Query 011212
Match_columns 491
No_of_seqs 183 out of 1217
Neff 4.7
Searched_HMMs 46136
Date Thu Mar 28 22:50:33 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/011212.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/011212hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0834 CDK9 kinase-activating 100.0 1.3E-34 2.8E-39 294.5 15.6 164 1-171 89-257 (323)
2 KOG0835 Cyclin L [General func 100.0 5.6E-28 1.2E-32 243.4 13.1 160 1-166 73-235 (367)
3 KOG0794 CDK8 kinase-activating 99.9 1.7E-24 3.7E-29 210.0 4.6 154 1-166 91-245 (264)
4 TIGR00569 ccl1 cyclin ccl1. Un 99.9 6.6E-23 1.4E-27 208.1 11.1 142 1-164 108-260 (305)
5 COG5333 CCL1 Cdk activating ki 99.8 6.6E-20 1.4E-24 184.3 11.7 116 1-130 95-211 (297)
6 PRK00423 tfb transcription ini 99.4 1.4E-12 3.1E-17 132.7 10.5 134 1-160 172-305 (310)
7 KOG2496 Cdk activating kinase 99.3 2.4E-12 5.2E-17 129.9 4.2 141 1-163 108-261 (325)
8 KOG0653 Cyclin B and related k 99.1 7E-11 1.5E-15 124.0 5.9 132 1-159 208-345 (391)
9 PF02984 Cyclin_C: Cyclin, C-t 99.1 2.8E-10 6.1E-15 97.0 6.6 89 68-163 1-93 (118)
10 KOG0654 G2/Mitotic-specific cy 99.1 8.2E-10 1.8E-14 114.8 11.1 136 1-164 187-327 (359)
11 COG5024 Cyclin [Cell division 99.0 3.1E-10 6.7E-15 120.7 6.3 132 1-160 263-400 (440)
12 KOG0656 G1/S-specific cyclin D 98.9 9.4E-10 2E-14 113.5 6.4 106 1-125 131-240 (335)
13 KOG0655 G1/S-specific cyclin E 98.7 2E-08 4.3E-13 103.0 5.8 154 1-185 196-361 (408)
14 smart00385 CYCLIN domain prese 98.6 1.2E-07 2.5E-12 74.7 7.8 80 73-156 2-82 (83)
15 COG1405 SUA7 Transcription ini 98.5 3.2E-07 6.9E-12 93.3 8.2 133 1-159 147-279 (285)
16 cd00043 CYCLIN Cyclin box fold 98.5 4.6E-07 1E-11 71.9 7.5 85 67-155 2-87 (88)
17 KOG1597 Transcription initiati 98.0 1.4E-05 3.1E-10 81.2 7.8 133 1-159 154-288 (308)
18 PF00382 TFIIB: Transcription 97.2 0.001 2.3E-08 53.6 6.2 70 74-147 1-70 (71)
19 PF00134 Cyclin_N: Cyclin, N-t 97.0 0.0001 2.3E-09 63.9 -1.2 46 1-66 81-127 (127)
20 PF00134 Cyclin_N: Cyclin, N-t 95.8 0.028 6.1E-07 48.7 6.8 85 73-160 37-123 (127)
21 PRK00423 tfb transcription ini 94.8 0.14 3E-06 52.8 9.0 88 70-161 125-212 (310)
22 TIGR00569 ccl1 cyclin ccl1. Un 92.6 0.24 5.1E-06 51.4 6.0 56 73-129 62-119 (305)
23 KOG1598 Transcription initiati 92.2 0.16 3.5E-06 55.9 4.5 78 51-128 144-226 (521)
24 KOG0834 CDK9 kinase-activating 87.9 0.79 1.7E-05 48.1 5.1 57 72-129 44-100 (323)
25 cd00043 CYCLIN Cyclin box fold 87.5 0.15 3.2E-06 40.1 -0.3 37 1-58 52-88 (88)
26 smart00385 CYCLIN domain prese 82.7 0.35 7.5E-06 37.6 -0.3 38 1-59 46-83 (83)
27 KOG0794 CDK8 kinase-activating 82.6 2.1 4.5E-05 43.3 5.0 73 87-160 60-145 (264)
28 COG1405 SUA7 Transcription ini 82.6 6.1 0.00013 40.8 8.6 100 54-157 76-183 (285)
29 KOG0656 G1/S-specific cyclin D 81.8 5.6 0.00012 42.1 8.0 83 48-131 50-144 (335)
30 KOG2496 Cdk activating kinase 76.2 4.2 9.2E-05 42.5 5.0 55 73-127 62-117 (325)
31 COG5333 CCL1 Cdk activating ki 74.3 4 8.6E-05 42.5 4.3 90 72-162 50-144 (297)
32 KOG1597 Transcription initiati 69.8 17 0.00036 38.1 7.5 88 70-161 107-194 (308)
33 KOG0835 Cyclin L [General func 67.7 27 0.00059 37.1 8.6 72 75-161 31-102 (367)
34 PF08613 Cyclin: Cyclin; Inte 64.2 31 0.00068 31.7 7.6 87 71-160 55-146 (149)
35 PF01857 RB_B: Retinoblastoma- 54.1 62 0.0013 30.0 7.6 54 73-127 17-72 (135)
36 KOG0653 Cyclin B and related k 40.5 83 0.0018 33.7 7.1 91 80-171 171-262 (391)
37 COG4009 Uncharacterized protei 37.3 23 0.00049 30.6 1.8 48 330-377 21-83 (88)
38 KOG0655 G1/S-specific cyclin E 36.5 1.3E+02 0.0028 32.5 7.5 111 50-161 120-239 (408)
39 COG5024 Cyclin [Cell division 34.2 47 0.001 36.6 4.1 80 87-166 232-311 (440)
40 COG5552 Uncharacterized conser 30.8 75 0.0016 27.2 3.8 55 109-166 16-70 (88)
41 PF07713 DUF1604: Protein of u 30.3 22 0.00048 30.9 0.7 17 348-364 59-75 (87)
42 PHA02690 hypothetical protein; 25.9 1E+02 0.0022 26.7 3.8 34 72-106 22-55 (90)
43 KOG4557 Origin recognition com 24.1 1.2E+02 0.0026 30.8 4.6 73 87-163 107-185 (262)
No 1
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=1.3e-34 Score=294.55 Aligned_cols=164 Identities=55% Similarity=0.893 Sum_probs=150.6
Q ss_pred CEEeeccCCCCCChHHHHHHHHHhhhccCCCChhhhccchHHHHHHHHHHHHHHHHHHHHcCCcccccCcHHHHHHHHHH
Q 011212 1 MFLAGKVEETPRPLKDVIIVSYEIIHKKDSTAPQRIRQQKEVYEQQKELILLGERVVLATLGFDLNVHHPYKPLVEAIKK 80 (491)
Q Consensus 1 LFLAsKVEEtprkLrDVI~Vs~~L~hkkdP~~~~~I~~~se~Yeq~Ke~IL~mErlILrtLgFDL~V~hPhkfLv~yLk~ 80 (491)
||||||+||+|++++|||.|+|.++++.+ +. ..+.|+++|+.|+.+|++||++|+|||+|.|||.||++|++.
T Consensus 89 lfLAgKvEetp~kl~dIi~~s~~~~~~~~------~~-~~~~~~~~~~~Iv~~E~~lL~tl~Fdl~v~hPy~~ll~~~k~ 161 (323)
T KOG0834|consen 89 LFLAGKVEETPRKLEDIIKVSYRYLNPKD------LE-LEEVYWELKERIVQLELLLLETLGFDLNVEHPYKYLLKYLKK 161 (323)
T ss_pred HHHHhhcccCcccHHHHHHHHHHHcCccc------cc-HHHHHHHHHHHHHHHHHHHHHHccCceeccCchHHHHHHHHH
Confidence 69999999999999999999999998754 11 578999999999999999999999999999999999999999
Q ss_pred hcccHH---HHHHHHHHHHHhhcCCccccccChHHHHHHHHHHHHHHhCcCCCCCCcccchhccC--CCHHHHHHHHHHH
Q 011212 81 FKVAQN---ALAQVAWNFVNDGLRTSLCLQFKPHHIAAGAIFLAAKFLKVKLPSDGDKVWWQEFD--VTPRQLEEVSNQM 155 (491)
Q Consensus 81 L~~~~~---~L~qlAw~fLnDSl~T~LcLqYpPsvIAaAAIyLA~kllgi~LPs~~~~~W~e~Lg--vt~eqL~eI~~eI 155 (491)
++.+.. .++++||+|+||+++|++||+|+|++||+|||+||+++.++.+|...+..||..|+ ++.+.|++|+.++
T Consensus 162 l~~~~~~~~~~a~~Aw~~~nD~~~t~~cL~y~p~~IAva~i~lA~~~~~~~~~~~~~~~w~~~~d~~vt~e~l~~i~~~~ 241 (323)
T KOG0834|consen 162 LKADENLKQPLAQAAWNFVNDSLRTTLCLQYSPHSIAVACIHLAAKLLGVELPSDTDKRWWREFDETVTNELLDDICHEF 241 (323)
T ss_pred hhhhhhccccHHHHHHHHhchhheeeeeEeecCcEEEeehhhHHHHHcCCCCCCCcccchhhhhcccCCHHHHHHHHHHH
Confidence 987654 59999999999999999999999999999999999999999999876668999998 9999999999999
Q ss_pred HHHHhhCCCCCCCCCc
Q 011212 156 LELYEQNRVPQSQGSE 171 (491)
Q Consensus 156 LeLY~~~r~~~~~~~~ 171 (491)
+.+|...........+
T Consensus 242 l~~y~~~~~~~~~~~~ 257 (323)
T KOG0834|consen 242 LDLYEQTPQRNHLLLN 257 (323)
T ss_pred HHHHhhcccccccccc
Confidence 9999988776655544
No 2
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=99.95 E-value=5.6e-28 Score=243.40 Aligned_cols=160 Identities=35% Similarity=0.669 Sum_probs=141.0
Q ss_pred CEEeeccCCCCCChHHHHHHHHHhhh--ccCCCChhhhccchHHHHHHHHHHHHHHHHHHHHcCCcccccCcHHHHHHHH
Q 011212 1 MFLAGKVEETPRPLKDVIIVSYEIIH--KKDSTAPQRIRQQKEVYEQQKELILLGERVVLATLGFDLNVHHPYKPLVEAI 78 (491)
Q Consensus 1 LFLAsKVEEtprkLrDVI~Vs~~L~h--kkdP~~~~~I~~~se~Yeq~Ke~IL~mErlILrtLgFDL~V~hPhkfLv~yL 78 (491)
|+||+|+||.|++++|||+|+++|.. +..+... .| -...|...+..++.+|+.||++|||++.|.|||++++.|+
T Consensus 73 v~LASKiEE~Prr~rdVinVFh~L~~r~~~~~~~~-~~--~~~~~~~lk~~~ir~e~~ILr~LGF~~Hv~hPhklii~YL 149 (367)
T KOG0835|consen 73 VLLASKIEEEPRRIRDVINVFHYLEQRRESEAAEH-LI--LARLYINLKMQVIRAERRILRELGFDVHVEHPHKLIIMYL 149 (367)
T ss_pred HHHHhhhccccccHhHHHHHHHHHHHHHhccCcch-hh--hhhHHhhhhhHHHHHHHHHHHHhCCeeeeeccHHHHHHHH
Confidence 46999999999999999999999854 2222211 12 2567788899999999999999999999999999999999
Q ss_pred HHhcccHH-HHHHHHHHHHHhhcCCccccccChHHHHHHHHHHHHHHhCcCCCCCCcccchhccCCCHHHHHHHHHHHHH
Q 011212 79 KKFKVAQN-ALAQVAWNFVNDGLRTSLCLQFKPHHIAAGAIFLAAKFLKVKLPSDGDKVWWQEFDVTPRQLEEVSNQMLE 157 (491)
Q Consensus 79 k~L~~~~~-~L~qlAw~fLnDSl~T~LcLqYpPsvIAaAAIyLA~kllgi~LPs~~~~~W~e~Lgvt~eqL~eI~~eILe 157 (491)
+.|++... .|.|.+|+|+||+++|++|+.|+|..|||||||||+..+++.||.. +.||..|+++.++|.+||-.++.
T Consensus 150 qtL~~~~~~~l~Q~~wNfmNDslRT~v~vry~pe~iACaciyLaAR~~eIpLp~~--P~Wf~~Fd~~k~eid~ic~~l~~ 227 (367)
T KOG0835|consen 150 QTLQLPPNLKLLQAAWNFMNDSLRTDVFVRYSPESIACACIYLAARNLEIPLPFQ--PHWFKAFDTTKREIDEICYRLIP 227 (367)
T ss_pred HHhcCCCchhHHHHHHHhhhhccccceeeecCHHHHHHHHHHHHHhhhcCCCCCC--ccHHHHcCCcHHHHHHHHHHHHH
Confidence 99988653 5899999999999999999999999999999999999999999875 48999999999999999999999
Q ss_pred HHhhCCCCC
Q 011212 158 LYEQNRVPQ 166 (491)
Q Consensus 158 LY~~~r~~~ 166 (491)
||.. ..|-
T Consensus 228 lY~~-~~p~ 235 (367)
T KOG0835|consen 228 LYKR-AKPD 235 (367)
T ss_pred HHHh-cccC
Confidence 9998 4443
No 3
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]
Probab=99.90 E-value=1.7e-24 Score=210.02 Aligned_cols=154 Identities=29% Similarity=0.551 Sum_probs=130.8
Q ss_pred CEEeeccCCCC-CChHHHHHHHHHhhhccCCCChhhhccchHHHHHHHHHHHHHHHHHHHHcCCcccccCcHHHHHHHHH
Q 011212 1 MFLAGKVEETP-RPLKDVIIVSYEIIHKKDSTAPQRIRQQKEVYEQQKELILLGERVVLATLGFDLNVHHPYKPLVEAIK 79 (491)
Q Consensus 1 LFLAsKVEEtp-rkLrDVI~Vs~~L~hkkdP~~~~~I~~~se~Yeq~Ke~IL~mErlILrtLgFDL~V~hPhkfLv~yLk 79 (491)
|||||||||+| ..+|-+++.+..+..+=. - -++.+.--...|++||+.||+.|++-|.|.|||+.|.++++
T Consensus 91 lyLAcKvEE~~i~~~r~l~~~a~~L~~~f~-~-------~~e~~~~~~~~I~e~Ef~llE~Ld~~LIVhHPYrsL~q~~q 162 (264)
T KOG0794|consen 91 LYLACKVEECPIVHIRLLVNEAKVLKTRFS-Y-------WPEKFPYERKDILEMEFYLLEALDCYLIVHHPYRSLLQFVQ 162 (264)
T ss_pred HHHHhhhhhcchHHHHHHHHHHHHHhhhcc-c-------chhhcCCCcCcchhhhhhHHhhhceeEEEecCCccHHHHHH
Confidence 68999999998 888888887776632211 0 01111112467999999999999999999999999999999
Q ss_pred HhcccHHHHHHHHHHHHHhhcCCccccccChHHHHHHHHHHHHHHhCcCCCCCCcccchhccCCCHHHHHHHHHHHHHHH
Q 011212 80 KFKVAQNALAQVAWNFVNDGLRTSLCLQFKPHHIAAGAIFLAAKFLKVKLPSDGDKVWWQEFDVTPRQLEEVSNQMLELY 159 (491)
Q Consensus 80 ~L~~~~~~L~qlAw~fLnDSl~T~LcLqYpPsvIAaAAIyLA~kllgi~LPs~~~~~W~e~Lgvt~eqL~eI~~eILeLY 159 (491)
..+..+..+.+.||.++||++++++||.|||++||+||||+|+...+.++| ..|+..+.++++.|.+|+.+|+++|
T Consensus 163 d~gi~d~~~l~~~W~ivNDSyr~Dl~Ll~PPh~IalAcl~Ia~~~~~k~~~----~~w~~el~vD~ekV~~~v~~I~~lY 238 (264)
T KOG0794|consen 163 DMGINDQKLLQLAWSIVNDSYRMDLCLLYPPHQIALACLYIACVIDEKDIP----KAWFAELSVDMEKVKDIVQEILKLY 238 (264)
T ss_pred HhcccchhhhhhhHhhhcchhhcceeeecCHHHHHHHHHHHHHhhcCCChH----HHHHHHHhccHHHHHHHHHHHHHHH
Confidence 999865578999999999999999999999999999999999999988766 4799999999999999999999999
Q ss_pred hhCCCCC
Q 011212 160 EQNRVPQ 166 (491)
Q Consensus 160 ~~~r~~~ 166 (491)
..++.-.
T Consensus 239 e~wk~~~ 245 (264)
T KOG0794|consen 239 ELWKIFD 245 (264)
T ss_pred HHHhhhh
Confidence 9887643
No 4
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=99.88 E-value=6.6e-23 Score=208.11 Aligned_cols=142 Identities=26% Similarity=0.325 Sum_probs=113.9
Q ss_pred CEEeeccCCCCCChHHHHHHHHHhhhccCCCChhhhccchHHHHHHHHHHHHHHHHHHHHcCCcccccCcHHHHHHHHHH
Q 011212 1 MFLAGKVEETPRPLKDVIIVSYEIIHKKDSTAPQRIRQQKEVYEQQKELILLGERVVLATLGFDLNVHHPYKPLVEAIKK 80 (491)
Q Consensus 1 LFLAsKVEEtprkLrDVI~Vs~~L~hkkdP~~~~~I~~~se~Yeq~Ke~IL~mErlILrtLgFDL~V~hPhkfLv~yLk~ 80 (491)
||||||+||+++++++|+.... .. +..+++.|+.+|++||++|+|+|.|+|||++|..|+..
T Consensus 108 lfLA~KvEE~~~si~~fv~~~~-----~~-------------~~~~~~~Il~~E~~lL~~L~F~L~V~hPyr~L~~~l~d 169 (305)
T TIGR00569 108 VFLACKVEEFNVSIDQFVGNLK-----ET-------------PLKALEQVLEYELLLIQQLNFHLIVHNPYRPLEGFLID 169 (305)
T ss_pred HHHHHhccccCcCHHHHHhhcc-----CC-------------chhhHHHHHHHHHHHHHHCCCcEEeeCccHHHHHHHHH
Confidence 6999999999999999987421 11 12357899999999999999999999999999999976
Q ss_pred hcc------cHHHHHHHHHHHHHhhcCCccccccChHHHHHHHHHHHHHHhCcCCCCCCcccchhccCC--CHHH---HH
Q 011212 81 FKV------AQNALAQVAWNFVNDGLRTSLCLQFKPHHIAAGAIFLAAKFLKVKLPSDGDKVWWQEFDV--TPRQ---LE 149 (491)
Q Consensus 81 L~~------~~~~L~qlAw~fLnDSl~T~LcLqYpPsvIAaAAIyLA~kllgi~LPs~~~~~W~e~Lgv--t~eq---L~ 149 (491)
++. ..+.+++.||.|+||+++|++||.|+|++||+||||+|+..+++.+|+. .| +.|++ +.+. |.
T Consensus 170 l~~~l~~~~~~~~l~q~a~~~lndsl~Td~~L~y~Ps~IAlAAI~lA~~~~~~~l~~~---~~-e~~~~~~~~~~~~~l~ 245 (305)
T TIGR00569 170 IKTRLPGLENPEYLRKHADKFLNRTLLTDAYLLYTPSQIALAAILHTASRAGLNMESY---LT-EQLSVPGNREELPQLI 245 (305)
T ss_pred HHHhhccccchHHHHHHHHHHHHHHHcCCceecCCHHHHHHHHHHHHHHHhCCCCccc---ch-hhhcccccHHHHHHHH
Confidence 642 2246899999999999999999999999999999999999999999974 35 77766 4444 55
Q ss_pred HHHHHHHHHHhhCCC
Q 011212 150 EVSNQMLELYEQNRV 164 (491)
Q Consensus 150 eI~~eILeLY~~~r~ 164 (491)
+.++.|..+......
T Consensus 246 ~~~~~~~~~~~~~~~ 260 (305)
T TIGR00569 246 DIMRELRILVKKYEE 260 (305)
T ss_pred HHHHHHHHHHHcCCC
Confidence 555555554444333
No 5
>COG5333 CCL1 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, cyclin H subunit [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]
Probab=99.81 E-value=6.6e-20 Score=184.35 Aligned_cols=116 Identities=41% Similarity=0.653 Sum_probs=100.2
Q ss_pred CEEeeccCCCCCChHHHHHHHHHhhhccCCCChhhhccchHHHHHHHHHHHHHHHHHHHHcCCcccccCcHHHHHHHHHH
Q 011212 1 MFLAGKVEETPRPLKDVIIVSYEIIHKKDSTAPQRIRQQKEVYEQQKELILLGERVVLATLGFDLNVHHPYKPLVEAIKK 80 (491)
Q Consensus 1 LFLAsKVEEtprkLrDVI~Vs~~L~hkkdP~~~~~I~~~se~Yeq~Ke~IL~mErlILrtLgFDL~V~hPhkfLv~yLk~ 80 (491)
||||||+|||| +||...++..++. .++.++.+|+.|+.+|+.||+.|+|||.|+|||+++..|++.
T Consensus 95 v~LA~K~ed~~---~~I~i~~~~~~~~-----------~se~~~~sr~~Il~~E~~lLEaL~fd~~V~hPy~~l~~f~~~ 160 (297)
T COG5333 95 VYLACKVEDTP---RDISIESFEARDL-----------WSEEPKSSRERILEYEFELLEALDFDLHVHHPYKYLEGFLKD 160 (297)
T ss_pred eeeeeeccccc---chhhHHHHHhhcc-----------ccccccccHHHHHHHHHHHHHHcccceEeccccHHHHHHHHH
Confidence 79999999995 4566655544321 345667789999999999999999999999999999999999
Q ss_pred hcccHH-HHHHHHHHHHHhhcCCccccccChHHHHHHHHHHHHHHhCcCCC
Q 011212 81 FKVAQN-ALAQVAWNFVNDGLRTSLCLQFKPHHIAAGAIFLAAKFLKVKLP 130 (491)
Q Consensus 81 L~~~~~-~L~qlAw~fLnDSl~T~LcLqYpPsvIAaAAIyLA~kllgi~LP 130 (491)
+..... .+.++||.|++|++++.+|+.|||++||+|||++|+...+.+++
T Consensus 161 ~q~~~~~~~~~~aw~~inDa~~t~~~llypphiIA~a~l~ia~~~~~~~~~ 211 (297)
T COG5333 161 LQEKDKYKLLQIAWKIINDALRTDLCLLYPPHIIALAALLIACEVLGMPII 211 (297)
T ss_pred HHhccHHHHHHHHHHHHHhhhhceeeeecChHHHHHHHHHHHHHhcCCccc
Confidence 876543 69999999999999999999999999999999999999887544
No 6
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=99.38 E-value=1.4e-12 Score=132.75 Aligned_cols=134 Identities=18% Similarity=0.222 Sum_probs=116.3
Q ss_pred CEEeeccCCCCCChHHHHHHHHHhhhccCCCChhhhccchHHHHHHHHHHHHHHHHHHHHcCCcccccCcHHHHHHHHHH
Q 011212 1 MFLAGKVEETPRPLKDVIIVSYEIIHKKDSTAPQRIRQQKEVYEQQKELILLGERVVLATLGFDLNVHHPYKPLVEAIKK 80 (491)
Q Consensus 1 LFLAsKVEEtprkLrDVI~Vs~~L~hkkdP~~~~~I~~~se~Yeq~Ke~IL~mErlILrtLgFDL~V~hPhkfLv~yLk~ 80 (491)
||+||+.+..|+.+++|+.++. ++ +.+|-.+++.|++.|+|++.+.+|+.|+.+|+..
T Consensus 172 lYiACR~~~~prtl~eI~~~~~-------------v~---------~k~i~~~~~~l~k~L~~~~~~~~p~~~i~r~~~~ 229 (310)
T PRK00423 172 LYAACRRCKVPRTLDEIAEVSR-------------VS---------RKEIGRCYRFLLRELNLKLPPTDPIDYVPRFASE 229 (310)
T ss_pred HHHHHHHcCCCcCHHHHHHHhC-------------CC---------HHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHH
Confidence 6899999999999999988753 11 3567888999999999999999999999999999
Q ss_pred hcccHHHHHHHHHHHHHhhcCCccccccChHHHHHHHHHHHHHHhCcCCCCCCcccchhccCCCHHHHHHHHHHHHHHHh
Q 011212 81 FKVAQNALAQVAWNFVNDGLRTSLCLQFKPHHIAAGAIFLAAKFLKVKLPSDGDKVWWQEFDVTPRQLEEVSNQMLELYE 160 (491)
Q Consensus 81 L~~~~~~L~qlAw~fLnDSl~T~LcLqYpPsvIAaAAIyLA~kllgi~LPs~~~~~W~e~Lgvt~eqL~eI~~eILeLY~ 160 (491)
|++.. .+.+.|+.+++++..+.++....|..||+||||+|+.+.+...+. +.-....+++...|...+.+|+..+.
T Consensus 230 L~L~~-~v~~~A~~i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~~g~~~t~---keIa~v~~Vs~~tI~~~ykel~~~l~ 305 (310)
T PRK00423 230 LGLSG-EVQKKAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLLGERRTQ---REVAEVAGVTEVTVRNRYKELAEKLD 305 (310)
T ss_pred cCCCH-HHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHhCCCCCH---HHHHHHcCCCHHHHHHHHHHHHHHhC
Confidence 99874 799999999999988888999999999999999999999876443 23456679999999999999987653
No 7
>KOG2496 consensus Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, cyclin H subunit [Cell cycle control, cell division, chromosome partitioning; Transcription; Replication, recombination and repair]
Probab=99.27 E-value=2.4e-12 Score=129.90 Aligned_cols=141 Identities=26% Similarity=0.356 Sum_probs=102.4
Q ss_pred CEEeeccCCCCCChHHHHHHHHHhhhccCCCChhhhccchHHHHHHHHHHHHHHHHHHHHcCCcccccCcHHHHHHHHHH
Q 011212 1 MFLAGKVEETPRPLKDVIIVSYEIIHKKDSTAPQRIRQQKEVYEQQKELILLGERVVLATLGFDLNVHHPYKPLVEAIKK 80 (491)
Q Consensus 1 LFLAsKVEEtprkLrDVI~Vs~~L~hkkdP~~~~~I~~~se~Yeq~Ke~IL~mErlILrtLgFDL~V~hPhkfLv~yLk~ 80 (491)
+|||||++|+.+++.+|+.-.. .++ |+..+.||.+|..+|+.|.|+|.|++||++|..|+..
T Consensus 108 ~flA~Kieef~ISieqFvkn~~-----~~~-------------~k~~e~vLk~E~~llqsL~f~L~vh~PyRPleGFl~D 169 (325)
T KOG2496|consen 108 FFLACKIEEFYISIEQFVKNMN-----GRK-------------WKTHEIVLKYEFLLLQSLKFSLTVHNPYRPLEGFLLD 169 (325)
T ss_pred HHHHhhhHhheecHHHHHhhcc-----Ccc-------------cccHHHHHhchHHHHHhhhhhheecCCCCchHHHHHH
Confidence 4899999999999999997532 111 3346889999999999999999999999999999887
Q ss_pred hcc------cHHHHHHHH--HHHHHhhcCCccccccChHHHHHHHHHHHHHHhCcCCCCCCcccchhcc-----CCCHHH
Q 011212 81 FKV------AQNALAQVA--WNFVNDGLRTSLCLQFKPHHIAAGAIFLAAKFLKVKLPSDGDKVWWQEF-----DVTPRQ 147 (491)
Q Consensus 81 L~~------~~~~L~qlA--w~fLnDSl~T~LcLqYpPsvIAaAAIyLA~kllgi~LPs~~~~~W~e~L-----gvt~eq 147 (491)
++. +.+.+.+.. ..|++..++|++++.|+|++||+|||..|.-..++.+-+ -....+ .-+...
T Consensus 170 ~kt~l~~~~n~d~~~~~~d~~~fl~~~lltDa~lLytPsQIALaAil~a~~~~~~~l~s----~~~e~l~~~enr~~~s~ 245 (325)
T KOG2496|consen 170 MKTRLPALENPDILRKHDDSKKFLDRALLTDAYLLYTPSQIALAAILHAAGRTGETLES----YLLESLGSQENREKLSE 245 (325)
T ss_pred HHHHHHhccCHHHHhhhhhHHHHHHHHHHhccceecChHHHHHHHHHHHhccccchHHH----HHHHHhcCccccccchh
Confidence 652 112333333 489999999999999999999999996665555543211 011112 233456
Q ss_pred HHHHHHHHHHHHhhCC
Q 011212 148 LEEVSNQMLELYEQNR 163 (491)
Q Consensus 148 L~eI~~eILeLY~~~r 163 (491)
+.+++..|..+-.+..
T Consensus 246 l~d~~~~~~nlvk~~~ 261 (325)
T KOG2496|consen 246 LLDILKKIRNLVKQYK 261 (325)
T ss_pred hHHHHHHHHHHHHhcc
Confidence 6677777666666555
No 8
>KOG0653 consensus Cyclin B and related kinase-activating proteins [Cell cycle control, cell division, chromosome partitioning]
Probab=99.11 E-value=7e-11 Score=124.03 Aligned_cols=132 Identities=25% Similarity=0.342 Sum_probs=106.2
Q ss_pred CE-EeeccCCCCCC-hHHHHHHHHHhhhccCCCChhhhccchHHHHHHHHHHHHHHHHHHHHcCCcccccCcHHHHHHHH
Q 011212 1 MF-LAGKVEETPRP-LKDVIIVSYEIIHKKDSTAPQRIRQQKEVYEQQKELILLGERVVLATLGFDLNVHHPYKPLVEAI 78 (491)
Q Consensus 1 LF-LAsKVEEtprk-LrDVI~Vs~~L~hkkdP~~~~~I~~~se~Yeq~Ke~IL~mErlILrtLgFDL~V~hPhkfLv~yL 78 (491)
|| ||||.||...+ +.|++.++ +..| .+++|+.||+.||.+|.|++.+++|+.||.+|+
T Consensus 208 lf~IA~K~EE~~~P~v~dlv~is------------------d~~~--s~~~il~mE~~il~~L~f~l~~p~~~~FLrr~~ 267 (391)
T KOG0653|consen 208 LLSIACKYEEISLPSVEDLVLIT------------------DGAY--SREEILRMEKYILNVLEFDLSVPTPLSFLRRFL 267 (391)
T ss_pred HHHHHHhhhhccCCccceeEeee------------------CCcc--chHHHHHHHHHHHhccCeeecCCchHHHHHHHH
Confidence 35 99999996444 67776643 2334 478999999999999999999999999999999
Q ss_pred HHhcccHHHHHHHHHHHHHhhcCCccccccChHHHHHHHHHHHHHHhCcCCCCCCcccchhcc----CCCHHHHHHHHHH
Q 011212 79 KKFKVAQNALAQVAWNFVNDGLRTSLCLQFKPHHIAAGAIFLAAKFLKVKLPSDGDKVWWQEF----DVTPRQLEEVSNQ 154 (491)
Q Consensus 79 k~L~~~~~~L~qlAw~fLnDSl~T~LcLqYpPsvIAaAAIyLA~kllgi~LPs~~~~~W~e~L----gvt~eqL~eI~~e 154 (491)
+....+ ....-++.+++..++...-.+.|+|+.+|+|++++|..+.... ..|...+ |+....+..+...
T Consensus 268 ka~~~d-~~~~~~~k~~~El~l~d~~~~~~~~s~~aaa~~~~~~~~~~~~------~~w~~~~~~~sg~~~~~~~~~~~~ 340 (391)
T KOG0653|consen 268 KAADYD-IKTRTLVKYLLELSLCDYSMLSIPPSSSAAASFTLALRMLSKG------DVWSPTLEHYSGYSESYLFECARS 340 (391)
T ss_pred Hhhhcc-hhHHHHHHHHHHHHHhhhHHhccCcHHHHHHHHHHHHHHhccC------CccCCCCeeccCCCcHHHHHHHHH
Confidence 998744 3566778889999888888999999999999999999998763 2487765 6655577777777
Q ss_pred HHHHH
Q 011212 155 MLELY 159 (491)
Q Consensus 155 ILeLY 159 (491)
+..+.
T Consensus 341 ~~~~~ 345 (391)
T KOG0653|consen 341 LSALS 345 (391)
T ss_pred HHHHH
Confidence 77643
No 9
>PF02984 Cyclin_C: Cyclin, C-terminal domain; InterPro: IPR004367 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. This is the C-terminal domain of cyclins.; GO: 0005634 nucleus; PDB: 3QHR_D 3QHW_B 1W98_B 1URC_D 2WMB_D 1H26_D 1GY3_B 2UUE_D 1E9H_D 2IW9_D ....
Probab=99.06 E-value=2.8e-10 Score=97.02 Aligned_cols=89 Identities=26% Similarity=0.331 Sum_probs=72.2
Q ss_pred cCcHHHHHHHHHHhcccHHHHHHHHHHHHHhhcCCccccccChHHHHHHHHHHHHHHhCcCCCCCCcccchhcc----CC
Q 011212 68 HHPYKPLVEAIKKFKVAQNALAQVAWNFVNDGLRTSLCLQFKPHHIAAGAIFLAAKFLKVKLPSDGDKVWWQEF----DV 143 (491)
Q Consensus 68 ~hPhkfLv~yLk~L~~~~~~L~qlAw~fLnDSl~T~LcLqYpPsvIAaAAIyLA~kllgi~LPs~~~~~W~e~L----gv 143 (491)
|+|+.||..|++..+. ...+..+|++|++.++.+.-++.|+|++||+|||++|...++.. ..|...+ ++
T Consensus 1 PTp~~Fl~~~~~~~~~-~~~~~~~a~~l~el~l~~~~fl~~~PS~iAaAai~lA~~~~~~~------~~~~~~l~~~t~~ 73 (118)
T PF02984_consen 1 PTPYDFLRRFLKISNA-DQEVRNLARYLLELSLLDYEFLQYPPSVIAAAAILLARKILGKE------PPWPESLEKLTGY 73 (118)
T ss_dssp --HHHHHHHHHTSSSH-HHHHHHHHHHHHHHHHHSHHHTTS-HHHHHHHHHHHHHHHHHSS------TCSHHHHHHHHTS
T ss_pred CcHHHHHHHHHHHcCC-cHHHHHHHHHHHHHHHhhccccCCCHHHHHHHHHHHHHHHhCcc------ccCCccchhhcCC
Confidence 6899999999665443 34799999999999999989999999999999999999998742 2576543 89
Q ss_pred CHHHHHHHHHHHHHHHhhCC
Q 011212 144 TPRQLEEVSNQMLELYEQNR 163 (491)
Q Consensus 144 t~eqL~eI~~eILeLY~~~r 163 (491)
+.++|..|+..|..++....
T Consensus 74 ~~~~l~~c~~~i~~~~~~~~ 93 (118)
T PF02984_consen 74 DKEDLKECIELIQELLSKAS 93 (118)
T ss_dssp -HHHHHHHHHHHHHHHHHCC
T ss_pred CHHHHHHHHHHHHHHHHhcC
Confidence 99999999999999998544
No 10
>KOG0654 consensus G2/Mitotic-specific cyclin A [Cell cycle control, cell division, chromosome partitioning]
Probab=99.06 E-value=8.2e-10 Score=114.83 Aligned_cols=136 Identities=22% Similarity=0.272 Sum_probs=113.6
Q ss_pred CEEeeccCC-CCCChHHHHHHHHHhhhccCCCChhhhccchHHHHHHHHHHHHHHHHHHHHcCCcccccCcHHHHHHHHH
Q 011212 1 MFLAGKVEE-TPRPLKDVIIVSYEIIHKKDSTAPQRIRQQKEVYEQQKELILLGERVVLATLGFDLNVHHPYKPLVEAIK 79 (491)
Q Consensus 1 LFLAsKVEE-tprkLrDVI~Vs~~L~hkkdP~~~~~I~~~se~Yeq~Ke~IL~mErlILrtLgFDL~V~hPhkfLv~yLk 79 (491)
+++|+|.|| .+..+.+++..+ +..| ++.+++.||..||..|.|.+..++...||..|+.
T Consensus 187 m~I~sk~ee~~~~~~~ef~~it------------------d~ty--~~~qv~~~~~~il~~l~~~~~~pt~~~~l~~~~~ 246 (359)
T KOG0654|consen 187 MLIASKYEEIKEPRVEEFCYIT------------------DNTY--TYWQVLRMEIDILNALTFELVRPTSKTFLRRFLR 246 (359)
T ss_pred ceeeccchhhcchHHHHHHhhh------------------hhhh--HHHHHHHHHHHHHHHhHHHHhCchHHHHHHHHHH
Confidence 478999999 466777777643 2344 3567999999999999999999999999999988
Q ss_pred HhcccHHHHHHHHHHHHHhhcCCccccccChHHHHHHHHHHHHHHhCcCCCCCCcccchhcc----CCCHHHHHHHHHHH
Q 011212 80 KFKVAQNALAQVAWNFVNDGLRTSLCLQFKPHHIAAGAIFLAAKFLKVKLPSDGDKVWWQEF----DVTPRQLEEVSNQM 155 (491)
Q Consensus 80 ~L~~~~~~L~qlAw~fLnDSl~T~LcLqYpPsvIAaAAIyLA~kllgi~LPs~~~~~W~e~L----gvt~eqL~eI~~eI 155 (491)
........+..+|.+++..+++.+.+|+|.|+.||+||++||...++. .+|...| +|+.+++..|+..|
T Consensus 247 ~~~~~~~~~e~~~~yl~elsll~~~~l~y~PSliAasAv~lA~~~~~~-------~pW~~~L~~~T~y~~edl~~~v~~L 319 (359)
T KOG0654|consen 247 VAQTPELQVEPLANYLTELSLLDYIFLKYLPSLIAASAVFLARLTLDF-------HPWNQTLEDYTGYKAEDLKPCVLDL 319 (359)
T ss_pred hhcchhHHHHHHHHHHHHhhhhhHHHhccChHHHHHHHHHHHHhhccC-------CCCchhhHHhhcccHHHHHHHHHHH
Confidence 865333467888999999999888899999999999999999999883 5798877 89999999999999
Q ss_pred HHHHhhCCC
Q 011212 156 LELYEQNRV 164 (491)
Q Consensus 156 LeLY~~~r~ 164 (491)
+ +|...+.
T Consensus 320 ~-~~l~~~~ 327 (359)
T KOG0654|consen 320 H-LYLNASG 327 (359)
T ss_pred h-cccCCCC
Confidence 9 7765444
No 11
>COG5024 Cyclin [Cell division and chromosome partitioning]
Probab=99.02 E-value=3.1e-10 Score=120.68 Aligned_cols=132 Identities=22% Similarity=0.261 Sum_probs=106.0
Q ss_pred CEEeeccCCC-CCChHHHHHHHHHhhhccCCCChhhhccchHHHHHHHHHHHHHHHHHHHHcCCcccccCcHHHHHHHHH
Q 011212 1 MFLAGKVEET-PRPLKDVIIVSYEIIHKKDSTAPQRIRQQKEVYEQQKELILLGERVVLATLGFDLNVHHPYKPLVEAIK 79 (491)
Q Consensus 1 LFLAsKVEEt-prkLrDVI~Vs~~L~hkkdP~~~~~I~~~se~Yeq~Ke~IL~mErlILrtLgFDL~V~hPhkfLv~yLk 79 (491)
||+|||+||. ...+++++.++.. .| .++.|+.+|+.||.+|+|++..|.|+.||.++.+
T Consensus 263 LfIa~K~EE~~~p~i~~l~~~t~g------------------~~--t~~~i~~aE~~ml~~l~f~is~P~P~sFLRriSk 322 (440)
T COG5024 263 LFIASKYEEVNCPSIKDLVYATDG------------------AF--TRDDIIRAERYMLEVLDFNISWPSPMSFLRRISK 322 (440)
T ss_pred HHHHHhHhHhcCHHHHHHHHHHcc------------------cc--cHHHHHHHHHHHhhhcccccCCCChHHHHHHHHh
Confidence 6999999995 4457777776532 22 4789999999999999999999999999888887
Q ss_pred HhcccHHHHHHHHHHHHHhhcCCccccccChHHHHHHHHHHHHHHhCcCCCCCCcccchhcc----C-CCHHHHHHHHHH
Q 011212 80 KFKVAQNALAQVAWNFVNDGLRTSLCLQFKPHHIAAGAIFLAAKFLKVKLPSDGDKVWWQEF----D-VTPRQLEEVSNQ 154 (491)
Q Consensus 80 ~L~~~~~~L~qlAw~fLnDSl~T~LcLqYpPsvIAaAAIyLA~kllgi~LPs~~~~~W~e~L----g-vt~eqL~eI~~e 154 (491)
+-.-+ ...+-.+-+++.-+....-++.++|+.+|+||.|+|...++.. .|-..| | ++..++..++..
T Consensus 323 a~dyd-~~srt~~k~~~e~s~~~~~f~~~~~S~~~aaa~~~s~~~~~~~-------~w~~~l~~ySg~y~~~~l~~~~~~ 394 (440)
T COG5024 323 ASDYD-IFSRTPAKFSSEISPVDYKFIQISPSWCAAAAMYLSRKILSQN-------QWDRTLIHYSGNYTNPDLKPLNES 394 (440)
T ss_pred hcccc-hhhhhhHhhhCCchHhhhhhccCCchHHHHHHHHHHHhhhccC-------CCCccccccCCCCCchhHHHHHHH
Confidence 76543 2445567777777776667788899999999999999998853 487777 4 888899999999
Q ss_pred HHHHHh
Q 011212 155 MLELYE 160 (491)
Q Consensus 155 ILeLY~ 160 (491)
+++...
T Consensus 395 ~~~~l~ 400 (440)
T COG5024 395 NKENLQ 400 (440)
T ss_pred HHHHhc
Confidence 888664
No 12
>KOG0656 consensus G1/S-specific cyclin D [Cell cycle control, cell division, chromosome partitioning]
Probab=98.95 E-value=9.4e-10 Score=113.47 Aligned_cols=106 Identities=27% Similarity=0.323 Sum_probs=80.8
Q ss_pred CEEeeccCCCCCCh-HHHHHHHHHhhhccCCCChhhhccchHHHHHHHHHHHHHHHHHHHHcCCcccccCcHHHHHHHHH
Q 011212 1 MFLAGKVEETPRPL-KDVIIVSYEIIHKKDSTAPQRIRQQKEVYEQQKELILLGERVVLATLGFDLNVHHPYKPLVEAIK 79 (491)
Q Consensus 1 LFLAsKVEEtprkL-rDVI~Vs~~L~hkkdP~~~~~I~~~se~Yeq~Ke~IL~mErlILrtLgFDL~V~hPhkfLv~yLk 79 (491)
|+||+|+||+.+++ -|+. |.| .. |-.-.+.|.+||.+||.+|+|+|...+|+.|+..|+.
T Consensus 131 LsLAsKmeE~~vPll~dl~-v~~----------------~~--~~feaktI~rmELLVLstL~Wrl~aVTP~sF~~~fl~ 191 (335)
T KOG0656|consen 131 LSLASKMEETDVPLLADLQ-VEY----------------TD--NVFEAKTIQRMELLVLSTLKWRLRAVTPFSFIDHFLS 191 (335)
T ss_pred HHHHHhhcCcCCchhhhhh-hcc----------------cc--ccccHHHHHHHHHHHHhhccccccCCCchHHHHHHHH
Confidence 57999999986443 2322 111 11 2223588999999999999999999999999999999
Q ss_pred HhcccH---HHHHHHHHHHHHhhcCCccccccChHHHHHHHHHHHHHHh
Q 011212 80 KFKVAQ---NALAQVAWNFVNDGLRTSLCLQFKPHHIAAGAIFLAAKFL 125 (491)
Q Consensus 80 ~L~~~~---~~L~qlAw~fLnDSl~T~LcLqYpPsvIAaAAIyLA~kll 125 (491)
++.... ..+...|..++-.+....-++.|+|++||+|++.++....
T Consensus 192 ki~~~~~~~~~~~~~~s~~ll~~~~d~~Fl~y~pSviAaa~~~~v~~~~ 240 (335)
T KOG0656|consen 192 KISQKDHNKHLFLKHASLFLLSVITDIKFLEYPPSVIAAAAILSVSASV 240 (335)
T ss_pred HcCcccchHHHHHHHHHHHHHHHhhhhhhhcCChHHHHHHHHHHHHHhh
Confidence 997532 2466777777777666677999999999999887766544
No 13
>KOG0655 consensus G1/S-specific cyclin E [Cell cycle control, cell division, chromosome partitioning]
Probab=98.69 E-value=2e-08 Score=103.00 Aligned_cols=154 Identities=19% Similarity=0.156 Sum_probs=107.8
Q ss_pred CEEeeccCC-CCCChHHHHHHHHHhhhccCCCChhhhccchHHHHHHHHHHHHHHHHHHHHcCCcccccCcHHHHHHHHH
Q 011212 1 MFLAGKVEE-TPRPLKDVIIVSYEIIHKKDSTAPQRIRQQKEVYEQQKELILLGERVVLATLGFDLNVHHPYKPLVEAIK 79 (491)
Q Consensus 1 LFLAsKVEE-tprkLrDVI~Vs~~L~hkkdP~~~~~I~~~se~Yeq~Ke~IL~mErlILrtLgFDL~V~hPhkfLv~yLk 79 (491)
||+|+|+|| .|.++-+|..|+. ..+ .-+.|+.||.+||++|+|+|...+.-.+|.-|++
T Consensus 196 LFIAAK~EEIYpPKl~eFAyvTD------------------gAc--s~ddIltmE~iilkal~W~l~PiTii~WL~vylQ 255 (408)
T KOG0655|consen 196 LFIAAKLEEIYPPKLIEFAYVTD------------------GAC--SEDDILTMELIILKALKWELSPITIISWLNVYLQ 255 (408)
T ss_pred HHHHHHHhhccCccccceeeecc------------------Ccc--chHHHHHHHHHHHHHhcccccceehHHHHHHHHH
Confidence 799999999 6889998887642 112 2478999999999999999999999999999999
Q ss_pred Hhccc-----------HHHHHHHHHHHHHhhcCCccccccChHHHHHHHHHHHHHHhCcCCCCCCcccchhccCCCHHHH
Q 011212 80 KFKVA-----------QNALAQVAWNFVNDGLRTSLCLQFKPHHIAAGAIFLAAKFLKVKLPSDGDKVWWQEFDVTPRQL 148 (491)
Q Consensus 80 ~L~~~-----------~~~L~qlAw~fLnDSl~T~LcLqYpPsvIAaAAIyLA~kllgi~LPs~~~~~W~e~Lgvt~eqL 148 (491)
..... ...+.|+|. +|..+.+.-=|+.|+-.+|||||||.-.... .--..-|+.+.+|
T Consensus 256 v~~~n~~~k~l~Pq~~~~efiqiaq-lLDlc~ldids~~fsYrilaAAal~h~~s~e----------~v~kaSG~~w~~i 324 (408)
T KOG0655|consen 256 VDALNDAPKVLLPQYSQEEFIQIAQ-LLDLCILDIDSLEFSYRILAAAALCHFTSIE----------VVKKASGLEWDSI 324 (408)
T ss_pred HHhcCCCCceeccccchHHHHHHHH-HHHHHHhccccccchHHHHHHHHHHHHhHHH----------HHHHcccccHHHH
Confidence 87542 234566665 5555555556899999999999998644321 1122336777899
Q ss_pred HHHHHHHHHHHhhCCCCCCCCCccccccCCCCCCCCC
Q 011212 149 EEVSNQMLELYEQNRVPQSQGSEVEGSAGGASSHRPQ 185 (491)
Q Consensus 149 ~eI~~eILeLY~~~r~~~~~~~~~e~~~~~~~~~~~~ 185 (491)
+.|+.-|.=+..--+......-...-.+...-.|-++
T Consensus 325 e~cv~wm~Pf~rvi~~~~~~~~~~~~kI~~eDsHnIQ 361 (408)
T KOG0655|consen 325 EECVDWMVPFVRVIKSTSPVKLKTFKKIPMEDSHNIQ 361 (408)
T ss_pred HHHHHHHHHHHHHHhhccchHhhhccCCCcccccchh
Confidence 9999988877765444433333233334444444444
No 14
>smart00385 CYCLIN domain present in cyclins, TFIIB and Retinoblastoma. A helical domain present in cyclins and TFIIB (twice) and Retinoblastoma (once). A protein recognition domain functioning in cell-cycle and transcription control.
Probab=98.64 E-value=1.2e-07 Score=74.71 Aligned_cols=80 Identities=23% Similarity=0.226 Sum_probs=67.1
Q ss_pred HHHHHHHHhcccHHHHHHHHHHHHHhhcCCccccccChHHHHHHHHHHHHHHhCcCCCCCCcccchhccCC-CHHHHHHH
Q 011212 73 PLVEAIKKFKVAQNALAQVAWNFVNDGLRTSLCLQFKPHHIAAGAIFLAAKFLKVKLPSDGDKVWWQEFDV-TPRQLEEV 151 (491)
Q Consensus 73 fLv~yLk~L~~~~~~L~qlAw~fLnDSl~T~LcLqYpPsvIAaAAIyLA~kllgi~LPs~~~~~W~e~Lgv-t~eqL~eI 151 (491)
||.+++..+++.. .+..+|++|+..++....++.++|+.||+||||+|+++.+...+. ..|....++ +.++|..+
T Consensus 2 ~l~~~~~~~~~~~-~~~~~a~~~~~~~l~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~---~~~~~~~~~~~~~~i~~~ 77 (83)
T smart00385 2 FLRRVCKALNLDP-ETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLAAKTEEIPPWT---KELVHYTGYFTEEEILRM 77 (83)
T ss_pred HHHHHHHHcCCCH-HHHHHHHHHHHHHHHHhhcccCCHHHHHHHHHHHHHHHhcCCCCc---hhHhHhhCCCCHHHHHHH
Confidence 7888999998864 799999999999987677888999999999999999999875332 245556677 99999999
Q ss_pred HHHHH
Q 011212 152 SNQML 156 (491)
Q Consensus 152 ~~eIL 156 (491)
...|+
T Consensus 78 ~~~il 82 (83)
T smart00385 78 EKLLL 82 (83)
T ss_pred HHHHh
Confidence 88876
No 15
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=98.49 E-value=3.2e-07 Score=93.31 Aligned_cols=133 Identities=19% Similarity=0.240 Sum_probs=110.0
Q ss_pred CEEeeccCCCCCChHHHHHHHHHhhhccCCCChhhhccchHHHHHHHHHHHHHHHHHHHHcCCcccccCcHHHHHHHHHH
Q 011212 1 MFLAGKVEETPRPLKDVIIVSYEIIHKKDSTAPQRIRQQKEVYEQQKELILLGERVVLATLGFDLNVHHPYKPLVEAIKK 80 (491)
Q Consensus 1 LFLAsKVEEtprkLrDVI~Vs~~L~hkkdP~~~~~I~~~se~Yeq~Ke~IL~mErlILrtLgFDL~V~hPhkfLv~yLk~ 80 (491)
||+||+....|+.+.+|+.+.. ++ +..|..+.+++.+.|+-.+....|..|+.+|+..
T Consensus 147 iY~acR~~~~prtl~eIa~a~~-------------V~---------~kei~rtyr~~~~~L~l~~~~~~p~~yi~rf~s~ 204 (285)
T COG1405 147 IYAACRINGVPRTLDEIAKALG-------------VS---------KKEIGRTYRLLVRELKLKIPPVDPSDYIPRFASK 204 (285)
T ss_pred HHHHHHHcCCCccHHHHHHHHC-------------CC---------HHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHH
Confidence 5778888888888888887643 11 3568888889999999999999999999999999
Q ss_pred hcccHHHHHHHHHHHHHhhcCCccccccChHHHHHHHHHHHHHHhCcCCCCCCcccchhccCCCHHHHHHHHHHHHHHH
Q 011212 81 FKVAQNALAQVAWNFVNDGLRTSLCLQFKPHHIAAGAIFLAAKFLKVKLPSDGDKVWWQEFDVTPRQLEEVSNQMLELY 159 (491)
Q Consensus 81 L~~~~~~L~qlAw~fLnDSl~T~LcLqYpPsvIAaAAIyLA~kllgi~LPs~~~~~W~e~Lgvt~eqL~eI~~eILeLY 159 (491)
|++. ..+...|..++..+..-.+...-.|..||+||||+|+.+++....+ ..-....++|+..|..-+.+|.+..
T Consensus 205 L~l~-~~v~~~a~ei~~~~~~~g~~~Gk~P~glAaaaiy~as~l~~~~~tq---~eva~v~~vtevTIrnrykel~~~~ 279 (285)
T COG1405 205 LGLS-DEVRRKAIEIVKKAKRAGLTAGKSPAGLAAAAIYLASLLLGERRTQ---KEVAKVAGVTEVTIRNRYKELADAL 279 (285)
T ss_pred cCCC-HHHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhCCchHH---HHHHHHhCCeeeHHHHHHHHHHHhh
Confidence 9998 5788999999999887777779999999999999999999965433 2345566999999998888877654
No 16
>cd00043 CYCLIN Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain.
Probab=98.49 E-value=4.6e-07 Score=71.89 Aligned_cols=85 Identities=20% Similarity=0.156 Sum_probs=69.0
Q ss_pred ccCcHHHHHHHHHHhcccHHHHHHHHHHHHHhhcCCccccccChHHHHHHHHHHHHHHhCcCCCCCCcccchhccCC-CH
Q 011212 67 VHHPYKPLVEAIKKFKVAQNALAQVAWNFVNDGLRTSLCLQFKPHHIAAGAIFLAAKFLKVKLPSDGDKVWWQEFDV-TP 145 (491)
Q Consensus 67 V~hPhkfLv~yLk~L~~~~~~L~qlAw~fLnDSl~T~LcLqYpPsvIAaAAIyLA~kllgi~LPs~~~~~W~e~Lgv-t~ 145 (491)
.++|+.||.+++..++... .+..+|++|++.++....+..+.|+.||+||||+|+++.+..+.. ..|....++ +.
T Consensus 2 ~~~~~~~l~~~~~~~~~~~-~~~~~A~~~~~~~~~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~---~~~~~~~~~~~~ 77 (88)
T cd00043 2 RPTPLDFLRRVAKALGLSP-ETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEEIPPWL---KDLVHVTGYATE 77 (88)
T ss_pred cchHHHHHHHHHHHcCCCH-HHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHcCCCCCH---HHHhHHhCCCCH
Confidence 4678999999999998874 788999999999998777889999999999999999998872111 234445577 88
Q ss_pred HHHHHHHHHH
Q 011212 146 RQLEEVSNQM 155 (491)
Q Consensus 146 eqL~eI~~eI 155 (491)
.+|..+...|
T Consensus 78 ~~i~~~e~~i 87 (88)
T cd00043 78 EEILRMEKLL 87 (88)
T ss_pred HHHHHHHHHh
Confidence 8888777665
No 17
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=98.01 E-value=1.4e-05 Score=81.24 Aligned_cols=133 Identities=14% Similarity=0.170 Sum_probs=97.7
Q ss_pred CEEeeccCCCCCChHHHHHHHHHhhhccCCCChhhhccchHHHHHHHHHHHHHHHHHHHHcCCccccc--CcHHHHHHHH
Q 011212 1 MFLAGKVEETPRPLKDVIIVSYEIIHKKDSTAPQRIRQQKEVYEQQKELILLGERVVLATLGFDLNVH--HPYKPLVEAI 78 (491)
Q Consensus 1 LFLAsKVEEtprkLrDVI~Vs~~L~hkkdP~~~~~I~~~se~Yeq~Ke~IL~mErlILrtLgFDL~V~--hPhkfLv~yL 78 (491)
||+||..++.||.+++|..++. +- +++|-++=.+|++.|+-.+... +.-.|+.+||
T Consensus 154 lyiACRq~~~pRT~kEI~~~an-v~---------------------kKEIgr~~K~i~~~l~~s~~~~s~~t~~~m~RFC 211 (308)
T KOG1597|consen 154 LYIACRQEDVPRTFKEISAVAN-VS---------------------KKEIGRCVKLIGEALETSVDLISISTGDFMPRFC 211 (308)
T ss_pred HHHHHHhcCCCchHHHHHHHHc-CC---------------------HHHHHHHHHHHHHHHhccchhhhhhHHHHHHHHH
Confidence 5789999999999999999875 21 3344445556777766655544 4788999999
Q ss_pred HHhcccHHHHHHHHHHHHHhhcCCccccccChHHHHHHHHHHHHHHhCcCCCCCCcccchhccCCCHHHHHHHHHHHHHH
Q 011212 79 KKFKVAQNALAQVAWNFVNDGLRTSLCLQFKPHHIAAGAIFLAAKFLKVKLPSDGDKVWWQEFDVTPRQLEEVSNQMLEL 158 (491)
Q Consensus 79 k~L~~~~~~L~qlAw~fLnDSl~T~LcLqYpPsvIAaAAIyLA~kllgi~LPs~~~~~W~e~Lgvt~eqL~eI~~eILeL 158 (491)
..|++.. .+...|-.++.-+-.-.++-.-.|-.||||+|||+..+....-+. +.--...||++..|+..++.|+..
T Consensus 212 s~L~L~~-~~q~aA~e~a~ka~~~~~~~gRsPiSIAAa~IYmisqls~~kkt~---keI~~vtgVaE~TIr~sYK~Lyp~ 287 (308)
T KOG1597|consen 212 SNLGLPK-SAQEAATEIAEKAEEMDIRAGRSPISIAAAAIYMISQLSDEKKTQ---KEIGEVTGVAEVTIRNSYKDLYPH 287 (308)
T ss_pred HhcCCCH-HHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHHHhccCcccH---HHHHHHhhhhHHHHHHHHHHHhhc
Confidence 9999874 555666666666554455556899999999999999998754333 223455689999999888887654
Q ss_pred H
Q 011212 159 Y 159 (491)
Q Consensus 159 Y 159 (491)
.
T Consensus 288 ~ 288 (308)
T KOG1597|consen 288 A 288 (308)
T ss_pred h
Confidence 3
No 18
>PF00382 TFIIB: Transcription factor TFIIB repeat; InterPro: IPR013150 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. In eukaryotes, transcription initiation of all protein encoding genes involves the polymerase II system. This sytem is modulated by both general and specific transcription factors. The general factors (which include TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIG and TFIIH) operate through common promoter elements, such as the TATA box. Transcription factor IIB (TFIIB) is of central importance in transcription of class II genes. It associates with TFIID-TFIIA bound to DNA (the DA complex) to form a ternary TFIID-IIA-IBB (DAB) complex, which is recognised by RNA polymerase II [, ]. TFIIB comprises ~315-340 residues and contains an imperfect C-terminal repeat of a 75-residue domain that may contribute to the symmetry of the folded protein. The basal archaeal transcription machinery resembles that of the eukaryotic polymerase II system and includes a homologue of TFIIB []. This entry represents a cyclin-like domain which is found repeated in the C-terminal region of a variety of eukaryotic TFIIB's and their archaeal counterparts. These domains individually form the typical cyclin fold, and in the transcription complex they straddle the C-terminal region of the TATA-binding protein - an interaction essential for the formation of the transcription initiation complex [, ].; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2PHG_A 1C9B_Q 1TFB_A 1VOL_A 3K7A_M 1AIS_B 1D3U_B.
Probab=97.18 E-value=0.001 Score=53.62 Aligned_cols=70 Identities=19% Similarity=0.193 Sum_probs=50.8
Q ss_pred HHHHHHHhcccHHHHHHHHHHHHHhhcCCccccccChHHHHHHHHHHHHHHhCcCCCCCCcccchhccCCCHHH
Q 011212 74 LVEAIKKFKVAQNALAQVAWNFVNDGLRTSLCLQFKPHHIAAGAIFLAAKFLKVKLPSDGDKVWWQEFDVTPRQ 147 (491)
Q Consensus 74 Lv~yLk~L~~~~~~L~qlAw~fLnDSl~T~LcLqYpPsvIAaAAIyLA~kllgi~LPs~~~~~W~e~Lgvt~eq 147 (491)
+.+|+..|++.. .+...|..++.......+.-.-.|..||+||||+|+...+.+.+. ..-...++++..+
T Consensus 1 I~r~~~~L~L~~-~v~~~A~~i~~~~~~~~~~~Gr~~~~iaAA~iY~acr~~~~~~t~---~eIa~~~~Vs~~t 70 (71)
T PF00382_consen 1 IPRICSKLGLPE-DVRERAKEIYKKAQERGLLKGRSPESIAAACIYLACRLNGVPRTL---KEIAEAAGVSEKT 70 (71)
T ss_dssp HHHHHHHTT--H-HHHHHHHHHHHHHHHTTTSTTS-HHHHHHHHHHHHHHHTTSSSSH---HHHHHHCTSSHHH
T ss_pred ChHHHhHcCCCH-HHHHHHHHHHHHHHHcCCcccCCHHHHHHHHHHHHHHHcCCCcCH---HHHHHHhCCCCCc
Confidence 457889998874 789999999988877777777889999999999999999876543 1233444555443
No 19
>PF00134 Cyclin_N: Cyclin, N-terminal domain; InterPro: IPR006671 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. Cyclins contain two domains of similar all-alpha fold, of which this entry is associated with the N-terminal domain.; PDB: 2W2H_B 3RGF_B 1KXU_A 1JKW_A 1URC_D 2WMB_D 1H26_D 1GY3_B 2UUE_D 1E9H_D ....
Probab=97.01 E-value=0.0001 Score=63.91 Aligned_cols=46 Identities=46% Similarity=0.699 Sum_probs=32.9
Q ss_pred CEEeeccCCC-CCChHHHHHHHHHhhhccCCCChhhhccchHHHHHHHHHHHHHHHHHHHHcCCccc
Q 011212 1 MFLAGKVEET-PRPLKDVIIVSYEIIHKKDSTAPQRIRQQKEVYEQQKELILLGERVVLATLGFDLN 66 (491)
Q Consensus 1 LFLAsKVEEt-prkLrDVI~Vs~~L~hkkdP~~~~~I~~~se~Yeq~Ke~IL~mErlILrtLgFDL~ 66 (491)
||||||++|. +..+.+++.++. ..| .+++|+.||+.||.+|+|+|+
T Consensus 81 l~lA~K~~e~~~~~~~~~~~~~~------------------~~~--~~~~i~~~E~~iL~~L~f~ln 127 (127)
T PF00134_consen 81 LFLASKMEEDNPPSISDLIRISD------------------NTF--TKKDILEMEREILSALNFDLN 127 (127)
T ss_dssp HHHHHHHHTSS--HHHHHHHHTT------------------TSS--HHHHHHHHHHHHHHHTTT---
T ss_pred HHHhhhhhccccchHHHHHHHHc------------------CCC--CHHHHHHHHHHHHHHCCCCcC
Confidence 5789999997 777888887641 122 268899999999999999985
No 20
>PF00134 Cyclin_N: Cyclin, N-terminal domain; InterPro: IPR006671 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. Cyclins contain two domains of similar all-alpha fold, of which this entry is associated with the N-terminal domain.; PDB: 2W2H_B 3RGF_B 1KXU_A 1JKW_A 1URC_D 2WMB_D 1H26_D 1GY3_B 2UUE_D 1E9H_D ....
Probab=95.84 E-value=0.028 Score=48.69 Aligned_cols=85 Identities=19% Similarity=0.192 Sum_probs=59.7
Q ss_pred HHHHHHHHhcccHHHHHHHHHHHHHhhcCCccccccChHHHHHHHHHHHHHHhCcCCCCCCcccchhcc--CCCHHHHHH
Q 011212 73 PLVEAIKKFKVAQNALAQVAWNFVNDGLRTSLCLQFKPHHIAAGAIFLAAKFLKVKLPSDGDKVWWQEF--DVTPRQLEE 150 (491)
Q Consensus 73 fLv~yLk~L~~~~~~L~qlAw~fLnDSl~T~LcLqYpPsvIAaAAIyLA~kllgi~LPs~~~~~W~e~L--gvt~eqL~e 150 (491)
|+...+..+++.. .+..+|..++...+....+....+..||+||+++|+++.....|.. ..|.... .++.++|..
T Consensus 37 ~i~~~~~~~~l~~-~~~~~A~~~~dr~~~~~~~~~~~~~li~~~cl~lA~K~~e~~~~~~--~~~~~~~~~~~~~~~i~~ 113 (127)
T PF00134_consen 37 WIIELCQRLKLSP-ETLHLAIYLFDRFLSKRPVNRSKLQLIALACLFLASKMEEDNPPSI--SDLIRISDNTFTKKDILE 113 (127)
T ss_dssp HHHHHHHHTT-BH-HHHHHHHHHHHHHHTTS-TTCCGHHHHHHHHHHHHHHHHTSS--HH--HHHHHHTTTSSHHHHHHH
T ss_pred HHHHHHHhcccch-hHHHHHHHHHHHHHhhcccccchhhhhhhhHHHHhhhhhccccchH--HHHHHHHcCCCCHHHHHH
Confidence 4556666666654 6778888888887765567889999999999999999987754431 1232222 578899988
Q ss_pred HHHHHHHHHh
Q 011212 151 VSNQMLELYE 160 (491)
Q Consensus 151 I~~eILeLY~ 160 (491)
.-..|+....
T Consensus 114 ~E~~iL~~L~ 123 (127)
T PF00134_consen 114 MEREILSALN 123 (127)
T ss_dssp HHHHHHHHTT
T ss_pred HHHHHHHHCC
Confidence 8888887654
No 21
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=94.76 E-value=0.14 Score=52.82 Aligned_cols=88 Identities=11% Similarity=0.077 Sum_probs=67.3
Q ss_pred cHHHHHHHHHHhcccHHHHHHHHHHHHHhhcCCccccccChHHHHHHHHHHHHHHhCcCCCCCCcccchhccCCCHHHHH
Q 011212 70 PYKPLVEAIKKFKVAQNALAQVAWNFVNDGLRTSLCLQFKPHHIAAGAIFLAAKFLKVKLPSDGDKVWWQEFDVTPRQLE 149 (491)
Q Consensus 70 PhkfLv~yLk~L~~~~~~L~qlAw~fLnDSl~T~LcLqYpPsvIAaAAIyLA~kllgi~LPs~~~~~W~e~Lgvt~eqL~ 149 (491)
.+..|..++..|++.. .+...|..|+..++.-.+.-......||+||||+|++..+.+... ..-...++++..+|.
T Consensus 125 a~~~I~~~~~~L~Lp~-~v~e~A~~iyk~~~~~~~~rgrs~~~i~AAclYiACR~~~~prtl---~eI~~~~~v~~k~i~ 200 (310)
T PRK00423 125 ALSELDRIASQLGLPR-SVREEAAVIYRKAVEKGLIRGRSIEGVVAAALYAACRRCKVPRTL---DEIAEVSRVSRKEIG 200 (310)
T ss_pred HHHHHHHHHHHcCCCH-HHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHcCCCcCH---HHHHHHhCCCHHHHH
Confidence 3446777777787764 788888888888776566678899999999999999998874322 123455689999999
Q ss_pred HHHHHHHHHHhh
Q 011212 150 EVSNQMLELYEQ 161 (491)
Q Consensus 150 eI~~eILeLY~~ 161 (491)
.++..|+..+..
T Consensus 201 ~~~~~l~k~L~~ 212 (310)
T PRK00423 201 RCYRFLLRELNL 212 (310)
T ss_pred HHHHHHHHHhCC
Confidence 999988887743
No 22
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=92.55 E-value=0.24 Score=51.43 Aligned_cols=56 Identities=18% Similarity=0.317 Sum_probs=43.6
Q ss_pred HHHHHHHHhc--ccHHHHHHHHHHHHHhhcCCccccccChHHHHHHHHHHHHHHhCcCC
Q 011212 73 PLVEAIKKFK--VAQNALAQVAWNFVNDGLRTSLCLQFKPHHIAAGAIFLAAKFLKVKL 129 (491)
Q Consensus 73 fLv~yLk~L~--~~~~~L~qlAw~fLnDSl~T~LcLqYpPsvIAaAAIyLA~kllgi~L 129 (491)
+|..++..|+ +.. .+..+|..|+...+.......|.|..||++|||||+++-...+
T Consensus 62 ~i~~~~~~lkp~Lpq-~viaTAivyf~RFy~~~Sv~~~~p~~Ia~tclfLA~KvEE~~~ 119 (305)
T TIGR00569 62 RLLDFCSAFKPTMPT-SVVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEEFNV 119 (305)
T ss_pred HHHHHHHHhcCCCCc-hHHHHHHHHHhHHhccCchhhcCHHHHHHHHHHHHHhccccCc
Confidence 3445555566 543 5677888899888877777899999999999999999877643
No 23
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=92.18 E-value=0.16 Score=55.88 Aligned_cols=78 Identities=14% Similarity=0.117 Sum_probs=64.8
Q ss_pred HHHHHHHHHHcCCc---ccccCcHHHHHHHHHHhcccH--HHHHHHHHHHHHhhcCCccccccChHHHHHHHHHHHHHHh
Q 011212 51 LLGERVVLATLGFD---LNVHHPYKPLVEAIKKFKVAQ--NALAQVAWNFVNDGLRTSLCLQFKPHHIAAGAIFLAAKFL 125 (491)
Q Consensus 51 L~mErlILrtLgFD---L~V~hPhkfLv~yLk~L~~~~--~~L~qlAw~fLnDSl~T~LcLqYpPsvIAaAAIyLA~kll 125 (491)
=.+=+.|...|.-+ +-...|.-|+.+|+..|.... +.++..|..+++.+.+..+...-.|..|+-|||++|+..+
T Consensus 144 G~~~l~l~~~L~i~en~~plvDpsL~i~Rfa~~L~~g~~~~~Vv~~a~~L~~rMkrdwm~tGRRPsglcGAaLliAar~h 223 (521)
T KOG1598|consen 144 GSNFLEVTDSLSIGENVSPLVDPSLYIVRFSCRLLFGDKTEDVAKTATRLAQRMKRDWMQTGRRPSGLCGAALLIAARMH 223 (521)
T ss_pred hHHHHHHHHHhccccccccccCcceeeechhHhhhcCCchHHHHHHHHHHHHHHHHHHHHhCCCccchhHHHHHHHHHHc
Confidence 33555677778877 666789999999999875432 4689999999999888888999999999999999999999
Q ss_pred CcC
Q 011212 126 KVK 128 (491)
Q Consensus 126 gi~ 128 (491)
++.
T Consensus 224 ~~~ 226 (521)
T KOG1598|consen 224 GFR 226 (521)
T ss_pred Ccc
Confidence 875
No 24
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=87.92 E-value=0.79 Score=48.09 Aligned_cols=57 Identities=23% Similarity=0.203 Sum_probs=42.8
Q ss_pred HHHHHHHHHhcccHHHHHHHHHHHHHhhcCCccccccChHHHHHHHHHHHHHHhCcCC
Q 011212 72 KPLVEAIKKFKVAQNALAQVAWNFVNDGLRTSLCLQFKPHHIAAGAIFLAAKFLKVKL 129 (491)
Q Consensus 72 kfLv~yLk~L~~~~~~L~qlAw~fLnDSl~T~LcLqYpPsvIAaAAIyLA~kllgi~L 129 (491)
.||..+...|++.... ..+|..|....++-..+-.|+|.+||++|||||.+.-....
T Consensus 44 ~fI~elg~~L~~~~~t-i~tA~~~~hRFy~~~s~~~~~~~~vA~sclfLAgKvEetp~ 100 (323)
T KOG0834|consen 44 KFIQELGVRLKMPQKT-IATAIVIFHRFYMFHSFKKFDPYTVAASCLFLAGKVEETPR 100 (323)
T ss_pred HHHHHHHHHcCCCccc-hhhhhhhhhhhhhhcccccCcHHHHHHHHHHHHhhcccCcc
Confidence 4667777777765433 35677777777766667799999999999999999876543
No 25
>cd00043 CYCLIN Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain.
Probab=87.53 E-value=0.15 Score=40.10 Aligned_cols=37 Identities=43% Similarity=0.540 Sum_probs=28.3
Q ss_pred CEEeeccCCCCCChHHHHHHHHHhhhccCCCChhhhccchHHHHHHHHHHHHHHHHHH
Q 011212 1 MFLAGKVEETPRPLKDVIIVSYEIIHKKDSTAPQRIRQQKEVYEQQKELILLGERVVL 58 (491)
Q Consensus 1 LFLAsKVEEtprkLrDVI~Vs~~L~hkkdP~~~~~I~~~se~Yeq~Ke~IL~mErlIL 58 (491)
||||||+++.+..+++++.++... ..++|..+|..||
T Consensus 52 l~lA~k~~~~~~~~~~~~~~~~~~---------------------~~~~i~~~e~~il 88 (88)
T cd00043 52 LYLAAKVEEIPPWLKDLVHVTGYA---------------------TEEEILRMEKLLL 88 (88)
T ss_pred HHHHHHHcCCCCCHHHHhHHhCCC---------------------CHHHHHHHHHHhC
Confidence 589999999999999998765310 2467888888764
No 26
>smart00385 CYCLIN domain present in cyclins, TFIIB and Retinoblastoma. A helical domain present in cyclins and TFIIB (twice) and Retinoblastoma (once). A protein recognition domain functioning in cell-cycle and transcription control.
Probab=82.75 E-value=0.35 Score=37.64 Aligned_cols=38 Identities=32% Similarity=0.445 Sum_probs=27.7
Q ss_pred CEEeeccCCCCCChHHHHHHHHHhhhccCCCChhhhccchHHHHHHHHHHHHHHHHHHH
Q 011212 1 MFLAGKVEETPRPLKDVIIVSYEIIHKKDSTAPQRIRQQKEVYEQQKELILLGERVVLA 59 (491)
Q Consensus 1 LFLAsKVEEtprkLrDVI~Vs~~L~hkkdP~~~~~I~~~se~Yeq~Ke~IL~mErlILr 59 (491)
||||||++|.++...+++.++.. | ..++|..+|+.||.
T Consensus 46 l~lA~k~~~~~~~~~~~~~~~~~-------------------~--~~~~i~~~~~~il~ 83 (83)
T smart00385 46 LYLAAKTEEIPPWTKELVHYTGY-------------------F--TEEEILRMEKLLLE 83 (83)
T ss_pred HHHHHHHhcCCCCchhHhHhhCC-------------------C--CHHHHHHHHHHHhC
Confidence 58899999988888887665321 1 24679999998873
No 27
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]
Probab=82.65 E-value=2.1 Score=43.32 Aligned_cols=73 Identities=15% Similarity=0.237 Sum_probs=49.5
Q ss_pred HHHHHHHHHHHhhcCCccccccChHHHHHHHHHHHHHHhCcCC-------------CCCCcccchhccCCCHHHHHHHHH
Q 011212 87 ALAQVAWNFVNDGLRTSLCLQFKPHHIAAGAIFLAAKFLKVKL-------------PSDGDKVWWQEFDVTPRQLEEVSN 153 (491)
Q Consensus 87 ~L~qlAw~fLnDSl~T~LcLqYpPsvIAaAAIyLA~kllgi~L-------------Ps~~~~~W~e~Lgvt~eqL~eI~~ 153 (491)
.+..+|..++...+.-.-.-.|.|..+|..|||||++.-.+.+ +...+ .|.+.+.+....|.++--
T Consensus 60 ~ViATAivY~rRfy~r~S~k~~~p~lla~TClyLAcKvEE~~i~~~r~l~~~a~~L~~~f~-~~~e~~~~~~~~I~e~Ef 138 (264)
T KOG0794|consen 60 RVIATAIVYFRRFYLRKSLKEIEPRLLAPTCLYLACKVEECPIVHIRLLVNEAKVLKTRFS-YWPEKFPYERKDILEMEF 138 (264)
T ss_pred HHHHHHHHHHHHHHHHHhhhccCHHHHHHHHHHHHhhhhhcchHHHHHHHHHHHHHhhhcc-cchhhcCCCcCcchhhhh
Confidence 5666777777776643446689999999999999999866531 21111 477777777777766666
Q ss_pred HHHHHHh
Q 011212 154 QMLELYE 160 (491)
Q Consensus 154 eILeLY~ 160 (491)
.+++.+.
T Consensus 139 ~llE~Ld 145 (264)
T KOG0794|consen 139 YLLEALD 145 (264)
T ss_pred hHHhhhc
Confidence 6665543
No 28
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=82.60 E-value=6.1 Score=40.82 Aligned_cols=100 Identities=11% Similarity=0.132 Sum_probs=65.2
Q ss_pred HHHHHHHcCCccccc--------CcHHHHHHHHHHhcccHHHHHHHHHHHHHhhcCCccccccChHHHHHHHHHHHHHHh
Q 011212 54 ERVVLATLGFDLNVH--------HPYKPLVEAIKKFKVAQNALAQVAWNFVNDGLRTSLCLQFKPHHIAAGAIFLAAKFL 125 (491)
Q Consensus 54 ErlILrtLgFDL~V~--------hPhkfLv~yLk~L~~~~~~L~qlAw~fLnDSl~T~LcLqYpPsvIAaAAIyLA~kll 125 (491)
+..-|+...+-..+. +....|..++..|++.. .+...|..+.-..+-..+.-.-....+++||||+|+...
T Consensus 76 ~~~rlr~~~~~~~v~~~~ernl~~a~~~l~~~~~~l~LP~-~v~e~A~~iyr~a~~~~l~rGRsie~v~AA~iY~acR~~ 154 (285)
T COG1405 76 KMYRLRKWQIRIRVSSAKERNLITALEELERIASALGLPE-SVRETAARIYRKAVDKGLLRGRSIESVAAACIYAACRIN 154 (285)
T ss_pred HHHHHHHHHhccccccchhhHHHHHHHHHHHHHHHhCCCc-hHHHHHHHHHHHHhhcCCCcCCcHHHHHHHHHHHHHHHc
Confidence 445556555555555 33445666666666653 577777777777666667777789999999999999998
Q ss_pred CcCCCCCCcccchhccCCCHHHHHHHHHHHHH
Q 011212 126 KVKLPSDGDKVWWQEFDVTPRQLEEVSNQMLE 157 (491)
Q Consensus 126 gi~LPs~~~~~W~e~Lgvt~eqL~eI~~eILe 157 (491)
+..... ..-...++++...|..+...|..
T Consensus 155 ~~prtl---~eIa~a~~V~~kei~rtyr~~~~ 183 (285)
T COG1405 155 GVPRTL---DEIAKALGVSKKEIGRTYRLLVR 183 (285)
T ss_pred CCCccH---HHHHHHHCCCHHHHHHHHHHHHH
Confidence 864322 11234446777777666664443
No 29
>KOG0656 consensus G1/S-specific cyclin D [Cell cycle control, cell division, chromosome partitioning]
Probab=81.82 E-value=5.6 Score=42.11 Aligned_cols=83 Identities=17% Similarity=0.179 Sum_probs=56.8
Q ss_pred HHHHHHHHHHHHHcCCccccc---CcH------HHHHHHHHHhcccHHHHHHHHHHHHHhhcCCccccccC---hHHHHH
Q 011212 48 ELILLGERVVLATLGFDLNVH---HPY------KPLVEAIKKFKVAQNALAQVAWNFVNDGLRTSLCLQFK---PHHIAA 115 (491)
Q Consensus 48 e~IL~mErlILrtLgFDL~V~---hPh------kfLv~yLk~L~~~~~~L~qlAw~fLnDSl~T~LcLqYp---PsvIAa 115 (491)
..++..|..-.-.+.+.+.+. +|+ .+|.+.+...+.. ..++-+|.+++...+...-+.++. -..||+
T Consensus 50 ~~ll~kEe~~~p~~~~~~~~~~~~~~~~R~~A~~WIl~V~~~~~~~-~~~~~LA~NYlDRFls~~~l~k~k~W~lQLlAv 128 (335)
T KOG0656|consen 50 ANLLEKEEQHNPSLDYFLCVQKLILSSMRKQALDWILKVCEEYNFE-PLVFLLAMNYLDRFLSSQKLPKDKPWMLQLLAV 128 (335)
T ss_pred HHHHHHHHHhCCCCchhhhcccccccHHHHHHHHHHHHHHHHhCCc-hHHHHHHHHHHHHhhcccccCCCchHHHHHHHH
Confidence 345556665555555444432 343 4555666655554 468889999998877655566777 788999
Q ss_pred HHHHHHHHHhCcCCCC
Q 011212 116 GAIFLAAKFLKVKLPS 131 (491)
Q Consensus 116 AAIyLA~kllgi~LPs 131 (491)
||+.||+++-...+|.
T Consensus 129 aCLsLAsKmeE~~vPl 144 (335)
T KOG0656|consen 129 ACLSLASKMEETDVPL 144 (335)
T ss_pred HHHHHHHhhcCcCCch
Confidence 9999999999887664
No 30
>KOG2496 consensus Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, cyclin H subunit [Cell cycle control, cell division, chromosome partitioning; Transcription; Replication, recombination and repair]
Probab=76.21 E-value=4.2 Score=42.51 Aligned_cols=55 Identities=25% Similarity=0.373 Sum_probs=44.8
Q ss_pred HHHHHHHHhccc-HHHHHHHHHHHHHhhcCCccccccChHHHHHHHHHHHHHHhCc
Q 011212 73 PLVEAIKKFKVA-QNALAQVAWNFVNDGLRTSLCLQFKPHHIAAGAIFLAAKFLKV 127 (491)
Q Consensus 73 fLv~yLk~L~~~-~~~L~qlAw~fLnDSl~T~LcLqYpPsvIAaAAIyLA~kllgi 127 (491)
.|++|+.++.-. ...+.-+|..|.-..++......|.|..|.++|+|+|++.-..
T Consensus 62 ~l~~f~~k~~p~lp~~Vv~TA~~fFkRffL~nsvme~~pk~I~~tc~flA~Kieef 117 (325)
T KOG2496|consen 62 SLVNFYSKFKPNLPTSVVSTAIEFFKRFFLENSVMEYSPKIIMATCFFLACKIEEF 117 (325)
T ss_pred HHHHHHHHhcCCCchHHHHHHHHHHHHHHHhcchhhcChHHHHHHHHHHHhhhHhh
Confidence 477777777532 1367888999999999988899999999999999999997543
No 31
>COG5333 CCL1 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, cyclin H subunit [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]
Probab=74.31 E-value=4 Score=42.53 Aligned_cols=90 Identities=13% Similarity=0.234 Sum_probs=59.2
Q ss_pred HHHHHHHHHhcccHHHHHHHHHHHHHhhcCCccccccChHHHHHHHHHHHHHHhCc--CCCCCC---cccchhccCCCHH
Q 011212 72 KPLVEAIKKFKVAQNALAQVAWNFVNDGLRTSLCLQFKPHHIAAGAIFLAAKFLKV--KLPSDG---DKVWWQEFDVTPR 146 (491)
Q Consensus 72 kfLv~yLk~L~~~~~~L~qlAw~fLnDSl~T~LcLqYpPsvIAaAAIyLA~kllgi--~LPs~~---~~~W~e~Lgvt~e 146 (491)
.++..++..|.+.. .+..+|..|+...++-.-.-.+++..||.+|||||++.-.. .+-... ...|.+..--+.+
T Consensus 50 k~i~~l~~~L~lp~-~~laTAi~~f~Rf~Lk~sv~e~~~~~vv~tcv~LA~K~ed~~~~I~i~~~~~~~~~se~~~~sr~ 128 (297)
T COG5333 50 KLIMDLCTRLNLPQ-TVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDTPRDISIESFEARDLWSEEPKSSRE 128 (297)
T ss_pred HHHHHHHHhcCCCc-chHHHHHHHHHHHHhhcccccccHHHHHHhheeeeeecccccchhhHHHHHhhccccccccccHH
Confidence 45666666666653 46677887887776555567999999999999999998773 221100 1236555556666
Q ss_pred HHHHHHHHHHHHHhhC
Q 011212 147 QLEEVSNQMLELYEQN 162 (491)
Q Consensus 147 qL~eI~~eILeLY~~~ 162 (491)
.|-.+-..|++.....
T Consensus 129 ~Il~~E~~lLEaL~fd 144 (297)
T COG5333 129 RILEYEFELLEALDFD 144 (297)
T ss_pred HHHHHHHHHHHHcccc
Confidence 6666666666665543
No 32
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=69.82 E-value=17 Score=38.05 Aligned_cols=88 Identities=14% Similarity=0.146 Sum_probs=51.3
Q ss_pred cHHHHHHHHHHhcccHHHHHHHHHHHHHhhcCCccccccChHHHHHHHHHHHHHHhCcCCCCCCcccchhccCCCHHHHH
Q 011212 70 PYKPLVEAIKKFKVAQNALAQVAWNFVNDGLRTSLCLQFKPHHIAAGAIFLAAKFLKVKLPSDGDKVWWQEFDVTPRQLE 149 (491)
Q Consensus 70 PhkfLv~yLk~L~~~~~~L~qlAw~fLnDSl~T~LcLqYpPsvIAaAAIyLA~kllgi~LPs~~~~~W~e~Lgvt~eqL~ 149 (491)
.+.-+..++..+.+.. .|...|..+.....-....=.-.-..||+||||+|++-.++ |... +.-....+++..+|-
T Consensus 107 a~~~I~~m~d~~~Lp~-~I~d~A~~ifk~v~~~k~lrGks~eai~AAclyiACRq~~~--pRT~-kEI~~~anv~kKEIg 182 (308)
T KOG1597|consen 107 AFKEITAMCDRLSLPA-TIKDRANEIFKLVEDSKLLRGKSVEALAAACLYIACRQEDV--PRTF-KEISAVANVSKKEIG 182 (308)
T ss_pred HHHHHHHHHHHhCCch-HHHHHHHHHHHHHHHhhhhcCccHHHHHHHHHHHHHHhcCC--CchH-HHHHHHHcCCHHHHH
Confidence 3445555666666542 34444444443333111222446678999999999988765 3210 111122278999999
Q ss_pred HHHHHHHHHHhh
Q 011212 150 EVSNQMLELYEQ 161 (491)
Q Consensus 150 eI~~eILeLY~~ 161 (491)
.|++.|++-+..
T Consensus 183 r~~K~i~~~l~~ 194 (308)
T KOG1597|consen 183 RCVKLIGEALET 194 (308)
T ss_pred HHHHHHHHHHhc
Confidence 999888887543
No 33
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=67.68 E-value=27 Score=37.14 Aligned_cols=72 Identities=13% Similarity=0.032 Sum_probs=44.5
Q ss_pred HHHHHHhcccHHHHHHHHHHHHHhhcCCccccccChHHHHHHHHHHHHHHhCcCCCCCCcccchhccCCCHHHHHHHHHH
Q 011212 75 VEAIKKFKVAQNALAQVAWNFVNDGLRTSLCLQFKPHHIAAGAIFLAAKFLKVKLPSDGDKVWWQEFDVTPRQLEEVSNQ 154 (491)
Q Consensus 75 v~yLk~L~~~~~~L~qlAw~fLnDSl~T~LcLqYpPsvIAaAAIyLA~kllgi~LPs~~~~~W~e~Lgvt~eqL~eI~~e 154 (491)
...+-.|.+.+ ....++..++...+...-++.|.-.+||+|||.||.++-... ....+|..+...
T Consensus 31 qea~ILL~L~q-~a~atgqVLFqRf~~~ks~v~~~~e~vv~ACv~LASKiEE~P--------------rr~rdVinVFh~ 95 (367)
T KOG0835|consen 31 QEAGILLNLPQ-VAMATGQVLFQRFCYSKSFVRHDFEIVVMACVLLASKIEEEP--------------RRIRDVINVFHY 95 (367)
T ss_pred HhhhHhhcCcH-HHHHHHHHHHHHHHhccccccccHHHHHHHHHHHHhhhcccc--------------ccHhHHHHHHHH
Confidence 33344444443 233445555556566666788888999999999999886531 234455555555
Q ss_pred HHHHHhh
Q 011212 155 MLELYEQ 161 (491)
Q Consensus 155 ILeLY~~ 161 (491)
|-.+|..
T Consensus 96 L~~r~~~ 102 (367)
T KOG0835|consen 96 LEQRRES 102 (367)
T ss_pred HHHHHhc
Confidence 5555554
No 34
>PF08613 Cyclin: Cyclin; InterPro: IPR013922 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. This entry includes cyclin PHO80 and other cyclins that partner with the cyclin-dependent kinase (CDK) PHO85. The PHO80/PHO85 cyclin-cdk complex is used for a regulatory process other than cell-cycle control []. This entry also includes other PHO80-like cyclins that are involved in the cell-cycle control. They belong to the P/U family and interact preferentially with CDKA1 [].; GO: 0019901 protein kinase binding, 0000079 regulation of cyclin-dependent protein kinase activity; PDB: 2PK9_D 2PMI_D.
Probab=64.23 E-value=31 Score=31.72 Aligned_cols=87 Identities=21% Similarity=0.280 Sum_probs=55.6
Q ss_pred HHHHHHHHHHhcccHHHHHHHHHHHHHhhcC----Ccccc-ccChHHHHHHHHHHHHHHhCcCCCCCCcccchhccCCCH
Q 011212 71 YKPLVEAIKKFKVAQNALAQVAWNFVNDGLR----TSLCL-QFKPHHIAAGAIFLAAKFLKVKLPSDGDKVWWQEFDVTP 145 (491)
Q Consensus 71 hkfLv~yLk~L~~~~~~L~qlAw~fLnDSl~----T~LcL-qYpPsvIAaAAIyLA~kllgi~LPs~~~~~W~e~Lgvt~ 145 (491)
..|+.++++...... .+.-+|..++..... ....+ .+.++-+-++||.+|.+++.-.--. ...|....|++.
T Consensus 55 ~~fl~ri~~~~~~s~-~~~i~aliYl~Rl~~~~~~~~~~~~~~~~~Rl~l~alilA~K~~~D~~~~--n~~~a~v~gis~ 131 (149)
T PF08613_consen 55 RDFLSRILKYTQCSP-ECLILALIYLDRLRQRSRKPNIPLNSSNIHRLFLTALILASKFLDDNTYS--NKSWAKVGGISL 131 (149)
T ss_dssp HHHHHHHHHHTT--H-HHHHHHHHHHHHHHH--H-TT---STTTHHHHHHHHHHHHHHHH-SS-----HHHHHHHHTS-H
T ss_pred HHHHHHHHHHcCCCh-HHHHHHHHHHHHHHHhhcccccccccchhHHHHHHHHHHHHhhccccccc--HHHHHhhcCCCH
Confidence 456666666655543 555566666655443 22222 4668889999999999998532111 246888889999
Q ss_pred HHHHHHHHHHHHHHh
Q 011212 146 RQLEEVSNQMLELYE 160 (491)
Q Consensus 146 eqL~eI~~eILeLY~ 160 (491)
.+|...-.++|.+..
T Consensus 132 ~eln~lE~~fL~~l~ 146 (149)
T PF08613_consen 132 KELNELEREFLKLLD 146 (149)
T ss_dssp HHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHHHCC
Confidence 999999999888764
No 35
>PF01857 RB_B: Retinoblastoma-associated protein B domain; InterPro: IPR002719 Retinoblastoma-like and retinoblastoma-associated proteins may have a function in cell cycle regulation. They form a complex with adenovirus E1A and SV40 large T antigen, and may bind and modulate the function of certain cellular proteins with which T and E1A compete for pocket binding. The proteins may act as tumor suppressors, and are potent inhibitors of E2F-mediated trans-activation. This domain has the cyclin fold []. The crystal structure of the Rb pocket bound to a nine-residue E7 peptide containing the LxCxE motif, shared by other Rb-binding viral and cellular proteins, shows that the LxCxE peptide binds a highly conserved groove on the B-box portion of the pocket; the A-box portion (see IPR002720 from INTERPRO) appears to be required for the stable folding of the B box. Also highly conserved is the extensive A-B interface, suggesting that it may be an additional protein-binding site. The A and B boxes each contain the cyclin-fold structural motif, with the LxCxE-binding site on the B-box cyclin fold being similar to a Cdk2-binding site of cyclin A and to a TBP-binding site of TFIIB []. The A and B boxes are found at the C-terminal end of the protein; the B-box is on C-terminal side of the A-box.; GO: 0051726 regulation of cell cycle, 0005634 nucleus; PDB: 1GUX_B 3POM_A 1GH6_B 1N4M_A 1O9K_H 4ELL_B 2R7G_C 4ELJ_A.
Probab=54.07 E-value=62 Score=29.97 Aligned_cols=54 Identities=20% Similarity=0.278 Sum_probs=40.8
Q ss_pred HHHHHHHHhcccHHHHHHHHHHHHHhhc--CCccccccChHHHHHHHHHHHHHHhCc
Q 011212 73 PLVEAIKKFKVAQNALAQVAWNFVNDGL--RTSLCLQFKPHHIAAGAIFLAAKFLKV 127 (491)
Q Consensus 73 fLv~yLk~L~~~~~~L~qlAw~fLnDSl--~T~LcLqYpPsvIAaAAIyLA~kllgi 127 (491)
-|..+|..|++.. .+...+|.++.-++ .|.|+.----.+|-+.|||..+++.+.
T Consensus 17 Rl~~LC~~L~l~~-~~~~~iwt~fe~~l~~~t~L~~dRHLDQiilCaiY~i~Kv~~~ 72 (135)
T PF01857_consen 17 RLQDLCERLDLSS-DLREKIWTCFEHSLTHHTELMKDRHLDQIILCAIYGICKVSKE 72 (135)
T ss_dssp HHHHHHHHHTTST-THHHHHHHHHHHHHHHSGGGGTTS-HHHHHHHHHHHHHHHTT-
T ss_pred HHHHHHHHcCCcH-HHHHHHHHHHHHHHHhhHHHHhcchHHHHHHHHHHHHHHhhcC
Confidence 3555666666653 57788899988877 567777778899999999999998874
No 36
>KOG0653 consensus Cyclin B and related kinase-activating proteins [Cell cycle control, cell division, chromosome partitioning]
Probab=40.48 E-value=83 Score=33.74 Aligned_cols=91 Identities=19% Similarity=0.191 Sum_probs=53.4
Q ss_pred HhcccHHHHHHHHHHHHHhhcCCccccccChHHHHHHHHH-HHHHHhCcCCCCCCcccchhccCCCHHHHHHHHHHHHHH
Q 011212 80 KFKVAQNALAQVAWNFVNDGLRTSLCLQFKPHHIAAGAIF-LAAKFLKVKLPSDGDKVWWQEFDVTPRQLEEVSNQMLEL 158 (491)
Q Consensus 80 ~L~~~~~~L~qlAw~fLnDSl~T~LcLqYpPsvIAaAAIy-LA~kllgi~LPs~~~~~W~e~Lgvt~eqL~eI~~eILeL 158 (491)
.|++.. +...+|.+++...+....+-.-.=..++++|++ +|+++-.+.+|......--..-.++.++|...-..|+..
T Consensus 171 ~F~L~~-ETL~LaVnliDRfL~~~~v~~~~lqLvgvsalf~IA~K~EE~~~P~v~dlv~isd~~~s~~~il~mE~~il~~ 249 (391)
T KOG0653|consen 171 KFGLSP-ETLYLAVNLIDRFLSKVKVPLKKLQLVGVSALLSIACKYEEISLPSVEDLVLITDGAYSREEILRMEKYILNV 249 (391)
T ss_pred hcCcCH-HHHHHHHHHHHHHHHHhcccHHHhhHHhHHHHHHHHHhhhhccCCccceeEeeeCCccchHHHHHHHHHHHhc
Confidence 344443 567889999844332212222333456777866 999996665664211000011147899999998889888
Q ss_pred HhhCCCCCCCCCc
Q 011212 159 YEQNRVPQSQGSE 171 (491)
Q Consensus 159 Y~~~r~~~~~~~~ 171 (491)
+...-.-+.+..-
T Consensus 250 L~f~l~~p~~~~F 262 (391)
T KOG0653|consen 250 LEFDLSVPTPLSF 262 (391)
T ss_pred cCeeecCCchHHH
Confidence 7776665544443
No 37
>COG4009 Uncharacterized protein conserved in archaea [Function unknown]
Probab=37.29 E-value=23 Score=30.56 Aligned_cols=48 Identities=31% Similarity=0.349 Sum_probs=27.0
Q ss_pred CHHHHHHHHHHhhhhcCCCc----------cccCCCCc---chhhhhhhcc--ccccchhhhH
Q 011212 330 DEDKVKAIREKRRKSRGEPT----------RKKDFMDE---DDLIERELED--IEIPVDDEKM 377 (491)
Q Consensus 330 ~~dkvka~~ek~~k~~g~~~----------~k~~~~d~---ddl~erele~--vela~e~~k~ 377 (491)
|--++||+|+|+.=+..+-. .-+=+.++ .+=++||||+ +++--..+++
T Consensus 21 ~Fv~~kA~l~k~~L~dDde~aIfnI~gT~Sy~V~Fl~~~~s~eev~~ele~mga~in~ds~~~ 83 (88)
T COG4009 21 DFVRLKAHLAKVDLNDDDELAIFNIEGTSSYYVVFLEEVESEEEVERELEDMGAEINRDSKAS 83 (88)
T ss_pred HHHHHHHHhcccccCCCCcEEEEEecCceeEEEEEEeccCCHHHHHHHHHHhCchhcccHHHH
Confidence 34478999999654433211 11212222 2457899998 6666555544
No 38
>KOG0655 consensus G1/S-specific cyclin E [Cell cycle control, cell division, chromosome partitioning]
Probab=36.49 E-value=1.3e+02 Score=32.47 Aligned_cols=111 Identities=15% Similarity=0.128 Sum_probs=59.3
Q ss_pred HHHHHHHHHHHcCCcccccCcH--------HHHHHHHHHhcccHHHHHHHHHHHHHhhcCCcc-ccccChHHHHHHHHHH
Q 011212 50 ILLGERVVLATLGFDLNVHHPY--------KPLVEAIKKFKVAQNALAQVAWNFVNDGLRTSL-CLQFKPHHIAAGAIFL 120 (491)
Q Consensus 50 IL~mErlILrtLgFDL~V~hPh--------kfLv~yLk~L~~~~~~L~qlAw~fLnDSl~T~L-cLqYpPsvIAaAAIyL 120 (491)
++.-|..-|+..-|--+-+.-- .+|...|...++.. ..+.+|..|+...+.|.. |.+--=..|..+|+|+
T Consensus 120 M~kkee~~l~~~~~l~qHpdlqp~mRaILlDWlmEVCEvykLHR-ETFyLAvDy~DRyl~t~~~v~kt~lQLIGitsLFI 198 (408)
T KOG0655|consen 120 MLKKEERYLRDKHFLEQHPDLQPQMRAILLDWLMEVCEVYKLHR-ETFYLAVDYFDRYLETQVEVSKTNLQLIGITSLFI 198 (408)
T ss_pred HHccchhhhhhhHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHhh-hHHHHHHHHHHHHHHHHHHhhhhhHHHhhHHHHHH
Confidence 4444555555555544433221 23334444444332 455677777766555543 4444556799999999
Q ss_pred HHHHhCcCCCCCCcccchhccCCCHHHHHHHHHHHHHHHhh
Q 011212 121 AAKFLKVKLPSDGDKVWWQEFDVTPRQLEEVSNQMLELYEQ 161 (491)
Q Consensus 121 A~kllgi~LPs~~~~~W~e~Lgvt~eqL~eI~~eILeLY~~ 161 (491)
|+++-.+-.|.-.+-..-..=-++.++|...-.-|++++..
T Consensus 199 AAK~EEIYpPKl~eFAyvTDgAcs~ddIltmE~iilkal~W 239 (408)
T KOG0655|consen 199 AAKLEEIYPPKLIEFAYVTDGACSEDDILTMELIILKALKW 239 (408)
T ss_pred HHHHhhccCccccceeeeccCccchHHHHHHHHHHHHHhcc
Confidence 99998886553110001111135666666655555555443
No 39
>COG5024 Cyclin [Cell division and chromosome partitioning]
Probab=34.24 E-value=47 Score=36.57 Aligned_cols=80 Identities=23% Similarity=0.214 Sum_probs=56.6
Q ss_pred HHHHHHHHHHHhhcCCccccccChHHHHHHHHHHHHHHhCcCCCCCCcccchhccCCCHHHHHHHHHHHHHHHhhCCCCC
Q 011212 87 ALAQVAWNFVNDGLRTSLCLQFKPHHIAAGAIFLAAKFLKVKLPSDGDKVWWQEFDVTPRQLEEVSNQMLELYEQNRVPQ 166 (491)
Q Consensus 87 ~L~qlAw~fLnDSl~T~LcLqYpPsvIAaAAIyLA~kllgi~LPs~~~~~W~e~Lgvt~eqL~eI~~eILeLY~~~r~~~ 166 (491)
...-+|.+|++..+-...+..-.=..+|++|+|+|+++-.+..|....-.-...-.++.++|...-..||..+...-.-|
T Consensus 232 eTL~lainiiDrfLs~~~v~l~k~QLvg~s~LfIa~K~EE~~~p~i~~l~~~t~g~~t~~~i~~aE~~ml~~l~f~is~P 311 (440)
T COG5024 232 ETLFLAINIIDRFLSSRVVSLEKYQLVGISALFIASKYEEVNCPSIKDLVYATDGAFTRDDIIRAERYMLEVLDFNISWP 311 (440)
T ss_pred hHHHHHHHHHHHHhccCcccHHHHHHHHHHHHHHHHhHhHhcCHHHHHHHHHHcccccHHHHHHHHHHHhhhcccccCCC
Confidence 45567888887777667777777789999999999999887666411001111225789999999999998877644433
No 40
>COG5552 Uncharacterized conserved protein [Function unknown]
Probab=30.83 E-value=75 Score=27.21 Aligned_cols=55 Identities=16% Similarity=0.329 Sum_probs=43.9
Q ss_pred ChHHHHHHHHHHHHHHhCcCCCCCCcccchhccCCCHHHHHHHHHHHHHHHhhCCCCC
Q 011212 109 KPHHIAAGAIFLAAKFLKVKLPSDGDKVWWQEFDVTPRQLEEVSNQMLELYEQNRVPQ 166 (491)
Q Consensus 109 pPsvIAaAAIyLA~kllgi~LPs~~~~~W~e~Lgvt~eqL~eI~~eILeLY~~~r~~~ 166 (491)
.|..|+.|++.+..++.|+.-|+. .--..|..-...|-.++.++|+.+...+.|.
T Consensus 16 T~~EvrdAAlQfVRKlSGtT~PS~---~n~~AFe~AV~~iaA~areLLDaLet~q~Pr 70 (88)
T COG5552 16 TPVEVRDAALQFVRKLSGTTHPSA---ANAEAFEAAVAEIAATARELLDALETRQQPR 70 (88)
T ss_pred CcHHHHHHHHHHHHHhcCCCCcch---hhHHHHHHHHHHHHHHHHHHHHhccccCCCC
Confidence 466799999999999999987763 3345677778899999999999888766653
No 41
>PF07713 DUF1604: Protein of unknown function (DUF1604); InterPro: IPR011666 This domain is found at the N terminus of several eukaryotic RNA processing proteins (e.g Q8N3B7 from SWISSPROT).
Probab=30.33 E-value=22 Score=30.91 Aligned_cols=17 Identities=53% Similarity=0.776 Sum_probs=14.2
Q ss_pred CccccCCCCcchhhhhh
Q 011212 348 PTRKKDFMDEDDLIERE 364 (491)
Q Consensus 348 ~~~k~~~~d~ddl~ere 364 (491)
..+--|+|||+||.|-.
T Consensus 59 ~q~~eDfMDeeD~~e~~ 75 (87)
T PF07713_consen 59 QQRPEDFMDEEDLAEFG 75 (87)
T ss_pred cCChhhccCHHHHHHhc
Confidence 45678999999999875
No 42
>PHA02690 hypothetical protein; Provisional
Probab=25.92 E-value=1e+02 Score=26.69 Aligned_cols=34 Identities=18% Similarity=0.279 Sum_probs=22.2
Q ss_pred HHHHHHHHHhcccHHHHHHHHHHHHHhhcCCcccc
Q 011212 72 KPLVEAIKKFKVAQNALAQVAWNFVNDGLRTSLCL 106 (491)
Q Consensus 72 kfLv~yLk~L~~~~~~L~qlAw~fLnDSl~T~LcL 106 (491)
.||..+...++.+. .+...+|.++.|.+.|-+.+
T Consensus 22 rYLeAIqrhlEgs~-plLR~~~RlLfDL~lTvfV~ 55 (90)
T PHA02690 22 RYLEAIQRHLEGST-PLLRQMWRLLFDLLLTVFVV 55 (90)
T ss_pred HHHHHHHHHHhcCC-HHHHHHHHHHHHHHHHHHHH
Confidence 45555555565544 56677899998888775433
No 43
>KOG4557 consensus Origin recognition complex, subunit 6 [Replication, recombination and repair]
Probab=24.12 E-value=1.2e+02 Score=30.81 Aligned_cols=73 Identities=21% Similarity=0.223 Sum_probs=51.2
Q ss_pred HHHHHHHHHHHhhcCC------ccccccChHHHHHHHHHHHHHHhCcCCCCCCcccchhccCCCHHHHHHHHHHHHHHHh
Q 011212 87 ALAQVAWNFVNDGLRT------SLCLQFKPHHIAAGAIFLAAKFLKVKLPSDGDKVWWQEFDVTPRQLEEVSNQMLELYE 160 (491)
Q Consensus 87 ~L~qlAw~fLnDSl~T------~LcLqYpPsvIAaAAIyLA~kllgi~LPs~~~~~W~e~Lgvt~eqL~eI~~eILeLY~ 160 (491)
.+...|..++.- |.. ..-+-|+-.+.++||+|+|++.+...+.-. .....-|+.+.++.-++.++-..|.
T Consensus 107 evi~~a~~vl~s-yk~~lpaT~~~~~D~SrP~ft~aA~~~ack~lKlKVdK~---kli~~sg~~~s~F~~l~kqler~~~ 182 (262)
T KOG4557|consen 107 EVIKSAQNVLSS-YKERLPATRRANADFSRPVFTAAAFYLACKKLKLKVDKL---KLIEVSGTSESEFSCLSKQLERNYK 182 (262)
T ss_pred HHHHHHHHHHHH-HHhcCchhhhcCCcccchHHHHHHHHHHHHHHHHhhhHh---hcccccCCCHHHHHHHHHHHHHHHH
Confidence 455666666643 211 245678888899999999999987654321 1233448999999999999999998
Q ss_pred hCC
Q 011212 161 QNR 163 (491)
Q Consensus 161 ~~r 163 (491)
+..
T Consensus 183 qv~ 185 (262)
T KOG4557|consen 183 QVS 185 (262)
T ss_pred Hhc
Confidence 743
Done!