Query 030687
Match_columns 173
No_of_seqs 206 out of 1237
Neff 6.4
Searched_HMMs 46136
Date Fri Mar 29 03:04:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030687.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030687hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0656 G1/S-specific cyclin D 100.0 2E-32 4.3E-37 236.1 11.3 111 62-173 40-150 (335)
2 KOG0655 G1/S-specific cyclin E 99.9 6.3E-25 1.4E-29 188.0 6.9 102 66-172 112-214 (408)
3 KOG0653 Cyclin B and related k 99.9 4.2E-23 9.1E-28 182.4 8.4 103 63-171 123-226 (391)
4 COG5024 Cyclin [Cell division 99.9 5.5E-23 1.2E-27 183.1 3.4 106 60-172 176-281 (440)
5 PF00134 Cyclin_N: Cyclin, N-t 99.8 2.3E-21 5.1E-26 143.8 6.8 98 69-171 1-98 (127)
6 KOG0654 G2/Mitotic-specific cy 99.5 3.9E-16 8.6E-21 136.2 -1.2 103 65-171 101-204 (359)
7 cd00043 CYCLIN Cyclin box fold 99.4 9.4E-13 2E-17 89.7 5.7 67 101-171 2-68 (88)
8 smart00385 CYCLIN domain prese 99.2 2E-11 4.4E-16 82.4 5.5 62 106-171 1-62 (83)
9 TIGR00569 ccl1 cyclin ccl1. Un 98.8 1.1E-08 2.4E-13 88.2 6.9 64 99-165 54-119 (305)
10 KOG0834 CDK9 kinase-activating 98.3 9.5E-07 2.1E-11 76.8 5.6 63 99-164 37-99 (323)
11 KOG0794 CDK8 kinase-activating 98.0 1.4E-05 2.9E-10 66.6 5.3 61 100-163 40-100 (264)
12 COG5333 CCL1 Cdk activating ki 97.9 1.8E-05 4E-10 67.9 4.9 63 98-163 42-104 (297)
13 KOG0835 Cyclin L [General func 97.4 0.00037 8.1E-09 60.7 6.7 63 98-163 20-82 (367)
14 PF08613 Cyclin: Cyclin; Inte 96.5 0.0078 1.7E-07 46.5 6.3 56 104-162 54-114 (149)
15 PF00382 TFIIB: Transcription 95.2 0.095 2.1E-06 35.2 6.2 54 108-164 1-54 (71)
16 KOG4164 Cyclin ik3-1/CABLES [C 94.6 0.036 7.9E-07 49.7 3.5 65 96-163 377-441 (497)
17 PRK00423 tfb transcription ini 94.4 0.19 4.1E-06 43.4 7.7 61 100-163 121-181 (310)
18 KOG2496 Cdk activating kinase 93.5 0.44 9.6E-06 41.5 8.0 55 108-165 63-119 (325)
19 PRK00423 tfb transcription ini 84.4 3.4 7.3E-05 35.7 6.5 56 105-163 220-275 (310)
20 KOG0834 CDK9 kinase-activating 84.1 0.93 2E-05 39.8 2.9 66 102-170 153-218 (323)
21 KOG1674 Cyclin [General functi 82.5 2.8 6E-05 34.6 5.0 57 107-163 81-144 (218)
22 COG1405 SUA7 Transcription ini 76.3 8.7 0.00019 33.1 6.2 57 103-162 193-249 (285)
23 PF02984 Cyclin_C: Cyclin, C-t 74.6 5 0.00011 28.3 3.8 54 106-162 5-58 (118)
24 KOG1597 Transcription initiati 70.4 11 0.00023 32.9 5.3 59 102-163 105-163 (308)
25 KOG0835 Cyclin L [General func 48.8 33 0.00072 30.5 4.7 23 146-168 182-204 (367)
26 COG1405 SUA7 Transcription ini 41.0 1.3E+02 0.0029 25.9 7.2 62 99-163 95-156 (285)
27 KOG1598 Transcription initiati 40.7 1.3E+02 0.0027 28.4 7.3 78 83-164 44-126 (521)
28 TIGR01446 DnaD_dom DnaD and ph 40.2 73 0.0016 20.9 4.4 31 94-128 11-41 (73)
29 PF14376 Haem_bd: Haem-binding 34.6 51 0.0011 25.0 3.3 35 77-111 102-136 (137)
30 TIGR00569 ccl1 cyclin ccl1. Un 34.2 1.6E+02 0.0034 25.6 6.6 42 123-167 185-226 (305)
31 PF12550 GCR1_C: Transcription 27.9 1.3E+02 0.0029 20.5 4.2 53 74-132 28-80 (81)
32 cd04441 DEP_2_DEP6 DEP (Dishev 26.4 70 0.0015 22.6 2.6 29 102-131 36-64 (85)
33 cd04449 DEP_DEPDC5-like DEP (D 25.8 76 0.0017 21.9 2.7 31 101-131 32-62 (83)
34 cd04443 DEP_GPR155 DEP (Dishev 24.9 80 0.0017 22.1 2.6 30 101-131 33-62 (83)
35 PF13591 MerR_2: MerR HTH fami 24.4 1.4E+02 0.003 20.6 3.8 29 106-134 46-74 (84)
36 cd04439 DEP_1_P-Rex DEP (Dishe 22.2 85 0.0018 21.8 2.3 30 101-131 31-60 (81)
37 cd04442 DEP_1_DEP6 DEP (Dishev 21.9 91 0.002 21.8 2.5 29 102-135 32-60 (82)
38 cd04438 DEP_dishevelled DEP (D 21.5 1E+02 0.0022 21.6 2.6 31 101-131 32-62 (84)
39 cd04447 DEP_BRCC3 DEP (Disheve 20.5 1.9E+02 0.004 20.9 3.9 39 101-139 32-72 (92)
40 cd04440 DEP_2_P-Rex DEP (Dishe 20.3 1E+02 0.0022 22.2 2.4 31 100-131 39-69 (93)
41 PF01857 RB_B: Retinoblastoma- 20.0 3.5E+02 0.0076 20.5 5.6 57 104-162 14-71 (135)
No 1
>KOG0656 consensus G1/S-specific cyclin D [Cell cycle control, cell division, chromosome partitioning]
Probab=99.98 E-value=2e-32 Score=236.13 Aligned_cols=111 Identities=51% Similarity=0.825 Sum_probs=104.6
Q ss_pred CCCCCHHHHHHHHHHHHhccCCCccchhhccCCCCCHHHHHHHHHHHHHHHHHhcCChhHHHHHHHHHHHHhhccccCCC
Q 030687 62 PFQTVSEELLREMAVKEGELLPKHDYLNRLRSGDLDSRVRREALDWILKAHAHYRFGPMSFCLSMNYLDRFLSVYELPKG 141 (173)
Q Consensus 62 pf~~y~~eil~~L~~~E~~~~p~~~yl~~~q~~~i~~~~R~~lvdWi~~v~~~~~l~~eT~~LAVnylDRfLs~~~v~~~ 141 (173)
+|..+++|++..|+++|+++.|..+|...++ ..+++.+|.++++||++||++++++++|++||||||||||+.+++++.
T Consensus 40 ~~~~~~e~~i~~ll~kEe~~~p~~~~~~~~~-~~~~~~~R~~A~~WIl~V~~~~~~~~~~~~LA~NYlDRFls~~~l~k~ 118 (335)
T KOG0656|consen 40 GFLLWDERVLANLLEKEEQHNPSLDYFLCVQ-KLILSSMRKQALDWILKVCEEYNFEPLVFLLAMNYLDRFLSSQKLPKD 118 (335)
T ss_pred ccccccHHHHHHHHHHHHHhCCCCchhhhcc-cccccHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHhhcccccCCC
Confidence 3567999999999999999999999776654 468889999999999999999999999999999999999999999999
Q ss_pred CCccchhhHHHHHHhhhhcccccCCCCCCCCC
Q 030687 142 KDWTVQLLTVACLSLAAKMEESEVPLLVELQV 173 (173)
Q Consensus 142 ~~w~lQLlgvaCL~LAaK~EE~~~P~~~dlqv 173 (173)
++|++||||+|||+|||||||+.+|.+.|+||
T Consensus 119 k~W~lQLlAvaCLsLAsKmeE~~vPll~dl~v 150 (335)
T KOG0656|consen 119 KPWMLQLLAVACLSLASKMEETDVPLLADLQV 150 (335)
T ss_pred chHHHHHHHHHHHHHHHhhcCcCCchhhhhhh
Confidence 99999999999999999999999999999997
No 2
>KOG0655 consensus G1/S-specific cyclin E [Cell cycle control, cell division, chromosome partitioning]
Probab=99.91 E-value=6.3e-25 Score=187.97 Aligned_cols=102 Identities=32% Similarity=0.560 Sum_probs=93.6
Q ss_pred CHHHHHHHHHHHHhccCCCccchhhccCCCCCHHHHHHHHHHHHHHHHHhcCChhHHHHHHHHHHHHhhcc-ccCCCCCc
Q 030687 66 VSEELLREMAVKEGELLPKHDYLNRLRSGDLDSRVRREALDWILKAHAHYRFGPMSFCLSMNYLDRFLSVY-ELPKGKDW 144 (173)
Q Consensus 66 y~~eil~~L~~~E~~~~p~~~yl~~~q~~~i~~~~R~~lvdWi~~v~~~~~l~~eT~~LAVnylDRfLs~~-~v~~~~~w 144 (173)
...+++..|+.||+.|+....++. |+++++++||++++|||++||+.|+|.+|||||||.|+||||... .+.+..
T Consensus 112 n~~eVW~lM~kkee~~l~~~~~l~--qHpdlqp~mRaILlDWlmEVCEvykLHRETFyLAvDy~DRyl~t~~~v~kt~-- 187 (408)
T KOG0655|consen 112 NSKEVWLLMLKKEERYLRDKHFLE--QHPDLQPQMRAILLDWLMEVCEVYKLHRETFYLAVDYFDRYLETQVEVSKTN-- 187 (408)
T ss_pred CHHHHHHHHHccchhhhhhhHHHh--hCCCCCHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhhh--
Confidence 678999999999999887766665 478999999999999999999999999999999999999999764 778877
Q ss_pred cchhhHHHHHHhhhhcccccCCCCCCCC
Q 030687 145 TVQLLTVACLSLAAKMEESEVPLLVELQ 172 (173)
Q Consensus 145 ~lQLlgvaCL~LAaK~EE~~~P~~~dlq 172 (173)
|||+|+||||||||+||++||++.+|.
T Consensus 188 -lQLIGitsLFIAAK~EEIYpPKl~eFA 214 (408)
T KOG0655|consen 188 -LQLIGITSLFIAAKLEEIYPPKLIEFA 214 (408)
T ss_pred -HHHhhHHHHHHHHHHhhccCcccccee
Confidence 999999999999999999999999874
No 3
>KOG0653 consensus Cyclin B and related kinase-activating proteins [Cell cycle control, cell division, chromosome partitioning]
Probab=99.88 E-value=4.2e-23 Score=182.36 Aligned_cols=103 Identities=27% Similarity=0.524 Sum_probs=93.9
Q ss_pred CCCCHHHHHHHHHHHHhccCCCccchhhccCCCCCHHHHHHHHHHHHHHHHHhcCChhHHHHHHHHHHHHhhccccCCCC
Q 030687 63 FQTVSEELLREMAVKEGELLPKHDYLNRLRSGDLDSRVRREALDWILKAHAHYRFGPMSFCLSMNYLDRFLSVYELPKGK 142 (173)
Q Consensus 63 f~~y~~eil~~L~~~E~~~~p~~~yl~~~q~~~i~~~~R~~lvdWi~~v~~~~~l~~eT~~LAVnylDRfLs~~~v~~~~ 142 (173)
..+|.++++.++..+|..+.|...+ .++++++..||.++|||+++||..|++.+||+|||||++||||+...++..+
T Consensus 123 ~~ey~~di~~~l~~~e~~~~p~~~~---~~~~e~~~~mR~iLvdwlvevh~~F~L~~ETL~LaVnliDRfL~~~~v~~~~ 199 (391)
T KOG0653|consen 123 IVEYVQDIFEYLRQLELEFLPLSYD---ISQSEIRAKMRAILVDWLVEVHEKFGLSPETLYLAVNLIDRFLSKVKVPLKK 199 (391)
T ss_pred HHHHHHHHHHHHHHHHHhhCchhhh---cccccccHHHHHHHHHHHHHhhhhcCcCHHHHHHHHHHHHHHHHHhcccHHH
Confidence 4589999999999999766776544 3467899999999999999999999999999999999999999999999998
Q ss_pred CccchhhHHHHHH-hhhhcccccCCCCCCC
Q 030687 143 DWTVQLLTVACLS-LAAKMEESEVPLLVEL 171 (173)
Q Consensus 143 ~w~lQLlgvaCL~-LAaK~EE~~~P~~~dl 171 (173)
+||+|++||+ ||+|+||..+|.+.||
T Consensus 200 ---lqLvgvsalf~IA~K~EE~~~P~v~dl 226 (391)
T KOG0653|consen 200 ---LQLVGVSALLSIACKYEEISLPSVEDL 226 (391)
T ss_pred ---hhHHhHHHHHHHHHhhhhccCCcccee
Confidence 9999999966 9999999999999887
No 4
>COG5024 Cyclin [Cell division and chromosome partitioning]
Probab=99.86 E-value=5.5e-23 Score=183.11 Aligned_cols=106 Identities=26% Similarity=0.460 Sum_probs=99.5
Q ss_pred CcCCCCCHHHHHHHHHHHHhccCCCccchhhccCCCCCHHHHHHHHHHHHHHHHHhcCChhHHHHHHHHHHHHhhccccC
Q 030687 60 FFPFQTVSEELLREMAVKEGELLPKHDYLNRLRSGDLDSRVRREALDWILKAHAHYRFGPMSFCLSMNYLDRFLSVYELP 139 (173)
Q Consensus 60 ~~pf~~y~~eil~~L~~~E~~~~p~~~yl~~~q~~~i~~~~R~~lvdWi~~v~~~~~l~~eT~~LAVnylDRfLs~~~v~ 139 (173)
.++ +|+.+|+.+|+++|..++|...|+.+ +..+...||..+++||.+||..|++-|+|++||||++||||+...++
T Consensus 176 mv~--Ey~~~Ife~l~k~e~~~lp~~~yl~k--q~~~~~~mR~~Lv~wlvevH~~F~llpeTL~lainiiDrfLs~~~v~ 251 (440)
T COG5024 176 MVP--EYASDIFEYLLKLELIDLPNPNYLIK--QSLYEWSMRSILVDWLVEVHGKFGLLPETLFLAINIIDRFLSSRVVS 251 (440)
T ss_pred chH--HHHHHHHHHHHHHHHHhcCcHHHHhh--cchhHHhHHHHHHHHHHHhcccccccchHHHHHHHHHHHHhccCccc
Confidence 346 99999999999999999999999654 66788899999999999999999999999999999999999999999
Q ss_pred CCCCccchhhHHHHHHhhhhcccccCCCCCCCC
Q 030687 140 KGKDWTVQLLTVACLSLAAKMEESEVPLLVELQ 172 (173)
Q Consensus 140 ~~~~w~lQLlgvaCL~LAaK~EE~~~P~~~dlq 172 (173)
-++ +||+|++||+||+|+||+++|.+.+|+
T Consensus 252 l~k---~QLvg~s~LfIa~K~EE~~~p~i~~l~ 281 (440)
T COG5024 252 LEK---YQLVGISALFIASKYEEVNCPSIKDLV 281 (440)
T ss_pred HHH---HHHHHHHHHHHHHhHhHhcCHHHHHHH
Confidence 999 999999999999999999999988875
No 5
>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=99.84 E-value=2.3e-21 Score=143.79 Aligned_cols=98 Identities=33% Similarity=0.630 Sum_probs=87.1
Q ss_pred HHHHHHHHHHhccCCCccchhhccCCCCCHHHHHHHHHHHHHHHHHhcCChhHHHHHHHHHHHHhhccccCCCCCccchh
Q 030687 69 ELLREMAVKEGELLPKHDYLNRLRSGDLDSRVRREALDWILKAHAHYRFGPMSFCLSMNYLDRFLSVYELPKGKDWTVQL 148 (173)
Q Consensus 69 eil~~L~~~E~~~~p~~~yl~~~q~~~i~~~~R~~lvdWi~~v~~~~~l~~eT~~LAVnylDRfLs~~~v~~~~~w~lQL 148 (173)
||+.+|+++|.++.|..+|++. +++++...|..+++||.+++..+++++.|+++|++|+|||+...++.+.+ +++
T Consensus 1 ~i~~~~~~~e~~~~~~~~~~~~--~~~~~~~~r~~~~~~i~~~~~~~~l~~~~~~~A~~~~dr~~~~~~~~~~~---~~l 75 (127)
T PF00134_consen 1 DIFRYLLEKELKYKPNPDYLEQ--QPEITPEMRQIIIDWIIELCQRLKLSPETLHLAIYLFDRFLSKRPVNRSK---LQL 75 (127)
T ss_dssp HHHHHHHHHHHHTTCCTTHGTG--TSSHHHHHHHHHHHHHHHHHHHTT-BHHHHHHHHHHHHHHHTTS-TTCCG---HHH
T ss_pred CHHHHHHHHHHHHCcCcccccc--ChhcCHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHhhcccccch---hhh
Confidence 7899999999999999999985 44789999999999999999999999999999999999999999988888 999
Q ss_pred hHHHHHHhhhhcccccCCCCCCC
Q 030687 149 LTVACLSLAAKMEESEVPLLVEL 171 (173)
Q Consensus 149 lgvaCL~LAaK~EE~~~P~~~dl 171 (173)
+|+||++||+|++|..+|.+.++
T Consensus 76 i~~~cl~lA~K~~e~~~~~~~~~ 98 (127)
T PF00134_consen 76 IALACLFLASKMEEDNPPSISDL 98 (127)
T ss_dssp HHHHHHHHHHHHHTSS--HHHHH
T ss_pred hhhhHHHHhhhhhccccchHHHH
Confidence 99999999999999988876543
No 6
>KOG0654 consensus G2/Mitotic-specific cyclin A [Cell cycle control, cell division, chromosome partitioning]
Probab=99.55 E-value=3.9e-16 Score=136.23 Aligned_cols=103 Identities=27% Similarity=0.480 Sum_probs=97.7
Q ss_pred CCHHHHHHHHHHHHhc-cCCCccchhhccCCCCCHHHHHHHHHHHHHHHHHhcCChhHHHHHHHHHHHHhhccccCCCCC
Q 030687 65 TVSEELLREMAVKEGE-LLPKHDYLNRLRSGDLDSRVRREALDWILKAHAHYRFGPMSFCLSMNYLDRFLSVYELPKGKD 143 (173)
Q Consensus 65 ~y~~eil~~L~~~E~~-~~p~~~yl~~~q~~~i~~~~R~~lvdWi~~v~~~~~l~~eT~~LAVnylDRfLs~~~v~~~~~ 143 (173)
.|..+|++++..-|.+ ++|.++|++.+|. ++++.||.++|+|.++|.+.+++..+|+|+++++.||||+...+.+.+
T Consensus 101 ~~~~~I~~~~r~~ei~~~rp~~~~~e~vq~-d~t~smrgilvdwlvevsee~r~~~e~l~ls~~~~drfl~~~~~~~~k- 178 (359)
T KOG0654|consen 101 KIAAKIYNTLRVSDIKSERPLPSKFEFVQA-DITPSMRGILVDWLVEVSEEYRLTFETLYLSVNYRDRFLSYKEVNKQK- 178 (359)
T ss_pred HHHHHHhhcccccchhhccCcccceeeeec-CCCcchhhhhhhhhhHHHHHHHhhhhheeecHHHHHHHhccCccHHHH-
Confidence 6899999999999999 9999999998864 899999999999999999999999999999999999999999999999
Q ss_pred ccchhhHHHHHHhhhhcccccCCCCCCC
Q 030687 144 WTVQLLTVACLSLAAKMEESEVPLLVEL 171 (173)
Q Consensus 144 w~lQLlgvaCL~LAaK~EE~~~P~~~dl 171 (173)
+|++|++|++||+|+||..+|.+.+|
T Consensus 179 --~ql~g~s~m~I~sk~ee~~~~~~~ef 204 (359)
T KOG0654|consen 179 --LQLVGISAMLIASKYEEIKEPRVEEF 204 (359)
T ss_pred --HHHhCcccceeeccchhhcchHHHHH
Confidence 99999999999999999999977665
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=99.37 E-value=9.4e-13 Score=89.74 Aligned_cols=67 Identities=36% Similarity=0.529 Sum_probs=60.5
Q ss_pred HHHHHHHHHHHHHHhcCChhHHHHHHHHHHHHhhccccCCCCCccchhhHHHHHHhhhhcccccCCCCCCC
Q 030687 101 RREALDWILKAHAHYRFGPMSFCLSMNYLDRFLSVYELPKGKDWTVQLLTVACLSLAAKMEESEVPLLVEL 171 (173)
Q Consensus 101 R~~lvdWi~~v~~~~~l~~eT~~LAVnylDRfLs~~~v~~~~~w~lQLlgvaCL~LAaK~EE~~~P~~~dl 171 (173)
|...++||.+++..++++++|.++|++++|||+....+.+.+ .+++|+||++||+|++|. +|...++
T Consensus 2 ~~~~~~~l~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~---~~~ia~a~l~lA~k~~~~-~~~~~~~ 68 (88)
T cd00043 2 RPTPLDFLRRVAKALGLSPETLTLAVNLLDRFLLDYSVLGRS---PSLVAAAALYLAAKVEEI-PPWLKDL 68 (88)
T ss_pred cchHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcccccCC---hHHHHHHHHHHHHHHcCC-CCCHHHH
Confidence 678899999999999999999999999999999998887666 999999999999999998 5665543
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=99.22 E-value=2e-11 Score=82.37 Aligned_cols=62 Identities=39% Similarity=0.537 Sum_probs=54.8
Q ss_pred HHHHHHHHHhcCChhHHHHHHHHHHHHhhccccCCCCCccchhhHHHHHHhhhhcccccCCCCCCC
Q 030687 106 DWILKAHAHYRFGPMSFCLSMNYLDRFLSVYELPKGKDWTVQLLTVACLSLAAKMEESEVPLLVEL 171 (173)
Q Consensus 106 dWi~~v~~~~~l~~eT~~LAVnylDRfLs~~~v~~~~~w~lQLlgvaCL~LAaK~EE~~~P~~~dl 171 (173)
+||.+++..+++++++.++|++++|||+....+.+.+ .+++|++|++||+|++|.. |...++
T Consensus 1 ~~l~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~---~~~ia~a~l~lA~k~~~~~-~~~~~~ 62 (83)
T smart00385 1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYS---PSLIAAAALYLAAKTEEIP-PWTKEL 62 (83)
T ss_pred CHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhcccCC---HHHHHHHHHHHHHHHhcCC-CCchhH
Confidence 5999999999999999999999999999977776666 9999999999999999986 444443
No 9
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=98.80 E-value=1.1e-08 Score=88.23 Aligned_cols=64 Identities=17% Similarity=0.277 Sum_probs=59.8
Q ss_pred HHHHHHHHHHHHHHHHhc--CChhHHHHHHHHHHHHhhccccCCCCCccchhhHHHHHHhhhhcccccC
Q 030687 99 RVRREALDWILKAHAHYR--FGPMSFCLSMNYLDRFLSVYELPKGKDWTVQLLTVACLSLAAKMEESEV 165 (173)
Q Consensus 99 ~~R~~lvdWi~~v~~~~~--l~~eT~~LAVnylDRfLs~~~v~~~~~w~lQLlgvaCL~LAaK~EE~~~ 165 (173)
..|.--...|.+++..++ +...|+..|+.||+||+....+...+ .+++++|||+||+|+||..+
T Consensus 54 ~l~~~y~~~i~~~~~~lkp~Lpq~viaTAivyf~RFy~~~Sv~~~~---p~~Ia~tclfLA~KvEE~~~ 119 (305)
T TIGR00569 54 DLVKYYEKRLLDFCSAFKPTMPTSVVGTAIMYFKRFYLNNSVMEYH---PKIIMLTCVFLACKVEEFNV 119 (305)
T ss_pred HHHHHHHHHHHHHHHHhcCCCCchHHHHHHHHHhHHhccCchhhcC---HHHHHHHHHHHHHhccccCc
Confidence 678888899999999999 99999999999999999999888777 99999999999999999854
No 10
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=98.31 E-value=9.5e-07 Score=76.83 Aligned_cols=63 Identities=22% Similarity=0.356 Sum_probs=59.9
Q ss_pred HHHHHHHHHHHHHHHHhcCChhHHHHHHHHHHHHhhccccCCCCCccchhhHHHHHHhhhhccccc
Q 030687 99 RVRREALDWILKAHAHYRFGPMSFCLSMNYLDRFLSVYELPKGKDWTVQLLTVACLSLAAKMEESE 164 (173)
Q Consensus 99 ~~R~~lvdWi~~v~~~~~l~~eT~~LAVnylDRfLs~~~v~~~~~w~lQLlgvaCL~LAaK~EE~~ 164 (173)
..|.....||.+++..+|+...|+..|+.|+.||.....+.+.. ...+|.+||+||+|+||+.
T Consensus 37 ~~r~~~~~fI~elg~~L~~~~~ti~tA~~~~hRFy~~~s~~~~~---~~~vA~sclfLAgKvEetp 99 (323)
T KOG0834|consen 37 RLRQEGAKFIQELGVRLKMPQKTIATAIVIFHRFYMFHSFKKFD---PYTVAASCLFLAGKVEETP 99 (323)
T ss_pred HHHHHHHHHHHHHHHHcCCCccchhhhhhhhhhhhhhcccccCc---HHHHHHHHHHHHhhcccCc
Confidence 78999999999999999999999999999999999999998887 7999999999999999973
No 11
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]
Probab=97.95 E-value=1.4e-05 Score=66.64 Aligned_cols=61 Identities=26% Similarity=0.347 Sum_probs=54.0
Q ss_pred HHHHHHHHHHHHHHHhcCChhHHHHHHHHHHHHhhccccCCCCCccchhhHHHHHHhhhhcccc
Q 030687 100 VRREALDWILKAHAHYRFGPMSFCLSMNYLDRFLSVYELPKGKDWTVQLLTVACLSLAAKMEES 163 (173)
Q Consensus 100 ~R~~lvdWi~~v~~~~~l~~eT~~LAVnylDRfLs~~~v~~~~~w~lQLlgvaCL~LAaK~EE~ 163 (173)
.+--.-+.|.+++++.++...++..|+.||-||+-+..+..-. ..|++.||++||+|+||.
T Consensus 40 l~i~~~n~I~~lg~~lklRQ~ViATAivY~rRfy~r~S~k~~~---p~lla~TClyLAcKvEE~ 100 (264)
T KOG0794|consen 40 LKIFMANVIQKLGQHLKLRQRVIATAIVYFRRFYLRKSLKEIE---PRLLAPTCLYLACKVEEC 100 (264)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccC---HHHHHHHHHHHHhhhhhc
Confidence 3445566788999999999999999999999999988877666 999999999999999997
No 12
>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=97.87 E-value=1.8e-05 Score=67.92 Aligned_cols=63 Identities=14% Similarity=0.239 Sum_probs=59.0
Q ss_pred HHHHHHHHHHHHHHHHHhcCChhHHHHHHHHHHHHhhccccCCCCCccchhhHHHHHHhhhhcccc
Q 030687 98 SRVRREALDWILKAHAHYRFGPMSFCLSMNYLDRFLSVYELPKGKDWTVQLLTVACLSLAAKMEES 163 (173)
Q Consensus 98 ~~~R~~lvdWi~~v~~~~~l~~eT~~LAVnylDRfLs~~~v~~~~~w~lQLlgvaCL~LAaK~EE~ 163 (173)
...|..-..||..+|.++++...++..||.+++||.....+..-. ++-++.||++||+|.||+
T Consensus 42 ~~l~i~~~k~i~~l~~~L~lp~~~laTAi~~f~Rf~Lk~sv~e~~---~~~vv~tcv~LA~K~ed~ 104 (297)
T COG5333 42 LNLVIYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEIS---LYSVVTTCVYLACKVEDT 104 (297)
T ss_pred hhHHHHHHHHHHHHHHhcCCCcchHHHHHHHHHHHHhhccccccc---HHHHHHhheeeeeecccc
Confidence 467888889999999999999999999999999999999988877 999999999999999995
No 13
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=97.44 E-value=0.00037 Score=60.70 Aligned_cols=63 Identities=19% Similarity=0.311 Sum_probs=58.4
Q ss_pred HHHHHHHHHHHHHHHHHhcCChhHHHHHHHHHHHHhhccccCCCCCccchhhHHHHHHhhhhcccc
Q 030687 98 SRVRREALDWILKAHAHYRFGPMSFCLSMNYLDRFLSVYELPKGKDWTVQLLTVACLSLAAKMEES 163 (173)
Q Consensus 98 ~~~R~~lvdWi~~v~~~~~l~~eT~~LAVnylDRfLs~~~v~~~~~w~lQLlgvaCL~LAaK~EE~ 163 (173)
...|.--+.||.+.+.-++|...+.+.+..+|-||...+.+-+.. +..++.||++||+|+||.
T Consensus 20 ~el~~LG~e~Iqea~ILL~L~q~a~atgqVLFqRf~~~ks~v~~~---~e~vv~ACv~LASKiEE~ 82 (367)
T KOG0835|consen 20 EELRILGCELIQEAGILLNLPQVAMATGQVLFQRFCYSKSFVRHD---FEIVVMACVLLASKIEEE 82 (367)
T ss_pred HHHHHHhHHHHHhhhHhhcCcHHHHHHHHHHHHHHHhcccccccc---HHHHHHHHHHHHhhhccc
Confidence 467888899999999999999999999999999999998887777 999999999999999996
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=96.54 E-value=0.0078 Score=46.52 Aligned_cols=56 Identities=23% Similarity=0.333 Sum_probs=43.8
Q ss_pred HHHHHHHHHHHhcCChhHHHHHHHHHHHHhh---cc--ccCCCCCccchhhHHHHHHhhhhccc
Q 030687 104 ALDWILKAHAHYRFGPMSFCLSMNYLDRFLS---VY--ELPKGKDWTVQLLTVACLSLAAKMEE 162 (173)
Q Consensus 104 lvdWi~~v~~~~~l~~eT~~LAVnylDRfLs---~~--~v~~~~~w~lQLlgvaCL~LAaK~EE 162 (173)
+.+++.++...-+++++++.+|..|+||+.. .. .+.... .+-+-++|+.+|+|+-+
T Consensus 54 i~~fl~ri~~~~~~s~~~~i~aliYl~Rl~~~~~~~~~~~~~~~---~~Rl~l~alilA~K~~~ 114 (149)
T PF08613_consen 54 IRDFLSRILKYTQCSPECLILALIYLDRLRQRSRKPNIPLNSSN---IHRLFLTALILASKFLD 114 (149)
T ss_dssp HHHHHHHHHHHTT--HHHHHHHHHHHHHHHH--H-TT---STTT---HHHHHHHHHHHHHHHH-
T ss_pred HHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhhcccccccccch---hHHHHHHHHHHHHhhcc
Confidence 7788999999999999999999999999998 22 233333 77899999999999944
No 15
>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=95.17 E-value=0.095 Score=35.21 Aligned_cols=54 Identities=11% Similarity=0.062 Sum_probs=42.4
Q ss_pred HHHHHHHhcCChhHHHHHHHHHHHHhhccccCCCCCccchhhHHHHHHhhhhccccc
Q 030687 108 ILKAHAHYRFGPMSFCLSMNYLDRFLSVYELPKGKDWTVQLLTVACLSLAAKMEESE 164 (173)
Q Consensus 108 i~~v~~~~~l~~eT~~LAVnylDRfLs~~~v~~~~~w~lQLlgvaCL~LAaK~EE~~ 164 (173)
|-+++..++|+..+.-.|..++.+-....-....+ ..-++++|+++|++.+...
T Consensus 1 I~r~~~~L~L~~~v~~~A~~i~~~~~~~~~~~Gr~---~~~iaAA~iY~acr~~~~~ 54 (71)
T PF00382_consen 1 IPRICSKLGLPEDVRERAKEIYKKAQERGLLKGRS---PESIAAACIYLACRLNGVP 54 (71)
T ss_dssp HHHHHHHTT--HHHHHHHHHHHHHHHHTTTSTTS----HHHHHHHHHHHHHHHTTSS
T ss_pred ChHHHhHcCCCHHHHHHHHHHHHHHHHcCCcccCC---HHHHHHHHHHHHHHHcCCC
Confidence 45789999999999999999998877765555444 8899999999999997653
No 16
>KOG4164 consensus Cyclin ik3-1/CABLES [Cell cycle control, cell division, chromosome partitioning]
Probab=94.56 E-value=0.036 Score=49.69 Aligned_cols=65 Identities=20% Similarity=0.235 Sum_probs=55.3
Q ss_pred CCHHHHHHHHHHHHHHHHHhcCChhHHHHHHHHHHHHhhccccCCCCCccchhhHHHHHHhhhhcccc
Q 030687 96 LDSRVRREALDWILKAHAHYRFGPMSFCLSMNYLDRFLSVYELPKGKDWTVQLLTVACLSLAAKMEES 163 (173)
Q Consensus 96 i~~~~R~~lvdWi~~v~~~~~l~~eT~~LAVnylDRfLs~~~v~~~~~w~lQLlgvaCL~LAaK~EE~ 163 (173)
+|...-+-+-.=|.++....++..-|+..|..||....-+..+.+.. -.|.|-|||.||+||.+.
T Consensus 377 LTLSKirSlKREMr~l~~d~~id~~TVa~AyVYFEKliLkglisK~N---RKlcAGAclLlaaKmnD~ 441 (497)
T KOG4164|consen 377 LTLSKIRSLKREMRELGEDCGIDVVTVAMAYVYFEKLILKGLISKQN---RKLCAGACLLLAAKMNDL 441 (497)
T ss_pred EeHHHHHHHHHHHHHhhhccCccceeehhHHHHHHHHHHhhhhhhhh---hhHHHHHHHHHHHHhhhh
Confidence 55544455566678889999999999999999999988888888877 899999999999999754
No 17
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=94.42 E-value=0.19 Score=43.40 Aligned_cols=61 Identities=8% Similarity=-0.100 Sum_probs=53.3
Q ss_pred HHHHHHHHHHHHHHHhcCChhHHHHHHHHHHHHhhccccCCCCCccchhhHHHHHHhhhhcccc
Q 030687 100 VRREALDWILKAHAHYRFGPMSFCLSMNYLDRFLSVYELPKGKDWTVQLLTVACLSLAAKMEES 163 (173)
Q Consensus 100 ~R~~lvdWi~~v~~~~~l~~eT~~LAVnylDRfLs~~~v~~~~~w~lQLlgvaCL~LAaK~EE~ 163 (173)
.-.....-|-.++..+++...+.-.|..++.++.....+.... ...+++||+++|+|.++.
T Consensus 121 ~l~~a~~~I~~~~~~L~Lp~~v~e~A~~iyk~~~~~~~~rgrs---~~~i~AAclYiACR~~~~ 181 (310)
T PRK00423 121 NLAFALSELDRIASQLGLPRSVREEAAVIYRKAVEKGLIRGRS---IEGVVAAALYAACRRCKV 181 (310)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCC---HHHHHHHHHHHHHHHcCC
Confidence 3355667788999999999999999999999999887777666 899999999999999876
No 18
>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=93.52 E-value=0.44 Score=41.45 Aligned_cols=55 Identities=15% Similarity=0.339 Sum_probs=44.0
Q ss_pred HHHHHHHh--cCChhHHHHHHHHHHHHhhccccCCCCCccchhhHHHHHHhhhhcccccC
Q 030687 108 ILKAHAHY--RFGPMSFCLSMNYLDRFLSVYELPKGKDWTVQLLTVACLSLAAKMEESEV 165 (173)
Q Consensus 108 i~~v~~~~--~l~~eT~~LAVnylDRfLs~~~v~~~~~w~lQLlgvaCL~LAaK~EE~~~ 165 (173)
+.+.+..| .+.+.++-.|+.+|-||.-...+..-. -..|..||+++|+|+||-++
T Consensus 63 l~~f~~k~~p~lp~~Vv~TA~~fFkRffL~nsvme~~---pk~I~~tc~flA~Kieef~I 119 (325)
T KOG2496|consen 63 LVNFYSKFKPNLPTSVVSTAIEFFKRFFLENSVMEYS---PKIIMATCFFLACKIEEFYI 119 (325)
T ss_pred HHHHHHHhcCCCchHHHHHHHHHHHHHHHhcchhhcC---hHHHHHHHHHHHhhhHhhee
Confidence 33444444 457888999999999998887777666 78899999999999999653
No 19
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=84.41 E-value=3.4 Score=35.68 Aligned_cols=56 Identities=9% Similarity=0.022 Sum_probs=43.4
Q ss_pred HHHHHHHHHHhcCChhHHHHHHHHHHHHhhccccCCCCCccchhhHHHHHHhhhhcccc
Q 030687 105 LDWILKAHAHYRFGPMSFCLSMNYLDRFLSVYELPKGKDWTVQLLTVACLSLAAKMEES 163 (173)
Q Consensus 105 vdWi~~v~~~~~l~~eT~~LAVnylDRfLs~~~v~~~~~w~lQLlgvaCL~LAaK~EE~ 163 (173)
-+.|...+..++++..+.-.|..++.+.....-....+ -.-+++||+++|++....
T Consensus 220 ~~~i~r~~~~L~L~~~v~~~A~~i~~~a~~~~l~~Gr~---P~sIAAAaIYlA~~~~g~ 275 (310)
T PRK00423 220 IDYVPRFASELGLSGEVQKKAIEILQKAKEKGLTSGKG---PTGLAAAAIYIASLLLGE 275 (310)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCC---HHHHHHHHHHHHHHHhCC
Confidence 47777888888888888888888888776544333334 889999999999998654
No 20
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=84.09 E-value=0.93 Score=39.76 Aligned_cols=66 Identities=21% Similarity=0.227 Sum_probs=45.4
Q ss_pred HHHHHHHHHHHHHhcCChhHHHHHHHHHHHHhhccccCCCCCccchhhHHHHHHhhhhcccccCCCCCC
Q 030687 102 REALDWILKAHAHYRFGPMSFCLSMNYLDRFLSVYELPKGKDWTVQLLTVACLSLAAKMEESEVPLLVE 170 (173)
Q Consensus 102 ~~lvdWi~~v~~~~~l~~eT~~LAVnylDRfLs~~~v~~~~~w~lQLlgvaCL~LAaK~EE~~~P~~~d 170 (173)
.-+++++.++-..-+........|.+++...+...-+-+-+ -+-+|++|++||+|+-...+|...+
T Consensus 153 ~~ll~~~k~l~~~~~~~~~~a~~Aw~~~nD~~~t~~cL~y~---p~~IAva~i~lA~~~~~~~~~~~~~ 218 (323)
T KOG0834|consen 153 KYLLKYLKKLKADENLKQPLAQAAWNFVNDSLRTTLCLQYS---PHSIAVACIHLAAKLLGVELPSDTD 218 (323)
T ss_pred HHHHHHHHHhhhhhhccccHHHHHHHHhchhheeeeeEeec---CcEEEeehhhHHHHHcCCCCCCCcc
Confidence 44566666665555555456677777777777655444444 7789999999999997776666544
No 21
>KOG1674 consensus Cyclin [General function prediction only]
Probab=82.54 E-value=2.8 Score=34.61 Aligned_cols=57 Identities=18% Similarity=0.379 Sum_probs=41.3
Q ss_pred HHHHHHHHhcCChhHHHHHHHHHHHHhhccc---cCCCC---Ccc-chhhHHHHHHhhhhcccc
Q 030687 107 WILKAHAHYRFGPMSFCLSMNYLDRFLSVYE---LPKGK---DWT-VQLLTVACLSLAAKMEES 163 (173)
Q Consensus 107 Wi~~v~~~~~l~~eT~~LAVnylDRfLs~~~---v~~~~---~w~-lQLlgvaCL~LAaK~EE~ 163 (173)
.+..+..+-+.+++++.+|..|||||....+ +.+.. ..+ ..-+-++|+.+|+|+.+.
T Consensus 81 yleri~k~~~~s~~~lv~al~Yldr~~~~~~~~~~~~~~~i~s~n~vhR~lit~v~vs~kf~~d 144 (218)
T KOG1674|consen 81 YLERIFKYSKCSPECLVLALVYLDRFVKQPQARSVKPQSLINSLNKVHRLLITTVTVSTKFLDD 144 (218)
T ss_pred HHHHHHHHhcCCchhhhhhhhhhhhhhhhhcccccCcccccccchhHHHHHHHHHHHHHhhccc
Confidence 4445777888999999999999999998733 22111 112 444678999999999853
No 22
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=76.26 E-value=8.7 Score=33.08 Aligned_cols=57 Identities=11% Similarity=0.026 Sum_probs=46.6
Q ss_pred HHHHHHHHHHHHhcCChhHHHHHHHHHHHHhhccccCCCCCccchhhHHHHHHhhhhccc
Q 030687 103 EALDWILKAHAHYRFGPMSFCLSMNYLDRFLSVYELPKGKDWTVQLLTVACLSLAAKMEE 162 (173)
Q Consensus 103 ~lvdWi~~v~~~~~l~~eT~~LAVnylDRfLs~~~v~~~~~w~lQLlgvaCL~LAaK~EE 162 (173)
+-.++|-..+..++|+.++--.|..+++............ -.-++++|+++|+++..
T Consensus 193 ~p~~yi~rf~s~L~l~~~v~~~a~ei~~~~~~~g~~~Gk~---P~glAaaaiy~as~l~~ 249 (285)
T COG1405 193 DPSDYIPRFASKLGLSDEVRRKAIEIVKKAKRAGLTAGKS---PAGLAAAAIYLASLLLG 249 (285)
T ss_pred CHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCcccCCC---chhHHHHHHHHHHHHhC
Confidence 3467788889999999999999999999988765444444 67789999999999854
No 23
>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=74.59 E-value=5 Score=28.25 Aligned_cols=54 Identities=19% Similarity=0.118 Sum_probs=35.5
Q ss_pred HHHHHHHHHhcCChhHHHHHHHHHHHHhhccccCCCCCccchhhHHHHHHhhhhccc
Q 030687 106 DWILKAHAHYRFGPMSFCLSMNYLDRFLSVYELPKGKDWTVQLLTVACLSLAAKMEE 162 (173)
Q Consensus 106 dWi~~v~~~~~l~~eT~~LAVnylDRfLs~~~v~~~~~w~lQLlgvaCL~LAaK~EE 162 (173)
+|+.......+...++..+|-.+++-.+....+-.-+ --++|++|+++|.++-.
T Consensus 5 ~Fl~~~~~~~~~~~~~~~~a~~l~el~l~~~~fl~~~---PS~iAaAai~lA~~~~~ 58 (118)
T PF02984_consen 5 DFLRRFLKISNADQEVRNLARYLLELSLLDYEFLQYP---PSVIAAAAILLARKILG 58 (118)
T ss_dssp HHHHHHHTSSSHHHHHHHHHHHHHHHHHHSHHHTTS----HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHcCCcHHHHHHHHHHHHHHHhhccccCCC---HHHHHHHHHHHHHHHhC
Confidence 4444443334445567777778888766665554444 67899999999999843
No 24
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=70.44 E-value=11 Score=32.91 Aligned_cols=59 Identities=17% Similarity=0.131 Sum_probs=48.2
Q ss_pred HHHHHHHHHHHHHhcCChhHHHHHHHHHHHHhhccccCCCCCccchhhHHHHHHhhhhcccc
Q 030687 102 REALDWILKAHAHYRFGPMSFCLSMNYLDRFLSVYELPKGKDWTVQLLTVACLSLAAKMEES 163 (173)
Q Consensus 102 ~~lvdWi~~v~~~~~l~~eT~~LAVnylDRfLs~~~v~~~~~w~lQLlgvaCL~LAaK~EE~ 163 (173)
.....=|..++...+|.....-.|=.++-++-......... .+-+..|||+||++-++.
T Consensus 105 ~~a~~~I~~m~d~~~Lp~~I~d~A~~ifk~v~~~k~lrGks---~eai~AAclyiACRq~~~ 163 (308)
T KOG1597|consen 105 KAAFKEITAMCDRLSLPATIKDRANEIFKLVEDSKLLRGKS---VEALAAACLYIACRQEDV 163 (308)
T ss_pred HHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHhhhhcCcc---HHHHHHHHHHHHHHhcCC
Confidence 34455567888999999888888888888888776666666 999999999999998875
No 25
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=48.81 E-value=33 Score=30.46 Aligned_cols=23 Identities=30% Similarity=0.488 Sum_probs=18.9
Q ss_pred chhhHHHHHHhhhhcccccCCCC
Q 030687 146 VQLLTVACLSLAAKMEESEVPLL 168 (173)
Q Consensus 146 lQLlgvaCL~LAaK~EE~~~P~~ 168 (173)
-.+|+.+|.++||.-+|+-.|..
T Consensus 182 pe~iACaciyLaAR~~eIpLp~~ 204 (367)
T KOG0835|consen 182 PESIACACIYLAARNLEIPLPFQ 204 (367)
T ss_pred HHHHHHHHHHHHHhhhcCCCCCC
Confidence 56899999999999999655543
No 26
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=41.03 E-value=1.3e+02 Score=25.86 Aligned_cols=62 Identities=11% Similarity=0.078 Sum_probs=52.7
Q ss_pred HHHHHHHHHHHHHHHHhcCChhHHHHHHHHHHHHhhccccCCCCCccchhhHHHHHHhhhhcccc
Q 030687 99 RVRREALDWILKAHAHYRFGPMSFCLSMNYLDRFLSVYELPKGKDWTVQLLTVACLSLAAKMEES 163 (173)
Q Consensus 99 ~~R~~lvdWi~~v~~~~~l~~eT~~LAVnylDRfLs~~~v~~~~~w~lQLlgvaCL~LAaK~EE~ 163 (173)
..-..+..-|-.++..+++.....-.|..++=+.+...-+.... .+-+.++|+++|++....
T Consensus 95 rnl~~a~~~l~~~~~~l~LP~~v~e~A~~iyr~a~~~~l~rGRs---ie~v~AA~iY~acR~~~~ 156 (285)
T COG1405 95 RNLITALEELERIASALGLPESVRETAARIYRKAVDKGLLRGRS---IESVAAACIYAACRINGV 156 (285)
T ss_pred hHHHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHhhcCCCcCCc---HHHHHHHHHHHHHHHcCC
Confidence 34556777788899999999999999999988888887777666 999999999999999765
No 27
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=40.72 E-value=1.3e+02 Score=28.36 Aligned_cols=78 Identities=14% Similarity=0.217 Sum_probs=56.5
Q ss_pred CCccchhhccCCCC-CHHHHHHHHH----HHHHHHHHhcCChhHHHHHHHHHHHHhhccccCCCCCccchhhHHHHHHhh
Q 030687 83 PKHDYLNRLRSGDL-DSRVRREALD----WILKAHAHYRFGPMSFCLSMNYLDRFLSVYELPKGKDWTVQLLTVACLSLA 157 (173)
Q Consensus 83 p~~~yl~~~q~~~i-~~~~R~~lvd----Wi~~v~~~~~l~~eT~~LAVnylDRfLs~~~v~~~~~w~lQLlgvaCL~LA 157 (173)
+...|+...|.+-- ....|...+. -|..++..+++.. ..-.|+|++---++..-.+... .+.+-.+||+|+
T Consensus 44 ~~G~~v~~~~~g~~~s~e~r~~t~~n~r~~i~~~~~~l~l~~-~~~~a~~~~k~a~~~nftkGr~---~~~vvasClY~v 119 (521)
T KOG1598|consen 44 AQGQFVRVGQSGAGSSLESREKTIYNARRLIEELTERLNLGN-KTEVAFNFFKLAPDRNFTKGRR---STEVVAACLYLV 119 (521)
T ss_pred cceeEEeccccCCccchHHHHHHHHHHHhHHHHHHHhcCcch-HHHHHHHHHHHHhhCCCCCCcc---hHHHHHHHHHHH
Confidence 55556555444322 3344443332 4678999999998 8889999998888877666666 999999999999
Q ss_pred hhccccc
Q 030687 158 AKMEESE 164 (173)
Q Consensus 158 aK~EE~~ 164 (173)
+..|-+.
T Consensus 120 cR~e~t~ 126 (521)
T KOG1598|consen 120 CRLEKTD 126 (521)
T ss_pred HHhhCCc
Confidence 9988664
No 28
>TIGR01446 DnaD_dom DnaD and phage-associated domain. This model represents the conserved domain of DnaD, part of Bacillus subtilis replication restart primosome, and of a number of phage-associated proteins. Members, both chromosomal or phage-associated, are found in the Bacillus/Clostridium group of Gram-positive bacteria.
Probab=40.25 E-value=73 Score=20.89 Aligned_cols=31 Identities=10% Similarity=0.115 Sum_probs=25.5
Q ss_pred CCCCHHHHHHHHHHHHHHHHHhcCChhHHHHHHHH
Q 030687 94 GDLDSRVRREALDWILKAHAHYRFGPMSFCLSMNY 128 (173)
Q Consensus 94 ~~i~~~~R~~lvdWi~~v~~~~~l~~eT~~LAVny 128 (173)
+.+++.....+.+|+ ..++++++.+..|+.+
T Consensus 11 r~ls~~e~~~i~~~~----~~~~~~~evI~~ai~~ 41 (73)
T TIGR01446 11 RMLSPFEMEDLKYWL----DEFGNSPELIKEALKE 41 (73)
T ss_pred CCCCHHHHHHHHHHH----HHhCCCHHHHHHHHHH
Confidence 358888899999987 4678889999888876
No 29
>PF14376 Haem_bd: Haem-binding domain
Probab=34.64 E-value=51 Score=25.05 Aligned_cols=35 Identities=20% Similarity=0.341 Sum_probs=28.1
Q ss_pred HHhccCCCccchhhccCCCCCHHHHHHHHHHHHHH
Q 030687 77 KEGELLPKHDYLNRLRSGDLDSRVRREALDWILKA 111 (173)
Q Consensus 77 ~E~~~~p~~~yl~~~q~~~i~~~~R~~lvdWi~~v 111 (173)
.+..-+|...|.--.....+|...|..+++|+.+.
T Consensus 102 I~~g~MP~~~Y~~~H~~a~Ls~~ek~~Ll~Wi~~~ 136 (137)
T PF14376_consen 102 IEDGEMPPPSYTLLHWEAKLSEEEKQALLNWIKEQ 136 (137)
T ss_pred HHcCCCChHHHhhhCCCCCCCHHHHHHHHHHHHHc
Confidence 35557898889776566679999999999999753
No 30
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=34.19 E-value=1.6e+02 Score=25.60 Aligned_cols=42 Identities=12% Similarity=0.010 Sum_probs=27.1
Q ss_pred HHHHHHHHHHhhccccCCCCCccchhhHHHHHHhhhhcccccCCC
Q 030687 123 CLSMNYLDRFLSVYELPKGKDWTVQLLTVACLSLAAKMEESEVPL 167 (173)
Q Consensus 123 ~LAVnylDRfLs~~~v~~~~~w~lQLlgvaCL~LAaK~EE~~~P~ 167 (173)
..|.++++..+...-.-.-. -+.||+||+++|+|..-...|.
T Consensus 185 q~a~~~lndsl~Td~~L~y~---Ps~IAlAAI~lA~~~~~~~l~~ 226 (305)
T TIGR00569 185 KHADKFLNRTLLTDAYLLYT---PSQIALAAILHTASRAGLNMES 226 (305)
T ss_pred HHHHHHHHHHHcCCceecCC---HHHHHHHHHHHHHHHhCCCCcc
Confidence 55667766544333222233 6789999999999986655554
No 31
>PF12550 GCR1_C: Transcriptional activator of glycolytic enzymes; InterPro: IPR022210 This domain family is found in eukaryotes, and is approximately 80 amino acids in length. This family is activates the transcription of glycolytic enzymes.
Probab=27.95 E-value=1.3e+02 Score=20.50 Aligned_cols=53 Identities=11% Similarity=0.122 Sum_probs=33.3
Q ss_pred HHHHHhccCCCccchhhccCCCCCHHHHHHHHHHHHHHHHHhcCChhHHHHHHHHHHHH
Q 030687 74 MAVKEGELLPKHDYLNRLRSGDLDSRVRREALDWILKAHAHYRFGPMSFCLSMNYLDRF 132 (173)
Q Consensus 74 L~~~E~~~~p~~~yl~~~q~~~i~~~~R~~lvdWi~~v~~~~~l~~eT~~LAVnylDRf 132 (173)
..+.|.+|... +-.. ....-+...|..+|++|.++....|++.+ -|+..+|.+
T Consensus 28 I~~le~~yG~~--WR~~-~~~~~~y~rRK~Ii~~I~~l~~~~g~~~~---~ai~~le~~ 80 (81)
T PF12550_consen 28 IRSLEKKYGSK--WRRD-SKERRTYSRRKVIIDFIERLANERGISEE---EAIEILEEI 80 (81)
T ss_pred HHHHHHHhChh--hccC-cccchhHHHHHHHHHHHHHHHHHcCCCHH---HHHHHHHhc
Confidence 45667776532 1111 01123457799999999999888777655 457777754
No 32
>cd04441 DEP_2_DEP6 DEP (Dishevelled, Egl-10, and Pleckstrin) domain 2 found in DEP6-like proteins. DEP6 proteins contain two DEP and a PDZ domain. Their function is unknown.
Probab=26.41 E-value=70 Score=22.58 Aligned_cols=29 Identities=21% Similarity=0.351 Sum_probs=15.9
Q ss_pred HHHHHHHHHHHHHhcCChhHHHHHHHHHHH
Q 030687 102 REALDWILKAHAHYRFGPMSFCLSMNYLDR 131 (173)
Q Consensus 102 ~~lvdWi~~v~~~~~l~~eT~~LAVnylDR 131 (173)
.++||||++-. ...-..+++.++-.++|.
T Consensus 36 sElVdWL~~~~-~~~sR~eAv~lgq~Ll~~ 64 (85)
T cd04441 36 SEFIDWLLQEG-EAESRREAVQLCRRLLEH 64 (85)
T ss_pred hHHHHHHHHcC-CCCCHHHHHHHHHHHHHC
Confidence 58999999854 222233444444444443
No 33
>cd04449 DEP_DEPDC5-like DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in DEPDC5-like proteins. DEPDC5, in human also known as KIAA0645, is a DEP domain containing protein of unknown function.
Probab=25.78 E-value=76 Score=21.87 Aligned_cols=31 Identities=13% Similarity=0.308 Sum_probs=16.6
Q ss_pred HHHHHHHHHHHHHHhcCChhHHHHHHHHHHH
Q 030687 101 RREALDWILKAHAHYRFGPMSFCLSMNYLDR 131 (173)
Q Consensus 101 R~~lvdWi~~v~~~~~l~~eT~~LAVnylDR 131 (173)
=.++|+||.+-.....-..+.+.++-.++|.
T Consensus 32 G~e~VdWL~~~~~~~~~r~eAv~lgq~Ll~~ 62 (83)
T cd04449 32 GSEAVSWLINNFEDVDTREEAVELGQELMNE 62 (83)
T ss_pred hHHHHHHHHHhCCCCCCHHHHHHHHHHHHHC
Confidence 4689999997433222233444444444443
No 34
>cd04443 DEP_GPR155 DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in GPR155-like proteins. GRP155-like proteins, also known as PGR22, contain an N-terminal permease domain, a central transmembrane region and a C-terminal DEP domain. They are orphan receptors of the class B G protein-coupled receptors. Their function is unknown.
Probab=24.88 E-value=80 Score=22.06 Aligned_cols=30 Identities=7% Similarity=0.134 Sum_probs=16.5
Q ss_pred HHHHHHHHHHHHHHhcCChhHHHHHHHHHHH
Q 030687 101 RREALDWILKAHAHYRFGPMSFCLSMNYLDR 131 (173)
Q Consensus 101 R~~lvdWi~~v~~~~~l~~eT~~LAVnylDR 131 (173)
=..+|+||++... -.-..+.+.++-.++|.
T Consensus 33 GselVdWL~~~~~-~~sR~eAv~lg~~Ll~~ 62 (83)
T cd04443 33 GCDLVSWLIEVGL-AQDRGEAVLYGRRLLQG 62 (83)
T ss_pred HHHHHHHHHHcCC-CCCHHHHHHHHHHHHHC
Confidence 4679999997521 11223455555555543
No 35
>PF13591 MerR_2: MerR HTH family regulatory protein
Probab=24.38 E-value=1.4e+02 Score=20.57 Aligned_cols=29 Identities=21% Similarity=0.280 Sum_probs=24.5
Q ss_pred HHHHHHHHHhcCChhHHHHHHHHHHHHhh
Q 030687 106 DWILKAHAHYRFGPMSFCLSMNYLDRFLS 134 (173)
Q Consensus 106 dWi~~v~~~~~l~~eT~~LAVnylDRfLs 134 (173)
.-+..++..++++.+.+.+.+.++||-=.
T Consensus 46 ~~~~rL~~Dl~in~~gi~lil~LLd~i~~ 74 (84)
T PF13591_consen 46 RRIRRLHRDLGINLEGIALILDLLDRIEQ 74 (84)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHHHHH
Confidence 34557899999999999999999999543
No 36
>cd04439 DEP_1_P-Rex DEP (Dishevelled, Egl-10, and Pleckstrin) domain 1 found in P-Rex-like proteins. The P-Rex family is the guanine-nucleotide exchange factor (GEF) for the small GTPase Rac that contains an N-terminal RhoGEF domain, two DEP and PDZ domains. Rac-GEF activity is stimulated by phosphatidylinositol (3,4,5)-trisphosphate (PtdIns(3,4,5)P3), a lipid second messenger, and by the G beta-gamma subunits of heterotrimeric G proteins. The DEP domains are not involved in mediating these stimuli, but may be of importance for basal and stimulated levels Rac-GEF activity.
Probab=22.18 E-value=85 Score=21.79 Aligned_cols=30 Identities=17% Similarity=0.226 Sum_probs=16.4
Q ss_pred HHHHHHHHHHHHHHhcCChhHHHHHHHHHHH
Q 030687 101 RREALDWILKAHAHYRFGPMSFCLSMNYLDR 131 (173)
Q Consensus 101 R~~lvdWi~~v~~~~~l~~eT~~LAVnylDR 131 (173)
=..+|+||++....- -..+.+.++-.++|.
T Consensus 31 GselVdWL~~~~~~~-~r~eAv~lg~~Ll~~ 60 (81)
T cd04439 31 GNEFVSWLLEIGEIS-KPEEGVNLGQALLEN 60 (81)
T ss_pred hHHHHHHHHHcCCCC-CHHHHHHHHHHHHHC
Confidence 357999999753211 123555555555554
No 37
>cd04442 DEP_1_DEP6 DEP (Dishevelled, Egl-10, and Pleckstrin) domain 1 found in DEP6-like proteins. DEP6 proteins contain two DEP and a PDZ domain. Their function is unknown.
Probab=21.90 E-value=91 Score=21.79 Aligned_cols=29 Identities=14% Similarity=0.460 Sum_probs=16.1
Q ss_pred HHHHHHHHHHHHHhcCChhHHHHHHHHHHHHhhc
Q 030687 102 REALDWILKAHAHYRFGPMSFCLSMNYLDRFLSV 135 (173)
Q Consensus 102 ~~lvdWi~~v~~~~~l~~eT~~LAVnylDRfLs~ 135 (173)
.++||||++... ..|-.-||.|--..|..
T Consensus 32 selVdWL~~~~~-----~~sR~eAv~lgq~Ll~~ 60 (82)
T cd04442 32 KELIDWLIEHKE-----ASDRETAIKIMQKLLDH 60 (82)
T ss_pred HHHHHHHHHcCC-----CCCHHHHHHHHHHHHHC
Confidence 578999996433 13444445544444443
No 38
>cd04438 DEP_dishevelled DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in dishevelled-like proteins. Dishevelled-like proteins play a key role in the transduction of the Wnt signal from the cell surface to the nucleus, which in turn is an important regulatory pathway for cellular development and growth. They contain an N-terminal DIX domain, a central PDZ domain, and a C-terminal DEP domain.
Probab=21.51 E-value=1e+02 Score=21.58 Aligned_cols=31 Identities=13% Similarity=0.143 Sum_probs=18.2
Q ss_pred HHHHHHHHHHHHHHhcCChhHHHHHHHHHHH
Q 030687 101 RREALDWILKAHAHYRFGPMSFCLSMNYLDR 131 (173)
Q Consensus 101 R~~lvdWi~~v~~~~~l~~eT~~LAVnylDR 131 (173)
=..+|+||++-.....-..+++.++-.+++.
T Consensus 32 GsdlVdWL~~~~~~~~~R~eAv~~g~~Ll~~ 62 (84)
T cd04438 32 GSDLVDWLLSHVEGLTDRREARKYASSLLKL 62 (84)
T ss_pred chHHHHHHHHhCCCCCCHHHHHHHHHHHHHC
Confidence 4579999987544333334555555555554
No 39
>cd04447 DEP_BRCC3 DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in BBRC3-like proteins. BBRC3, also known as DEPDC1B, is a DEP containing protein of unknown function.
Probab=20.55 E-value=1.9e+02 Score=20.90 Aligned_cols=39 Identities=23% Similarity=0.425 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHHHH-hcCC-hhHHHHHHHHHHHHhhccccC
Q 030687 101 RREALDWILKAHAH-YRFG-PMSFCLSMNYLDRFLSVYELP 139 (173)
Q Consensus 101 R~~lvdWi~~v~~~-~~l~-~eT~~LAVnylDRfLs~~~v~ 139 (173)
=.++|||+.+.... -+|+ ..|-..||.++-++|...-+.
T Consensus 32 gsEAVDwL~~~l~~n~~fg~~vtR~~av~l~qkll~~hVie 72 (92)
T cd04447 32 ASEAVDWLHELLRSNSNFGPEVTRQQTVQLLKKFLKNHVIE 72 (92)
T ss_pred hHHHHHHHHHHHHhccccCCCCCHHHHHHHHHHHHHcCCch
Confidence 36899999987432 2233 447788999999999876554
No 40
>cd04440 DEP_2_P-Rex DEP (Dishevelled, Egl-10, and Pleckstrin) domain 2 found in P-Rex-like proteins. The P-Rex family is the guanine-nucleotide exchange factor (GEF) for the small GTPase Rac that contains an N-terminal RhoGEF domain, two DEP and PDZ domains. Rac-GEF activity is stimulated by phosphatidylinositol (3,4,5)-trisphosphate (PtdIns(3,4,5)P3), a lipid second messenger, and the G beta-gamma subunits of heterotrimeric G proteins. The DEP domains are not involved in mediating these stimuli, but may be of importance for basal and stimulated levels Rac-GEF activity.
Probab=20.31 E-value=1e+02 Score=22.23 Aligned_cols=31 Identities=16% Similarity=0.317 Sum_probs=16.9
Q ss_pred HHHHHHHHHHHHHHHhcCChhHHHHHHHHHHH
Q 030687 100 VRREALDWILKAHAHYRFGPMSFCLSMNYLDR 131 (173)
Q Consensus 100 ~R~~lvdWi~~v~~~~~l~~eT~~LAVnylDR 131 (173)
.=.++|+|+++.. .-.-..+.+.+.-.++|.
T Consensus 39 vGsElVdWLi~~g-~~~tR~eAv~~gq~Ll~~ 69 (93)
T cd04440 39 PASKLVDWLLAQG-DCRTREEAVILGVGLCNN 69 (93)
T ss_pred chhHHHHHHHHcC-CCCCHHHHHHHHHHHHhC
Confidence 3468999999873 222333344444444443
No 41
>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=20.02 E-value=3.5e+02 Score=20.53 Aligned_cols=57 Identities=11% Similarity=0.037 Sum_probs=44.5
Q ss_pred HHHHHHHHHHHhcCChhHHHHHHHHHHHHhhcc-ccCCCCCccchhhHHHHHHhhhhccc
Q 030687 104 ALDWILKAHAHYRFGPMSFCLSMNYLDRFLSVY-ELPKGKDWTVQLLTVACLSLAAKMEE 162 (173)
Q Consensus 104 lvdWi~~v~~~~~l~~eT~~LAVnylDRfLs~~-~v~~~~~w~lQLlgvaCL~LAaK~EE 162 (173)
+..-+.++|..++++++..-.....++.-+... .+-.++ ++--+-+.|+++-+|+..
T Consensus 14 a~~Rl~~LC~~L~l~~~~~~~iwt~fe~~l~~~t~L~~dR--HLDQiilCaiY~i~Kv~~ 71 (135)
T PF01857_consen 14 AAVRLQDLCERLDLSSDLREKIWTCFEHSLTHHTELMKDR--HLDQIILCAIYGICKVSK 71 (135)
T ss_dssp HHHHHHHHHHHHTTSTTHHHHHHHHHHHHHHHSGGGGTTS---HHHHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHhhHHHHhcc--hHHHHHHHHHHHHHHhhc
Confidence 334566899999999998888889999988654 455444 688999999999999864
Done!