Query 033124
Match_columns 126
No_of_seqs 119 out of 1020
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 10:06:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033124.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033124hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0229 Conserved domain frequ 100.0 2.8E-42 6.2E-47 260.1 7.8 87 1-122 39-126 (140)
2 TIGR00357 methionine-R-sulfoxi 100.0 2.8E-41 6E-46 253.7 8.4 86 1-122 37-123 (134)
3 PRK00222 methionine sulfoxide 100.0 1.7E-40 3.8E-45 251.4 8.1 86 1-122 40-126 (142)
4 PF01641 SelR: SelR domain; I 100.0 1E-39 2.2E-44 242.4 6.6 86 1-121 34-120 (124)
5 PRK05508 methionine sulfoxide 100.0 2.1E-38 4.5E-43 234.2 7.9 83 1-122 30-114 (119)
6 KOG0856 Predicted pilin-like t 100.0 1.3E-35 2.8E-40 224.8 6.6 86 1-122 51-139 (146)
7 PRK14018 trifunctional thiored 100.0 2.8E-34 6.1E-39 252.2 8.3 86 1-122 415-502 (521)
8 PRK05550 bifunctional methioni 100.0 1.2E-33 2.5E-38 233.3 6.8 82 1-121 33-116 (283)
9 PF03226 Yippee-Mis18: Yippee 95.8 0.0095 2.1E-07 41.3 3.0 39 70-121 55-93 (96)
10 TIGR01384 TFS_arch transcripti 83.0 1.2 2.6E-05 31.0 2.5 20 68-87 58-77 (104)
11 PF04828 GFA: Glutathione-depe 81.1 2.3 5E-05 27.7 3.3 23 67-89 43-65 (92)
12 PF09855 DUF2082: Nucleic-acid 76.5 2 4.2E-05 28.8 1.8 27 5-39 1-27 (64)
13 PF10955 DUF2757: Protein of u 76.5 2.5 5.5E-05 29.4 2.5 14 1-14 1-14 (76)
14 PF08271 TF_Zn_Ribbon: TFIIB z 73.7 3 6.6E-05 25.0 2.0 14 1-14 16-29 (43)
15 PRK13130 H/ACA RNA-protein com 60.4 7.2 0.00016 25.6 1.9 23 6-28 19-41 (56)
16 KOG3507 DNA-directed RNA polym 57.1 7.6 0.00016 26.2 1.6 19 2-20 18-36 (62)
17 smart00659 RPOLCX RNA polymera 52.3 10 0.00022 23.4 1.5 13 4-16 2-14 (44)
18 PF15288 zf-CCHC_6: Zinc knuck 50.9 5 0.00011 24.8 -0.0 17 72-89 1-17 (40)
19 PF10058 DUF2296: Predicted in 50.3 11 0.00025 24.2 1.6 22 69-90 19-40 (54)
20 COG1645 Uncharacterized Zn-fin 41.8 8.3 0.00018 29.3 -0.1 11 4-14 28-38 (131)
21 PF03811 Zn_Tnp_IS1: InsA N-te 41.6 37 0.0008 20.2 2.7 26 68-94 1-26 (36)
22 PRK00398 rpoP DNA-directed RNA 40.8 36 0.00079 20.4 2.7 11 4-14 3-13 (46)
23 PF03604 DNA_RNApol_7kD: DNA d 39.1 19 0.0004 21.0 1.1 11 5-15 1-11 (32)
24 COG1594 RPB9 DNA-directed RNA 38.5 25 0.00053 25.6 2.0 18 70-87 70-87 (113)
25 PRK00423 tfb transcription ini 37.2 28 0.0006 29.0 2.3 29 2-40 28-56 (310)
26 COG1885 Uncharacterized protei 31.3 18 0.00039 27.0 0.3 13 2-14 47-59 (115)
27 TIGR02098 MJ0042_CXXC MJ0042 f 31.1 29 0.00063 19.8 1.1 12 71-82 24-35 (38)
28 TIGR02820 formald_GSH S-(hydro 30.8 47 0.001 26.3 2.6 19 69-87 86-104 (182)
29 KOG2691 RNA polymerase II subu 30.5 29 0.00062 25.9 1.2 20 69-88 69-89 (113)
30 PF10601 zf-LITAF-like: LITAF- 30.2 28 0.00061 22.8 1.1 16 69-84 55-70 (73)
31 PF11672 DUF3268: Protein of u 30.0 31 0.00066 25.1 1.3 23 73-97 32-55 (102)
32 COG1644 RPB10 DNA-directed RNA 29.6 17 0.00037 24.6 -0.1 17 71-87 3-19 (63)
33 COG1996 RPC10 DNA-directed RNA 29.6 26 0.00056 22.5 0.8 12 3-14 5-16 (49)
34 smart00714 LITAF Possible memb 28.6 24 0.00051 22.8 0.5 61 5-84 4-64 (67)
35 PRK05417 glutathione-dependent 28.2 86 0.0019 25.0 3.7 19 69-87 90-108 (191)
36 PF13248 zf-ribbon_3: zinc-rib 27.9 21 0.00045 19.4 0.1 8 7-14 19-26 (26)
37 PF06397 Desulfoferrod_N: Desu 27.8 33 0.00071 20.6 0.9 12 3-14 5-16 (36)
38 COG1405 SUA7 Transcription ini 26.8 49 0.0011 27.8 2.1 27 2-38 18-44 (285)
39 PF04135 Nop10p: Nucleolar RNA 26.6 42 0.00091 21.7 1.4 24 6-29 19-42 (53)
40 PF13842 Tnp_zf-ribbon_2: DDE_ 26.1 54 0.0012 18.8 1.6 13 70-82 14-26 (32)
41 PRK04016 DNA-directed RNA poly 25.8 25 0.00054 23.6 0.2 16 72-87 4-19 (62)
42 PF04810 zf-Sec23_Sec24: Sec23 25.5 29 0.00064 20.6 0.5 11 73-83 3-13 (40)
43 PF03117 Herpes_UL49_1: UL49 f 25.1 31 0.00068 28.8 0.7 20 5-31 106-125 (245)
44 PF13717 zinc_ribbon_4: zinc-r 24.9 45 0.00098 19.5 1.2 11 69-79 22-32 (36)
45 PF06170 DUF983: Protein of un 24.5 39 0.00084 23.6 1.0 22 70-91 6-28 (86)
46 COG2126 RPL37A Ribosomal prote 24.2 33 0.00072 23.0 0.6 18 69-86 13-30 (61)
47 COG3478 Predicted nucleic-acid 24.1 1E+02 0.0022 21.2 2.9 11 70-80 38-48 (68)
48 PF13719 zinc_ribbon_5: zinc-r 23.1 44 0.00095 19.5 0.9 11 69-79 22-32 (37)
49 PF06677 Auto_anti-p27: Sjogre 22.5 33 0.00073 21.0 0.3 9 6-14 19-27 (41)
50 cd00350 rubredoxin_like Rubred 22.2 42 0.0009 19.1 0.6 11 4-14 1-11 (33)
51 cd00729 rubredoxin_SM Rubredox 22.0 52 0.0011 19.0 1.0 11 4-14 2-12 (34)
52 PF11781 RRN7: RNA polymerase 21.0 51 0.0011 19.5 0.9 12 2-13 23-34 (36)
53 PRK00420 hypothetical protein; 20.9 36 0.00078 25.1 0.2 10 5-14 24-33 (112)
54 PF13408 Zn_ribbon_recom: Reco 20.9 51 0.0011 19.8 0.9 13 2-14 3-15 (58)
55 COG2260 Predicted Zn-ribbon RN 20.7 72 0.0016 21.3 1.6 23 6-28 19-41 (59)
56 PF13240 zinc_ribbon_2: zinc-r 20.0 57 0.0012 17.4 0.8 18 7-32 2-19 (23)
No 1
>COG0229 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=2.8e-42 Score=260.11 Aligned_cols=87 Identities=31% Similarity=0.644 Sum_probs=83.0
Q ss_pred CCcEEEecccccccCCCCCCCCCCCCccCCCCCcccccc-ccCCCCeEEeecCCcccccccccccCCCceEEEEecCccC
Q 033124 1 MASIYSCKECGTNLNLNTSHLYPATVYFPAGNKGTLSFA-MIDSTKFRLEKEDKIRPFFETLDYWGIQRKRTKIKCNNCG 79 (126)
Q Consensus 1 ~~G~Y~C~~Cg~~Lnlsss~~f~S~~Kf~sg~~GwpSF~-~i~~~~v~~~~d~~~~p~f~~~~s~g~~~~Rtev~C~~Cg 79 (126)
.+|+|+|++||.|| |+|++||+||| |||||+ ||++++|+..+|.++ +|.||||+|++|+
T Consensus 39 ~~GiY~c~~cg~pL-------F~S~~KfdSgc-GWPSF~~pi~~~~I~~~~D~S~------------gM~RtEVrc~~c~ 98 (140)
T COG0229 39 EKGIYVCIVCGEPL-------FSSEDKFDSGC-GWPSFTKPISPDAITYKEDRSH------------GMVRTEVRCANCD 98 (140)
T ss_pred CCceEEeecCCCcc-------ccccccccCCC-CCccccccCCcccceEeeccCC------------CcEEEEEEecCCC
Confidence 37999999999999 99999999999 999999 999999999999998 8899999999999
Q ss_pred CccccccCCCCCCCCCCCCcCCCCCCCCCCCceeEeeccceee
Q 033124 80 ALLGYIYDDGPPAVDTPGQFHFGPSQVIPRYPRYRLKTKALRI 122 (126)
Q Consensus 80 ~HLGhvF~Dgp~pt~~~~~~~~~~~~~~~~~~rY~i~~~AL~p 122 (126)
+||||||+|||+|+|+ +|||||++||+=
T Consensus 99 sHLGHVF~DGP~~tgg---------------lRYCINSasL~F 126 (140)
T COG0229 99 SHLGHVFPDGPPPTGG---------------LRYCINSASLRF 126 (140)
T ss_pred CccccccCCCCCCCCC---------------eeEeecchheee
Confidence 9999999999999984 899999999984
No 2
>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=100.00 E-value=2.8e-41 Score=253.71 Aligned_cols=86 Identities=33% Similarity=0.605 Sum_probs=81.3
Q ss_pred CCcEEEecccccccCCCCCCCCCCCCccCCCCCcccccc-ccCCCCeEEeecCCcccccccccccCCCceEEEEecCccC
Q 033124 1 MASIYSCKECGTNLNLNTSHLYPATVYFPAGNKGTLSFA-MIDSTKFRLEKEDKIRPFFETLDYWGIQRKRTKIKCNNCG 79 (126)
Q Consensus 1 ~~G~Y~C~~Cg~~Lnlsss~~f~S~~Kf~sg~~GwpSF~-~i~~~~v~~~~d~~~~p~f~~~~s~g~~~~Rtev~C~~Cg 79 (126)
.+|+|+|++||+|| |+|++||+||| |||||+ +|++++|++++|.++ +|+||||+|++||
T Consensus 37 ~~G~Y~C~~Cg~pL-------F~S~~KfdSg~-GWPSF~~~i~~~~V~~~~D~s~------------gm~RtEv~C~~Cg 96 (134)
T TIGR00357 37 EEGIYVDITCGEPL-------FSSEDKFDSGC-GWPSFYKPISEEVVAYERDESH------------GMIRTEVRCRNCD 96 (134)
T ss_pred CCeEEEccCCCCcc-------ccccchhcCCC-CCcCcCcccCCCceEEeecCCC------------CcEEEEEEecCCC
Confidence 37999999999999 99999999999 999999 998999999999887 7899999999999
Q ss_pred CccccccCCCCCCCCCCCCcCCCCCCCCCCCceeEeeccceee
Q 033124 80 ALLGYIYDDGPPAVDTPGQFHFGPSQVIPRYPRYRLKTKALRI 122 (126)
Q Consensus 80 ~HLGhvF~Dgp~pt~~~~~~~~~~~~~~~~~~rY~i~~~AL~p 122 (126)
+||||||+|||+||+ +|||||++||+=
T Consensus 97 ~HLGHVF~DGP~ptg----------------~RyCINs~sL~F 123 (134)
T TIGR00357 97 AHLGHVFDDGPEPTG----------------LRYCINSAALKF 123 (134)
T ss_pred CccCcccCCCCCCCC----------------ceEeecceeEec
Confidence 999999999998876 799999999973
No 3
>PRK00222 methionine sulfoxide reductase B; Provisional
Probab=100.00 E-value=1.7e-40 Score=251.43 Aligned_cols=86 Identities=31% Similarity=0.643 Sum_probs=81.3
Q ss_pred CCcEEEecccccccCCCCCCCCCCCCccCCCCCcccccc-ccCCCCeEEeecCCcccccccccccCCCceEEEEecCccC
Q 033124 1 MASIYSCKECGTNLNLNTSHLYPATVYFPAGNKGTLSFA-MIDSTKFRLEKEDKIRPFFETLDYWGIQRKRTKIKCNNCG 79 (126)
Q Consensus 1 ~~G~Y~C~~Cg~~Lnlsss~~f~S~~Kf~sg~~GwpSF~-~i~~~~v~~~~d~~~~p~f~~~~s~g~~~~Rtev~C~~Cg 79 (126)
.+|+|+|++||+|| |+|++||+||| |||||+ +|++++|++++|.++ +|.||||+|++||
T Consensus 40 ~~G~Y~C~~Cg~pL-------F~S~~Kf~Sg~-GWPSF~~~i~~~~V~~~~D~s~------------gm~RtEv~C~~Cg 99 (142)
T PRK00222 40 EKGIYVCIVCGEPL-------FSSDTKFDSGC-GWPSFTKPIDEEAIRELRDTSH------------GMVRTEVRCANCD 99 (142)
T ss_pred CCeEEEecCCCchh-------cCCcccccCCC-CCcCcCcccCCCceEEeeccCC------------CceEEEEEeCCCC
Confidence 37999999999999 99999999999 999999 998899999999887 7899999999999
Q ss_pred CccccccCCCCCCCCCCCCcCCCCCCCCCCCceeEeeccceee
Q 033124 80 ALLGYIYDDGPPAVDTPGQFHFGPSQVIPRYPRYRLKTKALRI 122 (126)
Q Consensus 80 ~HLGhvF~Dgp~pt~~~~~~~~~~~~~~~~~~rY~i~~~AL~p 122 (126)
+||||||+|||+|++ +|||||++||+=
T Consensus 100 ~HLGHVF~DGP~ptg----------------~RyCINs~sL~F 126 (142)
T PRK00222 100 SHLGHVFPDGPKPTG----------------LRYCINSASLKF 126 (142)
T ss_pred CccCcccCCCCCCCC----------------CEeeeceeeEEe
Confidence 999999999998876 799999999974
No 4
>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=100.00 E-value=1e-39 Score=242.44 Aligned_cols=86 Identities=33% Similarity=0.641 Sum_probs=78.1
Q ss_pred CCcEEEecccccccCCCCCCCCCCCCccCCCCCcccccc-ccCCCCeEEeecCCcccccccccccCCCceEEEEecCccC
Q 033124 1 MASIYSCKECGTNLNLNTSHLYPATVYFPAGNKGTLSFA-MIDSTKFRLEKEDKIRPFFETLDYWGIQRKRTKIKCNNCG 79 (126)
Q Consensus 1 ~~G~Y~C~~Cg~~Lnlsss~~f~S~~Kf~sg~~GwpSF~-~i~~~~v~~~~d~~~~p~f~~~~s~g~~~~Rtev~C~~Cg 79 (126)
.+|+|+|++||+|| |+|++||+||| |||||+ +|++++|+.+.|.++ +|+||||+|++||
T Consensus 34 ~~G~Y~C~~Cg~pL-------F~S~~Kf~Sg~-GWPSF~~~i~~~~v~~~~D~s~------------g~~R~Ev~C~~Cg 93 (124)
T PF01641_consen 34 EEGIYVCAVCGTPL-------FSSDTKFDSGC-GWPSFWQPIPGDAVKEREDFSH------------GMVRTEVRCARCG 93 (124)
T ss_dssp SSEEEEETTTS-EE-------EEGGGEETSSS-SSSEESSCSSTTSEEEEEEECT------------SSEEEEEEETTTC
T ss_pred CCEEEEcCCCCCcc-------ccCcccccCCc-CCccccCcCChHHEEEeccccC------------CceEEEEEecCCC
Confidence 37999999999999 99999999999 999999 998889999999886 7899999999999
Q ss_pred CccccccCCCCCCCCCCCCcCCCCCCCCCCCceeEeecccee
Q 033124 80 ALLGYIYDDGPPAVDTPGQFHFGPSQVIPRYPRYRLKTKALR 121 (126)
Q Consensus 80 ~HLGhvF~Dgp~pt~~~~~~~~~~~~~~~~~~rY~i~~~AL~ 121 (126)
+||||||+|||+|+. ++|||||++||+
T Consensus 94 ~HLGHVF~DGp~~~t---------------g~RyCINS~sL~ 120 (124)
T PF01641_consen 94 SHLGHVFDDGPPPPT---------------GLRYCINSASLK 120 (124)
T ss_dssp CEEEEEESTSSTTCT---------------SCEEEE-GGGEE
T ss_pred CccccEeCCCCCCCC---------------CcEEEeeeeeEE
Confidence 999999999998742 389999999996
No 5
>PRK05508 methionine sulfoxide reductase B; Provisional
Probab=100.00 E-value=2.1e-38 Score=234.23 Aligned_cols=83 Identities=30% Similarity=0.590 Sum_probs=74.0
Q ss_pred CCcEEEecccccccCCCCCCCCCCCCccCCCCCcccccc-ccCCCCeEEeecCCcccccccccccCCCceEEEEecCccC
Q 033124 1 MASIYSCKECGTNLNLNTSHLYPATVYFPAGNKGTLSFA-MIDSTKFRLEKEDKIRPFFETLDYWGIQRKRTKIKCNNCG 79 (126)
Q Consensus 1 ~~G~Y~C~~Cg~~Lnlsss~~f~S~~Kf~sg~~GwpSF~-~i~~~~v~~~~d~~~~p~f~~~~s~g~~~~Rtev~C~~Cg 79 (126)
.+|+|+|++||+|| |+|++||+||| |||||+ +|+ ++|+.++|.+ + +||||+|++||
T Consensus 30 ~~G~Y~C~~Cg~pL-------F~S~~KfdSg~-GWPSF~~~i~-~~v~~~~D~~-------------~-~RtEv~C~~C~ 86 (119)
T PRK05508 30 EKGTYVCKQCGAPL-------YRSEDKFKSGC-GWPSFDDEIK-GAVKRIPDAD-------------G-RRTEIVCANCG 86 (119)
T ss_pred CCeEEEecCCCCcc-------ccccccccCCC-CCcccCcccc-cceEEEecCC-------------C-cEEEEEeCCCC
Confidence 37999999999999 99999999999 999999 885 7899888865 2 69999999999
Q ss_pred CccccccCC-CCCCCCCCCCcCCCCCCCCCCCceeEeeccceee
Q 033124 80 ALLGYIYDD-GPPAVDTPGQFHFGPSQVIPRYPRYRLKTKALRI 122 (126)
Q Consensus 80 ~HLGhvF~D-gp~pt~~~~~~~~~~~~~~~~~~rY~i~~~AL~p 122 (126)
+||||||+| ||+||+ +|||||++||+=
T Consensus 87 ~HLGHVF~d~gp~ptg----------------~RyCINS~sL~F 114 (119)
T PRK05508 87 GHLGHVFEGEGFTPKN----------------TRHCVNSISLKF 114 (119)
T ss_pred CccCcccCCCCCCCCC----------------CEEeecceeEEe
Confidence 999999985 566665 899999999983
No 6
>KOG0856 consensus Predicted pilin-like transcription factor [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.3e-35 Score=224.78 Aligned_cols=86 Identities=29% Similarity=0.635 Sum_probs=80.1
Q ss_pred CCcEEEecccccccCCCCCCCCCCCCccCCCCCcccccc-ccCCCCeEEeecCCcccccccccccCCCceEEEEecCccC
Q 033124 1 MASIYSCKECGTNLNLNTSHLYPATVYFPAGNKGTLSFA-MIDSTKFRLEKEDKIRPFFETLDYWGIQRKRTKIKCNNCG 79 (126)
Q Consensus 1 ~~G~Y~C~~Cg~~Lnlsss~~f~S~~Kf~sg~~GwpSF~-~i~~~~v~~~~d~~~~p~f~~~~s~g~~~~Rtev~C~~Cg 79 (126)
.+|+|+|++|++|| |+|.+||+||| |||+|+ +|.+++|++.+|.+. +++|+||.|++||
T Consensus 51 e~GvY~C~~C~~pL-------ykS~tKfdsgc-GWPAF~e~i~~gaI~r~~d~s~------------~~~R~Ev~Ca~C~ 110 (146)
T KOG0856|consen 51 EEGVYVCAGCGTPL-------YKSTTKFDSGC-GWPAFFEAIGPGAITRTPDNSR------------GGRRTEVSCATCG 110 (146)
T ss_pred CCceEEEeecCCcc-------ccccccccCCC-CCchhhhccCCCceeeccccCC------------CCcceEEEEeecC
Confidence 47999999999999 99999999999 999998 888999999999887 6689999999999
Q ss_pred CccccccC-CCCC-CCCCCCCcCCCCCCCCCCCceeEeeccceee
Q 033124 80 ALLGYIYD-DGPP-AVDTPGQFHFGPSQVIPRYPRYRLKTKALRI 122 (126)
Q Consensus 80 ~HLGhvF~-Dgp~-pt~~~~~~~~~~~~~~~~~~rY~i~~~AL~p 122 (126)
+||||||. |||. ||+ .|||||++||.=
T Consensus 111 ~HLGHVF~~eG~~~Pt~----------------~R~CiNS~sL~F 139 (146)
T KOG0856|consen 111 GHLGHVFKGEGPKTPTD----------------ERHCINSVSLKF 139 (146)
T ss_pred CceeeeecCCCCCCCCC----------------ceeEeeeeeeee
Confidence 99999997 9987 776 699999999963
No 7
>PRK14018 trifunctional thioredoxin/methionine sulfoxide reductase A/B protein; Provisional
Probab=100.00 E-value=2.8e-34 Score=252.16 Aligned_cols=86 Identities=23% Similarity=0.399 Sum_probs=80.3
Q ss_pred CCcEEEecccccccCCCCCCCCCCCCccCCCCCcccccc-ccCCCCeEEeecCCcccccccccccCCCceEEEEecCccC
Q 033124 1 MASIYSCKECGTNLNLNTSHLYPATVYFPAGNKGTLSFA-MIDSTKFRLEKEDKIRPFFETLDYWGIQRKRTKIKCNNCG 79 (126)
Q Consensus 1 ~~G~Y~C~~Cg~~Lnlsss~~f~S~~Kf~sg~~GwpSF~-~i~~~~v~~~~d~~~~p~f~~~~s~g~~~~Rtev~C~~Cg 79 (126)
.+|+|+|++||+|| |+|.+||+||| |||||+ +|++++|++.+|.++ +|.||||+|++||
T Consensus 415 ~~G~y~c~~c~~pL-------f~s~~Kf~sg~-GWPsF~~~i~~~~v~~~~d~s~------------g~~R~Ev~c~~c~ 474 (521)
T PRK14018 415 KPGIYVDVVSGEPL-------FSSADKYDSGC-GWPSFTRPIDAKVVTEHDDFSY------------NMRRTEVRSRAAD 474 (521)
T ss_pred CCEEEEecCCCCcc-------ccCcccccCCC-CCcccCcccCcCceEEeeccCC------------CceEEEEEECCCC
Confidence 37999999999999 99999999999 999999 999999999999987 7899999999999
Q ss_pred CccccccCCCCCC-CCCCCCcCCCCCCCCCCCceeEeeccceee
Q 033124 80 ALLGYIYDDGPPA-VDTPGQFHFGPSQVIPRYPRYRLKTKALRI 122 (126)
Q Consensus 80 ~HLGhvF~Dgp~p-t~~~~~~~~~~~~~~~~~~rY~i~~~AL~p 122 (126)
+||||||+|||+| +| +|||||++||+=
T Consensus 475 ~HLGHvf~dgp~~~~g----------------~RyCiNs~~l~f 502 (521)
T PRK14018 475 SHLGHVFPDGPRDKGG----------------LRYCINGASLKF 502 (521)
T ss_pred CcCCcccCCCCCCCCC----------------CEeeeceeEEEe
Confidence 9999999999964 54 899999999973
No 8
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=100.00 E-value=1.2e-33 Score=233.30 Aligned_cols=82 Identities=30% Similarity=0.607 Sum_probs=72.7
Q ss_pred CCcEEEecccccccCCCCCCCCCCCCccCCCCCcccccc-ccCCCCeEEeecCCcccccccccccCCCceEEEEecCccC
Q 033124 1 MASIYSCKECGTNLNLNTSHLYPATVYFPAGNKGTLSFA-MIDSTKFRLEKEDKIRPFFETLDYWGIQRKRTKIKCNNCG 79 (126)
Q Consensus 1 ~~G~Y~C~~Cg~~Lnlsss~~f~S~~Kf~sg~~GwpSF~-~i~~~~v~~~~d~~~~p~f~~~~s~g~~~~Rtev~C~~Cg 79 (126)
.+|+|+|++||+|| |+|++||+||| |||||+ +|+ +++....|.+ +| ||||+|++||
T Consensus 33 ~~G~y~c~~c~~~L-------F~s~~Kf~sg~-GWPsF~~~~~-~~~~~~~d~~-------------~~-R~Ev~c~~c~ 89 (283)
T PRK05550 33 EKGVYLCRRCGAPL-------FRSEDKFNSGC-GWPSFDDEIP-GAVKRLPDAD-------------GR-RTEIVCANCG 89 (283)
T ss_pred CCcEEEcCCCCchh-------cCChhhccCCC-CCcCcCcccC-CccEEEEcCC-------------Cc-eEEEEecCCC
Confidence 37999999999999 99999999999 999999 885 5677777654 33 9999999999
Q ss_pred CccccccC-CCCCCCCCCCCcCCCCCCCCCCCceeEeecccee
Q 033124 80 ALLGYIYD-DGPPAVDTPGQFHFGPSQVIPRYPRYRLKTKALR 121 (126)
Q Consensus 80 ~HLGhvF~-Dgp~pt~~~~~~~~~~~~~~~~~~rY~i~~~AL~ 121 (126)
+||||||+ |||+||+ +|||||++||+
T Consensus 90 ~HLGHvF~ddgp~ptg----------------~RyCiNs~sL~ 116 (283)
T PRK05550 90 AHLGHVFEGEGLTPKN----------------TRHCVNSASLD 116 (283)
T ss_pred CccCcccCCCCCCCCC----------------ccccccccccc
Confidence 99999998 7777775 89999999997
No 9
>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=95.79 E-value=0.0095 Score=41.25 Aligned_cols=39 Identities=18% Similarity=0.578 Sum_probs=28.5
Q ss_pred EEEEecCccCCccccccCCCCCCCCCCCCcCCCCCCCCCCCceeEeecccee
Q 033124 70 RTKIKCNNCGALLGYIYDDGPPAVDTPGQFHFGPSQVIPRYPRYRLKTKALR 121 (126)
Q Consensus 70 Rtev~C~~Cg~HLGhvF~Dgp~pt~~~~~~~~~~~~~~~~~~rY~i~~~AL~ 121 (126)
-..|.|++|+.+||-.|..-+..-. -.. -+|.+..++|.
T Consensus 55 ~~~l~C~~C~~~lGwkY~~a~~~~~------------~k~-g~file~~~i~ 93 (96)
T PF03226_consen 55 VRDLFCSGCNTILGWKYESAPEEQK------------YKE-GKFILEKASIS 93 (96)
T ss_pred EEEeEcccCChhHCcEEEEcCHhHh------------hhC-CEEEEEhhHEE
Confidence 4689999999999999876654311 111 38999988875
No 10
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=82.96 E-value=1.2 Score=31.05 Aligned_cols=20 Identities=25% Similarity=0.634 Sum_probs=14.6
Q ss_pred ceEEEEecCccCCccccccC
Q 033124 68 RKRTKIKCNNCGALLGYIYD 87 (126)
Q Consensus 68 ~~Rtev~C~~Cg~HLGhvF~ 87 (126)
..++++.|.+||.+-...|.
T Consensus 58 ~~~~~~~Cp~Cg~~~a~f~~ 77 (104)
T TIGR01384 58 LPTTRVECPKCGHKEAYYWL 77 (104)
T ss_pred CCcccCCCCCCCCCeeEEEE
Confidence 35789999999866555543
No 11
>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=81.08 E-value=2.3 Score=27.68 Aligned_cols=23 Identities=17% Similarity=0.278 Sum_probs=15.3
Q ss_pred CceEEEEecCccCCccccccCCC
Q 033124 67 QRKRTKIKCNNCGALLGYIYDDG 89 (126)
Q Consensus 67 ~~~Rtev~C~~Cg~HLGhvF~Dg 89 (126)
........|++||.+|.......
T Consensus 43 ~~~~~r~FC~~CGs~l~~~~~~~ 65 (92)
T PF04828_consen 43 GKGVERYFCPTCGSPLFSEDERD 65 (92)
T ss_dssp TSSCEEEEETTT--EEEEEESST
T ss_pred CCcCcCcccCCCCCeeecccCCC
Confidence 44567899999999999763333
No 12
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=76.53 E-value=2 Score=28.80 Aligned_cols=27 Identities=26% Similarity=0.589 Sum_probs=19.7
Q ss_pred EEecccccccCCCCCCCCCCCCccCCCCCcccccc
Q 033124 5 YSCKECGTNLNLNTSHLYPATVYFPAGNKGTLSFA 39 (126)
Q Consensus 5 Y~C~~Cg~~Lnlsss~~f~S~~Kf~sg~~GwpSF~ 39 (126)
|.|..||..- |..+.--.+|. ||-.++
T Consensus 1 y~C~KCg~~~-------~e~~~v~~tgg-~~skiF 27 (64)
T PF09855_consen 1 YKCPKCGNEE-------YESGEVRATGG-GLSKIF 27 (64)
T ss_pred CCCCCCCCcc-------eecceEEccCC-eeEEEE
Confidence 7899999987 77777666665 665543
No 13
>PF10955 DUF2757: Protein of unknown function (DUF2757); InterPro: IPR020115 This entry contains proteins with no known function.
Probab=76.52 E-value=2.5 Score=29.35 Aligned_cols=14 Identities=50% Similarity=1.127 Sum_probs=13.2
Q ss_pred CCcEEEeccccccc
Q 033124 1 MASIYSCKECGTNL 14 (126)
Q Consensus 1 ~~G~Y~C~~Cg~~L 14 (126)
|+..|.|+.||..+
T Consensus 1 Mai~Y~CRHCg~~I 14 (76)
T PF10955_consen 1 MAIHYYCRHCGTKI 14 (76)
T ss_pred CceEEEecCCCCEE
Confidence 78899999999999
No 14
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=73.67 E-value=3 Score=25.00 Aligned_cols=14 Identities=29% Similarity=0.584 Sum_probs=10.7
Q ss_pred CCcEEEeccccccc
Q 033124 1 MASIYSCKECGTNL 14 (126)
Q Consensus 1 ~~G~Y~C~~Cg~~L 14 (126)
+.|.+.|..||.-|
T Consensus 16 ~~g~~vC~~CG~Vl 29 (43)
T PF08271_consen 16 ERGELVCPNCGLVL 29 (43)
T ss_dssp TTTEEEETTT-BBE
T ss_pred CCCeEECCCCCCEe
Confidence 36888999999887
No 15
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=60.39 E-value=7.2 Score=25.56 Aligned_cols=23 Identities=13% Similarity=0.338 Sum_probs=17.2
Q ss_pred EecccccccCCCCCCCCCCCCcc
Q 033124 6 SCKECGTNLNLNTSHLYPATVYF 28 (126)
Q Consensus 6 ~C~~Cg~~Lnlsss~~f~S~~Kf 28 (126)
.|..||.++...--.||+.++||
T Consensus 19 ~CP~CG~~t~~~~P~rfSp~D~y 41 (56)
T PRK13130 19 ICPVCGGKTKNPHPPRFSPEDKY 41 (56)
T ss_pred cCcCCCCCCCCCCCCCCCCCCcc
Confidence 47788888877777777777765
No 16
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=57.14 E-value=7.6 Score=26.15 Aligned_cols=19 Identities=32% Similarity=0.775 Sum_probs=14.5
Q ss_pred CcEEEecccccccCCCCCC
Q 033124 2 ASIYSCKECGTNLNLNTSH 20 (126)
Q Consensus 2 ~G~Y~C~~Cg~~Lnlsss~ 20 (126)
+-+|.|+-||.++.|.+-+
T Consensus 18 ~miYiCgdC~~en~lk~~D 36 (62)
T KOG3507|consen 18 TMIYICGDCGQENTLKRGD 36 (62)
T ss_pred cEEEEeccccccccccCCC
Confidence 3489999999998555544
No 17
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=52.35 E-value=10 Score=23.44 Aligned_cols=13 Identities=46% Similarity=1.114 Sum_probs=10.9
Q ss_pred EEEecccccccCC
Q 033124 4 IYSCKECGTNLNL 16 (126)
Q Consensus 4 ~Y~C~~Cg~~Lnl 16 (126)
+|.|+.||.+.++
T Consensus 2 ~Y~C~~Cg~~~~~ 14 (44)
T smart00659 2 IYICGECGRENEI 14 (44)
T ss_pred EEECCCCCCEeec
Confidence 6999999999733
No 18
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=50.93 E-value=5 Score=24.81 Aligned_cols=17 Identities=47% Similarity=1.064 Sum_probs=12.8
Q ss_pred EEecCccCCccccccCCC
Q 033124 72 KIKCNNCGALLGYIYDDG 89 (126)
Q Consensus 72 ev~C~~Cg~HLGhvF~Dg 89 (126)
++.|.+||+ +||.=.+.
T Consensus 1 k~kC~~CG~-~GH~~t~k 17 (40)
T PF15288_consen 1 KVKCKNCGA-FGHMRTNK 17 (40)
T ss_pred Ccccccccc-ccccccCc
Confidence 368999997 69985444
No 19
>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=50.30 E-value=11 Score=24.17 Aligned_cols=22 Identities=18% Similarity=0.318 Sum_probs=18.2
Q ss_pred eEEEEecCccCCccccccCCCC
Q 033124 69 KRTKIKCNNCGALLGYIYDDGP 90 (126)
Q Consensus 69 ~Rtev~C~~Cg~HLGhvF~Dgp 90 (126)
.|..|.|.+|..|=|-+....+
T Consensus 19 ~r~aLIC~~C~~hNGla~~~~~ 40 (54)
T PF10058_consen 19 NRYALICSKCFSHNGLAPKEEF 40 (54)
T ss_pred CceeEECcccchhhcccccccC
Confidence 6889999999999998864433
No 20
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=41.83 E-value=8.3 Score=29.33 Aligned_cols=11 Identities=45% Similarity=0.990 Sum_probs=9.9
Q ss_pred EEEeccccccc
Q 033124 4 IYSCKECGTNL 14 (126)
Q Consensus 4 ~Y~C~~Cg~~L 14 (126)
.++|..||.||
T Consensus 28 ~~hCp~Cg~PL 38 (131)
T COG1645 28 AKHCPKCGTPL 38 (131)
T ss_pred HhhCcccCCcc
Confidence 37899999999
No 21
>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=41.57 E-value=37 Score=20.18 Aligned_cols=26 Identities=15% Similarity=0.497 Sum_probs=16.7
Q ss_pred ceEEEEecCccCCccccccCCCCCCCC
Q 033124 68 RKRTKIKCNNCGALLGYIYDDGPPAVD 94 (126)
Q Consensus 68 ~~Rtev~C~~Cg~HLGhvF~Dgp~pt~ 94 (126)
|.-++|.|..|++..+ |..-|..+.|
T Consensus 1 Ma~i~v~CP~C~s~~~-v~k~G~~~~G 26 (36)
T PF03811_consen 1 MAKIDVHCPRCQSTEG-VKKNGKSPSG 26 (36)
T ss_pred CCcEeeeCCCCCCCCc-ceeCCCCCCC
Confidence 3568999999999864 3333443333
No 22
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=40.82 E-value=36 Score=20.43 Aligned_cols=11 Identities=36% Similarity=1.129 Sum_probs=10.1
Q ss_pred EEEeccccccc
Q 033124 4 IYSCKECGTNL 14 (126)
Q Consensus 4 ~Y~C~~Cg~~L 14 (126)
.|.|..||..+
T Consensus 3 ~y~C~~CG~~~ 13 (46)
T PRK00398 3 EYKCARCGREV 13 (46)
T ss_pred EEECCCCCCEE
Confidence 69999999997
No 23
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=39.05 E-value=19 Score=20.99 Aligned_cols=11 Identities=45% Similarity=1.280 Sum_probs=8.8
Q ss_pred EEecccccccC
Q 033124 5 YSCKECGTNLN 15 (126)
Q Consensus 5 Y~C~~Cg~~Ln 15 (126)
|.|+.||.+..
T Consensus 1 Y~C~~Cg~~~~ 11 (32)
T PF03604_consen 1 YICGECGAEVE 11 (32)
T ss_dssp EBESSSSSSE-
T ss_pred CCCCcCCCeeE
Confidence 88999998873
No 24
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=38.55 E-value=25 Score=25.61 Aligned_cols=18 Identities=33% Similarity=0.759 Sum_probs=14.2
Q ss_pred EEEEecCccCCccccccC
Q 033124 70 RTKIKCNNCGALLGYIYD 87 (126)
Q Consensus 70 Rtev~C~~Cg~HLGhvF~ 87 (126)
++++.|.+||.+=...|.
T Consensus 70 ~~~~~CpkCg~~ea~y~~ 87 (113)
T COG1594 70 TAKEKCPKCGNKEAYYWQ 87 (113)
T ss_pred cccccCCCCCCceeEEEe
Confidence 447899999998877663
No 25
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=37.19 E-value=28 Score=28.99 Aligned_cols=29 Identities=17% Similarity=0.327 Sum_probs=23.3
Q ss_pred CcEEEecccccccCCCCCCCCCCCCccCCCCCccccccc
Q 033124 2 ASIYSCKECGTNLNLNTSHLYPATVYFPAGNKGTLSFAM 40 (126)
Q Consensus 2 ~G~Y~C~~Cg~~Lnlsss~~f~S~~Kf~sg~~GwpSF~~ 40 (126)
.|.+.|..||.-| .+.--|.|. -|-+|..
T Consensus 28 ~Ge~vC~~CG~Vl---------~e~~iD~g~-EWR~f~~ 56 (310)
T PRK00423 28 RGEIVCADCGLVI---------EENIIDQGP-EWRAFDP 56 (310)
T ss_pred CCeEeecccCCcc---------cccccccCC-CccCCCc
Confidence 6899999999988 555567776 8999974
No 26
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=31.29 E-value=18 Score=26.96 Aligned_cols=13 Identities=31% Similarity=0.774 Sum_probs=11.8
Q ss_pred CcEEEeccccccc
Q 033124 2 ASIYSCKECGTNL 14 (126)
Q Consensus 2 ~G~Y~C~~Cg~~L 14 (126)
-|.++|..||.++
T Consensus 47 ~G~t~CP~Cg~~~ 59 (115)
T COG1885 47 VGSTSCPKCGEPF 59 (115)
T ss_pred cccccCCCCCCcc
Confidence 4889999999997
No 27
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=31.08 E-value=29 Score=19.80 Aligned_cols=12 Identities=33% Similarity=1.082 Sum_probs=9.8
Q ss_pred EEEecCccCCcc
Q 033124 71 TKIKCNNCGALL 82 (126)
Q Consensus 71 tev~C~~Cg~HL 82 (126)
.++.|.+|+..+
T Consensus 24 ~~v~C~~C~~~~ 35 (38)
T TIGR02098 24 GKVRCGKCGHVW 35 (38)
T ss_pred CEEECCCCCCEE
Confidence 489999998754
No 28
>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=30.83 E-value=47 Score=26.33 Aligned_cols=19 Identities=16% Similarity=0.382 Sum_probs=14.1
Q ss_pred eEEEEecCccCCccccccC
Q 033124 69 KRTKIKCNNCGALLGYIYD 87 (126)
Q Consensus 69 ~Rtev~C~~Cg~HLGhvF~ 87 (126)
...+..|.+||++|-+...
T Consensus 86 ~~~R~FC~~CGS~L~~~~~ 104 (182)
T TIGR02820 86 TIQRHACKGCGTHMYGRIE 104 (182)
T ss_pred CEEeecCCCCCCccccccc
Confidence 3455689999999966553
No 29
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=30.54 E-value=29 Score=25.92 Aligned_cols=20 Identities=20% Similarity=0.574 Sum_probs=16.1
Q ss_pred eE-EEEecCccCCccccccCC
Q 033124 69 KR-TKIKCNNCGALLGYIYDD 88 (126)
Q Consensus 69 ~R-tev~C~~Cg~HLGhvF~D 88 (126)
.| ....|.+||.+-+--|+.
T Consensus 69 Prts~~~C~~C~~~eavffQ~ 89 (113)
T KOG2691|consen 69 PRTSDKHCPKCGHREAVFFQA 89 (113)
T ss_pred CccccccCCccCCcceEEEec
Confidence 57 578899999998877764
No 30
>PF10601 zf-LITAF-like: LITAF-like zinc ribbon domain; InterPro: IPR006629 Members of this family display a conserved zinc ribbon structure [] with the motif C-XX-C- separated from the more C-terminal HX-C(P)X-C-X4-G-R motif by a variable region of usually 25-30 (hydrophobic) residues. Although it belongs to one of the zinc finger's fold groups (zinc ribbon), this particular domain was first identified in LPS-induced tumour necrosis alpha factor (LITAF) which is produced in mammalian cells after being challenged with lipopolysaccharide (LPS). The hydrophobic region probably inserts into the membrane rather than traversing it. Such an insertion brings together the N- and C-terminal C-XX-C motifs to form a compact Zn2+-binding structure [].
Probab=30.20 E-value=28 Score=22.76 Aligned_cols=16 Identities=50% Similarity=0.877 Sum_probs=14.0
Q ss_pred eEEEEecCccCCcccc
Q 033124 69 KRTKIKCNNCGALLGY 84 (126)
Q Consensus 69 ~Rtev~C~~Cg~HLGh 84 (126)
+-++-.|.+|++.||.
T Consensus 55 kd~~H~Cp~C~~~lg~ 70 (73)
T PF10601_consen 55 KDVYHYCPNCGAFLGT 70 (73)
T ss_pred cCceEECCCCCCEeEE
Confidence 4589999999999995
No 31
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=29.96 E-value=31 Score=25.07 Aligned_cols=23 Identities=26% Similarity=0.369 Sum_probs=16.5
Q ss_pred EecCccCCccc-cccCCCCCCCCCCC
Q 033124 73 IKCNNCGALLG-YIYDDGPPAVDTPG 97 (126)
Q Consensus 73 v~C~~Cg~HLG-hvF~Dgp~pt~~~~ 97 (126)
-+|..|++++| |-..+. |-|..+
T Consensus 32 y~C~~C~AyVG~H~~t~~--PlGtLA 55 (102)
T PF11672_consen 32 YVCTPCDAYVGCHPGTDI--PLGTLA 55 (102)
T ss_pred EECCCCCceeeeeCCCCC--cCcccC
Confidence 78999999999 765554 445433
No 32
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=29.64 E-value=17 Score=24.58 Aligned_cols=17 Identities=24% Similarity=0.888 Sum_probs=14.8
Q ss_pred EEEecCccCCccccccC
Q 033124 71 TKIKCNNCGALLGYIYD 87 (126)
Q Consensus 71 tev~C~~Cg~HLGhvF~ 87 (126)
+-|+|=.||.-+||.|+
T Consensus 3 iPiRCFsCGkvi~~~w~ 19 (63)
T COG1644 3 IPVRCFSCGKVIGHKWE 19 (63)
T ss_pred CceEeecCCCCHHHHHH
Confidence 35899999999999985
No 33
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=29.56 E-value=26 Score=22.46 Aligned_cols=12 Identities=33% Similarity=0.996 Sum_probs=9.4
Q ss_pred cEEEeccccccc
Q 033124 3 SIYSCKECGTNL 14 (126)
Q Consensus 3 G~Y~C~~Cg~~L 14 (126)
-.|.|+.||..+
T Consensus 5 ~~Y~C~~Cg~~~ 16 (49)
T COG1996 5 MEYKCARCGREV 16 (49)
T ss_pred EEEEhhhcCCee
Confidence 368888888885
No 34
>smart00714 LITAF Possible membrane-associated motif in LPS-induced tumor necrosis factor alpha factor (LITAF), also known as PIG7, and other animal proteins.
Probab=28.60 E-value=24 Score=22.81 Aligned_cols=61 Identities=25% Similarity=0.298 Sum_probs=34.1
Q ss_pred EEecccccccCCCCCCCCCCCCccCCCCCccccccccCCCCeEEeecCCcccccccccccCCCceEEEEecCccCCcccc
Q 033124 5 YSCKECGTNLNLNTSHLYPATVYFPAGNKGTLSFAMIDSTKFRLEKEDKIRPFFETLDYWGIQRKRTKIKCNNCGALLGY 84 (126)
Q Consensus 5 Y~C~~Cg~~Lnlsss~~f~S~~Kf~sg~~GwpSF~~i~~~~v~~~~d~~~~p~f~~~~s~g~~~~Rtev~C~~Cg~HLGh 84 (126)
-.|..|+... .+..++++|...|....-+- + .--.-+.|++.+ ..+.+.-.|.+|++.||.
T Consensus 4 i~Cp~C~~~~--------~T~v~~~~g~~t~~~~~ll~---~--~~~~~~iP~~~~------~~kd~~H~Cp~C~~~lg~ 64 (67)
T smart00714 4 LFCPRCQNNV--------TTRVETETGVCAWLICCLLF---L--LCFCCCLPCCLD------SFKDVNHYCPNCGAFLGT 64 (67)
T ss_pred eECCCCCCEE--------EEEEEEEeChHHHHHHHHHH---H--HHHHHHHHHhcc------cccCccEECCCCCCEeEE
Confidence 4677888774 56667777652233221110 0 000122355432 335688999999999994
No 35
>PRK05417 glutathione-dependent formaldehyde-activating enzyme; Provisional
Probab=28.15 E-value=86 Score=24.96 Aligned_cols=19 Identities=16% Similarity=0.382 Sum_probs=14.3
Q ss_pred eEEEEecCccCCccccccC
Q 033124 69 KRTKIKCNNCGALLGYIYD 87 (126)
Q Consensus 69 ~Rtev~C~~Cg~HLGhvF~ 87 (126)
...+-.|.+||.||-...+
T Consensus 90 ~i~R~FC~~CGS~L~~~~e 108 (191)
T PRK05417 90 TIQRHACKECGVHMYGRIE 108 (191)
T ss_pred CeEeeeCCCCCCccccccc
Confidence 4456699999999965544
No 36
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=27.89 E-value=21 Score=19.35 Aligned_cols=8 Identities=50% Similarity=1.468 Sum_probs=5.2
Q ss_pred eccccccc
Q 033124 7 CKECGTNL 14 (126)
Q Consensus 7 C~~Cg~~L 14 (126)
|..||++|
T Consensus 19 C~~CG~~L 26 (26)
T PF13248_consen 19 CPNCGAKL 26 (26)
T ss_pred ChhhCCCC
Confidence 66677665
No 37
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=27.81 E-value=33 Score=20.61 Aligned_cols=12 Identities=33% Similarity=1.104 Sum_probs=6.9
Q ss_pred cEEEeccccccc
Q 033124 3 SIYSCKECGTNL 14 (126)
Q Consensus 3 G~Y~C~~Cg~~L 14 (126)
-+|.|..||+-.
T Consensus 5 ~~YkC~~CGniV 16 (36)
T PF06397_consen 5 EFYKCEHCGNIV 16 (36)
T ss_dssp EEEE-TTT--EE
T ss_pred cEEEccCCCCEE
Confidence 479999999754
No 38
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=26.83 E-value=49 Score=27.79 Aligned_cols=27 Identities=22% Similarity=0.429 Sum_probs=22.9
Q ss_pred CcEEEecccccccCCCCCCCCCCCCccCCCCCccccc
Q 033124 2 ASIYSCKECGTNLNLNTSHLYPATVYFPAGNKGTLSF 38 (126)
Q Consensus 2 ~G~Y~C~~Cg~~Lnlsss~~f~S~~Kf~sg~~GwpSF 38 (126)
.|-++|+.||.-| .+...+.+- .|-.|
T Consensus 18 ~ge~VC~~CG~Vi---------~~~~id~gp-ewr~f 44 (285)
T COG1405 18 RGEIVCADCGLVL---------EDSLIDPGP-EWRAF 44 (285)
T ss_pred CCeEEeccCCEEe---------ccccccCCC-Ccccc
Confidence 4889999999998 556788887 99999
No 39
>PF04135 Nop10p: Nucleolar RNA-binding protein, Nop10p family; InterPro: IPR007264 H/ACA ribonucleoprotein particles (RNPs) are a family of RNA pseudouridine synthases that specify modification sites through guide RNAs. More than 100 mammalian H/ACA RNAs form an equal number of ribonucleoproteins (RNPs) by associating with the same four core proteins: Cbf5, Gar1, Nhp2 and Nop10. The function of these H/ACA RNPs is essential for biogenesis of the ribosome, splicing of precursor mRNAs (pre-mRNAs), maintenance of telomeres and probably for additional cellular processes []. Recent crystal structures of archaeal H/ACA protein complexes show how the same four proteins accommodate >100 distinct but related H/ACA RNAs []. The complex contains a stable core composed of Cbf5 and Nop10, to which Gar1 and Nhp2 subsequently bind, the complex interacts with snoRNAs []. In eukaryotes Nop10 is a nucleolar protein that is specifically associated with H/ACA snoRNAs. It is essential for normal 18S rRNA production and rRNA pseudouridylation by the ribonucleoprotein particles containing H/ACA snoRNAs (H/ACA snoRNPs). Nop10 is probably necessary for the stability of these RNPs [].; PDB: 2RFK_B 3LWR_B 2HVY_C 3HAX_C 3MQK_B 3LWO_B 3LWV_B 3HAY_C 3HJY_B 2EY4_E ....
Probab=26.59 E-value=42 Score=21.75 Aligned_cols=24 Identities=13% Similarity=0.379 Sum_probs=15.2
Q ss_pred EecccccccCCCCCCCCCCCCccC
Q 033124 6 SCKECGTNLNLNTSHLYPATVYFP 29 (126)
Q Consensus 6 ~C~~Cg~~Lnlsss~~f~S~~Kf~ 29 (126)
.|..||.+.--..-+||+.++||-
T Consensus 19 ~cp~cG~~T~~ahPaRFSPdDky~ 42 (53)
T PF04135_consen 19 KCPPCGGPTESAHPARFSPDDKYS 42 (53)
T ss_dssp BBTTTSSBSEESSSSSS-TTTTTC
T ss_pred ccCCCCCCCcCCcCCCCCCCCccH
Confidence 477778777555556777777663
No 40
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=26.07 E-value=54 Score=18.80 Aligned_cols=13 Identities=31% Similarity=0.754 Sum_probs=11.0
Q ss_pred EEEEecCccCCcc
Q 033124 70 RTKIKCNNCGALL 82 (126)
Q Consensus 70 Rtev~C~~Cg~HL 82 (126)
.|...|.+|+-+|
T Consensus 14 ~T~~~C~~C~v~l 26 (32)
T PF13842_consen 14 DTRYMCSKCDVPL 26 (32)
T ss_pred eeEEEccCCCCcc
Confidence 4999999998665
No 41
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=25.79 E-value=25 Score=23.61 Aligned_cols=16 Identities=19% Similarity=0.810 Sum_probs=14.2
Q ss_pred EEecCccCCccccccC
Q 033124 72 KIKCNNCGALLGYIYD 87 (126)
Q Consensus 72 ev~C~~Cg~HLGhvF~ 87 (126)
-|+|-.||.-+||.++
T Consensus 4 PvRCFTCGkvi~~~we 19 (62)
T PRK04016 4 PVRCFTCGKVIAEKWE 19 (62)
T ss_pred CeEecCCCCChHHHHH
Confidence 5899999999999875
No 42
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=25.52 E-value=29 Score=20.57 Aligned_cols=11 Identities=36% Similarity=1.065 Sum_probs=5.5
Q ss_pred EecCccCCccc
Q 033124 73 IKCNNCGALLG 83 (126)
Q Consensus 73 v~C~~Cg~HLG 83 (126)
++|++|++.|-
T Consensus 3 ~rC~~C~aylN 13 (40)
T PF04810_consen 3 VRCRRCRAYLN 13 (40)
T ss_dssp -B-TTT--BS-
T ss_pred cccCCCCCEEC
Confidence 68999999987
No 43
>PF03117 Herpes_UL49_1: UL49 family; InterPro: IPR004339 UL49 proteins are present in the viral tegument at the surface of the nucleocapsid []. Many of the nonconserved tegument proteins of alpha-herpes viruses play important roles during different steps of the viral replication cycle, such as the shutoff of host cell functions by the vhs protein encoded by UL41 and the transcriptional activation of viral immediate-early genes by the UL48 gene product, VP16. UL49 of Human herpesvirus 1 (HHV-1) has been shown to directly interact with VP16. The UL49 gene products of HHV-1 and Bovine herpesvirus 1 exhibit virus-independent intercellular trafficking of unknown biological function but are dispensable for productive viral replication. Envelope glycoprotein M (gM) and the complex formed by glycoproteins E (gE) and I (gI) are involved in the secondary envelopment of Suid herpesvirus 1 (Pseudorabies virus, PrV) particles in the cytoplasm of infected cells. In the absence of the gE-gI complex and gM, envelopment is blocked and capsids surrounded by tegument proteins accumulate in the cytoplasm. The cytoplasmic domains of gE and gM specifically interact with the C-terminal part of the UL49 gene product of PrV suggesting a role for the protein in secondary envelopment during herpesvirus virion maturation [].; GO: 0016032 viral reproduction, 0019033 viral tegument
Probab=25.11 E-value=31 Score=28.78 Aligned_cols=20 Identities=30% Similarity=0.502 Sum_probs=16.4
Q ss_pred EEecccccccCCCCCCCCCCCCccCCC
Q 033124 5 YSCKECGTNLNLNTSHLYPATVYFPAG 31 (126)
Q Consensus 5 Y~C~~Cg~~Lnlsss~~f~S~~Kf~sg 31 (126)
=.|..||+-| +--+.||..+
T Consensus 106 VvC~~CGhCL-------N~GK~K~~~~ 125 (245)
T PF03117_consen 106 VVCMECGHCL-------NFGKGKLKCG 125 (245)
T ss_pred EEeccCCchh-------hccchhhccc
Confidence 3699999999 7778888874
No 44
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=24.94 E-value=45 Score=19.46 Aligned_cols=11 Identities=45% Similarity=1.280 Sum_probs=9.0
Q ss_pred eEEEEecCccC
Q 033124 69 KRTKIKCNNCG 79 (126)
Q Consensus 69 ~Rtev~C~~Cg 79 (126)
...+|.|.+|+
T Consensus 22 ~g~~v~C~~C~ 32 (36)
T PF13717_consen 22 KGRKVRCSKCG 32 (36)
T ss_pred CCcEEECCCCC
Confidence 45699999996
No 45
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=24.49 E-value=39 Score=23.58 Aligned_cols=22 Identities=32% Similarity=0.706 Sum_probs=17.1
Q ss_pred EEEEecCccCCcccccc-CCCCC
Q 033124 70 RTKIKCNNCGALLGYIY-DDGPP 91 (126)
Q Consensus 70 Rtev~C~~Cg~HLGhvF-~Dgp~ 91 (126)
+..-.|..||-.++|.= +|||+
T Consensus 6 k~~~~C~~CG~d~~~~~adDgPA 28 (86)
T PF06170_consen 6 KVAPRCPHCGLDYSHARADDGPA 28 (86)
T ss_pred cCCCcccccCCccccCCcCccch
Confidence 45668999999999885 56664
No 46
>COG2126 RPL37A Ribosomal protein L37E [Translation, ribosomal structure and biogenesis]
Probab=24.20 E-value=33 Score=23.03 Aligned_cols=18 Identities=33% Similarity=0.669 Sum_probs=15.0
Q ss_pred eEEEEecCccCCcccccc
Q 033124 69 KRTKIKCNNCGALLGYIY 86 (126)
Q Consensus 69 ~Rtev~C~~Cg~HLGhvF 86 (126)
.+|-+.|++||.+-=||=
T Consensus 13 k~tH~~CRRCGr~syhv~ 30 (61)
T COG2126 13 KKTHIRCRRCGRRSYHVR 30 (61)
T ss_pred Ccceehhhhccchheeec
Confidence 478999999999887773
No 47
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=24.06 E-value=1e+02 Score=21.17 Aligned_cols=11 Identities=45% Similarity=0.927 Sum_probs=8.5
Q ss_pred EEEEecCccCC
Q 033124 70 RTKIKCNNCGA 80 (126)
Q Consensus 70 Rtev~C~~Cg~ 80 (126)
=+-+.|.+||=
T Consensus 38 f~~itCk~CgY 48 (68)
T COG3478 38 FIVITCKNCGY 48 (68)
T ss_pred EEEEEeccCCc
Confidence 36889999973
No 48
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=23.14 E-value=44 Score=19.52 Aligned_cols=11 Identities=36% Similarity=1.096 Sum_probs=8.9
Q ss_pred eEEEEecCccC
Q 033124 69 KRTKIKCNNCG 79 (126)
Q Consensus 69 ~Rtev~C~~Cg 79 (126)
...+|+|.+|+
T Consensus 22 ~~~~vrC~~C~ 32 (37)
T PF13719_consen 22 GGRKVRCPKCG 32 (37)
T ss_pred CCcEEECCCCC
Confidence 35699999996
No 49
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=22.48 E-value=33 Score=20.95 Aligned_cols=9 Identities=56% Similarity=1.372 Sum_probs=8.2
Q ss_pred Eeccccccc
Q 033124 6 SCKECGTNL 14 (126)
Q Consensus 6 ~C~~Cg~~L 14 (126)
+|..||.||
T Consensus 19 ~Cp~C~~PL 27 (41)
T PF06677_consen 19 HCPDCGTPL 27 (41)
T ss_pred ccCCCCCee
Confidence 688999999
No 50
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=22.16 E-value=42 Score=19.07 Aligned_cols=11 Identities=36% Similarity=0.821 Sum_probs=8.6
Q ss_pred EEEeccccccc
Q 033124 4 IYSCKECGTNL 14 (126)
Q Consensus 4 ~Y~C~~Cg~~L 14 (126)
.|.|..||+-.
T Consensus 1 ~~~C~~CGy~y 11 (33)
T cd00350 1 KYVCPVCGYIY 11 (33)
T ss_pred CEECCCCCCEE
Confidence 47888898874
No 51
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=22.02 E-value=52 Score=19.00 Aligned_cols=11 Identities=27% Similarity=0.809 Sum_probs=8.6
Q ss_pred EEEeccccccc
Q 033124 4 IYSCKECGTNL 14 (126)
Q Consensus 4 ~Y~C~~Cg~~L 14 (126)
.|.|..||+-.
T Consensus 2 ~~~C~~CG~i~ 12 (34)
T cd00729 2 VWVCPVCGYIH 12 (34)
T ss_pred eEECCCCCCEe
Confidence 58888888774
No 52
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=21.03 E-value=51 Score=19.46 Aligned_cols=12 Identities=33% Similarity=1.052 Sum_probs=10.0
Q ss_pred CcEEEecccccc
Q 033124 2 ASIYSCKECGTN 13 (126)
Q Consensus 2 ~G~Y~C~~Cg~~ 13 (126)
.|.|-|..||..
T Consensus 23 dG~~yC~~cG~~ 34 (36)
T PF11781_consen 23 DGFYYCDRCGHQ 34 (36)
T ss_pred CCEEEhhhCceE
Confidence 688999999875
No 53
>PRK00420 hypothetical protein; Validated
Probab=20.91 E-value=36 Score=25.08 Aligned_cols=10 Identities=40% Similarity=0.886 Sum_probs=8.9
Q ss_pred EEeccccccc
Q 033124 5 YSCKECGTNL 14 (126)
Q Consensus 5 Y~C~~Cg~~L 14 (126)
-+|..||.||
T Consensus 24 ~~CP~Cg~pL 33 (112)
T PRK00420 24 KHCPVCGLPL 33 (112)
T ss_pred CCCCCCCCcc
Confidence 4799999999
No 54
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=20.88 E-value=51 Score=19.78 Aligned_cols=13 Identities=23% Similarity=0.976 Sum_probs=11.4
Q ss_pred CcEEEeccccccc
Q 033124 2 ASIYSCKECGTNL 14 (126)
Q Consensus 2 ~G~Y~C~~Cg~~L 14 (126)
.|.-.|+.||.+|
T Consensus 3 ~g~l~C~~CG~~m 15 (58)
T PF13408_consen 3 SGLLRCGHCGSKM 15 (58)
T ss_pred CCcEEcccCCcEe
Confidence 5778899999998
No 55
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=20.73 E-value=72 Score=21.29 Aligned_cols=23 Identities=13% Similarity=0.455 Sum_probs=17.3
Q ss_pred EecccccccCCCCCCCCCCCCcc
Q 033124 6 SCKECGTNLNLNTSHLYPATVYF 28 (126)
Q Consensus 6 ~C~~Cg~~Lnlsss~~f~S~~Kf 28 (126)
.|..||.....+--.||+.+++|
T Consensus 19 ~Cp~CG~~t~~~~PprFSPeD~y 41 (59)
T COG2260 19 KCPVCGGDTKVPHPPRFSPEDKY 41 (59)
T ss_pred cCCCCCCccccCCCCCCCccchH
Confidence 57888888877777777777765
No 56
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=20.04 E-value=57 Score=17.41 Aligned_cols=18 Identities=22% Similarity=0.634 Sum_probs=11.3
Q ss_pred ecccccccCCCCCCCCCCCCccCCCC
Q 033124 7 CKECGTNLNLNTSHLYPATVYFPAGN 32 (126)
Q Consensus 7 C~~Cg~~Lnlsss~~f~S~~Kf~sg~ 32 (126)
|..||.+| ..+++|=..+
T Consensus 2 Cp~CG~~~--------~~~~~fC~~C 19 (23)
T PF13240_consen 2 CPNCGAEI--------EDDAKFCPNC 19 (23)
T ss_pred CcccCCCC--------CCcCcchhhh
Confidence 77888886 4455554444
Done!