Query 028408
Match_columns 209
No_of_seqs 194 out of 1282
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 11:03:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028408.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028408hhsearch_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 7E-71 1.5E-75 448.6 11.9 126 83-209 2-129 (140)
2 TIGR00357 methionine-R-sulfoxi 100.0 1E-69 2.2E-74 440.5 13.2 124 85-209 2-126 (134)
3 PRK00222 methionine sulfoxide 100.0 6.4E-69 1.4E-73 439.3 13.5 126 83-209 3-129 (142)
4 PF01641 SelR: SelR domain; I 100.0 1.4E-68 2.9E-73 429.0 10.2 122 87-209 1-124 (124)
5 PRK05508 methionine sulfoxide 100.0 3.2E-65 6.8E-70 407.2 12.0 115 92-209 2-117 (119)
6 KOG0856 Predicted pilin-like t 100.0 3.2E-64 6.9E-69 410.8 10.7 128 81-209 12-142 (146)
7 PRK14018 trifunctional thiored 100.0 4.3E-59 9.4E-64 443.1 13.4 129 80-209 375-505 (521)
8 PRK05550 bifunctional methioni 100.0 1.6E-58 3.4E-63 412.3 10.5 118 89-209 2-120 (283)
9 PF03226 Yippee-Mis18: Yippee 93.7 0.035 7.5E-07 41.8 1.4 81 123-204 2-92 (96)
10 TIGR01384 TFS_arch transcripti 78.4 2.5 5.3E-05 32.1 3.1 62 121-186 14-76 (104)
11 COG1645 Uncharacterized Zn-fin 69.0 1.6 3.5E-05 36.1 0.1 24 123-146 28-52 (131)
12 PF09855 DUF2082: Nucleic-acid 58.7 6.5 0.00014 28.7 1.6 43 124-179 1-43 (64)
13 PF11781 RRN7: RNA polymerase 58.6 4.5 9.7E-05 26.3 0.7 21 112-132 14-34 (36)
14 PRK00420 hypothetical protein; 54.1 7.2 0.00016 31.4 1.3 23 124-146 24-48 (112)
15 PF06677 Auto_anti-p27: Sjogre 52.3 6.2 0.00013 26.5 0.6 13 125-137 19-31 (41)
16 PRK04351 hypothetical protein; 49.2 30 0.00066 28.7 4.3 14 172-185 132-145 (149)
17 PF09814 HECT_2: HECT-like Ubi 48.0 25 0.00055 31.6 4.0 26 122-148 105-135 (354)
18 PF03811 Zn_Tnp_IS1: InsA N-te 47.5 24 0.00052 23.0 2.7 29 168-197 1-30 (36)
19 PHA03351 tegument protein UL16 46.9 8.5 0.00018 33.9 0.8 70 62-132 73-149 (235)
20 PF04828 GFA: Glutathione-depe 45.3 17 0.00037 25.6 2.0 31 171-205 47-77 (92)
21 PF02945 Endonuclease_7: Recom 44.9 6.9 0.00015 29.6 -0.1 43 125-186 24-66 (81)
22 smart00778 Prim_Zn_Ribbon Zinc 43.8 14 0.00031 24.3 1.3 16 115-130 17-32 (37)
23 PF01352 KRAB: KRAB box; Inte 39.0 32 0.0007 22.8 2.4 21 83-104 8-28 (41)
24 PF08271 TF_Zn_Ribbon: TFIIB z 38.5 19 0.00041 23.5 1.3 15 119-133 15-29 (43)
25 COG3791 Uncharacterized conser 36.0 15 0.00033 29.4 0.6 22 116-137 62-83 (133)
26 PRK03824 hypA hydrogenase nick 35.9 50 0.0011 26.8 3.6 27 110-137 56-83 (135)
27 PF07295 DUF1451: Protein of u 34.7 20 0.00043 29.9 1.1 42 82-133 81-122 (146)
28 PF06170 DUF983: Protein of un 31.6 25 0.00054 26.8 1.1 22 170-191 6-28 (86)
29 PF04502 DUF572: Family of unk 31.4 43 0.00092 30.8 2.8 50 124-190 41-93 (324)
30 PRK08624 hypothetical protein; 30.4 53 0.0011 31.5 3.3 19 119-137 55-76 (373)
31 PF10058 DUF2296: Predicted in 29.9 41 0.00088 23.6 1.9 26 168-193 18-43 (54)
32 PRK12495 hypothetical protein; 29.7 19 0.00042 32.4 0.2 14 121-134 40-53 (226)
33 COG3791 Uncharacterized conser 28.9 43 0.00093 26.8 2.1 28 174-205 71-98 (133)
34 PF15288 zf-CCHC_6: Zinc knuck 28.5 22 0.00047 24.0 0.3 15 173-188 2-16 (40)
35 PRK00423 tfb transcription ini 27.9 49 0.0011 30.1 2.5 32 118-151 25-56 (310)
36 cd04984 IgV_L_lambda Immunoglo 26.6 38 0.00083 24.5 1.3 13 117-129 71-83 (98)
37 COG1405 SUA7 Transcription ini 26.6 49 0.0011 30.3 2.3 30 118-149 15-44 (285)
38 PF09965 DUF2199: Uncharacteri 26.2 32 0.00069 28.8 0.9 25 124-158 1-25 (148)
39 PF04032 Rpr2: RNAse P Rpr2/Rp 25.6 99 0.0022 22.1 3.4 65 89-179 20-84 (85)
40 TIGR03655 anti_R_Lar restricti 25.5 57 0.0012 22.2 2.0 17 116-132 19-35 (53)
41 PF03119 DNA_ligase_ZBD: NAD-d 24.8 48 0.001 20.3 1.3 23 174-201 1-23 (28)
42 PF13719 zinc_ribbon_5: zinc-r 24.1 38 0.00082 21.7 0.8 17 167-187 20-36 (37)
43 PRK13130 H/ACA RNA-protein com 23.8 42 0.00092 24.0 1.1 13 125-137 19-31 (56)
44 PRK04179 rpl37e 50S ribosomal 23.3 43 0.00094 24.6 1.1 27 122-148 16-43 (62)
45 cd04980 IgV_L_kappa Immunoglob 23.2 42 0.0009 24.7 1.0 12 118-129 80-91 (106)
46 PRK00398 rpoP DNA-directed RNA 21.8 1.4E+02 0.003 19.6 3.2 11 123-133 3-13 (46)
47 PHA02565 49 recombination endo 21.3 49 0.0011 28.3 1.1 21 167-188 51-71 (157)
48 PF00047 ig: Immunoglobulin do 21.1 48 0.001 21.5 0.9 10 119-128 55-64 (64)
49 PTZ00073 60S ribosomal protein 20.9 51 0.0011 25.9 1.1 28 122-149 15-42 (91)
50 cd04983 IgV_TCR_alpha_like Imm 20.8 57 0.0012 23.6 1.3 14 117-130 78-91 (109)
51 TIGR02098 MJ0042_CXXC MJ0042 f 20.1 52 0.0011 20.5 0.8 11 172-182 25-35 (38)
52 PHA02540 61 DNA primase; Provi 20.0 49 0.0011 31.1 1.0 24 108-131 29-63 (337)
No 1
>COG0229 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=7e-71 Score=448.56 Aligned_cols=126 Identities=60% Similarity=1.034 Sum_probs=122.0
Q ss_pred CCCCHHHHHhcCCHHHHHHHhhcCCCCCccCCCCCCCCceEEEcccCCccccCCCCcccCCCCCccccccCC-CCcEEee
Q 028408 83 ASISDEEWKRRLTGEQYYITRQKGTERAFTGEYWNTKTPGTYHCICCDTPLFESSTKFDSGTGWPSYYQPIG-SNMKSKL 161 (209)
Q Consensus 83 ~~~s~~ewr~~Ltp~qy~Vlr~~GTE~pFsg~y~~~~~~GiY~C~~Cg~pLF~S~~KFdSg~GWPSF~~pi~-~~v~~~~ 161 (209)
+.++++|||++|||+||+|||++|||+||+|+||+++++|+|+|++||+|||+|++|||||||||||++||+ ++|.++.
T Consensus 2 ~~~sd~e~~~~Lt~~qy~Vtq~~gTE~pft~~y~~~~~~GiY~c~~cg~pLF~S~~KfdSgcGWPSF~~pi~~~~I~~~~ 81 (140)
T COG0229 2 IKPSDEELKEKLTPEQYRVTQNHGTERPFTGEYLDNKEKGIYVCIVCGEPLFSSEDKFDSGCGWPSFTKPISPDAITYKE 81 (140)
T ss_pred CccchHHHHHhcCHHHHHHHHhcCCCCCCCChhhcccCCceEEeecCCCccccccccccCCCCCccccccCCcccceEee
Confidence 357899999999999999999999999999999999999999999999999999999999999999999996 6899999
Q ss_pred cCCCCCCcEEEEEcCCCCCCccccCCCCCCCCC-ceeeecceeeeeeeC
Q 028408 162 DLSIIFMPRQEVLCAVCDAHLGHVFDDGPPPTG-KRYCINSASLKLKPK 209 (209)
Q Consensus 162 D~s~~gm~RtEV~C~~Cg~HLGHVF~DGP~Ptg-~RYCINS~sL~F~P~ 209 (209)
|.|+ ||.||||+|++||+||||||+|||+|+| +|||||||||+|+|+
T Consensus 82 D~S~-gM~RtEVrc~~c~sHLGHVF~DGP~~tgglRYCINSasL~Fip~ 129 (140)
T COG0229 82 DRSH-GMVRTEVRCANCDSHLGHVFPDGPPPTGGLRYCINSASLRFIPK 129 (140)
T ss_pred ccCC-CcEEEEEEecCCCCccccccCCCCCCCCCeeEeecchheeecch
Confidence 9997 9999999999999999999999999998 999999999999985
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=1e-69 Score=440.50 Aligned_cols=124 Identities=58% Similarity=0.982 Sum_probs=120.9
Q ss_pred CCHHHHHhcCCHHHHHHHhhcCCCCCccCCCCCCCCceEEEcccCCccccCCCCcccCCCCCccccccC-CCCcEEeecC
Q 028408 85 ISDEEWKRRLTGEQYYITRQKGTERAFTGEYWNTKTPGTYHCICCDTPLFESSTKFDSGTGWPSYYQPI-GSNMKSKLDL 163 (209)
Q Consensus 85 ~s~~ewr~~Ltp~qy~Vlr~~GTE~pFsg~y~~~~~~GiY~C~~Cg~pLF~S~~KFdSg~GWPSF~~pi-~~~v~~~~D~ 163 (209)
++++|||+.|||+||+|+|++|||+||||+||+++++|+|+|++||+|||+|++|||||||||||+++| +++|.++.|.
T Consensus 2 ~~~~ewr~~Lt~~qy~V~r~~gTE~pftg~y~~~~~~G~Y~C~~Cg~pLF~S~~KfdSg~GWPSF~~~i~~~~V~~~~D~ 81 (134)
T TIGR00357 2 PSDEELKKKLTPLQYEVTQNAGTEPPFTNEYWDNKEEGIYVDITCGEPLFSSEDKFDSGCGWPSFYKPISEEVVAYERDE 81 (134)
T ss_pred CCHHHHHHhCCHHHHHHHHHhCCCCCCCCCCCCCCCCeEEEccCCCCccccccchhcCCCCCcCcCcccCCCceEEeecC
Confidence 689999999999999999999999999999999999999999999999999999999999999999999 5789999999
Q ss_pred CCCCCcEEEEEcCCCCCCccccCCCCCCCCCceeeecceeeeeeeC
Q 028408 164 SIIFMPRQEVLCAVCDAHLGHVFDDGPPPTGKRYCINSASLKLKPK 209 (209)
Q Consensus 164 s~~gm~RtEV~C~~Cg~HLGHVF~DGP~Ptg~RYCINS~sL~F~P~ 209 (209)
++ ||+||||+|++||+||||||+|||+|||+||||||+||+|+|+
T Consensus 82 s~-gm~RtEv~C~~Cg~HLGHVF~DGP~ptg~RyCINs~sL~F~p~ 126 (134)
T TIGR00357 82 SH-GMIRTEVRCRNCDAHLGHVFDDGPEPTGLRYCINSAALKFIPL 126 (134)
T ss_pred CC-CcEEEEEEecCCCCccCcccCCCCCCCCceEeecceeEecccc
Confidence 96 9999999999999999999999999999999999999999984
No 3
>PRK00222 methionine sulfoxide reductase B; Provisional
Probab=100.00 E-value=6.4e-69 Score=439.33 Aligned_cols=126 Identities=60% Similarity=1.057 Sum_probs=122.2
Q ss_pred CCCCHHHHHhcCCHHHHHHHhhcCCCCCccCCCCCCCCceEEEcccCCccccCCCCcccCCCCCccccccCC-CCcEEee
Q 028408 83 ASISDEEWKRRLTGEQYYITRQKGTERAFTGEYWNTKTPGTYHCICCDTPLFESSTKFDSGTGWPSYYQPIG-SNMKSKL 161 (209)
Q Consensus 83 ~~~s~~ewr~~Ltp~qy~Vlr~~GTE~pFsg~y~~~~~~GiY~C~~Cg~pLF~S~~KFdSg~GWPSF~~pi~-~~v~~~~ 161 (209)
+.++++|||+.|||+||+|+|++||||||||+||+++++|+|+|++||+|||+|++|||||||||||+++|+ ++|+.+.
T Consensus 3 ~~~~~~ew~~~Lt~~qy~V~r~~gTE~pftg~~~~~~~~G~Y~C~~Cg~pLF~S~~Kf~Sg~GWPSF~~~i~~~~V~~~~ 82 (142)
T PRK00222 3 IEKSKEEWKKQLTPEQYRVTQEHGTERPFTGEYLDNKEKGIYVCIVCGEPLFSSDTKFDSGCGWPSFTKPIDEEAIRELR 82 (142)
T ss_pred ccCCHHHHHhhCCHHHHHHHHhcCCCCCCCCCCCCCCCCeEEEecCCCchhcCCcccccCCCCCcCcCcccCCCceEEee
Confidence 457999999999999999999999999999999999999999999999999999999999999999999995 7899999
Q ss_pred cCCCCCCcEEEEEcCCCCCCccccCCCCCCCCCceeeecceeeeeeeC
Q 028408 162 DLSIIFMPRQEVLCAVCDAHLGHVFDDGPPPTGKRYCINSASLKLKPK 209 (209)
Q Consensus 162 D~s~~gm~RtEV~C~~Cg~HLGHVF~DGP~Ptg~RYCINS~sL~F~P~ 209 (209)
|.++ ||.||||+|++||+||||||+|||+|||+||||||+||+|+|+
T Consensus 83 D~s~-gm~RtEv~C~~Cg~HLGHVF~DGP~ptg~RyCINs~sL~F~p~ 129 (142)
T PRK00222 83 DTSH-GMVRTEVRCANCDSHLGHVFPDGPKPTGLRYCINSASLKFIPK 129 (142)
T ss_pred ccCC-CceEEEEEeCCCCCccCcccCCCCCCCCCEeeeceeeEEeecc
Confidence 9986 9999999999999999999999999999999999999999985
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=1.4e-68 Score=428.99 Aligned_cols=122 Identities=66% Similarity=1.207 Sum_probs=115.4
Q ss_pred HHHHHhcCCHHHHHHHhhcCCCCCccCCCCCCCCceEEEcccCCccccCCCCcccCCCCCccccccCCC-CcEEeecCCC
Q 028408 87 DEEWKRRLTGEQYYITRQKGTERAFTGEYWNTKTPGTYHCICCDTPLFESSTKFDSGTGWPSYYQPIGS-NMKSKLDLSI 165 (209)
Q Consensus 87 ~~ewr~~Ltp~qy~Vlr~~GTE~pFsg~y~~~~~~GiY~C~~Cg~pLF~S~~KFdSg~GWPSF~~pi~~-~v~~~~D~s~ 165 (209)
|+|||++|||+||+|||++|||+||||+||+++++|+|+|++||+|||+|++|||||||||||+++|++ +|..+.|.++
T Consensus 1 d~ew~~~Lt~~qy~V~r~~gTE~pfsg~y~~~~~~G~Y~C~~Cg~pLF~S~~Kf~Sg~GWPSF~~~i~~~~v~~~~D~s~ 80 (124)
T PF01641_consen 1 DEEWRKRLTPEQYRVLREKGTERPFSGEYWDHKEEGIYVCAVCGTPLFSSDTKFDSGCGWPSFWQPIPGDAVKEREDFSH 80 (124)
T ss_dssp -HHHHHHSCHHHHHHHHHTTSSSTTSSGGCCTTSSEEEEETTTS-EEEEGGGEETSSSSSSEESSCSSTTSEEEEEEECT
T ss_pred CHHHHhhCCHHHHHHHHhcCCCCCCccCCcCCCCCEEEEcCCCCCccccCcccccCCcCCccccCcCChHHEEEeccccC
Confidence 789999999999999999999999999999999999999999999999999999999999999999986 8999999996
Q ss_pred CCCcEEEEEcCCCCCCccccCCCCCCC-CCceeeecceeeeeeeC
Q 028408 166 IFMPRQEVLCAVCDAHLGHVFDDGPPP-TGKRYCINSASLKLKPK 209 (209)
Q Consensus 166 ~gm~RtEV~C~~Cg~HLGHVF~DGP~P-tg~RYCINS~sL~F~P~ 209 (209)
||+||||+|++||+||||||+|||+| ||+||||||+||+|+|+
T Consensus 81 -g~~R~Ev~C~~Cg~HLGHVF~DGp~~~tg~RyCINS~sL~F~p~ 124 (124)
T PF01641_consen 81 -GMVRTEVRCARCGSHLGHVFDDGPPPPTGLRYCINSASLKFIPK 124 (124)
T ss_dssp -SSEEEEEEETTTCCEEEEEESTSSTTCTSCEEEE-GGGEEEEE-
T ss_pred -CceEEEEEecCCCCccccEeCCCCCCCCCcEEEeeeeeEEEecC
Confidence 99999999999999999999999987 69999999999999996
No 5
>PRK05508 methionine sulfoxide reductase B; Provisional
Probab=100.00 E-value=3.2e-65 Score=407.25 Aligned_cols=115 Identities=44% Similarity=0.804 Sum_probs=110.4
Q ss_pred hcCCHHHHHHHhhcCCCCCccCCCCCCCCceEEEcccCCccccCCCCcccCCCCCccccccCCCCcEEeecCCCCCCcEE
Q 028408 92 RRLTGEQYYITRQKGTERAFTGEYWNTKTPGTYHCICCDTPLFESSTKFDSGTGWPSYYQPIGSNMKSKLDLSIIFMPRQ 171 (209)
Q Consensus 92 ~~Ltp~qy~Vlr~~GTE~pFsg~y~~~~~~GiY~C~~Cg~pLF~S~~KFdSg~GWPSF~~pi~~~v~~~~D~s~~gm~Rt 171 (209)
++|||+||+|+|++||||||+|+||+++++|+|+|++||+|||+|++||||||||||||+||+++|+++.|.+ |.||
T Consensus 2 ~~Lt~~qy~V~r~~gTE~pftg~y~~~~~~G~Y~C~~Cg~pLF~S~~KfdSg~GWPSF~~~i~~~v~~~~D~~---~~Rt 78 (119)
T PRK05508 2 NELTPEEEAVILRKGTEPPFSGEYNDFFEKGTYVCKQCGAPLYRSEDKFKSGCGWPSFDDEIKGAVKRIPDAD---GRRT 78 (119)
T ss_pred CcCCHHHHHHHHhcCCCCCCCCCCcCcCCCeEEEecCCCCccccccccccCCCCCcccCcccccceEEEecCC---CcEE
Confidence 5899999999999999999999999999999999999999999999999999999999999999999999987 4699
Q ss_pred EEEcCCCCCCccccCC-CCCCCCCceeeecceeeeeeeC
Q 028408 172 EVLCAVCDAHLGHVFD-DGPPPTGKRYCINSASLKLKPK 209 (209)
Q Consensus 172 EV~C~~Cg~HLGHVF~-DGP~Ptg~RYCINS~sL~F~P~ 209 (209)
||+|++||+||||||+ |||+|||+|||||||||+|+|+
T Consensus 79 Ev~C~~C~~HLGHVF~d~gp~ptg~RyCINS~sL~F~p~ 117 (119)
T PRK05508 79 EIVCANCGGHLGHVFEGEGFTPKNTRHCVNSISLKFVPD 117 (119)
T ss_pred EEEeCCCCCccCcccCCCCCCCCCCEEeecceeEEeecC
Confidence 9999999999999998 5678999999999999999985
No 6
>KOG0856 consensus Predicted pilin-like transcription factor [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=3.2e-64 Score=410.81 Aligned_cols=128 Identities=48% Similarity=0.870 Sum_probs=123.0
Q ss_pred CCCCCCHHHHHhcCCHHHHHHHhhcCCCCCccCCCCCCCCceEEEcccCCccccCCCCcccCCCCCccccccC-CCCcEE
Q 028408 81 DYASISDEEWKRRLTGEQYYITRQKGTERAFTGEYWNTKTPGTYHCICCDTPLFESSTKFDSGTGWPSYYQPI-GSNMKS 159 (209)
Q Consensus 81 ~~~~~s~~ewr~~Ltp~qy~Vlr~~GTE~pFsg~y~~~~~~GiY~C~~Cg~pLF~S~~KFdSg~GWPSF~~pi-~~~v~~ 159 (209)
..++++++|||++||||||+|||++|||+||+|+|++++++|+|+|++|++|||+|++|||||||||+|++.| +++|..
T Consensus 12 ~~v~k~~~EWr~~LsPeQ~~v~RekgTE~p~tGey~~~~e~GvY~C~~C~~pLykS~tKfdsgcGWPAF~e~i~~gaI~r 91 (146)
T KOG0856|consen 12 GSVQKNDEEWRKVLSPEQFRVLREKGTERPGTGEYTKHFEEGVYVCAGCGTPLYKSTTKFDSGCGWPAFFEAIGPGAITR 91 (146)
T ss_pred cccccCHHHHHhhcCHHHhhhhHhhcccCCCCcccccccCCceEEEeecCCccccccccccCCCCCchhhhccCCCceee
Confidence 3467899999999999999999999999999999999999999999999999999999999999999999999 799999
Q ss_pred eecCCCCCCcEEEEEcCCCCCCccccCC-CCCC-CCCceeeecceeeeeeeC
Q 028408 160 KLDLSIIFMPRQEVLCAVCDAHLGHVFD-DGPP-PTGKRYCINSASLKLKPK 209 (209)
Q Consensus 160 ~~D~s~~gm~RtEV~C~~Cg~HLGHVF~-DGP~-Ptg~RYCINS~sL~F~P~ 209 (209)
..|.|. ||.|+||+|++||+||||||+ |||+ ||++|||||||||+|.|+
T Consensus 92 ~~d~s~-~~~R~Ev~Ca~C~~HLGHVF~~eG~~~Pt~~R~CiNS~sL~F~~~ 142 (146)
T KOG0856|consen 92 TPDNSR-GGRRTEVSCATCGGHLGHVFKGEGPKTPTDERHCINSVSLKFVPA 142 (146)
T ss_pred ccccCC-CCcceEEEEeecCCceeeeecCCCCCCCCCceeEeeeeeeeeccC
Confidence 999886 899999999999999999998 9998 999999999999999984
No 7
>PRK14018 trifunctional thioredoxin/methionine sulfoxide reductase A/B protein; Provisional
Probab=100.00 E-value=4.3e-59 Score=443.05 Aligned_cols=129 Identities=50% Similarity=0.788 Sum_probs=123.3
Q ss_pred CCCCCCCHHHHHhcCCHHHHHHHhhcCCCCCccCCCCCCCCceEEEcccCCccccCCCCcccCCCCCccccccCC-CCcE
Q 028408 80 VDYASISDEEWKRRLTGEQYYITRQKGTERAFTGEYWNTKTPGTYHCICCDTPLFESSTKFDSGTGWPSYYQPIG-SNMK 158 (209)
Q Consensus 80 ~~~~~~s~~ewr~~Ltp~qy~Vlr~~GTE~pFsg~y~~~~~~GiY~C~~Cg~pLF~S~~KFdSg~GWPSF~~pi~-~~v~ 158 (209)
.++..++++|||++|||+||+|+|++|||+||||+||+++++|+|+|++||+|||+|++|||||||||||++||+ ++|.
T Consensus 375 ~~~~~~~~~~~~~~Lt~~~y~v~~~~gtE~~f~~~~~~~~~~G~y~c~~c~~pLf~s~~Kf~sg~GWPsF~~~i~~~~v~ 454 (521)
T PRK14018 375 ATYKKPSDAELKRTLTEEQYQITQNAATERAFSHEYDHLFKPGIYVDVVSGEPLFSSADKYDSGCGWPSFTRPIDAKVVT 454 (521)
T ss_pred hhccCCChHHHhccCCHHHHHHHHhcCCCCCCCCCCcCCCCCEEEEecCCCCccccCcccccCCCCCcccCcccCcCceE
Confidence 347789999999999999999999999999999999999999999999999999999999999999999999997 5688
Q ss_pred EeecCCCCCCcEEEEEcCCCCCCccccCCCCCC-CCCceeeecceeeeeeeC
Q 028408 159 SKLDLSIIFMPRQEVLCAVCDAHLGHVFDDGPP-PTGKRYCINSASLKLKPK 209 (209)
Q Consensus 159 ~~~D~s~~gm~RtEV~C~~Cg~HLGHVF~DGP~-Ptg~RYCINS~sL~F~P~ 209 (209)
++.|.++ ||.||||+|++||+||||||+|||+ |||+||||||+||+|+|+
T Consensus 455 ~~~d~s~-g~~R~Ev~c~~c~~HLGHvf~dgp~~~~g~RyCiNs~~l~f~~~ 505 (521)
T PRK14018 455 EHDDFSY-NMRRTEVRSRAADSHLGHVFPDGPRDKGGLRYCINGASLKFIPL 505 (521)
T ss_pred EeeccCC-CceEEEEEECCCCCcCCcccCCCCCCCCCCEeeeceeEEEeecc
Confidence 8999986 9999999999999999999999996 699999999999999985
No 8
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=100.00 E-value=1.6e-58 Score=412.30 Aligned_cols=118 Identities=45% Similarity=0.854 Sum_probs=114.1
Q ss_pred HHHhcCCHHHHHHHhhcCCCCCccCCCCCCCCceEEEcccCCccccCCCCcccCCCCCccccccCCCCcEEeecCCCCCC
Q 028408 89 EWKRRLTGEQYYITRQKGTERAFTGEYWNTKTPGTYHCICCDTPLFESSTKFDSGTGWPSYYQPIGSNMKSKLDLSIIFM 168 (209)
Q Consensus 89 ewr~~Ltp~qy~Vlr~~GTE~pFsg~y~~~~~~GiY~C~~Cg~pLF~S~~KFdSg~GWPSF~~pi~~~v~~~~D~s~~gm 168 (209)
.||++|||+||+|+|++||||||+|+||+++++|+|+|++||+|||+|++|||||||||||++||+++|..+.|.+ ||
T Consensus 2 ~~~~~Lt~~~y~v~r~~gTE~pf~g~~~~~~~~G~y~c~~c~~~LF~s~~Kf~sg~GWPsF~~~~~~~~~~~~d~~--~~ 79 (283)
T PRK05550 2 DKMKSLTPFEYRVIEDKGTERPFSGEYYDHDEKGVYLCRRCGAPLFRSEDKFNSGCGWPSFDDEIPGAVKRLPDAD--GR 79 (283)
T ss_pred hhhhhCCHHHHHHHHhcCCCCCCCCcCcCCCCCcEEEcCCCCchhcCChhhccCCCCCcCcCcccCCccEEEEcCC--Cc
Confidence 6999999999999999999999999999999999999999999999999999999999999999999999999886 66
Q ss_pred cEEEEEcCCCCCCccccCC-CCCCCCCceeeecceeeeeeeC
Q 028408 169 PRQEVLCAVCDAHLGHVFD-DGPPPTGKRYCINSASLKLKPK 209 (209)
Q Consensus 169 ~RtEV~C~~Cg~HLGHVF~-DGP~Ptg~RYCINS~sL~F~P~ 209 (209)
||||+|++||+||||||+ |||+|||+||||||+||+|+|+
T Consensus 80 -R~Ev~c~~c~~HLGHvF~ddgp~ptg~RyCiNs~sL~f~p~ 120 (283)
T PRK05550 80 -RTEIVCANCGAHLGHVFEGEGLTPKNTRHCVNSASLDFVPA 120 (283)
T ss_pred -eEEEEecCCCCccCcccCCCCCCCCCccccccccccccCcc
Confidence 999999999999999998 8899999999999999999985
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=93.67 E-value=0.035 Score=41.78 Aligned_cols=81 Identities=19% Similarity=0.449 Sum_probs=47.7
Q ss_pred EEEcccCCccccCCCCccc-CCCCCcccc-ccCCCCcEEeecCCCCCC-----cEEEEEcCCCCCCccccCCCCCCC---
Q 028408 123 TYHCICCDTPLFESSTKFD-SGTGWPSYY-QPIGSNMKSKLDLSIIFM-----PRQEVLCAVCDAHLGHVFDDGPPP--- 192 (209)
Q Consensus 123 iY~C~~Cg~pLF~S~~KFd-Sg~GWPSF~-~pi~~~v~~~~D~s~~gm-----~RtEV~C~~Cg~HLGHVF~DGP~P--- 192 (209)
+|.|+.|.++|=+|..-.. .|..=++|- ..+...+...+.... |. .=..+.|++|+.+||=.+...|++
T Consensus 2 vf~C~~C~t~l~ds~~lvs~~g~~~~a~l~~~v~~~~~~~~~~~t-~~~~~~~~~~~l~C~~C~~~lGwkY~~a~~~~~~ 80 (96)
T PF03226_consen 2 VFQCKNCKTILADSNELVSFHGREGKAYLFNNVSNGVPVDRELMT-GETGGDHTVRDLFCSGCNTILGWKYESAPEEQKY 80 (96)
T ss_pred EEECCCCCCCcCCHHHheecCCCCccEEEEeeeeecccccceEEE-eeCCCCEEEEEeEcccCChhHCcEEEEcCHhHhh
Confidence 7999999999988776666 443224332 122222111110000 11 135799999999999999766654
Q ss_pred CCceeeecceee
Q 028408 193 TGKRYCINSASL 204 (209)
Q Consensus 193 tg~RYCINS~sL 204 (209)
---+|++.-++|
T Consensus 81 k~g~file~~~i 92 (96)
T PF03226_consen 81 KEGKFILEKASI 92 (96)
T ss_pred hCCEEEEEhhHE
Confidence 334566665554
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=78.41 E-value=2.5 Score=32.09 Aligned_cols=62 Identities=16% Similarity=0.297 Sum_probs=33.4
Q ss_pred ceEEEcccCCccccCC-CCcccCCCCCccccccCCCCcEEeecCCCCCCcEEEEEcCCCCCCccccC
Q 028408 121 PGTYHCICCDTPLFES-STKFDSGTGWPSYYQPIGSNMKSKLDLSIIFMPRQEVLCAVCDAHLGHVF 186 (209)
Q Consensus 121 ~GiY~C~~Cg~pLF~S-~~KFdSg~GWPSF~~pi~~~v~~~~D~s~~gm~RtEV~C~~Cg~HLGHVF 186 (209)
.+.|.|..||...... +.++..- -.+...+.+.+....|.. .+.+++++.|.+||.+-...|
T Consensus 14 ~~~~~C~~C~~~~~~~~~~~~v~~---~~~~~~~~~~~~~~~~~~-~~~~~~~~~Cp~Cg~~~a~f~ 76 (104)
T TIGR01384 14 NGVYVCPSCGYEKEKKPEDDYKVT---EKVKHKIKETIIIREEDS-ETLPTTRVECPKCGHKEAYYW 76 (104)
T ss_pred CCeEECcCCCCccccccccccEEE---EEeccccccceeeccccc-cCCCcccCCCCCCCCCeeEEE
Confidence 4799999999875543 1122100 011111112222233332 256789999999986655555
No 11
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=69.02 E-value=1.6 Score=36.10 Aligned_cols=24 Identities=38% Similarity=0.731 Sum_probs=16.8
Q ss_pred EEEcccCCccccCCCC-cccCCCCC
Q 028408 123 TYHCICCDTPLFESST-KFDSGTGW 146 (209)
Q Consensus 123 iY~C~~Cg~pLF~S~~-KFdSg~GW 146 (209)
-++|..||.|||.=+- -|=+-||.
T Consensus 28 ~~hCp~Cg~PLF~KdG~v~CPvC~~ 52 (131)
T COG1645 28 AKHCPKCGTPLFRKDGEVFCPVCGY 52 (131)
T ss_pred HhhCcccCCcceeeCCeEECCCCCc
Confidence 4899999999998332 25555554
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=58.74 E-value=6.5 Score=28.71 Aligned_cols=43 Identities=23% Similarity=0.502 Sum_probs=31.1
Q ss_pred EEcccCCccccCCCCcccCCCCCccccccCCCCcEEeecCCCCCCcEEEEEcCCCC
Q 028408 124 YHCICCDTPLFESSTKFDSGTGWPSYYQPIGSNMKSKLDLSIIFMPRQEVLCAVCD 179 (209)
Q Consensus 124 Y~C~~Cg~pLF~S~~KFdSg~GWPSF~~pi~~~v~~~~D~s~~gm~RtEV~C~~Cg 179 (209)
|.|..||..-|.++.--.+|.||-.+++ -.+ -.=+-|.|.+||
T Consensus 1 y~C~KCg~~~~e~~~v~~tgg~~skiFd-----------vq~--~~f~~v~C~~CG 43 (64)
T PF09855_consen 1 YKCPKCGNEEYESGEVRATGGGLSKIFD-----------VQN--KKFTTVSCTNCG 43 (64)
T ss_pred CCCCCCCCcceecceEEccCCeeEEEEE-----------ecC--cEEEEEECCCCC
Confidence 7899999999999888888888865322 111 012568999997
No 13
>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=58.63 E-value=4.5 Score=26.28 Aligned_cols=21 Identities=29% Similarity=0.631 Sum_probs=17.0
Q ss_pred cCCCCCCCCceEEEcccCCcc
Q 028408 112 TGEYWNTKTPGTYHCICCDTP 132 (209)
Q Consensus 112 sg~y~~~~~~GiY~C~~Cg~p 132 (209)
.|..|...++|.|+|+.||..
T Consensus 14 C~~~~~~~~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 14 CGSRWFYSDDGFYYCDRCGHQ 34 (36)
T ss_pred CCCeEeEccCCEEEhhhCceE
Confidence 556677788999999999864
No 14
>PRK00420 hypothetical protein; Validated
Probab=54.14 E-value=7.2 Score=31.38 Aligned_cols=23 Identities=35% Similarity=0.598 Sum_probs=14.3
Q ss_pred EEcccCCccccC--CCCcccCCCCC
Q 028408 124 YHCICCDTPLFE--SSTKFDSGTGW 146 (209)
Q Consensus 124 Y~C~~Cg~pLF~--S~~KFdSg~GW 146 (209)
-+|..||.|||. ....|=+.||=
T Consensus 24 ~~CP~Cg~pLf~lk~g~~~Cp~Cg~ 48 (112)
T PRK00420 24 KHCPVCGLPLFELKDGEVVCPVHGK 48 (112)
T ss_pred CCCCCCCCcceecCCCceECCCCCC
Confidence 467777777774 44455555554
No 15
>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=52.26 E-value=6.2 Score=26.47 Aligned_cols=13 Identities=46% Similarity=1.025 Sum_probs=10.7
Q ss_pred EcccCCccccCCC
Q 028408 125 HCICCDTPLFESS 137 (209)
Q Consensus 125 ~C~~Cg~pLF~S~ 137 (209)
+|..||.|||...
T Consensus 19 ~Cp~C~~PL~~~k 31 (41)
T PF06677_consen 19 HCPDCGTPLMRDK 31 (41)
T ss_pred ccCCCCCeeEEec
Confidence 6889999999743
No 16
>PRK04351 hypothetical protein; Provisional
Probab=49.25 E-value=30 Score=28.71 Aligned_cols=14 Identities=21% Similarity=0.567 Sum_probs=11.3
Q ss_pred EEEcCCCCCCcccc
Q 028408 172 EVLCAVCDAHLGHV 185 (209)
Q Consensus 172 EV~C~~Cg~HLGHV 185 (209)
.-+|.+|++.|-.+
T Consensus 132 ~yrCg~C~g~L~~~ 145 (149)
T PRK04351 132 RYRCGKCRGKLKLI 145 (149)
T ss_pred cEEeCCCCcEeeec
Confidence 57999999988544
No 17
>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=47.98 E-value=25 Score=31.62 Aligned_cols=26 Identities=27% Similarity=0.680 Sum_probs=18.4
Q ss_pred eEEEcccCCccccCCCCccc-----CCCCCcc
Q 028408 122 GTYHCICCDTPLFESSTKFD-----SGTGWPS 148 (209)
Q Consensus 122 GiY~C~~Cg~pLF~S~~KFd-----Sg~GWPS 148 (209)
-...|+.|+.+|..+ .+|. +...|-.
T Consensus 105 ~~~~C~~C~~~li~~-~~~~~~~~LPSe~W~e 135 (354)
T PF09814_consen 105 FSLCCRNCKNPLIPS-RNFKRWKDLPSENWAE 135 (354)
T ss_pred eEEECCCCCCcccCc-cccCEEecCCccchhh
Confidence 478999999999877 3333 4556643
No 18
>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=47.47 E-value=24 Score=22.98 Aligned_cols=29 Identities=38% Similarity=0.865 Sum_probs=20.3
Q ss_pred CcEEEEEcCCCCCCccccCCCCCCCCC-cee
Q 028408 168 MPRQEVLCAVCDAHLGHVFDDGPPPTG-KRY 197 (209)
Q Consensus 168 m~RtEV~C~~Cg~HLGHVF~DGP~Ptg-~RY 197 (209)
|.-|+|.|..|++..+ |..-|..+.| .||
T Consensus 1 Ma~i~v~CP~C~s~~~-v~k~G~~~~G~qry 30 (36)
T PF03811_consen 1 MAKIDVHCPRCQSTEG-VKKNGKSPSGHQRY 30 (36)
T ss_pred CCcEeeeCCCCCCCCc-ceeCCCCCCCCEeE
Confidence 5668999999999874 3444555544 676
No 19
>PHA03351 tegument protein UL16; Provisional
Probab=46.91 E-value=8.5 Score=33.89 Aligned_cols=70 Identities=24% Similarity=0.341 Sum_probs=46.0
Q ss_pred CCCCccccccccccccCCCCCC-CCCHHHHHhcCCHHHHHHHhhcCCC--CC----ccCCCCCCCCceEEEcccCCcc
Q 028408 62 KPDNIQGIHLLSSAEANRVDYA-SISDEEWKRRLTGEQYYITRQKGTE--RA----FTGEYWNTKTPGTYHCICCDTP 132 (209)
Q Consensus 62 ~~~~~~~~~~~~~~~~~~~~~~-~~s~~ewr~~Ltp~qy~Vlr~~GTE--~p----Fsg~y~~~~~~GiY~C~~Cg~p 132 (209)
+.+.+.|++..+|.+....|.+ -+++.|. ...|..||.|+|++--- -| |+...-++...|.|-|-.|.+-
T Consensus 73 sddeiigvaf~~q~nes~~d~wlykn~t~i-rnfs~i~~nilqdglkmr~vp~tklyt~rii~n~t~grydc~rceng 149 (235)
T PHA03351 73 SDDEIIGVAFTSQHNESVTDAWLYKNDTEI-RNFSDIQTNILQDGLKMRHVPVTKLYTHRIINNHTAGRYDCFRCENG 149 (235)
T ss_pred CccceEEEEEEeccCchhhhhhhhcCCcee-echhHHHHHHHhccceeeecchhhheehhhhccccccceeeEEecCC
Confidence 3456666666666544444432 2344444 47899999999985432 34 4555568899999999999763
No 20
>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=45.33 E-value=17 Score=25.61 Aligned_cols=31 Identities=19% Similarity=0.414 Sum_probs=20.5
Q ss_pred EEEEcCCCCCCccccCCCCCCCCCceeeecceeee
Q 028408 171 QEVLCAVCDAHLGHVFDDGPPPTGKRYCINSASLK 205 (209)
Q Consensus 171 tEV~C~~Cg~HLGHVF~DGP~Ptg~RYCINS~sL~ 205 (209)
.-..|++||++|.....+.| ..+-||..+|+
T Consensus 47 ~r~FC~~CGs~l~~~~~~~~----~~~~V~~g~ld 77 (92)
T PF04828_consen 47 ERYFCPTCGSPLFSEDERDP----DLVGVNAGTLD 77 (92)
T ss_dssp EEEEETTT--EEEEEESSTT----TEEEEEGGGBT
T ss_pred cCcccCCCCCeeecccCCCC----CEEEEEeEeeC
Confidence 44999999999997744433 37777777665
No 21
>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=44.90 E-value=6.9 Score=29.59 Aligned_cols=43 Identities=33% Similarity=0.546 Sum_probs=28.0
Q ss_pred EcccCCccccCCCCcccCCCCCccccccCCCCcEEeecCCCCCCcEEEEEcCCCCCCccccC
Q 028408 125 HCICCDTPLFESSTKFDSGTGWPSYYQPIGSNMKSKLDLSIIFMPRQEVLCAVCDAHLGHVF 186 (209)
Q Consensus 125 ~C~~Cg~pLF~S~~KFdSg~GWPSF~~pi~~~v~~~~D~s~~gm~RtEV~C~~Cg~HLGHVF 186 (209)
.|+.|+.|++....+. ....|-.. |..| -+.|..|+.=||++=
T Consensus 24 ~C~iC~~~~~~~~~~~-----------------~vDHdH~t-G~vR-GlLC~~CN~~lG~~~ 66 (81)
T PF02945_consen 24 RCAICGKPLPGESRKL-----------------VVDHDHKT-GRVR-GLLCRSCNTALGKVR 66 (81)
T ss_dssp E-TTT-SEEETTCGGC-----------------EEEE-TTT-TBEE-EEEEHHHHHHHHHCT
T ss_pred cCcCCCCCcccCCCcc-----------------eecCCCCC-CCch-hhhhhHHhhhhcccc
Confidence 8999999877553221 22334333 6677 799999999999983
No 22
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=43.80 E-value=14 Score=24.26 Aligned_cols=16 Identities=25% Similarity=0.731 Sum_probs=13.7
Q ss_pred CCCCCCceEEEcccCC
Q 028408 115 YWNTKTPGTYHCICCD 130 (209)
Q Consensus 115 y~~~~~~GiY~C~~Cg 130 (209)
|.|.+..|.|+|..|+
T Consensus 17 ~~d~~g~G~~~C~~Cg 32 (37)
T smart00778 17 FDDKDGRGTWFCSVCG 32 (37)
T ss_pred cccCCCCcCEEeCCCC
Confidence 6677788999999996
No 23
>PF01352 KRAB: KRAB box; InterPro: IPR001909 The Krueppel-associated box (KRAB) is a domain of around 75 amino acids that is found in the N-terminal part of about one third of eukaryotic Krueppel-type C2H2 zinc finger proteins (ZFPs) []. It is enriched in charged amino acids and can be divided into subregions A and B, which are predicted to fold into two amphipathic alpha-helices. The KRAB A and B boxes can be separated by variable spacer segments and many KRAB proteins contain only the A box []. The functions currently known for members of the KRAB-containing protein family include transcriptional repression of RNA polymerase I, II, and III promoters, binding and splicing of RNA, and control of nucleolus function. The KRAB domain functions as a transcriptional repressor when tethered to the template DNA by a DNA-binding domain. A sequence of 45 amino acids in the KRAB A subdomain has been shown to be necessary and sufficient for transcriptional repression. The B box does not repress by itself but does potentiate the repression exerted by the KRAB A subdomain [, ]. Gene silencing requires the binding of the KRAB domain to the RING-B box-coiled coil (RBCC) domain of the KAP-1/TIF1-beta corepressor. As KAP-1 binds to the heterochromatin proteins HP1, it has been proposed that the KRAB-ZFP-bound target gene could be silenced following recruitment to heterochromatin [, ]. KRAB-ZFPs probably constitute the single largest class of transcription factors within the human genome []. Although the function of KRAB-ZFPs is largely unknown, they appear to play important roles during cell differentiation and development. The KRAB domain is generally encoded by two exons. The regions coded by the two exons are known as KRAB-A and KRAB-B.; GO: 0003676 nucleic acid binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1V65_A.
Probab=39.05 E-value=32 Score=22.76 Aligned_cols=21 Identities=33% Similarity=0.490 Sum_probs=13.2
Q ss_pred CCCCHHHHHhcCCHHHHHHHhh
Q 028408 83 ASISDEEWKRRLTGEQYYITRQ 104 (209)
Q Consensus 83 ~~~s~~ewr~~Ltp~qy~Vlr~ 104 (209)
+.+|.+||. .|.|.|...-|+
T Consensus 8 v~fs~eEW~-~L~~~Qk~ly~d 28 (41)
T PF01352_consen 8 VYFSQEEWE-LLDPAQKNLYRD 28 (41)
T ss_dssp T---HHHHH-TS-HHHHHHHHH
T ss_pred EEcChhhcc-cccceecccchh
Confidence 468999998 799999765543
No 24
>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=38.50 E-value=19 Score=23.45 Aligned_cols=15 Identities=27% Similarity=0.501 Sum_probs=12.4
Q ss_pred CCceEEEcccCCccc
Q 028408 119 KTPGTYHCICCDTPL 133 (209)
Q Consensus 119 ~~~GiY~C~~Cg~pL 133 (209)
...|.++|..||.-|
T Consensus 15 ~~~g~~vC~~CG~Vl 29 (43)
T PF08271_consen 15 PERGELVCPNCGLVL 29 (43)
T ss_dssp TTTTEEEETTT-BBE
T ss_pred CCCCeEECCCCCCEe
Confidence 678999999999877
No 25
>COG3791 Uncharacterized conserved protein [Function unknown]
Probab=36.01 E-value=15 Score=29.42 Aligned_cols=22 Identities=27% Similarity=0.682 Sum_probs=16.9
Q ss_pred CCCCCceEEEcccCCccccCCC
Q 028408 116 WNTKTPGTYHCICCDTPLFESS 137 (209)
Q Consensus 116 ~~~~~~GiY~C~~Cg~pLF~S~ 137 (209)
......+.+.|..||.+||-..
T Consensus 62 ~~s~~~~r~FC~~CGs~l~~~~ 83 (133)
T COG3791 62 FSSGSAGRGFCPTCGSPLFWRG 83 (133)
T ss_pred eecCCCCCeecccCCCceEEec
Confidence 3455567779999999998753
No 26
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=35.93 E-value=50 Score=26.80 Aligned_cols=27 Identities=11% Similarity=0.303 Sum_probs=17.6
Q ss_pred CccCC-CCCCCCceEEEcccCCccccCCC
Q 028408 110 AFTGE-YWNTKTPGTYHCICCDTPLFESS 137 (209)
Q Consensus 110 pFsg~-y~~~~~~GiY~C~~Cg~pLF~S~ 137 (209)
++.|. +.=+..++.|.|..||.. |...
T Consensus 56 ~~ega~L~i~~~p~~~~C~~CG~~-~~~~ 83 (135)
T PRK03824 56 ILEGAEIIFEEEEAVLKCRNCGNE-WSLK 83 (135)
T ss_pred cccCCEEEEEecceEEECCCCCCE-Eecc
Confidence 45442 333467899999999943 5543
No 27
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=34.68 E-value=20 Score=29.91 Aligned_cols=42 Identities=24% Similarity=0.422 Sum_probs=26.3
Q ss_pred CCCCCHHHHHhcCCHHHHHHHhhcCCCCCccCCCCCCCCceEEEcccCCccc
Q 028408 82 YASISDEEWKRRLTGEQYYITRQKGTERAFTGEYWNTKTPGTYHCICCDTPL 133 (209)
Q Consensus 82 ~~~~s~~ewr~~Ltp~qy~Vlr~~GTE~pFsg~y~~~~~~GiY~C~~Cg~pL 133 (209)
..++|.=||.+.. .=++.+| .--+|+. -.+|+|+|..||..+
T Consensus 81 ItDkTqvEw~el~-----~d~~h~g--~Y~sGE~---~g~G~l~C~~Cg~~~ 122 (146)
T PF07295_consen 81 ITDKTQVEWAELA-----QDLEHHG--VYHSGEV---VGPGTLVCENCGHEV 122 (146)
T ss_pred hhchhHHHHHHHH-----HHHHhcC--CeecCcE---ecCceEecccCCCEE
Confidence 3467777786432 3344555 2335553 358999999999765
No 28
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=31.56 E-value=25 Score=26.83 Aligned_cols=22 Identities=32% Similarity=0.682 Sum_probs=17.9
Q ss_pred EEEEEcCCCCCCccccC-CCCCC
Q 028408 170 RQEVLCAVCDAHLGHVF-DDGPP 191 (209)
Q Consensus 170 RtEV~C~~Cg~HLGHVF-~DGP~ 191 (209)
.+.-+|..||.-++|.= +|||+
T Consensus 6 k~~~~C~~CG~d~~~~~adDgPA 28 (86)
T PF06170_consen 6 KVAPRCPHCGLDYSHARADDGPA 28 (86)
T ss_pred cCCCcccccCCccccCCcCccch
Confidence 45568999999999996 67874
No 29
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=31.40 E-value=43 Score=30.84 Aligned_cols=50 Identities=22% Similarity=0.549 Sum_probs=32.5
Q ss_pred EEcccCCccccCCCCcccCCCCCccccccCCCCcEEe-ecCCCCCCc--EEEEEcCCCCCCccccCCCCC
Q 028408 124 YHCICCDTPLFESSTKFDSGTGWPSYYQPIGSNMKSK-LDLSIIFMP--RQEVLCAVCDAHLGHVFDDGP 190 (209)
Q Consensus 124 Y~C~~Cg~pLF~S~~KFdSg~GWPSF~~pi~~~v~~~-~D~s~~gm~--RtEV~C~~Cg~HLGHVF~DGP 190 (209)
--|..||..++.. .||++ -+.+ .+..++|+. |-.++|..|++++ +|.--|
T Consensus 41 i~C~~C~~~I~kG-~rFNA--------------~Ke~v~~E~Yls~~I~rF~~kC~~C~~~i--~~kTDP 93 (324)
T PF04502_consen 41 IWCNTCGEYIYKG-VRFNA--------------RKEKVGNEKYLSTPIYRFYIKCPRCSNEI--EFKTDP 93 (324)
T ss_pred CcCCCCccccccc-eeeee--------------eeEecCCCccccceEEEEEEEcCCCCCEE--eeecCC
Confidence 3599999997764 46664 2222 233345654 8899999999976 564333
No 30
>PRK08624 hypothetical protein; Provisional
Probab=30.43 E-value=53 Score=31.54 Aligned_cols=19 Identities=26% Similarity=0.637 Sum_probs=13.8
Q ss_pred CCceEEEcc-cCCc--cccCCC
Q 028408 119 KTPGTYHCI-CCDT--PLFESS 137 (209)
Q Consensus 119 ~~~GiY~C~-~Cg~--pLF~S~ 137 (209)
.+.++|+|= +||. -.|.-=
T Consensus 55 pekq~yhCF~GCGa~GDVf~Fv 76 (373)
T PRK08624 55 IENDNFHCYTRCGDIFDVFELL 76 (373)
T ss_pred CCCCEEEEeCCCCCCCceeeeh
Confidence 467899998 9998 454433
No 31
>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=29.88 E-value=41 Score=23.61 Aligned_cols=26 Identities=19% Similarity=0.326 Sum_probs=21.2
Q ss_pred CcEEEEEcCCCCCCccccCCCCCCCC
Q 028408 168 MPRQEVLCAVCDAHLGHVFDDGPPPT 193 (209)
Q Consensus 168 m~RtEV~C~~Cg~HLGHVF~DGP~Pt 193 (209)
..|..+.|++|..|=|-+....+.+.
T Consensus 18 ~~r~aLIC~~C~~hNGla~~~~~~~i 43 (54)
T PF10058_consen 18 SNRYALICSKCFSHNGLAPKEEFEEI 43 (54)
T ss_pred cCceeEECcccchhhcccccccCCce
Confidence 45899999999999999986555554
No 32
>PRK12495 hypothetical protein; Provisional
Probab=29.68 E-value=19 Score=32.39 Aligned_cols=14 Identities=36% Similarity=0.821 Sum_probs=12.7
Q ss_pred ceEEEcccCCcccc
Q 028408 121 PGTYHCICCDTPLF 134 (209)
Q Consensus 121 ~GiY~C~~Cg~pLF 134 (209)
..-++|..||.|||
T Consensus 40 msa~hC~~CG~PIp 53 (226)
T PRK12495 40 MTNAHCDECGDPIF 53 (226)
T ss_pred cchhhcccccCccc
Confidence 46789999999999
No 33
>COG3791 Uncharacterized conserved protein [Function unknown]
Probab=28.86 E-value=43 Score=26.85 Aligned_cols=28 Identities=21% Similarity=0.310 Sum_probs=21.9
Q ss_pred EcCCCCCCccccCCCCCCCCCceeeecceeee
Q 028408 174 LCAVCDAHLGHVFDDGPPPTGKRYCINSASLK 205 (209)
Q Consensus 174 ~C~~Cg~HLGHVF~DGP~Ptg~RYCINS~sL~ 205 (209)
.|++||+||-+.-.|++ .-+=||-++|+
T Consensus 71 FC~~CGs~l~~~~~~~~----~~~~v~~~~ld 98 (133)
T COG3791 71 FCPTCGSPLFWRGPDED----PFVGVNAGALD 98 (133)
T ss_pred ecccCCCceEEecCCCC----ceEEEEEeeec
Confidence 99999999998877764 35667766665
No 34
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=28.49 E-value=22 Score=24.05 Aligned_cols=15 Identities=40% Similarity=0.875 Sum_probs=12.2
Q ss_pred EEcCCCCCCccccCCC
Q 028408 173 VLCAVCDAHLGHVFDD 188 (209)
Q Consensus 173 V~C~~Cg~HLGHVF~D 188 (209)
|+|.+||+ +||.=.+
T Consensus 2 ~kC~~CG~-~GH~~t~ 16 (40)
T PF15288_consen 2 VKCKNCGA-FGHMRTN 16 (40)
T ss_pred cccccccc-ccccccC
Confidence 68999997 6998654
No 35
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=27.86 E-value=49 Score=30.08 Aligned_cols=32 Identities=19% Similarity=0.486 Sum_probs=26.6
Q ss_pred CCCceEEEcccCCccccCCCCcccCCCCCccccc
Q 028408 118 TKTPGTYHCICCDTPLFESSTKFDSGTGWPSYYQ 151 (209)
Q Consensus 118 ~~~~GiY~C~~Cg~pLF~S~~KFdSg~GWPSF~~ 151 (209)
..+.|.++|..||.-| .+.-.|.|.-|-+|..
T Consensus 25 d~~~Ge~vC~~CG~Vl--~e~~iD~g~EWR~f~~ 56 (310)
T PRK00423 25 DYERGEIVCADCGLVI--EENIIDQGPEWRAFDP 56 (310)
T ss_pred ECCCCeEeecccCCcc--cccccccCCCccCCCc
Confidence 3578999999999876 4556788999999976
No 36
>cd04984 IgV_L_lambda Immunoglobulin (Ig) lambda light chain variable (V) domain. IgV_L_lambda: Immunoglobulin (Ig) light chain, lambda type, variable (V) domain. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. In Ig, each chain is composed of one variable domain (IgV) and one or more constant domains (IgC); these names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. There are five types of heavy chains (alpha, gamma, delta, epsilon, and mu), which determine the type of immunoglobulin: IgA, IgG, IgD, IgE, and IgM, respectively. In higher vertebrates, there are two types of light chain, designated kappa and lambda, which seem to be functionally identical, and can associate with any of the heavy chains.
Probab=26.62 E-value=38 Score=24.52 Aligned_cols=13 Identities=23% Similarity=0.478 Sum_probs=10.0
Q ss_pred CCCCceEEEcccC
Q 028408 117 NTKTPGTYHCICC 129 (209)
Q Consensus 117 ~~~~~GiY~C~~C 129 (209)
...+.|+|.|++-
T Consensus 71 ~~~Dsg~Y~C~~~ 83 (98)
T cd04984 71 QTEDEADYYCQVW 83 (98)
T ss_pred ChhhCEEEEEEEc
Confidence 3457899999874
No 37
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=26.58 E-value=49 Score=30.35 Aligned_cols=30 Identities=23% Similarity=0.582 Sum_probs=24.8
Q ss_pred CCCceEEEcccCCccccCCCCcccCCCCCccc
Q 028408 118 TKTPGTYHCICCDTPLFESSTKFDSGTGWPSY 149 (209)
Q Consensus 118 ~~~~GiY~C~~Cg~pLF~S~~KFdSg~GWPSF 149 (209)
..+.|-++|+.||.-| -+.-+|.|..|=.|
T Consensus 15 d~~~ge~VC~~CG~Vi--~~~~id~gpewr~f 44 (285)
T COG1405 15 DYERGEIVCADCGLVL--EDSLIDPGPEWRAF 44 (285)
T ss_pred eccCCeEEeccCCEEe--ccccccCCCCcccc
Confidence 3457999999999877 45568899999999
No 38
>PF09965 DUF2199: Uncharacterized protein conserved in bacteria (DUF2199); InterPro: IPR018697 This domain has no known function.
Probab=26.21 E-value=32 Score=28.78 Aligned_cols=25 Identities=28% Similarity=0.541 Sum_probs=19.0
Q ss_pred EEcccCCccccCCCCcccCCCCCccccccCCCCcE
Q 028408 124 YHCICCDTPLFESSTKFDSGTGWPSYYQPIGSNMK 158 (209)
Q Consensus 124 Y~C~~Cg~pLF~S~~KFdSg~GWPSF~~pi~~~v~ 158 (209)
|.|.+||+.- -|||||.-..|+.+.
T Consensus 1 y~C~~Cg~~h----------~~~P~~~~~~Pd~~~ 25 (148)
T PF09965_consen 1 YTCSCCGEEH----------EGLPSLGFDAPDYYY 25 (148)
T ss_pred CCCCcCCccC----------CCCcccccCCChhhh
Confidence 7899999864 488888777776543
No 39
>PF04032 Rpr2: RNAse P Rpr2/Rpp21/SNM1 subunit domain; InterPro: IPR007175 This family contains a ribonuclease P subunit of human and yeast. Other members of the family include the probable archaeal homologues. This subunit possibly binds the precursor tRNA [].; PDB: 2K3R_A 2KI7_B 2ZAE_B 1X0T_A.
Probab=25.59 E-value=99 Score=22.08 Aligned_cols=65 Identities=12% Similarity=0.132 Sum_probs=28.6
Q ss_pred HHHhcCCHHHHHHHhhcCCCCCccCCCCCCCCceEEEcccCCccccCCCCcccCCCCCccccccCCCCcEEeecCCCCCC
Q 028408 89 EWKRRLTGEQYYITRQKGTERAFTGEYWNTKTPGTYHCICCDTPLFESSTKFDSGTGWPSYYQPIGSNMKSKLDLSIIFM 168 (209)
Q Consensus 89 ewr~~Ltp~qy~Vlr~~GTE~pFsg~y~~~~~~GiY~C~~Cg~pLF~S~~KFdSg~GWPSF~~pi~~~v~~~~D~s~~gm 168 (209)
++-..+...-..|.++....-|- ++ -.-.|..||.+|-...+ -.|....+.. ..
T Consensus 20 ~lsr~y~~~~~~i~~k~~~~l~~--~~------kr~~Ck~C~~~liPG~~----------------~~vri~~~~~--~~ 73 (85)
T PF04032_consen 20 SLSRHYMKLMRKISKKTRIRLPP--EI------KRTICKKCGSLLIPGVN----------------CSVRIRKKKK--KK 73 (85)
T ss_dssp HHHHHHHHHHHHHHHHCT---ST--TC------CCTB-TTT--B--CTTT----------------EEEEEE---S--SS
T ss_pred HHHHHHHHHHHHHHHHhCCCCCh--HH------hcccccCCCCEEeCCCc----------------cEEEEEecCC--CC
Confidence 34444445556677765555332 22 12379999988742111 1122222222 24
Q ss_pred cEEEEEcCCCC
Q 028408 169 PRQEVLCAVCD 179 (209)
Q Consensus 169 ~RtEV~C~~Cg 179 (209)
..+.+.|..||
T Consensus 74 ~~l~~~C~~C~ 84 (85)
T PF04032_consen 74 NFLVYTCLNCG 84 (85)
T ss_dssp -EEEEEETTTT
T ss_pred CEEEEEccccC
Confidence 57999999997
No 40
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=25.54 E-value=57 Score=22.17 Aligned_cols=17 Identities=12% Similarity=0.319 Sum_probs=13.2
Q ss_pred CCCCCceEEEcccCCcc
Q 028408 116 WNTKTPGTYHCICCDTP 132 (209)
Q Consensus 116 ~~~~~~GiY~C~~Cg~p 132 (209)
.+....|+|.|..||.-
T Consensus 19 ~~~~~~~~~~C~~Cga~ 35 (53)
T TIGR03655 19 DPLDLSHYFECSTCGAS 35 (53)
T ss_pred CCCCCEEEEECCCCCCC
Confidence 45567788999999875
No 41
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 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 the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=24.81 E-value=48 Score=20.28 Aligned_cols=23 Identities=26% Similarity=0.504 Sum_probs=11.4
Q ss_pred EcCCCCCCccccCCCCCCCCCceeeecc
Q 028408 174 LCAVCDAHLGHVFDDGPPPTGKRYCINS 201 (209)
Q Consensus 174 ~C~~Cg~HLGHVF~DGP~Ptg~RYCINS 201 (209)
.|..||+.|=+. +|+ -..||+|+
T Consensus 1 ~CP~C~s~l~~~-~~e----v~~~C~N~ 23 (28)
T PF03119_consen 1 TCPVCGSKLVRE-EGE----VDIRCPNP 23 (28)
T ss_dssp B-TTT--BEEE--CCT----TCEEE--C
T ss_pred CcCCCCCEeEcC-CCC----EeEECCCC
Confidence 488999998743 332 25899998
No 42
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=24.14 E-value=38 Score=21.68 Aligned_cols=17 Identities=35% Similarity=0.679 Sum_probs=11.8
Q ss_pred CCcEEEEEcCCCCCCccccCC
Q 028408 167 FMPRQEVLCAVCDAHLGHVFD 187 (209)
Q Consensus 167 gm~RtEV~C~~Cg~HLGHVF~ 187 (209)
+.....|+|++|+ |+|.
T Consensus 20 ~~~~~~vrC~~C~----~~f~ 36 (37)
T PF13719_consen 20 PAGGRKVRCPKCG----HVFR 36 (37)
T ss_pred ccCCcEEECCCCC----cEee
Confidence 3445589999995 6653
No 43
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=23.81 E-value=42 Score=23.97 Aligned_cols=13 Identities=15% Similarity=0.337 Sum_probs=9.3
Q ss_pred EcccCCccccCCC
Q 028408 125 HCICCDTPLFESS 137 (209)
Q Consensus 125 ~C~~Cg~pLF~S~ 137 (209)
.|..||.++..+.
T Consensus 19 ~CP~CG~~t~~~~ 31 (56)
T PRK13130 19 ICPVCGGKTKNPH 31 (56)
T ss_pred cCcCCCCCCCCCC
Confidence 4888888886553
No 44
>PRK04179 rpl37e 50S ribosomal protein L37e; Reviewed
Probab=23.33 E-value=43 Score=24.65 Aligned_cols=27 Identities=19% Similarity=0.448 Sum_probs=24.1
Q ss_pred eEEEcccCCccccCCCCcccCCCCC-cc
Q 028408 122 GTYHCICCDTPLFESSTKFDSGTGW-PS 148 (209)
Q Consensus 122 GiY~C~~Cg~pLF~S~~KFdSg~GW-PS 148 (209)
-.-.|..||.--|....+.=+.||+ ||
T Consensus 16 tHt~CrRCG~~syh~qK~~CasCGygps 43 (62)
T PRK04179 16 THIRCRRCGRHSYNVRKKYCAACGFGRS 43 (62)
T ss_pred ccchhcccCcccccccccchhhcCCCcc
Confidence 4557999999999999999999999 75
No 45
>cd04980 IgV_L_kappa Immunoglobulin (Ig) light chain, kappa type, variable (V) domain. IgV_L_kappa: Immunoglobulin (Ig) light chain, kappa type, variable (V) domain. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. In Ig, each chain is composed of one variable domain (IgV) and one or more constant domains (IgC); these names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. There are five types of heavy chains (alpha, gamma, delta, epsilon, and mu), which determine the type of immunoglobulin: IgA, IgG, IgD, IgE, and IgM, respectively. In higher vertebrates, there are two types of light chain, designated kappa and lambda, which seem to be functionally identical, and can associate with any of the heavy chains.
Probab=23.19 E-value=42 Score=24.68 Aligned_cols=12 Identities=17% Similarity=0.401 Sum_probs=9.4
Q ss_pred CCCceEEEcccC
Q 028408 118 TKTPGTYHCICC 129 (209)
Q Consensus 118 ~~~~GiY~C~~C 129 (209)
..+.|+|.|+.-
T Consensus 80 ~~Dsg~Y~Ca~~ 91 (106)
T cd04980 80 PEDAAVYYCQQY 91 (106)
T ss_pred hHHCEEEEEEEe
Confidence 457899999873
No 46
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=21.80 E-value=1.4e+02 Score=19.57 Aligned_cols=11 Identities=27% Similarity=0.893 Sum_probs=8.0
Q ss_pred EEEcccCCccc
Q 028408 123 TYHCICCDTPL 133 (209)
Q Consensus 123 iY~C~~Cg~pL 133 (209)
.|.|..||..+
T Consensus 3 ~y~C~~CG~~~ 13 (46)
T PRK00398 3 EYKCARCGREV 13 (46)
T ss_pred EEECCCCCCEE
Confidence 57888888754
No 47
>PHA02565 49 recombination endonuclease VII; Provisional
Probab=21.26 E-value=49 Score=28.33 Aligned_cols=21 Identities=29% Similarity=0.515 Sum_probs=16.4
Q ss_pred CCcEEEEEcCCCCCCccccCCC
Q 028408 167 FMPRQEVLCAVCDAHLGHVFDD 188 (209)
Q Consensus 167 gm~RtEV~C~~Cg~HLGHVF~D 188 (209)
|-+| -+.|..|+.-||+|=++
T Consensus 51 G~VR-GLLC~~CN~~lG~~~~~ 71 (157)
T PHA02565 51 GRVR-GLLCNLCNALEGQMKHK 71 (157)
T ss_pred cccc-ccCchhhhhhhhhhhhh
Confidence 4445 58999999999998543
No 48
>PF00047 ig: Immunoglobulin domain The Prosite family only concerns antibodies and MHCs.; InterPro: IPR013151 Members of the immunoglobulin superfamily are found in hundreds of proteins of different functions. Examples include antibodies, the giant muscle kinase titin and receptor tyrosine kinases. Immunoglobulin-like domains may be involved in protein-protein and protein-ligand interactions. The Pfam alignments do not include the first and last strand of the immunoglobulin-like domain.; PDB: 1B6U_A 3O4O_C 3VH8_H 1BIH_A 2C9A_A 2V5Y_A 1BQH_K 2ATP_A 3B9K_A 1NEZ_H ....
Probab=21.10 E-value=48 Score=21.52 Aligned_cols=10 Identities=40% Similarity=1.092 Sum_probs=7.5
Q ss_pred CCceEEEccc
Q 028408 119 KTPGTYHCIC 128 (209)
Q Consensus 119 ~~~GiY~C~~ 128 (209)
.+.|+|.|.+
T Consensus 55 ~d~G~Y~C~v 64 (64)
T PF00047_consen 55 EDSGTYTCVV 64 (64)
T ss_dssp GGTEEEEEEE
T ss_pred HHCEEEEEEC
Confidence 3679999964
No 49
>PTZ00073 60S ribosomal protein L37; Provisional
Probab=20.88 E-value=51 Score=25.94 Aligned_cols=28 Identities=25% Similarity=0.396 Sum_probs=25.0
Q ss_pred eEEEcccCCccccCCCCcccCCCCCccc
Q 028408 122 GTYHCICCDTPLFESSTKFDSGTGWPSY 149 (209)
Q Consensus 122 GiY~C~~Cg~pLF~S~~KFdSg~GWPSF 149 (209)
-.-.|..||.--|.-..+.=+.||+|+=
T Consensus 15 tHtlCrRCG~~syH~qK~~CasCGypsa 42 (91)
T PTZ00073 15 THTLCRRCGKRSFHVQKKRCASCGYPSA 42 (91)
T ss_pred CcchhcccCccccccccccchhcCCchh
Confidence 4567999999999999999999999874
No 50
>cd04983 IgV_TCR_alpha_like Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) alpha chain and similar proteins. IgV_TCR_alpha: immunoglobulin (Ig) variable domain of the alpha chain of alpha/beta T-cell antigen receptors (TCRs). TCRs mediate antigen recognition by T lymphocytes, and are composed of alpha and beta, or gamma and delta, polypeptide chains with variable (V) and constant (C) regions. This group represents the variable domain of the alpha chain of TCRs and also includes the variable domain of delta chains of TCRs. Alpha/beta TCRs recognize antigen as peptide fragments presented by major histocompatibility complex (MHC) molecules. The variable domain of TCRs is responsible for antigen recognition, and is located at the N-terminus of the receptor. Gamma/delta TCRs recognize intact protein antigens; they recognize proteins antigens directly and without antigen processing, and MHC independently of the bound peptide.
Probab=20.81 E-value=57 Score=23.64 Aligned_cols=14 Identities=14% Similarity=0.479 Sum_probs=10.7
Q ss_pred CCCCceEEEcccCC
Q 028408 117 NTKTPGTYHCICCD 130 (209)
Q Consensus 117 ~~~~~GiY~C~~Cg 130 (209)
...+.|+|.|++..
T Consensus 78 ~~~DsG~Y~C~~~~ 91 (109)
T cd04983 78 QLSDSAVYFCALSE 91 (109)
T ss_pred CHHHCEEEEEEEec
Confidence 34578999999764
No 51
>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=20.06 E-value=52 Score=20.53 Aligned_cols=11 Identities=27% Similarity=0.631 Sum_probs=9.0
Q ss_pred EEEcCCCCCCc
Q 028408 172 EVLCAVCDAHL 182 (209)
Q Consensus 172 EV~C~~Cg~HL 182 (209)
+|+|.+||.-+
T Consensus 25 ~v~C~~C~~~~ 35 (38)
T TIGR02098 25 KVRCGKCGHVW 35 (38)
T ss_pred EEECCCCCCEE
Confidence 79999998654
No 52
>PHA02540 61 DNA primase; Provisional
Probab=20.01 E-value=49 Score=31.12 Aligned_cols=24 Identities=17% Similarity=0.522 Sum_probs=16.3
Q ss_pred CCCccCC---------CCCCCCce--EEEcccCCc
Q 028408 108 ERAFTGE---------YWNTKTPG--TYHCICCDT 131 (209)
Q Consensus 108 E~pFsg~---------y~~~~~~G--iY~C~~Cg~ 131 (209)
--||.|+ +|=..+.| +|+|=+||.
T Consensus 29 ~CPf~~ds~~~~~kpsF~V~p~k~~~~yhCFgCGa 63 (337)
T PHA02540 29 RCPICGDSQKDKNKARGWIYEKKDGGVFKCHNCGY 63 (337)
T ss_pred cCCCCCCccccCcCCcEEEeccCCceEEEecCCCC
Confidence 3577666 44344455 999999996
Done!