Query 038014
Match_columns 140
No_of_seqs 107 out of 695
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 06:39:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038014.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038014hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0869 CCAAT-binding factor, 100.0 2E-32 4.4E-37 210.0 10.9 111 25-135 19-129 (168)
2 KOG0871 Class 2 transcription 99.9 1.4E-26 3E-31 176.3 10.9 95 34-128 8-102 (156)
3 KOG0870 DNA polymerase epsilon 99.9 5.7E-26 1.2E-30 175.5 10.5 106 30-135 2-108 (172)
4 COG5150 Class 2 transcription 99.9 1.3E-21 2.7E-26 146.4 9.4 96 33-128 6-101 (148)
5 PF00808 CBFD_NFYB_HMF: Histon 99.8 1.7E-18 3.6E-23 114.5 7.4 64 38-102 2-65 (65)
6 COG2036 HHT1 Histones H3 and H 99.7 1.8E-18 4E-23 122.9 6.2 80 29-110 10-89 (91)
7 cd00076 H4 Histone H4, one of 99.5 7.1E-14 1.5E-18 98.3 7.8 71 38-110 13-83 (85)
8 PLN00035 histone H4; Provision 99.5 2E-13 4.4E-18 99.0 7.8 72 36-109 27-98 (103)
9 PTZ00015 histone H4; Provision 99.4 6.6E-13 1.4E-17 96.2 7.8 74 35-110 27-100 (102)
10 smart00417 H4 Histone H4. 99.3 6E-12 1.3E-16 86.5 5.6 62 37-100 12-73 (74)
11 smart00803 TAF TATA box bindin 99.3 2E-11 4.3E-16 81.7 6.9 64 38-103 2-65 (65)
12 smart00428 H3 Histone H3. 99.3 1.7E-11 3.7E-16 89.2 6.8 72 33-104 24-100 (105)
13 cd07981 TAF12 TATA Binding Pro 99.1 9.7E-10 2.1E-14 74.6 8.0 66 39-105 2-67 (72)
14 PLN00160 histone H3; Provision 99.0 5.6E-10 1.2E-14 80.3 6.6 71 33-103 16-90 (97)
15 PF00125 Histone: Core histone 99.0 5.7E-10 1.2E-14 74.8 6.1 68 36-103 3-73 (75)
16 PLN00161 histone H3; Provision 99.0 1.2E-09 2.5E-14 82.7 7.7 71 33-103 50-124 (135)
17 PLN00121 histone H3; Provision 99.0 6.7E-10 1.5E-14 84.2 5.9 71 33-103 57-130 (136)
18 COG5208 HAP5 CCAAT-binding fac 99.0 2.8E-10 6.1E-15 92.5 4.0 79 32-112 103-182 (286)
19 PTZ00018 histone H3; Provision 99.0 1.7E-09 3.8E-14 81.9 7.0 71 33-103 57-130 (136)
20 KOG3467 Histone H4 [Chromatin 98.8 1.4E-08 3.1E-13 72.1 6.7 69 38-108 29-97 (103)
21 smart00576 BTP Bromodomain tra 98.7 1.4E-07 2.9E-12 64.5 7.7 66 41-108 9-74 (77)
22 KOG1745 Histones H3 and H4 [Ch 98.7 1.4E-08 3.1E-13 76.9 3.0 75 32-106 57-134 (137)
23 KOG1657 CCAAT-binding factor, 98.6 4.6E-08 9.9E-13 80.1 4.1 87 33-121 69-159 (236)
24 cd00074 H2A Histone 2A; H2A is 98.5 3E-07 6.5E-12 67.9 6.4 70 34-104 16-85 (115)
25 cd07979 TAF9 TATA Binding Prot 98.5 4.1E-07 8.9E-12 67.1 7.1 78 42-121 5-83 (117)
26 PF15511 CENP-T: Centromere ki 98.5 2.5E-07 5.5E-12 80.7 5.7 64 34-97 347-414 (414)
27 KOG1659 Class 2 transcription 98.2 3.8E-06 8.2E-11 68.0 7.2 88 34-123 9-97 (224)
28 cd08050 TAF6 TATA Binding Prot 98.2 4.4E-06 9.5E-11 71.2 7.8 67 40-108 1-67 (343)
29 PF15630 CENP-S: Kinetochore c 98.1 1.2E-05 2.5E-10 55.5 6.3 62 43-104 10-72 (76)
30 COG5247 BUR6 Class 2 transcrip 98.0 1.6E-05 3.6E-10 57.9 5.9 79 37-117 22-101 (113)
31 PF07524 Bromo_TP: Bromodomain 98.0 5.4E-05 1.2E-09 51.3 7.8 65 42-108 10-74 (77)
32 COG5262 HTA1 Histone H2A [Chro 97.9 2.7E-05 5.8E-10 58.1 5.6 77 26-103 14-90 (132)
33 PF03847 TFIID_20kDa: Transcri 97.9 5.8E-05 1.2E-09 51.0 6.8 63 41-104 2-64 (68)
34 cd08048 TAF11 TATA Binding Pro 97.8 0.00011 2.3E-09 51.7 7.5 66 38-105 16-84 (85)
35 PF02969 TAF: TATA box binding 97.8 0.00014 3.1E-09 48.9 7.2 64 38-103 3-66 (66)
36 smart00427 H2B Histone H2B. 97.8 0.00013 2.8E-09 51.9 7.2 62 43-105 6-67 (89)
37 PF09415 CENP-X: CENP-S associ 97.7 6.8E-05 1.5E-09 51.2 4.0 65 40-104 1-67 (72)
38 PLN00158 histone H2B; Provisio 97.6 0.0004 8.8E-09 51.5 7.2 67 38-105 27-93 (116)
39 PF04719 TAFII28: hTAFII28-lik 97.5 0.0004 8.8E-09 49.4 6.7 67 38-105 23-90 (90)
40 PTZ00463 histone H2B; Provisio 97.5 0.00051 1.1E-08 51.0 7.2 63 42-105 32-94 (117)
41 smart00414 H2A Histone 2A. 97.4 0.00051 1.1E-08 50.1 6.0 69 35-104 6-74 (106)
42 PLN00154 histone H2A; Provisio 97.3 0.00074 1.6E-08 51.4 5.9 71 34-104 34-104 (136)
43 PTZ00017 histone H2A; Provisio 97.1 0.0011 2.3E-08 50.4 5.2 69 34-103 23-91 (134)
44 KOG1142 Transcription initiati 97.0 0.002 4.4E-08 53.5 6.4 76 35-111 151-229 (258)
45 PLN00153 histone H2A; Provisio 96.9 0.0034 7.4E-08 47.4 6.6 74 30-104 16-89 (129)
46 PF02291 TFIID-31kDa: Transcri 96.9 0.0041 8.9E-08 46.8 6.9 82 38-121 10-94 (129)
47 KOG1756 Histone 2A [Chromatin 96.9 0.0024 5.1E-08 48.2 5.6 71 32-103 21-91 (131)
48 PLN00156 histone H2AX; Provisi 96.9 0.0036 7.7E-08 47.8 6.6 70 33-103 24-93 (139)
49 KOG1658 DNA polymerase epsilon 96.9 0.00069 1.5E-08 52.6 2.3 69 35-105 56-125 (162)
50 PLN00157 histone H2A; Provisio 96.8 0.0026 5.7E-08 48.2 5.0 71 33-104 21-91 (132)
51 PF02269 TFIID-18kDa: Transcri 96.8 0.0018 4E-08 45.9 3.7 60 44-104 7-66 (93)
52 KOG1744 Histone H2B [Chromatin 96.4 0.013 2.7E-07 44.2 6.5 63 42-105 41-103 (127)
53 PF15510 CENP-W: Centromere ki 96.4 0.0056 1.2E-07 44.0 4.4 66 38-104 16-95 (102)
54 KOG3219 Transcription initiati 96.4 0.0039 8.4E-08 50.0 3.7 70 38-109 112-182 (195)
55 PTZ00252 histone H2A; Provisio 95.9 0.026 5.6E-07 42.9 5.7 69 34-103 21-91 (134)
56 cd07978 TAF13 The TATA Binding 95.5 0.28 6.1E-06 34.8 9.8 60 43-104 7-66 (92)
57 KOG3423 Transcription initiati 95.2 0.11 2.5E-06 40.9 7.3 69 38-108 86-168 (176)
58 KOG4336 TBP-associated transcr 94.6 0.23 4.9E-06 42.6 8.2 75 43-121 10-84 (323)
59 KOG2549 Transcription initiati 94.5 0.15 3.3E-06 46.6 7.4 66 40-107 13-78 (576)
60 KOG3334 Transcription initiati 92.2 0.72 1.6E-05 35.6 6.7 74 44-119 19-93 (148)
61 KOG2389 Predicted bromodomain 89.9 0.88 1.9E-05 39.6 5.9 69 38-108 29-97 (353)
62 TIGR03015 pepcterm_ATPase puta 89.6 1.3 2.7E-05 35.1 6.3 69 39-107 192-268 (269)
63 PRK00411 cdc6 cell division co 89.2 1.7 3.7E-05 36.5 7.1 70 41-110 209-287 (394)
64 COG5095 TAF6 Transcription ini 85.8 3.2 6.9E-05 36.4 6.8 66 41-108 8-73 (450)
65 TIGR02928 orc1/cdc6 family rep 85.6 4 8.7E-05 33.8 7.2 75 41-115 201-284 (365)
66 PF03540 TFIID_30kDa: Transcri 85.2 6 0.00013 25.4 6.3 48 38-87 2-49 (51)
67 KOG1757 Histone 2A [Chromatin 84.7 1.4 3E-05 33.0 3.6 67 33-103 25-95 (131)
68 cd08045 TAF4 TATA Binding Prot 84.0 11 0.00024 30.0 8.8 78 35-112 41-126 (212)
69 PF13654 AAA_32: AAA domain; P 83.2 5.5 0.00012 36.1 7.5 60 44-105 436-506 (509)
70 COG5162 Transcription initiati 81.8 9.6 0.00021 30.3 7.4 68 39-108 89-189 (197)
71 TIGR02902 spore_lonB ATP-depen 78.1 5.7 0.00012 35.8 5.9 69 39-107 263-334 (531)
72 TIGR00764 lon_rel lon-related 71.8 16 0.00034 33.8 7.1 50 57-106 330-392 (608)
73 COG1067 LonB Predicted ATP-dep 71.7 3.5 7.7E-05 38.5 2.9 48 57-104 338-398 (647)
74 PF08369 PCP_red: Proto-chloro 71.3 5.3 0.00011 24.6 2.8 42 59-101 2-44 (45)
75 PF13335 Mg_chelatase_2: Magne 71.3 15 0.00033 25.8 5.5 48 56-103 41-94 (96)
76 PF05236 TAF4: Transcription i 69.8 8 0.00017 31.7 4.3 74 34-107 39-120 (264)
77 COG5094 TAF9 Transcription ini 66.4 47 0.001 25.3 7.4 67 57-123 31-101 (145)
78 PF02861 Clp_N: Clp amino term 63.8 12 0.00027 22.2 3.4 35 81-115 1-35 (53)
79 PRK00080 ruvB Holliday junctio 59.2 38 0.00083 28.1 6.5 71 38-108 179-253 (328)
80 KOG2680 DNA helicase TIP49, TB 59.0 31 0.00068 30.5 6.1 50 54-103 374-427 (454)
81 PRK09862 putative ATP-dependen 55.9 48 0.001 30.1 7.0 60 56-115 437-502 (506)
82 TIGR02030 BchI-ChlI magnesium 55.7 51 0.0011 28.2 6.8 49 55-103 252-307 (337)
83 KOG3901 Transcription initiati 55.2 34 0.00073 25.2 4.8 49 53-104 23-71 (109)
84 PRK07452 DNA polymerase III su 54.5 54 0.0012 26.9 6.6 66 44-109 135-203 (326)
85 PF00531 Death: Death domain; 53.7 25 0.00054 22.7 3.7 30 89-118 54-83 (83)
86 PF09114 MotA_activ: Transcrip 53.6 22 0.00048 25.6 3.6 34 42-75 51-88 (96)
87 TIGR02442 Cob-chelat-sub cobal 53.6 48 0.001 30.6 6.7 49 55-103 247-302 (633)
88 TIGR02454 CbiQ_TIGR cobalt ABC 53.4 26 0.00056 26.6 4.3 38 91-128 112-160 (198)
89 PF09123 DUF1931: Domain of un 51.0 13 0.00029 28.4 2.3 53 44-98 1-53 (138)
90 PF12010 DUF3502: Domain of un 49.6 16 0.00035 27.0 2.5 59 60-125 72-133 (134)
91 TIGR01128 holA DNA polymerase 48.7 99 0.0021 24.6 7.2 66 38-103 110-176 (302)
92 COG1224 TIP49 DNA helicase TIP 48.1 36 0.00079 30.5 4.8 62 41-102 363-429 (450)
93 TIGR00635 ruvB Holliday juncti 48.0 88 0.0019 25.2 6.8 70 39-108 159-232 (305)
94 PRK13406 bchD magnesium chelat 47.6 43 0.00093 30.9 5.4 49 55-103 193-248 (584)
95 COG1474 CDC6 Cdc6-related prot 45.9 34 0.00075 29.6 4.3 74 42-115 193-275 (366)
96 PF07647 SAM_2: SAM domain (St 45.0 24 0.00053 22.1 2.6 24 93-116 4-27 (66)
97 smart00350 MCM minichromosome 44.7 82 0.0018 28.2 6.7 68 37-104 416-503 (509)
98 TIGR00368 Mg chelatase-related 44.2 54 0.0012 29.6 5.5 47 57-103 445-497 (499)
99 cd00166 SAM Sterile alpha moti 44.0 21 0.00046 21.6 2.1 24 94-117 3-26 (63)
100 PF02361 CbiQ: Cobalt transpor 43.5 38 0.00082 25.7 3.8 41 91-131 123-175 (224)
101 cd08316 Death_FAS_TNFRSF6 Deat 42.6 1.2E+02 0.0026 21.5 6.5 72 38-119 17-93 (97)
102 CHL00081 chlI Mg-protoporyphyr 42.5 1.2E+02 0.0025 26.4 7.0 49 55-103 265-320 (350)
103 COG5248 TAF19 Transcription in 42.1 99 0.0021 23.1 5.6 50 53-104 23-72 (126)
104 KOG1658 DNA polymerase epsilon 42.0 61 0.0013 25.4 4.7 89 38-128 11-111 (162)
105 PRK12402 replication factor C 41.5 90 0.0019 25.3 6.0 69 39-109 184-253 (337)
106 PTZ00361 26 proteosome regulat 40.4 34 0.00073 30.5 3.5 32 74-105 393-424 (438)
107 PF00536 SAM_1: SAM domain (St 40.2 31 0.00067 21.5 2.5 23 94-116 4-26 (64)
108 PF08823 PG_binding_2: Putativ 39.8 40 0.00086 22.8 3.0 32 95-126 18-55 (74)
109 PRK13407 bchI magnesium chelat 38.4 1.3E+02 0.0029 25.7 6.7 49 54-102 248-303 (334)
110 TIGR02031 BchD-ChlD magnesium 38.3 1.1E+02 0.0023 28.2 6.5 49 55-103 201-256 (589)
111 PLN00155 histone H2A; Provisio 37.0 58 0.0013 21.4 3.3 38 30-68 16-53 (58)
112 PF00356 LacI: Bacterial regul 37.0 81 0.0018 19.3 3.9 31 38-72 10-40 (46)
113 cd08313 Death_TNFR1 Death doma 36.3 1.4E+02 0.0031 20.4 5.7 71 38-113 8-78 (80)
114 smart00454 SAM Sterile alpha m 35.9 32 0.00069 20.9 2.0 25 93-117 4-28 (68)
115 PRK06585 holA DNA polymerase I 35.8 89 0.0019 25.9 5.2 62 42-103 145-208 (343)
116 TIGR01242 26Sp45 26S proteasom 35.3 48 0.001 28.0 3.5 32 73-104 331-362 (364)
117 PRK03992 proteasome-activating 34.8 49 0.0011 28.5 3.6 35 72-106 339-373 (389)
118 PRK13765 ATP-dependent proteas 34.6 67 0.0015 30.0 4.6 48 57-104 339-399 (637)
119 COG1724 Predicted RNA binding 34.1 23 0.00051 23.9 1.2 17 92-108 6-22 (66)
120 PRK02910 light-independent pro 33.7 1.3E+02 0.0028 27.1 6.1 53 53-106 465-518 (519)
121 PRK07914 hypothetical protein; 33.6 93 0.002 25.8 5.0 64 40-104 129-193 (320)
122 PRK14975 bifunctional 3'-5' ex 33.5 2.4E+02 0.0052 25.6 7.9 88 35-128 160-270 (553)
123 PTZ00454 26S protease regulato 32.3 56 0.0012 28.5 3.6 33 72-104 353-385 (398)
124 PRK05574 holA DNA polymerase I 32.0 1.5E+02 0.0033 24.0 5.9 67 38-104 145-212 (340)
125 COG5624 TAF61 Transcription in 30.8 50 0.0011 29.9 3.0 76 39-114 384-462 (505)
126 COG5251 TAF40 Transcription in 30.2 36 0.00078 27.3 1.8 63 38-102 115-178 (199)
127 PF13405 EF-hand_6: EF-hand do 29.9 50 0.0011 17.8 1.9 26 81-106 5-31 (31)
128 PF07499 RuvA_C: RuvA, C-termi 29.1 34 0.00073 20.8 1.2 13 96-108 4-16 (47)
129 KOG0785 Isocitrate dehydrogena 28.9 1.3E+02 0.0028 26.4 5.1 63 60-123 166-228 (365)
130 PF01077 NIR_SIR: Nitrite and 28.7 39 0.00085 24.9 1.7 73 15-118 80-153 (157)
131 PF07492 Trehalase_Ca-bi: Neut 28.1 32 0.00069 19.8 0.9 14 10-23 8-21 (30)
132 KOG1942 DNA helicase, TBP-inte 27.9 2E+02 0.0043 25.6 6.1 64 39-102 367-435 (456)
133 KOG1528 Salt-sensitive 3'-phos 27.1 2E+02 0.0044 25.1 5.9 79 28-107 40-125 (351)
134 PF11753 DUF3310: Protein of u 26.3 1.6E+02 0.0035 18.9 4.1 41 61-103 14-56 (60)
135 PRK05629 hypothetical protein; 26.1 1.9E+02 0.0042 23.8 5.6 48 55-103 143-190 (318)
136 COG1466 HolA DNA polymerase II 26.0 1.8E+02 0.0039 24.3 5.5 61 44-104 145-206 (334)
137 PTZ00373 60S Acidic ribosomal 25.6 1.7E+02 0.0037 21.5 4.6 28 81-108 8-35 (112)
138 smart00027 EH Eps15 homology d 25.4 1.5E+02 0.0032 20.0 4.1 28 81-108 15-42 (96)
139 PRK10423 transcriptional repre 25.1 57 0.0012 26.0 2.2 37 38-79 9-45 (327)
140 KOG0188 Alanyl-tRNA synthetase 24.8 5.3E+02 0.011 25.4 8.6 61 58-118 353-417 (895)
141 PLN00138 large subunit ribosom 24.5 1.8E+02 0.004 21.2 4.6 28 81-108 6-33 (113)
142 PF08681 DUF1778: Protein of u 24.2 28 0.00061 23.5 0.2 18 55-72 3-20 (80)
143 PRK14971 DNA polymerase III su 24.0 2.1E+02 0.0045 26.6 5.9 67 39-106 180-247 (614)
144 PF01922 SRP19: SRP19 protein; 24.0 39 0.00085 23.8 0.9 25 86-110 14-46 (95)
145 PRK08487 DNA polymerase III su 24.0 2.3E+02 0.0051 23.5 5.8 60 42-103 138-198 (328)
146 PRK05907 hypothetical protein; 23.5 1.7E+02 0.0037 24.7 4.8 72 55-126 151-232 (311)
147 smart00354 HTH_LACI helix_turn 23.5 1.4E+02 0.0031 19.1 3.6 33 37-73 10-42 (70)
148 KOG0784 Isocitrate dehydrogena 23.5 47 0.001 29.3 1.5 49 73-122 185-233 (375)
149 PRK14964 DNA polymerase III su 23.3 2.2E+02 0.0047 25.9 5.7 47 55-102 192-238 (491)
150 TIGR01052 top6b DNA topoisomer 23.2 1.3E+02 0.0028 27.4 4.3 58 49-120 426-483 (488)
151 KOG3468 NADH:ubiquinone oxidor 23.0 1E+02 0.0022 23.1 3.0 42 93-134 76-117 (128)
152 PRK00440 rfc replication facto 22.8 2.6E+02 0.0057 22.3 5.7 65 39-105 161-226 (319)
153 PTZ00183 centrin; Provisional 22.8 2.8E+02 0.006 19.4 5.5 18 86-103 63-80 (158)
154 PF09339 HTH_IclR: IclR helix- 22.8 45 0.00098 20.2 0.9 16 36-51 27-42 (52)
155 PRK10339 DNA-binding transcrip 22.2 97 0.0021 24.9 3.0 40 38-80 12-51 (327)
156 PF12767 SAGA-Tad1: Transcript 21.6 1.7E+02 0.0038 23.6 4.4 30 55-84 220-250 (252)
157 PF00403 HMA: Heavy-metal-asso 21.5 58 0.0013 20.0 1.3 16 93-108 47-62 (62)
158 PRK14961 DNA polymerase III su 21.3 3.9E+02 0.0084 22.6 6.7 65 40-105 179-244 (363)
159 COG1239 ChlI Mg-chelatase subu 21.1 2.4E+02 0.0053 25.4 5.5 49 55-103 265-320 (423)
160 PRK15485 cobalt transport prot 21.0 1.7E+02 0.0036 23.3 4.1 37 92-128 132-179 (225)
161 PRK09111 DNA polymerase III su 20.9 2.6E+02 0.0057 25.9 5.9 63 40-103 192-255 (598)
162 cd04752 Commd4 COMM_Domain con 20.5 4E+02 0.0087 20.4 9.7 51 69-126 43-94 (174)
163 PF03130 HEAT_PBS: PBS lyase H 20.4 1.6E+02 0.0034 15.6 2.7 22 99-120 6-27 (27)
164 COG1222 RPT1 ATP-dependent 26S 20.1 1.1E+02 0.0023 27.4 3.0 34 72-105 359-392 (406)
165 cd05833 Ribosomal_P2 Ribosomal 20.0 2.6E+02 0.0056 20.3 4.6 28 81-108 6-33 (109)
No 1
>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [Transcription]
Probab=99.98 E-value=2e-32 Score=209.98 Aligned_cols=111 Identities=68% Similarity=1.111 Sum_probs=105.5
Q ss_pred CCCCCCccccccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHh
Q 038014 25 GTDQDGVIKEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALAT 104 (140)
Q Consensus 25 ~~~~~~~~~~~d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~ 104 (140)
.|+.....+++|..||+|+|.||||..||.+.+|+|||++.+|+|+.+||.+|+++|.+.|.+++||||+++||+|||..
T Consensus 19 ~~~~~~~~reqDr~LPIANV~RIMK~~lP~naKIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIngdDllwAm~t 98 (168)
T KOG0869|consen 19 SPQSSLSLREQDRFLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASEKCQREKRKTINGDDLLWAMST 98 (168)
T ss_pred CCccccccchhhhhccHHHHHHHHHhcCCcccccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCcccHHHHHHHHHH
Confidence 56666789999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCchhHHHHHHHHHHHHHHHHHHhhhhccC
Q 038014 105 LGFDNYADQLKRYLHRYRELEGERANQNKAG 135 (140)
Q Consensus 105 lgf~~y~~~l~~~l~~~re~~~~kk~q~k~~ 135 (140)
|||++|+++|+.+|..||+++.++....+.+
T Consensus 99 LGFe~Y~eplkiyL~kYRe~e~e~~~~~~~~ 129 (168)
T KOG0869|consen 99 LGFENYAEPLKIYLQKYRELEGERGRSGKGG 129 (168)
T ss_pred cCcHhHHHHHHHHHHHHHHHhhhcccccccC
Confidence 9999999999999999999998887766655
No 2
>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=99.94 E-value=1.4e-26 Score=176.25 Aligned_cols=95 Identities=33% Similarity=0.662 Sum_probs=92.0
Q ss_pred cccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCchhHHH
Q 038014 34 EQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDNYADQ 113 (140)
Q Consensus 34 ~~d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~~y~~~ 113 (140)
.+++.||+|+|.+|||+.||.++||.+||+++|..||.+||+.|+++|+++|....||||.++||++||+.|||.+|++.
T Consensus 8 dde~sLPkAtv~KmIke~lP~d~rvakeareliincCvEFI~liSsEAneic~~e~KKTIa~EHV~KALe~LgF~eYiee 87 (156)
T KOG0871|consen 8 DDELSLPKATVNKMIKEMLPKDVRVAKEARELIINCCVEFINLISSEANEICNKEAKKTIAPEHVIKALENLGFGEYIEE 87 (156)
T ss_pred cccccCcHHHHHHHHHHhCCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHhHHhcccCCHHHHHHHHHHcchHHHHHH
Confidence 48899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHH
Q 038014 114 LKRYLHRYRELEGER 128 (140)
Q Consensus 114 l~~~l~~~re~~~~k 128 (140)
+.+.+++|+...+.+
T Consensus 88 ~~~vl~~~K~~~~~~ 102 (156)
T KOG0871|consen 88 AEEVLENCKEEAKKR 102 (156)
T ss_pred HHHHHHHHHHHHHHh
Confidence 999999999987754
No 3
>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription]
Probab=99.93 E-value=5.7e-26 Score=175.54 Aligned_cols=106 Identities=27% Similarity=0.449 Sum_probs=99.8
Q ss_pred CccccccccCchhHHHHHHhhhCCCC-ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCc
Q 038014 30 GVIKEQDRLLPIANVGRIMKQILPPN-AKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFD 108 (140)
Q Consensus 30 ~~~~~~d~~LP~A~V~RI~K~~lp~~-~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~ 108 (140)
...+++|+.||+|+|.||+|++||.. +.|++||+.+|+++|++|++||++.|++.|+.++||||+++||+.||++|+|.
T Consensus 2 e~eri~dl~lP~AiI~rlvke~l~E~~vsisKeA~~Ai~raAtVFv~~Lts~s~e~A~~q~rKt~sadDVl~aL~Eiefs 81 (172)
T KOG0870|consen 2 EDERIEDLNLPNAIITRLVKEVLPESNVSISKEARLAIARAATVFVIFLTSVSNEIAKDQKRKTISADDVLKALDEIEFS 81 (172)
T ss_pred cchhHHHhhccHHHHHHHHHHhCccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCcccHHHHHHHHHHhchH
Confidence 35678999999999999999999987 89999999999999999999999999999999999999999999999999999
Q ss_pred hhHHHHHHHHHHHHHHHHHHhhhhccC
Q 038014 109 NYADQLKRYLHRYRELEGERANQNKAG 135 (140)
Q Consensus 109 ~y~~~l~~~l~~~re~~~~kk~q~k~~ 135 (140)
.|.++|+..|+.|+...+.||..+...
T Consensus 82 ~f~~plk~~Le~yk~~~k~Kk~~~~~~ 108 (172)
T KOG0870|consen 82 SFVNPLKSALEAYKKAVKQKKLAKANK 108 (172)
T ss_pred HHhhHHHHHHHHHHHHHHHHHHhcccc
Confidence 999999999999999999888665543
No 4
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=99.86 E-value=1.3e-21 Score=146.42 Aligned_cols=96 Identities=27% Similarity=0.533 Sum_probs=92.5
Q ss_pred ccccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCchhHH
Q 038014 33 KEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDNYAD 112 (140)
Q Consensus 33 ~~~d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~~y~~ 112 (140)
..+++.||+|+|++.+-+.||.+..+.+||++.+..||.+||+.|+++|++.|..+.+|||.++||++||+.|||.+|++
T Consensus 6 ~dDe~sLPKATVqKMvS~iLp~dl~ftKearei~in~cieFi~~lsseAne~ce~EaKKTIa~EHviKALenLef~eyi~ 85 (148)
T COG5150 6 NDDENSLPKATVQKMVSSILPKDLVFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHVIKALENLEFEEYIE 85 (148)
T ss_pred ccccccCcHHHHHHHHHHhccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHhccHHHHHH
Confidence 34788999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHH
Q 038014 113 QLKRYLHRYRELEGER 128 (140)
Q Consensus 113 ~l~~~l~~~re~~~~k 128 (140)
.+.+.+.+|+..++.|
T Consensus 86 ~~~e~~~n~k~~qK~k 101 (148)
T COG5150 86 SCMEEHENYKSYQKQK 101 (148)
T ss_pred HHHHHHHHHHHHHhhc
Confidence 9999999999988765
No 5
>PF00808 CBFD_NFYB_HMF: Histone-like transcription factor (CBF/NF-Y) and archaeal histone; InterPro: IPR003958 The CCAAT-binding factor (CBF) is a mammalian transcription factor that binds to a CCAAT motif in the promoters of a wide variety of genes, including type I collagen and albumin. The factor is a heteromeric complex of A and B subunits, both of which are required for DNA-binding [, ]. The subunits can interact in the absence of DNA-binding, conserved regions in each being important in mediating this interaction. The A subunit can be split into 3 domains on the basis of sequence similarity, a non-conserved N-terminal 'A domain'; a highly-conserved central 'B domain' involved in DNA-binding; and a C-terminal 'C domain', which contains a number of glutamine and acidic residues involved in protein-protein interactions []. The A subunit shows striking similarity to the HAP3 subunit of the yeast CCAAT-binding heterotrimeric transcription factor [, ]. The Kluyveromyces lactis HAP3 protein has been predicted to contain a 4-cysteine zinc finger, which is thought to be present in similar HAP3 and CBF subunit A proteins, in which the third cysteine is replaced by a serine []. This domain is found in the CCAAT transcription factor and archaeal histones.; GO: 0043565 sequence-specific DNA binding, 0005622 intracellular; PDB: 1F1E_A 2BYM_D 2BYK_D 1HTA_A 1B67_A 1JFI_B 1KU5_B 1N1J_A 1BFM_A 1B6W_A ....
Probab=99.76 E-value=1.7e-18 Score=114.49 Aligned_cols=64 Identities=39% Similarity=0.618 Sum_probs=59.2
Q ss_pred cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHH
Q 038014 38 LLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWAL 102 (140)
Q Consensus 38 ~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~AL 102 (140)
.||.+.|+||||.. |+..+||+||..+|++|+++|+.+|+.+|++.|.+.+||||+++||..||
T Consensus 2 ~lP~a~vkri~k~~-~~~~~vs~ea~~~i~~a~e~Fi~~l~~~A~~~a~~~~rkti~~~Dv~~Av 65 (65)
T PF00808_consen 2 SLPLARVKRIMKSD-PDVMRVSKEAVEAIAKAAEEFIQYLAKEANEIAQRDKRKTITYEDVAKAV 65 (65)
T ss_dssp SS-HHHHHHHHHHT-STTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEE-HHHHHHHH
T ss_pred CCChHHHHHHhccC-CCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHC
Confidence 69999999999999 88889999999999999999999999999999999999999999999986
No 6
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=99.75 E-value=1.8e-18 Score=122.89 Aligned_cols=80 Identities=34% Similarity=0.474 Sum_probs=74.4
Q ss_pred CCccccccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCc
Q 038014 29 DGVIKEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFD 108 (140)
Q Consensus 29 ~~~~~~~d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~ 108 (140)
.+..+..+..||+++|.||||++.++ |||.+|.++|++++++|+..|+..|+++|.|+|||||+++||..|++.+||.
T Consensus 10 r~~~~~~~~~Lp~apv~Ri~r~~~~~--Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~DI~la~~~~~~~ 87 (91)
T COG2036 10 RRYQRSTDLLLPKAPVRRILRKAGAE--RVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLALKRLGRR 87 (91)
T ss_pred HhhhhhhhhhcCchHHHHHHHHHhHH--HhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHHHhccc
Confidence 34556788999999999999999654 9999999999999999999999999999999999999999999999999998
Q ss_pred hh
Q 038014 109 NY 110 (140)
Q Consensus 109 ~y 110 (140)
.|
T Consensus 88 ~~ 89 (91)
T COG2036 88 IY 89 (91)
T ss_pred cc
Confidence 65
No 7
>cd00076 H4 Histone H4, one of the four histones, along with H2A, H2B and H3, which forms the eukaryotic nucleosome core; along with H3, it plays a central role in nucleosome formation; histones bind to DNA and wrap the genetic material into "beads on a string" in which DNA (the string) is wrapped around small blobs of histones (the beads) at regular intervals; play a role in the inheritance of specialized chromosome structures and the control of gene activity; defects in the establishment of proper chromosome structure by histones may activate or silence genes aberrantly and thus lead to disease; the sequence of histone H4 has remained almost invariant in more than 2 billion years of evolution
Probab=99.51 E-value=7.1e-14 Score=98.27 Aligned_cols=71 Identities=21% Similarity=0.291 Sum_probs=67.3
Q ss_pred cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCchh
Q 038014 38 LLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDNY 110 (140)
Q Consensus 38 ~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~~y 110 (140)
.||+++|.||+|.. +..|||.|+.+.+.++.++|+..|..+|..+|+|++||||+++||..||++.|-.-|
T Consensus 13 gi~k~~I~RLarr~--GvkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~alkr~g~~~y 83 (85)
T cd00076 13 GITKPAIRRLARRG--GVKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLY 83 (85)
T ss_pred cCCHHHHHHHHHHc--CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHCCCCcc
Confidence 59999999999999 778999999999999999999999999999999999999999999999999986544
No 8
>PLN00035 histone H4; Provisional
Probab=99.47 E-value=2e-13 Score=99.03 Aligned_cols=72 Identities=21% Similarity=0.213 Sum_probs=67.2
Q ss_pred cccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCch
Q 038014 36 DRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDN 109 (140)
Q Consensus 36 d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~~ 109 (140)
...||+++|.||++.. +..|||.|+.+++.+..++|+..|+.+|..+|+|++||||+++||..||+.+|-.-
T Consensus 27 i~~ipk~~IrRLARr~--GvkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr~g~~l 98 (103)
T PLN00035 27 IQGITKPAIRRLARRG--GVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTL 98 (103)
T ss_pred hccCCHHHHHHHHHHc--CcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHcCCcC
Confidence 3469999999999999 77899999999999999999999999999999999999999999999999987543
No 9
>PTZ00015 histone H4; Provisional
Probab=99.42 E-value=6.6e-13 Score=96.19 Aligned_cols=74 Identities=22% Similarity=0.302 Sum_probs=68.6
Q ss_pred ccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCchh
Q 038014 35 QDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDNY 110 (140)
Q Consensus 35 ~d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~~y 110 (140)
..-.||+++|.||+|.. +..|||.|+.+.+.++.++|+..|+.+|..+|+|++||||+++||..||+..|-.-|
T Consensus 27 ~i~gI~k~~IrRLarr~--GvkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~AlKr~g~~~y 100 (102)
T PTZ00015 27 NIRGITKGAIRRLARRG--GVKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALKRQGRTLY 100 (102)
T ss_pred cccCCCHHHHHHHHHHc--CCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhcCCCCC
Confidence 34469999999999999 778999999999999999999999999999999999999999999999999886543
No 10
>smart00417 H4 Histone H4.
Probab=99.29 E-value=6e-12 Score=86.49 Aligned_cols=62 Identities=18% Similarity=0.266 Sum_probs=59.0
Q ss_pred ccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHH
Q 038014 37 RLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICW 100 (140)
Q Consensus 37 ~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ 100 (140)
-.||+++|.||+|.. +.-|||.++.+.+.+..++|+..|+.+|..+|+|+|||||+++||..
T Consensus 12 ~gI~k~~IrRLaRr~--GvkRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~~ 73 (74)
T smart00417 12 QGITKPAIRRLARRG--GVKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVY 73 (74)
T ss_pred cCCCHHHHHHHHHHc--CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHhee
Confidence 369999999999999 77799999999999999999999999999999999999999999974
No 11
>smart00803 TAF TATA box binding protein associated factor. TAFs (TATA box binding protein associated factors) are part of the transcription initiation factor TFIID multimeric protein complex. TFIID is composed of the TATA box binding protein (TBP) and a number of TAFs. The TAFs provide binding sites for many different transcriptional activators and co-activators that modulate transcription initiation by Pol II. TAF proteins adopt a histone-like fold.
Probab=99.26 E-value=2e-11 Score=81.73 Aligned_cols=64 Identities=27% Similarity=0.264 Sum_probs=61.1
Q ss_pred cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHH
Q 038014 38 LLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALA 103 (140)
Q Consensus 38 ~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe 103 (140)
.||+++|+||++.. +-.+||.|+..+|.+-++.|+..|..+|..+++|.|||||+++||..||+
T Consensus 2 ~~p~~~i~ria~~~--Gi~ris~~a~~~l~~~~e~rl~~i~~~A~k~~~hakRktlt~~DI~~Alk 65 (65)
T smart00803 2 WLPKETIKDVAESL--GIGNLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSALR 65 (65)
T ss_pred CCCHHHHHHHHHHC--CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCeecHHHHHHHhC
Confidence 58999999999999 66789999999999999999999999999999999999999999999984
No 12
>smart00428 H3 Histone H3.
Probab=99.25 E-value=1.7e-11 Score=89.25 Aligned_cols=72 Identities=21% Similarity=0.235 Sum_probs=66.1
Q ss_pred ccccccCchhHHHHHHhhhCCC-----CccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHh
Q 038014 33 KEQDRLLPIANVGRIMKQILPP-----NAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALAT 104 (140)
Q Consensus 33 ~~~d~~LP~A~V~RI~K~~lp~-----~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~ 104 (140)
+..++.+|+.++.|++++..++ +.+++.+|..+||+++|.|+..+...|+.+|.|+||+||+++|+..|..-
T Consensus 24 kst~lLI~k~pF~RLVREI~~~~~~~~~~R~~~~Al~aLQeasE~ylv~lfeda~~~a~HAkRvTl~~kDi~La~ri 100 (105)
T smart00428 24 KSTDLLIRKAPFQRLVREIAQKFTTGVDLRFQSSAIMALQEAAEAYLVGLFEDTNLLAIHAKRVTIMPKDIQLARRI 100 (105)
T ss_pred cCcccccccccHHHHHHHHHHHcCCCCCceeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccCcHhhHHHHHHH
Confidence 5678899999999999998643 68999999999999999999999999999999999999999999888643
No 13
>cd07981 TAF12 TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of the seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs function such as serving as activator-bind
Probab=99.06 E-value=9.7e-10 Score=74.56 Aligned_cols=66 Identities=20% Similarity=0.322 Sum_probs=61.8
Q ss_pred CchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhc
Q 038014 39 LPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATL 105 (140)
Q Consensus 39 LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~l 105 (140)
+++..+..++|+.-| ..+++.||.++|++.++.|+..++..|..+|+|.||+||.++||..+|++.
T Consensus 2 ~~k~~l~~lv~~id~-~~~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~~~tv~~~Di~l~l~r~ 67 (72)
T cd07981 2 LTKRKLQELLKEIDP-REQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQLHLERN 67 (72)
T ss_pred CcHHHHHHHHHhhCC-CCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHh
Confidence 678899999999965 589999999999999999999999999999999999999999999999863
No 14
>PLN00160 histone H3; Provisional
Probab=99.05 E-value=5.6e-10 Score=80.32 Aligned_cols=71 Identities=18% Similarity=0.143 Sum_probs=65.3
Q ss_pred ccccccCchhHHHHHHhhhCC----CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHH
Q 038014 33 KEQDRLLPIANVGRIMKQILP----PNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALA 103 (140)
Q Consensus 33 ~~~d~~LP~A~V~RI~K~~lp----~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe 103 (140)
+..++.||++++.|++++..+ ++.+++.+|..+||+++|.|+..+...++.+|.|+||.||++.|+..+..
T Consensus 16 kst~lLI~k~pF~RLVREI~~~~~~~~~Rfq~~Al~ALQeAsEayLv~lfed~~lca~HakRVTl~~kD~~L~~r 90 (97)
T PLN00160 16 KSTDLLIRRLPFARLVREIQMEMSREAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTIMPKDMQLARR 90 (97)
T ss_pred cchhhhhccccHHHHHHHHHHHcCCCCcEeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcccccchhhHHHHHH
Confidence 457889999999999999853 35899999999999999999999999999999999999999999988764
No 15
>PF00125 Histone: Core histone H2A/H2B/H3/H4 histone h2a signature histone h2b signature histone h3 signature histone h4 signature; InterPro: IPR007125 The core histones together with some other DNA binding proteins appear to form a superfamily defined by a common fold and distant sequence similarities [, ]. Some proteins contain local homology domains related to the histone fold [].; GO: 0003677 DNA binding; PDB: 2YFW_D 2YFV_B 1U35_H 2F8N_D 2PYO_D 2NQB_D 3AN2_C 3AZJ_C 3AV1_G 3AZM_G ....
Probab=99.04 E-value=5.7e-10 Score=74.79 Aligned_cols=68 Identities=28% Similarity=0.374 Sum_probs=62.6
Q ss_pred cccCchhHHHHHHhhhCCC---CccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHH
Q 038014 36 DRLLPIANVGRIMKQILPP---NAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALA 103 (140)
Q Consensus 36 d~~LP~A~V~RI~K~~lp~---~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe 103 (140)
...+|+.+|.|++|+..++ ..+||++|...|+.+++.|+..|...|..+|.+.||+||+++||..|++
T Consensus 3 ~~~~~~~~~~r~~r~i~~~~~~~~ris~~a~~~L~~~~E~~~~~il~~A~~~a~~~kR~tI~~~DI~~A~r 73 (75)
T PF00125_consen 3 RRLIPKFPFSRLLREIGEEILSKYRISSEALVALQSVLEYLLVEILEEAGNLARHAKRKTITPRDIQLAVR 73 (75)
T ss_dssp SHSSSHHHHHHHHHHHHHTTSSSSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTBSEEGHHHHHHHHH
T ss_pred ccccCceEEeeeeehhhcccccccccccccchhhhhhhhhhhhhhhhHHHHHHhhcCCcEecHHHHHHHHh
Confidence 4578999999999998653 2699999999999999999999999999999999999999999999985
No 16
>PLN00161 histone H3; Provisional
Probab=99.02 E-value=1.2e-09 Score=82.73 Aligned_cols=71 Identities=20% Similarity=0.232 Sum_probs=65.4
Q ss_pred ccccccCchhHHHHHHhhhC----CCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHH
Q 038014 33 KEQDRLLPIANVGRIMKQIL----PPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALA 103 (140)
Q Consensus 33 ~~~d~~LP~A~V~RI~K~~l----p~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe 103 (140)
+..++.||+.++.||+++.. +.+++++.+|..+||+++|.|+..|..+++-+|.|+||.||.+.|+..+..
T Consensus 50 kst~lLIpklPF~RLVREI~~~~~~~~~Rfq~~Al~ALQEAsEayLV~lFeda~lcaiHAkRVTlm~kDm~La~r 124 (135)
T PLN00161 50 KSTELLIRKLPFARLVREISNEMLREPFRWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMPKDMQLARR 124 (135)
T ss_pred cccccccccccHHHHHHHHHHhcCCCCcEeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccchhhHHHHHH
Confidence 56788999999999999985 346899999999999999999999999999999999999999999988864
No 17
>PLN00121 histone H3; Provisional
Probab=99.01 E-value=6.7e-10 Score=84.19 Aligned_cols=71 Identities=18% Similarity=0.209 Sum_probs=65.3
Q ss_pred ccccccCchhHHHHHHhhhCCC---CccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHH
Q 038014 33 KEQDRLLPIANVGRIMKQILPP---NAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALA 103 (140)
Q Consensus 33 ~~~d~~LP~A~V~RI~K~~lp~---~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe 103 (140)
+..++.||+.++.||+++...+ +++++.+|..+||+++|.|+..|..+++.+|.|++|.||++.|+..+..
T Consensus 57 kst~lLI~k~pF~RLVREI~~~~~~~~Rf~~~Al~ALQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~r 130 (136)
T PLN00121 57 KSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
T ss_pred cccccccccccHHHHHHHHHHHhCccceeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcceecchhhHHHHHH
Confidence 4468899999999999998643 6899999999999999999999999999999999999999999988763
No 18
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=99.00 E-value=2.8e-10 Score=92.53 Aligned_cols=79 Identities=27% Similarity=0.286 Sum_probs=72.2
Q ss_pred cccccccCchhHHHHHHhhhCCCCc-cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCchh
Q 038014 32 IKEQDRLLPIANVGRIMKQILPPNA-KISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDNY 110 (140)
Q Consensus 32 ~~~~d~~LP~A~V~RI~K~~lp~~~-rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~~y 110 (140)
+-..++.||.|+|+|+||-. +++ .||.||..++.+.++.||..|+..|.-.|++.+|+|+.-.||-.|+++.++.+|
T Consensus 103 ~~~k~h~LPlARIkkvMKtd--edVkMisaEaPvlFak~~EiFI~ELTmRAW~~ae~NkRRtLQksDia~Av~kSeMfDF 180 (286)
T COG5208 103 ILLKDHNLPLARIKKVMKTD--EDVKMISAEAPVLFAKITEIFIEELTMRAWINAEENKRRTLQKSDIAAAVKKSEMFDF 180 (286)
T ss_pred HHHHhccCcHHHHHHHHhcc--cchhheecccchHHHHHHHHHHHHHHHHHHHHHhHhhhhHHHHHHHHHHHHHHHHHhH
Confidence 44467789999999999998 666 499999999999999999999999999999999999999999999999988877
Q ss_pred HH
Q 038014 111 AD 112 (140)
Q Consensus 111 ~~ 112 (140)
.-
T Consensus 181 Li 182 (286)
T COG5208 181 LI 182 (286)
T ss_pred Hh
Confidence 53
No 19
>PTZ00018 histone H3; Provisional
Probab=98.97 E-value=1.7e-09 Score=81.93 Aligned_cols=71 Identities=18% Similarity=0.213 Sum_probs=65.2
Q ss_pred ccccccCchhHHHHHHhhhCC---CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHH
Q 038014 33 KEQDRLLPIANVGRIMKQILP---PNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALA 103 (140)
Q Consensus 33 ~~~d~~LP~A~V~RI~K~~lp---~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe 103 (140)
+..++.||+.++.||+++... .+++++.+|..+||+++|.|+..|..+++.+|.|++|.||++.|+..+..
T Consensus 57 kst~lLI~k~pF~RLVREI~~~~~~~~rf~~~al~aLQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~r 130 (136)
T PTZ00018 57 KSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
T ss_pred ccchhccccccHHHHHHHHHHHcCCcceeeHHHHHHHHHHHHHHHHHHhhhhHHHHHhhcceecchhhHHHHHH
Confidence 446889999999999999853 46899999999999999999999999999999999999999999988764
No 20
>KOG3467 consensus Histone H4 [Chromatin structure and dynamics]
Probab=98.81 E-value=1.4e-08 Score=72.07 Aligned_cols=69 Identities=23% Similarity=0.254 Sum_probs=64.7
Q ss_pred cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCc
Q 038014 38 LLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFD 108 (140)
Q Consensus 38 ~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~ 108 (140)
.+.+.+|+||.+.. +.-||+.-.-+.+..++.+|+..+...|..+++|++||||++.||+.+|+++|.-
T Consensus 29 gitKpaIRRlARr~--GVkRi~G~~yeE~~~~~k~fl~n~i~~A~~yt~HAKRKTvT~~dvv~~LKR~G~~ 97 (103)
T KOG3467|consen 29 GITKPAIRRLARRG--GVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRT 97 (103)
T ss_pred ccchHHHHHHHHhc--CcchhchhhHHHHHHHHHHHHHHHHHHHHHHHhhhhhceeeHHHHHHHHHHcCce
Confidence 47799999999999 6678999999999999999999999999999999999999999999999998754
No 21
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=98.67 E-value=1.4e-07 Score=64.51 Aligned_cols=66 Identities=21% Similarity=0.263 Sum_probs=60.1
Q ss_pred hhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCc
Q 038014 41 IANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFD 108 (140)
Q Consensus 41 ~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~ 108 (140)
+-.|.+|++.. +--+++.+|.+.|.+.++.|+..|+..+..+|+++||++++..||..||+++|+.
T Consensus 9 ~~~Vaqil~~~--Gf~~~~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~~~Dv~~Al~~~gi~ 74 (77)
T smart00576 9 RIAVAQILESA--GFDSFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPNLGDVVLALENLGIS 74 (77)
T ss_pred HHHHHHHHHHc--CccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCcc
Confidence 44677888887 4458999999999999999999999999999999999999999999999999974
No 22
>KOG1745 consensus Histones H3 and H4 [Chromatin structure and dynamics]
Probab=98.66 E-value=1.4e-08 Score=76.95 Aligned_cols=75 Identities=20% Similarity=0.228 Sum_probs=66.7
Q ss_pred cccccccCchhHHHHHHhhhC---CCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcC
Q 038014 32 IKEQDRLLPIANVGRIMKQIL---PPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLG 106 (140)
Q Consensus 32 ~~~~d~~LP~A~V~RI~K~~l---p~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lg 106 (140)
.+..|+.|++.+..|++++.. -.+.++...|+.+||++++.|+..|...++-+|.|+||.||.+.|+..|..-.|
T Consensus 57 QkstdLlI~K~PFqRlvrei~q~f~~dLrfqs~Ai~ALQeA~EayLv~LfEdtnlcAihAkRVTimpkdiQlArrirg 134 (137)
T KOG1745|consen 57 QKSTDLLIRKLPFQRLVREIAQDFKTDLRFQSSAIAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRG 134 (137)
T ss_pred HhhhHHHhhcCcHHHHhHHHHhcccccceehHHHHHHHHHHHHHHHHHhccccchhhhccceeEecccceehhhhccc
Confidence 346788999999999999553 347899999999999999999999999999999999999999999998876443
No 23
>KOG1657 consensus CCAAT-binding factor, subunit C (HAP5) [Transcription]
Probab=98.59 E-value=4.6e-08 Score=80.09 Aligned_cols=87 Identities=24% Similarity=0.294 Sum_probs=73.2
Q ss_pred ccccccCchhHHHHHHhhhCCCCc-cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhc---CCc
Q 038014 33 KEQDRLLPIANVGRIMKQILPPNA-KISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATL---GFD 108 (140)
Q Consensus 33 ~~~d~~LP~A~V~RI~K~~lp~~~-rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~l---gf~ 108 (140)
......||+++|++|||.. +++ .|+.||...+.+||+.||..|+..+...+...+|+|+...|+-.++..- +|.
T Consensus 69 d~~~~~lPlaRiKkimK~d--edv~mI~~Eapvl~aka~E~Fi~elt~~sw~~Tee~~rrtl~~sdia~av~~s~~fdFL 146 (236)
T KOG1657|consen 69 DFKNHILPLARIKKIMKSD--EDVSMITAEAPVLFAKACELFITELTLRSWVHTEENKRRTLQKSDIAAAVTQSETFDFL 146 (236)
T ss_pred chhhccCcHhhcccccccc--ccccccchhHHHHHHHHHHHHHHHHHHHhhhhhcccccccchHHHHHHHhccCCCccce
Confidence 3344579999999999999 555 6999999999999999999999999999999999999999999999874 444
Q ss_pred hhHHHHHHHHHHH
Q 038014 109 NYADQLKRYLHRY 121 (140)
Q Consensus 109 ~y~~~l~~~l~~~ 121 (140)
-.+-+-+...+.|
T Consensus 147 ~DivP~~~~~~~~ 159 (236)
T KOG1657|consen 147 RDIVPRKILAEKY 159 (236)
T ss_pred eccccchhccccc
Confidence 4444556656555
No 24
>cd00074 H2A Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins.
Probab=98.52 E-value=3e-07 Score=67.94 Aligned_cols=70 Identities=13% Similarity=0.178 Sum_probs=63.8
Q ss_pred cccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHh
Q 038014 34 EQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALAT 104 (140)
Q Consensus 34 ~~d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~ 104 (140)
-..+.||.++|.|+||+.- ...||+.+|...|..+.|-+...|...|...|++.+|++|+++||..|+..
T Consensus 16 ragL~fPV~ri~R~Lk~~~-~a~RVs~~A~VyLaAvLEYL~aEIlelA~n~ak~~k~krItp~hi~lAi~n 85 (115)
T cd00074 16 RAGLQFPVGRIHRYLKKGR-YAERVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKKRITPRHLQLAVRN 85 (115)
T ss_pred ccCccCcHHHHHHHHHcCc-cccccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEcHHHHHHHHhc
Confidence 3578999999999999852 247999999999999999999999999999999999999999999999874
No 25
>cd07979 TAF9 TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. The TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Human TAF9 has a paralogue gene (TAF9L) whi
Probab=98.51 E-value=4.1e-07 Score=67.13 Aligned_cols=78 Identities=12% Similarity=0.177 Sum_probs=66.0
Q ss_pred hHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCchhHH-HHHHHHHH
Q 038014 42 ANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDNYAD-QLKRYLHR 120 (140)
Q Consensus 42 A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~~y~~-~l~~~l~~ 120 (140)
..|.+|+|.. +..+++.+++..|.+.+..++..|..+|..+|+|+||+||+++||..|++..+-..|.+ +-+++|-+
T Consensus 5 ~~v~~iLk~~--Gv~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r~~~~f~~~p~~~~l~~ 82 (117)
T cd07979 5 RVIAAILKSM--GITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRVDYSFTSPPPRDFLLE 82 (117)
T ss_pred HHHHHHHHHC--CCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhccCCCCCCcHHHHHH
Confidence 3578888887 56799999999999999999999999999999999999999999999999766544544 35666544
Q ss_pred H
Q 038014 121 Y 121 (140)
Q Consensus 121 ~ 121 (140)
.
T Consensus 83 ~ 83 (117)
T cd07979 83 L 83 (117)
T ss_pred H
Confidence 3
No 26
>PF15511 CENP-T: Centromere kinetochore component CENP-T; PDB: 3B0D_T 3B0C_T 3VH5_T 3VH6_T.
Probab=98.46 E-value=2.5e-07 Score=80.71 Aligned_cols=64 Identities=22% Similarity=0.294 Sum_probs=48.2
Q ss_pred cccccCchhHHHHHHhhhCC----CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCccc
Q 038014 34 EQDRLLPIANVGRIMKQILP----PNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDD 97 (140)
Q Consensus 34 ~~d~~LP~A~V~RI~K~~lp----~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eD 97 (140)
+..-.||.+.|+|++..... .+++|++||..+|.+|..+|...|+..-..+|.|+|||||..+|
T Consensus 347 i~~P~lP~~~vK~la~~~ak~s~~sK~kiskdal~aleqasdwfFeQl~dDL~aYA~HAgRKTIdesD 414 (414)
T PF15511_consen 347 IPYPSLPPGVVKKLAQHFAKSSGGSKMKISKDALEALEQASDWFFEQLGDDLEAYAKHAGRKTIDESD 414 (414)
T ss_dssp -----S-HHHHHHHHHHHH-------S-B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHH
T ss_pred CCCCCCCccHHHHHHHHHHHhhcccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCCCC
Confidence 34446999999999877743 46899999999999999999999999999999999999998876
No 27
>KOG1659 consensus Class 2 transcription repressor NC2, alpha subunit (DRAP1) [Transcription]
Probab=98.24 E-value=3.8e-06 Score=67.99 Aligned_cols=88 Identities=11% Similarity=0.170 Sum_probs=75.3
Q ss_pred cccccCchhHHHHHHhhhCCCC-ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCchhHH
Q 038014 34 EQDRLLPIANVGRIMKQILPPN-AKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDNYAD 112 (140)
Q Consensus 34 ~~d~~LP~A~V~RI~K~~lp~~-~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~~y~~ 112 (140)
---..||.++|+|||... .+ .+|+.-....+.++.+.|+..|...+.+++...+-|||+++|+..+++.-.-.+|..
T Consensus 9 ~~~trfp~aRiKKIMQ~d--EdIGKvaqavPViisralElFl~~l~~~t~~~t~~~~aKt~s~~hlkq~v~~~~~FdFLk 86 (224)
T KOG1659|consen 9 KYKTRFPPARIKKIMQSD--EDIGKVAQAVPVIISRALELFLESLLQKTLEITRSRGAKTVSSSHLKQAVESDPKFDFLK 86 (224)
T ss_pred hhhccCCHHHHHHHHhhh--hhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhcCccccCHHHHHHHHhccchhHHHH
Confidence 334579999999999988 55 489999999999999999999999999999999999999999999999887777777
Q ss_pred HHHHHHHHHHH
Q 038014 113 QLKRYLHRYRE 123 (140)
Q Consensus 113 ~l~~~l~~~re 123 (140)
.+-..+..+..
T Consensus 87 ~~v~~vpd~~~ 97 (224)
T KOG1659|consen 87 EVVEKVPDRQQ 97 (224)
T ss_pred HHHHhcCCCcc
Confidence 65555443333
No 28
>cd08050 TAF6 TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and are involved in forming Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs functions such as serving as
Probab=98.23 E-value=4.4e-06 Score=71.18 Aligned_cols=67 Identities=19% Similarity=0.237 Sum_probs=60.9
Q ss_pred chhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCc
Q 038014 40 PIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFD 108 (140)
Q Consensus 40 P~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~ 108 (140)
|..+|+-|++.. +-.++++||..+|.+.++.++..|+.+|...++|.||||++++||-.||+.++.+
T Consensus 1 ~~~~i~~ia~~~--Gi~~~~~~a~~~La~~~e~~~~~i~~~A~k~~~hskR~~l~~~Di~~Al~~~n~e 67 (343)
T cd08050 1 PQESIKLIAESL--GIDSLSDEVAQLLAEDVEYRLREIIQEAAKFMRHSKRRKLTTSDVNHALRLRNVE 67 (343)
T ss_pred ChhHHHHHHHHc--CCCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHHhCCC
Confidence 567788888888 5559999999999999999999999999999999999999999999999976554
No 29
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=98.09 E-value=1.2e-05 Score=55.51 Aligned_cols=62 Identities=18% Similarity=0.230 Sum_probs=52.5
Q ss_pred HHHHHHhhhC-CCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHh
Q 038014 43 NVGRIMKQIL-PPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALAT 104 (140)
Q Consensus 43 ~V~RI~K~~l-p~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~ 104 (140)
+|.+|+.+.. +.++.+++.+..+|.+.+-.++..++.+---.|+|+||+||+.+||+...++
T Consensus 10 ~v~ki~ee~~~~~~~~~s~~~i~al~ELv~~q~~~~a~DLe~FAkHA~R~tI~~dDV~Ll~Rr 72 (76)
T PF15630_consen 10 TVGKIVEEEAKEKGVEVSPQFIAALTELVYKQLENLAKDLEAFAKHAGRSTINMDDVKLLARR 72 (76)
T ss_dssp HHHHHHHHCCCCTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHTTT
T ss_pred HHHHHHHHHHhccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHHHhhc
Confidence 5778888874 5578999999999999999999999999999999999999999999977653
No 30
>COG5247 BUR6 Class 2 transcription repressor NC2, alpha subunit (DRAP1 homolog) [Transcription]
Probab=98.01 E-value=1.6e-05 Score=57.87 Aligned_cols=79 Identities=14% Similarity=0.261 Sum_probs=68.7
Q ss_pred ccCchhHHHHHHhhhCCCC-ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCchhHHHHH
Q 038014 37 RLLPIANVGRIMKQILPPN-AKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDNYADQLK 115 (140)
Q Consensus 37 ~~LP~A~V~RI~K~~lp~~-~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~~y~~~l~ 115 (140)
..+|.|.|+|||... .+ .+|+.-......++.+.|+..|.....+.|+..+-|.|+.+++..|.+.-+=.+|...+.
T Consensus 22 trFP~ar~KkIMQ~d--eDiGKV~q~tPVIaskalE~Fl~~iv~~s~k~aR~~~skR~t~e~lk~a~~sdekFdFL~~~~ 99 (113)
T COG5247 22 TRFPIARLKKIMQLD--EDIGKVGQSTPVIASKALEMFLTEIVGLSLKEARKKSSKRMTSEFLKRATESDEKFDFLKNME 99 (113)
T ss_pred hcCCHHHHHHHHHhh--hhhhhhhhcchHHHHHHHHHHHHHHHHHHHHHHHhccchhhHHHHHHHHHhhhHHHHHHHHHH
Confidence 469999999999988 44 489999999999999999999999999999999999999999999998765555655544
Q ss_pred HH
Q 038014 116 RY 117 (140)
Q Consensus 116 ~~ 117 (140)
.+
T Consensus 100 ~~ 101 (113)
T COG5247 100 QF 101 (113)
T ss_pred Hh
Confidence 43
No 31
>PF07524 Bromo_TP: Bromodomain associated; InterPro: IPR006565 This bromodomain is found in eukaryotic transcription factors and PHD domain containing proteins (IPR001965 from INTERPRO). The tandem PHD finger-bromodomain is found in many chromatin-associated proteins. It is involved in gene silencing by the human co-repressor KRAB-associated protein 1 (KAP1). The tandem PHD finger-bromodomain of KAP1 has a distinct structure that joins the two protein modules. The first helix, alpha(Z), of an atypical bromodomain forms the central hydrophobic core that anchors the other three helices of the bromodomain on one side and the zinc binding PHD finger on the other []. The Rap1 GTPase-activating protein, Sipa1, is modulated by the cellular bromodomain protein, Brd4. Brd4 belongs to the BET family and is a multifunctional protein involved in transcription, replication, the signal transduction pathway, and cell cycle progression. All of these functions are linked to its association with acetylated chromatin. It has tandem bromodomains []. The dysregulation of the Brd4-associated pathways may play an important role in breast cancer progression []. Bovine papillomavirus type 1 E2 also binds to chromosomes in a complex with Brd4. Interaction with Brd4 is additionally important for E2-mediated transcriptional regulation [, ].
Probab=97.98 E-value=5.4e-05 Score=51.26 Aligned_cols=65 Identities=20% Similarity=0.265 Sum_probs=57.0
Q ss_pred hHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCc
Q 038014 42 ANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFD 108 (140)
Q Consensus 42 A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~ 108 (140)
-.|.+|++.. +=-.++..|.+.|...+..|+..|+..+..+|.+.||...+..||..||+++|+.
T Consensus 10 ~~va~il~~~--GF~~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~~~gi~ 74 (77)
T PF07524_consen 10 RSVAQILKHA--GFDSASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPNLQDVEQALEEMGIS 74 (77)
T ss_pred HHHHHHHHHc--CccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCC
Confidence 3455566665 2237999999999999999999999999999999999999999999999999984
No 32
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=97.91 E-value=2.7e-05 Score=58.13 Aligned_cols=77 Identities=13% Similarity=0.172 Sum_probs=65.9
Q ss_pred CCCCCccccccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHH
Q 038014 26 TDQDGVIKEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALA 103 (140)
Q Consensus 26 ~~~~~~~~~~d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe 103 (140)
-..++......+.+|...|+||||.. ...+||+++|...+.-|.+-.+..+..-|-..|+..|+|.|++.|+..|+.
T Consensus 14 r~~~s~sa~agl~fpvgrvkr~lk~~-~~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~kkkri~PrHlqlAIr 90 (132)
T COG5262 14 RVSQSRSAKAGLIFPVGRVKRLLKKG-NYRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRIIPRHLQLAIR 90 (132)
T ss_pred hhccchhhhcCccccHHHHHHHHHcC-ccceeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhcCcceechHHHHHHhc
Confidence 34455555567889999999999954 346899999999999999888888888899999999999999999999986
No 33
>PF03847 TFIID_20kDa: Transcription initiation factor TFIID subunit A; InterPro: IPR003228 Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription [].; GO: 0006352 transcription initiation, DNA-dependent, 0005669 transcription factor TFIID complex; PDB: 1H3O_B.
Probab=97.91 E-value=5.8e-05 Score=50.98 Aligned_cols=63 Identities=24% Similarity=0.325 Sum_probs=51.7
Q ss_pred hhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHh
Q 038014 41 IANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALAT 104 (140)
Q Consensus 41 ~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~ 104 (140)
+..+..++++.=| +..+..++.++|.+.+..||..+++.|...|+|.|-.||...||...|++
T Consensus 2 K~~l~~Lv~~iDp-~~~ld~~vee~Ll~laddFv~~v~~~ac~lAKhR~s~tle~~Dv~~~Ler 64 (68)
T PF03847_consen 2 KRKLQELVKQIDP-NEKLDPDVEELLLELADDFVDDVVSFACRLAKHRKSSTLEVKDVQLHLER 64 (68)
T ss_dssp HHHHHHHHHCC-S-S----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHHH
T ss_pred hHHHHHHHHHcCC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCHHHHHHHHHh
Confidence 4567888999844 78999999999999999999999999999999999999999999999875
No 34
>cd08048 TAF11 TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypothes
Probab=97.84 E-value=0.00011 Score=51.65 Aligned_cols=66 Identities=15% Similarity=0.188 Sum_probs=60.9
Q ss_pred cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC---CccCcccHHHHHHhc
Q 038014 38 LLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKR---KTVNGDDICWALATL 105 (140)
Q Consensus 38 ~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kR---KTI~~eDVl~ALe~l 105 (140)
.||++.|+|||...++ ..++.+...+|.-.+.+|+-.|...|.++..+.+. ..|.++||..|...|
T Consensus 16 ~f~k~~iKr~~~~~~~--~~v~~~v~i~v~glaKvFVGeivE~A~~V~~~~~~~~~~Pl~P~HireA~rrl 84 (85)
T cd08048 16 SFPKAAIKRLIQSVTG--QSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGEANTGPLQPRHLREAYRRL 84 (85)
T ss_pred hccHHHHHHHHHHHcC--CCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCCCCCcHHHHHHHHHh
Confidence 4999999999999965 78999999999999999999999999999888776 789999999999876
No 35
>PF02969 TAF: TATA box binding protein associated factor (TAF); InterPro: IPR004823 The TATA box binding protein associated factor (TAF) is part of the transcription initiation factor TFIID multimeric protein complex. TFIID plays a central role in mediating promoter responses to various activators and repressors. It binds tightly to TAFII-250 and directly interacts with TAFII-40. TFIID is composed of TATA binding protein (TBP)and a number of TBP-associated factors (TAFS). TAF proteins adopt a histone-like fold.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus; PDB: 1TAF_B.
Probab=97.80 E-value=0.00014 Score=48.92 Aligned_cols=64 Identities=25% Similarity=0.257 Sum_probs=51.3
Q ss_pred cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHH
Q 038014 38 LLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALA 103 (140)
Q Consensus 38 ~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe 103 (140)
.+|..+|+-+.... +-..++.|+...|.+-++--|..|..+|....+|.+|++++++||-.||+
T Consensus 3 ~~~~esvk~iAes~--Gi~~l~de~a~~La~dveyrlreiiq~a~kfm~hskR~~Lt~~Di~~ALr 66 (66)
T PF02969_consen 3 VFSQESVKDIAESL--GISNLSDEAAKALAEDVEYRLREIIQEALKFMRHSKRTKLTTDDINSALR 66 (66)
T ss_dssp ---HHHHHHHHHHT--T---B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH-
T ss_pred cCCHHHHHHHHHHc--CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhC
Confidence 47888998888887 44589999999999999999999999999999999999999999999985
No 36
>smart00427 H2B Histone H2B.
Probab=97.78 E-value=0.00013 Score=51.90 Aligned_cols=62 Identities=24% Similarity=0.373 Sum_probs=57.6
Q ss_pred HHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhc
Q 038014 43 NVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATL 105 (140)
Q Consensus 43 ~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~l 105 (140)
-|.|++|++-| +..||..+...+.--+..+...|+.+|...+.-.+|+||+..+|..|.+-+
T Consensus 6 Yi~kvLKqVhp-d~giS~kam~imnSfvnDiferIa~EAs~L~~~nkr~TltsreIqtAvrl~ 67 (89)
T smart00427 6 YIYKVLKQVHP-DTGISSKAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRLI 67 (89)
T ss_pred HHHHHHHHhCC-CccccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHH
Confidence 58999999987 679999999999999999999999999999999999999999999998654
No 37
>PF09415 CENP-X: CENP-S associating Centromere protein X; InterPro: IPR018552 Centromere protein X (CENP-X) is a component of the CENP-S complex. The CENP-S complex is composed of at least of CENP-S and CENP-X and is essential for the stable assembly of the outer kinetchore []. CENP-X is also a DNA-binding component of the Fanconi anemia (FA) core complex involved in DNA damage repair and genome maintenance. The FA complex is composed of CENPS, FANCA, FANCB, FANCC, FANCE, FANCF, FANCG, FANCL/PHF9, FANCM, FAAP24 and CENPX. Interacts with CENPS, FANCM and FAAP24 [, ].; PDB: 4DRB_L 4DRA_H 3V9R_D.
Probab=97.65 E-value=6.8e-05 Score=51.19 Aligned_cols=65 Identities=18% Similarity=0.278 Sum_probs=54.2
Q ss_pred chhHHHHHHhhhCC-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCc-cCcccHHHHHHh
Q 038014 40 PIANVGRIMKQILP-PNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKT-VNGDDICWALAT 104 (140)
Q Consensus 40 P~A~V~RI~K~~lp-~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKT-I~~eDVl~ALe~ 104 (140)
|+.+|.||++.... +..+|++||..++.+-...|+..-...|...++..|..+ |..+|+-+.+-.
T Consensus 1 p~~li~rll~~~f~~~~tkIs~dal~l~~eyl~iFV~EAv~Ra~~~a~~e~~~~~le~e~LEki~pq 67 (72)
T PF09415_consen 1 PPELIARLLHEHFKDDKTKISKDALKLSAEYLRIFVREAVARAAEQAEAEGDEGFLEVEHLEKILPQ 67 (72)
T ss_dssp -CHHHHHHHCTTSSSTT-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSEE-HHHHHHHCHC
T ss_pred ChHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHHH
Confidence 88999999998774 467999999999999999999999999999999999998 999999876543
No 38
>PLN00158 histone H2B; Provisional
Probab=97.55 E-value=0.0004 Score=51.51 Aligned_cols=67 Identities=21% Similarity=0.279 Sum_probs=60.5
Q ss_pred cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhc
Q 038014 38 LLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATL 105 (140)
Q Consensus 38 ~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~l 105 (140)
+--..-|.|++|++-| +..||..+...+.-....+..-|+.+|...|.-.+|+||+..+|..|++-+
T Consensus 27 esy~~YI~kVLKQVhP-d~gIS~kaM~ImnSfvnDiferIA~EAs~La~~nkr~TltsrEIqtAvrLv 93 (116)
T PLN00158 27 ETYKIYIYKVLKQVHP-DTGISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVRLI 93 (116)
T ss_pred ccHHHHHHHHHHHhCC-CCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHh
Confidence 4455679999999987 678999999999999999999999999999999999999999999998654
No 39
>PF04719 TAFII28: hTAFII28-like protein conserved region; InterPro: IPR006809 The general transcription factor, TFIID, consists of the TATA-binding protein (TBP) associated with a series of TBP-associated factors (TAFs) that together participate in the assembly of the transcription preinitiation complex. The conserved region is found at the C terminus of most member proteins. The crystal structure of hTAFII28 with hTAFII18 shows that this region is involved in the binding of these two subunits. The conserved region contains four alpha helices and three loops arranged as in histone H3 [, ].; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005634 nucleus; PDB: 1BH9_B 1BH8_B.
Probab=97.53 E-value=0.0004 Score=49.36 Aligned_cols=67 Identities=18% Similarity=0.218 Sum_probs=51.4
Q ss_pred cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCC-ccCcccHHHHHHhc
Q 038014 38 LLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRK-TVNGDDICWALATL 105 (140)
Q Consensus 38 ~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRK-TI~~eDVl~ALe~l 105 (140)
.||++.|+|||...++ +..|+.....++.-.+..|+-.|...|.+++...+.. .|.+.|+..|.++|
T Consensus 23 ~~~k~~ikkli~~~~~-~qsv~~~v~i~v~g~aKvFVGEiVE~A~~Vq~~~~~~~pl~P~hlreA~rrL 90 (90)
T PF04719_consen 23 SFNKAAIKKLINQVLG-NQSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGETGPLQPDHLREAYRRL 90 (90)
T ss_dssp ---HHHHHHHHHHHHS--S---HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SS--HHHHHHHHHHH
T ss_pred cCCHHHHHHHHHHHcC-CCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcHHHHHHHHhC
Confidence 5999999999999985 5799999999999999999999999999998866543 79999999998765
No 40
>PTZ00463 histone H2B; Provisional
Probab=97.50 E-value=0.00051 Score=51.00 Aligned_cols=63 Identities=22% Similarity=0.379 Sum_probs=57.7
Q ss_pred hHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhc
Q 038014 42 ANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATL 105 (140)
Q Consensus 42 A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~l 105 (140)
.-|.|++|++-| +..||..+...|+-.......-|+.+|...|.-.+|.||+..+|..|++-+
T Consensus 32 ~YI~KVLKqVhP-d~gIS~kaM~ImnSfvnDifErIA~EAs~La~~nkr~TltsrEIQtAvrLl 94 (117)
T PTZ00463 32 LYIFKVLKQVHP-DTGISRKSMNIMNSFLVDTFEKIATEASRLCKYTRRDTLSSREIQTAIRLV 94 (117)
T ss_pred HHHHHHHHhhCC-CCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHhhc
Confidence 349999999987 678999999999999999999999999999999999999999999998644
No 41
>smart00414 H2A Histone 2A.
Probab=97.40 E-value=0.00051 Score=50.07 Aligned_cols=69 Identities=10% Similarity=0.198 Sum_probs=61.3
Q ss_pred ccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHh
Q 038014 35 QDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALAT 104 (140)
Q Consensus 35 ~d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~ 104 (140)
..+.||.+.|.|+||+.-. ..||+..|...|.-+.|-+...|...|...|...+++.|+++|+..|+..
T Consensus 6 agL~fPVgRi~r~Lk~~~~-~~Rv~~~A~VyLaAvLEYLtaEILeLagn~a~~~k~~rItp~hi~lAi~n 74 (106)
T smart00414 6 AGLQFPVGRIHRLLRKGTY-AKRVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKRRITPRHLQLAIRN 74 (106)
T ss_pred CCccCchHHHHHHHHcCcc-ccccccccHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchHHHhhhccC
Confidence 4678999999999998732 45999999999999999888888888999999999999999999999864
No 42
>PLN00154 histone H2A; Provisional
Probab=97.28 E-value=0.00074 Score=51.37 Aligned_cols=71 Identities=14% Similarity=0.171 Sum_probs=61.1
Q ss_pred cccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHh
Q 038014 34 EQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALAT 104 (140)
Q Consensus 34 ~~d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~ 104 (140)
-..+.||.++|.|++|+...-..||+..|...|.-..|=+...|...|-..|...+++.|++.||..|+..
T Consensus 34 rAgL~FPVgRi~r~Lk~g~~~~~RVga~ApVYLAAVLEYLtAEVLELAGNaA~d~kk~RItPrHi~lAIrn 104 (136)
T PLN00154 34 RAGLQFPVGRIHRQLKQRVSAHGRVGATAAVYTAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRG 104 (136)
T ss_pred ccCccCchHHHHHHHHhhhhhccccccchHHHHHHHHHHHHHHHHHHHHHHHHhhCCceecHHHhhhhccC
Confidence 34788999999999999843356999999999998888777777778888899999999999999999853
No 43
>PTZ00017 histone H2A; Provisional
Probab=97.11 E-value=0.0011 Score=50.43 Aligned_cols=69 Identities=16% Similarity=0.192 Sum_probs=61.7
Q ss_pred cccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHH
Q 038014 34 EQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALA 103 (140)
Q Consensus 34 ~~d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe 103 (140)
-..+.||.+.|.|+||+.-. ..||+..|...|.-+.|-+...|...|...|...+++-|+++||..|+.
T Consensus 23 ragL~FPVgRi~R~Lk~g~~-a~RV~a~A~VYLAAVLEYLtaEILELAgNaa~d~kk~RItPrHi~lAI~ 91 (134)
T PTZ00017 23 KAGLQFPVGRVHRYLKKGRY-AKRVGAGAPVYLAAVLEYLTAEVLELAGNAAKDNKKKRITPRHIQLAIR 91 (134)
T ss_pred cCCcccchHHHHHHHhccch-hccccccchhhhHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHhhcc
Confidence 35788999999999998632 3599999999999999999999999999999999999999999999985
No 44
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=97.01 E-value=0.002 Score=53.54 Aligned_cols=76 Identities=17% Similarity=0.323 Sum_probs=66.3
Q ss_pred ccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHh---cCCchhH
Q 038014 35 QDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALAT---LGFDNYA 111 (140)
Q Consensus 35 ~d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~---lgf~~y~ 111 (140)
....|-+-.+.-+++.+- .+..|-+|+.+.|.+.|..||..|+..|...|+|.+..||-+.||...||+ +.|..|.
T Consensus 151 ~~~il~k~kl~dLvqqId-~~~~LD~dVedlLleiADdFV~sii~~sC~LAKHRKsdtlEvrDIqLhLEr~~Nm~iPgf~ 229 (258)
T KOG1142|consen 151 NNPILSKRKLDDLVQQID-GTTKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHRKSDTVEVRDIQLHLERNFNMEIPGFS 229 (258)
T ss_pred CCccccccchhHHHHhhc-CcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccchhheeeeeeccccccCCCcc
Confidence 444678888999999993 367899999999999999999999999999999999999999999999996 5555443
No 45
>PLN00153 histone H2A; Provisional
Probab=96.93 E-value=0.0034 Score=47.39 Aligned_cols=74 Identities=14% Similarity=0.155 Sum_probs=63.1
Q ss_pred CccccccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHh
Q 038014 30 GVIKEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALAT 104 (140)
Q Consensus 30 ~~~~~~d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~ 104 (140)
+-..-..+.||.+.|.|++|+.-. ..||+..|...|.-+.|-....|...|-..|...+++-|+++||..|+..
T Consensus 16 srS~ragL~FpVgRi~R~Lr~g~~-a~Rvga~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~n 89 (129)
T PLN00153 16 SRSAKAGLQFPVGRIARYLKKGKY-AERIGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKNRIVPRHIQLAIRN 89 (129)
T ss_pred CcccccCcccchHHHHHHHhcCch-hhccCCCchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHhhccC
Confidence 333445789999999999998633 45999999999999988888888888888999999999999999999853
No 46
>PF02291 TFIID-31kDa: Transcription initiation factor IID, 31kD subunit; InterPro: IPR003162 Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription []. TAFII-31 protein is a transcriptional coactivator of the p53 protein [].; GO: 0006352 transcription initiation, DNA-dependent; PDB: 1TAF_A.
Probab=96.92 E-value=0.0041 Score=46.83 Aligned_cols=82 Identities=18% Similarity=0.223 Sum_probs=48.4
Q ss_pred cCchh--HHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHH-hcCCchhHHHH
Q 038014 38 LLPIA--NVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALA-TLGFDNYADQL 114 (140)
Q Consensus 38 ~LP~A--~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe-~lgf~~y~~~l 114 (140)
.+|+. .|.-|+|+. +-......++..|.+.+-.|+..|..+|..+|.|+||++|+.+||..|++ ++++.-..++-
T Consensus 10 ~~PrDa~~i~~iL~~~--Gv~~yeprVv~qLLEfayRYt~~vL~DA~~ya~hA~~~~i~~~DVrLAi~~r~~~~f~~ppp 87 (129)
T PF02291_consen 10 SLPRDARVIHLILKSM--GVTEYEPRVVNQLLEFAYRYTSDVLEDAQVYADHAGRSTIDADDVRLAIQSRLDHSFTQPPP 87 (129)
T ss_dssp ---HHHHHHHHHHHHT--T---B-THHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHHHHT----------
T ss_pred cCChHHHHHHHHHHHc--CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHhhhccCCCC
Confidence 45552 345555665 44468888999999999999999999999999999999999999999999 56777777777
Q ss_pred HHHHHHH
Q 038014 115 KRYLHRY 121 (140)
Q Consensus 115 ~~~l~~~ 121 (140)
+++|-+.
T Consensus 88 re~llel 94 (129)
T PF02291_consen 88 REFLLEL 94 (129)
T ss_dssp -------
T ss_pred hHHHHHH
Confidence 7776544
No 47
>KOG1756 consensus Histone 2A [Chromatin structure and dynamics]
Probab=96.92 E-value=0.0024 Score=48.21 Aligned_cols=71 Identities=8% Similarity=0.173 Sum_probs=57.8
Q ss_pred cccccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHH
Q 038014 32 IKEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALA 103 (140)
Q Consensus 32 ~~~~d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe 103 (140)
..-..+.+|...|.|++|+. ....||+.+|...+.-+.+-....+...|-..++..++..|++.||..|+.
T Consensus 21 s~~agl~fPvgri~r~Lr~~-~~~~ri~~gapV~laavLeYL~Aeile~agnaardnkk~ri~PrH~~lAI~ 91 (131)
T KOG1756|consen 21 SSRAGLQFPVGRIHRLLRKG-RYAQRVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRITPRHLQLAIR 91 (131)
T ss_pred hhhcccccCHHHHHHHHHcc-chhhhccCCChHHHHHHHHHHHHHHHHHhHHHhhhcCccccChHHHHHHHh
Confidence 34467789999999999994 235799999999999776666666666666677888999999999999986
No 48
>PLN00156 histone H2AX; Provisional
Probab=96.92 E-value=0.0036 Score=47.84 Aligned_cols=70 Identities=13% Similarity=0.172 Sum_probs=60.3
Q ss_pred ccccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHH
Q 038014 33 KEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALA 103 (140)
Q Consensus 33 ~~~d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe 103 (140)
.-..+.||.++|.|++|+.-- ..||+..|...|.-+.|=....|...|-..|...+++.|+++||..|+.
T Consensus 24 ~rAgL~FPVgRi~R~Lk~g~y-a~RVga~ApVYLAAVLEYLtaEVLELAgNaa~d~kk~RItPrHi~lAIr 93 (139)
T PLN00156 24 SKAGLQFPVGRIARFLKAGKY-AERVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR 93 (139)
T ss_pred cccCcccchHHHHHHHhcCCh-hhccCCccHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHhhcc
Confidence 345788999999999998732 3599999999999988877777888888888999999999999999985
No 49
>KOG1658 consensus DNA polymerase epsilon, subunit C [Replication, recombination and repair]
Probab=96.86 E-value=0.00069 Score=52.62 Aligned_cols=69 Identities=23% Similarity=0.302 Sum_probs=60.7
Q ss_pred ccccCchhHHHHHHhhhCCCCcc-ccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhc
Q 038014 35 QDRLLPIANVGRIMKQILPPNAK-ISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATL 105 (140)
Q Consensus 35 ~d~~LP~A~V~RI~K~~lp~~~r-IskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~l 105 (140)
.-..||.++|+.+||.. ++++ ...+++.++.++++.||..|...+...+...+|||+.-.|+-.|++.-
T Consensus 56 ~l~rLpL~rik~vvkl~--pdl~l~~dea~~l~a~aaelfi~~Ln~~~~~~~q~~k~kt~qr~d~D~ai~~~ 125 (162)
T KOG1658|consen 56 SLSRLPLARIKQVVKLD--PDLTLLNDEASQLIAKAAELFIQELNDVAYTTAQLRKRKTEQRRDYDTAIEAV 125 (162)
T ss_pred hhhhccHHHHHhhccCC--cchhhhhhHHHHHHHHHHHHHHHHHHhccchhHHHHHhhhhhhhcccccccch
Confidence 34579999999999977 6776 667889999999999999999999999999999999999888877653
No 50
>PLN00157 histone H2A; Provisional
Probab=96.79 E-value=0.0026 Score=48.17 Aligned_cols=71 Identities=13% Similarity=0.159 Sum_probs=61.6
Q ss_pred ccccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHh
Q 038014 33 KEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALAT 104 (140)
Q Consensus 33 ~~~d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~ 104 (140)
.-..+.||...|.|++|+.-- ..||+..|...|.-+.|-....|...|-..|...+++-|+++||..|+..
T Consensus 21 ~ragL~FPVgRi~R~Lk~g~~-a~RIg~~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~n 91 (132)
T PLN00157 21 AKAGLQFPVGRIARYLKAGKY-ATRVGAGAPVYLAAVLEYLAAEVLELAGNAARDNKKSRIVPRHIQLAVRN 91 (132)
T ss_pred cccCcccchHHHHHHHhcCch-hhhcCCCcHhHHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHhhcccC
Confidence 345789999999999999632 46999999999999888888888888888999999999999999999853
No 51
>PF02269 TFIID-18kDa: Transcription initiation factor IID, 18kD subunit; InterPro: IPR003195 This family includes the Spt3 yeast transcription factors and the 18 kDa subunit from human transcription initiation factor IID (TFIID-18). Determination of the crystal structure reveals an atypical histone fold [].; GO: 0006366 transcription from RNA polymerase II promoter; PDB: 1BH9_A 1BH8_A.
Probab=96.76 E-value=0.0018 Score=45.85 Aligned_cols=60 Identities=17% Similarity=0.261 Sum_probs=29.4
Q ss_pred HHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHh
Q 038014 44 VGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALAT 104 (140)
Q Consensus 44 V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~ 104 (140)
|..+|-.- ++...-..|++.+|-+.+..||..+...|..+|...|+++|+.+|++-+|+.
T Consensus 7 I~~mMy~f-GD~~~P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~rg~~~i~~eDl~F~lR~ 66 (93)
T PF02269_consen 7 IRQMMYGF-GDVEEPLPETVDLVEDIVREYIIELCQEAMEVAQRRGSKKIKVEDLLFLLRK 66 (93)
T ss_dssp CHHHHHCT-TS-SS--HHHHHHHHHHHHHHHHHHHHHHHC---------------------
T ss_pred HHHHHHHc-CCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCcCcHHHHHHHHhc
Confidence 34445444 3445788999999999999999999999999999999999999999999985
No 52
>KOG1744 consensus Histone H2B [Chromatin structure and dynamics]
Probab=96.44 E-value=0.013 Score=44.24 Aligned_cols=63 Identities=29% Similarity=0.380 Sum_probs=56.9
Q ss_pred hHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhc
Q 038014 42 ANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATL 105 (140)
Q Consensus 42 A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~l 105 (140)
..|.|++|++-|+ .-|+..+...+.--.-.++..|+.+|...+.-.||.||+..++..|++-+
T Consensus 41 ~yv~kvlk~Vhpd-~gis~~a~~vmnsf~ndife~iA~ea~rla~y~krstisSreiqta~rLl 103 (127)
T KOG1744|consen 41 EYVYKVLKQVHPD-LGISSKAMGVMNSFVNDIFERIASEAGRLAHYNKRSTISSREIQTAVRLL 103 (127)
T ss_pred eehhhhhhcccCC-CCcCHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCcccHHHHHHHHHHh
Confidence 3477799999885 77999999999999999999999999999999999999999999988643
No 53
>PF15510 CENP-W: Centromere kinetochore component W
Probab=96.43 E-value=0.0056 Score=43.99 Aligned_cols=66 Identities=15% Similarity=0.190 Sum_probs=54.1
Q ss_pred cCchhHHHHHHhhhCCCCccccHHHHHH--------------HHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHH
Q 038014 38 LLPIANVGRIMKQILPPNAKISKEAKET--------------MQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALA 103 (140)
Q Consensus 38 ~LP~A~V~RI~K~~lp~~~rIskdA~~a--------------l~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe 103 (140)
.-|++.++|++|..-| ..|+....-.+ +.--|-.|++-|+.+|...|-.++-.||..+||+.|-+
T Consensus 16 kaPrgfLkrv~Kr~Kp-hlRl~~~~Dllv~~~~f~~~~~~~~vhLncLLFvhrLAEEaRtnA~EnK~~~Ik~~Hv~AaaK 94 (102)
T PF15510_consen 16 KAPRGFLKRVFKRQKP-HLRLETSGDLLVRFCPFSGWQWGGEVHLNCLLFVHRLAEEARTNACENKCGTIKKEHVLAAAK 94 (102)
T ss_pred hCchHHHHHHHHhcCC-ceeecccccHHHhhcccccccccceeehhHHHHHHHHHHHHHHHHHHHhhccccHHHHHHHHH
Confidence 5799999999998755 56655544444 55668899999999999999999999999999998865
Q ss_pred h
Q 038014 104 T 104 (140)
Q Consensus 104 ~ 104 (140)
.
T Consensus 95 v 95 (102)
T PF15510_consen 95 V 95 (102)
T ss_pred H
Confidence 3
No 54
>KOG3219 consensus Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=96.39 E-value=0.0039 Score=50.00 Aligned_cols=70 Identities=20% Similarity=0.220 Sum_probs=61.2
Q ss_pred cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCC-ccCcccHHHHHHhcCCch
Q 038014 38 LLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRK-TVNGDDICWALATLGFDN 109 (140)
Q Consensus 38 ~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRK-TI~~eDVl~ALe~lgf~~ 109 (140)
.||++.|+|||....+. .|+.-+..++.-.+.+|+-.|..+|.++|..-+.. .|.+.||-.|..+|+...
T Consensus 112 ~f~Ka~iKkL~~~itg~--~v~~nv~Ia~~GiaKvFVGEvVEeAl~V~~~~~e~~PLqP~HIREA~rrL~~qg 182 (195)
T KOG3219|consen 112 AFPKAQIKKLMSSITGQ--SVSENVAIAMAGIAKVFVGEVVEEALDVREEWGESGPLQPKHIREAYRRLKLQG 182 (195)
T ss_pred cCCHHHHHHHHHHHhCC--ccCcceeeeecchhhHhHHHHHHHHHHHHHHhccCCCCCcHHHHHHHHHHHhcC
Confidence 59999999999999653 39999999999999999999999999999877753 599999999998876543
No 55
>PTZ00252 histone H2A; Provisional
Probab=95.85 E-value=0.026 Score=42.92 Aligned_cols=69 Identities=12% Similarity=0.198 Sum_probs=52.8
Q ss_pred cccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHh--CCCCccCcccHHHHHH
Q 038014 34 EQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHK--EKRKTVNGDDICWALA 103 (140)
Q Consensus 34 ~~d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~--~kRKTI~~eDVl~ALe 103 (140)
-..+.||.+.|.|++|+.-- ..||+..|...|.-+.|=....|...|...|.. .+++-|+++||..|+.
T Consensus 21 rAGL~FPVgRi~R~Lr~g~y-a~RIga~ApVYLAAVLEYLtaEVLELAgnaa~d~~~kk~RItPrHi~lAIr 91 (134)
T PTZ00252 21 KAGLIFPVGRVGSLLRRGQY-ARRIGASGAVYMAAVLEYLTAELLELSVKAAAQQAKKPKRLTPRTVTLAVR 91 (134)
T ss_pred ccCccCchHHHHHHHHcCCc-ccccCCccHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccccHHHHHhhcc
Confidence 35789999999999998743 459999999888876655555555555555543 5678899999999985
No 56
>cd07978 TAF13 The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Several hy
Probab=95.55 E-value=0.28 Score=34.77 Aligned_cols=60 Identities=17% Similarity=0.276 Sum_probs=48.5
Q ss_pred HHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHh
Q 038014 43 NVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALAT 104 (140)
Q Consensus 43 ~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~ 104 (140)
-|+.+|-.- ++.-.-..|.+.+|-+.+..||..++..|.+.|. .+|.-++.+|++-+|+.
T Consensus 7 ei~~mmy~~-GD~~~P~~eTv~llE~iv~~~i~~l~~~a~~~A~-~r~~k~~~eD~~FliR~ 66 (92)
T cd07978 7 EIRQMMYGF-GDVQNPLPETVDLLEDIVVEYIIELCHKAAEVAQ-RRRGKVKVEDLIFLLRK 66 (92)
T ss_pred HHHHHHHHc-CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-cCCCCCCHHHHHHHHhc
Confidence 466666665 3334678899999999999999999999999998 44445699999999964
No 57
>KOG3423 consensus Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=95.15 E-value=0.11 Score=40.93 Aligned_cols=69 Identities=19% Similarity=0.246 Sum_probs=57.0
Q ss_pred cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC--------------CCccCcccHHHHHH
Q 038014 38 LLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEK--------------RKTVNGDDICWALA 103 (140)
Q Consensus 38 ~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~k--------------RKTI~~eDVl~ALe 103 (140)
.||-+.+.-.++.+ +-.....-.+-+|+-++..||..|+..|.+.|+-.+ |-|++-+|+-.||+
T Consensus 86 ~IPDavt~~yL~~a--Gf~~~D~rv~RLvsLaAQKfvSDIa~DA~Q~~k~r~~~~~~~~k~~~kdkK~tLtmeDL~~AL~ 163 (176)
T KOG3423|consen 86 TIPDAVTDHYLKKA--GFQTSDPRVKRLVSLAAQKFVSDIANDALQHSKIRTKTAIGKDKKQAKDKKYTLTMEDLSPALA 163 (176)
T ss_pred CCcHHHHHHHHHhc--CCCcCcHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccccccccccccceeeeHHHHHHHHH
Confidence 48888888888888 333455667788999999999999999999997443 55899999999999
Q ss_pred hcCCc
Q 038014 104 TLGFD 108 (140)
Q Consensus 104 ~lgf~ 108 (140)
+-|..
T Consensus 164 EyGin 168 (176)
T KOG3423|consen 164 EYGIN 168 (176)
T ss_pred HhCcc
Confidence 98875
No 58
>KOG4336 consensus TBP-associated transcription factor Prodos [Transcription]
Probab=94.57 E-value=0.23 Score=42.58 Aligned_cols=75 Identities=20% Similarity=0.298 Sum_probs=62.4
Q ss_pred HHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCchhHHHHHHHHHHH
Q 038014 43 NVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDNYADQLKRYLHRY 121 (140)
Q Consensus 43 ~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~~y~~~l~~~l~~~ 121 (140)
.|.-|.+.. +=--|++-|++.|.+....+|..++..+.-+|.++||...+..||...|-+||+. ++.|..+++.+
T Consensus 10 VV~~Ll~~~--gfd~is~~aletlvell~~yi~eigrq~~n~celagRT~pT~~Dv~l~Li~mnI~--v~sL~~~~q~~ 84 (323)
T KOG4336|consen 10 VVSNLLKTK--GFDSISNAALETLVELLQSYIREIGRQLHNYCELAGRTIPTQGDVKLTLIEMNIK--VSSLYAYFQKQ 84 (323)
T ss_pred HHHHHHHHh--CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcHHHHHHHHHHhCCC--hhhhHHHHHhc
Confidence 444455555 2235999999999999999999999999999999999999999999999999998 56666666544
No 59
>KOG2549 consensus Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=94.50 E-value=0.15 Score=46.64 Aligned_cols=66 Identities=23% Similarity=0.267 Sum_probs=58.0
Q ss_pred chhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCC
Q 038014 40 PIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGF 107 (140)
Q Consensus 40 P~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf 107 (140)
|.-.++-+++.. +-..|+.|+..+|.+-++.=|..++.+|.+.-.|.+|.+++.+||..||+-+..
T Consensus 13 ~~Es~k~vAEsl--Gi~nl~deaa~~La~dv~yrikEI~Q~aaKfm~hskR~kLtv~DV~~ALr~~nV 78 (576)
T KOG2549|consen 13 PKESVKVVAESL--GITNLNDEAALLLAEDVEYRIKEIVQDAAKFMVHSKRTKLTVDDVDYALRSLNV 78 (576)
T ss_pred cHHHHHHHHHHh--CccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcCcHHHHHHHHhhccc
Confidence 466777777766 456799999999999999999999999999999999999999999999996543
No 60
>KOG3334 consensus Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=92.20 E-value=0.72 Score=35.62 Aligned_cols=74 Identities=14% Similarity=0.229 Sum_probs=55.6
Q ss_pred HHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCchhHH-HHHHHHH
Q 038014 44 VGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDNYAD-QLKRYLH 119 (140)
Q Consensus 44 V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~~y~~-~l~~~l~ 119 (140)
|.-|+|+. +---...-...-|.+.+-.++..|...|.-++.|+++.||.++||..|++-..-..|.+ +=+++|-
T Consensus 19 i~~iL~s~--GI~eyEprVi~qlLefa~rYtt~vL~DA~vys~HA~ka~i~~eDVrlA~~~~~~~sf~~pPpRe~lL 93 (148)
T KOG3334|consen 19 IASILKSL--GIQEYEPRVINQLLEFAYRYTTTVLDDAKVYSSHAKKATIDAEDVRLAIQMRVDHSFTPPPPREFLL 93 (148)
T ss_pred HHHHHHHc--CccccChHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHhccccCCCCchHHHH
Confidence 34444444 22245666777788889999999999999999999999999999999999766666655 4444443
No 61
>KOG2389 consensus Predicted bromodomain transcription factor [Transcription]
Probab=89.91 E-value=0.88 Score=39.58 Aligned_cols=69 Identities=20% Similarity=0.225 Sum_probs=59.9
Q ss_pred cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCc
Q 038014 38 LLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFD 108 (140)
Q Consensus 38 ~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~ 108 (140)
.|-+..|..|+... +--....-|...|+.-+..||..|+..|..++...||.-.+..||+.||+.|+..
T Consensus 29 sla~~avaQIcqsl--g~~~~~~sale~Ltd~~~qyvQ~lgk~a~~~~n~anR~epnl~Div~Al~dls~s 97 (353)
T KOG2389|consen 29 SLARVAVAQICQSL--GYSSTQNSALETLTDVLQQYVQNLGKTAHRYSNLANRTEPNLFDIVLALQDLSAS 97 (353)
T ss_pred HHHHHHHHHHHHhc--CCcccccHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCccHHHHHHHHHHhhhh
Confidence 46777888888887 3335666699999999999999999999999999999999999999999987654
No 62
>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily. Members of this protein are marked as probable ATPases by the nucleotide binding P-loop motif GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of helicases, and extensive homology to ATPases of MSHA-type pilus systems and to GspA proteins associated with type II protein secretion systems.
Probab=89.62 E-value=1.3 Score=35.10 Aligned_cols=69 Identities=13% Similarity=0.241 Sum_probs=54.3
Q ss_pred CchhHHHHHHhhhCC-----CCccccHHHHHHHHHHHHH---HHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCC
Q 038014 39 LPIANVGRIMKQILP-----PNAKISKEAKETMQECVSE---FISFVTGEASDKCHKEKRKTVNGDDICWALATLGF 107 (140)
Q Consensus 39 LP~A~V~RI~K~~lp-----~~~rIskdA~~al~~aa~~---Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf 107 (140)
|....+..++...+. ....++.++...|.+.+.= .|..++..+...+-..+.++|+.++|..++.++.|
T Consensus 192 l~~~e~~~~l~~~l~~~g~~~~~~~~~~~~~~i~~~s~G~p~~i~~l~~~~~~~a~~~~~~~i~~~~v~~~~~~~~~ 268 (269)
T TIGR03015 192 LDREETREYIEHRLERAGNRDAPVFSEGAFDAIHRFSRGIPRLINILCDRLLLSAFLEEKREIGGEEVREVIAEIDF 268 (269)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCCCcCHHHHHHHHHHcCCcccHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhhc
Confidence 444556666554431 2346999999999988774 79999999999988899999999999999998864
No 63
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=89.18 E-value=1.7 Score=36.50 Aligned_cols=70 Identities=11% Similarity=0.106 Sum_probs=51.5
Q ss_pred hhHHHHHHhhhCCC---CccccHHHHHHHHHHH------HHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCchh
Q 038014 41 IANVGRIMKQILPP---NAKISKEAKETMQECV------SEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDNY 110 (140)
Q Consensus 41 ~A~V~RI~K~~lp~---~~rIskdA~~al~~aa------~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~~y 110 (140)
...+..|++..+.. ...++.++.+.+.+.+ -..+..+...|...|...++.+|+.+||..|++++....+
T Consensus 209 ~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~a~~~a~~~~~~~I~~~~v~~a~~~~~~~~~ 287 (394)
T PRK00411 209 ADEIFDILKDRVEEGFYPGVVDDEVLDLIADLTAREHGDARVAIDLLRRAGLIAEREGSRKVTEEDVRKAYEKSEIVHL 287 (394)
T ss_pred HHHHHHHHHHHHHhhcccCCCCHhHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHHHHHH
Confidence 45566666654421 2358899988888777 3455667788888999999999999999999998854443
No 64
>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=85.78 E-value=3.2 Score=36.35 Aligned_cols=66 Identities=23% Similarity=0.248 Sum_probs=56.4
Q ss_pred hhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCc
Q 038014 41 IANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFD 108 (140)
Q Consensus 41 ~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~ 108 (140)
+.+|+-++..- +-..|..|+..+|..-.+--|+.+..+|...-.|.+|..++-+||-.||+.++.+
T Consensus 8 ~et~KdvAesl--Gi~Ni~Dd~l~alamDlEYRI~ev~qea~KFmvhSKRtvLt~dDis~ALr~lNVe 73 (450)
T COG5095 8 KETLKDVAESL--GISNIDDDALRALAMDLEYRIKEVCQEASKFMVHSKRTVLTIDDISYALRSLNVE 73 (450)
T ss_pred HHHHHHHHHHc--CCcccccHHHHHHHHhHHHHHHHHHHHHHHHhhcccceeeeHHhHHHHHHhcCCC
Confidence 44555555544 3457999999999999999999999999999999999999999999999987654
No 65
>TIGR02928 orc1/cdc6 family replication initiation protein. Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.
Probab=85.60 E-value=4 Score=33.84 Aligned_cols=75 Identities=9% Similarity=0.061 Sum_probs=51.2
Q ss_pred hhHHHHHHhhhCC---CCccccHHHHHHHHHHHH------HHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCchhH
Q 038014 41 IANVGRIMKQILP---PNAKISKEAKETMQECVS------EFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDNYA 111 (140)
Q Consensus 41 ~A~V~RI~K~~lp---~~~rIskdA~~al~~aa~------~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~~y~ 111 (140)
...+..|++..+. ....++.++...+.+.+. ..+..+...|...|...++.+|+.+||..|+..+....+.
T Consensus 201 ~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~R~al~~l~~a~~~a~~~~~~~it~~~v~~a~~~~~~~~~~ 280 (365)
T TIGR02928 201 AEELRDILENRAEKAFYDGVLDDGVIPLCAALAAQEHGDARKAIDLLRVAGEIAEREGAERVTEDHVEKAQEKIEKDRLL 280 (365)
T ss_pred HHHHHHHHHHHHHhhccCCCCChhHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHH
Confidence 3446667765542 123588888777665442 3455566678888888899999999999999988655554
Q ss_pred HHHH
Q 038014 112 DQLK 115 (140)
Q Consensus 112 ~~l~ 115 (140)
..+.
T Consensus 281 ~~i~ 284 (365)
T TIGR02928 281 ELIR 284 (365)
T ss_pred HHHH
Confidence 4333
No 66
>PF03540 TFIID_30kDa: Transcription initiation factor TFIID 23-30kDa subunit; InterPro: IPR003923 Transcription initiation factor TFIID is a multimeric protein complex that plays a central role in mediating promoter responses to various activators and repressors. The complex includes TATA binding protein (TBP) and various TBP-associated factors (TAFS). TFIID a bona fide RNA polymerase II-specific TATA-binding protein-associated factor (TAF) and is essential for viability []. TFIID acts to nucleate the transcription complex, recruiting the rest of the factors through a direct interaction with TFIIB. The TBP subunit of TFIID is sufficient for TATA-element binding and TFIIB interaction, and can support basal transcription. The protein belongs to the TAF2H family.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus
Probab=85.24 E-value=6 Score=25.37 Aligned_cols=48 Identities=15% Similarity=0.188 Sum_probs=37.3
Q ss_pred cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 038014 38 LLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHK 87 (140)
Q Consensus 38 ~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~ 87 (140)
.+|-+.+.-+++.+ +--.-..-..-+++-++..||..++..|.++|+-
T Consensus 2 ~IPD~v~~~yL~~~--G~~~~D~rv~RLvSLaaQKFisdI~~dA~q~~k~ 49 (51)
T PF03540_consen 2 TIPDEVTDYYLERS--GFQTSDPRVKRLVSLAAQKFISDIANDAMQYCKI 49 (51)
T ss_pred CCCHHHHHHHHHHC--CCCCCCHhHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 47888888999888 2222334456688889999999999999999874
No 67
>KOG1757 consensus Histone 2A [Chromatin structure and dynamics]
Probab=84.67 E-value=1.4 Score=32.97 Aligned_cols=67 Identities=13% Similarity=0.243 Sum_probs=51.0
Q ss_pred ccccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhC----CCCccCcccHHHHHH
Q 038014 33 KEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKE----KRKTVNGDDICWALA 103 (140)
Q Consensus 33 ~~~d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~----kRKTI~~eDVl~ALe 103 (140)
....+.||..+|.|.+|.......|+..-+.... ...+.||+.+-.+.|..+ +-|.|++.|+..|++
T Consensus 25 ~raGlqFpVgRihr~LK~r~t~h~rVGataavy~----aaileYLTaEVLeLAgNasKdLKvKRitprHlqLAiR 95 (131)
T KOG1757|consen 25 ARAGLQFPVGRIHRHLKTRTTSHGRVGATAAVYS----AAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 95 (131)
T ss_pred HhcccccchHHHHHHHHHhcccccccchHHHHHH----HHHHHHHHHHHHHHcccccccceeeeccchhheeeec
Confidence 3456789999999999999777778876665433 335678888888877554 457899999988875
No 68
>cd08045 TAF4 TATA Binding Protein (TBP) Associated Factor 4 (TAF4) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 4 (TAF4) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryote. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypotheses are
Probab=83.96 E-value=11 Score=29.95 Aligned_cols=78 Identities=8% Similarity=0.095 Sum_probs=58.9
Q ss_pred ccccCchhHHHHHHhhhCCC-Cc-cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhC------CCCccCcccHHHHHHhcC
Q 038014 35 QDRLLPIANVGRIMKQILPP-NA-KISKEAKETMQECVSEFISFVTGEASDKCHKE------KRKTVNGDDICWALATLG 106 (140)
Q Consensus 35 ~d~~LP~A~V~RI~K~~lp~-~~-rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~------kRKTI~~eDVl~ALe~lg 106 (140)
....|....+.+.|...+.. +. .|+.|.+.+|+.||+.++..|.......|+|- ..+++...||..-|..|+
T Consensus 41 ~~~fl~~~~l~~~~~~i~~~~g~~~~~~d~~~lis~a~e~rlr~li~k~~~~s~hR~~~~~~~~r~~~~sdvr~qL~~l~ 120 (212)
T cd08045 41 DPSFLNPSPLAKKIRKIAKKHGLKEVDEDVLDLISLALEERLRNLLEKLIEVSEHRVDSEKEDERYEITSDVRKQLRFLE 120 (212)
T ss_pred hhhccCHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCceeecchHHHHHHHHH
Confidence 44567777777777666532 22 79999999999999999999999999999865 446677889988777665
Q ss_pred CchhHH
Q 038014 107 FDNYAD 112 (140)
Q Consensus 107 f~~y~~ 112 (140)
--+-..
T Consensus 121 ~~ek~e 126 (212)
T cd08045 121 QLEREE 126 (212)
T ss_pred HHHHHH
Confidence 444333
No 69
>PF13654 AAA_32: AAA domain; PDB: 3K1J_B.
Probab=83.16 E-value=5.5 Score=36.09 Aligned_cols=60 Identities=15% Similarity=0.176 Sum_probs=41.5
Q ss_pred HHHHHhhhCCCCccccHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHhCCCCccCcccHHHHHHhc
Q 038014 44 VGRIMKQILPPNAKISKEAKETMQECVSE-----------FISFVTGEASDKCHKEKRKTVNGDDICWALATL 105 (140)
Q Consensus 44 V~RI~K~~lp~~~rIskdA~~al~~aa~~-----------Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~l 105 (140)
|.+++++. +-..++.+|+..|-+.+.. -|..|..+|+.+|...+++.|+++||..|++.-
T Consensus 436 i~~~~~~~--~L~~~~~~Av~~li~~~~R~~q~kLsl~~~~l~~ll~EA~~~A~~~~~~~I~~~~V~~Ai~~r 506 (509)
T PF13654_consen 436 IASICQKE--GLPPFDRSAVARLIEYSARLDQDKLSLRFSWLADLLREANYWARKEGAKVITAEHVEQAIEER 506 (509)
T ss_dssp HHHHHHHH--SS--BBHHHHHHHHHHHHHCC-SEEE--HHHHHHHHHHHHHHHHHCT-SSB-HHHHHHHHHH-
T ss_pred HHHHHHhC--CCCCCCHHHHHHHHHHHHHHhCCEeCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHcc
Confidence 44444444 2225777777777766543 567788899999999999999999999999864
No 70
>COG5162 Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=81.77 E-value=9.6 Score=30.32 Aligned_cols=68 Identities=15% Similarity=0.189 Sum_probs=48.7
Q ss_pred CchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHh-------------------------------
Q 038014 39 LPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHK------------------------------- 87 (140)
Q Consensus 39 LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~------------------------------- 87 (140)
||-+.+.=.+-.+ +-.....-.+.+|.-.+..||..|+-.|.++.+-
T Consensus 89 iPd~v~DYyl~k~--Gf~~~D~rvKkLl~L~aqKFvsDiA~dayqYsrIr~~~sna~~t~~~a~~f~~gg~~~i~~~~~~ 166 (197)
T COG5162 89 IPDSVTDYYLEKA--GFVTSDQRVKKLLSLLAQKFVSDIAVDAYQYSRIRQGSSNAKATAQKAKRFAKGGASGIGSSGRR 166 (197)
T ss_pred ccHHHHHHHHHhc--CceeccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccchhhHHHHHHHHhcccccccccccc
Confidence 4555554444444 2234556677888999999999999999887641
Q ss_pred --CCCCccCcccHHHHHHhcCCc
Q 038014 88 --EKRKTVNGDDICWALATLGFD 108 (140)
Q Consensus 88 --~kRKTI~~eDVl~ALe~lgf~ 108 (140)
.++.+++..|+-.||++.|+.
T Consensus 167 ~dr~K~vltv~DLs~Al~EyGin 189 (197)
T COG5162 167 GDRKKPVLTVVDLSKALEEYGIN 189 (197)
T ss_pred cccCCceeeehHHHHHHHHhccc
Confidence 145678999999999998764
No 71
>TIGR02902 spore_lonB ATP-dependent protease LonB. Members of this protein are LonB, a paralog of the ATP-dependent protease La (LonA, TIGR00763). LonB proteins are found strictly, and almost universally, in endospore-forming bacteria. This protease was shown, in Bacillus subtilis, to be expressed specifically in the forespore, during sporulation, under control of sigma(F). The lonB gene, despite location immediately upstream of lonA, was shown to be monocistronic. LonB appears able to act on sigma(H) for post-translation control, but lonB mutation did not produce an obvious sporulation defect under the conditions tested. Note that additional paralogs of LonA and LonB occur in the Clostridium lineage and this model selects only one per species as the protein that corresponds to LonB in B. subtilis.
Probab=78.09 E-value=5.7 Score=35.83 Aligned_cols=69 Identities=20% Similarity=0.211 Sum_probs=47.6
Q ss_pred CchhHHHHHHhhhCCC-CccccHHHHHHHHHHHHH--HHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCC
Q 038014 39 LPIANVGRIMKQILPP-NAKISKEAKETMQECVSE--FISFVTGEASDKCHKEKRKTVNGDDICWALATLGF 107 (140)
Q Consensus 39 LP~A~V~RI~K~~lp~-~~rIskdA~~al~~aa~~--Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf 107 (140)
|+...+.+|++..+.. ++.++.++...|.+.+.. .+..+...|...|...+|++|+.+||.+++..-.|
T Consensus 263 L~~eei~~Il~~~a~k~~i~is~~al~~I~~y~~n~Rel~nll~~Aa~~A~~~~~~~It~~dI~~vl~~~~~ 334 (531)
T TIGR02902 263 LLDEEIKEIAKNAAEKIGINLEKHALELIVKYASNGREAVNIVQLAAGIALGEGRKRILAEDIEWVAENGNY 334 (531)
T ss_pred CCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHhhhhHHHHHHHHHHHHHHHhhCCCcEEcHHHHHHHhCCccc
Confidence 3345566677766532 467999999988776652 23344455666778889999999999999764433
No 72
>TIGR00764 lon_rel lon-related putative ATP-dependent protease. Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein.
Probab=71.83 E-value=16 Score=33.78 Aligned_cols=50 Identities=12% Similarity=0.092 Sum_probs=40.3
Q ss_pred cccHHHHHHHHHHHH-------------HHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcC
Q 038014 57 KISKEAKETMQECVS-------------EFISFVTGEASDKCHKEKRKTVNGDDICWALATLG 106 (140)
Q Consensus 57 rIskdA~~al~~aa~-------------~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lg 106 (140)
.++.+|+..|.+-+. .=+..|...|..+|..+++.+|+.+||..|++.-.
T Consensus 330 ~~s~~Av~~Li~~~~R~ag~r~~lsl~~R~L~~llR~A~~iA~~~~~~~I~~ehV~~Ai~~~~ 392 (608)
T TIGR00764 330 HFTRDAVEEIVREAQRRAGRKDHLTLRLRELGGLVRAAGDIAKSSGKVYVTAEHVLKAKKLAK 392 (608)
T ss_pred cCCHHHHHHHHHHHHHHHhcccccCCCHHHHHHHHHHHHHHHHhcCCceecHHHHHHHHHHHH
Confidence 689999998876443 34666777888899999999999999999987543
No 73
>COG1067 LonB Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]
Probab=71.70 E-value=3.5 Score=38.52 Aligned_cols=48 Identities=25% Similarity=0.284 Sum_probs=37.2
Q ss_pred cccHHHHHHHHHHHHH-------------HHHHHHHHHHHHHHhCCCCccCcccHHHHHHh
Q 038014 57 KISKEAKETMQECVSE-------------FISFVTGEASDKCHKEKRKTVNGDDICWALAT 104 (140)
Q Consensus 57 rIskdA~~al~~aa~~-------------Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~ 104 (140)
-++++|...|.+-+.. -+-.|...|..+|..++++-|+++||.+|++.
T Consensus 338 ~~~~~Av~~li~~a~R~Ag~~~~Ltl~~rdl~~lv~~A~~ia~~~~~~~I~ae~Ve~a~~~ 398 (647)
T COG1067 338 HLDKDAVEELIREAARRAGDQNKLTLRLRDLGNLVREAGDIAVSEGRKLITAEDVEEALQK 398 (647)
T ss_pred CCCHHHHHHHHHHHHHhccccceeccCHHHHHHHHHHhhHHHhcCCcccCcHHHHHHHHHh
Confidence 4777777666655543 23445558999999999999999999999987
No 74
>PF08369 PCP_red: Proto-chlorophyllide reductase 57 kD subunit; InterPro: IPR013580 This domain is found in bacteria and plant chloroplast proteins. It often appears at the C-terminal of nitrogenase component 1 type oxidoreductases (IPR000510 from INTERPRO) and sometimes independently in bacterial proteins such as the proto-chlorophyllide reductase subunit B of the cyanobacterium Synechocystis. This domain is also associated with chlorophyllide reductase subunit Z, converts chlorophylls (Chl) into bacteriochlorophylls (BChl) by reducing ring B of the tetrapyrrole.; GO: 0016491 oxidoreductase activity, 0015979 photosynthesis, 0015995 chlorophyll biosynthetic process, 0055114 oxidation-reduction process; PDB: 2KRU_A 2L09_A.
Probab=71.33 E-value=5.3 Score=24.64 Aligned_cols=42 Identities=12% Similarity=0.136 Sum_probs=28.3
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHHHH-HHHhCCCCccCcccHHHH
Q 038014 59 SKEAKETMQECVSEFISFVTGEASD-KCHKEKRKTVNGDDICWA 101 (140)
Q Consensus 59 skdA~~al~~aa~~Fi~~Las~A~~-~a~~~kRKTI~~eDVl~A 101 (140)
+.||...|.+. -.|+..-...+.+ +|...|...||.++|..|
T Consensus 2 ~~eA~~~L~~i-P~fvR~~~r~~~E~~Ar~~G~~~IT~e~v~~A 44 (45)
T PF08369_consen 2 TDEAEARLDRI-PFFVRKKLRDAAEKYARERGYDEITVEVVDAA 44 (45)
T ss_dssp -HHHHHHHCTS--HHHHHHHHHHHHHHHHHCT-SEE-HHHHHHH
T ss_pred CHHHHHHHHHC-CHHHHHHHHHHHHHHHHHcCCCeECHHHHHhh
Confidence 46777777774 6677765555444 899999999999998765
No 75
>PF13335 Mg_chelatase_2: Magnesium chelatase, subunit ChlI
Probab=71.27 E-value=15 Score=25.77 Aligned_cols=48 Identities=19% Similarity=0.243 Sum_probs=38.7
Q ss_pred ccccHHHHHHHHHHHHHH------HHHHHHHHHHHHHhCCCCccCcccHHHHHH
Q 038014 56 AKISKEAKETMQECVSEF------ISFVTGEASDKCHKEKRKTVNGDDICWALA 103 (140)
Q Consensus 56 ~rIskdA~~al~~aa~~F------i~~Las~A~~~a~~~kRKTI~~eDVl~ALe 103 (140)
..+++++...|..++..+ ++-|..-|.++|.-++...|+.+||..||.
T Consensus 41 ~~l~~~~~~~l~~~~~~~~lS~R~~~rilrvARTIADL~~~~~I~~~hi~EAl~ 94 (96)
T PF13335_consen 41 CPLSSEAKKLLEQAAEKLNLSARGYHRILRVARTIADLEGSERITREHIAEALS 94 (96)
T ss_pred cCCCHHHHHHHHHHHHHcCcCHHHHHHHHHHHHHHHhHcCCCCCCHHHHHHHHh
Confidence 357777777777777665 455667799999999999999999999984
No 76
>PF05236 TAF4: Transcription initiation factor TFIID component TAF4 family; InterPro: IPR007900 Accurate transcription initiation at protein-coding genes by RNA polymerase II requires the assembly of a multiprotein complex around the mRNA start site. Transcription factor TFIID is one of the general factors involved in this process. Yeast TFIID comprises the TATA binding protein and 14 TBP-associated factors (TAFIIs), nine of which contain histone-fold domains (IPR007124 from INTERPRO). The C-terminal region of the TFIID-specific yeast TAF4 (yTAF4) containing the HFD shares strong sequence similarity with Drosophila (d)TAF4 and human TAF4. A structure/function analysis of yTAF4 demonstrates that the HFD, a short conserved C-terminal domain (CCTD), and the region separating them are all required for yTAF4 function. This region of similarity is found in Transcription initiation factor TFIID component TAF4 []. ; GO: 0006352 transcription initiation, DNA-dependent, 0005669 transcription factor TFIID complex; PDB: 1H3O_C.
Probab=69.76 E-value=8 Score=31.66 Aligned_cols=74 Identities=11% Similarity=0.095 Sum_probs=33.9
Q ss_pred cccccCchhHHHHHHhhhCC--CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC------CccCcccHHHHHHhc
Q 038014 34 EQDRLLPIANVGRIMKQILP--PNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKR------KTVNGDDICWALATL 105 (140)
Q Consensus 34 ~~d~~LP~A~V~RI~K~~lp--~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kR------KTI~~eDVl~ALe~l 105 (140)
.++..|....+.+-|..... +...+..|.+.+|+-||+..|..|...+..+|+|--. .+....||-..|..|
T Consensus 39 ~~~~fL~~~~L~~~i~~i~~~~g~~~~~~d~l~llS~A~e~rLr~lie~~~~~s~hR~~~~~~~~~~~~~sdv~~qlr~l 118 (264)
T PF05236_consen 39 KEEPFLNPSPLQKRIQKIAKKHGLKSVDEDVLELLSLATEERLRNLIEKAIVLSRHRRDSSKSDPRYEIRSDVRKQLRFL 118 (264)
T ss_dssp -----S-HHHHHHHHHHHHHCTT--EE-TCHHHHHHHHHHHHHHHHHHHHH-----------------------------
T ss_pred ccccccCHHHHHHHHHHHHHHcCCcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccCCCcccccchHHHHHHHHH
Confidence 34556777777777766642 3457999999999999999999999999998876422 233467777666655
Q ss_pred CC
Q 038014 106 GF 107 (140)
Q Consensus 106 gf 107 (140)
.-
T Consensus 119 ~~ 120 (264)
T PF05236_consen 119 EQ 120 (264)
T ss_dssp --
T ss_pred HH
Confidence 43
No 77
>COG5094 TAF9 Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=66.41 E-value=47 Score=25.34 Aligned_cols=67 Identities=19% Similarity=0.190 Sum_probs=50.4
Q ss_pred cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCc---ccHHHHHHh-cCCchhHHHHHHHHHHHHH
Q 038014 57 KISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNG---DDICWALAT-LGFDNYADQLKRYLHRYRE 123 (140)
Q Consensus 57 rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~---eDVl~ALe~-lgf~~y~~~l~~~l~~~re 123 (140)
..+.....-+.+.|-.|...+..+|.-++++.||--++. +||..|+.. .|..---++=+++|-+.--
T Consensus 31 ~ye~~VplQLl~FAhRYTq~vl~Dalvya~htgrg~~a~l~veDvrLA~at~v~~~F~pppPke~llela~ 101 (145)
T COG5094 31 EYEPKVPLQLLEFAHRYTQDVLEDALVYAKHTGRGHIATLGVEDVRLALATKVGRHFVPPPPKEYLLELAT 101 (145)
T ss_pred hhCccchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHHHHHHHhcCCcCCCChHHHHHHHHH
Confidence 466677788889999999999999999999999986555 999999985 4444333455666654433
No 78
>PF02861 Clp_N: Clp amino terminal domain; InterPro: IPR004176 This short domain is found in one or two copies at the amino terminus of ClpA and ClpB proteins from bacteria and eukaryotes. The function of these domains is uncertain but they may form a protein binding site []. The proteins are thought to be subunits of ATP-dependent proteases which act as chaperones to target the proteases to substrates.; GO: 0019538 protein metabolic process; PDB: 3FH2_A 3ZRJ_A 3ZRI_A 1QVR_C 3FES_C 2Y1R_F 3PXG_D 2Y1Q_A 3PXI_C 2K77_A ....
Probab=63.84 E-value=12 Score=22.22 Aligned_cols=35 Identities=17% Similarity=0.088 Sum_probs=24.3
Q ss_pred HHHHHHhCCCCccCcccHHHHHHhcCCchhHHHHH
Q 038014 81 ASDKCHKEKRKTVNGDDICWALATLGFDNYADQLK 115 (140)
Q Consensus 81 A~~~a~~~kRKTI~~eDVl~ALe~lgf~~y~~~l~ 115 (140)
|.+.|...+...|+++|++.||=+.+=..+...++
T Consensus 1 A~~~A~~~~~~~i~~eHlL~all~~~~~~~~~il~ 35 (53)
T PF02861_consen 1 AQELARERGHQYISPEHLLLALLEDPDSIAARILK 35 (53)
T ss_dssp HHHHHHHTTBSSE-HHHHHHHHHHHTTSHHHHHHH
T ss_pred CHHHHHHcCCCcccHHHHHHHHHhhhhHHHHHHHH
Confidence 56788999999999999999976544333333333
No 79
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=59.18 E-value=38 Score=28.10 Aligned_cols=71 Identities=14% Similarity=0.164 Sum_probs=50.5
Q ss_pred cCchhHHHHHHhhhCC-CCccccHHHHHHHHHHHH---HHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCc
Q 038014 38 LLPIANVGRIMKQILP-PNAKISKEAKETMQECVS---EFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFD 108 (140)
Q Consensus 38 ~LP~A~V~RI~K~~lp-~~~rIskdA~~al~~aa~---~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~ 108 (140)
.++...+..|++..+. .++.++.++...|.+.+. ..+..+...+..++...+...|+.++|..+++.++..
T Consensus 179 ~~~~~e~~~il~~~~~~~~~~~~~~~~~~ia~~~~G~pR~a~~~l~~~~~~a~~~~~~~I~~~~v~~~l~~~~~~ 253 (328)
T PRK00080 179 FYTVEELEKIVKRSARILGVEIDEEGALEIARRSRGTPRIANRLLRRVRDFAQVKGDGVITKEIADKALDMLGVD 253 (328)
T ss_pred CCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCC
Confidence 3555666666665532 256899999988887763 3455556666677766677799999999999987655
No 80
>KOG2680 consensus DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=59.00 E-value=31 Score=30.48 Aligned_cols=50 Identities=22% Similarity=0.266 Sum_probs=42.4
Q ss_pred CCccccHHHHHHHHHHHH----HHHHHHHHHHHHHHHhCCCCccCcccHHHHHH
Q 038014 54 PNAKISKEAKETMQECVS----EFISFVTGEASDKCHKEKRKTVNGDDICWALA 103 (140)
Q Consensus 54 ~~~rIskdA~~al~~aa~----~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe 103 (140)
.++.++.||++.|.+..+ .|...|.+.|+..|.+.+-+++..+||..+-+
T Consensus 374 Edv~m~~~A~d~Lt~i~~~tsLRYai~Lit~a~~~~~krk~~~v~~~di~r~y~ 427 (454)
T KOG2680|consen 374 EDVEMNPDALDLLTKIGEATSLRYAIHLITAASLVCLKRKGKVVEVDDIERVYR 427 (454)
T ss_pred hccccCHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHhcCceeehhHHHHHHH
Confidence 468899999999887554 46777888899999999999999999998864
No 81
>PRK09862 putative ATP-dependent protease; Provisional
Probab=55.93 E-value=48 Score=30.14 Aligned_cols=60 Identities=12% Similarity=0.122 Sum_probs=44.6
Q ss_pred ccccHHHHHHHHHHHHHH------HHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCchhHHHHH
Q 038014 56 AKISKEAKETMQECVSEF------ISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDNYADQLK 115 (140)
Q Consensus 56 ~rIskdA~~al~~aa~~F------i~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~~y~~~l~ 115 (140)
..++.++...+..+...+ .+.|..-|..+|.-+||..|+.+||..|+.=-+++...-.+.
T Consensus 437 ~~l~~~~~~~l~~~~~~~~lS~Ra~~rlLrvARTiADL~g~~~V~~~hv~eAl~yR~~~~~~~~~~ 502 (506)
T PRK09862 437 CKLESEDARWLEETLIHLGLSIRAWQRLLKVARTIADIDQSDIITRQHLQEAVSYRAIDRLLIHLQ 502 (506)
T ss_pred hCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHhhcccHHHHHHH
Confidence 357777777777655443 566777899999999999999999999998666654444433
No 82
>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I. This model represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria.
Probab=55.66 E-value=51 Score=28.24 Aligned_cols=49 Identities=20% Similarity=0.127 Sum_probs=39.3
Q ss_pred CccccHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhCCCCccCcccHHHHHH
Q 038014 55 NAKISKEAKETMQECVSEFI-------SFVTGEASDKCHKEKRKTVNGDDICWALA 103 (140)
Q Consensus 55 ~~rIskdA~~al~~aa~~Fi-------~~Las~A~~~a~~~kRKTI~~eDVl~ALe 103 (140)
.+.|+.+....+...+..+= .++...|...|.-+||..|+++||..+..
T Consensus 252 ~V~v~d~~~~~i~~l~~~~~~~s~Ra~i~l~raArA~Aal~GR~~V~~dDv~~~a~ 307 (337)
T TIGR02030 252 QVTIPYDVLVKVAELCAELDVDGLRGELTLNRAAKALAAFEGRTEVTVDDIRRVAV 307 (337)
T ss_pred cCcCCHHHHHHHHHHHHHHCCCCCcHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 67899998888888766543 34666788899999999999999998765
No 83
>KOG3901 consensus Transcription initiation factor IID subunit [Transcription]
Probab=55.23 E-value=34 Score=25.20 Aligned_cols=49 Identities=22% Similarity=0.268 Sum_probs=39.3
Q ss_pred CCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHh
Q 038014 53 PPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALAT 104 (140)
Q Consensus 53 p~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~ 104 (140)
+++..=-.+++.+|-..+..||..++..|..+. +|--+..+|++-+|++
T Consensus 23 GDd~nP~~~tv~~Le~iV~~Yi~elt~~a~~~g---~rgk~~veD~~f~lRk 71 (109)
T KOG3901|consen 23 GDDVNPYPETVDLLEDIVLEYITELTHAAMEIG---KRGKVKVEDFKFLLRK 71 (109)
T ss_pred CCCCCccHhHHHHHHHHHHHHHHHHHHHHHHhc---ccCceeHHHHHHHHHh
Confidence 455666778999999999999999977777665 4555778999999975
No 84
>PRK07452 DNA polymerase III subunit delta; Validated
Probab=54.46 E-value=54 Score=26.91 Aligned_cols=66 Identities=12% Similarity=0.156 Sum_probs=46.6
Q ss_pred HHHHHhhhC-CCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHh--CCCCccCcccHHHHHHhcCCch
Q 038014 44 VGRIMKQIL-PPNAKISKEAKETMQECVSEFISFVTGEASDKCHK--EKRKTVNGDDICWALATLGFDN 109 (140)
Q Consensus 44 V~RI~K~~l-p~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~--~kRKTI~~eDVl~ALe~lgf~~ 109 (140)
+.+.|++.+ ..+..|+.+|...|..++.-=+..+..+-...+-- .++.+|+.+||...+....+.-
T Consensus 135 l~~~i~~~~~~~g~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~~It~~~V~~~v~~~~~~i 203 (326)
T PRK07452 135 LKQLVERTAQELGVKLTPEAAELLAEAVGNDSRRLYNELEKLALYAENSTKPISAEEVKALVSNTTQNS 203 (326)
T ss_pred HHHHHHHHHHHcCCCCCHHHHHHHHHHhCccHHHHHHHHHHHHHhccCCCCccCHHHHHHHhccCcCcH
Confidence 444444433 23678999999999999887666666666666655 4577899999998876655443
No 85
>PF00531 Death: Death domain; InterPro: IPR000488 The death domain (DD) is a homotypic protein interaction module composed of a bundle of six alpha-helices. DD is related in sequence and structure to the death effector domain (DED, see IPR001875 from INTERPRO) and the caspase recruitment domain (CARD, see IPR001315 from INTERPRO), which work in similar pathways and show similar interaction properties []. DD bind each other forming oligomers. Mammals have numerous and diverse DD-containing proteins []. Within these proteins, the DD domains can be found in combination with other domains, including: CARDs, DEDs, ankyrin repeats (IPR002110 from INTERPRO), caspase-like folds, kinase domains, leucine zippers (IPR002158 from INTERPRO), leucine-rich repeats (LRR) (IPR001611 from INTERPRO), TIR domains (IPR000157 from INTERPRO), and ZU5 domains (IPR000906 from INTERPRO) []. Some DD-containing proteins are involved in the regulation of apoptosis and inflammation through their activation of caspases and NF-kappaB, which typically involves interactions with TNF (tumour necrosis factor) cytokine receptors [, ]. In humans, eight of the over 30 known TNF receptors contain DD in their cytoplasmic tails; several of these TNF receptors use caspase activation as a signalling mechanism. The DD mediates self-association of these receptors, thus giving the signal to downstream events that lead to apoptosis. Other DD-containing proteins, such as ankyrin, MyD88 and pelle, are probably not directly involved in cell death signalling. DD-containing proteins also have links to innate immunity, communicating with Toll family receptors through bipartite adapter proteins such as MyD88 [].; GO: 0005515 protein binding, 0007165 signal transduction; PDB: 3OQ9_L 3EZQ_F 1E41_A 1E3Y_A 2GF5_A 2OF5_L 3EWV_E 3G5B_A 3MOP_L 2A9I_A ....
Probab=53.69 E-value=25 Score=22.71 Aligned_cols=30 Identities=20% Similarity=0.382 Sum_probs=24.2
Q ss_pred CCCccCcccHHHHHHhcCCchhHHHHHHHH
Q 038014 89 KRKTVNGDDICWALATLGFDNYADQLKRYL 118 (140)
Q Consensus 89 kRKTI~~eDVl~ALe~lgf~~y~~~l~~~l 118 (140)
....-+..+++.||+++|..+.+..++..|
T Consensus 54 ~~~~at~~~L~~aL~~~~~~d~~~~i~~~~ 83 (83)
T PF00531_consen 54 EGPNATVDQLIQALRDIGRNDLAEKIEQML 83 (83)
T ss_dssp HGSTSSHHHHHHHHHHTTHHHHHHHHHHH-
T ss_pred cCCCCcHHHHHHHHHHCCcHHHHHHHHhhC
Confidence 445667889999999999999988887654
No 86
>PF09114 MotA_activ: Transcription factor MotA, activation domain; InterPro: IPR015198 Transcription factor MotA is required for the activation of middle promoters in Bacteriophage T4, in addition to phage T4 co-activator AsiA, and sigma-70-containing Escherichia coli RNA polymerase. Phage T4 middle promoters have the sigma70 -10 DNA element, but not the -35 element; instead, they have a MotA box at -30 to which the transcription factor MotA binds []. MotA and AsiA interact with the C-terminal of sigma70 (region 4), which normally binds the -35 element and the beta-flap, thereby diverting sigma70 away from host promoters that require -35 element-binding to phage T4 middle promoters. Transcription factor MotA has two domains: an N-terminal domain required for binding to sigma70, and a C-terminal domain required for binding to the -30 MotA box element in the phage T4 middle promoter. This entry represents the N-terminal (activation) domain of MotA factors that binds sigma70. The N-terminal domain adopts an almost completely alpha-helical topology, with five alpha-helices and a short, two-stranded, beta-ribbon. Four alpha helices (alpha1, alpha3, alpha4 and alpha5) are amphipathic and pack their hydrophobic surfaces around the central helix alpha2 [].; PDB: 1BJA_B 1I1S_A.
Probab=53.62 E-value=22 Score=25.58 Aligned_cols=34 Identities=18% Similarity=0.316 Sum_probs=26.7
Q ss_pred hHHHHHHhhhC----CCCccccHHHHHHHHHHHHHHHH
Q 038014 42 ANVGRIMKQIL----PPNAKISKEAKETMQECVSEFIS 75 (140)
Q Consensus 42 A~V~RI~K~~l----p~~~rIskdA~~al~~aa~~Fi~ 75 (140)
++|.+++|..| +++..++.+..+.|+++++.|-.
T Consensus 51 SNIGvLIKkglIEKSGDGlv~T~~g~~Ii~~AA~l~a~ 88 (96)
T PF09114_consen 51 SNIGVLIKKGLIEKSGDGLVITEEGMDIIIQAAELWAQ 88 (96)
T ss_dssp HHHHHHHHTTSEEEETTEEEE-HHHHHHHHHHHHHHHH
T ss_pred HhHHHHHHcCcccccCCceEEechHHHHHHHHHHHHHh
Confidence 35666888876 45678999999999999999864
No 87
>TIGR02442 Cob-chelat-sub cobaltochelatase subunit. A number of genomes (actinobacteria, cyanobacteria, betaproteobacteria and pseudomonads) which apparently biosynthesize B12, encode a cobN gene but are demonstrably lacking cobS and cobT. These genomes do, however contain a homolog (modelled here) of the magnesium chelatase subunits BchI/BchD family. Aside from the cyanobacteria (which have a separate magnesium chelatase trimer), these species do not make chlorins, so do not have any use for a magnesium chelatase. Furthermore, in nearly all cases the members of this family are proximal to either CobN itself or other genes involved in cobalt transport or B12 biosynthesis.
Probab=53.61 E-value=48 Score=30.63 Aligned_cols=49 Identities=20% Similarity=0.205 Sum_probs=41.2
Q ss_pred CccccHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhCCCCccCcccHHHHHH
Q 038014 55 NAKISKEAKETMQECVSEFI-------SFVTGEASDKCHKEKRKTVNGDDICWALA 103 (140)
Q Consensus 55 ~~rIskdA~~al~~aa~~Fi-------~~Las~A~~~a~~~kRKTI~~eDVl~ALe 103 (140)
.+.|+.+....|...+..+- ..+...|...|.-.||.+|+.+||..|++
T Consensus 247 ~V~is~~~~~~l~~~~~~~~i~s~Ra~i~~~r~Ara~AaL~gr~~V~~~Dv~~A~~ 302 (633)
T TIGR02442 247 SVRISDSLIRFISELCIEFGVDGHRADIVMARAARALAALDGRRRVTAEDVREAAE 302 (633)
T ss_pred CCCCCHHHHHHHHHHHHHhCCCCccHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHH
Confidence 57899999999988887652 45666788889999999999999999886
No 88
>TIGR02454 CbiQ_TIGR cobalt ABC transporter, permease protein CbiQ. This model represents the permease component of the cobalt-specific ABC transporter. This model finds permeases which are generally next to the other subunits of the complex (CbiN and CbiO) or the cobalamin biosynthesis protein CbiM which is a transmembrane protein which likely interacts with the complex in some manner. In genomes which possess all of these subunits the ATPase is most likely running in the direction of import (for the biosynthesis of coenzyme B12). In other genomes, this subunit may be involved in the export of cobalt and/or other closely related heavy metals.
Probab=53.43 E-value=26 Score=26.64 Aligned_cols=38 Identities=26% Similarity=0.168 Sum_probs=32.3
Q ss_pred CccCcccHHHHHHhcCCc-----------hhHHHHHHHHHHHHHHHHHH
Q 038014 91 KTVNGDDICWALATLGFD-----------NYADQLKRYLHRYRELEGER 128 (140)
Q Consensus 91 KTI~~eDVl~ALe~lgf~-----------~y~~~l~~~l~~~re~~~~k 128 (140)
-|....|+..+|+++|++ .|+|.+.+..+.-++.++.|
T Consensus 112 ~TT~~~~l~~~l~~l~~P~~~~~~~~l~~Rfip~l~~e~~~i~~Aq~aR 160 (198)
T TIGR02454 112 LTTPFPELLSALRRLGVPPLLVEILLLTYRYLFVLLEELRRMLLAQRSR 160 (198)
T ss_pred HcCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 467889999999999987 68888888888888888877
No 89
>PF09123 DUF1931: Domain of unknown function (DUF1931); InterPro: IPR015207 This entry represents a set of hypothetical bacterial proteins containing a core of six alpha-helices, where one central helix is surrounded by the other five. The exact function of this family has not, as yet, been determined []. ; PDB: 1WWS_A 1WWI_A 1R4V_A.
Probab=51.02 E-value=13 Score=28.41 Aligned_cols=53 Identities=11% Similarity=0.223 Sum_probs=41.3
Q ss_pred HHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccH
Q 038014 44 VGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDI 98 (140)
Q Consensus 44 V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDV 98 (140)
+.|+++.+ .+.-|.|+-..-++..++.-+..|.-.|...|+.+||-+|...|+
T Consensus 1 fe~lFR~a--a~LdvdK~d~~r~~d~V~~Kl~DLl~va~~~Ak~ngRdvI~~~DL 53 (138)
T PF09123_consen 1 FERLFRKA--AGLDVDKNDAKRYSDFVEKKLYDLLLVAQENAKANGRDVIEPRDL 53 (138)
T ss_dssp HHHHHHHH--HS----HHHHHHHHHHHHHHHHHCCCCHHHHHHHTT-SEE-GGGS
T ss_pred ChHHHHHH--hccCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeeccccC
Confidence 46788888 456788888889999999999999999999999999999999886
No 90
>PF12010 DUF3502: Domain of unknown function (DUF3502); InterPro: IPR022627 This domain is about 140 amino acids in length and is functionally uncharacterised. It is found in bacteria C-terminal to PF01547 from PFAM.
Probab=49.57 E-value=16 Score=27.01 Aligned_cols=59 Identities=14% Similarity=0.227 Sum_probs=39.4
Q ss_pred HHHHHHHHHHHHHHHHHHHH---HHHHHHHhCCCCccCcccHHHHHHhcCCchhHHHHHHHHHHHHHHH
Q 038014 60 KEAKETMQECVSEFISFVTG---EASDKCHKEKRKTVNGDDICWALATLGFDNYADQLKRYLHRYRELE 125 (140)
Q Consensus 60 kdA~~al~~aa~~Fi~~Las---~A~~~a~~~kRKTI~~eDVl~ALe~lgf~~y~~~l~~~l~~~re~~ 125 (140)
......|..|..+.-.|... -..+. . -....++..|+..|++..+.+++..+++|+..+
T Consensus 72 s~Vk~Eiaa~~~v~~~Y~~~L~~G~vd~-e------~~~~~~~~kLk~AGidkV~~E~QkQlda~~~~~ 133 (134)
T PF12010_consen 72 SPVKNEIAACSNVWSEYYPPLETGLVDP-E------EALPEFNEKLKAAGIDKVIAELQKQLDAFLAAN 133 (134)
T ss_pred chhHHHHHHHHHHHHHHHHHHHccCCCH-H------HHHHHHHHHHHHhChHHHHHHHHHHHHHHHHhc
Confidence 44555666666665555433 22221 1 124667888889999999999999999997743
No 91
>TIGR01128 holA DNA polymerase III, delta subunit. subunit around DNA forming a DNA sliding clamp.
Probab=48.65 E-value=99 Score=24.65 Aligned_cols=66 Identities=14% Similarity=0.092 Sum_probs=45.5
Q ss_pred cCchhHHHHHHhhhCC-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHH
Q 038014 38 LLPIANVGRIMKQILP-PNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALA 103 (140)
Q Consensus 38 ~LP~A~V~RI~K~~lp-~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe 103 (140)
.++...+.+.+++.+. .+..|+.++...|...+.-=+..+-.+-...+--.+.++|+.+||...+.
T Consensus 110 ~~~~~~~~~~i~~~~~~~g~~i~~~a~~~l~~~~~~d~~~l~~el~KL~~~~~~~~It~e~I~~~~~ 176 (302)
T TIGR01128 110 TPKEQELPRWIQARLKKLGLRIDPDAVQLLAELVEGNLLAIAQELEKLALYAPDGKITLEDVEEAVS 176 (302)
T ss_pred CCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCcHHHHHHHHHHHHHhhCCCCCCCHHHHHHHHh
Confidence 3456666666666543 25789999999998888765666666666655544445799999977665
No 92
>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=48.14 E-value=36 Score=30.51 Aligned_cols=62 Identities=16% Similarity=0.161 Sum_probs=46.6
Q ss_pred hhHHHHHHhhhC-CCCccccHHHHHHHHHHHH----HHHHHHHHHHHHHHHhCCCCccCcccHHHHH
Q 038014 41 IANVGRIMKQIL-PPNAKISKEAKETMQECVS----EFISFVTGEASDKCHKEKRKTVNGDDICWAL 102 (140)
Q Consensus 41 ~A~V~RI~K~~l-p~~~rIskdA~~al~~aa~----~Fi~~Las~A~~~a~~~kRKTI~~eDVl~AL 102 (140)
..-|+-|++-.. -.++.++.||.+.|....+ .|...|.+-|..+|+..|+++|..+||..|-
T Consensus 363 ~~EireIi~iRa~ee~i~l~~~Ale~L~~ig~etSLRYa~qLL~pa~iiA~~rg~~~V~~~dVe~a~ 429 (450)
T COG1224 363 REEIREIIRIRAKEEDIELSDDALEYLTDIGEETSLRYAVQLLTPASIIAKRRGSKRVEVEDVERAK 429 (450)
T ss_pred HHHHHHHHHHhhhhhccccCHHHHHHHHhhchhhhHHHHHHhccHHHHHHHHhCCCeeehhHHHHHH
Confidence 334444544332 2367899999999987654 4666777789999999999999999999884
No 93
>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=47.96 E-value=88 Score=25.21 Aligned_cols=70 Identities=19% Similarity=0.163 Sum_probs=48.2
Q ss_pred CchhHHHHHHhhhCC-CCccccHHHHHHHHHHHH---HHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCc
Q 038014 39 LPIANVGRIMKQILP-PNAKISKEAKETMQECVS---EFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFD 108 (140)
Q Consensus 39 LP~A~V~RI~K~~lp-~~~rIskdA~~al~~aa~---~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~ 108 (140)
++...+..+++..+. .+..++.++...|.+.+. .++..+...+...+...+...|+.++|..++..+++.
T Consensus 159 l~~~e~~~il~~~~~~~~~~~~~~al~~ia~~~~G~pR~~~~ll~~~~~~a~~~~~~~it~~~v~~~l~~l~~~ 232 (305)
T TIGR00635 159 YTVEELAEIVSRSAGLLNVEIEPEAALEIARRSRGTPRIANRLLRRVRDFAQVRGQKIINRDIALKALEMLMID 232 (305)
T ss_pred CCHHHHHHHHHHHHHHhCCCcCHHHHHHHHHHhCCCcchHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHhCCC
Confidence 444556666665542 246789999988877653 3445555566677766666789999999999987554
No 94
>PRK13406 bchD magnesium chelatase subunit D; Provisional
Probab=47.62 E-value=43 Score=30.94 Aligned_cols=49 Identities=14% Similarity=0.106 Sum_probs=42.3
Q ss_pred CccccHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhCCCCccCcccHHHHHH
Q 038014 55 NAKISKEAKETMQECVSEFI-------SFVTGEASDKCHKEKRKTVNGDDICWALA 103 (140)
Q Consensus 55 ~~rIskdA~~al~~aa~~Fi-------~~Las~A~~~a~~~kRKTI~~eDVl~ALe 103 (140)
++.|+.+....+.+.|..|- ..+...|..+|.-+||..|+.+||..|+.
T Consensus 193 ~v~v~~~~l~~i~~~~~~~gv~S~Ra~i~llraARa~AaL~Gr~~V~~~dv~~Aa~ 248 (584)
T PRK13406 193 AVGPPPEAIAALCAAAAALGIASLRAPLLALRAARAAAALAGRTAVEEEDLALAAR 248 (584)
T ss_pred cCCCCHHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 78899999988888777764 46777889999999999999999999986
No 95
>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]
Probab=45.87 E-value=34 Score=29.57 Aligned_cols=74 Identities=15% Similarity=0.166 Sum_probs=51.8
Q ss_pred hHHHHHHhhhCCC---CccccHHHHHHHHHHH------HHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCchhHH
Q 038014 42 ANVGRIMKQILPP---NAKISKEAKETMQECV------SEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDNYAD 112 (140)
Q Consensus 42 A~V~RI~K~~lp~---~~rIskdA~~al~~aa------~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~~y~~ 112 (140)
.-+.-|++..... ...++.++...+..-+ ..+...+...|.+.|+..++.+|+.+||..|-++.+..-+..
T Consensus 193 ~el~~Il~~R~~~~~~~~~~~~~vl~lia~~~a~~~GDAR~aidilr~A~eiAe~~~~~~v~~~~v~~a~~~~~~~~~~~ 272 (366)
T COG1474 193 EELYDILRERVEEGFSAGVIDDDVLKLIAALVAAESGDARKAIDILRRAGEIAEREGSRKVSEDHVREAQEEIERDVLEE 272 (366)
T ss_pred HHHHHHHHHHHHhhccCCCcCccHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHhhCCCCcCHHHHHHHHHHhhHHHHHH
Confidence 4566666554321 3467777776665322 235667788899999999999999999999977777775555
Q ss_pred HHH
Q 038014 113 QLK 115 (140)
Q Consensus 113 ~l~ 115 (140)
.+.
T Consensus 273 ~~~ 275 (366)
T COG1474 273 VLK 275 (366)
T ss_pred HHH
Confidence 443
No 96
>PF07647 SAM_2: SAM domain (Sterile alpha motif); InterPro: IPR011510 The sterile alpha motif (SAM) domain is a putative protein interaction module present in a wide variety of proteins [] involved in many biological processes. The SAM domain that spreads over around 70 residues is found in diverse eukaryotic organisms []. SAM domains have been shown to homo- and hetero-oligomerise, forming multiple self-association architectures and also binding to various non-SAM domain-containing proteins [], nevertheless with a low affinity constant []. SAM domains also appear to possess the ability to bind RNA []. Smaug, a protein that helps to establish a morphogen gradient in Drosophila embryos by repressing the translation of nanos (nos) mRNA, binds to the 3' untranslated region (UTR) of nos mRNA via two similar hairpin structures. The 3D crystal structure of the Smaug RNA-binding region shows a cluster of positively charged residues on the Smaug-SAM domain, which could be the RNA-binding surface. This electropositive potential is unique among all previously determined SAM-domain structures and is conserved among Smaug-SAM homologs. These results suggest that the SAM domain might have a primary role in RNA binding. Structural analyses show that the SAM domain is arranged in a small five-helix bundle with two large interfaces []. In the case of the SAM domain of EphB2, each of these interfaces is able to form dimers. The presence of these two distinct intermonomers binding surface suggest that SAM could form extended polymeric structures []. This entry represents a second domain related to the SAM domain. ; GO: 0005515 protein binding; PDB: 1B0X_A 1X9X_B 1OW5_A 1V38_A 3BS7_A 3BS5_A 3TAD_A 3TAC_B 2K60_A 2DL0_A ....
Probab=45.04 E-value=24 Score=22.06 Aligned_cols=24 Identities=29% Similarity=0.578 Sum_probs=20.1
Q ss_pred cCcccHHHHHHhcCCchhHHHHHH
Q 038014 93 VNGDDICWALATLGFDNYADQLKR 116 (140)
Q Consensus 93 I~~eDVl~ALe~lgf~~y~~~l~~ 116 (140)
=+++||..-|+.+||+.|.+....
T Consensus 4 w~~~~v~~WL~~~gl~~y~~~f~~ 27 (66)
T PF07647_consen 4 WSPEDVAEWLKSLGLEQYADNFRE 27 (66)
T ss_dssp HCHHHHHHHHHHTTCGGGHHHHHH
T ss_pred CCHHHHHHHHHHCCcHHHHHHHHH
Confidence 467899999999999999887764
No 97
>smart00350 MCM minichromosome maintenance proteins.
Probab=44.74 E-value=82 Score=28.22 Aligned_cols=68 Identities=12% Similarity=0.089 Sum_probs=48.3
Q ss_pred ccCchhHHHHHHhhhCC-CCccccHHHHHHHHHHHHH-------------------HHHHHHHHHHHHHHhCCCCccCcc
Q 038014 37 RLLPIANVGRIMKQILP-PNAKISKEAKETMQECVSE-------------------FISFVTGEASDKCHKEKRKTVNGD 96 (140)
Q Consensus 37 ~~LP~A~V~RI~K~~lp-~~~rIskdA~~al~~aa~~-------------------Fi~~Las~A~~~a~~~kRKTI~~e 96 (140)
..++...+++.+.-+=. -.-+|++++...|.+.... .+..|...|--.|+-.+|.+|+.+
T Consensus 416 ~~~~~~~l~~yi~~ar~~~~P~ls~~~~~~i~~~y~~~R~~~~~~~~~~~~~~t~R~l~sliRla~A~A~l~~r~~V~~~ 495 (509)
T smart00350 416 VPISQEFLRKYIAYAREKIKPKLSEEAAEKLVKAYVDLRKEDSQSEARSSIPITVRQLESIIRLSEAHAKMRLSDVVEEA 495 (509)
T ss_pred ccCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhcccccccccccccCcCHHHHHHHHHHHHHHHHHcCCCccCHH
Confidence 35777788877755410 0125899999888664433 235666777788999999999999
Q ss_pred cHHHHHHh
Q 038014 97 DICWALAT 104 (140)
Q Consensus 97 DVl~ALe~ 104 (140)
||..|++-
T Consensus 496 Dv~~ai~l 503 (509)
T smart00350 496 DVEEAIRL 503 (509)
T ss_pred HHHHHHHH
Confidence 99999864
No 98
>TIGR00368 Mg chelatase-related protein. The N-terminal end matches very strongly a pfam Mg_chelatase domain.
Probab=44.19 E-value=54 Score=29.62 Aligned_cols=47 Identities=11% Similarity=0.186 Sum_probs=40.5
Q ss_pred cccHHHHHHHHHHHHHH------HHHHHHHHHHHHHhCCCCccCcccHHHHHH
Q 038014 57 KISKEAKETMQECVSEF------ISFVTGEASDKCHKEKRKTVNGDDICWALA 103 (140)
Q Consensus 57 rIskdA~~al~~aa~~F------i~~Las~A~~~a~~~kRKTI~~eDVl~ALe 103 (140)
.+++++...+.++...| .+.+..-|.++|.-+++..|..+||..|+.
T Consensus 445 ~l~~~~~~~l~~a~~~~~lS~R~~~rilrvArTiAdL~g~~~i~~~hv~eA~~ 497 (499)
T TIGR00368 445 KLSAIDANDLEGALNKLGLSSRATHRILKVARTIADLKEEKNISREHLAEAIE 497 (499)
T ss_pred CCCHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHh
Confidence 46888999888887776 566777899999999999999999999984
No 99
>cd00166 SAM Sterile alpha motif.; Widespread domain in signalling and nuclear proteins. In EPH-related tyrosine kinases, appears to mediate cell-cell initiated signal transduction via the binding of SH2-containing proteins to a conserved tyrosine that is phosphorylated. In many cases mediates homodimerization.
Probab=43.98 E-value=21 Score=21.58 Aligned_cols=24 Identities=29% Similarity=0.565 Sum_probs=20.3
Q ss_pred CcccHHHHHHhcCCchhHHHHHHH
Q 038014 94 NGDDICWALATLGFDNYADQLKRY 117 (140)
Q Consensus 94 ~~eDVl~ALe~lgf~~y~~~l~~~ 117 (140)
+.++|..-|+.+|+++|.+..++.
T Consensus 3 ~~~~V~~wL~~~~~~~y~~~f~~~ 26 (63)
T cd00166 3 SPEDVAEWLESLGLGQYADNFREN 26 (63)
T ss_pred CHHHHHHHHHHcChHHHHHHHHHc
Confidence 568899999999999999887654
No 100
>PF02361 CbiQ: Cobalt transport protein; InterPro: IPR003339 Cobalt transport proteins are most often found in cobalamin (vitamin B12) biosynthesis operons. Salmonella typhimurium synthesizes cobalamin (vitamin B12) de novo under anaerobic conditions. Not all Salmonella and Pseudomonas cobalamin synthetic genes have apparent homologs in the other species suggesting that the cobalamin biosynthetic pathways differ between the two organisms [].; GO: 0015087 cobalt ion transmembrane transporter activity, 0006824 cobalt ion transport, 0009236 cobalamin biosynthetic process
Probab=43.48 E-value=38 Score=25.74 Aligned_cols=41 Identities=24% Similarity=0.224 Sum_probs=34.1
Q ss_pred CccCcccHHHHHHhcCCch------------hHHHHHHHHHHHHHHHHHHhhh
Q 038014 91 KTVNGDDICWALATLGFDN------------YADQLKRYLHRYRELEGERANQ 131 (140)
Q Consensus 91 KTI~~eDVl~ALe~lgf~~------------y~~~l~~~l~~~re~~~~kk~q 131 (140)
.|.+++|+..+++.++++. |+|.+.+..+.-++.++.|...
T Consensus 123 ~tt~~~~l~~~l~~l~~P~~~~~~~i~l~~r~ip~l~~~~~~i~~A~~~Rg~~ 175 (224)
T PF02361_consen 123 LTTSPSDLISALRKLRLPYPKIALMISLTLRFIPLLLEEFKRIREAQRLRGVG 175 (224)
T ss_pred HHCCHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCC
Confidence 4788999999999999987 8888888888888888777433
No 101
>cd08316 Death_FAS_TNFRSF6 Death domain of FAS or TNF receptor superfamily member 6. Death Domain (DD) found in the FS7-associated cell surface antigen (FAS). FAS, also known as TNFRSF6 (TNF receptor superfamily member 6), APT1, CD95, FAS1, or APO-1, together with FADD (Fas-associating via Death Domain) and caspase 8, is an integral part of the death inducing signalling complex (DISC), which plays an important role in the induction of apoptosis and is activated by binding of the ligand FasL to FAS. FAS also plays a critical role in self-tolerance by eliminating cell types (autoreactive T and B cells) that contribute to autoimmunity. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in sign
Probab=42.57 E-value=1.2e+02 Score=21.48 Aligned_cols=72 Identities=7% Similarity=0.123 Sum_probs=42.8
Q ss_pred cCchhHHHHHHhhhCCCCccccHHHHHHHHH-----HHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCchhHH
Q 038014 38 LLPIANVGRIMKQILPPNAKISKEAKETMQE-----CVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDNYAD 112 (140)
Q Consensus 38 ~LP~A~V~RI~K~~lp~~~rIskdA~~al~~-----aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~~y~~ 112 (140)
.+|...+++++|.- .+|.-..+.+.. +.+.-+. .-.......|++ =+..+++.+|..+++..-++
T Consensus 17 ~~~~~~wK~faR~l-----glse~~Id~I~~~~~~d~~Eq~~q----mL~~W~~~~G~~-a~~~~Li~aLr~~~l~~~Ad 86 (97)
T cd08316 17 VMTLKDVKKFVRKS-----GLSEPKIDEIKLDNPQDTAEQKVQ----LLRAWYQSHGKT-GAYRTLIKTLRKAKLCTKAD 86 (97)
T ss_pred HcCHHHHHHHHHHc-----CCCHHHHHHHHHcCCCChHHHHHH----HHHHHHHHhCCC-chHHHHHHHHHHccchhHHH
Confidence 47777888888776 233333333331 1111111 112233444444 34789999999999999888
Q ss_pred HHHHHHH
Q 038014 113 QLKRYLH 119 (140)
Q Consensus 113 ~l~~~l~ 119 (140)
.++..++
T Consensus 87 ~I~~~l~ 93 (97)
T cd08316 87 KIQDIIE 93 (97)
T ss_pred HHHHHHH
Confidence 8877765
No 102
>CHL00081 chlI Mg-protoporyphyrin IX chelatase
Probab=42.51 E-value=1.2e+02 Score=26.36 Aligned_cols=49 Identities=18% Similarity=0.182 Sum_probs=41.0
Q ss_pred CccccHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhCCCCccCcccHHHHHH
Q 038014 55 NAKISKEAKETMQECVSEFI-------SFVTGEASDKCHKEKRKTVNGDDICWALA 103 (140)
Q Consensus 55 ~~rIskdA~~al~~aa~~Fi-------~~Las~A~~~a~~~kRKTI~~eDVl~ALe 103 (140)
.+.|+.+....|.+.+..+= .++...|.-.|--+||..|+++||..+..
T Consensus 265 ~V~v~~~~~~yi~~l~~~~~~~s~Ra~i~l~raArA~Aal~GR~~V~pdDv~~~a~ 320 (350)
T CHL00081 265 KVEIDYDLRVKISQICSELDVDGLRGDIVTNRAAKALAAFEGRTEVTPKDIFKVIT 320 (350)
T ss_pred CCccCHHHHHHHHHHHHHHCCCCChHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 68899999998888877753 35667788889999999999999998875
No 103
>COG5248 TAF19 Transcription initiation factor TFIID, subunit TAF13 [Transcription]
Probab=42.07 E-value=99 Score=23.10 Aligned_cols=50 Identities=18% Similarity=0.292 Sum_probs=41.8
Q ss_pred CCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHh
Q 038014 53 PPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALAT 104 (140)
Q Consensus 53 p~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~ 104 (140)
++.+.=..|...+|.+.+.-++..+...|...|. .|--+..+|+..||++
T Consensus 23 GDvv~P~~dt~~~L~e~V~dY~~~~ctna~~~Aq--~rnK~k~eDfkfaLr~ 72 (126)
T COG5248 23 GDVVAPRYDTAEALHEYVLDYMSILCTNAHNMAQ--VRNKTKTEDFKFALRR 72 (126)
T ss_pred CCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHH--hcccchHHHHHHHHhh
Confidence 4556677899999999999999999999999988 3445668999999985
No 104
>KOG1658 consensus DNA polymerase epsilon, subunit C [Replication, recombination and repair]
Probab=42.04 E-value=61 Score=25.43 Aligned_cols=89 Identities=15% Similarity=0.182 Sum_probs=53.8
Q ss_pred cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHH-----------H-HHHhCCCCccCcccHHHHHHhc
Q 038014 38 LLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEAS-----------D-KCHKEKRKTVNGDDICWALATL 105 (140)
Q Consensus 38 ~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~-----------~-~a~~~kRKTI~~eDVl~ALe~l 105 (140)
-||.+-+.||.|.. |.-+.=+.++..+...+++.|+..++..+. + +-+..---|+..++++.++.+.
T Consensus 11 ~~p~ekvkkiak~d-Pey~~te~~a~~etafatE~fvq~lv~~p~a~l~rLpL~rik~vvkl~pdl~l~~dea~~l~a~a 89 (162)
T KOG1658|consen 11 KLPMEKVKKIAKND-PEYMDTEDDAFVETAFATEQFVQVLVHLPQASLSRLPLARIKQVVKLDPDLTLLNDEASQLIAKA 89 (162)
T ss_pred cccHHHHHHhhcCC-chhhhcccchHHHHHHHHHHHHhhhhhhhhhhhhhccHHHHHhhccCCcchhhhhhHHHHHHHHH
Confidence 59999999999998 444556777777999999999888877221 1 1122223456666666665432
Q ss_pred CCchhHHHHHHHHHHHHHHHHHH
Q 038014 106 GFDNYADQLKRYLHRYRELEGER 128 (140)
Q Consensus 106 gf~~y~~~l~~~l~~~re~~~~k 128 (140)
-+.|+..|....-.+.+..++|
T Consensus 90 -aelfi~~Ln~~~~~~~q~~k~k 111 (162)
T KOG1658|consen 90 -AELFIQELNDVAYTTAQLRKRK 111 (162)
T ss_pred -HHHHHHHHHhccchhHHHHHhh
Confidence 2234444444433344433333
No 105
>PRK12402 replication factor C small subunit 2; Reviewed
Probab=41.50 E-value=90 Score=25.27 Aligned_cols=69 Identities=9% Similarity=0.031 Sum_probs=43.1
Q ss_pred CchhHHHHHHhhhCC-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCch
Q 038014 39 LPIANVGRIMKQILP-PNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDN 109 (140)
Q Consensus 39 LP~A~V~RI~K~~lp-~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~~ 109 (140)
++...+..+++..+. .+..++.++...|.+.+.-=+..+.......+. +..+|+.+||..++.....+.
T Consensus 184 ~~~~~~~~~l~~~~~~~~~~~~~~al~~l~~~~~gdlr~l~~~l~~~~~--~~~~It~~~v~~~~~~~~~~~ 253 (337)
T PRK12402 184 PTDDELVDVLESIAEAEGVDYDDDGLELIAYYAGGDLRKAILTLQTAAL--AAGEITMEAAYEALGDVGTDE 253 (337)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHH--cCCCCCHHHHHHHhCCCCCHH
Confidence 344566666665443 256799999999888774434444443433442 234799999998887655443
No 106
>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional
Probab=40.37 E-value=34 Score=30.48 Aligned_cols=32 Identities=25% Similarity=0.204 Sum_probs=27.9
Q ss_pred HHHHHHHHHHHHHhCCCCccCcccHHHHHHhc
Q 038014 74 ISFVTGEASDKCHKEKRKTVNGDDICWALATL 105 (140)
Q Consensus 74 i~~Las~A~~~a~~~kRKTI~~eDVl~ALe~l 105 (140)
|..|..+|...|.+.+|..|+.+||..|+++.
T Consensus 393 I~~i~~eA~~~Alr~~r~~Vt~~D~~~A~~~v 424 (438)
T PTZ00361 393 IKAICTEAGLLALRERRMKVTQADFRKAKEKV 424 (438)
T ss_pred HHHHHHHHHHHHHHhcCCccCHHHHHHHHHHH
Confidence 55677889999999999999999999998763
No 107
>PF00536 SAM_1: SAM domain (Sterile alpha motif); InterPro: IPR021129 The sterile alpha motif (SAM) domain is a putative protein interaction module present in a wide variety of proteins [] involved in many biological processes. The SAM domain that spreads over around 70 residues is found in diverse eukaryotic organisms []. SAM domains have been shown to homo- and hetero-oligomerise, forming multiple self-association architectures and also binding to various non-SAM domain-containing proteins [], nevertheless with a low affinity constant []. SAM domains also appear to possess the ability to bind RNA []. Smaug, a protein that helps to establish a morphogen gradient in Drosophila embryos by repressing the translation of nanos (nos) mRNA, binds to the 3' untranslated region (UTR) of nos mRNA via two similar hairpin structures. The 3D crystal structure of the Smaug RNA-binding region shows a cluster of positively charged residues on the Smaug-SAM domain, which could be the RNA-binding surface. This electropositive potential is unique among all previously determined SAM-domain structures and is conserved among Smaug-SAM homologs. These results suggest that the SAM domain might have a primary role in RNA binding. Structural analyses show that the SAM domain is arranged in a small five-helix bundle with two large interfaces []. In the case of the SAM domain of EphB2, each of these interfaces is able to form dimers. The presence of these two distinct intermonomers binding surface suggest that SAM could form extended polymeric structures []. This entry represents type 1 SAM domains. ; PDB: 2KIV_A 3HIL_B 3KKA_A 3K1R_B 3SEN_B 3SEI_B 1V85_A 2KE7_A 2EAM_A 1WWV_A ....
Probab=40.15 E-value=31 Score=21.48 Aligned_cols=23 Identities=26% Similarity=0.593 Sum_probs=19.7
Q ss_pred CcccHHHHHHhcCCchhHHHHHH
Q 038014 94 NGDDICWALATLGFDNYADQLKR 116 (140)
Q Consensus 94 ~~eDVl~ALe~lgf~~y~~~l~~ 116 (140)
++++|..-|+.+|++.|.+....
T Consensus 4 ~~~~V~~WL~~~~l~~y~~~F~~ 26 (64)
T PF00536_consen 4 SVEDVSEWLKSLGLEQYAENFEK 26 (64)
T ss_dssp SHHHHHHHHHHTTGGGGHHHHHH
T ss_pred CHHHHHHHHHHCCCHHHHHHHHc
Confidence 57899999999999999987743
No 108
>PF08823 PG_binding_2: Putative peptidoglycan binding domain; InterPro: IPR014927 This entry may be a peptidoglycan binding domain.
Probab=39.80 E-value=40 Score=22.82 Aligned_cols=32 Identities=19% Similarity=0.333 Sum_probs=26.2
Q ss_pred cccHHHHHHhcCC------chhHHHHHHHHHHHHHHHH
Q 038014 95 GDDICWALATLGF------DNYADQLKRYLHRYRELEG 126 (140)
Q Consensus 95 ~eDVl~ALe~lgf------~~y~~~l~~~l~~~re~~~ 126 (140)
++.|..+|.++|| +.+...+++.|..|..++.
T Consensus 18 ~~evq~~L~~lGyy~g~~~g~~d~a~~~Al~~~~g~EN 55 (74)
T PF08823_consen 18 AREVQEALKRLGYYKGEADGVWDEATEDALRAWAGTEN 55 (74)
T ss_pred HHHHHHHHHHcCCccCCCCCcccHHHHHHHHHHHHHhh
Confidence 3467789999999 6788899999998887664
No 109
>PRK13407 bchI magnesium chelatase subunit I; Provisional
Probab=38.38 E-value=1.3e+02 Score=25.67 Aligned_cols=49 Identities=10% Similarity=-0.016 Sum_probs=39.7
Q ss_pred CCccccHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhCCCCccCcccHHHHH
Q 038014 54 PNAKISKEAKETMQECVSEFI-------SFVTGEASDKCHKEKRKTVNGDDICWAL 102 (140)
Q Consensus 54 ~~~rIskdA~~al~~aa~~Fi-------~~Las~A~~~a~~~kRKTI~~eDVl~AL 102 (140)
+.+.|+.+....+.+.+..+= ..|...|...|--.||..|+++||..+.
T Consensus 248 ~~V~v~~~~~~yi~~l~~~~~~~s~Ra~i~l~~aA~a~A~l~Gr~~V~~~Di~~~~ 303 (334)
T PRK13407 248 PQLKTPNTVLHDCAALCIALGSDGLRGELTLLRAARALAAFEGAEAVGRSHLRSVA 303 (334)
T ss_pred CCcccCHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHHcCCCeeCHHHHHHHH
Confidence 367899999988888877653 2367788889999999999999997654
No 110
>TIGR02031 BchD-ChlD magnesium chelatase ATPase subunit D. This model represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria. Unlike subunit I (TIGR02030), this subunit is not found in archaea.
Probab=38.33 E-value=1.1e+02 Score=28.23 Aligned_cols=49 Identities=18% Similarity=0.198 Sum_probs=37.7
Q ss_pred CccccHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhCCCCccCcccHHHHHH
Q 038014 55 NAKISKEAKETMQECVSEFI-------SFVTGEASDKCHKEKRKTVNGDDICWALA 103 (140)
Q Consensus 55 ~~rIskdA~~al~~aa~~Fi-------~~Las~A~~~a~~~kRKTI~~eDVl~ALe 103 (140)
.+.|+.+....|.+.+..+- .++...|...|.-.||.+|+.+||..|..
T Consensus 201 ~V~i~~~~~~~l~~~~~~~gv~s~Ra~i~~~r~ArA~Aal~gr~~V~~~Dv~~a~~ 256 (589)
T TIGR02031 201 QVTISAEQVKELVLTAASLGISGHRADLFAVRAAKAHAALHGRTEVTEEDLKLAVE 256 (589)
T ss_pred CccCCHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHH
Confidence 57899998877776664432 24455677788899999999999999986
No 111
>PLN00155 histone H2A; Provisional
Probab=36.97 E-value=58 Score=21.42 Aligned_cols=38 Identities=13% Similarity=0.165 Sum_probs=27.7
Q ss_pred CccccccccCchhHHHHHHhhhCCCCccccHHHHHHHHH
Q 038014 30 GVIKEQDRLLPIANVGRIMKQILPPNAKISKEAKETMQE 68 (140)
Q Consensus 30 ~~~~~~d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~ 68 (140)
+...-..+.||...|.|.+|+.-. ..||+..|...+.-
T Consensus 16 srS~rAgL~FPVgri~r~Lr~g~~-a~Rvga~apVYlAA 53 (58)
T PLN00155 16 SRSAKAGLQFPVGRIARYLKKGKY-AERIGAGAPVYLAA 53 (58)
T ss_pred CcccccccccchHHHHHHHhcCCh-hhcccCCcHHHHHH
Confidence 333445789999999999999744 34888877765543
No 112
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=36.96 E-value=81 Score=19.28 Aligned_cols=31 Identities=23% Similarity=0.406 Sum_probs=25.6
Q ss_pred cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHH
Q 038014 38 LLPIANVGRIMKQILPPNAKISKEAKETMQECVSE 72 (140)
Q Consensus 38 ~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~ 72 (140)
.+..++|.|++... -+|+.+.++-+.+++++
T Consensus 10 gvS~~TVSr~ln~~----~~vs~~tr~rI~~~a~~ 40 (46)
T PF00356_consen 10 GVSKSTVSRVLNGP----PRVSEETRERILEAAEE 40 (46)
T ss_dssp TSSHHHHHHHHTTC----SSSTHHHHHHHHHHHHH
T ss_pred CcCHHHHHHHHhCC----CCCCHHHHHHHHHHHHH
Confidence 46788999988766 48999999999988776
No 113
>cd08313 Death_TNFR1 Death domain of Tumor Necrosis Factor Receptor 1. Death Domain (DD) found in tumor necrosis factor receptor-1 (TNFR-1). TNFR-1 has many names including TNFRSF1A, CD120a, p55, p60, and TNFR60. It activates two major intracellular signaling pathways that lead to the activation of the transcription factor NF-kB and the induction of cell death. Upon binding of its ligand TNF, TNFR-1 trimerizes which leads to the recruitment of an adaptor protein named TNFR-associated death domain protein (TRADD) through a DD/DD interaction. Mutations in the TNFRSF1A gene causes TNFR-associated periodic syndrome (TRAPS), a rare disorder characterized recurrent fever, myalgia, abdominal pain, conjunctivitis and skin eruptions. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation a
Probab=36.27 E-value=1.4e+02 Score=20.42 Aligned_cols=71 Identities=8% Similarity=0.004 Sum_probs=40.7
Q ss_pred cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCchhHHH
Q 038014 38 LLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDNYADQ 113 (140)
Q Consensus 38 ~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~~y~~~ 113 (140)
.+|....++++|.- .+|.--.+.+...-...-..+-..-...-...|+.--+..+++.||+++++..-++.
T Consensus 8 ~v~~~~wk~~~R~L-----Glse~~Id~ie~~~~~~~Eq~yqmL~~W~~~~g~~~At~~~L~~aLr~~~l~~~ae~ 78 (80)
T cd08313 8 EVPPRRWKEFVRRL-----GLSDNEIERVELDHRRCRDAQYQMLKVWKERGPRPYATLQHLLSVLRDMELVGCAED 78 (80)
T ss_pred hCCHHHHHHHHHHc-----CCCHHHHHHHHHhCCChHHHHHHHHHHHHHhcCCCcchHHHHHHHHHHcCcHHHHHH
Confidence 46778888888876 133333333332211111111112223445566667788999999999998865554
No 114
>smart00454 SAM Sterile alpha motif. Widespread domain in signalling and nuclear proteins. In EPH-related tyrosine kinases, appears to mediate cell-cell initiated signal transduction via the binding of SH2-containing proteins to a conserved tyrosine that is phosphorylated. In many cases mediates homodimerisation.
Probab=35.87 E-value=32 Score=20.92 Aligned_cols=25 Identities=20% Similarity=0.489 Sum_probs=20.4
Q ss_pred cCcccHHHHHHhcCCchhHHHHHHH
Q 038014 93 VNGDDICWALATLGFDNYADQLKRY 117 (140)
Q Consensus 93 I~~eDVl~ALe~lgf~~y~~~l~~~ 117 (140)
-+.++|..-|+.+||++|.+...+.
T Consensus 4 w~~~~v~~wL~~~g~~~y~~~f~~~ 28 (68)
T smart00454 4 WSPESVADWLESIGLEQYADNFRKN 28 (68)
T ss_pred CCHHHHHHHHHHCChHHHHHHHHHC
Confidence 4567888999999999998887654
No 115
>PRK06585 holA DNA polymerase III subunit delta; Reviewed
Probab=35.77 E-value=89 Score=25.86 Aligned_cols=62 Identities=11% Similarity=0.141 Sum_probs=41.2
Q ss_pred hHHHHHHhhhC-CCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHh-CCCCccCcccHHHHHH
Q 038014 42 ANVGRIMKQIL-PPNAKISKEAKETMQECVSEFISFVTGEASDKCHK-EKRKTVNGDDICWALA 103 (140)
Q Consensus 42 A~V~RI~K~~l-p~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~-~kRKTI~~eDVl~ALe 103 (140)
..+.+.+++.+ ..+.+|+.+|...|.+.+.-=+..+..+-...+-- .+.++|+.+||...+-
T Consensus 145 ~~l~~~i~~~~~~~g~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~It~edV~~lv~ 208 (343)
T PRK06585 145 RDLARLIDDELAEAGLRITPDARALLVALLGGDRLASRNEIEKLALYAHGKGEITLDDVRAVVG 208 (343)
T ss_pred HHHHHHHHHHHHHCCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHhC
Confidence 33344443333 22678999999999998887555666665555554 3456899999977654
No 116
>TIGR01242 26Sp45 26S proteasome subunit P45 family. Many proteins may score above the trusted cutoff because an internal
Probab=35.30 E-value=48 Score=27.97 Aligned_cols=32 Identities=25% Similarity=0.182 Sum_probs=27.3
Q ss_pred HHHHHHHHHHHHHHhCCCCccCcccHHHHHHh
Q 038014 73 FISFVTGEASDKCHKEKRKTVNGDDICWALAT 104 (140)
Q Consensus 73 Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~ 104 (140)
-+..+..+|...|...++..|+.+|+..|+++
T Consensus 331 dl~~l~~~A~~~a~~~~~~~i~~~d~~~a~~~ 362 (364)
T TIGR01242 331 DLKAICTEAGMFAIREERDYVTMDDFIKAVEK 362 (364)
T ss_pred HHHHHHHHHHHHHHHhCCCccCHHHHHHHHHH
Confidence 45567778888888899999999999999976
No 117
>PRK03992 proteasome-activating nucleotidase; Provisional
Probab=34.76 E-value=49 Score=28.51 Aligned_cols=35 Identities=17% Similarity=0.135 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcC
Q 038014 72 EFISFVTGEASDKCHKEKRKTVNGDDICWALATLG 106 (140)
Q Consensus 72 ~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lg 106 (140)
.-|..|..+|...|.+.++..|+.+|+..|++..-
T Consensus 339 adl~~l~~eA~~~a~~~~~~~i~~~d~~~A~~~~~ 373 (389)
T PRK03992 339 ADLKAICTEAGMFAIRDDRTEVTMEDFLKAIEKVM 373 (389)
T ss_pred HHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHh
Confidence 44566777888888889999999999999998753
No 118
>PRK13765 ATP-dependent protease Lon; Provisional
Probab=34.62 E-value=67 Score=30.05 Aligned_cols=48 Identities=13% Similarity=0.093 Sum_probs=38.4
Q ss_pred cccHHHHHHHHHHHHHH-------------HHHHHHHHHHHHHhCCCCccCcccHHHHHHh
Q 038014 57 KISKEAKETMQECVSEF-------------ISFVTGEASDKCHKEKRKTVNGDDICWALAT 104 (140)
Q Consensus 57 rIskdA~~al~~aa~~F-------------i~~Las~A~~~a~~~kRKTI~~eDVl~ALe~ 104 (140)
.++.+|+..|-+-++.- +..|..+|..+|+..+++.|+.+||..|+..
T Consensus 339 ~f~~eAVa~LI~~~~R~ag~r~~lsl~~~~l~~l~r~a~~~a~~~~~~~i~~~~v~~a~~~ 399 (637)
T PRK13765 339 HFDRDAVEEIIREAKRRAGRKGHLTLKLRDLGGLVRVAGDIARSEGAELTTAEHVLEAKKI 399 (637)
T ss_pred CCCHHHHHHHHHHHHHHhCCccccccCHHHHHHHHHHHHHHHHhhccceecHHHHHHHHHh
Confidence 58999888877755532 3347778999999999999999999999843
No 119
>COG1724 Predicted RNA binding protein (dsRBD-like fold), HicA family [General function prediction only]
Probab=34.06 E-value=23 Score=23.87 Aligned_cols=17 Identities=24% Similarity=0.421 Sum_probs=15.3
Q ss_pred ccCcccHHHHHHhcCCc
Q 038014 92 TVNGDDICWALATLGFD 108 (140)
Q Consensus 92 TI~~eDVl~ALe~lgf~ 108 (140)
.+++.+|+++|+.+||.
T Consensus 6 ~~~~ke~ik~Le~~Gf~ 22 (66)
T COG1724 6 RMKAKEVIKALEKDGFQ 22 (66)
T ss_pred cCCHHHHHHHHHhCCcE
Confidence 47889999999999997
No 120
>PRK02910 light-independent protochlorophyllide reductase subunit B; Provisional
Probab=33.71 E-value=1.3e+02 Score=27.13 Aligned_cols=53 Identities=11% Similarity=0.100 Sum_probs=42.2
Q ss_pred CCCccccHHHHHHHHHHHHHHHHHHHHHHH-HHHHhCCCCccCcccHHHHHHhcC
Q 038014 53 PPNAKISKEAKETMQECVSEFISFVTGEAS-DKCHKEKRKTVNGDDICWALATLG 106 (140)
Q Consensus 53 p~~~rIskdA~~al~~aa~~Fi~~Las~A~-~~a~~~kRKTI~~eDVl~ALe~lg 106 (140)
.+.+..+.||...|.+ .--|+..=..... +.|+..|...|+.+.|..|-..+|
T Consensus 465 ~~~~~w~~ea~~~l~~-~P~f~r~~~r~~~e~~a~~~g~~~it~~~~~~a~~~~~ 518 (519)
T PRK02910 465 DSELVWTPEAEAELKK-IPFFVRGKVRRNTEKFARERGLPEITLEVLYDAKAHFG 518 (519)
T ss_pred CCCCCCCHHHHHHHhh-CChhhHHHHHHHHHHHHHHcCCCeecHHHHHHHHHHhc
Confidence 3567899999999965 7788876555444 489999999999999999876654
No 121
>PRK07914 hypothetical protein; Reviewed
Probab=33.62 E-value=93 Score=25.76 Aligned_cols=64 Identities=8% Similarity=0.098 Sum_probs=43.1
Q ss_pred chhHHHHHHhhhCC-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHh
Q 038014 40 PIANVGRIMKQILP-PNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALAT 104 (140)
Q Consensus 40 P~A~V~RI~K~~lp-~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~ 104 (140)
+...+.+.|++.+. .+..|+.+|...|..++..=+..+..+--..+-..+ .+|+.+||...+..
T Consensus 129 ~~~~l~~wi~~~a~~~g~~i~~~A~~~L~~~~g~dl~~l~~EleKL~~~~~-~~It~e~V~~~v~~ 193 (320)
T PRK07914 129 KAAERADFVRKEFRSLRVKVDDDTVTALLDAVGSDLRELASACSQLVADTG-GAVDAAAVRRYHSG 193 (320)
T ss_pred CHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHCccHHHHHHHHHHHhcCCC-CCcCHHHHHHHcCC
Confidence 44554555544432 257899999999999987666666666555554333 57999998877653
No 122
>PRK14975 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Probab=33.50 E-value=2.4e+02 Score=25.61 Aligned_cols=88 Identities=14% Similarity=0.078 Sum_probs=54.2
Q ss_pred ccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHH----------HHHHHHHHHHHHHHHhCCCCc---cCcccHHHH
Q 038014 35 QDRLLPIANVGRIMKQILPPNAKISKEAKETMQECVS----------EFISFVTGEASDKCHKEKRKT---VNGDDICWA 101 (140)
Q Consensus 35 ~d~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~----------~Fi~~Las~A~~~a~~~kRKT---I~~eDVl~A 101 (140)
.++++|.+.|---|... ++.|..+....+..... .-+..|..+..+.+ |... =++.+|..+
T Consensus 160 ~~~E~~~~~~l~~me~~---Gi~~D~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~~~---g~~~~n~~S~~ql~~~ 233 (553)
T PRK14975 160 AAAESAGALAAAEMELA---GLPWDTDVHEALLAELLGPRPAAGGRPARLAELAAEIREAL---GRPRLNPDSPQQVLRA 233 (553)
T ss_pred HHHHhhHHHHHHHHHHh---CeEeCHHHHHHHHHHHhcccccccchHHHHHHHHHHHHHHh---CCCCCCCCCHHHHHHH
Confidence 34456666666666655 68888888876665555 45555555555444 4333 467889999
Q ss_pred HHhcCCc----------hhHHHHHHHHHHHHHHHHHH
Q 038014 102 LATLGFD----------NYADQLKRYLHRYRELEGER 128 (140)
Q Consensus 102 Le~lgf~----------~y~~~l~~~l~~~re~~~~k 128 (140)
|+++|+. .-.-|+-..+-+||+..|..
T Consensus 234 L~~~g~~~~~t~~~~L~~~~hp~~~~ile~r~~~kl~ 270 (553)
T PRK14975 234 LRRAGIELPSTRKWELREIDHPAVEPLLEYRKLSKLL 270 (553)
T ss_pred HHHCCCCCCCCcHHHhccCCCchHHHHHHHHHHHHHH
Confidence 9988885 00012334555777776654
No 123
>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional
Probab=32.34 E-value=56 Score=28.54 Aligned_cols=33 Identities=18% Similarity=0.117 Sum_probs=28.4
Q ss_pred HHHHHHHHHHHHHHHhCCCCccCcccHHHHHHh
Q 038014 72 EFISFVTGEASDKCHKEKRKTVNGDDICWALAT 104 (140)
Q Consensus 72 ~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~ 104 (140)
.=|..|..+|...|.+.+|..|+.+|+..|+++
T Consensus 353 aDI~~l~~eA~~~A~r~~~~~i~~~df~~A~~~ 385 (398)
T PTZ00454 353 ADIAAICQEAGMQAVRKNRYVILPKDFEKGYKT 385 (398)
T ss_pred HHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHH
Confidence 336678888999999999999999999999876
No 124
>PRK05574 holA DNA polymerase III subunit delta; Reviewed
Probab=32.04 E-value=1.5e+02 Score=24.03 Aligned_cols=67 Identities=15% Similarity=0.060 Sum_probs=45.1
Q ss_pred cCchhHHHHHHhhhCC-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHh
Q 038014 38 LLPIANVGRIMKQILP-PNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALAT 104 (140)
Q Consensus 38 ~LP~A~V~RI~K~~lp-~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~ 104 (140)
.++...+.+.++..+. .+..|+.+|...|.+.+..=+..+..+....+--.+-+.|+.+||...+-.
T Consensus 145 ~~~~~~~~~~i~~~~~~~g~~i~~~a~~~L~~~~~~d~~~l~~El~KL~l~~~~~~It~~~I~~~i~~ 212 (340)
T PRK05574 145 PPKEAELPQWIQQRLKQQGLQIDAAALQLLAERVEGNLLALAQELEKLALLYPDGKITLEDVEEAVPD 212 (340)
T ss_pred CCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCchHHHHHHHHHHHHhhcCCCCCCHHHHHHHHhh
Confidence 3556666666655553 257899999999999887766666666666654332222998888766543
No 125
>COG5624 TAF61 Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=30.75 E-value=50 Score=29.86 Aligned_cols=76 Identities=16% Similarity=0.163 Sum_probs=59.9
Q ss_pred CchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHh---cCCchhHHHH
Q 038014 39 LPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALAT---LGFDNYADQL 114 (140)
Q Consensus 39 LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~---lgf~~y~~~l 114 (140)
+-+-.+.-+.+..+.+..+|-.|.-+.+-.-+-.|+.-++.-+..+|+|-+-+||-+.|+-.-|++ +-++.|....
T Consensus 384 ~skrkL~el~~~~vd~eekie~eveelll~~ad~fve~vt~FsCrlakhrkSdtlevrD~qlhlErnwnIr~pGf~~d~ 462 (505)
T COG5624 384 DSKRKLEELQHGGVDEEEKIENEVEELLLSRADGFVEPVTEFSCRLAKHRKSDTLEVRDGQLHLERNWNIRCPGFVDDI 462 (505)
T ss_pred hhhhhHHHHHhhccCcceeccchHHHHHHhhhcccccccchheeEeeccCCCCceeeccceeeeccccceecCcchHHH
Confidence 334444445555555567899999999999999999999999999999999999999999988875 4455665543
No 126
>COG5251 TAF40 Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=30.22 E-value=36 Score=27.27 Aligned_cols=63 Identities=13% Similarity=-0.034 Sum_probs=45.9
Q ss_pred cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC-CCccCcccHHHHH
Q 038014 38 LLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEK-RKTVNGDDICWAL 102 (140)
Q Consensus 38 ~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~k-RKTI~~eDVl~AL 102 (140)
.||++.|++++-.++. -.|+...+..|+-.+.+|+-.+...|..+-..-+ --.+.+.|+..|.
T Consensus 115 ~lnKt~VKKlastV~n--QtVspNi~I~l~g~~KVfvGEiIElA~~Vq~~w~~sgpl~p~h~reay 178 (199)
T COG5251 115 SLNKTQVKKLASTVAN--QTVSPNIRIFLQGVGKVFVGEIIELAMIVQNKWLTSGPLIPFHKREAY 178 (199)
T ss_pred CCCHHHHHHHHHHHhc--cccCCCeeeeeechhHHHHHHHHHHHHHHHHHhcccCCCChHHHHHHH
Confidence 6999999999999963 4677777788888899999888877766533221 1126677776664
No 127
>PF13405 EF-hand_6: EF-hand domain; PDB: 2AMI_A 3QRX_A 1W7J_B 1OE9_B 1W7I_B 1KFU_S 1KFX_S 2BL0_B 1Y1X_B 3MSE_B ....
Probab=29.86 E-value=50 Score=17.77 Aligned_cols=26 Identities=19% Similarity=0.216 Sum_probs=19.7
Q ss_pred HHHHHHhCCCCccCcccHHHHHH-hcC
Q 038014 81 ASDKCHKEKRKTVNGDDICWALA-TLG 106 (140)
Q Consensus 81 A~~~a~~~kRKTI~~eDVl~ALe-~lg 106 (140)
+.......+.-+|+.+++..+|+ .+|
T Consensus 5 ~F~~~D~d~dG~I~~~el~~~l~~~lG 31 (31)
T PF13405_consen 5 AFKMFDKDGDGFIDFEELRAILRKSLG 31 (31)
T ss_dssp HHHHH-TTSSSEEEHHHHHHHHHHHTT
T ss_pred HHHHHCCCCCCcCcHHHHHHHHHHhcC
Confidence 45556677788999999999998 476
No 128
>PF07499 RuvA_C: RuvA, C-terminal domain; InterPro: IPR011114 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. The domain represents the C-terminal domain III of RuvA. This domain plays a significant role in the ATP-dependent branch migration of the hetero-duplex through direct contact with RuvB []. Within the Holliday junction, this domain makes no interaction with the DNA.; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination, 0009379 Holliday junction helicase complex; PDB: 1HJP_A 1CUK_A 1C7Y_A 1IXS_A 1IXR_B 1BVS_E 2ZTC_A 2ZTD_B 2H5X_A.
Probab=29.12 E-value=34 Score=20.81 Aligned_cols=13 Identities=38% Similarity=0.619 Sum_probs=11.2
Q ss_pred ccHHHHHHhcCCc
Q 038014 96 DDICWALATLGFD 108 (140)
Q Consensus 96 eDVl~ALe~lgf~ 108 (140)
+|++.||..|||.
T Consensus 4 ~d~~~AL~~LGy~ 16 (47)
T PF07499_consen 4 EDALEALISLGYS 16 (47)
T ss_dssp HHHHHHHHHTTS-
T ss_pred HHHHHHHHHcCCC
Confidence 6899999999998
No 129
>KOG0785 consensus Isocitrate dehydrogenase, alpha subunit [Amino acid transport and metabolism]
Probab=28.95 E-value=1.3e+02 Score=26.41 Aligned_cols=63 Identities=8% Similarity=0.028 Sum_probs=44.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCchhHHHHHHHHHHHHH
Q 038014 60 KEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDNYADQLKRYLHRYRE 123 (140)
Q Consensus 60 kdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~~y~~~l~~~l~~~re 123 (140)
.-.++.|....+.-...++..|.++|+..+|+.|+.-|=-+.|+.- =+-|.+.+++.-.+|.+
T Consensus 166 pGVvqsiK~IT~~AS~Ria~~AF~yAr~~~R~~vtvvHKaNImr~t-DGLFle~cre~a~~y~d 228 (365)
T KOG0785|consen 166 PGVVQSIKLITEAASRRIAEYAFEYARQNGRKRVTVVHKANIMRMT-DGLFLECCREVAKKYPD 228 (365)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCceEEEehhhhhhhc-chHHHHHHHHHhhhCCc
Confidence 3356666666666667788899999999999999988877776543 24566666666555443
No 130
>PF01077 NIR_SIR: Nitrite and sulphite reductase 4Fe-4S domain; InterPro: IPR006067 Sulphite reductases (SiRs) and related nitrite reductases (NiRs) catalyse the six-electron reduction reactions of sulphite to sulphide, and nitrite to ammonia, respectively. The Escherichia coli SiR enzyme is a complex composed of two proteins, a flavoprotein alpha-component (SiR-FP) and a hemoprotein beta-component (SiR-HP) (IPR005117 from INTERPRO), and has an alpha(8)beta(4) quaternary structure []. SiR-FP contains both FAD and FMN, while SiR-HP contains a Fe(4)S(4) cluster coupled to a siroheme through a cysteine bridge. Electrons are transferred from NADPH to FAD, and on to FMN in SiR-FP, from which they are transferred to the metal centre of SiR-HP, where they reduce the siroheme-bound sulphite. SiR-HP has a two-fold symmetry, which generates a distinctive three-domain alpha/beta fold that controls assembly and reactivity []. In the E. coli SiR-HP enzyme (1.8.1.2 from EC), the iron is bound to cysteine residues at positions 433, 439, 478 and 482, the latter also forming the siroheme ligand.; GO: 0016491 oxidoreductase activity, 0020037 heme binding, 0051536 iron-sulfur cluster binding, 0055114 oxidation-reduction process; PDB: 1ZJ8_B 1ZJ9_A 2AKJ_A 3VKT_A 3VKR_A 3VKS_A 3B0M_A 3B0N_A 3VKP_A 3B0J_A ....
Probab=28.66 E-value=39 Score=24.90 Aligned_cols=73 Identities=14% Similarity=0.240 Sum_probs=40.3
Q ss_pred CcccccCCCCCCCCCCccccccccCchhHHHHHHhhhCCCCccccH-HHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCcc
Q 038014 15 SYNFTVGASSGTDQDGVIKEQDRLLPIANVGRIMKQILPPNAKISK-EAKETMQECVSEFISFVTGEASDKCHKEKRKTV 93 (140)
Q Consensus 15 ~~~~~~~~~~~~~~~~~~~~~d~~LP~A~V~RI~K~~lp~~~rIsk-dA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI 93 (140)
-|++.+||..|............ ..+.. ++...+......|. .++..-
T Consensus 80 g~~v~vGG~~g~~~~~~~~~~~~------------------~~~~~ee~~~~i~~il~~y~-------------~~~~~~ 128 (157)
T PF01077_consen 80 GFDVYVGGGLGRHPRLGRELALA------------------GFVPEEEVLEVIEAILEYYR-------------GNREAR 128 (157)
T ss_dssp EEEEEES-BESTSTBEBEEEEEE------------------EEEEGGGHHHHHHHHHHHHH-------------S-HSSG
T ss_pred eeeeeecccccCCCCccceeecc------------------ccccHHHHHHHHHHHHHHHH-------------HhccCC
Confidence 58888888864433332222110 12333 35655555555543 223334
Q ss_pred CcccHHHHHHhcCCchhHHHHHHHH
Q 038014 94 NGDDICWALATLGFDNYADQLKRYL 118 (140)
Q Consensus 94 ~~eDVl~ALe~lgf~~y~~~l~~~l 118 (140)
..+-+..-++++|++.|...+++.+
T Consensus 129 ~~er~~~~i~r~G~e~~~~~v~~~~ 153 (157)
T PF01077_consen 129 KKERFKDFIERLGFEKFREEVEERL 153 (157)
T ss_dssp TT-SHHHHHHHHHHHHHHHHHHHTS
T ss_pred CCCCHHHHHHHHCHHHHHHHHHHHh
Confidence 4556788889999999988886654
No 131
>PF07492 Trehalase_Ca-bi: Neutral trehalase Ca2+ binding domain; InterPro: IPR011120 Neutral trehalases mobilise trehalose accumulated by fungal cells as a protective and storage carbohydrate. This family represents a calcium-binding domain similar to EF hand. Residues 97 and 108 in O42893 from SWISSPROT have been implicated in this interaction. It is thought that this domain may provide a general mechanism for regulating neutral trehalase activity in yeasts and filamentous fungi [].; GO: 0004555 alpha,alpha-trehalase activity, 0005509 calcium ion binding, 0005993 trehalose catabolic process, 0005737 cytoplasm
Probab=28.06 E-value=32 Score=19.81 Aligned_cols=14 Identities=21% Similarity=0.501 Sum_probs=12.3
Q ss_pred CCCCCCcccccCCC
Q 038014 10 ESYDNSYNFTVGAS 23 (140)
Q Consensus 10 ~~~~~~~~~~~~~~ 23 (140)
|-.|.+||||.-+.
T Consensus 8 EDTDgn~qITIeD~ 21 (30)
T PF07492_consen 8 EDTDGNFQITIEDT 21 (30)
T ss_pred cccCCCcEEEEecC
Confidence 66799999999887
No 132
>KOG1942 consensus DNA helicase, TBP-interacting protein [Replication, recombination and repair]
Probab=27.92 E-value=2e+02 Score=25.56 Aligned_cols=64 Identities=16% Similarity=0.147 Sum_probs=47.0
Q ss_pred CchhHHHHHHhhhCC-CCccccHHHHHHHHH----HHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHH
Q 038014 39 LPIANVGRIMKQILP-PNAKISKEAKETMQE----CVSEFISFVTGEASDKCHKEKRKTVNGDDICWAL 102 (140)
Q Consensus 39 LP~A~V~RI~K~~lp-~~~rIskdA~~al~~----aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~AL 102 (140)
.|...++.|++.... .+..+..+|...+.+ ..-.+...|.+-|..+|+-.||+.|..+||-..-
T Consensus 367 y~~~e~r~Ii~~Ra~~E~l~~~e~a~~~l~~~gt~tsLRy~vqLl~p~~~~ak~~g~~~i~v~dvee~~ 435 (456)
T KOG1942|consen 367 YDEEEIRQIIKIRAQVEGLQVEEEALDLLAEIGTSTSLRYAVQLLTPASILAKTNGRKEISVEDVEEVT 435 (456)
T ss_pred CCHHHHHHHHHHHHhhhcceecHHHHHHHHhhccchhHHHHHHhcCHHHHHHHHcCCceeecccHHHHH
Confidence 455566666655432 356899999988877 3334566667778899999999999999998663
No 133
>KOG1528 consensus Salt-sensitive 3'-phosphoadenosine-5'-phosphatase HAL2/SAL1 [Nucleotide transport and metabolism; Inorganic ion transport and metabolism]
Probab=27.05 E-value=2e+02 Score=25.12 Aligned_cols=79 Identities=13% Similarity=0.144 Sum_probs=51.8
Q ss_pred CCCccccccccCchhHHHHHHhhhCCCCc--cccHHHHHHHHHH-HHHHHHHHHHHHHH---HHHhCCC-CccCcccHHH
Q 038014 28 QDGVIKEQDRLLPIANVGRIMKQILPPNA--KISKEAKETMQEC-VSEFISFVTGEASD---KCHKEKR-KTVNGDDICW 100 (140)
Q Consensus 28 ~~~~~~~~d~~LP~A~V~RI~K~~lp~~~--rIskdA~~al~~a-a~~Fi~~Las~A~~---~a~~~kR-KTI~~eDVl~ 100 (140)
+.+|+...|+- -.|.|.-.+++.+|++- -|..|--.-|.+. ++.|+..++..-++ ....=+- .+++.+||++
T Consensus 40 D~SPVTvaDyG-~QAiVs~vL~~~f~~~p~slVaEEds~~Lr~n~~~~~l~~i~~lvnetl~s~~sy~~~~~ls~~dvl~ 118 (351)
T KOG1528|consen 40 DKSPVTVADYG-SQAIVSLVLEREFPDDPLSLVAEEDSGFLRKNGSEGLLSRITKLVNETLASDESYGDNSPLSSDDVLK 118 (351)
T ss_pred CCCCcchhhhh-HHHHHHHHHHHHcCCCCcceEeeccchhhhhhhhHHHHHHHHHHHHHHhhhhhhccCCCCCCHHHHHH
Confidence 55667777743 45778888899998764 5666666555554 56666666663333 2222233 7899999999
Q ss_pred HHHhcCC
Q 038014 101 ALATLGF 107 (140)
Q Consensus 101 ALe~lgf 107 (140)
|+..-+.
T Consensus 119 aID~G~s 125 (351)
T KOG1528|consen 119 AIDRGNS 125 (351)
T ss_pred HHhcccc
Confidence 9976543
No 134
>PF11753 DUF3310: Protein of unknwon function (DUF3310); InterPro: IPR021739 This entry is represented by Bacteriophage T7, Gp1.7. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=26.33 E-value=1.6e+02 Score=18.88 Aligned_cols=41 Identities=22% Similarity=0.222 Sum_probs=31.3
Q ss_pred HHHHHHHHH--HHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHH
Q 038014 61 EAKETMQEC--VSEFISFVTGEASDKCHKEKRKTVNGDDICWALA 103 (140)
Q Consensus 61 dA~~al~~a--a~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe 103 (140)
++.+.+ +. ...|+.+....|..++-+.++|.- .+|+.+|..
T Consensus 14 e~id~~-~~~~~~~~~~f~~gnaiKY~~R~~~K~~-~eDl~KA~~ 56 (60)
T PF11753_consen 14 ECIDFI-EQFTEEQFLGFCLGNAIKYLWRAGKKNG-IEDLKKAKW 56 (60)
T ss_pred cHHHHH-HHhcchhhhhHHHHHHHHHHHHHcccCc-HHHHHHHHH
Confidence 444555 33 458899999999999999999944 888888864
No 135
>PRK05629 hypothetical protein; Validated
Probab=26.14 E-value=1.9e+02 Score=23.81 Aligned_cols=48 Identities=8% Similarity=0.060 Sum_probs=35.6
Q ss_pred CccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHH
Q 038014 55 NAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALA 103 (140)
Q Consensus 55 ~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe 103 (140)
+.+|+.+|...|...+..=+..+..+--..+--. ..+|+.+||...+.
T Consensus 143 g~~i~~~A~~~L~~~~g~dl~~l~~EleKL~~~~-~~~It~e~V~~~v~ 190 (318)
T PRK05629 143 GVRPTPDVVHALLEGVGSDLRELASAISQLVEDT-QGNVTVEKVRAYYV 190 (318)
T ss_pred CCCCCHHHHHHHHHHHCccHHHHHHHHHHHHhcC-CCCcCHHHHHHHhC
Confidence 6789999999998888766666666655555433 45799999987754
No 136
>COG1466 HolA DNA polymerase III, delta subunit [DNA replication, recombination, and repair]
Probab=26.03 E-value=1.8e+02 Score=24.34 Aligned_cols=61 Identities=15% Similarity=0.128 Sum_probs=43.1
Q ss_pred HHHHHhhhC-CCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHh
Q 038014 44 VGRIMKQIL-PPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALAT 104 (140)
Q Consensus 44 V~RI~K~~l-p~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~ 104 (140)
+.+.++..+ ..+++|+.||...|-.+..-=+..+..+-...+--.+-++|+.+||..++-.
T Consensus 145 l~~~i~~~~~~~~l~i~~~a~~~L~~~~~~nl~~i~~Ei~KL~l~~~~~~I~~~~V~~~v~~ 206 (334)
T COG1466 145 LPQWIKKRAKELGLKIDQEAIQLLLEALGGNLLAIAQEIEKLALYAGDKEITLEDVEEVVSD 206 (334)
T ss_pred HHHHHHHHHHHcCCCCCHHHHHHHHHHhCCcHHHHHHHHHHHHHhCCCCcCCHHHHHHHHhc
Confidence 444444433 2268999999999999988666666666666554444449999999988865
No 137
>PTZ00373 60S Acidic ribosomal protein P2; Provisional
Probab=25.59 E-value=1.7e+02 Score=21.51 Aligned_cols=28 Identities=14% Similarity=0.127 Sum_probs=24.4
Q ss_pred HHHHHHhCCCCccCcccHHHHHHhcCCc
Q 038014 81 ASDKCHKEKRKTVNGDDICWALATLGFD 108 (140)
Q Consensus 81 A~~~a~~~kRKTI~~eDVl~ALe~lgf~ 108 (140)
|+-.|.-.|..++|.+||.+.|+..|.+
T Consensus 8 AYlL~~lgG~~~pTaddI~kIL~AaGve 35 (112)
T PTZ00373 8 AYLMCVLGGNENPTKKEVKNVLSAVNAD 35 (112)
T ss_pred HHHHHHHcCCCCCCHHHHHHHHHHcCCC
Confidence 5667888899999999999999988766
No 138
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=25.39 E-value=1.5e+02 Score=19.96 Aligned_cols=28 Identities=21% Similarity=0.147 Sum_probs=21.1
Q ss_pred HHHHHHhCCCCccCcccHHHHHHhcCCc
Q 038014 81 ASDKCHKEKRKTVNGDDICWALATLGFD 108 (140)
Q Consensus 81 A~~~a~~~kRKTI~~eDVl~ALe~lgf~ 108 (140)
+.......+.-.|+.++|..+|..+|+.
T Consensus 15 ~F~~~D~d~~G~Is~~el~~~l~~~~~~ 42 (96)
T smart00027 15 IFRSLDKNQDGTVTGAQAKPILLKSGLP 42 (96)
T ss_pred HHHHhCCCCCCeEeHHHHHHHHHHcCCC
Confidence 5555566777788888888888888775
No 139
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=25.09 E-value=57 Score=25.99 Aligned_cols=37 Identities=8% Similarity=0.266 Sum_probs=28.5
Q ss_pred cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHH
Q 038014 38 LLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTG 79 (140)
Q Consensus 38 ~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las 79 (140)
..-.+||.|.+... .+||.+.++-+.+++++ +.|.-.
T Consensus 9 gVS~~TVSrvLn~~----~~vs~~tr~rV~~~a~~-lgY~pn 45 (327)
T PRK10423 9 GVSTSTVSHVINKD----RFVSEAITAKVEAAIKE-LNYAPS 45 (327)
T ss_pred CCcHHHHHHHhCCC----CCCCHHHHHHHHHHHHH-HCCCcc
Confidence 45678999998644 47999999999999987 345443
No 140
>KOG0188 consensus Alanyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=24.81 E-value=5.3e+02 Score=25.40 Aligned_cols=61 Identities=16% Similarity=0.134 Sum_probs=39.6
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHH---HHHHHHhCC-CCccCcccHHHHHHhcCCchhHHHHHHHH
Q 038014 58 ISKEAKETMQECVSEFISFVTGE---ASDKCHKEK-RKTVNGDDICWALATLGFDNYADQLKRYL 118 (140)
Q Consensus 58 IskdA~~al~~aa~~Fi~~Las~---A~~~a~~~k-RKTI~~eDVl~ALe~lgf~~y~~~l~~~l 118 (140)
=+...++.|.+==..|..-|..- -...+...+ -+||.++++...-+..||+-=...|....
T Consensus 353 ~~~~v~diineEE~~F~ktl~rg~~~f~r~~~~~~~s~tipGd~~w~LydTyGfPvdlt~lmAee 417 (895)
T KOG0188|consen 353 DPQHVIDIINEEEAQFLKTLDRGRKLFDRVARELGSSKTIPGDVAWRLYDTYGFPVDLTELMAEE 417 (895)
T ss_pred CHHHHHHHhcHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchHHHHHHHhhcCCcHHHHHHHHHH
Confidence 33444555666556677666654 222344444 48999999988888999997666665544
No 141
>PLN00138 large subunit ribosomal protein LP2; Provisional
Probab=24.51 E-value=1.8e+02 Score=21.24 Aligned_cols=28 Identities=18% Similarity=0.081 Sum_probs=24.6
Q ss_pred HHHHHHhCCCCccCcccHHHHHHhcCCc
Q 038014 81 ASDKCHKEKRKTVNGDDICWALATLGFD 108 (140)
Q Consensus 81 A~~~a~~~kRKTI~~eDVl~ALe~lgf~ 108 (140)
|+-.|.-.|...+|.+||...|+..|.+
T Consensus 6 Ayll~~l~g~~~pta~dI~~IL~AaGve 33 (113)
T PLN00138 6 AYLLAVLGGNTCPSAEDLKDILGSVGAD 33 (113)
T ss_pred HHHHHHhcCCCCCCHHHHHHHHHHcCCc
Confidence 6677888889999999999999998776
No 142
>PF08681 DUF1778: Protein of unknown function (DUF1778); InterPro: IPR014795 This entry is represented by Vibrio phage ICP1, Orf50. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a family of uncharacterised proteins. The structure of one of the hypothetical proteins in this family has been solved and it forms a helix structure which may form interactions with DNA. ; PDB: 1Y9B_A.
Probab=24.17 E-value=28 Score=23.54 Aligned_cols=18 Identities=17% Similarity=0.361 Sum_probs=13.2
Q ss_pred CccccHHHHHHHHHHHHH
Q 038014 55 NAKISKEAKETMQECVSE 72 (140)
Q Consensus 55 ~~rIskdA~~al~~aa~~ 72 (140)
++|++.+.+..|.+++..
T Consensus 3 ~iR~~~e~k~li~~AA~~ 20 (80)
T PF08681_consen 3 EIRVTPEEKELIERAAAL 20 (80)
T ss_dssp EEE--HHHHHHHHHHHHH
T ss_pred eEecCHHHHHHHHHHHHH
Confidence 368999999999999765
No 143
>PRK14971 DNA polymerase III subunits gamma and tau; Provisional
Probab=24.05 E-value=2.1e+02 Score=26.57 Aligned_cols=67 Identities=7% Similarity=0.021 Sum_probs=36.4
Q ss_pred CchhHHHHHHhhhCC-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcC
Q 038014 39 LPIANVGRIMKQILP-PNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLG 106 (140)
Q Consensus 39 LP~A~V~RI~K~~lp-~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lg 106 (140)
++...+.+.++..+. .++.++.++...|.+.+.-=+..+.......+.-.+++ |+.++|...+....
T Consensus 180 ls~~ei~~~L~~ia~~egi~i~~~al~~La~~s~gdlr~al~~Lekl~~y~~~~-It~~~V~~~l~~~~ 247 (614)
T PRK14971 180 IQVADIVNHLQYVASKEGITAEPEALNVIAQKADGGMRDALSIFDQVVSFTGGN-ITYKSVIENLNILD 247 (614)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhccCC-ccHHHHHHHhCCCC
Confidence 444555555544332 25778888888877765544444444333333333433 77777766554333
No 144
>PF01922 SRP19: SRP19 protein; InterPro: IPR002778 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the SRP19 subunit. The SRP19 protein is unstructured but forms a compact core domain and two extended RNA-binding loops upon binding the signal recognition particle (SRP) RNA [].; GO: 0008312 7S RNA binding, 0006614 SRP-dependent cotranslational protein targeting to membrane, 0048500 signal recognition particle; PDB: 3DLU_A 3DLV_B 2J37_B 1MFQ_B 3KTV_D 1RY1_B 1JID_A 1KVV_A 1KVN_A 3KTW_B ....
Probab=24.03 E-value=39 Score=23.80 Aligned_cols=25 Identities=24% Similarity=0.258 Sum_probs=16.7
Q ss_pred HhCCCCc--------cCcccHHHHHHhcCCchh
Q 038014 86 HKEKRKT--------VNGDDICWALATLGFDNY 110 (140)
Q Consensus 86 ~~~kRKT--------I~~eDVl~ALe~lgf~~y 110 (140)
..+||+. .+.++|..|++.|||...
T Consensus 14 r~~GRrv~k~~aV~~P~~~EI~~a~~~Lgl~~~ 46 (95)
T PF01922_consen 14 RSEGRRVPKELAVENPTLEEIADACKKLGLPCV 46 (95)
T ss_dssp TTTT--SSTTTSBSS--HHHHHHHHHHTTSEEE
T ss_pred hhhccccChhhcCCCCCHHHHHHHHHHcCCCEE
Confidence 4566663 678999999999999743
No 145
>PRK08487 DNA polymerase III subunit delta; Validated
Probab=23.95 E-value=2.3e+02 Score=23.50 Aligned_cols=60 Identities=10% Similarity=0.040 Sum_probs=39.4
Q ss_pred hHHHHHHhhhCC-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHH
Q 038014 42 ANVGRIMKQILP-PNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALA 103 (140)
Q Consensus 42 A~V~RI~K~~lp-~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe 103 (140)
..+.+.+++.+. .+..|+.+|...|...+.-=+..+..+--..+-=.+ +|+.+||...+.
T Consensus 138 ~~l~~~i~~~~~~~g~~i~~~a~~~L~~~~g~dl~~l~~ELeKL~ly~~--~It~edV~~~v~ 198 (328)
T PRK08487 138 REALELLQERAKELGLDIDQNALNHLYFIHNEDLALAANELEKLAILNE--PITLKDIQELVF 198 (328)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCcHHHHHHHHHHHHHHhcC--CCCHHHHHHHhc
Confidence 334444444432 257899999999998887655555555555444433 699999988764
No 146
>PRK05907 hypothetical protein; Provisional
Probab=23.54 E-value=1.7e+02 Score=24.69 Aligned_cols=72 Identities=11% Similarity=-0.017 Sum_probs=46.0
Q ss_pred CccccHHHHHHHHHHH-HHHHHHHHHHHHHHHHh-CCCCccCcccHHHHHHh-cCCchhH--H-----HHHHHHHHHHHH
Q 038014 55 NAKISKEAKETMQECV-SEFISFVTGEASDKCHK-EKRKTVNGDDICWALAT-LGFDNYA--D-----QLKRYLHRYREL 124 (140)
Q Consensus 55 ~~rIskdA~~al~~aa-~~Fi~~Las~A~~~a~~-~kRKTI~~eDVl~ALe~-lgf~~y~--~-----~l~~~l~~~re~ 124 (140)
+..|+.+|...|-+.+ .-=+..+..+--..+-- ..+++|+.+||...+.+ +++.=|. + .....+.-|+.+
T Consensus 151 g~~i~~~a~~~L~~~~~~~nL~~l~~EleKL~ly~g~~~~It~e~V~~lv~~s~e~nIF~L~dai~~~~~~~Al~il~~L 230 (311)
T PRK05907 151 GISCSLGLASLFVSKFPQTGLFEILSEFQKLLCQMGKKESLEASDIQSFVVKKEAASLWKLRDALLRRDRVEGHSLLRSL 230 (311)
T ss_pred CCCcCHHHHHHHHHHccCCCHHHHHHHHHHHHHhcCCCCeECHHHHHHHhcCcccccHHHHHHHHHccCHHHHHHHHHHH
Confidence 5689999988888876 34444555555555554 56889999999988653 4555332 1 234455555555
Q ss_pred HH
Q 038014 125 EG 126 (140)
Q Consensus 125 ~~ 126 (140)
..
T Consensus 231 l~ 232 (311)
T PRK05907 231 LS 232 (311)
T ss_pred HH
Confidence 44
No 147
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=23.48 E-value=1.4e+02 Score=19.10 Aligned_cols=33 Identities=21% Similarity=0.381 Sum_probs=24.2
Q ss_pred ccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHH
Q 038014 37 RLLPIANVGRIMKQILPPNAKISKEAKETMQECVSEF 73 (140)
Q Consensus 37 ~~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~F 73 (140)
..+..++|.|++... ..|+.+.+..+.+++.++
T Consensus 10 ~gvS~~TVSr~ln~~----~~v~~~t~~~i~~~~~~~ 42 (70)
T smart00354 10 AGVSKATVSRVLNGN----GRVSEETREKVLAAMEEL 42 (70)
T ss_pred HCCCHHHHHHHHCCC----CCCCHHHHHHHHHHHHHh
Confidence 357788888877543 457888888888877774
No 148
>KOG0784 consensus Isocitrate dehydrogenase, gamma subunit [Amino acid transport and metabolism]
Probab=23.45 E-value=47 Score=29.26 Aligned_cols=49 Identities=16% Similarity=0.148 Sum_probs=37.6
Q ss_pred HHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCchhHHHHHHHHHHHH
Q 038014 73 FISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDNYADQLKRYLHRYR 122 (140)
Q Consensus 73 Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~~y~~~l~~~l~~~r 122 (140)
-...++..|.++|...|||-||+=|=-+ +-+||=+-|.+.+++....|.
T Consensus 185 kseRIaryAF~yA~k~gRKkVTaVHKAn-imKL~DGlFle~~~eva~~Yp 233 (375)
T KOG0784|consen 185 KSERIARYAFEYAKKNGRKKVTAVHKAN-IMKLGDGLFLESCQEVAKKYP 233 (375)
T ss_pred hhHHHHHHHHHHHHHhCCceEEEEeccC-ceecchhhHHHHHHHHHhcCC
Confidence 3445677899999999999999977665 346777788888887775554
No 149
>PRK14964 DNA polymerase III subunits gamma and tau; Provisional
Probab=23.27 E-value=2.2e+02 Score=25.86 Aligned_cols=47 Identities=11% Similarity=-0.010 Sum_probs=30.9
Q ss_pred CccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHH
Q 038014 55 NAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWAL 102 (140)
Q Consensus 55 ~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~AL 102 (140)
++.|+.++...|.+.+.-=+..+.+.-.+.+...+ .+|+.+||...|
T Consensus 192 gi~i~~eAL~lIa~~s~GslR~alslLdqli~y~~-~~It~e~V~~ll 238 (491)
T PRK14964 192 NIEHDEESLKLIAENSSGSMRNALFLLEQAAIYSN-NKISEKSVRDLL 238 (491)
T ss_pred CCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhcC-CCCCHHHHHHHH
Confidence 57899999999888775444444443333333333 479999988765
No 150
>TIGR01052 top6b DNA topoisomerase VI, B subunit. This model describes DNA topoisomerase VI, an archaeal type II DNA topoisomerase (DNA gyrase).
Probab=23.18 E-value=1.3e+02 Score=27.40 Aligned_cols=58 Identities=19% Similarity=0.321 Sum_probs=40.3
Q ss_pred hhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCchhHHHHHHHHHH
Q 038014 49 KQILPPNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFDNYADQLKRYLHR 120 (140)
Q Consensus 49 K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~~y~~~l~~~l~~ 120 (140)
|+++.+.--|-+|.+.||++||..-=.||...-...-...++++ |..|++.+-..|..
T Consensus 426 Ke~ia~~~ei~~ei~~al~~~~r~L~~~l~~~~~~~~~~~r~~~--------------~~~y~p~~a~~~~~ 483 (488)
T TIGR01052 426 KQSVADIPEIYNEIRLALMEVARRLRLYLSRKAREEEEIKRRKT--------------LEKYLPEIAKSLAY 483 (488)
T ss_pred hhhhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------------HHHHHHHHHHHHHH
Confidence 45544444688999999999999999999886665545444444 45666666665544
No 151
>KOG3468 consensus NADH:ubiquinone oxidoreductase, NDUFB7/B18 subunit [Energy production and conversion]
Probab=23.05 E-value=1e+02 Score=23.07 Aligned_cols=42 Identities=14% Similarity=0.263 Sum_probs=33.3
Q ss_pred cCcccHHHHHHhcCCchhHHHHHHHHHHHHHHHHHHhhhhcc
Q 038014 93 VNGDDICWALATLGFDNYADQLKRYLHRYRELEGERANQNKA 134 (140)
Q Consensus 93 I~~eDVl~ALe~lgf~~y~~~l~~~l~~~re~~~~kk~q~k~ 134 (140)
..++|=.-+-+.+++++|+.-++++-.+-+-+++.+|.++++
T Consensus 76 ~kC~~erh~~dkCEyed~vmRmkefeRErrlLqrq~r~e~~A 117 (128)
T KOG3468|consen 76 WKCEDERHVYDKCEYEDYVMRMKEFERERRLLQRQKRLEKNA 117 (128)
T ss_pred hhccccccchhhhhHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence 445666666778999999999999998888888877776654
No 152
>PRK00440 rfc replication factor C small subunit; Reviewed
Probab=22.84 E-value=2.6e+02 Score=22.26 Aligned_cols=65 Identities=14% Similarity=0.093 Sum_probs=38.5
Q ss_pred CchhHHHHHHhhhCC-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhc
Q 038014 39 LPIANVGRIMKQILP-PNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATL 105 (140)
Q Consensus 39 LP~A~V~RI~K~~lp-~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~l 105 (140)
++...+.++++..+. .++.|+.++...+.+.+.--+..+.......+. . .++|+.+||..++...
T Consensus 161 l~~~ei~~~l~~~~~~~~~~i~~~al~~l~~~~~gd~r~~~~~l~~~~~-~-~~~it~~~v~~~~~~~ 226 (319)
T PRK00440 161 LKKEAVAERLRYIAENEGIEITDDALEAIYYVSEGDMRKAINALQAAAA-T-GKEVTEEAVYKITGTA 226 (319)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHH-c-CCCCCHHHHHHHhCCC
Confidence 445555555555442 256799999988887765433333332222222 2 3689999998887543
No 153
>PTZ00183 centrin; Provisional
Probab=22.80 E-value=2.8e+02 Score=19.43 Aligned_cols=18 Identities=6% Similarity=0.121 Sum_probs=9.7
Q ss_pred HhCCCCccCcccHHHHHH
Q 038014 86 HKEKRKTVNGDDICWALA 103 (140)
Q Consensus 86 ~~~kRKTI~~eDVl~ALe 103 (140)
...+.-.|+.++++.++.
T Consensus 63 d~~~~g~i~~~eF~~~~~ 80 (158)
T PTZ00183 63 DKDGSGKIDFEEFLDIMT 80 (158)
T ss_pred CCCCCCcEeHHHHHHHHH
Confidence 344555566666655554
No 154
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=22.78 E-value=45 Score=20.22 Aligned_cols=16 Identities=25% Similarity=0.434 Sum_probs=12.4
Q ss_pred cccCchhHHHHHHhhh
Q 038014 36 DRLLPIANVGRIMKQI 51 (140)
Q Consensus 36 d~~LP~A~V~RI~K~~ 51 (140)
.+.+|++++.|+++.-
T Consensus 27 ~~gl~~stv~r~L~tL 42 (52)
T PF09339_consen 27 ALGLPKSTVHRLLQTL 42 (52)
T ss_dssp HHTS-HHHHHHHHHHH
T ss_pred HHCcCHHHHHHHHHHH
Confidence 4579999999999865
No 155
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=22.17 E-value=97 Score=24.88 Aligned_cols=40 Identities=20% Similarity=0.417 Sum_probs=29.8
Q ss_pred cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHH
Q 038014 38 LLPIANVGRIMKQILPPNAKISKEAKETMQECVSEFISFVTGE 80 (140)
Q Consensus 38 ~LP~A~V~RI~K~~lp~~~rIskdA~~al~~aa~~Fi~~Las~ 80 (140)
..-+++|.|.+... +..+||.+.++-+.+++++ +.|.-..
T Consensus 12 gVS~~TVSrvln~~--~~~~vs~~tr~rV~~~a~~-lgY~pn~ 51 (327)
T PRK10339 12 GVSLATVSRVLNDD--PTLNVKEETKHRILEIAEK-LEYKTSS 51 (327)
T ss_pred CCCHHhhhhhhcCC--CCCCcCHHHHHHHHHHHHH-hCCCCch
Confidence 46688999998755 3347999999999999988 3443333
No 156
>PF12767 SAGA-Tad1: Transcriptional regulator of RNA polII, SAGA, subunit; InterPro: IPR024738 The yeast Spt-Ada-Gcn5-Acetyl (SAGA) transferase complex is a multifunctional coactivator involved in multiple cellular processes [], including regulation of transcription by RNA polymerase II [, ]. It is formed of five major modular subunits and shows a high degree of structural conservation to human TFTC and STAGA []. This entry represents Ada1 (known as Tada1 in higher eukaryotes), one of the subunits that constitute the SAGA core. It also functions as a component of the SALSA and SLIK complexes. ; GO: 0070461 SAGA-type complex
Probab=21.55 E-value=1.7e+02 Score=23.61 Aligned_cols=30 Identities=7% Similarity=0.098 Sum_probs=26.5
Q ss_pred Cc-cccHHHHHHHHHHHHHHHHHHHHHHHHH
Q 038014 55 NA-KISKEAKETMQECVSEFISFVTGEASDK 84 (140)
Q Consensus 55 ~~-rIskdA~~al~~aa~~Fi~~Las~A~~~ 84 (140)
+. -|+.|+...|+-+++.|+..|.....+.
T Consensus 220 GL~gvs~~~a~ll~~ale~~LK~lI~s~l~~ 250 (252)
T PF12767_consen 220 GLGGVSDDCANLLNLALEVHLKNLIKSCLDL 250 (252)
T ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 44 7999999999999999999998877665
No 157
>PF00403 HMA: Heavy-metal-associated domain; InterPro: IPR006121 Proteins that transport heavy metals in micro-organisms and mammals share similarities in their sequences and structures. These proteins provide an important focus for research, some being involved in bacterial resistance to toxic metals, such as lead and cadmium, while others are involved in inherited human syndromes, such as Wilson's and Menke's diseases []. A conserved domain has been found in a number of these heavy metal transport or detoxification proteins []. The domain, which has been termed Heavy-Metal-Associated (HMA), contains two conserved cysteines that are probably involved in metal binding. Structure solution of the fourth HMA domain of the Menke's copper transporting ATPase shows a well-defined structure comprising a four-stranded antiparallel beta-sheet and two alpha helices packed in an alpha-beta sandwich fold []. This fold is common to other domains and is classified as "ferredoxin-like".; GO: 0046872 metal ion binding, 0030001 metal ion transport; PDB: 2VOY_A 1P6T_A 1KQK_A 2RML_A 1JWW_A 3K7R_F 1FES_A 1CC8_A 1FD8_A 2GGP_A ....
Probab=21.46 E-value=58 Score=19.95 Aligned_cols=16 Identities=19% Similarity=0.350 Sum_probs=12.8
Q ss_pred cCcccHHHHHHhcCCc
Q 038014 93 VNGDDICWALATLGFD 108 (140)
Q Consensus 93 I~~eDVl~ALe~lgf~ 108 (140)
++.++|..+++++||+
T Consensus 47 ~~~~~i~~~i~~~Gy~ 62 (62)
T PF00403_consen 47 TSIEKIIEAIEKAGYE 62 (62)
T ss_dssp SCHHHHHHHHHHTTSE
T ss_pred CCHHHHHHHHHHhCcC
Confidence 5668888999988874
No 158
>PRK14961 DNA polymerase III subunits gamma and tau; Provisional
Probab=21.35 E-value=3.9e+02 Score=22.62 Aligned_cols=65 Identities=11% Similarity=0.009 Sum_probs=34.7
Q ss_pred chhHHHHHHhhhCC-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhc
Q 038014 40 PIANVGRIMKQILP-PNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATL 105 (140)
Q Consensus 40 P~A~V~RI~K~~lp-~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~l 105 (140)
+...+..+++..+. .+..++.++...|.+.+.-=+..+-......+. -++..|+.+||..++...
T Consensus 179 ~~~el~~~L~~~~~~~g~~i~~~al~~ia~~s~G~~R~al~~l~~~~~-~~~~~It~~~v~~~l~~~ 244 (363)
T PRK14961 179 SEEKIFNFLKYILIKESIDTDEYALKLIAYHAHGSMRDALNLLEHAIN-LGKGNINIKNVTDMLGLL 244 (363)
T ss_pred CHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHH-hcCCCCCHHHHHHHHCCC
Confidence 34444444444332 246788888888776653222222222212222 256779999998876533
No 159
>COG1239 ChlI Mg-chelatase subunit ChlI [Coenzyme metabolism]
Probab=21.13 E-value=2.4e+02 Score=25.37 Aligned_cols=49 Identities=18% Similarity=0.221 Sum_probs=40.9
Q ss_pred CccccHHHHHHHHHHHHHHHH-------HHHHHHHHHHHhCCCCccCcccHHHHHH
Q 038014 55 NAKISKEAKETMQECVSEFIS-------FVTGEASDKCHKEKRKTVNGDDICWALA 103 (140)
Q Consensus 55 ~~rIskdA~~al~~aa~~Fi~-------~Las~A~~~a~~~kRKTI~~eDVl~ALe 103 (140)
.+.++.++...+...|..+-. .+...|...+.=.||.+++.+||..|++
T Consensus 265 ~V~l~~~~~~~ia~~~~~~~v~g~radi~~~r~a~a~aa~~Gr~~v~~~Di~~a~~ 320 (423)
T COG1239 265 EVELDDDAETKIAELCARLAVDGHRADIVVVRAAKALAALRGRTEVEEEDIREAAE 320 (423)
T ss_pred cccCcHHHHHHHHHHHHHhccCCCchhhHHHHHHHHHHHhcCceeeehhhHHHHHh
Confidence 678999999999988877654 3566677888999999999999999876
No 160
>PRK15485 cobalt transport protein CbiQ; Provisional
Probab=20.98 E-value=1.7e+02 Score=23.31 Aligned_cols=37 Identities=11% Similarity=-0.025 Sum_probs=28.0
Q ss_pred ccCcccHHHHHHhcCCc-----------hhHHHHHHHHHHHHHHHHHH
Q 038014 92 TVNGDDICWALATLGFD-----------NYADQLKRYLHRYRELEGER 128 (140)
Q Consensus 92 TI~~eDVl~ALe~lgf~-----------~y~~~l~~~l~~~re~~~~k 128 (140)
|-...|+..+|+++|++ .|++.+.+..+.-++.++.|
T Consensus 132 TT~~~~l~~~L~~l~vP~~~~~~~~l~~Rfi~~l~~e~~~i~~Aq~~R 179 (225)
T PRK15485 132 NLPFPQLIKLLKRAHIPRLLTEQILLTWRFIFILLEEAAAIRRAQSLR 179 (225)
T ss_pred hCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 34579999999999998 56677777777666666655
No 161
>PRK09111 DNA polymerase III subunits gamma and tau; Validated
Probab=20.86 E-value=2.6e+02 Score=25.90 Aligned_cols=63 Identities=8% Similarity=0.024 Sum_probs=38.3
Q ss_pred chhHHHHHHhhhCC-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHH
Q 038014 40 PIANVGRIMKQILP-PNAKISKEAKETMQECVSEFISFVTGEASDKCHKEKRKTVNGDDICWALA 103 (140)
Q Consensus 40 P~A~V~RI~K~~lp-~~~rIskdA~~al~~aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe 103 (140)
+...+.+.++..+. .+..|+.++...|.+.+.--+..+.....+.+.. +...|+.+||...+.
T Consensus 192 ~~~el~~~L~~i~~kegi~i~~eAl~lIa~~a~Gdlr~al~~Ldkli~~-g~g~It~e~V~~llg 255 (598)
T PRK09111 192 EADVLAAHLSRIAAKEGVEVEDEALALIARAAEGSVRDGLSLLDQAIAH-GAGEVTAEAVRDMLG 255 (598)
T ss_pred CHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHhh-cCCCcCHHHHHHHhC
Confidence 33444444444332 3578999999888887765555555544443333 345799988887653
No 162
>cd04752 Commd4 COMM_Domain containing protein 4. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=20.47 E-value=4e+02 Score=20.40 Aligned_cols=51 Identities=22% Similarity=0.311 Sum_probs=32.1
Q ss_pred HHHHHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhcCCc-hhHHHHHHHHHHHHHHHH
Q 038014 69 CVSEFISFVTGEASDKCHKEKRKTVNGDDICWALATLGFD-NYADQLKRYLHRYRELEG 126 (140)
Q Consensus 69 aa~~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~lgf~-~y~~~l~~~l~~~re~~~ 126 (140)
++...+.+|...|. |.-++++++..-|+.+||+ +.+..+.....++++...
T Consensus 43 ~~va~l~fiL~~A~-------k~n~~~~~l~~eL~~lglp~e~~~~l~~~~~~~~~~l~ 94 (174)
T cd04752 43 ASIAVLSFILSSAA-------KYNVDGESLSSELQQLGLPKEHATSLCRSYEEKQSKLQ 94 (174)
T ss_pred HHHHHHHHHHHHHH-------HcCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHH
Confidence 34445555555444 3449999999999999999 444444444455544443
No 163
>PF03130 HEAT_PBS: PBS lyase HEAT-like repeat; InterPro: IPR004155 These proteins contain a short bi-helical repeat that is related to HEAT. Cyanobacteria and red algae harvest light energy using macromolecular complexes known as phycobilisomes (PBS), peripherally attached to the photosynthetic membrane. The major components of PBS are the phycobiliproteins. These heterodimeric proteins are covalently attached to phycobilins: open-chain tetrapyrrole chromophores, which function as the photosynthetic light-harvesting pigments. Phycobiliproteins differ in sequence and in the nature and number of attached phycobilins to each of their subunits. These proteins include the lyase enzymes that specifically attach particular phycobilins to apophycobiliprotein subunits. The most comprehensively studied of these is the CpcE/Flyase P31967 from SWISSPROT, P31968 from SWISSPROT, which attaches phycocyanobilin (PCB) to the alpha subunit of apophycocyanin []. Similarly, MpeU/V attaches phycoerythrobilin to phycoerythrin II, while CpeY/Z is thought to be involved in phycoerythrobilin (PEB) attachment to phycoerythrin (PE) I (PEs I and II differ in sequence and in the number of attached molecules of PEB: PE I has five, PE II has six) []. All the reactions of the above lyases involve an apoprotein cysteine SH addition to a terminal delta 3,3'-double bond. Such a reaction is not possible in the case of phycoviolobilin (PVB), the phycobilin of alpha-phycoerythrocyanin (alpha-PEC). It is thought that in this case, PCB, not PVB, is first added to apo-alpha-PEC, and is then isomerized to PVB. The addition reaction has been shown to occur in the presence of either of the components of alpha-PEC-PVB lyase PecE or PecF (or both). The isomerisation reaction occurs only when both PecE and PecF components are present, i.e. the PecE/F phycobiliprotein lyase is also a phycobilin isomerase []. Another member of this family is the NblB protein, whose similarity to the phycobiliprotein lyases was previously noted []. This constitutively expressed protein is not known to have any lyase activity. It is thought to be involved in the coordination of PBS degradation with environmental nutrient limitation. It has been suggested that the similarity of NblB to the phycobiliprotein lyases is due to the ability to bind tetrapyrrole phycobilins via the common repeated motif [].; PDB: 1TE4_A.
Probab=20.35 E-value=1.6e+02 Score=15.61 Aligned_cols=22 Identities=23% Similarity=0.163 Sum_probs=17.2
Q ss_pred HHHHHhcCCchhHHHHHHHHHH
Q 038014 99 CWALATLGFDNYADQLKRYLHR 120 (140)
Q Consensus 99 l~ALe~lgf~~y~~~l~~~l~~ 120 (140)
..+|-.+|-...++.|.+.|++
T Consensus 6 a~aLg~igd~~ai~~L~~~L~d 27 (27)
T PF03130_consen 6 ARALGQIGDPRAIPALIEALED 27 (27)
T ss_dssp HHHHGGG-SHHHHHHHHHHHHH
T ss_pred HHHHHHcCCHHHHHHHHHHhcC
Confidence 5688889999999999888763
No 164
>COG1222 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]
Probab=20.11 E-value=1.1e+02 Score=27.43 Aligned_cols=34 Identities=21% Similarity=0.198 Sum_probs=29.5
Q ss_pred HHHHHHHHHHHHHHHhCCCCccCcccHHHHHHhc
Q 038014 72 EFISFVTGEASDKCHKEKRKTVNGDDICWALATL 105 (140)
Q Consensus 72 ~Fi~~Las~A~~~a~~~kRKTI~~eDVl~ALe~l 105 (140)
.=|.-+.++|--.|.++.|..|+.+|+++|.++.
T Consensus 359 AdlkaictEAGm~AiR~~R~~Vt~~DF~~Av~KV 392 (406)
T COG1222 359 ADLKAICTEAGMFAIRERRDEVTMEDFLKAVEKV 392 (406)
T ss_pred HHHHHHHHHHhHHHHHhccCeecHHHHHHHHHHH
Confidence 3467788889999999999999999999998763
No 165
>cd05833 Ribosomal_P2 Ribosomal protein P2. This subfamily represents the eukaryotic large ribosomal protein P2. Eukaryotic P1 and P2 are functionally equivalent to the bacterial protein L7/L12, but are not homologous to L7/L12. P2 is located in the L12 stalk, with proteins P1, P0, L11, and 28S rRNA. P1 and P2 are the only proteins in the ribosome to occur as multimers, always appearing as sets of heterodimers. Recent data indicate that eukaryotes have four copies (two heterodimers), while most archaeal species contain six copies of L12p (three homodimers). Bacteria may have four or six copies of L7/L12 (two or three homodimers) depending on the species. Experiments using S. cerevisiae P1 and P2 indicate that P1 proteins are positioned more internally with limited reactivity in the C-terminal domains, while P2 proteins seem to be more externally located and are more likely to interact with other cellular components. In lower eukaryotes, P1 and P2 are further subdivided into P1A, P1B, P2
Probab=20.03 E-value=2.6e+02 Score=20.25 Aligned_cols=28 Identities=14% Similarity=0.092 Sum_probs=24.0
Q ss_pred HHHHHHhCCCCccCcccHHHHHHhcCCc
Q 038014 81 ASDKCHKEKRKTVNGDDICWALATLGFD 108 (140)
Q Consensus 81 A~~~a~~~kRKTI~~eDVl~ALe~lgf~ 108 (140)
|+-.|.-.|..+||.+||...|+..|.+
T Consensus 6 AylL~~l~g~~~pTa~dI~~IL~AaGve 33 (109)
T cd05833 6 AYLLAVLGGNASPSAADVKKILGSVGVE 33 (109)
T ss_pred HHHHHHHcCCCCCCHHHHHHHHHHcCCC
Confidence 5667778888899999999999988765
Done!