Query psy4120
Match_columns 95
No_of_seqs 166 out of 1015
Neff 4.6
Searched_HMMs 46136
Date Fri Aug 16 17:28:56 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4120.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4120hhsearch_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 5.1E-48 1.1E-52 277.1 8.3 84 10-93 2-130 (140)
2 TIGR00357 methionine-R-sulfoxi 100.0 1.3E-47 2.7E-52 273.8 8.8 83 11-93 1-127 (134)
3 PRK00222 methionine sulfoxide 100.0 7.9E-47 1.7E-51 271.9 9.4 84 10-93 3-130 (142)
4 PF01641 SelR: SelR domain; I 100.0 7.1E-46 1.5E-50 261.8 9.0 79 14-92 1-124 (124)
5 KOG0856|consensus 100.0 2.4E-42 5.2E-47 248.7 8.0 90 5-94 9-144 (146)
6 PRK05508 methionine sulfoxide 100.0 3.4E-41 7.5E-46 236.9 8.3 75 19-93 2-118 (119)
7 PRK14018 trifunctional thiored 100.0 1.5E-39 3.3E-44 270.3 8.9 84 10-93 378-506 (521)
8 PRK05550 bifunctional methioni 100.0 1.9E-37 4.2E-42 242.6 6.7 79 15-94 1-122 (283)
9 PF03226 Yippee-Mis18: Yippee 85.0 0.58 1.3E-05 30.6 1.5 36 53-88 55-93 (96)
10 PF03811 Zn_Tnp_IS1: InsA N-te 76.0 3.7 8.1E-05 23.2 2.7 29 51-80 1-30 (36)
11 PF04828 GFA: Glutathione-depe 71.1 4.3 9.4E-05 24.9 2.4 31 55-89 48-78 (92)
12 COG3791 Uncharacterized conser 58.3 9.9 0.00022 26.5 2.5 35 48-88 64-98 (133)
13 PF13248 zf-ribbon_3: zinc-rib 53.1 5.5 0.00012 20.6 0.4 20 55-83 2-21 (26)
14 PF03119 DNA_ligase_ZBD: NAD-d 53.0 12 0.00025 20.0 1.6 23 57-84 1-23 (28)
15 PF10058 DUF2296: Predicted in 51.8 12 0.00025 22.9 1.7 26 51-76 18-43 (54)
16 PF14354 Lar_restr_allev: Rest 46.1 35 0.00076 20.1 3.2 26 37-63 7-37 (61)
17 PF15288 zf-CCHC_6: Zinc knuck 43.6 8.9 0.00019 22.5 0.3 15 56-71 2-16 (40)
18 PF06170 DUF983: Protein of un 41.0 12 0.00027 24.7 0.7 24 51-74 4-28 (86)
19 PF13719 zinc_ribbon_5: zinc-r 40.1 17 0.00037 20.2 1.1 17 50-70 20-36 (37)
20 COG3364 Zn-ribbon containing p 35.4 17 0.00037 25.6 0.7 12 57-72 4-15 (112)
21 PRK14891 50S ribosomal protein 35.1 28 0.00061 25.2 1.8 12 51-63 1-12 (131)
22 PF10601 zf-LITAF-like: LITAF- 34.8 23 0.0005 21.9 1.2 16 52-67 55-70 (73)
23 PRK00398 rpoP DNA-directed RNA 33.2 23 0.0005 20.2 0.9 12 54-65 2-13 (46)
24 PF01352 KRAB: KRAB box; Inte 32.8 48 0.001 18.9 2.2 22 7-29 5-26 (41)
25 TIGR02098 MJ0042_CXXC MJ0042 f 31.8 30 0.00066 18.7 1.2 12 54-65 24-35 (38)
26 PF05924 SAMP: SAMP Motif; In 31.4 6.5 0.00014 20.0 -1.4 9 78-86 6-14 (20)
27 PF10880 DUF2673: Protein of u 30.5 25 0.00054 22.4 0.8 18 13-30 42-59 (65)
28 PRK13267 archaemetzincin-like 29.7 16 0.00036 27.0 -0.2 19 65-90 133-152 (179)
29 PF04997 RNA_pol_Rpb1_1: RNA p 29.6 22 0.00047 26.2 0.5 9 61-69 67-75 (337)
30 COG3091 SprT Zn-dependent meta 29.5 31 0.00067 25.7 1.3 57 8-65 79-150 (156)
31 PF10122 Mu-like_Com: Mu-like 28.4 50 0.0011 20.3 1.9 18 51-69 20-37 (51)
32 PF11672 DUF3268: Protein of u 27.5 1.2E+02 0.0025 20.9 3.8 19 56-75 32-50 (102)
33 PF13005 zf-IS66: zinc-finger 27.1 29 0.00062 19.5 0.6 12 57-68 4-15 (47)
34 smart00834 CxxC_CXXC_SSSS Puta 26.8 43 0.00094 17.9 1.3 15 51-65 1-15 (41)
35 PF09723 Zn-ribbon_8: Zinc rib 26.7 43 0.00094 18.9 1.3 13 51-63 1-13 (42)
36 PF13842 Tnp_zf-ribbon_2: DDE_ 26.4 55 0.0012 17.8 1.6 12 54-65 15-26 (32)
37 PF07813 LTXXQ: LTXXQ motif fa 26.2 55 0.0012 20.3 1.8 16 15-30 82-97 (100)
38 PF13408 Zn_ribbon_recom: Reco 26.1 34 0.00074 19.5 0.8 13 56-68 6-18 (58)
39 PF05452 Clavanin: Clavanin; 26.0 37 0.00081 22.4 1.1 17 63-79 46-62 (80)
40 COG1644 RPB10 DNA-directed RNA 26.0 22 0.00048 22.8 -0.0 17 54-70 3-19 (63)
41 PF13101 DUF3945: Protein of u 25.9 35 0.00077 20.7 0.9 24 11-34 25-48 (59)
42 TIGR02605 CxxC_CxxC_SSSS putat 25.8 45 0.00098 19.1 1.3 13 51-63 1-13 (52)
43 PF04988 AKAP95: A-kinase anch 25.7 9.7 0.00021 28.5 -2.0 22 48-69 83-105 (165)
44 PRK09710 lar restriction allev 25.7 1E+02 0.0022 19.7 3.0 26 37-64 10-36 (64)
45 PF04810 zf-Sec23_Sec24: Sec23 24.9 32 0.00069 19.3 0.5 13 56-68 3-15 (40)
46 COG1996 RPC10 DNA-directed RNA 24.5 49 0.0011 20.1 1.3 14 52-65 3-16 (49)
47 COG1507 Uncharacterized conser 23.1 89 0.0019 23.4 2.7 30 49-82 19-54 (167)
48 PF09845 DUF2072: Zn-ribbon co 21.7 44 0.00096 24.1 0.8 13 57-73 3-15 (131)
49 PF00527 E7: E7 protein, Early 21.5 62 0.0013 21.5 1.5 18 50-67 47-64 (92)
50 PF05515 Viral_NABP: Viral nuc 21.3 19 0.00042 25.8 -1.1 32 30-67 39-76 (124)
51 PF09814 HECT_2: HECT-like Ubi 21.3 65 0.0014 25.1 1.7 15 54-68 192-206 (354)
52 KOG4465|consensus 21.0 50 0.0011 28.4 1.1 9 74-82 424-432 (598)
53 PF08271 TF_Zn_Ribbon: TFIIB z 20.6 60 0.0013 18.2 1.1 13 53-65 17-29 (43)
54 cd00233 VIP2 VIP2; A family of 20.6 76 0.0017 23.4 1.9 17 14-30 20-36 (201)
55 PF11781 RRN7: RNA polymerase 20.5 53 0.0011 18.3 0.8 22 55-82 8-29 (36)
56 PF07945 Toxin_16: Janus-atrac 20.5 48 0.001 18.8 0.6 12 72-83 24-35 (36)
57 COG2126 RPL37A Ribosomal prote 20.3 40 0.00087 21.5 0.3 23 48-70 7-31 (61)
No 1
>COG0229 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=5.1e-48 Score=277.14 Aligned_cols=84 Identities=55% Similarity=0.920 Sum_probs=79.2
Q ss_pred CCCCHHHHHhcCCHHHHHhhhhCCCCCCCCCC------------------------------------------ceeEE-
Q psy4120 10 CKIDKEELKKRLTPMQYHVTQEKGTERYIGSN------------------------------------------LLLLI- 46 (95)
Q Consensus 10 ~~~s~~ewk~~Lt~~qy~Vlr~~gTE~pfsg~------------------------------------------~v~~~- 46 (95)
.++++++||++|||+||+|||++|||+||+|+ +|.++
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 46899999999999999999999999999999 45555
Q ss_pred -eCCCceEEEEEcCCCCCccccccCCCCCCCC-ceeeeccceeeeeeCC
Q psy4120 47 -TNPDMVRTEVTCSKCDAHLGHVFNDGPAPTR-RRFCINSASVDFVPDH 93 (95)
Q Consensus 47 -~s~gm~R~Ev~C~~Cg~HLGHVF~DGP~ptg-~RyCiNs~sL~F~p~~ 93 (95)
.|+||.||||+|++|+|||||||+|||+||| +|||||||||+|+|.+
T Consensus 82 D~S~gM~RtEVrc~~c~sHLGHVF~DGP~~tgglRYCINSasL~Fip~~ 130 (140)
T COG0229 82 DRSHGMVRTEVRCANCDSHLGHVFPDGPPPTGGLRYCINSASLRFIPKE 130 (140)
T ss_pred ccCCCcEEEEEEecCCCCccccccCCCCCCCCCeeEeecchheeecchh
Confidence 8999999999999999999999999999998 9999999999999985
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=1.3e-47 Score=273.84 Aligned_cols=83 Identities=54% Similarity=0.935 Sum_probs=78.1
Q ss_pred CCCHHHHHhcCCHHHHHhhhhCCCCCCCCCC------------------------------------------ceeEE--
Q psy4120 11 KIDKEELKKRLTPMQYHVTQEKGTERYIGSN------------------------------------------LLLLI-- 46 (95)
Q Consensus 11 ~~s~~ewk~~Lt~~qy~Vlr~~gTE~pfsg~------------------------------------------~v~~~-- 46 (95)
+++++|||+.|||+||+|||++|||+||||+ +|.++
T Consensus 1 ~~~~~ewr~~Lt~~qy~V~r~~gTE~pftg~y~~~~~~G~Y~C~~Cg~pLF~S~~KfdSg~GWPSF~~~i~~~~V~~~~D 80 (134)
T TIGR00357 1 KPSDEELKKKLTPLQYEVTQNAGTEPPFTNEYWDNKEEGIYVDITCGEPLFSSEDKFDSGCGWPSFYKPISEEVVAYERD 80 (134)
T ss_pred CCCHHHHHHhCCHHHHHHHHHhCCCCCCCCCCCCCCCCeEEEccCCCCccccccchhcCCCCCcCcCcccCCCceEEeec
Confidence 4689999999999999999999999999999 45555
Q ss_pred eCCCceEEEEEcCCCCCccccccCCCCCCCCceeeeccceeeeeeCC
Q psy4120 47 TNPDMVRTEVTCSKCDAHLGHVFNDGPAPTRRRFCINSASVDFVPDH 93 (95)
Q Consensus 47 ~s~gm~R~Ev~C~~Cg~HLGHVF~DGP~ptg~RyCiNs~sL~F~p~~ 93 (95)
.|+||+||||+|++||+||||||+|||+|||+||||||+||+|+|+.
T Consensus 81 ~s~gm~RtEv~C~~Cg~HLGHVF~DGP~ptg~RyCINs~sL~F~p~~ 127 (134)
T TIGR00357 81 ESHGMIRTEVRCRNCDAHLGHVFDDGPEPTGLRYCINSAALKFIPLE 127 (134)
T ss_pred CCCCcEEEEEEecCCCCccCcccCCCCCCCCceEeecceeEecccch
Confidence 78999999999999999999999999999999999999999999975
No 3
>PRK00222 methionine sulfoxide reductase B; Provisional
Probab=100.00 E-value=7.9e-47 Score=271.92 Aligned_cols=84 Identities=57% Similarity=0.936 Sum_probs=79.0
Q ss_pred CCCCHHHHHhcCCHHHHHhhhhCCCCCCCCCC------------------------------------------ceeEE-
Q psy4120 10 CKIDKEELKKRLTPMQYHVTQEKGTERYIGSN------------------------------------------LLLLI- 46 (95)
Q Consensus 10 ~~~s~~ewk~~Lt~~qy~Vlr~~gTE~pfsg~------------------------------------------~v~~~- 46 (95)
++++++|||+.|||+||+|||++|||+||+|+ +|+++
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 56899999999999999999999999999999 45554
Q ss_pred -eCCCceEEEEEcCCCCCccccccCCCCCCCCceeeeccceeeeeeCC
Q psy4120 47 -TNPDMVRTEVTCSKCDAHLGHVFNDGPAPTRRRFCINSASVDFVPDH 93 (95)
Q Consensus 47 -~s~gm~R~Ev~C~~Cg~HLGHVF~DGP~ptg~RyCiNs~sL~F~p~~ 93 (95)
.++||.||||+|++||+||||||+|||+|||+||||||+||+|+|+.
T Consensus 83 D~s~gm~RtEv~C~~Cg~HLGHVF~DGP~ptg~RyCINs~sL~F~p~~ 130 (142)
T PRK00222 83 DTSHGMVRTEVRCANCDSHLGHVFPDGPKPTGLRYCINSASLKFIPKD 130 (142)
T ss_pred ccCCCceEEEEEeCCCCCccCcccCCCCCCCCCEeeeceeeEEeeccc
Confidence 78999999999999999999999999999999999999999999975
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=7.1e-46 Score=261.83 Aligned_cols=79 Identities=56% Similarity=0.955 Sum_probs=72.3
Q ss_pred HHHHHhcCCHHHHHhhhhCCCCCCCCCC------------------------------------------ceeEE--eCC
Q psy4120 14 KEELKKRLTPMQYHVTQEKGTERYIGSN------------------------------------------LLLLI--TNP 49 (95)
Q Consensus 14 ~~ewk~~Lt~~qy~Vlr~~gTE~pfsg~------------------------------------------~v~~~--~s~ 49 (95)
|+|||++|||+||+|||++|||+||||+ +|.+. .|+
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 6899999999999999999999999999 56655 889
Q ss_pred CceEEEEEcCCCCCccccccCCCCCC-CCceeeeccceeeeeeC
Q psy4120 50 DMVRTEVTCSKCDAHLGHVFNDGPAP-TRRRFCINSASVDFVPD 92 (95)
Q Consensus 50 gm~R~Ev~C~~Cg~HLGHVF~DGP~p-tg~RyCiNs~sL~F~p~ 92 (95)
||.||||+|++||+||||||+|||+| ||+||||||+||+|+|+
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
>KOG0856|consensus
Probab=100.00 E-value=2.4e-42 Score=248.73 Aligned_cols=90 Identities=43% Similarity=0.751 Sum_probs=83.6
Q ss_pred CCCCCCCCCHHHHHhcCCHHHHHhhhhCCCCCCCCCC------------------------------------------c
Q psy4120 5 NNAGGCKIDKEELKKRLTPMQYHVTQEKGTERYIGSN------------------------------------------L 42 (95)
Q Consensus 5 ~~~~~~~~s~~ewk~~Lt~~qy~Vlr~~gTE~pfsg~------------------------------------------~ 42 (95)
...++++++++|||+.|||+||+|||++|||+||+|+ +
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 4567899999999999999999999999999999999 4
Q ss_pred eeEE--eCCCceEEEEEcCCCCCccccccC-CCCC-CCCceeeeccceeeeeeCCC
Q psy4120 43 LLLI--TNPDMVRTEVTCSKCDAHLGHVFN-DGPA-PTRRRFCINSASVDFVPDHP 94 (95)
Q Consensus 43 v~~~--~s~gm~R~Ev~C~~Cg~HLGHVF~-DGP~-ptg~RyCiNs~sL~F~p~~~ 94 (95)
|+++ .|+||.|+||+|++||+||||||. |||. ||++||||||+||+|.|+..
T Consensus 89 I~r~~d~s~~~~R~Ev~Ca~C~~HLGHVF~~eG~~~Pt~~R~CiNS~sL~F~~~~~ 144 (146)
T KOG0856|consen 89 ITRTPDNSRGGRRTEVSCATCGGHLGHVFKGEGPKTPTDERHCINSVSLKFVPADS 144 (146)
T ss_pred eeeccccCCCCcceEEEEeecCCceeeeecCCCCCCCCCceeEeeeeeeeeccCCC
Confidence 5555 789999999999999999999998 9998 99999999999999999864
No 6
>PRK05508 methionine sulfoxide reductase B; Provisional
Probab=100.00 E-value=3.4e-41 Score=236.87 Aligned_cols=75 Identities=43% Similarity=0.752 Sum_probs=66.4
Q ss_pred hcCCHHHHHhhhhCCCCCCCCCC-----------------------------------------ceeEEeCCCceEEEEE
Q psy4120 19 KRLTPMQYHVTQEKGTERYIGSN-----------------------------------------LLLLITNPDMVRTEVT 57 (95)
Q Consensus 19 ~~Lt~~qy~Vlr~~gTE~pfsg~-----------------------------------------~v~~~~s~gm~R~Ev~ 57 (95)
+.|||+||+|||++|||+||+|+ +|.++....|.||||+
T Consensus 2 ~~Lt~~qy~V~r~~gTE~pftg~y~~~~~~G~Y~C~~Cg~pLF~S~~KfdSg~GWPSF~~~i~~~v~~~~D~~~~RtEv~ 81 (119)
T PRK05508 2 NELTPEEEAVILRKGTEPPFSGEYNDFFEKGTYVCKQCGAPLYRSEDKFKSGCGWPSFDDEIKGAVKRIPDADGRRTEIV 81 (119)
T ss_pred CcCCHHHHHHHHhcCCCCCCCCCCcCcCCCeEEEecCCCCccccccccccCCCCCcccCcccccceEEEecCCCcEEEEE
Confidence 57999999999999999999999 4555533336899999
Q ss_pred cCCCCCccccccC-CCCCCCCceeeeccceeeeeeCC
Q psy4120 58 CSKCDAHLGHVFN-DGPAPTRRRFCINSASVDFVPDH 93 (95)
Q Consensus 58 C~~Cg~HLGHVF~-DGP~ptg~RyCiNs~sL~F~p~~ 93 (95)
|++||+||||||+ |||+|||+|||||||||+|+|+.
T Consensus 82 C~~C~~HLGHVF~d~gp~ptg~RyCINS~sL~F~p~~ 118 (119)
T PRK05508 82 CANCGGHLGHVFEGEGFTPKNTRHCVNSISLKFVPDK 118 (119)
T ss_pred eCCCCCccCcccCCCCCCCCCCEEeecceeEEeecCC
Confidence 9999999999998 56789999999999999999975
No 7
>PRK14018 trifunctional thioredoxin/methionine sulfoxide reductase A/B protein; Provisional
Probab=100.00 E-value=1.5e-39 Score=270.28 Aligned_cols=84 Identities=43% Similarity=0.639 Sum_probs=77.7
Q ss_pred CCCCHHHHHhcCCHHHHHhhhhCCCCCCCCCC------------------------------------------ceeEE-
Q psy4120 10 CKIDKEELKKRLTPMQYHVTQEKGTERYIGSN------------------------------------------LLLLI- 46 (95)
Q Consensus 10 ~~~s~~ewk~~Lt~~qy~Vlr~~gTE~pfsg~------------------------------------------~v~~~- 46 (95)
.+++++|||+.|||+||+|||++|||+||||+ +|.+.
T Consensus 378 ~~~~~~~~~~~Lt~~~y~v~~~~gtE~~f~~~~~~~~~~G~y~c~~c~~pLf~s~~Kf~sg~GWPsF~~~i~~~~v~~~~ 457 (521)
T PRK14018 378 KKPSDAELKRTLTEEQYQITQNAATERAFSHEYDHLFKPGIYVDVVSGEPLFSSADKYDSGCGWPSFTRPIDAKVVTEHD 457 (521)
T ss_pred cCCChHHHhccCCHHHHHHHHhcCCCCCCCCCCcCCCCCEEEEecCCCCccccCcccccCCCCCcccCcccCcCceEEee
Confidence 35799999999999999999999999999999 35444
Q ss_pred -eCCCceEEEEEcCCCCCccccccCCCCC-CCCceeeeccceeeeeeCC
Q psy4120 47 -TNPDMVRTEVTCSKCDAHLGHVFNDGPA-PTRRRFCINSASVDFVPDH 93 (95)
Q Consensus 47 -~s~gm~R~Ev~C~~Cg~HLGHVF~DGP~-ptg~RyCiNs~sL~F~p~~ 93 (95)
.|+||.||||+|++||+||||||+|||+ |||+||||||+||+|+|+.
T Consensus 458 d~s~g~~R~Ev~c~~c~~HLGHvf~dgp~~~~g~RyCiNs~~l~f~~~~ 506 (521)
T PRK14018 458 DFSYNMRRTEVRSRAADSHLGHVFPDGPRDKGGLRYCINGASLKFIPLE 506 (521)
T ss_pred ccCCCceEEEEEECCCCCcCCcccCCCCCCCCCCEeeeceeEEEeecch
Confidence 7899999999999999999999999996 6999999999999999975
No 8
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=100.00 E-value=1.9e-37 Score=242.59 Aligned_cols=79 Identities=44% Similarity=0.820 Sum_probs=69.9
Q ss_pred HHHHhcCCHHHHHhhhhCCCCCCCCCC-----------------------------------------ceeEE-eCCCce
Q psy4120 15 EELKKRLTPMQYHVTQEKGTERYIGSN-----------------------------------------LLLLI-TNPDMV 52 (95)
Q Consensus 15 ~ewk~~Lt~~qy~Vlr~~gTE~pfsg~-----------------------------------------~v~~~-~s~gm~ 52 (95)
+.||+.|||+||+|||++||||||+|+ +|..+ ...||
T Consensus 1 ~~~~~~Lt~~~y~v~r~~gTE~pf~g~~~~~~~~G~y~c~~c~~~LF~s~~Kf~sg~GWPsF~~~~~~~~~~~~d~~~~- 79 (283)
T PRK05550 1 MDKMKSLTPFEYRVIEDKGTERPFSGEYYDHDEKGVYLCRRCGAPLFRSEDKFNSGCGWPSFDDEIPGAVKRLPDADGR- 79 (283)
T ss_pred ChhhhhCCHHHHHHHHhcCCCCCCCCcCcCCCCCcEEEcCCCCchhcCChhhccCCCCCcCcCcccCCccEEEEcCCCc-
Confidence 369999999999999999999999999 33333 23366
Q ss_pred EEEEEcCCCCCccccccC-CCCCCCCceeeeccceeeeeeCCC
Q psy4120 53 RTEVTCSKCDAHLGHVFN-DGPAPTRRRFCINSASVDFVPDHP 94 (95)
Q Consensus 53 R~Ev~C~~Cg~HLGHVF~-DGP~ptg~RyCiNs~sL~F~p~~~ 94 (95)
||||+|++||+||||||+ |||+|||+||||||+||+|+|+.+
T Consensus 80 R~Ev~c~~c~~HLGHvF~ddgp~ptg~RyCiNs~sL~f~p~~~ 122 (283)
T PRK05550 80 RTEIVCANCGAHLGHVFEGEGLTPKNTRHCVNSASLDFVPAEE 122 (283)
T ss_pred eEEEEecCCCCccCcccCCCCCCCCCccccccccccccCcccc
Confidence 999999999999999998 789999999999999999999853
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=84.96 E-value=0.58 Score=30.56 Aligned_cols=36 Identities=25% Similarity=0.622 Sum_probs=26.9
Q ss_pred EEEEEcCCCCCccccccCCCCCC---CCceeeeccceee
Q psy4120 53 RTEVTCSKCDAHLGHVFNDGPAP---TRRRFCINSASVD 88 (95)
Q Consensus 53 R~Ev~C~~Cg~HLGHVF~DGP~p---tg~RyCiNs~sL~ 88 (95)
=..+.|+.|+.+||..+..-|.. .--.|++.-++|.
T Consensus 55 ~~~l~C~~C~~~lGwkY~~a~~~~~~k~g~file~~~i~ 93 (96)
T PF03226_consen 55 VRDLFCSGCNTILGWKYESAPEEQKYKEGKFILEKASIS 93 (96)
T ss_pred EEEeEcccCChhHCcEEEEcCHhHhhhCCEEEEEhhHEE
Confidence 45799999999999999765543 3456777766664
No 10
>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=76.04 E-value=3.7 Score=23.25 Aligned_cols=29 Identities=31% Similarity=0.844 Sum_probs=21.3
Q ss_pred ceEEEEEcCCCCCccccccCCCCCCCC-cee
Q psy4120 51 MVRTEVTCSKCDAHLGHVFNDGPAPTR-RRF 80 (95)
Q Consensus 51 m~R~Ev~C~~Cg~HLGHVF~DGP~ptg-~Ry 80 (95)
|.-|+|.|..|++..+ |..-|-.+.| +||
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 6779999999999874 3345666655 676
No 11
>PF04828 GFA: Glutathione-dependent formaldehyde-activating enzyme; InterPro: IPR006913 The GFA family consists mainly of glutathione-dependent formaldehyde-activating enzymes, but also includes centromere protein V and a fission yeast protein described as uncharacterised lyase. Glutathione-dependent formaldehyde-activating enzyme catalyse the condensation of formaldehyde and glutathione to S-hydroxymethylglutathione. All known members of this family contain 5 strongly conserved cysteine residues.; GO: 0016846 carbon-sulfur lyase activity, 0008152 metabolic process; PDB: 3FAC_B 1XA8_A 1X6M_B.
Probab=71.13 E-value=4.3 Score=24.94 Aligned_cols=31 Identities=19% Similarity=0.311 Sum_probs=20.9
Q ss_pred EEEcCCCCCccccccCCCCCCCCceeeeccceeee
Q psy4120 55 EVTCSKCDAHLGHVFNDGPAPTRRRFCINSASVDF 89 (95)
Q Consensus 55 Ev~C~~Cg~HLGHVF~DGP~ptg~RyCiNs~sL~F 89 (95)
-..|+.||++|.......| ..+-|+..+|+-
T Consensus 48 r~FC~~CGs~l~~~~~~~~----~~~~V~~g~ld~ 78 (92)
T PF04828_consen 48 RYFCPTCGSPLFSEDERDP----DLVGVNAGTLDD 78 (92)
T ss_dssp EEEETTT--EEEEEESSTT----TEEEEEGGGBTT
T ss_pred CcccCCCCCeeecccCCCC----CEEEEEeEeeCC
Confidence 3899999999997644433 377788777753
No 12
>COG3791 Uncharacterized conserved protein [Function unknown]
Probab=58.34 E-value=9.9 Score=26.46 Aligned_cols=35 Identities=20% Similarity=0.230 Sum_probs=25.7
Q ss_pred CCCceEEEEEcCCCCCccccccCCCCCCCCceeeeccceee
Q psy4120 48 NPDMVRTEVTCSKCDAHLGHVFNDGPAPTRRRFCINSASVD 88 (95)
Q Consensus 48 s~gm~R~Ev~C~~Cg~HLGHVF~DGP~ptg~RyCiNs~sL~ 88 (95)
+....|. -|++||+||-+...|+. .-+=||-++|+
T Consensus 64 s~~~~r~--FC~~CGs~l~~~~~~~~----~~~~v~~~~ld 98 (133)
T COG3791 64 SGSAGRG--FCPTCGSPLFWRGPDED----PFVGVNAGALD 98 (133)
T ss_pred cCCCCCe--ecccCCCceEEecCCCC----ceEEEEEeeec
Confidence 3334444 99999999998877654 36777888887
No 13
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=53.09 E-value=5.5 Score=20.58 Aligned_cols=20 Identities=35% Similarity=0.896 Sum_probs=13.0
Q ss_pred EEEcCCCCCccccccCCCCCCCCceeeec
Q psy4120 55 EVTCSKCDAHLGHVFNDGPAPTRRRFCIN 83 (95)
Q Consensus 55 Ev~C~~Cg~HLGHVF~DGP~ptg~RyCiN 83 (95)
++.|.+||.-+ +.+.|||.|
T Consensus 2 ~~~Cp~Cg~~~---------~~~~~fC~~ 21 (26)
T PF13248_consen 2 EMFCPNCGAEI---------DPDAKFCPN 21 (26)
T ss_pred cCCCcccCCcC---------CcccccChh
Confidence 46789998732 244678765
No 14
>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=52.98 E-value=12 Score=19.95 Aligned_cols=23 Identities=26% Similarity=0.450 Sum_probs=11.5
Q ss_pred EcCCCCCccccccCCCCCCCCceeeecc
Q psy4120 57 TCSKCDAHLGHVFNDGPAPTRRRFCINS 84 (95)
Q Consensus 57 ~C~~Cg~HLGHVF~DGP~ptg~RyCiNs 84 (95)
.|..||+.|=.. +|+- ..||+|+
T Consensus 1 ~CP~C~s~l~~~-~~ev----~~~C~N~ 23 (28)
T PF03119_consen 1 TCPVCGSKLVRE-EGEV----DIRCPNP 23 (28)
T ss_dssp B-TTT--BEEE--CCTT----CEEE--C
T ss_pred CcCCCCCEeEcC-CCCE----eEECCCC
Confidence 488999998743 3322 5899998
No 15
>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=51.81 E-value=12 Score=22.86 Aligned_cols=26 Identities=27% Similarity=0.350 Sum_probs=20.7
Q ss_pred ceEEEEEcCCCCCccccccCCCCCCC
Q psy4120 51 MVRTEVTCSKCDAHLGHVFNDGPAPT 76 (95)
Q Consensus 51 m~R~Ev~C~~Cg~HLGHVF~DGP~pt 76 (95)
..|..+.|++|.+|=|-+....+.+.
T Consensus 18 ~~r~aLIC~~C~~hNGla~~~~~~~i 43 (54)
T PF10058_consen 18 SNRYALICSKCFSHNGLAPKEEFEEI 43 (54)
T ss_pred cCceeEECcccchhhcccccccCCce
Confidence 35888999999999999986555544
No 16
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=46.12 E-value=35 Score=20.11 Aligned_cols=26 Identities=27% Similarity=0.363 Sum_probs=16.8
Q ss_pred CCCCCceeEE-----eCCCceEEEEEcCCCCC
Q psy4120 37 YIGSNLLLLI-----TNPDMVRTEVTCSKCDA 63 (95)
Q Consensus 37 pfsg~~v~~~-----~s~gm~R~Ev~C~~Cg~ 63 (95)
||.|...... ...++. .-|.|..||+
T Consensus 7 PFCG~~~~~~~~~~~~~~~~~-~~V~C~~Cga 37 (61)
T PF14354_consen 7 PFCGSADVLIRQDEGFDYGMY-YYVECTDCGA 37 (61)
T ss_pred CCCCCcceEeecccCCCCCCE-EEEEcCCCCC
Confidence 8898744333 223332 6688999999
No 17
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=43.56 E-value=8.9 Score=22.48 Aligned_cols=15 Identities=40% Similarity=1.012 Sum_probs=11.7
Q ss_pred EEcCCCCCccccccCC
Q psy4120 56 VTCSKCDAHLGHVFND 71 (95)
Q Consensus 56 v~C~~Cg~HLGHVF~D 71 (95)
++|.+||+ +||.=.+
T Consensus 2 ~kC~~CG~-~GH~~t~ 16 (40)
T PF15288_consen 2 VKCKNCGA-FGHMRTN 16 (40)
T ss_pred cccccccc-ccccccC
Confidence 68999976 7997544
No 18
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=41.01 E-value=12 Score=24.70 Aligned_cols=24 Identities=29% Similarity=0.728 Sum_probs=18.5
Q ss_pred ceEEEEEcCCCCCcccccc-CCCCC
Q psy4120 51 MVRTEVTCSKCDAHLGHVF-NDGPA 74 (95)
Q Consensus 51 m~R~Ev~C~~Cg~HLGHVF-~DGP~ 74 (95)
..++.-+|..||--++|.= +|||+
T Consensus 4 ~Lk~~~~C~~CG~d~~~~~adDgPA 28 (86)
T PF06170_consen 4 YLKVAPRCPHCGLDYSHARADDGPA 28 (86)
T ss_pred cccCCCcccccCCccccCCcCccch
Confidence 3445568999999999985 57874
No 19
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=40.14 E-value=17 Score=20.18 Aligned_cols=17 Identities=41% Similarity=0.821 Sum_probs=11.4
Q ss_pred CceEEEEEcCCCCCccccccC
Q psy4120 50 DMVRTEVTCSKCDAHLGHVFN 70 (95)
Q Consensus 50 gm~R~Ev~C~~Cg~HLGHVF~ 70 (95)
+.....|+|++|+ |+|.
T Consensus 20 ~~~~~~vrC~~C~----~~f~ 36 (37)
T PF13719_consen 20 PAGGRKVRCPKCG----HVFR 36 (37)
T ss_pred ccCCcEEECCCCC----cEee
Confidence 3444579999994 6663
No 20
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=35.40 E-value=17 Score=25.61 Aligned_cols=12 Identities=58% Similarity=1.611 Sum_probs=10.3
Q ss_pred EcCCCCCccccccCCC
Q psy4120 57 TCSKCDAHLGHVFNDG 72 (95)
Q Consensus 57 ~C~~Cg~HLGHVF~DG 72 (95)
+|.+| ||||.||
T Consensus 4 ~CtrC----G~vf~~g 15 (112)
T COG3364 4 QCTRC----GEVFDDG 15 (112)
T ss_pred eeccc----ccccccc
Confidence 68888 6999997
No 21
>PRK14891 50S ribosomal protein L24e/unknown domain fusion protein; Provisional
Probab=35.09 E-value=28 Score=25.22 Aligned_cols=12 Identities=42% Similarity=0.639 Sum_probs=9.4
Q ss_pred ceEEEEEcCCCCC
Q psy4120 51 MVRTEVTCSKCDA 63 (95)
Q Consensus 51 m~R~Ev~C~~Cg~ 63 (95)
|+||+ .|+-||.
T Consensus 1 Mm~~e-~CsFcG~ 12 (131)
T PRK14891 1 MVETR-TCDYTGE 12 (131)
T ss_pred CCcee-eecCcCC
Confidence 67887 4999985
No 22
>PF10601 zf-LITAF-like: LITAF-like zinc ribbon domain; InterPro: IPR006629 Members of this family display a conserved zinc ribbon structure [] with the motif C-XX-C- separated from the more C-terminal HX-C(P)X-C-X4-G-R motif by a variable region of usually 25-30 (hydrophobic) residues. Although it belongs to one of the zinc finger's fold groups (zinc ribbon), this particular domain was first identified in LPS-induced tumour necrosis alpha factor (LITAF) which is produced in mammalian cells after being challenged with lipopolysaccharide (LPS). The hydrophobic region probably inserts into the membrane rather than traversing it. Such an insertion brings together the N- and C-terminal C-XX-C motifs to form a compact Zn2+-binding structure [].
Probab=34.76 E-value=23 Score=21.93 Aligned_cols=16 Identities=31% Similarity=0.590 Sum_probs=13.9
Q ss_pred eEEEEEcCCCCCcccc
Q psy4120 52 VRTEVTCSKCDAHLGH 67 (95)
Q Consensus 52 ~R~Ev~C~~Cg~HLGH 67 (95)
.-++-.|.+|+..||.
T Consensus 55 kd~~H~Cp~C~~~lg~ 70 (73)
T PF10601_consen 55 KDVYHYCPNCGAFLGT 70 (73)
T ss_pred cCceEECCCCCCEeEE
Confidence 4578899999999996
No 23
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=33.23 E-value=23 Score=20.17 Aligned_cols=12 Identities=25% Similarity=0.880 Sum_probs=9.3
Q ss_pred EEEEcCCCCCcc
Q psy4120 54 TEVTCSKCDAHL 65 (95)
Q Consensus 54 ~Ev~C~~Cg~HL 65 (95)
++++|.+||+-+
T Consensus 2 ~~y~C~~CG~~~ 13 (46)
T PRK00398 2 AEYKCARCGREV 13 (46)
T ss_pred CEEECCCCCCEE
Confidence 578999998754
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=32.77 E-value=48 Score=18.94 Aligned_cols=22 Identities=23% Similarity=0.243 Sum_probs=12.1
Q ss_pred CCCCCCCHHHHHhcCCHHHHHhh
Q psy4120 7 AGGCKIDKEELKKRLTPMQYHVT 29 (95)
Q Consensus 7 ~~~~~~s~~ewk~~Lt~~qy~Vl 29 (95)
+-.+.+|.+||. .|.|.|...-
T Consensus 5 Dvav~fs~eEW~-~L~~~Qk~ly 26 (41)
T PF01352_consen 5 DVAVYFSQEEWE-LLDPAQKNLY 26 (41)
T ss_dssp --TT---HHHHH-TS-HHHHHHH
T ss_pred EEEEEcChhhcc-cccceecccc
Confidence 345678999996 6899986643
No 25
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=31.83 E-value=30 Score=18.67 Aligned_cols=12 Identities=33% Similarity=0.736 Sum_probs=9.3
Q ss_pred EEEEcCCCCCcc
Q psy4120 54 TEVTCSKCDAHL 65 (95)
Q Consensus 54 ~Ev~C~~Cg~HL 65 (95)
.+|+|.+|+.-+
T Consensus 24 ~~v~C~~C~~~~ 35 (38)
T TIGR02098 24 GKVRCGKCGHVW 35 (38)
T ss_pred CEEECCCCCCEE
Confidence 379999998643
No 26
>PF05924 SAMP: SAMP Motif; InterPro: IPR009224 This short region is found repeated in the mid region of the adenomatous polyposis proteins (APCs). This motif binds axin [].; GO: 0008013 beta-catenin binding, 0016055 Wnt receptor signaling pathway; PDB: 1EMU_B 2RQU_B.
Probab=31.36 E-value=6.5 Score=20.01 Aligned_cols=9 Identities=44% Similarity=0.538 Sum_probs=6.7
Q ss_pred ceeeeccce
Q psy4120 78 RRFCINSAS 86 (95)
Q Consensus 78 ~RyCiNs~s 86 (95)
++-|||||-
T Consensus 6 L~~CI~sAm 14 (20)
T PF05924_consen 6 LQECIGSAM 14 (20)
T ss_dssp HHHHHHCTS
T ss_pred HHHHHHHhc
Confidence 467999983
No 27
>PF10880 DUF2673: Protein of unknown function (DUF2673); InterPro: IPR024247 This family of proteins with unknown function appears to be restricted to Rickettsiae spp.
Probab=30.49 E-value=25 Score=22.45 Aligned_cols=18 Identities=28% Similarity=0.388 Sum_probs=14.6
Q ss_pred CHHHHHhcCCHHHHHhhh
Q psy4120 13 DKEELKKRLTPMQYHVTQ 30 (95)
Q Consensus 13 s~~ewk~~Lt~~qy~Vlr 30 (95)
+...|.+.||..||..+-
T Consensus 42 ~qq~wvasltadqynmls 59 (65)
T PF10880_consen 42 DQQAWVASLTADQYNMLS 59 (65)
T ss_pred hHHHHHHHhhhhhhcccC
Confidence 356699999999998763
No 28
>PRK13267 archaemetzincin-like protein; Reviewed
Probab=29.75 E-value=16 Score=26.97 Aligned_cols=19 Identities=32% Similarity=0.648 Sum_probs=13.0
Q ss_pred cccccCCCCCCCCceeeecc-ceeeee
Q psy4120 65 LGHVFNDGPAPTRRRFCINS-ASVDFV 90 (95)
Q Consensus 65 LGHVF~DGP~ptg~RyCiNs-~sL~F~ 90 (95)
|||+| |+.||.|. +.+.|.
T Consensus 133 lGH~l-------GL~HC~~~~CvM~~s 152 (179)
T PRK13267 133 LGHTL-------GLEHCDNPRCVMNFS 152 (179)
T ss_pred HHHHc-------CCccCCCCCccCCCC
Confidence 78886 57889985 445543
No 29
>PF04997 RNA_pol_Rpb1_1: RNA polymerase Rpb1, domain 1; InterPro: IPR007080 RNA polymerases catalyse the DNA-dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). This domain, domain 1, represents the clamp domain, which is a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand [, ].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2Y0S_W 3QQC_A 1YNJ_D 1HQM_D 1YNN_D 1I6V_D 2GHO_D 2AUJ_D 1ZYR_D 1SMY_D ....
Probab=29.58 E-value=22 Score=26.22 Aligned_cols=9 Identities=44% Similarity=1.150 Sum_probs=6.9
Q ss_pred CCCcccccc
Q psy4120 61 CDAHLGHVF 69 (95)
Q Consensus 61 Cg~HLGHVF 69 (95)
|-+|.||+-
T Consensus 67 CpGHfGhI~ 75 (337)
T PF04997_consen 67 CPGHFGHIE 75 (337)
T ss_dssp CCCSEEEEE
T ss_pred cCCceeEEE
Confidence 558999973
No 30
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=29.50 E-value=31 Score=25.65 Aligned_cols=57 Identities=19% Similarity=0.205 Sum_probs=32.2
Q ss_pred CCCCCCHHHHHhcCC---------HHHHHhhhhCCCCCCCCCC------ceeEEeCCCceEEEEEcCCCCCcc
Q psy4120 8 GGCKIDKEELKKRLT---------PMQYHVTQEKGTERYIGSN------LLLLITNPDMVRTEVTCSKCDAHL 65 (95)
Q Consensus 8 ~~~~~s~~ewk~~Lt---------~~qy~Vlr~~gTE~pfsg~------~v~~~~s~gm~R~Ev~C~~Cg~HL 65 (95)
|.++.-++|||..|. ..++.|-.-++|--+|.=. .+..++..-.-+ +.+|..|++-|
T Consensus 79 gr~~phg~ewk~lm~qV~~l~~~~~h~~~~~~v~~~~~~Y~C~C~q~~l~~RRhn~~~~g~-~YrC~~C~gkL 150 (156)
T COG3091 79 GRYKPHGKEWKLLMQQVLGLRFCRTHQFEVQSVRRTTYPYRCQCQQHYLRIRRHNTVRRGE-VYRCGKCGGKL 150 (156)
T ss_pred CCCCCCchhHHHHHHHhCCCCCCccchHHHhhccccceeEEeecCCccchhhhcccccccc-eEEeccCCceE
Confidence 456778889987553 3566666666665555322 222221111112 68888888766
No 31
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=28.37 E-value=50 Score=20.29 Aligned_cols=18 Identities=28% Similarity=0.874 Sum_probs=13.4
Q ss_pred ceEEEEEcCCCCCcccccc
Q psy4120 51 MVRTEVTCSKCDAHLGHVF 69 (95)
Q Consensus 51 m~R~Ev~C~~Cg~HLGHVF 69 (95)
...+||.|.+|+. +-||=
T Consensus 20 ~~~leIKCpRC~t-iN~~~ 37 (51)
T PF10122_consen 20 VIELEIKCPRCKT-INHVR 37 (51)
T ss_pred ccEEEEECCCCCc-cceEe
Confidence 4579999999975 55553
No 32
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=27.50 E-value=1.2e+02 Score=20.88 Aligned_cols=19 Identities=32% Similarity=0.649 Sum_probs=13.7
Q ss_pred EEcCCCCCccccccCCCCCC
Q psy4120 56 VTCSKCDAHLGHVFNDGPAP 75 (95)
Q Consensus 56 v~C~~Cg~HLGHVF~DGP~p 75 (95)
.+|..|++..|=. .+.-.|
T Consensus 32 y~C~~C~AyVG~H-~~t~~P 50 (102)
T PF11672_consen 32 YVCTPCDAYVGCH-PGTDIP 50 (102)
T ss_pred EECCCCCceeeee-CCCCCc
Confidence 8999999999943 343344
No 33
>PF13005 zf-IS66: zinc-finger binding domain of transposase IS66 ; InterPro: IPR024474 This entry represents a predicted helix-turn-helix domain from insertion element IS66 transposases [].
Probab=27.08 E-value=29 Score=19.50 Aligned_cols=12 Identities=25% Similarity=0.886 Sum_probs=10.2
Q ss_pred EcCCCCCccccc
Q psy4120 57 TCSKCDAHLGHV 68 (95)
Q Consensus 57 ~C~~Cg~HLGHV 68 (95)
.|..||+.|..+
T Consensus 4 ~C~~Cg~~l~~i 15 (47)
T PF13005_consen 4 ACPDCGGELKEI 15 (47)
T ss_pred cCCCCCceeeEC
Confidence 699999999854
No 34
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=26.82 E-value=43 Score=17.95 Aligned_cols=15 Identities=27% Similarity=0.561 Sum_probs=11.0
Q ss_pred ceEEEEEcCCCCCcc
Q psy4120 51 MVRTEVTCSKCDAHL 65 (95)
Q Consensus 51 m~R~Ev~C~~Cg~HL 65 (95)
|..-|.+|..||.-.
T Consensus 1 Mp~Y~y~C~~Cg~~f 15 (41)
T smart00834 1 MPIYEYRCEDCGHTF 15 (41)
T ss_pred CCCEEEEcCCCCCEE
Confidence 556788999997633
No 35
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=26.70 E-value=43 Score=18.92 Aligned_cols=13 Identities=31% Similarity=0.621 Sum_probs=9.9
Q ss_pred ceEEEEEcCCCCC
Q psy4120 51 MVRTEVTCSKCDA 63 (95)
Q Consensus 51 m~R~Ev~C~~Cg~ 63 (95)
|..-|.+|..||.
T Consensus 1 MP~Yey~C~~Cg~ 13 (42)
T PF09723_consen 1 MPIYEYRCEECGH 13 (42)
T ss_pred CCCEEEEeCCCCC
Confidence 5567899999963
No 36
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=26.36 E-value=55 Score=17.77 Aligned_cols=12 Identities=58% Similarity=1.035 Sum_probs=10.5
Q ss_pred EEEEcCCCCCcc
Q psy4120 54 TEVTCSKCDAHL 65 (95)
Q Consensus 54 ~Ev~C~~Cg~HL 65 (95)
|-+.|+.|+-+|
T Consensus 15 T~~~C~~C~v~l 26 (32)
T PF13842_consen 15 TRYMCSKCDVPL 26 (32)
T ss_pred eEEEccCCCCcc
Confidence 889999999766
No 37
>PF07813 LTXXQ: LTXXQ motif family protein; InterPro: IPR012899 This five residue motif is found in a number of bacterial proteins bearing similarity to the protein CpxP (P32158 from SWISSPROT). This is a periplasmic protein that aids in combating extracytoplasmic protein-mediated toxicity, and may also be involved in the response to alkaline pH []. Another member of this family, Spy (P77754 from SWISSPROT) is also a periplasmic protein that may be involved in the response to stress []. The homology between CpxP and Spy may indicate that these two proteins are functionally related []. The motif is found repeated twice in many members of this entry. ; GO: 0042597 periplasmic space; PDB: 3ITF_B 3QZC_B 3OEO_D 3O39_A.
Probab=26.25 E-value=55 Score=20.30 Aligned_cols=16 Identities=31% Similarity=0.210 Sum_probs=11.6
Q ss_pred HHHHhcCCHHHHHhhh
Q psy4120 15 EELKKRLTPMQYHVTQ 30 (95)
Q Consensus 15 ~ewk~~Lt~~qy~Vlr 30 (95)
.++...|||+|...+.
T Consensus 82 ~~~~~vLt~eQk~~~~ 97 (100)
T PF07813_consen 82 HALYAVLTPEQKEKFD 97 (100)
T ss_dssp HHHHTTS-HHHHHHHH
T ss_pred HHHHhcCCHHHHHHHH
Confidence 4577899999988764
No 38
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=26.08 E-value=34 Score=19.46 Aligned_cols=13 Identities=15% Similarity=0.710 Sum_probs=11.1
Q ss_pred EEcCCCCCccccc
Q psy4120 56 VTCSKCDAHLGHV 68 (95)
Q Consensus 56 v~C~~Cg~HLGHV 68 (95)
|+|+.||..|-..
T Consensus 6 l~C~~CG~~m~~~ 18 (58)
T PF13408_consen 6 LRCGHCGSKMTRR 18 (58)
T ss_pred EEcccCCcEeEEE
Confidence 7899999998774
No 39
>PF05452 Clavanin: Clavanin; InterPro: IPR008453 This family consists of clavanin proteins from the haemocytes of the invertebrate Styela clava (Sea squirt), a solitary tunicate. The family is made up of four alpha-helical antimicrobial peptides, clavanins A, B, C and D. The tunicate peptides resemble magainins in size, primary sequence and antibacterial activity. Synthetic clavanin A displays comparable antimicrobial activity to magainins and cecropins. The presence of alpha-helical antimicrobial peptides in the haemocytes of a urochordate suggests that such peptides are primeval effectors of innate immunity in the vertebrate lineage [].; GO: 0005576 extracellular region
Probab=26.04 E-value=37 Score=22.41 Aligned_cols=17 Identities=24% Similarity=0.388 Sum_probs=11.8
Q ss_pred CccccccCCCCCCCCce
Q psy4120 63 AHLGHVFNDGPAPTRRR 79 (95)
Q Consensus 63 ~HLGHVF~DGP~ptg~R 79 (95)
-|.||||.|.-+..|+=
T Consensus 46 hgfshvfgddqqdngkf 62 (80)
T PF05452_consen 46 HGFSHVFGDDQQDNGKF 62 (80)
T ss_pred hcceeeccCccccCCee
Confidence 47899998766555543
No 40
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=26.00 E-value=22 Score=22.81 Aligned_cols=17 Identities=29% Similarity=0.751 Sum_probs=14.9
Q ss_pred EEEEcCCCCCccccccC
Q psy4120 54 TEVTCSKCDAHLGHVFN 70 (95)
Q Consensus 54 ~Ev~C~~Cg~HLGHVF~ 70 (95)
+-|+|=.||.=+||.|+
T Consensus 3 iPiRCFsCGkvi~~~w~ 19 (63)
T COG1644 3 IPVRCFSCGKVIGHKWE 19 (63)
T ss_pred CceEeecCCCCHHHHHH
Confidence 34899999999999985
No 41
>PF13101 DUF3945: Protein of unknown function (DUF3945)
Probab=25.91 E-value=35 Score=20.73 Aligned_cols=24 Identities=21% Similarity=0.160 Sum_probs=16.9
Q ss_pred CCCHHHHHhcCCHHHHHhhhhCCC
Q psy4120 11 KIDKEELKKRLTPMQYHVTQEKGT 34 (95)
Q Consensus 11 ~~s~~ewk~~Lt~~qy~Vlr~~gT 34 (95)
...+.-.-..||++|.+.|+++.+
T Consensus 25 ~ip~~i~g~~Ls~~q~~~L~~G~~ 48 (59)
T PF13101_consen 25 RIPDKIKGVELSPEQKEDLREGKP 48 (59)
T ss_pred cccceecCccCCHHHHHHHHCCCe
Confidence 344333446799999999998754
No 42
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=25.84 E-value=45 Score=19.06 Aligned_cols=13 Identities=31% Similarity=0.613 Sum_probs=9.8
Q ss_pred ceEEEEEcCCCCC
Q psy4120 51 MVRTEVTCSKCDA 63 (95)
Q Consensus 51 m~R~Ev~C~~Cg~ 63 (95)
|..-|.+|..||.
T Consensus 1 MP~Yey~C~~Cg~ 13 (52)
T TIGR02605 1 MPIYEYRCTACGH 13 (52)
T ss_pred CCCEEEEeCCCCC
Confidence 5567889999963
No 43
>PF04988 AKAP95: A-kinase anchoring protein 95 (AKAP95); InterPro: IPR007071 A-kinase (or PKA)-anchoring protein AKAP95 is implicated in mitotic chromosome condensation by acting as a targeting molecule for the condensin complex. The protein contains two zinc fingers which are thought to mediate the binding of AKAP95 to DNA [].; GO: 0003677 DNA binding, 0005634 nucleus
Probab=25.72 E-value=9.7 Score=28.53 Aligned_cols=22 Identities=27% Similarity=0.483 Sum_probs=17.0
Q ss_pred CCCceEEEE-EcCCCCCcccccc
Q psy4120 48 NPDMVRTEV-TCSKCDAHLGHVF 69 (95)
Q Consensus 48 s~gm~R~Ev-~C~~Cg~HLGHVF 69 (95)
.+.|.++|+ +|+.|+..+--+|
T Consensus 83 ehfm~KVEa~hCsACd~~IP~~~ 105 (165)
T PF04988_consen 83 EHFMKKVEAAHCSACDVFIPMQH 105 (165)
T ss_pred HHHHHHHHHhhhhHhhhhccCcH
Confidence 356889998 9999998875443
No 44
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=25.68 E-value=1e+02 Score=19.72 Aligned_cols=26 Identities=12% Similarity=0.294 Sum_probs=18.1
Q ss_pred CCCCCceeEE-eCCCceEEEEEcCCCCCc
Q psy4120 37 YIGSNLLLLI-TNPDMVRTEVTCSKCDAH 64 (95)
Q Consensus 37 pfsg~~v~~~-~s~gm~R~Ev~C~~Cg~H 64 (95)
||.|..+... .+.|.-+ +.|..|++=
T Consensus 10 PFCG~~~~~v~~~~g~~~--v~C~~CgA~ 36 (64)
T PRK09710 10 PFCGCPSVTVKAISGYYR--AKCNGCESR 36 (64)
T ss_pred CCCCCceeEEEecCceEE--EEcCCCCcC
Confidence 8999965554 4444333 899999984
No 45
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=24.94 E-value=32 Score=19.33 Aligned_cols=13 Identities=38% Similarity=0.820 Sum_probs=6.4
Q ss_pred EEcCCCCCccccc
Q psy4120 56 VTCSKCDAHLGHV 68 (95)
Q Consensus 56 v~C~~Cg~HLGHV 68 (95)
++|.+|++-|---
T Consensus 3 ~rC~~C~aylNp~ 15 (40)
T PF04810_consen 3 VRCRRCRAYLNPF 15 (40)
T ss_dssp -B-TTT--BS-TT
T ss_pred cccCCCCCEECCc
Confidence 6899999988654
No 46
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=24.52 E-value=49 Score=20.07 Aligned_cols=14 Identities=21% Similarity=0.688 Sum_probs=10.7
Q ss_pred eEEEEEcCCCCCcc
Q psy4120 52 VRTEVTCSKCDAHL 65 (95)
Q Consensus 52 ~R~Ev~C~~Cg~HL 65 (95)
..++..|++||.-+
T Consensus 3 ~~~~Y~C~~Cg~~~ 16 (49)
T COG1996 3 AMMEYKCARCGREV 16 (49)
T ss_pred ceEEEEhhhcCCee
Confidence 45678888888766
No 47
>COG1507 Uncharacterized conserved protein [Function unknown]
Probab=23.07 E-value=89 Score=23.43 Aligned_cols=30 Identities=27% Similarity=0.544 Sum_probs=20.3
Q ss_pred CCceEEEEEcCCCCCccccccC-----CC-CCCCCceeee
Q psy4120 49 PDMVRTEVTCSKCDAHLGHVFN-----DG-PAPTRRRFCI 82 (95)
Q Consensus 49 ~gm~R~Ev~C~~Cg~HLGHVF~-----DG-P~ptg~RyCi 82 (95)
-||.+|+++|.. +-=|=||. || |.|| +|-+
T Consensus 19 rgvl~I~~rcp~--g~P~VV~t~p~l~dg~PfPT--ly~l 54 (167)
T COG1507 19 RGVLKIAYRCPY--GEPGVVKTAPKLDDGTPFPT--LYYL 54 (167)
T ss_pred cCceEEEEECCC--CCceEEeecCCCCCCCcCCc--eeee
Confidence 589999999986 34566664 44 5565 6654
No 48
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=21.66 E-value=44 Score=24.11 Aligned_cols=13 Identities=62% Similarity=1.482 Sum_probs=10.4
Q ss_pred EcCCCCCccccccCCCC
Q psy4120 57 TCSKCDAHLGHVFNDGP 73 (95)
Q Consensus 57 ~C~~Cg~HLGHVF~DGP 73 (95)
+|.+| |++|.||-
T Consensus 3 ~Ct~C----g~~f~dgs 15 (131)
T PF09845_consen 3 QCTKC----GRVFEDGS 15 (131)
T ss_pred ccCcC----CCCcCCCc
Confidence 58888 68999885
No 49
>PF00527 E7: E7 protein, Early protein; InterPro: IPR000148 This family includes the E7 oncoprotein from various papillomaviruses []. Along with E5 and E6 their activities seem to be especially important for viral oncogenesis. E5 is located at the cell surface and reduces cell gap-gap junction communication. In cervical cancer E5 is expressed in earlier stages of neoplastic transformation of the cervical epithelium during viral infection. The role of E7 is less well understood but it has been shown to impede growth arrest signals in both NIH 3T3 cells and HFKs and that this correlates with elevated cdc25A gene expression. This deregulation of cdc25A is linked to disruption of cell cycle arrest [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2F8B_A 2EWL_A 2B9D_A.
Probab=21.48 E-value=62 Score=21.48 Aligned_cols=18 Identities=22% Similarity=0.504 Sum_probs=12.4
Q ss_pred CceEEEEEcCCCCCcccc
Q psy4120 50 DMVRTEVTCSKCDAHLGH 67 (95)
Q Consensus 50 gm~R~Ev~C~~Cg~HLGH 67 (95)
---||...|..|+.+|--
T Consensus 47 ~~Y~V~t~C~~C~~~lrl 64 (92)
T PF00527_consen 47 QPYRVVTCCGRCGKRLRL 64 (92)
T ss_dssp CEEEEEEEBTTT--EEEE
T ss_pred CCeEEEeECCCCCCEEEE
Confidence 345899999999988743
No 50
>PF05515 Viral_NABP: Viral nucleic acid binding ; InterPro: IPR008891 This family is common to ssRNA positive-strand viruses and are commonly described as nucleic acid binding proteins (NABP).
Probab=21.32 E-value=19 Score=25.76 Aligned_cols=32 Identities=13% Similarity=0.186 Sum_probs=21.3
Q ss_pred hhCCCCCCCCCC---ceeEE-eCCCceEEEEEcCCCCCcc--cc
Q psy4120 30 QEKGTERYIGSN---LLLLI-TNPDMVRTEVTCSKCDAHL--GH 67 (95)
Q Consensus 30 r~~gTE~pfsg~---~v~~~-~s~gm~R~Ev~C~~Cg~HL--GH 67 (95)
|..-.-.||.|. ++++. ..+| +|-.||.+| +|
T Consensus 39 R~~~q~kp~~G~SksA~KRRAkR~~------~C~~CG~~l~~~~ 76 (124)
T PF05515_consen 39 RKLSQNKPFNGTSKSAAKRRAKRYN------RCFKCGRYLHNNG 76 (124)
T ss_pred HHHHhcCCcCCCcHHHHHHHHHHhC------ccccccceeecCC
Confidence 333344699988 55544 4455 899999987 55
No 51
>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=21.25 E-value=65 Score=25.09 Aligned_cols=15 Identities=33% Similarity=0.848 Sum_probs=13.2
Q ss_pred EEEEcCCCCCccccc
Q psy4120 54 TEVTCSKCDAHLGHV 68 (95)
Q Consensus 54 ~Ev~C~~Cg~HLGHV 68 (95)
..|.|++|++-||-.
T Consensus 192 ~~v~C~~C~~~LG~~ 206 (354)
T PF09814_consen 192 RIVRCKRCSSQLGEK 206 (354)
T ss_pred cEEEeCCCCceeCCC
Confidence 469999999999973
No 52
>KOG4465|consensus
Probab=20.99 E-value=50 Score=28.44 Aligned_cols=9 Identities=56% Similarity=1.398 Sum_probs=8.0
Q ss_pred CCCCceeee
Q psy4120 74 APTRRRFCI 82 (95)
Q Consensus 74 ~ptg~RyCi 82 (95)
+|||+|||.
T Consensus 424 ~ptgkr~~l 432 (598)
T KOG4465|consen 424 EPTGKRFCL 432 (598)
T ss_pred CCCCceEEE
Confidence 589999996
No 53
>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=20.61 E-value=60 Score=18.17 Aligned_cols=13 Identities=38% Similarity=0.874 Sum_probs=8.8
Q ss_pred EEEEEcCCCCCcc
Q psy4120 53 RTEVTCSKCDAHL 65 (95)
Q Consensus 53 R~Ev~C~~Cg~HL 65 (95)
+-|+.|..||.=|
T Consensus 17 ~g~~vC~~CG~Vl 29 (43)
T PF08271_consen 17 RGELVCPNCGLVL 29 (43)
T ss_dssp TTEEEETTT-BBE
T ss_pred CCeEECCCCCCEe
Confidence 4578999995443
No 54
>cd00233 VIP2 VIP2; A family of actin-ADP-ribosylating toxin. A member of the Bacillus-prodiced vegetative insecticidal proteins (VIPs) possesses high specificity against the major insect pest, corn rootworms, and belongs to a classs of binary toxins and regulators of biological pathways distinct from classical A-B toxins. A novel family of insecticidal ADP-ribosyltransferses were isolated from Bacillus cereus during vegetative growth, where VIP1 likely targets insect cells and VIP2 ribosylates actin. VIP2 shares significant sequence similarity with enzymatic components of other binary toxins, Clostridium botulinum C2 toxin, C. perfringens iota toxin, C. piroforme toxin, C. piroforme toxin and C. difficile toxin.
Probab=20.57 E-value=76 Score=23.36 Aligned_cols=17 Identities=18% Similarity=0.317 Sum_probs=13.2
Q ss_pred HHHHHhcCCHHHHHhhh
Q psy4120 14 KEELKKRLTPMQYHVTQ 30 (95)
Q Consensus 14 ~~ewk~~Lt~~qy~Vlr 30 (95)
-++|++.||++|+..++
T Consensus 20 ~~~w~~~Lt~~e~~Ai~ 36 (201)
T cd00233 20 YKKWLKKLSPSEKEAIR 36 (201)
T ss_pred HHHHHhhCCHHHHHHHH
Confidence 45699999999977554
No 55
>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=20.51 E-value=53 Score=18.34 Aligned_cols=22 Identities=14% Similarity=0.342 Sum_probs=14.5
Q ss_pred EEEcCCCCCccccccCCCCCCCCceeee
Q psy4120 55 EVTCSKCDAHLGHVFNDGPAPTRRRFCI 82 (95)
Q Consensus 55 Ev~C~~Cg~HLGHVF~DGP~ptg~RyCi 82 (95)
...|..|++-++.. + -|.+||.
T Consensus 8 ~~~C~~C~~~~~~~-~-----dG~~yC~ 29 (36)
T PF11781_consen 8 NEPCPVCGSRWFYS-D-----DGFYYCD 29 (36)
T ss_pred CCcCCCCCCeEeEc-c-----CCEEEhh
Confidence 35699999984332 2 3678884
No 56
>PF07945 Toxin_16: Janus-atracotoxin; InterPro: IPR012499 This family includes three peptides secreted by the spider Hadronyche versuta (Blue mountains funnel-web spider) (P82226 from SWISSPROT, P82227 from SWISSPROT, P82228 from SWISSPROT). These are insect-selective, excitatory neurotoxins that may function by antagonising muscle acetylcholine receptors, or acetylcholine receptor subtypes present in other invertebrate neurons []. Janus atracotoxin-Hv1c (J-ACTX-Hv1c, P82228 from SWISSPROT) is organised into a disulphide-rich globular core (residues 3-19) and a beta-hairpin (residues 20-34). There are 4 disulphide bridges, one of which is a vicinal disulphide bridge; this is known to be unimportant in the maintenance of structure but critical for insecticidal activity []. ; GO: 0009405 pathogenesis, 0005576 extracellular region; PDB: 1DL0_A.
Probab=20.50 E-value=48 Score=18.82 Aligned_cols=12 Identities=42% Similarity=1.030 Sum_probs=7.8
Q ss_pred CCCCCCceeeec
Q psy4120 72 GPAPTRRRFCIN 83 (95)
Q Consensus 72 GP~ptg~RyCiN 83 (95)
||.|.|.-||-|
T Consensus 24 ~pe~ngvsycr~ 35 (36)
T PF07945_consen 24 GPEPNGVSYCRN 35 (36)
T ss_dssp E--TTS-EEEEE
T ss_pred ccCCCCceeecC
Confidence 688999999976
No 57
>COG2126 RPL37A Ribosomal protein L37E [Translation, ribosomal structure and biogenesis]
Probab=20.27 E-value=40 Score=21.48 Aligned_cols=23 Identities=22% Similarity=0.423 Sum_probs=18.0
Q ss_pred CCCc--eEEEEEcCCCCCccccccC
Q psy4120 48 NPDM--VRTEVTCSKCDAHLGHVFN 70 (95)
Q Consensus 48 s~gm--~R~Ev~C~~Cg~HLGHVF~ 70 (95)
|+|+ .++-++|.+||.|-=||=.
T Consensus 7 S~GKrnk~tH~~CRRCGr~syhv~k 31 (61)
T COG2126 7 SFGKRNKKTHIRCRRCGRRSYHVRK 31 (61)
T ss_pred cccccCCcceehhhhccchheeecc
Confidence 4454 3789999999999888854
Done!