Query 045194
Match_columns 157
No_of_seqs 143 out of 546
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 10:45:16 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045194.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045194hhsearch_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 6.9E-38 1.5E-42 247.5 10.6 97 2-98 26-122 (168)
2 KOG0871 Class 2 transcription 100.0 2.4E-30 5.1E-35 202.9 10.9 114 2-115 6-119 (156)
3 KOG0870 DNA polymerase epsilon 99.9 1.1E-25 2.4E-30 179.2 11.6 97 3-99 5-102 (172)
4 COG5150 Class 2 transcription 99.9 2.2E-24 4.7E-29 166.3 9.7 112 3-114 6-117 (148)
5 PF00808 CBFD_NFYB_HMF: Histon 99.8 3.6E-18 7.8E-23 115.7 7.9 64 8-72 2-65 (65)
6 COG2036 HHT1 Histones H3 and H 99.7 2.3E-17 5E-22 120.7 6.6 77 3-81 14-90 (91)
7 cd00076 H4 Histone H4, one of 99.3 2.3E-11 5E-16 88.0 8.0 71 8-80 13-83 (85)
8 PLN00035 histone H4; Provision 99.2 5.3E-11 1.1E-15 89.0 8.0 70 7-78 28-97 (103)
9 PTZ00015 histone H4; Provision 99.2 1.7E-10 3.7E-15 86.1 8.0 71 7-79 29-99 (102)
10 smart00803 TAF TATA box bindin 99.0 9.1E-10 2E-14 75.8 7.4 64 8-73 2-65 (65)
11 smart00417 H4 Histone H4. 99.0 1E-09 2.2E-14 77.7 6.0 63 7-71 12-74 (74)
12 smart00428 H3 Histone H3. 99.0 1.9E-09 4E-14 80.9 6.8 74 3-76 24-102 (105)
13 cd07981 TAF12 TATA Binding Pro 98.9 1E-08 2.2E-13 71.4 8.1 65 9-74 2-66 (72)
14 PF00125 Histone: Core histone 98.9 6.2E-09 1.3E-13 71.4 6.5 68 6-73 3-73 (75)
15 COG5208 HAP5 CCAAT-binding fac 98.7 9.4E-09 2E-13 86.4 4.4 77 5-83 106-183 (286)
16 PLN00121 histone H3; Provision 98.6 7.7E-08 1.7E-12 75.2 5.9 71 3-73 57-130 (136)
17 PLN00160 histone H3; Provision 98.6 1.3E-07 2.7E-12 70.2 6.6 71 3-73 16-90 (97)
18 PLN00161 histone H3; Provision 98.6 1.9E-07 4.1E-12 72.9 7.6 71 3-73 50-124 (135)
19 PTZ00018 histone H3; Provision 98.6 1.1E-07 2.4E-12 74.2 6.1 72 3-74 57-131 (136)
20 smart00576 BTP Bromodomain tra 98.5 9E-07 1.9E-11 62.1 7.9 66 11-78 9-74 (77)
21 cd00074 H2A Histone 2A; H2A is 98.3 1.9E-06 4.2E-11 65.5 6.9 68 6-74 18-85 (115)
22 KOG1657 CCAAT-binding factor, 98.3 6.6E-07 1.4E-11 75.3 4.5 83 7-91 73-159 (236)
23 cd07979 TAF9 TATA Binding Prot 98.2 7.2E-06 1.6E-10 62.2 7.4 78 12-91 5-83 (117)
24 PF15630 CENP-S: Kinetochore c 98.0 3.7E-05 8E-10 54.6 7.1 62 13-74 10-72 (76)
25 cd08050 TAF6 TATA Binding Prot 97.9 4.8E-05 1E-09 66.5 8.0 67 10-78 1-67 (343)
26 KOG1745 Histones H3 and H4 [Ch 97.8 1.1E-05 2.5E-10 63.1 2.8 74 3-76 58-134 (137)
27 smart00427 H2B Histone H2B. 97.8 9.6E-05 2.1E-09 54.2 7.3 62 13-75 6-67 (89)
28 PF15511 CENP-T: Centromere ki 97.8 3.9E-05 8.5E-10 68.9 6.2 60 8-67 351-414 (414)
29 PF07524 Bromo_TP: Bromodomain 97.8 0.0002 4.4E-09 49.7 8.1 65 12-78 10-74 (77)
30 PF03847 TFIID_20kDa: Transcri 97.7 0.00024 5.2E-09 49.4 7.4 63 11-74 2-64 (68)
31 KOG3467 Histone H4 [Chromatin 97.7 0.00018 3.8E-09 53.1 6.9 68 9-78 30-97 (103)
32 KOG1659 Class 2 transcription 97.6 0.00024 5.2E-09 59.5 7.6 83 8-92 13-96 (224)
33 PLN00158 histone H2B; Provisio 97.6 0.00029 6.2E-09 53.9 7.3 63 12-75 31-93 (116)
34 PTZ00463 histone H2B; Provisio 97.6 0.00036 7.7E-09 53.5 7.3 62 13-75 33-94 (117)
35 cd08048 TAF11 TATA Binding Pro 97.5 0.00059 1.3E-08 49.3 7.7 66 8-75 16-84 (85)
36 PF09415 CENP-X: CENP-S associ 97.5 0.00023 5E-09 50.0 4.6 64 10-73 1-66 (72)
37 COG5247 BUR6 Class 2 transcrip 97.3 0.00074 1.6E-08 51.0 6.4 78 8-87 23-101 (113)
38 COG5262 HTA1 Histone H2A [Chro 97.3 0.00059 1.3E-08 52.7 5.6 68 6-74 24-91 (132)
39 PF02969 TAF: TATA box binding 97.2 0.0027 5.9E-08 44.0 7.6 64 8-73 3-66 (66)
40 PF04719 TAFII28: hTAFII28-lik 97.2 0.0017 3.7E-08 47.5 6.8 67 8-75 23-90 (90)
41 smart00414 H2A Histone 2A. 97.1 0.0017 3.7E-08 48.7 6.3 68 6-74 7-74 (106)
42 PLN00154 histone H2A; Provisio 96.9 0.0028 6.2E-08 49.7 6.2 69 6-74 36-104 (136)
43 PTZ00017 histone H2A; Provisio 96.7 0.0036 7.8E-08 49.0 5.6 68 6-74 25-92 (134)
44 KOG1658 DNA polymerase epsilon 96.6 0.0018 4E-08 51.9 2.9 68 7-76 58-126 (162)
45 KOG1756 Histone 2A [Chromatin 96.5 0.0074 1.6E-07 47.0 5.9 68 6-74 25-92 (131)
46 KOG1744 Histone H2B [Chromatin 96.5 0.01 2.2E-07 46.2 6.6 62 13-75 42-103 (127)
47 KOG1142 Transcription initiati 96.5 0.0056 1.2E-07 52.5 5.4 67 6-73 152-218 (258)
48 PLN00157 histone H2A; Provisio 96.5 0.0064 1.4E-07 47.5 5.3 68 6-74 24-91 (132)
49 PLN00153 histone H2A; Provisio 96.4 0.0081 1.8E-07 46.8 5.5 68 6-74 22-89 (129)
50 PLN00156 histone H2AX; Provisi 96.4 0.0094 2E-07 47.0 5.8 68 6-74 27-94 (139)
51 PF02269 TFIID-18kDa: Transcri 96.2 0.0061 1.3E-07 44.4 3.7 59 15-74 8-66 (93)
52 PF15510 CENP-W: Centromere ki 95.9 0.015 3.2E-07 43.3 4.6 65 8-73 16-94 (102)
53 KOG3219 Transcription initiati 95.6 0.014 3.1E-07 48.2 3.9 70 7-78 111-181 (195)
54 PF02291 TFIID-31kDa: Transcri 95.4 0.085 1.8E-06 40.9 7.2 84 7-92 9-95 (129)
55 PTZ00252 histone H2A; Provisio 95.0 0.078 1.7E-06 41.6 6.1 68 6-74 23-92 (134)
56 KOG4336 TBP-associated transcr 94.0 0.36 7.8E-06 42.6 8.4 76 14-93 11-86 (323)
57 cd07978 TAF13 The TATA Binding 94.0 0.26 5.7E-06 36.0 6.5 78 13-94 7-84 (92)
58 KOG3423 Transcription initiati 90.7 1.5 3.2E-05 35.8 7.5 68 8-78 86-168 (176)
59 KOG2549 Transcription initiati 89.7 1.5 3.2E-05 41.6 7.6 66 11-78 14-79 (576)
60 TIGR03015 pepcterm_ATPase puta 89.2 1.4 3E-05 35.6 6.4 69 9-77 192-268 (269)
61 KOG2389 Predicted bromodomain 86.8 1.3 2.8E-05 39.8 5.0 70 7-78 28-97 (353)
62 PRK00411 cdc6 cell division co 86.7 4 8.6E-05 35.1 8.0 72 11-82 209-289 (394)
63 TIGR02928 orc1/cdc6 family rep 82.9 7.7 0.00017 32.9 8.0 74 12-85 202-284 (365)
64 PF13654 AAA_32: AAA domain; P 77.9 11 0.00023 35.2 7.7 49 27-75 447-506 (509)
65 KOG3334 Transcription initiati 75.6 8.4 0.00018 30.8 5.5 61 28-88 31-92 (148)
66 TIGR02902 spore_lonB ATP-depen 73.6 11 0.00023 35.1 6.5 64 11-75 265-332 (531)
67 COG5095 TAF6 Transcription ini 72.6 15 0.00033 33.3 6.9 54 25-78 20-73 (450)
68 KOG1757 Histone 2A [Chromatin 70.1 7.1 0.00015 30.2 3.8 64 6-73 28-95 (131)
69 TIGR00764 lon_rel lon-related 70.0 18 0.0004 34.3 7.3 49 27-75 330-391 (608)
70 PF08369 PCP_red: Proto-chloro 65.2 11 0.00024 23.9 3.4 42 29-71 2-44 (45)
71 PF02861 Clp_N: Clp amino term 63.8 11 0.00023 23.1 3.1 26 51-76 1-26 (53)
72 PF00531 Death: Death domain; 63.0 17 0.00038 24.1 4.3 60 28-88 24-83 (83)
73 COG1067 LonB Predicted ATP-dep 61.2 8.1 0.00018 37.2 3.2 48 27-74 338-398 (647)
74 KOG3901 Transcription initiati 60.6 24 0.00053 26.8 5.0 48 24-74 24-71 (109)
75 cd08045 TAF4 TATA Binding Prot 59.8 72 0.0016 26.0 8.2 77 7-83 43-127 (212)
76 COG5162 Transcription initiati 57.3 78 0.0017 26.1 7.8 68 8-78 88-189 (197)
77 PF13335 Mg_chelatase_2: Magne 56.5 44 0.00096 24.1 5.7 47 27-73 42-94 (96)
78 PF09114 MotA_activ: Transcrip 55.8 19 0.00042 26.8 3.7 34 12-45 51-88 (96)
79 KOG2680 DNA helicase TIP49, TB 54.9 59 0.0013 29.8 7.3 50 24-73 374-427 (454)
80 TIGR02030 BchI-ChlI magnesium 54.2 55 0.0012 28.8 7.0 53 19-72 247-306 (337)
81 PRK09862 putative ATP-dependen 52.4 60 0.0013 30.4 7.2 59 26-84 437-501 (506)
82 TIGR02442 Cob-chelat-sub cobal 52.2 52 0.0011 31.2 6.9 50 24-73 246-302 (633)
83 CHL00081 chlI Mg-protoporyphyr 48.0 51 0.0011 29.3 5.8 54 19-73 260-320 (350)
84 PRK00080 ruvB Holliday junctio 47.9 84 0.0018 26.7 7.0 70 10-79 181-254 (328)
85 PF07647 SAM_2: SAM domain (St 46.3 26 0.00055 22.6 2.8 24 63-86 4-27 (66)
86 COG5248 TAF19 Transcription in 46.1 62 0.0013 25.0 5.2 49 24-74 24-72 (126)
87 cd00166 SAM Sterile alpha moti 45.6 22 0.00048 22.1 2.4 24 64-87 3-26 (63)
88 TIGR01128 holA DNA polymerase 45.6 1E+02 0.0022 25.2 6.9 65 9-73 111-176 (302)
89 PF03540 TFIID_30kDa: Transcri 44.8 90 0.002 20.6 6.2 47 8-57 2-49 (51)
90 PRK07452 DNA polymerase III su 44.6 83 0.0018 26.5 6.4 65 14-78 135-202 (326)
91 COG1224 TIP49 DNA helicase TIP 44.3 79 0.0017 29.4 6.5 67 24-93 377-447 (450)
92 PF12010 DUF3502: Domain of un 43.7 23 0.00051 26.9 2.7 60 31-94 73-132 (134)
93 PRK13406 bchD magnesium chelat 43.5 54 0.0012 31.1 5.6 52 21-73 190-248 (584)
94 PRK12402 replication factor C 43.3 83 0.0018 26.1 6.2 71 9-81 184-255 (337)
95 cd04752 Commd4 COMM_Domain con 42.5 1.7E+02 0.0037 23.1 9.9 53 39-98 43-96 (174)
96 PF00536 SAM_1: SAM domain (St 42.0 31 0.00068 22.1 2.7 22 64-85 4-25 (64)
97 PRK13407 bchI magnesium chelat 41.0 89 0.0019 27.5 6.2 53 19-72 244-303 (334)
98 TIGR00635 ruvB Holliday juncti 40.9 1.2E+02 0.0027 24.9 6.8 67 12-78 162-232 (305)
99 PRK13765 ATP-dependent proteas 40.8 46 0.00099 32.0 4.7 47 27-73 339-398 (637)
100 TIGR02454 CbiQ_TIGR cobalt ABC 40.7 57 0.0012 25.3 4.5 38 61-98 112-160 (198)
101 smart00454 SAM Sterile alpha m 39.9 29 0.00063 21.7 2.3 25 63-87 4-28 (68)
102 smart00350 MCM minichromosome 39.7 1.4E+02 0.003 27.5 7.5 67 8-74 417-503 (509)
103 PF07499 RuvA_C: RuvA, C-termi 39.0 22 0.00047 22.4 1.5 14 66-79 4-17 (47)
104 TIGR02031 BchD-ChlD magnesium 38.2 1.1E+02 0.0023 29.0 6.6 55 18-73 195-256 (589)
105 PF02361 CbiQ: Cobalt transpor 37.5 57 0.0012 25.3 4.1 66 27-98 95-172 (224)
106 PF00356 LacI: Bacterial regul 36.6 80 0.0017 20.0 3.9 32 7-42 9-40 (46)
107 TIGR00368 Mg chelatase-related 36.1 89 0.0019 29.1 5.7 47 27-73 445-497 (499)
108 COG1474 CDC6 Cdc6-related prot 35.7 63 0.0014 28.7 4.5 60 27-86 211-276 (366)
109 TIGR01242 26Sp45 26S proteasom 34.4 54 0.0012 28.4 3.8 32 43-74 331-362 (364)
110 PTZ00361 26 proteosome regulat 34.2 52 0.0011 30.2 3.8 31 44-74 393-423 (438)
111 PRK03992 proteasome-activating 33.4 55 0.0012 29.0 3.8 34 43-76 340-373 (389)
112 PHA03328 nuclear egress lamina 33.3 58 0.0013 29.0 3.8 79 6-94 231-309 (316)
113 COG5251 TAF40 Transcription in 32.9 62 0.0013 26.8 3.6 61 8-72 115-178 (199)
114 PF05236 TAF4: Transcription i 32.7 80 0.0017 26.5 4.5 74 6-79 41-122 (264)
115 PF08823 PG_binding_2: Putativ 32.6 64 0.0014 22.5 3.3 31 66-96 19-55 (74)
116 PRK05574 holA DNA polymerase I 30.7 2.3E+02 0.0049 23.6 6.9 64 9-73 146-211 (340)
117 TIGR01052 top6b DNA topoisomer 30.3 91 0.002 29.2 4.7 58 19-90 426-483 (488)
118 PF12627 PolyA_pol_RNAbd: Prob 30.2 15 0.00033 23.7 -0.2 59 25-87 1-63 (64)
119 PRK10423 transcriptional repre 29.7 54 0.0012 26.8 2.9 37 8-49 9-45 (327)
120 PRK09526 lacI lac repressor; R 29.7 46 0.00099 27.5 2.5 37 8-49 16-52 (342)
121 COG1724 Predicted RNA binding 28.1 38 0.00083 23.7 1.4 17 62-78 6-22 (66)
122 PTZ00454 26S protease regulato 27.7 80 0.0017 28.4 3.8 31 44-74 355-385 (398)
123 TIGR01278 DPOR_BchB light-inde 26.7 1.3E+02 0.0027 27.8 5.0 52 24-76 459-511 (511)
124 PF11753 DUF3310: Protein of u 26.5 1.8E+02 0.0038 19.3 4.5 41 31-73 14-56 (60)
125 PF13405 EF-hand_6: EF-hand do 26.0 85 0.0018 17.4 2.5 26 51-76 5-31 (31)
126 PF09123 DUF1931: Domain of un 25.6 59 0.0013 25.7 2.3 54 14-69 1-54 (138)
127 PRK02910 light-independent pro 25.6 1.3E+02 0.0029 27.8 4.9 52 24-76 466-518 (519)
128 PRK06585 holA DNA polymerase I 25.2 2.3E+02 0.0051 24.0 6.1 49 25-73 159-208 (343)
129 PF06782 UPF0236: Uncharacteri 24.9 1.3E+02 0.0028 27.6 4.7 52 23-77 113-165 (470)
130 PRK14971 DNA polymerase III su 24.8 2E+02 0.0043 27.5 6.0 64 9-73 180-244 (614)
131 PRK07914 hypothetical protein; 24.4 1.7E+02 0.0037 24.8 5.1 62 11-73 130-192 (320)
132 COG1500 Predicted exosome subu 24.1 1.8E+02 0.004 24.9 5.1 70 13-85 71-143 (234)
133 PLN00138 large subunit ribosom 23.2 1.7E+02 0.0037 22.1 4.4 28 51-78 6-33 (113)
134 PF00403 HMA: Heavy-metal-asso 22.8 60 0.0013 20.5 1.6 16 63-78 47-62 (62)
135 PTZ00373 60S Acidic ribosomal 22.6 1.8E+02 0.0039 22.1 4.3 28 51-78 8-35 (112)
136 PRK14975 bifunctional 3'-5' ex 22.5 4.4E+02 0.0096 24.6 7.8 90 6-98 161-270 (553)
137 PF07928 Vps54: Vps54-like pro 21.9 30 0.00065 26.7 0.0 36 56-91 61-97 (135)
138 PRK00440 rfc replication facto 21.8 2.4E+02 0.0052 23.0 5.4 65 9-75 161-226 (319)
139 PF09957 DUF2191: Uncharacteri 21.6 2.3E+02 0.0049 18.0 4.3 39 60-98 2-42 (47)
140 PRK11303 DNA-binding transcrip 21.5 72 0.0016 26.1 2.2 38 8-47 11-48 (328)
141 KOG1528 Salt-sensitive 3'-phos 21.3 2.4E+02 0.0051 25.5 5.4 66 11-76 52-124 (351)
142 smart00354 HTH_LACI helix_turn 21.1 1.8E+02 0.0039 19.2 3.8 33 7-43 10-42 (70)
143 PRK09492 treR trehalose repres 21.1 96 0.0021 25.2 2.8 37 8-49 15-51 (315)
144 TIGR01481 ccpA catabolite cont 20.4 1.2E+02 0.0026 24.8 3.2 36 8-48 12-47 (329)
145 PF14434 Imm6: Immunity protei 20.3 3.9E+02 0.0086 20.3 6.6 50 35-85 9-65 (122)
146 PF09339 HTH_IclR: IclR helix- 20.3 55 0.0012 20.4 1.0 16 6-21 27-42 (52)
147 smart00027 EH Eps15 homology d 20.2 2.1E+02 0.0046 19.7 4.1 29 50-78 14-42 (96)
148 PRK14987 gluconate operon tran 20.1 89 0.0019 25.7 2.4 37 8-49 16-52 (331)
No 1
>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [Transcription]
Probab=100.00 E-value=6.9e-38 Score=247.46 Aligned_cols=97 Identities=67% Similarity=1.106 Sum_probs=95.3
Q ss_pred cccccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHhhCCCchhH
Q 045194 2 VEEQDKLLPIANVGKIMKQILPPRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALSTLGFDNYT 81 (157)
Q Consensus 2 ~~e~D~~LP~A~I~RImK~~LP~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~LgF~~y~ 81 (157)
.+++|+.||+|||.||||..||.+++|||||++.+|+|++|||+|||++|+++|..++|||||+|||||||..|||++|+
T Consensus 26 ~reqDr~LPIANV~RIMK~~lP~naKIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIngdDllwAm~tLGFe~Y~ 105 (168)
T KOG0869|consen 26 LREQDRFLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASEKCQREKRKTINGDDLLWAMSTLGFENYA 105 (168)
T ss_pred cchhhhhccHHHHHHHHHhcCCcccccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCcccHHHHHHHHHHcCcHhHH
Confidence 57899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHH
Q 045194 82 EAIVRYLHKYREDERER 98 (157)
Q Consensus 82 ~~L~~~L~~yre~~~~k 98 (157)
++|+.||.+||+.+.+|
T Consensus 106 eplkiyL~kYRe~e~e~ 122 (168)
T KOG0869|consen 106 EPLKIYLQKYRELEGER 122 (168)
T ss_pred HHHHHHHHHHHHHhhhc
Confidence 99999999999998887
No 2
>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=99.97 E-value=2.4e-30 Score=202.91 Aligned_cols=114 Identities=32% Similarity=0.611 Sum_probs=108.3
Q ss_pred cccccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHhhCCCchhH
Q 045194 2 VEEQDKLLPIANVGKIMKQILPPRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALSTLGFDNYT 81 (157)
Q Consensus 2 ~~e~D~~LP~A~I~RImK~~LP~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~LgF~~y~ 81 (157)
..++|+.||+|+|.+|||+.||.+++|.+||+++|.+||.+||++|+++||++|..+.||||+++||+.||+.|||.+|+
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 35678999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHhhhccCCccCCCcchhc
Q 045194 82 EAIVRYLHKYREDERERAKNQSKVTATSSNEDKA 115 (157)
Q Consensus 82 ~~L~~~L~~yre~~~~k~~nq~K~~~~~~t~~~~ 115 (157)
+.+.+.|+.|+.....|+....|...+|+|.+|+
T Consensus 86 ee~~~vl~~~K~~~~~~~~kssk~e~~Gi~eEEL 119 (156)
T KOG0871|consen 86 EEAEEVLENCKEEAKKRRRKSSKFEKSGIPEEEL 119 (156)
T ss_pred HHHHHHHHHHHHHHHHhhhhhhhHHhcCCCHHHH
Confidence 9999999999999887778888888899998854
No 3
>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription]
Probab=99.93 E-value=1.1e-25 Score=179.23 Aligned_cols=97 Identities=28% Similarity=0.511 Sum_probs=94.0
Q ss_pred ccccccCchhHHHHHHhhhCCCC-ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHhhCCCchhH
Q 045194 3 EEQDKLLPIANVGKIMKQILPPR-AKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALSTLGFDNYT 81 (157)
Q Consensus 3 ~e~D~~LP~A~I~RImK~~LP~~-~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~LgF~~y~ 81 (157)
+.+|+.||.|+|.||+|++||.. +.|||||+.+|+++|++||+||++.|+++|+.++||||+++||+.||+++||..|+
T Consensus 5 ri~dl~lP~AiI~rlvke~l~E~~vsisKeA~~Ai~raAtVFv~~Lts~s~e~A~~q~rKt~sadDVl~aL~Eiefs~f~ 84 (172)
T KOG0870|consen 5 RIEDLNLPNAIITRLVKEVLPESNVSISKEARLAIARAATVFVIFLTSVSNEIAKDQKRKTISADDVLKALDEIEFSSFV 84 (172)
T ss_pred hHHHhhccHHHHHHHHHHhCccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCcccHHHHHHHHHHhchHHHh
Confidence 45789999999999999999987 99999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHh
Q 045194 82 EAIVRYLHKYREDERERA 99 (157)
Q Consensus 82 ~~L~~~L~~yre~~~~k~ 99 (157)
.+|+..|+.|+...+.|+
T Consensus 85 ~plk~~Le~yk~~~k~Kk 102 (172)
T KOG0870|consen 85 NPLKSALEAYKKAVKQKK 102 (172)
T ss_pred hHHHHHHHHHHHHHHHHH
Confidence 999999999999999986
No 4
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=99.91 E-value=2.2e-24 Score=166.34 Aligned_cols=112 Identities=26% Similarity=0.494 Sum_probs=107.5
Q ss_pred ccccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHhhCCCchhHH
Q 045194 3 EEQDKLLPIANVGKIMKQILPPRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALSTLGFDNYTE 82 (157)
Q Consensus 3 ~e~D~~LP~A~I~RImK~~LP~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~LgF~~y~~ 82 (157)
.+++..||+|+|.+++-+.||.+..+.|||++.+++||.+||+.|+++|++.|..+.+|||.++||+.||+.|||.+|++
T Consensus 6 ~dDe~sLPKATVqKMvS~iLp~dl~ftKearei~in~cieFi~~lsseAne~ce~EaKKTIa~EHviKALenLef~eyi~ 85 (148)
T COG5150 6 NDDENSLPKATVQKMVSSILPKDLVFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHVIKALENLEFEEYIE 85 (148)
T ss_pred ccccccCcHHHHHHHHHHhccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHhccHHHHHH
Confidence 35678899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhhhccCCccCCCcchh
Q 045194 83 AIVRYLHKYREDERERAKNQSKVTATSSNEDK 114 (157)
Q Consensus 83 ~L~~~L~~yre~~~~k~~nq~K~~~~~~t~~~ 114 (157)
.+.+.+..|+..++.|.++..|..++|.+.+|
T Consensus 86 ~~~e~~~n~k~~qK~ke~k~sKFk~SGls~eE 117 (148)
T COG5150 86 SCMEEHENYKSYQKQKESKISKFKDSGLSMEE 117 (148)
T ss_pred HHHHHHHHHHHHHhhchhhhhHHHhcCCCHHH
Confidence 99999999999999999999999999998773
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=99.75 E-value=3.6e-18 Score=115.68 Aligned_cols=64 Identities=36% Similarity=0.597 Sum_probs=59.1
Q ss_pred cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHH
Q 045194 8 LLPIANVGKIMKQILPPRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWAL 72 (157)
Q Consensus 8 ~LP~A~I~RImK~~LP~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL 72 (157)
.||++.|.||||.. |+..+||+||..+|++|+++||.||+.+|++.|..++||||+++||..||
T Consensus 2 ~lP~a~vkri~k~~-~~~~~vs~ea~~~i~~a~e~Fi~~l~~~A~~~a~~~~rkti~~~Dv~~Av 65 (65)
T PF00808_consen 2 SLPLARVKRIMKSD-PDVMRVSKEAVEAIAKAAEEFIQYLAKEANEIAQRDKRKTITYEDVAKAV 65 (65)
T ss_dssp SS-HHHHHHHHHHT-STTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEE-HHHHHHHH
T ss_pred CCChHHHHHHhccC-CCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHC
Confidence 59999999999999 88889999999999999999999999999999999999999999999986
No 6
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=99.70 E-value=2.3e-17 Score=120.71 Aligned_cols=77 Identities=31% Similarity=0.457 Sum_probs=72.4
Q ss_pred ccccccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHhhCCCchhH
Q 045194 3 EEQDKLLPIANVGKIMKQILPPRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALSTLGFDNYT 81 (157)
Q Consensus 3 ~e~D~~LP~A~I~RImK~~LP~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~LgF~~y~ 81 (157)
+..|..||+++|.||||++.++ +||.+|++.|++++++|+..|+..|+++|.|+|||||+++||..|++.+||..|.
T Consensus 14 ~~~~~~Lp~apv~Ri~r~~~~~--Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~DI~la~~~~~~~~~~ 90 (91)
T COG2036 14 RSTDLLLPKAPVRRILRKAGAE--RVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLALKRLGRRIYG 90 (91)
T ss_pred hhhhhhcCchHHHHHHHHHhHH--HhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHHHhcccccc
Confidence 4567899999999999999765 9999999999999999999999999999999999999999999999999998763
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=99.27 E-value=2.3e-11 Score=88.03 Aligned_cols=71 Identities=18% Similarity=0.251 Sum_probs=66.4
Q ss_pred cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHhhCCCchh
Q 045194 8 LLPIANVGKIMKQILPPRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALSTLGFDNY 80 (157)
Q Consensus 8 ~LP~A~I~RImK~~LP~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~LgF~~y 80 (157)
.||++.|.||++.. +-.+||.|+.+.+.++..+|+..|..+|..+|.+.+||||+++||..||+..|-.-|
T Consensus 13 gi~k~~I~RLarr~--GvkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~alkr~g~~~y 83 (85)
T cd00076 13 GITKPAIRRLARRG--GVKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLY 83 (85)
T ss_pred cCCHHHHHHHHHHc--CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHCCCCcc
Confidence 59999999999998 567899999999999999999999999999999999999999999999999985533
No 8
>PLN00035 histone H4; Provisional
Probab=99.22 E-value=5.3e-11 Score=89.00 Aligned_cols=70 Identities=19% Similarity=0.210 Sum_probs=65.6
Q ss_pred ccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHhhCCCc
Q 045194 7 KLLPIANVGKIMKQILPPRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALSTLGFD 78 (157)
Q Consensus 7 ~~LP~A~I~RImK~~LP~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~LgF~ 78 (157)
..||++.|.||++.. +--+||.|+.+.+.+..++|+..|..+|..+|.+.+||||+++||..||+..|-.
T Consensus 28 ~~ipk~~IrRLARr~--GvkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr~g~~ 97 (103)
T PLN00035 28 QGITKPAIRRLARRG--GVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRT 97 (103)
T ss_pred ccCCHHHHHHHHHHc--CcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHcCCc
Confidence 359999999999998 5668999999999999999999999999999999999999999999999988754
No 9
>PTZ00015 histone H4; Provisional
Probab=99.15 E-value=1.7e-10 Score=86.13 Aligned_cols=71 Identities=17% Similarity=0.243 Sum_probs=66.4
Q ss_pred ccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHhhCCCch
Q 045194 7 KLLPIANVGKIMKQILPPRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALSTLGFDN 79 (157)
Q Consensus 7 ~~LP~A~I~RImK~~LP~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~LgF~~ 79 (157)
..||++.|.||++.. +--+||.|+.+.+.++.++|+..|..+|..+|.+.+||||+++||..||+..|-.-
T Consensus 29 ~gI~k~~IrRLarr~--GvkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~AlKr~g~~~ 99 (102)
T PTZ00015 29 RGITKGAIRRLARRG--GVKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALKRQGRTL 99 (102)
T ss_pred cCCCHHHHHHHHHHc--CCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhcCCCC
Confidence 469999999999998 56789999999999999999999999999999999999999999999999988643
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=99.05 E-value=9.1e-10 Score=75.77 Aligned_cols=64 Identities=23% Similarity=0.242 Sum_probs=60.3
Q ss_pred cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHh
Q 045194 8 LLPIANVGKIMKQILPPRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALS 73 (157)
Q Consensus 8 ~LP~A~I~RImK~~LP~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~ 73 (157)
.||.++|.||++.. +--+||.|+...|.+-++.|+.-|..+|...+.+.+||||+++||-.||+
T Consensus 2 ~~p~~~i~ria~~~--Gi~ris~~a~~~l~~~~e~rl~~i~~~A~k~~~hakRktlt~~DI~~Alk 65 (65)
T smart00803 2 WLPKETIKDVAESL--GIGNLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSALR 65 (65)
T ss_pred CCCHHHHHHHHHHC--CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCeecHHHHHHHhC
Confidence 58999999999997 45579999999999999999999999999999999999999999999984
No 11
>smart00417 H4 Histone H4.
Probab=98.99 E-value=1e-09 Score=77.71 Aligned_cols=63 Identities=17% Similarity=0.227 Sum_probs=58.7
Q ss_pred ccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHH
Q 045194 7 KLLPIANVGKIMKQILPPRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWA 71 (157)
Q Consensus 7 ~~LP~A~I~RImK~~LP~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~A 71 (157)
..||++.|.||++.. +--+||.++.+.+.+..++|+..|..+|..+|.+.+||||+++||..|
T Consensus 12 ~gI~k~~IrRLaRr~--GvkRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~~a 74 (74)
T smart00417 12 QGITKPAIRRLARRG--GVKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVYA 74 (74)
T ss_pred cCCCHHHHHHHHHHc--CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHheeC
Confidence 369999999999998 566899999999999999999999999999999999999999999753
No 12
>smart00428 H3 Histone H3.
Probab=98.96 E-value=1.9e-09 Score=80.89 Aligned_cols=74 Identities=19% Similarity=0.224 Sum_probs=67.1
Q ss_pred ccccccCchhHHHHHHhhhCCC-----CccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHhhCC
Q 045194 3 EEQDKLLPIANVGKIMKQILPP-----RAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALSTLG 76 (157)
Q Consensus 3 ~e~D~~LP~A~I~RImK~~LP~-----~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~Lg 76 (157)
+..++.+|+....|++++.... +.+++.+|..+||++++.|+.-+...|+..+.+.||+||.++|+..|..--|
T Consensus 24 kst~lLI~k~pF~RLVREI~~~~~~~~~~R~~~~Al~aLQeasE~ylv~lfeda~~~a~HAkRvTl~~kDi~La~rir~ 102 (105)
T smart00428 24 KSTDLLIRKAPFQRLVREIAQKFTTGVDLRFQSSAIMALQEAAEAYLVGLFEDTNLLAIHAKRVTIMPKDIQLARRIRG 102 (105)
T ss_pred cCcccccccccHHHHHHHHHHHcCCCCCceeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccCcHhhHHHHHHHhc
Confidence 4578999999999999998753 7899999999999999999999999999999999999999999988865433
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=1e-08 Score=71.41 Aligned_cols=65 Identities=20% Similarity=0.357 Sum_probs=61.2
Q ss_pred CchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHhh
Q 045194 9 LPIANVGKIMKQILPPRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALST 74 (157)
Q Consensus 9 LP~A~I~RImK~~LP~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~ 74 (157)
|++..+..++++.-| +.+|+.||.++|++.+.+|+.-++..|...|++.||+||.++||..+|+.
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 678889999999866 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=6.2e-09 Score=71.42 Aligned_cols=68 Identities=24% Similarity=0.340 Sum_probs=62.4
Q ss_pred cccCchhHHHHHHhhhCCC---CccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHh
Q 045194 6 DKLLPIANVGKIMKQILPP---RAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALS 73 (157)
Q Consensus 6 D~~LP~A~I~RImK~~LP~---~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~ 73 (157)
+..+|...|.|+.|+..++ ..+||++|..+|+..++.|+.-|...|...|.+.||+||++.||..|++
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 4678999999999998753 2699999999999999999999999999999999999999999999985
No 15
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=98.74 E-value=9.4e-09 Score=86.36 Aligned_cols=77 Identities=27% Similarity=0.307 Sum_probs=70.9
Q ss_pred ccccCchhHHHHHHhhhCCCCcc-ccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHhhCCCchhHHH
Q 045194 5 QDKLLPIANVGKIMKQILPPRAK-ISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALSTLGFDNYTEA 83 (157)
Q Consensus 5 ~D~~LP~A~I~RImK~~LP~~~k-ISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~LgF~~y~~~ 83 (157)
.+..||+|.|.|+||-. ++++ ||.||..++.+.++.||..||-.|+-.+++++|+|+--.||..|++.-++.||+-.
T Consensus 106 k~h~LPlARIkkvMKtd--edVkMisaEaPvlFak~~EiFI~ELTmRAW~~ae~NkRRtLQksDia~Av~kSeMfDFLid 183 (286)
T COG5208 106 KDHNLPLARIKKVMKTD--EDVKMISAEAPVLFAKITEIFIEELTMRAWINAEENKRRTLQKSDIAAAVKKSEMFDFLID 183 (286)
T ss_pred HhccCcHHHHHHHHhcc--cchhheecccchHHHHHHHHHHHHHHHHHHHHHhHhhhhHHHHHHHHHHHHHHHHHhHHhh
Confidence 35689999999999966 6776 99999999999999999999999999999999999999999999999998888644
No 16
>PLN00121 histone H3; Provisional
Probab=98.61 E-value=7.7e-08 Score=75.16 Aligned_cols=71 Identities=15% Similarity=0.189 Sum_probs=65.8
Q ss_pred ccccccCchhHHHHHHhhhCC---CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHh
Q 045194 3 EEQDKLLPIANVGKIMKQILP---PRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALS 73 (157)
Q Consensus 3 ~e~D~~LP~A~I~RImK~~LP---~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~ 73 (157)
+..|+.+|+....||++++.. .+.++..+|..+||++++.|+.-+...++-.+.+.+|.||.+.|+..++.
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 456899999999999999975 37899999999999999999999999999999999999999999988864
No 17
>PLN00160 histone H3; Provisional
Probab=98.61 E-value=1.3e-07 Score=70.23 Aligned_cols=71 Identities=15% Similarity=0.129 Sum_probs=65.2
Q ss_pred ccccccCchhHHHHHHhhhCC----CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHh
Q 045194 3 EEQDKLLPIANVGKIMKQILP----PRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALS 73 (157)
Q Consensus 3 ~e~D~~LP~A~I~RImK~~LP----~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~ 73 (157)
+..++.+|++...|++++... .+.++..+|..+||++++.|+.-+...|+-.|.+.||.||.+.|+..|..
T Consensus 16 kst~lLI~k~pF~RLVREI~~~~~~~~~Rfq~~Al~ALQeAsEayLv~lfed~~lca~HakRVTl~~kD~~L~~r 90 (97)
T PLN00160 16 KSTDLLIRRLPFARLVREIQMEMSREAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTIMPKDMQLARR 90 (97)
T ss_pred cchhhhhccccHHHHHHHHHHHcCCCCcEeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcccccchhhHHHHHH
Confidence 457889999999999999864 35899999999999999999999999999999999999999999988764
No 18
>PLN00161 histone H3; Provisional
Probab=98.60 E-value=1.9e-07 Score=72.90 Aligned_cols=71 Identities=15% Similarity=0.212 Sum_probs=65.3
Q ss_pred ccccccCchhHHHHHHhhhCC----CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHh
Q 045194 3 EEQDKLLPIANVGKIMKQILP----PRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALS 73 (157)
Q Consensus 3 ~e~D~~LP~A~I~RImK~~LP----~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~ 73 (157)
+..++.+|++...|+++++.. .+.++..+|..+||++++.|+.-+...|+-.|.+.+|.||.+.|+..|..
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 456889999999999999863 46899999999999999999999999999999999999999999988864
No 19
>PTZ00018 histone H3; Provisional
Probab=98.58 E-value=1.1e-07 Score=74.24 Aligned_cols=72 Identities=15% Similarity=0.183 Sum_probs=66.0
Q ss_pred ccccccCchhHHHHHHhhhCC---CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHhh
Q 045194 3 EEQDKLLPIANVGKIMKQILP---PRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALST 74 (157)
Q Consensus 3 ~e~D~~LP~A~I~RImK~~LP---~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~ 74 (157)
+..|+.+|+....||++++.. .+.++..+|.++||++++.|+.-+...++-.+.+.+|.||.+.|+..+..-
T Consensus 57 kst~lLI~k~pF~RLVREI~~~~~~~~rf~~~al~aLQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~ri 131 (136)
T PTZ00018 57 KSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRI 131 (136)
T ss_pred ccchhccccccHHHHHHHHHHHcCCcceeeHHHHHHHHHHHHHHHHHHhhhhHHHHHhhcceecchhhHHHHHHh
Confidence 456899999999999999864 478999999999999999999999999999999999999999999888643
No 20
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=98.48 E-value=9e-07 Score=62.06 Aligned_cols=66 Identities=20% Similarity=0.246 Sum_probs=59.7
Q ss_pred hhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHhhCCCc
Q 045194 11 IANVGKIMKQILPPRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALSTLGFD 78 (157)
Q Consensus 11 ~A~I~RImK~~LP~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~LgF~ 78 (157)
+-.|.+|++.. +--+++.+|.+.|.+....|+..|+..+..+|.+.||++++..||..||+++|+.
T Consensus 9 ~~~Vaqil~~~--Gf~~~~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~~~Dv~~Al~~~gi~ 74 (77)
T smart00576 9 RIAVAQILESA--GFDSFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPNLGDVVLALENLGIS 74 (77)
T ss_pred HHHHHHHHHHc--CccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCcc
Confidence 44577788876 3458999999999999999999999999999999999999999999999999974
No 21
>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=98.32 E-value=1.9e-06 Score=65.50 Aligned_cols=68 Identities=10% Similarity=0.148 Sum_probs=62.2
Q ss_pred cccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHhh
Q 045194 6 DKLLPIANVGKIMKQILPPRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALST 74 (157)
Q Consensus 6 D~~LP~A~I~RImK~~LP~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~ 74 (157)
.+.||.+.|.|+||+.- ...+|+.+|...|..+.+-+...|...|...|.+.+|++|+++||..|+..
T Consensus 18 gL~fPV~ri~R~Lk~~~-~a~RVs~~A~VyLaAvLEYL~aEIlelA~n~ak~~k~krItp~hi~lAi~n 85 (115)
T cd00074 18 GLQFPVGRIHRYLKKGR-YAERVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKKRITPRHLQLAVRN 85 (115)
T ss_pred CccCcHHHHHHHHHcCc-cccccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEcHHHHHHHHhc
Confidence 57899999999999843 257999999999999999999999999999999999999999999999864
No 22
>KOG1657 consensus CCAAT-binding factor, subunit C (HAP5) [Transcription]
Probab=98.31 E-value=6.6e-07 Score=75.35 Aligned_cols=83 Identities=24% Similarity=0.287 Sum_probs=71.1
Q ss_pred ccCchhHHHHHHhhhCCCCc-cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHhhCCCchhHH---
Q 045194 7 KLLPIANVGKIMKQILPPRA-KISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALSTLGFDNYTE--- 82 (157)
Q Consensus 7 ~~LP~A~I~RImK~~LP~~~-kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~LgF~~y~~--- 82 (157)
..||++.|.+|||.. +++ +|+.||..++.+||+.||..|+..|+..+...+|+|+...|+-.|+..-.-.+|+.
T Consensus 73 ~~lPlaRiKkimK~d--edv~mI~~Eapvl~aka~E~Fi~elt~~sw~~Tee~~rrtl~~sdia~av~~s~~fdFL~Div 150 (236)
T KOG1657|consen 73 HILPLARIKKIMKSD--EDVSMITAEAPVLFAKACELFITELTLRSWVHTEENKRRTLQKSDIAAAVTQSETFDFLRDIV 150 (236)
T ss_pred ccCcHhhcccccccc--ccccccchhHHHHHHHHHHHHHHHHHHHhhhhhcccccccchHHHHHHHhccCCCccceeccc
Confidence 469999999999977 555 59999999999999999999999999999999999999999999999776666543
Q ss_pred HHHHHHHHH
Q 045194 83 AIVRYLHKY 91 (157)
Q Consensus 83 ~L~~~L~~y 91 (157)
+-+...++|
T Consensus 151 P~~~~~~~~ 159 (236)
T KOG1657|consen 151 PRKILAEKY 159 (236)
T ss_pred cchhccccc
Confidence 334445555
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=98.19 E-value=7.2e-06 Score=62.18 Aligned_cols=78 Identities=14% Similarity=0.187 Sum_probs=65.4
Q ss_pred hHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHhhCCCchhHHH-HHHHHHH
Q 045194 12 ANVGKIMKQILPPRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALSTLGFDNYTEA-IVRYLHK 90 (157)
Q Consensus 12 A~I~RImK~~LP~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~LgF~~y~~~-L~~~L~~ 90 (157)
..|.+|+|+. +..+++.+++..|.+.+..++.-|..+|...|.+.||+||+.+||..|++..+-..|..+ -+++|-.
T Consensus 5 ~~v~~iLk~~--Gv~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r~~~~f~~~p~~~~l~~ 82 (117)
T cd07979 5 RVIAAILKSM--GITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRVDYSFTSPPPRDFLLE 82 (117)
T ss_pred HHHHHHHHHC--CCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhccCCCCCCcHHHHHH
Confidence 3578888886 456899999999999999999999999999999999999999999999997776555443 5555543
Q ss_pred H
Q 045194 91 Y 91 (157)
Q Consensus 91 y 91 (157)
+
T Consensus 83 ~ 83 (117)
T cd07979 83 L 83 (117)
T ss_pred H
Confidence 3
No 24
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=97.97 E-value=3.7e-05 Score=54.61 Aligned_cols=62 Identities=18% Similarity=0.216 Sum_probs=52.8
Q ss_pred HHHHHHhhhC-CCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHhh
Q 045194 13 NVGKIMKQIL-PPRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALST 74 (157)
Q Consensus 13 ~I~RImK~~L-P~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~ 74 (157)
.|.+|+.+.. +.++.+|+.+..+|.+.+-.++..++..---.|+|+||+||+.+||+...++
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 5788888874 5678999999999999999999999999999999999999999999977654
No 25
>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=97.89 E-value=4.8e-05 Score=66.54 Aligned_cols=67 Identities=18% Similarity=0.217 Sum_probs=59.1
Q ss_pred chhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHhhCCCc
Q 045194 10 PIANVGKIMKQILPPRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALSTLGFD 78 (157)
Q Consensus 10 P~A~I~RImK~~LP~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~LgF~ 78 (157)
|..+|.-|++.. +-.++++||..+|.+.++.++..|..+|...+++.||||++++||-.||+.++.+
T Consensus 1 ~~~~i~~ia~~~--Gi~~~~~~a~~~La~~~e~~~~~i~~~A~k~~~hskR~~l~~~Di~~Al~~~n~e 67 (343)
T cd08050 1 PQESIKLIAESL--GIDSLSDEVAQLLAEDVEYRLREIIQEAAKFMRHSKRRKLTTSDVNHALRLRNVE 67 (343)
T ss_pred ChhHHHHHHHHc--CCCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHHhCCC
Confidence 445677777766 3449999999999999999999999999999999999999999999999977665
No 26
>KOG1745 consensus Histones H3 and H4 [Chromatin structure and dynamics]
Probab=97.84 E-value=1.1e-05 Score=63.14 Aligned_cols=74 Identities=18% Similarity=0.212 Sum_probs=65.2
Q ss_pred ccccccCchhHHHHHHhhhCC---CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHhhCC
Q 045194 3 EEQDKLLPIANVGKIMKQILP---PRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALSTLG 76 (157)
Q Consensus 3 ~e~D~~LP~A~I~RImK~~LP---~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~Lg 76 (157)
+..|+++++....|++++..+ .+.++...|+.+||++++.|+.-|.-.+|-.|.+.||.||.+.||-.|..-.|
T Consensus 58 kstdLlI~K~PFqRlvrei~q~f~~dLrfqs~Ai~ALQeA~EayLv~LfEdtnlcAihAkRVTimpkdiQlArrirg 134 (137)
T KOG1745|consen 58 KSTDLLIRKLPFQRLVREIAQDFKTDLRFQSSAIAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRG 134 (137)
T ss_pred hhhHHHhhcCcHHHHhHHHHhcccccceehHHHHHHHHHHHHHHHHHhccccchhhhccceeEecccceehhhhccc
Confidence 346888999999999995544 58899999999999999999999999999999999999999999988876544
No 27
>smart00427 H2B Histone H2B.
Probab=97.82 E-value=9.6e-05 Score=54.17 Aligned_cols=62 Identities=23% Similarity=0.332 Sum_probs=57.3
Q ss_pred HHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHhhC
Q 045194 13 NVGKIMKQILPPRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALSTL 75 (157)
Q Consensus 13 ~I~RImK~~LP~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~L 75 (157)
-|+|+.|++-| +..||..|...|.-.+..+..-|+.+|...|.-.+|+||+..+|..|.+-+
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 48999999987 779999999999999999999999999999999999999999999998654
No 28
>PF15511 CENP-T: Centromere kinetochore component CENP-T; PDB: 3B0D_T 3B0C_T 3VH5_T 3VH6_T.
Probab=97.82 E-value=3.9e-05 Score=68.87 Aligned_cols=60 Identities=23% Similarity=0.370 Sum_probs=47.5
Q ss_pred cCchhHHHHHHhhhCC----CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchh
Q 045194 8 LLPIANVGKIMKQILP----PRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDD 67 (157)
Q Consensus 8 ~LP~A~I~RImK~~LP----~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eD 67 (157)
.||.+.|.|++..... .+++|++||..+|.+|...|-..|...-.-+|.|+|||||...|
T Consensus 351 ~lP~~~vK~la~~~ak~s~~sK~kiskdal~aleqasdwfFeQl~dDL~aYA~HAgRKTIdesD 414 (414)
T PF15511_consen 351 SLPPGVVKKLAQHFAKSSGGSKMKISKDALEALEQASDWFFEQLGDDLEAYAKHAGRKTIDESD 414 (414)
T ss_dssp -S-HHHHHHHHHHHH-------S-B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHH
T ss_pred CCCccHHHHHHHHHHHhhcccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCCCC
Confidence 4888999888877754 57899999999999999999999999999999999999998876
No 29
>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=97.78 E-value=0.0002 Score=49.71 Aligned_cols=65 Identities=20% Similarity=0.247 Sum_probs=56.9
Q ss_pred hHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHhhCCCc
Q 045194 12 ANVGKIMKQILPPRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALSTLGFD 78 (157)
Q Consensus 12 A~I~RImK~~LP~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~LgF~ 78 (157)
-.|.+|++.+ +=-.++..|.+.|.+.+..||..|+..+...|.+.||...+..||..||+++|+.
T Consensus 10 ~~va~il~~~--GF~~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~~~gi~ 74 (77)
T PF07524_consen 10 RSVAQILKHA--GFDSASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPNLQDVEQALEEMGIS 74 (77)
T ss_pred HHHHHHHHHc--CccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCC
Confidence 3455666655 2236999999999999999999999999999999999999999999999999984
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=97.69 E-value=0.00024 Score=49.39 Aligned_cols=63 Identities=21% Similarity=0.299 Sum_probs=51.1
Q ss_pred hhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHhh
Q 045194 11 IANVGKIMKQILPPRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALST 74 (157)
Q Consensus 11 ~A~I~RImK~~LP~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~ 74 (157)
+..+..+|+++- ++..+..|+.++|.+.|.+||.-++..|...|++-|-.||...||.-.|++
T Consensus 2 K~~l~~Lv~~iD-p~~~ld~~vee~Ll~laddFv~~v~~~ac~lAKhR~s~tle~~Dv~~~Ler 64 (68)
T PF03847_consen 2 KRKLQELVKQID-PNEKLDPDVEELLLELADDFVDDVVSFACRLAKHRKSSTLEVKDVQLHLER 64 (68)
T ss_dssp HHHHHHHHHCC--SS----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHHH
T ss_pred hHHHHHHHHHcC-CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCHHHHHHHHHh
Confidence 346788899975 488999999999999999999999999999999999999999999988864
No 31
>KOG3467 consensus Histone H4 [Chromatin structure and dynamics]
Probab=97.69 E-value=0.00018 Score=53.10 Aligned_cols=68 Identities=19% Similarity=0.237 Sum_probs=60.0
Q ss_pred CchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHhhCCCc
Q 045194 9 LPIANVGKIMKQILPPRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALSTLGFD 78 (157)
Q Consensus 9 LP~A~I~RImK~~LP~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~LgF~ 78 (157)
+-+-+|.||.+.. +--+|+.-.-+.+...+.+||..+-+.|..++.+.+||||++-||+-+|+..|.-
T Consensus 30 itKpaIRRlARr~--GVkRi~G~~yeE~~~~~k~fl~n~i~~A~~yt~HAKRKTvT~~dvv~~LKR~G~~ 97 (103)
T KOG3467|consen 30 ITKPAIRRLARRG--GVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRT 97 (103)
T ss_pred cchHHHHHHHHhc--CcchhchhhHHHHHHHHHHHHHHHHHHHHHHHhhhhhceeeHHHHHHHHHHcCce
Confidence 4566888888876 3346888888899999999999999999999999999999999999999998864
No 32
>KOG1659 consensus Class 2 transcription repressor NC2, alpha subunit (DRAP1) [Transcription]
Probab=97.62 E-value=0.00024 Score=59.46 Aligned_cols=83 Identities=14% Similarity=0.186 Sum_probs=73.3
Q ss_pred cCchhHHHHHHhhhCCCC-ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHhhCCCchhHHHHHH
Q 045194 8 LLPIANVGKIMKQILPPR-AKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALSTLGFDNYTEAIVR 86 (157)
Q Consensus 8 ~LP~A~I~RImK~~LP~~-~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~LgF~~y~~~L~~ 86 (157)
.+|.|.|.|||... .+ .+|+.-.-..+.++.+.|+.-|...+.++++..+-|||+++|+..|+..-.-.||+..+..
T Consensus 13 rfp~aRiKKIMQ~d--EdIGKvaqavPViisralElFl~~l~~~t~~~t~~~~aKt~s~~hlkq~v~~~~~FdFLk~~v~ 90 (224)
T KOG1659|consen 13 RFPPARIKKIMQSD--EDIGKVAQAVPVIISRALELFLESLLQKTLEITRSRGAKTVSSSHLKQAVESDPKFDFLKEVVE 90 (224)
T ss_pred cCCHHHHHHHHhhh--hhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhcCccccCHHHHHHHHhccchhHHHHHHHH
Confidence 48999999999865 44 4899999999999999999999999999999999999999999999999998899988666
Q ss_pred HHHHHH
Q 045194 87 YLHKYR 92 (157)
Q Consensus 87 ~L~~yr 92 (157)
....+.
T Consensus 91 ~vpd~~ 96 (224)
T KOG1659|consen 91 KVPDRQ 96 (224)
T ss_pred hcCCCc
Confidence 554333
No 33
>PLN00158 histone H2B; Provisional
Probab=97.61 E-value=0.00029 Score=53.93 Aligned_cols=63 Identities=22% Similarity=0.302 Sum_probs=57.8
Q ss_pred hHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHhhC
Q 045194 12 ANVGKIMKQILPPRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALSTL 75 (157)
Q Consensus 12 A~I~RImK~~LP~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~L 75 (157)
.-|+|++|++-| +..||..|...|.-....+..-|+.||...|.-.+|+||+..+|..|++-+
T Consensus 31 ~YI~kVLKQVhP-d~gIS~kaM~ImnSfvnDiferIA~EAs~La~~nkr~TltsrEIqtAvrLv 93 (116)
T PLN00158 31 IYIYKVLKQVHP-DTGISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVRLI 93 (116)
T ss_pred HHHHHHHHHhCC-CCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHh
Confidence 459999999987 778999999999999999999999999999999999999999999998654
No 34
>PTZ00463 histone H2B; Provisional
Probab=97.57 E-value=0.00036 Score=53.48 Aligned_cols=62 Identities=24% Similarity=0.358 Sum_probs=57.0
Q ss_pred HHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHhhC
Q 045194 13 NVGKIMKQILPPRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALSTL 75 (157)
Q Consensus 13 ~I~RImK~~LP~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~L 75 (157)
-|+|++|++-| +.-||..|...|.-.......-|+.||...|.-.+|.||++.+|..|++-+
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 48999999987 778999999999998999899999999999999999999999999998654
No 35
>cd08048 TAF11 TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypothes
Probab=97.53 E-value=0.00059 Score=49.35 Aligned_cols=66 Identities=15% Similarity=0.203 Sum_probs=60.8
Q ss_pred cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC---CccCchhHHHHHhhC
Q 045194 8 LLPIANVGKIMKQILPPRAKISKEAKQTMQECATEFISFVTGEASDKCHKENR---KTVNGDDICWALSTL 75 (157)
Q Consensus 8 ~LP~A~I~RImK~~LP~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kR---KTI~~eDVl~AL~~L 75 (157)
.||++.|.|||...++ ..++.+...+|.-.+.+||..|..+|.++..+.+. .-|.++||-.|.+.|
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 4999999999999985 78999999999999999999999999999987666 789999999999876
No 36
>PF09415 CENP-X: CENP-S associating Centromere protein X; InterPro: IPR018552 Centromere protein X (CENP-X) is a component of the CENP-S complex. The CENP-S complex is composed of at least of CENP-S and CENP-X and is essential for the stable assembly of the outer kinetchore []. CENP-X is also a DNA-binding component of the Fanconi anemia (FA) core complex involved in DNA damage repair and genome maintenance. The FA complex is composed of CENPS, FANCA, FANCB, FANCC, FANCE, FANCF, FANCG, FANCL/PHF9, FANCM, FAAP24 and CENPX. Interacts with CENPS, FANCM and FAAP24 [, ].; PDB: 4DRB_L 4DRA_H 3V9R_D.
Probab=97.45 E-value=0.00023 Score=50.03 Aligned_cols=64 Identities=17% Similarity=0.276 Sum_probs=53.3
Q ss_pred chhHHHHHHhhhCC-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCc-cCchhHHHHHh
Q 045194 10 PIANVGKIMKQILP-PRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKT-VNGDDICWALS 73 (157)
Q Consensus 10 P~A~I~RImK~~LP-~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKT-I~~eDVl~AL~ 73 (157)
|..+|.||++.... ++.+|++||..++.+....||..-...|.+.+..+|... |..+|+-+.+-
T Consensus 1 p~~li~rll~~~f~~~~tkIs~dal~l~~eyl~iFV~EAv~Ra~~~a~~e~~~~~le~e~LEki~p 66 (72)
T PF09415_consen 1 PPELIARLLHEHFKDDKTKISKDALKLSAEYLRIFVREAVARAAEQAEAEGDEGFLEVEHLEKILP 66 (72)
T ss_dssp -CHHHHHHHCTTSSSTT-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSEE-HHHHHHHCH
T ss_pred ChHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHH
Confidence 78999999997764 578999999999999999999999999999999999988 99999877553
No 37
>COG5247 BUR6 Class 2 transcription repressor NC2, alpha subunit (DRAP1 homolog) [Transcription]
Probab=97.33 E-value=0.00074 Score=50.95 Aligned_cols=78 Identities=15% Similarity=0.232 Sum_probs=68.5
Q ss_pred cCchhHHHHHHhhhCCCC-ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHhhCCCchhHHHHHH
Q 045194 8 LLPIANVGKIMKQILPPR-AKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALSTLGFDNYTEAIVR 86 (157)
Q Consensus 8 ~LP~A~I~RImK~~LP~~-~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~LgF~~y~~~L~~ 86 (157)
.+|+|.|.|||.-. .+ .+|+.-......++.+.|+..|-....+.++..+-|.|+.+++..|.+.-.=.||+..+..
T Consensus 23 rFP~ar~KkIMQ~d--eDiGKV~q~tPVIaskalE~Fl~~iv~~s~k~aR~~~skR~t~e~lk~a~~sdekFdFL~~~~~ 100 (113)
T COG5247 23 RFPIARLKKIMQLD--EDIGKVGQSTPVIASKALEMFLTEIVGLSLKEARKKSSKRMTSEFLKRATESDEKFDFLKNMEQ 100 (113)
T ss_pred cCCHHHHHHHHHhh--hhhhhhhhcchHHHHHHHHHHHHHHHHHHHHHHHhccchhhHHHHHHHHHhhhHHHHHHHHHHH
Confidence 58999999999854 44 4899999999999999999999999999999999999999999999988777777766654
Q ss_pred H
Q 045194 87 Y 87 (157)
Q Consensus 87 ~ 87 (157)
+
T Consensus 101 ~ 101 (113)
T COG5247 101 F 101 (113)
T ss_pred h
Confidence 4
No 38
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=97.30 E-value=0.00059 Score=52.70 Aligned_cols=68 Identities=13% Similarity=0.209 Sum_probs=60.7
Q ss_pred cccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHhh
Q 045194 6 DKLLPIANVGKIMKQILPPRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALST 74 (157)
Q Consensus 6 D~~LP~A~I~RImK~~LP~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~ 74 (157)
.+.+|...|.|+||.. ...+||+++|...+.-|.+=.+..|+.-|-..|...++|.|.+.|+-.|++.
T Consensus 24 gl~fpvgrvkr~lk~~-~~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~kkkri~PrHlqlAIrn 91 (132)
T COG5262 24 GLIFPVGRVKRLLKKG-NYRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRIIPRHLQLAIRN 91 (132)
T ss_pred CccccHHHHHHHHHcC-ccceeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhcCcceechHHHHHHhcC
Confidence 4679999999999944 3578999999999999998888888888999999999999999999999863
No 39
>PF02969 TAF: TATA box binding protein associated factor (TAF); InterPro: IPR004823 The TATA box binding protein associated factor (TAF) is part of the transcription initiation factor TFIID multimeric protein complex. TFIID plays a central role in mediating promoter responses to various activators and repressors. It binds tightly to TAFII-250 and directly interacts with TAFII-40. TFIID is composed of TATA binding protein (TBP)and a number of TBP-associated factors (TAFS). TAF proteins adopt a histone-like fold.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus; PDB: 1TAF_B.
Probab=97.20 E-value=0.0027 Score=44.01 Aligned_cols=64 Identities=22% Similarity=0.236 Sum_probs=48.9
Q ss_pred cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHh
Q 045194 8 LLPIANVGKIMKQILPPRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALS 73 (157)
Q Consensus 8 ~LP~A~I~RImK~~LP~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~ 73 (157)
.+|..+|.-+.... +-..++.|+...|.+=++--|..|..+|.....+.+|++++++||=.||+
T Consensus 3 ~~~~esvk~iAes~--Gi~~l~de~a~~La~dveyrlreiiq~a~kfm~hskR~~Lt~~Di~~ALr 66 (66)
T PF02969_consen 3 VFSQESVKDIAESL--GISNLSDEAAKALAEDVEYRLREIIQEALKFMRHSKRTKLTTDDINSALR 66 (66)
T ss_dssp ---HHHHHHHHHHT--T---B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH-
T ss_pred cCCHHHHHHHHHHc--CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhC
Confidence 36777776666554 23479999999999999999999999999999999999999999999985
No 40
>PF04719 TAFII28: hTAFII28-like protein conserved region; InterPro: IPR006809 The general transcription factor, TFIID, consists of the TATA-binding protein (TBP) associated with a series of TBP-associated factors (TAFs) that together participate in the assembly of the transcription preinitiation complex. The conserved region is found at the C terminus of most member proteins. The crystal structure of hTAFII28 with hTAFII18 shows that this region is involved in the binding of these two subunits. The conserved region contains four alpha helices and three loops arranged as in histone H3 [, ].; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005634 nucleus; PDB: 1BH9_B 1BH8_B.
Probab=97.19 E-value=0.0017 Score=47.54 Aligned_cols=67 Identities=19% Similarity=0.222 Sum_probs=52.0
Q ss_pred cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC-CccCchhHHHHHhhC
Q 045194 8 LLPIANVGKIMKQILPPRAKISKEAKQTMQECATEFISFVTGEASDKCHKENR-KTVNGDDICWALSTL 75 (157)
Q Consensus 8 ~LP~A~I~RImK~~LP~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kR-KTI~~eDVl~AL~~L 75 (157)
.||++.|.|||...+. +..|+.....+|.-.+..||..|-.+|.+++...+. .-|.+.|+-.|.+.|
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 5999999999999984 678999999999999999999999999999986554 389999999998765
No 41
>smart00414 H2A Histone 2A.
Probab=97.10 E-value=0.0017 Score=48.73 Aligned_cols=68 Identities=7% Similarity=0.167 Sum_probs=59.4
Q ss_pred cccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHhh
Q 045194 6 DKLLPIANVGKIMKQILPPRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALST 74 (157)
Q Consensus 6 D~~LP~A~I~RImK~~LP~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~ 74 (157)
.+.+|.+.|.|+||+.-- ..+|+..|...|..+.+-+...|...|...|...+++.|+++||..|+..
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 578999999999998642 45999999999999888887887777888899999999999999999865
No 42
>PLN00154 histone H2A; Provisional
Probab=96.91 E-value=0.0028 Score=49.71 Aligned_cols=69 Identities=12% Similarity=0.139 Sum_probs=57.1
Q ss_pred cccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHhh
Q 045194 6 DKLLPIANVGKIMKQILPPRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALST 74 (157)
Q Consensus 6 D~~LP~A~I~RImK~~LP~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~ 74 (157)
.+.||...|.|++|+-..-..||+..|...|.-..+=+...|...|-..|...+++-|++.||..|+..
T Consensus 36 gL~FPVgRi~r~Lk~g~~~~~RVga~ApVYLAAVLEYLtAEVLELAGNaA~d~kk~RItPrHi~lAIrn 104 (136)
T PLN00154 36 GLQFPVGRIHRQLKQRVSAHGRVGATAAVYTAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRG 104 (136)
T ss_pred CccCchHHHHHHHHhhhhhccccccchHHHHHHHHHHHHHHHHHHHHHHHHhhCCceecHHHhhhhccC
Confidence 478999999999999753356999999999887776555556666777889999999999999999864
No 43
>PTZ00017 histone H2A; Provisional
Probab=96.75 E-value=0.0036 Score=49.02 Aligned_cols=68 Identities=13% Similarity=0.158 Sum_probs=59.3
Q ss_pred cccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHhh
Q 045194 6 DKLLPIANVGKIMKQILPPRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALST 74 (157)
Q Consensus 6 D~~LP~A~I~RImK~~LP~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~ 74 (157)
.+.||...|.|+||+.-- ..+|+..|...|.-+.+-+...|...|...|...+++-|+++||..|+..
T Consensus 25 gL~FPVgRi~R~Lk~g~~-a~RV~a~A~VYLAAVLEYLtaEILELAgNaa~d~kk~RItPrHi~lAI~n 92 (134)
T PTZ00017 25 GLQFPVGRVHRYLKKGRY-AKRVGAGAPVYLAAVLEYLTAEVLELAGNAAKDNKKKRITPRHIQLAIRN 92 (134)
T ss_pred CcccchHHHHHHHhccch-hccccccchhhhHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHhhccC
Confidence 478999999999998632 45999999999999888888888888888899999999999999999853
No 44
>KOG1658 consensus DNA polymerase epsilon, subunit C [Replication, recombination and repair]
Probab=96.57 E-value=0.0018 Score=51.90 Aligned_cols=68 Identities=26% Similarity=0.361 Sum_probs=59.3
Q ss_pred ccCchhHHHHHHhhhCCCCcc-ccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHhhCC
Q 045194 7 KLLPIANVGKIMKQILPPRAK-ISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALSTLG 76 (157)
Q Consensus 7 ~~LP~A~I~RImK~~LP~~~k-ISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~Lg 76 (157)
..||++.|..+|| +++++. ...|++.+|.+++..||.+|...++..+...+|||+.-.|+=.|++.-+
T Consensus 58 ~rLpL~rik~vvk--l~pdl~l~~dea~~l~a~aaelfi~~Ln~~~~~~~q~~k~kt~qr~d~D~ai~~~d 126 (162)
T KOG1658|consen 58 SRLPLARIKQVVK--LDPDLTLLNDEASQLIAKAAELFIQELNDVAYTTAQLRKRKTEQRRDYDTAIEAVD 126 (162)
T ss_pred hhccHHHHHhhcc--CCcchhhhhhHHHHHHHHHHHHHHHHHHhccchhHHHHHhhhhhhhcccccccchH
Confidence 5699999999999 568887 5567889999999999999999999999999999999988877775543
No 45
>KOG1756 consensus Histone 2A [Chromatin structure and dynamics]
Probab=96.52 E-value=0.0074 Score=47.02 Aligned_cols=68 Identities=6% Similarity=0.156 Sum_probs=54.8
Q ss_pred cccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHhh
Q 045194 6 DKLLPIANVGKIMKQILPPRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALST 74 (157)
Q Consensus 6 D~~LP~A~I~RImK~~LP~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~ 74 (157)
.+.+|...|.|++|+. .-..+|+.+|...|.-|.+=.+..|+..|-..+..+++.-|++.||..|+..
T Consensus 25 gl~fPvgri~r~Lr~~-~~~~ri~~gapV~laavLeYL~Aeile~agnaardnkk~ri~PrH~~lAI~N 92 (131)
T KOG1756|consen 25 GLQFPVGRIHRLLRKG-RYAQRVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRITPRHLQLAIRN 92 (131)
T ss_pred ccccCHHHHHHHHHcc-chhhhccCCChHHHHHHHHHHHHHHHHHhHHHhhhcCccccChHHHHHHHhC
Confidence 5689999999999993 2356899999999996666555555555666678889999999999999963
No 46
>KOG1744 consensus Histone H2B [Chromatin structure and dynamics]
Probab=96.52 E-value=0.01 Score=46.15 Aligned_cols=62 Identities=27% Similarity=0.357 Sum_probs=56.6
Q ss_pred HHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHhhC
Q 045194 13 NVGKIMKQILPPRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALSTL 75 (157)
Q Consensus 13 ~I~RImK~~LP~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~L 75 (157)
-|+|++|++-|+ .-|+.++...|.-..-.|...|+.+|+..+.-.||.||+..+|..|.+-|
T Consensus 42 yv~kvlk~Vhpd-~gis~~a~~vmnsf~ndife~iA~ea~rla~y~krstisSreiqta~rLl 103 (127)
T KOG1744|consen 42 YVYKVLKQVHPD-LGISSKAMGVMNSFVNDIFERIASEAGRLAHYNKRSTISSREIQTAVRLL 103 (127)
T ss_pred ehhhhhhcccCC-CCcCHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCcccHHHHHHHHHHh
Confidence 478899999885 77999999999999999999999999999999999999999999988543
No 47
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=96.47 E-value=0.0056 Score=52.50 Aligned_cols=67 Identities=19% Similarity=0.311 Sum_probs=60.8
Q ss_pred cccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHh
Q 045194 6 DKLLPIANVGKIMKQILPPRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALS 73 (157)
Q Consensus 6 D~~LP~A~I~RImK~~LP~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~ 73 (157)
+..|=+-.|.-+++++- ++.+|-+|+.++|.+.|..||..|+..|...|++-+..||-..||...|+
T Consensus 152 ~~il~k~kl~dLvqqId-~~~~LD~dVedlLleiADdFV~sii~~sC~LAKHRKsdtlEvrDIqLhLE 218 (258)
T KOG1142|consen 152 NPILSKRKLDDLVQQID-GTTKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHRKSDTVEVRDIQLHLE 218 (258)
T ss_pred CccccccchhHHHHhhc-CcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccchhheeeeee
Confidence 45566777888999984 47899999999999999999999999999999999999999999999998
No 48
>PLN00157 histone H2A; Provisional
Probab=96.46 E-value=0.0064 Score=47.50 Aligned_cols=68 Identities=10% Similarity=0.129 Sum_probs=57.9
Q ss_pred cccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHhh
Q 045194 6 DKLLPIANVGKIMKQILPPRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALST 74 (157)
Q Consensus 6 D~~LP~A~I~RImK~~LP~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~ 74 (157)
.+.+|...|.|++|+.-- ..+|+..|...|.-+.+-....|...|...|...+++-|+++||..|+..
T Consensus 24 gL~FPVgRi~R~Lk~g~~-a~RIg~~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~n 91 (132)
T PLN00157 24 GLQFPVGRIARYLKAGKY-ATRVGAGAPVYLAAVLEYLAAEVLELAGNAARDNKKSRIVPRHIQLAVRN 91 (132)
T ss_pred CcccchHHHHHHHhcCch-hhhcCCCcHhHHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHhhcccC
Confidence 478999999999999632 46899999999988877777777777888899999999999999999853
No 49
>PLN00153 histone H2A; Provisional
Probab=96.40 E-value=0.0081 Score=46.78 Aligned_cols=68 Identities=12% Similarity=0.148 Sum_probs=58.3
Q ss_pred cccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHhh
Q 045194 6 DKLLPIANVGKIMKQILPPRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALST 74 (157)
Q Consensus 6 D~~LP~A~I~RImK~~LP~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~ 74 (157)
.+.+|...|.|++|+.-. ..+|+..|...|.-+.+=....|...|...|...+++-|+++||..|+..
T Consensus 22 gL~FpVgRi~R~Lr~g~~-a~Rvga~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~n 89 (129)
T PLN00153 22 GLQFPVGRIARYLKKGKY-AERIGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKNRIVPRHIQLAIRN 89 (129)
T ss_pred CcccchHHHHHHHhcCch-hhccCCCchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHhhccC
Confidence 478999999999998643 46899999999988887777777777888899999999999999999853
No 50
>PLN00156 histone H2AX; Provisional
Probab=96.38 E-value=0.0094 Score=46.98 Aligned_cols=68 Identities=10% Similarity=0.139 Sum_probs=56.6
Q ss_pred cccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHhh
Q 045194 6 DKLLPIANVGKIMKQILPPRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALST 74 (157)
Q Consensus 6 D~~LP~A~I~RImK~~LP~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~ 74 (157)
.+.+|...|.|++++.-- ..||+..|...|.-+.+=....|...|...|...+++-|+++||..|+..
T Consensus 27 gL~FPVgRi~R~Lk~g~y-a~RVga~ApVYLAAVLEYLtaEVLELAgNaa~d~kk~RItPrHi~lAIrn 94 (139)
T PLN00156 27 GLQFPVGRIARFLKAGKY-AERVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRN 94 (139)
T ss_pred CcccchHHHHHHHhcCCh-hhccCCccHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHhhccC
Confidence 478999999999998632 45899999999888776666666666777889999999999999999853
No 51
>PF02269 TFIID-18kDa: Transcription initiation factor IID, 18kD subunit; InterPro: IPR003195 This family includes the Spt3 yeast transcription factors and the 18 kDa subunit from human transcription initiation factor IID (TFIID-18). Determination of the crystal structure reveals an atypical histone fold [].; GO: 0006366 transcription from RNA polymerase II promoter; PDB: 1BH9_A 1BH8_A.
Probab=96.21 E-value=0.0061 Score=44.42 Aligned_cols=59 Identities=15% Similarity=0.236 Sum_probs=28.6
Q ss_pred HHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHhh
Q 045194 15 GKIMKQILPPRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALST 74 (157)
Q Consensus 15 ~RImK~~LP~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~ 74 (157)
..+|-. .++...-..|.+.+|-+.+.+||..+...|...|...|++.|+.+|++-+|+.
T Consensus 8 ~~mMy~-fGD~~~P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~rg~~~i~~eDl~F~lR~ 66 (93)
T PF02269_consen 8 RQMMYG-FGDVEEPLPETVDLVEDIVREYIIELCQEAMEVAQRRGSKKIKVEDLLFLLRK 66 (93)
T ss_dssp HHHHHC-TTS-SS--HHHHHHHHHHHHHHHHHHHHHHHC---------------------
T ss_pred HHHHHH-cCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCcCcHHHHHHHHhc
Confidence 344443 33345688999999999999999999999999999999999999999999985
No 52
>PF15510 CENP-W: Centromere kinetochore component W
Probab=95.94 E-value=0.015 Score=43.27 Aligned_cols=65 Identities=12% Similarity=0.182 Sum_probs=54.0
Q ss_pred cCchhHHHHHHhhhCCCCccccHHHHHH--------------HHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHh
Q 045194 8 LLPIANVGKIMKQILPPRAKISKEAKQT--------------MQECATEFISFVTGEASDKCHKENRKTVNGDDICWALS 73 (157)
Q Consensus 8 ~LP~A~I~RImK~~LP~~~kISkDA~~a--------------l~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~ 73 (157)
.-|++.+.|++|..-| ..++....-.+ +.--|-.||+-|+-||...|-+++=.||..+||+.|-+
T Consensus 16 kaPrgfLkrv~Kr~Kp-hlRl~~~~Dllv~~~~f~~~~~~~~vhLncLLFvhrLAEEaRtnA~EnK~~~Ik~~Hv~AaaK 94 (102)
T PF15510_consen 16 KAPRGFLKRVFKRQKP-HLRLETSGDLLVRFCPFSGWQWGGEVHLNCLLFVHRLAEEARTNACENKCGTIKKEHVLAAAK 94 (102)
T ss_pred hCchHHHHHHHHhcCC-ceeecccccHHHhhcccccccccceeehhHHHHHHHHHHHHHHHHHHHhhccccHHHHHHHHH
Confidence 4699999999998765 66665554444 56678899999999999999999999999999998865
No 53
>KOG3219 consensus Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=95.64 E-value=0.014 Score=48.21 Aligned_cols=70 Identities=23% Similarity=0.238 Sum_probs=61.1
Q ss_pred ccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC-CccCchhHHHHHhhCCCc
Q 045194 7 KLLPIANVGKIMKQILPPRAKISKEAKQTMQECATEFISFVTGEASDKCHKENR-KTVNGDDICWALSTLGFD 78 (157)
Q Consensus 7 ~~LP~A~I~RImK~~LP~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kR-KTI~~eDVl~AL~~LgF~ 78 (157)
..||++.|.|||..+.... |+.-+..+|+-.+.+||..|--+|.++|..-+. --|-+.||-.|.+.|+..
T Consensus 111 s~f~Ka~iKkL~~~itg~~--v~~nv~Ia~~GiaKvFVGEvVEeAl~V~~~~~e~~PLqP~HIREA~rrL~~q 181 (195)
T KOG3219|consen 111 SAFPKAQIKKLMSSITGQS--VSENVAIAMAGIAKVFVGEVVEEALDVREEWGESGPLQPKHIREAYRRLKLQ 181 (195)
T ss_pred hcCCHHHHHHHHHHHhCCc--cCcceeeeecchhhHhHHHHHHHHHHHHHHhccCCCCCcHHHHHHHHHHHhc
Confidence 3699999999999997533 999999999999999999999999999986665 468999999998887654
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=95.39 E-value=0.085 Score=40.91 Aligned_cols=84 Identities=20% Similarity=0.232 Sum_probs=46.4
Q ss_pred ccCchh--HHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHh-hCCCchhHHH
Q 045194 7 KLLPIA--NVGKIMKQILPPRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALS-TLGFDNYTEA 83 (157)
Q Consensus 7 ~~LP~A--~I~RImK~~LP~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~-~LgF~~y~~~ 83 (157)
-.+|+. .|.-|+|+. +-......+...|.+.+-.|+.-|-.+|..++.+.||++|+.+||..|++ .+++.-..++
T Consensus 9 ~~~PrDa~~i~~iL~~~--Gv~~yeprVv~qLLEfayRYt~~vL~DA~~ya~hA~~~~i~~~DVrLAi~~r~~~~f~~pp 86 (129)
T PF02291_consen 9 KSLPRDARVIHLILKSM--GVTEYEPRVVNQLLEFAYRYTSDVLEDAQVYADHAGRSTIDADDVRLAIQSRLDHSFTQPP 86 (129)
T ss_dssp ----HHHHHHHHHHHHT--T---B-THHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHHHHT---------
T ss_pred ccCChHHHHHHHHHHHc--CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHhhhccCCC
Confidence 345652 334444444 22246777888999999999999999999999999999999999999998 6677666666
Q ss_pred HHHHHHHHH
Q 045194 84 IVRYLHKYR 92 (157)
Q Consensus 84 L~~~L~~yr 92 (157)
-+++|-..-
T Consensus 87 pre~llelA 95 (129)
T PF02291_consen 87 PREFLLELA 95 (129)
T ss_dssp ---------
T ss_pred ChHHHHHHH
Confidence 666665443
No 55
>PTZ00252 histone H2A; Provisional
Probab=95.02 E-value=0.078 Score=41.61 Aligned_cols=68 Identities=10% Similarity=0.171 Sum_probs=49.1
Q ss_pred cccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHh--cCCCccCchhHHHHHhh
Q 045194 6 DKLLPIANVGKIMKQILPPRAKISKEAKQTMQECATEFISFVTGEASDKCHK--ENRKTVNGDDICWALST 74 (157)
Q Consensus 6 D~~LP~A~I~RImK~~LP~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~--~kRKTI~~eDVl~AL~~ 74 (157)
.+.+|...|.|++++.-- ..+|+.-|...|.-+.+=....|...|...|.. .+++-|+++||..|+..
T Consensus 23 GL~FPVgRi~R~Lr~g~y-a~RIga~ApVYLAAVLEYLtaEVLELAgnaa~d~~~kk~RItPrHi~lAIrN 92 (134)
T PTZ00252 23 GLIFPVGRVGSLLRRGQY-ARRIGASGAVYMAAVLEYLTAELLELSVKAAAQQAKKPKRLTPRTVTLAVRH 92 (134)
T ss_pred CccCchHHHHHHHHcCCc-ccccCCccHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccccHHHHHhhccC
Confidence 478999999999998743 468999998888765543333333334444433 57789999999999853
No 56
>KOG4336 consensus TBP-associated transcription factor Prodos [Transcription]
Probab=93.99 E-value=0.36 Score=42.65 Aligned_cols=76 Identities=18% Similarity=0.261 Sum_probs=63.5
Q ss_pred HHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHhhCCCchhHHHHHHHHHHHHH
Q 045194 14 VGKIMKQILPPRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALSTLGFDNYTEAIVRYLHKYRE 93 (157)
Q Consensus 14 I~RImK~~LP~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~LgF~~y~~~L~~~L~~yre 93 (157)
|.-|.++.. ---|++-|.+.|.+....+|.-|...+..+|...||-..+.-||..+|-++|+. +..|..+++++-.
T Consensus 11 V~~Ll~~~g--fd~is~~aletlvell~~yi~eigrq~~n~celagRT~pT~~Dv~l~Li~mnI~--v~sL~~~~q~~~~ 86 (323)
T KOG4336|consen 11 VSNLLKTKG--FDSISNAALETLVELLQSYIREIGRQLHNYCELAGRTIPTQGDVKLTLIEMNIK--VSSLYAYFQKQEF 86 (323)
T ss_pred HHHHHHHhC--chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcHHHHHHHHHHhCCC--hhhhHHHHHhccc
Confidence 444444442 224999999999999999999999999999999999999999999999999998 5667777765554
No 57
>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=93.96 E-value=0.26 Score=35.98 Aligned_cols=78 Identities=14% Similarity=0.158 Sum_probs=55.9
Q ss_pred HHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHhhCCCchhHHHHHHHHHHHH
Q 045194 13 NVGKIMKQILPPRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALSTLGFDNYTEAIVRYLHKYR 92 (157)
Q Consensus 13 ~I~RImK~~LP~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~LgF~~y~~~L~~~L~~yr 92 (157)
-|.-+|-.. ++...-..|.+.+|-+.+.+||.-|+.+|.+.|. .+|.-|+.||++-+|+.- .-.+.-++.+|.--.
T Consensus 7 ei~~mmy~~-GD~~~P~~eTv~llE~iv~~~i~~l~~~a~~~A~-~r~~k~~~eD~~FliR~D--~~Kl~Rl~~lL~~k~ 82 (92)
T cd07978 7 EIRQMMYGF-GDVQNPLPETVDLLEDIVVEYIIELCHKAAEVAQ-RRRGKVKVEDLIFLLRKD--PKKLARLRELLSMKD 82 (92)
T ss_pred HHHHHHHHc-CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-cCCCCCCHHHHHHHHhcC--HHHHHHHHHHHHHHH
Confidence 355566543 3344578899999999999999999999999998 444445999999999642 234445555555434
Q ss_pred HH
Q 045194 93 ED 94 (157)
Q Consensus 93 e~ 94 (157)
+.
T Consensus 83 ~~ 84 (92)
T cd07978 83 EL 84 (92)
T ss_pred HH
Confidence 43
No 58
>KOG3423 consensus Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=90.66 E-value=1.5 Score=35.85 Aligned_cols=68 Identities=19% Similarity=0.275 Sum_probs=56.0
Q ss_pred cCchhHHHHHHhhhCCCCcc-ccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC--------------CCccCchhHHHHH
Q 045194 8 LLPIANVGKIMKQILPPRAK-ISKEAKQTMQECATEFISFVTGEASDKCHKEN--------------RKTVNGDDICWAL 72 (157)
Q Consensus 8 ~LP~A~I~RImK~~LP~~~k-ISkDA~~al~~~ateFI~~ltseA~e~~~~~k--------------RKTI~~eDVl~AL 72 (157)
.||=+.+.-.++.+ ++. ...-.+.+|.=++-.||+-|+..|.+.|+-.+ |-|++-+|+-.||
T Consensus 86 ~IPDavt~~yL~~a---Gf~~~D~rv~RLvsLaAQKfvSDIa~DA~Q~~k~r~~~~~~~~k~~~kdkK~tLtmeDL~~AL 162 (176)
T KOG3423|consen 86 TIPDAVTDHYLKKA---GFQTSDPRVKRLVSLAAQKFVSDIANDALQHSKIRTKTAIGKDKKQAKDKKYTLTMEDLSPAL 162 (176)
T ss_pred CCcHHHHHHHHHhc---CCCcCcHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccccccccccccceeeeHHHHHHHH
Confidence 58888888888877 443 44556788999999999999999999997443 4589999999999
Q ss_pred hhCCCc
Q 045194 73 STLGFD 78 (157)
Q Consensus 73 ~~LgF~ 78 (157)
.+.|+.
T Consensus 163 ~EyGin 168 (176)
T KOG3423|consen 163 AEYGIN 168 (176)
T ss_pred HHhCcc
Confidence 999975
No 59
>KOG2549 consensus Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=89.66 E-value=1.5 Score=41.61 Aligned_cols=66 Identities=20% Similarity=0.222 Sum_probs=54.8
Q ss_pred hhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHhhCCCc
Q 045194 11 IANVGKIMKQILPPRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALSTLGFD 78 (157)
Q Consensus 11 ~A~I~RImK~~LP~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~LgF~ 78 (157)
.-.+.-++ +.+ +-..|+.|+..+|.+=.+.=|..|..+|.+.-.+.+|.+++.+||-.||+.+..+
T Consensus 14 ~Es~k~vA-Esl-Gi~nl~deaa~~La~dv~yrikEI~Q~aaKfm~hskR~kLtv~DV~~ALr~~nVe 79 (576)
T KOG2549|consen 14 KESVKVVA-ESL-GITNLNDEAALLLAEDVEYRIKEIVQDAAKFMVHSKRTKLTVDDVDYALRSLNVE 79 (576)
T ss_pred HHHHHHHH-HHh-CccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcCcHHHHHHHHhhcccc
Confidence 44444444 444 3446999999999999999999999999999999999999999999999966543
No 60
>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily. Members of this protein are marked as probable ATPases by the nucleotide binding P-loop motif GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of helicases, and extensive homology to ATPases of MSHA-type pilus systems and to GspA proteins associated with type II protein secretion systems.
Probab=89.15 E-value=1.4 Score=35.63 Aligned_cols=69 Identities=12% Similarity=0.237 Sum_probs=53.4
Q ss_pred CchhHHHHHHhhhCC-----CCccccHHHHHHHHHHHHH---HHHHHHHHHHHHHHhcCCCccCchhHHHHHhhCCC
Q 045194 9 LPIANVGKIMKQILP-----PRAKISKEAKQTMQECATE---FISFVTGEASDKCHKENRKTVNGDDICWALSTLGF 77 (157)
Q Consensus 9 LP~A~I~RImK~~LP-----~~~kISkDA~~al~~~ate---FI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~LgF 77 (157)
|....+..++...+. ....++.++.+.|.+.+.= .|+.+...|...+...+.++|+.++|-.++.++.|
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 333445555544331 2346999999999988875 79999999999988899999999999999998874
No 61
>KOG2389 consensus Predicted bromodomain transcription factor [Transcription]
Probab=86.77 E-value=1.3 Score=39.79 Aligned_cols=70 Identities=20% Similarity=0.196 Sum_probs=58.4
Q ss_pred ccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHhhCCCc
Q 045194 7 KLLPIANVGKIMKQILPPRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALSTLGFD 78 (157)
Q Consensus 7 ~~LP~A~I~RImK~~LP~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~LgF~ 78 (157)
+.|-+..|..|+... + .-....-|.+.|+..+..||.-|+..|..++...||--.+..||+.||+.|+..
T Consensus 28 ~sla~~avaQIcqsl-g-~~~~~~sale~Ltd~~~qyvQ~lgk~a~~~~n~anR~epnl~Div~Al~dls~s 97 (353)
T KOG2389|consen 28 FSLARVAVAQICQSL-G-YSSTQNSALETLTDVLQQYVQNLGKTAHRYSNLANRTEPNLFDIVLALQDLSAS 97 (353)
T ss_pred HHHHHHHHHHHHHhc-C-CcccccHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCccHHHHHHHHHHhhhh
Confidence 346667777887664 3 223445599999999999999999999999999999999999999999988766
No 62
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=86.66 E-value=4 Score=35.12 Aligned_cols=72 Identities=13% Similarity=0.130 Sum_probs=50.5
Q ss_pred hhHHHHHHhhhCCC---CccccHHHHHHHHHHH------HHHHHHHHHHHHHHHHhcCCCccCchhHHHHHhhCCCchhH
Q 045194 11 IANVGKIMKQILPP---RAKISKEAKQTMQECA------TEFISFVTGEASDKCHKENRKTVNGDDICWALSTLGFDNYT 81 (157)
Q Consensus 11 ~A~I~RImK~~LP~---~~kISkDA~~al~~~a------teFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~LgF~~y~ 81 (157)
...+..|++..+.. ...++.++.+.+.+.+ --.+..+...|.+.|...++.+|+.+||..|+..+....+.
T Consensus 209 ~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~a~~~a~~~~~~~I~~~~v~~a~~~~~~~~~~ 288 (394)
T PRK00411 209 ADEIFDILKDRVEEGFYPGVVDDEVLDLIADLTAREHGDARVAIDLLRRAGLIAEREGSRKVTEEDVRKAYEKSEIVHLS 288 (394)
T ss_pred HHHHHHHHHHHHHhhcccCCCCHhHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHHHHHHH
Confidence 34455555544321 2358899988888777 33455666788888988999999999999999988544443
Q ss_pred H
Q 045194 82 E 82 (157)
Q Consensus 82 ~ 82 (157)
.
T Consensus 289 ~ 289 (394)
T PRK00411 289 E 289 (394)
T ss_pred H
Confidence 3
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=82.92 E-value=7.7 Score=32.91 Aligned_cols=74 Identities=14% Similarity=0.065 Sum_probs=49.6
Q ss_pred hHHHHHHhhhCC---CCccccHHHHHHHHHHHH------HHHHHHHHHHHHHHHhcCCCccCchhHHHHHhhCCCchhHH
Q 045194 12 ANVGKIMKQILP---PRAKISKEAKQTMQECAT------EFISFVTGEASDKCHKENRKTVNGDDICWALSTLGFDNYTE 82 (157)
Q Consensus 12 A~I~RImK~~LP---~~~kISkDA~~al~~~at------eFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~LgF~~y~~ 82 (157)
..+..|++..+. ....++.++...+.+.+. -.+..+...|.+.|..+++.+|+.+||..|+..+..+.+..
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 335555554432 123478888777665442 23444566778888888999999999999999986665555
Q ss_pred HHH
Q 045194 83 AIV 85 (157)
Q Consensus 83 ~L~ 85 (157)
.+.
T Consensus 282 ~i~ 284 (365)
T TIGR02928 282 LIR 284 (365)
T ss_pred HHH
Confidence 444
No 64
>PF13654 AAA_32: AAA domain; PDB: 3K1J_B.
Probab=77.89 E-value=11 Score=35.19 Aligned_cols=49 Identities=16% Similarity=0.219 Sum_probs=38.7
Q ss_pred cccHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHhcCCCccCchhHHHHHhhC
Q 045194 27 KISKEAKQTMQECATE-----------FISFVTGEASDKCHKENRKTVNGDDICWALSTL 75 (157)
Q Consensus 27 kISkDA~~al~~~ate-----------FI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~L 75 (157)
-++.+|+..|.+.+.. -|.-|..+|+-+|..++++.|+++||..|++.-
T Consensus 447 ~~~~~Av~~li~~~~R~~q~kLsl~~~~l~~ll~EA~~~A~~~~~~~I~~~~V~~Ai~~r 506 (509)
T PF13654_consen 447 PFDRSAVARLIEYSARLDQDKLSLRFSWLADLLREANYWARKEGAKVITAEHVEQAIEER 506 (509)
T ss_dssp -BBHHHHHHHHHHHHHCC-SEEE--HHHHHHHHHHHHHHHHHCT-SSB-HHHHHHHHHH-
T ss_pred CCCHHHHHHHHHHHHHHhCCEeCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHcc
Confidence 4888888888776653 567777999999999999999999999999753
No 65
>KOG3334 consensus Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=75.60 E-value=8.4 Score=30.77 Aligned_cols=61 Identities=15% Similarity=0.204 Sum_probs=47.5
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHhhCCCchhHH-HHHHHH
Q 045194 28 ISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALSTLGFDNYTE-AIVRYL 88 (157)
Q Consensus 28 ISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~LgF~~y~~-~L~~~L 88 (157)
...-....|.+.+--++.-|...|.-++.+.++.+|.++||..|++..+=-.|.. +=+++|
T Consensus 31 yEprVi~qlLefa~rYtt~vL~DA~vys~HA~ka~i~~eDVrlA~~~~~~~sf~~pPpRe~l 92 (148)
T KOG3334|consen 31 YEPRVINQLLEFAYRYTTTVLDDAKVYSSHAKKATIDAEDVRLAIQMRVDHSFTPPPPREFL 92 (148)
T ss_pred cChHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHhccccCCCCchHHH
Confidence 3344455567777777888889999999999999999999999999777777766 334444
No 66
>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=73.63 E-value=11 Score=35.05 Aligned_cols=64 Identities=20% Similarity=0.241 Sum_probs=44.1
Q ss_pred hhHHHHHHhhhCC-CCccccHHHHHHHHHHHH---HHHHHHHHHHHHHHHhcCCCccCchhHHHHHhhC
Q 045194 11 IANVGKIMKQILP-PRAKISKEAKQTMQECAT---EFISFVTGEASDKCHKENRKTVNGDDICWALSTL 75 (157)
Q Consensus 11 ~A~I~RImK~~LP-~~~kISkDA~~al~~~at---eFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~L 75 (157)
...+..|++..+. .++.|++++.+.|.+.+. +.++. ...|...|..++|++|+.+||.+++..-
T Consensus 265 ~eei~~Il~~~a~k~~i~is~~al~~I~~y~~n~Rel~nl-l~~Aa~~A~~~~~~~It~~dI~~vl~~~ 332 (531)
T TIGR02902 265 DEEIKEIAKNAAEKIGINLEKHALELIVKYASNGREAVNI-VQLAAGIALGEGRKRILAEDIEWVAENG 332 (531)
T ss_pred HHHHHHHHHHHHHHcCCCcCHHHHHHHHHhhhhHHHHHHH-HHHHHHHHhhCCCcEEcHHHHHHHhCCc
Confidence 3445556666553 246799999998877665 23333 3455567888899999999999997543
No 67
>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=72.55 E-value=15 Score=33.32 Aligned_cols=54 Identities=26% Similarity=0.255 Sum_probs=49.3
Q ss_pred CccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHhhCCCc
Q 045194 25 RAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALSTLGFD 78 (157)
Q Consensus 25 ~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~LgF~ 78 (157)
-..|..|+..+|.--.+==|+.+..+|...-.+.+|..++.+||-.||+.|+.+
T Consensus 20 i~Ni~Dd~l~alamDlEYRI~ev~qea~KFmvhSKRtvLt~dDis~ALr~lNVe 73 (450)
T COG5095 20 ISNIDDDALRALAMDLEYRIKEVCQEASKFMVHSKRTVLTIDDISYALRSLNVE 73 (450)
T ss_pred CcccccHHHHHHHHhHHHHHHHHHHHHHHHhhcccceeeeHHhHHHHHHhcCCC
Confidence 446999999999998888899999999999999999999999999999988655
No 68
>KOG1757 consensus Histone 2A [Chromatin structure and dynamics]
Probab=70.08 E-value=7.1 Score=30.23 Aligned_cols=64 Identities=11% Similarity=0.232 Sum_probs=49.9
Q ss_pred cccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC----CCccCchhHHHHHh
Q 045194 6 DKLLPIANVGKIMKQILPPRAKISKEAKQTMQECATEFISFVTGEASDKCHKEN----RKTVNGDDICWALS 73 (157)
Q Consensus 6 D~~LP~A~I~RImK~~LP~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~k----RKTI~~eDVl~AL~ 73 (157)
.+.+|...|.|.+|.-.....++..-+.... ...+.|||.|-.+.|.+.. -|.|++.|+-.|++
T Consensus 28 GlqFpVgRihr~LK~r~t~h~rVGataavy~----aaileYLTaEVLeLAgNasKdLKvKRitprHlqLAiR 95 (131)
T KOG1757|consen 28 GLQFPVGRIHRHLKTRTTSHGRVGATAAVYS----AAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 95 (131)
T ss_pred ccccchHHHHHHHHHhcccccccchHHHHHH----HHHHHHHHHHHHHHcccccccceeeeccchhheeeec
Confidence 4689999999999999887888876665443 3457799999888875543 47899999988875
No 69
>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=69.99 E-value=18 Score=34.26 Aligned_cols=49 Identities=12% Similarity=0.116 Sum_probs=39.5
Q ss_pred cccHHHHHHHHHHHH-------------HHHHHHHHHHHHHHHhcCCCccCchhHHHHHhhC
Q 045194 27 KISKEAKQTMQECAT-------------EFISFVTGEASDKCHKENRKTVNGDDICWALSTL 75 (157)
Q Consensus 27 kISkDA~~al~~~at-------------eFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~L 75 (157)
.++.+|...|.+-++ -=|.-|..+|..+|..+++.+|+.+||..|++.-
T Consensus 330 ~~s~~Av~~Li~~~~R~ag~r~~lsl~~R~L~~llR~A~~iA~~~~~~~I~~ehV~~Ai~~~ 391 (608)
T TIGR00764 330 HFTRDAVEEIVREAQRRAGRKDHLTLRLRELGGLVRAAGDIAKSSGKVYVTAEHVLKAKKLA 391 (608)
T ss_pred cCCHHHHHHHHHHHHHHHhcccccCCCHHHHHHHHHHHHHHHHhcCCceecHHHHHHHHHHH
Confidence 689999988876544 3355566788889989999999999999998754
No 70
>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=65.16 E-value=11 Score=23.92 Aligned_cols=42 Identities=12% Similarity=0.143 Sum_probs=25.6
Q ss_pred cHHHHHHHHHHHHHHHH-HHHHHHHHHHHhcCCCccCchhHHHH
Q 045194 29 SKEAKQTMQECATEFIS-FVTGEASDKCHKENRKTVNGDDICWA 71 (157)
Q Consensus 29 SkDA~~al~~~ateFI~-~ltseA~e~~~~~kRKTI~~eDVl~A 71 (157)
+.||...|.+. =.|+- .|-..+-..|...|...|+.++|..|
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 45666665554 23443 33455677789999999999988765
No 71
>PF02861 Clp_N: Clp amino terminal domain; InterPro: IPR004176 This short domain is found in one or two copies at the amino terminus of ClpA and ClpB proteins from bacteria and eukaryotes. The function of these domains is uncertain but they may form a protein binding site []. The proteins are thought to be subunits of ATP-dependent proteases which act as chaperones to target the proteases to substrates.; GO: 0019538 protein metabolic process; PDB: 3FH2_A 3ZRJ_A 3ZRI_A 1QVR_C 3FES_C 2Y1R_F 3PXG_D 2Y1Q_A 3PXI_C 2K77_A ....
Probab=63.75 E-value=11 Score=23.13 Aligned_cols=26 Identities=12% Similarity=0.146 Sum_probs=21.0
Q ss_pred HHHHHHhcCCCccCchhHHHHHhhCC
Q 045194 51 ASDKCHKENRKTVNGDDICWALSTLG 76 (157)
Q Consensus 51 A~e~~~~~kRKTI~~eDVl~AL~~Lg 76 (157)
|.+.|...+...|+.+|++.||=.-+
T Consensus 1 A~~~A~~~~~~~i~~eHlL~all~~~ 26 (53)
T PF02861_consen 1 AQELARERGHQYISPEHLLLALLEDP 26 (53)
T ss_dssp HHHHHHHTTBSSE-HHHHHHHHHHHT
T ss_pred CHHHHHHcCCCcccHHHHHHHHHhhh
Confidence 56789999999999999999975544
No 72
>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=62.96 E-value=17 Score=24.14 Aligned_cols=60 Identities=18% Similarity=0.252 Sum_probs=37.6
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHhhCCCchhHHHHHHHH
Q 045194 28 ISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALSTLGFDNYTEAIVRYL 88 (157)
Q Consensus 28 ISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~LgF~~y~~~L~~~L 88 (157)
++..-.+.|...... ...=+.+............-+.++++.||+.+|..+-++.|+.+|
T Consensus 24 ~~~~~i~~i~~~~~~-~~~~~~~~L~~W~~~~~~~at~~~L~~aL~~~~~~d~~~~i~~~~ 83 (83)
T PF00531_consen 24 LSESEIENIEEENPD-LREQTYEMLQRWRQREGPNATVDQLIQALRDIGRNDLAEKIEQML 83 (83)
T ss_dssp S-HHHHHHHHHHSTS-HHHHHHHHHHHHHHHHGSTSSHHHHHHHHHHTTHHHHHHHHHHH-
T ss_pred cCHHHHHHHHHhCCC-hHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHCCcHHHHHHHHhhC
Confidence 555555555554422 222233333444444455667889999999999999999988765
No 73
>COG1067 LonB Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]
Probab=61.24 E-value=8.1 Score=37.20 Aligned_cols=48 Identities=25% Similarity=0.305 Sum_probs=35.9
Q ss_pred cccHHHHHHHHHHHHHH-------------HHHHHHHHHHHHHhcCCCccCchhHHHHHhh
Q 045194 27 KISKEAKQTMQECATEF-------------ISFVTGEASDKCHKENRKTVNGDDICWALST 74 (157)
Q Consensus 27 kISkDA~~al~~~ateF-------------I~~ltseA~e~~~~~kRKTI~~eDVl~AL~~ 74 (157)
-++++|..-|.+-+..- +.-|-.+|..+|..++++-|+++||.+|++.
T Consensus 338 ~~~~~Av~~li~~a~R~Ag~~~~Ltl~~rdl~~lv~~A~~ia~~~~~~~I~ae~Ve~a~~~ 398 (647)
T COG1067 338 HLDKDAVEELIREAARRAGDQNKLTLRLRDLGNLVREAGDIAVSEGRKLITAEDVEEALQK 398 (647)
T ss_pred CCCHHHHHHHHHHHHHhccccceeccCHHHHHHHHHHhhHHHhcCCcccCcHHHHHHHHHh
Confidence 37777766655544432 2334449999999999999999999999976
No 74
>KOG3901 consensus Transcription initiation factor IID subunit [Transcription]
Probab=60.61 E-value=24 Score=26.84 Aligned_cols=48 Identities=19% Similarity=0.223 Sum_probs=38.8
Q ss_pred CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHhh
Q 045194 24 PRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALST 74 (157)
Q Consensus 24 ~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~ 74 (157)
++..=-.|.+++|...+.+||..++..|..+. +|--+..||++-+|+.
T Consensus 24 Dd~nP~~~tv~~Le~iV~~Yi~elt~~a~~~g---~rgk~~veD~~f~lRk 71 (109)
T KOG3901|consen 24 DDVNPYPETVDLLEDIVLEYITELTHAAMEIG---KRGKVKVEDFKFLLRK 71 (109)
T ss_pred CCCCccHhHHHHHHHHHHHHHHHHHHHHHHhc---ccCceeHHHHHHHHHh
Confidence 44456678899999999999999988888776 4556788999999863
No 75
>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=59.84 E-value=72 Score=25.96 Aligned_cols=77 Identities=10% Similarity=0.084 Sum_probs=54.6
Q ss_pred ccCchhHHHHHHhhhCCC-Cc-cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhc------CCCccCchhHHHHHhhCCCc
Q 045194 7 KLLPIANVGKIMKQILPP-RA-KISKEAKQTMQECATEFISFVTGEASDKCHKE------NRKTVNGDDICWALSTLGFD 78 (157)
Q Consensus 7 ~~LP~A~I~RImK~~LP~-~~-kISkDA~~al~~~ateFI~~ltseA~e~~~~~------kRKTI~~eDVl~AL~~LgF~ 78 (157)
..|....|.+.|...+.. +. .|+.|...+|.-||.+++..|.......|.+- .-.++-..||-..|..|+--
T Consensus 43 ~fl~~~~l~~~~~~i~~~~g~~~~~~d~~~lis~a~e~rlr~li~k~~~~s~hR~~~~~~~~r~~~~sdvr~qL~~l~~~ 122 (212)
T cd08045 43 SFLNPSPLAKKIRKIAKKHGLKEVDEDVLDLISLALEERLRNLLEKLIEVSEHRVDSEKEDERYEITSDVRKQLRFLEQL 122 (212)
T ss_pred hccCHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCceeecchHHHHHHHHHHH
Confidence 345555666666555432 22 69999999999999999999999999988753 33556677888777666554
Q ss_pred hhHHH
Q 045194 79 NYTEA 83 (157)
Q Consensus 79 ~y~~~ 83 (157)
+..+.
T Consensus 123 ek~e~ 127 (212)
T cd08045 123 EREEE 127 (212)
T ss_pred HHHHH
Confidence 44443
No 76
>COG5162 Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=57.33 E-value=78 Score=26.11 Aligned_cols=68 Identities=16% Similarity=0.223 Sum_probs=47.4
Q ss_pred cCchhHHHHHHhhhCCCCcc-ccHHHHHHHHHHHHHHHHHHHHHHHHHHH-h------------------c---------
Q 045194 8 LLPIANVGKIMKQILPPRAK-ISKEAKQTMQECATEFISFVTGEASDKCH-K------------------E--------- 58 (157)
Q Consensus 8 ~LP~A~I~RImK~~LP~~~k-ISkDA~~al~~~ateFI~~ltseA~e~~~-~------------------~--------- 58 (157)
.||-+.+-=.|-.+ ++. ...-.+.+|.-.+..||+-|+..|.++.+ + .
T Consensus 88 liPd~v~DYyl~k~---Gf~~~D~rvKkLl~L~aqKFvsDiA~dayqYsrIr~~~sna~~t~~~a~~f~~gg~~~i~~~~ 164 (197)
T COG5162 88 LIPDSVTDYYLEKA---GFVTSDQRVKKLLSLLAQKFVSDIAVDAYQYSRIRQGSSNAKATAQKAKRFAKGGASGIGSSG 164 (197)
T ss_pred CccHHHHHHHHHhc---CceeccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccchhhHHHHHHHHhcccccccccc
Confidence 35555555555443 333 34456778888999999999988876642 1 1
Q ss_pred -----CCCccCchhHHHHHhhCCCc
Q 045194 59 -----NRKTVNGDDICWALSTLGFD 78 (157)
Q Consensus 59 -----kRKTI~~eDVl~AL~~LgF~ 78 (157)
++-+++..|+-.||++.|+.
T Consensus 165 ~~~dr~K~vltv~DLs~Al~EyGin 189 (197)
T COG5162 165 RRGDRKKPVLTVVDLSKALEEYGIN 189 (197)
T ss_pred cccccCCceeeehHHHHHHHHhccc
Confidence 55678999999999998875
No 77
>PF13335 Mg_chelatase_2: Magnesium chelatase, subunit ChlI
Probab=56.51 E-value=44 Score=24.10 Aligned_cols=47 Identities=23% Similarity=0.279 Sum_probs=39.5
Q ss_pred cccHHHHHHHHHHHHHH------HHHHHHHHHHHHHhcCCCccCchhHHHHHh
Q 045194 27 KISKEAKQTMQECATEF------ISFVTGEASDKCHKENRKTVNGDDICWALS 73 (157)
Q Consensus 27 kISkDA~~al~~~ateF------I~~ltseA~e~~~~~kRKTI~~eDVl~AL~ 73 (157)
.+++++..+|..++..| ++-|..-|..+|--++...|..+||..||.
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 58888888888888766 455667789999999999999999999984
No 78
>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=55.84 E-value=19 Score=26.76 Aligned_cols=34 Identities=21% Similarity=0.307 Sum_probs=27.7
Q ss_pred hHHHHHHhhhC----CCCccccHHHHHHHHHHHHHHHH
Q 045194 12 ANVGKIMKQIL----PPRAKISKEAKQTMQECATEFIS 45 (157)
Q Consensus 12 A~I~RImK~~L----P~~~kISkDA~~al~~~ateFI~ 45 (157)
++|.+++|.-| .++..++.++.+.|+++++.|-.
T Consensus 51 SNIGvLIKkglIEKSGDGlv~T~~g~~Ii~~AA~l~a~ 88 (96)
T PF09114_consen 51 SNIGVLIKKGLIEKSGDGLVITEEGMDIIIQAAELWAQ 88 (96)
T ss_dssp HHHHHHHHTTSEEEETTEEEE-HHHHHHHHHHHHHHHH
T ss_pred HhHHHHHHcCcccccCCceEEechHHHHHHHHHHHHHh
Confidence 56888999887 35678999999999999998754
No 79
>KOG2680 consensus DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=54.93 E-value=59 Score=29.76 Aligned_cols=50 Identities=20% Similarity=0.245 Sum_probs=41.5
Q ss_pred CCccccHHHHHHHHHHHHH----HHHHHHHHHHHHHHhcCCCccCchhHHHHHh
Q 045194 24 PRAKISKEAKQTMQECATE----FISFVTGEASDKCHKENRKTVNGDDICWALS 73 (157)
Q Consensus 24 ~~~kISkDA~~al~~~ate----FI~~ltseA~e~~~~~kRKTI~~eDVl~AL~ 73 (157)
.++.++.||++.|.....+ |-.+|-..|+..|.+.+-+++..+||-.+.+
T Consensus 374 Edv~m~~~A~d~Lt~i~~~tsLRYai~Lit~a~~~~~krk~~~v~~~di~r~y~ 427 (454)
T KOG2680|consen 374 EDVEMNPDALDLLTKIGEATSLRYAIHLITAASLVCLKRKGKVVEVDDIERVYR 427 (454)
T ss_pred hccccCHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHhcCceeehhHHHHHHH
Confidence 4788999999998776543 5566677889999999999999999998874
No 80
>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=54.15 E-value=55 Score=28.81 Aligned_cols=53 Identities=23% Similarity=0.238 Sum_probs=40.8
Q ss_pred hhhCCCCccccHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCccCchhHHHHH
Q 045194 19 KQILPPRAKISKEAKQTMQECATEFI-------SFVTGEASDKCHKENRKTVNGDDICWAL 72 (157)
Q Consensus 19 K~~LP~~~kISkDA~~al~~~ateFI-------~~ltseA~e~~~~~kRKTI~~eDVl~AL 72 (157)
++.++ .+.|+.+....+.+.+..+= .++...|...|.-+||..|+++||..+.
T Consensus 247 ~~~~~-~V~v~d~~~~~i~~l~~~~~~~s~Ra~i~l~raArA~Aal~GR~~V~~dDv~~~a 306 (337)
T TIGR02030 247 QNLLP-QVTIPYDVLVKVAELCAELDVDGLRGELTLNRAAKALAAFEGRTEVTVDDIRRVA 306 (337)
T ss_pred HHHhc-cCcCCHHHHHHHHHHHHHHCCCCCcHHHHHHHHHHHHHHHcCCCCCCHHHHHHHH
Confidence 34454 78899999988888776653 2455677888889999999999998765
No 81
>PRK09862 putative ATP-dependent protease; Provisional
Probab=52.38 E-value=60 Score=30.40 Aligned_cols=59 Identities=12% Similarity=0.101 Sum_probs=45.3
Q ss_pred ccccHHHHHHHHHHHHHH------HHHHHHHHHHHHHhcCCCccCchhHHHHHhhCCCchhHHHH
Q 045194 26 AKISKEAKQTMQECATEF------ISFVTGEASDKCHKENRKTVNGDDICWALSTLGFDNYTEAI 84 (157)
Q Consensus 26 ~kISkDA~~al~~~ateF------I~~ltseA~e~~~~~kRKTI~~eDVl~AL~~LgF~~y~~~L 84 (157)
+.++.++...+.+....+ .+.|..-|..+|--++|..|+.+||..|+.--+++...-.+
T Consensus 437 ~~l~~~~~~~l~~~~~~~~lS~Ra~~rlLrvARTiADL~g~~~V~~~hv~eAl~yR~~~~~~~~~ 501 (506)
T PRK09862 437 CKLESEDARWLEETLIHLGLSIRAWQRLLKVARTIADIDQSDIITRQHLQEAVSYRAIDRLLIHL 501 (506)
T ss_pred hCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHhhcccHHHHHH
Confidence 467888888777765544 56677788999999999999999999999866666444443
No 82
>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=52.23 E-value=52 Score=31.23 Aligned_cols=50 Identities=22% Similarity=0.274 Sum_probs=42.0
Q ss_pred CCccccHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCccCchhHHHHHh
Q 045194 24 PRAKISKEAKQTMQECATEFI-------SFVTGEASDKCHKENRKTVNGDDICWALS 73 (157)
Q Consensus 24 ~~~kISkDA~~al~~~ateFI-------~~ltseA~e~~~~~kRKTI~~eDVl~AL~ 73 (157)
+.+.|+.++...|.+.+..+- .++...|.-.|.-+||.+|+.+||..|+.
T Consensus 246 ~~V~is~~~~~~l~~~~~~~~i~s~Ra~i~~~r~Ara~AaL~gr~~V~~~Dv~~A~~ 302 (633)
T TIGR02442 246 PSVRISDSLIRFISELCIEFGVDGHRADIVMARAARALAALDGRRRVTAEDVREAAE 302 (633)
T ss_pred CCCCCCHHHHHHHHHHHHHhCCCCccHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHH
Confidence 478899999999999887762 45667788888999999999999998874
No 83
>CHL00081 chlI Mg-protoporyphyrin IX chelatase
Probab=47.96 E-value=51 Score=29.35 Aligned_cols=54 Identities=19% Similarity=0.295 Sum_probs=43.4
Q ss_pred hhhCCCCccccHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCccCchhHHHHHh
Q 045194 19 KQILPPRAKISKEAKQTMQECATEFI-------SFVTGEASDKCHKENRKTVNGDDICWALS 73 (157)
Q Consensus 19 K~~LP~~~kISkDA~~al~~~ateFI-------~~ltseA~e~~~~~kRKTI~~eDVl~AL~ 73 (157)
++.++ .+.|+.+....|.+.|..+= .++...|.-.|--+||..|+++||..+..
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 44454 78899999999998888764 35667788888899999999999987753
No 84
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=47.91 E-value=84 Score=26.73 Aligned_cols=70 Identities=16% Similarity=0.183 Sum_probs=46.3
Q ss_pred chhHHHHHHhhhCC-CCccccHHHHHHHHHHHH---HHHHHHHHHHHHHHHhcCCCccCchhHHHHHhhCCCch
Q 045194 10 PIANVGKIMKQILP-PRAKISKEAKQTMQECAT---EFISFVTGEASDKCHKENRKTVNGDDICWALSTLGFDN 79 (157)
Q Consensus 10 P~A~I~RImK~~LP-~~~kISkDA~~al~~~at---eFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~LgF~~ 79 (157)
+...+..|++..+. .++.++.|+...|.+.+. -.+..+...+.+.+...+...|+.++|..++..++.+.
T Consensus 181 ~~~e~~~il~~~~~~~~~~~~~~~~~~ia~~~~G~pR~a~~~l~~~~~~a~~~~~~~I~~~~v~~~l~~~~~~~ 254 (328)
T PRK00080 181 TVEELEKIVKRSARILGVEIDEEGALEIARRSRGTPRIANRLLRRVRDFAQVKGDGVITKEIADKALDMLGVDE 254 (328)
T ss_pred CHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCc
Confidence 33444445544332 356799998888776663 23444445566666666677899999999999877663
No 85
>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=46.26 E-value=26 Score=22.61 Aligned_cols=24 Identities=21% Similarity=0.440 Sum_probs=20.5
Q ss_pred cCchhHHHHHhhCCCchhHHHHHH
Q 045194 63 VNGDDICWALSTLGFDNYTEAIVR 86 (157)
Q Consensus 63 I~~eDVl~AL~~LgF~~y~~~L~~ 86 (157)
=+++||..-|..+||..|.+.+..
T Consensus 4 w~~~~v~~WL~~~gl~~y~~~f~~ 27 (66)
T PF07647_consen 4 WSPEDVAEWLKSLGLEQYADNFRE 27 (66)
T ss_dssp HCHHHHHHHHHHTTCGGGHHHHHH
T ss_pred CCHHHHHHHHHHCCcHHHHHHHHH
Confidence 467899999999999999987765
No 86
>COG5248 TAF19 Transcription initiation factor TFIID, subunit TAF13 [Transcription]
Probab=46.06 E-value=62 Score=25.03 Aligned_cols=49 Identities=14% Similarity=0.279 Sum_probs=41.1
Q ss_pred CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHhh
Q 045194 24 PRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALST 74 (157)
Q Consensus 24 ~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~ 74 (157)
+.+.=.-|..++|.+.+.-+++.+..+|...|. .|--+..||..-||+.
T Consensus 24 Dvv~P~~dt~~~L~e~V~dY~~~~ctna~~~Aq--~rnK~k~eDfkfaLr~ 72 (126)
T COG5248 24 DVVAPRYDTAEALHEYVLDYMSILCTNAHNMAQ--VRNKTKTEDFKFALRR 72 (126)
T ss_pred CCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHH--hcccchHHHHHHHHhh
Confidence 445567789999999999999999999999988 4556778999999974
No 87
>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=45.62 E-value=22 Score=22.08 Aligned_cols=24 Identities=21% Similarity=0.422 Sum_probs=20.3
Q ss_pred CchhHHHHHhhCCCchhHHHHHHH
Q 045194 64 NGDDICWALSTLGFDNYTEAIVRY 87 (157)
Q Consensus 64 ~~eDVl~AL~~LgF~~y~~~L~~~ 87 (157)
+.++|..-|+.+|+++|++.+...
T Consensus 3 ~~~~V~~wL~~~~~~~y~~~f~~~ 26 (63)
T cd00166 3 SPEDVAEWLESLGLGQYADNFREN 26 (63)
T ss_pred CHHHHHHHHHHcChHHHHHHHHHc
Confidence 578999999999999998887654
No 88
>TIGR01128 holA DNA polymerase III, delta subunit. subunit around DNA forming a DNA sliding clamp.
Probab=45.57 E-value=1e+02 Score=25.20 Aligned_cols=65 Identities=14% Similarity=0.074 Sum_probs=42.9
Q ss_pred CchhHHHHHHhhhCC-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHh
Q 045194 9 LPIANVGKIMKQILP-PRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALS 73 (157)
Q Consensus 9 LP~A~I~RImK~~LP-~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~ 73 (157)
+....+.+.+++.+. .+..|+.++...|...+.-=+..+..+-...|.-.+.++|+.+||...+.
T Consensus 111 ~~~~~~~~~i~~~~~~~g~~i~~~a~~~l~~~~~~d~~~l~~el~KL~~~~~~~~It~e~I~~~~~ 176 (302)
T TIGR01128 111 PKEQELPRWIQARLKKLGLRIDPDAVQLLAELVEGNLLAIAQELEKLALYAPDGKITLEDVEEAVS 176 (302)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCcHHHHHHHHHHHHHhhCCCCCCCHHHHHHHHh
Confidence 445556666666553 35689999999988877654555555666655543444799999876654
No 89
>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=44.78 E-value=90 Score=20.62 Aligned_cols=47 Identities=17% Similarity=0.234 Sum_probs=34.9
Q ss_pred cCchhHHHHHHhhhCCCCcc-ccHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 045194 8 LLPIANVGKIMKQILPPRAK-ISKEAKQTMQECATEFISFVTGEASDKCHK 57 (157)
Q Consensus 8 ~LP~A~I~RImK~~LP~~~k-ISkDA~~al~~~ateFI~~ltseA~e~~~~ 57 (157)
.+|=+.+.-+++.+ ++. -..-.+.+|.=++..||.-|+..|.+.|+-
T Consensus 2 ~IPD~v~~~yL~~~---G~~~~D~rv~RLvSLaaQKFisdI~~dA~q~~k~ 49 (51)
T PF03540_consen 2 TIPDEVTDYYLERS---GFQTSDPRVKRLVSLAAQKFISDIANDAMQYCKI 49 (51)
T ss_pred CCCHHHHHHHHHHC---CCCCCCHhHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 36777777777776 333 233446778889999999999999999874
No 90
>PRK07452 DNA polymerase III subunit delta; Validated
Probab=44.62 E-value=83 Score=26.47 Aligned_cols=65 Identities=11% Similarity=0.124 Sum_probs=46.0
Q ss_pred HHHHHhhhCC-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHh--cCCCccCchhHHHHHhhCCCc
Q 045194 14 VGKIMKQILP-PRAKISKEAKQTMQECATEFISFVTGEASDKCHK--ENRKTVNGDDICWALSTLGFD 78 (157)
Q Consensus 14 I~RImK~~LP-~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~--~kRKTI~~eDVl~AL~~LgF~ 78 (157)
+.+.|++.+. .+..|+.+|...|.+++.-=...+..+-...+.- .++.+|+.+||...+....+.
T Consensus 135 l~~~i~~~~~~~g~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~~It~~~V~~~v~~~~~~ 202 (326)
T PRK07452 135 LKQLVERTAQELGVKLTPEAAELLAEAVGNDSRRLYNELEKLALYAENSTKPISAEEVKALVSNTTQN 202 (326)
T ss_pred HHHHHHHHHHHcCCCCCHHHHHHHHHHhCccHHHHHHHHHHHHHhccCCCCccCHHHHHHHhccCcCc
Confidence 4444444332 3678999999999998886556666666666654 557889999999887666544
No 91
>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=44.33 E-value=79 Score=29.36 Aligned_cols=67 Identities=22% Similarity=0.317 Sum_probs=47.9
Q ss_pred CCccccHHHHHHHHHHHHH----HHHHHHHHHHHHHHhcCCCccCchhHHHHHhhCCCchhHHHHHHHHHHHHH
Q 045194 24 PRAKISKEAKQTMQECATE----FISFVTGEASDKCHKENRKTVNGDDICWALSTLGFDNYTEAIVRYLHKYRE 93 (157)
Q Consensus 24 ~~~kISkDA~~al~~~ate----FI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~LgF~~y~~~L~~~L~~yre 93 (157)
.++.+++||.+.|....++ |..-|..-|+.+|...|+++|..+||-.|-+ | |-|-... -+|++.|+.
T Consensus 377 e~i~l~~~Ale~L~~ig~etSLRYa~qLL~pa~iiA~~rg~~~V~~~dVe~a~~-l-F~D~krS-v~~v~~~~~ 447 (450)
T COG1224 377 EDIELSDDALEYLTDIGEETSLRYAVQLLTPASIIAKRRGSKRVEVEDVERAKE-L-FLDVKRS-VEYVEKYEG 447 (450)
T ss_pred hccccCHHHHHHHHhhchhhhHHHHHHhccHHHHHHHHhCCCeeehhHHHHHHH-H-HhhHHHH-HHHHHHHHh
Confidence 4778999999999876654 4555566789999999999999999998843 2 3333222 345555554
No 92
>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=43.69 E-value=23 Score=26.87 Aligned_cols=60 Identities=10% Similarity=0.177 Sum_probs=38.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHhhCCCchhHHHHHHHHHHHHHH
Q 045194 31 EAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALSTLGFDNYTEAIVRYLHKYRED 94 (157)
Q Consensus 31 DA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~LgF~~y~~~L~~~L~~yre~ 94 (157)
..+.-|..|..+.-.|...-..-... ---.-..+...|+..|++..+.+++..|+.|+..
T Consensus 73 ~Vk~Eiaa~~~v~~~Y~~~L~~G~vd----~e~~~~~~~~kLk~AGidkV~~E~QkQlda~~~~ 132 (134)
T PF12010_consen 73 PVKNEIAACSNVWSEYYPPLETGLVD----PEEALPEFNEKLKAAGIDKVIAELQKQLDAFLAA 132 (134)
T ss_pred hhHHHHHHHHHHHHHHHHHHHccCCC----HHHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHh
Confidence 34455666666655554432211110 0112346778899999999999999999999875
No 93
>PRK13406 bchD magnesium chelatase subunit D; Provisional
Probab=43.52 E-value=54 Score=31.14 Aligned_cols=52 Identities=19% Similarity=0.179 Sum_probs=44.2
Q ss_pred hCCCCccccHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCccCchhHHHHHh
Q 045194 21 ILPPRAKISKEAKQTMQECATEFI-------SFVTGEASDKCHKENRKTVNGDDICWALS 73 (157)
Q Consensus 21 ~LP~~~kISkDA~~al~~~ateFI-------~~ltseA~e~~~~~kRKTI~~eDVl~AL~ 73 (157)
.++ ++.|+.+....+.+.|..|= .++...|.-+|--+||..|+.+||..|+.
T Consensus 190 rl~-~v~v~~~~l~~i~~~~~~~gv~S~Ra~i~llraARa~AaL~Gr~~V~~~dv~~Aa~ 248 (584)
T PRK13406 190 RLP-AVGPPPEAIAALCAAAAALGIASLRAPLLALRAARAAAALAGRTAVEEEDLALAAR 248 (584)
T ss_pred HHc-cCCCCHHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 454 88999999999888888774 46778889999999999999999999874
No 94
>PRK12402 replication factor C small subunit 2; Reviewed
Probab=43.33 E-value=83 Score=26.09 Aligned_cols=71 Identities=8% Similarity=0.014 Sum_probs=41.7
Q ss_pred CchhHHHHHHhhhCC-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHhhCCCchhH
Q 045194 9 LPIANVGKIMKQILP-PRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALSTLGFDNYT 81 (157)
Q Consensus 9 LP~A~I~RImK~~LP-~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~LgF~~y~ 81 (157)
++...+..+++..+. .+..++.++...|.+.+.-=+..+.......+. +..+|+.+||..++.....++.+
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 344555666655443 356799999988887763222222222233332 23479999998888765544333
No 95
>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=42.48 E-value=1.7e+02 Score=23.15 Aligned_cols=53 Identities=19% Similarity=0.370 Sum_probs=41.6
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHhhCCCc-hhHHHHHHHHHHHHHHHHHH
Q 045194 39 CATEFISFVTGEASDKCHKENRKTVNGDDICWALSTLGFD-NYTEAIVRYLHKYREDERER 98 (157)
Q Consensus 39 ~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~LgF~-~y~~~L~~~L~~yre~~~~k 98 (157)
.+.+.+.||..+|.. .-++++++..-|+.|||+ +.++.+......+|+.-...
T Consensus 43 ~~va~l~fiL~~A~k-------~n~~~~~l~~eL~~lglp~e~~~~l~~~~~~~~~~l~~~ 96 (174)
T cd04752 43 ASIAVLSFILSSAAK-------YNVDGESLSSELQQLGLPKEHATSLCRSYEEKQSKLQES 96 (174)
T ss_pred HHHHHHHHHHHHHHH-------cCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 556677777766653 448999999999999999 68888888888888876665
No 96
>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=42.05 E-value=31 Score=22.11 Aligned_cols=22 Identities=27% Similarity=0.496 Sum_probs=19.3
Q ss_pred CchhHHHHHhhCCCchhHHHHH
Q 045194 64 NGDDICWALSTLGFDNYTEAIV 85 (157)
Q Consensus 64 ~~eDVl~AL~~LgF~~y~~~L~ 85 (157)
++++|..-|+.+|++.|++...
T Consensus 4 ~~~~V~~WL~~~~l~~y~~~F~ 25 (64)
T PF00536_consen 4 SVEDVSEWLKSLGLEQYAENFE 25 (64)
T ss_dssp SHHHHHHHHHHTTGGGGHHHHH
T ss_pred CHHHHHHHHHHCCCHHHHHHHH
Confidence 5789999999999999998763
No 97
>PRK13407 bchI magnesium chelatase subunit I; Provisional
Probab=41.00 E-value=89 Score=27.53 Aligned_cols=53 Identities=11% Similarity=0.041 Sum_probs=41.5
Q ss_pred hhhCCCCccccHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCccCchhHHHHH
Q 045194 19 KQILPPRAKISKEAKQTMQECATEFI-------SFVTGEASDKCHKENRKTVNGDDICWAL 72 (157)
Q Consensus 19 K~~LP~~~kISkDA~~al~~~ateFI-------~~ltseA~e~~~~~kRKTI~~eDVl~AL 72 (157)
++.++ .+.|+.+....+.+.+..+= .+|...|.-.|.-+||..|+++||..+.
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 34443 78899999999988887764 2366778888999999999999996544
No 98
>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=40.89 E-value=1.2e+02 Score=24.95 Aligned_cols=67 Identities=18% Similarity=0.165 Sum_probs=43.0
Q ss_pred hHHHHHHhhhCC-CCccccHHHHHHHHHHHH---HHHHHHHHHHHHHHHhcCCCccCchhHHHHHhhCCCc
Q 045194 12 ANVGKIMKQILP-PRAKISKEAKQTMQECAT---EFISFVTGEASDKCHKENRKTVNGDDICWALSTLGFD 78 (157)
Q Consensus 12 A~I~RImK~~LP-~~~kISkDA~~al~~~at---eFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~LgF~ 78 (157)
..+..+++..+. .+..++.++...|.+.+. -++..+...+.+.+...+...|+.++|..++..++++
T Consensus 162 ~e~~~il~~~~~~~~~~~~~~al~~ia~~~~G~pR~~~~ll~~~~~~a~~~~~~~it~~~v~~~l~~l~~~ 232 (305)
T TIGR00635 162 EELAEIVSRSAGLLNVEIEPEAALEIARRSRGTPRIANRLLRRVRDFAQVRGQKIINRDIALKALEMLMID 232 (305)
T ss_pred HHHHHHHHHHHHHhCCCcCHHHHHHHHHHhCCCcchHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHhCCC
Confidence 334444444332 246788898887777543 2234444455666655666789999999999987655
No 99
>PRK13765 ATP-dependent protease Lon; Provisional
Probab=40.84 E-value=46 Score=32.04 Aligned_cols=47 Identities=13% Similarity=0.116 Sum_probs=38.3
Q ss_pred cccHHHHHHHHHHHHHH-------------HHHHHHHHHHHHHhcCCCccCchhHHHHHh
Q 045194 27 KISKEAKQTMQECATEF-------------ISFVTGEASDKCHKENRKTVNGDDICWALS 73 (157)
Q Consensus 27 kISkDA~~al~~~ateF-------------I~~ltseA~e~~~~~kRKTI~~eDVl~AL~ 73 (157)
.++.+|...|.+-++.- |.-|-.+|..+|+.++++.|+++||..|+.
T Consensus 339 ~f~~eAVa~LI~~~~R~ag~r~~lsl~~~~l~~l~r~a~~~a~~~~~~~i~~~~v~~a~~ 398 (637)
T PRK13765 339 HFDRDAVEEIIREAKRRAGRKGHLTLKLRDLGGLVRVAGDIARSEGAELTTAEHVLEAKK 398 (637)
T ss_pred CCCHHHHHHHHHHHHHHhCCccccccCHHHHHHHHHHHHHHHHhhccceecHHHHHHHHH
Confidence 58999988887766532 233678899999999999999999999974
No 100
>TIGR02454 CbiQ_TIGR cobalt ABC transporter, permease protein CbiQ. This model represents the permease component of the cobalt-specific ABC transporter. This model finds permeases which are generally next to the other subunits of the complex (CbiN and CbiO) or the cobalamin biosynthesis protein CbiM which is a transmembrane protein which likely interacts with the complex in some manner. In genomes which possess all of these subunits the ATPase is most likely running in the direction of import (for the biosynthesis of coenzyme B12). In other genomes, this subunit may be involved in the export of cobalt and/or other closely related heavy metals.
Probab=40.69 E-value=57 Score=25.35 Aligned_cols=38 Identities=24% Similarity=0.253 Sum_probs=30.2
Q ss_pred CccCchhHHHHHhhCCCc-----------hhHHHHHHHHHHHHHHHHHH
Q 045194 61 KTVNGDDICWALSTLGFD-----------NYTEAIVRYLHKYREDERER 98 (157)
Q Consensus 61 KTI~~eDVl~AL~~LgF~-----------~y~~~L~~~L~~yre~~~~k 98 (157)
-|.+..|+..+|+.+|+. .|++.+.+..+.-+++++.|
T Consensus 112 ~TT~~~~l~~~l~~l~~P~~~~~~~~l~~Rfip~l~~e~~~i~~Aq~aR 160 (198)
T TIGR02454 112 LTTPFPELLSALRRLGVPPLLVEILLLTYRYLFVLLEELRRMLLAQRSR 160 (198)
T ss_pred HcCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 467889999999999986 46677777777777777776
No 101
>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=39.93 E-value=29 Score=21.68 Aligned_cols=25 Identities=12% Similarity=0.352 Sum_probs=20.6
Q ss_pred cCchhHHHHHhhCCCchhHHHHHHH
Q 045194 63 VNGDDICWALSTLGFDNYTEAIVRY 87 (157)
Q Consensus 63 I~~eDVl~AL~~LgF~~y~~~L~~~ 87 (157)
-+.++|..-|..+||.+|++.+.+.
T Consensus 4 w~~~~v~~wL~~~g~~~y~~~f~~~ 28 (68)
T smart00454 4 WSPESVADWLESIGLEQYADNFRKN 28 (68)
T ss_pred CCHHHHHHHHHHCChHHHHHHHHHC
Confidence 4668899999999999988877655
No 102
>smart00350 MCM minichromosome maintenance proteins.
Probab=39.73 E-value=1.4e+02 Score=27.52 Aligned_cols=67 Identities=12% Similarity=0.122 Sum_probs=46.3
Q ss_pred cCchhHHHHHHhhhCC-CCccccHHHHHHHHHHHHHH-------------------HHHHHHHHHHHHHhcCCCccCchh
Q 045194 8 LLPIANVGKIMKQILP-PRAKISKEAKQTMQECATEF-------------------ISFVTGEASDKCHKENRKTVNGDD 67 (157)
Q Consensus 8 ~LP~A~I~RImK~~LP-~~~kISkDA~~al~~~ateF-------------------I~~ltseA~e~~~~~kRKTI~~eD 67 (157)
.++...+.+.+.-+=. -.-.|++++.+.|.+...+. +..|..-|.-.|+-.+|.+|+.+|
T Consensus 417 ~~~~~~l~~yi~~ar~~~~P~ls~~~~~~i~~~y~~~R~~~~~~~~~~~~~~t~R~l~sliRla~A~A~l~~r~~V~~~D 496 (509)
T smart00350 417 PISQEFLRKYIAYAREKIKPKLSEEAAEKLVKAYVDLRKEDSQSEARSSIPITVRQLESIIRLSEAHAKMRLSDVVEEAD 496 (509)
T ss_pred cCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhcccccccccccccCcCHHHHHHHHHHHHHHHHHcCCCccCHHH
Confidence 4677777776643310 01258999999887655442 245556677788899999999999
Q ss_pred HHHHHhh
Q 045194 68 ICWALST 74 (157)
Q Consensus 68 Vl~AL~~ 74 (157)
|..|++-
T Consensus 497 v~~ai~l 503 (509)
T smart00350 497 VEEAIRL 503 (509)
T ss_pred HHHHHHH
Confidence 9999864
No 103
>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=38.97 E-value=22 Score=22.40 Aligned_cols=14 Identities=36% Similarity=0.570 Sum_probs=11.8
Q ss_pred hhHHHHHhhCCCch
Q 045194 66 DDICWALSTLGFDN 79 (157)
Q Consensus 66 eDVl~AL~~LgF~~ 79 (157)
+|++.||..|||..
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 68999999999983
No 104
>TIGR02031 BchD-ChlD magnesium chelatase ATPase subunit D. This model represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria. Unlike subunit I (TIGR02030), this subunit is not found in archaea.
Probab=38.18 E-value=1.1e+02 Score=28.97 Aligned_cols=55 Identities=22% Similarity=0.314 Sum_probs=40.5
Q ss_pred HhhhCCCCccccHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCccCchhHHHHHh
Q 045194 18 MKQILPPRAKISKEAKQTMQECATEFI-------SFVTGEASDKCHKENRKTVNGDDICWALS 73 (157)
Q Consensus 18 mK~~LP~~~kISkDA~~al~~~ateFI-------~~ltseA~e~~~~~kRKTI~~eDVl~AL~ 73 (157)
+++.++ .+.|+.+....|.+.+..+= .++...|.-.|.-+||.+|+.+||..|..
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 344454 78899999888777665431 24456677778889999999999998874
No 105
>PF02361 CbiQ: Cobalt transport protein; InterPro: IPR003339 Cobalt transport proteins are most often found in cobalamin (vitamin B12) biosynthesis operons. Salmonella typhimurium synthesizes cobalamin (vitamin B12) de novo under anaerobic conditions. Not all Salmonella and Pseudomonas cobalamin synthetic genes have apparent homologs in the other species suggesting that the cobalamin biosynthetic pathways differ between the two organisms [].; GO: 0015087 cobalt ion transmembrane transporter activity, 0006824 cobalt ion transport, 0009236 cobalamin biosynthetic process
Probab=37.51 E-value=57 Score=25.35 Aligned_cols=66 Identities=18% Similarity=0.191 Sum_probs=44.4
Q ss_pred cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHhhCCCch------------hHHHHHHHHHHHHHH
Q 045194 27 KISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALSTLGFDN------------YTEAIVRYLHKYRED 94 (157)
Q Consensus 27 kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~LgF~~------------y~~~L~~~L~~yre~ 94 (157)
.+..+. +..++..++..+..-..-..- =.|.+++|++.+++.+++.. |++.+.+.++.-+++
T Consensus 95 ~i~~~g---~~~~~~~~lr~~~~~~~~~~~---~~tt~~~~l~~~l~~l~~P~~~~~~~i~l~~r~ip~l~~~~~~i~~A 168 (224)
T PF02361_consen 95 SITQEG---LIYAALLALRILAILLASLLF---ILTTSPSDLISALRKLRLPYPKIALMISLTLRFIPLLLEEFKRIREA 168 (224)
T ss_pred hhhHHH---HHHHHHHHHHHHHHHHHHHHH---HHHCCHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344554 344444444444433333222 24789999999999999987 788888888888888
Q ss_pred HHHH
Q 045194 95 ERER 98 (157)
Q Consensus 95 ~~~k 98 (157)
++.|
T Consensus 169 ~~~R 172 (224)
T PF02361_consen 169 QRLR 172 (224)
T ss_pred HHHc
Confidence 8777
No 106
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=36.58 E-value=80 Score=19.96 Aligned_cols=32 Identities=19% Similarity=0.369 Sum_probs=26.5
Q ss_pred ccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHH
Q 045194 7 KLLPIANVGKIMKQILPPRAKISKEAKQTMQECATE 42 (157)
Q Consensus 7 ~~LP~A~I~RImK~~LP~~~kISkDA~~al~~~ate 42 (157)
..+-.++|.|++... -.||.+.++-|.+++.+
T Consensus 9 agvS~~TVSr~ln~~----~~vs~~tr~rI~~~a~~ 40 (46)
T PF00356_consen 9 AGVSKSTVSRVLNGP----PRVSEETRERILEAAEE 40 (46)
T ss_dssp HTSSHHHHHHHHTTC----SSSTHHHHHHHHHHHHH
T ss_pred HCcCHHHHHHHHhCC----CCCCHHHHHHHHHHHHH
Confidence 357789999999875 37999999999988876
No 107
>TIGR00368 Mg chelatase-related protein. The N-terminal end matches very strongly a pfam Mg_chelatase domain.
Probab=36.08 E-value=89 Score=29.06 Aligned_cols=47 Identities=11% Similarity=0.160 Sum_probs=40.6
Q ss_pred cccHHHHHHHHHHHHHH------HHHHHHHHHHHHHhcCCCccCchhHHHHHh
Q 045194 27 KISKEAKQTMQECATEF------ISFVTGEASDKCHKENRKTVNGDDICWALS 73 (157)
Q Consensus 27 kISkDA~~al~~~ateF------I~~ltseA~e~~~~~kRKTI~~eDVl~AL~ 73 (157)
.+++++...|.++...| .+-|..-|..+|--+++..|..+||..|+.
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 566677889999999999999999999984
No 108
>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]
Probab=35.73 E-value=63 Score=28.73 Aligned_cols=60 Identities=13% Similarity=0.127 Sum_probs=43.1
Q ss_pred cccHHHHHHHHHHH------HHHHHHHHHHHHHHHHhcCCCccCchhHHHHHhhCCCchhHHHHHH
Q 045194 27 KISKEAKQTMQECA------TEFISFVTGEASDKCHKENRKTVNGDDICWALSTLGFDNYTEAIVR 86 (157)
Q Consensus 27 kISkDA~~al~~~a------teFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~LgF~~y~~~L~~ 86 (157)
.++.++...+..-+ ..+..-+...|.++|..+++.+|+.+||..|-++.+..-+.+.+..
T Consensus 211 ~~~~~vl~lia~~~a~~~GDAR~aidilr~A~eiAe~~~~~~v~~~~v~~a~~~~~~~~~~~~~~~ 276 (366)
T COG1474 211 VIDDDVLKLIAALVAAESGDARKAIDILRRAGEIAEREGSRKVSEDHVREAQEEIERDVLEEVLKT 276 (366)
T ss_pred CcCccHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHhhCCCCcCHHHHHHHHHHhhHHHHHHHHHc
Confidence 46666655544322 2344566778999999999999999999999877777766665443
No 109
>TIGR01242 26Sp45 26S proteasome subunit P45 family. Many proteins may score above the trusted cutoff because an internal
Probab=34.37 E-value=54 Score=28.38 Aligned_cols=32 Identities=25% Similarity=0.181 Sum_probs=27.3
Q ss_pred HHHHHHHHHHHHHHhcCCCccCchhHHHHHhh
Q 045194 43 FISFVTGEASDKCHKENRKTVNGDDICWALST 74 (157)
Q Consensus 43 FI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~ 74 (157)
-|..|..+|...|...++..|+.+|+..|++.
T Consensus 331 dl~~l~~~A~~~a~~~~~~~i~~~d~~~a~~~ 362 (364)
T TIGR01242 331 DLKAICTEAGMFAIREERDYVTMDDFIKAVEK 362 (364)
T ss_pred HHHHHHHHHHHHHHHhCCCccCHHHHHHHHHH
Confidence 34567778888898999999999999999875
No 110
>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional
Probab=34.15 E-value=52 Score=30.16 Aligned_cols=31 Identities=26% Similarity=0.168 Sum_probs=27.3
Q ss_pred HHHHHHHHHHHHHhcCCCccCchhHHHHHhh
Q 045194 44 ISFVTGEASDKCHKENRKTVNGDDICWALST 74 (157)
Q Consensus 44 I~~ltseA~e~~~~~kRKTI~~eDVl~AL~~ 74 (157)
|..|..+|...|.+++|..|+.+||..|++.
T Consensus 393 I~~i~~eA~~~Alr~~r~~Vt~~D~~~A~~~ 423 (438)
T PTZ00361 393 IKAICTEAGLLALRERRMKVTQADFRKAKEK 423 (438)
T ss_pred HHHHHHHHHHHHHHhcCCccCHHHHHHHHHH
Confidence 5567788999999999999999999999875
No 111
>PRK03992 proteasome-activating nucleotidase; Provisional
Probab=33.44 E-value=55 Score=28.96 Aligned_cols=34 Identities=18% Similarity=0.158 Sum_probs=27.8
Q ss_pred HHHHHHHHHHHHHHhcCCCccCchhHHHHHhhCC
Q 045194 43 FISFVTGEASDKCHKENRKTVNGDDICWALSTLG 76 (157)
Q Consensus 43 FI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~Lg 76 (157)
=|..|..+|...|.++++..|+.+|+..|++..-
T Consensus 340 dl~~l~~eA~~~a~~~~~~~i~~~d~~~A~~~~~ 373 (389)
T PRK03992 340 DLKAICTEAGMFAIRDDRTEVTMEDFLKAIEKVM 373 (389)
T ss_pred HHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHh
Confidence 3556677888888889999999999999987653
No 112
>PHA03328 nuclear egress lamina protein UL31; Provisional
Probab=33.30 E-value=58 Score=29.03 Aligned_cols=79 Identities=22% Similarity=0.341 Sum_probs=49.0
Q ss_pred cccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHhhCCCchhHHHHH
Q 045194 6 DKLLPIANVGKIMKQILPPRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALSTLGFDNYTEAIV 85 (157)
Q Consensus 6 D~~LP~A~I~RImK~~LP~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~LgF~~y~~~L~ 85 (157)
++-||-.-|.+|+-. +| +.+|+-|... .-||..+..++--....+..-+|+++||..+|..|+|++ +-+.
T Consensus 231 slHL~~~~L~~Ll~n-~~-gY~i~adv~~------~~fvL~v~~~~~~~~~~~~~~~V~~~dIy~k~~dL~f~d--El~~ 300 (316)
T PHA03328 231 SLHLHYRLIDRLLTA-CP-GYRIIAHVWQ------TTFVLVVRRDAERQTTDADVPAVSAEDIYCKMCDLNFDG--ELLL 300 (316)
T ss_pred cccchHHHHHHHHHh-CC-CCeEEEEEec------ceEEEEEeeCCCCCCccccccccCHHHHHHHHhCCCCCh--HHHH
Confidence 344555555555444 44 6666655432 235555554443345667889999999999999999996 3344
Q ss_pred HHHHHHHHH
Q 045194 86 RYLHKYRED 94 (157)
Q Consensus 86 ~~L~~yre~ 94 (157)
+|..-|...
T Consensus 301 Ey~kly~~f 309 (316)
T PHA03328 301 EYKRLYATF 309 (316)
T ss_pred HHHHHHHHH
Confidence 555555443
No 113
>COG5251 TAF40 Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=32.89 E-value=62 Score=26.83 Aligned_cols=61 Identities=13% Similarity=0.006 Sum_probs=45.0
Q ss_pred cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC---ccCchhHHHHH
Q 045194 8 LLPIANVGKIMKQILPPRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRK---TVNGDDICWAL 72 (157)
Q Consensus 8 ~LP~A~I~RImK~~LP~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRK---TI~~eDVl~AL 72 (157)
.||++.|.+++-.++ +-.|+...+.+|+-.+.+|+..|---|..+- +++. -+.+.|+-.|.
T Consensus 115 ~lnKt~VKKlastV~--nQtVspNi~I~l~g~~KVfvGEiIElA~~Vq--~~w~~sgpl~p~h~reay 178 (199)
T COG5251 115 SLNKTQVKKLASTVA--NQTVSPNIRIFLQGVGKVFVGEIIELAMIVQ--NKWLTSGPLIPFHKREAY 178 (199)
T ss_pred CCCHHHHHHHHHHHh--ccccCCCeeeeeechhHHHHHHHHHHHHHHH--HHhcccCCCChHHHHHHH
Confidence 699999999999997 4557777788889999999988876665443 2233 36666666554
No 114
>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=32.70 E-value=80 Score=26.50 Aligned_cols=74 Identities=11% Similarity=0.059 Sum_probs=32.8
Q ss_pred cccCchhHHHHHHhhhCC--CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC------CccCchhHHHHHhhCCC
Q 045194 6 DKLLPIANVGKIMKQILP--PRAKISKEAKQTMQECATEFISFVTGEASDKCHKENR------KTVNGDDICWALSTLGF 77 (157)
Q Consensus 6 D~~LP~A~I~RImK~~LP--~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kR------KTI~~eDVl~AL~~LgF 77 (157)
+..|....+.+-|.++.. +...|..|...+|.-||.++|..|-..+..+|.+--. .+.-..||-..|..|.-
T Consensus 41 ~~fL~~~~L~~~i~~i~~~~g~~~~~~d~l~llS~A~e~rLr~lie~~~~~s~hR~~~~~~~~~~~~~sdv~~qlr~l~~ 120 (264)
T PF05236_consen 41 EPFLNPSPLQKRIQKIAKKHGLKSVDEDVLELLSLATEERLRNLIEKAIVLSRHRRDSSKSDPRYEIRSDVRKQLRFLEQ 120 (264)
T ss_dssp ---S-HHHHHHHHHHHHHCTT--EE-TCHHHHHHHHHHHHHHHHHHHHH-------------------------------
T ss_pred ccccCHHHHHHHHHHHHHHcCCcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccCCCcccccchHHHHHHHHHHH
Confidence 445666666666665542 3457999999999999999999999999988865221 12235567666655544
Q ss_pred ch
Q 045194 78 DN 79 (157)
Q Consensus 78 ~~ 79 (157)
-+
T Consensus 121 ~e 122 (264)
T PF05236_consen 121 LE 122 (264)
T ss_dssp --
T ss_pred HH
Confidence 33
No 115
>PF08823 PG_binding_2: Putative peptidoglycan binding domain; InterPro: IPR014927 This entry may be a peptidoglycan binding domain.
Probab=32.61 E-value=64 Score=22.49 Aligned_cols=31 Identities=26% Similarity=0.373 Sum_probs=25.2
Q ss_pred hhHHHHHhhCCC------chhHHHHHHHHHHHHHHHH
Q 045194 66 DDICWALSTLGF------DNYTEAIVRYLHKYREDER 96 (157)
Q Consensus 66 eDVl~AL~~LgF------~~y~~~L~~~L~~yre~~~ 96 (157)
+.|..+|..||| +.|-+.++..|..|...+.
T Consensus 19 ~evq~~L~~lGyy~g~~~g~~d~a~~~Al~~~~g~EN 55 (74)
T PF08823_consen 19 REVQEALKRLGYYKGEADGVWDEATEDALRAWAGTEN 55 (74)
T ss_pred HHHHHHHHHcCCccCCCCCcccHHHHHHHHHHHHHhh
Confidence 457789999999 6788888999988887653
No 116
>PRK05574 holA DNA polymerase III subunit delta; Reviewed
Probab=30.70 E-value=2.3e+02 Score=23.63 Aligned_cols=64 Identities=17% Similarity=0.087 Sum_probs=43.6
Q ss_pred CchhHHHHHHhhhCC-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhc-CCCccCchhHHHHHh
Q 045194 9 LPIANVGKIMKQILP-PRAKISKEAKQTMQECATEFISFVTGEASDKCHKE-NRKTVNGDDICWALS 73 (157)
Q Consensus 9 LP~A~I~RImK~~LP-~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~-kRKTI~~eDVl~AL~ 73 (157)
+....+.+.|++.+. .+..|+.+|...|.+.+..=+..+..+-...+.-. +++ |+.+||-..+.
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 445555666655553 36689999999999888766666677777766533 333 99988875544
No 117
>TIGR01052 top6b DNA topoisomerase VI, B subunit. This model describes DNA topoisomerase VI, an archaeal type II DNA topoisomerase (DNA gyrase).
Probab=30.25 E-value=91 Score=29.22 Aligned_cols=58 Identities=22% Similarity=0.328 Sum_probs=39.9
Q ss_pred hhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHhhCCCchhHHHHHHHHHH
Q 045194 19 KQILPPRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALSTLGFDNYTEAIVRYLHK 90 (157)
Q Consensus 19 K~~LP~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~LgF~~y~~~L~~~L~~ 90 (157)
|+++.+.--|-+|.+.+|++||...=.||...-...-..+++++ |..|++.+.+.|..
T Consensus 426 Ke~ia~~~ei~~ei~~al~~~~r~L~~~l~~~~~~~~~~~r~~~--------------~~~y~p~~a~~~~~ 483 (488)
T TIGR01052 426 KQSVADIPEIYNEIRLALMEVARRLRLYLSRKAREEEEIKRRKT--------------LEKYLPEIAKSLAY 483 (488)
T ss_pred hhhhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------------HHHHHHHHHHHHHH
Confidence 34443334588899999999999999999976655555544444 45666666666543
No 118
>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=30.16 E-value=15 Score=23.68 Aligned_cols=59 Identities=24% Similarity=0.299 Sum_probs=32.6
Q ss_pred CccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcc---CchhHHHHHhhCCCchhH-HHHHHH
Q 045194 25 RAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTV---NGDDICWALSTLGFDNYT-EAIVRY 87 (157)
Q Consensus 25 ~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI---~~eDVl~AL~~LgF~~y~-~~L~~~ 87 (157)
+.+|.++...+|.+++. .+..|+.+ .-..+=.|.+ .+...+..|.++|+-+++ +.+..+
T Consensus 1 gF~ie~~t~~ai~~~~~-~L~~is~E---Ri~~El~kil~~~~~~~~~~~l~~~gll~~ifP~l~~a 63 (64)
T PF12627_consen 1 GFKIEPETEEAIKENAE-LLSKISKE---RIREELEKILSSPNPSRAFKLLDELGLLEYIFPELDAA 63 (64)
T ss_dssp T-EE-HHHHHHHHHHGG-GGGGS-HH---HHHHHHHHHHTSTTHHHHHHHHHHTTCHHHHSTTHHT-
T ss_pred CCccCHHHHHHHHHHHH-HHhcCCHH---HHHHHHHHHHcCCCHHHHHHHHHHcCCHHHHCcccccc
Confidence 35688888888888776 44444433 3222333333 345566777788877664 555443
No 119
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=29.71 E-value=54 Score=26.77 Aligned_cols=37 Identities=8% Similarity=0.229 Sum_probs=29.1
Q ss_pred cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHH
Q 045194 8 LLPIANVGKIMKQILPPRAKISKEAKQTMQECATEFISFVTG 49 (157)
Q Consensus 8 ~LP~A~I~RImK~~LP~~~kISkDA~~al~~~ateFI~~lts 49 (157)
..-++||.|.+... -+||.+.++-+.+++.+ +.|.-.
T Consensus 9 gVS~~TVSrvLn~~----~~vs~~tr~rV~~~a~~-lgY~pn 45 (327)
T PRK10423 9 GVSTSTVSHVINKD----RFVSEAITAKVEAAIKE-LNYAPS 45 (327)
T ss_pred CCcHHHHHHHhCCC----CCCCHHHHHHHHHHHHH-HCCCcc
Confidence 46689999999753 36999999999999987 455543
No 120
>PRK09526 lacI lac repressor; Reviewed
Probab=29.71 E-value=46 Score=27.45 Aligned_cols=37 Identities=14% Similarity=0.410 Sum_probs=29.9
Q ss_pred cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHH
Q 045194 8 LLPIANVGKIMKQILPPRAKISKEAKQTMQECATEFISFVTG 49 (157)
Q Consensus 8 ~LP~A~I~RImK~~LP~~~kISkDA~~al~~~ateFI~~lts 49 (157)
..-++||.|++... .+||.+.++-+.+++.+ +.|.-.
T Consensus 16 GVS~~TVSrvLn~~----~~vs~~tr~rV~~~a~e-lgY~pn 52 (342)
T PRK09526 16 GVSYQTVSRVLNQA----SHVSAKTREKVEAAMAE-LNYVPN 52 (342)
T ss_pred CCCHHHHHHHhcCC----CCCCHHHHHHHHHHHHH-HCCCcC
Confidence 46688999999753 36999999999999999 667543
No 121
>COG1724 Predicted RNA binding protein (dsRBD-like fold), HicA family [General function prediction only]
Probab=28.07 E-value=38 Score=23.67 Aligned_cols=17 Identities=24% Similarity=0.425 Sum_probs=15.2
Q ss_pred ccCchhHHHHHhhCCCc
Q 045194 62 TVNGDDICWALSTLGFD 78 (157)
Q Consensus 62 TI~~eDVl~AL~~LgF~ 78 (157)
.+++.+|+.+|+.+||.
T Consensus 6 ~~~~ke~ik~Le~~Gf~ 22 (66)
T COG1724 6 RMKAKEVIKALEKDGFQ 22 (66)
T ss_pred cCCHHHHHHHHHhCCcE
Confidence 47889999999999996
No 122
>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional
Probab=27.71 E-value=80 Score=28.37 Aligned_cols=31 Identities=23% Similarity=0.210 Sum_probs=27.2
Q ss_pred HHHHHHHHHHHHHhcCCCccCchhHHHHHhh
Q 045194 44 ISFVTGEASDKCHKENRKTVNGDDICWALST 74 (157)
Q Consensus 44 I~~ltseA~e~~~~~kRKTI~~eDVl~AL~~ 74 (157)
|..|..+|...|..++|..|+.+|+..|++.
T Consensus 355 I~~l~~eA~~~A~r~~~~~i~~~df~~A~~~ 385 (398)
T PTZ00454 355 IAAICQEAGMQAVRKNRYVILPKDFEKGYKT 385 (398)
T ss_pred HHHHHHHHHHHHHHcCCCccCHHHHHHHHHH
Confidence 6677788888899999999999999999875
No 123
>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=26.71 E-value=1.3e+02 Score=27.82 Aligned_cols=52 Identities=13% Similarity=0.153 Sum_probs=39.0
Q ss_pred CCccccHHHHHHHHHHHHHHH-HHHHHHHHHHHHhcCCCccCchhHHHHHhhCC
Q 045194 24 PRAKISKEAKQTMQECATEFI-SFVTGEASDKCHKENRKTVNGDDICWALSTLG 76 (157)
Q Consensus 24 ~~~kISkDA~~al~~~ateFI-~~ltseA~e~~~~~kRKTI~~eDVl~AL~~Lg 76 (157)
+.+.++.||...|.+. =-|+ .-+-..+-+.|++.|...|+.+.|..|=..+|
T Consensus 459 ~~~~w~~ea~~~l~~~-P~f~r~~~r~~~e~~a~~~g~~~it~~~~~~a~~~~~ 511 (511)
T TIGR01278 459 GELGWTAEAEAELKKV-PFFVRGKVRRNTENFARERGYSVITLEVIYAAKEHFG 511 (511)
T ss_pred CCCCcCHHHHHHHhhC-ChhhhHHHHHHHHHHHHHcCCCEEcHHHHHHHHHhcC
Confidence 3467999999998653 3333 34445677789999999999999998876654
No 124
>PF11753 DUF3310: Protein of unknwon function (DUF3310); InterPro: IPR021739 This entry is represented by Bacteriophage T7, Gp1.7. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=26.47 E-value=1.8e+02 Score=19.34 Aligned_cols=41 Identities=22% Similarity=0.265 Sum_probs=31.8
Q ss_pred HHHHHHHHH--HHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHh
Q 045194 31 EAKQTMQEC--ATEFISFVTGEASDKCHKENRKTVNGDDICWALS 73 (157)
Q Consensus 31 DA~~al~~~--ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~ 73 (157)
|..+.| +. ...|..|....|...+.+.++|. .-+|+.+|..
T Consensus 14 e~id~~-~~~~~~~~~~f~~gnaiKY~~R~~~K~-~~eDl~KA~~ 56 (60)
T PF11753_consen 14 ECIDFI-EQFTEEQFLGFCLGNAIKYLWRAGKKN-GIEDLKKAKW 56 (60)
T ss_pred cHHHHH-HHhcchhhhhHHHHHHHHHHHHHcccC-cHHHHHHHHH
Confidence 455555 44 44899999999999999999993 4788888764
No 125
>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=25.99 E-value=85 Score=17.39 Aligned_cols=26 Identities=19% Similarity=0.240 Sum_probs=19.2
Q ss_pred HHHHHHhcCCCccCchhHHHHHh-hCC
Q 045194 51 ASDKCHKENRKTVNGDDICWALS-TLG 76 (157)
Q Consensus 51 A~e~~~~~kRKTI~~eDVl~AL~-~Lg 76 (157)
+....-.++--.|+.+++..+|+ .||
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 34455567778999999999998 576
No 126
>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=25.64 E-value=59 Score=25.75 Aligned_cols=54 Identities=7% Similarity=0.159 Sum_probs=38.7
Q ss_pred HHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHH
Q 045194 14 VGKIMKQILPPRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDIC 69 (157)
Q Consensus 14 I~RImK~~LP~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl 69 (157)
+.|+++.+. +.-|.|+-..-+.+.+..=+.-|.--|.+.|+.+||-+|...|+=
T Consensus 1 fe~lFR~aa--~LdvdK~d~~r~~d~V~~Kl~DLl~va~~~Ak~ngRdvI~~~DLP 54 (138)
T PF09123_consen 1 FERLFRKAA--GLDVDKNDAKRYSDFVEKKLYDLLLVAQENAKANGRDVIEPRDLP 54 (138)
T ss_dssp HHHHHHHHH--S----HHHHHHHHHHHHHHHHHCCCCHHHHHHHTT-SEE-GGGS-
T ss_pred ChHHHHHHh--ccCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeeccccCC
Confidence 357788774 455778888888888888788788889999999999999998863
No 127
>PRK02910 light-independent protochlorophyllide reductase subunit B; Provisional
Probab=25.61 E-value=1.3e+02 Score=27.79 Aligned_cols=52 Identities=12% Similarity=0.121 Sum_probs=39.4
Q ss_pred CCccccHHHHHHHHHHHHHHHH-HHHHHHHHHHHhcCCCccCchhHHHHHhhCC
Q 045194 24 PRAKISKEAKQTMQECATEFIS-FVTGEASDKCHKENRKTVNGDDICWALSTLG 76 (157)
Q Consensus 24 ~~~kISkDA~~al~~~ateFI~-~ltseA~e~~~~~kRKTI~~eDVl~AL~~Lg 76 (157)
+.+.++.||...|.+ .=-|+. -+-..+-+.|+..|...|+.+.|..|-..+|
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 333443 3445667788999999999999999877654
No 128
>PRK06585 holA DNA polymerase III subunit delta; Reviewed
Probab=25.23 E-value=2.3e+02 Score=23.96 Aligned_cols=49 Identities=10% Similarity=0.034 Sum_probs=35.0
Q ss_pred CccccHHHHHHHHHHHHHHHHHHHHHHHHHHHh-cCCCccCchhHHHHHh
Q 045194 25 RAKISKEAKQTMQECATEFISFVTGEASDKCHK-ENRKTVNGDDICWALS 73 (157)
Q Consensus 25 ~~kISkDA~~al~~~ateFI~~ltseA~e~~~~-~kRKTI~~eDVl~AL~ 73 (157)
+.+|+.+|...|.+.+.-=...+..+-...+.- .+.++|+.+||...+.
T Consensus 159 g~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~It~edV~~lv~ 208 (343)
T PRK06585 159 GLRITPDARALLVALLGGDRLASRNEIEKLALYAHGKGEITLDDVRAVVG 208 (343)
T ss_pred CCCCCHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHhC
Confidence 678999999999988876444555555555543 4456899999976644
No 129
>PF06782 UPF0236: Uncharacterised protein family (UPF0236); InterPro: IPR009620 This is a group of proteins of unknown function.
Probab=24.87 E-value=1.3e+02 Score=27.61 Aligned_cols=52 Identities=23% Similarity=0.312 Sum_probs=41.2
Q ss_pred CCCccccHHHHHHHHHHHHHHHHHHHHHHHHHH-HhcCCCccCchhHHHHHhhCCC
Q 045194 23 PPRAKISKEAKQTMQECATEFISFVTGEASDKC-HKENRKTVNGDDICWALSTLGF 77 (157)
Q Consensus 23 P~~~kISkDA~~al~~~ateFI~~ltseA~e~~-~~~kRKTI~~eDVl~AL~~LgF 77 (157)
++..+||.+++..+.+.|++ .+| ..|.+.- ...+...|+.+-|..+++.+|+
T Consensus 113 ~~~~R~S~~~~~~i~~~a~~-~sY--r~aa~~l~~~~~~~~iS~~tV~~~v~~~g~ 165 (470)
T PF06782_consen 113 KKYQRISPELKEKIVELATE-MSY--RKAAEILEELLGNVSISKQTVWNIVKEAGF 165 (470)
T ss_pred CcccchhHHHHHHHHHHHhh-cCH--HHHHHHHhhccCCCccCHHHHHHHHHhccc
Confidence 45679999999999998887 555 3444444 4567899999999999999993
No 130
>PRK14971 DNA polymerase III subunits gamma and tau; Provisional
Probab=24.84 E-value=2e+02 Score=27.49 Aligned_cols=64 Identities=8% Similarity=0.021 Sum_probs=32.2
Q ss_pred CchhHHHHHHhhhCC-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHh
Q 045194 9 LPIANVGKIMKQILP-PRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALS 73 (157)
Q Consensus 9 LP~A~I~RImK~~LP-~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~ 73 (157)
|+...+.+.++..+. .++.++.++..+|.+.+.-=+..+-.+....+.-.+++ |+.++|...+.
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 334445444544332 36778888888876655432333333333333222333 66666655443
No 131
>PRK07914 hypothetical protein; Reviewed
Probab=24.43 E-value=1.7e+02 Score=24.83 Aligned_cols=62 Identities=10% Similarity=0.127 Sum_probs=41.2
Q ss_pred hhHHHHHHhhhCC-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHh
Q 045194 11 IANVGKIMKQILP-PRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALS 73 (157)
Q Consensus 11 ~A~I~RImK~~LP-~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~ 73 (157)
-..+.+.|++.+. .+..|+.+|...|.+++..=+..+..+-...+...+ .+|+.+||-..+.
T Consensus 130 ~~~l~~wi~~~a~~~g~~i~~~A~~~L~~~~g~dl~~l~~EleKL~~~~~-~~It~e~V~~~v~ 192 (320)
T PRK07914 130 AAERADFVRKEFRSLRVKVDDDTVTALLDAVGSDLRELASACSQLVADTG-GAVDAAAVRRYHS 192 (320)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHCccHHHHHHHHHHHhcCCC-CCcCHHHHHHHcC
Confidence 4444455544443 366899999999999987656666666555554333 5699888876644
No 132
>COG1500 Predicted exosome subunit [Translation, ribosomal structure and biogenesis]
Probab=24.14 E-value=1.8e+02 Score=24.90 Aligned_cols=70 Identities=16% Similarity=0.210 Sum_probs=49.6
Q ss_pred HHHHHHhhhCC-CCccccHHHHHHHHHHH-HHHHHHHHHHHHHHHHhcCCCccCchhHHHHHhhCCCc-hhHHHHH
Q 045194 13 NVGKIMKQILP-PRAKISKEAKQTMQECA-TEFISFVTGEASDKCHKENRKTVNGDDICWALSTLGFD-NYTEAIV 85 (157)
Q Consensus 13 ~I~RImK~~LP-~~~kISkDA~~al~~~a-teFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~LgF~-~y~~~L~ 85 (157)
.+..|+++.|. +.+.++.+-+..|++.- ...|++|++.|.+ -..+.-..+.-|-.||++++|. ++....+
T Consensus 71 d~~eI~~eIl~kGeiQlTaeqR~~m~e~k~rqIi~~IsRn~Id---P~t~~P~Pp~rIe~Ameeakv~id~~K~ae 143 (234)
T COG1500 71 DPDEIAEEILKKGEIQLTAEQRREMLEEKKRQIINIISRNAID---PQTKAPHPPARIEKAMEEAKVHIDPFKSAE 143 (234)
T ss_pred CHHHHHHHHHhcCceeccHHHHHHHHHHHHHHHHHHHHHhccC---CCCCCCCCHHHHHHHHHhcCcccCCCCCHH
Confidence 36666666665 45779988877766655 4667788877655 3455678888999999999998 5544433
No 133
>PLN00138 large subunit ribosomal protein LP2; Provisional
Probab=23.20 E-value=1.7e+02 Score=22.09 Aligned_cols=28 Identities=18% Similarity=0.098 Sum_probs=24.9
Q ss_pred HHHHHHhcCCCccCchhHHHHHhhCCCc
Q 045194 51 ASDKCHKENRKTVNGDDICWALSTLGFD 78 (157)
Q Consensus 51 A~e~~~~~kRKTI~~eDVl~AL~~LgF~ 78 (157)
|.-.|.-.|...++.+||...|+..|.+
T Consensus 6 Ayll~~l~g~~~pta~dI~~IL~AaGve 33 (113)
T PLN00138 6 AYLLAVLGGNTCPSAEDLKDILGSVGAD 33 (113)
T ss_pred HHHHHHhcCCCCCCHHHHHHHHHHcCCc
Confidence 5667888899999999999999999887
No 134
>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=22.83 E-value=60 Score=20.48 Aligned_cols=16 Identities=19% Similarity=0.354 Sum_probs=13.4
Q ss_pred cCchhHHHHHhhCCCc
Q 045194 63 VNGDDICWALSTLGFD 78 (157)
Q Consensus 63 I~~eDVl~AL~~LgF~ 78 (157)
++.++|..+++.+||+
T Consensus 47 ~~~~~i~~~i~~~Gy~ 62 (62)
T PF00403_consen 47 TSIEKIIEAIEKAGYE 62 (62)
T ss_dssp SCHHHHHHHHHHTTSE
T ss_pred CCHHHHHHHHHHhCcC
Confidence 5668899999999985
No 135
>PTZ00373 60S Acidic ribosomal protein P2; Provisional
Probab=22.57 E-value=1.8e+02 Score=22.06 Aligned_cols=28 Identities=18% Similarity=0.158 Sum_probs=24.9
Q ss_pred HHHHHHhcCCCccCchhHHHHHhhCCCc
Q 045194 51 ASDKCHKENRKTVNGDDICWALSTLGFD 78 (157)
Q Consensus 51 A~e~~~~~kRKTI~~eDVl~AL~~LgF~ 78 (157)
|.-.|.-.|..+++.+||...|+..|.+
T Consensus 8 AYlL~~lgG~~~pTaddI~kIL~AaGve 35 (112)
T PTZ00373 8 AYLMCVLGGNENPTKKEVKNVLSAVNAD 35 (112)
T ss_pred HHHHHHHcCCCCCCHHHHHHHHHHcCCC
Confidence 5667888899999999999999999887
No 136
>PRK14975 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Probab=22.46 E-value=4.4e+02 Score=24.57 Aligned_cols=90 Identities=11% Similarity=0.060 Sum_probs=56.9
Q ss_pred cccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHH----------HHHHHHHHHHHHHHHhcCCCccCchhHHHHHhhC
Q 045194 6 DKLLPIANVGKIMKQILPPRAKISKEAKQTMQECAT----------EFISFVTGEASDKCHKENRKTVNGDDICWALSTL 75 (157)
Q Consensus 6 D~~LP~A~I~RImK~~LP~~~kISkDA~~al~~~at----------eFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~L 75 (157)
++++|.+.|---|... ++.|..+....+..-.. .-+.-|..+..+......=--=++.+|..+|+.+
T Consensus 161 ~~E~~~~~~l~~me~~---Gi~~D~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~~~g~~~~n~~S~~ql~~~L~~~ 237 (553)
T PRK14975 161 AAESAGALAAAEMELA---GLPWDTDVHEALLAELLGPRPAAGGRPARLAELAAEIREALGRPRLNPDSPQQVLRALRRA 237 (553)
T ss_pred HHHhhHHHHHHHHHHh---CeEeCHHHHHHHHHHHhcccccccchHHHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHC
Confidence 4567888888888776 78898888766655544 4555666555554422111234678899999999
Q ss_pred CCc----------hhHHHHHHHHHHHHHHHHHH
Q 045194 76 GFD----------NYTEAIVRYLHKYREDERER 98 (157)
Q Consensus 76 gF~----------~y~~~L~~~L~~yre~~~~k 98 (157)
|+. .-..++-..+-+||...+..
T Consensus 238 g~~~~~t~~~~L~~~~hp~~~~ile~r~~~kl~ 270 (553)
T PRK14975 238 GIELPSTRKWELREIDHPAVEPLLEYRKLSKLL 270 (553)
T ss_pred CCCCCCCcHHHhccCCCchHHHHHHHHHHHHHH
Confidence 884 01113445566788877665
No 137
>PF07928 Vps54: Vps54-like protein; InterPro: IPR012501 This family contains various proteins that are homologues of the yeast Vps54 protein, such as the rat homologue (Q9JMK8 from SWISSPROT), the human homologue (Q86YF7 from SWISSPROT), and the mouse homologue (Q8R3X1 from SWISSPROT). In yeast, Vps54 associates with Vps52 and Vps53 proteins to form a trimolecular complex that is involved in protein transport between Golgi, endosomal, and vacuolar compartments []. All Vps54 homologues contain a coiled coil region (not found in the region featured in this family) and multiple dileucine motifs []. ; GO: 0042147 retrograde transport, endosome to Golgi; PDB: 3N1E_B 3N1B_B.
Probab=21.92 E-value=30 Score=26.70 Aligned_cols=36 Identities=17% Similarity=0.277 Sum_probs=0.0
Q ss_pred HhcCCCccCchhHHHHHhhCCCc-hhHHHHHHHHHHH
Q 045194 56 HKENRKTVNGDDICWALSTLGFD-NYTEAIVRYLHKY 91 (157)
Q Consensus 56 ~~~kRKTI~~eDVl~AL~~LgF~-~y~~~L~~~L~~y 91 (157)
+..|-|+|++.|+--|-+.|+|- .+++.++++++..
T Consensus 61 ~~agLK~IT~KhLALasq~L~~~~~lip~i~~~~~~~ 97 (135)
T PF07928_consen 61 RSAGLKTITAKHLALASQSLSFIISLIPYIREFFERH 97 (135)
T ss_dssp -------------------------------------
T ss_pred hccCcCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 45678999999999999999998 7888888888765
No 138
>PRK00440 rfc replication factor C small subunit; Reviewed
Probab=21.76 E-value=2.4e+02 Score=23.05 Aligned_cols=65 Identities=12% Similarity=0.089 Sum_probs=37.1
Q ss_pred CchhHHHHHHhhhCC-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCchhHHHHHhhC
Q 045194 9 LPIANVGKIMKQILP-PRAKISKEAKQTMQECATEFISFVTGEASDKCHKENRKTVNGDDICWALSTL 75 (157)
Q Consensus 9 LP~A~I~RImK~~LP-~~~kISkDA~~al~~~ateFI~~ltseA~e~~~~~kRKTI~~eDVl~AL~~L 75 (157)
++...+.++++..+. .++.|+.++...|.+.+.--+..+-.+-...+. . .++|+.+||..++...
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 334445555554442 356799999888877764322222222222222 2 3689999998887544
No 139
>PF09957 DUF2191: Uncharacterized protein conserved in bacteria (DUF2191); InterPro: IPR019239 This entry, found in various hypothetical prokaryotic proteins, has no known function.
Probab=21.58 E-value=2.3e+02 Score=18.00 Aligned_cols=39 Identities=26% Similarity=0.272 Sum_probs=28.7
Q ss_pred CCccCchhHH--HHHhhCCCchhHHHHHHHHHHHHHHHHHH
Q 045194 60 RKTVNGDDIC--WALSTLGFDNYTEAIVRYLHKYREDERER 98 (157)
Q Consensus 60 RKTI~~eDVl--~AL~~LgF~~y~~~L~~~L~~yre~~~~k 98 (157)
|.||.-+|=+ .|++-.|+..-.+.+...|..|-...+.+
T Consensus 2 rTti~iDd~Ll~eA~~l~g~~tk~~~V~~ALr~~i~r~~~~ 42 (47)
T PF09957_consen 2 RTTIDIDDELLAEAMRLTGTKTKKEAVNEALRELIRRRKRR 42 (47)
T ss_pred cceEeeCHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHH
Confidence 4566655533 78888899999888888888887765544
No 140
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=21.51 E-value=72 Score=26.09 Aligned_cols=38 Identities=5% Similarity=0.107 Sum_probs=28.5
Q ss_pred cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHH
Q 045194 8 LLPIANVGKIMKQILPPRAKISKEAKQTMQECATEFISFV 47 (157)
Q Consensus 8 ~LP~A~I~RImK~~LP~~~kISkDA~~al~~~ateFI~~l 47 (157)
..-++||.|++...- ...+||.+.++.+.+++.+ +.|.
T Consensus 11 GVS~~TVSrvLn~~~-~~~~Vs~~tr~rV~~~a~e-lgY~ 48 (328)
T PRK11303 11 GVSRTTASYVINGKA-KQYRVSDKTVEKVMAVVRE-HNYH 48 (328)
T ss_pred CCCHHHHHHHHcCCC-CCCCcCHHHHHHHHHHHHH-hCCC
Confidence 456899999997641 1136999999999999988 3443
No 141
>KOG1528 consensus Salt-sensitive 3'-phosphoadenosine-5'-phosphatase HAL2/SAL1 [Nucleotide transport and metabolism; Inorganic ion transport and metabolism]
Probab=21.33 E-value=2.4e+02 Score=25.50 Aligned_cols=66 Identities=14% Similarity=0.193 Sum_probs=42.9
Q ss_pred hhHHHHHHhhhCCCCc--cccHHHHHHHHHH-HHHHHHHHHHHHHH---HHHhcCC-CccCchhHHHHHhhCC
Q 045194 11 IANVGKIMKQILPPRA--KISKEAKQTMQEC-ATEFISFVTGEASD---KCHKENR-KTVNGDDICWALSTLG 76 (157)
Q Consensus 11 ~A~I~RImK~~LP~~~--kISkDA~~al~~~-ateFI~~ltseA~e---~~~~~kR-KTI~~eDVl~AL~~Lg 76 (157)
.|.|.-.+++.+|++- -+..|--..|.+. ++.|+.-|+.--++ ....=+- ..++.+||+.|+..-+
T Consensus 52 QAiVs~vL~~~f~~~p~slVaEEds~~Lr~n~~~~~l~~i~~lvnetl~s~~sy~~~~~ls~~dvl~aID~G~ 124 (351)
T KOG1528|consen 52 QAIVSLVLEREFPDDPLSLVAEEDSGFLRKNGSEGLLSRITKLVNETLASDESYGDNSPLSSDDVLKAIDRGN 124 (351)
T ss_pred HHHHHHHHHHHcCCCCcceEeeccchhhhhhhhHHHHHHHHHHHHHHhhhhhhccCCCCCCHHHHHHHHhccc
Confidence 4677888899998654 4666666555554 55666667663333 2222222 7899999999997543
No 142
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=21.12 E-value=1.8e+02 Score=19.23 Aligned_cols=33 Identities=15% Similarity=0.318 Sum_probs=23.8
Q ss_pred ccCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHH
Q 045194 7 KLLPIANVGKIMKQILPPRAKISKEAKQTMQECATEF 43 (157)
Q Consensus 7 ~~LP~A~I~RImK~~LP~~~kISkDA~~al~~~ateF 43 (157)
..+..++|.|++... ..|+.+.+..+.+++.++
T Consensus 10 ~gvS~~TVSr~ln~~----~~v~~~t~~~i~~~~~~~ 42 (70)
T smart00354 10 AGVSKATVSRVLNGN----GRVSEETREKVLAAMEEL 42 (70)
T ss_pred HCCCHHHHHHHHCCC----CCCCHHHHHHHHHHHHHh
Confidence 456778888877643 347888888888877764
No 143
>PRK09492 treR trehalose repressor; Provisional
Probab=21.07 E-value=96 Score=25.18 Aligned_cols=37 Identities=11% Similarity=0.279 Sum_probs=28.9
Q ss_pred cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHH
Q 045194 8 LLPIANVGKIMKQILPPRAKISKEAKQTMQECATEFISFVTG 49 (157)
Q Consensus 8 ~LP~A~I~RImK~~LP~~~kISkDA~~al~~~ateFI~~lts 49 (157)
.+-++||.|++... .+||.+.++-+.+++.+ +.|.-.
T Consensus 15 gVS~~TVSrvLn~~----~~vs~~tr~rV~~~a~e-lgY~pn 51 (315)
T PRK09492 15 GVGKSTVSRVLNNE----SGVSEETRERVEAVINQ-HGFSPS 51 (315)
T ss_pred CCCHHHHhHHhCCC----CCCCHHHHHHHHHHHHH-HCCCcC
Confidence 46788999999753 36999999999999988 445443
No 144
>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=20.44 E-value=1.2e+02 Score=24.83 Aligned_cols=36 Identities=8% Similarity=0.278 Sum_probs=28.8
Q ss_pred cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHH
Q 045194 8 LLPIANVGKIMKQILPPRAKISKEAKQTMQECATEFISFVT 48 (157)
Q Consensus 8 ~LP~A~I~RImK~~LP~~~kISkDA~~al~~~ateFI~~lt 48 (157)
.+-.+||.|++... .+||.+.++-+.+++.+ +.|.-
T Consensus 12 gvS~~TVSrvLn~~----~~vs~~tr~rV~~~a~~-lgY~p 47 (329)
T TIGR01481 12 GVSMATVSRVVNGN----PNVKPATRKKVLEVIKR-LDYRP 47 (329)
T ss_pred CCCHHHHHHHhCCC----CCCCHHHHHHHHHHHHH-HCCCC
Confidence 46688999999764 36999999999999988 45544
No 145
>PF14434 Imm6: Immunity protein Imm6
Probab=20.31 E-value=3.9e+02 Score=20.27 Aligned_cols=50 Identities=26% Similarity=0.327 Sum_probs=34.3
Q ss_pred HHHHHHHHHH-----HHHHHHHHHHHHh--cCCCccCchhHHHHHhhCCCchhHHHHH
Q 045194 35 TMQECATEFI-----SFVTGEASDKCHK--ENRKTVNGDDICWALSTLGFDNYTEAIV 85 (157)
Q Consensus 35 al~~~ateFI-----~~ltseA~e~~~~--~kRKTI~~eDVl~AL~~LgF~~y~~~L~ 85 (157)
.|.++...+| .++..+|.+.|.. +| +.++++++..-|...++.+...-+.
T Consensus 9 ~iae~~~~~I~~~~~~~~~~~aL~~cw~wle~-~~~~~D~LY~lldn~D~~gi~~~~~ 65 (122)
T PF14434_consen 9 AIAEKLVDYIKKSEYGEFVREALDACWKWLEG-KEVTGDELYSLLDNEDENGIFIFMQ 65 (122)
T ss_pred HHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHc-CCCCHHHHHHHHhCcccccHHHHHH
Confidence 3444444444 3444889999863 44 8999999999998888876555433
No 146
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=20.26 E-value=55 Score=20.43 Aligned_cols=16 Identities=19% Similarity=0.395 Sum_probs=12.2
Q ss_pred cccCchhHHHHHHhhh
Q 045194 6 DKLLPIANVGKIMKQI 21 (157)
Q Consensus 6 D~~LP~A~I~RImK~~ 21 (157)
...+|+++++|+++.-
T Consensus 27 ~~gl~~stv~r~L~tL 42 (52)
T PF09339_consen 27 ALGLPKSTVHRLLQTL 42 (52)
T ss_dssp HHTS-HHHHHHHHHHH
T ss_pred HHCcCHHHHHHHHHHH
Confidence 4579999999999764
No 147
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=20.15 E-value=2.1e+02 Score=19.75 Aligned_cols=29 Identities=21% Similarity=0.142 Sum_probs=22.2
Q ss_pred HHHHHHHhcCCCccCchhHHHHHhhCCCc
Q 045194 50 EASDKCHKENRKTVNGDDICWALSTLGFD 78 (157)
Q Consensus 50 eA~e~~~~~kRKTI~~eDVl~AL~~LgF~ 78 (157)
.+...+-.++.-.|+.++|..+|..+|+.
T Consensus 14 ~~F~~~D~d~~G~Is~~el~~~l~~~~~~ 42 (96)
T smart00027 14 QIFRSLDKNQDGTVTGAQAKPILLKSGLP 42 (96)
T ss_pred HHHHHhCCCCCCeEeHHHHHHHHHHcCCC
Confidence 34455556777789999999999988876
No 148
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=20.08 E-value=89 Score=25.73 Aligned_cols=37 Identities=8% Similarity=0.264 Sum_probs=29.2
Q ss_pred cCchhHHHHHHhhhCCCCccccHHHHHHHHHHHHHHHHHHHH
Q 045194 8 LLPIANVGKIMKQILPPRAKISKEAKQTMQECATEFISFVTG 49 (157)
Q Consensus 8 ~LP~A~I~RImK~~LP~~~kISkDA~~al~~~ateFI~~lts 49 (157)
..-++||.|++... .+||.+.++-+.+++.+ +.|.-.
T Consensus 16 gVS~~TVSrvLn~~----~~vs~~tr~rV~~~a~e-lgY~pn 52 (331)
T PRK14987 16 GVTKMTVSRFLRNP----EQVSVALRGKIAAALDE-LGYIPN 52 (331)
T ss_pred CCCHHHhhhhhCCC----CCCCHHHHHHHHHHHHH-hCCCcc
Confidence 45678999988653 36999999999999998 667543
Done!