Query 026677
Match_columns 235
No_of_seqs 113 out of 337
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 11:11:02 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026677.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026677hhsearch_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 3E-96 7E-101 631.8 14.4 190 45-234 5-194 (216)
2 PTZ00396 Casein kinase II subu 100.0 1.6E-91 3.4E-96 625.2 16.7 193 43-235 17-209 (251)
3 PF01214 CK_II_beta: Casein ki 100.0 3E-89 6.5E-94 587.3 8.9 184 48-231 1-184 (184)
4 COG5041 SKB2 Casein kinase II, 100.0 2.6E-86 5.7E-91 574.6 10.0 188 45-234 22-209 (242)
5 PRK05978 hypothetical protein; 80.0 1.9 4.1E-05 36.5 3.2 41 137-186 24-64 (148)
6 PF01927 Mut7-C: Mut7-C RNAse 74.0 3.3 7.1E-05 34.2 3.0 52 132-186 72-136 (147)
7 COG1656 Uncharacterized conser 69.2 5 0.00011 34.7 3.1 63 122-187 65-143 (165)
8 smart00647 IBR In Between Ring 51.7 24 0.00052 24.0 3.6 24 137-160 7-32 (64)
9 PF14205 Cys_rich_KTR: Cystein 49.8 7.1 0.00015 28.1 0.6 11 172-182 26-36 (55)
10 KOG4684 Uncharacterized conser 48.8 16 0.00035 33.3 2.8 37 148-184 140-180 (275)
11 PF06827 zf-FPG_IleRS: Zinc fi 46.2 9.1 0.0002 23.3 0.6 10 174-183 21-30 (30)
12 PF06677 Auto_anti-p27: Sjogre 45.4 18 0.00038 24.3 1.9 23 148-181 19-41 (41)
13 PF06044 DRP: Dam-replacing fa 44.6 4.7 0.0001 37.0 -1.2 58 147-211 32-101 (254)
14 PF05191 ADK_lid: Adenylate ki 44.3 15 0.00032 23.9 1.4 13 174-186 1-13 (36)
15 PRK00420 hypothetical protein; 42.2 29 0.00064 28.1 3.1 30 147-187 24-53 (112)
16 COG0401 Uncharacterized homolo 41.0 8.2 0.00018 27.8 -0.2 13 119-131 43-55 (56)
17 PF08772 NOB1_Zn_bind: Nin one 40.8 10 0.00023 28.5 0.3 13 171-183 21-33 (73)
18 PRK00432 30S ribosomal protein 40.5 13 0.00028 25.8 0.8 10 173-182 19-28 (50)
19 TIGR02098 MJ0042_CXXC MJ0042 f 39.9 14 0.00031 23.4 0.8 28 154-184 8-35 (38)
20 COG2888 Predicted Zn-ribbon RN 39.1 19 0.00042 26.3 1.5 17 167-183 20-36 (61)
21 PF03811 Zn_Tnp_IS1: InsA N-te 35.6 21 0.00046 23.3 1.1 12 171-182 2-13 (36)
22 PF13719 zinc_ribbon_5: zinc-r 34.7 19 0.00042 23.2 0.8 29 154-185 8-36 (37)
23 PF11238 DUF3039: Protein of u 34.5 9.7 0.00021 27.7 -0.7 28 151-185 28-55 (58)
24 KOG2828 Acetyl-CoA hydrolase [ 34.1 17 0.00036 35.7 0.6 19 122-140 400-418 (454)
25 PF11335 DUF3137: Protein of u 33.7 18 0.00039 29.3 0.7 17 122-138 62-78 (142)
26 PF10601 zf-LITAF-like: LITAF- 33.2 27 0.00058 25.4 1.5 19 169-187 2-20 (73)
27 PF09788 Tmemb_55A: Transmembr 32.9 38 0.00083 31.3 2.7 38 148-185 125-168 (256)
28 COG4416 Com Mu-like prophage p 32.2 21 0.00047 25.8 0.8 17 168-184 18-34 (60)
29 PF13717 zinc_ribbon_4: zinc-r 31.4 29 0.00062 22.4 1.2 15 173-187 1-15 (36)
30 PF01485 IBR: IBR domain; Int 27.8 79 0.0017 21.3 3.1 43 144-186 16-60 (64)
31 KOG1973 Chromatin remodeling p 26.8 34 0.00074 31.3 1.3 38 142-182 228-267 (274)
32 COG1579 Zn-ribbon protein, pos 26.8 18 0.0004 32.9 -0.4 34 151-184 197-231 (239)
33 COG1631 RPL42A Ribosomal prote 26.4 29 0.00062 27.5 0.6 13 172-184 6-18 (94)
34 KOG1773 Stress responsive prot 25.5 19 0.00042 26.5 -0.4 15 119-133 45-59 (63)
35 PF06222 Phage_TAC: Phage tail 25.5 28 0.00061 29.0 0.5 34 90-129 79-112 (127)
36 KOG0435 Leucyl-tRNA synthetase 25.4 43 0.00094 35.3 1.9 57 143-203 427-502 (876)
37 PF02150 RNA_POL_M_15KD: RNA p 25.2 23 0.00051 22.7 -0.0 14 175-188 2-15 (35)
38 PF03966 Trm112p: Trm112p-like 23.7 39 0.00084 24.3 0.9 12 173-184 52-63 (68)
39 COG5034 TNG2 Chromatin remodel 23.7 49 0.0011 30.7 1.7 39 140-183 225-270 (271)
40 smart00661 RPOL9 RNA polymeras 22.6 40 0.00087 22.4 0.7 12 176-187 2-13 (52)
41 PRK14890 putative Zn-ribbon RN 22.2 59 0.0013 23.7 1.6 16 168-183 19-34 (59)
42 PF00471 Ribosomal_L33: Riboso 22.1 61 0.0013 22.3 1.6 16 167-182 25-40 (48)
43 PRK14810 formamidopyrimidine-D 21.4 58 0.0012 29.7 1.7 26 148-181 246-271 (272)
44 COG3809 Uncharacterized protei 21.3 41 0.00088 26.1 0.6 12 174-185 21-32 (88)
45 PF10588 NADH-G_4Fe-4S_3: NADH 21.1 1.7E+02 0.0036 19.3 3.5 40 87-127 2-41 (41)
46 COG4098 comFA Superfamily II D 20.9 39 0.00085 33.1 0.6 13 159-181 55-67 (441)
47 PF08121 Toxin_33: Waglerin fa 20.8 59 0.0013 19.0 1.1 15 212-226 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=3e-96 Score=631.84 Aligned_cols=190 Identities=71% Similarity=1.301 Sum_probs=183.7
Q ss_pred CCCChHHHHhCCCCCeeEEecCcccccCCCccCCCCCCCCCHHHHHHHHcCCCCCCCCCCChhhHHHHHHHHHHHhcccc
Q 026677 45 DDTSWISWFCNLRGNEFFCEVDDEYIQDDFNLCGLSSQVPYYDYALDLILDVESSHGDMFTEEQNELVESAAEMLYGLIH 124 (235)
Q Consensus 45 ~~~sWI~wFcs~~gneff~eVdedyI~D~FNL~GL~~~v~~y~~aL~~ILd~~~~~~~~~~~~~~~~ie~~A~~LYGLIH 124 (235)
++.+||+|||+++|||||||||+|||+|+|||+||+.+||+|++||++|||.+++++....+++.+++|++|++||||||
T Consensus 5 ee~sWI~wFc~~~GnEffceVdeeyIqD~FNltgL~~~Vp~y~~ald~ILD~~~~~~~e~~~~~~~~iE~aae~LYGLIH 84 (216)
T KOG3092|consen 5 EEVSWISWFCGLRGNEFFCEVDEEYIQDRFNLTGLSEQVPNYRQALDLILDLEPDDELEDNAEQSELIESAAEMLYGLIH 84 (216)
T ss_pred cccchHHHHhcCCCCeeeEecCHHHhhhhhccccccccCchHHHHHHHhhcCCCCcccccchhHHHHHHHHHHHHHHhhh
Confidence 55579999999999999999999999999999999999999999999999999888766666677899999999999999
Q ss_pred ceeeeChHHHHHHHHhhhcCcccCCCCcCCCCCCccccccCCCCCCccceeecCCCCccccCCCCCCCcccccccCCchh
Q 026677 125 VRYILTSKGMAAMLEKYKNYDFGRCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPKCEDIYYPRSKYQGNIDGAYFGTTFP 204 (235)
Q Consensus 125 ARYIlT~~Gl~~M~eKy~~g~FG~CPRv~C~~q~lLPiGlSd~pg~~~VKlyCP~C~DvY~P~s~~~~~iDGAyFGtsFp 204 (235)
||||+|.+||++|++||++++||+||||+|++|+|||+|+||+||+++||+|||+|.|||.|+|+++.+|||||||||||
T Consensus 85 aRYIlT~~Gl~~M~eKy~~~dFG~CPRV~C~~q~~LPvGLsDipg~~~VklYCP~C~dvY~P~ssr~~~iDGa~fGtsFP 164 (216)
T KOG3092|consen 85 ARYILTNRGLAAMLEKYKNGDFGRCPRVYCCGQPVLPVGLSDIPGKSTVKLYCPSCEDVYIPKSSRHGNIDGAYFGTSFP 164 (216)
T ss_pred heeeechHHHHHHHHHHhcCCCCcCCcccccCCccccccccCCCCcceEEEeCCCcccccccccccccccccchhcCCCc
Confidence 99999999999999999999999999999999999999999999999999999999999999999989999999999999
Q ss_pred hHHHHHhCCCCCCCCCCCcceeeeeeeecC
Q 026677 205 HLFLMTYGHLKPQKATQSYVPRVFGFKLHK 234 (235)
Q Consensus 205 h~fl~~yp~l~p~~~~~~y~PrIfGFki~~ 234 (235)
|||||+||++.|+++.++|+|||||||||+
T Consensus 165 hmff~~~p~l~P~r~~~~yvPriyGFkih~ 194 (216)
T KOG3092|consen 165 HMFFMTHPELRPKRPTEQYVPRIYGFKIHK 194 (216)
T ss_pred hhHHHhccccCCCcchhhhcchheeeeeCc
Confidence 999999999999999999999999999997
No 2
>PTZ00396 Casein kinase II subunit beta; Provisional
Probab=100.00 E-value=1.6e-91 Score=625.16 Aligned_cols=193 Identities=53% Similarity=1.046 Sum_probs=182.4
Q ss_pred CCCCCChHHHHhCCCCCeeEEecCcccccCCCccCCCCCCCCCHHHHHHHHcCCCCCCCCCCChhhHHHHHHHHHHHhcc
Q 026677 43 DGDDTSWISWFCNLRGNEFFCEVDDEYIQDDFNLCGLSSQVPYYDYALDLILDVESSHGDMFTEEQNELVESAAEMLYGL 122 (235)
Q Consensus 43 ~~~~~sWI~wFcs~~gneff~eVdedyI~D~FNL~GL~~~v~~y~~aL~~ILd~~~~~~~~~~~~~~~~ie~~A~~LYGL 122 (235)
++++.+||+|||+++||+|||+||+|||+|+||||||+.+||+|++||+||||.+.++++...++..+.++++|++||||
T Consensus 17 s~~~~sWI~wF~~~~gne~f~~Vd~dyI~D~FNl~GL~~~v~~y~~al~~Ild~~~~~~~~~~~~~~~~i~~~a~~LYGL 96 (251)
T PTZ00396 17 SEESMGWIEWFCSLKGHEFLCEVDEDFIRDEFNLYGLKSKFPFYNEALDMILDSEPPDDEDLEDEQFLEVYQEASDLYGL 96 (251)
T ss_pred CCCcCcHHHHHhCCCCCeeEEEeCHHHhcCcchhhCccccccCHHHHHHHHcCCCCCccccccchhHHHHHHHHHHHHHH
Confidence 34677999999999999999999999999999999999999999999999999987765444556678899999999999
Q ss_pred ccceeeeChHHHHHHHHhhhcCcccCCCCcCCCCCCccccccCCCCCCccceeecCCCCccccCCCCCCCcccccccCCc
Q 026677 123 IHVRYILTSKGMAAMLEKYKNYDFGRCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPKCEDIYYPRSKYQGNIDGAYFGTT 202 (235)
Q Consensus 123 IHARYIlT~~Gl~~M~eKy~~g~FG~CPRv~C~~q~lLPiGlSd~pg~~~VKlyCP~C~DvY~P~s~~~~~iDGAyFGts 202 (235)
||||||+|++||++|++||++|+||+||||+|++|+|||||+||+||+++||+|||+|+|||+|++.++..|||||||||
T Consensus 97 IHARyI~T~~Gl~~M~eKY~~g~FG~CPRv~C~~q~~LPvGlSd~~g~~~VKlyCP~C~DvY~p~s~~~~~iDGA~FGts 176 (251)
T PTZ00396 97 IHARFITTPKGLALMREKYLQGKFGHCPRVLCEGQNVLPIGLSDVLKTSRVKVYCPRCQEVYHPKKSSLLDIDGAFFGTS 176 (251)
T ss_pred HhHhHhcCHHHHHHHHHHhhCCCCCCCCCccCCCCcccccccCCCcCcCceeEeCCCchhhcCCCCccccccccceecCc
Confidence 99999999999999999999999999999999999999999999999999999999999999999877669999999999
Q ss_pred hhhHHHHHhCCCCCCCCCCCcceeeeeeeecCC
Q 026677 203 FPHLFLMTYGHLKPQKATQSYVPRVFGFKLHKP 235 (235)
Q Consensus 203 Fph~fl~~yp~l~p~~~~~~y~PrIfGFki~~~ 235 (235)
|||||+|+||++.|++++++|+|||||||||++
T Consensus 177 Fph~fl~~~p~l~p~~~~~~yvPrifGFki~~~ 209 (251)
T PTZ00396 177 FPHLFLMTYPELIPTKPPQYYVPKIFGFKVHKK 209 (251)
T ss_pred HHHHHHHhccccCCCCCCCccCCeeeeEEeccc
Confidence 999999999999999999999999999999964
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=3e-89 Score=587.32 Aligned_cols=184 Identities=64% Similarity=1.221 Sum_probs=153.4
Q ss_pred ChHHHHhCCCCCeeEEecCcccccCCCccCCCCCCCCCHHHHHHHHcCCCCCCCCCCChhhHHHHHHHHHHHhcccccee
Q 026677 48 SWISWFCNLRGNEFFCEVDDEYIQDDFNLCGLSSQVPYYDYALDLILDVESSHGDMFTEEQNELVESAAEMLYGLIHVRY 127 (235)
Q Consensus 48 sWI~wFcs~~gneff~eVdedyI~D~FNL~GL~~~v~~y~~aL~~ILd~~~~~~~~~~~~~~~~ie~~A~~LYGLIHARY 127 (235)
+||+|||+++||+||||||+|||+|+|||+||+++||+|++||++|||.+.++++..++++.+.++++|++|||||||||
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 69999999999999999999999999999999999999999999999998876555566678889999999999999999
Q ss_pred eeChHHHHHHHHhhhcCcccCCCCcCCCCCCccccccCCCCCCccceeecCCCCccccCCCCCCCcccccccCCchhhHH
Q 026677 128 ILTSKGMAAMLEKYKNYDFGRCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPKCEDIYYPRSKYQGNIDGAYFGTTFPHLF 207 (235)
Q Consensus 128 IlT~~Gl~~M~eKy~~g~FG~CPRv~C~~q~lLPiGlSd~pg~~~VKlyCP~C~DvY~P~s~~~~~iDGAyFGtsFph~f 207 (235)
|+|++||++|++||++|+||+||||+|++|+|||||+||+||+++||||||+|+|||+|++.+.++||||||||||||||
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 99999999999999999999999999999999999999999999999999999999999887788999999999999999
Q ss_pred HHHhCCCCCCCCCCCcceeeeeee
Q 026677 208 LMTYGHLKPQKATQSYVPRVFGFK 231 (235)
Q Consensus 208 l~~yp~l~p~~~~~~y~PrIfGFk 231 (235)
+|+||++.|+.+.++|+|||||||
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=2.6e-86 Score=574.55 Aligned_cols=188 Identities=54% Similarity=1.131 Sum_probs=178.2
Q ss_pred CCCChHHHHhCCCCCeeEEecCcccccCCCccCCCCCCCCCHHHHHHHHcCCCCCCCCCCChhhHHHHHHHHHHHhcccc
Q 026677 45 DDTSWISWFCNLRGNEFFCEVDDEYIQDDFNLCGLSSQVPYYDYALDLILDVESSHGDMFTEEQNELVESAAEMLYGLIH 124 (235)
Q Consensus 45 ~~~sWI~wFcs~~gneff~eVdedyI~D~FNL~GL~~~v~~y~~aL~~ILd~~~~~~~~~~~~~~~~ie~~A~~LYGLIH 124 (235)
+...||+|||+++||||||+||++||+|.|||+||+..||+|.+||++|||...+.. ..+.+.+.||.+|++||||||
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 333799999999999999999999999999999999999999999999999876543 233446789999999999999
Q ss_pred ceeeeChHHHHHHHHhhhcCcccCCCCcCCCCCCccccccCCCCCCccceeecCCCCccccCCCCCCCcccccccCCchh
Q 026677 125 VRYILTSKGMAAMLEKYKNYDFGRCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPKCEDIYYPRSKYQGNIDGAYFGTTFP 204 (235)
Q Consensus 125 ARYIlT~~Gl~~M~eKy~~g~FG~CPRv~C~~q~lLPiGlSd~pg~~~VKlyCP~C~DvY~P~s~~~~~iDGAyFGtsFp 204 (235)
||||+|..||++|++||+.++||+||||+||+|+|||+||||+||+++||||||+|.|+|.|+|+++..|||||||||||
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 026677 205 HLFLMTYGHLKPQKATQSYVPRVFGFKLHK 234 (235)
Q Consensus 205 h~fl~~yp~l~p~~~~~~y~PrIfGFki~~ 234 (235)
|||+++||++.|+++.+.|+|||||||||+
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=79.96 E-value=1.9 Score=36.53 Aligned_cols=41 Identities=17% Similarity=0.220 Sum_probs=32.3
Q ss_pred HHHhhhcCcccCCCCcCCCCCCccccccCCCCCCccceeecCCCCccccC
Q 026677 137 MLEKYKNYDFGRCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPKCEDIYYP 186 (235)
Q Consensus 137 M~eKy~~g~FG~CPRv~C~~q~lLPiGlSd~pg~~~VKlyCP~C~DvY~P 186 (235)
+..-..+|-.|+||| |..-+++= +--+|+--||.|..-|.+
T Consensus 24 ~~~~~~rGl~grCP~--CG~G~LF~-------g~Lkv~~~C~~CG~~~~~ 64 (148)
T PRK05978 24 VGRAMWRGFRGRCPA--CGEGKLFR-------AFLKPVDHCAACGEDFTH 64 (148)
T ss_pred hHHHHHHHHcCcCCC--CCCCcccc-------cccccCCCccccCCcccc
Confidence 445677899999998 77777762 455788899999999975
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=73.97 E-value=3.3 Score=34.24 Aligned_cols=52 Identities=31% Similarity=0.776 Sum_probs=32.8
Q ss_pred HHHHHHHHhhh-----cCcccCCCCcCCCCCCccccccCCCCC--------CccceeecCCCCccccC
Q 026677 132 KGMAAMLEKYK-----NYDFGRCPRVYCCGQPCLPVGQSDIPR--------SSTVKIYCPKCEDIYYP 186 (235)
Q Consensus 132 ~Gl~~M~eKy~-----~g~FG~CPRv~C~~q~lLPiGlSd~pg--------~~~VKlyCP~C~DvY~P 186 (235)
+=|.++.+++. +..|.+||+ ||+ ++.|+...+..+ ....=..||.|+.||=+
T Consensus 72 ~QL~ev~~~~~l~~~~~~~~sRC~~--CN~-~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiyW~ 136 (147)
T PF01927_consen 72 EQLREVLERFGLKLRLDPIFSRCPK--CNG-PLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIYWE 136 (147)
T ss_pred HHHHHHHHHcCCccccCCCCCccCC--CCc-EeeechhhccccccCccccccCCeEEECCCCCCEecc
Confidence 34444555553 445899986 666 788886654422 22234679999999954
No 7
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=69.24 E-value=5 Score=34.70 Aligned_cols=63 Identities=27% Similarity=0.460 Sum_probs=42.9
Q ss_pred cccceeeeChHHHHHHHHh---hh-----cCcccCCCCcCCCCCCccccccCC--------CCCCccceeecCCCCcccc
Q 026677 122 LIHVRYILTSKGMAAMLEK---YK-----NYDFGRCPRVYCCGQPCLPVGQSD--------IPRSSTVKIYCPKCEDIYY 185 (235)
Q Consensus 122 LIHARYIlT~~Gl~~M~eK---y~-----~g~FG~CPRv~C~~q~lLPiGlSd--------~pg~~~VKlyCP~C~DvY~ 185 (235)
.++|=||-+..=.+||.+= +. +-+|-+||. ||+ +|+++-... +.+....-..||+|..+|=
T Consensus 65 g~~~i~i~~~s~~~Ql~e~~~~~~l~~~~~~e~~RCp~--CN~-~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~CgkiYW 141 (165)
T COG1656 65 GIKAILIRSDSIEEQLAEFLARLGLKPRLFPEFSRCPE--CNG-ELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKIYW 141 (165)
T ss_pred cCceEEEeCCCHHHHHHHHHHHhccchhcccccccCcc--cCC-EeccCcHHHHhhccchhhhhcccceeECCCCccccc
Confidence 3677788888777777765 22 334889994 877 677776655 2233344455999999997
Q ss_pred CC
Q 026677 186 PR 187 (235)
Q Consensus 186 P~ 187 (235)
|-
T Consensus 142 ~G 143 (165)
T COG1656 142 KG 143 (165)
T ss_pred Cc
Confidence 63
No 8
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=51.70 E-value=24 Score=23.97 Aligned_cols=24 Identities=29% Similarity=0.588 Sum_probs=15.4
Q ss_pred HHHhhhc--CcccCCCCcCCCCCCcc
Q 026677 137 MLEKYKN--YDFGRCPRVYCCGQPCL 160 (235)
Q Consensus 137 M~eKy~~--g~FG~CPRv~C~~q~lL 160 (235)
+.++|.+ ..+-.||+..|+..-.+
T Consensus 7 ~~~~~i~~~~~~~~CP~~~C~~~~~~ 32 (64)
T smart00647 7 LLESYVESNPDLKWCPAPDCSAAIIV 32 (64)
T ss_pred HHHHHHhcCCCccCCCCCCCcceEEe
Confidence 4444533 46778999999764433
No 9
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=49.77 E-value=7.1 Score=28.07 Aligned_cols=11 Identities=45% Similarity=1.407 Sum_probs=8.7
Q ss_pred cceeecCCCCc
Q 026677 172 TVKIYCPKCED 182 (235)
Q Consensus 172 ~VKlyCP~C~D 182 (235)
..-||||+|+.
T Consensus 26 NfPlyCpKCK~ 36 (55)
T PF14205_consen 26 NFPLYCPKCKQ 36 (55)
T ss_pred cccccCCCCCc
Confidence 44799999964
No 10
>KOG4684 consensus Uncharacterized conserved protein, contains C4-type Zn-finger [General function prediction only]
Probab=48.75 E-value=16 Score=33.32 Aligned_cols=37 Identities=19% Similarity=0.557 Sum_probs=25.9
Q ss_pred CCCCcCCCCC----CccccccCCCCCCccceeecCCCCccc
Q 026677 148 RCPRVYCCGQ----PCLPVGQSDIPRSSTVKIYCPKCEDIY 184 (235)
Q Consensus 148 ~CPRv~C~~q----~lLPiGlSd~pg~~~VKlyCP~C~DvY 184 (235)
.|||-+|++- ++.|--++..+.-..+++-|-.|+++|
T Consensus 140 ACPRpnCkRiInL~p~~~~p~~P~~~P~gcRV~CgHC~~tF 180 (275)
T KOG4684|consen 140 ACPRPNCKRIINLDPLIEKPRDPGTAPTGCRVKCGHCNETF 180 (275)
T ss_pred ccCCCCcceeeecCCCCCCCCCCCCCCcceEEEecCcccee
Confidence 3999999863 334434444444456899999999998
No 11
>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=46.24 E-value=9.1 Score=23.31 Aligned_cols=10 Identities=30% Similarity=1.265 Sum_probs=7.1
Q ss_pred eeecCCCCcc
Q 026677 174 KIYCPKCEDI 183 (235)
Q Consensus 174 KlyCP~C~Dv 183 (235)
--|||+|++|
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 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=45.39 E-value=18 Score=24.35 Aligned_cols=23 Identities=48% Similarity=1.223 Sum_probs=15.4
Q ss_pred CCCCcCCCCCCccccccCCCCCCccceeecCCCC
Q 026677 148 RCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPKCE 181 (235)
Q Consensus 148 ~CPRv~C~~q~lLPiGlSd~pg~~~VKlyCP~C~ 181 (235)
.||. | +.|++. +. .+ ++|||.|.
T Consensus 19 ~Cp~--C-~~PL~~----~k--~g--~~~Cv~C~ 41 (41)
T PF06677_consen 19 HCPD--C-GTPLMR----DK--DG--KIYCVSCG 41 (41)
T ss_pred ccCC--C-CCeeEE----ec--CC--CEECCCCC
Confidence 6884 7 677775 11 22 68999994
No 13
>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=44.60 E-value=4.7 Score=36.99 Aligned_cols=58 Identities=34% Similarity=0.749 Sum_probs=26.0
Q ss_pred cCCCCcCCCCCCccccccCCCCCCccc-eeecCCCCccccCCCCCC---C-cccccccC-------CchhhHHHHHh
Q 026677 147 GRCPRVYCCGQPCLPVGQSDIPRSSTV-KIYCPKCEDIYYPRSKYQ---G-NIDGAYFG-------TTFPHLFLMTY 211 (235)
Q Consensus 147 G~CPRv~C~~q~lLPiGlSd~pg~~~V-KlyCP~C~DvY~P~s~~~---~-~iDGAyFG-------tsFph~fl~~y 211 (235)
+.||+ |+..++-=+ +.-.+| -.|||+|++-|.-+|... . -.||||-- .+=|.+|||+|
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 444444333 334445 578999999998875321 1 34999963 24577778877
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=44.33 E-value=15 Score=23.89 Aligned_cols=13 Identities=46% Similarity=1.007 Sum_probs=10.9
Q ss_pred eeecCCCCccccC
Q 026677 174 KIYCPKCEDIYYP 186 (235)
Q Consensus 174 KlyCP~C~DvY~P 186 (235)
+..||.|..+||-
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
>PRK00420 hypothetical protein; Validated
Probab=42.22 E-value=29 Score=28.12 Aligned_cols=30 Identities=23% Similarity=0.643 Sum_probs=20.8
Q ss_pred cCCCCcCCCCCCccccccCCCCCCccceeecCCCCccccCC
Q 026677 147 GRCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPKCEDIYYPR 187 (235)
Q Consensus 147 G~CPRv~C~~q~lLPiGlSd~pg~~~VKlyCP~C~DvY~P~ 187 (235)
+.||. |. .|++ +...-+.|||.|..++.-.
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 78998 65 3443 2133389999999999753
No 16
>COG0401 Uncharacterized homolog of Blt101 [Function unknown]
Probab=41.02 E-value=8.2 Score=27.84 Aligned_cols=13 Identities=31% Similarity=0.749 Sum_probs=11.0
Q ss_pred HhccccceeeeCh
Q 026677 119 LYGLIHVRYILTS 131 (235)
Q Consensus 119 LYGLIHARYIlT~ 131 (235)
+=|+|||=||++.
T Consensus 43 ~PGiiHA~yvi~~ 55 (56)
T COG0401 43 IPGIIHALYVILR 55 (56)
T ss_pred hhhhHhheEEEEe
Confidence 4589999999875
No 17
>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=40.82 E-value=10 Score=28.48 Aligned_cols=13 Identities=38% Similarity=1.042 Sum_probs=5.6
Q ss_pred ccceeecCCCCcc
Q 026677 171 STVKIYCPKCEDI 183 (235)
Q Consensus 171 ~~VKlyCP~C~Dv 183 (235)
.+-|+|||+|.--
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 18
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=40.55 E-value=13 Score=25.81 Aligned_cols=10 Identities=30% Similarity=1.168 Sum_probs=5.4
Q ss_pred ceeecCCCCc
Q 026677 173 VKIYCPKCED 182 (235)
Q Consensus 173 VKlyCP~C~D 182 (235)
++-|||+|..
T Consensus 19 ~~~fCP~Cg~ 28 (50)
T PRK00432 19 KNKFCPRCGS 28 (50)
T ss_pred ccCcCcCCCc
Confidence 3446666654
No 19
>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=39.91 E-value=14 Score=23.38 Aligned_cols=28 Identities=21% Similarity=0.387 Sum_probs=16.2
Q ss_pred CCCCCccccccCCCCCCccceeecCCCCccc
Q 026677 154 CCGQPCLPVGQSDIPRSSTVKIYCPKCEDIY 184 (235)
Q Consensus 154 C~~q~lLPiGlSd~pg~~~VKlyCP~C~DvY 184 (235)
|..+.-+|-..- +....++-||+|+..+
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 20
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=39.10 E-value=19 Score=26.35 Aligned_cols=17 Identities=35% Similarity=0.960 Sum_probs=14.5
Q ss_pred CCCCccceeecCCCCcc
Q 026677 167 IPRSSTVKIYCPKCEDI 183 (235)
Q Consensus 167 ~pg~~~VKlyCP~C~Dv 183 (235)
.|++..|+-.||+|.++
T Consensus 20 ~p~e~~v~F~CPnCGe~ 36 (61)
T COG2888 20 APGETAVKFPCPNCGEV 36 (61)
T ss_pred ccCCceeEeeCCCCCce
Confidence 37889999999999943
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=35.63 E-value=21 Score=23.28 Aligned_cols=12 Identities=25% Similarity=1.143 Sum_probs=10.1
Q ss_pred ccceeecCCCCc
Q 026677 171 STVKIYCPKCED 182 (235)
Q Consensus 171 ~~VKlyCP~C~D 182 (235)
.+|.+.||+|+.
T Consensus 2 a~i~v~CP~C~s 13 (36)
T PF03811_consen 2 AKIDVHCPRCQS 13 (36)
T ss_pred CcEeeeCCCCCC
Confidence 478999999974
No 22
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=34.69 E-value=19 Score=23.17 Aligned_cols=29 Identities=24% Similarity=0.547 Sum_probs=18.8
Q ss_pred CCCCCccccccCCCCCCccceeecCCCCcccc
Q 026677 154 CCGQPCLPVGQSDIPRSSTVKIYCPKCEDIYY 185 (235)
Q Consensus 154 C~~q~lLPiGlSd~pg~~~VKlyCP~C~DvY~ 185 (235)
|+...-||-. ..+.+..++-||+|+.++.
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 5544444432 2446677999999998874
No 23
>PF11238 DUF3039: Protein of unknown function (DUF3039); InterPro: IPR021400 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=34.46 E-value=9.7 Score=27.67 Aligned_cols=28 Identities=29% Similarity=0.636 Sum_probs=17.8
Q ss_pred CcCCCCCCccccccCCCCCCccceeecCCCCcccc
Q 026677 151 RVYCCGQPCLPVGQSDIPRSSTVKIYCPKCEDIYY 185 (235)
Q Consensus 151 Rv~C~~q~lLPiGlSd~pg~~~VKlyCP~C~DvY~ 185 (235)
+.+|.. +.|.+.+..+ ..| ||.|++||.
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 24
>KOG2828 consensus Acetyl-CoA hydrolase [Energy production and conversion]
Probab=34.12 E-value=17 Score=35.70 Aligned_cols=19 Identities=32% Similarity=0.630 Sum_probs=15.7
Q ss_pred cccceeeeChHHHHHHHHh
Q 026677 122 LIHVRYILTSKGMAAMLEK 140 (235)
Q Consensus 122 LIHARYIlT~~Gl~~M~eK 140 (235)
--|++||+|+.||..+.-|
T Consensus 400 rah~~y~VTEhGiA~L~Gk 418 (454)
T KOG2828|consen 400 RAHLDYLVTEHGIADLWGK 418 (454)
T ss_pred ccceeEEEecccHHHHhCC
Confidence 3599999999999987533
No 25
>PF11335 DUF3137: Protein of unknown function (DUF3137) ; InterPro: IPR021484 This bacterial family of proteins has no known function.
Probab=33.69 E-value=18 Score=29.32 Aligned_cols=17 Identities=41% Similarity=0.604 Sum_probs=14.0
Q ss_pred cccceeeeChHHHHHHH
Q 026677 122 LIHVRYILTSKGMAAML 138 (235)
Q Consensus 122 LIHARYIlT~~Gl~~M~ 138 (235)
.+.|||||||.=|+.+.
T Consensus 62 ~~~AryiLtP~~mE~L~ 78 (142)
T PF11335_consen 62 QVEARYILTPSFMERLL 78 (142)
T ss_pred HHHHHHhCCHHHHHHHH
Confidence 35799999999887665
No 26
>PF10601 zf-LITAF-like: LITAF-like zinc ribbon domain; InterPro: IPR006629 Members of this family display a conserved zinc ribbon structure [] with the motif C-XX-C- separated from the more C-terminal HX-C(P)X-C-X4-G-R motif by a variable region of usually 25-30 (hydrophobic) residues. Although it belongs to one of the zinc finger's fold groups (zinc ribbon), this particular domain was first identified in LPS-induced tumour necrosis alpha factor (LITAF) which is produced in mammalian cells after being challenged with lipopolysaccharide (LPS). The hydrophobic region probably inserts into the membrane rather than traversing it. Such an insertion brings together the N- and C-terminal C-XX-C motifs to form a compact Zn2+-binding structure [].
Probab=33.24 E-value=27 Score=25.35 Aligned_cols=19 Identities=37% Similarity=0.856 Sum_probs=15.4
Q ss_pred CCccceeecCCCCccccCC
Q 026677 169 RSSTVKIYCPKCEDIYYPR 187 (235)
Q Consensus 169 g~~~VKlyCP~C~DvY~P~ 187 (235)
+..++.++||.|+..=.+.
T Consensus 2 ~~~p~~~~CP~C~~~~~T~ 20 (73)
T PF10601_consen 2 GPEPVRIYCPYCQQQVQTR 20 (73)
T ss_pred CCCceeeECCCCCCEEEEE
Confidence 5678999999999887653
No 27
>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=32.87 E-value=38 Score=31.25 Aligned_cols=38 Identities=24% Similarity=0.637 Sum_probs=24.4
Q ss_pred CCCCcCCCCCCcc-cc--cc-CCCC--CCccceeecCCCCcccc
Q 026677 148 RCPRVYCCGQPCL-PV--GQ-SDIP--RSSTVKIYCPKCEDIYY 185 (235)
Q Consensus 148 ~CPRv~C~~q~lL-Pi--Gl-Sd~p--g~~~VKlyCP~C~DvY~ 185 (235)
.|||-+|++--.| |. |- +..+ .-.++++-|+.|++.+.
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 3999999975333 22 11 1111 22578999999999985
No 28
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=32.19 E-value=21 Score=25.79 Aligned_cols=17 Identities=18% Similarity=0.698 Sum_probs=13.2
Q ss_pred CCCccceeecCCCCccc
Q 026677 168 PRSSTVKIYCPKCEDIY 184 (235)
Q Consensus 168 pg~~~VKlyCP~C~DvY 184 (235)
-+++-++.-||+|+.|=
T Consensus 18 ~~~~yle~KCPrCK~vN 34 (60)
T COG4416 18 EGQAYLEKKCPRCKEVN 34 (60)
T ss_pred ccceeeeecCCccceee
Confidence 34567889999998764
No 29
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=31.44 E-value=29 Score=22.35 Aligned_cols=15 Identities=33% Similarity=0.766 Sum_probs=12.2
Q ss_pred ceeecCCCCccccCC
Q 026677 173 VKIYCPKCEDIYYPR 187 (235)
Q Consensus 173 VKlyCP~C~DvY~P~ 187 (235)
+++-||+|+-.|.-+
T Consensus 1 M~i~Cp~C~~~y~i~ 15 (36)
T PF13717_consen 1 MIITCPNCQAKYEID 15 (36)
T ss_pred CEEECCCCCCEEeCC
Confidence 478899999999743
No 30
>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=27.83 E-value=79 Score=21.26 Aligned_cols=43 Identities=19% Similarity=0.226 Sum_probs=16.8
Q ss_pred CcccCCCCcCCCCCCccccccCCC--CCCccceeecCCCCccccC
Q 026677 144 YDFGRCPRVYCCGQPCLPVGQSDI--PRSSTVKIYCPKCEDIYYP 186 (235)
Q Consensus 144 g~FG~CPRv~C~~q~lLPiGlSd~--pg~~~VKlyCP~C~DvY~P 186 (235)
..+-.||+..|+..-...-|.... -=..-=..||..|+.-+|+
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 344589999999754444333321 0000114556666665554
No 31
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=26.85 E-value=34 Score=31.28 Aligned_cols=38 Identities=26% Similarity=0.518 Sum_probs=26.9
Q ss_pred hcCcccCCCCcCCC-CCCccc-cccCCCCCCccceeecCCCCc
Q 026677 142 KNYDFGRCPRVYCC-GQPCLP-VGQSDIPRSSTVKIYCPKCED 182 (235)
Q Consensus 142 ~~g~FG~CPRv~C~-~q~lLP-iGlSd~pg~~~VKlyCP~C~D 182 (235)
.-|.++-|=+..|. .--=+| |||...|.. |.|||+|+.
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 35677778888887 444455 599866644 499999964
No 32
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=26.83 E-value=18 Score=32.89 Aligned_cols=34 Identities=26% Similarity=0.494 Sum_probs=24.6
Q ss_pred CcCCCCCC-ccccccCCCCCCccceeecCCCCccc
Q 026677 151 RVYCCGQP-CLPVGQSDIPRSSTVKIYCPKCEDIY 184 (235)
Q Consensus 151 Rv~C~~q~-lLPiGlSd~pg~~~VKlyCP~C~DvY 184 (235)
.--|.|++ .||.+........-=-++||.|.-|-
T Consensus 197 g~~C~GC~m~l~~~~~~~V~~~d~iv~CP~CgRIL 231 (239)
T COG1579 197 GRVCGGCHMKLPSQTLSKVRKKDEIVFCPYCGRIL 231 (239)
T ss_pred CCcccCCeeeecHHHHHHHhcCCCCccCCccchHH
Confidence 34588887 68887765555565568999998764
No 33
>COG1631 RPL42A Ribosomal protein L44E [Translation, ribosomal structure and biogenesis]
Probab=26.39 E-value=29 Score=27.52 Aligned_cols=13 Identities=31% Similarity=0.874 Sum_probs=10.5
Q ss_pred cceeecCCCCccc
Q 026677 172 TVKIYCPKCEDIY 184 (235)
Q Consensus 172 ~VKlyCP~C~DvY 184 (235)
+++.|||.|+..=
T Consensus 6 ~~~tyCp~CkkhT 18 (94)
T COG1631 6 KRRTYCPYCKKHT 18 (94)
T ss_pred ceeecCcccccce
Confidence 6789999998643
No 34
>KOG1773 consensus Stress responsive protein [General function prediction only]
Probab=25.53 E-value=19 Score=26.52 Aligned_cols=15 Identities=40% Similarity=0.793 Sum_probs=12.2
Q ss_pred HhccccceeeeChHH
Q 026677 119 LYGLIHVRYILTSKG 133 (235)
Q Consensus 119 LYGLIHARYIlT~~G 133 (235)
+=|+|||=|+++-++
T Consensus 45 iPgiIhA~yii~~~~ 59 (63)
T KOG1773|consen 45 IPGIIHAIYIIFFRG 59 (63)
T ss_pred hHHHHhhEEEEEEec
Confidence 458999999997654
No 35
>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=25.52 E-value=28 Score=28.99 Aligned_cols=34 Identities=29% Similarity=0.707 Sum_probs=17.4
Q ss_pred HHHHcCCCCCCCCCCChhhHHHHHHHHHHHhccccceeee
Q 026677 90 LDLILDVESSHGDMFTEEQNELVESAAEMLYGLIHVRYIL 129 (235)
Q Consensus 90 L~~ILd~~~~~~~~~~~~~~~~ie~~A~~LYGLIHARYIl 129 (235)
+++++|.+.. -.|.+++.+.+ ...||-.|||-+-
T Consensus 79 idVL~dE~~~--rVFsd~D~~~V----~~~YGPVHaRLl~ 112 (127)
T PF06222_consen 79 IDVLLDEDGQ--RVFSDDDAEQV----AAIYGPVHARLLR 112 (127)
T ss_dssp HHHEE-TTS---BSS-GGGHHHH----HCC--HHHHHHHH
T ss_pred hHHHhcCCCC--cccCcchHHHH----HHHhchHHHHHHH
Confidence 4566665443 34555554443 3489999999653
No 36
>KOG0435 consensus Leucyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=25.38 E-value=43 Score=35.30 Aligned_cols=57 Identities=25% Similarity=0.638 Sum_probs=37.4
Q ss_pred cCcccC-CCCcCCCCCCccccccCCCCCCcc------------------ceeecCCCCccccCCCCCCCcccccccCCch
Q 026677 143 NYDFGR-CPRVYCCGQPCLPVGQSDIPRSST------------------VKIYCPKCEDIYYPRSKYQGNIDGAYFGTTF 203 (235)
Q Consensus 143 ~g~FG~-CPRv~C~~q~lLPiGlSd~pg~~~------------------VKlyCP~C~DvY~P~s~~~~~iDGAyFGtsF 203 (235)
+.-+|+ =|-|.|..+--+||-+|+-|=.-+ |+.-||+|++ |-...-...| .|+++++
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 334564 688999998888888887765443 8899999998 4222221333 5666655
No 37
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=25.19 E-value=23 Score=22.71 Aligned_cols=14 Identities=36% Similarity=1.355 Sum_probs=11.4
Q ss_pred eecCCCCccccCCC
Q 026677 175 IYCPKCEDIYYPRS 188 (235)
Q Consensus 175 lyCP~C~DvY~P~s 188 (235)
.|||.|+.+-.|+.
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 49999999998864
No 38
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=23.73 E-value=39 Score=24.29 Aligned_cols=12 Identities=33% Similarity=0.993 Sum_probs=11.0
Q ss_pred ceeecCCCCccc
Q 026677 173 VKIYCPKCEDIY 184 (235)
Q Consensus 173 VKlyCP~C~DvY 184 (235)
=.|.||.|+-+|
T Consensus 52 g~L~Cp~c~r~Y 63 (68)
T PF03966_consen 52 GELICPECGREY 63 (68)
T ss_dssp TEEEETTTTEEE
T ss_pred CEEEcCCCCCEE
Confidence 489999999999
No 39
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=23.66 E-value=49 Score=30.74 Aligned_cols=39 Identities=33% Similarity=0.774 Sum_probs=26.3
Q ss_pred hhhcCcccCCCCcCCCCCCc------cc-cccCCCCCCccceeecCCCCcc
Q 026677 140 KYKNYDFGRCPRVYCCGQPC------LP-VGQSDIPRSSTVKIYCPKCEDI 183 (235)
Q Consensus 140 Ky~~g~FG~CPRv~C~~q~l------LP-iGlSd~pg~~~VKlyCP~C~Dv 183 (235)
..++.-||. =|.|.+.+| || |||..-|+ -+.|||-|++.
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 347888885 444554443 45 49987663 48999999864
No 40
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=22.62 E-value=40 Score=22.37 Aligned_cols=12 Identities=42% Similarity=1.453 Sum_probs=10.2
Q ss_pred ecCCCCccccCC
Q 026677 176 YCPKCEDIYYPR 187 (235)
Q Consensus 176 yCP~C~DvY~P~ 187 (235)
|||.|+.+-.++
T Consensus 2 FCp~Cg~~l~~~ 13 (52)
T smart00661 2 FCPKCGNMLIPK 13 (52)
T ss_pred CCCCCCCccccc
Confidence 899999888765
No 41
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=22.17 E-value=59 Score=23.70 Aligned_cols=16 Identities=44% Similarity=1.190 Sum_probs=12.5
Q ss_pred CCCccceeecCCCCcc
Q 026677 168 PRSSTVKIYCPKCEDI 183 (235)
Q Consensus 168 pg~~~VKlyCP~C~Dv 183 (235)
|.+..|+..||+|.++
T Consensus 19 ~~~~~~~F~CPnCG~~ 34 (59)
T PRK14890 19 PREKAVKFLCPNCGEV 34 (59)
T ss_pred CCCccCEeeCCCCCCe
Confidence 4455789999999765
No 42
>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=22.15 E-value=61 Score=22.34 Aligned_cols=16 Identities=38% Similarity=1.038 Sum_probs=12.6
Q ss_pred CCCCccceeecCCCCc
Q 026677 167 IPRSSTVKIYCPKCED 182 (235)
Q Consensus 167 ~pg~~~VKlyCP~C~D 182 (235)
.|..=.++-|||.|+.
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 43
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=21.42 E-value=58 Score=29.66 Aligned_cols=26 Identities=31% Similarity=0.732 Sum_probs=15.5
Q ss_pred CCCCcCCCCCCccccccCCCCCCccceeecCCCC
Q 026677 148 RCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPKCE 181 (235)
Q Consensus 148 ~CPRv~C~~q~lLPiGlSd~pg~~~VKlyCP~C~ 181 (235)
.||| |.. ++.=+... ++.--|||.|+
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 35578999997
No 44
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.33 E-value=41 Score=26.15 Aligned_cols=12 Identities=33% Similarity=1.190 Sum_probs=10.0
Q ss_pred eeecCCCCcccc
Q 026677 174 KIYCPKCEDIYY 185 (235)
Q Consensus 174 KlyCP~C~DvY~ 185 (235)
--|||+|+-|..
T Consensus 21 iD~CPrCrGVWL 32 (88)
T COG3809 21 IDYCPRCRGVWL 32 (88)
T ss_pred eeeCCccccEee
Confidence 459999999985
No 45
>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=21.08 E-value=1.7e+02 Score=19.26 Aligned_cols=40 Identities=20% Similarity=0.254 Sum_probs=15.2
Q ss_pred HHHHHHHcCCCCCCCCCCChhhHHHHHHHHHHHhcccccee
Q 026677 87 DYALDLILDVESSHGDMFTEEQNELVESAAEMLYGLIHVRY 127 (235)
Q Consensus 87 ~~aL~~ILd~~~~~~~~~~~~~~~~ie~~A~~LYGLIHARY 127 (235)
+.+|++||...+-+...=+....=.++..| .-||+-++||
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 468999998765443221112222333343 4699999987
No 46
>COG4098 comFA Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [DNA replication, recombination, and repair]
Probab=20.94 E-value=39 Score=33.07 Aligned_cols=13 Identities=46% Similarity=1.109 Sum_probs=10.5
Q ss_pred ccccccCCCCCCccceeecCCCC
Q 026677 159 CLPVGQSDIPRSSTVKIYCPKCE 181 (235)
Q Consensus 159 lLPiGlSd~pg~~~VKlyCP~C~ 181 (235)
-||+| ++||++|-
T Consensus 55 ~lp~~----------~~YCr~Cl 67 (441)
T COG4098 55 KLPCG----------CLYCRNCL 67 (441)
T ss_pred ccccc----------eEeehhhh
Confidence 57777 89999984
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=20.76 E-value=59 Score=18.95 Aligned_cols=15 Identities=33% Similarity=0.658 Sum_probs=11.4
Q ss_pred CCCCCCCCCCCccee
Q 026677 212 GHLKPQKATQSYVPR 226 (235)
Q Consensus 212 p~l~p~~~~~~y~Pr 226 (235)
|++.|-.++-.|+||
T Consensus 4 pdlrpcyppchyipr 18 (22)
T PF08121_consen 4 PDLRPCYPPCHYIPR 18 (22)
T ss_pred CccccCCCCccccCC
Confidence 677777777778876
Done!