Query 026135
Match_columns 243
No_of_seqs 197 out of 1227
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 04:11:38 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026135.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026135hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0048 Transcription factor, 99.6 2.8E-16 6.1E-21 139.5 6.4 58 2-61 67-124 (238)
2 PLN03212 Transcription repress 99.5 3.3E-14 7.2E-19 128.4 7.4 63 2-66 83-145 (249)
3 PLN03091 hypothetical protein; 99.4 2E-13 4.4E-18 131.5 6.9 62 2-65 72-133 (459)
4 PF13921 Myb_DNA-bind_6: Myb-l 99.0 4E-10 8.7E-15 79.6 3.9 52 2-55 3-54 (60)
5 PF00249 Myb_DNA-binding: Myb- 98.8 3.2E-09 6.9E-14 72.6 4.1 41 2-44 6-48 (48)
6 smart00717 SANT SANT SWI3, AD 98.8 5.8E-09 1.3E-13 68.2 4.5 42 2-45 6-48 (49)
7 cd00167 SANT 'SWI3, ADA2, N-Co 98.7 2.7E-08 5.8E-13 64.2 4.7 40 2-43 4-44 (45)
8 PLN03212 Transcription repress 98.6 2E-08 4.3E-13 91.3 3.9 59 2-61 30-89 (249)
9 KOG0048 Transcription factor, 98.5 7.8E-08 1.7E-12 85.7 2.4 60 2-62 14-74 (238)
10 PLN03091 hypothetical protein; 98.4 1.9E-07 4.1E-12 90.7 2.9 57 2-59 19-76 (459)
11 COG5147 REB1 Myb superfamily p 96.4 0.0032 7E-08 62.8 4.2 46 2-49 77-122 (512)
12 COG5147 REB1 Myb superfamily p 96.4 0.0019 4E-08 64.4 2.3 60 1-61 24-83 (512)
13 KOG0049 Transcription factor, 96.2 0.0059 1.3E-07 62.7 5.0 54 2-56 365-418 (939)
14 KOG0050 mRNA splicing protein 96.2 0.0041 8.9E-08 62.2 3.6 54 3-57 13-66 (617)
15 KOG0051 RNA polymerase I termi 93.8 0.061 1.3E-06 54.8 4.0 43 2-47 389-431 (607)
16 KOG0049 Transcription factor, 91.2 0.27 5.9E-06 51.0 4.6 45 3-48 418-462 (939)
17 PF08281 Sigma70_r4_2: Sigma-7 90.3 0.7 1.5E-05 31.4 4.7 40 1-43 11-50 (54)
18 PF08914 Myb_DNA-bind_2: Rap1 89.1 0.52 1.1E-05 34.9 3.5 46 2-48 7-61 (65)
19 KOG0050 mRNA splicing protein 89.0 0.37 8.1E-06 48.7 3.4 45 2-49 64-108 (617)
20 PF13837 Myb_DNA-bind_4: Myb/S 88.5 0.61 1.3E-05 34.5 3.6 48 2-49 6-69 (90)
21 KOG0457 Histone acetyltransfer 85.5 1.1 2.3E-05 44.4 4.3 41 2-43 77-117 (438)
22 TIGR02894 DNA_bind_RsfA transc 82.6 1.6 3.5E-05 38.0 3.7 48 2-50 9-61 (161)
23 COG5114 Histone acetyltransfer 80.4 1.9 4.1E-05 41.7 3.6 39 3-43 69-108 (432)
24 TIGR01557 myb_SHAQKYF myb-like 80.2 4 8.7E-05 29.4 4.5 41 2-43 8-53 (57)
25 PRK13923 putative spore coat p 74.0 4.3 9.3E-05 35.6 3.8 46 2-48 10-60 (170)
26 PF13873 Myb_DNA-bind_5: Myb/S 73.9 4.5 9.7E-05 29.5 3.4 44 2-45 7-70 (78)
27 PF13404 HTH_AsnC-type: AsnC-t 70.0 9.6 0.00021 25.6 4.0 40 1-42 1-40 (42)
28 PRK11179 DNA-binding transcrip 68.0 10 0.00022 31.4 4.6 47 1-49 7-53 (153)
29 PF09111 SLIDE: SLIDE; InterP 63.3 10 0.00022 31.2 3.7 45 2-47 54-113 (118)
30 PRK09047 RNA polymerase factor 60.4 26 0.00056 28.0 5.6 39 2-43 108-146 (161)
31 PF12776 Myb_DNA-bind_3: Myb/S 60.1 20 0.00043 26.7 4.6 45 2-46 4-64 (96)
32 PF04545 Sigma70_r4: Sigma-70, 59.6 20 0.00044 24.0 4.1 42 2-46 6-47 (50)
33 PRK11169 leucine-responsive tr 59.6 12 0.00025 31.5 3.5 46 1-48 12-57 (164)
34 cd06171 Sigma70_r4 Sigma70, re 57.0 30 0.00066 21.6 4.5 39 2-43 12-50 (55)
35 smart00344 HTH_ASNC helix_turn 54.1 27 0.00059 26.5 4.5 48 1-50 1-48 (108)
36 COG5259 RSC8 RSC chromatin rem 51.3 19 0.0004 36.5 3.9 40 2-43 284-323 (531)
37 KOG1279 Chromatin remodeling f 50.8 22 0.00048 36.0 4.4 40 2-43 258-297 (506)
38 PRK04217 hypothetical protein; 50.7 34 0.00073 27.8 4.7 39 2-43 44-82 (110)
39 PRK09642 RNA polymerase sigma 48.9 45 0.00097 26.8 5.2 38 2-42 108-145 (160)
40 KOG2656 DNA methyltransferase 48.4 18 0.0004 35.8 3.3 51 2-54 135-191 (445)
41 PRK12545 RNA polymerase sigma 44.4 49 0.0011 28.1 5.0 47 2-51 141-190 (201)
42 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 41.3 42 0.0009 23.8 3.4 35 4-41 8-42 (50)
43 PRK09647 RNA polymerase sigma 40.1 65 0.0014 27.7 5.2 39 2-43 140-178 (203)
44 PRK09637 RNA polymerase sigma 37.7 65 0.0014 27.0 4.7 38 2-42 108-145 (181)
45 PRK12516 RNA polymerase sigma 37.1 97 0.0021 26.1 5.7 38 2-42 118-155 (187)
46 smart00595 MADF subfamily of S 37.0 40 0.00087 24.8 3.0 23 20-43 29-51 (89)
47 PF10545 MADF_DNA_bdg: Alcohol 36.1 39 0.00085 24.0 2.7 25 20-44 28-53 (85)
48 KOG3173 Predicted Zn-finger pr 35.0 24 0.00053 30.5 1.7 19 181-200 106-126 (167)
49 KOG0051 RNA polymerase I termi 33.0 58 0.0013 33.8 4.3 49 1-49 440-512 (607)
50 PF08706 D5_N: D5 N terminal l 32.8 17 0.00036 28.5 0.3 17 226-242 99-115 (150)
51 COG5118 BDP1 Transcription ini 32.4 65 0.0014 32.1 4.3 43 2-46 370-412 (507)
52 PRK12527 RNA polymerase sigma 31.9 1.1E+02 0.0023 24.6 4.9 39 2-43 107-145 (159)
53 PF13325 MCRS_N: N-terminal re 31.6 94 0.002 27.9 4.9 49 2-50 78-132 (199)
54 PRK12520 RNA polymerase sigma 29.9 1.1E+02 0.0023 25.5 4.8 39 2-43 133-171 (191)
55 TIGR02960 SigX5 RNA polymerase 29.4 1.7E+02 0.0036 26.5 6.2 44 2-49 144-187 (324)
56 PLN03142 Probable chromatin-re 29.1 71 0.0015 35.1 4.4 46 2-49 931-989 (1033)
57 PF01388 ARID: ARID/BRIGHT DNA 26.4 1.4E+02 0.0031 22.2 4.5 27 20-46 59-90 (92)
58 KOG4282 Transcription factor G 26.3 88 0.0019 29.2 4.0 30 20-49 85-118 (345)
59 cd08319 Death_RAIDD Death doma 25.9 93 0.002 23.9 3.4 32 5-39 2-33 (83)
60 PF11035 SnAPC_2_like: Small n 25.8 1.3E+02 0.0028 29.2 5.0 39 3-43 28-69 (344)
61 PRK12524 RNA polymerase sigma 24.3 1.5E+02 0.0033 24.8 4.8 38 2-42 138-175 (196)
62 TIGR02959 SigZ RNA polymerase 21.7 2E+02 0.0043 23.6 4.9 38 2-42 102-139 (170)
63 PRK12540 RNA polymerase sigma 21.7 2.1E+02 0.0046 23.9 5.1 46 2-50 113-161 (182)
64 PRK11922 RNA polymerase sigma 20.8 1E+02 0.0022 26.9 3.0 38 2-42 151-188 (231)
65 cd08317 Death_ank Death domain 20.7 1.1E+02 0.0023 23.0 2.8 32 5-39 4-35 (84)
66 TIGR03001 Sig-70_gmx1 RNA poly 20.6 1.9E+02 0.004 25.9 4.8 37 2-41 163-199 (244)
67 PRK09636 RNA polymerase sigma 20.5 1.9E+02 0.0041 26.1 4.8 45 2-50 117-161 (293)
No 1
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.63 E-value=2.8e-16 Score=139.51 Aligned_cols=58 Identities=59% Similarity=1.035 Sum_probs=54.2
Q ss_pred hhhHHHHHHHHHHhCCcCcHHHHhccCCCCChHHHHHHHHHHHHhhhhhCCCCCCCCCCC
Q 026135 2 KKMNSLSNSIASLVTSKSSWSLIAGRLPGRTDNEIKNYWNTHIRRKLLNRGIDPATHRPL 61 (243)
Q Consensus 2 ~EEDelLi~l~s~~Gn~~kWs~IA~~LpGRTdn~IKNrWn~~lrrkl~~~~~~p~t~rpl 61 (243)
+|||++||++|+.+|| ||+.||++|||||||+|||||+++++|++...++++.+..+.
T Consensus 67 ~eEe~~Ii~lH~~~GN--rWs~IA~~LPGRTDNeIKN~Wnt~lkkkl~~~~~~~~~~~~~ 124 (238)
T KOG0048|consen 67 DEEEDLIIKLHALLGN--RWSLIAGRLPGRTDNEVKNHWNTHLKKKLLKMGIDPSTHRPS 124 (238)
T ss_pred HHHHHHHHHHHHHHCc--HHHHHHhhCCCcCHHHHHHHHHHHHHHHHHHcCCCCCccccc
Confidence 6999999999999999 999999999999999999999999999999988877776654
No 2
>PLN03212 Transcription repressor MYB5; Provisional
Probab=99.50 E-value=3.3e-14 Score=128.42 Aligned_cols=63 Identities=57% Similarity=1.050 Sum_probs=59.6
Q ss_pred hhhHHHHHHHHHHhCCcCcHHHHhccCCCCChHHHHHHHHHHHHhhhhhCCCCCCCCCCCCCCCC
Q 026135 2 KKMNSLSNSIASLVTSKSSWSLIAGRLPGRTDNEIKNYWNTHIRRKLLNRGIDPATHRPLNEPAV 66 (243)
Q Consensus 2 ~EEDelLi~l~s~~Gn~~kWs~IA~~LpGRTdn~IKNrWn~~lrrkl~~~~~~p~t~rpl~~~~~ 66 (243)
+|||++|+++|.++|+ +|+.||++|||||+++|||||+.+++++++..+++|.+++|+.....
T Consensus 83 ~EED~lLlel~~~~Gn--KWs~IAk~LpGRTDnqIKNRWns~LrK~l~r~~i~p~~~kp~~~~~~ 145 (249)
T PLN03212 83 SDEEDLILRLHRLLGN--RWSLIAGRIPGRTDNEIKNYWNTHLRKKLLRQGIDPQTHKPLDANNI 145 (249)
T ss_pred hHHHHHHHHHHHhccc--cHHHHHhhcCCCCHHHHHHHHHHHHhHHHHhcCCCCCCCCCCCcccc
Confidence 6899999999999999 99999999999999999999999999999999999999999876543
No 3
>PLN03091 hypothetical protein; Provisional
Probab=99.42 E-value=2e-13 Score=131.52 Aligned_cols=62 Identities=48% Similarity=0.888 Sum_probs=59.4
Q ss_pred hhhHHHHHHHHHHhCCcCcHHHHhccCCCCChHHHHHHHHHHHHhhhhhCCCCCCCCCCCCCCC
Q 026135 2 KKMNSLSNSIASLVTSKSSWSLIAGRLPGRTDNEIKNYWNTHIRRKLLNRGIDPATHRPLNEPA 65 (243)
Q Consensus 2 ~EEDelLi~l~s~~Gn~~kWs~IA~~LpGRTdn~IKNrWn~~lrrkl~~~~~~p~t~rpl~~~~ 65 (243)
+|||++|+++|.+||+ +|+.||++|||||+++|||||+.++|++++.++++|.+|+|+.+..
T Consensus 72 ~EED~lLLeL~k~~Gn--KWskIAk~LPGRTDnqIKNRWnslLKKklr~~~I~p~t~kpl~e~E 133 (459)
T PLN03091 72 QQEENLIIELHAVLGN--RWSQIAAQLPGRTDNEIKNLWNSCLKKKLRQRGIDPNTHKPLSEVE 133 (459)
T ss_pred HHHHHHHHHHHHHhCc--chHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCCCCCCCCccccc
Confidence 7999999999999999 9999999999999999999999999999999999999999998643
No 4
>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=98.99 E-value=4e-10 Score=79.55 Aligned_cols=52 Identities=25% Similarity=0.415 Sum_probs=43.8
Q ss_pred hhhHHHHHHHHHHhCCcCcHHHHhccCCCCChHHHHHHHHHHHHhhhhhCCCCC
Q 026135 2 KKMNSLSNSIASLVTSKSSWSLIAGRLPGRTDNEIKNYWNTHIRRKLLNRGIDP 55 (243)
Q Consensus 2 ~EEDelLi~l~s~~Gn~~kWs~IA~~LpGRTdn~IKNrWn~~lrrkl~~~~~~p 55 (243)
+|||++|+.+|..+|+ +|..||.+|+.||..+|++||+.+|++.+....+++
T Consensus 3 ~eEd~~L~~~~~~~g~--~W~~Ia~~l~~Rt~~~~~~r~~~~l~~~~~~~~wt~ 54 (60)
T PF13921_consen 3 KEEDELLLELVKKYGN--DWKKIAEHLGNRTPKQCRNRWRNHLRPKISRGPWTK 54 (60)
T ss_dssp HHHHHHHHHHHHHHTS---HHHHHHHSTTS-HHHHHHHHHHTTSTTSTSSSSSH
T ss_pred HHHHHHHHHHHHHHCc--CHHHHHHHHCcCCHHHHHHHHHHHCcccccCCCcCH
Confidence 6999999999999999 999999999669999999999998877666655543
No 5
>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=98.85 E-value=3.2e-09 Score=72.59 Aligned_cols=41 Identities=20% Similarity=0.383 Sum_probs=38.7
Q ss_pred hhhHHHHHHHHHHhCCcCc-HHHHhccCC-CCChHHHHHHHHHHH
Q 026135 2 KKMNSLSNSIASLVTSKSS-WSLIAGRLP-GRTDNEIKNYWNTHI 44 (243)
Q Consensus 2 ~EEDelLi~l~s~~Gn~~k-Ws~IA~~Lp-GRTdn~IKNrWn~~l 44 (243)
+|||++|++++.++|. . |..||..|| |||..+|++||+.++
T Consensus 6 ~eE~~~l~~~v~~~g~--~~W~~Ia~~~~~~Rt~~qc~~~~~~~~ 48 (48)
T PF00249_consen 6 EEEDEKLLEAVKKYGK--DNWKKIAKRMPGGRTAKQCRSRYQNLL 48 (48)
T ss_dssp HHHHHHHHHHHHHSTT--THHHHHHHHHSSSSTHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHHhCC--cHHHHHHHHcCCCCCHHHHHHHHHhhC
Confidence 6899999999999998 6 999999999 999999999999864
No 6
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=98.82 E-value=5.8e-09 Score=68.15 Aligned_cols=42 Identities=26% Similarity=0.565 Sum_probs=39.7
Q ss_pred hhhHHHHHHHHHHhC-CcCcHHHHhccCCCCChHHHHHHHHHHHH
Q 026135 2 KKMNSLSNSIASLVT-SKSSWSLIAGRLPGRTDNEIKNYWNTHIR 45 (243)
Q Consensus 2 ~EEDelLi~l~s~~G-n~~kWs~IA~~LpGRTdn~IKNrWn~~lr 45 (243)
++||++|+.++..+| . .|..||..|++||+.+|++||+.+++
T Consensus 6 ~~E~~~l~~~~~~~g~~--~w~~Ia~~~~~rt~~~~~~~~~~~~~ 48 (49)
T smart00717 6 EEEDELLIELVKKYGKN--NWEKIAKELPGRTAEQCRERWNNLLK 48 (49)
T ss_pred HHHHHHHHHHHHHHCcC--CHHHHHHHcCCCCHHHHHHHHHHHcC
Confidence 689999999999999 8 99999999999999999999998764
No 7
>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=98.70 E-value=2.7e-08 Score=64.24 Aligned_cols=40 Identities=25% Similarity=0.483 Sum_probs=38.1
Q ss_pred hhhHHHHHHHHHHhC-CcCcHHHHhccCCCCChHHHHHHHHHH
Q 026135 2 KKMNSLSNSIASLVT-SKSSWSLIAGRLPGRTDNEIKNYWNTH 43 (243)
Q Consensus 2 ~EEDelLi~l~s~~G-n~~kWs~IA~~LpGRTdn~IKNrWn~~ 43 (243)
+|||++|+.++..+| . .|..||..|++|+..+|++||+.+
T Consensus 4 ~eE~~~l~~~~~~~g~~--~w~~Ia~~~~~rs~~~~~~~~~~~ 44 (45)
T cd00167 4 EEEDELLLEAVKKYGKN--NWEKIAKELPGRTPKQCRERWRNL 44 (45)
T ss_pred HHHHHHHHHHHHHHCcC--CHHHHHhHcCCCCHHHHHHHHHHh
Confidence 689999999999999 7 999999999999999999999875
No 8
>PLN03212 Transcription repressor MYB5; Provisional
Probab=98.65 E-value=2e-08 Score=91.26 Aligned_cols=59 Identities=14% Similarity=0.198 Sum_probs=53.6
Q ss_pred hhhHHHHHHHHHHhCCcCcHHHHhccC-CCCChHHHHHHHHHHHHhhhhhCCCCCCCCCCC
Q 026135 2 KKMNSLSNSIASLVTSKSSWSLIAGRL-PGRTDNEIKNYWNTHIRRKLLNRGIDPATHRPL 61 (243)
Q Consensus 2 ~EEDelLi~l~s~~Gn~~kWs~IA~~L-pGRTdn~IKNrWn~~lrrkl~~~~~~p~t~rpl 61 (243)
+|||++|++++..+|.. +|..||+++ +|||+++|+.||..+|++.+....|++.+..-+
T Consensus 30 ~EEDe~L~~lV~kyG~~-nW~~IAk~~g~gRT~KQCReRW~N~L~P~I~kgpWT~EED~lL 89 (249)
T PLN03212 30 VEEDEILVSFIKKEGEG-RWRSLPKRAGLLRCGKSCRLRWMNYLRPSVKRGGITSDEEDLI 89 (249)
T ss_pred HHHHHHHHHHHHHhCcc-cHHHHHHhhhcCCCcchHHHHHHHhhchhcccCCCChHHHHHH
Confidence 79999999999999943 899999998 699999999999999999999999988876644
No 9
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=98.45 E-value=7.8e-08 Score=85.67 Aligned_cols=60 Identities=7% Similarity=0.043 Sum_probs=55.4
Q ss_pred hhhHHHHHHHHHHhCCcCcHHHHhccCC-CCChHHHHHHHHHHHHhhhhhCCCCCCCCCCCC
Q 026135 2 KKMNSLSNSIASLVTSKSSWSLIAGRLP-GRTDNEIKNYWNTHIRRKLLNRGIDPATHRPLN 62 (243)
Q Consensus 2 ~EEDelLi~l~s~~Gn~~kWs~IA~~Lp-GRTdn~IKNrWn~~lrrkl~~~~~~p~t~rpl~ 62 (243)
.|||++|++++..+|.. +|..|++.++ ||++.+|+-||..|||+.++...+++.+.+.+-
T Consensus 14 ~EED~~L~~~V~~~G~~-~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ikrg~fT~eEe~~Ii 74 (238)
T KOG0048|consen 14 QEEDLTQIRSIKSFGKH-NGTALPKLAGLRRCGKSCRLRWTNYLRPDLKRGNFSDEEEDLII 74 (238)
T ss_pred hHHHHHHHHHHHHhCCC-CcchhhhhcCCCccchHHHHHhhcccCCCccCCCCCHHHHHHHH
Confidence 69999999999999963 7999999999 999999999999999999999999988777653
No 10
>PLN03091 hypothetical protein; Provisional
Probab=98.37 E-value=1.9e-07 Score=90.72 Aligned_cols=57 Identities=11% Similarity=0.124 Sum_probs=51.6
Q ss_pred hhhHHHHHHHHHHhCCcCcHHHHhccC-CCCChHHHHHHHHHHHHhhhhhCCCCCCCCC
Q 026135 2 KKMNSLSNSIASLVTSKSSWSLIAGRL-PGRTDNEIKNYWNTHIRRKLLNRGIDPATHR 59 (243)
Q Consensus 2 ~EEDelLi~l~s~~Gn~~kWs~IA~~L-pGRTdn~IKNrWn~~lrrkl~~~~~~p~t~r 59 (243)
+|||++|++++..+|.. +|..||+.+ +||++++||.||+.+|++.+++..|++.+..
T Consensus 19 pEEDe~L~~~V~kyG~~-nWs~IAk~~g~gRT~KQCRERW~NyLdP~IkKgpWT~EED~ 76 (459)
T PLN03091 19 PEEDEKLLRHITKYGHG-CWSSVPKQAGLQRCGKSCRLRWINYLRPDLKRGTFSQQEEN 76 (459)
T ss_pred HHHHHHHHHHHHHhCcC-CHHHHhhhhccCcCcchHhHHHHhccCCcccCCCCCHHHHH
Confidence 69999999999999953 899999998 4999999999999999999999988877663
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=96.40 E-value=0.0032 Score=62.77 Aligned_cols=46 Identities=13% Similarity=0.142 Sum_probs=42.6
Q ss_pred hhhHHHHHHHHHHhCCcCcHHHHhccCCCCChHHHHHHHHHHHHhhhh
Q 026135 2 KKMNSLSNSIASLVTSKSSWSLIAGRLPGRTDNEIKNYWNTHIRRKLL 49 (243)
Q Consensus 2 ~EEDelLi~l~s~~Gn~~kWs~IA~~LpGRTdn~IKNrWn~~lrrkl~ 49 (243)
.|||+.|+.++.++|+ +|+.||..++||++.+|.+||+..+.....
T Consensus 77 ~eed~~li~l~~~~~~--~wstia~~~d~rt~~~~~ery~~~~~~~~s 122 (512)
T COG5147 77 EEEDEQLIDLDKELGT--QWSTIADYKDRRTAQQCVERYVNTLEDLSS 122 (512)
T ss_pred HHHHHHHHHHHHhcCc--hhhhhccccCccchHHHHHHHHHHhhhhhc
Confidence 5899999999999999 999999999999999999999987776555
No 12
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=96.38 E-value=0.0019 Score=64.45 Aligned_cols=60 Identities=18% Similarity=0.351 Sum_probs=52.3
Q ss_pred ChhhHHHHHHHHHHhCCcCcHHHHhccCCCCChHHHHHHHHHHHHhhhhhCCCCCCCCCCC
Q 026135 1 MKKMNSLSNSIASLVTSKSSWSLIAGRLPGRTDNEIKNYWNTHIRRKLLNRGIDPATHRPL 61 (243)
Q Consensus 1 ~~EEDelLi~l~s~~Gn~~kWs~IA~~LpGRTdn~IKNrWn~~lrrkl~~~~~~p~t~rpl 61 (243)
+..||+.+..++..+|.+ .|+.||..|.-|+.+++++||+.++.+.+....+......-+
T Consensus 24 ~~~EDe~l~~~vk~l~~n-nws~vas~~~~~~~kq~~~rw~~~lnp~lk~~~~~~eed~~l 83 (512)
T COG5147 24 KRTEDEDLKALVKKLGPN-NWSKVASLLISSTGKQSSNRWNNHLNPQLKKKNWSEEEDEQL 83 (512)
T ss_pred CCcchhHHHHHHhhcccc-cHHHHHHHhcccccccccchhhhhhchhcccccccHHHHHHH
Confidence 467999999999999954 899999999999999999999999999999888766654443
No 13
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=96.24 E-value=0.0059 Score=62.71 Aligned_cols=54 Identities=15% Similarity=0.260 Sum_probs=48.5
Q ss_pred hhhHHHHHHHHHHhCCcCcHHHHhccCCCCChHHHHHHHHHHHHhhhhhCCCCCC
Q 026135 2 KKMNSLSNSIASLVTSKSSWSLIAGRLPGRTDNEIKNYWNTHIRRKLLNRGIDPA 56 (243)
Q Consensus 2 ~EEDelLi~l~s~~Gn~~kWs~IA~~LpGRTdn~IKNrWn~~lrrkl~~~~~~p~ 56 (243)
.+||-+|+..+++||.+ -|.+|...+|||++.+|+.||...|.+.++...|+-.
T Consensus 365 ~~ED~~L~~AV~~Yg~k-dw~k~R~~vPnRSdsQcR~RY~nvL~~s~K~~rW~l~ 418 (939)
T KOG0049|consen 365 DQEDVLLVCAVSRYGAK-DWAKVRQAVPNRSDSQCRERYTNVLNRSAKVERWTLV 418 (939)
T ss_pred CHHHHHHHHHHHHhCcc-chhhHHHhcCCccHHHHHHHHHHHHHHhhccCceeec
Confidence 58999999999999963 7999999999999999999999999998888777543
No 14
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=96.20 E-value=0.0041 Score=62.21 Aligned_cols=54 Identities=15% Similarity=0.238 Sum_probs=48.7
Q ss_pred hhHHHHHHHHHHhCCcCcHHHHhccCCCCChHHHHHHHHHHHHhhhhhCCCCCCC
Q 026135 3 KMNSLSNSIASLVTSKSSWSLIAGRLPGRTDNEIKNYWNTHIRRKLLNRGIDPAT 57 (243)
Q Consensus 3 EEDelLi~l~s~~Gn~~kWs~IA~~LpGRTdn~IKNrWn~~lrrkl~~~~~~p~t 57 (243)
-||++|-..+..+|.+ +|+.|+++|+-.+..+|++||+.++.+.++...|....
T Consensus 13 tEdeilkaav~kyg~n-qws~i~sll~~kt~rqC~~rw~e~ldp~i~~tews~ee 66 (617)
T KOG0050|consen 13 TEDEVLKAAVMKYGKN-QWSRIASLLNRKTARQCKARWEEWLDPAIKKTEWSREE 66 (617)
T ss_pred cHHHHHHHHHHHcchH-HHHHHHHHHhhcchhHHHHHHHHHhCHHHhhhhhhhhH
Confidence 4899999999999943 99999999999999999999999999999988886553
No 15
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=93.85 E-value=0.061 Score=54.79 Aligned_cols=43 Identities=14% Similarity=0.302 Sum_probs=39.6
Q ss_pred hhhHHHHHHHHHHhCCcCcHHHHhccCCCCChHHHHHHHHHHHHhh
Q 026135 2 KKMNSLSNSIASLVTSKSSWSLIAGRLPGRTDNEIKNYWNTHIRRK 47 (243)
Q Consensus 2 ~EEDelLi~l~s~~Gn~~kWs~IA~~LpGRTdn~IKNrWn~~lrrk 47 (243)
+||++.|..+|.++|+ .|..|++.| ||....|+.||..+.+..
T Consensus 389 ~ee~eeL~~l~~~~g~--~W~~Ig~~l-gr~P~~crd~wr~~~~~g 431 (607)
T KOG0051|consen 389 PEEEEELKKLVVEHGN--DWKEIGKAL-GRMPMDCRDRWRQYVKCG 431 (607)
T ss_pred cchHHHHHHHHHHhcc--cHHHHHHHH-ccCcHHHHHHHHHhhccc
Confidence 6899999999999999 999999998 999999999999876554
No 16
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=91.24 E-value=0.27 Score=50.99 Aligned_cols=45 Identities=18% Similarity=0.175 Sum_probs=35.8
Q ss_pred hhHHHHHHHHHHhCCcCcHHHHhccCCCCChHHHHHHHHHHHHhhh
Q 026135 3 KMNSLSNSIASLVTSKSSWSLIAGRLPGRTDNEIKNYWNTHIRRKL 48 (243)
Q Consensus 3 EEDelLi~l~s~~Gn~~kWs~IA~~LpGRTdn~IKNrWn~~lrrkl 48 (243)
.||+.||.++..||.. .|.+||..||.||..+...|-...++.++
T Consensus 418 ~edeqL~~~V~~YG~g-~WakcA~~Lp~~t~~q~~rrR~R~~~~k~ 462 (939)
T KOG0049|consen 418 VEDEQLLYAVKVYGKG-NWAKCAMLLPKKTSRQLRRRRLRLIAAKL 462 (939)
T ss_pred cchHHHHHHHHHHccc-hHHHHHHHccccchhHHHHHHHHHHHHHH
Confidence 4889999999999943 99999999999999776665555554443
No 17
>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=90.29 E-value=0.7 Score=31.41 Aligned_cols=40 Identities=15% Similarity=0.128 Sum_probs=31.1
Q ss_pred ChhhHHHHHHHHHHhCCcCcHHHHhccCCCCChHHHHHHHHHH
Q 026135 1 MKKMNSLSNSIASLVTSKSSWSLIAGRLPGRTDNEIKNYWNTH 43 (243)
Q Consensus 1 ~~EEDelLi~l~s~~Gn~~kWs~IA~~LpGRTdn~IKNrWn~~ 43 (243)
|++++..++.++-..|- .|..||..| |.+.+.|+.+...-
T Consensus 11 L~~~~r~i~~l~~~~g~--s~~eIa~~l-~~s~~~v~~~l~ra 50 (54)
T PF08281_consen 11 LPERQREIFLLRYFQGM--SYAEIAEIL-GISESTVKRRLRRA 50 (54)
T ss_dssp S-HHHHHHHHHHHTS-----HHHHHHHC-TS-HHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHCc--CHHHHHHHH-CcCHHHHHHHHHHH
Confidence 56889999999999998 999999999 99999999976654
No 18
>PF08914 Myb_DNA-bind_2: Rap1 Myb domain; InterPro: IPR015010 Rap1 Myb adopts a canonical three-helix bundle tertiary structure, with the second and third helices forming a helix-turn-helix variant motif. The function is unclear but it may either interact with DNA via an adaptor protein or it may be only involved in protein-protein interactions []. ; PDB: 1FEX_A.
Probab=89.13 E-value=0.52 Score=34.92 Aligned_cols=46 Identities=13% Similarity=0.203 Sum_probs=32.3
Q ss_pred hhhHHHHHHHHHHh--------CCcCcHHHHhccCC-CCChHHHHHHHHHHHHhhh
Q 026135 2 KKMNSLSNSIASLV--------TSKSSWSLIAGRLP-GRTDNEIKNYWNTHIRRKL 48 (243)
Q Consensus 2 ~EEDelLi~l~s~~--------Gn~~kWs~IA~~Lp-GRTdn~IKNrWn~~lrrkl 48 (243)
.|||++|++.+.++ ||. -|..++..-| .+|=.+.|+||..+|+.+.
T Consensus 7 ~edD~~l~~~v~~~~~~~~~~~Gn~-iwk~le~~~~t~HtwQSwR~Ry~K~L~~~~ 61 (65)
T PF08914_consen 7 EEDDAALLDYVKENERQGGSVSGNK-IWKELEEKHPTRHTWQSWRDRYLKHLRGRP 61 (65)
T ss_dssp HHHHHHHHHHHHHT--STTTTTSSH-HHHHHHHS-SSS--SHHHHHHHHHHT----
T ss_pred HHHHHHHHHHHHHhccCCCCCchHH-HHHHHHHHcCCCCCHHHHHHHHHHHHhccc
Confidence 68999999999443 441 4999999988 9999999999988887664
No 19
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=88.96 E-value=0.37 Score=48.70 Aligned_cols=45 Identities=20% Similarity=0.319 Sum_probs=40.8
Q ss_pred hhhHHHHHHHHHHhCCcCcHHHHhccCCCCChHHHHHHHHHHHHhhhh
Q 026135 2 KKMNSLSNSIASLVTSKSSWSLIAGRLPGRTDNEIKNYWNTHIRRKLL 49 (243)
Q Consensus 2 ~EEDelLi~l~s~~Gn~~kWs~IA~~LpGRTdn~IKNrWn~~lrrkl~ 49 (243)
.|||+.|+++..++-. .|..||..| ||+.++|-.||+.++--...
T Consensus 64 ~eederlLhlakl~p~--qwrtIa~i~-gr~~~qc~eRy~~ll~~~~s 108 (617)
T KOG0050|consen 64 REEDERLLHLAKLEPT--QWRTIADIM-GRTSQQCLERYNNLLDVYVS 108 (617)
T ss_pred hhHHHHHHHHHHhcCC--ccchHHHHh-hhhHHHHHHHHHHHHHHHHh
Confidence 5899999999999999 999999987 99999999999988766554
No 20
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=88.51 E-value=0.61 Score=34.51 Aligned_cols=48 Identities=21% Similarity=0.282 Sum_probs=32.0
Q ss_pred hhhHHHHHHHHHH------hC---Cc---CcHHHHhccC----CCCChHHHHHHHHHHHHhhhh
Q 026135 2 KKMNSLSNSIASL------VT---SK---SSWSLIAGRL----PGRTDNEIKNYWNTHIRRKLL 49 (243)
Q Consensus 2 ~EEDelLi~l~s~------~G---n~---~kWs~IA~~L----pGRTdn~IKNrWn~~lrrkl~ 49 (243)
.+|-.+||+++.. ++ .. ..|..||..| -.||..+|+++|+.+.++...
T Consensus 6 ~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~~~Yk~ 69 (90)
T PF13837_consen 6 DEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNLKKKYKK 69 (90)
T ss_dssp HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHHHHHHC
T ss_pred HHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHH
Confidence 4677788887776 32 10 1499999998 479999999999996555443
No 21
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=85.55 E-value=1.1 Score=44.35 Aligned_cols=41 Identities=22% Similarity=0.225 Sum_probs=35.9
Q ss_pred hhhHHHHHHHHHHhCCcCcHHHHhccCCCCChHHHHHHHHHH
Q 026135 2 KKMNSLSNSIASLVTSKSSWSLIAGRLPGRTDNEIKNYWNTH 43 (243)
Q Consensus 2 ~EEDelLi~l~s~~Gn~~kWs~IA~~LpGRTdn~IKNrWn~~ 43 (243)
-+||-+||+....||-. +|..||.++.-|+..+||.+|..+
T Consensus 77 adEEilLLea~~t~G~G-NW~dIA~hIGtKtkeeck~hy~k~ 117 (438)
T KOG0457|consen 77 ADEEILLLEAAETYGFG-NWQDIADHIGTKTKEECKEHYLKH 117 (438)
T ss_pred hHHHHHHHHHHHHhCCC-cHHHHHHHHcccchHHHHHHHHHH
Confidence 37889999999999932 899999999999999999998643
No 22
>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=82.58 E-value=1.6 Score=37.97 Aligned_cols=48 Identities=19% Similarity=0.230 Sum_probs=33.9
Q ss_pred hhhHHHHHHHHHHh---CCc--CcHHHHhccCCCCChHHHHHHHHHHHHhhhhh
Q 026135 2 KKMNSLSNSIASLV---TSK--SSWSLIAGRLPGRTDNEIKNYWNTHIRRKLLN 50 (243)
Q Consensus 2 ~EEDelLi~l~s~~---Gn~--~kWs~IA~~LpGRTdn~IKNrWn~~lrrkl~~ 50 (243)
+|||.||-+.+-.+ |.- .-...+++.| +||.-+|.=|||+++|+++..
T Consensus 9 ~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L-~RTsAACGFRWNs~VRkqY~~ 61 (161)
T TIGR02894 9 HEEDLLLAETVLRHIREGSTQLSAFEEVGRAL-NRTAAACGFRWNAYVRKQYEE 61 (161)
T ss_pred cHHHHHHHHHHHHHHhcchHHHHHHHHHHHHH-cccHHHhcchHHHHHHHHHHH
Confidence 46776665544333 420 0367778887 999999999999999987643
No 23
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=80.36 E-value=1.9 Score=41.71 Aligned_cols=39 Identities=21% Similarity=0.244 Sum_probs=35.4
Q ss_pred hhHHHHHHHHHHhC-CcCcHHHHhccCCCCChHHHHHHHHHH
Q 026135 3 KMNSLSNSIASLVT-SKSSWSLIAGRLPGRTDNEIKNYWNTH 43 (243)
Q Consensus 3 EEDelLi~l~s~~G-n~~kWs~IA~~LpGRTdn~IKNrWn~~ 43 (243)
+||-+||+.-..+| . +|.-||.++..|+..+||.+|..+
T Consensus 69 dEEllli~~~~TlGlG--NW~dIadyiGsr~kee~k~HylK~ 108 (432)
T COG5114 69 DEELLLIECLDTLGLG--NWEDIADYIGSRAKEEIKSHYLKM 108 (432)
T ss_pred hHHHHHHHHHHhcCCC--cHHHHHHHHhhhhhHHHHHHHHHH
Confidence 68899999999999 5 899999999999999999998643
No 24
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=80.16 E-value=4 Score=29.40 Aligned_cols=41 Identities=10% Similarity=0.161 Sum_probs=34.3
Q ss_pred hhhHHHHHHHHHHhCCcCcH---HHHhccCC--CCChHHHHHHHHHH
Q 026135 2 KKMNSLSNSIASLVTSKSSW---SLIAGRLP--GRTDNEIKNYWNTH 43 (243)
Q Consensus 2 ~EEDelLi~l~s~~Gn~~kW---s~IA~~Lp--GRTdn~IKNrWn~~ 43 (243)
+||.++.++.+..+|-. .| ..|+..|. +.|..+|+.+...|
T Consensus 8 ~eeh~~Fl~ai~~~G~g-~~a~pk~I~~~~~~~~lT~~qV~SH~QKy 53 (57)
T TIGR01557 8 EDLHDRFLQAVQKLGGP-DWATPKRILELMVVDGLTRDQVASHLQKY 53 (57)
T ss_pred HHHHHHHHHHHHHhCCC-cccchHHHHHHcCCCCCCHHHHHHHHHHH
Confidence 68999999999999932 89 99999874 33999999988765
No 25
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=73.97 E-value=4.3 Score=35.59 Aligned_cols=46 Identities=15% Similarity=0.294 Sum_probs=31.0
Q ss_pred hhhHHHHHHHHHHhCCc--Cc---HHHHhccCCCCChHHHHHHHHHHHHhhh
Q 026135 2 KKMNSLSNSIASLVTSK--SS---WSLIAGRLPGRTDNEIKNYWNTHIRRKL 48 (243)
Q Consensus 2 ~EEDelLi~l~s~~Gn~--~k---Ws~IA~~LpGRTdn~IKNrWn~~lrrkl 48 (243)
.|||.+|-+.+-.++.. .+ ...++..| +||.-+|.-|||+++|++.
T Consensus 10 ~e~d~llae~vl~~i~eg~tql~afe~~g~~L-~rt~aac~fRwNs~vrk~Y 60 (170)
T PRK13923 10 QERDGLLAEVVLRHIREGGTQLKAFEEVGDAL-KRTAAACGFRWNSVVRKQY 60 (170)
T ss_pred hHHHHHHHHHHHHHHhccchHHHHHHHHHHHH-hhhHHHHHhHHHHHHHHHH
Confidence 46666665555555420 02 45555666 9999999999999998644
No 26
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=73.92 E-value=4.5 Score=29.54 Aligned_cols=44 Identities=16% Similarity=0.274 Sum_probs=33.3
Q ss_pred hhhHHHHHHHHHHh-----CCc----------CcHHHHhccC-----CCCChHHHHHHHHHHHH
Q 026135 2 KKMNSLSNSIASLV-----TSK----------SSWSLIAGRL-----PGRTDNEIKNYWNTHIR 45 (243)
Q Consensus 2 ~EEDelLi~l~s~~-----Gn~----------~kWs~IA~~L-----pGRTdn~IKNrWn~~lr 45 (243)
.+|.++|++++..+ |.. ..|..|+..| +.|+..++|..|..+..
T Consensus 7 ~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk~ 70 (78)
T PF13873_consen 7 EEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLKS 70 (78)
T ss_pred HHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHH
Confidence 57888888887765 300 1499999988 47999999999987543
No 27
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=69.95 E-value=9.6 Score=25.63 Aligned_cols=40 Identities=10% Similarity=0.211 Sum_probs=31.1
Q ss_pred ChhhHHHHHHHHHHhCCcCcHHHHhccCCCCChHHHHHHHHH
Q 026135 1 MKKMNSLSNSIASLVTSKSSWSLIAGRLPGRTDNEIKNYWNT 42 (243)
Q Consensus 1 ~~EEDelLi~l~s~~Gn~~kWs~IA~~LpGRTdn~IKNrWn~ 42 (243)
|++=|..|+.+...-|.. .|..||..+ |=+...|.+|+..
T Consensus 1 lD~~D~~Il~~Lq~d~r~-s~~~la~~l-glS~~~v~~Ri~r 40 (42)
T PF13404_consen 1 LDELDRKILRLLQEDGRR-SYAELAEEL-GLSESTVRRRIRR 40 (42)
T ss_dssp --HHHHHHHHHHHH-TTS--HHHHHHHH-TS-HHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHcCCc-cHHHHHHHH-CcCHHHHHHHHHH
Confidence 677899999999988853 799999998 9999999999865
No 28
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=67.96 E-value=10 Score=31.37 Aligned_cols=47 Identities=6% Similarity=0.065 Sum_probs=39.3
Q ss_pred ChhhHHHHHHHHHHhCCcCcHHHHhccCCCCChHHHHHHHHHHHHhhhh
Q 026135 1 MKKMNSLSNSIASLVTSKSSWSLIAGRLPGRTDNEIKNYWNTHIRRKLL 49 (243)
Q Consensus 1 ~~EEDelLi~l~s~~Gn~~kWs~IA~~LpGRTdn~IKNrWn~~lrrkl~ 49 (243)
|++-|..|+++-..=|.. .|+.||+.+ |-+...|++||..+...-+.
T Consensus 7 lD~~D~~Il~~Lq~d~R~-s~~eiA~~l-glS~~tV~~Ri~rL~~~GvI 53 (153)
T PRK11179 7 IDNLDRGILEALMENART-PYAELAKQF-GVSPGTIHVRVEKMKQAGII 53 (153)
T ss_pred cCHHHHHHHHHHHHcCCC-CHHHHHHHH-CcCHHHHHHHHHHHHHCCCe
Confidence 467899999998888853 899999999 99999999999876655543
No 29
>PF09111 SLIDE: SLIDE; InterPro: IPR015195 The SLIDE domain adopts a secondary structure comprising a main core of three alpha-helices. It has a role in DNA binding, contacting DNA target sites similar to c-Myb (IPR014778 from INTERPRO) repeats or homeodomains []. ; GO: 0003676 nucleic acid binding, 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006338 chromatin remodeling, 0005634 nucleus; PDB: 2NOG_A 2Y9Y_A 2Y9Z_A 1OFC_X.
Probab=63.33 E-value=10 Score=31.18 Aligned_cols=45 Identities=18% Similarity=0.216 Sum_probs=36.7
Q ss_pred hhhHHHHHHHHHHhCC---cCcHHHHhcc------------CCCCChHHHHHHHHHHHHhh
Q 026135 2 KKMNSLSNSIASLVTS---KSSWSLIAGR------------LPGRTDNEIKNYWNTHIRRK 47 (243)
Q Consensus 2 ~EEDelLi~l~s~~Gn---~~kWs~IA~~------------LpGRTdn~IKNrWn~~lrrk 47 (243)
+|||..|+-+...+|- . .|..|... |..||...|..|-+++|+--
T Consensus 54 eeEDRfLl~~~~~~G~~~~~-~~e~Ik~~Ir~~p~FrFDwf~kSRt~~el~rR~~tLi~~i 113 (118)
T PF09111_consen 54 EEEDRFLLCMLYKYGYDAEG-NWEKIKQEIRESPLFRFDWFFKSRTPQELQRRCNTLIKLI 113 (118)
T ss_dssp HHHHHHHHHHHHHHTTTSTT-HHHHHHHHHHH-CGGCT-HHHHTS-HHHHHHHHHHHHHHH
T ss_pred cHHHHHHHHHHHHhCCCCCc-hHHHHHHHHHhCCCcccchhcccCCHHHHHHHHHHHHHHH
Confidence 6899999999999994 3 79888763 37899999999999887643
No 30
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=60.43 E-value=26 Score=27.95 Aligned_cols=39 Identities=8% Similarity=0.008 Sum_probs=33.2
Q ss_pred hhhHHHHHHHHHHhCCcCcHHHHhccCCCCChHHHHHHHHHH
Q 026135 2 KKMNSLSNSIASLVTSKSSWSLIAGRLPGRTDNEIKNYWNTH 43 (243)
Q Consensus 2 ~EEDelLi~l~s~~Gn~~kWs~IA~~LpGRTdn~IKNrWn~~ 43 (243)
+++...++.|+-..|- ....||..| |-+.+.||++...-
T Consensus 108 p~~~r~v~~l~~~~g~--s~~EIA~~l-gis~~tV~~~l~ra 146 (161)
T PRK09047 108 PARQREAFLLRYWEDM--DVAETAAAM-GCSEGSVKTHCSRA 146 (161)
T ss_pred CHHHHHHHHHHHHhcC--CHHHHHHHH-CCCHHHHHHHHHHH
Confidence 4667778888878887 899999999 99999999998743
No 31
>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=60.13 E-value=20 Score=26.70 Aligned_cols=45 Identities=20% Similarity=0.365 Sum_probs=29.5
Q ss_pred hhhHHHHHHHHHHh---CCc--------CcHHHHhccC---C--CCChHHHHHHHHHHHHh
Q 026135 2 KKMNSLSNSIASLV---TSK--------SSWSLIAGRL---P--GRTDNEIKNYWNTHIRR 46 (243)
Q Consensus 2 ~EEDelLi~l~s~~---Gn~--------~kWs~IA~~L---p--GRTdn~IKNrWn~~lrr 46 (243)
++++++|+++..+. |+. .-|..|+..| + ..+..+|||||..+-+.
T Consensus 4 ~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~lk~~ 64 (96)
T PF12776_consen 4 PEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTLKKD 64 (96)
T ss_pred hHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHHHHH
Confidence 45677777766443 431 0299999988 3 33678999999875433
No 32
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 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 is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; 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: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=59.65 E-value=20 Score=23.96 Aligned_cols=42 Identities=12% Similarity=0.158 Sum_probs=31.1
Q ss_pred hhhHHHHHHHHHHhCCcCcHHHHhccCCCCChHHHHHHHHHHHHh
Q 026135 2 KKMNSLSNSIASLVTSKSSWSLIAGRLPGRTDNEIKNYWNTHIRR 46 (243)
Q Consensus 2 ~EEDelLi~l~s~~Gn~~kWs~IA~~LpGRTdn~IKNrWn~~lrr 46 (243)
.+++..||.++-.-|- .|..||..| |-+...|+.+-..-+++
T Consensus 6 ~~~er~vi~~~y~~~~--t~~eIa~~l-g~s~~~V~~~~~~al~k 47 (50)
T PF04545_consen 6 PPREREVIRLRYFEGL--TLEEIAERL-GISRSTVRRILKRALKK 47 (50)
T ss_dssp -HHHHHHHHHHHTST---SHHHHHHHH-TSCHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHhcCCC--CHHHHHHHH-CCcHHHHHHHHHHHHHH
Confidence 4566777777766666 899999998 88999999877655543
No 33
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=59.63 E-value=12 Score=31.46 Aligned_cols=46 Identities=9% Similarity=-0.021 Sum_probs=38.6
Q ss_pred ChhhHHHHHHHHHHhCCcCcHHHHhccCCCCChHHHHHHHHHHHHhhh
Q 026135 1 MKKMNSLSNSIASLVTSKSSWSLIAGRLPGRTDNEIKNYWNTHIRRKL 48 (243)
Q Consensus 1 ~~EEDelLi~l~s~~Gn~~kWs~IA~~LpGRTdn~IKNrWn~~lrrkl 48 (243)
+++-|..|+.+-+.-|.. .|+.||+.+ |-+...|.+||+.+.+..+
T Consensus 12 lD~~D~~IL~~Lq~d~R~-s~~eiA~~l-glS~~tv~~Ri~rL~~~Gv 57 (164)
T PRK11169 12 LDRIDRNILNELQKDGRI-SNVELSKRV-GLSPTPCLERVRRLERQGF 57 (164)
T ss_pred HHHHHHHHHHHhccCCCC-CHHHHHHHH-CcCHHHHHHHHHHHHHCCC
Confidence 467789999888888853 899999998 9999999999977666554
No 34
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=57.04 E-value=30 Score=21.65 Aligned_cols=39 Identities=13% Similarity=0.020 Sum_probs=29.4
Q ss_pred hhhHHHHHHHHHHhCCcCcHHHHhccCCCCChHHHHHHHHHH
Q 026135 2 KKMNSLSNSIASLVTSKSSWSLIAGRLPGRTDNEIKNYWNTH 43 (243)
Q Consensus 2 ~EEDelLi~l~s~~Gn~~kWs~IA~~LpGRTdn~IKNrWn~~ 43 (243)
.+++..++.++-.-|- .+..||..| |-+...|+.+++..
T Consensus 12 ~~~~~~~~~~~~~~~~--~~~~ia~~~-~~s~~~i~~~~~~~ 50 (55)
T cd06171 12 PEREREVILLRFGEGL--SYEEIAEIL-GISRSTVRQRLHRA 50 (55)
T ss_pred CHHHHHHHHHHHhcCC--CHHHHHHHH-CcCHHHHHHHHHHH
Confidence 3556677777766777 899999997 78888888776653
No 35
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=54.15 E-value=27 Score=26.55 Aligned_cols=48 Identities=8% Similarity=0.075 Sum_probs=40.1
Q ss_pred ChhhHHHHHHHHHHhCCcCcHHHHhccCCCCChHHHHHHHHHHHHhhhhh
Q 026135 1 MKKMNSLSNSIASLVTSKSSWSLIAGRLPGRTDNEIKNYWNTHIRRKLLN 50 (243)
Q Consensus 1 ~~EEDelLi~l~s~~Gn~~kWs~IA~~LpGRTdn~IKNrWn~~lrrkl~~ 50 (243)
|++.|..|+.+...-|.. .|..||+.+ |-+...|..+++.+....+..
T Consensus 1 ld~~D~~il~~L~~~~~~-~~~~la~~l-~~s~~tv~~~l~~L~~~g~i~ 48 (108)
T smart00344 1 LDEIDRKILEELQKDARI-SLAELAKKV-GLSPSTVHNRVKRLEEEGVIK 48 (108)
T ss_pred CCHHHHHHHHHHHHhCCC-CHHHHHHHH-CcCHHHHHHHHHHHHHCCCee
Confidence 578899999999888853 899999998 999999999998877665543
No 36
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=51.28 E-value=19 Score=36.49 Aligned_cols=40 Identities=10% Similarity=0.070 Sum_probs=36.3
Q ss_pred hhhHHHHHHHHHHhCCcCcHHHHhccCCCCChHHHHHHHHHH
Q 026135 2 KKMNSLSNSIASLVTSKSSWSLIAGRLPGRTDNEIKNYWNTH 43 (243)
Q Consensus 2 ~EEDelLi~l~s~~Gn~~kWs~IA~~LpGRTdn~IKNrWn~~ 43 (243)
.+|..||++.+++||- .|.+||++..-+|-.+|=-+|-.+
T Consensus 284 ~qE~~LLLEGIe~ygD--dW~kVA~HVgtKt~EqCIl~FL~L 323 (531)
T COG5259 284 RQELLLLLEGIEMYGD--DWDKVARHVGTKTKEQCILHFLQL 323 (531)
T ss_pred HHHHHHHHHHHHHhhh--hHHHHHHHhCCCCHHHHHHHHHcC
Confidence 5788999999999999 999999999999999998888643
No 37
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=50.81 E-value=22 Score=36.01 Aligned_cols=40 Identities=8% Similarity=0.124 Sum_probs=36.6
Q ss_pred hhhHHHHHHHHHHhCCcCcHHHHhccCCCCChHHHHHHHHHH
Q 026135 2 KKMNSLSNSIASLVTSKSSWSLIAGRLPGRTDNEIKNYWNTH 43 (243)
Q Consensus 2 ~EEDelLi~l~s~~Gn~~kWs~IA~~LpGRTdn~IKNrWn~~ 43 (243)
++|..+|++.+.+||- .|.+||.+...||-.+|--++..+
T Consensus 258 ~qE~lLLLE~ie~y~d--dW~kVa~hVg~ks~eqCI~kFL~L 297 (506)
T KOG1279|consen 258 EQETLLLLEAIEMYGD--DWNKVADHVGTKSQEQCILKFLRL 297 (506)
T ss_pred HHHHHHHHHHHHHhcc--cHHHHHhccCCCCHHHHHHHHHhc
Confidence 5799999999999999 999999999999999998887644
No 38
>PRK04217 hypothetical protein; Provisional
Probab=50.74 E-value=34 Score=27.85 Aligned_cols=39 Identities=5% Similarity=-0.048 Sum_probs=33.2
Q ss_pred hhhHHHHHHHHHHhCCcCcHHHHhccCCCCChHHHHHHHHHH
Q 026135 2 KKMNSLSNSIASLVTSKSSWSLIAGRLPGRTDNEIKNYWNTH 43 (243)
Q Consensus 2 ~EEDelLi~l~s~~Gn~~kWs~IA~~LpGRTdn~IKNrWn~~ 43 (243)
.+++..++.++..-|- ....||+.| |.+...|+++|+..
T Consensus 44 t~eereai~l~~~eGl--S~~EIAk~L-GIS~sTV~r~L~RA 82 (110)
T PRK04217 44 TYEEFEALRLVDYEGL--TQEEAGKRM-GVSRGTVWRALTSA 82 (110)
T ss_pred CHHHHHHHHHHHHcCC--CHHHHHHHH-CcCHHHHHHHHHHH
Confidence 4566778888877887 999999998 99999999999864
No 39
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=48.93 E-value=45 Score=26.76 Aligned_cols=38 Identities=11% Similarity=-0.151 Sum_probs=31.8
Q ss_pred hhhHHHHHHHHHHhCCcCcHHHHhccCCCCChHHHHHHHHH
Q 026135 2 KKMNSLSNSIASLVTSKSSWSLIAGRLPGRTDNEIKNYWNT 42 (243)
Q Consensus 2 ~EEDelLi~l~s~~Gn~~kWs~IA~~LpGRTdn~IKNrWn~ 42 (243)
+++...++.++-..|- ....||..| |-+.+.||++...
T Consensus 108 p~~~r~v~~l~~~~g~--s~~EIA~~l-gis~~tV~~~l~R 145 (160)
T PRK09642 108 PENYRDVVLAHYLEEK--SYQEIALQE-KIEVKTVEMKLYR 145 (160)
T ss_pred CHHHHHHHHHHHHhCC--CHHHHHHHH-CCCHHHHHHHHHH
Confidence 4556777888878887 899999998 9999999999764
No 40
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=48.36 E-value=18 Score=35.78 Aligned_cols=51 Identities=20% Similarity=0.223 Sum_probs=44.3
Q ss_pred hhhHHHHHHHHHHhCCcCcHHHHhcc-----CCC-CChHHHHHHHHHHHHhhhhhCCCC
Q 026135 2 KKMNSLSNSIASLVTSKSSWSLIAGR-----LPG-RTDNEIKNYWNTHIRRKLLNRGID 54 (243)
Q Consensus 2 ~EEDelLi~l~s~~Gn~~kWs~IA~~-----LpG-RTdn~IKNrWn~~lrrkl~~~~~~ 54 (243)
+||-+.|.+|-..|-= +|-.||.+ ++- ||-..+|.||+...|..++.+.-.
T Consensus 135 keETD~LF~lck~fDL--Rf~VIaDRyd~qq~~~sRTvEdLKeRyY~v~r~l~kAr~~s 191 (445)
T KOG2656|consen 135 KEETDYLFDLCKRFDL--RFFVIADRYDNQQYKKSRTVEDLKERYYSVCRKLLKARAPS 191 (445)
T ss_pred HHHHHHHHHHHHhcCe--eEEEEeeccchhhccccccHHHHHHHHHHHHHHHHHccCCC
Confidence 6888999999999998 99999999 666 999999999999888887765444
No 41
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=44.37 E-value=49 Score=28.14 Aligned_cols=47 Identities=13% Similarity=0.027 Sum_probs=35.8
Q ss_pred hhhHHHHHHHHHHhCCcCcHHHHhccCCCCChHHHHHHHHH---HHHhhhhhC
Q 026135 2 KKMNSLSNSIASLVTSKSSWSLIAGRLPGRTDNEIKNYWNT---HIRRKLLNR 51 (243)
Q Consensus 2 ~EEDelLi~l~s~~Gn~~kWs~IA~~LpGRTdn~IKNrWn~---~lrrkl~~~ 51 (243)
+++...|+.|+-..|- .-..||..| |.+.+.||.+... .||+.+...
T Consensus 141 p~~~r~v~~L~~~eg~--s~~EIA~~l-gis~~tVk~~l~RAr~~Lr~~l~~~ 190 (201)
T PRK12545 141 PEQIGRVFMMREFLDF--EIDDICTEL-TLTANHCSVLLYRARTRLRTCLSEK 190 (201)
T ss_pred CHHHHHHHHHHHHcCC--CHHHHHHHH-CcCHHHHHHHHHHHHHHHHHHHHHH
Confidence 4567778888878887 899999998 9999999998763 344444433
No 42
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=41.29 E-value=42 Score=23.83 Aligned_cols=35 Identities=20% Similarity=0.306 Sum_probs=24.3
Q ss_pred hHHHHHHHHHHhCCcCcHHHHhccCCCCChHHHHHHHH
Q 026135 4 MNSLSNSIASLVTSKSSWSLIAGRLPGRTDNEIKNYWN 41 (243)
Q Consensus 4 EDelLi~l~s~~Gn~~kWs~IA~~LpGRTdn~IKNrWn 41 (243)
+|+-.|.+..++|- +-..||+++ ||+-+.|+++-+
T Consensus 8 ~Eqaqid~m~qlG~--s~~~isr~i-~RSr~~Ir~yl~ 42 (50)
T PF11427_consen 8 AEQAQIDVMHQLGM--SLREISRRI-GRSRTCIRRYLK 42 (50)
T ss_dssp HHHHHHHHHHHTT----HHHHHHHH-T--HHHHHHHHH
T ss_pred HHHHHHHHHHHhch--hHHHHHHHh-CccHHHHHHHhc
Confidence 45555666669998 999999998 999999988743
No 43
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=40.14 E-value=65 Score=27.69 Aligned_cols=39 Identities=13% Similarity=0.086 Sum_probs=32.4
Q ss_pred hhhHHHHHHHHHHhCCcCcHHHHhccCCCCChHHHHHHHHHH
Q 026135 2 KKMNSLSNSIASLVTSKSSWSLIAGRLPGRTDNEIKNYWNTH 43 (243)
Q Consensus 2 ~EEDelLi~l~s~~Gn~~kWs~IA~~LpGRTdn~IKNrWn~~ 43 (243)
+++...++.|+-..|- +-..||..| |-+.+.|++++..-
T Consensus 140 ~~~~r~v~~L~~~~g~--s~~EIA~~L-gis~~tV~~~l~RA 178 (203)
T PRK09647 140 PPEFRAAVVLCDIEGL--SYEEIAATL-GVKLGTVRSRIHRG 178 (203)
T ss_pred CHHHHHHHHHHHHcCC--CHHHHHHHH-CCCHHHHHHHHHHH
Confidence 4566777778778887 899999998 99999999998743
No 44
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=37.66 E-value=65 Score=26.96 Aligned_cols=38 Identities=18% Similarity=0.064 Sum_probs=33.0
Q ss_pred hhhHHHHHHHHHHhCCcCcHHHHhccCCCCChHHHHHHHHH
Q 026135 2 KKMNSLSNSIASLVTSKSSWSLIAGRLPGRTDNEIKNYWNT 42 (243)
Q Consensus 2 ~EEDelLi~l~s~~Gn~~kWs~IA~~LpGRTdn~IKNrWn~ 42 (243)
.+++..|+.+.-..|- .+..||..| |-+.+.|+++...
T Consensus 108 ~~~~r~i~~l~~~~g~--~~~EIA~~l-gis~~tV~~~l~R 145 (181)
T PRK09637 108 PEKYAEALRLTELEGL--SQKEIAEKL-GLSLSGAKSRVQR 145 (181)
T ss_pred CHHHHHHHHHHHhcCC--CHHHHHHHh-CCCHHHHHHHHHH
Confidence 4677888888888898 999999998 9999999999864
No 45
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=37.10 E-value=97 Score=26.09 Aligned_cols=38 Identities=13% Similarity=-0.019 Sum_probs=32.8
Q ss_pred hhhHHHHHHHHHHhCCcCcHHHHhccCCCCChHHHHHHHHH
Q 026135 2 KKMNSLSNSIASLVTSKSSWSLIAGRLPGRTDNEIKNYWNT 42 (243)
Q Consensus 2 ~EEDelLi~l~s~~Gn~~kWs~IA~~LpGRTdn~IKNrWn~ 42 (243)
++++..|+.|+-..|- .+..||..| |-+.+.||.+-..
T Consensus 118 p~~~r~i~~L~~~~g~--s~~EIA~~L-gis~~tVk~~l~R 155 (187)
T PRK12516 118 PDDQREAIILVGASGF--AYEEAAEIC-GCAVGTIKSRVNR 155 (187)
T ss_pred CHHHHHHHHHHHHcCC--CHHHHHHHH-CCCHHHHHHHHHH
Confidence 5677888888888898 999999998 9999999998764
No 46
>smart00595 MADF subfamily of SANT domain.
Probab=37.01 E-value=40 Score=24.81 Aligned_cols=23 Identities=35% Similarity=0.651 Sum_probs=20.2
Q ss_pred cHHHHhccCCCCChHHHHHHHHHH
Q 026135 20 SWSLIAGRLPGRTDNEIKNYWNTH 43 (243)
Q Consensus 20 kWs~IA~~LpGRTdn~IKNrWn~~ 43 (243)
-|..||..| |-+...|+.+|+.+
T Consensus 29 aW~~Ia~~l-~~~~~~~~~kw~~L 51 (89)
T smart00595 29 AWEEIAEEL-GLSVEECKKRWKNL 51 (89)
T ss_pred HHHHHHHHH-CcCHHHHHHHHHHH
Confidence 599999999 44999999999865
No 47
>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=36.08 E-value=39 Score=23.99 Aligned_cols=25 Identities=24% Similarity=0.433 Sum_probs=20.4
Q ss_pred cHHHHhccCCC-CChHHHHHHHHHHH
Q 026135 20 SWSLIAGRLPG-RTDNEIKNYWNTHI 44 (243)
Q Consensus 20 kWs~IA~~LpG-RTdn~IKNrWn~~l 44 (243)
-|..||..|.. -+...|+.+|..+-
T Consensus 28 aw~~Ia~~l~~~~~~~~~~~~w~~Lr 53 (85)
T PF10545_consen 28 AWQEIARELGKEFSVDDCKKRWKNLR 53 (85)
T ss_pred HHHHHHHHHccchhHHHHHHHHHHHH
Confidence 59999999953 57788999998753
No 48
>KOG3173 consensus Predicted Zn-finger protein [General function prediction only]
Probab=35.02 E-value=24 Score=30.54 Aligned_cols=19 Identities=37% Similarity=1.017 Sum_probs=16.2
Q ss_pred eeeeee--ecCCcCCCCccccC
Q 026135 181 SLCLAC--SLGLQNSKGCSCNN 200 (243)
Q Consensus 181 ~vC~~c--sLG~~~~~~CsC~~ 200 (243)
..||.| .+|+++ -.|.|++
T Consensus 106 ~rC~~C~kk~gltg-f~CrCG~ 126 (167)
T KOG3173|consen 106 KRCFKCRKKVGLTG-FKCRCGN 126 (167)
T ss_pred hhhhhhhhhhcccc-cccccCC
Confidence 459999 589999 9999984
No 49
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=33.02 E-value=58 Score=33.84 Aligned_cols=49 Identities=10% Similarity=0.142 Sum_probs=38.1
Q ss_pred ChhhHHHHHHHHH-------Hh-------C----------CcCcHHHHhccCCCCChHHHHHHHHHHHHhhhh
Q 026135 1 MKKMNSLSNSIAS-------LV-------T----------SKSSWSLIAGRLPGRTDNEIKNYWNTHIRRKLL 49 (243)
Q Consensus 1 ~~EEDelLi~l~s-------~~-------G----------n~~kWs~IA~~LpGRTdn~IKNrWn~~lrrkl~ 49 (243)
+.||+++|+++++ ++ | ....|..|+..+.-|+--+|+-.|+.++.+...
T Consensus 440 s~eEe~~Llk~V~~~~~~~~q~q~~n~~~~~q~sp~s~~~d~I~Wt~vse~~~TR~~~qCr~Kw~kl~~~~s~ 512 (607)
T KOG0051|consen 440 SIEEEEKLLKTVNEMIREALQPQASNTDTGLQESPESTLKDDINWTLVSEMLGTRSRIQCRYKWYKLTTSPSF 512 (607)
T ss_pred hHHHHHHHHHHHHHHHHHhhcccccccchhhhcCccccccCCcchhhhhHhhcCCCcchHHHHHHHHHhhHHh
Confidence 4689999999985 33 1 011699999999999999999999988766543
No 50
>PF08706 D5_N: D5 N terminal like; InterPro: IPR014818 This domain is found in D5 proteins of DNA viruses and bacteriophage P4 DNA primase.
Probab=32.75 E-value=17 Score=28.53 Aligned_cols=17 Identities=41% Similarity=0.792 Sum_probs=15.3
Q ss_pred cccccccccccccccCC
Q 026135 226 DFLGLKSGVLDYRSLEM 242 (243)
Q Consensus 226 dFlglk~~~ld~r~lem 242 (243)
+.|++++||||+++-++
T Consensus 99 ~~i~~~NGvldl~tg~l 115 (150)
T PF08706_consen 99 NLINFKNGVLDLRTGEL 115 (150)
T ss_pred CEEecCCEEEECCCCee
Confidence 69999999999998775
No 51
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=32.42 E-value=65 Score=32.15 Aligned_cols=43 Identities=23% Similarity=0.241 Sum_probs=36.4
Q ss_pred hhhHHHHHHHHHHhCCcCcHHHHhccCCCCChHHHHHHHHHHHHh
Q 026135 2 KKMNSLSNSIASLVTSKSSWSLIAGRLPGRTDNEIKNYWNTHIRR 46 (243)
Q Consensus 2 ~EEDelLi~l~s~~Gn~~kWs~IA~~LpGRTdn~IKNrWn~~lrr 46 (243)
.+|-++..+..++||- -+++|+..||.|.-.+||-.|...-++
T Consensus 370 ~~e~ekFYKALs~wGt--dF~LIs~lfP~R~RkqIKaKfi~Eek~ 412 (507)
T COG5118 370 KKEIEKFYKALSIWGT--DFSLISSLFPNRERKQIKAKFIKEEKV 412 (507)
T ss_pred HHHHHHHHHHHHHhcc--hHHHHHHhcCchhHHHHHHHHHHHhhh
Confidence 3566778888899998 999999999999999999988765443
No 52
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=31.87 E-value=1.1e+02 Score=24.61 Aligned_cols=39 Identities=18% Similarity=0.025 Sum_probs=33.3
Q ss_pred hhhHHHHHHHHHHhCCcCcHHHHhccCCCCChHHHHHHHHHH
Q 026135 2 KKMNSLSNSIASLVTSKSSWSLIAGRLPGRTDNEIKNYWNTH 43 (243)
Q Consensus 2 ~EEDelLi~l~s~~Gn~~kWs~IA~~LpGRTdn~IKNrWn~~ 43 (243)
++++..|+.|+-..|- .-..||..| |-+.+.|++|...-
T Consensus 107 ~~~~r~v~~l~~~~~~--s~~eIA~~l-gis~~tv~~~l~ra 145 (159)
T PRK12527 107 PPACRDSFLLRKLEGL--SHQQIAEHL-GISRSLVEKHIVNA 145 (159)
T ss_pred CHHHHHHHHHHHHcCC--CHHHHHHHh-CCCHHHHHHHHHHH
Confidence 5778888888877887 899999998 99999999998743
No 53
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=31.57 E-value=94 Score=27.93 Aligned_cols=49 Identities=20% Similarity=0.335 Sum_probs=30.8
Q ss_pred hhhHHHHHHHHHHhCCc-CcHHHHhc-----cCCCCChHHHHHHHHHHHHhhhhh
Q 026135 2 KKMNSLSNSIASLVTSK-SSWSLIAG-----RLPGRTDNEIKNYWNTHIRRKLLN 50 (243)
Q Consensus 2 ~EEDelLi~l~s~~Gn~-~kWs~IA~-----~LpGRTdn~IKNrWn~~lrrkl~~ 50 (243)
.+||++|...-....+. ..+..|=. +-++||...+.++|....+-.++.
T Consensus 78 ~~EE~lL~~v~s~~~p~le~Fq~LL~~n~~vFh~sRTak~L~~HW~lmkqy~LL~ 132 (199)
T PF13325_consen 78 KEEEQLLGTVASSSQPSLETFQELLDKNRSVFHPSRTAKSLQDHWRLMKQYHLLP 132 (199)
T ss_pred HHHHHHHHhhhhccCCcHHHHHHHHHhChhhhccccCHHHHHHHHHHHHHhchhh
Confidence 57888887765444330 12433322 238999999999999655555554
No 54
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=29.92 E-value=1.1e+02 Score=25.46 Aligned_cols=39 Identities=8% Similarity=-0.134 Sum_probs=32.8
Q ss_pred hhhHHHHHHHHHHhCCcCcHHHHhccCCCCChHHHHHHHHHH
Q 026135 2 KKMNSLSNSIASLVTSKSSWSLIAGRLPGRTDNEIKNYWNTH 43 (243)
Q Consensus 2 ~EEDelLi~l~s~~Gn~~kWs~IA~~LpGRTdn~IKNrWn~~ 43 (243)
++++..++.|+-..|- .-..||..| |-+.+.||++...-
T Consensus 133 p~~~r~v~~l~~~~g~--s~~EIA~~l-gis~~tV~~~l~Ra 171 (191)
T PRK12520 133 PPRTGRVFMMREWLEL--ETEEICQEL-QITATNAWVLLYRA 171 (191)
T ss_pred CHHHHHHHHHHHHcCC--CHHHHHHHH-CCCHHHHHHHHHHH
Confidence 4667778888878887 899999998 99999999998743
No 55
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=29.42 E-value=1.7e+02 Score=26.48 Aligned_cols=44 Identities=11% Similarity=0.026 Sum_probs=35.0
Q ss_pred hhhHHHHHHHHHHhCCcCcHHHHhccCCCCChHHHHHHHHHHHHhhhh
Q 026135 2 KKMNSLSNSIASLVTSKSSWSLIAGRLPGRTDNEIKNYWNTHIRRKLL 49 (243)
Q Consensus 2 ~EEDelLi~l~s~~Gn~~kWs~IA~~LpGRTdn~IKNrWn~~lrrkl~ 49 (243)
++++..++.|+...|- ....||..| |.+.+.||++...- +++++
T Consensus 144 p~~~R~v~~L~~~~g~--s~~EIA~~l-gis~~tV~~~l~Ra-r~~Lr 187 (324)
T TIGR02960 144 PPRQRAVLLLRDVLGW--RAAETAELL-GTSTASVNSALQRA-RATLD 187 (324)
T ss_pred CHHHhhHhhhHHHhCC--CHHHHHHHH-CCCHHHHHHHHHHH-HHHHH
Confidence 4567778888888888 999999998 99999999998653 34444
No 56
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=29.05 E-value=71 Score=35.11 Aligned_cols=46 Identities=15% Similarity=0.217 Sum_probs=38.2
Q ss_pred hhhHHHHHHHHHHhC-CcCcHHHHhc------------cCCCCChHHHHHHHHHHHHhhhh
Q 026135 2 KKMNSLSNSIASLVT-SKSSWSLIAG------------RLPGRTDNEIKNYWNTHIRRKLL 49 (243)
Q Consensus 2 ~EEDelLi~l~s~~G-n~~kWs~IA~------------~LpGRTdn~IKNrWn~~lrrkl~ 49 (243)
+|||..|+-....+| . +|..|.. +|..||...|+.|.+++|+--.+
T Consensus 931 ~~~d~~~~~~~~~~g~~--~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~~l~~~~~~ 989 (1033)
T PLN03142 931 EECDRFMLCMVHKLGYG--NWDELKAAFRTSPLFRFDWFVKSRTPQELARRCDTLIRLIEK 989 (1033)
T ss_pred HHHHHHHHHHHHHhccc--hHHHHHHHHHhCCceeeehhhccCCHHHHHHHHHHHHHHHHH
Confidence 689999999999999 5 8999844 23799999999999988766433
No 57
>PF01388 ARID: ARID/BRIGHT DNA binding domain; InterPro: IPR001606 Members of the recently discovered ARID (AT-rich interaction domain; also known as BRIGHT domain)) family of DNA-binding proteins are found in fungi and invertebrate and vertebrate metazoans. ARID-encoding genes are involved in a variety of biological processes including embryonic development, cell lineage gene regulation and cell cycle control. Although the specific roles of this domain and of ARID-containing proteins in transcriptional regulation are yet to be elucidated, they include both positive and negative transcriptional regulation and a likely involvement in the modification of chromatin structure []. The basic structure of the ARID domain domain appears to be a series of six alpha-helices separated by beta-strands, loops, or turns, but the structured region may extend to an additional helix at either or both ends of the basic six. Based on primary sequence homology, they can be partitioned into three structural classes: Minimal ARID proteins that consist of a core domain formed by six alpha helices; ARID proteins that supplement the core domain with an N-terminal alpha-helix; and Extended-ARID proteins, which contain the core domain and additional alpha-helices at their N- and C-termini. The human SWI-SNF complex protein p270 is an ARID family member with non-sequence-specific DNA binding activity. The ARID consensus and other structural features are common to both p270 and yeast SWI1, suggesting that p270 is a human counterpart of SWI1 []. The approximately 100-residue ARID sequence is present in a series of proteins strongly implicated in the regulation of cell growth, development, and tissue-specific gene expression. Although about a dozen ARID proteins can be identified from database searches, to date, only Bright (a regulator of B-cell-specific gene expression), dead ringer (a Drosophila melanogaster gene product required for normal development), and MRF-2 (which represses expression from the Cytomegalovirus enhancer) have been analyzed directly in regard to their DNA binding properties. Each binds preferentially to AT-rich sites. In contrast, p270 shows no sequence preference in its DNA binding activity, thereby demonstrating that AT-rich binding is not an intrinsic property of ARID domains and that ARID family proteins may be involved in a wider range of DNA interactions [].; GO: 0003677 DNA binding, 0005622 intracellular; PDB: 1C20_A 1KQQ_A 2JRZ_A 2LM1_A 2YQE_A 2JXJ_A 2EH9_A 2CXY_A 2LI6_A 1KN5_A ....
Probab=26.40 E-value=1.4e+02 Score=22.17 Aligned_cols=27 Identities=15% Similarity=0.331 Sum_probs=19.5
Q ss_pred cHHHHhccCCC---CC--hHHHHHHHHHHHHh
Q 026135 20 SWSLIAGRLPG---RT--DNEIKNYWNTHIRR 46 (243)
Q Consensus 20 kWs~IA~~LpG---RT--dn~IKNrWn~~lrr 46 (243)
+|..||..|.- .+ ...+|..|..+|..
T Consensus 59 ~W~~va~~lg~~~~~~~~~~~L~~~Y~~~L~~ 90 (92)
T PF01388_consen 59 KWREVARKLGFPPSSTSAAQQLRQHYEKYLLP 90 (92)
T ss_dssp THHHHHHHTTS-TTSCHHHHHHHHHHHHHTHH
T ss_pred hHHHHHHHhCCCCCCCcHHHHHHHHHHHHhHh
Confidence 69999999832 12 36789988877653
No 58
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=26.26 E-value=88 Score=29.17 Aligned_cols=30 Identities=13% Similarity=0.193 Sum_probs=24.1
Q ss_pred cHHHHhccC----CCCChHHHHHHHHHHHHhhhh
Q 026135 20 SWSLIAGRL----PGRTDNEIKNYWNTHIRRKLL 49 (243)
Q Consensus 20 kWs~IA~~L----pGRTdn~IKNrWn~~lrrkl~ 49 (243)
-|..||+.| -=|++.+||++|..+.++.-+
T Consensus 85 ~We~va~k~~~~g~~rs~~qck~K~~nl~k~Yk~ 118 (345)
T KOG4282|consen 85 LWEEVARKMAELGYPRSPKQCKAKIENLKKKYKK 118 (345)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHH
Confidence 499999966 468999999999987665543
No 59
>cd08319 Death_RAIDD Death domain of RIP-associated ICH-1 homologous protein with a death domain. Death domain (DD) of RAIDD (RIP-associated ICH-1 homologous protein with a death domain), also known as CRADD (Caspase and RIP adaptor). RAIDD is an adaptor protein that together with the p53-inducible protein PIDD and caspase-2, forms the PIDDosome complex, which is required for caspase-2 activation and plays a role in mediating stress-induced apoptosis. RAIDD contains an N-terminal Caspase Activation and Recruitment Domain (CARD), which interacts with the caspase-2 CARD, and a C-terminal DD, which interacts with the DD of PIDD. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD, DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other pr
Probab=25.90 E-value=93 Score=23.95 Aligned_cols=32 Identities=19% Similarity=0.328 Sum_probs=26.1
Q ss_pred HHHHHHHHHHhCCcCcHHHHhccCCCCChHHHHHH
Q 026135 5 NSLSNSIASLVTSKSSWSLIAGRLPGRTDNEIKNY 39 (243)
Q Consensus 5 DelLi~l~s~~Gn~~kWs~IA~~LpGRTdn~IKNr 39 (243)
|+-|..+...+|. .|..+|.+| |=++..|...
T Consensus 2 ~~~L~~la~~LG~--~W~~Lar~L-gls~~~I~~i 33 (83)
T cd08319 2 DRELNQLAQRLGP--EWEQVLLDL-GLSQTDIYRC 33 (83)
T ss_pred HHHHHHHHHHHhh--hHHHHHHHc-CCCHHHHHHH
Confidence 4567788899999 999999998 7777776553
No 60
>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=25.83 E-value=1.3e+02 Score=29.24 Aligned_cols=39 Identities=21% Similarity=0.347 Sum_probs=29.8
Q ss_pred hhHHHHHHHHHHhCCcCcH---HHHhccCCCCChHHHHHHHHHH
Q 026135 3 KMNSLSNSIASLVTSKSSW---SLIAGRLPGRTDNEIKNYWNTH 43 (243)
Q Consensus 3 EEDelLi~l~s~~Gn~~kW---s~IA~~LpGRTdn~IKNrWn~~ 43 (243)
|.-++|.-|...-|. .+ ..|++.|+||+..+|++.-+.+
T Consensus 28 Ekr~Llr~Lqar~g~--~epd~ael~~~l~~Rs~aEI~~fl~~L 69 (344)
T PF11035_consen 28 EKRQLLRLLQARRGQ--PEPDAAELAKELPGRSEAEIRDFLQQL 69 (344)
T ss_pred HHHHHHHHHHHhcCC--CCcCHHHHHhhccCcCHHHHHHHHHHH
Confidence 455666667776675 54 6899999999999999976543
No 61
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=24.28 E-value=1.5e+02 Score=24.78 Aligned_cols=38 Identities=8% Similarity=-0.059 Sum_probs=32.0
Q ss_pred hhhHHHHHHHHHHhCCcCcHHHHhccCCCCChHHHHHHHHH
Q 026135 2 KKMNSLSNSIASLVTSKSSWSLIAGRLPGRTDNEIKNYWNT 42 (243)
Q Consensus 2 ~EEDelLi~l~s~~Gn~~kWs~IA~~LpGRTdn~IKNrWn~ 42 (243)
+++...|+.|+-..|- .+..||..| |=+.+.|+++-..
T Consensus 138 ~~~~r~i~~L~~~~g~--s~~eIA~~l-gis~~tV~~~l~R 175 (196)
T PRK12524 138 PERQRQAVVLRHIEGL--SNPEIAEVM-EIGVEAVESLTAR 175 (196)
T ss_pred CHHHHHHHHHHHHcCC--CHHHHHHHH-CcCHHHHHHHHHH
Confidence 5667778888878888 999999998 9999999998764
No 62
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=21.73 E-value=2e+02 Score=23.58 Aligned_cols=38 Identities=18% Similarity=0.044 Sum_probs=31.9
Q ss_pred hhhHHHHHHHHHHhCCcCcHHHHhccCCCCChHHHHHHHHH
Q 026135 2 KKMNSLSNSIASLVTSKSSWSLIAGRLPGRTDNEIKNYWNT 42 (243)
Q Consensus 2 ~EEDelLi~l~s~~Gn~~kWs~IA~~LpGRTdn~IKNrWn~ 42 (243)
.+++..++.|+-..|- .-..||..| |-+...|+++...
T Consensus 102 ~~~~r~v~~l~~~~g~--s~~eIA~~l-gis~~tV~~~l~R 139 (170)
T TIGR02959 102 PDEYREAIRLTELEGL--SQQEIAEKL-GLSLSGAKSRVQR 139 (170)
T ss_pred CHHHHHHHHHHHHcCC--CHHHHHHHH-CCCHHHHHHHHHH
Confidence 4567778888878887 899999998 9999999998864
No 63
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=21.67 E-value=2.1e+02 Score=23.90 Aligned_cols=46 Identities=15% Similarity=0.028 Sum_probs=35.1
Q ss_pred hhhHHHHHHHHHHhCCcCcHHHHhccCCCCChHHHHHHHH---HHHHhhhhh
Q 026135 2 KKMNSLSNSIASLVTSKSSWSLIAGRLPGRTDNEIKNYWN---THIRRKLLN 50 (243)
Q Consensus 2 ~EEDelLi~l~s~~Gn~~kWs~IA~~LpGRTdn~IKNrWn---~~lrrkl~~ 50 (243)
+++...++.|+-..|- ....||..| |-+.+.|+.+-+ ..|++.+..
T Consensus 113 p~~~R~v~~L~~~~g~--s~~EIA~~L-gis~~tV~~~l~RAr~~Lr~~l~~ 161 (182)
T PRK12540 113 PQDQREALILVGASGF--SYEDAAAIC-GCAVGTIKSRVNRARSKLSALLYV 161 (182)
T ss_pred CHHHHHHhhHHHHcCC--CHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHh
Confidence 4667778888778888 899999998 899999999866 334444443
No 64
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=20.76 E-value=1e+02 Score=26.87 Aligned_cols=38 Identities=13% Similarity=0.029 Sum_probs=30.8
Q ss_pred hhhHHHHHHHHHHhCCcCcHHHHhccCCCCChHHHHHHHHH
Q 026135 2 KKMNSLSNSIASLVTSKSSWSLIAGRLPGRTDNEIKNYWNT 42 (243)
Q Consensus 2 ~EEDelLi~l~s~~Gn~~kWs~IA~~LpGRTdn~IKNrWn~ 42 (243)
++++..|+.++-..|- ....||..| |.+...||+++..
T Consensus 151 ~~~~r~i~~l~~~~g~--s~~EIAe~l-gis~~tVk~~l~R 188 (231)
T PRK11922 151 PDAFRAVFVLRVVEEL--SVEETAQAL-GLPEETVKTRLHR 188 (231)
T ss_pred CHHHhhhheeehhcCC--CHHHHHHHH-CcCHHHHHHHHHH
Confidence 3556667777666777 899999998 9999999999874
No 65
>cd08317 Death_ank Death domain associated with Ankyrins. Death Domain (DD) associated with Ankyrins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. Ankyrins function as adaptor proteins and they interact, through ANK repeats, with structurally diverse membrane proteins, including ion channels/pumps, calcium release channels, and cell adhesion molecules. They play critical roles in the proper expression and membrane localization of these proteins. In mammals, this family includes ankyrin-R for restricted (or ANK1), ankyrin-B for broadly expressed (or ANK2) and ankyrin-G for general or giant (or ANK3). They are expressed in different combinations in many tissues and play non-overlapping functions. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-associati
Probab=20.68 E-value=1.1e+02 Score=22.98 Aligned_cols=32 Identities=25% Similarity=0.460 Sum_probs=25.4
Q ss_pred HHHHHHHHHHhCCcCcHHHHhccCCCCChHHHHHH
Q 026135 5 NSLSNSIASLVTSKSSWSLIAGRLPGRTDNEIKNY 39 (243)
Q Consensus 5 DelLi~l~s~~Gn~~kWs~IA~~LpGRTdn~IKNr 39 (243)
|..|..+...+|. .|..+|++| |=++..|...
T Consensus 4 ~~~l~~ia~~lG~--dW~~LAr~L-g~~~~dI~~i 35 (84)
T cd08317 4 DIRLADISNLLGS--DWPQLAREL-GVSETDIDLI 35 (84)
T ss_pred cchHHHHHHHHhh--HHHHHHHHc-CCCHHHHHHH
Confidence 4566777889998 999999999 6777766653
No 66
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.
Probab=20.57 E-value=1.9e+02 Score=25.93 Aligned_cols=37 Identities=5% Similarity=-0.063 Sum_probs=31.0
Q ss_pred hhhHHHHHHHHHHhCCcCcHHHHhccCCCCChHHHHHHHH
Q 026135 2 KKMNSLSNSIASLVTSKSSWSLIAGRLPGRTDNEIKNYWN 41 (243)
Q Consensus 2 ~EEDelLi~l~s~~Gn~~kWs~IA~~LpGRTdn~IKNrWn 41 (243)
++++..++.|+-.-|- .+..||..| |-+.+.||.+-.
T Consensus 163 p~~~R~v~~L~~~eg~--S~~EIA~~L-gis~~TVk~rl~ 199 (244)
T TIGR03001 163 SERERHLLRLHFVDGL--SMDRIGAMY-QVHRSTVSRWVA 199 (244)
T ss_pred CHHHHHHHHHHHHcCC--CHHHHHHHH-CcCHHHHHHHHH
Confidence 4566777888877887 899999998 999999999876
No 67
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=20.50 E-value=1.9e+02 Score=26.13 Aligned_cols=45 Identities=13% Similarity=0.224 Sum_probs=36.2
Q ss_pred hhhHHHHHHHHHHhCCcCcHHHHhccCCCCChHHHHHHHHHHHHhhhhh
Q 026135 2 KKMNSLSNSIASLVTSKSSWSLIAGRLPGRTDNEIKNYWNTHIRRKLLN 50 (243)
Q Consensus 2 ~EEDelLi~l~s~~Gn~~kWs~IA~~LpGRTdn~IKNrWn~~lrrkl~~ 50 (243)
.+++..++.|+...|- .-..||..| |.+...||.+.+. .|++++.
T Consensus 117 ~~~~R~v~~L~~~~g~--s~~EIA~~l-g~s~~tVk~~l~R-Ar~~Lr~ 161 (293)
T PRK09636 117 SPLERAAFLLHDVFGV--PFDEIASTL-GRSPAACRQLASR-ARKHVRA 161 (293)
T ss_pred CHHHHHHHHHHHHhCC--CHHHHHHHH-CCCHHHHHHHHHH-HHHHHHh
Confidence 4567778888888898 999999998 9999999999865 3555554
Done!