Query 025330
Match_columns 254
No_of_seqs 137 out of 337
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 04:45:32 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025330.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025330hhsearch_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 1.3E-75 2.9E-80 513.0 13.0 156 95-250 2-157 (216)
2 PTZ00396 Casein kinase II subu 100.0 8E-71 1.7E-75 497.6 14.2 154 97-250 18-171 (251)
3 PF01214 CK_II_beta: Casein ki 100.0 2.3E-70 5E-75 475.0 8.1 150 101-250 1-150 (184)
4 COG5041 SKB2 Casein kinase II, 100.0 5.9E-66 1.3E-70 455.9 8.9 149 100-250 24-172 (242)
5 PF01927 Mut7-C: Mut7-C RNAse 78.3 2.2 4.7E-05 35.7 3.1 43 196-241 88-138 (147)
6 PF15235 GRIN_C: G protein-reg 68.2 3.9 8.5E-05 35.1 2.2 24 11-34 55-78 (137)
7 COG1656 Uncharacterized conser 65.0 6 0.00013 34.9 2.8 63 176-241 66-144 (165)
8 PRK05978 hypothetical protein; 59.6 6.1 0.00013 34.1 1.9 42 190-240 24-65 (148)
9 smart00647 IBR In Between Ring 57.3 19 0.00041 24.8 3.8 22 190-211 7-30 (64)
10 PF14205 Cys_rich_KTR: Cystein 52.7 6 0.00013 29.3 0.6 11 225-235 26-36 (55)
11 PRK00432 30S ribosomal protein 46.7 8.3 0.00018 27.4 0.5 9 227-235 20-28 (50)
12 PF06827 zf-FPG_IleRS: Zinc fi 46.1 8.9 0.00019 23.9 0.6 10 227-236 21-30 (30)
13 PF08772 NOB1_Zn_bind: Nin one 45.1 8.4 0.00018 29.7 0.4 12 224-235 21-32 (73)
14 PF05191 ADK_lid: Adenylate ki 44.2 15 0.00033 24.5 1.5 15 227-241 1-15 (36)
15 TIGR02098 MJ0042_CXXC MJ0042 f 42.2 11 0.00025 24.3 0.6 29 207-238 8-36 (38)
16 KOG4684 Uncharacterized conser 41.9 24 0.00052 33.0 2.9 38 201-238 140-181 (275)
17 PF06677 Auto_anti-p27: Sjogre 39.8 21 0.00046 24.6 1.7 23 201-234 19-41 (41)
18 COG2888 Predicted Zn-ribbon RN 39.5 19 0.00041 27.2 1.5 17 220-236 20-36 (61)
19 KOG1973 Chromatin remodeling p 39.2 16 0.00035 33.8 1.4 39 194-235 227-267 (274)
20 PF11238 DUF3039: Protein of u 37.8 7.6 0.00016 29.0 -0.8 28 204-238 28-55 (58)
21 PF03811 Zn_Tnp_IS1: InsA N-te 36.7 20 0.00043 24.1 1.1 12 224-235 2-13 (36)
22 PF01485 IBR: IBR domain; Int 35.4 53 0.0012 22.5 3.2 43 197-239 16-60 (64)
23 PF13717 zinc_ribbon_4: zinc-r 35.0 22 0.00048 23.5 1.2 16 226-241 1-16 (36)
24 PF10601 zf-LITAF-like: LITAF- 33.4 28 0.00061 25.7 1.6 17 222-238 2-18 (73)
25 PF13719 zinc_ribbon_5: zinc-r 31.6 22 0.00049 23.4 0.7 29 207-238 8-36 (37)
26 PF11335 DUF3137: Protein of u 31.2 22 0.00048 29.2 0.8 18 175-192 62-79 (142)
27 PF02150 RNA_POL_M_15KD: RNA p 31.0 15 0.00032 24.3 -0.2 15 228-242 2-16 (35)
28 COG1631 RPL42A Ribosomal prote 30.9 21 0.00046 29.0 0.7 12 224-235 5-16 (94)
29 COG0401 Uncharacterized homolo 30.1 15 0.00032 27.3 -0.3 13 172-184 43-55 (56)
30 COG4098 comFA Superfamily II D 29.7 22 0.00047 35.5 0.6 13 212-234 55-67 (441)
31 COG4416 Com Mu-like prophage p 29.7 25 0.00054 26.3 0.8 19 220-238 17-35 (60)
32 smart00661 RPOL9 RNA polymeras 29.6 26 0.00056 23.8 0.8 13 229-241 2-14 (52)
33 PRK01103 formamidopyrimidine/5 29.1 36 0.00078 31.3 1.9 12 224-235 262-273 (274)
34 PF09788 Tmemb_55A: Transmembr 27.3 55 0.0012 30.9 2.8 38 201-238 125-168 (256)
35 PRK14810 formamidopyrimidine-D 27.1 37 0.0008 31.3 1.6 26 201-234 246-271 (272)
36 PF03966 Trm112p: Trm112p-like 26.6 30 0.00066 25.3 0.8 14 225-238 51-64 (68)
37 COG1545 Predicted nucleic-acid 26.5 39 0.00085 28.4 1.5 19 226-244 28-46 (140)
38 PRK00420 hypothetical protein; 26.2 43 0.00092 27.8 1.7 31 200-241 24-54 (112)
39 KOG2828 Acetyl-CoA hydrolase [ 26.0 24 0.00052 35.4 0.2 16 176-191 401-416 (454)
40 COG5034 TNG2 Chromatin remodel 25.7 42 0.00092 31.8 1.7 41 193-236 225-270 (271)
41 PF00471 Ribosomal_L33: Riboso 23.8 52 0.0011 23.3 1.5 16 220-235 25-40 (48)
42 COG1579 Zn-ribbon protein, pos 23.7 22 0.00047 33.0 -0.5 34 205-238 198-232 (239)
43 COG3809 Uncharacterized protei 23.2 35 0.00076 27.3 0.6 11 228-238 22-32 (88)
44 PRK14890 putative Zn-ribbon RN 23.0 55 0.0012 24.5 1.6 16 221-236 19-34 (59)
45 COG2816 NPY1 NTP pyrophosphohy 22.9 61 0.0013 30.9 2.2 41 190-242 104-144 (279)
46 COG5252 Uncharacterized conser 22.8 66 0.0014 30.6 2.4 39 179-217 136-179 (299)
47 PRK00504 rpmG 50S ribosomal pr 22.1 44 0.00094 24.0 0.9 16 220-235 27-42 (50)
48 PRK00241 nudC NADH pyrophospha 21.9 65 0.0014 29.6 2.2 34 198-241 98-131 (256)
49 PRK12495 hypothetical protein; 21.4 97 0.0021 28.8 3.1 15 225-239 56-70 (226)
50 PF06222 Phage_TAC: Phage tail 21.2 36 0.00077 29.1 0.3 33 143-181 79-111 (127)
51 PRK00595 rpmG 50S ribosomal pr 21.2 51 0.0011 23.8 1.1 16 220-235 30-45 (53)
52 PF08756 YfkB: YfkB-like domai 20.3 81 0.0018 27.7 2.3 30 185-214 102-136 (153)
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=1.3e-75 Score=512.99 Aligned_cols=156 Identities=71% Similarity=1.234 Sum_probs=149.6
Q ss_pred CCCCCCChHHHHhCCCCCeeEEecCcccccCCCccCCCCCCCCCHHHHHHHHcCCCCCCCCCCchHHHHHHHHHHHHHhh
Q 025330 95 SDGDDTSWISWFCNLRGNEFFCEVDDEYIQDDFNLCGLSSQVPYYDYALDLILDVESSHGDMFTEEQNELVESAAEMLYG 174 (254)
Q Consensus 95 s~~ed~sWI~wFcsl~gneffceVDedYI~D~FNL~GL~~~Vp~Y~~ALd~ILd~e~~~~d~~~~~~~~~ie~~A~~LYG 174 (254)
+++++.+||+|||+++|||||||||+|||+|+|||+||+.+||+|++||++|||+++.++.+..+++.++||++|++|||
T Consensus 2 s~see~sWI~wFc~~~GnEffceVdeeyIqD~FNltgL~~~Vp~y~~ald~ILD~~~~~~~e~~~~~~~~iE~aae~LYG 81 (216)
T KOG3092|consen 2 SSSEEVSWISWFCGLRGNEFFCEVDEEYIQDRFNLTGLSEQVPNYRQALDLILDLEPDDELEDNAEQSELIESAAEMLYG 81 (216)
T ss_pred CcccccchHHHHhcCCCCeeeEecCHHHhhhhhccccccccCchHHHHHHHhhcCCCCcccccchhHHHHHHHHHHHHHH
Confidence 34466679999999999999999999999999999999999999999999999999988777777778999999999999
Q ss_pred hccccceeChHHHHHHHHhhhcCCCCCCCcccCCCCCccccccCCCCCCccceeeCCCCCccccCCCCCCcCCccc
Q 025330 175 LIHVRYILTSKGMAAMLEKYKNYDFGRCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPKCEDIYYPRSKYQGSILKI 250 (254)
Q Consensus 175 LIHARYIlT~~GL~~M~eKY~~g~FG~CPRv~C~gq~lLPiGlSD~pg~stVKlYCP~C~DVY~P~s~~~~~IDG~ 250 (254)
|||||||||.+||++|++||++++||+||||+|++|+|||+||||+|++++||+|||+|+|||.|+|+++++|||+
T Consensus 82 LIHaRYIlT~~Gl~~M~eKy~~~dFG~CPRV~C~~q~~LPvGLsDipg~~~VklYCP~C~dvY~P~ssr~~~iDGa 157 (216)
T KOG3092|consen 82 LIHARYILTNRGLAAMLEKYKNGDFGRCPRVYCCGQPVLPVGLSDIPGKSTVKLYCPSCEDVYIPKSSRHGNIDGA 157 (216)
T ss_pred hhhheeeechHHHHHHHHHHhcCCCCcCCcccccCCccccccccCCCCcceEEEeCCCcccccccccccccccccc
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999996
No 2
>PTZ00396 Casein kinase II subunit beta; Provisional
Probab=100.00 E-value=8e-71 Score=497.64 Aligned_cols=154 Identities=48% Similarity=0.952 Sum_probs=145.2
Q ss_pred CCCCChHHHHhCCCCCeeEEecCcccccCCCccCCCCCCCCCHHHHHHHHcCCCCCCCCCCchHHHHHHHHHHHHHhhhc
Q 025330 97 GDDTSWISWFCNLRGNEFFCEVDDEYIQDDFNLCGLSSQVPYYDYALDLILDVESSHGDMFTEEQNELVESAAEMLYGLI 176 (254)
Q Consensus 97 ~ed~sWI~wFcsl~gneffceVDedYI~D~FNL~GL~~~Vp~Y~~ALd~ILd~e~~~~d~~~~~~~~~ie~~A~~LYGLI 176 (254)
.++.+||+|||+++||+|||+||+|||+|+||||||+.+||+|++||+||||.+++.+...+++....++++|++|||||
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 45679999999999999999999999999999999999999999999999999876654445566788999999999999
Q ss_pred cccceeChHHHHHHHHhhhcCCCCCCCcccCCCCCccccccCCCCCCccceeeCCCCCccccCCCCCCcCCccc
Q 025330 177 HVRYILTSKGMAAMLEKYKNYDFGRCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPKCEDIYYPRSKYQGSILKI 250 (254)
Q Consensus 177 HARYIlT~~GL~~M~eKY~~g~FG~CPRv~C~gq~lLPiGlSD~pg~stVKlYCP~C~DVY~P~s~~~~~IDG~ 250 (254)
|||||+|++||++|++||++|+||+||||+|++|+|||||+||+||+++||+|||+|+|||+|++.++..|||+
T Consensus 98 HARyI~T~~Gl~~M~eKY~~g~FG~CPRv~C~~q~~LPvGlSd~~g~~~VKlyCP~C~DvY~p~s~~~~~iDGA 171 (251)
T PTZ00396 98 HARFITTPKGLALMREKYLQGKFGHCPRVLCEGQNVLPIGLSDVLKTSRVKVYCPRCQEVYHPKKSSLLDIDGA 171 (251)
T ss_pred hHhHhcCHHHHHHHHHHhhCCCCCCCCCccCCCCcccccccCCCcCcCceeEeCCCchhhcCCCCccccccccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999887799996
No 3
>PF01214 CK_II_beta: Casein kinase II regulatory subunit; InterPro: IPR000704 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. Casein kinase, a ubiquitous, well-conserved protein kinase involved in cell metabolism and differentiation, is characterised by its preference for Ser or Thr in acidic stretches of amino acids. The enzyme is a tetramer of 2 alpha- and 2 beta-subunits [, ]. However, some species (e.g., mammals) possess 2 related forms of the alpha-subunit (alpha and alpha'), while others (e.g., fungi) possess 2 related beta-subunits (beta and beta') []. The alpha-subunit is the catalytic unit and contains regions characteristic of serine/threonine protein kinases. The beta-subunit is believed to be regulatory, possessing an N-terminal auto-phosphorylation site, an internal acidic domain, and a potential metal-binding motif []. The beta subunit is a highly conserved protein of about 25kDa that contains, in its central section, a cysteine-rich motif, CX(n)C, that could be involved in binding a metal such as zinc []. The mammalian beta-subunit gene promoter shares common features with those of other mammalian protein kinases and is closely related to the promoter of the regulatory subunit of cAMP-dependent protein kinase [].; GO: 0019887 protein kinase regulator activity, 0005956 protein kinase CK2 complex; PDB: 2R6M_B 1RQF_K 1DS5_G 1QF8_B 3EED_A 4DGL_A 1JWH_D.
Probab=100.00 E-value=2.3e-70 Score=474.98 Aligned_cols=150 Identities=61% Similarity=1.151 Sum_probs=126.9
Q ss_pred ChHHHHhCCCCCeeEEecCcccccCCCccCCCCCCCCCHHHHHHHHcCCCCCCCCCCchHHHHHHHHHHHHHhhhccccc
Q 025330 101 SWISWFCNLRGNEFFCEVDDEYIQDDFNLCGLSSQVPYYDYALDLILDVESSHGDMFTEEQNELVESAAEMLYGLIHVRY 180 (254)
Q Consensus 101 sWI~wFcsl~gneffceVDedYI~D~FNL~GL~~~Vp~Y~~ALd~ILd~e~~~~d~~~~~~~~~ie~~A~~LYGLIHARY 180 (254)
+||+|||+++||+||||||+|||+|+|||+||+.+||+|++||++|||.+.+.++..++.+.+.++++|++|||||||||
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 69999999999999999999999999999999999999999999999998776555666678889999999999999999
Q ss_pred eeChHHHHHHHHhhhcCCCCCCCcccCCCCCccccccCCCCCCccceeeCCCCCccccCCCCCCcCCccc
Q 025330 181 ILTSKGMAAMLEKYKNYDFGRCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPKCEDIYYPRSKYQGSILKI 250 (254)
Q Consensus 181 IlT~~GL~~M~eKY~~g~FG~CPRv~C~gq~lLPiGlSD~pg~stVKlYCP~C~DVY~P~s~~~~~IDG~ 250 (254)
|+|++||++|++||++|+||+||||+|++|+|||||+||+||+++||||||+|+|||+|++.++..|||+
T Consensus 81 I~T~~Gl~~m~eKy~~g~FG~CPRv~C~~~~lLPiGlsd~~g~~~vKlyCP~C~dvY~p~~~~~~~iDGA 150 (184)
T PF01214_consen 81 ILTPRGLEQMKEKYEQGDFGRCPRVYCNGQPLLPIGLSDTPGESTVKLYCPRCKDVYHPPSSRHSNIDGA 150 (184)
T ss_dssp TTSHHHHHHHHHHHHTTTT-B-SBGGGTT-B-EEEBS-SSTTS-BBEEEETTTTEEE--SSGGGTTSBGG
T ss_pred hhcHHHHHHHHHhhcCCcCCcCCcccCCCCceeCccCCCCCCccceeEECCCCccccCCCCccccceecc
Confidence 9999999999999999999999999999999999999999999999999999999999988999999997
No 4
>COG5041 SKB2 Casein kinase II, beta subunit [Signal transduction mechanisms / Cell division and chromosome partitioning / Transcription]
Probab=100.00 E-value=5.9e-66 Score=455.86 Aligned_cols=149 Identities=55% Similarity=1.077 Sum_probs=140.5
Q ss_pred CChHHHHhCCCCCeeEEecCcccccCCCccCCCCCCCCCHHHHHHHHcCCCCCCCCCCchHHHHHHHHHHHHHhhhcccc
Q 025330 100 TSWISWFCNLRGNEFFCEVDDEYIQDDFNLCGLSSQVPYYDYALDLILDVESSHGDMFTEEQNELVESAAEMLYGLIHVR 179 (254)
Q Consensus 100 ~sWI~wFcsl~gneffceVDedYI~D~FNL~GL~~~Vp~Y~~ALd~ILd~e~~~~d~~~~~~~~~ie~~A~~LYGLIHAR 179 (254)
..||+|||+++||||||+||++||+|.|||+||+..||+|.+||++|||...+. .+.+.+-+.||.+|+.||||||||
T Consensus 24 ~~Wi~~F~~rkg~eyfc~V~~efIeDrFNltgL~~~Vp~y~~~ldlILD~~~~~--~~e~~~~d~iE~sa~~LYgLIHaR 101 (242)
T COG5041 24 DEWIDWFCSRKGNEYFCEVPEEFIEDRFNLTGLSREVPHYSEVLDLILDKLAPS--NLENDEVDIIEESARQLYGLIHAR 101 (242)
T ss_pred HHHHHHHHcCCCCeeeeeCCHHHHHhhhhccchhhccchHHHHHHHHHhccCCc--chhhhhhHHHHHHHHHHHHHHHhh
Confidence 379999999999999999999999999999999999999999999999987543 233334578999999999999999
Q ss_pred ceeChHHHHHHHHhhhcCCCCCCCcccCCCCCccccccCCCCCCccceeeCCCCCccccCCCCCCcCCccc
Q 025330 180 YILTSKGMAAMLEKYKNYDFGRCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPKCEDIYYPRSKYQGSILKI 250 (254)
Q Consensus 180 YIlT~~GL~~M~eKY~~g~FG~CPRv~C~gq~lLPiGlSD~pg~stVKlYCP~C~DVY~P~s~~~~~IDG~ 250 (254)
||+|..||++|++||+.++||+||||+||+|+|||+||||+||+++||||||+|.|||.|+|+++..|||.
T Consensus 102 yIiT~~GL~~m~eKy~~~efG~CPRv~Cn~~~vLPvGLsDi~g~~~vkLyCpsC~dlY~p~Ssr~~~iDGa 172 (242)
T COG5041 102 YIITKSGLQAMLEKYKSREFGACPRVYCNGQQVLPVGLSDIPGKSSVKLYCPSCEDLYLPKSSRHQSIDGA 172 (242)
T ss_pred heeeHHHHHHHHHHHhhcccCCCCcccccCcceeccccccCCCCceeEEecCchhhhcCcccccccccccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999996
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=78.30 E-value=2.2 Score=35.73 Aligned_cols=43 Identities=35% Similarity=0.806 Sum_probs=29.2
Q ss_pred cCCCCCCCcccCCCCCccccccCCCCC--------CccceeeCCCCCccccCCC
Q 025330 196 NYDFGRCPRVYCCGQPCLPVGQSDIPR--------SSTVKIYCPKCEDIYYPRS 241 (254)
Q Consensus 196 ~g~FG~CPRv~C~gq~lLPiGlSD~pg--------~stVKlYCP~C~DVY~P~s 241 (254)
+..|-+||. ||+ ++.|+...++.+ ....=..||.|+.||=+=+
T Consensus 88 ~~~~sRC~~--CN~-~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiyW~Gs 138 (147)
T PF01927_consen 88 DPIFSRCPK--CNG-PLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIYWEGS 138 (147)
T ss_pred CCCCCccCC--CCc-EeeechhhccccccCccccccCCeEEECCCCCCEecccc
Confidence 445899986 655 788886654422 2233567999999997643
No 6
>PF15235 GRIN_C: G protein-regulated inducer of neurite outgrowth C-terminus
Probab=68.19 E-value=3.9 Score=35.13 Aligned_cols=24 Identities=29% Similarity=0.479 Sum_probs=21.8
Q ss_pred ccccccCccchhhhhHHHHhhhhc
Q 025330 11 KSEIVAGPLDRKRINDALDKHLEK 34 (254)
Q Consensus 11 ~~~~~~~~~~~~~~~~~~~~~~~~ 34 (254)
-=||+|.++|-.-+..|+.||||+
T Consensus 55 TWEVYGAs~DpEvLG~AIQkHLE~ 78 (137)
T PF15235_consen 55 TWEVYGASVDPEVLGMAIQKHLER 78 (137)
T ss_pred eEEEeccccCHHHHHHHHHHHHHH
Confidence 347999999999999999999997
No 7
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=64.99 E-value=6 Score=34.92 Aligned_cols=63 Identities=29% Similarity=0.495 Sum_probs=43.0
Q ss_pred ccccceeChHHHHHHHHh---hh-----cCCCCCCCcccCCCCCccccccCC--------CCCCccceeeCCCCCccccC
Q 025330 176 IHVRYILTSKGMAAMLEK---YK-----NYDFGRCPRVYCCGQPCLPVGQSD--------IPRSSTVKIYCPKCEDIYYP 239 (254)
Q Consensus 176 IHARYIlT~~GL~~M~eK---Y~-----~g~FG~CPRv~C~gq~lLPiGlSD--------~pg~stVKlYCP~C~DVY~P 239 (254)
+++=||.+..=..+|.+= +. .-.|-+||. ||+ +++++--.. +.+....-..||+|..+|=|
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 334889994 755 588886655 22344444559999999977
Q ss_pred CC
Q 025330 240 RS 241 (254)
Q Consensus 240 ~s 241 (254)
-+
T Consensus 143 Gs 144 (165)
T COG1656 143 GS 144 (165)
T ss_pred ch
Confidence 54
No 8
>PRK05978 hypothetical protein; Provisional
Probab=59.56 E-value=6.1 Score=34.12 Aligned_cols=42 Identities=17% Similarity=0.219 Sum_probs=33.4
Q ss_pred HHHhhhcCCCCCCCcccCCCCCccccccCCCCCCccceeeCCCCCccccCC
Q 025330 190 MLEKYKNYDFGRCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPKCEDIYYPR 240 (254)
Q Consensus 190 M~eKY~~g~FG~CPRv~C~gq~lLPiGlSD~pg~stVKlYCP~C~DVY~P~ 240 (254)
+..-..+|-.|+||| |..-+++= +--+|.-.||.|..-|.+.
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 445678899999997 77777762 5667888999999999864
No 9
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=57.26 E-value=19 Score=24.83 Aligned_cols=22 Identities=32% Similarity=0.631 Sum_probs=14.4
Q ss_pred HHHhhhc--CCCCCCCcccCCCCC
Q 025330 190 MLEKYKN--YDFGRCPRVYCCGQP 211 (254)
Q Consensus 190 M~eKY~~--g~FG~CPRv~C~gq~ 211 (254)
+.++|.. ..+-.||+..|...-
T Consensus 7 ~~~~~i~~~~~~~~CP~~~C~~~~ 30 (64)
T smart00647 7 LLESYVESNPDLKWCPAPDCSAAI 30 (64)
T ss_pred HHHHHHhcCCCccCCCCCCCcceE
Confidence 3444533 467789999996543
No 10
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=52.66 E-value=6 Score=29.26 Aligned_cols=11 Identities=45% Similarity=1.407 Sum_probs=8.8
Q ss_pred cceeeCCCCCc
Q 025330 225 TVKIYCPKCED 235 (254)
Q Consensus 225 tVKlYCP~C~D 235 (254)
..-||||+|+.
T Consensus 26 NfPlyCpKCK~ 36 (55)
T PF14205_consen 26 NFPLYCPKCKQ 36 (55)
T ss_pred cccccCCCCCc
Confidence 44699999985
No 11
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=46.71 E-value=8.3 Score=27.45 Aligned_cols=9 Identities=33% Similarity=1.361 Sum_probs=4.3
Q ss_pred eeeCCCCCc
Q 025330 227 KIYCPKCED 235 (254)
Q Consensus 227 KlYCP~C~D 235 (254)
+.|||+|..
T Consensus 20 ~~fCP~Cg~ 28 (50)
T PRK00432 20 NKFCPRCGS 28 (50)
T ss_pred cCcCcCCCc
Confidence 335555544
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=46.11 E-value=8.9 Score=23.90 Aligned_cols=10 Identities=30% Similarity=1.265 Sum_probs=7.0
Q ss_pred eeeCCCCCcc
Q 025330 227 KIYCPKCEDI 236 (254)
Q Consensus 227 KlYCP~C~DV 236 (254)
--|||+|.+|
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
>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=45.13 E-value=8.4 Score=29.68 Aligned_cols=12 Identities=42% Similarity=1.151 Sum_probs=5.5
Q ss_pred ccceeeCCCCCc
Q 025330 224 STVKIYCPKCED 235 (254)
Q Consensus 224 stVKlYCP~C~D 235 (254)
.+-|.|||+|.-
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 577999999974
No 14
>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=44.22 E-value=15 Score=24.45 Aligned_cols=15 Identities=40% Similarity=0.820 Sum_probs=11.9
Q ss_pred eeeCCCCCccccCCC
Q 025330 227 KIYCPKCEDIYYPRS 241 (254)
Q Consensus 227 KlYCP~C~DVY~P~s 241 (254)
+..||.|..+|+...
T Consensus 1 Rr~C~~Cg~~Yh~~~ 15 (36)
T PF05191_consen 1 RRICPKCGRIYHIEF 15 (36)
T ss_dssp EEEETTTTEEEETTT
T ss_pred CcCcCCCCCcccccc
Confidence 357999999998643
No 15
>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=42.24 E-value=11 Score=24.33 Aligned_cols=29 Identities=24% Similarity=0.461 Sum_probs=18.0
Q ss_pred CCCCCccccccCCCCCCccceeeCCCCCcccc
Q 025330 207 CCGQPCLPVGQSDIPRSSTVKIYCPKCEDIYY 238 (254)
Q Consensus 207 C~gq~lLPiGlSD~pg~stVKlYCP~C~DVY~ 238 (254)
|..+.-+|-.. ......++.||+|+..+.
T Consensus 8 C~~~~~v~~~~---~~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 8 CKTSFRVVDSQ---LGANGGKVRCGKCGHVWY 36 (38)
T ss_pred CCCEEEeCHHH---cCCCCCEEECCCCCCEEE
Confidence 65555566433 223445888999987663
No 16
>KOG4684 consensus Uncharacterized conserved protein, contains C4-type Zn-finger [General function prediction only]
Probab=41.90 E-value=24 Score=33.02 Aligned_cols=38 Identities=18% Similarity=0.543 Sum_probs=25.3
Q ss_pred CCCcccCCCC----CccccccCCCCCCccceeeCCCCCcccc
Q 025330 201 RCPRVYCCGQ----PCLPVGQSDIPRSSTVKIYCPKCEDIYY 238 (254)
Q Consensus 201 ~CPRv~C~gq----~lLPiGlSD~pg~stVKlYCP~C~DVY~ 238 (254)
-|||-+|++- ++.|--++..+.-..+++-|-.|+++|.
T Consensus 140 ACPRpnCkRiInL~p~~~~p~~P~~~P~gcRV~CgHC~~tFL 181 (275)
T KOG4684|consen 140 ACPRPNCKRIINLDPLIEKPRDPGTAPTGCRVKCGHCNETFL 181 (275)
T ss_pred ccCCCCcceeeecCCCCCCCCCCCCCCcceEEEecCccceee
Confidence 5999999863 2333333333333558999999999884
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=39.80 E-value=21 Score=24.58 Aligned_cols=23 Identities=48% Similarity=1.292 Sum_probs=15.7
Q ss_pred CCCcccCCCCCccccccCCCCCCccceeeCCCCC
Q 025330 201 RCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPKCE 234 (254)
Q Consensus 201 ~CPRv~C~gq~lLPiGlSD~pg~stVKlYCP~C~ 234 (254)
.||. | +.|++. + +.. ++|||.|.
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 7994 7 777775 2 222 57999995
No 18
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=39.49 E-value=19 Score=27.19 Aligned_cols=17 Identities=35% Similarity=0.960 Sum_probs=14.5
Q ss_pred CCCCccceeeCCCCCcc
Q 025330 220 IPRSSTVKIYCPKCEDI 236 (254)
Q Consensus 220 ~pg~stVKlYCP~C~DV 236 (254)
.|++..|+..||+|.++
T Consensus 20 ~p~e~~v~F~CPnCGe~ 36 (61)
T COG2888 20 APGETAVKFPCPNCGEV 36 (61)
T ss_pred ccCCceeEeeCCCCCce
Confidence 37889999999999954
No 19
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=39.20 E-value=16 Score=33.82 Aligned_cols=39 Identities=23% Similarity=0.469 Sum_probs=28.6
Q ss_pred hhcCCCCCCCcccCC-CCCccc-cccCCCCCCccceeeCCCCCc
Q 025330 194 YKNYDFGRCPRVYCC-GQPCLP-VGQSDIPRSSTVKIYCPKCED 235 (254)
Q Consensus 194 Y~~g~FG~CPRv~C~-gq~lLP-iGlSD~pg~stVKlYCP~C~D 235 (254)
-.-|.++-|=+..|. .-.=+| |||...|.-. .|||+|..
T Consensus 227 vsyg~Mi~CDn~~C~~eWFH~~CVGL~~~Pkgk---WyC~~C~~ 267 (274)
T KOG1973|consen 227 VSYGKMIGCDNPGCPIEWFHFTCVGLKTKPKGK---WYCPRCKA 267 (274)
T ss_pred cccccccccCCCCCCcceEEEeccccccCCCCc---ccchhhhh
Confidence 345778888888887 444455 4999777443 99999975
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=37.81 E-value=7.6 Score=29.01 Aligned_cols=28 Identities=36% Similarity=0.968 Sum_probs=17.2
Q ss_pred cccCCCCCccccccCCCCCCccceeeCCCCCcccc
Q 025330 204 RVYCCGQPCLPVGQSDIPRSSTVKIYCPKCEDIYY 238 (254)
Q Consensus 204 Rv~C~gq~lLPiGlSD~pg~stVKlYCP~C~DVY~ 238 (254)
+.+| |.-..| +.+ |...+| ||.|++||.
T Consensus 28 vALC-Gk~wvp-~rd--p~~~PV---CP~Ck~iye 55 (58)
T PF11238_consen 28 VALC-GKVWVP-TRD--PKPFPV---CPECKEIYE 55 (58)
T ss_pred Eeee-CceeCC-CCC--CCCCCC---CcCHHHHHH
Confidence 5677 443444 333 333444 999999995
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=36.74 E-value=20 Score=24.05 Aligned_cols=12 Identities=25% Similarity=1.143 Sum_probs=10.2
Q ss_pred ccceeeCCCCCc
Q 025330 224 STVKIYCPKCED 235 (254)
Q Consensus 224 stVKlYCP~C~D 235 (254)
.+|.+.||+|..
T Consensus 2 a~i~v~CP~C~s 13 (36)
T PF03811_consen 2 AKIDVHCPRCQS 13 (36)
T ss_pred CcEeeeCCCCCC
Confidence 478999999985
No 22
>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=35.43 E-value=53 Score=22.45 Aligned_cols=43 Identities=19% Similarity=0.226 Sum_probs=18.5
Q ss_pred CCCCCCCcccCCCCCccccccCCC--CCCccceeeCCCCCccccC
Q 025330 197 YDFGRCPRVYCCGQPCLPVGQSDI--PRSSTVKIYCPKCEDIYYP 239 (254)
Q Consensus 197 g~FG~CPRv~C~gq~lLPiGlSD~--pg~stVKlYCP~C~DVY~P 239 (254)
..+-.||+..|...-..+-+.... -=..-=..||..|..-+|+
T Consensus 16 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~ 60 (64)
T PF01485_consen 16 PNIRWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPWHE 60 (64)
T ss_dssp --CC--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSESCT
T ss_pred CCccCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCcccCC
Confidence 344599999997654333333321 1111225667777776665
No 23
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=35.03 E-value=22 Score=23.46 Aligned_cols=16 Identities=31% Similarity=0.729 Sum_probs=12.8
Q ss_pred ceeeCCCCCccccCCC
Q 025330 226 VKIYCPKCEDIYYPRS 241 (254)
Q Consensus 226 VKlYCP~C~DVY~P~s 241 (254)
+++-||+|+-.|.-+.
T Consensus 1 M~i~Cp~C~~~y~i~d 16 (36)
T PF13717_consen 1 MIITCPNCQAKYEIDD 16 (36)
T ss_pred CEEECCCCCCEEeCCH
Confidence 4788999999997543
No 24
>PF10601 zf-LITAF-like: LITAF-like zinc ribbon domain; InterPro: IPR006629 Members of this family display a conserved zinc ribbon structure [] with the motif C-XX-C- separated from the more C-terminal HX-C(P)X-C-X4-G-R motif by a variable region of usually 25-30 (hydrophobic) residues. Although it belongs to one of the zinc finger's fold groups (zinc ribbon), this particular domain was first identified in LPS-induced tumour necrosis alpha factor (LITAF) which is produced in mammalian cells after being challenged with lipopolysaccharide (LPS). The hydrophobic region probably inserts into the membrane rather than traversing it. Such an insertion brings together the N- and C-terminal C-XX-C motifs to form a compact Zn2+-binding structure [].
Probab=33.43 E-value=28 Score=25.69 Aligned_cols=17 Identities=35% Similarity=0.862 Sum_probs=13.7
Q ss_pred CCccceeeCCCCCcccc
Q 025330 222 RSSTVKIYCPKCEDIYY 238 (254)
Q Consensus 222 g~stVKlYCP~C~DVY~ 238 (254)
+..++.++||.|+..=.
T Consensus 2 ~~~p~~~~CP~C~~~~~ 18 (73)
T PF10601_consen 2 GPEPVRIYCPYCQQQVQ 18 (73)
T ss_pred CCCceeeECCCCCCEEE
Confidence 56789999999997543
No 25
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=31.58 E-value=22 Score=23.45 Aligned_cols=29 Identities=28% Similarity=0.599 Sum_probs=19.7
Q ss_pred CCCCCccccccCCCCCCccceeeCCCCCcccc
Q 025330 207 CCGQPCLPVGQSDIPRSSTVKIYCPKCEDIYY 238 (254)
Q Consensus 207 C~gq~lLPiGlSD~pg~stVKlYCP~C~DVY~ 238 (254)
|....-||- +.......++-||+|+.++.
T Consensus 8 C~~~f~v~~---~~l~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 8 CQTRFRVPD---DKLPAGGRKVRCPKCGHVFR 36 (37)
T ss_pred CCceEEcCH---HHcccCCcEEECCCCCcEee
Confidence 555555543 23446777999999998874
No 26
>PF11335 DUF3137: Protein of unknown function (DUF3137) ; InterPro: IPR021484 This bacterial family of proteins has no known function.
Probab=31.18 E-value=22 Score=29.18 Aligned_cols=18 Identities=44% Similarity=0.637 Sum_probs=14.4
Q ss_pred hccccceeChHHHHHHHH
Q 025330 175 LIHVRYILTSKGMAAMLE 192 (254)
Q Consensus 175 LIHARYIlT~~GL~~M~e 192 (254)
.+.|||||||.=|+.+.+
T Consensus 62 ~~~AryiLtP~~mE~L~~ 79 (142)
T PF11335_consen 62 QVEARYILTPSFMERLLE 79 (142)
T ss_pred HHHHHHhCCHHHHHHHHH
Confidence 456799999999887754
No 27
>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=31.03 E-value=15 Score=24.29 Aligned_cols=15 Identities=33% Similarity=1.276 Sum_probs=12.0
Q ss_pred eeCCCCCccccCCCC
Q 025330 228 IYCPKCEDIYYPRSK 242 (254)
Q Consensus 228 lYCP~C~DVY~P~s~ 242 (254)
.|||.|..+-.|+..
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 599999999988653
No 28
>COG1631 RPL42A Ribosomal protein L44E [Translation, ribosomal structure and biogenesis]
Probab=30.93 E-value=21 Score=28.97 Aligned_cols=12 Identities=33% Similarity=1.063 Sum_probs=9.9
Q ss_pred ccceeeCCCCCc
Q 025330 224 STVKIYCPKCED 235 (254)
Q Consensus 224 stVKlYCP~C~D 235 (254)
-+++.|||.|..
T Consensus 5 K~~~tyCp~Ckk 16 (94)
T COG1631 5 KKRRTYCPYCKK 16 (94)
T ss_pred cceeecCccccc
Confidence 368899999975
No 29
>COG0401 Uncharacterized homolog of Blt101 [Function unknown]
Probab=30.06 E-value=15 Score=27.33 Aligned_cols=13 Identities=31% Similarity=0.749 Sum_probs=11.0
Q ss_pred HhhhccccceeCh
Q 025330 172 LYGLIHVRYILTS 184 (254)
Q Consensus 172 LYGLIHARYIlT~ 184 (254)
+=|+|||=||++.
T Consensus 43 ~PGiiHA~yvi~~ 55 (56)
T COG0401 43 IPGIIHALYVILR 55 (56)
T ss_pred hhhhHhheEEEEe
Confidence 5589999999874
No 30
>COG4098 comFA Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [DNA replication, recombination, and repair]
Probab=29.75 E-value=22 Score=35.54 Aligned_cols=13 Identities=46% Similarity=1.109 Sum_probs=10.5
Q ss_pred ccccccCCCCCCccceeeCCCCC
Q 025330 212 CLPVGQSDIPRSSTVKIYCPKCE 234 (254)
Q Consensus 212 lLPiGlSD~pg~stVKlYCP~C~ 234 (254)
-||+| ++||++|-
T Consensus 55 ~lp~~----------~~YCr~Cl 67 (441)
T COG4098 55 KLPCG----------CLYCRNCL 67 (441)
T ss_pred ccccc----------eEeehhhh
Confidence 57777 89999884
No 31
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=29.73 E-value=25 Score=26.28 Aligned_cols=19 Identities=16% Similarity=0.564 Sum_probs=14.1
Q ss_pred CCCCccceeeCCCCCcccc
Q 025330 220 IPRSSTVKIYCPKCEDIYY 238 (254)
Q Consensus 220 ~pg~stVKlYCP~C~DVY~ 238 (254)
.-++.-+++-||+|+.|-.
T Consensus 17 a~~~~yle~KCPrCK~vN~ 35 (60)
T COG4416 17 AEGQAYLEKKCPRCKEVNE 35 (60)
T ss_pred cccceeeeecCCccceeee
Confidence 3456678899999988743
No 32
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=29.55 E-value=26 Score=23.75 Aligned_cols=13 Identities=38% Similarity=1.346 Sum_probs=10.5
Q ss_pred eCCCCCccccCCC
Q 025330 229 YCPKCEDIYYPRS 241 (254)
Q Consensus 229 YCP~C~DVY~P~s 241 (254)
|||.|..+-.|+.
T Consensus 2 FCp~Cg~~l~~~~ 14 (52)
T smart00661 2 FCPKCGNMLIPKE 14 (52)
T ss_pred CCCCCCCcccccc
Confidence 8999988887763
No 33
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=29.06 E-value=36 Score=31.27 Aligned_cols=12 Identities=25% Similarity=1.135 Sum_probs=9.3
Q ss_pred ccceeeCCCCCc
Q 025330 224 STVKIYCPKCED 235 (254)
Q Consensus 224 stVKlYCP~C~D 235 (254)
++.--|||.|+.
T Consensus 262 gR~t~~CP~CQ~ 273 (274)
T PRK01103 262 GRSTFFCPRCQK 273 (274)
T ss_pred CCCcEECcCCCC
Confidence 356689999984
No 34
>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=27.33 E-value=55 Score=30.90 Aligned_cols=38 Identities=24% Similarity=0.615 Sum_probs=24.8
Q ss_pred CCCcccCCCCCcc-cc--ccC-CCC--CCccceeeCCCCCcccc
Q 025330 201 RCPRVYCCGQPCL-PV--GQS-DIP--RSSTVKIYCPKCEDIYY 238 (254)
Q Consensus 201 ~CPRv~C~gq~lL-Pi--GlS-D~p--g~stVKlYCP~C~DVY~ 238 (254)
.|||-+|++--.| |. |.. ..+ .-.++.+-|+.|.+.|.
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 5999999875333 22 111 111 22578999999999985
No 35
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=27.09 E-value=37 Score=31.32 Aligned_cols=26 Identities=31% Similarity=0.768 Sum_probs=16.2
Q ss_pred CCCcccCCCCCccccccCCCCCCccceeeCCCCC
Q 025330 201 RCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPKCE 234 (254)
Q Consensus 201 ~CPRv~C~gq~lLPiGlSD~pg~stVKlYCP~C~ 234 (254)
.||| | |.++.=+.+. ++.--|||.|+
T Consensus 246 pCpr--C-G~~I~~~~~~-----gR~t~~CP~CQ 271 (272)
T PRK14810 246 PCLN--C-KTPIRRVVVA-----GRSSHYCPHCQ 271 (272)
T ss_pred cCCC--C-CCeeEEEEEC-----CCccEECcCCc
Confidence 6887 7 4444333222 36678999997
No 36
>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=26.60 E-value=30 Score=25.32 Aligned_cols=14 Identities=29% Similarity=0.776 Sum_probs=11.8
Q ss_pred cceeeCCCCCcccc
Q 025330 225 TVKIYCPKCEDIYY 238 (254)
Q Consensus 225 tVKlYCP~C~DVY~ 238 (254)
.=.|.||.|+-+|-
T Consensus 51 eg~L~Cp~c~r~YP 64 (68)
T PF03966_consen 51 EGELICPECGREYP 64 (68)
T ss_dssp TTEEEETTTTEEEE
T ss_pred CCEEEcCCCCCEEe
Confidence 34899999999994
No 37
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=26.46 E-value=39 Score=28.42 Aligned_cols=19 Identities=32% Similarity=0.877 Sum_probs=14.2
Q ss_pred ceeeCCCCCccccCCCCCC
Q 025330 226 VKIYCPKCEDIYYPRSKYQ 244 (254)
Q Consensus 226 VKlYCP~C~DVY~P~s~~~ 244 (254)
+-..|++|.-+|.|+....
T Consensus 28 ~g~kC~~CG~v~~PPr~~C 46 (140)
T COG1545 28 LGTKCKKCGRVYFPPRAYC 46 (140)
T ss_pred EEEEcCCCCeEEcCCcccC
Confidence 3567999999999876543
No 38
>PRK00420 hypothetical protein; Validated
Probab=26.22 E-value=43 Score=27.79 Aligned_cols=31 Identities=29% Similarity=0.728 Sum_probs=21.5
Q ss_pred CCCCcccCCCCCccccccCCCCCCccceeeCCCCCccccCCC
Q 025330 200 GRCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPKCEDIYYPRS 241 (254)
Q Consensus 200 G~CPRv~C~gq~lLPiGlSD~pg~stVKlYCP~C~DVY~P~s 241 (254)
.+||. | |.|++= ...-+.|||.|..++.-.+
T Consensus 24 ~~CP~--C-g~pLf~--------lk~g~~~Cp~Cg~~~~v~~ 54 (112)
T PRK00420 24 KHCPV--C-GLPLFE--------LKDGEVVCPVHGKVYIVKS 54 (112)
T ss_pred CCCCC--C-CCccee--------cCCCceECCCCCCeeeecc
Confidence 79998 6 455542 1334789999999987543
No 39
>KOG2828 consensus Acetyl-CoA hydrolase [Energy production and conversion]
Probab=25.96 E-value=24 Score=35.40 Aligned_cols=16 Identities=31% Similarity=0.744 Sum_probs=14.4
Q ss_pred ccccceeChHHHHHHH
Q 025330 176 IHVRYILTSKGMAAML 191 (254)
Q Consensus 176 IHARYIlT~~GL~~M~ 191 (254)
-|++||+|+.||+.+.
T Consensus 401 ah~~y~VTEhGiA~L~ 416 (454)
T KOG2828|consen 401 AHLDYLVTEHGIADLW 416 (454)
T ss_pred cceeEEEecccHHHHh
Confidence 5999999999999874
No 40
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=25.67 E-value=42 Score=31.84 Aligned_cols=41 Identities=29% Similarity=0.700 Sum_probs=27.4
Q ss_pred hhhcCCCCC---CCcccCCCC-Cccc-cccCCCCCCccceeeCCCCCcc
Q 025330 193 KYKNYDFGR---CPRVYCCGQ-PCLP-VGQSDIPRSSTVKIYCPKCEDI 236 (254)
Q Consensus 193 KY~~g~FG~---CPRv~C~gq-~lLP-iGlSD~pg~stVKlYCP~C~DV 236 (254)
..++.-||. |-...|+.. .=|| |||..-|+ -+.|||-|++.
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 367888994 555555432 1255 49987773 58999999874
No 41
>PF00471 Ribosomal_L33: Ribosomal protein L33; InterPro: IPR001705 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L33 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L33 has been shown to be on the surface of 50S subunit. L33 belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, , ], groups: Eubacterial L33. Algal and plant chloroplast L33. Cyanelle L33. L33 is a small protein of 49 to 66 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3PIO_1 3PIP_1 3PYT_3 3MS1_3 3F1F_6 3F1H_6 3MRZ_3 3PYO_3 3D5B_6 3D5D_6 ....
Probab=23.81 E-value=52 Score=23.29 Aligned_cols=16 Identities=38% Similarity=1.038 Sum_probs=12.7
Q ss_pred CCCCccceeeCCCCCc
Q 025330 220 IPRSSTVKIYCPKCED 235 (254)
Q Consensus 220 ~pg~stVKlYCP~C~D 235 (254)
.|..-.++-|||.|+.
T Consensus 25 ~~~rL~lkKycp~~~k 40 (48)
T PF00471_consen 25 TPERLELKKYCPRCRK 40 (48)
T ss_dssp SSSSSEEEEEETSSSS
T ss_pred CCceeeEeccCCCCCC
Confidence 3556678999999975
No 42
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=23.68 E-value=22 Score=33.00 Aligned_cols=34 Identities=29% Similarity=0.580 Sum_probs=24.2
Q ss_pred ccCCCCC-ccccccCCCCCCccceeeCCCCCcccc
Q 025330 205 VYCCGQP-CLPVGQSDIPRSSTVKIYCPKCEDIYY 238 (254)
Q Consensus 205 v~C~gq~-lLPiGlSD~pg~stVKlYCP~C~DVY~ 238 (254)
--|.|++ .||.+.........=-+|||.|.-|-+
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 3577877 588876655555555689999998743
No 43
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.18 E-value=35 Score=27.29 Aligned_cols=11 Identities=36% Similarity=1.361 Sum_probs=9.5
Q ss_pred eeCCCCCcccc
Q 025330 228 IYCPKCEDIYY 238 (254)
Q Consensus 228 lYCP~C~DVY~ 238 (254)
-|||+|.-|..
T Consensus 22 D~CPrCrGVWL 32 (88)
T COG3809 22 DYCPRCRGVWL 32 (88)
T ss_pred eeCCccccEee
Confidence 49999999984
No 44
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=22.97 E-value=55 Score=24.54 Aligned_cols=16 Identities=44% Similarity=1.190 Sum_probs=12.3
Q ss_pred CCCccceeeCCCCCcc
Q 025330 221 PRSSTVKIYCPKCEDI 236 (254)
Q Consensus 221 pg~stVKlYCP~C~DV 236 (254)
|....|+..||+|.++
T Consensus 19 ~~~~~~~F~CPnCG~~ 34 (59)
T PRK14890 19 PREKAVKFLCPNCGEV 34 (59)
T ss_pred CCCccCEeeCCCCCCe
Confidence 4455799999999765
No 45
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=22.86 E-value=61 Score=30.88 Aligned_cols=41 Identities=39% Similarity=0.852 Sum_probs=29.8
Q ss_pred HHHhhhcCCCCCCCcccCCCCCccccccCCCCCCccceeeCCCCCccccCCCC
Q 025330 190 MLEKYKNYDFGRCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPKCEDIYYPRSK 242 (254)
Q Consensus 190 M~eKY~~g~FG~CPRv~C~gq~lLPiGlSD~pg~stVKlYCP~C~DVY~P~s~ 242 (254)
+.+.+....| ||+ | |.-..+.....|..||.|+..+.|+-.
T Consensus 104 l~~w~~~~RF--Cg~--C--------G~~~~~~~~g~~~~C~~cg~~~fPR~d 144 (279)
T COG2816 104 LLEWYRSHRF--CGR--C--------GTKTYPREGGWARVCPKCGHEHFPRID 144 (279)
T ss_pred HHHHHhhCcC--CCC--C--------CCcCccccCceeeeCCCCCCccCCCCC
Confidence 3445555555 654 3 444677889999999999999999753
No 46
>COG5252 Uncharacterized conserved protein, contains CCCH-type Zn-finger protein [General function prediction only]
Probab=22.81 E-value=66 Score=30.55 Aligned_cols=39 Identities=26% Similarity=0.430 Sum_probs=35.7
Q ss_pred cceeChHHHHHHHHhhhcCCCC---CCCcc--cCCCCCcccccc
Q 025330 179 RYILTSKGMAAMLEKYKNYDFG---RCPRV--YCCGQPCLPVGQ 217 (254)
Q Consensus 179 RYIlT~~GL~~M~eKY~~g~FG---~CPRv--~C~gq~lLPiGl 217 (254)
-+|-|.+=++-+.+-..+|.|| .||+- .|-.-+-||.|.
T Consensus 136 P~intd~VCkffieA~e~GkYgw~W~CPng~~~C~y~H~Lp~Gy 179 (299)
T COG5252 136 PWINTDRVCKFFIEAMESGKYGWGWTCPNGNMRCSYIHKLPDGY 179 (299)
T ss_pred CCCChhHHHHHHHHHHhcCCccceeeCCCCCceeeeeeccCccc
Confidence 7888999999999999999999 89998 899999999985
No 47
>PRK00504 rpmG 50S ribosomal protein L33; Validated
Probab=22.10 E-value=44 Score=24.03 Aligned_cols=16 Identities=31% Similarity=0.993 Sum_probs=12.4
Q ss_pred CCCCccceeeCCCCCc
Q 025330 220 IPRSSTVKIYCPKCED 235 (254)
Q Consensus 220 ~pg~stVKlYCP~C~D 235 (254)
.|..-.+|-|||.|+.
T Consensus 27 ~~~rLelkKycp~c~k 42 (50)
T PRK00504 27 TPERLELKKFCPRCNK 42 (50)
T ss_pred CCceEEEECcCCCCCC
Confidence 4556678999999975
No 48
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=21.91 E-value=65 Score=29.55 Aligned_cols=34 Identities=32% Similarity=0.816 Sum_probs=24.4
Q ss_pred CCCCCCcccCCCCCccccccCCCCCCccceeeCCCCCccccCCC
Q 025330 198 DFGRCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPKCEDIYYPRS 241 (254)
Q Consensus 198 ~FG~CPRv~C~gq~lLPiGlSD~pg~stVKlYCP~C~DVY~P~s 241 (254)
.+-.||+. |+++.+ ..+..+..||.|..++.|+.
T Consensus 98 ~~~fC~~C---G~~~~~-------~~~~~~~~C~~c~~~~yp~~ 131 (256)
T PRK00241 98 SHRFCGYC---GHPMHP-------SKTEWAMLCPHCRERYYPRI 131 (256)
T ss_pred cCcccccc---CCCCee-------cCCceeEECCCCCCEECCCC
Confidence 46779874 334433 25677899999999999864
No 49
>PRK12495 hypothetical protein; Provisional
Probab=21.36 E-value=97 Score=28.81 Aligned_cols=15 Identities=20% Similarity=0.618 Sum_probs=12.2
Q ss_pred cceeeCCCCCccccC
Q 025330 225 TVKIYCPKCEDIYYP 239 (254)
Q Consensus 225 tVKlYCP~C~DVY~P 239 (254)
.=+.|||.|+.++.-
T Consensus 56 pG~~~Cp~CQ~~~~~ 70 (226)
T PRK12495 56 DGQEFCPTCQQPVTE 70 (226)
T ss_pred CCeeECCCCCCcccc
Confidence 346899999999973
No 50
>PF06222 Phage_TAC: Phage tail assembly chaperone; InterPro: IPR010411 This entry is represented by Bacteriophage HK97, Gp13 and Gp14. These are two overlapping reading frames []. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. These proteins include several putative tail assembly chaperones encoded by phages of Gram-negative bacteria.; PDB: 2OB9_A.
Probab=21.18 E-value=36 Score=29.07 Aligned_cols=33 Identities=30% Similarity=0.738 Sum_probs=17.5
Q ss_pred HHHHcCCCCCCCCCCchHHHHHHHHHHHHHhhhccccce
Q 025330 143 LDLILDVESSHGDMFTEEQNELVESAAEMLYGLIHVRYI 181 (254)
Q Consensus 143 Ld~ILd~e~~~~d~~~~~~~~~ie~~A~~LYGLIHARYI 181 (254)
+++++|.+. .-.|++++.+.+ ...||-.|+|-+
T Consensus 79 idVL~dE~~--~rVFsd~D~~~V----~~~YGPVHaRLl 111 (127)
T PF06222_consen 79 IDVLLDEDG--QRVFSDDDAEQV----AAIYGPVHARLL 111 (127)
T ss_dssp HHHEE-TTS---BSS-GGGHHHH----HCC--HHHHHHH
T ss_pred hHHHhcCCC--CcccCcchHHHH----HHHhchHHHHHH
Confidence 455566543 245666655544 358999999954
No 51
>PRK00595 rpmG 50S ribosomal protein L33; Validated
Probab=21.15 E-value=51 Score=23.76 Aligned_cols=16 Identities=25% Similarity=0.378 Sum_probs=12.3
Q ss_pred CCCCccceeeCCCCCc
Q 025330 220 IPRSSTVKIYCPKCED 235 (254)
Q Consensus 220 ~pg~stVKlYCP~C~D 235 (254)
.|..-.++-|||.|+.
T Consensus 30 ~~~rL~lkKycp~~~k 45 (53)
T PRK00595 30 TPEKLELKKYDPVLRK 45 (53)
T ss_pred CCCceEEECcCCCCCC
Confidence 3555678999999985
No 52
>PF08756 YfkB: YfkB-like domain; InterPro: IPR014866 YfkB is adjacent to YfkA in Bacillus subtilis. In other bacterial species, it is fused to this protein. As YfkA contains a Radical SAM domain it suggests this domain is interacts with them.
Probab=20.26 E-value=81 Score=27.67 Aligned_cols=30 Identities=20% Similarity=0.588 Sum_probs=23.6
Q ss_pred HHHHHHHHhhhcCCCC-----CCCcccCCCCCccc
Q 025330 185 KGMAAMLEKYKNYDFG-----RCPRVYCCGQPCLP 214 (254)
Q Consensus 185 ~GL~~M~eKY~~g~FG-----~CPRv~C~gq~lLP 214 (254)
..|..+.++|.+..-- +||-|.|.|-++|=
T Consensus 102 d~L~~~f~~W~~~~l~~slnCHCp~v~ClGPN~LV 136 (153)
T PF08756_consen 102 DSLTDAFDRWLDSPLAKSLNCHCPAVKCLGPNVLV 136 (153)
T ss_pred CcHHHHHHHHhcCcccccccCcCCcccccCCCeee
Confidence 4578888888765443 89999999999884
Done!