Query 025072
Match_columns 258
No_of_seqs 180 out of 748
Neff 3.7
Searched_HMMs 46136
Date Fri Mar 29 02:27:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025072.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025072hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0048 Transcription factor, 99.2 4.4E-12 9.5E-17 112.9 4.0 36 2-37 82-117 (238)
2 PLN03212 Transcription repress 98.6 4.7E-08 1E-12 89.7 4.9 41 2-42 98-138 (249)
3 PLN03091 hypothetical protein; 98.6 1.2E-07 2.5E-12 93.0 6.7 42 2-43 87-128 (459)
4 smart00717 SANT SANT SWI3, AD 97.1 0.00034 7.3E-09 45.3 2.0 26 2-27 22-47 (49)
5 cd00167 SANT 'SWI3, ADA2, N-Co 96.8 0.0012 2.5E-08 42.3 2.5 25 2-26 20-44 (45)
6 PF00249 Myb_DNA-binding: Myb- 96.5 0.0013 2.8E-08 45.1 1.4 24 3-26 23-47 (48)
7 PF13921 Myb_DNA-bind_6: Myb-l 96.2 0.0011 2.4E-08 46.7 -0.3 27 2-28 18-44 (60)
8 PLN03212 Transcription repress 89.3 0.21 4.5E-06 46.6 1.8 34 2-35 46-80 (249)
9 PLN03091 hypothetical protein; 72.8 1.2 2.7E-05 44.7 0.2 31 2-32 35-66 (459)
10 PF02260 FATC: FATC domain; I 71.2 1.4 3.1E-05 29.0 0.2 15 116-130 16-30 (33)
11 COG5147 REB1 Myb superfamily p 58.4 3.5 7.6E-05 42.0 0.2 35 2-36 41-75 (512)
12 PF13837 Myb_DNA-bind_4: Myb/S 56.6 9 0.0002 28.3 2.1 33 3-36 36-72 (90)
13 KOG0048 Transcription factor, 49.2 4.4 9.6E-05 36.4 -0.7 37 3-39 31-68 (238)
14 PF10545 MADF_DNA_bdg: Alcohol 45.4 25 0.00054 25.2 2.9 24 3-26 28-52 (85)
15 COG5147 REB1 Myb superfamily p 44.7 16 0.00036 37.4 2.5 31 2-32 92-122 (512)
16 KOG0050 mRNA splicing protein 42.7 16 0.00034 38.0 2.0 35 2-36 28-62 (617)
17 smart00595 MADF subfamily of S 42.4 31 0.00068 25.5 3.1 23 3-26 29-51 (89)
18 PF13873 Myb_DNA-bind_5: Myb/S 36.8 43 0.00094 24.5 3.1 23 3-25 40-67 (78)
19 PF11035 SnAPC_2_like: Small n 33.8 64 0.0014 31.7 4.5 29 4-33 47-75 (344)
20 KOG0049 Transcription factor, 30.4 42 0.0009 36.1 2.8 32 3-34 382-413 (939)
21 PF08281 Sigma70_r4_2: Sigma-7 26.5 83 0.0018 21.2 2.9 23 3-26 28-50 (54)
22 KOG0049 Transcription factor, 24.1 1.4E+02 0.0031 32.3 5.3 22 114-135 577-598 (939)
23 KOG4282 Transcription factor G 24.0 91 0.002 29.2 3.6 37 2-39 84-124 (345)
24 TIGR02894 DNA_bind_RsfA transc 21.2 70 0.0015 28.4 2.1 27 5-32 34-60 (161)
25 PF12776 Myb_DNA-bind_3: Myb/S 21.1 1E+02 0.0022 23.0 2.8 28 4-32 34-66 (96)
No 1
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.24 E-value=4.4e-12 Score=112.90 Aligned_cols=36 Identities=61% Similarity=1.000 Sum_probs=34.1
Q ss_pred CcHHHHhCcCCCCChHHHHHHHHHHHHHHHHhhcCC
Q 025072 2 SRWAAIASYLPQRTDNDIKNYWNTHLKKKLKKLQTG 37 (258)
Q Consensus 2 NkWs~IAk~LPGRTDN~IKNrWnt~LkKklk~~~s~ 37 (258)
|||++||++|||||||+||||||++||||+.+++.+
T Consensus 82 NrWs~IA~~LPGRTDNeIKN~Wnt~lkkkl~~~~~~ 117 (238)
T KOG0048|consen 82 NRWSLIAGRLPGRTDNEVKNHWNTHLKKKLLKMGID 117 (238)
T ss_pred cHHHHHHhhCCCcCHHHHHHHHHHHHHHHHHHcCCC
Confidence 899999999999999999999999999999998843
No 2
>PLN03212 Transcription repressor MYB5; Provisional
Probab=98.59 E-value=4.7e-08 Score=89.67 Aligned_cols=41 Identities=51% Similarity=0.916 Sum_probs=36.7
Q ss_pred CcHHHHhCcCCCCChHHHHHHHHHHHHHHHHhhcCCCCCCC
Q 025072 2 SRWAAIASYLPQRTDNDIKNYWNTHLKKKLKKLQTGSDGGQ 42 (258)
Q Consensus 2 NkWs~IAk~LPGRTDN~IKNrWnt~LkKklk~~~s~~~~~~ 42 (258)
++|+.||++|||||||.|||||+++++|++++.+..+...+
T Consensus 98 nKWs~IAk~LpGRTDnqIKNRWns~LrK~l~r~~i~p~~~k 138 (249)
T PLN03212 98 NRWSLIAGRIPGRTDNEIKNYWNTHLRKKLLRQGIDPQTHK 138 (249)
T ss_pred ccHHHHHhhcCCCCHHHHHHHHHHHHhHHHHhcCCCCCCCC
Confidence 68999999999999999999999999999988777666553
No 3
>PLN03091 hypothetical protein; Provisional
Probab=98.55 E-value=1.2e-07 Score=93.01 Aligned_cols=42 Identities=48% Similarity=0.821 Sum_probs=38.1
Q ss_pred CcHHHHhCcCCCCChHHHHHHHHHHHHHHHHhhcCCCCCCCC
Q 025072 2 SRWAAIASYLPQRTDNDIKNYWNTHLKKKLKKLQTGSDGGQN 43 (258)
Q Consensus 2 NkWs~IAk~LPGRTDN~IKNrWnt~LkKklk~~~s~~~~~~~ 43 (258)
+||++||++|||||||.|||||+.+|||++++.+..+..+++
T Consensus 87 nKWskIAk~LPGRTDnqIKNRWnslLKKklr~~~I~p~t~kp 128 (459)
T PLN03091 87 NRWSQIAAQLPGRTDNEIKNLWNSCLKKKLRQRGIDPNTHKP 128 (459)
T ss_pred cchHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCCCCCCCC
Confidence 689999999999999999999999999999998887766554
No 4
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=97.08 E-value=0.00034 Score=45.35 Aligned_cols=26 Identities=38% Similarity=0.762 Sum_probs=23.8
Q ss_pred CcHHHHhCcCCCCChHHHHHHHHHHH
Q 025072 2 SRWAAIASYLPQRTDNDIKNYWNTHL 27 (258)
Q Consensus 2 NkWs~IAk~LPGRTDN~IKNrWnt~L 27 (258)
..|..||.+||+||+++|++||+..+
T Consensus 22 ~~w~~Ia~~~~~rt~~~~~~~~~~~~ 47 (49)
T smart00717 22 NNWEKIAKELPGRTAEQCRERWNNLL 47 (49)
T ss_pred CCHHHHHHHcCCCCHHHHHHHHHHHc
Confidence 57999999999999999999999754
No 5
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=96.77 E-value=0.0012 Score=42.33 Aligned_cols=25 Identities=32% Similarity=0.686 Sum_probs=22.9
Q ss_pred CcHHHHhCcCCCCChHHHHHHHHHH
Q 025072 2 SRWAAIASYLPQRTDNDIKNYWNTH 26 (258)
Q Consensus 2 NkWs~IAk~LPGRTDN~IKNrWnt~ 26 (258)
..|..||..|++||.++|++||+..
T Consensus 20 ~~w~~Ia~~~~~rs~~~~~~~~~~~ 44 (45)
T cd00167 20 NNWEKIAKELPGRTPKQCRERWRNL 44 (45)
T ss_pred CCHHHHHhHcCCCCHHHHHHHHHHh
Confidence 4799999999999999999999853
No 6
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=96.48 E-value=0.0013 Score=45.08 Aligned_cols=24 Identities=25% Similarity=0.563 Sum_probs=22.3
Q ss_pred cHHHHhCcCC-CCChHHHHHHHHHH
Q 025072 3 RWAAIASYLP-QRTDNDIKNYWNTH 26 (258)
Q Consensus 3 kWs~IAk~LP-GRTDN~IKNrWnt~ 26 (258)
.|..||.+|| |||...|++||+.+
T Consensus 23 ~W~~Ia~~~~~~Rt~~qc~~~~~~~ 47 (48)
T PF00249_consen 23 NWKKIAKRMPGGRTAKQCRSRYQNL 47 (48)
T ss_dssp HHHHHHHHHSSSSTHHHHHHHHHHH
T ss_pred HHHHHHHHcCCCCCHHHHHHHHHhh
Confidence 4999999999 99999999999864
No 7
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=96.17 E-value=0.0011 Score=46.72 Aligned_cols=27 Identities=37% Similarity=0.753 Sum_probs=21.8
Q ss_pred CcHHHHhCcCCCCChHHHHHHHHHHHH
Q 025072 2 SRWAAIASYLPQRTDNDIKNYWNTHLK 28 (258)
Q Consensus 2 NkWs~IAk~LPGRTDN~IKNrWnt~Lk 28 (258)
+.|..||.+|+.||..+|++||+..|+
T Consensus 18 ~~W~~Ia~~l~~Rt~~~~~~r~~~~l~ 44 (60)
T PF13921_consen 18 NDWKKIAEHLGNRTPKQCRNRWRNHLR 44 (60)
T ss_dssp S-HHHHHHHSTTS-HHHHHHHHHHTTS
T ss_pred cCHHHHHHHHCcCCHHHHHHHHHHHCc
Confidence 579999999966999999999997553
No 8
>PLN03212 Transcription repressor MYB5; Provisional
Probab=89.35 E-value=0.21 Score=46.57 Aligned_cols=34 Identities=18% Similarity=0.367 Sum_probs=29.0
Q ss_pred CcHHHHhCcC-CCCChHHHHHHHHHHHHHHHHhhc
Q 025072 2 SRWAAIASYL-PQRTDNDIKNYWNTHLKKKLKKLQ 35 (258)
Q Consensus 2 NkWs~IAk~L-PGRTDN~IKNrWnt~LkKklk~~~ 35 (258)
++|..||+++ +|||+..++.||+.+|+-.+++..
T Consensus 46 ~nW~~IAk~~g~gRT~KQCReRW~N~L~P~I~kgp 80 (249)
T PLN03212 46 GRWRSLPKRAGLLRCGKSCRLRWMNYLRPSVKRGG 80 (249)
T ss_pred ccHHHHHHhhhcCCCcchHHHHHHHhhchhcccCC
Confidence 4799999998 799999999999998877665543
No 9
>PLN03091 hypothetical protein; Provisional
Probab=72.81 E-value=1.2 Score=44.67 Aligned_cols=31 Identities=23% Similarity=0.447 Sum_probs=26.0
Q ss_pred CcHHHHhCcC-CCCChHHHHHHHHHHHHHHHH
Q 025072 2 SRWAAIASYL-PQRTDNDIKNYWNTHLKKKLK 32 (258)
Q Consensus 2 NkWs~IAk~L-PGRTDN~IKNrWnt~LkKklk 32 (258)
..|..||+++ +||++..++.||+.+|.-.|+
T Consensus 35 ~nWs~IAk~~g~gRT~KQCRERW~NyLdP~Ik 66 (459)
T PLN03091 35 GCWSSVPKQAGLQRCGKSCRLRWINYLRPDLK 66 (459)
T ss_pred CCHHHHhhhhccCcCcchHhHHHHhccCCccc
Confidence 4699999998 599999999999977755544
No 10
>PF02260 FATC: FATC domain; InterPro: IPR003152 The FATC domain is found at the C-terminal end of the PIK-related kinases. Members of the family of PIK-related kinases may act as intracellular sensors that govern radial and horizontal pathways [].; GO: 0005515 protein binding; PDB: 2KIT_A 1W1N_A 2KIO_A.
Probab=71.17 E-value=1.4 Score=29.03 Aligned_cols=15 Identities=40% Similarity=0.937 Sum_probs=13.2
Q ss_pred ccchHhHHHHHhhhh
Q 025072 116 ASNAENISRLLQNWM 130 (258)
Q Consensus 116 Ass~eNIsrlL~gWm 130 (258)
|.+.+|++||-.|||
T Consensus 16 At~~~nLa~my~GW~ 30 (33)
T PF02260_consen 16 ATDPENLARMYIGWM 30 (33)
T ss_dssp HHHHHHHHHHCTSS-
T ss_pred HcCHHHHHHHhcchh
Confidence 678999999999998
No 11
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=58.44 E-value=3.5 Score=42.05 Aligned_cols=35 Identities=37% Similarity=0.624 Sum_probs=29.6
Q ss_pred CcHHHHhCcCCCCChHHHHHHHHHHHHHHHHhhcC
Q 025072 2 SRWAAIASYLPQRTDNDIKNYWNTHLKKKLKKLQT 36 (258)
Q Consensus 2 NkWs~IAk~LPGRTDN~IKNrWnt~LkKklk~~~s 36 (258)
|.|++||..|.-|+.+.+++||+.++...+++...
T Consensus 41 nnws~vas~~~~~~~kq~~~rw~~~lnp~lk~~~~ 75 (512)
T COG5147 41 NNWSKVASLLISSTGKQSSNRWNNHLNPQLKKKNW 75 (512)
T ss_pred ccHHHHHHHhcccccccccchhhhhhchhcccccc
Confidence 56999999998899999999999888777665443
No 12
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=56.64 E-value=9 Score=28.31 Aligned_cols=33 Identities=42% Similarity=0.694 Sum_probs=24.1
Q ss_pred cHHHHhCcC----CCCChHHHHHHHHHHHHHHHHhhcC
Q 025072 3 RWAAIASYL----PQRTDNDIKNYWNTHLKKKLKKLQT 36 (258)
Q Consensus 3 kWs~IAk~L----PGRTDN~IKNrWnt~LkKklk~~~s 36 (258)
.|..||..| ..||...|+++|+. |++++++...
T Consensus 36 ~w~~Ia~~l~~~G~~rt~~qc~~Kw~~-L~~~Yk~~k~ 72 (90)
T PF13837_consen 36 VWKEIAEELAEHGYNRTPEQCRNKWKN-LKKKYKKIKD 72 (90)
T ss_dssp HHHHHHHHHHHHC----HHHHHHHHHH-HHHHHHCSSS
T ss_pred HHHHHHHHHHHcCCCCCHHHHHHHHHH-HHHHHHHHHh
Confidence 488999887 57999999999996 7777877654
No 13
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=49.22 E-value=4.4 Score=36.44 Aligned_cols=37 Identities=16% Similarity=0.279 Sum_probs=31.8
Q ss_pred cHHHHhCcCC-CCChHHHHHHHHHHHHHHHHhhcCCCC
Q 025072 3 RWAAIASYLP-QRTDNDIKNYWNTHLKKKLKKLQTGSD 39 (258)
Q Consensus 3 kWs~IAk~LP-GRTDN~IKNrWnt~LkKklk~~~s~~~ 39 (258)
+|..|++.++ ||++-.++-||.-+|+-.+++-.-+.+
T Consensus 31 ~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ikrg~fT~e 68 (238)
T KOG0048|consen 31 NGTALPKLAGLRRCGKSCRLRWTNYLRPDLKRGNFSDE 68 (238)
T ss_pred CcchhhhhcCCCccchHHHHHhhcccCCCccCCCCCHH
Confidence 6999999999 999999999999999888876554443
No 14
>PF10545 MADF_DNA_bdg: Alcohol dehydrogenase transcription factor Myb/SANT-like; InterPro: IPR006578 The MADF (myb/SANT-like domain in Adf-1) domain is an approximately 80-amino-acid module that directs sequence specific DNA binding to a site consisting of multiple tri-nucleotide repeats. The MADF domain is found in one or more copies in eukaryotic and viral proteins and is often associated with the BESS domain []. MADF is related to the Myb DNA-binding domain (IPR001005 from INTERPRO). The retroviral oncogene v-myb, and its cellular counterpart c-myb, are nuclear DNA-binding proteins that specifically recognise the sequence YAAC(G/T)G. It is likely that the MADF domain is more closely related to the myb/SANT domain than it is to other HTH domains. Some proteins known to contain a MADF domain are listed below: Drosophila Adf-1, a transcription factor first identified on the basis of its interaction with the alcohol dehydrogenase promoter but that binds the promoters of a diverse group of genes []. Drosophila Dorsal-interacting protein 3 (Dip3), which functions both as an activator to bind DNA in a sequence specific manner and a coactivator to stimulate synergistic activation by Dorsal and Twist []. Drosophila Stonewall (Stwl), a putative transcription factor required for maintenance of female germline stem cells as well as oocyte differentiation.
Probab=45.41 E-value=25 Score=25.17 Aligned_cols=24 Identities=29% Similarity=0.526 Sum_probs=19.6
Q ss_pred cHHHHhCcCCC-CChHHHHHHHHHH
Q 025072 3 RWAAIASYLPQ-RTDNDIKNYWNTH 26 (258)
Q Consensus 3 kWs~IAk~LPG-RTDN~IKNrWnt~ 26 (258)
-|..||..|.. -+.+.|+.+|+.+
T Consensus 28 aw~~Ia~~l~~~~~~~~~~~~w~~L 52 (85)
T PF10545_consen 28 AWQEIARELGKEFSVDDCKKRWKNL 52 (85)
T ss_pred HHHHHHHHHccchhHHHHHHHHHHH
Confidence 39999999943 5788999999963
No 15
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=44.74 E-value=16 Score=37.36 Aligned_cols=31 Identities=23% Similarity=0.440 Sum_probs=27.1
Q ss_pred CcHHHHhCcCCCCChHHHHHHHHHHHHHHHH
Q 025072 2 SRWAAIASYLPQRTDNDIKNYWNTHLKKKLK 32 (258)
Q Consensus 2 NkWs~IAk~LPGRTDN~IKNrWnt~LkKklk 32 (258)
++|..||.++||||+..+.++|+-.+.....
T Consensus 92 ~~wstia~~~d~rt~~~~~ery~~~~~~~~s 122 (512)
T COG5147 92 TQWSTIADYKDRRTAQQCVERYVNTLEDLSS 122 (512)
T ss_pred chhhhhccccCccchHHHHHHHHHHhhhhhc
Confidence 5799999999999999999999977766544
No 16
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=42.65 E-value=16 Score=37.98 Aligned_cols=35 Identities=31% Similarity=0.574 Sum_probs=31.1
Q ss_pred CcHHHHhCcCCCCChHHHHHHHHHHHHHHHHhhcC
Q 025072 2 SRWAAIASYLPQRTDNDIKNYWNTHLKKKLKKLQT 36 (258)
Q Consensus 2 NkWs~IAk~LPGRTDN~IKNrWnt~LkKklk~~~s 36 (258)
|.|++|++.|+.-+....|+||+-++--.|++..-
T Consensus 28 nqws~i~sll~~kt~rqC~~rw~e~ldp~i~~tew 62 (617)
T KOG0050|consen 28 NQWSRIASLLNRKTARQCKARWEEWLDPAIKKTEW 62 (617)
T ss_pred HHHHHHHHHHhhcchhHHHHHHHHHhCHHHhhhhh
Confidence 67999999999999999999999988777776654
No 17
>smart00595 MADF subfamily of SANT domain.
Probab=42.41 E-value=31 Score=25.54 Aligned_cols=23 Identities=26% Similarity=0.511 Sum_probs=20.0
Q ss_pred cHHHHhCcCCCCChHHHHHHHHHH
Q 025072 3 RWAAIASYLPQRTDNDIKNYWNTH 26 (258)
Q Consensus 3 kWs~IAk~LPGRTDN~IKNrWnt~ 26 (258)
-|..||..| |-+..+||.+|+.+
T Consensus 29 aW~~Ia~~l-~~~~~~~~~kw~~L 51 (89)
T smart00595 29 AWEEIAEEL-GLSVEECKKRWKNL 51 (89)
T ss_pred HHHHHHHHH-CcCHHHHHHHHHHH
Confidence 399999999 55999999999953
No 18
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=36.76 E-value=43 Score=24.46 Aligned_cols=23 Identities=30% Similarity=0.643 Sum_probs=18.7
Q ss_pred cHHHHhCcC-----CCCChHHHHHHHHH
Q 025072 3 RWAAIASYL-----PQRTDNDIKNYWNT 25 (258)
Q Consensus 3 kWs~IAk~L-----PGRTDN~IKNrWnt 25 (258)
.|..|+..| +.||...||.+|.-
T Consensus 40 ~W~~I~~~lN~~~~~~Rs~~~lkkkW~n 67 (78)
T PF13873_consen 40 AWEEIAEELNALGPGKRSWKQLKKKWKN 67 (78)
T ss_pred HHHHHHHHHHhcCCCCCCHHHHHHHHHH
Confidence 388888876 47899999999984
No 19
>PF11035 SnAPC_2_like: Small nuclear RNA activating complex subunit 2-like; InterPro: IPR021281 This family of proteins is SnAPC subunit 2-like. SnAPC allows the transcription of human small nuclear RNA genes to occur by recognition of the proximal sequence element [].
Probab=33.81 E-value=64 Score=31.70 Aligned_cols=29 Identities=28% Similarity=0.591 Sum_probs=23.0
Q ss_pred HHHHhCcCCCCChHHHHHHHHHHHHHHHHh
Q 025072 4 WAAIASYLPQRTDNDIKNYWNTHLKKKLKK 33 (258)
Q Consensus 4 Ws~IAk~LPGRTDN~IKNrWnt~LkKklk~ 33 (258)
...|+++|+||+.-+|.++-+ +||.++.+
T Consensus 47 ~ael~~~l~~Rs~aEI~~fl~-~LK~rvar 75 (344)
T PF11035_consen 47 AAELAKELPGRSEAEIRDFLQ-QLKGRVAR 75 (344)
T ss_pred HHHHHhhccCcCHHHHHHHHH-HHHHHHHH
Confidence 367999999999999999887 45555433
No 20
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=30.41 E-value=42 Score=36.15 Aligned_cols=32 Identities=22% Similarity=0.502 Sum_probs=27.6
Q ss_pred cHHHHhCcCCCCChHHHHHHHHHHHHHHHHhh
Q 025072 3 RWAAIASYLPQRTDNDIKNYWNTHLKKKLKKL 34 (258)
Q Consensus 3 kWs~IAk~LPGRTDN~IKNrWnt~LkKklk~~ 34 (258)
-|++|...+|||+|-.++.||...|.+++|..
T Consensus 382 dw~k~R~~vPnRSdsQcR~RY~nvL~~s~K~~ 413 (939)
T KOG0049|consen 382 DWAKVRQAVPNRSDSQCRERYTNVLNRSAKVE 413 (939)
T ss_pred chhhHHHhcCCccHHHHHHHHHHHHHHhhccC
Confidence 39999999999999999999988777776543
No 21
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=26.46 E-value=83 Score=21.22 Aligned_cols=23 Identities=22% Similarity=0.310 Sum_probs=17.9
Q ss_pred cHHHHhCcCCCCChHHHHHHHHHH
Q 025072 3 RWAAIASYLPQRTDNDIKNYWNTH 26 (258)
Q Consensus 3 kWs~IAk~LPGRTDN~IKNrWnt~ 26 (258)
.|..||..+ |.+.+.|+++....
T Consensus 28 s~~eIa~~l-~~s~~~v~~~l~ra 50 (54)
T PF08281_consen 28 SYAEIAEIL-GISESTVKRRLRRA 50 (54)
T ss_dssp -HHHHHHHC-TS-HHHHHHHHHHH
T ss_pred CHHHHHHHH-CcCHHHHHHHHHHH
Confidence 478999999 99999999976643
No 22
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=24.08 E-value=1.4e+02 Score=32.30 Aligned_cols=22 Identities=18% Similarity=0.218 Sum_probs=17.9
Q ss_pred ccccchHhHHHHHhhhhcCCCC
Q 025072 114 PYASNAENISRLLQNWMKNPPK 135 (258)
Q Consensus 114 ~YAss~eNIsrlL~gWm~~~p~ 135 (258)
.-.+|-.-|+|.+-.||+--++
T Consensus 577 ~~Vssl~~V~R~~v~~~~~R~~ 598 (939)
T KOG0049|consen 577 EIVSSLLTVTRVDVRYMIERSK 598 (939)
T ss_pred ccccchhHHHHHhhhhcccchH
Confidence 3567888899999999987766
No 23
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=23.97 E-value=91 Score=29.23 Aligned_cols=37 Identities=27% Similarity=0.385 Sum_probs=29.6
Q ss_pred CcHHHHhCcC----CCCChHHHHHHHHHHHHHHHHhhcCCCC
Q 025072 2 SRWAAIASYL----PQRTDNDIKNYWNTHLKKKLKKLQTGSD 39 (258)
Q Consensus 2 NkWs~IAk~L----PGRTDN~IKNrWnt~LkKklk~~~s~~~ 39 (258)
+.|..||..+ --||+-.||++|.. |+|++++......
T Consensus 84 ~~We~va~k~~~~g~~rs~~qck~K~~n-l~k~Yk~~k~~~~ 124 (345)
T KOG4282|consen 84 PLWEEVARKMAELGYPRSPKQCKAKIEN-LKKKYKKEKAKKE 124 (345)
T ss_pred cHHHHHHHHHHHhCCCCCHHHHHHHHHH-HHHHHHHHhcccC
Confidence 4599999855 57999999999995 7788888876544
No 24
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=21.23 E-value=70 Score=28.42 Aligned_cols=27 Identities=22% Similarity=0.395 Sum_probs=23.5
Q ss_pred HHHhCcCCCCChHHHHHHHHHHHHHHHH
Q 025072 5 AAIASYLPQRTDNDIKNYWNTHLKKKLK 32 (258)
Q Consensus 5 s~IAk~LPGRTDN~IKNrWnt~LkKklk 32 (258)
..+++.| +||.-++-=|||..+||++.
T Consensus 34 eEvg~~L-~RTsAACGFRWNs~VRkqY~ 60 (161)
T TIGR02894 34 EEVGRAL-NRTAAACGFRWNAYVRKQYE 60 (161)
T ss_pred HHHHHHH-cccHHHhcchHHHHHHHHHH
Confidence 4567788 99999999999999998764
No 25
>PF12776 Myb_DNA-bind_3: Myb/SANT-like DNA-binding domain; InterPro: IPR024752 This domain, found in a range of uncharacterised proteins, may be related to Myb/SANT-like DNA binding domains.
Probab=21.08 E-value=1e+02 Score=22.96 Aligned_cols=28 Identities=39% Similarity=0.713 Sum_probs=19.5
Q ss_pred HHHHhCcC---CCC--ChHHHHHHHHHHHHHHHH
Q 025072 4 WAAIASYL---PQR--TDNDIKNYWNTHLKKKLK 32 (258)
Q Consensus 4 Ws~IAk~L---PGR--TDN~IKNrWnt~LkKklk 32 (258)
|..|+..| +|+ |...|||+|.. ||+..+
T Consensus 34 w~~i~~~~~~~~~~~~t~~qlknk~~~-lk~~y~ 66 (96)
T PF12776_consen 34 WNNIAEEFNEKTGLNYTKKQLKNKWKT-LKKDYR 66 (96)
T ss_pred HHHHHHHHHHHhCCcccHHHHHHHHHH-HHHHHH
Confidence 77788777 333 67889999985 555443
Done!