Query 026009
Match_columns 245
No_of_seqs 114 out of 333
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 02:38:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026009.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026009hhsearch_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 1.1E-95 2E-100 633.1 14.3 192 53-244 3-194 (216)
2 PTZ00396 Casein kinase II subu 100.0 2.5E-91 5.5E-96 628.0 16.6 204 42-245 5-209 (251)
3 PF01214 CK_II_beta: Casein ki 100.0 1E-88 2.2E-93 587.8 8.9 184 58-241 1-184 (184)
4 COG5041 SKB2 Casein kinase II, 100.0 9.8E-86 2.1E-90 575.4 9.9 188 55-244 22-209 (242)
5 PRK05978 hypothetical protein; 82.3 1.4 3E-05 37.7 3.2 42 147-197 24-65 (148)
6 PF01927 Mut7-C: Mut7-C RNAse 75.1 2.9 6.2E-05 34.8 2.9 41 153-196 88-136 (147)
7 COG1656 Uncharacterized conser 71.3 4.2 9.1E-05 35.5 3.1 62 133-197 66-143 (165)
8 KOG4684 Uncharacterized conser 50.7 14 0.00031 34.0 2.8 36 159-194 141-180 (275)
9 smart00647 IBR In Between Ring 50.3 25 0.00055 24.0 3.5 23 147-169 7-31 (64)
10 PF14205 Cys_rich_KTR: Cystein 48.9 7.5 0.00016 28.2 0.6 11 182-192 26-36 (55)
11 PF06044 DRP: Dam-replacing fa 46.8 4.3 9.3E-05 37.6 -1.1 58 157-221 32-101 (254)
12 PF06677 Auto_anti-p27: Sjogre 45.9 17 0.00037 24.7 1.9 23 158-191 19-41 (41)
13 PRK00420 hypothetical protein; 45.2 24 0.00052 28.9 3.1 30 157-197 24-53 (112)
14 PF05191 ADK_lid: Adenylate ki 44.5 14 0.00031 24.2 1.4 13 184-196 1-13 (36)
15 PF06827 zf-FPG_IleRS: Zinc fi 43.8 10 0.00023 23.3 0.6 10 184-193 21-30 (30)
16 TIGR02098 MJ0042_CXXC MJ0042 f 43.2 12 0.00025 24.0 0.8 28 164-194 8-35 (38)
17 COG2888 Predicted Zn-ribbon RN 39.9 19 0.0004 26.7 1.5 17 177-193 20-36 (61)
18 PRK00432 30S ribosomal protein 39.8 14 0.0003 25.9 0.8 10 183-192 19-28 (50)
19 PF08772 NOB1_Zn_bind: Nin one 39.6 11 0.00024 28.6 0.3 13 181-193 21-33 (73)
20 COG0401 Uncharacterized homolo 37.9 9.7 0.00021 27.7 -0.2 13 129-141 43-55 (56)
21 PF03811 Zn_Tnp_IS1: InsA N-te 36.4 20 0.00043 23.6 1.1 12 181-192 2-13 (36)
22 PF11238 DUF3039: Protein of u 35.3 9.2 0.0002 28.1 -0.7 28 161-195 28-55 (58)
23 PF13717 zinc_ribbon_4: zinc-r 34.6 24 0.00051 23.0 1.2 15 183-197 1-15 (36)
24 COG4416 Com Mu-like prophage p 34.1 19 0.00042 26.3 0.8 17 178-194 18-34 (60)
25 PF10601 zf-LITAF-like: LITAF- 34.0 25 0.00055 25.7 1.5 19 179-197 2-20 (73)
26 PF13719 zinc_ribbon_5: zinc-r 33.7 20 0.00044 23.3 0.8 29 164-195 8-36 (37)
27 KOG0435 Leucyl-tRNA synthetase 33.4 26 0.00056 37.2 1.9 57 153-213 427-502 (876)
28 PF09788 Tmemb_55A: Transmembr 32.9 38 0.00082 31.6 2.7 37 159-195 126-168 (256)
29 COG5034 TNG2 Chromatin remodel 32.1 28 0.00061 32.6 1.7 39 150-193 225-270 (271)
30 KOG1973 Chromatin remodeling p 31.5 25 0.00055 32.4 1.3 38 152-192 228-267 (274)
31 KOG2828 Acetyl-CoA hydrolase [ 29.9 22 0.00048 35.2 0.7 19 132-150 400-418 (454)
32 PF11335 DUF3137: Protein of u 28.7 24 0.00052 28.8 0.6 50 132-197 62-111 (142)
33 COG1631 RPL42A Ribosomal prote 27.6 26 0.00057 28.0 0.6 13 182-194 6-18 (94)
34 COG4098 comFA Superfamily II D 27.1 25 0.00055 34.6 0.6 13 169-191 55-67 (441)
35 PF03966 Trm112p: Trm112p-like 24.9 36 0.00077 24.7 0.9 13 183-195 52-64 (68)
36 smart00531 TFIIE Transcription 24.0 40 0.00087 28.0 1.1 42 151-196 94-135 (147)
37 PF01485 IBR: IBR domain; Int 24.0 1E+02 0.0022 20.9 3.0 42 155-196 17-60 (64)
38 COG3809 Uncharacterized protei 23.7 34 0.00074 26.8 0.6 12 184-195 21-32 (88)
39 KOG1773 Stress responsive prot 23.7 22 0.00047 26.5 -0.4 15 129-143 45-59 (63)
40 PRK14810 formamidopyrimidine-D 23.4 49 0.0011 30.3 1.7 26 158-191 246-271 (272)
41 COG1579 Zn-ribbon protein, pos 23.4 23 0.00051 32.5 -0.4 33 162-194 198-231 (239)
42 PF02150 RNA_POL_M_15KD: RNA p 23.2 27 0.00058 22.7 -0.0 14 185-198 2-15 (35)
43 PF00471 Ribosomal_L33: Riboso 22.7 59 0.0013 22.6 1.6 17 177-193 25-41 (48)
44 PF10588 NADH-G_4Fe-4S_3: NADH 22.5 1.5E+02 0.0032 19.7 3.5 40 97-137 2-41 (41)
45 PRK14890 putative Zn-ribbon RN 22.1 59 0.0013 24.0 1.5 16 178-193 19-34 (59)
46 smart00661 RPOL9 RNA polymeras 21.7 43 0.00093 22.4 0.7 12 186-197 2-13 (52)
47 PF08121 Toxin_33: Waglerin fa 21.6 55 0.0012 19.3 1.1 15 222-236 4-18 (22)
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=1.1e-95 Score=633.07 Aligned_cols=192 Identities=70% Similarity=1.289 Sum_probs=184.6
Q ss_pred CCCCCChHHHHhCCCCCeeEEecCcccccCCCccCCCCCCCCCHHHHHHHHcCCCCCCCCCCChhhHHHHHHHHHHHhcc
Q 026009 53 DGDDTSWISWFCNLRGNEFFCEVDDEYIQDDFNLCGLSSQVPYYDYALDLILDVESSHGDMFTEEQNELVESAAEMLYGL 132 (245)
Q Consensus 53 ~~~~~sWI~wFcsl~gneff~eVdedyI~D~FNL~GL~~~V~~y~~aL~~ILd~~~~~~~~~~~~~~~~ie~~A~~LYGL 132 (245)
++++.+||+|||+++|||||||||+|||+|+|||+||+.+||+|++||++|||.+++++....+++.+++|++|++||||
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 34455799999999999999999999999999999999999999999999999998887766666778999999999999
Q ss_pred ccceeeeChHHHHHHHHhhhcCccccCCCccCCCCCccccccCCCCCCccceeecCCCCccccCCCCCCCcccccccCCc
Q 026009 133 IHVRYILTSKGMAAMLEKYKNYDFGRCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPKCEDIYYPRSKYQGNIDGAYFGTT 212 (245)
Q Consensus 133 IHARYIlT~~Gl~~M~eKY~~g~FG~CPRv~C~~q~lLPiGlSd~pg~s~VKlyCP~C~DvY~P~s~~~~~iDGAyFGts 212 (245)
||||||+|.+||++|++||++++||+||||+|++|+|||+|+||+||+++||+|||+|+|||.|+|+++++|||||||||
T Consensus 83 IHaRYIlT~~Gl~~M~eKy~~~dFG~CPRV~C~~q~~LPvGLsDipg~~~VklYCP~C~dvY~P~ssr~~~iDGa~fGts 162 (216)
T KOG3092|consen 83 IHARYILTNRGLAAMLEKYKNGDFGRCPRVYCCGQPVLPVGLSDIPGKSTVKLYCPSCEDVYIPKSSRHGNIDGAYFGTS 162 (216)
T ss_pred hhheeeechHHHHHHHHHHhcCCCCcCCcccccCCccccccccCCCCcceEEEeCCCcccccccccccccccccchhcCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhHHHHHhCCCCCCCCCCCcceeeeeeeecC
Q 026009 213 FPHLFLMTYGHLKPQKATQSYVPRVFGFKLHK 244 (245)
Q Consensus 213 Fphlfl~~yP~l~p~~~~~~Y~PrIfGFkI~~ 244 (245)
|||||||+||++.|+++.++|+|||||||||+
T Consensus 163 FPhmff~~~p~l~P~r~~~~yvPriyGFkih~ 194 (216)
T KOG3092|consen 163 FPHMFFMTHPELRPKRPTEQYVPRIYGFKIHK 194 (216)
T ss_pred CchhHHHhccccCCCcchhhhcchheeeeeCc
Confidence 99999999999999999999999999999997
No 2
>PTZ00396 Casein kinase II subunit beta; Provisional
Probab=100.00 E-value=2.5e-91 Score=628.00 Aligned_cols=204 Identities=52% Similarity=1.005 Sum_probs=187.3
Q ss_pred ccccccCCCCC-CCCCCChHHHHhCCCCCeeEEecCcccccCCCccCCCCCCCCCHHHHHHHHcCCCCCCCCCCChhhHH
Q 026009 42 TDSEESDVSGS-DGDDTSWISWFCNLRGNEFFCEVDDEYIQDDFNLCGLSSQVPYYDYALDLILDVESSHGDMFTEEQNE 120 (245)
Q Consensus 42 ~~~~~s~~s~~-~~~~~sWI~wFcsl~gneff~eVdedyI~D~FNL~GL~~~V~~y~~aL~~ILd~~~~~~~~~~~~~~~ 120 (245)
.++++++++++ ++++.+||+|||+++||+|||+||+|||+|+|||+||+.+|++|++||+||||.++++++...++..+
T Consensus 5 ~~~~~~~~~~~~s~~~~sWI~wF~~~~gne~f~~Vd~dyI~D~FNl~GL~~~v~~y~~al~~Ild~~~~~~~~~~~~~~~ 84 (251)
T PTZ00396 5 FSDEESSYSEEPSEESMGWIEWFCSLKGHEFLCEVDEDFIRDEFNLYGLKSKFPFYNEALDMILDSEPPDDEDLEDEQFL 84 (251)
T ss_pred cccccccccccCCCCcCcHHHHHhCCCCCeeEEEeCHHHhcCcchhhCccccccCHHHHHHHHcCCCCCccccccchhHH
Confidence 33444444433 35677999999999999999999999999999999999999999999999999987765544556778
Q ss_pred HHHHHHHHHhccccceeeeChHHHHHHHHhhhcCccccCCCccCCCCCccccccCCCCCCccceeecCCCCccccCCCCC
Q 026009 121 LVESAAEMLYGLIHVRYILTSKGMAAMLEKYKNYDFGRCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPKCEDIYYPRSKY 200 (245)
Q Consensus 121 ~ie~~A~~LYGLIHARYIlT~~Gl~~M~eKY~~g~FG~CPRv~C~~q~lLPiGlSd~pg~s~VKlyCP~C~DvY~P~s~~ 200 (245)
.++++|++||||||||||+|++||++|++||++|+||+||||+|++|+|||||+||+||+++||+|||+|+|||+|++.+
T Consensus 85 ~i~~~a~~LYGLIHARyI~T~~Gl~~M~eKY~~g~FG~CPRv~C~~q~~LPvGlSd~~g~~~VKlyCP~C~DvY~p~s~~ 164 (251)
T PTZ00396 85 EVYQEASDLYGLIHARFITTPKGLALMREKYLQGKFGHCPRVLCEGQNVLPIGLSDVLKTSRVKVYCPRCQEVYHPKKSS 164 (251)
T ss_pred HHHHHHHHHHHHHhHhHhcCHHHHHHHHHHhhCCCCCCCCCccCCCCcccccccCCCcCcCceeEeCCCchhhcCCCCcc
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999877
Q ss_pred CCcccccccCCchhhHHHHHhCCCCCCCCCCCcceeeeeeeecCC
Q 026009 201 QGNIDGAYFGTTFPHLFLMTYGHLKPQKATQSYVPRVFGFKLHKP 245 (245)
Q Consensus 201 ~~~iDGAyFGtsFphlfl~~yP~l~p~~~~~~Y~PrIfGFkI~~~ 245 (245)
+..||||||||||||||+|+||++.|+++.++|+|||||||||++
T Consensus 165 ~~~iDGA~FGtsFph~fl~~~p~l~p~~~~~~yvPrifGFki~~~ 209 (251)
T PTZ00396 165 LLDIDGAFFGTSFPHLFLMTYPELIPTKPPQYYVPKIFGFKVHKK 209 (251)
T ss_pred ccccccceecCcHHHHHHHhccccCCCCCCCccCCeeeeEEeccc
Confidence 669999999999999999999999999999999999999999964
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=1e-88 Score=587.81 Aligned_cols=184 Identities=64% Similarity=1.221 Sum_probs=153.6
Q ss_pred ChHHHHhCCCCCeeEEecCcccccCCCccCCCCCCCCCHHHHHHHHcCCCCCCCCCCChhhHHHHHHHHHHHhcccccee
Q 026009 58 SWISWFCNLRGNEFFCEVDDEYIQDDFNLCGLSSQVPYYDYALDLILDVESSHGDMFTEEQNELVESAAEMLYGLIHVRY 137 (245)
Q Consensus 58 sWI~wFcsl~gneff~eVdedyI~D~FNL~GL~~~V~~y~~aL~~ILd~~~~~~~~~~~~~~~~ie~~A~~LYGLIHARY 137 (245)
+||+|||+++||+||||||+|||+|+|||+||+++||+|++||++|||.+.++++..++++.+.++++|++|||||||||
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 69999999999999999999999999999999999999999999999998876555666778889999999999999999
Q ss_pred eeChHHHHHHHHhhhcCccccCCCccCCCCCccccccCCCCCCccceeecCCCCccccCCCCCCCcccccccCCchhhHH
Q 026009 138 ILTSKGMAAMLEKYKNYDFGRCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPKCEDIYYPRSKYQGNIDGAYFGTTFPHLF 217 (245)
Q Consensus 138 IlT~~Gl~~M~eKY~~g~FG~CPRv~C~~q~lLPiGlSd~pg~s~VKlyCP~C~DvY~P~s~~~~~iDGAyFGtsFphlf 217 (245)
|+|++||++|++||++|+||+||||+|++|+|||+|+||+||+++||||||+|+|||+|++.++++||||||||||||||
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 026009 218 LMTYGHLKPQKATQSYVPRVFGFK 241 (245)
Q Consensus 218 l~~yP~l~p~~~~~~Y~PrIfGFk 241 (245)
+|+||++.|+.+.++|+|||||||
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=9.8e-86 Score=575.44 Aligned_cols=188 Identities=54% Similarity=1.131 Sum_probs=178.3
Q ss_pred CCCChHHHHhCCCCCeeEEecCcccccCCCccCCCCCCCCCHHHHHHHHcCCCCCCCCCCChhhHHHHHHHHHHHhcccc
Q 026009 55 DDTSWISWFCNLRGNEFFCEVDDEYIQDDFNLCGLSSQVPYYDYALDLILDVESSHGDMFTEEQNELVESAAEMLYGLIH 134 (245)
Q Consensus 55 ~~~sWI~wFcsl~gneff~eVdedyI~D~FNL~GL~~~V~~y~~aL~~ILd~~~~~~~~~~~~~~~~ie~~A~~LYGLIH 134 (245)
+...||+|||+++||||||+||++||+|.|||+||+..||+|++||++|||...++. ..+.+.+.||.+|++||||||
T Consensus 22 ~y~~Wi~~F~~rkg~eyfc~V~~efIeDrFNltgL~~~Vp~y~~~ldlILD~~~~~~--~e~~~~d~iE~sa~~LYgLIH 99 (242)
T COG5041 22 EYDEWIDWFCSRKGNEYFCEVPEEFIEDRFNLTGLSREVPHYSEVLDLILDKLAPSN--LENDEVDIIEESARQLYGLIH 99 (242)
T ss_pred HHHHHHHHHHcCCCCeeeeeCCHHHHHhhhhccchhhccchHHHHHHHHHhccCCcc--hhhhhhHHHHHHHHHHHHHHH
Confidence 344799999999999999999999999999999999999999999999999876543 233446789999999999999
Q ss_pred ceeeeChHHHHHHHHhhhcCccccCCCccCCCCCccccccCCCCCCccceeecCCCCccccCCCCCCCcccccccCCchh
Q 026009 135 VRYILTSKGMAAMLEKYKNYDFGRCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPKCEDIYYPRSKYQGNIDGAYFGTTFP 214 (245)
Q Consensus 135 ARYIlT~~Gl~~M~eKY~~g~FG~CPRv~C~~q~lLPiGlSd~pg~s~VKlyCP~C~DvY~P~s~~~~~iDGAyFGtsFp 214 (245)
||||+|..||++|.+||+.++||+||||+||+|+|||+||||+||+++||||||+|.|||.|+|+++..|||||||||||
T Consensus 100 aRyIiT~~GL~~m~eKy~~~efG~CPRv~Cn~~~vLPvGLsDi~g~~~vkLyCpsC~dlY~p~Ssr~~~iDGa~fGtSFP 179 (242)
T COG5041 100 ARYIITKSGLQAMLEKYKSREFGACPRVYCNGQQVLPVGLSDIPGKSSVKLYCPSCEDLYLPKSSRHQSIDGAFFGTSFP 179 (242)
T ss_pred hhheeeHHHHHHHHHHHhhcccCCCCcccccCcceeccccccCCCCceeEEecCchhhhcCcccccccccccchhccCCc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHhCCCCCCCCCCCcceeeeeeeecC
Q 026009 215 HLFLMTYGHLKPQKATQSYVPRVFGFKLHK 244 (245)
Q Consensus 215 hlfl~~yP~l~p~~~~~~Y~PrIfGFkI~~ 244 (245)
|||+++||++.|+++.+.|+|||||||||+
T Consensus 180 h~f~~~~pel~p~~~~e~YiprIfGfri~~ 209 (242)
T COG5041 180 HMFLQTFPELFPKRSCERYIPRIFGFRIHS 209 (242)
T ss_pred hHHHHhchhhcCCcchhhhcceeeeeEeeh
Confidence 999999999999999999999999999986
No 5
>PRK05978 hypothetical protein; Provisional
Probab=82.31 E-value=1.4 Score=37.68 Aligned_cols=42 Identities=17% Similarity=0.219 Sum_probs=32.8
Q ss_pred HHHhhhcCccccCCCccCCCCCccccccCCCCCCccceeecCCCCccccCC
Q 026009 147 MLEKYKNYDFGRCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPKCEDIYYPR 197 (245)
Q Consensus 147 M~eKY~~g~FG~CPRv~C~~q~lLPiGlSd~pg~s~VKlyCP~C~DvY~P~ 197 (245)
+..-..+|-.|+||| |..-+++= +--+|+--||.|..-|.+.
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 445678899999998 77777762 5567888999999999753
No 6
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=75.12 E-value=2.9 Score=34.83 Aligned_cols=41 Identities=34% Similarity=0.835 Sum_probs=27.6
Q ss_pred cCccccCCCccCCCCCccccccCCCCC--------CccceeecCCCCccccC
Q 026009 153 NYDFGRCPRVYCCGQPCLPVGQSDIPR--------SSTVKIYCPKCEDIYYP 196 (245)
Q Consensus 153 ~g~FG~CPRv~C~~q~lLPiGlSd~pg--------~s~VKlyCP~C~DvY~P 196 (245)
+..|.+||+ ||+ ++.|+...+..+ ....=..||.|+.||=+
T Consensus 88 ~~~~sRC~~--CN~-~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiyW~ 136 (147)
T PF01927_consen 88 DPIFSRCPK--CNG-PLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIYWE 136 (147)
T ss_pred CCCCCccCC--CCc-EeeechhhccccccCccccccCCeEEECCCCCCEecc
Confidence 445899986 666 788886554322 22235679999999954
No 7
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=71.28 E-value=4.2 Score=35.48 Aligned_cols=62 Identities=27% Similarity=0.491 Sum_probs=42.5
Q ss_pred ccceeeeChHHHHHHHHh---hh-----cCccccCCCccCCCCCccccccCC--------CCCCccceeecCCCCccccC
Q 026009 133 IHVRYILTSKGMAAMLEK---YK-----NYDFGRCPRVYCCGQPCLPVGQSD--------IPRSSTVKIYCPKCEDIYYP 196 (245)
Q Consensus 133 IHARYIlT~~Gl~~M~eK---Y~-----~g~FG~CPRv~C~~q~lLPiGlSd--------~pg~s~VKlyCP~C~DvY~P 196 (245)
+++=||-+..=.+||.+= +. +-+|-+||. ||+ +++++-... +.+....-..||+|..+|=+
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 677788888877787765 21 344889994 777 688776655 22333444559999999975
Q ss_pred C
Q 026009 197 R 197 (245)
Q Consensus 197 ~ 197 (245)
-
T Consensus 143 G 143 (165)
T COG1656 143 G 143 (165)
T ss_pred c
Confidence 3
No 8
>KOG4684 consensus Uncharacterized conserved protein, contains C4-type Zn-finger [General function prediction only]
Probab=50.66 E-value=14 Score=33.96 Aligned_cols=36 Identities=19% Similarity=0.578 Sum_probs=25.5
Q ss_pred CCCccCCCC----CccccccCCCCCCccceeecCCCCccc
Q 026009 159 CPRVYCCGQ----PCLPVGQSDIPRSSTVKIYCPKCEDIY 194 (245)
Q Consensus 159 CPRv~C~~q----~lLPiGlSd~pg~s~VKlyCP~C~DvY 194 (245)
|||-+|++- ++.|--++..+.-..+++-|-.|++.|
T Consensus 141 CPRpnCkRiInL~p~~~~p~~P~~~P~gcRV~CgHC~~tF 180 (275)
T KOG4684|consen 141 CPRPNCKRIINLDPLIEKPRDPGTAPTGCRVKCGHCNETF 180 (275)
T ss_pred cCCCCcceeeecCCCCCCCCCCCCCCcceEEEecCcccee
Confidence 999999863 333434444444456899999999988
No 9
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=50.34 E-value=25 Score=24.05 Aligned_cols=23 Identities=30% Similarity=0.588 Sum_probs=14.8
Q ss_pred HHHhhhc--CccccCCCccCCCCCc
Q 026009 147 MLEKYKN--YDFGRCPRVYCCGQPC 169 (245)
Q Consensus 147 M~eKY~~--g~FG~CPRv~C~~q~l 169 (245)
+.++|.+ ..+-.||+..|+..-.
T Consensus 7 ~~~~~i~~~~~~~~CP~~~C~~~~~ 31 (64)
T smart00647 7 LLESYVESNPDLKWCPAPDCSAAII 31 (64)
T ss_pred HHHHHHhcCCCccCCCCCCCcceEE
Confidence 3444433 4677899999976433
No 10
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=48.87 E-value=7.5 Score=28.25 Aligned_cols=11 Identities=45% Similarity=1.407 Sum_probs=8.7
Q ss_pred cceeecCCCCc
Q 026009 182 TVKIYCPKCED 192 (245)
Q Consensus 182 ~VKlyCP~C~D 192 (245)
..-||||+|+.
T Consensus 26 NfPlyCpKCK~ 36 (55)
T PF14205_consen 26 NFPLYCPKCKQ 36 (55)
T ss_pred cccccCCCCCc
Confidence 34799999964
No 11
>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=46.82 E-value=4.3 Score=37.60 Aligned_cols=58 Identities=34% Similarity=0.749 Sum_probs=25.9
Q ss_pred ccCCCccCCCCCccccccCCCCCCccc-eeecCCCCccccCCCCCC---C-cccccccC-------CchhhHHHHHh
Q 026009 157 GRCPRVYCCGQPCLPVGQSDIPRSSTV-KIYCPKCEDIYYPRSKYQ---G-NIDGAYFG-------TTFPHLFLMTY 221 (245)
Q Consensus 157 G~CPRv~C~~q~lLPiGlSd~pg~s~V-KlyCP~C~DvY~P~s~~~---~-~iDGAyFG-------tsFphlfl~~y 221 (245)
+.||+ |+..++-=+ +.-.+| -.|||+|++-|.-+|... . -.||||-- .+=|.+|+|+|
T Consensus 32 ~yCP~--Cg~~~L~~f-----~NN~PVaDF~C~~C~eeyELKSk~~~l~~~I~dGAY~Tmi~Ri~s~~NPnfffl~Y 101 (254)
T PF06044_consen 32 MYCPN--CGSKPLSKF-----ENNRPVADFYCPNCNEEYELKSKKKKLSNKINDGAYHTMIERITSDNNPNFFFLTY 101 (254)
T ss_dssp ---TT--T--SS-EE-------------EEE-TTT--EEEEEEEESS--SEEEEEEHHHHHHHHHTT---EEEEEEE
T ss_pred CcCCC--CCChhHhhc-----cCCCccceeECCCCchHHhhhhhccccCCcccCccHHHHHHHhhccCCCCEEEEEe
Confidence 46886 444333322 344555 578999999999875331 1 34999963 24577788887
No 12
>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=45.86 E-value=17 Score=24.68 Aligned_cols=23 Identities=48% Similarity=1.292 Sum_probs=15.4
Q ss_pred cCCCccCCCCCccccccCCCCCCccceeecCCCC
Q 026009 158 RCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPKCE 191 (245)
Q Consensus 158 ~CPRv~C~~q~lLPiGlSd~pg~s~VKlyCP~C~ 191 (245)
+||. | +.|++. + +.+ ++|||.|.
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 6994 7 677775 1 122 68999994
No 13
>PRK00420 hypothetical protein; Validated
Probab=45.22 E-value=24 Score=28.88 Aligned_cols=30 Identities=23% Similarity=0.643 Sum_probs=20.8
Q ss_pred ccCCCccCCCCCccccccCCCCCCccceeecCCCCccccCC
Q 026009 157 GRCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPKCEDIYYPR 197 (245)
Q Consensus 157 G~CPRv~C~~q~lLPiGlSd~pg~s~VKlyCP~C~DvY~P~ 197 (245)
++||. |. .|++ +...-+.|||.|..++.-.
T Consensus 24 ~~CP~--Cg-~pLf--------~lk~g~~~Cp~Cg~~~~v~ 53 (112)
T PRK00420 24 KHCPV--CG-LPLF--------ELKDGEVVCPVHGKVYIVK 53 (112)
T ss_pred CCCCC--CC-Ccce--------ecCCCceECCCCCCeeeec
Confidence 79998 65 3433 2233489999999999754
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=44.53 E-value=14 Score=24.18 Aligned_cols=13 Identities=46% Similarity=1.007 Sum_probs=10.9
Q ss_pred eeecCCCCccccC
Q 026009 184 KIYCPKCEDIYYP 196 (245)
Q Consensus 184 KlyCP~C~DvY~P 196 (245)
+..||.|..+||.
T Consensus 1 Rr~C~~Cg~~Yh~ 13 (36)
T PF05191_consen 1 RRICPKCGRIYHI 13 (36)
T ss_dssp EEEETTTTEEEET
T ss_pred CcCcCCCCCcccc
Confidence 3579999999985
No 15
>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=43.75 E-value=10 Score=23.26 Aligned_cols=10 Identities=30% Similarity=1.265 Sum_probs=7.1
Q ss_pred eeecCCCCcc
Q 026009 184 KIYCPKCEDI 193 (245)
Q Consensus 184 KlyCP~C~Dv 193 (245)
--|||+|.+|
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 16
>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=43.18 E-value=12 Score=24.01 Aligned_cols=28 Identities=21% Similarity=0.387 Sum_probs=16.6
Q ss_pred CCCCCccccccCCCCCCccceeecCCCCccc
Q 026009 164 CCGQPCLPVGQSDIPRSSTVKIYCPKCEDIY 194 (245)
Q Consensus 164 C~~q~lLPiGlSd~pg~s~VKlyCP~C~DvY 194 (245)
|..+.-+|-..- +....++-||+|+...
T Consensus 8 C~~~~~v~~~~~---~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 8 CKTSFRVVDSQL---GANGGKVRCGKCGHVW 35 (38)
T ss_pred CCCEEEeCHHHc---CCCCCEEECCCCCCEE
Confidence 555555554332 2334478888887765
No 17
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=39.86 E-value=19 Score=26.73 Aligned_cols=17 Identities=35% Similarity=0.960 Sum_probs=14.5
Q ss_pred CCCCccceeecCCCCcc
Q 026009 177 IPRSSTVKIYCPKCEDI 193 (245)
Q Consensus 177 ~pg~s~VKlyCP~C~Dv 193 (245)
.|++..|+-.||+|.++
T Consensus 20 ~p~e~~v~F~CPnCGe~ 36 (61)
T COG2888 20 APGETAVKFPCPNCGEV 36 (61)
T ss_pred ccCCceeEeeCCCCCce
Confidence 37889999999999954
No 18
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=39.76 E-value=14 Score=25.94 Aligned_cols=10 Identities=30% Similarity=1.168 Sum_probs=5.1
Q ss_pred ceeecCCCCc
Q 026009 183 VKIYCPKCED 192 (245)
Q Consensus 183 VKlyCP~C~D 192 (245)
++-|||+|..
T Consensus 19 ~~~fCP~Cg~ 28 (50)
T PRK00432 19 KNKFCPRCGS 28 (50)
T ss_pred ccCcCcCCCc
Confidence 3445555554
No 19
>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=39.57 E-value=11 Score=28.60 Aligned_cols=13 Identities=38% Similarity=1.042 Sum_probs=5.6
Q ss_pred ccceeecCCCCcc
Q 026009 181 STVKIYCPKCEDI 193 (245)
Q Consensus 181 s~VKlyCP~C~Dv 193 (245)
.+-|.|||+|.--
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 4569999999753
No 20
>COG0401 Uncharacterized homolog of Blt101 [Function unknown]
Probab=37.92 E-value=9.7 Score=27.74 Aligned_cols=13 Identities=31% Similarity=0.749 Sum_probs=11.0
Q ss_pred HhccccceeeeCh
Q 026009 129 LYGLIHVRYILTS 141 (245)
Q Consensus 129 LYGLIHARYIlT~ 141 (245)
+=|+|||-|+++.
T Consensus 43 ~PGiiHA~yvi~~ 55 (56)
T COG0401 43 IPGIIHALYVILR 55 (56)
T ss_pred hhhhHhheEEEEe
Confidence 5589999999875
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=36.37 E-value=20 Score=23.62 Aligned_cols=12 Identities=25% Similarity=1.143 Sum_probs=10.2
Q ss_pred ccceeecCCCCc
Q 026009 181 STVKIYCPKCED 192 (245)
Q Consensus 181 s~VKlyCP~C~D 192 (245)
++|.+.||+|+.
T Consensus 2 a~i~v~CP~C~s 13 (36)
T PF03811_consen 2 AKIDVHCPRCQS 13 (36)
T ss_pred CcEeeeCCCCCC
Confidence 578999999974
No 22
>PF11238 DUF3039: Protein of unknown function (DUF3039); InterPro: IPR021400 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=35.29 E-value=9.2 Score=28.06 Aligned_cols=28 Identities=29% Similarity=0.636 Sum_probs=18.0
Q ss_pred CccCCCCCccccccCCCCCCccceeecCCCCcccc
Q 026009 161 RVYCCGQPCLPVGQSDIPRSSTVKIYCPKCEDIYY 195 (245)
Q Consensus 161 Rv~C~~q~lLPiGlSd~pg~s~VKlyCP~C~DvY~ 195 (245)
+.+|.. +.|.+.+..+ ..| ||.|++||.
T Consensus 28 vALCGk--~wvp~rdp~~--~PV---CP~Ck~iye 55 (58)
T PF11238_consen 28 VALCGK--VWVPTRDPKP--FPV---CPECKEIYE 55 (58)
T ss_pred EeeeCc--eeCCCCCCCC--CCC---CcCHHHHHH
Confidence 566664 4555554333 444 999999995
No 23
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=34.55 E-value=24 Score=22.98 Aligned_cols=15 Identities=33% Similarity=0.766 Sum_probs=12.4
Q ss_pred ceeecCCCCccccCC
Q 026009 183 VKIYCPKCEDIYYPR 197 (245)
Q Consensus 183 VKlyCP~C~DvY~P~ 197 (245)
+++-||+|+-.|.-+
T Consensus 1 M~i~Cp~C~~~y~i~ 15 (36)
T PF13717_consen 1 MIITCPNCQAKYEID 15 (36)
T ss_pred CEEECCCCCCEEeCC
Confidence 578899999999754
No 24
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=34.08 E-value=19 Score=26.32 Aligned_cols=17 Identities=18% Similarity=0.698 Sum_probs=13.3
Q ss_pred CCCccceeecCCCCccc
Q 026009 178 PRSSTVKIYCPKCEDIY 194 (245)
Q Consensus 178 pg~s~VKlyCP~C~DvY 194 (245)
-+++-++.-||||+.|=
T Consensus 18 ~~~~yle~KCPrCK~vN 34 (60)
T COG4416 18 EGQAYLEKKCPRCKEVN 34 (60)
T ss_pred ccceeeeecCCccceee
Confidence 34667889999998874
No 25
>PF10601 zf-LITAF-like: LITAF-like zinc ribbon domain; InterPro: IPR006629 Members of this family display a conserved zinc ribbon structure [] with the motif C-XX-C- separated from the more C-terminal HX-C(P)X-C-X4-G-R motif by a variable region of usually 25-30 (hydrophobic) residues. Although it belongs to one of the zinc finger's fold groups (zinc ribbon), this particular domain was first identified in LPS-induced tumour necrosis alpha factor (LITAF) which is produced in mammalian cells after being challenged with lipopolysaccharide (LPS). The hydrophobic region probably inserts into the membrane rather than traversing it. Such an insertion brings together the N- and C-terminal C-XX-C motifs to form a compact Zn2+-binding structure [].
Probab=34.04 E-value=25 Score=25.70 Aligned_cols=19 Identities=37% Similarity=0.856 Sum_probs=15.5
Q ss_pred CCccceeecCCCCccccCC
Q 026009 179 RSSTVKIYCPKCEDIYYPR 197 (245)
Q Consensus 179 g~s~VKlyCP~C~DvY~P~ 197 (245)
+..++.++||+|+..=.+.
T Consensus 2 ~~~p~~~~CP~C~~~~~T~ 20 (73)
T PF10601_consen 2 GPEPVRIYCPYCQQQVQTR 20 (73)
T ss_pred CCCceeeECCCCCCEEEEE
Confidence 5678999999999887653
No 26
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=33.74 E-value=20 Score=23.30 Aligned_cols=29 Identities=24% Similarity=0.547 Sum_probs=19.0
Q ss_pred CCCCCccccccCCCCCCccceeecCCCCcccc
Q 026009 164 CCGQPCLPVGQSDIPRSSTVKIYCPKCEDIYY 195 (245)
Q Consensus 164 C~~q~lLPiGlSd~pg~s~VKlyCP~C~DvY~ 195 (245)
|+...-||-. ..+.+..++-||+|+.++.
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 2446677999999998873
No 27
>KOG0435 consensus Leucyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=33.44 E-value=26 Score=37.18 Aligned_cols=57 Identities=25% Similarity=0.638 Sum_probs=38.3
Q ss_pred cCcccc-CCCccCCCCCccccccCCCCCCcc------------------ceeecCCCCccccCCCCCCCcccccccCCch
Q 026009 153 NYDFGR-CPRVYCCGQPCLPVGQSDIPRSST------------------VKIYCPKCEDIYYPRSKYQGNIDGAYFGTTF 213 (245)
Q Consensus 153 ~g~FG~-CPRv~C~~q~lLPiGlSd~pg~s~------------------VKlyCP~C~DvY~P~s~~~~~iDGAyFGtsF 213 (245)
+.-+|+ =|-|.|..+--+||-+|+-|=.-+ |+.-||+|++ |....-...| .|+++++
T Consensus 427 QRyWGTPIPivhc~~cG~vpVpes~LPV~LP~l~~~~~kG~Pls~~~e~vn~~cP~cg~---pAkRETDTMD-TFvDSsW 502 (876)
T KOG0435|consen 427 QRYWGTPIPIVHCDDCGAVPVPESELPVTLPELNDFTPKGPPLSKADEWVNVDCPRCGE---PAKRETDTMD-TFVDSSW 502 (876)
T ss_pred hhccCCCcceEEcCCCCcccCcHHHCCcccccccccCCCCCcccchhhheeccCccCCC---cccccccccc-hhhccce
Confidence 444564 689999999988888887765444 8899999998 4322221333 5555554
No 28
>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=32.89 E-value=38 Score=31.56 Aligned_cols=37 Identities=24% Similarity=0.660 Sum_probs=23.7
Q ss_pred CCCccCCCCCcc-cc--cc-CCCC--CCccceeecCCCCcccc
Q 026009 159 CPRVYCCGQPCL-PV--GQ-SDIP--RSSTVKIYCPKCEDIYY 195 (245)
Q Consensus 159 CPRv~C~~q~lL-Pi--Gl-Sd~p--g~s~VKlyCP~C~DvY~ 195 (245)
|||-+|++--.| |. |- +..+ .-.++++-|++|++.+.
T Consensus 126 CPRp~CkRiI~L~~~~~~p~~~~~~~~p~~~rv~CghC~~~Fl 168 (256)
T PF09788_consen 126 CPRPNCKRIINLGPSHQGPVTPPVPTQPGSCRVICGHCSNTFL 168 (256)
T ss_pred CCCCCCcceEEeCCccCCCCCCCCCCCCCceeEECCCCCCcEe
Confidence 999999974333 22 01 1111 22578999999999985
No 29
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=32.15 E-value=28 Score=32.59 Aligned_cols=39 Identities=33% Similarity=0.774 Sum_probs=27.3
Q ss_pred hhhcCccccCCCccCCCCCc------cc-cccCCCCCCccceeecCCCCcc
Q 026009 150 KYKNYDFGRCPRVYCCGQPC------LP-VGQSDIPRSSTVKIYCPKCEDI 193 (245)
Q Consensus 150 KY~~g~FG~CPRv~C~~q~l------LP-iGlSd~pg~s~VKlyCP~C~Dv 193 (245)
..+++-||. =|.|.+.+| || |||..-|+ -+.|||-|++.
T Consensus 225 fCqqvSyGq--MVaCDn~nCkrEWFH~~CVGLk~pPK---G~WYC~eCk~~ 270 (271)
T COG5034 225 FCQQVSYGQ--MVACDNANCKREWFHLECVGLKEPPK---GKWYCPECKKA 270 (271)
T ss_pred Eeccccccc--ceecCCCCCchhheeccccccCCCCC---CcEeCHHhHhc
Confidence 468899995 455555443 45 49987664 48999999874
No 30
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=31.48 E-value=25 Score=32.39 Aligned_cols=38 Identities=26% Similarity=0.518 Sum_probs=27.0
Q ss_pred hcCccccCCCccCC-CCCccc-cccCCCCCCccceeecCCCCc
Q 026009 152 KNYDFGRCPRVYCC-GQPCLP-VGQSDIPRSSTVKIYCPKCED 192 (245)
Q Consensus 152 ~~g~FG~CPRv~C~-~q~lLP-iGlSd~pg~s~VKlyCP~C~D 192 (245)
.-|.++-|=...|. .--=+| |||...|.. |.|||+|+.
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 45677778888887 444455 599976654 499999964
No 31
>KOG2828 consensus Acetyl-CoA hydrolase [Energy production and conversion]
Probab=29.87 E-value=22 Score=35.18 Aligned_cols=19 Identities=32% Similarity=0.630 Sum_probs=15.8
Q ss_pred cccceeeeChHHHHHHHHh
Q 026009 132 LIHVRYILTSKGMAAMLEK 150 (245)
Q Consensus 132 LIHARYIlT~~Gl~~M~eK 150 (245)
--|++||+|+.|+..+.-|
T Consensus 400 rah~~y~VTEhGiA~L~Gk 418 (454)
T KOG2828|consen 400 RAHLDYLVTEHGIADLWGK 418 (454)
T ss_pred ccceeEEEecccHHHHhCC
Confidence 3599999999999987543
No 32
>PF11335 DUF3137: Protein of unknown function (DUF3137) ; InterPro: IPR021484 This bacterial family of proteins has no known function.
Probab=28.74 E-value=24 Score=28.80 Aligned_cols=50 Identities=30% Similarity=0.468 Sum_probs=29.3
Q ss_pred cccceeeeChHHHHHHHHhhhcCccccCCCccCCCCCccccccCCCCCCccceeecCCCCccccCC
Q 026009 132 LIHVRYILTSKGMAAMLEKYKNYDFGRCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPKCEDIYYPR 197 (245)
Q Consensus 132 LIHARYIlT~~Gl~~M~eKY~~g~FG~CPRv~C~~q~lLPiGlSd~pg~s~VKlyCP~C~DvY~P~ 197 (245)
.+.|||||||.=|+.+.+ +.+.. |. |+.++ ...+++-+..+.=++.+.|+
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 456899999998887764 22222 32 12221 22356666666666777754
No 33
>COG1631 RPL42A Ribosomal protein L44E [Translation, ribosomal structure and biogenesis]
Probab=27.61 E-value=26 Score=28.00 Aligned_cols=13 Identities=31% Similarity=0.874 Sum_probs=10.5
Q ss_pred cceeecCCCCccc
Q 026009 182 TVKIYCPKCEDIY 194 (245)
Q Consensus 182 ~VKlyCP~C~DvY 194 (245)
+++.|||.|+..=
T Consensus 6 ~~~tyCp~CkkhT 18 (94)
T COG1631 6 KRRTYCPYCKKHT 18 (94)
T ss_pred ceeecCcccccce
Confidence 6789999998643
No 34
>COG4098 comFA Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [DNA replication, recombination, and repair]
Probab=27.13 E-value=25 Score=34.62 Aligned_cols=13 Identities=46% Similarity=1.109 Sum_probs=10.4
Q ss_pred ccccccCCCCCCccceeecCCCC
Q 026009 169 CLPVGQSDIPRSSTVKIYCPKCE 191 (245)
Q Consensus 169 lLPiGlSd~pg~s~VKlyCP~C~ 191 (245)
-||+| ++||++|-
T Consensus 55 ~lp~~----------~~YCr~Cl 67 (441)
T COG4098 55 KLPCG----------CLYCRNCL 67 (441)
T ss_pred ccccc----------eEeehhhh
Confidence 57777 89999984
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=24.89 E-value=36 Score=24.70 Aligned_cols=13 Identities=31% Similarity=0.838 Sum_probs=11.3
Q ss_pred ceeecCCCCcccc
Q 026009 183 VKIYCPKCEDIYY 195 (245)
Q Consensus 183 VKlyCP~C~DvY~ 195 (245)
=.|.||.|+-+|-
T Consensus 52 g~L~Cp~c~r~YP 64 (68)
T PF03966_consen 52 GELICPECGREYP 64 (68)
T ss_dssp TEEEETTTTEEEE
T ss_pred CEEEcCCCCCEEe
Confidence 4899999999993
No 36
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=23.99 E-value=40 Score=28.02 Aligned_cols=42 Identities=17% Similarity=0.391 Sum_probs=23.4
Q ss_pred hhcCccccCCCccCCCCCccccccCCCCCCccceeecCCCCccccC
Q 026009 151 YKNYDFGRCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPKCEDIYYP 196 (245)
Q Consensus 151 Y~~g~FG~CPRv~C~~q~lLPiGlSd~pg~s~VKlyCP~C~DvY~P 196 (245)
-.+..|=.||+ |+..--.=-.+. ....+.+.-||.|+..-..
T Consensus 94 e~~~~~Y~Cp~--C~~~y~~~ea~~--~~d~~~~f~Cp~Cg~~l~~ 135 (147)
T smart00531 94 ETNNAYYKCPN--CQSKYTFLEANQ--LLDMDGTFTCPRCGEELEE 135 (147)
T ss_pred ccCCcEEECcC--CCCEeeHHHHHH--hcCCCCcEECCCCCCEEEE
Confidence 34566778997 664332111111 0012456899999887654
No 37
>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=23.97 E-value=1e+02 Score=20.90 Aligned_cols=42 Identities=19% Similarity=0.256 Sum_probs=16.3
Q ss_pred ccccCCCccCCCCCccccccCCC--CCCccceeecCCCCccccC
Q 026009 155 DFGRCPRVYCCGQPCLPVGQSDI--PRSSTVKIYCPKCEDIYYP 196 (245)
Q Consensus 155 ~FG~CPRv~C~~q~lLPiGlSd~--pg~s~VKlyCP~C~DvY~P 196 (245)
.+-.||+..|+.--...-|.... -=..-=..||..|+.-+|+
T Consensus 17 ~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~ 60 (64)
T PF01485_consen 17 NIRWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPWHE 60 (64)
T ss_dssp -CC--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSESCT
T ss_pred CccCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCcccCC
Confidence 44589999999754433333321 0000114555566555553
No 38
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.69 E-value=34 Score=26.84 Aligned_cols=12 Identities=33% Similarity=1.190 Sum_probs=10.0
Q ss_pred eeecCCCCcccc
Q 026009 184 KIYCPKCEDIYY 195 (245)
Q Consensus 184 KlyCP~C~DvY~ 195 (245)
--|||+|+-|..
T Consensus 21 iD~CPrCrGVWL 32 (88)
T COG3809 21 IDYCPRCRGVWL 32 (88)
T ss_pred eeeCCccccEee
Confidence 359999999985
No 39
>KOG1773 consensus Stress responsive protein [General function prediction only]
Probab=23.67 E-value=22 Score=26.50 Aligned_cols=15 Identities=40% Similarity=0.793 Sum_probs=12.2
Q ss_pred HhccccceeeeChHH
Q 026009 129 LYGLIHVRYILTSKG 143 (245)
Q Consensus 129 LYGLIHARYIlT~~G 143 (245)
+=|+|||-|+++.+|
T Consensus 45 iPgiIhA~yii~~~~ 59 (63)
T KOG1773|consen 45 IPGIIHAIYIIFFRG 59 (63)
T ss_pred hHHHHhhEEEEEEec
Confidence 458999999997654
No 40
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=23.44 E-value=49 Score=30.33 Aligned_cols=26 Identities=31% Similarity=0.732 Sum_probs=15.6
Q ss_pred cCCCccCCCCCccccccCCCCCCccceeecCCCC
Q 026009 158 RCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPKCE 191 (245)
Q Consensus 158 ~CPRv~C~~q~lLPiGlSd~pg~s~VKlyCP~C~ 191 (245)
.||| |.. ++.=+.+. ++---|||.|+
T Consensus 246 pCpr--CG~-~I~~~~~~-----gR~t~~CP~CQ 271 (272)
T PRK14810 246 PCLN--CKT-PIRRVVVA-----GRSSHYCPHCQ 271 (272)
T ss_pred cCCC--CCC-eeEEEEEC-----CCccEECcCCc
Confidence 4888 753 33222222 35678999997
No 41
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=23.36 E-value=23 Score=32.50 Aligned_cols=33 Identities=27% Similarity=0.538 Sum_probs=23.1
Q ss_pred ccCCCCCc-cccccCCCCCCccceeecCCCCccc
Q 026009 162 VYCCGQPC-LPVGQSDIPRSSTVKIYCPKCEDIY 194 (245)
Q Consensus 162 v~C~~q~l-LPiGlSd~pg~s~VKlyCP~C~DvY 194 (245)
--|.||++ ||.+........-=-++||.|.-+-
T Consensus 198 ~~C~GC~m~l~~~~~~~V~~~d~iv~CP~CgRIL 231 (239)
T COG1579 198 RVCGGCHMKLPSQTLSKVRKKDEIVFCPYCGRIL 231 (239)
T ss_pred CcccCCeeeecHHHHHHHhcCCCCccCCccchHH
Confidence 35777774 7887665555555568999998764
No 42
>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=23.21 E-value=27 Score=22.65 Aligned_cols=14 Identities=36% Similarity=1.355 Sum_probs=11.4
Q ss_pred eecCCCCccccCCC
Q 026009 185 IYCPKCEDIYYPRS 198 (245)
Q Consensus 185 lyCP~C~DvY~P~s 198 (245)
.|||.|+.+-.|+.
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 48999999998864
No 43
>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=22.69 E-value=59 Score=22.64 Aligned_cols=17 Identities=35% Similarity=0.935 Sum_probs=12.8
Q ss_pred CCCCccceeecCCCCcc
Q 026009 177 IPRSSTVKIYCPKCEDI 193 (245)
Q Consensus 177 ~pg~s~VKlyCP~C~Dv 193 (245)
.|..=.++-|||.|+..
T Consensus 25 ~~~rL~lkKycp~~~kh 41 (48)
T PF00471_consen 25 TPERLELKKYCPRCRKH 41 (48)
T ss_dssp SSSSSEEEEEETSSSSE
T ss_pred CCceeeEeccCCCCCCE
Confidence 35566789999999753
No 44
>PF10588 NADH-G_4Fe-4S_3: NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; InterPro: IPR019574 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. This entry describes the G subunit (one of 14 subunits, A to N) of the NADH-quinone oxidoreductase complex I which generally couples NADH and ubiquinone oxidation/reduction in bacteria and mammalian mitochondria while translocating protons, but may act on NADPH and/or plastoquinone in cyanobacteria and plant chloroplasts. This family does not contain related subunits from formate dehydrogenase complexes. This entry represents the iron-sulphur binding domain of the G subunit.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 3M9S_C 2FUG_L 3IAS_L 2YBB_3 3IAM_3 3I9V_3.
Probab=22.50 E-value=1.5e+02 Score=19.72 Aligned_cols=40 Identities=20% Similarity=0.254 Sum_probs=15.4
Q ss_pred HHHHHHHcCCCCCCCCCCChhhHHHHHHHHHHHhcccccee
Q 026009 97 DYALDLILDVESSHGDMFTEEQNELVESAAEMLYGLIHVRY 137 (245)
Q Consensus 97 ~~aL~~ILd~~~~~~~~~~~~~~~~ie~~A~~LYGLIHARY 137 (245)
+.+|++||...+.+...=+....=.++..| .-||+-++||
T Consensus 2 r~~lelll~~H~~dC~~C~~~G~CeLQ~~~-~~~gv~~~~f 41 (41)
T PF10588_consen 2 RTVLELLLANHPLDCPTCDKNGNCELQDLA-YEYGVDEQRF 41 (41)
T ss_dssp HHHHHHHHTT----TTT-TTGGG-HHHHHH-HHH-S-----
T ss_pred HHHHHHHHhCCCCcCcCCCCCCCCHHHHHH-HHhCCCcCCC
Confidence 468999998776543221112222333333 3699999987
No 45
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=22.12 E-value=59 Score=23.96 Aligned_cols=16 Identities=44% Similarity=1.190 Sum_probs=12.5
Q ss_pred CCCccceeecCCCCcc
Q 026009 178 PRSSTVKIYCPKCEDI 193 (245)
Q Consensus 178 pg~s~VKlyCP~C~Dv 193 (245)
|++..|+..||+|.++
T Consensus 19 ~~~~~~~F~CPnCG~~ 34 (59)
T PRK14890 19 PREKAVKFLCPNCGEV 34 (59)
T ss_pred CCCccCEeeCCCCCCe
Confidence 4455789999999765
No 46
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=21.74 E-value=43 Score=22.43 Aligned_cols=12 Identities=42% Similarity=1.453 Sum_probs=10.1
Q ss_pred ecCCCCccccCC
Q 026009 186 YCPKCEDIYYPR 197 (245)
Q Consensus 186 yCP~C~DvY~P~ 197 (245)
|||.|+.+-.++
T Consensus 2 FCp~Cg~~l~~~ 13 (52)
T smart00661 2 FCPKCGNMLIPK 13 (52)
T ss_pred CCCCCCCccccc
Confidence 899999887765
No 47
>PF08121 Toxin_33: Waglerin family; InterPro: IPR012637 This family consists of the lethal peptides (waglerins) that are found in the venom of Trimeresurus wagleri (Wagler's pit viper) (Tropidolaemus wagleri). Waglerins are 22-24 residue lethal peptides and are competitive antagonist of the muscle nicotinic receptor (nAChR). Waglerin-1 possesses a distinctive selectivity for the alpha-epsilon interface binding site of the mouse nAChR [].; GO: 0030550 acetylcholine receptor inhibitor activity, 0005576 extracellular region
Probab=21.59 E-value=55 Score=19.33 Aligned_cols=15 Identities=33% Similarity=0.658 Sum_probs=11.8
Q ss_pred CCCCCCCCCCCccee
Q 026009 222 GHLKPQKATQSYVPR 236 (245)
Q Consensus 222 P~l~p~~~~~~Y~Pr 236 (245)
|++.|-.++-.|+||
T Consensus 4 pdlrpcyppchyipr 18 (22)
T PF08121_consen 4 PDLRPCYPPCHYIPR 18 (22)
T ss_pred CccccCCCCccccCC
Confidence 678887777788886
Done!