Query 019948
Match_columns 333
No_of_seqs 221 out of 519
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 05:48:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019948.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019948hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR01557 myb_SHAQKYF myb-like 99.8 4.9E-19 1.1E-23 133.0 5.8 53 93-145 1-57 (57)
2 PF00249 Myb_DNA-binding: Myb- 99.4 5.1E-13 1.1E-17 95.0 5.2 45 96-141 2-47 (48)
3 cd00167 SANT 'SWI3, ADA2, N-Co 99.0 4.4E-10 9.4E-15 75.3 5.2 44 97-141 1-44 (45)
4 smart00717 SANT SANT SWI3, AD 99.0 3.8E-10 8.3E-15 76.3 5.0 46 96-142 2-47 (49)
5 KOG0457 Histone acetyltransfer 98.6 5.3E-08 1.1E-12 98.0 5.1 50 96-146 73-122 (438)
6 PF13921 Myb_DNA-bind_6: Myb-l 98.6 7.4E-08 1.6E-12 70.6 4.4 42 98-141 1-42 (60)
7 KOG0724 Zuotin and related mol 98.4 1.5E-07 3.3E-12 89.7 2.7 79 89-167 158-241 (335)
8 PLN03212 Transcription repress 98.2 3.6E-06 7.7E-11 80.0 6.7 49 94-142 24-72 (249)
9 PLN03091 hypothetical protein; 98.0 7E-06 1.5E-10 83.4 6.0 52 91-142 10-61 (459)
10 KOG4329 DNA-binding protein [G 98.0 3.7E-05 8E-10 77.0 9.9 57 90-150 272-328 (445)
11 COG5259 RSC8 RSC chromatin rem 97.9 8.4E-06 1.8E-10 83.3 4.8 41 96-138 280-320 (531)
12 COG5114 Histone acetyltransfer 97.9 1.1E-05 2.4E-10 79.7 4.3 49 96-145 64-112 (432)
13 PLN03212 Transcription repress 97.6 0.00011 2.4E-09 70.0 6.1 46 95-142 78-123 (249)
14 PLN03091 hypothetical protein; 97.5 0.0002 4.3E-09 73.1 6.7 48 95-144 67-114 (459)
15 KOG1279 Chromatin remodeling f 97.5 0.00012 2.6E-09 75.7 5.1 45 93-139 251-295 (506)
16 PLN03162 golden-2 like transcr 97.3 0.0027 5.8E-08 64.3 11.3 58 89-146 231-291 (526)
17 KOG0048 Transcription factor, 97.0 0.00082 1.8E-08 62.4 4.3 47 95-142 9-56 (238)
18 KOG0049 Transcription factor, 96.4 0.0045 9.7E-08 66.3 5.7 46 96-142 361-406 (939)
19 KOG4167 Predicted DNA-binding 96.3 0.003 6.4E-08 68.1 3.6 49 95-148 619-667 (907)
20 KOG0048 Transcription factor, 95.9 0.019 4.1E-07 53.4 6.1 43 94-138 61-103 (238)
21 KOG0049 Transcription factor, 95.3 0.02 4.2E-07 61.6 4.5 46 93-139 410-455 (939)
22 COG5118 BDP1 Transcription ini 94.9 0.039 8.5E-07 56.2 5.0 59 76-136 343-404 (507)
23 PF00098 zf-CCHC: Zinc knuckle 94.7 0.024 5.2E-07 34.1 1.9 18 3-20 1-18 (18)
24 KOG4468 Polycomb-group transcr 94.6 0.046 1E-06 58.3 5.0 50 95-145 88-146 (782)
25 PLN03142 Probable chromatin-re 94.5 0.05 1.1E-06 60.9 5.3 49 97-146 826-874 (1033)
26 KOG3554 Histone deacetylase co 94.5 0.034 7.4E-07 57.9 3.6 52 92-147 282-333 (693)
27 KOG0724 Zuotin and related mol 94.2 0.011 2.4E-07 56.7 -0.4 49 97-147 55-103 (335)
28 KOG3841 TEF-1 and related tran 93.9 0.25 5.4E-06 50.5 8.4 48 93-141 74-141 (455)
29 PF15288 zf-CCHC_6: Zinc knuck 93.7 0.033 7.2E-07 40.1 1.3 20 3-22 2-23 (40)
30 PF14392 zf-CCHC_4: Zinc knuck 92.9 0.038 8.3E-07 40.1 0.6 19 1-19 30-48 (49)
31 PF13837 Myb_DNA-bind_4: Myb/S 92.7 0.24 5.2E-06 38.2 4.8 51 96-146 2-68 (90)
32 KOG0050 mRNA splicing protein 91.5 0.17 3.7E-06 53.3 3.5 48 93-141 5-52 (617)
33 smart00426 TEA TEA domain. 90.9 0.32 7E-06 38.7 3.8 44 95-139 3-66 (68)
34 PF09111 SLIDE: SLIDE; InterP 90.6 0.56 1.2E-05 40.3 5.3 51 93-144 47-111 (118)
35 KOG1194 Predicted DNA-binding 85.7 1.3 2.9E-05 46.3 5.2 46 96-146 188-233 (534)
36 PF01285 TEA: TEA/ATTS domain 83.9 1.3 2.7E-05 45.6 4.2 48 93-141 47-112 (431)
37 smart00343 ZnF_C2HC zinc finge 82.0 0.74 1.6E-05 29.1 1.1 18 4-21 1-18 (26)
38 KOG0051 RNA polymerase I termi 81.6 1.9 4.2E-05 46.2 4.6 50 94-144 435-509 (607)
39 COG5147 REB1 Myb superfamily p 81.3 0.98 2.1E-05 47.5 2.3 55 90-145 15-69 (512)
40 PLN03142 Probable chromatin-re 75.7 6 0.00013 44.9 6.4 48 94-141 925-983 (1033)
41 PF14952 zf-tcix: Putative tre 75.0 1.7 3.8E-05 32.1 1.4 19 3-21 12-31 (44)
42 PF13248 zf-ribbon_3: zinc-rib 72.6 1.9 4.1E-05 27.7 1.0 25 1-25 1-26 (26)
43 KOG0385 Chromatin remodeling c 71.4 5.6 0.00012 44.4 4.7 50 96-147 796-845 (971)
44 PF13873 Myb_DNA-bind_5: Myb/S 71.0 11 0.00024 28.7 5.1 46 96-141 3-68 (78)
45 COG5147 REB1 Myb superfamily p 69.8 7.3 0.00016 41.2 5.0 44 94-139 71-114 (512)
46 COG5082 AIR1 Arginine methyltr 69.4 2.6 5.6E-05 39.4 1.5 18 2-19 97-114 (190)
47 KOG2009 Transcription initiati 67.9 5.3 0.00011 42.9 3.6 46 89-136 403-448 (584)
48 KOG4282 Transcription factor G 66.1 14 0.0003 36.0 5.8 55 95-149 54-120 (345)
49 KOG0051 RNA polymerase I termi 65.3 7.7 0.00017 41.9 4.2 46 94-142 383-428 (607)
50 PF12776 Myb_DNA-bind_3: Myb/S 62.8 24 0.00053 27.4 5.7 48 97-145 1-64 (96)
51 PF06461 DUF1086: Domain of Un 60.3 39 0.00084 30.6 7.0 49 97-146 40-90 (145)
52 PF08914 Myb_DNA-bind_2: Rap1 58.9 20 0.00042 28.0 4.4 48 95-142 2-57 (65)
53 PF04504 DUF573: Protein of un 56.6 8.2 0.00018 31.9 2.1 33 96-129 5-44 (98)
54 PF08074 CHDCT2: CHDCT2 (NUC03 53.8 7.4 0.00016 36.0 1.5 29 94-122 2-30 (173)
55 KOG0384 Chromodomain-helicase 53.3 8 0.00017 44.9 2.0 51 94-147 1132-1195(1373)
56 PF11035 SnAPC_2_like: Small n 51.4 41 0.0009 34.1 6.3 52 92-144 18-72 (344)
57 PF02509 Rota_NS35: Rotavirus 48.9 9.1 0.0002 37.9 1.4 53 96-156 195-256 (316)
58 KOG1194 Predicted DNA-binding 43.7 35 0.00075 36.2 4.6 49 94-144 368-416 (534)
59 COG5082 AIR1 Arginine methyltr 38.3 16 0.00035 34.2 1.2 18 2-19 60-77 (190)
60 PF10571 UPF0547: Uncharacteri 37.9 16 0.00035 23.9 0.8 9 2-10 14-22 (26)
61 CHL00112 rpl28 ribosomal prote 34.1 20 0.00044 27.9 1.0 14 1-14 1-17 (63)
62 smart00501 BRIGHT BRIGHT, ARID 33.8 99 0.0021 24.6 4.9 42 103-145 35-87 (93)
63 KOG0050 mRNA splicing protein 32.3 42 0.0009 36.2 3.2 44 95-141 59-102 (617)
64 PF01388 ARID: ARID/BRIGHT DNA 31.7 85 0.0018 24.6 4.2 42 103-144 39-90 (92)
65 PHA00442 host recBCD nuclease 31.4 46 0.00099 26.0 2.5 23 101-123 26-48 (59)
66 PTZ00368 universal minicircle 31.2 31 0.00068 29.6 1.8 18 4-21 54-71 (148)
67 PTZ00368 universal minicircle 31.0 32 0.0007 29.5 1.8 19 3-21 78-96 (148)
68 KOG0119 Splicing factor 1/bran 28.9 30 0.00065 36.9 1.5 18 4-21 287-304 (554)
69 PF08792 A2L_zn_ribbon: A2L zi 28.4 27 0.00057 24.0 0.7 10 3-12 4-13 (33)
70 PF13325 MCRS_N: N-terminal re 27.7 71 0.0015 30.2 3.6 46 94-139 72-123 (199)
71 PF00191 Annexin: Annexin; In 27.6 66 0.0014 23.4 2.7 40 104-145 4-43 (66)
72 PF13917 zf-CCHC_3: Zinc knuck 27.2 37 0.0008 24.7 1.3 19 2-20 4-22 (42)
73 PRK00359 rpmB 50S ribosomal pr 26.7 32 0.0007 27.6 1.0 10 1-10 1-10 (76)
74 PF05634 APO_RNA-bind: APO RNA 26.7 36 0.00079 32.3 1.5 19 3-21 99-122 (204)
75 PF13696 zf-CCHC_2: Zinc knuck 26.5 32 0.0007 23.8 0.8 19 3-21 9-27 (32)
76 KOG0487 Transcription factor A 24.7 54 0.0012 32.9 2.3 57 89-150 233-295 (308)
77 PF13240 zinc_ribbon_2: zinc-r 24.6 36 0.00079 21.5 0.8 19 4-22 1-20 (23)
78 KOG4400 E3 ubiquitin ligase in 24.3 43 0.00092 31.5 1.5 18 4-21 145-162 (261)
79 PF09297 zf-NADH-PPase: NADH p 23.4 49 0.0011 21.9 1.2 25 2-26 3-32 (32)
80 KOG0119 Splicing factor 1/bran 21.7 48 0.001 35.5 1.4 24 2-26 261-284 (554)
No 1
>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=99.77 E-value=4.9e-19 Score=133.01 Aligned_cols=53 Identities=51% Similarity=0.727 Sum_probs=48.8
Q ss_pred CCCCCCCHHHHHHHHHHHHHcCCCCh---hhhhhhhcCCC-CHHHHHhHHHHHHHHH
Q 019948 93 KKGVPWTEEEHRMFLLGLQKLGKGDW---RGIARNYVVSR-TPTQVASHAQKYFIRQ 145 (333)
Q Consensus 93 kk~~~WTeEEH~~FL~GLekyGkGdW---k~IA~~~V~TR-Tp~QV~SHAQKYF~r~ 145 (333)
|++..||+|||++||+||+.||.|+| +.|++.++.++ |+.||+|||||||+++
T Consensus 1 k~r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~~k~ 57 (57)
T TIGR01557 1 KPRVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYRLKQ 57 (57)
T ss_pred CCCCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHHccC
Confidence 45689999999999999999999999 99997777899 9999999999999863
No 2
>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=99.39 E-value=5.1e-13 Score=95.03 Aligned_cols=45 Identities=40% Similarity=0.671 Sum_probs=40.8
Q ss_pred CCCCHHHHHHHHHHHHHcCCCChhhhhhhhcC-CCCHHHHHhHHHHH
Q 019948 96 VPWTEEEHRMFLLGLQKLGKGDWRGIARNYVV-SRTPTQVASHAQKY 141 (333)
Q Consensus 96 ~~WTeEEH~~FL~GLekyGkGdWk~IA~~~V~-TRTp~QV~SHAQKY 141 (333)
.+||+||+.+|++|+++||.++|+.||+ +|+ +||..||++|+++|
T Consensus 2 ~~Wt~eE~~~l~~~v~~~g~~~W~~Ia~-~~~~~Rt~~qc~~~~~~~ 47 (48)
T PF00249_consen 2 GPWTEEEDEKLLEAVKKYGKDNWKKIAK-RMPGGRTAKQCRSRYQNL 47 (48)
T ss_dssp -SS-HHHHHHHHHHHHHSTTTHHHHHHH-HHSSSSTHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHhCCcHHHHHHH-HcCCCCCHHHHHHHHHhh
Confidence 5899999999999999999977999995 788 99999999999987
No 3
>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=99.03 E-value=4.4e-10 Score=75.25 Aligned_cols=44 Identities=39% Similarity=0.729 Sum_probs=40.9
Q ss_pred CCCHHHHHHHHHHHHHcCCCChhhhhhhhcCCCCHHHHHhHHHHH
Q 019948 97 PWTEEEHRMFLLGLQKLGKGDWRGIARNYVVSRTPTQVASHAQKY 141 (333)
Q Consensus 97 ~WTeEEH~~FL~GLekyGkGdWk~IA~~~V~TRTp~QV~SHAQKY 141 (333)
.||+||+.+|+.++.+||.++|..|| .++++||..||+.|++++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia-~~~~~rs~~~~~~~~~~~ 44 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIA-KELPGRTPKQCRERWRNL 44 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHH-hHcCCCCHHHHHHHHHHh
Confidence 59999999999999999977999999 589999999999998765
No 4
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.03 E-value=3.8e-10 Score=76.34 Aligned_cols=46 Identities=30% Similarity=0.525 Sum_probs=42.0
Q ss_pred CCCCHHHHHHHHHHHHHcCCCChhhhhhhhcCCCCHHHHHhHHHHHH
Q 019948 96 VPWTEEEHRMFLLGLQKLGKGDWRGIARNYVVSRTPTQVASHAQKYF 142 (333)
Q Consensus 96 ~~WTeEEH~~FL~GLekyGkGdWk~IA~~~V~TRTp~QV~SHAQKYF 142 (333)
..||+||..+|+.++..||.++|..|| .++++||+.||+.++.+++
T Consensus 2 ~~Wt~~E~~~l~~~~~~~g~~~w~~Ia-~~~~~rt~~~~~~~~~~~~ 47 (49)
T smart00717 2 GEWTEEEDELLIELVKKYGKNNWEKIA-KELPGRTAEQCRERWNNLL 47 (49)
T ss_pred CCCCHHHHHHHHHHHHHHCcCCHHHHH-HHcCCCCHHHHHHHHHHHc
Confidence 589999999999999999977999999 5899999999999887654
No 5
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=98.58 E-value=5.3e-08 Score=97.99 Aligned_cols=50 Identities=26% Similarity=0.551 Sum_probs=47.6
Q ss_pred CCCCHHHHHHHHHHHHHcCCCChhhhhhhhcCCCCHHHHHhHHHHHHHHHh
Q 019948 96 VPWTEEEHRMFLLGLQKLGKGDWRGIARNYVVSRTPTQVASHAQKYFIRQS 146 (333)
Q Consensus 96 ~~WTeEEH~~FL~GLekyGkGdWk~IA~~~V~TRTp~QV~SHAQKYF~r~~ 146 (333)
..||.+|..+||+|++.||-|+|..|| ++|+|||..+|+.|+-|+|++..
T Consensus 73 ~~WtadEEilLLea~~t~G~GNW~dIA-~hIGtKtkeeck~hy~k~fv~s~ 122 (438)
T KOG0457|consen 73 PSWTADEEILLLEAAETYGFGNWQDIA-DHIGTKTKEECKEHYLKHFVNSP 122 (438)
T ss_pred CCCChHHHHHHHHHHHHhCCCcHHHHH-HHHcccchHHHHHHHHHHHhcCc
Confidence 589999999999999999999999999 69999999999999999999764
No 6
>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=98.57 E-value=7.4e-08 Score=70.56 Aligned_cols=42 Identities=36% Similarity=0.642 Sum_probs=35.7
Q ss_pred CCHHHHHHHHHHHHHcCCCChhhhhhhhcCCCCHHHHHhHHHHH
Q 019948 98 WTEEEHRMFLLGLQKLGKGDWRGIARNYVVSRTPTQVASHAQKY 141 (333)
Q Consensus 98 WTeEEH~~FL~GLekyGkGdWk~IA~~~V~TRTp~QV~SHAQKY 141 (333)
||+||..+++.++++||. +|+.||+ ++++||+.||+.+.+++
T Consensus 1 WT~eEd~~L~~~~~~~g~-~W~~Ia~-~l~~Rt~~~~~~r~~~~ 42 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGN-DWKKIAE-HLGNRTPKQCRNRWRNH 42 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS--HHHHHH-HSTTS-HHHHHHHHHHT
T ss_pred CCHHHHHHHHHHHHHHCc-CHHHHHH-HHCcCCHHHHHHHHHHH
Confidence 999999999999999996 9999995 78999999999888763
No 7
>KOG0724 consensus Zuotin and related molecular chaperones (DnaJ superfamily), contains DNA-binding domains [Posttranslational modification, protein turnover, chaperones]
Probab=98.38 E-value=1.5e-07 Score=89.68 Aligned_cols=79 Identities=47% Similarity=0.642 Sum_probs=73.1
Q ss_pred ccCcCCCCCCCHHHHHHHHHHHHHcCCCChhhhhhhhcCCCCHHHHHhHHH-----HHHHHHhhhccccCCCccccccCC
Q 019948 89 SRERKKGVPWTEEEHRMFLLGLQKLGKGDWRGIARNYVVSRTPTQVASHAQ-----KYFIRQSNVSRRKRRSSLFDIVAD 163 (333)
Q Consensus 89 ~~~rkk~~~WTeEEH~~FL~GLekyGkGdWk~IA~~~V~TRTp~QV~SHAQ-----KYF~r~~~~~krkrR~Sl~D~~~~ 163 (333)
...++++..|++.+|.+|+.++.++|+++|..|.++++.+|++.|+.+||| +||.+.....+.++|.+++|++..
T Consensus 158 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~s~a~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~ 237 (335)
T KOG0724|consen 158 EELRRKGTPVTERERKLVLLALKKDGKIDWRKISQNVEKERTPEQVASHAQEKAFEKALARQKSGEEEKRRKSIEDITTA 237 (335)
T ss_pred hhhhhccchhHHHHHHHHHhhhcccccccceechhhhhhhhcchhhhhhhhhhhhHHHHHHHhhhccccccchhhhhhcc
Confidence 566778899999999999999999999999999999999999999999999 999999999999999999999887
Q ss_pred CCCC
Q 019948 164 EPLD 167 (333)
Q Consensus 164 ~~~d 167 (333)
....
T Consensus 238 ~~~~ 241 (335)
T KOG0724|consen 238 SEAE 241 (335)
T ss_pred chhh
Confidence 6543
No 8
>PLN03212 Transcription repressor MYB5; Provisional
Probab=98.17 E-value=3.6e-06 Score=80.04 Aligned_cols=49 Identities=27% Similarity=0.501 Sum_probs=43.5
Q ss_pred CCCCCCHHHHHHHHHHHHHcCCCChhhhhhhhcCCCCHHHHHhHHHHHH
Q 019948 94 KGVPWTEEEHRMFLLGLQKLGKGDWRGIARNYVVSRTPTQVASHAQKYF 142 (333)
Q Consensus 94 k~~~WTeEEH~~FL~GLekyGkGdWk~IA~~~V~TRTp~QV~SHAQKYF 142 (333)
+..+||+||..+++..+++||.++|+.||+.+...||..||+.+..+|+
T Consensus 24 KRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L 72 (249)
T PLN03212 24 KRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYL 72 (249)
T ss_pred cCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhh
Confidence 4569999999999999999999999999963336999999999998886
No 9
>PLN03091 hypothetical protein; Provisional
Probab=98.03 E-value=7e-06 Score=83.37 Aligned_cols=52 Identities=19% Similarity=0.403 Sum_probs=43.7
Q ss_pred CcCCCCCCCHHHHHHHHHHHHHcCCCChhhhhhhhcCCCCHHHHHhHHHHHH
Q 019948 91 ERKKGVPWTEEEHRMFLLGLQKLGKGDWRGIARNYVVSRTPTQVASHAQKYF 142 (333)
Q Consensus 91 ~rkk~~~WTeEEH~~FL~GLekyGkGdWk~IA~~~V~TRTp~QV~SHAQKYF 142 (333)
.+.+.+.||.||.++++.++++||.++|+.||+.+...||..|||.+..+|+
T Consensus 10 qklrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyL 61 (459)
T PLN03091 10 QKLRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYL 61 (459)
T ss_pred CCCcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhcc
Confidence 3344579999999999999999999999999963335899999999877664
No 10
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=97.98 E-value=3.7e-05 Score=77.00 Aligned_cols=57 Identities=30% Similarity=0.450 Sum_probs=48.0
Q ss_pred cCcCCCCCCCHHHHHHHHHHHHHcCCCChhhhhhhhcCCCCHHHHHhHHHHHHHHHhhhcc
Q 019948 90 RERKKGVPWTEEEHRMFLLGLQKLGKGDWRGIARNYVVSRTPTQVASHAQKYFIRQSNVSR 150 (333)
Q Consensus 90 ~~rkk~~~WTeEEH~~FL~GLekyGkGdWk~IA~~~V~TRTp~QV~SHAQKYF~r~~~~~k 150 (333)
.-|..---|+++|.+.|-+||+.||| |+..|-++-|+||+...| ..-||+|++..+.
T Consensus 272 ~~rd~l~~wsEeEcr~FEegl~~yGK-DF~lIr~nkvrtRsvgEl---VeyYYlWKkSery 328 (445)
T KOG4329|consen 272 TVRDDLSGWSEEECRNFEEGLELYGK-DFHLIRANKVRTRSVGEL---VEYYYLWKKSERY 328 (445)
T ss_pred ecccccccCCHHHHHHHHHHHHHhcc-cHHHHHhcccccchHHHH---HHHHHHhhcCcch
Confidence 33444457999999999999999999 999999999999999999 4468888876654
No 11
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=97.95 E-value=8.4e-06 Score=83.31 Aligned_cols=41 Identities=32% Similarity=0.591 Sum_probs=38.6
Q ss_pred CCCCHHHHHHHHHHHHHcCCCChhhhhhhhcCCCCHHHHHhHH
Q 019948 96 VPWTEEEHRMFLLGLQKLGKGDWRGIARNYVVSRTPTQVASHA 138 (333)
Q Consensus 96 ~~WTeEEH~~FL~GLekyGkGdWk~IA~~~V~TRTp~QV~SHA 138 (333)
..||.+|-.++|+||+.||. ||.+||+ +|+|||..||--|.
T Consensus 280 k~WS~qE~~LLLEGIe~ygD-dW~kVA~-HVgtKt~EqCIl~F 320 (531)
T COG5259 280 KNWSRQELLLLLEGIEMYGD-DWDKVAR-HVGTKTKEQCILHF 320 (531)
T ss_pred ccccHHHHHHHHHHHHHhhh-hHHHHHH-HhCCCCHHHHHHHH
Confidence 48999999999999999998 9999995 99999999998875
No 12
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.88 E-value=1.1e-05 Score=79.65 Aligned_cols=49 Identities=31% Similarity=0.617 Sum_probs=46.3
Q ss_pred CCCCHHHHHHHHHHHHHcCCCChhhhhhhhcCCCCHHHHHhHHHHHHHHH
Q 019948 96 VPWTEEEHRMFLLGLQKLGKGDWRGIARNYVVSRTPTQVASHAQKYFIRQ 145 (333)
Q Consensus 96 ~~WTeEEH~~FL~GLekyGkGdWk~IA~~~V~TRTp~QV~SHAQKYF~r~ 145 (333)
.-|+.+|..+|++|++.+|-|+|..|| .||++|+-..|++|+-|||+.-
T Consensus 64 e~WgadEEllli~~~~TlGlGNW~dIa-dyiGsr~kee~k~HylK~y~es 112 (432)
T COG5114 64 EGWGADEELLLIECLDTLGLGNWEDIA-DYIGSRAKEEIKSHYLKMYDES 112 (432)
T ss_pred CCcCchHHHHHHHHHHhcCCCcHHHHH-HHHhhhhhHHHHHHHHHHHhhc
Confidence 579999999999999999999999999 6999999999999999998853
No 13
>PLN03212 Transcription repressor MYB5; Provisional
Probab=97.60 E-value=0.00011 Score=70.04 Aligned_cols=46 Identities=22% Similarity=0.242 Sum_probs=41.2
Q ss_pred CCCCCHHHHHHHHHHHHHcCCCChhhhhhhhcCCCCHHHHHhHHHHHH
Q 019948 95 GVPWTEEEHRMFLLGLQKLGKGDWRGIARNYVVSRTPTQVASHAQKYF 142 (333)
Q Consensus 95 ~~~WTeEEH~~FL~GLekyGkGdWk~IA~~~V~TRTp~QV~SHAQKYF 142 (333)
..+||+||.++.++...+||. .|..||+ +++.||..||+.+...++
T Consensus 78 kgpWT~EED~lLlel~~~~Gn-KWs~IAk-~LpGRTDnqIKNRWns~L 123 (249)
T PLN03212 78 RGGITSDEEDLILRLHRLLGN-RWSLIAG-RIPGRTDNEIKNYWNTHL 123 (249)
T ss_pred cCCCChHHHHHHHHHHHhccc-cHHHHHh-hcCCCCHHHHHHHHHHHH
Confidence 369999999999999999997 8999995 999999999998876544
No 14
>PLN03091 hypothetical protein; Provisional
Probab=97.50 E-value=0.0002 Score=73.09 Aligned_cols=48 Identities=17% Similarity=0.299 Sum_probs=42.2
Q ss_pred CCCCCHHHHHHHHHHHHHcCCCChhhhhhhhcCCCCHHHHHhHHHHHHHH
Q 019948 95 GVPWTEEEHRMFLLGLQKLGKGDWRGIARNYVVSRTPTQVASHAQKYFIR 144 (333)
Q Consensus 95 ~~~WTeEEH~~FL~GLekyGkGdWk~IA~~~V~TRTp~QV~SHAQKYF~r 144 (333)
.++||+||.+++|+..++||. .|..|| .+++.||..||+.+......|
T Consensus 67 KgpWT~EED~lLLeL~k~~Gn-KWskIA-k~LPGRTDnqIKNRWnslLKK 114 (459)
T PLN03091 67 RGTFSQQEENLIIELHAVLGN-RWSQIA-AQLPGRTDNEIKNLWNSCLKK 114 (459)
T ss_pred CCCCCHHHHHHHHHHHHHhCc-chHHHH-HhcCCCCHHHHHHHHHHHHHH
Confidence 369999999999999999998 999999 599999999999887654433
No 15
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=97.49 E-value=0.00012 Score=75.72 Aligned_cols=45 Identities=24% Similarity=0.456 Sum_probs=40.7
Q ss_pred CCCCCCCHHHHHHHHHHHHHcCCCChhhhhhhhcCCCCHHHHHhHHH
Q 019948 93 KKGVPWTEEEHRMFLLGLQKLGKGDWRGIARNYVVSRTPTQVASHAQ 139 (333)
Q Consensus 93 kk~~~WTeEEH~~FL~GLekyGkGdWk~IA~~~V~TRTp~QV~SHAQ 139 (333)
..+..||++|-.++|+||++||- ||.+|| .+|+|||..||-.|.-
T Consensus 251 ~~~~~WT~qE~lLLLE~ie~y~d-dW~kVa-~hVg~ks~eqCI~kFL 295 (506)
T KOG1279|consen 251 SARPNWTEQETLLLLEAIEMYGD-DWNKVA-DHVGTKSQEQCILKFL 295 (506)
T ss_pred cCCCCccHHHHHHHHHHHHHhcc-cHHHHH-hccCCCCHHHHHHHHH
Confidence 34568999999999999999998 999999 6999999999988753
No 16
>PLN03162 golden-2 like transcription factor; Provisional
Probab=97.26 E-value=0.0027 Score=64.29 Aligned_cols=58 Identities=33% Similarity=0.385 Sum_probs=43.9
Q ss_pred ccCcCCCCCCCHHHHHHHHHHHHHcCC--CChhhhhh-hhcCCCCHHHHHhHHHHHHHHHh
Q 019948 89 SRERKKGVPWTEEEHRMFLLGLQKLGK--GDWRGIAR-NYVVSRTPTQVASHAQKYFIRQS 146 (333)
Q Consensus 89 ~~~rkk~~~WTeEEH~~FL~GLekyGk--GdWk~IA~-~~V~TRTp~QV~SHAQKYF~r~~ 146 (333)
...||.+..||.|=|++|+++++++|- --=|+|-+ .=|..=|..+|+||-|||...++
T Consensus 231 ~g~KKpRLrWTpELH~rFVeAV~qLG~dKATPK~ILelMnV~GLTRenVKSHLQKYRl~rk 291 (526)
T PLN03162 231 PGKKKAKVDWTPELHRRFVHAVEQLGVEKAFPSRILELMGVQCLTRHNIASHLQKYRSHRR 291 (526)
T ss_pred CCCCCCcccCCHHHHHHHHHHHHHhCcCccchHHHHHHcCCCCcCHHHHHHHHHHHHHhcc
Confidence 345677899999999999999999992 12234432 12677899999999999966543
No 17
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=96.98 E-value=0.00082 Score=62.40 Aligned_cols=47 Identities=19% Similarity=0.344 Sum_probs=43.2
Q ss_pred CCCCCHHHHHHHHHHHHHcCCCChhhhhhhhcC-CCCHHHHHhHHHHHH
Q 019948 95 GVPWTEEEHRMFLLGLQKLGKGDWRGIARNYVV-SRTPTQVASHAQKYF 142 (333)
Q Consensus 95 ~~~WTeEEH~~FL~GLekyGkGdWk~IA~~~V~-TRTp~QV~SHAQKYF 142 (333)
.++||.||..+++.-+++||.|.|..|++ ..+ -|+-.|||-..-.|.
T Consensus 9 kGpWt~EED~~L~~~V~~~G~~~W~~i~k-~~gl~R~GKSCRlRW~NyL 56 (238)
T KOG0048|consen 9 KGPWTQEEDLTQIRSIKSFGKHNGTALPK-LAGLRRCGKSCRLRWTNYL 56 (238)
T ss_pred CCCCChHHHHHHHHHHHHhCCCCcchhhh-hcCCCccchHHHHHhhccc
Confidence 37999999999999999999999999995 788 999999999887773
No 18
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=96.45 E-value=0.0045 Score=66.27 Aligned_cols=46 Identities=20% Similarity=0.468 Sum_probs=41.8
Q ss_pred CCCCHHHHHHHHHHHHHcCCCChhhhhhhhcCCCCHHHHHhHHHHHH
Q 019948 96 VPWTEEEHRMFLLGLQKLGKGDWRGIARNYVVSRTPTQVASHAQKYF 142 (333)
Q Consensus 96 ~~WTeEEH~~FL~GLekyGkGdWk~IA~~~V~TRTp~QV~SHAQKYF 142 (333)
++||.+|..+++.|+.+||..||-+|- ..|+.|+-.|||..+.+.+
T Consensus 361 g~wt~~ED~~L~~AV~~Yg~kdw~k~R-~~vPnRSdsQcR~RY~nvL 406 (939)
T KOG0049|consen 361 GRWTDQEDVLLVCAVSRYGAKDWAKVR-QAVPNRSDSQCRERYTNVL 406 (939)
T ss_pred CCCCCHHHHHHHHHHHHhCccchhhHH-HhcCCccHHHHHHHHHHHH
Confidence 699999999999999999999999998 5999999999999765443
No 19
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=96.32 E-value=0.003 Score=68.08 Aligned_cols=49 Identities=24% Similarity=0.369 Sum_probs=44.2
Q ss_pred CCCCCHHHHHHHHHHHHHcCCCChhhhhhhhcCCCCHHHHHhHHHHHHHHHhhh
Q 019948 95 GVPWTEEEHRMFLLGLQKLGKGDWRGIARNYVVSRTPTQVASHAQKYFIRQSNV 148 (333)
Q Consensus 95 ~~~WTeEEH~~FL~GLekyGkGdWk~IA~~~V~TRTp~QV~SHAQKYF~r~~~~ 148 (333)
...||..|.++|-.||-.|-| |+..|+ .+|+|||..|| .|-||.|.+-.
T Consensus 619 Sd~WTp~E~~lF~kA~y~~~K-DF~~v~-km~~~KtVaqC---VeyYYtWKK~~ 667 (907)
T KOG4167|consen 619 SDKWTPLERKLFNKALYTYSK-DFIFVQ-KMVKSKTVAQC---VEYYYTWKKIM 667 (907)
T ss_pred cccccHHHHHHHHHHHHHhcc-cHHHHH-HHhccccHHHH---HHHHHHHHHhc
Confidence 357999999999999999999 999999 59999999999 77788888754
No 20
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=95.85 E-value=0.019 Score=53.42 Aligned_cols=43 Identities=28% Similarity=0.390 Sum_probs=39.2
Q ss_pred CCCCCCHHHHHHHHHHHHHcCCCChhhhhhhhcCCCCHHHHHhHH
Q 019948 94 KGVPWTEEEHRMFLLGLQKLGKGDWRGIARNYVVSRTPTQVASHA 138 (333)
Q Consensus 94 k~~~WTeEEH~~FL~GLekyGkGdWk~IA~~~V~TRTp~QV~SHA 138 (333)
+++.||+||.++.+++=.+||- .|..|| .+++.||--.|+.|-
T Consensus 61 krg~fT~eEe~~Ii~lH~~~GN-rWs~IA-~~LPGRTDNeIKN~W 103 (238)
T KOG0048|consen 61 KRGNFSDEEEDLIIKLHALLGN-RWSLIA-GRLPGRTDNEVKNHW 103 (238)
T ss_pred cCCCCCHHHHHHHHHHHHHHCc-HHHHHH-hhCCCcCHHHHHHHH
Confidence 3579999999999999999997 899999 599999999997774
No 21
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=95.30 E-value=0.02 Score=61.60 Aligned_cols=46 Identities=26% Similarity=0.421 Sum_probs=41.1
Q ss_pred CCCCCCCHHHHHHHHHHHHHcCCCChhhhhhhhcCCCCHHHHHhHHH
Q 019948 93 KKGVPWTEEEHRMFLLGLQKLGKGDWRGIARNYVVSRTPTQVASHAQ 139 (333)
Q Consensus 93 kk~~~WTeEEH~~FL~GLekyGkGdWk~IA~~~V~TRTp~QV~SHAQ 139 (333)
-|...||-.|.+++|..+++||+|.|-+|| .|++-||-.|..+.-.
T Consensus 410 ~K~~rW~l~edeqL~~~V~~YG~g~WakcA-~~Lp~~t~~q~~rrR~ 455 (939)
T KOG0049|consen 410 AKVERWTLVEDEQLLYAVKVYGKGNWAKCA-MLLPKKTSRQLRRRRL 455 (939)
T ss_pred hccCceeecchHHHHHHHHHHccchHHHHH-HHccccchhHHHHHHH
Confidence 355799999999999999999999999999 5999999999877543
No 22
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=94.85 E-value=0.039 Score=56.24 Aligned_cols=59 Identities=20% Similarity=0.321 Sum_probs=47.6
Q ss_pred CCCCCCCCCCC---CCccCcCCCCCCCHHHHHHHHHHHHHcCCCChhhhhhhhcCCCCHHHHHh
Q 019948 76 GYASEDFVPGS---SSSRERKKGVPWTEEEHRMFLLGLQKLGKGDWRGIARNYVVSRTPTQVAS 136 (333)
Q Consensus 76 gY~Sd~~v~~s---~~~~~rkk~~~WTeEEH~~FL~GLekyGkGdWk~IA~~~V~TRTp~QV~S 136 (333)
-|.-++..... ++...+++..+||.+|-++|-.||..+|- |+..|+ +++++|...||..
T Consensus 343 E~veen~~ar~vts~t~g~~~~~~~Ws~~e~ekFYKALs~wGt-dF~LIs-~lfP~R~RkqIKa 404 (507)
T COG5118 343 EVVEENPFARIVTSSTFGKKKGALRWSKKEIEKFYKALSIWGT-DFSLIS-SLFPNRERKQIKA 404 (507)
T ss_pred HHhhccchhheeecccccCCCCCCcccHHHHHHHHHHHHHhcc-hHHHHH-HhcCchhHHHHHH
Confidence 45555543332 22466677889999999999999999998 999999 6999999999965
No 23
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=94.72 E-value=0.024 Score=34.06 Aligned_cols=18 Identities=44% Similarity=1.187 Sum_probs=16.7
Q ss_pred cccCCCCCCCCCCCCCCC
Q 019948 3 RRCSHCSHNGHNSRTCPN 20 (333)
Q Consensus 3 R~CS~c~~~GHnsrtc~~ 20 (333)
|+|-.||..||-++-||.
T Consensus 1 ~~C~~C~~~GH~~~~Cp~ 18 (18)
T PF00098_consen 1 RKCFNCGEPGHIARDCPK 18 (18)
T ss_dssp SBCTTTSCSSSCGCTSSS
T ss_pred CcCcCCCCcCcccccCcc
Confidence 689999999999999984
No 24
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=94.59 E-value=0.046 Score=58.27 Aligned_cols=50 Identities=30% Similarity=0.462 Sum_probs=40.2
Q ss_pred CCCCCHHHHHHHHHHHHHcCCCChhhh---------hhhhcCCCCHHHHHhHHHHHHHHH
Q 019948 95 GVPWTEEEHRMFLLGLQKLGKGDWRGI---------ARNYVVSRTPTQVASHAQKYFIRQ 145 (333)
Q Consensus 95 ~~~WTeEEH~~FL~GLekyGkGdWk~I---------A~~~V~TRTp~QV~SHAQKYF~r~ 145 (333)
.+.||.+|..-|..||+.+|| |+..| +..-+..||--||+-||-+-..++
T Consensus 88 ktaWt~~E~~~Ffdal~~~GK-dFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~~~m 146 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVGK-DFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLVRRM 146 (782)
T ss_pred ccccchhhHHHHHHHHHHhcc-cHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHHHHH
Confidence 468999999999999999999 99999 113477889999988765544444
No 25
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=94.50 E-value=0.05 Score=60.89 Aligned_cols=49 Identities=22% Similarity=0.472 Sum_probs=44.8
Q ss_pred CCCHHHHHHHHHHHHHcCCCChhhhhhhhcCCCCHHHHHhHHHHHHHHHh
Q 019948 97 PWTEEEHRMFLLGLQKLGKGDWRGIARNYVVSRTPTQVASHAQKYFIRQS 146 (333)
Q Consensus 97 ~WTeEEH~~FL~GLekyGkGdWk~IA~~~V~TRTp~QV~SHAQKYF~r~~ 146 (333)
.||..+-..|+.|.++||+.+...|| ..|.+||+.+|+-+++-|+.|..
T Consensus 826 ~w~~~~f~~f~~~~~~~gr~~~~~i~-~~~~~k~~~ev~~y~~~f~~~~~ 874 (1033)
T PLN03142 826 TWSRRDFNAFIRACEKYGRNDIKSIA-SEMEGKTEEEVERYAKVFWERYK 874 (1033)
T ss_pred cccHHHHHHHHHHHHHhCHhHHHHHH-HHhcCCCHHHHHHHHHHHHHhhh
Confidence 49999999999999999999999999 58999999999999988876643
No 26
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=94.46 E-value=0.034 Score=57.94 Aligned_cols=52 Identities=23% Similarity=0.547 Sum_probs=44.0
Q ss_pred cCCCCCCCHHHHHHHHHHHHHcCCCChhhhhhhhcCCCCHHHHHhHHHHHHHHHhh
Q 019948 92 RKKGVPWTEEEHRMFLLGLQKLGKGDWRGIARNYVVSRTPTQVASHAQKYFIRQSN 147 (333)
Q Consensus 92 rkk~~~WTeEEH~~FL~GLekyGkGdWk~IA~~~V~TRTp~QV~SHAQKYF~r~~~ 147 (333)
|..-.-|+.-|-.+|.++|+|||| |+..|-+.|++=|+.+-| .+-||++...
T Consensus 282 RDemEEWSasEanLFEeALeKyGK-DFndIrqdfLPWKSl~sI---veyYYmwKtt 333 (693)
T KOG3554|consen 282 RDEMEEWSASEANLFEEALEKYGK-DFNDIRQDFLPWKSLTSI---VEYYYMWKTT 333 (693)
T ss_pred hhhhhhccchhhHHHHHHHHHhcc-cHHHHHHhhcchHHHHHH---HHHHHHHhhh
Confidence 334468999999999999999999 999999999999987776 6667777653
No 27
>KOG0724 consensus Zuotin and related molecular chaperones (DnaJ superfamily), contains DNA-binding domains [Posttranslational modification, protein turnover, chaperones]
Probab=94.23 E-value=0.011 Score=56.73 Aligned_cols=49 Identities=18% Similarity=0.094 Sum_probs=45.3
Q ss_pred CCCHHHHHHHHHHHHHcCCCChhhhhhhhcCCCCHHHHHhHHHHHHHHHhh
Q 019948 97 PWTEEEHRMFLLGLQKLGKGDWRGIARNYVVSRTPTQVASHAQKYFIRQSN 147 (333)
Q Consensus 97 ~WTeEEH~~FL~GLekyGkGdWk~IA~~~V~TRTp~QV~SHAQKYF~r~~~ 147 (333)
.||++||..|.++|..| +-.|+.|- .|++.++..|.++|+|+||.....
T Consensus 55 ~~t~~~~~~~~~~l~~~-~~~~~~~~-~~~~~~~~v~~~~~~~~~~p~~~~ 103 (335)
T KOG0724|consen 55 RRTPDSWDKFAEALPLE-KRLEDKIE-EYIGLVFDVNIRESGQKPFPKYGK 103 (335)
T ss_pred ccchhhhhHHHhcCccc-cccchhHH-hhhhhHHHHhhhhccCCCccccCc
Confidence 59999999999999999 45999999 599999999999999999988864
No 28
>KOG3841 consensus TEF-1 and related transcription factor, TEAD family [Transcription]
Probab=93.94 E-value=0.25 Score=50.46 Aligned_cols=48 Identities=31% Similarity=0.373 Sum_probs=39.2
Q ss_pred CCCCCCCHHHHHHHHHHHHHcC---------------CCChhhhhhhhc-----CCCCHHHHHhHHHHH
Q 019948 93 KKGVPWTEEEHRMFLLGLQKLG---------------KGDWRGIARNYV-----VSRTPTQVASHAQKY 141 (333)
Q Consensus 93 kk~~~WTeEEH~~FL~GLekyG---------------kGdWk~IA~~~V-----~TRTp~QV~SHAQKY 141 (333)
-.-+-|+++=...|++||..|- .|+=..||+ || +|||..||.||-|=.
T Consensus 74 daegvWSpdIEqsFqEALaiyppcGrrKIilsdegkmyGRNELIar-YIKlrtgktRTrKQVSSHIQVl 141 (455)
T KOG3841|consen 74 DAEGVWSPDIEQSFQEALAIYPPCGRRKIILSDEGKMYGRNELIAR-YIKLRTGKTRTRKQVSSHIQVL 141 (455)
T ss_pred ccccccChhHHHHHHHHHhhcCCCCceeEEEccCccccchHHHHHH-HHHHhcCCchhHHHHHHHHHHH
Confidence 4457899999999999999875 245567886 76 599999999999944
No 29
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=93.71 E-value=0.033 Score=40.11 Aligned_cols=20 Identities=30% Similarity=0.807 Sum_probs=16.9
Q ss_pred cccCCCCCCCCC--CCCCCCCc
Q 019948 3 RRCSHCSHNGHN--SRTCPNRG 22 (333)
Q Consensus 3 R~CS~c~~~GHn--srtc~~~g 22 (333)
+||..||.+||. +|+||-..
T Consensus 2 ~kC~~CG~~GH~~t~k~CP~~~ 23 (40)
T PF15288_consen 2 VKCKNCGAFGHMRTNKRCPMYC 23 (40)
T ss_pred ccccccccccccccCccCCCCC
Confidence 799999999995 48999653
No 30
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=92.93 E-value=0.038 Score=40.11 Aligned_cols=19 Identities=42% Similarity=1.130 Sum_probs=17.2
Q ss_pred CCcccCCCCCCCCCCCCCC
Q 019948 1 MTRRCSHCSHNGHNSRTCP 19 (333)
Q Consensus 1 m~R~CS~c~~~GHnsrtc~ 19 (333)
+.+.|.+||..||..+.|+
T Consensus 30 lp~~C~~C~~~gH~~~~C~ 48 (49)
T PF14392_consen 30 LPRFCFHCGRIGHSDKECP 48 (49)
T ss_pred cChhhcCCCCcCcCHhHcC
Confidence 4578999999999999997
No 31
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=92.66 E-value=0.24 Score=38.23 Aligned_cols=51 Identities=22% Similarity=0.418 Sum_probs=31.4
Q ss_pred CCCCHHHHHHHHHHHHH------cC-----CC--Chhhhhhhh---cCCCCHHHHHhHHHHHHHHHh
Q 019948 96 VPWTEEEHRMFLLGLQK------LG-----KG--DWRGIARNY---VVSRTPTQVASHAQKYFIRQS 146 (333)
Q Consensus 96 ~~WTeEEH~~FL~GLek------yG-----kG--dWk~IA~~~---V~TRTp~QV~SHAQKYF~r~~ 146 (333)
..||++|...||..+.. |+ ++ -|+.||..+ --.||+.||+.....-..+-.
T Consensus 2 ~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~~~Yk 68 (90)
T PF13837_consen 2 RNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNLKKKYK 68 (90)
T ss_dssp -SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHH
Confidence 47999999999998877 32 22 599998632 237999999887754433333
No 32
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=91.46 E-value=0.17 Score=53.30 Aligned_cols=48 Identities=25% Similarity=0.488 Sum_probs=43.3
Q ss_pred CCCCCCCHHHHHHHHHHHHHcCCCChhhhhhhhcCCCCHHHHHhHHHHH
Q 019948 93 KKGVPWTEEEHRMFLLGLQKLGKGDWRGIARNYVVSRTPTQVASHAQKY 141 (333)
Q Consensus 93 kk~~~WTeEEH~~FL~GLekyGkGdWk~IA~~~V~TRTp~QV~SHAQKY 141 (333)
.+++-|+.-|.+..-.|+.+||+..|..|+ .....+|+.||....-+|
T Consensus 5 ~kggvwrntEdeilkaav~kyg~nqws~i~-sll~~kt~rqC~~rw~e~ 52 (617)
T KOG0050|consen 5 IKGGVWRNTEDEVLKAAVMKYGKNQWSRIA-SLLNRKTARQCKARWEEW 52 (617)
T ss_pred EecceecccHHHHHHHHHHHcchHHHHHHH-HHHhhcchhHHHHHHHHH
Confidence 467899999999999999999999999999 599999999998766555
No 33
>smart00426 TEA TEA domain.
Probab=90.91 E-value=0.32 Score=38.70 Aligned_cols=44 Identities=32% Similarity=0.413 Sum_probs=33.3
Q ss_pred CCCCCHHHHHHHHHHHHHcCCCChhh---------------hhhhhc-----CCCCHHHHHhHHH
Q 019948 95 GVPWTEEEHRMFLLGLQKLGKGDWRG---------------IARNYV-----VSRTPTQVASHAQ 139 (333)
Q Consensus 95 ~~~WTeEEH~~FL~GLekyGkGdWk~---------------IA~~~V-----~TRTp~QV~SHAQ 139 (333)
...|.++=...|++||+.|-+-.+++ |+ +|+ ..||..||.||-|
T Consensus 3 ~~vWp~~lE~Af~~aL~~~~~~g~~kik~~~r~k~~gRNelIs-~YI~~~tGk~Rt~KQVsShIQ 66 (68)
T smart00426 3 EGVWSPDIEQAFQEALAIYPPCGRRKIILSDEGKMYGRNELIA-RYIKLRTGKTRTRKQVSSHIQ 66 (68)
T ss_pred CCcCcHHHHHHHHHHHHHcCccCcccchhhhcCcccchhHHHH-HHHHHHhCCccchhhhcchhe
Confidence 35799999999999999987533332 33 233 4799999999987
No 34
>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=90.64 E-value=0.56 Score=40.31 Aligned_cols=51 Identities=33% Similarity=0.586 Sum_probs=40.3
Q ss_pred CCCCCCCHHHHHHHHHHHHHcCC---CChhhhhh-----------hhcCCCCHHHHHhHHHHHHHH
Q 019948 93 KKGVPWTEEEHRMFLLGLQKLGK---GDWRGIAR-----------NYVVSRTPTQVASHAQKYFIR 144 (333)
Q Consensus 93 kk~~~WTeEEH~~FL~GLekyGk---GdWk~IA~-----------~~V~TRTp~QV~SHAQKYF~r 144 (333)
.++..||+||.+-.|..+.+||- |.|..|-. -|+.|||+..+.=++. +.++
T Consensus 47 ~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir~~p~FrFDwf~kSRt~~el~rR~~-tLi~ 111 (118)
T PF09111_consen 47 NKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIRESPLFRFDWFFKSRTPQELQRRCN-TLIK 111 (118)
T ss_dssp SS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHHH-CGGCT-HHHHTS-HHHHHHHHH-HHHH
T ss_pred CCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHHhCCCcccchhcccCCHHHHHHHHH-HHHH
Confidence 44579999999999999999999 99999953 4789999999988885 4433
No 35
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=85.71 E-value=1.3 Score=46.27 Aligned_cols=46 Identities=26% Similarity=0.452 Sum_probs=38.0
Q ss_pred CCCCHHHHHHHHHHHHHcCCCChhhhhhhhcCCCCHHHHHhHHHHHHHHHh
Q 019948 96 VPWTEEEHRMFLLGLQKLGKGDWRGIARNYVVSRTPTQVASHAQKYFIRQS 146 (333)
Q Consensus 96 ~~WTeEEH~~FL~GLekyGkGdWk~IA~~~V~TRTp~QV~SHAQKYF~r~~ 146 (333)
..||.||--+|-.+++.||+ ++.+|- ..++-|+..-+ .|-||-+.+
T Consensus 188 d~WT~Ed~vlFe~aF~~~GK-~F~kIr-q~LP~rsLaSl---vqyYy~~KK 233 (534)
T KOG1194|consen 188 DEWTAEDIVLFEQAFQFFGK-DFHKIR-QALPHRSLASL---VQYYYSWKK 233 (534)
T ss_pred ccchHHHHHHHHHHHHHhcc-cHHHHH-HHccCccHHHH---HHHHHHHHH
Confidence 47999999999999999999 999999 48999997666 554544443
No 36
>PF01285 TEA: TEA/ATTS domain family; InterPro: IPR000818 Transcriptional enhancer activators are nuclear proteins that contain a TEA/ATTSdomain, a DNA-binding region of 66-68 amino acids. The TEA/ATTS domain is found in the N-termini of certain gene regulatory proteins, such as the Simian virus 40 (SV40) enhancer factor TEF-1, yeast trans-acting factor TEC-1 (which is required for TY1 enhancer activity), and the Aspergillus abaA regulatory gene product. SV40 and retroviral enhancers, and those to which TEF-1, TEC-1 and abaA proteins bind, contain GT-IIC sites: the TEA/ATTS domain may therefore recognise and bind such sites. Secondary structure predictions suggest the presence of 3 helices, but have not confirmed the presence of the helix-turn-helix motif characteristic of many DNA-binding proteins: DNA-binding may therefore be effected by a different mechanism [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3L15_B 2HZD_A 3KYS_A 3JUA_C 4EAZ_B.
Probab=83.86 E-value=1.3 Score=45.61 Aligned_cols=48 Identities=27% Similarity=0.334 Sum_probs=30.0
Q ss_pred CCCCCCCHHHHHHHHHHHHHcCCCChh-------------hhhhhhc-----CCCCHHHHHhHHHHH
Q 019948 93 KKGVPWTEEEHRMFLLGLQKLGKGDWR-------------GIARNYV-----VSRTPTQVASHAQKY 141 (333)
Q Consensus 93 kk~~~WTeEEH~~FL~GLekyGkGdWk-------------~IA~~~V-----~TRTp~QV~SHAQKY 141 (333)
+....|+++=+..|++||..|-+-.++ .|+ .|| .+||..||.||.|-.
T Consensus 47 ~~~~vw~~~~e~af~~al~~~~~~g~~k~~~~~~~~grn~li~-~yi~~~tg~~rt~kqvsshiqvl 112 (431)
T PF01285_consen 47 DGEGVWPPDIEQAFQEALAIYPPCGRRKLSDEGKMYGRNELIS-DYIKLKTGKTRTRKQVSSHIQVL 112 (431)
T ss_dssp GGS--S-HHHHHHHHHHHHHS-SSS---HHHH-----THHHHH-HHHHHHHS----SHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHhCCCCCCcccccccccccchhHHH-HHHHHHhCcccchhHHHHHHHHH
Confidence 445789999999999999998744333 345 254 579999999999955
No 37
>smart00343 ZnF_C2HC zinc finger.
Probab=82.03 E-value=0.74 Score=29.07 Aligned_cols=18 Identities=39% Similarity=1.149 Sum_probs=15.9
Q ss_pred ccCCCCCCCCCCCCCCCC
Q 019948 4 RCSHCSHNGHNSRTCPNR 21 (333)
Q Consensus 4 ~CS~c~~~GHnsrtc~~~ 21 (333)
+|..||..||.++.|+..
T Consensus 1 ~C~~CG~~GH~~~~C~~~ 18 (26)
T smart00343 1 KCYNCGKEGHIARDCPKX 18 (26)
T ss_pred CCccCCCCCcchhhCCcc
Confidence 599999999999999843
No 38
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=81.57 E-value=1.9 Score=46.20 Aligned_cols=50 Identities=18% Similarity=0.262 Sum_probs=39.5
Q ss_pred CCCCCCHHHHHHHHHHHH-------Hc-------C----C-------CChhhhhhhhcCCCCHHHHHhHHHHHHHH
Q 019948 94 KGVPWTEEEHRMFLLGLQ-------KL-------G----K-------GDWRGIARNYVVSRTPTQVASHAQKYFIR 144 (333)
Q Consensus 94 k~~~WTeEEH~~FL~GLe-------ky-------G----k-------GdWk~IA~~~V~TRTp~QV~SHAQKYF~r 144 (333)
++..||.||.+++|..++ .| | . =.|..|+. .++||+..||+.|.+|-..+
T Consensus 435 ~r~~Ws~eEe~~Llk~V~~~~~~~~q~q~~n~~~~~q~sp~s~~~d~I~Wt~vse-~~~TR~~~qCr~Kw~kl~~~ 509 (607)
T KOG0051|consen 435 NRGAWSIEEEEKLLKTVNEMIREALQPQASNTDTGLQESPESTLKDDINWTLVSE-MLGTRSRIQCRYKWYKLTTS 509 (607)
T ss_pred ccCcchHHHHHHHHHHHHHHHHHhhcccccccchhhhcCccccccCCcchhhhhH-hhcCCCcchHHHHHHHHHhh
Confidence 457999999999999996 34 1 1 17999995 99999999999877665443
No 39
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=81.32 E-value=0.98 Score=47.52 Aligned_cols=55 Identities=22% Similarity=0.378 Sum_probs=44.4
Q ss_pred cCcCCCCCCCHHHHHHHHHHHHHcCCCChhhhhhhhcCCCCHHHHHhHHHHHHHHH
Q 019948 90 RERKKGVPWTEEEHRMFLLGLQKLGKGDWRGIARNYVVSRTPTQVASHAQKYFIRQ 145 (333)
Q Consensus 90 ~~rkk~~~WTeEEH~~FL~GLekyGkGdWk~IA~~~V~TRTp~QV~SHAQKYF~r~ 145 (333)
+...+++.|+..|....+.+.++||...|-.||..|+. ||..|++.|-..|...+
T Consensus 15 ~~~~k~gsw~~~EDe~l~~~vk~l~~nnws~vas~~~~-~~~kq~~~rw~~~lnp~ 69 (512)
T COG5147 15 QTKRKGGSWKRTEDEDLKALVKKLGPNNWSKVASLLIS-STGKQSSNRWNNHLNPQ 69 (512)
T ss_pred cceecCCCCCCcchhHHHHHHhhcccccHHHHHHHhcc-cccccccchhhhhhchh
Confidence 33445569999999999999999999999999975555 99999999886564444
No 40
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=75.74 E-value=6 Score=44.92 Aligned_cols=48 Identities=35% Similarity=0.614 Sum_probs=40.9
Q ss_pred CCCCCCHHHHHHHHHHHHHcCCCChhhhhh-----------hhcCCCCHHHHHhHHHHH
Q 019948 94 KGVPWTEEEHRMFLLGLQKLGKGDWRGIAR-----------NYVVSRTPTQVASHAQKY 141 (333)
Q Consensus 94 k~~~WTeEEH~~FL~GLekyGkGdWk~IA~-----------~~V~TRTp~QV~SHAQKY 141 (333)
++..||+||.+..|-.+.+||.|.|..|-. -|+.|||+..+.=++.-.
T Consensus 925 ~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~~l 983 (1033)
T PLN03142 925 KGKLYNEECDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELARRCDTL 983 (1033)
T ss_pred CCCcCCHHHHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHHHHHHHH
Confidence 345799999999999999999999999932 478999999998888533
No 41
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=75.03 E-value=1.7 Score=32.06 Aligned_cols=19 Identities=37% Similarity=1.001 Sum_probs=16.3
Q ss_pred cccCCCC-CCCCCCCCCCCC
Q 019948 3 RRCSHCS-HNGHNSRTCPNR 21 (333)
Q Consensus 3 R~CS~c~-~~GHnsrtc~~~ 21 (333)
|||.+|| .||+-+--|-|.
T Consensus 12 rkCp~CGt~NG~R~~~CKN~ 31 (44)
T PF14952_consen 12 RKCPKCGTYNGTRGLSCKNK 31 (44)
T ss_pred ccCCcCcCccCcccccccCC
Confidence 8999999 889988778765
No 42
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=72.55 E-value=1.9 Score=27.67 Aligned_cols=25 Identities=32% Similarity=0.808 Sum_probs=18.5
Q ss_pred CCcccCCCCCC-CCCCCCCCCCceEE
Q 019948 1 MTRRCSHCSHN-GHNSRTCPNRGVKI 25 (333)
Q Consensus 1 m~R~CS~c~~~-GHnsrtc~~~g~~L 25 (333)
|.+.|.+||+. --..+-|++=|-+|
T Consensus 1 m~~~Cp~Cg~~~~~~~~fC~~CG~~L 26 (26)
T PF13248_consen 1 MEMFCPNCGAEIDPDAKFCPNCGAKL 26 (26)
T ss_pred CcCCCcccCCcCCcccccChhhCCCC
Confidence 88999999973 44677888755443
No 43
>KOG0385 consensus Chromatin remodeling complex WSTF-ISWI, small subunit [Transcription]
Probab=71.41 E-value=5.6 Score=44.39 Aligned_cols=50 Identities=28% Similarity=0.491 Sum_probs=44.3
Q ss_pred CCCCHHHHHHHHHHHHHcCCCChhhhhhhhcCCCCHHHHHhHHHHHHHHHhh
Q 019948 96 VPWTEEEHRMFLLGLQKLGKGDWRGIARNYVVSRTPTQVASHAQKYFIRQSN 147 (333)
Q Consensus 96 ~~WTeEEH~~FL~GLekyGkGdWk~IA~~~V~TRTp~QV~SHAQKYF~r~~~ 147 (333)
..||+.+-..|+.|-++||++|-..|++ -|-. |+..|..+|.-||.|+..
T Consensus 796 t~w~k~df~~fi~a~eKygr~di~~ia~-~~e~-~~eev~~y~rvfwer~~e 845 (971)
T KOG0385|consen 796 TNWTKRDFNQFIKANEKYGRDDIENIAA-EVEG-TPEEVGEYARVFWERLEE 845 (971)
T ss_pred cchhhhhHHHHHHHhhccCcchhhhhHH-hhcC-CHHHHHHHHHHHHHHHHH
Confidence 3599999999999999999999999996 4444 999999999988888864
No 44
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=71.01 E-value=11 Score=28.67 Aligned_cols=46 Identities=20% Similarity=0.289 Sum_probs=34.8
Q ss_pred CCCCHHHHHHHHHHHHHcC----------------CCChhhhhhhh----cCCCCHHHHHhHHHHH
Q 019948 96 VPWTEEEHRMFLLGLQKLG----------------KGDWRGIARNY----VVSRTPTQVASHAQKY 141 (333)
Q Consensus 96 ~~WTeEEH~~FL~GLekyG----------------kGdWk~IA~~~----V~TRTp~QV~SHAQKY 141 (333)
..||.+|...+++-+++|- ..-|..|+..| .+.||..|++-..+++
T Consensus 3 ~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nl 68 (78)
T PF13873_consen 3 PNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNL 68 (78)
T ss_pred CCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHH
Confidence 4799999999999999973 23799997533 3489999997644433
No 45
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=69.80 E-value=7.3 Score=41.24 Aligned_cols=44 Identities=32% Similarity=0.489 Sum_probs=38.3
Q ss_pred CCCCCCHHHHHHHHHHHHHcCCCChhhhhhhhcCCCCHHHHHhHHH
Q 019948 94 KGVPWTEEEHRMFLLGLQKLGKGDWRGIARNYVVSRTPTQVASHAQ 139 (333)
Q Consensus 94 k~~~WTeEEH~~FL~GLekyGkGdWk~IA~~~V~TRTp~QV~SHAQ 139 (333)
+...|++||.+..+..=..+|- .|..|+ .+++.||-.||...+.
T Consensus 71 k~~~~~~eed~~li~l~~~~~~-~wstia-~~~d~rt~~~~~ery~ 114 (512)
T COG5147 71 KKKNWSEEEDEQLIDLDKELGT-QWSTIA-DYKDRRTAQQCVERYV 114 (512)
T ss_pred ccccccHHHHHHHHHHHHhcCc-hhhhhc-cccCccchHHHHHHHH
Confidence 4468999999999999999998 799999 5999999999944333
No 46
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=69.44 E-value=2.6 Score=39.38 Aligned_cols=18 Identities=39% Similarity=1.040 Sum_probs=15.7
Q ss_pred CcccCCCCCCCCCCCCCC
Q 019948 2 TRRCSHCSHNGHNSRTCP 19 (333)
Q Consensus 2 ~R~CS~c~~~GHnsrtc~ 19 (333)
+.+|.+||-+||-+|-|+
T Consensus 97 ~~~C~~Cg~~GH~~~dC~ 114 (190)
T COG5082 97 PKKCYNCGETGHLSRDCN 114 (190)
T ss_pred ccccccccccCccccccC
Confidence 458999999999999994
No 47
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=67.92 E-value=5.3 Score=42.89 Aligned_cols=46 Identities=22% Similarity=0.376 Sum_probs=40.9
Q ss_pred ccCcCCCCCCCHHHHHHHHHHHHHcCCCChhhhhhhhcCCCCHHHHHh
Q 019948 89 SRERKKGVPWTEEEHRMFLLGLQKLGKGDWRGIARNYVVSRTPTQVAS 136 (333)
Q Consensus 89 ~~~rkk~~~WTeEEH~~FL~GLekyGkGdWk~IA~~~V~TRTp~QV~S 136 (333)
+..+.....||.+|-.+|-.+|..+|- ++.-|+ +..+.|+..||+-
T Consensus 403 ~sk~~~~~~w~~se~e~fyka~~~~gs-~~slis-~l~p~R~rk~iK~ 448 (584)
T KOG2009|consen 403 YSKKLETDKWDASETELFYKALSERGS-DFSLIS-NLFPLRDRKQIKA 448 (584)
T ss_pred ccCccccCcccchhhHHhhhHHhhhcc-cccccc-cccccccHHHHHH
Confidence 455556789999999999999999998 999999 7999999999953
No 48
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=66.10 E-value=14 Score=35.96 Aligned_cols=55 Identities=22% Similarity=0.358 Sum_probs=40.0
Q ss_pred CCCCCHHHHHHHHHHHHH----cCCC-----Chhhhhh---hhcCCCCHHHHHhHHHHHHHHHhhhc
Q 019948 95 GVPWTEEEHRMFLLGLQK----LGKG-----DWRGIAR---NYVVSRTPTQVASHAQKYFIRQSNVS 149 (333)
Q Consensus 95 ~~~WTeEEH~~FL~GLek----yGkG-----dWk~IA~---~~V~TRTp~QV~SHAQKYF~r~~~~~ 149 (333)
...|+.+|-+.+|+...+ |..| .|..||+ ..---||+.||+.-..+...+.++.+
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~k~Yk~~k 120 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLKKKYKKEK 120 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHh
Confidence 479999999999988765 3344 5999986 35567999999887655544444443
No 49
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=65.35 E-value=7.7 Score=41.86 Aligned_cols=46 Identities=26% Similarity=0.499 Sum_probs=39.9
Q ss_pred CCCCCCHHHHHHHHHHHHHcCCCChhhhhhhhcCCCCHHHHHhHHHHHH
Q 019948 94 KGVPWTEEEHRMFLLGLQKLGKGDWRGIARNYVVSRTPTQVASHAQKYF 142 (333)
Q Consensus 94 k~~~WTeEEH~~FL~GLekyGkGdWk~IA~~~V~TRTp~QV~SHAQKYF 142 (333)
+.+.||+||.+....-....|. +|+.|++ .+ .|.|.-|+.+...|-
T Consensus 383 ~rg~wt~ee~eeL~~l~~~~g~-~W~~Ig~-~l-gr~P~~crd~wr~~~ 428 (607)
T KOG0051|consen 383 KRGKWTPEEEEELKKLVVEHGN-DWKEIGK-AL-GRMPMDCRDRWRQYV 428 (607)
T ss_pred ccCCCCcchHHHHHHHHHHhcc-cHHHHHH-HH-ccCcHHHHHHHHHhh
Confidence 5679999999999999999996 9999995 44 577999999998773
No 50
>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=62.85 E-value=24 Score=27.42 Aligned_cols=48 Identities=25% Similarity=0.385 Sum_probs=33.5
Q ss_pred CCCHHHHHHHHHHHHHc-------CCC-----Chhhhhhh----hcCCCCHHHHHhHHHHHHHHH
Q 019948 97 PWTEEEHRMFLLGLQKL-------GKG-----DWRGIARN----YVVSRTPTQVASHAQKYFIRQ 145 (333)
Q Consensus 97 ~WTeEEH~~FL~GLeky-------GkG-----dWk~IA~~----~V~TRTp~QV~SHAQKYF~r~ 145 (333)
.||+++.+.||+.|... +.| .|+.|++. +-...|..||++|.+ .+++.
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~-~lk~~ 64 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWK-TLKKD 64 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHH-HHHHH
Confidence 49999999999998553 122 57777653 345668999999975 43433
No 51
>PF06461 DUF1086: Domain of Unknown Function (DUF1086); InterPro: IPR009462 This entry represents several eukaryotic domains of unknown function, which are present in chromodomain helicase DNA binding proteins. This domain is often found in conjunction with IPR000330 from INTERPRO, IPR001650 from INTERPRO, IPR009463 from INTERPRO, IPR000953 from INTERPRO and IPR001965 from INTERPRO.
Probab=60.27 E-value=39 Score=30.61 Aligned_cols=49 Identities=12% Similarity=0.379 Sum_probs=40.7
Q ss_pred CCCHHHHHHHHHHHHHcCCC--ChhhhhhhhcCCCCHHHHHhHHHHHHHHHh
Q 019948 97 PWTEEEHRMFLLGLQKLGKG--DWRGIARNYVVSRTPTQVASHAQKYFIRQS 146 (333)
Q Consensus 97 ~WTeEEH~~FL~GLekyGkG--dWk~IA~~~V~TRTp~QV~SHAQKYF~r~~ 146 (333)
-++..+.+.||.++-+||-| +|+-+-+ -+.-||...++.|+--|+..+.
T Consensus 40 GFn~rQR~~Fln~vMR~G~~~f~~~w~~~-~Lr~Ks~~ei~aY~~LFm~HL~ 90 (145)
T PF06461_consen 40 GFNPRQRKAFLNAVMRYGMGAFDWKWFVP-RLRGKSEKEIRAYGSLFMRHLC 90 (145)
T ss_pred ccCHHHHHHHHHHHHHHCcCcccchHHhh-hhccccHHHHHHHHHHHHHHhc
Confidence 46888999999999999987 8888874 7999999999999964444443
No 52
>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=58.89 E-value=20 Score=27.96 Aligned_cols=48 Identities=17% Similarity=0.207 Sum_probs=29.3
Q ss_pred CCCCCHHHHHHHHHHHHHcCC--------CChhhhhhhhcCCCCHHHHHhHHHHHH
Q 019948 95 GVPWTEEEHRMFLLGLQKLGK--------GDWRGIARNYVVSRTPTQVASHAQKYF 142 (333)
Q Consensus 95 ~~~WTeEEH~~FL~GLekyGk--------GdWk~IA~~~V~TRTp~QV~SHAQKYF 142 (333)
+.+.|+||...++.-|..+.+ .-|+.+++.++...|-.=-+.|+-|.+
T Consensus 2 R~~fT~edD~~l~~~v~~~~~~~~~~~Gn~iwk~le~~~~t~HtwQSwR~Ry~K~L 57 (65)
T PF08914_consen 2 RTPFTEEDDAALLDYVKENERQGGSVSGNKIWKELEEKHPTRHTWQSWRDRYLKHL 57 (65)
T ss_dssp -----HHHHHHHHHHHHHT--STTTTTSSHHHHHHHHS-SSS--SHHHHHHHHHHT
T ss_pred CCCCCHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence 368999999999999966542 259999987776677666777665553
No 53
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=56.60 E-value=8.2 Score=31.93 Aligned_cols=33 Identities=30% Similarity=0.588 Sum_probs=25.3
Q ss_pred CCCCHHHHHHHHHHHHHc----CCC---ChhhhhhhhcCCC
Q 019948 96 VPWTEEEHRMFLLGLQKL----GKG---DWRGIARNYVVSR 129 (333)
Q Consensus 96 ~~WTeEEH~~FL~GLeky----GkG---dWk~IA~~~V~TR 129 (333)
..||+|+...+|+||-.| |.. ||...- .+|.-.
T Consensus 5 R~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~-~~vk~~ 44 (98)
T PF04504_consen 5 RLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFY-DFVKGS 44 (98)
T ss_pred CCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHH-HHHHHH
Confidence 479999999999999998 632 777766 455544
No 54
>PF08074 CHDCT2: CHDCT2 (NUC038) domain; InterPro: IPR012957 The CHDCT2 C-terminal domain is found in PHD/RING fingers and chromo domain-associated CHD-like helicases [].; GO: 0003677 DNA binding, 0005524 ATP binding, 0008270 zinc ion binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=53.84 E-value=7.4 Score=35.97 Aligned_cols=29 Identities=28% Similarity=0.573 Sum_probs=26.0
Q ss_pred CCCCCCHHHHHHHHHHHHHcCCCChhhhh
Q 019948 94 KGVPWTEEEHRMFLLGLQKLGKGDWRGIA 122 (333)
Q Consensus 94 k~~~WTeEEH~~FL~GLekyGkGdWk~IA 122 (333)
....|-.+-+-.+|.|+-++|.|.|..|.
T Consensus 2 ~~~iw~r~hdywll~gi~~hgy~rwqdi~ 30 (173)
T PF08074_consen 2 EYEIWHRRHDYWLLAGIVKHGYGRWQDIQ 30 (173)
T ss_pred hhhhhhhhhhHHHHhHHhhccchhHHHHh
Confidence 34689999999999999999999999995
No 55
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=53.32 E-value=8 Score=44.89 Aligned_cols=51 Identities=25% Similarity=0.583 Sum_probs=37.4
Q ss_pred CCCCCCHHHHHHHHHHHHHcCCCChhhhh---------hhh----cCCCCHHHHHhHHHHHHHHHhh
Q 019948 94 KGVPWTEEEHRMFLLGLQKLGKGDWRGIA---------RNY----VVSRTPTQVASHAQKYFIRQSN 147 (333)
Q Consensus 94 k~~~WTeEEH~~FL~GLekyGkGdWk~IA---------~~~----V~TRTp~QV~SHAQKYF~r~~~ 147 (333)
....|..+|...||.|+-+||.|.|..|- +.| ++ +..|.+..| .|...+..
T Consensus 1132 ~~~~W~~e~Ds~LLiGI~khGygswe~Ir~Dp~L~l~dKi~~~e~~P--~a~~L~~R~-~yLls~~~ 1195 (1373)
T KOG0384|consen 1132 WDCDWGSEDDSMLLIGIFKHGYGSWEAIRLDPDLGLTDKIFLVETVP--QAKHLQRRA-DYLLSLLR 1195 (1373)
T ss_pred cccCCCchhhhhHhhhhhhcccccHHHhccCccccchhhhcccccCC--chHHHHHHH-HHHHHHHh
Confidence 46789999999999999999999999992 111 22 245565555 57766653
No 56
>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=51.44 E-value=41 Score=34.11 Aligned_cols=52 Identities=21% Similarity=0.234 Sum_probs=39.9
Q ss_pred cCCCCCCCHHHHHHHHHHHHHcCCC---ChhhhhhhhcCCCCHHHHHhHHHHHHHH
Q 019948 92 RKKGVPWTEEEHRMFLLGLQKLGKG---DWRGIARNYVVSRTPTQVASHAQKYFIR 144 (333)
Q Consensus 92 rkk~~~WTeEEH~~FL~GLekyGkG---dWk~IA~~~V~TRTp~QV~SHAQKYF~r 144 (333)
......||..|.+.+|.+|+--... |...|++ .|..|+..||+..-|+.=.|
T Consensus 18 ~~gp~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~-~l~~Rs~aEI~~fl~~LK~r 72 (344)
T PF11035_consen 18 VTGPAAWSAREKRQLLRLLQARRGQPEPDAAELAK-ELPGRSEAEIRDFLQQLKGR 72 (344)
T ss_pred CCCcccCcHHHHHHHHHHHHHhcCCCCcCHHHHHh-hccCcCHHHHHHHHHHHHHH
Confidence 3446799999999999999975322 4456774 89999999999988766433
No 57
>PF02509 Rota_NS35: Rotavirus non-structural protein 35; InterPro: IPR003668 Rotavirus non-structural protein 2 (NSP2) is a basic protein which possesses RNA-binding activity and is essential for genome replication []. It may also be important for viral RNA packaging.; GO: 0003723 RNA binding, 0019079 viral genome replication; PDB: 2GU0_B 2R8F_A 2R7P_A 2R7C_A 1L9V_A 2R7J_A.
Probab=48.87 E-value=9.1 Score=37.95 Aligned_cols=53 Identities=21% Similarity=0.350 Sum_probs=36.5
Q ss_pred CCCCHHHHHHHHHHHHH---------cCCCChhhhhhhhcCCCCHHHHHhHHHHHHHHHhhhccccCCCc
Q 019948 96 VPWTEEEHRMFLLGLQK---------LGKGDWRGIARNYVVSRTPTQVASHAQKYFIRQSNVSRRKRRSS 156 (333)
Q Consensus 96 ~~WTeEEH~~FL~GLek---------yGkGdWk~IA~~~V~TRTp~QV~SHAQKYF~r~~~~~krkrR~S 156 (333)
.+=.+.+.+.|..-|+- +|+|.||-+- -.||++||...|...++-+|+++..+
T Consensus 195 ~pi~d~~~kelvAelrwqyNkFAvItHGkgHyRvV~--------ys~v~nHAdRv~at~ks~~K~~~~~~ 256 (316)
T PF02509_consen 195 TPISDSNVKELVAELRWQYNKFAVITHGKGHYRVVK--------YSSVANHADRVYATFKSNKKTGSQFS 256 (316)
T ss_dssp S---HHHHHHHHHHHHHHTTTEEEEESSSSCEEEEE--------GGGHHHHHHHHHHHHCTTCCTT----
T ss_pred CCCchHHHHHHHHHHHHhhcceEEEeccCceEEEEe--------hHHhhhhHHHHHHHHhcccccCCccc
Confidence 35556666677666653 6899999886 57999999999999998877655433
No 58
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=43.75 E-value=35 Score=36.24 Aligned_cols=49 Identities=4% Similarity=-0.120 Sum_probs=41.6
Q ss_pred CCCCCCHHHHHHHHHHHHHcCCCChhhhhhhhcCCCCHHHHHhHHHHHHHH
Q 019948 94 KGVPWTEEEHRMFLLGLQKLGKGDWRGIARNYVVSRTPTQVASHAQKYFIR 144 (333)
Q Consensus 94 k~~~WTeEEH~~FL~GLekyGkGdWk~IA~~~V~TRTp~QV~SHAQKYF~r 144 (333)
-+..||.+|..+.+.+|++||+ +...|+ -.|+-++-.|+..-.-.|-.|
T Consensus 368 ~n~~~~T~~~la~v~~I~~~~~-~~~pl~-wrik~t~cmee~e~l~~~~Rr 416 (534)
T KOG1194|consen 368 MNRCFDTPAALALIDNIKRKHH-MCVPLV-WRVKQTKCMEENEILNEEARR 416 (534)
T ss_pred hccccCcHHHHHHHHHHHHhcc-Ccchhh-hHhcCcchhhHHHHHHHHHHH
Confidence 3479999999999999999999 888888 689999999998766666333
No 59
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=38.33 E-value=16 Score=34.22 Aligned_cols=18 Identities=44% Similarity=1.066 Sum_probs=16.6
Q ss_pred CcccCCCCCCCCCCCCCC
Q 019948 2 TRRCSHCSHNGHNSRTCP 19 (333)
Q Consensus 2 ~R~CS~c~~~GHnsrtc~ 19 (333)
.++|--||.+||-.|-||
T Consensus 60 ~~~C~nCg~~GH~~~DCP 77 (190)
T COG5082 60 NPVCFNCGQNGHLRRDCP 77 (190)
T ss_pred ccccchhcccCcccccCC
Confidence 368999999999999999
No 60
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=37.86 E-value=16 Score=23.87 Aligned_cols=9 Identities=33% Similarity=1.025 Sum_probs=7.6
Q ss_pred CcccCCCCC
Q 019948 2 TRRCSHCSH 10 (333)
Q Consensus 2 ~R~CS~c~~ 10 (333)
+++|.|||+
T Consensus 14 ~~~Cp~CG~ 22 (26)
T PF10571_consen 14 AKFCPHCGY 22 (26)
T ss_pred cCcCCCCCC
Confidence 578999996
No 61
>CHL00112 rpl28 ribosomal protein L28; Provisional
Probab=34.10 E-value=20 Score=27.94 Aligned_cols=14 Identities=29% Similarity=0.719 Sum_probs=11.2
Q ss_pred CCcccCCCCC---CCCC
Q 019948 1 MTRRCSHCSH---NGHN 14 (333)
Q Consensus 1 m~R~CS~c~~---~GHn 14 (333)
|+|+|--||. .|+|
T Consensus 1 Msr~C~i~GK~~~~Gn~ 17 (63)
T CHL00112 1 MSKKCQLTGKKANNGYT 17 (63)
T ss_pred CCCeeccCCCcCccCce
Confidence 9999999994 5543
No 62
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=33.78 E-value=99 Score=24.57 Aligned_cols=42 Identities=24% Similarity=0.567 Sum_probs=26.5
Q ss_pred HHHHHHHHHHcC-------CCChhhhhhhhcCCC----CHHHHHhHHHHHHHHH
Q 019948 103 HRMFLLGLQKLG-------KGDWRGIARNYVVSR----TPTQVASHAQKYFIRQ 145 (333)
Q Consensus 103 H~~FL~GLekyG-------kGdWk~IA~~~V~TR----Tp~QV~SHAQKYF~r~ 145 (333)
+.+|.. +.+.| ...|+.|++.+--.. ...+++.|++||..-.
T Consensus 35 ~~Ly~~-V~~~GG~~~v~~~~~W~~Va~~lg~~~~~~~~~~~lk~~Y~k~L~~y 87 (93)
T smart00501 35 YRLYRL-VQERGGYDQVTKDKKWKEIARELGIPDTSTSAASSLRKHYERYLLPF 87 (93)
T ss_pred HHHHHH-HHHccCHHHHcCCCCHHHHHHHhCCCcccchHHHHHHHHHHHHhHHH
Confidence 455554 44444 358999997554333 3677888888885543
No 63
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=32.27 E-value=42 Score=36.20 Aligned_cols=44 Identities=25% Similarity=0.407 Sum_probs=37.6
Q ss_pred CCCCCHHHHHHHHHHHHHcCCCChhhhhhhhcCCCCHHHHHhHHHHH
Q 019948 95 GVPWTEEEHRMFLLGLQKLGKGDWRGIARNYVVSRTPTQVASHAQKY 141 (333)
Q Consensus 95 ~~~WTeEEH~~FL~GLekyGkGdWk~IA~~~V~TRTp~QV~SHAQKY 141 (333)
.+-|+.||.++.|.....+-. -|+-|+. +-.||..||--++.+-
T Consensus 59 ~tews~eederlLhlakl~p~-qwrtIa~--i~gr~~~qc~eRy~~l 102 (617)
T KOG0050|consen 59 KTEWSREEDERLLHLAKLEPT-QWRTIAD--IMGRTSQQCLERYNNL 102 (617)
T ss_pred hhhhhhhHHHHHHHHHHhcCC-ccchHHH--HhhhhHHHHHHHHHHH
Confidence 368999999999999999997 9999995 5669999997776544
No 64
>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=31.71 E-value=85 Score=24.57 Aligned_cols=42 Identities=26% Similarity=0.540 Sum_probs=25.6
Q ss_pred HHHHHHHHHHcC------CCChhhhhhhh-cC-CCC--HHHHHhHHHHHHHH
Q 019948 103 HRMFLLGLQKLG------KGDWRGIARNY-VV-SRT--PTQVASHAQKYFIR 144 (333)
Q Consensus 103 H~~FL~GLekyG------kGdWk~IA~~~-V~-TRT--p~QV~SHAQKYF~r 144 (333)
+.+|..-.+.-| .++|..|++.+ +. +.+ ..|++.|+.+|+..
T Consensus 39 ~~Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~~~~~~~~~L~~~Y~~~L~~ 90 (92)
T PF01388_consen 39 YKLYKAVMKRGGFDKVTKNKKWREVARKLGFPPSSTSAAQQLRQHYEKYLLP 90 (92)
T ss_dssp HHHHHHHHHHTSHHHHHHHTTHHHHHHHTTS-TTSCHHHHHHHHHHHHHTHH
T ss_pred HHHHHHHHhCcCcccCcccchHHHHHHHhCCCCCCCcHHHHHHHHHHHHhHh
Confidence 445554444434 35899999755 22 122 36899999888653
No 65
>PHA00442 host recBCD nuclease inhibitor
Probab=31.40 E-value=46 Score=25.97 Aligned_cols=23 Identities=30% Similarity=0.616 Sum_probs=20.2
Q ss_pred HHHHHHHHHHHHcCCCChhhhhh
Q 019948 101 EEHRMFLLGLQKLGKGDWRGIAR 123 (333)
Q Consensus 101 EEH~~FL~GLekyGkGdWk~IA~ 123 (333)
|-...||.+|+-.|-.+|.++..
T Consensus 26 ek~~~~L~~Lea~GVDNW~Gy~e 48 (59)
T PHA00442 26 EKDNEFLKALRACGVDNWDGYMD 48 (59)
T ss_pred HHhhHHHHHHHHcCCcchhhHHH
Confidence 55678999999999999999974
No 66
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=31.18 E-value=31 Score=29.61 Aligned_cols=18 Identities=44% Similarity=1.099 Sum_probs=11.1
Q ss_pred ccCCCCCCCCCCCCCCCC
Q 019948 4 RCSHCSHNGHNSRTCPNR 21 (333)
Q Consensus 4 ~CS~c~~~GHnsrtc~~~ 21 (333)
.|..|+..||-++.||..
T Consensus 54 ~C~~Cg~~GH~~~~Cp~~ 71 (148)
T PTZ00368 54 SCYNCGKTGHLSRECPEA 71 (148)
T ss_pred ccCCCCCcCcCcccCCCc
Confidence 466666666666666653
No 67
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=30.98 E-value=32 Score=29.53 Aligned_cols=19 Identities=58% Similarity=1.281 Sum_probs=17.3
Q ss_pred cccCCCCCCCCCCCCCCCC
Q 019948 3 RRCSHCSHNGHNSRTCPNR 21 (333)
Q Consensus 3 R~CS~c~~~GHnsrtc~~~ 21 (333)
+.|..|+..||.++.|+.+
T Consensus 78 ~~C~~Cg~~GH~~~~C~~~ 96 (148)
T PTZ00368 78 RSCYNCGQTGHISRECPNR 96 (148)
T ss_pred cccCcCCCCCcccccCCCc
Confidence 4699999999999999985
No 68
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=28.90 E-value=30 Score=36.94 Aligned_cols=18 Identities=33% Similarity=0.626 Sum_probs=10.8
Q ss_pred ccCCCCCCCCCCCCCCCC
Q 019948 4 RCSHCSHNGHNSRTCPNR 21 (333)
Q Consensus 4 ~CS~c~~~GHnsrtc~~~ 21 (333)
.|-+||-.||+++.|+..
T Consensus 287 ~c~~cg~~gH~~~dc~~~ 304 (554)
T KOG0119|consen 287 VCKICGPLGHISIDCKVN 304 (554)
T ss_pred cccccCCcccccccCCCc
Confidence 566666666666666544
No 69
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=28.42 E-value=27 Score=24.00 Aligned_cols=10 Identities=50% Similarity=1.351 Sum_probs=8.5
Q ss_pred cccCCCCCCC
Q 019948 3 RRCSHCSHNG 12 (333)
Q Consensus 3 R~CS~c~~~G 12 (333)
++|+.|+++|
T Consensus 4 ~~C~~C~~~~ 13 (33)
T PF08792_consen 4 KKCSKCGGNG 13 (33)
T ss_pred eEcCCCCCCe
Confidence 6899999886
No 70
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=27.70 E-value=71 Score=30.15 Aligned_cols=46 Identities=13% Similarity=0.161 Sum_probs=35.4
Q ss_pred CCCCCCHHHHHHHHHHHHHcC--CCChhhhh----hhhcCCCCHHHHHhHHH
Q 019948 94 KGVPWTEEEHRMFLLGLQKLG--KGDWRGIA----RNYVVSRTPTQVASHAQ 139 (333)
Q Consensus 94 k~~~WTeEEH~~FL~GLekyG--kGdWk~IA----~~~V~TRTp~QV~SHAQ 139 (333)
....||.+|.+++...-.... ...|++|- ..|-.+||+.+...|.|
T Consensus 72 ~kalfS~~EE~lL~~v~s~~~p~le~Fq~LL~~n~~vFh~sRTak~L~~HW~ 123 (199)
T PF13325_consen 72 SKALFSKEEEQLLGTVASSSQPSLETFQELLDKNRSVFHPSRTAKSLQDHWR 123 (199)
T ss_pred ccCCCCHHHHHHHHhhhhccCCcHHHHHHHHHhChhhhccccCHHHHHHHHH
Confidence 347999999999888765543 34677772 25889999999999987
No 71
>PF00191 Annexin: Annexin; InterPro: IPR018502 The annexins (or lipocortins) are a family of proteins that bind to phospholipids in a calcium-dependent manner []. They are distributed ubiquitously in different tissues and cell types of higher and lower eukaryotes, including mammals, fish, birds, Drosophila melanogaster (Fruit fly), Xenopus laevis (African clawed frog), Caenorhabditis elegans , Dictyostelium discoideum (Slime mold) and Neurospora crassa [, ]. Annexins are absent from yeasts and prokaryotes []. The plant annexins are somewhat distinct from those found in other taxa []. Most eukaryotic species have 1-20 annexin (ANX) genes. All annexins share a core domain made up of four similar repeats, each approximately 70 amino acids long []. Each individual annexin repeat (sometimes referred to as endonexin folds) is folded into five alpha-helices, and in turn are wound into a right-handed super-helix; they usually contain a characteristic 'type 2' motif for binding calcium ions with the sequence 'GxGT-[38 residues]-D/E'. Animal and fungal annexins also have variable amino-terminal domains. The core domains of most vertebrate annexins have been analysed by X-ray crystallography, revealing conservation of their secondary and tertiary structures despite only 45-55% amino-acid identity among individual members. The four repeats pack into a structure that resembles a flattened disc, with a slightly convex surface on which the Ca 2+ -binding loops are located and a concave surface at which the amino and carboxyl termini come into close apposition. Annexins are traditionally thought of as calcium-dependent phospholipid-binding proteins, but recent work suggests a more complex set of functions. The famiy has been linked with inhibition of phospholipase activity, exocytosis and endoctyosis, signal transduction, organisation of the extracellular matrix, resistance to reactive oxygen species and DNA replication [].; GO: 0005509 calcium ion binding, 0005544 calcium-dependent phospholipid binding; PDB: 1N44_A 1BC1_A 2IE6_A 2H0M_A 1A8B_A 2H0K_A 1BCW_A 1BCZ_A 1N42_A 1BC0_A ....
Probab=27.58 E-value=66 Score=23.43 Aligned_cols=40 Identities=20% Similarity=0.279 Sum_probs=31.8
Q ss_pred HHHHHHHHHcCCCChhhhhhhhcCCCCHHHHHhHHHHHHHHH
Q 019948 104 RMFLLGLQKLGKGDWRGIARNYVVSRTPTQVASHAQKYFIRQ 145 (333)
Q Consensus 104 ~~FL~GLekyGkGdWk~IA~~~V~TRTp~QV~SHAQKYF~r~ 145 (333)
+++-.|++..|..++.-|. .+.+|++.|++.=.+.|...-
T Consensus 4 ~~l~~a~~~~g~de~~li~--Il~~rs~~ql~~i~~~Y~~~~ 43 (66)
T PF00191_consen 4 ELLHAALKGWGTDEDVLIE--ILCTRSPAQLRAIKQAYKKKY 43 (66)
T ss_dssp HHHHHHHSSSSSTHHHHHH--HHHHSTHHHHHHHHHHHHHHH
T ss_pred HHHHHHccCCCCChhHhhh--HHhhhcccccceeehhhhhhh
Confidence 4778889999976666665 688999999999888885544
No 72
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=27.19 E-value=37 Score=24.66 Aligned_cols=19 Identities=42% Similarity=1.055 Sum_probs=17.2
Q ss_pred CcccCCCCCCCCCCCCCCC
Q 019948 2 TRRCSHCSHNGHNSRTCPN 20 (333)
Q Consensus 2 ~R~CS~c~~~GHnsrtc~~ 20 (333)
..+|-.|+..||=..-|++
T Consensus 4 ~~~CqkC~~~GH~tyeC~~ 22 (42)
T PF13917_consen 4 RVRCQKCGQKGHWTYECPN 22 (42)
T ss_pred CCcCcccCCCCcchhhCCC
Confidence 3689999999999999995
No 73
>PRK00359 rpmB 50S ribosomal protein L28; Reviewed
Probab=26.72 E-value=32 Score=27.58 Aligned_cols=10 Identities=30% Similarity=0.617 Sum_probs=9.2
Q ss_pred CCcccCCCCC
Q 019948 1 MTRRCSHCSH 10 (333)
Q Consensus 1 m~R~CS~c~~ 10 (333)
|+|+|--||.
T Consensus 1 Msr~C~i~GK 10 (76)
T PRK00359 1 MSRVCEITGK 10 (76)
T ss_pred CCCccccCCC
Confidence 9999999994
No 74
>PF05634 APO_RNA-bind: APO RNA-binding; InterPro: IPR008512 This family consists of plant APO (accumulation of photosystem 1) proteins.
Probab=26.71 E-value=36 Score=32.33 Aligned_cols=19 Identities=37% Similarity=0.812 Sum_probs=15.6
Q ss_pred cccCCCC-----CCCCCCCCCCCC
Q 019948 3 RRCSHCS-----HNGHNSRTCPNR 21 (333)
Q Consensus 3 R~CS~c~-----~~GHnsrtc~~~ 21 (333)
..|.+|+ .-||.-|||...
T Consensus 99 ~~C~~C~EVHVG~~GH~irtC~g~ 122 (204)
T PF05634_consen 99 KACGYCPEVHVGPVGHKIRTCGGF 122 (204)
T ss_pred eecCCCCCeEECCCcccccccCCC
Confidence 5799994 789999999753
No 75
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=26.51 E-value=32 Score=23.84 Aligned_cols=19 Identities=32% Similarity=0.887 Sum_probs=16.8
Q ss_pred cccCCCCCCCCCCCCCCCC
Q 019948 3 RRCSHCSHNGHNSRTCPNR 21 (333)
Q Consensus 3 R~CS~c~~~GHnsrtc~~~ 21 (333)
..|--|+..||--+.||..
T Consensus 9 Y~C~~C~~~GH~i~dCP~~ 27 (32)
T PF13696_consen 9 YVCHRCGQKGHWIQDCPTN 27 (32)
T ss_pred CEeecCCCCCccHhHCCCC
Confidence 4699999999999999963
No 76
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=24.69 E-value=54 Score=32.86 Aligned_cols=57 Identities=26% Similarity=0.366 Sum_probs=41.1
Q ss_pred ccCcCCCCCCCHH------HHHHHHHHHHHcCCCChhhhhhhhcCCCCHHHHHhHHHHHHHHHhhhcc
Q 019948 89 SRERKKGVPWTEE------EHRMFLLGLQKLGKGDWRGIARNYVVSRTPTQVASHAQKYFIRQSNVSR 150 (333)
Q Consensus 89 ~~~rkk~~~WTeE------EH~~FL~GLekyGkGdWk~IA~~~V~TRTp~QV~SHAQKYF~r~~~~~k 150 (333)
++-|||+.+.|+. -.-+|=.=|.|=-| ..|++ .-.=|-+||+.-.|+=-+|.|++.|
T Consensus 233 ~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR---~ElSr--~lNLTeRQVKIWFQNRRMK~KK~~r 295 (308)
T KOG0487|consen 233 RRGRKKRCPYTKHQTLELEKEFLFNMYITKEKR---LELSR--TLNLTERQVKIWFQNRRMKEKKVNR 295 (308)
T ss_pred cccccccCCchHHHHHHHHHHHHHHHHHhHHHH---HHHHH--hcccchhheeeeehhhhhHHhhhhh
Confidence 7889999999983 23344455555444 77886 5567899999988877777776664
No 77
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=24.58 E-value=36 Score=21.50 Aligned_cols=19 Identities=32% Similarity=0.903 Sum_probs=12.7
Q ss_pred ccCCCC-CCCCCCCCCCCCc
Q 019948 4 RCSHCS-HNGHNSRTCPNRG 22 (333)
Q Consensus 4 ~CS~c~-~~GHnsrtc~~~g 22 (333)
+|.+|| .+=-+++.|+.=|
T Consensus 1 ~Cp~CG~~~~~~~~fC~~CG 20 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKFCPNCG 20 (23)
T ss_pred CCcccCCCCCCcCcchhhhC
Confidence 588888 4445677777644
No 78
>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=24.29 E-value=43 Score=31.53 Aligned_cols=18 Identities=39% Similarity=1.056 Sum_probs=14.9
Q ss_pred ccCCCCCCCCCCCCCCCC
Q 019948 4 RCSHCSHNGHNSRTCPNR 21 (333)
Q Consensus 4 ~CS~c~~~GHnsrtc~~~ 21 (333)
+|-.||..||-++-|+..
T Consensus 145 ~Cy~Cg~~GH~s~~C~~~ 162 (261)
T KOG4400|consen 145 KCYSCGEQGHISDDCPEN 162 (261)
T ss_pred ccCCCCcCCcchhhCCCC
Confidence 488899999999999854
No 79
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=23.40 E-value=49 Score=21.87 Aligned_cols=25 Identities=32% Similarity=0.768 Sum_probs=12.7
Q ss_pred CcccCCCCC-----CCCCCCCCCCCceEEe
Q 019948 2 TRRCSHCSH-----NGHNSRTCPNRGVKIF 26 (333)
Q Consensus 2 ~R~CS~c~~-----~GHnsrtc~~~g~~LF 26 (333)
.|-|+.||. .+--+|-||.=|...|
T Consensus 3 ~rfC~~CG~~t~~~~~g~~r~C~~Cg~~~y 32 (32)
T PF09297_consen 3 HRFCGRCGAPTKPAPGGWARRCPSCGHEHY 32 (32)
T ss_dssp TSB-TTT--BEEE-SSSS-EEESSSS-EE-
T ss_pred CcccCcCCccccCCCCcCEeECCCCcCEeC
Confidence 367888883 4445677777666554
No 80
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=21.66 E-value=48 Score=35.52 Aligned_cols=24 Identities=33% Similarity=0.872 Sum_probs=20.3
Q ss_pred CcccCCCCCCCCCCCCCCCCceEEe
Q 019948 2 TRRCSHCSHNGHNSRTCPNRGVKIF 26 (333)
Q Consensus 2 ~R~CS~c~~~GHnsrtc~~~g~~LF 26 (333)
.|.|.-||.-||..--||+| +-+|
T Consensus 261 ~~~c~~cg~~~H~q~~cp~r-~~~~ 284 (554)
T KOG0119|consen 261 NRACRNCGSTGHKQYDCPGR-IPNT 284 (554)
T ss_pred cccccccCCCccccccCCcc-cccc
Confidence 37999999999999999999 4433
Done!