Query 030714
Match_columns 173
No_of_seqs 149 out of 586
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 03:29:38 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030714.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030714hhsearch_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 1.2E-41 2.6E-46 273.2 13.8 119 1-120 1-120 (168)
2 KOG0871 Class 2 transcription 100.0 1.2E-29 2.5E-34 202.3 8.9 111 26-140 6-116 (156)
3 KOG0870 DNA polymerase epsilon 99.9 1.4E-24 3.1E-29 175.8 8.1 94 25-118 3-97 (172)
4 COG5150 Class 2 transcription 99.9 8.1E-23 1.8E-27 160.3 8.9 100 26-125 5-104 (148)
5 PF00808 CBFD_NFYB_HMF: Histon 99.8 7.1E-19 1.5E-23 121.1 7.5 64 32-96 2-65 (65)
6 COG2036 HHT1 Histones H3 and H 99.7 1.2E-17 2.7E-22 124.2 6.1 79 25-105 12-90 (91)
7 cd00076 H4 Histone H4, one of 99.2 5.7E-11 1.2E-15 87.5 8.1 72 31-104 12-83 (85)
8 PLN00035 histone H4; Provision 99.2 1.1E-10 2.4E-15 88.7 8.2 76 26-103 23-98 (103)
9 PTZ00015 histone H4; Provision 99.1 3.2E-10 6.9E-15 86.1 8.2 77 26-104 24-100 (102)
10 smart00803 TAF TATA box bindin 99.0 2.4E-09 5.1E-14 74.9 7.3 64 32-97 2-65 (65)
11 smart00428 H3 Histone H3. 98.9 2.3E-09 5E-14 81.8 6.9 74 26-99 23-101 (105)
12 smart00417 H4 Histone H4. 98.9 2.1E-09 4.5E-14 77.4 5.9 64 30-95 11-74 (74)
13 cd07981 TAF12 TATA Binding Pro 98.9 9.7E-09 2.1E-13 72.8 8.2 65 33-98 2-66 (72)
14 PF00125 Histone: Core histone 98.9 4.8E-09 1E-13 73.2 6.1 68 30-97 3-73 (75)
15 PLN00121 histone H3; Provision 98.6 8.7E-08 1.9E-12 76.1 6.0 71 27-97 57-130 (136)
16 PLN00161 histone H3; Provision 98.6 1.8E-07 4E-12 74.2 7.8 71 27-97 50-124 (135)
17 PLN00160 histone H3; Provision 98.6 1.4E-07 3.1E-12 71.2 6.7 72 26-97 15-90 (97)
18 COG5208 HAP5 CCAAT-binding fac 98.6 5.8E-08 1.3E-12 83.0 4.2 77 29-107 106-183 (286)
19 KOG1657 CCAAT-binding factor, 98.6 1.2E-07 2.7E-12 81.1 6.2 87 30-117 72-161 (236)
20 PTZ00018 histone H3; Provision 98.6 1.3E-07 2.8E-12 75.2 5.8 71 27-97 57-130 (136)
21 smart00576 BTP Bromodomain tra 98.4 1.6E-06 3.5E-11 61.8 8.0 66 35-102 9-74 (77)
22 cd00074 H2A Histone 2A; H2A is 98.3 1.4E-06 3.1E-11 67.4 6.6 69 29-98 17-85 (115)
23 cd07979 TAF9 TATA Binding Prot 98.1 2E-05 4.4E-10 60.7 8.2 78 37-116 6-84 (117)
24 KOG1745 Histones H3 and H4 [Ch 97.9 7.6E-06 1.7E-10 65.2 2.9 75 26-100 57-134 (137)
25 KOG1142 Transcription initiati 97.9 6.2E-05 1.3E-09 65.4 8.5 92 5-97 125-218 (258)
26 cd08050 TAF6 TATA Binding Prot 97.9 6.2E-05 1.3E-09 67.0 8.1 66 34-101 1-66 (343)
27 PF15630 CENP-S: Kinetochore c 97.8 6.6E-05 1.4E-09 54.2 6.7 62 37-98 10-72 (76)
28 PF15511 CENP-T: Centromere ki 97.8 3.1E-05 6.8E-10 70.7 5.9 64 28-91 347-414 (414)
29 smart00427 H2B Histone H2B. 97.8 0.00012 2.5E-09 54.7 7.4 62 37-99 6-67 (89)
30 PF03847 TFIID_20kDa: Transcri 97.8 0.00013 2.8E-09 51.6 6.8 63 35-98 2-64 (68)
31 KOG1659 Class 2 transcription 97.7 0.0001 2.3E-09 62.6 6.3 84 31-115 12-95 (224)
32 PF07524 Bromo_TP: Bromodomain 97.6 0.00051 1.1E-08 48.5 8.2 64 37-102 11-74 (77)
33 cd08048 TAF11 TATA Binding Pro 97.6 0.00048 1E-08 50.7 7.9 66 32-99 16-84 (85)
34 PLN00158 histone H2B; Provisio 97.6 0.00037 8.1E-09 54.2 7.5 64 35-99 30-93 (116)
35 KOG3467 Histone H4 [Chromatin 97.6 0.00035 7.5E-09 52.5 6.9 69 32-102 29-97 (103)
36 PTZ00463 histone H2B; Provisio 97.5 0.00045 9.8E-09 53.8 7.4 62 37-99 33-94 (117)
37 PF09415 CENP-X: CENP-S associ 97.4 0.00022 4.8E-09 51.0 4.2 65 34-98 1-67 (72)
38 COG5262 HTA1 Histone H2A [Chro 97.3 0.00047 1E-08 54.1 5.3 68 29-97 23-90 (132)
39 PF04719 TAFII28: hTAFII28-lik 97.3 0.0013 2.7E-08 49.1 6.9 67 32-99 23-90 (90)
40 COG5247 BUR6 Class 2 transcrip 97.2 0.0016 3.5E-08 50.0 7.1 80 29-109 20-99 (113)
41 smart00414 H2A Histone 2A. 97.1 0.0016 3.4E-08 49.8 6.2 68 30-98 7-74 (106)
42 PF02969 TAF: TATA box binding 96.9 0.0063 1.4E-07 42.9 7.5 64 32-97 3-66 (66)
43 KOG1658 DNA polymerase epsilon 96.9 0.00066 1.4E-08 55.3 2.4 65 31-97 58-123 (162)
44 PLN00154 histone H2A; Provisio 96.8 0.0036 7.8E-08 50.0 6.1 69 29-97 35-103 (136)
45 PTZ00017 histone H2A; Provisio 96.7 0.0039 8.6E-08 49.6 5.4 68 29-97 24-91 (134)
46 PF15510 CENP-W: Centromere ki 96.6 0.0034 7.5E-08 47.4 4.6 67 31-98 15-95 (102)
47 KOG1744 Histone H2B [Chromatin 96.4 0.012 2.5E-07 46.6 6.7 60 38-98 43-102 (127)
48 PLN00157 histone H2A; Provisio 96.3 0.0076 1.6E-07 47.9 5.2 68 29-97 23-90 (132)
49 PLN00153 histone H2A; Provisio 96.3 0.0092 2E-07 47.3 5.4 68 29-97 21-88 (129)
50 PLN00156 histone H2AX; Provisi 96.3 0.011 2.4E-07 47.4 5.7 68 29-97 26-93 (139)
51 KOG1756 Histone 2A [Chromatin 96.2 0.012 2.7E-07 46.6 5.8 68 29-97 24-91 (131)
52 PF02269 TFIID-18kDa: Transcri 96.2 0.0071 1.5E-07 44.8 3.9 60 38-98 7-66 (93)
53 KOG3219 Transcription initiati 95.2 0.025 5.5E-07 47.6 4.2 69 32-102 112-181 (195)
54 PF02291 TFIID-31kDa: Transcri 94.9 0.14 3.1E-06 40.4 7.4 86 29-116 7-95 (129)
55 cd07978 TAF13 The TATA Binding 94.9 0.25 5.5E-06 36.7 8.3 59 37-97 7-65 (92)
56 PTZ00252 histone H2A; Provisio 94.9 0.081 1.8E-06 42.3 6.0 68 29-97 22-91 (134)
57 KOG4336 TBP-associated transcr 92.7 0.67 1.5E-05 41.7 8.2 76 38-117 11-86 (323)
58 TIGR03015 pepcterm_ATPase puta 91.6 0.62 1.4E-05 38.4 6.4 69 33-101 192-268 (269)
59 KOG3423 Transcription initiati 89.9 1.7 3.7E-05 36.1 7.4 69 32-102 86-168 (176)
60 PRK00411 cdc6 cell division co 88.8 2.2 4.8E-05 37.4 7.8 70 35-104 209-287 (394)
61 KOG2389 Predicted bromodomain 87.0 1.7 3.8E-05 39.6 6.1 70 31-102 28-97 (353)
62 KOG2549 Transcription initiati 86.2 2.7 5.9E-05 40.6 7.2 66 34-101 13-78 (576)
63 TIGR02928 orc1/cdc6 family rep 85.6 4.3 9.4E-05 35.1 7.7 74 36-109 202-284 (365)
64 TIGR02902 spore_lonB ATP-depen 80.7 4.2 9.1E-05 38.4 6.1 66 35-101 265-334 (531)
65 PF13654 AAA_32: AAA domain; P 78.6 9.4 0.0002 36.2 7.7 59 38-99 436-506 (509)
66 TIGR00764 lon_rel lon-related 76.6 9.8 0.00021 36.7 7.3 50 51-100 330-392 (608)
67 COG1067 LonB Predicted ATP-dep 76.5 2.4 5.1E-05 41.5 3.1 49 51-100 338-400 (647)
68 KOG2680 DNA helicase TIP49, TB 73.6 14 0.0003 34.2 7.1 60 38-97 363-427 (454)
69 PF13335 Mg_chelatase_2: Magne 73.5 13 0.00027 27.5 5.7 47 51-97 42-94 (96)
70 cd08045 TAF4 TATA Binding Prot 73.1 18 0.0004 30.0 7.3 79 29-107 41-127 (212)
71 KOG3334 Transcription initiati 71.3 13 0.00029 30.2 5.7 65 52-116 31-96 (148)
72 COG1224 TIP49 DNA helicase TIP 69.3 15 0.00033 34.4 6.4 82 33-117 361-447 (450)
73 COG5095 TAF6 Transcription ini 69.2 10 0.00023 34.9 5.3 52 50-101 21-72 (450)
74 KOG1757 Histone 2A [Chromatin 66.9 9.2 0.0002 30.2 3.9 65 29-97 27-95 (131)
75 PF08369 PCP_red: Proto-chloro 66.7 7.9 0.00017 25.1 3.0 42 53-95 2-44 (45)
76 PF00531 Death: Death domain; 66.5 10 0.00022 25.8 3.7 61 51-112 23-83 (83)
77 COG5248 TAF19 Transcription in 63.5 42 0.00091 26.4 6.9 48 48-97 24-71 (126)
78 KOG3901 Transcription initiati 62.4 20 0.00044 27.8 4.9 47 48-97 24-70 (109)
79 PRK13765 ATP-dependent proteas 61.8 18 0.00039 35.4 5.6 48 51-98 339-399 (637)
80 PF02861 Clp_N: Clp amino term 61.6 6.8 0.00015 24.5 1.9 25 75-99 1-25 (53)
81 PRK00080 ruvB Holliday junctio 60.3 35 0.00077 29.6 6.8 71 33-103 180-254 (328)
82 TIGR00635 ruvB Holliday juncti 60.1 38 0.00082 28.6 6.8 71 33-103 159-233 (305)
83 TIGR02030 BchI-ChlI magnesium 59.7 40 0.00086 30.3 7.1 54 43-97 247-307 (337)
84 TIGR02442 Cob-chelat-sub cobal 57.6 38 0.00082 32.7 7.0 49 49-97 247-302 (633)
85 cd04752 Commd4 COMM_Domain con 54.7 38 0.00083 27.4 5.7 48 63-117 43-91 (174)
86 PRK09862 putative ATP-dependen 54.2 46 0.001 31.7 6.9 54 50-103 437-496 (506)
87 PRK13406 bchD magnesium chelat 52.9 32 0.00069 33.2 5.7 59 37-97 183-248 (584)
88 TIGR01128 holA DNA polymerase 51.5 60 0.0013 27.0 6.6 66 32-97 110-176 (302)
89 COG5624 TAF61 Transcription in 51.3 8.1 0.00018 36.4 1.4 77 31-107 382-461 (505)
90 smart00350 MCM minichromosome 51.3 72 0.0016 29.9 7.7 65 31-98 416-503 (509)
91 COG5162 Transcription initiati 49.8 1E+02 0.0022 25.9 7.4 51 52-102 106-189 (197)
92 PLN00138 large subunit ribosom 49.7 45 0.00098 25.7 5.1 44 70-115 3-46 (113)
93 CHL00081 chlI Mg-protoporyphyr 49.4 48 0.001 30.1 6.0 54 43-97 260-320 (350)
94 TIGR01052 top6b DNA topoisomer 48.3 24 0.00052 33.6 4.0 60 43-116 426-485 (488)
95 TIGR00368 Mg chelatase-related 47.9 44 0.00096 31.6 5.7 47 51-97 445-497 (499)
96 PRK12402 replication factor C 47.0 48 0.001 28.0 5.4 71 33-105 184-255 (337)
97 PTZ00373 60S Acidic ribosomal 46.6 58 0.0013 25.2 5.2 44 69-114 4-47 (112)
98 COG1474 CDC6 Cdc6-related prot 46.2 77 0.0017 28.7 6.8 71 37-107 194-273 (366)
99 PRK13407 bchI magnesium chelat 45.8 66 0.0014 28.9 6.2 53 43-96 244-303 (334)
100 PF05236 TAF4: Transcription i 45.6 32 0.00068 29.5 4.0 77 27-103 38-122 (264)
101 PF09114 MotA_activ: Transcrip 44.2 33 0.00072 26.0 3.4 33 36-68 51-87 (96)
102 TIGR02031 BchD-ChlD magnesium 43.9 78 0.0017 30.4 6.8 55 42-97 195-256 (589)
103 PRK07452 DNA polymerase III su 40.9 74 0.0016 27.3 5.6 64 38-101 135-201 (326)
104 PRK05932 RNA polymerase factor 40.8 42 0.00091 31.4 4.4 81 29-123 351-448 (455)
105 PF07647 SAM_2: SAM domain (St 40.1 31 0.00067 22.6 2.5 24 86-109 3-26 (66)
106 COG1508 RpoN DNA-directed RNA 39.0 77 0.0017 30.0 5.8 85 25-123 332-436 (444)
107 PRK03992 proteasome-activating 38.5 40 0.00086 30.4 3.7 35 66-100 339-373 (389)
108 PF12627 PolyA_pol_RNAbd: Prob 38.4 8 0.00017 25.5 -0.6 59 49-111 1-63 (64)
109 PF08681 DUF1778: Protein of u 38.1 28 0.00061 24.7 2.2 50 49-98 3-60 (80)
110 PTZ00361 26 proteosome regulat 37.7 39 0.00086 31.5 3.7 32 68-99 393-424 (438)
111 PRK05574 holA DNA polymerase I 37.5 93 0.002 26.4 5.7 64 33-97 146-211 (340)
112 TIGR01242 26Sp45 26S proteasom 37.1 44 0.00094 29.5 3.7 32 67-98 331-362 (364)
113 cd05833 Ribosomal_P2 Ribosomal 36.9 97 0.0021 23.7 5.1 31 70-102 3-33 (109)
114 cd00166 SAM Sterile alpha moti 36.9 28 0.00062 22.0 1.9 24 88-111 3-26 (63)
115 PF12010 DUF3502: Domain of un 36.3 35 0.00076 26.4 2.7 61 54-118 72-132 (134)
116 PF00356 LacI: Bacterial regul 35.9 75 0.0016 20.5 3.8 32 32-67 10-41 (46)
117 KOG1528 Salt-sensitive 3'-phos 35.1 1E+02 0.0022 28.3 5.7 74 26-100 44-124 (351)
118 PF07499 RuvA_C: RuvA, C-termi 35.0 24 0.00051 22.6 1.3 14 90-103 4-17 (47)
119 PF00536 SAM_1: SAM domain (St 34.9 40 0.00088 22.0 2.5 21 88-108 4-24 (64)
120 PRK09526 lacI lac repressor; R 33.6 28 0.0006 29.3 1.8 40 32-76 16-55 (342)
121 PF13405 EF-hand_6: EF-hand do 33.3 39 0.00084 19.2 1.9 26 75-100 5-31 (31)
122 cd00823 TopoIIB_Trans TopoIIB_ 32.1 83 0.0018 25.7 4.2 34 43-76 111-144 (151)
123 smart00027 EH Eps15 homology d 32.1 78 0.0017 22.4 3.7 28 75-102 15-42 (96)
124 PF09123 DUF1931: Domain of un 31.9 43 0.00093 27.0 2.5 53 38-92 1-53 (138)
125 COG1389 DNA topoisomerase VI, 31.5 36 0.00078 32.8 2.3 46 43-88 434-479 (538)
126 PTZ00454 26S protease regulato 31.4 60 0.0013 29.7 3.7 32 68-99 355-386 (398)
127 PRK14868 DNA topoisomerase VI 31.1 60 0.0013 32.9 3.9 56 29-87 614-669 (795)
128 COG1222 RPT1 ATP-dependent 26S 29.9 79 0.0017 29.6 4.2 50 50-99 338-392 (406)
129 smart00454 SAM Sterile alpha m 29.7 41 0.00089 21.3 1.8 25 87-111 4-28 (68)
130 PRK12469 RNA polymerase factor 29.2 86 0.0019 29.8 4.4 81 29-123 377-474 (481)
131 PTZ00183 centrin; Provisional 29.2 1.7E+02 0.0038 21.4 5.4 22 77-98 60-81 (158)
132 PRK12728 fliE flagellar hook-b 28.2 2.3E+02 0.0049 21.4 5.8 63 55-119 32-98 (102)
133 PF03540 TFIID_30kDa: Transcri 28.1 1.9E+02 0.0042 19.4 6.3 48 32-81 2-49 (51)
134 COG1466 HolA DNA polymerase II 27.6 1.3E+02 0.0028 26.4 5.0 50 49-98 157-206 (334)
135 PRK07914 hypothetical protein; 27.3 1.2E+02 0.0026 26.3 4.7 63 34-97 129-192 (320)
136 PF13499 EF-hand_7: EF-hand do 26.9 1.6E+02 0.0036 18.7 4.4 46 74-119 4-50 (66)
137 COG1724 Predicted RNA binding 26.8 39 0.00085 24.1 1.3 17 86-102 6-22 (66)
138 PRK14975 bifunctional 3'-5' ex 26.6 2.9E+02 0.0063 26.3 7.5 90 29-121 160-269 (553)
139 PRK02910 light-independent pro 26.4 1.2E+02 0.0025 28.6 4.8 52 48-100 466-518 (519)
140 PRK00440 rfc replication facto 26.3 1.3E+02 0.0027 25.2 4.6 65 33-99 161-226 (319)
141 PRK14867 DNA topoisomerase VI 26.2 84 0.0018 31.2 3.9 52 51-116 592-643 (659)
142 TIGR02903 spore_lon_C ATP-depe 26.2 1.2E+02 0.0027 29.3 5.0 72 35-106 355-437 (615)
143 PHA03328 nuclear egress lamina 26.1 70 0.0015 29.1 3.1 79 28-116 229-307 (316)
144 PRK10423 transcriptional repre 26.0 53 0.0012 27.3 2.3 37 33-74 10-46 (327)
145 COG5251 TAF40 Transcription in 25.7 99 0.0021 26.1 3.7 61 32-96 115-178 (199)
146 smart00354 HTH_LACI helix_turn 25.6 1.1E+02 0.0025 20.6 3.5 32 32-67 11-42 (70)
147 TIGR01278 DPOR_BchB light-inde 25.4 1.3E+02 0.0027 28.3 4.8 51 49-100 460-511 (511)
148 PF10728 DUF2520: Domain of un 25.2 2.2E+02 0.0048 22.0 5.5 71 36-117 14-87 (132)
149 PRK04184 DNA topoisomerase VI 24.6 55 0.0012 31.5 2.3 55 43-97 431-487 (535)
150 PRK14987 gluconate operon tran 24.3 46 0.001 27.9 1.6 39 32-75 16-54 (331)
151 PRK14971 DNA polymerase III su 24.2 1.5E+02 0.0032 28.8 5.2 64 33-97 180-244 (614)
152 cd00051 EFh EF-hand, calcium b 23.9 1.6E+02 0.0035 17.1 4.2 39 77-115 7-45 (63)
153 PRK06585 holA DNA polymerase I 23.5 1.9E+02 0.004 25.0 5.3 60 38-97 147-208 (343)
154 PF00403 HMA: Heavy-metal-asso 22.7 55 0.0012 21.0 1.4 16 87-102 47-62 (62)
155 cd00052 EH Eps15 homology doma 22.2 2E+02 0.0043 18.0 4.0 25 77-101 6-30 (67)
156 PF12668 DUF3791: Protein of u 21.7 93 0.002 20.9 2.4 30 83-112 13-42 (62)
157 PTZ00184 calmodulin; Provision 21.6 2.3E+02 0.005 20.3 4.7 40 74-113 88-127 (149)
158 PRK10727 DNA-binding transcrip 21.5 58 0.0013 27.5 1.6 39 33-76 13-51 (343)
159 PRK09492 treR trehalose repres 21.4 73 0.0016 26.4 2.2 38 32-74 15-52 (315)
160 TIGR01481 ccpA catabolite cont 21.1 89 0.0019 26.0 2.7 38 32-74 12-49 (329)
161 PF14644 DUF4456: Domain of un 20.1 1.7E+02 0.0038 24.2 4.2 43 52-95 149-191 (208)
162 CHL00076 chlB photochlorophyll 20.1 2E+02 0.0044 27.1 5.1 51 49-100 461-512 (513)
No 1
>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [Transcription]
Probab=100.00 E-value=1.2e-41 Score=273.24 Aligned_cols=119 Identities=71% Similarity=1.140 Sum_probs=106.8
Q ss_pred CCCCCCCCCCCCCCCCCCCCC-CCCCCCcccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 030714 1 MAEAPTSPAGGSHESGGEQSP-HAGGVREQDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKC 79 (173)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~-~~~~~~e~D~~LP~A~I~RImK~~LP~~~rISkDA~~al~~ca~eFI~~LtseA~d~c 79 (173)
|++++..+ ++.|+.++.+.+ .+..++++|++||+|||.||||+.||.+++|+||||+.+|+|++|||+|||+||+++|
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 56665555 456666655444 3457999999999999999999999999999999999999999999999999999999
Q ss_pred HhcCCCCcCchhhHHHHHhcCCcchhhHHHHHHHHHHcccc
Q 030714 80 QKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLMRYREGDT 120 (173)
Q Consensus 80 ~~~kRKTIs~eDVl~AL~~LgF~~yv~~Lk~~L~~yre~~~ 120 (173)
.+++||||++|||||||.+|||++|+++|+.||.+|||.+.
T Consensus 80 ~~EkRKTIngdDllwAm~tLGFe~Y~eplkiyL~kYRe~e~ 120 (168)
T KOG0869|consen 80 QREKRKTINGDDLLWAMSTLGFENYAEPLKIYLQKYRELEG 120 (168)
T ss_pred HHHhcCcccHHHHHHHHHHcCcHhHHHHHHHHHHHHHHHhh
Confidence 99999999999999999999999999999999999998643
No 2
>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=99.96 E-value=1.2e-29 Score=202.29 Aligned_cols=111 Identities=32% Similarity=0.572 Sum_probs=103.6
Q ss_pred CCcccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCcchh
Q 030714 26 VREQDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYI 105 (173)
Q Consensus 26 ~~e~D~~LP~A~I~RImK~~LP~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~~LgF~~yv 105 (173)
...+|+.||+|+|.+|||+.||.+++|.+||+++|++||.+||++|+++||++|.++.||||++|||++||+.|||.+|+
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 46789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHHHcccccCCCCCCCCCccccccCCCC
Q 030714 106 DPLKAYLMRYREGDTKGSARGGDGSAKRDTIGALP 140 (173)
Q Consensus 106 ~~Lk~~L~~yre~~~~~s~k~~~~~~~~~~~~~~~ 140 (173)
+.+...|+.|++...+. +++++|.+.+|++.
T Consensus 86 ee~~~vl~~~K~~~~~~----~~kssk~e~~Gi~e 116 (156)
T KOG0871|consen 86 EEAEEVLENCKEEAKKR----RRKSSKFEKSGIPE 116 (156)
T ss_pred HHHHHHHHHHHHHHHHh----hhhhhhHHhcCCCH
Confidence 99999999999876543 56688888899873
No 3
>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription]
Probab=99.91 E-value=1.4e-24 Score=175.76 Aligned_cols=94 Identities=34% Similarity=0.591 Sum_probs=90.4
Q ss_pred CCCcccccCchhHHHHHHHhhCCCC-CcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCcc
Q 030714 25 GVREQDRYLPIANISRIMKKALPAN-GKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFED 103 (173)
Q Consensus 25 ~~~e~D~~LP~A~I~RImK~~LP~~-~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~~LgF~~ 103 (173)
..+.+|+.||+|+|.||+|++||.. +.|+|||+.+|+++|++||+||++.|+++|+.++||||+++||+.||++++|..
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 4578999999999999999999986 899999999999999999999999999999999999999999999999999999
Q ss_pred hhhHHHHHHHHHHcc
Q 030714 104 YIDPLKAYLMRYREG 118 (173)
Q Consensus 104 yv~~Lk~~L~~yre~ 118 (173)
|+.+|+..|+.|+-.
T Consensus 83 f~~plk~~Le~yk~~ 97 (172)
T KOG0870|consen 83 FVNPLKSALEAYKKA 97 (172)
T ss_pred HhhHHHHHHHHHHHH
Confidence 999999999999943
No 4
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=99.88 E-value=8.1e-23 Score=160.27 Aligned_cols=100 Identities=25% Similarity=0.493 Sum_probs=94.1
Q ss_pred CCcccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCcchh
Q 030714 26 VREQDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYI 105 (173)
Q Consensus 26 ~~e~D~~LP~A~I~RImK~~LP~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~~LgF~~yv 105 (173)
...+++.||+|+|.+.+.+.||.+..++|||++.+++||.+||+.|+++||+.|.++.+|||.++||++||+.|+|.+|+
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 45688999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHHHcccccCCCC
Q 030714 106 DPLKAYLMRYREGDTKGSAR 125 (173)
Q Consensus 106 ~~Lk~~L~~yre~~~~~s~k 125 (173)
+.+.+.+..|++.++.+.+|
T Consensus 85 ~~~~e~~~n~k~~qK~ke~k 104 (148)
T COG5150 85 ESCMEEHENYKSYQKQKESK 104 (148)
T ss_pred HHHHHHHHHHHHHHhhchhh
Confidence 99999999999887655433
No 5
>PF00808 CBFD_NFYB_HMF: Histone-like transcription factor (CBF/NF-Y) and archaeal histone; InterPro: IPR003958 The CCAAT-binding factor (CBF) is a mammalian transcription factor that binds to a CCAAT motif in the promoters of a wide variety of genes, including type I collagen and albumin. The factor is a heteromeric complex of A and B subunits, both of which are required for DNA-binding [, ]. The subunits can interact in the absence of DNA-binding, conserved regions in each being important in mediating this interaction. The A subunit can be split into 3 domains on the basis of sequence similarity, a non-conserved N-terminal 'A domain'; a highly-conserved central 'B domain' involved in DNA-binding; and a C-terminal 'C domain', which contains a number of glutamine and acidic residues involved in protein-protein interactions []. The A subunit shows striking similarity to the HAP3 subunit of the yeast CCAAT-binding heterotrimeric transcription factor [, ]. The Kluyveromyces lactis HAP3 protein has been predicted to contain a 4-cysteine zinc finger, which is thought to be present in similar HAP3 and CBF subunit A proteins, in which the third cysteine is replaced by a serine []. This domain is found in the CCAAT transcription factor and archaeal histones.; GO: 0043565 sequence-specific DNA binding, 0005622 intracellular; PDB: 1F1E_A 2BYM_D 2BYK_D 1HTA_A 1B67_A 1JFI_B 1KU5_B 1N1J_A 1BFM_A 1B6W_A ....
Probab=99.78 E-value=7.1e-19 Score=121.07 Aligned_cols=64 Identities=36% Similarity=0.624 Sum_probs=59.2
Q ss_pred cCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHH
Q 030714 32 YLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAM 96 (173)
Q Consensus 32 ~LP~A~I~RImK~~LP~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL 96 (173)
.||++.|.||||.. |++.+||+||.++|++|+++||.||+.+|++.|.+++||||+++||..||
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 87889999999999999999999999999999999999999999999986
No 6
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=99.71 E-value=1.2e-17 Score=124.16 Aligned_cols=79 Identities=30% Similarity=0.465 Sum_probs=75.1
Q ss_pred CCCcccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCcch
Q 030714 25 GVREQDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDY 104 (173)
Q Consensus 25 ~~~e~D~~LP~A~I~RImK~~LP~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~~LgF~~y 104 (173)
..+..|..||+++|.||||+..++ |||.+|+++|++|+++|+..|+..|++.|.++|||||+++||..|++.+||..|
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 467889999999999999999985 999999999999999999999999999999999999999999999999999866
Q ss_pred h
Q 030714 105 I 105 (173)
Q Consensus 105 v 105 (173)
.
T Consensus 90 ~ 90 (91)
T COG2036 90 G 90 (91)
T ss_pred c
Confidence 4
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=99.22 E-value=5.7e-11 Score=87.45 Aligned_cols=72 Identities=19% Similarity=0.337 Sum_probs=66.8
Q ss_pred ccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCcch
Q 030714 31 RYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDY 104 (173)
Q Consensus 31 ~~LP~A~I~RImK~~LP~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~~LgF~~y 104 (173)
-.||++.|.||+|... ..+||.|+.+.+.++.++|+..|..+|...|++.+||||+++||..||+..|-.-|
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 46899999999999999999999999999999999999999999999999986544
No 8
>PLN00035 histone H4; Provisional
Probab=99.18 E-value=1.1e-10 Score=88.74 Aligned_cols=76 Identities=16% Similarity=0.253 Sum_probs=68.6
Q ss_pred CCcccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCcc
Q 030714 26 VREQDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFED 103 (173)
Q Consensus 26 ~~e~D~~LP~A~I~RImK~~LP~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~~LgF~~ 103 (173)
.++....||++.|.||++... ..+||.|+.+.+.+..++|+..|..+|...|++.+||||+++||..||+..|=.-
T Consensus 23 ~~d~i~~ipk~~IrRLARr~G--vkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr~g~~l 98 (103)
T PLN00035 23 LRDNIQGITKPAIRRLARRGG--VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTL 98 (103)
T ss_pred HHhhhccCCHHHHHHHHHHcC--cccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHcCCcC
Confidence 344455699999999999996 4699999999999999999999999999999999999999999999999877543
No 9
>PTZ00015 histone H4; Provisional
Probab=99.12 E-value=3.2e-10 Score=86.12 Aligned_cols=77 Identities=19% Similarity=0.359 Sum_probs=69.8
Q ss_pred CCcccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCcch
Q 030714 26 VREQDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDY 104 (173)
Q Consensus 26 ~~e~D~~LP~A~I~RImK~~LP~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~~LgF~~y 104 (173)
.++....||++.|.||+|...- .|||.|+.+.+.++.++|+..|..+|...|++.+||||+++||..||+..|-.-|
T Consensus 24 ~r~~i~gI~k~~IrRLarr~Gv--kRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~AlKr~g~~~y 100 (102)
T PTZ00015 24 LRDNIRGITKGAIRRLARRGGV--KRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALKRQGRTLY 100 (102)
T ss_pred HhhcccCCCHHHHHHHHHHcCC--ccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhcCCCCC
Confidence 3455667999999999999964 6899999999999999999999999999999999999999999999998886443
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=98.97 E-value=2.4e-09 Score=74.95 Aligned_cols=64 Identities=25% Similarity=0.281 Sum_probs=60.4
Q ss_pred cCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHH
Q 030714 32 YLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (173)
Q Consensus 32 ~LP~A~I~RImK~~LP~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~ 97 (173)
.||+++|.||++...- .+||.|+...|.+-++.|+.-|..+|...+++.+||||+++||-.||+
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 5899999999999864 479999999999999999999999999999999999999999999984
No 11
>smart00428 H3 Histone H3.
Probab=98.95 E-value=2.3e-09 Score=81.76 Aligned_cols=74 Identities=16% Similarity=0.170 Sum_probs=67.1
Q ss_pred CCcccccCchhHHHHHHHhhCCC-----CCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhc
Q 030714 26 VREQDRYLPIANISRIMKKALPA-----NGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATL 99 (173)
Q Consensus 26 ~~e~D~~LP~A~I~RImK~~LP~-----~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~~L 99 (173)
....++.+|+..+.|++++...+ +.+|+.+|+.+||++++.|+.-+...|+..+.+.||+||.++|+..|..-.
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 45678999999999999998754 679999999999999999999999999999999999999999998886533
No 12
>smart00417 H4 Histone H4.
Probab=98.93 E-value=2.1e-09 Score=77.43 Aligned_cols=64 Identities=17% Similarity=0.289 Sum_probs=59.2
Q ss_pred cccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHH
Q 030714 30 DRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWA 95 (173)
Q Consensus 30 D~~LP~A~I~RImK~~LP~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~A 95 (173)
-..||++.|.||+|...- -+||.++.+.+.+..++|+..|..+|...|++.+||||+++||..|
T Consensus 11 i~gI~k~~IrRLaRr~Gv--kRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~~a 74 (74)
T smart00417 11 IQGITKPAIRRLARRGGV--KRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVYA 74 (74)
T ss_pred hcCCCHHHHHHHHHHcCc--chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHheeC
Confidence 346999999999999964 6899999999999999999999999999999999999999999753
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=98.90 E-value=9.7e-09 Score=72.75 Aligned_cols=65 Identities=15% Similarity=0.324 Sum_probs=61.4
Q ss_pred CchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHh
Q 030714 33 LPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMAT 98 (173)
Q Consensus 33 LP~A~I~RImK~~LP~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~~ 98 (173)
|++..+..++|+.-| ..+|+.||.++|++.+.+|+.-++..|...|++.||+||..+||..+|++
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 677889999999977 68999999999999999999999999999999999999999999999975
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=98.88 E-value=4.8e-09 Score=73.18 Aligned_cols=68 Identities=25% Similarity=0.331 Sum_probs=62.3
Q ss_pred cccCchhHHHHHHHhhCCC---CCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHH
Q 030714 30 DRYLPIANISRIMKKALPA---NGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (173)
Q Consensus 30 D~~LP~A~I~RImK~~LP~---~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~ 97 (173)
+..+|+..|.|+.|+..++ ..+|+++|..+|+..++.|+.-|..+|...|.+.||+||+++||..|+.
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 4568899999999988774 2699999999999999999999999999999999999999999999985
No 15
>PLN00121 histone H3; Provisional
Probab=98.60 E-value=8.7e-08 Score=76.15 Aligned_cols=71 Identities=14% Similarity=0.165 Sum_probs=65.5
Q ss_pred CcccccCchhHHHHHHHhhCCC---CCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHH
Q 030714 27 REQDRYLPIANISRIMKKALPA---NGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (173)
Q Consensus 27 ~e~D~~LP~A~I~RImK~~LP~---~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~ 97 (173)
...|+.||+..+.|++++...+ +.+++.+|.++||++++.|+..|...++-.+.+.||.||.+.|+..++.
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 4468999999999999998754 7899999999999999999999999999999999999999999987764
No 16
>PLN00161 histone H3; Provisional
Probab=98.60 E-value=1.8e-07 Score=74.23 Aligned_cols=71 Identities=15% Similarity=0.186 Sum_probs=65.1
Q ss_pred CcccccCchhHHHHHHHhhCC----CCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHH
Q 030714 27 REQDRYLPIANISRIMKKALP----ANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (173)
Q Consensus 27 ~e~D~~LP~A~I~RImK~~LP----~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~ 97 (173)
...++.+|+..+.|++++... .+.+++.+|.++||++++.|+.-|...|+-.|.+.||.||.+.|+..|..
T Consensus 50 kst~lLIpklPF~RLVREI~~~~~~~~~Rfq~~Al~ALQEAsEayLV~lFeda~lcaiHAkRVTlm~kDm~La~r 124 (135)
T PLN00161 50 KSTELLIRKLPFARLVREISNEMLREPFRWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMPKDMQLARR 124 (135)
T ss_pred cccccccccccHHHHHHHHHHhcCCCCcEeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccchhhHHHHHH
Confidence 557889999999999999853 36899999999999999999999999999999999999999999988764
No 17
>PLN00160 histone H3; Provisional
Probab=98.60 E-value=1.4e-07 Score=71.15 Aligned_cols=72 Identities=15% Similarity=0.102 Sum_probs=65.4
Q ss_pred CCcccccCchhHHHHHHHhhCC----CCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHH
Q 030714 26 VREQDRYLPIANISRIMKKALP----ANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (173)
Q Consensus 26 ~~e~D~~LP~A~I~RImK~~LP----~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~ 97 (173)
....++.+|++.+.|++++... .+.+++.+|..+||++++.|+.-+...++-.|.+.||.||.+.|+.-|..
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 3457899999999999999864 35899999999999999999999999999999999999999999988764
No 18
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=98.56 E-value=5.8e-08 Score=83.01 Aligned_cols=77 Identities=26% Similarity=0.343 Sum_probs=69.2
Q ss_pred ccccCchhHHHHHHHhhCCCCCc-ccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCcchhhH
Q 030714 29 QDRYLPIANISRIMKKALPANGK-IAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYIDP 107 (173)
Q Consensus 29 ~D~~LP~A~I~RImK~~LP~~~r-ISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~~LgF~~yv~~ 107 (173)
.+..||+|.|+|+||..- ++| ||.||-.++.+.|+.||..||..|.-.+++++|+|+--.||..|+++-+..+|+-.
T Consensus 106 k~h~LPlARIkkvMKtde--dVkMisaEaPvlFak~~EiFI~ELTmRAW~~ae~NkRRtLQksDia~Av~kSeMfDFLid 183 (286)
T COG5208 106 KDHNLPLARIKKVMKTDE--DVKMISAEAPVLFAKITEIFIEELTMRAWINAEENKRRTLQKSDIAAAVKKSEMFDFLID 183 (286)
T ss_pred HhccCcHHHHHHHHhccc--chhheecccchHHHHHHHHHHHHHHHHHHHHHhHhhhhHHHHHHHHHHHHHHHHHhHHhh
Confidence 456799999999999664 454 99999999999999999999999999999999999999999999998887776544
No 19
>KOG1657 consensus CCAAT-binding factor, subunit C (HAP5) [Transcription]
Probab=98.56 E-value=1.2e-07 Score=81.09 Aligned_cols=87 Identities=26% Similarity=0.345 Sum_probs=76.2
Q ss_pred cccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHH---hcCCcchhh
Q 030714 30 DRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA---TLGFEDYID 106 (173)
Q Consensus 30 D~~LP~A~I~RImK~~LP~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~---~LgF~~yv~ 106 (173)
...||++.|++|||..-. .-.|+.||..++.+||+.||..|+..|+..+...+|+|+...||..|+. ..+|.-.+-
T Consensus 72 ~~~lPlaRiKkimK~ded-v~mI~~Eapvl~aka~E~Fi~elt~~sw~~Tee~~rrtl~~sdia~av~~s~~fdFL~Div 150 (236)
T KOG1657|consen 72 NHILPLARIKKIMKSDED-VSMITAEAPVLFAKACELFITELTLRSWVHTEENKRRTLQKSDIAAAVTQSETFDFLRDIV 150 (236)
T ss_pred hccCcHhhcccccccccc-ccccchhHHHHHHHHHHHHHHHHHHHhhhhhcccccccchHHHHHHHhccCCCccceeccc
Confidence 457999999999997753 3369999999999999999999999999999999999999999999998 566777777
Q ss_pred HHHHHHHHHHc
Q 030714 107 PLKAYLMRYRE 117 (173)
Q Consensus 107 ~Lk~~L~~yre 117 (173)
+.+..+++|..
T Consensus 151 P~~~~~~~~~~ 161 (236)
T KOG1657|consen 151 PRKILAEKYPS 161 (236)
T ss_pred cchhccccccc
Confidence 88888888743
No 20
>PTZ00018 histone H3; Provisional
Probab=98.56 E-value=1.3e-07 Score=75.21 Aligned_cols=71 Identities=14% Similarity=0.169 Sum_probs=65.2
Q ss_pred CcccccCchhHHHHHHHhhCC---CCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHH
Q 030714 27 REQDRYLPIANISRIMKKALP---ANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (173)
Q Consensus 27 ~e~D~~LP~A~I~RImK~~LP---~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~ 97 (173)
...|+.||+..+.||+++... .+.+++.+|+++||++++.|+..|...++..|.+.||.||.+.|+..|..
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 456899999999999999864 36899999999999999999999999999999999999999999987764
No 21
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=98.42 E-value=1.6e-06 Score=61.82 Aligned_cols=66 Identities=18% Similarity=0.261 Sum_probs=59.5
Q ss_pred hhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCc
Q 030714 35 IANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFE 102 (173)
Q Consensus 35 ~A~I~RImK~~LP~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~~LgF~ 102 (173)
+-.|.+|+|...= -+++.+|+++|.+....|+..|+..+...|++.+|++++..||..||+++|+.
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 3457788887753 37999999999999999999999999999999999999999999999999974
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=98.34 E-value=1.4e-06 Score=67.37 Aligned_cols=69 Identities=17% Similarity=0.233 Sum_probs=62.7
Q ss_pred ccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHh
Q 030714 29 QDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMAT 98 (173)
Q Consensus 29 ~D~~LP~A~I~RImK~~LP~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~~ 98 (173)
..+.||.+.|.|+||+.-- ..||+.+|...|..+.+.+..-|...|...|+..+|++|+++||..|+..
T Consensus 17 agL~fPV~ri~R~Lk~~~~-a~RVs~~A~VyLaAvLEYL~aEIlelA~n~ak~~k~krItp~hi~lAi~n 85 (115)
T cd00074 17 AGLQFPVGRIHRYLKKGRY-AERVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKKRITPRHLQLAVRN 85 (115)
T ss_pred cCccCcHHHHHHHHHcCcc-ccccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEcHHHHHHHHhc
Confidence 3688999999999998432 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=98.08 E-value=2e-05 Score=60.73 Aligned_cols=78 Identities=14% Similarity=0.200 Sum_probs=65.9
Q ss_pred HHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCcchhh-HHHHHHHHH
Q 030714 37 NISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYID-PLKAYLMRY 115 (173)
Q Consensus 37 ~I~RImK~~LP~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~~LgF~~yv~-~Lk~~L~~y 115 (173)
.|.+|+|+.. ..+++.++...|.+.+..++.-|..+|...|++.+|+||+.+||.-|++...-..|.. +-+++|.+.
T Consensus 6 ~v~~iLk~~G--v~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r~~~~f~~~p~~~~l~~~ 83 (117)
T cd07979 6 VIAAILKSMG--ITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRVDYSFTSPPPRDFLLEL 83 (117)
T ss_pred HHHHHHHHCC--CCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhccCCCCCCcHHHHHHH
Confidence 5788888873 3589999999999999999999999999999999999999999999999665544444 466777655
Q ss_pred H
Q 030714 116 R 116 (173)
Q Consensus 116 r 116 (173)
-
T Consensus 84 a 84 (117)
T cd07979 84 A 84 (117)
T ss_pred H
Confidence 5
No 24
>KOG1745 consensus Histones H3 and H4 [Chromatin structure and dynamics]
Probab=97.91 E-value=7.6e-06 Score=65.20 Aligned_cols=75 Identities=16% Similarity=0.194 Sum_probs=66.0
Q ss_pred CCcccccCchhHHHHHHHhhCC---CCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcC
Q 030714 26 VREQDRYLPIANISRIMKKALP---ANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLG 100 (173)
Q Consensus 26 ~~e~D~~LP~A~I~RImK~~LP---~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~~Lg 100 (173)
.+..|+.+++....|++|+..+ .+.++...|+.+||++++.|+.-|.-.+|-.+.+.||.||.+.||--|..-.|
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 3457889999999999995543 47899999999999999999999999999999999999999999998876544
No 25
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=97.89 E-value=6.2e-05 Score=65.41 Aligned_cols=92 Identities=17% Similarity=0.298 Sum_probs=72.6
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCC--cccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 030714 5 PTSPAGGSHESGGEQSPHAGGVR--EQDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKE 82 (173)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~--e~D~~LP~A~I~RImK~~LP~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~ 82 (173)
|.-+.||+.+.|+..|+...... +.+..|=+-.|.-++++.-+ +.+|-+|+.++|.+.|..||..|+..|-..|++.
T Consensus 125 P~~~~~g~~~g~~~sp~~s~s~~~~~~~~il~k~kl~dLvqqId~-~~~LD~dVedlLleiADdFV~sii~~sC~LAKHR 203 (258)
T KOG1142|consen 125 PVIGSQGSVSGGGTSPAGSSSQDEPGNNPILSKRKLDDLVQQIDG-TTKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHR 203 (258)
T ss_pred CCCCCCCccCCCCCCCCcccccccCCCCccccccchhHHHHhhcC-cccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 33333455554444444333322 34556778889999999855 7899999999999999999999999999999999
Q ss_pred CCCCcCchhhHHHHH
Q 030714 83 KRKTINGDDLLWAMA 97 (173)
Q Consensus 83 kRKTIs~eDVl~AL~ 97 (173)
|..||-..||...|+
T Consensus 204 KsdtlEvrDIqLhLE 218 (258)
T KOG1142|consen 204 KSDTVEVRDIQLHLE 218 (258)
T ss_pred ccCccchhheeeeee
Confidence 999999999999998
No 26
>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=6.2e-05 Score=66.98 Aligned_cols=66 Identities=18% Similarity=0.188 Sum_probs=57.8
Q ss_pred chhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCC
Q 030714 34 PIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGF 101 (173)
Q Consensus 34 P~A~I~RImK~~LP~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~~LgF 101 (173)
|..+|.-|.+...- .++++||..+|.+.++.++..|..+|...+++.||||++.+||-.||+.++.
T Consensus 1 ~~~~i~~ia~~~Gi--~~~~~~a~~~La~~~e~~~~~i~~~A~k~~~hskR~~l~~~Di~~Al~~~n~ 66 (343)
T cd08050 1 PQESIKLIAESLGI--DSLSDEVAQLLAEDVEYRLREIIQEAAKFMRHSKRRKLTTSDVNHALRLRNV 66 (343)
T ss_pred ChhHHHHHHHHcCC--CcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHHhCC
Confidence 44567777776642 4899999999999999999999999999999999999999999999996554
No 27
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=97.85 E-value=6.6e-05 Score=54.25 Aligned_cols=62 Identities=15% Similarity=0.193 Sum_probs=52.5
Q ss_pred HHHHHHHhhC-CCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHh
Q 030714 37 NISRIMKKAL-PANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMAT 98 (173)
Q Consensus 37 ~I~RImK~~L-P~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~~ 98 (173)
.|.||+.+.. +.++.+++++..+|.+.+-.++..++..-.-.|++.||+||+.|||+-...+
T Consensus 10 ~v~ki~ee~~~~~~~~~s~~~i~al~ELv~~q~~~~a~DLe~FAkHA~R~tI~~dDV~Ll~Rr 72 (76)
T PF15630_consen 10 TVGKIVEEEAKEKGVEVSPQFIAALTELVYKQLENLAKDLEAFAKHAGRSTINMDDVKLLARR 72 (76)
T ss_dssp HHHHHHHHCCCCTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHTTT
T ss_pred HHHHHHHHHHhccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHHHhhc
Confidence 5788999885 4578899999999999999999999999999999999999999999977653
No 28
>PF15511 CENP-T: Centromere kinetochore component CENP-T; PDB: 3B0D_T 3B0C_T 3VH5_T 3VH6_T.
Probab=97.83 E-value=3.1e-05 Score=70.70 Aligned_cols=64 Identities=20% Similarity=0.280 Sum_probs=47.8
Q ss_pred cccccCchhHHHHHHHhhCC----CCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchh
Q 030714 28 EQDRYLPIANISRIMKKALP----ANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDD 91 (173)
Q Consensus 28 e~D~~LP~A~I~RImK~~LP----~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eD 91 (173)
..--.||.+.|+|++..... .+++|+|||..+|.+|...|...|+..-.-+|.|.|||||..+|
T Consensus 347 i~~P~lP~~~vK~la~~~ak~s~~sK~kiskdal~aleqasdwfFeQl~dDL~aYA~HAgRKTIdesD 414 (414)
T PF15511_consen 347 IPYPSLPPGVVKKLAQHFAKSSGGSKMKISKDALEALEQASDWFFEQLGDDLEAYAKHAGRKTIDESD 414 (414)
T ss_dssp -----S-HHHHHHHHHHHH-------S-B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHH
T ss_pred CCCCCCCccHHHHHHHHHHHhhcccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCCCC
Confidence 34456999999998887754 47899999999999999999999999999999999999999876
No 29
>smart00427 H2B Histone H2B.
Probab=97.79 E-value=0.00012 Score=54.67 Aligned_cols=62 Identities=21% Similarity=0.350 Sum_probs=57.6
Q ss_pred HHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhc
Q 030714 37 NISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATL 99 (173)
Q Consensus 37 ~I~RImK~~LP~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~~L 99 (173)
-|+|++|++-| +.-||..|...|.-.+..+..-|+.||...|.-.+|+||+..+|..|.+-+
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 568999999999999999999999999999999999999999999998644
No 30
>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=97.75 E-value=0.00013 Score=51.64 Aligned_cols=63 Identities=19% Similarity=0.306 Sum_probs=51.4
Q ss_pred hhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHh
Q 030714 35 IANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMAT 98 (173)
Q Consensus 35 ~A~I~RImK~~LP~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~~ 98 (173)
+..+..++++.-| +.++.+|+.++|.++|.+||.-++..|-..|++.+-.||...||.-.|++
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 3467888998866 78999999999999999999999999999999999999999999998874
No 31
>KOG1659 consensus Class 2 transcription repressor NC2, alpha subunit (DRAP1) [Transcription]
Probab=97.68 E-value=0.0001 Score=62.64 Aligned_cols=84 Identities=17% Similarity=0.214 Sum_probs=71.0
Q ss_pred ccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCcchhhHHHH
Q 030714 31 RYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKA 110 (173)
Q Consensus 31 ~~LP~A~I~RImK~~LP~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~~LgF~~yv~~Lk~ 110 (173)
-.||.+.|.|||...-. -.||+.-+-..+.++.+.|+.-|-..+.++++..+-|||+++|+..++..-.-.+|+..+-.
T Consensus 12 trfp~aRiKKIMQ~dEd-IGKvaqavPViisralElFl~~l~~~t~~~t~~~~aKt~s~~hlkq~v~~~~~FdFLk~~v~ 90 (224)
T KOG1659|consen 12 TRFPPARIKKIMQSDED-IGKVAQAVPVIISRALELFLESLLQKTLEITRSRGAKTVSSSHLKQAVESDPKFDFLKEVVE 90 (224)
T ss_pred ccCCHHHHHHHHhhhhh-hhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhcCccccCHHHHHHHHhccchhHHHHHHHH
Confidence 35899999999997654 45899999999999999999999999999999999999999999999987766677665444
Q ss_pred HHHHH
Q 030714 111 YLMRY 115 (173)
Q Consensus 111 ~L~~y 115 (173)
.+..+
T Consensus 91 ~vpd~ 95 (224)
T KOG1659|consen 91 KVPDR 95 (224)
T ss_pred hcCCC
Confidence 44333
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=97.61 E-value=0.00051 Score=48.51 Aligned_cols=64 Identities=19% Similarity=0.270 Sum_probs=56.0
Q ss_pred HHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCc
Q 030714 37 NISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFE 102 (173)
Q Consensus 37 ~I~RImK~~LP~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~~LgF~ 102 (173)
.|.+|++...= -.++..|.+.|.+.+..||..|+..+...|...+|...+..||..||+++|+.
T Consensus 11 ~va~il~~~GF--~~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~~~gi~ 74 (77)
T PF07524_consen 11 SVAQILKHAGF--DSASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPNLQDVEQALEEMGIS 74 (77)
T ss_pred HHHHHHHHcCc--cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCC
Confidence 45556655431 26999999999999999999999999999999999999999999999999984
No 33
>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=97.58 E-value=0.00048 Score=50.67 Aligned_cols=66 Identities=20% Similarity=0.211 Sum_probs=61.3
Q ss_pred cCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC---CCcCchhhHHHHHhc
Q 030714 32 YLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKR---KTINGDDLLWAMATL 99 (173)
Q Consensus 32 ~LP~A~I~RImK~~LP~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kR---KTIs~eDVl~AL~~L 99 (173)
.||++.|.|||...++ ..++.+...+|.-.+.+||--|.-+|.++..+.+. .-|.|+||-+|...|
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 4999999999999997 68999999999999999999999999999988775 789999999999876
No 34
>PLN00158 histone H2B; Provisional
Probab=97.56 E-value=0.00037 Score=54.24 Aligned_cols=64 Identities=17% Similarity=0.310 Sum_probs=58.7
Q ss_pred hhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhc
Q 030714 35 IANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATL 99 (173)
Q Consensus 35 ~A~I~RImK~~LP~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~~L 99 (173)
..-|+|++|++-| +..||..+...|.-.+..+..-|+.||...|.-.+|+||+..+|..|.+-+
T Consensus 30 ~~YI~kVLKQVhP-d~gIS~kaM~ImnSfvnDiferIA~EAs~La~~nkr~TltsrEIqtAvrLv 93 (116)
T PLN00158 30 KIYIYKVLKQVHP-DTGISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVRLI 93 (116)
T ss_pred HHHHHHHHHHhCC-CCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHh
Confidence 4459999999999 578999999999999999999999999999999999999999999998643
No 35
>KOG3467 consensus Histone H4 [Chromatin structure and dynamics]
Probab=97.55 E-value=0.00035 Score=52.47 Aligned_cols=69 Identities=17% Similarity=0.268 Sum_probs=61.4
Q ss_pred cCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCc
Q 030714 32 YLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFE 102 (173)
Q Consensus 32 ~LP~A~I~RImK~~LP~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~~LgF~ 102 (173)
-+-+-+|.||.+... .-+|+----+.+...+.+||..+-+.|...+++.+||||++-||+-+|++.|.-
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 356778999999875 357888888889999999999999999999999999999999999999998864
No 36
>PTZ00463 histone H2B; Provisional
Probab=97.52 E-value=0.00045 Score=53.84 Aligned_cols=62 Identities=19% Similarity=0.386 Sum_probs=57.4
Q ss_pred HHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhc
Q 030714 37 NISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATL 99 (173)
Q Consensus 37 ~I~RImK~~LP~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~~L 99 (173)
-|+|++|++-| +.-||..|...|.-.+.....-|+.||...|.-.+|+||+..+|..|.+-+
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 39999999999 578999999999999999999999999999999999999999999998643
No 37
>PF09415 CENP-X: CENP-S associating Centromere protein X; InterPro: IPR018552 Centromere protein X (CENP-X) is a component of the CENP-S complex. The CENP-S complex is composed of at least of CENP-S and CENP-X and is essential for the stable assembly of the outer kinetchore []. CENP-X is also a DNA-binding component of the Fanconi anemia (FA) core complex involved in DNA damage repair and genome maintenance. The FA complex is composed of CENPS, FANCA, FANCB, FANCC, FANCE, FANCF, FANCG, FANCL/PHF9, FANCM, FAAP24 and CENPX. Interacts with CENPS, FANCM and FAAP24 [, ].; PDB: 4DRB_L 4DRA_H 3V9R_D.
Probab=97.42 E-value=0.00022 Score=51.01 Aligned_cols=65 Identities=20% Similarity=0.297 Sum_probs=53.9
Q ss_pred chhHHHHHHHhhCC-CCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCC-cCchhhHHHHHh
Q 030714 34 PIANISRIMKKALP-ANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKT-INGDDLLWAMAT 98 (173)
Q Consensus 34 P~A~I~RImK~~LP-~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKT-Is~eDVl~AL~~ 98 (173)
|..+|.||++.... ++.+|++||..++.+....||.--...|.+.++.++..+ |..+|+-+.+-.
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 78899999997774 578999999999999999999999999999999999888 999999876543
No 38
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=97.32 E-value=0.00047 Score=54.14 Aligned_cols=68 Identities=19% Similarity=0.239 Sum_probs=61.0
Q ss_pred ccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHH
Q 030714 29 QDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (173)
Q Consensus 29 ~D~~LP~A~I~RImK~~LP~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~ 97 (173)
.-+.+|...|.||||..- -.+||+++|...+.-|.+-.+..|+..|-..|+..++|.|.|.|+-.|+.
T Consensus 23 agl~fpvgrvkr~lk~~~-~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~kkkri~PrHlqlAIr 90 (132)
T COG5262 23 AGLIFPVGRVKRLLKKGN-YRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRIIPRHLQLAIR 90 (132)
T ss_pred cCccccHHHHHHHHHcCc-cceeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhcCcceechHHHHHHhc
Confidence 567899999999999443 36899999999999999988888888899999999999999999999986
No 39
>PF04719 TAFII28: hTAFII28-like protein conserved region; InterPro: IPR006809 The general transcription factor, TFIID, consists of the TATA-binding protein (TBP) associated with a series of TBP-associated factors (TAFs) that together participate in the assembly of the transcription preinitiation complex. The conserved region is found at the C terminus of most member proteins. The crystal structure of hTAFII28 with hTAFII18 shows that this region is involved in the binding of these two subunits. The conserved region contains four alpha helices and three loops arranged as in histone H3 [, ].; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005634 nucleus; PDB: 1BH9_B 1BH8_B.
Probab=97.26 E-value=0.0013 Score=49.12 Aligned_cols=67 Identities=21% Similarity=0.229 Sum_probs=52.3
Q ss_pred cCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC-CCcCchhhHHHHHhc
Q 030714 32 YLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKR-KTINGDDLLWAMATL 99 (173)
Q Consensus 32 ~LP~A~I~RImK~~LP~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kR-KTIs~eDVl~AL~~L 99 (173)
.||++.|.|||...+. +..|+.....+|.-.+..||--|-.+|.+++.+.+. .-|.|+|+-+|..+|
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 4999999999999996 578999999999999999999999999999987653 379999999998765
No 40
>COG5247 BUR6 Class 2 transcription repressor NC2, alpha subunit (DRAP1 homolog) [Transcription]
Probab=97.20 E-value=0.0016 Score=49.98 Aligned_cols=80 Identities=18% Similarity=0.274 Sum_probs=67.2
Q ss_pred ccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCcchhhHH
Q 030714 29 QDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPL 108 (173)
Q Consensus 29 ~D~~LP~A~I~RImK~~LP~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~~LgF~~yv~~L 108 (173)
--..+|+|.|.|||.-.-+ -.+|+.-.-....++.+.|+..|-.++.+.++..+-|.|+.+++..|.+.-.=-+|...+
T Consensus 20 ~ktrFP~ar~KkIMQ~deD-iGKV~q~tPVIaskalE~Fl~~iv~~s~k~aR~~~skR~t~e~lk~a~~sdekFdFL~~~ 98 (113)
T COG5247 20 KKTRFPIARLKKIMQLDED-IGKVGQSTPVIASKALEMFLTEIVGLSLKEARKKSSKRMTSEFLKRATESDEKFDFLKNM 98 (113)
T ss_pred hhhcCCHHHHHHHHHhhhh-hhhhhhcchHHHHHHHHHHHHHHHHHHHHHHHhccchhhHHHHHHHHHhhhHHHHHHHHH
Confidence 3457999999999986643 458999999999999999999999999999999999999999999998865555555444
Q ss_pred H
Q 030714 109 K 109 (173)
Q Consensus 109 k 109 (173)
.
T Consensus 99 ~ 99 (113)
T COG5247 99 E 99 (113)
T ss_pred H
Confidence 3
No 41
>smart00414 H2A Histone 2A.
Probab=97.10 E-value=0.0016 Score=49.77 Aligned_cols=68 Identities=15% Similarity=0.257 Sum_probs=59.7
Q ss_pred cccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHh
Q 030714 30 DRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMAT 98 (173)
Q Consensus 30 D~~LP~A~I~RImK~~LP~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~~ 98 (173)
.+.||.+.|.|+||+.-- ..||+..|...|.-|.+=+...|-..|...|...+++.|+++||..|+..
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 35999999999999888888888888888899999999999999999864
No 42
>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=96.93 E-value=0.0063 Score=42.93 Aligned_cols=64 Identities=19% Similarity=0.204 Sum_probs=48.7
Q ss_pred cCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHH
Q 030714 32 YLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (173)
Q Consensus 32 ~LP~A~I~RImK~~LP~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~ 97 (173)
.+|..+|.-+.... . -..++.|+..+|.+=++--|..|..+|....++.+|++++.+||-.||+
T Consensus 3 ~~~~esvk~iAes~-G-i~~l~de~a~~La~dveyrlreiiq~a~kfm~hskR~~Lt~~Di~~ALr 66 (66)
T PF02969_consen 3 VFSQESVKDIAESL-G-ISNLSDEAAKALAEDVEYRLREIIQEALKFMRHSKRTKLTTDDINSALR 66 (66)
T ss_dssp ---HHHHHHHHHHT-T----B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH-
T ss_pred cCCHHHHHHHHHHc-C-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhC
Confidence 35677776665554 3 2369999999999999999999999999999999999999999999985
No 43
>KOG1658 consensus DNA polymerase epsilon, subunit C [Replication, recombination and repair]
Probab=96.87 E-value=0.00066 Score=55.34 Aligned_cols=65 Identities=26% Similarity=0.328 Sum_probs=56.9
Q ss_pred ccCchhHHHHHHHhhCCCCCc-ccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHH
Q 030714 31 RYLPIANISRIMKKALPANGK-IAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (173)
Q Consensus 31 ~~LP~A~I~RImK~~LP~~~r-ISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~ 97 (173)
..||++.|..+|| ++++++ ..+|++.++.+++..||.+|...++..+...+|||+.-.|+=.|++
T Consensus 58 ~rLpL~rik~vvk--l~pdl~l~~dea~~l~a~aaelfi~~Ln~~~~~~~q~~k~kt~qr~d~D~ai~ 123 (162)
T KOG1658|consen 58 SRLPLARIKQVVK--LDPDLTLLNDEASQLIAKAAELFIQELNDVAYTTAQLRKRKTEQRRDYDTAIE 123 (162)
T ss_pred hhccHHHHHhhcc--CCcchhhhhhHHHHHHHHHHHHHHHHHHhccchhHHHHHhhhhhhhccccccc
Confidence 5799999999999 666776 5677899999999999999999999999999999998887766654
No 44
>PLN00154 histone H2A; Provisional
Probab=96.81 E-value=0.0036 Score=50.00 Aligned_cols=69 Identities=19% Similarity=0.250 Sum_probs=58.1
Q ss_pred ccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHH
Q 030714 29 QDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (173)
Q Consensus 29 ~D~~LP~A~I~RImK~~LP~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~ 97 (173)
-.+.||.+.|.|++|+..--..||+..|...|.-+.+=+..-|...|-..|+..+++-|++.||..|+.
T Consensus 35 AgL~FPVgRi~r~Lk~g~~~~~RVga~ApVYLAAVLEYLtAEVLELAGNaA~d~kk~RItPrHi~lAIr 103 (136)
T PLN00154 35 AGLQFPVGRIHRQLKQRVSAHGRVGATAAVYTAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 103 (136)
T ss_pred cCccCchHHHHHHHHhhhhhccccccchHHHHHHHHHHHHHHHHHHHHHHHHhhCCceecHHHhhhhcc
Confidence 468899999999999986434699999998888877666666666677888999999999999999985
No 45
>PTZ00017 histone H2A; Provisional
Probab=96.67 E-value=0.0039 Score=49.64 Aligned_cols=68 Identities=15% Similarity=0.226 Sum_probs=60.1
Q ss_pred ccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHH
Q 030714 29 QDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (173)
Q Consensus 29 ~D~~LP~A~I~RImK~~LP~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~ 97 (173)
-.+.||.+.|.|++|+.-- ..||+..|...|.-+.+-+..-|-..|...|...+++-|+++||..|+.
T Consensus 24 agL~FPVgRi~R~Lk~g~~-a~RV~a~A~VYLAAVLEYLtaEILELAgNaa~d~kk~RItPrHi~lAI~ 91 (134)
T PTZ00017 24 AGLQFPVGRVHRYLKKGRY-AKRVGAGAPVYLAAVLEYLTAEVLELAGNAAKDNKKKRITPRHIQLAIR 91 (134)
T ss_pred CCcccchHHHHHHHhccch-hccccccchhhhHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHhhcc
Confidence 4688999999999998643 3599999999999998888888888888899999999999999999985
No 46
>PF15510 CENP-W: Centromere kinetochore component W
Probab=96.65 E-value=0.0034 Score=47.41 Aligned_cols=67 Identities=21% Similarity=0.255 Sum_probs=55.9
Q ss_pred ccCchhHHHHHHHhhCCCCCcccHHHHHH--------------HHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHH
Q 030714 31 RYLPIANISRIMKKALPANGKIAKDAKDT--------------VQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAM 96 (173)
Q Consensus 31 ~~LP~A~I~RImK~~LP~~~rISkDA~~a--------------l~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL 96 (173)
+.-|++.+.|++|..-| ..++....-.+ +.--|-.||+-|+-||...|=+++-.||..|||+.|-
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 45799999999998887 56766655444 5667889999999999988888999999999999986
Q ss_pred Hh
Q 030714 97 AT 98 (173)
Q Consensus 97 ~~ 98 (173)
+.
T Consensus 94 Kv 95 (102)
T PF15510_consen 94 KV 95 (102)
T ss_pred HH
Confidence 53
No 47
>KOG1744 consensus Histone H2B [Chromatin structure and dynamics]
Probab=96.44 E-value=0.012 Score=46.65 Aligned_cols=60 Identities=23% Similarity=0.325 Sum_probs=55.8
Q ss_pred HHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHh
Q 030714 38 ISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMAT 98 (173)
Q Consensus 38 I~RImK~~LP~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~~ 98 (173)
|+|++|++-|+ .-|+.++...|.-...+|+-.|+.+|+..+.-.+|.||+..+|..|..-
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 67799999996 6799999999999999999999999999999999999999999998753
No 48
>PLN00157 histone H2A; Provisional
Probab=96.34 E-value=0.0076 Score=47.93 Aligned_cols=68 Identities=13% Similarity=0.186 Sum_probs=58.8
Q ss_pred ccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHH
Q 030714 29 QDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (173)
Q Consensus 29 ~D~~LP~A~I~RImK~~LP~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~ 97 (173)
-.+.||...|.|++|+.-- ..||+..|...|.-+.+-++.-|-..|...|...+++-|+++||..|+.
T Consensus 23 agL~FPVgRi~R~Lk~g~~-a~RIg~~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~ 90 (132)
T PLN00157 23 AGLQFPVGRIARYLKAGKY-ATRVGAGAPVYLAAVLEYLAAEVLELAGNAARDNKKSRIVPRHIQLAVR 90 (132)
T ss_pred cCcccchHHHHHHHhcCch-hhhcCCCcHhHHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHhhccc
Confidence 3688999999999999643 3599999999999888777777777788889999999999999999985
No 49
>PLN00153 histone H2A; Provisional
Probab=96.30 E-value=0.0092 Score=47.29 Aligned_cols=68 Identities=16% Similarity=0.218 Sum_probs=59.3
Q ss_pred ccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHH
Q 030714 29 QDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (173)
Q Consensus 29 ~D~~LP~A~I~RImK~~LP~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~ 97 (173)
-.+.||...|.|++|+.-- ..||+..|...|.-+.+-.+.-|...|...|...+++-|+++||..|+.
T Consensus 21 agL~FpVgRi~R~Lr~g~~-a~Rvga~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~ 88 (129)
T PLN00153 21 AGLQFPVGRIARYLKKGKY-AERIGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKNRIVPRHIQLAIR 88 (129)
T ss_pred cCcccchHHHHHHHhcCch-hhccCCCchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHhhcc
Confidence 4688999999999998654 3599999999999888877777777788889999999999999999985
No 50
>PLN00156 histone H2AX; Provisional
Probab=96.26 E-value=0.011 Score=47.43 Aligned_cols=68 Identities=13% Similarity=0.201 Sum_probs=57.6
Q ss_pred ccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHH
Q 030714 29 QDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (173)
Q Consensus 29 ~D~~LP~A~I~RImK~~LP~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~ 97 (173)
-.+.||...|.|++|+.-- ..||+..|...|.-|.+=...-|...|-..|...+++-|+++||..|+.
T Consensus 26 AgL~FPVgRi~R~Lk~g~y-a~RVga~ApVYLAAVLEYLtaEVLELAgNaa~d~kk~RItPrHi~lAIr 93 (139)
T PLN00156 26 AGLQFPVGRIARFLKAGKY-AERVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR 93 (139)
T ss_pred cCcccchHHHHHHHhcCCh-hhccCCccHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHhhcc
Confidence 3678999999999998643 3599999999988887766666777777888899999999999999985
No 51
>KOG1756 consensus Histone 2A [Chromatin structure and dynamics]
Probab=96.24 E-value=0.012 Score=46.59 Aligned_cols=68 Identities=16% Similarity=0.245 Sum_probs=54.9
Q ss_pred ccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHH
Q 030714 29 QDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (173)
Q Consensus 29 ~D~~LP~A~I~RImK~~LP~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~ 97 (173)
..+.+|...|.|++|+.= --.+|+.+|...|.-|.+=....|+..|-..++.+++.-|++.||..|+.
T Consensus 24 agl~fPvgri~r~Lr~~~-~~~ri~~gapV~laavLeYL~Aeile~agnaardnkk~ri~PrH~~lAI~ 91 (131)
T KOG1756|consen 24 AGLQFPVGRIHRLLRKGR-YAQRVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRITPRHLQLAIR 91 (131)
T ss_pred cccccCHHHHHHHHHccc-hhhhccCCChHHHHHHHHHHHHHHHHHhHHHhhhcCccccChHHHHHHHh
Confidence 568899999999999932 24689999999999766655555555566667788899999999999986
No 52
>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=96.15 E-value=0.0071 Score=44.84 Aligned_cols=60 Identities=25% Similarity=0.308 Sum_probs=29.5
Q ss_pred HHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHh
Q 030714 38 ISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMAT 98 (173)
Q Consensus 38 I~RImK~~LP~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~~ 98 (173)
|..+|-.-.. ...-..|+..+|-+.+.+||..|..+|...|...++++|+.||++-+|..
T Consensus 7 I~~mMy~fGD-~~~P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~rg~~~i~~eDl~F~lR~ 66 (93)
T PF02269_consen 7 IRQMMYGFGD-VEEPLPETVDLVEDIVREYIIELCQEAMEVAQRRGSKKIKVEDLLFLLRK 66 (93)
T ss_dssp CHHHHHCTTS--SS--HHHHHHHHHHHHHHHHHHHHHHHC---------------------
T ss_pred HHHHHHHcCC-CCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCcCcHHHHHHHHhc
Confidence 3445554443 45788999999999999999999999999999999999999999999984
No 53
>KOG3219 consensus Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=95.24 E-value=0.025 Score=47.61 Aligned_cols=69 Identities=14% Similarity=0.191 Sum_probs=60.8
Q ss_pred cCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC-CCcCchhhHHHHHhcCCc
Q 030714 32 YLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKR-KTINGDDLLWAMATLGFE 102 (173)
Q Consensus 32 ~LP~A~I~RImK~~LP~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kR-KTIs~eDVl~AL~~LgF~ 102 (173)
.||++.|.|||...... .|+.-+..+|.-.+.+||--|--+|.++|..-+. --|.|.||-.|...|...
T Consensus 112 ~f~Ka~iKkL~~~itg~--~v~~nv~Ia~~GiaKvFVGEvVEeAl~V~~~~~e~~PLqP~HIREA~rrL~~q 181 (195)
T KOG3219|consen 112 AFPKAQIKKLMSSITGQ--SVSENVAIAMAGIAKVFVGEVVEEALDVREEWGESGPLQPKHIREAYRRLKLQ 181 (195)
T ss_pred cCCHHHHHHHHHHHhCC--ccCcceeeeecchhhHhHHHHHHHHHHHHHHhccCCCCCcHHHHHHHHHHHhc
Confidence 59999999999999873 3999999999999999999999999999987764 459999999998877654
No 54
>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=94.94 E-value=0.14 Score=40.36 Aligned_cols=86 Identities=21% Similarity=0.245 Sum_probs=47.0
Q ss_pred ccccCchh--HHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHH-hcCCcchh
Q 030714 29 QDRYLPIA--NISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA-TLGFEDYI 105 (173)
Q Consensus 29 ~D~~LP~A--~I~RImK~~LP~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~-~LgF~~yv 105 (173)
+.-.+|+. .|.-|+|+.. .......+...|.+.+-.|+.-|-..|...+.+.+|++|+.+||..|++ .+++.-.-
T Consensus 7 ~~~~~PrDa~~i~~iL~~~G--v~~yeprVv~qLLEfayRYt~~vL~DA~~ya~hA~~~~i~~~DVrLAi~~r~~~~f~~ 84 (129)
T PF02291_consen 7 QSKSLPRDARVIHLILKSMG--VTEYEPRVVNQLLEFAYRYTSDVLEDAQVYADHAGRSTIDADDVRLAIQSRLDHSFTQ 84 (129)
T ss_dssp ------HHHHHHHHHHHHTT-----B-THHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHHHHT-------
T ss_pred CCccCChHHHHHHHHHHHcC--CcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHhhhccC
Confidence 34456763 2444555442 2347778889999999999999999999999999999999999999999 67777666
Q ss_pred hHHHHHHHHHH
Q 030714 106 DPLKAYLMRYR 116 (173)
Q Consensus 106 ~~Lk~~L~~yr 116 (173)
.+-+++|.+.-
T Consensus 85 pppre~llelA 95 (129)
T PF02291_consen 85 PPPREFLLELA 95 (129)
T ss_dssp -----------
T ss_pred CCChHHHHHHH
Confidence 77777775554
No 55
>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=94.92 E-value=0.25 Score=36.70 Aligned_cols=59 Identities=19% Similarity=0.297 Sum_probs=48.7
Q ss_pred HHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHH
Q 030714 37 NISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (173)
Q Consensus 37 ~I~RImK~~LP~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~ 97 (173)
-|..+|--... +..-..|...+|-+.+.+||.-|+.+|.+.|. .+|.-|+.||++-+|.
T Consensus 7 ei~~mmy~~GD-~~~P~~eTv~llE~iv~~~i~~l~~~a~~~A~-~r~~k~~~eD~~FliR 65 (92)
T cd07978 7 EIRQMMYGFGD-VQNPLPETVDLLEDIVVEYIIELCHKAAEVAQ-RRRGKVKVEDLIFLLR 65 (92)
T ss_pred HHHHHHHHcCC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-cCCCCCCHHHHHHHHh
Confidence 46666766654 44678899999999999999999999999998 4444469999999997
No 56
>PTZ00252 histone H2A; Provisional
Probab=94.91 E-value=0.081 Score=42.26 Aligned_cols=68 Identities=7% Similarity=0.165 Sum_probs=50.4
Q ss_pred ccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHh--cCCCCcCchhhHHHHH
Q 030714 29 QDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQK--EKRKTINGDDLLWAMA 97 (173)
Q Consensus 29 ~D~~LP~A~I~RImK~~LP~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~--~kRKTIs~eDVl~AL~ 97 (173)
-.+.||...|.|++|+.-- ..||+.-|...|.-+.+=...-|-..|...|.. .+++-|+++||..|+.
T Consensus 22 AGL~FPVgRi~R~Lr~g~y-a~RIga~ApVYLAAVLEYLtaEVLELAgnaa~d~~~kk~RItPrHi~lAIr 91 (134)
T PTZ00252 22 AGLIFPVGRVGSLLRRGQY-ARRIGASGAVYMAAVLEYLTAELLELSVKAAAQQAKKPKRLTPRTVTLAVR 91 (134)
T ss_pred cCccCchHHHHHHHHcCCc-ccccCCccHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccccHHHHHhhcc
Confidence 3689999999999998765 359999998888776554444444444445543 5678899999999985
No 57
>KOG4336 consensus TBP-associated transcription factor Prodos [Transcription]
Probab=92.67 E-value=0.67 Score=41.70 Aligned_cols=76 Identities=18% Similarity=0.295 Sum_probs=63.5
Q ss_pred HHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCcchhhHHHHHHHHHHc
Q 030714 38 ISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLMRYRE 117 (173)
Q Consensus 38 I~RImK~~LP~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~~LgF~~yv~~Lk~~L~~yre 117 (173)
|..|.++.+=+ .|++-|++.|.+....+|.-|...+...|...+|-..+.-||...|-++|+. +..|..+++++.-
T Consensus 11 V~~Ll~~~gfd--~is~~aletlvell~~yi~eigrq~~n~celagRT~pT~~Dv~l~Li~mnI~--v~sL~~~~q~~~~ 86 (323)
T KOG4336|consen 11 VSNLLKTKGFD--SISNAALETLVELLQSYIREIGRQLHNYCELAGRTIPTQGDVKLTLIEMNIK--VSSLYAYFQKQEF 86 (323)
T ss_pred HHHHHHHhCch--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcHHHHHHHHHHhCCC--hhhhHHHHHhccc
Confidence 34444444332 4999999999999999999999999999999999999999999999999997 5677777766654
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=91.63 E-value=0.62 Score=38.36 Aligned_cols=69 Identities=14% Similarity=0.243 Sum_probs=54.3
Q ss_pred CchhHHHHHHHhhCC-----CCCcccHHHHHHHHHHHHH---HHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCC
Q 030714 33 LPIANISRIMKKALP-----ANGKIAKDAKDTVQECVSE---FISFITSEASDKCQKEKRKTINGDDLLWAMATLGF 101 (173)
Q Consensus 33 LP~A~I~RImK~~LP-----~~~rISkDA~~al~~ca~e---FI~~LtseA~d~c~~~kRKTIs~eDVl~AL~~LgF 101 (173)
|....+..++...+. ....+++++.+.|.+.+.= .|+.++..|...+-.++.++|+.++|..++.++.|
T Consensus 192 l~~~e~~~~l~~~l~~~g~~~~~~~~~~~~~~i~~~s~G~p~~i~~l~~~~~~~a~~~~~~~i~~~~v~~~~~~~~~ 268 (269)
T TIGR03015 192 LDREETREYIEHRLERAGNRDAPVFSEGAFDAIHRFSRGIPRLINILCDRLLLSAFLEEKREIGGEEVREVIAEIDF 268 (269)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCCCcCHHHHHHHHHHcCCcccHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhhc
Confidence 444555555554431 2346999999999998875 79999999998888889999999999999998875
No 59
>KOG3423 consensus Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=89.91 E-value=1.7 Score=36.11 Aligned_cols=69 Identities=25% Similarity=0.242 Sum_probs=55.5
Q ss_pred cCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC--------------CCCcCchhhHHHHH
Q 030714 32 YLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEK--------------RKTINGDDLLWAMA 97 (173)
Q Consensus 32 ~LP~A~I~RImK~~LP~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~k--------------RKTIs~eDVl~AL~ 97 (173)
.||=+.+.-+++.+.= .....-.+-+|.=++-.||+-|+..|...|+-.. |-|++-+|+-.||+
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 5888888888887742 2344556778999999999999999999997443 55899999999999
Q ss_pred hcCCc
Q 030714 98 TLGFE 102 (173)
Q Consensus 98 ~LgF~ 102 (173)
+.|..
T Consensus 164 EyGin 168 (176)
T KOG3423|consen 164 EYGIN 168 (176)
T ss_pred HhCcc
Confidence 98873
No 60
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=88.80 E-value=2.2 Score=37.35 Aligned_cols=70 Identities=13% Similarity=0.171 Sum_probs=50.6
Q ss_pred hhHHHHHHHhhCCC---CCcccHHHHHHHHHHH------HHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCcch
Q 030714 35 IANISRIMKKALPA---NGKIAKDAKDTVQECV------SEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDY 104 (173)
Q Consensus 35 ~A~I~RImK~~LP~---~~rISkDA~~al~~ca------~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~~LgF~~y 104 (173)
...+..|++..+.. ...++.++.+.+.+.+ -..+..+...|.+.|...++.+|+.+||.+|++.+....+
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 2358999998888877 3345566678888898899999999999999998844333
No 61
>KOG2389 consensus Predicted bromodomain transcription factor [Transcription]
Probab=87.00 E-value=1.7 Score=39.63 Aligned_cols=70 Identities=14% Similarity=0.162 Sum_probs=59.2
Q ss_pred ccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCc
Q 030714 31 RYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFE 102 (173)
Q Consensus 31 ~~LP~A~I~RImK~~LP~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~~LgF~ 102 (173)
..|-+..|..|+....-.. ...-|.+.|+..+..||.-|+..|...+...+|--.+..||+.||++|+..
T Consensus 28 ~sla~~avaQIcqslg~~~--~~~sale~Ltd~~~qyvQ~lgk~a~~~~n~anR~epnl~Div~Al~dls~s 97 (353)
T KOG2389|consen 28 FSLARVAVAQICQSLGYSS--TQNSALETLTDVLQQYVQNLGKTAHRYSNLANRTEPNLFDIVLALQDLSAS 97 (353)
T ss_pred HHHHHHHHHHHHHhcCCcc--cccHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCccHHHHHHHHHHhhhh
Confidence 3577777888887664433 444499999999999999999999999999999999999999999987763
No 62
>KOG2549 consensus Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=86.25 E-value=2.7 Score=40.58 Aligned_cols=66 Identities=21% Similarity=0.273 Sum_probs=54.5
Q ss_pred chhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCC
Q 030714 34 PIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGF 101 (173)
Q Consensus 34 P~A~I~RImK~~LP~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~~LgF 101 (173)
|.-.+. .|-+.+. -..|++|+..+|.+-++.=|.-|+-+|.+.-.+.||.+++.+||-.||+.+..
T Consensus 13 ~~Es~k-~vAEslG-i~nl~deaa~~La~dv~yrikEI~Q~aaKfm~hskR~kLtv~DV~~ALr~~nV 78 (576)
T KOG2549|consen 13 PKESVK-VVAESLG-ITNLNDEAALLLAEDVEYRIKEIVQDAAKFMVHSKRTKLTVDDVDYALRSLNV 78 (576)
T ss_pred cHHHHH-HHHHHhC-ccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcCcHHHHHHHHhhccc
Confidence 344444 4445554 34599999999999999999999999999999999999999999999995543
No 63
>TIGR02928 orc1/cdc6 family replication initiation protein. Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.
Probab=85.57 E-value=4.3 Score=35.06 Aligned_cols=74 Identities=8% Similarity=0.131 Sum_probs=50.4
Q ss_pred hHHHHHHHhhCC---CCCcccHHHHHHHHHHHH------HHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCcchhh
Q 030714 36 ANISRIMKKALP---ANGKIAKDAKDTVQECVS------EFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYID 106 (173)
Q Consensus 36 A~I~RImK~~LP---~~~rISkDA~~al~~ca~------eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~~LgF~~yv~ 106 (173)
..+..|++..+. ....+.+|+.+.+.+.+. -.+..+...|.+.|..+++.+|+.+||..|++.+....+..
T Consensus 202 ~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~R~al~~l~~a~~~a~~~~~~~it~~~v~~a~~~~~~~~~~~ 281 (365)
T TIGR02928 202 EELRDILENRAEKAFYDGVLDDGVIPLCAALAAQEHGDARKAIDLLRVAGEIAEREGAERVTEDHVEKAQEKIEKDRLLE 281 (365)
T ss_pred HHHHHHHHHHHHhhccCCCCChhHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHH
Confidence 346666665542 123588888887766543 23444566777888888999999999999999886555544
Q ss_pred HHH
Q 030714 107 PLK 109 (173)
Q Consensus 107 ~Lk 109 (173)
.++
T Consensus 282 ~i~ 284 (365)
T TIGR02928 282 LIR 284 (365)
T ss_pred HHH
Confidence 333
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=80.71 E-value=4.2 Score=38.35 Aligned_cols=66 Identities=23% Similarity=0.300 Sum_probs=45.7
Q ss_pred hhHHHHHHHhhCCC-CCcccHHHHHHHHHHHH---HHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCC
Q 030714 35 IANISRIMKKALPA-NGKIAKDAKDTVQECVS---EFISFITSEASDKCQKEKRKTINGDDLLWAMATLGF 101 (173)
Q Consensus 35 ~A~I~RImK~~LP~-~~rISkDA~~al~~ca~---eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~~LgF 101 (173)
...+.+|++..+.. +..|++++.+.|.+.+. +.++.| ..|...|..++|++|+.+||.|++..-.|
T Consensus 265 ~eei~~Il~~~a~k~~i~is~~al~~I~~y~~n~Rel~nll-~~Aa~~A~~~~~~~It~~dI~~vl~~~~~ 334 (531)
T TIGR02902 265 DEEIKEIAKNAAEKIGINLEKHALELIVKYASNGREAVNIV-QLAAGIALGEGRKRILAEDIEWVAENGNY 334 (531)
T ss_pred HHHHHHHHHHHHHHcCCCcCHHHHHHHHHhhhhHHHHHHHH-HHHHHHHhhCCCcEEcHHHHHHHhCCccc
Confidence 34466666666542 46799999998877765 333333 34556777789999999999999764433
No 65
>PF13654 AAA_32: AAA domain; PDB: 3K1J_B.
Probab=78.63 E-value=9.4 Score=36.21 Aligned_cols=59 Identities=24% Similarity=0.304 Sum_probs=43.4
Q ss_pred HHHHHHhh-CCCCCcccHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhc
Q 030714 38 ISRIMKKA-LPANGKIAKDAKDTVQECVSE-----------FISFITSEASDKCQKEKRKTINGDDLLWAMATL 99 (173)
Q Consensus 38 I~RImK~~-LP~~~rISkDA~~al~~ca~e-----------FI~~LtseA~d~c~~~kRKTIs~eDVl~AL~~L 99 (173)
|.+++++. |+ .++.+|...|.+.+.. -|.-|-.||+..|+.+++++|+++||..|++.-
T Consensus 436 i~~~~~~~~L~---~~~~~Av~~li~~~~R~~q~kLsl~~~~l~~ll~EA~~~A~~~~~~~I~~~~V~~Ai~~r 506 (509)
T PF13654_consen 436 IASICQKEGLP---PFDRSAVARLIEYSARLDQDKLSLRFSWLADLLREANYWARKEGAKVITAEHVEQAIEER 506 (509)
T ss_dssp HHHHHHHHSS-----BBHHHHHHHHHHHHHCC-SEEE--HHHHHHHHHHHHHHHHHCT-SSB-HHHHHHHHHH-
T ss_pred HHHHHHhCCCC---CCCHHHHHHHHHHHHHHhCCEeCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHcc
Confidence 45555544 22 4899998888887653 567788999999999999999999999999853
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=76.57 E-value=9.8 Score=36.71 Aligned_cols=50 Identities=12% Similarity=0.145 Sum_probs=40.2
Q ss_pred cccHHHHHHHHHHHH-------------HHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcC
Q 030714 51 KIAKDAKDTVQECVS-------------EFISFITSEASDKCQKEKRKTINGDDLLWAMATLG 100 (173)
Q Consensus 51 rISkDA~~al~~ca~-------------eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~~Lg 100 (173)
.++++|.+.|.+.++ -=|.-|-.+|..+|..+++.+|+.+||.+|++.-.
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 699999998886544 23555677888899999999999999999997543
No 67
>COG1067 LonB Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]
Probab=76.50 E-value=2.4 Score=41.51 Aligned_cols=49 Identities=24% Similarity=0.309 Sum_probs=37.4
Q ss_pred cccHHHHHHHHHHHH--------------HHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcC
Q 030714 51 KIAKDAKDTVQECVS--------------EFISFITSEASDKCQKEKRKTINGDDLLWAMATLG 100 (173)
Q Consensus 51 rISkDA~~al~~ca~--------------eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~~Lg 100 (173)
.++++|..-|.+-+. .-...|. +|.++|..++++-|+++||.+|++.-.
T Consensus 338 ~~~~~Av~~li~~a~R~Ag~~~~Ltl~~rdl~~lv~-~A~~ia~~~~~~~I~ae~Ve~a~~~~~ 400 (647)
T COG1067 338 HLDKDAVEELIREAARRAGDQNKLTLRLRDLGNLVR-EAGDIAVSEGRKLITAEDVEEALQKRE 400 (647)
T ss_pred CCCHHHHHHHHHHHHHhccccceeccCHHHHHHHHH-HhhHHHhcCCcccCcHHHHHHHHHhhh
Confidence 477777666655544 3344444 999999999999999999999998743
No 68
>KOG2680 consensus DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=73.62 E-value=14 Score=34.24 Aligned_cols=60 Identities=22% Similarity=0.293 Sum_probs=46.1
Q ss_pred HHHHHHhhCC-CCCcccHHHHHHHHHHHHH----HHHHHHHHHHHHHHhcCCCCcCchhhHHHHH
Q 030714 38 ISRIMKKALP-ANGKIAKDAKDTVQECVSE----FISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (173)
Q Consensus 38 I~RImK~~LP-~~~rISkDA~~al~~ca~e----FI~~LtseA~d~c~~~kRKTIs~eDVl~AL~ 97 (173)
|..|++--.. +++.++.||++.|.+...+ |..+|-+.|+.+|.+.|-+++..+||-.+.+
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 4444443332 4678999999999876654 5566667789999999999999999999964
No 69
>PF13335 Mg_chelatase_2: Magnesium chelatase, subunit ChlI
Probab=73.48 E-value=13 Score=27.48 Aligned_cols=47 Identities=15% Similarity=0.211 Sum_probs=39.7
Q ss_pred cccHHHHHHHHHHHHHH------HHHHHHHHHHHHHhcCCCCcCchhhHHHHH
Q 030714 51 KIAKDAKDTVQECVSEF------ISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (173)
Q Consensus 51 rISkDA~~al~~ca~eF------I~~LtseA~d~c~~~kRKTIs~eDVl~AL~ 97 (173)
.+++++..+|..++..| ++-|..-|..+|.-++...|..+||..||.
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 47888888888888766 455667788999999999999999999984
No 70
>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=73.10 E-value=18 Score=29.99 Aligned_cols=79 Identities=10% Similarity=0.153 Sum_probs=58.4
Q ss_pred ccccCchhHHHHHHHhhCCCCC--cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhc------CCCCcCchhhHHHHHhcC
Q 030714 29 QDRYLPIANISRIMKKALPANG--KIAKDAKDTVQECVSEFISFITSEASDKCQKE------KRKTINGDDLLWAMATLG 100 (173)
Q Consensus 29 ~D~~LP~A~I~RImK~~LP~~~--rISkDA~~al~~ca~eFI~~LtseA~d~c~~~------kRKTIs~eDVl~AL~~Lg 100 (173)
+..+|....|.+.|...+.... .|+.|...+|.-||.+++..|-......|++- ...++--.||-.-|..|+
T Consensus 41 ~~~fl~~~~l~~~~~~i~~~~g~~~~~~d~~~lis~a~e~rlr~li~k~~~~s~hR~~~~~~~~r~~~~sdvr~qL~~l~ 120 (212)
T cd08045 41 DPSFLNPSPLAKKIRKIAKKHGLKEVDEDVLDLISLALEERLRNLLEKLIEVSEHRVDSEKEDERYEITSDVRKQLRFLE 120 (212)
T ss_pred hhhccCHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCceeecchHHHHHHHHH
Confidence 4456777777776666665322 69999999999999999999999999888765 345666778877776665
Q ss_pred CcchhhH
Q 030714 101 FEDYIDP 107 (173)
Q Consensus 101 F~~yv~~ 107 (173)
--+..+.
T Consensus 121 ~~ek~e~ 127 (212)
T cd08045 121 QLEREEE 127 (212)
T ss_pred HHHHHHH
Confidence 5444443
No 71
>KOG3334 consensus Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=71.28 E-value=13 Score=30.22 Aligned_cols=65 Identities=14% Similarity=0.242 Sum_probs=51.6
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCcchhh-HHHHHHHHHH
Q 030714 52 IAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYID-PLKAYLMRYR 116 (173)
Q Consensus 52 ISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~~LgF~~yv~-~Lk~~L~~yr 116 (173)
...-...-|-+.+--++.-|-..|.-.+.+.+|.||..|||-.|++...=..|.. +=+++|-++-
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 4555666777888888888899999999999999999999999999666656655 5566665554
No 72
>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=69.29 E-value=15 Score=34.45 Aligned_cols=82 Identities=17% Similarity=0.238 Sum_probs=58.7
Q ss_pred CchhHHHHHHHhhCC-CCCcccHHHHHHHHHHHHH----HHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCcchhhH
Q 030714 33 LPIANISRIMKKALP-ANGKIAKDAKDTVQECVSE----FISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYIDP 107 (173)
Q Consensus 33 LP~A~I~RImK~~LP-~~~rISkDA~~al~~ca~e----FI~~LtseA~d~c~~~kRKTIs~eDVl~AL~~LgF~~yv~~ 107 (173)
.++.-|.-|++--.. .++.+++||.+.|....++ |..-|-.-|+.+|++.++++|..+||-.|-+ =|.|-...
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 345556666664433 3678999999999887665 4555666788999999999999999999843 35555444
Q ss_pred HHHHHHHHHc
Q 030714 108 LKAYLMRYRE 117 (173)
Q Consensus 108 Lk~~L~~yre 117 (173)
.+ |++.|++
T Consensus 439 v~-~v~~~~~ 447 (450)
T COG1224 439 VE-YVEKYEG 447 (450)
T ss_pred HH-HHHHHHh
Confidence 43 6667664
No 73
>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=69.21 E-value=10 Score=34.91 Aligned_cols=52 Identities=25% Similarity=0.268 Sum_probs=48.0
Q ss_pred CcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCC
Q 030714 50 GKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGF 101 (173)
Q Consensus 50 ~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~~LgF 101 (173)
..|.+|+..+|..-.+-=|+-+..+|...-.+.||..++-+||-.||..|..
T Consensus 21 ~Ni~Dd~l~alamDlEYRI~ev~qea~KFmvhSKRtvLt~dDis~ALr~lNV 72 (450)
T COG5095 21 SNIDDDALRALAMDLEYRIKEVCQEASKFMVHSKRTVLTIDDISYALRSLNV 72 (450)
T ss_pred cccccHHHHHHHHhHHHHHHHHHHHHHHHhhcccceeeeHHhHHHHHHhcCC
Confidence 4699999999999999999999999999999999999999999999998754
No 74
>KOG1757 consensus Histone 2A [Chromatin structure and dynamics]
Probab=66.91 E-value=9.2 Score=30.15 Aligned_cols=65 Identities=20% Similarity=0.327 Sum_probs=49.6
Q ss_pred ccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhc----CCCCcCchhhHHHHH
Q 030714 29 QDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKE----KRKTINGDDLLWAMA 97 (173)
Q Consensus 29 ~D~~LP~A~I~RImK~~LP~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~----kRKTIs~eDVl~AL~ 97 (173)
.-+.||...|.|.+|.-.....+|..-+... ....+.|||.|-.+.+.+. +-|.|++.|+..|+.
T Consensus 27 aGlqFpVgRihr~LK~r~t~h~rVGataavy----~aaileYLTaEVLeLAgNasKdLKvKRitprHlqLAiR 95 (131)
T KOG1757|consen 27 AGLQFPVGRIHRHLKTRTTSHGRVGATAAVY----SAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 95 (131)
T ss_pred cccccchHHHHHHHHHhcccccccchHHHHH----HHHHHHHHHHHHHHHcccccccceeeeccchhheeeec
Confidence 4578999999999999988777876544332 2335678999888887655 457899999988875
No 75
>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=66.70 E-value=7.9 Score=25.10 Aligned_cols=42 Identities=12% Similarity=0.081 Sum_probs=26.6
Q ss_pred cHHHHHHHHHHHHHHHHHH-HHHHHHHHHhcCCCCcCchhhHHH
Q 030714 53 AKDAKDTVQECVSEFISFI-TSEASDKCQKEKRKTINGDDLLWA 95 (173)
Q Consensus 53 SkDA~~al~~ca~eFI~~L-tseA~d~c~~~kRKTIs~eDVl~A 95 (173)
+.||...|.+. =.|+.-- =..+-..|+..|...|+.++|..|
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 56777777765 4455433 334447788899999999998876
No 76
>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=66.50 E-value=10 Score=25.75 Aligned_cols=61 Identities=15% Similarity=0.262 Sum_probs=39.8
Q ss_pred cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCcchhhHHHHHH
Q 030714 51 KIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYL 112 (173)
Q Consensus 51 rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~~LgF~~yv~~Lk~~L 112 (173)
-++..-.+.|..+... ..--+.+............-+.++++.||.++|..+.++.|+.+|
T Consensus 23 g~~~~~i~~i~~~~~~-~~~~~~~~L~~W~~~~~~~at~~~L~~aL~~~~~~d~~~~i~~~~ 83 (83)
T PF00531_consen 23 GLSESEIENIEEENPD-LREQTYEMLQRWRQREGPNATVDQLIQALRDIGRNDLAEKIEQML 83 (83)
T ss_dssp TS-HHHHHHHHHHSTS-HHHHHHHHHHHHHHHHGSTSSHHHHHHHHHHTTHHHHHHHHHHH-
T ss_pred CcCHHHHHHHHHhCCC-hHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHCCcHHHHHHHHhhC
Confidence 3666666666664432 333333344445555556678899999999999999999888764
No 77
>COG5248 TAF19 Transcription initiation factor TFIID, subunit TAF13 [Transcription]
Probab=63.54 E-value=42 Score=26.42 Aligned_cols=48 Identities=19% Similarity=0.328 Sum_probs=41.3
Q ss_pred CCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHH
Q 030714 48 ANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (173)
Q Consensus 48 ~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~ 97 (173)
+.+.=..|..++|.+.+..+++.+...|...|+ .|-.+..||..-||+
T Consensus 24 Dvv~P~~dt~~~L~e~V~dY~~~~ctna~~~Aq--~rnK~k~eDfkfaLr 71 (126)
T COG5248 24 DVVAPRYDTAEALHEYVLDYMSILCTNAHNMAQ--VRNKTKTEDFKFALR 71 (126)
T ss_pred CCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHH--hcccchHHHHHHHHh
Confidence 355677899999999999999999999999998 444577899999997
No 78
>KOG3901 consensus Transcription initiation factor IID subunit [Transcription]
Probab=62.42 E-value=20 Score=27.76 Aligned_cols=47 Identities=19% Similarity=0.284 Sum_probs=38.4
Q ss_pred CCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHH
Q 030714 48 ANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (173)
Q Consensus 48 ~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~ 97 (173)
++..=-.|..++|-..+.+||.-++..|..+. +|--+.-||++-+|+
T Consensus 24 Dd~nP~~~tv~~Le~iV~~Yi~elt~~a~~~g---~rgk~~veD~~f~lR 70 (109)
T KOG3901|consen 24 DDVNPYPETVDLLEDIVLEYITELTHAAMEIG---KRGKVKVEDFKFLLR 70 (109)
T ss_pred CCCCccHhHHHHHHHHHHHHHHHHHHHHHHhc---ccCceeHHHHHHHHH
Confidence 34456678999999999999999988777776 455578899999997
No 79
>PRK13765 ATP-dependent protease Lon; Provisional
Probab=61.85 E-value=18 Score=35.39 Aligned_cols=48 Identities=15% Similarity=0.148 Sum_probs=39.1
Q ss_pred cccHHHHHHHHHHHHHH-------------HHHHHHHHHHHHHhcCCCCcCchhhHHHHHh
Q 030714 51 KIAKDAKDTVQECVSEF-------------ISFITSEASDKCQKEKRKTINGDDLLWAMAT 98 (173)
Q Consensus 51 rISkDA~~al~~ca~eF-------------I~~LtseA~d~c~~~kRKTIs~eDVl~AL~~ 98 (173)
.|+++|...|.+-++.- |.-|-.+|..+|+.++++.|+.+||..|+..
T Consensus 339 ~f~~eAVa~LI~~~~R~ag~r~~lsl~~~~l~~l~r~a~~~a~~~~~~~i~~~~v~~a~~~ 399 (637)
T PRK13765 339 HFDRDAVEEIIREAKRRAGRKGHLTLKLRDLGGLVRVAGDIARSEGAELTTAEHVLEAKKI 399 (637)
T ss_pred CCCHHHHHHHHHHHHHHhCCccccccCHHHHHHHHHHHHHHHHhhccceecHHHHHHHHHh
Confidence 59999988888766632 2337788999999999999999999999843
No 80
>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=61.61 E-value=6.8 Score=24.52 Aligned_cols=25 Identities=20% Similarity=0.262 Sum_probs=20.2
Q ss_pred HHHHHHhcCCCCcCchhhHHHHHhc
Q 030714 75 ASDKCQKEKRKTINGDDLLWAMATL 99 (173)
Q Consensus 75 A~d~c~~~kRKTIs~eDVl~AL~~L 99 (173)
|.+.|+..+...|+++|++.||=.-
T Consensus 1 A~~~A~~~~~~~i~~eHlL~all~~ 25 (53)
T PF02861_consen 1 AQELARERGHQYISPEHLLLALLED 25 (53)
T ss_dssp HHHHHHHTTBSSE-HHHHHHHHHHH
T ss_pred CHHHHHHcCCCcccHHHHHHHHHhh
Confidence 5678899999999999999996543
No 81
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=60.26 E-value=35 Score=29.56 Aligned_cols=71 Identities=13% Similarity=0.167 Sum_probs=49.0
Q ss_pred CchhHHHHHHHhhCC-CCCcccHHHHHHHHHHHHH---HHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCcc
Q 030714 33 LPIANISRIMKKALP-ANGKIAKDAKDTVQECVSE---FISFITSEASDKCQKEKRKTINGDDLLWAMATLGFED 103 (173)
Q Consensus 33 LP~A~I~RImK~~LP-~~~rISkDA~~al~~ca~e---FI~~LtseA~d~c~~~kRKTIs~eDVl~AL~~LgF~~ 103 (173)
++...+..|++.... .++.++.|+...|.+.|.= ++..+...+.+.+...+.+.|+.++|..+++.++.+.
T Consensus 180 ~~~~e~~~il~~~~~~~~~~~~~~~~~~ia~~~~G~pR~a~~~l~~~~~~a~~~~~~~I~~~~v~~~l~~~~~~~ 254 (328)
T PRK00080 180 YTVEELEKIVKRSARILGVEIDEEGALEIARRSRGTPRIANRLLRRVRDFAQVKGDGVITKEIADKALDMLGVDE 254 (328)
T ss_pred CCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCc
Confidence 455566666665533 2567999998888776632 2444444566666666677899999999999887654
No 82
>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=60.10 E-value=38 Score=28.57 Aligned_cols=71 Identities=18% Similarity=0.204 Sum_probs=47.0
Q ss_pred CchhHHHHHHHhhCC-CCCcccHHHHHHHHHHHHH---HHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCcc
Q 030714 33 LPIANISRIMKKALP-ANGKIAKDAKDTVQECVSE---FISFITSEASDKCQKEKRKTINGDDLLWAMATLGFED 103 (173)
Q Consensus 33 LP~A~I~RImK~~LP-~~~rISkDA~~al~~ca~e---FI~~LtseA~d~c~~~kRKTIs~eDVl~AL~~LgF~~ 103 (173)
++...+..|++.... .+..++.|+...|.+.+.= ++..+...+.+.+...+...|+.++|..++..++++.
T Consensus 159 l~~~e~~~il~~~~~~~~~~~~~~al~~ia~~~~G~pR~~~~ll~~~~~~a~~~~~~~it~~~v~~~l~~l~~~~ 233 (305)
T TIGR00635 159 YTVEELAEIVSRSAGLLNVEIEPEAALEIARRSRGTPRIANRLLRRVRDFAQVRGQKIINRDIALKALEMLMIDE 233 (305)
T ss_pred CCHHHHHHHHHHHHHHhCCCcCHHHHHHHHHHhCCCcchHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHhCCCC
Confidence 344556666665443 2467999998888776532 3344444555666666667799999999999876653
No 83
>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=59.67 E-value=40 Score=30.25 Aligned_cols=54 Identities=22% Similarity=0.198 Sum_probs=41.3
Q ss_pred HhhCCCCCcccHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCCcCchhhHHHHH
Q 030714 43 KKALPANGKIAKDAKDTVQECVSEFI-------SFITSEASDKCQKEKRKTINGDDLLWAMA 97 (173)
Q Consensus 43 K~~LP~~~rISkDA~~al~~ca~eFI-------~~LtseA~d~c~~~kRKTIs~eDVl~AL~ 97 (173)
++.++ .+.|+++.+..+.+.+..+= .++...|...|--++|..|+++||..+..
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 44555 67899999998888777652 23556677788889999999999998764
No 84
>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=57.56 E-value=38 Score=32.72 Aligned_cols=49 Identities=16% Similarity=0.184 Sum_probs=41.3
Q ss_pred CCcccHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCCcCchhhHHHHH
Q 030714 49 NGKIAKDAKDTVQECVSEFI-------SFITSEASDKCQKEKRKTINGDDLLWAMA 97 (173)
Q Consensus 49 ~~rISkDA~~al~~ca~eFI-------~~LtseA~d~c~~~kRKTIs~eDVl~AL~ 97 (173)
.+.|+.++++.|.+.+..+- .++...|..+|.-++|.+|+.+||..|+.
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 45666777888899999999999999886
No 85
>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=54.70 E-value=38 Score=27.38 Aligned_cols=48 Identities=21% Similarity=0.312 Sum_probs=35.5
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCc-chhhHHHHHHHHHHc
Q 030714 63 CVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFE-DYIDPLKAYLMRYRE 117 (173)
Q Consensus 63 ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~~LgF~-~yv~~Lk~~L~~yre 117 (173)
.+.+.++||-.+|. |.-++++++..-|+.|||+ +.++.+......+++
T Consensus 43 ~~va~l~fiL~~A~-------k~n~~~~~l~~eL~~lglp~e~~~~l~~~~~~~~~ 91 (174)
T cd04752 43 ASIAVLSFILSSAA-------KYNVDGESLSSELQQLGLPKEHATSLCRSYEEKQS 91 (174)
T ss_pred HHHHHHHHHHHHHH-------HcCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHH
Confidence 45666777777666 4459999999999999996 666666666666664
No 86
>PRK09862 putative ATP-dependent protease; Provisional
Probab=54.22 E-value=46 Score=31.69 Aligned_cols=54 Identities=11% Similarity=0.109 Sum_probs=42.4
Q ss_pred CcccHHHHHHHHHHHHHH------HHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCcc
Q 030714 50 GKIAKDAKDTVQECVSEF------ISFITSEASDKCQKEKRKTINGDDLLWAMATLGFED 103 (173)
Q Consensus 50 ~rISkDA~~al~~ca~eF------I~~LtseA~d~c~~~kRKTIs~eDVl~AL~~LgF~~ 103 (173)
..+++++...+.+....+ .+.|..-|..+|.-++|..|+.+||..|+.--+++.
T Consensus 437 ~~l~~~~~~~l~~~~~~~~lS~Ra~~rlLrvARTiADL~g~~~V~~~hv~eAl~yR~~~~ 496 (506)
T PRK09862 437 CKLESEDARWLEETLIHLGLSIRAWQRLLKVARTIADIDQSDIITRQHLQEAVSYRAIDR 496 (506)
T ss_pred hCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHhhcccH
Confidence 467888888777765544 566777888999999999999999999997555543
No 87
>PRK13406 bchD magnesium chelatase subunit D; Provisional
Probab=52.94 E-value=32 Score=33.24 Aligned_cols=59 Identities=15% Similarity=0.141 Sum_probs=47.2
Q ss_pred HHHHHHHhhCCCCCcccHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCCcCchhhHHHHH
Q 030714 37 NISRIMKKALPANGKIAKDAKDTVQECVSEFI-------SFITSEASDKCQKEKRKTINGDDLLWAMA 97 (173)
Q Consensus 37 ~I~RImK~~LP~~~rISkDA~~al~~ca~eFI-------~~LtseA~d~c~~~kRKTIs~eDVl~AL~ 97 (173)
.|.+.- +.++ ++.|+.+.+..+.++|..|= .++...|..+|--++|.+|+.+||..|+.
T Consensus 183 ~I~~AR-~rl~-~v~v~~~~l~~i~~~~~~~gv~S~Ra~i~llraARa~AaL~Gr~~V~~~dv~~Aa~ 248 (584)
T PRK13406 183 DIAAAR-ARLP-AVGPPPEAIAALCAAAAALGIASLRAPLLALRAARAAAALAGRTAVEEEDLALAAR 248 (584)
T ss_pred HHHHHH-HHHc-cCCCCHHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 344333 3455 78999999998888887774 46778888999999999999999999986
No 88
>TIGR01128 holA DNA polymerase III, delta subunit. subunit around DNA forming a DNA sliding clamp.
Probab=51.50 E-value=60 Score=27.05 Aligned_cols=66 Identities=18% Similarity=0.113 Sum_probs=46.1
Q ss_pred cCchhHHHHHHHhhCCC-CCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHH
Q 030714 32 YLPIANISRIMKKALPA-NGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (173)
Q Consensus 32 ~LP~A~I~RImK~~LP~-~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~ 97 (173)
.+....+.+++++.+.. +..|++++...|.+.+.-=+..+-.+-...|.-.+.++|+.+||...+.
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 34566666667666543 5679999999998887755566666666665554445799999987765
No 89
>COG5624 TAF61 Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=51.34 E-value=8.1 Score=36.44 Aligned_cols=77 Identities=12% Similarity=0.201 Sum_probs=63.6
Q ss_pred ccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHh---cCCcchhhH
Q 030714 31 RYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMAT---LGFEDYIDP 107 (173)
Q Consensus 31 ~~LP~A~I~RImK~~LP~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~~---LgF~~yv~~ 107 (173)
+.+-+-.+.-+.+..++...+|-.|.-+++-..+-.|+--++..+-..+++-+-+||-..||-.-|++ +-++.|++.
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 45566667777888878788999999999999999999999999989999999999999999877773 334566654
No 90
>smart00350 MCM minichromosome maintenance proteins.
Probab=51.32 E-value=72 Score=29.86 Aligned_cols=65 Identities=9% Similarity=0.144 Sum_probs=45.4
Q ss_pred ccCchhHHHHHHH---h-hCCCCCcccHHHHHHHHHHHHHHH-------------------HHHHHHHHHHHHhcCCCCc
Q 030714 31 RYLPIANISRIMK---K-ALPANGKIAKDAKDTVQECVSEFI-------------------SFITSEASDKCQKEKRKTI 87 (173)
Q Consensus 31 ~~LP~A~I~RImK---~-~LP~~~rISkDA~~al~~ca~eFI-------------------~~LtseA~d~c~~~kRKTI 87 (173)
..++...+.+.+. + ..| +|++++.+.|.+...+.= ..|-..|--.|+-..|.+|
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 4567777777664 3 334 589999998877554421 3444556667888899999
Q ss_pred CchhhHHHHHh
Q 030714 88 NGDDLLWAMAT 98 (173)
Q Consensus 88 s~eDVl~AL~~ 98 (173)
+.+||..|++-
T Consensus 493 ~~~Dv~~ai~l 503 (509)
T smart00350 493 EEADVEEAIRL 503 (509)
T ss_pred CHHHHHHHHHH
Confidence 99999999753
No 91
>COG5162 Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=49.79 E-value=1e+02 Score=25.94 Aligned_cols=51 Identities=20% Similarity=0.211 Sum_probs=39.1
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHHHh-------------------c--------------CCCCcCchhhHHHHHh
Q 030714 52 IAKDAKDTVQECVSEFISFITSEASDKCQK-------------------E--------------KRKTINGDDLLWAMAT 98 (173)
Q Consensus 52 ISkDA~~al~~ca~eFI~~LtseA~d~c~~-------------------~--------------kRKTIs~eDVl~AL~~ 98 (173)
...-.+.+|.-.+..||+-|+..|.+..+- . ++.+++..|+-.||++
T Consensus 106 ~D~rvKkLl~L~aqKFvsDiA~dayqYsrIr~~~sna~~t~~~a~~f~~gg~~~i~~~~~~~dr~K~vltv~DLs~Al~E 185 (197)
T COG5162 106 SDQRVKKLLSLLAQKFVSDIAVDAYQYSRIRQGSSNAKATAQKAKRFAKGGASGIGSSGRRGDRKKPVLTVVDLSKALEE 185 (197)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccchhhHHHHHHHHhcccccccccccccccCCceeeehHHHHHHHH
Confidence 444567888899999999999888765421 1 4567889999999998
Q ss_pred cCCc
Q 030714 99 LGFE 102 (173)
Q Consensus 99 LgF~ 102 (173)
.|+.
T Consensus 186 yGin 189 (197)
T COG5162 186 YGIN 189 (197)
T ss_pred hccc
Confidence 8873
No 92
>PLN00138 large subunit ribosomal protein LP2; Provisional
Probab=49.75 E-value=45 Score=25.72 Aligned_cols=44 Identities=14% Similarity=0.081 Sum_probs=32.8
Q ss_pred HHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCcchhhHHHHHHHHH
Q 030714 70 FITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLMRY 115 (173)
Q Consensus 70 ~LtseA~d~c~~~kRKTIs~eDVl~AL~~LgF~~yv~~Lk~~L~~y 115 (173)
||+ |+-.|.-.++..|+.+||...|+..|.+---..++.++...
T Consensus 3 yva--Ayll~~l~g~~~pta~dI~~IL~AaGvevd~~~~~~f~~~L 46 (113)
T PLN00138 3 VVA--AYLLAVLGGNTCPSAEDLKDILGSVGADADDDRIELLLSEV 46 (113)
T ss_pred HHH--HHHHHHhcCCCCCCHHHHHHHHHHcCCcccHHHHHHHHHHH
Confidence 554 77788888999999999999999998863333444444444
No 93
>CHL00081 chlI Mg-protoporyphyrin IX chelatase
Probab=49.40 E-value=48 Score=30.08 Aligned_cols=54 Identities=19% Similarity=0.238 Sum_probs=43.7
Q ss_pred HhhCCCCCcccHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCCcCchhhHHHHH
Q 030714 43 KKALPANGKIAKDAKDTVQECVSEFI-------SFITSEASDKCQKEKRKTINGDDLLWAMA 97 (173)
Q Consensus 43 K~~LP~~~rISkDA~~al~~ca~eFI-------~~LtseA~d~c~~~kRKTIs~eDVl~AL~ 97 (173)
++.++ .+.|+++.+..+.+.|..+= .++...|.-.|--++|..|+++||..+..
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 45555 57899999999999888863 35666677788889999999999998865
No 94
>TIGR01052 top6b DNA topoisomerase VI, B subunit. This model describes DNA topoisomerase VI, an archaeal type II DNA topoisomerase (DNA gyrase).
Probab=48.32 E-value=24 Score=33.57 Aligned_cols=60 Identities=17% Similarity=0.290 Sum_probs=41.8
Q ss_pred HhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCcchhhHHHHHHHHHH
Q 030714 43 KKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLMRYR 116 (173)
Q Consensus 43 K~~LP~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~~LgF~~yv~~Lk~~L~~yr 116 (173)
|+++.+.--|-+|.+.||++||...=.||...-...-+++++++ |..|++.+-..|...-
T Consensus 426 Ke~ia~~~ei~~ei~~al~~~~r~L~~~l~~~~~~~~~~~r~~~--------------~~~y~p~~a~~~~~~~ 485 (488)
T TIGR01052 426 KQSVADIPEIYNEIRLALMEVARRLRLYLSRKAREEEEIKRRKT--------------LEKYLPEIAKSLAYIL 485 (488)
T ss_pred hhhhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------------HHHHHHHHHHHHHHHh
Confidence 34444344688899999999999999999987665555555544 4567776666665543
No 95
>TIGR00368 Mg chelatase-related protein. The N-terminal end matches very strongly a pfam Mg_chelatase domain.
Probab=47.86 E-value=44 Score=31.61 Aligned_cols=47 Identities=15% Similarity=0.191 Sum_probs=40.6
Q ss_pred cccHHHHHHHHHHHHHH------HHHHHHHHHHHHHhcCCCCcCchhhHHHHH
Q 030714 51 KIAKDAKDTVQECVSEF------ISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (173)
Q Consensus 51 rISkDA~~al~~ca~eF------I~~LtseA~d~c~~~kRKTIs~eDVl~AL~ 97 (173)
.++++++..|.+++..| .+-|..-|..+|.-+++..|..+||.+|+.
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 46889999999888876 566777889999999999999999999984
No 96
>PRK12402 replication factor C small subunit 2; Reviewed
Probab=47.04 E-value=48 Score=28.04 Aligned_cols=71 Identities=7% Similarity=0.033 Sum_probs=43.2
Q ss_pred CchhHHHHHHHhhCC-CCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCcchh
Q 030714 33 LPIANISRIMKKALP-ANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYI 105 (173)
Q Consensus 33 LP~A~I~RImK~~LP-~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~~LgF~~yv 105 (173)
++...+..++++.+. .+..++.++.+.|.+.+.-=+..+-......|. +.++|+.+||..++.....++.+
T Consensus 184 ~~~~~~~~~l~~~~~~~~~~~~~~al~~l~~~~~gdlr~l~~~l~~~~~--~~~~It~~~v~~~~~~~~~~~~i 255 (337)
T PRK12402 184 PTDDELVDVLESIAEAEGVDYDDDGLELIAYYAGGDLRKAILTLQTAAL--AAGEITMEAAYEALGDVGTDEVI 255 (337)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHH--cCCCCCHHHHHHHhCCCCCHHHH
Confidence 444566666666544 245799999999888773323333333333332 23479999999988765544333
No 97
>PTZ00373 60S Acidic ribosomal protein P2; Provisional
Probab=46.64 E-value=58 Score=25.20 Aligned_cols=44 Identities=9% Similarity=0.142 Sum_probs=32.1
Q ss_pred HHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCcchhhHHHHHHHH
Q 030714 69 SFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLMR 114 (173)
Q Consensus 69 ~~LtseA~d~c~~~kRKTIs~eDVl~AL~~LgF~~yv~~Lk~~L~~ 114 (173)
.||+ |+-.|.-.++.+|+.+||.+.|+..|.+---..++.++..
T Consensus 4 kyva--AYlL~~lgG~~~pTaddI~kIL~AaGveVd~~~~~l~~~~ 47 (112)
T PTZ00373 4 KYVA--AYLMCVLGGNENPTKKEVKNVLSAVNADVEDDVLDNFFKS 47 (112)
T ss_pred HHHH--HHHHHHHcCCCCCCHHHHHHHHHHcCCCccHHHHHHHHHH
Confidence 3554 6778888899999999999999998885333344444443
No 98
>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]
Probab=46.23 E-value=77 Score=28.72 Aligned_cols=71 Identities=14% Similarity=0.178 Sum_probs=48.4
Q ss_pred HHHHHHHhhCCC---CCcccHHHHHHHHHHHH------HHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCcchhhH
Q 030714 37 NISRIMKKALPA---NGKIAKDAKDTVQECVS------EFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYIDP 107 (173)
Q Consensus 37 ~I~RImK~~LP~---~~rISkDA~~al~~ca~------eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~~LgF~~yv~~ 107 (173)
-|.-|+++-... ...++.++.+++...+. .+..-|...|.++|+++++.+|+.+||..|-+..+..-+.+.
T Consensus 194 el~~Il~~R~~~~~~~~~~~~~vl~lia~~~a~~~GDAR~aidilr~A~eiAe~~~~~~v~~~~v~~a~~~~~~~~~~~~ 273 (366)
T COG1474 194 ELYDILRERVEEGFSAGVIDDDVLKLIAALVAAESGDARKAIDILRRAGEIAEREGSRKVSEDHVREAQEEIERDVLEEV 273 (366)
T ss_pred HHHHHHHHHHHhhccCCCcCccHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHhhCCCCcCHHHHHHHHHHhhHHHHHHH
Confidence 355555554321 34678877776664332 244566678999999999999999999999766665544443
No 99
>PRK13407 bchI magnesium chelatase subunit I; Provisional
Probab=45.78 E-value=66 Score=28.87 Aligned_cols=53 Identities=11% Similarity=0.031 Sum_probs=41.9
Q ss_pred HhhCCCCCcccHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCCcCchhhHHHH
Q 030714 43 KKALPANGKIAKDAKDTVQECVSEFI-------SFITSEASDKCQKEKRKTINGDDLLWAM 96 (173)
Q Consensus 43 K~~LP~~~rISkDA~~al~~ca~eFI-------~~LtseA~d~c~~~kRKTIs~eDVl~AL 96 (173)
++.++ .+.|+++.+..+.+.|..+= .+|...|.-.|--++|..|+++||..+.
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 44455 57899999999999887764 2366777888999999999999996654
No 100
>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=45.56 E-value=32 Score=29.46 Aligned_cols=77 Identities=9% Similarity=0.099 Sum_probs=35.4
Q ss_pred CcccccCchhHHHHHHHhhCCC--CCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC------CCcCchhhHHHHHh
Q 030714 27 REQDRYLPIANISRIMKKALPA--NGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKR------KTINGDDLLWAMAT 98 (173)
Q Consensus 27 ~e~D~~LP~A~I~RImK~~LP~--~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kR------KTIs~eDVl~AL~~ 98 (173)
..++.+|-...+.+.|.+.... ...|..|...+|.-||.+.|..|-..+..+|++-.. .+....||-..|..
T Consensus 38 ~~~~~fL~~~~L~~~i~~i~~~~g~~~~~~d~l~llS~A~e~rLr~lie~~~~~s~hR~~~~~~~~~~~~~sdv~~qlr~ 117 (264)
T PF05236_consen 38 EKEEPFLNPSPLQKRIQKIAKKHGLKSVDEDVLELLSLATEERLRNLIEKAIVLSRHRRDSSKSDPRYEIRSDVRKQLRF 117 (264)
T ss_dssp ------S-HHHHHHHHHHHHHCTT--EE-TCHHHHHHHHHHHHHHHHHHHHH----------------------------
T ss_pred cccccccCHHHHHHHHHHHHHHcCCcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccCCCcccccchHHHHHHHH
Confidence 4567788888888888777643 346999999999999999999999999888865421 13335677666665
Q ss_pred cCCcc
Q 030714 99 LGFED 103 (173)
Q Consensus 99 LgF~~ 103 (173)
|.-.+
T Consensus 118 l~~~e 122 (264)
T PF05236_consen 118 LEQLE 122 (264)
T ss_dssp -----
T ss_pred HHHHH
Confidence 55433
No 101
>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=44.17 E-value=33 Score=26.03 Aligned_cols=33 Identities=21% Similarity=0.318 Sum_probs=26.8
Q ss_pred hHHHHHHHhhC----CCCCcccHHHHHHHHHHHHHHH
Q 030714 36 ANISRIMKKAL----PANGKIAKDAKDTVQECVSEFI 68 (173)
Q Consensus 36 A~I~RImK~~L----P~~~rISkDA~~al~~ca~eFI 68 (173)
++|.+++|+.| .+...++.++.+.|+++++.|-
T Consensus 51 SNIGvLIKkglIEKSGDGlv~T~~g~~Ii~~AA~l~a 87 (96)
T PF09114_consen 51 SNIGVLIKKGLIEKSGDGLVITEEGMDIIIQAAELWA 87 (96)
T ss_dssp HHHHHHHHTTSEEEETTEEEE-HHHHHHHHHHHHHHH
T ss_pred HhHHHHHHcCcccccCCceEEechHHHHHHHHHHHHH
Confidence 56888999887 3467899999999999999983
No 102
>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=43.90 E-value=78 Score=30.45 Aligned_cols=55 Identities=16% Similarity=0.232 Sum_probs=40.3
Q ss_pred HHhhCCCCCcccHHHHHHHHHHHHHH-------HHHHHHHHHHHHHhcCCCCcCchhhHHHHH
Q 030714 42 MKKALPANGKIAKDAKDTVQECVSEF-------ISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (173)
Q Consensus 42 mK~~LP~~~rISkDA~~al~~ca~eF-------I~~LtseA~d~c~~~kRKTIs~eDVl~AL~ 97 (173)
+++.++ .+.|+.+..+.|.+.|..+ -.++...|.-.|.-++|.+|+++||..|..
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 344455 5789999987777766543 124455666778888999999999999986
No 103
>PRK07452 DNA polymerase III subunit delta; Validated
Probab=40.90 E-value=74 Score=27.25 Aligned_cols=64 Identities=11% Similarity=0.149 Sum_probs=46.0
Q ss_pred HHHHHHhhCC-CCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHh--cCCCCcCchhhHHHHHhcCC
Q 030714 38 ISRIMKKALP-ANGKIAKDAKDTVQECVSEFISFITSEASDKCQK--EKRKTINGDDLLWAMATLGF 101 (173)
Q Consensus 38 I~RImK~~LP-~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~--~kRKTIs~eDVl~AL~~LgF 101 (173)
+.++|++.+. .+..|+.+|...|.+++.-=...+..|-...|.- .++.+|+.+||...+....+
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 4444444433 2568999999999999887666666666666654 45778999999988765554
No 104
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=40.81 E-value=42 Score=31.41 Aligned_cols=81 Identities=14% Similarity=0.252 Sum_probs=53.7
Q ss_pred ccccCchhHHHHHHHhhC---CCC---------CcccHH-----HHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchh
Q 030714 29 QDRYLPIANISRIMKKAL---PAN---------GKIAKD-----AKDTVQECVSEFISFITSEASDKCQKEKRKTINGDD 91 (173)
Q Consensus 29 ~D~~LP~A~I~RImK~~L---P~~---------~rISkD-----A~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eD 91 (173)
+++.|-.+||.|+++... |-+ ..++.+ +.+.|.....+ -+...+++|-++.+.
T Consensus 351 e~lglheSTVSRav~~Kyv~tp~Gi~~lk~FFs~~~~~~~g~~~S~~~Ik~~Ik~----------lI~~Ed~~~PlSD~~ 420 (455)
T PRK05932 351 EELGMHESTISRATTNKYMATPRGIFELKYFFSSAVSTDGGGEASSTAIRALIKK----------LIAAENPKKPLSDSK 420 (455)
T ss_pred HHhCCCccchhhhhcCceeecCCceEEHHHhcccccCCCCCccccHHHHHHHHHH----------HHHhcCCCCCCCHHH
Confidence 567888999999998763 211 011111 22333333322 255677889999999
Q ss_pred hHHHHHhcCCcchhhHHHHHHHHHHcccccCC
Q 030714 92 LLWAMATLGFEDYIDPLKAYLMRYREGDTKGS 123 (173)
Q Consensus 92 Vl~AL~~LgF~~yv~~Lk~~L~~yre~~~~~s 123 (173)
|...|+.-|+. -.+..+.+||+...-.+
T Consensus 421 I~~~L~~~Gi~----IaRRTVaKYRe~L~Ip~ 448 (455)
T PRK05932 421 IAELLKEQGID----VARRTVAKYREALNIPS 448 (455)
T ss_pred HHHHHHHcCCC----eehHHHHHHHHHcCCCC
Confidence 99999998884 55788999998765543
No 105
>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=40.06 E-value=31 Score=22.61 Aligned_cols=24 Identities=29% Similarity=0.509 Sum_probs=19.9
Q ss_pred CcCchhhHHHHHhcCCcchhhHHH
Q 030714 86 TINGDDLLWAMATLGFEDYIDPLK 109 (173)
Q Consensus 86 TIs~eDVl~AL~~LgF~~yv~~Lk 109 (173)
+=+++||..-|+.+||.+|++..+
T Consensus 3 ~w~~~~v~~WL~~~gl~~y~~~f~ 26 (66)
T PF07647_consen 3 TWSPEDVAEWLKSLGLEQYADNFR 26 (66)
T ss_dssp GHCHHHHHHHHHHTTCGGGHHHHH
T ss_pred CCCHHHHHHHHHHCCcHHHHHHHH
Confidence 346789999999999998888655
No 106
>COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]
Probab=39.03 E-value=77 Score=30.00 Aligned_cols=85 Identities=18% Similarity=0.265 Sum_probs=55.7
Q ss_pred CCCc--ccccCchhHHHHHHHhhCCCC------------CcccHH------HHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 030714 25 GVRE--QDRYLPIANISRIMKKALPAN------------GKIAKD------AKDTVQECVSEFISFITSEASDKCQKEKR 84 (173)
Q Consensus 25 ~~~e--~D~~LP~A~I~RImK~~LP~~------------~rISkD------A~~al~~ca~eFI~~LtseA~d~c~~~kR 84 (173)
++++ +++.+=-++|.|++++..-.. ..|+.+ ..++|..-... -+...+++
T Consensus 332 ~LrdvA~~i~~HESTISRai~nKy~~tprG~feLK~FFs~~i~s~~gg~~~S~~~Ik~~Ik~----------lI~~E~~~ 401 (444)
T COG1508 332 VLRDVADEIGMHESTISRAITNKYLATPRGLFELKYFFSSSLASSEGGEASSTEAIKALIKK----------LIEAEDKK 401 (444)
T ss_pred cHHHHHHHhCccHHHHHHHHhcccccCCcceeeHHHHHHHhccCCCCCccccHHHHHHHHHH----------HHhhccCC
Confidence 4444 667888899999999875321 011111 01122221111 25566778
Q ss_pred CCcCchhhHHHHHhcCCcchhhHHHHHHHHHHcccccCC
Q 030714 85 KTINGDDLLWAMATLGFEDYIDPLKAYLMRYREGDTKGS 123 (173)
Q Consensus 85 KTIs~eDVl~AL~~LgF~~yv~~Lk~~L~~yre~~~~~s 123 (173)
|-++.+.|...|++-| ++..+..+++||+..+-.+
T Consensus 402 ~pLSD~kIa~lLkekG----i~iARRTVAKYRe~L~I~s 436 (444)
T COG1508 402 KPLSDSKIAELLKEKG----IDVARRTVAKYREELNIPS 436 (444)
T ss_pred CCCCHHHHHHHHHHcC----CchhHHhHHHHHHHcCCCc
Confidence 8999999999999888 5688899999998776543
No 107
>PRK03992 proteasome-activating nucleotidase; Provisional
Probab=38.47 E-value=40 Score=30.42 Aligned_cols=35 Identities=20% Similarity=0.228 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcC
Q 030714 66 EFISFITSEASDKCQKEKRKTINGDDLLWAMATLG 100 (173)
Q Consensus 66 eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~~Lg 100 (173)
-=|..|..+|...|.+++++.|+.+|+..|++..-
T Consensus 339 adl~~l~~eA~~~a~~~~~~~i~~~d~~~A~~~~~ 373 (389)
T PRK03992 339 ADLKAICTEAGMFAIRDDRTEVTMEDFLKAIEKVM 373 (389)
T ss_pred HHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHh
Confidence 34566778888888899999999999999997653
No 108
>PF12627 PolyA_pol_RNAbd: Probable RNA and SrmB- binding site of polymerase A; PDB: 1OU5_B 3H38_A 3H3A_B 3H39_B 3H37_A 3AQN_A 3AQK_A 3AQM_B 3AQL_B 1MIY_A ....
Probab=38.42 E-value=8 Score=25.50 Aligned_cols=59 Identities=25% Similarity=0.375 Sum_probs=33.6
Q ss_pred CCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCc---CchhhHHHHHhcCCcchh-hHHHHH
Q 030714 49 NGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTI---NGDDLLWAMATLGFEDYI-DPLKAY 111 (173)
Q Consensus 49 ~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTI---s~eDVl~AL~~LgF~~yv-~~Lk~~ 111 (173)
+++|.+++..+|.+++. .+..|+.+- -..+=.|.+ .+...+..|.++|+.+++ +.++..
T Consensus 1 gF~ie~~t~~ai~~~~~-~L~~is~ER---i~~El~kil~~~~~~~~~~~l~~~gll~~ifP~l~~a 63 (64)
T PF12627_consen 1 GFKIEPETEEAIKENAE-LLSKISKER---IREELEKILSSPNPSRAFKLLDELGLLEYIFPELDAA 63 (64)
T ss_dssp T-EE-HHHHHHHHHHGG-GGGGS-HHH---HHHHHHHHHTSTTHHHHHHHHHHTTCHHHHSTTHHT-
T ss_pred CCccCHHHHHHHHHHHH-HHhcCCHHH---HHHHHHHHHcCCCHHHHHHHHHHcCCHHHHCcccccc
Confidence 35788888888888877 455555442 222223333 345566777788877664 555443
No 109
>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=38.06 E-value=28 Score=24.72 Aligned_cols=50 Identities=18% Similarity=0.355 Sum_probs=27.8
Q ss_pred CCcccHHHHHHHHHHHH-------HHHHHHHHHHHHHH-HhcCCCCcCchhhHHHHHh
Q 030714 49 NGKIAKDAKDTVQECVS-------EFISFITSEASDKC-QKEKRKTINGDDLLWAMAT 98 (173)
Q Consensus 49 ~~rISkDA~~al~~ca~-------eFI~~LtseA~d~c-~~~kRKTIs~eDVl~AL~~ 98 (173)
++|++.+.++.|.+++. .||.-.+.++.+.. ..+..-+++.+|.-.-++.
T Consensus 3 ~iR~~~e~k~li~~AA~~~G~sls~Fi~~aa~~~A~~~i~~~~~~~Ls~~~~~~f~~a 60 (80)
T PF08681_consen 3 EIRVTPEEKELIERAAALSGVSLSDFILSAALEAAEEVIEEHERIRLSAEDFEAFMAA 60 (80)
T ss_dssp EEE--HHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHH
T ss_pred eEecCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhcceeEcCHHHHHHHHHH
Confidence 36899999999999975 56555554444332 2233445666654444333
No 110
>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional
Probab=37.73 E-value=39 Score=31.47 Aligned_cols=32 Identities=25% Similarity=0.258 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHHHhcCCCCcCchhhHHHHHhc
Q 030714 68 ISFITSEASDKCQKEKRKTINGDDLLWAMATL 99 (173)
Q Consensus 68 I~~LtseA~d~c~~~kRKTIs~eDVl~AL~~L 99 (173)
|..|..+|...|.+++|..|+.+||..|++..
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 66788889999999999999999999999763
No 111
>PRK05574 holA DNA polymerase III subunit delta; Reviewed
Probab=37.52 E-value=93 Score=26.44 Aligned_cols=64 Identities=17% Similarity=0.097 Sum_probs=45.7
Q ss_pred CchhHHHHHHHhhCC-CCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhc-CCCCcCchhhHHHHH
Q 030714 33 LPIANISRIMKKALP-ANGKIAKDAKDTVQECVSEFISFITSEASDKCQKE-KRKTINGDDLLWAMA 97 (173)
Q Consensus 33 LP~A~I~RImK~~LP-~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~-kRKTIs~eDVl~AL~ 97 (173)
+....+.+.|++.+. .+..|+.+|...|.+.+..=+..+..|-...|.-. +++ |+.+||-..+.
T Consensus 146 ~~~~~~~~~i~~~~~~~g~~i~~~a~~~L~~~~~~d~~~l~~El~KL~l~~~~~~-It~~~I~~~i~ 211 (340)
T PRK05574 146 PKEAELPQWIQQRLKQQGLQIDAAALQLLAERVEGNLLALAQELEKLALLYPDGK-ITLEDVEEAVP 211 (340)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCchHHHHHHHHHHHHhhcCCCC-CCHHHHHHHHh
Confidence 555666666666554 25689999999999988876777777777766543 334 99999876655
No 112
>TIGR01242 26Sp45 26S proteasome subunit P45 family. Many proteins may score above the trusted cutoff because an internal
Probab=37.09 E-value=44 Score=29.50 Aligned_cols=32 Identities=25% Similarity=0.267 Sum_probs=27.6
Q ss_pred HHHHHHHHHHHHHHhcCCCCcCchhhHHHHHh
Q 030714 67 FISFITSEASDKCQKEKRKTINGDDLLWAMAT 98 (173)
Q Consensus 67 FI~~LtseA~d~c~~~kRKTIs~eDVl~AL~~ 98 (173)
-|..|..+|...|.+.++..|+.+|+..|++.
T Consensus 331 dl~~l~~~A~~~a~~~~~~~i~~~d~~~a~~~ 362 (364)
T TIGR01242 331 DLKAICTEAGMFAIREERDYVTMDDFIKAVEK 362 (364)
T ss_pred HHHHHHHHHHHHHHHhCCCccCHHHHHHHHHH
Confidence 35577788888898999999999999999975
No 113
>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=36.91 E-value=97 Score=23.68 Aligned_cols=31 Identities=13% Similarity=0.164 Sum_probs=26.3
Q ss_pred HHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCc
Q 030714 70 FITSEASDKCQKEKRKTINGDDLLWAMATLGFE 102 (173)
Q Consensus 70 ~LtseA~d~c~~~kRKTIs~eDVl~AL~~LgF~ 102 (173)
||+ |+-.|.-.++..|+.+||...|+..|.+
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 454 6778888889899999999999998875
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=36.91 E-value=28 Score=21.98 Aligned_cols=24 Identities=21% Similarity=0.425 Sum_probs=19.6
Q ss_pred CchhhHHHHHhcCCcchhhHHHHH
Q 030714 88 NGDDLLWAMATLGFEDYIDPLKAY 111 (173)
Q Consensus 88 s~eDVl~AL~~LgF~~yv~~Lk~~ 111 (173)
+.++|..-|+.+|+++|++.++..
T Consensus 3 ~~~~V~~wL~~~~~~~y~~~f~~~ 26 (63)
T cd00166 3 SPEDVAEWLESLGLGQYADNFREN 26 (63)
T ss_pred CHHHHHHHHHHcChHHHHHHHHHc
Confidence 578999999999998888876543
No 115
>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=36.28 E-value=35 Score=26.38 Aligned_cols=61 Identities=10% Similarity=0.176 Sum_probs=39.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCcchhhHHHHHHHHHHcc
Q 030714 54 KDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLMRYREG 118 (173)
Q Consensus 54 kDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~~LgF~~yv~~Lk~~L~~yre~ 118 (173)
...+.-|..|..+.-.|......=... ---.-..+...|+..|++.++.++...|++|++.
T Consensus 72 s~Vk~Eiaa~~~v~~~Y~~~L~~G~vd----~e~~~~~~~~kLk~AGidkV~~E~QkQlda~~~~ 132 (134)
T PF12010_consen 72 SPVKNEIAACSNVWSEYYPPLETGLVD----PEEALPEFNEKLKAAGIDKVIAELQKQLDAFLAA 132 (134)
T ss_pred chhHHHHHHHHHHHHHHHHHHHccCCC----HHHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHh
Confidence 344556666666665555433221100 0112456788889999999999999999999864
No 116
>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=35.91 E-value=75 Score=20.49 Aligned_cols=32 Identities=13% Similarity=0.419 Sum_probs=26.2
Q ss_pred cCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHH
Q 030714 32 YLPIANISRIMKKALPANGKIAKDAKDTVQECVSEF 67 (173)
Q Consensus 32 ~LP~A~I~RImK~~LP~~~rISkDA~~al~~ca~eF 67 (173)
.+-+++|.|++... -+|+.+.++-|.+++.+.
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 46678999998866 379999999999988763
No 117
>KOG1528 consensus Salt-sensitive 3'-phosphoadenosine-5'-phosphatase HAL2/SAL1 [Nucleotide transport and metabolism; Inorganic ion transport and metabolism]
Probab=35.11 E-value=1e+02 Score=28.26 Aligned_cols=74 Identities=19% Similarity=0.254 Sum_probs=48.8
Q ss_pred CCcccccCchhHHHHHHHhhCCCCC--cccHHHHHHHHHH-HHHHHHHHHHHHHH-HHHhc--CC-CCcCchhhHHHHHh
Q 030714 26 VREQDRYLPIANISRIMKKALPANG--KIAKDAKDTVQEC-VSEFISFITSEASD-KCQKE--KR-KTINGDDLLWAMAT 98 (173)
Q Consensus 26 ~~e~D~~LP~A~I~RImK~~LP~~~--rISkDA~~al~~c-a~eFI~~LtseA~d-~c~~~--kR-KTIs~eDVl~AL~~ 98 (173)
++.-|+- --|.|.-.+++.+|+.- .|..|-...|.+. ++.|+.-|+..-++ .+..+ +- +.++.+||++|++.
T Consensus 44 VTvaDyG-~QAiVs~vL~~~f~~~p~slVaEEds~~Lr~n~~~~~l~~i~~lvnetl~s~~sy~~~~~ls~~dvl~aID~ 122 (351)
T KOG1528|consen 44 VTVADYG-SQAIVSLVLEREFPDDPLSLVAEEDSGFLRKNGSEGLLSRITKLVNETLASDESYGDNSPLSSDDVLKAIDR 122 (351)
T ss_pred cchhhhh-HHHHHHHHHHHHcCCCCcceEeeccchhhhhhhhHHHHHHHHHHHHHHhhhhhhccCCCCCCHHHHHHHHhc
Confidence 4555543 35778889999999654 4666666666655 56777777774444 22222 23 78999999999985
Q ss_pred cC
Q 030714 99 LG 100 (173)
Q Consensus 99 Lg 100 (173)
-+
T Consensus 123 G~ 124 (351)
T KOG1528|consen 123 GN 124 (351)
T ss_pred cc
Confidence 43
No 118
>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=34.96 E-value=24 Score=22.63 Aligned_cols=14 Identities=36% Similarity=0.672 Sum_probs=11.7
Q ss_pred hhhHHHHHhcCCcc
Q 030714 90 DDLLWAMATLGFED 103 (173)
Q Consensus 90 eDVl~AL~~LgF~~ 103 (173)
+|++.||..|||..
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 68999999999973
No 119
>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=34.89 E-value=40 Score=21.97 Aligned_cols=21 Identities=24% Similarity=0.455 Sum_probs=18.6
Q ss_pred CchhhHHHHHhcCCcchhhHH
Q 030714 88 NGDDLLWAMATLGFEDYIDPL 108 (173)
Q Consensus 88 s~eDVl~AL~~LgF~~yv~~L 108 (173)
++++|..-|+.+|+++|++..
T Consensus 4 ~~~~V~~WL~~~~l~~y~~~F 24 (64)
T PF00536_consen 4 SVEDVSEWLKSLGLEQYAENF 24 (64)
T ss_dssp SHHHHHHHHHHTTGGGGHHHH
T ss_pred CHHHHHHHHHHCCCHHHHHHH
Confidence 578999999999999998875
No 120
>PRK09526 lacI lac repressor; Reviewed
Probab=33.58 E-value=28 Score=29.25 Aligned_cols=40 Identities=13% Similarity=0.469 Sum_probs=31.0
Q ss_pred cCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHH
Q 030714 32 YLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEAS 76 (173)
Q Consensus 32 ~LP~A~I~RImK~~LP~~~rISkDA~~al~~ca~eFI~~LtseA~ 76 (173)
..-+++|.|++... .+||++.++-+.+++.+ +.|.-..+.
T Consensus 16 GVS~~TVSrvLn~~----~~vs~~tr~rV~~~a~e-lgY~pn~~a 55 (342)
T PRK09526 16 GVSYQTVSRVLNQA----SHVSAKTREKVEAAMAE-LNYVPNRVA 55 (342)
T ss_pred CCCHHHHHHHhcCC----CCCCHHHHHHHHHHHHH-HCCCcCHHH
Confidence 45678999998753 36999999999999999 567654333
No 121
>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=33.31 E-value=39 Score=19.22 Aligned_cols=26 Identities=23% Similarity=0.234 Sum_probs=20.2
Q ss_pred HHHHHHhcCCCCcCchhhHHHHH-hcC
Q 030714 75 ASDKCQKEKRKTINGDDLLWAMA-TLG 100 (173)
Q Consensus 75 A~d~c~~~kRKTIs~eDVl~AL~-~Lg 100 (173)
+....-.++.-+|+.+++..+|+ .||
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 44566677888999999999998 576
No 122
>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=32.13 E-value=83 Score=25.72 Aligned_cols=34 Identities=18% Similarity=0.319 Sum_probs=26.6
Q ss_pred HhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHH
Q 030714 43 KKALPANGKIAKDAKDTVQECVSEFISFITSEAS 76 (173)
Q Consensus 43 K~~LP~~~rISkDA~~al~~ca~eFI~~LtseA~ 76 (173)
|+++.+.--|-+|.+.+|++||...=.||...-.
T Consensus 111 KeaIadvpEI~~EIrlAl~~~~R~L~~~l~kk~~ 144 (151)
T cd00823 111 KEAIADIPEIEEEIKLALQEVARKLKRYLSKKRK 144 (151)
T ss_pred hhhhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4555544468899999999999999999986544
No 123
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=32.10 E-value=78 Score=22.44 Aligned_cols=28 Identities=14% Similarity=0.141 Sum_probs=22.2
Q ss_pred HHHHHHhcCCCCcCchhhHHHHHhcCCc
Q 030714 75 ASDKCQKEKRKTINGDDLLWAMATLGFE 102 (173)
Q Consensus 75 A~d~c~~~kRKTIs~eDVl~AL~~LgF~ 102 (173)
+...+-.++.-+|+.++|..+|..+|+.
T Consensus 15 ~F~~~D~d~~G~Is~~el~~~l~~~~~~ 42 (96)
T smart00027 15 IFRSLDKNQDGTVTGAQAKPILLKSGLP 42 (96)
T ss_pred HHHHhCCCCCCeEeHHHHHHHHHHcCCC
Confidence 4456667778889999999999988875
No 124
>PF09123 DUF1931: Domain of unknown function (DUF1931); InterPro: IPR015207 This entry represents a set of hypothetical bacterial proteins containing a core of six alpha-helices, where one central helix is surrounded by the other five. The exact function of this family has not, as yet, been determined []. ; PDB: 1WWS_A 1WWI_A 1R4V_A.
Probab=31.95 E-value=43 Score=26.99 Aligned_cols=53 Identities=19% Similarity=0.256 Sum_probs=40.1
Q ss_pred HHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhh
Q 030714 38 ISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDL 92 (173)
Q Consensus 38 I~RImK~~LP~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDV 92 (173)
+.||.+.+.. .-|.|+-..-+...++.=+.-|.-.|.+.|+.++|.+|.+.|+
T Consensus 1 fe~lFR~aa~--LdvdK~d~~r~~d~V~~Kl~DLl~va~~~Ak~ngRdvI~~~DL 53 (138)
T PF09123_consen 1 FERLFRKAAG--LDVDKNDAKRYSDFVEKKLYDLLLVAQENAKANGRDVIEPRDL 53 (138)
T ss_dssp HHHHHHHHHS------HHHHHHHHHHHHHHHHHCCCCHHHHHHHTT-SEE-GGGS
T ss_pred ChHHHHHHhc--cCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeeccccC
Confidence 3577888764 5577888888888888888888888999999999999999886
No 125
>COG1389 DNA topoisomerase VI, subunit B [DNA replication, recombination, and repair]
Probab=31.49 E-value=36 Score=32.77 Aligned_cols=46 Identities=17% Similarity=0.344 Sum_probs=36.7
Q ss_pred HhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcC
Q 030714 43 KKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTIN 88 (173)
Q Consensus 43 K~~LP~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs 88 (173)
|+++.+.--|-+|.+.|+++||.+.=+||+....+.-+.+++++|.
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 3444434458899999999999999999999999887777777653
No 126
>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional
Probab=31.42 E-value=60 Score=29.72 Aligned_cols=32 Identities=25% Similarity=0.233 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHHHhcCCCCcCchhhHHHHHhc
Q 030714 68 ISFITSEASDKCQKEKRKTINGDDLLWAMATL 99 (173)
Q Consensus 68 I~~LtseA~d~c~~~kRKTIs~eDVl~AL~~L 99 (173)
|..|..+|...|.+++|+.|+.+|+..|++..
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 127
>PRK14868 DNA topoisomerase VI subunit B; Provisional
Probab=31.12 E-value=60 Score=32.93 Aligned_cols=56 Identities=20% Similarity=0.340 Sum_probs=39.7
Q ss_pred ccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCc
Q 030714 29 QDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTI 87 (173)
Q Consensus 29 ~D~~LP~A~I~RImK~~LP~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTI 87 (173)
-...+|-.... |+++.+.--|-+|.+.+|++||.+.=.||...-...-++++++++
T Consensus 614 aST~VPfts~s---KeaIA~vpEI~~EI~lAl~~~aR~Lk~yl~k~~~~~~~~~k~~~~ 669 (795)
T PRK14868 614 ASTNVPFTSES---KDAIANVPEIEDEIELAIREAARELKSYLNKRRSMQKRREKQDVL 669 (795)
T ss_pred eecCCCCCCcc---hhhhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33445544433 455554456999999999999999999999877766666666654
No 128
>COG1222 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]
Probab=29.92 E-value=79 Score=29.64 Aligned_cols=50 Identities=22% Similarity=0.323 Sum_probs=38.7
Q ss_pred CcccHHH-HHHHHHHHHHH----HHHHHHHHHHHHHhcCCCCcCchhhHHHHHhc
Q 030714 50 GKIAKDA-KDTVQECVSEF----ISFITSEASDKCQKEKRKTINGDDLLWAMATL 99 (173)
Q Consensus 50 ~rISkDA-~~al~~ca~eF----I~~LtseA~d~c~~~kRKTIs~eDVl~AL~~L 99 (173)
+.+++|. .+.|.+++..| |.-|+.||--.|.++.|+.|+-+|.++|.++.
T Consensus 338 M~l~~dvd~e~la~~~~g~sGAdlkaictEAGm~AiR~~R~~Vt~~DF~~Av~KV 392 (406)
T COG1222 338 MNLADDVDLELLARLTEGFSGADLKAICTEAGMFAIRERRDEVTMEDFLKAVEKV 392 (406)
T ss_pred ccCccCcCHHHHHHhcCCCchHHHHHHHHHHhHHHHHhccCeecHHHHHHHHHHH
Confidence 4555554 45566655554 77889999999999999999999999998743
No 129
>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=29.67 E-value=41 Score=21.34 Aligned_cols=25 Identities=16% Similarity=0.353 Sum_probs=19.6
Q ss_pred cCchhhHHHHHhcCCcchhhHHHHH
Q 030714 87 INGDDLLWAMATLGFEDYIDPLKAY 111 (173)
Q Consensus 87 Is~eDVl~AL~~LgF~~yv~~Lk~~ 111 (173)
-+.++|..-|+.+||.+|++.++..
T Consensus 4 w~~~~v~~wL~~~g~~~y~~~f~~~ 28 (68)
T smart00454 4 WSPESVADWLESIGLEQYADNFRKN 28 (68)
T ss_pred CCHHHHHHHHHHCChHHHHHHHHHC
Confidence 4678899999999999877766543
No 130
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=29.20 E-value=86 Score=29.81 Aligned_cols=81 Identities=17% Similarity=0.201 Sum_probs=53.8
Q ss_pred ccccCchhHHHHHHHhhC---CCC---------CcccHH-----HHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchh
Q 030714 29 QDRYLPIANISRIMKKAL---PAN---------GKIAKD-----AKDTVQECVSEFISFITSEASDKCQKEKRKTINGDD 91 (173)
Q Consensus 29 ~D~~LP~A~I~RImK~~L---P~~---------~rISkD-----A~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eD 91 (173)
+++.|--+||.|+++... |-+ ..|+.+ +.++|.....++ +...+++|-++-+.
T Consensus 377 e~lglHeSTVSRa~~~KY~~tp~GifeLK~FFs~~v~~~~g~~~Ss~~Ik~~Ik~l----------I~~Ed~~kPLSD~~ 446 (481)
T PRK12469 377 EELGLHESTISRATGNKYMATPRGTFEFKHFFPRKLEAAGGGECSAAAVRALIKEM----------IAAEQAGDPLSDVA 446 (481)
T ss_pred HHhCCCcchhhHHhcCceeecCCceEeHHHhhccccCCCCCccccHHHHHHHHHHH----------HHhcCCCCCCCHHH
Confidence 567888999999998763 211 012111 222333332222 55677899999999
Q ss_pred hHHHHHhcCCcchhhHHHHHHHHHHcccccCC
Q 030714 92 LLWAMATLGFEDYIDPLKAYLMRYREGDTKGS 123 (173)
Q Consensus 92 Vl~AL~~LgF~~yv~~Lk~~L~~yre~~~~~s 123 (173)
|...|+.-|+. -.+..+.+|||...-.+
T Consensus 447 I~~~L~~~GI~----IARRTVAKYRe~L~Ips 474 (481)
T PRK12469 447 LAEMLAGRGVL----IARRTVAKYREAMKIPP 474 (481)
T ss_pred HHHHHHhcCCC----eechhHHHHHHHcCCCC
Confidence 99999988874 56678999998776543
No 131
>PTZ00183 centrin; Provisional
Probab=29.19 E-value=1.7e+02 Score=21.43 Aligned_cols=22 Identities=18% Similarity=0.246 Sum_probs=14.0
Q ss_pred HHHHhcCCCCcCchhhHHHHHh
Q 030714 77 DKCQKEKRKTINGDDLLWAMAT 98 (173)
Q Consensus 77 d~c~~~kRKTIs~eDVl~AL~~ 98 (173)
..+..++...|+.++.+.++..
T Consensus 60 ~~~d~~~~g~i~~~eF~~~~~~ 81 (158)
T PTZ00183 60 ADVDKDGSGKIDFEEFLDIMTK 81 (158)
T ss_pred HHhCCCCCCcEeHHHHHHHHHH
Confidence 3344556667777777777654
No 132
>PRK12728 fliE flagellar hook-basal body protein FliE; Provisional
Probab=28.22 E-value=2.3e+02 Score=21.37 Aligned_cols=63 Identities=13% Similarity=0.174 Sum_probs=39.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH--HHhcCCCCcCchhhHHHHH--hcCCcchhhHHHHHHHHHHccc
Q 030714 55 DAKDTVQECVSEFISFITSEASDK--CQKEKRKTINGDDLLWAMA--TLGFEDYIDPLKAYLMRYREGD 119 (173)
Q Consensus 55 DA~~al~~ca~eFI~~LtseA~d~--c~~~kRKTIs~eDVl~AL~--~LgF~~yv~~Lk~~L~~yre~~ 119 (173)
.+.+.|.++... ++..-.+|.+. +-..|. +++..||+-|++ .+.|.-.+.--...++.|+|..
T Consensus 32 sF~~~L~~ai~~-vn~~q~~a~~~~~~~~~G~-~~~lhevmiA~~kA~lslq~~vqVRNKlv~AYqEIM 98 (102)
T PRK12728 32 SFSDFLKEALNK-VNELQVEADNSTEKLVKGE-IVDLHDVMIAAQKASISLQLTVQIRNKVVEAYQEIM 98 (102)
T ss_pred CHHHHHHHHHHH-HHHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455556555555 33333333322 223344 789999999998 5556666777778888999864
No 133
>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=28.06 E-value=1.9e+02 Score=19.43 Aligned_cols=48 Identities=19% Similarity=0.200 Sum_probs=34.9
Q ss_pred cCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 030714 32 YLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQK 81 (173)
Q Consensus 32 ~LP~A~I~RImK~~LP~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~ 81 (173)
.+|=+-+.-+++.+.=+ .-..-.+-+|.=++..||+-|+..|.+.|+-
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 36777777788777531 1223345688888999999999999998864
No 134
>COG1466 HolA DNA polymerase III, delta subunit [DNA replication, recombination, and repair]
Probab=27.59 E-value=1.3e+02 Score=26.42 Aligned_cols=50 Identities=18% Similarity=0.120 Sum_probs=40.0
Q ss_pred CCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHh
Q 030714 49 NGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMAT 98 (173)
Q Consensus 49 ~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~~ 98 (173)
+.+|++||.+.|..+..-=+..+.+|-...|--..-++|+.+||..++..
T Consensus 157 ~l~i~~~a~~~L~~~~~~nl~~i~~Ei~KL~l~~~~~~I~~~~V~~~v~~ 206 (334)
T COG1466 157 GLKIDQEAIQLLLEALGGNLLAIAQEIEKLALYAGDKEITLEDVEEVVSD 206 (334)
T ss_pred CCCCCHHHHHHHHHHhCCcHHHHHHHHHHHHHhCCCCcCCHHHHHHHHhc
Confidence 57899999999999998767777777776665555449999999988763
No 135
>PRK07914 hypothetical protein; Reviewed
Probab=27.30 E-value=1.2e+02 Score=26.32 Aligned_cols=63 Identities=11% Similarity=0.144 Sum_probs=41.9
Q ss_pred chhHHHHHHHhhCCC-CCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHH
Q 030714 34 PIANISRIMKKALPA-NGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (173)
Q Consensus 34 P~A~I~RImK~~LP~-~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~ 97 (173)
+-..+.+.|++.+-. +.+|+.||...|.+++..=+..|..|-...+-..+ .+|+.+||...+.
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 344445555544432 56899999999999997666666666555554333 5698888877654
No 136
>PF13499 EF-hand_7: EF-hand domain pair; PDB: 1TCF_A 2TN4_A 1TN4_A 1A2X_A 2CT9_B 2OTG_B 2OS8_B 1SNL_A 3O4Y_A 3J04_E ....
Probab=26.87 E-value=1.6e+02 Score=18.73 Aligned_cols=46 Identities=26% Similarity=0.280 Sum_probs=33.0
Q ss_pred HHHHHHHhcCCCCcCchhhHHHHHhcCCcchhhHHHHHHHH-HHccc
Q 030714 74 EASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLMR-YREGD 119 (173)
Q Consensus 74 eA~d~c~~~kRKTIs~eDVl~AL~~LgF~~yv~~Lk~~L~~-yre~~ 119 (173)
++...+-.++.-.|+.+++..++..++..-....+...++. |+..+
T Consensus 4 ~~F~~~D~d~~G~i~~~el~~~~~~~~~~~~~~~~~~~~~~~~~~~D 50 (66)
T PF13499_consen 4 EAFKKFDKDGDGYISKEELRRALKHLGRDMSDEESDEMIDQIFREFD 50 (66)
T ss_dssp HHHHHHSTTSSSEEEHHHHHHHHHHTTSHSTHHHHHHHHHHHHHHHT
T ss_pred HHHHHHcCCccCCCCHHHHHHHHHHhcccccHHHHHHHHHHHHHHhC
Confidence 34566677778889999999999999987655555555544 44444
No 137
>COG1724 Predicted RNA binding protein (dsRBD-like fold), HicA family [General function prediction only]
Probab=26.79 E-value=39 Score=24.07 Aligned_cols=17 Identities=18% Similarity=0.481 Sum_probs=15.2
Q ss_pred CcCchhhHHHHHhcCCc
Q 030714 86 TINGDDLLWAMATLGFE 102 (173)
Q Consensus 86 TIs~eDVl~AL~~LgF~ 102 (173)
.+++.+|+++|+.+||.
T Consensus 6 ~~~~ke~ik~Le~~Gf~ 22 (66)
T COG1724 6 RMKAKEVIKALEKDGFQ 22 (66)
T ss_pred cCCHHHHHHHHHhCCcE
Confidence 47889999999999996
No 138
>PRK14975 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Probab=26.59 E-value=2.9e+02 Score=26.26 Aligned_cols=90 Identities=14% Similarity=0.111 Sum_probs=54.1
Q ss_pred ccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHH----------HHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHh
Q 030714 29 QDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVS----------EFISFITSEASDKCQKEKRKTINGDDLLWAMAT 98 (173)
Q Consensus 29 ~D~~LP~A~I~RImK~~LP~~~rISkDA~~al~~ca~----------eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~~ 98 (173)
.++++|.+.|-.-|... ++.|..+....+..-.. .-+.-|..+..+......=.-=++.+|.++|+.
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 34456666666666555 47788887666655554 555666666665542221123467899999999
Q ss_pred cCCc----------chhhHHHHHHHHHHccccc
Q 030714 99 LGFE----------DYIDPLKAYLMRYREGDTK 121 (173)
Q Consensus 99 LgF~----------~yv~~Lk~~L~~yre~~~~ 121 (173)
+|+. .-..|+-..+-+||+..+.
T Consensus 237 ~g~~~~~t~~~~L~~~~hp~~~~ile~r~~~kl 269 (553)
T PRK14975 237 AGIELPSTRKWELREIDHPAVEPLLEYRKLSKL 269 (553)
T ss_pred CCCCCCCCcHHHhccCCCchHHHHHHHHHHHHH
Confidence 8884 1112344566688876554
No 139
>PRK02910 light-independent protochlorophyllide reductase subunit B; Provisional
Probab=26.37 E-value=1.2e+02 Score=28.65 Aligned_cols=52 Identities=13% Similarity=0.145 Sum_probs=39.0
Q ss_pred CCCcccHHHHHHHHHHHHHHHH-HHHHHHHHHHHhcCCCCcCchhhHHHHHhcC
Q 030714 48 ANGKIAKDAKDTVQECVSEFIS-FITSEASDKCQKEKRKTINGDDLLWAMATLG 100 (173)
Q Consensus 48 ~~~rISkDA~~al~~ca~eFI~-~LtseA~d~c~~~kRKTIs~eDVl~AL~~Lg 100 (173)
+.+.++.||...|.+ .=-|+. -+=..+-+.|++.+...|+.+.|..|-..+|
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 456799999999965 455554 3334445778899999999999999977654
No 140
>PRK00440 rfc replication factor C small subunit; Reviewed
Probab=26.31 E-value=1.3e+02 Score=25.17 Aligned_cols=65 Identities=9% Similarity=0.055 Sum_probs=38.4
Q ss_pred CchhHHHHHHHhhCC-CCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhc
Q 030714 33 LPIANISRIMKKALP-ANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATL 99 (173)
Q Consensus 33 LP~A~I~RImK~~LP-~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~~L 99 (173)
++...+.++++..+. .+..|+.++.+.+.+.+.--+..+-.+-...+. . .++|+.+||..++...
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 344555555555443 256799999999888765333333222222222 2 4679999998887543
No 141
>PRK14867 DNA topoisomerase VI subunit B; Provisional
Probab=26.17 E-value=84 Score=31.17 Aligned_cols=52 Identities=19% Similarity=0.314 Sum_probs=36.3
Q ss_pred cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCcchhhHHHHHHHHHH
Q 030714 51 KIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLMRYR 116 (173)
Q Consensus 51 rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~~LgF~~yv~~Lk~~L~~yr 116 (173)
-|-+|.+.||++||.+.=.||...-...-++++++++ ..|++.+-..|...-
T Consensus 592 eI~~Ei~lAl~~~~r~L~~~l~~~~~~~~~~~k~~~~--------------~~y~p~~a~~l~~~~ 643 (659)
T PRK14867 592 EIFNEIRQALMICARELEKYISRIRREKEEEQKRKYV--------------MKYAVIFAEGLASIT 643 (659)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------------HHHHHHHHHHHHHHh
Confidence 4677888899999999999999866655555555543 345555555555443
No 142
>TIGR02903 spore_lon_C ATP-dependent protease, Lon family. Members of this protein family resemble the widely distributed ATP-dependent protease La, also called Lon and LonA. It resembles even more closely LonB, which is a LonA paralog found in genomes if and only if the species is capable of endospore formation (as in Bacillus subtilis, Clostridium tetani, and select other members of the Firmicutes) and expressed specifically in the forespore compartment. Members of this family are restricted to a subset of spore-forming species, and are very likely to participate in the program of endospore formation. We propose the designation LonC.
Probab=26.16 E-value=1.2e+02 Score=29.29 Aligned_cols=72 Identities=14% Similarity=0.204 Sum_probs=45.5
Q ss_pred hhHHHHHHHhhCCC-CCcccHHHHHHHHHHH---HHHHHHHHHHHH----H---HHHhcCCCCcCchhhHHHHHhcCCcc
Q 030714 35 IANISRIMKKALPA-NGKIAKDAKDTVQECV---SEFISFITSEAS----D---KCQKEKRKTINGDDLLWAMATLGFED 103 (173)
Q Consensus 35 ~A~I~RImK~~LP~-~~rISkDA~~al~~ca---~eFI~~LtseA~----d---~c~~~kRKTIs~eDVl~AL~~LgF~~ 103 (173)
...+..|++..+.. +..++.++.++|.+++ ...++.|..... . .+...++.+|+.+||.+++..--|..
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 34566777766543 3568999999998865 334444432211 1 12233456899999999998877765
Q ss_pred hhh
Q 030714 104 YID 106 (173)
Q Consensus 104 yv~ 106 (173)
|..
T Consensus 435 ~~~ 437 (615)
T TIGR02903 435 YEK 437 (615)
T ss_pred chh
Confidence 543
No 143
>PHA03328 nuclear egress lamina protein UL31; Provisional
Probab=26.12 E-value=70 Score=29.06 Aligned_cols=79 Identities=18% Similarity=0.302 Sum_probs=48.4
Q ss_pred cccccCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCcchhhH
Q 030714 28 EQDRYLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYIDP 107 (173)
Q Consensus 28 e~D~~LP~A~I~RImK~~LP~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~~LgF~~yv~~ 107 (173)
..++.||=.-|.+|+-. +| +.+|.-|... .-||..+....--....+..-||+++||..++.+|+|++- -
T Consensus 229 ~~slHL~~~~L~~Ll~n-~~-gY~i~adv~~------~~fvL~v~~~~~~~~~~~~~~~V~~~dIy~k~~dL~f~dE--l 298 (316)
T PHA03328 229 GKSLHLHYRLIDRLLTA-CP-GYRIIAHVWQ------TTFVLVVRRDAERQTTDADVPAVSAEDIYCKMCDLNFDGE--L 298 (316)
T ss_pred CCcccchHHHHHHHHHh-CC-CCeEEEEEec------ceEEEEEeeCCCCCCccccccccCHHHHHHHHhCCCCChH--H
Confidence 35566776666655554 45 5565554321 2455555533332445667899999999999999999742 2
Q ss_pred HHHHHHHHH
Q 030714 108 LKAYLMRYR 116 (173)
Q Consensus 108 Lk~~L~~yr 116 (173)
+.+|..-|.
T Consensus 299 ~~Ey~kly~ 307 (316)
T PHA03328 299 LLEYKRLYA 307 (316)
T ss_pred HHHHHHHHH
Confidence 234444444
No 144
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=26.04 E-value=53 Score=27.26 Aligned_cols=37 Identities=14% Similarity=0.363 Sum_probs=28.9
Q ss_pred CchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHH
Q 030714 33 LPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSE 74 (173)
Q Consensus 33 LP~A~I~RImK~~LP~~~rISkDA~~al~~ca~eFI~~Ltse 74 (173)
+-+++|.|.+... .+||++.++-+.+++.+. .|.-+.
T Consensus 10 VS~~TVSrvLn~~----~~vs~~tr~rV~~~a~~l-gY~pn~ 46 (327)
T PRK10423 10 VSTSTVSHVINKD----RFVSEAITAKVEAAIKEL-NYAPSA 46 (327)
T ss_pred CcHHHHHHHhCCC----CCCCHHHHHHHHHHHHHH-CCCccH
Confidence 4578999999653 369999999999999885 555443
No 145
>COG5251 TAF40 Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=25.73 E-value=99 Score=26.14 Aligned_cols=61 Identities=11% Similarity=-0.004 Sum_probs=46.6
Q ss_pred cCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC---CcCchhhHHHH
Q 030714 32 YLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRK---TINGDDLLWAM 96 (173)
Q Consensus 32 ~LP~A~I~RImK~~LP~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRK---TIs~eDVl~AL 96 (173)
.||+++|.+++-.++. -.|+...+.+|+-.+.+|+--|--.|..+ ++++. -+.+.|+-.|.
T Consensus 115 ~lnKt~VKKlastV~n--QtVspNi~I~l~g~~KVfvGEiIElA~~V--q~~w~~sgpl~p~h~reay 178 (199)
T COG5251 115 SLNKTQVKKLASTVAN--QTVSPNIRIFLQGVGKVFVGEIIELAMIV--QNKWLTSGPLIPFHKREAY 178 (199)
T ss_pred CCCHHHHHHHHHHHhc--cccCCCeeeeeechhHHHHHHHHHHHHHH--HHHhcccCCCChHHHHHHH
Confidence 5999999999999985 46888888899999999998877666533 23333 36777777664
No 146
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=25.59 E-value=1.1e+02 Score=20.60 Aligned_cols=32 Identities=19% Similarity=0.496 Sum_probs=21.9
Q ss_pred cCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHH
Q 030714 32 YLPIANISRIMKKALPANGKIAKDAKDTVQECVSEF 67 (173)
Q Consensus 32 ~LP~A~I~RImK~~LP~~~rISkDA~~al~~ca~eF 67 (173)
.+.+++|.|++... ..|+.+.++.+.+++.++
T Consensus 11 gvS~~TVSr~ln~~----~~v~~~t~~~i~~~~~~~ 42 (70)
T smart00354 11 GVSKATVSRVLNGN----GRVSEETREKVLAAMEEL 42 (70)
T ss_pred CCCHHHHHHHHCCC----CCCCHHHHHHHHHHHHHh
Confidence 46677777777533 347777777777777765
No 147
>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=25.39 E-value=1.3e+02 Score=28.33 Aligned_cols=51 Identities=12% Similarity=0.154 Sum_probs=38.2
Q ss_pred CCcccHHHHHHHHHHHHHHHH-HHHHHHHHHHHhcCCCCcCchhhHHHHHhcC
Q 030714 49 NGKIAKDAKDTVQECVSEFIS-FITSEASDKCQKEKRKTINGDDLLWAMATLG 100 (173)
Q Consensus 49 ~~rISkDA~~al~~ca~eFI~-~LtseA~d~c~~~kRKTIs~eDVl~AL~~Lg 100 (173)
.+.++.||...|.+ .=-|+. -+=..+-..|++.+...|+.+.|..|=..+|
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 46799999999965 444554 3444455778999999999999999876654
No 148
>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=25.15 E-value=2.2e+02 Score=22.04 Aligned_cols=71 Identities=13% Similarity=0.130 Sum_probs=45.7
Q ss_pred hHHHHHHHhhCCCCCcccHHHHHHHHHHH---HHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHHhcCCcchhhHHHHHH
Q 030714 36 ANISRIMKKALPANGKIAKDAKDTVQECV---SEFISFITSEASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYL 112 (173)
Q Consensus 36 A~I~RImK~~LP~~~rISkDA~~al~~ca---~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~~LgF~~yv~~Lk~~L 112 (173)
..+.+|+++.......|..+-|....-++ +-|+.+|...|.+.+.+.+ |..++.+.+|. +-++..+
T Consensus 14 ~~l~~l~~~lg~~~~~i~~~~r~~yHaAav~asNf~~~L~~~a~~ll~~~g---i~~~~a~~~L~--------PLi~~t~ 82 (132)
T PF10728_consen 14 EVLQELAKELGGRPFEIDSEQRALYHAAAVFASNFLVALYALAAELLEQAG---IDFEEALEALL--------PLIRETL 82 (132)
T ss_dssp HHHHHHHHHTTSEEEE--GGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----SHHH--HHHH--------HHHHHHH
T ss_pred HHHHHHHHHhCCceEEeCHHhHHHHHHHHHHHHhhHHHHHHHHHHHHHHcC---CCchhHHHHHH--------HHHHHHH
Confidence 45778888877767789999988887765 4788888888888887763 55555444443 4455566
Q ss_pred HHHHc
Q 030714 113 MRYRE 117 (173)
Q Consensus 113 ~~yre 117 (173)
++..+
T Consensus 83 ~n~~~ 87 (132)
T PF10728_consen 83 ENILQ 87 (132)
T ss_dssp HHHHH
T ss_pred HHHHh
Confidence 65553
No 149
>PRK04184 DNA topoisomerase VI subunit B; Validated
Probab=24.62 E-value=55 Score=31.54 Aligned_cols=55 Identities=20% Similarity=0.317 Sum_probs=39.5
Q ss_pred HhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcC--chhhHHHHH
Q 030714 43 KKALPANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTIN--GDDLLWAMA 97 (173)
Q Consensus 43 K~~LP~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs--~eDVl~AL~ 97 (173)
|+++.+.--|-+|.+.+|++||...=.||...-...-.+++++++. -.+|..+|.
T Consensus 431 Ke~ia~~~ei~~ei~~al~~~~r~L~~~l~~~~~~~~~~~k~~~~~~y~p~~a~~~~ 487 (535)
T PRK04184 431 KEAIADVPEIEKEIRLALQEVARKLKKYLSRKRKEEEAKKKAKTFEKYIPEIARKLA 487 (535)
T ss_pred hhhhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4445444568899999999999999999998777666666666543 234555554
No 150
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=24.27 E-value=46 Score=27.91 Aligned_cols=39 Identities=13% Similarity=0.370 Sum_probs=29.7
Q ss_pred cCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHH
Q 030714 32 YLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEA 75 (173)
Q Consensus 32 ~LP~A~I~RImK~~LP~~~rISkDA~~al~~ca~eFI~~LtseA 75 (173)
..-+++|.|++... .+|+.+.++-+.+.+.+ +.|.-..+
T Consensus 16 gVS~~TVSrvLn~~----~~vs~~tr~rV~~~a~e-lgY~pn~~ 54 (331)
T PRK14987 16 GVTKMTVSRFLRNP----EQVSVALRGKIAAALDE-LGYIPNRA 54 (331)
T ss_pred CCCHHHhhhhhCCC----CCCCHHHHHHHHHHHHH-hCCCccHH
Confidence 35678899988643 37999999999999999 56665443
No 151
>PRK14971 DNA polymerase III subunits gamma and tau; Provisional
Probab=24.18 E-value=1.5e+02 Score=28.81 Aligned_cols=64 Identities=8% Similarity=0.009 Sum_probs=33.1
Q ss_pred CchhHHHHHHHhhCC-CCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHHHH
Q 030714 33 LPIANISRIMKKALP-ANGKIAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWAMA 97 (173)
Q Consensus 33 LP~A~I~RImK~~LP-~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~AL~ 97 (173)
|+...|.+.+++.+. .++.+++++..+|.+.+.-=+..+-.+....+.-.+++ |+.++|...+.
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 444445555544332 25678898888877765433333333333333223333 66666665543
No 152
>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=23.88 E-value=1.6e+02 Score=17.11 Aligned_cols=39 Identities=21% Similarity=0.207 Sum_probs=26.2
Q ss_pred HHHHhcCCCCcCchhhHHHHHhcCCcchhhHHHHHHHHH
Q 030714 77 DKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLMRY 115 (173)
Q Consensus 77 d~c~~~kRKTIs~eDVl~AL~~LgF~~yv~~Lk~~L~~y 115 (173)
..+..++.-.|+.+|+..+++.++...-.+.+...+..+
T Consensus 7 ~~~d~~~~g~l~~~e~~~~l~~~~~~~~~~~~~~~~~~~ 45 (63)
T cd00051 7 RLFDKDGDGTISADELKAALKSLGEGLSEEEIDEMIREV 45 (63)
T ss_pred HHhCCCCCCcCcHHHHHHHHHHhCCCCCHHHHHHHHHHh
Confidence 344455556789999999999988665555555555444
No 153
>PRK06585 holA DNA polymerase III subunit delta; Reviewed
Probab=23.54 E-value=1.9e+02 Score=25.02 Aligned_cols=60 Identities=17% Similarity=0.152 Sum_probs=39.7
Q ss_pred HHHHHHhhCC-CCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHh-cCCCCcCchhhHHHHH
Q 030714 38 ISRIMKKALP-ANGKIAKDAKDTVQECVSEFISFITSEASDKCQK-EKRKTINGDDLLWAMA 97 (173)
Q Consensus 38 I~RImK~~LP-~~~rISkDA~~al~~ca~eFI~~LtseA~d~c~~-~kRKTIs~eDVl~AL~ 97 (173)
+.+++++.+. .+.+|+.||...|.+++.-=...+..|-...+.- .+.++|+.+||...+.
T Consensus 147 l~~~i~~~~~~~g~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~It~edV~~lv~ 208 (343)
T PRK06585 147 LARLIDDELAEAGLRITPDARALLVALLGGDRLASRNEIEKLALYAHGKGEITLDDVRAVVG 208 (343)
T ss_pred HHHHHHHHHHHCCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHhC
Confidence 3344443332 2578999999999998886555555555555543 3456799999977654
No 154
>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=22.73 E-value=55 Score=21.03 Aligned_cols=16 Identities=19% Similarity=0.406 Sum_probs=13.6
Q ss_pred cCchhhHHHHHhcCCc
Q 030714 87 INGDDLLWAMATLGFE 102 (173)
Q Consensus 87 Is~eDVl~AL~~LgF~ 102 (173)
++.++|..+++.+||+
T Consensus 47 ~~~~~i~~~i~~~Gy~ 62 (62)
T PF00403_consen 47 TSIEKIIEAIEKAGYE 62 (62)
T ss_dssp SCHHHHHHHHHHTTSE
T ss_pred CCHHHHHHHHHHhCcC
Confidence 5678899999999985
No 155
>cd00052 EH Eps15 homology domain; found in proteins implicated in endocytosis, vesicle transport, and signal transduction. The alignment contains a pair of EF-hand motifs, typically one of them is canonical and binds to Ca2+, while the other may not bind to Ca2+. A hydrophobic binding pocket is formed by residues from both EF-hand motifs. The EH domain binds to proteins containing NPF (class I), [WF]W or SWG (class II), or H[TS]F (class III) sequence motifs.
Probab=22.17 E-value=2e+02 Score=18.01 Aligned_cols=25 Identities=16% Similarity=0.210 Sum_probs=18.5
Q ss_pred HHHHhcCCCCcCchhhHHHHHhcCC
Q 030714 77 DKCQKEKRKTINGDDLLWAMATLGF 101 (173)
Q Consensus 77 d~c~~~kRKTIs~eDVl~AL~~LgF 101 (173)
.....++.-.|+.+++..+|..+|+
T Consensus 6 ~~~D~~~~G~i~~~el~~~l~~~g~ 30 (67)
T cd00052 6 RSLDPDGDGLISGDEARPFLGKSGL 30 (67)
T ss_pred HHhCCCCCCcCcHHHHHHHHHHcCC
Confidence 3344556667888999999888887
No 156
>PF12668 DUF3791: Protein of unknown function (DUF3791); InterPro: IPR024269 This entry represents proteins of unknown function.
Probab=21.69 E-value=93 Score=20.88 Aligned_cols=30 Identities=27% Similarity=0.314 Sum_probs=22.3
Q ss_pred CCCCcCchhhHHHHHhcCCcchhhHHHHHH
Q 030714 83 KRKTINGDDLLWAMATLGFEDYIDPLKAYL 112 (173)
Q Consensus 83 kRKTIs~eDVl~AL~~LgF~~yv~~Lk~~L 112 (173)
+|+-|++++++.-+++.+.-+|+.+--..|
T Consensus 13 ~~~~~s~~ea~~~~~~~~~~~~i~~~Yd~l 42 (62)
T PF12668_consen 13 KKLNISGEEAYNYFKRSGVIDYIIDCYDVL 42 (62)
T ss_pred HHHCcCHHHHHHHHHHcCcHHHHHHcchHH
Confidence 355689999999999888877776654444
No 157
>PTZ00184 calmodulin; Provisional
Probab=21.60 E-value=2.3e+02 Score=20.34 Aligned_cols=40 Identities=18% Similarity=0.180 Sum_probs=27.4
Q ss_pred HHHHHHHhcCCCCcCchhhHHHHHhcCCcchhhHHHHHHH
Q 030714 74 EASDKCQKEKRKTINGDDLLWAMATLGFEDYIDPLKAYLM 113 (173)
Q Consensus 74 eA~d~c~~~kRKTIs~eDVl~AL~~LgF~~yv~~Lk~~L~ 113 (173)
.+...+..+++-.|+.+|+..+|..+|+.---+.++..+.
T Consensus 88 ~~F~~~D~~~~g~i~~~e~~~~l~~~~~~~~~~~~~~~~~ 127 (149)
T PTZ00184 88 EAFKVFDRDGNGFISAAELRHVMTNLGEKLTDEEVDEMIR 127 (149)
T ss_pred HHHHhhCCCCCCeEeHHHHHHHHHHHCCCCCHHHHHHHHH
Confidence 3445555567778999999999999887644444554443
No 158
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=21.49 E-value=58 Score=27.55 Aligned_cols=39 Identities=15% Similarity=0.400 Sum_probs=30.0
Q ss_pred CchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHH
Q 030714 33 LPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSEAS 76 (173)
Q Consensus 33 LP~A~I~RImK~~LP~~~rISkDA~~al~~ca~eFI~~LtseA~ 76 (173)
+-+++|.|++... .+||.+.++-+.+++.+ +.|.-..+.
T Consensus 13 VS~~TVSrvLn~~----~~Vs~~tr~rV~~~a~e-lgY~pn~~a 51 (343)
T PRK10727 13 VSVATVSRVINNS----PKASEASRLAVHSAMES-LSYHPNANA 51 (343)
T ss_pred CCHHHHHHHhCCC----CCCCHHHHHHHHHHHHH-HCCCCCHHH
Confidence 4578999998653 36999999999999998 466554443
No 159
>PRK09492 treR trehalose repressor; Provisional
Probab=21.39 E-value=73 Score=26.37 Aligned_cols=38 Identities=13% Similarity=0.406 Sum_probs=29.2
Q ss_pred cCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHH
Q 030714 32 YLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSE 74 (173)
Q Consensus 32 ~LP~A~I~RImK~~LP~~~rISkDA~~al~~ca~eFI~~Ltse 74 (173)
.+-+++|.|++... .+||.+.++-+.+++.+. .|.-..
T Consensus 15 gVS~~TVSrvLn~~----~~vs~~tr~rV~~~a~el-gY~pn~ 52 (315)
T PRK09492 15 GVGKSTVSRVLNNE----SGVSEETRERVEAVINQH-GFSPSK 52 (315)
T ss_pred CCCHHHHhHHhCCC----CCCCHHHHHHHHHHHHHH-CCCcCH
Confidence 45678999998753 479999999999999885 455443
No 160
>TIGR01481 ccpA catabolite control protein A. Catabolite control protein A is a LacI family global transcriptional regulator found in Gram-positive bacteria. CcpA is involved in repressing carbohydrate utilization genes [ex: alpha-amylase (amyE), acetyl-coenzyme A synthase (acsA)] and in activating genes involved in transporting excess carbon from the cell [ex: acetate kinase (ackA), alpha-acetolactate synthase (alsS)]. Additionally, disruption of CcpA in Bacillus megaterium, Staphylococcus xylosus, Lactobacillus casei and Lactocacillus pentosus also decreases growth rate, which suggests CcpA is involved in the regulation of other metabolic pathways.
Probab=21.13 E-value=89 Score=26.02 Aligned_cols=38 Identities=13% Similarity=0.333 Sum_probs=29.1
Q ss_pred cCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHH
Q 030714 32 YLPIANISRIMKKALPANGKIAKDAKDTVQECVSEFISFITSE 74 (173)
Q Consensus 32 ~LP~A~I~RImK~~LP~~~rISkDA~~al~~ca~eFI~~Ltse 74 (173)
.+-+++|.|++... .+||++.++-+.+++++. .|.-..
T Consensus 12 gvS~~TVSrvLn~~----~~vs~~tr~rV~~~a~~l-gY~pn~ 49 (329)
T TIGR01481 12 GVSMATVSRVVNGN----PNVKPATRKKVLEVIKRL-DYRPNA 49 (329)
T ss_pred CCCHHHHHHHhCCC----CCCCHHHHHHHHHHHHHH-CCCCCH
Confidence 35578999998753 379999999999999885 554443
No 161
>PF14644 DUF4456: Domain of unknown function (DUF4456)
Probab=20.07 E-value=1.7e+02 Score=24.18 Aligned_cols=43 Identities=12% Similarity=0.076 Sum_probs=33.7
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcCchhhHHH
Q 030714 52 IAKDAKDTVQECVSEFISFITSEASDKCQKEKRKTINGDDLLWA 95 (173)
Q Consensus 52 ISkDA~~al~~ca~eFI~~LtseA~d~c~~~kRKTIs~eDVl~A 95 (173)
.+....+.+.+++..||.-|+......+.-=. .-|+++||...
T Consensus 149 ~~~~l~~~~~~~a~~f~~~l~~~~~~ll~~lD-~~vt~dDl~~~ 191 (208)
T PF14644_consen 149 FWEKLLEEVRKEAQMFVARLAQFTEKLLLLLD-EVVTPDDLQPP 191 (208)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-cCCCHHHcCCC
Confidence 56677888899999999999988886665554 66888888654
No 162
>CHL00076 chlB photochlorophyllide reductase subunit B
Probab=20.06 E-value=2e+02 Score=27.14 Aligned_cols=51 Identities=8% Similarity=0.090 Sum_probs=39.5
Q ss_pred CCcccHHHHHHHHHHHHHHHH-HHHHHHHHHHHhcCCCCcCchhhHHHHHhcC
Q 030714 49 NGKIAKDAKDTVQECVSEFIS-FITSEASDKCQKEKRKTINGDDLLWAMATLG 100 (173)
Q Consensus 49 ~~rISkDA~~al~~ca~eFI~-~LtseA~d~c~~~kRKTIs~eDVl~AL~~Lg 100 (173)
.+.++.||...|.+. =-|+. -+=..+-..|++++...|+.|.|..|=..+|
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 467999999999987 44554 3334445778899999999999999977665
Done!