Query 030547
Match_columns 175
No_of_seqs 159 out of 598
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 15:23:38 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030547.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030547hhsearch_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 8.2E-43 1.8E-47 280.5 14.7 149 1-152 1-150 (168)
2 KOG0871 Class 2 transcription 100.0 2.7E-29 5.9E-34 200.6 9.2 110 26-141 6-115 (156)
3 KOG0870 DNA polymerase epsilon 99.9 3.2E-27 6.9E-32 191.5 9.4 103 25-127 3-106 (172)
4 COG5150 Class 2 transcription 99.9 6.3E-23 1.4E-27 161.2 9.5 98 26-123 5-102 (148)
5 PF00808 CBFD_NFYB_HMF: Histon 99.8 1.5E-18 3.2E-23 119.7 7.9 64 32-96 2-65 (65)
6 COG2036 HHT1 Histones H3 and H 99.7 2.8E-17 6E-22 122.5 6.9 79 25-105 12-90 (91)
7 cd00076 H4 Histone H4, one of 99.2 1.2E-10 2.6E-15 85.9 8.5 72 31-104 12-83 (85)
8 PLN00035 histone H4; Provision 99.1 2.2E-10 4.9E-15 87.3 8.6 75 26-102 23-97 (103)
9 PTZ00015 histone H4; Provision 99.1 6E-10 1.3E-14 84.8 8.6 77 26-104 24-100 (102)
10 smart00803 TAF TATA box bindin 98.9 4.3E-09 9.4E-14 73.8 7.6 64 32-97 2-65 (65)
11 smart00428 H3 Histone H3. 98.9 4E-09 8.7E-14 80.6 7.2 74 26-99 23-101 (105)
12 smart00417 H4 Histone H4. 98.9 4.1E-09 8.9E-14 76.1 6.0 65 29-95 10-74 (74)
13 cd07981 TAF12 TATA Binding Pro 98.8 2.2E-08 4.7E-13 71.1 8.5 65 33-98 2-66 (72)
14 PF00125 Histone: Core histone 98.8 1E-08 2.2E-13 71.6 6.6 68 30-97 3-73 (75)
15 PLN00161 histone H3; Provision 98.6 2.3E-07 5E-12 73.8 7.6 72 26-97 49-124 (135)
16 PLN00160 histone H3; Provision 98.6 1.9E-07 4E-12 70.7 6.7 72 26-97 15-90 (97)
17 PLN00121 histone H3; Provision 98.6 1.4E-07 2.9E-12 75.2 6.1 71 27-97 57-130 (136)
18 COG5208 HAP5 CCAAT-binding fac 98.6 5.6E-08 1.2E-12 83.3 4.0 78 29-108 106-184 (286)
19 PTZ00018 histone H3; Provision 98.5 1.7E-07 3.7E-12 74.7 6.0 71 27-97 57-130 (136)
20 KOG1657 CCAAT-binding factor, 98.5 2.2E-07 4.8E-12 79.7 5.8 87 28-115 70-159 (236)
21 smart00576 BTP Bromodomain tra 98.3 3.9E-06 8.5E-11 59.9 8.3 66 35-102 9-74 (77)
22 cd00074 H2A Histone 2A; H2A is 98.2 5.4E-06 1.2E-10 64.3 7.1 68 30-98 18-85 (115)
23 cd07979 TAF9 TATA Binding Prot 98.0 3.7E-05 8E-10 59.4 8.9 79 36-116 5-84 (117)
24 cd08050 TAF6 TATA Binding Prot 97.8 7E-05 1.5E-09 66.8 8.4 67 34-102 1-67 (343)
25 PF15630 CENP-S: Kinetochore c 97.8 7.3E-05 1.6E-09 54.1 6.7 61 37-97 10-71 (76)
26 smart00427 H2B Histone H2B. 97.8 0.00013 2.8E-09 54.6 7.7 62 37-99 6-67 (89)
27 KOG1745 Histones H3 and H4 [Ch 97.8 1.6E-05 3.5E-10 63.5 2.7 75 26-100 57-134 (137)
28 PF15511 CENP-T: Centromere ki 97.7 5.9E-05 1.3E-09 69.0 6.3 66 26-91 345-414 (414)
29 PF03847 TFIID_20kDa: Transcri 97.7 0.00027 5.8E-09 50.1 7.3 63 35-98 2-64 (68)
30 KOG3467 Histone H4 [Chromatin 97.6 0.00033 7.2E-09 52.7 7.3 69 32-102 29-97 (103)
31 PLN00158 histone H2B; Provisio 97.6 0.00041 8.9E-09 54.1 7.8 65 34-99 29-93 (116)
32 PF07524 Bromo_TP: Bromodomain 97.5 0.00084 1.8E-08 47.5 8.5 63 37-102 11-74 (77)
33 KOG1142 Transcription initiati 97.5 0.00043 9.2E-09 60.4 8.2 69 28-97 150-218 (258)
34 PTZ00463 histone H2B; Provisio 97.5 0.00051 1.1E-08 53.7 7.7 62 37-99 33-94 (117)
35 cd08048 TAF11 TATA Binding Pro 97.4 0.00096 2.1E-08 49.2 8.1 66 32-99 16-84 (85)
36 PF09415 CENP-X: CENP-S associ 97.4 0.00019 4.1E-09 51.4 4.2 65 34-98 1-67 (72)
37 PF04719 TAFII28: hTAFII28-lik 97.2 0.002 4.4E-08 48.1 7.3 67 32-99 23-90 (90)
38 KOG1659 Class 2 transcription 97.2 0.0009 2E-08 57.1 6.0 81 31-112 12-92 (224)
39 COG5262 HTA1 Histone H2A [Chro 97.2 0.00097 2.1E-08 52.5 5.7 67 30-97 24-90 (132)
40 PF02969 TAF: TATA box binding 97.0 0.006 1.3E-07 43.1 7.8 64 32-97 3-66 (66)
41 smart00414 H2A Histone 2A. 96.9 0.0036 7.9E-08 47.9 6.3 68 30-98 7-74 (106)
42 COG5247 BUR6 Class 2 transcrip 96.8 0.0062 1.3E-07 46.9 7.2 80 29-109 20-99 (113)
43 PLN00154 histone H2A; Provisio 96.6 0.0066 1.4E-07 48.6 6.4 68 30-97 36-103 (136)
44 KOG1744 Histone H2B [Chromatin 96.6 0.0089 1.9E-07 47.4 6.9 60 38-98 43-102 (127)
45 PTZ00017 histone H2A; Provisio 96.4 0.0086 1.9E-07 47.8 5.7 67 30-97 25-91 (134)
46 PF15510 CENP-W: Centromere ki 96.3 0.0081 1.7E-07 45.5 5.0 67 31-98 15-95 (102)
47 KOG1658 DNA polymerase epsilon 96.2 0.0026 5.5E-08 52.1 2.0 66 31-98 58-124 (162)
48 PF02269 TFIID-18kDa: Transcri 96.2 0.0064 1.4E-07 45.2 3.8 59 39-98 8-66 (93)
49 PLN00156 histone H2AX; Provisi 96.1 0.036 7.8E-07 44.6 8.0 67 30-97 27-93 (139)
50 KOG1756 Histone 2A [Chromatin 96.0 0.023 4.9E-07 45.2 6.1 68 29-97 24-91 (131)
51 PLN00157 histone H2A; Provisio 95.9 0.017 3.7E-07 46.0 5.4 67 30-97 24-90 (132)
52 PLN00153 histone H2A; Provisio 95.9 0.021 4.5E-07 45.4 5.6 67 30-97 22-88 (129)
53 cd07978 TAF13 The TATA Binding 94.8 0.25 5.5E-06 36.8 8.1 74 37-114 7-80 (92)
54 KOG3219 Transcription initiati 94.6 0.05 1.1E-06 46.0 4.3 69 32-102 112-181 (195)
55 PF02291 TFIID-31kDa: Transcri 93.8 0.35 7.6E-06 38.3 7.4 86 28-115 6-94 (129)
56 PTZ00252 histone H2A; Provisio 93.8 0.22 4.8E-06 39.9 6.2 63 30-97 23-91 (134)
57 KOG4336 TBP-associated transcr 92.7 0.78 1.7E-05 41.4 8.6 77 37-117 10-86 (323)
58 TIGR03015 pepcterm_ATPase puta 91.8 0.7 1.5E-05 38.1 6.9 70 33-102 192-269 (269)
59 KOG3423 Transcription initiati 90.7 1.6 3.4E-05 36.4 7.8 69 32-102 86-168 (176)
60 PRK00411 cdc6 cell division co 88.7 2.4 5.1E-05 37.2 7.9 70 35-104 209-287 (394)
61 TIGR02928 orc1/cdc6 family rep 86.3 3.8 8.2E-05 35.5 7.7 75 35-109 201-284 (365)
62 KOG2549 Transcription initiati 85.6 4.6 9.9E-05 39.2 8.4 65 35-101 14-78 (576)
63 KOG2389 Predicted bromodomain 82.9 3.9 8.5E-05 37.5 6.4 69 31-101 28-96 (353)
64 TIGR02902 spore_lonB ATP-depen 81.3 4.2 9.1E-05 38.4 6.3 64 35-99 265-332 (531)
65 PF13654 AAA_32: AAA domain; P 79.1 10 0.00022 36.1 8.1 49 51-99 447-506 (509)
66 TIGR00764 lon_rel lon-related 78.4 9.1 0.0002 37.0 7.6 50 51-100 330-392 (608)
67 COG1067 LonB Predicted ATP-dep 77.6 2.3 4.9E-05 41.7 3.4 49 51-99 338-399 (647)
68 cd08045 TAF4 TATA Binding Prot 72.2 18 0.00039 30.1 7.1 80 28-107 40-127 (212)
69 PF08369 PCP_red: Proto-chloro 71.2 6.6 0.00014 25.5 3.3 42 53-95 2-44 (45)
70 PF13335 Mg_chelatase_2: Magne 70.9 18 0.00038 26.8 6.0 47 51-97 42-94 (96)
71 KOG3334 Transcription initiati 70.1 15 0.00033 29.9 5.9 65 52-116 31-96 (148)
72 COG5095 TAF6 Transcription ini 69.4 12 0.00026 34.7 5.6 53 50-102 21-73 (450)
73 KOG2680 DNA helicase TIP49, TB 69.0 22 0.00049 33.0 7.3 60 38-97 363-427 (454)
74 cd04752 Commd4 COMM_Domain con 67.1 21 0.00046 28.9 6.3 50 63-119 43-93 (174)
75 PF02861 Clp_N: Clp amino term 65.9 5.9 0.00013 24.9 2.3 26 75-100 1-26 (53)
76 PRK00080 ruvB Holliday junctio 65.5 30 0.00066 30.0 7.3 72 32-103 179-254 (328)
77 COG1224 TIP49 DNA helicase TIP 63.4 23 0.0005 33.4 6.4 82 33-117 361-447 (450)
78 KOG3901 Transcription initiati 62.2 23 0.00051 27.5 5.2 48 48-98 24-71 (109)
79 TIGR00635 ruvB Holliday juncti 62.1 47 0.001 28.1 7.7 70 33-102 159-232 (305)
80 COG5248 TAF19 Transcription in 61.1 26 0.00055 27.7 5.3 49 48-98 24-72 (126)
81 KOG1757 Histone 2A [Chromatin 61.1 13 0.00029 29.3 3.8 65 29-97 27-95 (131)
82 TIGR01128 holA DNA polymerase 59.5 49 0.0011 27.6 7.3 66 32-97 110-176 (302)
83 TIGR02442 Cob-chelat-sub cobal 57.3 42 0.00091 32.5 7.3 49 49-97 247-302 (633)
84 TIGR02030 BchI-ChlI magnesium 56.8 53 0.0011 29.5 7.4 54 43-97 247-307 (337)
85 PRK09862 putative ATP-dependen 56.4 43 0.00094 31.9 7.1 55 50-104 437-497 (506)
86 PF00531 Death: Death domain; 55.1 20 0.00044 24.3 3.6 30 83-112 54-83 (83)
87 PRK13406 bchD magnesium chelat 54.2 33 0.00072 33.2 6.0 52 45-97 190-248 (584)
88 PRK13765 ATP-dependent proteas 52.2 38 0.00082 33.2 6.1 47 51-97 339-398 (637)
89 PRK12402 replication factor C 51.3 36 0.00078 28.8 5.3 70 33-104 184-254 (337)
90 COG1222 RPT1 ATP-dependent 26S 50.7 27 0.00059 32.7 4.6 75 25-99 313-392 (406)
91 TIGR01052 top6b DNA topoisomer 48.8 20 0.00043 34.2 3.6 59 43-115 426-484 (488)
92 TIGR00368 Mg chelatase-related 47.4 50 0.0011 31.3 6.0 47 51-97 445-497 (499)
93 smart00350 MCM minichromosome 47.3 69 0.0015 30.1 6.9 65 31-98 416-503 (509)
94 PRK05574 holA DNA polymerase I 45.9 66 0.0014 27.4 6.1 66 32-97 145-211 (340)
95 PF05236 TAF4: Transcription i 45.3 33 0.00072 29.4 4.1 78 26-103 37-122 (264)
96 PRK07452 DNA polymerase III su 45.3 59 0.0013 27.9 5.7 64 38-101 135-201 (326)
97 COG5162 Transcription initiati 45.1 1.4E+02 0.003 25.2 7.6 49 53-101 107-188 (197)
98 CHL00081 chlI Mg-protoporyphyr 44.7 85 0.0018 28.6 6.8 54 43-97 260-320 (350)
99 PLN00138 large subunit ribosom 44.7 71 0.0015 24.7 5.5 31 70-102 3-33 (113)
100 PF08823 PG_binding_2: Putativ 44.2 41 0.00089 24.0 3.8 31 90-120 19-55 (74)
101 TIGR02031 BchD-ChlD magnesium 43.6 87 0.0019 30.2 7.1 55 42-97 195-256 (589)
102 COG1474 CDC6 Cdc6-related prot 43.4 97 0.0021 28.1 7.0 73 36-108 193-274 (366)
103 PF07647 SAM_2: SAM domain (St 43.3 30 0.00064 22.8 2.8 25 86-110 3-27 (66)
104 TIGR01242 26Sp45 26S proteasom 42.8 35 0.00075 30.2 4.0 33 67-99 331-363 (364)
105 PTZ00373 60S Acidic ribosomal 42.1 88 0.0019 24.3 5.6 32 69-102 4-35 (112)
106 PTZ00361 26 proteosome regulat 42.1 35 0.00075 31.9 4.0 32 68-99 393-424 (438)
107 PRK03992 proteasome-activating 42.0 36 0.00078 30.7 4.0 34 67-100 340-373 (389)
108 KOG1528 Salt-sensitive 3'-phos 41.3 78 0.0017 29.0 5.9 75 25-100 43-124 (351)
109 COG5624 TAF61 Transcription in 40.6 14 0.00031 34.9 1.2 78 31-108 382-462 (505)
110 PF09114 MotA_activ: Transcrip 40.3 43 0.00093 25.5 3.5 32 36-67 51-86 (96)
111 PRK13407 bchI magnesium chelat 39.6 1E+02 0.0022 27.7 6.5 53 43-96 244-303 (334)
112 PF00356 LacI: Bacterial regul 39.4 63 0.0014 20.9 3.8 32 32-67 10-41 (46)
113 PF08681 DUF1778: Protein of u 38.8 26 0.00057 24.9 2.2 51 49-99 3-61 (80)
114 cd00166 SAM Sterile alpha moti 37.6 27 0.00058 22.1 1.9 24 88-111 3-26 (63)
115 PF00536 SAM_1: SAM domain (St 37.4 39 0.00084 22.1 2.7 22 88-109 4-25 (64)
116 COG5251 TAF40 Transcription in 37.3 52 0.0011 27.8 3.9 61 32-96 115-178 (199)
117 PTZ00454 26S protease regulato 36.5 46 0.00099 30.5 3.8 32 68-99 355-386 (398)
118 PF12010 DUF3502: Domain of un 36.4 34 0.00075 26.5 2.6 60 54-117 72-131 (134)
119 COG1466 HolA DNA polymerase II 35.3 90 0.002 27.4 5.4 61 38-98 145-206 (334)
120 COG1724 Predicted RNA binding 35.0 27 0.00058 25.0 1.6 17 86-102 6-22 (66)
121 PF12627 PolyA_pol_RNAbd: Prob 34.3 7.7 0.00017 25.6 -1.2 59 49-111 1-63 (64)
122 PF07499 RuvA_C: RuvA, C-termi 33.7 30 0.00065 22.2 1.6 14 90-103 4-17 (47)
123 cd05833 Ribosomal_P2 Ribosomal 33.6 1.4E+02 0.003 22.9 5.5 31 70-102 3-33 (109)
124 COG1389 DNA topoisomerase VI, 32.9 34 0.00073 33.0 2.4 46 43-88 434-479 (538)
125 cd00823 TopoIIB_Trans TopoIIB_ 32.8 78 0.0017 25.9 4.2 33 43-75 111-143 (151)
126 PRK07914 hypothetical protein; 32.7 94 0.002 27.0 5.0 63 34-97 129-192 (320)
127 smart00454 SAM Sterile alpha m 31.4 37 0.0008 21.6 1.8 26 86-111 3-28 (68)
128 PF13405 EF-hand_6: EF-hand do 31.4 55 0.0012 18.6 2.4 26 75-100 5-31 (31)
129 smart00027 EH Eps15 homology d 31.4 96 0.0021 22.0 4.1 28 75-102 15-42 (96)
130 PRK02910 light-independent pro 31.3 96 0.0021 29.3 5.2 52 48-100 466-518 (519)
131 TIGR01278 DPOR_BchB light-inde 31.2 98 0.0021 29.1 5.2 51 49-100 460-511 (511)
132 PRK14868 DNA topoisomerase VI 30.6 55 0.0012 33.2 3.6 70 26-98 611-682 (795)
133 PF10728 DUF2520: Domain of un 30.2 1.8E+02 0.004 22.5 5.8 58 36-96 14-74 (132)
134 PRK06585 holA DNA polymerase I 29.4 1.4E+02 0.0031 25.8 5.6 62 36-97 145-208 (343)
135 PRK00440 rfc replication facto 28.8 1E+02 0.0022 25.8 4.4 65 33-99 161-226 (319)
136 PRK09526 lacI lac repressor; R 28.1 56 0.0012 27.5 2.8 37 32-73 16-52 (342)
137 PRK14975 bifunctional 3'-5' ex 28.0 3.8E+02 0.0082 25.5 8.6 89 29-120 160-268 (553)
138 PTZ00183 centrin; Provisional 26.9 2.5E+02 0.0054 20.6 5.9 20 79-98 62-81 (158)
139 PF11753 DUF3310: Protein of u 26.5 1.9E+02 0.0042 19.6 4.7 42 55-98 14-57 (60)
140 PRK14867 DNA topoisomerase VI 26.1 76 0.0016 31.5 3.6 37 51-87 592-628 (659)
141 PRK04184 DNA topoisomerase VI 25.8 52 0.0011 31.8 2.4 57 43-99 431-489 (535)
142 PRK14971 DNA polymerase III su 25.6 1.3E+02 0.0028 29.3 5.1 64 33-97 180-244 (614)
143 PHA03328 nuclear egress lamina 25.4 81 0.0018 28.7 3.4 69 27-103 228-296 (316)
144 TIGR03261 phnS2 putative 2-ami 25.2 1.7E+02 0.0038 25.0 5.4 60 61-120 260-330 (334)
145 TIGR02903 spore_lon_C ATP-depe 24.8 1.5E+02 0.0033 28.7 5.4 72 35-106 355-437 (615)
146 PF00403 HMA: Heavy-metal-asso 24.8 53 0.0011 21.2 1.7 16 87-102 47-62 (62)
147 CHL00076 chlB photochlorophyll 24.5 1.6E+02 0.0034 27.9 5.3 51 49-100 461-512 (513)
148 PRK12728 fliE flagellar hook-b 24.0 3.2E+02 0.0069 20.6 6.4 38 81-119 59-98 (102)
149 cd00051 EFh EF-hand, calcium b 23.9 1.6E+02 0.0035 17.1 4.6 38 78-115 8-45 (63)
150 PTZ00184 calmodulin; Provision 23.8 2.5E+02 0.0053 20.2 5.3 38 74-111 88-125 (149)
151 PLN02900 alanyl-tRNA synthetas 23.2 3.2E+02 0.0069 28.3 7.5 29 80-108 404-433 (936)
152 PF03540 TFIID_30kDa: Transcri 23.1 2.5E+02 0.0053 19.0 6.3 48 32-81 2-49 (51)
153 PF02718 Herpes_UL31: Herpesvi 22.6 1.3E+02 0.0028 26.6 4.1 78 26-118 177-254 (258)
154 COG5340 Predicted transcriptio 22.6 1.3E+02 0.0028 26.7 4.0 54 26-79 148-207 (269)
155 PRK05932 RNA polymerase factor 22.1 1.5E+02 0.0033 27.8 4.6 41 76-120 405-445 (455)
156 TIGR02639 ClpA ATP-dependent C 22.1 1.2E+02 0.0026 29.8 4.2 23 74-96 11-33 (731)
157 smart00354 HTH_LACI helix_turn 22.0 1.5E+02 0.0032 20.1 3.5 32 32-67 11-42 (70)
158 PRK10727 DNA-binding transcrip 21.8 82 0.0018 26.7 2.6 37 33-74 13-49 (343)
159 PF09339 HTH_IclR: IclR helix- 21.6 49 0.0011 21.1 1.0 17 30-46 27-43 (52)
160 PF09239 Topo-VIb_trans: Topoi 21.4 97 0.0021 25.6 2.9 33 43-75 120-152 (160)
161 PF02361 CbiQ: Cobalt transpor 21.3 4.1E+02 0.0089 20.9 7.7 63 51-119 95-169 (224)
162 PF12668 DUF3791: Protein of u 20.5 1.1E+02 0.0024 20.6 2.6 30 84-113 14-43 (62)
163 cd00083 HLH Helix-loop-helix d 20.5 1.8E+02 0.0038 18.4 3.5 35 40-74 24-58 (60)
164 PRK14987 gluconate operon tran 20.4 93 0.002 26.1 2.7 37 32-73 16-52 (331)
165 PRK05907 hypothetical protein; 20.1 2.5E+02 0.0054 24.9 5.4 72 49-120 151-232 (311)
No 1
>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [Transcription]
Probab=100.00 E-value=8.2e-43 Score=280.52 Aligned_cols=149 Identities=62% Similarity=0.992 Sum_probs=124.8
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCC-CCCCcccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 030547 1 MAEAPTSPAGGSHESGGEQSPHA-GGVREQDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKC 79 (175)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~d~~LP~A~V~RImK~~LP~~~kISkDA~~al~~~aseFI~~LtseA~~~~ 79 (175)
|++++..+ ++.++.||.+.+.+ ..++++|++||+|+|.||||+.||.+.||||||++.+|+|++|||+|||++|+++|
T Consensus 1 m~~s~~~~-~~~~e~~g~~~~~~~~~~reqDr~LPIANV~RIMK~~lP~naKIsKDAKE~vQECVSEfISFvT~EAsekC 79 (168)
T KOG0869|consen 1 MAESDHDS-GGGDENGGNSSPQSSLSLREQDRFLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASEKC 79 (168)
T ss_pred CCCCcCCC-CccccCCcccCCccccccchhhhhccHHHHHHHHHhcCCcccccchHHHHHHHHHHHHHHHHHhhHHHHHH
Confidence 56666655 45677766554443 67999999999999999999999999999999999999999999999999999999
Q ss_pred HhcCCCccChhhHHHHHHHcCCCcchHHHHHHHHHHHHHhhcccCCCCCCCCCCCCCcCCCCCCCcccccccC
Q 030547 80 QKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLMRYREMEGDTKGSARGGDGSAKRDTIGALPGQNAQYALQG 152 (175)
Q Consensus 80 ~~~kRKTI~~eDVl~AL~~LgF~~yv~~Lk~~L~~yre~~~~kk~~~k~~~~~~k~~~~~~~~~~~~~~~~~~ 152 (175)
.+++|||||+|||||||..|||++|+++|+.||.+|||+++++....+.+... .+.-...-+...+++.||
T Consensus 80 ~~EkRKTIngdDllwAm~tLGFe~Y~eplkiyL~kYRe~e~e~~~~~~~~~~~--~~~~~~~~~~~~~~~~~g 150 (168)
T KOG0869|consen 80 QREKRKTINGDDLLWAMSTLGFENYAEPLKIYLQKYRELEGERGRSGKGGQMT--GGNGIDEHGPSGEVPEQG 150 (168)
T ss_pred HHHhcCcccHHHHHHHHHHcCcHhHHHHHHHHHHHHHHHhhhcccccccCccc--ccccccccCCCcCCCCCC
Confidence 99999999999999999999999999999999999999999888877666522 232222334445566665
No 2
>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=99.96 E-value=2.7e-29 Score=200.60 Aligned_cols=110 Identities=31% Similarity=0.564 Sum_probs=99.7
Q ss_pred CCcccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHHcCCCcch
Q 030547 26 VREQDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYI 105 (175)
Q Consensus 26 ~~~~d~~LP~A~V~RImK~~LP~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~~yv 105 (175)
-..+|+.||+|+|.+|||+.||.+++|.+||++.|.+||.+||+.|+++||++|.++.||||++|||++||+.|||.+|+
T Consensus 6 ~~dde~sLPkAtv~KmIke~lP~d~rvakeareliincCvEFI~liSsEAneic~~e~KKTIa~EHV~KALe~LgF~eYi 85 (156)
T KOG0871|consen 6 KEDDELSLPKATVNKMIKEMLPKDVRVAKEARELIINCCVEFINLISSEANEICNKEAKKTIAPEHVIKALENLGFGEYI 85 (156)
T ss_pred cccccccCcHHHHHHHHHHhCCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHhHHhcccCCHHHHHHHHHHcchHHHH
Confidence 45788999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHhhcccCCCCCCCCCCCCCcCCCC
Q 030547 106 DPLKAYLMRYREMEGDTKGSARGGDGSAKRDTIGAL 141 (175)
Q Consensus 106 ~~Lk~~L~~yre~~~~kk~~~k~~~~~~k~~~~~~~ 141 (175)
+.+.+.|+.|+..... ....++|-..+|.+
T Consensus 86 ee~~~vl~~~K~~~~~------~~~kssk~e~~Gi~ 115 (156)
T KOG0871|consen 86 EEAEEVLENCKEEAKK------RRRKSSKFEKSGIP 115 (156)
T ss_pred HHHHHHHHHHHHHHHH------hhhhhhhHHhcCCC
Confidence 9999999999986642 22335666667765
No 3
>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription]
Probab=99.94 E-value=3.2e-27 Score=191.54 Aligned_cols=103 Identities=32% Similarity=0.526 Sum_probs=98.4
Q ss_pred CCCcccccCchhHHHHHHHhhCCCC-CcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHHcCCCc
Q 030547 25 GVREQDRYLPIANISRIMKKALPAN-GKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFED 103 (175)
Q Consensus 25 ~~~~~d~~LP~A~V~RImK~~LP~~-~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~~ 103 (175)
..+++|+.||+|+|.||+|++||+. +.|+|||+.+|+++|++||+|||+.|+++|+.++||||+++|||.||++|+|..
T Consensus 3 ~eri~dl~lP~AiI~rlvke~l~E~~vsisKeA~~Ai~raAtVFv~~Lts~s~e~A~~q~rKt~sadDVl~aL~Eiefs~ 82 (172)
T KOG0870|consen 3 DERIEDLNLPNAIITRLVKEVLPESNVSISKEARLAIARAATVFVIFLTSVSNEIAKDQKRKTISADDVLKALDEIEFSS 82 (172)
T ss_pred chhHHHhhccHHHHHHHHHHhCccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCcccHHHHHHHHHHhchHH
Confidence 4688999999999999999999986 899999999999999999999999999999999999999999999999999999
Q ss_pred chHHHHHHHHHHHHHhhcccCCCC
Q 030547 104 YIDPLKAYLMRYREMEGDTKGSAR 127 (175)
Q Consensus 104 yv~~Lk~~L~~yre~~~~kk~~~k 127 (175)
|+.+|+..|+.||...++||.++.
T Consensus 83 f~~plk~~Le~yk~~~k~Kk~~~~ 106 (172)
T KOG0870|consen 83 FVNPLKSALEAYKKAVKQKKLAKA 106 (172)
T ss_pred HhhHHHHHHHHHHHHHHHHHHhcc
Confidence 999999999999999888887654
No 4
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=99.89 E-value=6.3e-23 Score=161.20 Aligned_cols=98 Identities=26% Similarity=0.507 Sum_probs=93.0
Q ss_pred CCcccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHHcCCCcch
Q 030547 26 VREQDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYI 105 (175)
Q Consensus 26 ~~~~d~~LP~A~V~RImK~~LP~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~~yv 105 (175)
-..+++.||+|+|.++|-+.||.+..+.|||++.+++||.+||+.|+++||+.|..+.+|||.++||++||+.|+|.+|+
T Consensus 5 ~~dDe~sLPKATVqKMvS~iLp~dl~ftKearei~in~cieFi~~lsseAne~ce~EaKKTIa~EHviKALenLef~eyi 84 (148)
T COG5150 5 KNDDENSLPKATVQKMVSSILPKDLVFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHVIKALENLEFEEYI 84 (148)
T ss_pred cccccccCcHHHHHHHHHHhccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHhccHHHHH
Confidence 45678999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHhhccc
Q 030547 106 DPLKAYLMRYREMEGDTK 123 (175)
Q Consensus 106 ~~Lk~~L~~yre~~~~kk 123 (175)
+.+.+.++.|+..++.|.
T Consensus 85 ~~~~e~~~n~k~~qK~ke 102 (148)
T COG5150 85 ESCMEEHENYKSYQKQKE 102 (148)
T ss_pred HHHHHHHHHHHHHHhhch
Confidence 999999999998875443
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=99.77 E-value=1.5e-18 Score=119.70 Aligned_cols=64 Identities=36% Similarity=0.624 Sum_probs=59.4
Q ss_pred cCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHH
Q 030547 32 YLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAM 96 (175)
Q Consensus 32 ~LP~A~V~RImK~~LP~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL 96 (175)
.||++.|.||||.. |++.+||+||.++|++|+++||.||+.+|++.|.+++||||+++||..||
T Consensus 2 ~lP~a~vkri~k~~-~~~~~vs~ea~~~i~~a~e~Fi~~l~~~A~~~a~~~~rkti~~~Dv~~Av 65 (65)
T PF00808_consen 2 SLPLARVKRIMKSD-PDVMRVSKEAVEAIAKAAEEFIQYLAKEANEIAQRDKRKTITYEDVAKAV 65 (65)
T ss_dssp SS-HHHHHHHHHHT-STTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEE-HHHHHHHH
T ss_pred CCChHHHHHHhccC-CCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHC
Confidence 69999999999999 88899999999999999999999999999999999999999999999986
No 6
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=99.70 E-value=2.8e-17 Score=122.52 Aligned_cols=79 Identities=30% Similarity=0.465 Sum_probs=75.2
Q ss_pred CCCcccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHHcCCCcc
Q 030547 25 GVREQDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDY 104 (175)
Q Consensus 25 ~~~~~d~~LP~A~V~RImK~~LP~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~~y 104 (175)
..+..+..||+++|.||||++.++ +||.+|+++|++|+++|+..|+..|++.|.+.|||||+++||..|++.+||..|
T Consensus 12 ~~~~~~~~Lp~apv~Ri~r~~~~~--Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~DI~la~~~~~~~~~ 89 (91)
T COG2036 12 YQRSTDLLLPKAPVRRILRKAGAE--RVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLALKRLGRRIY 89 (91)
T ss_pred hhhhhhhhcCchHHHHHHHHHhHH--HhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHHHhccccc
Confidence 467889999999999999999986 999999999999999999999999999999999999999999999999999866
Q ss_pred h
Q 030547 105 I 105 (175)
Q Consensus 105 v 105 (175)
.
T Consensus 90 ~ 90 (91)
T COG2036 90 G 90 (91)
T ss_pred c
Confidence 3
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=99.19 E-value=1.2e-10 Score=85.94 Aligned_cols=72 Identities=19% Similarity=0.337 Sum_probs=66.7
Q ss_pred ccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHHcCCCcc
Q 030547 31 RYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDY 104 (175)
Q Consensus 31 ~~LP~A~V~RImK~~LP~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~~y 104 (175)
..||++.|.||++... ..+||.|+.+.+.++..+|+..|..+|...|++.+||||+++||..||+..|-.-|
T Consensus 12 ~gi~k~~I~RLarr~G--vkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~alkr~g~~~y 83 (85)
T cd00076 12 KGITKPAIRRLARRGG--VKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLY 83 (85)
T ss_pred ccCCHHHHHHHHHHcC--cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHCCCCcc
Confidence 3599999999999996 46999999999999999999999999999999999999999999999999985543
No 8
>PLN00035 histone H4; Provisional
Probab=99.15 E-value=2.2e-10 Score=87.27 Aligned_cols=75 Identities=16% Similarity=0.275 Sum_probs=68.3
Q ss_pred CCcccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHHcCCC
Q 030547 26 VREQDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFE 102 (175)
Q Consensus 26 ~~~~d~~LP~A~V~RImK~~LP~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~ 102 (175)
.++....||++.|.||++... ..+||.|+.+.+.+..++|+.-|..+|...|++.+||||+++||..||+..|-.
T Consensus 23 ~~d~i~~ipk~~IrRLARr~G--vkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr~g~~ 97 (103)
T PLN00035 23 LRDNIQGITKPAIRRLARRGG--VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRT 97 (103)
T ss_pred HHhhhccCCHHHHHHHHHHcC--cccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHcCCc
Confidence 344555699999999999996 459999999999999999999999999999999999999999999999988754
No 9
>PTZ00015 histone H4; Provisional
Probab=99.09 E-value=6e-10 Score=84.80 Aligned_cols=77 Identities=19% Similarity=0.357 Sum_probs=69.7
Q ss_pred CCcccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHHcCCCcc
Q 030547 26 VREQDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDY 104 (175)
Q Consensus 26 ~~~~d~~LP~A~V~RImK~~LP~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~~y 104 (175)
.++....||++.|.||++... ..+||.|+.+.+.++..+|+..|..+|...|++.+||||+++||..||+..|-.-|
T Consensus 24 ~r~~i~gI~k~~IrRLarr~G--vkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~AlKr~g~~~y 100 (102)
T PTZ00015 24 LRDNIRGITKGAIRRLARRGG--VKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALKRQGRTLY 100 (102)
T ss_pred HhhcccCCCHHHHHHHHHHcC--CccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhcCCCCC
Confidence 455666799999999999996 35899999999999999999999999999999999999999999999999886443
No 10
>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=98.94 E-value=4.3e-09 Score=73.77 Aligned_cols=64 Identities=25% Similarity=0.281 Sum_probs=60.3
Q ss_pred cCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHH
Q 030547 32 YLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (175)
Q Consensus 32 ~LP~A~V~RImK~~LP~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (175)
.||+++|.||++...- .+||.|+...|.+-++.|+.-|..+|...+++.+||||+++||-.||+
T Consensus 2 ~~p~~~i~ria~~~Gi--~ris~~a~~~l~~~~e~rl~~i~~~A~k~~~hakRktlt~~DI~~Alk 65 (65)
T smart00803 2 WLPKETIKDVAESLGI--GNLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSALR 65 (65)
T ss_pred CCCHHHHHHHHHHCCC--ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCeecHHHHHHHhC
Confidence 5899999999999853 479999999999999999999999999999999999999999999984
No 11
>smart00428 H3 Histone H3.
Probab=98.91 E-value=4e-09 Score=80.62 Aligned_cols=74 Identities=16% Similarity=0.170 Sum_probs=67.6
Q ss_pred CCcccccCchhHHHHHHHhhCCC-----CCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHHc
Q 030547 26 VREQDRYLPIANISRIMKKALPA-----NGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATL 99 (175)
Q Consensus 26 ~~~~d~~LP~A~V~RImK~~LP~-----~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~L 99 (175)
.+..++.+|+....|++++...+ +.+|+.+|..+||++++.|+.-+...|+..|.+.||+||.++|+.-|..-.
T Consensus 23 Qkst~lLI~k~pF~RLVREI~~~~~~~~~~R~~~~Al~aLQeasE~ylv~lfeda~~~a~HAkRvTl~~kDi~La~rir 101 (105)
T smart00428 23 QKSTDLLIRKAPFQRLVREIAQKFTTGVDLRFQSSAIMALQEAAEAYLVGLFEDTNLLAIHAKRVTIMPKDIQLARRIR 101 (105)
T ss_pred ccCcccccccccHHHHHHHHHHHcCCCCCceeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccCcHhhHHHHHHHh
Confidence 46788999999999999998864 679999999999999999999999999999999999999999998886433
No 12
>smart00417 H4 Histone H4.
Probab=98.89 E-value=4.1e-09 Score=76.05 Aligned_cols=65 Identities=17% Similarity=0.288 Sum_probs=59.4
Q ss_pred ccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHH
Q 030547 29 QDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWA 95 (175)
Q Consensus 29 ~d~~LP~A~V~RImK~~LP~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~A 95 (175)
.-..||++.|.||++...- -+||.|+.+.+.+...+|+..|..+|...|++.+||||+++||..|
T Consensus 10 ~i~gI~k~~IrRLaRr~Gv--kRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~~a 74 (74)
T smart00417 10 NIQGITKPAIRRLARRGGV--KRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVYA 74 (74)
T ss_pred hhcCCCHHHHHHHHHHcCc--chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHheeC
Confidence 3346999999999999963 5899999999999999999999999999999999999999999753
No 13
>cd07981 TAF12 TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of the seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs function such as serving as activator-bind
Probab=98.85 E-value=2.2e-08 Score=71.11 Aligned_cols=65 Identities=15% Similarity=0.324 Sum_probs=61.3
Q ss_pred CchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHH
Q 030547 33 LPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMAT 98 (175)
Q Consensus 33 LP~A~V~RImK~~LP~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~ 98 (175)
|++..+..++|+.=| +.+|+.||.++|++.+.+|+.-++..|...|++.||+||..+||..+|++
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 677889999999976 58999999999999999999999999999999999999999999999975
No 14
>PF00125 Histone: Core histone H2A/H2B/H3/H4 histone h2a signature histone h2b signature histone h3 signature histone h4 signature; InterPro: IPR007125 The core histones together with some other DNA binding proteins appear to form a superfamily defined by a common fold and distant sequence similarities [, ]. Some proteins contain local homology domains related to the histone fold [].; GO: 0003677 DNA binding; PDB: 2YFW_D 2YFV_B 1U35_H 2F8N_D 2PYO_D 2NQB_D 3AN2_C 3AZJ_C 3AV1_G 3AZM_G ....
Probab=98.84 E-value=1e-08 Score=71.63 Aligned_cols=68 Identities=25% Similarity=0.331 Sum_probs=62.8
Q ss_pred cccCchhHHHHHHHhhCCC---CCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHH
Q 030547 30 DRYLPIANISRIMKKALPA---NGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (175)
Q Consensus 30 d~~LP~A~V~RImK~~LP~---~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (175)
+..+|+..|.|+.|+..++ ..+|+++|...|+.+++.|+.-|...|...|...||+||+++||..|++
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 4578999999999999874 2699999999999999999999999999999999999999999999985
No 15
>PLN00161 histone H3; Provisional
Probab=98.57 E-value=2.3e-07 Score=73.80 Aligned_cols=72 Identities=15% Similarity=0.177 Sum_probs=65.9
Q ss_pred CCcccccCchhHHHHHHHhhCC----CCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHH
Q 030547 26 VREQDRYLPIANISRIMKKALP----ANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (175)
Q Consensus 26 ~~~~d~~LP~A~V~RImK~~LP----~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (175)
.+..++.+|+..+.|++++... .+.+|+.+|.++||++++.|+.-|...|+-.|.+.+|.||.+.|+.-|..
T Consensus 49 Qkst~lLIpklPF~RLVREI~~~~~~~~~Rfq~~Al~ALQEAsEayLV~lFeda~lcaiHAkRVTlm~kDm~La~r 124 (135)
T PLN00161 49 QKSTELLIRKLPFARLVREISNEMLREPFRWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMPKDMQLARR 124 (135)
T ss_pred ccccccccccccHHHHHHHHHHhcCCCCcEeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccchhhHHHHHH
Confidence 3677889999999999999864 36899999999999999999999999999999999999999999988864
No 16
>PLN00160 histone H3; Provisional
Probab=98.57 E-value=1.9e-07 Score=70.66 Aligned_cols=72 Identities=15% Similarity=0.102 Sum_probs=65.8
Q ss_pred CCcccccCchhHHHHHHHhhCC----CCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHH
Q 030547 26 VREQDRYLPIANISRIMKKALP----ANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (175)
Q Consensus 26 ~~~~d~~LP~A~V~RImK~~LP----~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (175)
.+..++.+|++...|++++... ++.+++.+|..+||++++.|+.-+...++-.|.+.||.||.+.|+.-|..
T Consensus 15 Qkst~lLI~k~pF~RLVREI~~~~~~~~~Rfq~~Al~ALQeAsEayLv~lfed~~lca~HakRVTl~~kD~~L~~r 90 (97)
T PLN00160 15 QKSTDLLIRRLPFARLVREIQMEMSREAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTIMPKDMQLARR 90 (97)
T ss_pred ccchhhhhccccHHHHHHHHHHHcCCCCcEeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcccccchhhHHHHHH
Confidence 4567899999999999999864 35899999999999999999999999999999999999999999987764
No 17
>PLN00121 histone H3; Provisional
Probab=98.56 E-value=1.4e-07 Score=75.22 Aligned_cols=71 Identities=14% Similarity=0.165 Sum_probs=66.1
Q ss_pred CcccccCchhHHHHHHHhhCCC---CCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHH
Q 030547 27 REQDRYLPIANISRIMKKALPA---NGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (175)
Q Consensus 27 ~~~d~~LP~A~V~RImK~~LP~---~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (175)
+..++.+|+..+.||+++...+ +.+|+.+|.++||++++.|+.-|...++-.|.+.+|.||.+.|+.-|..
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 5678999999999999999865 7899999999999999999999999999999999999999999987763
No 18
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=98.56 E-value=5.6e-08 Score=83.30 Aligned_cols=78 Identities=26% Similarity=0.362 Sum_probs=70.4
Q ss_pred ccccCchhHHHHHHHhhCCCCCc-ccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHHcCCCcchHH
Q 030547 29 QDRYLPIANISRIMKKALPANGK-IAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYIDP 107 (175)
Q Consensus 29 ~d~~LP~A~V~RImK~~LP~~~k-ISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~~yv~~ 107 (175)
.+..||.|.|.|+||-. +++| ||.||-.++.++|+.||.-||-.|.-.+++++|+|+--.||..|+++-++-||+-.
T Consensus 106 k~h~LPlARIkkvMKtd--edVkMisaEaPvlFak~~EiFI~ELTmRAW~~ae~NkRRtLQksDia~Av~kSeMfDFLid 183 (286)
T COG5208 106 KDHNLPLARIKKVMKTD--EDVKMISAEAPVLFAKITEIFIEELTMRAWINAEENKRRTLQKSDIAAAVKKSEMFDFLID 183 (286)
T ss_pred HhccCcHHHHHHHHhcc--cchhheecccchHHHHHHHHHHHHHHHHHHHHHhHhhhhHHHHHHHHHHHHHHHHHhHHhh
Confidence 45679999999999965 4554 99999999999999999999999999999999999999999999999988887654
Q ss_pred H
Q 030547 108 L 108 (175)
Q Consensus 108 L 108 (175)
+
T Consensus 184 i 184 (286)
T COG5208 184 I 184 (286)
T ss_pred h
Confidence 4
No 19
>PTZ00018 histone H3; Provisional
Probab=98.54 E-value=1.7e-07 Score=74.66 Aligned_cols=71 Identities=14% Similarity=0.169 Sum_probs=65.6
Q ss_pred CcccccCchhHHHHHHHhhCC---CCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHH
Q 030547 27 REQDRYLPIANISRIMKKALP---ANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (175)
Q Consensus 27 ~~~d~~LP~A~V~RImK~~LP---~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (175)
+..|+.+|+..+.||+++... .+.++..+|.++||++++.|+.-|...++-.|.+.+|.||.+.|+.-|..
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 567899999999999999875 36899999999999999999999999999999999999999999987764
No 20
>KOG1657 consensus CCAAT-binding factor, subunit C (HAP5) [Transcription]
Probab=98.48 E-value=2.2e-07 Score=79.73 Aligned_cols=87 Identities=25% Similarity=0.314 Sum_probs=72.5
Q ss_pred cccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHHc---CCCcc
Q 030547 28 EQDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATL---GFEDY 104 (175)
Q Consensus 28 ~~d~~LP~A~V~RImK~~LP~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~L---gF~~y 104 (175)
.....||++.|.+|||..= +.-.|+.||...+.+||+.||..|+..|+..+...+|+|+...|+-.|+..- +|.-.
T Consensus 70 ~~~~~lPlaRiKkimK~de-dv~mI~~Eapvl~aka~E~Fi~elt~~sw~~Tee~~rrtl~~sdia~av~~s~~fdFL~D 148 (236)
T KOG1657|consen 70 FKNHILPLARIKKIMKSDE-DVSMITAEAPVLFAKACELFITELTLRSWVHTEENKRRTLQKSDIAAAVTQSETFDFLRD 148 (236)
T ss_pred hhhccCcHhhccccccccc-cccccchhHHHHHHHHHHHHHHHHHHHhhhhhcccccccchHHHHHHHhccCCCccceec
Confidence 3345799999999999773 2337999999999999999999999999999999999999999999999854 44444
Q ss_pred hHHHHHHHHHH
Q 030547 105 IDPLKAYLMRY 115 (175)
Q Consensus 105 v~~Lk~~L~~y 115 (175)
+-+.+..+++|
T Consensus 149 ivP~~~~~~~~ 159 (236)
T KOG1657|consen 149 IVPRKILAEKY 159 (236)
T ss_pred cccchhccccc
Confidence 44666666666
No 21
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=98.33 E-value=3.9e-06 Score=59.92 Aligned_cols=66 Identities=18% Similarity=0.261 Sum_probs=59.1
Q ss_pred hhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHHcCCC
Q 030547 35 IANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFE 102 (175)
Q Consensus 35 ~A~V~RImK~~LP~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~ 102 (175)
+-.|.+|+|.+.= -+++.+|.++|.+....|+.-|+..+...|...+|++++..||..||+++|+.
T Consensus 9 ~~~Vaqil~~~Gf--~~~~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~~~Dv~~Al~~~gi~ 74 (77)
T smart00576 9 RIAVAQILESAGF--DSFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPNLGDVVLALENLGIS 74 (77)
T ss_pred HHHHHHHHHHcCc--cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCcc
Confidence 3457788887742 38999999999999999999999999999999999999999999999999973
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=98.20 E-value=5.4e-06 Score=64.28 Aligned_cols=68 Identities=18% Similarity=0.237 Sum_probs=61.9
Q ss_pred cccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHH
Q 030547 30 DRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMAT 98 (175)
Q Consensus 30 d~~LP~A~V~RImK~~LP~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~ 98 (175)
.+.||.+.|.|+||+.-- ..||+.+|...|..+.+.+..-|...|...|+..+|++|+++||..|+..
T Consensus 18 gL~fPV~ri~R~Lk~~~~-a~RVs~~A~VyLaAvLEYL~aEIlelA~n~ak~~k~krItp~hi~lAi~n 85 (115)
T cd00074 18 GLQFPVGRIHRYLKKGRY-AERVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKKRITPRHLQLAVRN 85 (115)
T ss_pred CccCcHHHHHHHHHcCcc-ccccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEcHHHHHHHHhc
Confidence 688999999999998432 36999999999999999999999999999999999999999999999863
No 23
>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=98.05 E-value=3.7e-05 Score=59.43 Aligned_cols=79 Identities=14% Similarity=0.195 Sum_probs=66.1
Q ss_pred hHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHHcCCCcchHH-HHHHHHH
Q 030547 36 ANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYIDP-LKAYLMR 114 (175)
Q Consensus 36 A~V~RImK~~LP~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~~yv~~-Lk~~L~~ 114 (175)
..|.||+|+.. ..+++.+++..|.+.+..++.-|..+|...|++.+|+||+.+||.-|++...-..|..+ -+++|-.
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 35788888873 34899999999999999999999999999999999999999999999997666555544 6666655
Q ss_pred HH
Q 030547 115 YR 116 (175)
Q Consensus 115 yr 116 (175)
+-
T Consensus 83 ~a 84 (117)
T cd07979 83 LA 84 (117)
T ss_pred HH
Confidence 43
No 24
>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=97.85 E-value=7e-05 Score=66.80 Aligned_cols=67 Identities=19% Similarity=0.202 Sum_probs=58.2
Q ss_pred chhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHHcCCC
Q 030547 34 PIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFE 102 (175)
Q Consensus 34 P~A~V~RImK~~LP~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~ 102 (175)
|..+|.-|++... -.++++||..+|.+.++.++.-|..+|...+++.||||++++||-.||+.++.+
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 3456666777663 238999999999999999999999999999999999999999999999976654
No 25
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=97.83 E-value=7.3e-05 Score=54.15 Aligned_cols=61 Identities=15% Similarity=0.198 Sum_probs=52.2
Q ss_pred HHHHHHHhhC-CCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHH
Q 030547 37 NISRIMKKAL-PANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (175)
Q Consensus 37 ~V~RImK~~L-P~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (175)
.|.||+.+.. +.++.+++++.-+|.+.+-.++..++..-.-.|++.||+||+.+||+-..+
T Consensus 10 ~v~ki~ee~~~~~~~~~s~~~i~al~ELv~~q~~~~a~DLe~FAkHA~R~tI~~dDV~Ll~R 71 (76)
T PF15630_consen 10 TVGKIVEEEAKEKGVEVSPQFIAALTELVYKQLENLAKDLEAFAKHAGRSTINMDDVKLLAR 71 (76)
T ss_dssp HHHHHHHHCCCCTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHTT
T ss_pred HHHHHHHHHHhccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHHHhh
Confidence 5789999885 457899999999999999999999999999999999999999999987654
No 26
>smart00427 H2B Histone H2B.
Probab=97.80 E-value=0.00013 Score=54.56 Aligned_cols=62 Identities=21% Similarity=0.350 Sum_probs=57.3
Q ss_pred HHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHHc
Q 030547 37 NISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATL 99 (175)
Q Consensus 37 ~V~RImK~~LP~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~L 99 (175)
-|+|+.|++-| +.-||..|...|.-.+..+..-|+.+|...|...+|+||+.++|..|.+-+
T Consensus 6 Yi~kvLKqVhp-d~giS~kam~imnSfvnDiferIa~EAs~L~~~nkr~TltsreIqtAvrl~ 67 (89)
T smart00427 6 YIYKVLKQVHP-DTGISSKAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRLI 67 (89)
T ss_pred HHHHHHHHhCC-CccccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHH
Confidence 48999999999 468999999999999999999999999999999999999999999998644
No 27
>KOG1745 consensus Histones H3 and H4 [Chromatin structure and dynamics]
Probab=97.76 E-value=1.6e-05 Score=63.47 Aligned_cols=75 Identities=16% Similarity=0.194 Sum_probs=66.5
Q ss_pred CCcccccCchhHHHHHHHhhCC---CCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHHcC
Q 030547 26 VREQDRYLPIANISRIMKKALP---ANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLG 100 (175)
Q Consensus 26 ~~~~d~~LP~A~V~RImK~~LP---~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~Lg 100 (175)
.+..|+.+++....|++++..+ .+.+|...|..+||++++.|+.-|.-.+|-+|.+.||.||.+.||--|..-.|
T Consensus 57 QkstdLlI~K~PFqRlvrei~q~f~~dLrfqs~Ai~ALQeA~EayLv~LfEdtnlcAihAkRVTimpkdiQlArrirg 134 (137)
T KOG1745|consen 57 QKSTDLLIRKLPFQRLVREIAQDFKTDLRFQSSAIAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRG 134 (137)
T ss_pred HhhhHHHhhcCcHHHHhHHHHhcccccceehHHHHHHHHHHHHHHHHHhccccchhhhccceeEecccceehhhhccc
Confidence 4567889999999999995554 47899999999999999999999999999999999999999999998876443
No 28
>PF15511 CENP-T: Centromere kinetochore component CENP-T; PDB: 3B0D_T 3B0C_T 3VH5_T 3VH6_T.
Probab=97.74 E-value=5.9e-05 Score=69.02 Aligned_cols=66 Identities=20% Similarity=0.257 Sum_probs=48.1
Q ss_pred CCcccccCchhHHHHHHHhhCC----CCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhh
Q 030547 26 VREQDRYLPIANISRIMKKALP----ANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDD 91 (175)
Q Consensus 26 ~~~~d~~LP~A~V~RImK~~LP----~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eD 91 (175)
.++.--.||.+.|.|++..... .+++|+|||..+|.+|...|...|...-..+|++.|||||..+|
T Consensus 345 hgi~~P~lP~~~vK~la~~~ak~s~~sK~kiskdal~aleqasdwfFeQl~dDL~aYA~HAgRKTIdesD 414 (414)
T PF15511_consen 345 HGIPYPSLPPGVVKKLAQHFAKSSGGSKMKISKDALEALEQASDWFFEQLGDDLEAYAKHAGRKTIDESD 414 (414)
T ss_dssp -------S-HHHHHHHHHHHH-------S-B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHH
T ss_pred CCCCCCCCCccHHHHHHHHHHHhhcccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCCCC
Confidence 5566667999999999888854 46899999999999999999999999999999999999999877
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=97.66 E-value=0.00027 Score=50.14 Aligned_cols=63 Identities=19% Similarity=0.306 Sum_probs=51.3
Q ss_pred hhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHH
Q 030547 35 IANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMAT 98 (175)
Q Consensus 35 ~A~V~RImK~~LP~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~ 98 (175)
+..+..++++.=| +.++..|+.++|.+.|.+||.-++..|-..|++.+-.||...||...|++
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 3467888998855 78999999999999999999999999999999999999999999999874
No 30
>KOG3467 consensus Histone H4 [Chromatin structure and dynamics]
Probab=97.59 E-value=0.00033 Score=52.69 Aligned_cols=69 Identities=17% Similarity=0.268 Sum_probs=61.6
Q ss_pred cCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHHcCCC
Q 030547 32 YLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFE 102 (175)
Q Consensus 32 ~LP~A~V~RImK~~LP~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~ 102 (175)
-+-+-+|.||.+... .-+|+--.-+.+..++.+||..+-+.|...+.+.+||||++-||+-+|++.|.-
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 466888999999875 347888888899999999999999999999999999999999999999998753
No 31
>PLN00158 histone H2B; Provisional
Probab=97.57 E-value=0.00041 Score=54.12 Aligned_cols=65 Identities=17% Similarity=0.290 Sum_probs=58.8
Q ss_pred chhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHHc
Q 030547 34 PIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATL 99 (175)
Q Consensus 34 P~A~V~RImK~~LP~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~L 99 (175)
-..-|+|++|++-| +.-||..+...|+-.+..+..-|+.||...|...+|+||+..+|..|.+-+
T Consensus 29 y~~YI~kVLKQVhP-d~gIS~kaM~ImnSfvnDiferIA~EAs~La~~nkr~TltsrEIqtAvrLv 93 (116)
T PLN00158 29 YKIYIYKVLKQVHP-DTGISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVRLI 93 (116)
T ss_pred HHHHHHHHHHHhCC-CCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHh
Confidence 34569999999998 568999999999999999999999999999999999999999999998544
No 32
>PF07524 Bromo_TP: Bromodomain associated; InterPro: IPR006565 This bromodomain is found in eukaryotic transcription factors and PHD domain containing proteins (IPR001965 from INTERPRO). The tandem PHD finger-bromodomain is found in many chromatin-associated proteins. It is involved in gene silencing by the human co-repressor KRAB-associated protein 1 (KAP1). The tandem PHD finger-bromodomain of KAP1 has a distinct structure that joins the two protein modules. The first helix, alpha(Z), of an atypical bromodomain forms the central hydrophobic core that anchors the other three helices of the bromodomain on one side and the zinc binding PHD finger on the other []. The Rap1 GTPase-activating protein, Sipa1, is modulated by the cellular bromodomain protein, Brd4. Brd4 belongs to the BET family and is a multifunctional protein involved in transcription, replication, the signal transduction pathway, and cell cycle progression. All of these functions are linked to its association with acetylated chromatin. It has tandem bromodomains []. The dysregulation of the Brd4-associated pathways may play an important role in breast cancer progression []. Bovine papillomavirus type 1 E2 also binds to chromosomes in a complex with Brd4. Interaction with Brd4 is additionally important for E2-mediated transcriptional regulation [, ].
Probab=97.53 E-value=0.00084 Score=47.48 Aligned_cols=63 Identities=19% Similarity=0.292 Sum_probs=55.8
Q ss_pred HHHHHHHhhCCCCC-cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHHcCCC
Q 030547 37 NISRIMKKALPANG-KIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFE 102 (175)
Q Consensus 37 ~V~RImK~~LP~~~-kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~ 102 (175)
.|.+|++.+ +. .++..|.+.|...+..||..|...+...|...+|...+..||..||+++|+.
T Consensus 11 ~va~il~~~---GF~~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~~~gi~ 74 (77)
T PF07524_consen 11 SVAQILKHA---GFDSASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPNLQDVEQALEEMGIS 74 (77)
T ss_pred HHHHHHHHc---CccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCC
Confidence 455566554 23 7999999999999999999999999999999999999999999999999983
No 33
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=97.53 E-value=0.00043 Score=60.40 Aligned_cols=69 Identities=16% Similarity=0.278 Sum_probs=62.5
Q ss_pred cccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHH
Q 030547 28 EQDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (175)
Q Consensus 28 ~~d~~LP~A~V~RImK~~LP~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (175)
..+..|=+-.|.-+++++-+ +.+|-+|+.+.|.+.|..||.-|+..|-..|++.|..||-..||...||
T Consensus 150 ~~~~il~k~kl~dLvqqId~-~~~LD~dVedlLleiADdFV~sii~~sC~LAKHRKsdtlEvrDIqLhLE 218 (258)
T KOG1142|consen 150 GNNPILSKRKLDDLVQQIDG-TTKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHRKSDTVEVRDIQLHLE 218 (258)
T ss_pred CCCccccccchhHHHHhhcC-cccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccchhheeeeee
Confidence 33455777889999999854 6799999999999999999999999999999999999999999999998
No 34
>PTZ00463 histone H2B; Provisional
Probab=97.52 E-value=0.00051 Score=53.66 Aligned_cols=62 Identities=19% Similarity=0.386 Sum_probs=57.1
Q ss_pred HHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHHc
Q 030547 37 NISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATL 99 (175)
Q Consensus 37 ~V~RImK~~LP~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~L 99 (175)
-|+|++|++-| +.-||..|...|+-.+.....-|+.||...|...+|+||+..+|..|.+-+
T Consensus 33 YI~KVLKqVhP-d~gIS~kaM~ImnSfvnDifErIA~EAs~La~~nkr~TltsrEIQtAvrLl 94 (117)
T PTZ00463 33 YIFKVLKQVHP-DTGISRKSMNIMNSFLVDTFEKIATEASRLCKYTRRDTLSSREIQTAIRLV 94 (117)
T ss_pred HHHHHHHhhCC-CCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHhhc
Confidence 49999999998 568999999999999999999999999999999999999999999998543
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=97.45 E-value=0.00096 Score=49.18 Aligned_cols=66 Identities=20% Similarity=0.211 Sum_probs=61.5
Q ss_pred cCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC---CccChhhHHHHHHHc
Q 030547 32 YLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKR---KTINGDDLLWAMATL 99 (175)
Q Consensus 32 ~LP~A~V~RImK~~LP~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kR---KTI~~eDVl~AL~~L 99 (175)
.||++.|.|||...++ ..++.+...+|.-.+.+||--|..+|.++..+.+. .-|.++||-+|...|
T Consensus 16 ~f~k~~iKr~~~~~~~--~~v~~~v~i~v~glaKvFVGeivE~A~~V~~~~~~~~~~Pl~P~HireA~rrl 84 (85)
T cd08048 16 SFPKAAIKRLIQSVTG--QSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGEANTGPLQPRHLREAYRRL 84 (85)
T ss_pred hccHHHHHHHHHHHcC--CCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCCCCCcHHHHHHHHHh
Confidence 4999999999999986 78999999999999999999999999999988776 789999999999876
No 36
>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=97.44 E-value=0.00019 Score=51.43 Aligned_cols=65 Identities=20% Similarity=0.297 Sum_probs=54.1
Q ss_pred chhHHHHHHHhhCC-CCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCc-cChhhHHHHHHH
Q 030547 34 PIANISRIMKKALP-ANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKT-INGDDLLWAMAT 98 (175)
Q Consensus 34 P~A~V~RImK~~LP-~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKT-I~~eDVl~AL~~ 98 (175)
|..+|.||++.... ++.+|++||..++.+....||.--...|.+.++.++..+ |..+|+-+.+-.
T Consensus 1 p~~li~rll~~~f~~~~tkIs~dal~l~~eyl~iFV~EAv~Ra~~~a~~e~~~~~le~e~LEki~pq 67 (72)
T PF09415_consen 1 PPELIARLLHEHFKDDKTKISKDALKLSAEYLRIFVREAVARAAEQAEAEGDEGFLEVEHLEKILPQ 67 (72)
T ss_dssp -CHHHHHHHCTTSSSTT-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSEE-HHHHHHHCHC
T ss_pred ChHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHHH
Confidence 78999999998774 478999999999999999999999999999999999888 999999886543
No 37
>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=97.19 E-value=0.002 Score=48.11 Aligned_cols=67 Identities=21% Similarity=0.235 Sum_probs=52.1
Q ss_pred cCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC-ccChhhHHHHHHHc
Q 030547 32 YLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRK-TINGDDLLWAMATL 99 (175)
Q Consensus 32 ~LP~A~V~RImK~~LP~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRK-TI~~eDVl~AL~~L 99 (175)
.||++.|.|||...+. |..|+.....+|.-.+..||--|-.+|.+++.+.+.. -|.+.|+-+|..+|
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 4999999999999995 5789999999999999999999999999999876643 79999999998765
No 38
>KOG1659 consensus Class 2 transcription repressor NC2, alpha subunit (DRAP1) [Transcription]
Probab=97.17 E-value=0.0009 Score=57.14 Aligned_cols=81 Identities=17% Similarity=0.242 Sum_probs=70.2
Q ss_pred ccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHHcCCCcchHHHHH
Q 030547 31 RYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKA 110 (175)
Q Consensus 31 ~~LP~A~V~RImK~~LP~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~~yv~~Lk~ 110 (175)
-.+|.+.|.|||...= +-.||+.-.-..+.++.+.|+.-|...+.++++..+-|||+++|+..|...-.-.+|+..+-.
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 4589999999998663 245899999999999999999999999999999999999999999999998777777776544
Q ss_pred HH
Q 030547 111 YL 112 (175)
Q Consensus 111 ~L 112 (175)
.+
T Consensus 91 ~v 92 (224)
T KOG1659|consen 91 KV 92 (224)
T ss_pred hc
Confidence 33
No 39
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=97.17 E-value=0.00097 Score=52.51 Aligned_cols=67 Identities=19% Similarity=0.254 Sum_probs=59.5
Q ss_pred cccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHH
Q 030547 30 DRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (175)
Q Consensus 30 d~~LP~A~V~RImK~~LP~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (175)
-+.+|...|.||||.. .-.+||+++|...+..|.+-.+.-|+..|-..|...++|.|.+.|+-.|+.
T Consensus 24 gl~fpvgrvkr~lk~~-~~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~kkkri~PrHlqlAIr 90 (132)
T COG5262 24 GLIFPVGRVKRLLKKG-NYRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRIIPRHLQLAIR 90 (132)
T ss_pred CccccHHHHHHHHHcC-ccceeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhcCcceechHHHHHHhc
Confidence 4679999999999944 347899999999999998888888888888899999999999999999986
No 40
>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=96.98 E-value=0.006 Score=43.13 Aligned_cols=64 Identities=19% Similarity=0.190 Sum_probs=48.5
Q ss_pred cCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHH
Q 030547 32 YLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (175)
Q Consensus 32 ~LP~A~V~RImK~~LP~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (175)
.+|..+|.-+..... -..++.|+...|.+=++--|..|..+|....++.+|++++.+||-.||+
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 367777766555542 2379999999999999999999999999999999999999999999985
No 41
>smart00414 H2A Histone 2A.
Probab=96.86 E-value=0.0036 Score=47.89 Aligned_cols=68 Identities=15% Similarity=0.257 Sum_probs=58.6
Q ss_pred cccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHH
Q 030547 30 DRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMAT 98 (175)
Q Consensus 30 d~~LP~A~V~RImK~~LP~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~ 98 (175)
.+.||.+.|.|+||+.-- ..+|+..|...|..+.+-+...|-..|...|...+++.|+++||..|+..
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 578999999999998743 35999999999998888777777777888899999999999999999864
No 42
>COG5247 BUR6 Class 2 transcription repressor NC2, alpha subunit (DRAP1 homolog) [Transcription]
Probab=96.81 E-value=0.0062 Score=46.94 Aligned_cols=80 Identities=18% Similarity=0.275 Sum_probs=67.5
Q ss_pred ccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHHcCCCcchHHH
Q 030547 29 QDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPL 108 (175)
Q Consensus 29 ~d~~LP~A~V~RImK~~LP~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~~yv~~L 108 (175)
.-..+|+|.|.|||.-.- +-.+|+.-.-....++.+.|+..|-.+..+.++..+-|.|+.+++..|.+.-+=-+|...+
T Consensus 20 ~ktrFP~ar~KkIMQ~de-DiGKV~q~tPVIaskalE~Fl~~iv~~s~k~aR~~~skR~t~e~lk~a~~sdekFdFL~~~ 98 (113)
T COG5247 20 KKTRFPIARLKKIMQLDE-DIGKVGQSTPVIASKALEMFLTEIVGLSLKEARKKSSKRMTSEFLKRATESDEKFDFLKNM 98 (113)
T ss_pred hhhcCCHHHHHHHHHhhh-hhhhhhhcchHHHHHHHHHHHHHHHHHHHHHHHhccchhhHHHHHHHHHhhhHHHHHHHHH
Confidence 344699999999998553 2458999999999999999999999999999999999999999999999876655565544
Q ss_pred H
Q 030547 109 K 109 (175)
Q Consensus 109 k 109 (175)
.
T Consensus 99 ~ 99 (113)
T COG5247 99 E 99 (113)
T ss_pred H
Confidence 3
No 43
>PLN00154 histone H2A; Provisional
Probab=96.62 E-value=0.0066 Score=48.62 Aligned_cols=68 Identities=19% Similarity=0.255 Sum_probs=55.5
Q ss_pred cccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHH
Q 030547 30 DRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (175)
Q Consensus 30 d~~LP~A~V~RImK~~LP~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (175)
.+.||.+.|.|++|+...-..||+..|...|..+.+=+..-|...|-..|...+++-|++.||..|+.
T Consensus 36 gL~FPVgRi~r~Lk~g~~~~~RVga~ApVYLAAVLEYLtAEVLELAGNaA~d~kk~RItPrHi~lAIr 103 (136)
T PLN00154 36 GLQFPVGRIHRQLKQRVSAHGRVGATAAVYTAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 103 (136)
T ss_pred CccCchHHHHHHHHhhhhhccccccchHHHHHHHHHHHHHHHHHHHHHHHHhhCCceecHHHhhhhcc
Confidence 67899999999999986435699999998888766555555555566778999999999999999985
No 44
>KOG1744 consensus Histone H2B [Chromatin structure and dynamics]
Probab=96.60 E-value=0.0089 Score=47.39 Aligned_cols=60 Identities=23% Similarity=0.325 Sum_probs=55.8
Q ss_pred HHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHH
Q 030547 38 ISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMAT 98 (175)
Q Consensus 38 V~RImK~~LP~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~ 98 (175)
|.|++|++-|+ .-|+.++...++-...+|+..|+.+|+..+...+|.||+..+|..|.+-
T Consensus 43 v~kvlk~Vhpd-~gis~~a~~vmnsf~ndife~iA~ea~rla~y~krstisSreiqta~rL 102 (127)
T KOG1744|consen 43 VYKVLKQVHPD-LGISSKAMGVMNSFVNDIFERIASEAGRLAHYNKRSTISSREIQTAVRL 102 (127)
T ss_pred hhhhhhcccCC-CCcCHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCcccHHHHHHHHHH
Confidence 77899999996 6699999999999999999999999999999999999999999998753
No 45
>PTZ00017 histone H2A; Provisional
Probab=96.38 E-value=0.0086 Score=47.83 Aligned_cols=67 Identities=15% Similarity=0.231 Sum_probs=58.3
Q ss_pred cccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHH
Q 030547 30 DRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (175)
Q Consensus 30 d~~LP~A~V~RImK~~LP~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (175)
.+.||...|.|++|+.-- ..||+..|...|..+.+-+..-|...|-..|...+++-|+++||..|+.
T Consensus 25 gL~FPVgRi~R~Lk~g~~-a~RV~a~A~VYLAAVLEYLtaEILELAgNaa~d~kk~RItPrHi~lAI~ 91 (134)
T PTZ00017 25 GLQFPVGRVHRYLKKGRY-AKRVGAGAPVYLAAVLEYLTAEVLELAGNAAKDNKKKRITPRHIQLAIR 91 (134)
T ss_pred CcccchHHHHHHHhccch-hccccccchhhhHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHhhcc
Confidence 688999999999998643 3599999999999888877777777788889999999999999999985
No 46
>PF15510 CENP-W: Centromere kinetochore component W
Probab=96.34 E-value=0.0081 Score=45.53 Aligned_cols=67 Identities=21% Similarity=0.255 Sum_probs=54.8
Q ss_pred ccCchhHHHHHHHhhCCCCCcccHHHHHH--------------HHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHH
Q 030547 31 RYLPIANISRIMKKALPANGKIAKDAKDT--------------VQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAM 96 (175)
Q Consensus 31 ~~LP~A~V~RImK~~LP~~~kISkDA~~a--------------l~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL 96 (175)
..-|++.+.|++|..-| ..++....-.. +.--|-.||+-|+-||...|=+++-.||+.+||+.|.
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 45665544444 5666889999999999999988999999999999987
Q ss_pred HH
Q 030547 97 AT 98 (175)
Q Consensus 97 ~~ 98 (175)
+.
T Consensus 94 Kv 95 (102)
T PF15510_consen 94 KV 95 (102)
T ss_pred HH
Confidence 64
No 47
>KOG1658 consensus DNA polymerase epsilon, subunit C [Replication, recombination and repair]
Probab=96.23 E-value=0.0026 Score=52.08 Aligned_cols=66 Identities=26% Similarity=0.326 Sum_probs=56.9
Q ss_pred ccCchhHHHHHHHhhCCCCCc-ccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHH
Q 030547 31 RYLPIANISRIMKKALPANGK-IAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMAT 98 (175)
Q Consensus 31 ~~LP~A~V~RImK~~LP~~~k-ISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~ 98 (175)
..||.+.|..+|| ++++.+ ...|++.++.+++..||.+|...++..+...+|||+.-.|+=.|.+.
T Consensus 58 ~rLpL~rik~vvk--l~pdl~l~~dea~~l~a~aaelfi~~Ln~~~~~~~q~~k~kt~qr~d~D~ai~~ 124 (162)
T KOG1658|consen 58 SRLPLARIKQVVK--LDPDLTLLNDEASQLIAKAAELFIQELNDVAYTTAQLRKRKTEQRRDYDTAIEA 124 (162)
T ss_pred hhccHHHHHhhcc--CCcchhhhhhHHHHHHHHHHHHHHHHHHhccchhHHHHHhhhhhhhcccccccc
Confidence 5699999999998 556776 55678999999999999999999999999999999998887766653
No 48
>PF02269 TFIID-18kDa: Transcription initiation factor IID, 18kD subunit; InterPro: IPR003195 This family includes the Spt3 yeast transcription factors and the 18 kDa subunit from human transcription initiation factor IID (TFIID-18). Determination of the crystal structure reveals an atypical histone fold [].; GO: 0006366 transcription from RNA polymerase II promoter; PDB: 1BH9_A 1BH8_A.
Probab=96.19 E-value=0.0064 Score=45.17 Aligned_cols=59 Identities=24% Similarity=0.293 Sum_probs=28.8
Q ss_pred HHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHH
Q 030547 39 SRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMAT 98 (175)
Q Consensus 39 ~RImK~~LP~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~ 98 (175)
..+|-.-. +...-..|...+|-+.+.+||..|...|...|...|+++|+.+|++.+|+.
T Consensus 8 ~~mMy~fG-D~~~P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~rg~~~i~~eDl~F~lR~ 66 (93)
T PF02269_consen 8 RQMMYGFG-DVEEPLPETVDLVEDIVREYIIELCQEAMEVAQRRGSKKIKVEDLLFLLRK 66 (93)
T ss_dssp HHHHHCTT-S-SS--HHHHHHHHHHHHHHHHHHHHHHHC---------------------
T ss_pred HHHHHHcC-CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCcCcHHHHHHHHhc
Confidence 34444433 345788999999999999999999999999999999999999999999984
No 49
>PLN00156 histone H2AX; Provisional
Probab=96.12 E-value=0.036 Score=44.56 Aligned_cols=67 Identities=13% Similarity=0.205 Sum_probs=55.2
Q ss_pred cccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHH
Q 030547 30 DRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (175)
Q Consensus 30 d~~LP~A~V~RImK~~LP~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (175)
.+.||...|.|++|+.-- ..||+..|...|.-+.+=...-|...|-..|...+++-|+++||..|+.
T Consensus 27 gL~FPVgRi~R~Lk~g~y-a~RVga~ApVYLAAVLEYLtaEVLELAgNaa~d~kk~RItPrHi~lAIr 93 (139)
T PLN00156 27 GLQFPVGRIARFLKAGKY-AERVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR 93 (139)
T ss_pred CcccchHHHHHHHhcCCh-hhccCCccHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHhhcc
Confidence 678999999999998643 3599999998888776655555555666778899999999999999985
No 50
>KOG1756 consensus Histone 2A [Chromatin structure and dynamics]
Probab=95.97 E-value=0.023 Score=45.24 Aligned_cols=68 Identities=16% Similarity=0.252 Sum_probs=52.8
Q ss_pred ccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHH
Q 030547 29 QDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (175)
Q Consensus 29 ~d~~LP~A~V~RImK~~LP~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (175)
..+.+|...|.|++|+. .--.+|+.+|...+.-|.+=....|+..|-..+..+++.-|+++||..|+.
T Consensus 24 agl~fPvgri~r~Lr~~-~~~~ri~~gapV~laavLeYL~Aeile~agnaardnkk~ri~PrH~~lAI~ 91 (131)
T KOG1756|consen 24 AGLQFPVGRIHRLLRKG-RYAQRVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRITPRHLQLAIR 91 (131)
T ss_pred cccccCHHHHHHHHHcc-chhhhccCCChHHHHHHHHHHHHHHHHHhHHHhhhcCccccChHHHHHHHh
Confidence 45789999999999993 224689999999999655444444444455566788899999999999986
No 51
>PLN00157 histone H2A; Provisional
Probab=95.94 E-value=0.017 Score=46.01 Aligned_cols=67 Identities=13% Similarity=0.190 Sum_probs=56.6
Q ss_pred cccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHH
Q 030547 30 DRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (175)
Q Consensus 30 d~~LP~A~V~RImK~~LP~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (175)
.+.||...|.|++|+.-- ..||+..|...|.-+.+-++.-|...|-..|...+++-|+++||..|+.
T Consensus 24 gL~FPVgRi~R~Lk~g~~-a~RIg~~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~ 90 (132)
T PLN00157 24 GLQFPVGRIARYLKAGKY-ATRVGAGAPVYLAAVLEYLAAEVLELAGNAARDNKKSRIVPRHIQLAVR 90 (132)
T ss_pred CcccchHHHHHHHhcCch-hhhcCCCcHhHHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHhhccc
Confidence 688999999999999643 3599999999988877666666666677888999999999999999985
No 52
>PLN00153 histone H2A; Provisional
Probab=95.88 E-value=0.021 Score=45.38 Aligned_cols=67 Identities=16% Similarity=0.223 Sum_probs=57.2
Q ss_pred cccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHH
Q 030547 30 DRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (175)
Q Consensus 30 d~~LP~A~V~RImK~~LP~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (175)
.+.||...|.|++|+.-- ..||+..|...|.-+.+-++.-|...|-..|...+++-|+++||..|+.
T Consensus 22 gL~FpVgRi~R~Lr~g~~-a~Rvga~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~ 88 (129)
T PLN00153 22 GLQFPVGRIARYLKKGKY-AERIGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKNRIVPRHIQLAIR 88 (129)
T ss_pred CcccchHHHHHHHhcCch-hhccCCCchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHhhcc
Confidence 688999999999998654 3599999999998887766666666777888999999999999999985
No 53
>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=94.81 E-value=0.25 Score=36.77 Aligned_cols=74 Identities=18% Similarity=0.254 Sum_probs=54.4
Q ss_pred HHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHHcCCCcchHHHHHHHHH
Q 030547 37 NISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLMR 114 (175)
Q Consensus 37 ~V~RImK~~LP~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~~yv~~Lk~~L~~ 114 (175)
-|..+|-... +...-..|...+|-+.+.+||.-|+.+|.+.|. .+|.-|+.||++-+|+.= .-.+..++.+|.-
T Consensus 7 ei~~mmy~~G-D~~~P~~eTv~llE~iv~~~i~~l~~~a~~~A~-~r~~k~~~eD~~FliR~D--~~Kl~Rl~~lL~~ 80 (92)
T cd07978 7 EIRQMMYGFG-DVQNPLPETVDLLEDIVVEYIIELCHKAAEVAQ-RRRGKVKVEDLIFLLRKD--PKKLARLRELLSM 80 (92)
T ss_pred HHHHHHHHcC-CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-cCCCCCCHHHHHHHHhcC--HHHHHHHHHHHHH
Confidence 3566666554 345678899999999999999999999999999 444456999999999631 2233444455443
No 54
>KOG3219 consensus Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=94.62 E-value=0.05 Score=45.97 Aligned_cols=69 Identities=14% Similarity=0.188 Sum_probs=60.5
Q ss_pred cCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC-CccChhhHHHHHHHcCCC
Q 030547 32 YLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKR-KTINGDDLLWAMATLGFE 102 (175)
Q Consensus 32 ~LP~A~V~RImK~~LP~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kR-KTI~~eDVl~AL~~LgF~ 102 (175)
.||++.|.|||..... ..|+.-+..+++-.+.+||--|--+|.++|...+. --|-+.||-.|...|...
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 4999999999999985 34999999999999999999999999999987774 358899999998877654
No 55
>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=93.83 E-value=0.35 Score=38.26 Aligned_cols=86 Identities=21% Similarity=0.249 Sum_probs=46.5
Q ss_pred cccccCchh--HHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHH-HcCCCcc
Q 030547 28 EQDRYLPIA--NISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA-TLGFEDY 104 (175)
Q Consensus 28 ~~d~~LP~A--~V~RImK~~LP~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~-~LgF~~y 104 (175)
...-.+|+. .|.-|+|+.. -......+...|.+.+-.|+.-|-..|...+.+.+|++|+.+||..|++ .+++.-.
T Consensus 6 ~~~~~~PrDa~~i~~iL~~~G--v~~yeprVv~qLLEfayRYt~~vL~DA~~ya~hA~~~~i~~~DVrLAi~~r~~~~f~ 83 (129)
T PF02291_consen 6 SQSKSLPRDARVIHLILKSMG--VTEYEPRVVNQLLEFAYRYTSDVLEDAQVYADHAGRSTIDADDVRLAIQSRLDHSFT 83 (129)
T ss_dssp -------HHHHHHHHHHHHTT-----B-THHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHHHHT------
T ss_pred CCCccCChHHHHHHHHHHHcC--CcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHhhhcc
Confidence 344567763 3444555442 1256777888899999999999999999999999999999999999999 6677666
Q ss_pred hHHHHHHHHHH
Q 030547 105 IDPLKAYLMRY 115 (175)
Q Consensus 105 v~~Lk~~L~~y 115 (175)
.++-+++|-+.
T Consensus 84 ~pppre~llel 94 (129)
T PF02291_consen 84 QPPPREFLLEL 94 (129)
T ss_dssp -----------
T ss_pred CCCChHHHHHH
Confidence 66666666554
No 56
>PTZ00252 histone H2A; Provisional
Probab=93.76 E-value=0.22 Score=39.88 Aligned_cols=63 Identities=11% Similarity=0.274 Sum_probs=48.5
Q ss_pred cccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHH----Hh--cCCCccChhhHHHHHH
Q 030547 30 DRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKC----QK--EKRKTINGDDLLWAMA 97 (175)
Q Consensus 30 d~~LP~A~V~RImK~~LP~~~kISkDA~~al~~~aseFI~~LtseA~~~~----~~--~kRKTI~~eDVl~AL~ 97 (175)
.+.||...|.|++|+.-- ..||+.-|...|..+ +.||++|-.+.+ .+ .+++-|+++||..|+.
T Consensus 23 GL~FPVgRi~R~Lr~g~y-a~RIga~ApVYLAAV----LEYLtaEVLELAgnaa~d~~~kk~RItPrHi~lAIr 91 (134)
T PTZ00252 23 GLIFPVGRVGSLLRRGQY-ARRIGASGAVYMAAV----LEYLTAELLELSVKAAAQQAKKPKRLTPRTVTLAVR 91 (134)
T ss_pred CccCchHHHHHHHHcCCc-ccccCCccHHHHHHH----HHHHHHHHHHHHHHHHHhccCCcccccHHHHHhhcc
Confidence 678999999999998754 359999888877765 446666555544 32 5678999999999985
No 57
>KOG4336 consensus TBP-associated transcription factor Prodos [Transcription]
Probab=92.66 E-value=0.78 Score=41.39 Aligned_cols=77 Identities=18% Similarity=0.282 Sum_probs=64.6
Q ss_pred HHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHHcCCCcchHHHHHHHHHHH
Q 030547 37 NISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLMRYR 116 (175)
Q Consensus 37 ~V~RImK~~LP~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~~yv~~Lk~~L~~yr 116 (175)
.|.-|.++.+=+ .|++-|++.|.+....+|.-|...+...|...||...+.-||...|-++||. +..|..+++++.
T Consensus 10 VV~~Ll~~~gfd--~is~~aletlvell~~yi~eigrq~~n~celagRT~pT~~Dv~l~Li~mnI~--v~sL~~~~q~~~ 85 (323)
T KOG4336|consen 10 VVSNLLKTKGFD--SISNAALETLVELLQSYIREIGRQLHNYCELAGRTIPTQGDVKLTLIEMNIK--VSSLYAYFQKQE 85 (323)
T ss_pred HHHHHHHHhCch--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcHHHHHHHHHHhCCC--hhhhHHHHHhcc
Confidence 344555555432 5999999999999999999999999999999999999999999999999997 677777777655
Q ss_pred H
Q 030547 117 E 117 (175)
Q Consensus 117 e 117 (175)
.
T Consensus 86 ~ 86 (323)
T KOG4336|consen 86 F 86 (323)
T ss_pred c
Confidence 3
No 58
>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=91.78 E-value=0.7 Score=38.14 Aligned_cols=70 Identities=16% Similarity=0.257 Sum_probs=54.7
Q ss_pred CchhHHHHHHHhhCC-----CCCcccHHHHHHHHHHHHH---HHHHHHHHHHHHHHhcCCCccChhhHHHHHHHcCCC
Q 030547 33 LPIANISRIMKKALP-----ANGKIAKDAKDTVQECVSE---FISFITSEASDKCQKEKRKTINGDDLLWAMATLGFE 102 (175)
Q Consensus 33 LP~A~V~RImK~~LP-----~~~kISkDA~~al~~~ase---FI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~ 102 (175)
|...-+..++...+. ....+++++.+.|.+.+.= .|+.+...|...+-.++.++|+.++|..++.++.|+
T Consensus 192 l~~~e~~~~l~~~l~~~g~~~~~~~~~~~~~~i~~~s~G~p~~i~~l~~~~~~~a~~~~~~~i~~~~v~~~~~~~~~~ 269 (269)
T TIGR03015 192 LDREETREYIEHRLERAGNRDAPVFSEGAFDAIHRFSRGIPRLINILCDRLLLSAFLEEKREIGGEEVREVIAEIDFE 269 (269)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCCCcCHHHHHHHHHHcCCcccHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhhcC
Confidence 444555555554431 2346999999999998875 799999999988888899999999999999998753
No 59
>KOG3423 consensus Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=90.70 E-value=1.6 Score=36.43 Aligned_cols=69 Identities=25% Similarity=0.242 Sum_probs=55.2
Q ss_pred cCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC--------------CCccChhhHHHHHH
Q 030547 32 YLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEK--------------RKTINGDDLLWAMA 97 (175)
Q Consensus 32 ~LP~A~V~RImK~~LP~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~k--------------RKTI~~eDVl~AL~ 97 (175)
.||-+.+.-.++.+.= .....-.+-+|.-++-.||+-|+..|.+.|+-.. |-|++-+|+-.||+
T Consensus 86 ~IPDavt~~yL~~aGf--~~~D~rv~RLvsLaAQKfvSDIa~DA~Q~~k~r~~~~~~~~k~~~kdkK~tLtmeDL~~AL~ 163 (176)
T KOG3423|consen 86 TIPDAVTDHYLKKAGF--QTSDPRVKRLVSLAAQKFVSDIANDALQHSKIRTKTAIGKDKKQAKDKKYTLTMEDLSPALA 163 (176)
T ss_pred CCcHHHHHHHHHhcCC--CcCcHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccccccccccccceeeeHHHHHHHHH
Confidence 5898988888888742 1234455678888999999999999999996443 55899999999999
Q ss_pred HcCCC
Q 030547 98 TLGFE 102 (175)
Q Consensus 98 ~LgF~ 102 (175)
+.|..
T Consensus 164 EyGin 168 (176)
T KOG3423|consen 164 EYGIN 168 (176)
T ss_pred HhCcc
Confidence 99873
No 60
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=88.69 E-value=2.4 Score=37.24 Aligned_cols=70 Identities=13% Similarity=0.171 Sum_probs=50.4
Q ss_pred hhHHHHHHHhhCCC---CCcccHHHHHHHHHHH------HHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHHcCCCcc
Q 030547 35 IANISRIMKKALPA---NGKIAKDAKDTVQECV------SEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDY 104 (175)
Q Consensus 35 ~A~V~RImK~~LP~---~~kISkDA~~al~~~a------seFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~~y 104 (175)
...+..|++..+.. ...++.++.+.+.+.+ -..+..+...|.+.|...++.+|+.+||.+|++++....+
T Consensus 209 ~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~a~~~a~~~~~~~I~~~~v~~a~~~~~~~~~ 287 (394)
T PRK00411 209 ADEIFDILKDRVEEGFYPGVVDDEVLDLIADLTAREHGDARVAIDLLRRAGLIAEREGSRKVTEEDVRKAYEKSEIVHL 287 (394)
T ss_pred HHHHHHHHHHHHHhhcccCCCCHhHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHHHHHH
Confidence 45566666654421 2358999988888777 3344556678888899999999999999999998854433
No 61
>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=86.28 E-value=3.8 Score=35.51 Aligned_cols=75 Identities=8% Similarity=0.125 Sum_probs=50.5
Q ss_pred hhHHHHHHHhhCC---CCCcccHHHHHHHHHHHH------HHHHHHHHHHHHHHHhcCCCccChhhHHHHHHHcCCCcch
Q 030547 35 IANISRIMKKALP---ANGKIAKDAKDTVQECVS------EFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYI 105 (175)
Q Consensus 35 ~A~V~RImK~~LP---~~~kISkDA~~al~~~as------eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~~yv 105 (175)
..-+..|++..+. ....+..|+...+.+.+. -.+..+...|.+.|..+++.+|+.+||.+|++.+....++
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 3446666665442 123588888877766443 2334455567788888899999999999999988655554
Q ss_pred HHHH
Q 030547 106 DPLK 109 (175)
Q Consensus 106 ~~Lk 109 (175)
..++
T Consensus 281 ~~i~ 284 (365)
T TIGR02928 281 ELIR 284 (365)
T ss_pred HHHH
Confidence 4443
No 62
>KOG2549 consensus Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=85.58 E-value=4.6 Score=39.17 Aligned_cols=65 Identities=20% Similarity=0.252 Sum_probs=54.2
Q ss_pred hhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHHcCC
Q 030547 35 IANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGF 101 (175)
Q Consensus 35 ~A~V~RImK~~LP~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF 101 (175)
+-.+ +.|-+.+. -..|+.|+..+|.+=++.=|.-|+-+|.+.-.+.+|.+++.+||-.||+.+..
T Consensus 14 ~Es~-k~vAEslG-i~nl~deaa~~La~dv~yrikEI~Q~aaKfm~hskR~kLtv~DV~~ALr~~nV 78 (576)
T KOG2549|consen 14 KESV-KVVAESLG-ITNLNDEAALLLAEDVEYRIKEIVQDAAKFMVHSKRTKLTVDDVDYALRSLNV 78 (576)
T ss_pred HHHH-HHHHHHhC-ccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcCcHHHHHHHHhhccc
Confidence 4444 44555553 23599999999999999999999999999999999999999999999996544
No 63
>KOG2389 consensus Predicted bromodomain transcription factor [Transcription]
Probab=82.92 E-value=3.9 Score=37.48 Aligned_cols=69 Identities=14% Similarity=0.164 Sum_probs=58.9
Q ss_pred ccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHHcCC
Q 030547 31 RYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGF 101 (175)
Q Consensus 31 ~~LP~A~V~RImK~~LP~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF 101 (175)
..|-+..|..|+....=.. ...-|.+.|+..+..||.-|+..|...+.-.+|.-.|..||+.||+.|+.
T Consensus 28 ~sla~~avaQIcqslg~~~--~~~sale~Ltd~~~qyvQ~lgk~a~~~~n~anR~epnl~Div~Al~dls~ 96 (353)
T KOG2389|consen 28 FSLARVAVAQICQSLGYSS--TQNSALETLTDVLQQYVQNLGKTAHRYSNLANRTEPNLFDIVLALQDLSA 96 (353)
T ss_pred HHHHHHHHHHHHHhcCCcc--cccHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCccHHHHHHHHHHhhh
Confidence 3577778888887764333 34449999999999999999999999999999999999999999998876
No 64
>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=81.32 E-value=4.2 Score=38.43 Aligned_cols=64 Identities=23% Similarity=0.280 Sum_probs=44.8
Q ss_pred hhHHHHHHHhhCCC-CCcccHHHHHHHHHHHH---HHHHHHHHHHHHHHHhcCCCccChhhHHHHHHHc
Q 030547 35 IANISRIMKKALPA-NGKIAKDAKDTVQECVS---EFISFITSEASDKCQKEKRKTINGDDLLWAMATL 99 (175)
Q Consensus 35 ~A~V~RImK~~LP~-~~kISkDA~~al~~~as---eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~L 99 (175)
..-+.+|++..+.. +..|++++.+.|.+.+. +.++.| ..|...|..++|++|+.+||.|++..-
T Consensus 265 ~eei~~Il~~~a~k~~i~is~~al~~I~~y~~n~Rel~nll-~~Aa~~A~~~~~~~It~~dI~~vl~~~ 332 (531)
T TIGR02902 265 DEEIKEIAKNAAEKIGINLEKHALELIVKYASNGREAVNIV-QLAAGIALGEGRKRILAEDIEWVAENG 332 (531)
T ss_pred HHHHHHHHHHHHHHcCCCcCHHHHHHHHHhhhhHHHHHHHH-HHHHHHHhhCCCcEEcHHHHHHHhCCc
Confidence 34466666666542 46799999998877765 333333 345567788899999999999997543
No 65
>PF13654 AAA_32: AAA domain; PDB: 3K1J_B.
Probab=79.10 E-value=10 Score=36.06 Aligned_cols=49 Identities=18% Similarity=0.201 Sum_probs=38.9
Q ss_pred cccHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHhcCCCccChhhHHHHHHHc
Q 030547 51 KIAKDAKDTVQECVSE-----------FISFITSEASDKCQKEKRKTINGDDLLWAMATL 99 (175)
Q Consensus 51 kISkDA~~al~~~ase-----------FI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~L 99 (175)
.++.+|...|.+.+.. .|.-|-.+|+..|..+++++|+++||..|++.-
T Consensus 447 ~~~~~Av~~li~~~~R~~q~kLsl~~~~l~~ll~EA~~~A~~~~~~~I~~~~V~~Ai~~r 506 (509)
T PF13654_consen 447 PFDRSAVARLIEYSARLDQDKLSLRFSWLADLLREANYWARKEGAKVITAEHVEQAIEER 506 (509)
T ss_dssp -BBHHHHHHHHHHHHHCC-SEEE--HHHHHHHHHHHHHHHHHCT-SSB-HHHHHHHHHH-
T ss_pred CCCHHHHHHHHHHHHHHhCCEeCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHcc
Confidence 5889998888887653 566777899999999999999999999999864
No 66
>TIGR00764 lon_rel lon-related putative ATP-dependent protease. Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein.
Probab=78.44 E-value=9.1 Score=37.00 Aligned_cols=50 Identities=12% Similarity=0.145 Sum_probs=40.0
Q ss_pred cccHHHHHHHHHHHH-------------HHHHHHHHHHHHHHHhcCCCccChhhHHHHHHHcC
Q 030547 51 KIAKDAKDTVQECVS-------------EFISFITSEASDKCQKEKRKTINGDDLLWAMATLG 100 (175)
Q Consensus 51 kISkDA~~al~~~as-------------eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~Lg 100 (175)
.++++|...|.+.++ -=|.-|-.+|..+|..+++.+|+.+||.+|++.-.
T Consensus 330 ~~s~~Av~~Li~~~~R~ag~r~~lsl~~R~L~~llR~A~~iA~~~~~~~I~~ehV~~Ai~~~~ 392 (608)
T TIGR00764 330 HFTRDAVEEIVREAQRRAGRKDHLTLRLRELGGLVRAAGDIAKSSGKVYVTAEHVLKAKKLAK 392 (608)
T ss_pred cCCHHHHHHHHHHHHHHHhcccccCCCHHHHHHHHHHHHHHHHhcCCceecHHHHHHHHHHHH
Confidence 699999999886544 23455667888899999999999999999997543
No 67
>COG1067 LonB Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]
Probab=77.61 E-value=2.3 Score=41.70 Aligned_cols=49 Identities=24% Similarity=0.264 Sum_probs=37.6
Q ss_pred cccHHHHHHHHHHHHH-------------HHHHHHHHHHHHHHhcCCCccChhhHHHHHHHc
Q 030547 51 KIAKDAKDTVQECVSE-------------FISFITSEASDKCQKEKRKTINGDDLLWAMATL 99 (175)
Q Consensus 51 kISkDA~~al~~~ase-------------FI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~L 99 (175)
-++++|..-|.+-+.. -+.-|-.+|.++|..++++-|+++||.+|++.-
T Consensus 338 ~~~~~Av~~li~~a~R~Ag~~~~Ltl~~rdl~~lv~~A~~ia~~~~~~~I~ae~Ve~a~~~~ 399 (647)
T COG1067 338 HLDKDAVEELIREAARRAGDQNKLTLRLRDLGNLVREAGDIAVSEGRKLITAEDVEEALQKR 399 (647)
T ss_pred CCCHHHHHHHHHHHHHhccccceeccCHHHHHHHHHHhhHHHhcCCcccCcHHHHHHHHHhh
Confidence 4788887766665543 233344499999999999999999999999873
No 68
>cd08045 TAF4 TATA Binding Protein (TBP) Associated Factor 4 (TAF4) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 4 (TAF4) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryote. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypotheses are
Probab=72.22 E-value=18 Score=30.09 Aligned_cols=80 Identities=10% Similarity=0.156 Sum_probs=59.0
Q ss_pred cccccCchhHHHHHHHhhCCCCC--cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhc------CCCccChhhHHHHHHHc
Q 030547 28 EQDRYLPIANISRIMKKALPANG--KIAKDAKDTVQECVSEFISFITSEASDKCQKE------KRKTINGDDLLWAMATL 99 (175)
Q Consensus 28 ~~d~~LP~A~V~RImK~~LP~~~--kISkDA~~al~~~aseFI~~LtseA~~~~~~~------kRKTI~~eDVl~AL~~L 99 (175)
.+..+|....|.+.|...+.... .|+.|....|.-||.+++..|-......|++- ...++-..||-.-|..|
T Consensus 40 ~~~~fl~~~~l~~~~~~i~~~~g~~~~~~d~~~lis~a~e~rlr~li~k~~~~s~hR~~~~~~~~r~~~~sdvr~qL~~l 119 (212)
T cd08045 40 KDPSFLNPSPLAKKIRKIAKKHGLKEVDEDVLDLISLALEERLRNLLEKLIEVSEHRVDSEKEDERYEITSDVRKQLRFL 119 (212)
T ss_pred chhhccCHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCceeecchHHHHHHHH
Confidence 33456777777777777765433 69999999999999999999999998888764 34566678887777666
Q ss_pred CCCcchHH
Q 030547 100 GFEDYIDP 107 (175)
Q Consensus 100 gF~~yv~~ 107 (175)
+--+..+.
T Consensus 120 ~~~ek~e~ 127 (212)
T cd08045 120 EQLEREEE 127 (212)
T ss_pred HHHHHHHH
Confidence 55444433
No 69
>PF08369 PCP_red: Proto-chlorophyllide reductase 57 kD subunit; InterPro: IPR013580 This domain is found in bacteria and plant chloroplast proteins. It often appears at the C-terminal of nitrogenase component 1 type oxidoreductases (IPR000510 from INTERPRO) and sometimes independently in bacterial proteins such as the proto-chlorophyllide reductase subunit B of the cyanobacterium Synechocystis. This domain is also associated with chlorophyllide reductase subunit Z, converts chlorophylls (Chl) into bacteriochlorophylls (BChl) by reducing ring B of the tetrapyrrole.; GO: 0016491 oxidoreductase activity, 0015979 photosynthesis, 0015995 chlorophyll biosynthetic process, 0055114 oxidation-reduction process; PDB: 2KRU_A 2L09_A.
Probab=71.20 E-value=6.6 Score=25.53 Aligned_cols=42 Identities=12% Similarity=0.120 Sum_probs=27.9
Q ss_pred cHHHHHHHHHHHHHHHH-HHHHHHHHHHHhcCCCccChhhHHHH
Q 030547 53 AKDAKDTVQECVSEFIS-FITSEASDKCQKEKRKTINGDDLLWA 95 (175)
Q Consensus 53 SkDA~~al~~~aseFI~-~LtseA~~~~~~~kRKTI~~eDVl~A 95 (175)
+.||...|.+. -.||. -|-..+-..|...|...||.++|..|
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 56777777775 45554 34445667889999999999999876
No 70
>PF13335 Mg_chelatase_2: Magnesium chelatase, subunit ChlI
Probab=70.94 E-value=18 Score=26.75 Aligned_cols=47 Identities=15% Similarity=0.211 Sum_probs=39.3
Q ss_pred cccHHHHHHHHHHHHHH------HHHHHHHHHHHHHhcCCCccChhhHHHHHH
Q 030547 51 KIAKDAKDTVQECVSEF------ISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (175)
Q Consensus 51 kISkDA~~al~~~aseF------I~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (175)
.+++++...|..++..| ++-|...|..+|--++...|..+||..||.
T Consensus 42 ~l~~~~~~~l~~~~~~~~lS~R~~~rilrvARTIADL~~~~~I~~~hi~EAl~ 94 (96)
T PF13335_consen 42 PLSSEAKKLLEQAAEKLNLSARGYHRILRVARTIADLEGSERITREHIAEALS 94 (96)
T ss_pred CCCHHHHHHHHHHHHHcCcCHHHHHHHHHHHHHHHhHcCCCCCCHHHHHHHHh
Confidence 57888888888887766 445666889999999999999999999984
No 71
>KOG3334 consensus Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=70.12 E-value=15 Score=29.92 Aligned_cols=65 Identities=14% Similarity=0.242 Sum_probs=50.2
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHHcCCCcchH-HHHHHHHHHH
Q 030547 52 IAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYID-PLKAYLMRYR 116 (175)
Q Consensus 52 ISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~~yv~-~Lk~~L~~yr 116 (175)
...-...-|-+.+=-++.-|-..|.-.+.+.++.||.++||..|+....=-.|.. +=+++|-++-
T Consensus 31 yEprVi~qlLefa~rYtt~vL~DA~vys~HA~ka~i~~eDVrlA~~~~~~~sf~~pPpRe~lL~lA 96 (148)
T KOG3334|consen 31 YEPRVINQLLEFAYRYTTTVLDDAKVYSSHAKKATIDAEDVRLAIQMRVDHSFTPPPPREFLLELA 96 (148)
T ss_pred cChHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHhccccCCCCchHHHHHHH
Confidence 4455556677777777888888999999999999999999999999776666666 5555555543
No 72
>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=69.42 E-value=12 Score=34.66 Aligned_cols=53 Identities=26% Similarity=0.286 Sum_probs=48.5
Q ss_pred CcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHHcCCC
Q 030547 50 GKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFE 102 (175)
Q Consensus 50 ~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~ 102 (175)
..|..|+..+|..-.+-=|+-+..+|...-.+.||..++-+||-.||+.|..+
T Consensus 21 ~Ni~Dd~l~alamDlEYRI~ev~qea~KFmvhSKRtvLt~dDis~ALr~lNVe 73 (450)
T COG5095 21 SNIDDDALRALAMDLEYRIKEVCQEASKFMVHSKRTVLTIDDISYALRSLNVE 73 (450)
T ss_pred cccccHHHHHHHHhHHHHHHHHHHHHHHHhhcccceeeeHHhHHHHHHhcCCC
Confidence 36999999999999999999999999999999999999999999999988653
No 73
>KOG2680 consensus DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=69.00 E-value=22 Score=33.01 Aligned_cols=60 Identities=22% Similarity=0.293 Sum_probs=45.5
Q ss_pred HHHHHHhhCC-CCCcccHHHHHHHHHHHHH----HHHHHHHHHHHHHHhcCCCccChhhHHHHHH
Q 030547 38 ISRIMKKALP-ANGKIAKDAKDTVQECVSE----FISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (175)
Q Consensus 38 V~RImK~~LP-~~~kISkDA~~al~~~ase----FI~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (175)
|..|.+--.. +++.++.||++.|.+...+ |-.+|-+.|+.+|.+.|-+++..+||-.+.+
T Consensus 363 ~~~IL~iRc~EEdv~m~~~A~d~Lt~i~~~tsLRYai~Lit~a~~~~~krk~~~v~~~di~r~y~ 427 (454)
T KOG2680|consen 363 IKKILRIRCQEEDVEMNPDALDLLTKIGEATSLRYAIHLITAASLVCLKRKGKVVEVDDIERVYR 427 (454)
T ss_pred HHHHHHhhhhhhccccCHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHhcCceeehhHHHHHHH
Confidence 4444444333 4788999999999876554 4455666788899999999999999999974
No 74
>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=67.06 E-value=21 Score=28.91 Aligned_cols=50 Identities=20% Similarity=0.272 Sum_probs=37.2
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHHcCCC-cchHHHHHHHHHHHHHh
Q 030547 63 CVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFE-DYIDPLKAYLMRYREME 119 (175)
Q Consensus 63 ~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~-~yv~~Lk~~L~~yre~~ 119 (175)
.+.+.+.||-..|. |.-++.+++..-|+.|||+ +.++.+......+|+..
T Consensus 43 ~~va~l~fiL~~A~-------k~n~~~~~l~~eL~~lglp~e~~~~l~~~~~~~~~~l 93 (174)
T cd04752 43 ASIAVLSFILSSAA-------KYNVDGESLSSELQQLGLPKEHATSLCRSYEEKQSKL 93 (174)
T ss_pred HHHHHHHHHHHHHH-------HcCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHH
Confidence 55667778877666 5669999999999999996 66666666666666543
No 75
>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=65.89 E-value=5.9 Score=24.86 Aligned_cols=26 Identities=19% Similarity=0.231 Sum_probs=21.2
Q ss_pred HHHHHHhcCCCccChhhHHHHHHHcC
Q 030547 75 ASDKCQKEKRKTINGDDLLWAMATLG 100 (175)
Q Consensus 75 A~~~~~~~kRKTI~~eDVl~AL~~Lg 100 (175)
|.+.|...+...|+.+|++.||=+-+
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 56789999999999999999975544
No 76
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=65.52 E-value=30 Score=30.05 Aligned_cols=72 Identities=13% Similarity=0.194 Sum_probs=49.8
Q ss_pred cCchhHHHHHHHhhCC-CCCcccHHHHHHHHHHHH---HHHHHHHHHHHHHHHhcCCCccChhhHHHHHHHcCCCc
Q 030547 32 YLPIANISRIMKKALP-ANGKIAKDAKDTVQECVS---EFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFED 103 (175)
Q Consensus 32 ~LP~A~V~RImK~~LP-~~~kISkDA~~al~~~as---eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~~ 103 (175)
.++...+..|++.... .++.++.|+...|.+.|. -++..+...+.+.+...+.+.|+.++|..+++.++...
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 3555666666665543 267899999888887663 23444444556666666677999999999999887654
No 77
>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=63.38 E-value=23 Score=33.39 Aligned_cols=82 Identities=17% Similarity=0.233 Sum_probs=57.8
Q ss_pred CchhHHHHHHHhhCC-CCCcccHHHHHHHHHHHHH----HHHHHHHHHHHHHHhcCCCccChhhHHHHHHHcCCCcchHH
Q 030547 33 LPIANISRIMKKALP-ANGKIAKDAKDTVQECVSE----FISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYIDP 107 (175)
Q Consensus 33 LP~A~V~RImK~~LP-~~~kISkDA~~al~~~ase----FI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~~yv~~ 107 (175)
.++.-|.-|++--.. +++.+++||.+.|....++ +..-|-+-|+.+|++.++++|..+||-.|-+ =|.|-...
T Consensus 361 y~~~EireIi~iRa~ee~i~l~~~Ale~L~~ig~etSLRYa~qLL~pa~iiA~~rg~~~V~~~dVe~a~~--lF~D~krS 438 (450)
T COG1224 361 YSREEIREIIRIRAKEEDIELSDDALEYLTDIGEETSLRYAVQLLTPASIIAKRRGSKRVEVEDVERAKE--LFLDVKRS 438 (450)
T ss_pred CCHHHHHHHHHHhhhhhccccCHHHHHHHHhhchhhhHHHHHHhccHHHHHHHHhCCCeeehhHHHHHHH--HHhhHHHH
Confidence 445556666664443 3788999999999877655 4444556788999999999999999999943 24444444
Q ss_pred HHHHHHHHHH
Q 030547 108 LKAYLMRYRE 117 (175)
Q Consensus 108 Lk~~L~~yre 117 (175)
. +|++.|++
T Consensus 439 v-~~v~~~~~ 447 (450)
T COG1224 439 V-EYVEKYEG 447 (450)
T ss_pred H-HHHHHHHh
Confidence 3 46677664
No 78
>KOG3901 consensus Transcription initiation factor IID subunit [Transcription]
Probab=62.23 E-value=23 Score=27.49 Aligned_cols=48 Identities=19% Similarity=0.279 Sum_probs=38.4
Q ss_pred CCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHH
Q 030547 48 ANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMAT 98 (175)
Q Consensus 48 ~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~ 98 (175)
++..=-.|.+++|-..+.+||.-++..|..+. +|--+..||++-+|++
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 44456678899999999999999987777766 4445788999999973
No 79
>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=62.10 E-value=47 Score=28.06 Aligned_cols=70 Identities=19% Similarity=0.200 Sum_probs=46.7
Q ss_pred CchhHHHHHHHhhCC-CCCcccHHHHHHHHHHHH---HHHHHHHHHHHHHHHhcCCCccChhhHHHHHHHcCCC
Q 030547 33 LPIANISRIMKKALP-ANGKIAKDAKDTVQECVS---EFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFE 102 (175)
Q Consensus 33 LP~A~V~RImK~~LP-~~~kISkDA~~al~~~as---eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~ 102 (175)
+....+..|++.... .+..++.|+...|.+.+. -++..+...+.+.+...+...|+.++|..++..++++
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 444556666665543 256799999888877653 2233444445566655666789999999999987665
No 80
>COG5248 TAF19 Transcription initiation factor TFIID, subunit TAF13 [Transcription]
Probab=61.08 E-value=26 Score=27.66 Aligned_cols=49 Identities=18% Similarity=0.320 Sum_probs=41.4
Q ss_pred CCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHH
Q 030547 48 ANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMAT 98 (175)
Q Consensus 48 ~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~ 98 (175)
+...=.-|..++|.+.+.-+++.+...|...|+. |-.+..||...||++
T Consensus 24 Dvv~P~~dt~~~L~e~V~dY~~~~ctna~~~Aq~--rnK~k~eDfkfaLr~ 72 (126)
T COG5248 24 DVVAPRYDTAEALHEYVLDYMSILCTNAHNMAQV--RNKTKTEDFKFALRR 72 (126)
T ss_pred CCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHh--cccchHHHHHHHHhh
Confidence 4556678999999999999999999999999983 445678999999973
No 81
>KOG1757 consensus Histone 2A [Chromatin structure and dynamics]
Probab=61.07 E-value=13 Score=29.34 Aligned_cols=65 Identities=20% Similarity=0.327 Sum_probs=49.3
Q ss_pred ccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhc----CCCccChhhHHHHHH
Q 030547 29 QDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKE----KRKTINGDDLLWAMA 97 (175)
Q Consensus 29 ~d~~LP~A~V~RImK~~LP~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~----kRKTI~~eDVl~AL~ 97 (175)
.-+.+|...|.|.+|.-.....++..-+..-. ...+.|||.|-.+.|... +-|.|++.|+..|++
T Consensus 27 aGlqFpVgRihr~LK~r~t~h~rVGataavy~----aaileYLTaEVLeLAgNasKdLKvKRitprHlqLAiR 95 (131)
T KOG1757|consen 27 AGLQFPVGRIHRHLKTRTTSHGRVGATAAVYS----AAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 95 (131)
T ss_pred cccccchHHHHHHHHHhcccccccchHHHHHH----HHHHHHHHHHHHHHcccccccceeeeccchhheeeec
Confidence 34689999999999999887788765443322 345679999888877554 457899999988875
No 82
>TIGR01128 holA DNA polymerase III, delta subunit. subunit around DNA forming a DNA sliding clamp.
Probab=59.48 E-value=49 Score=27.65 Aligned_cols=66 Identities=18% Similarity=0.113 Sum_probs=47.7
Q ss_pred cCchhHHHHHHHhhCCC-CCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHH
Q 030547 32 YLPIANISRIMKKALPA-NGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (175)
Q Consensus 32 ~LP~A~V~RImK~~LP~-~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (175)
.+....+.+++++.+.. +..|+.++...|.+.+.-=+..+..+-...|.-.+.++|+.+||...+.
T Consensus 110 ~~~~~~~~~~i~~~~~~~g~~i~~~a~~~l~~~~~~d~~~l~~el~KL~~~~~~~~It~e~I~~~~~ 176 (302)
T TIGR01128 110 TPKEQELPRWIQARLKKLGLRIDPDAVQLLAELVEGNLLAIAQELEKLALYAPDGKITLEDVEEAVS 176 (302)
T ss_pred CCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCcHHHHHHHHHHHHHhhCCCCCCCHHHHHHHHh
Confidence 35566677777766653 5689999999998888765666666666666655555799999987765
No 83
>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=57.33 E-value=42 Score=32.47 Aligned_cols=49 Identities=16% Similarity=0.184 Sum_probs=41.6
Q ss_pred CCcccHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCccChhhHHHHHH
Q 030547 49 NGKIAKDAKDTVQECVSEFI-------SFITSEASDKCQKEKRKTINGDDLLWAMA 97 (175)
Q Consensus 49 ~~kISkDA~~al~~~aseFI-------~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (175)
.+.|+.++++.|.+.+..+- .++...|..+|.-++|.+|+.+||..|++
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 57899999999999887762 45667788899999999999999999885
No 84
>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I. This model represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria.
Probab=56.79 E-value=53 Score=29.54 Aligned_cols=54 Identities=22% Similarity=0.198 Sum_probs=41.1
Q ss_pred HhhCCCCCcccHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCccChhhHHHHHH
Q 030547 43 KKALPANGKIAKDAKDTVQECVSEFI-------SFITSEASDKCQKEKRKTINGDDLLWAMA 97 (175)
Q Consensus 43 K~~LP~~~kISkDA~~al~~~aseFI-------~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (175)
++.++ .+.|+.+.+..+.+.|..+= .++...|...|.-++|..|+++||..+..
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 44454 57899988888888776652 34556777888999999999999998764
No 85
>PRK09862 putative ATP-dependent protease; Provisional
Probab=56.42 E-value=43 Score=31.94 Aligned_cols=55 Identities=11% Similarity=0.107 Sum_probs=42.8
Q ss_pred CcccHHHHHHHHHHHHHH------HHHHHHHHHHHHHhcCCCccChhhHHHHHHHcCCCcc
Q 030547 50 GKIAKDAKDTVQECVSEF------ISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDY 104 (175)
Q Consensus 50 ~kISkDA~~al~~~aseF------I~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~~y 104 (175)
..+++++...+.+++..+ .++|...|..+|.-++|..|+.+||..|+.=-+++..
T Consensus 437 ~~l~~~~~~~l~~~~~~~~lS~Ra~~rlLrvARTiADL~g~~~V~~~hv~eAl~yR~~~~~ 497 (506)
T PRK09862 437 CKLESEDARWLEETLIHLGLSIRAWQRLLKVARTIADIDQSDIITRQHLQEAVSYRAIDRL 497 (506)
T ss_pred hCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHhhcccHH
Confidence 367788888777755444 5667778999999999999999999999975555533
No 86
>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=55.13 E-value=20 Score=24.27 Aligned_cols=30 Identities=20% Similarity=0.351 Sum_probs=24.7
Q ss_pred CCCccChhhHHHHHHHcCCCcchHHHHHHH
Q 030547 83 KRKTINGDDLLWAMATLGFEDYIDPLKAYL 112 (175)
Q Consensus 83 kRKTI~~eDVl~AL~~LgF~~yv~~Lk~~L 112 (175)
....-+.++++.||+++|..+.++.++.+|
T Consensus 54 ~~~~at~~~L~~aL~~~~~~d~~~~i~~~~ 83 (83)
T PF00531_consen 54 EGPNATVDQLIQALRDIGRNDLAEKIEQML 83 (83)
T ss_dssp HGSTSSHHHHHHHHHHTTHHHHHHHHHHH-
T ss_pred cCCCCcHHHHHHHHHHCCcHHHHHHHHhhC
Confidence 345678889999999999999999888764
No 87
>PRK13406 bchD magnesium chelatase subunit D; Provisional
Probab=54.16 E-value=33 Score=33.23 Aligned_cols=52 Identities=15% Similarity=0.135 Sum_probs=44.9
Q ss_pred hCCCCCcccHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCccChhhHHHHHH
Q 030547 45 ALPANGKIAKDAKDTVQECVSEFI-------SFITSEASDKCQKEKRKTINGDDLLWAMA 97 (175)
Q Consensus 45 ~LP~~~kISkDA~~al~~~aseFI-------~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (175)
.++ ++.|+.+....+.++|..|= .+|...|..+|--++|.+|+.+||..|+.
T Consensus 190 rl~-~v~v~~~~l~~i~~~~~~~gv~S~Ra~i~llraARa~AaL~Gr~~V~~~dv~~Aa~ 248 (584)
T PRK13406 190 RLP-AVGPPPEAIAALCAAAAALGIASLRAPLLALRAARAAAALAGRTAVEEEDLALAAR 248 (584)
T ss_pred HHc-cCCCCHHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 444 78999999999888888774 47778899999999999999999999985
No 88
>PRK13765 ATP-dependent protease Lon; Provisional
Probab=52.19 E-value=38 Score=33.24 Aligned_cols=47 Identities=15% Similarity=0.155 Sum_probs=38.4
Q ss_pred cccHHHHHHHHHHHHHH-------------HHHHHHHHHHHHHhcCCCccChhhHHHHHH
Q 030547 51 KIAKDAKDTVQECVSEF-------------ISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (175)
Q Consensus 51 kISkDA~~al~~~aseF-------------I~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (175)
.|+++|...|.+-++.- |.-|-.+|..+|+.++++.|+.+||..|+.
T Consensus 339 ~f~~eAVa~LI~~~~R~ag~r~~lsl~~~~l~~l~r~a~~~a~~~~~~~i~~~~v~~a~~ 398 (637)
T PRK13765 339 HFDRDAVEEIIREAKRRAGRKGHLTLKLRDLGGLVRVAGDIARSEGAELTTAEHVLEAKK 398 (637)
T ss_pred CCCHHHHHHHHHHHHHHhCCccccccCHHHHHHHHHHHHHHHHhhccceecHHHHHHHHH
Confidence 68999988888766632 223677899999999999999999999984
No 89
>PRK12402 replication factor C small subunit 2; Reviewed
Probab=51.33 E-value=36 Score=28.85 Aligned_cols=70 Identities=6% Similarity=0.014 Sum_probs=43.3
Q ss_pred CchhHHHHHHHhhCC-CCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHHcCCCcc
Q 030547 33 LPIANISRIMKKALP-ANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDY 104 (175)
Q Consensus 33 LP~A~V~RImK~~LP-~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~~y 104 (175)
++...+.++++..+. .+..++.++.+.|.+.+.-=+..+-......|. +.++|+.+||..++.....++.
T Consensus 184 ~~~~~~~~~l~~~~~~~~~~~~~~al~~l~~~~~gdlr~l~~~l~~~~~--~~~~It~~~v~~~~~~~~~~~~ 254 (337)
T PRK12402 184 PTDDELVDVLESIAEAEGVDYDDDGLELIAYYAGGDLRKAILTLQTAAL--AAGEITMEAAYEALGDVGTDEV 254 (337)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHH--cCCCCCHHHHHHHhCCCCCHHH
Confidence 445566666666554 256799999999988873323333333333332 2347999999998876554433
No 90
>COG1222 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]
Probab=50.70 E-value=27 Score=32.66 Aligned_cols=75 Identities=20% Similarity=0.191 Sum_probs=49.4
Q ss_pred CCCcccccCchhHHHHHHHhhCCCCCcccHHH-HHHHHHHHHHH----HHHHHHHHHHHHHhcCCCccChhhHHHHHHHc
Q 030547 25 GVREQDRYLPIANISRIMKKALPANGKIAKDA-KDTVQECVSEF----ISFITSEASDKCQKEKRKTINGDDLLWAMATL 99 (175)
Q Consensus 25 ~~~~~d~~LP~A~V~RImK~~LP~~~kISkDA-~~al~~~aseF----I~~LtseA~~~~~~~kRKTI~~eDVl~AL~~L 99 (175)
.-|.-++.||-.-=.+-|=+..-..|.+++|. .+.|.+++.-| |.-|..||--.|.++.|..|+-+|.++|.+++
T Consensus 313 ~DRkIEfplPd~~gR~~Il~IHtrkM~l~~dvd~e~la~~~~g~sGAdlkaictEAGm~AiR~~R~~Vt~~DF~~Av~KV 392 (406)
T COG1222 313 FDRKIEFPLPDEEGRAEILKIHTRKMNLADDVDLELLARLTEGFSGADLKAICTEAGMFAIRERRDEVTMEDFLKAVEKV 392 (406)
T ss_pred ccceeecCCCCHHHHHHHHHHHhhhccCccCcCHHHHHHhcCCCchHHHHHHHHHHhHHHHHhccCeecHHHHHHHHHHH
Confidence 34445556664333322222222235566655 45566665555 77889999999999999999999999998654
No 91
>TIGR01052 top6b DNA topoisomerase VI, B subunit. This model describes DNA topoisomerase VI, an archaeal type II DNA topoisomerase (DNA gyrase).
Probab=48.80 E-value=20 Score=34.17 Aligned_cols=59 Identities=17% Similarity=0.308 Sum_probs=39.8
Q ss_pred HhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHHcCCCcchHHHHHHHHHH
Q 030547 43 KKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLMRY 115 (175)
Q Consensus 43 K~~LP~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~~yv~~Lk~~L~~y 115 (175)
|+++.+.--|-+|.+.||++||...=.||...-...-.++++++ |..|++.+-..|...
T Consensus 426 Ke~ia~~~ei~~ei~~al~~~~r~L~~~l~~~~~~~~~~~r~~~--------------~~~y~p~~a~~~~~~ 484 (488)
T TIGR01052 426 KQSVADIPEIYNEIRLALMEVARRLRLYLSRKAREEEEIKRRKT--------------LEKYLPEIAKSLAYI 484 (488)
T ss_pred hhhhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------------HHHHHHHHHHHHHHH
Confidence 44444344688899999999999999999876665555554444 345666665555443
No 92
>TIGR00368 Mg chelatase-related protein. The N-terminal end matches very strongly a pfam Mg_chelatase domain.
Probab=47.36 E-value=50 Score=31.35 Aligned_cols=47 Identities=15% Similarity=0.191 Sum_probs=40.7
Q ss_pred cccHHHHHHHHHHHHHH------HHHHHHHHHHHHHhcCCCccChhhHHHHHH
Q 030547 51 KIAKDAKDTVQECVSEF------ISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (175)
Q Consensus 51 kISkDA~~al~~~aseF------I~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (175)
.++++++..|.+++..| .+-|...|..+|.-+++..|..+||..|+.
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 56889999999888876 556677899999999999999999999984
No 93
>smart00350 MCM minichromosome maintenance proteins.
Probab=47.34 E-value=69 Score=30.07 Aligned_cols=65 Identities=11% Similarity=0.170 Sum_probs=45.7
Q ss_pred ccCchhHHHHHHHhh----CCCCCcccHHHHHHHHHHHHHH-------------------HHHHHHHHHHHHHhcCCCcc
Q 030547 31 RYLPIANISRIMKKA----LPANGKIAKDAKDTVQECVSEF-------------------ISFITSEASDKCQKEKRKTI 87 (175)
Q Consensus 31 ~~LP~A~V~RImK~~----LP~~~kISkDA~~al~~~aseF-------------------I~~LtseA~~~~~~~kRKTI 87 (175)
..++...+.+.+.-+ .| +|++++.+.|.+...+. +..|...|.-.|+-..|.+|
T Consensus 416 ~~~~~~~l~~yi~~ar~~~~P---~ls~~~~~~i~~~y~~~R~~~~~~~~~~~~~~t~R~l~sliRla~A~A~l~~r~~V 492 (509)
T smart00350 416 VPISQEFLRKYIAYAREKIKP---KLSEEAAEKLVKAYVDLRKEDSQSEARSSIPITVRQLESIIRLSEAHAKMRLSDVV 492 (509)
T ss_pred ccCCHHHHHHHHHHHHhcCCC---CCCHHHHHHHHHHHHHhcccccccccccccCcCHHHHHHHHHHHHHHHHHcCCCcc
Confidence 356777777666433 33 68999998887654442 24455667777888889999
Q ss_pred ChhhHHHHHHH
Q 030547 88 NGDDLLWAMAT 98 (175)
Q Consensus 88 ~~eDVl~AL~~ 98 (175)
+.+||..|++-
T Consensus 493 ~~~Dv~~ai~l 503 (509)
T smart00350 493 EEADVEEAIRL 503 (509)
T ss_pred CHHHHHHHHHH
Confidence 99999998753
No 94
>PRK05574 holA DNA polymerase III subunit delta; Reviewed
Probab=45.88 E-value=66 Score=27.41 Aligned_cols=66 Identities=15% Similarity=0.055 Sum_probs=47.3
Q ss_pred cCchhHHHHHHHhhCCC-CCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHH
Q 030547 32 YLPIANISRIMKKALPA-NGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (175)
Q Consensus 32 ~LP~A~V~RImK~~LP~-~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (175)
.+....+.+.|+..+-. +..|+.+|...|.+.+..=+..+..|-...|.-.+-+.|+.+||-..+.
T Consensus 145 ~~~~~~~~~~i~~~~~~~g~~i~~~a~~~L~~~~~~d~~~l~~El~KL~l~~~~~~It~~~I~~~i~ 211 (340)
T PRK05574 145 PPKEAELPQWIQQRLKQQGLQIDAAALQLLAERVEGNLLALAQELEKLALLYPDGKITLEDVEEAVP 211 (340)
T ss_pred CCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCchHHHHHHHHHHHHhhcCCCCCCHHHHHHHHh
Confidence 35566666666666643 6689999999999998876777777777776544322399999876655
No 95
>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=45.31 E-value=33 Score=29.40 Aligned_cols=78 Identities=9% Similarity=0.112 Sum_probs=36.3
Q ss_pred CCcccccCchhHHHHHHHhhCCCC--CcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC------CccChhhHHHHHH
Q 030547 26 VREQDRYLPIANISRIMKKALPAN--GKIAKDAKDTVQECVSEFISFITSEASDKCQKEKR------KTINGDDLLWAMA 97 (175)
Q Consensus 26 ~~~~d~~LP~A~V~RImK~~LP~~--~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kR------KTI~~eDVl~AL~ 97 (175)
...++.+|-...+.+-|.+....+ ..|..|...+|.-||.++|..|-..+..+|++-.. .+....||-..|.
T Consensus 37 ~~~~~~fL~~~~L~~~i~~i~~~~g~~~~~~d~l~llS~A~e~rLr~lie~~~~~s~hR~~~~~~~~~~~~~sdv~~qlr 116 (264)
T PF05236_consen 37 SEKEEPFLNPSPLQKRIQKIAKKHGLKSVDEDVLELLSLATEERLRNLIEKAIVLSRHRRDSSKSDPRYEIRSDVRKQLR 116 (264)
T ss_dssp -------S-HHHHHHHHHHHHHCTT--EE-TCHHHHHHHHHHHHHHHHHHHHH---------------------------
T ss_pred ccccccccCHHHHHHHHHHHHHHcCCcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccCCCcccccchHHHHHHH
Confidence 346677888888888888877543 46999999999999999999999999888865432 1334667777666
Q ss_pred HcCCCc
Q 030547 98 TLGFED 103 (175)
Q Consensus 98 ~LgF~~ 103 (175)
.|.--+
T Consensus 117 ~l~~~e 122 (264)
T PF05236_consen 117 FLEQLE 122 (264)
T ss_dssp ------
T ss_pred HHHHHH
Confidence 555433
No 96
>PRK07452 DNA polymerase III subunit delta; Validated
Probab=45.29 E-value=59 Score=27.90 Aligned_cols=64 Identities=11% Similarity=0.149 Sum_probs=46.6
Q ss_pred HHHHHHhhCC-CCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHh--cCCCccChhhHHHHHHHcCC
Q 030547 38 ISRIMKKALP-ANGKIAKDAKDTVQECVSEFISFITSEASDKCQK--EKRKTINGDDLLWAMATLGF 101 (175)
Q Consensus 38 V~RImK~~LP-~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~--~kRKTI~~eDVl~AL~~LgF 101 (175)
+.+.|++.+- .+..|+.+|...|.+++.-=...+..+-...|.- .++.+|+.+||...+....+
T Consensus 135 l~~~i~~~~~~~g~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~~It~~~V~~~v~~~~~ 201 (326)
T PRK07452 135 LKQLVERTAQELGVKLTPEAAELLAEAVGNDSRRLYNELEKLALYAENSTKPISAEEVKALVSNTTQ 201 (326)
T ss_pred HHHHHHHHHHHcCCCCCHHHHHHHHHHhCccHHHHHHHHHHHHHhccCCCCccCHHHHHHHhccCcC
Confidence 4454444443 3678999999999999887666676777776665 45778999999988766554
No 97
>COG5162 Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=45.10 E-value=1.4e+02 Score=25.17 Aligned_cols=49 Identities=20% Similarity=0.234 Sum_probs=37.5
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHh---------------------------------cCCCccChhhHHHHHHHc
Q 030547 53 AKDAKDTVQECVSEFISFITSEASDKCQK---------------------------------EKRKTINGDDLLWAMATL 99 (175)
Q Consensus 53 SkDA~~al~~~aseFI~~LtseA~~~~~~---------------------------------~kRKTI~~eDVl~AL~~L 99 (175)
..-.+-+|.-.+..||+-|+-.|.+..+- .++.+++..|+-.||++.
T Consensus 107 D~rvKkLl~L~aqKFvsDiA~dayqYsrIr~~~sna~~t~~~a~~f~~gg~~~i~~~~~~~dr~K~vltv~DLs~Al~Ey 186 (197)
T COG5162 107 DQRVKKLLSLLAQKFVSDIAVDAYQYSRIRQGSSNAKATAQKAKRFAKGGASGIGSSGRRGDRKKPVLTVVDLSKALEEY 186 (197)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccchhhHHHHHHHHhcccccccccccccccCCceeeehHHHHHHHHh
Confidence 34457788888999999998877654421 156678999999999998
Q ss_pred CC
Q 030547 100 GF 101 (175)
Q Consensus 100 gF 101 (175)
|+
T Consensus 187 Gi 188 (197)
T COG5162 187 GI 188 (197)
T ss_pred cc
Confidence 87
No 98
>CHL00081 chlI Mg-protoporyphyrin IX chelatase
Probab=44.71 E-value=85 Score=28.55 Aligned_cols=54 Identities=19% Similarity=0.238 Sum_probs=43.9
Q ss_pred HhhCCCCCcccHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCccChhhHHHHHH
Q 030547 43 KKALPANGKIAKDAKDTVQECVSEFI-------SFITSEASDKCQKEKRKTINGDDLLWAMA 97 (175)
Q Consensus 43 K~~LP~~~kISkDA~~al~~~aseFI-------~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (175)
++.++ .+.|+.+.+..|.+.|..+= .++...|.-.|--++|..|+++||..+..
T Consensus 260 r~~~~-~V~v~~~~~~yi~~l~~~~~~~s~Ra~i~l~raArA~Aal~GR~~V~pdDv~~~a~ 320 (350)
T CHL00081 260 QNLLP-KVEIDYDLRVKISQICSELDVDGLRGDIVTNRAAKALAAFEGRTEVTPKDIFKVIT 320 (350)
T ss_pred HHhcC-CCccCHHHHHHHHHHHHHHCCCCChHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 44555 57899999999988888763 46667788889999999999999998875
No 99
>PLN00138 large subunit ribosomal protein LP2; Provisional
Probab=44.71 E-value=71 Score=24.70 Aligned_cols=31 Identities=13% Similarity=0.097 Sum_probs=27.0
Q ss_pred HHHHHHHHHHHhcCCCccChhhHHHHHHHcCCC
Q 030547 70 FITSEASDKCQKEKRKTINGDDLLWAMATLGFE 102 (175)
Q Consensus 70 ~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~ 102 (175)
||+ |+-.|.-.+...||.+||.+.|+..|.+
T Consensus 3 yva--Ayll~~l~g~~~pta~dI~~IL~AaGve 33 (113)
T PLN00138 3 VVA--AYLLAVLGGNTCPSAEDLKDILGSVGAD 33 (113)
T ss_pred HHH--HHHHHHhcCCCCCCHHHHHHHHHHcCCc
Confidence 554 6778888999999999999999999875
No 100
>PF08823 PG_binding_2: Putative peptidoglycan binding domain; InterPro: IPR014927 This entry may be a peptidoglycan binding domain.
Probab=44.20 E-value=41 Score=23.99 Aligned_cols=31 Identities=16% Similarity=0.253 Sum_probs=26.4
Q ss_pred hhHHHHHHHcCC------CcchHHHHHHHHHHHHHhh
Q 030547 90 DDLLWAMATLGF------EDYIDPLKAYLMRYREMEG 120 (175)
Q Consensus 90 eDVl~AL~~LgF------~~yv~~Lk~~L~~yre~~~ 120 (175)
+.|..+|..||| +.|-+.++..|..|..+++
T Consensus 19 ~evq~~L~~lGyy~g~~~g~~d~a~~~Al~~~~g~EN 55 (74)
T PF08823_consen 19 REVQEALKRLGYYKGEADGVWDEATEDALRAWAGTEN 55 (74)
T ss_pred HHHHHHHHHcCCccCCCCCcccHHHHHHHHHHHHHhh
Confidence 467889999999 7888999999999987654
No 101
>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=43.57 E-value=87 Score=30.18 Aligned_cols=55 Identities=16% Similarity=0.232 Sum_probs=40.4
Q ss_pred HHhhCCCCCcccHHHHHHHHHHHHHH-------HHHHHHHHHHHHHhcCCCccChhhHHHHHH
Q 030547 42 MKKALPANGKIAKDAKDTVQECVSEF-------ISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (175)
Q Consensus 42 mK~~LP~~~kISkDA~~al~~~aseF-------I~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (175)
+++.++ .+.|+.+....|.+.|..+ -.++...|.-.|.-++|.+|+.+||..|..
T Consensus 195 ar~~~~-~V~i~~~~~~~l~~~~~~~gv~s~Ra~i~~~r~ArA~Aal~gr~~V~~~Dv~~a~~ 256 (589)
T TIGR02031 195 ARELLP-QVTISAEQVKELVLTAASLGISGHRADLFAVRAAKAHAALHGRTEVTEEDLKLAVE 256 (589)
T ss_pred HHHhcC-CccCCHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHH
Confidence 344444 5789999887777766543 224556677788889999999999999975
No 102
>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]
Probab=43.37 E-value=97 Score=28.14 Aligned_cols=73 Identities=15% Similarity=0.191 Sum_probs=48.7
Q ss_pred hHHHHHHHhhCCC---CCcccHHHHHHHHHHHH------HHHHHHHHHHHHHHHhcCCCccChhhHHHHHHHcCCCcchH
Q 030547 36 ANISRIMKKALPA---NGKIAKDAKDTVQECVS------EFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYID 106 (175)
Q Consensus 36 A~V~RImK~~LP~---~~kISkDA~~al~~~as------eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~~yv~ 106 (175)
.-|.-|+++-.-. ...++.++...+...+. .+..-|...|.++|.++++.+|+.+||..|-++.+..-+.+
T Consensus 193 ~el~~Il~~R~~~~~~~~~~~~~vl~lia~~~a~~~GDAR~aidilr~A~eiAe~~~~~~v~~~~v~~a~~~~~~~~~~~ 272 (366)
T COG1474 193 EELYDILRERVEEGFSAGVIDDDVLKLIAALVAAESGDARKAIDILRRAGEIAEREGSRKVSEDHVREAQEEIERDVLEE 272 (366)
T ss_pred HHHHHHHHHHHHhhccCCCcCccHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHhhCCCCcCHHHHHHHHHHhhHHHHHH
Confidence 3455555544331 34677777666653322 23455667789999999999999999999977777665544
Q ss_pred HH
Q 030547 107 PL 108 (175)
Q Consensus 107 ~L 108 (175)
.+
T Consensus 273 ~~ 274 (366)
T COG1474 273 VL 274 (366)
T ss_pred HH
Confidence 43
No 103
>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=43.30 E-value=30 Score=22.77 Aligned_cols=25 Identities=28% Similarity=0.489 Sum_probs=20.8
Q ss_pred ccChhhHHHHHHHcCCCcchHHHHH
Q 030547 86 TINGDDLLWAMATLGFEDYIDPLKA 110 (175)
Q Consensus 86 TI~~eDVl~AL~~LgF~~yv~~Lk~ 110 (175)
+=+++||..-|+.+||++|.+.++.
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 104
>TIGR01242 26Sp45 26S proteasome subunit P45 family. Many proteins may score above the trusted cutoff because an internal
Probab=42.76 E-value=35 Score=30.20 Aligned_cols=33 Identities=24% Similarity=0.277 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHHHHhcCCCccChhhHHHHHHHc
Q 030547 67 FISFITSEASDKCQKEKRKTINGDDLLWAMATL 99 (175)
Q Consensus 67 FI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~L 99 (175)
-|..|..+|...|.+.++..|+.+|+..|++..
T Consensus 331 dl~~l~~~A~~~a~~~~~~~i~~~d~~~a~~~~ 363 (364)
T TIGR01242 331 DLKAICTEAGMFAIREERDYVTMDDFIKAVEKV 363 (364)
T ss_pred HHHHHHHHHHHHHHHhCCCccCHHHHHHHHHHh
Confidence 355777888999999999999999999999763
No 105
>PTZ00373 60S Acidic ribosomal protein P2; Provisional
Probab=42.11 E-value=88 Score=24.26 Aligned_cols=32 Identities=6% Similarity=0.161 Sum_probs=27.3
Q ss_pred HHHHHHHHHHHHhcCCCccChhhHHHHHHHcCCC
Q 030547 69 SFITSEASDKCQKEKRKTINGDDLLWAMATLGFE 102 (175)
Q Consensus 69 ~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~ 102 (175)
.||+ |+-.|.-.++.+||.+||.+.|+..|.+
T Consensus 4 kyva--AYlL~~lgG~~~pTaddI~kIL~AaGve 35 (112)
T PTZ00373 4 KYVA--AYLMCVLGGNENPTKKEVKNVLSAVNAD 35 (112)
T ss_pred HHHH--HHHHHHHcCCCCCCHHHHHHHHHHcCCC
Confidence 3554 6778888999999999999999998875
No 106
>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional
Probab=42.06 E-value=35 Score=31.92 Aligned_cols=32 Identities=25% Similarity=0.258 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHHHhcCCCccChhhHHHHHHHc
Q 030547 68 ISFITSEASDKCQKEKRKTINGDDLLWAMATL 99 (175)
Q Consensus 68 I~~LtseA~~~~~~~kRKTI~~eDVl~AL~~L 99 (175)
|..|..+|...|.+++|..|+.+||..|++..
T Consensus 393 I~~i~~eA~~~Alr~~r~~Vt~~D~~~A~~~v 424 (438)
T PTZ00361 393 IKAICTEAGLLALRERRMKVTQADFRKAKEKV 424 (438)
T ss_pred HHHHHHHHHHHHHHhcCCccCHHHHHHHHHHH
Confidence 56778889999999999999999999999764
No 107
>PRK03992 proteasome-activating nucleotidase; Provisional
Probab=42.00 E-value=36 Score=30.74 Aligned_cols=34 Identities=21% Similarity=0.234 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHHHHhcCCCccChhhHHHHHHHcC
Q 030547 67 FISFITSEASDKCQKEKRKTINGDDLLWAMATLG 100 (175)
Q Consensus 67 FI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~Lg 100 (175)
=|..|..+|...|.+++++.|+.+|+..|++.+-
T Consensus 340 dl~~l~~eA~~~a~~~~~~~i~~~d~~~A~~~~~ 373 (389)
T PRK03992 340 DLKAICTEAGMFAIRDDRTEVTMEDFLKAIEKVM 373 (389)
T ss_pred HHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHh
Confidence 4556777888889899999999999999997653
No 108
>KOG1528 consensus Salt-sensitive 3'-phosphoadenosine-5'-phosphatase HAL2/SAL1 [Nucleotide transport and metabolism; Inorganic ion transport and metabolism]
Probab=41.30 E-value=78 Score=29.05 Aligned_cols=75 Identities=19% Similarity=0.244 Sum_probs=51.2
Q ss_pred CCCcccccCchhHHHHHHHhhCCCCC--cccHHHHHHHHHH-HHHHHHHHHHHHHH-HHHhc--CC-CccChhhHHHHHH
Q 030547 25 GVREQDRYLPIANISRIMKKALPANG--KIAKDAKDTVQEC-VSEFISFITSEASD-KCQKE--KR-KTINGDDLLWAMA 97 (175)
Q Consensus 25 ~~~~~d~~LP~A~V~RImK~~LP~~~--kISkDA~~al~~~-aseFI~~LtseA~~-~~~~~--kR-KTI~~eDVl~AL~ 97 (175)
+|+.-|+- -.|.|.-.+++.+|+.- .+..|-...|.+. ++.|+.-|+..-|+ .+..+ +- +.++.+||++|+.
T Consensus 43 PVTvaDyG-~QAiVs~vL~~~f~~~p~slVaEEds~~Lr~n~~~~~l~~i~~lvnetl~s~~sy~~~~~ls~~dvl~aID 121 (351)
T KOG1528|consen 43 PVTVADYG-SQAIVSLVLEREFPDDPLSLVAEEDSGFLRKNGSEGLLSRITKLVNETLASDESYGDNSPLSSDDVLKAID 121 (351)
T ss_pred Ccchhhhh-HHHHHHHHHHHHcCCCCcceEeeccchhhhhhhhHHHHHHHHHHHHHHhhhhhhccCCCCCCHHHHHHHHh
Confidence 46666654 35789999999999754 5777766666665 56677777774443 22222 22 7899999999997
Q ss_pred HcC
Q 030547 98 TLG 100 (175)
Q Consensus 98 ~Lg 100 (175)
.-+
T Consensus 122 ~G~ 124 (351)
T KOG1528|consen 122 RGN 124 (351)
T ss_pred ccc
Confidence 544
No 109
>COG5624 TAF61 Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=40.61 E-value=14 Score=34.94 Aligned_cols=78 Identities=12% Similarity=0.210 Sum_probs=63.6
Q ss_pred ccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHH---cCCCcchHH
Q 030547 31 RYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMAT---LGFEDYIDP 107 (175)
Q Consensus 31 ~~LP~A~V~RImK~~LP~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~---LgF~~yv~~ 107 (175)
+.+-+-.+.-+.+..+....+|-.|.-+.+-..+..|+.-++.-+-..+++.+-+||-+.||-.-|++ +-++.|+..
T Consensus 382 Rl~skrkL~el~~~~vd~eekie~eveelll~~ad~fve~vt~FsCrlakhrkSdtlevrD~qlhlErnwnIr~pGf~~d 461 (505)
T COG5624 382 RLDSKRKLEELQHGGVDEEEKIENEVEELLLSRADGFVEPVTEFSCRLAKHRKSDTLEVRDGQLHLERNWNIRCPGFVDD 461 (505)
T ss_pred hhhhhhhHHHHHhhccCcceeccchHHHHHHhhhcccccccchheeEeeccCCCCceeeccceeeeccccceecCcchHH
Confidence 34566667777788877777999999999999999999999988888889999999999999877763 334677765
Q ss_pred H
Q 030547 108 L 108 (175)
Q Consensus 108 L 108 (175)
.
T Consensus 462 ~ 462 (505)
T COG5624 462 I 462 (505)
T ss_pred H
Confidence 4
No 110
>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=40.32 E-value=43 Score=25.50 Aligned_cols=32 Identities=22% Similarity=0.336 Sum_probs=26.2
Q ss_pred hHHHHHHHhhC----CCCCcccHHHHHHHHHHHHHH
Q 030547 36 ANISRIMKKAL----PANGKIAKDAKDTVQECVSEF 67 (175)
Q Consensus 36 A~V~RImK~~L----P~~~kISkDA~~al~~~aseF 67 (175)
++|.+++|..| .++..++.++.+.|+++++.|
T Consensus 51 SNIGvLIKkglIEKSGDGlv~T~~g~~Ii~~AA~l~ 86 (96)
T PF09114_consen 51 SNIGVLIKKGLIEKSGDGLVITEEGMDIIIQAAELW 86 (96)
T ss_dssp HHHHHHHHTTSEEEETTEEEE-HHHHHHHHHHHHHH
T ss_pred HhHHHHHHcCcccccCCceEEechHHHHHHHHHHHH
Confidence 46778999887 346689999999999999998
No 111
>PRK13407 bchI magnesium chelatase subunit I; Provisional
Probab=39.60 E-value=1e+02 Score=27.69 Aligned_cols=53 Identities=11% Similarity=0.031 Sum_probs=41.4
Q ss_pred HhhCCCCCcccHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCccChhhHHHHH
Q 030547 43 KKALPANGKIAKDAKDTVQECVSEFI-------SFITSEASDKCQKEKRKTINGDDLLWAM 96 (175)
Q Consensus 43 K~~LP~~~kISkDA~~al~~~aseFI-------~~LtseA~~~~~~~kRKTI~~eDVl~AL 96 (175)
++.++ .+.|+.+....+.+.|..+= .+|...|...|.-+||..|+++||..+.
T Consensus 244 ~~~~~-~V~v~~~~~~yi~~l~~~~~~~s~Ra~i~l~~aA~a~A~l~Gr~~V~~~Di~~~~ 303 (334)
T PRK13407 244 RARLP-QLKTPNTVLHDCAALCIALGSDGLRGELTLLRAARALAAFEGAEAVGRSHLRSVA 303 (334)
T ss_pred HHhcC-CcccCHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHHcCCCeeCHHHHHHHH
Confidence 34454 57899999998888887763 2466778888999999999999996654
No 112
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=39.38 E-value=63 Score=20.92 Aligned_cols=32 Identities=13% Similarity=0.419 Sum_probs=25.9
Q ss_pred cCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHH
Q 030547 32 YLPIANISRIMKKALPANGKIAKDAKDTVQECVSEF 67 (175)
Q Consensus 32 ~LP~A~V~RImK~~LP~~~kISkDA~~al~~~aseF 67 (175)
.+-+++|.|++... .+|+.+.++-|.+++.+.
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 45678999998866 389999999999887763
No 113
>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=38.79 E-value=26 Score=24.93 Aligned_cols=51 Identities=20% Similarity=0.367 Sum_probs=27.0
Q ss_pred CCcccHHHHHHHHHHHH-------HHHHHHHHHHHHH-HHhcCCCccChhhHHHHHHHc
Q 030547 49 NGKIAKDAKDTVQECVS-------EFISFITSEASDK-CQKEKRKTINGDDLLWAMATL 99 (175)
Q Consensus 49 ~~kISkDA~~al~~~as-------eFI~~LtseA~~~-~~~~kRKTI~~eDVl~AL~~L 99 (175)
++|++.+.++.|.++|. .||.-.+.++.+. -..+..-+++.+|.-.-++.|
T Consensus 3 ~iR~~~e~k~li~~AA~~~G~sls~Fi~~aa~~~A~~~i~~~~~~~Ls~~~~~~f~~aL 61 (80)
T PF08681_consen 3 EIRVTPEEKELIERAAALSGVSLSDFILSAALEAAEEVIEEHERIRLSAEDFEAFMAAL 61 (80)
T ss_dssp EEE--HHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHH
T ss_pred eEecCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhcceeEcCHHHHHHHHHHH
Confidence 36899999999999975 4554444433322 222334455555544443333
No 114
>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=37.63 E-value=27 Score=22.14 Aligned_cols=24 Identities=21% Similarity=0.425 Sum_probs=19.8
Q ss_pred ChhhHHHHHHHcCCCcchHHHHHH
Q 030547 88 NGDDLLWAMATLGFEDYIDPLKAY 111 (175)
Q Consensus 88 ~~eDVl~AL~~LgF~~yv~~Lk~~ 111 (175)
+.++|..-|+.+|+++|++.++..
T Consensus 3 ~~~~V~~wL~~~~~~~y~~~f~~~ 26 (63)
T cd00166 3 SPEDVAEWLESLGLGQYADNFREN 26 (63)
T ss_pred CHHHHHHHHHHcChHHHHHHHHHc
Confidence 678999999999998888877553
No 115
>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=37.43 E-value=39 Score=22.11 Aligned_cols=22 Identities=23% Similarity=0.453 Sum_probs=19.4
Q ss_pred ChhhHHHHHHHcCCCcchHHHH
Q 030547 88 NGDDLLWAMATLGFEDYIDPLK 109 (175)
Q Consensus 88 ~~eDVl~AL~~LgF~~yv~~Lk 109 (175)
++++|..-|+.+|++.|++..+
T Consensus 4 ~~~~V~~WL~~~~l~~y~~~F~ 25 (64)
T PF00536_consen 4 SVEDVSEWLKSLGLEQYAENFE 25 (64)
T ss_dssp SHHHHHHHHHHTTGGGGHHHHH
T ss_pred CHHHHHHHHHHCCCHHHHHHHH
Confidence 6789999999999999998763
No 116
>COG5251 TAF40 Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=37.28 E-value=52 Score=27.81 Aligned_cols=61 Identities=13% Similarity=0.000 Sum_probs=46.0
Q ss_pred cCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC---ccChhhHHHHH
Q 030547 32 YLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRK---TINGDDLLWAM 96 (175)
Q Consensus 32 ~LP~A~V~RImK~~LP~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRK---TI~~eDVl~AL 96 (175)
.||++.|.+++..++ |-.|+...+.+|+-.+.+|+--|--.|..+- +++. -+.+.|+-.|.
T Consensus 115 ~lnKt~VKKlastV~--nQtVspNi~I~l~g~~KVfvGEiIElA~~Vq--~~w~~sgpl~p~h~reay 178 (199)
T COG5251 115 SLNKTQVKKLASTVA--NQTVSPNIRIFLQGVGKVFVGEIIELAMIVQ--NKWLTSGPLIPFHKREAY 178 (199)
T ss_pred CCCHHHHHHHHHHHh--ccccCCCeeeeeechhHHHHHHHHHHHHHHH--HHhcccCCCChHHHHHHH
Confidence 599999999999998 4578888888999999999988876665332 2332 36677776664
No 117
>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional
Probab=36.55 E-value=46 Score=30.54 Aligned_cols=32 Identities=25% Similarity=0.233 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHHHhcCCCccChhhHHHHHHHc
Q 030547 68 ISFITSEASDKCQKEKRKTINGDDLLWAMATL 99 (175)
Q Consensus 68 I~~LtseA~~~~~~~kRKTI~~eDVl~AL~~L 99 (175)
|..|..+|...|.+++|..|+.+|+..|++..
T Consensus 355 I~~l~~eA~~~A~r~~~~~i~~~df~~A~~~v 386 (398)
T PTZ00454 355 IAAICQEAGMQAVRKNRYVILPKDFEKGYKTV 386 (398)
T ss_pred HHHHHHHHHHHHHHcCCCccCHHHHHHHHHHH
Confidence 66788889999999999999999999998753
No 118
>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=36.38 E-value=34 Score=26.48 Aligned_cols=60 Identities=10% Similarity=0.176 Sum_probs=41.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHHcCCCcchHHHHHHHHHHHH
Q 030547 54 KDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLMRYRE 117 (175)
Q Consensus 54 kDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~~yv~~Lk~~L~~yre 117 (175)
...+..|..|..+.-.|......-... ---.-..+...|+..|++.++.++...|++|+.
T Consensus 72 s~Vk~Eiaa~~~v~~~Y~~~L~~G~vd----~e~~~~~~~~kLk~AGidkV~~E~QkQlda~~~ 131 (134)
T PF12010_consen 72 SPVKNEIAACSNVWSEYYPPLETGLVD----PEEALPEFNEKLKAAGIDKVIAELQKQLDAFLA 131 (134)
T ss_pred chhHHHHHHHHHHHHHHHHHHHccCCC----HHHHHHHHHHHHHHhChHHHHHHHHHHHHHHHH
Confidence 445667777777776666443221110 112245678889999999999999999999985
No 119
>COG1466 HolA DNA polymerase III, delta subunit [DNA replication, recombination, and repair]
Probab=35.29 E-value=90 Score=27.43 Aligned_cols=61 Identities=18% Similarity=0.150 Sum_probs=45.8
Q ss_pred HHHHHHhhCCC-CCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHH
Q 030547 38 ISRIMKKALPA-NGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMAT 98 (175)
Q Consensus 38 V~RImK~~LP~-~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~ 98 (175)
+.+.|+..+-. +.+|++||.+.|..+..-=+..|.++-...+--.+-++|+.+||..++..
T Consensus 145 l~~~i~~~~~~~~l~i~~~a~~~L~~~~~~nl~~i~~Ei~KL~l~~~~~~I~~~~V~~~v~~ 206 (334)
T COG1466 145 LPQWIKKRAKELGLKIDQEAIQLLLEALGGNLLAIAQEIEKLALYAGDKEITLEDVEEVVSD 206 (334)
T ss_pred HHHHHHHHHHHcCCCCCHHHHHHHHHHhCCcHHHHHHHHHHHHHhCCCCcCCHHHHHHHHhc
Confidence 44444444432 67999999999999998777777777777776666559999999988764
No 120
>COG1724 Predicted RNA binding protein (dsRBD-like fold), HicA family [General function prediction only]
Probab=35.01 E-value=27 Score=24.95 Aligned_cols=17 Identities=18% Similarity=0.481 Sum_probs=15.4
Q ss_pred ccChhhHHHHHHHcCCC
Q 030547 86 TINGDDLLWAMATLGFE 102 (175)
Q Consensus 86 TI~~eDVl~AL~~LgF~ 102 (175)
.+++.||+++|+.+||.
T Consensus 6 ~~~~ke~ik~Le~~Gf~ 22 (66)
T COG1724 6 RMKAKEVIKALEKDGFQ 22 (66)
T ss_pred cCCHHHHHHHHHhCCcE
Confidence 47899999999999996
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=34.29 E-value=7.7 Score=25.63 Aligned_cols=59 Identities=25% Similarity=0.394 Sum_probs=32.1
Q ss_pred CCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcc---ChhhHHHHHHHcCCCcch-HHHHHH
Q 030547 49 NGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTI---NGDDLLWAMATLGFEDYI-DPLKAY 111 (175)
Q Consensus 49 ~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI---~~eDVl~AL~~LgF~~yv-~~Lk~~ 111 (175)
+++|.++...+|.+++. .+..|+.+ .-..+=.|.+ ++...+..|.++|+-+++ +.++.+
T Consensus 1 gF~ie~~t~~ai~~~~~-~L~~is~E---Ri~~El~kil~~~~~~~~~~~l~~~gll~~ifP~l~~a 63 (64)
T PF12627_consen 1 GFKIEPETEEAIKENAE-LLSKISKE---RIREELEKILSSPNPSRAFKLLDELGLLEYIFPELDAA 63 (64)
T ss_dssp T-EE-HHHHHHHHHHGG-GGGGS-HH---HHHHHHHHHHTSTTHHHHHHHHHHTTCHHHHSTTHHT-
T ss_pred CCccCHHHHHHHHHHHH-HHhcCCHH---HHHHHHHHHHcCCCHHHHHHHHHHcCCHHHHCcccccc
Confidence 35678888888887776 44455433 2222222233 455667777788876664 555443
No 122
>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=33.66 E-value=30 Score=22.20 Aligned_cols=14 Identities=36% Similarity=0.672 Sum_probs=11.8
Q ss_pred hhHHHHHHHcCCCc
Q 030547 90 DDLLWAMATLGFED 103 (175)
Q Consensus 90 eDVl~AL~~LgF~~ 103 (175)
+|++.||..|||..
T Consensus 4 ~d~~~AL~~LGy~~ 17 (47)
T PF07499_consen 4 EDALEALISLGYSK 17 (47)
T ss_dssp HHHHHHHHHTTS-H
T ss_pred HHHHHHHHHcCCCH
Confidence 69999999999973
No 123
>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=33.62 E-value=1.4e+02 Score=22.88 Aligned_cols=31 Identities=13% Similarity=0.164 Sum_probs=26.4
Q ss_pred HHHHHHHHHHHhcCCCccChhhHHHHHHHcCCC
Q 030547 70 FITSEASDKCQKEKRKTINGDDLLWAMATLGFE 102 (175)
Q Consensus 70 ~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~ 102 (175)
||+ |+-.|.-.++.+||.+||...|+..|.+
T Consensus 3 yva--AylL~~l~g~~~pTa~dI~~IL~AaGve 33 (109)
T cd05833 3 YVA--AYLLAVLGGNASPSAADVKKILGSVGVE 33 (109)
T ss_pred HHH--HHHHHHHcCCCCCCHHHHHHHHHHcCCC
Confidence 554 6778888889999999999999998874
No 124
>COG1389 DNA topoisomerase VI, subunit B [DNA replication, recombination, and repair]
Probab=32.88 E-value=34 Score=33.02 Aligned_cols=46 Identities=17% Similarity=0.344 Sum_probs=36.4
Q ss_pred HhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccC
Q 030547 43 KKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTIN 88 (175)
Q Consensus 43 K~~LP~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~ 88 (175)
|+++.+.--|-+|.+.|+++||.+.=+||+....+.-..+++++|.
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 3444333457799999999999999999999988887777777763
No 125
>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=32.82 E-value=78 Score=25.94 Aligned_cols=33 Identities=18% Similarity=0.328 Sum_probs=26.1
Q ss_pred HhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHH
Q 030547 43 KKALPANGKIAKDAKDTVQECVSEFISFITSEA 75 (175)
Q Consensus 43 K~~LP~~~kISkDA~~al~~~aseFI~~LtseA 75 (175)
|+++.+.--|-+|.+.||++||...=.||...-
T Consensus 111 KeaIadvpEI~~EIrlAl~~~~R~L~~~l~kk~ 143 (151)
T cd00823 111 KEAIADIPEIEEEIKLALQEVARKLKRYLSKKR 143 (151)
T ss_pred hhhhcCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455554446889999999999999999997643
No 126
>PRK07914 hypothetical protein; Reviewed
Probab=32.65 E-value=94 Score=26.98 Aligned_cols=63 Identities=11% Similarity=0.144 Sum_probs=42.9
Q ss_pred chhHHHHHHHhhCCC-CCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHH
Q 030547 34 PIANISRIMKKALPA-NGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (175)
Q Consensus 34 P~A~V~RImK~~LP~-~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (175)
+...+.+.|++.+-. +..|+.||...|.+++..=+..|..|-...+...+ .+|+.+||...+.
T Consensus 129 ~~~~l~~wi~~~a~~~g~~i~~~A~~~L~~~~g~dl~~l~~EleKL~~~~~-~~It~e~V~~~v~ 192 (320)
T PRK07914 129 KAAERADFVRKEFRSLRVKVDDDTVTALLDAVGSDLRELASACSQLVADTG-GAVDAAAVRRYHS 192 (320)
T ss_pred CHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHCccHHHHHHHHHHHhcCCC-CCcCHHHHHHHcC
Confidence 445555555555543 56899999999999997666666666555554333 5799888877654
No 127
>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=31.40 E-value=37 Score=21.63 Aligned_cols=26 Identities=15% Similarity=0.340 Sum_probs=20.7
Q ss_pred ccChhhHHHHHHHcCCCcchHHHHHH
Q 030547 86 TINGDDLLWAMATLGFEDYIDPLKAY 111 (175)
Q Consensus 86 TI~~eDVl~AL~~LgF~~yv~~Lk~~ 111 (175)
.-+.++|..-|+.+||++|++.++..
T Consensus 3 ~w~~~~v~~wL~~~g~~~y~~~f~~~ 28 (68)
T smart00454 3 QWSPESVADWLESIGLEQYADNFRKN 28 (68)
T ss_pred CCCHHHHHHHHHHCChHHHHHHHHHC
Confidence 34678899999999999888876553
No 128
>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=31.38 E-value=55 Score=18.60 Aligned_cols=26 Identities=23% Similarity=0.234 Sum_probs=19.9
Q ss_pred HHHHHHhcCCCccChhhHHHHHH-HcC
Q 030547 75 ASDKCQKEKRKTINGDDLLWAMA-TLG 100 (175)
Q Consensus 75 A~~~~~~~kRKTI~~eDVl~AL~-~Lg 100 (175)
+....-.++.-+|+.+++..+|+ .||
T Consensus 5 ~F~~~D~d~dG~I~~~el~~~l~~~lG 31 (31)
T PF13405_consen 5 AFKMFDKDGDGFIDFEELRAILRKSLG 31 (31)
T ss_dssp HHHHH-TTSSSEEEHHHHHHHHHHHTT
T ss_pred HHHHHCCCCCCcCcHHHHHHHHHHhcC
Confidence 44566677788999999999998 576
No 129
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=31.35 E-value=96 Score=21.99 Aligned_cols=28 Identities=14% Similarity=0.141 Sum_probs=21.5
Q ss_pred HHHHHHhcCCCccChhhHHHHHHHcCCC
Q 030547 75 ASDKCQKEKRKTINGDDLLWAMATLGFE 102 (175)
Q Consensus 75 A~~~~~~~kRKTI~~eDVl~AL~~LgF~ 102 (175)
+...+-.++.-.|+.++|..+|..+|+.
T Consensus 15 ~F~~~D~d~~G~Is~~el~~~l~~~~~~ 42 (96)
T smart00027 15 IFRSLDKNQDGTVTGAQAKPILLKSGLP 42 (96)
T ss_pred HHHHhCCCCCCeEeHHHHHHHHHHcCCC
Confidence 4455666777789999999999888874
No 130
>PRK02910 light-independent protochlorophyllide reductase subunit B; Provisional
Probab=31.32 E-value=96 Score=29.28 Aligned_cols=52 Identities=13% Similarity=0.145 Sum_probs=40.5
Q ss_pred CCCcccHHHHHHHHHHHHHHHH-HHHHHHHHHHHhcCCCccChhhHHHHHHHcC
Q 030547 48 ANGKIAKDAKDTVQECVSEFIS-FITSEASDKCQKEKRKTINGDDLLWAMATLG 100 (175)
Q Consensus 48 ~~~kISkDA~~al~~~aseFI~-~LtseA~~~~~~~kRKTI~~eDVl~AL~~Lg 100 (175)
+.+.++.||...|.+ .--|+. -+-..+.+.|+..|...|+.+.|..|-..+|
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 456899999999965 555554 4445566788999999999999999977654
No 131
>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=31.24 E-value=98 Score=29.13 Aligned_cols=51 Identities=12% Similarity=0.154 Sum_probs=39.7
Q ss_pred CCcccHHHHHHHHHHHHHHHH-HHHHHHHHHHHhcCCCccChhhHHHHHHHcC
Q 030547 49 NGKIAKDAKDTVQECVSEFIS-FITSEASDKCQKEKRKTINGDDLLWAMATLG 100 (175)
Q Consensus 49 ~~kISkDA~~al~~~aseFI~-~LtseA~~~~~~~kRKTI~~eDVl~AL~~Lg 100 (175)
.+.++.||...|.+ .--|+. -+-..+...|+..+...|+.+.|..|=+.+|
T Consensus 460 ~~~w~~ea~~~l~~-~P~f~r~~~r~~~e~~a~~~g~~~it~~~~~~a~~~~~ 511 (511)
T TIGR01278 460 ELGWTAEAEAELKK-VPFFVRGKVRRNTENFARERGYSVITLEVIYAAKEHFG 511 (511)
T ss_pred CCCcCHHHHHHHhh-CChhhhHHHHHHHHHHHHHcCCCEEcHHHHHHHHHhcC
Confidence 46899999999965 444554 4555666889999999999999999976654
No 132
>PRK14868 DNA topoisomerase VI subunit B; Provisional
Probab=30.64 E-value=55 Score=33.23 Aligned_cols=70 Identities=19% Similarity=0.281 Sum_probs=45.5
Q ss_pred CCcccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccC--hhhHHHHHHH
Q 030547 26 VREQDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTIN--GDDLLWAMAT 98 (175)
Q Consensus 26 ~~~~d~~LP~A~V~RImK~~LP~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~--~eDVl~AL~~ 98 (175)
|-+-...+|-.... |+++.+.--|-+|.+.||++||.+.=.||...-...-++++++++. --+|..+|.+
T Consensus 611 VhvaST~VPfts~s---KeaIA~vpEI~~EI~lAl~~~aR~Lk~yl~k~~~~~~~~~k~~~~~kylp~~a~~l~~ 682 (795)
T PRK14868 611 VHVASTNVPFTSES---KDAIANVPEIEDEIELAIREAARELKSYLNKRRSMQKRREKQDVLGTILPEMATKVAE 682 (795)
T ss_pred EEEeecCCCCCCcc---hhhhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444455544433 4555544468999999999999999999998776666666665543 2344444443
No 133
>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=30.16 E-value=1.8e+02 Score=22.53 Aligned_cols=58 Identities=14% Similarity=0.155 Sum_probs=38.6
Q ss_pred hHHHHHHHhhCCCCCcccHHHHHHHHHHH---HHHHHHHHHHHHHHHHhcCCCccChhhHHHHH
Q 030547 36 ANISRIMKKALPANGKIAKDAKDTVQECV---SEFISFITSEASDKCQKEKRKTINGDDLLWAM 96 (175)
Q Consensus 36 A~V~RImK~~LP~~~kISkDA~~al~~~a---seFI~~LtseA~~~~~~~kRKTI~~eDVl~AL 96 (175)
..+.+|+++.-.....|..+-|....-++ +.|+..|...|.+.+.+. -|..++.+.+|
T Consensus 14 ~~l~~l~~~lg~~~~~i~~~~r~~yHaAav~asNf~~~L~~~a~~ll~~~---gi~~~~a~~~L 74 (132)
T PF10728_consen 14 EVLQELAKELGGRPFEIDSEQRALYHAAAVFASNFLVALYALAAELLEQA---GIDFEEALEAL 74 (132)
T ss_dssp HHHHHHHHHTTSEEEE--GGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHT---T-SHHH--HHH
T ss_pred HHHHHHHHHhCCceEEeCHHhHHHHHHHHHHHHhhHHHHHHHHHHHHHHc---CCCchhHHHHH
Confidence 45777888877666789999999888775 478888888888888766 34554444443
No 134
>PRK06585 holA DNA polymerase III subunit delta; Reviewed
Probab=29.38 E-value=1.4e+02 Score=25.81 Aligned_cols=62 Identities=16% Similarity=0.156 Sum_probs=41.3
Q ss_pred hHHHHHHHhhCC-CCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHh-cCCCccChhhHHHHHH
Q 030547 36 ANISRIMKKALP-ANGKIAKDAKDTVQECVSEFISFITSEASDKCQK-EKRKTINGDDLLWAMA 97 (175)
Q Consensus 36 A~V~RImK~~LP-~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~-~kRKTI~~eDVl~AL~ 97 (175)
..+.+.+++.+- .+.+|+.||...|.+++.-=...+..+-...+.- .+.++|+.+||...+.
T Consensus 145 ~~l~~~i~~~~~~~g~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~It~edV~~lv~ 208 (343)
T PRK06585 145 RDLARLIDDELAEAGLRITPDARALLVALLGGDRLASRNEIEKLALYAHGKGEITLDDVRAVVG 208 (343)
T ss_pred HHHHHHHHHHHHHCCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHhC
Confidence 334444444443 3678999999999998886555566665666554 3356899999876644
No 135
>PRK00440 rfc replication factor C small subunit; Reviewed
Probab=28.82 E-value=1e+02 Score=25.83 Aligned_cols=65 Identities=9% Similarity=0.055 Sum_probs=38.9
Q ss_pred CchhHHHHHHHhhCC-CCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHHc
Q 030547 33 LPIANISRIMKKALP-ANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATL 99 (175)
Q Consensus 33 LP~A~V~RImK~~LP-~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~L 99 (175)
++...+.++++..+. .+..|+.++.+.|.+.+.--+..+-.+-...+. . .++|+.+||..++...
T Consensus 161 l~~~ei~~~l~~~~~~~~~~i~~~al~~l~~~~~gd~r~~~~~l~~~~~-~-~~~it~~~v~~~~~~~ 226 (319)
T PRK00440 161 LKKEAVAERLRYIAENEGIEITDDALEAIYYVSEGDMRKAINALQAAAA-T-GKEVTEEAVYKITGTA 226 (319)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHH-c-CCCCCHHHHHHHhCCC
Confidence 445555556655543 256799999999888765333332222222222 2 3689999998887543
No 136
>PRK09526 lacI lac repressor; Reviewed
Probab=28.11 E-value=56 Score=27.48 Aligned_cols=37 Identities=14% Similarity=0.493 Sum_probs=30.0
Q ss_pred cCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHH
Q 030547 32 YLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITS 73 (175)
Q Consensus 32 ~LP~A~V~RImK~~LP~~~kISkDA~~al~~~aseFI~~Lts 73 (175)
-.-++||.|++... .+||++.++-+.+++.+ +.|.-.
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 46689999999753 37999999999999999 567543
No 137
>PRK14975 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Probab=27.98 E-value=3.8e+02 Score=25.54 Aligned_cols=89 Identities=15% Similarity=0.142 Sum_probs=54.1
Q ss_pred ccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHH----------HHHHHHHHHHHHHHHhcCCCccChhhHHHHHHH
Q 030547 29 QDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVS----------EFISFITSEASDKCQKEKRKTINGDDLLWAMAT 98 (175)
Q Consensus 29 ~d~~LP~A~V~RImK~~LP~~~kISkDA~~al~~~as----------eFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~ 98 (175)
.++++|.+.|.--|... ++.|..+....+..-.. .-+.-|..+..+......=-.=++.+|.++|+.
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 44566777776666655 57888887766665554 555666665555443211123467899999999
Q ss_pred cCCC----------cchHHHHHHHHHHHHHhh
Q 030547 99 LGFE----------DYIDPLKAYLMRYREMEG 120 (175)
Q Consensus 99 LgF~----------~yv~~Lk~~L~~yre~~~ 120 (175)
+|+. .-..++-..|-+||+..+
T Consensus 237 ~g~~~~~t~~~~L~~~~hp~~~~ile~r~~~k 268 (553)
T PRK14975 237 AGIELPSTRKWELREIDHPAVEPLLEYRKLSK 268 (553)
T ss_pred CCCCCCCCcHHHhccCCCchHHHHHHHHHHHH
Confidence 9884 111234455667787654
No 138
>PTZ00183 centrin; Provisional
Probab=26.89 E-value=2.5e+02 Score=20.61 Aligned_cols=20 Identities=20% Similarity=0.267 Sum_probs=11.6
Q ss_pred HHhcCCCccChhhHHHHHHH
Q 030547 79 CQKEKRKTINGDDLLWAMAT 98 (175)
Q Consensus 79 ~~~~kRKTI~~eDVl~AL~~ 98 (175)
+..++...|+.++.+.++..
T Consensus 62 ~d~~~~g~i~~~eF~~~~~~ 81 (158)
T PTZ00183 62 VDKDGSGKIDFEEFLDIMTK 81 (158)
T ss_pred hCCCCCCcEeHHHHHHHHHH
Confidence 33455556666666666543
No 139
>PF11753 DUF3310: Protein of unknwon function (DUF3310); InterPro: IPR021739 This entry is represented by Bacteriophage T7, Gp1.7. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=26.53 E-value=1.9e+02 Score=19.58 Aligned_cols=42 Identities=21% Similarity=0.192 Sum_probs=31.7
Q ss_pred HHHHHHHHH--HHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHH
Q 030547 55 DAKDTVQEC--VSEFISFITSEASDKCQKEKRKTINGDDLLWAMAT 98 (175)
Q Consensus 55 DA~~al~~~--aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~ 98 (175)
|..+.+ +. ...|+.|....|...+-+.++|. .-+|+.+|..=
T Consensus 14 e~id~~-~~~~~~~~~~f~~gnaiKY~~R~~~K~-~~eDl~KA~~Y 57 (60)
T PF11753_consen 14 ECIDFI-EQFTEEQFLGFCLGNAIKYLWRAGKKN-GIEDLKKAKWY 57 (60)
T ss_pred cHHHHH-HHhcchhhhhHHHHHHHHHHHHHcccC-cHHHHHHHHHH
Confidence 444555 33 34899999999999999999994 48888888753
No 140
>PRK14867 DNA topoisomerase VI subunit B; Provisional
Probab=26.07 E-value=76 Score=31.53 Aligned_cols=37 Identities=22% Similarity=0.442 Sum_probs=28.5
Q ss_pred cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcc
Q 030547 51 KIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTI 87 (175)
Q Consensus 51 kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI 87 (175)
-|-+|.+.||++||.+.=.||...-...-++++++++
T Consensus 592 eI~~Ei~lAl~~~~r~L~~~l~~~~~~~~~~~k~~~~ 628 (659)
T PRK14867 592 EIFNEIRQALMICARELEKYISRIRREKEEEQKRKYV 628 (659)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4677888899999999999999866655555555553
No 141
>PRK04184 DNA topoisomerase VI subunit B; Validated
Probab=25.81 E-value=52 Score=31.78 Aligned_cols=57 Identities=19% Similarity=0.322 Sum_probs=41.2
Q ss_pred HhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccC--hhhHHHHHHHc
Q 030547 43 KKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTIN--GDDLLWAMATL 99 (175)
Q Consensus 43 K~~LP~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~--~eDVl~AL~~L 99 (175)
|+++.+.--|-+|.+.||++||...=.||...-...-.+++++++. -.+|.++|.++
T Consensus 431 Ke~ia~~~ei~~ei~~al~~~~r~L~~~l~~~~~~~~~~~k~~~~~~y~p~~a~~~~~~ 489 (535)
T PRK04184 431 KEAIADVPEIEKEIRLALQEVARKLKKYLSRKRKEEEAKKKAKTFEKYIPEIARKLAEI 489 (535)
T ss_pred hhhhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4555444468899999999999999999998777666666666553 34566666543
No 142
>PRK14971 DNA polymerase III subunits gamma and tau; Provisional
Probab=25.56 E-value=1.3e+02 Score=29.28 Aligned_cols=64 Identities=8% Similarity=0.009 Sum_probs=33.9
Q ss_pred CchhHHHHHHHhhCC-CCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHH
Q 030547 33 LPIANISRIMKKALP-ANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (175)
Q Consensus 33 LP~A~V~RImK~~LP-~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~ 97 (175)
|+...+.+.+++.+. .+..++.++...|.+.+.-=+..+-.+....+.-.+++ |+.++|...+.
T Consensus 180 ls~~ei~~~L~~ia~~egi~i~~~al~~La~~s~gdlr~al~~Lekl~~y~~~~-It~~~V~~~l~ 244 (614)
T PRK14971 180 IQVADIVNHLQYVASKEGITAEPEALNVIAQKADGGMRDALSIFDQVVSFTGGN-ITYKSVIENLN 244 (614)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhccCC-ccHHHHHHHhC
Confidence 444555555554332 36788998888877765433333333333333333333 66666655443
No 143
>PHA03328 nuclear egress lamina protein UL31; Provisional
Probab=25.37 E-value=81 Score=28.71 Aligned_cols=69 Identities=16% Similarity=0.313 Sum_probs=44.7
Q ss_pred CcccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHHcCCCc
Q 030547 27 REQDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFED 103 (175)
Q Consensus 27 ~~~d~~LP~A~V~RImK~~LP~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~~ 103 (175)
..+++-||-.-|.+|+-. +| +-+|.-|... +-||..+....--..-.+..-||+++||..++.+|+|++
T Consensus 228 ~~~slHL~~~~L~~Ll~n-~~-gY~i~adv~~------~~fvL~v~~~~~~~~~~~~~~~V~~~dIy~k~~dL~f~d 296 (316)
T PHA03328 228 PGKSLHLHYRLIDRLLTA-CP-GYRIIAHVWQ------TTFVLVVRRDAERQTTDADVPAVSAEDIYCKMCDLNFDG 296 (316)
T ss_pred CCCcccchHHHHHHHHHh-CC-CCeEEEEEec------ceEEEEEeeCCCCCCccccccccCHHHHHHHHhCCCCCh
Confidence 344556776666665554 45 5555554322 345555554333345667788999999999999999974
No 144
>TIGR03261 phnS2 putative 2-aminoethylphosphonate ABC transporter, periplasmic 2-aminoethylphosphonate-binding protein. This ABC transporter extracellular solute-binding protein is found in a number of genomes in operon-like contexts strongly suggesting a substrate specificity for 2-aminoethylphosphonate (2-AEP). The characterized PhnSTUV system is absent in the genomes in which this system is found. These genomes encode systems for the catabolism of 2-AEP, making the need for a 2-AEP-specific transporter likely.
Probab=25.21 E-value=1.7e+02 Score=24.98 Aligned_cols=60 Identities=8% Similarity=0.074 Sum_probs=37.3
Q ss_pred HHHHHHHHHHHHHHHH-HHHHhcCCCccC----------hhhHHHHHHHcCCCcchHHHHHHHHHHHHHhh
Q 030547 61 QECVSEFISFITSEAS-DKCQKEKRKTIN----------GDDLLWAMATLGFEDYIDPLKAYLMRYREMEG 120 (175)
Q Consensus 61 ~~~aseFI~~LtseA~-~~~~~~kRKTI~----------~eDVl~AL~~LgF~~yv~~Lk~~L~~yre~~~ 120 (175)
.++|..||.|+.+... ..-.+.....++ ++++...+-.+++..+.+.....+++|.....
T Consensus 260 ~e~A~~fidfllS~e~Q~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~rw~~~~~ 330 (334)
T TIGR03261 260 NDAAKKLVDWSISDEAMELYAKNYAVVATPGVAKPDAGFPKNVEDLLIKNDFVWAAANRDKILEEWSKRYG 330 (334)
T ss_pred HHHHHHHHHHHcCHHHHHHHHhcCcccccCCcccCcccCCcchhhhcccCCHHHHHHhHHHHHHHHHHHhh
Confidence 3789999999976533 332233322211 12444445566777778888899999987765
No 145
>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=24.85 E-value=1.5e+02 Score=28.72 Aligned_cols=72 Identities=14% Similarity=0.193 Sum_probs=45.4
Q ss_pred hhHHHHHHHhhCCC-CCcccHHHHHHHHHHH---HHHHHHHHHHH----HH---HHHhcCCCccChhhHHHHHHHcCCCc
Q 030547 35 IANISRIMKKALPA-NGKIAKDAKDTVQECV---SEFISFITSEA----SD---KCQKEKRKTINGDDLLWAMATLGFED 103 (175)
Q Consensus 35 ~A~V~RImK~~LP~-~~kISkDA~~al~~~a---seFI~~LtseA----~~---~~~~~kRKTI~~eDVl~AL~~LgF~~ 103 (175)
..-+..|++..+.. +..++.++..+|.+++ ...++.|.... .. .+...++.+|+.+||.+++..--|..
T Consensus 355 ~edi~~Il~~~a~~~~v~ls~eal~~L~~ys~~gRraln~L~~~~~~~~~~~~~~~~~~~~~~I~~edv~~~l~~~r~~~ 434 (615)
T TIGR02903 355 PEDIALIVLNAAEKINVHLAAGVEELIARYTIEGRKAVNILADVYGYALYRAAEAGKENDKVTITQDDVYEVIQISRLSP 434 (615)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHCCCcHHHHHHHHHHHHHHHHHHHHHhccCCCCeeECHHHHHHHhCCCcCcc
Confidence 35566677766543 4568999999988865 34444443221 11 12233456899999999998777765
Q ss_pred chH
Q 030547 104 YID 106 (175)
Q Consensus 104 yv~ 106 (175)
|..
T Consensus 435 ~~~ 437 (615)
T TIGR02903 435 YEK 437 (615)
T ss_pred chh
Confidence 554
No 146
>PF00403 HMA: Heavy-metal-associated domain; InterPro: IPR006121 Proteins that transport heavy metals in micro-organisms and mammals share similarities in their sequences and structures. These proteins provide an important focus for research, some being involved in bacterial resistance to toxic metals, such as lead and cadmium, while others are involved in inherited human syndromes, such as Wilson's and Menke's diseases []. A conserved domain has been found in a number of these heavy metal transport or detoxification proteins []. The domain, which has been termed Heavy-Metal-Associated (HMA), contains two conserved cysteines that are probably involved in metal binding. Structure solution of the fourth HMA domain of the Menke's copper transporting ATPase shows a well-defined structure comprising a four-stranded antiparallel beta-sheet and two alpha helices packed in an alpha-beta sandwich fold []. This fold is common to other domains and is classified as "ferredoxin-like".; GO: 0046872 metal ion binding, 0030001 metal ion transport; PDB: 2VOY_A 1P6T_A 1KQK_A 2RML_A 1JWW_A 3K7R_F 1FES_A 1CC8_A 1FD8_A 2GGP_A ....
Probab=24.85 E-value=53 Score=21.17 Aligned_cols=16 Identities=19% Similarity=0.406 Sum_probs=13.8
Q ss_pred cChhhHHHHHHHcCCC
Q 030547 87 INGDDLLWAMATLGFE 102 (175)
Q Consensus 87 I~~eDVl~AL~~LgF~ 102 (175)
++.++|..+++.+||+
T Consensus 47 ~~~~~i~~~i~~~Gy~ 62 (62)
T PF00403_consen 47 TSIEKIIEAIEKAGYE 62 (62)
T ss_dssp SCHHHHHHHHHHTTSE
T ss_pred CCHHHHHHHHHHhCcC
Confidence 6678999999999984
No 147
>CHL00076 chlB photochlorophyllide reductase subunit B
Probab=24.54 E-value=1.6e+02 Score=27.91 Aligned_cols=51 Identities=8% Similarity=0.090 Sum_probs=40.8
Q ss_pred CCcccHHHHHHHHHHHHHHHH-HHHHHHHHHHHhcCCCccChhhHHHHHHHcC
Q 030547 49 NGKIAKDAKDTVQECVSEFIS-FITSEASDKCQKEKRKTINGDDLLWAMATLG 100 (175)
Q Consensus 49 ~~kISkDA~~al~~~aseFI~-~LtseA~~~~~~~kRKTI~~eDVl~AL~~Lg 100 (175)
.+.++.||...|.+. --|+. -+-..+...|+.++...|+.+.|..|=.++|
T Consensus 461 ~~~w~~ea~~~l~~i-P~f~r~~~r~~~e~~a~~~g~~~it~~~~~~a~~~~~ 512 (513)
T CHL00076 461 DLIWSPESQLELSKI-PGFVRGKVKRNTEKFARQNGITNITVEVMYAAKEALS 512 (513)
T ss_pred CCCCCHHHHHHHHhC-CHHhHHHHHHHHHHHHHHcCCCeEcHHHHHHHHHhhC
Confidence 467999999999998 55554 4445566788999999999999999977765
No 148
>PRK12728 fliE flagellar hook-basal body protein FliE; Provisional
Probab=24.00 E-value=3.2e+02 Score=20.60 Aligned_cols=38 Identities=11% Similarity=0.184 Sum_probs=28.1
Q ss_pred hcCCCccChhhHHHHHHH--cCCCcchHHHHHHHHHHHHHh
Q 030547 81 KEKRKTINGDDLLWAMAT--LGFEDYIDPLKAYLMRYREME 119 (175)
Q Consensus 81 ~~kRKTI~~eDVl~AL~~--LgF~~yv~~Lk~~L~~yre~~ 119 (175)
..|. +++..||.-|+++ +.|.-.+.-=...++.|+|+.
T Consensus 59 ~~G~-~~~lhevmiA~~kA~lslq~~vqVRNKlv~AYqEIM 98 (102)
T PRK12728 59 VKGE-IVDLHDVMIAAQKASISLQLTVQIRNKVVEAYQEIM 98 (102)
T ss_pred HcCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444 8899999999985 555556666667888999875
No 149
>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=23.87 E-value=1.6e+02 Score=17.13 Aligned_cols=38 Identities=21% Similarity=0.215 Sum_probs=25.1
Q ss_pred HHHhcCCCccChhhHHHHHHHcCCCcchHHHHHHHHHH
Q 030547 78 KCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLMRY 115 (175)
Q Consensus 78 ~~~~~kRKTI~~eDVl~AL~~LgF~~yv~~Lk~~L~~y 115 (175)
.+..++.-.|+.+|+..+++.++...-.+.+...+..+
T Consensus 8 ~~d~~~~g~l~~~e~~~~l~~~~~~~~~~~~~~~~~~~ 45 (63)
T cd00051 8 LFDKDGDGTISADELKAALKSLGEGLSEEEIDEMIREV 45 (63)
T ss_pred HhCCCCCCcCcHHHHHHHHHHhCCCCCHHHHHHHHHHh
Confidence 34455555789999999999988665555555544443
No 150
>PTZ00184 calmodulin; Provisional
Probab=23.80 E-value=2.5e+02 Score=20.22 Aligned_cols=38 Identities=18% Similarity=0.179 Sum_probs=26.3
Q ss_pred HHHHHHHhcCCCccChhhHHHHHHHcCCCcchHHHHHH
Q 030547 74 EASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAY 111 (175)
Q Consensus 74 eA~~~~~~~kRKTI~~eDVl~AL~~LgF~~yv~~Lk~~ 111 (175)
.+...+-.+++-.|+.+|+..+|..+|+.--...++..
T Consensus 88 ~~F~~~D~~~~g~i~~~e~~~~l~~~~~~~~~~~~~~~ 125 (149)
T PTZ00184 88 EAFKVFDRDGNGFISAAELRHVMTNLGEKLTDEEVDEM 125 (149)
T ss_pred HHHHhhCCCCCCeEeHHHHHHHHHHHCCCCCHHHHHHH
Confidence 34455555677789999999999999875433444443
No 151
>PLN02900 alanyl-tRNA synthetase
Probab=23.21 E-value=3.2e+02 Score=28.32 Aligned_cols=29 Identities=21% Similarity=0.416 Sum_probs=22.1
Q ss_pred HhcCCCccChhhHHHHHHHcCCC-cchHHH
Q 030547 80 QKEKRKTINGDDLLWAMATLGFE-DYIDPL 108 (175)
Q Consensus 80 ~~~kRKTI~~eDVl~AL~~LgF~-~yv~~L 108 (175)
+.+++++|+++|+++.-+..||+ |....+
T Consensus 404 ~~~~~~~l~g~~af~LydTyGfP~dlt~~i 433 (936)
T PLN02900 404 KANGGPVLSGKDAFLLYDTYGFPVDLTELM 433 (936)
T ss_pred hhcCCCcCCHHHHHHHHhccCCCHHHHHHH
Confidence 34456789999999999999996 444443
No 152
>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=23.06 E-value=2.5e+02 Score=18.95 Aligned_cols=48 Identities=19% Similarity=0.200 Sum_probs=34.2
Q ss_pred cCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 030547 32 YLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQK 81 (175)
Q Consensus 32 ~LP~A~V~RImK~~LP~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~ 81 (175)
.+|-+.+.-+++.+.=+ .-..-.+-+|.=++..||+-|+..|.+.|+-
T Consensus 2 ~IPD~v~~~yL~~~G~~--~~D~rv~RLvSLaaQKFisdI~~dA~q~~k~ 49 (51)
T PF03540_consen 2 TIPDEVTDYYLERSGFQ--TSDPRVKRLVSLAAQKFISDIANDAMQYCKI 49 (51)
T ss_pred CCCHHHHHHHHHHCCCC--CCCHhHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 46777788888877522 1222335577788889999999999988863
No 153
>PF02718 Herpes_UL31: Herpesvirus UL31-like protein; InterPro: IPR021152 This is a family of Herpesvirus proteins, belong to the UL31 family, which including UL31, UL53, and the product of ORF69 in some strains. The proteins in this family have no known function.
Probab=22.63 E-value=1.3e+02 Score=26.56 Aligned_cols=78 Identities=21% Similarity=0.376 Sum_probs=47.5
Q ss_pred CCcccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHHcCCCcch
Q 030547 26 VREQDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYI 105 (175)
Q Consensus 26 ~~~~d~~LP~A~V~RImK~~LP~~~kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~~yv 105 (175)
...+++-||-.-|.+|+-.. | +-+|+-|... .-||.-++..+ ..+..-+|.++||..++.+|+|+
T Consensus 177 F~~~~lHl~~~~i~~ll~n~-~-~Y~i~~dv~~------~~fvL~v~~~~----~~~~~~~I~~~~I~~ki~dld~~--- 241 (258)
T PF02718_consen 177 FPGKSLHLHERCIRQLLDNC-P-GYKISADVWQ------GTFVLVVRPDR----EEQTSPKIDADDIYCKICDLDFP--- 241 (258)
T ss_pred ECCCCccchHHHHHHHHHhC-C-CCeEEEEEec------CEEEEEEEeCC----CcCCCcccCHHHHHHHHHcCCCC---
Confidence 34566778877777666655 4 5555544321 12333333221 22347789999999999999998
Q ss_pred HHHHHHHHHHHHH
Q 030547 106 DPLKAYLMRYREM 118 (175)
Q Consensus 106 ~~Lk~~L~~yre~ 118 (175)
.+|+...++|...
T Consensus 242 dEl~~ey~k~~~~ 254 (258)
T PF02718_consen 242 DELKEEYEKYYAL 254 (258)
T ss_pred hHHHHHHHHHHHH
Confidence 4555555555543
No 154
>COG5340 Predicted transcriptional regulator [Transcription]
Probab=22.59 E-value=1.3e+02 Score=26.68 Aligned_cols=54 Identities=9% Similarity=0.182 Sum_probs=43.5
Q ss_pred CCcccccCchhHHHHHHHhhCCC-----CC-cccHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 030547 26 VREQDRYLPIANISRIMKKALPA-----NG-KIAKDAKDTVQECVSEFISFITSEASDKC 79 (175)
Q Consensus 26 ~~~~d~~LP~A~V~RImK~~LP~-----~~-kISkDA~~al~~~aseFI~~LtseA~~~~ 79 (175)
-.++.+..|.+++.|-+++.+.. +. -++|-.+.+....+++|..|+-..+|-.+
T Consensus 148 T~Ie~~~VpvttlaKTi~DC~~kP~YCGG~~~~akAl~aa~e~a~~e~t~Yl~R~~n~Aa 207 (269)
T COG5340 148 TSIEGTVVPVTTLAKTIVDCADKPEYCGGIRELAKALVAADEQACSEATEYLQRLDNGAA 207 (269)
T ss_pred cceeeeeeehHHHHHHHHHHhcCccccCCHHHHHHHHHHhHHHHHHHHHHHHHhccchHH
Confidence 34566679999999999999975 33 48888999999999999999877766443
No 155
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=22.11 E-value=1.5e+02 Score=27.83 Aligned_cols=41 Identities=12% Similarity=0.227 Sum_probs=33.7
Q ss_pred HHHHHhcCCCccChhhHHHHHHHcCCCcchHHHHHHHHHHHHHhh
Q 030547 76 SDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLMRYREMEG 120 (175)
Q Consensus 76 ~~~~~~~kRKTI~~eDVl~AL~~LgF~~yv~~Lk~~L~~yre~~~ 120 (175)
.-+...++++-++.+.|...|++-|+. .-+.-+.+||+..+
T Consensus 405 ~lI~~Ed~~~PlSD~~I~~~L~~~Gi~----IaRRTVaKYRe~L~ 445 (455)
T PRK05932 405 KLIAAENPKKPLSDSKIAELLKEQGID----VARRTVAKYREALN 445 (455)
T ss_pred HHHHhcCCCCCCCHHHHHHHHHHcCCC----eehHHHHHHHHHcC
Confidence 346678888999999999999998884 55778899998764
No 156
>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA.
Probab=22.07 E-value=1.2e+02 Score=29.78 Aligned_cols=23 Identities=17% Similarity=0.374 Sum_probs=20.1
Q ss_pred HHHHHHHhcCCCccChhhHHHHH
Q 030547 74 EASDKCQKEKRKTINGDDLLWAM 96 (175)
Q Consensus 74 eA~~~~~~~kRKTI~~eDVl~AL 96 (175)
.|.+.|.+-+..-|+++|++.||
T Consensus 11 ~A~~~A~~~~h~~V~~EHLLlaL 33 (731)
T TIGR02639 11 AALEEAKKRRHEFVTLEHILLAL 33 (731)
T ss_pred HHHHHHHHhCCCcCcHHHHHHHH
Confidence 47788999999999999999886
No 157
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=22.01 E-value=1.5e+02 Score=20.11 Aligned_cols=32 Identities=19% Similarity=0.496 Sum_probs=18.9
Q ss_pred cCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHH
Q 030547 32 YLPIANISRIMKKALPANGKIAKDAKDTVQECVSEF 67 (175)
Q Consensus 32 ~LP~A~V~RImK~~LP~~~kISkDA~~al~~~aseF 67 (175)
.+.+++|.|++... ..|+.+.++.+.+++.++
T Consensus 11 gvS~~TVSr~ln~~----~~v~~~t~~~i~~~~~~~ 42 (70)
T smart00354 11 GVSKATVSRVLNGN----GRVSEETREKVLAAMEEL 42 (70)
T ss_pred CCCHHHHHHHHCCC----CCCCHHHHHHHHHHHHHh
Confidence 35566666666432 346666666666666554
No 158
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=21.76 E-value=82 Score=26.66 Aligned_cols=37 Identities=16% Similarity=0.415 Sum_probs=28.8
Q ss_pred CchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHH
Q 030547 33 LPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSE 74 (175)
Q Consensus 33 LP~A~V~RImK~~LP~~~kISkDA~~al~~~aseFI~~Ltse 74 (175)
+-++||.|++... .+||.+.++-+.+++.+ +.|.-..
T Consensus 13 VS~~TVSrvLn~~----~~Vs~~tr~rV~~~a~e-lgY~pn~ 49 (343)
T PRK10727 13 VSVATVSRVINNS----PKASEASRLAVHSAMES-LSYHPNA 49 (343)
T ss_pred CCHHHHHHHhCCC----CCCCHHHHHHHHHHHHH-HCCCCCH
Confidence 5578999999653 37999999999999998 4565443
No 159
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=21.64 E-value=49 Score=21.13 Aligned_cols=17 Identities=18% Similarity=0.393 Sum_probs=13.0
Q ss_pred cccCchhHHHHHHHhhC
Q 030547 30 DRYLPIANISRIMKKAL 46 (175)
Q Consensus 30 d~~LP~A~V~RImK~~L 46 (175)
.+.+|+++++|+++.-.
T Consensus 27 ~~gl~~stv~r~L~tL~ 43 (52)
T PF09339_consen 27 ALGLPKSTVHRLLQTLV 43 (52)
T ss_dssp HHTS-HHHHHHHHHHHH
T ss_pred HHCcCHHHHHHHHHHHH
Confidence 45799999999998654
No 160
>PF09239 Topo-VIb_trans: Topoisomerase VI B subunit, transducer; InterPro: IPR015320 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils []. This entry represents subunit B of topoisomerase VI, an ATP-dependent type IIB enzyme. Members of this family adopt a structure consisting of a four-stranded beta-sheet backed by three alpha-helices, the last of which is over 50 amino acids long and extends from the body of the protein by several turns. This domain has been proposed to mediate intersubunit communication by structurally transducing signals from the ATP binding and hydrolysis domains to the DNA binding and cleavage domains of the gyrase holoenzyme []. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0006265 DNA topological change, 0005694 chromosome; PDB: 2ZBK_F 2HKJ_A 1Z5B_A 1Z5C_B 1MX0_F 1Z5A_A 1MU5_A 1Z59_A 2Q2E_B.
Probab=21.45 E-value=97 Score=25.62 Aligned_cols=33 Identities=21% Similarity=0.465 Sum_probs=24.6
Q ss_pred HhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHH
Q 030547 43 KKALPANGKIAKDAKDTVQECVSEFISFITSEA 75 (175)
Q Consensus 43 K~~LP~~~kISkDA~~al~~~aseFI~~LtseA 75 (175)
|+++.+.--|-+|.+.||++||...=.||....
T Consensus 120 KeaIa~~pEI~~Ei~lAl~e~~R~L~~yl~rk~ 152 (160)
T PF09239_consen 120 KEAIADVPEIEKEIRLALQECARKLKKYLSRKR 152 (160)
T ss_dssp SSSB---HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hhhhcCcHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444444446889999999999999999997643
No 161
>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=21.28 E-value=4.1e+02 Score=20.88 Aligned_cols=63 Identities=17% Similarity=0.148 Sum_probs=39.6
Q ss_pred cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhhHHHHHHHcCCCc------------chHHHHHHHHHHHHH
Q 030547 51 KIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFED------------YIDPLKAYLMRYREM 118 (175)
Q Consensus 51 kISkDA~~al~~~aseFI~~LtseA~~~~~~~kRKTI~~eDVl~AL~~LgF~~------------yv~~Lk~~L~~yre~ 118 (175)
.+..+. +..++..++..+..-..-..- -.|.+.+|++.+++.+.+.. |++.+.+.+++-++.
T Consensus 95 ~i~~~g---~~~~~~~~lr~~~~~~~~~~~---~~tt~~~~l~~~l~~l~~P~~~~~~~i~l~~r~ip~l~~~~~~i~~A 168 (224)
T PF02361_consen 95 SITQEG---LIYAALLALRILAILLASLLF---ILTTSPSDLISALRKLRLPYPKIALMISLTLRFIPLLLEEFKRIREA 168 (224)
T ss_pred hhhHHH---HHHHHHHHHHHHHHHHHHHHH---HHHCCHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344443 444555555444443333222 23899999999999999987 777777666666554
Q ss_pred h
Q 030547 119 E 119 (175)
Q Consensus 119 ~ 119 (175)
+
T Consensus 169 ~ 169 (224)
T PF02361_consen 169 Q 169 (224)
T ss_pred H
Confidence 4
No 162
>PF12668 DUF3791: Protein of unknown function (DUF3791); InterPro: IPR024269 This entry represents proteins of unknown function.
Probab=20.53 E-value=1.1e+02 Score=20.57 Aligned_cols=30 Identities=23% Similarity=0.264 Sum_probs=23.6
Q ss_pred CCccChhhHHHHHHHcCCCcchHHHHHHHH
Q 030547 84 RKTINGDDLLWAMATLGFEDYIDPLKAYLM 113 (175)
Q Consensus 84 RKTI~~eDVl~AL~~LgF~~yv~~Lk~~L~ 113 (175)
|.-|++++++.-+++.+.-+|+.+.-..|.
T Consensus 14 ~~~~s~~ea~~~~~~~~~~~~i~~~Yd~lH 43 (62)
T PF12668_consen 14 KLNISGEEAYNYFKRSGVIDYIIDCYDVLH 43 (62)
T ss_pred HHCcCHHHHHHHHHHcCcHHHHHHcchHHH
Confidence 667899999999999988778776555443
No 163
>cd00083 HLH Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and
Probab=20.50 E-value=1.8e+02 Score=18.43 Aligned_cols=35 Identities=14% Similarity=0.162 Sum_probs=24.0
Q ss_pred HHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHH
Q 030547 40 RIMKKALPANGKIAKDAKDTVQECVSEFISFITSE 74 (175)
Q Consensus 40 RImK~~LP~~~kISkDA~~al~~~aseFI~~Ltse 74 (175)
...+..+|......+-.+..|-+.|..||.+|...
T Consensus 24 ~~L~~llp~~~~~~k~~k~~iL~~a~~yI~~L~~~ 58 (60)
T cd00083 24 DELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQEL 58 (60)
T ss_pred HHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Confidence 34566677653345555688888888999998654
No 164
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=20.44 E-value=93 Score=26.12 Aligned_cols=37 Identities=11% Similarity=0.365 Sum_probs=28.7
Q ss_pred cCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHH
Q 030547 32 YLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITS 73 (175)
Q Consensus 32 ~LP~A~V~RImK~~LP~~~kISkDA~~al~~~aseFI~~Lts 73 (175)
-.-++||.|++... .+||.+.++-+.+++.+ +.|.-.
T Consensus 16 gVS~~TVSrvLn~~----~~vs~~tr~rV~~~a~e-lgY~pn 52 (331)
T PRK14987 16 GVTKMTVSRFLRNP----EQVSVALRGKIAAALDE-LGYIPN 52 (331)
T ss_pred CCCHHHhhhhhCCC----CCCCHHHHHHHHHHHHH-hCCCcc
Confidence 35678999988643 37999999999999988 556543
No 165
>PRK05907 hypothetical protein; Provisional
Probab=20.08 E-value=2.5e+02 Score=24.86 Aligned_cols=72 Identities=10% Similarity=-0.065 Sum_probs=47.0
Q ss_pred CCcccHHHHHHHHHHH-HHHHHHHHHHHHHHHHh-cCCCccChhhHHHHHH-HcCCC--cchH-----HHHHHHHHHHHH
Q 030547 49 NGKIAKDAKDTVQECV-SEFISFITSEASDKCQK-EKRKTINGDDLLWAMA-TLGFE--DYID-----PLKAYLMRYREM 118 (175)
Q Consensus 49 ~~kISkDA~~al~~~a-seFI~~LtseA~~~~~~-~kRKTI~~eDVl~AL~-~LgF~--~yv~-----~Lk~~L~~yre~ 118 (175)
+.+|+++|...|.+.+ .-=+..|..|-...|.- ..+++|+.+||...+. .++|. +.++ ..+..+.-|+++
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 5689999988888877 33444666666666665 5588999999988854 45554 2222 234556666665
Q ss_pred hh
Q 030547 119 EG 120 (175)
Q Consensus 119 ~~ 120 (175)
..
T Consensus 231 l~ 232 (311)
T PRK05907 231 LS 232 (311)
T ss_pred HH
Confidence 43
Done!