Query 037001
Match_columns 284
No_of_seqs 132 out of 346
Neff 4.2
Searched_HMMs 46136
Date Fri Mar 29 07:34:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/037001.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/037001hhsearch_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 3.5E-96 8E-101 650.6 14.3 193 92-284 3-195 (216)
2 PTZ00396 Casein kinase II subu 100.0 3.4E-90 7.4E-95 633.3 16.8 193 92-284 17-209 (251)
3 PF01214 CK_II_beta: Casein ki 100.0 6.1E-88 1.3E-92 594.4 8.7 184 97-280 1-184 (184)
4 COG5041 SKB2 Casein kinase II, 100.0 1.5E-84 3.3E-89 580.8 10.1 185 97-283 25-209 (242)
5 PF01927 Mut7-C: Mut7-C RNAse 74.4 3.2 6.9E-05 35.4 3.1 51 182-235 73-136 (147)
6 PRK05978 hypothetical protein; 73.7 3.1 6.8E-05 36.4 2.9 41 186-235 24-64 (148)
7 PF15235 GRIN_C: G protein-reg 63.9 3.9 8.4E-05 35.7 1.4 24 11-34 55-78 (137)
8 COG1656 Uncharacterized conser 53.6 12 0.00027 33.5 2.8 63 172-237 66-144 (165)
9 PF06044 DRP: Dam-replacing fa 48.9 3.6 7.9E-05 39.0 -1.3 58 196-260 32-101 (254)
10 KOG4684 Uncharacterized conser 47.9 17 0.00036 34.4 2.8 37 197-233 140-180 (275)
11 PF14205 Cys_rich_KTR: Cystein 46.3 8.4 0.00018 28.8 0.5 11 221-231 26-36 (55)
12 smart00647 IBR In Between Ring 45.3 33 0.00072 24.0 3.5 23 186-208 7-31 (64)
13 PRK00420 hypothetical protein; 44.8 25 0.00054 29.6 3.2 30 196-236 24-53 (112)
14 PF06827 zf-FPG_IleRS: Zinc fi 37.9 14 0.00031 23.3 0.6 10 223-232 21-30 (30)
15 PF08772 NOB1_Zn_bind: Nin one 37.4 13 0.00029 29.0 0.4 13 220-232 21-33 (73)
16 PF05191 ADK_lid: Adenylate ki 36.6 22 0.00048 24.0 1.4 13 224-236 2-14 (36)
17 PF06677 Auto_anti-p27: Sjogre 34.0 30 0.00066 24.1 1.8 23 197-230 19-41 (41)
18 COG2888 Predicted Zn-ribbon RN 33.8 26 0.00056 26.8 1.5 18 216-233 20-37 (61)
19 PF13717 zinc_ribbon_4: zinc-r 32.9 25 0.00055 23.5 1.2 15 222-236 1-15 (36)
20 PF11238 DUF3039: Protein of u 32.1 11 0.00024 28.5 -0.8 10 225-234 46-55 (58)
21 PF03811 Zn_Tnp_IS1: InsA N-te 31.3 27 0.00057 23.8 1.1 12 220-231 2-13 (36)
22 PRK00432 30S ribosomal protein 30.9 22 0.00048 25.6 0.7 9 223-231 20-28 (50)
23 PF09788 Tmemb_55A: Transmembr 28.8 49 0.0011 31.7 2.8 38 197-234 125-168 (256)
24 KOG1973 Chromatin remodeling p 28.8 30 0.00065 32.6 1.4 38 191-231 228-267 (274)
25 COG0401 Uncharacterized homolo 27.7 17 0.00036 27.4 -0.4 13 168-180 43-55 (56)
26 PF10601 zf-LITAF-like: LITAF- 26.9 39 0.00084 25.3 1.5 19 218-236 2-20 (73)
27 PF11335 DUF3137: Protein of u 26.9 27 0.00058 29.2 0.6 50 171-236 62-111 (142)
28 COG1631 RPL42A Ribosomal prote 26.3 28 0.00062 28.6 0.6 14 220-233 5-18 (94)
29 TIGR02098 MJ0042_CXXC MJ0042 f 24.7 43 0.00093 21.9 1.2 15 222-236 1-15 (38)
30 PF13719 zinc_ribbon_5: zinc-r 24.7 35 0.00077 22.8 0.8 29 203-234 8-36 (37)
31 COG4416 Com Mu-like prophage p 24.3 35 0.00076 25.8 0.7 17 218-234 19-35 (60)
32 PF02150 RNA_POL_M_15KD: RNA p 23.7 26 0.00057 23.4 0.0 14 224-237 2-15 (35)
33 COG4098 comFA Superfamily II D 23.3 33 0.00072 34.7 0.6 8 223-230 60-67 (441)
34 COG1096 Predicted RNA-binding 21.8 50 0.0011 30.3 1.4 24 197-232 151-174 (188)
35 PF03966 Trm112p: Trm112p-like 21.7 44 0.00095 24.9 0.9 12 222-233 52-63 (68)
36 smart00661 RPOL9 RNA polymeras 21.6 44 0.00095 23.0 0.8 12 225-236 2-13 (52)
37 KOG2828 Acetyl-CoA hydrolase [ 21.6 37 0.0008 34.6 0.5 17 171-187 400-416 (454)
38 PRK14810 formamidopyrimidine-D 21.5 55 0.0012 30.7 1.6 26 197-230 246-271 (272)
39 COG1579 Zn-ribbon protein, pos 21.0 27 0.00059 32.9 -0.5 34 201-234 198-232 (239)
40 COG5034 TNG2 Chromatin remodel 20.7 61 0.0013 31.2 1.8 41 189-232 225-270 (271)
41 PF14774 FAM177: FAM177 family 20.6 29 0.00063 29.6 -0.3 48 92-143 56-107 (123)
42 COG5252 Uncharacterized conser 20.1 76 0.0016 30.6 2.2 40 175-214 136-180 (299)
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=3.5e-96 Score=650.62 Aligned_cols=193 Identities=69% Similarity=1.287 Sum_probs=186.1
Q ss_pred CCCCCchHHHHhCCCCCeeEEecCcccccCCCccCCCCCCCCCHHHHHHHHcCCCCCCCCCCchhhHHHHHHHHHHHhcc
Q 037001 92 EGDDTSWISWFCNLRGNEFFCEVDDDYIQDDFNLCGLSGQVPYYDYALDLILDVESSHGEMFTEEQNELVESAAEMLYGL 171 (284)
Q Consensus 92 ~~e~~sWI~wFcsl~gneffceVDedYI~D~FNL~GL~~~Vp~Y~~AL~~ILd~~~~~~~~~~~~~~~~ie~~A~~LYGL 171 (284)
++++.+||+|||+++|||||||||+|||+|+|||+||+.+||+|++||++|||+++.++.++.+++.++||++|++||||
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 44566799999999999999999999999999999999999999999999999998887777777789999999999999
Q ss_pred cccceeeChHHHHHHHHhhccCccCCCCcccCCCCCccccccCCCCCCccceeecCCCCccccCCCCCCCcccccccCCc
Q 037001 172 IHARYILTTKGMAAMLDKYKNYDFGRCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPRCEDIYYPRSKYQGNIDGAYFGTT 251 (284)
Q Consensus 172 IHARYIlT~~GL~~M~eKY~~g~FG~CPRv~C~gq~lLPiGlSD~pg~stVKlYCP~C~DVY~P~s~~~~~IDGAyFGts 251 (284)
||||||||.+||++|++||++++||+||||+|++|+|||+||||+|++++||||||+|+|||.|+|+++.+|||||||||
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 hhhHHHHHhCCCCCCCCCCCcceeeeeeeecCC
Q 037001 252 FPHLFLMTYGHLKPQKAVQSYAPRVFGFKIHKP 284 (284)
Q Consensus 252 FpHlFl~~yp~l~p~~~~~~YvPrIFGFKIh~~ 284 (284)
|||||||+||++.|+++.++|||||||||||+.
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=3.4e-90 Score=633.27 Aligned_cols=193 Identities=53% Similarity=1.046 Sum_probs=182.8
Q ss_pred CCCCCchHHHHhCCCCCeeEEecCcccccCCCccCCCCCCCCCHHHHHHHHcCCCCCCCCCCchhhHHHHHHHHHHHhcc
Q 037001 92 EGDDTSWISWFCNLRGNEFFCEVDDDYIQDDFNLCGLSGQVPYYDYALDLILDVESSHGEMFTEEQNELVESAAEMLYGL 171 (284)
Q Consensus 92 ~~e~~sWI~wFcsl~gneffceVDedYI~D~FNL~GL~~~Vp~Y~~AL~~ILd~~~~~~~~~~~~~~~~ie~~A~~LYGL 171 (284)
+.++.+||+|||+++||+|||+||+|||+|+||||||+.+||||++||+||||.+..+++..+++..+.++++|++||||
T Consensus 17 s~~~~sWI~wF~~~~gne~f~~Vd~dyI~D~FNl~GL~~~v~~y~~al~~Ild~~~~~~~~~~~~~~~~i~~~a~~LYGL 96 (251)
T PTZ00396 17 SEESMGWIEWFCSLKGHEFLCEVDEDFIRDEFNLYGLKSKFPFYNEALDMILDSEPPDDEDLEDEQFLEVYQEASDLYGL 96 (251)
T ss_pred CCCcCcHHHHHhCCCCCeeEEEeCHHHhcCcchhhCccccccCHHHHHHHHcCCCCCccccccchhHHHHHHHHHHHHHH
Confidence 34667899999999999999999999999999999999999999999999999987665555566778899999999999
Q ss_pred cccceeeChHHHHHHHHhhccCccCCCCcccCCCCCccccccCCCCCCccceeecCCCCccccCCCCCCCcccccccCCc
Q 037001 172 IHARYILTTKGMAAMLDKYKNYDFGRCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPRCEDIYYPRSKYQGNIDGAYFGTT 251 (284)
Q Consensus 172 IHARYIlT~~GL~~M~eKY~~g~FG~CPRv~C~gq~lLPiGlSD~pg~stVKlYCP~C~DVY~P~s~~~~~IDGAyFGts 251 (284)
||||||+|++||++|++||++|+||+||||+|++|+|||||+||+||+++||+|||+|+|||+|++.++..|||||||||
T Consensus 97 IHARyI~T~~Gl~~M~eKY~~g~FG~CPRv~C~~q~~LPvGlSd~~g~~~VKlyCP~C~DvY~p~s~~~~~iDGA~FGts 176 (251)
T PTZ00396 97 IHARFITTPKGLALMREKYLQGKFGHCPRVLCEGQNVLPIGLSDVLKTSRVKVYCPRCQEVYHPKKSSLLDIDGAFFGTS 176 (251)
T ss_pred HhHhHhcCHHHHHHHHHHhhCCCCCCCCCccCCCCcccccccCCCcCcCceeEeCCCchhhcCCCCccccccccceecCc
Confidence 99999999999999999999999999999999999999999999999999999999999999999877668999999999
Q ss_pred hhhHHHHHhCCCCCCCCCCCcceeeeeeeecCC
Q 037001 252 FPHLFLMTYGHLKPQKAVQSYAPRVFGFKIHKP 284 (284)
Q Consensus 252 FpHlFl~~yp~l~p~~~~~~YvPrIFGFKIh~~ 284 (284)
|||||||+||++.|+++.++|+|||||||||++
T Consensus 177 Fph~fl~~~p~l~p~~~~~~yvPrifGFki~~~ 209 (251)
T PTZ00396 177 FPHLFLMTYPELIPTKPPQYYVPKIFGFKVHKK 209 (251)
T ss_pred HHHHHHHhccccCCCCCCCccCCeeeeEEeccc
Confidence 999999999999999999999999999999963
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=6.1e-88 Score=594.38 Aligned_cols=184 Identities=64% Similarity=1.219 Sum_probs=153.7
Q ss_pred chHHHHhCCCCCeeEEecCcccccCCCccCCCCCCCCCHHHHHHHHcCCCCCCCCCCchhhHHHHHHHHHHHhcccccce
Q 037001 97 SWISWFCNLRGNEFFCEVDDDYIQDDFNLCGLSGQVPYYDYALDLILDVESSHGEMFTEEQNELVESAAEMLYGLIHARY 176 (284)
Q Consensus 97 sWI~wFcsl~gneffceVDedYI~D~FNL~GL~~~Vp~Y~~AL~~ILd~~~~~~~~~~~~~~~~ie~~A~~LYGLIHARY 176 (284)
+||+|||+++||+||||||+|||+|+|||+||+++||+|++||++|||.+..+++..++++.+.++++|++|||||||||
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 69999999999999999999999999999999999999999999999998776556666778889999999999999999
Q ss_pred eeChHHHHHHHHhhccCccCCCCcccCCCCCccccccCCCCCCccceeecCCCCccccCCCCCCCcccccccCCchhhHH
Q 037001 177 ILTTKGMAAMLDKYKNYDFGRCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPRCEDIYYPRSKYQGNIDGAYFGTTFPHLF 256 (284)
Q Consensus 177 IlT~~GL~~M~eKY~~g~FG~CPRv~C~gq~lLPiGlSD~pg~stVKlYCP~C~DVY~P~s~~~~~IDGAyFGtsFpHlF 256 (284)
|+|++||++|++||++|+||+||||+|++|+|||||+||+||+++||||||+|+|||+|++.++.+||||||||||||||
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 99999999999999999999999999999999999999999999999999999999999888888999999999999999
Q ss_pred HHHhCCCCCCCCCCCcceeeeeee
Q 037001 257 LMTYGHLKPQKAVQSYAPRVFGFK 280 (284)
Q Consensus 257 l~~yp~l~p~~~~~~YvPrIFGFK 280 (284)
+|+||++.|+.+.++|+|||||||
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=1.5e-84 Score=580.81 Aligned_cols=185 Identities=55% Similarity=1.139 Sum_probs=176.7
Q ss_pred chHHHHhCCCCCeeEEecCcccccCCCccCCCCCCCCCHHHHHHHHcCCCCCCCCCCchhhHHHHHHHHHHHhcccccce
Q 037001 97 SWISWFCNLRGNEFFCEVDDDYIQDDFNLCGLSGQVPYYDYALDLILDVESSHGEMFTEEQNELVESAAEMLYGLIHARY 176 (284)
Q Consensus 97 sWI~wFcsl~gneffceVDedYI~D~FNL~GL~~~Vp~Y~~AL~~ILd~~~~~~~~~~~~~~~~ie~~A~~LYGLIHARY 176 (284)
.||+|||+++||||||+||++||+|.|||+||+..||+|.+||++|||...+. .+.+.+-+.||.+|+.|||||||||
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 79999999999999999999999999999999999999999999999986544 2333445789999999999999999
Q ss_pred eeChHHHHHHHHhhccCccCCCCcccCCCCCccccccCCCCCCccceeecCCCCccccCCCCCCCcccccccCCchhhHH
Q 037001 177 ILTTKGMAAMLDKYKNYDFGRCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPRCEDIYYPRSKYQGNIDGAYFGTTFPHLF 256 (284)
Q Consensus 177 IlT~~GL~~M~eKY~~g~FG~CPRv~C~gq~lLPiGlSD~pg~stVKlYCP~C~DVY~P~s~~~~~IDGAyFGtsFpHlF 256 (284)
|+|..||++|++||+.++||+||||+||+|+|||+||||+||+++||||||+|.|||.|+|+++..||||||||||||||
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 037001 257 LMTYGHLKPQKAVQSYAPRVFGFKIHK 283 (284)
Q Consensus 257 l~~yp~l~p~~~~~~YvPrIFGFKIh~ 283 (284)
|++||++.|+++.+.|+|||||||||+
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=74.40 E-value=3.2 Score=35.38 Aligned_cols=51 Identities=29% Similarity=0.783 Sum_probs=32.1
Q ss_pred HHHHHHHhhc-----cCccCCCCcccCCCCCccccccCCCC--------CCccceeecCCCCccccC
Q 037001 182 GMAAMLDKYK-----NYDFGRCPRVYCCGQPCLPVGQSDIP--------RSSTVKIYCPRCEDIYYP 235 (284)
Q Consensus 182 GL~~M~eKY~-----~g~FG~CPRv~C~gq~lLPiGlSD~p--------g~stVKlYCP~C~DVY~P 235 (284)
=|..+.+.|. +..|-+||. ||+ ++.|+...+.. .....=..||.|+.||=+
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 3444444443 445899986 555 78888655432 222335679999999954
No 6
>PRK05978 hypothetical protein; Provisional
Probab=73.69 E-value=3.1 Score=36.44 Aligned_cols=41 Identities=17% Similarity=0.212 Sum_probs=31.9
Q ss_pred HHHhhccCccCCCCcccCCCCCccccccCCCCCCccceeecCCCCccccC
Q 037001 186 MLDKYKNYDFGRCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPRCEDIYYP 235 (284)
Q Consensus 186 M~eKY~~g~FG~CPRv~C~gq~lLPiGlSD~pg~stVKlYCP~C~DVY~P 235 (284)
+..-..+|-.|+||| |..-+++= +--+|.-.||.|..-|.+
T Consensus 24 ~~~~~~rGl~grCP~--CG~G~LF~-------g~Lkv~~~C~~CG~~~~~ 64 (148)
T PRK05978 24 VGRAMWRGFRGRCPA--CGEGKLFR-------AFLKPVDHCAACGEDFTH 64 (148)
T ss_pred hHHHHHHHHcCcCCC--CCCCcccc-------cccccCCCccccCCcccc
Confidence 344577899999997 77776662 455788899999999965
No 7
>PF15235 GRIN_C: G protein-regulated inducer of neurite outgrowth C-terminus
Probab=63.91 E-value=3.9 Score=35.65 Aligned_cols=24 Identities=38% Similarity=0.414 Sum_probs=22.1
Q ss_pred CcccccCccchhhhhHHHHhhhhc
Q 037001 11 KSEVVVGPVDRKRINDALDKQLER 34 (284)
Q Consensus 11 ~~~~~~~~~~~~~~~~~~~~~~~~ 34 (284)
.=||+|+.+|-.-+.-|+.||||+
T Consensus 55 TWEVYGAs~DpEvLG~AIQkHLE~ 78 (137)
T PF15235_consen 55 TWEVYGASVDPEVLGMAIQKHLER 78 (137)
T ss_pred eEEEeccccCHHHHHHHHHHHHHH
Confidence 348999999999999999999997
No 8
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=53.62 E-value=12 Score=33.47 Aligned_cols=63 Identities=27% Similarity=0.497 Sum_probs=41.8
Q ss_pred cccceeeChHHHHHHHHh---hc-----cCccCCCCcccCCCCCccccccCC--------CCCCccceeecCCCCccccC
Q 037001 172 IHARYILTTKGMAAMLDK---YK-----NYDFGRCPRVYCCGQPCLPVGQSD--------IPRSSTVKIYCPRCEDIYYP 235 (284)
Q Consensus 172 IHARYIlT~~GL~~M~eK---Y~-----~g~FG~CPRv~C~gq~lLPiGlSD--------~pg~stVKlYCP~C~DVY~P 235 (284)
+++=||.+..=.+||.+= +. .-.|-+||. ||+ +|+++--.. +.+....-..||+|..+|=+
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 677788887777777664 22 334889995 654 577776554 22333444559999999976
Q ss_pred CC
Q 037001 236 RS 237 (284)
Q Consensus 236 ~s 237 (284)
-+
T Consensus 143 Gs 144 (165)
T COG1656 143 GS 144 (165)
T ss_pred ch
Confidence 43
No 9
>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=48.90 E-value=3.6 Score=39.02 Aligned_cols=58 Identities=34% Similarity=0.746 Sum_probs=26.4
Q ss_pred CCCCcccCCCCCccccccCCCCCCccc-eeecCCCCccccCCCCCC--C--cccccccC-------CchhhHHHHHh
Q 037001 196 GRCPRVYCCGQPCLPVGQSDIPRSSTV-KIYCPRCEDIYYPRSKYQ--G--NIDGAYFG-------TTFPHLFLMTY 260 (284)
Q Consensus 196 G~CPRv~C~gq~lLPiGlSD~pg~stV-KlYCP~C~DVY~P~s~~~--~--~IDGAyFG-------tsFpHlFl~~y 260 (284)
+.||+ |..-++-=+ +.-.+| -.|||+|.+-|.-+|+.. + -.||||-- .+=|.+|||+|
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 46775 443333322 444555 578999999999876431 1 34999963 24688888888
No 10
>KOG4684 consensus Uncharacterized conserved protein, contains C4-type Zn-finger [General function prediction only]
Probab=47.95 E-value=17 Score=34.45 Aligned_cols=37 Identities=19% Similarity=0.557 Sum_probs=25.7
Q ss_pred CCCcccCCCC----CccccccCCCCCCccceeecCCCCccc
Q 037001 197 RCPRVYCCGQ----PCLPVGQSDIPRSSTVKIYCPRCEDIY 233 (284)
Q Consensus 197 ~CPRv~C~gq----~lLPiGlSD~pg~stVKlYCP~C~DVY 233 (284)
.|||-+|++- |+.|--.+..+.-..+++-|-.|+++|
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 333333444444456899999999998
No 11
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=46.25 E-value=8.4 Score=28.84 Aligned_cols=11 Identities=36% Similarity=1.392 Sum_probs=8.6
Q ss_pred cceeecCCCCc
Q 037001 221 TVKIYCPRCED 231 (284)
Q Consensus 221 tVKlYCP~C~D 231 (284)
..-||||+|+.
T Consensus 26 NfPlyCpKCK~ 36 (55)
T PF14205_consen 26 NFPLYCPKCKQ 36 (55)
T ss_pred cccccCCCCCc
Confidence 34799999964
No 12
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=45.32 E-value=33 Score=24.03 Aligned_cols=23 Identities=26% Similarity=0.575 Sum_probs=14.7
Q ss_pred HHHhhcc--CccCCCCcccCCCCCc
Q 037001 186 MLDKYKN--YDFGRCPRVYCCGQPC 208 (284)
Q Consensus 186 M~eKY~~--g~FG~CPRv~C~gq~l 208 (284)
+.++|.. ..+-.||+..|...-.
T Consensus 7 ~~~~~i~~~~~~~~CP~~~C~~~~~ 31 (64)
T smart00647 7 LLESYVESNPDLKWCPAPDCSAAII 31 (64)
T ss_pred HHHHHHhcCCCccCCCCCCCcceEE
Confidence 3444433 4677899999965433
No 13
>PRK00420 hypothetical protein; Validated
Probab=44.79 E-value=25 Score=29.60 Aligned_cols=30 Identities=23% Similarity=0.629 Sum_probs=21.0
Q ss_pred CCCCcccCCCCCccccccCCCCCCccceeecCCCCccccCC
Q 037001 196 GRCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPRCEDIYYPR 236 (284)
Q Consensus 196 G~CPRv~C~gq~lLPiGlSD~pg~stVKlYCP~C~DVY~P~ 236 (284)
.+||. |. .|++= ...-+.|||.|..++.-.
T Consensus 24 ~~CP~--Cg-~pLf~--------lk~g~~~Cp~Cg~~~~v~ 53 (112)
T PRK00420 24 KHCPV--CG-LPLFE--------LKDGEVVCPVHGKVYIVK 53 (112)
T ss_pred CCCCC--CC-Cccee--------cCCCceECCCCCCeeeec
Confidence 79998 53 55542 123389999999999754
No 14
>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=37.90 E-value=14 Score=23.31 Aligned_cols=10 Identities=40% Similarity=1.331 Sum_probs=7.0
Q ss_pred eeecCCCCcc
Q 037001 223 KIYCPRCEDI 232 (284)
Q Consensus 223 KlYCP~C~DV 232 (284)
--|||+|.+|
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 15
>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=37.43 E-value=13 Score=29.00 Aligned_cols=13 Identities=31% Similarity=1.030 Sum_probs=5.6
Q ss_pred ccceeecCCCCcc
Q 037001 220 STVKIYCPRCEDI 232 (284)
Q Consensus 220 stVKlYCP~C~DV 232 (284)
.+-|+|||+|.--
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 4669999999753
No 16
>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=36.59 E-value=22 Score=24.01 Aligned_cols=13 Identities=38% Similarity=0.935 Sum_probs=11.0
Q ss_pred eecCCCCccccCC
Q 037001 224 IYCPRCEDIYYPR 236 (284)
Q Consensus 224 lYCP~C~DVY~P~ 236 (284)
..||.|..+||..
T Consensus 2 r~C~~Cg~~Yh~~ 14 (36)
T PF05191_consen 2 RICPKCGRIYHIE 14 (36)
T ss_dssp EEETTTTEEEETT
T ss_pred cCcCCCCCccccc
Confidence 5799999999854
No 17
>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=34.02 E-value=30 Score=24.14 Aligned_cols=23 Identities=48% Similarity=1.288 Sum_probs=15.7
Q ss_pred CCCcccCCCCCccccccCCCCCCccceeecCCCC
Q 037001 197 RCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPRCE 230 (284)
Q Consensus 197 ~CPRv~C~gq~lLPiGlSD~pg~stVKlYCP~C~ 230 (284)
.||. | +.|++. + +.. ++|||.|.
T Consensus 19 ~Cp~--C-~~PL~~----~--k~g--~~~Cv~C~ 41 (41)
T PF06677_consen 19 HCPD--C-GTPLMR----D--KDG--KIYCVSCG 41 (41)
T ss_pred ccCC--C-CCeeEE----e--cCC--CEECCCCC
Confidence 7884 7 777775 1 122 68999995
No 18
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=33.78 E-value=26 Score=26.80 Aligned_cols=18 Identities=33% Similarity=0.848 Sum_probs=14.9
Q ss_pred CCCCccceeecCCCCccc
Q 037001 216 IPRSSTVKIYCPRCEDIY 233 (284)
Q Consensus 216 ~pg~stVKlYCP~C~DVY 233 (284)
.|++..|+..||+|.++-
T Consensus 20 ~p~e~~v~F~CPnCGe~~ 37 (61)
T COG2888 20 APGETAVKFPCPNCGEVE 37 (61)
T ss_pred ccCCceeEeeCCCCCcee
Confidence 378899999999999543
No 19
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=32.94 E-value=25 Score=23.52 Aligned_cols=15 Identities=33% Similarity=0.755 Sum_probs=12.4
Q ss_pred ceeecCCCCccccCC
Q 037001 222 VKIYCPRCEDIYYPR 236 (284)
Q Consensus 222 VKlYCP~C~DVY~P~ 236 (284)
+++-||+|+-.|.-+
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 20
>PF11238 DUF3039: Protein of unknown function (DUF3039); InterPro: IPR021400 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=32.06 E-value=11 Score=28.54 Aligned_cols=10 Identities=50% Similarity=1.428 Sum_probs=8.8
Q ss_pred ecCCCCcccc
Q 037001 225 YCPRCEDIYY 234 (284)
Q Consensus 225 YCP~C~DVY~ 234 (284)
-||.|++||.
T Consensus 46 VCP~Ck~iye 55 (58)
T PF11238_consen 46 VCPECKEIYE 55 (58)
T ss_pred CCcCHHHHHH
Confidence 3999999995
No 21
>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=31.33 E-value=27 Score=23.76 Aligned_cols=12 Identities=33% Similarity=1.198 Sum_probs=10.1
Q ss_pred ccceeecCCCCc
Q 037001 220 STVKIYCPRCED 231 (284)
Q Consensus 220 stVKlYCP~C~D 231 (284)
.+|.+.||+|..
T Consensus 2 a~i~v~CP~C~s 13 (36)
T PF03811_consen 2 AKIDVHCPRCQS 13 (36)
T ss_pred CcEeeeCCCCCC
Confidence 478999999974
No 22
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=30.88 E-value=22 Score=25.64 Aligned_cols=9 Identities=44% Similarity=1.435 Sum_probs=4.1
Q ss_pred eeecCCCCc
Q 037001 223 KIYCPRCED 231 (284)
Q Consensus 223 KlYCP~C~D 231 (284)
+-|||+|..
T Consensus 20 ~~fCP~Cg~ 28 (50)
T PRK00432 20 NKFCPRCGS 28 (50)
T ss_pred cCcCcCCCc
Confidence 335555543
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=28.83 E-value=49 Score=31.68 Aligned_cols=38 Identities=18% Similarity=0.484 Sum_probs=24.6
Q ss_pred CCCcccCCCCCccccc----cCCCC--CCccceeecCCCCcccc
Q 037001 197 RCPRVYCCGQPCLPVG----QSDIP--RSSTVKIYCPRCEDIYY 234 (284)
Q Consensus 197 ~CPRv~C~gq~lLPiG----lSD~p--g~stVKlYCP~C~DVY~ 234 (284)
.|||-+|++--.|.=- .+..+ .-.++.+-|++|.+.|.
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 5999999875333211 11111 22578999999999985
No 24
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=28.79 E-value=30 Score=32.64 Aligned_cols=38 Identities=29% Similarity=0.536 Sum_probs=27.6
Q ss_pred ccCccCCCCcccCC-CCCccc-cccCCCCCCccceeecCCCCc
Q 037001 191 KNYDFGRCPRVYCC-GQPCLP-VGQSDIPRSSTVKIYCPRCED 231 (284)
Q Consensus 191 ~~g~FG~CPRv~C~-gq~lLP-iGlSD~pg~stVKlYCP~C~D 231 (284)
.-|.++-|=...|. ..-=+| |||...|.- |.|||.|..
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 45778888888887 444455 599866644 499999964
No 25
>COG0401 Uncharacterized homolog of Blt101 [Function unknown]
Probab=27.69 E-value=17 Score=27.37 Aligned_cols=13 Identities=38% Similarity=0.807 Sum_probs=10.9
Q ss_pred HhcccccceeeCh
Q 037001 168 LYGLIHARYILTT 180 (284)
Q Consensus 168 LYGLIHARYIlT~ 180 (284)
+=|+|||=||++.
T Consensus 43 ~PGiiHA~yvi~~ 55 (56)
T COG0401 43 IPGIIHALYVILR 55 (56)
T ss_pred hhhhHhheEEEEe
Confidence 5589999999874
No 26
>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=26.95 E-value=39 Score=25.34 Aligned_cols=19 Identities=37% Similarity=0.861 Sum_probs=15.4
Q ss_pred CCccceeecCCCCccccCC
Q 037001 218 RSSTVKIYCPRCEDIYYPR 236 (284)
Q Consensus 218 g~stVKlYCP~C~DVY~P~ 236 (284)
+..++.++||.|+..=.+.
T Consensus 2 ~~~p~~~~CP~C~~~~~T~ 20 (73)
T PF10601_consen 2 GPEPVRIYCPYCQQQVQTR 20 (73)
T ss_pred CCCceeeECCCCCCEEEEE
Confidence 4678999999999877654
No 27
>PF11335 DUF3137: Protein of unknown function (DUF3137) ; InterPro: IPR021484 This bacterial family of proteins has no known function.
Probab=26.93 E-value=27 Score=29.19 Aligned_cols=50 Identities=30% Similarity=0.474 Sum_probs=28.5
Q ss_pred ccccceeeChHHHHHHHHhhccCccCCCCcccCCCCCccccccCCCCCCccceeecCCCCccccCC
Q 037001 171 LIHARYILTTKGMAAMLDKYKNYDFGRCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPRCEDIYYPR 236 (284)
Q Consensus 171 LIHARYIlT~~GL~~M~eKY~~g~FG~CPRv~C~gq~lLPiGlSD~pg~stVKlYCP~C~DVY~P~ 236 (284)
.+.|||||||.=|+.+.+ +.+.. |. |+.++ ...+++-+..+.=++.+.|+
T Consensus 62 ~~~AryiLtP~~mE~L~~-l~~~~-~~------------~i~~~--f~~~~lyiai~~~~~~Fe~~ 111 (142)
T PF11335_consen 62 QVEARYILTPSFMERLLE-LRERF-GG------------PISLS--FDGNKLYIAIPSGRDLFEPS 111 (142)
T ss_pred HHHHHHhCCHHHHHHHHH-HHHhc-CC------------CEEEE--EeCCEEEEEEeCCcccccCC
Confidence 356799999998887653 22222 22 11111 22356666666666777654
No 28
>COG1631 RPL42A Ribosomal protein L44E [Translation, ribosomal structure and biogenesis]
Probab=26.28 E-value=28 Score=28.63 Aligned_cols=14 Identities=29% Similarity=0.821 Sum_probs=10.9
Q ss_pred ccceeecCCCCccc
Q 037001 220 STVKIYCPRCEDIY 233 (284)
Q Consensus 220 stVKlYCP~C~DVY 233 (284)
.+++.|||.|...=
T Consensus 5 K~~~tyCp~CkkhT 18 (94)
T COG1631 5 KKRRTYCPYCKKHT 18 (94)
T ss_pred cceeecCcccccce
Confidence 36899999997643
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=24.73 E-value=43 Score=21.92 Aligned_cols=15 Identities=27% Similarity=0.809 Sum_probs=11.6
Q ss_pred ceeecCCCCccccCC
Q 037001 222 VKIYCPRCEDIYYPR 236 (284)
Q Consensus 222 VKlYCP~C~DVY~P~ 236 (284)
+++=||+|...|.-.
T Consensus 1 M~~~CP~C~~~~~v~ 15 (38)
T TIGR02098 1 MRIQCPNCKTSFRVV 15 (38)
T ss_pred CEEECCCCCCEEEeC
Confidence 467899999998643
No 30
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=24.72 E-value=35 Score=22.82 Aligned_cols=29 Identities=21% Similarity=0.541 Sum_probs=18.9
Q ss_pred CCCCCccccccCCCCCCccceeecCCCCcccc
Q 037001 203 CCGQPCLPVGQSDIPRSSTVKIYCPRCEDIYY 234 (284)
Q Consensus 203 C~gq~lLPiGlSD~pg~stVKlYCP~C~DVY~ 234 (284)
|+...-||-. .......++-||+|+.++.
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 5555444432 2346677999999998873
No 31
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=24.31 E-value=35 Score=25.81 Aligned_cols=17 Identities=24% Similarity=0.694 Sum_probs=13.1
Q ss_pred CCccceeecCCCCcccc
Q 037001 218 RSSTVKIYCPRCEDIYY 234 (284)
Q Consensus 218 g~stVKlYCP~C~DVY~ 234 (284)
+++-+++-||+|+.|-.
T Consensus 19 ~~~yle~KCPrCK~vN~ 35 (60)
T COG4416 19 GQAYLEKKCPRCKEVNE 35 (60)
T ss_pred cceeeeecCCccceeee
Confidence 45677899999988743
No 32
>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=23.72 E-value=26 Score=23.39 Aligned_cols=14 Identities=36% Similarity=1.336 Sum_probs=11.5
Q ss_pred eecCCCCccccCCC
Q 037001 224 IYCPRCEDIYYPRS 237 (284)
Q Consensus 224 lYCP~C~DVY~P~s 237 (284)
.|||.|..+-.|+.
T Consensus 2 ~FCp~C~nlL~p~~ 15 (35)
T PF02150_consen 2 RFCPECGNLLYPKE 15 (35)
T ss_dssp -BETTTTSBEEEEE
T ss_pred eeCCCCCccceEcC
Confidence 59999999998864
No 33
>COG4098 comFA Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [DNA replication, recombination, and repair]
Probab=23.32 E-value=33 Score=34.74 Aligned_cols=8 Identities=38% Similarity=1.140 Sum_probs=6.9
Q ss_pred eeecCCCC
Q 037001 223 KIYCPRCE 230 (284)
Q Consensus 223 KlYCP~C~ 230 (284)
++||++|-
T Consensus 60 ~~YCr~Cl 67 (441)
T COG4098 60 CLYCRNCL 67 (441)
T ss_pred eEeehhhh
Confidence 89999984
No 34
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=21.79 E-value=50 Score=30.26 Aligned_cols=24 Identities=38% Similarity=1.007 Sum_probs=16.2
Q ss_pred CCCcccCCCCCccccccCCCCCCccceeecCCCCcc
Q 037001 197 RCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPRCEDI 232 (284)
Q Consensus 197 ~CPRv~C~gq~lLPiGlSD~pg~stVKlYCP~C~DV 232 (284)
.|+| | +++|.+-| ..|+||+|.-+
T Consensus 151 ~Csr--C-~~~L~~~~---------~~l~Cp~Cg~t 174 (188)
T COG1096 151 RCSR--C-RAPLVKKG---------NMLKCPNCGNT 174 (188)
T ss_pred EccC--C-CcceEEcC---------cEEECCCCCCE
Confidence 4666 3 56666633 37999999754
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=21.70 E-value=44 Score=24.88 Aligned_cols=12 Identities=33% Similarity=0.971 Sum_probs=11.0
Q ss_pred ceeecCCCCccc
Q 037001 222 VKIYCPRCEDIY 233 (284)
Q Consensus 222 VKlYCP~C~DVY 233 (284)
=.|.||.|+-+|
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 489999999999
No 36
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=21.61 E-value=44 Score=22.99 Aligned_cols=12 Identities=33% Similarity=1.439 Sum_probs=10.3
Q ss_pred ecCCCCccccCC
Q 037001 225 YCPRCEDIYYPR 236 (284)
Q Consensus 225 YCP~C~DVY~P~ 236 (284)
|||.|..+-.++
T Consensus 2 FCp~Cg~~l~~~ 13 (52)
T smart00661 2 FCPKCGNMLIPK 13 (52)
T ss_pred CCCCCCCccccc
Confidence 899999988765
No 37
>KOG2828 consensus Acetyl-CoA hydrolase [Energy production and conversion]
Probab=21.56 E-value=37 Score=34.57 Aligned_cols=17 Identities=29% Similarity=0.593 Sum_probs=14.8
Q ss_pred ccccceeeChHHHHHHH
Q 037001 171 LIHARYILTTKGMAAML 187 (284)
Q Consensus 171 LIHARYIlT~~GL~~M~ 187 (284)
--|++||+|+.|++.+.
T Consensus 400 rah~~y~VTEhGiA~L~ 416 (454)
T KOG2828|consen 400 RAHLDYLVTEHGIADLW 416 (454)
T ss_pred ccceeEEEecccHHHHh
Confidence 35999999999999874
No 38
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=21.49 E-value=55 Score=30.74 Aligned_cols=26 Identities=31% Similarity=0.746 Sum_probs=15.8
Q ss_pred CCCcccCCCCCccccccCCCCCCccceeecCCCC
Q 037001 197 RCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPRCE 230 (284)
Q Consensus 197 ~CPRv~C~gq~lLPiGlSD~pg~stVKlYCP~C~ 230 (284)
.||| |. .++.=+.+. ++.--|||.|+
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 35678999997
No 39
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=20.98 E-value=27 Score=32.88 Aligned_cols=34 Identities=29% Similarity=0.601 Sum_probs=23.7
Q ss_pred ccCCCCCc-cccccCCCCCCccceeecCCCCcccc
Q 037001 201 VYCCGQPC-LPVGQSDIPRSSTVKIYCPRCEDIYY 234 (284)
Q Consensus 201 v~C~gq~l-LPiGlSD~pg~stVKlYCP~C~DVY~ 234 (284)
--|.||++ ||.+........-=-+|||.|.-|-+
T Consensus 198 ~~C~GC~m~l~~~~~~~V~~~d~iv~CP~CgRILy 232 (239)
T COG1579 198 RVCGGCHMKLPSQTLSKVRKKDEIVFCPYCGRILY 232 (239)
T ss_pred CcccCCeeeecHHHHHHHhcCCCCccCCccchHHH
Confidence 35777774 78876655555555689999987643
No 40
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=20.68 E-value=61 Score=31.22 Aligned_cols=41 Identities=29% Similarity=0.694 Sum_probs=26.6
Q ss_pred hhccCccCC---CCcccCCCC-Cccc-cccCCCCCCccceeecCCCCcc
Q 037001 189 KYKNYDFGR---CPRVYCCGQ-PCLP-VGQSDIPRSSTVKIYCPRCEDI 232 (284)
Q Consensus 189 KY~~g~FG~---CPRv~C~gq-~lLP-iGlSD~pg~stVKlYCP~C~DV 232 (284)
..++.-||. |-...|+.. -=|| |||..-|+ -+.|||-|++.
T Consensus 225 fCqqvSyGqMVaCDn~nCkrEWFH~~CVGLk~pPK---G~WYC~eCk~~ 270 (271)
T COG5034 225 FCQQVSYGQMVACDNANCKREWFHLECVGLKEPPK---GKWYCPECKKA 270 (271)
T ss_pred EecccccccceecCCCCCchhheeccccccCCCCC---CcEeCHHhHhc
Confidence 368889994 444444431 1145 48887663 58999999874
No 41
>PF14774 FAM177: FAM177 family
Probab=20.58 E-value=29 Score=29.58 Aligned_cols=48 Identities=23% Similarity=0.611 Sum_probs=30.8
Q ss_pred CCCCCchHHHHh---CCCCCeeEEecCcccccCCC-ccCCCCCCCCCHHHHHHHHc
Q 037001 92 EGDDTSWISWFC---NLRGNEFFCEVDDDYIQDDF-NLCGLSGQVPYYDYALDLIL 143 (284)
Q Consensus 92 ~~e~~sWI~wFc---sl~gneffceVDedYI~D~F-NL~GL~~~Vp~Y~~AL~~IL 143 (284)
+....+|..|+- ..-|+..|.-+ ||+-..| ++.||.. |.|+.||+-.-
T Consensus 56 dp~~l~w~~~~~~~~~~~~~~~l~~~--d~~Ge~lA~~fGit~--~KYqy~idey~ 107 (123)
T PF14774_consen 56 DPSKLTWGPWLWFWAWRVGTKSLSGC--DYLGEKLASFFGITS--PKYQYAIDEYY 107 (123)
T ss_pred CcccCCcHHHHHHHHHHHHHhHhhHH--hhhhhHHHHHhCCCc--hHHHHHHHHHH
Confidence 445568998774 22445444333 5666655 5779977 89999997543
No 42
>COG5252 Uncharacterized conserved protein, contains CCCH-type Zn-finger protein [General function prediction only]
Probab=20.06 E-value=76 Score=30.57 Aligned_cols=40 Identities=23% Similarity=0.399 Sum_probs=36.5
Q ss_pred ceeeChHHHHHHHHhhccCccC---CCCcc--cCCCCCccccccC
Q 037001 175 RYILTTKGMAAMLDKYKNYDFG---RCPRV--YCCGQPCLPVGQS 214 (284)
Q Consensus 175 RYIlT~~GL~~M~eKY~~g~FG---~CPRv--~C~gq~lLPiGlS 214 (284)
-+|-|.+=++-..+-..+|.|| .||+- .|-.-+-||.|..
T Consensus 136 P~intd~VCkffieA~e~GkYgw~W~CPng~~~C~y~H~Lp~GyV 180 (299)
T COG5252 136 PWINTDRVCKFFIEAMESGKYGWGWTCPNGNMRCSYIHKLPDGYV 180 (299)
T ss_pred CCCChhHHHHHHHHHHhcCCccceeeCCCCCceeeeeeccCccce
Confidence 7888999999999999999999 89998 8999999999863
Done!