Query 021351
Match_columns 313
No_of_seqs 211 out of 560
Neff 3.3
Searched_HMMs 46136
Date Fri Mar 29 09:33:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021351.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021351hhsearch_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 2.6E-18 5.6E-23 128.0 5.7 53 90-142 1-57 (57)
2 PF00249 Myb_DNA-binding: Myb- 99.5 1.8E-14 3.8E-19 101.3 5.4 46 93-139 2-48 (48)
3 cd00167 SANT 'SWI3, ADA2, N-Co 99.2 2.2E-11 4.8E-16 80.3 5.3 45 94-139 1-45 (45)
4 smart00717 SANT SANT SWI3, AD 99.2 3.1E-11 6.7E-16 80.5 5.8 46 93-139 2-47 (49)
5 KOG0457 Histone acetyltransfer 99.0 6.8E-10 1.5E-14 110.3 5.3 50 92-142 72-121 (438)
6 PF13921 Myb_DNA-bind_6: Myb-l 98.9 9.5E-10 2.1E-14 79.5 4.5 43 95-139 1-43 (60)
7 PLN03212 Transcription repress 98.7 1.2E-08 2.6E-13 95.6 5.9 50 89-139 22-72 (249)
8 PLN03091 hypothetical protein; 98.7 1.6E-08 3.4E-13 101.2 4.9 52 87-139 9-61 (459)
9 KOG0048 Transcription factor, 98.4 1.9E-07 4.1E-12 85.1 4.5 47 92-139 9-56 (238)
10 COG5114 Histone acetyltransfer 98.3 6.1E-07 1.3E-11 87.8 4.5 59 93-159 64-122 (432)
11 PLN03212 Transcription repress 98.3 1.7E-06 3.6E-11 81.5 6.4 51 90-142 76-126 (249)
12 COG5259 RSC8 RSC chromatin rem 98.2 1.1E-06 2.3E-11 88.9 4.4 41 93-135 280-320 (531)
13 KOG0724 Zuotin and related mol 98.2 8E-07 1.7E-11 83.5 2.7 75 85-159 157-236 (335)
14 PLN03091 hypothetical protein; 98.2 3.9E-06 8.4E-11 84.4 6.8 50 91-142 66-115 (459)
15 KOG1279 Chromatin remodeling f 98.0 7.1E-06 1.5E-10 83.6 5.2 42 92-135 253-294 (506)
16 KOG4329 DNA-binding protein [G 97.8 2.5E-05 5.5E-10 77.6 5.0 49 92-144 277-325 (445)
17 KOG0048 Transcription factor, 97.6 0.00013 2.7E-09 66.8 6.6 50 90-141 60-109 (238)
18 KOG0049 Transcription factor, 97.5 0.00011 2.5E-09 77.3 5.8 50 91-141 359-408 (939)
19 PLN03162 golden-2 like transcr 96.9 0.0022 4.9E-08 64.4 6.7 57 88-145 233-293 (526)
20 KOG0049 Transcription factor, 96.7 0.0016 3.5E-08 69.0 4.8 47 90-137 410-456 (939)
21 KOG4167 Predicted DNA-binding 96.3 0.0067 1.5E-07 65.0 5.8 48 92-144 619-666 (907)
22 KOG0050 mRNA splicing protein 96.1 0.0051 1.1E-07 63.8 3.7 49 90-139 5-53 (617)
23 PF13837 Myb_DNA-bind_4: Myb/S 95.9 0.019 4.1E-07 43.8 5.3 53 94-147 3-72 (90)
24 COG5118 BDP1 Transcription ini 95.4 0.023 5.1E-07 57.4 5.2 46 87-134 360-405 (507)
25 KOG4468 Polycomb-group transcr 95.3 0.023 5.1E-07 60.0 5.1 52 92-144 88-148 (782)
26 smart00426 TEA TEA domain. 95.2 0.024 5.1E-07 44.7 3.5 43 93-136 4-66 (68)
27 KOG3554 Histone deacetylase co 94.8 0.021 4.6E-07 59.0 2.9 51 89-143 282-332 (693)
28 PF00098 zf-CCHC: Zinc knuckle 94.6 0.027 5.9E-07 33.7 2.0 18 3-20 1-18 (18)
29 PF09111 SLIDE: SLIDE; InterP 94.4 0.084 1.8E-06 44.9 5.2 52 90-142 47-112 (118)
30 KOG0724 Zuotin and related mol 94.2 0.011 2.4E-07 55.9 -0.5 48 95-144 56-103 (335)
31 PLN03142 Probable chromatin-re 94.0 0.08 1.7E-06 58.6 5.5 50 92-142 823-873 (1033)
32 KOG0051 RNA polymerase I termi 93.7 0.085 1.8E-06 55.6 4.7 53 90-143 434-511 (607)
33 COG5147 REB1 Myb superfamily p 93.6 0.04 8.6E-07 57.0 2.2 55 88-143 16-70 (512)
34 PF14392 zf-CCHC_4: Zinc knuck 93.4 0.031 6.6E-07 40.2 0.7 19 1-19 30-48 (49)
35 PF15288 zf-CCHC_6: Zinc knuck 92.8 0.055 1.2E-06 38.8 1.2 20 3-22 2-23 (40)
36 KOG3841 TEF-1 and related tran 92.3 0.2 4.3E-06 50.8 4.9 49 90-139 74-142 (455)
37 PF01285 TEA: TEA/ATTS domain 92.2 0.16 3.5E-06 51.4 4.2 48 90-138 47-112 (431)
38 PF13873 Myb_DNA-bind_5: Myb/S 91.6 0.5 1.1E-05 35.7 5.3 51 93-143 3-73 (78)
39 PF08914 Myb_DNA-bind_2: Rap1 90.9 0.42 9.1E-06 36.8 4.3 51 92-142 2-60 (65)
40 KOG0051 RNA polymerase I termi 90.2 0.33 7.1E-06 51.4 4.2 48 91-141 383-430 (607)
41 KOG1194 Predicted DNA-binding 89.8 0.6 1.3E-05 48.3 5.6 41 93-135 188-228 (534)
42 PF12776 Myb_DNA-bind_3: Myb/S 89.0 1 2.2E-05 34.7 5.2 60 94-153 1-76 (96)
43 COG5147 REB1 Myb superfamily p 87.4 0.86 1.9E-05 47.4 4.9 53 90-144 70-122 (512)
44 KOG4282 Transcription factor G 86.2 1.4 3.1E-05 42.1 5.4 57 92-148 54-122 (345)
45 smart00343 ZnF_C2HC zinc finge 84.5 0.52 1.1E-05 29.5 1.1 17 4-20 1-17 (26)
46 PLN03142 Probable chromatin-re 84.4 2.2 4.7E-05 47.8 6.5 50 92-142 926-986 (1033)
47 KOG0050 mRNA splicing protein 76.5 2.7 5.8E-05 44.4 3.6 49 91-142 58-106 (617)
48 PF04504 DUF573: Protein of un 70.3 9.4 0.0002 31.3 4.8 39 94-133 6-56 (98)
49 PF06461 DUF1086: Domain of Un 69.5 13 0.00027 33.4 5.7 49 95-144 41-91 (145)
50 KOG0385 Chromatin remodeling c 67.4 8.2 0.00018 42.8 4.9 52 93-146 796-847 (971)
51 KOG0384 Chromodomain-helicase 66.6 3.5 7.5E-05 47.3 2.0 54 91-145 1132-1196(1373)
52 KOG2009 Transcription initiati 64.9 6.6 0.00014 41.8 3.6 47 85-133 402-448 (584)
53 PRK13923 putative spore coat p 63.8 8.9 0.00019 35.0 3.7 48 92-140 5-57 (170)
54 COG5082 AIR1 Arginine methyltr 63.6 3.8 8.3E-05 38.0 1.4 18 2-19 97-114 (190)
55 PF13325 MCRS_N: N-terminal re 63.3 9 0.0002 35.7 3.8 49 89-137 70-124 (199)
56 TIGR02894 DNA_bind_RsfA transc 57.9 15 0.00032 33.5 4.0 49 92-142 4-58 (161)
57 PF11035 SnAPC_2_like: Small n 57.8 27 0.00059 35.1 6.2 53 89-142 18-73 (344)
58 KOG1194 Predicted DNA-binding 50.6 23 0.00051 37.2 4.6 48 93-142 370-417 (534)
59 PF13248 zf-ribbon_3: zinc-rib 49.3 11 0.00025 23.9 1.4 20 1-20 1-21 (26)
60 PF09420 Nop16: Ribosome bioge 45.8 58 0.0013 28.6 5.8 48 90-138 112-162 (164)
61 PF14952 zf-tcix: Putative tre 44.6 14 0.00029 27.3 1.4 18 3-20 12-30 (44)
62 PHA00442 host recBCD nuclease 43.8 23 0.00049 27.5 2.5 24 96-119 24-47 (59)
63 PF08074 CHDCT2: CHDCT2 (NUC03 42.4 15 0.00033 33.7 1.7 27 93-119 4-30 (173)
64 PF01388 ARID: ARID/BRIGHT DNA 39.7 74 0.0016 24.6 5.0 28 113-141 58-90 (92)
65 PF10571 UPF0547: Uncharacteri 38.9 16 0.00034 23.8 0.9 10 2-11 14-23 (26)
66 COG5082 AIR1 Arginine methyltr 38.9 16 0.00034 34.0 1.2 18 2-19 60-77 (190)
67 smart00501 BRIGHT BRIGHT, ARID 37.3 1E+02 0.0022 24.2 5.5 32 113-144 54-89 (93)
68 PTZ00368 universal minicircle 35.7 31 0.00068 29.2 2.5 19 3-21 53-71 (148)
69 PF08281 Sigma70_r4_2: Sigma-7 31.0 1.8E+02 0.0039 20.1 5.4 37 98-137 13-49 (54)
70 PF08792 A2L_zn_ribbon: A2L zi 28.6 26 0.00057 23.9 0.7 10 3-12 4-13 (33)
71 KOG0119 Splicing factor 1/bran 28.3 29 0.00064 36.7 1.3 19 3-21 286-304 (554)
72 PTZ00368 universal minicircle 27.2 40 0.00086 28.6 1.7 16 4-19 29-44 (148)
73 KOG2656 DNA methyltransferase 27.1 74 0.0016 33.1 3.8 43 93-136 131-178 (445)
74 PF00191 Annexin: Annexin; In 26.8 79 0.0017 22.7 3.0 40 101-142 4-43 (66)
75 PF13696 zf-CCHC_2: Zinc knuck 26.2 33 0.00071 23.7 0.8 18 3-20 9-26 (32)
76 PF05634 APO_RNA-bind: APO RNA 25.2 50 0.0011 31.2 2.1 20 3-22 99-123 (204)
77 PF13917 zf-CCHC_3: Zinc knuck 23.7 45 0.00098 24.1 1.2 19 2-20 4-22 (42)
78 PF06397 Desulfoferrod_N: Desu 23.3 31 0.00067 24.3 0.3 8 4-11 8-15 (36)
79 KOG4400 E3 ubiquitin ligase in 22.8 43 0.00093 31.1 1.2 18 4-21 145-162 (261)
80 PF06170 DUF983: Protein of un 21.3 41 0.0009 27.3 0.7 13 1-13 7-19 (86)
81 PLN00111 accumulation of photo 21.3 61 0.0013 33.3 2.0 20 3-22 121-145 (399)
82 TIGR02937 sigma70-ECF RNA poly 21.1 3.1E+02 0.0067 21.0 5.5 45 95-143 111-155 (158)
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=2.6e-18 Score=127.96 Aligned_cols=53 Identities=49% Similarity=0.691 Sum_probs=47.7
Q ss_pred cCCCccCHHHHHHHHHHHHHcCCCCH---HhhhhhhcCCC-CHHHHHHHHHHHHHHH
Q 021351 90 KRGVPWTEDEHRLFLLGLQKVGKGDW---RGISRNFVKTR-TPTQVASHAQKYFLRR 142 (313)
Q Consensus 90 Kkg~~WTeEEh~lFLegLekyGkGdW---k~IAr~~V~TR-T~~QVrSHAQKYFir~ 142 (313)
|.+..||+|||++||+||+.||.|+| +.|++.++.+| |+.||+||+||||+++
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 99995566688 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=99.52 E-value=1.8e-14 Score=101.33 Aligned_cols=46 Identities=35% Similarity=0.616 Sum_probs=41.3
Q ss_pred CccCHHHHHHHHHHHHHcCCCCHHhhhhhhcC-CCCHHHHHHHHHHHH
Q 021351 93 VPWTEDEHRLFLLGLQKVGKGDWRGISRNFVK-TRTPTQVASHAQKYF 139 (313)
Q Consensus 93 ~~WTeEEh~lFLegLekyGkGdWk~IAr~~V~-TRT~~QVrSHAQKYF 139 (313)
.+||+||+++|++||++||.++|+.|| .+|+ +||..||++|+++|.
T Consensus 2 ~~Wt~eE~~~l~~~v~~~g~~~W~~Ia-~~~~~~Rt~~qc~~~~~~~~ 48 (48)
T PF00249_consen 2 GPWTEEEDEKLLEAVKKYGKDNWKKIA-KRMPGGRTAKQCRSRYQNLL 48 (48)
T ss_dssp -SS-HHHHHHHHHHHHHSTTTHHHHHH-HHHSSSSTHHHHHHHHHHHT
T ss_pred CCCCHHHHHHHHHHHHHhCCcHHHHHH-HHcCCCCCHHHHHHHHHhhC
Confidence 469999999999999999997799999 6888 999999999999883
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=99.22 E-value=2.2e-11 Score=80.35 Aligned_cols=45 Identities=36% Similarity=0.701 Sum_probs=41.6
Q ss_pred ccCHHHHHHHHHHHHHcCCCCHHhhhhhhcCCCCHHHHHHHHHHHH
Q 021351 94 PWTEDEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASHAQKYF 139 (313)
Q Consensus 94 ~WTeEEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSHAQKYF 139 (313)
+||+||+++|+.++.+||.++|..|| .++++||..||+.|+++++
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 7999999999999987763
No 4
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.21 E-value=3.1e-11 Score=80.49 Aligned_cols=46 Identities=28% Similarity=0.499 Sum_probs=42.3
Q ss_pred CccCHHHHHHHHHHHHHcCCCCHHhhhhhhcCCCCHHHHHHHHHHHH
Q 021351 93 VPWTEDEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASHAQKYF 139 (313)
Q Consensus 93 ~~WTeEEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSHAQKYF 139 (313)
..||+||+++|+.++.+||.++|..|| .++++||+.||+.++.+++
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 469999999999999999966999999 7999999999999987664
No 5
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=98.95 E-value=6.8e-10 Score=110.31 Aligned_cols=50 Identities=30% Similarity=0.578 Sum_probs=47.0
Q ss_pred CCccCHHHHHHHHHHHHHcCCCCHHhhhhhhcCCCCHHHHHHHHHHHHHHH
Q 021351 92 GVPWTEDEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASHAQKYFLRR 142 (313)
Q Consensus 92 g~~WTeEEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSHAQKYFir~ 142 (313)
...||.+|+.+||+|++.||-|+|..|| +||+|||.++|+.|+.|+|++.
T Consensus 72 ~~~WtadEEilLLea~~t~G~GNW~dIA-~hIGtKtkeeck~hy~k~fv~s 121 (438)
T KOG0457|consen 72 DPSWTADEEILLLEAAETYGFGNWQDIA-DHIGTKTKEECKEHYLKHFVNS 121 (438)
T ss_pred CCCCChHHHHHHHHHHHHhCCCcHHHHH-HHHcccchHHHHHHHHHHHhcC
Confidence 3459999999999999999999999999 8999999999999999999854
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=98.94 E-value=9.5e-10 Score=79.52 Aligned_cols=43 Identities=33% Similarity=0.661 Sum_probs=37.0
Q ss_pred cCHHHHHHHHHHHHHcCCCCHHhhhhhhcCCCCHHHHHHHHHHHH
Q 021351 95 WTEDEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASHAQKYF 139 (313)
Q Consensus 95 WTeEEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSHAQKYF 139 (313)
||+||++++++++++||. +|+.|| .++++||+.||+.|+.+++
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 6889999999999988744
No 7
>PLN03212 Transcription repressor MYB5; Provisional
Probab=98.75 E-value=1.2e-08 Score=95.64 Aligned_cols=50 Identities=22% Similarity=0.455 Sum_probs=44.9
Q ss_pred ccCCCccCHHHHHHHHHHHHHcCCCCHHhhhhhhc-CCCCHHHHHHHHHHHH
Q 021351 89 RKRGVPWTEDEHRLFLLGLQKVGKGDWRGISRNFV-KTRTPTQVASHAQKYF 139 (313)
Q Consensus 89 rKkg~~WTeEEh~lFLegLekyGkGdWk~IAr~~V-~TRT~~QVrSHAQKYF 139 (313)
..+..+||+||++++++++++||.++|+.|| ..+ ..||..|||.+|.+|+
T Consensus 22 glKRg~WT~EEDe~L~~lV~kyG~~nW~~IA-k~~g~gRT~KQCReRW~N~L 72 (249)
T PLN03212 22 GMKRGPWTVEEDEILVSFIKKEGEGRWRSLP-KRAGLLRCGKSCRLRWMNYL 72 (249)
T ss_pred CCcCCCCCHHHHHHHHHHHHHhCcccHHHHH-HhhhcCCCcchHHHHHHHhh
Confidence 3456679999999999999999999999999 566 5899999999999997
No 8
>PLN03091 hypothetical protein; Provisional
Probab=98.69 E-value=1.6e-08 Score=101.23 Aligned_cols=52 Identities=19% Similarity=0.399 Sum_probs=45.4
Q ss_pred ccccCCCccCHHHHHHHHHHHHHcCCCCHHhhhhhhcC-CCCHHHHHHHHHHHH
Q 021351 87 RERKRGVPWTEDEHRLFLLGLQKVGKGDWRGISRNFVK-TRTPTQVASHAQKYF 139 (313)
Q Consensus 87 ~~rKkg~~WTeEEh~lFLegLekyGkGdWk~IAr~~V~-TRT~~QVrSHAQKYF 139 (313)
+.+.++.+||.||+++++++|++||.++|+.|| .+++ +||.+|||.+|.+|+
T Consensus 9 KqklrKg~WTpEEDe~L~~~V~kyG~~nWs~IA-k~~g~gRT~KQCRERW~NyL 61 (459)
T PLN03091 9 KQKLRKGLWSPEEDEKLLRHITKYGHGCWSSVP-KQAGLQRCGKSCRLRWINYL 61 (459)
T ss_pred CCCCcCCCCCHHHHHHHHHHHHHhCcCCHHHHh-hhhccCcCcchHhHHHHhcc
Confidence 344556679999999999999999999999999 5665 899999999999875
No 9
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=98.44 E-value=1.9e-07 Score=85.13 Aligned_cols=47 Identities=17% Similarity=0.336 Sum_probs=44.8
Q ss_pred CCccCHHHHHHHHHHHHHcCCCCHHhhhhhhcC-CCCHHHHHHHHHHHH
Q 021351 92 GVPWTEDEHRLFLLGLQKVGKGDWRGISRNFVK-TRTPTQVASHAQKYF 139 (313)
Q Consensus 92 g~~WTeEEh~lFLegLekyGkGdWk~IAr~~V~-TRT~~QVrSHAQKYF 139 (313)
.++||.||++++.+.|++||.|+|..|+ ...+ -|+.+|||.+|-+|+
T Consensus 9 kGpWt~EED~~L~~~V~~~G~~~W~~i~-k~~gl~R~GKSCRlRW~NyL 56 (238)
T KOG0048|consen 9 KGPWTQEEDLTQIRSIKSFGKHNGTALP-KLAGLRRCGKSCRLRWTNYL 56 (238)
T ss_pred CCCCChHHHHHHHHHHHHhCCCCcchhh-hhcCCCccchHHHHHhhccc
Confidence 5889999999999999999999999999 6888 899999999999997
No 10
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=98.29 E-value=6.1e-07 Score=87.78 Aligned_cols=59 Identities=29% Similarity=0.561 Sum_probs=51.5
Q ss_pred CccCHHHHHHHHHHHHHcCCCCHHhhhhhhcCCCCHHHHHHHHHHHHHHHhhcccccCCCCcccccc
Q 021351 93 VPWTEDEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASHAQKYFLRRFNQNKRRRRSSLFDITA 159 (313)
Q Consensus 93 ~~WTeEEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSHAQKYFir~~~~~k~krR~Sl~di~~ 159 (313)
.-|+.+|+.+|+++++.+|-|+|..|| .|||+|+.+.|++|+.|||+-- +=+-|-||+.
T Consensus 64 e~WgadEEllli~~~~TlGlGNW~dIa-dyiGsr~kee~k~HylK~y~es-------~~ypl~~i~~ 122 (432)
T COG5114 64 EGWGADEELLLIECLDTLGLGNWEDIA-DYIGSRAKEEIKSHYLKMYDES-------KYYPLPDITQ 122 (432)
T ss_pred CCcCchHHHHHHHHHHhcCCCcHHHHH-HHHhhhhhHHHHHHHHHHHhhc-------cccccccccc
Confidence 459999999999999999999999999 8999999999999999999742 2345667766
No 11
>PLN03212 Transcription repressor MYB5; Provisional
Probab=98.26 E-value=1.7e-06 Score=81.49 Aligned_cols=51 Identities=20% Similarity=0.242 Sum_probs=44.9
Q ss_pred cCCCccCHHHHHHHHHHHHHcCCCCHHhhhhhhcCCCCHHHHHHHHHHHHHHH
Q 021351 90 KRGVPWTEDEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASHAQKYFLRR 142 (313)
Q Consensus 90 Kkg~~WTeEEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSHAQKYFir~ 142 (313)
-+..+||+||++++++.+.+||. .|..|| .+++.||..||+.||..++.+.
T Consensus 76 I~kgpWT~EED~lLlel~~~~Gn-KWs~IA-k~LpGRTDnqIKNRWns~LrK~ 126 (249)
T PLN03212 76 VKRGGITSDEEDLILRLHRLLGN-RWSLIA-GRIPGRTDNEIKNYWNTHLRKK 126 (249)
T ss_pred cccCCCChHHHHHHHHHHHhccc-cHHHHH-hhcCCCCHHHHHHHHHHHHhHH
Confidence 34568999999999999999997 899999 7999999999999987666443
No 12
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=98.22 E-value=1.1e-06 Score=88.94 Aligned_cols=41 Identities=32% Similarity=0.582 Sum_probs=38.6
Q ss_pred CccCHHHHHHHHHHHHHcCCCCHHhhhhhhcCCCCHHHHHHHH
Q 021351 93 VPWTEDEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASHA 135 (313)
Q Consensus 93 ~~WTeEEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSHA 135 (313)
-.||.+|..++|+||++||. ||.+|| .+|+|||++||-.|.
T Consensus 280 k~WS~qE~~LLLEGIe~ygD-dW~kVA-~HVgtKt~EqCIl~F 320 (531)
T COG5259 280 KNWSRQELLLLLEGIEMYGD-DWDKVA-RHVGTKTKEQCILHF 320 (531)
T ss_pred ccccHHHHHHHHHHHHHhhh-hHHHHH-HHhCCCCHHHHHHHH
Confidence 36999999999999999998 999999 799999999999884
No 13
>KOG0724 consensus Zuotin and related molecular chaperones (DnaJ superfamily), contains DNA-binding domains [Posttranslational modification, protein turnover, chaperones]
Probab=98.19 E-value=8e-07 Score=83.52 Aligned_cols=75 Identities=51% Similarity=0.708 Sum_probs=70.4
Q ss_pred CCccccCCCccCHHHHHHHHHHHHHcCCCCHHhhhhhhcCCCCHHHHHHHHH-----HHHHHHhhcccccCCCCcccccc
Q 021351 85 RSRERKRGVPWTEDEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASHAQ-----KYFLRRFNQNKRRRRSSLFDITA 159 (313)
Q Consensus 85 ~~~~rKkg~~WTeEEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSHAQ-----KYFir~~~~~k~krR~Sl~di~~ 159 (313)
...+++++..|++.+|.+|+.++.+||+++|..|+++++.+|++.|+.+|+| +|+.+....++.++|.+++++..
T Consensus 157 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~s~a~~~~~~~~~~~~~~~~~~~~~~s~~~~~~ 236 (335)
T KOG0724|consen 157 AEELRRKGTPVTERERKLVLLALKKDGKIDWRKISQNVEKERTPEQVASHAQEKAFEKALARQKSGEEEKRRKSIEDITT 236 (335)
T ss_pred hhhhhhccchhHHHHHHHHHhhhcccccccceechhhhhhhhcchhhhhhhhhhhhHHHHHHHhhhccccccchhhhhhc
Confidence 3456778999999999999999999999999999999999999999999999 99999999999999999999987
No 14
>PLN03091 hypothetical protein; Provisional
Probab=98.15 E-value=3.9e-06 Score=84.42 Aligned_cols=50 Identities=14% Similarity=0.294 Sum_probs=44.8
Q ss_pred CCCccCHHHHHHHHHHHHHcCCCCHHhhhhhhcCCCCHHHHHHHHHHHHHHH
Q 021351 91 RGVPWTEDEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASHAQKYFLRR 142 (313)
Q Consensus 91 kg~~WTeEEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSHAQKYFir~ 142 (313)
+..+||+||++++|+.+++||. +|..|| .+++.||..||+.||...+.|.
T Consensus 66 kKgpWT~EED~lLLeL~k~~Gn-KWskIA-k~LPGRTDnqIKNRWnslLKKk 115 (459)
T PLN03091 66 KRGTFSQQEENLIIELHAVLGN-RWSQIA-AQLPGRTDNEIKNLWNSCLKKK 115 (459)
T ss_pred cCCCCCHHHHHHHHHHHHHhCc-chHHHH-HhcCCCCHHHHHHHHHHHHHHH
Confidence 3568999999999999999998 999999 7999999999999998665554
No 15
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=97.99 E-value=7.1e-06 Score=83.62 Aligned_cols=42 Identities=29% Similarity=0.529 Sum_probs=39.3
Q ss_pred CCccCHHHHHHHHHHHHHcCCCCHHhhhhhhcCCCCHHHHHHHH
Q 021351 92 GVPWTEDEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASHA 135 (313)
Q Consensus 92 g~~WTeEEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSHA 135 (313)
+..||++|..++|+||++||. ||.+|| .+|+|||..||-.|.
T Consensus 253 ~~~WT~qE~lLLLE~ie~y~d-dW~kVa-~hVg~ks~eqCI~kF 294 (506)
T KOG1279|consen 253 RPNWTEQETLLLLEAIEMYGD-DWNKVA-DHVGTKSQEQCILKF 294 (506)
T ss_pred CCCccHHHHHHHHHHHHHhcc-cHHHHH-hccCCCCHHHHHHHH
Confidence 456999999999999999999 999999 899999999999973
No 16
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=97.79 E-value=2.5e-05 Score=77.57 Aligned_cols=49 Identities=35% Similarity=0.522 Sum_probs=43.5
Q ss_pred CCccCHHHHHHHHHHHHHcCCCCHHhhhhhhcCCCCHHHHHHHHHHHHHHHhh
Q 021351 92 GVPWTEDEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASHAQKYFLRRFN 144 (313)
Q Consensus 92 g~~WTeEEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSHAQKYFir~~~ 144 (313)
...|++||++.|.+||+.||| ||..|.++-|.||+...|..+ ||++.+.
T Consensus 277 l~~wsEeEcr~FEegl~~yGK-DF~lIr~nkvrtRsvgElVey---YYlWKkS 325 (445)
T KOG4329|consen 277 LSGWSEEECRNFEEGLELYGK-DFHLIRANKVRTRSVGELVEY---YYLWKKS 325 (445)
T ss_pred cccCCHHHHHHHHHHHHHhcc-cHHHHHhcccccchHHHHHHH---HHHhhcC
Confidence 456999999999999999999 999999999999999999765 7776443
No 17
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=97.63 E-value=0.00013 Score=66.83 Aligned_cols=50 Identities=18% Similarity=0.294 Sum_probs=44.1
Q ss_pred cCCCccCHHHHHHHHHHHHHcCCCCHHhhhhhhcCCCCHHHHHHHHHHHHHH
Q 021351 90 KRGVPWTEDEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASHAQKYFLR 141 (313)
Q Consensus 90 Kkg~~WTeEEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSHAQKYFir 141 (313)
-++..||+||+++.+++-.+||- +|..|| .+++.||--.|+.||.-...|
T Consensus 60 ikrg~fT~eEe~~Ii~lH~~~GN-rWs~IA-~~LPGRTDNeIKN~Wnt~lkk 109 (238)
T KOG0048|consen 60 LKRGNFSDEEEDLIIKLHALLGN-RWSLIA-GRLPGRTDNEVKNHWNTHLKK 109 (238)
T ss_pred ccCCCCCHHHHHHHHHHHHHHCc-HHHHHH-hhCCCcCHHHHHHHHHHHHHH
Confidence 34667999999999999999998 899999 799999999999998655533
No 18
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=97.54 E-value=0.00011 Score=77.32 Aligned_cols=50 Identities=22% Similarity=0.453 Sum_probs=44.8
Q ss_pred CCCccCHHHHHHHHHHHHHcCCCCHHhhhhhhcCCCCHHHHHHHHHHHHHH
Q 021351 91 RGVPWTEDEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASHAQKYFLR 141 (313)
Q Consensus 91 kg~~WTeEEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSHAQKYFir 141 (313)
+.++||.+|+.+++.|+++||..+|-.|- ..|+.|+..|||.+|.+.+.+
T Consensus 359 khg~wt~~ED~~L~~AV~~Yg~kdw~k~R-~~vPnRSdsQcR~RY~nvL~~ 408 (939)
T KOG0049|consen 359 KHGRWTDQEDVLLVCAVSRYGAKDWAKVR-QAVPNRSDSQCRERYTNVLNR 408 (939)
T ss_pred cCCCCCCHHHHHHHHHHHHhCccchhhHH-HhcCCccHHHHHHHHHHHHHH
Confidence 45679999999999999999999999997 899999999999998765544
No 19
>PLN03162 golden-2 like transcription factor; Provisional
Probab=96.89 E-value=0.0022 Score=64.41 Aligned_cols=57 Identities=32% Similarity=0.429 Sum_probs=44.8
Q ss_pred cccCCCccCHHHHHHHHHHHHHcCC--CCHHhhhhhh--cCCCCHHHHHHHHHHHHHHHhhc
Q 021351 88 ERKRGVPWTEDEHRLFLLGLQKVGK--GDWRGISRNF--VKTRTPTQVASHAQKYFLRRFNQ 145 (313)
Q Consensus 88 ~rKkg~~WTeEEh~lFLegLekyGk--GdWk~IAr~~--V~TRT~~QVrSHAQKYFir~~~~ 145 (313)
.||.+..||+|=|++|++||++.|. --=|.|- ++ |..=|..+|+||-|||.+.++++
T Consensus 233 ~KKpRLrWTpELH~rFVeAV~qLG~dKATPK~IL-elMnV~GLTRenVKSHLQKYRl~rk~l 293 (526)
T PLN03162 233 KKKAKVDWTPELHRRFVHAVEQLGVEKAFPSRIL-ELMGVQCLTRHNIASHLQKYRSHRRHL 293 (526)
T ss_pred CCCCcccCCHHHHHHHHHHHHHhCcCccchHHHH-HHcCCCCcCHHHHHHHHHHHHHhcccc
Confidence 5677889999999999999999993 1233443 34 45679999999999998877644
No 20
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=96.75 E-value=0.0016 Score=68.99 Aligned_cols=47 Identities=21% Similarity=0.422 Sum_probs=41.4
Q ss_pred cCCCccCHHHHHHHHHHHHHcCCCCHHhhhhhhcCCCCHHHHHHHHHH
Q 021351 90 KRGVPWTEDEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASHAQK 137 (313)
Q Consensus 90 Kkg~~WTeEEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSHAQK 137 (313)
-|...||-.|++++|.+|++||+|.|-+|| .+++.||.+|.+..-..
T Consensus 410 ~K~~rW~l~edeqL~~~V~~YG~g~WakcA-~~Lp~~t~~q~~rrR~R 456 (939)
T KOG0049|consen 410 AKVERWTLVEDEQLLYAVKVYGKGNWAKCA-MLLPKKTSRQLRRRRLR 456 (939)
T ss_pred hccCceeecchHHHHHHHHHHccchHHHHH-HHccccchhHHHHHHHH
Confidence 345679999999999999999999999999 89999999888765443
No 21
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=96.27 E-value=0.0067 Score=64.97 Aligned_cols=48 Identities=27% Similarity=0.371 Sum_probs=42.2
Q ss_pred CCccCHHHHHHHHHHHHHcCCCCHHhhhhhhcCCCCHHHHHHHHHHHHHHHhh
Q 021351 92 GVPWTEDEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASHAQKYFLRRFN 144 (313)
Q Consensus 92 g~~WTeEEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSHAQKYFir~~~ 144 (313)
...||..|.++|-.||-.|-| ||..|+ ..|++||..||..+ ||.|.+-
T Consensus 619 Sd~WTp~E~~lF~kA~y~~~K-DF~~v~-km~~~KtVaqCVey---YYtWKK~ 666 (907)
T KOG4167|consen 619 SDKWTPLERKLFNKALYTYSK-DFIFVQ-KMVKSKTVAQCVEY---YYTWKKI 666 (907)
T ss_pred cccccHHHHHHHHHHHHHhcc-cHHHHH-HHhccccHHHHHHH---HHHHHHh
Confidence 467999999999999999999 999999 79999999999765 6666543
No 22
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=96.08 E-value=0.0051 Score=63.75 Aligned_cols=49 Identities=20% Similarity=0.508 Sum_probs=45.3
Q ss_pred cCCCccCHHHHHHHHHHHHHcCCCCHHhhhhhhcCCCCHHHHHHHHHHHH
Q 021351 90 KRGVPWTEDEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASHAQKYF 139 (313)
Q Consensus 90 Kkg~~WTeEEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSHAQKYF 139 (313)
.+++.|+.-|++.+-.|+.+||+..|..|+ ....-+|+.||+..|.+|.
T Consensus 5 ~kggvwrntEdeilkaav~kyg~nqws~i~-sll~~kt~rqC~~rw~e~l 53 (617)
T KOG0050|consen 5 IKGGVWRNTEDEVLKAAVMKYGKNQWSRIA-SLLNRKTARQCKARWEEWL 53 (617)
T ss_pred EecceecccHHHHHHHHHHHcchHHHHHHH-HHHhhcchhHHHHHHHHHh
Confidence 456779999999999999999999999999 7999999999999998874
No 23
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=95.90 E-value=0.019 Score=43.79 Aligned_cols=53 Identities=19% Similarity=0.380 Sum_probs=35.3
Q ss_pred ccCHHHHHHHHHHHHH------cC-----CC--CHHhhhhhhcC----CCCHHHHHHHHHHHHHHHhhccc
Q 021351 94 PWTEDEHRLFLLGLQK------VG-----KG--DWRGISRNFVK----TRTPTQVASHAQKYFLRRFNQNK 147 (313)
Q Consensus 94 ~WTeEEh~lFLegLek------yG-----kG--dWk~IAr~~V~----TRT~~QVrSHAQKYFir~~~~~k 147 (313)
.||++|-..||+.+.. ++ ++ -|+.||. .+. .||+.||+..+.+-..+-.+.+.
T Consensus 3 ~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~-~l~~~G~~rt~~qc~~Kw~~L~~~Yk~~k~ 72 (90)
T PF13837_consen 3 NWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAE-ELAEHGYNRTPEQCRNKWKNLKKKYKKIKD 72 (90)
T ss_dssp SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHH-HHHHHC----HHHHHHHHHHHHHHHHCSSS
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHH-HHHHcCCCCCHHHHHHHHHHHHHHHHHHHh
Confidence 5999999999999887 21 12 5999994 442 69999999998765555544433
No 24
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=95.39 E-value=0.023 Score=57.41 Aligned_cols=46 Identities=24% Similarity=0.428 Sum_probs=42.1
Q ss_pred ccccCCCccCHHHHHHHHHHHHHcCCCCHHhhhhhhcCCCCHHHHHHH
Q 021351 87 RERKRGVPWTEDEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASH 134 (313)
Q Consensus 87 ~~rKkg~~WTeEEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSH 134 (313)
-.++...+||.+|-++|-.||..+|. ||..|| +++++|...||+.-
T Consensus 360 g~~~~~~~Ws~~e~ekFYKALs~wGt-dF~LIs-~lfP~R~RkqIKaK 405 (507)
T COG5118 360 GKKKGALRWSKKEIEKFYKALSIWGT-DFSLIS-SLFPNRERKQIKAK 405 (507)
T ss_pred cCCCCCCcccHHHHHHHHHHHHHhcc-hHHHHH-HhcCchhHHHHHHH
Confidence 35677789999999999999999999 999999 89999999999864
No 25
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=95.31 E-value=0.023 Score=59.96 Aligned_cols=52 Identities=27% Similarity=0.424 Sum_probs=41.9
Q ss_pred CCccCHHHHHHHHHHHHHcCCCCHHhh---------hhhhcCCCCHHHHHHHHHHHHHHHhh
Q 021351 92 GVPWTEDEHRLFLLGLQKVGKGDWRGI---------SRNFVKTRTPTQVASHAQKYFLRRFN 144 (313)
Q Consensus 92 g~~WTeEEh~lFLegLekyGkGdWk~I---------Ar~~V~TRT~~QVrSHAQKYFir~~~ 144 (313)
+..||-.|+..|..||+.+|+ ||..| +..-+..||.-|||-||.+-..+..+
T Consensus 88 ktaWt~~E~~~Ffdal~~~GK-dFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~~~m~k 148 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVGK-DFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLVRRMNK 148 (782)
T ss_pred ccccchhhHHHHHHHHHHhcc-cHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHHHHHHh
Confidence 457999999999999999999 99999 22456778999999887655555543
No 26
>smart00426 TEA TEA domain.
Probab=95.15 E-value=0.024 Score=44.71 Aligned_cols=43 Identities=35% Similarity=0.435 Sum_probs=32.7
Q ss_pred CccCHHHHHHHHHHHHHcCC-C--------------CHHhhhhhhc-----CCCCHHHHHHHHH
Q 021351 93 VPWTEDEHRLFLLGLQKVGK-G--------------DWRGISRNFV-----KTRTPTQVASHAQ 136 (313)
Q Consensus 93 ~~WTeEEh~lFLegLekyGk-G--------------dWk~IAr~~V-----~TRT~~QVrSHAQ 136 (313)
.-|.++=+..|++||+.|-+ | +=..|+ +|+ ..||++||-||-|
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 45999999999999998865 2 223455 454 3599999999976
No 27
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=94.75 E-value=0.021 Score=59.00 Aligned_cols=51 Identities=27% Similarity=0.548 Sum_probs=43.5
Q ss_pred ccCCCccCHHHHHHHHHHHHHcCCCCHHhhhhhhcCCCCHHHHHHHHHHHHHHHh
Q 021351 89 RKRGVPWTEDEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASHAQKYFLRRF 143 (313)
Q Consensus 89 rKkg~~WTeEEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSHAQKYFir~~ 143 (313)
|-....|+..|-.+|.+||+|||+ |+..|-++|++=|+.+-+..+ ||++..
T Consensus 282 RDemEEWSasEanLFEeALeKyGK-DFndIrqdfLPWKSl~sIvey---YYmwKt 332 (693)
T KOG3554|consen 282 RDEMEEWSASEANLFEEALEKYGK-DFNDIRQDFLPWKSLTSIVEY---YYMWKT 332 (693)
T ss_pred hhhhhhccchhhHHHHHHHHHhcc-cHHHHHHhhcchHHHHHHHHH---HHHHhh
Confidence 455667999999999999999999 999999999999998888665 555543
No 28
>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=94.64 E-value=0.027 Score=33.66 Aligned_cols=18 Identities=44% Similarity=1.126 Sum_probs=16.6
Q ss_pred CccCCCCCCCCCCCCCCC
Q 021351 3 RSCSQCGNNGHNSRTCAE 20 (313)
Q Consensus 3 R~CS~Cgn~GHNsRTC~~ 20 (313)
|+|-.||..||-+|-|+.
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 689999999999999983
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=94.40 E-value=0.084 Score=44.85 Aligned_cols=52 Identities=29% Similarity=0.581 Sum_probs=41.1
Q ss_pred cCCCccCHHHHHHHHHHHHHcCC---CCHHhhhh-----------hhcCCCCHHHHHHHHHHHHHHH
Q 021351 90 KRGVPWTEDEHRLFLLGLQKVGK---GDWRGISR-----------NFVKTRTPTQVASHAQKYFLRR 142 (313)
Q Consensus 90 Kkg~~WTeEEh~lFLegLekyGk---GdWk~IAr-----------~~V~TRT~~QVrSHAQKYFir~ 142 (313)
.++..||+||++-+|-.+.+||- |.|..|-+ -|+.+||+..+.-++. ++++.
T Consensus 47 ~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir~~p~FrFDwf~kSRt~~el~rR~~-tLi~~ 112 (118)
T PF09111_consen 47 NKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIRESPLFRFDWFFKSRTPQELQRRCN-TLIKL 112 (118)
T ss_dssp SS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHHH-CGGCT-HHHHTS-HHHHHHHHH-HHHHH
T ss_pred CCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHHhCCCcccchhcccCCHHHHHHHHH-HHHHH
Confidence 34556999999999999999999 99999954 4789999999998886 55544
No 30
>KOG0724 consensus Zuotin and related molecular chaperones (DnaJ superfamily), contains DNA-binding domains [Posttranslational modification, protein turnover, chaperones]
Probab=94.21 E-value=0.011 Score=55.86 Aligned_cols=48 Identities=19% Similarity=0.083 Sum_probs=45.1
Q ss_pred cCHHHHHHHHHHHHHcCCCCHHhhhhhhcCCCCHHHHHHHHHHHHHHHhh
Q 021351 95 WTEDEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASHAQKYFLRRFN 144 (313)
Q Consensus 95 WTeEEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSHAQKYFir~~~ 144 (313)
||++||..|.++|..| +..|..|- .|++.++..|.++|+|+||.+...
T Consensus 56 ~t~~~~~~~~~~l~~~-~~~~~~~~-~~~~~~~~v~~~~~~~~~~p~~~~ 103 (335)
T KOG0724|consen 56 RTPDSWDKFAEALPLE-KRLEDKIE-EYIGLVFDVNIRESGQKPFPKYGK 103 (335)
T ss_pred cchhhhhHHHhcCccc-cccchhHH-hhhhhHHHHhhhhccCCCccccCc
Confidence 9999999999999999 55999998 899999999999999999988775
No 31
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=94.00 E-value=0.08 Score=58.64 Aligned_cols=50 Identities=22% Similarity=0.484 Sum_probs=45.0
Q ss_pred CC-ccCHHHHHHHHHHHHHcCCCCHHhhhhhhcCCCCHHHHHHHHHHHHHHH
Q 021351 92 GV-PWTEDEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASHAQKYFLRR 142 (313)
Q Consensus 92 g~-~WTeEEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSHAQKYFir~ 142 (313)
|. .||..+=..|+.|.++||+.+...|| ..|.+||+.+|+.+++-|+.|.
T Consensus 823 gf~~w~~~~f~~f~~~~~~~gr~~~~~i~-~~~~~k~~~ev~~y~~~f~~~~ 873 (1033)
T PLN03142 823 GFSTWSRRDFNAFIRACEKYGRNDIKSIA-SEMEGKTEEEVERYAKVFWERY 873 (1033)
T ss_pred CcCcccHHHHHHHHHHHHHhCHhHHHHHH-HHhcCCCHHHHHHHHHHHHHhh
Confidence 44 49999999999999999999999999 7999999999999888777554
No 32
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=93.66 E-value=0.085 Score=55.58 Aligned_cols=53 Identities=19% Similarity=0.258 Sum_probs=42.9
Q ss_pred cCCCccCHHHHHHHHHHHH-------Hc-------CC-----------CCHHhhhhhhcCCCCHHHHHHHHHHHHHHHh
Q 021351 90 KRGVPWTEDEHRLFLLGLQ-------KV-------GK-----------GDWRGISRNFVKTRTPTQVASHAQKYFLRRF 143 (313)
Q Consensus 90 Kkg~~WTeEEh~lFLegLe-------ky-------Gk-----------GdWk~IAr~~V~TRT~~QVrSHAQKYFir~~ 143 (313)
.+..+||.||++++|..++ .| |. =.|..|+ +.++||+..|||.||+|-..+-.
T Consensus 434 ~~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 434 RNRGAWSIEEEEKLLKTVNEMIREALQPQASNTDTGLQESPESTLKDDINWTLVS-EMLGTRSRIQCRYKWYKLTTSPS 511 (607)
T ss_pred cccCcchHHHHHHHHHHHHHHHHHhhcccccccchhhhcCccccccCCcchhhhh-HhhcCCCcchHHHHHHHHHhhHH
Confidence 3556799999999999996 33 11 1799999 69999999999999988766544
No 33
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=93.62 E-value=0.04 Score=56.97 Aligned_cols=55 Identities=15% Similarity=0.375 Sum_probs=45.7
Q ss_pred cccCCCccCHHHHHHHHHHHHHcCCCCHHhhhhhhcCCCCHHHHHHHHHHHHHHHh
Q 021351 88 ERKRGVPWTEDEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASHAQKYFLRRF 143 (313)
Q Consensus 88 ~rKkg~~WTeEEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSHAQKYFir~~ 143 (313)
...+++.|+..|++.++-++++||..+|..|| ..+..||..||+.|+..|...+.
T Consensus 16 ~~~k~gsw~~~EDe~l~~~vk~l~~nnws~va-s~~~~~~~kq~~~rw~~~lnp~l 70 (512)
T COG5147 16 TKRKGGSWKRTEDEDLKALVKKLGPNNWSKVA-SLLISSTGKQSSNRWNNHLNPQL 70 (512)
T ss_pred ceecCCCCCCcchhHHHHHHhhcccccHHHHH-HHhcccccccccchhhhhhchhc
Confidence 34455689999999999999999999999999 45555999999999977765443
No 34
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=93.36 E-value=0.031 Score=40.21 Aligned_cols=19 Identities=37% Similarity=1.034 Sum_probs=17.1
Q ss_pred CCCccCCCCCCCCCCCCCC
Q 021351 1 MSRSCSQCGNNGHNSRTCA 19 (313)
Q Consensus 1 m~R~CS~Cgn~GHNsRTC~ 19 (313)
+.+.|.+||..||..+.|+
T Consensus 30 lp~~C~~C~~~gH~~~~C~ 48 (49)
T PF14392_consen 30 LPRFCFHCGRIGHSDKECP 48 (49)
T ss_pred cChhhcCCCCcCcCHhHcC
Confidence 3578999999999999997
No 35
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=92.81 E-value=0.055 Score=38.81 Aligned_cols=20 Identities=30% Similarity=0.724 Sum_probs=17.7
Q ss_pred CccCCCCCCCCCC--CCCCCCC
Q 021351 3 RSCSQCGNNGHNS--RTCAEAG 22 (313)
Q Consensus 3 R~CS~Cgn~GHNs--RTC~~~~ 22 (313)
+||..||.+||.. |+||-..
T Consensus 2 ~kC~~CG~~GH~~t~k~CP~~~ 23 (40)
T PF15288_consen 2 VKCKNCGAFGHMRTNKRCPMYC 23 (40)
T ss_pred ccccccccccccccCccCCCCC
Confidence 7999999999976 8999765
No 36
>KOG3841 consensus TEF-1 and related transcription factor, TEAD family [Transcription]
Probab=92.30 E-value=0.2 Score=50.78 Aligned_cols=49 Identities=33% Similarity=0.373 Sum_probs=40.0
Q ss_pred cCCCccCHHHHHHHHHHHHHcCC---------------CCHHhhhhhhc-----CCCCHHHHHHHHHHHH
Q 021351 90 KRGVPWTEDEHRLFLLGLQKVGK---------------GDWRGISRNFV-----KTRTPTQVASHAQKYF 139 (313)
Q Consensus 90 Kkg~~WTeEEh~lFLegLekyGk---------------GdWk~IAr~~V-----~TRT~~QVrSHAQKYF 139 (313)
-..+.|+++=++.|+|||..|-. |+=..||| || +|||.+||-||-|=.-
T Consensus 74 daegvWSpdIEqsFqEALaiyppcGrrKIilsdegkmyGRNELIar-YIKlrtgktRTrKQVSSHIQVla 142 (455)
T KOG3841|consen 74 DAEGVWSPDIEQSFQEALAIYPPCGRRKIILSDEGKMYGRNELIAR-YIKLRTGKTRTRKQVSSHIQVLA 142 (455)
T ss_pred ccccccChhHHHHHHHHHhhcCCCCceeEEEccCccccchHHHHHH-HHHHhcCCchhHHHHHHHHHHHH
Confidence 44456999999999999998842 67888994 87 5899999999998443
No 37
>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=92.24 E-value=0.16 Score=51.39 Aligned_cols=48 Identities=33% Similarity=0.380 Sum_probs=32.1
Q ss_pred cCCCccCHHHHHHHHHHHHHcCC-------------CCHHhhhhhhc-----CCCCHHHHHHHHHHH
Q 021351 90 KRGVPWTEDEHRLFLLGLQKVGK-------------GDWRGISRNFV-----KTRTPTQVASHAQKY 138 (313)
Q Consensus 90 Kkg~~WTeEEh~lFLegLekyGk-------------GdWk~IAr~~V-----~TRT~~QVrSHAQKY 138 (313)
+....|++|=+..|++||+.|-+ |+=+.|+ .|| .+||.+||.+|.|-.
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 44556999999999999998854 4556677 576 469999999999854
No 38
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=91.61 E-value=0.5 Score=35.71 Aligned_cols=51 Identities=16% Similarity=0.245 Sum_probs=39.7
Q ss_pred CccCHHHHHHHHHHHHHc-----CC-----------CCHHhhhhhh----cCCCCHHHHHHHHHHHHHHHh
Q 021351 93 VPWTEDEHRLFLLGLQKV-----GK-----------GDWRGISRNF----VKTRTPTQVASHAQKYFLRRF 143 (313)
Q Consensus 93 ~~WTeEEh~lFLegLeky-----Gk-----------GdWk~IAr~~----V~TRT~~QVrSHAQKYFir~~ 143 (313)
..||.+|.+.|++.|++| |+ .-|..|+..| .+.||..|++..|.++-....
T Consensus 3 ~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk~~~K 73 (78)
T PF13873_consen 3 PNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLKSKAK 73 (78)
T ss_pred CCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHH
Confidence 459999999999999998 42 3799998543 137999999998887655443
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=90.87 E-value=0.42 Score=36.83 Aligned_cols=51 Identities=16% Similarity=0.216 Sum_probs=31.8
Q ss_pred CCccCHHHHHHHHHHHHHcCC--------CCHHhhhhhhcCCCCHHHHHHHHHHHHHHH
Q 021351 92 GVPWTEDEHRLFLLGLQKVGK--------GDWRGISRNFVKTRTPTQVASHAQKYFLRR 142 (313)
Q Consensus 92 g~~WTeEEh~lFLegLekyGk--------GdWk~IAr~~V~TRT~~QVrSHAQKYFir~ 142 (313)
.++.|+||+..+++.|..+.. .-|+.+++.++...|-.--|.|+.|.+...
T Consensus 2 R~~fT~edD~~l~~~v~~~~~~~~~~~Gn~iwk~le~~~~t~HtwQSwR~Ry~K~L~~~ 60 (65)
T PF08914_consen 2 RTPFTEEDDAALLDYVKENERQGGSVSGNKIWKELEEKHPTRHTWQSWRDRYLKHLRGR 60 (65)
T ss_dssp -----HHHHHHHHHHHHHT--STTTTTSSHHHHHHHHS-SSS--SHHHHHHHHHHT---
T ss_pred CCCCCHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcc
Confidence 357999999999999966532 259999987776788888888877666543
No 40
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=90.24 E-value=0.33 Score=51.36 Aligned_cols=48 Identities=21% Similarity=0.407 Sum_probs=41.1
Q ss_pred CCCccCHHHHHHHHHHHHHcCCCCHHhhhhhhcCCCCHHHHHHHHHHHHHH
Q 021351 91 RGVPWTEDEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASHAQKYFLR 141 (313)
Q Consensus 91 kg~~WTeEEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSHAQKYFir 141 (313)
+.+.||+||.+.+.....++|. +|..|+ ..+ .|.|.-||.||..|-.-
T Consensus 383 ~rg~wt~ee~eeL~~l~~~~g~-~W~~Ig-~~l-gr~P~~crd~wr~~~~~ 430 (607)
T KOG0051|consen 383 KRGKWTPEEEEELKKLVVEHGN-DWKEIG-KAL-GRMPMDCRDRWRQYVKC 430 (607)
T ss_pred ccCCCCcchHHHHHHHHHHhcc-cHHHHH-HHH-ccCcHHHHHHHHHhhcc
Confidence 4566999999999999999997 999999 455 57899999999987643
No 41
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=89.76 E-value=0.6 Score=48.35 Aligned_cols=41 Identities=24% Similarity=0.377 Sum_probs=36.9
Q ss_pred CccCHHHHHHHHHHHHHcCCCCHHhhhhhhcCCCCHHHHHHHH
Q 021351 93 VPWTEDEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASHA 135 (313)
Q Consensus 93 ~~WTeEEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSHA 135 (313)
-.||.||--+|-.+++.||+ ++.+|- ..++-|+..-++-++
T Consensus 188 d~WT~Ed~vlFe~aF~~~GK-~F~kIr-q~LP~rsLaSlvqyY 228 (534)
T KOG1194|consen 188 DEWTAEDIVLFEQAFQFFGK-DFHKIR-QALPHRSLASLVQYY 228 (534)
T ss_pred ccchHHHHHHHHHHHHHhcc-cHHHHH-HHccCccHHHHHHHH
Confidence 45999999999999999999 999998 799999988886554
No 42
>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=89.00 E-value=1 Score=34.69 Aligned_cols=60 Identities=23% Similarity=0.320 Sum_probs=39.6
Q ss_pred ccCHHHHHHHHHHHHHc---C----CC-----CHHhhhhhhc----CCCCHHHHHHHHHHHHHHHhhcccccCCCC
Q 021351 94 PWTEDEHRLFLLGLQKV---G----KG-----DWRGISRNFV----KTRTPTQVASHAQKYFLRRFNQNKRRRRSS 153 (313)
Q Consensus 94 ~WTeEEh~lFLegLeky---G----kG-----dWk~IAr~~V----~TRT~~QVrSHAQKYFir~~~~~k~krR~S 153 (313)
.||+++++.||+.|... | .+ .|..|++.|. ...|..||+.|+...-.+....+.-+..++
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~lk~~y~~~~~l~~~sg 76 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTLKKDYRIWKELRNHSG 76 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHHHHHHHHHHHHHcCCC
Confidence 49999999999998654 2 11 5888875443 347899999998654333344444444444
No 43
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=87.38 E-value=0.86 Score=47.43 Aligned_cols=53 Identities=17% Similarity=0.324 Sum_probs=45.7
Q ss_pred cCCCccCHHHHHHHHHHHHHcCCCCHHhhhhhhcCCCCHHHHHHHHHHHHHHHhh
Q 021351 90 KRGVPWTEDEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASHAQKYFLRRFN 144 (313)
Q Consensus 90 Kkg~~WTeEEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSHAQKYFir~~~ 144 (313)
.+...|++||++.++..-..+|- .|..|| .++..||..||...|.+-+.....
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 34567999999999999999999 799999 899999999998887766665554
No 44
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=86.16 E-value=1.4 Score=42.11 Aligned_cols=57 Identities=16% Similarity=0.354 Sum_probs=42.2
Q ss_pred CCccCHHHHHHHHHHHHHc----CCC-----CHHhhhhhhc---CCCCHHHHHHHHHHHHHHHhhcccc
Q 021351 92 GVPWTEDEHRLFLLGLQKV----GKG-----DWRGISRNFV---KTRTPTQVASHAQKYFLRRFNQNKR 148 (313)
Q Consensus 92 g~~WTeEEh~lFLegLeky----GkG-----dWk~IAr~~V---~TRT~~QVrSHAQKYFir~~~~~k~ 148 (313)
...|+.||-..||++..+. ..+ .|..||+.+- --||+.||+.-+.+...+.++.+.+
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 4679999999999987643 223 5999996333 3599999999887776666655443
No 45
>smart00343 ZnF_C2HC zinc finger.
Probab=84.51 E-value=0.52 Score=29.52 Aligned_cols=17 Identities=41% Similarity=1.152 Sum_probs=15.6
Q ss_pred ccCCCCCCCCCCCCCCC
Q 021351 4 SCSQCGNNGHNSRTCAE 20 (313)
Q Consensus 4 ~CS~Cgn~GHNsRTC~~ 20 (313)
+|..||..||.++.|+.
T Consensus 1 ~C~~CG~~GH~~~~C~~ 17 (26)
T smart00343 1 KCYNCGKEGHIARDCPK 17 (26)
T ss_pred CCccCCCCCcchhhCCc
Confidence 59999999999999983
No 46
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=84.43 E-value=2.2 Score=47.80 Aligned_cols=50 Identities=32% Similarity=0.629 Sum_probs=41.5
Q ss_pred CCccCHHHHHHHHHHHHHcCCCCHHhhhh-----------hhcCCCCHHHHHHHHHHHHHHH
Q 021351 92 GVPWTEDEHRLFLLGLQKVGKGDWRGISR-----------NFVKTRTPTQVASHAQKYFLRR 142 (313)
Q Consensus 92 g~~WTeEEh~lFLegLekyGkGdWk~IAr-----------~~V~TRT~~QVrSHAQKYFir~ 142 (313)
+-.||+||++.+|-.+.+||.|+|..|-. -|+++||+..+.-++. ++++.
T Consensus 926 ~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~-~l~~~ 986 (1033)
T PLN03142 926 GKLYNEECDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELARRCD-TLIRL 986 (1033)
T ss_pred CCcCCHHHHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHHHHHH-HHHHH
Confidence 34599999999999999999999999943 5789999999988886 44443
No 47
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=76.49 E-value=2.7 Score=44.44 Aligned_cols=49 Identities=18% Similarity=0.319 Sum_probs=40.9
Q ss_pred CCCccCHHHHHHHHHHHHHcCCCCHHhhhhhhcCCCCHHHHHHHHHHHHHHH
Q 021351 91 RGVPWTEDEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASHAQKYFLRR 142 (313)
Q Consensus 91 kg~~WTeEEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSHAQKYFir~ 142 (313)
+.+-|+.||++++|.+...+-. -|+.|+ . +-.||..||-.++++-.-..
T Consensus 58 ~~tews~eederlLhlakl~p~-qwrtIa-~-i~gr~~~qc~eRy~~ll~~~ 106 (617)
T KOG0050|consen 58 KKTEWSREEDERLLHLAKLEPT-QWRTIA-D-IMGRTSQQCLERYNNLLDVY 106 (617)
T ss_pred hhhhhhhhHHHHHHHHHHhcCC-ccchHH-H-HhhhhHHHHHHHHHHHHHHH
Confidence 4566999999999999999998 999999 3 44699999999988654433
No 48
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=70.30 E-value=9.4 Score=31.26 Aligned_cols=39 Identities=31% Similarity=0.560 Sum_probs=28.8
Q ss_pred ccCHHHHHHHHHHHHHc----CC---CCHHhhhhhhcCCC-----CHHHHHH
Q 021351 94 PWTEDEHRLFLLGLQKV----GK---GDWRGISRNFVKTR-----TPTQVAS 133 (313)
Q Consensus 94 ~WTeEEh~lFLegLeky----Gk---GdWk~IAr~~V~TR-----T~~QVrS 133 (313)
-||+|++..+|+||-.| |. -||...- ++|... |..|+..
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 39999999999999988 64 2777776 566544 5566644
No 49
>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=69.52 E-value=13 Score=33.41 Aligned_cols=49 Identities=12% Similarity=0.377 Sum_probs=41.8
Q ss_pred cCHHHHHHHHHHHHHcCCC--CHHhhhhhhcCCCCHHHHHHHHHHHHHHHhh
Q 021351 95 WTEDEHRLFLLGLQKVGKG--DWRGISRNFVKTRTPTQVASHAQKYFLRRFN 144 (313)
Q Consensus 95 WTeEEh~lFLegLekyGkG--dWk~IAr~~V~TRT~~QVrSHAQKYFir~~~ 144 (313)
++..+.+.||.+|.+||-| +|+-+- .-+.-||..+++.++-=|+.++..
T Consensus 41 Fn~rQR~~Fln~vMR~G~~~f~~~w~~-~~Lr~Ks~~ei~aY~~LFm~HL~E 91 (145)
T PF06461_consen 41 FNPRQRKAFLNAVMRYGMGAFDWKWFV-PRLRGKSEKEIRAYGSLFMRHLCE 91 (145)
T ss_pred cCHHHHHHHHHHHHHHCcCcccchHHh-hhhccccHHHHHHHHHHHHHHhcC
Confidence 7889999999999999998 898887 588999999999998755555543
No 50
>KOG0385 consensus Chromatin remodeling complex WSTF-ISWI, small subunit [Transcription]
Probab=67.42 E-value=8.2 Score=42.85 Aligned_cols=52 Identities=25% Similarity=0.416 Sum_probs=45.3
Q ss_pred CccCHHHHHHHHHHHHHcCCCCHHhhhhhhcCCCCHHHHHHHHHHHHHHHhhcc
Q 021351 93 VPWTEDEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASHAQKYFLRRFNQN 146 (313)
Q Consensus 93 ~~WTeEEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSHAQKYFir~~~~~ 146 (313)
..||+.+-..|+.|-++||++|-..||+ -|-. |+..|..++.-||-++..+.
T Consensus 796 t~w~k~df~~fi~a~eKygr~di~~ia~-~~e~-~~eev~~y~rvfwer~~el~ 847 (971)
T KOG0385|consen 796 TNWTKRDFNQFIKANEKYGRDDIENIAA-EVEG-TPEEVGEYARVFWERLEELS 847 (971)
T ss_pred cchhhhhHHHHHHHhhccCcchhhhhHH-hhcC-CHHHHHHHHHHHHHHHHHhh
Confidence 3499999999999999999999999995 5555 99999999998888887643
No 51
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=66.57 E-value=3.5 Score=47.26 Aligned_cols=54 Identities=24% Similarity=0.582 Sum_probs=38.4
Q ss_pred CCCccCHHHHHHHHHHHHHcCCCCHHhhhh---------hh-cC-CCCHHHHHHHHHHHHHHHhhc
Q 021351 91 RGVPWTEDEHRLFLLGLQKVGKGDWRGISR---------NF-VK-TRTPTQVASHAQKYFLRRFNQ 145 (313)
Q Consensus 91 kg~~WTeEEh~lFLegLekyGkGdWk~IAr---------~~-V~-TRT~~QVrSHAQKYFir~~~~ 145 (313)
...-|..||+..||.||-+||.|.|..|-- .| +- -=+..|.+.++ .|++.+.+.
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 567799999999999999999999999921 11 01 12345666655 587776543
No 52
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=64.95 E-value=6.6 Score=41.78 Aligned_cols=47 Identities=26% Similarity=0.409 Sum_probs=41.6
Q ss_pred CCccccCCCccCHHHHHHHHHHHHHcCCCCHHhhhhhhcCCCCHHHHHH
Q 021351 85 RSRERKRGVPWTEDEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVAS 133 (313)
Q Consensus 85 ~~~~rKkg~~WTeEEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrS 133 (313)
...++.....||.+|-++|-.+|..+|- ++..|+ +....|+..||+-
T Consensus 402 t~sk~~~~~~w~~se~e~fyka~~~~gs-~~slis-~l~p~R~rk~iK~ 448 (584)
T KOG2009|consen 402 TYSKKLETDKWDASETELFYKALSERGS-DFSLIS-NLFPLRDRKQIKA 448 (584)
T ss_pred hccCccccCcccchhhHHhhhHHhhhcc-cccccc-cccccccHHHHHH
Confidence 3345566788999999999999999998 999999 8999999999975
No 53
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=63.82 E-value=8.9 Score=35.00 Aligned_cols=48 Identities=13% Similarity=0.107 Sum_probs=35.0
Q ss_pred CCccCHHHHHHHHHHHHHcCCCCHHhhhhhhc-----CCCCHHHHHHHHHHHHH
Q 021351 92 GVPWTEDEHRLFLLGLQKVGKGDWRGISRNFV-----KTRTPTQVASHAQKYFL 140 (313)
Q Consensus 92 g~~WTeEEh~lFLegLekyGkGdWk~IAr~~V-----~TRT~~QVrSHAQKYFi 140 (313)
.-.||+||+.++.+-+-+|++-.=..++ .|- =.||..+|..+|..|..
T Consensus 5 qdawt~e~d~llae~vl~~i~eg~tql~-afe~~g~~L~rt~aac~fRwNs~vr 57 (170)
T PRK13923 5 QDAWTQERDGLLAEVVLRHIREGGTQLK-AFEEVGDALKRTAAACGFRWNSVVR 57 (170)
T ss_pred hhhhhhHHHHHHHHHHHHHHhccchHHH-HHHHHHHHHhhhHHHHHhHHHHHHH
Confidence 3469999999999999988874333443 222 25999999999955544
No 54
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=63.64 E-value=3.8 Score=37.98 Aligned_cols=18 Identities=44% Similarity=1.123 Sum_probs=16.0
Q ss_pred CCccCCCCCCCCCCCCCC
Q 021351 2 SRSCSQCGNNGHNSRTCA 19 (313)
Q Consensus 2 ~R~CS~Cgn~GHNsRTC~ 19 (313)
..+|.+||-+||=+|-|+
T Consensus 97 ~~~C~~Cg~~GH~~~dC~ 114 (190)
T COG5082 97 PKKCYNCGETGHLSRDCN 114 (190)
T ss_pred ccccccccccCccccccC
Confidence 358999999999999994
No 55
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=63.31 E-value=9 Score=35.65 Aligned_cols=49 Identities=12% Similarity=0.148 Sum_probs=37.1
Q ss_pred ccCCCccCHHHHHHHHHHHHHcC--CCCHHhhhh----hhcCCCCHHHHHHHHHH
Q 021351 89 RKRGVPWTEDEHRLFLLGLQKVG--KGDWRGISR----NFVKTRTPTQVASHAQK 137 (313)
Q Consensus 89 rKkg~~WTeEEh~lFLegLekyG--kGdWk~IAr----~~V~TRT~~QVrSHAQK 137 (313)
.....+||.+|++++........ ...|..|=. -|-.+||+.+...||+-
T Consensus 70 iq~kalfS~~EE~lL~~v~s~~~p~le~Fq~LL~~n~~vFh~sRTak~L~~HW~l 124 (199)
T PF13325_consen 70 IQSKALFSKEEEQLLGTVASSSQPSLETFQELLDKNRSVFHPSRTAKSLQDHWRL 124 (199)
T ss_pred ccccCCCCHHHHHHHHhhhhccCCcHHHHHHHHHhChhhhccccCHHHHHHHHHH
Confidence 34568899999999998765543 246777721 47789999999999983
No 56
>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=57.93 E-value=15 Score=33.45 Aligned_cols=49 Identities=18% Similarity=0.321 Sum_probs=37.6
Q ss_pred CCccCHHHHHHHHHHHHHcCC-C-----CHHhhhhhhcCCCCHHHHHHHHHHHHHHH
Q 021351 92 GVPWTEDEHRLFLLGLQKVGK-G-----DWRGISRNFVKTRTPTQVASHAQKYFLRR 142 (313)
Q Consensus 92 g~~WTeEEh~lFLegLekyGk-G-----dWk~IAr~~V~TRT~~QVrSHAQKYFir~ 142 (313)
.-.||+||+.++.+.+-+|=+ | -+..+++ -=.||+.-|..+|..|..++
T Consensus 4 QDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~--~L~RTsAACGFRWNs~VRkq 58 (161)
T TIGR02894 4 QDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGR--ALNRTAAACGFRWNAYVRKQ 58 (161)
T ss_pred ccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHH--HHcccHHHhcchHHHHHHHH
Confidence 346999999999999988844 2 4555552 12799999999999887765
No 57
>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=57.78 E-value=27 Score=35.08 Aligned_cols=53 Identities=21% Similarity=0.243 Sum_probs=40.6
Q ss_pred ccCCCccCHHHHHHHHHHHHHc-CC--CCHHhhhhhhcCCCCHHHHHHHHHHHHHHH
Q 021351 89 RKRGVPWTEDEHRLFLLGLQKV-GK--GDWRGISRNFVKTRTPTQVASHAQKYFLRR 142 (313)
Q Consensus 89 rKkg~~WTeEEh~lFLegLeky-Gk--GdWk~IAr~~V~TRT~~QVrSHAQKYFir~ 142 (313)
.+....||..|.+.+|.+|+-. |+ =|-..|+ ..+.+|...||+..-|+.-.|.
T Consensus 18 ~~gp~~Ws~rEkr~Llr~Lqar~g~~epd~ael~-~~l~~Rs~aEI~~fl~~LK~rv 73 (344)
T PF11035_consen 18 VTGPAAWSAREKRQLLRLLQARRGQPEPDAAELA-KELPGRSEAEIRDFLQQLKGRV 73 (344)
T ss_pred CCCcccCcHHHHHHHHHHHHHhcCCCCcCHHHHH-hhccCcCHHHHHHHHHHHHHHH
Confidence 3456789999999999999965 33 1555777 5899999999998877654443
No 58
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=50.59 E-value=23 Score=37.18 Aligned_cols=48 Identities=6% Similarity=-0.090 Sum_probs=42.2
Q ss_pred CccCHHHHHHHHHHHHHcCCCCHHhhhhhhcCCCCHHHHHHHHHHHHHHH
Q 021351 93 VPWTEDEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASHAQKYFLRR 142 (313)
Q Consensus 93 ~~WTeEEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSHAQKYFir~ 142 (313)
..||.+|..+.+.+|++||+ +...|+ ..|+-++..|+..-..+|-.|+
T Consensus 370 ~~~~T~~~la~v~~I~~~~~-~~~pl~-wrik~t~cmee~e~l~~~~Rr~ 417 (534)
T KOG1194|consen 370 RCFDTPAALALIDNIKRKHH-MCVPLV-WRVKQTKCMEENEILNEEARRQ 417 (534)
T ss_pred cccCcHHHHHHHHHHHHhcc-Ccchhh-hHhcCcchhhHHHHHHHHHHHH
Confidence 56999999999999999999 899999 7999999999988777775554
No 59
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=49.34 E-value=11 Score=23.88 Aligned_cols=20 Identities=25% Similarity=0.780 Sum_probs=14.8
Q ss_pred CCCccCCCCCC-CCCCCCCCC
Q 021351 1 MSRSCSQCGNN-GHNSRTCAE 20 (313)
Q Consensus 1 m~R~CS~Cgn~-GHNsRTC~~ 20 (313)
|.+.|.+||.. --..+-|+.
T Consensus 1 m~~~Cp~Cg~~~~~~~~fC~~ 21 (26)
T PF13248_consen 1 MEMFCPNCGAEIDPDAKFCPN 21 (26)
T ss_pred CcCCCcccCCcCCcccccChh
Confidence 88999999984 345566763
No 60
>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=45.78 E-value=58 Score=28.56 Aligned_cols=48 Identities=25% Similarity=0.390 Sum_probs=38.0
Q ss_pred cCCCccCHHHHHHHHHHHHHcCCCCHHhhhhhhc-CC--CCHHHHHHHHHHH
Q 021351 90 KRGVPWTEDEHRLFLLGLQKVGKGDWRGISRNFV-KT--RTPTQVASHAQKY 138 (313)
Q Consensus 90 Kkg~~WTeEEh~lFLegLekyGkGdWk~IAr~~V-~T--RT~~QVrSHAQKY 138 (313)
+....=|++|.+-....|++||. |++.++++.= .. .|+.|++--..+|
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 55666889999999999999997 9999996432 22 6899998776665
No 61
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=44.65 E-value=14 Score=27.34 Aligned_cols=18 Identities=39% Similarity=1.055 Sum_probs=14.0
Q ss_pred CccCCCC-CCCCCCCCCCC
Q 021351 3 RSCSQCG-NNGHNSRTCAE 20 (313)
Q Consensus 3 R~CS~Cg-n~GHNsRTC~~ 20 (313)
|||.+|| .||+-+--|.+
T Consensus 12 rkCp~CGt~NG~R~~~CKN 30 (44)
T PF14952_consen 12 RKCPKCGTYNGTRGLSCKN 30 (44)
T ss_pred ccCCcCcCccCcccccccC
Confidence 8999999 46877766764
No 62
>PHA00442 host recBCD nuclease inhibitor
Probab=43.85 E-value=23 Score=27.51 Aligned_cols=24 Identities=25% Similarity=0.565 Sum_probs=21.0
Q ss_pred CHHHHHHHHHHHHHcCCCCHHhhh
Q 021351 96 TEDEHRLFLLGLQKVGKGDWRGIS 119 (313)
Q Consensus 96 TeEEh~lFLegLekyGkGdWk~IA 119 (313)
+-|-+..||++|+-+|-.+|.++.
T Consensus 24 sLek~~~~L~~Lea~GVDNW~Gy~ 47 (59)
T PHA00442 24 SLEKDNEFLKALRACGVDNWDGYM 47 (59)
T ss_pred HHHHhhHHHHHHHHcCCcchhhHH
Confidence 346677899999999999999997
No 63
>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=42.37 E-value=15 Score=33.73 Aligned_cols=27 Identities=30% Similarity=0.649 Sum_probs=24.8
Q ss_pred CccCHHHHHHHHHHHHHcCCCCHHhhh
Q 021351 93 VPWTEDEHRLFLLGLQKVGKGDWRGIS 119 (313)
Q Consensus 93 ~~WTeEEh~lFLegLekyGkGdWk~IA 119 (313)
.-|-.+-+-.+|.|+-+||.|+|..|.
T Consensus 4 ~iw~r~hdywll~gi~~hgy~rwqdi~ 30 (173)
T PF08074_consen 4 EIWHRRHDYWLLAGIVKHGYGRWQDIQ 30 (173)
T ss_pred hhhhhhhhHHHHhHHhhccchhHHHHh
Confidence 359999999999999999999999996
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=39.68 E-value=74 Score=24.59 Aligned_cols=28 Identities=32% Similarity=0.646 Sum_probs=20.4
Q ss_pred CCHHhhhhhhcCC---CC--HHHHHHHHHHHHHH
Q 021351 113 GDWRGISRNFVKT---RT--PTQVASHAQKYFLR 141 (313)
Q Consensus 113 GdWk~IAr~~V~T---RT--~~QVrSHAQKYFir 141 (313)
++|..|++.+ +- .+ ..+++.|+.+|+..
T Consensus 58 ~~W~~va~~l-g~~~~~~~~~~~L~~~Y~~~L~~ 90 (92)
T PF01388_consen 58 KKWREVARKL-GFPPSSTSAAQQLRQHYEKYLLP 90 (92)
T ss_dssp TTHHHHHHHT-TS-TTSCHHHHHHHHHHHHHTHH
T ss_pred chHHHHHHHh-CCCCCCCcHHHHHHHHHHHHhHh
Confidence 5899999644 32 22 47899999999764
No 65
>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=38.87 E-value=16 Score=23.82 Aligned_cols=10 Identities=30% Similarity=1.099 Sum_probs=8.0
Q ss_pred CCccCCCCCC
Q 021351 2 SRSCSQCGNN 11 (313)
Q Consensus 2 ~R~CS~Cgn~ 11 (313)
+++|.|||+.
T Consensus 14 ~~~Cp~CG~~ 23 (26)
T PF10571_consen 14 AKFCPHCGYD 23 (26)
T ss_pred cCcCCCCCCC
Confidence 5789999963
No 66
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=38.87 E-value=16 Score=34.00 Aligned_cols=18 Identities=44% Similarity=1.053 Sum_probs=16.6
Q ss_pred CCccCCCCCCCCCCCCCC
Q 021351 2 SRSCSQCGNNGHNSRTCA 19 (313)
Q Consensus 2 ~R~CS~Cgn~GHNsRTC~ 19 (313)
.++|--||++||-.|-||
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=37.32 E-value=1e+02 Score=24.18 Aligned_cols=32 Identities=22% Similarity=0.452 Sum_probs=22.8
Q ss_pred CCHHhhhhhhcC----CCCHHHHHHHHHHHHHHHhh
Q 021351 113 GDWRGISRNFVK----TRTPTQVASHAQKYFLRRFN 144 (313)
Q Consensus 113 GdWk~IAr~~V~----TRT~~QVrSHAQKYFir~~~ 144 (313)
..|..|++.+-- |....+++.|+++|+.-...
T Consensus 54 ~~W~~Va~~lg~~~~~~~~~~~lk~~Y~k~L~~yE~ 89 (93)
T smart00501 54 KKWKEIARELGIPDTSTSAASSLRKHYERYLLPFER 89 (93)
T ss_pred CCHHHHHHHhCCCcccchHHHHHHHHHHHHhHHHHH
Confidence 589999954332 23468899999999776554
No 68
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=35.69 E-value=31 Score=29.23 Aligned_cols=19 Identities=63% Similarity=1.240 Sum_probs=12.1
Q ss_pred CccCCCCCCCCCCCCCCCC
Q 021351 3 RSCSQCGNNGHNSRTCAEA 21 (313)
Q Consensus 3 R~CS~Cgn~GHNsRTC~~~ 21 (313)
+.|..||..||-++.|+..
T Consensus 53 ~~C~~Cg~~GH~~~~Cp~~ 71 (148)
T PTZ00368 53 RSCYNCGKTGHLSRECPEA 71 (148)
T ss_pred cccCCCCCcCcCcccCCCc
Confidence 3566666666666666654
No 69
>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=31.05 E-value=1.8e+02 Score=20.09 Aligned_cols=37 Identities=14% Similarity=0.206 Sum_probs=21.9
Q ss_pred HHHHHHHHHHHHcCCCCHHhhhhhhcCCCCHHHHHHHHHH
Q 021351 98 DEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASHAQK 137 (313)
Q Consensus 98 EEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSHAQK 137 (313)
++++..+...-..|. .|+.|| ..++ .|...|+.|.++
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 444555555566677 999999 4554 778888777544
No 70
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=28.57 E-value=26 Score=23.87 Aligned_cols=10 Identities=60% Similarity=1.561 Sum_probs=8.3
Q ss_pred CccCCCCCCC
Q 021351 3 RSCSQCGNNG 12 (313)
Q Consensus 3 R~CS~Cgn~G 12 (313)
++|+.||++|
T Consensus 4 ~~C~~C~~~~ 13 (33)
T PF08792_consen 4 KKCSKCGGNG 13 (33)
T ss_pred eEcCCCCCCe
Confidence 6799998887
No 71
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=28.35 E-value=29 Score=36.73 Aligned_cols=19 Identities=37% Similarity=0.732 Sum_probs=15.9
Q ss_pred CccCCCCCCCCCCCCCCCC
Q 021351 3 RSCSQCGNNGHNSRTCAEA 21 (313)
Q Consensus 3 R~CS~Cgn~GHNsRTC~~~ 21 (313)
+.|-+||-.||+++-|...
T Consensus 286 n~c~~cg~~gH~~~dc~~~ 304 (554)
T KOG0119|consen 286 NVCKICGPLGHISIDCKVN 304 (554)
T ss_pred ccccccCCcccccccCCCc
Confidence 4799999999999999854
No 72
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=27.17 E-value=40 Score=28.60 Aligned_cols=16 Identities=50% Similarity=1.203 Sum_probs=11.3
Q ss_pred ccCCCCCCCCCCCCCC
Q 021351 4 SCSQCGNNGHNSRTCA 19 (313)
Q Consensus 4 ~CS~Cgn~GHNsRTC~ 19 (313)
.|..||..||-++.|+
T Consensus 29 ~C~~Cg~~GH~~~~Cp 44 (148)
T PTZ00368 29 PCYKCGEPGHLSRECP 44 (148)
T ss_pred cCccCCCCCcCcccCc
Confidence 5666888888666664
No 73
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=27.07 E-value=74 Score=33.05 Aligned_cols=43 Identities=14% Similarity=0.247 Sum_probs=36.4
Q ss_pred CccCHHHHHHHHHHHHHcCCCCHHhhhhh-----hcCCCCHHHHHHHHH
Q 021351 93 VPWTEDEHRLFLLGLQKVGKGDWRGISRN-----FVKTRTPTQVASHAQ 136 (313)
Q Consensus 93 ~~WTeEEh~lFLegLekyGkGdWk~IAr~-----~V~TRT~~QVrSHAQ 136 (313)
..||.||-+-+.+..++|.- +|--||.. |-.+||.+..+.++-
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 45999999999999999998 88888854 444599999998863
No 74
>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=26.82 E-value=79 Score=22.73 Aligned_cols=40 Identities=25% Similarity=0.273 Sum_probs=31.7
Q ss_pred HHHHHHHHHcCCCCHHhhhhhhcCCCCHHHHHHHHHHHHHHH
Q 021351 101 RLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASHAQKYFLRR 142 (313)
Q Consensus 101 ~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSHAQKYFir~ 142 (313)
+++-+|++..|..++.-|. .+.+|+..|.+.=.+.|....
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 4788899999986666665 888999999998888776554
No 75
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=26.17 E-value=33 Score=23.69 Aligned_cols=18 Identities=33% Similarity=0.925 Sum_probs=16.5
Q ss_pred CccCCCCCCCCCCCCCCC
Q 021351 3 RSCSQCGNNGHNSRTCAE 20 (313)
Q Consensus 3 R~CS~Cgn~GHNsRTC~~ 20 (313)
..|--|+.-||--+.||.
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 76
>PF05634 APO_RNA-bind: APO RNA-binding; InterPro: IPR008512 This family consists of plant APO (accumulation of photosystem 1) proteins.
Probab=25.19 E-value=50 Score=31.20 Aligned_cols=20 Identities=40% Similarity=0.926 Sum_probs=16.4
Q ss_pred CccCCC-----CCCCCCCCCCCCCC
Q 021351 3 RSCSQC-----GNNGHNSRTCAEAG 22 (313)
Q Consensus 3 R~CS~C-----gn~GHNsRTC~~~~ 22 (313)
..|.+| |.-||.-|||....
T Consensus 99 ~~C~~C~EVHVG~~GH~irtC~g~k 123 (204)
T PF05634_consen 99 KACGYCPEVHVGPVGHKIRTCGGFK 123 (204)
T ss_pred eecCCCCCeEECCCcccccccCCCC
Confidence 569999 67899999998543
No 77
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=23.69 E-value=45 Score=24.06 Aligned_cols=19 Identities=32% Similarity=0.906 Sum_probs=17.0
Q ss_pred CCccCCCCCCCCCCCCCCC
Q 021351 2 SRSCSQCGNNGHNSRTCAE 20 (313)
Q Consensus 2 ~R~CS~Cgn~GHNsRTC~~ 20 (313)
...|-.|+..||=..-|+.
T Consensus 4 ~~~CqkC~~~GH~tyeC~~ 22 (42)
T PF13917_consen 4 RVRCQKCGQKGHWTYECPN 22 (42)
T ss_pred CCcCcccCCCCcchhhCCC
Confidence 3689999999999999994
No 78
>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=23.32 E-value=31 Score=24.27 Aligned_cols=8 Identities=50% Similarity=1.335 Sum_probs=3.9
Q ss_pred ccCCCCCC
Q 021351 4 SCSQCGNN 11 (313)
Q Consensus 4 ~CS~Cgn~ 11 (313)
||.+|||.
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 78999874
No 79
>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=22.77 E-value=43 Score=31.09 Aligned_cols=18 Identities=44% Similarity=1.043 Sum_probs=15.7
Q ss_pred ccCCCCCCCCCCCCCCCC
Q 021351 4 SCSQCGNNGHNSRTCAEA 21 (313)
Q Consensus 4 ~CS~Cgn~GHNsRTC~~~ 21 (313)
+|-.||+.||=++-|+..
T Consensus 145 ~Cy~Cg~~GH~s~~C~~~ 162 (261)
T KOG4400|consen 145 KCYSCGEQGHISDDCPEN 162 (261)
T ss_pred ccCCCCcCCcchhhCCCC
Confidence 599999999999999953
No 80
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=21.30 E-value=41 Score=27.26 Aligned_cols=13 Identities=23% Similarity=0.713 Sum_probs=9.3
Q ss_pred CCCccCCCCCCCC
Q 021351 1 MSRSCSQCGNNGH 13 (313)
Q Consensus 1 m~R~CS~Cgn~GH 13 (313)
|..+|++||..=+
T Consensus 7 ~~~~C~~CG~d~~ 19 (86)
T PF06170_consen 7 VAPRCPHCGLDYS 19 (86)
T ss_pred CCCcccccCCccc
Confidence 4578999997543
No 81
>PLN00111 accumulation of photosystem one; Provisional
Probab=21.27 E-value=61 Score=33.34 Aligned_cols=20 Identities=45% Similarity=0.989 Sum_probs=16.4
Q ss_pred CccCCC-----CCCCCCCCCCCCCC
Q 021351 3 RSCSQC-----GNNGHNSRTCAEAG 22 (313)
Q Consensus 3 R~CS~C-----gn~GHNsRTC~~~~ 22 (313)
+.|.+| |.-||.-|||....
T Consensus 121 ~~C~~C~EVHVG~~GH~irtC~g~k 145 (399)
T PLN00111 121 HACKFCSEVHVGKVGHLIRTCRGPG 145 (399)
T ss_pred eecCcCCceeECCCCccccccCCcc
Confidence 578888 57899999998654
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=21.14 E-value=3.1e+02 Score=21.05 Aligned_cols=45 Identities=13% Similarity=0.186 Sum_probs=27.8
Q ss_pred cCHHHHHHHHHHHHHcCCCCHHhhhhhhcCCCCHHHHHHHHHHHHHHHh
Q 021351 95 WTEDEHRLFLLGLQKVGKGDWRGISRNFVKTRTPTQVASHAQKYFLRRF 143 (313)
Q Consensus 95 WTeEEh~lFLegLekyGkGdWk~IAr~~V~TRT~~QVrSHAQKYFir~~ 143 (313)
+++.|.+.|...+ ..|. .|..|| ..++. +...|+.+.++-..++.
T Consensus 111 L~~~~~~ii~~~~-~~g~-s~~eIA-~~l~~-s~~~v~~~~~~~~~kl~ 155 (158)
T TIGR02937 111 LPEREREVLVLRY-LEGL-SYKEIA-EILGI-SVGTVKRRLKRARKKLR 155 (158)
T ss_pred CCHHHHHHHhhHH-hcCC-CHHHHH-HHHCC-CHHHHHHHHHHHHHHHH
Confidence 5666666654332 2465 899999 56665 66666666555544443
Done!