Query 025636
Match_columns 250
No_of_seqs 117 out of 337
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 07:54:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025636.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025636hhsearch_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 5.3E-96 1E-100 637.5 14.3 193 58-250 3-195 (216)
2 PTZ00396 Casein kinase II subu 100.0 1.1E-90 2.4E-95 625.8 16.6 193 58-250 17-209 (251)
3 PF01214 CK_II_beta: Casein ki 100.0 9.8E-89 2.1E-93 589.6 8.6 184 63-246 1-184 (184)
4 COG5041 SKB2 Casein kinase II, 100.0 9.9E-86 2.2E-90 577.5 9.9 188 60-249 22-209 (242)
5 PRK05978 hypothetical protein; 77.2 2.5 5.3E-05 36.3 3.1 41 152-201 24-64 (148)
6 PF01927 Mut7-C: Mut7-C RNAse 72.3 3.8 8.3E-05 34.2 3.0 41 158-201 88-136 (147)
7 COG1656 Uncharacterized conser 68.2 5.3 0.00011 35.0 3.1 62 138-202 66-143 (165)
8 KOG4684 Uncharacterized conser 52.4 13 0.00028 34.4 2.8 36 164-199 141-180 (275)
9 smart00647 IBR In Between Ring 49.7 26 0.00056 24.1 3.5 23 152-174 7-31 (64)
10 PRK00420 hypothetical protein; 48.4 14 0.00031 30.4 2.2 30 162-202 24-53 (112)
11 PF06677 Auto_anti-p27: Sjogre 46.2 17 0.00036 24.8 1.9 23 163-196 19-41 (41)
12 PF14205 Cys_rich_KTR: Cystein 45.8 8.7 0.00019 28.1 0.5 11 187-197 26-36 (55)
13 PF06827 zf-FPG_IleRS: Zinc fi 43.5 11 0.00023 23.3 0.6 10 189-198 21-30 (30)
14 PF05191 ADK_lid: Adenylate ki 40.3 19 0.00041 23.8 1.4 13 189-201 1-13 (36)
15 TIGR02098 MJ0042_CXXC MJ0042 f 40.3 14 0.0003 23.7 0.8 28 169-199 8-35 (38)
16 PF06044 DRP: Dam-replacing fa 40.1 6 0.00013 36.8 -1.3 58 162-226 32-101 (254)
17 PRK00432 30S ribosomal protein 37.7 15 0.00033 25.8 0.8 9 189-197 20-28 (50)
18 PF03811 Zn_Tnp_IS1: InsA N-te 36.2 20 0.00044 23.7 1.1 12 186-197 2-13 (36)
19 COG0401 Uncharacterized homolo 36.0 11 0.00024 27.6 -0.2 13 134-146 43-55 (56)
20 PF09788 Tmemb_55A: Transmembr 35.5 33 0.00071 32.1 2.7 38 163-200 125-168 (256)
21 PF08772 NOB1_Zn_bind: Nin one 35.1 15 0.00032 28.1 0.3 11 186-196 21-31 (73)
22 COG2888 Predicted Zn-ribbon RN 34.4 25 0.00055 26.2 1.5 17 182-198 20-36 (61)
23 PF13719 zinc_ribbon_5: zinc-r 33.5 21 0.00045 23.4 0.8 29 169-200 8-36 (37)
24 PF13717 zinc_ribbon_4: zinc-r 32.8 26 0.00057 22.9 1.2 15 188-202 1-15 (36)
25 PF10601 zf-LITAF-like: LITAF- 32.7 27 0.00059 25.6 1.5 19 184-202 2-20 (73)
26 PF11238 DUF3039: Protein of u 31.5 11 0.00025 27.7 -0.7 28 166-200 28-55 (58)
27 COG4416 Com Mu-like prophage p 30.2 24 0.00053 25.9 0.8 18 183-200 18-35 (60)
28 KOG2828 Acetyl-CoA hydrolase [ 29.3 23 0.0005 35.2 0.7 19 137-155 400-418 (454)
29 PF11335 DUF3137: Protein of u 29.0 23 0.00049 29.0 0.6 50 137-202 62-111 (142)
30 PF06222 Phage_TAC: Phage tail 28.5 21 0.00045 30.2 0.2 34 105-144 79-112 (127)
31 PF01485 IBR: IBR domain; Int 26.0 91 0.002 21.2 3.1 42 160-201 17-60 (64)
32 KOG1973 Chromatin remodeling p 25.3 38 0.00082 31.3 1.4 38 157-197 228-267 (274)
33 COG1631 RPL42A Ribosomal prote 24.9 32 0.00068 27.7 0.6 11 187-197 6-16 (94)
34 COG5034 TNG2 Chromatin remodel 24.5 47 0.001 31.3 1.8 39 155-198 225-270 (271)
35 KOG0435 Leucyl-tRNA synthetase 23.9 48 0.001 35.4 1.9 57 158-218 427-502 (876)
36 KOG1773 Stress responsive prot 22.5 24 0.00052 26.4 -0.4 15 134-148 45-59 (63)
37 PF08121 Toxin_33: Waglerin fa 22.3 52 0.0011 19.6 1.1 15 227-241 4-18 (22)
38 PF10588 NADH-G_4Fe-4S_3: NADH 22.2 1.5E+02 0.0033 19.8 3.5 40 102-142 2-41 (41)
39 PRK14810 formamidopyrimidine-D 22.1 54 0.0012 30.2 1.7 26 163-196 246-271 (272)
40 PF02150 RNA_POL_M_15KD: RNA p 22.1 29 0.00064 22.6 -0.0 14 190-203 2-15 (35)
41 PF03966 Trm112p: Trm112p-like 21.6 45 0.00099 24.2 0.9 13 188-200 52-64 (68)
42 smart00661 RPOL9 RNA polymeras 20.8 46 0.001 22.4 0.8 12 191-202 2-13 (52)
43 COG4098 comFA Superfamily II D 20.5 41 0.00088 33.4 0.6 8 189-196 60-67 (441)
44 COG3809 Uncharacterized protei 20.4 44 0.00095 26.4 0.6 12 189-200 21-32 (88)
45 smart00531 TFIIE Transcription 20.2 50 0.0011 27.5 1.0 47 150-201 88-135 (147)
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=5.3e-96 Score=637.49 Aligned_cols=193 Identities=70% Similarity=1.295 Sum_probs=185.3
Q ss_pred CCCCCchHHHHhCCCCCeeEEecCcccccCCCccCCCCCCCCCHHHHHHHHcCCCCCCCCCCChhhHHHHHHHHHHHhcc
Q 025636 58 DGDDTSWISWFCNLRGNEFFCEVDDEYIQDDFNLCGLSSQVPYYDYALDLILDVESSHGDMFTEEQNELVESAAEMLYGL 137 (250)
Q Consensus 58 ~~e~~sWI~wFcs~~gneff~eVdedyI~D~FNL~GL~~~V~~y~~AL~~ILd~~~~~~~~~~d~~~~~ie~~A~~LYGL 137 (250)
++++.+||+|||+++|||||||||+|||+|+|||+||+.+||+|++||++|||.+++++....+++.+++|++|++||||
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 34555799999999999999999999999999999999999999999999999998887766666778999999999999
Q ss_pred ccceeeeChHHHHHHHHhhccCccCCCCCcCCCCCCccccccCCCCCCccceeecCCCCccccCCCCCCCcccccccCCc
Q 025636 138 IHVRYILTSKGMAAMLEKYKNYDFGRCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPKCEDIYYPRSKYQGNIDGAYFGTT 217 (250)
Q Consensus 138 IHARYIlT~~Gl~~M~eKy~~g~FG~CPRv~C~~q~lLPiGlSd~pg~s~VKlyCP~C~DvY~P~s~~~~~iDGAyFGts 217 (250)
||||||+|.+||++|++||++++||+||||+|++|+|||+||||+||+++||+|||+|+|||.|+|+++++|||||||||
T Consensus 83 IHaRYIlT~~Gl~~M~eKy~~~dFG~CPRV~C~~q~~LPvGLsDipg~~~VklYCP~C~dvY~P~ssr~~~iDGa~fGts 162 (216)
T KOG3092|consen 83 IHARYILTNRGLAAMLEKYKNGDFGRCPRVYCCGQPVLPVGLSDIPGKSTVKLYCPSCEDVYIPKSSRHGNIDGAYFGTS 162 (216)
T ss_pred hhheeeechHHHHHHHHHHhcCCCCcCCcccccCCccccccccCCCCcceEEEeCCCcccccccccccccccccchhcCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhHHHHHhCCCCCCCCCCccceeeeeeeecCC
Q 025636 218 FPHLFLMTYGHLKPQKATQSYVPRVFGFKLHKP 250 (250)
Q Consensus 218 Fph~Fl~~yP~l~p~~~~~~Y~PrIfGFkI~~~ 250 (250)
|||||+|+||++.|+++.++|+|||||||||+.
T Consensus 163 FPhmff~~~p~l~P~r~~~~yvPriyGFkih~~ 195 (216)
T KOG3092|consen 163 FPHMFFMTHPELRPKRPTEQYVPRIYGFKIHKP 195 (216)
T ss_pred CchhHHHhccccCCCcchhhhcchheeeeeCch
Confidence 999999999999999999999999999999973
No 2
>PTZ00396 Casein kinase II subunit beta; Provisional
Probab=100.00 E-value=1.1e-90 Score=625.76 Aligned_cols=193 Identities=53% Similarity=1.046 Sum_probs=183.2
Q ss_pred CCCCCchHHHHhCCCCCeeEEecCcccccCCCccCCCCCCCCCHHHHHHHHcCCCCCCCCCCChhhHHHHHHHHHHHhcc
Q 025636 58 DGDDTSWISWFCNLRGNEFFCEVDDEYIQDDFNLCGLSSQVPYYDYALDLILDVESSHGDMFTEEQNELVESAAEMLYGL 137 (250)
Q Consensus 58 ~~e~~sWI~wFcs~~gneff~eVdedyI~D~FNL~GL~~~V~~y~~AL~~ILd~~~~~~~~~~d~~~~~ie~~A~~LYGL 137 (250)
++++.+||+|||+++||+|||+||+|||+|+||||||+.+||+|++||+||||.++++++..+++..+.++++|++||||
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 46677999999999999999999999999999999999999999999999999987765545566778899999999999
Q ss_pred ccceeeeChHHHHHHHHhhccCccCCCCCcCCCCCCccccccCCCCCCccceeecCCCCccccCCCCCCCcccccccCCc
Q 025636 138 IHVRYILTSKGMAAMLEKYKNYDFGRCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPKCEDIYYPRSKYQGNIDGAYFGTT 217 (250)
Q Consensus 138 IHARYIlT~~Gl~~M~eKy~~g~FG~CPRv~C~~q~lLPiGlSd~pg~s~VKlyCP~C~DvY~P~s~~~~~iDGAyFGts 217 (250)
||||||+|++||++|++||++|+||+||||+|++|+|||||+||+||+++||+|||+|+|||+|++.++..|||||||||
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 025636 218 FPHLFLMTYGHLKPQKATQSYVPRVFGFKLHKP 250 (250)
Q Consensus 218 Fph~Fl~~yP~l~p~~~~~~Y~PrIfGFkI~~~ 250 (250)
|||||+|+||++.|++++++|+|||||||||++
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=9.8e-89 Score=589.58 Aligned_cols=184 Identities=64% Similarity=1.221 Sum_probs=153.9
Q ss_pred chHHHHhCCCCCeeEEecCcccccCCCccCCCCCCCCCHHHHHHHHcCCCCCCCCCCChhhHHHHHHHHHHHhcccccee
Q 025636 63 SWISWFCNLRGNEFFCEVDDEYIQDDFNLCGLSSQVPYYDYALDLILDVESSHGDMFTEEQNELVESAAEMLYGLIHVRY 142 (250)
Q Consensus 63 sWI~wFcs~~gneff~eVdedyI~D~FNL~GL~~~V~~y~~AL~~ILd~~~~~~~~~~d~~~~~ie~~A~~LYGLIHARY 142 (250)
+||+|||+++||+||||||+|||+|+|||+||+++||+|++||++|||.+.++++..++++.+.++++|++|||||||||
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 69999999999999999999999999999999999999999999999998876556667778899999999999999999
Q ss_pred eeChHHHHHHHHhhccCccCCCCCcCCCCCCccccccCCCCCCccceeecCCCCccccCCCCCCCcccccccCCchhhHH
Q 025636 143 ILTSKGMAAMLEKYKNYDFGRCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPKCEDIYYPRSKYQGNIDGAYFGTTFPHLF 222 (250)
Q Consensus 143 IlT~~Gl~~M~eKy~~g~FG~CPRv~C~~q~lLPiGlSd~pg~s~VKlyCP~C~DvY~P~s~~~~~iDGAyFGtsFph~F 222 (250)
|+|++||++|++||++|+||+||||+|++|+|||||+||+||+++||||||+|+|||+|++.+.++||||||||||||||
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 025636 223 LMTYGHLKPQKATQSYVPRVFGFK 246 (250)
Q Consensus 223 l~~yP~l~p~~~~~~Y~PrIfGFk 246 (250)
+|+||++.|+.+.++|+|||||||
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=9.9e-86 Score=577.53 Aligned_cols=188 Identities=54% Similarity=1.131 Sum_probs=178.3
Q ss_pred CCCchHHHHhCCCCCeeEEecCcccccCCCccCCCCCCCCCHHHHHHHHcCCCCCCCCCCChhhHHHHHHHHHHHhcccc
Q 025636 60 DDTSWISWFCNLRGNEFFCEVDDEYIQDDFNLCGLSSQVPYYDYALDLILDVESSHGDMFTEEQNELVESAAEMLYGLIH 139 (250)
Q Consensus 60 e~~sWI~wFcs~~gneff~eVdedyI~D~FNL~GL~~~V~~y~~AL~~ILd~~~~~~~~~~d~~~~~ie~~A~~LYGLIH 139 (250)
+...||+|||+++||||||+||++||+|+|||+||+..||+|++||++|||...++. ..+.+-+.||.+|++||||||
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 334799999999999999999999999999999999999999999999999876543 233445789999999999999
Q ss_pred ceeeeChHHHHHHHHhhccCccCCCCCcCCCCCCccccccCCCCCCccceeecCCCCccccCCCCCCCcccccccCCchh
Q 025636 140 VRYILTSKGMAAMLEKYKNYDFGRCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPKCEDIYYPRSKYQGNIDGAYFGTTFP 219 (250)
Q Consensus 140 ARYIlT~~Gl~~M~eKy~~g~FG~CPRv~C~~q~lLPiGlSd~pg~s~VKlyCP~C~DvY~P~s~~~~~iDGAyFGtsFp 219 (250)
||||+|..||++|++||+.++||+||||+||+|+|||+||||+||+++||||||+|.|||.|+|+++..|||||||||||
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 025636 220 HLFLMTYGHLKPQKATQSYVPRVFGFKLHK 249 (250)
Q Consensus 220 h~Fl~~yP~l~p~~~~~~Y~PrIfGFkI~~ 249 (250)
|||+++||++.|+++.+.|+|||||||||+
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=77.18 E-value=2.5 Score=36.30 Aligned_cols=41 Identities=17% Similarity=0.220 Sum_probs=32.2
Q ss_pred HHHhhccCccCCCCCcCCCCCCccccccCCCCCCccceeecCCCCccccC
Q 025636 152 MLEKYKNYDFGRCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPKCEDIYYP 201 (250)
Q Consensus 152 M~eKy~~g~FG~CPRv~C~~q~lLPiGlSd~pg~s~VKlyCP~C~DvY~P 201 (250)
+..-..+|-.|+||| |..-+++= +--+|+-.||.|..-|.+
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 556788899999999975
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=72.29 E-value=3.8 Score=34.20 Aligned_cols=41 Identities=34% Similarity=0.835 Sum_probs=27.7
Q ss_pred cCccCCCCCcCCCCCCccccccCCCCC--------CccceeecCCCCccccC
Q 025636 158 NYDFGRCPRVYCCGQPCLPVGQSDIPR--------SSTVKIYCPKCEDIYYP 201 (250)
Q Consensus 158 ~g~FG~CPRv~C~~q~lLPiGlSd~pg--------~s~VKlyCP~C~DvY~P 201 (250)
+..|.+||+ ||+ ++.|+.-.+..+ ....=-.||+|+.||=+
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 22234579999999954
No 7
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=68.22 E-value=5.3 Score=35.02 Aligned_cols=62 Identities=27% Similarity=0.491 Sum_probs=42.2
Q ss_pred ccceeeeChHHHHHHHHh---hc-----cCccCCCCCcCCCCCCccccccCC--------CCCCccceeecCCCCccccC
Q 025636 138 IHVRYILTSKGMAAMLEK---YK-----NYDFGRCPRVYCCGQPCLPVGQSD--------IPRSSTVKIYCPKCEDIYYP 201 (250)
Q Consensus 138 IHARYIlT~~Gl~~M~eK---y~-----~g~FG~CPRv~C~~q~lLPiGlSd--------~pg~s~VKlyCP~C~DvY~P 201 (250)
++|=||-+..=.+||.+= +. +-+|-+||. ||+ +|+++--.. +.+....-..||+|..+|=|
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 677788887777777764 22 345889994 777 688776655 22333334559999999975
Q ss_pred C
Q 025636 202 R 202 (250)
Q Consensus 202 ~ 202 (250)
-
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=52.38 E-value=13 Score=34.38 Aligned_cols=36 Identities=19% Similarity=0.578 Sum_probs=25.7
Q ss_pred CCCcCCCCC----CccccccCCCCCCccceeecCCCCccc
Q 025636 164 CPRVYCCGQ----PCLPVGQSDIPRSSTVKIYCPKCEDIY 199 (250)
Q Consensus 164 CPRv~C~~q----~lLPiGlSd~pg~s~VKlyCP~C~DvY 199 (250)
|||-+|++- ++.|--++..+.-..+++-|-.|+|.|
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 344444444444456899999999988
No 9
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=49.72 E-value=26 Score=24.10 Aligned_cols=23 Identities=30% Similarity=0.588 Sum_probs=14.8
Q ss_pred HHHhhcc--CccCCCCCcCCCCCCc
Q 025636 152 MLEKYKN--YDFGRCPRVYCCGQPC 174 (250)
Q Consensus 152 M~eKy~~--g~FG~CPRv~C~~q~l 174 (250)
+.++|.+ ..+-.||+..|+..-.
T Consensus 7 ~~~~~i~~~~~~~~CP~~~C~~~~~ 31 (64)
T smart00647 7 LLESYVESNPDLKWCPAPDCSAAII 31 (64)
T ss_pred HHHHHHhcCCCccCCCCCCCcceEE
Confidence 3444433 4677899999976433
No 10
>PRK00420 hypothetical protein; Validated
Probab=48.37 E-value=14 Score=30.36 Aligned_cols=30 Identities=23% Similarity=0.643 Sum_probs=20.8
Q ss_pred CCCCCcCCCCCCccccccCCCCCCccceeecCCCCccccCC
Q 025636 162 GRCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPKCEDIYYPR 202 (250)
Q Consensus 162 G~CPRv~C~~q~lLPiGlSd~pg~s~VKlyCP~C~DvY~P~ 202 (250)
++||. |. .|++ +...-+.|||.|..++.-.
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 55 4443 2123389999999998753
No 11
>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=46.22 E-value=17 Score=24.84 Aligned_cols=23 Identities=48% Similarity=1.292 Sum_probs=15.6
Q ss_pred CCCCcCCCCCCccccccCCCCCCccceeecCCCC
Q 025636 163 RCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPKCE 196 (250)
Q Consensus 163 ~CPRv~C~~q~lLPiGlSd~pg~s~VKlyCP~C~ 196 (250)
+||. | +.|++. + +.+ ++|||.|.
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 6894 7 677775 1 122 68999995
No 12
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=45.78 E-value=8.7 Score=28.06 Aligned_cols=11 Identities=45% Similarity=1.407 Sum_probs=8.8
Q ss_pred cceeecCCCCc
Q 025636 187 TVKIYCPKCED 197 (250)
Q Consensus 187 ~VKlyCP~C~D 197 (250)
..-||||+|+.
T Consensus 26 NfPlyCpKCK~ 36 (55)
T PF14205_consen 26 NFPLYCPKCKQ 36 (55)
T ss_pred cccccCCCCCc
Confidence 44799999984
No 13
>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=43.55 E-value=11 Score=23.35 Aligned_cols=10 Identities=30% Similarity=1.265 Sum_probs=7.1
Q ss_pred eeecCCCCcc
Q 025636 189 KIYCPKCEDI 198 (250)
Q Consensus 189 KlyCP~C~Dv 198 (250)
--|||+|++|
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 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=40.28 E-value=19 Score=23.77 Aligned_cols=13 Identities=46% Similarity=1.007 Sum_probs=10.9
Q ss_pred eeecCCCCccccC
Q 025636 189 KIYCPKCEDIYYP 201 (250)
Q Consensus 189 KlyCP~C~DvY~P 201 (250)
+..||.|..+|+.
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
>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=40.26 E-value=14 Score=23.73 Aligned_cols=28 Identities=21% Similarity=0.387 Sum_probs=16.6
Q ss_pred CCCCCccccccCCCCCCccceeecCCCCccc
Q 025636 169 CCGQPCLPVGQSDIPRSSTVKIYCPKCEDIY 199 (250)
Q Consensus 169 C~~q~lLPiGlSd~pg~s~VKlyCP~C~DvY 199 (250)
|..+.-+|-..- .....++-||+|+.+.
T Consensus 8 C~~~~~v~~~~~---~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 8 CKTSFRVVDSQL---GANGGKVRCGKCGHVW 35 (38)
T ss_pred CCCEEEeCHHHc---CCCCCEEECCCCCCEE
Confidence 555555554332 2334478888888665
No 16
>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=40.11 E-value=6 Score=36.78 Aligned_cols=58 Identities=34% Similarity=0.749 Sum_probs=25.9
Q ss_pred CCCCCcCCCCCCccccccCCCCCCccc-eeecCCCCccccCCCCCC---C-cccccccC-------CchhhHHHHHh
Q 025636 162 GRCPRVYCCGQPCLPVGQSDIPRSSTV-KIYCPKCEDIYYPRSKYQ---G-NIDGAYFG-------TTFPHLFLMTY 226 (250)
Q Consensus 162 G~CPRv~C~~q~lLPiGlSd~pg~s~V-KlyCP~C~DvY~P~s~~~---~-~iDGAyFG-------tsFph~Fl~~y 226 (250)
+.||+ |...++-=+ +...+| -.|||+|++-|.-+|... . -.||||-- .+=|.+|+|+|
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 46876 444433322 445555 578999999998875431 1 34999963 24577788887
No 17
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=37.72 E-value=15 Score=25.83 Aligned_cols=9 Identities=33% Similarity=1.361 Sum_probs=4.3
Q ss_pred eeecCCCCc
Q 025636 189 KIYCPKCED 197 (250)
Q Consensus 189 KlyCP~C~D 197 (250)
+-|||+|..
T Consensus 20 ~~fCP~Cg~ 28 (50)
T PRK00432 20 NKFCPRCGS 28 (50)
T ss_pred cCcCcCCCc
Confidence 335555544
No 18
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=36.20 E-value=20 Score=23.72 Aligned_cols=12 Identities=25% Similarity=1.143 Sum_probs=10.3
Q ss_pred ccceeecCCCCc
Q 025636 186 STVKIYCPKCED 197 (250)
Q Consensus 186 s~VKlyCP~C~D 197 (250)
++|.+.||+|+.
T Consensus 2 a~i~v~CP~C~s 13 (36)
T PF03811_consen 2 AKIDVHCPRCQS 13 (36)
T ss_pred CcEeeeCCCCCC
Confidence 578999999984
No 19
>COG0401 Uncharacterized homolog of Blt101 [Function unknown]
Probab=36.04 E-value=11 Score=27.61 Aligned_cols=13 Identities=31% Similarity=0.749 Sum_probs=11.0
Q ss_pred HhccccceeeeCh
Q 025636 134 LYGLIHVRYILTS 146 (250)
Q Consensus 134 LYGLIHARYIlT~ 146 (250)
+=|+|||=||++.
T Consensus 43 ~PGiiHA~yvi~~ 55 (56)
T COG0401 43 IPGIIHALYVILR 55 (56)
T ss_pred hhhhHhheEEEEe
Confidence 4589999999875
No 20
>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=35.49 E-value=33 Score=32.11 Aligned_cols=38 Identities=18% Similarity=0.484 Sum_probs=24.3
Q ss_pred CCCCcCCCCCCccccc----cCCCC--CCccceeecCCCCcccc
Q 025636 163 RCPRVYCCGQPCLPVG----QSDIP--RSSTVKIYCPKCEDIYY 200 (250)
Q Consensus 163 ~CPRv~C~~q~lLPiG----lSd~p--g~s~VKlyCP~C~DvY~ 200 (250)
.|||-+|++--.|.=- .+..+ .-.++++-|+.|++.+.
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 3999999974333211 11111 22578999999999985
No 21
>PF08772 NOB1_Zn_bind: Nin one binding (NOB1) Zn-ribbon like; InterPro: IPR014881 This entry corresponds to a zinc ribbon and is found on the RNA binding protein NOB1. ; PDB: 2CON_A.
Probab=35.13 E-value=15 Score=28.10 Aligned_cols=11 Identities=45% Similarity=1.189 Sum_probs=5.3
Q ss_pred ccceeecCCCC
Q 025636 186 STVKIYCPKCE 196 (250)
Q Consensus 186 s~VKlyCP~C~ 196 (250)
.+-|.|||+|.
T Consensus 21 ~~~k~FCp~CG 31 (73)
T PF08772_consen 21 DMTKQFCPKCG 31 (73)
T ss_dssp -SS--S-SSS-
T ss_pred CCCceeCcccC
Confidence 46699999998
No 22
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=34.40 E-value=25 Score=26.16 Aligned_cols=17 Identities=35% Similarity=0.960 Sum_probs=14.5
Q ss_pred CCCCccceeecCCCCcc
Q 025636 182 IPRSSTVKIYCPKCEDI 198 (250)
Q Consensus 182 ~pg~s~VKlyCP~C~Dv 198 (250)
.|++..|+-.||+|.++
T Consensus 20 ~p~e~~v~F~CPnCGe~ 36 (61)
T COG2888 20 APGETAVKFPCPNCGEV 36 (61)
T ss_pred ccCCceeEeeCCCCCce
Confidence 37889999999999954
No 23
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=33.52 E-value=21 Score=23.36 Aligned_cols=29 Identities=24% Similarity=0.547 Sum_probs=19.0
Q ss_pred CCCCCccccccCCCCCCccceeecCCCCcccc
Q 025636 169 CCGQPCLPVGQSDIPRSSTVKIYCPKCEDIYY 200 (250)
Q Consensus 169 C~~q~lLPiGlSd~pg~s~VKlyCP~C~DvY~ 200 (250)
|+...-||-. ..+.+..++-||+|+.++.
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 24
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=32.81 E-value=26 Score=22.87 Aligned_cols=15 Identities=33% Similarity=0.766 Sum_probs=12.3
Q ss_pred ceeecCCCCccccCC
Q 025636 188 VKIYCPKCEDIYYPR 202 (250)
Q Consensus 188 VKlyCP~C~DvY~P~ 202 (250)
+++-||+|+-.|.-+
T Consensus 1 M~i~Cp~C~~~y~i~ 15 (36)
T PF13717_consen 1 MIITCPNCQAKYEID 15 (36)
T ss_pred CEEECCCCCCEEeCC
Confidence 578899999999743
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=32.70 E-value=27 Score=25.61 Aligned_cols=19 Identities=37% Similarity=0.856 Sum_probs=15.3
Q ss_pred CCccceeecCCCCccccCC
Q 025636 184 RSSTVKIYCPKCEDIYYPR 202 (250)
Q Consensus 184 g~s~VKlyCP~C~DvY~P~ 202 (250)
+.+++.++||.|+..=.+.
T Consensus 2 ~~~p~~~~CP~C~~~~~T~ 20 (73)
T PF10601_consen 2 GPEPVRIYCPYCQQQVQTR 20 (73)
T ss_pred CCCceeeECCCCCCEEEEE
Confidence 5678999999999877553
No 26
>PF11238 DUF3039: Protein of unknown function (DUF3039); InterPro: IPR021400 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=31.49 E-value=11 Score=27.72 Aligned_cols=28 Identities=25% Similarity=0.551 Sum_probs=17.6
Q ss_pred CcCCCCCCccccccCCCCCCccceeecCCCCcccc
Q 025636 166 RVYCCGQPCLPVGQSDIPRSSTVKIYCPKCEDIYY 200 (250)
Q Consensus 166 Rv~C~~q~lLPiGlSd~pg~s~VKlyCP~C~DvY~ 200 (250)
+.+|.. +.|.+.+.. ...| ||.|++||.
T Consensus 28 vALCGk--~wvp~rdp~--~~PV---CP~Ck~iye 55 (58)
T PF11238_consen 28 VALCGK--VWVPTRDPK--PFPV---CPECKEIYE 55 (58)
T ss_pred EeeeCc--eeCCCCCCC--CCCC---CcCHHHHHH
Confidence 556654 445544433 3444 999999995
No 27
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=30.15 E-value=24 Score=25.94 Aligned_cols=18 Identities=17% Similarity=0.610 Sum_probs=13.6
Q ss_pred CCCccceeecCCCCcccc
Q 025636 183 PRSSTVKIYCPKCEDIYY 200 (250)
Q Consensus 183 pg~s~VKlyCP~C~DvY~ 200 (250)
-+++-++.-||||+.|-.
T Consensus 18 ~~~~yle~KCPrCK~vN~ 35 (60)
T COG4416 18 EGQAYLEKKCPRCKEVNE 35 (60)
T ss_pred ccceeeeecCCccceeee
Confidence 345677899999998743
No 28
>KOG2828 consensus Acetyl-CoA hydrolase [Energy production and conversion]
Probab=29.31 E-value=23 Score=35.21 Aligned_cols=19 Identities=32% Similarity=0.630 Sum_probs=15.7
Q ss_pred cccceeeeChHHHHHHHHh
Q 025636 137 LIHVRYILTSKGMAAMLEK 155 (250)
Q Consensus 137 LIHARYIlT~~Gl~~M~eK 155 (250)
--|++||+|+.||+.+.-|
T Consensus 400 rah~~y~VTEhGiA~L~Gk 418 (454)
T KOG2828|consen 400 RAHLDYLVTEHGIADLWGK 418 (454)
T ss_pred ccceeEEEecccHHHHhCC
Confidence 3599999999999987543
No 29
>PF11335 DUF3137: Protein of unknown function (DUF3137) ; InterPro: IPR021484 This bacterial family of proteins has no known function.
Probab=29.02 E-value=23 Score=29.04 Aligned_cols=50 Identities=30% Similarity=0.468 Sum_probs=29.0
Q ss_pred cccceeeeChHHHHHHHHhhccCccCCCCCcCCCCCCccccccCCCCCCccceeecCCCCccccCC
Q 025636 137 LIHVRYILTSKGMAAMLEKYKNYDFGRCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPKCEDIYYPR 202 (250)
Q Consensus 137 LIHARYIlT~~Gl~~M~eKy~~g~FG~CPRv~C~~q~lLPiGlSd~pg~s~VKlyCP~C~DvY~P~ 202 (250)
-+.|||||||.=|+.+.+ +.+.. |. |+.++ ...+++-+..+.=++.+.|+
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 356799999998887764 22222 32 12222 22356666666666777754
No 30
>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=28.46 E-value=21 Score=30.17 Aligned_cols=34 Identities=29% Similarity=0.707 Sum_probs=17.9
Q ss_pred HHHHcCCCCCCCCCCChhhHHHHHHHHHHHhccccceeee
Q 025636 105 LDLILDVESSHGDMFTEEQNELVESAAEMLYGLIHVRYIL 144 (250)
Q Consensus 105 L~~ILd~~~~~~~~~~d~~~~~ie~~A~~LYGLIHARYIl 144 (250)
+++++|.+.. -.|.++..+.+ ...||-.|||-+-
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 5666776443 35556555544 3489999999643
No 31
>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=26.01 E-value=91 Score=21.21 Aligned_cols=42 Identities=19% Similarity=0.256 Sum_probs=16.4
Q ss_pred ccCCCCCcCCCCCCccccccCCC--CCCccceeecCCCCccccC
Q 025636 160 DFGRCPRVYCCGQPCLPVGQSDI--PRSSTVKIYCPKCEDIYYP 201 (250)
Q Consensus 160 ~FG~CPRv~C~~q~lLPiGlSd~--pg~s~VKlyCP~C~DvY~P 201 (250)
.+-.||+..|+.--..+-|.... -=..-=..||..|+.-+|+
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 44589999999754443333321 0000114555566655553
No 32
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=25.33 E-value=38 Score=31.34 Aligned_cols=38 Identities=26% Similarity=0.518 Sum_probs=26.6
Q ss_pred ccCccCCCCCcCCC-CCCccc-cccCCCCCCccceeecCCCCc
Q 025636 157 KNYDFGRCPRVYCC-GQPCLP-VGQSDIPRSSTVKIYCPKCED 197 (250)
Q Consensus 157 ~~g~FG~CPRv~C~-~q~lLP-iGlSd~pg~s~VKlyCP~C~D 197 (250)
.-|.++.|=...|. .--=+| |||...|.. |.|||+|+.
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 45667777777777 444444 599976654 499999984
No 33
>COG1631 RPL42A Ribosomal protein L44E [Translation, ribosomal structure and biogenesis]
Probab=24.85 E-value=32 Score=27.68 Aligned_cols=11 Identities=36% Similarity=1.156 Sum_probs=9.5
Q ss_pred cceeecCCCCc
Q 025636 187 TVKIYCPKCED 197 (250)
Q Consensus 187 ~VKlyCP~C~D 197 (250)
+++.|||.|+.
T Consensus 6 ~~~tyCp~Ckk 16 (94)
T COG1631 6 KRRTYCPYCKK 16 (94)
T ss_pred ceeecCccccc
Confidence 67899999984
No 34
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=24.49 E-value=47 Score=31.29 Aligned_cols=39 Identities=33% Similarity=0.774 Sum_probs=27.1
Q ss_pred hhccCccCCCCCcCCCCCCc------cc-cccCCCCCCccceeecCCCCcc
Q 025636 155 KYKNYDFGRCPRVYCCGQPC------LP-VGQSDIPRSSTVKIYCPKCEDI 198 (250)
Q Consensus 155 Ky~~g~FG~CPRv~C~~q~l------LP-iGlSd~pg~s~VKlyCP~C~Dv 198 (250)
..++.-||. =|.|.+.+| || |||..-|+ -+.|||-|++.
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 444544443 45 59987664 48999999864
No 35
>KOG0435 consensus Leucyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=23.85 E-value=48 Score=35.43 Aligned_cols=57 Identities=25% Similarity=0.638 Sum_probs=38.3
Q ss_pred cCccCC-CCCcCCCCCCccccccCCCCCCcc------------------ceeecCCCCccccCCCCCCCcccccccCCch
Q 025636 158 NYDFGR-CPRVYCCGQPCLPVGQSDIPRSST------------------VKIYCPKCEDIYYPRSKYQGNIDGAYFGTTF 218 (250)
Q Consensus 158 ~g~FG~-CPRv~C~~q~lLPiGlSd~pg~s~------------------VKlyCP~C~DvY~P~s~~~~~iDGAyFGtsF 218 (250)
+.-+|+ =|-|.|..+--+||-+|+-|=.-+ |+.-||+|++ |....-...| .|+++++
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 688999998888888887765444 8899999997 4322222333 5666655
No 36
>KOG1773 consensus Stress responsive protein [General function prediction only]
Probab=22.52 E-value=24 Score=26.42 Aligned_cols=15 Identities=40% Similarity=0.793 Sum_probs=12.2
Q ss_pred HhccccceeeeChHH
Q 025636 134 LYGLIHVRYILTSKG 148 (250)
Q Consensus 134 LYGLIHARYIlT~~G 148 (250)
+=|+|||-|+++.++
T Consensus 45 iPgiIhA~yii~~~~ 59 (63)
T KOG1773|consen 45 IPGIIHAIYIIFFRG 59 (63)
T ss_pred hHHHHhhEEEEEEec
Confidence 458999999997654
No 37
>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=22.29 E-value=52 Score=19.56 Aligned_cols=15 Identities=33% Similarity=0.658 Sum_probs=11.8
Q ss_pred CCCCCCCCCCcccee
Q 025636 227 GHLKPQKATQSYVPR 241 (250)
Q Consensus 227 P~l~p~~~~~~Y~Pr 241 (250)
|+|.|-.++-.|+||
T Consensus 4 pdlrpcyppchyipr 18 (22)
T PF08121_consen 4 PDLRPCYPPCHYIPR 18 (22)
T ss_pred CccccCCCCccccCC
Confidence 678887777788886
No 38
>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=22.16 E-value=1.5e+02 Score=19.76 Aligned_cols=40 Identities=20% Similarity=0.233 Sum_probs=15.4
Q ss_pred HHHHHHHcCCCCCCCCCCChhhHHHHHHHHHHHhcccccee
Q 025636 102 DYALDLILDVESSHGDMFTEEQNELVESAAEMLYGLIHVRY 142 (250)
Q Consensus 102 ~~AL~~ILd~~~~~~~~~~d~~~~~ie~~A~~LYGLIHARY 142 (250)
+.+|++||...+.+...=+....=.++..|. -||+-++||
T Consensus 2 r~~lelll~~H~~dC~~C~~~G~CeLQ~~~~-~~gv~~~~f 41 (41)
T PF10588_consen 2 RTVLELLLANHPLDCPTCDKNGNCELQDLAY-EYGVDEQRF 41 (41)
T ss_dssp HHHHHHHHTT----TTT-TTGGG-HHHHHHH-HH-S-----
T ss_pred HHHHHHHHhCCCCcCcCCCCCCCCHHHHHHH-HhCCCcCCC
Confidence 4689999988755432211122223333343 699999987
No 39
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=22.10 E-value=54 Score=30.15 Aligned_cols=26 Identities=31% Similarity=0.746 Sum_probs=15.8
Q ss_pred CCCCcCCCCCCccccccCCCCCCccceeecCCCC
Q 025636 163 RCPRVYCCGQPCLPVGQSDIPRSSTVKIYCPKCE 196 (250)
Q Consensus 163 ~CPRv~C~~q~lLPiGlSd~pg~s~VKlyCP~C~ 196 (250)
.||| |. .++.=+.+. ++---|||.|+
T Consensus 246 pCpr--CG-~~I~~~~~~-----gR~t~~CP~CQ 271 (272)
T PRK14810 246 PCLN--CK-TPIRRVVVA-----GRSSHYCPHCQ 271 (272)
T ss_pred cCCC--CC-CeeEEEEEC-----CCccEECcCCc
Confidence 4888 75 333322222 35678999998
No 40
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=22.07 E-value=29 Score=22.58 Aligned_cols=14 Identities=36% Similarity=1.355 Sum_probs=11.4
Q ss_pred eecCCCCccccCCC
Q 025636 190 IYCPKCEDIYYPRS 203 (250)
Q Consensus 190 lyCP~C~DvY~P~s 203 (250)
.|||.|..+-.|+.
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 41
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=21.61 E-value=45 Score=24.24 Aligned_cols=13 Identities=31% Similarity=0.838 Sum_probs=11.3
Q ss_pred ceeecCCCCcccc
Q 025636 188 VKIYCPKCEDIYY 200 (250)
Q Consensus 188 VKlyCP~C~DvY~ 200 (250)
=.|.||.|+-+|-
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 42
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=20.75 E-value=46 Score=22.35 Aligned_cols=12 Identities=42% Similarity=1.453 Sum_probs=10.1
Q ss_pred ecCCCCccccCC
Q 025636 191 YCPKCEDIYYPR 202 (250)
Q Consensus 191 yCP~C~DvY~P~ 202 (250)
|||.|+.+-.|+
T Consensus 2 FCp~Cg~~l~~~ 13 (52)
T smart00661 2 FCPKCGNMLIPK 13 (52)
T ss_pred CCCCCCCccccc
Confidence 899999887765
No 43
>COG4098 comFA Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [DNA replication, recombination, and repair]
Probab=20.46 E-value=41 Score=33.40 Aligned_cols=8 Identities=38% Similarity=1.161 Sum_probs=6.9
Q ss_pred eeecCCCC
Q 025636 189 KIYCPKCE 196 (250)
Q Consensus 189 KlyCP~C~ 196 (250)
++||++|-
T Consensus 60 ~~YCr~Cl 67 (441)
T COG4098 60 CLYCRNCL 67 (441)
T ss_pred eEeehhhh
Confidence 89999885
No 44
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.40 E-value=44 Score=26.38 Aligned_cols=12 Identities=33% Similarity=1.190 Sum_probs=10.1
Q ss_pred eeecCCCCcccc
Q 025636 189 KIYCPKCEDIYY 200 (250)
Q Consensus 189 KlyCP~C~DvY~ 200 (250)
--|||+|.-|..
T Consensus 21 iD~CPrCrGVWL 32 (88)
T COG3809 21 IDYCPRCRGVWL 32 (88)
T ss_pred eeeCCccccEee
Confidence 359999999985
No 45
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=20.18 E-value=50 Score=27.52 Aligned_cols=47 Identities=21% Similarity=0.392 Sum_probs=25.6
Q ss_pred HHHHHhhccCccCCCCCcCCCCCCcc-ccccCCCCCCccceeecCCCCccccC
Q 025636 150 AAMLEKYKNYDFGRCPRVYCCGQPCL-PVGQSDIPRSSTVKIYCPKCEDIYYP 201 (250)
Q Consensus 150 ~~M~eKy~~g~FG~CPRv~C~~q~lL-PiGlSd~pg~s~VKlyCP~C~DvY~P 201 (250)
+...+.-.+..|=.||+ |+..--. -.-.... .+.+.-||.|+..-.+
T Consensus 88 ~~~l~~e~~~~~Y~Cp~--C~~~y~~~ea~~~~d---~~~~f~Cp~Cg~~l~~ 135 (147)
T smart00531 88 EDKLEDETNNAYYKCPN--CQSKYTFLEANQLLD---MDGTFTCPRCGEELEE 135 (147)
T ss_pred HHHHhcccCCcEEECcC--CCCEeeHHHHHHhcC---CCCcEECCCCCCEEEE
Confidence 33333334667778997 6643221 1111111 2456899999977654
Done!