Query 023888
Match_columns 275
No_of_seqs 139 out of 352
Neff 4.2
Searched_HMMs 46136
Date Fri Mar 29 07:23:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023888.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023888hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3092 Casein kinase II, beta 100.0 2.3E-86 5E-91 585.6 12.0 180 96-275 3-195 (216)
2 PTZ00396 Casein kinase II subu 100.0 6.1E-81 1.3E-85 569.8 15.3 179 97-275 18-209 (251)
3 PF01214 CK_II_beta: Casein ki 100.0 2.6E-78 5.7E-83 530.9 7.3 171 101-271 1-184 (184)
4 COG5041 SKB2 Casein kinase II, 100.0 1.4E-75 2.9E-80 521.2 8.1 172 101-274 25-209 (242)
5 PRK05978 hypothetical protein; 72.4 2.9 6.2E-05 36.5 2.3 39 180-227 27-65 (148)
6 PF01927 Mut7-C: Mut7-C RNAse 65.1 4.1 8.8E-05 34.6 1.8 43 181-226 86-136 (147)
7 PF15235 GRIN_C: G protein-reg 51.5 7.8 0.00017 33.6 1.2 23 12-34 56-78 (137)
8 PF06044 DRP: Dam-replacing fa 50.0 3.3 7.2E-05 39.1 -1.4 58 187-251 32-101 (254)
9 COG1656 Uncharacterized conser 48.5 9.9 0.00021 33.9 1.4 44 181-227 92-143 (165)
10 PF14205 Cys_rich_KTR: Cystein 47.5 8.1 0.00018 28.8 0.6 10 213-222 27-36 (55)
11 PRK00420 hypothetical protein; 47.1 16 0.00035 30.5 2.4 30 187-227 24-53 (112)
12 KOG4684 Uncharacterized conser 46.0 18 0.0004 34.0 2.8 37 188-224 140-180 (275)
13 PF06827 zf-FPG_IleRS: Zinc fi 42.3 11 0.00024 23.7 0.6 10 214-223 21-30 (30)
14 PF08772 NOB1_Zn_bind: Nin one 41.4 10 0.00022 29.5 0.3 13 211-223 21-33 (73)
15 COG2888 Predicted Zn-ribbon RN 37.0 22 0.00047 27.1 1.5 17 208-224 21-37 (61)
16 PRK00432 30S ribosomal protein 35.8 17 0.00037 26.1 0.7 8 214-221 37-44 (50)
17 PF05191 ADK_lid: Adenylate ki 34.9 18 0.00038 24.4 0.7 12 215-226 2-13 (36)
18 PF06677 Auto_anti-p27: Sjogre 34.3 30 0.00064 24.1 1.7 23 188-221 19-41 (41)
19 PF03811 Zn_Tnp_IS1: InsA N-te 33.6 24 0.00052 23.8 1.1 13 211-223 2-14 (36)
20 PF13717 zinc_ribbon_4: zinc-r 33.0 25 0.00054 23.4 1.2 15 213-227 1-15 (36)
21 PF11238 DUF3039: Protein of u 32.4 11 0.00023 28.4 -0.8 10 216-225 46-55 (58)
22 PF13719 zinc_ribbon_5: zinc-r 30.4 24 0.00053 23.5 0.8 29 194-225 8-36 (37)
23 PF09788 Tmemb_55A: Transmembr 28.8 48 0.0011 31.5 2.7 38 188-225 125-168 (256)
24 PF10601 zf-LITAF-like: LITAF- 28.8 35 0.00077 25.4 1.5 18 209-226 2-19 (73)
25 KOG1973 Chromatin remodeling p 28.7 30 0.00064 32.5 1.3 46 172-222 220-267 (274)
26 COG1631 RPL42A Ribosomal prote 27.3 27 0.00059 28.6 0.7 11 212-222 6-16 (94)
27 COG1579 Zn-ribbon protein, pos 27.1 17 0.00038 34.0 -0.5 35 191-225 197-232 (239)
28 COG4416 Com Mu-like prophage p 27.0 30 0.00065 26.0 0.8 16 209-224 19-34 (60)
29 TIGR02098 MJ0042_CXXC MJ0042 f 25.6 40 0.00086 22.0 1.2 15 213-227 1-15 (38)
30 PF03966 Trm112p: Trm112p-like 25.5 32 0.0007 25.5 0.8 12 213-224 52-63 (68)
31 PF02150 RNA_POL_M_15KD: RNA p 25.2 21 0.00045 23.8 -0.3 15 215-229 2-16 (35)
32 COG1096 Predicted RNA-binding 25.0 36 0.00079 31.0 1.1 26 186-223 149-174 (188)
33 smart00647 IBR In Between Ring 24.3 83 0.0018 21.8 2.7 16 184-199 16-31 (64)
34 smart00661 RPOL9 RNA polymeras 24.1 37 0.0008 23.2 0.8 12 216-227 2-13 (52)
35 COG4098 comFA Superfamily II D 23.6 32 0.0007 34.6 0.6 14 199-222 55-68 (441)
36 COG5034 TNG2 Chromatin remodel 23.2 49 0.0011 31.7 1.7 46 170-223 220-270 (271)
37 COG2816 NPY1 NTP pyrophosphohy 22.9 60 0.0013 31.2 2.2 36 203-238 118-156 (279)
38 PRK14890 putative Zn-ribbon RN 21.2 62 0.0014 24.4 1.6 16 208-223 19-34 (59)
39 COG3809 Uncharacterized protei 21.1 40 0.00087 27.1 0.6 12 215-226 22-33 (88)
40 PF00471 Ribosomal_L33: Riboso 20.6 67 0.0014 23.0 1.5 16 207-222 25-40 (48)
41 PF01485 IBR: IBR domain; Int 20.2 1.4E+02 0.003 20.6 3.1 42 185-226 17-60 (64)
No 1
>KOG3092 consensus Casein kinase II, beta subunit [Signal transduction mechanisms; Cell cycle control, cell division, chromosome partitioning; Transcription]
Probab=100.00 E-value=2.3e-86 Score=585.62 Aligned_cols=180 Identities=71% Similarity=1.305 Sum_probs=172.6
Q ss_pred CCCCCChHHHHhCCCCCeeEEecCcccccCCCccCCCCCCCCCHHHHHHHHcCCCCCCCCCCchhhHHHHHHHHHHHHcc
Q 023888 96 DGDDTSWISWFCNLRGNEFFCEVDDEYIQDDFNLCGLSSQVPYYDYALDLILDVESSHGDMFTEEQNELVESAAEMLYGL 175 (275)
Q Consensus 96 ~~e~~sWI~wFcsl~gneff~eVDedYI~D~FNL~GL~~~Vp~y~~AL~lILd~~~~~~~~~~~~~~~~ie~~A~~LYGL 175 (275)
++++.+||+|||+++|||||||||+|||+|+|||+||+.+||+|++||++|||+++.++.+..+++.++||++|++||||
T Consensus 3 ~see~sWI~wFc~~~GnEffceVdeeyIqD~FNltgL~~~Vp~y~~ald~ILD~~~~~~~e~~~~~~~~iE~aae~LYGL 82 (216)
T KOG3092|consen 3 SSEEVSWISWFCGLRGNEFFCEVDEEYIQDRFNLTGLSEQVPNYRQALDLILDLEPDDELEDNAEQSELIESAAEMLYGL 82 (216)
T ss_pred cccccchHHHHhcCCCCeeeEecCHHHhhhhhccccccccCchHHHHHHHhhcCCCCcccccchhHHHHHHHHHHHHHHh
Confidence 34566799999999999999999999999999999999999999999999999998877777777789999999999999
Q ss_pred cc-------------cccccccccCCCCcccCCCCCccccccCCCCCcccceEeCCCCCccccCCCCCCccccccccCCc
Q 023888 176 IH-------------LEKYKNYDFGRCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPKCEDIYYPRSKYQGNIDGAYFGTT 242 (275)
Q Consensus 176 IH-------------~eKY~~g~FG~CPRv~C~gq~lLPiGlSD~pg~stVKlYCP~C~DVY~P~s~~~~~IDGAyFGts 242 (275)
|| ++||++++||+||||+|++|+|||||+||+||+++||||||+|+|||.|+++++++|||||||||
T Consensus 83 IHaRYIlT~~Gl~~M~eKy~~~dFG~CPRV~C~~q~~LPvGLsDipg~~~VklYCP~C~dvY~P~ssr~~~iDGa~fGts 162 (216)
T KOG3092|consen 83 IHARYILTNRGLAAMLEKYKNGDFGRCPRVYCCGQPVLPVGLSDIPGKSTVKLYCPSCEDVYIPKSSRHGNIDGAYFGTS 162 (216)
T ss_pred hhheeeechHHHHHHHHHHhcCCCCcCCcccccCCccccccccCCCCcceEEEeCCCcccccccccccccccccchhcCC
Confidence 99 79999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhHHHHHHhCCCCCCCCCCCcceeeeeeeecCC
Q 023888 243 FPHLFLMTYGHLKPQKATQSYVPRVFGFKLHKP 275 (275)
Q Consensus 243 FpHlFl~~yP~l~P~~~~~~YvPrIFGFKIh~~ 275 (275)
|||||||+||++.|+++.++|||||||||||+.
T Consensus 163 FPhmff~~~p~l~P~r~~~~yvPriyGFkih~~ 195 (216)
T KOG3092|consen 163 FPHMFFMTHPELRPKRPTEQYVPRIYGFKIHKP 195 (216)
T ss_pred CchhHHHhccccCCCcchhhhcchheeeeeCch
Confidence 999999999999999999999999999999973
No 2
>PTZ00396 Casein kinase II subunit beta; Provisional
Probab=100.00 E-value=6.1e-81 Score=569.81 Aligned_cols=179 Identities=53% Similarity=1.064 Sum_probs=169.3
Q ss_pred CCCCChHHHHhCCCCCeeEEecCcccccCCCccCCCCCCCCCHHHHHHHHcCCCCCCCCCCchhhHHHHHHHHHHHHccc
Q 023888 97 GDDTSWISWFCNLRGNEFFCEVDDEYIQDDFNLCGLSSQVPYYDYALDLILDVESSHGDMFTEEQNELVESAAEMLYGLI 176 (275)
Q Consensus 97 ~e~~sWI~wFcsl~gneff~eVDedYI~D~FNL~GL~~~Vp~y~~AL~lILd~~~~~~~~~~~~~~~~ie~~A~~LYGLI 176 (275)
.++.+||+|||+++||+|||+||+|||+|+||||||+.+|++|++||+||||.+...++..+++..+.++++|++|||||
T Consensus 18 ~~~~sWI~wF~~~~gne~f~~Vd~dyI~D~FNl~GL~~~v~~y~~al~~Ild~~~~~~~~~~~~~~~~i~~~a~~LYGLI 97 (251)
T PTZ00396 18 EESMGWIEWFCSLKGHEFLCEVDEDFIRDEFNLYGLKSKFPFYNEALDMILDSEPPDDEDLEDEQFLEVYQEASDLYGLI 97 (251)
T ss_pred CCcCcHHHHHhCCCCCeeEEEeCHHHhcCcchhhCccccccCHHHHHHHHcCCCCCccccccchhHHHHHHHHHHHHHHH
Confidence 45679999999999999999999999999999999999999999999999999876654455567788999999999999
Q ss_pred c-------------cccccccccCCCCcccCCCCCccccccCCCCCcccceEeCCCCCccccCCCCCCccccccccCCch
Q 023888 177 H-------------LEKYKNYDFGRCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPKCEDIYYPRSKYQGNIDGAYFGTTF 243 (275)
Q Consensus 177 H-------------~eKY~~g~FG~CPRv~C~gq~lLPiGlSD~pg~stVKlYCP~C~DVY~P~s~~~~~IDGAyFGtsF 243 (275)
| ++||++|+||+||||+|++|+|||||+||+||+++||||||+|+|||+|++.++..||||||||||
T Consensus 98 HARyI~T~~Gl~~M~eKY~~g~FG~CPRv~C~~q~~LPvGlSd~~g~~~VKlyCP~C~DvY~p~s~~~~~iDGA~FGtsF 177 (251)
T PTZ00396 98 HARFITTPKGLALMREKYLQGKFGHCPRVLCEGQNVLPIGLSDVLKTSRVKVYCPRCQEVYHPKKSSLLDIDGAFFGTSF 177 (251)
T ss_pred hHhHhcCHHHHHHHHHHhhCCCCCCCCCccCCCCcccccccCCCcCcCceeEeCCCchhhcCCCCccccccccceecCcH
Confidence 9 799999999999999999999999999999999999999999999999999887799999999999
Q ss_pred hHHHHHHhCCCCCCCCCCCcceeeeeeeecCC
Q 023888 244 PHLFLMTYGHLKPQKATQSYVPRVFGFKLHKP 275 (275)
Q Consensus 244 pHlFl~~yP~l~P~~~~~~YvPrIFGFKIh~~ 275 (275)
||||||+||++.|+++.++|+|||||||||.+
T Consensus 178 ph~fl~~~p~l~p~~~~~~yvPrifGFki~~~ 209 (251)
T PTZ00396 178 PHLFLMTYPELIPTKPPQYYVPKIFGFKVHKK 209 (251)
T ss_pred HHHHHHhccccCCCCCCCccCCeeeeEEeccc
Confidence 99999999999999999999999999999963
No 3
>PF01214 CK_II_beta: Casein kinase II regulatory subunit; InterPro: IPR000704 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. Casein kinase, a ubiquitous, well-conserved protein kinase involved in cell metabolism and differentiation, is characterised by its preference for Ser or Thr in acidic stretches of amino acids. The enzyme is a tetramer of 2 alpha- and 2 beta-subunits [, ]. However, some species (e.g., mammals) possess 2 related forms of the alpha-subunit (alpha and alpha'), while others (e.g., fungi) possess 2 related beta-subunits (beta and beta') []. The alpha-subunit is the catalytic unit and contains regions characteristic of serine/threonine protein kinases. The beta-subunit is believed to be regulatory, possessing an N-terminal auto-phosphorylation site, an internal acidic domain, and a potential metal-binding motif []. The beta subunit is a highly conserved protein of about 25kDa that contains, in its central section, a cysteine-rich motif, CX(n)C, that could be involved in binding a metal such as zinc []. The mammalian beta-subunit gene promoter shares common features with those of other mammalian protein kinases and is closely related to the promoter of the regulatory subunit of cAMP-dependent protein kinase [].; GO: 0019887 protein kinase regulator activity, 0005956 protein kinase CK2 complex; PDB: 2R6M_B 1RQF_K 1DS5_G 1QF8_B 3EED_A 4DGL_A 1JWH_D.
Probab=100.00 E-value=2.6e-78 Score=530.94 Aligned_cols=171 Identities=64% Similarity=1.236 Sum_probs=140.5
Q ss_pred ChHHHHhCCCCCeeEEecCcccccCCCccCCCCCCCCCHHHHHHHHcCCCCCCCCCCchhhHHHHHHHHHHHHcccc---
Q 023888 101 SWISWFCNLRGNEFFCEVDDEYIQDDFNLCGLSSQVPYYDYALDLILDVESSHGDMFTEEQNELVESAAEMLYGLIH--- 177 (275)
Q Consensus 101 sWI~wFcsl~gneff~eVDedYI~D~FNL~GL~~~Vp~y~~AL~lILd~~~~~~~~~~~~~~~~ie~~A~~LYGLIH--- 177 (275)
+||+|||+++||+||||||+|||+|+|||+||+++||+|++||++|||.+..+++..+++..+.++++|++||||||
T Consensus 1 sWI~~F~~~~~~~~f~~Vd~dyI~D~FNl~GL~~~v~~y~~al~~Ild~~~~~~~~~~~~~~~~i~~~a~~LYGLIHaRy 80 (184)
T PF01214_consen 1 SWIDWFCSLKGNEFFCEVDEDYIEDSFNLYGLSSQVPNYDEALDMILDKEPDEDEESDDESDDEIEKSAEMLYGLIHARY 80 (184)
T ss_dssp -HHHHHHHSTTTTT-----HHHHHSGGGGTTGGGTSTTHHHHHHHHTT----TTTTTTTCCHHHHHHHHHHHHHHHHHHH
T ss_pred CHHHHHhCCCCCeEEEEeCHHHHhCcchhcChhhccccHHHHHHHHcCCCcccchhccchhHHHHHHHHHHHHhhhHHHH
Confidence 69999999999999999999999999999999999999999999999998766555666678899999999999999
Q ss_pred ----------cccccccccCCCCcccCCCCCccccccCCCCCcccceEeCCCCCccccCCCCCCccccccccCCchhHHH
Q 023888 178 ----------LEKYKNYDFGRCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPKCEDIYYPRSKYQGNIDGAYFGTTFPHLF 247 (275)
Q Consensus 178 ----------~eKY~~g~FG~CPRv~C~gq~lLPiGlSD~pg~stVKlYCP~C~DVY~P~s~~~~~IDGAyFGtsFpHlF 247 (275)
++||++|+||+||||+|++|+|||||+||+||+++||||||+|+|||+|+++++.+||||||||||||||
T Consensus 81 I~T~~Gl~~m~eKy~~g~FG~CPRv~C~~~~lLPiGlsd~~g~~~vKlyCP~C~dvY~p~~~~~~~iDGA~FG~sFph~f 160 (184)
T PF01214_consen 81 ILTPRGLEQMKEKYEQGDFGRCPRVYCNGQPLLPIGLSDTPGESTVKLYCPRCKDVYHPPSSRHSNIDGAYFGPSFPHLF 160 (184)
T ss_dssp TTSHHHHHHHHHHHHTTTT-B-SBGGGTT-B-EEEBS-SSTTS-BBEEEETTTTEEE--SSGGGTTSBGGGTTSSHHHHH
T ss_pred hhcHHHHHHHHHhhcCCcCCcCCcccCCCCceeCccCCCCCCccceeEECCCCccccCCCCccccceeccccCCccHHHH
Confidence 7899999999999999999999999999999999999999999999999888999999999999999999
Q ss_pred HHHhCCCCCCCCCCCcceeeeeee
Q 023888 248 LMTYGHLKPQKATQSYVPRVFGFK 271 (275)
Q Consensus 248 l~~yP~l~P~~~~~~YvPrIFGFK 271 (275)
+|+||++.|+.+.++|+|||||||
T Consensus 161 ~~~~p~~~~~~~~~~y~PrifGFk 184 (184)
T PF01214_consen 161 LMTYPELIPSPPPKPYVPRIFGFK 184 (184)
T ss_dssp HHH-GGGS-SS-SS----ECTTCE
T ss_pred HHHCccccCCCCCCccCCcccccC
Confidence 999999999999999999999998
No 4
>COG5041 SKB2 Casein kinase II, beta subunit [Signal transduction mechanisms / Cell division and chromosome partitioning / Transcription]
Probab=100.00 E-value=1.4e-75 Score=521.21 Aligned_cols=172 Identities=55% Similarity=1.157 Sum_probs=163.5
Q ss_pred ChHHHHhCCCCCeeEEecCcccccCCCccCCCCCCCCCHHHHHHHHcCCCCCCCCCCchhhHHHHHHHHHHHHcccc---
Q 023888 101 SWISWFCNLRGNEFFCEVDDEYIQDDFNLCGLSSQVPYYDYALDLILDVESSHGDMFTEEQNELVESAAEMLYGLIH--- 177 (275)
Q Consensus 101 sWI~wFcsl~gneff~eVDedYI~D~FNL~GL~~~Vp~y~~AL~lILd~~~~~~~~~~~~~~~~ie~~A~~LYGLIH--- 177 (275)
.||+|||+++||||||+||++||+|.|||+||+..||+|.+||++|||...+. .+.+.+-+.||.+|+.||||||
T Consensus 25 ~Wi~~F~~rkg~eyfc~V~~efIeDrFNltgL~~~Vp~y~~~ldlILD~~~~~--~~e~~~~d~iE~sa~~LYgLIHaRy 102 (242)
T COG5041 25 EWIDWFCSRKGNEYFCEVPEEFIEDRFNLTGLSREVPHYSEVLDLILDKLAPS--NLENDEVDIIEESARQLYGLIHARY 102 (242)
T ss_pred HHHHHHHcCCCCeeeeeCCHHHHHhhhhccchhhccchHHHHHHHHHhccCCc--chhhhhhHHHHHHHHHHHHHHHhhh
Confidence 79999999999999999999999999999999999999999999999987543 2333345789999999999999
Q ss_pred ----------cccccccccCCCCcccCCCCCccccccCCCCCcccceEeCCCCCccccCCCCCCccccccccCCchhHHH
Q 023888 178 ----------LEKYKNYDFGRCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPKCEDIYYPRSKYQGNIDGAYFGTTFPHLF 247 (275)
Q Consensus 178 ----------~eKY~~g~FG~CPRv~C~gq~lLPiGlSD~pg~stVKlYCP~C~DVY~P~s~~~~~IDGAyFGtsFpHlF 247 (275)
++||+.++||+||||+||+|+|||+||||+||+++||||||+|.|||.|+|++++.||||||||||||||
T Consensus 103 IiT~~GL~~m~eKy~~~efG~CPRv~Cn~~~vLPvGLsDi~g~~~vkLyCpsC~dlY~p~Ssr~~~iDGa~fGtSFPh~f 182 (242)
T COG5041 103 IITKSGLQAMLEKYKSREFGACPRVYCNGQQVLPVGLSDIPGKSSVKLYCPSCEDLYLPKSSRHQSIDGAFFGTSFPHMF 182 (242)
T ss_pred eeeHHHHHHHHHHHhhcccCCCCcccccCcceeccccccCCCCceeEEecCchhhhcCcccccccccccchhccCCchHH
Confidence 7999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhCCCCCCCCCCCcceeeeeeeecC
Q 023888 248 LMTYGHLKPQKATQSYVPRVFGFKLHK 274 (275)
Q Consensus 248 l~~yP~l~P~~~~~~YvPrIFGFKIh~ 274 (275)
|++||++.|+++.+.|+|||||||||+
T Consensus 183 ~~~~pel~p~~~~e~YiprIfGfri~~ 209 (242)
T COG5041 183 LQTFPELFPKRSCERYIPRIFGFRIHS 209 (242)
T ss_pred HHhchhhcCCcchhhhcceeeeeEeeh
Confidence 999999999999999999999999986
No 5
>PRK05978 hypothetical protein; Provisional
Probab=72.42 E-value=2.9 Score=36.52 Aligned_cols=39 Identities=18% Similarity=0.256 Sum_probs=30.9
Q ss_pred cccccccCCCCcccCCCCCccccccCCCCCcccceEeCCCCCccccCC
Q 023888 180 KYKNYDFGRCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPKCEDIYYPR 227 (275)
Q Consensus 180 KY~~g~FG~CPRv~C~gq~lLPiGlSD~pg~stVKlYCP~C~DVY~P~ 227 (275)
-..+|-.|+||| |..-+++= +--+|.-.||.|..-|.+.
T Consensus 27 ~~~rGl~grCP~--CG~G~LF~-------g~Lkv~~~C~~CG~~~~~~ 65 (148)
T PRK05978 27 AMWRGFRGRCPA--CGEGKLFR-------AFLKPVDHCAACGEDFTHH 65 (148)
T ss_pred HHHHHHcCcCCC--CCCCcccc-------cccccCCCccccCCccccC
Confidence 467889999998 77776662 5567888999999999754
No 6
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=65.13 E-value=4.1 Score=34.56 Aligned_cols=43 Identities=33% Similarity=0.772 Sum_probs=29.1
Q ss_pred ccccccCCCCcccCCCCCccccccCCCC--------CcccceEeCCCCCccccC
Q 023888 181 YKNYDFGRCPRVYCCGQPCLPVGQSDIP--------RSSTVKIYCPKCEDIYYP 226 (275)
Q Consensus 181 Y~~g~FG~CPRv~C~gq~lLPiGlSD~p--------g~stVKlYCP~C~DVY~P 226 (275)
..+..|-+||. ||+ ++.|+...++. .....=..||.|+.||=+
T Consensus 86 ~~~~~~sRC~~--CN~-~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiyW~ 136 (147)
T PF01927_consen 86 RLDPIFSRCPK--CNG-PLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIYWE 136 (147)
T ss_pred ccCCCCCccCC--CCc-EeeechhhccccccCccccccCCeEEECCCCCCEecc
Confidence 44566999986 655 78888665442 222335679999999954
No 7
>PF15235 GRIN_C: G protein-regulated inducer of neurite outgrowth C-terminus
Probab=51.52 E-value=7.8 Score=33.64 Aligned_cols=23 Identities=30% Similarity=0.498 Sum_probs=21.2
Q ss_pred cccccCccchhhhhHHHHhhhhc
Q 023888 12 SEIVAGPLDRKRINDALDKHLEK 34 (275)
Q Consensus 12 ~~~~~~~~~~~~~~~~~~~~~~~ 34 (275)
=||+|++||-.-+..|+.||||+
T Consensus 56 WEVYGAs~DpEvLG~AIQkHLE~ 78 (137)
T PF15235_consen 56 WEVYGASVDPEVLGMAIQKHLER 78 (137)
T ss_pred EEEeccccCHHHHHHHHHHHHHH
Confidence 36899999999999999999997
No 8
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=49.95 E-value=3.3 Score=39.12 Aligned_cols=58 Identities=34% Similarity=0.736 Sum_probs=26.7
Q ss_pred CCCCcccCCCCCccccccCCCCCcccc-eEeCCCCCccccCCCCC----CccccccccC-------CchhHHHHHHh
Q 023888 187 GRCPRVYCCGQPCLPVGQSDIPRSSTV-KIYCPKCEDIYYPRSKY----QGNIDGAYFG-------TTFPHLFLMTY 251 (275)
Q Consensus 187 G~CPRv~C~gq~lLPiGlSD~pg~stV-KlYCP~C~DVY~P~s~~----~~~IDGAyFG-------tsFpHlFl~~y 251 (275)
+.||+ |..-++-=+ +....| -.|||+|.+-|.-+|.. ..-.||||-- .+=|.+|||+|
T Consensus 32 ~yCP~--Cg~~~L~~f-----~NN~PVaDF~C~~C~eeyELKSk~~~l~~~I~dGAY~Tmi~Ri~s~~NPnfffl~Y 101 (254)
T PF06044_consen 32 MYCPN--CGSKPLSKF-----ENNRPVADFYCPNCNEEYELKSKKKKLSNKINDGAYHTMIERITSDNNPNFFFLTY 101 (254)
T ss_dssp ---TT--T--SS-EE-------------EEE-TTT--EEEEEEEESS--SEEEEEEHHHHHHHHHTT---EEEEEEE
T ss_pred CcCCC--CCChhHhhc-----cCCCccceeECCCCchHHhhhhhccccCCcccCccHHHHHHHhhccCCCCEEEEEe
Confidence 45876 433333322 344455 47899999999887643 2247999963 24577788888
No 9
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=48.50 E-value=9.9 Score=33.92 Aligned_cols=44 Identities=32% Similarity=0.659 Sum_probs=29.6
Q ss_pred ccccccCCCCcccCCCCCccccccCC--------CCCcccceEeCCCCCccccCC
Q 023888 181 YKNYDFGRCPRVYCCGQPCLPVGQSD--------IPRSSTVKIYCPKCEDIYYPR 227 (275)
Q Consensus 181 Y~~g~FG~CPRv~C~gq~lLPiGlSD--------~pg~stVKlYCP~C~DVY~P~ 227 (275)
...-+|-+||. ||+ +|+++--.. +.+....-..||+|..||=+-
T Consensus 92 ~~~~e~~RCp~--CN~-~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~CgkiYW~G 143 (165)
T COG1656 92 RLFPEFSRCPE--CNG-ELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKIYWKG 143 (165)
T ss_pred hcccccccCcc--cCC-EeccCcHHHHhhccchhhhhcccceeECCCCcccccCc
Confidence 45566899995 654 577776655 223444445599999999653
No 10
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=47.48 E-value=8.1 Score=28.79 Aligned_cols=10 Identities=50% Similarity=1.530 Sum_probs=8.2
Q ss_pred ceEeCCCCCc
Q 023888 213 VKIYCPKCED 222 (275)
Q Consensus 213 VKlYCP~C~D 222 (275)
.-||||+|+.
T Consensus 27 fPlyCpKCK~ 36 (55)
T PF14205_consen 27 FPLYCPKCKQ 36 (55)
T ss_pred ccccCCCCCc
Confidence 3699999985
No 11
>PRK00420 hypothetical protein; Validated
Probab=47.07 E-value=16 Score=30.53 Aligned_cols=30 Identities=27% Similarity=0.728 Sum_probs=20.8
Q ss_pred CCCCcccCCCCCccccccCCCCCcccceEeCCCCCccccCC
Q 023888 187 GRCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPKCEDIYYPR 227 (275)
Q Consensus 187 G~CPRv~C~gq~lLPiGlSD~pg~stVKlYCP~C~DVY~P~ 227 (275)
..||. | |.|++= ...-+.|||.|+.++.-.
T Consensus 24 ~~CP~--C-g~pLf~--------lk~g~~~Cp~Cg~~~~v~ 53 (112)
T PRK00420 24 KHCPV--C-GLPLFE--------LKDGEVVCPVHGKVYIVK 53 (112)
T ss_pred CCCCC--C-CCccee--------cCCCceECCCCCCeeeec
Confidence 78998 5 455542 133469999999998654
No 12
>KOG4684 consensus Uncharacterized conserved protein, contains C4-type Zn-finger [General function prediction only]
Probab=45.97 E-value=18 Score=34.00 Aligned_cols=37 Identities=19% Similarity=0.557 Sum_probs=24.8
Q ss_pred CCCcccCCCC----CccccccCCCCCcccceEeCCCCCccc
Q 023888 188 RCPRVYCCGQ----PCLPVGQSDIPRSSTVKIYCPKCEDIY 224 (275)
Q Consensus 188 ~CPRv~C~gq----~lLPiGlSD~pg~stVKlYCP~C~DVY 224 (275)
.|||-+|++- ++.|--.+..+.-..+++-|-.|+++|
T Consensus 140 ACPRpnCkRiInL~p~~~~p~~P~~~P~gcRV~CgHC~~tF 180 (275)
T KOG4684|consen 140 ACPRPNCKRIINLDPLIEKPRDPGTAPTGCRVKCGHCNETF 180 (275)
T ss_pred ccCCCCcceeeecCCCCCCCCCCCCCCcceEEEecCcccee
Confidence 4999999853 333333333333445899999999988
No 13
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 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 domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=42.34 E-value=11 Score=23.70 Aligned_cols=10 Identities=30% Similarity=1.265 Sum_probs=7.0
Q ss_pred eEeCCCCCcc
Q 023888 214 KIYCPKCEDI 223 (275)
Q Consensus 214 KlYCP~C~DV 223 (275)
--|||+|.+|
T Consensus 21 ~~~C~rCq~v 30 (30)
T PF06827_consen 21 TYLCPRCQKV 30 (30)
T ss_dssp EEE-TTTCCH
T ss_pred CeECcCCcCC
Confidence 3689999875
No 14
>PF08772 NOB1_Zn_bind: Nin one binding (NOB1) Zn-ribbon like; InterPro: IPR014881 This entry corresponds to a zinc ribbon and is found on the RNA binding protein NOB1. ; PDB: 2CON_A.
Probab=41.40 E-value=10 Score=29.52 Aligned_cols=13 Identities=38% Similarity=1.042 Sum_probs=5.8
Q ss_pred ccceEeCCCCCcc
Q 023888 211 STVKIYCPKCEDI 223 (275)
Q Consensus 211 stVKlYCP~C~DV 223 (275)
.+-|+|||+|.--
T Consensus 21 ~~~k~FCp~CGn~ 33 (73)
T PF08772_consen 21 DMTKQFCPKCGNA 33 (73)
T ss_dssp -SS--S-SSS--S
T ss_pred CCCceeCcccCCC
Confidence 5679999999854
No 15
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=36.99 E-value=22 Score=27.06 Aligned_cols=17 Identities=35% Similarity=0.923 Sum_probs=14.6
Q ss_pred CCcccceEeCCCCCccc
Q 023888 208 PRSSTVKIYCPKCEDIY 224 (275)
Q Consensus 208 pg~stVKlYCP~C~DVY 224 (275)
|++..|+..||+|.++-
T Consensus 21 p~e~~v~F~CPnCGe~~ 37 (61)
T COG2888 21 PGETAVKFPCPNCGEVE 37 (61)
T ss_pred cCCceeEeeCCCCCcee
Confidence 78899999999999543
No 16
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=35.77 E-value=17 Score=26.11 Aligned_cols=8 Identities=38% Similarity=0.937 Sum_probs=3.7
Q ss_pred eEeCCCCC
Q 023888 214 KIYCPKCE 221 (275)
Q Consensus 214 KlYCP~C~ 221 (275)
.+.|++|.
T Consensus 37 r~~C~~Cg 44 (50)
T PRK00432 37 RWHCGKCG 44 (50)
T ss_pred cEECCCcC
Confidence 34455444
No 17
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=34.87 E-value=18 Score=24.38 Aligned_cols=12 Identities=50% Similarity=1.015 Sum_probs=10.6
Q ss_pred EeCCCCCccccC
Q 023888 215 IYCPKCEDIYYP 226 (275)
Q Consensus 215 lYCP~C~DVY~P 226 (275)
..||.|..||+.
T Consensus 2 r~C~~Cg~~Yh~ 13 (36)
T PF05191_consen 2 RICPKCGRIYHI 13 (36)
T ss_dssp EEETTTTEEEET
T ss_pred cCcCCCCCcccc
Confidence 579999999985
No 18
>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=34.32 E-value=30 Score=24.07 Aligned_cols=23 Identities=48% Similarity=1.239 Sum_probs=15.3
Q ss_pred CCCcccCCCCCccccccCCCCCcccceEeCCCCC
Q 023888 188 RCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPKCE 221 (275)
Q Consensus 188 ~CPRv~C~gq~lLPiGlSD~pg~stVKlYCP~C~ 221 (275)
.||. | +.|++. + +. =++|||.|.
T Consensus 19 ~Cp~--C-~~PL~~----~--k~--g~~~Cv~C~ 41 (41)
T PF06677_consen 19 HCPD--C-GTPLMR----D--KD--GKIYCVSCG 41 (41)
T ss_pred ccCC--C-CCeeEE----e--cC--CCEECCCCC
Confidence 5884 7 777775 1 12 258999995
No 19
>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=33.56 E-value=24 Score=23.85 Aligned_cols=13 Identities=23% Similarity=1.040 Sum_probs=10.8
Q ss_pred ccceEeCCCCCcc
Q 023888 211 STVKIYCPKCEDI 223 (275)
Q Consensus 211 stVKlYCP~C~DV 223 (275)
.+|.+.||+|+..
T Consensus 2 a~i~v~CP~C~s~ 14 (36)
T PF03811_consen 2 AKIDVHCPRCQST 14 (36)
T ss_pred CcEeeeCCCCCCC
Confidence 4788999999864
No 20
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=33.01 E-value=25 Score=23.43 Aligned_cols=15 Identities=33% Similarity=0.766 Sum_probs=12.3
Q ss_pred ceEeCCCCCccccCC
Q 023888 213 VKIYCPKCEDIYYPR 227 (275)
Q Consensus 213 VKlYCP~C~DVY~P~ 227 (275)
+++-||+|+-.|.-+
T Consensus 1 M~i~Cp~C~~~y~i~ 15 (36)
T PF13717_consen 1 MIITCPNCQAKYEID 15 (36)
T ss_pred CEEECCCCCCEEeCC
Confidence 578899999999644
No 21
>PF11238 DUF3039: Protein of unknown function (DUF3039); InterPro: IPR021400 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=32.38 E-value=11 Score=28.45 Aligned_cols=10 Identities=50% Similarity=1.454 Sum_probs=8.7
Q ss_pred eCCCCCcccc
Q 023888 216 YCPKCEDIYY 225 (275)
Q Consensus 216 YCP~C~DVY~ 225 (275)
-||.|++||.
T Consensus 46 VCP~Ck~iye 55 (58)
T PF11238_consen 46 VCPECKEIYE 55 (58)
T ss_pred CCcCHHHHHH
Confidence 3999999994
No 22
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=30.41 E-value=24 Score=23.48 Aligned_cols=29 Identities=24% Similarity=0.547 Sum_probs=18.8
Q ss_pred CCCCCccccccCCCCCcccceEeCCCCCcccc
Q 023888 194 CCGQPCLPVGQSDIPRSSTVKIYCPKCEDIYY 225 (275)
Q Consensus 194 C~gq~lLPiGlSD~pg~stVKlYCP~C~DVY~ 225 (275)
|....-||-. .......++-||+|+.++.
T Consensus 8 C~~~f~v~~~---~l~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 8 CQTRFRVPDD---KLPAGGRKVRCPKCGHVFR 36 (37)
T ss_pred CCceEEcCHH---HcccCCcEEECCCCCcEee
Confidence 5444444432 2446677999999998873
No 23
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=28.84 E-value=48 Score=31.55 Aligned_cols=38 Identities=24% Similarity=0.626 Sum_probs=24.4
Q ss_pred CCCcccCCCCCcc-cc--c-cCCCC--CcccceEeCCCCCcccc
Q 023888 188 RCPRVYCCGQPCL-PV--G-QSDIP--RSSTVKIYCPKCEDIYY 225 (275)
Q Consensus 188 ~CPRv~C~gq~lL-Pi--G-lSD~p--g~stVKlYCP~C~DVY~ 225 (275)
.|||-+|++--.| |. | .+..+ .-.++.+-|+.|++.|.
T Consensus 125 aCPRp~CkRiI~L~~~~~~p~~~~~~~~p~~~rv~CghC~~~Fl 168 (256)
T PF09788_consen 125 ACPRPNCKRIINLGPSHQGPVTPPVPTQPGSCRVICGHCSNTFL 168 (256)
T ss_pred cCCCCCCcceEEeCCccCCCCCCCCCCCCCceeEECCCCCCcEe
Confidence 4999999965333 22 1 11111 22578999999999985
No 24
>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=28.80 E-value=35 Score=25.44 Aligned_cols=18 Identities=33% Similarity=0.816 Sum_probs=14.6
Q ss_pred CcccceEeCCCCCccccC
Q 023888 209 RSSTVKIYCPKCEDIYYP 226 (275)
Q Consensus 209 g~stVKlYCP~C~DVY~P 226 (275)
+..++.++||.|+..=.+
T Consensus 2 ~~~p~~~~CP~C~~~~~T 19 (73)
T PF10601_consen 2 GPEPVRIYCPYCQQQVQT 19 (73)
T ss_pred CCCceeeECCCCCCEEEE
Confidence 467899999999987544
No 25
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=28.73 E-value=30 Score=32.53 Aligned_cols=46 Identities=22% Similarity=0.463 Sum_probs=31.4
Q ss_pred HHcccccccccccccCCCCcccCC-CCCccc-cccCCCCCcccceEeCCCCCc
Q 023888 172 LYGLIHLEKYKNYDFGRCPRVYCC-GQPCLP-VGQSDIPRSSTVKIYCPKCED 222 (275)
Q Consensus 172 LYGLIH~eKY~~g~FG~CPRv~C~-gq~lLP-iGlSD~pg~stVKlYCP~C~D 222 (275)
+|-+-+ --.-|.++-|=+..|. .--=+| |||...|.-. .|||+|..
T Consensus 220 ~yC~Cn--qvsyg~Mi~CDn~~C~~eWFH~~CVGL~~~Pkgk---WyC~~C~~ 267 (274)
T KOG1973|consen 220 TYCICN--QVSYGKMIGCDNPGCPIEWFHFTCVGLKTKPKGK---WYCPRCKA 267 (274)
T ss_pred EEEEec--ccccccccccCCCCCCcceEEEeccccccCCCCc---ccchhhhh
Confidence 666665 2344677788888887 443344 5998766443 99999975
No 26
>COG1631 RPL42A Ribosomal protein L44E [Translation, ribosomal structure and biogenesis]
Probab=27.27 E-value=27 Score=28.61 Aligned_cols=11 Identities=36% Similarity=1.156 Sum_probs=9.6
Q ss_pred cceEeCCCCCc
Q 023888 212 TVKIYCPKCED 222 (275)
Q Consensus 212 tVKlYCP~C~D 222 (275)
+++.|||.|..
T Consensus 6 ~~~tyCp~Ckk 16 (94)
T COG1631 6 KRRTYCPYCKK 16 (94)
T ss_pred ceeecCccccc
Confidence 68899999985
No 27
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=27.05 E-value=17 Score=34.02 Aligned_cols=35 Identities=29% Similarity=0.554 Sum_probs=24.4
Q ss_pred cccCCCCC-ccccccCCCCCcccceEeCCCCCcccc
Q 023888 191 RVYCCGQP-CLPVGQSDIPRSSTVKIYCPKCEDIYY 225 (275)
Q Consensus 191 Rv~C~gq~-lLPiGlSD~pg~stVKlYCP~C~DVY~ 225 (275)
.--|.||+ .||.+........-=-+|||.|.-|-+
T Consensus 197 g~~C~GC~m~l~~~~~~~V~~~d~iv~CP~CgRILy 232 (239)
T COG1579 197 GRVCGGCHMKLPSQTLSKVRKKDEIVFCPYCGRILY 232 (239)
T ss_pred CCcccCCeeeecHHHHHHHhcCCCCccCCccchHHH
Confidence 34588887 688876655444555589999998743
No 28
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=26.96 E-value=30 Score=26.02 Aligned_cols=16 Identities=19% Similarity=0.752 Sum_probs=12.7
Q ss_pred CcccceEeCCCCCccc
Q 023888 209 RSSTVKIYCPKCEDIY 224 (275)
Q Consensus 209 g~stVKlYCP~C~DVY 224 (275)
+++-+++-||+|+.|-
T Consensus 19 ~~~yle~KCPrCK~vN 34 (60)
T COG4416 19 GQAYLEKKCPRCKEVN 34 (60)
T ss_pred cceeeeecCCccceee
Confidence 4567789999999874
No 29
>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=25.63 E-value=40 Score=21.95 Aligned_cols=15 Identities=27% Similarity=0.820 Sum_probs=11.5
Q ss_pred ceEeCCCCCccccCC
Q 023888 213 VKIYCPKCEDIYYPR 227 (275)
Q Consensus 213 VKlYCP~C~DVY~P~ 227 (275)
+++=||+|...|.-.
T Consensus 1 M~~~CP~C~~~~~v~ 15 (38)
T TIGR02098 1 MRIQCPNCKTSFRVV 15 (38)
T ss_pred CEEECCCCCCEEEeC
Confidence 467899999988543
No 30
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=25.45 E-value=32 Score=25.48 Aligned_cols=12 Identities=33% Similarity=0.993 Sum_probs=10.9
Q ss_pred ceEeCCCCCccc
Q 023888 213 VKIYCPKCEDIY 224 (275)
Q Consensus 213 VKlYCP~C~DVY 224 (275)
=.|.||.|+.+|
T Consensus 52 g~L~Cp~c~r~Y 63 (68)
T PF03966_consen 52 GELICPECGREY 63 (68)
T ss_dssp TEEEETTTTEEE
T ss_pred CEEEcCCCCCEE
Confidence 479999999999
No 31
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=25.15 E-value=21 Score=23.76 Aligned_cols=15 Identities=33% Similarity=1.276 Sum_probs=11.8
Q ss_pred EeCCCCCccccCCCC
Q 023888 215 IYCPKCEDIYYPRSK 229 (275)
Q Consensus 215 lYCP~C~DVY~P~s~ 229 (275)
.|||.|+.+-.|+..
T Consensus 2 ~FCp~C~nlL~p~~~ 16 (35)
T PF02150_consen 2 RFCPECGNLLYPKED 16 (35)
T ss_dssp -BETTTTSBEEEEEE
T ss_pred eeCCCCCccceEcCC
Confidence 599999999888643
No 32
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=25.03 E-value=36 Score=31.00 Aligned_cols=26 Identities=35% Similarity=1.045 Sum_probs=17.9
Q ss_pred cCCCCcccCCCCCccccccCCCCCcccceEeCCCCCcc
Q 023888 186 FGRCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPKCEDI 223 (275)
Q Consensus 186 FG~CPRv~C~gq~lLPiGlSD~pg~stVKlYCP~C~DV 223 (275)
|-.|+| | +++|.+-|. .|+||+|+-+
T Consensus 149 ~A~Csr--C-~~~L~~~~~---------~l~Cp~Cg~t 174 (188)
T COG1096 149 YARCSR--C-RAPLVKKGN---------MLKCPNCGNT 174 (188)
T ss_pred EEEccC--C-CcceEEcCc---------EEECCCCCCE
Confidence 456777 3 666766443 5999999866
No 33
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=24.28 E-value=83 Score=21.83 Aligned_cols=16 Identities=25% Similarity=0.480 Sum_probs=11.3
Q ss_pred cccCCCCcccCCCCCc
Q 023888 184 YDFGRCPRVYCCGQPC 199 (275)
Q Consensus 184 g~FG~CPRv~C~gq~l 199 (275)
..+-.||+..|...-.
T Consensus 16 ~~~~~CP~~~C~~~~~ 31 (64)
T smart00647 16 PDLKWCPAPDCSAAII 31 (64)
T ss_pred CCccCCCCCCCcceEE
Confidence 3566899999965433
No 34
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=24.11 E-value=37 Score=23.24 Aligned_cols=12 Identities=42% Similarity=1.453 Sum_probs=10.2
Q ss_pred eCCCCCccccCC
Q 023888 216 YCPKCEDIYYPR 227 (275)
Q Consensus 216 YCP~C~DVY~P~ 227 (275)
|||.|+.+-.++
T Consensus 2 FCp~Cg~~l~~~ 13 (52)
T smart00661 2 FCPKCGNMLIPK 13 (52)
T ss_pred CCCCCCCccccc
Confidence 899999987765
No 35
>COG4098 comFA Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [DNA replication, recombination, and repair]
Probab=23.65 E-value=32 Score=34.64 Aligned_cols=14 Identities=43% Similarity=0.959 Sum_probs=10.7
Q ss_pred ccccccCCCCCcccceEeCCCCCc
Q 023888 199 CLPVGQSDIPRSSTVKIYCPKCED 222 (275)
Q Consensus 199 lLPiGlSD~pg~stVKlYCP~C~D 222 (275)
-||+| ++||++|--
T Consensus 55 ~lp~~----------~~YCr~Cl~ 68 (441)
T COG4098 55 KLPCG----------CLYCRNCLM 68 (441)
T ss_pred ccccc----------eEeehhhhh
Confidence 57777 799998853
No 36
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=23.25 E-value=49 Score=31.68 Aligned_cols=46 Identities=33% Similarity=0.679 Sum_probs=30.4
Q ss_pred HHHHcccccccccccccCC---CCcccCCCCC-ccc-cccCCCCCcccceEeCCCCCcc
Q 023888 170 EMLYGLIHLEKYKNYDFGR---CPRVYCCGQP-CLP-VGQSDIPRSSTVKIYCPKCEDI 223 (275)
Q Consensus 170 ~~LYGLIH~eKY~~g~FG~---CPRv~C~gq~-lLP-iGlSD~pg~stVKlYCP~C~DV 223 (275)
+.||- .-++.-||. |-...|+..= =|| |||..-| .-++|||-|++.
T Consensus 220 e~lYC-----fCqqvSyGqMVaCDn~nCkrEWFH~~CVGLk~pP---KG~WYC~eCk~~ 270 (271)
T COG5034 220 EELYC-----FCQQVSYGQMVACDNANCKREWFHLECVGLKEPP---KGKWYCPECKKA 270 (271)
T ss_pred ceeEE-----EecccccccceecCCCCCchhheeccccccCCCC---CCcEeCHHhHhc
Confidence 34676 578889996 5555554321 144 5888766 357999999874
No 37
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=22.87 E-value=60 Score=31.23 Aligned_cols=36 Identities=31% Similarity=0.528 Sum_probs=27.2
Q ss_pred ccCCCCCcccceEeCCCCCccccCCCCC---Cccccccc
Q 023888 203 GQSDIPRSSTVKIYCPKCEDIYYPRSKY---QGNIDGAY 238 (275)
Q Consensus 203 GlSD~pg~stVKlYCP~C~DVY~P~s~~---~~~IDGAy 238 (275)
|.-..+.....|..||+|+..+.|+-.. ...++|..
T Consensus 118 G~~~~~~~~g~~~~C~~cg~~~fPR~dP~vIv~v~~~~~ 156 (279)
T COG2816 118 GTKTYPREGGWARVCPKCGHEHFPRIDPCVIVAVIRGDE 156 (279)
T ss_pred CCcCccccCceeeeCCCCCCccCCCCCCeEEEEEecCCc
Confidence 4445688999999999999999997532 33466665
No 38
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=21.22 E-value=62 Score=24.44 Aligned_cols=16 Identities=44% Similarity=1.190 Sum_probs=12.5
Q ss_pred CCcccceEeCCCCCcc
Q 023888 208 PRSSTVKIYCPKCEDI 223 (275)
Q Consensus 208 pg~stVKlYCP~C~DV 223 (275)
|.+..|+..||+|.++
T Consensus 19 ~~~~~~~F~CPnCG~~ 34 (59)
T PRK14890 19 PREKAVKFLCPNCGEV 34 (59)
T ss_pred CCCccCEeeCCCCCCe
Confidence 4455789999999865
No 39
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.14 E-value=40 Score=27.13 Aligned_cols=12 Identities=33% Similarity=1.229 Sum_probs=10.0
Q ss_pred EeCCCCCccccC
Q 023888 215 IYCPKCEDIYYP 226 (275)
Q Consensus 215 lYCP~C~DVY~P 226 (275)
-|||+|.-|..-
T Consensus 22 D~CPrCrGVWLD 33 (88)
T COG3809 22 DYCPRCRGVWLD 33 (88)
T ss_pred eeCCccccEeec
Confidence 599999999853
No 40
>PF00471 Ribosomal_L33: Ribosomal protein L33; InterPro: IPR001705 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L33 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L33 has been shown to be on the surface of 50S subunit. L33 belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, , ], groups: Eubacterial L33. Algal and plant chloroplast L33. Cyanelle L33. L33 is a small protein of 49 to 66 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3PIO_1 3PIP_1 3PYT_3 3MS1_3 3F1F_6 3F1H_6 3MRZ_3 3PYO_3 3D5B_6 3D5D_6 ....
Probab=20.57 E-value=67 Score=22.96 Aligned_cols=16 Identities=38% Similarity=1.038 Sum_probs=12.4
Q ss_pred CCCcccceEeCCCCCc
Q 023888 207 IPRSSTVKIYCPKCED 222 (275)
Q Consensus 207 ~pg~stVKlYCP~C~D 222 (275)
.|..-.++-|||.|+.
T Consensus 25 ~~~rL~lkKycp~~~k 40 (48)
T PF00471_consen 25 TPERLELKKYCPRCRK 40 (48)
T ss_dssp SSSSSEEEEEETSSSS
T ss_pred CCceeeEeccCCCCCC
Confidence 3556678999999975
No 41
>PF01485 IBR: IBR domain; InterPro: IPR002867 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 cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=20.22 E-value=1.4e+02 Score=20.63 Aligned_cols=42 Identities=19% Similarity=0.256 Sum_probs=16.8
Q ss_pred ccCCCCcccCCCCCccccccCCC--CCcccceEeCCCCCccccC
Q 023888 185 DFGRCPRVYCCGQPCLPVGQSDI--PRSSTVKIYCPKCEDIYYP 226 (275)
Q Consensus 185 ~FG~CPRv~C~gq~lLPiGlSD~--pg~stVKlYCP~C~DVY~P 226 (275)
.+-.||+..|..--...-+.... -=..-=..||..|+.-+|+
T Consensus 17 ~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~ 60 (64)
T PF01485_consen 17 NIRWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPWHE 60 (64)
T ss_dssp -CC--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSESCT
T ss_pred CccCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCcccCC
Confidence 34489999997654433333321 0000114566666666654
Done!