Query 022223
Match_columns 300
No_of_seqs 217 out of 557
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 08:57:55 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022223.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022223hhsearch_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 99.7 2.9E-18 6.2E-23 127.1 5.9 53 90-142 1-57 (57)
2 PF00249 Myb_DNA-binding: Myb- 99.5 2.4E-14 5.2E-19 100.3 5.3 45 93-138 2-47 (48)
3 cd00167 SANT 'SWI3, ADA2, N-Co 99.2 2.7E-11 5.8E-16 79.7 5.3 45 94-139 1-45 (45)
4 smart00717 SANT SANT SWI3, AD 99.2 3.7E-11 8.1E-16 79.9 5.8 46 93-139 2-47 (49)
5 PF13921 Myb_DNA-bind_6: Myb-l 98.9 1.1E-09 2.5E-14 78.9 4.5 43 95-139 1-43 (60)
6 KOG0457 Histone acetyltransfer 98.9 1.1E-09 2.3E-14 108.5 5.3 50 93-143 73-122 (438)
7 PLN03212 Transcription repress 98.7 2E-08 4.4E-13 93.8 5.7 50 90-140 23-73 (249)
8 PLN03091 hypothetical protein; 98.6 2.8E-08 6.1E-13 99.0 5.0 51 88-139 10-61 (459)
9 KOG0048 Transcription factor, 98.4 3.4E-07 7.4E-12 83.2 4.1 48 92-140 9-57 (238)
10 COG5114 Histone acetyltransfer 98.3 5.3E-07 1.2E-11 87.8 4.4 49 93-142 64-112 (432)
11 KOG0724 Zuotin and related mol 98.3 3.4E-07 7.4E-12 85.8 2.7 78 85-162 157-239 (335)
12 KOG4329 DNA-binding protein [G 98.3 2.9E-06 6.2E-11 83.7 8.4 53 90-146 275-327 (445)
13 PLN03212 Transcription repress 98.2 5.1E-06 1.1E-10 77.9 8.9 49 91-141 77-125 (249)
14 COG5259 RSC8 RSC chromatin rem 98.1 1.8E-06 4E-11 86.9 4.4 40 93-134 280-319 (531)
15 PLN03091 hypothetical protein; 98.1 6.7E-06 1.4E-10 82.4 6.7 49 92-142 67-115 (459)
16 KOG1279 Chromatin remodeling f 98.0 8.7E-06 1.9E-10 82.7 5.2 42 91-134 252-293 (506)
17 KOG0048 Transcription factor, 97.6 0.00017 3.7E-09 65.7 6.5 48 90-139 60-107 (238)
18 KOG0049 Transcription factor, 97.5 0.00012 2.6E-09 76.9 5.7 52 91-143 359-410 (939)
19 PLN03162 golden-2 like transcr 97.1 0.00091 2E-08 66.8 6.4 58 87-145 232-293 (526)
20 KOG0049 Transcription factor, 96.8 0.0014 3E-08 69.2 4.7 47 91-138 411-457 (939)
21 KOG3554 Histone deacetylase co 96.7 0.0019 4.2E-08 66.1 4.6 52 88-143 281-332 (693)
22 KOG4167 Predicted DNA-binding 96.2 0.0061 1.3E-07 65.0 5.2 49 92-145 619-667 (907)
23 KOG0050 mRNA splicing protein 95.9 0.0072 1.6E-07 62.4 3.7 50 90-140 5-54 (617)
24 KOG4468 Polycomb-group transcr 95.7 0.015 3.2E-07 61.1 5.0 51 92-143 88-147 (782)
25 COG5118 BDP1 Transcription ini 95.4 0.026 5.5E-07 56.9 5.4 50 83-134 356-405 (507)
26 PF13837 Myb_DNA-bind_4: Myb/S 95.4 0.036 7.9E-07 42.1 5.1 52 93-145 2-70 (90)
27 PF00098 zf-CCHC: Zinc knuckle 94.6 0.029 6.4E-07 33.3 2.1 17 3-19 1-17 (18)
28 PLN03142 Probable chromatin-re 94.5 0.055 1.2E-06 59.6 5.4 49 94-143 826-874 (1033)
29 PF09111 SLIDE: SLIDE; InterP 94.5 0.088 1.9E-06 44.5 5.5 51 90-141 47-111 (118)
30 KOG0724 Zuotin and related mol 94.4 0.0092 2E-07 56.2 -0.5 49 94-144 55-103 (335)
31 smart00426 TEA TEA domain. 94.4 0.035 7.6E-07 43.5 2.7 43 93-136 4-66 (68)
32 PF14392 zf-CCHC_4: Zinc knuck 93.6 0.026 5.7E-07 40.3 0.6 19 1-19 30-48 (49)
33 KOG0051 RNA polymerase I termi 93.5 0.089 1.9E-06 55.2 4.5 52 91-143 435-511 (607)
34 KOG0051 RNA polymerase I termi 93.2 0.1 2.3E-06 54.7 4.5 50 91-143 383-432 (607)
35 PF15288 zf-CCHC_6: Zinc knuck 93.0 0.049 1.1E-06 38.8 1.2 20 3-22 2-23 (40)
36 COG5147 REB1 Myb superfamily p 92.6 0.071 1.5E-06 54.9 2.3 54 89-143 17-70 (512)
37 KOG1194 Predicted DNA-binding 92.1 0.23 4.9E-06 51.1 5.1 42 92-135 187-228 (534)
38 KOG3841 TEF-1 and related tran 90.8 0.34 7.3E-06 48.9 4.7 48 90-138 74-141 (455)
39 PF08914 Myb_DNA-bind_2: Rap1 90.8 0.49 1.1E-05 36.3 4.6 50 92-141 2-59 (65)
40 PF01285 TEA: TEA/ATTS domain 90.1 0.31 6.8E-06 49.2 3.8 48 90-138 47-112 (431)
41 PF13873 Myb_DNA-bind_5: Myb/S 89.2 1.1 2.3E-05 33.8 5.2 49 93-141 3-71 (78)
42 PLN03142 Probable chromatin-re 87.0 1.3 2.8E-05 49.3 6.3 51 92-142 926-987 (1033)
43 KOG0050 mRNA splicing protein 86.5 0.72 1.6E-05 48.2 3.8 45 91-138 58-102 (617)
44 COG5147 REB1 Myb superfamily p 86.2 1.1 2.4E-05 46.5 4.9 53 90-144 70-122 (512)
45 KOG4282 Transcription factor G 85.0 1.7 3.6E-05 41.5 5.3 57 92-148 54-122 (345)
46 smart00343 ZnF_C2HC zinc finge 84.8 0.5 1.1E-05 29.5 1.1 17 4-20 1-17 (26)
47 PF12776 Myb_DNA-bind_3: Myb/S 84.0 2.9 6.2E-05 32.1 5.3 45 94-138 1-61 (96)
48 TIGR02894 DNA_bind_RsfA transc 82.8 1.3 2.8E-05 39.8 3.3 49 92-142 4-58 (161)
49 PRK13923 putative spore coat p 76.1 3 6.5E-05 37.8 3.5 47 92-140 5-57 (170)
50 KOG0385 Chromatin remodeling c 73.8 4.9 0.00011 44.3 4.9 52 92-145 795-846 (971)
51 PF06461 DUF1086: Domain of Un 69.1 13 0.00028 33.2 5.6 50 95-145 41-92 (145)
52 KOG0384 Chromodomain-helicase 68.6 3 6.5E-05 47.5 2.0 54 91-145 1132-1196(1373)
53 KOG2009 Transcription initiati 67.8 5.4 0.00012 42.2 3.5 49 83-133 400-448 (584)
54 PF04504 DUF573: Protein of un 66.4 12 0.00027 30.4 4.7 39 94-133 6-56 (98)
55 COG5082 AIR1 Arginine methyltr 65.2 3.4 7.4E-05 38.1 1.4 18 2-19 97-114 (190)
56 PF08074 CHDCT2: CHDCT2 (NUC03 57.8 6.3 0.00014 36.0 1.7 29 91-119 2-30 (173)
57 KOG1194 Predicted DNA-binding 55.4 18 0.00039 37.8 4.6 49 92-142 369-417 (534)
58 PF11035 SnAPC_2_like: Small n 53.4 35 0.00077 34.1 6.1 49 90-139 19-70 (344)
59 PF13325 MCRS_N: N-terminal re 52.2 18 0.00039 33.6 3.7 48 90-137 71-124 (199)
60 PF13248 zf-ribbon_3: zinc-rib 46.7 13 0.00029 23.4 1.4 19 1-19 1-20 (26)
61 PF14952 zf-tcix: Putative tre 46.2 12 0.00027 27.3 1.4 18 3-20 12-30 (44)
62 PHA00442 host recBCD nuclease 44.6 23 0.0005 27.3 2.6 24 96-119 24-47 (59)
63 PF09420 Nop16: Ribosome bioge 44.1 65 0.0014 28.1 5.8 48 90-138 112-162 (164)
64 PF10571 UPF0547: Uncharacteri 42.6 12 0.00027 24.1 0.8 10 2-11 14-23 (26)
65 PF01388 ARID: ARID/BRIGHT DNA 38.6 77 0.0017 24.4 4.9 28 113-141 58-90 (92)
66 COG5082 AIR1 Arginine methyltr 38.2 16 0.00036 33.7 1.2 18 2-19 60-77 (190)
67 smart00501 BRIGHT BRIGHT, ARID 36.4 1E+02 0.0023 24.0 5.4 31 113-144 54-89 (93)
68 PF08281 Sigma70_r4_2: Sigma-7 36.0 1.3E+02 0.0028 20.8 5.2 37 98-137 13-49 (54)
69 PTZ00368 universal minicircle 35.8 31 0.00067 29.1 2.4 19 3-21 53-71 (148)
70 PF13404 HTH_AsnC-type: AsnC-t 33.0 1.3E+02 0.0029 20.9 4.9 38 98-137 3-40 (42)
71 KOG1878 Nuclear receptor coreg 31.6 7.4 0.00016 45.2 -2.5 47 86-134 219-265 (1672)
72 PF00191 Annexin: Annexin; In 29.7 63 0.0014 23.1 2.9 41 101-143 4-44 (66)
73 PF08792 A2L_zn_ribbon: A2L zi 29.0 25 0.00055 23.8 0.7 10 3-12 4-13 (33)
74 KOG0119 Splicing factor 1/bran 29.0 28 0.00061 36.7 1.3 19 3-21 286-304 (554)
75 PF05634 APO_RNA-bind: APO RNA 28.7 39 0.00085 31.7 2.0 20 3-22 99-123 (204)
76 PF06397 Desulfoferrod_N: Desu 28.1 20 0.00042 25.1 -0.0 8 4-11 8-15 (36)
77 PRK11179 DNA-binding transcrip 26.7 1.3E+02 0.0027 25.6 4.6 38 97-136 8-45 (153)
78 PTZ00368 universal minicircle 26.0 42 0.00092 28.3 1.7 17 3-19 28-44 (148)
79 PF13696 zf-CCHC_2: Zinc knuck 24.6 36 0.00078 23.3 0.8 18 3-20 9-26 (32)
80 PLN00111 accumulation of photo 24.5 48 0.001 33.9 2.0 20 3-22 121-145 (399)
81 KOG4400 E3 ubiquitin ligase in 24.1 39 0.00084 31.3 1.2 18 4-21 145-162 (261)
82 TIGR02937 sigma70-ECF RNA poly 23.5 2.5E+02 0.0054 21.5 5.4 45 94-142 110-154 (158)
83 smart00344 HTH_ASNC helix_turn 23.5 1.7E+02 0.0037 22.7 4.6 38 97-136 2-39 (108)
84 PF13917 zf-CCHC_3: Zinc knuck 22.8 48 0.001 23.8 1.2 19 2-20 4-22 (42)
85 PRK11169 leucine-responsive tr 22.6 1.5E+02 0.0034 25.4 4.5 39 97-137 13-51 (164)
86 PF06170 DUF983: Protein of un 22.3 38 0.00083 27.3 0.7 16 1-16 7-22 (86)
87 PF02954 HTH_8: Bacterial regu 22.3 1.8E+02 0.0039 19.8 4.0 25 98-124 5-29 (42)
88 KOG2656 DNA methyltransferase 21.5 1E+02 0.0022 31.9 3.6 43 93-136 131-178 (445)
89 CHL00112 rpl28 ribosomal prote 20.4 46 0.00099 25.6 0.7 12 1-12 1-12 (63)
90 PHA03074 late transcription fa 20.4 44 0.00096 31.7 0.8 13 3-15 5-17 (225)
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=99.74 E-value=2.9e-18 Score=127.14 Aligned_cols=53 Identities=49% Similarity=0.691 Sum_probs=47.6
Q ss_pred cCCCccCHHHHHHHHHHHHHcCCCCH---HhHhhhhcCCC-CHHHHHHHHHHHHHHh
Q 022223 90 KRGVPWTEDEHRLFLLGLQKVGKGDW---RGISRNFVKTR-TPTQVASHAQKYFLRR 142 (300)
Q Consensus 90 Kkg~~WTeEEh~lFLegLekyGkGdW---k~IAr~~V~TR-T~~QVrSHAQKYF~r~ 142 (300)
|++..||+|||++||+||+.||.|+| +.|++.++.++ |+.||+||+||||+++
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 45678999999999999999999999 99995556688 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=99.51 E-value=2.4e-14 Score=100.31 Aligned_cols=45 Identities=36% Similarity=0.615 Sum_probs=40.8
Q ss_pred CccCHHHHHHHHHHHHHcCCCCHHhHhhhhcC-CCCHHHHHHHHHHH
Q 022223 93 VPWTEDEHRLFLLGLQKVGKGDWRGISRNFVK-TRTPTQVASHAQKY 138 (300)
Q Consensus 93 ~~WTeEEh~lFLegLekyGkGdWk~IAr~~V~-TRT~~QVrSHAQKY 138 (300)
.+||+||+++|++||++||.++|+.|| .+|+ +||..||++|+++|
T Consensus 2 ~~Wt~eE~~~l~~~v~~~g~~~W~~Ia-~~~~~~Rt~~qc~~~~~~~ 47 (48)
T PF00249_consen 2 GPWTEEEDEKLLEAVKKYGKDNWKKIA-KRMPGGRTAKQCRSRYQNL 47 (48)
T ss_dssp -SS-HHHHHHHHHHHHHSTTTHHHHHH-HHHSSSSTHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHhCCcHHHHHH-HHcCCCCCHHHHHHHHHhh
Confidence 469999999999999999997799999 6888 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=99.21 E-value=2.7e-11 Score=79.73 Aligned_cols=45 Identities=36% Similarity=0.701 Sum_probs=41.5
Q ss_pred ccCHHHHHHHHHHHHHcCCCCHHhHhhhhcCCCCHHHHHHHHHHHH
Q 022223 94 PWTEDEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASHAQKYF 139 (300)
Q Consensus 94 ~WTeEEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSHAQKYF 139 (300)
+||+||+++|+.++.+||.++|..|| .++++||..||+.|+++++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia-~~~~~rs~~~~~~~~~~~~ 45 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIA-KELPGRTPKQCRERWRNLL 45 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHH-hHcCCCCHHHHHHHHHHhC
Confidence 59999999999999999966999999 7999999999999987653
No 4
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.20 E-value=3.7e-11 Score=79.88 Aligned_cols=46 Identities=28% Similarity=0.499 Sum_probs=42.1
Q ss_pred CccCHHHHHHHHHHHHHcCCCCHHhHhhhhcCCCCHHHHHHHHHHHH
Q 022223 93 VPWTEDEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASHAQKYF 139 (300)
Q Consensus 93 ~~WTeEEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSHAQKYF 139 (300)
..||+||+.+|+.++.+||.++|..|| .++++||..||+.++.+++
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 479999999999999999966999999 7999999999999987654
No 5
>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=98.93 E-value=1.1e-09 Score=78.86 Aligned_cols=43 Identities=33% Similarity=0.661 Sum_probs=36.7
Q ss_pred cCHHHHHHHHHHHHHcCCCCHHhHhhhhcCCCCHHHHHHHHHHHH
Q 022223 95 WTEDEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASHAQKYF 139 (300)
Q Consensus 95 WTeEEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSHAQKYF 139 (300)
||+||++++++++++||. +|..|| .++++||+.||+.|+.+++
T Consensus 1 WT~eEd~~L~~~~~~~g~-~W~~Ia-~~l~~Rt~~~~~~r~~~~l 43 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGN-DWKKIA-EHLGNRTPKQCRNRWRNHL 43 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS--HHHHH-HHSTTS-HHHHHHHHHHTT
T ss_pred CCHHHHHHHHHHHHHHCc-CHHHHH-HHHCcCCHHHHHHHHHHHC
Confidence 999999999999999996 999999 6889999999999987643
No 6
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=98.92 E-value=1.1e-09 Score=108.45 Aligned_cols=50 Identities=30% Similarity=0.552 Sum_probs=47.5
Q ss_pred CccCHHHHHHHHHHHHHcCCCCHHhHhhhhcCCCCHHHHHHHHHHHHHHhh
Q 022223 93 VPWTEDEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASHAQKYFLRRF 143 (300)
Q Consensus 93 ~~WTeEEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSHAQKYF~r~~ 143 (300)
..||.+|+.+||+|++.||-|||..|| ++|||||.++|+.|+.|+|++..
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 469999999999999999999999999 89999999999999999999765
No 7
>PLN03212 Transcription repressor MYB5; Provisional
Probab=98.70 E-value=2e-08 Score=93.76 Aligned_cols=50 Identities=22% Similarity=0.447 Sum_probs=44.5
Q ss_pred cCCCccCHHHHHHHHHHHHHcCCCCHHhHhhhhc-CCCCHHHHHHHHHHHHH
Q 022223 90 KRGVPWTEDEHRLFLLGLQKVGKGDWRGISRNFV-KTRTPTQVASHAQKYFL 140 (300)
Q Consensus 90 Kkg~~WTeEEh~lFLegLekyGkGdWk~IAr~~V-~TRT~~QVrSHAQKYF~ 140 (300)
-+..+||+||++++++++++||.++|+.|| ..+ ..||..|||.+|.+|+.
T Consensus 23 lKRg~WT~EEDe~L~~lV~kyG~~nW~~IA-k~~g~gRT~KQCReRW~N~L~ 73 (249)
T PLN03212 23 MKRGPWTVEEDEILVSFIKKEGEGRWRSLP-KRAGLLRCGKSCRLRWMNYLR 73 (249)
T ss_pred CcCCCCCHHHHHHHHHHHHHhCcccHHHHH-HhhhcCCCcchHHHHHHHhhc
Confidence 345679999999999999999998999999 566 58999999999999973
No 8
>PLN03091 hypothetical protein; Provisional
Probab=98.64 E-value=2.8e-08 Score=99.04 Aligned_cols=51 Identities=20% Similarity=0.389 Sum_probs=44.5
Q ss_pred cccCCCccCHHHHHHHHHHHHHcCCCCHHhHhhhhcC-CCCHHHHHHHHHHHH
Q 022223 88 ERKRGVPWTEDEHRLFLLGLQKVGKGDWRGISRNFVK-TRTPTQVASHAQKYF 139 (300)
Q Consensus 88 ~rKkg~~WTeEEh~lFLegLekyGkGdWk~IAr~~V~-TRT~~QVrSHAQKYF 139 (300)
.+.+...||+||++++++++++||.++|..|| .+++ .||.+|||.+|.+|+
T Consensus 10 qklrKg~WTpEEDe~L~~~V~kyG~~nWs~IA-k~~g~gRT~KQCRERW~NyL 61 (459)
T PLN03091 10 QKLRKGLWSPEEDEKLLRHITKYGHGCWSSVP-KQAGLQRCGKSCRLRWINYL 61 (459)
T ss_pred CCCcCCCCCHHHHHHHHHHHHHhCcCCHHHHh-hhhccCcCcchHhHHHHhcc
Confidence 34455679999999999999999999999999 5665 899999999998775
No 9
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=98.35 E-value=3.4e-07 Score=83.23 Aligned_cols=48 Identities=17% Similarity=0.314 Sum_probs=44.7
Q ss_pred CCccCHHHHHHHHHHHHHcCCCCHHhHhhhhcC-CCCHHHHHHHHHHHHH
Q 022223 92 GVPWTEDEHRLFLLGLQKVGKGDWRGISRNFVK-TRTPTQVASHAQKYFL 140 (300)
Q Consensus 92 g~~WTeEEh~lFLegLekyGkGdWk~IAr~~V~-TRT~~QVrSHAQKYF~ 140 (300)
..+||.||++++.+.|++||.|+|..|+ +..+ -|+.+|||.+|-+|+.
T Consensus 9 kGpWt~EED~~L~~~V~~~G~~~W~~i~-k~~gl~R~GKSCRlRW~NyLr 57 (238)
T KOG0048|consen 9 KGPWTQEEDLTQIRSIKSFGKHNGTALP-KLAGLRRCGKSCRLRWTNYLR 57 (238)
T ss_pred CCCCChHHHHHHHHHHHHhCCCCcchhh-hhcCCCccchHHHHHhhcccC
Confidence 4789999999999999999999999999 6888 8999999999998853
No 10
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=98.31 E-value=5.3e-07 Score=87.77 Aligned_cols=49 Identities=27% Similarity=0.603 Sum_probs=46.2
Q ss_pred CccCHHHHHHHHHHHHHcCCCCHHhHhhhhcCCCCHHHHHHHHHHHHHHh
Q 022223 93 VPWTEDEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASHAQKYFLRR 142 (300)
Q Consensus 93 ~~WTeEEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSHAQKYF~r~ 142 (300)
.-|+.+|+.+|+++++..|-|+|..|| .|||+|+..+|++|+-|||...
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 459999999999999999999999999 8999999999999999999853
No 11
>KOG0724 consensus Zuotin and related molecular chaperones (DnaJ superfamily), contains DNA-binding domains [Posttranslational modification, protein turnover, chaperones]
Probab=98.29 E-value=3.4e-07 Score=85.76 Aligned_cols=78 Identities=50% Similarity=0.695 Sum_probs=72.8
Q ss_pred CCccccCCCccCHHHHHHHHHHHHHcCCCCHHhHhhhhcCCCCHHHHHHHHH-----HHHHHhhhcccccCCCccccccc
Q 022223 85 RSRERKRGVPWTEDEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASHAQ-----KYFLRRFNQNKRRRRSSLFDITA 159 (300)
Q Consensus 85 ~~~~rKkg~~WTeEEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSHAQ-----KYF~r~~~~~k~krr~Sl~dit~ 159 (300)
....++++..|++.+|.+|+.++.+||+++|..|+++++.+|++.|+.+|+| +|+.+.....+.++|.+++|++.
T Consensus 157 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~s~a~~~~~~~~~~~~~~~~~~~~~~s~~~~~~ 236 (335)
T KOG0724|consen 157 AEELRRKGTPVTERERKLVLLALKKDGKIDWRKISQNVEKERTPEQVASHAQEKAFEKALARQKSGEEEKRRKSIEDITT 236 (335)
T ss_pred hhhhhhccchhHHHHHHHHHhhhcccccccceechhhhhhhhcchhhhhhhhhhhhHHHHHHHhhhccccccchhhhhhc
Confidence 3456778999999999999999999999999999999999999999999999 99999999999999999999988
Q ss_pred ccc
Q 022223 160 SST 162 (300)
Q Consensus 160 ~~~ 162 (300)
...
T Consensus 237 ~~~ 239 (335)
T KOG0724|consen 237 ASE 239 (335)
T ss_pred cch
Confidence 765
No 12
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=98.27 E-value=2.9e-06 Score=83.75 Aligned_cols=53 Identities=32% Similarity=0.496 Sum_probs=47.1
Q ss_pred cCCCccCHHHHHHHHHHHHHcCCCCHHhHhhhhcCCCCHHHHHHHHHHHHHHhhhcc
Q 022223 90 KRGVPWTEDEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASHAQKYFLRRFNQN 146 (300)
Q Consensus 90 Kkg~~WTeEEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSHAQKYF~r~~~~~ 146 (300)
.....|++||++.|.+||+.||| ||..|.++.|.||+..+|..+ ||++.+...
T Consensus 275 d~l~~wsEeEcr~FEegl~~yGK-DF~lIr~nkvrtRsvgElVey---YYlWKkSer 327 (445)
T KOG4329|consen 275 DDLSGWSEEECRNFEEGLELYGK-DFHLIRANKVRTRSVGELVEY---YYLWKKSER 327 (445)
T ss_pred cccccCCHHHHHHHHHHHHHhcc-cHHHHHhcccccchHHHHHHH---HHHhhcCcc
Confidence 34678999999999999999999 999999999999999999877 788776653
No 13
>PLN03212 Transcription repressor MYB5; Provisional
Probab=98.23 E-value=5.1e-06 Score=77.94 Aligned_cols=49 Identities=20% Similarity=0.245 Sum_probs=43.4
Q ss_pred CCCccCHHHHHHHHHHHHHcCCCCHHhHhhhhcCCCCHHHHHHHHHHHHHH
Q 022223 91 RGVPWTEDEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASHAQKYFLR 141 (300)
Q Consensus 91 kg~~WTeEEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSHAQKYF~r 141 (300)
+..+||+||++++++.+.+||. .|..|| .+++.||..||+.||..++.+
T Consensus 77 ~kgpWT~EED~lLlel~~~~Gn-KWs~IA-k~LpGRTDnqIKNRWns~LrK 125 (249)
T PLN03212 77 KRGGITSDEEDLILRLHRLLGN-RWSLIA-GRIPGRTDNEIKNYWNTHLRK 125 (249)
T ss_pred ccCCCChHHHHHHHHHHHhccc-cHHHHH-hhcCCCCHHHHHHHHHHHHhH
Confidence 4568999999999999999997 899999 699999999999998765543
No 14
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=98.15 E-value=1.8e-06 Score=86.92 Aligned_cols=40 Identities=33% Similarity=0.615 Sum_probs=38.2
Q ss_pred CccCHHHHHHHHHHHHHcCCCCHHhHhhhhcCCCCHHHHHHH
Q 022223 93 VPWTEDEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASH 134 (300)
Q Consensus 93 ~~WTeEEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSH 134 (300)
..||.+|..++|+||+.||. ||.+|| .+|+|||++||-.|
T Consensus 280 k~WS~qE~~LLLEGIe~ygD-dW~kVA-~HVgtKt~EqCIl~ 319 (531)
T COG5259 280 KNWSRQELLLLLEGIEMYGD-DWDKVA-RHVGTKTKEQCILH 319 (531)
T ss_pred ccccHHHHHHHHHHHHHhhh-hHHHHH-HHhCCCCHHHHHHH
Confidence 37999999999999999998 999999 79999999999988
No 15
>PLN03091 hypothetical protein; Provisional
Probab=98.07 E-value=6.7e-06 Score=82.42 Aligned_cols=49 Identities=14% Similarity=0.282 Sum_probs=43.8
Q ss_pred CCccCHHHHHHHHHHHHHcCCCCHHhHhhhhcCCCCHHHHHHHHHHHHHHh
Q 022223 92 GVPWTEDEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASHAQKYFLRR 142 (300)
Q Consensus 92 g~~WTeEEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSHAQKYF~r~ 142 (300)
..+||+||++++|+.+++||. .|..|| .+++.||..||+.||...+.|.
T Consensus 67 KgpWT~EED~lLLeL~k~~Gn-KWskIA-k~LPGRTDnqIKNRWnslLKKk 115 (459)
T PLN03091 67 RGTFSQQEENLIIELHAVLGN-RWSQIA-AQLPGRTDNEIKNLWNSCLKKK 115 (459)
T ss_pred CCCCCHHHHHHHHHHHHHhCc-chHHHH-HhcCCCCHHHHHHHHHHHHHHH
Confidence 458999999999999999998 899999 7999999999999987665543
No 16
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=97.96 E-value=8.7e-06 Score=82.65 Aligned_cols=42 Identities=29% Similarity=0.543 Sum_probs=39.6
Q ss_pred CCCccCHHHHHHHHHHHHHcCCCCHHhHhhhhcCCCCHHHHHHH
Q 022223 91 RGVPWTEDEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASH 134 (300)
Q Consensus 91 kg~~WTeEEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSH 134 (300)
.+..||++|..++|+||++||- ||.+|| .+|+|||..||-.|
T Consensus 252 ~~~~WT~qE~lLLLE~ie~y~d-dW~kVa-~hVg~ks~eqCI~k 293 (506)
T KOG1279|consen 252 ARPNWTEQETLLLLEAIEMYGD-DWNKVA-DHVGTKSQEQCILK 293 (506)
T ss_pred CCCCccHHHHHHHHHHHHHhcc-cHHHHH-hccCCCCHHHHHHH
Confidence 3567999999999999999998 999999 89999999999998
No 17
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=97.56 E-value=0.00017 Score=65.74 Aligned_cols=48 Identities=19% Similarity=0.302 Sum_probs=42.4
Q ss_pred cCCCccCHHHHHHHHHHHHHcCCCCHHhHhhhhcCCCCHHHHHHHHHHHH
Q 022223 90 KRGVPWTEDEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASHAQKYF 139 (300)
Q Consensus 90 Kkg~~WTeEEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSHAQKYF 139 (300)
-+...||+||+++.+++-.+||- .|..|| .+++.||--.|+.||.-..
T Consensus 60 ikrg~fT~eEe~~Ii~lH~~~GN-rWs~IA-~~LPGRTDNeIKN~Wnt~l 107 (238)
T KOG0048|consen 60 LKRGNFSDEEEDLIIKLHALLGN-RWSLIA-GRLPGRTDNEVKNHWNTHL 107 (238)
T ss_pred ccCCCCCHHHHHHHHHHHHHHCc-HHHHHH-hhCCCcCHHHHHHHHHHHH
Confidence 34667999999999999999998 799999 7999999999999975444
No 18
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=97.54 E-value=0.00012 Score=76.88 Aligned_cols=52 Identities=21% Similarity=0.420 Sum_probs=45.8
Q ss_pred CCCccCHHHHHHHHHHHHHcCCCCHHhHhhhhcCCCCHHHHHHHHHHHHHHhh
Q 022223 91 RGVPWTEDEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASHAQKYFLRRF 143 (300)
Q Consensus 91 kg~~WTeEEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSHAQKYF~r~~ 143 (300)
+-.+||.+|+.+++.|+.+||..+|-+|- ..|+.|+..|||.+|.+.+.+..
T Consensus 359 khg~wt~~ED~~L~~AV~~Yg~kdw~k~R-~~vPnRSdsQcR~RY~nvL~~s~ 410 (939)
T KOG0049|consen 359 KHGRWTDQEDVLLVCAVSRYGAKDWAKVR-QAVPNRSDSQCRERYTNVLNRSA 410 (939)
T ss_pred cCCCCCCHHHHHHHHHHHHhCccchhhHH-HhcCCccHHHHHHHHHHHHHHhh
Confidence 34579999999999999999999999997 89999999999999777665544
No 19
>PLN03162 golden-2 like transcription factor; Provisional
Probab=97.12 E-value=0.00091 Score=66.79 Aligned_cols=58 Identities=31% Similarity=0.416 Sum_probs=45.1
Q ss_pred ccccCCCccCHHHHHHHHHHHHHcCC--CCHHhHhhhh--cCCCCHHHHHHHHHHHHHHhhhc
Q 022223 87 RERKRGVPWTEDEHRLFLLGLQKVGK--GDWRGISRNF--VKTRTPTQVASHAQKYFLRRFNQ 145 (300)
Q Consensus 87 ~~rKkg~~WTeEEh~lFLegLekyGk--GdWk~IAr~~--V~TRT~~QVrSHAQKYF~r~~~~ 145 (300)
..||.+..||+|=|++|++||++.|. --=|.|- ++ |..-|..+|+||-|||...+.++
T Consensus 232 g~KKpRLrWTpELH~rFVeAV~qLG~dKATPK~IL-elMnV~GLTRenVKSHLQKYRl~rk~l 293 (526)
T PLN03162 232 GKKKAKVDWTPELHRRFVHAVEQLGVEKAFPSRIL-ELMGVQCLTRHNIASHLQKYRSHRRHL 293 (526)
T ss_pred CCCCCcccCCHHHHHHHHHHHHHhCcCccchHHHH-HHcCCCCcCHHHHHHHHHHHHHhcccc
Confidence 35667889999999999999999993 1233443 23 55689999999999998887643
No 20
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=96.80 E-value=0.0014 Score=69.17 Aligned_cols=47 Identities=21% Similarity=0.425 Sum_probs=41.4
Q ss_pred CCCccCHHHHHHHHHHHHHcCCCCHHhHhhhhcCCCCHHHHHHHHHHH
Q 022223 91 RGVPWTEDEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASHAQKY 138 (300)
Q Consensus 91 kg~~WTeEEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSHAQKY 138 (300)
|...||-.|+++++.++++||+|.|-+|| .+++.||..|.+..-..+
T Consensus 411 K~~rW~l~edeqL~~~V~~YG~g~WakcA-~~Lp~~t~~q~~rrR~R~ 457 (939)
T KOG0049|consen 411 KVERWTLVEDEQLLYAVKVYGKGNWAKCA-MLLPKKTSRQLRRRRLRL 457 (939)
T ss_pred ccCceeecchHHHHHHHHHHccchHHHHH-HHccccchhHHHHHHHHH
Confidence 45669999999999999999999999999 899999998887665443
No 21
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=96.68 E-value=0.0019 Score=66.06 Aligned_cols=52 Identities=27% Similarity=0.519 Sum_probs=45.3
Q ss_pred cccCCCccCHHHHHHHHHHHHHcCCCCHHhHhhhhcCCCCHHHHHHHHHHHHHHhh
Q 022223 88 ERKRGVPWTEDEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASHAQKYFLRRF 143 (300)
Q Consensus 88 ~rKkg~~WTeEEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSHAQKYF~r~~ 143 (300)
=|.....|+.-|-.+|.+||+|||| ||..|-++|++=|+.+-+..+ ||++..
T Consensus 281 CRDemEEWSasEanLFEeALeKyGK-DFndIrqdfLPWKSl~sIvey---YYmwKt 332 (693)
T KOG3554|consen 281 CRDEMEEWSASEANLFEEALEKYGK-DFNDIRQDFLPWKSLTSIVEY---YYMWKT 332 (693)
T ss_pred ehhhhhhccchhhHHHHHHHHHhcc-cHHHHHHhhcchHHHHHHHHH---HHHHhh
Confidence 3566788999999999999999999 999999999999998888776 666654
No 22
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=96.22 E-value=0.0061 Score=64.99 Aligned_cols=49 Identities=27% Similarity=0.356 Sum_probs=43.3
Q ss_pred CCccCHHHHHHHHHHHHHcCCCCHHhHhhhhcCCCCHHHHHHHHHHHHHHhhhc
Q 022223 92 GVPWTEDEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASHAQKYFLRRFNQ 145 (300)
Q Consensus 92 g~~WTeEEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSHAQKYF~r~~~~ 145 (300)
-..||..|.++|-.||-.|-| ||..|+ ..|++||..||..+ ||.+.+-.
T Consensus 619 Sd~WTp~E~~lF~kA~y~~~K-DF~~v~-km~~~KtVaqCVey---YYtWKK~~ 667 (907)
T KOG4167|consen 619 SDKWTPLERKLFNKALYTYSK-DFIFVQ-KMVKSKTVAQCVEY---YYTWKKIM 667 (907)
T ss_pred cccccHHHHHHHHHHHHHhcc-cHHHHH-HHhccccHHHHHHH---HHHHHHhc
Confidence 356999999999999999998 999999 79999999999877 77766543
No 23
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=95.87 E-value=0.0072 Score=62.40 Aligned_cols=50 Identities=20% Similarity=0.471 Sum_probs=45.3
Q ss_pred cCCCccCHHHHHHHHHHHHHcCCCCHHhHhhhhcCCCCHHHHHHHHHHHHH
Q 022223 90 KRGVPWTEDEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASHAQKYFL 140 (300)
Q Consensus 90 Kkg~~WTeEEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSHAQKYF~ 140 (300)
.++..|+.-|++.+-.|+.+||+..|..|+ ..+.-+|+.||...|.+|..
T Consensus 5 ~kggvwrntEdeilkaav~kyg~nqws~i~-sll~~kt~rqC~~rw~e~ld 54 (617)
T KOG0050|consen 5 IKGGVWRNTEDEVLKAAVMKYGKNQWSRIA-SLLNRKTARQCKARWEEWLD 54 (617)
T ss_pred EecceecccHHHHHHHHHHHcchHHHHHHH-HHHhhcchhHHHHHHHHHhC
Confidence 457779999999999999999999999999 79999999999999887743
No 24
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=95.65 E-value=0.015 Score=61.07 Aligned_cols=51 Identities=27% Similarity=0.427 Sum_probs=41.4
Q ss_pred CCccCHHHHHHHHHHHHHcCCCCHHhH---------hhhhcCCCCHHHHHHHHHHHHHHhh
Q 022223 92 GVPWTEDEHRLFLLGLQKVGKGDWRGI---------SRNFVKTRTPTQVASHAQKYFLRRF 143 (300)
Q Consensus 92 g~~WTeEEh~lFLegLekyGkGdWk~I---------Ar~~V~TRT~~QVrSHAQKYF~r~~ 143 (300)
.+.||-.|++.|..||+.+|| ||.+| +..-+..||.-|||-||.+-..+..
T Consensus 88 ktaWt~~E~~~Ffdal~~~GK-dFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~~~m~ 147 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVGK-DFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLVRRMN 147 (782)
T ss_pred ccccchhhHHHHHHHHHHhcc-cHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHHHHHH
Confidence 568999999999999999999 99999 2245778999999988655544443
No 25
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=95.38 E-value=0.026 Score=56.87 Aligned_cols=50 Identities=24% Similarity=0.391 Sum_probs=44.1
Q ss_pred ccCCccccCCCccCHHHHHHHHHHHHHcCCCCHHhHhhhhcCCCCHHHHHHH
Q 022223 83 SGRSRERKRGVPWTEDEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASH 134 (300)
Q Consensus 83 s~~~~~rKkg~~WTeEEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSH 134 (300)
++.--.++...+||.+|-++|-.||..+|- ||..|+ +++++|...||..-
T Consensus 356 s~t~g~~~~~~~Ws~~e~ekFYKALs~wGt-dF~LIs-~lfP~R~RkqIKaK 405 (507)
T COG5118 356 SSTFGKKKGALRWSKKEIEKFYKALSIWGT-DFSLIS-SLFPNRERKQIKAK 405 (507)
T ss_pred cccccCCCCCCcccHHHHHHHHHHHHHhcc-hHHHHH-HhcCchhHHHHHHH
Confidence 444445677889999999999999999998 999999 89999999999864
No 26
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=95.36 E-value=0.036 Score=42.06 Aligned_cols=52 Identities=19% Similarity=0.366 Sum_probs=33.9
Q ss_pred CccCHHHHHHHHHHHHH------cC-----CC--CHHhHhhhhcC----CCCHHHHHHHHHHHHHHhhhc
Q 022223 93 VPWTEDEHRLFLLGLQK------VG-----KG--DWRGISRNFVK----TRTPTQVASHAQKYFLRRFNQ 145 (300)
Q Consensus 93 ~~WTeEEh~lFLegLek------yG-----kG--dWk~IAr~~V~----TRT~~QVrSHAQKYF~r~~~~ 145 (300)
..||++|-..||+.+.. ++ ++ -|+.||. .+. .||+.||+..+.+-..+-.+.
T Consensus 2 ~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~-~l~~~G~~rt~~qc~~Kw~~L~~~Yk~~ 70 (90)
T PF13837_consen 2 RNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAE-ELAEHGYNRTPEQCRNKWKNLKKKYKKI 70 (90)
T ss_dssp -SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHH-HHHHHC----HHHHHHHHHHHHHHHHCS
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHH-HHHHcCCCCCHHHHHHHHHHHHHHHHHH
Confidence 36999999999998887 21 12 5999994 442 699999999987654444443
No 27
>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=94.58 E-value=0.029 Score=33.28 Aligned_cols=17 Identities=47% Similarity=1.169 Sum_probs=16.2
Q ss_pred CccCCCCCCCCCCCCCC
Q 022223 3 RSCSQCGNNGHNSRTCA 19 (300)
Q Consensus 3 R~CS~Cgn~GHNsRTC~ 19 (300)
|+|-.||..||-+|.|+
T Consensus 1 ~~C~~C~~~GH~~~~Cp 17 (18)
T PF00098_consen 1 RKCFNCGEPGHIARDCP 17 (18)
T ss_dssp SBCTTTSCSSSCGCTSS
T ss_pred CcCcCCCCcCcccccCc
Confidence 68999999999999998
No 28
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=94.47 E-value=0.055 Score=59.61 Aligned_cols=49 Identities=20% Similarity=0.426 Sum_probs=44.6
Q ss_pred ccCHHHHHHHHHHHHHcCCCCHHhHhhhhcCCCCHHHHHHHHHHHHHHhh
Q 022223 94 PWTEDEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASHAQKYFLRRF 143 (300)
Q Consensus 94 ~WTeEEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSHAQKYF~r~~ 143 (300)
.||..+=..|+.|.++||+.|...|| ..|.+||+.+|+.+++-|+.|..
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 59999999999999999999999999 78999999999999888776643
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=94.45 E-value=0.088 Score=44.53 Aligned_cols=51 Identities=29% Similarity=0.607 Sum_probs=40.5
Q ss_pred cCCCccCHHHHHHHHHHHHHcCC---CCHHhHhh-----------hhcCCCCHHHHHHHHHHHHHH
Q 022223 90 KRGVPWTEDEHRLFLLGLQKVGK---GDWRGISR-----------NFVKTRTPTQVASHAQKYFLR 141 (300)
Q Consensus 90 Kkg~~WTeEEh~lFLegLekyGk---GdWk~IAr-----------~~V~TRT~~QVrSHAQKYF~r 141 (300)
.++..||+||++-+|-.+.+||. |.|..|-+ -|+.+||+..+.-++. ++++
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 44557999999999999999999 99999964 4789999999998886 4443
No 30
>KOG0724 consensus Zuotin and related molecular chaperones (DnaJ superfamily), contains DNA-binding domains [Posttranslational modification, protein turnover, chaperones]
Probab=94.44 E-value=0.0092 Score=56.22 Aligned_cols=49 Identities=16% Similarity=0.046 Sum_probs=45.4
Q ss_pred ccCHHHHHHHHHHHHHcCCCCHHhHhhhhcCCCCHHHHHHHHHHHHHHhhh
Q 022223 94 PWTEDEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASHAQKYFLRRFN 144 (300)
Q Consensus 94 ~WTeEEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSHAQKYF~r~~~ 144 (300)
.||++||..|.++|..|+ -.|..|- .|++.++..|.++|+|+||-....
T Consensus 55 ~~t~~~~~~~~~~l~~~~-~~~~~~~-~~~~~~~~v~~~~~~~~~~p~~~~ 103 (335)
T KOG0724|consen 55 RRTPDSWDKFAEALPLEK-RLEDKIE-EYIGLVFDVNIRESGQKPFPKYGK 103 (335)
T ss_pred ccchhhhhHHHhcCcccc-ccchhHH-hhhhhHHHHhhhhccCCCccccCc
Confidence 399999999999999994 5999998 899999999999999999988775
No 31
>smart00426 TEA TEA domain.
Probab=94.36 E-value=0.035 Score=43.52 Aligned_cols=43 Identities=33% Similarity=0.387 Sum_probs=32.2
Q ss_pred CccCHHHHHHHHHHHHHcCCCC-H--------------HhHhhhhc-----CCCCHHHHHHHHH
Q 022223 93 VPWTEDEHRLFLLGLQKVGKGD-W--------------RGISRNFV-----KTRTPTQVASHAQ 136 (300)
Q Consensus 93 ~~WTeEEh~lFLegLekyGkGd-W--------------k~IAr~~V-----~TRT~~QVrSHAQ 136 (300)
.-|.++=+..|++||+.|-+-. | +.|+ +|+ ..||.+||.||-|
T Consensus 4 ~vWp~~lE~Af~~aL~~~~~~g~~kik~~~r~k~~gRNelIs-~YI~~~tGk~Rt~KQVsShIQ 66 (68)
T smart00426 4 GVWSPDIEQAFQEALAIYPPCGRRKIILSDEGKMYGRNELIA-RYIKLRTGKTRTRKQVSSHIQ 66 (68)
T ss_pred CcCcHHHHHHHHHHHHHcCccCcccchhhhcCcccchhHHHH-HHHHHHhCCccchhhhcchhe
Confidence 3599999999999999887522 2 3344 344 3599999999976
No 32
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=93.59 E-value=0.026 Score=40.34 Aligned_cols=19 Identities=37% Similarity=1.034 Sum_probs=17.1
Q ss_pred CCCccCCCCCCCCCCCCCC
Q 022223 1 MSRSCSQCGNNGHNSRTCA 19 (300)
Q Consensus 1 m~R~CS~Cgn~GHNsRTC~ 19 (300)
+.+.|.+||..||..+.|+
T Consensus 30 lp~~C~~C~~~gH~~~~C~ 48 (49)
T PF14392_consen 30 LPRFCFHCGRIGHSDKECP 48 (49)
T ss_pred cChhhcCCCCcCcCHhHcC
Confidence 3578999999999999997
No 33
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=93.51 E-value=0.089 Score=55.20 Aligned_cols=52 Identities=19% Similarity=0.246 Sum_probs=42.0
Q ss_pred CCCccCHHHHHHHHHHHH-------Hc-------CC-----------CCHHhHhhhhcCCCCHHHHHHHHHHHHHHhh
Q 022223 91 RGVPWTEDEHRLFLLGLQ-------KV-------GK-----------GDWRGISRNFVKTRTPTQVASHAQKYFLRRF 143 (300)
Q Consensus 91 kg~~WTeEEh~lFLegLe-------ky-------Gk-----------GdWk~IAr~~V~TRT~~QVrSHAQKYF~r~~ 143 (300)
+..+||.||.+++|..++ .| |. =+|..|+ +.++||+..|||.||+|-..+-.
T Consensus 435 ~r~~Ws~eEe~~Llk~V~~~~~~~~q~q~~n~~~~~q~sp~s~~~d~I~Wt~vs-e~~~TR~~~qCr~Kw~kl~~~~s 511 (607)
T KOG0051|consen 435 NRGAWSIEEEEKLLKTVNEMIREALQPQASNTDTGLQESPESTLKDDINWTLVS-EMLGTRSRIQCRYKWYKLTTSPS 511 (607)
T ss_pred ccCcchHHHHHHHHHHHHHHHHHhhcccccccchhhhcCccccccCCcchhhhh-HhhcCCCcchHHHHHHHHHhhHH
Confidence 556799999999999996 44 11 1699999 69999999999999887655443
No 34
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=93.22 E-value=0.1 Score=54.69 Aligned_cols=50 Identities=20% Similarity=0.366 Sum_probs=43.0
Q ss_pred CCCccCHHHHHHHHHHHHHcCCCCHHhHhhhhcCCCCHHHHHHHHHHHHHHhh
Q 022223 91 RGVPWTEDEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASHAQKYFLRRF 143 (300)
Q Consensus 91 kg~~WTeEEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSHAQKYF~r~~ 143 (300)
+...||+||.+.+......+|. +|..|+ +.++ |.|.-||.++..|-.--.
T Consensus 383 ~rg~wt~ee~eeL~~l~~~~g~-~W~~Ig-~~lg-r~P~~crd~wr~~~~~g~ 432 (607)
T KOG0051|consen 383 KRGKWTPEEEEELKKLVVEHGN-DWKEIG-KALG-RMPMDCRDRWRQYVKCGS 432 (607)
T ss_pred ccCCCCcchHHHHHHHHHHhcc-cHHHHH-HHHc-cCcHHHHHHHHHhhcccc
Confidence 4556999999999999999996 999999 6776 899999999998755443
No 35
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=93.02 E-value=0.049 Score=38.80 Aligned_cols=20 Identities=30% Similarity=0.724 Sum_probs=17.5
Q ss_pred CccCCCCCCCCCC--CCCCCCC
Q 022223 3 RSCSQCGNNGHNS--RTCAEAG 22 (300)
Q Consensus 3 R~CS~Cgn~GHNs--RTC~~~~ 22 (300)
+||..||.+||.. |+||-..
T Consensus 2 ~kC~~CG~~GH~~t~k~CP~~~ 23 (40)
T PF15288_consen 2 VKCKNCGAFGHMRTNKRCPMYC 23 (40)
T ss_pred ccccccccccccccCccCCCCC
Confidence 7999999999976 8999665
No 36
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=92.64 E-value=0.071 Score=54.94 Aligned_cols=54 Identities=15% Similarity=0.375 Sum_probs=44.6
Q ss_pred ccCCCccCHHHHHHHHHHHHHcCCCCHHhHhhhhcCCCCHHHHHHHHHHHHHHhh
Q 022223 89 RKRGVPWTEDEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASHAQKYFLRRF 143 (300)
Q Consensus 89 rKkg~~WTeEEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSHAQKYF~r~~ 143 (300)
..++..|+..|++.++-++++||..+|..||. .+..||..||+.|+..|...+.
T Consensus 17 ~~k~gsw~~~EDe~l~~~vk~l~~nnws~vas-~~~~~~~kq~~~rw~~~lnp~l 70 (512)
T COG5147 17 KRKGGSWKRTEDEDLKALVKKLGPNNWSKVAS-LLISSTGKQSSNRWNNHLNPQL 70 (512)
T ss_pred eecCCCCCCcchhHHHHHHhhcccccHHHHHH-Hhcccccccccchhhhhhchhc
Confidence 34455899999999999999999999999995 5555999999999866655443
No 37
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=92.13 E-value=0.23 Score=51.07 Aligned_cols=42 Identities=24% Similarity=0.355 Sum_probs=38.0
Q ss_pred CCccCHHHHHHHHHHHHHcCCCCHHhHhhhhcCCCCHHHHHHHH
Q 022223 92 GVPWTEDEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASHA 135 (300)
Q Consensus 92 g~~WTeEEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSHA 135 (300)
-..||.||--+|..+++.||+ +|++|- ..++-|+...++-+|
T Consensus 187 ~d~WT~Ed~vlFe~aF~~~GK-~F~kIr-q~LP~rsLaSlvqyY 228 (534)
T KOG1194|consen 187 PDEWTAEDIVLFEQAFQFFGK-DFHKIR-QALPHRSLASLVQYY 228 (534)
T ss_pred cccchHHHHHHHHHHHHHhcc-cHHHHH-HHccCccHHHHHHHH
Confidence 456999999999999999999 999998 799999998887764
No 38
>KOG3841 consensus TEF-1 and related transcription factor, TEAD family [Transcription]
Probab=90.82 E-value=0.34 Score=48.95 Aligned_cols=48 Identities=33% Similarity=0.396 Sum_probs=39.3
Q ss_pred cCCCccCHHHHHHHHHHHHHcCC---------------CCHHhHhhhhc-----CCCCHHHHHHHHHHH
Q 022223 90 KRGVPWTEDEHRLFLLGLQKVGK---------------GDWRGISRNFV-----KTRTPTQVASHAQKY 138 (300)
Q Consensus 90 Kkg~~WTeEEh~lFLegLekyGk---------------GdWk~IAr~~V-----~TRT~~QVrSHAQKY 138 (300)
-...-|+++=++.|+|||..|-. |+=..||| || .|||.+||-||-|=.
T Consensus 74 daegvWSpdIEqsFqEALaiyppcGrrKIilsdegkmyGRNELIar-YIKlrtgktRTrKQVSSHIQVl 141 (455)
T KOG3841|consen 74 DAEGVWSPDIEQSFQEALAIYPPCGRRKIILSDEGKMYGRNELIAR-YIKLRTGKTRTRKQVSSHIQVL 141 (455)
T ss_pred ccccccChhHHHHHHHHHhhcCCCCceeEEEccCccccchHHHHHH-HHHHhcCCchhHHHHHHHHHHH
Confidence 44456999999999999998752 67889995 77 579999999999844
No 39
>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=90.76 E-value=0.49 Score=36.27 Aligned_cols=50 Identities=16% Similarity=0.263 Sum_probs=31.6
Q ss_pred CCccCHHHHHHHHHHHHHcC------CCC--HHhHhhhhcCCCCHHHHHHHHHHHHHH
Q 022223 92 GVPWTEDEHRLFLLGLQKVG------KGD--WRGISRNFVKTRTPTQVASHAQKYFLR 141 (300)
Q Consensus 92 g~~WTeEEh~lFLegLekyG------kGd--Wk~IAr~~V~TRT~~QVrSHAQKYF~r 141 (300)
++++|+||+..+++.|..+. .|+ |+.+++.++...|-.--|.|+.|.+..
T Consensus 2 R~~fT~edD~~l~~~v~~~~~~~~~~~Gn~iwk~le~~~~t~HtwQSwR~Ry~K~L~~ 59 (65)
T PF08914_consen 2 RTPFTEEDDAALLDYVKENERQGGSVSGNKIWKELEEKHPTRHTWQSWRDRYLKHLRG 59 (65)
T ss_dssp -----HHHHHHHHHHHHHT--STTTTTSSHHHHHHHHS-SSS--SHHHHHHHHHHT--
T ss_pred CCCCCHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHcCCCCCHHHHHHHHHHHHhc
Confidence 35799999999999996553 244 999998777678888888986665543
No 40
>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=90.09 E-value=0.31 Score=49.16 Aligned_cols=48 Identities=33% Similarity=0.380 Sum_probs=31.8
Q ss_pred cCCCccCHHHHHHHHHHHHHcCC-------------CCHHhHhhhhcC-----CCCHHHHHHHHHHH
Q 022223 90 KRGVPWTEDEHRLFLLGLQKVGK-------------GDWRGISRNFVK-----TRTPTQVASHAQKY 138 (300)
Q Consensus 90 Kkg~~WTeEEh~lFLegLekyGk-------------GdWk~IAr~~V~-----TRT~~QVrSHAQKY 138 (300)
+...-|+++=+..|++||+.|-+ |+=+.|+ .||. +||.+||.||-|-.
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 34456999999999999998865 3445666 5654 59999999999944
No 41
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=89.16 E-value=1.1 Score=33.78 Aligned_cols=49 Identities=16% Similarity=0.281 Sum_probs=37.7
Q ss_pred CccCHHHHHHHHHHHHHc-----CC-----------CCHHhHhhhh----cCCCCHHHHHHHHHHHHHH
Q 022223 93 VPWTEDEHRLFLLGLQKV-----GK-----------GDWRGISRNF----VKTRTPTQVASHAQKYFLR 141 (300)
Q Consensus 93 ~~WTeEEh~lFLegLeky-----Gk-----------GdWk~IAr~~----V~TRT~~QVrSHAQKYF~r 141 (300)
..||.+|.+.|++.|++| |+ .-|..|+..| .+.||..|++..+.++-..
T Consensus 3 ~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk~~ 71 (78)
T PF13873_consen 3 PNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLKSK 71 (78)
T ss_pred CCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHH
Confidence 359999999999999987 31 3699998533 2369999999887766443
No 42
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=87.00 E-value=1.3 Score=49.30 Aligned_cols=51 Identities=29% Similarity=0.544 Sum_probs=42.3
Q ss_pred CCccCHHHHHHHHHHHHHcCCCCHHhHhh-----------hhcCCCCHHHHHHHHHHHHHHh
Q 022223 92 GVPWTEDEHRLFLLGLQKVGKGDWRGISR-----------NFVKTRTPTQVASHAQKYFLRR 142 (300)
Q Consensus 92 g~~WTeEEh~lFLegLekyGkGdWk~IAr-----------~~V~TRT~~QVrSHAQKYF~r~ 142 (300)
+..||+||++.+|-.+.+||.|+|..|-. -|+.+||+.++.-++.--..-.
T Consensus 926 ~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~~l~~~~ 987 (1033)
T PLN03142 926 GKLYNEECDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELARRCDTLIRLI 987 (1033)
T ss_pred CCcCCHHHHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHHHHHHHHHHHH
Confidence 44699999999999999999999999943 5788999999998886443333
No 43
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=86.50 E-value=0.72 Score=48.22 Aligned_cols=45 Identities=20% Similarity=0.396 Sum_probs=39.5
Q ss_pred CCCccCHHHHHHHHHHHHHcCCCCHHhHhhhhcCCCCHHHHHHHHHHH
Q 022223 91 RGVPWTEDEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASHAQKY 138 (300)
Q Consensus 91 kg~~WTeEEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSHAQKY 138 (300)
+.+-|+.||++++|++...+-. -|+-|+ ..|+ ||..||-.++++-
T Consensus 58 ~~tews~eederlLhlakl~p~-qwrtIa-~i~g-r~~~qc~eRy~~l 102 (617)
T KOG0050|consen 58 KKTEWSREEDERLLHLAKLEPT-QWRTIA-DIMG-RTSQQCLERYNNL 102 (617)
T ss_pred hhhhhhhhHHHHHHHHHHhcCC-ccchHH-HHhh-hhHHHHHHHHHHH
Confidence 3456999999999999999997 899999 6666 9999999998764
No 44
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=86.20 E-value=1.1 Score=46.49 Aligned_cols=53 Identities=17% Similarity=0.324 Sum_probs=45.8
Q ss_pred cCCCccCHHHHHHHHHHHHHcCCCCHHhHhhhhcCCCCHHHHHHHHHHHHHHhhh
Q 022223 90 KRGVPWTEDEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASHAQKYFLRRFN 144 (300)
Q Consensus 90 Kkg~~WTeEEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSHAQKYF~r~~~ 144 (300)
.+...|++||++.+++.-..+|- .|..|+ .+++.||..||...|.+-+....+
T Consensus 70 lk~~~~~~eed~~li~l~~~~~~-~wstia-~~~d~rt~~~~~ery~~~~~~~~s 122 (512)
T COG5147 70 LKKKNWSEEEDEQLIDLDKELGT-QWSTIA-DYKDRRTAQQCVERYVNTLEDLSS 122 (512)
T ss_pred cccccccHHHHHHHHHHHHhcCc-hhhhhc-cccCccchHHHHHHHHHHhhhhhc
Confidence 34567999999999999999998 799999 899999999998887766665554
No 45
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=84.98 E-value=1.7 Score=41.48 Aligned_cols=57 Identities=16% Similarity=0.334 Sum_probs=41.6
Q ss_pred CCccCHHHHHHHHHHHHHc----CCC-----CHHhHhhhh---cCCCCHHHHHHHHHHHHHHhhhcccc
Q 022223 92 GVPWTEDEHRLFLLGLQKV----GKG-----DWRGISRNF---VKTRTPTQVASHAQKYFLRRFNQNKR 148 (300)
Q Consensus 92 g~~WTeEEh~lFLegLeky----GkG-----dWk~IAr~~---V~TRT~~QVrSHAQKYF~r~~~~~k~ 148 (300)
...|++||-+.||++..+. ..+ .|..||+++ ---||+.||+..+.+-..+..+.+.+
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~k~Yk~~k~~ 122 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLKKKYKKEKAK 122 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHhcc
Confidence 4789999999999987642 223 499999633 23499999998887766666655443
No 46
>smart00343 ZnF_C2HC zinc finger.
Probab=84.79 E-value=0.5 Score=29.45 Aligned_cols=17 Identities=41% Similarity=1.152 Sum_probs=15.5
Q ss_pred ccCCCCCCCCCCCCCCC
Q 022223 4 SCSQCGNNGHNSRTCAE 20 (300)
Q Consensus 4 ~CS~Cgn~GHNsRTC~~ 20 (300)
+|..||..||.++.|+.
T Consensus 1 ~C~~CG~~GH~~~~C~~ 17 (26)
T smart00343 1 KCYNCGKEGHIARDCPK 17 (26)
T ss_pred CCccCCCCCcchhhCCc
Confidence 59999999999999983
No 47
>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=84.03 E-value=2.9 Score=32.12 Aligned_cols=45 Identities=24% Similarity=0.421 Sum_probs=32.2
Q ss_pred ccCHHHHHHHHHHHHHc-------CCC-----CHHhHhhhh----cCCCCHHHHHHHHHHH
Q 022223 94 PWTEDEHRLFLLGLQKV-------GKG-----DWRGISRNF----VKTRTPTQVASHAQKY 138 (300)
Q Consensus 94 ~WTeEEh~lFLegLeky-------GkG-----dWk~IAr~~----V~TRT~~QVrSHAQKY 138 (300)
.||+++++.||+.|... +.+ .|..|++.| -...|..||+.|+...
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~l 61 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTL 61 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHH
Confidence 49999999999998654 112 477786533 2346889999997644
No 48
>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=82.80 E-value=1.3 Score=39.85 Aligned_cols=49 Identities=14% Similarity=0.260 Sum_probs=38.8
Q ss_pred CCccCHHHHHHHHHHHHHcCC------CCHHhHhhhhcCCCCHHHHHHHHHHHHHHh
Q 022223 92 GVPWTEDEHRLFLLGLQKVGK------GDWRGISRNFVKTRTPTQVASHAQKYFLRR 142 (300)
Q Consensus 92 g~~WTeEEh~lFLegLekyGk------GdWk~IAr~~V~TRT~~QVrSHAQKYF~r~ 142 (300)
-..||+||+.++.+.+.+|=+ ..|..++ ..+ +||+.-|..+|..|..++
T Consensus 4 QDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg-~~L-~RTsAACGFRWNs~VRkq 58 (161)
T TIGR02894 4 QDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVG-RAL-NRTAAACGFRWNAYVRKQ 58 (161)
T ss_pred ccccccHHHHHHHHHHHHHHhcchHHHHHHHHHH-HHH-cccHHHhcchHHHHHHHH
Confidence 347999999999999998854 2577777 344 499999999998886654
No 49
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=76.10 E-value=3 Score=37.77 Aligned_cols=47 Identities=11% Similarity=0.166 Sum_probs=34.4
Q ss_pred CCccCHHHHHHHHHHHHHcCCCC------HHhHhhhhcCCCCHHHHHHHHHHHHH
Q 022223 92 GVPWTEDEHRLFLLGLQKVGKGD------WRGISRNFVKTRTPTQVASHAQKYFL 140 (300)
Q Consensus 92 g~~WTeEEh~lFLegLekyGkGd------Wk~IAr~~V~TRT~~QVrSHAQKYF~ 140 (300)
...||+||+.++.+-+..|++-. +..++ ..+ .||..+|..+|..|..
T Consensus 5 qdawt~e~d~llae~vl~~i~eg~tql~afe~~g-~~L-~rt~aac~fRwNs~vr 57 (170)
T PRK13923 5 QDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVG-DAL-KRTAAACGFRWNSVVR 57 (170)
T ss_pred hhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHH-HHH-hhhHHHHHhHHHHHHH
Confidence 34699999999999999998732 34444 223 4999999999955543
No 50
>KOG0385 consensus Chromatin remodeling complex WSTF-ISWI, small subunit [Transcription]
Probab=73.76 E-value=4.9 Score=44.26 Aligned_cols=52 Identities=25% Similarity=0.377 Sum_probs=44.9
Q ss_pred CCccCHHHHHHHHHHHHHcCCCCHHhHhhhhcCCCCHHHHHHHHHHHHHHhhhc
Q 022223 92 GVPWTEDEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASHAQKYFLRRFNQ 145 (300)
Q Consensus 92 g~~WTeEEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSHAQKYF~r~~~~ 145 (300)
-..||+.+-..|+.|-++||++|-..||+ -|-. |+..|..++.-||-+++..
T Consensus 795 ft~w~k~df~~fi~a~eKygr~di~~ia~-~~e~-~~eev~~y~rvfwer~~el 846 (971)
T KOG0385|consen 795 FTNWTKRDFNQFIKANEKYGRDDIENIAA-EVEG-TPEEVGEYARVFWERLEEL 846 (971)
T ss_pred ccchhhhhHHHHHHHhhccCcchhhhhHH-hhcC-CHHHHHHHHHHHHHHHHHh
Confidence 34599999999999999999999999995 4554 9999999999888887654
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=69.08 E-value=13 Score=33.16 Aligned_cols=50 Identities=12% Similarity=0.368 Sum_probs=42.8
Q ss_pred cCHHHHHHHHHHHHHcCCC--CHHhHhhhhcCCCCHHHHHHHHHHHHHHhhhc
Q 022223 95 WTEDEHRLFLLGLQKVGKG--DWRGISRNFVKTRTPTQVASHAQKYFLRRFNQ 145 (300)
Q Consensus 95 WTeEEh~lFLegLekyGkG--dWk~IAr~~V~TRT~~QVrSHAQKYF~r~~~~ 145 (300)
++..+.+.||.++.+||-| +|+-+- .-+.-||..+++.++-=|+.++...
T Consensus 41 Fn~rQR~~Fln~vMR~G~~~f~~~w~~-~~Lr~Ks~~ei~aY~~LFm~HL~E~ 92 (145)
T PF06461_consen 41 FNPRQRKAFLNAVMRYGMGAFDWKWFV-PRLRGKSEKEIRAYGSLFMRHLCEP 92 (145)
T ss_pred cCHHHHHHHHHHHHHHCcCcccchHHh-hhhccccHHHHHHHHHHHHHHhcCC
Confidence 6788999999999999987 799888 5788899999999998777776643
No 52
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=68.64 E-value=3 Score=47.53 Aligned_cols=54 Identities=20% Similarity=0.520 Sum_probs=37.9
Q ss_pred CCCccCHHHHHHHHHHHHHcCCCCHHhHhh-------hhcC----CCCHHHHHHHHHHHHHHhhhc
Q 022223 91 RGVPWTEDEHRLFLLGLQKVGKGDWRGISR-------NFVK----TRTPTQVASHAQKYFLRRFNQ 145 (300)
Q Consensus 91 kg~~WTeEEh~lFLegLekyGkGdWk~IAr-------~~V~----TRT~~QVrSHAQKYF~r~~~~ 145 (300)
...-|..||+..||.||-+||.|+|..|-- +-|. --+..|.+.++ .|+..+.+.
T Consensus 1132 ~~~~W~~e~Ds~LLiGI~khGygswe~Ir~Dp~L~l~dKi~~~e~~P~a~~L~~R~-~yLls~~~~ 1196 (1373)
T KOG0384|consen 1132 WDCDWGSEDDSMLLIGIFKHGYGSWEAIRLDPDLGLTDKIFLVETVPQAKHLQRRA-DYLLSLLRK 1196 (1373)
T ss_pred cccCCCchhhhhHhhhhhhcccccHHHhccCccccchhhhcccccCCchHHHHHHH-HHHHHHHhh
Confidence 567799999999999999999999999931 1111 12345555554 477766543
No 53
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=67.77 E-value=5.4 Score=42.22 Aligned_cols=49 Identities=24% Similarity=0.383 Sum_probs=43.0
Q ss_pred ccCCccccCCCccCHHHHHHHHHHHHHcCCCCHHhHhhhhcCCCCHHHHHH
Q 022223 83 SGRSRERKRGVPWTEDEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVAS 133 (300)
Q Consensus 83 s~~~~~rKkg~~WTeEEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrS 133 (300)
......+.....||.+|-++|-.+|..+|- ++..|+ +....|+..||+-
T Consensus 400 ~~t~sk~~~~~~w~~se~e~fyka~~~~gs-~~slis-~l~p~R~rk~iK~ 448 (584)
T KOG2009|consen 400 YATYSKKLETDKWDASETELFYKALSERGS-DFSLIS-NLFPLRDRKQIKA 448 (584)
T ss_pred hhhccCccccCcccchhhHHhhhHHhhhcc-cccccc-cccccccHHHHHH
Confidence 344455667888999999999999999998 999999 8999999999975
No 54
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=66.37 E-value=12 Score=30.43 Aligned_cols=39 Identities=31% Similarity=0.560 Sum_probs=28.0
Q ss_pred ccCHHHHHHHHHHHHHc----CC---CCHHhHhhhhcCCC-----CHHHHHH
Q 022223 94 PWTEDEHRLFLLGLQKV----GK---GDWRGISRNFVKTR-----TPTQVAS 133 (300)
Q Consensus 94 ~WTeEEh~lFLegLeky----Gk---GdWk~IAr~~V~TR-----T~~QVrS 133 (300)
-||+|++..+|+||-.| |. -||...- ++|... |..|+..
T Consensus 6 ~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~-~~vk~~l~~~~s~~Ql~~ 56 (98)
T PF04504_consen 6 LWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFY-DFVKGSLSFDVSKNQLYD 56 (98)
T ss_pred CCCchHHHHHHHHHHHHHHhcCCCCCccHHHHH-HHHHHHccCCCCHHHHHH
Confidence 49999999999999988 63 2677766 555443 4455543
No 55
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=65.20 E-value=3.4 Score=38.09 Aligned_cols=18 Identities=44% Similarity=1.123 Sum_probs=16.1
Q ss_pred CCccCCCCCCCCCCCCCC
Q 022223 2 SRSCSQCGNNGHNSRTCA 19 (300)
Q Consensus 2 ~R~CS~Cgn~GHNsRTC~ 19 (300)
..+|.+||-+||=+|-|+
T Consensus 97 ~~~C~~Cg~~GH~~~dC~ 114 (190)
T COG5082 97 PKKCYNCGETGHLSRDCN 114 (190)
T ss_pred ccccccccccCccccccC
Confidence 358999999999999994
No 56
>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=57.80 E-value=6.3 Score=35.97 Aligned_cols=29 Identities=28% Similarity=0.563 Sum_probs=26.0
Q ss_pred CCCccCHHHHHHHHHHHHHcCCCCHHhHh
Q 022223 91 RGVPWTEDEHRLFLLGLQKVGKGDWRGIS 119 (300)
Q Consensus 91 kg~~WTeEEh~lFLegLekyGkGdWk~IA 119 (300)
...-|-.+-+-.+|.|+-+||.|+|..|.
T Consensus 2 ~~~iw~r~hdywll~gi~~hgy~rwqdi~ 30 (173)
T PF08074_consen 2 EYEIWHRRHDYWLLAGIVKHGYGRWQDIQ 30 (173)
T ss_pred hhhhhhhhhhHHHHhHHhhccchhHHHHh
Confidence 34569999999999999999999999996
No 57
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=55.37 E-value=18 Score=37.81 Aligned_cols=49 Identities=6% Similarity=-0.086 Sum_probs=42.3
Q ss_pred CCccCHHHHHHHHHHHHHcCCCCHHhHhhhhcCCCCHHHHHHHHHHHHHHh
Q 022223 92 GVPWTEDEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASHAQKYFLRR 142 (300)
Q Consensus 92 g~~WTeEEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSHAQKYF~r~ 142 (300)
...||.+|..+.+.+|++||+ ++..|+ ..|+.++..|+....-+|-.|+
T Consensus 369 n~~~~T~~~la~v~~I~~~~~-~~~pl~-wrik~t~cmee~e~l~~~~Rr~ 417 (534)
T KOG1194|consen 369 NRCFDTPAALALIDNIKRKHH-MCVPLV-WRVKQTKCMEENEILNEEARRQ 417 (534)
T ss_pred ccccCcHHHHHHHHHHHHhcc-Ccchhh-hHhcCcchhhHHHHHHHHHHHH
Confidence 467999999999999999999 899999 7999999999987766664444
No 58
>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=53.39 E-value=35 Score=34.13 Aligned_cols=49 Identities=20% Similarity=0.287 Sum_probs=38.4
Q ss_pred cCCCccCHHHHHHHHHHHHHc-CC--CCHHhHhhhhcCCCCHHHHHHHHHHHH
Q 022223 90 KRGVPWTEDEHRLFLLGLQKV-GK--GDWRGISRNFVKTRTPTQVASHAQKYF 139 (300)
Q Consensus 90 Kkg~~WTeEEh~lFLegLeky-Gk--GdWk~IAr~~V~TRT~~QVrSHAQKYF 139 (300)
+....||..|.+.+|.+|+-- |+ =|-..|+ ..+.+|+..||+..-|+.-
T Consensus 19 ~gp~~Ws~rEkr~Llr~Lqar~g~~epd~ael~-~~l~~Rs~aEI~~fl~~LK 70 (344)
T PF11035_consen 19 TGPAAWSAREKRQLLRLLQARRGQPEPDAAELA-KELPGRSEAEIRDFLQQLK 70 (344)
T ss_pred CCcccCcHHHHHHHHHHHHHhcCCCCcCHHHHH-hhccCcCHHHHHHHHHHHH
Confidence 446789999999999999965 32 2555777 5899999999998776543
No 59
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=52.22 E-value=18 Score=33.57 Aligned_cols=48 Identities=13% Similarity=0.167 Sum_probs=36.6
Q ss_pred cCCCccCHHHHHHHHHHHHHcC--CCCHHhHhh----hhcCCCCHHHHHHHHHH
Q 022223 90 KRGVPWTEDEHRLFLLGLQKVG--KGDWRGISR----NFVKTRTPTQVASHAQK 137 (300)
Q Consensus 90 Kkg~~WTeEEh~lFLegLekyG--kGdWk~IAr----~~V~TRT~~QVrSHAQK 137 (300)
.....||.+|++++........ ...|.+|=. -|-.+||+.+...||+-
T Consensus 71 q~kalfS~~EE~lL~~v~s~~~p~le~Fq~LL~~n~~vFh~sRTak~L~~HW~l 124 (199)
T PF13325_consen 71 QSKALFSKEEEQLLGTVASSSQPSLETFQELLDKNRSVFHPSRTAKSLQDHWRL 124 (199)
T ss_pred cccCCCCHHHHHHHHhhhhccCCcHHHHHHHHHhChhhhccccCHHHHHHHHHH
Confidence 4567899999999998765543 246777721 47788999999999983
No 60
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=46.74 E-value=13 Score=23.42 Aligned_cols=19 Identities=26% Similarity=0.805 Sum_probs=14.1
Q ss_pred CCCccCCCCCC-CCCCCCCC
Q 022223 1 MSRSCSQCGNN-GHNSRTCA 19 (300)
Q Consensus 1 m~R~CS~Cgn~-GHNsRTC~ 19 (300)
|.+.|.+||.. --..+-|+
T Consensus 1 m~~~Cp~Cg~~~~~~~~fC~ 20 (26)
T PF13248_consen 1 MEMFCPNCGAEIDPDAKFCP 20 (26)
T ss_pred CcCCCcccCCcCCcccccCh
Confidence 78999999984 33456666
No 61
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=46.20 E-value=12 Score=27.34 Aligned_cols=18 Identities=39% Similarity=1.055 Sum_probs=13.9
Q ss_pred CccCCCC-CCCCCCCCCCC
Q 022223 3 RSCSQCG-NNGHNSRTCAE 20 (300)
Q Consensus 3 R~CS~Cg-n~GHNsRTC~~ 20 (300)
|||.+|| .||+-+--|.+
T Consensus 12 rkCp~CGt~NG~R~~~CKN 30 (44)
T PF14952_consen 12 RKCPKCGTYNGTRGLSCKN 30 (44)
T ss_pred ccCCcCcCccCcccccccC
Confidence 8999999 46777766764
No 62
>PHA00442 host recBCD nuclease inhibitor
Probab=44.56 E-value=23 Score=27.26 Aligned_cols=24 Identities=25% Similarity=0.565 Sum_probs=20.7
Q ss_pred CHHHHHHHHHHHHHcCCCCHHhHh
Q 022223 96 TEDEHRLFLLGLQKVGKGDWRGIS 119 (300)
Q Consensus 96 TeEEh~lFLegLekyGkGdWk~IA 119 (300)
+-|-+..||++|+-.|-.+|.++.
T Consensus 24 sLek~~~~L~~Lea~GVDNW~Gy~ 47 (59)
T PHA00442 24 SLEKDNEFLKALRACGVDNWDGYM 47 (59)
T ss_pred HHHHhhHHHHHHHHcCCcchhhHH
Confidence 345667899999999999999997
No 63
>PF09420 Nop16: Ribosome biogenesis protein Nop16; InterPro: IPR019002 Nucleolar protein 16 (Nop16) is a protein involved in the biogenesis of the 60S ribosomal subunit.
Probab=44.11 E-value=65 Score=28.12 Aligned_cols=48 Identities=25% Similarity=0.390 Sum_probs=37.8
Q ss_pred cCCCccCHHHHHHHHHHHHHcCCCCHHhHhhhhc-CC--CCHHHHHHHHHHH
Q 022223 90 KRGVPWTEDEHRLFLLGLQKVGKGDWRGISRNFV-KT--RTPTQVASHAQKY 138 (300)
Q Consensus 90 Kkg~~WTeEEh~lFLegLekyGkGdWk~IAr~~V-~T--RT~~QVrSHAQKY 138 (300)
+....=+++|.......|++||. |++.++++.= .. .|+.|++--..+|
T Consensus 112 ~~~~~ls~~e~~~i~~Li~KhGd-Dy~aMarD~KLN~~Q~T~~qlrrki~~~ 162 (164)
T PF09420_consen 112 KKPRRLSEREIEYIEYLIEKHGD-DYKAMARDRKLNYMQHTPGQLRRKIRKY 162 (164)
T ss_pred cCCCCCCHHHHHHHHHHHHHHCc-cHHHHhccCCCCcccCCHHHHHHHHHHh
Confidence 55667899999999999999997 9999996322 11 6999998776665
No 64
>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=42.61 E-value=12 Score=24.08 Aligned_cols=10 Identities=30% Similarity=1.099 Sum_probs=8.0
Q ss_pred CCccCCCCCC
Q 022223 2 SRSCSQCGNN 11 (300)
Q Consensus 2 ~R~CS~Cgn~ 11 (300)
+++|.|||+.
T Consensus 14 ~~~Cp~CG~~ 23 (26)
T PF10571_consen 14 AKFCPHCGYD 23 (26)
T ss_pred cCcCCCCCCC
Confidence 5789999973
No 65
>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=38.65 E-value=77 Score=24.40 Aligned_cols=28 Identities=29% Similarity=0.558 Sum_probs=20.0
Q ss_pred CCHHhHhhhhcCCCC-----HHHHHHHHHHHHHH
Q 022223 113 GDWRGISRNFVKTRT-----PTQVASHAQKYFLR 141 (300)
Q Consensus 113 GdWk~IAr~~V~TRT-----~~QVrSHAQKYF~r 141 (300)
+.|..|++ .++--. ..+++.||.+|+..
T Consensus 58 ~~W~~va~-~lg~~~~~~~~~~~L~~~Y~~~L~~ 90 (92)
T PF01388_consen 58 KKWREVAR-KLGFPPSSTSAAQQLRQHYEKYLLP 90 (92)
T ss_dssp TTHHHHHH-HTTS-TTSCHHHHHHHHHHHHHTHH
T ss_pred chHHHHHH-HhCCCCCCCcHHHHHHHHHHHHhHh
Confidence 57999996 443322 47899999998764
No 66
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=38.24 E-value=16 Score=33.72 Aligned_cols=18 Identities=44% Similarity=1.053 Sum_probs=16.6
Q ss_pred CCccCCCCCCCCCCCCCC
Q 022223 2 SRSCSQCGNNGHNSRTCA 19 (300)
Q Consensus 2 ~R~CS~Cgn~GHNsRTC~ 19 (300)
.++|--||++||-.|-|+
T Consensus 60 ~~~C~nCg~~GH~~~DCP 77 (190)
T COG5082 60 NPVCFNCGQNGHLRRDCP 77 (190)
T ss_pred ccccchhcccCcccccCC
Confidence 368999999999999999
No 67
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=36.44 E-value=1e+02 Score=24.02 Aligned_cols=31 Identities=19% Similarity=0.418 Sum_probs=22.3
Q ss_pred CCHHhHhhhhcCCC-----CHHHHHHHHHHHHHHhhh
Q 022223 113 GDWRGISRNFVKTR-----TPTQVASHAQKYFLRRFN 144 (300)
Q Consensus 113 GdWk~IAr~~V~TR-----T~~QVrSHAQKYF~r~~~ 144 (300)
..|..|++ .++-. ...+++.|+++|+.....
T Consensus 54 ~~W~~Va~-~lg~~~~~~~~~~~lk~~Y~k~L~~yE~ 89 (93)
T smart00501 54 KKWKEIAR-ELGIPDTSTSAASSLRKHYERYLLPFER 89 (93)
T ss_pred CCHHHHHH-HhCCCcccchHHHHHHHHHHHHhHHHHH
Confidence 47999995 44432 367889999999776553
No 68
>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=36.02 E-value=1.3e+02 Score=20.77 Aligned_cols=37 Identities=14% Similarity=0.206 Sum_probs=22.8
Q ss_pred HHHHHHHHHHHHcCCCCHHhHhhhhcCCCCHHHHHHHHHH
Q 022223 98 DEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASHAQK 137 (300)
Q Consensus 98 EEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSHAQK 137 (300)
++++..+...-..|. .|+.|| ..++ .|...|+.|.++
T Consensus 13 ~~~r~i~~l~~~~g~-s~~eIa-~~l~-~s~~~v~~~l~r 49 (54)
T PF08281_consen 13 ERQREIFLLRYFQGM-SYAEIA-EILG-ISESTVKRRLRR 49 (54)
T ss_dssp HHHHHHHHHHHTS----HHHHH-HHCT-S-HHHHHHHHHH
T ss_pred HHHHHHHHHHHHHCc-CHHHHH-HHHC-cCHHHHHHHHHH
Confidence 444555555566776 899999 5665 888888887654
No 69
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=35.83 E-value=31 Score=29.14 Aligned_cols=19 Identities=63% Similarity=1.240 Sum_probs=11.9
Q ss_pred CccCCCCCCCCCCCCCCCC
Q 022223 3 RSCSQCGNNGHNSRTCAEA 21 (300)
Q Consensus 3 R~CS~Cgn~GHNsRTC~~~ 21 (300)
+.|..||..||-++.|+..
T Consensus 53 ~~C~~Cg~~GH~~~~Cp~~ 71 (148)
T PTZ00368 53 RSCYNCGKTGHLSRECPEA 71 (148)
T ss_pred cccCCCCCcCcCcccCCCc
Confidence 3566666666666666553
No 70
>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=33.01 E-value=1.3e+02 Score=20.88 Aligned_cols=38 Identities=16% Similarity=0.232 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHHcCCCCHHhHhhhhcCCCCHHHHHHHHHH
Q 022223 98 DEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASHAQK 137 (300)
Q Consensus 98 EEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSHAQK 137 (300)
+=+++.|..|+.-|+-.|..|| ..++ =|...|..+.++
T Consensus 3 ~~D~~Il~~Lq~d~r~s~~~la-~~lg-lS~~~v~~Ri~r 40 (42)
T PF13404_consen 3 ELDRKILRLLQEDGRRSYAELA-EELG-LSESTVRRRIRR 40 (42)
T ss_dssp HHHHHHHHHHHH-TTS-HHHHH-HHHT-S-HHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCccHHHHH-HHHC-cCHHHHHHHHHH
Confidence 4578899999999999999999 5777 566677666543
No 71
>KOG1878 consensus Nuclear receptor coregulator SMRT/SMRTER, contains Myb-like domains [Transcription]
Probab=31.64 E-value=7.4 Score=45.21 Aligned_cols=47 Identities=19% Similarity=0.403 Sum_probs=41.3
Q ss_pred CccccCCCccCHHHHHHHHHHHHHcCCCCHHhHhhhhcCCCCHHHHHHH
Q 022223 86 SRERKRGVPWTEDEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASH 134 (300)
Q Consensus 86 ~~~rKkg~~WTeEEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSH 134 (300)
++.+.....|+++||+.|-.=+..+-+ ++..|+ +|+--+|..||.-+
T Consensus 219 ~k~~~~~n~Ws~~Ek~~fk~rf~~H~k-nf~~~a-s~~erkSv~d~vlf 265 (1672)
T KOG1878|consen 219 HKDRQRMNEWSPEEKELFKSRFAQHVK-NFGLIA-SFFERKSVSDCVLF 265 (1672)
T ss_pred cchHHHhhhccccccccccchhhhcCc-chhhhh-hhhcccchhhceee
Confidence 345567888999999999999999997 999999 89988999999866
No 72
>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=29.74 E-value=63 Score=23.13 Aligned_cols=41 Identities=24% Similarity=0.225 Sum_probs=32.2
Q ss_pred HHHHHHHHHcCCCCHHhHhhhhcCCCCHHHHHHHHHHHHHHhh
Q 022223 101 RLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASHAQKYFLRRF 143 (300)
Q Consensus 101 ~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSHAQKYF~r~~ 143 (300)
+++-+|++..|..++.-|. .+.+|+..|.+.=.+.|.....
T Consensus 4 ~~l~~a~~~~g~de~~li~--Il~~rs~~ql~~i~~~Y~~~~g 44 (66)
T PF00191_consen 4 ELLHAALKGWGTDEDVLIE--ILCTRSPAQLRAIKQAYKKKYG 44 (66)
T ss_dssp HHHHHHHSSSSSTHHHHHH--HHHHSTHHHHHHHHHHHHHHHS
T ss_pred HHHHHHccCCCCChhHhhh--HHhhhcccccceeehhhhhhhH
Confidence 4788899999976666665 7889999999988887765543
No 73
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=29.00 E-value=25 Score=23.78 Aligned_cols=10 Identities=60% Similarity=1.561 Sum_probs=8.3
Q ss_pred CccCCCCCCC
Q 022223 3 RSCSQCGNNG 12 (300)
Q Consensus 3 R~CS~Cgn~G 12 (300)
++|+.||++|
T Consensus 4 ~~C~~C~~~~ 13 (33)
T PF08792_consen 4 KKCSKCGGNG 13 (33)
T ss_pred eEcCCCCCCe
Confidence 6799998887
No 74
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=28.95 E-value=28 Score=36.66 Aligned_cols=19 Identities=37% Similarity=0.732 Sum_probs=15.6
Q ss_pred CccCCCCCCCCCCCCCCCC
Q 022223 3 RSCSQCGNNGHNSRTCAEA 21 (300)
Q Consensus 3 R~CS~Cgn~GHNsRTC~~~ 21 (300)
+.|-+||-.||+++-|...
T Consensus 286 n~c~~cg~~gH~~~dc~~~ 304 (554)
T KOG0119|consen 286 NVCKICGPLGHISIDCKVN 304 (554)
T ss_pred ccccccCCcccccccCCCc
Confidence 4789999999999999843
No 75
>PF05634 APO_RNA-bind: APO RNA-binding; InterPro: IPR008512 This family consists of plant APO (accumulation of photosystem 1) proteins.
Probab=28.71 E-value=39 Score=31.69 Aligned_cols=20 Identities=40% Similarity=0.926 Sum_probs=16.4
Q ss_pred CccCCC-----CCCCCCCCCCCCCC
Q 022223 3 RSCSQC-----GNNGHNSRTCAEAG 22 (300)
Q Consensus 3 R~CS~C-----gn~GHNsRTC~~~~ 22 (300)
..|.+| |.-||.-|||....
T Consensus 99 ~~C~~C~EVHVG~~GH~irtC~g~k 123 (204)
T PF05634_consen 99 KACGYCPEVHVGPVGHKIRTCGGFK 123 (204)
T ss_pred eecCCCCCeEECCCcccccccCCCC
Confidence 469999 67899999998543
No 76
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=28.07 E-value=20 Score=25.07 Aligned_cols=8 Identities=50% Similarity=1.335 Sum_probs=4.0
Q ss_pred ccCCCCCC
Q 022223 4 SCSQCGNN 11 (300)
Q Consensus 4 ~CS~Cgn~ 11 (300)
||.+|||.
T Consensus 8 kC~~CGni 15 (36)
T PF06397_consen 8 KCEHCGNI 15 (36)
T ss_dssp E-TTT--E
T ss_pred EccCCCCE
Confidence 79999984
No 77
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=26.68 E-value=1.3e+02 Score=25.60 Aligned_cols=38 Identities=11% Similarity=0.198 Sum_probs=31.0
Q ss_pred HHHHHHHHHHHHHcCCCCHHhHhhhhcCCCCHHHHHHHHH
Q 022223 97 EDEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASHAQ 136 (300)
Q Consensus 97 eEEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSHAQ 136 (300)
++.+++.|+.|++=|+-.|..|| ..++ -+...|+.+.+
T Consensus 8 D~~D~~Il~~Lq~d~R~s~~eiA-~~lg-lS~~tV~~Ri~ 45 (153)
T PRK11179 8 DNLDRGILEALMENARTPYAELA-KQFG-VSPGTIHVRVE 45 (153)
T ss_pred CHHHHHHHHHHHHcCCCCHHHHH-HHHC-cCHHHHHHHHH
Confidence 46789999999999999999999 4666 57777776654
No 78
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=25.99 E-value=42 Score=28.29 Aligned_cols=17 Identities=53% Similarity=1.224 Sum_probs=11.7
Q ss_pred CccCCCCCCCCCCCCCC
Q 022223 3 RSCSQCGNNGHNSRTCA 19 (300)
Q Consensus 3 R~CS~Cgn~GHNsRTC~ 19 (300)
..|..||..||-++.|+
T Consensus 28 ~~C~~Cg~~GH~~~~Cp 44 (148)
T PTZ00368 28 RPCYKCGEPGHLSRECP 44 (148)
T ss_pred ccCccCCCCCcCcccCc
Confidence 35666888888666664
No 79
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=24.59 E-value=36 Score=23.31 Aligned_cols=18 Identities=33% Similarity=0.925 Sum_probs=16.5
Q ss_pred CccCCCCCCCCCCCCCCC
Q 022223 3 RSCSQCGNNGHNSRTCAE 20 (300)
Q Consensus 3 R~CS~Cgn~GHNsRTC~~ 20 (300)
..|--|+.-||--+.|+.
T Consensus 9 Y~C~~C~~~GH~i~dCP~ 26 (32)
T PF13696_consen 9 YVCHRCGQKGHWIQDCPT 26 (32)
T ss_pred CEeecCCCCCccHhHCCC
Confidence 469999999999999996
No 80
>PLN00111 accumulation of photosystem one; Provisional
Probab=24.53 E-value=48 Score=33.89 Aligned_cols=20 Identities=45% Similarity=0.989 Sum_probs=16.3
Q ss_pred CccCCC-----CCCCCCCCCCCCCC
Q 022223 3 RSCSQC-----GNNGHNSRTCAEAG 22 (300)
Q Consensus 3 R~CS~C-----gn~GHNsRTC~~~~ 22 (300)
+.|.+| |.-||.-|||....
T Consensus 121 ~~C~~C~EVHVG~~GH~irtC~g~k 145 (399)
T PLN00111 121 HACKFCSEVHVGKVGHLIRTCRGPG 145 (399)
T ss_pred eecCcCCceeECCCCccccccCCcc
Confidence 568888 67999999999654
No 81
>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=24.14 E-value=39 Score=31.26 Aligned_cols=18 Identities=44% Similarity=1.043 Sum_probs=15.7
Q ss_pred ccCCCCCCCCCCCCCCCC
Q 022223 4 SCSQCGNNGHNSRTCAEA 21 (300)
Q Consensus 4 ~CS~Cgn~GHNsRTC~~~ 21 (300)
+|-.||+.||=++-|+..
T Consensus 145 ~Cy~Cg~~GH~s~~C~~~ 162 (261)
T KOG4400|consen 145 KCYSCGEQGHISDDCPEN 162 (261)
T ss_pred ccCCCCcCCcchhhCCCC
Confidence 599999999999999943
No 82
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=23.54 E-value=2.5e+02 Score=21.50 Aligned_cols=45 Identities=13% Similarity=0.192 Sum_probs=28.6
Q ss_pred ccCHHHHHHHHHHHHHcCCCCHHhHhhhhcCCCCHHHHHHHHHHHHHHh
Q 022223 94 PWTEDEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASHAQKYFLRR 142 (300)
Q Consensus 94 ~WTeEEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSHAQKYF~r~ 142 (300)
.+++.|.+.|..- -..|. .|..|| ...+. +...|+.+.++-..++
T Consensus 110 ~L~~~~~~ii~~~-~~~g~-s~~eIA-~~l~~-s~~~v~~~~~~~~~kl 154 (158)
T TIGR02937 110 KLPEREREVLVLR-YLEGL-SYKEIA-EILGI-SVGTVKRRLKRARKKL 154 (158)
T ss_pred hCCHHHHHHHhhH-HhcCC-CHHHHH-HHHCC-CHHHHHHHHHHHHHHH
Confidence 3666666666433 23465 899999 57775 7777777665554444
No 83
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=23.50 E-value=1.7e+02 Score=22.73 Aligned_cols=38 Identities=21% Similarity=0.256 Sum_probs=30.2
Q ss_pred HHHHHHHHHHHHHcCCCCHHhHhhhhcCCCCHHHHHHHHH
Q 022223 97 EDEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASHAQ 136 (300)
Q Consensus 97 eEEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSHAQ 136 (300)
++.++++|..|+..|.-.|..|+ ..++ -+...|+.+.+
T Consensus 2 d~~D~~il~~L~~~~~~~~~~la-~~l~-~s~~tv~~~l~ 39 (108)
T smart00344 2 DEIDRKILEELQKDARISLAELA-KKVG-LSPSTVHNRVK 39 (108)
T ss_pred CHHHHHHHHHHHHhCCCCHHHHH-HHHC-cCHHHHHHHHH
Confidence 35788999999999988999999 4665 56777777654
No 84
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=22.80 E-value=48 Score=23.77 Aligned_cols=19 Identities=32% Similarity=0.906 Sum_probs=17.0
Q ss_pred CCccCCCCCCCCCCCCCCC
Q 022223 2 SRSCSQCGNNGHNSRTCAE 20 (300)
Q Consensus 2 ~R~CS~Cgn~GHNsRTC~~ 20 (300)
...|-.||..||=..-|+.
T Consensus 4 ~~~CqkC~~~GH~tyeC~~ 22 (42)
T PF13917_consen 4 RVRCQKCGQKGHWTYECPN 22 (42)
T ss_pred CCcCcccCCCCcchhhCCC
Confidence 3679999999999999994
No 85
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=22.58 E-value=1.5e+02 Score=25.39 Aligned_cols=39 Identities=26% Similarity=0.232 Sum_probs=31.2
Q ss_pred HHHHHHHHHHHHHcCCCCHHhHhhhhcCCCCHHHHHHHHHH
Q 022223 97 EDEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASHAQK 137 (300)
Q Consensus 97 eEEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSHAQK 137 (300)
+|-+++.|..|++-|+-.|..|| .-++ -+..-|+.+.++
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA-~~lg-lS~~tv~~Ri~r 51 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELS-KRVG-LSPTPCLERVRR 51 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHH-HHHC-cCHHHHHHHHHH
Confidence 66789999999999999999999 4666 566667666543
No 86
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=22.29 E-value=38 Score=27.28 Aligned_cols=16 Identities=25% Similarity=0.725 Sum_probs=10.5
Q ss_pred CCCccCCCCCCCCCCC
Q 022223 1 MSRSCSQCGNNGHNSR 16 (300)
Q Consensus 1 m~R~CS~Cgn~GHNsR 16 (300)
|..+|++||..=+--|
T Consensus 7 ~~~~C~~CG~d~~~~~ 22 (86)
T PF06170_consen 7 VAPRCPHCGLDYSHAR 22 (86)
T ss_pred CCCcccccCCccccCC
Confidence 4578999997543333
No 87
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=22.28 E-value=1.8e+02 Score=19.76 Aligned_cols=25 Identities=24% Similarity=0.408 Sum_probs=19.6
Q ss_pred HHHHHHHHHHHHcCCCCHHhHhhhhcC
Q 022223 98 DEHRLFLLGLQKVGKGDWRGISRNFVK 124 (300)
Q Consensus 98 EEh~lFLegLekyGkGdWk~IAr~~V~ 124 (300)
=|...+.++|+++| |+....|+ .+|
T Consensus 5 ~E~~~i~~aL~~~~-gn~~~aA~-~Lg 29 (42)
T PF02954_consen 5 FEKQLIRQALERCG-GNVSKAAR-LLG 29 (42)
T ss_dssp HHHHHHHHHHHHTT-T-HHHHHH-HHT
T ss_pred HHHHHHHHHHHHhC-CCHHHHHH-HHC
Confidence 47888999999999 59999994 555
No 88
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=21.48 E-value=1e+02 Score=31.89 Aligned_cols=43 Identities=14% Similarity=0.247 Sum_probs=35.7
Q ss_pred CccCHHHHHHHHHHHHHcCCCCHHhHhhh-----hcCCCCHHHHHHHHH
Q 022223 93 VPWTEDEHRLFLLGLQKVGKGDWRGISRN-----FVKTRTPTQVASHAQ 136 (300)
Q Consensus 93 ~~WTeEEh~lFLegLekyGkGdWk~IAr~-----~V~TRT~~QVrSHAQ 136 (300)
..||.||-+-+.+..++|.- +|--|+-. |=.+||.+..+.++-
T Consensus 131 n~WskeETD~LF~lck~fDL-Rf~VIaDRyd~qq~~~sRTvEdLKeRyY 178 (445)
T KOG2656|consen 131 NSWSKEETDYLFDLCKRFDL-RFFVIADRYDNQQYKKSRTVEDLKERYY 178 (445)
T ss_pred ccccHHHHHHHHHHHHhcCe-eEEEEeeccchhhccccccHHHHHHHHH
Confidence 46999999999999999997 78888743 344499999998863
No 89
>CHL00112 rpl28 ribosomal protein L28; Provisional
Probab=20.44 E-value=46 Score=25.64 Aligned_cols=12 Identities=33% Similarity=0.767 Sum_probs=10.1
Q ss_pred CCCccCCCCCCC
Q 022223 1 MSRSCSQCGNNG 12 (300)
Q Consensus 1 m~R~CS~Cgn~G 12 (300)
|+|+|--||.--
T Consensus 1 Msr~C~i~GK~~ 12 (63)
T CHL00112 1 MSKKCQLTGKKA 12 (63)
T ss_pred CCCeeccCCCcC
Confidence 899999999743
No 90
>PHA03074 late transcription factor VLTF-3; Provisional
Probab=20.41 E-value=44 Score=31.66 Aligned_cols=13 Identities=46% Similarity=0.851 Sum_probs=10.6
Q ss_pred CccCCCCCCCCCC
Q 022223 3 RSCSQCGNNGHNS 15 (300)
Q Consensus 3 R~CS~Cgn~GHNs 15 (300)
++||.|++||==+
T Consensus 5 ~~C~~C~~ngiv~ 17 (225)
T PHA03074 5 KLCSGCRHNGIVS 17 (225)
T ss_pred hhcCCCCCCCeee
Confidence 7899999998533
Done!