Query 023046
Match_columns 288
No_of_seqs 138 out of 347
Neff 4.2
Searched_HMMs 46136
Date Fri Mar 29 08:03:36 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023046.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023046hhsearch_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 3.6E-96 8E-101 651.7 14.2 192 96-287 3-194 (216)
2 PTZ00396 Casein kinase II subu 100.0 2.8E-90 6E-95 635.0 17.4 192 97-288 18-209 (251)
3 PF01214 CK_II_beta: Casein ki 100.0 5E-88 1.1E-92 595.9 9.7 184 101-284 1-184 (184)
4 COG5041 SKB2 Casein kinase II, 100.0 8.8E-85 1.9E-89 583.4 10.1 185 101-287 25-209 (242)
5 PF01927 Mut7-C: Mut7-C RNAse 72.3 3.8 8.3E-05 34.9 3.1 51 186-239 73-136 (147)
6 PRK05978 hypothetical protein; 71.4 4.3 9.4E-05 35.6 3.2 42 190-240 24-65 (148)
7 PF15235 GRIN_C: G protein-reg 68.1 3.8 8.3E-05 35.8 2.2 23 12-34 56-78 (137)
8 COG1656 Uncharacterized conser 52.1 13 0.00028 33.5 2.7 62 176-240 66-143 (165)
9 smart00647 IBR In Between Ring 48.0 31 0.00067 24.3 3.7 24 190-213 7-32 (64)
10 PF06044 DRP: Dam-replacing fa 48.0 3.7 8.1E-05 39.0 -1.4 58 200-264 32-101 (254)
11 PF14205 Cys_rich_KTR: Cystein 46.3 8.6 0.00019 28.9 0.6 11 225-235 26-36 (55)
12 PF06827 zf-FPG_IleRS: Zinc fi 41.4 12 0.00025 23.8 0.6 10 227-236 21-30 (30)
13 KOG4684 Uncharacterized conser 40.1 26 0.00056 33.3 2.8 37 201-237 140-180 (275)
14 PF08772 NOB1_Zn_bind: Nin one 35.4 15 0.00032 28.8 0.4 12 224-235 21-32 (73)
15 PRK00420 hypothetical protein; 35.4 44 0.00095 28.2 3.2 30 200-240 24-53 (112)
16 PF06677 Auto_anti-p27: Sjogre 31.9 35 0.00075 23.9 1.8 23 201-234 19-41 (41)
17 PF11238 DUF3039: Protein of u 31.4 11 0.00024 28.5 -0.8 10 229-238 46-55 (58)
18 PF03811 Zn_Tnp_IS1: InsA N-te 30.8 27 0.00059 23.7 1.1 12 224-235 2-13 (36)
19 PF05191 ADK_lid: Adenylate ki 30.7 24 0.00052 23.9 0.8 12 228-239 2-13 (36)
20 PRK00432 30S ribosomal protein 30.4 23 0.0005 25.6 0.7 9 227-235 20-28 (50)
21 COG2888 Predicted Zn-ribbon RN 30.1 32 0.00069 26.4 1.4 17 220-236 20-36 (61)
22 PF13717 zinc_ribbon_4: zinc-r 30.0 30 0.00065 23.2 1.2 15 226-240 1-15 (36)
23 KOG1973 Chromatin remodeling p 29.7 28 0.00062 32.9 1.4 38 195-235 228-267 (274)
24 PF13719 zinc_ribbon_5: zinc-r 29.4 26 0.00056 23.5 0.8 18 221-238 19-36 (37)
25 TIGR02098 MJ0042_CXXC MJ0042 f 27.8 29 0.00064 22.8 0.8 29 207-238 8-36 (38)
26 PF11335 DUF3137: Protein of u 27.4 29 0.00062 29.1 0.9 17 175-191 62-78 (142)
27 COG0401 Uncharacterized homolo 26.8 16 0.00034 27.6 -0.7 13 172-184 43-55 (56)
28 COG1631 RPL42A Ribosomal prote 26.0 29 0.00063 28.6 0.6 11 225-235 6-16 (94)
29 COG4416 Com Mu-like prophage p 25.9 31 0.00068 26.1 0.7 16 222-237 19-34 (60)
30 PF09788 Tmemb_55A: Transmembr 25.8 59 0.0013 31.2 2.7 38 201-238 125-168 (256)
31 PF10601 zf-LITAF-like: LITAF- 25.8 42 0.00091 25.2 1.4 18 222-239 2-19 (73)
32 COG1579 Zn-ribbon protein, pos 24.3 21 0.00047 33.6 -0.5 34 204-237 197-231 (239)
33 COG4098 comFA Superfamily II D 23.4 33 0.00071 34.8 0.6 13 212-234 55-67 (441)
34 COG5034 TNG2 Chromatin remodel 23.3 49 0.0011 31.9 1.7 38 194-236 226-270 (271)
35 PF03966 Trm112p: Trm112p-like 23.1 39 0.00085 25.2 0.8 13 226-238 52-64 (68)
36 PF02150 RNA_POL_M_15KD: RNA p 22.2 28 0.00061 23.3 -0.1 15 228-242 2-16 (35)
37 KOG2384 Major histocompatibili 21.6 38 0.00083 31.7 0.6 51 225-285 82-134 (223)
38 PRK14810 formamidopyrimidine-D 21.3 55 0.0012 30.8 1.6 26 201-234 246-271 (272)
39 COG3809 Uncharacterized protei 21.1 41 0.00088 27.3 0.6 12 227-238 21-32 (88)
40 smart00661 RPOL9 RNA polymeras 20.7 47 0.001 22.9 0.8 12 229-240 2-13 (52)
41 COG2816 NPY1 NTP pyrophosphohy 20.4 71 0.0015 31.0 2.1 50 190-251 104-156 (279)
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=3.6e-96 Score=651.72 Aligned_cols=192 Identities=70% Similarity=1.289 Sum_probs=185.6
Q ss_pred CCCCCChHHHHhCCCCCeeEEecCcccccCCCccCCCCCCCCCHHHHHHHHcCCCCCCCCCCChhhHHHHHHHHHHHhcc
Q 023046 96 DGDDTSWISWFCNLRGNEFFCEVDDEYIQDDFNLCGLSSQVPYYDYALDLILDVESSHGDMFTEEQNELVESAAEMLYGL 175 (288)
Q Consensus 96 ~~e~~sWI~wFcsl~gneff~eVdedyI~D~FNL~GL~~~Vp~y~~AL~~ILd~e~~~~~~~~~~~~~~ie~~A~~LYGL 175 (288)
++++.+||+|||+++|||||||||+|||+|+|||+||+.+||+|++||++|||+++.++.+..+++.++||++|++||||
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 34566799999999999999999999999999999999999999999999999998887777777789999999999999
Q ss_pred cccccccChHHHHHHHHHhhcCccCCCCcccCCCCCccccccCCCCCCccceeecCCCCccccCCCCCCCcccccccCCc
Q 023046 176 IHVRYILTSKGMAAMLEKYKNYDFGRCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPKCEDIYYPRSKYQGNIDGAYFGTT 255 (288)
Q Consensus 176 IHARYIlT~~GL~~M~eKY~~g~FG~CPRv~C~gq~lLPiGlSD~pg~stVKlYCP~C~DVY~P~s~~~~~IDGAyFGts 255 (288)
||||||||.+||++|++||++++||+||||+|++|+|||+|+||+||+++||||||+|+|||.|+++++.+|||||||||
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 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhHHHHHHhCCCCCCCCCCCcceeEeeeeecC
Q 023046 256 FPHLFLMTYGHLKPQKATQSYVPRVFGFKLHK 287 (288)
Q Consensus 256 FpH~Fl~~yP~l~P~~~~~~YvPrIFGFKIh~ 287 (288)
|||||||+||++.|+++.++|||||||||||+
T Consensus 163 FPhmff~~~p~l~P~r~~~~yvPriyGFkih~ 194 (216)
T KOG3092|consen 163 FPHMFFMTHPELRPKRPTEQYVPRIYGFKIHK 194 (216)
T ss_pred CchhHHHhccccCCCcchhhhcchheeeeeCc
Confidence 99999999999999999999999999999997
No 2
>PTZ00396 Casein kinase II subunit beta; Provisional
Probab=100.00 E-value=2.8e-90 Score=634.99 Aligned_cols=192 Identities=53% Similarity=1.051 Sum_probs=182.8
Q ss_pred CCCCChHHHHhCCCCCeeEEecCcccccCCCccCCCCCCCCCHHHHHHHHcCCCCCCCCCCChhhHHHHHHHHHHHhccc
Q 023046 97 GDDTSWISWFCNLRGNEFFCEVDDEYIQDDFNLCGLSSQVPYYDYALDLILDVESSHGDMFTEEQNELVESAAEMLYGLI 176 (288)
Q Consensus 97 ~e~~sWI~wFcsl~gneff~eVdedyI~D~FNL~GL~~~Vp~y~~AL~~ILd~e~~~~~~~~~~~~~~ie~~A~~LYGLI 176 (288)
.++.+||+|||+++||+|||+||+|||+|+||||||+.+||+|++||+||||.+.++++..+++..+.++++|++|||||
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 45679999999999999999999999999999999999999999999999999876655455667788999999999999
Q ss_pred ccccccChHHHHHHHHHhhcCccCCCCcccCCCCCccccccCCCCCCccceeecCCCCccccCCCCCCCcccccccCCch
Q 023046 177 HVRYILTSKGMAAMLEKYKNYDFGRCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPKCEDIYYPRSKYQGNIDGAYFGTTF 256 (288)
Q Consensus 177 HARYIlT~~GL~~M~eKY~~g~FG~CPRv~C~gq~lLPiGlSD~pg~stVKlYCP~C~DVY~P~s~~~~~IDGAyFGtsF 256 (288)
|||||+|++||++|++||++|+||+||||+|++|+|||||+||+||+++||+|||+|+|||+|++.++..||||||||||
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 99999999999999999999999999999999999999999999999999999999999999999877799999999999
Q ss_pred hHHHHHHhCCCCCCCCCCCcceeEeeeeecCC
Q 023046 257 PHLFLMTYGHLKPQKATQSYVPRVFGFKLHKP 288 (288)
Q Consensus 257 pH~Fl~~yP~l~P~~~~~~YvPrIFGFKIh~~ 288 (288)
||||||+||++.|+++.++|+|||||||||++
T Consensus 178 ph~fl~~~p~l~p~~~~~~yvPrifGFki~~~ 209 (251)
T PTZ00396 178 PHLFLMTYPELIPTKPPQYYVPKIFGFKVHKK 209 (251)
T ss_pred HHHHHHhccccCCCCCCCccCCeeeeEEeccc
Confidence 99999999999999999999999999999964
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=5e-88 Score=595.90 Aligned_cols=184 Identities=64% Similarity=1.221 Sum_probs=154.0
Q ss_pred ChHHHHhCCCCCeeEEecCcccccCCCccCCCCCCCCCHHHHHHHHcCCCCCCCCCCChhhHHHHHHHHHHHhccccccc
Q 023046 101 SWISWFCNLRGNEFFCEVDDEYIQDDFNLCGLSSQVPYYDYALDLILDVESSHGDMFTEEQNELVESAAEMLYGLIHVRY 180 (288)
Q Consensus 101 sWI~wFcsl~gneff~eVdedyI~D~FNL~GL~~~Vp~y~~AL~~ILd~e~~~~~~~~~~~~~~ie~~A~~LYGLIHARY 180 (288)
+||+|||+++||+||||||+|||+|+|||+||+++||+|++||++|||.+.++++..++++.+.++++|++|||||||||
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 69999999999999999999999999999999999999999999999998776555666677899999999999999999
Q ss_pred ccChHHHHHHHHHhhcCccCCCCcccCCCCCccccccCCCCCCccceeecCCCCccccCCCCCCCcccccccCCchhHHH
Q 023046 181 ILTSKGMAAMLEKYKNYDFGRCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPKCEDIYYPRSKYQGNIDGAYFGTTFPHLF 260 (288)
Q Consensus 181 IlT~~GL~~M~eKY~~g~FG~CPRv~C~gq~lLPiGlSD~pg~stVKlYCP~C~DVY~P~s~~~~~IDGAyFGtsFpH~F 260 (288)
|+|++||++|++||++|+||+||||+|++|+|||||+||+||+++||||||+|+|||+|+++++.+||||||||||||||
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 99999999999999999999999999999999999999999999999999999999999888999999999999999999
Q ss_pred HHHhCCCCCCCCCCCcceeEeeee
Q 023046 261 LMTYGHLKPQKATQSYVPRVFGFK 284 (288)
Q Consensus 261 l~~yP~l~P~~~~~~YvPrIFGFK 284 (288)
+|+||++.|+.+.++|+|||||||
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=8.8e-85 Score=583.44 Aligned_cols=185 Identities=55% Similarity=1.144 Sum_probs=177.2
Q ss_pred ChHHHHhCCCCCeeEEecCcccccCCCccCCCCCCCCCHHHHHHHHcCCCCCCCCCCChhhHHHHHHHHHHHhccccccc
Q 023046 101 SWISWFCNLRGNEFFCEVDDEYIQDDFNLCGLSSQVPYYDYALDLILDVESSHGDMFTEEQNELVESAAEMLYGLIHVRY 180 (288)
Q Consensus 101 sWI~wFcsl~gneff~eVdedyI~D~FNL~GL~~~Vp~y~~AL~~ILd~e~~~~~~~~~~~~~~ie~~A~~LYGLIHARY 180 (288)
.||+|||+++||||||+||++||+|.|||+||+..||+|.+||++|||...+. .+.+.+-+.||.+|+.|||||||||
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 79999999999999999999999999999999999999999999999987653 2333445789999999999999999
Q ss_pred ccChHHHHHHHHHhhcCccCCCCcccCCCCCccccccCCCCCCccceeecCCCCccccCCCCCCCcccccccCCchhHHH
Q 023046 181 ILTSKGMAAMLEKYKNYDFGRCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPKCEDIYYPRSKYQGNIDGAYFGTTFPHLF 260 (288)
Q Consensus 181 IlT~~GL~~M~eKY~~g~FG~CPRv~C~gq~lLPiGlSD~pg~stVKlYCP~C~DVY~P~s~~~~~IDGAyFGtsFpH~F 260 (288)
|+|..||++|++||+.++||+||||+||+|+|||+||||+||+++||||||+|.|||.|+|+++..||||||||||||||
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 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhCCCCCCCCCCCcceeEeeeeecC
Q 023046 261 LMTYGHLKPQKATQSYVPRVFGFKLHK 287 (288)
Q Consensus 261 l~~yP~l~P~~~~~~YvPrIFGFKIh~ 287 (288)
|++||++.|+++.+.|+|||||||||+
T Consensus 183 ~~~~pel~p~~~~e~YiprIfGfri~~ 209 (242)
T COG5041 183 LQTFPELFPKRSCERYIPRIFGFRIHS 209 (242)
T ss_pred HHhchhhcCCcchhhhcceeeeeEeeh
Confidence 999999999999999999999999986
No 5
>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=72.30 E-value=3.8 Score=34.94 Aligned_cols=51 Identities=31% Similarity=0.788 Sum_probs=32.3
Q ss_pred HHHHHHHHhh-----cCccCCCCcccCCCCCccccccCCCC--------CCccceeecCCCCccccC
Q 023046 186 GMAAMLEKYK-----NYDFGRCPRVYCCGQPCLPVGQSDIP--------RSSTVKIYCPKCEDIYYP 239 (288)
Q Consensus 186 GL~~M~eKY~-----~g~FG~CPRv~C~gq~lLPiGlSD~p--------g~stVKlYCP~C~DVY~P 239 (288)
=|..+.+.|. ...|-+||. ||+ ++.|+...++. .....=..||.|+.||=+
T Consensus 73 QL~ev~~~~~l~~~~~~~~sRC~~--CN~-~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiyW~ 136 (147)
T PF01927_consen 73 QLREVLERFGLKLRLDPIFSRCPK--CNG-PLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIYWE 136 (147)
T ss_pred HHHHHHHHcCCccccCCCCCccCC--CCc-EeeechhhccccccCccccccCCeEEECCCCCCEecc
Confidence 3444445553 445899986 655 78888665442 222335679999999954
No 6
>PRK05978 hypothetical protein; Provisional
Probab=71.43 E-value=4.3 Score=35.65 Aligned_cols=42 Identities=17% Similarity=0.219 Sum_probs=32.6
Q ss_pred HHHHhhcCccCCCCcccCCCCCccccccCCCCCCccceeecCCCCccccCC
Q 023046 190 MLEKYKNYDFGRCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPKCEDIYYPR 240 (288)
Q Consensus 190 M~eKY~~g~FG~CPRv~C~gq~lLPiGlSD~pg~stVKlYCP~C~DVY~P~ 240 (288)
+..-..+|-.|+||| |..-+++= +--+|.-.||.|..-|.+.
T Consensus 24 ~~~~~~rGl~grCP~--CG~G~LF~-------g~Lkv~~~C~~CG~~~~~~ 65 (148)
T PRK05978 24 VGRAMWRGFRGRCPA--CGEGKLFR-------AFLKPVDHCAACGEDFTHH 65 (148)
T ss_pred hHHHHHHHHcCcCCC--CCCCcccc-------cccccCCCccccCCccccC
Confidence 445677899999998 77776662 4567888999999988754
No 7
>PF15235 GRIN_C: G protein-regulated inducer of neurite outgrowth C-terminus
Probab=68.07 E-value=3.8 Score=35.77 Aligned_cols=23 Identities=30% Similarity=0.498 Sum_probs=21.4
Q ss_pred cccccCccchhhhhHHHhhhhhc
Q 023046 12 SEIVAGPLDRKRINDALDKHLEK 34 (288)
Q Consensus 12 ~~~~~~~~~~~~~~~~~~~~~~~ 34 (288)
=||+|+++|-.-+..|++||||+
T Consensus 56 WEVYGAs~DpEvLG~AIQkHLE~ 78 (137)
T PF15235_consen 56 WEVYGASVDPEVLGMAIQKHLER 78 (137)
T ss_pred EEEeccccCHHHHHHHHHHHHHH
Confidence 47899999999999999999997
No 8
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=52.14 E-value=13 Score=33.46 Aligned_cols=62 Identities=27% Similarity=0.491 Sum_probs=41.4
Q ss_pred cccccccChHHHHHHHHH---hh-----cCccCCCCcccCCCCCccccccCC--------CCCCccceeecCCCCccccC
Q 023046 176 IHVRYILTSKGMAAMLEK---YK-----NYDFGRCPRVYCCGQPCLPVGQSD--------IPRSSTVKIYCPKCEDIYYP 239 (288)
Q Consensus 176 IHARYIlT~~GL~~M~eK---Y~-----~g~FG~CPRv~C~gq~lLPiGlSD--------~pg~stVKlYCP~C~DVY~P 239 (288)
+++=||.+..=.++|.+= +. .-+|-+||. ||+ +|+++--.. +.+....-..||+|..+|=+
T Consensus 66 ~~~i~i~~~s~~~Ql~e~~~~~~l~~~~~~e~~RCp~--CN~-~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~CgkiYW~ 142 (165)
T COG1656 66 IKAILIRSDSIEEQLAEFLARLGLKPRLFPEFSRCPE--CNG-ELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKIYWK 142 (165)
T ss_pred CceEEEeCCCHHHHHHHHHHHhccchhcccccccCcc--cCC-EeccCcHHHHhhccchhhhhcccceeECCCCcccccC
Confidence 677788877777777665 32 344889995 654 577776655 22344444559999999976
Q ss_pred C
Q 023046 240 R 240 (288)
Q Consensus 240 ~ 240 (288)
-
T Consensus 143 G 143 (165)
T COG1656 143 G 143 (165)
T ss_pred c
Confidence 3
No 9
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=48.03 E-value=31 Score=24.25 Aligned_cols=24 Identities=29% Similarity=0.588 Sum_probs=15.3
Q ss_pred HHHHhhc--CccCCCCcccCCCCCcc
Q 023046 190 MLEKYKN--YDFGRCPRVYCCGQPCL 213 (288)
Q Consensus 190 M~eKY~~--g~FG~CPRv~C~gq~lL 213 (288)
+.++|.. ..+-.||+..|...-.+
T Consensus 7 ~~~~~i~~~~~~~~CP~~~C~~~~~~ 32 (64)
T smart00647 7 LLESYVESNPDLKWCPAPDCSAAIIV 32 (64)
T ss_pred HHHHHHhcCCCccCCCCCCCcceEEe
Confidence 4445533 46778999999654333
No 10
>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=48.02 E-value=3.7 Score=39.02 Aligned_cols=58 Identities=34% Similarity=0.736 Sum_probs=26.9
Q ss_pred CCCCcccCCCCCccccccCCCCCCccc-eeecCCCCccccCCCCC----CCcccccccC-------CchhHHHHHHh
Q 023046 200 GRCPRVYCCGQPCLPVGQSDIPRSSTV-KIYCPKCEDIYYPRSKY----QGNIDGAYFG-------TTFPHLFLMTY 264 (288)
Q Consensus 200 G~CPRv~C~gq~lLPiGlSD~pg~stV-KlYCP~C~DVY~P~s~~----~~~IDGAyFG-------tsFpH~Fl~~y 264 (288)
..||+ |...++-=+ +....| -.|||+|.+-|.-+|.. ....||||-- .+=|.+|||+|
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 46886 433333322 445555 57899999999887743 2247999963 24677888888
No 11
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=46.26 E-value=8.6 Score=28.86 Aligned_cols=11 Identities=45% Similarity=1.407 Sum_probs=8.8
Q ss_pred cceeecCCCCc
Q 023046 225 TVKIYCPKCED 235 (288)
Q Consensus 225 tVKlYCP~C~D 235 (288)
..-||||+|+.
T Consensus 26 NfPlyCpKCK~ 36 (55)
T PF14205_consen 26 NFPLYCPKCKQ 36 (55)
T ss_pred cccccCCCCCc
Confidence 34799999975
No 12
>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=41.39 E-value=12 Score=23.78 Aligned_cols=10 Identities=30% Similarity=1.265 Sum_probs=7.0
Q ss_pred eeecCCCCcc
Q 023046 227 KIYCPKCEDI 236 (288)
Q Consensus 227 KlYCP~C~DV 236 (288)
--|||+|.+|
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 4689999875
No 13
>KOG4684 consensus Uncharacterized conserved protein, contains C4-type Zn-finger [General function prediction only]
Probab=40.15 E-value=26 Score=33.29 Aligned_cols=37 Identities=19% Similarity=0.557 Sum_probs=25.0
Q ss_pred CCCcccCCCC----CccccccCCCCCCccceeecCCCCccc
Q 023046 201 RCPRVYCCGQ----PCLPVGQSDIPRSSTVKIYCPKCEDIY 237 (288)
Q Consensus 201 ~CPRv~C~gq----~lLPiGlSD~pg~stVKlYCP~C~DVY 237 (288)
.|||-+|++- ++.|--++..+.-..+++-|-.|+++|
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 5999999863 333333333333455899999999988
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=35.39 E-value=15 Score=28.81 Aligned_cols=12 Identities=42% Similarity=1.151 Sum_probs=5.3
Q ss_pred ccceeecCCCCc
Q 023046 224 STVKIYCPKCED 235 (288)
Q Consensus 224 stVKlYCP~C~D 235 (288)
.+-|+|||+|.-
T Consensus 21 ~~~k~FCp~CGn 32 (73)
T PF08772_consen 21 DMTKQFCPKCGN 32 (73)
T ss_dssp -SS--S-SSS--
T ss_pred CCCceeCcccCC
Confidence 466999999975
No 15
>PRK00420 hypothetical protein; Validated
Probab=35.36 E-value=44 Score=28.21 Aligned_cols=30 Identities=27% Similarity=0.738 Sum_probs=20.9
Q ss_pred CCCCcccCCCCCccccccCCCCCCccceeecCCCCccccCC
Q 023046 200 GRCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPKCEDIYYPR 240 (288)
Q Consensus 200 G~CPRv~C~gq~lLPiGlSD~pg~stVKlYCP~C~DVY~P~ 240 (288)
..||. | |.|++ +...-+.|||.|..++.-.
T Consensus 24 ~~CP~--C-g~pLf--------~lk~g~~~Cp~Cg~~~~v~ 53 (112)
T PRK00420 24 KHCPV--C-GLPLF--------ELKDGEVVCPVHGKVYIVK 53 (112)
T ss_pred CCCCC--C-CCcce--------ecCCCceECCCCCCeeeec
Confidence 79998 5 35543 2133489999999998754
No 16
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=31.90 E-value=35 Score=23.93 Aligned_cols=23 Identities=48% Similarity=1.239 Sum_probs=15.7
Q ss_pred CCCcccCCCCCccccccCCCCCCccceeecCCCC
Q 023046 201 RCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPKCE 234 (288)
Q Consensus 201 ~CPRv~C~gq~lLPiGlSD~pg~stVKlYCP~C~ 234 (288)
.||. | +.|++. + +. =++|||.|.
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 7884 7 777775 1 12 268999994
No 17
>PF11238 DUF3039: Protein of unknown function (DUF3039); InterPro: IPR021400 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=31.39 E-value=11 Score=28.53 Aligned_cols=10 Identities=50% Similarity=1.454 Sum_probs=8.8
Q ss_pred ecCCCCcccc
Q 023046 229 YCPKCEDIYY 238 (288)
Q Consensus 229 YCP~C~DVY~ 238 (288)
-||.|++||.
T Consensus 46 VCP~Ck~iye 55 (58)
T PF11238_consen 46 VCPECKEIYE 55 (58)
T ss_pred CCcCHHHHHH
Confidence 4999999995
No 18
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=30.76 E-value=27 Score=23.75 Aligned_cols=12 Identities=25% Similarity=1.143 Sum_probs=10.2
Q ss_pred ccceeecCCCCc
Q 023046 224 STVKIYCPKCED 235 (288)
Q Consensus 224 stVKlYCP~C~D 235 (288)
.+|.+.||+|..
T Consensus 2 a~i~v~CP~C~s 13 (36)
T PF03811_consen 2 AKIDVHCPRCQS 13 (36)
T ss_pred CcEeeeCCCCCC
Confidence 478999999975
No 19
>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=30.72 E-value=24 Score=23.92 Aligned_cols=12 Identities=50% Similarity=1.015 Sum_probs=10.5
Q ss_pred eecCCCCccccC
Q 023046 228 IYCPKCEDIYYP 239 (288)
Q Consensus 228 lYCP~C~DVY~P 239 (288)
..||.|..||+.
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 20
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=30.38 E-value=23 Score=25.61 Aligned_cols=9 Identities=33% Similarity=1.361 Sum_probs=4.6
Q ss_pred eeecCCCCc
Q 023046 227 KIYCPKCED 235 (288)
Q Consensus 227 KlYCP~C~D 235 (288)
+-|||+|..
T Consensus 20 ~~fCP~Cg~ 28 (50)
T PRK00432 20 NKFCPRCGS 28 (50)
T ss_pred cCcCcCCCc
Confidence 445555544
No 21
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=30.15 E-value=32 Score=26.36 Aligned_cols=17 Identities=35% Similarity=0.960 Sum_probs=14.6
Q ss_pred CCCCccceeecCCCCcc
Q 023046 220 IPRSSTVKIYCPKCEDI 236 (288)
Q Consensus 220 ~pg~stVKlYCP~C~DV 236 (288)
.|++..|+..||+|.++
T Consensus 20 ~p~e~~v~F~CPnCGe~ 36 (61)
T COG2888 20 APGETAVKFPCPNCGEV 36 (61)
T ss_pred ccCCceeEeeCCCCCce
Confidence 37889999999999854
No 22
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=30.04 E-value=30 Score=23.24 Aligned_cols=15 Identities=33% Similarity=0.766 Sum_probs=12.2
Q ss_pred ceeecCCCCccccCC
Q 023046 226 VKIYCPKCEDIYYPR 240 (288)
Q Consensus 226 VKlYCP~C~DVY~P~ 240 (288)
+++-||+|+-.|.-+
T Consensus 1 M~i~Cp~C~~~y~i~ 15 (36)
T PF13717_consen 1 MIITCPNCQAKYEID 15 (36)
T ss_pred CEEECCCCCCEEeCC
Confidence 578899999999744
No 23
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=29.65 E-value=28 Score=32.88 Aligned_cols=38 Identities=26% Similarity=0.518 Sum_probs=27.3
Q ss_pred hcCccCCCCcccCC-CCCccc-cccCCCCCCccceeecCCCCc
Q 023046 195 KNYDFGRCPRVYCC-GQPCLP-VGQSDIPRSSTVKIYCPKCED 235 (288)
Q Consensus 195 ~~g~FG~CPRv~C~-gq~lLP-iGlSD~pg~stVKlYCP~C~D 235 (288)
.-|.++-|=...|. ..-=+| |||...|.- |.|||+|+.
T Consensus 228 syg~Mi~CDn~~C~~eWFH~~CVGL~~~Pkg---kWyC~~C~~ 267 (274)
T KOG1973|consen 228 SYGKMIGCDNPGCPIEWFHFTCVGLKTKPKG---KWYCPRCKA 267 (274)
T ss_pred ccccccccCCCCCCcceEEEeccccccCCCC---cccchhhhh
Confidence 35777888888887 444445 599876644 499999975
No 24
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=29.38 E-value=26 Score=23.53 Aligned_cols=18 Identities=28% Similarity=0.731 Sum_probs=14.1
Q ss_pred CCCccceeecCCCCcccc
Q 023046 221 PRSSTVKIYCPKCEDIYY 238 (288)
Q Consensus 221 pg~stVKlYCP~C~DVY~ 238 (288)
......++-||+|+.++.
T Consensus 19 l~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 19 LPAGGRKVRCPKCGHVFR 36 (37)
T ss_pred cccCCcEEECCCCCcEee
Confidence 446677999999998873
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=27.77 E-value=29 Score=22.77 Aligned_cols=29 Identities=24% Similarity=0.463 Sum_probs=18.2
Q ss_pred CCCCCccccccCCCCCCccceeecCCCCcccc
Q 023046 207 CCGQPCLPVGQSDIPRSSTVKIYCPKCEDIYY 238 (288)
Q Consensus 207 C~gq~lLPiGlSD~pg~stVKlYCP~C~DVY~ 238 (288)
|..+.-+|-..- .....++.||+|+.++.
T Consensus 8 C~~~~~v~~~~~---~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 8 CKTSFRVVDSQL---GANGGKVRCGKCGHVWY 36 (38)
T ss_pred CCCEEEeCHHHc---CCCCCEEECCCCCCEEE
Confidence 555555664432 24445899999987753
No 26
>PF11335 DUF3137: Protein of unknown function (DUF3137) ; InterPro: IPR021484 This bacterial family of proteins has no known function.
Probab=27.38 E-value=29 Score=29.10 Aligned_cols=17 Identities=41% Similarity=0.604 Sum_probs=13.7
Q ss_pred ccccccccChHHHHHHH
Q 023046 175 LIHVRYILTSKGMAAML 191 (288)
Q Consensus 175 LIHARYIlT~~GL~~M~ 191 (288)
-+.|||||||.=|+.+.
T Consensus 62 ~~~AryiLtP~~mE~L~ 78 (142)
T PF11335_consen 62 QVEARYILTPSFMERLL 78 (142)
T ss_pred HHHHHHhCCHHHHHHHH
Confidence 35699999999877665
No 27
>COG0401 Uncharacterized homolog of Blt101 [Function unknown]
Probab=26.84 E-value=16 Score=27.58 Aligned_cols=13 Identities=31% Similarity=0.749 Sum_probs=10.9
Q ss_pred HhcccccccccCh
Q 023046 172 LYGLIHVRYILTS 184 (288)
Q Consensus 172 LYGLIHARYIlT~ 184 (288)
+=|+|||=||++.
T Consensus 43 ~PGiiHA~yvi~~ 55 (56)
T COG0401 43 IPGIIHALYVILR 55 (56)
T ss_pred hhhhHhheEEEEe
Confidence 5589999999874
No 28
>COG1631 RPL42A Ribosomal protein L44E [Translation, ribosomal structure and biogenesis]
Probab=25.96 E-value=29 Score=28.65 Aligned_cols=11 Identities=36% Similarity=1.156 Sum_probs=9.6
Q ss_pred cceeecCCCCc
Q 023046 225 TVKIYCPKCED 235 (288)
Q Consensus 225 tVKlYCP~C~D 235 (288)
+++.|||.|..
T Consensus 6 ~~~tyCp~Ckk 16 (94)
T COG1631 6 KRRTYCPYCKK 16 (94)
T ss_pred ceeecCccccc
Confidence 67899999975
No 29
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=25.94 E-value=31 Score=26.12 Aligned_cols=16 Identities=19% Similarity=0.752 Sum_probs=12.7
Q ss_pred CCccceeecCCCCccc
Q 023046 222 RSSTVKIYCPKCEDIY 237 (288)
Q Consensus 222 g~stVKlYCP~C~DVY 237 (288)
+++-+++-||+|+.|-
T Consensus 19 ~~~yle~KCPrCK~vN 34 (60)
T COG4416 19 GQAYLEKKCPRCKEVN 34 (60)
T ss_pred cceeeeecCCccceee
Confidence 4567789999998874
No 30
>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=25.83 E-value=59 Score=31.20 Aligned_cols=38 Identities=24% Similarity=0.615 Sum_probs=24.7
Q ss_pred CCCcccCCCCCcc-cc--ccC-CCC--CCccceeecCCCCcccc
Q 023046 201 RCPRVYCCGQPCL-PV--GQS-DIP--RSSTVKIYCPKCEDIYY 238 (288)
Q Consensus 201 ~CPRv~C~gq~lL-Pi--GlS-D~p--g~stVKlYCP~C~DVY~ 238 (288)
.|||-+|++--.| |. |.. ..+ .-.++.+-|+.|++.|.
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 5999999875433 22 111 111 23578999999999985
No 31
>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=25.75 E-value=42 Score=25.22 Aligned_cols=18 Identities=33% Similarity=0.816 Sum_probs=14.4
Q ss_pred CCccceeecCCCCccccC
Q 023046 222 RSSTVKIYCPKCEDIYYP 239 (288)
Q Consensus 222 g~stVKlYCP~C~DVY~P 239 (288)
+..++.++||.|+..=.+
T Consensus 2 ~~~p~~~~CP~C~~~~~T 19 (73)
T PF10601_consen 2 GPEPVRIYCPYCQQQVQT 19 (73)
T ss_pred CCCceeeECCCCCCEEEE
Confidence 467899999999986544
No 32
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=24.28 E-value=21 Score=33.64 Aligned_cols=34 Identities=26% Similarity=0.494 Sum_probs=24.7
Q ss_pred cccCCCCC-ccccccCCCCCCccceeecCCCCccc
Q 023046 204 RVYCCGQP-CLPVGQSDIPRSSTVKIYCPKCEDIY 237 (288)
Q Consensus 204 Rv~C~gq~-lLPiGlSD~pg~stVKlYCP~C~DVY 237 (288)
.--|.||+ .||.+........-=-+|||.|.-|-
T Consensus 197 g~~C~GC~m~l~~~~~~~V~~~d~iv~CP~CgRIL 231 (239)
T COG1579 197 GRVCGGCHMKLPSQTLSKVRKKDEIVFCPYCGRIL 231 (239)
T ss_pred CCcccCCeeeecHHHHHHHhcCCCCccCCccchHH
Confidence 34588888 58887766555565668999998764
No 33
>COG4098 comFA Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [DNA replication, recombination, and repair]
Probab=23.37 E-value=33 Score=34.85 Aligned_cols=13 Identities=46% Similarity=1.109 Sum_probs=10.5
Q ss_pred ccccccCCCCCCccceeecCCCC
Q 023046 212 CLPVGQSDIPRSSTVKIYCPKCE 234 (288)
Q Consensus 212 lLPiGlSD~pg~stVKlYCP~C~ 234 (288)
-||+| ++||++|-
T Consensus 55 ~lp~~----------~~YCr~Cl 67 (441)
T COG4098 55 KLPCG----------CLYCRNCL 67 (441)
T ss_pred ccccc----------eEeehhhh
Confidence 57777 89999984
No 34
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=23.34 E-value=49 Score=31.90 Aligned_cols=38 Identities=34% Similarity=0.823 Sum_probs=26.2
Q ss_pred hhcCccCCCCcccCCCCCc------cc-cccCCCCCCccceeecCCCCcc
Q 023046 194 YKNYDFGRCPRVYCCGQPC------LP-VGQSDIPRSSTVKIYCPKCEDI 236 (288)
Q Consensus 194 Y~~g~FG~CPRv~C~gq~l------LP-iGlSD~pg~stVKlYCP~C~DV 236 (288)
.++.-||. =|.|.+.+| || |||..-|. -++|||-|++.
T Consensus 226 CqqvSyGq--MVaCDn~nCkrEWFH~~CVGLk~pPK---G~WYC~eCk~~ 270 (271)
T COG5034 226 CQQVSYGQ--MVACDNANCKREWFHLECVGLKEPPK---GKWYCPECKKA 270 (271)
T ss_pred eccccccc--ceecCCCCCchhheeccccccCCCCC---CcEeCHHhHhc
Confidence 57788884 455555443 55 48887663 48999999874
No 35
>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=23.06 E-value=39 Score=25.19 Aligned_cols=13 Identities=31% Similarity=0.838 Sum_probs=11.2
Q ss_pred ceeecCCCCcccc
Q 023046 226 VKIYCPKCEDIYY 238 (288)
Q Consensus 226 VKlYCP~C~DVY~ 238 (288)
=.|.||.|+.+|-
T Consensus 52 g~L~Cp~c~r~YP 64 (68)
T PF03966_consen 52 GELICPECGREYP 64 (68)
T ss_dssp TEEEETTTTEEEE
T ss_pred CEEEcCCCCCEEe
Confidence 4899999999983
No 36
>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=22.20 E-value=28 Score=23.32 Aligned_cols=15 Identities=33% Similarity=1.276 Sum_probs=11.8
Q ss_pred eecCCCCccccCCCC
Q 023046 228 IYCPKCEDIYYPRSK 242 (288)
Q Consensus 228 lYCP~C~DVY~P~s~ 242 (288)
.|||.|..+-.|+..
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 599999999888653
No 37
>KOG2384 consensus Major histocompatibility complex protein BAT4, contains G-patch and ankyrin domains [General function prediction only]
Probab=21.59 E-value=38 Score=31.68 Aligned_cols=51 Identities=33% Similarity=0.661 Sum_probs=31.7
Q ss_pred cceeecCCCCccccCCCCCCCcccccccCCchhHHHHHHhCCCCCCCCCC--CcceeEeeeee
Q 023046 225 TVKIYCPKCEDIYYPRSKYQGNIDGAYFGTTFPHLFLMTYGHLKPQKATQ--SYVPRVFGFKL 285 (288)
Q Consensus 225 tVKlYCP~C~DVY~P~s~~~~~IDGAyFGtsFpH~Fl~~yP~l~P~~~~~--~YvPrIFGFKI 285 (288)
.---||-.| |+|.|.++.-.++ ||-.|+|-+.. .|..+.. ..-|+--|||+
T Consensus 82 e~lfyCE~C-d~~ip~~~~snH~------tSttHllsl~~---~pa~k~~p~~i~pks~GyrL 134 (223)
T KOG2384|consen 82 EALFYCEVC-DIYIPNSKKSNHF------TSTTHLLSLQH---IPANKFQPHLIKPKSLGYRL 134 (223)
T ss_pred Cccchhhhh-hhhccCCCCccch------hhHHHHhhhcc---CCCCCCCCCcCCCCCchHHH
Confidence 446799999 9999987543333 67788887654 2322222 23456666654
No 38
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=21.34 E-value=55 Score=30.78 Aligned_cols=26 Identities=31% Similarity=0.746 Sum_probs=15.6
Q ss_pred CCCcccCCCCCccccccCCCCCCccceeecCCCC
Q 023046 201 RCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPKCE 234 (288)
Q Consensus 201 ~CPRv~C~gq~lLPiGlSD~pg~stVKlYCP~C~ 234 (288)
.||| |. .++.=+.+. ++.--|||.|+
T Consensus 246 pCpr--CG-~~I~~~~~~-----gR~t~~CP~CQ 271 (272)
T PRK14810 246 PCLN--CK-TPIRRVVVA-----GRSSHYCPHCQ 271 (272)
T ss_pred cCCC--CC-CeeEEEEEC-----CCccEECcCCc
Confidence 6887 64 444322222 35568999997
No 39
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.13 E-value=41 Score=27.30 Aligned_cols=12 Identities=33% Similarity=1.190 Sum_probs=9.9
Q ss_pred eeecCCCCcccc
Q 023046 227 KIYCPKCEDIYY 238 (288)
Q Consensus 227 KlYCP~C~DVY~ 238 (288)
--|||+|.-|..
T Consensus 21 iD~CPrCrGVWL 32 (88)
T COG3809 21 IDYCPRCRGVWL 32 (88)
T ss_pred eeeCCccccEee
Confidence 359999999974
No 40
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=20.74 E-value=47 Score=22.89 Aligned_cols=12 Identities=42% Similarity=1.453 Sum_probs=10.1
Q ss_pred ecCCCCccccCC
Q 023046 229 YCPKCEDIYYPR 240 (288)
Q Consensus 229 YCP~C~DVY~P~ 240 (288)
|||.|..+-.++
T Consensus 2 FCp~Cg~~l~~~ 13 (52)
T smart00661 2 FCPKCGNMLIPK 13 (52)
T ss_pred CCCCCCCccccc
Confidence 899999887765
No 41
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=20.40 E-value=71 Score=30.97 Aligned_cols=50 Identities=34% Similarity=0.629 Sum_probs=34.1
Q ss_pred HHHHhhcCccCCCCcccCCCCCccccccCCCCCCccceeecCCCCccccCCCCC---CCcccccc
Q 023046 190 MLEKYKNYDFGRCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPKCEDIYYPRSKY---QGNIDGAY 251 (288)
Q Consensus 190 M~eKY~~g~FG~CPRv~C~gq~lLPiGlSD~pg~stVKlYCP~C~DVY~P~s~~---~~~IDGAy 251 (288)
+.+.+....| ||+. |.-..+.....|..||+|...+.|+-.. ...++|..
T Consensus 104 l~~w~~~~RF--Cg~C----------G~~~~~~~~g~~~~C~~cg~~~fPR~dP~vIv~v~~~~~ 156 (279)
T COG2816 104 LLEWYRSHRF--CGRC----------GTKTYPREGGWARVCPKCGHEHFPRIDPCVIVAVIRGDE 156 (279)
T ss_pred HHHHHhhCcC--CCCC----------CCcCccccCceeeeCCCCCCccCCCCCCeEEEEEecCCc
Confidence 4445555554 5552 4456688999999999999999997543 23456665
Done!