in a number of other signalling proteins including AF6, rasfadin, SNX27, CYR1, and STE50.
Probab=27.70 E-value=34 Score=17.67 Aligned_cols=15 Identities=47% Similarity=0.789 Sum_probs=13.5
Q ss_pred CEEEEEEEECCCCCC
Q ss_conf 024787873146897
Q 537021.9.peg.8 7 TYRAILLYSQEMTPN 21 (43)
Q Consensus 7 tyraillysqemtpn 21 (43)
-|+.|++-||+-||.
T Consensus 17 ~YKSIllt~qDktP~ 31 (87)
T cd00153 17 LYKSILLTSQDKAPQ 31 (87)
T ss_pred EEEEEEEECCCCCHH
T ss_conf 799999852886779
No 7
>PRK11470 hypothetical protein; Provisional
Probab=24.10 E-value=62 Score=16.25 Aligned_cols=24 Identities=29% Similarity=0.375 Sum_probs=18.2
Q ss_pred CCCCCEEEEEEEEEEECCEEEEEE
Q ss_conf 897450440144488336378850
Q 537021.9.peg.8 19 TPNKKWCHCGIFFQVVGNGFLLLN 42 (43)
Q Consensus 19 tpnkkwchcgiffqvvgngfllln 42 (43)
..+-.|-||||.+..-|++++.+.
T Consensus 30 aT~S~~sHvGIIv~~~G~~~~V~E 53 (200)
T PRK11470 30 ASNCWSNHVGIIIGHNGEDFLVAE 53 (200)
T ss_pred HHCCCCCCEEEEEEECCCCEEEEE
T ss_conf 748975524799985598408998
No 8
>COG4802 FtrB Ferredoxin-thioredoxin reductase, catalytic subunit [Energy production and conversion]
Probab=23.25 E-value=37 Score=17.48 Aligned_cols=12 Identities=25% Similarity=0.858 Sum_probs=9.3
Q ss_pred CCCEEEEEEEEE
Q ss_conf 745044014448
Q 537021.9.peg.8 21 NKKWCHCGIFFQ 32 (43)
Q Consensus 21 nkkwchcgiffq 32 (43)
..+-||||.|+.
T Consensus 78 e~g~C~C~Lyl~ 89 (110)
T COG4802 78 EYGECYCGLYLS 89 (110)
T ss_pred HHCCEEEEEEEC
T ss_conf 507454888846
No 9
>COG5610 Predicted hydrolase (HAD superfamily) [General function prediction only]
Probab=20.20 E-value=43 Score=17.13 Aligned_cols=15 Identities=47% Similarity=0.847 Sum_probs=11.8
Q ss_pred ECCCCCCCCEEEEEE
Q ss_conf 314689745044014
Q 537021.9.peg.8 15 SQEMTPNKKWCHCGI 29 (43)
Q Consensus 15 sqemtpnkkwchcgi 29 (43)
.+|-..+++|-|||-
T Consensus 168 k~EnVd~~~w~H~GD 182 (635)
T COG5610 168 KLENVDPKKWIHCGD 182 (635)
T ss_pred HHCCCCHHHEEEECC
T ss_conf 631798113578457
No 10
>TIGR01130 ER_PDI_fam protein disulfide isomerases; InterPro: IPR005792 This family represents eukaryotic protein disulphide isomerases retained in the endoplasmic reticulum (ER) and other closely related forms. Some members have been assigned alternative or additional functions such as prolyl 4-hydroxylase and dolichyl-diphosphooligosaccharide-protein glycotransferase. Members of this family have at least two protein-disulphide domains, each similar to thioredoxin but with the redox-active disulphide in the motif PWCGHCK, and an ER retention signal at the extreme C-terminus (KDEL, HDEL, and similar motifs). ; GO: 0016853 isomerase activity, 0005783 endoplasmic reticulum.
Probab=17.76 E-value=34 Score=17.65 Aligned_cols=4 Identities=100% Similarity=3.590 Sum_probs=0.0
Q ss_pred EE-EE
Q ss_conf 04-40
Q 537021.9.peg.8 24 WC-HC 27 (43)
Q Consensus 24 wc-hc 27 (43)
|| ||
T Consensus 29 WCGHC 33 (522)
T TIGR01130 29 WCGHC 33 (522)
T ss_pred CCCHH
T ss_conf 34411
Done!