Query 028947
Match_columns 201
No_of_seqs 178 out of 1280
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 05:03:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028947.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028947hhsearch_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 4.3E-71 9.3E-76 447.7 12.0 126 75-201 2-129 (140)
2 TIGR00357 methionine-R-sulfoxi 100.0 5.7E-70 1.2E-74 439.6 13.0 124 77-201 2-126 (134)
3 PRK00222 methionine sulfoxide 100.0 2.9E-69 6.3E-74 439.1 13.4 126 75-201 3-129 (142)
4 PF01641 SelR: SelR domain; I 100.0 7.7E-69 1.7E-73 428.1 10.2 122 79-201 1-124 (124)
5 PRK05508 methionine sulfoxide 100.0 1.1E-65 2.4E-70 407.8 11.8 115 84-201 2-117 (119)
6 KOG0856 Predicted pilin-like t 100.0 3.2E-64 7E-69 408.9 10.4 131 70-201 9-142 (146)
7 PRK14018 trifunctional thiored 100.0 2.5E-59 5.5E-64 441.9 13.3 131 70-201 373-505 (521)
8 PRK05550 bifunctional methioni 100.0 6.7E-59 1.4E-63 412.3 10.5 119 80-201 1-120 (283)
9 PF03226 Yippee-Mis18: Yippee 94.5 0.026 5.7E-07 42.2 2.2 81 115-196 2-92 (96)
10 TIGR01384 TFS_arch transcripti 73.6 3.9 8.5E-05 30.8 3.1 62 113-178 14-76 (104)
11 COG1645 Uncharacterized Zn-fin 70.7 1.4 3.1E-05 36.3 0.1 24 115-138 28-52 (131)
12 PF09855 DUF2082: Nucleic-acid 60.9 5.5 0.00012 28.9 1.6 43 116-171 1-43 (64)
13 PF11781 RRN7: RNA polymerase 59.1 4.5 9.8E-05 26.1 0.8 21 104-124 14-34 (36)
14 PRK00420 hypothetical protein; 52.6 7.4 0.00016 31.2 1.2 23 116-138 24-48 (112)
15 PF04828 GFA: Glutathione-depe 51.2 13 0.00028 26.1 2.1 33 161-197 45-77 (92)
16 PF06677 Auto_anti-p27: Sjogre 50.2 7.1 0.00015 26.1 0.6 14 116-129 18-31 (41)
17 PF03811 Zn_Tnp_IS1: InsA N-te 47.1 24 0.00053 22.8 2.7 29 160-189 1-30 (36)
18 smart00778 Prim_Zn_Ribbon Zinc 46.9 13 0.00028 24.3 1.4 17 107-123 17-33 (37)
19 PF02945 Endonuclease_7: Recom 43.4 7.3 0.00016 29.3 -0.2 44 117-179 24-67 (81)
20 PF06170 DUF983: Protein of un 39.0 16 0.00035 27.7 1.1 22 162-183 6-28 (86)
21 COG3791 Uncharacterized conser 38.6 14 0.00029 29.5 0.7 22 107-128 61-82 (133)
22 PF08271 TF_Zn_Ribbon: TFIIB z 38.0 21 0.00045 23.1 1.4 15 111-125 15-29 (43)
23 PF07295 DUF1451: Protein of u 36.8 18 0.00038 30.0 1.1 42 74-125 81-122 (146)
24 PF01352 KRAB: KRAB box; Inte 35.9 40 0.00086 22.2 2.5 21 75-96 8-28 (41)
25 COG3791 Uncharacterized conser 35.3 28 0.0006 27.8 2.0 28 166-197 71-98 (133)
26 PF10058 DUF2296: Predicted in 33.7 32 0.0007 24.0 1.8 26 160-185 18-43 (54)
27 PF15288 zf-CCHC_6: Zinc knuck 33.4 16 0.00035 24.6 0.3 15 165-180 2-16 (40)
28 PRK12495 hypothetical protein; 32.0 17 0.00036 32.6 0.2 16 111-126 38-53 (226)
29 COG1405 SUA7 Transcription ini 27.7 46 0.001 30.3 2.3 30 110-141 15-44 (285)
30 PRK00423 tfb transcription ini 27.3 51 0.0011 29.7 2.5 32 110-143 25-56 (310)
31 cd04984 IgV_L_lambda Immunoglo 26.9 37 0.00079 24.4 1.3 12 110-121 72-83 (98)
32 PF09965 DUF2199: Uncharacteri 26.6 31 0.00067 28.7 0.9 25 116-150 1-25 (148)
33 TIGR03655 anti_R_Lar restricti 26.1 52 0.0011 22.2 1.8 17 108-124 19-35 (53)
34 PRK13130 H/ACA RNA-protein com 25.1 38 0.00083 24.1 1.0 13 117-129 19-31 (56)
35 PF13719 zinc_ribbon_5: zinc-r 24.3 37 0.00081 21.6 0.8 17 159-179 20-36 (37)
36 cd04980 IgV_L_kappa Immunoglob 23.8 38 0.00083 24.7 0.9 12 110-121 80-91 (106)
37 PRK08624 hypothetical protein; 23.2 1.3E+02 0.0028 28.8 4.4 22 110-131 54-78 (373)
38 PHA02540 61 DNA primase; Provi 22.2 42 0.00092 31.4 1.0 18 107-124 45-64 (337)
39 PF03119 DNA_ligase_ZBD: NAD-d 22.0 59 0.0013 19.8 1.3 23 166-193 1-23 (28)
40 PRK04179 rpl37e 50S ribosomal 21.9 48 0.001 24.3 1.1 27 114-140 16-43 (62)
41 COG1885 Uncharacterized protei 21.7 35 0.00076 27.6 0.3 15 111-125 45-59 (115)
42 PF00047 ig: Immunoglobulin do 21.3 43 0.00093 21.6 0.7 10 111-120 55-64 (64)
43 TIGR02098 MJ0042_CXXC MJ0042 f 20.9 48 0.001 20.6 0.8 12 163-174 24-35 (38)
44 PF13717 zinc_ribbon_4: zinc-r 20.7 56 0.0012 20.8 1.1 11 161-171 22-32 (36)
45 TIGR03831 YgiT_finger YgiT-typ 20.6 47 0.001 20.8 0.7 18 112-129 29-46 (46)
46 cd05862 Ig1_VEGFR First immuno 20.5 56 0.0012 23.4 1.2 22 110-131 59-81 (86)
47 cd04983 IgV_TCR_alpha_like Imm 20.2 58 0.0013 23.4 1.2 14 110-123 79-92 (109)
48 PTZ00073 60S ribosomal protein 20.1 55 0.0012 25.7 1.1 28 114-141 15-42 (91)
No 1
>COG0229 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=4.3e-71 Score=447.70 Aligned_cols=126 Identities=60% Similarity=1.034 Sum_probs=121.7
Q ss_pred CCCCHHHHHhcCCHHHHHHHhhcCCCCCccCCCCCCCCCeEEEcccCCcccccCCCcccCCCCCccccccCC-CCceeee
Q 028947 75 ASISDEEWKRRLTGEQYYITRQKGTERAFTGEYWNTKTPGTYHCICCDTPLFESSTKFDSGTGWPSYYQPIG-SNMKSKL 153 (201)
Q Consensus 75 ~~~sd~ewk~~LTp~qy~V~r~~GTE~pfsG~y~~~~~~G~Y~C~~Cg~pLFsS~~KFdSg~GWPSF~~~i~-~~V~~~~ 153 (201)
+.++|+|||++|||+||+|||++|||+||+|+||+++++|+|+|++||+|||+|++|||||||||||++||. ++|+++.
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 457899999999999999999999999999999999999999999999999999999999999999999996 6899999
Q ss_pred cCCCCCccEEEEEcCCCCCCccccCCCCCCCCC-ceeeeccceeeeeeC
Q 028947 154 DLSIIFMPRQEVLCAVCDAHLGHVFDDGPPPTG-KRYCINSASLKLKPK 201 (201)
Q Consensus 154 D~s~~gm~RtEV~C~~Cg~HLGHVF~DGP~ptg-~RYCINS~sL~F~p~ 201 (201)
|.|+ ||.||||+|++||+||||||+|||+||| +|||||||||+|+|+
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 9996 9999999999999999999999999998 999999999999984
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=5.7e-70 Score=439.63 Aligned_cols=124 Identities=58% Similarity=0.982 Sum_probs=120.5
Q ss_pred CCHHHHHhcCCHHHHHHHhhcCCCCCccCCCCCCCCCeEEEcccCCcccccCCCcccCCCCCccccccC-CCCceeeecC
Q 028947 77 ISDEEWKRRLTGEQYYITRQKGTERAFTGEYWNTKTPGTYHCICCDTPLFESSTKFDSGTGWPSYYQPI-GSNMKSKLDL 155 (201)
Q Consensus 77 ~sd~ewk~~LTp~qy~V~r~~GTE~pfsG~y~~~~~~G~Y~C~~Cg~pLFsS~~KFdSg~GWPSF~~~i-~~~V~~~~D~ 155 (201)
++|+|||+.|||+||+|+|++|||+||||+||+++++|+|+|++||+|||+|++|||||||||||+++| +++|+++.|.
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 589999999999999999999999999999999999999999999999999999999999999999999 5789999999
Q ss_pred CCCCccEEEEEcCCCCCCccccCCCCCCCCCceeeeccceeeeeeC
Q 028947 156 SIIFMPRQEVLCAVCDAHLGHVFDDGPPPTGKRYCINSASLKLKPK 201 (201)
Q Consensus 156 s~~gm~RtEV~C~~Cg~HLGHVF~DGP~ptg~RYCINS~sL~F~p~ 201 (201)
++ ||+||||+|++||+||||||+|||+|||+||||||+||+|+|+
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 86 9999999999999999999999999999999999999999984
No 3
>PRK00222 methionine sulfoxide reductase B; Provisional
Probab=100.00 E-value=2.9e-69 Score=439.05 Aligned_cols=126 Identities=60% Similarity=1.057 Sum_probs=121.9
Q ss_pred CCCCHHHHHhcCCHHHHHHHhhcCCCCCccCCCCCCCCCeEEEcccCCcccccCCCcccCCCCCccccccCC-CCceeee
Q 028947 75 ASISDEEWKRRLTGEQYYITRQKGTERAFTGEYWNTKTPGTYHCICCDTPLFESSTKFDSGTGWPSYYQPIG-SNMKSKL 153 (201)
Q Consensus 75 ~~~sd~ewk~~LTp~qy~V~r~~GTE~pfsG~y~~~~~~G~Y~C~~Cg~pLFsS~~KFdSg~GWPSF~~~i~-~~V~~~~ 153 (201)
+.++|+|||+.|||+||+|+|++||||||||+||+++++|+|+|++||+|||+|++|||||||||||+++|+ ++|+.+.
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 cCCCCCccEEEEEcCCCCCCccccCCCCCCCCCceeeeccceeeeeeC
Q 028947 154 DLSIIFMPRQEVLCAVCDAHLGHVFDDGPPPTGKRYCINSASLKLKPK 201 (201)
Q Consensus 154 D~s~~gm~RtEV~C~~Cg~HLGHVF~DGP~ptg~RYCINS~sL~F~p~ 201 (201)
|.++ ||.||||+|++||+||||||+|||+|||+||||||+||+|+|+
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 9886 9999999999999999999999999999999999999999984
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=7.7e-69 Score=428.12 Aligned_cols=122 Identities=66% Similarity=1.207 Sum_probs=115.2
Q ss_pred HHHHHhcCCHHHHHHHhhcCCCCCccCCCCCCCCCeEEEcccCCcccccCCCcccCCCCCccccccCCC-CceeeecCCC
Q 028947 79 DEEWKRRLTGEQYYITRQKGTERAFTGEYWNTKTPGTYHCICCDTPLFESSTKFDSGTGWPSYYQPIGS-NMKSKLDLSI 157 (201)
Q Consensus 79 d~ewk~~LTp~qy~V~r~~GTE~pfsG~y~~~~~~G~Y~C~~Cg~pLFsS~~KFdSg~GWPSF~~~i~~-~V~~~~D~s~ 157 (201)
|+|||++|||+||+|||++|||+||||+||+++++|+|+|++||+|||+|++||+||||||||+++|++ +|..+.|.++
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 8999999886
Q ss_pred CCccEEEEEcCCCCCCccccCCCCCCC-CCceeeeccceeeeeeC
Q 028947 158 IFMPRQEVLCAVCDAHLGHVFDDGPPP-TGKRYCINSASLKLKPK 201 (201)
Q Consensus 158 ~gm~RtEV~C~~Cg~HLGHVF~DGP~p-tg~RYCINS~sL~F~p~ 201 (201)
||+||||+|++||+||||||+|||+| ||+||||||+||+|+|+
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=1.1e-65 Score=407.81 Aligned_cols=115 Identities=44% Similarity=0.804 Sum_probs=110.2
Q ss_pred hcCCHHHHHHHhhcCCCCCccCCCCCCCCCeEEEcccCCcccccCCCcccCCCCCccccccCCCCceeeecCCCCCccEE
Q 028947 84 RRLTGEQYYITRQKGTERAFTGEYWNTKTPGTYHCICCDTPLFESSTKFDSGTGWPSYYQPIGSNMKSKLDLSIIFMPRQ 163 (201)
Q Consensus 84 ~~LTp~qy~V~r~~GTE~pfsG~y~~~~~~G~Y~C~~Cg~pLFsS~~KFdSg~GWPSF~~~i~~~V~~~~D~s~~gm~Rt 163 (201)
++|||+||+|+|++||||||+|+||+++++|+|+|++||+|||+|++|||||||||||+++|+++|+.+.|.+ |.||
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 5899999999999999999999999999999999999999999999999999999999999998999999976 4699
Q ss_pred EEEcCCCCCCccccCC-CCCCCCCceeeeccceeeeeeC
Q 028947 164 EVLCAVCDAHLGHVFD-DGPPPTGKRYCINSASLKLKPK 201 (201)
Q Consensus 164 EV~C~~Cg~HLGHVF~-DGP~ptg~RYCINS~sL~F~p~ 201 (201)
||+|++||+||||||+ |||+|||+|||||||||+|+|+
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=408.92 Aligned_cols=131 Identities=47% Similarity=0.855 Sum_probs=124.5
Q ss_pred cccCCCCCCHHHHHhcCCHHHHHHHhhcCCCCCccCCCCCCCCCeEEEcccCCcccccCCCcccCCCCCccccccC-CCC
Q 028947 70 NRVDYASISDEEWKRRLTGEQYYITRQKGTERAFTGEYWNTKTPGTYHCICCDTPLFESSTKFDSGTGWPSYYQPI-GSN 148 (201)
Q Consensus 70 ~~~~~~~~sd~ewk~~LTp~qy~V~r~~GTE~pfsG~y~~~~~~G~Y~C~~Cg~pLFsS~~KFdSg~GWPSF~~~i-~~~ 148 (201)
.+...++++|+|||+.||||||+|||++|||+||+|+|++++++|+|+|++|++|||+|++|||||||||+|++.| +++
T Consensus 9 ~~~~~v~k~~~EWr~~LsPeQ~~v~RekgTE~p~tGey~~~~e~GvY~C~~C~~pLykS~tKfdsgcGWPAF~e~i~~ga 88 (146)
T KOG0856|consen 9 PKTGSVQKNDEEWRKVLSPEQFRVLREKGTERPGTGEYTKHFEEGVYVCAGCGTPLYKSTTKFDSGCGWPAFFEAIGPGA 88 (146)
T ss_pred CCCcccccCHHHHHhhcCHHHhhhhHhhcccCCCCcccccccCCceEEEeecCCccccccccccCCCCCchhhhccCCCc
Confidence 3455678999999999999999999999999999999999999999999999999999999999999999999999 788
Q ss_pred ceeeecCCCCCccEEEEEcCCCCCCccccCC-CCCC-CCCceeeeccceeeeeeC
Q 028947 149 MKSKLDLSIIFMPRQEVLCAVCDAHLGHVFD-DGPP-PTGKRYCINSASLKLKPK 201 (201)
Q Consensus 149 V~~~~D~s~~gm~RtEV~C~~Cg~HLGHVF~-DGP~-ptg~RYCINS~sL~F~p~ 201 (201)
|....|.+. +|.|+||+|++||+||||||+ |||. ||++|||||||||+|.|+
T Consensus 89 I~r~~d~s~-~~~R~Ev~Ca~C~~HLGHVF~~eG~~~Pt~~R~CiNS~sL~F~~~ 142 (146)
T KOG0856|consen 89 ITRTPDNSR-GGRRTEVSCATCGGHLGHVFKGEGPKTPTDERHCINSVSLKFVPA 142 (146)
T ss_pred eeeccccCC-CCcceEEEEeecCCceeeeecCCCCCCCCCceeEeeeeeeeeccC
Confidence 998888875 899999999999999999998 9998 999999999999999984
No 7
>PRK14018 trifunctional thioredoxin/methionine sulfoxide reductase A/B protein; Provisional
Probab=100.00 E-value=2.5e-59 Score=441.95 Aligned_cols=131 Identities=49% Similarity=0.781 Sum_probs=124.1
Q ss_pred cccCCCCCCHHHHHhcCCHHHHHHHhhcCCCCCccCCCCCCCCCeEEEcccCCcccccCCCcccCCCCCccccccCC-CC
Q 028947 70 NRVDYASISDEEWKRRLTGEQYYITRQKGTERAFTGEYWNTKTPGTYHCICCDTPLFESSTKFDSGTGWPSYYQPIG-SN 148 (201)
Q Consensus 70 ~~~~~~~~sd~ewk~~LTp~qy~V~r~~GTE~pfsG~y~~~~~~G~Y~C~~Cg~pLFsS~~KFdSg~GWPSF~~~i~-~~ 148 (201)
.+..+..++++|||++|||+||+|||++|||+||||+||+++++|+|+|++||+|||+|++|||||||||||+++|+ ++
T Consensus 373 ~~~~~~~~~~~~~~~~Lt~~~y~v~~~~gtE~~f~~~~~~~~~~G~y~c~~c~~pLf~s~~Kf~sg~GWPsF~~~i~~~~ 452 (521)
T PRK14018 373 DAATYKKPSDAELKRTLTEEQYQITQNAATERAFSHEYDHLFKPGIYVDVVSGEPLFSSADKYDSGCGWPSFTRPIDAKV 452 (521)
T ss_pred chhhccCCChHHHhccCCHHHHHHHHhcCCCCCCCCCCcCCCCCEEEEecCCCCccccCcccccCCCCCcccCcccCcCc
Confidence 34557889999999999999999999999999999999999999999999999999999999999999999999997 56
Q ss_pred ceeeecCCCCCccEEEEEcCCCCCCccccCCCCCC-CCCceeeeccceeeeeeC
Q 028947 149 MKSKLDLSIIFMPRQEVLCAVCDAHLGHVFDDGPP-PTGKRYCINSASLKLKPK 201 (201)
Q Consensus 149 V~~~~D~s~~gm~RtEV~C~~Cg~HLGHVF~DGP~-ptg~RYCINS~sL~F~p~ 201 (201)
|.++.|.++ ||.||||+|++||+||||||+|||+ |||+||||||+||+|+|+
T Consensus 453 v~~~~d~s~-g~~R~Ev~c~~c~~HLGHvf~dgp~~~~g~RyCiNs~~l~f~~~ 505 (521)
T PRK14018 453 VTEHDDFSY-NMRRTEVRSRAADSHLGHVFPDGPRDKGGLRYCINGASLKFIPL 505 (521)
T ss_pred eEEeeccCC-CceEEEEEECCCCCcCCcccCCCCCCCCCCEeeeceeEEEeecc
Confidence 888899886 9999999999999999999999996 699999999999999984
No 8
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=100.00 E-value=6.7e-59 Score=412.31 Aligned_cols=119 Identities=45% Similarity=0.841 Sum_probs=114.2
Q ss_pred HHHHhcCCHHHHHHHhhcCCCCCccCCCCCCCCCeEEEcccCCcccccCCCcccCCCCCccccccCCCCceeeecCCCCC
Q 028947 80 EEWKRRLTGEQYYITRQKGTERAFTGEYWNTKTPGTYHCICCDTPLFESSTKFDSGTGWPSYYQPIGSNMKSKLDLSIIF 159 (201)
Q Consensus 80 ~ewk~~LTp~qy~V~r~~GTE~pfsG~y~~~~~~G~Y~C~~Cg~pLFsS~~KFdSg~GWPSF~~~i~~~V~~~~D~s~~g 159 (201)
++||++|||+||+|+|++||||||+|+||+++++|+|+|++||+|||+|++|||||||||||+++|+++|+.+.|.+ |
T Consensus 1 ~~~~~~Lt~~~y~v~r~~gTE~pf~g~~~~~~~~G~y~c~~c~~~LF~s~~Kf~sg~GWPsF~~~~~~~~~~~~d~~--~ 78 (283)
T PRK05550 1 MDKMKSLTPFEYRVIEDKGTERPFSGEYYDHDEKGVYLCRRCGAPLFRSEDKFNSGCGWPSFDDEIPGAVKRLPDAD--G 78 (283)
T ss_pred ChhhhhCCHHHHHHHHhcCCCCCCCCcCcCCCCCcEEEcCCCCchhcCChhhccCCCCCcCcCcccCCccEEEEcCC--C
Confidence 36999999999999999999999999999999999999999999999999999999999999999999999998876 6
Q ss_pred ccEEEEEcCCCCCCccccCC-CCCCCCCceeeeccceeeeeeC
Q 028947 160 MPRQEVLCAVCDAHLGHVFD-DGPPPTGKRYCINSASLKLKPK 201 (201)
Q Consensus 160 m~RtEV~C~~Cg~HLGHVF~-DGP~ptg~RYCINS~sL~F~p~ 201 (201)
| ||||+|++||+||||||+ |||+|||+||||||+||+|+|+
T Consensus 79 ~-R~Ev~c~~c~~HLGHvF~ddgp~ptg~RyCiNs~sL~f~p~ 120 (283)
T PRK05550 79 R-RTEIVCANCGAHLGHVFEGEGLTPKNTRHCVNSASLDFVPA 120 (283)
T ss_pred c-eEEEEecCCCCccCcccCCCCCCCCCccccccccccccCcc
Confidence 6 999999999999999998 8899999999999999999984
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=94.51 E-value=0.026 Score=42.18 Aligned_cols=81 Identities=19% Similarity=0.449 Sum_probs=48.9
Q ss_pred EEEcccCCcccccCCCccc-CCCCCcccc-ccCCCCceeeecCCCCCc-----cEEEEEcCCCCCCccccCCCCCCC---
Q 028947 115 TYHCICCDTPLFESSTKFD-SGTGWPSYY-QPIGSNMKSKLDLSIIFM-----PRQEVLCAVCDAHLGHVFDDGPPP--- 184 (201)
Q Consensus 115 ~Y~C~~Cg~pLFsS~~KFd-Sg~GWPSF~-~~i~~~V~~~~D~s~~gm-----~RtEV~C~~Cg~HLGHVF~DGP~p--- 184 (201)
+|.|+.|.++|=+|..-.. +|..=++|- ..+...+........ |. .=..+.|++|+.+||=.+...|..
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 7999999999987776666 443334432 222222211111000 11 135899999999999999876654
Q ss_pred CCceeeecccee
Q 028947 185 TGKRYCINSASL 196 (201)
Q Consensus 185 tg~RYCINS~sL 196 (201)
.--+|++.-++|
T Consensus 81 k~g~file~~~i 92 (96)
T PF03226_consen 81 KEGKFILEKASI 92 (96)
T ss_pred hCCEEEEEhhHE
Confidence 344677666555
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=73.58 E-value=3.9 Score=30.78 Aligned_cols=62 Identities=16% Similarity=0.297 Sum_probs=32.8
Q ss_pred CeEEEcccCCcccccC-CCcccCCCCCccccccCCCCceeeecCCCCCccEEEEEcCCCCCCccccC
Q 028947 113 PGTYHCICCDTPLFES-STKFDSGTGWPSYYQPIGSNMKSKLDLSIIFMPRQEVLCAVCDAHLGHVF 178 (201)
Q Consensus 113 ~G~Y~C~~Cg~pLFsS-~~KFdSg~GWPSF~~~i~~~V~~~~D~s~~gm~RtEV~C~~Cg~HLGHVF 178 (201)
.+.|.|..||...... +.++..- -.+...+.+.+....|.. .+.+++++.|.+||.+-...|
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 4789999999875442 1122100 011111112222222322 256789999999986655555
No 11
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=70.67 E-value=1.4 Score=36.25 Aligned_cols=24 Identities=38% Similarity=0.731 Sum_probs=17.4
Q ss_pred EEEcccCCcccccCCC-cccCCCCC
Q 028947 115 TYHCICCDTPLFESST-KFDSGTGW 138 (201)
Q Consensus 115 ~Y~C~~Cg~pLFsS~~-KFdSg~GW 138 (201)
-+||..||.|||.=+- -|=+-||.
T Consensus 28 ~~hCp~Cg~PLF~KdG~v~CPvC~~ 52 (131)
T COG1645 28 AKHCPKCGTPLFRKDGEVFCPVCGY 52 (131)
T ss_pred HhhCcccCCcceeeCCeEECCCCCc
Confidence 4799999999998332 35566664
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=60.93 E-value=5.5 Score=28.92 Aligned_cols=43 Identities=23% Similarity=0.521 Sum_probs=31.0
Q ss_pred EEcccCCcccccCCCcccCCCCCccccccCCCCceeeecCCCCCccEEEEEcCCCC
Q 028947 116 YHCICCDTPLFESSTKFDSGTGWPSYYQPIGSNMKSKLDLSIIFMPRQEVLCAVCD 171 (201)
Q Consensus 116 Y~C~~Cg~pLFsS~~KFdSg~GWPSF~~~i~~~V~~~~D~s~~gm~RtEV~C~~Cg 171 (201)
|.|..||..-|.++.--.+|.||-.+++ |. .. .=+-|.|.+||
T Consensus 1 y~C~KCg~~~~e~~~v~~tgg~~skiFd-----vq----~~----~f~~v~C~~CG 43 (64)
T PF09855_consen 1 YKCPKCGNEEYESGEVRATGGGLSKIFD-----VQ----NK----KFTTVSCTNCG 43 (64)
T ss_pred CCCCCCCCcceecceEEccCCeeEEEEE-----ec----Cc----EEEEEECCCCC
Confidence 7899999999988888788888865421 11 11 12578899997
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=59.09 E-value=4.5 Score=26.13 Aligned_cols=21 Identities=29% Similarity=0.631 Sum_probs=16.4
Q ss_pred cCCCCCCCCCeEEEcccCCcc
Q 028947 104 TGEYWNTKTPGTYHCICCDTP 124 (201)
Q Consensus 104 sG~y~~~~~~G~Y~C~~Cg~p 124 (201)
-|..|...+.|.|.|+.||..
T Consensus 14 C~~~~~~~~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 14 CGSRWFYSDDGFYYCDRCGHQ 34 (36)
T ss_pred CCCeEeEccCCEEEhhhCceE
Confidence 455577778999999999864
No 14
>PRK00420 hypothetical protein; Validated
Probab=52.62 E-value=7.4 Score=31.15 Aligned_cols=23 Identities=35% Similarity=0.598 Sum_probs=16.1
Q ss_pred EEcccCCccccc--CCCcccCCCCC
Q 028947 116 YHCICCDTPLFE--SSTKFDSGTGW 138 (201)
Q Consensus 116 Y~C~~Cg~pLFs--S~~KFdSg~GW 138 (201)
-+|..||.|||. ....|=+.||=
T Consensus 24 ~~CP~Cg~pLf~lk~g~~~Cp~Cg~ 48 (112)
T PRK00420 24 KHCPVCGLPLFELKDGEVVCPVHGK 48 (112)
T ss_pred CCCCCCCCcceecCCCceECCCCCC
Confidence 578888888885 55556666665
No 15
>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=51.21 E-value=13 Score=26.07 Aligned_cols=33 Identities=18% Similarity=0.353 Sum_probs=21.5
Q ss_pred cEEEEEcCCCCCCccccCCCCCCCCCceeeeccceee
Q 028947 161 PRQEVLCAVCDAHLGHVFDDGPPPTGKRYCINSASLK 197 (201)
Q Consensus 161 ~RtEV~C~~Cg~HLGHVF~DGP~ptg~RYCINS~sL~ 197 (201)
...-..|++||++|.....+.| ..+-||..+|+
T Consensus 45 ~~~r~FC~~CGs~l~~~~~~~~----~~~~V~~g~ld 77 (92)
T PF04828_consen 45 GVERYFCPTCGSPLFSEDERDP----DLVGVNAGTLD 77 (92)
T ss_dssp SCEEEEETTT--EEEEEESSTT----TEEEEEGGGBT
T ss_pred cCcCcccCCCCCeeecccCCCC----CEEEEEeEeeC
Confidence 3455999999999997644433 37777777665
No 16
>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=50.21 E-value=7.1 Score=26.06 Aligned_cols=14 Identities=43% Similarity=0.888 Sum_probs=11.1
Q ss_pred EEcccCCcccccCC
Q 028947 116 YHCICCDTPLFESS 129 (201)
Q Consensus 116 Y~C~~Cg~pLFsS~ 129 (201)
-+|..||.|||...
T Consensus 18 ~~Cp~C~~PL~~~k 31 (41)
T PF06677_consen 18 EHCPDCGTPLMRDK 31 (41)
T ss_pred CccCCCCCeeEEec
Confidence 36889999999743
No 17
>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=47.05 E-value=24 Score=22.82 Aligned_cols=29 Identities=38% Similarity=0.865 Sum_probs=20.6
Q ss_pred ccEEEEEcCCCCCCccccCCCCCCCCC-cee
Q 028947 160 MPRQEVLCAVCDAHLGHVFDDGPPPTG-KRY 189 (201)
Q Consensus 160 m~RtEV~C~~Cg~HLGHVF~DGP~ptg-~RY 189 (201)
|.-|+|.|..|++..+ |..-|..+.| +||
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 3344655554 676
No 18
>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=46.93 E-value=13 Score=24.35 Aligned_cols=17 Identities=24% Similarity=0.700 Sum_probs=13.9
Q ss_pred CCCCCCCeEEEcccCCc
Q 028947 107 YWNTKTPGTYHCICCDT 123 (201)
Q Consensus 107 y~~~~~~G~Y~C~~Cg~ 123 (201)
|.+.+..|.|+|..|+.
T Consensus 17 ~~d~~g~G~~~C~~Cg~ 33 (37)
T smart00778 17 FDDKDGRGTWFCSVCGA 33 (37)
T ss_pred cccCCCCcCEEeCCCCC
Confidence 66667789999999963
No 19
>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=43.44 E-value=7.3 Score=29.30 Aligned_cols=44 Identities=34% Similarity=0.588 Sum_probs=27.8
Q ss_pred EcccCCcccccCCCcccCCCCCccccccCCCCceeeecCCCCCccEEEEEcCCCCCCccccCC
Q 028947 117 HCICCDTPLFESSTKFDSGTGWPSYYQPIGSNMKSKLDLSIIFMPRQEVLCAVCDAHLGHVFD 179 (201)
Q Consensus 117 ~C~~Cg~pLFsS~~KFdSg~GWPSF~~~i~~~V~~~~D~s~~gm~RtEV~C~~Cg~HLGHVF~ 179 (201)
.|+.|+.|++....+. +.. .|... |..| -+.|..|..-||++=+
T Consensus 24 ~C~iC~~~~~~~~~~~----------------~vD-HdH~t-G~vR-GlLC~~CN~~lG~~~D 67 (81)
T PF02945_consen 24 RCAICGKPLPGESRKL----------------VVD-HDHKT-GRVR-GLLCRSCNTALGKVRD 67 (81)
T ss_dssp E-TTT-SEEETTCGGC----------------EEE-E-TTT-TBEE-EEEEHHHHHHHHHCTT
T ss_pred cCcCCCCCcccCCCcc----------------eec-CCCCC-CCch-hhhhhHHhhhhccccC
Confidence 8999999876542221 222 23232 6677 8999999999999833
No 20
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=38.97 E-value=16 Score=27.73 Aligned_cols=22 Identities=32% Similarity=0.682 Sum_probs=17.6
Q ss_pred EEEEEcCCCCCCccccC-CCCCC
Q 028947 162 RQEVLCAVCDAHLGHVF-DDGPP 183 (201)
Q Consensus 162 RtEV~C~~Cg~HLGHVF-~DGP~ 183 (201)
.+.-+|..||.-++|.= +|||+
T Consensus 6 k~~~~C~~CG~d~~~~~adDgPA 28 (86)
T PF06170_consen 6 KVAPRCPHCGLDYSHARADDGPA 28 (86)
T ss_pred cCCCcccccCCccccCCcCccch
Confidence 34567999999999986 57874
No 21
>COG3791 Uncharacterized conserved protein [Function unknown]
Probab=38.58 E-value=14 Score=29.53 Aligned_cols=22 Identities=32% Similarity=0.794 Sum_probs=17.1
Q ss_pred CCCCCCCeEEEcccCCcccccC
Q 028947 107 YWNTKTPGTYHCICCDTPLFES 128 (201)
Q Consensus 107 y~~~~~~G~Y~C~~Cg~pLFsS 128 (201)
|......+.+.|..||.+||..
T Consensus 61 ~~~s~~~~r~FC~~CGs~l~~~ 82 (133)
T COG3791 61 YFSSGSAGRGFCPTCGSPLFWR 82 (133)
T ss_pred EeecCCCCCeecccCCCceEEe
Confidence 3345567778999999999865
No 22
>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=37.96 E-value=21 Score=23.14 Aligned_cols=15 Identities=27% Similarity=0.501 Sum_probs=12.4
Q ss_pred CCCeEEEcccCCccc
Q 028947 111 KTPGTYHCICCDTPL 125 (201)
Q Consensus 111 ~~~G~Y~C~~Cg~pL 125 (201)
.+.|.++|..||.-|
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 23
>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=36.79 E-value=18 Score=30.02 Aligned_cols=42 Identities=24% Similarity=0.415 Sum_probs=26.0
Q ss_pred CCCCCHHHHHhcCCHHHHHHHhhcCCCCCccCCCCCCCCCeEEEcccCCccc
Q 028947 74 YASISDEEWKRRLTGEQYYITRQKGTERAFTGEYWNTKTPGTYHCICCDTPL 125 (201)
Q Consensus 74 ~~~~sd~ewk~~LTp~qy~V~r~~GTE~pfsG~y~~~~~~G~Y~C~~Cg~pL 125 (201)
..++|.-||.+-. +=++.+| ---+|+.- .+|+|+|..||..+
T Consensus 81 ItDkTqvEw~el~-----~d~~h~g--~Y~sGE~~---g~G~l~C~~Cg~~~ 122 (146)
T PF07295_consen 81 ITDKTQVEWAELA-----QDLEHHG--VYHSGEVV---GPGTLVCENCGHEV 122 (146)
T ss_pred hhchhHHHHHHHH-----HHHHhcC--CeecCcEe---cCceEecccCCCEE
Confidence 3456666775332 2244555 33355544 48999999999865
No 24
>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=35.86 E-value=40 Score=22.23 Aligned_cols=21 Identities=33% Similarity=0.490 Sum_probs=13.3
Q ss_pred CCCCHHHHHhcCCHHHHHHHhh
Q 028947 75 ASISDEEWKRRLTGEQYYITRQ 96 (201)
Q Consensus 75 ~~~sd~ewk~~LTp~qy~V~r~ 96 (201)
+.+|.+||. .|.|.|...-|+
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 568999997 899999765553
No 25
>COG3791 Uncharacterized conserved protein [Function unknown]
Probab=35.33 E-value=28 Score=27.77 Aligned_cols=28 Identities=21% Similarity=0.310 Sum_probs=21.9
Q ss_pred EcCCCCCCccccCCCCCCCCCceeeeccceee
Q 028947 166 LCAVCDAHLGHVFDDGPPPTGKRYCINSASLK 197 (201)
Q Consensus 166 ~C~~Cg~HLGHVF~DGP~ptg~RYCINS~sL~ 197 (201)
.|.+||+||-+.-.|+. .-+=||-++|+
T Consensus 71 FC~~CGs~l~~~~~~~~----~~~~v~~~~ld 98 (133)
T COG3791 71 FCPTCGSPLFWRGPDED----PFVGVNAGALD 98 (133)
T ss_pred ecccCCCceEEecCCCC----ceEEEEEeeec
Confidence 99999999998877764 35667777766
No 26
>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=33.71 E-value=32 Score=24.00 Aligned_cols=26 Identities=19% Similarity=0.326 Sum_probs=21.1
Q ss_pred ccEEEEEcCCCCCCccccCCCCCCCC
Q 028947 160 MPRQEVLCAVCDAHLGHVFDDGPPPT 185 (201)
Q Consensus 160 m~RtEV~C~~Cg~HLGHVF~DGP~pt 185 (201)
..|..+.|++|..|=|-+....+.+.
T Consensus 18 ~~r~aLIC~~C~~hNGla~~~~~~~i 43 (54)
T PF10058_consen 18 SNRYALICSKCFSHNGLAPKEEFEEI 43 (54)
T ss_pred cCceeEECcccchhhcccccccCCce
Confidence 35899999999999999986555554
No 27
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=33.35 E-value=16 Score=24.57 Aligned_cols=15 Identities=40% Similarity=0.875 Sum_probs=12.1
Q ss_pred EEcCCCCCCccccCCC
Q 028947 165 VLCAVCDAHLGHVFDD 180 (201)
Q Consensus 165 V~C~~Cg~HLGHVF~D 180 (201)
|.|.+||+ +||.-.+
T Consensus 2 ~kC~~CG~-~GH~~t~ 16 (40)
T PF15288_consen 2 VKCKNCGA-FGHMRTN 16 (40)
T ss_pred cccccccc-ccccccC
Confidence 68999998 6998654
No 28
>PRK12495 hypothetical protein; Provisional
Probab=31.97 E-value=17 Score=32.62 Aligned_cols=16 Identities=38% Similarity=0.762 Sum_probs=13.7
Q ss_pred CCCeEEEcccCCcccc
Q 028947 111 KTPGTYHCICCDTPLF 126 (201)
Q Consensus 111 ~~~G~Y~C~~Cg~pLF 126 (201)
-...-++|..||.|||
T Consensus 38 atmsa~hC~~CG~PIp 53 (226)
T PRK12495 38 ATMTNAHCDECGDPIF 53 (226)
T ss_pred cccchhhcccccCccc
Confidence 3456899999999999
No 29
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=27.66 E-value=46 Score=30.32 Aligned_cols=30 Identities=23% Similarity=0.582 Sum_probs=25.0
Q ss_pred CCCCeEEEcccCCcccccCCCcccCCCCCccc
Q 028947 110 TKTPGTYHCICCDTPLFESSTKFDSGTGWPSY 141 (201)
Q Consensus 110 ~~~~G~Y~C~~Cg~pLFsS~~KFdSg~GWPSF 141 (201)
..+.|.++|+.||.=| -+.-+|.|..|=.|
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 3458999999999877 45568999999999
No 30
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=27.29 E-value=51 Score=29.72 Aligned_cols=32 Identities=19% Similarity=0.486 Sum_probs=26.6
Q ss_pred CCCCeEEEcccCCcccccCCCcccCCCCCccccc
Q 028947 110 TKTPGTYHCICCDTPLFESSTKFDSGTGWPSYYQ 143 (201)
Q Consensus 110 ~~~~G~Y~C~~Cg~pLFsS~~KFdSg~GWPSF~~ 143 (201)
..+.|.++|..||.=| .+.-.|.|.-|-+|..
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 3579999999999876 4566788999999976
No 31
>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=26.94 E-value=37 Score=24.45 Aligned_cols=12 Identities=25% Similarity=0.498 Sum_probs=9.7
Q ss_pred CCCCeEEEcccC
Q 028947 110 TKTPGTYHCICC 121 (201)
Q Consensus 110 ~~~~G~Y~C~~C 121 (201)
..+.|+|.|++-
T Consensus 72 ~~Dsg~Y~C~~~ 83 (98)
T cd04984 72 TEDEADYYCQVW 83 (98)
T ss_pred hhhCEEEEEEEc
Confidence 457899999874
No 32
>PF09965 DUF2199: Uncharacterized protein conserved in bacteria (DUF2199); InterPro: IPR018697 This domain has no known function.
Probab=26.56 E-value=31 Score=28.68 Aligned_cols=25 Identities=28% Similarity=0.541 Sum_probs=18.6
Q ss_pred EEcccCCcccccCCCcccCCCCCccccccCCCCce
Q 028947 116 YHCICCDTPLFESSTKFDSGTGWPSYYQPIGSNMK 150 (201)
Q Consensus 116 Y~C~~Cg~pLFsS~~KFdSg~GWPSF~~~i~~~V~ 150 (201)
|.|.+||+.- -|||+|.-..++.+.
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 588888766665443
No 33
>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=26.14 E-value=52 Score=22.23 Aligned_cols=17 Identities=12% Similarity=0.319 Sum_probs=13.1
Q ss_pred CCCCCCeEEEcccCCcc
Q 028947 108 WNTKTPGTYHCICCDTP 124 (201)
Q Consensus 108 ~~~~~~G~Y~C~~Cg~p 124 (201)
.+....|+|.|..||.-
T Consensus 19 ~~~~~~~~~~C~~Cga~ 35 (53)
T TIGR03655 19 DPLDLSHYFECSTCGAS 35 (53)
T ss_pred CCCCCEEEEECCCCCCC
Confidence 45567888899999875
No 34
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=25.13 E-value=38 Score=24.07 Aligned_cols=13 Identities=15% Similarity=0.337 Sum_probs=9.5
Q ss_pred EcccCCcccccCC
Q 028947 117 HCICCDTPLFESS 129 (201)
Q Consensus 117 ~C~~Cg~pLFsS~ 129 (201)
.|..||.++.++-
T Consensus 19 ~CP~CG~~t~~~~ 31 (56)
T PRK13130 19 ICPVCGGKTKNPH 31 (56)
T ss_pred cCcCCCCCCCCCC
Confidence 4888888886554
No 35
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=24.33 E-value=37 Score=21.59 Aligned_cols=17 Identities=35% Similarity=0.679 Sum_probs=12.0
Q ss_pred CccEEEEEcCCCCCCccccCC
Q 028947 159 FMPRQEVLCAVCDAHLGHVFD 179 (201)
Q Consensus 159 gm~RtEV~C~~Cg~HLGHVF~ 179 (201)
+.....|+|++|+ |+|.
T Consensus 20 ~~~~~~vrC~~C~----~~f~ 36 (37)
T PF13719_consen 20 PAGGRKVRCPKCG----HVFR 36 (37)
T ss_pred ccCCcEEECCCCC----cEee
Confidence 4445699999995 6653
No 36
>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=23.80 E-value=38 Score=24.71 Aligned_cols=12 Identities=17% Similarity=0.401 Sum_probs=9.5
Q ss_pred CCCCeEEEcccC
Q 028947 110 TKTPGTYHCICC 121 (201)
Q Consensus 110 ~~~~G~Y~C~~C 121 (201)
..+.|+|.|+.-
T Consensus 80 ~~Dsg~Y~Ca~~ 91 (106)
T cd04980 80 PEDAAVYYCQQY 91 (106)
T ss_pred hHHCEEEEEEEe
Confidence 457899999873
No 37
>PRK08624 hypothetical protein; Provisional
Probab=23.21 E-value=1.3e+02 Score=28.84 Aligned_cols=22 Identities=27% Similarity=0.563 Sum_probs=15.4
Q ss_pred CCCCeEEEcc-cCCc--ccccCCCc
Q 028947 110 TKTPGTYHCI-CCDT--PLFESSTK 131 (201)
Q Consensus 110 ~~~~G~Y~C~-~Cg~--pLFsS~~K 131 (201)
+.+.++|+|= +||. ..|.-=.+
T Consensus 54 ~pekq~yhCF~GCGa~GDVf~Fv~~ 78 (373)
T PRK08624 54 YIENDNFHCYTRCGDIFDVFELLCK 78 (373)
T ss_pred cCCCCEEEEeCCCCCCCceeeehhh
Confidence 3467899998 9998 55554433
No 38
>PHA02540 61 DNA primase; Provisional
Probab=22.24 E-value=42 Score=31.36 Aligned_cols=18 Identities=17% Similarity=0.521 Sum_probs=12.3
Q ss_pred CCCCCCCe--EEEcccCCcc
Q 028947 107 YWNTKTPG--TYHCICCDTP 124 (201)
Q Consensus 107 y~~~~~~G--~Y~C~~Cg~p 124 (201)
+|=+.+.| +|+|=+||.-
T Consensus 45 F~V~p~k~~~~yhCFgCGa~ 64 (337)
T PHA02540 45 GWIYEKKDGGVFKCHNCGYH 64 (337)
T ss_pred EEEeccCCceEEEecCCCCC
Confidence 33334455 9999999963
No 39
>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=21.96 E-value=59 Score=19.78 Aligned_cols=23 Identities=26% Similarity=0.504 Sum_probs=11.4
Q ss_pred EcCCCCCCccccCCCCCCCCCceeeecc
Q 028947 166 LCAVCDAHLGHVFDDGPPPTGKRYCINS 193 (201)
Q Consensus 166 ~C~~Cg~HLGHVF~DGP~ptg~RYCINS 193 (201)
.|-.||+.|=+. +|+ -..||+|.
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 488899998743 222 25899998
No 40
>PRK04179 rpl37e 50S ribosomal protein L37e; Reviewed
Probab=21.89 E-value=48 Score=24.28 Aligned_cols=27 Identities=19% Similarity=0.448 Sum_probs=24.2
Q ss_pred eEEEcccCCcccccCCCcccCCCCC-cc
Q 028947 114 GTYHCICCDTPLFESSTKFDSGTGW-PS 140 (201)
Q Consensus 114 G~Y~C~~Cg~pLFsS~~KFdSg~GW-PS 140 (201)
-.-.|..||.--|....|.=+.||+ ||
T Consensus 16 tHt~CrRCG~~syh~qK~~CasCGygps 43 (62)
T PRK04179 16 THIRCRRCGRHSYNVRKKYCAACGFGRS 43 (62)
T ss_pred ccchhcccCcccccccccchhhcCCCcc
Confidence 3567999999999999999999999 76
No 41
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=21.72 E-value=35 Score=27.65 Aligned_cols=15 Identities=27% Similarity=0.649 Sum_probs=13.2
Q ss_pred CCCeEEEcccCCccc
Q 028947 111 KTPGTYHCICCDTPL 125 (201)
Q Consensus 111 ~~~G~Y~C~~Cg~pL 125 (201)
-+-|.+.|..||+++
T Consensus 45 ie~G~t~CP~Cg~~~ 59 (115)
T COG1885 45 IEVGSTSCPKCGEPF 59 (115)
T ss_pred EecccccCCCCCCcc
Confidence 378999999999986
No 42
>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=21.29 E-value=43 Score=21.62 Aligned_cols=10 Identities=40% Similarity=1.092 Sum_probs=7.3
Q ss_pred CCCeEEEccc
Q 028947 111 KTPGTYHCIC 120 (201)
Q Consensus 111 ~~~G~Y~C~~ 120 (201)
.+.|.|.|.+
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 3688898864
No 43
>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=20.93 E-value=48 Score=20.55 Aligned_cols=12 Identities=25% Similarity=0.551 Sum_probs=9.3
Q ss_pred EEEEcCCCCCCc
Q 028947 163 QEVLCAVCDAHL 174 (201)
Q Consensus 163 tEV~C~~Cg~HL 174 (201)
.+|+|.+||.-+
T Consensus 24 ~~v~C~~C~~~~ 35 (38)
T TIGR02098 24 GKVRCGKCGHVW 35 (38)
T ss_pred CEEECCCCCCEE
Confidence 389999998654
No 44
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=20.70 E-value=56 Score=20.77 Aligned_cols=11 Identities=27% Similarity=0.751 Sum_probs=8.9
Q ss_pred cEEEEEcCCCC
Q 028947 161 PRQEVLCAVCD 171 (201)
Q Consensus 161 ~RtEV~C~~Cg 171 (201)
....|.|.+||
T Consensus 22 ~g~~v~C~~C~ 32 (36)
T PF13717_consen 22 KGRKVRCSKCG 32 (36)
T ss_pred CCcEEECCCCC
Confidence 35699999995
No 45
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=20.62 E-value=47 Score=20.79 Aligned_cols=18 Identities=11% Similarity=0.357 Sum_probs=13.9
Q ss_pred CCeEEEcccCCcccccCC
Q 028947 112 TPGTYHCICCDTPLFESS 129 (201)
Q Consensus 112 ~~G~Y~C~~Cg~pLFsS~ 129 (201)
.--.+.|..||..+|+.+
T Consensus 29 ~vp~~~C~~CGE~~~~~~ 46 (46)
T TIGR03831 29 NVPALVCPQCGEEYLDAE 46 (46)
T ss_pred CCCccccccCCCEeeCCC
Confidence 345678999999999753
No 46
>cd05862 Ig1_VEGFR First immunoglobulin (Ig)-like domain of vascular endothelial growth factor (VEGF) receptor(R). IG1_VEGFR: first immunoglobulin (Ig)-like domain of vascular endothelial growth factor (VEGF) receptor(R). The VEGFRs have an extracellular component with seven Ig-like domains, a transmembrane segment, and an intracellular tyrosine kinase domain interrupted by a kinase-insert domain. The VEGFR family consists of three members, VEGFR-1 (Flt-1), VEGFR-2 (KDR/Flk-1) and VEGFR-3 (Flt-4). VEGF_A interacts with both VEGFR-1 and VEGFR-2. VEGFR-1 binds strongest to VEGF, VEGF-2 binds more weakly. VEGFR-3 appears not to bind VEGF, but binds other members of the VEGF family (VEGF-C and -D). VEGFRs bind VEGFs with high affinity with the IG-like domains. VEGF-A is important to the growth and maintenance of vascular endothelial cells and to the development of new blood- and lymphatic-vessels in physiological and pathological states. VEGFR-2 is a major mediator of the mitogenic, angioge
Probab=20.48 E-value=56 Score=23.41 Aligned_cols=22 Identities=23% Similarity=0.377 Sum_probs=13.8
Q ss_pred CCCCeEEEccc-CCcccccCCCc
Q 028947 110 TKTPGTYHCIC-CDTPLFESSTK 131 (201)
Q Consensus 110 ~~~~G~Y~C~~-Cg~pLFsS~~K 131 (201)
..+.|.|.|++ ++.-.+.+.++
T Consensus 59 ~~DsG~Y~C~a~n~~~~~~~~t~ 81 (86)
T cd05862 59 LSDLGRYTCTASSGQMIAKNSTI 81 (86)
T ss_pred cccCEEEEEEEeecceEecccEE
Confidence 56899999965 33444444443
No 47
>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=20.17 E-value=58 Score=23.43 Aligned_cols=14 Identities=14% Similarity=0.498 Sum_probs=10.7
Q ss_pred CCCCeEEEcccCCc
Q 028947 110 TKTPGTYHCICCDT 123 (201)
Q Consensus 110 ~~~~G~Y~C~~Cg~ 123 (201)
..+.|+|.|++...
T Consensus 79 ~~DsG~Y~C~~~~~ 92 (109)
T cd04983 79 LSDSAVYFCALSES 92 (109)
T ss_pred HHHCEEEEEEEecC
Confidence 45789999997643
No 48
>PTZ00073 60S ribosomal protein L37; Provisional
Probab=20.14 E-value=55 Score=25.66 Aligned_cols=28 Identities=25% Similarity=0.396 Sum_probs=25.1
Q ss_pred eEEEcccCCcccccCCCcccCCCCCccc
Q 028947 114 GTYHCICCDTPLFESSTKFDSGTGWPSY 141 (201)
Q Consensus 114 G~Y~C~~Cg~pLFsS~~KFdSg~GWPSF 141 (201)
-.-.|..||.--|.-..+.=+.||+|+=
T Consensus 15 tHtlCrRCG~~syH~qK~~CasCGypsa 42 (91)
T PTZ00073 15 THTLCRRCGKRSFHVQKKRCASCGYPSA 42 (91)
T ss_pred CcchhcccCccccccccccchhcCCchh
Confidence 3568999999999999999999999974
Done!