Query 011310
Match_columns 489
No_of_seqs 230 out of 1361
Neff 4.1
Searched_HMMs 46136
Date Thu Mar 28 23:55:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/011310.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/011310hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0653 Cyclin B and related k 100.0 3.9E-32 8.4E-37 280.6 11.1 140 349-489 109-253 (391)
2 COG5024 Cyclin [Cell division 100.0 8.6E-31 1.9E-35 274.1 7.2 136 354-489 170-307 (440)
3 KOG0655 G1/S-specific cyclin E 100.0 2.2E-29 4.8E-34 253.9 5.5 125 365-489 113-240 (408)
4 PF00134 Cyclin_N: Cyclin, N-t 99.9 6.1E-27 1.3E-31 200.8 8.8 123 367-489 1-125 (127)
5 KOG0656 G1/S-specific cyclin D 99.9 1.1E-23 2.4E-28 214.5 9.7 128 362-489 42-176 (335)
6 KOG0654 G2/Mitotic-specific cy 99.8 9.6E-22 2.1E-26 201.9 2.4 140 350-489 87-231 (359)
7 cd00043 CYCLIN Cyclin box fold 99.5 2.8E-14 6E-19 112.1 6.6 86 396-483 1-88 (88)
8 smart00385 CYCLIN domain prese 99.4 1.1E-13 2.4E-18 107.8 5.3 82 402-484 1-83 (83)
9 TIGR00569 ccl1 cyclin ccl1. Un 99.3 4.7E-12 1E-16 128.5 7.6 94 395-489 54-153 (305)
10 KOG0834 CDK9 kinase-activating 99.0 7.7E-10 1.7E-14 113.4 6.8 96 393-489 35-145 (323)
11 COG5333 CCL1 Cdk activating ki 98.5 3.4E-07 7.3E-12 93.1 7.3 96 393-489 41-144 (297)
12 KOG0835 Cyclin L [General func 98.3 9.3E-07 2E-11 90.9 6.7 96 393-489 19-135 (367)
13 KOG0794 CDK8 kinase-activating 98.3 6.3E-07 1.4E-11 88.7 3.9 93 397-489 41-147 (264)
14 PF08613 Cyclin: Cyclin; Inte 98.2 2.5E-06 5.5E-11 77.9 7.0 89 400-489 54-148 (149)
15 KOG4164 Cyclin ik3-1/CABLES [C 97.2 9.3E-05 2E-09 78.1 0.6 132 356-488 339-477 (497)
16 KOG2496 Cdk activating kinase 97.2 0.0012 2.6E-08 68.0 7.9 87 402-489 61-153 (325)
17 PRK00423 tfb transcription ini 96.9 0.0041 8.9E-08 63.5 8.8 89 398-488 123-212 (310)
18 PF00382 TFIIB: Transcription 93.3 0.14 3E-06 41.1 4.4 63 405-468 2-64 (71)
19 KOG1674 Cyclin [General functi 92.7 0.28 6E-06 48.4 6.5 87 400-488 78-176 (218)
20 KOG1597 Transcription initiati 89.7 0.73 1.6E-05 47.9 6.1 83 403-487 110-193 (308)
21 PF02984 Cyclin_C: Cyclin, C-t 86.9 1.4 3E-05 37.0 5.2 83 401-484 4-87 (118)
22 PRK00423 tfb transcription ini 81.5 4.7 0.0001 41.5 7.3 84 401-486 220-304 (310)
23 KOG1675 Predicted cyclin [Gene 78.8 2.2 4.7E-05 44.8 3.8 76 413-488 206-284 (343)
24 KOG0834 CDK9 kinase-activating 78.8 3 6.6E-05 43.8 4.9 88 399-486 154-245 (323)
25 COG1405 SUA7 Transcription ini 77.4 9 0.0002 39.6 7.8 90 396-487 96-186 (285)
26 KOG0835 Cyclin L [General func 54.7 38 0.00083 36.2 7.0 52 411-462 152-205 (367)
27 COG1405 SUA7 Transcription ini 46.8 24 0.00052 36.5 4.1 57 399-455 193-249 (285)
28 PF01857 RB_B: Retinoblastoma- 29.5 67 0.0015 29.7 3.7 66 400-466 14-81 (135)
29 PF14376 Haem_bd: Haem-binding 28.7 86 0.0019 28.9 4.3 37 370-406 97-135 (137)
30 PF03903 Phage_T4_gp36: Phage 23.1 1.1E+02 0.0024 30.8 4.2 34 44-77 33-75 (219)
No 1
>KOG0653 consensus Cyclin B and related kinase-activating proteins [Cell cycle control, cell division, chromosome partitioning]
Probab=99.97 E-value=3.9e-32 Score=280.61 Aligned_cols=140 Identities=45% Similarity=0.768 Sum_probs=130.0
Q ss_pred CCCCC--CCCCcchhhhhHHHHHHHHHHHHhcCCCCccccccCCCCCHHHHHHHHHHHHHHhhhcccchhHHHHHHHHHH
Q 011310 349 LPGID--DDCNQLEVAEYVDEIYHYYWVMEAQNPPLENYMSSQTDITPQMRGILINWLIEVHLKFDLMPETLYLMVILLD 426 (489)
Q Consensus 349 lpdiD--D~~dpl~v~EYaeDIyqyLr~rE~~~~p~~nYL~~QpeIT~kmRaiLIDWLiEV~~kFkLs~ETLfLAVnLLD 426 (489)
+.|+| |..+|+++.||++|||.||+.+|..+.| ..|+..|+++++.||.+|+|||++||.+|+|.+|||||||+|+|
T Consensus 109 ~~dl~~~d~~~~~~~~ey~~di~~~l~~~e~~~~p-~~~~~~~~e~~~~mR~iLvdwlvevh~~F~L~~ETL~LaVnliD 187 (391)
T KOG0653|consen 109 ILDLDSEDKSDPSMIVEYVQDIFEYLRQLELEFLP-LSYDISQSEIRAKMRAILVDWLVEVHEKFGLSPETLYLAVNLID 187 (391)
T ss_pred ccCcchhcccCcHHHHHHHHHHHHHHHHHHHhhCc-hhhhcccccccHHHHHHHHHHHHHhhhhcCcCHHHHHHHHHHHH
Confidence 44555 7789999999999999999999963343 45668899999999999999999999999999999999999999
Q ss_pred HhhhccccCCCCeeEehhhhhh-hhhccCccCCCCHHHHHHHh-ccCCHHHHHHHHH-HhHhcCCC
Q 011310 427 RYLSEVKIKKNEMQLVGLTSLL-LASKYEDFWHPRVKDLISIS-ETYTRDHMLRMVC-ILNGLNLF 489 (489)
Q Consensus 427 RYLS~~~V~r~kLQLVGiTCLf-IASKyEEi~pP~L~dLV~I~-naYTkeqIL~ME~-IL~tLdWD 489 (489)
|||+...|++.+|||||++||| ||+||||.++|.+.||++++ ++||++||++||+ ||++|+|+
T Consensus 188 RfL~~~~v~~~~lqLvgvsalf~IA~K~EE~~~P~v~dlv~isd~~~s~~~il~mE~~il~~L~f~ 253 (391)
T KOG0653|consen 188 RFLSKVKVPLKKLQLVGVSALLSIACKYEEISLPSVEDLVLITDGAYSREEILRMEKYILNVLEFD 253 (391)
T ss_pred HHHHHhcccHHHhhHHhHHHHHHHHHhhhhccCCccceeEeeeCCccchHHHHHHHHHHHhccCee
Confidence 9999988999999999999976 99999999999999999999 9999999999999 99999996
No 2
>COG5024 Cyclin [Cell division and chromosome partitioning]
Probab=99.96 E-value=8.6e-31 Score=274.09 Aligned_cols=136 Identities=39% Similarity=0.687 Sum_probs=134.0
Q ss_pred CCCCcchhhhhHHHHHHHHHHHHhcCCCCccccccCCCCCHHHHHHHHHHHHHHhhhcccchhHHHHHHHHHHHhhhccc
Q 011310 354 DDCNQLEVAEYVDEIYHYYWVMEAQNPPLENYMSSQTDITPQMRGILINWLIEVHLKFDLMPETLYLMVILLDRYLSEVK 433 (489)
Q Consensus 354 D~~dpl~v~EYaeDIyqyLr~rE~~~~p~~nYL~~QpeIT~kmRaiLIDWLiEV~~kFkLs~ETLfLAVnLLDRYLS~~~ 433 (489)
+.+||+++.||+.+||.|+..+|..+.|.+.||..|+++.+.||.+|++||++||.+|+|.||||||||+|+||||+...
T Consensus 170 ~~~d~~mv~Ey~~~Ife~l~k~e~~~lp~~~yl~kq~~~~~~mR~~Lv~wlvevH~~F~llpeTL~lainiiDrfLs~~~ 249 (440)
T COG5024 170 DQEDPLMVPEYASDIFEYLLKLELIDLPNPNYLIKQSLYEWSMRSILVDWLVEVHGKFGLLPETLFLAINIIDRFLSSRV 249 (440)
T ss_pred cccCccchHHHHHHHHHHHHHHHHHhcCcHHHHhhcchhHHhHHHHHHHHHHHhcccccccchHHHHHHHHHHHHhccCc
Confidence 67899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCeeEehhhhhhhhhccCccCCCCHHHHHHHh-ccCCHHHHHHHHH-HhHhcCCC
Q 011310 434 IKKNEMQLVGLTSLLLASKYEDFWHPRVKDLISIS-ETYTRDHMLRMVC-ILNGLNLF 489 (489)
Q Consensus 434 V~r~kLQLVGiTCLfIASKyEEi~pP~L~dLV~I~-naYTkeqIL~ME~-IL~tLdWD 489 (489)
+..+++||+|++||||||||||+++|.+.+|++++ ++|+.++|+.||+ ||.+|+|+
T Consensus 250 v~l~k~QLvg~s~LfIa~K~EE~~~p~i~~l~~~t~g~~t~~~i~~aE~~ml~~l~f~ 307 (440)
T COG5024 250 VSLEKYQLVGISALFIASKYEEVNCPSIKDLVYATDGAFTRDDIIRAERYMLEVLDFN 307 (440)
T ss_pred ccHHHHHHHHHHHHHHHHhHhHhcCHHHHHHHHHHcccccHHHHHHHHHHHhhhcccc
Confidence 99999999999999999999999999999999999 9999999999999 99999995
No 3
>KOG0655 consensus G1/S-specific cyclin E [Cell cycle control, cell division, chromosome partitioning]
Probab=99.95 E-value=2.2e-29 Score=253.93 Aligned_cols=125 Identities=33% Similarity=0.611 Sum_probs=120.2
Q ss_pred HHHHHHHHHHHHhcCCCCccccccCCCCCHHHHHHHHHHHHHHhhhcccchhHHHHHHHHHHHhhhc-cccCCCCeeEeh
Q 011310 365 VDEIYHYYWVMEAQNPPLENYMSSQTDITPQMRGILINWLIEVHLKFDLMPETLYLMVILLDRYLSE-VKIKKNEMQLVG 443 (489)
Q Consensus 365 aeDIyqyLr~rE~~~~p~~nYL~~QpeIT~kmRaiLIDWLiEV~~kFkLs~ETLfLAVnLLDRYLS~-~~V~r~kLQLVG 443 (489)
..++|..|..+|..+.....|+.+||++.|+||+||+|||+|||+.++|..||||||+-||||||.. ..+.+..|||||
T Consensus 113 ~~eVW~lM~kkee~~l~~~~~l~qHpdlqp~mRaILlDWlmEVCEvykLHRETFyLAvDy~DRyl~t~~~v~kt~lQLIG 192 (408)
T KOG0655|consen 113 SKEVWLLMLKKEERYLRDKHFLEQHPDLQPQMRAILLDWLMEVCEVYKLHRETFYLAVDYFDRYLETQVEVSKTNLQLIG 192 (408)
T ss_pred HHHHHHHHHccchhhhhhhHHHhhCCCCCHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhhhHHHhh
Confidence 4799999999999988888899999999999999999999999999999999999999999999974 679999999999
Q ss_pred hhhhhhhhccCccCCCCHHHHHHHh-ccCCHHHHHHHHH-HhHhcCCC
Q 011310 444 LTSLLLASKYEDFWHPRVKDLISIS-ETYTRDHMLRMVC-ILNGLNLF 489 (489)
Q Consensus 444 iTCLfIASKyEEi~pP~L~dLV~I~-naYTkeqIL~ME~-IL~tLdWD 489 (489)
++|||||+|+||++||.+.+|+|++ ++||.++|+.||. ||+.|+|+
T Consensus 193 itsLFIAAK~EEIYpPKl~eFAyvTDgAcs~ddIltmE~iilkal~W~ 240 (408)
T KOG0655|consen 193 ITSLFIAAKLEEIYPPKLIEFAYVTDGACSEDDILTMELIILKALKWE 240 (408)
T ss_pred HHHHHHHHHHhhccCccccceeeeccCccchHHHHHHHHHHHHHhccc
Confidence 9999999999999999999999999 9999999999999 99999996
No 4
>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=99.94 E-value=6.1e-27 Score=200.80 Aligned_cols=123 Identities=41% Similarity=0.711 Sum_probs=115.8
Q ss_pred HHHHHHHHHHhcCCCCccccccCCCCCHHHHHHHHHHHHHHhhhcccchhHHHHHHHHHHHhhhccccCCCCeeEehhhh
Q 011310 367 EIYHYYWVMEAQNPPLENYMSSQTDITPQMRGILINWLIEVHLKFDLMPETLYLMVILLDRYLSEVKIKKNEMQLVGLTS 446 (489)
Q Consensus 367 DIyqyLr~rE~~~~p~~nYL~~QpeIT~kmRaiLIDWLiEV~~kFkLs~ETLfLAVnLLDRYLS~~~V~r~kLQLVGiTC 446 (489)
|||++|++.|.++.+.+.|+..|++++..+|..+++||++++..++++++|+|+|+.|||||+....+.+.+++++|++|
T Consensus 1 ~i~~~~~~~e~~~~~~~~~~~~~~~~~~~~r~~~~~~i~~~~~~~~l~~~~~~~A~~~~dr~~~~~~~~~~~~~li~~~c 80 (127)
T PF00134_consen 1 DIFRYLLEKELKYKPNPDYLEQQPEITPEMRQIIIDWIIELCQRLKLSPETLHLAIYLFDRFLSKRPVNRSKLQLIALAC 80 (127)
T ss_dssp HHHHHHHHHHHHTTCCTTHGTGTSSHHHHHHHHHHHHHHHHHHHTT-BHHHHHHHHHHHHHHHTTS-TTCCGHHHHHHHH
T ss_pred CHHHHHHHHHHHHCcCccccccChhcCHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHhhcccccchhhhhhhhH
Confidence 79999999999998889999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhccCccCCCCHHHHHHHh-ccCCHHHHHHHHH-HhHhcCCC
Q 011310 447 LLLASKYEDFWHPRVKDLISIS-ETYTRDHMLRMVC-ILNGLNLF 489 (489)
Q Consensus 447 LfIASKyEEi~pP~L~dLV~I~-naYTkeqIL~ME~-IL~tLdWD 489 (489)
|+||+|+||..+|.+.+++.++ +.|+.++|++||+ ||.+|+|+
T Consensus 81 l~lA~K~~e~~~~~~~~~~~~~~~~~~~~~i~~~E~~iL~~L~f~ 125 (127)
T PF00134_consen 81 LFLASKMEEDNPPSISDLIRISDNTFTKKDILEMEREILSALNFD 125 (127)
T ss_dssp HHHHHHHHTSS--HHHHHHHHTTTSSHHHHHHHHHHHHHHHTTT-
T ss_pred HHHhhhhhccccchHHHHHHHHcCCCCHHHHHHHHHHHHHHCCCC
Confidence 9999999999999999999999 9999999999999 99999997
No 5
>KOG0656 consensus G1/S-specific cyclin D [Cell cycle control, cell division, chromosome partitioning]
Probab=99.89 E-value=1.1e-23 Score=214.48 Aligned_cols=128 Identities=26% Similarity=0.414 Sum_probs=116.7
Q ss_pred hhhHHHHHHHHHHHHhcCCCCcc-ccccCCCCCHHHHHHHHHHHHHHhhhcccchhHHHHHHHHHHHhhhccccCCCC--
Q 011310 362 AEYVDEIYHYYWVMEAQNPPLEN-YMSSQTDITPQMRGILINWLIEVHLKFDLMPETLYLMVILLDRYLSEVKIKKNE-- 438 (489)
Q Consensus 362 ~EYaeDIyqyLr~rE~~~~p~~n-YL~~QpeIT~kmRaiLIDWLiEV~~kFkLs~ETLfLAVnLLDRYLS~~~V~r~k-- 438 (489)
.-+.++++..|...|.++.|..+ |+..|..+++.||.++++||++||.++++.+++++||||||||||+.+.+++.+
T Consensus 42 ~~~~e~~i~~ll~kEe~~~p~~~~~~~~~~~~~~~~R~~A~~WIl~V~~~~~~~~~~~~LA~NYlDRFls~~~l~k~k~W 121 (335)
T KOG0656|consen 42 LLWDERVLANLLEKEEQHNPSLDYFLCVQKLILSSMRKQALDWILKVCEEYNFEPLVFLLAMNYLDRFLSSQKLPKDKPW 121 (335)
T ss_pred ccccHHHHHHHHHHHHHhCCCCchhhhcccccccHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHhhcccccCCCchH
Confidence 34557888888888888887777 566899999999999999999999999999999999999999999999999999
Q ss_pred -eeEehhhhhhhhhccCccCCCCHHHHHH-Hh-ccCCHHHHHHHHH-HhHhcCCC
Q 011310 439 -MQLVGLTSLLLASKYEDFWHPRVKDLIS-IS-ETYTRDHMLRMVC-ILNGLNLF 489 (489)
Q Consensus 439 -LQLVGiTCLfIASKyEEi~pP~L~dLV~-I~-naYTkeqIL~ME~-IL~tLdWD 489 (489)
+||+|++||+||||+||...|.+-|+.. .+ +.|..+.|.+||+ ||.+|+|.
T Consensus 122 ~lQLlAvaCLsLAsKmeE~~vPll~dl~v~~~~~~feaktI~rmELLVLstL~Wr 176 (335)
T KOG0656|consen 122 MLQLLAVACLSLASKMEETDVPLLADLQVEYTDNVFEAKTIQRMELLVLSTLKWR 176 (335)
T ss_pred HHHHHHHHHHHHHHhhcCcCCchhhhhhhccccccccHHHHHHHHHHHHhhcccc
Confidence 9999999999999999998788887754 44 9999999999999 99999995
No 6
>KOG0654 consensus G2/Mitotic-specific cyclin A [Cell cycle control, cell division, chromosome partitioning]
Probab=99.83 E-value=9.6e-22 Score=201.92 Aligned_cols=140 Identities=41% Similarity=0.625 Sum_probs=133.6
Q ss_pred CCCC-CCCCcchhhhhHHHHHHHHHHHHhc-CCCCcccccc-CCCCCHHHHHHHHHHHHHHhhhcccchhHHHHHHHHHH
Q 011310 350 PGID-DDCNQLEVAEYVDEIYHYYWVMEAQ-NPPLENYMSS-QTDITPQMRGILINWLIEVHLKFDLMPETLYLMVILLD 426 (489)
Q Consensus 350 pdiD-D~~dpl~v~EYaeDIyqyLr~rE~~-~~p~~nYL~~-QpeIT~kmRaiLIDWLiEV~~kFkLs~ETLfLAVnLLD 426 (489)
.+|| +..+|++|..|+.+||+|++..|.. ..|.++||.. |.++++.||.+|+||+++|.+.+.+..++|||+++++|
T Consensus 87 ~~~ds~~~dp~~c~~~~~~I~~~~r~~ei~~~rp~~~~~e~vq~d~t~smrgilvdwlvevsee~r~~~e~l~ls~~~~d 166 (359)
T KOG0654|consen 87 MRIDSVGEDPQMCLKIAAKIYNTLRVSDIKSERPLPSKFEFVQADITPSMRGILVDWLVEVSEEYRLTFETLYLSVNYRD 166 (359)
T ss_pred cchhhcccchHHHHHHHHHHhhcccccchhhccCcccceeeeecCCCcchhhhhhhhhhHHHHHHHhhhhheeecHHHHH
Confidence 4555 5679999999999999999999999 8899999985 99999999999999999999999999999999999999
Q ss_pred HhhhccccCCCCeeEehhhhhhhhhccCccCCCCHHHHHHHh-ccCCHHHHHHHHH-HhHhcCCC
Q 011310 427 RYLSEVKIKKNEMQLVGLTSLLLASKYEDFWHPRVKDLISIS-ETYTRDHMLRMVC-ILNGLNLF 489 (489)
Q Consensus 427 RYLS~~~V~r~kLQLVGiTCLfIASKyEEi~pP~L~dLV~I~-naYTkeqIL~ME~-IL~tLdWD 489 (489)
|||....+.+.++||+|.+|++||+||||+.+|.+++|++++ +.|+..|+..||. ||..|.|+
T Consensus 167 rfl~~~~~~~~k~ql~g~s~m~I~sk~ee~~~~~~~ef~~itd~ty~~~qv~~~~~~il~~l~~~ 231 (359)
T KOG0654|consen 167 RFLSYKEVNKQKLQLVGISAMLIASKYEEIKEPRVEEFCYITDNTYTYWQVLRMEIDILNALTFE 231 (359)
T ss_pred HHhccCccHHHHHHHhCcccceeeccchhhcchHHHHHHhhhhhhhHHHHHHHHHHHHHHHhHHH
Confidence 999999999999999999999999999999999999999999 9999999999999 99998763
No 7
>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=99.51 E-value=2.8e-14 Score=112.07 Aligned_cols=86 Identities=37% Similarity=0.546 Sum_probs=80.2
Q ss_pred HHHHHHHHHHHHhhhcccchhHHHHHHHHHHHhhhccccCCCCeeEehhhhhhhhhccCccCCCCHHHHHHHh-ccCCHH
Q 011310 396 MRGILINWLIEVHLKFDLMPETLYLMVILLDRYLSEVKIKKNEMQLVGLTSLLLASKYEDFWHPRVKDLISIS-ETYTRD 474 (489)
Q Consensus 396 mRaiLIDWLiEV~~kFkLs~ETLfLAVnLLDRYLS~~~V~r~kLQLVGiTCLfIASKyEEi~pP~L~dLV~I~-naYTke 474 (489)
+|..+++||.+++..++++++++++|+.|+|||+....+.+.+++++|++||+||+|++|. ++.+.+++..+ .. +.+
T Consensus 1 ~~~~~~~~l~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~ia~a~l~lA~k~~~~-~~~~~~~~~~~~~~-~~~ 78 (88)
T cd00043 1 MRPTPLDFLRRVAKALGLSPETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEEI-PPWLKDLVHVTGYA-TEE 78 (88)
T ss_pred CcchHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHcCC-CCCHHHHhHHhCCC-CHH
Confidence 3678899999999999999999999999999999999999999999999999999999999 89999998887 43 999
Q ss_pred HHHHHHH-Hh
Q 011310 475 HMLRMVC-IL 483 (489)
Q Consensus 475 qIL~ME~-IL 483 (489)
+|..||+ ||
T Consensus 79 ~i~~~e~~il 88 (88)
T cd00043 79 EILRMEKLLL 88 (88)
T ss_pred HHHHHHHHhC
Confidence 9999999 75
No 8
>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=99.44 E-value=1.1e-13 Score=107.84 Aligned_cols=82 Identities=38% Similarity=0.548 Sum_probs=74.6
Q ss_pred HHHHHHhhhcccchhHHHHHHHHHHHhhhccccCCCCeeEehhhhhhhhhccCccCCCCHHHHHHHhccCCHHHHHHHHH
Q 011310 402 NWLIEVHLKFDLMPETLYLMVILLDRYLSEVKIKKNEMQLVGLTSLLLASKYEDFWHPRVKDLISISETYTRDHMLRMVC 481 (489)
Q Consensus 402 DWLiEV~~kFkLs~ETLfLAVnLLDRYLS~~~V~r~kLQLVGiTCLfIASKyEEi~pP~L~dLV~I~naYTkeqIL~ME~ 481 (489)
+||.+++..+++++++.++|+.|+|||+....+.+...+++|++||+||+|++|.. |...++...++.|+.++|..||+
T Consensus 1 ~~l~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~ia~a~l~lA~k~~~~~-~~~~~~~~~~~~~~~~~i~~~~~ 79 (83)
T smart00385 1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLAAKTEEIP-PWTKELVHYTGYFTEEEILRMEK 79 (83)
T ss_pred CHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhcccCCHHHHHHHHHHHHHHHhcCC-CCchhHhHhhCCCCHHHHHHHHH
Confidence 59999999999999999999999999999877888999999999999999999985 67788888883389999999999
Q ss_pred -HhH
Q 011310 482 -ILN 484 (489)
Q Consensus 482 -IL~ 484 (489)
||.
T Consensus 80 ~il~ 83 (83)
T smart00385 80 LLLE 83 (83)
T ss_pred HHhC
Confidence 873
No 9
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=99.29 E-value=4.7e-12 Score=128.54 Aligned_cols=94 Identities=16% Similarity=0.284 Sum_probs=86.5
Q ss_pred HHHHHHHHHHHHHhhhcc--cchhHHHHHHHHHHHhhhccccCCCCeeEehhhhhhhhhccCccCCCCHHHHHHHh-cc-
Q 011310 395 QMRGILINWLIEVHLKFD--LMPETLYLMVILLDRYLSEVKIKKNEMQLVGLTSLLLASKYEDFWHPRVKDLISIS-ET- 470 (489)
Q Consensus 395 kmRaiLIDWLiEV~~kFk--Ls~ETLfLAVnLLDRYLS~~~V~r~kLQLVGiTCLfIASKyEEi~pP~L~dLV~I~-na- 470 (489)
.+|..-..+|.++|..|+ |.++|++.|+.||+||+....+...+.++|++||||||||+||.. ..+.+|+... ..
T Consensus 54 ~l~~~y~~~i~~~~~~lkp~Lpq~viaTAivyf~RFy~~~Sv~~~~p~~Ia~tclfLA~KvEE~~-~si~~fv~~~~~~~ 132 (305)
T TIGR00569 54 DLVKYYEKRLLDFCSAFKPTMPTSVVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEEFN-VSIDQFVGNLKETP 132 (305)
T ss_pred HHHHHHHHHHHHHHHHhcCCCCchHHHHHHHHHhHHhccCchhhcCHHHHHHHHHHHHHhccccC-cCHHHHHhhccCCc
Confidence 578888899999999999 999999999999999999999999999999999999999999995 5789998877 43
Q ss_pred -CCHHHHHHHHH-HhHhcCCC
Q 011310 471 -YTRDHMLRMVC-ILNGLNLF 489 (489)
Q Consensus 471 -YTkeqIL~ME~-IL~tLdWD 489 (489)
+..++|+.||. ||+.|+|+
T Consensus 133 ~~~~~~Il~~E~~lL~~L~F~ 153 (305)
T TIGR00569 133 LKALEQVLEYELLLIQQLNFH 153 (305)
T ss_pred hhhHHHHHHHHHHHHHHCCCc
Confidence 47799999999 99999996
No 10
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=98.97 E-value=7.7e-10 Score=113.44 Aligned_cols=96 Identities=18% Similarity=0.330 Sum_probs=87.6
Q ss_pred CHHHHHHHHHHHHHHhhhcccchhHHHHHHHHHHHhhhccccCCCCeeEehhhhhhhhhccCccCCCCHHHHHHHh-ccC
Q 011310 393 TPQMRGILINWLIEVHLKFDLMPETLYLMVILLDRYLSEVKIKKNEMQLVGLTSLLLASKYEDFWHPRVKDLISIS-ETY 471 (489)
Q Consensus 393 T~kmRaiLIDWLiEV~~kFkLs~ETLfLAVnLLDRYLS~~~V~r~kLQLVGiTCLfIASKyEEi~pP~L~dLV~I~-naY 471 (489)
....|.....||++++.++++.+-|+..|+.||.||+....+...+...+|++|||||+|.||. |..++|++..+ ..+
T Consensus 35 E~~~r~~~~~fI~elg~~L~~~~~ti~tA~~~~hRFy~~~s~~~~~~~~vA~sclfLAgKvEet-p~kl~dIi~~s~~~~ 113 (323)
T KOG0834|consen 35 ELRLRQEGAKFIQELGVRLKMPQKTIATAIVIFHRFYMFHSFKKFDPYTVAASCLFLAGKVEET-PRKLEDIIKVSYRYL 113 (323)
T ss_pred HHHHHHHHHHHHHHHHHHcCCCccchhhhhhhhhhhhhhcccccCcHHHHHHHHHHHHhhcccC-cccHHHHHHHHHHHc
Confidence 3468999999999999999999999999999999999999999999999999999999999987 67899998888 444
Q ss_pred C-------------HHHHHHHHH-HhHhcCCC
Q 011310 472 T-------------RDHMLRMVC-ILNGLNLF 489 (489)
Q Consensus 472 T-------------keqIL~ME~-IL~tLdWD 489 (489)
. ++.|+..|. ||++|.||
T Consensus 114 ~~~~~~~~~~~~~~~~~Iv~~E~~lL~tl~Fd 145 (323)
T KOG0834|consen 114 NPKDLELEEVYWELKERIVQLELLLLETLGFD 145 (323)
T ss_pred CcccccHHHHHHHHHHHHHHHHHHHHHHccCc
Confidence 3 577999999 99999997
No 11
>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=98.46 E-value=3.4e-07 Score=93.14 Aligned_cols=96 Identities=15% Similarity=0.211 Sum_probs=79.9
Q ss_pred CHHHHHHHHHHHHHHhhhcccchhHHHHHHHHHHHhhhccccCCCCeeEehhhhhhhhhccCccCCCCHHHHHHHh----
Q 011310 393 TPQMRGILINWLIEVHLKFDLMPETLYLMVILLDRYLSEVKIKKNEMQLVGLTSLLLASKYEDFWHPRVKDLISIS---- 468 (489)
Q Consensus 393 T~kmRaiLIDWLiEV~~kFkLs~ETLfLAVnLLDRYLS~~~V~r~kLQLVGiTCLfIASKyEEi~pP~L~dLV~I~---- 468 (489)
....|..-.-|+..+|.+++|...++-.||.+|+||+....+..-.++-|+.||+++|+|.||. +-.+.-.....
T Consensus 41 e~~l~i~~~k~i~~l~~~L~lp~~~laTAi~~f~Rf~Lk~sv~e~~~~~vv~tcv~LA~K~ed~-~~~I~i~~~~~~~~~ 119 (297)
T COG5333 41 ELNLVIYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDT-PRDISIESFEARDLW 119 (297)
T ss_pred hhhHHHHHHHHHHHHHHhcCCCcchHHHHHHHHHHHHhhcccccccHHHHHHhheeeeeecccc-cchhhHHHHHhhccc
Confidence 3456777789999999999999999999999999999999999999999999999999999995 11122111111
Q ss_pred ---ccCCHHHHHHHHH-HhHhcCCC
Q 011310 469 ---ETYTRDHMLRMVC-ILNGLNLF 489 (489)
Q Consensus 469 ---naYTkeqIL~ME~-IL~tLdWD 489 (489)
-.-+++.|+.+|. ||+.|+||
T Consensus 120 se~~~~sr~~Il~~E~~lLEaL~fd 144 (297)
T COG5333 120 SEEPKSSRERILEYEFELLEALDFD 144 (297)
T ss_pred cccccccHHHHHHHHHHHHHHcccc
Confidence 2346889999999 99999997
No 12
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=98.32 E-value=9.3e-07 Score=90.94 Aligned_cols=96 Identities=20% Similarity=0.289 Sum_probs=82.0
Q ss_pred CHHHHHHHHHHHHHHhhhcccchhHHHHHHHHHHHhhhccccCCCCeeEehhhhhhhhhccCccCCCCHHHHHHHh-c--
Q 011310 393 TPQMRGILINWLIEVHLKFDLMPETLYLMVILLDRYLSEVKIKKNEMQLVGLTSLLLASKYEDFWHPRVKDLISIS-E-- 469 (489)
Q Consensus 393 T~kmRaiLIDWLiEV~~kFkLs~ETLfLAVnLLDRYLS~~~V~r~kLQLVGiTCLfIASKyEEi~pP~L~dLV~I~-n-- 469 (489)
....|..-+.||.+-+.-++|+..+.+.+..||-||+....+-+.++..++++|++||||+||. |-.+.|++.+. +
T Consensus 19 e~el~~LG~e~Iqea~ILL~L~q~a~atgqVLFqRf~~~ks~v~~~~e~vv~ACv~LASKiEE~-Prr~rdVinVFh~L~ 97 (367)
T KOG0835|consen 19 EEELRILGCELIQEAGILLNLPQVAMATGQVLFQRFCYSKSFVRHDFEIVVMACVLLASKIEEE-PRRIRDVINVFHYLE 97 (367)
T ss_pred HHHHHHHhHHHHHhhhHhhcCcHHHHHHHHHHHHHHHhccccccccHHHHHHHHHHHHhhhccc-cccHhHHHHHHHHHH
Confidence 4567888899999999999999999999999999999999999999999999999999999987 45566654433 1
Q ss_pred -cC----------------CHHHHHHHHH-HhHhcCCC
Q 011310 470 -TY----------------TRDHMLRMVC-ILNGLNLF 489 (489)
Q Consensus 470 -aY----------------TkeqIL~ME~-IL~tLdWD 489 (489)
.| .+.++..+|. ||..|+||
T Consensus 98 ~r~~~~~~~~~~~~~~~~~lk~~~ir~e~~ILr~LGF~ 135 (367)
T KOG0835|consen 98 QRRESEAAEHLILARLYINLKMQVIRAERRILRELGFD 135 (367)
T ss_pred HHHhccCcchhhhhhHHhhhhhHHHHHHHHHHHHhCCe
Confidence 11 2567899999 99999997
No 13
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]
Probab=98.26 E-value=6.3e-07 Score=88.65 Aligned_cols=93 Identities=20% Similarity=0.322 Sum_probs=75.5
Q ss_pred HHHHHHHHHHHhhhcccchhHHHHHHHHHHHhhhccccCCCCeeEehhhhhhhhhccCccCCCCHHHHHHHh--------
Q 011310 397 RGILINWLIEVHLKFDLMPETLYLMVILLDRYLSEVKIKKNEMQLVGLTSLLLASKYEDFWHPRVKDLISIS-------- 468 (489)
Q Consensus 397 RaiLIDWLiEV~~kFkLs~ETLfLAVnLLDRYLS~~~V~r~kLQLVGiTCLfIASKyEEi~pP~L~dLV~I~-------- 468 (489)
+--..+.+..++++++|...++..|+.||-||+.+.++..-++.|++.||+++|||.||.-.-.++-++...
T Consensus 41 ~i~~~n~I~~lg~~lklRQ~ViATAivY~rRfy~r~S~k~~~p~lla~TClyLAcKvEE~~i~~~r~l~~~a~~L~~~f~ 120 (264)
T KOG0794|consen 41 KIFMANVIQKLGQHLKLRQRVIATAIVYFRRFYLRKSLKEIEPRLLAPTCLYLACKVEECPIVHIRLLVNEAKVLKTRFS 120 (264)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCHHHHHHHHHHHHhhhhhcchHHHHHHHHHHHHHhhhcc
Confidence 334445577889999999999999999999999999999999999999999999999998422333333221
Q ss_pred -----ccCCHHHHHHHHH-HhHhcCCC
Q 011310 469 -----ETYTRDHMLRMVC-ILNGLNLF 489 (489)
Q Consensus 469 -----naYTkeqIL~ME~-IL~tLdWD 489 (489)
..|...+|++||. +|+.|+++
T Consensus 121 ~~~e~~~~~~~~I~e~Ef~llE~Ld~~ 147 (264)
T KOG0794|consen 121 YWPEKFPYERKDILEMEFYLLEALDCY 147 (264)
T ss_pred cchhhcCCCcCcchhhhhhHHhhhcee
Confidence 3467788999999 99999874
No 14
>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=98.24 E-value=2.5e-06 Score=77.94 Aligned_cols=89 Identities=22% Similarity=0.248 Sum_probs=68.4
Q ss_pred HHHHHHHHhhhcccchhHHHHHHHHHHHhhh---cc--ccCCCCeeEehhhhhhhhhccCccCCCCHHHHHHHhccCCHH
Q 011310 400 LINWLIEVHLKFDLMPETLYLMVILLDRYLS---EV--KIKKNEMQLVGLTSLLLASKYEDFWHPRVKDLISISETYTRD 474 (489)
Q Consensus 400 LIDWLiEV~~kFkLs~ETLfLAVnLLDRYLS---~~--~V~r~kLQLVGiTCLfIASKyEEi~pP~L~dLV~I~naYTke 474 (489)
+.+|+..++...+++++++.+|+.|+||+.. .. .+......-+-++||.||+||-+.....-..+..+++ ++.+
T Consensus 54 i~~fl~ri~~~~~~s~~~~i~aliYl~Rl~~~~~~~~~~~~~~~~~Rl~l~alilA~K~~~D~~~~n~~~a~v~g-is~~ 132 (149)
T PF08613_consen 54 IRDFLSRILKYTQCSPECLILALIYLDRLRQRSRKPNIPLNSSNIHRLFLTALILASKFLDDNTYSNKSWAKVGG-ISLK 132 (149)
T ss_dssp HHHHHHHHHHHTT--HHHHHHHHHHHHHHHH--H-TT---STTTHHHHHHHHHHHHHHHH-SS---HHHHHHHHT-S-HH
T ss_pred HHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhhcccccccccchhHHHHHHHHHHHHhhcccccccHHHHHhhcC-CCHH
Confidence 7889999999999999999999999999998 22 3556667788999999999997766666666665554 6999
Q ss_pred HHHHHHH-HhHhcCCC
Q 011310 475 HMLRMVC-ILNGLNLF 489 (489)
Q Consensus 475 qIL~ME~-IL~tLdWD 489 (489)
||-.||+ .|..|+|+
T Consensus 133 eln~lE~~fL~~l~~~ 148 (149)
T PF08613_consen 133 ELNELEREFLKLLDYN 148 (149)
T ss_dssp HHHHHHHHHHHHTTT-
T ss_pred HHHHHHHHHHHHCCCc
Confidence 9999999 99999996
No 15
>KOG4164 consensus Cyclin ik3-1/CABLES [Cell cycle control, cell division, chromosome partitioning]
Probab=97.22 E-value=9.3e-05 Score=78.05 Aligned_cols=132 Identities=19% Similarity=0.242 Sum_probs=102.4
Q ss_pred CCcchhhhhHHHHHHHHHHHHhcCCCCccccccCCC--CCH-HHHHHHHHHHHHHhhhcccchhHHHHHHHHHHHhhhcc
Q 011310 356 CNQLEVAEYVDEIYHYYWVMEAQNPPLENYMSSQTD--ITP-QMRGILINWLIEVHLKFDLMPETLYLMVILLDRYLSEV 432 (489)
Q Consensus 356 ~dpl~v~EYaeDIyqyLr~rE~~~~p~~nYL~~Qpe--IT~-kmRaiLIDWLiEV~~kFkLs~ETLfLAVnLLDRYLS~~ 432 (489)
-+++.+.+|.-...+|.+....+...+..|-..-|. +|. ++|. |-.-|.++....++..-|+..|..||....-+.
T Consensus 339 k~~l~F~symttvidyVrpsdlKkdmNe~FreKfP~IkLTLSKirS-lKREMr~l~~d~~id~~TVa~AyVYFEKliLkg 417 (497)
T KOG4164|consen 339 KRVLIFSSYMTTVIDYVRPSDLKKDMNETFREKFPHIKLTLSKIRS-LKREMRELGEDCGIDVVTVAMAYVYFEKLILKG 417 (497)
T ss_pred cceeEeccccceeEEEechHHHHHHHhHHHHHhCCeeEEeHHHHHH-HHHHHHHhhhccCccceeehhHHHHHHHHHHhh
Confidence 356777777766666655544332222333333333 233 3444 445588889999999999999999999999999
Q ss_pred ccCCCCeeEehhhhhhhhhccCccCCCCHHHHHHHh---ccCCHHHHHHHHH-HhHhcCC
Q 011310 433 KIKKNEMQLVGLTSLLLASKYEDFWHPRVKDLISIS---ETYTRDHMLRMVC-ILNGLNL 488 (489)
Q Consensus 433 ~V~r~kLQLVGiTCLfIASKyEEi~pP~L~dLV~I~---naYTkeqIL~ME~-IL~tLdW 488 (489)
.+.+.+-.|.|-+||++|+|+.+..-..+..|+.-. -.+.+.|++..|. ||-+|+|
T Consensus 418 lisK~NRKlcAGAclLlaaKmnD~Kks~vKslIek~Ee~fR~nrrdLia~Ef~VlvaLef 477 (497)
T KOG4164|consen 418 LISKQNRKLCAGACLLLAAKMNDLKKSTVKSLIEKLEEQFRLNRRDLIAFEFPVLVALEF 477 (497)
T ss_pred hhhhhhhhHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHhcccHHhhhhhhhhHHHhhhh
Confidence 999999999999999999999998888899998766 6788999999999 9999988
No 16
>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=97.17 E-value=0.0012 Score=67.97 Aligned_cols=87 Identities=18% Similarity=0.311 Sum_probs=73.3
Q ss_pred HHHHHHhhhc--ccchhHHHHHHHHHHHhhhccccCCCCeeEehhhhhhhhhccCccCCCCHHHHHHHh---ccCCHHHH
Q 011310 402 NWLIEVHLKF--DLMPETLYLMVILLDRYLSEVKIKKNEMQLVGLTSLLLASKYEDFWHPRVKDLISIS---ETYTRDHM 476 (489)
Q Consensus 402 DWLiEV~~kF--kLs~ETLfLAVnLLDRYLS~~~V~r~kLQLVGiTCLfIASKyEEi~pP~L~dLV~I~---naYTkeqI 476 (489)
..+++.+.+| .+.++++-.|+.+|-||+-...|..-.-..|-+||+|+|+|.||.+ ..+++|+.-. ..=+.+.|
T Consensus 61 ~~l~~f~~k~~p~lp~~Vv~TA~~fFkRffL~nsvme~~pk~I~~tc~flA~Kieef~-ISieqFvkn~~~~~~k~~e~v 139 (325)
T KOG2496|consen 61 LSLVNFYSKFKPNLPTSVVSTAIEFFKRFFLENSVMEYSPKIIMATCFFLACKIEEFY-ISIEQFVKNMNGRKWKTHEIV 139 (325)
T ss_pred HHHHHHHHHhcCCCchHHHHHHHHHHHHHHHhcchhhcChHHHHHHHHHHHhhhHhhe-ecHHHHHhhccCcccccHHHH
Confidence 3344455554 4678899999999999999988888889999999999999999875 7799998876 34678999
Q ss_pred HHHHH-HhHhcCCC
Q 011310 477 LRMVC-ILNGLNLF 489 (489)
Q Consensus 477 L~ME~-IL~tLdWD 489 (489)
+..|. +|+.|+|+
T Consensus 140 Lk~E~~llqsL~f~ 153 (325)
T KOG2496|consen 140 LKYEFLLLQSLKFS 153 (325)
T ss_pred HhchHHHHHhhhhh
Confidence 99999 99999996
No 17
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=96.87 E-value=0.0041 Score=63.54 Aligned_cols=89 Identities=15% Similarity=0.168 Sum_probs=77.4
Q ss_pred HHHHHHHHHHhhhcccchhHHHHHHHHHHHhhhccccCCCCeeEehhhhhhhhhccCccCCCCHHHHHHHhccCCHHHHH
Q 011310 398 GILINWLIEVHLKFDLMPETLYLMVILLDRYLSEVKIKKNEMQLVGLTSLLLASKYEDFWHPRVKDLISISETYTRDHML 477 (489)
Q Consensus 398 aiLIDWLiEV~~kFkLs~ETLfLAVnLLDRYLS~~~V~r~kLQLVGiTCLfIASKyEEi~pP~L~dLV~I~naYTkeqIL 477 (489)
.....-|-+++..++|+..+.-.|..|+.+++....+.......++++||||||+.++. |-++.+++.+++ .+..+|-
T Consensus 123 ~~a~~~I~~~~~~L~Lp~~v~e~A~~iyk~~~~~~~~rgrs~~~i~AAclYiACR~~~~-prtl~eI~~~~~-v~~k~i~ 200 (310)
T PRK00423 123 AFALSELDRIASQLGLPRSVREEAAVIYRKAVEKGLIRGRSIEGVVAAALYAACRRCKV-PRTLDEIAEVSR-VSRKEIG 200 (310)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHcCC-CcCHHHHHHHhC-CCHHHHH
Confidence 44556688899999999999999999999999988888888999999999999998655 788999877773 3778999
Q ss_pred HHHH-HhHhcCC
Q 011310 478 RMVC-ILNGLNL 488 (489)
Q Consensus 478 ~ME~-IL~tLdW 488 (489)
+.++ |++.|++
T Consensus 201 ~~~~~l~k~L~~ 212 (310)
T PRK00423 201 RCYRFLLRELNL 212 (310)
T ss_pred HHHHHHHHHhCC
Confidence 9999 9999876
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=93.27 E-value=0.14 Score=41.13 Aligned_cols=63 Identities=10% Similarity=0.101 Sum_probs=51.0
Q ss_pred HHHhhhcccchhHHHHHHHHHHHhhhccccCCCCeeEehhhhhhhhhccCccCCCCHHHHHHHh
Q 011310 405 IEVHLKFDLMPETLYLMVILLDRYLSEVKIKKNEMQLVGLTSLLLASKYEDFWHPRVKDLISIS 468 (489)
Q Consensus 405 iEV~~kFkLs~ETLfLAVnLLDRYLS~~~V~r~kLQLVGiTCLfIASKyEEi~pP~L~dLV~I~ 468 (489)
-.+|..++|+.++.-.|..++++-....-+......-++++|+++||+.+.. +.++.++...+
T Consensus 2 ~r~~~~L~L~~~v~~~A~~i~~~~~~~~~~~Gr~~~~iaAA~iY~acr~~~~-~~t~~eIa~~~ 64 (71)
T PF00382_consen 2 PRICSKLGLPEDVRERAKEIYKKAQERGLLKGRSPESIAAACIYLACRLNGV-PRTLKEIAEAA 64 (71)
T ss_dssp HHHHHHTT--HHHHHHHHHHHHHHHHTTTSTTS-HHHHHHHHHHHHHHHTTS-SSSHHHHHHHC
T ss_pred hHHHhHcCCCHHHHHHHHHHHHHHHHcCCcccCCHHHHHHHHHHHHHHHcCC-CcCHHHHHHHh
Confidence 4689999999999999999999988887777778899999999999998754 66788876654
No 19
>KOG1674 consensus Cyclin [General function prediction only]
Probab=92.73 E-value=0.28 Score=48.39 Aligned_cols=87 Identities=18% Similarity=0.273 Sum_probs=62.9
Q ss_pred HHHHHHHHhhhcccchhHHHHHHHHHHHhhhccc---cCCCC-------eeEehhhhhhhhhccCccCCCCHHHHHHHh-
Q 011310 400 LINWLIEVHLKFDLMPETLYLMVILLDRYLSEVK---IKKNE-------MQLVGLTSLLLASKYEDFWHPRVKDLISIS- 468 (489)
Q Consensus 400 LIDWLiEV~~kFkLs~ETLfLAVnLLDRYLS~~~---V~r~k-------LQLVGiTCLfIASKyEEi~pP~L~dLV~I~- 468 (489)
+-+++.++......+++++.+|..|||||..... +.+.. ..=+-++|+.+|+|+.+...- ..-.+.-
T Consensus 78 i~~yleri~k~~~~s~~~lv~al~Yldr~~~~~~~~~~~~~~~i~s~n~vhR~lit~v~vs~kf~~d~~y--~n~~~a~v 155 (218)
T KOG1674|consen 78 IRQYLERIFKYSKCSPECLVLALVYLDRFVKQPQARSVKPQSLINSLNKVHRLLITTVTVSTKFLDDVYY--SNAYYAKV 155 (218)
T ss_pred hHHHHHHHHHHhcCCchhhhhhhhhhhhhhhhhcccccCcccccccchhHHHHHHHHHHHHHhhccchhh--hHHHHHHh
Confidence 3456677777888999999999999999998632 11111 222568999999999865321 2222222
Q ss_pred ccCCHHHHHHHHH-HhHhcCC
Q 011310 469 ETYTRDHMLRMVC-ILNGLNL 488 (489)
Q Consensus 469 naYTkeqIL~ME~-IL~tLdW 488 (489)
+..+.+|+-.+|. .|..++|
T Consensus 156 ggl~~~eln~lE~~~l~~~~~ 176 (218)
T KOG1674|consen 156 GGLTTDELNKLELDLLFLLDF 176 (218)
T ss_pred CCCChHhhhhhhHHHHhhCCe
Confidence 8888999999999 9988887
No 20
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=89.66 E-value=0.73 Score=47.85 Aligned_cols=83 Identities=12% Similarity=0.144 Sum_probs=69.6
Q ss_pred HHHHHhhhcccchhHHHHHHHHHHHhhhccccCCCCeeEehhhhhhhhhccCccCCCCHHHHHHHhccCCHHHHHHHHH-
Q 011310 403 WLIEVHLKFDLMPETLYLMVILLDRYLSEVKIKKNEMQLVGLTSLLLASKYEDFWHPRVKDLISISETYTRDHMLRMVC- 481 (489)
Q Consensus 403 WLiEV~~kFkLs~ETLfLAVnLLDRYLS~~~V~r~kLQLVGiTCLfIASKyEEi~pP~L~dLV~I~naYTkeqIL~ME~- 481 (489)
-+..+++..+|....--.|-.+|-+|...+...-...+-++++||+|||.-++. |-++.++..+++ .++.||-+.=+
T Consensus 110 ~I~~m~d~~~Lp~~I~d~A~~ifk~v~~~k~lrGks~eai~AAclyiACRq~~~-pRT~kEI~~~an-v~kKEIgr~~K~ 187 (308)
T KOG1597|consen 110 EITAMCDRLSLPATIKDRANEIFKLVEDSKLLRGKSVEALAAACLYIACRQEDV-PRTFKEISAVAN-VSKKEIGRCVKL 187 (308)
T ss_pred HHHHHHHHhCCchHHHHHHHHHHHHHHHhhhhcCccHHHHHHHHHHHHHHhcCC-CchHHHHHHHHc-CCHHHHHHHHHH
Confidence 366788999999988889999999999877888888999999999999998766 667777766667 88899988877
Q ss_pred HhHhcC
Q 011310 482 ILNGLN 487 (489)
Q Consensus 482 IL~tLd 487 (489)
|+..|+
T Consensus 188 i~~~l~ 193 (308)
T KOG1597|consen 188 IGEALE 193 (308)
T ss_pred HHHHHh
Confidence 877764
No 21
>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=86.94 E-value=1.4 Score=37.02 Aligned_cols=83 Identities=17% Similarity=0.171 Sum_probs=53.9
Q ss_pred HHHHHHHhhhcccchhHHHHHHHHHHHhhhccccCCCCeeEehhhhhhhhhccCccCCCCHHHHHHHhccCCHHHHHHHH
Q 011310 401 INWLIEVHLKFDLMPETLYLMVILLDRYLSEVKIKKNEMQLVGLTSLLLASKYEDFWHPRVKDLISISETYTRDHMLRMV 480 (489)
Q Consensus 401 IDWLiEV~~kFkLs~ETLfLAVnLLDRYLS~~~V~r~kLQLVGiTCLfIASKyEEi~pP~L~dLV~I~naYTkeqIL~ME 480 (489)
.+||-......+...++-++|-.+++..|....+-.-.--+||++|+++|.+.-...++-...+..++ .|+.++|..+=
T Consensus 4 ~~Fl~~~~~~~~~~~~~~~~a~~l~el~l~~~~fl~~~PS~iAaAai~lA~~~~~~~~~~~~~l~~~t-~~~~~~l~~c~ 82 (118)
T PF02984_consen 4 YDFLRRFLKISNADQEVRNLARYLLELSLLDYEFLQYPPSVIAAAAILLARKILGKEPPWPESLEKLT-GYDKEDLKECI 82 (118)
T ss_dssp HHHHHHHHTSSSHHHHHHHHHHHHHHHHHHSHHHTTS-HHHHHHHHHHHHHHHHHSSTCSHHHHHHHH-TS-HHHHHHHH
T ss_pred HHHHHHHHHHcCCcHHHHHHHHHHHHHHHhhccccCCCHHHHHHHHHHHHHHHhCccccCCccchhhc-CCCHHHHHHHH
Confidence 34555554445556778889999999877776677777789999999999999542222233343444 55777776654
Q ss_pred H-HhH
Q 011310 481 C-ILN 484 (489)
Q Consensus 481 ~-IL~ 484 (489)
. |..
T Consensus 83 ~~i~~ 87 (118)
T PF02984_consen 83 ELIQE 87 (118)
T ss_dssp HHHHH
T ss_pred HHHHH
Confidence 4 443
No 22
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=81.46 E-value=4.7 Score=41.47 Aligned_cols=84 Identities=10% Similarity=0.053 Sum_probs=63.9
Q ss_pred HHHHHHHhhhcccchhHHHHHHHHHHHhhhccccCCCCeeEehhhhhhhhhccCccCCCCHHHHHHHhccCCHHHHHHHH
Q 011310 401 INWLIEVHLKFDLMPETLYLMVILLDRYLSEVKIKKNEMQLVGLTSLLLASKYEDFWHPRVKDLISISETYTRDHMLRMV 480 (489)
Q Consensus 401 IDWLiEV~~kFkLs~ETLfLAVnLLDRYLS~~~V~r~kLQLVGiTCLfIASKyEEi~pP~L~dLV~I~naYTkeqIL~ME 480 (489)
.++|-..|..|+|+.++.-.|..++.+.....-.......-|+++|+|||++.... +.++.++..++ ..+...|...=
T Consensus 220 ~~~i~r~~~~L~L~~~v~~~A~~i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~~g~-~~t~keIa~v~-~Vs~~tI~~~y 297 (310)
T PRK00423 220 IDYVPRFASELGLSGEVQKKAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLLGE-RRTQREVAEVA-GVTEVTVRNRY 297 (310)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHhCC-CCCHHHHHHHc-CCCHHHHHHHH
Confidence 58899999999999999999999999888766667788899999999999998754 46777776655 23444454443
Q ss_pred H-HhHhc
Q 011310 481 C-ILNGL 486 (489)
Q Consensus 481 ~-IL~tL 486 (489)
+ |+..|
T Consensus 298 kel~~~l 304 (310)
T PRK00423 298 KELAEKL 304 (310)
T ss_pred HHHHHHh
Confidence 3 44443
No 23
>KOG1675 consensus Predicted cyclin [General function prediction only]
Probab=78.85 E-value=2.2 Score=44.81 Aligned_cols=76 Identities=21% Similarity=0.138 Sum_probs=55.3
Q ss_pred cchhHHHHHHHHHHHhhhccccC--CCCeeEehhhhhhhhhccCccCCCCHHHHHHHhccCCHHHHHHHHH-HhHhcCC
Q 011310 413 LMPETLYLMVILLDRYLSEVKIK--KNEMQLVGLTSLLLASKYEDFWHPRVKDLISISETYTRDHMLRMVC-ILNGLNL 488 (489)
Q Consensus 413 Ls~ETLfLAVnLLDRYLS~~~V~--r~kLQLVGiTCLfIASKyEEi~pP~L~dLV~I~naYTkeqIL~ME~-IL~tLdW 488 (489)
|.-+.--..+.|++|.+....+. +.....+...+.|+|+|......--=-|++.|+.-.|.+|+.+||+ +|..|+|
T Consensus 206 lta~~aiitL~~~erl~~~~e~~~~p~~w~r~~~g~il~sskv~~dqs~wnvdycqIlKd~tveDmNe~ERqfLelLqf 284 (343)
T KOG1675|consen 206 LTAECDIITLVYAERLLWLAERDPCPRNWSRAVLGEILLSSKVYDDQSVWNVDYCEILKDQSVDDMNALERQFLELLQF 284 (343)
T ss_pred hhhccchHHHHhhHhhhhHhhcCCCcchhhhhhhhhheehhhhhhhhhcccHHHHHHHhhccHhhHHHHHHHHHHHHhh
Confidence 33333344457888888765544 6667777777899999996654333356777776668999999999 9999987
No 24
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=78.80 E-value=3 Score=43.78 Aligned_cols=88 Identities=15% Similarity=0.091 Sum_probs=58.2
Q ss_pred HHHHHHHHHhhhcccchhHHHHHHHHHHHhhhccccCCCCeeEehhhhhhhhhccCccCCCCHHHH--HHHh-ccCCHHH
Q 011310 399 ILINWLIEVHLKFDLMPETLYLMVILLDRYLSEVKIKKNEMQLVGLTSLLLASKYEDFWHPRVKDL--ISIS-ETYTRDH 475 (489)
Q Consensus 399 iLIDWLiEV~~kFkLs~ETLfLAVnLLDRYLS~~~V~r~kLQLVGiTCLfIASKyEEi~pP~L~dL--V~I~-naYTkeq 475 (489)
-|++|+..+-..-.........|.+++-..+...-+-.-+.+-||++||+||+++-....|...+- .... ...|.++
T Consensus 154 ~ll~~~k~l~~~~~~~~~~a~~Aw~~~nD~~~t~~cL~y~p~~IAva~i~lA~~~~~~~~~~~~~~~w~~~~d~~vt~e~ 233 (323)
T KOG0834|consen 154 YLLKYLKKLKADENLKQPLAQAAWNFVNDSLRTTLCLQYSPHSIAVACIHLAAKLLGVELPSDTDKRWWREFDETVTNEL 233 (323)
T ss_pred HHHHHHHHhhhhhhccccHHHHHHHHhchhheeeeeEeecCcEEEeehhhHHHHHcCCCCCCCcccchhhhhcccCCHHH
Confidence 344444444433333333556666666666655556677788999999999999977655555544 3344 6688999
Q ss_pred HHHHHH-HhHhc
Q 011310 476 MLRMVC-ILNGL 486 (489)
Q Consensus 476 IL~ME~-IL~tL 486 (489)
+..+.. +|..+
T Consensus 234 l~~i~~~~l~~y 245 (323)
T KOG0834|consen 234 LDDICHEFLDLY 245 (323)
T ss_pred HHHHHHHHHHHH
Confidence 988888 77654
No 25
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=77.38 E-value=9 Score=39.56 Aligned_cols=90 Identities=7% Similarity=0.062 Sum_probs=74.9
Q ss_pred HHHHHHHHHHHHhhhcccchhHHHHHHHHHHHhhhccccCCCCeeEehhhhhhhhhccCccCCCCHHHHHHHhccCCHHH
Q 011310 396 MRGILINWLIEVHLKFDLMPETLYLMVILLDRYLSEVKIKKNEMQLVGLTSLLLASKYEDFWHPRVKDLISISETYTRDH 475 (489)
Q Consensus 396 mRaiLIDWLiEV~~kFkLs~ETLfLAVnLLDRYLS~~~V~r~kLQLVGiTCLfIASKyEEi~pP~L~dLV~I~naYTkeq 475 (489)
.-.....-|-.++..++|...+.-.|..++=..+...-+.....+-+.++|+++||+.... |-++.+++.+.. -++.+
T Consensus 96 nl~~a~~~l~~~~~~l~LP~~v~e~A~~iyr~a~~~~l~rGRsie~v~AA~iY~acR~~~~-prtl~eIa~a~~-V~~ke 173 (285)
T COG1405 96 NLITALEELERIASALGLPESVRETAARIYRKAVDKGLLRGRSIESVAAACIYAACRINGV-PRTLDEIAKALG-VSKKE 173 (285)
T ss_pred HHHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHhhcCCCcCCcHHHHHHHHHHHHHHHcCC-CccHHHHHHHHC-CCHHH
Confidence 3455667788899999999999999999999999988888999999999999999999766 667777776664 45688
Q ss_pred HHHHHH-HhHhcC
Q 011310 476 MLRMVC-ILNGLN 487 (489)
Q Consensus 476 IL~ME~-IL~tLd 487 (489)
|.++.+ +...|+
T Consensus 174 i~rtyr~~~~~L~ 186 (285)
T COG1405 174 IGRTYRLLVRELK 186 (285)
T ss_pred HHHHHHHHHHhcC
Confidence 988888 777664
No 26
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=54.68 E-value=38 Score=36.19 Aligned_cols=52 Identities=13% Similarity=0.126 Sum_probs=36.7
Q ss_pred cccchhH--HHHHHHHHHHhhhccccCCCCeeEehhhhhhhhhccCccCCCCHH
Q 011310 411 FDLMPET--LYLMVILLDRYLSEVKIKKNEMQLVGLTSLLLASKYEDFWHPRVK 462 (489)
Q Consensus 411 FkLs~ET--LfLAVnLLDRYLS~~~V~r~kLQLVGiTCLfIASKyEEi~pP~L~ 462 (489)
+++.++- +-.+.||+.--|-..-+-+..-.+|+++|+++|+.-+|+-.|...
T Consensus 152 L~~~~~~~l~Q~~wNfmNDslRT~v~vry~pe~iACaciyLaAR~~eIpLp~~P 205 (367)
T KOG0835|consen 152 LQLPPNLKLLQAAWNFMNDSLRTDVFVRYSPESIACACIYLAARNLEIPLPFQP 205 (367)
T ss_pred hcCCCchhHHHHHHHhhhhccccceeeecCHHHHHHHHHHHHHhhhcCCCCCCc
Confidence 3444433 455666666666666667777889999999999999996555444
No 27
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=46.84 E-value=24 Score=36.50 Aligned_cols=57 Identities=11% Similarity=0.001 Sum_probs=50.6
Q ss_pred HHHHHHHHHhhhcccchhHHHHHHHHHHHhhhccccCCCCeeEehhhhhhhhhccCc
Q 011310 399 ILINWLIEVHLKFDLMPETLYLMVILLDRYLSEVKIKKNEMQLVGLTSLLLASKYED 455 (489)
Q Consensus 399 iLIDWLiEV~~kFkLs~ETLfLAVnLLDRYLS~~~V~r~kLQLVGiTCLfIASKyEE 455 (489)
.-.+++-..+..++|+.++--.|+.|++............-.=++++|++||+.+..
T Consensus 193 ~p~~yi~rf~s~L~l~~~v~~~a~ei~~~~~~~g~~~Gk~P~glAaaaiy~as~l~~ 249 (285)
T COG1405 193 DPSDYIPRFASKLGLSDEVRRKAIEIVKKAKRAGLTAGKSPAGLAAAAIYLASLLLG 249 (285)
T ss_pred CHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhC
Confidence 345788899999999999999999999999988777777788899999999999976
No 28
>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=29.52 E-value=67 Score=29.75 Aligned_cols=66 Identities=15% Similarity=0.142 Sum_probs=49.0
Q ss_pred HHHHHHHHhhhcccchhHHHHHHHHHHHhhhcc--ccCCCCeeEehhhhhhhhhccCccCCCCHHHHHH
Q 011310 400 LINWLIEVHLKFDLMPETLYLMVILLDRYLSEV--KIKKNEMQLVGLTSLLLASKYEDFWHPRVKDLIS 466 (489)
Q Consensus 400 LIDWLiEV~~kFkLs~ETLfLAVnLLDRYLS~~--~V~r~kLQLVGiTCLfIASKyEEi~pP~L~dLV~ 466 (489)
..--|.++|..++++++..-....+|+..|... -+.-.+|--+-++|+++-+|... ..++..+++.
T Consensus 14 a~~Rl~~LC~~L~l~~~~~~~iwt~fe~~l~~~t~L~~dRHLDQiilCaiY~i~Kv~~-~~~sF~~Ii~ 81 (135)
T PF01857_consen 14 AAVRLQDLCERLDLSSDLREKIWTCFEHSLTHHTELMKDRHLDQIILCAIYGICKVSK-EELSFKDIIK 81 (135)
T ss_dssp HHHHHHHHHHHHTTSTTHHHHHHHHHHHHHHHSGGGGTTS-HHHHHHHHHHHHHHHTT--S--HHHHHH
T ss_pred HHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHhhHHHHhcchHHHHHHHHHHHHHHhhc-CCCCHHHHHH
Confidence 334577899999999998888889999998753 35667788899999999999866 4555556543
No 29
>PF14376 Haem_bd: Haem-binding domain
Probab=28.71 E-value=86 Score=28.85 Aligned_cols=37 Identities=22% Similarity=0.381 Sum_probs=29.2
Q ss_pred HHHHHHHhcCCCCccccccCCC--CCHHHHHHHHHHHHH
Q 011310 370 HYYWVMEAQNPPLENYMSSQTD--ITPQMRGILINWLIE 406 (489)
Q Consensus 370 qyLr~rE~~~~p~~nYL~~Qpe--IT~kmRaiLIDWLiE 406 (489)
+-....|...+|...|+-.|++ +++..|..|++|+-+
T Consensus 97 ~i~~~I~~g~MP~~~Y~~~H~~a~Ls~~ek~~Ll~Wi~~ 135 (137)
T PF14376_consen 97 KIEEVIEDGEMPPPSYTLLHWEAKLSEEEKQALLNWIKE 135 (137)
T ss_pred HHHHHHHcCCCChHHHhhhCCCCCCCHHHHHHHHHHHHH
Confidence 3334445567888999988877 999999999999865
No 30
>PF03903 Phage_T4_gp36: Phage T4 tail fibre; InterPro: IPR005601 Irreversible binding of T-even bacteriophages to Escherichia coli is mediated by the short tail fibres, which serve as inextensible stays during DNA injection. Short tail fibres are exceptionally stable elongated trimers of gene product 12 (gp12), a 56 kDa protein. The N-terminal region of gp12 is important for phage attachment, the central region forms a long shaft, while a C-terminal globular region is implicated in binding to the bacterial lipopolysaccharide core. The distal half-fibre contains two molecules each of gp36 and gp37 and one molecule of gp35.
Probab=23.13 E-value=1.1e+02 Score=30.78 Aligned_cols=34 Identities=29% Similarity=0.547 Sum_probs=22.8
Q ss_pred eeeEEeecccccccc---------chhhhcccccCCCcccccc
Q 011310 44 RNFKVYSENEMVKED---------SNTIKNSVPVKNGAALASA 77 (489)
Q Consensus 44 ~~~~~~~~~~~~~~~---------~~~~~~~~~~~~g~~~~~~ 77 (489)
..||||+||.+---. --++.+-|.|++|...-.+
T Consensus 33 k~~~iYTE~dKPqA~dndfVSKanGGT~~~~V~f~~gv~v~~~ 75 (219)
T PF03903_consen 33 KGFKIYTENDKPQATDNDFVSKANGGTYKGNVQFNQGVSVGFA 75 (219)
T ss_pred cceeeeccccCCcccccCeeEeccCccccceEEEeccceeecc
Confidence 579999998543211 1156788888888766643
Done!