Query psy10861
Match_columns 498
No_of_seqs 317 out of 563
Neff 4.0
Searched_HMMs 46136
Date Fri Aug 16 20:20:08 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy10861.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/10861hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3092|consensus 100.0 1.2E-80 2.5E-85 587.1 13.2 199 151-446 2-200 (216)
2 PTZ00396 Casein kinase II subu 100.0 4.3E-73 9.4E-78 556.1 15.8 200 150-446 15-214 (251)
3 COG5041 SKB2 Casein kinase II, 100.0 3E-72 6.5E-77 533.6 10.7 203 150-451 18-220 (242)
4 PF01214 CK_II_beta: Casein ki 100.0 3.3E-71 7.2E-76 522.2 12.6 184 157-437 1-184 (184)
5 KOG3092|consensus 100.0 4.9E-47 1.1E-51 358.9 8.2 174 81-394 8-187 (216)
6 PTZ00396 Casein kinase II subu 100.0 3.7E-41 8.1E-46 330.9 10.0 166 76-381 17-182 (251)
7 PF01214 CK_II_beta: Casein ki 100.0 3.1E-41 6.7E-46 318.8 8.1 159 81-379 1-159 (184)
8 COG5041 SKB2 Casein kinase II, 99.8 6.4E-22 1.4E-26 189.8 3.8 63 72-148 14-78 (242)
9 PF06044 DRP: Dam-replacing fa 89.1 0.07 1.5E-06 53.9 -1.5 62 320-417 32-101 (254)
10 PF01927 Mut7-C: Mut7-C RNAse 83.3 1 2.2E-05 41.6 2.9 22 316-340 88-109 (147)
11 PF13717 zinc_ribbon_4: zinc-r 77.2 1.6 3.4E-05 31.8 1.6 35 346-390 1-35 (36)
12 TIGR02098 MJ0042_CXXC MJ0042 f 71.7 1.8 3.8E-05 31.1 0.8 31 321-356 4-34 (38)
13 PF13719 zinc_ribbon_5: zinc-r 69.5 2.4 5.2E-05 30.9 1.1 34 347-390 2-35 (37)
14 PRK00420 hypothetical protein; 66.5 8.5 0.00019 35.0 4.1 50 279-358 2-51 (112)
15 PRK00241 nudC NADH pyrophospha 65.5 4.1 8.9E-05 41.1 2.1 17 343-359 113-129 (256)
16 KOG4684|consensus 65.4 4.8 0.0001 40.7 2.6 71 322-415 141-215 (275)
17 PF06044 DRP: Dam-replacing fa 64.1 2.2 4.7E-05 43.5 -0.1 39 347-396 31-69 (254)
18 PRK03564 formate dehydrogenase 63.4 29 0.00063 36.5 7.9 48 319-388 187-234 (309)
19 PRK05978 hypothetical protein; 62.6 6.1 0.00013 37.4 2.6 39 311-358 25-63 (148)
20 PF03966 Trm112p: Trm112p-like 61.5 3.5 7.5E-05 33.4 0.7 17 313-332 1-17 (68)
21 COG1656 Uncharacterized conser 59.3 9.4 0.0002 36.9 3.2 60 296-358 66-141 (165)
22 PF04216 FdhE: Protein involve 58.3 5.1 0.00011 40.6 1.4 47 320-388 173-219 (290)
23 PRK14714 DNA polymerase II lar 57.7 12 0.00026 45.8 4.4 40 12-51 321-360 (1337)
24 COG2816 NPY1 NTP pyrophosphohy 56.6 7.7 0.00017 40.2 2.3 40 309-360 103-142 (279)
25 PF13453 zf-TFIIB: Transcripti 53.6 9 0.0002 28.2 1.7 29 321-358 1-30 (41)
26 PF09297 zf-NADH-PPase: NADH p 53.0 5.4 0.00012 28.0 0.4 15 374-388 15-29 (32)
27 PF10058 DUF2296: Predicted in 52.8 13 0.00029 29.5 2.6 36 341-387 16-51 (54)
28 PF10083 DUF2321: Uncharacteri 52.0 7.8 0.00017 37.2 1.4 14 379-393 67-80 (158)
29 PF06827 zf-FPG_IleRS: Zinc fi 50.6 8.6 0.00019 26.5 1.1 28 321-356 3-30 (30)
30 PF13719 zinc_ribbon_5: zinc-r 50.0 10 0.00022 27.6 1.5 33 321-358 4-36 (37)
31 TIGR01562 FdhE formate dehydro 48.4 18 0.00038 38.0 3.5 50 318-388 183-232 (305)
32 COG2816 NPY1 NTP pyrophosphohy 47.8 20 0.00044 37.3 3.7 42 348-404 112-156 (279)
33 PF09788 Tmemb_55A: Transmembr 45.8 22 0.00048 36.6 3.6 55 322-390 126-187 (256)
34 PF06677 Auto_anti-p27: Sjogre 44.0 17 0.00036 27.6 1.8 24 320-354 18-41 (41)
35 smart00647 IBR In Between Ring 41.0 58 0.0012 24.8 4.5 31 317-353 16-46 (64)
36 PF14205 Cys_rich_KTR: Cystein 40.1 17 0.00038 29.4 1.5 7 347-353 28-34 (55)
37 PRK00432 30S ribosomal protein 39.6 15 0.00032 28.8 1.0 10 346-355 19-28 (50)
38 PF07191 zinc-ribbons_6: zinc- 38.8 20 0.00043 30.3 1.7 36 321-388 3-38 (70)
39 COG1545 Predicted nucleic-acid 38.4 18 0.0004 33.5 1.6 15 347-361 29-43 (140)
40 COG4260 Membrane protease subu 37.9 18 0.00039 38.1 1.6 41 315-389 302-343 (345)
41 COG1645 Uncharacterized Zn-fin 36.4 23 0.00049 33.2 1.8 26 320-357 29-55 (131)
42 PF03811 Zn_Tnp_IS1: InsA N-te 35.9 33 0.00073 25.3 2.3 12 344-355 2-13 (36)
43 PF01927 Mut7-C: Mut7-C RNAse 35.2 23 0.00049 32.7 1.7 44 347-392 91-136 (147)
44 smart00661 RPOL9 RNA polymeras 35.2 26 0.00056 26.3 1.7 7 347-353 20-26 (52)
45 PRK00241 nudC NADH pyrophospha 35.1 40 0.00087 34.1 3.5 19 377-395 114-132 (256)
46 PF09538 FYDLN_acid: Protein o 35.1 21 0.00046 32.1 1.4 13 381-393 27-39 (108)
47 COG2888 Predicted Zn-ribbon RN 34.9 21 0.00045 29.5 1.2 15 341-355 21-35 (61)
48 PRK04023 DNA polymerase II lar 33.4 40 0.00086 40.8 3.6 50 82-143 412-461 (1121)
49 PF05191 ADK_lid: Adenylate ki 31.8 33 0.00072 25.2 1.7 11 348-358 2-12 (36)
50 TIGR01384 TFS_arch transcripti 31.4 27 0.00059 30.1 1.5 11 347-357 16-26 (104)
51 PF12773 DZR: Double zinc ribb 31.3 39 0.00085 25.3 2.1 13 345-357 27-39 (50)
52 PF13248 zf-ribbon_3: zinc-rib 29.1 24 0.00052 23.8 0.6 9 347-355 2-10 (26)
53 PRK14890 putative Zn-ribbon RN 28.5 40 0.00087 27.7 1.8 16 341-356 19-34 (59)
54 PF13240 zinc_ribbon_2: zinc-r 26.3 31 0.00067 23.0 0.7 10 349-358 1-10 (23)
55 COG3677 Transposase and inacti 25.8 33 0.00072 31.6 1.1 36 344-390 27-63 (129)
56 PF00301 Rubredoxin: Rubredoxi 24.9 67 0.0015 25.0 2.4 39 347-387 1-41 (47)
57 KOG2239|consensus 24.8 99 0.0021 31.1 4.1 68 26-93 102-171 (209)
58 TIGR00100 hypA hydrogenase nic 24.7 45 0.00097 29.9 1.6 17 343-359 66-82 (115)
59 PF11238 DUF3039: Protein of u 24.4 26 0.00056 28.7 0.0 10 382-391 46-55 (58)
60 PRK12380 hydrogenase nickel in 23.5 48 0.001 29.7 1.6 16 344-359 67-82 (113)
61 smart00531 TFIIE Transcription 22.2 49 0.0011 30.6 1.5 23 304-328 84-106 (147)
62 PF12812 PDZ_1: PDZ-like domai 22.1 49 0.0011 27.9 1.3 60 31-92 2-62 (78)
63 PF02150 RNA_POL_M_15KD: RNA p 22.0 27 0.00058 25.4 -0.2 14 348-361 2-15 (35)
64 TIGR02300 FYDLN_acid conserved 21.9 53 0.0012 30.8 1.6 13 381-393 27-39 (129)
65 PF01485 IBR: IBR domain; Int 21.8 81 0.0018 23.9 2.4 29 319-353 18-46 (64)
66 PRK14559 putative protein seri 21.6 1E+02 0.0022 35.6 4.1 32 382-414 29-60 (645)
67 COG1096 Predicted RNA-binding 20.5 57 0.0012 32.3 1.6 25 319-355 149-173 (188)
68 PRK06450 threonine synthase; V 20.4 63 0.0014 33.8 2.0 14 345-358 1-14 (338)
69 PRK00564 hypA hydrogenase nick 20.1 69 0.0015 28.8 1.9 17 343-359 67-83 (117)
No 1
>KOG3092|consensus
Probab=100.00 E-value=1.2e-80 Score=587.11 Aligned_cols=199 Identities=73% Similarity=1.308 Sum_probs=173.1
Q ss_pred CCcccchhHHhhhcCCCCccccccChhhhccccccCCcccccccHHHHHHHHcCCCCCCcccCCCCChhhHHHHHHhhhh
Q psy10861 151 SSSEEVSWISWFCGLRGNEFFCEVDEDYIQDKFNLTGLNEQVPHYRQALDMILDLEPDDELEDNPNQSDLIEQASEMLYG 230 (498)
Q Consensus 151 ssse~~sWI~wF~~~~gne~f~eVDeDfI~D~FNL~GL~~~vp~y~~ALdlIld~~~~~~~e~~~~~~~lIe~sAe~LYG 230 (498)
+++++.|||+|||+++|||||||||+|||+|+|||+||+.+||+|++|||+|||.+++++++++++
T Consensus 2 s~see~sWI~wFc~~~GnEffceVdeeyIqD~FNltgL~~~Vp~y~~ald~ILD~~~~~~~e~~~~-------------- 67 (216)
T KOG3092|consen 2 SSSEEVSWISWFCGLRGNEFFCEVDEEYIQDRFNLTGLSEQVPNYRQALDLILDLEPDDELEDNAE-------------- 67 (216)
T ss_pred CcccccchHHHHhcCCCCeeeEecCHHHhhhhhccccccccCchHHHHHHHhhcCCCCcccccchh--------------
Confidence 456777899999999999999999999999999999999999999999999999988776655433
Q ss_pred hhhhhhhhccchhhhHHhhhccCCCCCCCccccCCCCCcCCCcccCCCCCCchhHHHHHHHHhhhhhcceeeChhhHHHH
Q psy10861 231 LIHARYILTNRGIGQMIEKYQTGDFGHCPRVYCESQPMLPIDDELEDNPNQSDLIEQASEMLYGLIHARYILTNRGIGQM 310 (498)
Q Consensus 231 LIHARYIlT~rGL~~M~EKY~~gdFG~CPRv~C~~q~vLPVG~~Lsd~p~~~d~i~~~a~~LYgliHaRyi~T~~Gl~~m 310 (498)
++|+||.+|++||||||||||+|++||++|
T Consensus 68 --------------------------------------------------~~~~iE~aae~LYGLIHaRYIlT~~Gl~~M 97 (216)
T KOG3092|consen 68 --------------------------------------------------QSELIESAAEMLYGLIHARYILTNRGLAAM 97 (216)
T ss_pred --------------------------------------------------HHHHHHHHHHHHHHhhhheeeechHHHHHH
Confidence 235566666666667777777777777777
Q ss_pred HHhhcCCCccccCCcCCCCCCccccccCCCCCCccceEecCCCcccccCCCCCCcccCCCCCCCCccccccccCCCcccc
Q psy10861 311 IEKYQTGDFGHCPRVYCESQPMLPIGLSDVPGEAMVKSYCPKCMDVYTPKSSRHHHTDGLSDVPGEAMVKSYCPKCMDVY 390 (498)
Q Consensus 311 ~~Ky~~~~FG~CPRv~C~~~~~LP~G~sd~~~~~~vklYCP~C~dvY~p~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~ 390 (498)
.+||++++||+||||+|++|+|||+|+||+||+++||||||+|+|||.|
T Consensus 98 ~eKy~~~dFG~CPRV~C~~q~~LPvGLsDipg~~~VklYCP~C~dvY~P------------------------------- 146 (216)
T KOG3092|consen 98 LEKYKNGDFGRCPRVYCCGQPVLPVGLSDIPGKSTVKLYCPSCEDVYIP------------------------------- 146 (216)
T ss_pred HHHHhcCCCCcCCcccccCCccccccccCCCCcceEEEeCCCccccccc-------------------------------
Confidence 7777777888888888889999999999999999999999999999995
Q ss_pred cCCCCCCCCccccccCCchhhHHHhhcCCCCCCCCCCCcCCCcCCCccCCCCCcch
Q psy10861 391 TPKSSRHHHTDGAYFGTGFPHMLFMVHPEYRPKRPVNQFVPSSRNDELEDNPNQSD 446 (498)
Q Consensus 391 ~p~~~~~~~iDGa~fG~sFph~f~~~~p~~~p~~~~~~~~p~I~GFKLhdnpnQSD 446 (498)
++||+.+||||||||||||||||+||+++|+++.++|||||||||||+.+.+..
T Consensus 147 --~ssr~~~iDGa~fGtsFPhmff~~~p~l~P~r~~~~yvPriyGFkih~~a~~~~ 200 (216)
T KOG3092|consen 147 --KSSRHGNIDGAYFGTSFPHMFFMTHPELRPKRPTEQYVPRIYGFKIHKPAYTGP 200 (216)
T ss_pred --ccccccccccchhcCCCchhHHHhccccCCCcchhhhcchheeeeeCchhhccH
Confidence 455677899999999999999999999999999999999999999999875555
No 2
>PTZ00396 Casein kinase II subunit beta; Provisional
Probab=100.00 E-value=4.3e-73 Score=556.05 Aligned_cols=200 Identities=50% Similarity=0.939 Sum_probs=171.7
Q ss_pred CCCcccchhHHhhhcCCCCccccccChhhhccccccCCcccccccHHHHHHHHcCCCCCCcccCCCCChhhHHHHHHhhh
Q psy10861 150 MSSSEEVSWISWFCGLRGNEFFCEVDEDYIQDKFNLTGLNEQVPHYRQALDMILDLEPDDELEDNPNQSDLIEQASEMLY 229 (498)
Q Consensus 150 ~ssse~~sWI~wF~~~~gne~f~eVDeDfI~D~FNL~GL~~~vp~y~~ALdlIld~~~~~~~e~~~~~~~lIe~sAe~LY 229 (498)
++|+++.+||+|||+++||+|||+||+|||+|+|||+||+..|++|++||++|+|...+++.+....
T Consensus 15 ~~s~~~~sWI~wF~~~~gne~f~~Vd~dyI~D~FNl~GL~~~v~~y~~al~~Ild~~~~~~~~~~~~------------- 81 (251)
T PTZ00396 15 EPSEESMGWIEWFCSLKGHEFLCEVDEDFIRDEFNLYGLKSKFPFYNEALDMILDSEPPDDEDLEDE------------- 81 (251)
T ss_pred cCCCCcCcHHHHHhCCCCCeeEEEeCHHHhcCcchhhCccccccCHHHHHHHHcCCCCCccccccch-------------
Confidence 3456677999999999999999999999999999999999999999999999999876543211111
Q ss_pred hhhhhhhhhccchhhhHHhhhccCCCCCCCccccCCCCCcCCCcccCCCCCCchhHHHHHHHHhhhhhcceeeChhhHHH
Q psy10861 230 GLIHARYILTNRGIGQMIEKYQTGDFGHCPRVYCESQPMLPIDDELEDNPNQSDLIEQASEMLYGLIHARYILTNRGIGQ 309 (498)
Q Consensus 230 GLIHARYIlT~rGL~~M~EKY~~gdFG~CPRv~C~~q~vLPVG~~Lsd~p~~~d~i~~~a~~LYgliHaRyi~T~~Gl~~ 309 (498)
..+.++.+|.+||||||||||+|++||++
T Consensus 82 ---------------------------------------------------~~~~i~~~a~~LYGLIHARyI~T~~Gl~~ 110 (251)
T PTZ00396 82 ---------------------------------------------------QFLEVYQEASDLYGLIHARFITTPKGLAL 110 (251)
T ss_pred ---------------------------------------------------hHHHHHHHHHHHHHHHhHhHhcCHHHHHH
Confidence 12345566777777777778888888888
Q ss_pred HHHhhcCCCccccCCcCCCCCCccccccCCCCCCccceEecCCCcccccCCCCCCcccCCCCCCCCccccccccCCCccc
Q psy10861 310 MIEKYQTGDFGHCPRVYCESQPMLPIGLSDVPGEAMVKSYCPKCMDVYTPKSSRHHHTDGLSDVPGEAMVKSYCPKCMDV 389 (498)
Q Consensus 310 m~~Ky~~~~FG~CPRv~C~~~~~LP~G~sd~~~~~~vklYCP~C~dvY~p~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~ 389 (498)
|++||++++||+||||+|++|||||||+||+||+++||||||+|+|||+|++
T Consensus 111 M~eKY~~g~FG~CPRv~C~~q~~LPvGlSd~~g~~~VKlyCP~C~DvY~p~s---------------------------- 162 (251)
T PTZ00396 111 MREKYLQGKFGHCPRVLCEGQNVLPIGLSDVLKTSRVKVYCPRCQEVYHPKK---------------------------- 162 (251)
T ss_pred HHHHhhCCCCCCCCCccCCCCcccccccCCCcCcCceeEeCCCchhhcCCCC----------------------------
Confidence 8888888888889999999999999999999999999999999999999644
Q ss_pred ccCCCCCCCCccccccCCchhhHHHhhcCCCCCCCCCCCcCCCcCCCccCCCCCcch
Q psy10861 390 YTPKSSRHHHTDGAYFGTGFPHMLFMVHPEYRPKRPVNQFVPSSRNDELEDNPNQSD 446 (498)
Q Consensus 390 ~~p~~~~~~~iDGa~fG~sFph~f~~~~p~~~p~~~~~~~~p~I~GFKLhdnpnQSD 446 (498)
+++..||||||||||||||||+||+++|.++..+|+|||||||||+.+....
T Consensus 163 -----~~~~~iDGA~FGtsFph~fl~~~p~l~p~~~~~~yvPrifGFki~~~~~~~~ 214 (251)
T PTZ00396 163 -----SSLLDIDGAFFGTSFPHLFLMTYPELIPTKPPQYYVPKIFGFKVHKKKSSKE 214 (251)
T ss_pred -----ccccccccceecCcHHHHHHHhccccCCCCCCCccCCeeeeEEecccccccc
Confidence 4456899999999999999999999999999999999999999998764443
No 3
>COG5041 SKB2 Casein kinase II, beta subunit [Signal transduction mechanisms / Cell division and chromosome partitioning / Transcription]
Probab=100.00 E-value=3e-72 Score=533.59 Aligned_cols=203 Identities=50% Similarity=1.016 Sum_probs=174.3
Q ss_pred CCCcccchhHHhhhcCCCCccccccChhhhccccccCCcccccccHHHHHHHHcCCCCCCcccCCCCChhhHHHHHHhhh
Q psy10861 150 MSSSEEVSWISWFCGLRGNEFFCEVDEDYIQDKFNLTGLNEQVPHYRQALDMILDLEPDDELEDNPNQSDLIEQASEMLY 229 (498)
Q Consensus 150 ~ssse~~sWI~wF~~~~gne~f~eVDeDfI~D~FNL~GL~~~vp~y~~ALdlIld~~~~~~~e~~~~~~~lIe~sAe~LY 229 (498)
.||++..+||+|||+++||||||+||+|||+|+||++||+..||+|++|+++|+|...++..+... .+.||.+|++||
T Consensus 18 sds~~y~~Wi~~F~~rkg~eyfc~V~~efIeDrFNltgL~~~Vp~y~~~ldlILD~~~~~~~e~~~--~d~iE~sa~~LY 95 (242)
T COG5041 18 SDSSEYDEWIDWFCSRKGNEYFCEVPEEFIEDRFNLTGLSREVPHYSEVLDLILDKLAPSNLENDE--VDIIEESARQLY 95 (242)
T ss_pred cccHHHHHHHHHHHcCCCCeeeeeCCHHHHHhhhhccchhhccchHHHHHHHHHhccCCcchhhhh--hHHHHHHHHHHH
Confidence 344555689999999999999999999999999999999999999999999999998776554322 478999999999
Q ss_pred hhhhhhhhhccchhhhHHhhhccCCCCCCCccccCCCCCcCCCcccCCCCCCchhHHHHHHHHhhhhhcceeeChhhHHH
Q psy10861 230 GLIHARYILTNRGIGQMIEKYQTGDFGHCPRVYCESQPMLPIDDELEDNPNQSDLIEQASEMLYGLIHARYILTNRGIGQ 309 (498)
Q Consensus 230 GLIHARYIlT~rGL~~M~EKY~~gdFG~CPRv~C~~q~vLPVG~~Lsd~p~~~d~i~~~a~~LYgliHaRyi~T~~Gl~~ 309 (498)
||||||||+|+.||++|+|||+.++||+||||+
T Consensus 96 gLIHaRyIiT~~GL~~m~eKy~~~efG~CPRv~----------------------------------------------- 128 (242)
T COG5041 96 GLIHARYIITKSGLQAMLEKYKSREFGACPRVY----------------------------------------------- 128 (242)
T ss_pred HHHHhhheeeHHHHHHHHHHHhhcccCCCCccc-----------------------------------------------
Confidence 999999988888888888887777776666555
Q ss_pred HHHhhcCCCccccCCcCCCCCCccccccCCCCCCccceEecCCCcccccCCCCCCcccCCCCCCCCccccccccCCCccc
Q psy10861 310 MIEKYQTGDFGHCPRVYCESQPMLPIGLSDVPGEAMVKSYCPKCMDVYTPKSSRHHHTDGLSDVPGEAMVKSYCPKCMDV 389 (498)
Q Consensus 310 m~~Ky~~~~FG~CPRv~C~~~~~LP~G~sd~~~~~~vklYCP~C~dvY~p~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~ 389 (498)
|++|+|||+|+||+||.++||||||+|.|+|.|
T Consensus 129 -----------------Cn~~~vLPvGLsDi~g~~~vkLyCpsC~dlY~p------------------------------ 161 (242)
T COG5041 129 -----------------CNGQQVLPVGLSDIPGKSSVKLYCPSCEDLYLP------------------------------ 161 (242)
T ss_pred -----------------ccCcceeccccccCCCCceeEEecCchhhhcCc------------------------------
Confidence 555566666688889999999999999999995
Q ss_pred ccCCCCCCCCccccccCCchhhHHHhhcCCCCCCCCCCCcCCCcCCCccCCCCCcchhHHHH
Q psy10861 390 YTPKSSRHHHTDGAYFGTGFPHMLFMVHPEYRPKRPVNQFVPSSRNDELEDNPNQSDLIEQA 451 (498)
Q Consensus 390 ~~p~~~~~~~iDGa~fG~sFph~f~~~~p~~~p~~~~~~~~p~I~GFKLhdnpnQSDLie~~ 451 (498)
+++||..|||||||||||||||++||++.|+++.+.|+|||||||||+.+....+.++.
T Consensus 162 ---~Ssr~~~iDGa~fGtSFPh~f~~~~pel~p~~~~e~YiprIfGfri~~~a~~~~~~e~~ 220 (242)
T COG5041 162 ---KSSRHQSIDGAFFGTSFPHMFLQTFPELFPKRSCERYIPRIFGFRIHSHADTGPRMEWL 220 (242)
T ss_pred ---ccccccccccchhccCCchHHHHhchhhcCCcchhhhcceeeeeEeehhhccccHHHHH
Confidence 55667789999999999999999999999999999999999999999987555555544
No 4
>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=3.3e-71 Score=522.20 Aligned_cols=184 Identities=64% Similarity=1.206 Sum_probs=139.3
Q ss_pred hhHHhhhcCCCCccccccChhhhccccccCCcccccccHHHHHHHHcCCCCCCcccCCCCChhhHHHHHHhhhhhhhhhh
Q psy10861 157 SWISWFCGLRGNEFFCEVDEDYIQDKFNLTGLNEQVPHYRQALDMILDLEPDDELEDNPNQSDLIEQASEMLYGLIHARY 236 (498)
Q Consensus 157 sWI~wF~~~~gne~f~eVDeDfI~D~FNL~GL~~~vp~y~~ALdlIld~~~~~~~e~~~~~~~lIe~sAe~LYGLIHARY 236 (498)
|||+|||+++||+||||||+|||+|+|||+||+++||+|++||++|+|.+.+++.+.+..
T Consensus 1 sWI~~F~~~~~~~~f~~Vd~dyI~D~FNl~GL~~~v~~y~~al~~Ild~~~~~~~~~~~~-------------------- 60 (184)
T PF01214_consen 1 SWIDWFCSLKGNEFFCEVDEDYIEDSFNLYGLSSQVPNYDEALDMILDKEPDEDEESDDE-------------------- 60 (184)
T ss_dssp -HHHHHHHSTTTTT-----HHHHHSGGGGTTGGGTSTTHHHHHHHHTT----TTTTTTTC--------------------
T ss_pred CHHHHHhCCCCCeEEEEeCHHHHhCcchhcChhhccccHHHHHHHHcCCCcccchhccch--------------------
Confidence 699999999999999999999999999999999999999999999999876543221112
Q ss_pred hhccchhhhHHhhhccCCCCCCCccccCCCCCcCCCcccCCCCCCchhHHHHHHHHhhhhhcceeeChhhHHHHHHhhcC
Q psy10861 237 ILTNRGIGQMIEKYQTGDFGHCPRVYCESQPMLPIDDELEDNPNQSDLIEQASEMLYGLIHARYILTNRGIGQMIEKYQT 316 (498)
Q Consensus 237 IlT~rGL~~M~EKY~~gdFG~CPRv~C~~q~vLPVG~~Lsd~p~~~d~i~~~a~~LYgliHaRyi~T~~Gl~~m~~Ky~~ 316 (498)
+.+.++++|++||||||||||+|++||++|++||++
T Consensus 61 --------------------------------------------~~~~i~~~a~~LYGLIHaRyI~T~~Gl~~m~eKy~~ 96 (184)
T PF01214_consen 61 --------------------------------------------SDDEIEKSAEMLYGLIHARYILTPRGLEQMKEKYEQ 96 (184)
T ss_dssp --------------------------------------------CHHHHHHHHHHHHHHHHHHHTTSHHHHHHHHHHHHT
T ss_pred --------------------------------------------hHHHHHHHHHHHHhhhHHHHhhcHHHHHHHHHhhcC
Confidence 245566666777777777778888888888888888
Q ss_pred CCccccCCcCCCCCCccccccCCCCCCccceEecCCCcccccCCCCCCcccCCCCCCCCccccccccCCCcccccCCCCC
Q psy10861 317 GDFGHCPRVYCESQPMLPIGLSDVPGEAMVKSYCPKCMDVYTPKSSRHHHTDGLSDVPGEAMVKSYCPKCMDVYTPKSSR 396 (498)
Q Consensus 317 ~~FG~CPRv~C~~~~~LP~G~sd~~~~~~vklYCP~C~dvY~p~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~p~~~~ 396 (498)
++||+||||+|++|+|||+|+||+||+++||||||+|+|||+| ++++
T Consensus 97 g~FG~CPRv~C~~~~lLPiGlsd~~g~~~vKlyCP~C~dvY~p---------------------------------~~~~ 143 (184)
T PF01214_consen 97 GDFGRCPRVYCNGQPLLPIGLSDTPGESTVKLYCPRCKDVYHP---------------------------------PSSR 143 (184)
T ss_dssp TTT-B-SBGGGTT-B-EEEBS-SSTTS-BBEEEETTTTEEE-----------------------------------SSGG
T ss_pred CcCCcCCcccCCCCceeCccCCCCCCccceeEECCCCccccCC---------------------------------CCcc
Confidence 8888899999999999999999999999999999999999995 3456
Q ss_pred CCCccccccCCchhhHHHhhcCCCCCCCCCCCcCCCcCCCc
Q psy10861 397 HHHTDGAYFGTGFPHMLFMVHPEYRPKRPVNQFVPSSRNDE 437 (498)
Q Consensus 397 ~~~iDGa~fG~sFph~f~~~~p~~~p~~~~~~~~p~I~GFK 437 (498)
+.+||||||||||||||+|+||++.|+.+..+|+|||||||
T Consensus 144 ~~~iDGA~FG~sFph~f~~~~p~~~~~~~~~~y~PrifGFk 184 (184)
T PF01214_consen 144 HSNIDGAYFGPSFPHLFLMTYPELIPSPPPKPYVPRIFGFK 184 (184)
T ss_dssp GTTSBGGGTTSSHHHHHHHH-GGGS-SS-SS----ECTTCE
T ss_pred ccceeccccCCccHHHHHHHCccccCCCCCCccCCcccccC
Confidence 78999999999999999999999999999999999999997
No 5
>KOG3092|consensus
Probab=100.00 E-value=4.9e-47 Score=358.92 Aligned_cols=174 Identities=53% Similarity=0.896 Sum_probs=147.7
Q ss_pred hhhhhcccccCCCCcccchHHHhhhccccccCChhhhhcccCccCccccCCChHHHHHHHhcCCCCCCCCCCcccchhHH
Q psy10861 81 DYIQDKFNLTGLNEQVPHYRQALDMILDLEPVDEDYIQDKFNLTGLNEQVPHYRQALDMILDLEPGSLKMSSSEEVSWIS 160 (498)
Q Consensus 81 d~i~d~fnl~gl~~~v~~~~~al~~i~~l~EVdedfIeD~FNLtGL~~~Vp~Y~eALdmILD~e~~d~~~ssse~~sWI~ 160 (498)
+||.|++++.| ||+ +||||+|||+|+||||||+.+||+|++|||+|||++++++.++.++
T Consensus 8 sWI~wFc~~~G-nEf-------------fceVdeeyIqD~FNltgL~~~Vp~y~~ald~ILD~~~~~~~e~~~~------ 67 (216)
T KOG3092|consen 8 SWISWFCGLRG-NEF-------------FCEVDEEYIQDRFNLTGLSEQVPNYRQALDLILDLEPDDELEDNAE------ 67 (216)
T ss_pred chHHHHhcCCC-Cee-------------eEecCHHHhhhhhccccccccCchHHHHHHHhhcCCCCcccccchh------
Confidence 49999999999 433 9999999999999999999999999999999999998765321110
Q ss_pred hhhcCCCCccccccChhhhccccccCCcccccccHHHHHHHHcCCCCCCcccCCCCChhhHHHHHHhhhhhhhhhhhhcc
Q psy10861 161 WFCGLRGNEFFCEVDEDYIQDKFNLTGLNEQVPHYRQALDMILDLEPDDELEDNPNQSDLIEQASEMLYGLIHARYILTN 240 (498)
Q Consensus 161 wF~~~~gne~f~eVDeDfI~D~FNL~GL~~~vp~y~~ALdlIld~~~~~~~e~~~~~~~lIe~sAe~LYGLIHARYIlT~ 240 (498)
.-| +||++|++||||||||||+|+
T Consensus 68 -------------------------------------~~~-------------------~iE~aae~LYGLIHaRYIlT~ 91 (216)
T KOG3092|consen 68 -------------------------------------QSE-------------------LIESAAEMLYGLIHARYILTN 91 (216)
T ss_pred -------------------------------------HHH-------------------HHHHHHHHHHHhhhheeeech
Confidence 001 268899999999999999999
Q ss_pred chhhhHHhhhccCCCCCCCccccCCCCCcCCCcccCCCCCCchhHHHHHHHHhhhhhcceeeChhhHHHHHHhhcCCCcc
Q psy10861 241 RGIGQMIEKYQTGDFGHCPRVYCESQPMLPIDDELEDNPNQSDLIEQASEMLYGLIHARYILTNRGIGQMIEKYQTGDFG 320 (498)
Q Consensus 241 rGL~~M~EKY~~gdFG~CPRv~C~~q~vLPVG~~Lsd~p~~~d~i~~~a~~LYgliHaRyi~T~~Gl~~m~~Ky~~~~FG 320 (498)
+||++|+|||++++||+||||+|++|+||||| |+|+|+. ++++||
T Consensus 92 ~Gl~~M~eKy~~~dFG~CPRV~C~~q~~LPvG--LsDipg~------~~VklY--------------------------- 136 (216)
T KOG3092|consen 92 RGLAAMLEKYKNGDFGRCPRVYCCGQPVLPVG--LSDIPGK------STVKLY--------------------------- 136 (216)
T ss_pred HHHHHHHHHHhcCCCCcCCcccccCCcccccc--ccCCCCc------ceEEEe---------------------------
Confidence 99999999999999999999999999999999 8888886 457788
Q ss_pred ccCCcCCCCCCccccccCCCCCCccceEecCCCcccccCCCCCCcccCCCCCCCCcccccc-----cc-CCCcccccCCC
Q psy10861 321 HCPRVYCESQPMLPIGLSDVPGEAMVKSYCPKCMDVYTPKSSRHHHTDGLSDVPGEAMVKS-----YC-PKCMDVYTPKS 394 (498)
Q Consensus 321 ~CPRv~C~~~~~LP~G~sd~~~~~~vklYCP~C~dvY~p~~~~~~~~~g~~~~~~~~~~~~-----~~-~~~~~~~~p~~ 394 (498)
||+ |+ ++|-|+. . ||+++|||+|||||+++.. .= .+..+.|.||.
T Consensus 137 -CP~--C~------------------dvY~P~s----s----r~~~iDGa~fGtsFPhmff~~~p~l~P~r~~~~yvPri 187 (216)
T KOG3092|consen 137 -CPS--CE------------------DVYIPKS----S----RHGNIDGAYFGTSFPHMFFMTHPELRPKRPTEQYVPRI 187 (216)
T ss_pred -CCC--cc------------------ccccccc----c----cccccccchhcCCCchhHHHhccccCCCcchhhhcchh
Confidence 999 99 9999998 3 7899999999999999833 11 22336677764
No 6
>PTZ00396 Casein kinase II subunit beta; Provisional
Probab=100.00 E-value=3.7e-41 Score=330.92 Aligned_cols=166 Identities=43% Similarity=0.662 Sum_probs=139.4
Q ss_pred CCCchhhhhhcccccCCCCcccchHHHhhhccccccCChhhhhcccCccCccccCCChHHHHHHHhcCCCCCCCCCCccc
Q psy10861 76 PQIDEDYIQDKFNLTGLNEQVPHYRQALDMILDLEPVDEDYIQDKFNLTGLNEQVPHYRQALDMILDLEPGSLKMSSSEE 155 (498)
Q Consensus 76 ~e~ded~i~d~fnl~gl~~~v~~~~~al~~i~~l~EVdedfIeD~FNLtGL~~~Vp~Y~eALdmILD~e~~d~~~ssse~ 155 (498)
.+.+++||.|+.++.| |+| |||||+|||+|+||||||+.+||+|++||+||||.+++++++.+++
T Consensus 17 s~~~~sWI~wF~~~~g-ne~-------------f~~Vd~dyI~D~FNl~GL~~~v~~y~~al~~Ild~~~~~~~~~~~~- 81 (251)
T PTZ00396 17 SEESMGWIEWFCSLKG-HEF-------------LCEVDEDFIRDEFNLYGLKSKFPFYNEALDMILDSEPPDDEDLEDE- 81 (251)
T ss_pred CCCcCcHHHHHhCCCC-Cee-------------EEEeCHHHhcCcchhhCccccccCHHHHHHHHcCCCCCccccccch-
Confidence 3455679999999999 545 9999999999999999999999999999999999987543111000
Q ss_pred chhHHhhhcCCCCccccccChhhhccccccCCcccccccHHHHHHHHcCCCCCCcccCCCCChhhHHHHHHhhhhhhhhh
Q psy10861 156 VSWISWFCGLRGNEFFCEVDEDYIQDKFNLTGLNEQVPHYRQALDMILDLEPDDELEDNPNQSDLIEQASEMLYGLIHAR 235 (498)
Q Consensus 156 ~sWI~wF~~~~gne~f~eVDeDfI~D~FNL~GL~~~vp~y~~ALdlIld~~~~~~~e~~~~~~~lIe~sAe~LYGLIHAR 235 (498)
. . . .++++|+.||||||||
T Consensus 82 --------------------------~---------------------------~--~------~i~~~a~~LYGLIHAR 100 (251)
T PTZ00396 82 --------------------------Q---------------------------F--L------EVYQEASDLYGLIHAR 100 (251)
T ss_pred --------------------------h---------------------------H--H------HHHHHHHHHHHHHhHh
Confidence 0 0 0 1467889999999999
Q ss_pred hhhccchhhhHHhhhccCCCCCCCccccCCCCCcCCCcccCCCCCCchhHHHHHHHHhhhhhcceeeChhhHHHHHHhhc
Q psy10861 236 YILTNRGIGQMIEKYQTGDFGHCPRVYCESQPMLPIDDELEDNPNQSDLIEQASEMLYGLIHARYILTNRGIGQMIEKYQ 315 (498)
Q Consensus 236 YIlT~rGL~~M~EKY~~gdFG~CPRv~C~~q~vLPVG~~Lsd~p~~~d~i~~~a~~LYgliHaRyi~T~~Gl~~m~~Ky~ 315 (498)
||+|++||++|++||++|+||+||||+|++|+||||| |||+|+.+. ++||
T Consensus 101 yI~T~~Gl~~M~eKY~~g~FG~CPRv~C~~q~~LPvG--lSd~~g~~~------VKly---------------------- 150 (251)
T PTZ00396 101 FITTPKGLALMREKYLQGKFGHCPRVLCEGQNVLPIG--LSDVLKTSR------VKVY---------------------- 150 (251)
T ss_pred HhcCHHHHHHHHHHhhCCCCCCCCCccCCCCcccccc--cCCCcCcCc------eeEe----------------------
Confidence 9999999999999999999999999999999999999 888888654 6677
Q ss_pred CCCccccCCcCCCCCCccccccCCCCCCccceEecCCCcccccCCCCCCcccCCCCCCCCcccccc
Q psy10861 316 TGDFGHCPRVYCESQPMLPIGLSDVPGEAMVKSYCPKCMDVYTPKSSRHHHTDGLSDVPGEAMVKS 381 (498)
Q Consensus 316 ~~~FG~CPRv~C~~~~~LP~G~sd~~~~~~vklYCP~C~dvY~p~~~~~~~~~g~~~~~~~~~~~~ 381 (498)
||| |+ +||=|+... . .++|||+|||+|+++..
T Consensus 151 ------CP~--C~------------------DvY~p~s~~--~------~~iDGA~FGtsFph~fl 182 (251)
T PTZ00396 151 ------CPR--CQ------------------EVYHPKKSS--L------LDIDGAFFGTSFPHLFL 182 (251)
T ss_pred ------CCC--ch------------------hhcCCCCcc--c------cccccceecCcHHHHHH
Confidence 999 99 999998632 2 15899999999999843
No 7
>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=3.1e-41 Score=318.76 Aligned_cols=159 Identities=55% Similarity=0.946 Sum_probs=120.9
Q ss_pred hhhhhcccccCCCCcccchHHHhhhccccccCChhhhhcccCccCccccCCChHHHHHHHhcCCCCCCCCCCcccchhHH
Q psy10861 81 DYIQDKFNLTGLNEQVPHYRQALDMILDLEPVDEDYIQDKFNLTGLNEQVPHYRQALDMILDLEPGSLKMSSSEEVSWIS 160 (498)
Q Consensus 81 d~i~d~fnl~gl~~~v~~~~~al~~i~~l~EVdedfIeD~FNLtGL~~~Vp~Y~eALdmILD~e~~d~~~ssse~~sWI~ 160 (498)
+||+|+.++.| |+| |||||+|||+|+|||+||+++||+|++||+||||.+++++++.+.+.
T Consensus 1 sWI~~F~~~~~-~~~-------------f~~Vd~dyI~D~FNl~GL~~~v~~y~~al~~Ild~~~~~~~~~~~~~----- 61 (184)
T PF01214_consen 1 SWIDWFCSLKG-NEF-------------FCEVDEDYIEDSFNLYGLSSQVPNYDEALDMILDKEPDEDEESDDES----- 61 (184)
T ss_dssp -HHHHHHHSTT-TTT------------------HHHHHSGGGGTTGGGTSTTHHHHHHHHTT----TTTTTTTCC-----
T ss_pred CHHHHHhCCCC-CeE-------------EEEeCHHHHhCcchhcChhhccccHHHHHHHHcCCCcccchhccchh-----
Confidence 59999999998 544 99999999999999999999999999999999999876431111000
Q ss_pred hhhcCCCCccccccChhhhccccccCCcccccccHHHHHHHHcCCCCCCcccCCCCChhhHHHHHHhhhhhhhhhhhhcc
Q psy10861 161 WFCGLRGNEFFCEVDEDYIQDKFNLTGLNEQVPHYRQALDMILDLEPDDELEDNPNQSDLIEQASEMLYGLIHARYILTN 240 (498)
Q Consensus 161 wF~~~~gne~f~eVDeDfI~D~FNL~GL~~~vp~y~~ALdlIld~~~~~~~e~~~~~~~lIe~sAe~LYGLIHARYIlT~ 240 (498)
.+ .++++|++||||||||||+|+
T Consensus 62 ---------------~~------------------------------------------~i~~~a~~LYGLIHaRyI~T~ 84 (184)
T PF01214_consen 62 ---------------DD------------------------------------------EIEKSAEMLYGLIHARYILTP 84 (184)
T ss_dssp ---------------HH------------------------------------------HHHHHHHHHHHHHHHHHTTSH
T ss_pred ---------------HH------------------------------------------HHHHHHHHHHhhhHHHHhhcH
Confidence 00 147789999999999999999
Q ss_pred chhhhHHhhhccCCCCCCCccccCCCCCcCCCcccCCCCCCchhHHHHHHHHhhhhhcceeeChhhHHHHHHhhcCCCcc
Q psy10861 241 RGIGQMIEKYQTGDFGHCPRVYCESQPMLPIDDELEDNPNQSDLIEQASEMLYGLIHARYILTNRGIGQMIEKYQTGDFG 320 (498)
Q Consensus 241 rGL~~M~EKY~~gdFG~CPRv~C~~q~vLPVG~~Lsd~p~~~d~i~~~a~~LYgliHaRyi~T~~Gl~~m~~Ky~~~~FG 320 (498)
+||++|+|||++|+||+||||+|++|+||||| +||+|+++. ++||
T Consensus 85 ~Gl~~m~eKy~~g~FG~CPRv~C~~~~lLPiG--lsd~~g~~~------vKly--------------------------- 129 (184)
T PF01214_consen 85 RGLEQMKEKYEQGDFGRCPRVYCNGQPLLPIG--LSDTPGEST------VKLY--------------------------- 129 (184)
T ss_dssp HHHHHHHHHHHTTTT-B-SBGGGTT-B-EEEB--S-SSTTS-B------BEEE---------------------------
T ss_pred HHHHHHHHhhcCCcCCcCCcccCCCCceeCcc--CCCCCCccc------eeEE---------------------------
Confidence 99999999999999999999999999999999 899998865 5677
Q ss_pred ccCCcCCCCCCccccccCCCCCCccceEecCCCcccccCCCCCCcccCCCCCCCCcccc
Q psy10861 321 HCPRVYCESQPMLPIGLSDVPGEAMVKSYCPKCMDVYTPKSSRHHHTDGLSDVPGEAMV 379 (498)
Q Consensus 321 ~CPRv~C~~~~~LP~G~sd~~~~~~vklYCP~C~dvY~p~~~~~~~~~g~~~~~~~~~~ 379 (498)
||| |+ ++|-|+- + +|.++|||+|||+|+++
T Consensus 130 -CP~--C~------------------dvY~p~~-----~---~~~~iDGA~FG~sFph~ 159 (184)
T PF01214_consen 130 -CPR--CK------------------DVYHPPS-----S---RHSNIDGAYFGPSFPHL 159 (184)
T ss_dssp -ETT--TT------------------EEE--SS-----G---GGTTSBGGGTTSSHHHH
T ss_pred -CCC--Cc------------------cccCCCC-----c---cccceeccccCCccHHH
Confidence 999 99 9999944 2 46789999999999998
No 8
>COG5041 SKB2 Casein kinase II, beta subunit [Signal transduction mechanisms / Cell division and chromosome partitioning / Transcription]
Probab=99.84 E-value=6.4e-22 Score=189.82 Aligned_cols=63 Identities=41% Similarity=0.614 Sum_probs=53.6
Q ss_pred CCCCCCCchh--hhhhcccccCCCCcccchHHHhhhccccccCChhhhhcccCccCccccCCChHHHHHHHhcCCCCCC
Q psy10861 72 KRRDPQIDED--YIQDKFNLTGLNEQVPHYRQALDMILDLEPVDEDYIQDKFNLTGLNEQVPHYRQALDMILDLEPGSL 148 (498)
Q Consensus 72 ~~~~~e~ded--~i~d~fnl~gl~~~v~~~~~al~~i~~l~EVdedfIeD~FNLtGL~~~Vp~Y~eALdmILD~e~~d~ 148 (498)
.+++.+.++. ||.|++..+| |++ +||||+|||+|+||||||+..||+|++|||+|||..+.+.
T Consensus 14 ~~d~sds~~y~~Wi~~F~~rkg-~ey-------------fc~V~~efIeDrFNltgL~~~Vp~y~~~ldlILD~~~~~~ 78 (242)
T COG5041 14 SDDDSDSSEYDEWIDWFCSRKG-NEY-------------FCEVPEEFIEDRFNLTGLSREVPHYSEVLDLILDKLAPSN 78 (242)
T ss_pred cccccccHHHHHHHHHHHcCCC-Cee-------------eeeCCHHHHHhhhhccchhhccchHHHHHHHHHhccCCcc
Confidence 3444455554 9999999999 544 9999999999999999999999999999999999987654
No 9
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=89.11 E-value=0.07 Score=53.94 Aligned_cols=62 Identities=31% Similarity=0.650 Sum_probs=27.9
Q ss_pred cccCCcCCCCCCccccccCCCCCCccc-eEecCCCcccccCCCCCCcccCCCCCCCCccccccccCCCcccccCCCCCCC
Q psy10861 320 GHCPRVYCESQPMLPIGLSDVPGEAMV-KSYCPKCMDVYTPKSSRHHHTDGLSDVPGEAMVKSYCPKCMDVYTPKSSRHH 398 (498)
Q Consensus 320 G~CPRv~C~~~~~LP~G~sd~~~~~~v-klYCP~C~dvY~p~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~p~~~~~~ 398 (498)
.+||+ |+.-++--++ ....| +.|||+|.+-|.-||.+ + .-...
T Consensus 32 ~yCP~--Cg~~~L~~f~-----NN~PVaDF~C~~C~eeyELKSk~-----------------------~------~l~~~ 75 (254)
T PF06044_consen 32 MYCPN--CGSKPLSKFE-----NNRPVADFYCPNCNEEYELKSKK-----------------------K------KLSNK 75 (254)
T ss_dssp ---TT--T--SS-EE-------------EEE-TTT--EEEEEEEE-----------------------S------S--SE
T ss_pred CcCCC--CCChhHhhcc-----CCCccceeECCCCchHHhhhhhc-----------------------c------ccCCc
Confidence 46999 8877655443 23333 88899998888854421 0 00123
Q ss_pred CccccccC-------CchhhHHHhhc
Q psy10861 399 HTDGAYFG-------TGFPHMLFMVH 417 (498)
Q Consensus 399 ~iDGa~fG-------~sFph~f~~~~ 417 (498)
-.||||-- .+=|.+|||.|
T Consensus 76 I~dGAY~Tmi~Ri~s~~NPnfffl~Y 101 (254)
T PF06044_consen 76 INDGAYHTMIERITSDNNPNFFFLTY 101 (254)
T ss_dssp EEEEEHHHHHHHHHTT---EEEEEEE
T ss_pred ccCccHHHHHHHhhccCCCCEEEEEe
Confidence 45999963 24688899999
No 10
>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=83.32 E-value=1 Score=41.58 Aligned_cols=22 Identities=32% Similarity=0.919 Sum_probs=16.4
Q ss_pred CCCccccCCcCCCCCCccccccCCC
Q psy10861 316 TGDFGHCPRVYCESQPMLPIGLSDV 340 (498)
Q Consensus 316 ~~~FG~CPRv~C~~~~~LP~G~sd~ 340 (498)
...|..||. ||+ ++.|+...+.
T Consensus 88 ~~~~sRC~~--CN~-~L~~v~~~~v 109 (147)
T PF01927_consen 88 DPIFSRCPK--CNG-PLRPVSKEEV 109 (147)
T ss_pred CCCCCccCC--CCc-Eeeechhhcc
Confidence 445899999 997 7888865543
No 11
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=77.24 E-value=1.6 Score=31.85 Aligned_cols=35 Identities=26% Similarity=0.524 Sum_probs=20.6
Q ss_pred ceEecCCCcccccCCCCCCcccCCCCCCCCccccccccCCCcccc
Q psy10861 346 VKSYCPKCMDVYTPKSSRHHHTDGLSDVPGEAMVKSYCPKCMDVY 390 (498)
Q Consensus 346 vklYCP~C~dvY~p~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~ 390 (498)
+++-||+|+-.|.-..+ .+ ...+++..|++|..+|
T Consensus 1 M~i~Cp~C~~~y~i~d~---~i-------p~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 1 MIITCPNCQAKYEIDDE---KI-------PPKGRKVRCSKCGHVF 35 (36)
T ss_pred CEEECCCCCCEEeCCHH---HC-------CCCCcEEECCCCCCEe
Confidence 36778888777762111 11 1345577788887665
No 12
>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=71.72 E-value=1.8 Score=31.07 Aligned_cols=31 Identities=29% Similarity=0.508 Sum_probs=15.2
Q ss_pred ccCCcCCCCCCccccccCCCCCCccceEecCCCccc
Q psy10861 321 HCPRVYCESQPMLPIGLSDVPGEAMVKSYCPKCMDV 356 (498)
Q Consensus 321 ~CPRv~C~~~~~LP~G~sd~~~~~~vklYCP~C~dv 356 (498)
.||+ |..+.-+|-..- +....++-||+|+..
T Consensus 4 ~CP~--C~~~~~v~~~~~---~~~~~~v~C~~C~~~ 34 (38)
T TIGR02098 4 QCPN--CKTSFRVVDSQL---GANGGKVRCGKCGHV 34 (38)
T ss_pred ECCC--CCCEEEeCHHHc---CCCCCEEECCCCCCE
Confidence 3666 665554543322 222335666666443
No 13
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=69.53 E-value=2.4 Score=30.91 Aligned_cols=34 Identities=26% Similarity=0.542 Sum_probs=17.2
Q ss_pred eEecCCCcccccCCCCCCcccCCCCCCCCccccccccCCCcccc
Q psy10861 347 KSYCPKCMDVYTPKSSRHHHTDGLSDVPGEAMVKSYCPKCMDVY 390 (498)
Q Consensus 347 klYCP~C~dvY~p~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~ 390 (498)
++-||+|.-.|.-+.+ .. ...+.+..|++|..+|
T Consensus 2 ~i~CP~C~~~f~v~~~--------~l--~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 2 IITCPNCQTRFRVPDD--------KL--PAGGRKVRCPKCGHVF 35 (37)
T ss_pred EEECCCCCceEEcCHH--------Hc--ccCCcEEECCCCCcEe
Confidence 4567777666651110 00 1234456677776555
No 14
>PRK00420 hypothetical protein; Validated
Probab=66.46 E-value=8.5 Score=34.96 Aligned_cols=50 Identities=30% Similarity=0.702 Sum_probs=31.4
Q ss_pred CCCchhHHHHHHHHhhhhhcceeeChhhHHHHHHhhcCCCccccCCcCCCCCCccccccCCCCCCccceEecCCCccccc
Q psy10861 279 PNQSDLIEQASEMLYGLIHARYILTNRGIGQMIEKYQTGDFGHCPRVYCESQPMLPIGLSDVPGEAMVKSYCPKCMDVYT 358 (498)
Q Consensus 279 p~~~d~i~~~a~~LYgliHaRyi~T~~Gl~~m~~Ky~~~~FG~CPRv~C~~~~~LP~G~sd~~~~~~vklYCP~C~dvY~ 358 (498)
|...+.+..+|+.|. +|- .|.. .+||. |. .|++=. ..-++|||.|..++.
T Consensus 2 ~~~~~~~k~~a~~Ll-----------~Ga-~ml~-------~~CP~--Cg-~pLf~l--------k~g~~~Cp~Cg~~~~ 51 (112)
T PRK00420 2 MESEDIVKKAAELLL-----------KGA-KMLS-------KHCPV--CG-LPLFEL--------KDGEVVCPVHGKVYI 51 (112)
T ss_pred CccHHHHHHHHHHHH-----------hHH-HHcc-------CCCCC--CC-Ccceec--------CCCceECCCCCCeee
Confidence 445577777777776 232 2322 67999 87 443311 223899999988776
No 15
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=65.50 E-value=4.1 Score=41.08 Aligned_cols=17 Identities=29% Similarity=0.767 Sum_probs=9.8
Q ss_pred CccceEecCCCcccccC
Q psy10861 343 EAMVKSYCPKCMDVYTP 359 (498)
Q Consensus 343 ~~~vklYCP~C~dvY~p 359 (498)
.+..+..||+|..++-|
T Consensus 113 ~~~~~~~C~~c~~~~yp 129 (256)
T PRK00241 113 KTEWAMLCPHCRERYYP 129 (256)
T ss_pred CCceeEECCCCCCEECC
Confidence 44556666666655554
No 16
>KOG4684|consensus
Probab=65.39 E-value=4.8 Score=40.67 Aligned_cols=71 Identities=20% Similarity=0.485 Sum_probs=48.8
Q ss_pred cCCcCCCC----CCccccccCCCCCCccceEecCCCcccccCCCCCCcccCCCCCCCCccccccccCCCcccccCCCCCC
Q psy10861 322 CPRVYCES----QPMLPIGLSDVPGEAMVKSYCPKCMDVYTPKSSRHHHTDGLSDVPGEAMVKSYCPKCMDVYTPKSSRH 397 (498)
Q Consensus 322 CPRv~C~~----~~~LP~G~sd~~~~~~vklYCP~C~dvY~p~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~p~~~~~ 397 (498)
|||-+|.+ .|+.|--.+..+.-.++++-|-.|++.|. -+.+....-.||.|.+|.+
T Consensus 141 CPRpnCkRiInL~p~~~~p~~P~~~P~gcRV~CgHC~~tFL--------------fnt~tnaLArCPHCrKvSs------ 200 (275)
T KOG4684|consen 141 CPRPNCKRIINLDPLIEKPRDPGTAPTGCRVKCGHCNETFL--------------FNTLTNALARCPHCRKVSS------ 200 (275)
T ss_pred cCCCCcceeeecCCCCCCCCCCCCCCcceEEEecCccceee--------------hhhHHHHHhcCCcccchhh------
Confidence 99999986 34445445555555679999999999997 2345556779999965542
Q ss_pred CCccccccCCchhhHHHh
Q psy10861 398 HHTDGAYFGTGFPHMLFM 415 (498)
Q Consensus 398 ~~iDGa~fG~sFph~f~~ 415 (498)
=|.-|-.+=+-+||+
T Consensus 201 ---vGsrfar~Ra~~ffi 215 (275)
T KOG4684|consen 201 ---VGSRFARRRALLFFI 215 (275)
T ss_pred ---hhhHHhhhhhHHHHH
Confidence 355566665666654
No 17
>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=64.14 E-value=2.2 Score=43.54 Aligned_cols=39 Identities=28% Similarity=0.617 Sum_probs=18.0
Q ss_pred eEecCCCcccccCCCCCCcccCCCCCCCCccccccccCCCcccccCCCCC
Q psy10861 347 KSYCPKCMDVYTPKSSRHHHTDGLSDVPGEAMVKSYCPKCMDVYTPKSSR 396 (498)
Q Consensus 347 klYCP~C~dvY~p~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~p~~~~ 396 (498)
.+|||+|...+. +.|..+-+-...||+.|.+-|..|+..
T Consensus 31 n~yCP~Cg~~~L-----------~~f~NN~PVaDF~C~~C~eeyELKSk~ 69 (254)
T PF06044_consen 31 NMYCPNCGSKPL-----------SKFENNRPVADFYCPNCNEEYELKSKK 69 (254)
T ss_dssp H---TTT--SS------------EE--------EEE-TTT--EEEEEEEE
T ss_pred CCcCCCCCChhH-----------hhccCCCccceeECCCCchHHhhhhhc
Confidence 689999977765 234556677788999999999999765
No 18
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=63.40 E-value=29 Score=36.49 Aligned_cols=48 Identities=21% Similarity=0.480 Sum_probs=33.6
Q ss_pred ccccCCcCCCCCCccccccCCCCCCccceEecCCCcccccCCCCCCcccCCCCCCCCccccccccCCCcc
Q psy10861 319 FGHCPRVYCESQPMLPIGLSDVPGEAMVKSYCPKCMDVYTPKSSRHHHTDGLSDVPGEAMVKSYCPKCMD 388 (498)
Q Consensus 319 FG~CPRv~C~~~~~LP~G~sd~~~~~~vklYCP~C~dvY~p~~~~~~~~~g~~~~~~~~~~~~~~~~~~~ 388 (498)
-++||- |.+.|++-+-.. ...++.=-++|..|.--++ .++.-||.|++
T Consensus 187 ~~~CPv--CGs~P~~s~v~~-~~~~G~RyL~CslC~teW~-------------------~~R~~C~~Cg~ 234 (309)
T PRK03564 187 RQFCPV--CGSMPVSSVVQI-GTTQGLRYLHCNLCESEWH-------------------VVRVKCSNCEQ 234 (309)
T ss_pred CCCCCC--CCCcchhheeec-cCCCCceEEEcCCCCCccc-------------------ccCccCCCCCC
Confidence 488999 999987654322 1234556899999944444 56678999985
No 19
>PRK05978 hypothetical protein; Provisional
Probab=62.64 E-value=6.1 Score=37.42 Aligned_cols=39 Identities=21% Similarity=0.393 Sum_probs=23.8
Q ss_pred HHhhcCCCccccCCcCCCCCCccccccCCCCCCccceEecCCCccccc
Q psy10861 311 IEKYQTGDFGHCPRVYCESQPMLPIGLSDVPGEAMVKSYCPKCMDVYT 358 (498)
Q Consensus 311 ~~Ky~~~~FG~CPRv~C~~~~~LP~G~sd~~~~~~vklYCP~C~dvY~ 358 (498)
..-..+|-.|+||| |..-+++= +--+|.-.||.|..-|.
T Consensus 25 ~~~~~rGl~grCP~--CG~G~LF~-------g~Lkv~~~C~~CG~~~~ 63 (148)
T PRK05978 25 GRAMWRGFRGRCPA--CGEGKLFR-------AFLKPVDHCAACGEDFT 63 (148)
T ss_pred HHHHHHHHcCcCCC--CCCCcccc-------cccccCCCccccCCccc
Confidence 34456678899999 98666542 23344555666655554
No 20
>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=61.53 E-value=3.5 Score=33.45 Aligned_cols=17 Identities=29% Similarity=0.677 Sum_probs=11.5
Q ss_pred hhcCCCccccCCcCCCCCCc
Q psy10861 313 KYQTGDFGHCPRVYCESQPM 332 (498)
Q Consensus 313 Ky~~~~FG~CPRv~C~~~~~ 332 (498)
|+..-.|..||. |.+ |+
T Consensus 1 k~~llniL~Cp~--ck~-pL 17 (68)
T PF03966_consen 1 KLLLLNILACPV--CKG-PL 17 (68)
T ss_dssp BGGGCGTBB-TT--TSS-BE
T ss_pred ChhHHhhhcCCC--CCC-cc
Confidence 455667889997 876 55
No 21
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=59.33 E-value=9.4 Score=36.92 Aligned_cols=60 Identities=25% Similarity=0.398 Sum_probs=33.7
Q ss_pred hhcceeeChhhHHHHHHh---h-----cCCCccccCCcCCCCCCccccccCCC--------CCCccceEecCCCccccc
Q psy10861 296 IHARYILTNRGIGQMIEK---Y-----QTGDFGHCPRVYCESQPMLPIGLSDV--------PGEAMVKSYCPKCMDVYT 358 (498)
Q Consensus 296 iHaRyi~T~~Gl~~m~~K---y-----~~~~FG~CPRv~C~~~~~LP~G~sd~--------~~~~~vklYCP~C~dvY~ 358 (498)
+++=||-+..=.+||.+= + ....|-.||. || .+++++-...+ ......=..||+|..+|=
T Consensus 66 ~~~i~i~~~s~~~Ql~e~~~~~~l~~~~~~e~~RCp~--CN-~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~CgkiYW 141 (165)
T COG1656 66 IKAILIRSDSIEEQLAEFLARLGLKPRLFPEFSRCPE--CN-GELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKIYW 141 (165)
T ss_pred CceEEEeCCCHHHHHHHHHHHhccchhcccccccCcc--cC-CEeccCcHHHHhhccchhhhhcccceeECCCCccccc
Confidence 455566666655665553 2 2345889999 98 45666655441 122222233777766665
No 22
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=58.29 E-value=5.1 Score=40.65 Aligned_cols=47 Identities=30% Similarity=0.615 Sum_probs=24.2
Q ss_pred cccCCcCCCCCCccccccCCCCCCccceEecCCCcccccCCCCCCcccCCCCCCCCccccccccCCCcc
Q psy10861 320 GHCPRVYCESQPMLPIGLSDVPGEAMVKSYCPKCMDVYTPKSSRHHHTDGLSDVPGEAMVKSYCPKCMD 388 (498)
Q Consensus 320 G~CPRv~C~~~~~LP~G~sd~~~~~~vklYCP~C~dvY~p~~~~~~~~~g~~~~~~~~~~~~~~~~~~~ 388 (498)
|+||- |.+.|++=+=..+.. ++.=.++|..|.--+ ..++..||.|++
T Consensus 173 g~CPv--CGs~P~~s~l~~~~~-~G~R~L~Cs~C~t~W-------------------~~~R~~Cp~Cg~ 219 (290)
T PF04216_consen 173 GYCPV--CGSPPVLSVLRGGER-EGKRYLHCSLCGTEW-------------------RFVRIKCPYCGN 219 (290)
T ss_dssp SS-TT--T---EEEEEEE-------EEEEEETTT--EE-------------------E--TTS-TTT--
T ss_pred CcCCC--CCCcCceEEEecCCC-CccEEEEcCCCCCee-------------------eecCCCCcCCCC
Confidence 89999 999988766555544 456789999994444 455668999974
No 23
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=57.70 E-value=12 Score=45.81 Aligned_cols=40 Identities=23% Similarity=0.350 Sum_probs=19.4
Q ss_pred ecCccccccccccCCceeEeeccceeeeeeeeehhhHHHH
Q psy10861 12 VGGSSVKKTAKDSGPALLRIETDEKIGLYGFKIHSLAYQL 51 (498)
Q Consensus 12 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 51 (498)
+||-.|-.--...|---||---...-|+--.-+||-.--|
T Consensus 321 iaGRPvfs~Ps~~GGFRLRYGRsRntGfAt~g~~PAtm~l 360 (1337)
T PRK14714 321 IGGRPVFSHPSRNGGFRLRYGRSRNTGFATAGVHPATMHL 360 (1337)
T ss_pred hcCCccccCCCCCCceeeeecccccccccccccCHHHHHH
Confidence 3444444444444444555544444444445577755443
No 24
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=56.57 E-value=7.7 Score=40.23 Aligned_cols=40 Identities=35% Similarity=0.666 Sum_probs=28.6
Q ss_pred HHHHhhcCCCccccCCcCCCCCCccccccCCCCCCccceEecCCCcccccCC
Q psy10861 309 QMIEKYQTGDFGHCPRVYCESQPMLPIGLSDVPGEAMVKSYCPKCMDVYTPK 360 (498)
Q Consensus 309 ~m~~Ky~~~~FG~CPRv~C~~~~~LP~G~sd~~~~~~vklYCP~C~dvY~p~ 360 (498)
++.+.+.+..| ||+ .|--..+.+...+..||+|+..+-|+
T Consensus 103 ~l~~w~~~~RF--Cg~----------CG~~~~~~~~g~~~~C~~cg~~~fPR 142 (279)
T COG2816 103 QLLEWYRSHRF--CGR----------CGTKTYPREGGWARVCPKCGHEHFPR 142 (279)
T ss_pred HHHHHHhhCcC--CCC----------CCCcCccccCceeeeCCCCCCccCCC
Confidence 34566777777 888 36666777777888888887766653
No 25
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=53.60 E-value=9 Score=28.20 Aligned_cols=29 Identities=34% Similarity=0.913 Sum_probs=18.4
Q ss_pred ccCCcCCCCCCccccccCCCCCCccceEe-cCCCccccc
Q psy10861 321 HCPRVYCESQPMLPIGLSDVPGEAMVKSY-CPKCMDVYT 358 (498)
Q Consensus 321 ~CPRv~C~~~~~LP~G~sd~~~~~~vklY-CP~C~dvY~ 358 (498)
.||+ |+. .|-++-+. .|.++ ||+|.-++.
T Consensus 1 ~CP~--C~~-~l~~~~~~------~~~id~C~~C~G~W~ 30 (41)
T PF13453_consen 1 KCPR--CGT-ELEPVRLG------DVEIDVCPSCGGIWF 30 (41)
T ss_pred CcCC--CCc-ccceEEEC------CEEEEECCCCCeEEc
Confidence 4888 876 56666662 24444 888865554
No 26
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=53.05 E-value=5.4 Score=27.98 Aligned_cols=15 Identities=27% Similarity=0.605 Sum_probs=7.5
Q ss_pred CCccccccccCCCcc
Q psy10861 374 PGEAMVKSYCPKCMD 388 (498)
Q Consensus 374 ~~~~~~~~~~~~~~~ 388 (498)
+...+-.+.||.|+.
T Consensus 15 ~~~~g~~r~C~~Cg~ 29 (32)
T PF09297_consen 15 PAPGGWARRCPSCGH 29 (32)
T ss_dssp E-SSSS-EEESSSS-
T ss_pred CCCCcCEeECCCCcC
Confidence 334455677777753
No 27
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=52.81 E-value=13 Score=29.49 Aligned_cols=36 Identities=22% Similarity=0.454 Sum_probs=27.4
Q ss_pred CCCccceEecCCCcccccCCCCCCcccCCCCCCCCccccccccCCCc
Q psy10861 341 PGEAMVKSYCPKCMDVYTPKSSRHHHTDGLSDVPGEAMVKSYCPKCM 387 (498)
Q Consensus 341 ~~~~~vklYCP~C~dvY~p~~~~~~~~~g~~~~~~~~~~~~~~~~~~ 387 (498)
.-+.+..|-|++| +.-.|......+..++.+||.|.
T Consensus 16 ~~~~r~aLIC~~C-----------~~hNGla~~~~~~~i~y~C~~Cg 51 (54)
T PF10058_consen 16 SPSNRYALICSKC-----------FSHNGLAPKEEFEEIQYRCPYCG 51 (54)
T ss_pred cccCceeEECccc-----------chhhcccccccCCceEEEcCCCC
Confidence 3456778889999 12357776788888999999995
No 28
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=52.02 E-value=7.8 Score=37.23 Aligned_cols=14 Identities=43% Similarity=0.935 Sum_probs=12.2
Q ss_pred cccccCCCcccccCC
Q psy10861 379 VKSYCPKCMDVYTPK 393 (498)
Q Consensus 379 ~~~~~~~~~~~~~p~ 393 (498)
+.+||-.|++.| |+
T Consensus 67 ~PsYC~~CGkpy-PW 80 (158)
T PF10083_consen 67 APSYCHNCGKPY-PW 80 (158)
T ss_pred CChhHHhCCCCC-ch
Confidence 588999999888 76
No 29
>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=50.60 E-value=8.6 Score=26.45 Aligned_cols=28 Identities=36% Similarity=0.903 Sum_probs=12.6
Q ss_pred ccCCcCCCCCCccccccCCCCCCccceEecCCCccc
Q psy10861 321 HCPRVYCESQPMLPIGLSDVPGEAMVKSYCPKCMDV 356 (498)
Q Consensus 321 ~CPRv~C~~~~~LP~G~sd~~~~~~vklYCP~C~dv 356 (498)
.||| |.+. +..++... .=--|||+|.+|
T Consensus 3 ~C~r--C~~~-~~~~~~~~-----r~~~~C~rCq~v 30 (30)
T PF06827_consen 3 KCPR--CWNY-IEDIGING-----RSTYLCPRCQKV 30 (30)
T ss_dssp B-TT--T--B-BEEEEETT-----EEEEE-TTTCCH
T ss_pred cCcc--CCCc-ceEeEecC-----CCCeECcCCcCC
Confidence 4888 7632 44444422 224678888653
No 30
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=49.99 E-value=10 Score=27.63 Aligned_cols=33 Identities=30% Similarity=0.650 Sum_probs=23.9
Q ss_pred ccCCcCCCCCCccccccCCCCCCccceEecCCCccccc
Q psy10861 321 HCPRVYCESQPMLPIGLSDVPGEAMVKSYCPKCMDVYT 358 (498)
Q Consensus 321 ~CPRv~C~~~~~LP~G~sd~~~~~~vklYCP~C~dvY~ 358 (498)
.||+ |+..--||-. ..+.+..++-||+|+.+|.
T Consensus 4 ~CP~--C~~~f~v~~~---~l~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 4 TCPN--CQTRFRVPDD---KLPAGGRKVRCPKCGHVFR 36 (37)
T ss_pred ECCC--CCceEEcCHH---HcccCCcEEECCCCCcEee
Confidence 5999 9977655543 2446677999999987764
No 31
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=48.42 E-value=18 Score=37.95 Aligned_cols=50 Identities=20% Similarity=0.478 Sum_probs=33.3
Q ss_pred CccccCCcCCCCCCccccccCCCCCCccceEecCCCcccccCCCCCCcccCCCCCCCCccccccccCCCcc
Q psy10861 318 DFGHCPRVYCESQPMLPIGLSDVPGEAMVKSYCPKCMDVYTPKSSRHHHTDGLSDVPGEAMVKSYCPKCMD 388 (498)
Q Consensus 318 ~FG~CPRv~C~~~~~LP~G~sd~~~~~~vklYCP~C~dvY~p~~~~~~~~~g~~~~~~~~~~~~~~~~~~~ 388 (498)
.-|+||- |.+.|++-+=......++.=-++|..|.--++ .++.-||.|++
T Consensus 183 ~~~~CPv--CGs~P~~s~~~~~~~~~G~RyL~CslC~teW~-------------------~~R~~C~~Cg~ 232 (305)
T TIGR01562 183 SRTLCPA--CGSPPVASMVRQGGKETGLRYLSCSLCATEWH-------------------YVRVKCSHCEE 232 (305)
T ss_pred CCCcCCC--CCChhhhhhhcccCCCCCceEEEcCCCCCccc-------------------ccCccCCCCCC
Confidence 3578999 99988654322211224455799999955444 56678999974
No 32
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=47.75 E-value=20 Score=37.27 Aligned_cols=42 Identities=24% Similarity=0.420 Sum_probs=29.1
Q ss_pred EecCCCcccccCCCCCCcccCCCCCCCCccccccccCCCcccccCCCCCCC---Cccccc
Q psy10861 348 SYCPKCMDVYTPKSSRHHHTDGLSDVPGEAMVKSYCPKCMDVYTPKSSRHH---HTDGAY 404 (498)
Q Consensus 348 lYCP~C~dvY~p~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~p~~~~~~---~iDGa~ 404 (498)
=|||+|.-==. +...+.++.||+|...+.|+..... .++|..
T Consensus 112 RFCg~CG~~~~---------------~~~~g~~~~C~~cg~~~fPR~dP~vIv~v~~~~~ 156 (279)
T COG2816 112 RFCGRCGTKTY---------------PREGGWARVCPKCGHEHFPRIDPCVIVAVIRGDE 156 (279)
T ss_pred cCCCCCCCcCc---------------cccCceeeeCCCCCCccCCCCCCeEEEEEecCCc
Confidence 38999953332 3446789999999999999965432 345554
No 33
>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=45.77 E-value=22 Score=36.56 Aligned_cols=55 Identities=22% Similarity=0.465 Sum_probs=32.6
Q ss_pred cCCcCCCCCCcc-cc---ccCCCC--CCccceEecCCCcccccCCCCCCcccCCCCCCCCcc-ccccccCCCcccc
Q psy10861 322 CPRVYCESQPML-PI---GLSDVP--GEAMVKSYCPKCMDVYTPKSSRHHHTDGLSDVPGEA-MVKSYCPKCMDVY 390 (498)
Q Consensus 322 CPRv~C~~~~~L-P~---G~sd~~--~~~~vklYCP~C~dvY~p~~~~~~~~~g~~~~~~~~-~~~~~~~~~~~~~ 390 (498)
|||-+|.+-=.| |. -.+..+ ...++++-|+.|.+.|. | +.+. ...-.||.|.++.
T Consensus 126 CPRp~CkRiI~L~~~~~~p~~~~~~~~p~~~rv~CghC~~~Fl-------------~-~~~~~~tlARCPHCrKvS 187 (256)
T PF09788_consen 126 CPRPNCKRIINLGPSHQGPVTPPVPTQPGSCRVICGHCSNTFL-------------F-NTLTSNTLARCPHCRKVS 187 (256)
T ss_pred CCCCCCcceEEeCCccCCCCCCCCCCCCCceeEECCCCCCcEe-------------c-cCCCCCccccCCCCceec
Confidence 999999863222 22 111111 22578999999999886 1 1222 2345899996544
No 34
>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=44.03 E-value=17 Score=27.61 Aligned_cols=24 Identities=42% Similarity=1.077 Sum_probs=16.1
Q ss_pred cccCCcCCCCCCccccccCCCCCCccceEecCCCc
Q psy10861 320 GHCPRVYCESQPMLPIGLSDVPGEAMVKSYCPKCM 354 (498)
Q Consensus 320 G~CPRv~C~~~~~LP~G~sd~~~~~~vklYCP~C~ 354 (498)
-+||. | +.|++. +. + =++|||.|.
T Consensus 18 ~~Cp~--C-~~PL~~----~k--~--g~~~Cv~C~ 41 (41)
T PF06677_consen 18 EHCPD--C-GTPLMR----DK--D--GKIYCVSCG 41 (41)
T ss_pred CccCC--C-CCeeEE----ec--C--CCEECCCCC
Confidence 46997 8 577775 11 1 168999993
No 35
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=41.00 E-value=58 Score=24.83 Aligned_cols=31 Identities=29% Similarity=0.731 Sum_probs=19.6
Q ss_pred CCccccCCcCCCCCCccccccCCCCCCccceEecCCC
Q psy10861 317 GDFGHCPRVYCESQPMLPIGLSDVPGEAMVKSYCPKC 353 (498)
Q Consensus 317 ~~FG~CPRv~C~~~~~LP~G~sd~~~~~~vklYCP~C 353 (498)
..+-.||+..|+..-..+ + +....++-||.|
T Consensus 16 ~~~~~CP~~~C~~~~~~~----~--~~~~~~v~C~~C 46 (64)
T smart00647 16 PDLKWCPAPDCSAAIIVT----E--EEGCNRVTCPKC 46 (64)
T ss_pred CCccCCCCCCCcceEEec----C--CCCCCeeECCCC
Confidence 466679988897432221 1 234457889999
No 36
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=40.14 E-value=17 Score=29.42 Aligned_cols=7 Identities=71% Similarity=1.848 Sum_probs=4.2
Q ss_pred eEecCCC
Q psy10861 347 KSYCPKC 353 (498)
Q Consensus 347 klYCP~C 353 (498)
-||||+|
T Consensus 28 PlyCpKC 34 (55)
T PF14205_consen 28 PLYCPKC 34 (55)
T ss_pred cccCCCC
Confidence 4566666
No 37
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=39.59 E-value=15 Score=28.76 Aligned_cols=10 Identities=30% Similarity=1.152 Sum_probs=6.0
Q ss_pred ceEecCCCcc
Q psy10861 346 VKSYCPKCMD 355 (498)
Q Consensus 346 vklYCP~C~d 355 (498)
+.-|||+|..
T Consensus 19 ~~~fCP~Cg~ 28 (50)
T PRK00432 19 KNKFCPRCGS 28 (50)
T ss_pred ccCcCcCCCc
Confidence 3447777744
No 38
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=38.78 E-value=20 Score=30.31 Aligned_cols=36 Identities=31% Similarity=0.838 Sum_probs=22.0
Q ss_pred ccCCcCCCCCCccccccCCCCCCccceEecCCCcccccCCCCCCcccCCCCCCCCccccccccCCCcc
Q psy10861 321 HCPRVYCESQPMLPIGLSDVPGEAMVKSYCPKCMDVYTPKSSRHHHTDGLSDVPGEAMVKSYCPKCMD 388 (498)
Q Consensus 321 ~CPRv~C~~~~~LP~G~sd~~~~~~vklYCP~C~dvY~p~~~~~~~~~g~~~~~~~~~~~~~~~~~~~ 388 (498)
.||. |. ++|-|.| -..+|..|..-|. +..+||-|.+
T Consensus 3 ~CP~--C~-~~L~~~~---------~~~~C~~C~~~~~--------------------~~a~CPdC~~ 38 (70)
T PF07191_consen 3 TCPK--CQ-QELEWQG---------GHYHCEACQKDYK--------------------KEAFCPDCGQ 38 (70)
T ss_dssp B-SS--S--SBEEEET---------TEEEETTT--EEE--------------------EEEE-TTT-S
T ss_pred cCCC--CC-CccEEeC---------CEEECccccccce--------------------ecccCCCccc
Confidence 5888 87 5566666 3788999988886 4568999963
No 39
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=38.36 E-value=18 Score=33.49 Aligned_cols=15 Identities=40% Similarity=0.797 Sum_probs=12.0
Q ss_pred eEecCCCcccccCCC
Q psy10861 347 KSYCPKCMDVYTPKS 361 (498)
Q Consensus 347 klYCP~C~dvY~p~~ 361 (498)
-..|++|..+|.|+.
T Consensus 29 g~kC~~CG~v~~PPr 43 (140)
T COG1545 29 GTKCKKCGRVYFPPR 43 (140)
T ss_pred EEEcCCCCeEEcCCc
Confidence 567889999999863
No 40
>COG4260 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]
Probab=37.92 E-value=18 Score=38.14 Aligned_cols=41 Identities=22% Similarity=0.491 Sum_probs=25.9
Q ss_pred cCCCccccCCcCCCCCCccccccCCCCCCccceEecCCCcccccCCCCCCcccCCCCCCCCccc-cccccCCCccc
Q psy10861 315 QTGDFGHCPRVYCESQPMLPIGLSDVPGEAMVKSYCPKCMDVYTPKSSRHHHTDGLSDVPGEAM-VKSYCPKCMDV 389 (498)
Q Consensus 315 ~~~~FG~CPRv~C~~~~~LP~G~sd~~~~~~vklYCP~C~dvY~p~~~~~~~~~g~~~~~~~~~-~~~~~~~~~~~ 389 (498)
....-+.||| |... + |||.|.-... +.|+. .-..||-|.+-
T Consensus 302 ~pa~t~~~~r--~~k~----------------n-fc~ncG~~~t---------------~~~~ng~a~fcp~cgq~ 343 (345)
T COG4260 302 APAATWPCAR--CAKL----------------N-FCLNCGCGTT---------------ADFDNGKAKFCPECGQG 343 (345)
T ss_pred CCcccCcchh--cccc----------------c-cccccCcccc---------------cCCccchhhhChhhcCC
Confidence 3445578999 8722 2 9999953333 33443 45589999753
No 41
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=36.44 E-value=23 Score=33.21 Aligned_cols=26 Identities=31% Similarity=0.892 Sum_probs=17.5
Q ss_pred cccCCcCCCCCCccccccCCCCCCccceEecCCCc-ccc
Q psy10861 320 GHCPRVYCESQPMLPIGLSDVPGEAMVKSYCPKCM-DVY 357 (498)
Q Consensus 320 G~CPRv~C~~~~~LP~G~sd~~~~~~vklYCP~C~-dvY 357 (498)
-+||. |. .||+= .+=++|||-|. .++
T Consensus 29 ~hCp~--Cg-~PLF~---------KdG~v~CPvC~~~~~ 55 (131)
T COG1645 29 KHCPK--CG-TPLFR---------KDGEVFCPVCGYREV 55 (131)
T ss_pred hhCcc--cC-Cccee---------eCCeEECCCCCceEE
Confidence 46999 76 55443 33389999997 444
No 42
>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=35.90 E-value=33 Score=25.28 Aligned_cols=12 Identities=33% Similarity=0.949 Sum_probs=9.7
Q ss_pred ccceEecCCCcc
Q psy10861 344 AMVKSYCPKCMD 355 (498)
Q Consensus 344 ~~vklYCP~C~d 355 (498)
++|.|.||+|..
T Consensus 2 a~i~v~CP~C~s 13 (36)
T PF03811_consen 2 AKIDVHCPRCQS 13 (36)
T ss_pred CcEeeeCCCCCC
Confidence 578999999943
No 43
>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=35.23 E-value=23 Score=32.71 Aligned_cols=44 Identities=27% Similarity=0.363 Sum_probs=24.0
Q ss_pred eEecCCCcccccCCCCCCcccCCCC--CCCCccccccccCCCcccccC
Q psy10861 347 KSYCPKCMDVYTPKSSRHHHTDGLS--DVPGEAMVKSYCPKCMDVYTP 392 (498)
Q Consensus 347 klYCP~C~dvY~p~~~~~~~~~g~~--~~~~~~~~~~~~~~~~~~~~p 392 (498)
---||.|+....|-+.. .+.+.- .+.........||+|++||=+
T Consensus 91 ~sRC~~CN~~L~~v~~~--~v~~~vp~~v~~~~~~f~~C~~C~kiyW~ 136 (147)
T PF01927_consen 91 FSRCPKCNGPLRPVSKE--EVKDRVPPYVYETYDEFWRCPGCGKIYWE 136 (147)
T ss_pred CCccCCCCcEeeechhh--ccccccCccccccCCeEEECCCCCCEecc
Confidence 34599999887653211 111110 011111225689999999955
No 44
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=35.18 E-value=26 Score=26.28 Aligned_cols=7 Identities=43% Similarity=1.146 Sum_probs=3.5
Q ss_pred eEecCCC
Q psy10861 347 KSYCPKC 353 (498)
Q Consensus 347 klYCP~C 353 (498)
...||.|
T Consensus 20 ~~vC~~C 26 (52)
T smart00661 20 RFVCRKC 26 (52)
T ss_pred EEECCcC
Confidence 4445555
No 45
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=35.12 E-value=40 Score=34.09 Aligned_cols=19 Identities=26% Similarity=0.700 Sum_probs=15.5
Q ss_pred cccccccCCCcccccCCCC
Q psy10861 377 AMVKSYCPKCMDVYTPKSS 395 (498)
Q Consensus 377 ~~~~~~~~~~~~~~~p~~~ 395 (498)
.+.+.+|++|+.++.|+.+
T Consensus 114 ~~~~~~C~~c~~~~yp~~~ 132 (256)
T PRK00241 114 TEWAMLCPHCRERYYPRIA 132 (256)
T ss_pred CceeEECCCCCCEECCCCC
Confidence 4567899999999999743
No 46
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=35.11 E-value=21 Score=32.11 Aligned_cols=13 Identities=38% Similarity=1.012 Sum_probs=9.7
Q ss_pred cccCCCcccccCC
Q psy10861 381 SYCPKCMDVYTPK 393 (498)
Q Consensus 381 ~~~~~~~~~~~p~ 393 (498)
-.||+|+.+|.|.
T Consensus 27 ivCP~CG~~~~~~ 39 (108)
T PF09538_consen 27 IVCPKCGTEFPPE 39 (108)
T ss_pred ccCCCCCCccCcc
Confidence 3699998888654
No 47
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=34.88 E-value=21 Score=29.53 Aligned_cols=15 Identities=53% Similarity=1.088 Sum_probs=13.2
Q ss_pred CCCccceEecCCCcc
Q psy10861 341 PGEAMVKSYCPKCMD 355 (498)
Q Consensus 341 ~~~~~vklYCP~C~d 355 (498)
|++..|+..||.|.+
T Consensus 21 p~e~~v~F~CPnCGe 35 (61)
T COG2888 21 PGETAVKFPCPNCGE 35 (61)
T ss_pred cCCceeEeeCCCCCc
Confidence 778899999999974
No 48
>PRK04023 DNA polymerase II large subunit; Validated
Probab=33.44 E-value=40 Score=40.81 Aligned_cols=50 Identities=14% Similarity=0.234 Sum_probs=27.1
Q ss_pred hhhhcccccCCCCcccchHHHhhhccccccCChhhhhcccCccCccccCCChHHHHHHHhcC
Q psy10861 82 YIQDKFNLTGLNEQVPHYRQALDMILDLEPVDEDYIQDKFNLTGLNEQVPHYRQALDMILDL 143 (498)
Q Consensus 82 ~i~d~fnl~gl~~~v~~~~~al~~i~~l~EVdedfIeD~FNLtGL~~~Vp~Y~eALdmILD~ 143 (498)
|++.--.|---+=-.+||.|-++-- -..++.++ +|+ -|.-.+|+++-.+.
T Consensus 412 FlENNhpL~Ps~y~~EWW~qe~~~~--~~~~~~~~--------~l~--~p~~~eA~~~s~~~ 461 (1121)
T PRK04023 412 FLENNHPLLPSSYCEEWWIQELEAA--GAEYEPEF--------DLE--NPSQEEALKISEEY 461 (1121)
T ss_pred hhhcCCcCCCccccHHHHHHHHHhc--ccccCccc--------ccc--CCCHHHHHHHHHHc
Confidence 4454444544332346887776642 22333222 122 28888999887765
No 49
>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=31.78 E-value=33 Score=25.17 Aligned_cols=11 Identities=45% Similarity=1.201 Sum_probs=9.7
Q ss_pred EecCCCccccc
Q psy10861 348 SYCPKCMDVYT 358 (498)
Q Consensus 348 lYCP~C~dvY~ 358 (498)
..||+|..+|+
T Consensus 2 r~C~~Cg~~Yh 12 (36)
T PF05191_consen 2 RICPKCGRIYH 12 (36)
T ss_dssp EEETTTTEEEE
T ss_pred cCcCCCCCccc
Confidence 56999999998
No 50
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=31.45 E-value=27 Score=30.05 Aligned_cols=11 Identities=27% Similarity=0.476 Sum_probs=6.3
Q ss_pred eEecCCCcccc
Q psy10861 347 KSYCPKCMDVY 357 (498)
Q Consensus 347 klYCP~C~dvY 357 (498)
.++||.|.-.+
T Consensus 16 ~~~C~~C~~~~ 26 (104)
T TIGR01384 16 VYVCPSCGYEK 26 (104)
T ss_pred eEECcCCCCcc
Confidence 56666665443
No 51
>PF12773 DZR: Double zinc ribbon
Probab=31.33 E-value=39 Score=25.29 Aligned_cols=13 Identities=31% Similarity=0.639 Sum_probs=7.9
Q ss_pred cceEecCCCcccc
Q psy10861 345 MVKSYCPKCMDVY 357 (498)
Q Consensus 345 ~vklYCP~C~dvY 357 (498)
...++||+|....
T Consensus 27 ~~~~~C~~Cg~~~ 39 (50)
T PF12773_consen 27 QSKKICPNCGAEN 39 (50)
T ss_pred CCCCCCcCCcCCC
Confidence 3466777775553
No 52
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=29.09 E-value=24 Score=23.83 Aligned_cols=9 Identities=33% Similarity=1.202 Sum_probs=6.8
Q ss_pred eEecCCCcc
Q psy10861 347 KSYCPKCMD 355 (498)
Q Consensus 347 klYCP~C~d 355 (498)
.++||+|..
T Consensus 2 ~~~Cp~Cg~ 10 (26)
T PF13248_consen 2 EMFCPNCGA 10 (26)
T ss_pred cCCCcccCC
Confidence 468999965
No 53
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=28.46 E-value=40 Score=27.71 Aligned_cols=16 Identities=50% Similarity=0.976 Sum_probs=11.6
Q ss_pred CCCccceEecCCCccc
Q psy10861 341 PGEAMVKSYCPKCMDV 356 (498)
Q Consensus 341 ~~~~~vklYCP~C~dv 356 (498)
|.+..|+..||.|.++
T Consensus 19 ~~~~~~~F~CPnCG~~ 34 (59)
T PRK14890 19 PREKAVKFLCPNCGEV 34 (59)
T ss_pred CCCccCEeeCCCCCCe
Confidence 3445689999999654
No 54
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=26.30 E-value=31 Score=22.98 Aligned_cols=10 Identities=40% Similarity=1.089 Sum_probs=6.1
Q ss_pred ecCCCccccc
Q psy10861 349 YCPKCMDVYT 358 (498)
Q Consensus 349 YCP~C~dvY~ 358 (498)
|||+|..-..
T Consensus 1 ~Cp~CG~~~~ 10 (23)
T PF13240_consen 1 YCPNCGAEIE 10 (23)
T ss_pred CCcccCCCCC
Confidence 6888854443
No 55
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=25.81 E-value=33 Score=31.55 Aligned_cols=36 Identities=17% Similarity=0.389 Sum_probs=20.8
Q ss_pred ccceEecCCCcccccCCCCCCcccCCCCCCCCcc-ccccccCCCcccc
Q psy10861 344 AMVKSYCPKCMDVYTPKSSRHHHTDGLSDVPGEA-MVKSYCPKCMDVY 390 (498)
Q Consensus 344 ~~vklYCP~C~dvY~p~~~~~~~~~g~~~~~~~~-~~~~~~~~~~~~~ 390 (498)
..++++||.|.--+. .+ -|.... ..+..|++|...|
T Consensus 27 ~~~~~~cP~C~s~~~---~k--------~g~~~~~~qRyrC~~C~~tf 63 (129)
T COG3677 27 QITKVNCPRCKSSNV---VK--------IGGIRRGHQRYKCKSCGSTF 63 (129)
T ss_pred hcccCcCCCCCccce---ee--------ECCccccccccccCCcCcce
Confidence 345788888854441 11 123334 3456899997555
No 56
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=24.90 E-value=67 Score=25.00 Aligned_cols=39 Identities=28% Similarity=0.571 Sum_probs=24.2
Q ss_pred eEecCCCcccccCCCCCCcccCCCCCCCCcccccc--ccCCCc
Q psy10861 347 KSYCPKCMDVYTPKSSRHHHTDGLSDVPGEAMVKS--YCPKCM 387 (498)
Q Consensus 347 klYCP~C~dvY~p~~~~~~~~~g~~~~~~~~~~~~--~~~~~~ 387 (498)
|--|+.|.=||.|..-. ...|.--||.|..+.. .||-|.
T Consensus 1 ky~C~~CgyvYd~~~Gd--~~~~i~pGt~F~~Lp~~w~CP~C~ 41 (47)
T PF00301_consen 1 KYQCPVCGYVYDPEKGD--PENGIPPGTPFEDLPDDWVCPVCG 41 (47)
T ss_dssp EEEETTTSBEEETTTBB--GGGTB-TT--GGGS-TT-B-TTTS
T ss_pred CcCCCCCCEEEcCCcCC--cccCcCCCCCHHHCCCCCcCcCCC
Confidence 34699999999975422 2345566788888854 899996
No 57
>KOG2239|consensus
Probab=24.84 E-value=99 Score=31.10 Aligned_cols=68 Identities=26% Similarity=0.335 Sum_probs=37.9
Q ss_pred CceeEe-eccceeeeeeeeehhhHHHHHHHHHhccCCCceeEEeccCCCC-CCCCchhhhhhcccccCCC
Q psy10861 26 PALLRI-ETDEKIGLYGFKIHSLAYQLQQNAAANFKTPVRAVSYNTGKRR-DPQIDEDYIQDKFNLTGLN 93 (498)
Q Consensus 26 ~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~e~ded~i~d~fnl~gl~ 93 (498)
|-..|+ -+|--|-+=.-||--|.-|+|.+||.+||-|=.+-.--.+..+ .+...|+=.+..-+.|||+
T Consensus 102 PdVyKsp~sdtYiiFGeakiedls~q~q~~aae~fk~~~~~~~~~~~~~~~~~~~~ee~dEeeVD~tgve 171 (209)
T KOG2239|consen 102 PDVYKSPASDTYIIFGEAKIEDLSQQAQMQAAERFKVPQEAPGLIQEDTSATPPAQEESDEEEVDETGVE 171 (209)
T ss_pred CceeccCCCceEEEecccccchhHHHHHHHHHHhccCCccccccccccccCCCccccccchhccCcccCc
Confidence 333444 2333344445788999999999999999998444332222222 2322222222235667766
No 58
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=24.70 E-value=45 Score=29.91 Aligned_cols=17 Identities=24% Similarity=0.641 Sum_probs=12.9
Q ss_pred CccceEecCCCcccccC
Q psy10861 343 EAMVKSYCPKCMDVYTP 359 (498)
Q Consensus 343 ~~~vklYCP~C~dvY~p 359 (498)
.-.+..+|+.|...|.+
T Consensus 66 ~~p~~~~C~~Cg~~~~~ 82 (115)
T TIGR00100 66 DEPVECECEDCSEEVSP 82 (115)
T ss_pred eeCcEEEcccCCCEEec
Confidence 34568999999877764
No 59
>PF11238 DUF3039: Protein of unknown function (DUF3039); InterPro: IPR021400 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=24.36 E-value=26 Score=28.75 Aligned_cols=10 Identities=40% Similarity=1.424 Sum_probs=8.3
Q ss_pred ccCCCccccc
Q psy10861 382 YCPKCMDVYT 391 (498)
Q Consensus 382 ~~~~~~~~~~ 391 (498)
.||.|.+||.
T Consensus 46 VCP~Ck~iye 55 (58)
T PF11238_consen 46 VCPECKEIYE 55 (58)
T ss_pred CCcCHHHHHH
Confidence 8999988873
No 60
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=23.55 E-value=48 Score=29.70 Aligned_cols=16 Identities=19% Similarity=0.451 Sum_probs=12.2
Q ss_pred ccceEecCCCcccccC
Q psy10861 344 AMVKSYCPKCMDVYTP 359 (498)
Q Consensus 344 ~~vklYCP~C~dvY~p 359 (498)
-.++++|+.|+..|.+
T Consensus 67 vp~~~~C~~Cg~~~~~ 82 (113)
T PRK12380 67 KPAQAWCWDCSQVVEI 82 (113)
T ss_pred eCcEEEcccCCCEEec
Confidence 4568999999877763
No 61
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=22.16 E-value=49 Score=30.56 Aligned_cols=23 Identities=17% Similarity=0.618 Sum_probs=13.6
Q ss_pred hhhHHHHHHhhcCCCccccCCcCCC
Q psy10861 304 NRGIGQMIEKYQTGDFGHCPRVYCE 328 (498)
Q Consensus 304 ~~Gl~~m~~Ky~~~~FG~CPRv~C~ 328 (498)
.+-|+...+.-....|-.||+ |+
T Consensus 84 ~~~L~~~l~~e~~~~~Y~Cp~--C~ 106 (147)
T smart00531 84 RKRLEDKLEDETNNAYYKCPN--CQ 106 (147)
T ss_pred HHHHHHHHhcccCCcEEECcC--CC
Confidence 344444444445667778887 66
No 62
>PF12812 PDZ_1: PDZ-like domain
Probab=22.09 E-value=49 Score=27.89 Aligned_cols=60 Identities=18% Similarity=0.183 Sum_probs=41.3
Q ss_pred eeccceeeeeeeeehhhHHHHHHHHHhccCCCceeEEeccCCCCCCC-CchhhhhhcccccCC
Q psy10861 31 IETDEKIGLYGFKIHSLAYQLQQNAAANFKTPVRAVSYNTGKRRDPQ-IDEDYIQDKFNLTGL 92 (498)
Q Consensus 31 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e-~ded~i~d~fnl~gl 92 (498)
|+|+.-+-.-|=.+|+|.||.-.|-. ++.+|--+....|+-.+-- +...||...-|-+-.
T Consensus 2 itp~r~v~~~Ga~f~~Ls~q~aR~~~--~~~~gv~v~~~~g~~~~~~~i~~g~iI~~Vn~kpt 62 (78)
T PF12812_consen 2 ITPSRFVEVCGAVFHDLSYQQARQYG--IPVGGVYVAVSGGSLAFAGGISKGFIITSVNGKPT 62 (78)
T ss_pred ccCCEEEEEcCeecccCCHHHHHHhC--CCCCEEEEEecCCChhhhCCCCCCeEEEeECCcCC
Confidence 67888889999999999999877664 3344555555555554444 677777766654443
No 63
>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=22.00 E-value=27 Score=25.38 Aligned_cols=14 Identities=36% Similarity=1.101 Sum_probs=8.3
Q ss_pred EecCCCcccccCCC
Q psy10861 348 SYCPKCMDVYTPKS 361 (498)
Q Consensus 348 lYCP~C~dvY~p~~ 361 (498)
.|||.|+.+-.|+.
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 36777766666543
No 64
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=21.85 E-value=53 Score=30.79 Aligned_cols=13 Identities=15% Similarity=0.432 Sum_probs=9.7
Q ss_pred cccCCCcccccCC
Q psy10861 381 SYCPKCMDVYTPK 393 (498)
Q Consensus 381 ~~~~~~~~~~~p~ 393 (498)
-.||+|+.+|.|.
T Consensus 27 ~vcP~cg~~~~~~ 39 (129)
T TIGR02300 27 AVSPYTGEQFPPE 39 (129)
T ss_pred ccCCCcCCccCcc
Confidence 4799998887554
No 65
>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=21.83 E-value=81 Score=23.93 Aligned_cols=29 Identities=28% Similarity=0.512 Sum_probs=12.2
Q ss_pred ccccCCcCCCCCCccccccCCCCCCccceEecCCC
Q psy10861 319 FGHCPRVYCESQPMLPIGLSDVPGEAMVKSYCPKC 353 (498)
Q Consensus 319 FG~CPRv~C~~~~~LP~G~sd~~~~~~vklYCP~C 353 (498)
+-.||+..|+.--...-+... -.+.||.|
T Consensus 18 ~~~Cp~~~C~~~~~~~~~~~~------~~~~C~~C 46 (64)
T PF01485_consen 18 IRWCPNPDCEYIIEKDDGCNS------PIVTCPSC 46 (64)
T ss_dssp CC--TTSST---ECS-SSTTS--------CCTTSC
T ss_pred ccCCCCCCCcccEEecCCCCC------CeeECCCC
Confidence 346999999843222222111 14788888
No 66
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=21.55 E-value=1e+02 Score=35.57 Aligned_cols=32 Identities=28% Similarity=0.406 Sum_probs=16.6
Q ss_pred ccCCCcccccCCCCCCCCccccccCCchhhHHH
Q psy10861 382 YCPKCMDVYTPKSSRHHHTDGAYFGTGFPHMLF 414 (498)
Q Consensus 382 ~~~~~~~~~~p~~~~~~~iDGa~fG~sFph~f~ 414 (498)
.||+|+..- |...++-.-=|+..|+-..-+..
T Consensus 29 ~Cp~CG~~~-~~~~~fC~~CG~~~~~~~~~~~~ 60 (645)
T PRK14559 29 PCPQCGTEV-PVDEAHCPNCGAETGTIWWAIIA 60 (645)
T ss_pred cCCCCCCCC-CcccccccccCCcccchhhhhcc
Confidence 577776443 33333333345666666655543
No 67
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=20.52 E-value=57 Score=32.30 Aligned_cols=25 Identities=28% Similarity=0.837 Sum_probs=15.9
Q ss_pred ccccCCcCCCCCCccccccCCCCCCccceEecCCCcc
Q psy10861 319 FGHCPRVYCESQPMLPIGLSDVPGEAMVKSYCPKCMD 355 (498)
Q Consensus 319 FG~CPRv~C~~~~~LP~G~sd~~~~~~vklYCP~C~d 355 (498)
|-.|+| |. ++|.+- .-.|+||+|.-
T Consensus 149 ~A~Csr--C~-~~L~~~---------~~~l~Cp~Cg~ 173 (188)
T COG1096 149 YARCSR--CR-APLVKK---------GNMLKCPNCGN 173 (188)
T ss_pred EEEccC--CC-cceEEc---------CcEEECCCCCC
Confidence 345888 76 455552 23789999943
No 68
>PRK06450 threonine synthase; Validated
Probab=20.45 E-value=63 Score=33.83 Aligned_cols=14 Identities=43% Similarity=0.643 Sum_probs=11.8
Q ss_pred cceEecCCCccccc
Q psy10861 345 MVKSYCPKCMDVYT 358 (498)
Q Consensus 345 ~vklYCP~C~dvY~ 358 (498)
+|++.|++|..-|.
T Consensus 1 ~~~~~C~~Cg~~~~ 14 (338)
T PRK06450 1 MVKEVCMKCGKERE 14 (338)
T ss_pred CceeEECCcCCcCC
Confidence 47899999988885
No 69
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=20.10 E-value=69 Score=28.84 Aligned_cols=17 Identities=29% Similarity=0.769 Sum_probs=12.5
Q ss_pred CccceEecCCCcccccC
Q psy10861 343 EAMVKSYCPKCMDVYTP 359 (498)
Q Consensus 343 ~~~vklYCP~C~dvY~p 359 (498)
.-.+..+|+.|+..+.+
T Consensus 67 ~vp~~~~C~~Cg~~~~~ 83 (117)
T PRK00564 67 DEKVELECKDCSHVFKP 83 (117)
T ss_pred ecCCEEEhhhCCCcccc
Confidence 34568999999877763
Done!