Query 047769
Match_columns 131
No_of_seqs 174 out of 438
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 02:58:26 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/047769.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/047769hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00035 histone H4; Provision 100.0 1.1E-45 2.4E-50 266.8 9.9 103 29-131 1-103 (103)
2 PTZ00015 histone H4; Provision 100.0 4E-43 8.6E-48 253.1 9.9 101 29-129 1-102 (102)
3 KOG3467 Histone H4 [Chromatin 100.0 2.9E-43 6.3E-48 248.8 8.1 103 29-131 1-103 (103)
4 cd00076 H4 Histone H4, one of 100.0 4.9E-38 1.1E-42 220.2 8.7 85 45-129 1-85 (85)
5 smart00417 H4 Histone H4. 100.0 3.3E-31 7.1E-36 181.6 6.1 74 45-118 1-74 (74)
6 PLN00163 histone H4; Provision 99.9 1.5E-25 3.2E-30 147.1 2.5 59 29-87 1-59 (59)
7 COG2036 HHT1 Histones H3 and H 99.9 4.8E-24 1E-28 151.2 7.0 90 40-129 2-91 (91)
8 smart00803 TAF TATA box bindin 99.9 2.5E-22 5.4E-27 134.1 7.9 64 57-120 2-65 (65)
9 cd08050 TAF6 TATA Binding Prot 99.6 5.5E-15 1.2E-19 124.3 9.0 72 59-130 1-73 (343)
10 PF02969 TAF: TATA box binding 99.5 3.1E-14 6.8E-19 95.7 8.2 64 57-120 3-66 (66)
11 cd07979 TAF9 TATA Binding Prot 99.5 2.7E-14 5.8E-19 104.8 8.4 68 61-130 5-72 (117)
12 smart00576 BTP Bromodomain tra 99.5 9.5E-14 2E-18 94.6 7.6 70 56-125 5-74 (77)
13 PF15511 CENP-T: Centromere ki 99.4 9.1E-13 2E-17 113.7 7.3 69 46-114 338-414 (414)
14 PF00125 Histone: Core histone 99.4 3.4E-12 7.4E-17 85.0 7.8 66 56-121 4-74 (75)
15 KOG0869 CCAAT-binding factor, 99.3 3.4E-12 7.3E-17 98.6 7.4 82 47-128 22-105 (168)
16 cd07981 TAF12 TATA Binding Pro 99.3 8.3E-12 1.8E-16 84.4 8.4 65 58-122 2-67 (72)
17 PF00808 CBFD_NFYB_HMF: Histon 99.3 2.4E-11 5.3E-16 79.6 8.7 63 57-119 2-65 (65)
18 KOG2549 Transcription initiati 99.3 1E-11 2.2E-16 110.6 8.6 74 58-131 12-86 (576)
19 COG5095 TAF6 Transcription ini 99.3 2.2E-11 4.8E-16 103.8 8.4 75 57-131 5-80 (450)
20 PF07524 Bromo_TP: Bromodomain 99.1 6.2E-10 1.3E-14 75.2 8.5 68 57-124 6-73 (77)
21 PF15630 CENP-S: Kinetochore c 99.1 4.7E-10 1E-14 77.2 7.3 61 62-122 10-73 (76)
22 cd00074 H2A Histone 2A; H2A is 99.0 1.8E-09 4E-14 79.5 8.9 65 57-121 20-85 (115)
23 smart00428 H3 Histone H3. 98.9 2.4E-09 5.2E-14 77.8 6.6 69 57-125 29-104 (105)
24 PF02291 TFIID-31kDa: Transcri 98.9 6.8E-09 1.5E-13 77.8 8.1 66 57-122 10-77 (129)
25 KOG3334 Transcription initiati 98.7 9.9E-08 2.1E-12 72.9 8.7 67 57-123 11-79 (148)
26 PLN00161 histone H3; Provision 98.3 7.1E-06 1.5E-10 62.2 9.0 69 57-125 55-129 (135)
27 PLN00160 histone H3; Provision 98.3 3.5E-06 7.5E-11 60.6 6.6 68 57-124 21-94 (97)
28 KOG0870 DNA polymerase epsilon 98.3 5.5E-06 1.2E-10 64.8 8.1 69 57-125 10-81 (172)
29 PLN00121 histone H3; Provision 98.2 2.1E-06 4.6E-11 65.1 5.5 68 57-124 62-134 (136)
30 PTZ00018 histone H3; Provision 98.2 3E-06 6.6E-11 64.2 5.6 68 57-124 62-134 (136)
31 PF03847 TFIID_20kDa: Transcri 98.2 1.4E-05 3.1E-10 53.9 8.1 64 59-122 1-65 (68)
32 KOG2389 Predicted bromodomain 98.2 3.6E-06 7.8E-11 72.0 6.3 75 52-126 24-98 (353)
33 COG5094 TAF9 Transcription ini 98.1 9.4E-06 2E-10 61.3 6.0 60 62-121 19-81 (145)
34 PLN00153 histone H2A; Provisio 98.0 2.3E-05 4.9E-10 59.0 7.5 87 29-120 1-88 (129)
35 PLN00154 histone H2A; Provisio 98.0 5E-05 1.1E-09 57.7 9.0 64 57-120 38-103 (136)
36 KOG4336 TBP-associated transcr 98.0 2.5E-05 5.4E-10 66.1 7.8 68 58-125 6-73 (323)
37 PLN00157 histone H2A; Provisio 97.9 4.3E-05 9.4E-10 57.7 7.4 64 57-120 26-90 (132)
38 PLN00156 histone H2AX; Provisi 97.9 7.4E-05 1.6E-09 56.9 8.2 81 40-120 10-93 (139)
39 KOG1142 Transcription initiati 97.9 6.2E-05 1.3E-09 62.3 8.0 78 53-130 150-229 (258)
40 PTZ00017 histone H2A; Provisio 97.9 8.1E-05 1.8E-09 56.4 7.9 64 57-120 27-91 (134)
41 KOG0871 Class 2 transcription 97.8 0.00014 3E-09 56.1 7.5 75 53-127 8-84 (156)
42 KOG1756 Histone 2A [Chromatin 97.7 0.00018 3.9E-09 54.2 7.3 88 29-120 1-91 (131)
43 PF02269 TFIID-18kDa: Transcri 97.4 0.00022 4.7E-09 50.4 3.8 61 63-123 7-68 (93)
44 smart00414 H2A Histone 2A. 97.4 0.00071 1.5E-08 49.2 6.4 64 57-120 9-73 (106)
45 COG5262 HTA1 Histone H2A [Chro 97.3 0.0011 2.5E-08 49.6 7.2 64 57-120 26-90 (132)
46 PLN00158 histone H2B; Provisio 97.3 0.0023 5E-08 47.5 8.3 62 60-121 30-92 (116)
47 PTZ00463 histone H2B; Provisio 97.1 0.0052 1.1E-07 45.7 8.7 60 62-121 33-93 (117)
48 smart00427 H2B Histone H2B. 96.9 0.0063 1.4E-07 43.3 7.6 60 62-121 6-66 (89)
49 cd07978 TAF13 The TATA Binding 96.9 0.007 1.5E-07 42.9 7.5 61 61-122 6-67 (92)
50 cd08048 TAF11 TATA Binding Pro 96.8 0.0095 2.1E-07 41.7 7.6 66 57-122 16-84 (85)
51 KOG1745 Histones H3 and H4 [Ch 96.8 0.00098 2.1E-08 50.7 2.5 68 57-124 63-135 (137)
52 KOG3423 Transcription initiati 96.6 0.019 4.2E-07 45.2 8.8 74 52-125 81-168 (176)
53 PTZ00252 histone H2A; Provisio 96.2 0.024 5.1E-07 43.1 7.0 64 57-120 25-91 (134)
54 PF09415 CENP-X: CENP-S associ 96.1 0.015 3.3E-07 39.5 5.1 61 59-119 1-65 (72)
55 COG5150 Class 2 transcription 96.1 0.028 6E-07 42.8 6.9 70 56-125 10-81 (148)
56 COG5208 HAP5 CCAAT-binding fac 95.9 0.017 3.7E-07 47.6 5.3 66 56-121 108-174 (286)
57 PF03540 TFIID_30kDa: Transcri 95.9 0.052 1.1E-06 35.0 6.4 48 57-104 2-49 (51)
58 PF04719 TAFII28: hTAFII28-lik 95.8 0.06 1.3E-06 38.2 7.3 66 57-122 23-90 (90)
59 KOG1744 Histone H2B [Chromatin 95.2 0.084 1.8E-06 39.8 6.5 47 75-121 56-102 (127)
60 KOG1657 CCAAT-binding factor, 94.8 0.054 1.2E-06 44.4 4.7 67 55-121 72-139 (236)
61 PF13654 AAA_32: AAA domain; P 94.7 0.16 3.5E-06 45.5 8.0 61 62-122 435-506 (509)
62 cd08045 TAF4 TATA Binding Prot 94.3 0.28 6E-06 38.8 7.8 61 62-122 53-119 (212)
63 KOG1659 Class 2 transcription 94.1 0.19 4.2E-06 41.0 6.6 67 55-121 11-78 (224)
64 PLN00155 histone H2A; Provisio 93.5 0.16 3.4E-06 33.6 4.2 33 57-89 24-57 (58)
65 PF05236 TAF4: Transcription i 93.2 0.14 3E-06 41.8 4.2 61 62-122 52-118 (264)
66 TIGR00764 lon_rel lon-related 91.5 0.97 2.1E-05 41.3 8.0 59 63-121 318-390 (608)
67 KOG3901 Transcription initiati 91.1 0.77 1.7E-05 33.8 5.6 42 77-121 30-71 (109)
68 TIGR02902 spore_lonB ATP-depen 90.9 1 2.2E-05 40.3 7.4 64 57-121 262-331 (531)
69 COG5248 TAF19 Transcription in 89.7 1.2 2.6E-05 33.2 5.7 59 62-122 14-73 (126)
70 KOG3219 Transcription initiati 89.3 0.59 1.3E-05 37.6 4.1 67 57-123 112-179 (195)
71 COG5247 BUR6 Class 2 transcrip 88.6 3.3 7.2E-05 30.5 7.3 64 57-120 23-87 (113)
72 COG5162 Transcription initiati 88.0 4.8 0.0001 32.1 8.3 71 55-125 86-189 (197)
73 COG1067 LonB Predicted ATP-dep 87.0 2.8 6.1E-05 39.0 7.5 59 63-121 327-398 (647)
74 PRK07452 DNA polymerase III su 86.3 1.9 4.2E-05 35.1 5.6 62 62-124 138-201 (326)
75 TIGR03015 pepcterm_ATPase puta 85.5 4 8.7E-05 31.8 6.8 68 55-122 189-266 (269)
76 cd08313 Death_TNFR1 Death doma 85.1 4.4 9.5E-05 28.0 6.0 68 54-124 5-72 (80)
77 PRK00411 cdc6 cell division co 84.0 4 8.7E-05 33.9 6.5 68 55-122 204-282 (394)
78 PRK06585 holA DNA polymerase I 83.5 3.4 7.3E-05 34.0 5.8 60 63-123 151-211 (343)
79 PRK05574 holA DNA polymerase I 82.7 4.9 0.00011 32.5 6.4 60 63-123 155-214 (340)
80 TIGR01128 holA DNA polymerase 81.7 6.7 0.00014 31.1 6.7 59 63-122 120-178 (302)
81 PRK07914 hypothetical protein; 80.6 4.8 0.0001 33.2 5.7 58 63-122 137-194 (320)
82 PF12767 SAGA-Tad1: Transcript 80.2 4.4 9.6E-05 32.7 5.3 40 63-102 212-251 (252)
83 KOG1757 Histone 2A [Chromatin 80.0 3.6 7.7E-05 30.9 4.3 64 57-120 30-95 (131)
84 PRK08487 DNA polymerase III su 78.6 7.5 0.00016 32.2 6.3 58 62-122 143-200 (328)
85 PF08369 PCP_red: Proto-chloro 78.2 5.6 0.00012 24.5 4.1 41 77-118 3-44 (45)
86 PRK05907 hypothetical protein; 78.0 6.8 0.00015 32.9 5.9 58 63-121 143-202 (311)
87 PRK13765 ATP-dependent proteas 75.1 10 0.00022 35.2 6.6 51 71-121 336-399 (637)
88 PRK05629 hypothetical protein; 73.7 12 0.00026 30.8 6.2 58 63-122 135-192 (318)
89 PF06971 Put_DNA-bind_N: Putat 73.3 3.5 7.7E-05 26.1 2.3 28 57-84 2-38 (50)
90 TIGR02928 orc1/cdc6 family rep 73.0 23 0.00049 29.0 7.7 68 55-122 196-274 (365)
91 smart00350 MCM minichromosome 72.9 15 0.00033 32.6 7.0 66 57-122 417-504 (509)
92 PRK12402 replication factor C 72.8 10 0.00022 30.5 5.5 56 63-121 193-248 (337)
93 PF13335 Mg_chelatase_2: Magne 70.7 26 0.00057 24.4 6.6 58 57-120 31-94 (96)
94 COG1224 TIP49 DNA helicase TIP 67.8 17 0.00038 32.4 6.2 62 59-121 362-431 (450)
95 COG5624 TAF61 Transcription in 66.6 2 4.3E-05 38.5 0.1 94 37-130 362-459 (505)
96 PRK00440 rfc replication facto 66.4 19 0.00041 28.6 5.8 56 63-121 170-225 (319)
97 cd08784 Death_DRs Death Domain 66.1 27 0.00058 23.5 5.7 67 54-124 5-71 (79)
98 PRK00080 ruvB Holliday junctio 63.8 34 0.00074 28.2 6.9 74 55-129 177-257 (328)
99 COG1466 HolA DNA polymerase II 62.8 26 0.00056 29.2 6.1 60 62-122 148-207 (334)
100 PRK14970 DNA polymerase III su 59.6 25 0.00053 29.3 5.4 56 63-120 176-231 (367)
101 TIGR02397 dnaX_nterm DNA polym 58.8 27 0.00058 28.4 5.4 56 63-120 185-240 (355)
102 PRK14964 DNA polymerase III su 58.7 23 0.0005 31.9 5.4 55 63-119 184-238 (491)
103 PF09288 UBA_3: Fungal ubiquit 58.4 13 0.00028 24.3 2.8 36 56-91 19-54 (55)
104 TIGR03420 DnaA_homol_Hda DnaA 57.0 52 0.0011 24.8 6.5 61 57-119 158-225 (226)
105 TIGR02030 BchI-ChlI magnesium 56.1 48 0.001 28.2 6.7 48 73-120 253-307 (337)
106 PRK09087 hypothetical protein; 55.6 95 0.0021 24.5 8.0 59 62-122 161-222 (226)
107 TIGR02442 Cob-chelat-sub cobal 55.2 40 0.00088 30.9 6.5 48 74-121 249-303 (633)
108 PRK08903 DnaA regulatory inact 54.8 74 0.0016 24.4 7.1 57 62-120 165-224 (227)
109 PRK14955 DNA polymerase III su 54.5 39 0.00084 28.9 5.9 62 57-119 185-254 (397)
110 PTZ00361 26 proteosome regulat 54.4 19 0.00042 31.8 4.1 35 88-122 390-424 (438)
111 TIGR00635 ruvB Holliday juncti 54.3 94 0.002 24.8 7.8 67 56-123 157-230 (305)
112 PRK04195 replication factor C 52.6 37 0.00079 29.8 5.6 54 63-119 169-222 (482)
113 CHL00081 chlI Mg-protoporyphyr 52.3 81 0.0018 27.2 7.5 62 59-120 252-320 (350)
114 PRK09111 DNA polymerase III su 52.1 35 0.00075 31.4 5.5 56 63-120 200-255 (598)
115 PF00493 MCM: MCM2/3/5 family 51.5 14 0.00031 30.9 2.8 66 57-122 241-326 (331)
116 cd08780 Death_TRADD Death Doma 51.4 56 0.0012 23.4 5.3 62 63-125 16-81 (90)
117 cd08315 Death_TRAILR_DR4_DR5 D 51.3 43 0.00093 23.5 4.8 66 55-124 14-79 (96)
118 TIGR00368 Mg chelatase-related 50.6 57 0.0012 29.3 6.6 46 75-120 446-497 (499)
119 PF00356 LacI: Bacterial regul 49.8 44 0.00095 20.5 4.1 31 57-89 10-40 (46)
120 PRK06645 DNA polymerase III su 49.8 41 0.00088 30.4 5.5 65 55-120 184-254 (507)
121 PRK13407 bchI magnesium chelat 49.7 73 0.0016 27.1 6.8 62 58-119 235-303 (334)
122 KOG0784 Isocitrate dehydrogena 49.6 8.2 0.00018 33.8 1.1 36 77-112 172-207 (375)
123 PRK08727 hypothetical protein; 48.2 1.1E+02 0.0023 24.1 7.1 66 55-122 159-231 (233)
124 COG1737 RpiR Transcriptional r 47.5 82 0.0018 25.6 6.6 63 57-121 47-126 (281)
125 PRK00149 dnaA chromosomal repl 46.7 74 0.0016 27.5 6.5 57 64-122 290-349 (450)
126 PRK13406 bchD magnesium chelat 46.5 94 0.002 28.6 7.4 54 68-121 189-249 (584)
127 PRK03992 proteasome-activating 46.3 33 0.00072 29.3 4.3 36 87-122 337-372 (389)
128 cd08316 Death_FAS_TNFRSF6 Deat 46.2 97 0.0021 22.0 6.0 64 57-124 17-81 (97)
129 PRK09862 putative ATP-dependen 46.1 92 0.002 28.2 7.2 32 91-122 461-492 (506)
130 TIGR01242 26Sp45 26S proteasom 44.4 36 0.00079 28.4 4.2 42 80-121 317-362 (364)
131 PTZ00454 26S protease regulato 44.4 34 0.00074 29.7 4.1 34 89-122 353-386 (398)
132 PRK14962 DNA polymerase III su 43.9 67 0.0015 28.6 5.9 60 57-121 175-241 (472)
133 KOG1658 DNA polymerase epsilon 42.8 15 0.00033 28.7 1.5 68 56-123 58-126 (162)
134 COG4907 Predicted membrane pro 42.3 16 0.00035 33.5 1.8 26 17-42 563-590 (595)
135 TIGR00362 DnaA chromosomal rep 41.8 1.4E+02 0.003 25.3 7.3 57 63-121 277-336 (405)
136 PRK14961 DNA polymerase III su 41.3 71 0.0015 26.9 5.4 64 55-120 175-242 (363)
137 PRK08084 DNA replication initi 41.2 1.7E+02 0.0038 22.9 7.4 56 63-120 176-234 (235)
138 cd08306 Death_FADD Fas-associa 40.2 85 0.0018 21.4 4.8 62 61-126 14-76 (86)
139 PRK14963 DNA polymerase III su 40.0 69 0.0015 28.8 5.4 62 56-120 173-238 (504)
140 TIGR02031 BchD-ChlD magnesium 38.9 86 0.0019 28.6 5.9 48 74-121 203-257 (589)
141 PRK06620 hypothetical protein; 38.4 1.8E+02 0.0038 22.8 7.0 56 62-119 155-213 (214)
142 PRK14954 DNA polymerase III su 38.1 1E+02 0.0022 28.6 6.3 62 57-119 185-254 (620)
143 TIGR03280 methan_mark_11 putat 38.1 45 0.00097 28.3 3.7 38 94-131 232-269 (292)
144 COG5251 TAF40 Transcription in 38.0 25 0.00054 28.2 2.0 65 57-121 115-180 (199)
145 PRK06893 DNA replication initi 37.5 1.9E+02 0.0042 22.5 7.1 55 63-119 170-227 (229)
146 cd08318 Death_NMPP84 Death dom 36.9 1.3E+02 0.0029 20.3 5.9 60 61-124 19-78 (86)
147 PRK14971 DNA polymerase III su 36.8 86 0.0019 28.9 5.6 62 57-120 179-244 (614)
148 PF09123 DUF1931: Domain of un 36.0 30 0.00064 26.5 2.1 52 64-115 2-53 (138)
149 PF07766 LETM1: LETM1-like pro 35.8 1.8E+02 0.0038 23.9 6.8 71 55-128 168-238 (268)
150 cd06456 M3A_DCP_Oligopeptidase 34.8 1.5E+02 0.0033 25.8 6.6 66 65-130 15-96 (422)
151 PRK14087 dnaA chromosomal repl 34.2 2E+02 0.0043 25.3 7.3 60 63-122 284-348 (450)
152 PRK13531 regulatory ATPase Rav 33.8 2.5E+02 0.0055 25.6 8.0 62 57-118 206-280 (498)
153 PF12909 DUF3832: Protein of u 33.7 91 0.002 22.0 4.2 33 77-109 36-68 (89)
154 CHL00176 ftsH cell division pr 33.7 58 0.0012 30.2 4.0 34 89-122 390-423 (638)
155 PRK11302 DNA-binding transcrip 32.9 2.2E+02 0.0047 22.5 6.8 22 57-78 45-66 (284)
156 TIGR01241 FtsH_fam ATP-depende 32.8 67 0.0015 28.2 4.1 43 80-122 249-295 (495)
157 cd01392 HTH_LacI Helix-turn-he 32.5 1.1E+02 0.0023 17.9 4.0 31 57-89 8-38 (52)
158 PF11705 RNA_pol_3_Rpc31: DNA- 32.5 28 0.0006 27.8 1.6 10 29-38 1-10 (233)
159 PRK14950 DNA polymerase III su 32.3 1.2E+02 0.0027 27.4 5.8 57 63-121 188-244 (585)
160 TIGR01278 DPOR_BchB light-inde 32.1 1E+02 0.0022 27.4 5.2 48 74-122 462-510 (511)
161 PF02042 RWP-RK: RWP-RK domain 31.7 46 0.001 21.3 2.2 20 57-76 26-45 (52)
162 cd08319 Death_RAIDD Death doma 31.6 1.4E+02 0.0031 20.4 4.9 64 62-129 15-81 (83)
163 PRK06305 DNA polymerase III su 31.4 1.2E+02 0.0026 26.6 5.5 61 57-119 179-243 (451)
164 KOG0480 DNA replication licens 30.7 2.4E+02 0.0053 27.1 7.5 82 47-128 545-649 (764)
165 PF02971 FTCD: Formiminotransf 30.6 1.3E+02 0.0028 23.2 4.9 58 62-130 72-136 (145)
166 KOG3902 Histone acetyltransfer 30.3 2E+02 0.0044 25.1 6.4 59 63-121 30-89 (352)
167 PTZ00111 DNA replication licen 30.1 1.8E+02 0.0038 28.7 6.7 36 88-123 770-805 (915)
168 PRK14958 DNA polymerase III su 30.0 1.5E+02 0.0032 26.7 5.8 61 55-120 175-242 (509)
169 TIGR02903 spore_lon_C ATP-depe 29.6 1.5E+02 0.0032 27.3 5.9 67 57-124 352-432 (615)
170 PRK02910 light-independent pro 29.6 1.2E+02 0.0026 27.1 5.2 49 74-123 469-518 (519)
171 PRK14952 DNA polymerase III su 29.2 1.3E+02 0.0028 27.7 5.5 59 57-119 176-241 (584)
172 PF01726 LexA_DNA_bind: LexA D 29.1 95 0.0021 20.2 3.5 28 57-87 23-50 (65)
173 PLN03238 probable histone acet 28.8 1.1E+02 0.0024 26.1 4.6 52 73-124 195-249 (290)
174 PLN03239 histone acetyltransfe 28.2 1.3E+02 0.0028 26.4 5.0 52 73-124 253-310 (351)
175 PRK10733 hflB ATP-dependent me 28.2 85 0.0018 28.9 4.1 34 89-122 359-392 (644)
176 PRK14086 dnaA chromosomal repl 28.1 2.8E+02 0.0061 26.0 7.4 57 63-121 455-514 (617)
177 COG4130 Predicted sugar epimer 28.1 96 0.0021 26.0 4.0 67 56-123 47-128 (272)
178 CHL00206 ycf2 Ycf2; Provisiona 27.7 80 0.0017 33.8 4.1 35 88-122 1843-1877(2281)
179 PF13846 DUF4196: Domain of un 27.6 40 0.00087 25.0 1.5 41 3-54 55-95 (112)
180 PF00725 3HCDH: 3-hydroxyacyl- 27.5 1.3E+02 0.0029 19.9 4.1 36 87-125 4-40 (97)
181 cd08815 Death_TNFRSF25_DR3 Dea 27.3 2.1E+02 0.0046 19.7 6.2 63 55-123 6-68 (77)
182 COG0325 Predicted enzyme with 27.1 1.5E+02 0.0033 24.4 5.0 40 88-128 4-54 (228)
183 COG2344 AT-rich DNA-binding pr 26.9 1E+02 0.0022 25.2 3.9 48 57-107 6-62 (211)
184 PF00531 Death: Death domain; 26.1 1.5E+02 0.0033 18.8 4.0 18 107-124 55-72 (83)
185 PF07261 DnaB_2: Replication i 26.1 1.8E+02 0.0038 18.4 5.5 44 66-109 4-49 (77)
186 COG1239 ChlI Mg-chelatase subu 26.0 1.8E+02 0.004 26.0 5.6 28 94-121 294-321 (423)
187 cd08779 Death_PIDD Death Domai 25.7 2.2E+02 0.0048 19.3 6.2 60 62-124 15-75 (86)
188 PF02459 Adeno_terminal: Adeno 25.7 1.3E+02 0.0029 27.8 4.8 39 85-123 447-485 (548)
189 PRK08451 DNA polymerase III su 24.9 2.2E+02 0.0049 26.0 6.1 60 55-119 173-239 (535)
190 COG3854 SpoIIIAA ncharacterize 24.9 44 0.00095 28.5 1.5 63 58-130 9-75 (308)
191 PRK14959 DNA polymerase III su 24.6 2.1E+02 0.0046 26.7 6.0 61 57-119 177-241 (624)
192 PF13443 HTH_26: Cro/C1-type H 24.6 84 0.0018 19.2 2.5 36 57-93 21-56 (63)
193 PRK14957 DNA polymerase III su 24.2 1.8E+02 0.004 26.5 5.5 60 56-120 176-242 (546)
194 PF12146 Hydrolase_4: Putative 24.2 31 0.00068 23.0 0.4 26 101-130 25-50 (79)
195 PRK14953 DNA polymerase III su 24.1 2.3E+02 0.0049 25.3 5.9 55 63-119 187-241 (486)
196 cd01670 Death Death Domain: a 24.0 2E+02 0.0043 18.2 5.9 60 61-124 11-70 (79)
197 PF06798 PrkA: PrkA serine pro 23.9 2.6E+02 0.0055 23.0 5.8 57 64-122 179-237 (254)
198 smart00354 HTH_LACI helix_turn 23.6 1.8E+02 0.0038 18.6 4.0 32 57-90 11-42 (70)
199 PF07830 PP2C_C: Protein serin 23.6 2.6E+02 0.0056 19.4 5.3 49 71-122 9-57 (81)
200 PRK05896 DNA polymerase III su 23.6 2.5E+02 0.0055 26.2 6.3 60 57-118 177-240 (605)
201 PF02861 Clp_N: Clp amino term 23.4 1.1E+02 0.0023 17.9 2.7 26 98-123 1-26 (53)
202 PF01418 HTH_6: Helix-turn-hel 22.8 1E+02 0.0023 20.2 2.8 21 57-77 45-65 (77)
203 PF06144 DNA_pol3_delta: DNA p 22.7 1.9E+02 0.004 20.8 4.4 39 62-101 132-170 (172)
204 PRK14088 dnaA chromosomal repl 22.5 4.1E+02 0.0089 23.2 7.1 56 63-120 272-330 (440)
205 cd08317 Death_ank Death domain 22.3 2.5E+02 0.0053 18.7 5.6 60 61-124 16-76 (84)
206 TIGR02366 DHAK_reg probable di 22.2 1.3E+02 0.0027 21.8 3.4 20 57-76 20-39 (176)
207 cd07064 AlkD_like_1 A new stru 22.1 1.6E+02 0.0034 23.1 4.1 61 55-117 20-84 (208)
208 COG4463 CtsR Transcriptional r 21.8 48 0.001 25.7 1.1 39 83-121 4-48 (153)
209 PRK07764 DNA polymerase III su 21.5 2.2E+02 0.0049 27.4 5.7 62 57-119 178-243 (824)
210 PLN03025 replication factor C 21.4 2.4E+02 0.0052 23.0 5.3 52 63-117 167-218 (319)
211 PF02978 SRP_SPB: Signal pepti 21.4 1.3E+02 0.0029 21.3 3.3 30 55-90 68-97 (104)
212 PRK06647 DNA polymerase III su 21.3 2.8E+02 0.006 25.3 6.0 58 57-119 177-241 (563)
213 PRK08691 DNA polymerase III su 21.2 2.6E+02 0.0055 26.8 5.9 61 57-122 177-244 (709)
214 PTZ00124 adenosine deaminase; 20.8 1.7E+02 0.0038 25.1 4.4 17 57-73 47-63 (362)
215 PF13338 DUF4095: Domain of un 20.6 37 0.0008 23.1 0.2 25 57-81 1-25 (124)
216 PRK11557 putative DNA-binding 20.4 3.9E+02 0.0084 21.1 6.1 22 57-78 41-62 (278)
217 CHL00076 chlB photochlorophyll 20.4 2.5E+02 0.0053 25.2 5.4 49 74-123 463-512 (513)
218 PRK05563 DNA polymerase III su 20.4 2.9E+02 0.0063 25.1 5.9 58 57-119 177-241 (559)
219 PRK12422 chromosomal replicati 20.3 5.1E+02 0.011 22.8 7.3 57 63-121 280-342 (445)
220 PRK06911 rpsN 30S ribosomal pr 20.1 1.2E+02 0.0025 21.7 2.8 37 18-70 53-90 (100)
No 1
>PLN00035 histone H4; Provisional
Probab=100.00 E-value=1.1e-45 Score=266.78 Aligned_cols=103 Identities=100% Similarity=1.472 Sum_probs=102.0
Q ss_pred ccCCCCCCccCCCCCCccccccccccccccchHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCc
Q 047769 29 MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRK 108 (131)
Q Consensus 29 m~g~gkggkg~gk~g~kR~rKvlrd~i~gIpk~aIrRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RK 108 (131)
|+|+||||+|+|++|+|||+|+++|+|++||+++|+||||++|++|||++||+++++++++|+++|++||++||+||+||
T Consensus 1 m~~~~k~~~g~g~~g~kr~~k~~~d~i~~ipk~~IrRLARr~GvkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RK 80 (103)
T PLN00035 1 MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRK 80 (103)
T ss_pred CCCCCCCCCCCCCCcchHHHHHHHhhhccCCHHHHHHHHHHcCcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eecHHHHHHHHHHcCCcccccCC
Q 047769 109 TVTAMDVVYALKRQGRTLYGFGG 131 (131)
Q Consensus 109 TVt~~DV~~ALkr~G~~lYGF~~ 131 (131)
||+++||++||+++|+|||||++
T Consensus 81 TV~~~DV~~Alkr~g~~lyGf~~ 103 (103)
T PLN00035 81 TVTAMDVVYALKRQGRTLYGFGG 103 (103)
T ss_pred cCcHHHHHHHHHHcCCcCCCCCC
Confidence 99999999999999999999985
No 2
>PTZ00015 histone H4; Provisional
Probab=100.00 E-value=4e-43 Score=253.11 Aligned_cols=101 Identities=84% Similarity=1.223 Sum_probs=99.7
Q ss_pred ccCCCCCCccCC-CCCCccccccccccccccchHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCC
Q 047769 29 MSGRGKGGKGLG-KGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARR 107 (131)
Q Consensus 29 m~g~gkggkg~g-k~g~kR~rKvlrd~i~gIpk~aIrRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~R 107 (131)
|+|+||||+|+| +||+|||||+++|++++||+|+|+|||+++|++|||++||++++++++.|+++|++||++||+||+|
T Consensus 1 ~~~~~k~~~~~~~~g~~kr~rk~~r~~i~gI~k~~IrRLarr~GvkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~R 80 (102)
T PTZ00015 1 MSGMGKGKKSLGAKGGQKRQKKVLRDNIRGITKGAIRRLARRGGVKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARR 80 (102)
T ss_pred CCCcccCCCccccccchhhHHHHHhhcccCCCHHHHHHHHHHcCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 789999999999 8899999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ceecHHHHHHHHHHcCCccccc
Q 047769 108 KTVTAMDVVYALKRQGRTLYGF 129 (131)
Q Consensus 108 KTVt~~DV~~ALkr~G~~lYGF 129 (131)
||||++||++||++||+|||||
T Consensus 81 KTVt~~DV~~AlKr~g~~~ygf 102 (102)
T PTZ00015 81 KTVTAMDVVYALKRQGRTLYGF 102 (102)
T ss_pred CcccHHHHHHHHHhcCCCCCCC
Confidence 9999999999999999999999
No 3
>KOG3467 consensus Histone H4 [Chromatin structure and dynamics]
Probab=100.00 E-value=2.9e-43 Score=248.84 Aligned_cols=103 Identities=98% Similarity=1.462 Sum_probs=102.0
Q ss_pred ccCCCCCCccCCCCCCccccccccccccccchHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCc
Q 047769 29 MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRK 108 (131)
Q Consensus 29 m~g~gkggkg~gk~g~kR~rKvlrd~i~gIpk~aIrRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RK 108 (131)
|+++|+||||+||||+|||||+++|+|++|+||+|+||||++||+||+..+|+|++.+++.|+++++.+|++|++||+||
T Consensus 1 Ms~r~~g~KG~~KG~AKrHRK~LsDnIqgitKpaIRRlARr~GVkRi~G~~yeE~~~~~k~fl~n~i~~A~~yt~HAKRK 80 (103)
T KOG3467|consen 1 MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRK 80 (103)
T ss_pred CCCcCccccccccchHHHHHHHHHhhccccchHHHHHHHHhcCcchhchhhHHHHHHHHHHHHHHHHHHHHHHHhhhhhc
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eecHHHHHHHHHHcCCcccccCC
Q 047769 109 TVTAMDVVYALKRQGRTLYGFGG 131 (131)
Q Consensus 109 TVt~~DV~~ALkr~G~~lYGF~~ 131 (131)
|||++||+++|+|||++||||+|
T Consensus 81 TvT~~dvv~~LKR~G~~~~g~~~ 103 (103)
T KOG3467|consen 81 TVTAMDVVYALKRQGRTLYGFGG 103 (103)
T ss_pred eeeHHHHHHHHHHcCceeeccCC
Confidence 99999999999999999999986
No 4
>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=100.00 E-value=4.9e-38 Score=220.16 Aligned_cols=85 Identities=87% Similarity=1.288 Sum_probs=84.5
Q ss_pred ccccccccccccccchHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHcCC
Q 047769 45 KRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGR 124 (131)
Q Consensus 45 kR~rKvlrd~i~gIpk~aIrRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~G~ 124 (131)
|||||+++|+|++||+|+|+|||+++|++|||+++|+++++++++|+++|++||++||+||+|||||++||++||++||+
T Consensus 1 kr~r~~~~~~~~gi~k~~I~RLarr~GvkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~alkr~g~ 80 (85)
T cd00076 1 KRHRKVLRDNIKGITKPAIRRLARRGGVKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKRQGR 80 (85)
T ss_pred CchhHHHHHhhccCCHHHHHHHHHHcCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHCCC
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccc
Q 047769 125 TLYGF 129 (131)
Q Consensus 125 ~lYGF 129 (131)
|||||
T Consensus 81 ~~ygf 85 (85)
T cd00076 81 TLYGY 85 (85)
T ss_pred CccCC
Confidence 99999
No 5
>smart00417 H4 Histone H4.
Probab=99.97 E-value=3.3e-31 Score=181.58 Aligned_cols=74 Identities=92% Similarity=1.314 Sum_probs=72.5
Q ss_pred ccccccccccccccchHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHH
Q 047769 45 KRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYA 118 (131)
Q Consensus 45 kR~rKvlrd~i~gIpk~aIrRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~A 118 (131)
+||+|+++|+|+|||+|+|+|||+++|++|||+++|++++++++.|+++|++||++||+||+||||+++||++|
T Consensus 1 ~r~~~~~~d~i~gI~k~~IrRLaRr~GvkRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~~a 74 (74)
T smart00417 1 RRHKKVLRDNIQGITKPAIRRLARRGGVKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVYA 74 (74)
T ss_pred CchhHHHHhhhcCCCHHHHHHHHHHcCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHheeC
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999875
No 6
>PLN00163 histone H4; Provisional
Probab=99.91 E-value=1.5e-25 Score=147.12 Aligned_cols=59 Identities=98% Similarity=1.458 Sum_probs=57.3
Q ss_pred ccCCCCCCccCCCCCCccccccccccccccchHHHHHHHHhcCccccchHHHHHHHHHH
Q 047769 29 MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVL 87 (131)
Q Consensus 29 m~g~gkggkg~gk~g~kR~rKvlrd~i~gIpk~aIrRLArr~GvkRIS~~ay~el~~vl 87 (131)
|+|+||||+|+||+|+|||+|+++|+|++||+|+|+||||++||+|||..+|+|++++|
T Consensus 1 m~g~gkggkglGkggaKRhrk~lrd~i~gItKpaIrRLARRgGVKRIs~~iY~e~R~vl 59 (59)
T PLN00163 1 MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRTVL 59 (59)
T ss_pred CCCCCCCCCccCCccchhHHHHHHHhhcccchHHHHHHHHhcCceeecchhhHhHhccC
Confidence 88999999999999999999999999999999999999999999999999999999864
No 7
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=99.90 E-value=4.8e-24 Score=151.20 Aligned_cols=90 Identities=41% Similarity=0.602 Sum_probs=86.5
Q ss_pred CCCCCccccccccccccccchHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHH
Q 047769 40 GKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYAL 119 (131)
Q Consensus 40 gk~g~kR~rKvlrd~i~gIpk~aIrRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~AL 119 (131)
|..|.+.+++.+++....||+++|+||+|+.|.+|||++|.++++++++.|+++|+++|+.||.|||||||+++||.+|+
T Consensus 2 ~~~~~~~~r~~~~~~~~~Lp~apv~Ri~r~~~~~Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~DI~la~ 81 (91)
T COG2036 2 GAVGLKEIRRYQRSTDLLLPKAPVRRILRKAGAERVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLAL 81 (91)
T ss_pred CcchHHHHHhhhhhhhhhcCchHHHHHHHHHhHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHH
Confidence 55678889999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHcCCccccc
Q 047769 120 KRQGRTLYGF 129 (131)
Q Consensus 120 kr~G~~lYGF 129 (131)
+.+|..+|++
T Consensus 82 ~~~~~~~~~~ 91 (91)
T COG2036 82 KRLGRRIYGE 91 (91)
T ss_pred HHhccccccC
Confidence 9999998875
No 8
>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=99.87 E-value=2.5e-22 Score=134.09 Aligned_cols=64 Identities=20% Similarity=0.345 Sum_probs=62.5
Q ss_pred ccchHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHH
Q 047769 57 GITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALK 120 (131)
Q Consensus 57 gIpk~aIrRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALk 120 (131)
.+|+++|+|||+++|++|||++++++|++.+++|+++|+++|++|++|++|||||++||.+||+
T Consensus 2 ~~p~~~i~ria~~~Gi~ris~~a~~~l~~~~e~rl~~i~~~A~k~~~hakRktlt~~DI~~Alk 65 (65)
T smart00803 2 WLPKETIKDVAESLGIGNLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSALR 65 (65)
T ss_pred CCCHHHHHHHHHHCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCeecHHHHHHHhC
Confidence 4899999999999999999999999999999999999999999999999999999999999985
No 9
>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=99.58 E-value=5.5e-15 Score=124.34 Aligned_cols=72 Identities=25% Similarity=0.450 Sum_probs=69.6
Q ss_pred chHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHcC-CcccccC
Q 047769 59 TKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQG-RTLYGFG 130 (131)
Q Consensus 59 pk~aIrRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~G-~~lYGF~ 130 (131)
|+.+|+-+|++.|+.++|+++..+|.+.+++++++|+++|++||+|++|||++++||..||+..+ +|+|||.
T Consensus 1 ~~~~i~~ia~~~Gi~~~~~~a~~~La~~~e~~~~~i~~~A~k~~~hskR~~l~~~Di~~Al~~~n~eplyG~~ 73 (343)
T cd08050 1 PQESIKLIAESLGIDSLSDEVAQLLAEDVEYRLREIIQEAAKFMRHSKRRKLTTSDVNHALRLRNVEPLYGFS 73 (343)
T ss_pred ChhHHHHHHHHcCCCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHHhCCCcccCCC
Confidence 46789999999999999999999999999999999999999999999999999999999999988 9999996
No 10
>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=99.55 E-value=3.1e-14 Score=95.69 Aligned_cols=64 Identities=19% Similarity=0.351 Sum_probs=53.7
Q ss_pred ccchHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHH
Q 047769 57 GITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALK 120 (131)
Q Consensus 57 gIpk~aIrRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALk 120 (131)
-+|+.+|+.+|++.|+..+++++...|.+.+++++.+|+++|.+|++|++|+++|++||..|||
T Consensus 3 ~~~~esvk~iAes~Gi~~l~de~a~~La~dveyrlreiiq~a~kfm~hskR~~Lt~~Di~~ALr 66 (66)
T PF02969_consen 3 VFSQESVKDIAESLGISNLSDEAAKALAEDVEYRLREIIQEALKFMRHSKRTKLTTDDINSALR 66 (66)
T ss_dssp ---HHHHHHHHHHTT---B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH-
T ss_pred cCCHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhC
Confidence 4789999999999999999999999999999999999999999999999999999999999996
No 11
>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=99.54 E-value=2.7e-14 Score=104.85 Aligned_cols=68 Identities=22% Similarity=0.351 Sum_probs=63.4
Q ss_pred HHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHcCCcccccC
Q 047769 61 PAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTLYGFG 130 (131)
Q Consensus 61 ~aIrRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~G~~lYGF~ 130 (131)
..|.+|+++.|+.+++++|..+|.++++.|.++|++||..||+||+|+||+++||.+|++..+. |.|.
T Consensus 5 ~~v~~iLk~~Gv~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r~~--~~f~ 72 (117)
T cd07979 5 RVIAAILKSMGITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRVD--YSFT 72 (117)
T ss_pred HHHHHHHHHCCCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhc--cCCC
Confidence 3589999999999999999999999999999999999999999999999999999999988665 6664
No 12
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=99.50 E-value=9.5e-14 Score=94.55 Aligned_cols=70 Identities=23% Similarity=0.333 Sum_probs=66.0
Q ss_pred cccchHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHcCCc
Q 047769 56 QGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRT 125 (131)
Q Consensus 56 ~gIpk~aIrRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~G~~ 125 (131)
+.+-+.+|.+|++..|++++++++.+.+.++++.|+.++++.+..||+|+||++++..||.+||+.+|..
T Consensus 5 ~~ll~~~Vaqil~~~Gf~~~~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~~~Dv~~Al~~~gi~ 74 (77)
T smart00576 5 FALLRIAVAQILESAGFDSFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPNLGDVVLALENLGIS 74 (77)
T ss_pred HHHHHHHHHHHHHHcCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCcc
Confidence 3456789999999999999999999999999999999999999999999999999999999999998854
No 13
>PF15511 CENP-T: Centromere kinetochore component CENP-T; PDB: 3B0D_T 3B0C_T 3VH5_T 3VH6_T.
Probab=99.38 E-value=9.1e-13 Score=113.69 Aligned_cols=69 Identities=26% Similarity=0.349 Sum_probs=48.2
Q ss_pred cccccccccccc--cchHHHHHHHHhc------CccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHH
Q 047769 46 RHRKVLRDNIQG--ITKPAIRRLARRG------GVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMD 114 (131)
Q Consensus 46 R~rKvlrd~i~g--Ipk~aIrRLArr~------GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~D 114 (131)
+.+|+.+..|.+ +|...||+||.+. +-.+||+++|++|.++++|||+|++.|+.+||+|||||||+.+|
T Consensus 338 k~~k~Skhgi~~P~lP~~~vK~la~~~ak~s~~sK~kiskdal~aleqasdwfFeQl~dDL~aYA~HAgRKTIdesD 414 (414)
T PF15511_consen 338 KQKKVSKHGIPYPSLPPGVVKKLAQHFAKSSGGSKMKISKDALEALEQASDWFFEQLGDDLEAYAKHAGRKTIDESD 414 (414)
T ss_dssp --------------S-HHHHHHHHHHHH-------S-B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHH
T ss_pred cccCCCCCCCCCCCCCccHHHHHHHHHHHhhcccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCCCC
Confidence 567788888885 9999999999776 34899999999999999999999999999999999999999988
No 14
>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=99.36 E-value=3.4e-12 Score=85.00 Aligned_cols=66 Identities=32% Similarity=0.394 Sum_probs=62.3
Q ss_pred cccchHHHHHHHHhcCc-----cccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHH
Q 047769 56 QGITKPAIRRLARRGGV-----KRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKR 121 (131)
Q Consensus 56 ~gIpk~aIrRLArr~Gv-----kRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr 121 (131)
..||+.+|.|+++..+. .|||.++++.|..++|.|+.+|+++|..+|.|++|+||++.||..|++.
T Consensus 4 ~~~~~~~~~r~~r~i~~~~~~~~ris~~a~~~L~~~~E~~~~~il~~A~~~a~~~kR~tI~~~DI~~A~r~ 74 (75)
T PF00125_consen 4 RLIPKFPFSRLLREIGEEILSKYRISSEALVALQSVLEYLLVEILEEAGNLARHAKRKTITPRDIQLAVRI 74 (75)
T ss_dssp HSSSHHHHHHHHHHHHHTTSSSSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTBSEEGHHHHHHHHHH
T ss_pred cccCceEEeeeeehhhcccccccccccccchhhhhhhhhhhhhhhhHHHHHHhhcCCcEecHHHHHHHHhc
Confidence 36899999999999877 4999999999999999999999999999999999999999999999974
No 15
>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [Transcription]
Probab=99.34 E-value=3.4e-12 Score=98.63 Aligned_cols=82 Identities=20% Similarity=0.270 Sum_probs=75.6
Q ss_pred ccccccccccccchHHHHHHHHhcC--ccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHcCC
Q 047769 47 HRKVLRDNIQGITKPAIRRLARRGG--VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGR 124 (131)
Q Consensus 47 ~rKvlrd~i~gIpk~aIrRLArr~G--vkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~G~ 124 (131)
..-.+++..+.+|.+.|-||+++.= -..||+||.+.+.+++.+|+..|..+|..-|+..+|||||.+||++||..+|+
T Consensus 22 ~~~~~reqDr~LPIANV~RIMK~~lP~naKIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIngdDllwAm~tLGF 101 (168)
T KOG0869|consen 22 SSLSLREQDRFLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASEKCQREKRKTINGDDLLWAMSTLGF 101 (168)
T ss_pred cccccchhhhhccHHHHHHHHHhcCCcccccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCcccHHHHHHHHHHcCc
Confidence 3456799999999999999999974 36699999999999999999999999999999999999999999999999998
Q ss_pred cccc
Q 047769 125 TLYG 128 (131)
Q Consensus 125 ~lYG 128 (131)
..|.
T Consensus 102 e~Y~ 105 (168)
T KOG0869|consen 102 ENYA 105 (168)
T ss_pred HhHH
Confidence 8773
No 16
>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=99.33 E-value=8.3e-12 Score=84.36 Aligned_cols=65 Identities=22% Similarity=0.322 Sum_probs=59.7
Q ss_pred cchHHHHHHHHhc-CccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHc
Q 047769 58 ITKPAIRRLARRG-GVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 122 (131)
Q Consensus 58 Ipk~aIrRLArr~-GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~ 122 (131)
+++..+..|.+.. +-.|++++|.++|.++++.|+.+|+.+|+.+|.|+||+||++.||.++|+++
T Consensus 2 ~~k~~l~~lv~~id~~~~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~~~tv~~~Di~l~l~r~ 67 (72)
T cd07981 2 LTKRKLQELLKEIDPREQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQLHLERN 67 (72)
T ss_pred CcHHHHHHHHHhhCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHh
Confidence 5677788888776 3489999999999999999999999999999999999999999999999986
No 17
>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=99.30 E-value=2.4e-11 Score=79.60 Aligned_cols=63 Identities=22% Similarity=0.342 Sum_probs=57.8
Q ss_pred ccchHHHHHHHHhc-CccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHH
Q 047769 57 GITKPAIRRLARRG-GVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYAL 119 (131)
Q Consensus 57 gIpk~aIrRLArr~-GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~AL 119 (131)
.||.+.|+||++.. ++.+||.++.+.+..+.+.|++.++.+|...|++.+||||+.+||..||
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 SLPLARVKRIMKSDPDVMRVSKEAVEAIAKAAEEFIQYLAKEANEIAQRDKRKTITYEDVAKAV 65 (65)
T ss_dssp SS-HHHHHHHHHHTSTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEE-HHHHHHHH
T ss_pred CCChHHHHHHhccCCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHC
Confidence 58999999999998 8899999999999999999999999999999999999999999999986
No 18
>KOG2549 consensus Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=99.29 E-value=1e-11 Score=110.64 Aligned_cols=74 Identities=24% Similarity=0.425 Sum_probs=71.1
Q ss_pred cchHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHcC-CcccccCC
Q 047769 58 ITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQG-RTLYGFGG 131 (131)
Q Consensus 58 Ipk~aIrRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~G-~~lYGF~~ 131 (131)
.|+.+++-+|++.|++.+++++...|.+.+++.+++|++||++|+.|++|.++|++||.+||+..+ +|+|||++
T Consensus 12 s~~Es~k~vAEslGi~nl~deaa~~La~dv~yrikEI~Q~aaKfm~hskR~kLtv~DV~~ALr~~nVep~yg~~s 86 (576)
T KOG2549|consen 12 SPKESVKVVAESLGITNLNDEAALLLAEDVEYRIKEIVQDAAKFMVHSKRTKLTVDDVDYALRSLNVEPLYGFGA 86 (576)
T ss_pred CcHHHHHHHHHHhCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcCcHHHHHHHHhhcccccccCccc
Confidence 458999999999999999999999999999999999999999999999999999999999999988 99999974
No 19
>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=99.25 E-value=2.2e-11 Score=103.79 Aligned_cols=75 Identities=23% Similarity=0.368 Sum_probs=72.3
Q ss_pred ccchHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHcC-CcccccCC
Q 047769 57 GITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQG-RTLYGFGG 131 (131)
Q Consensus 57 gIpk~aIrRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~G-~~lYGF~~ 131 (131)
-+++.+|+.+|++.|+..|.+|+..++...+|+++.+|+++|++|+.|++|..+|.+||-+||+..+ +|||||++
T Consensus 5 ~ws~et~KdvAeslGi~Ni~Dd~l~alamDlEYRI~ev~qea~KFmvhSKRtvLt~dDis~ALr~lNVePLyGyd~ 80 (450)
T COG5095 5 LWSKETLKDVAESLGISNIDDDALRALAMDLEYRIKEVCQEASKFMVHSKRTVLTIDDISYALRSLNVEPLYGYDP 80 (450)
T ss_pred eecHHHHHHHHHHcCCcccccHHHHHHHHhHHHHHHHHHHHHHHHhhcccceeeeHHhHHHHHHhcCCCcccCCCC
Confidence 4678999999999999999999999999999999999999999999999999999999999999988 99999985
No 20
>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=99.11 E-value=6.2e-10 Score=75.23 Aligned_cols=68 Identities=24% Similarity=0.374 Sum_probs=64.3
Q ss_pred ccchHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHcCC
Q 047769 57 GITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGR 124 (131)
Q Consensus 57 gIpk~aIrRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~G~ 124 (131)
.+-+..|..++++.|+..+++.+.+.|.+++..|++++.+.+..||+|++|...+..||..||+..|.
T Consensus 6 ~~l~~~va~il~~~GF~~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~~~gi 73 (77)
T PF07524_consen 6 SLLRRSVAQILKHAGFDSASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPNLQDVEQALEEMGI 73 (77)
T ss_pred HHHHHHHHHHHHHcCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCC
Confidence 44567899999999999999999999999999999999999999999999999999999999999885
No 21
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=99.09 E-value=4.7e-10 Score=77.23 Aligned_cols=61 Identities=20% Similarity=0.294 Sum_probs=51.7
Q ss_pred HHHHHHHhcCc---cccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHc
Q 047769 62 AIRRLARRGGV---KRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 122 (131)
Q Consensus 62 aIrRLArr~Gv---kRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~ 122 (131)
+|.+|++..+. ..+|+.+..+|.+.+..++++++.|...||+||||+||+.+||.+..+++
T Consensus 10 ~v~ki~ee~~~~~~~~~s~~~i~al~ELv~~q~~~~a~DLe~FAkHA~R~tI~~dDV~Ll~Rrn 73 (76)
T PF15630_consen 10 TVGKIVEEEAKEKGVEVSPQFIAALTELVYKQLENLAKDLEAFAKHAGRSTINMDDVKLLARRN 73 (76)
T ss_dssp HHHHHHHHCCCCTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHTTT-
T ss_pred HHHHHHHHHHhccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHHHhhcC
Confidence 57788888753 34999999999999999999999999999999999999999999998764
No 22
>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=99.03 E-value=1.8e-09 Score=79.45 Aligned_cols=65 Identities=15% Similarity=0.164 Sum_probs=61.8
Q ss_pred ccchHHHHHHHHh-cCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHH
Q 047769 57 GITKPAIRRLARR-GGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKR 121 (131)
Q Consensus 57 gIpk~aIrRLArr-~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr 121 (131)
-||...|.|+++. .+..|||+++...|..+||++..+|++-|..+|+|++|++|+++||.+|++.
T Consensus 20 ~fPV~ri~R~Lk~~~~a~RVs~~A~VyLaAvLEYL~aEIlelA~n~ak~~k~krItp~hi~lAi~n 85 (115)
T cd00074 20 QFPVGRIHRYLKKGRYAERVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKKRITPRHLQLAVRN 85 (115)
T ss_pred cCcHHHHHHHHHcCccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEcHHHHHHHHhc
Confidence 4899999999997 6889999999999999999999999999999999999999999999999964
No 23
>smart00428 H3 Histone H3.
Probab=98.94 E-value=2.4e-09 Score=77.83 Aligned_cols=69 Identities=22% Similarity=0.261 Sum_probs=59.6
Q ss_pred ccchHHHHHHHHhcC-------ccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHcCCc
Q 047769 57 GITKPAIRRLARRGG-------VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRT 125 (131)
Q Consensus 57 gIpk~aIrRLArr~G-------vkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~G~~ 125 (131)
-||+.+..||.|... --|++++|..+|.+++|.|+.++.+||..+|.||+|+||++.|+.+|.+-.|..
T Consensus 29 LI~k~pF~RLVREI~~~~~~~~~~R~~~~Al~aLQeasE~ylv~lfeda~~~a~HAkRvTl~~kDi~La~rir~~~ 104 (105)
T smart00428 29 LIRKAPFQRLVREIAQKFTTGVDLRFQSSAIMALQEAAEAYLVGLFEDTNLLAIHAKRVTIMPKDIQLARRIRGER 104 (105)
T ss_pred ccccccHHHHHHHHHHHcCCCCCceeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccCcHhhHHHHHHHhccC
Confidence 588888777665432 249999999999999999999999999999999999999999999998766543
No 24
>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=98.91 E-value=6.8e-09 Score=77.79 Aligned_cols=66 Identities=24% Similarity=0.367 Sum_probs=53.7
Q ss_pred ccchHH--HHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHc
Q 047769 57 GITKPA--IRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 122 (131)
Q Consensus 57 gIpk~a--IrRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~ 122 (131)
.+|+.+ |..|++..||....+.+...|.+++..|..+|+.||..|++||+|++|+++||.+|++.+
T Consensus 10 ~~PrDa~~i~~iL~~~Gv~~yeprVv~qLLEfayRYt~~vL~DA~~ya~hA~~~~i~~~DVrLAi~~r 77 (129)
T PF02291_consen 10 SLPRDARVIHLILKSMGVTEYEPRVVNQLLEFAYRYTSDVLEDAQVYADHAGRSTIDADDVRLAIQSR 77 (129)
T ss_dssp ---HHHHHHHHHHHHTT---B-THHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHHHHT
T ss_pred cCChHHHHHHHHHHHcCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHH
Confidence 456654 889999999999999999999999999999999999999999999999999999999743
No 25
>KOG3334 consensus Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=98.71 E-value=9.9e-08 Score=72.95 Aligned_cols=67 Identities=24% Similarity=0.368 Sum_probs=62.0
Q ss_pred ccchHH--HHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHcC
Q 047769 57 GITKPA--IRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQG 123 (131)
Q Consensus 57 gIpk~a--IrRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~G 123 (131)
+-|+.+ |..|++..||+-.++.+...|.++...|...|+.||..|++||++.||+++||.+|+..+.
T Consensus 11 ~~pkDa~~i~~iL~s~GI~eyEprVi~qlLefa~rYtt~vL~DA~vys~HA~ka~i~~eDVrlA~~~~~ 79 (148)
T KOG3334|consen 11 GVPKDARVIASILKSLGIQEYEPRVINQLLEFAYRYTTTVLDDAKVYSSHAKKATIDAEDVRLAIQMRV 79 (148)
T ss_pred CCcHHHHHHHHHHHHcCccccChHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHh
Confidence 455655 8899999999999999999999999999999999999999999999999999999998654
No 26
>PLN00161 histone H3; Provisional
Probab=98.28 E-value=7.1e-06 Score=62.18 Aligned_cols=69 Identities=23% Similarity=0.200 Sum_probs=59.2
Q ss_pred ccchHHHHHHHHhc------CccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHcCCc
Q 047769 57 GITKPAIRRLARRG------GVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRT 125 (131)
Q Consensus 57 gIpk~aIrRLArr~------GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~G~~ 125 (131)
-||+.+..||.|.. .--|+..++..+|.++.|.||-++.+|+..+|-||+|-||...|+.++.+-.|..
T Consensus 55 LIpklPF~RLVREI~~~~~~~~~Rfq~~Al~ALQEAsEayLV~lFeda~lcaiHAkRVTlm~kDm~La~rirg~~ 129 (135)
T PLN00161 55 LIRKLPFARLVREISNEMLREPFRWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMPKDMQLARRIRGPI 129 (135)
T ss_pred ccccccHHHHHHHHHHhcCCCCcEeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccchhhHHHHHHhcccc
Confidence 48888866666542 2368999999999999999999999999999999999999999999998655543
No 27
>PLN00160 histone H3; Provisional
Probab=98.25 E-value=3.5e-06 Score=60.64 Aligned_cols=68 Identities=21% Similarity=0.224 Sum_probs=58.6
Q ss_pred ccchHHHHHHHHhc------CccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHcCC
Q 047769 57 GITKPAIRRLARRG------GVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGR 124 (131)
Q Consensus 57 gIpk~aIrRLArr~------GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~G~ 124 (131)
-||+.+..||.|.. ..-|+..+|..+|.++.|.|+-++.+|+..+|-||+|.|+...|+.++.+-.|.
T Consensus 21 LI~k~pF~RLVREI~~~~~~~~~Rfq~~Al~ALQeAsEayLv~lfed~~lca~HakRVTl~~kD~~L~~rirg~ 94 (97)
T PLN00160 21 LIRRLPFARLVREIQMEMSREAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTIMPKDMQLARRIRGQ 94 (97)
T ss_pred hhccccHHHHHHHHHHHcCCCCcEeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcccccchhhHHHHHHhhcc
Confidence 57888866665543 236899999999999999999999999999999999999999999999865553
No 28
>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription]
Probab=98.25 E-value=5.5e-06 Score=64.77 Aligned_cols=69 Identities=20% Similarity=0.179 Sum_probs=64.1
Q ss_pred ccchHHHHHHHHhcCccc---cchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHcCCc
Q 047769 57 GITKPAIRRLARRGGVKR---ISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRT 125 (131)
Q Consensus 57 gIpk~aIrRLArr~GvkR---IS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~G~~ 125 (131)
.+|.+.|.||++..=-+. ||.+|..++......|+-.+.--|-.+|...+|||++++||..||..++++
T Consensus 10 ~lP~AiI~rlvke~l~E~~vsisKeA~~Ai~raAtVFv~~Lts~s~e~A~~q~rKt~sadDVl~aL~Eiefs 81 (172)
T KOG0870|consen 10 NLPNAIITRLVKEVLPESNVSISKEARLAIARAATVFVIFLTSVSNEIAKDQKRKTISADDVLKALDEIEFS 81 (172)
T ss_pred hccHHHHHHHHHHhCccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCcccHHHHHHHHHHhchH
Confidence 589999999999876544 999999999999999999999999999999999999999999999998865
No 29
>PLN00121 histone H3; Provisional
Probab=98.25 E-value=2.1e-06 Score=65.08 Aligned_cols=68 Identities=22% Similarity=0.244 Sum_probs=58.8
Q ss_pred ccchHHHHHHHHhcC-----ccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHcCC
Q 047769 57 GITKPAIRRLARRGG-----VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGR 124 (131)
Q Consensus 57 gIpk~aIrRLArr~G-----vkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~G~ 124 (131)
-||+.+..||.|..- --|+..+|..+|.++.|.||-++.+|+..+|-||+|-||...|+.++.+-.|.
T Consensus 62 LI~k~pF~RLVREI~~~~~~~~Rf~~~Al~ALQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~rirg~ 134 (136)
T PLN00121 62 LIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 134 (136)
T ss_pred ccccccHHHHHHHHHHHhCccceeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcceecchhhHHHHHHhccc
Confidence 488888766665432 24999999999999999999999999999999999999999999999865554
No 30
>PTZ00018 histone H3; Provisional
Probab=98.20 E-value=3e-06 Score=64.22 Aligned_cols=68 Identities=22% Similarity=0.244 Sum_probs=58.8
Q ss_pred ccchHHHHHHHHhcC-----ccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHcCC
Q 047769 57 GITKPAIRRLARRGG-----VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGR 124 (131)
Q Consensus 57 gIpk~aIrRLArr~G-----vkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~G~ 124 (131)
-||+.+..||.|..- --|+..++..+|.++.|.||-++.+|+..+|-||+|.||...|+.++.+-.|.
T Consensus 62 LI~k~pF~RLVREI~~~~~~~~rf~~~al~aLQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~rirg~ 134 (136)
T PTZ00018 62 LIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 134 (136)
T ss_pred ccccccHHHHHHHHHHHcCCcceeeHHHHHHHHHHHHHHHHHHhhhhHHHHHhhcceecchhhHHHHHHhccc
Confidence 488888777665431 24999999999999999999999999999999999999999999999865553
No 31
>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=98.19 E-value=1.4e-05 Score=53.87 Aligned_cols=64 Identities=19% Similarity=0.277 Sum_probs=51.8
Q ss_pred chHHHHHHHHhcCc-cccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHc
Q 047769 59 TKPAIRRLARRGGV-KRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 122 (131)
Q Consensus 59 pk~aIrRLArr~Gv-kRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~ 122 (131)
+|..+..|.+.... ..+.+++.+.|.++.+.|+++|+..|...|.|-+-.|++..||.+.|+|+
T Consensus 1 ~K~~l~~Lv~~iDp~~~ld~~vee~Ll~laddFv~~v~~~ac~lAKhR~s~tle~~Dv~~~Ler~ 65 (68)
T PF03847_consen 1 SKRKLQELVKQIDPNEKLDPDVEELLLELADDFVDDVVSFACRLAKHRKSSTLEVKDVQLHLERN 65 (68)
T ss_dssp -HHHHHHHHHCC-SS----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHHHH
T ss_pred ChHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCHHHHHHHHHhh
Confidence 46667778887764 77999999999999999999999999999999999999999999999986
No 32
>KOG2389 consensus Predicted bromodomain transcription factor [Transcription]
Probab=98.18 E-value=3.6e-06 Score=72.01 Aligned_cols=75 Identities=20% Similarity=0.313 Sum_probs=70.1
Q ss_pred cccccccchHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHcCCcc
Q 047769 52 RDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTL 126 (131)
Q Consensus 52 rd~i~gIpk~aIrRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~G~~l 126 (131)
.++...+.+.+|.+|+.+.|.......+.+.|.+++..|+.++.+.|..|+++++|...+..||+.||+.++-.+
T Consensus 24 ~~ya~sla~~avaQIcqslg~~~~~~sale~Ltd~~~qyvQ~lgk~a~~~~n~anR~epnl~Div~Al~dls~s~ 98 (353)
T KOG2389|consen 24 AEYAFSLARVAVAQICQSLGYSSTQNSALETLTDVLQQYVQNLGKTAHRYSNLANRTEPNLFDIVLALQDLSASL 98 (353)
T ss_pred HHHHHHHHHHHHHHHHHhcCCcccccHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCccHHHHHHHHHHhhhhc
Confidence 456668999999999999999999999999999999999999999999999999999999999999999987553
No 33
>COG5094 TAF9 Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=98.08 E-value=9.4e-06 Score=61.29 Aligned_cols=60 Identities=22% Similarity=0.319 Sum_probs=54.8
Q ss_pred HHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceec---HHHHHHHHHH
Q 047769 62 AIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVT---AMDVVYALKR 121 (131)
Q Consensus 62 aIrRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt---~~DV~~ALkr 121 (131)
-|.-|+++.|+...++.+--+|.++...|..+|++||..|++|+||-.++ ++||.+|+..
T Consensus 19 lihliL~Slgi~~ye~~VplQLl~FAhRYTq~vl~Dalvya~htgrg~~a~l~veDvrLA~at 81 (145)
T COG5094 19 LIHLILRSLGIEEYEPKVPLQLLEFAHRYTQDVLEDALVYAKHTGRGHIATLGVEDVRLALAT 81 (145)
T ss_pred HHHHHHHhcCchhhCccchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHHHHHH
Confidence 37788999999999999999999999999999999999999999998555 5999999954
No 34
>PLN00153 histone H2A; Provisional
Probab=98.05 E-value=2.3e-05 Score=59.03 Aligned_cols=87 Identities=21% Similarity=0.323 Sum_probs=68.8
Q ss_pred ccCCCCCCccCCCCCCccccccccccccccchHHHHHHHHhcC-ccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCC
Q 047769 29 MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGG-VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARR 107 (131)
Q Consensus 29 m~g~gkggkg~gk~g~kR~rKvlrd~i~gIpk~aIrRLArr~G-vkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~R 107 (131)
|+|+|||++ ...|...+..+..+ -+|..-|.|+++.+. .+||+..+.-.|..+||+...+|++-|...+...++
T Consensus 1 m~g~~~~~~----~~~k~~srS~ragL-~FpVgRi~R~Lr~g~~a~Rvga~A~VYLAAVLEYLtaEVLELAgnaa~d~kk 75 (129)
T PLN00153 1 MAGRGKGKT----SGKKAVSRSAKAGL-QFPVGRIARYLKKGKYAERIGAGAPVYLAAVLEYLTAEVLELAGNAARDNKK 75 (129)
T ss_pred CCCCCCCCc----cccCccCcccccCc-ccchHHHHHHHhcCchhhccCCCchHHHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 788877321 11122223333333 479999999998764 589999999999999999999999999999999999
Q ss_pred ceecHHHHHHHHH
Q 047769 108 KTVTAMDVVYALK 120 (131)
Q Consensus 108 KTVt~~DV~~ALk 120 (131)
+-|++..+.+|++
T Consensus 76 ~RItPrHi~lAI~ 88 (129)
T PLN00153 76 NRIVPRHIQLAIR 88 (129)
T ss_pred CccChHHHHhhcc
Confidence 9999999999984
No 35
>PLN00154 histone H2A; Provisional
Probab=98.02 E-value=5e-05 Score=57.66 Aligned_cols=64 Identities=16% Similarity=0.155 Sum_probs=60.1
Q ss_pred ccchHHHHHHHHhcC--ccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHH
Q 047769 57 GITKPAIRRLARRGG--VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALK 120 (131)
Q Consensus 57 gIpk~aIrRLArr~G--vkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALk 120 (131)
.+|..-|.|+++.+. ..||+..+--.|..+||+...+|++-|-..|...+++-|+..+|.+|++
T Consensus 38 ~FPVgRi~r~Lk~g~~~~~RVga~ApVYLAAVLEYLtAEVLELAGNaA~d~kk~RItPrHi~lAIr 103 (136)
T PLN00154 38 QFPVGRIHRQLKQRVSAHGRVGATAAVYTAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 103 (136)
T ss_pred cCchHHHHHHHHhhhhhccccccchHHHHHHHHHHHHHHHHHHHHHHHHhhCCceecHHHhhhhcc
Confidence 479999999999986 5799999999999999999999999999999999999999999999985
No 36
>KOG4336 consensus TBP-associated transcription factor Prodos [Transcription]
Probab=98.00 E-value=2.5e-05 Score=66.13 Aligned_cols=68 Identities=24% Similarity=0.304 Sum_probs=63.4
Q ss_pred cchHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHcCCc
Q 047769 58 ITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRT 125 (131)
Q Consensus 58 Ipk~aIrRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~G~~ 125 (131)
|-.+.|..|+...|+.-||.-+.+.|.+.+..|+.+|.+.+..||+|+||...|..||.+.|.++|..
T Consensus 6 vl~~VV~~Ll~~~gfd~is~~aletlvell~~yi~eigrq~~n~celagRT~pT~~Dv~l~Li~mnI~ 73 (323)
T KOG4336|consen 6 VLAPVVSNLLKTKGFDSISNAALETLVELLQSYIREIGRQLHNYCELAGRTIPTQGDVKLTLIEMNIK 73 (323)
T ss_pred HHHHHHHHHHHHhCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcHHHHHHHHHHhCCC
Confidence 34566888999999999999999999999999999999999999999999999999999999999853
No 37
>PLN00157 histone H2A; Provisional
Probab=97.94 E-value=4.3e-05 Score=57.74 Aligned_cols=64 Identities=14% Similarity=0.168 Sum_probs=59.3
Q ss_pred ccchHHHHHHHHhcC-ccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHH
Q 047769 57 GITKPAIRRLARRGG-VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALK 120 (131)
Q Consensus 57 gIpk~aIrRLArr~G-vkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALk 120 (131)
-+|..-|.|+++.+- ..||+..+.-.|..+||+...+|++-|...|...+++-|+..+|.+|++
T Consensus 26 ~FPVgRi~R~Lk~g~~a~RIg~~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~ 90 (132)
T PLN00157 26 QFPVGRIARYLKAGKYATRVGAGAPVYLAAVLEYLAAEVLELAGNAARDNKKSRIVPRHIQLAVR 90 (132)
T ss_pred ccchHHHHHHHhcCchhhhcCCCcHhHHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHhhccc
Confidence 479999999998853 5899999999999999999999999999999999999999999999984
No 38
>PLN00156 histone H2AX; Provisional
Probab=97.91 E-value=7.4e-05 Score=56.92 Aligned_cols=81 Identities=19% Similarity=0.286 Sum_probs=67.2
Q ss_pred CCCCCccccccccccccc--cchHHHHHHHHhcC-ccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHH
Q 047769 40 GKGGAKRHRKVLRDNIQG--ITKPAIRRLARRGG-VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVV 116 (131)
Q Consensus 40 gk~g~kR~rKvlrd~i~g--Ipk~aIrRLArr~G-vkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~ 116 (131)
|+||.++.....+..=-+ +|..-|.|+++.+. .+||+..+.-.|..+||+...+|++-|-..+...+++-|+...+.
T Consensus 10 ~~g~~~~~k~~srS~rAgL~FPVgRi~R~Lk~g~ya~RVga~ApVYLAAVLEYLtaEVLELAgNaa~d~kk~RItPrHi~ 89 (139)
T PLN00156 10 GRGKPKATKSVSRSSKAGLQFPVGRIARFLKAGKYAERVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQ 89 (139)
T ss_pred CCCcccccCCcCcccccCcccchHHHHHHHhcCChhhccCCccHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHH
Confidence 455555544444433333 78889999998864 589999999999999999999999999999999999999999999
Q ss_pred HHHH
Q 047769 117 YALK 120 (131)
Q Consensus 117 ~ALk 120 (131)
+|++
T Consensus 90 lAIr 93 (139)
T PLN00156 90 LAVR 93 (139)
T ss_pred hhcc
Confidence 9984
No 39
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=97.88 E-value=6.2e-05 Score=62.30 Aligned_cols=78 Identities=17% Similarity=0.282 Sum_probs=68.7
Q ss_pred ccccccchHHHHHHHHhcC-ccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHc-CCcccccC
Q 047769 53 DNIQGITKPAIRRLARRGG-VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ-GRTLYGFG 130 (131)
Q Consensus 53 d~i~gIpk~aIrRLArr~G-vkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~-G~~lYGF~ 130 (131)
++.+-+.|.-+..|.+..- -+.+.+++-+-|.++.+.|++.|+.-|..+|.|-+-.||.+-||.+.|||. +..+=||+
T Consensus 150 ~~~~il~k~kl~dLvqqId~~~~LD~dVedlLleiADdFV~sii~~sC~LAKHRKsdtlEvrDIqLhLEr~~Nm~iPgf~ 229 (258)
T KOG1142|consen 150 GNNPILSKRKLDDLVQQIDGTTKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHRKSDTVEVRDIQLHLERNFNMEIPGFS 229 (258)
T ss_pred CCCccccccchhHHHHhhcCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccchhheeeeeeccccccCCCcc
Confidence 4556788888888888874 477999999999999999999999999999999999999999999999994 56666775
No 40
>PTZ00017 histone H2A; Provisional
Probab=97.88 E-value=8.1e-05 Score=56.37 Aligned_cols=64 Identities=17% Similarity=0.226 Sum_probs=59.6
Q ss_pred ccchHHHHHHHHhc-CccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHH
Q 047769 57 GITKPAIRRLARRG-GVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALK 120 (131)
Q Consensus 57 gIpk~aIrRLArr~-GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALk 120 (131)
-+|..-|.|+++.+ -..||+..+.-.|..+||++..+|++-|...+...+++-|++.+|.+|++
T Consensus 27 ~FPVgRi~R~Lk~g~~a~RV~a~A~VYLAAVLEYLtaEILELAgNaa~d~kk~RItPrHi~lAI~ 91 (134)
T PTZ00017 27 QFPVGRVHRYLKKGRYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAAKDNKKKRITPRHIQLAIR 91 (134)
T ss_pred ccchHHHHHHHhccchhccccccchhhhHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHhhcc
Confidence 47999999999876 46899999999999999999999999999999999999999999999985
No 41
>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=97.76 E-value=0.00014 Score=56.13 Aligned_cols=75 Identities=17% Similarity=0.200 Sum_probs=67.6
Q ss_pred ccccccchHHHHHHHHhcCc--cccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHcCCccc
Q 047769 53 DNIQGITKPAIRRLARRGGV--KRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTLY 127 (131)
Q Consensus 53 d~i~gIpk~aIrRLArr~Gv--kRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~G~~lY 127 (131)
|..-.||+++|..|.+..=- -||..++-+-+.++.-+|+.-|..+|-..|+...+|||..+-|+-||+.+|+.=|
T Consensus 8 dde~sLPkAtv~KmIke~lP~d~rvakeareliincCvEFI~liSsEAneic~~e~KKTIa~EHV~KALe~LgF~eY 84 (156)
T KOG0871|consen 8 DDELSLPKATVNKMIKEMLPKDVRVAKEARELIINCCVEFINLISSEANEICNKEAKKTIAPEHVIKALENLGFGEY 84 (156)
T ss_pred cccccCcHHHHHHHHHHhCCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHhHHhcccCCHHHHHHHHHHcchHHH
Confidence 33448999999999988754 6899999999999999999999999999999999999999999999999987544
No 42
>KOG1756 consensus Histone 2A [Chromatin structure and dynamics]
Probab=97.70 E-value=0.00018 Score=54.20 Aligned_cols=88 Identities=24% Similarity=0.322 Sum_probs=69.3
Q ss_pred ccCCCCCCccCCCCCCcccccccccccc--ccchHHHHHHHHh-cCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Q 047769 29 MSGRGKGGKGLGKGGAKRHRKVLRDNIQ--GITKPAIRRLARR-GGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHA 105 (131)
Q Consensus 29 m~g~gkggkg~gk~g~kR~rKvlrd~i~--gIpk~aIrRLArr-~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA 105 (131)
|+|++++|++ +.++..+..+..-. -+|...|.|++|. -...|||..+--.+..+||+...+|++-|-..++..
T Consensus 1 ~s~~~k~gk~----~~~~~~~~srs~~agl~fPvgri~r~Lr~~~~~~ri~~gapV~laavLeYL~Aeile~agnaardn 76 (131)
T KOG1756|consen 1 MSGRGKGGKA----KPRAKAKSSRSSRAGLQFPVGRIHRLLRKGRYAQRVGAGAPVYLAAVLEYLTAEILELAGNAARDN 76 (131)
T ss_pred CCccCCCCcc----cchhhhhcchhhhcccccCHHHHHHHHHccchhhhccCCChHHHHHHHHHHHHHHHHHhHHHhhhc
Confidence 5677776543 22222222222222 3788899999999 357999999999999999999999999999999999
Q ss_pred CCceecHHHHHHHHH
Q 047769 106 RRKTVTAMDVVYALK 120 (131)
Q Consensus 106 ~RKTVt~~DV~~ALk 120 (131)
+++-|+..-+.+|+.
T Consensus 77 kk~ri~PrH~~lAI~ 91 (131)
T KOG1756|consen 77 KKTRITPRHLQLAIR 91 (131)
T ss_pred CccccChHHHHHHHh
Confidence 999999999999995
No 43
>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=97.37 E-value=0.00022 Score=50.40 Aligned_cols=61 Identities=13% Similarity=0.279 Sum_probs=29.7
Q ss_pred HHHHHHhcC-ccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHcC
Q 047769 63 IRRLARRGG-VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQG 123 (131)
Q Consensus 63 IrRLArr~G-vkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~G 123 (131)
|+.|+-..| +..-+++...-+.+++..|+.+++..|..+|...|+++++.+|++++|++.-
T Consensus 7 I~~mMy~fGD~~~P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~rg~~~i~~eDl~F~lR~D~ 68 (93)
T PF02269_consen 7 IRQMMYGFGDVEEPLPETVDLVEDIVREYIIELCQEAMEVAQRRGSKKIKVEDLLFLLRKDP 68 (93)
T ss_dssp CHHHHHCTTS-SS--HHHHHHHHHHHHHHHHHHHHHHHC-----------------------
T ss_pred HHHHHHHcCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCcCcHHHHHHHHhcCH
Confidence 445555555 4678889999999999999999999999999999999999999999998753
No 44
>smart00414 H2A Histone 2A.
Probab=97.36 E-value=0.00071 Score=49.21 Aligned_cols=64 Identities=20% Similarity=0.263 Sum_probs=59.8
Q ss_pred ccchHHHHHHHHhcC-ccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHH
Q 047769 57 GITKPAIRRLARRGG-VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALK 120 (131)
Q Consensus 57 gIpk~aIrRLArr~G-vkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALk 120 (131)
-+|..-|.|+++.+- ..||+..+.-.|..+||+...+|++-|...+...+++.|++.++..|+.
T Consensus 9 ~fPVgRi~r~Lk~~~~~~Rv~~~A~VyLaAvLEYLtaEILeLagn~a~~~k~~rItp~hi~lAi~ 73 (106)
T smart00414 9 QFPVGRIHRLLRKGTYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKRRITPRHLQLAIR 73 (106)
T ss_pred cCchHHHHHHHHcCccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchHHHhhhcc
Confidence 478999999998874 6899999999999999999999999999999999999999999999985
No 45
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=97.32 E-value=0.0011 Score=49.57 Aligned_cols=64 Identities=16% Similarity=0.181 Sum_probs=59.3
Q ss_pred ccchHHHHHHHHhc-CccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHH
Q 047769 57 GITKPAIRRLARRG-GVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALK 120 (131)
Q Consensus 57 gIpk~aIrRLArr~-GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALk 120 (131)
-+|..-|+|++++. ...||+.++.-.+..|+++...+|++-|-..|...+.|.|+.-.+-+|++
T Consensus 26 ~fpvgrvkr~lk~~~~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~kkkri~PrHlqlAIr 90 (132)
T COG5262 26 IFPVGRVKRLLKKGNYRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRIIPRHLQLAIR 90 (132)
T ss_pred cccHHHHHHHHHcCccceeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhcCcceechHHHHHHhc
Confidence 47899999999944 67999999999999999999999999999999999999999999998885
No 46
>PLN00158 histone H2B; Provisional
Probab=97.27 E-value=0.0023 Score=47.51 Aligned_cols=62 Identities=16% Similarity=0.170 Sum_probs=54.0
Q ss_pred hHHHHHHHHhcCc-cccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHH
Q 047769 60 KPAIRRLARRGGV-KRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKR 121 (131)
Q Consensus 60 k~aIrRLArr~Gv-kRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr 121 (131)
...|.++++..-. ..||..+...+..++.+.||.|+.+|...+...+|.|++..||..|.+.
T Consensus 30 ~~YI~kVLKQVhPd~gIS~kaM~ImnSfvnDiferIA~EAs~La~~nkr~TltsrEIqtAvrL 92 (116)
T PLN00158 30 KIYIYKVLKQVHPDTGISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVRL 92 (116)
T ss_pred HHHHHHHHHHhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHH
Confidence 3457777776543 4489999999999999999999999999999999999999999999875
No 47
>PTZ00463 histone H2B; Provisional
Probab=97.10 E-value=0.0052 Score=45.70 Aligned_cols=60 Identities=17% Similarity=0.164 Sum_probs=52.7
Q ss_pred HHHHHHHhcCc-cccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHH
Q 047769 62 AIRRLARRGGV-KRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKR 121 (131)
Q Consensus 62 aIrRLArr~Gv-kRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr 121 (131)
-|.++++..-. .-||..+...+..++.+.||.|+.+|...+...+|.|++..||..|.+.
T Consensus 33 YI~KVLKqVhPd~gIS~kaM~ImnSfvnDifErIA~EAs~La~~nkr~TltsrEIQtAvrL 93 (117)
T PTZ00463 33 YIFKVLKQVHPDTGISRKSMNIMNSFLVDTFEKIATEASRLCKYTRRDTLSSREIQTAIRL 93 (117)
T ss_pred HHHHHHHhhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHhh
Confidence 36777776533 4489999999999999999999999999999999999999999999875
No 48
>smart00427 H2B Histone H2B.
Probab=96.95 E-value=0.0063 Score=43.28 Aligned_cols=60 Identities=12% Similarity=0.164 Sum_probs=51.7
Q ss_pred HHHHHHHhcCc-cccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHH
Q 047769 62 AIRRLARRGGV-KRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKR 121 (131)
Q Consensus 62 aIrRLArr~Gv-kRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr 121 (131)
.|.++++..-. .-||..+...+..++.+.++.|+.+|...+...+|+|++..||..|.+.
T Consensus 6 Yi~kvLKqVhpd~giS~kam~imnSfvnDiferIa~EAs~L~~~nkr~TltsreIqtAvrl 66 (89)
T smart00427 6 YIYKVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRL 66 (89)
T ss_pred HHHHHHHHhCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHH
Confidence 35566665432 3499999999999999999999999999999999999999999999875
No 49
>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=96.89 E-value=0.007 Score=42.87 Aligned_cols=61 Identities=16% Similarity=0.269 Sum_probs=52.1
Q ss_pred HHHHHHHHhcC-ccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHc
Q 047769 61 PAIRRLARRGG-VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 122 (131)
Q Consensus 61 ~aIrRLArr~G-vkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~ 122 (131)
..|+.|+--.| +..-+++....+.+++..|+.+++..|...|. .+|..++.+|++++|++-
T Consensus 6 ~ei~~mmy~~GD~~~P~~eTv~llE~iv~~~i~~l~~~a~~~A~-~r~~k~~~eD~~FliR~D 67 (92)
T cd07978 6 KEIRQMMYGFGDVQNPLPETVDLLEDIVVEYIIELCHKAAEVAQ-RRRGKVKVEDLIFLLRKD 67 (92)
T ss_pred HHHHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-cCCCCCCHHHHHHHHhcC
Confidence 45777887777 45677888999999999999999999999999 677778999999999763
No 50
>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=96.82 E-value=0.0095 Score=41.71 Aligned_cols=66 Identities=20% Similarity=0.275 Sum_probs=60.1
Q ss_pred ccchHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCC---ceecHHHHHHHHHHc
Q 047769 57 GITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARR---KTVTAMDVVYALKRQ 122 (131)
Q Consensus 57 gIpk~aIrRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~R---KTVt~~DV~~ALkr~ 122 (131)
.+|++.|+||+...--..+|+++...+..+.+.|+-+|++.|....+.-+. .-+.+..|..|.+++
T Consensus 16 ~f~k~~iKr~~~~~~~~~v~~~v~i~v~glaKvFVGeivE~A~~V~~~~~~~~~~Pl~P~HireA~rrl 84 (85)
T cd08048 16 SFPKAAIKRLIQSVTGQSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGEANTGPLQPRHLREAYRRL 84 (85)
T ss_pred hccHHHHHHHHHHHcCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCCCCCcHHHHHHHHHh
Confidence 499999999998876689999999999999999999999999999998665 789999999999875
No 51
>KOG1745 consensus Histones H3 and H4 [Chromatin structure and dynamics]
Probab=96.77 E-value=0.00098 Score=50.73 Aligned_cols=68 Identities=22% Similarity=0.260 Sum_probs=58.1
Q ss_pred ccchHHHHHHHH---hcC--ccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHcCC
Q 047769 57 GITKPAIRRLAR---RGG--VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGR 124 (131)
Q Consensus 57 gIpk~aIrRLAr---r~G--vkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~G~ 124 (131)
-|.+.+-.||++ ..+ .-|+..+|..+|.++.|.||-.+.+|+-.+|-||+|-||..-||-+|.+-.|.
T Consensus 63 lI~K~PFqRlvrei~q~f~~dLrfqs~Ai~ALQeA~EayLv~LfEdtnlcAihAkRVTimpkdiQlArrirg~ 135 (137)
T KOG1745|consen 63 LIRKLPFQRLVREIAQDFKTDLRFQSSAIAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 135 (137)
T ss_pred HhhcCcHHHHhHHHHhcccccceehHHHHHHHHHHHHHHHHHhccccchhhhccceeEecccceehhhhcccC
Confidence 466777777776 222 36899999999999999999999999999999999999999999999876553
No 52
>KOG3423 consensus Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=96.61 E-value=0.019 Score=45.23 Aligned_cols=74 Identities=16% Similarity=0.193 Sum_probs=64.9
Q ss_pred cccccccchHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCC--------------CceecHHHHHH
Q 047769 52 RDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHAR--------------RKTVTAMDVVY 117 (131)
Q Consensus 52 rd~i~gIpk~aIrRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~--------------RKTVt~~DV~~ 117 (131)
.|.-.-||.+.+.-++..+|+......+..-+.=....|+.+|+.||..||+-.. +-|+|.+|..-
T Consensus 81 ddYtP~IPDavt~~yL~~aGf~~~D~rv~RLvsLaAQKfvSDIa~DA~Q~~k~r~~~~~~~~k~~~kdkK~tLtmeDL~~ 160 (176)
T KOG3423|consen 81 DDYTPTIPDAVTDHYLKKAGFQTSDPRVKRLVSLAAQKFVSDIANDALQHSKIRTKTAIGKDKKQAKDKKYTLTMEDLSP 160 (176)
T ss_pred hcCCCCCcHHHHHHHHHhcCCCcCcHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccccccccccccceeeeHHHHHH
Confidence 4455679999999999999999999999999999999999999999999998543 44999999999
Q ss_pred HHHHcCCc
Q 047769 118 ALKRQGRT 125 (131)
Q Consensus 118 ALkr~G~~ 125 (131)
||+..|..
T Consensus 161 AL~EyGin 168 (176)
T KOG3423|consen 161 ALAEYGIN 168 (176)
T ss_pred HHHHhCcc
Confidence 99997743
No 53
>PTZ00252 histone H2A; Provisional
Probab=96.21 E-value=0.024 Score=43.10 Aligned_cols=64 Identities=20% Similarity=0.226 Sum_probs=57.5
Q ss_pred ccchHHHHHHHHhcC-ccccchHHHHHHHHHHHHHHHHHHHHHHHHHhh--CCCceecHHHHHHHHH
Q 047769 57 GITKPAIRRLARRGG-VKRISGLIYEETRGVLKIFLENVIRDAVTYTEH--ARRKTVTAMDVVYALK 120 (131)
Q Consensus 57 gIpk~aIrRLArr~G-vkRIS~~ay~el~~vle~fle~I~~dAv~yaeH--A~RKTVt~~DV~~ALk 120 (131)
-+|..-|.|+++.+. ..||+..+.-.|..+||+...+|++-|...|.. .+++-|+...|.+|++
T Consensus 25 ~FPVgRi~R~Lr~g~ya~RIga~ApVYLAAVLEYLtaEVLELAgnaa~d~~~kk~RItPrHi~lAIr 91 (134)
T PTZ00252 25 IFPVGRVGSLLRRGQYARRIGASGAVYMAAVLEYLTAELLELSVKAAAQQAKKPKRLTPRTVTLAVR 91 (134)
T ss_pred cCchHHHHHHHHcCCcccccCCccHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccccHHHHHhhcc
Confidence 489999999998876 589999999999999999999999999999865 5778899999999984
No 54
>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=96.12 E-value=0.015 Score=39.52 Aligned_cols=61 Identities=18% Similarity=0.190 Sum_probs=49.3
Q ss_pred chHHHHHHHHhc---CccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCce-ecHHHHHHHH
Q 047769 59 TKPAIRRLARRG---GVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKT-VTAMDVVYAL 119 (131)
Q Consensus 59 pk~aIrRLArr~---GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKT-Vt~~DV~~AL 119 (131)
|+..|.||.+.. --.|||+++...+.+.++.|..+.+..|+.-++-.+-.+ |+.+|+...+
T Consensus 1 p~~li~rll~~~f~~~~tkIs~dal~l~~eyl~iFV~EAv~Ra~~~a~~e~~~~~le~e~LEki~ 65 (72)
T PF09415_consen 1 PPELIARLLHEHFKDDKTKISKDALKLSAEYLRIFVREAVARAAEQAEAEGDEGFLEVEHLEKIL 65 (72)
T ss_dssp -CHHHHHHHCTTSSSTT-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSEE-HHHHHHHC
T ss_pred ChHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHH
Confidence 678899999732 247899999999999999999999999999999999988 9999987654
No 55
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=96.11 E-value=0.028 Score=42.82 Aligned_cols=70 Identities=16% Similarity=0.105 Sum_probs=61.7
Q ss_pred cccchHHHHHHHHhcCcc--ccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHcCCc
Q 047769 56 QGITKPAIRRLARRGGVK--RISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRT 125 (131)
Q Consensus 56 ~gIpk~aIrRLArr~Gvk--RIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~G~~ 125 (131)
..+||++|..+.-..--+ -+..++-+.+-++.-+|+--+..+|-..|+....|||.++.|+-||+.+++.
T Consensus 10 ~sLPKATVqKMvS~iLp~dl~ftKearei~in~cieFi~~lsseAne~ce~EaKKTIa~EHviKALenLef~ 81 (148)
T COG5150 10 NSLPKATVQKMVSSILPKDLVFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHVIKALENLEFE 81 (148)
T ss_pred ccCcHHHHHHHHHHhccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHhccHH
Confidence 379999999998765432 3778999999999999999999999999999999999999999999988754
No 56
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=95.90 E-value=0.017 Score=47.63 Aligned_cols=66 Identities=23% Similarity=0.318 Sum_probs=61.6
Q ss_pred cccchHHHHHHHHhc-CccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHH
Q 047769 56 QGITKPAIRRLARRG-GVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKR 121 (131)
Q Consensus 56 ~gIpk~aIrRLArr~-GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr 121 (131)
..+|.+-|+++++.- +|+=||.+|---+....|.|++++.-.|-..|+..+|+|+.-.||..|++.
T Consensus 108 h~LPlARIkkvMKtdedVkMisaEaPvlFak~~EiFI~ELTmRAW~~ae~NkRRtLQksDia~Av~k 174 (286)
T COG5208 108 HNLPLARIKKVMKTDEDVKMISAEAPVLFAKITEIFIEELTMRAWINAEENKRRTLQKSDIAAAVKK 174 (286)
T ss_pred ccCcHHHHHHHHhcccchhheecccchHHHHHHHHHHHHHHHHHHHHHhHhhhhHHHHHHHHHHHHH
Confidence 468999999999875 799999999999999999999999999999999999999999999999975
No 57
>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=95.88 E-value=0.052 Score=34.97 Aligned_cols=48 Identities=15% Similarity=0.208 Sum_probs=44.4
Q ss_pred ccchHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 047769 57 GITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEH 104 (131)
Q Consensus 57 gIpk~aIrRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeH 104 (131)
-||..-+.-+++++|++.-...+..-+.=+...|+.+|+.||..|++.
T Consensus 2 ~IPD~v~~~yL~~~G~~~~D~rv~RLvSLaaQKFisdI~~dA~q~~k~ 49 (51)
T PF03540_consen 2 TIPDEVTDYYLERSGFQTSDPRVKRLVSLAAQKFISDIANDAMQYCKI 49 (51)
T ss_pred CCCHHHHHHHHHHCCCCCCCHhHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 488999999999999999899999999999999999999999999875
No 58
>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=95.85 E-value=0.06 Score=38.21 Aligned_cols=66 Identities=18% Similarity=0.252 Sum_probs=49.0
Q ss_pred ccchHHHHHHHHhcCc-cccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCc-eecHHHHHHHHHHc
Q 047769 57 GITKPAIRRLARRGGV-KRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRK-TVTAMDVVYALKRQ 122 (131)
Q Consensus 57 gIpk~aIrRLArr~Gv-kRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RK-TVt~~DV~~ALkr~ 122 (131)
.++|+.|++|+...-- ..+|+.+.-.+..+.+.|+-+|++.|....+.-+-. .++...+..|.+++
T Consensus 23 ~~~k~~ikkli~~~~~~qsv~~~v~i~v~g~aKvFVGEiVE~A~~Vq~~~~~~~pl~P~hlreA~rrL 90 (90)
T PF04719_consen 23 SFNKAAIKKLINQVLGNQSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGETGPLQPDHLREAYRRL 90 (90)
T ss_dssp ---HHHHHHHHHHHHS-S---HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SS--HHHHHHHHHHH
T ss_pred cCCHHHHHHHHHHHcCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcHHHHHHHHhC
Confidence 5899999999988644 789999999999999999999999999998854433 78888888888763
No 59
>KOG1744 consensus Histone H2B [Chromatin structure and dynamics]
Probab=95.21 E-value=0.084 Score=39.82 Aligned_cols=47 Identities=15% Similarity=0.215 Sum_probs=44.7
Q ss_pred cchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHH
Q 047769 75 ISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKR 121 (131)
Q Consensus 75 IS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr 121 (131)
||..+...+..++.++|+.|+.+|-.+++.-+|.||+..+|..|.+.
T Consensus 56 is~~a~~vmnsf~ndife~iA~ea~rla~y~krstisSreiqta~rL 102 (127)
T KOG1744|consen 56 ISSKAMGVMNSFVNDIFERIASEAGRLAHYNKRSTISSREIQTAVRL 102 (127)
T ss_pred cCHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCcccHHHHHHHHHH
Confidence 89999999999999999999999999999999999999999998865
No 60
>KOG1657 consensus CCAAT-binding factor, subunit C (HAP5) [Transcription]
Probab=94.76 E-value=0.054 Score=44.40 Aligned_cols=67 Identities=15% Similarity=0.199 Sum_probs=61.7
Q ss_pred ccccchHHHHHHHHhc-CccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHH
Q 047769 55 IQGITKPAIRRLARRG-GVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKR 121 (131)
Q Consensus 55 i~gIpk~aIrRLArr~-GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr 121 (131)
+..+|.+.|++|.++- .+.-|+.++.--+..++|.|+.++...+-.+|+-.+|+|+...|+..+...
T Consensus 72 ~~~lPlaRiKkimK~dedv~mI~~Eapvl~aka~E~Fi~elt~~sw~~Tee~~rrtl~~sdia~av~~ 139 (236)
T KOG1657|consen 72 NHILPLARIKKIMKSDEDVSMITAEAPVLFAKACELFITELTLRSWVHTEENKRRTLQKSDIAAAVTQ 139 (236)
T ss_pred hccCcHhhccccccccccccccchhHHHHHHHHHHHHHHHHHHHhhhhhcccccccchHHHHHHHhcc
Confidence 4479999999999875 578899999999999999999999999999999999999999999999864
No 61
>PF13654 AAA_32: AAA domain; PDB: 3K1J_B.
Probab=94.70 E-value=0.16 Score=45.55 Aligned_cols=61 Identities=16% Similarity=0.236 Sum_probs=49.5
Q ss_pred HHHHHHHhcCccccchHHHHHHHHHHHH-----------HHHHHHHHHHHHHhhCCCceecHHHHHHHHHHc
Q 047769 62 AIRRLARRGGVKRISGLIYEETRGVLKI-----------FLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 122 (131)
Q Consensus 62 aIrRLArr~GvkRIS~~ay~el~~vle~-----------fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~ 122 (131)
-|..++++.|...++.+|+.+|.+.... .+.+++++|..+|+..+.+.|+++||..|++..
T Consensus 435 ~i~~~~~~~~L~~~~~~Av~~li~~~~R~~q~kLsl~~~~l~~ll~EA~~~A~~~~~~~I~~~~V~~Ai~~r 506 (509)
T PF13654_consen 435 FIASICQKEGLPPFDRSAVARLIEYSARLDQDKLSLRFSWLADLLREANYWARKEGAKVITAEHVEQAIEER 506 (509)
T ss_dssp HHHHHHHHHSS--BBHHHHHHHHHHHHHCC-SEEE--HHHHHHHHHHHHHHHHHCT-SSB-HHHHHHHHHH-
T ss_pred HHHHHHHhCCCCCCCHHHHHHHHHHHHHHhCCEeCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHcc
Confidence 3677888899999999999999877543 688999999999999999999999999999865
No 62
>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=94.30 E-value=0.28 Score=38.83 Aligned_cols=61 Identities=21% Similarity=0.310 Sum_probs=52.3
Q ss_pred HHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhC------CCceecHHHHHHHHHHc
Q 047769 62 AIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHA------RRKTVTAMDVVYALKRQ 122 (131)
Q Consensus 62 aIrRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA------~RKTVt~~DV~~ALkr~ 122 (131)
.|.+++...|++-+++++++.+..+++.|+..|+.+++..++|- .-..+-..||..-|+.+
T Consensus 53 ~~~~i~~~~g~~~~~~d~~~lis~a~e~rlr~li~k~~~~s~hR~~~~~~~~r~~~~sdvr~qL~~l 119 (212)
T cd08045 53 KIRKIAKKHGLKEVDEDVLDLISLALEERLRNLLEKLIEVSEHRVDSEKEDERYEITSDVRKQLRFL 119 (212)
T ss_pred HHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCceeecchHHHHHHHH
Confidence 47788999999999999999999999999999999999999995 33566677887776653
No 63
>KOG1659 consensus Class 2 transcription repressor NC2, alpha subunit (DRAP1) [Transcription]
Probab=94.13 E-value=0.19 Score=40.99 Aligned_cols=67 Identities=15% Similarity=0.285 Sum_probs=59.0
Q ss_pred ccccchHHHHHHHHhc-CccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHH
Q 047769 55 IQGITKPAIRRLARRG-GVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKR 121 (131)
Q Consensus 55 i~gIpk~aIrRLArr~-GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr 121 (131)
..-+|.+-|++|+..- -|-+|...+--.+...||-|++.+++.+...|+--+-|||+++-++.|...
T Consensus 11 ~trfp~aRiKKIMQ~dEdIGKvaqavPViisralElFl~~l~~~t~~~t~~~~aKt~s~~hlkq~v~~ 78 (224)
T KOG1659|consen 11 KTRFPPARIKKIMQSDEDIGKVAQAVPVIISRALELFLESLLQKTLEITRSRGAKTVSSSHLKQAVES 78 (224)
T ss_pred hccCCHHHHHHHHhhhhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhcCccccCHHHHHHHHhc
Confidence 3468899999999764 467888888888899999999999999999999999999999999999843
No 64
>PLN00155 histone H2A; Provisional
Probab=93.53 E-value=0.16 Score=33.60 Aligned_cols=33 Identities=21% Similarity=0.189 Sum_probs=26.3
Q ss_pred ccchHHHHHHHHhcC-ccccchHHHHHHHHHHHH
Q 047769 57 GITKPAIRRLARRGG-VKRISGLIYEETRGVLKI 89 (131)
Q Consensus 57 gIpk~aIrRLArr~G-vkRIS~~ay~el~~vle~ 89 (131)
-+|..-|.|+++.+- .+||+..+---+..+||+
T Consensus 24 ~FPVgri~r~Lr~g~~a~Rvga~apVYlAAVLEY 57 (58)
T PLN00155 24 QFPVGRIARYLKKGKYAERIGAGAPVYLAAVLEY 57 (58)
T ss_pred ccchHHHHHHHhcCChhhcccCCcHHHHHHHHHh
Confidence 478889999998765 489998877778777764
No 65
>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=93.17 E-value=0.14 Score=41.77 Aligned_cols=61 Identities=23% Similarity=0.278 Sum_probs=32.8
Q ss_pred HHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCc------eecHHHHHHHHHHc
Q 047769 62 AIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRK------TVTAMDVVYALKRQ 122 (131)
Q Consensus 62 aIrRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RK------TVt~~DV~~ALkr~ 122 (131)
.|.+|+...|...+++|+++-|.-+++.||.+|+.+++..++|--.- +....||...|+.+
T Consensus 52 ~i~~i~~~~g~~~~~~d~l~llS~A~e~rLr~lie~~~~~s~hR~~~~~~~~~~~~~sdv~~qlr~l 118 (264)
T PF05236_consen 52 RIQKIAKKHGLKSVDEDVLELLSLATEERLRNLIEKAIVLSRHRRDSSKSDPRYEIRSDVRKQLRFL 118 (264)
T ss_dssp HHHHHHHCTT--EE-TCHHHHHHHHHHHHHHHHHHHHH-----------------------------
T ss_pred HHHHHHHHcCCcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccCCCcccccchHHHHHHHHH
Confidence 37788888899999999999999999999999999999999984332 33466776666543
No 66
>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=91.54 E-value=0.97 Score=41.27 Aligned_cols=59 Identities=20% Similarity=0.177 Sum_probs=47.4
Q ss_pred HHHHHHhcC-ccccchHHHHHHHHHHH-------------HHHHHHHHHHHHHHhhCCCceecHHHHHHHHHH
Q 047769 63 IRRLARRGG-VKRISGLIYEETRGVLK-------------IFLENVIRDAVTYTEHARRKTVTAMDVVYALKR 121 (131)
Q Consensus 63 IrRLArr~G-vkRIS~~ay~el~~vle-------------~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr 121 (131)
|.+.+++.| ...+|+++.+++.+... .-+.+|++.|..+|+..+..+|+.+||..|++.
T Consensus 318 i~~~~~r~G~l~~~s~~Av~~Li~~~~R~ag~r~~lsl~~R~L~~llR~A~~iA~~~~~~~I~~ehV~~Ai~~ 390 (608)
T TIGR00764 318 VAQEVKKDGRIPHFTRDAVEEIVREAQRRAGRKDHLTLRLRELGGLVRAAGDIAKSSGKVYVTAEHVLKAKKL 390 (608)
T ss_pred HHHHHHHhCCCCcCCHHHHHHHHHHHHHHHhcccccCCCHHHHHHHHHHHHHHHHhcCCceecHHHHHHHHHH
Confidence 444455554 67899999999876533 568899999999999999999999999998764
No 67
>KOG3901 consensus Transcription initiation factor IID subunit [Transcription]
Probab=91.06 E-value=0.77 Score=33.78 Aligned_cols=42 Identities=12% Similarity=0.238 Sum_probs=33.1
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHH
Q 047769 77 GLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKR 121 (131)
Q Consensus 77 ~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr 121 (131)
++..+.|.+++-.|+.+++..|.... +|-.+..+|+.++|++
T Consensus 30 ~~tv~~Le~iV~~Yi~elt~~a~~~g---~rgk~~veD~~f~lRk 71 (109)
T KOG3901|consen 30 PETVDLLEDIVLEYITELTHAAMEIG---KRGKVKVEDFKFLLRK 71 (109)
T ss_pred HhHHHHHHHHHHHHHHHHHHHHHHhc---ccCceeHHHHHHHHHh
Confidence 45677788888888888866665554 6777999999999986
No 68
>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=90.92 E-value=1 Score=40.32 Aligned_cols=64 Identities=16% Similarity=0.155 Sum_probs=47.0
Q ss_pred ccchHHHHHHH----HhcCccccchHHHHHHHHHHH--HHHHHHHHHHHHHHhhCCCceecHHHHHHHHHH
Q 047769 57 GITKPAIRRLA----RRGGVKRISGLIYEETRGVLK--IFLENVIRDAVTYTEHARRKTVTAMDVVYALKR 121 (131)
Q Consensus 57 gIpk~aIrRLA----rr~GvkRIS~~ay~el~~vle--~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr 121 (131)
.++...+..|+ ++.|+ .+++++++.+..... ..+.++++.|..+|...+|++|+.+||.+++..
T Consensus 262 pL~~eei~~Il~~~a~k~~i-~is~~al~~I~~y~~n~Rel~nll~~Aa~~A~~~~~~~It~~dI~~vl~~ 331 (531)
T TIGR02902 262 PLLDEEIKEIAKNAAEKIGI-NLEKHALELIVKYASNGREAVNIVQLAAGIALGEGRKRILAEDIEWVAEN 331 (531)
T ss_pred CCCHHHHHHHHHHHHHHcCC-CcCHHHHHHHHHhhhhHHHHHHHHHHHHHHHhhCCCcEEcHHHHHHHhCC
Confidence 44455555555 44454 489999887655432 457788899988898889999999999999963
No 69
>COG5248 TAF19 Transcription initiation factor TFIID, subunit TAF13 [Transcription]
Probab=89.68 E-value=1.2 Score=33.25 Aligned_cols=59 Identities=19% Similarity=0.173 Sum_probs=45.6
Q ss_pred HHHHHHHhcC-ccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHc
Q 047769 62 AIRRLARRGG-VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 122 (131)
Q Consensus 62 aIrRLArr~G-vkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~ 122 (131)
.|+.|+=.-| +-.=-.+..+.|.+.+..|+..++-.|...|+ .|-.+..+|..+||++-
T Consensus 14 DikslmYayGDvv~P~~dt~~~L~e~V~dY~~~~ctna~~~Aq--~rnK~k~eDfkfaLr~D 73 (126)
T COG5248 14 DIKSLMYAYGDVVAPRYDTAEALHEYVLDYMSILCTNAHNMAQ--VRNKTKTEDFKFALRRD 73 (126)
T ss_pred HHHHHHHHhCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHH--hcccchHHHHHHHHhhC
Confidence 3455554444 33334567788999999999999999999998 67779999999999874
No 70
>KOG3219 consensus Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=89.34 E-value=0.59 Score=37.57 Aligned_cols=67 Identities=18% Similarity=0.255 Sum_probs=57.1
Q ss_pred ccchHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCc-eecHHHHHHHHHHcC
Q 047769 57 GITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRK-TVTAMDVVYALKRQG 123 (131)
Q Consensus 57 gIpk~aIrRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RK-TVt~~DV~~ALkr~G 123 (131)
++||+.|++|+...--.-||+-+.-++..+.+.|.-+|++.|...++.-+-. -+....|-.|.+|++
T Consensus 112 ~f~Ka~iKkL~~~itg~~v~~nv~Ia~~GiaKvFVGEvVEeAl~V~~~~~e~~PLqP~HIREA~rrL~ 179 (195)
T KOG3219|consen 112 AFPKAQIKKLMSSITGQSVSENVAIAMAGIAKVFVGEVVEEALDVREEWGESGPLQPKHIREAYRRLK 179 (195)
T ss_pred cCCHHHHHHHHHHHhCCccCcceeeeecchhhHhHHHHHHHHHHHHHHhccCCCCCcHHHHHHHHHHH
Confidence 7999999999987633339999999999999999999999999999876543 688899999888743
No 71
>COG5247 BUR6 Class 2 transcription repressor NC2, alpha subunit (DRAP1 homolog) [Transcription]
Probab=88.60 E-value=3.3 Score=30.48 Aligned_cols=64 Identities=9% Similarity=0.147 Sum_probs=54.1
Q ss_pred ccchHHHHHHHHhc-CccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHH
Q 047769 57 GITKPAIRRLARRG-GVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALK 120 (131)
Q Consensus 57 gIpk~aIrRLArr~-GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALk 120 (131)
-+|.+-|++|+.-- .+-.|+...--.....||.|+..|++.+.+.|+.-+-|-+|++-++.|..
T Consensus 23 rFP~ar~KkIMQ~deDiGKV~q~tPVIaskalE~Fl~~iv~~s~k~aR~~~skR~t~e~lk~a~~ 87 (113)
T COG5247 23 RFPIARLKKIMQLDEDIGKVGQSTPVIASKALEMFLTEIVGLSLKEARKKSSKRMTSEFLKRATE 87 (113)
T ss_pred cCCHHHHHHHHHhhhhhhhhhhcchHHHHHHHHHHHHHHHHHHHHHHHhccchhhHHHHHHHHHh
Confidence 58999999998643 45667777667778899999999999999999998888899999888874
No 72
>COG5162 Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=88.03 E-value=4.8 Score=32.05 Aligned_cols=71 Identities=17% Similarity=0.218 Sum_probs=59.7
Q ss_pred ccccchHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhh--------C---------------------
Q 047769 55 IQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEH--------A--------------------- 105 (131)
Q Consensus 55 i~gIpk~aIrRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeH--------A--------------------- 105 (131)
-.-||...+.=.+...|+......+..-|.-....|+.+|+.||-.|.+- +
T Consensus 86 ~PliPd~v~DYyl~k~Gf~~~D~rvKkLl~L~aqKFvsDiA~dayqYsrIr~~~sna~~t~~~a~~f~~gg~~~i~~~~~ 165 (197)
T COG5162 86 TPLIPDSVTDYYLEKAGFVTSDQRVKKLLSLLAQKFVSDIAVDAYQYSRIRQGSSNAKATAQKAKRFAKGGASGIGSSGR 165 (197)
T ss_pred CCCccHHHHHHHHHhcCceeccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccchhhHHHHHHHHhccccccccccc
Confidence 34688888889999999998888888888888999999999999988752 1
Q ss_pred ----CCceecHHHHHHHHHHcCCc
Q 047769 106 ----RRKTVTAMDVVYALKRQGRT 125 (131)
Q Consensus 106 ----~RKTVt~~DV~~ALkr~G~~ 125 (131)
+..++|+.|...||...|..
T Consensus 166 ~~dr~K~vltv~DLs~Al~EyGin 189 (197)
T COG5162 166 RGDRKKPVLTVVDLSKALEEYGIN 189 (197)
T ss_pred ccccCCceeeehHHHHHHHHhccc
Confidence 45588999999999987754
No 73
>COG1067 LonB Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]
Probab=87.03 E-value=2.8 Score=38.97 Aligned_cols=59 Identities=31% Similarity=0.326 Sum_probs=49.6
Q ss_pred HHHHHHhcCccccchHHHHHHHHHHHHH-------------HHHHHHHHHHHHhhCCCceecHHHHHHHHHH
Q 047769 63 IRRLARRGGVKRISGLIYEETRGVLKIF-------------LENVIRDAVTYTEHARRKTVTAMDVVYALKR 121 (131)
Q Consensus 63 IrRLArr~GvkRIS~~ay~el~~vle~f-------------le~I~~dAv~yaeHA~RKTVt~~DV~~ALkr 121 (131)
++.+++.+....++.+|+++|-..+..+ +.++++.|-.+|+-.+++-|+++||..|++.
T Consensus 327 ~q~v~~d~~ip~~~~~Av~~li~~a~R~Ag~~~~Ltl~~rdl~~lv~~A~~ia~~~~~~~I~ae~Ve~a~~~ 398 (647)
T COG1067 327 VQELARDGNIPHLDKDAVEELIREAARRAGDQNKLTLRLRDLGNLVREAGDIAVSEGRKLITAEDVEEALQK 398 (647)
T ss_pred HHHHHhcCCCCCCCHHHHHHHHHHHHHhccccceeccCHHHHHHHHHHhhHHHhcCCcccCcHHHHHHHHHh
Confidence 4556667788888888888887776654 5688999999999999999999999999986
No 74
>PRK07452 DNA polymerase III subunit delta; Validated
Probab=86.33 E-value=1.9 Score=35.14 Aligned_cols=62 Identities=15% Similarity=0.076 Sum_probs=51.8
Q ss_pred HHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhh--CCCceecHHHHHHHHHHcCC
Q 047769 62 AIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEH--ARRKTVTAMDVVYALKRQGR 124 (131)
Q Consensus 62 aIrRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeH--A~RKTVt~~DV~~ALkr~G~ 124 (131)
-|+..|++.|.+ |++++.+.|.+.+..=+..+..+..+.+-+ .+..+||.+||...+-....
T Consensus 138 ~i~~~~~~~g~~-i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~~It~~~V~~~v~~~~~ 201 (326)
T PRK07452 138 LVERTAQELGVK-LTPEAAELLAEAVGNDSRRLYNELEKLALYAENSTKPISAEEVKALVSNTTQ 201 (326)
T ss_pred HHHHHHHHcCCC-CCHHHHHHHHHHhCccHHHHHHHHHHHHHhccCCCCccCHHHHHHHhccCcC
Confidence 477888889977 999999999999988888888888888888 45788999999988754433
No 75
>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=85.54 E-value=4 Score=31.83 Aligned_cols=68 Identities=7% Similarity=0.102 Sum_probs=52.1
Q ss_pred ccccchHHHHHHH----HhcCc---cccchHHHHHHHHHHHH---HHHHHHHHHHHHHhhCCCceecHHHHHHHHHHc
Q 047769 55 IQGITKPAIRRLA----RRGGV---KRISGLIYEETRGVLKI---FLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 122 (131)
Q Consensus 55 i~gIpk~aIrRLA----rr~Gv---kRIS~~ay~el~~vle~---fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~ 122 (131)
+..++...+..++ +..|. ..+++++++.+.+...- ++..++..+...+--.+.++|+.++|..++...
T Consensus 189 l~~l~~~e~~~~l~~~l~~~g~~~~~~~~~~~~~~i~~~s~G~p~~i~~l~~~~~~~a~~~~~~~i~~~~v~~~~~~~ 266 (269)
T TIGR03015 189 LGPLDREETREYIEHRLERAGNRDAPVFSEGAFDAIHRFSRGIPRLINILCDRLLLSAFLEEKREIGGEEVREVIAEI 266 (269)
T ss_pred CCCCCHHHHHHHHHHHHHHcCCCCCCCcCHHHHHHHHHHcCCcccHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHh
Confidence 5566666655544 44553 35999999999988664 688888888888777788999999999999874
No 76
>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=85.07 E-value=4.4 Score=27.95 Aligned_cols=68 Identities=13% Similarity=0.095 Sum_probs=53.0
Q ss_pred cccccchHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHcCC
Q 047769 54 NIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGR 124 (131)
Q Consensus 54 ~i~gIpk~aIrRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~G~ 124 (131)
....+|.+..+++||+.| +|+.-.+.+...-...-|++.+-.-...+-.|+..-|.++++.||+..+.
T Consensus 5 v~d~v~~~~wk~~~R~LG---lse~~Id~ie~~~~~~~Eq~yqmL~~W~~~~g~~~At~~~L~~aLr~~~l 72 (80)
T cd08313 5 VLDEVPPRRWKEFVRRLG---LSDNEIERVELDHRRCRDAQYQMLKVWKERGPRPYATLQHLLSVLRDMEL 72 (80)
T ss_pred HHHhCCHHHHHHHHHHcC---CCHHHHHHHHHhCCChHHHHHHHHHHHHHhcCCCcchHHHHHHHHHHcCc
Confidence 345789999999999999 66666666665444555677777778888888878899999999998764
No 77
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=84.01 E-value=4 Score=33.89 Aligned_cols=68 Identities=16% Similarity=0.154 Sum_probs=50.1
Q ss_pred ccccchHHHHHHHHh---cC--ccccchHHHHHHHHHH------HHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHc
Q 047769 55 IQGITKPAIRRLARR---GG--VKRISGLIYEETRGVL------KIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 122 (131)
Q Consensus 55 i~gIpk~aIrRLArr---~G--vkRIS~~ay~el~~vl------e~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~ 122 (131)
...++...+..+++. .+ -.-+++++.+.+.+.. -.++-+++..|..+|...++.+|+.+||..|+...
T Consensus 204 f~py~~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~a~~~a~~~~~~~I~~~~v~~a~~~~ 282 (394)
T PRK00411 204 FPPYTADEIFDILKDRVEEGFYPGVVDDEVLDLIADLTAREHGDARVAIDLLRRAGLIAEREGSRKVTEEDVRKAYEKS 282 (394)
T ss_pred cCCCCHHHHHHHHHHHHHhhcccCCCCHhHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHH
Confidence 334555655555432 12 2358899998888877 34556888999999999999999999999999865
No 78
>PRK06585 holA DNA polymerase III subunit delta; Reviewed
Probab=83.51 E-value=3.4 Score=34.04 Aligned_cols=60 Identities=13% Similarity=-0.020 Sum_probs=48.1
Q ss_pred HHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCC-CceecHHHHHHHHHHcC
Q 047769 63 IRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHAR-RKTVTAMDVVYALKRQG 123 (131)
Q Consensus 63 IrRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~-RKTVt~~DV~~ALkr~G 123 (131)
|...|+..|.+ |++++.+.|.+.+..=+..+..+..+.+-.++ .++||.+||...+-...
T Consensus 151 i~~~~~~~g~~-i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~It~edV~~lv~~~~ 211 (343)
T PRK06585 151 IDDELAEAGLR-ITPDARALLVALLGGDRLASRNEIEKLALYAHGKGEITLDDVRAVVGDAS 211 (343)
T ss_pred HHHHHHHCCCC-CCHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHhCCcc
Confidence 77888999976 99999999999988877777777777666643 56899999988875543
No 79
>PRK05574 holA DNA polymerase III subunit delta; Reviewed
Probab=82.72 E-value=4.9 Score=32.53 Aligned_cols=60 Identities=13% Similarity=0.079 Sum_probs=47.0
Q ss_pred HHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHcC
Q 047769 63 IRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQG 123 (131)
Q Consensus 63 IrRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~G 123 (131)
|+..++..|+. |++++.+.+.+.+..=+..+..+..+.+-.++-+.||.+||...+-...
T Consensus 155 i~~~~~~~g~~-i~~~a~~~L~~~~~~d~~~l~~El~KL~l~~~~~~It~~~I~~~i~~~~ 214 (340)
T PRK05574 155 IQQRLKQQGLQ-IDAAALQLLAERVEGNLLALAQELEKLALLYPDGKITLEDVEEAVPDSA 214 (340)
T ss_pred HHHHHHHcCCC-CCHHHHHHHHHHhCchHHHHHHHHHHHHhhcCCCCCCHHHHHHHHhhhh
Confidence 67778888976 9999999999998877777777777777665323399999998876543
No 80
>TIGR01128 holA DNA polymerase III, delta subunit. subunit around DNA forming a DNA sliding clamp.
Probab=81.69 E-value=6.7 Score=31.13 Aligned_cols=59 Identities=15% Similarity=0.083 Sum_probs=44.1
Q ss_pred HHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHc
Q 047769 63 IRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 122 (131)
Q Consensus 63 IrRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~ 122 (131)
|+..+++.|++ |++++.+.+.+.+..=+..+..+..+.+-.++-++||.+||...+-..
T Consensus 120 i~~~~~~~g~~-i~~~a~~~l~~~~~~d~~~l~~el~KL~~~~~~~~It~e~I~~~~~~~ 178 (302)
T TIGR01128 120 IQARLKKLGLR-IDPDAVQLLAELVEGNLLAIAQELEKLALYAPDGKITLEDVEEAVSDS 178 (302)
T ss_pred HHHHHHHcCCC-CCHHHHHHHHHHhCcHHHHHHHHHHHHHhhCCCCCCCHHHHHHHHhhh
Confidence 66777788866 999999999988876566665666665555555579999998877543
No 81
>PRK07914 hypothetical protein; Reviewed
Probab=80.64 E-value=4.8 Score=33.20 Aligned_cols=58 Identities=14% Similarity=0.036 Sum_probs=47.9
Q ss_pred HHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHc
Q 047769 63 IRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 122 (131)
Q Consensus 63 IrRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~ 122 (131)
|...|++.|++ |++++.+.|.+.+..=+..+..+..+.+-+.+ .+||.+||...+-..
T Consensus 137 i~~~a~~~g~~-i~~~A~~~L~~~~g~dl~~l~~EleKL~~~~~-~~It~e~V~~~v~~~ 194 (320)
T PRK07914 137 VRKEFRSLRVK-VDDDTVTALLDAVGSDLRELASACSQLVADTG-GAVDAAAVRRYHSGK 194 (320)
T ss_pred HHHHHHHcCCC-CCHHHHHHHHHHHCccHHHHHHHHHHHhcCCC-CCcCHHHHHHHcCCC
Confidence 77888899977 99999999999988778888888777765555 579999999887554
No 82
>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=80.15 E-value=4.4 Score=32.72 Aligned_cols=40 Identities=18% Similarity=0.274 Sum_probs=35.7
Q ss_pred HHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHH
Q 047769 63 IRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYT 102 (131)
Q Consensus 63 IrRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~ya 102 (131)
+..+|...|..-+|.++.+-+.-.++.||.+|+..++..+
T Consensus 212 m~~ia~e~GL~gvs~~~a~ll~~ale~~LK~lI~s~l~~~ 251 (252)
T PF12767_consen 212 MEQIAWEHGLGGVSDDCANLLNLALEVHLKNLIKSCLDLV 251 (252)
T ss_pred HHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 5567788899889999999999999999999999988764
No 83
>KOG1757 consensus Histone 2A [Chromatin structure and dynamics]
Probab=80.04 E-value=3.6 Score=30.87 Aligned_cols=64 Identities=14% Similarity=0.158 Sum_probs=50.5
Q ss_pred ccchHHHHHHHHhc--CccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHH
Q 047769 57 GITKPAIRRLARRG--GVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALK 120 (131)
Q Consensus 57 gIpk~aIrRLArr~--GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALk 120 (131)
.+|..-|.|.++.- .-.|+-..+.-....++++...+|++-|-..+..-+=|-||.-..-+|++
T Consensus 30 qFpVgRihr~LK~r~t~h~rVGataavy~aaileYLTaEVLeLAgNasKdLKvKRitprHlqLAiR 95 (131)
T KOG1757|consen 30 QFPVGRIHRHLKTRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 95 (131)
T ss_pred ccchHHHHHHHHHhcccccccchHHHHHHHHHHHHHHHHHHHHcccccccceeeeccchhheeeec
Confidence 47888899888653 55788888888888999999999998888877777777788776666653
No 84
>PRK08487 DNA polymerase III subunit delta; Validated
Probab=78.59 E-value=7.5 Score=32.22 Aligned_cols=58 Identities=10% Similarity=-0.017 Sum_probs=48.9
Q ss_pred HHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHc
Q 047769 62 AIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 122 (131)
Q Consensus 62 aIrRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~ 122 (131)
-|+..|+..|.+ |+++|.+.+.+.+..=+..+..+..+.+-..+ +||.+||....-..
T Consensus 143 ~i~~~~~~~g~~-i~~~a~~~L~~~~g~dl~~l~~ELeKL~ly~~--~It~edV~~~v~~~ 200 (328)
T PRK08487 143 LLQERAKELGLD-IDQNALNHLYFIHNEDLALAANELEKLAILNE--PITLKDIQELVFGL 200 (328)
T ss_pred HHHHHHHHhCCC-CCHHHHHHHHHHhCcHHHHHHHHHHHHHHhcC--CCCHHHHHHHhccc
Confidence 377888889977 99999999999988888888888888777765 69999999887543
No 85
>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=78.24 E-value=5.6 Score=24.52 Aligned_cols=41 Identities=20% Similarity=0.196 Sum_probs=23.7
Q ss_pred hHHHHHHHHHHHHHHHHHHHH-HHHHHhhCCCceecHHHHHHH
Q 047769 77 GLIYEETRGVLKIFLENVIRD-AVTYTEHARRKTVTAMDVVYA 118 (131)
Q Consensus 77 ~~ay~el~~vle~fle~I~~d-Av~yaeHA~RKTVt~~DV~~A 118 (131)
++|-..|..+ =.|+...+++ +..||...|...||.+.|..|
T Consensus 3 ~eA~~~L~~i-P~fvR~~~r~~~E~~Ar~~G~~~IT~e~v~~A 44 (45)
T PF08369_consen 3 DEAEARLDRI-PFFVRKKLRDAAEKYARERGYDEITVEVVDAA 44 (45)
T ss_dssp HHHHHHHCTS--HHHHHHHHHHHHHHHHHCT-SEE-HHHHHHH
T ss_pred HHHHHHHHHC-CHHHHHHHHHHHHHHHHHcCCCeECHHHHHhh
Confidence 3444444443 3355455544 457899999999999888654
No 86
>PRK05907 hypothetical protein; Provisional
Probab=77.96 E-value=6.8 Score=32.89 Aligned_cols=58 Identities=10% Similarity=0.071 Sum_probs=48.2
Q ss_pred HHHHHHhcCccccchHHHHHHHHHH-HHHHHHHHHHHHHHHhh-CCCceecHHHHHHHHHH
Q 047769 63 IRRLARRGGVKRISGLIYEETRGVL-KIFLENVIRDAVTYTEH-ARRKTVTAMDVVYALKR 121 (131)
Q Consensus 63 IrRLArr~GvkRIS~~ay~el~~vl-e~fle~I~~dAv~yaeH-A~RKTVt~~DV~~ALkr 121 (131)
|.+.+++.|.+ |+.++.+.+.+.+ ..=+..+.++..+.+-+ ..+++||.+||....-.
T Consensus 143 i~~~~~~~g~~-i~~~a~~~L~~~~~~~nL~~l~~EleKL~ly~g~~~~It~e~V~~lv~~ 202 (311)
T PRK05907 143 LIQRAKELGIS-CSLGLASLFVSKFPQTGLFEILSEFQKLLCQMGKKESLEASDIQSFVVK 202 (311)
T ss_pred HHHHHHHcCCC-cCHHHHHHHHHHccCCCHHHHHHHHHHHHHhcCCCCeECHHHHHHHhcC
Confidence 66777888855 9999999999877 57788899999998888 45889999999987644
No 87
>PRK13765 ATP-dependent protease Lon; Provisional
Probab=75.08 E-value=10 Score=35.19 Aligned_cols=51 Identities=22% Similarity=0.053 Sum_probs=41.6
Q ss_pred CccccchHHHHHHHHHHH-------------HHHHHHHHHHHHHHhhCCCceecHHHHHHHHHH
Q 047769 71 GVKRISGLIYEETRGVLK-------------IFLENVIRDAVTYTEHARRKTVTAMDVVYALKR 121 (131)
Q Consensus 71 GvkRIS~~ay~el~~vle-------------~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr 121 (131)
....+++++.+++-+... .-+.++++.|..+|+..+++.|+.+||..|+++
T Consensus 336 ~l~~f~~eAVa~LI~~~~R~ag~r~~lsl~~~~l~~l~r~a~~~a~~~~~~~i~~~~v~~a~~~ 399 (637)
T PRK13765 336 KIPHFDRDAVEEIIREAKRRAGRKGHLTLKLRDLGGLVRVAGDIARSEGAELTTAEHVLEAKKI 399 (637)
T ss_pred CCCCCCHHHHHHHHHHHHHHhCCccccccCHHHHHHHHHHHHHHHHhhccceecHHHHHHHHHh
Confidence 456789998888876544 345569999999999999999999999988865
No 88
>PRK05629 hypothetical protein; Validated
Probab=73.75 E-value=12 Score=30.76 Aligned_cols=58 Identities=12% Similarity=0.019 Sum_probs=45.8
Q ss_pred HHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHc
Q 047769 63 IRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 122 (131)
Q Consensus 63 IrRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~ 122 (131)
|...|++.|.+ |++++.+.|.+.+..=+..+-.+..+.+-+.+ .+||.+||...+-.+
T Consensus 135 i~~~~~~~g~~-i~~~A~~~L~~~~g~dl~~l~~EleKL~~~~~-~~It~e~V~~~v~~~ 192 (318)
T PRK05629 135 VTQEFKNHGVR-PTPDVVHALLEGVGSDLRELASAISQLVEDTQ-GNVTVEKVRAYYVGV 192 (318)
T ss_pred HHHHHHHcCCC-CCHHHHHHHHHHHCccHHHHHHHHHHHHhcCC-CCcCHHHHHHHhCCC
Confidence 77888889977 99999999998887777777777776665544 479999999876544
No 89
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=73.27 E-value=3.5 Score=26.12 Aligned_cols=28 Identities=39% Similarity=0.553 Sum_probs=19.1
Q ss_pred ccchHHHHHHH---------HhcCccccchHHHHHHH
Q 047769 57 GITKPAIRRLA---------RRGGVKRISGLIYEETR 84 (131)
Q Consensus 57 gIpk~aIrRLA---------rr~GvkRIS~~ay~el~ 84 (131)
.||+++|+||. ...|+++||..-..+..
T Consensus 2 ~Ip~~ti~RL~~Y~r~L~~l~~~G~~~vSS~~La~~~ 38 (50)
T PF06971_consen 2 KIPKATIRRLPLYLRYLEQLKEEGVERVSSQELAEAL 38 (50)
T ss_dssp S-SHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHHHHHHHcCCeeECHHHHHHHH
Confidence 58999999986 56799999977655544
No 90
>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=73.02 E-value=23 Score=29.03 Aligned_cols=68 Identities=12% Similarity=0.028 Sum_probs=47.8
Q ss_pred ccccchHHHHHHHHhc---C--ccccchHHHHHHHHHHH------HHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHc
Q 047769 55 IQGITKPAIRRLARRG---G--VKRISGLIYEETRGVLK------IFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 122 (131)
Q Consensus 55 i~gIpk~aIrRLArr~---G--vkRIS~~ay~el~~vle------~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~ 122 (131)
++..+...+..++++- + -.-+++++.+.+.+... ..+.++++.|..+|.-.++.+|+.+||..|+...
T Consensus 196 f~p~~~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~R~al~~l~~a~~~a~~~~~~~it~~~v~~a~~~~ 274 (365)
T TIGR02928 196 FPPYDAEELRDILENRAEKAFYDGVLDDGVIPLCAALAAQEHGDARKAIDLLRVAGEIAEREGAERVTEDHVEKAQEKI 274 (365)
T ss_pred eCCCCHHHHHHHHHHHHHhhccCCCCChhHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHH
Confidence 3455666666666432 1 12377888777766553 4566788899999988889999999999988654
No 91
>smart00350 MCM minichromosome maintenance proteins.
Probab=72.86 E-value=15 Score=32.58 Aligned_cols=66 Identities=20% Similarity=0.127 Sum_probs=47.3
Q ss_pred ccchHHHHHHH---HhcCccccchHHHHHHHHHHHH-------------------HHHHHHHHHHHHHhhCCCceecHHH
Q 047769 57 GITKPAIRRLA---RRGGVKRISGLIYEETRGVLKI-------------------FLENVIRDAVTYTEHARRKTVTAMD 114 (131)
Q Consensus 57 gIpk~aIrRLA---rr~GvkRIS~~ay~el~~vle~-------------------fle~I~~dAv~yaeHA~RKTVt~~D 114 (131)
.++...+++.. |.--...+|+++.+.+.+.... .++.+++-|.++|.-..|.+|+.+|
T Consensus 417 ~~~~~~l~~yi~~ar~~~~P~ls~~~~~~i~~~y~~~R~~~~~~~~~~~~~~t~R~l~sliRla~A~A~l~~r~~V~~~D 496 (509)
T smart00350 417 PISQEFLRKYIAYAREKIKPKLSEEAAEKLVKAYVDLRKEDSQSEARSSIPITVRQLESIIRLSEAHAKMRLSDVVEEAD 496 (509)
T ss_pred cCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhcccccccccccccCcCHHHHHHHHHHHHHHHHHcCCCccCHHH
Confidence 45666666443 4312235888887776654222 3478899999999999999999999
Q ss_pred HHHHHHHc
Q 047769 115 VVYALKRQ 122 (131)
Q Consensus 115 V~~ALkr~ 122 (131)
|..|++-.
T Consensus 497 v~~ai~l~ 504 (509)
T smart00350 497 VEEAIRLL 504 (509)
T ss_pred HHHHHHHH
Confidence 99998753
No 92
>PRK12402 replication factor C small subunit 2; Reviewed
Probab=72.76 E-value=10 Score=30.51 Aligned_cols=56 Identities=18% Similarity=-0.019 Sum_probs=40.4
Q ss_pred HHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHH
Q 047769 63 IRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKR 121 (131)
Q Consensus 63 IrRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr 121 (131)
+++++++.|+. +++++.+.+.+...-=+++++..+..++. +..+||.+||..++..
T Consensus 193 l~~~~~~~~~~-~~~~al~~l~~~~~gdlr~l~~~l~~~~~--~~~~It~~~v~~~~~~ 248 (337)
T PRK12402 193 LESIAEAEGVD-YDDDGLELIAYYAGGDLRKAILTLQTAAL--AAGEITMEAAYEALGD 248 (337)
T ss_pred HHHHHHHcCCC-CCHHHHHHHHHHcCCCHHHHHHHHHHHHH--cCCCCCHHHHHHHhCC
Confidence 55666677876 99999999988776556666666665553 3347999999887754
No 93
>PF13335 Mg_chelatase_2: Magnesium chelatase, subunit ChlI
Probab=70.67 E-value=26 Score=24.45 Aligned_cols=58 Identities=14% Similarity=0.166 Sum_probs=46.4
Q ss_pred ccchHHHHHHHHhcCccccchHHHHHHHHHHHHH------HHHHHHHHHHHHhhCCCceecHHHHHHHHH
Q 047769 57 GITKPAIRRLARRGGVKRISGLIYEETRGVLKIF------LENVIRDAVTYTEHARRKTVTAMDVVYALK 120 (131)
Q Consensus 57 gIpk~aIrRLArr~GvkRIS~~ay~el~~vle~f------le~I~~dAv~yaeHA~RKTVt~~DV~~ALk 120 (131)
.+|-..|.+.+. +++++...|..+++.+ +..|++=|-+.|..++...|+.+||..||.
T Consensus 31 ~l~~~~l~~~~~------l~~~~~~~l~~~~~~~~lS~R~~~rilrvARTIADL~~~~~I~~~hi~EAl~ 94 (96)
T PF13335_consen 31 QLPGEELRKYCP------LSSEAKKLLEQAAEKLNLSARGYHRILRVARTIADLEGSERITREHIAEALS 94 (96)
T ss_pred cCCHHHHHhHcC------CCHHHHHHHHHHHHHcCcCHHHHHHHHHHHHHHHhHcCCCCCCHHHHHHHHh
Confidence 577777777653 7777777777766654 567888899999999999999999999984
No 94
>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=67.78 E-value=17 Score=32.44 Aligned_cols=62 Identities=18% Similarity=0.175 Sum_probs=48.6
Q ss_pred chHHHHHHHHh----cCccccchHHHHHHHHH----HHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHH
Q 047769 59 TKPAIRRLARR----GGVKRISGLIYEETRGV----LKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKR 121 (131)
Q Consensus 59 pk~aIrRLArr----~GvkRIS~~ay~el~~v----le~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr 121 (131)
+...|+.|.+. .++. +|++|.+.|.+. .-.|.-|++.-|...|+..|+++|..+||..|-+.
T Consensus 362 ~~~EireIi~iRa~ee~i~-l~~~Ale~L~~ig~etSLRYa~qLL~pa~iiA~~rg~~~V~~~dVe~a~~l 431 (450)
T COG1224 362 SREEIREIIRIRAKEEDIE-LSDDALEYLTDIGEETSLRYAVQLLTPASIIAKRRGSKRVEVEDVERAKEL 431 (450)
T ss_pred CHHHHHHHHHHhhhhhccc-cCHHHHHHHHhhchhhhHHHHHHhccHHHHHHHHhCCCeeehhHHHHHHHH
Confidence 34445555533 3444 899999999876 45788999999999999999999999999988653
No 95
>COG5624 TAF61 Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=66.59 E-value=2 Score=38.51 Aligned_cols=94 Identities=21% Similarity=0.201 Sum_probs=71.4
Q ss_pred ccCCCCCCcccccccccc-ccccchHHHHHHHHhc--CccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHH
Q 047769 37 KGLGKGGAKRHRKVLRDN-IQGITKPAIRRLARRG--GVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAM 113 (131)
Q Consensus 37 kg~gk~g~kR~rKvlrd~-i~gIpk~aIrRLArr~--GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~ 113 (131)
.||...|.-|-.---+|+ -+-.+|+.++.|.+.+ +-+.|..++-+-|.+....|.+.|..=+..||.|-+-+|+.+-
T Consensus 362 ~gl~Tpg~~k~p~ye~D~~~Rl~skrkL~el~~~~vd~eekie~eveelll~~ad~fve~vt~FsCrlakhrkSdtlevr 441 (505)
T COG5624 362 GGLATPGRDKGPLYERDDLWRLDSKRKLEELQHGGVDEEEKIENEVEELLLSRADGFVEPVTEFSCRLAKHRKSDTLEVR 441 (505)
T ss_pred cccCCCcccCCCchhcchhhhhhhhhhHHHHHhhccCcceeccchHHHHHHhhhcccccccchheeEeeccCCCCceeec
Confidence 345444533322222455 5567888888888665 3477999999999999999999999999999999999999999
Q ss_pred HHHHHHHHcC-CcccccC
Q 047769 114 DVVYALKRQG-RTLYGFG 130 (131)
Q Consensus 114 DV~~ALkr~G-~~lYGF~ 130 (131)
||-+-|+|.- ..+=||.
T Consensus 442 D~qlhlErnwnIr~pGf~ 459 (505)
T COG5624 442 DGQLHLERNWNIRCPGFV 459 (505)
T ss_pred cceeeeccccceecCcch
Confidence 9999999864 3344774
No 96
>PRK00440 rfc replication factor C small subunit; Reviewed
Probab=66.37 E-value=19 Score=28.61 Aligned_cols=56 Identities=20% Similarity=0.129 Sum_probs=40.5
Q ss_pred HHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHH
Q 047769 63 IRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKR 121 (131)
Q Consensus 63 IrRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr 121 (131)
+..+++..|+. +++++.+.+.+...--+..++.....++..+ ++||.+||..++..
T Consensus 170 l~~~~~~~~~~-i~~~al~~l~~~~~gd~r~~~~~l~~~~~~~--~~it~~~v~~~~~~ 225 (319)
T PRK00440 170 LRYIAENEGIE-ITDDALEAIYYVSEGDMRKAINALQAAAATG--KEVTEEAVYKITGT 225 (319)
T ss_pred HHHHHHHcCCC-CCHHHHHHHHHHcCCCHHHHHHHHHHHHHcC--CCCCHHHHHHHhCC
Confidence 45666667875 9999999998887666666666666665543 67999998877643
No 97
>cd08784 Death_DRs Death Domain of Death Receptors. Death domain (DD) found in death receptor proteins. Death receptors are members of the tumor necrosis factor (TNF) receptor superfamily, characterized by having a cytoplasmic DD. Known members of the family are Fas (CD95/APO-1), TNF-receptor 1 (TNFR1/TNFRSF1A/p55/CD120a), TNF-related apoptosis-inducing ligand receptor 1 (TRAIL-R1 /DR4), and receptor 2 (TRAIL-R2/DR5/APO-2/KILLER), as well as Death Receptor 3 (DR3/APO-3/TRAMP/WSL-1/LARD). They are involved in apoptosis signaling pathways. 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 signaling pathways and can recruit other proteins into signaling complexes.
Probab=66.07 E-value=27 Score=23.45 Aligned_cols=67 Identities=15% Similarity=0.076 Sum_probs=47.5
Q ss_pred cccccchHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHcCC
Q 047769 54 NIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGR 124 (131)
Q Consensus 54 ~i~gIpk~aIrRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~G~ 124 (131)
.+..+|....+++||+.|+ |+.-.+.+...-...-+++.+-....-+-.|+ .-|.+..+.||+..|.
T Consensus 5 v~~~v~~~~Wk~laR~LGl---s~~~I~~ie~~~~~~~eq~~~mL~~W~~k~G~-~At~~~L~~aL~~~~~ 71 (79)
T cd08784 5 VFEEVPFDQHKRFFRKLGL---SDNEIKVAELDNPQHRDRVYELLRIWRNKEGR-KATLNTLIKALKDLDQ 71 (79)
T ss_pred HHHHCCHHHHHHHHHHcCC---CHHHHHHHHHcCCchHHHHHHHHHHHHhccCc-CcHHHHHHHHHHHccc
Confidence 3456788889999999994 45555555443323346666667777777777 6689999999998774
No 98
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=63.80 E-value=34 Score=28.15 Aligned_cols=74 Identities=15% Similarity=0.106 Sum_probs=49.6
Q ss_pred ccccchHHHHHHHH----hcCccccchHHHHHHHHHHH---HHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHcCCccc
Q 047769 55 IQGITKPAIRRLAR----RGGVKRISGLIYEETRGVLK---IFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTLY 127 (131)
Q Consensus 55 i~gIpk~aIrRLAr----r~GvkRIS~~ay~el~~vle---~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~G~~lY 127 (131)
+..++...+..+.+ ..++. +++++.+.+.+... ..+..+++.+..++.-.+...|+.++|..++...+...+
T Consensus 177 l~~~~~~e~~~il~~~~~~~~~~-~~~~~~~~ia~~~~G~pR~a~~~l~~~~~~a~~~~~~~I~~~~v~~~l~~~~~~~~ 255 (328)
T PRK00080 177 LEFYTVEELEKIVKRSARILGVE-IDEEGALEIARRSRGTPRIANRLLRRVRDFAQVKGDGVITKEIADKALDMLGVDEL 255 (328)
T ss_pred cCCCCHHHHHHHHHHHHHHcCCC-cCHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCcC
Confidence 34566666554443 44544 89999888886653 345666666666776556678999999999988765544
Q ss_pred cc
Q 047769 128 GF 129 (131)
Q Consensus 128 GF 129 (131)
|.
T Consensus 256 ~l 257 (328)
T PRK00080 256 GL 257 (328)
T ss_pred CC
Confidence 43
No 99
>COG1466 HolA DNA polymerase III, delta subunit [DNA replication, recombination, and repair]
Probab=62.82 E-value=26 Score=29.20 Aligned_cols=60 Identities=20% Similarity=0.092 Sum_probs=51.4
Q ss_pred HHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHc
Q 047769 62 AIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 122 (131)
Q Consensus 62 aIrRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~ 122 (131)
-|.+.++..|++ |+++|.+.+...++.=+..+..+..+.+-.++=++||.+||..++-.-
T Consensus 148 ~i~~~~~~~~l~-i~~~a~~~L~~~~~~nl~~i~~Ei~KL~l~~~~~~I~~~~V~~~v~~~ 207 (334)
T COG1466 148 WIKKRAKELGLK-IDQEAIQLLLEALGGNLLAIAQEIEKLALYAGDKEITLEDVEEVVSDV 207 (334)
T ss_pred HHHHHHHHcCCC-CCHHHHHHHHHHhCCcHHHHHHHHHHHHHhCCCCcCCHHHHHHHHhcc
Confidence 366667778866 999999999999999999999999999888877799999999888553
No 100
>PRK14970 DNA polymerase III subunits gamma and tau; Provisional
Probab=59.57 E-value=25 Score=29.27 Aligned_cols=56 Identities=13% Similarity=0.078 Sum_probs=37.1
Q ss_pred HHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHH
Q 047769 63 IRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALK 120 (131)
Q Consensus 63 IrRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALk 120 (131)
+.++|++.|++ +++++.+.+.+...-=+..+.......+.+++.. ||.+||..++.
T Consensus 176 l~~~~~~~g~~-i~~~al~~l~~~~~gdlr~~~~~lekl~~y~~~~-it~~~v~~~~~ 231 (367)
T PRK14970 176 LAGIAVKEGIK-FEDDALHIIAQKADGALRDALSIFDRVVTFCGKN-ITRQAVTENLN 231 (367)
T ss_pred HHHHHHHcCCC-CCHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCCC-CCHHHHHHHhC
Confidence 45566677875 9999999988876544444444444444444544 89888886653
No 101
>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau. This model represents the well-conserved first ~ 365 amino acids of the translation of the dnaX gene. The full-length product of the dnaX gene in the model bacterium E. coli is the DNA polymerase III tau subunit. A translational frameshift leads to early termination and a truncated protein subunit gamma, about 1/3 shorter than tau and present in roughly equal amounts. This frameshift mechanism is not necessarily universal for species with DNA polymerase III but appears conserved in the exterme thermophile Thermus thermophilis.
Probab=58.83 E-value=27 Score=28.44 Aligned_cols=56 Identities=16% Similarity=0.138 Sum_probs=34.6
Q ss_pred HHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHH
Q 047769 63 IRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALK 120 (131)
Q Consensus 63 IrRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALk 120 (131)
++..++..|++ +++++.+.+.+...--+..+...+...+.+++ +.||.+||..++.
T Consensus 185 l~~~~~~~g~~-i~~~a~~~l~~~~~g~~~~a~~~lekl~~~~~-~~it~~~v~~~~~ 240 (355)
T TIGR02397 185 LKKILDKEGIK-IEDEALELIARAADGSLRDALSLLDQLISFGN-GNITYEDVNELLG 240 (355)
T ss_pred HHHHHHHcCCC-CCHHHHHHHHHHcCCChHHHHHHHHHHHhhcC-CCCCHHHHHHHhC
Confidence 44455567764 89999888887765444444444444444444 3488888876553
No 102
>PRK14964 DNA polymerase III subunits gamma and tau; Provisional
Probab=58.71 E-value=23 Score=31.89 Aligned_cols=55 Identities=7% Similarity=-0.038 Sum_probs=37.9
Q ss_pred HHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHH
Q 047769 63 IRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYAL 119 (131)
Q Consensus 63 IrRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~AL 119 (131)
+.++++..|+. |++++.+.+.+...--+..++......+.+++ .+||.+||...|
T Consensus 184 L~~ia~~Egi~-i~~eAL~lIa~~s~GslR~alslLdqli~y~~-~~It~e~V~~ll 238 (491)
T PRK14964 184 LVDIAKKENIE-HDEESLKLIAENSSGSMRNALFLLEQAAIYSN-NKISEKSVRDLL 238 (491)
T ss_pred HHHHHHHcCCC-CCHHHHHHHHHHcCCCHHHHHHHHHHHHHhcC-CCCCHHHHHHHH
Confidence 45556667764 99999999887765555555555544455555 479999998765
No 103
>PF09288 UBA_3: Fungal ubiquitin-associated domain ; InterPro: IPR015368 This C-terminal domain is found in ubiquitin binding proteins, it adopts a structure consisting of a three alpha-helix bundle. This domain is predominantly found in fungi []. ; PDB: 1TTE_A.
Probab=58.39 E-value=13 Score=24.32 Aligned_cols=36 Identities=25% Similarity=0.452 Sum_probs=21.3
Q ss_pred cccchHHHHHHHHhcCccccchHHHHHHHHHHHHHH
Q 047769 56 QGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFL 91 (131)
Q Consensus 56 ~gIpk~aIrRLArr~GvkRIS~~ay~el~~vle~fl 91 (131)
.|+++..|-..+|+.|++++.+.-.+.-..++++.|
T Consensus 19 mGF~~dkVvevlrrlgik~~n~~dn~t~~~ilEELL 54 (55)
T PF09288_consen 19 MGFERDKVVEVLRRLGIKSMNGVDNETENKILEELL 54 (55)
T ss_dssp HT--HHHHHHHHHHS--SS--SS--HHHHHHHHHHT
T ss_pred cCCcHHHHHHHHHHhCCCCCCCccchhHHHHHHHHh
Confidence 489999999999999999988666666555565543
No 104
>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda. Members of this protein family are Hda (Homologous to DnaA). These proteins are about half the length of DnaA and homologous over length of Hda. In the model species Escherichia coli, the initiation of DNA replication requires DnaA bound to ATP rather than ADP; Hda helps facilitate the conversion of DnaA-ATP to DnaA-ADP.
Probab=56.98 E-value=52 Score=24.81 Aligned_cols=61 Identities=11% Similarity=-0.011 Sum_probs=41.7
Q ss_pred ccchHHHHHHH----HhcCccccchHHHHHHHHHHH---HHHHHHHHHHHHHHhhCCCceecHHHHHHHH
Q 047769 57 GITKPAIRRLA----RRGGVKRISGLIYEETRGVLK---IFLENVIRDAVTYTEHARRKTVTAMDVVYAL 119 (131)
Q Consensus 57 gIpk~aIrRLA----rr~GvkRIS~~ay~el~~vle---~fle~I~~dAv~yaeHA~RKTVt~~DV~~AL 119 (131)
.++...+..++ .+.|+ .+++++.+.|..... ..+.++++++..++.-++ ++||.+.|...|
T Consensus 158 ~l~~~e~~~~l~~~~~~~~~-~~~~~~l~~L~~~~~gn~r~L~~~l~~~~~~~~~~~-~~i~~~~~~~~~ 225 (226)
T TIGR03420 158 PLSDEEKIAALQSRAARRGL-QLPDEVADYLLRHGSRDMGSLMALLDALDRASLAAK-RKITIPFVKEVL 225 (226)
T ss_pred CCCHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHhC-CCCCHHHHHHHh
Confidence 44444444433 34554 499999999887543 457778888887776666 479999988776
No 105
>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=56.14 E-value=48 Score=28.25 Aligned_cols=48 Identities=15% Similarity=0.013 Sum_probs=36.6
Q ss_pred cccchHHHHHHHHHHHHHH-------HHHHHHHHHHHhhCCCceecHHHHHHHHH
Q 047769 73 KRISGLIYEETRGVLKIFL-------ENVIRDAVTYTEHARRKTVTAMDVVYALK 120 (131)
Q Consensus 73 kRIS~~ay~el~~vle~fl-------e~I~~dAv~yaeHA~RKTVt~~DV~~ALk 120 (131)
-.||+++.+.+.+.....= ..+++-|-++|--.||..|+.+||..+..
T Consensus 253 V~v~d~~~~~i~~l~~~~~~~s~Ra~i~l~raArA~Aal~GR~~V~~dDv~~~a~ 307 (337)
T TIGR02030 253 VTIPYDVLVKVAELCAELDVDGLRGELTLNRAAKALAAFEGRTEVTVDDIRRVAV 307 (337)
T ss_pred CcCCHHHHHHHHHHHHHHCCCCCcHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 3477777777777655432 23678888999999999999999997764
No 106
>PRK09087 hypothetical protein; Validated
Probab=55.56 E-value=95 Score=24.52 Aligned_cols=59 Identities=8% Similarity=-0.048 Sum_probs=41.3
Q ss_pred HHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHH---HHHHHHhhCCCceecHHHHHHHHHHc
Q 047769 62 AIRRLARRGGVKRISGLIYEETRGVLKIFLENVIR---DAVTYTEHARRKTVTAMDVVYALKRQ 122 (131)
Q Consensus 62 aIrRLArr~GvkRIS~~ay~el~~vle~fle~I~~---dAv~yaeHA~RKTVt~~DV~~ALkr~ 122 (131)
.+++.++..|+ .+++++.+.+.+-+..=++.+.. ....++...+|+ ||...|..+|+..
T Consensus 161 iL~~~~~~~~~-~l~~ev~~~La~~~~r~~~~l~~~l~~L~~~~~~~~~~-it~~~~~~~l~~~ 222 (226)
T PRK09087 161 VIFKLFADRQL-YVDPHVVYYLVSRMERSLFAAQTIVDRLDRLALERKSR-ITRALAAEVLNEM 222 (226)
T ss_pred HHHHHHHHcCC-CCCHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhCCC-CCHHHHHHHHHhh
Confidence 34555555565 49999999998877666655554 444556555654 9999999999764
No 107
>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=55.19 E-value=40 Score=30.86 Aligned_cols=48 Identities=27% Similarity=0.142 Sum_probs=38.5
Q ss_pred ccchHHHHHHHHHHHHH-------HHHHHHHHHHHHhhCCCceecHHHHHHHHHH
Q 047769 74 RISGLIYEETRGVLKIF-------LENVIRDAVTYTEHARRKTVTAMDVVYALKR 121 (131)
Q Consensus 74 RIS~~ay~el~~vle~f-------le~I~~dAv~yaeHA~RKTVt~~DV~~ALkr 121 (131)
.||+++.+.+.+....+ ...+++-|-++|...+|.+|+.+||..|++-
T Consensus 249 ~is~~~~~~l~~~~~~~~i~s~Ra~i~~~r~Ara~AaL~gr~~V~~~Dv~~A~~l 303 (633)
T TIGR02442 249 RISDSLIRFISELCIEFGVDGHRADIVMARAARALAALDGRRRVTAEDVREAAEL 303 (633)
T ss_pred CCCHHHHHHHHHHHHHhCCCCccHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHH
Confidence 47888888887776554 2457788889999999999999999888764
No 108
>PRK08903 DnaA regulatory inactivator Hda; Validated
Probab=54.78 E-value=74 Score=24.36 Aligned_cols=57 Identities=14% Similarity=0.137 Sum_probs=41.6
Q ss_pred HHHHHHHhcCccccchHHHHHHHHHHH---HHHHHHHHHHHHHHhhCCCceecHHHHHHHHH
Q 047769 62 AIRRLARRGGVKRISGLIYEETRGVLK---IFLENVIRDAVTYTEHARRKTVTAMDVVYALK 120 (131)
Q Consensus 62 aIrRLArr~GvkRIS~~ay~el~~vle---~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALk 120 (131)
.+.+++.+.|+. +++++.+.|..... ..+.+++++...++...+ +.||-..|..+|.
T Consensus 165 ~l~~~~~~~~v~-l~~~al~~L~~~~~gn~~~l~~~l~~l~~~~~~~~-~~i~~~~~~~~l~ 224 (227)
T PRK08903 165 ALKAAAAERGLQ-LADEVPDYLLTHFRRDMPSLMALLDALDRYSLEQK-RPVTLPLLREMLA 224 (227)
T ss_pred HHHHHHHHcCCC-CCHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHhC-CCCCHHHHHHHHh
Confidence 344555566744 99999999998654 346667777777777767 5899999988874
No 109
>PRK14955 DNA polymerase III subunits gamma and tau; Provisional
Probab=54.49 E-value=39 Score=28.89 Aligned_cols=62 Identities=8% Similarity=0.100 Sum_probs=40.4
Q ss_pred ccchHHH----HHHHHhcCccccchHHHHHHHHHHHHHHHHHHH---HHHHHHh-hCCCceecHHHHHHHH
Q 047769 57 GITKPAI----RRLARRGGVKRISGLIYEETRGVLKIFLENVIR---DAVTYTE-HARRKTVTAMDVVYAL 119 (131)
Q Consensus 57 gIpk~aI----rRLArr~GvkRIS~~ay~el~~vle~fle~I~~---dAv~yae-HA~RKTVt~~DV~~AL 119 (131)
.++...+ .++++..|+. |++++.+.+.+...--+..+.. .+..|+. +...++||.+||..++
T Consensus 185 ~l~~~ei~~~l~~~~~~~g~~-i~~~al~~l~~~s~g~lr~a~~~L~kl~~~~~~~~~~~~It~~~v~~~v 254 (397)
T PRK14955 185 RIPLEEIQQQLQGICEAEGIS-VDADALQLIGRKAQGSMRDAQSILDQVIAFSVESEGEGSIRYDKVAELL 254 (397)
T ss_pred CCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHcCCCHHHHHHHHHHHHHhccccCCCCccCHHHHHHHH
Confidence 3444444 4444445654 9999999988877665554444 4455654 4567799999887655
No 110
>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional
Probab=54.42 E-value=19 Score=31.82 Aligned_cols=35 Identities=20% Similarity=0.140 Sum_probs=30.6
Q ss_pred HHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHc
Q 047769 88 KIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 122 (131)
Q Consensus 88 e~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~ 122 (131)
-.-+..|+.+|...|...+|..|+.+|+..|+++.
T Consensus 390 gAdI~~i~~eA~~~Alr~~r~~Vt~~D~~~A~~~v 424 (438)
T PTZ00361 390 GADIKAICTEAGLLALRERRMKVTQADFRKAKEKV 424 (438)
T ss_pred HHHHHHHHHHHHHHHHHhcCCccCHHHHHHHHHHH
Confidence 33477899999999999999999999999999873
No 111
>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=54.33 E-value=94 Score=24.81 Aligned_cols=67 Identities=13% Similarity=0.016 Sum_probs=44.1
Q ss_pred cccchHHHHHH----HHhcCccccchHHHHHHHHHHHH---HHHHHHHHHHHHHhhCCCceecHHHHHHHHHHcC
Q 047769 56 QGITKPAIRRL----ARRGGVKRISGLIYEETRGVLKI---FLENVIRDAVTYTEHARRKTVTAMDVVYALKRQG 123 (131)
Q Consensus 56 ~gIpk~aIrRL----Arr~GvkRIS~~ay~el~~vle~---fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~G 123 (131)
..++...+..+ +...++ .+++++.+.+.+...- .+.+++..+..++...+...|+.++|..++....
T Consensus 157 ~~l~~~e~~~il~~~~~~~~~-~~~~~al~~ia~~~~G~pR~~~~ll~~~~~~a~~~~~~~it~~~v~~~l~~l~ 230 (305)
T TIGR00635 157 EFYTVEELAEIVSRSAGLLNV-EIEPEAALEIARRSRGTPRIANRLLRRVRDFAQVRGQKIINRDIALKALEMLM 230 (305)
T ss_pred CCCCHHHHHHHHHHHHHHhCC-CcCHHHHHHHHHHhCCCcchHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHhC
Confidence 34555544444 444455 4889998888876432 3455666666677666667799999999998743
No 112
>PRK04195 replication factor C large subunit; Provisional
Probab=52.57 E-value=37 Score=29.78 Aligned_cols=54 Identities=20% Similarity=0.172 Sum_probs=42.0
Q ss_pred HHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHH
Q 047769 63 IRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYAL 119 (131)
Q Consensus 63 IrRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~AL 119 (131)
+++++++.|+. +++++++.+.+...--++.++.++..++. ++..++.+||...+
T Consensus 169 L~~i~~~egi~-i~~eaL~~Ia~~s~GDlR~ain~Lq~~a~--~~~~it~~~v~~~~ 222 (482)
T PRK04195 169 LKRICRKEGIE-CDDEALKEIAERSGGDLRSAINDLQAIAE--GYGKLTLEDVKTLG 222 (482)
T ss_pred HHHHHHHcCCC-CCHHHHHHHHHHcCCCHHHHHHHHHHHhc--CCCCCcHHHHHHhh
Confidence 45666667875 89999999998887788888888888765 45568898887665
No 113
>CHL00081 chlI Mg-protoporyphyrin IX chelatase
Probab=52.35 E-value=81 Score=27.18 Aligned_cols=62 Identities=13% Similarity=-0.007 Sum_probs=43.5
Q ss_pred chHHHHHHHHhcCccccchHHHHHHHHHHHHHH-------HHHHHHHHHHHhhCCCceecHHHHHHHHH
Q 047769 59 TKPAIRRLARRGGVKRISGLIYEETRGVLKIFL-------ENVIRDAVTYTEHARRKTVTAMDVVYALK 120 (131)
Q Consensus 59 pk~aIrRLArr~GvkRIS~~ay~el~~vle~fl-------e~I~~dAv~yaeHA~RKTVt~~DV~~ALk 120 (131)
....|...-+..---.||+++.+.+.+.+...= ..+++-|-++|--+||..|+.+||..+..
T Consensus 252 ~~~~I~~ar~~~~~V~v~~~~~~yi~~l~~~~~~~s~Ra~i~l~raArA~Aal~GR~~V~pdDv~~~a~ 320 (350)
T CHL00081 252 LRSKIVAAQNLLPKVEIDYDLRVKISQICSELDVDGLRGDIVTNRAAKALAAFEGRTEVTPKDIFKVIT 320 (350)
T ss_pred CHHHHHHHHHhcCCCccCHHHHHHHHHHHHHHCCCCChHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 344444444443334478888877777766542 24667788999999999999999998765
No 114
>PRK09111 DNA polymerase III subunits gamma and tau; Validated
Probab=52.10 E-value=35 Score=31.41 Aligned_cols=56 Identities=18% Similarity=0.103 Sum_probs=39.2
Q ss_pred HHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHH
Q 047769 63 IRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALK 120 (131)
Q Consensus 63 IrRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALk 120 (131)
++++++..|+. |++++.+.+.....-.+..++......+.++ ...||.+||...+-
T Consensus 200 L~~i~~kegi~-i~~eAl~lIa~~a~Gdlr~al~~Ldkli~~g-~g~It~e~V~~llg 255 (598)
T PRK09111 200 LSRIAAKEGVE-VEDEALALIARAAEGSVRDGLSLLDQAIAHG-AGEVTAEAVRDMLG 255 (598)
T ss_pred HHHHHHHcCCC-CCHHHHHHHHHHcCCCHHHHHHHHHHHHhhc-CCCcCHHHHHHHhC
Confidence 45555667766 9999998888877766666655554544453 45799999987663
No 115
>PF00493 MCM: MCM2/3/5 family This family extends the MCM domain of Prosite.; InterPro: IPR001208 MCM proteins are DNA-dependent ATPases required for the initiation of eukaryotic DNA replication [, , ]. In eukaryotes there is a family of six proteins, MCM2 to MCM7. They were first identified in yeast where most of them have a direct role in the initiation of chromosomal DNA replication by interacting directly with autonomously replicating sequences (ARS). They were thus called minichromosome maintenance proteins, MCM proteins []. This family is also present in the archebacteria in 1 to 4 copies. Methanocaldococcus jannaschii (Methanococcus jannaschii) has four members, MJ0363, MJ0961, MJ1489 and MJECL13. The "MCM motif" contains Walker-A and Walker-B type nucleotide binding motifs. The diagnostic sequence defining the MCMs is IDEFDKM. Only Mcm2 (aka Cdc19 or Nda1) has been subjected to mutational analysis in this region, and most mutations abolish its activity []. The presence of a putative ATP-binding domain implies that these proteins may be involved in an ATP-consuming step in the initiation of DNA replication in eukaryotes. The MCM proteins bind together in a large complex []. Within this complex, individual subunits associate with different affinities, and there is a tightly associated core of Mcm4 (Cdc21), Mcm6 (Mis5) and Mcm7 []. This core complex in human MCMs has been associated with helicase activity in vitro [], leading to the suggestion that the MCM proteins are the eukaryotic replicative helicase. Schizosaccharomyces pombe (Fission yeast) MCMs, like those in metazoans, are found in the nucleus throughout the cell cycle. This is in contrast to the Saccharomyces cerevisiae (Baker's yeast) in which MCM proteins move in and out of the nucleus during each cell cycle. The assembly of the MCM complex in S. pombe is required for MCM localisation, ensuring that only intact MCM complexes remain in the nucleus [].; GO: 0003677 DNA binding, 0005524 ATP binding, 0006260 DNA replication; PDB: 3F8T_A 3F9V_A.
Probab=51.54 E-value=14 Score=30.91 Aligned_cols=66 Identities=24% Similarity=0.139 Sum_probs=44.7
Q ss_pred ccchHHHHH---HHHhcCccccchHHHHHHHHHH-----------------HHHHHHHHHHHHHHHhhCCCceecHHHHH
Q 047769 57 GITKPAIRR---LARRGGVKRISGLIYEETRGVL-----------------KIFLENVIRDAVTYTEHARRKTVTAMDVV 116 (131)
Q Consensus 57 gIpk~aIrR---LArr~GvkRIS~~ay~el~~vl-----------------e~fle~I~~dAv~yaeHA~RKTVt~~DV~ 116 (131)
.+|..-+++ .||..=...+|+++.+.+.+.. -..|+-+++=|.+.|+-.-|.+|+.+||.
T Consensus 241 ~~~~~~lr~yI~yar~~~~P~ls~ea~~~I~~~Yv~lR~~~~~~~~~~~iT~R~LeSLIRLseA~AKl~lr~~V~~~Dv~ 320 (331)
T PF00493_consen 241 PISEDLLRKYIAYARQNIHPVLSEEAKELIINYYVELRKESKSNNKSIPITIRQLESLIRLSEAHAKLRLRDEVTEEDVE 320 (331)
T ss_dssp TT-HCCCHHHHHHHHHHC--EE-HHCHHHHHHHHCCCCHCHHCHSS-B-SSCCCCCHHHHHHHHHHHCTTSSECSHHHHH
T ss_pred ccCHHHHHHHHHHHHhhcccccCHHHHHHHHHHHHHhcccccccccccccchhhHHHHHHHHHHHHHHhccCceeHHHHH
Confidence 445544443 3452223458888877776541 12457899999999999999999999999
Q ss_pred HHHHHc
Q 047769 117 YALKRQ 122 (131)
Q Consensus 117 ~ALkr~ 122 (131)
.|++-.
T Consensus 321 ~Ai~L~ 326 (331)
T PF00493_consen 321 EAIRLF 326 (331)
T ss_dssp HHHHHH
T ss_pred HHHHHH
Confidence 998753
No 116
>cd08780 Death_TRADD Death Domain of Tumor Necrosis Factor Receptor 1-Associated Death Domain protein. Death domain (DD) of TRADD (TNF Receptor 1-Associated Death Domain or TNFRSF1A-associated via death domain) protein. TRADD is a central signaling adaptor for TNF-receptor 1 (TNFR1), mediating activation of Nuclear Factor -kappaB (NF-kB) and c-Jun N-terminal kinase (JNK), as well as caspase-dependent apoptosis. It also carries important immunological roles including germinal center formation, DR3-mediated T-cell stimulation, and TNFalpha-mediated inflammatory responses. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into s
Probab=51.39 E-value=56 Score=23.37 Aligned_cols=62 Identities=15% Similarity=0.132 Sum_probs=41.4
Q ss_pred HHHHHHhcCc--cccchHHHHHHHHHHH-H-HHHHHHHHHHHHHhhCCCceecHHHHHHHHHHcCCc
Q 047769 63 IRRLARRGGV--KRISGLIYEETRGVLK-I-FLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRT 125 (131)
Q Consensus 63 IrRLArr~Gv--kRIS~~ay~el~~vle-~-fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~G~~ 125 (131)
.+++||+.|- .-+++...+.+...-+ + .-|++-+-...+.+..|++ -|....+.||+..+.+
T Consensus 16 WK~laR~Lg~~cral~d~~ID~I~~~y~r~gL~EqvyQ~L~~W~~~eg~~-Atv~~Lv~AL~~c~l~ 81 (90)
T cd08780 16 WKPVGRSLQKNCRALRDPAIDNLAYEYDREGLYEQAYQLLRRFIQSEGKK-ATLQRLVQALEENGLT 81 (90)
T ss_pred HHHHHHHHcccccccchhHHHHHHhhcccccHHHHHHHHHHHHHHhcccc-chHHHHHHHHHHccch
Confidence 5677777772 2366666666653222 2 3455555566777777877 9999999999987754
No 117
>cd08315 Death_TRAILR_DR4_DR5 Death domain of Tumor necrosis factor-Related Apoptosis-Inducing Ligand Receptors. Death Domain (DD) found in Tumor necrosis factor-Related Apoptosis-Inducing Ligand (TRAIL) Receptors. In mammals, this family includes TRAILR1 (also called DR4 or TNFRSF10A) and TRAILR2 (also called DR5, TNFRSF10B, or KILLER). They function as receptors for the cytokine TRAIL and are involved in apoptosis signaling pathways. TRAIL preferentially induces apoptosis in cancer cells while exhibiting little toxicity in normal cells. 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 signaling pathways and can recruit other proteins into signaling complexes.
Probab=51.26 E-value=43 Score=23.49 Aligned_cols=66 Identities=18% Similarity=0.232 Sum_probs=45.0
Q ss_pred ccccchHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHcCC
Q 047769 55 IQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGR 124 (131)
Q Consensus 55 i~gIpk~aIrRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~G~ 124 (131)
...+|....+++||+.| +|+.-.+.+...-..--+++.+-.....+-.|+ .-|...++.||+..+.
T Consensus 14 ~~~V~~~~Wk~laR~LG---Lse~~I~~i~~~~~~~~eq~~qmL~~W~~~~G~-~At~~~L~~aL~~~~~ 79 (96)
T cd08315 14 IKEVPFDSWNRLMRQLG---LSENEIDVAKANERVTREQLYQMLLTWVNKTGR-KASVNTLLDALEAIGL 79 (96)
T ss_pred HHHCCHHHHHHHHHHcC---CCHHHHHHHHHHCCCCHHHHHHHHHHHHHhhCC-CcHHHHHHHHHHHccc
Confidence 45678888999999999 455555555443222256666667777776666 5668888888888764
No 118
>TIGR00368 Mg chelatase-related protein. The N-terminal end matches very strongly a pfam Mg_chelatase domain.
Probab=50.63 E-value=57 Score=29.30 Aligned_cols=46 Identities=15% Similarity=0.271 Sum_probs=36.7
Q ss_pred cchHHHHHHHHHHHHH------HHHHHHHHHHHHhhCCCceecHHHHHHHHH
Q 047769 75 ISGLIYEETRGVLKIF------LENVIRDAVTYTEHARRKTVTAMDVVYALK 120 (131)
Q Consensus 75 IS~~ay~el~~vle~f------le~I~~dAv~yaeHA~RKTVt~~DV~~ALk 120 (131)
+++++.+.+.++++.+ ...|++=|-++|..+++..|+.+||..|+.
T Consensus 446 l~~~~~~~l~~a~~~~~lS~R~~~rilrvArTiAdL~g~~~i~~~hv~eA~~ 497 (499)
T TIGR00368 446 LSAIDANDLEGALNKLGLSSRATHRILKVARTIADLKEEKNISREHLAEAIE 497 (499)
T ss_pred CCHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHh
Confidence 4556666666555554 567899999999999999999999999984
No 119
>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=49.81 E-value=44 Score=20.50 Aligned_cols=31 Identities=19% Similarity=0.244 Sum_probs=23.5
Q ss_pred ccchHHHHHHHHhcCccccchHHHHHHHHHHHH
Q 047769 57 GITKPAIRRLARRGGVKRISGLIYEETRGVLKI 89 (131)
Q Consensus 57 gIpk~aIrRLArr~GvkRIS~~ay~el~~vle~ 89 (131)
|++.++|.|.+... .+||++..+.+.+++++
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 67888888888655 57888887777776654
No 120
>PRK06645 DNA polymerase III subunits gamma and tau; Validated
Probab=49.79 E-value=41 Score=30.37 Aligned_cols=65 Identities=3% Similarity=-0.057 Sum_probs=40.7
Q ss_pred ccccchHH----HHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCC--CceecHHHHHHHHH
Q 047769 55 IQGITKPA----IRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHAR--RKTVTAMDVVYALK 120 (131)
Q Consensus 55 i~gIpk~a----IrRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~--RKTVt~~DV~~ALk 120 (131)
++.++... ++++++..|+. +++++++.+.....--+..++...-..+.+++ ...||.+||...+-
T Consensus 184 f~~ls~~el~~~L~~i~~~egi~-ie~eAL~~Ia~~s~GslR~al~~Ldkai~~~~~~~~~It~~~V~~llg 254 (507)
T PRK06645 184 LRRLSFEEIFKLLEYITKQENLK-TDIEALRIIAYKSEGSARDAVSILDQAASMSAKSDNIISPQVINQMLG 254 (507)
T ss_pred ccCCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHcCCCHHHHHHHHHHHHHhhccCCCCcCHHHHHHHHC
Confidence 34455544 45566677754 89999998887765555555444444333332 34799999987763
No 121
>PRK13407 bchI magnesium chelatase subunit I; Provisional
Probab=49.72 E-value=73 Score=27.13 Aligned_cols=62 Identities=8% Similarity=0.013 Sum_probs=44.7
Q ss_pred cchHHHHHHHHhcCccccchHHHHHHHHHHHHHHH-------HHHHHHHHHHhhCCCceecHHHHHHHH
Q 047769 58 ITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLE-------NVIRDAVTYTEHARRKTVTAMDVVYAL 119 (131)
Q Consensus 58 Ipk~aIrRLArr~GvkRIS~~ay~el~~vle~fle-------~I~~dAv~yaeHA~RKTVt~~DV~~AL 119 (131)
+....|..+-+..---.||+++.+.+.+++...=. .+++.|.++|-..||..|+.+||..+.
T Consensus 235 ~~~~~i~~a~~~~~~V~v~~~~~~yi~~l~~~~~~~s~Ra~i~l~~aA~a~A~l~Gr~~V~~~Di~~~~ 303 (334)
T PRK13407 235 QLRGRILGARARLPQLKTPNTVLHDCAALCIALGSDGLRGELTLLRAARALAAFEGAEAVGRSHLRSVA 303 (334)
T ss_pred CCHHHHHHHHHhcCCcccCHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHHcCCCeeCHHHHHHHH
Confidence 33445555544444455888888888887665321 278899999999999999999996554
No 122
>KOG0784 consensus Isocitrate dehydrogenase, gamma subunit [Amino acid transport and metabolism]
Probab=49.60 E-value=8.2 Score=33.80 Aligned_cols=36 Identities=31% Similarity=0.316 Sum_probs=30.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecH
Q 047769 77 GLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTA 112 (131)
Q Consensus 77 ~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~ 112 (131)
+.+.|.|.=+.+.-.+.|++-|..||...+||.||+
T Consensus 172 pGVVEsLKVvT~~kseRIaryAF~yA~k~gRKkVTa 207 (375)
T KOG0784|consen 172 PGVVESLKVVTRFKSERIARYAFEYAKKNGRKKVTA 207 (375)
T ss_pred cchhheeeeehhhhhHHHHHHHHHHHHHhCCceEEE
Confidence 355666666777888999999999999999999986
No 123
>PRK08727 hypothetical protein; Validated
Probab=48.21 E-value=1.1e+02 Score=24.12 Aligned_cols=66 Identities=14% Similarity=0.016 Sum_probs=42.0
Q ss_pred ccccchHHHHHHHHh----cCccccchHHHHHHHHHHH---HHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHc
Q 047769 55 IQGITKPAIRRLARR----GGVKRISGLIYEETRGVLK---IFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 122 (131)
Q Consensus 55 i~gIpk~aIrRLArr----~GvkRIS~~ay~el~~vle---~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~ 122 (131)
++.+....+..++++ -|+ .+++++.+.|.+... ..+.++++.+..++-..+| .||.+.|...|..+
T Consensus 159 l~~~~~e~~~~iL~~~a~~~~l-~l~~e~~~~La~~~~rd~r~~l~~L~~l~~~~~~~~~-~it~~~~~~~l~~~ 231 (233)
T PRK08727 159 LPVLDDVARAAVLRERAQRRGL-ALDEAAIDWLLTHGERELAGLVALLDRLDRESLAAKR-RVTVPFLRRVLEEG 231 (233)
T ss_pred ecCCCHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhCC-CCCHHHHHHHHhhc
Confidence 334444454444443 455 489999998887765 3334446666655555565 69999999988654
No 124
>COG1737 RpiR Transcriptional regulators [Transcription]
Probab=47.50 E-value=82 Score=25.65 Aligned_cols=63 Identities=17% Similarity=0.230 Sum_probs=38.5
Q ss_pred ccchHHHHHHHHhcCccccchHHHHHHHHHHHH-----------------HHHHHHHHHHHHHhhCCCceecHHHHHHHH
Q 047769 57 GITKPAIRRLARRGGVKRISGLIYEETRGVLKI-----------------FLENVIRDAVTYTEHARRKTVTAMDVVYAL 119 (131)
Q Consensus 57 gIpk~aIrRLArr~GvkRIS~~ay~el~~vle~-----------------fle~I~~dAv~yaeHA~RKTVt~~DV~~AL 119 (131)
+++.++|-|+|++.|.+-+++- ...+++.+.. .+++++.+.....++. .+.++.+++..|.
T Consensus 47 ~VS~aTv~Rf~~kLGf~Gf~ef-k~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~t-~~~l~~~~l~~av 124 (281)
T COG1737 47 GVSPATVVRFARKLGFEGFSEF-KLALAQELAEGRAQLLREIAEDDGPESILEKLLAANIAALERT-LNLLDEEALERAV 124 (281)
T ss_pred CCCHHHHHHHHHHcCCCCHHHH-HHHHHHHHhhccchhhcccCCCCCHHHHHHHHHHHHHHHHHHH-HHhcCHHHHHHHH
Confidence 6789999999999998877743 3344444422 4555555555554442 2345566665555
Q ss_pred HH
Q 047769 120 KR 121 (131)
Q Consensus 120 kr 121 (131)
+.
T Consensus 125 ~~ 126 (281)
T COG1737 125 EL 126 (281)
T ss_pred HH
Confidence 54
No 125
>PRK00149 dnaA chromosomal replication initiation protein; Reviewed
Probab=46.69 E-value=74 Score=27.51 Aligned_cols=57 Identities=18% Similarity=0.206 Sum_probs=37.2
Q ss_pred HHHHHhcCccccchHHHHHHHHHHH---HHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHc
Q 047769 64 RRLARRGGVKRISGLIYEETRGVLK---IFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 122 (131)
Q Consensus 64 rRLArr~GvkRIS~~ay~el~~vle---~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~ 122 (131)
++.++..|+. +++++.+.+.+.+. .-|+.++.....|+...+|. ||.+.+..+|+..
T Consensus 290 ~~~~~~~~~~-l~~e~l~~ia~~~~~~~R~l~~~l~~l~~~~~~~~~~-it~~~~~~~l~~~ 349 (450)
T PRK00149 290 KKKAEEEGID-LPDEVLEFIAKNITSNVRELEGALNRLIAYASLTGKP-ITLELAKEALKDL 349 (450)
T ss_pred HHHHHHcCCC-CCHHHHHHHHcCcCCCHHHHHHHHHHHHHHHHhhCCC-CCHHHHHHHHHHh
Confidence 3444443443 88888888876544 34556666677777766654 7888888888753
No 126
>PRK13406 bchD magnesium chelatase subunit D; Provisional
Probab=46.55 E-value=94 Score=28.58 Aligned_cols=54 Identities=15% Similarity=-0.028 Sum_probs=42.4
Q ss_pred HhcCccccchHHHHHHHHHHHHHH-------HHHHHHHHHHHhhCCCceecHHHHHHHHHH
Q 047769 68 RRGGVKRISGLIYEETRGVLKIFL-------ENVIRDAVTYTEHARRKTVTAMDVVYALKR 121 (131)
Q Consensus 68 rr~GvkRIS~~ay~el~~vle~fl-------e~I~~dAv~yaeHA~RKTVt~~DV~~ALkr 121 (131)
++.+--.+++++.+.+.+++..+- ..+++-|-++|--+||.+|+.+||..|+.-
T Consensus 189 ~rl~~v~v~~~~l~~i~~~~~~~gv~S~Ra~i~llraARa~AaL~Gr~~V~~~dv~~Aa~l 249 (584)
T PRK13406 189 ARLPAVGPPPEAIAALCAAAAALGIASLRAPLLALRAARAAAALAGRTAVEEEDLALAARL 249 (584)
T ss_pred HHHccCCCCHHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence 333445688888888777666653 367888999999999999999999998864
No 127
>PRK03992 proteasome-activating nucleotidase; Provisional
Probab=46.27 E-value=33 Score=29.33 Aligned_cols=36 Identities=19% Similarity=0.209 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHc
Q 047769 87 LKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 122 (131)
Q Consensus 87 le~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~ 122 (131)
.-.-++.++++|..+|-..+++.|+.+|+..|++..
T Consensus 337 sgadl~~l~~eA~~~a~~~~~~~i~~~d~~~A~~~~ 372 (389)
T PRK03992 337 SGADLKAICTEAGMFAIRDDRTEVTMEDFLKAIEKV 372 (389)
T ss_pred CHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHH
Confidence 335678889999999999999999999999999875
No 128
>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=46.16 E-value=97 Score=21.95 Aligned_cols=64 Identities=11% Similarity=0.134 Sum_probs=44.1
Q ss_pred ccchHHHHHHHHhcCccccchHHHHHHHHHH-HHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHcCC
Q 047769 57 GITKPAIRRLARRGGVKRISGLIYEETRGVL-KIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGR 124 (131)
Q Consensus 57 gIpk~aIrRLArr~GvkRIS~~ay~el~~vl-e~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~G~ 124 (131)
.+|...++++||+.| +|+.-.+++...- ...-|++.+-.-.+.+-.|++. +..+.+.+|+..+.
T Consensus 17 ~~~~~~wK~faR~lg---lse~~Id~I~~~~~~d~~Eq~~qmL~~W~~~~G~~a-~~~~Li~aLr~~~l 81 (97)
T cd08316 17 VMTLKDVKKFVRKSG---LSEPKIDEIKLDNPQDTAEQKVQLLRAWYQSHGKTG-AYRTLIKTLRKAKL 81 (97)
T ss_pred HcCHHHHHHHHHHcC---CCHHHHHHHHHcCCCChHHHHHHHHHHHHHHhCCCc-hHHHHHHHHHHccc
Confidence 577888999999999 5666566655332 3445777777777777655543 35788888887763
No 129
>PRK09862 putative ATP-dependent protease; Provisional
Probab=46.10 E-value=92 Score=28.22 Aligned_cols=32 Identities=13% Similarity=0.168 Sum_probs=27.7
Q ss_pred HHHHHHHHHHHHhhCCCceecHHHHHHHHHHc
Q 047769 91 LENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 122 (131)
Q Consensus 91 le~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~ 122 (131)
...+++=|-++|..++|..|+.+||..|+.-.
T Consensus 461 ~~rlLrvARTiADL~g~~~V~~~hv~eAl~yR 492 (506)
T PRK09862 461 WQRLLKVARTIADIDQSDIITRQHLQEAVSYR 492 (506)
T ss_pred HHHHHHHHHHHHHHcCCCCCCHHHHHHHHHhh
Confidence 34678888999999999999999999999643
No 130
>TIGR01242 26Sp45 26S proteasome subunit P45 family. Many proteins may score above the trusted cutoff because an internal
Probab=44.41 E-value=36 Score=28.45 Aligned_cols=42 Identities=19% Similarity=0.230 Sum_probs=33.3
Q ss_pred HHHHHHHHH----HHHHHHHHHHHHHHhhCCCceecHHHHHHHHHH
Q 047769 80 YEETRGVLK----IFLENVIRDAVTYTEHARRKTVTAMDVVYALKR 121 (131)
Q Consensus 80 y~el~~vle----~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr 121 (131)
++++....+ .-+..++.+|...|-..++..|+.+|+..|++.
T Consensus 317 ~~~la~~t~g~sg~dl~~l~~~A~~~a~~~~~~~i~~~d~~~a~~~ 362 (364)
T TIGR01242 317 LEAIAKMTEGASGADLKAICTEAGMFAIREERDYVTMDDFIKAVEK 362 (364)
T ss_pred HHHHHHHcCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHH
Confidence 445554443 456788899999998999999999999999975
No 131
>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional
Probab=44.36 E-value=34 Score=29.70 Aligned_cols=34 Identities=12% Similarity=0.056 Sum_probs=30.4
Q ss_pred HHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHc
Q 047769 89 IFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 122 (131)
Q Consensus 89 ~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~ 122 (131)
.=+..++++|...|-..+|..|+.+|+..|+++.
T Consensus 353 aDI~~l~~eA~~~A~r~~~~~i~~~df~~A~~~v 386 (398)
T PTZ00454 353 ADIAAICQEAGMQAVRKNRYVILPKDFEKGYKTV 386 (398)
T ss_pred HHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHHH
Confidence 3477899999999999999999999999999884
No 132
>PRK14962 DNA polymerase III subunits gamma and tau; Provisional
Probab=43.90 E-value=67 Score=28.58 Aligned_cols=60 Identities=15% Similarity=0.068 Sum_probs=36.9
Q ss_pred ccchHHHH----HHHHhcCccccchHHHHHHHHHHHH---HHHHHHHHHHHHHhhCCCceecHHHHHHHHHH
Q 047769 57 GITKPAIR----RLARRGGVKRISGLIYEETRGVLKI---FLENVIRDAVTYTEHARRKTVTAMDVVYALKR 121 (131)
Q Consensus 57 gIpk~aIr----RLArr~GvkRIS~~ay~el~~vle~---fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr 121 (131)
.++...+. ++++..|+ .+++++.+.+.+...- .+.+.++.+..|+ +. .||.+||..++..
T Consensus 175 ~l~~~el~~~L~~i~~~egi-~i~~eal~~Ia~~s~GdlR~aln~Le~l~~~~---~~-~It~e~V~~~l~~ 241 (472)
T PRK14962 175 NISDELIIKRLQEVAEAEGI-EIDREALSFIAKRASGGLRDALTMLEQVWKFS---EG-KITLETVHEALGL 241 (472)
T ss_pred CccHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHHhCCCHHHHHHHHHHHHHhc---CC-CCCHHHHHHHHcC
Confidence 45555544 44444565 4999999998875432 3444444444443 33 3999999888743
No 133
>KOG1658 consensus DNA polymerase epsilon, subunit C [Replication, recombination and repair]
Probab=42.82 E-value=15 Score=28.74 Aligned_cols=68 Identities=13% Similarity=0.141 Sum_probs=52.5
Q ss_pred cccchHHHHHHHHhcC-ccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHcC
Q 047769 56 QGITKPAIRRLARRGG-VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQG 123 (131)
Q Consensus 56 ~gIpk~aIrRLArr~G-vkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~G 123 (131)
.-+|...|+.+.+--- +.=...+|...+....+-|++.+..++-.+++..+|||+.--|+..|++.-.
T Consensus 58 ~rLpL~rik~vvkl~pdl~l~~dea~~l~a~aaelfi~~Ln~~~~~~~q~~k~kt~qr~d~D~ai~~~d 126 (162)
T KOG1658|consen 58 SRLPLARIKQVVKLDPDLTLLNDEASQLIAKAAELFIQELNDVAYTTAQLRKRKTEQRRDYDTAIEAVD 126 (162)
T ss_pred hhccHHHHHhhccCCcchhhhhhHHHHHHHHHHHHHHHHHHhccchhHHHHHhhhhhhhcccccccchH
Confidence 3466666776665432 3334556777788899999999999999999999999999999888876543
No 134
>COG4907 Predicted membrane protein [Function unknown]
Probab=42.28 E-value=16 Score=33.48 Aligned_cols=26 Identities=42% Similarity=0.648 Sum_probs=14.3
Q ss_pred eecCCCccccccccCCCCC--CccCCCC
Q 047769 17 IYSSDTQYQRKIMSGRGKG--GKGLGKG 42 (131)
Q Consensus 17 ~~~~~~~~~~~~m~g~gkg--gkg~gk~ 42 (131)
.|++-++++|...+|+|.| |.|+|.|
T Consensus 563 aysa~a~S~~~~~~GGG~G~~gGg~GGG 590 (595)
T COG4907 563 AYSAIASSRRSSSSGGGGGFSGGGSGGG 590 (595)
T ss_pred hhhcccccccCCCCCCCCCcCCCCCCCC
Confidence 3555666666666666554 2344443
No 135
>TIGR00362 DnaA chromosomal replication initiator protein DnaA. DnaA is involved in DNA biosynthesis; initiation of chromosome replication and can also be transcription regulator. The C-terminal of the family hits the pfam bacterial DnaA (bac_dnaA) domain family. For a review, see Kaguni (2006).
Probab=41.84 E-value=1.4e+02 Score=25.31 Aligned_cols=57 Identities=18% Similarity=0.224 Sum_probs=34.3
Q ss_pred HHHHHHhcCccccchHHHHHHHHHHH---HHHHHHHHHHHHHHhhCCCceecHHHHHHHHHH
Q 047769 63 IRRLARRGGVKRISGLIYEETRGVLK---IFLENVIRDAVTYTEHARRKTVTAMDVVYALKR 121 (131)
Q Consensus 63 IrRLArr~GvkRIS~~ay~el~~vle---~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr 121 (131)
+++.++..+. .+++++.+.+.+.+. .-|+.++.....|+...+|. ||.+.+..+|+.
T Consensus 277 l~~~~~~~~~-~l~~e~l~~ia~~~~~~~r~l~~~l~~l~~~a~~~~~~-it~~~~~~~L~~ 336 (405)
T TIGR00362 277 LQKKAEEEGL-ELPDEVLEFIAKNIRSNVRELEGALNRLLAYASLTGKP-ITLELAKEALKD 336 (405)
T ss_pred HHHHHHHcCC-CCCHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHhCCC-CCHHHHHHHHHH
Confidence 3444444454 378888888776544 23555666666666655543 666666666654
No 136
>PRK14961 DNA polymerase III subunits gamma and tau; Provisional
Probab=41.25 E-value=71 Score=26.91 Aligned_cols=64 Identities=6% Similarity=-0.021 Sum_probs=36.0
Q ss_pred ccccchHHHH----HHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHH
Q 047769 55 IQGITKPAIR----RLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALK 120 (131)
Q Consensus 55 i~gIpk~aIr----RLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALk 120 (131)
+..++...+. ++++..|+ .+++++.+.+.+...-=+..++..+...+.. ++..|+.+||..++.
T Consensus 175 ~~~l~~~el~~~L~~~~~~~g~-~i~~~al~~ia~~s~G~~R~al~~l~~~~~~-~~~~It~~~v~~~l~ 242 (363)
T PRK14961 175 LKIISEEKIFNFLKYILIKESI-DTDEYALKLIAYHAHGSMRDALNLLEHAINL-GKGNINIKNVTDMLG 242 (363)
T ss_pred CCCCCHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHHcCCCHHHHHHHHHHHHHh-cCCCCCHHHHHHHHC
Confidence 3345555444 44445564 4888888887766443333333333222223 466799999987664
No 137
>PRK08084 DNA replication initiation factor; Provisional
Probab=41.21 E-value=1.7e+02 Score=22.91 Aligned_cols=56 Identities=21% Similarity=0.039 Sum_probs=32.8
Q ss_pred HHHHHHhcCccccchHHHHHHHHHHH---HHHHHHHHHHHHHHhhCCCceecHHHHHHHHH
Q 047769 63 IRRLARRGGVKRISGLIYEETRGVLK---IFLENVIRDAVTYTEHARRKTVTAMDVVYALK 120 (131)
Q Consensus 63 IrRLArr~GvkRIS~~ay~el~~vle---~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALk 120 (131)
+++.|..-|+. +|+++++.+..-+. .-++.++.....++-..+|+ ||.+-|..+|.
T Consensus 176 l~~~a~~~~~~-l~~~v~~~L~~~~~~d~r~l~~~l~~l~~~~l~~~~~-it~~~~k~~l~ 234 (235)
T PRK08084 176 LQLRARLRGFE-LPEDVGRFLLKRLDREMRTLFMTLDQLDRASITAQRK-LTIPFVKEILK 234 (235)
T ss_pred HHHHHHHcCCC-CCHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHhcCCC-CCHHHHHHHHc
Confidence 34434444654 99999999987655 23334444432233334554 88888877763
No 138
>cd08306 Death_FADD Fas-associated Death Domain protein-protein interaction domain. Death domain (DD) found in FAS-associated via death domain (FADD). FADD is a component of the death-inducing signaling complex (DISC) and serves as an adaptor in the signaling pathway of death receptor proteins. It modulates apoptosis as well as non-apoptotic processes such as cell cycle progression, survival, innate immune signaling, and hematopoiesis. FADD contains an N-terminal DED and a C-terminal DD. Its DD interacts with the DD of the activated death receptor, FAS, and its DED recruits the initiator caspases, caspase-8 and -10, to the DISC complex via a homotypic interaction with the N-terminal DED of the caspase. 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),
Probab=40.19 E-value=85 Score=21.37 Aligned_cols=62 Identities=23% Similarity=0.263 Sum_probs=41.2
Q ss_pred HHHHHHHHhcCccccchHHHHHHHHHH-HHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHcCCcc
Q 047769 61 PAIRRLARRGGVKRISGLIYEETRGVL-KIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTL 126 (131)
Q Consensus 61 ~aIrRLArr~GvkRIS~~ay~el~~vl-e~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~G~~l 126 (131)
+..++|||+.| +|+.-.+.+...- ...-+++.+-...+.+..| +.-|..-+..||+..+...
T Consensus 14 ~~Wk~laR~LG---lse~~Id~i~~~~~~~~~eq~~~mL~~W~~~~g-~~At~~~L~~aL~~~~l~~ 76 (86)
T cd08306 14 RDWRKLARKLG---LSETKIESIEEAHPRNLREQVRQSLREWKKIKK-KEAKVADLIKALRDCQLNL 76 (86)
T ss_pred hhHHHHHHHcC---CCHHHHHHHHHHCCCCHHHHHHHHHHHHHHhHC-cchHHHHHHHHHHHcCcHH
Confidence 45778899988 5555555554332 2233556666667777777 5668888999999887643
No 139
>PRK14963 DNA polymerase III subunits gamma and tau; Provisional
Probab=40.04 E-value=69 Score=28.76 Aligned_cols=62 Identities=18% Similarity=0.075 Sum_probs=42.3
Q ss_pred cccchHHH----HHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHH
Q 047769 56 QGITKPAI----RRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALK 120 (131)
Q Consensus 56 ~gIpk~aI----rRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALk 120 (131)
..++...+ +++++..|++ +++++.+.+.+...--+..++......+.. ..+||.+||..++.
T Consensus 173 ~~ls~~el~~~L~~i~~~egi~-i~~~Al~~ia~~s~GdlR~aln~Lekl~~~--~~~It~~~V~~~l~ 238 (504)
T PRK14963 173 RRLTEEEIAGKLRRLLEAEGRE-AEPEALQLVARLADGAMRDAESLLERLLAL--GTPVTRKQVEEALG 238 (504)
T ss_pred cCCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHcCCCHHHHHHHHHHHHhc--CCCCCHHHHHHHHC
Confidence 34555554 4556667865 899999999887776666666555555444 34799999887753
No 140
>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=38.88 E-value=86 Score=28.63 Aligned_cols=48 Identities=21% Similarity=0.049 Sum_probs=36.4
Q ss_pred ccchHHHHHHHHHHHHH-------HHHHHHHHHHHHhhCCCceecHHHHHHHHHH
Q 047769 74 RISGLIYEETRGVLKIF-------LENVIRDAVTYTEHARRKTVTAMDVVYALKR 121 (131)
Q Consensus 74 RIS~~ay~el~~vle~f-------le~I~~dAv~yaeHA~RKTVt~~DV~~ALkr 121 (131)
.||+++.+.+.+..-.+ ...+++-|-++|--.+|.+|+.+||..|.+-
T Consensus 203 ~i~~~~~~~l~~~~~~~gv~s~Ra~i~~~r~ArA~Aal~gr~~V~~~Dv~~a~~l 257 (589)
T TIGR02031 203 TISAEQVKELVLTAASLGISGHRADLFAVRAAKAHAALHGRTEVTEEDLKLAVEL 257 (589)
T ss_pred cCCHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHH
Confidence 47777777776654332 2245678889999999999999999998864
No 141
>PRK06620 hypothetical protein; Validated
Probab=38.42 E-value=1.8e+02 Score=22.79 Aligned_cols=56 Identities=18% Similarity=0.067 Sum_probs=33.4
Q ss_pred HHHHHHHhcCccccchHHHHHHHHHHH---HHHHHHHHHHHHHHhhCCCceecHHHHHHHH
Q 047769 62 AIRRLARRGGVKRISGLIYEETRGVLK---IFLENVIRDAVTYTEHARRKTVTAMDVVYAL 119 (131)
Q Consensus 62 aIrRLArr~GvkRIS~~ay~el~~vle---~fle~I~~dAv~yaeHA~RKTVt~~DV~~AL 119 (131)
.+++.+...|+ .+++++.+-+...+. ..+++++.....++...+| .||...|..+|
T Consensus 155 ~l~k~~~~~~l-~l~~ev~~~L~~~~~~d~r~l~~~l~~l~~~~~~~~~-~it~~~~~~~l 213 (214)
T PRK06620 155 LIFKHFSISSV-TISRQIIDFLLVNLPREYSKIIEILENINYFALISKR-KITISLVKEVL 213 (214)
T ss_pred HHHHHHHHcCC-CCCHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHcCC-CCCHHHHHHHh
Confidence 34455554554 399999998886543 2233333334344555554 58888887766
No 142
>PRK14954 DNA polymerase III subunits gamma and tau; Provisional
Probab=38.09 E-value=1e+02 Score=28.58 Aligned_cols=62 Identities=13% Similarity=0.067 Sum_probs=40.7
Q ss_pred ccchHHH----HHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhC----CCceecHHHHHHHH
Q 047769 57 GITKPAI----RRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHA----RRKTVTAMDVVYAL 119 (131)
Q Consensus 57 gIpk~aI----rRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA----~RKTVt~~DV~~AL 119 (131)
.++...| .++++..|++ |++++.+.+.+...--+..++...-..+.++ ..++||.+||..++
T Consensus 185 ~l~~~ei~~~L~~i~~~egi~-I~~eal~~La~~s~Gdlr~al~eLeKL~~y~~~~~~~~~It~~~V~~lv 254 (620)
T PRK14954 185 RIPLDEIQSQLQMICRAEGIQ-IDADALQLIARKAQGSMRDAQSILDQVIAFSVGSEAEKVIAYQGVAELL 254 (620)
T ss_pred CCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHhCCCHHHHHHHHHHHHHhccccccCCccCHHHHHHHH
Confidence 4554444 4455555644 9999999988877766666655554444443 37789998887765
No 143
>TIGR03280 methan_mark_11 putative methanogenesis marker protein 11. Members of this protein family, to date, are found in a completed prokaryotic genome if and only if the species is one of the archaeal methanogens. The exact function is unknown, but likely is linked to methanogenesis or a process closely connected to it.
Probab=38.08 E-value=45 Score=28.32 Aligned_cols=38 Identities=16% Similarity=0.248 Sum_probs=32.6
Q ss_pred HHHHHHHHHhhCCCceecHHHHHHHHHHcCCcccccCC
Q 047769 94 VIRDAVTYTEHARRKTVTAMDVVYALKRQGRTLYGFGG 131 (131)
Q Consensus 94 I~~dAv~yaeHA~RKTVt~~DV~~ALkr~G~~lYGF~~ 131 (131)
+-.....|...|++.-|+.+|....+++.|..+++|.+
T Consensus 232 ~p~~L~~fg~~Ak~~vvt~eeA~~~a~~~gi~l~~~~g 269 (292)
T TIGR03280 232 PPKELKEYGNKAKREMVSIEEAERVAERNNIEIIEVTG 269 (292)
T ss_pred CcHHHHHHHHHHHhceeCHHHHHHHHHHCCcEEEEeCC
Confidence 34456889999999999999999999999988888753
No 144
>COG5251 TAF40 Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=38.00 E-value=25 Score=28.21 Aligned_cols=65 Identities=18% Similarity=0.184 Sum_probs=52.6
Q ss_pred ccchHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCC-ceecHHHHHHHHHH
Q 047769 57 GITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARR-KTVTAMDVVYALKR 121 (131)
Q Consensus 57 gIpk~aIrRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~R-KTVt~~DV~~ALkr 121 (131)
+++|..|+.+|-..--.-||+-+.-.+..+-+.|.-+|++-|.+.-+.-+- -.+..+|+-.|.+.
T Consensus 115 ~lnKt~VKKlastV~nQtVspNi~I~l~g~~KVfvGEiIElA~~Vq~~w~~sgpl~p~h~reayr~ 180 (199)
T COG5251 115 SLNKTQVKKLASTVANQTVSPNIRIFLQGVGKVFVGEIIELAMIVQNKWLTSGPLIPFHKREAYRY 180 (199)
T ss_pred CCCHHHHHHHHHHHhccccCCCeeeeeechhHHHHHHHHHHHHHHHHHhcccCCCChHHHHHHHHH
Confidence 799999999998887788999999999999999999999988877654222 24667777766654
No 145
>PRK06893 DNA replication initiation factor; Validated
Probab=37.47 E-value=1.9e+02 Score=22.51 Aligned_cols=55 Identities=20% Similarity=0.081 Sum_probs=33.6
Q ss_pred HHHHHHhcCccccchHHHHHHHHHHH---HHHHHHHHHHHHHHhhCCCceecHHHHHHHH
Q 047769 63 IRRLARRGGVKRISGLIYEETRGVLK---IFLENVIRDAVTYTEHARRKTVTAMDVVYAL 119 (131)
Q Consensus 63 IrRLArr~GvkRIS~~ay~el~~vle---~fle~I~~dAv~yaeHA~RKTVt~~DV~~AL 119 (131)
+++.|..-|+ .+++++.+.+..-+. ..+..++......+-..+| .||...|..+|
T Consensus 170 L~~~a~~~~l-~l~~~v~~~L~~~~~~d~r~l~~~l~~l~~~~~~~~~-~it~~~v~~~L 227 (229)
T PRK06893 170 LQRNAYQRGI-ELSDEVANFLLKRLDRDMHTLFDALDLLDKASLQAQR-KLTIPFVKEIL 227 (229)
T ss_pred HHHHHHHcCC-CCCHHHHHHHHHhccCCHHHHHHHHHHHHHHHHhcCC-CCCHHHHHHHh
Confidence 3344444454 489999988886654 3344444444333334455 59999988876
No 146
>cd08318 Death_NMPP84 Death domain of Nuclear Matrix Protein P84. Death domain (DD) found in the Nuclear Matrix Protein P84 (also known as HPR1 or THOC1). HPR1/p84 resides in the nuclear matrix and is part of the THO complex, also called TREX (transcription/export) complex, which functions in mRNP biogenesis at the interface between transcription and export of mRNA from the nucleus. Mice lacking THOC1 have abnormal testis development and are sterile. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=36.87 E-value=1.3e+02 Score=20.32 Aligned_cols=60 Identities=12% Similarity=0.041 Sum_probs=39.9
Q ss_pred HHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHcCC
Q 047769 61 PAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGR 124 (131)
Q Consensus 61 ~aIrRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~G~ 124 (131)
...++||++.|+ |+.-.+.+...-...-+++.+-...+.+..|. .-|.+-...||+..|.
T Consensus 19 ~~Wk~Lar~LGl---s~~dI~~i~~~~~~~~eq~~~mL~~W~~r~g~-~AT~~~L~~aL~~~~~ 78 (86)
T cd08318 19 EDWKTLAPHLEM---KDKEIRAIESDSEDIKMQAKQLLVAWQDREGS-QATPETLITALNAAGL 78 (86)
T ss_pred hhHHHHHHHcCC---CHHHHHHHHhcCCCHHHHHHHHHHHHHHhcCc-cccHHHHHHHHHHcCc
Confidence 357789999995 44444545433333456666666677777774 4688889999998774
No 147
>PRK14971 DNA polymerase III subunits gamma and tau; Provisional
Probab=36.78 E-value=86 Score=28.87 Aligned_cols=62 Identities=11% Similarity=0.045 Sum_probs=39.2
Q ss_pred ccchHHH----HHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHH
Q 047769 57 GITKPAI----RRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALK 120 (131)
Q Consensus 57 gIpk~aI----rRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALk 120 (131)
.++...| +++|+..|+. +++++.+.+.+...--+..++...-..+.+++.+ |+.+||...+.
T Consensus 179 ~ls~~ei~~~L~~ia~~egi~-i~~~al~~La~~s~gdlr~al~~Lekl~~y~~~~-It~~~V~~~l~ 244 (614)
T PRK14971 179 RIQVADIVNHLQYVASKEGIT-AEPEALNVIAQKADGGMRDALSIFDQVVSFTGGN-ITYKSVIENLN 244 (614)
T ss_pred CCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHcCCCHHHHHHHHHHHHHhccCC-ccHHHHHHHhC
Confidence 3444444 4555667864 8888888888766555555555554444445544 88888876654
No 148
>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=35.99 E-value=30 Score=26.53 Aligned_cols=52 Identities=13% Similarity=0.103 Sum_probs=38.3
Q ss_pred HHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHH
Q 047769 64 RRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDV 115 (131)
Q Consensus 64 rRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV 115 (131)
.++.|.+.-=-|..+=.+.+.++++.-+-+++.-|..-|...||..|...|+
T Consensus 2 e~lFR~aa~LdvdK~d~~r~~d~V~~Kl~DLl~va~~~Ak~ngRdvI~~~DL 53 (138)
T PF09123_consen 2 ERLFRKAAGLDVDKNDAKRYSDFVEKKLYDLLLVAQENAKANGRDVIEPRDL 53 (138)
T ss_dssp HHHHHHHHS----HHHHHHHHHHHHHHHHHCCCCHHHHHHHTT-SEE-GGGS
T ss_pred hHHHHHHhccCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeeccccC
Confidence 4566655433366777888999999999999999999999999999998885
No 149
>PF07766 LETM1: LETM1-like protein; InterPro: IPR011685 This is a group of mainly hypothetical eukaryotic proteins. Putative features found in LETM1, such as a transmembrane domain and a CK2 and PKC phosphorylation site [], are relatively conserved throughout the family. Deletion of LETM1 is thought to be involved in the development of Wolf-Hirschhorn syndrome in humans []. A member of this family, P91927 from SWISSPROT, is known to be expressed in the mitochondria of Drosophila melanogaster [], suggesting that this may be a group of mitochondrial proteins.; PDB: 3SKQ_A.
Probab=35.76 E-value=1.8e+02 Score=23.88 Aligned_cols=71 Identities=17% Similarity=0.219 Sum_probs=52.3
Q ss_pred ccccchHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHcCCcccc
Q 047769 55 IQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTLYG 128 (131)
Q Consensus 55 i~gIpk~aIrRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~G~~lYG 128 (131)
+..++.+-++.|++-.|+..+..+.+ ++.-+..++..|..|=...... |=..++.+++..|+..-|..-.|
T Consensus 168 Ld~Lsr~~L~~L~r~~~l~~~~~~~~--lr~rL~~~~~~l~~dD~~i~~e-Gv~~Ls~~EL~~Ac~~RGl~~~~ 238 (268)
T PF07766_consen 168 LDNLSRPHLRALCRLLGLTPFGPSSL--LRRRLRKRLRYLKQDDRLIKRE-GVDSLSEEELQDACYERGLRSTG 238 (268)
T ss_dssp HHHS-HHHHHHHHHHTT----SSHHH--HHHHHHHHHHHHHHHHHHHHHH--GGGS-HHHHHHHHHHTT---TT
T ss_pred cccCCHHHHHHHHHHhccCcCCchHH--HHHHHHHHHHHHHHHHHHHHHh-ccccCCHHHHHHHHHHhCCCcCC
Confidence 44688888999999999988887766 7888999999999988887777 88899999999999998854444
No 150
>cd06456 M3A_DCP_Oligopeptidase_A Peptidase family M3 dipeptidyl carboxypeptidase (DCP; Dcp II; peptidyl dipeptidase; EC 3.4.15.5). This metal-binding M3A family also includes oligopeptidase A (OpdA; EC 3.4.24.70) enzyme. DCP cleaves dipeptides off the C-termini of various peptides and proteins, the smallest substrate being N-blocked tripeptides and unblocked tetrapeptides. DCP from E. coli is inhibited by the anti-hypertensive drug captopril, an inhibitor of the mammalian angiotensin converting enzyme (ACE, also called peptidyl dipeptidase A). Oligopeptidase A (OpdA) may play a specific role in the degradation of signal peptides after they are released from precursor forms of secreted proteins. It can also cleave N-acetyl-L-Ala.
Probab=34.84 E-value=1.5e+02 Score=25.80 Aligned_cols=66 Identities=14% Similarity=0.203 Sum_probs=40.9
Q ss_pred HHHHhcCccccchHHHHH----HHHHHHHHHHHHHHHHHHHHh------------hCCCceecHHHHHHHHHHcCCcccc
Q 047769 65 RLARRGGVKRISGLIYEE----TRGVLKIFLENVIRDAVTYTE------------HARRKTVTAMDVVYALKRQGRTLYG 128 (131)
Q Consensus 65 RLArr~GvkRIS~~ay~e----l~~vle~fle~I~~dAv~yae------------HA~RKTVt~~DV~~ALkr~G~~lYG 128 (131)
++|+-.|.+..++-+++. -.+.+..|++++.+.+...++ ..+-.++..-|+.+..+.+....|.
T Consensus 15 e~A~llG~~s~a~~~l~~~ma~sp~~v~~Fl~~l~~~~~p~~~~e~~~L~~~~~~~~~~~~l~~wD~~yy~~~~~~~~~~ 94 (422)
T cd06456 15 EKAKLLGFENYAEYSLADKMAKSPEAVLEFLEDLAPKAKPQAKKELAELQAFAKEEGGEDELEPWDWAYYSEKLRKEKYD 94 (422)
T ss_pred HHHHHcCCCCHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHhcC
Confidence 567777777666665552 225566666666655443222 2333468899999999877666666
Q ss_pred cC
Q 047769 129 FG 130 (131)
Q Consensus 129 F~ 130 (131)
|+
T Consensus 95 ~d 96 (422)
T cd06456 95 LD 96 (422)
T ss_pred CC
Confidence 53
No 151
>PRK14087 dnaA chromosomal replication initiation protein; Provisional
Probab=34.22 E-value=2e+02 Score=25.31 Aligned_cols=60 Identities=8% Similarity=0.085 Sum_probs=39.5
Q ss_pred HHHHHHhcCcc-ccchHHHHHHHHHHH---HHHHHHHHHHHHHHhhCC-CceecHHHHHHHHHHc
Q 047769 63 IRRLARRGGVK-RISGLIYEETRGVLK---IFLENVIRDAVTYTEHAR-RKTVTAMDVVYALKRQ 122 (131)
Q Consensus 63 IrRLArr~Gvk-RIS~~ay~el~~vle---~fle~I~~dAv~yaeHA~-RKTVt~~DV~~ALkr~ 122 (131)
+++.++..|.. .+++++.+.+.+.+. .-++.++..+..++-... .+.||.+.|..+|+..
T Consensus 284 L~~~~~~~gl~~~l~~evl~~Ia~~~~gd~R~L~gaL~~l~~~a~~~~~~~~it~~~v~~~l~~~ 348 (450)
T PRK14087 284 IKKEIKNQNIKQEVTEEAINFISNYYSDDVRKIKGSVSRLNFWSQQNPEEKIITIEIVSDLFRDI 348 (450)
T ss_pred HHHHHHhcCCCCCCCHHHHHHHHHccCCCHHHHHHHHHHHHHHHhcccCCCCCCHHHHHHHHhhc
Confidence 44445555653 699999998887654 445555555555555442 3579999999988764
No 152
>PRK13531 regulatory ATPase RavA; Provisional
Probab=33.83 E-value=2.5e+02 Score=25.61 Aligned_cols=62 Identities=13% Similarity=0.159 Sum_probs=45.7
Q ss_pred ccchHHHHHHHHhcCccccchHHHHHHHHHHHH-------------HHHHHHHHHHHHHhhCCCceecHHHHHHH
Q 047769 57 GITKPAIRRLARRGGVKRISGLIYEETRGVLKI-------------FLENVIRDAVTYTEHARRKTVTAMDVVYA 118 (131)
Q Consensus 57 gIpk~aIrRLArr~GvkRIS~~ay~el~~vle~-------------fle~I~~dAv~yaeHA~RKTVt~~DV~~A 118 (131)
.|+...+..+-+..---.|++.+.+.+.+.... ....+++-|-++|=-.||..|+.+||..+
T Consensus 206 vis~eel~~lq~~v~~V~v~d~v~eyI~~L~~~lr~~r~~~~~SpR~~~~l~~~akA~A~l~GR~~V~p~Dv~ll 280 (498)
T PRK13531 206 QITDEEYQQWQKEIGKITLPDHVFELIFQLRQQLDALPNAPYVSDRRWKKAIRLLQASAFFSGRDAIAPIDLILL 280 (498)
T ss_pred CCCHHHHHHHHHHhcceeCCHHHHHHHHHHHHHHhcCCCCCCcCcHHHHHHHHHHHHHHHHCCCCCCCHHHHHHh
Confidence 466676666665554456888888877776642 34457788888999999999999999943
No 153
>PF12909 DUF3832: Protein of unknown function (DUF3832); InterPro: IPR024308 This domain found in bacteria and Acanthamoeba polyphaga mimivirus (APMV) L591 protein has no known function. In Q0AZ30 from SWISSPROT and other uncharacterised proteins this domain is found C-terminal, while the N terminus shows remote homology to the bacterial toxin/antitoxin 'addiction module' (PF12910 from PFAM).; PDB: 3K6Q_C.
Probab=33.74 E-value=91 Score=21.97 Aligned_cols=33 Identities=12% Similarity=0.137 Sum_probs=27.4
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCce
Q 047769 77 GLIYEETRGVLKIFLENVIRDAVTYTEHARRKT 109 (131)
Q Consensus 77 ~~ay~el~~vle~fle~I~~dAv~yaeHA~RKT 109 (131)
++|.+++.+.+.+|.++=..+.--|.++.+|+.
T Consensus 36 eeA~~~lie~l~dYAedy~~~~~~~~~apnR~~ 68 (89)
T PF12909_consen 36 EEAIEDLIEDLRDYAEDYMNRFPLFYNAPNRRH 68 (89)
T ss_dssp HHHHHHHHHHHHHHHHHHHHTHHHHHTSTTTGG
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccc
Confidence 477888888888888888888988888888874
No 154
>CHL00176 ftsH cell division protein; Validated
Probab=33.67 E-value=58 Score=30.24 Aligned_cols=34 Identities=24% Similarity=0.348 Sum_probs=29.6
Q ss_pred HHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHc
Q 047769 89 IFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 122 (131)
Q Consensus 89 ~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~ 122 (131)
.-+++++.+|...+.-.+++.|+.+|+..|+.+.
T Consensus 390 aDL~~lvneAal~a~r~~~~~It~~dl~~Ai~rv 423 (638)
T CHL00176 390 ADLANLLNEAAILTARRKKATITMKEIDTAIDRV 423 (638)
T ss_pred HHHHHHHHHHHHHHHHhCCCCcCHHHHHHHHHHH
Confidence 3578889999888888888999999999999875
No 155
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=32.87 E-value=2.2e+02 Score=22.49 Aligned_cols=22 Identities=18% Similarity=0.469 Sum_probs=18.4
Q ss_pred ccchHHHHHHHHhcCccccchH
Q 047769 57 GITKPAIRRLARRGGVKRISGL 78 (131)
Q Consensus 57 gIpk~aIrRLArr~GvkRIS~~ 78 (131)
+.+.++|-|+|++.|.+-+++-
T Consensus 45 ~vS~aTv~Rf~kklG~~gf~e~ 66 (284)
T PRK11302 45 NVSEPTVNRFCRSLDTKGFPDF 66 (284)
T ss_pred CCCHHHHHHHHHHcCCCCHHHH
Confidence 6788999999999998877643
No 156
>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH. HflB(FtsH) is a pleiotropic protein required for correct cell division in bacteria. It has ATP-dependent zinc metalloprotease activity. It was formerly designated cell division protein FtsH.
Probab=32.79 E-value=67 Score=28.21 Aligned_cols=43 Identities=16% Similarity=0.200 Sum_probs=32.8
Q ss_pred HHHHHHHHH----HHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHc
Q 047769 80 YEETRGVLK----IFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 122 (131)
Q Consensus 80 y~el~~vle----~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~ 122 (131)
.+++.+... .-+++++++|...+...+++.|+.+|+..|+++.
T Consensus 249 l~~la~~t~G~sgadl~~l~~eA~~~a~~~~~~~i~~~~l~~a~~~~ 295 (495)
T TIGR01241 249 LKAVARRTPGFSGADLANLLNEAALLAARKNKTEITMNDIEEAIDRV 295 (495)
T ss_pred HHHHHHhCCCCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHH
Confidence 444544433 4578888888888877788899999999999875
No 157
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=32.53 E-value=1.1e+02 Score=17.89 Aligned_cols=31 Identities=16% Similarity=0.209 Sum_probs=20.4
Q ss_pred ccchHHHHHHHHhcCccccchHHHHHHHHHHHH
Q 047769 57 GITKPAIRRLARRGGVKRISGLIYEETRGVLKI 89 (131)
Q Consensus 57 gIpk~aIrRLArr~GvkRIS~~ay~el~~vle~ 89 (131)
+++.++|.++.+. -..+|++....+.+++.+
T Consensus 8 gvs~~tvs~~l~g--~~~vs~~~~~~i~~~~~~ 38 (52)
T cd01392 8 GVSVATVSRVLNG--KPRVSEETRERVLAAAEE 38 (52)
T ss_pred CcCHHHHHHHHcC--CCCCCHHHHHHHHHHHHH
Confidence 6788888888763 335777666666555544
No 158
>PF11705 RNA_pol_3_Rpc31: DNA-directed RNA polymerase III subunit Rpc31; InterPro: IPR024661 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. RNA polymerase III contains seventeen subunits in yeasts and in human cells. Twelve of these are akin to RNA polymerase I or II and the other five are RNA polymerase III-specific, and form the functionally distinct groups: (i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31, Rpc34 and Rpc82 form a cluster of enzyme-specific subunits that contribute to transcription initiation in Saccharomyces cerevisiae and Homo sapiens. There is evidence that these subunits are anchored at or near the N-terminal Zn-fold of Rpc1, itself prolonged by a highly conserved but RNA polymerase III-specific domain []. This entry represents the Rpc31 subunit.
Probab=32.46 E-value=28 Score=27.81 Aligned_cols=10 Identities=70% Similarity=1.146 Sum_probs=6.3
Q ss_pred ccCCCCCCcc
Q 047769 29 MSGRGKGGKG 38 (131)
Q Consensus 29 m~g~gkggkg 38 (131)
|||||.|+.|
T Consensus 1 MSgRGggrg~ 10 (233)
T PF11705_consen 1 MSGRGGGRGG 10 (233)
T ss_pred CCCCCCCCCC
Confidence 8877765543
No 159
>PRK14950 DNA polymerase III subunits gamma and tau; Provisional
Probab=32.34 E-value=1.2e+02 Score=27.43 Aligned_cols=57 Identities=11% Similarity=0.047 Sum_probs=36.4
Q ss_pred HHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHH
Q 047769 63 IRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKR 121 (131)
Q Consensus 63 IrRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr 121 (131)
+..++...|+. |++++.+.+.+...--+..++.....++.+. ..+||.+||..++..
T Consensus 188 L~~~a~~egl~-i~~eal~~La~~s~Gdlr~al~~LekL~~y~-~~~It~e~V~~ll~~ 244 (585)
T PRK14950 188 LRKIAAAEGIN-LEPGALEAIARAATGSMRDAENLLQQLATTY-GGEISLSQVQSLLGI 244 (585)
T ss_pred HHHHHHHcCCC-CCHHHHHHHHHHcCCCHHHHHHHHHHHHHhc-CCCCCHHHHHHHhcC
Confidence 34455556755 8999998888776554555555444444443 346999998766543
No 160
>TIGR01278 DPOR_BchB light-independent protochlorophyllide reductase, B subunit. This enzyme describes the B subunit of the dark form protochlorophyllide reductase, a nitrogenase-like enzyme. This subunit shows homology to the nitrogenase molybdenum-iron protein. It catalyzes a step in bacteriochlorophyll biosynthesis.
Probab=32.10 E-value=1e+02 Score=27.45 Aligned_cols=48 Identities=15% Similarity=0.131 Sum_probs=34.8
Q ss_pred ccchHHHHHHHHHHHHHH-HHHHHHHHHHHhhCCCceecHHHHHHHHHHc
Q 047769 74 RISGLIYEETRGVLKIFL-ENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 122 (131)
Q Consensus 74 RIS~~ay~el~~vle~fl-e~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~ 122 (131)
.-|++|-.+|.++ =.|+ ..+=+.+..||+..|...||.+.+..|=...
T Consensus 462 ~w~~ea~~~l~~~-P~f~r~~~r~~~e~~a~~~g~~~it~~~~~~a~~~~ 510 (511)
T TIGR01278 462 GWTAEAEAELKKV-PFFVRGKVRRNTENFARERGYSVITLEVIYAAKEHF 510 (511)
T ss_pred CcCHHHHHHHhhC-ChhhhHHHHHHHHHHHHHcCCCEEcHHHHHHHHHhc
Confidence 4677777777654 2333 4555667789999999999999998775543
No 161
>PF02042 RWP-RK: RWP-RK domain; InterPro: IPR003035 This domain is named RWP-RK after a conserved motif at the C terminus of the domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [].
Probab=31.67 E-value=46 Score=21.27 Aligned_cols=20 Identities=30% Similarity=0.602 Sum_probs=17.1
Q ss_pred ccchHHHHHHHHhcCccccc
Q 047769 57 GITKPAIRRLARRGGVKRIS 76 (131)
Q Consensus 57 gIpk~aIrRLArr~GvkRIS 76 (131)
++....++|++|+.|+.|=.
T Consensus 26 gv~~T~LKr~CR~~GI~RWP 45 (52)
T PF02042_consen 26 GVSVTTLKRRCRRLGIPRWP 45 (52)
T ss_pred CCCHHHHHHHHHHcCCCCCC
Confidence 67888899999999998754
No 162
>cd08319 Death_RAIDD Death domain of RIP-associated ICH-1 homologous protein with a death domain. Death domain (DD) of RAIDD (RIP-associated ICH-1 homologous protein with a death domain), also known as CRADD (Caspase and RIP adaptor). RAIDD is an adaptor protein that together with the p53-inducible protein PIDD and caspase-2, forms the PIDDosome complex, which is required for caspase-2 activation and plays a role in mediating stress-induced apoptosis. RAIDD contains an N-terminal Caspase Activation and Recruitment Domain (CARD), which interacts with the caspase-2 CARD, and a C-terminal DD, which interacts with the DD of PIDD. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD, DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other pr
Probab=31.58 E-value=1.4e+02 Score=20.42 Aligned_cols=64 Identities=13% Similarity=0.124 Sum_probs=41.2
Q ss_pred HHHHHHHhcCccccchHHHHHHHHH-HHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHcC--Cccccc
Q 047769 62 AIRRLARRGGVKRISGLIYEETRGV-LKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQG--RTLYGF 129 (131)
Q Consensus 62 aIrRLArr~GvkRIS~~ay~el~~v-le~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~G--~~lYGF 129 (131)
..+.+|++.|+ |+.-.+.+... -..--+++-+-....-+-.| +.-|.+..+.||+..+ ...|.|
T Consensus 15 ~W~~Lar~Lgl---s~~~I~~i~~~~p~~l~eQv~~mL~~W~~r~G-~~ATv~~L~~aL~~~~~~~~~~~~ 81 (83)
T cd08319 15 EWEQVLLDLGL---SQTDIYRCKENHPHNVQSQIVEALVKWRQRFG-KKATVQSLIQSLKAVEVDPSVLQF 81 (83)
T ss_pred hHHHHHHHcCC---CHHHHHHHHHhCCCCHHHHHHHHHHHHHHhcC-CCCcHHHHHHHHHHcCCCHHHHHh
Confidence 45677888774 34444444432 22334566666677777666 6788899999999876 455555
No 163
>PRK06305 DNA polymerase III subunits gamma and tau; Validated
Probab=31.41 E-value=1.2e+02 Score=26.65 Aligned_cols=61 Identities=16% Similarity=0.018 Sum_probs=33.9
Q ss_pred ccchHHHHHH----HHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHH
Q 047769 57 GITKPAIRRL----ARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYAL 119 (131)
Q Consensus 57 gIpk~aIrRL----Arr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~AL 119 (131)
.++...|..+ ++..|++ +++++.+.+.....-=+..++......+...+ ..|+.+||..++
T Consensus 179 ~l~~~el~~~L~~~~~~eg~~-i~~~al~~L~~~s~gdlr~a~~~Lekl~~~~~-~~It~~~V~~l~ 243 (451)
T PRK06305 179 RIPEETIIDKLALIAKQEGIE-TSREALLPIARAAQGSLRDAESLYDYVVGLFP-KSLDPDSVAKAL 243 (451)
T ss_pred CCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHcCCCHHHHHHHHHHHHHhcc-CCcCHHHHHHHH
Confidence 4555555543 3445654 89998888877654434433333333222223 338888876654
No 164
>KOG0480 consensus DNA replication licensing factor, MCM6 component [Replication, recombination and repair]
Probab=30.69 E-value=2.4e+02 Score=27.11 Aligned_cols=82 Identities=21% Similarity=0.108 Sum_probs=58.8
Q ss_pred cccccccccc--ccchHHHHHHHHh--cCccccchHHHHHHHHHH-------------------HHHHHHHHHHHHHHHh
Q 047769 47 HRKVLRDNIQ--GITKPAIRRLARR--GGVKRISGLIYEETRGVL-------------------KIFLENVIRDAVTYTE 103 (131)
Q Consensus 47 ~rKvlrd~i~--gIpk~aIrRLArr--~GvkRIS~~ay~el~~vl-------------------e~fle~I~~dAv~yae 103 (131)
|+.+....-. .+|..-|++..+= -=..++|.++.+.+.+.. -.=||.+++-+.+.|+
T Consensus 545 h~~i~~~~~~~~~~~~e~vrkYi~yAR~~~P~ls~ea~~~lve~Y~~lR~~~~~~~~~~s~~ITvRqLESlIRLsEA~Ar 624 (764)
T KOG0480|consen 545 HRGIDDATERVCVYTLEQVRKYIRYARNFKPKLSKEASEMLVEKYKGLRQRDAQGNNRSSYRITVRQLESLIRLSEARAR 624 (764)
T ss_pred hccccccccccccccHHHHHHHHHHHHhcCccccHHHHHHHHHHHHHHHHhhccccCcccccccHHHHHHHHHHHHHHHh
Confidence 4444433333 7888888855432 223668888877766442 2347788999999999
Q ss_pred hCCCceecHHHHHHHHHHcCCcccc
Q 047769 104 HARRKTVTAMDVVYALKRQGRTLYG 128 (131)
Q Consensus 104 HA~RKTVt~~DV~~ALkr~G~~lYG 128 (131)
-.=|..||.+||..|.+-+.+.+|.
T Consensus 625 ~~~~devt~~~v~ea~eLlk~Siv~ 649 (764)
T KOG0480|consen 625 VECRDEVTKEDVEEAVELLKKSIVR 649 (764)
T ss_pred hhhhhhccHHHHHHHHHHHHhhhee
Confidence 9999999999999999988777664
No 165
>PF02971 FTCD: Formiminotransferase domain; InterPro: IPR013802 The formiminotransferase (FT) domain of formiminotransferase-cyclodeaminase (FTCD) forms a homodimer, with each protomer being comprised of two subdomains. The formiminotransferase domain has an N-terminal subdomain that is made up of a six-stranded mixed beta-pleated sheet and five alpha helices, which are arranged on the external surface of the beta sheet. This, in turn, faces the beta-sheet of the C-terminal subdomain to form a double beta-sheet layer. The two subdomains are separated by a short linker sequence, which is not thought to be any more flexible than the remainder of the molecule. The substrate is predicted to form a number of contacts with residues found in both the N-terminal and C-terminal subdomains []. In humans, deficiency of this enzyme results in a disease phenotype []. This entry represents the C-terminal subdomain of the formiminotransferase domain.; GO: 0005542 folic acid binding, 0016740 transferase activity, 0008152 metabolic process; PDB: 1QD1_B 2PFD_C.
Probab=30.64 E-value=1.3e+02 Score=23.22 Aligned_cols=58 Identities=21% Similarity=0.306 Sum_probs=33.3
Q ss_pred HHHHHHHhcCccccchHH-----HHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHH-HHHHHcC-CcccccC
Q 047769 62 AIRRLARRGGVKRISGLI-----YEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVV-YALKRQG-RTLYGFG 130 (131)
Q Consensus 62 aIrRLArr~GvkRIS~~a-----y~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~-~ALkr~G-~~lYGF~ 130 (131)
.|++.|++-|+.=+..++ .+++.++.++|++ -.++.+++.++++ .|.+++| ..+.-|+
T Consensus 72 ~v~~eA~~~Gv~v~gsElVGlvP~~Alldaa~yyl~-----------~e~~~~~~e~~~i~lav~~LGL~~l~pF~ 136 (145)
T PF02971_consen 72 EVKREAARYGVPVVGSELVGLVPLDALLDAAEYYLQ-----------KENFFILPEEQKIRLAVKRLGLDSLSPFD 136 (145)
T ss_dssp HHHHHHHCTT--EEEEEEES-B-HHHHHHHHHHHHH-----------HCT----SHHHHHHHHHHCCTTTSSS---
T ss_pred HHHHHHHHhCCCccceEEEccccHHHHHHHHHHHhc-----------ccccccCChHHHHHHHHHHcCccccCCCC
Confidence 478888999986665554 4566666666665 4566677777754 6778888 5555554
No 166
>KOG3902 consensus Histone acetyltransferase PCAF/SAGA, subunit SUPT3H/SPT3 [Transcription]
Probab=30.26 E-value=2e+02 Score=25.06 Aligned_cols=59 Identities=8% Similarity=0.160 Sum_probs=44.8
Q ss_pred HHHHH-HhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHH
Q 047769 63 IRRLA-RRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKR 121 (131)
Q Consensus 63 IrRLA-rr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr 121 (131)
|..++ ..+-+.+=+.+-..-+.+.+.-=+-+++..|...+..+|-.-||.+|+++.++.
T Consensus 30 iQqmmf~sGei~~P~pett~Lved~V~gqvie~l~qa~eia~lrgsr~Itpedliflir~ 89 (352)
T KOG3902|consen 30 IQQMMFQSGEIPDPLPETTNLVEDNVRGQVIESLVQANEIADLRGSRSITPEDLIFLIRH 89 (352)
T ss_pred HHHHHHHhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCccccChHHHHHHhhc
Confidence 33444 344466666666666667777777788888999999999999999999998853
No 167
>PTZ00111 DNA replication licensing factor MCM4; Provisional
Probab=30.05 E-value=1.8e+02 Score=28.66 Aligned_cols=36 Identities=19% Similarity=0.234 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHcC
Q 047769 88 KIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQG 123 (131)
Q Consensus 88 e~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~G 123 (131)
-.-||.+++=|.+.|+-.=+.+|+.+||..|++-.-
T Consensus 770 ~RqLEsLIRLsEA~AK~rLs~~Vt~~Dv~~Ai~L~~ 805 (915)
T PTZ00111 770 SRMISSIIRISVSLARMRLSTVVTPADALQAVQIVK 805 (915)
T ss_pred HHHHHHHHHHHHHHhhhcCcCcccHHHHHHHHHHHH
Confidence 345788999999999999999999999999987654
No 168
>PRK14958 DNA polymerase III subunits gamma and tau; Provisional
Probab=29.97 E-value=1.5e+02 Score=26.69 Aligned_cols=61 Identities=13% Similarity=0.140 Sum_probs=38.4
Q ss_pred ccccchHHH----HHHHHhcCccccchHHHHHHHHHHHH---HHHHHHHHHHHHHhhCCCceecHHHHHHHHH
Q 047769 55 IQGITKPAI----RRLARRGGVKRISGLIYEETRGVLKI---FLENVIRDAVTYTEHARRKTVTAMDVVYALK 120 (131)
Q Consensus 55 i~gIpk~aI----rRLArr~GvkRIS~~ay~el~~vle~---fle~I~~dAv~yaeHA~RKTVt~~DV~~ALk 120 (131)
+..++...| +++++..|+. +++++++.+.....- .+.+++..++.| +...||.+||...+-
T Consensus 175 f~~l~~~~i~~~l~~il~~egi~-~~~~al~~ia~~s~GslR~al~lLdq~ia~----~~~~It~~~V~~~lg 242 (509)
T PRK14958 175 LAQLPPLQIAAHCQHLLKEENVE-FENAALDLLARAANGSVRDALSLLDQSIAY----GNGKVLIADVKTMLG 242 (509)
T ss_pred cCCCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHcCCcHHHHHHHHHHHHhc----CCCCcCHHHHHHHHC
Confidence 334566554 3567777865 888888887766443 333444445544 345699999987763
No 169
>TIGR02903 spore_lon_C ATP-dependent protease, Lon family. Members of this protein family resemble the widely distributed ATP-dependent protease La, also called Lon and LonA. It resembles even more closely LonB, which is a LonA paralog found in genomes if and only if the species is capable of endospore formation (as in Bacillus subtilis, Clostridium tetani, and select other members of the Firmicutes) and expressed specifically in the forespore compartment. Members of this family are restricted to a subset of spore-forming species, and are very likely to participate in the program of endospore formation. We propose the designation LonC.
Probab=29.60 E-value=1.5e+02 Score=27.28 Aligned_cols=67 Identities=16% Similarity=0.104 Sum_probs=41.5
Q ss_pred ccchHHHHHHHHh----cCccccchHHHHHHHHHHH--HHHHHHHHHHHHHH--------hhCCCceecHHHHHHHHHHc
Q 047769 57 GITKPAIRRLARR----GGVKRISGLIYEETRGVLK--IFLENVIRDAVTYT--------EHARRKTVTAMDVVYALKRQ 122 (131)
Q Consensus 57 gIpk~aIrRLArr----~GvkRIS~~ay~el~~vle--~fle~I~~dAv~ya--------eHA~RKTVt~~DV~~ALkr~ 122 (131)
.++...+..|+++ .++ .+++++.+.+....- ...-+++.++..++ +..+..+|+.+||..+++..
T Consensus 352 pls~edi~~Il~~~a~~~~v-~ls~eal~~L~~ys~~gRraln~L~~~~~~~~~~~~~~~~~~~~~~I~~edv~~~l~~~ 430 (615)
T TIGR02903 352 PLTPEDIALIVLNAAEKINV-HLAAGVEELIARYTIEGRKAVNILADVYGYALYRAAEAGKENDKVTITQDDVYEVIQIS 430 (615)
T ss_pred CCCHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHCCCcHHHHHHHHHHHHHHHHHHHHHhccCCCCeeECHHHHHHHhCCC
Confidence 3455555555544 454 488888888875421 23345667776554 22345689999999999765
Q ss_pred CC
Q 047769 123 GR 124 (131)
Q Consensus 123 G~ 124 (131)
..
T Consensus 431 r~ 432 (615)
T TIGR02903 431 RL 432 (615)
T ss_pred cC
Confidence 43
No 170
>PRK02910 light-independent protochlorophyllide reductase subunit B; Provisional
Probab=29.58 E-value=1.2e+02 Score=27.11 Aligned_cols=49 Identities=14% Similarity=0.115 Sum_probs=35.4
Q ss_pred ccchHHHHHHHHHHHHHH-HHHHHHHHHHHhhCCCceecHHHHHHHHHHcC
Q 047769 74 RISGLIYEETRGVLKIFL-ENVIRDAVTYTEHARRKTVTAMDVVYALKRQG 123 (131)
Q Consensus 74 RIS~~ay~el~~vle~fl-e~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~G 123 (131)
.-+++|-.+|.++ =.|+ ..+=+.+..||+..|...||.+.+..|-...|
T Consensus 469 ~w~~ea~~~l~~~-P~f~r~~~r~~~e~~a~~~g~~~it~~~~~~a~~~~~ 518 (519)
T PRK02910 469 VWTPEAEAELKKI-PFFVRGKVRRNTEKFARERGLPEITLEVLYDAKAHFG 518 (519)
T ss_pred CCCHHHHHHHhhC-ChhhHHHHHHHHHHHHHHcCCCeecHHHHHHHHHHhc
Confidence 4677777777653 3344 44445667899999999999999988866543
No 171
>PRK14952 DNA polymerase III subunits gamma and tau; Provisional
Probab=29.22 E-value=1.3e+02 Score=27.68 Aligned_cols=59 Identities=17% Similarity=0.102 Sum_probs=34.0
Q ss_pred ccchHH----HHHHHHhcCccccchHHHHHHHHHHHHH---HHHHHHHHHHHHhhCCCceecHHHHHHHH
Q 047769 57 GITKPA----IRRLARRGGVKRISGLIYEETRGVLKIF---LENVIRDAVTYTEHARRKTVTAMDVVYAL 119 (131)
Q Consensus 57 gIpk~a----IrRLArr~GvkRIS~~ay~el~~vle~f---le~I~~dAv~yaeHA~RKTVt~~DV~~AL 119 (131)
.++... +.++++..|+. ++++++..+.....-= +.++++.++.| .+...||.+||...+
T Consensus 176 ~l~~~~i~~~L~~i~~~egi~-i~~~al~~Ia~~s~GdlR~aln~Ldql~~~---~~~~~It~~~v~~ll 241 (584)
T PRK14952 176 LLPPRTMRALIARICEQEGVV-VDDAVYPLVIRAGGGSPRDTLSVLDQLLAG---AADTHVTYQRALGLL 241 (584)
T ss_pred CCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHcCCCHHHHHHHHHHHHhc---cCCCCcCHHHHHHHH
Confidence 455554 44555666754 8888887776553332 33334444444 345668888876654
No 172
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=29.11 E-value=95 Score=20.20 Aligned_cols=28 Identities=29% Similarity=0.412 Sum_probs=16.0
Q ss_pred ccchHHHHHHHHhcCccccchHHHHHHHHHH
Q 047769 57 GITKPAIRRLARRGGVKRISGLIYEETRGVL 87 (131)
Q Consensus 57 gIpk~aIrRLArr~GvkRIS~~ay~el~~vl 87 (131)
|.| |+++.||+..|++ |........+.|
T Consensus 23 G~~-Pt~rEIa~~~g~~--S~~tv~~~L~~L 50 (65)
T PF01726_consen 23 GYP-PTVREIAEALGLK--STSTVQRHLKAL 50 (65)
T ss_dssp SS----HHHHHHHHTSS--SHHHHHHHHHHH
T ss_pred CCC-CCHHHHHHHhCCC--ChHHHHHHHHHH
Confidence 566 6899999999987 444443333333
No 173
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=28.81 E-value=1.1e+02 Score=26.11 Aligned_cols=52 Identities=19% Similarity=0.192 Sum_probs=36.3
Q ss_pred cccchHHHHHHHHHHHHHHHHHHHH---HHHHHhhCCCceecHHHHHHHHHHcCC
Q 047769 73 KRISGLIYEETRGVLKIFLENVIRD---AVTYTEHARRKTVTAMDVVYALKRQGR 124 (131)
Q Consensus 73 kRIS~~ay~el~~vle~fle~I~~d---Av~yaeHA~RKTVt~~DV~~ALkr~G~ 124 (131)
+.+|+.-.-..+.....-+-+.+.+ .+...+-+..+-++.+||+.+|+.+|.
T Consensus 195 kPLSdlG~~sY~~YW~~~il~~L~~~~~~isi~~is~~T~i~~~Dii~tL~~l~~ 249 (290)
T PLN03238 195 RPLSDLGKVSFRSYWTRVLLEQLRDVKGDVSIKDLSLATGIRGEDIVSTLQSLNL 249 (290)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHhcCCCccHHHHHHHhCCCHHHHHHHHHHCCc
Confidence 4477776666665555555444433 456666777888999999999998874
No 174
>PLN03239 histone acetyltransferase; Provisional
Probab=28.22 E-value=1.3e+02 Score=26.36 Aligned_cols=52 Identities=19% Similarity=0.279 Sum_probs=35.8
Q ss_pred cccchHHHHHHHHHHHHHHHHHHHH------HHHHHhhCCCceecHHHHHHHHHHcCC
Q 047769 73 KRISGLIYEETRGVLKIFLENVIRD------AVTYTEHARRKTVTAMDVVYALKRQGR 124 (131)
Q Consensus 73 kRIS~~ay~el~~vle~fle~I~~d------Av~yaeHA~RKTVt~~DV~~ALkr~G~ 124 (131)
+.+|+.-.-..+.....-+-+.+.+ .+...+-+..+-++.+||+.+|+.+|.
T Consensus 253 kPLSdlG~~sY~~YW~~~il~~L~~~~~~~~~~si~dis~~Tgi~~~DIi~tL~~l~~ 310 (351)
T PLN03239 253 KPMSDLGQQAYIPYWGSTIVDFLLNHSGNDSSLSIMDIAKKTSIMAEDIVFALNQLGI 310 (351)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHhccCCCCCccHHHHHHHhCCCHHHHHHHHHHCCc
Confidence 4477776666665544444444433 256677777888999999999999883
No 175
>PRK10733 hflB ATP-dependent metalloprotease; Reviewed
Probab=28.16 E-value=85 Score=28.90 Aligned_cols=34 Identities=15% Similarity=0.299 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHc
Q 047769 89 IFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 122 (131)
Q Consensus 89 ~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~ 122 (131)
.-+.+++++|..+|-..++..|+.+|+..|+.+.
T Consensus 359 adl~~l~~eAa~~a~r~~~~~i~~~d~~~a~~~v 392 (644)
T PRK10733 359 ADLANLVNEAALFAARGNKRVVSMVEFEKAKDKI 392 (644)
T ss_pred HHHHHHHHHHHHHHHHcCCCcccHHHHHHHHHHH
Confidence 3788999999999999999999999999998753
No 176
>PRK14086 dnaA chromosomal replication initiation protein; Provisional
Probab=28.13 E-value=2.8e+02 Score=25.98 Aligned_cols=57 Identities=14% Similarity=0.120 Sum_probs=33.4
Q ss_pred HHHHHHhcCccccchHHHHHHHHHHH---HHHHHHHHHHHHHHhhCCCceecHHHHHHHHHH
Q 047769 63 IRRLARRGGVKRISGLIYEETRGVLK---IFLENVIRDAVTYTEHARRKTVTAMDVVYALKR 121 (131)
Q Consensus 63 IrRLArr~GvkRIS~~ay~el~~vle---~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr 121 (131)
+++.|+.-|+. +++++.+-|..-+. ..|+.++.....|+.-.+ +.||.+.+..+|+.
T Consensus 455 L~kka~~r~l~-l~~eVi~yLa~r~~rnvR~LegaL~rL~a~a~~~~-~~itl~la~~vL~~ 514 (617)
T PRK14086 455 LRKKAVQEQLN-APPEVLEFIASRISRNIRELEGALIRVTAFASLNR-QPVDLGLTEIVLRD 514 (617)
T ss_pred HHHHHHhcCCC-CCHHHHHHHHHhccCCHHHHHHHHHHHHHHHHhhC-CCCCHHHHHHHHHH
Confidence 44445555543 78888888876655 444555555555555544 34666666666654
No 177
>COG4130 Predicted sugar epimerase [Carbohydrate transport and metabolism]
Probab=28.09 E-value=96 Score=26.05 Aligned_cols=67 Identities=21% Similarity=0.189 Sum_probs=42.7
Q ss_pred cccchHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCce---------------ecHHHHHHHHH
Q 047769 56 QGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKT---------------VTAMDVVYALK 120 (131)
Q Consensus 56 ~gIpk~aIrRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKT---------------Vt~~DV~~ALk 120 (131)
.+.|.+.|+.+|+..|+.=||=.+.--..+..+..- .=++....||.-.|-|+ +.-+|.+.||+
T Consensus 47 dg~p~a~vka~Aek~Gl~IvSINAlypFn~wt~~~~-a~a~~la~yA~acGA~aLvlcPlNd~s~~~~~vr~~~lv~Alk 125 (272)
T COG4130 47 DGTPAAEVKALAEKAGLTIVSINALYPFNEWTEERV-AEARGLADYAAACGAKALVLCPLNDGSWPGTAVRREDLVEALK 125 (272)
T ss_pred CCCCHHHHHHHHHHcCcEEEEeeccccccccChHHH-HHHHHHHHHHHhcCCceEEEEeccCCCCCCcccchHHHHHHHH
Confidence 378999999999999998888666544432221111 11233445555555443 45688999999
Q ss_pred HcC
Q 047769 121 RQG 123 (131)
Q Consensus 121 r~G 123 (131)
++-
T Consensus 126 aLk 128 (272)
T COG4130 126 ALK 128 (272)
T ss_pred Hhh
Confidence 864
No 178
>CHL00206 ycf2 Ycf2; Provisional
Probab=27.75 E-value=80 Score=33.83 Aligned_cols=35 Identities=17% Similarity=0.211 Sum_probs=32.0
Q ss_pred HHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHc
Q 047769 88 KIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 122 (131)
Q Consensus 88 e~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~ 122 (131)
=.=+.+++.+|...|-..+++.|+.+|+..|+.||
T Consensus 1843 GADLanLvNEAaliAirq~ks~Id~~~I~~Al~Rq 1877 (2281)
T CHL00206 1843 ARDLVALTNEALSISITQKKSIIDTNTIRSALHRQ 1877 (2281)
T ss_pred HHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHHH
Confidence 45578899999999999999999999999999987
No 179
>PF13846 DUF4196: Domain of unknown function (DUF4196)
Probab=27.57 E-value=40 Score=24.97 Aligned_cols=41 Identities=39% Similarity=0.541 Sum_probs=28.7
Q ss_pred ccccceeeeeeeEEeecCCCccccccccCCCCCCccCCCCCCcccccccccc
Q 047769 3 EVRNKKVKLSRITLIYSSDTQYQRKIMSGRGKGGKGLGKGGAKRHRKVLRDN 54 (131)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~m~g~gkggkg~gk~g~kR~rKvlrd~ 54 (131)
-.+.|+-++|- ++||||.....-+ +.-|.++||.|++..|.
T Consensus 55 Ik~gkRkr~SS--vm~DSDdSdDSDi---------lvrkv~~KR~rrv~eds 95 (112)
T PF13846_consen 55 IKRGKRKRLSS--VMYDSDDSDDSDI---------LVRKVGAKRPRRVVEDS 95 (112)
T ss_pred hcccccceeee--eeecCCccccchh---------hhhhhhccccceeccCc
Confidence 35666777776 8899887654442 23467899999998764
No 180
>PF00725 3HCDH: 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; InterPro: IPR006108 3-hydroxyacyl-CoA dehydrogenase (1.1.1.35 from EC) (HCDH) [] is an enzyme involved in fatty acid metabolism, it catalyzes the reduction of 3-hydroxyacyl-CoA to 3-oxoacyl-CoA. Most eukaryotic cells have 2 fatty-acid beta-oxidation systems, one located in mitochondria and the other in peroxisomes. In peroxisomes 3-hydroxyacyl-CoA dehydrogenase forms, with enoyl-CoA hydratase (ECH) and 3,2-trans-enoyl-CoA isomerase (ECI) a multifunctional enzyme where the N-terminal domain bears the hydratase/isomerase activities and the C-terminal domain the dehydrogenase activity. There are two mitochondrial enzymes: one which is monofunctional and the other which is, like its peroxisomal counterpart, multifunctional. In Escherichia coli (gene fadB) and Pseudomonas fragi (gene faoA) HCDH is part of a multifunctional enzyme which also contains an ECH/ECI domain as well as a 3-hydroxybutyryl-CoA epimerase domain []. There are two major region of similarities in the sequences of proteins of the HCDH family, the first one located in the N-terminal, corresponds to the NAD-binding site, the second one is located in the centre of the sequence. This represents the C-terminal domain which is also found in lambda crystallin. Some proteins include two copies of this domain.; GO: 0003857 3-hydroxyacyl-CoA dehydrogenase activity, 0016491 oxidoreductase activity, 0006631 fatty acid metabolic process, 0055114 oxidation-reduction process; PDB: 3MOG_A 2WTB_A 3ADP_A 3ADO_A 1WDL_B 2D3T_B 1WDK_A 1WDM_B 3K6J_A 1ZCJ_A ....
Probab=27.53 E-value=1.3e+02 Score=19.91 Aligned_cols=36 Identities=17% Similarity=0.273 Sum_probs=27.2
Q ss_pred HHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHH-cCCc
Q 047769 87 LKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKR-QGRT 125 (131)
Q Consensus 87 le~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr-~G~~ 125 (131)
++..+-.++.+|....+..- ++++||..+++. .|.|
T Consensus 4 ~nRl~~~~~~ea~~l~~egv---as~~~ID~~~~~~~G~p 40 (97)
T PF00725_consen 4 VNRLLAALLNEAARLVEEGV---ASPEDIDRAMRYGLGFP 40 (97)
T ss_dssp HHHHHHHHHHHHHHHHHTTS---SSHHHHHHHHHHHHTHS
T ss_pred HHHHHHHHHHHHHHHHHHcC---CCHHHHHHHHHHhCCCC
Confidence 34556667777888888643 689999999998 7766
No 181
>cd08815 Death_TNFRSF25_DR3 Death domain of Tumor Necrosis Factor Receptor superfamily 25. Death Domain (DD) found in Tumor Necrosis Factor (TNF) receptor superfamily 25 (TNFRSF25), also known as TRAMP (TNF receptor-related apoptosis-mediating protein), LARD, APO-3, WSL-1, or DR3 (Death Receptor-3). TNFRSF25 is primarily expressed in T cells, is activated by binding to its ligand TL1A, and plays an important role in T-cell function. 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 signaling pathways and can recruit other proteins into signaling complexes.
Probab=27.34 E-value=2.1e+02 Score=19.74 Aligned_cols=63 Identities=14% Similarity=0.184 Sum_probs=37.7
Q ss_pred ccccchHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHcC
Q 047769 55 IQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQG 123 (131)
Q Consensus 55 i~gIpk~aIrRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~G 123 (131)
...+|.+-.++++|+.|+.-.+ ++.....-..+=+..-.-..+..+-.+ -+.+++..+|++++
T Consensus 6 ~D~VP~~~wk~F~R~LGLsdn~---Ie~~E~~~~~~rda~y~ML~~W~~q~~---a~~n~Ll~aL~~m~ 68 (77)
T cd08815 6 MDAVPARRWKEFVRTLGLREAE---IEAVELEIGRFRDQQYEMLKRWRQQQP---AGLDAVYAALERMG 68 (77)
T ss_pred eccCChHHHHHHHHHcCCcHhH---HHHHHhcccchHHHHHHHHHHHHHcCC---CcHHHHHHHHHHHH
Confidence 4578999999999999964333 333322211122344444445555442 46788888888765
No 182
>COG0325 Predicted enzyme with a TIM-barrel fold [General function prediction only]
Probab=27.11 E-value=1.5e+02 Score=24.40 Aligned_cols=40 Identities=35% Similarity=0.373 Sum_probs=29.6
Q ss_pred HHHHHHHHHHHHHHHhhCCC-----------ceecHHHHHHHHHHcCCcccc
Q 047769 88 KIFLENVIRDAVTYTEHARR-----------KTVTAMDVVYALKRQGRTLYG 128 (131)
Q Consensus 88 e~fle~I~~dAv~yaeHA~R-----------KTVt~~DV~~ALkr~G~~lYG 128 (131)
..-++.|...-.+.++.++| ||+.++||..|++ .|..-+|
T Consensus 4 ~~nl~~v~~~I~~a~~~a~R~~~~V~LvAVSK~~~~~~I~~~~~-aG~r~fG 54 (228)
T COG0325 4 KENLAAVRERIAAAAERAGRNPGSVTLVAVSKTVPAEDIREAYE-AGQRHFG 54 (228)
T ss_pred HHHHHHHHHHHHHHHHHcCCCCCcEEEEEEeCCCCHHHHHHHHH-cCChhhc
Confidence 34456666666777888888 7899999998885 6766555
No 183
>COG2344 AT-rich DNA-binding protein [General function prediction only]
Probab=26.94 E-value=1e+02 Score=25.17 Aligned_cols=48 Identities=29% Similarity=0.401 Sum_probs=33.6
Q ss_pred ccchHHHHHHH------H---hcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCC
Q 047769 57 GITKPAIRRLA------R---RGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARR 107 (131)
Q Consensus 57 gIpk~aIrRLA------r---r~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~R 107 (131)
.||+++++||- + ..|+.|+|+. |+.+.+..=-.+|=+|..-|-+..+|
T Consensus 6 ~IP~AT~kRL~~YyR~le~l~a~~v~rvsS~---els~~~~vdsatIRrDfSYFG~lGkr 62 (211)
T COG2344 6 KIPKATAKRLPLYYRVLERLHASGVERVSSK---ELSEALGVDSATIRRDFSYFGELGKR 62 (211)
T ss_pred cCCHHHHHHhHHHHHHHHHHHHcCCceecHH---HHHHHhCCCHHHHhhhhHHHHhcCCC
Confidence 58999988774 3 6799999964 55666666666666776666665444
No 184
>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=26.08 E-value=1.5e+02 Score=18.76 Aligned_cols=18 Identities=28% Similarity=0.388 Sum_probs=13.2
Q ss_pred CceecHHHHHHHHHHcCC
Q 047769 107 RKTVTAMDVVYALKRQGR 124 (131)
Q Consensus 107 RKTVt~~DV~~ALkr~G~ 124 (131)
...-|..+++.||+..|+
T Consensus 55 ~~~at~~~L~~aL~~~~~ 72 (83)
T PF00531_consen 55 GPNATVDQLIQALRDIGR 72 (83)
T ss_dssp GSTSSHHHHHHHHHHTTH
T ss_pred CCCCcHHHHHHHHHHCCc
Confidence 345678888888888763
No 185
>PF07261 DnaB_2: Replication initiation and membrane attachment; InterPro: IPR006343 This entry represents a domain found in several bacterial replication initiation and membrane attachment proteins, DnaB and DnaD. The DnaD protein is a component of the PriA primosome. The PriA primosome functions to recruit the replication fork helicase onto the DNA []. Members, both chromosomal or phage-associated, are found in the Bacillus/Clostridium group of Gram-positive bacteria []. The DnaB protein is essential for both replication initiation and membrane attachment of the origin region of the chromosome and Plasmid pUB110 in Bacillus subtilis. It is known that there are two different classes (DnaBI and DnaBII) in the DnaB mutants; DnaBI is essential for both chromosome and pUB110 replication, whereas DnaBII is necessary only for chromosome replication []. This domain tends to be found towards the C terminus of DnaB and DnaD proteins and is alpha helical in nature.; PDB: 2I5U_A 2ZC2_A.
Probab=26.08 E-value=1.8e+02 Score=18.35 Aligned_cols=44 Identities=14% Similarity=0.163 Sum_probs=32.8
Q ss_pred HHHhcCccccchHHHHHHHHHHH--HHHHHHHHHHHHHHhhCCCce
Q 047769 66 LARRGGVKRISGLIYEETRGVLK--IFLENVIRDAVTYTEHARRKT 109 (131)
Q Consensus 66 LArr~GvkRIS~~ay~el~~vle--~fle~I~~dAv~yaeHA~RKT 109 (131)
..+......+|+...+.+...++ .|-.+++..|+.||--.+..+
T Consensus 4 ~~e~~~~~~~s~~e~~~l~~~~~~~~~~~~~v~~ai~~~~~~~~~~ 49 (77)
T PF07261_consen 4 FYEKNFGRPPSPSEIEKLEKWIDDYGFSPEVVNEAIEYALENNKRS 49 (77)
T ss_dssp HHHCCCTSS--HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCT--S
T ss_pred HHHHHcCCCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHcCCCC
Confidence 34555456789999999999999 999999999999999655555
No 186
>COG1239 ChlI Mg-chelatase subunit ChlI [Coenzyme metabolism]
Probab=25.95 E-value=1.8e+02 Score=26.05 Aligned_cols=28 Identities=25% Similarity=0.223 Sum_probs=22.9
Q ss_pred HHHHHHHHHhhCCCceecHHHHHHHHHH
Q 047769 94 VIRDAVTYTEHARRKTVTAMDVVYALKR 121 (131)
Q Consensus 94 I~~dAv~yaeHA~RKTVt~~DV~~ALkr 121 (131)
+.+-+.++|...||.+|+.+||..|+.-
T Consensus 294 ~~r~a~a~aa~~Gr~~v~~~Di~~a~~l 321 (423)
T COG1239 294 VVRAAKALAALRGRTEVEEEDIREAAEL 321 (423)
T ss_pred HHHHHHHHHHhcCceeeehhhHHHHHhh
Confidence 4455678889999999999999988753
No 187
>cd08779 Death_PIDD Death Domain of p53-induced protein with a death domain. Death domain (DD) found in PIDD (p53-induced protein with a death domain) and similar proteins. PIDD is a component of the PIDDosome complex, which is an oligomeric caspase-activating complex involved in caspase-2 activation and plays a role in mediating stress-induced apoptosis. The PIDDosome complex is composed of three components, PIDD, RAIDD and caspase-2, which interact through their DDs and DD-like domains. The DD of PIDD interacts with the DD of RAIDD, which also contains a Caspase Activation and Recruitment Domain (CARD) that interacts with the caspase-2 CARD. Autoproteolysis of PIDD determines the downstream signaling event, between pro-survival NF-kB or pro-death caspase-2 activation. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members
Probab=25.70 E-value=2.2e+02 Score=19.32 Aligned_cols=60 Identities=13% Similarity=0.098 Sum_probs=38.0
Q ss_pred HHHHHHHhcCccccchHHHHHHHHH-HHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHcCC
Q 047769 62 AIRRLARRGGVKRISGLIYEETRGV-LKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGR 124 (131)
Q Consensus 62 aIrRLArr~GvkRIS~~ay~el~~v-le~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~G~ 124 (131)
..++||++.|+ |+.-.+.+... -...-+++..-...+.+..+...-|..-+..||+..|+
T Consensus 15 ~Wk~lar~LGl---se~~Id~Ie~~~~~dl~eq~~~mL~~W~~~~~~~~atv~~L~~AL~~~gr 75 (86)
T cd08779 15 DWQAIGLHLGL---SYRELQRIKYNNRDDLDEQIFDMLFSWAQRQAGDPDAVGKLVTALEESGR 75 (86)
T ss_pred HHHHHHHHcCC---CHHHHHHHHHHCccCHHHHHHHHHHHHHHhcCCCchHHHHHHHHHHHcCH
Confidence 46788888884 44444444433 13334555555667777766655667888889988774
No 188
>PF02459 Adeno_terminal: Adenoviral DNA terminal protein; InterPro: IPR003391 The genome of adenovirus contains a protein covalently bound to the 5' end of each strand of the linear DNA molecule []. Since adenovirus DNA replication is initiated at the termini of the DNA molecule it has been proposed that the terminal protein serves as the primer for initiation of replication. However, the priming function now appears to reside in the precursor form of the terminal protein (pTP) found on the 5' ends of nascent DNA strands replicated in vitro [, ] and as a component of DNA-protein complexes isolated from virions of the protease-deficient adenovirus serotype 2 (Ad2) mutant tsl. The pTP is encoded by the leftward-transcribed strand of the viral genome and comprises part of a transcription unit that also encodes the single-strand DNA binding protein [].; GO: 0003677 DNA binding, 0006260 DNA replication
Probab=25.70 E-value=1.3e+02 Score=27.83 Aligned_cols=39 Identities=15% Similarity=0.231 Sum_probs=34.2
Q ss_pred HHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHcC
Q 047769 85 GVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQG 123 (131)
Q Consensus 85 ~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~G 123 (131)
..+......|++|....+++||+-.++.+|+...|....
T Consensus 447 ~aF~~l~~RI~~Dl~~~verag~~~~~~ee~e~~l~dI~ 485 (548)
T PF02459_consen 447 NAFSQLMRRISRDLLATVERAGRGELEEEEIEQFLADIA 485 (548)
T ss_pred cHHHHHHHHHHHHHHHHHhccCcccCCHHHHHHHHHHhc
Confidence 346677889999999999999999999999999998754
No 189
>PRK08451 DNA polymerase III subunits gamma and tau; Validated
Probab=24.90 E-value=2.2e+02 Score=25.98 Aligned_cols=60 Identities=17% Similarity=0.186 Sum_probs=36.8
Q ss_pred ccccchHHH----HHHHHhcCccccchHHHHHHHHHHHH---HHHHHHHHHHHHHhhCCCceecHHHHHHHH
Q 047769 55 IQGITKPAI----RRLARRGGVKRISGLIYEETRGVLKI---FLENVIRDAVTYTEHARRKTVTAMDVVYAL 119 (131)
Q Consensus 55 i~gIpk~aI----rRLArr~GvkRIS~~ay~el~~vle~---fle~I~~dAv~yaeHA~RKTVt~~DV~~AL 119 (131)
...++...| +++++..|+. +++++++.+.....- .+.+++..|+.|+ +..||.+||...+
T Consensus 173 F~~Ls~~ei~~~L~~Il~~EGi~-i~~~Al~~Ia~~s~GdlR~alnlLdqai~~~----~~~It~~~V~~~l 239 (535)
T PRK08451 173 FKQIPQNSIISHLKTILEKEGVS-YEPEALEILARSGNGSLRDTLTLLDQAIIYC----KNAITESKVADML 239 (535)
T ss_pred cCCCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHcCCcHHHHHHHHHHHHHhc----CCCCCHHHHHHHh
Confidence 345666654 4445577864 899999888876443 3334444555555 3458887776543
No 190
>COG3854 SpoIIIAA ncharacterized protein conserved in bacteria [Function unknown]
Probab=24.90 E-value=44 Score=28.51 Aligned_cols=63 Identities=22% Similarity=0.294 Sum_probs=40.9
Q ss_pred cchHHHHHHHHhcCccccchHHHHHHHHH---HHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHcC-CcccccC
Q 047769 58 ITKPAIRRLARRGGVKRISGLIYEETRGV---LKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQG-RTLYGFG 130 (131)
Q Consensus 58 Ipk~aIrRLArr~GvkRIS~~ay~el~~v---le~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~G-~~lYGF~ 130 (131)
|=..+|+++.++ +++ +..+.++ +..-++-+...-..|-.|.+ ||.+|.-++|.+++ +.+|+|.
T Consensus 9 iLPe~i~~~l~~-----~p~--~~~l~Evri~v~Rp~e~~~~~~~vyl~~~~---vT~ed~~~~~~rls~ysiys~e 75 (308)
T COG3854 9 ILPEKIRQILKE-----IPD--RNNLEEVRIRVNRPLEAIFPGQPVYLSYIG---VTKEDLQKTLNRLSGYSIYSVE 75 (308)
T ss_pred hChHHHHHHHHh-----CCc--cccceeeEeecCCCceEecCCCceeccccc---ccHHHHHHHHHHhcccccccch
Confidence 334556666643 443 3333332 34444445555567778877 99999999999987 8999874
No 191
>PRK14959 DNA polymerase III subunits gamma and tau; Provisional
Probab=24.56 E-value=2.1e+02 Score=26.75 Aligned_cols=61 Identities=8% Similarity=-0.016 Sum_probs=34.3
Q ss_pred ccchHHHH----HHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHH
Q 047769 57 GITKPAIR----RLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYAL 119 (131)
Q Consensus 57 gIpk~aIr----RLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~AL 119 (131)
.++...|. ++++..|+. |++++++.+.....--+..++...-..+. .+..+||.+||..++
T Consensus 177 pLs~~eL~~~L~~il~~egi~-id~eal~lIA~~s~GdlR~Al~lLeqll~-~g~~~It~d~V~~~l 241 (624)
T PRK14959 177 RLSEAGLEAHLTKVLGREGVD-YDPAAVRLIARRAAGSVRDSMSLLGQVLA-LGESRLTIDGARGVL 241 (624)
T ss_pred CCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHcCCCHHHHHHHHHHHHH-hcCCCcCHHHHHHHh
Confidence 45555444 444456654 88888888777655434433333333232 244578888776554
No 192
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=24.55 E-value=84 Score=19.16 Aligned_cols=36 Identities=22% Similarity=0.237 Sum_probs=19.3
Q ss_pred ccchHHHHHHHHhcCccccchHHHHHHHHHHHHHHHH
Q 047769 57 GITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLEN 93 (131)
Q Consensus 57 gIpk~aIrRLArr~GvkRIS~~ay~el~~vle~fle~ 93 (131)
+|+.++|.++.. +....++-+..+.+.+++.-=+++
T Consensus 21 gis~~tl~~~~~-~~~~~~~~~~l~~ia~~l~~~~~e 56 (63)
T PF13443_consen 21 GISRSTLSRILN-GKPSNPSLDTLEKIAKALNCSPEE 56 (63)
T ss_dssp T--HHHHHHHHT-TT-----HHHHHHHHHHHT--HHH
T ss_pred CcCHHHHHHHHh-cccccccHHHHHHHHHHcCCCHHH
Confidence 788888888886 335678877777777776554444
No 193
>PRK14957 DNA polymerase III subunits gamma and tau; Provisional
Probab=24.19 E-value=1.8e+02 Score=26.54 Aligned_cols=60 Identities=10% Similarity=0.083 Sum_probs=36.7
Q ss_pred cccchHHHH----HHHHhcCccccchHHHHHHHHHHHH---HHHHHHHHHHHHHhhCCCceecHHHHHHHHH
Q 047769 56 QGITKPAIR----RLARRGGVKRISGLIYEETRGVLKI---FLENVIRDAVTYTEHARRKTVTAMDVVYALK 120 (131)
Q Consensus 56 ~gIpk~aIr----RLArr~GvkRIS~~ay~el~~vle~---fle~I~~dAv~yaeHA~RKTVt~~DV~~ALk 120 (131)
..++...|. +++++.|+ .+++++++.+.....- .+.+.++.++.|+ + ..|+.+||..++.
T Consensus 176 ~~Ls~~eI~~~L~~il~~egi-~~e~~Al~~Ia~~s~GdlR~alnlLek~i~~~---~-~~It~~~V~~~l~ 242 (546)
T PRK14957 176 KHISQADIKDQLKIILAKENI-NSDEQSLEYIAYHAKGSLRDALSLLDQAISFC---G-GELKQAQIKQMLG 242 (546)
T ss_pred CCCCHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhc---c-CCCCHHHHHHHHc
Confidence 345555544 44556675 4888888887766544 3334444455553 3 5688888887653
No 194
>PF12146 Hydrolase_4: Putative lysophospholipase; InterPro: IPR022742 This domain is found in bacteria and eukaryotes and is approximately 110 amino acids in length. Many members are annotated as being lysophospholipases, and others as alpha-beta hydrolase fold-containing proteins.
Probab=24.17 E-value=31 Score=22.99 Aligned_cols=26 Identities=23% Similarity=0.482 Sum_probs=17.8
Q ss_pred HHhhCCCceecHHHHHHHHHHcCCcccccC
Q 047769 101 YTEHARRKTVTAMDVVYALKRQGRTLYGFG 130 (131)
Q Consensus 101 yaeHA~RKTVt~~DV~~ALkr~G~~lYGF~ 130 (131)
++||++| -.++...|..+|...|+||
T Consensus 25 ~~eh~~r----y~~~a~~L~~~G~~V~~~D 50 (79)
T PF12146_consen 25 FGEHSGR----YAHLAEFLAEQGYAVFAYD 50 (79)
T ss_pred cHHHHHH----HHHHHHHHHhCCCEEEEEC
Confidence 3556664 5567777778888877775
No 195
>PRK14953 DNA polymerase III subunits gamma and tau; Provisional
Probab=24.10 E-value=2.3e+02 Score=25.35 Aligned_cols=55 Identities=9% Similarity=-0.037 Sum_probs=32.6
Q ss_pred HHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHH
Q 047769 63 IRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYAL 119 (131)
Q Consensus 63 IrRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~AL 119 (131)
+.+++++.|+. +++++.+.+.+...-=+..++..+-..+.++ ...||.+||..++
T Consensus 187 L~~i~k~egi~-id~~al~~La~~s~G~lr~al~~Ldkl~~~~-~~~It~~~V~~~l 241 (486)
T PRK14953 187 LKRICNEEKIE-YEEKALDLLAQASEGGMRDAASLLDQASTYG-EGKVTIKVVEEFL 241 (486)
T ss_pred HHHHHHHcCCC-CCHHHHHHHHHHcCCCHHHHHHHHHHHHHhc-CCCcCHHHHHHHh
Confidence 45566677864 8889888887765443333333333322333 2358888887765
No 196
>cd01670 Death Death Domain: a protein-protein interaction domain. Death Domains (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. Structural analysis of DD-DD complexes show that the domains interact with each other in many different ways. DD-containing proteins serve as adaptors in signaling pathways and they can recruit other proteins into signaling complexes. In mammals, they are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways. In invertebrates, they are involved in transcriptional regulation of zygotic patterning genes in insect embryogenesis, and are components of the ToII/NF-kappaB pathway, a conserved innate immune pathway in a
Probab=24.03 E-value=2e+02 Score=18.17 Aligned_cols=60 Identities=20% Similarity=0.225 Sum_probs=35.2
Q ss_pred HHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHcCC
Q 047769 61 PAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGR 124 (131)
Q Consensus 61 ~aIrRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~G~ 124 (131)
...++||++.| +|..-.+.+...-....++..+=.....+-.+. .-|.++...||+..++
T Consensus 11 ~~W~~la~~Lg---l~~~~I~~i~~~~~~~~~~~~~mL~~W~~~~~~-~at~~~L~~aL~~~~~ 70 (79)
T cd01670 11 KDWKKLARKLG---LSDGEIDQIEEDNPRVREQAYQLLLKWEEREGD-NATVGNLIEALREIGR 70 (79)
T ss_pred hHHHHHHHHhC---CCHHHHHHHHHhCCCHHHHHHHHHHHHHhccCc-CcHHHHHHHHHHHcCH
Confidence 56788999988 454545555443332123322223333333333 7889999999998775
No 197
>PF06798 PrkA: PrkA serine protein kinase C-terminal domain; InterPro: IPR010650 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. This entry is found at the C terminus of PrkA proteins - bacterial and archaeal serine kinases approximately 630 residues in length. PrkA possesses the A-motif of nucleotide-binding proteins and exhibits distant homology to eukaryotic protein kinases []. Note that many of these are hypothetical.
Probab=23.89 E-value=2.6e+02 Score=23.02 Aligned_cols=57 Identities=19% Similarity=0.262 Sum_probs=40.9
Q ss_pred HHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHh-hCC-CceecHHHHHHHHHHc
Q 047769 64 RRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTE-HAR-RKTVTAMDVVYALKRQ 122 (131)
Q Consensus 64 rRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yae-HA~-RKTVt~~DV~~ALkr~ 122 (131)
.++++.+ +.++-+.++.|+++++.+|..=.+|++.+.. -++ .-+=+-.+|...+.++
T Consensus 179 ~~~~~~g--~~~~~~~~e~Lr~~iEkkL~~d~~~~~~~~t~~~k~~d~e~~~~~~~~i~rL 237 (254)
T PF06798_consen 179 SALAREG--KKFDYTSYERLREAIEKKLFSDVKDLIKIITESSKTPDKEQQRKIDEVIERL 237 (254)
T ss_pred HHHHcCC--CCCChhhhHHHHHHHHHHHHHHHHHHHHhcchhccCCCHHHHHHHHHHHHHH
Confidence 5555544 6788899999999999999988999998876 333 2233345566666665
No 198
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=23.64 E-value=1.8e+02 Score=18.63 Aligned_cols=32 Identities=22% Similarity=0.393 Sum_probs=18.9
Q ss_pred ccchHHHHHHHHhcCccccchHHHHHHHHHHHHH
Q 047769 57 GITKPAIRRLARRGGVKRISGLIYEETRGVLKIF 90 (131)
Q Consensus 57 gIpk~aIrRLArr~GvkRIS~~ay~el~~vle~f 90 (131)
+++.++|.|++. |-..||++..+.+.++++++
T Consensus 11 gvS~~TVSr~ln--~~~~v~~~t~~~i~~~~~~~ 42 (70)
T smart00354 11 GVSKATVSRVLN--GNGRVSEETREKVLAAMEEL 42 (70)
T ss_pred CCCHHHHHHHHC--CCCCCCHHHHHHHHHHHHHh
Confidence 677777777764 33456666555555544443
No 199
>PF07830 PP2C_C: Protein serine/threonine phosphatase 2C, C-terminal domain; InterPro: IPR012911 Protein phosphatase 2C (PP2C) is involved in regulating cellular responses to stress in various eukaryotes. It consists of two domains: an N-terminal catalytic domain and a C-terminal domain characteristic of mammalian PP2Cs. This domain consists of three antiparallel alpha helices, one of which packs against two corresponding alpha-helices of the N-terminal domain. The C-terminal domain does not seem to play a role in catalysis, but it may provide protein substrate specificity due to the cleft that is created between it and the catalytic domain []. ; GO: 0000287 magnesium ion binding, 0004721 phosphoprotein phosphatase activity, 0030145 manganese ion binding; PDB: 2P8E_A 3FXL_A 3FXO_A 1A6Q_A 3FXK_A 3FXM_A 3FXJ_A.
Probab=23.57 E-value=2.6e+02 Score=19.37 Aligned_cols=49 Identities=14% Similarity=0.264 Sum_probs=21.9
Q ss_pred CccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHc
Q 047769 71 GVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 122 (131)
Q Consensus 71 GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~ 122 (131)
|+-++|++|.+.=.+ |+.+|++.+++.+.-... ....+...|...|...
T Consensus 9 gAPkvs~EAv~~E~e-Ld~~l~~rv~ei~~~~~~--~~~~~l~~V~~~L~~e 57 (81)
T PF07830_consen 9 GAPKVSEEAVKKEAE-LDKYLEQRVEEIIEKSSE--EENPDLVYVMRTLASE 57 (81)
T ss_dssp TS----HHHHHHHHH-HHHHHHHHHHHHT------------HHHHHHHHHHT
T ss_pred CCCCCCHHHHHHHHH-HHHHHHHHHHHHHHHhcc--cCCCCHHHHHHHHHhc
Confidence 567788888765433 777777777766654332 3334444555555443
No 200
>PRK05896 DNA polymerase III subunits gamma and tau; Validated
Probab=23.56 E-value=2.5e+02 Score=26.18 Aligned_cols=60 Identities=7% Similarity=0.130 Sum_probs=35.3
Q ss_pred ccchHHHH----HHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHH
Q 047769 57 GITKPAIR----RLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYA 118 (131)
Q Consensus 57 gIpk~aIr----RLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~A 118 (131)
.++...+. ++++..|+ .+++++.+.+.+...--+..++......+...+.. |+.+||..+
T Consensus 177 ~Ls~~eL~~~L~~il~kegi-~Is~eal~~La~lS~GdlR~AlnlLekL~~y~~~~-It~e~V~el 240 (605)
T PRK05896 177 KLNNSELQELLKSIAKKEKI-KIEDNAIDKIADLADGSLRDGLSILDQLSTFKNSE-IDIEDINKT 240 (605)
T ss_pred CCCHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHHcCCcHHHHHHHHHHHHhhcCCC-CCHHHHHHH
Confidence 45554444 34444564 38899888887776654554444444444455533 888776654
No 201
>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=23.36 E-value=1.1e+02 Score=17.86 Aligned_cols=26 Identities=12% Similarity=0.152 Sum_probs=19.9
Q ss_pred HHHHHhhCCCceecHHHHHHHHHHcC
Q 047769 98 AVTYTEHARRKTVTAMDVVYALKRQG 123 (131)
Q Consensus 98 Av~yaeHA~RKTVt~~DV~~ALkr~G 123 (131)
|...|...+...|+++.+.+||=.+.
T Consensus 1 A~~~A~~~~~~~i~~eHlL~all~~~ 26 (53)
T PF02861_consen 1 AQELARERGHQYISPEHLLLALLEDP 26 (53)
T ss_dssp HHHHHHHTTBSSE-HHHHHHHHHHHT
T ss_pred CHHHHHHcCCCcccHHHHHHHHHhhh
Confidence 56778888999999999999975443
No 202
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []. Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=22.76 E-value=1e+02 Score=20.16 Aligned_cols=21 Identities=19% Similarity=0.444 Sum_probs=15.2
Q ss_pred ccchHHHHHHHHhcCccccch
Q 047769 57 GITKPAIRRLARRGGVKRISG 77 (131)
Q Consensus 57 gIpk~aIrRLArr~GvkRIS~ 77 (131)
+++.++|-|++++.|..-+++
T Consensus 45 ~vS~sti~Rf~kkLG~~gf~e 65 (77)
T PF01418_consen 45 GVSPSTIVRFCKKLGFSGFKE 65 (77)
T ss_dssp TS-HHHHHHHHHHCTTTCHHH
T ss_pred CCCHHHHHHHHHHhCCCCHHH
Confidence 678888888888888765543
No 203
>PF06144 DNA_pol3_delta: DNA polymerase III, delta subunit; InterPro: IPR010372 DNA polymerase III, delta subunit (2.7.7.7 from EC) is required for, along with delta' subunit, the assembly of the processivity factor beta(2) onto primed DNA in the DNA polymerase III holoenzyme-catalysed reaction []. The delta subunit is also known as HolA.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication, 0009360 DNA polymerase III complex; PDB: 3GLG_F 1XXH_A 1JQL_B 3GLF_F 1JQJ_C 3GLI_F.
Probab=22.66 E-value=1.9e+02 Score=20.77 Aligned_cols=39 Identities=15% Similarity=0.037 Sum_probs=26.4
Q ss_pred HHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHH
Q 047769 62 AIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTY 101 (131)
Q Consensus 62 aIrRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~y 101 (131)
-|+..+++.|+. |++++.+.|.+.+..=+..+..+..+.
T Consensus 132 ~i~~~~~~~g~~-i~~~a~~~L~~~~~~d~~~l~~EleKL 170 (172)
T PF06144_consen 132 WIKERAKKNGLK-IDPDAAQYLIERVGNDLSLLQNELEKL 170 (172)
T ss_dssp HHHHHHHHTT-E-E-HHHHHHHHHHHTT-HHHHHHHHHHH
T ss_pred HHHHHHHHcCCC-CCHHHHHHHHHHhChHHHHHHHHHHHh
Confidence 377888888875 999999999887776666666555443
No 204
>PRK14088 dnaA chromosomal replication initiation protein; Provisional
Probab=22.51 E-value=4.1e+02 Score=23.22 Aligned_cols=56 Identities=14% Similarity=0.149 Sum_probs=29.4
Q ss_pred HHHHHHhcCccccchHHHHHHHHHHHH---HHHHHHHHHHHHHhhCCCceecHHHHHHHHH
Q 047769 63 IRRLARRGGVKRISGLIYEETRGVLKI---FLENVIRDAVTYTEHARRKTVTAMDVVYALK 120 (131)
Q Consensus 63 IrRLArr~GvkRIS~~ay~el~~vle~---fle~I~~dAv~yaeHA~RKTVt~~DV~~ALk 120 (131)
+++.++..++. +++++++.+.+-+.. .|+.++.....|+...++ .+|.+.+..+|+
T Consensus 272 L~~~~~~~~~~-l~~ev~~~Ia~~~~~~~R~L~g~l~~l~~~~~~~~~-~it~~~a~~~L~ 330 (440)
T PRK14088 272 ARKMLEIEHGE-LPEEVLNFVAENVDDNLRRLRGAIIKLLVYKETTGE-EVDLKEAILLLK 330 (440)
T ss_pred HHHHHHhcCCC-CCHHHHHHHHhccccCHHHHHHHHHHHHHHHHHhCC-CCCHHHHHHHHH
Confidence 34444444543 778877777765432 334444444455554443 255555555554
No 205
>cd08317 Death_ank Death domain associated with Ankyrins. Death Domain (DD) associated with Ankyrins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. Ankyrins function as adaptor proteins and they interact, through ANK repeats, with structurally diverse membrane proteins, including ion channels/pumps, calcium release channels, and cell adhesion molecules. They play critical roles in the proper expression and membrane localization of these proteins. In mammals, this family includes ankyrin-R for restricted (or ANK1), ankyrin-B for broadly expressed (or ANK2) and ankyrin-G for general or giant (or ANK3). They are expressed in different combinations in many tissues and play non-overlapping functions. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-associati
Probab=22.34 E-value=2.5e+02 Score=18.69 Aligned_cols=60 Identities=20% Similarity=0.168 Sum_probs=38.3
Q ss_pred HHHHHHHHhcCccccchHHHHHHHH-HHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHcCC
Q 047769 61 PAIRRLARRGGVKRISGLIYEETRG-VLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGR 124 (131)
Q Consensus 61 ~aIrRLArr~GvkRIS~~ay~el~~-vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~G~ 124 (131)
...++||+..|+. ..-.+.+.. .-..-.+++.+-.....+..|+ ..|.+..+.||+..|+
T Consensus 16 ~dW~~LAr~Lg~~---~~dI~~i~~~~~~~~~eq~~~mL~~W~~r~g~-~at~~~L~~AL~~i~r 76 (84)
T cd08317 16 SDWPQLARELGVS---ETDIDLIKAENPNSLAQQAQAMLKLWLEREGK-KATGNSLEKALKKIGR 76 (84)
T ss_pred hHHHHHHHHcCCC---HHHHHHHHHHCCCCHHHHHHHHHHHHHHhcCC-cchHHHHHHHHHHcCh
Confidence 4567899999844 322333322 1122236666666777777775 5788999999998875
No 206
>TIGR02366 DHAK_reg probable dihydroxyacetone kinase regulator. The seed alignment for this family was built from a set of closely related uncharacterized proteins associated with operons for the type of bacterial dihydroxyacetone kinase that transfers PEP-derived phosphate from a phosphoprotein, as in phosphotransferase system transport, rather than from ATP. Members have a TetR transcriptional regulator domain (pfam00440) at the N-terminus and sequence homology throughout.
Probab=22.25 E-value=1.3e+02 Score=21.82 Aligned_cols=20 Identities=10% Similarity=0.311 Sum_probs=16.4
Q ss_pred ccchHHHHHHHHhcCccccc
Q 047769 57 GITKPAIRRLARRGGVKRIS 76 (131)
Q Consensus 57 gIpk~aIrRLArr~GvkRIS 76 (131)
++.+-+|..||+++||.|-+
T Consensus 20 ~~~~ITV~~I~~~AgvsR~T 39 (176)
T TIGR02366 20 AFSKISVSDIMSTAQIRRQT 39 (176)
T ss_pred CCccCCHHHHHHHhCCCHHH
Confidence 67777899999999987643
No 207
>cd07064 AlkD_like_1 A new structural DNA glycosylase containing HEAT-like repeats. This domain represents a new and uncharacterized structural superfamily of DNA glycosylases that form an alpha-alpha superhelix fold that are not belong to the identified five structural DNA glycosylase superfamilies (UDG, AAG/MNPG, MutM/Fpg and helix-hairpin-helix). DNA glycosylases removing alkylated base residues have been identified in all organisms investigated and may be universally present in nature. DNA glycosylases catalyze the first step in Base Excision Repair (BER) pathway by cleaving damaged DNA bases within double strand DNA to produce an abasic site. The resulting abasic site is further processed by AP endonuclease, phosphodiesterase, DNA polymerases, and DNA ligase functions to restore the DNA to an undamaged state. All glycosylase examined to date utilize a similar strategy for binding DNA and base flipping despite their structural diversity. The known structures for members of this fa
Probab=22.10 E-value=1.6e+02 Score=23.06 Aligned_cols=61 Identities=18% Similarity=0.073 Sum_probs=33.0
Q ss_pred ccccchHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHH----HhhCCCceecHHHHHH
Q 047769 55 IQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTY----TEHARRKTVTAMDVVY 117 (131)
Q Consensus 55 i~gIpk~aIrRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~y----aeHA~RKTVt~~DV~~ 117 (131)
.-||+.|.++.+|+..+.+ ++.+..+++.+.+..+.+.-.+++--+ ... .++..+.+|+..
T Consensus 20 f~Gv~~P~~R~lak~~~~~-~~~~~~~~~~~l~~~Lw~~~~~E~r~~al~~l~~-~~~~~~~~~~~~ 84 (208)
T cd07064 20 FYGIKTPERRALSKPFLKE-SKLPDKEELWELVLELWQQPEREYQYVAIDLLRK-YKKFLTPEDLPL 84 (208)
T ss_pred cCCCChHHHHHHHHHHHHH-cCCCcHHHHHHHHHHHHcchHHHHHHHHHHHHHH-HHhcCCHHHHHH
Confidence 4499999999999988642 221123344444444444443333222 222 345567777443
No 208
>COG4463 CtsR Transcriptional repressor of class III stress genes [Transcription]
Probab=21.77 E-value=48 Score=25.74 Aligned_cols=39 Identities=15% Similarity=0.411 Sum_probs=32.2
Q ss_pred HHHHHHHHHHHHHHHH------HHHHhhCCCceecHHHHHHHHHH
Q 047769 83 TRGVLKIFLENVIRDA------VTYTEHARRKTVTAMDVVYALKR 121 (131)
Q Consensus 83 l~~vle~fle~I~~dA------v~yaeHA~RKTVt~~DV~~ALkr 121 (131)
+.+.+|.|+.+++.++ ++-++.|.+..+-++.|.|.++.
T Consensus 4 ~SDiIE~YlK~ll~es~~~ivEIkRselAd~FqcVPSQINYVIkT 48 (153)
T COG4463 4 TSDIIEAYLKELLEESTEEIVEIKRSELADQFQCVPSQINYVIKT 48 (153)
T ss_pred hHHHHHHHHHHHHHhcccchhhhhHHHHhhhcccchhheeeeeee
Confidence 4577889999999888 67788899998888888888764
No 209
>PRK07764 DNA polymerase III subunits gamma and tau; Validated
Probab=21.55 E-value=2.2e+02 Score=27.35 Aligned_cols=62 Identities=15% Similarity=0.034 Sum_probs=32.6
Q ss_pred ccchHHHH----HHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHH
Q 047769 57 GITKPAIR----RLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYAL 119 (131)
Q Consensus 57 gIpk~aIr----RLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~AL 119 (131)
.++...|. ++++..|+. |+++++..+.....--+..++..+-+++-.++...||.+||...+
T Consensus 178 ~l~~~~l~~~L~~il~~EGv~-id~eal~lLa~~sgGdlR~Al~eLEKLia~~~~~~IT~e~V~all 243 (824)
T PRK07764 178 LVPPEVMRGYLERICAQEGVP-VEPGVLPLVIRAGGGSVRDSLSVLDQLLAGAGPEGVTYERAVALL 243 (824)
T ss_pred CCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHcCCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHh
Confidence 45555544 444445754 788887776655443333333333333333445558777665443
No 210
>PLN03025 replication factor C subunit; Provisional
Probab=21.42 E-value=2.4e+02 Score=23.04 Aligned_cols=52 Identities=8% Similarity=-0.091 Sum_probs=31.5
Q ss_pred HHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHH
Q 047769 63 IRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVY 117 (131)
Q Consensus 63 IrRLArr~GvkRIS~~ay~el~~vle~fle~I~~dAv~yaeHA~RKTVt~~DV~~ 117 (131)
++++|+..|+. +++++++.+.+...-=++.++....... .+...||.+||..
T Consensus 167 L~~i~~~egi~-i~~~~l~~i~~~~~gDlR~aln~Lq~~~--~~~~~i~~~~v~~ 218 (319)
T PLN03025 167 LMKVVEAEKVP-YVPEGLEAIIFTADGDMRQALNNLQATH--SGFGFVNQENVFK 218 (319)
T ss_pred HHHHHHHcCCC-CCHHHHHHHHHHcCCCHHHHHHHHHHHH--hcCCCCCHHHHHH
Confidence 45666777875 8899988887665544444444443222 2334688777753
No 211
>PF02978 SRP_SPB: Signal peptide binding domain; InterPro: IPR004125 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 M domain of the 54 kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species. These proteins include Escherichia coli and Bacillus subtilis ffh protein (P48), which seems to be the prokaryotic counterpart of SRP54; signal recognition particle receptor alpha subunit (docking protein), an integral membrane GTP-binding protein which ensures, in conjunction with SRP, the correct targeting of nascent secretory proteins to the endoplasmic reticulum membrane; bacterial FtsY protein, which is believed to play a similar role to that of the docking protein in eukaryotes; the pilA protein from Neisseria gonorrhoeae, the homologue of ftsY; and bacterial flagellar biosynthesis protein flhF.; GO: 0008312 7S RNA binding, 0006614 SRP-dependent cotranslational protein targeting to membrane, 0048500 signal recognition particle; PDB: 2FFH_B 3NDB_B 2V3C_C 1QZW_G 1QZX_B 3KL4_A 2JQE_A 1HQ1_A 1RY1_W 1MFQ_C ....
Probab=21.36 E-value=1.3e+02 Score=21.34 Aligned_cols=30 Identities=30% Similarity=0.441 Sum_probs=19.6
Q ss_pred ccccchHHHHHHHHhcCccccchHHHHHHHHHHHHH
Q 047769 55 IQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIF 90 (131)
Q Consensus 55 i~gIpk~aIrRLArr~GvkRIS~~ay~el~~vle~f 90 (131)
-.-|..+-++|||+-.|+. .+++.+.++.|
T Consensus 68 p~ll~~sR~~RIA~GSG~~------~~eV~~ll~~f 97 (104)
T PF02978_consen 68 PKLLNESRRRRIARGSGTT------VQEVNELLKQF 97 (104)
T ss_dssp GGGHHHHHHHHHHHHTTS-------HHHHHHHHHHH
T ss_pred ccccchHHHHHHHHHcCCC------HHHHHHHHHHH
Confidence 3345556789999999965 45566666655
No 212
>PRK06647 DNA polymerase III subunits gamma and tau; Validated
Probab=21.27 E-value=2.8e+02 Score=25.34 Aligned_cols=58 Identities=7% Similarity=0.032 Sum_probs=33.7
Q ss_pred ccchHHH----HHHHHhcCccccchHHHHHHHHHHHHH---HHHHHHHHHHHHhhCCCceecHHHHHHHH
Q 047769 57 GITKPAI----RRLARRGGVKRISGLIYEETRGVLKIF---LENVIRDAVTYTEHARRKTVTAMDVVYAL 119 (131)
Q Consensus 57 gIpk~aI----rRLArr~GvkRIS~~ay~el~~vle~f---le~I~~dAv~yaeHA~RKTVt~~DV~~AL 119 (131)
.++...+ +++++..|+. +++++.+.+.....-- +.+.+..++.|+ + ..+|.+||..++
T Consensus 177 ~l~~~el~~~L~~i~~~egi~-id~eAl~lLa~~s~GdlR~alslLdklis~~---~-~~It~e~V~~ll 241 (563)
T PRK06647 177 LLSLEKIYNMLKKVCLEDQIK-YEDEALKWIAYKSTGSVRDAYTLFDQVVSFS---D-SDITLEQIRSKM 241 (563)
T ss_pred CCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHcCCCHHHHHHHHHHHHhhc---C-CCCCHHHHHHHh
Confidence 3444544 4445556755 8889888877654432 333334444453 3 348888877765
No 213
>PRK08691 DNA polymerase III subunits gamma and tau; Validated
Probab=21.18 E-value=2.6e+02 Score=26.76 Aligned_cols=61 Identities=8% Similarity=0.010 Sum_probs=39.2
Q ss_pred ccchHH----HHHHHHhcCccccchHHHHHHHHHHH---HHHHHHHHHHHHHHhhCCCceecHHHHHHHHHHc
Q 047769 57 GITKPA----IRRLARRGGVKRISGLIYEETRGVLK---IFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 122 (131)
Q Consensus 57 gIpk~a----IrRLArr~GvkRIS~~ay~el~~vle---~fle~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~ 122 (131)
.++... ++++++..|+. |++++++.+.+... ..+.+++..++.| +...|+.+||...|-..
T Consensus 177 ~Ls~eeI~~~L~~Il~kEgi~-id~eAL~~Ia~~A~GslRdAlnLLDqaia~----g~g~It~e~V~~lLG~~ 244 (709)
T PRK08691 177 NMTAQQVADHLAHVLDSEKIA-YEPPALQLLGRAAAGSMRDALSLLDQAIAL----GSGKVAENDVRQMIGAV 244 (709)
T ss_pred CCCHHHHHHHHHHHHHHcCCC-cCHHHHHHHHHHhCCCHHHHHHHHHHHHHh----cCCCcCHHHHHHHHccc
Confidence 455554 44566677765 89999988887754 3444445555555 23468988888776543
No 214
>PTZ00124 adenosine deaminase; Provisional
Probab=20.84 E-value=1.7e+02 Score=25.10 Aligned_cols=17 Identities=6% Similarity=-0.013 Sum_probs=14.3
Q ss_pred ccchHHHHHHHHhcCcc
Q 047769 57 GITKPAIRRLARRGGVK 73 (131)
Q Consensus 57 gIpk~aIrRLArr~Gvk 73 (131)
.|+..++..||++.|+.
T Consensus 47 si~~~tl~~La~~~~~~ 63 (362)
T PTZ00124 47 CFSVDFFLSCIRKYNLQ 63 (362)
T ss_pred CCCHHHHHHHHHHcCCC
Confidence 57888999999998863
No 215
>PF13338 DUF4095: Domain of unknown function (DUF4095)
Probab=20.58 E-value=37 Score=23.15 Aligned_cols=25 Identities=44% Similarity=0.804 Sum_probs=22.4
Q ss_pred ccchHHHHHHHHhcCccccchHHHH
Q 047769 57 GITKPAIRRLARRGGVKRISGLIYE 81 (131)
Q Consensus 57 gIpk~aIrRLArr~GvkRIS~~ay~ 81 (131)
|++...++++++++.+.|+...+|-
T Consensus 1 G~sr~~l~~~~~~G~l~rl~rGvY~ 25 (124)
T PF13338_consen 1 GISRRALRRLVRRGELIRLRRGVYA 25 (124)
T ss_pred CcCHHHHHHHHHCCCEEEeeCCEEE
Confidence 6788999999999999999888876
No 216
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=20.43 E-value=3.9e+02 Score=21.12 Aligned_cols=22 Identities=23% Similarity=0.543 Sum_probs=18.5
Q ss_pred ccchHHHHHHHHhcCccccchH
Q 047769 57 GITKPAIRRLARRGGVKRISGL 78 (131)
Q Consensus 57 gIpk~aIrRLArr~GvkRIS~~ 78 (131)
+.+.++|-|+|++.|.+-+++-
T Consensus 41 ~vS~aTv~Rf~kklG~~Gf~ef 62 (278)
T PRK11557 41 GVSQSSVVKFAQKLGYKGFPAL 62 (278)
T ss_pred CCCHHHHHHHHHHcCCCCHHHH
Confidence 6789999999999999877644
No 217
>CHL00076 chlB photochlorophyllide reductase subunit B
Probab=20.41 E-value=2.5e+02 Score=25.23 Aligned_cols=49 Identities=14% Similarity=0.037 Sum_probs=36.5
Q ss_pred ccchHHHHHHHHHHHHHH-HHHHHHHHHHHhhCCCceecHHHHHHHHHHcC
Q 047769 74 RISGLIYEETRGVLKIFL-ENVIRDAVTYTEHARRKTVTAMDVVYALKRQG 123 (131)
Q Consensus 74 RIS~~ay~el~~vle~fl-e~I~~dAv~yaeHA~RKTVt~~DV~~ALkr~G 123 (131)
.-|++|-.+|.++ =.|+ ..+=+.+..||+..|...||.+.+..|=.+.|
T Consensus 463 ~w~~ea~~~l~~i-P~f~r~~~r~~~e~~a~~~g~~~it~~~~~~a~~~~~ 512 (513)
T CHL00076 463 IWSPESQLELSKI-PGFVRGKVKRNTEKFARQNGITNITVEVMYAAKEALS 512 (513)
T ss_pred CCCHHHHHHHHhC-CHHhHHHHHHHHHHHHHHcCCCeEcHHHHHHHHHhhC
Confidence 4678888888776 3344 45555677899999999999999887755443
No 218
>PRK05563 DNA polymerase III subunits gamma and tau; Validated
Probab=20.36 E-value=2.9e+02 Score=25.07 Aligned_cols=58 Identities=12% Similarity=0.123 Sum_probs=33.5
Q ss_pred ccchHHH----HHHHHhcCccccchHHHHHHHHHHHH---HHHHHHHHHHHHHhhCCCceecHHHHHHHH
Q 047769 57 GITKPAI----RRLARRGGVKRISGLIYEETRGVLKI---FLENVIRDAVTYTEHARRKTVTAMDVVYAL 119 (131)
Q Consensus 57 gIpk~aI----rRLArr~GvkRIS~~ay~el~~vle~---fle~I~~dAv~yaeHA~RKTVt~~DV~~AL 119 (131)
.++...| +.+++..|+. +++++.+.+.....- .+.+++..+..|+ ...||.+||..++
T Consensus 177 ~~~~~ei~~~L~~i~~~egi~-i~~~al~~ia~~s~G~~R~al~~Ldq~~~~~----~~~It~~~V~~vl 241 (559)
T PRK05563 177 RISVEDIVERLKYILDKEGIE-YEDEALRLIARAAEGGMRDALSILDQAISFG----DGKVTYEDALEVT 241 (559)
T ss_pred CCCHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHcCCCHHHHHHHHHHHHHhc----cCCCCHHHHHHHh
Confidence 4444444 4445566764 888888777655332 2334444455553 3458888877654
No 219
>PRK12422 chromosomal replication initiation protein; Provisional
Probab=20.33 E-value=5.1e+02 Score=22.82 Aligned_cols=57 Identities=18% Similarity=0.141 Sum_probs=34.7
Q ss_pred HHHHHHhcCccccchHHHHHHHHHHH---HHHHHHHHHH---HHHHhhCCCceecHHHHHHHHHH
Q 047769 63 IRRLARRGGVKRISGLIYEETRGVLK---IFLENVIRDA---VTYTEHARRKTVTAMDVVYALKR 121 (131)
Q Consensus 63 IrRLArr~GvkRIS~~ay~el~~vle---~fle~I~~dA---v~yaeHA~RKTVt~~DV~~ALkr 121 (131)
+++.++..|+ .+++++.+.+..-+. .-|+..+... +.|+.-.+ ..+|.+++..+|+.
T Consensus 280 L~~k~~~~~~-~l~~evl~~la~~~~~dir~L~g~l~~l~~~~a~~~~~~-~~i~~~~~~~~l~~ 342 (445)
T PRK12422 280 LERKAEALSI-RIEETALDFLIEALSSNVKSLLHALTLLAKRVAYKKLSH-QLLYVDDIKALLHD 342 (445)
T ss_pred HHHHHHHcCC-CCCHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHhhC-CCCCHHHHHHHHHH
Confidence 4455555564 488888887765433 3344444444 35666555 35788888877764
No 220
>PRK06911 rpsN 30S ribosomal protein S14; Reviewed
Probab=20.09 E-value=1.2e+02 Score=21.73 Aligned_cols=37 Identities=24% Similarity=0.343 Sum_probs=24.8
Q ss_pred ecCCCcc-ccccccCCCCCCccCCCCCCccccccccccccccchHHHHHHHHhc
Q 047769 18 YSSDTQY-QRKIMSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRG 70 (131)
Q Consensus 18 ~~~~~~~-~~~~m~g~gkggkg~gk~g~kR~rKvlrd~i~gIpk~aIrRLArr~ 70 (131)
|+|++.. .||+++|+..| +.+++ +|+.-.++.+|..+
T Consensus 53 nss~~R~rNRC~~TGR~Rg--------------v~r~F--gLsRi~~Rela~~G 90 (100)
T PRK06911 53 NSNPVRYVTRCKQCGRPHA--------------VYRKF--NLCRICLRQQLMVG 90 (100)
T ss_pred ccCcchhhcccCCCCCCcc--------------ccccc--CchHHHHHHHHHcC
Confidence 5566543 58999988763 22322 78888888888776
Done!