Query 036580
Match_columns 186
No_of_seqs 173 out of 713
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 03:25:36 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/036580.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/036580hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0869 CCAAT-binding factor, 100.0 7.6E-38 1.6E-42 254.4 15.6 125 1-127 1-129 (168)
2 KOG0871 Class 2 transcription 99.9 2.5E-25 5.4E-30 179.8 11.0 95 26-120 8-102 (156)
3 KOG0870 DNA polymerase epsilon 99.9 1.5E-24 3.2E-29 177.9 11.4 106 24-129 4-110 (172)
4 COG5150 Class 2 transcription 99.8 1.3E-20 2.8E-25 149.8 10.0 96 27-122 8-103 (148)
5 PF00808 CBFD_NFYB_HMF: Histon 99.8 5.9E-19 1.3E-23 122.9 8.3 64 30-94 2-65 (65)
6 COG2036 HHT1 Histones H3 and H 99.8 2E-18 4.3E-23 130.0 7.3 77 24-102 13-89 (91)
7 cd00076 H4 Histone H4, one of 99.5 6.6E-14 1.4E-18 104.3 8.9 71 30-102 13-83 (85)
8 PLN00035 histone H4; Provision 99.5 1.3E-13 2.7E-18 106.1 8.9 73 28-102 27-99 (103)
9 PTZ00015 histone H4; Provision 99.5 3.2E-13 7E-18 103.7 9.0 75 26-102 26-100 (102)
10 smart00417 H4 Histone H4. 99.3 2.3E-12 5E-17 93.9 6.3 63 29-93 12-74 (74)
11 smart00803 TAF TATA box bindin 99.3 7.9E-12 1.7E-16 88.5 7.6 64 30-95 2-65 (65)
12 KOG1657 CCAAT-binding factor, 99.2 1.7E-11 3.7E-16 105.9 7.0 90 23-113 67-159 (236)
13 smart00428 H3 Histone H3. 99.2 4.5E-11 9.7E-16 92.3 7.4 72 24-95 23-99 (105)
14 COG5208 HAP5 CCAAT-binding fac 99.2 1.7E-11 3.6E-16 105.7 4.7 81 25-106 104-184 (286)
15 cd07981 TAF12 TATA Binding Pro 99.1 4.3E-10 9.4E-15 80.6 8.9 65 31-96 2-66 (72)
16 PF00125 Histone: Core histone 99.1 2.1E-10 4.6E-15 81.0 6.7 68 28-95 3-73 (75)
17 PLN00160 histone H3; Provision 99.0 9.4E-10 2E-14 83.9 6.7 71 25-95 16-90 (97)
18 PLN00161 histone H3; Provision 99.0 1.6E-09 3.5E-14 86.9 7.6 71 25-95 50-124 (135)
19 PLN00121 histone H3; Provision 99.0 9E-10 1.9E-14 88.5 5.9 71 25-95 57-130 (136)
20 PTZ00018 histone H3; Provision 98.9 1.4E-09 3.1E-14 87.4 6.1 71 25-95 57-130 (136)
21 KOG3467 Histone H4 [Chromatin 98.9 8.5E-09 1.8E-13 78.0 7.7 69 30-100 29-97 (103)
22 cd00074 H2A Histone 2A; H2A is 98.7 3.5E-08 7.6E-13 77.2 7.4 69 27-96 17-85 (115)
23 smart00576 BTP Bromodomain tra 98.7 1.3E-07 2.8E-12 68.3 8.7 66 33-100 9-74 (77)
24 cd07979 TAF9 TATA Binding Prot 98.7 2.4E-07 5.2E-12 72.3 9.8 79 34-114 5-84 (117)
25 KOG1745 Histones H3 and H4 [Ch 98.4 8.7E-08 1.9E-12 77.2 2.2 73 24-96 57-132 (137)
26 PF15511 CENP-T: Centromere ki 98.4 4.2E-07 9E-12 83.9 6.6 60 30-89 351-414 (414)
27 cd08050 TAF6 TATA Binding Prot 98.3 2E-06 4.3E-11 77.4 8.8 67 32-100 1-67 (343)
28 KOG1659 Class 2 transcription 98.3 1.4E-06 3.1E-11 74.7 6.3 81 29-110 12-92 (224)
29 PF03847 TFIID_20kDa: Transcri 98.2 1.1E-05 2.3E-10 57.9 7.8 63 33-96 2-64 (68)
30 PF02969 TAF: TATA box binding 98.1 3E-05 6.5E-10 55.4 8.2 64 30-95 3-66 (66)
31 PF15630 CENP-S: Kinetochore c 98.1 1.6E-05 3.4E-10 58.2 6.9 62 35-96 10-72 (76)
32 COG5262 HTA1 Histone H2A [Chro 98.0 1.1E-05 2.3E-10 64.1 6.1 69 27-96 23-91 (132)
33 PF07524 Bromo_TP: Bromodomain 98.0 6.5E-05 1.4E-09 53.8 8.8 65 34-100 10-74 (77)
34 COG5247 BUR6 Class 2 transcrip 97.9 2.4E-05 5.2E-10 60.7 6.2 77 30-107 23-99 (113)
35 cd08048 TAF11 TATA Binding Pro 97.9 5.7E-05 1.2E-09 56.3 8.1 66 30-97 16-84 (85)
36 smart00414 H2A Histone 2A. 97.8 5.8E-05 1.3E-09 58.4 6.6 68 28-96 7-74 (106)
37 smart00427 H2B Histone H2B. 97.8 0.00015 3.2E-09 54.8 8.1 61 35-96 6-66 (89)
38 PLN00154 histone H2A; Provisio 97.7 8.7E-05 1.9E-09 59.9 6.6 70 27-96 35-104 (136)
39 PF09415 CENP-X: CENP-S associ 97.7 8.1E-05 1.8E-09 53.9 4.7 64 32-95 1-66 (72)
40 PTZ00017 histone H2A; Provisio 97.7 0.00011 2.5E-09 59.1 6.0 69 27-96 24-92 (134)
41 PF04719 TAFII28: hTAFII28-lik 97.6 0.00042 9.1E-09 52.3 7.8 67 30-97 23-90 (90)
42 PLN00158 histone H2B; Provisio 97.6 0.00046 1E-08 54.4 8.1 64 32-96 29-92 (116)
43 KOG1658 DNA polymerase epsilon 97.5 3.3E-05 7.2E-10 63.6 1.5 67 29-96 58-124 (162)
44 KOG1142 Transcription initiati 97.5 0.00022 4.7E-09 62.9 6.7 70 26-96 150-219 (258)
45 PTZ00463 histone H2B; Provisio 97.5 0.00057 1.2E-08 54.0 8.0 61 35-96 33-93 (117)
46 PLN00156 histone H2AX; Provisi 97.5 0.0003 6.6E-09 57.0 6.3 69 27-96 26-94 (139)
47 PLN00157 histone H2A; Provisio 97.5 0.00025 5.4E-09 57.0 5.7 69 27-96 23-91 (132)
48 PLN00153 histone H2A; Provisio 97.5 0.00028 6.1E-09 56.6 5.9 69 27-96 21-89 (129)
49 KOG1756 Histone 2A [Chromatin 97.4 0.00041 9E-09 55.6 6.5 69 27-96 24-92 (131)
50 PF02269 TFIID-18kDa: Transcri 97.2 0.00042 9E-09 52.1 3.9 60 36-96 7-66 (93)
51 PF15510 CENP-W: Centromere ki 97.2 0.001 2.2E-08 51.0 5.4 67 29-96 15-95 (102)
52 cd07978 TAF13 The TATA Binding 97.1 0.012 2.5E-07 44.4 10.4 61 34-96 6-66 (92)
53 PF02291 TFIID-31kDa: Transcri 97.0 0.0034 7.4E-08 50.2 7.7 84 30-115 10-96 (129)
54 PTZ00252 histone H2A; Provisio 97.0 0.0023 5E-08 51.6 6.6 69 27-96 22-92 (134)
55 KOG1744 Histone H2B [Chromatin 96.7 0.0073 1.6E-07 48.4 7.2 61 35-96 42-102 (127)
56 KOG3219 Transcription initiati 96.6 0.003 6.5E-08 53.8 4.8 69 30-100 112-181 (195)
57 KOG3423 Transcription initiati 95.5 0.088 1.9E-06 44.2 8.1 69 30-100 86-168 (176)
58 KOG2549 Transcription initiati 95.5 0.065 1.4E-06 52.0 8.3 66 31-98 12-77 (576)
59 KOG4336 TBP-associated transcr 95.3 0.12 2.6E-06 47.0 8.9 77 36-116 11-87 (323)
60 KOG3334 Transcription initiati 95.1 0.2 4.4E-06 41.1 9.0 81 36-118 19-100 (148)
61 TIGR03015 pepcterm_ATPase puta 92.7 0.52 1.1E-05 39.3 7.2 70 30-99 191-268 (269)
62 COG5095 TAF6 Transcription ini 92.0 0.67 1.4E-05 43.0 7.5 66 33-100 8-73 (450)
63 KOG2389 Predicted bromodomain 91.4 0.64 1.4E-05 42.9 6.7 69 30-100 29-97 (353)
64 PRK00411 cdc6 cell division co 90.3 1.3 2.9E-05 39.2 7.7 70 31-100 207-285 (394)
65 KOG1757 Histone 2A [Chromatin 90.1 0.42 9E-06 38.1 3.7 65 27-95 27-95 (131)
66 cd08045 TAF4 TATA Binding Prot 89.6 2 4.4E-05 36.2 7.9 75 27-101 41-123 (212)
67 TIGR02928 orc1/cdc6 family rep 88.6 2.2 4.7E-05 37.4 7.7 72 33-104 201-281 (365)
68 PF13335 Mg_chelatase_2: Magne 86.6 4.7 0.0001 30.2 7.3 58 30-95 31-94 (96)
69 PF13654 AAA_32: AAA domain; P 84.9 5 0.00011 38.5 8.4 59 36-96 436-505 (509)
70 COG5162 Transcription initiati 83.7 6.9 0.00015 33.2 7.7 68 31-100 89-189 (197)
71 PF03540 TFIID_30kDa: Transcri 83.4 6.9 0.00015 26.8 6.3 48 30-79 2-49 (51)
72 TIGR02902 spore_lonB ATP-depen 83.2 4.1 8.9E-05 38.9 7.1 66 31-96 263-331 (531)
73 KOG3901 Transcription initiati 82.8 9.5 0.00021 30.0 7.6 48 46-96 24-71 (109)
74 PF08369 PCP_red: Proto-chloro 82.0 2.4 5.1E-05 28.0 3.5 42 51-93 2-44 (45)
75 TIGR00764 lon_rel lon-related 80.5 7.9 0.00017 37.8 8.0 48 49-96 330-390 (608)
76 COG5094 TAF9 Transcription ini 79.5 18 0.00039 29.4 8.4 74 47-120 29-106 (145)
77 PF05236 TAF4: Transcription i 76.8 3.5 7.5E-05 35.8 4.0 73 26-98 39-119 (264)
78 KOG2680 DNA helicase TIP49, TB 76.4 13 0.00027 35.0 7.6 51 46-96 374-428 (454)
79 COG1224 TIP49 DNA helicase TIP 74.9 15 0.00033 34.9 7.8 82 31-115 361-447 (450)
80 PRK00080 ruvB Holliday junctio 72.9 37 0.00079 29.9 9.5 72 30-101 179-254 (328)
81 TIGR00635 ruvB Holliday juncti 72.5 32 0.00069 29.4 8.8 70 31-100 159-232 (305)
82 COG1067 LonB Predicted ATP-dep 71.9 4.5 9.7E-05 40.1 3.8 48 49-96 338-398 (647)
83 PF09123 DUF1931: Domain of un 69.6 4.2 9.1E-05 33.2 2.6 69 36-116 1-69 (138)
84 COG5248 TAF19 Transcription in 69.2 33 0.00072 27.3 7.4 58 36-96 15-72 (126)
85 COG5251 TAF40 Transcription in 68.4 8.3 0.00018 32.9 4.2 62 30-95 115-179 (199)
86 PRK09862 putative ATP-dependen 65.9 27 0.00057 33.7 7.6 53 48-100 437-495 (506)
87 TIGR02442 Cob-chelat-sub cobal 65.5 27 0.00058 34.2 7.6 49 47-95 247-302 (633)
88 TIGR00368 Mg chelatase-related 64.8 18 0.0004 34.6 6.2 47 49-95 445-497 (499)
89 PF08681 DUF1778: Protein of u 64.4 6.2 0.00013 28.5 2.4 52 47-98 3-62 (80)
90 PRK13406 bchD magnesium chelat 62.4 22 0.00047 34.8 6.4 59 35-95 183-248 (584)
91 smart00350 MCM minichromosome 61.3 46 0.001 31.6 8.2 68 29-96 416-503 (509)
92 TIGR02030 BchI-ChlI magnesium 60.7 45 0.00098 30.3 7.7 54 41-95 247-307 (337)
93 KOG1658 DNA polymerase epsilon 60.4 27 0.00058 29.2 5.7 98 28-127 9-118 (162)
94 PRK12402 replication factor C 58.1 30 0.00065 29.7 5.9 68 31-100 184-252 (337)
95 COG1474 CDC6 Cdc6-related prot 57.7 35 0.00076 31.3 6.5 69 34-102 193-270 (366)
96 PF00356 LacI: Bacterial regul 56.5 24 0.00051 23.2 3.9 32 30-65 10-41 (46)
97 PRK07452 DNA polymerase III su 55.2 43 0.00093 29.1 6.5 53 47-99 147-201 (326)
98 PF02861 Clp_N: Clp amino term 55.2 25 0.00054 22.2 3.8 26 73-98 1-26 (53)
99 TIGR01128 holA DNA polymerase 53.6 90 0.002 26.3 8.0 65 31-95 111-176 (302)
100 CHL00081 chlI Mg-protoporyphyr 51.5 64 0.0014 29.7 7.2 60 34-95 254-320 (350)
101 COG1222 RPT1 ATP-dependent 26S 50.8 26 0.00057 33.1 4.6 49 48-96 338-391 (406)
102 PF00531 Death: Death domain; 50.4 33 0.00071 23.5 4.1 29 82-110 55-83 (83)
103 PF09114 MotA_activ: Transcrip 48.8 35 0.00077 26.2 4.2 34 34-67 51-88 (96)
104 PRK13407 bchI magnesium chelat 47.8 71 0.0015 29.0 6.8 59 34-94 238-303 (334)
105 PRK14975 bifunctional 3'-5' ex 47.8 1.5E+02 0.0033 28.5 9.4 93 27-122 160-272 (553)
106 COG5624 TAF61 Transcription in 47.5 16 0.00034 35.1 2.6 76 30-105 383-461 (505)
107 TIGR02031 BchD-ChlD magnesium 47.4 77 0.0017 30.9 7.4 54 41-95 196-256 (589)
108 PRK13765 ATP-dependent proteas 46.9 61 0.0013 32.2 6.7 48 49-96 339-399 (637)
109 PRK05932 RNA polymerase factor 46.3 40 0.00086 32.0 5.1 79 27-119 351-446 (455)
110 PTZ00361 26 proteosome regulat 45.3 32 0.0007 32.5 4.4 31 66-96 393-423 (438)
111 KOG1528 Salt-sensitive 3'-phos 43.6 67 0.0015 29.8 5.9 76 20-96 40-122 (351)
112 PRK03992 proteasome-activating 43.2 39 0.00084 30.9 4.5 34 64-97 339-372 (389)
113 PRK06585 holA DNA polymerase I 43.0 75 0.0016 27.9 6.1 49 47-95 159-208 (343)
114 PRK12728 fliE flagellar hook-b 42.9 1.5E+02 0.0033 22.6 7.1 64 53-118 32-99 (102)
115 TIGR01242 26Sp45 26S proteasom 42.6 39 0.00085 30.2 4.3 32 65-96 331-362 (364)
116 PRK05574 holA DNA polymerase I 42.2 1E+02 0.0022 26.5 6.8 66 31-96 146-212 (340)
117 PF08823 PG_binding_2: Putativ 41.2 56 0.0012 23.6 4.2 32 88-119 19-56 (74)
118 PTZ00454 26S protease regulato 40.1 43 0.00093 31.1 4.3 31 66-96 355-385 (398)
119 PTZ00183 centrin; Provisional 39.9 1.3E+02 0.0028 22.4 6.3 21 76-96 61-81 (158)
120 PRK07914 hypothetical protein; 39.4 85 0.0018 27.6 5.9 62 33-95 130-192 (320)
121 PF12627 PolyA_pol_RNAbd: Prob 38.7 19 0.0004 24.0 1.3 57 48-108 2-62 (64)
122 PRK14700 recombination factor 37.9 1.3E+02 0.0027 27.5 6.8 66 30-96 38-114 (300)
123 PF12010 DUF3502: Domain of un 37.3 33 0.00073 26.9 2.7 61 52-116 72-132 (134)
124 smart00354 HTH_LACI helix_turn 37.2 56 0.0012 22.5 3.6 32 30-65 11-42 (70)
125 PF11753 DUF3310: Protein of u 37.2 1.1E+02 0.0024 21.0 5.1 41 53-95 14-56 (60)
126 PLN00155 histone H2A; Provisio 37.0 32 0.0007 24.2 2.3 36 27-63 21-56 (58)
127 PF13405 EF-hand_6: EF-hand do 36.6 50 0.0011 19.0 2.8 27 72-98 4-31 (31)
128 COG1466 HolA DNA polymerase II 35.9 1.2E+02 0.0027 26.9 6.4 50 47-96 157-206 (334)
129 TIGR02395 rpoN_sigma RNA polym 35.8 1E+02 0.0022 29.0 6.1 79 27-119 326-422 (429)
130 PF07647 SAM_2: SAM domain (St 35.7 56 0.0012 21.6 3.3 25 84-108 3-27 (66)
131 PRK09526 lacI lac repressor; R 34.8 37 0.00081 28.9 2.8 37 30-71 16-52 (342)
132 cd00166 SAM Sterile alpha moti 34.2 41 0.00088 21.5 2.3 24 86-109 3-26 (63)
133 TIGR01052 top6b DNA topoisomer 33.2 49 0.0011 31.9 3.6 44 41-84 426-469 (488)
134 PRK05907 hypothetical protein; 33.2 1.1E+02 0.0025 27.3 5.7 73 47-119 151-233 (311)
135 TIGR01241 FtsH_fam ATP-depende 33.1 1.1E+02 0.0024 28.6 5.9 61 37-98 231-296 (495)
136 smart00027 EH Eps15 homology d 32.4 1.1E+02 0.0023 22.0 4.5 28 73-100 15-42 (96)
137 PF00536 SAM_1: SAM domain (St 32.3 63 0.0014 21.3 3.1 23 86-108 4-26 (64)
138 PRK00440 rfc replication facto 32.2 1E+02 0.0022 26.1 5.0 64 31-96 161-225 (319)
139 COG4453 Uncharacterized protei 32.2 1.8E+02 0.0039 22.3 5.8 65 47-111 14-87 (95)
140 PLN00138 large subunit ribosom 32.0 1.5E+02 0.0032 23.2 5.5 40 73-112 6-45 (113)
141 PF12668 DUF3791: Protein of u 31.7 78 0.0017 21.6 3.5 31 81-111 13-43 (62)
142 PTZ00373 60S Acidic ribosomal 31.3 1.5E+02 0.0034 23.2 5.5 39 73-111 8-46 (112)
143 PRK08487 DNA polymerase III su 30.9 1.9E+02 0.004 25.6 6.7 47 47-95 152-198 (328)
144 cd08316 Death_FAS_TNFRSF6 Deat 30.7 2.4E+02 0.0051 21.3 8.6 72 30-111 17-93 (97)
145 PF10835 DUF2573: Protein of u 30.1 85 0.0018 23.6 3.6 71 54-124 4-80 (82)
146 PTZ00009 heat shock 70 kDa pro 30.0 4.8E+02 0.01 25.6 9.9 13 31-43 512-524 (653)
147 PF13499 EF-hand_7: EF-hand do 29.7 1.3E+02 0.0028 19.5 4.3 42 72-113 4-45 (66)
148 PRK03902 manganese transport t 29.4 2.1E+02 0.0045 22.1 6.0 87 27-115 30-135 (142)
149 cd08313 Death_TNFR1 Death doma 29.4 2.3E+02 0.0049 20.7 6.4 70 30-104 8-77 (80)
150 PRK09111 DNA polymerase III su 29.3 1.4E+02 0.0031 29.4 6.1 62 32-94 192-254 (598)
151 PRK02910 light-independent pro 29.0 1.2E+02 0.0025 29.1 5.4 52 46-98 466-518 (519)
152 CHL00076 chlB photochlorophyll 28.8 1.2E+02 0.0027 28.9 5.5 52 46-98 460-512 (513)
153 TIGR02639 ClpA ATP-dependent C 28.4 3.5E+02 0.0077 26.9 8.7 69 32-100 346-433 (731)
154 PF02847 MA3: MA3 domain; Int 28.2 1.5E+02 0.0032 21.5 4.8 15 82-96 66-80 (113)
155 PF08397 IMD: IRSp53/MIM homol 28.1 1.6E+02 0.0034 24.7 5.5 59 53-116 24-99 (219)
156 PF07499 RuvA_C: RuvA, C-termi 28.0 1.3E+02 0.0029 19.3 4.0 14 87-100 3-16 (47)
157 PRK14964 DNA polymerase III su 28.0 1.6E+02 0.0034 28.4 6.1 47 47-94 192-238 (491)
158 PRK10727 DNA-binding transcrip 27.8 54 0.0012 28.1 2.7 32 30-65 12-43 (343)
159 TIGR01278 DPOR_BchB light-inde 27.7 1.3E+02 0.0028 28.7 5.4 52 46-98 459-511 (511)
160 PRK14987 gluconate operon tran 27.6 56 0.0012 27.8 2.7 31 30-64 16-46 (331)
161 PF02049 FliE: Flagellar hook- 27.5 2.6E+02 0.0055 20.7 7.2 66 52-118 25-93 (96)
162 smart00454 SAM Sterile alpha m 27.4 59 0.0013 20.9 2.3 26 84-109 3-28 (68)
163 PRK14955 DNA polymerase III su 27.3 3.7E+02 0.008 24.5 8.1 48 47-94 203-254 (397)
164 PF10728 DUF2520: Domain of un 27.0 2.9E+02 0.0062 21.7 6.5 59 33-94 13-74 (132)
165 CHL00176 ftsH cell division pr 27.0 1.6E+02 0.0034 29.3 6.0 64 34-97 356-423 (638)
166 cd00051 EFh EF-hand, calcium b 26.9 1.4E+02 0.0031 17.6 5.1 33 76-108 8-40 (63)
167 TIGR02903 spore_lon_C ATP-depe 26.8 1.3E+02 0.0029 29.4 5.5 70 33-103 355-436 (615)
168 PRK05629 hypothetical protein; 26.5 2.2E+02 0.0047 24.9 6.3 48 47-95 143-190 (318)
169 KOG3557 Epidermal growth facto 26.4 81 0.0018 31.9 3.9 32 98-129 279-310 (721)
170 COG1500 Predicted exosome subu 26.2 4.4E+02 0.0095 23.4 8.0 74 36-112 72-148 (234)
171 KOG1942 DNA helicase, TBP-inte 26.2 1.6E+02 0.0035 27.8 5.5 65 30-94 366-435 (456)
172 COG1724 Predicted RNA binding 26.0 54 0.0012 23.7 2.0 18 84-101 6-23 (66)
173 KOG0785 Isocitrate dehydrogena 25.9 99 0.0022 28.9 4.1 66 50-116 164-229 (365)
174 KOG4717 Serine/threonine prote 25.5 1.5E+02 0.0033 30.0 5.5 73 48-120 240-349 (864)
175 cd01392 HTH_LacI Helix-turn-he 25.1 1.1E+02 0.0024 19.0 3.2 32 30-65 8-39 (52)
176 TIGR02454 CbiQ_TIGR cobalt ABC 25.1 1.5E+02 0.0033 23.7 4.7 18 83-100 112-129 (198)
177 PRK07764 DNA polymerase III su 24.8 1.7E+02 0.0036 30.1 5.8 61 31-91 179-240 (824)
178 PRK14971 DNA polymerase III su 24.8 1.6E+02 0.0036 28.9 5.6 63 31-94 180-243 (614)
179 KOG0729 26S proteasome regulat 24.8 67 0.0015 29.9 2.8 48 49-96 365-417 (435)
180 COG1239 ChlI Mg-chelatase subu 24.5 1.9E+02 0.004 27.8 5.7 49 47-95 265-320 (423)
181 TIGR01481 ccpA catabolite cont 24.4 91 0.002 26.3 3.4 32 30-65 12-43 (329)
182 PTZ00184 calmodulin; Provision 24.4 2.8E+02 0.0061 20.2 5.7 30 71-100 87-116 (149)
183 KOG2008 BTK-associated SH3-dom 24.3 76 0.0016 29.8 3.0 70 48-122 75-145 (426)
184 cd04752 Commd4 COMM_Domain con 24.0 4E+02 0.0087 21.7 10.0 53 61-120 43-96 (174)
185 cd05833 Ribosomal_P2 Ribosomal 23.6 2.5E+02 0.0053 21.8 5.4 28 73-100 6-33 (109)
186 PF02361 CbiQ: Cobalt transpor 23.5 1.5E+02 0.0033 23.7 4.4 37 83-119 123-171 (224)
187 KOG2256 Predicted protein invo 23.1 3.5E+02 0.0075 27.5 7.5 80 30-121 538-620 (661)
188 COG1389 DNA topoisomerase VI, 23.1 61 0.0013 31.7 2.3 46 41-86 434-479 (538)
189 TIGR02397 dnaX_nterm DNA polym 22.9 2.4E+02 0.0051 24.4 5.8 62 33-95 178-240 (355)
190 PRK10423 transcriptional repre 22.7 98 0.0021 26.0 3.3 32 30-65 9-40 (327)
191 PF03477 ATP-cone: ATP cone do 22.4 53 0.0011 23.2 1.4 55 31-96 13-67 (90)
192 PRK10703 DNA-binding transcrip 22.4 1E+02 0.0022 26.3 3.3 32 30-65 12-43 (341)
193 PLN02900 alanyl-tRNA synthetas 22.2 6.1E+02 0.013 26.6 9.3 28 78-105 404-432 (936)
194 cd00052 EH Eps15 homology doma 22.0 2.2E+02 0.0048 18.0 4.9 24 76-99 7-30 (67)
195 PF12767 SAGA-Tad1: Transcript 21.8 2.4E+02 0.0052 24.2 5.5 28 49-76 223-250 (252)
196 PRK06645 DNA polymerase III su 21.5 2.2E+02 0.0047 27.5 5.6 65 31-95 187-254 (507)
197 KOG0027 Calmodulin and related 21.2 3.9E+02 0.0085 20.6 8.1 42 69-110 86-127 (151)
198 PRK11303 DNA-binding transcrip 20.8 1.3E+02 0.0028 25.3 3.7 35 30-65 11-45 (328)
199 PRK14963 DNA polymerase III su 20.7 2.5E+02 0.0055 26.9 5.9 61 31-93 175-236 (504)
200 cd00823 TopoIIB_Trans TopoIIB_ 20.7 1.7E+02 0.0037 24.2 4.2 34 41-74 111-144 (151)
201 PRK14954 DNA polymerase III su 20.7 4E+02 0.0087 26.5 7.4 64 31-94 186-254 (620)
202 KOG0921 Dosage compensation co 20.6 1.7E+02 0.0037 31.3 4.9 26 48-73 1088-1116(1282)
203 PRK06474 hypothetical protein; 20.5 1.8E+02 0.0039 23.9 4.3 14 30-43 38-51 (178)
No 1
>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [Transcription]
Probab=100.00 E-value=7.6e-38 Score=254.41 Aligned_cols=125 Identities=78% Similarity=1.186 Sum_probs=114.1
Q ss_pred CCCCCCCCCCcccccCCC----CCCCCCcccccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 036580 1 MGDSDNDSGGERERQHGS----SRELSPREQDRFLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASDK 76 (186)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~----~~e~~~re~d~~LPkA~V~RImK~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~ 76 (186)
|++||.++++. +.+++ .+.++++++|++||+|+|.||||+.||.+.+|||||++.+|+|+.+||++||.+|.+.
T Consensus 1 m~~s~~~~~~~--~e~~g~~~~~~~~~~reqDr~LPIANV~RIMK~~lP~naKIsKDAKE~vQECVSEfISFvT~EAsek 78 (168)
T KOG0869|consen 1 MAESDHDSGGG--DENGGNSSPQSSLSLREQDRFLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASEK 78 (168)
T ss_pred CCCCcCCCCcc--ccCCcccCCccccccchhhhhccHHHHHHHHHhcCCcccccchHHHHHHHHHHHHHHHHHhhHHHHH
Confidence 78889888665 33333 2567899999999999999999999999999999999999999999999999999999
Q ss_pred HHhcCCCccCHHHHHHHHHHcCCccchHHHHHHHHHHHHHHHhhhhcCCCC
Q 036580 77 CQREKRKTINGDDLLWAMTTLGFEEYVEPLKVYLQRFREMEGEKMARDKDA 127 (186)
Q Consensus 77 a~~~kRKTIt~eDVl~AL~~LgF~dyi~~Lk~~L~~~re~~~~K~~~kk~~ 127 (186)
|++++||||+.+||+|||.+|||++|+++|+.||.+|||+++++....+..
T Consensus 79 C~~EkRKTIngdDllwAm~tLGFe~Y~eplkiyL~kYRe~e~e~~~~~~~~ 129 (168)
T KOG0869|consen 79 CQREKRKTINGDDLLWAMSTLGFENYAEPLKIYLQKYRELEGERGRSGKGG 129 (168)
T ss_pred HHHHhcCcccHHHHHHHHHHcCcHhHHHHHHHHHHHHHHHhhhcccccccC
Confidence 999999999999999999999999999999999999999998887655554
No 2
>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=99.93 E-value=2.5e-25 Score=179.76 Aligned_cols=95 Identities=32% Similarity=0.659 Sum_probs=90.1
Q ss_pred ccccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHcCCccchHH
Q 036580 26 EQDRFLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMTTLGFEEYVEP 105 (186)
Q Consensus 26 e~d~~LPkA~V~RImK~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~LgF~dyi~~ 105 (186)
.+++.||+|+|.+|||+.||.++||.+||+++|.+||.+||+.|+++|+++|..+.||||.++||++||+.|||.+|++.
T Consensus 8 dde~sLPkAtv~KmIke~lP~d~rvakeareliincCvEFI~liSsEAneic~~e~KKTIa~EHV~KALe~LgF~eYiee 87 (156)
T KOG0871|consen 8 DDELSLPKATVNKMIKEMLPKDVRVAKEARELIINCCVEFINLISSEANEICNKEAKKTIAPEHVIKALENLGFGEYIEE 87 (156)
T ss_pred cccccCcHHHHHHHHHHhCCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHhHHhcccCCHHHHHHHHHHcchHHHHHH
Confidence 34567999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHhh
Q 036580 106 LKVYLQRFREMEGEK 120 (186)
Q Consensus 106 Lk~~L~~~re~~~~K 120 (186)
+.+.|++|+.....+
T Consensus 88 ~~~vl~~~K~~~~~~ 102 (156)
T KOG0871|consen 88 AEEVLENCKEEAKKR 102 (156)
T ss_pred HHHHHHHHHHHHHHh
Confidence 999999999876543
No 3
>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription]
Probab=99.92 E-value=1.5e-24 Score=177.91 Aligned_cols=106 Identities=30% Similarity=0.518 Sum_probs=100.5
Q ss_pred CcccccCCchhHHHHHHHhhCCCC-cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHcCCccc
Q 036580 24 PREQDRFLPIANVSRIMKKALPAN-AKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMTTLGFEEY 102 (186)
Q Consensus 24 ~re~d~~LPkA~V~RImK~alP~~-~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~LgF~dy 102 (186)
.+.+|+.||+|+|.||+|+.||.. +.|++||+.+|++++++||+||++.|+++|..++||||+++||+.||+.|+|..|
T Consensus 4 eri~dl~lP~AiI~rlvke~l~E~~vsisKeA~~Ai~raAtVFv~~Lts~s~e~A~~q~rKt~sadDVl~aL~Eiefs~f 83 (172)
T KOG0870|consen 4 ERIEDLNLPNAIITRLVKEVLPESNVSISKEARLAIARAATVFVIFLTSVSNEIAKDQKRKTISADDVLKALDEIEFSSF 83 (172)
T ss_pred hhHHHhhccHHHHHHHHHHhCccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCcccHHHHHHHHHHhchHHH
Confidence 467899999999999999999976 8999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHHHHHHHHhhhhcCCCCCC
Q 036580 103 VEPLKVYLQRFREMEGEKMARDKDAPP 129 (186)
Q Consensus 103 i~~Lk~~L~~~re~~~~K~~~kk~~~~ 129 (186)
+.||+..|+.|+...++|+.++..+.-
T Consensus 84 ~~plk~~Le~yk~~~k~Kk~~~~~~~e 110 (172)
T KOG0870|consen 84 VNPLKSALEAYKKAVKQKKLAKANKSE 110 (172)
T ss_pred hhHHHHHHHHHHHHHHHHHHhcccccc
Confidence 999999999999999999887776643
No 4
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=99.84 E-value=1.3e-20 Score=149.76 Aligned_cols=96 Identities=28% Similarity=0.522 Sum_probs=91.2
Q ss_pred cccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHcCCccchHHH
Q 036580 27 QDRFLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMTTLGFEEYVEPL 106 (186)
Q Consensus 27 ~d~~LPkA~V~RImK~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~LgF~dyi~~L 106 (186)
+++.||+|+|.+++-+.||.+..+++||++.|++||-+||+.|+++|++.|+.+.+|||.++||++||+.|+|.+|++.|
T Consensus 8 De~sLPKATVqKMvS~iLp~dl~ftKearei~in~cieFi~~lsseAne~ce~EaKKTIa~EHviKALenLef~eyi~~~ 87 (148)
T COG5150 8 DENSLPKATVQKMVSSILPKDLVFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHVIKALENLEFEEYIESC 87 (148)
T ss_pred ccccCcHHHHHHHHHHhccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHhccHHHHHHHH
Confidence 34569999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhhhh
Q 036580 107 KVYLQRFREMEGEKMA 122 (186)
Q Consensus 107 k~~L~~~re~~~~K~~ 122 (186)
.+.+.+|+..++.|..
T Consensus 88 ~e~~~n~k~~qK~ke~ 103 (148)
T COG5150 88 MEEHENYKSYQKQKES 103 (148)
T ss_pred HHHHHHHHHHHhhchh
Confidence 9999999998877643
No 5
>PF00808 CBFD_NFYB_HMF: Histone-like transcription factor (CBF/NF-Y) and archaeal histone; InterPro: IPR003958 The CCAAT-binding factor (CBF) is a mammalian transcription factor that binds to a CCAAT motif in the promoters of a wide variety of genes, including type I collagen and albumin. The factor is a heteromeric complex of A and B subunits, both of which are required for DNA-binding [, ]. The subunits can interact in the absence of DNA-binding, conserved regions in each being important in mediating this interaction. The A subunit can be split into 3 domains on the basis of sequence similarity, a non-conserved N-terminal 'A domain'; a highly-conserved central 'B domain' involved in DNA-binding; and a C-terminal 'C domain', which contains a number of glutamine and acidic residues involved in protein-protein interactions []. The A subunit shows striking similarity to the HAP3 subunit of the yeast CCAAT-binding heterotrimeric transcription factor [, ]. The Kluyveromyces lactis HAP3 protein has been predicted to contain a 4-cysteine zinc finger, which is thought to be present in similar HAP3 and CBF subunit A proteins, in which the third cysteine is replaced by a serine []. This domain is found in the CCAAT transcription factor and archaeal histones.; GO: 0043565 sequence-specific DNA binding, 0005622 intracellular; PDB: 1F1E_A 2BYM_D 2BYK_D 1HTA_A 1B67_A 1JFI_B 1KU5_B 1N1J_A 1BFM_A 1B6W_A ....
Probab=99.78 E-value=5.9e-19 Score=122.88 Aligned_cols=64 Identities=42% Similarity=0.645 Sum_probs=59.3
Q ss_pred CCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHH
Q 036580 30 FLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAM 94 (186)
Q Consensus 30 ~LPkA~V~RImK~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL 94 (186)
.||+++|+||||.. |++.+||+||.++|++|+++||.+|+.+|++.|++++||||+++||..||
T Consensus 2 ~lP~a~vkri~k~~-~~~~~vs~ea~~~i~~a~e~Fi~~l~~~A~~~a~~~~rkti~~~Dv~~Av 65 (65)
T PF00808_consen 2 SLPLARVKRIMKSD-PDVMRVSKEAVEAIAKAAEEFIQYLAKEANEIAQRDKRKTITYEDVAKAV 65 (65)
T ss_dssp SS-HHHHHHHHHHT-STTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEE-HHHHHHHH
T ss_pred CCChHHHHHHhccC-CCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHC
Confidence 59999999999999 88899999999999999999999999999999999999999999999986
No 6
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=99.75 E-value=2e-18 Score=129.98 Aligned_cols=77 Identities=34% Similarity=0.536 Sum_probs=73.1
Q ss_pred CcccccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHcCCccc
Q 036580 24 PREQDRFLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMTTLGFEEY 102 (186)
Q Consensus 24 ~re~d~~LPkA~V~RImK~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~LgF~dy 102 (186)
.+..+..||+++|.||||+..++ |||.+|+++|++|+++|+..|+..|+++|.|+|||||+++||..|++.++|.-|
T Consensus 13 ~~~~~~~Lp~apv~Ri~r~~~~~--Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~DI~la~~~~~~~~~ 89 (91)
T COG2036 13 QRSTDLLLPKAPVRRILRKAGAE--RVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLALKRLGRRIY 89 (91)
T ss_pred hhhhhhhcCchHHHHHHHHHhHH--HhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHHHhccccc
Confidence 46788899999999999999964 999999999999999999999999999999999999999999999999999765
No 7
>cd00076 H4 Histone H4, one of the four histones, along with H2A, H2B and H3, which forms the eukaryotic nucleosome core; along with H3, it plays a central role in nucleosome formation; histones bind to DNA and wrap the genetic material into "beads on a string" in which DNA (the string) is wrapped around small blobs of histones (the beads) at regular intervals; play a role in the inheritance of specialized chromosome structures and the control of gene activity; defects in the establishment of proper chromosome structure by histones may activate or silence genes aberrantly and thus lead to disease; the sequence of histone H4 has remained almost invariant in more than 2 billion years of evolution
Probab=99.52 E-value=6.6e-14 Score=104.25 Aligned_cols=71 Identities=20% Similarity=0.324 Sum_probs=67.3
Q ss_pred CCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHcCCccc
Q 036580 30 FLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMTTLGFEEY 102 (186)
Q Consensus 30 ~LPkA~V~RImK~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~LgF~dy 102 (186)
.||++.|.||+|... ..|||.|+.+.+.++.++|+..|..+|..+|+|++||||+++||..||++.|-.-|
T Consensus 13 gi~k~~I~RLarr~G--vkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~alkr~g~~~y 83 (85)
T cd00076 13 GITKPAIRRLARRGG--VKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLY 83 (85)
T ss_pred cCCHHHHHHHHHHcC--cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHCCCCcc
Confidence 599999999999997 78999999999999999999999999999999999999999999999999986544
No 8
>PLN00035 histone H4; Provisional
Probab=99.49 E-value=1.3e-13 Score=106.10 Aligned_cols=73 Identities=19% Similarity=0.262 Sum_probs=67.7
Q ss_pred ccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHcCCccc
Q 036580 28 DRFLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMTTLGFEEY 102 (186)
Q Consensus 28 d~~LPkA~V~RImK~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~LgF~dy 102 (186)
...||+++|.||+|... ..|||.|+.+++.+..++|+..|+.+|..+|+|++||||+++||..||+.+|-.-|
T Consensus 27 i~~ipk~~IrRLARr~G--vkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr~g~~ly 99 (103)
T PLN00035 27 IQGITKPAIRRLARRGG--VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTLY 99 (103)
T ss_pred hccCCHHHHHHHHHHcC--cccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHcCCcCC
Confidence 34599999999999997 78999999999999999999999999999999999999999999999998875443
No 9
>PTZ00015 histone H4; Provisional
Probab=99.46 E-value=3.2e-13 Score=103.68 Aligned_cols=75 Identities=21% Similarity=0.347 Sum_probs=69.1
Q ss_pred ccccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHcCCccc
Q 036580 26 EQDRFLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMTTLGFEEY 102 (186)
Q Consensus 26 e~d~~LPkA~V~RImK~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~LgF~dy 102 (186)
.....||+++|.||+|... ..|||.|+.+.+.++.++|+..|+.+|..+|+|++||||+++||..||+.+|-.-|
T Consensus 26 ~~i~gI~k~~IrRLarr~G--vkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~AlKr~g~~~y 100 (102)
T PTZ00015 26 DNIRGITKGAIRRLARRGG--VKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALKRQGRTLY 100 (102)
T ss_pred hcccCCCHHHHHHHHHHcC--CccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhcCCCCC
Confidence 3445799999999999997 78999999999999999999999999999999999999999999999999876544
No 10
>smart00417 H4 Histone H4.
Probab=99.34 E-value=2.3e-12 Score=93.85 Aligned_cols=63 Identities=17% Similarity=0.297 Sum_probs=59.7
Q ss_pred cCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHH
Q 036580 29 RFLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWA 93 (186)
Q Consensus 29 ~~LPkA~V~RImK~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~A 93 (186)
..||+++|.||+|... ..|||.++.+.+.+..++|+..|+.+|..+|+|++||||+++||..|
T Consensus 12 ~gI~k~~IrRLaRr~G--vkRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~~a 74 (74)
T smart00417 12 QGITKPAIRRLARRGG--VKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVYA 74 (74)
T ss_pred cCCCHHHHHHHHHHcC--cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHheeC
Confidence 3699999999999997 78999999999999999999999999999999999999999999754
No 11
>smart00803 TAF TATA box binding protein associated factor. TAFs (TATA box binding protein associated factors) are part of the transcription initiation factor TFIID multimeric protein complex. TFIID is composed of the TATA box binding protein (TBP) and a number of TAFs. The TAFs provide binding sites for many different transcriptional activators and co-activators that modulate transcription initiation by Pol II. TAF proteins adopt a histone-like fold.
Probab=99.31 E-value=7.9e-12 Score=88.54 Aligned_cols=64 Identities=22% Similarity=0.242 Sum_probs=61.1
Q ss_pred CCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHH
Q 036580 30 FLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMT 95 (186)
Q Consensus 30 ~LPkA~V~RImK~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~ 95 (186)
.||+++|+||++... ..+||.|+..+|.+.++.|+..|..+|.++++|.+||||+.+||..||+
T Consensus 2 ~~p~~~i~ria~~~G--i~ris~~a~~~l~~~~e~rl~~i~~~A~k~~~hakRktlt~~DI~~Alk 65 (65)
T smart00803 2 WLPKETIKDVAESLG--IGNLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSALR 65 (65)
T ss_pred CCCHHHHHHHHHHCC--CccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCeecHHHHHHHhC
Confidence 589999999999986 6799999999999999999999999999999999999999999999984
No 12
>KOG1657 consensus CCAAT-binding factor, subunit C (HAP5) [Transcription]
Probab=99.23 E-value=1.7e-11 Score=105.93 Aligned_cols=90 Identities=22% Similarity=0.344 Sum_probs=78.7
Q ss_pred CCcccccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH---cCC
Q 036580 23 SPREQDRFLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMTT---LGF 99 (186)
Q Consensus 23 ~~re~d~~LPkA~V~RImK~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~---LgF 99 (186)
........||+++|++|||.. ++...|+.||..++.+||+.||..|+..|+..++..+|+|+...|+..|+.. ++|
T Consensus 67 ~~d~~~~~lPlaRiKkimK~d-edv~mI~~Eapvl~aka~E~Fi~elt~~sw~~Tee~~rrtl~~sdia~av~~s~~fdF 145 (236)
T KOG1657|consen 67 QLDFKNHILPLARIKKIMKSD-EDVSMITAEAPVLFAKACELFITELTLRSWVHTEENKRRTLQKSDIAAAVTQSETFDF 145 (236)
T ss_pred ccchhhccCcHhhcccccccc-ccccccchhHHHHHHHHHHHHHHHHHHHhhhhhcccccccchHHHHHHHhccCCCccc
Confidence 334455679999999999998 4566899999999999999999999999999999999999999999999985 566
Q ss_pred ccchHHHHHHHHHH
Q 036580 100 EEYVEPLKVYLQRF 113 (186)
Q Consensus 100 ~dyi~~Lk~~L~~~ 113 (186)
.-.+-|.+..+++|
T Consensus 146 L~DivP~~~~~~~~ 159 (236)
T KOG1657|consen 146 LRDIVPRKILAEKY 159 (236)
T ss_pred eeccccchhccccc
Confidence 66666888888888
No 13
>smart00428 H3 Histone H3.
Probab=99.21 E-value=4.5e-11 Score=92.26 Aligned_cols=72 Identities=17% Similarity=0.212 Sum_probs=66.2
Q ss_pred CcccccCCchhHHHHHHHhhCCC-----CcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHH
Q 036580 24 PREQDRFLPIANVSRIMKKALPA-----NAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMT 95 (186)
Q Consensus 24 ~re~d~~LPkA~V~RImK~alP~-----~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~ 95 (186)
.+.+++.||+.++.|++++...+ +.||+.+|+++||+++|.|+..|...|+.+|.|+||+||+++|+..|..
T Consensus 23 Qkst~lLI~k~pF~RLVREI~~~~~~~~~~R~~~~Al~aLQeasE~ylv~lfeda~~~a~HAkRvTl~~kDi~La~r 99 (105)
T smart00428 23 QKSTDLLIRKAPFQRLVREIAQKFTTGVDLRFQSSAIMALQEAAEAYLVGLFEDTNLLAIHAKRVTIMPKDIQLARR 99 (105)
T ss_pred ccCcccccccccHHHHHHHHHHHcCCCCCceeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccCcHhhHHHHHH
Confidence 36778899999999999998753 6799999999999999999999999999999999999999999988864
No 14
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=99.19 E-value=1.7e-11 Score=105.73 Aligned_cols=81 Identities=22% Similarity=0.267 Sum_probs=73.1
Q ss_pred cccccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHcCCccchH
Q 036580 25 REQDRFLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMTTLGFEEYVE 104 (186)
Q Consensus 25 re~d~~LPkA~V~RImK~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~LgF~dyi~ 104 (186)
-..++.||+|+|+|+||-.- ++..||.||..++.++||.||..||..||-.|++++|+|+...||..|+++-++.||+-
T Consensus 104 ~~k~h~LPlARIkkvMKtde-dVkMisaEaPvlFak~~EiFI~ELTmRAW~~ae~NkRRtLQksDia~Av~kSeMfDFLi 182 (286)
T COG5208 104 LLKDHNLPLARIKKVMKTDE-DVKMISAEAPVLFAKITEIFIEELTMRAWINAEENKRRTLQKSDIAAAVKKSEMFDFLI 182 (286)
T ss_pred HHHhccCcHHHHHHHHhccc-chhheecccchHHHHHHHHHHHHHHHHHHHHHhHhhhhHHHHHHHHHHHHHHHHHhHHh
Confidence 34567899999999999885 46679999999999999999999999999999999999999999999999988888765
Q ss_pred HH
Q 036580 105 PL 106 (186)
Q Consensus 105 ~L 106 (186)
.+
T Consensus 183 di 184 (286)
T COG5208 183 DI 184 (286)
T ss_pred hh
Confidence 43
No 15
>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=99.13 E-value=4.3e-10 Score=80.64 Aligned_cols=65 Identities=18% Similarity=0.327 Sum_probs=62.0
Q ss_pred CchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 036580 31 LPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMTT 96 (186)
Q Consensus 31 LPkA~V~RImK~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~ 96 (186)
|++..+..++|+.-| ..+|+.||.++|++.++.|+..|+..|..+|+|.+|+||..+||..+|++
T Consensus 2 ~~k~~l~~lv~~id~-~~~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~~~tv~~~Di~l~l~r 66 (72)
T cd07981 2 LTKRKLQELLKEIDP-REQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQLHLER 66 (72)
T ss_pred CcHHHHHHHHHhhCC-CCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence 688899999999987 58999999999999999999999999999999999999999999999986
No 16
>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=99.11 E-value=2.1e-10 Score=80.96 Aligned_cols=68 Identities=25% Similarity=0.348 Sum_probs=62.4
Q ss_pred ccCCchhHHHHHHHhhCCC---CcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHH
Q 036580 28 DRFLPIANVSRIMKKALPA---NAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMT 95 (186)
Q Consensus 28 d~~LPkA~V~RImK~alP~---~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~ 95 (186)
...+|+..|.|++|+..++ ..+||++|.+.|+.+++.|+..|...|..+|.+.||+||+++||..|++
T Consensus 3 ~~~~~~~~~~r~~r~i~~~~~~~~ris~~a~~~L~~~~E~~~~~il~~A~~~a~~~kR~tI~~~DI~~A~r 73 (75)
T PF00125_consen 3 RRLIPKFPFSRLLREIGEEILSKYRISSEALVALQSVLEYLLVEILEEAGNLARHAKRKTITPRDIQLAVR 73 (75)
T ss_dssp SHSSSHHHHHHHHHHHHHTTSSSSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTBSEEGHHHHHHHHH
T ss_pred ccccCceEEeeeeehhhcccccccccccccchhhhhhhhhhhhhhhhHHHHHHhhcCCcEecHHHHHHHHh
Confidence 4568999999999998753 1699999999999999999999999999999999999999999999986
No 17
>PLN00160 histone H3; Provisional
Probab=99.00 E-value=9.4e-10 Score=83.93 Aligned_cols=71 Identities=15% Similarity=0.124 Sum_probs=65.3
Q ss_pred cccccCCchhHHHHHHHhhCC----CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHH
Q 036580 25 REQDRFLPIANVSRIMKKALP----ANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMT 95 (186)
Q Consensus 25 re~d~~LPkA~V~RImK~alP----~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~ 95 (186)
+.+++.||+.++.|++++... ++.|+..+|..+||+++|.|+..|...++..|.|+||.||+++|+..+..
T Consensus 16 kst~lLI~k~pF~RLVREI~~~~~~~~~Rfq~~Al~ALQeAsEayLv~lfed~~lca~HakRVTl~~kD~~L~~r 90 (97)
T PLN00160 16 KSTDLLIRRLPFARLVREIQMEMSREAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTIMPKDMQLARR 90 (97)
T ss_pred cchhhhhccccHHHHHHHHHHHcCCCCcEeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcccccchhhHHHHHH
Confidence 567889999999999999863 35899999999999999999999999999999999999999999987764
No 18
>PLN00161 histone H3; Provisional
Probab=98.98 E-value=1.6e-09 Score=86.95 Aligned_cols=71 Identities=15% Similarity=0.207 Sum_probs=65.4
Q ss_pred cccccCCchhHHHHHHHhhCC----CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHH
Q 036580 25 REQDRFLPIANVSRIMKKALP----ANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMT 95 (186)
Q Consensus 25 re~d~~LPkA~V~RImK~alP----~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~ 95 (186)
+..++.||+.++.|++++... .+.++..+|+++||+++|.|+..|...++.+|.|+||.||++.|+..+..
T Consensus 50 kst~lLIpklPF~RLVREI~~~~~~~~~Rfq~~Al~ALQEAsEayLV~lFeda~lcaiHAkRVTlm~kDm~La~r 124 (135)
T PLN00161 50 KSTELLIRKLPFARLVREISNEMLREPFRWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMPKDMQLARR 124 (135)
T ss_pred cccccccccccHHHHHHHHHHhcCCCCcEeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccchhhHHHHHH
Confidence 667889999999999999863 36899999999999999999999999999999999999999999987764
No 19
>PLN00121 histone H3; Provisional
Probab=98.97 E-value=9e-10 Score=88.53 Aligned_cols=71 Identities=14% Similarity=0.185 Sum_probs=65.6
Q ss_pred cccccCCchhHHHHHHHhhCCC---CcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHH
Q 036580 25 REQDRFLPIANVSRIMKKALPA---NAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMT 95 (186)
Q Consensus 25 re~d~~LPkA~V~RImK~alP~---~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~ 95 (186)
+.+++.||+..+.||+++...+ +.++..+|+++||+++|.|+..|...++.+|.|.+|.||++.|+..+..
T Consensus 57 kst~lLI~k~pF~RLVREI~~~~~~~~Rf~~~Al~ALQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~r 130 (136)
T PLN00121 57 KSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
T ss_pred cccccccccccHHHHHHHHHHHhCccceeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcceecchhhHHHHHH
Confidence 5678899999999999998753 6899999999999999999999999999999999999999999987763
No 20
>PTZ00018 histone H3; Provisional
Probab=98.95 E-value=1.4e-09 Score=87.35 Aligned_cols=71 Identities=14% Similarity=0.189 Sum_probs=65.3
Q ss_pred cccccCCchhHHHHHHHhhCC---CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHH
Q 036580 25 REQDRFLPIANVSRIMKKALP---ANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMT 95 (186)
Q Consensus 25 re~d~~LPkA~V~RImK~alP---~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~ 95 (186)
+.+++.||+..+.||+++... .+.++..+|+++||+++|.|+..|...++.+|.|++|.||++.|+..+..
T Consensus 57 kst~lLI~k~pF~RLVREI~~~~~~~~rf~~~al~aLQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~r 130 (136)
T PTZ00018 57 KSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
T ss_pred ccchhccccccHHHHHHHHHHHcCCcceeeHHHHHHHHHHHHHHHHHHhhhhHHHHHhhcceecchhhHHHHHH
Confidence 567889999999999999863 36899999999999999999999999999999999999999999987763
No 21
>KOG3467 consensus Histone H4 [Chromatin structure and dynamics]
Probab=98.88 E-value=8.5e-09 Score=77.97 Aligned_cols=69 Identities=20% Similarity=0.271 Sum_probs=65.3
Q ss_pred CCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHcCCc
Q 036580 30 FLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMTTLGFE 100 (186)
Q Consensus 30 ~LPkA~V~RImK~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~LgF~ 100 (186)
-|.+.+|+||.+... +.||+.-..+.+..++.+||..+...|..+++|++||||++.||+.+|+++|.-
T Consensus 29 gitKpaIRRlARr~G--VkRi~G~~yeE~~~~~k~fl~n~i~~A~~yt~HAKRKTvT~~dvv~~LKR~G~~ 97 (103)
T KOG3467|consen 29 GITKPAIRRLARRGG--VKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRT 97 (103)
T ss_pred ccchHHHHHHHHhcC--cchhchhhHHHHHHHHHHHHHHHHHHHHHHHhhhhhceeeHHHHHHHHHHcCce
Confidence 478999999999986 789999999999999999999999999999999999999999999999998764
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=98.74 E-value=3.5e-08 Score=77.21 Aligned_cols=69 Identities=17% Similarity=0.227 Sum_probs=63.2
Q ss_pred cccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 036580 27 QDRFLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMTT 96 (186)
Q Consensus 27 ~d~~LPkA~V~RImK~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~ 96 (186)
..+.||.++|.|+||+..- ..||+.+|...|..+.|.+...|...|...|.+.+|++|+++||..|+..
T Consensus 17 agL~fPV~ri~R~Lk~~~~-a~RVs~~A~VyLaAvLEYL~aEIlelA~n~ak~~k~krItp~hi~lAi~n 85 (115)
T cd00074 17 AGLQFPVGRIHRYLKKGRY-AERVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKKRITPRHLQLAVRN 85 (115)
T ss_pred cCccCcHHHHHHHHHcCcc-ccccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEcHHHHHHHHhc
Confidence 3577999999999998432 57999999999999999999999999999999999999999999999974
No 23
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=98.70 E-value=1.3e-07 Score=68.30 Aligned_cols=66 Identities=21% Similarity=0.261 Sum_probs=60.7
Q ss_pred hhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHcCCc
Q 036580 33 IANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMTTLGFE 100 (186)
Q Consensus 33 kA~V~RImK~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~LgF~ 100 (186)
+-.|.+|+|... -.+++.+|+++|.+.++.|+..|+..+..+|++.+|++++..||..||+++|+.
T Consensus 9 ~~~Vaqil~~~G--f~~~~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~~~Dv~~Al~~~gi~ 74 (77)
T smart00576 9 RIAVAQILESAG--FDSFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPNLGDVVLALENLGIS 74 (77)
T ss_pred HHHHHHHHHHcC--ccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCcc
Confidence 456788888875 569999999999999999999999999999999999999999999999999874
No 24
>cd07979 TAF9 TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. The TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Human TAF9 has a paralogue gene (TAF9L) whi
Probab=98.66 E-value=2.4e-07 Score=72.31 Aligned_cols=79 Identities=14% Similarity=0.173 Sum_probs=66.8
Q ss_pred hHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHcCCccchH-HHHHHHHH
Q 036580 34 ANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMTTLGFEEYVE-PLKVYLQR 112 (186)
Q Consensus 34 A~V~RImK~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~LgF~dyi~-~Lk~~L~~ 112 (186)
..|.+|+|+.. ..+++.+++..|.+.+..++..|..+|..+|+|++|+||+.+||..|++...-..|.. +-+++|-+
T Consensus 5 ~~v~~iLk~~G--v~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r~~~~f~~~p~~~~l~~ 82 (117)
T cd07979 5 RVIAAILKSMG--ITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRVDYSFTSPPPRDFLLE 82 (117)
T ss_pred HHHHHHHHHCC--CCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhccCCCCCCcHHHHHH
Confidence 36889999875 6799999999999999999999999999999999999999999999999765544544 45666654
Q ss_pred HH
Q 036580 113 FR 114 (186)
Q Consensus 113 ~r 114 (186)
.-
T Consensus 83 ~a 84 (117)
T cd07979 83 LA 84 (117)
T ss_pred HH
Confidence 44
No 25
>KOG1745 consensus Histones H3 and H4 [Chromatin structure and dynamics]
Probab=98.45 E-value=8.7e-08 Score=77.17 Aligned_cols=73 Identities=15% Similarity=0.201 Sum_probs=65.6
Q ss_pred CcccccCCchhHHHHHHHhhCC---CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 036580 24 PREQDRFLPIANVSRIMKKALP---ANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMTT 96 (186)
Q Consensus 24 ~re~d~~LPkA~V~RImK~alP---~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~ 96 (186)
.+.+|+.|++.++.|++|+..+ .+.++...|+.+||+++|.|+..|...+|-+|.|+||.||++.||..|..-
T Consensus 57 QkstdLlI~K~PFqRlvrei~q~f~~dLrfqs~Ai~ALQeA~EayLv~LfEdtnlcAihAkRVTimpkdiQlArri 132 (137)
T KOG1745|consen 57 QKSTDLLIRKLPFQRLVREIAQDFKTDLRFQSSAIAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRI 132 (137)
T ss_pred HhhhHHHhhcCcHHHHhHHHHhcccccceehHHHHHHHHHHHHHHHHHhccccchhhhccceeEecccceehhhhc
Confidence 3578889999999999995543 478999999999999999999999999999999999999999999988754
No 26
>PF15511 CENP-T: Centromere kinetochore component CENP-T; PDB: 3B0D_T 3B0C_T 3VH5_T 3VH6_T.
Probab=98.43 E-value=4.2e-07 Score=83.88 Aligned_cols=60 Identities=27% Similarity=0.351 Sum_probs=48.3
Q ss_pred CCchhHHHHHHHhhCC----CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHH
Q 036580 30 FLPIANVSRIMKKALP----ANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDD 89 (186)
Q Consensus 30 ~LPkA~V~RImK~alP----~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eD 89 (186)
.||.+.|+||+..... ...+|++||+.+|.+|.++|...|...--.||+|+|||||..+|
T Consensus 351 ~lP~~~vK~la~~~ak~s~~sK~kiskdal~aleqasdwfFeQl~dDL~aYA~HAgRKTIdesD 414 (414)
T PF15511_consen 351 SLPPGVVKKLAQHFAKSSGGSKMKISKDALEALEQASDWFFEQLGDDLEAYAKHAGRKTIDESD 414 (414)
T ss_dssp -S-HHHHHHHHHHHH-------S-B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHH
T ss_pred CCCccHHHHHHHHHHHhhcccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCCCC
Confidence 4999999999877753 46899999999999999999999999999999999999999887
No 27
>cd08050 TAF6 TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and are involved in forming Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs functions such as serving as
Probab=98.35 E-value=2e-06 Score=77.39 Aligned_cols=67 Identities=18% Similarity=0.197 Sum_probs=61.2
Q ss_pred chhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHcCCc
Q 036580 32 PIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMTTLGFE 100 (186)
Q Consensus 32 PkA~V~RImK~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~LgF~ 100 (186)
|..+|+-|++... ..++++||..+|.+.++.++..|+.+|.+.++|.|||||+.+||-.||+.++.+
T Consensus 1 ~~~~i~~ia~~~G--i~~~~~~a~~~La~~~e~~~~~i~~~A~k~~~hskR~~l~~~Di~~Al~~~n~e 67 (343)
T cd08050 1 PQESIKLIAESLG--IDSLSDEVAQLLAEDVEYRLREIIQEAAKFMRHSKRRKLTTSDVNHALRLRNVE 67 (343)
T ss_pred ChhHHHHHHHHcC--CCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHHhCCC
Confidence 5678888888885 569999999999999999999999999999999999999999999999976554
No 28
>KOG1659 consensus Class 2 transcription repressor NC2, alpha subunit (DRAP1) [Transcription]
Probab=98.29 E-value=1.4e-06 Score=74.71 Aligned_cols=81 Identities=12% Similarity=0.178 Sum_probs=71.5
Q ss_pred cCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHcCCccchHHHHH
Q 036580 29 RFLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMTTLGFEEYVEPLKV 108 (186)
Q Consensus 29 ~~LPkA~V~RImK~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~LgF~dyi~~Lk~ 108 (186)
..||.++|+|||...- |.-+|+.-....+.++.|.|+..|...+.++++..+-|||+++|+..+++.-.-+||+..+-.
T Consensus 12 trfp~aRiKKIMQ~dE-dIGKvaqavPViisralElFl~~l~~~t~~~t~~~~aKt~s~~hlkq~v~~~~~FdFLk~~v~ 90 (224)
T KOG1659|consen 12 TRFPPARIKKIMQSDE-DIGKVAQAVPVIISRALELFLESLLQKTLEITRSRGAKTVSSSHLKQAVESDPKFDFLKEVVE 90 (224)
T ss_pred ccCCHHHHHHHHhhhh-hhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhcCccccCHHHHHHHHhccchhHHHHHHHH
Confidence 3699999999998874 567999999999999999999999999999999999999999999999998777777666444
Q ss_pred HH
Q 036580 109 YL 110 (186)
Q Consensus 109 ~L 110 (186)
.+
T Consensus 91 ~v 92 (224)
T KOG1659|consen 91 KV 92 (224)
T ss_pred hc
Confidence 33
No 29
>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=98.18 E-value=1.1e-05 Score=57.89 Aligned_cols=63 Identities=21% Similarity=0.306 Sum_probs=52.3
Q ss_pred hhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 036580 33 IANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMTT 96 (186)
Q Consensus 33 kA~V~RImK~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~ 96 (186)
+..+..++++.-| ...+.+|+.++|.+.+..||..++..|...|+|.+-.||...||...|++
T Consensus 2 K~~l~~Lv~~iDp-~~~ld~~vee~Ll~laddFv~~v~~~ac~lAKhR~s~tle~~Dv~~~Ler 64 (68)
T PF03847_consen 2 KRKLQELVKQIDP-NEKLDPDVEELLLELADDFVDDVVSFACRLAKHRKSSTLEVKDVQLHLER 64 (68)
T ss_dssp HHHHHHHHHCC-S-S----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHHH
T ss_pred hHHHHHHHHHcCC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCHHHHHHHHHh
Confidence 4578889999976 78999999999999999999999999999999999999999999999985
No 30
>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=98.07 E-value=3e-05 Score=55.42 Aligned_cols=64 Identities=20% Similarity=0.202 Sum_probs=51.6
Q ss_pred CCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHH
Q 036580 30 FLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMT 95 (186)
Q Consensus 30 ~LPkA~V~RImK~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~ 95 (186)
.+|..+|+-+..... ...++.|+...|.+-++.-|..|..+|.+++.|.+|++++.+||-.||+
T Consensus 3 ~~~~esvk~iAes~G--i~~l~de~a~~La~dveyrlreiiq~a~kfm~hskR~~Lt~~Di~~ALr 66 (66)
T PF02969_consen 3 VFSQESVKDIAESLG--ISNLSDEAAKALAEDVEYRLREIIQEALKFMRHSKRTKLTTDDINSALR 66 (66)
T ss_dssp ---HHHHHHHHHHTT-----B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH-
T ss_pred cCCHHHHHHHHHHcC--CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhC
Confidence 478889988888775 5689999999999999999999999999999999999999999999985
No 31
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=98.07 E-value=1.6e-05 Score=58.20 Aligned_cols=62 Identities=18% Similarity=0.211 Sum_probs=52.3
Q ss_pred HHHHHHHhhC-CCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 036580 35 NVSRIMKKAL-PANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMTT 96 (186)
Q Consensus 35 ~V~RImK~al-P~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~ 96 (186)
+|.+|+.+.. +.+..+|+.+..+|.+.+-.++..++.+--..|+|+||+||+.+||+...++
T Consensus 10 ~v~ki~ee~~~~~~~~~s~~~i~al~ELv~~q~~~~a~DLe~FAkHA~R~tI~~dDV~Ll~Rr 72 (76)
T PF15630_consen 10 TVGKIVEEEAKEKGVEVSPQFIAALTELVYKQLENLAKDLEAFAKHAGRSTINMDDVKLLARR 72 (76)
T ss_dssp HHHHHHHHCCCCTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHTTT
T ss_pred HHHHHHHHHHhccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHHHhhc
Confidence 5778888875 4577899999999999999999999999999999999999999999877643
No 32
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=98.05 E-value=1.1e-05 Score=64.06 Aligned_cols=69 Identities=19% Similarity=0.264 Sum_probs=62.9
Q ss_pred cccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 036580 27 QDRFLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMTT 96 (186)
Q Consensus 27 ~d~~LPkA~V~RImK~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~ 96 (186)
.-+.+|..+|+||||.. .-.+||+++|...+..|++..+..|+..|-..|...++|.|++.|+..|+..
T Consensus 23 agl~fpvgrvkr~lk~~-~~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~kkkri~PrHlqlAIrn 91 (132)
T COG5262 23 AGLIFPVGRVKRLLKKG-NYRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRIIPRHLQLAIRN 91 (132)
T ss_pred cCccccHHHHHHHHHcC-ccceeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhcCcceechHHHHHHhcC
Confidence 45679999999999954 3478999999999999999999999999999999999999999999999874
No 33
>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=98.00 E-value=6.5e-05 Score=53.77 Aligned_cols=65 Identities=20% Similarity=0.252 Sum_probs=57.7
Q ss_pred hHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHcCCc
Q 036580 34 ANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMTTLGFE 100 (186)
Q Consensus 34 A~V~RImK~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~LgF~ 100 (186)
-.|.+|++... =..++..|++.|.+.+..||..|+..+..+|++.+|...+..||..||+++|+.
T Consensus 10 ~~va~il~~~G--F~~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~~~gi~ 74 (77)
T PF07524_consen 10 RSVAQILKHAG--FDSASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPNLQDVEQALEEMGIS 74 (77)
T ss_pred HHHHHHHHHcC--ccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCC
Confidence 35666666654 347999999999999999999999999999999999999999999999999983
No 34
>COG5247 BUR6 Class 2 transcription repressor NC2, alpha subunit (DRAP1 homolog) [Transcription]
Probab=97.95 E-value=2.4e-05 Score=60.71 Aligned_cols=77 Identities=14% Similarity=0.256 Sum_probs=67.2
Q ss_pred CCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHcCCccchHHHH
Q 036580 30 FLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMTTLGFEEYVEPLK 107 (186)
Q Consensus 30 ~LPkA~V~RImK~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~LgF~dyi~~Lk 107 (186)
.+|+|+|+|||...- |.-+|+.-......++.|.|+..|..++.+.|+..+-|.|+.+++..|.+.-+=.||+....
T Consensus 23 rFP~ar~KkIMQ~de-DiGKV~q~tPVIaskalE~Fl~~iv~~s~k~aR~~~skR~t~e~lk~a~~sdekFdFL~~~~ 99 (113)
T COG5247 23 RFPIARLKKIMQLDE-DIGKVGQSTPVIASKALEMFLTEIVGLSLKEARKKSSKRMTSEFLKRATESDEKFDFLKNME 99 (113)
T ss_pred cCCHHHHHHHHHhhh-hhhhhhhcchHHHHHHHHHHHHHHHHHHHHHHHhccchhhHHHHHHHHHhhhHHHHHHHHHH
Confidence 699999999998874 56799999999999999999999999999999999999999999999998755555554443
No 35
>cd08048 TAF11 TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypothes
Probab=97.95 E-value=5.7e-05 Score=56.29 Aligned_cols=66 Identities=18% Similarity=0.216 Sum_probs=61.1
Q ss_pred CCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC---CccCHHHHHHHHHHc
Q 036580 30 FLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASDKCQREKR---KTINGDDLLWAMTTL 97 (186)
Q Consensus 30 ~LPkA~V~RImK~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kR---KTIt~eDVl~AL~~L 97 (186)
.||++.|+|||...+ +..++.+...+|.-.+.+||-.|..+|.++..+.+. .-|.++||..|.+.|
T Consensus 16 ~f~k~~iKr~~~~~~--~~~v~~~v~i~v~glaKvFVGeivE~A~~V~~~~~~~~~~Pl~P~HireA~rrl 84 (85)
T cd08048 16 SFPKAAIKRLIQSVT--GQSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGEANTGPLQPRHLREAYRRL 84 (85)
T ss_pred hccHHHHHHHHHHHc--CCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCCCCCcHHHHHHHHHh
Confidence 499999999999998 479999999999999999999999999999887665 789999999999876
No 36
>smart00414 H2A Histone 2A.
Probab=97.83 E-value=5.8e-05 Score=58.36 Aligned_cols=68 Identities=15% Similarity=0.250 Sum_probs=62.2
Q ss_pred ccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 036580 28 DRFLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMTT 96 (186)
Q Consensus 28 d~~LPkA~V~RImK~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~ 96 (186)
.+.||.++|.|+||+.-- ..||+..|...|..+.|.+..+|...|...|...+++.|+++||..|+..
T Consensus 7 gL~fPVgRi~r~Lk~~~~-~~Rv~~~A~VyLaAvLEYLtaEILeLagn~a~~~k~~rItp~hi~lAi~n 74 (106)
T smart00414 7 GLQFPVGRIHRLLRKGTY-AKRVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKRRITPRHLQLAIRN 74 (106)
T ss_pred CccCchHHHHHHHHcCcc-ccccccccHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchHHHhhhccC
Confidence 467999999999999742 46999999999999999999999999999999999999999999999864
No 37
>smart00427 H2B Histone H2B.
Probab=97.80 E-value=0.00015 Score=54.83 Aligned_cols=61 Identities=20% Similarity=0.331 Sum_probs=57.2
Q ss_pred HHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 036580 35 NVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMTT 96 (186)
Q Consensus 35 ~V~RImK~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~ 96 (186)
-|.|++|+.-|+ ..||..|...++-.+..+...|+.+|...|.-.+|+||+..+|..|++-
T Consensus 6 Yi~kvLKqVhpd-~giS~kam~imnSfvnDiferIa~EAs~L~~~nkr~TltsreIqtAvrl 66 (89)
T smart00427 6 YIYKVLKQVHPD-TGISSKAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRL 66 (89)
T ss_pred HHHHHHHHhCCC-ccccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHH
Confidence 489999999984 6899999999999999999999999999999999999999999999865
No 38
>PLN00154 histone H2A; Provisional
Probab=97.75 E-value=8.7e-05 Score=59.93 Aligned_cols=70 Identities=17% Similarity=0.203 Sum_probs=63.5
Q ss_pred cccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 036580 27 QDRFLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMTT 96 (186)
Q Consensus 27 ~d~~LPkA~V~RImK~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~ 96 (186)
-.+.||.++|.|++|+...-..||+..|...|.-+.|.+...|...|-..|...+++-|++.||..|+..
T Consensus 35 AgL~FPVgRi~r~Lk~g~~~~~RVga~ApVYLAAVLEYLtAEVLELAGNaA~d~kk~RItPrHi~lAIrn 104 (136)
T PLN00154 35 AGLQFPVGRIHRQLKQRVSAHGRVGATAAVYTAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRG 104 (136)
T ss_pred cCccCchHHHHHHHHhhhhhccccccchHHHHHHHHHHHHHHHHHHHHHHHHhhCCceecHHHhhhhccC
Confidence 3678999999999999753356999999999999999999999999999999999999999999999864
No 39
>PF09415 CENP-X: CENP-S associating Centromere protein X; InterPro: IPR018552 Centromere protein X (CENP-X) is a component of the CENP-S complex. The CENP-S complex is composed of at least of CENP-S and CENP-X and is essential for the stable assembly of the outer kinetchore []. CENP-X is also a DNA-binding component of the Fanconi anemia (FA) core complex involved in DNA damage repair and genome maintenance. The FA complex is composed of CENPS, FANCA, FANCB, FANCC, FANCE, FANCF, FANCG, FANCL/PHF9, FANCM, FAAP24 and CENPX. Interacts with CENPS, FANCM and FAAP24 [, ].; PDB: 4DRB_L 4DRA_H 3V9R_D.
Probab=97.66 E-value=8.1e-05 Score=53.93 Aligned_cols=64 Identities=20% Similarity=0.315 Sum_probs=53.6
Q ss_pred chhHHHHHHHhhCC-CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCc-cCHHHHHHHHH
Q 036580 32 PIANVSRIMKKALP-ANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKT-INGDDLLWAMT 95 (186)
Q Consensus 32 PkA~V~RImK~alP-~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKT-It~eDVl~AL~ 95 (186)
|..+|.||++.... +..+|++||..++.+....||..-...|...++.++..+ |..+|+.+.+-
T Consensus 1 p~~li~rll~~~f~~~~tkIs~dal~l~~eyl~iFV~EAv~Ra~~~a~~e~~~~~le~e~LEki~p 66 (72)
T PF09415_consen 1 PPELIARLLHEHFKDDKTKISKDALKLSAEYLRIFVREAVARAAEQAEAEGDEGFLEVEHLEKILP 66 (72)
T ss_dssp -CHHHHHHHCTTSSSTT-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSEE-HHHHHHHCH
T ss_pred ChHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHH
Confidence 88999999997763 578999999999999999999999999999999999888 99999987654
No 40
>PTZ00017 histone H2A; Provisional
Probab=97.66 E-value=0.00011 Score=59.12 Aligned_cols=69 Identities=17% Similarity=0.225 Sum_probs=62.8
Q ss_pred cccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 036580 27 QDRFLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMTT 96 (186)
Q Consensus 27 ~d~~LPkA~V~RImK~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~ 96 (186)
-.+.||..+|.|+||+.-- ..||+..|...|.-+.|.+...|...|...|...+++-|+++||..|+..
T Consensus 24 agL~FPVgRi~R~Lk~g~~-a~RV~a~A~VYLAAVLEYLtaEILELAgNaa~d~kk~RItPrHi~lAI~n 92 (134)
T PTZ00017 24 AGLQFPVGRVHRYLKKGRY-AKRVGAGAPVYLAAVLEYLTAEVLELAGNAAKDNKKKRITPRHIQLAIRN 92 (134)
T ss_pred CCcccchHHHHHHHhccch-hccccccchhhhHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHhhccC
Confidence 3678999999999998642 46999999999999999999999999999999999999999999999963
No 41
>PF04719 TAFII28: hTAFII28-like protein conserved region; InterPro: IPR006809 The general transcription factor, TFIID, consists of the TATA-binding protein (TBP) associated with a series of TBP-associated factors (TAFs) that together participate in the assembly of the transcription preinitiation complex. The conserved region is found at the C terminus of most member proteins. The crystal structure of hTAFII28 with hTAFII18 shows that this region is involved in the binding of these two subunits. The conserved region contains four alpha helices and three loops arranged as in histone H3 [, ].; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005634 nucleus; PDB: 1BH9_B 1BH8_B.
Probab=97.58 E-value=0.00042 Score=52.31 Aligned_cols=67 Identities=19% Similarity=0.224 Sum_probs=52.4
Q ss_pred CCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC-CccCHHHHHHHHHHc
Q 036580 30 FLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASDKCQREKR-KTINGDDLLWAMTTL 97 (186)
Q Consensus 30 ~LPkA~V~RImK~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kR-KTIt~eDVl~AL~~L 97 (186)
.||++.|+|||...+. +..|+.-...+|.-.+.+||-.|..+|.+++.+.+. .-|.+.|+-.|.++|
T Consensus 23 ~~~k~~ikkli~~~~~-~qsv~~~v~i~v~g~aKvFVGEiVE~A~~Vq~~~~~~~pl~P~hlreA~rrL 90 (90)
T PF04719_consen 23 SFNKAAIKKLINQVLG-NQSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGETGPLQPDHLREAYRRL 90 (90)
T ss_dssp ---HHHHHHHHHHHHS--S---HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SS--HHHHHHHHHHH
T ss_pred cCCHHHHHHHHHHHcC-CCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcHHHHHHHHhC
Confidence 4999999999999983 479999999999999999999999999999886554 489999999998875
No 42
>PLN00158 histone H2B; Provisional
Probab=97.57 E-value=0.00046 Score=54.44 Aligned_cols=64 Identities=16% Similarity=0.273 Sum_probs=58.8
Q ss_pred chhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 036580 32 PIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMTT 96 (186)
Q Consensus 32 PkA~V~RImK~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~ 96 (186)
-..-|.|++|+.-| +..||..|...++-.+..+...|+.+|...|.-.+|+||+..+|..|++-
T Consensus 29 y~~YI~kVLKQVhP-d~gIS~kaM~ImnSfvnDiferIA~EAs~La~~nkr~TltsrEIqtAvrL 92 (116)
T PLN00158 29 YKIYIYKVLKQVHP-DTGISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVRL 92 (116)
T ss_pred HHHHHHHHHHHhCC-CCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHH
Confidence 34569999999998 57899999999999999999999999999999999999999999999864
No 43
>KOG1658 consensus DNA polymerase epsilon, subunit C [Replication, recombination and repair]
Probab=97.55 E-value=3.3e-05 Score=63.65 Aligned_cols=67 Identities=24% Similarity=0.306 Sum_probs=59.8
Q ss_pred cCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 036580 29 RFLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMTT 96 (186)
Q Consensus 29 ~~LPkA~V~RImK~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~ 96 (186)
..||+++|+.+||.. |+......|++.++.++++.||..|...++..++..+|||+...|+-.|++.
T Consensus 58 ~rLpL~rik~vvkl~-pdl~l~~dea~~l~a~aaelfi~~Ln~~~~~~~q~~k~kt~qr~d~D~ai~~ 124 (162)
T KOG1658|consen 58 SRLPLARIKQVVKLD-PDLTLLNDEASQLIAKAAELFIQELNDVAYTTAQLRKRKTEQRRDYDTAIEA 124 (162)
T ss_pred hhccHHHHHhhccCC-cchhhhhhHHHHHHHHHHHHHHHHHHhccchhHHHHHhhhhhhhcccccccc
Confidence 569999999999986 4555577889999999999999999999999999999999999998887764
No 44
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=97.55 E-value=0.00022 Score=62.86 Aligned_cols=70 Identities=13% Similarity=0.269 Sum_probs=64.2
Q ss_pred ccccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 036580 26 EQDRFLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMTT 96 (186)
Q Consensus 26 e~d~~LPkA~V~RImK~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~ 96 (186)
..+..|-+..|..+++..-+ +..|-+|+.++|.+.|..||..|+..|...|+|.|..||...||...|++
T Consensus 150 ~~~~il~k~kl~dLvqqId~-~~~LD~dVedlLleiADdFV~sii~~sC~LAKHRKsdtlEvrDIqLhLEr 219 (258)
T KOG1142|consen 150 GNNPILSKRKLDDLVQQIDG-TTKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHRKSDTVEVRDIQLHLER 219 (258)
T ss_pred CCCccccccchhHHHHhhcC-cccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccchhheeeeeec
Confidence 34556888999999999964 78999999999999999999999999999999999999999999999995
No 45
>PTZ00463 histone H2B; Provisional
Probab=97.52 E-value=0.00057 Score=53.97 Aligned_cols=61 Identities=18% Similarity=0.370 Sum_probs=56.9
Q ss_pred HHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 036580 35 NVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMTT 96 (186)
Q Consensus 35 ~V~RImK~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~ 96 (186)
-|.|++|+.-| +..||..|...++-.+....+.|+.+|...|.-.+|.||+..+|..|++-
T Consensus 33 YI~KVLKqVhP-d~gIS~kaM~ImnSfvnDifErIA~EAs~La~~nkr~TltsrEIQtAvrL 93 (117)
T PTZ00463 33 YIFKVLKQVHP-DTGISRKSMNIMNSFLVDTFEKIATEASRLCKYTRRDTLSSREIQTAIRL 93 (117)
T ss_pred HHHHHHHhhCC-CCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHhh
Confidence 49999999998 57899999999999999999999999999999999999999999999864
No 46
>PLN00156 histone H2AX; Provisional
Probab=97.48 E-value=0.0003 Score=56.99 Aligned_cols=69 Identities=13% Similarity=0.195 Sum_probs=62.6
Q ss_pred cccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 036580 27 QDRFLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMTT 96 (186)
Q Consensus 27 ~d~~LPkA~V~RImK~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~ 96 (186)
-.+.||..+|.|++|+.-- ..||+..|...|.-+.|..+..|...|...|...+++-|+++||..|+..
T Consensus 26 AgL~FPVgRi~R~Lk~g~y-a~RVga~ApVYLAAVLEYLtaEVLELAgNaa~d~kk~RItPrHi~lAIrn 94 (139)
T PLN00156 26 AGLQFPVGRIARFLKAGKY-AERVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRN 94 (139)
T ss_pred cCcccchHHHHHHHhcCCh-hhccCCccHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHhhccC
Confidence 3678999999999999643 46999999999999999999999999999999999999999999999863
No 47
>PLN00157 histone H2A; Provisional
Probab=97.48 E-value=0.00025 Score=57.02 Aligned_cols=69 Identities=13% Similarity=0.185 Sum_probs=62.8
Q ss_pred cccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 036580 27 QDRFLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMTT 96 (186)
Q Consensus 27 ~d~~LPkA~V~RImK~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~ 96 (186)
-.+.||..+|.|++|+.-- ..||+..|...|.-+.|.++..|...|...|...+++-|+++||..|+..
T Consensus 23 agL~FPVgRi~R~Lk~g~~-a~RIg~~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~n 91 (132)
T PLN00157 23 AGLQFPVGRIARYLKAGKY-ATRVGAGAPVYLAAVLEYLAAEVLELAGNAARDNKKSRIVPRHIQLAVRN 91 (132)
T ss_pred cCcccchHHHHHHHhcCch-hhhcCCCcHhHHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHhhcccC
Confidence 3678999999999999642 46999999999999999999999999999999999999999999999864
No 48
>PLN00153 histone H2A; Provisional
Probab=97.47 E-value=0.00028 Score=56.55 Aligned_cols=69 Identities=16% Similarity=0.212 Sum_probs=63.0
Q ss_pred cccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 036580 27 QDRFLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMTT 96 (186)
Q Consensus 27 ~d~~LPkA~V~RImK~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~ 96 (186)
-.+.||..+|.|++|+.-- ..||+..|...|.-+.|.++..|...|...|...+++-|+++||..|+..
T Consensus 21 agL~FpVgRi~R~Lr~g~~-a~Rvga~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~n 89 (129)
T PLN00153 21 AGLQFPVGRIARYLKKGKY-AERIGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKNRIVPRHIQLAIRN 89 (129)
T ss_pred cCcccchHHHHHHHhcCch-hhccCCCchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHhhccC
Confidence 4678999999999998653 46999999999999999999999999999999999999999999999863
No 49
>KOG1756 consensus Histone 2A [Chromatin structure and dynamics]
Probab=97.44 E-value=0.00041 Score=55.58 Aligned_cols=69 Identities=13% Similarity=0.239 Sum_probs=61.7
Q ss_pred cccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 036580 27 QDRFLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMTT 96 (186)
Q Consensus 27 ~d~~LPkA~V~RImK~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~ 96 (186)
..+.+|..+|.|++|+. .-..||+.+|...+.-|.+.....|+..|-..+..+++.-|+++||..|+..
T Consensus 24 agl~fPvgri~r~Lr~~-~~~~ri~~gapV~laavLeYL~Aeile~agnaardnkk~ri~PrH~~lAI~N 92 (131)
T KOG1756|consen 24 AGLQFPVGRIHRLLRKG-RYAQRVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRITPRHLQLAIRN 92 (131)
T ss_pred cccccCHHHHHHHHHcc-chhhhccCCChHHHHHHHHHHHHHHHHHhHHHhhhcCccccChHHHHHHHhC
Confidence 45679999999999993 2357999999999999999999999999999999999999999999999974
No 50
>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=97.21 E-value=0.00042 Score=52.10 Aligned_cols=60 Identities=23% Similarity=0.295 Sum_probs=30.4
Q ss_pred HHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 036580 36 VSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMTT 96 (186)
Q Consensus 36 V~RImK~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~ 96 (186)
|..+|-.-. |...-..|+..+|-+.+.+||..|+.+|...|...++++|+.+|++.+|+.
T Consensus 7 I~~mMy~fG-D~~~P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~rg~~~i~~eDl~F~lR~ 66 (93)
T PF02269_consen 7 IRQMMYGFG-DVEEPLPETVDLVEDIVREYIIELCQEAMEVAQRRGSKKIKVEDLLFLLRK 66 (93)
T ss_dssp CHHHHHCTT-S-SS--HHHHHHHHHHHHHHHHHHHHHHHC---------------------
T ss_pred HHHHHHHcC-CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCcCcHHHHHHHHhc
Confidence 445565554 566788999999999999999999999999999999999999999999985
No 51
>PF15510 CENP-W: Centromere kinetochore component W
Probab=97.15 E-value=0.001 Score=50.96 Aligned_cols=67 Identities=21% Similarity=0.256 Sum_probs=56.2
Q ss_pred cCCchhHHHHHHHhhCCCCcccCHHHHHH--------------HHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHH
Q 036580 29 RFLPIANVSRIMKKALPANAKISKDAKET--------------VQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAM 94 (186)
Q Consensus 29 ~~LPkA~V~RImK~alP~~~rISkDA~~a--------------i~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL 94 (186)
..-|+..++|++|+.-| ..|+...+-.+ +.--|-.||+.|+.+|...|=+++-.||..+||+.|.
T Consensus 15 rkaPrgfLkrv~Kr~Kp-hlRl~~~~Dllv~~~~f~~~~~~~~vhLncLLFvhrLAEEaRtnA~EnK~~~Ik~~Hv~Aaa 93 (102)
T PF15510_consen 15 RKAPRGFLKRVFKRQKP-HLRLETSGDLLVRFCPFSGWQWGGEVHLNCLLFVHRLAEEARTNACENKCGTIKKEHVLAAA 93 (102)
T ss_pred HhCchHHHHHHHHhcCC-ceeecccccHHHhhcccccccccceeehhHHHHHHHHHHHHHHHHHHHhhccccHHHHHHHH
Confidence 35799999999998877 56766555444 5667889999999999999999999999999999887
Q ss_pred HH
Q 036580 95 TT 96 (186)
Q Consensus 95 ~~ 96 (186)
+.
T Consensus 94 Kv 95 (102)
T PF15510_consen 94 KV 95 (102)
T ss_pred HH
Confidence 64
No 52
>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=97.06 E-value=0.012 Score=44.44 Aligned_cols=61 Identities=15% Similarity=0.262 Sum_probs=51.2
Q ss_pred hHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 036580 34 ANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMTT 96 (186)
Q Consensus 34 A~V~RImK~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~ 96 (186)
.-|+.+|--.. ++..-..|...+|-+.+.+||..|+.+|...|. .+|.-|+.+|++.+|+.
T Consensus 6 ~ei~~mmy~~G-D~~~P~~eTv~llE~iv~~~i~~l~~~a~~~A~-~r~~k~~~eD~~FliR~ 66 (92)
T cd07978 6 KEIRQMMYGFG-DVQNPLPETVDLLEDIVVEYIIELCHKAAEVAQ-RRRGKVKVEDLIFLLRK 66 (92)
T ss_pred HHHHHHHHHcC-CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-cCCCCCCHHHHHHHHhc
Confidence 34677777765 456778999999999999999999999999998 45555699999999975
No 53
>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=97.03 E-value=0.0034 Score=50.16 Aligned_cols=84 Identities=20% Similarity=0.209 Sum_probs=49.0
Q ss_pred CCch--hHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHH-HcCCccchHHH
Q 036580 30 FLPI--ANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMT-TLGFEEYVEPL 106 (186)
Q Consensus 30 ~LPk--A~V~RImK~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~-~LgF~dyi~~L 106 (186)
.+|+ -.|.-|+|+.. .......+...|.+.+-.|+..|..+|..++.|++|++|+.+||..|++ ++++.-...+-
T Consensus 10 ~~PrDa~~i~~iL~~~G--v~~yeprVv~qLLEfayRYt~~vL~DA~~ya~hA~~~~i~~~DVrLAi~~r~~~~f~~ppp 87 (129)
T PF02291_consen 10 SLPRDARVIHLILKSMG--VTEYEPRVVNQLLEFAYRYTSDVLEDAQVYADHAGRSTIDADDVRLAIQSRLDHSFTQPPP 87 (129)
T ss_dssp ---HHHHHHHHHHHHTT-----B-THHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHHHHT----------
T ss_pred cCChHHHHHHHHHHHcC--CcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHhhhccCCCC
Confidence 4665 24556666664 5567888899999999999999999999999999999999999999999 56776666666
Q ss_pred HHHHHHHHH
Q 036580 107 KVYLQRFRE 115 (186)
Q Consensus 107 k~~L~~~re 115 (186)
+++|.+.-+
T Consensus 88 re~llelA~ 96 (129)
T PF02291_consen 88 REFLLELAR 96 (129)
T ss_dssp ---------
T ss_pred hHHHHHHHH
Confidence 776655443
No 54
>PTZ00252 histone H2A; Provisional
Probab=97.00 E-value=0.0023 Score=51.63 Aligned_cols=69 Identities=9% Similarity=0.169 Sum_probs=60.3
Q ss_pred cccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHh--cCCCccCHHHHHHHHHH
Q 036580 27 QDRFLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASDKCQR--EKRKTINGDDLLWAMTT 96 (186)
Q Consensus 27 ~d~~LPkA~V~RImK~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~--~kRKTIt~eDVl~AL~~ 96 (186)
-.+.||..+|.|++|+.-- ..||+.-|...|.-+.|.....|...|...|.+ .+++-|+++||..|+..
T Consensus 22 AGL~FPVgRi~R~Lr~g~y-a~RIga~ApVYLAAVLEYLtaEVLELAgnaa~d~~~kk~RItPrHi~lAIrN 92 (134)
T PTZ00252 22 AGLIFPVGRVGSLLRRGQY-ARRIGASGAVYMAAVLEYLTAELLELSVKAAAQQAKKPKRLTPRTVTLAVRH 92 (134)
T ss_pred cCccCchHHHHHHHHcCCc-ccccCCccHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccccHHHHHhhccC
Confidence 4578999999999998753 469999999999999999999999989888865 67889999999999863
No 55
>KOG1744 consensus Histone H2B [Chromatin structure and dynamics]
Probab=96.72 E-value=0.0073 Score=48.38 Aligned_cols=61 Identities=23% Similarity=0.322 Sum_probs=56.1
Q ss_pred HHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 036580 35 NVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMTT 96 (186)
Q Consensus 35 ~V~RImK~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~ 96 (186)
-|.|++|+.-|+ .-|+.++...++-.+..|+..|+.+|...+.-.+|.||+-.+|..|++-
T Consensus 42 yv~kvlk~Vhpd-~gis~~a~~vmnsf~ndife~iA~ea~rla~y~krstisSreiqta~rL 102 (127)
T KOG1744|consen 42 YVYKVLKQVHPD-LGISSKAMGVMNSFVNDIFERIASEAGRLAHYNKRSTISSREIQTAVRL 102 (127)
T ss_pred ehhhhhhcccCC-CCcCHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCcccHHHHHHHHHH
Confidence 367799999987 6799999999999999999999999999999999999999999998854
No 56
>KOG3219 consensus Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=96.63 E-value=0.003 Score=53.80 Aligned_cols=69 Identities=16% Similarity=0.192 Sum_probs=61.1
Q ss_pred CCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC-CccCHHHHHHHHHHcCCc
Q 036580 30 FLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASDKCQREKR-KTINGDDLLWAMTTLGFE 100 (186)
Q Consensus 30 ~LPkA~V~RImK~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kR-KTIt~eDVl~AL~~LgF~ 100 (186)
.||+++|+|||..... ..|+.-+..+++-.+.+||-.|..+|.++|...+. --|.+.||-.|..+|...
T Consensus 112 ~f~Ka~iKkL~~~itg--~~v~~nv~Ia~~GiaKvFVGEvVEeAl~V~~~~~e~~PLqP~HIREA~rrL~~q 181 (195)
T KOG3219|consen 112 AFPKAQIKKLMSSITG--QSVSENVAIAMAGIAKVFVGEVVEEALDVREEWGESGPLQPKHIREAYRRLKLQ 181 (195)
T ss_pred cCCHHHHHHHHHHHhC--CccCcceeeeecchhhHhHHHHHHHHHHHHHHhccCCCCCcHHHHHHHHHHHhc
Confidence 5999999999999984 34999999999999999999999999999997665 479999999999887554
No 57
>KOG3423 consensus Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=95.50 E-value=0.088 Score=44.22 Aligned_cols=69 Identities=22% Similarity=0.241 Sum_probs=57.5
Q ss_pred CCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC--------------CCccCHHHHHHHHH
Q 036580 30 FLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASDKCQREK--------------RKTINGDDLLWAMT 95 (186)
Q Consensus 30 ~LPkA~V~RImK~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~k--------------RKTIt~eDVl~AL~ 95 (186)
.||-+.+.-+++.+. ....-.-.+-+|.=++-.||+.|+..|.++|+-.. |-|++-+|+..||+
T Consensus 86 ~IPDavt~~yL~~aG--f~~~D~rv~RLvsLaAQKfvSDIa~DA~Q~~k~r~~~~~~~~k~~~kdkK~tLtmeDL~~AL~ 163 (176)
T KOG3423|consen 86 TIPDAVTDHYLKKAG--FQTSDPRVKRLVSLAAQKFVSDIANDALQHSKIRTKTAIGKDKKQAKDKKYTLTMEDLSPALA 163 (176)
T ss_pred CCcHHHHHHHHHhcC--CCcCcHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccccccccccccceeeeHHHHHHHHH
Confidence 599999999999886 33445566788999999999999999999998433 45899999999999
Q ss_pred HcCCc
Q 036580 96 TLGFE 100 (186)
Q Consensus 96 ~LgF~ 100 (186)
+.|+.
T Consensus 164 EyGin 168 (176)
T KOG3423|consen 164 EYGIN 168 (176)
T ss_pred HhCcc
Confidence 98874
No 58
>KOG2549 consensus Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=95.49 E-value=0.065 Score=51.95 Aligned_cols=66 Identities=20% Similarity=0.211 Sum_probs=58.7
Q ss_pred CchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHcC
Q 036580 31 LPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMTTLG 98 (186)
Q Consensus 31 LPkA~V~RImK~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~Lg 98 (186)
-|.-.++-+++... ...|+.|+..+|.+-++.=|..|+.+|.++..|.||.+++.+||..||+.+.
T Consensus 12 s~~Es~k~vAEslG--i~nl~deaa~~La~dv~yrikEI~Q~aaKfm~hskR~kLtv~DV~~ALr~~n 77 (576)
T KOG2549|consen 12 SPKESVKVVAESLG--ITNLNDEAALLLAEDVEYRIKEIVQDAAKFMVHSKRTKLTVDDVDYALRSLN 77 (576)
T ss_pred CcHHHHHHHHHHhC--ccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcCcHHHHHHHHhhcc
Confidence 34777777777765 6679999999999999999999999999999999999999999999999653
No 59
>KOG4336 consensus TBP-associated transcription factor Prodos [Transcription]
Probab=95.32 E-value=0.12 Score=47.01 Aligned_cols=77 Identities=22% Similarity=0.293 Sum_probs=66.0
Q ss_pred HHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHcCCccchHHHHHHHHHHHH
Q 036580 36 VSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMTTLGFEEYVEPLKVYLQRFRE 115 (186)
Q Consensus 36 V~RImK~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~LgF~dyi~~Lk~~L~~~re 115 (186)
|.-|.+..+ ---|++-|++.|.+.+..+|..|...+.-+|++++|-..+..||...|-++||. +..|..+++++..
T Consensus 11 V~~Ll~~~g--fd~is~~aletlvell~~yi~eigrq~~n~celagRT~pT~~Dv~l~Li~mnI~--v~sL~~~~q~~~~ 86 (323)
T KOG4336|consen 11 VSNLLKTKG--FDSISNAALETLVELLQSYIREIGRQLHNYCELAGRTIPTQGDVKLTLIEMNIK--VSSLYAYFQKQEF 86 (323)
T ss_pred HHHHHHHhC--chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcHHHHHHHHHHhCCC--hhhhHHHHHhccc
Confidence 444445544 235999999999999999999999999999999999999999999999999998 7788888887765
Q ss_pred H
Q 036580 116 M 116 (186)
Q Consensus 116 ~ 116 (186)
.
T Consensus 87 s 87 (323)
T KOG4336|consen 87 S 87 (323)
T ss_pred h
Confidence 3
No 60
>KOG3334 consensus Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=95.12 E-value=0.2 Score=41.09 Aligned_cols=81 Identities=15% Similarity=0.198 Sum_probs=59.6
Q ss_pred HHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHcCCccchH-HHHHHHHHHH
Q 036580 36 VSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMTTLGFEEYVE-PLKVYLQRFR 114 (186)
Q Consensus 36 V~RImK~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~LgF~dyi~-~Lk~~L~~~r 114 (186)
|.-|+|+.. ..-...-...-|.+.+=.++..|...|.-++.|+++.||..+||..|++...-..|.. +=+++|-++-
T Consensus 19 i~~iL~s~G--I~eyEprVi~qlLefa~rYtt~vL~DA~vys~HA~ka~i~~eDVrlA~~~~~~~sf~~pPpRe~lL~lA 96 (148)
T KOG3334|consen 19 IASILKSLG--IQEYEPRVINQLLEFAYRYTTTVLDDAKVYSSHAKKATIDAEDVRLAIQMRVDHSFTPPPPREFLLELA 96 (148)
T ss_pred HHHHHHHcC--ccccChHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHhccccCCCCchHHHHHHH
Confidence 444555543 3345566667788888889999999999999999999999999999999765555655 5566665554
Q ss_pred HHHH
Q 036580 115 EMEG 118 (186)
Q Consensus 115 e~~~ 118 (186)
...+
T Consensus 97 ~~rN 100 (148)
T KOG3334|consen 97 AERN 100 (148)
T ss_pred Hhhc
Confidence 4444
No 61
>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=92.69 E-value=0.52 Score=39.30 Aligned_cols=70 Identities=13% Similarity=0.214 Sum_probs=55.5
Q ss_pred CCchhHHHHHHHhhCC-----CCcccCHHHHHHHHHHHHH---HHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHcCC
Q 036580 30 FLPIANVSRIMKKALP-----ANAKISKDAKETVQECVSE---FISFVTGEASDKCQREKRKTINGDDLLWAMTTLGF 99 (186)
Q Consensus 30 ~LPkA~V~RImK~alP-----~~~rISkDA~~ai~k~aee---FI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~LgF 99 (186)
.|....+..++...+. ....+++++.+.|.+.+.- .|..++..+...+-..+.++|+.++|..++.++.|
T Consensus 191 ~l~~~e~~~~l~~~l~~~g~~~~~~~~~~~~~~i~~~s~G~p~~i~~l~~~~~~~a~~~~~~~i~~~~v~~~~~~~~~ 268 (269)
T TIGR03015 191 PLDREETREYIEHRLERAGNRDAPVFSEGAFDAIHRFSRGIPRLINILCDRLLLSAFLEEKREIGGEEVREVIAEIDF 268 (269)
T ss_pred CCCHHHHHHHHHHHHHHcCCCCCCCcCHHHHHHHHHHcCCcccHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhhc
Confidence 3555666666654431 1346999999999998875 79999999999888889999999999999998875
No 62
>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=92.00 E-value=0.67 Score=43.02 Aligned_cols=66 Identities=23% Similarity=0.215 Sum_probs=57.6
Q ss_pred hhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHcCCc
Q 036580 33 IANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMTTLGFE 100 (186)
Q Consensus 33 kA~V~RImK~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~LgF~ 100 (186)
+.+|+-.+.... ...|.+|+..+|..-.|.=|..+..+|.+.-.|.||..++-+||-.||+.|..+
T Consensus 8 ~et~KdvAeslG--i~Ni~Dd~l~alamDlEYRI~ev~qea~KFmvhSKRtvLt~dDis~ALr~lNVe 73 (450)
T COG5095 8 KETLKDVAESLG--ISNIDDDALRALAMDLEYRIKEVCQEASKFMVHSKRTVLTIDDISYALRSLNVE 73 (450)
T ss_pred HHHHHHHHHHcC--CcccccHHHHHHHHhHHHHHHHHHHHHHHHhhcccceeeeHHhHHHHHHhcCCC
Confidence 456666665543 568999999999999999999999999999999999999999999999988654
No 63
>KOG2389 consensus Predicted bromodomain transcription factor [Transcription]
Probab=91.39 E-value=0.64 Score=42.91 Aligned_cols=69 Identities=17% Similarity=0.178 Sum_probs=59.7
Q ss_pred CCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHcCCc
Q 036580 30 FLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMTTLGFE 100 (186)
Q Consensus 30 ~LPkA~V~RImK~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~LgF~ 100 (186)
.|-+..|..|+.... -.....-|++.|+..+..||..|+..|..++...+|.-.+..||+.||+.|+..
T Consensus 29 sla~~avaQIcqslg--~~~~~~sale~Ltd~~~qyvQ~lgk~a~~~~n~anR~epnl~Div~Al~dls~s 97 (353)
T KOG2389|consen 29 SLARVAVAQICQSLG--YSSTQNSALETLTDVLQQYVQNLGKTAHRYSNLANRTEPNLFDIVLALQDLSAS 97 (353)
T ss_pred HHHHHHHHHHHHhcC--CcccccHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCccHHHHHHHHHHhhhh
Confidence 577788889987765 334555599999999999999999999999999999999999999999987553
No 64
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=90.30 E-value=1.3 Score=39.18 Aligned_cols=70 Identities=10% Similarity=0.131 Sum_probs=51.9
Q ss_pred CchhHHHHHHHhhCCC---CcccCHHHHHHHHHHH------HHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHcCCc
Q 036580 31 LPIANVSRIMKKALPA---NAKISKDAKETVQECV------SEFISFVTGEASDKCQREKRKTINGDDLLWAMTTLGFE 100 (186)
Q Consensus 31 LPkA~V~RImK~alP~---~~rISkDA~~ai~k~a------eeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~LgF~ 100 (186)
+....+..|++..+.. ...++.++.+.+.+.+ -..+..|...|...|...++.+|+.+||..|++.+...
T Consensus 207 y~~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~a~~~a~~~~~~~I~~~~v~~a~~~~~~~ 285 (394)
T PRK00411 207 YTADEIFDILKDRVEEGFYPGVVDDEVLDLIADLTAREHGDARVAIDLLRRAGLIAEREGSRKVTEEDVRKAYEKSEIV 285 (394)
T ss_pred CCHHHHHHHHHHHHHhhcccCCCCHhHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHHHH
Confidence 3355666776655421 2358999998888877 33556777888888998999999999999999987433
No 65
>KOG1757 consensus Histone 2A [Chromatin structure and dynamics]
Probab=90.05 E-value=0.42 Score=38.09 Aligned_cols=65 Identities=17% Similarity=0.258 Sum_probs=48.4
Q ss_pred cccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHH----hcCCCccCHHHHHHHHH
Q 036580 27 QDRFLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASDKCQ----REKRKTINGDDLLWAMT 95 (186)
Q Consensus 27 ~d~~LPkA~V~RImK~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~----~~kRKTIt~eDVl~AL~ 95 (186)
.-+.||..+|.|.+|.......||..-+...... .+.|||.+-.+.|. .-|-|.|++.|+..|++
T Consensus 27 aGlqFpVgRihr~LK~r~t~h~rVGataavy~aa----ileYLTaEVLeLAgNasKdLKvKRitprHlqLAiR 95 (131)
T KOG1757|consen 27 AGLQFPVGRIHRHLKTRTTSHGRVGATAAVYSAA----ILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 95 (131)
T ss_pred cccccchHHHHHHHHHhcccccccchHHHHHHHH----HHHHHHHHHHHHcccccccceeeeccchhheeeec
Confidence 4467999999999999987778887766655544 45566666666554 44458899999988875
No 66
>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=89.65 E-value=2 Score=36.17 Aligned_cols=75 Identities=11% Similarity=0.117 Sum_probs=57.0
Q ss_pred cccCCchhHHHHHHHhhCCC--CcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhc------CCCccCHHHHHHHHHHcC
Q 036580 27 QDRFLPIANVSRIMKKALPA--NAKISKDAKETVQECVSEFISFVTGEASDKCQRE------KRKTINGDDLLWAMTTLG 98 (186)
Q Consensus 27 ~d~~LPkA~V~RImK~alP~--~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~------kRKTIt~eDVl~AL~~Lg 98 (186)
...+|....|.+.|...+.. ...|+.|.+.+|..||+.++..|.......|+|. ...++...||-..|..|+
T Consensus 41 ~~~fl~~~~l~~~~~~i~~~~g~~~~~~d~~~lis~a~e~rlr~li~k~~~~s~hR~~~~~~~~r~~~~sdvr~qL~~l~ 120 (212)
T cd08045 41 DPSFLNPSPLAKKIRKIAKKHGLKEVDEDVLDLISLALEERLRNLLEKLIEVSEHRVDSEKEDERYEITSDVRKQLRFLE 120 (212)
T ss_pred hhhccCHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCceeecchHHHHHHHHH
Confidence 33567777777777666532 1279999999999999999999999999999875 336677888888776654
Q ss_pred Ccc
Q 036580 99 FEE 101 (186)
Q Consensus 99 F~d 101 (186)
-.+
T Consensus 121 ~~e 123 (212)
T cd08045 121 QLE 123 (212)
T ss_pred HHH
Confidence 443
No 67
>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=88.64 E-value=2.2 Score=37.36 Aligned_cols=72 Identities=10% Similarity=0.091 Sum_probs=50.9
Q ss_pred hhHHHHHHHhhCC---CCcccCHHHHHHHHHHHH------HHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHcCCccch
Q 036580 33 IANVSRIMKKALP---ANAKISKDAKETVQECVS------EFISFVTGEASDKCQREKRKTINGDDLLWAMTTLGFEEYV 103 (186)
Q Consensus 33 kA~V~RImK~alP---~~~rISkDA~~ai~k~ae------eFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~LgF~dyi 103 (186)
...+..|++..+. ....+++|+...+.+.+. ..+..+...|...|..+++.+|+.+||..|+..+....+.
T Consensus 201 ~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~R~al~~l~~a~~~a~~~~~~~it~~~v~~a~~~~~~~~~~ 280 (365)
T TIGR02928 201 AEELRDILENRAEKAFYDGVLDDGVIPLCAALAAQEHGDARKAIDLLRVAGEIAEREGAERVTEDHVEKAQEKIEKDRLL 280 (365)
T ss_pred HHHHHHHHHHHHHhhccCCCCChhHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHH
Confidence 4456777766542 123588888887766553 3455677788888988889999999999999987544443
Q ss_pred H
Q 036580 104 E 104 (186)
Q Consensus 104 ~ 104 (186)
.
T Consensus 281 ~ 281 (365)
T TIGR02928 281 E 281 (365)
T ss_pred H
Confidence 3
No 68
>PF13335 Mg_chelatase_2: Magnesium chelatase, subunit ChlI
Probab=86.56 E-value=4.7 Score=30.21 Aligned_cols=58 Identities=16% Similarity=0.228 Sum_probs=47.0
Q ss_pred CCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHH------HHHHHHHHHHHHHhcCCCccCHHHHHHHHH
Q 036580 30 FLPIANVSRIMKKALPANAKISKDAKETVQECVSEF------ISFVTGEASDKCQREKRKTINGDDLLWAMT 95 (186)
Q Consensus 30 ~LPkA~V~RImK~alP~~~rISkDA~~ai~k~aeeF------I~~Lts~A~~~a~~~kRKTIt~eDVl~AL~ 95 (186)
.||-..|.+. ..+++++..+|.+++..| +.-|..-|.++|.-++...|..+||..||.
T Consensus 31 ~l~~~~l~~~--------~~l~~~~~~~l~~~~~~~~lS~R~~~rilrvARTIADL~~~~~I~~~hi~EAl~ 94 (96)
T PF13335_consen 31 QLPGEELRKY--------CPLSSEAKKLLEQAAEKLNLSARGYHRILRVARTIADLEGSERITREHIAEALS 94 (96)
T ss_pred cCCHHHHHhH--------cCCCHHHHHHHHHHHHHcCcCHHHHHHHHHHHHHHHhHcCCCCCCHHHHHHHHh
Confidence 3555555443 367888999999888776 567888899999999999999999999984
No 69
>PF13654 AAA_32: AAA domain; PDB: 3K1J_B.
Probab=84.88 E-value=5 Score=38.52 Aligned_cols=59 Identities=17% Similarity=0.197 Sum_probs=42.3
Q ss_pred HHHHHHhhCCCCcccCHHHHHHHHHHHH-----------HHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 036580 36 VSRIMKKALPANAKISKDAKETVQECVS-----------EFISFVTGEASDKCQREKRKTINGDDLLWAMTT 96 (186)
Q Consensus 36 V~RImK~alP~~~rISkDA~~ai~k~ae-----------eFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~ 96 (186)
|.+++++.- -..++.+|+..|-+.+. .-|..|..+|+.+|+.+++++|+++||..|++.
T Consensus 436 i~~~~~~~~--L~~~~~~Av~~li~~~~R~~q~kLsl~~~~l~~ll~EA~~~A~~~~~~~I~~~~V~~Ai~~ 505 (509)
T PF13654_consen 436 IASICQKEG--LPPFDRSAVARLIEYSARLDQDKLSLRFSWLADLLREANYWARKEGAKVITAEHVEQAIEE 505 (509)
T ss_dssp HHHHHHHHS--S--BBHHHHHHHHHHHHHCC-SEEE--HHHHHHHHHHHHHHHHHCT-SSB-HHHHHHHHHH
T ss_pred HHHHHHhCC--CCCCCHHHHHHHHHHHHHHhCCEeCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHc
Confidence 444444432 23578888777776653 367888999999999999999999999999975
No 70
>COG5162 Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=83.72 E-value=6.9 Score=33.17 Aligned_cols=68 Identities=18% Similarity=0.189 Sum_probs=47.1
Q ss_pred CchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHh-c-----------------------------
Q 036580 31 LPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASDKCQR-E----------------------------- 80 (186)
Q Consensus 31 LPkA~V~RImK~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~-~----------------------------- 80 (186)
||-+.+.=.|..+. -.....-.+.+|.-.+..||+.|+..|.++.+- .
T Consensus 89 iPd~v~DYyl~k~G--f~~~D~rvKkLl~L~aqKFvsDiA~dayqYsrIr~~~sna~~t~~~a~~f~~gg~~~i~~~~~~ 166 (197)
T COG5162 89 IPDSVTDYYLEKAG--FVTSDQRVKKLLSLLAQKFVSDIAVDAYQYSRIRQGSSNAKATAQKAKRFAKGGASGIGSSGRR 166 (197)
T ss_pred ccHHHHHHHHHhcC--ceeccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccchhhHHHHHHHHhcccccccccccc
Confidence 44444444444432 233455667888999999999999999886541 1
Q ss_pred ---CCCccCHHHHHHHHHHcCCc
Q 036580 81 ---KRKTINGDDLLWAMTTLGFE 100 (186)
Q Consensus 81 ---kRKTIt~eDVl~AL~~LgF~ 100 (186)
++.+++..|+..||++.|+.
T Consensus 167 ~dr~K~vltv~DLs~Al~EyGin 189 (197)
T COG5162 167 GDRKKPVLTVVDLSKALEEYGIN 189 (197)
T ss_pred cccCCceeeehHHHHHHHHhccc
Confidence 45578899999999987763
No 71
>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=83.45 E-value=6.9 Score=26.81 Aligned_cols=48 Identities=17% Similarity=0.200 Sum_probs=37.2
Q ss_pred CCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 036580 30 FLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASDKCQR 79 (186)
Q Consensus 30 ~LPkA~V~RImK~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~ 79 (186)
.||-+.+.-+++++.= ..-..-.+-+|.=++..||..|+..|.++|+.
T Consensus 2 ~IPD~v~~~yL~~~G~--~~~D~rv~RLvSLaaQKFisdI~~dA~q~~k~ 49 (51)
T PF03540_consen 2 TIPDEVTDYYLERSGF--QTSDPRVKRLVSLAAQKFISDIANDAMQYCKI 49 (51)
T ss_pred CCCHHHHHHHHHHCCC--CCCCHhHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 4788889999988862 12233446688889999999999999999874
No 72
>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=83.20 E-value=4.1 Score=38.91 Aligned_cols=66 Identities=23% Similarity=0.243 Sum_probs=47.2
Q ss_pred CchhHHHHHHHhhCC-CCcccCHHHHHHHHHHHHH--HHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 036580 31 LPIANVSRIMKKALP-ANAKISKDAKETVQECVSE--FISFVTGEASDKCQREKRKTINGDDLLWAMTT 96 (186)
Q Consensus 31 LPkA~V~RImK~alP-~~~rISkDA~~ai~k~aee--FI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~ 96 (186)
|....+.+|++..+. ....|++++.+.|.+.+.. .+..+...|..+|..++|++|+.+||.|++..
T Consensus 263 L~~eei~~Il~~~a~k~~i~is~~al~~I~~y~~n~Rel~nll~~Aa~~A~~~~~~~It~~dI~~vl~~ 331 (531)
T TIGR02902 263 LLDEEIKEIAKNAAEKIGINLEKHALELIVKYASNGREAVNIVQLAAGIALGEGRKRILAEDIEWVAEN 331 (531)
T ss_pred CCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHhhhhHHHHHHHHHHHHHHHhhCCCcEEcHHHHHHHhCC
Confidence 344557777777663 2457999999988777652 23444555666777788999999999999754
No 73
>KOG3901 consensus Transcription initiation factor IID subunit [Transcription]
Probab=82.80 E-value=9.5 Score=29.97 Aligned_cols=48 Identities=17% Similarity=0.278 Sum_probs=40.4
Q ss_pred CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 036580 46 ANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMTT 96 (186)
Q Consensus 46 ~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~ 96 (186)
|+..=-.|++++|-..+.+||..++..|..+. +|-.+.-||++.+|++
T Consensus 24 Dd~nP~~~tv~~Le~iV~~Yi~elt~~a~~~g---~rgk~~veD~~f~lRk 71 (109)
T KOG3901|consen 24 DDVNPYPETVDLLEDIVLEYITELTHAAMEIG---KRGKVKVEDFKFLLRK 71 (109)
T ss_pred CCCCccHhHHHHHHHHHHHHHHHHHHHHHHhc---ccCceeHHHHHHHHHh
Confidence 55666688999999999999999988887766 5666788999999985
No 74
>PF08369 PCP_red: Proto-chlorophyllide reductase 57 kD subunit; InterPro: IPR013580 This domain is found in bacteria and plant chloroplast proteins. It often appears at the C-terminal of nitrogenase component 1 type oxidoreductases (IPR000510 from INTERPRO) and sometimes independently in bacterial proteins such as the proto-chlorophyllide reductase subunit B of the cyanobacterium Synechocystis. This domain is also associated with chlorophyllide reductase subunit Z, converts chlorophylls (Chl) into bacteriochlorophylls (BChl) by reducing ring B of the tetrapyrrole.; GO: 0016491 oxidoreductase activity, 0015979 photosynthesis, 0015995 chlorophyll biosynthetic process, 0055114 oxidation-reduction process; PDB: 2KRU_A 2L09_A.
Probab=82.03 E-value=2.4 Score=27.97 Aligned_cols=42 Identities=12% Similarity=0.113 Sum_probs=29.8
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHH-HHHhcCCCccCHHHHHHH
Q 036580 51 SKDAKETVQECVSEFISFVTGEASD-KCQREKRKTINGDDLLWA 93 (186)
Q Consensus 51 SkDA~~ai~k~aeeFI~~Lts~A~~-~a~~~kRKTIt~eDVl~A 93 (186)
+.||...|.+. -.|+.--...+.+ +|...|...|+.++|..|
T Consensus 2 ~~eA~~~L~~i-P~fvR~~~r~~~E~~Ar~~G~~~IT~e~v~~A 44 (45)
T PF08369_consen 2 TDEAEARLDRI-PFFVRKKLRDAAEKYARERGYDEITVEVVDAA 44 (45)
T ss_dssp -HHHHHHHCTS--HHHHHHHHHHHHHHHHHCT-SEE-HHHHHHH
T ss_pred CHHHHHHHHHC-CHHHHHHHHHHHHHHHHHcCCCeECHHHHHhh
Confidence 56788888775 7788766666555 888999999999998765
No 75
>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=80.48 E-value=7.9 Score=37.83 Aligned_cols=48 Identities=15% Similarity=0.169 Sum_probs=40.3
Q ss_pred ccCHHHHHHHHHHHH-------------HHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 036580 49 KISKDAKETVQECVS-------------EFISFVTGEASDKCQREKRKTINGDDLLWAMTT 96 (186)
Q Consensus 49 rISkDA~~ai~k~ae-------------eFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~ 96 (186)
.++++|+..|.+-+. .=|..|..+|..+|..+++.+|+.+||..|++.
T Consensus 330 ~~s~~Av~~Li~~~~R~ag~r~~lsl~~R~L~~llR~A~~iA~~~~~~~I~~ehV~~Ai~~ 390 (608)
T TIGR00764 330 HFTRDAVEEIVREAQRRAGRKDHLTLRLRELGGLVRAAGDIAKSSGKVYVTAEHVLKAKKL 390 (608)
T ss_pred cCCHHHHHHHHHHHHHHHhcccccCCCHHHHHHHHHHHHHHHHhcCCceecHHHHHHHHHH
Confidence 799999988876443 456778888988999889999999999999975
No 76
>COG5094 TAF9 Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=79.50 E-value=18 Score=29.41 Aligned_cols=74 Identities=19% Similarity=0.164 Sum_probs=54.8
Q ss_pred CcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccC---HHHHHHHHHHcCCccchH-HHHHHHHHHHHHHHhh
Q 036580 47 NAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTIN---GDDLLWAMTTLGFEEYVE-PLKVYLQRFREMEGEK 120 (186)
Q Consensus 47 ~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt---~eDVl~AL~~LgF~dyi~-~Lk~~L~~~re~~~~K 120 (186)
....+.-...-+.+.+-.+-..|...|.-+++|.+|-.|. .+||..|+..-=--.|++ +-+++|-+.--+.+.|
T Consensus 29 i~~ye~~VplQLl~FAhRYTq~vl~Dalvya~htgrg~~a~l~veDvrLA~at~v~~~F~pppPke~llela~erN~K 106 (145)
T COG5094 29 IEEYEPKVPLQLLEFAHRYTQDVLEDALVYAKHTGRGHIATLGVEDVRLALATKVGRHFVPPPPKEYLLELATERNSK 106 (145)
T ss_pred chhhCccchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHHHHHHHhcCCcCCCChHHHHHHHHHHhcCC
Confidence 4456666778888999999999999999999999996554 599999998543344554 5577776655444433
No 77
>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=76.78 E-value=3.5 Score=35.81 Aligned_cols=73 Identities=12% Similarity=0.127 Sum_probs=34.2
Q ss_pred ccccCCchhHHHHHHHhhCC--CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC------CccCHHHHHHHHHHc
Q 036580 26 EQDRFLPIANVSRIMKKALP--ANAKISKDAKETVQECVSEFISFVTGEASDKCQREKR------KTINGDDLLWAMTTL 97 (186)
Q Consensus 26 e~d~~LPkA~V~RImK~alP--~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kR------KTIt~eDVl~AL~~L 97 (186)
.++.+|....+.+.|.+... ....|..|.+.+|.-||++.|..|...+..+|+|-.. .+....||-..|..|
T Consensus 39 ~~~~fL~~~~L~~~i~~i~~~~g~~~~~~d~l~llS~A~e~rLr~lie~~~~~s~hR~~~~~~~~~~~~~sdv~~qlr~l 118 (264)
T PF05236_consen 39 KEEPFLNPSPLQKRIQKIAKKHGLKSVDEDVLELLSLATEERLRNLIEKAIVLSRHRRDSSKSDPRYEIRSDVRKQLRFL 118 (264)
T ss_dssp -----S-HHHHHHHHHHHHHCTT--EE-TCHHHHHHHHHHHHHHHHHHHHH-----------------------------
T ss_pred ccccccCHHHHHHHHHHHHHHcCCcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccCCCcccccchHHHHHHHHH
Confidence 34567887777777766653 2457999999999999999999999999999987432 133456676666544
Q ss_pred C
Q 036580 98 G 98 (186)
Q Consensus 98 g 98 (186)
.
T Consensus 119 ~ 119 (264)
T PF05236_consen 119 E 119 (264)
T ss_dssp -
T ss_pred H
Confidence 3
No 78
>KOG2680 consensus DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=76.39 E-value=13 Score=34.97 Aligned_cols=51 Identities=18% Similarity=0.254 Sum_probs=42.6
Q ss_pred CCcccCHHHHHHHHHHHH----HHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 036580 46 ANAKISKDAKETVQECVS----EFISFVTGEASDKCQREKRKTINGDDLLWAMTT 96 (186)
Q Consensus 46 ~~~rISkDA~~ai~k~ae----eFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~ 96 (186)
.++.++.||++.|.+..+ .|..+|...|+..|.+.|-+++..+||..+.+-
T Consensus 374 Edv~m~~~A~d~Lt~i~~~tsLRYai~Lit~a~~~~~krk~~~v~~~di~r~y~L 428 (454)
T KOG2680|consen 374 EDVEMNPDALDLLTKIGEATSLRYAIHLITAASLVCLKRKGKVVEVDDIERVYRL 428 (454)
T ss_pred hccccCHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHhcCceeehhHHHHHHHH
Confidence 467899999999987654 366677788899999999999999999998753
No 79
>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=74.93 E-value=15 Score=34.95 Aligned_cols=82 Identities=18% Similarity=0.251 Sum_probs=56.8
Q ss_pred CchhHHHHHHHhhCC-CCcccCHHHHHHHHHHHHH----HHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHcCCccchHH
Q 036580 31 LPIANVSRIMKKALP-ANAKISKDAKETVQECVSE----FISFVTGEASDKCQREKRKTINGDDLLWAMTTLGFEEYVEP 105 (186)
Q Consensus 31 LPkA~V~RImK~alP-~~~rISkDA~~ai~k~aee----FI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~LgF~dyi~~ 105 (186)
.+..-|+-|++-... .++.+++||++.|.+.-++ +...|..-|..+|+..++++|..+||..|-+- |.| +..
T Consensus 361 y~~~EireIi~iRa~ee~i~l~~~Ale~L~~ig~etSLRYa~qLL~pa~iiA~~rg~~~V~~~dVe~a~~l--F~D-~kr 437 (450)
T COG1224 361 YSREEIREIIRIRAKEEDIELSDDALEYLTDIGEETSLRYAVQLLTPASIIAKRRGSKRVEVEDVERAKEL--FLD-VKR 437 (450)
T ss_pred CCHHHHHHHHHHhhhhhccccCHHHHHHHHhhchhhhHHHHHHhccHHHHHHHHhCCCeeehhHHHHHHHH--Hhh-HHH
Confidence 445556666654432 4678999999999876554 55566677888999999999999999988643 322 223
Q ss_pred HHHHHHHHHH
Q 036580 106 LKVYLQRFRE 115 (186)
Q Consensus 106 Lk~~L~~~re 115 (186)
--+|+++|++
T Consensus 438 Sv~~v~~~~~ 447 (450)
T COG1224 438 SVEYVEKYEG 447 (450)
T ss_pred HHHHHHHHHh
Confidence 3456666654
No 80
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=72.92 E-value=37 Score=29.86 Aligned_cols=72 Identities=15% Similarity=0.219 Sum_probs=52.0
Q ss_pred CCchhHHHHHHHhhCC-CCcccCHHHHHHHHHHHH---HHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHcCCcc
Q 036580 30 FLPIANVSRIMKKALP-ANAKISKDAKETVQECVS---EFISFVTGEASDKCQREKRKTINGDDLLWAMTTLGFEE 101 (186)
Q Consensus 30 ~LPkA~V~RImK~alP-~~~rISkDA~~ai~k~ae---eFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~LgF~d 101 (186)
.++...+..|++.... ....++.|+...|.+.|. ..+..+...+.+++...+.+.|+.++|..+++.++...
T Consensus 179 ~~~~~e~~~il~~~~~~~~~~~~~~~~~~ia~~~~G~pR~a~~~l~~~~~~a~~~~~~~I~~~~v~~~l~~~~~~~ 254 (328)
T PRK00080 179 FYTVEELEKIVKRSARILGVEIDEEGALEIARRSRGTPRIANRLLRRVRDFAQVKGDGVITKEIADKALDMLGVDE 254 (328)
T ss_pred CCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCc
Confidence 3556666667765542 356799999988887773 44666666677777766677899999999999876653
No 81
>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=72.54 E-value=32 Score=29.42 Aligned_cols=70 Identities=19% Similarity=0.207 Sum_probs=49.8
Q ss_pred CchhHHHHHHHhhCC-CCcccCHHHHHHHHHHHH---HHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHcCCc
Q 036580 31 LPIANVSRIMKKALP-ANAKISKDAKETVQECVS---EFISFVTGEASDKCQREKRKTINGDDLLWAMTTLGFE 100 (186)
Q Consensus 31 LPkA~V~RImK~alP-~~~rISkDA~~ai~k~ae---eFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~LgF~ 100 (186)
++...+..|++.... ....++.++...|.+.+. .++..+...+...+...+...|+.++|..++..+++.
T Consensus 159 l~~~e~~~il~~~~~~~~~~~~~~al~~ia~~~~G~pR~~~~ll~~~~~~a~~~~~~~it~~~v~~~l~~l~~~ 232 (305)
T TIGR00635 159 YTVEELAEIVSRSAGLLNVEIEPEAALEIARRSRGTPRIANRLLRRVRDFAQVRGQKIINRDIALKALEMLMID 232 (305)
T ss_pred CCHHHHHHHHHHHHHHhCCCcCHHHHHHHHHHhCCCcchHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHhCCC
Confidence 455666666665542 245789999988888763 3455666667777766666789999999999987654
No 82
>COG1067 LonB Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]
Probab=71.94 E-value=4.5 Score=40.14 Aligned_cols=48 Identities=27% Similarity=0.284 Sum_probs=35.9
Q ss_pred ccCHHHHHHHHHHHHH-------------HHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 036580 49 KISKDAKETVQECVSE-------------FISFVTGEASDKCQREKRKTINGDDLLWAMTT 96 (186)
Q Consensus 49 rISkDA~~ai~k~aee-------------FI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~ 96 (186)
-++++|...|.+-+.. -|-.|..+|..+|..++++-|+++||.+|++.
T Consensus 338 ~~~~~Av~~li~~a~R~Ag~~~~Ltl~~rdl~~lv~~A~~ia~~~~~~~I~ae~Ve~a~~~ 398 (647)
T COG1067 338 HLDKDAVEELIREAARRAGDQNKLTLRLRDLGNLVREAGDIAVSEGRKLITAEDVEEALQK 398 (647)
T ss_pred CCCHHHHHHHHHHHHHhccccceeccCHHHHHHHHHHhhHHHhcCCcccCcHHHHHHHHHh
Confidence 4666665555544432 34455669999999999999999999999986
No 83
>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=69.61 E-value=4.2 Score=33.18 Aligned_cols=69 Identities=19% Similarity=0.296 Sum_probs=50.3
Q ss_pred HHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHcCCccchHHHHHHHHHHHH
Q 036580 36 VSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMTTLGFEEYVEPLKVYLQRFRE 115 (186)
Q Consensus 36 V~RImK~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~LgF~dyi~~Lk~~L~~~re 115 (186)
+.||++.+. ..-|.|+-..-+.+.++.=+..|.--|...|+.++|-+|...|+=-. .-+++.+.+||+
T Consensus 1 fe~lFR~aa--~LdvdK~d~~r~~d~V~~Kl~DLl~va~~~Ak~ngRdvI~~~DLPIT----------kGlqesi~~Fr~ 68 (138)
T PF09123_consen 1 FERLFRKAA--GLDVDKNDAKRYSDFVEKKLYDLLLVAQENAKANGRDVIEPRDLPIT----------KGLQESIREFRK 68 (138)
T ss_dssp HHHHHHHHH--S----HHHHHHHHHHHHHHHHHCCCCHHHHHHHTT-SEE-GGGS-------------HHHHHHHHHHHT
T ss_pred ChHHHHHHh--ccCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeeccccCCcc----------HHHHHHHHHHHH
Confidence 468888887 56788999999999999999999999999999999999999987322 345566666665
Q ss_pred H
Q 036580 116 M 116 (186)
Q Consensus 116 ~ 116 (186)
+
T Consensus 69 l 69 (138)
T PF09123_consen 69 L 69 (138)
T ss_dssp T
T ss_pred c
Confidence 5
No 84
>COG5248 TAF19 Transcription initiation factor TFIID, subunit TAF13 [Transcription]
Probab=69.22 E-value=33 Score=27.35 Aligned_cols=58 Identities=19% Similarity=0.301 Sum_probs=45.7
Q ss_pred HHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 036580 36 VSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMTT 96 (186)
Q Consensus 36 V~RImK~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~ 96 (186)
|+-+|-.- .|+..-..|..++|.+.+..++..+...|...|+ .|-.+..+|+..||++
T Consensus 15 ikslmYay-GDvv~P~~dt~~~L~e~V~dY~~~~ctna~~~Aq--~rnK~k~eDfkfaLr~ 72 (126)
T COG5248 15 IKSLMYAY-GDVVAPRYDTAEALHEYVLDYMSILCTNAHNMAQ--VRNKTKTEDFKFALRR 72 (126)
T ss_pred HHHHHHHh-CCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHH--hcccchHHHHHHHHhh
Confidence 33444333 3566777899999999999999999999999888 4555688999999985
No 85
>COG5251 TAF40 Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=68.36 E-value=8.3 Score=32.85 Aligned_cols=62 Identities=15% Similarity=0.002 Sum_probs=50.8
Q ss_pred CCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC---ccCHHHHHHHHH
Q 036580 30 FLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRK---TINGDDLLWAMT 95 (186)
Q Consensus 30 ~LPkA~V~RImK~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRK---TIt~eDVl~AL~ 95 (186)
.||++.|++++-..+ +-.|+.-.+..|+-.+.+|+-.|...|..+- +++. -+.+.|+-.|..
T Consensus 115 ~lnKt~VKKlastV~--nQtVspNi~I~l~g~~KVfvGEiIElA~~Vq--~~w~~sgpl~p~h~reayr 179 (199)
T COG5251 115 SLNKTQVKKLASTVA--NQTVSPNIRIFLQGVGKVFVGEIIELAMIVQ--NKWLTSGPLIPFHKREAYR 179 (199)
T ss_pred CCCHHHHHHHHHHHh--ccccCCCeeeeeechhHHHHHHHHHHHHHHH--HHhcccCCCChHHHHHHHH
Confidence 599999999999998 6788888899999999999999998885543 3343 478888887764
No 86
>PRK09862 putative ATP-dependent protease; Provisional
Probab=65.91 E-value=27 Score=33.74 Aligned_cols=53 Identities=11% Similarity=0.121 Sum_probs=41.7
Q ss_pred cccCHHHHHHHHHHHHHH------HHHHHHHHHHHHHhcCCCccCHHHHHHHHHHcCCc
Q 036580 48 AKISKDAKETVQECVSEF------ISFVTGEASDKCQREKRKTINGDDLLWAMTTLGFE 100 (186)
Q Consensus 48 ~rISkDA~~ai~k~aeeF------I~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~LgF~ 100 (186)
..+++++...+.++...+ .+.|...|.++|.-++|..|+.+||..|+.--.++
T Consensus 437 ~~l~~~~~~~l~~~~~~~~lS~Ra~~rlLrvARTiADL~g~~~V~~~hv~eAl~yR~~~ 495 (506)
T PRK09862 437 CKLESEDARWLEETLIHLGLSIRAWQRLLKVARTIADIDQSDIITRQHLQEAVSYRAID 495 (506)
T ss_pred hCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHhhccc
Confidence 357777877777765544 56788889999999999999999999999743333
No 87
>TIGR02442 Cob-chelat-sub cobaltochelatase subunit. A number of genomes (actinobacteria, cyanobacteria, betaproteobacteria and pseudomonads) which apparently biosynthesize B12, encode a cobN gene but are demonstrably lacking cobS and cobT. These genomes do, however contain a homolog (modelled here) of the magnesium chelatase subunits BchI/BchD family. Aside from the cyanobacteria (which have a separate magnesium chelatase trimer), these species do not make chlorins, so do not have any use for a magnesium chelatase. Furthermore, in nearly all cases the members of this family are proximal to either CobN itself or other genes involved in cobalt transport or B12 biosynthesis.
Probab=65.49 E-value=27 Score=34.16 Aligned_cols=49 Identities=18% Similarity=0.207 Sum_probs=41.7
Q ss_pred CcccCHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCccCHHHHHHHHH
Q 036580 47 NAKISKDAKETVQECVSEFI-------SFVTGEASDKCQREKRKTINGDDLLWAMT 95 (186)
Q Consensus 47 ~~rISkDA~~ai~k~aeeFI-------~~Lts~A~~~a~~~kRKTIt~eDVl~AL~ 95 (186)
.+.|+.+++..|.+.+..+- ..+...|..+|.-++|.+|+.+||..|++
T Consensus 247 ~V~is~~~~~~l~~~~~~~~i~s~Ra~i~~~r~Ara~AaL~gr~~V~~~Dv~~A~~ 302 (633)
T TIGR02442 247 SVRISDSLIRFISELCIEFGVDGHRADIVMARAARALAALDGRRRVTAEDVREAAE 302 (633)
T ss_pred CCCCCHHHHHHHHHHHHHhCCCCccHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHH
Confidence 57899999999999887662 46677788889999999999999999886
No 88
>TIGR00368 Mg chelatase-related protein. The N-terminal end matches very strongly a pfam Mg_chelatase domain.
Probab=64.78 E-value=18 Score=34.59 Aligned_cols=47 Identities=15% Similarity=0.174 Sum_probs=41.9
Q ss_pred ccCHHHHHHHHHHHHHH------HHHHHHHHHHHHHhcCCCccCHHHHHHHHH
Q 036580 49 KISKDAKETVQECVSEF------ISFVTGEASDKCQREKRKTINGDDLLWAMT 95 (186)
Q Consensus 49 rISkDA~~ai~k~aeeF------I~~Lts~A~~~a~~~kRKTIt~eDVl~AL~ 95 (186)
.+++++...+.++++.| ++.|..-|.++|.-+++..|..+||..|+.
T Consensus 445 ~l~~~~~~~l~~a~~~~~lS~R~~~rilrvArTiAdL~g~~~i~~~hv~eA~~ 497 (499)
T TIGR00368 445 KLSAIDANDLEGALNKLGLSSRATHRILKVARTIADLKEEKNISREHLAEAIE 497 (499)
T ss_pred CCCHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHh
Confidence 56889999999998876 678889999999999999999999999984
No 89
>PF08681 DUF1778: Protein of unknown function (DUF1778); InterPro: IPR014795 This entry is represented by Vibrio phage ICP1, Orf50. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a family of uncharacterised proteins. The structure of one of the hypothetical proteins in this family has been solved and it forms a helix structure which may form interactions with DNA. ; PDB: 1Y9B_A.
Probab=64.43 E-value=6.2 Score=28.52 Aligned_cols=52 Identities=19% Similarity=0.354 Sum_probs=29.5
Q ss_pred CcccCHHHHHHHHHHHH-------HHHHHHHHHHHHHHH-hcCCCccCHHHHHHHHHHcC
Q 036580 47 NAKISKDAKETVQECVS-------EFISFVTGEASDKCQ-REKRKTINGDDLLWAMTTLG 98 (186)
Q Consensus 47 ~~rISkDA~~ai~k~ae-------eFI~~Lts~A~~~a~-~~kRKTIt~eDVl~AL~~Lg 98 (186)
++||+.+.++.|.+++. .||...+.++.+... ....-+++.+|...-++.|+
T Consensus 3 ~iR~~~e~k~li~~AA~~~G~sls~Fi~~aa~~~A~~~i~~~~~~~Ls~~~~~~f~~aLd 62 (80)
T PF08681_consen 3 EIRVTPEEKELIERAAALSGVSLSDFILSAALEAAEEVIEEHERIRLSAEDFEAFMAALD 62 (80)
T ss_dssp EEE--HHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH
T ss_pred eEecCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhcceeEcCHHHHHHHHHHHh
Confidence 46899999999999984 565555544444322 22334566666554444443
No 90
>PRK13406 bchD magnesium chelatase subunit D; Provisional
Probab=62.43 E-value=22 Score=34.85 Aligned_cols=59 Identities=14% Similarity=0.159 Sum_probs=47.8
Q ss_pred HHHHHHHhhCCCCcccCHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCccCHHHHHHHHH
Q 036580 35 NVSRIMKKALPANAKISKDAKETVQECVSEFI-------SFVTGEASDKCQREKRKTINGDDLLWAMT 95 (186)
Q Consensus 35 ~V~RImK~alP~~~rISkDA~~ai~k~aeeFI-------~~Lts~A~~~a~~~kRKTIt~eDVl~AL~ 95 (186)
.|.+.-+ .++ ++.|+.+.+..+.++|..|- ..|...|..+|.-++|.+|+.+||..|+.
T Consensus 183 ~I~~AR~-rl~-~v~v~~~~l~~i~~~~~~~gv~S~Ra~i~llraARa~AaL~Gr~~V~~~dv~~Aa~ 248 (584)
T PRK13406 183 DIAAARA-RLP-AVGPPPEAIAALCAAAAALGIASLRAPLLALRAARAAAALAGRTAVEEEDLALAAR 248 (584)
T ss_pred HHHHHHH-HHc-cCCCCHHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 4444433 344 78999999999888887774 47888899999999999999999999985
No 91
>smart00350 MCM minichromosome maintenance proteins.
Probab=61.30 E-value=46 Score=31.55 Aligned_cols=68 Identities=10% Similarity=0.095 Sum_probs=49.7
Q ss_pred cCCchhHHHHHHHhhCC-CCcccCHHHHHHHHHHHHH-------------------HHHHHHHHHHHHHHhcCCCccCHH
Q 036580 29 RFLPIANVSRIMKKALP-ANAKISKDAKETVQECVSE-------------------FISFVTGEASDKCQREKRKTINGD 88 (186)
Q Consensus 29 ~~LPkA~V~RImK~alP-~~~rISkDA~~ai~k~aee-------------------FI~~Lts~A~~~a~~~kRKTIt~e 88 (186)
..++...+++.+.-+-- -.-.|++++.+.|.+.... .+..|...|-..|+-..|.+|+.+
T Consensus 416 ~~~~~~~l~~yi~~ar~~~~P~ls~~~~~~i~~~y~~~R~~~~~~~~~~~~~~t~R~l~sliRla~A~A~l~~r~~V~~~ 495 (509)
T smart00350 416 VPISQEFLRKYIAYAREKIKPKLSEEAAEKLVKAYVDLRKEDSQSEARSSIPITVRQLESIIRLSEAHAKMRLSDVVEEA 495 (509)
T ss_pred ccCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhcccccccccccccCcCHHHHHHHHHHHHHHHHHcCCCccCHH
Confidence 35788888887754421 0126899999988765433 335677777778999999999999
Q ss_pred HHHHHHHH
Q 036580 89 DLLWAMTT 96 (186)
Q Consensus 89 DVl~AL~~ 96 (186)
||..|++-
T Consensus 496 Dv~~ai~l 503 (509)
T smart00350 496 DVEEAIRL 503 (509)
T ss_pred HHHHHHHH
Confidence 99999864
No 92
>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=60.69 E-value=45 Score=30.29 Aligned_cols=54 Identities=22% Similarity=0.215 Sum_probs=41.5
Q ss_pred HhhCCCCcccCHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCccCHHHHHHHHH
Q 036580 41 KKALPANAKISKDAKETVQECVSEFI-------SFVTGEASDKCQREKRKTINGDDLLWAMT 95 (186)
Q Consensus 41 K~alP~~~rISkDA~~ai~k~aeeFI-------~~Lts~A~~~a~~~kRKTIt~eDVl~AL~ 95 (186)
++.++ .+.|+++.+..+.+.|..+= .++...|-.+|--++|..|+++||..++.
T Consensus 247 ~~~~~-~V~v~d~~~~~i~~l~~~~~~~s~Ra~i~l~raArA~Aal~GR~~V~~dDv~~~a~ 307 (337)
T TIGR02030 247 QNLLP-QVTIPYDVLVKVAELCAELDVDGLRGELTLNRAAKALAAFEGRTEVTVDDIRRVAV 307 (337)
T ss_pred HHHhc-cCcCCHHHHHHHHHHHHHHCCCCCcHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 33444 57899999888888776553 34667777788899999999999998764
No 93
>KOG1658 consensus DNA polymerase epsilon, subunit C [Replication, recombination and repair]
Probab=60.40 E-value=27 Score=29.24 Aligned_cols=98 Identities=15% Similarity=0.209 Sum_probs=60.0
Q ss_pred ccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHH-----------HHH-HhcCCCccCHHHHHHHHH
Q 036580 28 DRFLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEAS-----------DKC-QREKRKTINGDDLLWAMT 95 (186)
Q Consensus 28 d~~LPkA~V~RImK~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~-----------~~a-~~~kRKTIt~eDVl~AL~ 95 (186)
.--||++-++||.|.. |.-+.=+.+|..+...+++.|+..++..+. +.| +..--.|+..++++.++.
T Consensus 9 ~p~~p~ekvkkiak~d-Pey~~te~~a~~etafatE~fvq~lv~~p~a~l~rLpL~rik~vvkl~pdl~l~~dea~~l~a 87 (162)
T KOG1658|consen 9 SPKLPMEKVKKIAKND-PEYMDTEDDAFVETAFATEQFVQVLVHLPQASLSRLPLARIKQVVKLDPDLTLLNDEASQLIA 87 (162)
T ss_pred CccccHHHHHHhhcCC-chhhhcccchHHHHHHHHHHHHhhhhhhhhhhhhhccHHHHHhhccCCcchhhhhhHHHHHHH
Confidence 3469999999999987 545556777888999999999988888221 111 112234667777776665
Q ss_pred HcCCccchHHHHHHHHHHHHHHHhhhhcCCCC
Q 036580 96 TLGFEEYVEPLKVYLQRFREMEGEKMARDKDA 127 (186)
Q Consensus 96 ~LgF~dyi~~Lk~~L~~~re~~~~K~~~kk~~ 127 (186)
.- -+.|+..|....-.+......|+-.+++-
T Consensus 88 ~a-aelfi~~Ln~~~~~~~q~~k~kt~qr~d~ 118 (162)
T KOG1658|consen 88 KA-AELFIQELNDVAYTTAQLRKRKTEQRRDY 118 (162)
T ss_pred HH-HHHHHHHHHhccchhHHHHHhhhhhhhcc
Confidence 31 12344444444444444444444455544
No 94
>PRK12402 replication factor C small subunit 2; Reviewed
Probab=58.07 E-value=30 Score=29.66 Aligned_cols=68 Identities=7% Similarity=0.012 Sum_probs=42.5
Q ss_pred CchhHHHHHHHhhCC-CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHcCCc
Q 036580 31 LPIANVSRIMKKALP-ANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMTTLGFE 100 (186)
Q Consensus 31 LPkA~V~RImK~alP-~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~LgF~ 100 (186)
++...+..++++.+. ....|+.++...|.+.+.-=+..+.......+. ...+|+.+||..++.....+
T Consensus 184 ~~~~~~~~~l~~~~~~~~~~~~~~al~~l~~~~~gdlr~l~~~l~~~~~--~~~~It~~~v~~~~~~~~~~ 252 (337)
T PRK12402 184 PTDDELVDVLESIAEAEGVDYDDDGLELIAYYAGGDLRKAILTLQTAAL--AAGEITMEAAYEALGDVGTD 252 (337)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHH--cCCCCCHHHHHHHhCCCCCH
Confidence 444556666665443 245799999999988874434444444444442 23479999999888754433
No 95
>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]
Probab=57.67 E-value=35 Score=31.33 Aligned_cols=69 Identities=13% Similarity=0.176 Sum_probs=50.5
Q ss_pred hHHHHHHHhhCC---CCcccCHHHHHHHHHHH------HHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHcCCccc
Q 036580 34 ANVSRIMKKALP---ANAKISKDAKETVQECV------SEFISFVTGEASDKCQREKRKTINGDDLLWAMTTLGFEEY 102 (186)
Q Consensus 34 A~V~RImK~alP---~~~rISkDA~~ai~k~a------eeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~LgF~dy 102 (186)
.-|.-|+++... ....++.++..++..-+ ..+...|...|.++|+.+++.+|+.+||..|-+..+..-+
T Consensus 193 ~el~~Il~~R~~~~~~~~~~~~~vl~lia~~~a~~~GDAR~aidilr~A~eiAe~~~~~~v~~~~v~~a~~~~~~~~~ 270 (366)
T COG1474 193 EELYDILRERVEEGFSAGVIDDDVLKLIAALVAAESGDARKAIDILRRAGEIAEREGSRKVSEDHVREAQEEIERDVL 270 (366)
T ss_pred HHHHHHHHHHHHhhccCCCcCccHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHhhCCCCcCHHHHHHHHHHhhHHHH
Confidence 456667666542 23468888877776443 3466788899999999999999999999999666555433
No 96
>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=56.48 E-value=24 Score=23.20 Aligned_cols=32 Identities=22% Similarity=0.450 Sum_probs=26.9
Q ss_pred CCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHH
Q 036580 30 FLPIANVSRIMKKALPANAKISKDAKETVQECVSEF 65 (186)
Q Consensus 30 ~LPkA~V~RImK~alP~~~rISkDA~~ai~k~aeeF 65 (186)
.+.+++|.|++... .+||.+.++-|.+++++.
T Consensus 10 gvS~~TVSr~ln~~----~~vs~~tr~rI~~~a~~l 41 (46)
T PF00356_consen 10 GVSKSTVSRVLNGP----PRVSEETRERILEAAEEL 41 (46)
T ss_dssp TSSHHHHHHHHTTC----SSSTHHHHHHHHHHHHHH
T ss_pred CcCHHHHHHHHhCC----CCCCHHHHHHHHHHHHHH
Confidence 47789999999775 489999999999988764
No 97
>PRK07452 DNA polymerase III subunit delta; Validated
Probab=55.25 E-value=43 Score=29.10 Aligned_cols=53 Identities=15% Similarity=0.140 Sum_probs=41.8
Q ss_pred CcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHh--cCCCccCHHHHHHHHHHcCC
Q 036580 47 NAKISKDAKETVQECVSEFISFVTGEASDKCQR--EKRKTINGDDLLWAMTTLGF 99 (186)
Q Consensus 47 ~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~--~kRKTIt~eDVl~AL~~LgF 99 (186)
+..|+.+|...|.+++..=+..+..+-.+.+.- .++.+|+.+||...+....+
T Consensus 147 g~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~~It~~~V~~~v~~~~~ 201 (326)
T PRK07452 147 GVKLTPEAAELLAEAVGNDSRRLYNELEKLALYAENSTKPISAEEVKALVSNTTQ 201 (326)
T ss_pred CCCCCHHHHHHHHHHhCccHHHHHHHHHHHHHhccCCCCccCHHHHHHHhccCcC
Confidence 578999999999999987666777777776665 45788999999987765543
No 98
>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=55.20 E-value=25 Score=22.16 Aligned_cols=26 Identities=19% Similarity=0.220 Sum_probs=20.6
Q ss_pred HHHHHHhcCCCccCHHHHHHHHHHcC
Q 036580 73 ASDKCQREKRKTINGDDLLWAMTTLG 98 (186)
Q Consensus 73 A~~~a~~~kRKTIt~eDVl~AL~~Lg 98 (186)
|.+.|+..+...|+.+||+.||=...
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 55688899999999999999976543
No 99
>TIGR01128 holA DNA polymerase III, delta subunit. subunit around DNA forming a DNA sliding clamp.
Probab=53.55 E-value=90 Score=26.32 Aligned_cols=65 Identities=17% Similarity=0.132 Sum_probs=44.5
Q ss_pred CchhHHHHHHHhhCC-CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHH
Q 036580 31 LPIANVSRIMKKALP-ANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMT 95 (186)
Q Consensus 31 LPkA~V~RImK~alP-~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~ 95 (186)
+....+.+++++.+. .+..|+.++...|.+.+..=+..+..+-.+.|.-.+.++|+.+||...+.
T Consensus 111 ~~~~~~~~~i~~~~~~~g~~i~~~a~~~l~~~~~~d~~~l~~el~KL~~~~~~~~It~e~I~~~~~ 176 (302)
T TIGR01128 111 PKEQELPRWIQARLKKLGLRIDPDAVQLLAELVEGNLLAIAQELEKLALYAPDGKITLEDVEEAVS 176 (302)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCcHHHHHHHHHHHHHhhCCCCCCCHHHHHHHHh
Confidence 445556656655443 25689999999998888765555666666655544445799999987765
No 100
>CHL00081 chlI Mg-protoporyphyrin IX chelatase
Probab=51.49 E-value=64 Score=29.68 Aligned_cols=60 Identities=18% Similarity=0.268 Sum_probs=45.4
Q ss_pred hHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCccCHHHHHHHHH
Q 036580 34 ANVSRIMKKALPANAKISKDAKETVQECVSEFI-------SFVTGEASDKCQREKRKTINGDDLLWAMT 95 (186)
Q Consensus 34 A~V~RImK~alP~~~rISkDA~~ai~k~aeeFI-------~~Lts~A~~~a~~~kRKTIt~eDVl~AL~ 95 (186)
..|... ++.++ .+.|+++.+..|.+.|..+= .+|...|...|--++|..|+++||..+..
T Consensus 254 ~~I~~a-r~~~~-~V~v~~~~~~yi~~l~~~~~~~s~Ra~i~l~raArA~Aal~GR~~V~pdDv~~~a~ 320 (350)
T CHL00081 254 SKIVAA-QNLLP-KVEIDYDLRVKISQICSELDVDGLRGDIVTNRAAKALAAFEGRTEVTPKDIFKVIT 320 (350)
T ss_pred HHHHHH-HHhcC-CCccCHHHHHHHHHHHHHHCCCCChHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 344443 34444 57899999999988887753 35667777788899999999999998875
No 101
>COG1222 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]
Probab=50.82 E-value=26 Score=33.12 Aligned_cols=49 Identities=22% Similarity=0.323 Sum_probs=40.0
Q ss_pred cccCHHH-HHHHHHHHHHH----HHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 036580 48 AKISKDA-KETVQECVSEF----ISFVTGEASDKCQREKRKTINGDDLLWAMTT 96 (186)
Q Consensus 48 ~rISkDA-~~ai~k~aeeF----I~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~ 96 (186)
+.+++|. .+.|.++++.| |..|..+|--+|.++.|..|+.+|++.|.++
T Consensus 338 M~l~~dvd~e~la~~~~g~sGAdlkaictEAGm~AiR~~R~~Vt~~DF~~Av~K 391 (406)
T COG1222 338 MNLADDVDLELLARLTEGFSGADLKAICTEAGMFAIRERRDEVTMEDFLKAVEK 391 (406)
T ss_pred ccCccCcCHHHHHHhcCCCchHHHHHHHHHHhHHHHHhccCeecHHHHHHHHHH
Confidence 4555554 56677776666 7789999999999999999999999999875
No 102
>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=50.38 E-value=33 Score=23.50 Aligned_cols=29 Identities=21% Similarity=0.337 Sum_probs=23.6
Q ss_pred CCccCHHHHHHHHHHcCCccchHHHHHHH
Q 036580 82 RKTINGDDLLWAMTTLGFEEYVEPLKVYL 110 (186)
Q Consensus 82 RKTIt~eDVl~AL~~LgF~dyi~~Lk~~L 110 (186)
...-+..+++.||++++..+-++.++.+|
T Consensus 55 ~~~at~~~L~~aL~~~~~~d~~~~i~~~~ 83 (83)
T PF00531_consen 55 GPNATVDQLIQALRDIGRNDLAEKIEQML 83 (83)
T ss_dssp GSTSSHHHHHHHHHHTTHHHHHHHHHHH-
T ss_pred CCCCcHHHHHHHHHHCCcHHHHHHHHhhC
Confidence 44567889999999999998888887654
No 103
>PF09114 MotA_activ: Transcription factor MotA, activation domain; InterPro: IPR015198 Transcription factor MotA is required for the activation of middle promoters in Bacteriophage T4, in addition to phage T4 co-activator AsiA, and sigma-70-containing Escherichia coli RNA polymerase. Phage T4 middle promoters have the sigma70 -10 DNA element, but not the -35 element; instead, they have a MotA box at -30 to which the transcription factor MotA binds []. MotA and AsiA interact with the C-terminal of sigma70 (region 4), which normally binds the -35 element and the beta-flap, thereby diverting sigma70 away from host promoters that require -35 element-binding to phage T4 middle promoters. Transcription factor MotA has two domains: an N-terminal domain required for binding to sigma70, and a C-terminal domain required for binding to the -30 MotA box element in the phage T4 middle promoter. This entry represents the N-terminal (activation) domain of MotA factors that binds sigma70. The N-terminal domain adopts an almost completely alpha-helical topology, with five alpha-helices and a short, two-stranded, beta-ribbon. Four alpha helices (alpha1, alpha3, alpha4 and alpha5) are amphipathic and pack their hydrophobic surfaces around the central helix alpha2 [].; PDB: 1BJA_B 1I1S_A.
Probab=48.76 E-value=35 Score=26.24 Aligned_cols=34 Identities=15% Similarity=0.322 Sum_probs=27.2
Q ss_pred hHHHHHHHhhC----CCCcccCHHHHHHHHHHHHHHHH
Q 036580 34 ANVSRIMKKAL----PANAKISKDAKETVQECVSEFIS 67 (186)
Q Consensus 34 A~V~RImK~al----P~~~rISkDA~~ai~k~aeeFI~ 67 (186)
++|-+|+|..+ .|...++.++.+.|+++++.|-.
T Consensus 51 SNIGvLIKkglIEKSGDGlv~T~~g~~Ii~~AA~l~a~ 88 (96)
T PF09114_consen 51 SNIGVLIKKGLIEKSGDGLVITEEGMDIIIQAAELWAQ 88 (96)
T ss_dssp HHHHHHHHTTSEEEETTEEEE-HHHHHHHHHHHHHHHH
T ss_pred HhHHHHHHcCcccccCCceEEechHHHHHHHHHHHHHh
Confidence 45777999887 35678999999999999999953
No 104
>PRK13407 bchI magnesium chelatase subunit I; Provisional
Probab=47.82 E-value=71 Score=29.04 Aligned_cols=59 Identities=10% Similarity=0.037 Sum_probs=43.8
Q ss_pred hHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCccCHHHHHHHH
Q 036580 34 ANVSRIMKKALPANAKISKDAKETVQECVSEFI-------SFVTGEASDKCQREKRKTINGDDLLWAM 94 (186)
Q Consensus 34 A~V~RImK~alP~~~rISkDA~~ai~k~aeeFI-------~~Lts~A~~~a~~~kRKTIt~eDVl~AL 94 (186)
..|..+ ++.++ .+.|+++....|.+.|..+= .+|...|...|-.++|..|+++||..+.
T Consensus 238 ~~i~~a-~~~~~-~V~v~~~~~~yi~~l~~~~~~~s~Ra~i~l~~aA~a~A~l~Gr~~V~~~Di~~~~ 303 (334)
T PRK13407 238 GRILGA-RARLP-QLKTPNTVLHDCAALCIALGSDGLRGELTLLRAARALAAFEGAEAVGRSHLRSVA 303 (334)
T ss_pred HHHHHH-HHhcC-CcccCHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHHcCCCeeCHHHHHHHH
Confidence 344444 33344 57899999999988887653 2377778888999999999999997655
No 105
>PRK14975 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Probab=47.76 E-value=1.5e+02 Score=28.54 Aligned_cols=93 Identities=17% Similarity=0.115 Sum_probs=61.5
Q ss_pred cccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHH----------HHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 036580 27 QDRFLPIANVSRIMKKALPANAKISKDAKETVQECVS----------EFISFVTGEASDKCQREKRKTINGDDLLWAMTT 96 (186)
Q Consensus 27 ~d~~LPkA~V~RImK~alP~~~rISkDA~~ai~k~ae----------eFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~ 96 (186)
.++.+|.+.|---|... .+.|..+....+...+. .-+..|..+..+.+...-=.-=++++|..+|++
T Consensus 160 ~~~E~~~~~~l~~me~~---Gi~~D~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~~~g~~~~n~~S~~ql~~~L~~ 236 (553)
T PRK14975 160 AAAESAGALAAAEMELA---GLPWDTDVHEALLAELLGPRPAAGGRPARLAELAAEIREALGRPRLNPDSPQQVLRALRR 236 (553)
T ss_pred HHHHhhHHHHHHHHHHh---CeEeCHHHHHHHHHHHhcccccccchHHHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHH
Confidence 34467777777777766 47888888777776666 666777777666542211133478999999998
Q ss_pred cCCc----------cchHHHHHHHHHHHHHHHhhhh
Q 036580 97 LGFE----------EYVEPLKVYLQRFREMEGEKMA 122 (186)
Q Consensus 97 LgF~----------dyi~~Lk~~L~~~re~~~~K~~ 122 (186)
+|+. .-..|+-..+-+||+..+...+
T Consensus 237 ~g~~~~~t~~~~L~~~~hp~~~~ile~r~~~kl~st 272 (553)
T PRK14975 237 AGIELPSTRKWELREIDHPAVEPLLEYRKLSKLLSA 272 (553)
T ss_pred CCCCCCCCcHHHhccCCCchHHHHHHHHHHHHHHHH
Confidence 8884 1122455677788887765543
No 106
>COG5624 TAF61 Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=47.55 E-value=16 Score=35.09 Aligned_cols=76 Identities=13% Similarity=0.180 Sum_probs=62.4
Q ss_pred CCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH---cCCccchHH
Q 036580 30 FLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMTT---LGFEEYVEP 105 (186)
Q Consensus 30 ~LPkA~V~RImK~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~---LgF~dyi~~ 105 (186)
.+-+-.+.-+.+..+....+|-.|.-+++-..+..|+.-++.-+..+++|.+-+||-..||-.-|++ +=++.|+..
T Consensus 383 l~skrkL~el~~~~vd~eekie~eveelll~~ad~fve~vt~FsCrlakhrkSdtlevrD~qlhlErnwnIr~pGf~~d 461 (505)
T COG5624 383 LDSKRKLEELQHGGVDEEEKIENEVEELLLSRADGFVEPVTEFSCRLAKHRKSDTLEVRDGQLHLERNWNIRCPGFVDD 461 (505)
T ss_pred hhhhhhHHHHHhhccCcceeccchHHHHHHhhhcccccccchheeEeeccCCCCceeeccceeeeccccceecCcchHH
Confidence 4566666777777776778999999999999999999999999999999999999999999877774 333455443
No 107
>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=47.39 E-value=77 Score=30.89 Aligned_cols=54 Identities=19% Similarity=0.271 Sum_probs=39.2
Q ss_pred HhhCCCCcccCHHHHHHHHHHHHHH-------HHHHHHHHHHHHHhcCCCccCHHHHHHHHH
Q 036580 41 KKALPANAKISKDAKETVQECVSEF-------ISFVTGEASDKCQREKRKTINGDDLLWAMT 95 (186)
Q Consensus 41 K~alP~~~rISkDA~~ai~k~aeeF-------I~~Lts~A~~~a~~~kRKTIt~eDVl~AL~ 95 (186)
++.++ .+.|+.+....|.+.|-.+ -.++...|...|.-++|.+|+.+||..|+.
T Consensus 196 r~~~~-~V~i~~~~~~~l~~~~~~~gv~s~Ra~i~~~r~ArA~Aal~gr~~V~~~Dv~~a~~ 256 (589)
T TIGR02031 196 RELLP-QVTISAEQVKELVLTAASLGISGHRADLFAVRAAKAHAALHGRTEVTEEDLKLAVE 256 (589)
T ss_pred HHhcC-CccCCHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHH
Confidence 33444 5789999887776666433 224556666788889999999999999885
No 108
>PRK13765 ATP-dependent protease Lon; Provisional
Probab=46.93 E-value=61 Score=32.19 Aligned_cols=48 Identities=17% Similarity=0.140 Sum_probs=38.7
Q ss_pred ccCHHHHHHHHHHHHH-------------HHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 036580 49 KISKDAKETVQECVSE-------------FISFVTGEASDKCQREKRKTINGDDLLWAMTT 96 (186)
Q Consensus 49 rISkDA~~ai~k~aee-------------FI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~ 96 (186)
.|+++|+..|-+-.+. =|..|..+|..+|+.++++.|+.+||..|+..
T Consensus 339 ~f~~eAVa~LI~~~~R~ag~r~~lsl~~~~l~~l~r~a~~~a~~~~~~~i~~~~v~~a~~~ 399 (637)
T PRK13765 339 HFDRDAVEEIIREAKRRAGRKGHLTLKLRDLGGLVRVAGDIARSEGAELTTAEHVLEAKKI 399 (637)
T ss_pred CCCHHHHHHHHHHHHHHhCCccccccCHHHHHHHHHHHHHHHHhhccceecHHHHHHHHHh
Confidence 6899888777765542 34458888999999999999999999999843
No 109
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=46.29 E-value=40 Score=32.00 Aligned_cols=79 Identities=11% Similarity=0.262 Sum_probs=53.8
Q ss_pred cccCCchhHHHHHHHhhC---CC---------CcccCHH-----HHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHH
Q 036580 27 QDRFLPIANVSRIMKKAL---PA---------NAKISKD-----AKETVQECVSEFISFVTGEASDKCQREKRKTINGDD 89 (186)
Q Consensus 27 ~d~~LPkA~V~RImK~al---P~---------~~rISkD-----A~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eD 89 (186)
+++.|-.+||.|+++..- |- ...++.+ +.+.|.+....+ +...++++-++-+.
T Consensus 351 e~lglheSTVSRav~~Kyv~tp~Gi~~lk~FFs~~~~~~~g~~~S~~~Ik~~Ik~l----------I~~Ed~~~PlSD~~ 420 (455)
T PRK05932 351 EELGMHESTISRATTNKYMATPRGIFELKYFFSSAVSTDGGGEASSTAIRALIKKL----------IAAENPKKPLSDSK 420 (455)
T ss_pred HHhCCCccchhhhhcCceeecCCceEEHHHhcccccCCCCCccccHHHHHHHHHHH----------HHhcCCCCCCCHHH
Confidence 455789999999997653 21 0111111 223333333333 46678899999999
Q ss_pred HHHHHHHcCCccchHHHHHHHHHHHHHHHh
Q 036580 90 LLWAMTTLGFEEYVEPLKVYLQRFREMEGE 119 (186)
Q Consensus 90 Vl~AL~~LgF~dyi~~Lk~~L~~~re~~~~ 119 (186)
|...|+.-|+. ..+..+.+||+..+=
T Consensus 421 I~~~L~~~Gi~----IaRRTVaKYRe~L~I 446 (455)
T PRK05932 421 IAELLKEQGID----VARRTVAKYREALNI 446 (455)
T ss_pred HHHHHHHcCCC----eehHHHHHHHHHcCC
Confidence 99999998885 678999999997653
No 110
>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional
Probab=45.28 E-value=32 Score=32.48 Aligned_cols=31 Identities=26% Similarity=0.230 Sum_probs=27.8
Q ss_pred HHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 036580 66 ISFVTGEASDKCQREKRKTINGDDLLWAMTT 96 (186)
Q Consensus 66 I~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~ 96 (186)
|..|..+|...|.+.+|..|+.+||..|+++
T Consensus 393 I~~i~~eA~~~Alr~~r~~Vt~~D~~~A~~~ 423 (438)
T PTZ00361 393 IKAICTEAGLLALRERRMKVTQADFRKAKEK 423 (438)
T ss_pred HHHHHHHHHHHHHHhcCCccCHHHHHHHHHH
Confidence 6678888999999999999999999999876
No 111
>KOG1528 consensus Salt-sensitive 3'-phosphoadenosine-5'-phosphatase HAL2/SAL1 [Nucleotide transport and metabolism; Inorganic ion transport and metabolism]
Probab=43.61 E-value=67 Score=29.80 Aligned_cols=76 Identities=14% Similarity=0.198 Sum_probs=51.2
Q ss_pred CCCCCcccccCCchhHHHHHHHhhCCCCc--ccCHHHHHHHHHH-HHHHHHHHHHHHHH-HHHh--cCC-CccCHHHHHH
Q 036580 20 RELSPREQDRFLPIANVSRIMKKALPANA--KISKDAKETVQEC-VSEFISFVTGEASD-KCQR--EKR-KTINGDDLLW 92 (186)
Q Consensus 20 ~e~~~re~d~~LPkA~V~RImK~alP~~~--rISkDA~~ai~k~-aeeFI~~Lts~A~~-~a~~--~kR-KTIt~eDVl~ 92 (186)
+..++..-|+ =-.|.|.-.+++.+|+.- -|..|--.-|.+. ++.|+..|+..-++ ++.. =+- ++++.+||+.
T Consensus 40 D~SPVTvaDy-G~QAiVs~vL~~~f~~~p~slVaEEds~~Lr~n~~~~~l~~i~~lvnetl~s~~sy~~~~~ls~~dvl~ 118 (351)
T KOG1528|consen 40 DKSPVTVADY-GSQAIVSLVLEREFPDDPLSLVAEEDSGFLRKNGSEGLLSRITKLVNETLASDESYGDNSPLSSDDVLK 118 (351)
T ss_pred CCCCcchhhh-hHHHHHHHHHHHHcCCCCcceEeeccchhhhhhhhHHHHHHHHHHHHHHhhhhhhccCCCCCCHHHHHH
Confidence 4455555554 346788888999998655 5777666666665 67788888774444 2222 223 7899999999
Q ss_pred HHHH
Q 036580 93 AMTT 96 (186)
Q Consensus 93 AL~~ 96 (186)
|+..
T Consensus 119 aID~ 122 (351)
T KOG1528|consen 119 AIDR 122 (351)
T ss_pred HHhc
Confidence 9975
No 112
>PRK03992 proteasome-activating nucleotidase; Provisional
Probab=43.21 E-value=39 Score=30.89 Aligned_cols=34 Identities=21% Similarity=0.253 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHc
Q 036580 64 EFISFVTGEASDKCQREKRKTINGDDLLWAMTTL 97 (186)
Q Consensus 64 eFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~L 97 (186)
.=|..|..+|...|.+++++.|+.+|+..|++.+
T Consensus 339 adl~~l~~eA~~~a~~~~~~~i~~~d~~~A~~~~ 372 (389)
T PRK03992 339 ADLKAICTEAGMFAIRDDRTEVTMEDFLKAIEKV 372 (389)
T ss_pred HHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHH
Confidence 3466778888888888899999999999999764
No 113
>PRK06585 holA DNA polymerase III subunit delta; Reviewed
Probab=43.03 E-value=75 Score=27.86 Aligned_cols=49 Identities=14% Similarity=0.062 Sum_probs=36.4
Q ss_pred CcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHh-cCCCccCHHHHHHHHH
Q 036580 47 NAKISKDAKETVQECVSEFISFVTGEASDKCQR-EKRKTINGDDLLWAMT 95 (186)
Q Consensus 47 ~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~-~kRKTIt~eDVl~AL~ 95 (186)
..+|+.+|...|.+++..=+..+..+-.+.+.- ...++|+.+||...+.
T Consensus 159 g~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~It~edV~~lv~ 208 (343)
T PRK06585 159 GLRITPDARALLVALLGGDRLASRNEIEKLALYAHGKGEITLDDVRAVVG 208 (343)
T ss_pred CCCCCHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHhC
Confidence 578999999999999886555555655555553 3456899999987654
No 114
>PRK12728 fliE flagellar hook-basal body protein FliE; Provisional
Probab=42.87 E-value=1.5e+02 Score=22.65 Aligned_cols=64 Identities=11% Similarity=0.183 Sum_probs=40.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH--HHhcCCCccCHHHHHHHHHH--cCCccchHHHHHHHHHHHHHHH
Q 036580 53 DAKETVQECVSEFISFVTGEASDK--CQREKRKTINGDDLLWAMTT--LGFEEYVEPLKVYLQRFREMEG 118 (186)
Q Consensus 53 DA~~ai~k~aeeFI~~Lts~A~~~--a~~~kRKTIt~eDVl~AL~~--LgF~dyi~~Lk~~L~~~re~~~ 118 (186)
...+.|.+++.. +..+-.+|.+. +-..|. ++...||+-|+++ +-|.-.+.--.+.++.|+|+.+
T Consensus 32 sF~~~L~~ai~~-vn~~q~~a~~~~~~~~~G~-~~~lhevmiA~~kA~lslq~~vqVRNKlv~AYqEIMr 99 (102)
T PRK12728 32 SFSDFLKEALNK-VNELQVEADNSTEKLVKGE-IVDLHDVMIAAQKASISLQLTVQIRNKVVEAYQEIMR 99 (102)
T ss_pred CHHHHHHHHHHH-HHHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 455566666555 33333333332 223344 7899999999996 4555556666788999999754
No 115
>TIGR01242 26Sp45 26S proteasome subunit P45 family. Many proteins may score above the trusted cutoff because an internal
Probab=42.63 E-value=39 Score=30.17 Aligned_cols=32 Identities=25% Similarity=0.251 Sum_probs=27.7
Q ss_pred HHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 036580 65 FISFVTGEASDKCQREKRKTINGDDLLWAMTT 96 (186)
Q Consensus 65 FI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~ 96 (186)
-|..|..+|...|.+.++..|+.+|+..|++.
T Consensus 331 dl~~l~~~A~~~a~~~~~~~i~~~d~~~a~~~ 362 (364)
T TIGR01242 331 DLKAICTEAGMFAIREERDYVTMDDFIKAVEK 362 (364)
T ss_pred HHHHHHHHHHHHHHHhCCCccCHHHHHHHHHH
Confidence 45577888888888999999999999999976
No 116
>PRK05574 holA DNA polymerase III subunit delta; Reviewed
Probab=42.24 E-value=1e+02 Score=26.51 Aligned_cols=66 Identities=15% Similarity=0.077 Sum_probs=44.4
Q ss_pred CchhHHHHHHHhhCC-CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 036580 31 LPIANVSRIMKKALP-ANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMTT 96 (186)
Q Consensus 31 LPkA~V~RImK~alP-~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~ 96 (186)
++...+.+.++..+. ....|+.+|...|.+.+..=+..+..+....+.-.+-+.|+.+||...+..
T Consensus 146 ~~~~~~~~~i~~~~~~~g~~i~~~a~~~L~~~~~~d~~~l~~El~KL~l~~~~~~It~~~I~~~i~~ 212 (340)
T PRK05574 146 PKEAELPQWIQQRLKQQGLQIDAAALQLLAERVEGNLLALAQELEKLALLYPDGKITLEDVEEAVPD 212 (340)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCchHHHHHHHHHHHHhhcCCCCCCHHHHHHHHhh
Confidence 455555555554442 356899999999999987766667777767665332223999999876653
No 117
>PF08823 PG_binding_2: Putative peptidoglycan binding domain; InterPro: IPR014927 This entry may be a peptidoglycan binding domain.
Probab=41.20 E-value=56 Score=23.59 Aligned_cols=32 Identities=19% Similarity=0.240 Sum_probs=26.6
Q ss_pred HHHHHHHHHcCC------ccchHHHHHHHHHHHHHHHh
Q 036580 88 DDLLWAMTTLGF------EEYVEPLKVYLQRFREMEGE 119 (186)
Q Consensus 88 eDVl~AL~~LgF------~dyi~~Lk~~L~~~re~~~~ 119 (186)
+.|..+|.+||| ..+-+.++..|..|..+++=
T Consensus 19 ~evq~~L~~lGyy~g~~~g~~d~a~~~Al~~~~g~ENf 56 (74)
T PF08823_consen 19 REVQEALKRLGYYKGEADGVWDEATEDALRAWAGTENF 56 (74)
T ss_pred HHHHHHHHHcCCccCCCCCcccHHHHHHHHHHHHHhhH
Confidence 467788999999 57888999999999987664
No 118
>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional
Probab=40.14 E-value=43 Score=31.07 Aligned_cols=31 Identities=26% Similarity=0.226 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 036580 66 ISFVTGEASDKCQREKRKTINGDDLLWAMTT 96 (186)
Q Consensus 66 I~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~ 96 (186)
|..|..+|...|.+++|..|+.+|+..|+++
T Consensus 355 I~~l~~eA~~~A~r~~~~~i~~~df~~A~~~ 385 (398)
T PTZ00454 355 IAAICQEAGMQAVRKNRYVILPKDFEKGYKT 385 (398)
T ss_pred HHHHHHHHHHHHHHcCCCccCHHHHHHHHHH
Confidence 7788889999999999999999999999876
No 119
>PTZ00183 centrin; Provisional
Probab=39.94 E-value=1.3e+02 Score=22.43 Aligned_cols=21 Identities=19% Similarity=0.284 Sum_probs=11.3
Q ss_pred HHHhcCCCccCHHHHHHHHHH
Q 036580 76 KCQREKRKTINGDDLLWAMTT 96 (186)
Q Consensus 76 ~a~~~kRKTIt~eDVl~AL~~ 96 (186)
.+..++..+|+.++++.++..
T Consensus 61 ~~d~~~~g~i~~~eF~~~~~~ 81 (158)
T PTZ00183 61 DVDKDGSGKIDFEEFLDIMTK 81 (158)
T ss_pred HhCCCCCCcEeHHHHHHHHHH
Confidence 334445555666666655543
No 120
>PRK07914 hypothetical protein; Reviewed
Probab=39.36 E-value=85 Score=27.56 Aligned_cols=62 Identities=10% Similarity=0.144 Sum_probs=40.8
Q ss_pred hhHHHHHHHhhCC-CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHH
Q 036580 33 IANVSRIMKKALP-ANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMT 95 (186)
Q Consensus 33 kA~V~RImK~alP-~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~ 95 (186)
-..+.+.|++.+- ....|+.+|...|.+++..=+..|..+-.+.+-..+ .+|+.+||...+.
T Consensus 130 ~~~l~~wi~~~a~~~g~~i~~~A~~~L~~~~g~dl~~l~~EleKL~~~~~-~~It~e~V~~~v~ 192 (320)
T PRK07914 130 AAERADFVRKEFRSLRVKVDDDTVTALLDAVGSDLRELASACSQLVADTG-GAVDAAAVRRYHS 192 (320)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHCccHHHHHHHHHHHhcCCC-CCcCHHHHHHHcC
Confidence 3443444433332 256899999999999997666666666555554333 5799999987655
No 121
>PF12627 PolyA_pol_RNAbd: Probable RNA and SrmB- binding site of polymerase A; PDB: 1OU5_B 3H38_A 3H3A_B 3H39_B 3H37_A 3AQN_A 3AQK_A 3AQM_B 3AQL_B 1MIY_A ....
Probab=38.71 E-value=19 Score=24.02 Aligned_cols=57 Identities=25% Similarity=0.380 Sum_probs=28.9
Q ss_pred cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcc---CHHHHHHHHHHcCCccch-HHHHH
Q 036580 48 AKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTI---NGDDLLWAMTTLGFEEYV-EPLKV 108 (186)
Q Consensus 48 ~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTI---t~eDVl~AL~~LgF~dyi-~~Lk~ 108 (186)
.+|.+++..+|.+++. .+..|+.+-.. .+=.|.+ .+...+..|.++|+.+++ +.+..
T Consensus 2 F~ie~~t~~ai~~~~~-~L~~is~ERi~---~El~kil~~~~~~~~~~~l~~~gll~~ifP~l~~ 62 (64)
T PF12627_consen 2 FKIEPETEEAIKENAE-LLSKISKERIR---EELEKILSSPNPSRAFKLLDELGLLEYIFPELDA 62 (64)
T ss_dssp -EE-HHHHHHHHHHGG-GGGGS-HHHHH---HHHHHHHTSTTHHHHHHHHHHTTCHHHHSTTHHT
T ss_pred CccCHHHHHHHHHHHH-HHhcCCHHHHH---HHHHHHHcCCCHHHHHHHHHHcCCHHHHCccccc
Confidence 3566777777777666 44444433211 1111111 456667777788877664 44443
No 122
>PRK14700 recombination factor protein RarA; Provisional
Probab=37.87 E-value=1.3e+02 Score=27.51 Aligned_cols=66 Identities=14% Similarity=0.162 Sum_probs=44.0
Q ss_pred CCchhHHHHHHHhhCCC-------CcccCHHHHHHHHHHH----HHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 036580 30 FLPIANVSRIMKKALPA-------NAKISKDAKETVQECV----SEFISFVTGEASDKCQREKRKTINGDDLLWAMTT 96 (186)
Q Consensus 30 ~LPkA~V~RImK~alP~-------~~rISkDA~~ai~k~a----eeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~ 96 (186)
.|....|.+|+++++.+ ...|++|++..|.+.| ..++..| ..|...+.......|+.++|..++..
T Consensus 38 ~L~~~di~~il~ral~~~~~~~~~~~~i~~~al~~ia~~a~GDaR~aLN~L-E~a~~~~~~~~~~~it~~~~~~~~~~ 114 (300)
T PRK14700 38 RLSLVATQKLIEKALSQDEVLAKHKFKIDDGLYNAMHNYNEGDCRKILNLL-ERMFLISTRGDEIYLNKELFDQAVGE 114 (300)
T ss_pred CCCHHHHHHHHHHHHHhhhccCCcCCCcCHHHHHHHHHhcCCHHHHHHHHH-HHHHhhccccCCCccCHHHHHHHHhH
Confidence 47778888999888853 2579999999999876 3344333 22333232333345899999888864
No 123
>PF12010 DUF3502: Domain of unknown function (DUF3502); InterPro: IPR022627 This domain is about 140 amino acids in length and is functionally uncharacterised. It is found in bacteria C-terminal to PF01547 from PFAM.
Probab=37.34 E-value=33 Score=26.85 Aligned_cols=61 Identities=10% Similarity=0.170 Sum_probs=38.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHcCCccchHHHHHHHHHHHHH
Q 036580 52 KDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMTTLGFEEYVEPLKVYLQRFREM 116 (186)
Q Consensus 52 kDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~LgF~dyi~~Lk~~L~~~re~ 116 (186)
...+..|..|..+.-.|......=.. ----...++...|+..|++..+.+++..|++|++.
T Consensus 72 s~Vk~Eiaa~~~v~~~Y~~~L~~G~v----d~e~~~~~~~~kLk~AGidkV~~E~QkQlda~~~~ 132 (134)
T PF12010_consen 72 SPVKNEIAACSNVWSEYYPPLETGLV----DPEEALPEFNEKLKAAGIDKVIAELQKQLDAFLAA 132 (134)
T ss_pred chhHHHHHHHHHHHHHHHHHHHccCC----CHHHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHh
Confidence 34455666666665555444321111 01113456677888899999999999999999864
No 124
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=37.22 E-value=56 Score=22.50 Aligned_cols=32 Identities=25% Similarity=0.444 Sum_probs=24.2
Q ss_pred CCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHH
Q 036580 30 FLPIANVSRIMKKALPANAKISKDAKETVQECVSEF 65 (186)
Q Consensus 30 ~LPkA~V~RImK~alP~~~rISkDA~~ai~k~aeeF 65 (186)
.+.+++|.|++... ..|+.+.++.|.+++.++
T Consensus 11 gvS~~TVSr~ln~~----~~v~~~t~~~i~~~~~~~ 42 (70)
T smart00354 11 GVSKATVSRVLNGN----GRVSEETREKVLAAMEEL 42 (70)
T ss_pred CCCHHHHHHHHCCC----CCCCHHHHHHHHHHHHHh
Confidence 47788888887543 467888888888888776
No 125
>PF11753 DUF3310: Protein of unknwon function (DUF3310); InterPro: IPR021739 This entry is represented by Bacteriophage T7, Gp1.7. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=37.18 E-value=1.1e+02 Score=20.98 Aligned_cols=41 Identities=24% Similarity=0.272 Sum_probs=32.4
Q ss_pred HHHHHHHHH--HHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHH
Q 036580 53 DAKETVQEC--VSEFISFVTGEASDKCQREKRKTINGDDLLWAMT 95 (186)
Q Consensus 53 DA~~ai~k~--aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~ 95 (186)
|+.+.+ +. .+.|+.+....|.+++-+.++|. ..+|+.+|..
T Consensus 14 e~id~~-~~~~~~~~~~f~~gnaiKY~~R~~~K~-~~eDl~KA~~ 56 (60)
T PF11753_consen 14 ECIDFI-EQFTEEQFLGFCLGNAIKYLWRAGKKN-GIEDLKKAKW 56 (60)
T ss_pred cHHHHH-HHhcchhhhhHHHHHHHHHHHHHcccC-cHHHHHHHHH
Confidence 445555 44 45899999999999999999995 4899998874
No 126
>PLN00155 histone H2A; Provisional
Probab=36.99 E-value=32 Score=24.23 Aligned_cols=36 Identities=17% Similarity=0.274 Sum_probs=28.0
Q ss_pred cccCCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHH
Q 036580 27 QDRFLPIANVSRIMKKALPANAKISKDAKETVQECVS 63 (186)
Q Consensus 27 ~d~~LPkA~V~RImK~alP~~~rISkDA~~ai~k~ae 63 (186)
..+.||..+|.|++|+.-. ..||+.-|..-+.-..|
T Consensus 21 AgL~FPVgri~r~Lr~g~~-a~Rvga~apVYlAAVLE 56 (58)
T PLN00155 21 AGLQFPVGRIARYLKKGKY-AERIGAGAPVYLAAVLE 56 (58)
T ss_pred cccccchHHHHHHHhcCCh-hhcccCCcHHHHHHHHH
Confidence 4678999999999999764 45898888777665543
No 127
>PF13405 EF-hand_6: EF-hand domain; PDB: 2AMI_A 3QRX_A 1W7J_B 1OE9_B 1W7I_B 1KFU_S 1KFX_S 2BL0_B 1Y1X_B 3MSE_B ....
Probab=36.60 E-value=50 Score=19.00 Aligned_cols=27 Identities=22% Similarity=0.268 Sum_probs=20.6
Q ss_pred HHHHHHHhcCCCccCHHHHHHHHH-HcC
Q 036580 72 EASDKCQREKRKTINGDDLLWAMT-TLG 98 (186)
Q Consensus 72 ~A~~~a~~~kRKTIt~eDVl~AL~-~Lg 98 (186)
.+......++.-+|+.+++..+|+ .||
T Consensus 4 ~~F~~~D~d~dG~I~~~el~~~l~~~lG 31 (31)
T PF13405_consen 4 EAFKMFDKDGDGFIDFEELRAILRKSLG 31 (31)
T ss_dssp HHHHHH-TTSSSEEEHHHHHHHHHHHTT
T ss_pred HHHHHHCCCCCCcCcHHHHHHHHHHhcC
Confidence 345566777888999999999998 465
No 128
>COG1466 HolA DNA polymerase III, delta subunit [DNA replication, recombination, and repair]
Probab=35.95 E-value=1.2e+02 Score=26.89 Aligned_cols=50 Identities=16% Similarity=0.143 Sum_probs=40.5
Q ss_pred CcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 036580 47 NAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMTT 96 (186)
Q Consensus 47 ~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~ 96 (186)
..+|++||.+.|..+.+-=+..+..+-...+--..-++|+.+||..++..
T Consensus 157 ~l~i~~~a~~~L~~~~~~nl~~i~~Ei~KL~l~~~~~~I~~~~V~~~v~~ 206 (334)
T COG1466 157 GLKIDQEAIQLLLEALGGNLLAIAQEIEKLALYAGDKEITLEDVEEVVSD 206 (334)
T ss_pred CCCCCHHHHHHHHHHhCCcHHHHHHHHHHHHHhCCCCcCCHHHHHHHHhc
Confidence 57999999999999999777777777777666545449999999988764
No 129
>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., PubMed:15231786). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations
Probab=35.80 E-value=1e+02 Score=28.98 Aligned_cols=79 Identities=15% Similarity=0.299 Sum_probs=53.3
Q ss_pred cccCCchhHHHHHHHhhC---CC---------CcccCH-H-----HHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHH
Q 036580 27 QDRFLPIANVSRIMKKAL---PA---------NAKISK-D-----AKETVQECVSEFISFVTGEASDKCQREKRKTINGD 88 (186)
Q Consensus 27 ~d~~LPkA~V~RImK~al---P~---------~~rISk-D-----A~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~e 88 (186)
+++.|-.+||.|+++..- |- ...++. + +.+.|.+...+. +...+++|-++-+
T Consensus 326 ~~lglheSTVSRav~~Kyi~tp~Gi~~lk~FFs~~~~~~~~g~~~S~~~Ik~~I~~l----------I~~E~~~~PlSD~ 395 (429)
T TIGR02395 326 EELGLHESTISRAINNKYLQTPRGVFELKYFFSRGVQTDSGEGEVSSTAIKALIKEL----------IAAEDKRKPLSDQ 395 (429)
T ss_pred HHhCCCccchhhhhcCceEecCCceEEHHHhcCCccCCCCCCCccCHHHHHHHHHHH----------HHhcCCCCCCCHH
Confidence 455789999999997653 21 011111 0 223333333333 4667889999999
Q ss_pred HHHHHHHHcCCccchHHHHHHHHHHHHHHHh
Q 036580 89 DLLWAMTTLGFEEYVEPLKVYLQRFREMEGE 119 (186)
Q Consensus 89 DVl~AL~~LgF~dyi~~Lk~~L~~~re~~~~ 119 (186)
.|...|+.-|+. ..+..+.+||+..+=
T Consensus 396 ~I~~~L~~~Gi~----IaRRTVaKYRe~L~I 422 (429)
T TIGR02395 396 KIAELLKEKGIK----IARRTVAKYREELGI 422 (429)
T ss_pred HHHHHHHhcCCC----eehHHHHHHHHHcCC
Confidence 999999998864 678999999987653
No 130
>PF07647 SAM_2: SAM domain (Sterile alpha motif); InterPro: IPR011510 The sterile alpha motif (SAM) domain is a putative protein interaction module present in a wide variety of proteins [] involved in many biological processes. The SAM domain that spreads over around 70 residues is found in diverse eukaryotic organisms []. SAM domains have been shown to homo- and hetero-oligomerise, forming multiple self-association architectures and also binding to various non-SAM domain-containing proteins [], nevertheless with a low affinity constant []. SAM domains also appear to possess the ability to bind RNA []. Smaug, a protein that helps to establish a morphogen gradient in Drosophila embryos by repressing the translation of nanos (nos) mRNA, binds to the 3' untranslated region (UTR) of nos mRNA via two similar hairpin structures. The 3D crystal structure of the Smaug RNA-binding region shows a cluster of positively charged residues on the Smaug-SAM domain, which could be the RNA-binding surface. This electropositive potential is unique among all previously determined SAM-domain structures and is conserved among Smaug-SAM homologs. These results suggest that the SAM domain might have a primary role in RNA binding. Structural analyses show that the SAM domain is arranged in a small five-helix bundle with two large interfaces []. In the case of the SAM domain of EphB2, each of these interfaces is able to form dimers. The presence of these two distinct intermonomers binding surface suggest that SAM could form extended polymeric structures []. This entry represents a second domain related to the SAM domain. ; GO: 0005515 protein binding; PDB: 1B0X_A 1X9X_B 1OW5_A 1V38_A 3BS7_A 3BS5_A 3TAD_A 3TAC_B 2K60_A 2DL0_A ....
Probab=35.66 E-value=56 Score=21.65 Aligned_cols=25 Identities=24% Similarity=0.466 Sum_probs=20.6
Q ss_pred ccCHHHHHHHHHHcCCccchHHHHH
Q 036580 84 TINGDDLLWAMTTLGFEEYVEPLKV 108 (186)
Q Consensus 84 TIt~eDVl~AL~~LgF~dyi~~Lk~ 108 (186)
+=+.+||..-|+.+||.+|.+..+.
T Consensus 3 ~w~~~~v~~WL~~~gl~~y~~~f~~ 27 (66)
T PF07647_consen 3 TWSPEDVAEWLKSLGLEQYADNFRE 27 (66)
T ss_dssp GHCHHHHHHHHHHTTCGGGHHHHHH
T ss_pred CCCHHHHHHHHHHCCcHHHHHHHHH
Confidence 3468899999999999999887654
No 131
>PRK09526 lacI lac repressor; Reviewed
Probab=34.79 E-value=37 Score=28.85 Aligned_cols=37 Identities=24% Similarity=0.507 Sum_probs=28.9
Q ss_pred CCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHH
Q 036580 30 FLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTG 71 (186)
Q Consensus 30 ~LPkA~V~RImK~alP~~~rISkDA~~ai~k~aeeFI~~Lts 71 (186)
..-++||.|++... .+||++.++-|.+++++ +.|.-.
T Consensus 16 GVS~~TVSrvLn~~----~~vs~~tr~rV~~~a~e-lgY~pn 52 (342)
T PRK09526 16 GVSYQTVSRVLNQA----SHVSAKTREKVEAAMAE-LNYVPN 52 (342)
T ss_pred CCCHHHHHHHhcCC----CCCCHHHHHHHHHHHHH-HCCCcC
Confidence 46788999998653 47999999999999988 445433
No 132
>cd00166 SAM Sterile alpha motif.; Widespread domain in signalling and nuclear proteins. In EPH-related tyrosine kinases, appears to mediate cell-cell initiated signal transduction via the binding of SH2-containing proteins to a conserved tyrosine that is phosphorylated. In many cases mediates homodimerization.
Probab=34.15 E-value=41 Score=21.53 Aligned_cols=24 Identities=17% Similarity=0.393 Sum_probs=20.2
Q ss_pred CHHHHHHHHHHcCCccchHHHHHH
Q 036580 86 NGDDLLWAMTTLGFEEYVEPLKVY 109 (186)
Q Consensus 86 t~eDVl~AL~~LgF~dyi~~Lk~~ 109 (186)
+.++|..-|+.+++++|++.++..
T Consensus 3 ~~~~V~~wL~~~~~~~y~~~f~~~ 26 (63)
T cd00166 3 SPEDVAEWLESLGLGQYADNFREN 26 (63)
T ss_pred CHHHHHHHHHHcChHHHHHHHHHc
Confidence 678999999999999888887653
No 133
>TIGR01052 top6b DNA topoisomerase VI, B subunit. This model describes DNA topoisomerase VI, an archaeal type II DNA topoisomerase (DNA gyrase).
Probab=33.23 E-value=49 Score=31.92 Aligned_cols=44 Identities=16% Similarity=0.298 Sum_probs=32.8
Q ss_pred HhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCc
Q 036580 41 KKALPANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKT 84 (186)
Q Consensus 41 K~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKT 84 (186)
|+++.+.--|-+|.+.+|++||...=.||...-...-+..++++
T Consensus 426 Ke~ia~~~ei~~ei~~al~~~~r~L~~~l~~~~~~~~~~~r~~~ 469 (488)
T TIGR01052 426 KQSVADIPEIYNEIRLALMEVARRLRLYLSRKAREEEEIKRRKT 469 (488)
T ss_pred hhhhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45554555788999999999999999999987666555544444
No 134
>PRK05907 hypothetical protein; Provisional
Probab=33.19 E-value=1.1e+02 Score=27.34 Aligned_cols=73 Identities=7% Similarity=-0.041 Sum_probs=47.4
Q ss_pred CcccCHHHHHHHHHHH-HHHHHHHHHHHHHHHHh-cCCCccCHHHHHHHHH-HcCCc--cchH-----HHHHHHHHHHHH
Q 036580 47 NAKISKDAKETVQECV-SEFISFVTGEASDKCQR-EKRKTINGDDLLWAMT-TLGFE--EYVE-----PLKVYLQRFREM 116 (186)
Q Consensus 47 ~~rISkDA~~ai~k~a-eeFI~~Lts~A~~~a~~-~kRKTIt~eDVl~AL~-~LgF~--dyi~-----~Lk~~L~~~re~ 116 (186)
+.+|+.+|...|.+.+ ..=+..|..+-.+.|.- ..+++|+.+||...+. .+.+. +.++ ..+..++-|+++
T Consensus 151 g~~i~~~a~~~L~~~~~~~nL~~l~~EleKL~ly~g~~~~It~e~V~~lv~~s~e~nIF~L~dai~~~~~~~Al~il~~L 230 (311)
T PRK05907 151 GISCSLGLASLFVSKFPQTGLFEILSEFQKLLCQMGKKESLEASDIQSFVVKKEAASLWKLRDALLRRDRVEGHSLLRSL 230 (311)
T ss_pred CCCcCHHHHHHHHHHccCCCHHHHHHHHHHHHHhcCCCCeECHHHHHHHhcCcccccHHHHHHHHHccCHHHHHHHHHHH
Confidence 4689999988888877 34445666666666554 5688999999998765 33433 3332 234555556655
Q ss_pred HHh
Q 036580 117 EGE 119 (186)
Q Consensus 117 ~~~ 119 (186)
..+
T Consensus 231 l~~ 233 (311)
T PRK05907 231 LSD 233 (311)
T ss_pred HHh
Confidence 443
No 135
>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=33.07 E-value=1.1e+02 Score=28.64 Aligned_cols=61 Identities=18% Similarity=0.161 Sum_probs=37.6
Q ss_pred HHHHHhhCCCCcccC-HHHHHHHHHHHH----HHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHcC
Q 036580 37 SRIMKKALPANAKIS-KDAKETVQECVS----EFISFVTGEASDKCQREKRKTINGDDLLWAMTTLG 98 (186)
Q Consensus 37 ~RImK~alP~~~rIS-kDA~~ai~k~ae----eFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~Lg 98 (186)
..|++..+. ...+. ......|.+.+. -=|..|..+|...+.+.+++.|+.+|+..|+++.-
T Consensus 231 ~~il~~~l~-~~~~~~~~~l~~la~~t~G~sgadl~~l~~eA~~~a~~~~~~~i~~~~l~~a~~~~~ 296 (495)
T TIGR01241 231 EEILKVHAK-NKKLAPDVDLKAVARRTPGFSGADLANLLNEAALLAARKNKTEITMNDIEEAIDRVI 296 (495)
T ss_pred HHHHHHHHh-cCCCCcchhHHHHHHhCCCCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHh
Confidence 556666553 22222 222334444433 23556666776677777889999999999999763
No 136
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=32.39 E-value=1.1e+02 Score=22.03 Aligned_cols=28 Identities=11% Similarity=0.134 Sum_probs=21.5
Q ss_pred HHHHHHhcCCCccCHHHHHHHHHHcCCc
Q 036580 73 ASDKCQREKRKTINGDDLLWAMTTLGFE 100 (186)
Q Consensus 73 A~~~a~~~kRKTIt~eDVl~AL~~LgF~ 100 (186)
+...+..++.-+|+.++|..+|..+++.
T Consensus 15 ~F~~~D~d~~G~Is~~el~~~l~~~~~~ 42 (96)
T smart00027 15 IFRSLDKNQDGTVTGAQAKPILLKSGLP 42 (96)
T ss_pred HHHHhCCCCCCeEeHHHHHHHHHHcCCC
Confidence 4445666777889999999999888775
No 137
>PF00536 SAM_1: SAM domain (Sterile alpha motif); InterPro: IPR021129 The sterile alpha motif (SAM) domain is a putative protein interaction module present in a wide variety of proteins [] involved in many biological processes. The SAM domain that spreads over around 70 residues is found in diverse eukaryotic organisms []. SAM domains have been shown to homo- and hetero-oligomerise, forming multiple self-association architectures and also binding to various non-SAM domain-containing proteins [], nevertheless with a low affinity constant []. SAM domains also appear to possess the ability to bind RNA []. Smaug, a protein that helps to establish a morphogen gradient in Drosophila embryos by repressing the translation of nanos (nos) mRNA, binds to the 3' untranslated region (UTR) of nos mRNA via two similar hairpin structures. The 3D crystal structure of the Smaug RNA-binding region shows a cluster of positively charged residues on the Smaug-SAM domain, which could be the RNA-binding surface. This electropositive potential is unique among all previously determined SAM-domain structures and is conserved among Smaug-SAM homologs. These results suggest that the SAM domain might have a primary role in RNA binding. Structural analyses show that the SAM domain is arranged in a small five-helix bundle with two large interfaces []. In the case of the SAM domain of EphB2, each of these interfaces is able to form dimers. The presence of these two distinct intermonomers binding surface suggest that SAM could form extended polymeric structures []. This entry represents type 1 SAM domains. ; PDB: 2KIV_A 3HIL_B 3KKA_A 3K1R_B 3SEN_B 3SEI_B 1V85_A 2KE7_A 2EAM_A 1WWV_A ....
Probab=32.34 E-value=63 Score=21.30 Aligned_cols=23 Identities=26% Similarity=0.453 Sum_probs=19.8
Q ss_pred CHHHHHHHHHHcCCccchHHHHH
Q 036580 86 NGDDLLWAMTTLGFEEYVEPLKV 108 (186)
Q Consensus 86 t~eDVl~AL~~LgF~dyi~~Lk~ 108 (186)
+.++|..-|+.++++.|++..+.
T Consensus 4 ~~~~V~~WL~~~~l~~y~~~F~~ 26 (64)
T PF00536_consen 4 SVEDVSEWLKSLGLEQYAENFEK 26 (64)
T ss_dssp SHHHHHHHHHHTTGGGGHHHHHH
T ss_pred CHHHHHHHHHHCCCHHHHHHHHc
Confidence 67899999999999999987743
No 138
>PRK00440 rfc replication factor C small subunit; Reviewed
Probab=32.23 E-value=1e+02 Score=26.14 Aligned_cols=64 Identities=13% Similarity=0.085 Sum_probs=39.0
Q ss_pred CchhHHHHHHHhhCC-CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 036580 31 LPIANVSRIMKKALP-ANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMTT 96 (186)
Q Consensus 31 LPkA~V~RImK~alP-~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~ 96 (186)
++...+.++++..+. ....|+.++.+.|.+.+.--+..+.......+.. .++|+.+||..++..
T Consensus 161 l~~~ei~~~l~~~~~~~~~~i~~~al~~l~~~~~gd~r~~~~~l~~~~~~--~~~it~~~v~~~~~~ 225 (319)
T PRK00440 161 LKKEAVAERLRYIAENEGIEITDDALEAIYYVSEGDMRKAINALQAAAAT--GKEVTEEAVYKITGT 225 (319)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHc--CCCCCHHHHHHHhCC
Confidence 444555555554432 2457999999999888754433333333333332 468999999887754
No 139
>COG4453 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.16 E-value=1.8e+02 Score=22.33 Aligned_cols=65 Identities=15% Similarity=0.261 Sum_probs=43.2
Q ss_pred CcccCHHHHHHHHHHH-------HHHHHHHHHHHHH-HHHhcCCCccCHHHHHHHHHHcCCcc-chHHHHHHHH
Q 036580 47 NAKISKDAKETVQECV-------SEFISFVTGEASD-KCQREKRKTINGDDLLWAMTTLGFEE-YVEPLKVYLQ 111 (186)
Q Consensus 47 ~~rISkDA~~ai~k~a-------eeFI~~Lts~A~~-~a~~~kRKTIt~eDVl~AL~~LgF~d-yi~~Lk~~L~ 111 (186)
+.|++.|.+++|.+++ +.|+..-+.++.+ +-.++.+-.++.+|-..-|..|+=+. =-+.|+..++
T Consensus 14 nlR~~~d~~~Li~~AAai~g~s~tdFvl~aA~~~A~~vi~~~~~~~L~e~~~~~fl~~LD~P~~pn~~L~~a~~ 87 (95)
T COG4453 14 NLRLTPDQRDLIDRAAAIEGKSLTDFVLSAALEAAEDVIEDQRRFILDEEDYRRFLAALDNPPSPNPKLKRAMA 87 (95)
T ss_pred eeecCHHHHHHHHHHHHHHCCcHHHHHHHHHHHHHHHHHHhhHHHhCCHHHHHHHHHHhcCCCCCCHHHHHHHh
Confidence 6799999999999988 4577666655444 33455566778888777777776653 2333444333
No 140
>PLN00138 large subunit ribosomal protein LP2; Provisional
Probab=32.04 E-value=1.5e+02 Score=23.21 Aligned_cols=40 Identities=13% Similarity=0.084 Sum_probs=29.1
Q ss_pred HHHHHHhcCCCccCHHHHHHHHHHcCCccchHHHHHHHHH
Q 036580 73 ASDKCQREKRKTINGDDLLWAMTTLGFEEYVEPLKVYLQR 112 (186)
Q Consensus 73 A~~~a~~~kRKTIt~eDVl~AL~~LgF~dyi~~Lk~~L~~ 112 (186)
|+-.|.-.+..+|+.+||...|+..|.+---..++.++..
T Consensus 6 Ayll~~l~g~~~pta~dI~~IL~AaGvevd~~~~~~f~~~ 45 (113)
T PLN00138 6 AYLLAVLGGNTCPSAEDLKDILGSVGADADDDRIELLLSE 45 (113)
T ss_pred HHHHHHhcCCCCCCHHHHHHHHHHcCCcccHHHHHHHHHH
Confidence 4557888889999999999999999876333344444443
No 141
>PF12668 DUF3791: Protein of unknown function (DUF3791); InterPro: IPR024269 This entry represents proteins of unknown function.
Probab=31.68 E-value=78 Score=21.57 Aligned_cols=31 Identities=19% Similarity=0.275 Sum_probs=24.6
Q ss_pred CCCccCHHHHHHHHHHcCCccchHHHHHHHH
Q 036580 81 KRKTINGDDLLWAMTTLGFEEYVEPLKVYLQ 111 (186)
Q Consensus 81 kRKTIt~eDVl~AL~~LgF~dyi~~Lk~~L~ 111 (186)
+|+-|+++++...+++.+.-+|+.+..+.|.
T Consensus 13 ~~~~~s~~ea~~~~~~~~~~~~i~~~Yd~lH 43 (62)
T PF12668_consen 13 KKLNISGEEAYNYFKRSGVIDYIIDCYDVLH 43 (62)
T ss_pred HHHCcCHHHHHHHHHHcCcHHHHHHcchHHH
Confidence 4677899999999999988888776655543
No 142
>PTZ00373 60S Acidic ribosomal protein P2; Provisional
Probab=31.28 E-value=1.5e+02 Score=23.17 Aligned_cols=39 Identities=8% Similarity=0.096 Sum_probs=28.2
Q ss_pred HHHHHHhcCCCccCHHHHHHHHHHcCCccchHHHHHHHH
Q 036580 73 ASDKCQREKRKTINGDDLLWAMTTLGFEEYVEPLKVYLQ 111 (186)
Q Consensus 73 A~~~a~~~kRKTIt~eDVl~AL~~LgF~dyi~~Lk~~L~ 111 (186)
|+-.|.-.+..+|+.+||...|+..|.+---..+..++.
T Consensus 8 AYlL~~lgG~~~pTaddI~kIL~AaGveVd~~~~~l~~~ 46 (112)
T PTZ00373 8 AYLMCVLGGNENPTKKEVKNVLSAVNADVEDDVLDNFFK 46 (112)
T ss_pred HHHHHHHcCCCCCCHHHHHHHHHHcCCCccHHHHHHHHH
Confidence 445778888999999999999999887633333444443
No 143
>PRK08487 DNA polymerase III subunit delta; Validated
Probab=30.87 E-value=1.9e+02 Score=25.57 Aligned_cols=47 Identities=13% Similarity=0.065 Sum_probs=34.9
Q ss_pred CcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHH
Q 036580 47 NAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMT 95 (186)
Q Consensus 47 ~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~ 95 (186)
...|+.+|...|...+.-=+..|..+--+.+.=.+ +|+.+||...+.
T Consensus 152 g~~i~~~a~~~L~~~~g~dl~~l~~ELeKL~ly~~--~It~edV~~~v~ 198 (328)
T PRK08487 152 GLDIDQNALNHLYFIHNEDLALAANELEKLAILNE--PITLKDIQELVF 198 (328)
T ss_pred CCCCCHHHHHHHHHHhCcHHHHHHHHHHHHHHhcC--CCCHHHHHHHhc
Confidence 56899999999999887655556665555554433 799999998764
No 144
>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=30.70 E-value=2.4e+02 Score=21.33 Aligned_cols=72 Identities=7% Similarity=0.162 Sum_probs=44.7
Q ss_pred CCchhHHHHHHHhhCCCCcccCHHHHHHHHH-----HHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHcCCccchH
Q 036580 30 FLPIANVSRIMKKALPANAKISKDAKETVQE-----CVSEFISFVTGEASDKCQREKRKTINGDDLLWAMTTLGFEEYVE 104 (186)
Q Consensus 30 ~LPkA~V~RImK~alP~~~rISkDA~~ai~k-----~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~LgF~dyi~ 104 (186)
.+|...+++++++.. ||.-..+.|.. +.+-.+..| ....+..|++- +..+++.+|..+++..-++
T Consensus 17 ~~~~~~wK~faR~lg-----lse~~Id~I~~~~~~d~~Eq~~qmL----~~W~~~~G~~a-~~~~Li~aLr~~~l~~~Ad 86 (97)
T cd08316 17 VMTLKDVKKFVRKSG-----LSEPKIDEIKLDNPQDTAEQKVQLL----RAWYQSHGKTG-AYRTLIKTLRKAKLCTKAD 86 (97)
T ss_pred HcCHHHHHHHHHHcC-----CCHHHHHHHHHcCCCChHHHHHHHH----HHHHHHhCCCc-hHHHHHHHHHHccchhHHH
Confidence 378888899888763 34433333331 112222222 22455555554 5799999999999998888
Q ss_pred HHHHHHH
Q 036580 105 PLKVYLQ 111 (186)
Q Consensus 105 ~Lk~~L~ 111 (186)
.++..++
T Consensus 87 ~I~~~l~ 93 (97)
T cd08316 87 KIQDIIE 93 (97)
T ss_pred HHHHHHH
Confidence 8876654
No 145
>PF10835 DUF2573: Protein of unknown function (DUF2573); InterPro: IPR020393 This entry contains proteins with no known function.
Probab=30.05 E-value=85 Score=23.57 Aligned_cols=71 Identities=15% Similarity=0.264 Sum_probs=52.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHc------CCccchHHHHHHHHHHHHHHHhhhhcC
Q 036580 54 AKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMTTL------GFEEYVEPLKVYLQRFREMEGEKMARD 124 (186)
Q Consensus 54 A~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~L------gF~dyi~~Lk~~L~~~re~~~~K~~~k 124 (186)
..+.|.-.++.|-..|+.+++..-...=++-+-+.+|.++|=-| -+.+-...++..+++.|+++.++++.+
T Consensus 4 l~eq~dgLveKytELL~Ge~~~e~~EkVk~W~lYshiaKsMPpL~kHWN~~~PeaK~~ik~li~~Ik~lNe~~r~~~ 80 (82)
T PF10835_consen 4 LQEQFDGLVEKYTELLLGETSPEMKEKVKQWALYSHIAKSMPPLAKHWNGTYPEAKEEIKELIEEIKQLNEAHRANK 80 (82)
T ss_pred HHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHhCcHHHHhhcccCchHHHHHHHHHHHHHHHHHHHHhhc
Confidence 44556666777777788888776666667778888888877644 466777888999999999888777654
No 146
>PTZ00009 heat shock 70 kDa protein; Provisional
Probab=29.99 E-value=4.8e+02 Score=25.64 Aligned_cols=13 Identities=31% Similarity=0.608 Sum_probs=7.5
Q ss_pred CchhHHHHHHHhh
Q 036580 31 LPIANVSRIMKKA 43 (186)
Q Consensus 31 LPkA~V~RImK~a 43 (186)
|....|.++.+..
T Consensus 512 ls~~~i~~~~~~~ 524 (653)
T PTZ00009 512 LSKADIDRMVNEA 524 (653)
T ss_pred ccHHHHHHHHHHH
Confidence 5555666665554
No 147
>PF13499 EF-hand_7: EF-hand domain pair; PDB: 1TCF_A 2TN4_A 1TN4_A 1A2X_A 2CT9_B 2OTG_B 2OS8_B 1SNL_A 3O4Y_A 3J04_E ....
Probab=29.72 E-value=1.3e+02 Score=19.52 Aligned_cols=42 Identities=21% Similarity=0.250 Sum_probs=30.8
Q ss_pred HHHHHHHhcCCCccCHHHHHHHHHHcCCccchHHHHHHHHHH
Q 036580 72 EASDKCQREKRKTINGDDLLWAMTTLGFEEYVEPLKVYLQRF 113 (186)
Q Consensus 72 ~A~~~a~~~kRKTIt~eDVl~AL~~LgF~dyi~~Lk~~L~~~ 113 (186)
++......++.-.|+.+++..+++.++..-....+...++.+
T Consensus 4 ~~F~~~D~d~~G~i~~~el~~~~~~~~~~~~~~~~~~~~~~~ 45 (66)
T PF13499_consen 4 EAFKKFDKDGDGYISKEELRRALKHLGRDMSDEESDEMIDQI 45 (66)
T ss_dssp HHHHHHSTTSSSEEEHHHHHHHHHHTTSHSTHHHHHHHHHHH
T ss_pred HHHHHHcCCccCCCCHHHHHHHHHHhcccccHHHHHHHHHHH
Confidence 455667777788899999999999988766555666655543
No 148
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=29.44 E-value=2.1e+02 Score=22.09 Aligned_cols=87 Identities=9% Similarity=0.053 Sum_probs=45.7
Q ss_pred cccCCchhHHHHHHHhhCC---------CCcccCHHHHHHHHH------HHHHHHHHHHH---HHH-HHHHhcCCCccCH
Q 036580 27 QDRFLPIANVSRIMKKALP---------ANAKISKDAKETVQE------CVSEFISFVTG---EAS-DKCQREKRKTING 87 (186)
Q Consensus 27 ~d~~LPkA~V~RImK~alP---------~~~rISkDA~~ai~k------~aeeFI~~Lts---~A~-~~a~~~kRKTIt~ 87 (186)
+.+.+..++|.++++...- ..+.++...+..... ..+.|+..|.. .+. +.|.-+ -.|++
T Consensus 30 ~~l~vs~~svs~~l~~L~~~Gli~~~~~~~i~LT~~G~~~a~~~~~~h~~~e~~l~~l~~~~~~~~~~a~~iE--H~ls~ 107 (142)
T PRK03902 30 EALSVHPSSVTKMVQKLDKDEYLIYEKYRGLVLTPKGKKIGKRLVYRHELLEQFLRIIGVDESKIYNDVEGIE--HHLSW 107 (142)
T ss_pred HHhCCChhHHHHHHHHHHHCCCEEEecCceEEECHHHHHHHHHHHHHHHHHHHHHHHhCcCHHHHHHHHHHHh--hcCCH
Confidence 3456889999999866532 124467766554433 23666655432 111 122222 23444
Q ss_pred HHHHHHHHHcCCccchHHHHHHHHHHHH
Q 036580 88 DDLLWAMTTLGFEEYVEPLKVYLQRFRE 115 (186)
Q Consensus 88 eDVl~AL~~LgF~dyi~~Lk~~L~~~re 115 (186)
+=+...-+-++|....+.+.+.+++|+.
T Consensus 108 e~~~rl~~~~~~~~~~p~~~~~~~~~~~ 135 (142)
T PRK03902 108 NAIDRIGDLVQYFEEDPDRLETLRAVQK 135 (142)
T ss_pred HHHHHHHHHHcchhhCcHHHHHHHHHHH
Confidence 4343333346777666666666666543
No 149
>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=29.44 E-value=2.3e+02 Score=20.72 Aligned_cols=70 Identities=13% Similarity=0.018 Sum_probs=39.3
Q ss_pred CCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHcCCccchH
Q 036580 30 FLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMTTLGFEEYVE 104 (186)
Q Consensus 30 ~LPkA~V~RImK~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~LgF~dyi~ 104 (186)
.+|....++++++.. +|.--.+.|...-...-.-+-..-...-+..++.--+..+++.||+.+++..-++
T Consensus 8 ~v~~~~wk~~~R~LG-----lse~~Id~ie~~~~~~~Eq~yqmL~~W~~~~g~~~At~~~L~~aLr~~~l~~~ae 77 (80)
T cd08313 8 EVPPRRWKEFVRRLG-----LSDNEIERVELDHRRCRDAQYQMLKVWKERGPRPYATLQHLLSVLRDMELVGCAE 77 (80)
T ss_pred hCCHHHHHHHHHHcC-----CCHHHHHHHHHhCCChHHHHHHHHHHHHHhcCCCcchHHHHHHHHHHcCcHHHHH
Confidence 378888999998864 3333333332221111011111112244556665668899999999998865444
No 150
>PRK09111 DNA polymerase III subunits gamma and tau; Validated
Probab=29.31 E-value=1.4e+02 Score=29.35 Aligned_cols=62 Identities=2% Similarity=-0.005 Sum_probs=38.0
Q ss_pred chhHHHHHHHhhCC-CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHH
Q 036580 32 PIANVSRIMKKALP-ANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAM 94 (186)
Q Consensus 32 PkA~V~RImK~alP-~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL 94 (186)
+...+.+.+++.+. ....|+.++..+|.+.+.--+..+..+..+.+.. +.+.|+.+||...+
T Consensus 192 ~~~el~~~L~~i~~kegi~i~~eAl~lIa~~a~Gdlr~al~~Ldkli~~-g~g~It~e~V~~ll 254 (598)
T PRK09111 192 EADVLAAHLSRIAAKEGVEVEDEALALIARAAEGSVRDGLSLLDQAIAH-GAGEVTAEAVRDML 254 (598)
T ss_pred CHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHhh-cCCCcCHHHHHHHh
Confidence 33344444444322 2568999999999988776555555554443333 34578888887654
No 151
>PRK02910 light-independent protochlorophyllide reductase subunit B; Provisional
Probab=29.05 E-value=1.2e+02 Score=29.06 Aligned_cols=52 Identities=12% Similarity=0.123 Sum_probs=41.7
Q ss_pred CCcccCHHHHHHHHHHHHHHHHHHHHHHHH-HHHhcCCCccCHHHHHHHHHHcC
Q 036580 46 ANAKISKDAKETVQECVSEFISFVTGEASD-KCQREKRKTINGDDLLWAMTTLG 98 (186)
Q Consensus 46 ~~~rISkDA~~ai~k~aeeFI~~Lts~A~~-~a~~~kRKTIt~eDVl~AL~~Lg 98 (186)
+...++.||...|.+ +--|+.--.....+ +|++.+...|+.+.|..|-..++
T Consensus 466 ~~~~w~~ea~~~l~~-~P~f~r~~~r~~~e~~a~~~g~~~it~~~~~~a~~~~~ 518 (519)
T PRK02910 466 SELVWTPEAEAELKK-IPFFVRGKVRRNTEKFARERGLPEITLEVLYDAKAHFG 518 (519)
T ss_pred CCCCCCHHHHHHHhh-CChhhHHHHHHHHHHHHHHcCCCeecHHHHHHHHHHhc
Confidence 467899999999965 77888766655555 88999999999999998876653
No 152
>CHL00076 chlB photochlorophyllide reductase subunit B
Probab=28.79 E-value=1.2e+02 Score=28.93 Aligned_cols=52 Identities=10% Similarity=0.095 Sum_probs=41.8
Q ss_pred CCcccCHHHHHHHHHHHHHHHHHHHHHHHH-HHHhcCCCccCHHHHHHHHHHcC
Q 036580 46 ANAKISKDAKETVQECVSEFISFVTGEASD-KCQREKRKTINGDDLLWAMTTLG 98 (186)
Q Consensus 46 ~~~rISkDA~~ai~k~aeeFI~~Lts~A~~-~a~~~kRKTIt~eDVl~AL~~Lg 98 (186)
+...++.||...|.+. --|+.-=...+.+ +|+.++...|+.+.|..|=..++
T Consensus 460 ~~~~w~~ea~~~l~~i-P~f~r~~~r~~~e~~a~~~g~~~it~~~~~~a~~~~~ 512 (513)
T CHL00076 460 SDLIWSPESQLELSKI-PGFVRGKVKRNTEKFARQNGITNITVEVMYAAKEALS 512 (513)
T ss_pred CCCCCCHHHHHHHHhC-CHHhHHHHHHHHHHHHHHcCCCeEcHHHHHHHHHhhC
Confidence 3567999999999998 7777765555544 88999999999999998866654
No 153
>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA.
Probab=28.36 E-value=3.5e+02 Score=26.91 Aligned_cols=69 Identities=20% Similarity=0.258 Sum_probs=45.5
Q ss_pred chhHHHHHHHhhCC-----CCcccCHHHHHHHHHHHHHHHHH---------HHHHHHHHHHh----cCCCccCHHHHHHH
Q 036580 32 PIANVSRIMKKALP-----ANAKISKDAKETVQECVSEFISF---------VTGEASDKCQR----EKRKTINGDDLLWA 93 (186)
Q Consensus 32 PkA~V~RImK~alP-----~~~rISkDA~~ai~k~aeeFI~~---------Lts~A~~~a~~----~kRKTIt~eDVl~A 93 (186)
....+..|++...+ -.+.|+++|..++.+.+..||.. |..+|...+.- ..+.+|+.+||..+
T Consensus 346 ~~~~~~~il~~~~~~~e~~~~v~i~~~al~~~~~ls~ryi~~r~~P~kai~lld~a~a~~~~~~~~~~~~~v~~~~i~~~ 425 (731)
T TIGR02639 346 SIEETVKILKGLKEKYEEFHHVKYSDEALEAAVELSARYINDRFLPDKAIDVIDEAGASFRLRPKAKKKANVSVKDIENV 425 (731)
T ss_pred CHHHHHHHHHHHHHHHHhccCcccCHHHHHHHHHhhhcccccccCCHHHHHHHHHhhhhhhcCcccccccccCHHHHHHH
Confidence 34445556664443 24679999999999999888743 33444332221 12567999999999
Q ss_pred HHHc-CCc
Q 036580 94 MTTL-GFE 100 (186)
Q Consensus 94 L~~L-gF~ 100 (186)
+..+ |++
T Consensus 426 i~~~tgiP 433 (731)
T TIGR02639 426 VAKMAHIP 433 (731)
T ss_pred HHHHhCCC
Confidence 9975 665
No 154
>PF02847 MA3: MA3 domain; InterPro: IPR003891 This entry represents the MI domain (after MA-3 and eIF4G), it is a protein-protein interaction module of ~130 amino acids [, , ]. It appears in several translation factors and is found in: One copy in plant and animal eIF4G 1 and 2 (DAP-5/NAT1/p97) Two copies in the animal programmed cell death protein 4 (PDCD4) or MA-3 that is induced during programmed cell death and inhibits neoplastic transformation Four tandem-repeated copies in a group of uncharacterised plant proteins The MI domain consists of seven alpha-helices, which pack into a globular form. The packing arrangement consists of repeating pairs of antiparallel helices packed one upon the other such that a superhelical axis is generated perpendicular to the alpha-helical axes []. The MI domain has also been named MA3 domain.; PDB: 2ION_A 2IOL_B 2NSZ_A 3EIQ_C 2HM8_A 2KZT_B 2IOS_A 2RG8_B 2ZU6_E 3EIJ_A ....
Probab=28.24 E-value=1.5e+02 Score=21.51 Aligned_cols=15 Identities=20% Similarity=0.271 Sum_probs=10.6
Q ss_pred CCccCHHHHHHHHHH
Q 036580 82 RKTINGDDLLWAMTT 96 (186)
Q Consensus 82 RKTIt~eDVl~AL~~ 96 (186)
++.|+.+++..++++
T Consensus 66 ~~~~~~~~~~~gf~~ 80 (113)
T PF02847_consen 66 RKLISKEQFQEGFED 80 (113)
T ss_dssp TTSS-HHHHHHHHHH
T ss_pred cCCCCHHHHHHHHHH
Confidence 567888888888774
No 155
>PF08397 IMD: IRSp53/MIM homology domain; InterPro: IPR013606 The IMD (IRSp53 and MIM (missing in metastases) homology) domain is a BAR-like domain of approximately 250 amino acids found at the N-terminal in the insulin receptor tyrosine kinase substrate p53 (IRSp53) and in the evolutionarily related IRSp53/MIM family. In IRSp53, a ubiquitous regulator o the actin cytoskeleton, the IMD domain acts as conserved F-actin bundling domain involved in filopodium formation. Filopodium-inducing IMD activity is regulated by Cdc42 and Rac1 (Rho-family GTPases) and is SH3-independent [, , ]. The IRSp53/MIM family is a novel F-actin bundling protein family that includes invertebrate relatives: Vertebrate MIM (missing in metastasis), an actin-binding scaffold protein that may be involved in cancer metastasis. Vertebrate ABBA-1, a MIM-related protein. Vertebrate brain-specific angiogenesis inhibitor 1-associated protein 2 (BAI1-associated protein 2) or insulin receptor tyrosine kinase substrate p53 (IRSp53), a multifunctional adaptor protein that links Rac1 with a Wiskott-Aldrich syndrome family verprolin-homologous protein 2 (WAVE2) to induce lamellipodia or Cdc42 with Mena to induce filopodia []. Vertebrate brain-specific angiogenesis inhibitor 1-associated protein 2-like proteins 1 and 2 (BAI1-associated protein 2-like proteins 1 and 2). Drosophila melanogaster (Fruit fly) CG32082-PA. Caenorhabditis elegans M04F3.5 protein. The vertebrate IRSp53/MIM family is divided into two major groups: the IRSp53 subfamily and the MIM/ABBA subfamily. The putative invertebrate homologues are positioned between them. The IRSp53 subfamily members contain an SH3 domain, and the MIM/ABBA subfamily proteins contain a WH2 (WASP-homology 2) domain. The vertebrate SH3-containing subfamily is further divided into three groups according to the presence or absence of the WWB and the half-CRIB motif. The IMD domain can bind to and bundle actin filaments, bind to membranes and interact with the small GTPase Rac [, ]. The IMD domain folds as a coiled coil of three extended alpha-helices and a shorter C-terminal helix. Helix 4 packs tightly against the other three helices, and thus represents an integral part of the domain. The fold of the IMD domain closely resembles that of the BAR (Bin-Amphiphysin-RVS) domain, a functional module serving both as a sensor and inducer of membrane curvature []. The WH2 domain performs a scaffolding function [].; GO: 0008093 cytoskeletal adaptor activity, 0017124 SH3 domain binding, 0007165 signal transduction, 0046847 filopodium assembly; PDB: 2D1L_A 3OK8_B 1WDZ_B 1Y2O_A 2YKT_A.
Probab=28.10 E-value=1.6e+02 Score=24.74 Aligned_cols=59 Identities=15% Similarity=0.265 Sum_probs=33.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHc------------C----C-ccchHHHHHHHHHHHH
Q 036580 53 DAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMTTL------------G----F-EEYVEPLKVYLQRFRE 115 (186)
Q Consensus 53 DA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~L------------g----F-~dyi~~Lk~~L~~~re 115 (186)
-|+.++..|+..|+.-|...+.. |....- ..||=.+|.++ . | .+++.||+..++.|+.
T Consensus 24 ~al~~~~~a~~~f~dal~ki~~~-A~~s~~----s~~lG~~L~~~s~~~r~i~~~~~~~~~~~~~~li~pLe~~~e~d~k 98 (219)
T PF08397_consen 24 KALRAMSQAAAAFFDALQKIGDM-ASNSRG----SKELGDALMQISEVHRRIENELEEVFKAFHSELIQPLEKKLEEDKK 98 (219)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHH-HHTSSS----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHh-ccCCCc----cccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35677778888887777665533 322111 22332222211 1 1 2678888888888876
Q ss_pred H
Q 036580 116 M 116 (186)
Q Consensus 116 ~ 116 (186)
.
T Consensus 99 ~ 99 (219)
T PF08397_consen 99 Y 99 (219)
T ss_dssp H
T ss_pred H
Confidence 4
No 156
>PF07499 RuvA_C: RuvA, C-terminal domain; InterPro: IPR011114 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. The domain represents the C-terminal domain III of RuvA. This domain plays a significant role in the ATP-dependent branch migration of the hetero-duplex through direct contact with RuvB []. Within the Holliday junction, this domain makes no interaction with the DNA.; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination, 0009379 Holliday junction helicase complex; PDB: 1HJP_A 1CUK_A 1C7Y_A 1IXS_A 1IXR_B 1BVS_E 2ZTC_A 2ZTD_B 2H5X_A.
Probab=28.05 E-value=1.3e+02 Score=19.34 Aligned_cols=14 Identities=36% Similarity=0.560 Sum_probs=11.7
Q ss_pred HHHHHHHHHHcCCc
Q 036580 87 GDDLLWAMTTLGFE 100 (186)
Q Consensus 87 ~eDVl~AL~~LgF~ 100 (186)
.+|++.||..|||.
T Consensus 3 ~~d~~~AL~~LGy~ 16 (47)
T PF07499_consen 3 LEDALEALISLGYS 16 (47)
T ss_dssp HHHHHHHHHHTTS-
T ss_pred HHHHHHHHHHcCCC
Confidence 37899999999998
No 157
>PRK14964 DNA polymerase III subunits gamma and tau; Provisional
Probab=28.01 E-value=1.6e+02 Score=28.42 Aligned_cols=47 Identities=9% Similarity=-0.019 Sum_probs=31.2
Q ss_pred CcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHH
Q 036580 47 NAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAM 94 (186)
Q Consensus 47 ~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL 94 (186)
+..|+.+|...|.+.+.-=+..+.+.-.+.+...+ .+|+.+||...|
T Consensus 192 gi~i~~eAL~lIa~~s~GslR~alslLdqli~y~~-~~It~e~V~~ll 238 (491)
T PRK14964 192 NIEHDEESLKLIAENSSGSMRNALFLLEQAAIYSN-NKISEKSVRDLL 238 (491)
T ss_pred CCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhcC-CCCCHHHHHHHH
Confidence 56899999999998875444444444333343333 479999987654
No 158
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=27.75 E-value=54 Score=28.08 Aligned_cols=32 Identities=22% Similarity=0.400 Sum_probs=26.4
Q ss_pred CCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHH
Q 036580 30 FLPIANVSRIMKKALPANAKISKDAKETVQECVSEF 65 (186)
Q Consensus 30 ~LPkA~V~RImK~alP~~~rISkDA~~ai~k~aeeF 65 (186)
.+-++||.|.+... .+||.+.++-|.+++++.
T Consensus 12 GVS~~TVSrvLn~~----~~Vs~~tr~rV~~~a~el 43 (343)
T PRK10727 12 GVSVATVSRVINNS----PKASEASRLAVHSAMESL 43 (343)
T ss_pred CCCHHHHHHHhCCC----CCCCHHHHHHHHHHHHHH
Confidence 36788999998653 379999999999999874
No 159
>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=27.74 E-value=1.3e+02 Score=28.69 Aligned_cols=52 Identities=12% Similarity=0.132 Sum_probs=40.5
Q ss_pred CCcccCHHHHHHHHHHHHHHHHHHHHHHHH-HHHhcCCCccCHHHHHHHHHHcC
Q 036580 46 ANAKISKDAKETVQECVSEFISFVTGEASD-KCQREKRKTINGDDLLWAMTTLG 98 (186)
Q Consensus 46 ~~~rISkDA~~ai~k~aeeFI~~Lts~A~~-~a~~~kRKTIt~eDVl~AL~~Lg 98 (186)
+...++.||...|.+ +--|+.-=.....+ +|++++..+|+.+.|..|=+.++
T Consensus 459 ~~~~w~~ea~~~l~~-~P~f~r~~~r~~~e~~a~~~g~~~it~~~~~~a~~~~~ 511 (511)
T TIGR01278 459 GELGWTAEAEAELKK-VPFFVRGKVRRNTENFARERGYSVITLEVIYAAKEHFG 511 (511)
T ss_pred CCCCcCHHHHHHHhh-CChhhhHHHHHHHHHHHHHcCCCEEcHHHHHHHHHhcC
Confidence 356899999999954 77777755555444 88999999999999988866543
No 160
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=27.64 E-value=56 Score=27.77 Aligned_cols=31 Identities=16% Similarity=0.294 Sum_probs=24.9
Q ss_pred CCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHH
Q 036580 30 FLPIANVSRIMKKALPANAKISKDAKETVQECVSE 64 (186)
Q Consensus 30 ~LPkA~V~RImK~alP~~~rISkDA~~ai~k~aee 64 (186)
..-++||.|++... .+||.+.++-|.+++++
T Consensus 16 gVS~~TVSrvLn~~----~~vs~~tr~rV~~~a~e 46 (331)
T PRK14987 16 GVTKMTVSRFLRNP----EQVSVALRGKIAAALDE 46 (331)
T ss_pred CCCHHHhhhhhCCC----CCCCHHHHHHHHHHHHH
Confidence 46678888888543 37999999999999877
No 161
>PF02049 FliE: Flagellar hook-basal body complex protein FliE; InterPro: IPR001624 Four genes from the major Bacillus subtilis chemotaxis locus have been shown to encode proteins that are similar to the Salmonella typhimurium FlgB, FlgC, FlgG and FliF proteins; a further gene product is similar to the Escherichia coli FliE protein []. All of these proteins are thought to form part of the hook-basal body complex of the bacterial flagella []. The FlgB, FlgC and FlgG proteins are components of the proximal and distal rods; FliF forms the M-ring that anchors the rod assembly to the membrane; but the role of FliE has not yet been determined []. The similarity between the proteins in these two organisms suggests that the structures of the M-ring and the rod may be similar []. Nevertheless, some differences in size and amino acid composition between some of the homologues suggest the basal body proteins may be organised slightly differently within B. subtilis []. From gel electrophoresis and autoradiography of 35S-labelled S. typhimurium hook-basal body complexes and the deduced number of sulphur-containing residues in FliE, the stoichiometry of the protein in the hook-basal body complex has been estimated to be about nine subunits []. FliE does not undergo cleavage of a signal peptide, nor does it show any similarity to the axial components like the rod or hook proteins, which are thought to be exported by the flagellum-specific export pathway []. On this evidence, it has been suggested that FliE may be in the vicinity of the MS ring, perhaps acting as an adaptor protein between ring and rod substructures [].; GO: 0003774 motor activity, 0005198 structural molecule activity, 0001539 ciliary or flagellar motility, 0009288 bacterial-type flagellum
Probab=27.53 E-value=2.6e+02 Score=20.68 Aligned_cols=66 Identities=9% Similarity=0.132 Sum_probs=39.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH-HHhcCCCccCHHHHHHHHHH--cCCccchHHHHHHHHHHHHHHH
Q 036580 52 KDAKETVQECVSEFISFVTGEASDK-CQREKRKTINGDDLLWAMTT--LGFEEYVEPLKVYLQRFREMEG 118 (186)
Q Consensus 52 kDA~~ai~k~aeeFI~~Lts~A~~~-a~~~kRKTIt~eDVl~AL~~--LgF~dyi~~Lk~~L~~~re~~~ 118 (186)
.++.+.|.+++...-.......... .-..|. .+...||+-|+++ +-|.-.+.--.+.++.|+|+.+
T Consensus 25 ~~F~~~l~~al~~vn~~q~~a~~~~~~~~~G~-~~dl~~vmia~~kA~lslq~~vqVRnK~v~AYqEImr 93 (96)
T PF02049_consen 25 ASFSDVLKNALDEVNQTQQQADQMAQAFATGE-SVDLHEVMIAMQKASLSLQLAVQVRNKAVEAYQEIMR 93 (96)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3444555555554444333322222 223344 8899999999996 4555556666788999999754
No 162
>smart00454 SAM Sterile alpha motif. Widespread domain in signalling and nuclear proteins. In EPH-related tyrosine kinases, appears to mediate cell-cell initiated signal transduction via the binding of SH2-containing proteins to a conserved tyrosine that is phosphorylated. In many cases mediates homodimerisation.
Probab=27.38 E-value=59 Score=20.87 Aligned_cols=26 Identities=12% Similarity=0.318 Sum_probs=20.8
Q ss_pred ccCHHHHHHHHHHcCCccchHHHHHH
Q 036580 84 TINGDDLLWAMTTLGFEEYVEPLKVY 109 (186)
Q Consensus 84 TIt~eDVl~AL~~LgF~dyi~~Lk~~ 109 (186)
.-+.++|..-|+.+||.+|+..+++.
T Consensus 3 ~w~~~~v~~wL~~~g~~~y~~~f~~~ 28 (68)
T smart00454 3 QWSPESVADWLESIGLEQYADNFRKN 28 (68)
T ss_pred CCCHHHHHHHHHHCChHHHHHHHHHC
Confidence 34678999999999999888877554
No 163
>PRK14955 DNA polymerase III subunits gamma and tau; Provisional
Probab=27.27 E-value=3.7e+02 Score=24.51 Aligned_cols=48 Identities=10% Similarity=0.010 Sum_probs=29.7
Q ss_pred CcccCHHHHHHHHHHHHHHHHHHHHHHH---HHHH-hcCCCccCHHHHHHHH
Q 036580 47 NAKISKDAKETVQECVSEFISFVTGEAS---DKCQ-REKRKTINGDDLLWAM 94 (186)
Q Consensus 47 ~~rISkDA~~ai~k~aeeFI~~Lts~A~---~~a~-~~kRKTIt~eDVl~AL 94 (186)
...|+.++...|.+.+.-=+..+..+.. .++. ...+++|+.+||...+
T Consensus 203 g~~i~~~al~~l~~~s~g~lr~a~~~L~kl~~~~~~~~~~~~It~~~v~~~v 254 (397)
T PRK14955 203 GISVDADALQLIGRKAQGSMRDAQSILDQVIAFSVESEGEGSIRYDKVAELL 254 (397)
T ss_pred CCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhccccCCCCccCHHHHHHHH
Confidence 3568999988887777553333333322 2332 2346789998887654
No 164
>PF10728 DUF2520: Domain of unknown function (DUF2520); InterPro: IPR018931 This presumed domain is found C-terminal to a Rossmann-like domain suggesting that these proteins are oxidoreductases. ; PDB: 3D1L_A 2I76_A 3DFU_A.
Probab=27.01 E-value=2.9e+02 Score=21.71 Aligned_cols=59 Identities=14% Similarity=0.177 Sum_probs=40.3
Q ss_pred hhHHHHHHHhhCCCCcccCHHHHHHHHHHH---HHHHHHHHHHHHHHHHhcCCCccCHHHHHHHH
Q 036580 33 IANVSRIMKKALPANAKISKDAKETVQECV---SEFISFVTGEASDKCQREKRKTINGDDLLWAM 94 (186)
Q Consensus 33 kA~V~RImK~alP~~~rISkDA~~ai~k~a---eeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL 94 (186)
+..+++|+++.......|..+-+....-++ ..|+..|...|.+.++.. -|..++.+.+|
T Consensus 13 ~~~l~~l~~~lg~~~~~i~~~~r~~yHaAav~asNf~~~L~~~a~~ll~~~---gi~~~~a~~~L 74 (132)
T PF10728_consen 13 LEVLQELAKELGGRPFEIDSEQRALYHAAAVFASNFLVALYALAAELLEQA---GIDFEEALEAL 74 (132)
T ss_dssp HHHHHHHHHHTTSEEEE--GGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHT---T-SHHH--HHH
T ss_pred HHHHHHHHHHhCCceEEeCHHhHHHHHHHHHHHHhhHHHHHHHHHHHHHHc---CCCchhHHHHH
Confidence 356778888887667789999888887765 578888888898888776 35665544444
No 165
>CHL00176 ftsH cell division protein; Validated
Probab=26.96 E-value=1.6e+02 Score=29.25 Aligned_cols=64 Identities=16% Similarity=0.082 Sum_probs=39.5
Q ss_pred hHHHHHHHhhCCCCcccCHHHHHHHHHHHH----HHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHc
Q 036580 34 ANVSRIMKKALPANAKISKDAKETVQECVS----EFISFVTGEASDKCQREKRKTINGDDLLWAMTTL 97 (186)
Q Consensus 34 A~V~RImK~alP~~~rISkDA~~ai~k~ae----eFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~L 97 (186)
.....|++..+.............|.+.+. .=|..|..+|.-.|.+.+++.|+.+||..|++++
T Consensus 356 ~~R~~IL~~~l~~~~~~~d~~l~~lA~~t~G~sgaDL~~lvneAal~a~r~~~~~It~~dl~~Ai~rv 423 (638)
T CHL00176 356 EGRLDILKVHARNKKLSPDVSLELIARRTPGFSGADLANLLNEAAILTARRKKATITMKEIDTAIDRV 423 (638)
T ss_pred HHHHHHHHHHHhhcccchhHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHhCCCCcCHHHHHHHHHHH
Confidence 334456665553211223333444544333 2356667777667778888999999999999875
No 166
>cd00051 EFh EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers.
Probab=26.93 E-value=1.4e+02 Score=17.58 Aligned_cols=33 Identities=24% Similarity=0.255 Sum_probs=21.2
Q ss_pred HHHhcCCCccCHHHHHHHHHHcCCccchHHHHH
Q 036580 76 KCQREKRKTINGDDLLWAMTTLGFEEYVEPLKV 108 (186)
Q Consensus 76 ~a~~~kRKTIt~eDVl~AL~~LgF~dyi~~Lk~ 108 (186)
.+..++.-.|+.+|+..+++.++...-.+.++.
T Consensus 8 ~~d~~~~g~l~~~e~~~~l~~~~~~~~~~~~~~ 40 (63)
T cd00051 8 LFDKDGDGTISADELKAALKSLGEGLSEEEIDE 40 (63)
T ss_pred HhCCCCCCcCcHHHHHHHHHHhCCCCCHHHHHH
Confidence 444555567888889888888875543333333
No 167
>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=26.83 E-value=1.3e+02 Score=29.39 Aligned_cols=70 Identities=13% Similarity=0.215 Sum_probs=43.2
Q ss_pred hhHHHHHHHhhCCC-CcccCHHHHHHHHHHH---HHHHHHHHHHHHHH--------HHhcCCCccCHHHHHHHHHHcCCc
Q 036580 33 IANVSRIMKKALPA-NAKISKDAKETVQECV---SEFISFVTGEASDK--------CQREKRKTINGDDLLWAMTTLGFE 100 (186)
Q Consensus 33 kA~V~RImK~alP~-~~rISkDA~~ai~k~a---eeFI~~Lts~A~~~--------a~~~kRKTIt~eDVl~AL~~LgF~ 100 (186)
...+..|++..+.. ...++.++.++|.+++ ...+..|.. +..+ +...++.+|+.+||..++..--|.
T Consensus 355 ~edi~~Il~~~a~~~~v~ls~eal~~L~~ys~~gRraln~L~~-~~~~~~~~~~~~~~~~~~~~I~~edv~~~l~~~r~~ 433 (615)
T TIGR02903 355 PEDIALIVLNAAEKINVHLAAGVEELIARYTIEGRKAVNILAD-VYGYALYRAAEAGKENDKVTITQDDVYEVIQISRLS 433 (615)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHCCCcHHHHHHHHHH-HHHHHHHHHHHhccCCCCeeECHHHHHHHhCCCcCc
Confidence 45577777776532 3468999999988765 233333322 1111 223345689999999998876665
Q ss_pred cch
Q 036580 101 EYV 103 (186)
Q Consensus 101 dyi 103 (186)
.|.
T Consensus 434 ~~~ 436 (615)
T TIGR02903 434 PYE 436 (615)
T ss_pred cch
Confidence 444
No 168
>PRK05629 hypothetical protein; Validated
Probab=26.46 E-value=2.2e+02 Score=24.91 Aligned_cols=48 Identities=8% Similarity=0.057 Sum_probs=35.3
Q ss_pred CcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHH
Q 036580 47 NAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMT 95 (186)
Q Consensus 47 ~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~ 95 (186)
..+|+.+|...|.+.+..=+..|..+--+.|.-. ..+|+.+||...+.
T Consensus 143 g~~i~~~A~~~L~~~~g~dl~~l~~EleKL~~~~-~~~It~e~V~~~v~ 190 (318)
T PRK05629 143 GVRPTPDVVHALLEGVGSDLRELASAISQLVEDT-QGNVTVEKVRAYYV 190 (318)
T ss_pred CCCCCHHHHHHHHHHHCccHHHHHHHHHHHHhcC-CCCcCHHHHHHHhC
Confidence 5689999999998888765556666555555433 45799999987654
No 169
>KOG3557 consensus Epidermal growth factor receptor kinase substrate [Signal transduction mechanisms]
Probab=26.45 E-value=81 Score=31.92 Aligned_cols=32 Identities=25% Similarity=0.341 Sum_probs=25.4
Q ss_pred CCccchHHHHHHHHHHHHHHHhhhhcCCCCCC
Q 036580 98 GFEEYVEPLKVYLQRFREMEGEKMARDKDAPP 129 (186)
Q Consensus 98 gF~dyi~~Lk~~L~~~re~~~~K~~~kk~~~~ 129 (186)
+++.|+..|+...+.+||++..|+..|...+.
T Consensus 279 DIE~FvaRLQkAAeA~reLe~Rkr~~K~~k~~ 310 (721)
T KOG3557|consen 279 DIESFVARLQKAAEAARELEQRKRGRKSKKRA 310 (721)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhcccccCCC
Confidence 45678999999999999999988865544443
No 170
>COG1500 Predicted exosome subunit [Translation, ribosomal structure and biogenesis]
Probab=26.25 E-value=4.4e+02 Score=23.40 Aligned_cols=74 Identities=12% Similarity=0.168 Sum_probs=49.8
Q ss_pred HHHHHHhhCC-CCcccCHHHHHHHHHHHHH-HHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHcCCc-cchHHHHHHHHH
Q 036580 36 VSRIMKKALP-ANAKISKDAKETVQECVSE-FISFVTGEASDKCQREKRKTINGDDLLWAMTTLGFE-EYVEPLKVYLQR 112 (186)
Q Consensus 36 V~RImK~alP-~~~rISkDA~~ai~k~aee-FI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~LgF~-dyi~~Lk~~L~~ 112 (186)
+..|+++.+. ....++.+-+..+++.... .|++|+..|.+ -..+.-+.+.-|..||++++|. ++..+.++...+
T Consensus 72 ~~eI~~eIl~kGeiQlTaeqR~~m~e~k~rqIi~~IsRn~Id---P~t~~P~Pp~rIe~Ameeakv~id~~K~ae~Qv~e 148 (234)
T COG1500 72 PDEIAEEILKKGEIQLTAEQRREMLEEKKRQIINIISRNAID---PQTKAPHPPARIEKAMEEAKVHIDPFKSAEEQVQE 148 (234)
T ss_pred HHHHHHHHHhcCceeccHHHHHHHHHHHHHHHHHHHHHhccC---CCCCCCCCHHHHHHHHHhcCcccCCCCCHHHHHHH
Confidence 4444444442 2578999998888877765 44577765543 3345688999999999999996 665555554443
No 171
>KOG1942 consensus DNA helicase, TBP-interacting protein [Replication, recombination and repair]
Probab=26.23 E-value=1.6e+02 Score=27.82 Aligned_cols=65 Identities=15% Similarity=0.122 Sum_probs=46.5
Q ss_pred CCchhHHHHHHHhhCC-CCcccCHHHHHHHHHHH----HHHHHHHHHHHHHHHHhcCCCccCHHHHHHHH
Q 036580 30 FLPIANVSRIMKKALP-ANAKISKDAKETVQECV----SEFISFVTGEASDKCQREKRKTINGDDLLWAM 94 (186)
Q Consensus 30 ~LPkA~V~RImK~alP-~~~rISkDA~~ai~k~a----eeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL 94 (186)
..|-..++.|++.... .+..+..+|.+.+.+.. -.+...|..-|+..|+-.+|+.|..+||-.+-
T Consensus 366 ~y~~~e~r~Ii~~Ra~~E~l~~~e~a~~~l~~~gt~tsLRy~vqLl~p~~~~ak~~g~~~i~v~dvee~~ 435 (456)
T KOG1942|consen 366 PYDEEEIRQIIKIRAQVEGLQVEEEALDLLAEIGTSTSLRYAVQLLTPASILAKTNGRKEISVEDVEEVT 435 (456)
T ss_pred cCCHHHHHHHHHHHHhhhcceecHHHHHHHHhhccchhHHHHHHhcCHHHHHHHHcCCceeecccHHHHH
Confidence 3556667777765542 45679999999887732 23444455567788999999999999997654
No 172
>COG1724 Predicted RNA binding protein (dsRBD-like fold), HicA family [General function prediction only]
Probab=25.99 E-value=54 Score=23.69 Aligned_cols=18 Identities=17% Similarity=0.401 Sum_probs=15.8
Q ss_pred ccCHHHHHHHHHHcCCcc
Q 036580 84 TINGDDLLWAMTTLGFEE 101 (186)
Q Consensus 84 TIt~eDVl~AL~~LgF~d 101 (186)
.+++.||+++|+.+||..
T Consensus 6 ~~~~ke~ik~Le~~Gf~~ 23 (66)
T COG1724 6 RMKAKEVIKALEKDGFQL 23 (66)
T ss_pred cCCHHHHHHHHHhCCcEE
Confidence 478999999999999973
No 173
>KOG0785 consensus Isocitrate dehydrogenase, alpha subunit [Amino acid transport and metabolism]
Probab=25.89 E-value=99 Score=28.85 Aligned_cols=66 Identities=8% Similarity=0.077 Sum_probs=47.1
Q ss_pred cCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHcCCccchHHHHHHHHHHHHH
Q 036580 50 ISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMTTLGFEEYVEPLKVYLQRFREM 116 (186)
Q Consensus 50 ISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~LgF~dyi~~Lk~~L~~~re~ 116 (186)
|-.-..+.|...++.-...|+.-|.++|+.++|+.|+.-|=.+.|+.-+ .-|.+.+++.-++|-++
T Consensus 164 vvpGVvqsiK~IT~~AS~Ria~~AF~yAr~~~R~~vtvvHKaNImr~tD-GLFle~cre~a~~y~dI 229 (365)
T KOG0785|consen 164 VVPGVVQSIKLITEAASRRIAEYAFEYARQNGRKRVTVVHKANIMRMTD-GLFLECCREVAKKYPDI 229 (365)
T ss_pred ccccHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCceEEEehhhhhhhcc-hHHHHHHHHHhhhCCcc
Confidence 3344667777777777788899999999999999998777666665432 24566666666655544
No 174
>KOG4717 consensus Serine/threonine protein kinase [Signal transduction mechanisms]
Probab=25.50 E-value=1.5e+02 Score=29.98 Aligned_cols=73 Identities=15% Similarity=0.272 Sum_probs=50.0
Q ss_pred cccCHHHHHHHHHHH------HHHHHHHHHHHHHHHHhcCCCc---------------------------cCHHHHHHHH
Q 036580 48 AKISKDAKETVQECV------SEFISFVTGEASDKCQREKRKT---------------------------INGDDLLWAM 94 (186)
Q Consensus 48 ~rISkDA~~ai~k~a------eeFI~~Lts~A~~~a~~~kRKT---------------------------It~eDVl~AL 94 (186)
.-||+|++++|+... ..-++.|.+.+|-.+...+-.| -+.|||+.||
T Consensus 240 shvS~eCrdLI~sMLvRdPkkRAslEeI~s~~Wlq~~D~~~sT~iPLvsr~~L~ee~Ha~IIq~Mv~G~IAs~e~Il~aL 319 (864)
T KOG4717|consen 240 SHVSKECRDLIQSMLVRDPKKRASLEEIVSTSWLQAGDRGLSTAIPLVSRHHLPEEAHATIIQQMVAGAIASEEDILRAL 319 (864)
T ss_pred hhhhHHHHHHHHHHHhcCchhhccHHHHhccccccCCCCCccccCceeehhhCChHHHHHHHHHHhcccccCHHHHHHHH
Confidence 368999999998754 2234555555555544443222 3678999999
Q ss_pred HHcCCc----cchHHHHHHHHHHHHHHHhh
Q 036580 95 TTLGFE----EYVEPLKVYLQRFREMEGEK 120 (186)
Q Consensus 95 ~~LgF~----dyi~~Lk~~L~~~re~~~~K 120 (186)
+.-.+- -|.--.+..|..|||.+.++
T Consensus 320 e~n~YNhiTATYfLLAEr~Lr~~rEe~aq~ 349 (864)
T KOG4717|consen 320 ENNEYNHITATYFLLAERVLRSYREEQAQE 349 (864)
T ss_pred hccccchhhhHHHHHHHHHHHHHHHHHHHh
Confidence 987764 45666788899999987766
No 175
>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=25.07 E-value=1.1e+02 Score=19.04 Aligned_cols=32 Identities=25% Similarity=0.476 Sum_probs=20.2
Q ss_pred CCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHH
Q 036580 30 FLPIANVSRIMKKALPANAKISKDAKETVQECVSEF 65 (186)
Q Consensus 30 ~LPkA~V~RImK~alP~~~rISkDA~~ai~k~aeeF 65 (186)
.+..++|.|+++.. ..|+.+....|.+++.++
T Consensus 8 gvs~~tvs~~l~g~----~~vs~~~~~~i~~~~~~l 39 (52)
T cd01392 8 GVSVATVSRVLNGK----PRVSEETRERVLAAAEEL 39 (52)
T ss_pred CcCHHHHHHHHcCC----CCCCHHHHHHHHHHHHHh
Confidence 46677777777643 256676666666666554
No 176
>TIGR02454 CbiQ_TIGR cobalt ABC transporter, permease protein CbiQ. This model represents the permease component of the cobalt-specific ABC transporter. This model finds permeases which are generally next to the other subunits of the complex (CbiN and CbiO) or the cobalamin biosynthesis protein CbiM which is a transmembrane protein which likely interacts with the complex in some manner. In genomes which possess all of these subunits the ATPase is most likely running in the direction of import (for the biosynthesis of coenzyme B12). In other genomes, this subunit may be involved in the export of cobalt and/or other closely related heavy metals.
Probab=25.06 E-value=1.5e+02 Score=23.67 Aligned_cols=18 Identities=33% Similarity=0.287 Sum_probs=15.9
Q ss_pred CccCHHHHHHHHHHcCCc
Q 036580 83 KTINGDDLLWAMTTLGFE 100 (186)
Q Consensus 83 KTIt~eDVl~AL~~LgF~ 100 (186)
.|....|+..+|++++++
T Consensus 112 ~TT~~~~l~~~l~~l~~P 129 (198)
T TIGR02454 112 LTTPFPELLSALRRLGVP 129 (198)
T ss_pred HcCCHHHHHHHHHHcCCC
Confidence 467899999999999986
No 177
>PRK07764 DNA polymerase III subunits gamma and tau; Validated
Probab=24.80 E-value=1.7e+02 Score=30.11 Aligned_cols=61 Identities=3% Similarity=-0.027 Sum_probs=32.6
Q ss_pred CchhHHHHHHHhhCC-CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHH
Q 036580 31 LPIANVSRIMKKALP-ANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLL 91 (186)
Q Consensus 31 LPkA~V~RImK~alP-~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl 91 (186)
|+...|.+++++.+. .++.|+++++.+|.+.+.-=+..+.++..+.+.-.+...|+.+||.
T Consensus 179 l~~~~l~~~L~~il~~EGv~id~eal~lLa~~sgGdlR~Al~eLEKLia~~~~~~IT~e~V~ 240 (824)
T PRK07764 179 VPPEVMRGYLERICAQEGVPVEPGVLPLVIRAGGGSVRDSLSVLDQLLAGAGPEGVTYERAV 240 (824)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHhhcCCCCCCHHHHH
Confidence 556666666666542 2467888888877766544333333333333332234456666443
No 178
>PRK14971 DNA polymerase III subunits gamma and tau; Provisional
Probab=24.78 E-value=1.6e+02 Score=28.92 Aligned_cols=63 Identities=5% Similarity=0.015 Sum_probs=33.2
Q ss_pred CchhHHHHHHHhhCC-CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHH
Q 036580 31 LPIANVSRIMKKALP-ANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAM 94 (186)
Q Consensus 31 LPkA~V~RImK~alP-~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL 94 (186)
|+...|.+.+++.+. ....|+.++..+|.+.+.-=+..+..+....+.-.+++ |+.++|...+
T Consensus 180 ls~~ei~~~L~~ia~~egi~i~~~al~~La~~s~gdlr~al~~Lekl~~y~~~~-It~~~V~~~l 243 (614)
T PRK14971 180 IQVADIVNHLQYVASKEGITAEPEALNVIAQKADGGMRDALSIFDQVVSFTGGN-ITYKSVIENL 243 (614)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhccCC-ccHHHHHHHh
Confidence 444555555544321 24678898888887766443333333333333223333 7776666544
No 179
>KOG0729 consensus 26S proteasome regulatory complex, ATPase RPT1 [Posttranslational modification, protein turnover, chaperones]
Probab=24.76 E-value=67 Score=29.92 Aligned_cols=48 Identities=25% Similarity=0.268 Sum_probs=35.9
Q ss_pred ccCHHHH-HHHHHHH----HHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 036580 49 KISKDAK-ETVQECV----SEFISFVTGEASDKCQREKRKTINGDDLLWAMTT 96 (186)
Q Consensus 49 rISkDA~-~ai~k~a----eeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~ 96 (186)
.|-+|.+ ++|.+.| -.=|..+..+|--+|.++.||+.+.+|.+.|+..
T Consensus 365 sverdir~ellarlcpnstgaeirsvcteagmfairarrk~atekdfl~av~k 417 (435)
T KOG0729|consen 365 SVERDIRFELLARLCPNSTGAEIRSVCTEAGMFAIRARRKVATEKDFLDAVNK 417 (435)
T ss_pred ccccchhHHHHHhhCCCCcchHHHHHHHHhhHHHHHHHhhhhhHHHHHHHHHH
Confidence 4445543 4555544 3446778888999999999999999999999875
No 180
>COG1239 ChlI Mg-chelatase subunit ChlI [Coenzyme metabolism]
Probab=24.46 E-value=1.9e+02 Score=27.77 Aligned_cols=49 Identities=16% Similarity=0.235 Sum_probs=39.7
Q ss_pred CcccCHHHHHHHHHHHHHHHH-------HHHHHHHHHHHhcCCCccCHHHHHHHHH
Q 036580 47 NAKISKDAKETVQECVSEFIS-------FVTGEASDKCQREKRKTINGDDLLWAMT 95 (186)
Q Consensus 47 ~~rISkDA~~ai~k~aeeFI~-------~Lts~A~~~a~~~kRKTIt~eDVl~AL~ 95 (186)
.+.++.++...+.+.|..+-. .++..|..++.-.+|.+++.+||..|++
T Consensus 265 ~V~l~~~~~~~ia~~~~~~~v~g~radi~~~r~a~a~aa~~Gr~~v~~~Di~~a~~ 320 (423)
T COG1239 265 EVELDDDAETKIAELCARLAVDGHRADIVVVRAAKALAALRGRTEVEEEDIREAAE 320 (423)
T ss_pred cccCcHHHHHHHHHHHHHhccCCCchhhHHHHHHHHHHHhcCceeeehhhHHHHHh
Confidence 577889999999888877643 3566677788888999999999998875
No 181
>TIGR01481 ccpA catabolite control protein A. Catabolite control protein A is a LacI family global transcriptional regulator found in Gram-positive bacteria. CcpA is involved in repressing carbohydrate utilization genes [ex: alpha-amylase (amyE), acetyl-coenzyme A synthase (acsA)] and in activating genes involved in transporting excess carbon from the cell [ex: acetate kinase (ackA), alpha-acetolactate synthase (alsS)]. Additionally, disruption of CcpA in Bacillus megaterium, Staphylococcus xylosus, Lactobacillus casei and Lactocacillus pentosus also decreases growth rate, which suggests CcpA is involved in the regulation of other metabolic pathways.
Probab=24.41 E-value=91 Score=26.31 Aligned_cols=32 Identities=19% Similarity=0.374 Sum_probs=26.2
Q ss_pred CCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHH
Q 036580 30 FLPIANVSRIMKKALPANAKISKDAKETVQECVSEF 65 (186)
Q Consensus 30 ~LPkA~V~RImK~alP~~~rISkDA~~ai~k~aeeF 65 (186)
.+-++||.|++... .+||++.++.|.+++++.
T Consensus 12 gvS~~TVSrvLn~~----~~vs~~tr~rV~~~a~~l 43 (329)
T TIGR01481 12 GVSMATVSRVVNGN----PNVKPATRKKVLEVIKRL 43 (329)
T ss_pred CCCHHHHHHHhCCC----CCCCHHHHHHHHHHHHHH
Confidence 46788999998764 379999999999998764
No 182
>PTZ00184 calmodulin; Provisional
Probab=24.39 E-value=2.8e+02 Score=20.15 Aligned_cols=30 Identities=30% Similarity=0.317 Sum_probs=23.4
Q ss_pred HHHHHHHHhcCCCccCHHHHHHHHHHcCCc
Q 036580 71 GEASDKCQREKRKTINGDDLLWAMTTLGFE 100 (186)
Q Consensus 71 s~A~~~a~~~kRKTIt~eDVl~AL~~LgF~ 100 (186)
..+......+++-.|+.+|+..+|..+++.
T Consensus 87 ~~~F~~~D~~~~g~i~~~e~~~~l~~~~~~ 116 (149)
T PTZ00184 87 KEAFKVFDRDGNGFISAAELRHVMTNLGEK 116 (149)
T ss_pred HHHHHhhCCCCCCeEeHHHHHHHHHHHCCC
Confidence 445555666777889999999999988765
No 183
>KOG2008 consensus BTK-associated SH3-domain binding protein SAB [Signal transduction mechanisms]
Probab=24.29 E-value=76 Score=29.76 Aligned_cols=70 Identities=20% Similarity=0.266 Sum_probs=36.7
Q ss_pred cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHcCCc-cchHHHHHHHHHHHHHHHhhhh
Q 036580 48 AKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMTTLGFE-EYVEPLKVYLQRFREMEGEKMA 122 (186)
Q Consensus 48 ~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~LgF~-dyi~~Lk~~L~~~re~~~~K~~ 122 (186)
.++-..++...|+++..|=..-+ ....|+.. ..|..+-++.- ..+.|+ .|++-|.-.++..+|.++++..
T Consensus 75 k~~er~~r~e~QkAa~~FeRat~--vl~~Akeq--Vsl~~~sL~~~-~~~~~~~~~~evlnh~~qrV~EaE~e~t~ 145 (426)
T KOG2008|consen 75 KRVERQARLEAQKAAQDFERATE--VLRAAKEQ--VSLAEQSLLED-DKRQFDSAWQEVLNHATQRVMEAEQEKTR 145 (426)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHH--HHHHHHHhhcc-hhhhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35777889999999999943211 11122110 01111111100 233443 6777777777777777766644
No 184
>cd04752 Commd4 COMM_Domain containing protein 4. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=23.98 E-value=4e+02 Score=21.71 Aligned_cols=53 Identities=19% Similarity=0.275 Sum_probs=34.9
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHcCCc-cchHHHHHHHHHHHHHHHhh
Q 036580 61 CVSEFISFVTGEASDKCQREKRKTINGDDLLWAMTTLGFE-EYVEPLKVYLQRFREMEGEK 120 (186)
Q Consensus 61 ~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~LgF~-dyi~~Lk~~L~~~re~~~~K 120 (186)
++-..+.+|...|. |.-++++++..-|+.|||+ +.++.+...+.++++...++
T Consensus 43 ~~va~l~fiL~~A~-------k~n~~~~~l~~eL~~lglp~e~~~~l~~~~~~~~~~l~~~ 96 (174)
T cd04752 43 ASIAVLSFILSSAA-------KYNVDGESLSSELQQLGLPKEHATSLCRSYEEKQSKLQES 96 (174)
T ss_pred HHHHHHHHHHHHHH-------HcCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 34445556665553 3449999999999999998 55555656666666544433
No 185
>cd05833 Ribosomal_P2 Ribosomal protein P2. This subfamily represents the eukaryotic large ribosomal protein P2. Eukaryotic P1 and P2 are functionally equivalent to the bacterial protein L7/L12, but are not homologous to L7/L12. P2 is located in the L12 stalk, with proteins P1, P0, L11, and 28S rRNA. P1 and P2 are the only proteins in the ribosome to occur as multimers, always appearing as sets of heterodimers. Recent data indicate that eukaryotes have four copies (two heterodimers), while most archaeal species contain six copies of L12p (three homodimers). Bacteria may have four or six copies of L7/L12 (two or three homodimers) depending on the species. Experiments using S. cerevisiae P1 and P2 indicate that P1 proteins are positioned more internally with limited reactivity in the C-terminal domains, while P2 proteins seem to be more externally located and are more likely to interact with other cellular components. In lower eukaryotes, P1 and P2 are further subdivided into P1A, P1B, P2
Probab=23.61 E-value=2.5e+02 Score=21.77 Aligned_cols=28 Identities=14% Similarity=0.057 Sum_probs=23.6
Q ss_pred HHHHHHhcCCCccCHHHHHHHHHHcCCc
Q 036580 73 ASDKCQREKRKTINGDDLLWAMTTLGFE 100 (186)
Q Consensus 73 A~~~a~~~kRKTIt~eDVl~AL~~LgF~ 100 (186)
|+-.|.-.++.+|+.+||...|+..|.+
T Consensus 6 AylL~~l~g~~~pTa~dI~~IL~AaGve 33 (109)
T cd05833 6 AYLLAVLGGNASPSAADVKKILGSVGVE 33 (109)
T ss_pred HHHHHHHcCCCCCCHHHHHHHHHHcCCC
Confidence 3447777888899999999999998875
No 186
>PF02361 CbiQ: Cobalt transport protein; InterPro: IPR003339 Cobalt transport proteins are most often found in cobalamin (vitamin B12) biosynthesis operons. Salmonella typhimurium synthesizes cobalamin (vitamin B12) de novo under anaerobic conditions. Not all Salmonella and Pseudomonas cobalamin synthetic genes have apparent homologs in the other species suggesting that the cobalamin biosynthetic pathways differ between the two organisms [].; GO: 0015087 cobalt ion transmembrane transporter activity, 0006824 cobalt ion transport, 0009236 cobalamin biosynthetic process
Probab=23.54 E-value=1.5e+02 Score=23.69 Aligned_cols=37 Identities=24% Similarity=0.291 Sum_probs=25.8
Q ss_pred CccCHHHHHHHHHHcCCcc------------chHHHHHHHHHHHHHHHh
Q 036580 83 KTINGDDLLWAMTTLGFEE------------YVEPLKVYLQRFREMEGE 119 (186)
Q Consensus 83 KTIt~eDVl~AL~~LgF~d------------yi~~Lk~~L~~~re~~~~ 119 (186)
.|.+.+|++.+++.+.++. |++.+.+.+++-++.++.
T Consensus 123 ~tt~~~~l~~~l~~l~~P~~~~~~~i~l~~r~ip~l~~~~~~i~~A~~~ 171 (224)
T PF02361_consen 123 LTTSPSDLISALRKLRLPYPKIALMISLTLRFIPLLLEEFKRIREAQRL 171 (224)
T ss_pred HHCCHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4789999999999999887 455555555444444433
No 187
>KOG2256 consensus Predicted protein involved in nuclear export of pre-ribosomes [Translation, ribosomal structure and biogenesis]
Probab=23.08 E-value=3.5e+02 Score=27.47 Aligned_cols=80 Identities=16% Similarity=0.268 Sum_probs=53.4
Q ss_pred CCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHH--H-HHHcCCccchHHH
Q 036580 30 FLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLW--A-MTTLGFEEYVEPL 106 (186)
Q Consensus 30 ~LPkA~V~RImK~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~--A-L~~LgF~dyi~~L 106 (186)
..|+.++++++|+.-+ . -+.+-+.-||..|=..+.=++++..+++..+.|-.. | .+.+.... .||
T Consensus 538 ~p~i~rLk~f~k~skn--~--------~~~r~v~~li~kle~ns~FV~~kR~~v~F~pnD~~~V~afe~~~~~~~--TPl 605 (661)
T KOG2256|consen 538 LPVIMRLKSFLKESKN--G--------NYKRVVKQLIEKLEENSKFVLEKRNKVKFSPNDQQAVSAFEQDLDWNK--TPL 605 (661)
T ss_pred HHHHHHHHHHHHHhcc--H--------HHHHHHHHHHHHHHHHHHHHHHHHhcCccCCCcHHHHHHHHHHHHccC--CcH
Confidence 4667889999998863 2 244555566666666666677777778777766432 2 22444444 799
Q ss_pred HHHHHHHHHHHHhhh
Q 036580 107 KVYLQRFREMEGEKM 121 (186)
Q Consensus 107 k~~L~~~re~~~~K~ 121 (186)
..|...||+...+|+
T Consensus 606 ~~yy~~~rk~~~~k~ 620 (661)
T KOG2256|consen 606 GQYYSSWRKVREEKN 620 (661)
T ss_pred HHHHHHHHHHHHHHH
Confidence 999999998765543
No 188
>COG1389 DNA topoisomerase VI, subunit B [DNA replication, recombination, and repair]
Probab=23.07 E-value=61 Score=31.71 Aligned_cols=46 Identities=20% Similarity=0.369 Sum_probs=36.7
Q ss_pred HhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccC
Q 036580 41 KKALPANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTIN 86 (186)
Q Consensus 41 K~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt 86 (186)
|+++.++--|-+|.+.++++||...=.||.......-+.+++++|.
T Consensus 434 KqsIa~vpeIe~Eir~Al~evaRkL~~yLsrk~r~~e~~~K~~~i~ 479 (538)
T COG1389 434 KQSIADVPEIENEIRLALMEVARKLKLYLSRKRREMEERKKRKTIE 479 (538)
T ss_pred chhccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4444444568899999999999999999999998877777777654
No 189
>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=22.87 E-value=2.4e+02 Score=24.43 Aligned_cols=62 Identities=15% Similarity=0.116 Sum_probs=33.2
Q ss_pred hhHHHHHHHhhCC-CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHH
Q 036580 33 IANVSRIMKKALP-ANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMT 95 (186)
Q Consensus 33 kA~V~RImK~alP-~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~ 95 (186)
...+..+++..+. ....|+.++...|.+.+.--+..+..+....+.-.+ +.|+.+||..++.
T Consensus 178 ~~~l~~~l~~~~~~~g~~i~~~a~~~l~~~~~g~~~~a~~~lekl~~~~~-~~it~~~v~~~~~ 240 (355)
T TIGR02397 178 LEDIVERLKKILDKEGIKIEDEALELIARAADGSLRDALSLLDQLISFGN-GNITYEDVNELLG 240 (355)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCChHHHHHHHHHHHhhcC-CCCCHHHHHHHhC
Confidence 3444444444321 245788888888777765433333333333232222 3488888866553
No 190
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=22.65 E-value=98 Score=26.01 Aligned_cols=32 Identities=19% Similarity=0.310 Sum_probs=26.6
Q ss_pred CCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHH
Q 036580 30 FLPIANVSRIMKKALPANAKISKDAKETVQECVSEF 65 (186)
Q Consensus 30 ~LPkA~V~RImK~alP~~~rISkDA~~ai~k~aeeF 65 (186)
.+-++||.|.+... .+||++.++-|.+++++.
T Consensus 9 gVS~~TVSrvLn~~----~~vs~~tr~rV~~~a~~l 40 (327)
T PRK10423 9 GVSTSTVSHVINKD----RFVSEAITAKVEAAIKEL 40 (327)
T ss_pred CCcHHHHHHHhCCC----CCCCHHHHHHHHHHHHHH
Confidence 36789999999653 379999999999998875
No 191
>PF03477 ATP-cone: ATP cone domain; InterPro: IPR005144 The ATP-cone is an evolutionarily mobile, ATP-binding regulatory domain which is found in a variety of proteins including ribonucleotide reductases, phosphoglycerate kinases and transcriptional regulators []. In ribonucleotide reductase protein R1 (P28903 from SWISSPROT) from Escherichia coli this domain is located at the N terminus, and is composed mostly of helices []. It forms part of the allosteric effector region and contains the general allosteric activity site in a cleft located at the tip of the N-terminal region []. This site binds either ATP (activating) or dATP (inhibitory), with the base bound in a hydrophobic pocket and the phosphates bound to basic residues. Substrate binding to this site is thought to affect enzyme activity by altering the relative positions of the two subunits of ribonucleotide reductase.; PDB: 2XO4_A 1RLR_A 7R1R_B 5R1R_A 2XO5_B 2XAW_A 2R1R_C 2XAY_B 2X0X_C 2XAZ_A ....
Probab=22.40 E-value=53 Score=23.23 Aligned_cols=55 Identities=16% Similarity=0.291 Sum_probs=26.0
Q ss_pred CchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 036580 31 LPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMTT 96 (186)
Q Consensus 31 LPkA~V~RImK~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~AL~~ 96 (186)
|=..-|.+.+..+......++.+.... |+.+.........+..|+.++|..++..
T Consensus 13 F~~~KI~~~i~~a~~~~~~~~~~~~~~-----------i~~~V~~~l~~~~~~~is~~eI~~~v~~ 67 (90)
T PF03477_consen 13 FDREKIVRAIEKACEASRELSEEDAEE-----------IASEVENKLYDSGKEEISTEEIQDIVEN 67 (90)
T ss_dssp S-HHHHHHHHHTTCTTTSTTTST-HHH-----------HHHHHHTC-ST----TEEHHHHHHHHHH
T ss_pred ecHHHHHHHHHHHHHhcccccHHHHHH-----------HHHHHHHHHHhccCCCeeHHHHHHHHHH
Confidence 334555566666552122334333333 3333444455555668999998887764
No 192
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=22.39 E-value=1e+02 Score=26.27 Aligned_cols=32 Identities=16% Similarity=0.344 Sum_probs=26.5
Q ss_pred CCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHH
Q 036580 30 FLPIANVSRIMKKALPANAKISKDAKETVQECVSEF 65 (186)
Q Consensus 30 ~LPkA~V~RImK~alP~~~rISkDA~~ai~k~aeeF 65 (186)
.+-++||.|.++.. .+||++.++-|.+++++.
T Consensus 12 gVS~~TVSrvLn~~----~~vs~~tr~~V~~~a~el 43 (341)
T PRK10703 12 GVSTTTVSHVINKT----RFVAEETRNAVWAAIKEL 43 (341)
T ss_pred CCCHHHHHHHHcCC----CCCCHHHHHHHHHHHHHH
Confidence 46789999999753 379999999999998775
No 193
>PLN02900 alanyl-tRNA synthetase
Probab=22.15 E-value=6.1e+02 Score=26.64 Aligned_cols=28 Identities=21% Similarity=0.393 Sum_probs=21.5
Q ss_pred HhcCCCccCHHHHHHHHHHcCCc-cchHH
Q 036580 78 QREKRKTINGDDLLWAMTTLGFE-EYVEP 105 (186)
Q Consensus 78 ~~~kRKTIt~eDVl~AL~~LgF~-dyi~~ 105 (186)
+.+++++|+.+|+.....+.||+ |....
T Consensus 404 ~~~~~~~l~g~~af~LydTyGfP~dlt~~ 432 (936)
T PLN02900 404 KANGGPVLSGKDAFLLYDTYGFPVDLTEL 432 (936)
T ss_pred hhcCCCcCCHHHHHHHHhccCCCHHHHHH
Confidence 33456789999999999999997 44443
No 194
>cd00052 EH Eps15 homology domain; found in proteins implicated in endocytosis, vesicle transport, and signal transduction. The alignment contains a pair of EF-hand motifs, typically one of them is canonical and binds to Ca2+, while the other may not bind to Ca2+. A hydrophobic binding pocket is formed by residues from both EF-hand motifs. The EH domain binds to proteins containing NPF (class I), [WF]W or SWG (class II), or H[TS]F (class III) sequence motifs.
Probab=22.04 E-value=2.2e+02 Score=18.04 Aligned_cols=24 Identities=17% Similarity=0.196 Sum_probs=17.1
Q ss_pred HHHhcCCCccCHHHHHHHHHHcCC
Q 036580 76 KCQREKRKTINGDDLLWAMTTLGF 99 (186)
Q Consensus 76 ~a~~~kRKTIt~eDVl~AL~~LgF 99 (186)
....++.-+|+.+++..+|..+++
T Consensus 7 ~~D~~~~G~i~~~el~~~l~~~g~ 30 (67)
T cd00052 7 SLDPDGDGLISGDEARPFLGKSGL 30 (67)
T ss_pred HhCCCCCCcCcHHHHHHHHHHcCC
Confidence 344555667888888888888776
No 195
>PF12767 SAGA-Tad1: Transcriptional regulator of RNA polII, SAGA, subunit; InterPro: IPR024738 The yeast Spt-Ada-Gcn5-Acetyl (SAGA) transferase complex is a multifunctional coactivator involved in multiple cellular processes [], including regulation of transcription by RNA polymerase II [, ]. It is formed of five major modular subunits and shows a high degree of structural conservation to human TFTC and STAGA []. This entry represents Ada1 (known as Tada1 in higher eukaryotes), one of the subunits that constitute the SAGA core. It also functions as a component of the SALSA and SLIK complexes. ; GO: 0070461 SAGA-type complex
Probab=21.80 E-value=2.4e+02 Score=24.23 Aligned_cols=28 Identities=11% Similarity=0.126 Sum_probs=25.5
Q ss_pred ccCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 036580 49 KISKDAKETVQECVSEFISFVTGEASDK 76 (186)
Q Consensus 49 rISkDA~~ai~k~aeeFI~~Lts~A~~~ 76 (186)
-|+.||..+|+-+++.|+..|.....+.
T Consensus 223 gvs~~~a~ll~~ale~~LK~lI~s~l~~ 250 (252)
T PF12767_consen 223 GVSDDCANLLNLALEVHLKNLIKSCLDL 250 (252)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 7999999999999999999998877664
No 196
>PRK06645 DNA polymerase III subunits gamma and tau; Validated
Probab=21.46 E-value=2.2e+02 Score=27.54 Aligned_cols=65 Identities=8% Similarity=0.010 Sum_probs=37.7
Q ss_pred CchhHHHHHHHhhCC-CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhc--CCCccCHHHHHHHHH
Q 036580 31 LPIANVSRIMKKALP-ANAKISKDAKETVQECVSEFISFVTGEASDKCQRE--KRKTINGDDLLWAMT 95 (186)
Q Consensus 31 LPkA~V~RImK~alP-~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~--kRKTIt~eDVl~AL~ 95 (186)
|+...+..+++..+. .+..|+.+|...|.+.+.--+..+.++-...+... ....|+.+||...+-
T Consensus 187 ls~~el~~~L~~i~~~egi~ie~eAL~~Ia~~s~GslR~al~~Ldkai~~~~~~~~~It~~~V~~llg 254 (507)
T PRK06645 187 LSFEEIFKLLEYITKQENLKTDIEALRIIAYKSEGSARDAVSILDQAASMSAKSDNIISPQVINQMLG 254 (507)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhhccCCCCcCHHHHHHHHC
Confidence 444445545544442 25679999999998877554444444333322221 234789988876654
No 197
>KOG0027 consensus Calmodulin and related proteins (EF-Hand superfamily) [Signal transduction mechanisms]
Probab=21.20 E-value=3.9e+02 Score=20.58 Aligned_cols=42 Identities=21% Similarity=0.140 Sum_probs=33.1
Q ss_pred HHHHHHHHHHhcCCCccCHHHHHHHHHHcCCccchHHHHHHH
Q 036580 69 VTGEASDKCQREKRKTINGDDLLWAMTTLGFEEYVEPLKVYL 110 (186)
Q Consensus 69 Lts~A~~~a~~~kRKTIt~eDVl~AL~~LgF~dyi~~Lk~~L 110 (186)
-..+|...-..++.-.|+++++...|..||...-.++++.-+
T Consensus 86 el~eaF~~fD~d~~G~Is~~el~~~l~~lg~~~~~~e~~~mi 127 (151)
T KOG0027|consen 86 ELKEAFRVFDKDGDGFISASELKKVLTSLGEKLTDEECKEMI 127 (151)
T ss_pred HHHHHHHHHccCCCCcCcHHHHHHHHHHhCCcCCHHHHHHHH
Confidence 447788888888999999999999999999876644444433
No 198
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=20.82 E-value=1.3e+02 Score=25.34 Aligned_cols=35 Identities=17% Similarity=0.180 Sum_probs=26.8
Q ss_pred CCchhHHHHHHHhhCCCCcccCHHHHHHHHHHHHHH
Q 036580 30 FLPIANVSRIMKKALPANAKISKDAKETVQECVSEF 65 (186)
Q Consensus 30 ~LPkA~V~RImK~alP~~~rISkDA~~ai~k~aeeF 65 (186)
.+-++||.|++.... ...+||.+.++.|.+++++.
T Consensus 11 GVS~~TVSrvLn~~~-~~~~Vs~~tr~rV~~~a~el 45 (328)
T PRK11303 11 GVSRTTASYVINGKA-KQYRVSDKTVEKVMAVVREH 45 (328)
T ss_pred CCCHHHHHHHHcCCC-CCCCcCHHHHHHHHHHHHHh
Confidence 367899999996642 11379999999999998774
No 199
>PRK14963 DNA polymerase III subunits gamma and tau; Provisional
Probab=20.71 E-value=2.5e+02 Score=26.90 Aligned_cols=61 Identities=8% Similarity=0.030 Sum_probs=38.2
Q ss_pred CchhHHHHHHHhhCC-CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHH
Q 036580 31 LPIANVSRIMKKALP-ANAKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWA 93 (186)
Q Consensus 31 LPkA~V~RImK~alP-~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~~kRKTIt~eDVl~A 93 (186)
|+...|...++..+. ....|+.++..+|.+.+.-=+..+.......+.. ..+|+.+||...
T Consensus 175 ls~~el~~~L~~i~~~egi~i~~~Al~~ia~~s~GdlR~aln~Lekl~~~--~~~It~~~V~~~ 236 (504)
T PRK14963 175 LTEEEIAGKLRRLLEAEGREAEPEALQLVARLADGAMRDAESLLERLLAL--GTPVTRKQVEEA 236 (504)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHhc--CCCCCHHHHHHH
Confidence 556666555555432 2567899999999888766555555444443332 346888887654
No 200
>cd00823 TopoIIB_Trans TopoIIB_Trans: Transducer domain, having a ribosomal S5 domain 2-like fold, of the type found in proteins of the type IIB family of DNA topoisomerases similar to Sulfolobus shibatae topoisomerase VI (topoVI). The sole representative of the Type IIB family is topo VI. Topo VI enzymes are heterotetramers found in archaea and plants. S. shibatae topoVI relaxes both positive and negative supercoils, and in addition has a strong decatenase activity. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes.
Probab=20.67 E-value=1.7e+02 Score=24.22 Aligned_cols=34 Identities=18% Similarity=0.330 Sum_probs=26.6
Q ss_pred HhhCCCCcccCHHHHHHHHHHHHHHHHHHHHHHH
Q 036580 41 KKALPANAKISKDAKETVQECVSEFISFVTGEAS 74 (186)
Q Consensus 41 K~alP~~~rISkDA~~ai~k~aeeFI~~Lts~A~ 74 (186)
|+++.+.--|-+|.+.+|++||...-.||...-.
T Consensus 111 KeaIadvpEI~~EIrlAl~~~~R~L~~~l~kk~~ 144 (151)
T cd00823 111 KEAIADIPEIEEEIKLALQEVARKLKRYLSKKRK 144 (151)
T ss_pred hhhhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4555455568889999999999999999987653
No 201
>PRK14954 DNA polymerase III subunits gamma and tau; Provisional
Probab=20.66 E-value=4e+02 Score=26.45 Aligned_cols=64 Identities=11% Similarity=0.093 Sum_probs=36.7
Q ss_pred CchhHHHHHHHhhCC-CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHh----cCCCccCHHHHHHHH
Q 036580 31 LPIANVSRIMKKALP-ANAKISKDAKETVQECVSEFISFVTGEASDKCQR----EKRKTINGDDLLWAM 94 (186)
Q Consensus 31 LPkA~V~RImK~alP-~~~rISkDA~~ai~k~aeeFI~~Lts~A~~~a~~----~kRKTIt~eDVl~AL 94 (186)
|+...|.+.+++.+. ....|+.++...|.+.+.-=+..+..+-...+.- ..+++|+.+||...+
T Consensus 186 l~~~ei~~~L~~i~~~egi~I~~eal~~La~~s~Gdlr~al~eLeKL~~y~~~~~~~~~It~~~V~~lv 254 (620)
T PRK14954 186 IPLDEIQSQLQMICRAEGIQIDADALQLIARKAQGSMRDAQSILDQVIAFSVGSEAEKVIAYQGVAELL 254 (620)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHHHhccccccCCccCHHHHHHHH
Confidence 444444444443322 1456999999888877765444444443332222 346788988886654
No 202
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=20.57 E-value=1.7e+02 Score=31.28 Aligned_cols=26 Identities=15% Similarity=0.245 Sum_probs=13.5
Q ss_pred cccCHHHHH---HHHHHHHHHHHHHHHHH
Q 036580 48 AKISKDAKE---TVQECVSEFISFVTGEA 73 (186)
Q Consensus 48 ~rISkDA~~---ai~k~aeeFI~~Lts~A 73 (186)
.+||-||.. .|.-|.|..|..++..-
T Consensus 1088 lqIshEaAAcItgLr~AmEaLvvev~knP 1116 (1282)
T KOG0921|consen 1088 LQISHEAAACITGLRPAMEALVVEVCKNP 1116 (1282)
T ss_pred EeccHHHHHHHhhhHHHHHHHHHHHhcCh
Confidence 456766643 34455555554444433
No 203
>PRK06474 hypothetical protein; Provisional
Probab=20.46 E-value=1.8e+02 Score=23.88 Aligned_cols=14 Identities=21% Similarity=0.287 Sum_probs=11.5
Q ss_pred CCchhHHHHHHHhh
Q 036580 30 FLPIANVSRIMKKA 43 (186)
Q Consensus 30 ~LPkA~V~RImK~a 43 (186)
.+|.++|+|.+|.-
T Consensus 38 ~is~aTvYrhL~~L 51 (178)
T PRK06474 38 DVPQATLYRHLQTM 51 (178)
T ss_pred CCCHHHHHHHHHHH
Confidence 59999999988654
Done!