Query 032293
Match_columns 143
No_of_seqs 126 out of 556
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 12:11:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032293.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032293hhsearch_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 2.6E-31 5.7E-36 204.3 10.0 101 6-111 26-126 (168)
2 KOG0870 DNA polymerase epsilon 100.0 4.5E-30 9.6E-35 198.8 9.7 107 5-115 3-109 (172)
3 KOG0871 Class 2 transcription 100.0 3.5E-29 7.6E-34 190.9 9.3 100 8-112 8-107 (156)
4 COG5150 Class 2 transcription 99.9 1.4E-24 3.1E-29 162.6 9.5 100 8-112 7-106 (148)
5 PF00808 CBFD_NFYB_HMF: Histon 99.8 2.1E-18 4.6E-23 114.4 7.7 64 12-81 2-65 (65)
6 COG2036 HHT1 Histones H3 and H 99.6 4.9E-16 1.1E-20 110.8 7.1 76 8-90 15-90 (91)
7 cd00076 H4 Histone H4, one of 99.3 3.8E-11 8.3E-16 84.7 8.5 71 12-89 13-83 (85)
8 PLN00035 histone H4; Provision 99.2 8.5E-11 1.8E-15 85.6 8.6 69 12-87 29-97 (103)
9 PTZ00015 histone H4; Provision 99.2 2.3E-10 4.9E-15 83.2 8.5 71 12-89 30-100 (102)
10 smart00803 TAF TATA box bindin 99.0 1.2E-09 2.6E-14 73.3 7.5 64 12-82 2-65 (65)
11 smart00428 H3 Histone H3. 99.0 1.4E-09 3E-14 79.5 7.2 76 8-83 25-100 (105)
12 smart00417 H4 Histone H4. 99.0 1.8E-09 4E-14 74.4 6.4 62 12-80 13-74 (74)
13 PF00125 Histone: Core histone 98.9 4.5E-09 9.7E-14 70.7 6.7 71 10-82 3-73 (75)
14 cd07981 TAF12 TATA Binding Pro 98.9 1.3E-08 2.8E-13 69.3 8.3 65 13-83 2-66 (72)
15 COG5208 HAP5 CCAAT-binding fac 98.7 7.3E-09 1.6E-13 84.6 3.8 80 6-91 103-182 (286)
16 PLN00160 histone H3; Provision 98.7 6.2E-08 1.3E-12 69.9 6.3 74 8-82 17-90 (97)
17 PLN00161 histone H3; Provision 98.6 1E-07 2.2E-12 72.4 6.8 73 9-82 52-124 (135)
18 PLN00121 histone H3; Provision 98.6 1.2E-07 2.6E-12 72.2 5.9 73 8-82 58-130 (136)
19 PTZ00018 histone H3; Provision 98.6 1.4E-07 3E-12 71.8 6.0 72 9-82 59-130 (136)
20 KOG1657 CCAAT-binding factor, 98.5 1.2E-07 2.5E-12 78.0 5.0 83 12-100 74-159 (236)
21 smart00576 BTP Bromodomain tra 98.4 1.6E-06 3.5E-11 59.4 8.2 65 16-87 10-74 (77)
22 cd00074 H2A Histone 2A; H2A is 98.4 1.2E-06 2.5E-11 65.0 7.0 68 10-83 18-85 (115)
23 cd07979 TAF9 TATA Binding Prot 98.2 1.1E-05 2.3E-10 59.8 9.0 80 17-103 6-86 (117)
24 PF15630 CENP-S: Kinetochore c 98.0 3.3E-05 7.2E-10 53.4 7.0 63 17-83 10-72 (76)
25 cd08050 TAF6 TATA Binding Prot 97.9 6.7E-05 1.5E-09 64.2 8.3 67 14-87 1-67 (343)
26 KOG3467 Histone H4 [Chromatin 97.8 0.00011 2.3E-09 52.6 7.4 68 13-87 30-97 (103)
27 PF15511 CENP-T: Centromere ki 97.8 4.1E-05 8.8E-10 67.2 6.3 67 9-76 348-414 (414)
28 smart00427 H2B Histone H2B. 97.8 0.00012 2.6E-09 52.2 7.5 63 16-84 5-67 (89)
29 KOG1745 Histones H3 and H4 [Ch 97.8 1.3E-05 2.7E-10 61.2 2.5 75 8-84 59-133 (137)
30 KOG1659 Class 2 transcription 97.8 0.0001 2.2E-09 60.0 7.2 78 12-95 13-90 (224)
31 PF07524 Bromo_TP: Bromodomain 97.8 0.0003 6.5E-09 47.8 8.5 52 36-87 23-74 (77)
32 cd08048 TAF11 TATA Binding Pro 97.7 0.00021 4.6E-09 50.3 7.6 66 12-84 16-84 (85)
33 PF09415 CENP-X: CENP-S associ 97.7 7.9E-05 1.7E-09 51.0 4.7 66 14-83 1-67 (72)
34 PF03847 TFIID_20kDa: Transcri 97.7 0.00037 8.1E-09 47.2 7.6 63 15-83 2-64 (68)
35 PLN00158 histone H2B; Provisio 97.6 0.0003 6.6E-09 52.3 7.5 64 15-84 30-93 (116)
36 COG5262 HTA1 Histone H2A [Chro 97.6 0.00017 3.7E-09 54.0 5.7 67 10-82 24-90 (132)
37 PTZ00463 histone H2B; Provisio 97.6 0.00041 8.9E-09 51.6 7.5 62 17-84 33-94 (117)
38 PF04719 TAFII28: hTAFII28-lik 97.5 0.00065 1.4E-08 48.4 7.4 67 12-84 23-90 (90)
39 PF02969 TAF: TATA box binding 97.4 0.0013 2.7E-08 44.4 7.8 64 12-82 3-66 (66)
40 COG5247 BUR6 Class 2 transcrip 97.3 0.00095 2E-08 48.9 6.1 78 11-94 22-99 (113)
41 smart00414 H2A Histone 2A. 97.3 0.001 2.2E-08 48.6 6.3 68 10-83 7-74 (106)
42 PTZ00017 histone H2A; Provisio 97.0 0.0017 3.8E-08 49.4 5.8 68 10-83 25-92 (134)
43 PLN00154 histone H2A; Provisio 96.9 0.0027 5.9E-08 48.4 6.2 69 10-83 36-104 (136)
44 PF15510 CENP-W: Centromere ki 96.9 0.0021 4.6E-08 46.2 5.0 66 12-83 16-95 (102)
45 KOG1756 Histone 2A [Chromatin 96.8 0.004 8.6E-08 47.1 6.1 68 9-82 24-91 (131)
46 PLN00153 histone H2A; Provisio 96.8 0.0037 8E-08 47.4 5.7 68 10-83 22-89 (129)
47 PLN00157 histone H2A; Provisio 96.8 0.0034 7.5E-08 47.7 5.6 68 10-83 24-91 (132)
48 PLN00156 histone H2AX; Provisi 96.8 0.0043 9.3E-08 47.5 6.1 68 10-83 27-94 (139)
49 KOG1744 Histone H2B [Chromatin 96.4 0.015 3.2E-07 44.0 6.9 62 17-84 42-103 (127)
50 KOG1658 DNA polymerase epsilon 96.2 0.0032 6.9E-08 49.1 2.3 66 12-84 59-125 (162)
51 PF02291 TFIID-31kDa: Transcri 96.1 0.036 7.8E-07 41.9 7.6 88 7-101 5-95 (129)
52 KOG1142 Transcription initiati 96.1 0.012 2.5E-07 49.2 5.1 71 13-89 155-228 (258)
53 PF02269 TFIID-18kDa: Transcri 96.0 0.0098 2.1E-07 42.2 3.8 49 35-83 18-66 (93)
54 KOG3219 Transcription initiati 95.8 0.012 2.6E-07 47.4 3.8 70 12-88 112-182 (195)
55 PTZ00252 histone H2A; Provisio 95.8 0.037 8E-07 42.2 6.3 68 10-83 23-92 (134)
56 cd07978 TAF13 The TATA Binding 94.3 0.34 7.4E-06 34.4 7.5 59 18-83 8-66 (92)
57 KOG3423 Transcription initiati 94.2 0.32 6.9E-06 38.5 7.7 69 12-87 86-168 (176)
58 TIGR03015 pepcterm_ATPase puta 92.7 0.47 1E-05 37.7 6.7 74 13-86 192-268 (269)
59 KOG4336 TBP-associated transcr 91.8 1.3 2.9E-05 38.1 8.6 66 35-102 21-86 (323)
60 KOG2549 Transcription initiati 90.7 1.3 2.8E-05 40.9 7.9 65 14-85 13-77 (576)
61 PRK00411 cdc6 cell division co 88.7 2.6 5.6E-05 35.6 7.9 73 15-89 209-287 (394)
62 KOG3334 Transcription initiati 88.6 7.1 0.00015 30.3 9.4 70 36-105 30-100 (148)
63 KOG2389 Predicted bromodomain 86.4 2.3 5E-05 37.1 6.3 69 12-87 29-97 (353)
64 TIGR02928 orc1/cdc6 family rep 83.4 6.9 0.00015 32.6 7.7 76 16-93 202-283 (365)
65 PF09114 MotA_activ: Transcrip 78.1 2.2 4.8E-05 30.7 2.6 38 16-54 51-88 (96)
66 PF13335 Mg_chelatase_2: Magne 76.5 12 0.00027 26.3 6.1 47 36-82 42-94 (96)
67 PF13654 AAA_32: AAA domain; P 76.0 9.8 0.00021 34.6 6.7 49 36-84 447-506 (509)
68 TIGR02902 spore_lonB ATP-depen 75.2 10 0.00022 34.4 6.7 63 17-84 267-332 (531)
69 PF02861 Clp_N: Clp amino term 73.5 3.5 7.6E-05 24.8 2.3 25 60-84 1-25 (53)
70 COG5095 TAF6 Transcription ini 73.2 10 0.00022 33.4 5.8 54 34-87 20-73 (450)
71 cd08045 TAF4 TATA Binding Prot 72.5 15 0.00032 29.3 6.3 77 10-89 42-124 (212)
72 PF03540 TFIID_30kDa: Transcri 72.2 23 0.0005 22.7 6.0 48 12-66 2-49 (51)
73 COG1067 LonB Predicted ATP-dep 70.4 4.8 0.00011 37.8 3.5 33 51-84 367-399 (647)
74 COG5162 Transcription initiati 70.0 31 0.00067 27.6 7.4 68 13-87 89-189 (197)
75 PF08369 PCP_red: Proto-chloro 63.2 12 0.00026 23.0 3.2 42 38-80 2-44 (45)
76 PF04552 Sigma54_DBD: Sigma-54 62.8 15 0.00032 28.5 4.3 84 6-107 54-153 (160)
77 KOG1757 Histone 2A [Chromatin 62.2 12 0.00025 28.2 3.5 68 6-82 24-95 (131)
78 TIGR00635 ruvB Holliday juncti 61.9 44 0.00095 27.1 7.2 72 13-88 159-233 (305)
79 PRK09862 putative ATP-dependen 61.5 36 0.00078 31.0 7.2 59 35-93 437-501 (506)
80 COG5251 TAF40 Transcription in 61.0 12 0.00025 30.1 3.5 64 12-82 115-179 (199)
81 TIGR00764 lon_rel lon-related 60.3 26 0.00056 32.5 6.2 50 36-85 330-392 (608)
82 PRK00080 ruvB Holliday junctio 59.9 46 0.00099 27.7 7.2 72 13-88 180-254 (328)
83 KOG2680 DNA helicase TIP49, TB 59.3 43 0.00092 29.7 6.9 49 34-82 375-427 (454)
84 cd04752 Commd4 COMM_Domain con 54.4 51 0.0011 25.5 6.1 52 48-106 43-95 (174)
85 TIGR02442 Cob-chelat-sub cobal 54.4 49 0.0011 30.7 7.0 49 34-82 247-302 (633)
86 TIGR02030 BchI-ChlI magnesium 53.6 62 0.0013 27.8 7.1 49 34-82 252-307 (337)
87 PRK13406 bchD magnesium chelat 52.8 35 0.00076 31.6 5.7 49 34-82 193-248 (584)
88 PRK12402 replication factor C 51.9 47 0.001 27.0 5.9 70 12-87 183-252 (337)
89 PRK07452 DNA polymerase III su 50.8 58 0.0013 26.8 6.3 66 18-87 135-202 (326)
90 KOG3901 Transcription initiati 50.6 58 0.0013 24.1 5.4 46 35-83 26-71 (109)
91 TIGR00368 Mg chelatase-related 50.6 46 0.00099 30.2 6.0 47 36-82 445-497 (499)
92 PF05236 TAF4: Transcription i 49.8 30 0.00065 28.4 4.4 56 9-67 40-95 (264)
93 TIGR01128 holA DNA polymerase 49.4 1E+02 0.0022 24.7 7.4 67 12-82 110-176 (302)
94 PF07647 SAM_2: SAM domain (St 48.9 25 0.00055 22.1 3.1 25 71-95 3-27 (66)
95 PF07499 RuvA_C: RuvA, C-termi 47.8 13 0.00028 22.7 1.5 14 75-88 4-17 (47)
96 CHL00081 chlI Mg-protoporyphyr 46.3 73 0.0016 27.7 6.4 49 34-82 265-320 (350)
97 COG1508 RpoN DNA-directed RNA 46.2 1E+02 0.0022 27.9 7.4 87 6-110 335-438 (444)
98 cd00166 SAM Sterile alpha moti 45.9 20 0.00044 21.7 2.2 24 72-95 2-25 (63)
99 PF00536 SAM_1: SAM domain (St 45.1 30 0.00065 21.6 3.0 22 73-94 4-25 (64)
100 PF12010 DUF3502: Domain of un 43.3 28 0.0006 25.8 2.9 61 40-104 73-133 (134)
101 PRK05932 RNA polymerase factor 42.6 71 0.0015 28.7 5.9 85 6-108 348-448 (455)
102 PF00531 Death: Death domain; 42.3 57 0.0012 21.0 4.1 29 69-97 55-83 (83)
103 PF09339 HTH_IclR: IclR helix- 42.2 17 0.00037 22.3 1.4 19 8-26 25-43 (52)
104 PRK13407 bchI magnesium chelat 40.6 94 0.002 26.7 6.2 48 34-81 249-303 (334)
105 COG1224 TIP49 DNA helicase TIP 40.0 63 0.0014 29.1 5.1 48 34-81 378-429 (450)
106 PRK13765 ATP-dependent proteas 39.9 53 0.0012 30.8 4.8 47 36-82 339-398 (637)
107 COG1474 CDC6 Cdc6-related prot 39.6 50 0.0011 28.7 4.4 59 35-93 210-274 (366)
108 TIGR02031 BchD-ChlD magnesium 39.6 1.1E+02 0.0023 28.3 6.7 49 34-82 201-256 (589)
109 PRK07914 hypothetical protein; 39.1 75 0.0016 26.4 5.2 64 14-82 129-192 (320)
110 TIGR02454 CbiQ_TIGR cobalt ABC 38.9 53 0.0012 25.0 4.0 38 70-107 112-160 (198)
111 smart00454 SAM Sterile alpha m 36.6 33 0.00072 20.9 2.2 26 71-96 3-28 (68)
112 TIGR01242 26Sp45 26S proteasom 35.4 59 0.0013 27.5 4.1 32 52-83 331-362 (364)
113 PRK05574 holA DNA polymerase I 34.7 1.5E+02 0.0032 24.2 6.3 67 12-83 145-212 (340)
114 PRK03992 proteasome-activating 34.2 64 0.0014 27.9 4.2 35 52-86 340-374 (389)
115 COG1724 Predicted RNA binding 34.0 32 0.0007 23.3 1.8 17 71-87 6-22 (66)
116 PTZ00361 26 proteosome regulat 33.3 64 0.0014 28.8 4.1 32 53-84 393-424 (438)
117 PF08823 PG_binding_2: Putativ 32.5 91 0.002 21.1 3.9 31 75-105 19-55 (74)
118 PLN00138 large subunit ribosom 32.2 1.3E+02 0.0029 22.0 5.0 28 60-87 6-33 (113)
119 COG5248 TAF19 Transcription in 31.9 1.7E+02 0.0037 21.9 5.5 47 35-83 26-72 (126)
120 PF02361 CbiQ: Cobalt transpor 31.5 76 0.0016 24.1 3.9 42 70-111 123-176 (224)
121 TIGR02395 rpoN_sigma RNA polym 31.4 1.5E+02 0.0032 26.4 6.1 87 6-109 323-425 (429)
122 PRK12469 RNA polymerase factor 31.2 1.4E+02 0.0031 27.1 6.0 85 6-107 374-473 (481)
123 PF00356 LacI: Bacterial regul 30.9 96 0.0021 19.0 3.5 35 8-51 6-40 (46)
124 TIGR01764 excise DNA binding d 30.6 65 0.0014 18.3 2.6 38 8-45 8-46 (49)
125 PRK02910 light-independent pro 30.2 1.1E+02 0.0024 27.6 5.2 52 33-85 466-518 (519)
126 PF14434 Imm6: Immunity protei 29.8 2.3E+02 0.005 20.9 6.0 47 43-90 8-61 (122)
127 PF07928 Vps54: Vps54-like pro 29.8 18 0.00038 27.3 0.0 36 65-100 61-97 (135)
128 PTZ00373 60S Acidic ribosomal 29.3 1.7E+02 0.0037 21.5 5.2 28 60-87 8-35 (112)
129 PF00403 HMA: Heavy-metal-asso 28.9 49 0.0011 20.4 2.0 16 72-87 47-62 (62)
130 COG1500 Predicted exosome subu 28.8 2.2E+02 0.0048 23.7 6.2 73 14-93 68-142 (234)
131 PF13405 EF-hand_6: EF-hand do 28.7 66 0.0014 17.3 2.3 26 60-85 5-31 (31)
132 PRK06585 holA DNA polymerase I 28.6 1.9E+02 0.0041 24.0 6.0 63 16-82 145-208 (343)
133 PTZ00454 26S protease regulato 27.7 94 0.002 27.3 4.2 32 53-84 355-386 (398)
134 TIGR01278 DPOR_BchB light-inde 26.7 1.3E+02 0.0028 27.1 5.0 51 34-85 460-511 (511)
135 smart00350 MCM minichromosome 26.7 1.9E+02 0.0041 26.0 6.0 69 12-84 417-504 (509)
136 smart00027 EH Eps15 homology d 25.9 1.6E+02 0.0035 19.9 4.3 28 60-87 15-42 (96)
137 cd05833 Ribosomal_P2 Ribosomal 24.6 2.2E+02 0.0049 20.7 5.1 28 60-87 6-33 (109)
138 PRK00440 rfc replication facto 24.1 2.2E+02 0.0048 22.8 5.5 66 13-84 161-226 (319)
139 PF03484 B5: tRNA synthetase B 23.0 59 0.0013 21.2 1.6 19 70-88 17-35 (70)
140 PF09123 DUF1931: Domain of un 22.9 63 0.0014 24.8 1.9 52 19-77 2-53 (138)
141 PRK14971 DNA polymerase III su 21.6 2.3E+02 0.005 26.4 5.7 65 13-82 180-244 (614)
142 PF03979 Sigma70_r1_1: Sigma-7 21.5 1.2E+02 0.0027 20.4 3.0 44 63-106 13-57 (82)
143 PRK08487 DNA polymerase III su 21.4 2.8E+02 0.0061 23.1 5.8 64 13-82 135-198 (328)
144 PF13713 BRX_N: Transcription 21.0 1.5E+02 0.0032 18.0 2.9 21 46-66 7-27 (39)
145 PF12668 DUF3791: Protein of u 21.0 1E+02 0.0022 19.8 2.4 30 68-97 13-42 (62)
146 TIGR02639 ClpA ATP-dependent C 20.9 3.3E+02 0.0071 25.7 6.6 37 34-82 75-111 (731)
147 CHL00076 chlB photochlorophyll 20.7 2.2E+02 0.0047 25.8 5.2 51 34-85 461-512 (513)
148 PRK12728 fliE flagellar hook-b 20.6 3.3E+02 0.0072 19.5 6.9 91 11-105 5-99 (102)
149 COG1466 HolA DNA polymerase II 20.3 3.7E+02 0.008 22.5 6.3 62 17-83 144-206 (334)
150 KOG0093 GTPase Rab3, small G p 20.0 54 0.0012 26.1 1.0 55 38-92 105-164 (193)
151 PF03130 HEAT_PBS: PBS lyase H 20.0 1.2E+02 0.0027 16.1 2.3 23 77-99 5-27 (27)
No 1
>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [Transcription]
Probab=99.97 E-value=2.6e-31 Score=204.35 Aligned_cols=101 Identities=27% Similarity=0.488 Sum_probs=93.8
Q ss_pred cchhhccCchhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHhhcC
Q 032293 6 VVPEAEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEID 85 (143)
Q Consensus 6 ~~~Ed~~LP~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~lg 85 (143)
+-.+|-.||+|+|.||||..||. +.+|||||++.+|+|+++||+|||++|++.|..++||||+++||||||..||
T Consensus 26 ~reqDr~LPIANV~RIMK~~lP~-----naKIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIngdDllwAm~tLG 100 (168)
T KOG0869|consen 26 LREQDRFLPIANVSRIMKKALPA-----NAKISKDAKETVQECVSEFISFVTGEASEKCQREKRKTINGDDLLWAMSTLG 100 (168)
T ss_pred cchhhhhccHHHHHHHHHhcCCc-----ccccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCcccHHHHHHHHHHcC
Confidence 34567789999999999999995 8999999999999999999999999999999999999999999999999999
Q ss_pred cccchHHHHHHHHHHHHHhhccccCc
Q 032293 86 FTEFVDPLRDSLDEFRQKNAGKRAGT 111 (143)
Q Consensus 86 F~~yi~~l~~~l~~~ke~~~~Kk~~~ 111 (143)
|++|+++|+.||..||+....+....
T Consensus 101 Fe~Y~eplkiyL~kYRe~e~e~~~~~ 126 (168)
T KOG0869|consen 101 FENYAEPLKIYLQKYRELEGERGRSG 126 (168)
T ss_pred cHhHHHHHHHHHHHHHHHhhhccccc
Confidence 99999999999999999866655543
No 2
>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription]
Probab=99.96 E-value=4.5e-30 Score=198.83 Aligned_cols=107 Identities=36% Similarity=0.672 Sum_probs=99.7
Q ss_pred ccchhhccCchhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHhhc
Q 032293 5 KVVPEAEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEI 84 (143)
Q Consensus 5 k~~~Ed~~LP~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~l 84 (143)
-..++++.||+|+|.||+|++||+ +++.|||||+.+|+++|++||+|||+.|+++|+.++||||+++||+.||.+|
T Consensus 3 ~eri~dl~lP~AiI~rlvke~l~E----~~vsisKeA~~Ai~raAtVFv~~Lts~s~e~A~~q~rKt~sadDVl~aL~Ei 78 (172)
T KOG0870|consen 3 DERIEDLNLPNAIITRLVKEVLPE----SNVSISKEARLAIARAATVFVIFLTSVSNEIAKDQKRKTISADDVLKALDEI 78 (172)
T ss_pred chhHHHhhccHHHHHHHHHHhCcc----ccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCcccHHHHHHHHHHh
Confidence 345689999999999999999997 3699999999999999999999999999999999999999999999999999
Q ss_pred CcccchHHHHHHHHHHHHHhhccccCccCCH
Q 032293 85 DFTEFVDPLRDSLDEFRQKNAGKRAGTSKSK 115 (143)
Q Consensus 85 gF~~yi~~l~~~l~~~ke~~~~Kk~~~~~~~ 115 (143)
+|+.|+.||+..|+.|+..+++|+.....+.
T Consensus 79 efs~f~~plk~~Le~yk~~~k~Kk~~~~~~~ 109 (172)
T KOG0870|consen 79 EFSSFVNPLKSALEAYKKAVKQKKLAKANKS 109 (172)
T ss_pred chHHHhhHHHHHHHHHHHHHHHHHHhccccc
Confidence 9999999999999999999999988755333
No 3
>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=99.96 E-value=3.5e-29 Score=190.93 Aligned_cols=100 Identities=29% Similarity=0.549 Sum_probs=95.0
Q ss_pred hhhccCchhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHhhcCcc
Q 032293 8 PEAEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFT 87 (143)
Q Consensus 8 ~Ed~~LP~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~lgF~ 87 (143)
.+++.||+++|.+|||+.||. +++|.+||+++|..||.+||++|+++||++|....||||+++||++||+.|||.
T Consensus 8 dde~sLPkAtv~KmIke~lP~-----d~rvakeareliincCvEFI~liSsEAneic~~e~KKTIa~EHV~KALe~LgF~ 82 (156)
T KOG0871|consen 8 DDELSLPKATVNKMIKEMLPK-----DVRVAKEARELIINCCVEFINLISSEANEICNKEAKKTIAPEHVIKALENLGFG 82 (156)
T ss_pred cccccCcHHHHHHHHHHhCCc-----ccccchHHHHHHHHHHHHHHHHHHHHHHHHHhHHhcccCCHHHHHHHHHHcchH
Confidence 467899999999999999995 899999999999999999999999999999999999999999999999999999
Q ss_pred cchHHHHHHHHHHHHHhhccccCcc
Q 032293 88 EFVDPLRDSLDEFRQKNAGKRAGTS 112 (143)
Q Consensus 88 ~yi~~l~~~l~~~ke~~~~Kk~~~~ 112 (143)
+|++.+...|++|+..+.+++.++.
T Consensus 83 eYiee~~~vl~~~K~~~~~~~~kss 107 (156)
T KOG0871|consen 83 EYIEEAEEVLENCKEEAKKRRRKSS 107 (156)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhhhh
Confidence 9999999999999999988777654
No 4
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=99.91 E-value=1.4e-24 Score=162.59 Aligned_cols=100 Identities=29% Similarity=0.529 Sum_probs=95.7
Q ss_pred hhhccCchhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHhhcCcc
Q 032293 8 PEAEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFT 87 (143)
Q Consensus 8 ~Ed~~LP~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~lgF~ 87 (143)
.+.+.||+|+|.++|.+.||. +..++|||+++|+.||.+||+.|+++||++|..+.+|||+++||++||++|||.
T Consensus 7 dDe~sLPKATVqKMvS~iLp~-----dl~ftKearei~in~cieFi~~lsseAne~ce~EaKKTIa~EHviKALenLef~ 81 (148)
T COG5150 7 DDENSLPKATVQKMVSSILPK-----DLVFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHVIKALENLEFE 81 (148)
T ss_pred cccccCcHHHHHHHHHHhccc-----cccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHhccHH
Confidence 477899999999999999996 899999999999999999999999999999999999999999999999999999
Q ss_pred cchHHHHHHHHHHHHHhhccccCcc
Q 032293 88 EFVDPLRDSLDEFRQKNAGKRAGTS 112 (143)
Q Consensus 88 ~yi~~l~~~l~~~ke~~~~Kk~~~~ 112 (143)
+||+.|.+.+..|+..+++|.++.+
T Consensus 82 eyi~~~~e~~~n~k~~qK~ke~k~s 106 (148)
T COG5150 82 EYIESCMEEHENYKSYQKQKESKIS 106 (148)
T ss_pred HHHHHHHHHHHHHHHHHhhchhhhh
Confidence 9999999999999999999888754
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=99.76 E-value=2.1e-18 Score=114.38 Aligned_cols=64 Identities=41% Similarity=0.619 Sum_probs=58.3
Q ss_pred cCchhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHH
Q 032293 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAI 81 (143)
Q Consensus 12 ~LP~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL 81 (143)
.||.+.|.||||.. |+ ..+||+||..+|++|+++||.||+.+|+++|..++||||+++||..||
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-PD-----VMRVSKEAVEAIAKAAEEFIQYLAKEANEIAQRDKRKTITYEDVAKAV 65 (65)
T ss_dssp SS-HHHHHHHHHHT-ST-----TSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEE-HHHHHHHH
T ss_pred CCChHHHHHHhccC-CC-----ccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHC
Confidence 69999999999999 63 678999999999999999999999999999999999999999999986
No 6
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=99.64 E-value=4.9e-16 Score=110.77 Aligned_cols=76 Identities=22% Similarity=0.334 Sum_probs=70.8
Q ss_pred hhhccCchhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHhhcCcc
Q 032293 8 PEAEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFT 87 (143)
Q Consensus 8 ~Ed~~LP~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~lgF~ 87 (143)
.-+..||+++|.||||.+.+ -+||.+|...|++|.++|+..|+..|+++|.++|||||+++||..|++.+||.
T Consensus 15 ~~~~~Lp~apv~Ri~r~~~~-------~Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~DI~la~~~~~~~ 87 (91)
T COG2036 15 STDLLLPKAPVRRILRKAGA-------ERVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLALKRLGRR 87 (91)
T ss_pred hhhhhcCchHHHHHHHHHhH-------HHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHHHhccc
Confidence 34568999999999999985 39999999999999999999999999999999999999999999999999997
Q ss_pred cch
Q 032293 88 EFV 90 (143)
Q Consensus 88 ~yi 90 (143)
.|.
T Consensus 88 ~~~ 90 (91)
T COG2036 88 IYG 90 (91)
T ss_pred ccc
Confidence 663
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=99.26 E-value=3.8e-11 Score=84.66 Aligned_cols=71 Identities=17% Similarity=0.220 Sum_probs=66.4
Q ss_pred cCchhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHhhcCcccc
Q 032293 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFTEF 89 (143)
Q Consensus 12 ~LP~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~lgF~~y 89 (143)
.||++.|.||++.. |..+||.|+...+.++...|+..|...|..+|.+++||||+++||..||+..|-.-|
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 367999999999999999999999999999999999999999999999999985443
No 8
>PLN00035 histone H4; Provisional
Probab=99.21 E-value=8.5e-11 Score=85.57 Aligned_cols=69 Identities=19% Similarity=0.203 Sum_probs=65.1
Q ss_pred cCchhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHhhcCcc
Q 032293 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFT 87 (143)
Q Consensus 12 ~LP~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~lgF~ 87 (143)
.||++.|.||++..- ..+||.++...+.+....|+..|...|..+|.+++||||+++||..||+..|-.
T Consensus 29 ~ipk~~IrRLARr~G-------vkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr~g~~ 97 (103)
T PLN00035 29 GITKPAIRRLARRGG-------VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRT 97 (103)
T ss_pred cCCHHHHHHHHHHcC-------cccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHcCCc
Confidence 499999999999983 679999999999999999999999999999999999999999999999988754
No 9
>PTZ00015 histone H4; Provisional
Probab=99.15 E-value=2.3e-10 Score=83.22 Aligned_cols=71 Identities=17% Similarity=0.241 Sum_probs=66.2
Q ss_pred cCchhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHhhcCcccc
Q 032293 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFTEF 89 (143)
Q Consensus 12 ~LP~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~lgF~~y 89 (143)
.||++.|.||++.. |..+||.|+.+.+..+...|+..|...|..+|.+++||||+++||..||+..|-.-|
T Consensus 30 gI~k~~IrRLarr~-------GvkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~AlKr~g~~~y 100 (102)
T PTZ00015 30 GITKGAIRRLARRG-------GVKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALKRQGRTLY 100 (102)
T ss_pred CCCHHHHHHHHHHc-------CCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhcCCCCC
Confidence 59999999999998 367999999999999999999999999999999999999999999999999885433
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=99.04 E-value=1.2e-09 Score=73.26 Aligned_cols=64 Identities=22% Similarity=0.237 Sum_probs=60.3
Q ss_pred cCchhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHh
Q 032293 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIE 82 (143)
Q Consensus 12 ~LP~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~ 82 (143)
.||.++|.||++... --+||.|+...|.+-.+.|+.-|...|..++.+.+|+||+++||-.||+
T Consensus 2 ~~p~~~i~ria~~~G-------i~ris~~a~~~l~~~~e~rl~~i~~~A~k~~~hakRktlt~~DI~~Alk 65 (65)
T smart00803 2 WLPKETIKDVAESLG-------IGNLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSALR 65 (65)
T ss_pred CCCHHHHHHHHHHCC-------CccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCeecHHHHHHHhC
Confidence 589999999999883 5689999999999999999999999999999999999999999999984
No 11
>smart00428 H3 Histone H3.
Probab=99.00 E-value=1.4e-09 Score=79.46 Aligned_cols=76 Identities=21% Similarity=0.265 Sum_probs=68.0
Q ss_pred hhhccCchhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHhh
Q 032293 8 PEAEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (143)
Q Consensus 8 ~Ed~~LP~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~ 83 (143)
+.++.+|+....|++++...+..++.+.+|+.+|..+||++++.|+.-+...|+..|.+.||+||.+.|+.-|..-
T Consensus 25 st~lLI~k~pF~RLVREI~~~~~~~~~~R~~~~Al~aLQeasE~ylv~lfeda~~~a~HAkRvTl~~kDi~La~ri 100 (105)
T smart00428 25 STDLLIRKAPFQRLVREIAQKFTTGVDLRFQSSAIMALQEAAEAYLVGLFEDTNLLAIHAKRVTIMPKDIQLARRI 100 (105)
T ss_pred CcccccccccHHHHHHHHHHHcCCCCCceeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccCcHhhHHHHHHH
Confidence 3467899999999999999876543368999999999999999999999999999999999999999999888643
No 12
>smart00417 H4 Histone H4.
Probab=98.97 E-value=1.8e-09 Score=74.38 Aligned_cols=62 Identities=18% Similarity=0.209 Sum_probs=58.3
Q ss_pred cCchhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHH
Q 032293 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKA 80 (143)
Q Consensus 12 ~LP~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~A 80 (143)
.||++.|.||++.. |.-+||.++...+.+....|+..|...|..+|.+++||||+++||..|
T Consensus 13 gI~k~~IrRLaRr~-------GvkRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~~a 74 (74)
T smart00417 13 GITKPAIRRLARRG-------GVKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVYA 74 (74)
T ss_pred CCCHHHHHHHHHHc-------CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHheeC
Confidence 69999999999998 367999999999999999999999999999999999999999999753
No 13
>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=98.92 E-value=4.5e-09 Score=70.67 Aligned_cols=71 Identities=18% Similarity=0.311 Sum_probs=63.6
Q ss_pred hccCchhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHh
Q 032293 10 AEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIE 82 (143)
Q Consensus 10 d~~LP~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~ 82 (143)
...+|+..|.|+.++..++.. ...+||.+|..+|+.+++.|+.-|...|..+|.+.+|+||++.||..|+.
T Consensus 3 ~~~~~~~~~~r~~r~i~~~~~--~~~ris~~a~~~L~~~~E~~~~~il~~A~~~a~~~kR~tI~~~DI~~A~r 73 (75)
T PF00125_consen 3 RRLIPKFPFSRLLREIGEEIL--SKYRISSEALVALQSVLEYLLVEILEEAGNLARHAKRKTITPRDIQLAVR 73 (75)
T ss_dssp SHSSSHHHHHHHHHHHHHTTS--SSSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTBSEEGHHHHHHHHH
T ss_pred ccccCceEEeeeeehhhcccc--cccccccccchhhhhhhhhhhhhhhhHHHHHHhhcCCcEecHHHHHHHHh
Confidence 356899999999999987432 12799999999999999999999999999999999999999999999985
No 14
>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=98.89 E-value=1.3e-08 Score=69.26 Aligned_cols=65 Identities=22% Similarity=0.236 Sum_probs=61.1
Q ss_pred CchhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHhh
Q 032293 13 LPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (143)
Q Consensus 13 LP~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~ 83 (143)
||+..+..++++.=| ..+|+.||..+|++.+..|+.-++..|..+|++.||+||.++||.-+|+.
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 678889999999865 58999999999999999999999999999999999999999999999975
No 15
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=98.74 E-value=7.3e-09 Score=84.56 Aligned_cols=80 Identities=23% Similarity=0.365 Sum_probs=70.3
Q ss_pred cchhhccCchhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHhhcC
Q 032293 6 VVPEAEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEID 85 (143)
Q Consensus 6 ~~~Ed~~LP~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~lg 85 (143)
+..-+..||.|.|.|+||-.= +.-.||.||..+|.+.|+.||..||..|+-.+++++|+|+--.||..|++..+
T Consensus 103 ~~~k~h~LPlARIkkvMKtde------dVkMisaEaPvlFak~~EiFI~ELTmRAW~~ae~NkRRtLQksDia~Av~kSe 176 (286)
T COG5208 103 ILLKDHNLPLARIKKVMKTDE------DVKMISAEAPVLFAKITEIFIEELTMRAWINAEENKRRTLQKSDIAAAVKKSE 176 (286)
T ss_pred HHHHhccCcHHHHHHHHhccc------chhheecccchHHHHHHHHHHHHHHHHHHHHHhHhhhhHHHHHHHHHHHHHHH
Confidence 444566899999999999863 23489999999999999999999999999999999999999999999999888
Q ss_pred cccchH
Q 032293 86 FTEFVD 91 (143)
Q Consensus 86 F~~yi~ 91 (143)
..+|+-
T Consensus 177 MfDFLi 182 (286)
T COG5208 177 MFDFLI 182 (286)
T ss_pred HHhHHh
Confidence 666553
No 16
>PLN00160 histone H3; Provisional
Probab=98.67 E-value=6.2e-08 Score=69.95 Aligned_cols=74 Identities=22% Similarity=0.150 Sum_probs=66.1
Q ss_pred hhhccCchhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHh
Q 032293 8 PEAEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIE 82 (143)
Q Consensus 8 ~Ed~~LP~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~ 82 (143)
+.++.+|+....|++++......+ .+.+++.+|..+||++++.|+.-+...++..|.+.+|.||.+.|+.-|..
T Consensus 17 st~lLI~k~pF~RLVREI~~~~~~-~~~Rfq~~Al~ALQeAsEayLv~lfed~~lca~HakRVTl~~kD~~L~~r 90 (97)
T PLN00160 17 STDLLIRRLPFARLVREIQMEMSR-EAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTIMPKDMQLARR 90 (97)
T ss_pred chhhhhccccHHHHHHHHHHHcCC-CCcEeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcccccchhhHHHHHH
Confidence 346789999999999999875432 25899999999999999999999999999999999999999999988764
No 17
>PLN00161 histone H3; Provisional
Probab=98.63 E-value=1e-07 Score=72.42 Aligned_cols=73 Identities=23% Similarity=0.180 Sum_probs=65.9
Q ss_pred hhccCchhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHh
Q 032293 9 EAEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIE 82 (143)
Q Consensus 9 Ed~~LP~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~ 82 (143)
-++.+|+..+.|++++...+..+ .+++++.+|..+||++++.|+.-|...||..|.+.+|.||.+.|+..|..
T Consensus 52 t~lLIpklPF~RLVREI~~~~~~-~~~Rfq~~Al~ALQEAsEayLV~lFeda~lcaiHAkRVTlm~kDm~La~r 124 (135)
T PLN00161 52 TELLIRKLPFARLVREISNEMLR-EPFRWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMPKDMQLARR 124 (135)
T ss_pred cccccccccHHHHHHHHHHhcCC-CCcEeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccchhhHHHHHH
Confidence 35689999999999999876543 36999999999999999999999999999999999999999999988864
No 18
>PLN00121 histone H3; Provisional
Probab=98.58 E-value=1.2e-07 Score=72.19 Aligned_cols=73 Identities=25% Similarity=0.275 Sum_probs=66.3
Q ss_pred hhhccCchhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHh
Q 032293 8 PEAEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIE 82 (143)
Q Consensus 8 ~Ed~~LP~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~ 82 (143)
+.++.+|+..+.||+++...... .+++++.+|..+||++++.|+..|...++..|.+.+|.||.+.|+..+..
T Consensus 58 st~lLI~k~pF~RLVREI~~~~~--~~~Rf~~~Al~ALQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~r 130 (136)
T PLN00121 58 STELLIRKLPFQRLVREIAQDFK--TDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
T ss_pred ccccccccccHHHHHHHHHHHhC--ccceeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcceecchhhHHHHHH
Confidence 35778999999999999987653 36899999999999999999999999999999999999999999988764
No 19
>PTZ00018 histone H3; Provisional
Probab=98.57 E-value=1.4e-07 Score=71.84 Aligned_cols=72 Identities=25% Similarity=0.277 Sum_probs=65.6
Q ss_pred hhccCchhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHh
Q 032293 9 EAEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIE 82 (143)
Q Consensus 9 Ed~~LP~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~ 82 (143)
-++.+|+..+.||+++...+.. .+++++.+|..+||++++.|+..|...++..|.+.+|.||.+.|+..|..
T Consensus 59 t~lLI~k~pF~RLVREI~~~~~--~~~rf~~~al~aLQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~r 130 (136)
T PTZ00018 59 TELLIRKLPFQRLVREIAQDFK--TDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
T ss_pred chhccccccHHHHHHHHHHHcC--CcceeeHHHHHHHHHHHHHHHHHHhhhhHHHHHhhcceecchhhHHHHHH
Confidence 4678999999999999987543 36899999999999999999999999999999999999999999988764
No 20
>KOG1657 consensus CCAAT-binding factor, subunit C (HAP5) [Transcription]
Probab=98.53 E-value=1.2e-07 Score=77.96 Aligned_cols=83 Identities=19% Similarity=0.339 Sum_probs=72.0
Q ss_pred cCchhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHhhcC---ccc
Q 032293 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEID---FTE 88 (143)
Q Consensus 12 ~LP~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~lg---F~~ 88 (143)
.||++.|.+|||..-. .-.|+.||..++.+||+.||..|+..|+..+...+|+|+...|+..|+..-. |.-
T Consensus 74 ~lPlaRiKkimK~ded------v~mI~~Eapvl~aka~E~Fi~elt~~sw~~Tee~~rrtl~~sdia~av~~s~~fdFL~ 147 (236)
T KOG1657|consen 74 ILPLARIKKIMKSDED------VSMITAEAPVLFAKACELFITELTLRSWVHTEENKRRTLQKSDIAAAVTQSETFDFLR 147 (236)
T ss_pred cCcHhhcccccccccc------ccccchhHHHHHHHHHHHHHHHHHHHhhhhhcccccccchHHHHHHHhccCCCcccee
Confidence 7999999999999831 3489999999999999999999999999999999999999999999999644 444
Q ss_pred chHHHHHHHHHH
Q 032293 89 FVDPLRDSLDEF 100 (143)
Q Consensus 89 yi~~l~~~l~~~ 100 (143)
.+-|.+..++.|
T Consensus 148 DivP~~~~~~~~ 159 (236)
T KOG1657|consen 148 DIVPRKILAEKY 159 (236)
T ss_pred ccccchhccccc
Confidence 555567777777
No 21
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=98.44 E-value=1.6e-06 Score=59.38 Aligned_cols=65 Identities=22% Similarity=0.273 Sum_probs=58.0
Q ss_pred hHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHhhcCcc
Q 032293 16 TIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFT 87 (143)
Q Consensus 16 a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~lgF~ 87 (143)
-.|.+|++.+ |--+++..|.+.|.+....|+..|+..+..+|.+.||+++++.||..||.++|+.
T Consensus 10 ~~Vaqil~~~-------Gf~~~~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~~~Dv~~Al~~~gi~ 74 (77)
T smart00576 10 IAVAQILESA-------GFDSFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPNLGDVVLALENLGIS 74 (77)
T ss_pred HHHHHHHHHc-------CccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCcc
Confidence 3566666666 3458999999999999999999999999999999999999999999999999974
No 22
>cd00074 H2A Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins.
Probab=98.39 E-value=1.2e-06 Score=64.99 Aligned_cols=68 Identities=13% Similarity=0.170 Sum_probs=62.4
Q ss_pred hccCchhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHhh
Q 032293 10 AEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (143)
Q Consensus 10 d~~LP~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~ 83 (143)
.+.||.+.|.|+|++.-. ..+|+.+|...|..+.+.+..-|...|...|...+|++|+++||..|+..
T Consensus 18 gL~fPV~ri~R~Lk~~~~------a~RVs~~A~VyLaAvLEYL~aEIlelA~n~ak~~k~krItp~hi~lAi~n 85 (115)
T cd00074 18 GLQFPVGRIHRYLKKGRY------AERVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKKRITPRHLQLAVRN 85 (115)
T ss_pred CccCcHHHHHHHHHcCcc------ccccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEcHHHHHHHHhc
Confidence 467999999999998432 57999999999999999999999999999999999999999999999974
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=98.23 E-value=1.1e-05 Score=59.75 Aligned_cols=80 Identities=20% Similarity=0.200 Sum_probs=66.8
Q ss_pred HHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHhhcCcccch-HHHHH
Q 032293 17 IVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFTEFV-DPLRD 95 (143)
Q Consensus 17 ~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~lgF~~yi-~~l~~ 95 (143)
.|.+|+|+. |...++.+++..|.+.+..++.-|...|...|.++||+||+++||.-|++..+-..|. ++-++
T Consensus 6 ~v~~iLk~~-------Gv~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r~~~~f~~~p~~~ 78 (117)
T cd07979 6 VIAAILKSM-------GITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRVDYSFTSPPPRD 78 (117)
T ss_pred HHHHHHHHC-------CCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhccCCCCCCcHH
Confidence 677888876 3568999999999999999999999999999999999999999999999976654444 44666
Q ss_pred HHHHHHHH
Q 032293 96 SLDEFRQK 103 (143)
Q Consensus 96 ~l~~~ke~ 103 (143)
+|-++-..
T Consensus 79 ~l~~~a~~ 86 (117)
T cd07979 79 FLLELARE 86 (117)
T ss_pred HHHHHHHH
Confidence 66655443
No 24
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=97.99 E-value=3.3e-05 Score=53.40 Aligned_cols=63 Identities=21% Similarity=0.280 Sum_probs=52.5
Q ss_pred HHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHhh
Q 032293 17 IVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (143)
Q Consensus 17 ~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~ 83 (143)
+|.+|+.+.... .++.+|+.+..+|.+.+-.++..++..-.-+|+++||+||+++||+-..+.
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 TVGKIVEEEAKE----KGVEVSPQFIAALTELVYKQLENLAKDLEAFAKHAGRSTINMDDVKLLARR 72 (76)
T ss_dssp HHHHHHHHCCCC----TTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHTTT
T ss_pred HHHHHHHHHHhc----cCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHHHhhc
Confidence 578888887532 378999999999999999999999999999999999999999999977653
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=97.87 E-value=6.7e-05 Score=64.17 Aligned_cols=67 Identities=15% Similarity=0.213 Sum_probs=58.5
Q ss_pred chhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHhhcCcc
Q 032293 14 PKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFT 87 (143)
Q Consensus 14 P~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~lgF~ 87 (143)
|..+|.-|++.. |..++++||..+|.+.++.++..|..+|...+++.+|+|++++||-.||+.++.+
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 455677777766 2459999999999999999999999999999999999999999999999966543
No 26
>KOG3467 consensus Histone H4 [Chromatin structure and dynamics]
Probab=97.83 E-value=0.00011 Score=52.57 Aligned_cols=68 Identities=19% Similarity=0.208 Sum_probs=60.9
Q ss_pred CchhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHhhcCcc
Q 032293 13 LPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFT 87 (143)
Q Consensus 13 LP~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~lgF~ 87 (143)
+.+-+|.||.+... .-+|+--.-.-+..++.+||..+-+-|...+.+++||||++-||+-+|+.+|..
T Consensus 30 itKpaIRRlARr~G-------VkRi~G~~yeE~~~~~k~fl~n~i~~A~~yt~HAKRKTvT~~dvv~~LKR~G~~ 97 (103)
T KOG3467|consen 30 ITKPAIRRLARRGG-------VKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRT 97 (103)
T ss_pred cchHHHHHHHHhcC-------cchhchhhHHHHHHHHHHHHHHHHHHHHHHHhhhhhceeeHHHHHHHHHHcCce
Confidence 55778999998873 458888888889999999999999999999999999999999999999998854
No 27
>PF15511 CENP-T: Centromere kinetochore component CENP-T; PDB: 3B0D_T 3B0C_T 3VH5_T 3VH6_T.
Probab=97.82 E-value=4.1e-05 Score=67.22 Aligned_cols=67 Identities=24% Similarity=0.379 Sum_probs=48.1
Q ss_pred hhccCchhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHH
Q 032293 9 EAEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAED 76 (143)
Q Consensus 9 Ed~~LP~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eD 76 (143)
+.-.||.+.|.|++...... +....++|++||..+|.+|...|...|..---.+|.|+|||||...|
T Consensus 348 ~~P~lP~~~vK~la~~~ak~-s~~sK~kiskdal~aleqasdwfFeQl~dDL~aYA~HAgRKTIdesD 414 (414)
T PF15511_consen 348 PYPSLPPGVVKKLAQHFAKS-SGGSKMKISKDALEALEQASDWFFEQLGDDLEAYAKHAGRKTIDESD 414 (414)
T ss_dssp ----S-HHHHHHHHHHHH--------S-B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHH
T ss_pred CCCCCCccHHHHHHHHHHHh-hcccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCCCC
Confidence 34469999999998877642 11237899999999999999999999999999999999999999876
No 28
>smart00427 H2B Histone H2B.
Probab=97.82 E-value=0.00012 Score=52.17 Aligned_cols=63 Identities=16% Similarity=0.274 Sum_probs=56.9
Q ss_pred hHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHhhc
Q 032293 16 TIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEI 84 (143)
Q Consensus 16 a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~l 84 (143)
.-|+|++|++-| +.-||..|...+.--...+..-|+.+|...|..++|+||++.+|..|++-+
T Consensus 5 ~Yi~kvLKqVhp------d~giS~kam~imnSfvnDiferIa~EAs~L~~~nkr~TltsreIqtAvrl~ 67 (89)
T smart00427 5 IYIYKVLKQVHP------DTGISSKAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRLI 67 (89)
T ss_pred HHHHHHHHHhCC------CccccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHH
Confidence 358999999988 578999999999988888888899999999999999999999999998654
No 29
>KOG1745 consensus Histones H3 and H4 [Chromatin structure and dynamics]
Probab=97.81 E-value=1.3e-05 Score=61.17 Aligned_cols=75 Identities=23% Similarity=0.225 Sum_probs=65.2
Q ss_pred hhhccCchhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHhhc
Q 032293 8 PEAEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEI 84 (143)
Q Consensus 8 ~Ed~~LP~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~l 84 (143)
+.++.+++....|++++..+... .++++...|..+||++++.|+.-|.-.+|-+|.+.+|.||.+.||--|..--
T Consensus 59 stdLlI~K~PFqRlvrei~q~f~--~dLrfqs~Ai~ALQeA~EayLv~LfEdtnlcAihAkRVTimpkdiQlArrir 133 (137)
T KOG1745|consen 59 STDLLIRKLPFQRLVREIAQDFK--TDLRFQSSAIAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIR 133 (137)
T ss_pred hhHHHhhcCcHHHHhHHHHhccc--ccceehHHHHHHHHHHHHHHHHHhccccchhhhccceeEecccceehhhhcc
Confidence 35778889999999997665432 2789999999999999999999999999999999999999999998887543
No 30
>KOG1659 consensus Class 2 transcription repressor NC2, alpha subunit (DRAP1) [Transcription]
Probab=97.77 E-value=0.0001 Score=59.99 Aligned_cols=78 Identities=12% Similarity=0.254 Sum_probs=68.5
Q ss_pred cCchhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHhhcCcccchH
Q 032293 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFTEFVD 91 (143)
Q Consensus 12 ~LP~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~lgF~~yi~ 91 (143)
.||.+.|.|||...=. --+|+.-+...+.++.+.|+.-|-..+.+++...+-|||+++|+..++..-.-.+|+.
T Consensus 13 rfp~aRiKKIMQ~dEd------IGKvaqavPViisralElFl~~l~~~t~~~t~~~~aKt~s~~hlkq~v~~~~~FdFLk 86 (224)
T KOG1659|consen 13 RFPPARIKKIMQSDED------IGKVAQAVPVIISRALELFLESLLQKTLEITRSRGAKTVSSSHLKQAVESDPKFDFLK 86 (224)
T ss_pred cCCHHHHHHHHhhhhh------hhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhcCccccCHHHHHHHHhccchhHHHH
Confidence 6999999999987631 3489999999999999999999999999999999999999999999999887667766
Q ss_pred HHHH
Q 032293 92 PLRD 95 (143)
Q Consensus 92 ~l~~ 95 (143)
.+-.
T Consensus 87 ~~v~ 90 (224)
T KOG1659|consen 87 EVVE 90 (224)
T ss_pred HHHH
Confidence 6433
No 31
>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=97.75 E-value=0.0003 Score=47.76 Aligned_cols=52 Identities=25% Similarity=0.341 Sum_probs=50.3
Q ss_pred cccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHhhcCcc
Q 032293 36 SVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFT 87 (143)
Q Consensus 36 ~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~lgF~ 87 (143)
.++..|.+.|...+..||..|+..+...|...+|...++.||..||.++|+.
T Consensus 23 ~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~~~gi~ 74 (77)
T PF07524_consen 23 SASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPNLQDVEQALEEMGIS 74 (77)
T ss_pred ccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCC
Confidence 7899999999999999999999999999999999999999999999999984
No 32
>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=97.73 E-value=0.00021 Score=50.31 Aligned_cols=66 Identities=18% Similarity=0.368 Sum_probs=60.1
Q ss_pred cCchhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCC---CCCChHHHHHHHhhc
Q 032293 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKR---QTINAEDVLKAIEEI 84 (143)
Q Consensus 12 ~LP~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kR---KTIs~eDVl~AL~~l 84 (143)
.||++.|.|||...++ ..++.+...+|.-.+.+||.-|.-+|.++....+. ..|.|.||-.|...|
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 5999999999999983 67899999999999999999999999999987655 889999999998876
No 33
>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=97.68 E-value=7.9e-05 Score=51.02 Aligned_cols=66 Identities=21% Similarity=0.381 Sum_probs=54.7
Q ss_pred chhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCC-CChHHHHHHHhh
Q 032293 14 PKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQT-INAEDVLKAIEE 83 (143)
Q Consensus 14 P~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKT-Is~eDVl~AL~~ 83 (143)
|..+|.||++....+ ...+|++||..++++....||.--...|...+...+..+ |..+|+-+.+-.
T Consensus 1 p~~li~rll~~~f~~----~~tkIs~dal~l~~eyl~iFV~EAv~Ra~~~a~~e~~~~~le~e~LEki~pq 67 (72)
T PF09415_consen 1 PPELIARLLHEHFKD----DKTKISKDALKLSAEYLRIFVREAVARAAEQAEAEGDEGFLEVEHLEKILPQ 67 (72)
T ss_dssp -CHHHHHHHCTTSSS----TT-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSEE-HHHHHHHCHC
T ss_pred ChHHHHHHHHHHhcC----CCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHHH
Confidence 889999999977753 478999999999999999999999999999999999988 999999876543
No 34
>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=97.65 E-value=0.00037 Score=47.17 Aligned_cols=63 Identities=22% Similarity=0.222 Sum_probs=51.2
Q ss_pred hhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHhh
Q 032293 15 KTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (143)
Q Consensus 15 ~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~ 83 (143)
+..+.-+|++.=| +..+..++.++|.+.|..||.-++..|-..|++.+-.||...||.-.|+.
T Consensus 2 K~~l~~Lv~~iDp------~~~ld~~vee~Ll~laddFv~~v~~~ac~lAKhR~s~tle~~Dv~~~Ler 64 (68)
T PF03847_consen 2 KRKLQELVKQIDP------NEKLDPDVEELLLELADDFVDDVVSFACRLAKHRKSSTLEVKDVQLHLER 64 (68)
T ss_dssp HHHHHHHHHCC-S------S----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHHH
T ss_pred hHHHHHHHHHcCC------CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCHHHHHHHHHh
Confidence 3467888999865 68999999999999999999999999999999999999999999998874
No 35
>PLN00158 histone H2B; Provisional
Probab=97.63 E-value=0.0003 Score=52.30 Aligned_cols=64 Identities=16% Similarity=0.265 Sum_probs=57.4
Q ss_pred hhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHhhc
Q 032293 15 KTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEI 84 (143)
Q Consensus 15 ~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~l 84 (143)
...|+|++|++-| +.-||..+...|.--...+..-|+.+|...|.-++|.||++.+|..|++-+
T Consensus 30 ~~YI~kVLKQVhP------d~gIS~kaM~ImnSfvnDiferIA~EAs~La~~nkr~TltsrEIqtAvrLv 93 (116)
T PLN00158 30 KIYIYKVLKQVHP------DTGISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVRLI 93 (116)
T ss_pred HHHHHHHHHHhCC------CCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHh
Confidence 3569999999988 577999999999988888888899999999999999999999999998654
No 36
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=97.59 E-value=0.00017 Score=53.99 Aligned_cols=67 Identities=15% Similarity=0.186 Sum_probs=59.9
Q ss_pred hccCchhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHh
Q 032293 10 AEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIE 82 (143)
Q Consensus 10 d~~LP~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~ 82 (143)
-+.||.+.|.||||..- ..++|+++|...+.-|.+-.+..|+.-|-..|...+++.|.|.|+-.|+.
T Consensus 24 gl~fpvgrvkr~lk~~~------~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~kkkri~PrHlqlAIr 90 (132)
T COG5262 24 GLIFPVGRVKRLLKKGN------YRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRIIPRHLQLAIR 90 (132)
T ss_pred CccccHHHHHHHHHcCc------cceeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhcCcceechHHHHHHhc
Confidence 35799999999999542 37999999999999998888888888888899999999999999999987
No 37
>PTZ00463 histone H2B; Provisional
Probab=97.57 E-value=0.00041 Score=51.64 Aligned_cols=62 Identities=16% Similarity=0.300 Sum_probs=55.8
Q ss_pred HHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHhhc
Q 032293 17 IVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEI 84 (143)
Q Consensus 17 ~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~l 84 (143)
-|+|++|++-| +.-||..|...|.--......-|+.+|...|.-.+|.||++.+|..|++-+
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 59999999988 577999999999988888888899999999999999999999999998644
No 38
>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=97.49 E-value=0.00065 Score=48.44 Aligned_cols=67 Identities=16% Similarity=0.358 Sum_probs=51.9
Q ss_pred cCchhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCC-CCCChHHHHHHHhhc
Q 032293 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKR-QTINAEDVLKAIEEI 84 (143)
Q Consensus 12 ~LP~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kR-KTIs~eDVl~AL~~l 84 (143)
.||++.|.|||...+. +..|+.....++.=.+.+||-.|-..|.+++...+. ..|.|.|+-.|...|
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 6999999999999984 578999999999999999999999999999976554 489999999998765
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=97.43 E-value=0.0013 Score=44.43 Aligned_cols=64 Identities=16% Similarity=0.232 Sum_probs=48.9
Q ss_pred cCchhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHh
Q 032293 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIE 82 (143)
Q Consensus 12 ~LP~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~ 82 (143)
.+|..+|.-+.-.. |-..++.|+...|.+=++--|..|...|..+..+.+|++++++||-.||+
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 24489999999999999999999999999999999999999999999985
No 40
>COG5247 BUR6 Class 2 transcription repressor NC2, alpha subunit (DRAP1 homolog) [Transcription]
Probab=97.26 E-value=0.00095 Score=48.88 Aligned_cols=78 Identities=9% Similarity=0.167 Sum_probs=66.4
Q ss_pred ccCchhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHhhcCcccch
Q 032293 11 EELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFTEFV 90 (143)
Q Consensus 11 ~~LP~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~lgF~~yi 90 (143)
..||.|.|.|||.-.-+ --+|+.-......++.+.|+..|-..+-..|+..+-+.|+.+++..|.+.-+=.+|+
T Consensus 22 trFP~ar~KkIMQ~deD------iGKV~q~tPVIaskalE~Fl~~iv~~s~k~aR~~~skR~t~e~lk~a~~sdekFdFL 95 (113)
T COG5247 22 TRFPIARLKKIMQLDED------IGKVGQSTPVIASKALEMFLTEIVGLSLKEARKKSSKRMTSEFLKRATESDEKFDFL 95 (113)
T ss_pred hcCCHHHHHHHHHhhhh------hhhhhhcchHHHHHHHHHHHHHHHHHHHHHHHhccchhhHHHHHHHHHhhhHHHHHH
Confidence 36999999999987631 348899999999999999999999999999999999999999999999876655565
Q ss_pred HHHH
Q 032293 91 DPLR 94 (143)
Q Consensus 91 ~~l~ 94 (143)
..+.
T Consensus 96 ~~~~ 99 (113)
T COG5247 96 KNME 99 (113)
T ss_pred HHHH
Confidence 5443
No 41
>smart00414 H2A Histone 2A.
Probab=97.26 E-value=0.001 Score=48.65 Aligned_cols=68 Identities=13% Similarity=0.194 Sum_probs=60.0
Q ss_pred hccCchhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHhh
Q 032293 10 AEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (143)
Q Consensus 10 d~~LP~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~ 83 (143)
.+.||.+.|.|+|++.-. ..+|+..|...|.-+.+-+...|-..|-..|...+++.|++.||..|+..
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 467999999999998742 46999999999999888888888888888999999999999999999974
No 42
>PTZ00017 histone H2A; Provisional
Probab=97.03 E-value=0.0017 Score=49.41 Aligned_cols=68 Identities=18% Similarity=0.188 Sum_probs=60.1
Q ss_pred hccCchhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHhh
Q 032293 10 AEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (143)
Q Consensus 10 d~~LP~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~ 83 (143)
.+.||.+.|.|+|++.-. ..+|+..|...|.-+.+-+...|...|-..|...+++-|+|.||..|+..
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 467999999999998642 46999999999999888888888888888999999999999999999963
No 43
>PLN00154 histone H2A; Provisional
Probab=96.95 E-value=0.0027 Score=48.44 Aligned_cols=69 Identities=16% Similarity=0.148 Sum_probs=57.5
Q ss_pred hccCchhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHhh
Q 032293 10 AEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (143)
Q Consensus 10 d~~LP~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~ 83 (143)
.+.||.+.|.|++|+-... ..+|+..|...|.-+.+-+...|.-.|-..|...+++-|++.||..|+..
T Consensus 36 gL~FPVgRi~r~Lk~g~~~-----~~RVga~ApVYLAAVLEYLtAEVLELAGNaA~d~kk~RItPrHi~lAIrn 104 (136)
T PLN00154 36 GLQFPVGRIHRQLKQRVSA-----HGRVGATAAVYTAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRG 104 (136)
T ss_pred CccCchHHHHHHHHhhhhh-----ccccccchHHHHHHHHHHHHHHHHHHHHHHHHhhCCceecHHHhhhhccC
Confidence 4679999999999997521 46999999999988777666666667777888999999999999999964
No 44
>PF15510 CENP-W: Centromere kinetochore component W
Probab=96.91 E-value=0.0021 Score=46.24 Aligned_cols=66 Identities=26% Similarity=0.346 Sum_probs=54.1
Q ss_pred cCchhHHHHHHhccccCCCCCCcccccHHHHHH--------------HHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHH
Q 032293 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLA--------------FCESARIFIHYLSATANDICKESKRQTINAEDV 77 (143)
Q Consensus 12 ~LP~a~V~RI~K~~Lp~~~~~~~~~IskdA~~a--------------l~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDV 77 (143)
.-|++.+.|++|..-|. .++....-.+ +.-.|-.||+-|+-+|...|=+++=.||.++||
T Consensus 16 kaPrgfLkrv~Kr~Kph------lRl~~~~Dllv~~~~f~~~~~~~~vhLncLLFvhrLAEEaRtnA~EnK~~~Ik~~Hv 89 (102)
T PF15510_consen 16 KAPRGFLKRVFKRQKPH------LRLETSGDLLVRFCPFSGWQWGGEVHLNCLLFVHRLAEEARTNACENKCGTIKKEHV 89 (102)
T ss_pred hCchHHHHHHHHhcCCc------eeecccccHHHhhcccccccccceeehhHHHHHHHHHHHHHHHHHHHhhccccHHHH
Confidence 46999999999988773 5555444444 566789999999999999888889999999999
Q ss_pred HHHHhh
Q 032293 78 LKAIEE 83 (143)
Q Consensus 78 l~AL~~ 83 (143)
+.|-+-
T Consensus 90 ~AaaKv 95 (102)
T PF15510_consen 90 LAAAKV 95 (102)
T ss_pred HHHHHH
Confidence 998753
No 45
>KOG1756 consensus Histone 2A [Chromatin structure and dynamics]
Probab=96.83 E-value=0.004 Score=47.13 Aligned_cols=68 Identities=13% Similarity=0.185 Sum_probs=54.1
Q ss_pred hhccCchhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHh
Q 032293 9 EAEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIE 82 (143)
Q Consensus 9 Ed~~LP~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~ 82 (143)
..+-||.+.|.|++|+.= ...+|+..|...+.-|.+-.+..|+..|-..+..+++.-|+|.||..|+.
T Consensus 24 agl~fPvgri~r~Lr~~~------~~~ri~~gapV~laavLeYL~Aeile~agnaardnkk~ri~PrH~~lAI~ 91 (131)
T KOG1756|consen 24 AGLQFPVGRIHRLLRKGR------YAQRVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRITPRHLQLAIR 91 (131)
T ss_pred cccccCHHHHHHHHHccc------hhhhccCCChHHHHHHHHHHHHHHHHHhHHHhhhcCccccChHHHHHHHh
Confidence 456799999999999942 26899999999998655544455555555567788999999999999997
No 46
>PLN00153 histone H2A; Provisional
Probab=96.78 E-value=0.0037 Score=47.36 Aligned_cols=68 Identities=13% Similarity=0.157 Sum_probs=59.0
Q ss_pred hccCchhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHhh
Q 032293 10 AEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (143)
Q Consensus 10 d~~LP~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~ 83 (143)
.+.||.+.|.|++++.-. ..+|+..|...|.-+.+-++..|...|-..|...+++-|+|.||..|+..
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 468999999999998643 57999999999998888777777778888889999999999999999963
No 47
>PLN00157 histone H2A; Provisional
Probab=96.78 E-value=0.0034 Score=47.68 Aligned_cols=68 Identities=13% Similarity=0.157 Sum_probs=58.5
Q ss_pred hccCchhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHhh
Q 032293 10 AEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (143)
Q Consensus 10 d~~LP~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~ 83 (143)
.+.||.+.|.|++++.-- ..+|+..|...|.-+.+-++..|...|-..|...+++-|++.||..|+..
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 467999999999999642 57999999999988877777777777888889999999999999999964
No 48
>PLN00156 histone H2AX; Provisional
Probab=96.78 E-value=0.0043 Score=47.55 Aligned_cols=68 Identities=13% Similarity=0.153 Sum_probs=57.6
Q ss_pred hccCchhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHhh
Q 032293 10 AEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (143)
Q Consensus 10 d~~LP~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~ 83 (143)
.+.||.+.|.|++++.-- ..+|+..|...|.-+.+-....|...|-..|...+++-|+|.||..|+..
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 467999999999998642 46999999999988877666777777777888899999999999999963
No 49
>KOG1744 consensus Histone H2B [Chromatin structure and dynamics]
Probab=96.42 E-value=0.015 Score=43.98 Aligned_cols=62 Identities=18% Similarity=0.279 Sum_probs=55.5
Q ss_pred HHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHhhc
Q 032293 17 IVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEI 84 (143)
Q Consensus 17 ~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~l 84 (143)
.|+|++|++-| +.-|+..+..++.--...|+-.|+.+|+..+.-.+|.||+..+|..|+.-|
T Consensus 42 yv~kvlk~Vhp------d~gis~~a~~vmnsf~ndife~iA~ea~rla~y~krstisSreiqta~rLl 103 (127)
T KOG1744|consen 42 YVYKVLKQVHP------DLGISSKAMGVMNSFVNDIFERIASEAGRLAHYNKRSTISSREIQTAVRLL 103 (127)
T ss_pred ehhhhhhcccC------CCCcCHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCcccHHHHHHHHHHh
Confidence 47889999987 356999999999999999999999999999999999999999999988543
No 50
>KOG1658 consensus DNA polymerase epsilon, subunit C [Replication, recombination and repair]
Probab=96.21 E-value=0.0032 Score=49.12 Aligned_cols=66 Identities=29% Similarity=0.382 Sum_probs=55.7
Q ss_pred cCchhHHHHHHhccccCCCCCCcc-cccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHhhc
Q 032293 12 ELPKTIVRRVVKDKLHNCSPDTDI-SVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEI 84 (143)
Q Consensus 12 ~LP~a~V~RI~K~~Lp~~~~~~~~-~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~l 84 (143)
.||.+.|..+|+-. | ++ ....+++.++.+++..||..|+..++..+...+|+|+.-.|+-.|++.-
T Consensus 59 rLpL~rik~vvkl~-p------dl~l~~dea~~l~a~aaelfi~~Ln~~~~~~~q~~k~kt~qr~d~D~ai~~~ 125 (162)
T KOG1658|consen 59 RLPLARIKQVVKLD-P------DLTLLNDEASQLIAKAAELFIQELNDVAYTTAQLRKRKTEQRRDYDTAIEAV 125 (162)
T ss_pred hccHHHHHhhccCC-c------chhhhhhHHHHHHHHHHHHHHHHHHhccchhHHHHHhhhhhhhcccccccch
Confidence 58888888888765 2 45 5567789999999999999999999999999999999988887776543
No 51
>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=96.13 E-value=0.036 Score=41.88 Aligned_cols=88 Identities=22% Similarity=0.261 Sum_probs=48.0
Q ss_pred chhhccCchh--HHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHh-h
Q 032293 7 VPEAEELPKT--IVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIE-E 83 (143)
Q Consensus 7 ~~Ed~~LP~a--~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~-~ 83 (143)
......+|+. .|.-|+++. |-......+...|.+-+--|+.-|-..|..+|.+++|.+|+.+||--|++ .
T Consensus 5 ~~~~~~~PrDa~~i~~iL~~~-------Gv~~yeprVv~qLLEfayRYt~~vL~DA~~ya~hA~~~~i~~~DVrLAi~~r 77 (129)
T PF02291_consen 5 DSQSKSLPRDARVIHLILKSM-------GVTEYEPRVVNQLLEFAYRYTSDVLEDAQVYADHAGRSTIDADDVRLAIQSR 77 (129)
T ss_dssp --------HHHHHHHHHHHHT-------T---B-THHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHHHHT
T ss_pred CCCCccCChHHHHHHHHHHHc-------CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHH
Confidence 3445567774 455555554 23467788899999999999999999999999999999999999999999 5
Q ss_pred cCcccchHHHHHHHHHHH
Q 032293 84 IDFTEFVDPLRDSLDEFR 101 (143)
Q Consensus 84 lgF~~yi~~l~~~l~~~k 101 (143)
+++...-++-+++|-..-
T Consensus 78 ~~~~f~~pppre~llelA 95 (129)
T PF02291_consen 78 LDHSFTQPPPREFLLELA 95 (129)
T ss_dssp ------------------
T ss_pred HhhhccCCCChHHHHHHH
Confidence 777777777666665543
No 52
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=96.07 E-value=0.012 Score=49.23 Aligned_cols=71 Identities=18% Similarity=0.258 Sum_probs=60.7
Q ss_pred CchhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHhh---cCcccc
Q 032293 13 LPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE---IDFTEF 89 (143)
Q Consensus 13 LP~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~---lgF~~y 89 (143)
|-+-.|.-+++.+- ++..|-.|+.++|.+.|..||..|+..|-..|++.+..||-..||.-.|++ +.|..|
T Consensus 155 l~k~kl~dLvqqId------~~~~LD~dVedlLleiADdFV~sii~~sC~LAKHRKsdtlEvrDIqLhLEr~~Nm~iPgf 228 (258)
T KOG1142|consen 155 LSKRKLDDLVQQID------GTTKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHRKSDTVEVRDIQLHLERNFNMEIPGF 228 (258)
T ss_pred ccccchhHHHHhhc------CcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccchhheeeeeeccccccCCCc
Confidence 44556777788774 378999999999999999999999999999999999999999999999993 445444
No 53
>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=95.99 E-value=0.0098 Score=42.25 Aligned_cols=49 Identities=16% Similarity=0.196 Sum_probs=24.8
Q ss_pred ccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHhh
Q 032293 35 ISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (143)
Q Consensus 35 ~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~ 83 (143)
..-..|+..+|-+....||..|...|..+|...|+++|+.+|++-+|+.
T Consensus 18 ~~P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~rg~~~i~~eDl~F~lR~ 66 (93)
T PF02269_consen 18 EEPLPETVDLVEDIVREYIIELCQEAMEVAQRRGSKKIKVEDLLFLLRK 66 (93)
T ss_dssp SS--HHHHHHHHHHHHHHHHHHHHHHHC---------------------
T ss_pred CCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCcCcHHHHHHHHhc
Confidence 4668999999999999999999999999999999999999999999984
No 54
>KOG3219 consensus Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=95.77 E-value=0.012 Score=47.36 Aligned_cols=70 Identities=16% Similarity=0.306 Sum_probs=61.6
Q ss_pred cCchhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCC-CCCChHHHHHHHhhcCccc
Q 032293 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKR-QTINAEDVLKAIEEIDFTE 88 (143)
Q Consensus 12 ~LP~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kR-KTIs~eDVl~AL~~lgF~~ 88 (143)
.||+++|.|||..... ..|+.-+..+++=-+.+||--|--+|.++|...+. -.|.|.||-.|...|....
T Consensus 112 ~f~Ka~iKkL~~~itg-------~~v~~nv~Ia~~GiaKvFVGEvVEeAl~V~~~~~e~~PLqP~HIREA~rrL~~qg 182 (195)
T KOG3219|consen 112 AFPKAQIKKLMSSITG-------QSVSENVAIAMAGIAKVFVGEVVEEALDVREEWGESGPLQPKHIREAYRRLKLQG 182 (195)
T ss_pred cCCHHHHHHHHHHHhC-------CccCcceeeeecchhhHhHHHHHHHHHHHHHHhccCCCCCcHHHHHHHHHHHhcC
Confidence 6999999999999984 33899999999999999999999999999987665 4799999999999887654
No 55
>PTZ00252 histone H2A; Provisional
Probab=95.77 E-value=0.037 Score=42.21 Aligned_cols=68 Identities=9% Similarity=0.066 Sum_probs=49.9
Q ss_pred hccCchhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHh--cCCCCCChHHHHHHHhh
Q 032293 10 AEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKE--SKRQTINAEDVLKAIEE 83 (143)
Q Consensus 10 d~~LP~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~--~kRKTIs~eDVl~AL~~ 83 (143)
.+.||.+.|.|++++.-- ..+|+.-|...|.-+.+-....|...|-..|.. .+++-|++.||..|+..
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 468999999999998743 469999998888765544444444444444433 57789999999999964
No 56
>cd07978 TAF13 The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Several hy
Probab=94.31 E-value=0.34 Score=34.43 Aligned_cols=59 Identities=12% Similarity=0.176 Sum_probs=46.8
Q ss_pred HHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHhh
Q 032293 18 VRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (143)
Q Consensus 18 V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~ 83 (143)
|..+|--... ...-..|...+|-+....||..|+..|..+|. .++.-|+.+|++-+|+.
T Consensus 8 i~~mmy~~GD------~~~P~~eTv~llE~iv~~~i~~l~~~a~~~A~-~r~~k~~~eD~~FliR~ 66 (92)
T cd07978 8 IRQMMYGFGD------VQNPLPETVDLLEDIVVEYIIELCHKAAEVAQ-RRRGKVKVEDLIFLLRK 66 (92)
T ss_pred HHHHHHHcCC------CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-cCCCCCCHHHHHHHHhc
Confidence 5555555432 23458899999999999999999999999998 44555699999999963
No 57
>KOG3423 consensus Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=94.19 E-value=0.32 Score=38.53 Aligned_cols=69 Identities=16% Similarity=0.194 Sum_probs=56.2
Q ss_pred cCchhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcC--------------CCCCChHHH
Q 032293 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESK--------------RQTINAEDV 77 (143)
Q Consensus 12 ~LP~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~k--------------RKTIs~eDV 77 (143)
.||-+.+.-.++.+.= ...-.-.+.+|.=++..||..|+..|.+.|+-.. |-|++-+|+
T Consensus 86 ~IPDavt~~yL~~aGf-------~~~D~rv~RLvsLaAQKfvSDIa~DA~Q~~k~r~~~~~~~~k~~~kdkK~tLtmeDL 158 (176)
T KOG3423|consen 86 TIPDAVTDHYLKKAGF-------QTSDPRVKRLVSLAAQKFVSDIANDALQHSKIRTKTAIGKDKKQAKDKKYTLTMEDL 158 (176)
T ss_pred CCcHHHHHHHHHhcCC-------CcCcHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccccccccccccceeeeHHHH
Confidence 5899999999888742 2334456788999999999999999999997443 458999999
Q ss_pred HHHHhhcCcc
Q 032293 78 LKAIEEIDFT 87 (143)
Q Consensus 78 l~AL~~lgF~ 87 (143)
-.||.+.|..
T Consensus 159 ~~AL~EyGin 168 (176)
T KOG3423|consen 159 SPALAEYGIN 168 (176)
T ss_pred HHHHHHhCcc
Confidence 9999999874
No 58
>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily. Members of this protein are marked as probable ATPases by the nucleotide binding P-loop motif GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of helicases, and extensive homology to ATPases of MSHA-type pilus systems and to GspA proteins associated with type II protein secretion systems.
Probab=92.70 E-value=0.47 Score=37.71 Aligned_cols=74 Identities=22% Similarity=0.248 Sum_probs=54.9
Q ss_pred CchhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHH---HHHHHHHHHHHHhHhcCCCCCChHHHHHHHhhcCc
Q 032293 13 LPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARI---FIHYLSATANDICKESKRQTINAEDVLKAIEEIDF 86 (143)
Q Consensus 13 LP~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~---FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~lgF 86 (143)
|...-+..++...+..........++.++...|.+.+.= .|+.+...|...+-..+.++|+.++|-.++.++.|
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 333445555544442111112356899999999998875 79999999999988889999999999999998875
No 59
>KOG4336 consensus TBP-associated transcription factor Prodos [Transcription]
Probab=91.83 E-value=1.3 Score=38.07 Aligned_cols=66 Identities=18% Similarity=0.242 Sum_probs=57.5
Q ss_pred ccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHhhcCcccchHHHHHHHHHHHH
Q 032293 35 ISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFTEFVDPLRDSLDEFRQ 102 (143)
Q Consensus 35 ~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~lgF~~yi~~l~~~l~~~ke 102 (143)
-.|++-|++-|.+....+|.-+...+...|...||-..|.-||...|-.|||. +..|..+++.+-.
T Consensus 21 d~is~~aletlvell~~yi~eigrq~~n~celagRT~pT~~Dv~l~Li~mnI~--v~sL~~~~q~~~~ 86 (323)
T KOG4336|consen 21 DSISNAALETLVELLQSYIREIGRQLHNYCELAGRTIPTQGDVKLTLIEMNIK--VSSLYAYFQKQEF 86 (323)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcHHHHHHHHHHhCCC--hhhhHHHHHhccc
Confidence 36999999999999999999999999999999999999999999999999986 4556665554433
No 60
>KOG2549 consensus Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=90.71 E-value=1.3 Score=40.92 Aligned_cols=65 Identities=26% Similarity=0.365 Sum_probs=54.6
Q ss_pred chhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHhhcC
Q 032293 14 PKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEID 85 (143)
Q Consensus 14 P~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~lg 85 (143)
|.-.+. .|-+.+ |-..|+.|+..+|..=.+.=|.-|...|.++-.+.+|.+++.+||..||..+.
T Consensus 13 ~~Es~k-~vAEsl------Gi~nl~deaa~~La~dv~yrikEI~Q~aaKfm~hskR~kLtv~DV~~ALr~~n 77 (576)
T KOG2549|consen 13 PKESVK-VVAESL------GITNLNDEAALLLAEDVEYRIKEIVQDAAKFMVHSKRTKLTVDDVDYALRSLN 77 (576)
T ss_pred cHHHHH-HHHHHh------CccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcCcHHHHHHHHhhcc
Confidence 344444 444455 35579999999999999999999999999999999999999999999999654
No 61
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=88.67 E-value=2.6 Score=35.57 Aligned_cols=73 Identities=18% Similarity=0.165 Sum_probs=49.8
Q ss_pred hhHHHHHHhccccCCCCCCcccccHHHHHHHHHHH------HHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHhhcCccc
Q 032293 15 KTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESA------RIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFTE 88 (143)
Q Consensus 15 ~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a------~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~lgF~~ 88 (143)
..-+..|++..+...- ....++.++...+.+.+ --++..+...|...|...++.+|+.+||..|+..+....
T Consensus 209 ~~e~~~il~~r~~~~~--~~~~~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~a~~~a~~~~~~~I~~~~v~~a~~~~~~~~ 286 (394)
T PRK00411 209 ADEIFDILKDRVEEGF--YPGVVDDEVLDLIADLTAREHGDARVAIDLLRRAGLIAEREGSRKVTEEDVRKAYEKSEIVH 286 (394)
T ss_pred HHHHHHHHHHHHHhhc--ccCCCCHhHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHHHHH
Confidence 3445555555442100 02357889988887766 334556667888888888999999999999999885444
Q ss_pred c
Q 032293 89 F 89 (143)
Q Consensus 89 y 89 (143)
+
T Consensus 287 ~ 287 (394)
T PRK00411 287 L 287 (394)
T ss_pred H
Confidence 3
No 62
>KOG3334 consensus Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=88.56 E-value=7.1 Score=30.29 Aligned_cols=70 Identities=24% Similarity=0.208 Sum_probs=54.0
Q ss_pred cccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHhhcCcccchH-HHHHHHHHHHHHhh
Q 032293 36 SVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFTEFVD-PLRDSLDEFRQKNA 105 (143)
Q Consensus 36 ~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~lgF~~yi~-~l~~~l~~~ke~~~ 105 (143)
-...-....|.+-+--++.-|...|.-.+.+.++.||.++||-.|++...--+|.. +=+++|-++-....
T Consensus 30 eyEprVi~qlLefa~rYtt~vL~DA~vys~HA~ka~i~~eDVrlA~~~~~~~sf~~pPpRe~lL~lA~~rN 100 (148)
T KOG3334|consen 30 EYEPRVINQLLEFAYRYTTTVLDDAKVYSSHAKKATIDAEDVRLAIQMRVDHSFTPPPPREFLLELAAERN 100 (148)
T ss_pred ccChHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHhccccCCCCchHHHHHHHHhhc
Confidence 44555666777788888888889999999999999999999999999766555554 55676666655544
No 63
>KOG2389 consensus Predicted bromodomain transcription factor [Transcription]
Probab=86.41 E-value=2.3 Score=37.12 Aligned_cols=69 Identities=17% Similarity=0.256 Sum_probs=56.9
Q ss_pred cCchhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHhhcCcc
Q 032293 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFT 87 (143)
Q Consensus 12 ~LP~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~lgF~ 87 (143)
.|-+..|..|+.... --....-|...|+..+..||+-|+..|..++...||--.+..||+.||++|+.+
T Consensus 29 sla~~avaQIcqslg-------~~~~~~sale~Ltd~~~qyvQ~lgk~a~~~~n~anR~epnl~Div~Al~dls~s 97 (353)
T KOG2389|consen 29 SLARVAVAQICQSLG-------YSSTQNSALETLTDVLQQYVQNLGKTAHRYSNLANRTEPNLFDIVLALQDLSAS 97 (353)
T ss_pred HHHHHHHHHHHHhcC-------CcccccHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCccHHHHHHHHHHhhhh
Confidence 455667788876653 123334499999999999999999999999999999999999999999988754
No 64
>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=83.38 E-value=6.9 Score=32.56 Aligned_cols=76 Identities=14% Similarity=0.173 Sum_probs=48.5
Q ss_pred hHHHHHHhccccCCCCCCcccccHHHHHHHHHHHH------HHHHHHHHHHHHHhHhcCCCCCChHHHHHHHhhcCcccc
Q 032293 16 TIVRRVVKDKLHNCSPDTDISVHKDALLAFCESAR------IFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFTEF 89 (143)
Q Consensus 16 a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~------~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~lgF~~y 89 (143)
.-+..|++..+...- .+..++.++...+.+.+. -.+..+...|...|...++.+|+.+||..|+..+..+.+
T Consensus 202 ~e~~~il~~r~~~~~--~~~~~~~~~l~~i~~~~~~~~Gd~R~al~~l~~a~~~a~~~~~~~it~~~v~~a~~~~~~~~~ 279 (365)
T TIGR02928 202 EELRDILENRAEKAF--YDGVLDDGVIPLCAALAAQEHGDARKAIDLLRVAGEIAEREGAERVTEDHVEKAQEKIEKDRL 279 (365)
T ss_pred HHHHHHHHHHHHhhc--cCCCCChhHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHH
Confidence 345566655442100 023477888776655332 234445667778888888999999999999998865555
Q ss_pred hHHH
Q 032293 90 VDPL 93 (143)
Q Consensus 90 i~~l 93 (143)
+..+
T Consensus 280 ~~~i 283 (365)
T TIGR02928 280 LELI 283 (365)
T ss_pred HHHH
Confidence 5444
No 65
>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=78.08 E-value=2.2 Score=30.74 Aligned_cols=38 Identities=13% Similarity=0.262 Sum_probs=32.3
Q ss_pred hHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHH
Q 032293 16 TIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIH 54 (143)
Q Consensus 16 a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~ 54 (143)
++|.+|||.-|=..++|| ..++.++.+.|+++++.|-.
T Consensus 51 SNIGvLIKkglIEKSGDG-lv~T~~g~~Ii~~AA~l~a~ 88 (96)
T PF09114_consen 51 SNIGVLIKKGLIEKSGDG-LVITEEGMDIIIQAAELWAQ 88 (96)
T ss_dssp HHHHHHHHTTSEEEETTE-EEE-HHHHHHHHHHHHHHHH
T ss_pred HhHHHHHHcCcccccCCc-eEEechHHHHHHHHHHHHHh
Confidence 578889999998777776 89999999999999999854
No 66
>PF13335 Mg_chelatase_2: Magnesium chelatase, subunit ChlI
Probab=76.46 E-value=12 Score=26.33 Aligned_cols=47 Identities=17% Similarity=0.226 Sum_probs=39.2
Q ss_pred cccHHHHHHHHHHHHHH------HHHHHHHHHHHhHhcCCCCCChHHHHHHHh
Q 032293 36 SVHKDALLAFCESARIF------IHYLSATANDICKESKRQTINAEDVLKAIE 82 (143)
Q Consensus 36 ~IskdA~~al~~~a~~F------I~~lt~~A~~~a~~~kRKTIs~eDVl~AL~ 82 (143)
.++.++..+|..++..| ++-|..-|..||-=++...|+.+||..||.
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 46788888888887766 455667889999999999999999999984
No 67
>PF13654 AAA_32: AAA domain; PDB: 3K1J_B.
Probab=76.00 E-value=9.8 Score=34.61 Aligned_cols=49 Identities=27% Similarity=0.287 Sum_probs=37.3
Q ss_pred cccHHHHHHHHHHHH-----------HHHHHHHHHHHHHhHhcCCCCCChHHHHHHHhhc
Q 032293 36 SVHKDALLAFCESAR-----------IFIHYLSATANDICKESKRQTINAEDVLKAIEEI 84 (143)
Q Consensus 36 ~IskdA~~al~~~a~-----------~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~l 84 (143)
-++.+|+..|.+.+. ..|.-|-.+|+.+|...++.+|+++||..|++.-
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 467777777766554 3567788999999999999999999999999763
No 68
>TIGR02902 spore_lonB ATP-dependent protease LonB. Members of this protein are LonB, a paralog of the ATP-dependent protease La (LonA, TIGR00763). LonB proteins are found strictly, and almost universally, in endospore-forming bacteria. This protease was shown, in Bacillus subtilis, to be expressed specifically in the forespore, during sporulation, under control of sigma(F). The lonB gene, despite location immediately upstream of lonA, was shown to be monocistronic. LonB appears able to act on sigma(H) for post-translation control, but lonB mutation did not produce an obvious sporulation defect under the conditions tested. Note that additional paralogs of LonA and LonB occur in the Clostridium lineage and this model selects only one per species as the protein that corresponds to LonB in B. subtilis.
Probab=75.23 E-value=10 Score=34.38 Aligned_cols=63 Identities=22% Similarity=0.226 Sum_probs=42.2
Q ss_pred HHHHHHhccccCCCCCCcccccHHHHHHHHHHHH---HHHHHHHHHHHHHhHhcCCCCCChHHHHHHHhhc
Q 032293 17 IVRRVVKDKLHNCSPDTDISVHKDALLAFCESAR---IFIHYLSATANDICKESKRQTINAEDVLKAIEEI 84 (143)
Q Consensus 17 ~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~---~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~l 84 (143)
-+..|++..+.. .++.|+.++..+|.+.+. ..++.| ..|..+|...+|++|+.+||.+++..-
T Consensus 267 ei~~Il~~~a~k----~~i~is~~al~~I~~y~~n~Rel~nll-~~Aa~~A~~~~~~~It~~dI~~vl~~~ 332 (531)
T TIGR02902 267 EIKEIAKNAAEK----IGINLEKHALELIVKYASNGREAVNIV-QLAAGIALGEGRKRILAEDIEWVAENG 332 (531)
T ss_pred HHHHHHHHHHHH----cCCCcCHHHHHHHHHhhhhHHHHHHHH-HHHHHHHhhCCCcEEcHHHHHHHhCCc
Confidence 344555555432 247789999988877665 233333 345567777889999999999997543
No 69
>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=73.47 E-value=3.5 Score=24.80 Aligned_cols=25 Identities=32% Similarity=0.409 Sum_probs=20.3
Q ss_pred HHHHhHhcCCCCCChHHHHHHHhhc
Q 032293 60 ANDICKESKRQTINAEDVLKAIEEI 84 (143)
Q Consensus 60 A~~~a~~~kRKTIs~eDVl~AL~~l 84 (143)
|.++|...+...|+++|++.||=.-
T Consensus 1 A~~~A~~~~~~~i~~eHlL~all~~ 25 (53)
T PF02861_consen 1 AQELARERGHQYISPEHLLLALLED 25 (53)
T ss_dssp HHHHHHHTTBSSE-HHHHHHHHHHH
T ss_pred CHHHHHHcCCCcccHHHHHHHHHhh
Confidence 5678899999999999999996543
No 70
>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=73.23 E-value=10 Score=33.41 Aligned_cols=54 Identities=20% Similarity=0.265 Sum_probs=49.6
Q ss_pred cccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHhhcCcc
Q 032293 34 DISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFT 87 (143)
Q Consensus 34 ~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~lgF~ 87 (143)
--.|..|+..+|.--.+-=|+-+-.+|..+-.+.+|..++-+||-.||..|+.+
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 457999999999999999999999999999999999999999999999987643
No 71
>cd08045 TAF4 TATA Binding Protein (TBP) Associated Factor 4 (TAF4) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 4 (TAF4) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryote. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypotheses are
Probab=72.55 E-value=15 Score=29.30 Aligned_cols=77 Identities=12% Similarity=0.050 Sum_probs=56.7
Q ss_pred hccCchhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhc------CCCCCChHHHHHHHhh
Q 032293 10 AEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKES------KRQTINAEDVLKAIEE 83 (143)
Q Consensus 10 d~~LP~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~------kRKTIs~eDVl~AL~~ 83 (143)
...|....|.+.|...+... |-..|+.|+..+|+-||..++..|-.....+|.+- .-.++-..||-.-|..
T Consensus 42 ~~fl~~~~l~~~~~~i~~~~---g~~~~~~d~~~lis~a~e~rlr~li~k~~~~s~hR~~~~~~~~r~~~~sdvr~qL~~ 118 (212)
T cd08045 42 PSFLNPSPLAKKIRKIAKKH---GLKEVDEDVLDLISLALEERLRNLLEKLIEVSEHRVDSEKEDERYEITSDVRKQLRF 118 (212)
T ss_pred hhccCHHHHHHHHHHHHHHc---CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCceeecchHHHHHHH
Confidence 34677777777777776542 11279999999999999999999999999988764 3356667788777766
Q ss_pred cCcccc
Q 032293 84 IDFTEF 89 (143)
Q Consensus 84 lgF~~y 89 (143)
|+--+.
T Consensus 119 l~~~ek 124 (212)
T cd08045 119 LEQLER 124 (212)
T ss_pred HHHHHH
Confidence 554433
No 72
>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=72.24 E-value=23 Score=22.72 Aligned_cols=48 Identities=15% Similarity=0.186 Sum_probs=36.7
Q ss_pred cCchhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHh
Q 032293 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKE 66 (143)
Q Consensus 12 ~LP~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~ 66 (143)
.+|-+.+.-++..+.=++ -..-..-+++=++..||..|+..|.+.|+-
T Consensus 2 ~IPD~v~~~yL~~~G~~~-------~D~rv~RLvSLaaQKFisdI~~dA~q~~k~ 49 (51)
T PF03540_consen 2 TIPDEVTDYYLERSGFQT-------SDPRVKRLVSLAAQKFISDIANDAMQYCKI 49 (51)
T ss_pred CCCHHHHHHHHHHCCCCC-------CCHhHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 478888888888875332 123346688889999999999999999863
No 73
>COG1067 LonB Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]
Probab=70.41 E-value=4.8 Score=37.76 Aligned_cols=33 Identities=30% Similarity=0.341 Sum_probs=27.3
Q ss_pred HHHHHHHHHHHHHhHhcCCCCCChHHHHHHHhhc
Q 032293 51 IFIHYLSATANDICKESKRQTINAEDVLKAIEEI 84 (143)
Q Consensus 51 ~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~l 84 (143)
.-...|. .|..+|..++++-|+++||.+|++..
T Consensus 367 dl~~lv~-~A~~ia~~~~~~~I~ae~Ve~a~~~~ 399 (647)
T COG1067 367 DLGNLVR-EAGDIAVSEGRKLITAEDVEEALQKR 399 (647)
T ss_pred HHHHHHH-HhhHHHhcCCcccCcHHHHHHHHHhh
Confidence 3344444 99999999999999999999999873
No 74
>COG5162 Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=70.00 E-value=31 Score=27.57 Aligned_cols=68 Identities=15% Similarity=0.259 Sum_probs=46.6
Q ss_pred CchhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhH-hc------------------------
Q 032293 13 LPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICK-ES------------------------ 67 (143)
Q Consensus 13 LP~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~-~~------------------------ 67 (143)
||-+.+.=.|-.+ |-.....-.+-+|.-.+..||+.|+..|++..+ ..
T Consensus 89 iPd~v~DYyl~k~-------Gf~~~D~rvKkLl~L~aqKFvsDiA~dayqYsrIr~~~sna~~t~~~a~~f~~gg~~~i~ 161 (197)
T COG5162 89 IPDSVTDYYLEKA-------GFVTSDQRVKKLLSLLAQKFVSDIAVDAYQYSRIRQGSSNAKATAQKAKRFAKGGASGIG 161 (197)
T ss_pred ccHHHHHHHHHhc-------CceeccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccchhhHHHHHHHHhccccccc
Confidence 4555554444443 223344556788888999999999998887542 11
Q ss_pred --------CCCCCChHHHHHHHhhcCcc
Q 032293 68 --------KRQTINAEDVLKAIEEIDFT 87 (143)
Q Consensus 68 --------kRKTIs~eDVl~AL~~lgF~ 87 (143)
++-+++..|+-.||.+.|+.
T Consensus 162 ~~~~~~dr~K~vltv~DLs~Al~EyGin 189 (197)
T COG5162 162 SSGRRGDRKKPVLTVVDLSKALEEYGIN 189 (197)
T ss_pred ccccccccCCceeeehHHHHHHHHhccc
Confidence 45678899999999988864
No 75
>PF08369 PCP_red: Proto-chlorophyllide reductase 57 kD subunit; InterPro: IPR013580 This domain is found in bacteria and plant chloroplast proteins. It often appears at the C-terminal of nitrogenase component 1 type oxidoreductases (IPR000510 from INTERPRO) and sometimes independently in bacterial proteins such as the proto-chlorophyllide reductase subunit B of the cyanobacterium Synechocystis. This domain is also associated with chlorophyllide reductase subunit Z, converts chlorophylls (Chl) into bacteriochlorophylls (BChl) by reducing ring B of the tetrapyrrole.; GO: 0016491 oxidoreductase activity, 0015979 photosynthesis, 0015995 chlorophyll biosynthetic process, 0055114 oxidation-reduction process; PDB: 2KRU_A 2L09_A.
Probab=63.16 E-value=12 Score=23.05 Aligned_cols=42 Identities=19% Similarity=0.139 Sum_probs=26.1
Q ss_pred cHHHHHHHHHHHHHHHHHHH-HHHHHHhHhcCCCCCChHHHHHH
Q 032293 38 HKDALLAFCESARIFIHYLS-ATANDICKESKRQTINAEDVLKA 80 (143)
Q Consensus 38 skdA~~al~~~a~~FI~~lt-~~A~~~a~~~kRKTIs~eDVl~A 80 (143)
+.||...|.+. =.|+.--. ..+-..|...|...||.++|..|
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 45666666664 34554333 44455899999999999999876
No 76
>PF04552 Sigma54_DBD: Sigma-54, DNA binding domain; InterPro: IPR007634 This DNA-binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore, this region contains a putative helix-turn-helix motif. At the C terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins [].; PDB: 2AHQ_A 2O9L_A 2O8K_A.
Probab=62.82 E-value=15 Score=28.54 Aligned_cols=84 Identities=15% Similarity=0.260 Sum_probs=30.5
Q ss_pred cchhhccCchhHHHHHHhccccCCCC---------------CCcccccHHHHH-HHHHHHHHHHHHHHHHHHHHhHhcCC
Q 032293 6 VVPEAEELPKTIVRRVVKDKLHNCSP---------------DTDISVHKDALL-AFCESARIFIHYLSATANDICKESKR 69 (143)
Q Consensus 6 ~~~Ed~~LP~a~V~RI~K~~Lp~~~~---------------~~~~~IskdA~~-al~~~a~~FI~~lt~~A~~~a~~~kR 69 (143)
.+++.+.|..+||.|+++...=+++. +.+..+|.++.. .| ..-+..+++.
T Consensus 54 ~iA~~lgl~~STVSRav~~Ky~~t~~Gi~plk~fF~~~~~~~~~~~~S~~~ik~~i--------------~~lI~~Ed~~ 119 (160)
T PF04552_consen 54 DIADELGLHESTVSRAVKNKYIQTPRGIFPLKDFFSRSVSSGSGEEFSSEAIKARI--------------KELIEEEDKK 119 (160)
T ss_dssp -------------------------------S-----SS--SS-SS---TTH-HHH--------------HHHHTTS-TT
T ss_pred HHHHHhCCCHhHHHHHHcCceeecCCeeeeHHHhccccccCCCCcccHHHHHHHHH--------------HHHHHhcCCC
Confidence 45688899999999999876533321 001113333322 22 2246667788
Q ss_pred CCCChHHHHHHHhhcCcccchHHHHHHHHHHHHHhhcc
Q 032293 70 QTINAEDVLKAIEEIDFTEFVDPLRDSLDEFRQKNAGK 107 (143)
Q Consensus 70 KTIs~eDVl~AL~~lgF~~yi~~l~~~l~~~ke~~~~K 107 (143)
+.+|-+.|...|..-| +..-...+..||+...--
T Consensus 120 ~PlSD~~i~~~L~~~g----i~isRRTVaKYR~~L~Ip 153 (160)
T PF04552_consen 120 KPLSDQEIAELLKEEG----IKISRRTVAKYREELGIP 153 (160)
T ss_dssp S---HHHHHHHHTTTT----S---HHHHHHHHHHHT-S
T ss_pred CCCCHHHHHHHHHHcC----CCccHHHHHHHHHHcCCC
Confidence 9999999999998776 667788899999987643
No 77
>KOG1757 consensus Histone 2A [Chromatin structure and dynamics]
Probab=62.20 E-value=12 Score=28.17 Aligned_cols=68 Identities=16% Similarity=0.236 Sum_probs=50.0
Q ss_pred cchhhccCchhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCC----CCCChHHHHHHH
Q 032293 6 VVPEAEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKR----QTINAEDVLKAI 81 (143)
Q Consensus 6 ~~~Ed~~LP~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kR----KTIs~eDVl~AL 81 (143)
.+...+.||...|.|.+|.-... ..+|..-+.... .-.+.|||.+-.+.|.+..+ |.|+|.|+..|+
T Consensus 24 s~raGlqFpVgRihr~LK~r~t~-----h~rVGataavy~----aaileYLTaEVLeLAgNasKdLKvKRitprHlqLAi 94 (131)
T KOG1757|consen 24 SARAGLQFPVGRIHRHLKTRTTS-----HGRVGATAAVYS----AAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAI 94 (131)
T ss_pred HHhcccccchHHHHHHHHHhccc-----ccccchHHHHHH----HHHHHHHHHHHHHHcccccccceeeeccchhheeee
Confidence 34566789999999999998752 456665443332 34578999999888765543 789999998887
Q ss_pred h
Q 032293 82 E 82 (143)
Q Consensus 82 ~ 82 (143)
+
T Consensus 95 R 95 (131)
T KOG1757|consen 95 R 95 (131)
T ss_pred c
Confidence 6
No 78
>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=61.89 E-value=44 Score=27.10 Aligned_cols=72 Identities=18% Similarity=0.236 Sum_probs=46.8
Q ss_pred CchhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHH---HHHHHHHHHHHHHhHhcCCCCCChHHHHHHHhhcCccc
Q 032293 13 LPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESAR---IFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFTE 88 (143)
Q Consensus 13 LP~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~---~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~lgF~~ 88 (143)
++...+..+++..+.. .++.++.++...|.+.+. -++..+...+...+...+...|+.++|..++..++++.
T Consensus 159 l~~~e~~~il~~~~~~----~~~~~~~~al~~ia~~~~G~pR~~~~ll~~~~~~a~~~~~~~it~~~v~~~l~~l~~~~ 233 (305)
T TIGR00635 159 YTVEELAEIVSRSAGL----LNVEIEPEAALEIARRSRGTPRIANRLLRRVRDFAQVRGQKIINRDIALKALEMLMIDE 233 (305)
T ss_pred CCHHHHHHHHHHHHHH----hCCCcCHHHHHHHHHHhCCCcchHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHhCCCC
Confidence 3344455555554432 246788999888877653 23344455566666555667899999999999876553
No 79
>PRK09862 putative ATP-dependent protease; Provisional
Probab=61.49 E-value=36 Score=31.05 Aligned_cols=59 Identities=12% Similarity=0.088 Sum_probs=44.5
Q ss_pred ccccHHHHHHHHHHHHHH------HHHHHHHHHHHhHhcCCCCCChHHHHHHHhhcCcccchHHH
Q 032293 35 ISVHKDALLAFCESARIF------IHYLSATANDICKESKRQTINAEDVLKAIEEIDFTEFVDPL 93 (143)
Q Consensus 35 ~~IskdA~~al~~~a~~F------I~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~lgF~~yi~~l 93 (143)
+.++.++...+..++..+ .+.|..-|..+|-=++|..|+++||..|+.--+++..+-.+
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 356777777777665544 56777888899999999999999999999866555444333
No 80
>COG5251 TAF40 Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=61.04 E-value=12 Score=30.07 Aligned_cols=64 Identities=13% Similarity=0.094 Sum_probs=49.9
Q ss_pred cCchhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcC-CCCCChHHHHHHHh
Q 032293 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESK-RQTINAEDVLKAIE 82 (143)
Q Consensus 12 ~LP~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~k-RKTIs~eDVl~AL~ 82 (143)
.||++.|.+++..++ +..|+...+.+|+-.+.+|+..|--.|..+-..-+ --.+.+.|+-.|..
T Consensus 115 ~lnKt~VKKlastV~-------nQtVspNi~I~l~g~~KVfvGEiIElA~~Vq~~w~~sgpl~p~h~reayr 179 (199)
T COG5251 115 SLNKTQVKKLASTVA-------NQTVSPNIRIFLQGVGKVFVGEIIELAMIVQNKWLTSGPLIPFHKREAYR 179 (199)
T ss_pred CCCHHHHHHHHHHHh-------ccccCCCeeeeeechhHHHHHHHHHHHHHHHHHhcccCCCChHHHHHHHH
Confidence 699999999999998 46788888889999999999988877766533211 12478888877754
No 81
>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=60.27 E-value=26 Score=32.46 Aligned_cols=50 Identities=30% Similarity=0.287 Sum_probs=39.6
Q ss_pred cccHHHHHHHHHHHH-------------HHHHHHHHHHHHHhHhcCCCCCChHHHHHHHhhcC
Q 032293 36 SVHKDALLAFCESAR-------------IFIHYLSATANDICKESKRQTINAEDVLKAIEEID 85 (143)
Q Consensus 36 ~IskdA~~al~~~a~-------------~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~lg 85 (143)
.++.+|...|.+-++ -=|.-|-..|+.+|...+..+|+.+||..|++.-.
T Consensus 330 ~~s~~Av~~Li~~~~R~ag~r~~lsl~~R~L~~llR~A~~iA~~~~~~~I~~ehV~~Ai~~~~ 392 (608)
T TIGR00764 330 HFTRDAVEEIVREAQRRAGRKDHLTLRLRELGGLVRAAGDIAKSSGKVYVTAEHVLKAKKLAK 392 (608)
T ss_pred cCCHHHHHHHHHHHHHHHhcccccCCCHHHHHHHHHHHHHHHHhcCCceecHHHHHHHHHHHH
Confidence 588999888876444 34556677888899888999999999999997554
No 82
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=59.94 E-value=46 Score=27.72 Aligned_cols=72 Identities=15% Similarity=0.209 Sum_probs=49.0
Q ss_pred CchhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHH---HHHHHHHHHHHHHhHhcCCCCCChHHHHHHHhhcCccc
Q 032293 13 LPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESAR---IFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFTE 88 (143)
Q Consensus 13 LP~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~---~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~lgF~~ 88 (143)
++...+..|++..+.. .++.++.++...|.+.|. -++..+...+..++...+...|+.++|..++..++...
T Consensus 180 ~~~~e~~~il~~~~~~----~~~~~~~~~~~~ia~~~~G~pR~a~~~l~~~~~~a~~~~~~~I~~~~v~~~l~~~~~~~ 254 (328)
T PRK00080 180 YTVEELEKIVKRSARI----LGVEIDEEGALEIARRSRGTPRIANRLLRRVRDFAQVKGDGVITKEIADKALDMLGVDE 254 (328)
T ss_pred CCHHHHHHHHHHHHHH----cCCCcCHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCc
Confidence 4445555555555432 257899999888877663 23444555566666666667999999999999887654
No 83
>KOG2680 consensus DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=59.28 E-value=43 Score=29.75 Aligned_cols=49 Identities=18% Similarity=0.339 Sum_probs=41.1
Q ss_pred cccccHHHHHHHHHHHH----HHHHHHHHHHHHHhHhcCCCCCChHHHHHHHh
Q 032293 34 DISVHKDALLAFCESAR----IFIHYLSATANDICKESKRQTINAEDVLKAIE 82 (143)
Q Consensus 34 ~~~IskdA~~al~~~a~----~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~ 82 (143)
++.++.||++.|.+-.. -|..+|-+.|+.+|.+.+-+++..+||-.+-.
T Consensus 375 dv~m~~~A~d~Lt~i~~~tsLRYai~Lit~a~~~~~krk~~~v~~~di~r~y~ 427 (454)
T KOG2680|consen 375 DVEMNPDALDLLTKIGEATSLRYAIHLITAASLVCLKRKGKVVEVDDIERVYR 427 (454)
T ss_pred ccccCHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHhcCceeehhHHHHHHH
Confidence 68899999999876543 46667777899999999999999999999864
No 84
>cd04752 Commd4 COMM_Domain containing protein 4. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=54.44 E-value=51 Score=25.50 Aligned_cols=52 Identities=13% Similarity=0.298 Sum_probs=37.7
Q ss_pred HHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHhhcCcc-cchHHHHHHHHHHHHHhhc
Q 032293 48 SARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFT-EFVDPLRDSLDEFRQKNAG 106 (143)
Q Consensus 48 ~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~lgF~-~yi~~l~~~l~~~ke~~~~ 106 (143)
++...++||-..|. |.-++++++..-|+.|||+ +.+..+...+..++.....
T Consensus 43 ~~va~l~fiL~~A~-------k~n~~~~~l~~eL~~lglp~e~~~~l~~~~~~~~~~l~~ 95 (174)
T cd04752 43 ASIAVLSFILSSAA-------KYNVDGESLSSELQQLGLPKEHATSLCRSYEEKQSKLQE 95 (174)
T ss_pred HHHHHHHHHHHHHH-------HcCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHH
Confidence 45566666666554 3449999999999999997 5777777777777766543
No 85
>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=54.41 E-value=49 Score=30.65 Aligned_cols=49 Identities=20% Similarity=0.242 Sum_probs=41.5
Q ss_pred cccccHHHHHHHHHHHHHHH-------HHHHHHHHHHhHhcCCCCCChHHHHHHHh
Q 032293 34 DISVHKDALLAFCESARIFI-------HYLSATANDICKESKRQTINAEDVLKAIE 82 (143)
Q Consensus 34 ~~~IskdA~~al~~~a~~FI-------~~lt~~A~~~a~~~kRKTIs~eDVl~AL~ 82 (143)
.+.|+.+....|...+..+- .++...|..+|.=++|.+|+.+||..|+.
T Consensus 247 ~V~is~~~~~~l~~~~~~~~i~s~Ra~i~~~r~Ara~AaL~gr~~V~~~Dv~~A~~ 302 (633)
T TIGR02442 247 SVRISDSLIRFISELCIEFGVDGHRADIVMARAARALAALDGRRRVTAEDVREAAE 302 (633)
T ss_pred CCCCCHHHHHHHHHHHHHhCCCCccHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHH
Confidence 58899999999998887762 45667788888899999999999999886
No 86
>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=53.62 E-value=62 Score=27.80 Aligned_cols=49 Identities=14% Similarity=0.219 Sum_probs=38.7
Q ss_pred cccccHHHHHHHHHHHHHHH-------HHHHHHHHHHhHhcCCCCCChHHHHHHHh
Q 032293 34 DISVHKDALLAFCESARIFI-------HYLSATANDICKESKRQTINAEDVLKAIE 82 (143)
Q Consensus 34 ~~~IskdA~~al~~~a~~FI-------~~lt~~A~~~a~~~kRKTIs~eDVl~AL~ 82 (143)
.+.|+.+....+...|..+= .++...|...|--+||..|+++||..+..
T Consensus 252 ~V~v~d~~~~~i~~l~~~~~~~s~Ra~i~l~raArA~Aal~GR~~V~~dDv~~~a~ 307 (337)
T TIGR02030 252 QVTIPYDVLVKVAELCAELDVDGLRGELTLNRAAKALAAFEGRTEVTVDDIRRVAV 307 (337)
T ss_pred cCcCCHHHHHHHHHHHHHHCCCCCcHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 58899998888888766552 34566777788889999999999998764
No 87
>PRK13406 bchD magnesium chelatase subunit D; Provisional
Probab=52.81 E-value=35 Score=31.62 Aligned_cols=49 Identities=18% Similarity=0.231 Sum_probs=42.9
Q ss_pred cccccHHHHHHHHHHHHHHH-------HHHHHHHHHHhHhcCCCCCChHHHHHHHh
Q 032293 34 DISVHKDALLAFCESARIFI-------HYLSATANDICKESKRQTINAEDVLKAIE 82 (143)
Q Consensus 34 ~~~IskdA~~al~~~a~~FI-------~~lt~~A~~~a~~~kRKTIs~eDVl~AL~ 82 (143)
++.|+.+....+...|..|= .++...|..+|-=+||.+|+.+||..|+.
T Consensus 193 ~v~v~~~~l~~i~~~~~~~gv~S~Ra~i~llraARa~AaL~Gr~~V~~~dv~~Aa~ 248 (584)
T PRK13406 193 AVGPPPEAIAALCAAAAALGIASLRAPLLALRAARAAAALAGRTAVEEEDLALAAR 248 (584)
T ss_pred cCCCCHHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 68899999998888888774 47788888999999999999999999985
No 88
>PRK12402 replication factor C small subunit 2; Reviewed
Probab=51.86 E-value=47 Score=27.02 Aligned_cols=70 Identities=11% Similarity=0.040 Sum_probs=42.5
Q ss_pred cCchhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHhhcCcc
Q 032293 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFT 87 (143)
Q Consensus 12 ~LP~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~lgF~ 87 (143)
.++...+..+++..+.. .++.++.++...|.+.+.-=+..+-......+. +..+|+.+||..++.....+
T Consensus 183 ~~~~~~~~~~l~~~~~~----~~~~~~~~al~~l~~~~~gdlr~l~~~l~~~~~--~~~~It~~~v~~~~~~~~~~ 252 (337)
T PRK12402 183 APTDDELVDVLESIAEA----EGVDYDDDGLELIAYYAGGDLRKAILTLQTAAL--AAGEITMEAAYEALGDVGTD 252 (337)
T ss_pred CCCHHHHHHHHHHHHHH----cCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHH--cCCCCCHHHHHHHhCCCCCH
Confidence 34455666666666543 246789999988888763222223232333332 23479999999988765443
No 89
>PRK07452 DNA polymerase III subunit delta; Validated
Probab=50.85 E-value=58 Score=26.83 Aligned_cols=66 Identities=12% Similarity=0.151 Sum_probs=46.9
Q ss_pred HHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHh--cCCCCCChHHHHHHHhhcCcc
Q 032293 18 VRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKE--SKRQTINAEDVLKAIEEIDFT 87 (143)
Q Consensus 18 V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~--~kRKTIs~eDVl~AL~~lgF~ 87 (143)
+.+.|++.+.. .+..|+.+|...|..++.-=...+..+-..++.- .++.+|+.+||...+....+.
T Consensus 135 l~~~i~~~~~~----~g~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~~It~~~V~~~v~~~~~~ 202 (326)
T PRK07452 135 LKQLVERTAQE----LGVKLTPEAAELLAEAVGNDSRRLYNELEKLALYAENSTKPISAEEVKALVSNTTQN 202 (326)
T ss_pred HHHHHHHHHHH----cCCCCCHHHHHHHHHHhCccHHHHHHHHHHHHHhccCCCCccCHHHHHHHhccCcCc
Confidence 45555554432 2588999999999998886566666666666654 457789999999887665543
No 90
>KOG3901 consensus Transcription initiation factor IID subunit [Transcription]
Probab=50.64 E-value=58 Score=24.06 Aligned_cols=46 Identities=17% Similarity=0.204 Sum_probs=38.1
Q ss_pred ccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHhh
Q 032293 35 ISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (143)
Q Consensus 35 ~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~ 83 (143)
..=-.+++.+|-.-...||..++..|..+. +|--+..+|++-+|+.
T Consensus 26 ~nP~~~tv~~Le~iV~~Yi~elt~~a~~~g---~rgk~~veD~~f~lRk 71 (109)
T KOG3901|consen 26 VNPYPETVDLLEDIVLEYITELTHAAMEIG---KRGKVKVEDFKFLLRK 71 (109)
T ss_pred CCccHhHHHHHHHHHHHHHHHHHHHHHHhc---ccCceeHHHHHHHHHh
Confidence 445678899999999999999988888887 5556788999999974
No 91
>TIGR00368 Mg chelatase-related protein. The N-terminal end matches very strongly a pfam Mg_chelatase domain.
Probab=50.62 E-value=46 Score=30.19 Aligned_cols=47 Identities=17% Similarity=0.169 Sum_probs=40.6
Q ss_pred cccHHHHHHHHHHHHHH------HHHHHHHHHHHhHhcCCCCCChHHHHHHHh
Q 032293 36 SVHKDALLAFCESARIF------IHYLSATANDICKESKRQTINAEDVLKAIE 82 (143)
Q Consensus 36 ~IskdA~~al~~~a~~F------I~~lt~~A~~~a~~~kRKTIs~eDVl~AL~ 82 (143)
.++.++..+|.+++..| ++-|..-|..+|.=+++..|+.+||..||.
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 46888999999888877 566777889999999999999999999984
No 92
>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=49.80 E-value=30 Score=28.39 Aligned_cols=56 Identities=14% Similarity=0.083 Sum_probs=35.3
Q ss_pred hhccCchhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhc
Q 032293 9 EAEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKES 67 (143)
Q Consensus 9 Ed~~LP~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~ 67 (143)
+...|....+.+.|....... |...|..|...+|.-||..+|..|-..+..+|.+-
T Consensus 40 ~~~fL~~~~L~~~i~~i~~~~---g~~~~~~d~l~llS~A~e~rLr~lie~~~~~s~hR 95 (264)
T PF05236_consen 40 EEPFLNPSPLQKRIQKIAKKH---GLKSVDEDVLELLSLATEERLRNLIEKAIVLSRHR 95 (264)
T ss_dssp ----S-HHHHHHHHHHHHHCT---T--EE-TCHHHHHHHHHHHHHHHHHHHHH------
T ss_pred cccccCHHHHHHHHHHHHHHc---CCcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 445677777777777766532 35689999999999999999999999999988653
No 93
>TIGR01128 holA DNA polymerase III, delta subunit. subunit around DNA forming a DNA sliding clamp.
Probab=49.41 E-value=1e+02 Score=24.67 Aligned_cols=67 Identities=15% Similarity=0.189 Sum_probs=47.0
Q ss_pred cCchhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHh
Q 032293 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIE 82 (143)
Q Consensus 12 ~LP~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~ 82 (143)
.++...+.+++++.+.. .+..|+.++...|...+.-=+..+..+-..+|.-.+.++|+.+||...+.
T Consensus 110 ~~~~~~~~~~i~~~~~~----~g~~i~~~a~~~l~~~~~~d~~~l~~el~KL~~~~~~~~It~e~I~~~~~ 176 (302)
T TIGR01128 110 TPKEQELPRWIQARLKK----LGLRIDPDAVQLLAELVEGNLLAIAQELEKLALYAPDGKITLEDVEEAVS 176 (302)
T ss_pred CCCHHHHHHHHHHHHHH----cCCCCCHHHHHHHHHHhCcHHHHHHHHHHHHHhhCCCCCCCHHHHHHHHh
Confidence 45566677777776653 25789999999998877655556666666665543444799999987765
No 94
>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=48.89 E-value=25 Score=22.05 Aligned_cols=25 Identities=24% Similarity=0.522 Sum_probs=20.9
Q ss_pred CCChHHHHHHHhhcCcccchHHHHH
Q 032293 71 TINAEDVLKAIEEIDFTEFVDPLRD 95 (143)
Q Consensus 71 TIs~eDVl~AL~~lgF~~yi~~l~~ 95 (143)
+=++++|..-|..+||..|.+....
T Consensus 3 ~w~~~~v~~WL~~~gl~~y~~~f~~ 27 (66)
T PF07647_consen 3 TWSPEDVAEWLKSLGLEQYADNFRE 27 (66)
T ss_dssp GHCHHHHHHHHHHTTCGGGHHHHHH
T ss_pred CCCHHHHHHHHHHCCcHHHHHHHHH
Confidence 3478999999999999999987754
No 95
>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=47.83 E-value=13 Score=22.74 Aligned_cols=14 Identities=29% Similarity=0.643 Sum_probs=11.8
Q ss_pred HHHHHHHhhcCccc
Q 032293 75 EDVLKAIEEIDFTE 88 (143)
Q Consensus 75 eDVl~AL~~lgF~~ 88 (143)
+|++.||..|||..
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 68999999999984
No 96
>CHL00081 chlI Mg-protoporyphyrin IX chelatase
Probab=46.30 E-value=73 Score=27.69 Aligned_cols=49 Identities=12% Similarity=0.197 Sum_probs=40.7
Q ss_pred cccccHHHHHHHHHHHHHHH-------HHHHHHHHHHhHhcCCCCCChHHHHHHHh
Q 032293 34 DISVHKDALLAFCESARIFI-------HYLSATANDICKESKRQTINAEDVLKAIE 82 (143)
Q Consensus 34 ~~~IskdA~~al~~~a~~FI-------~~lt~~A~~~a~~~kRKTIs~eDVl~AL~ 82 (143)
.+.|+.+....+.+.|..+= .++...|.-.|-=+||..|+++||..+..
T Consensus 265 ~V~v~~~~~~yi~~l~~~~~~~s~Ra~i~l~raArA~Aal~GR~~V~pdDv~~~a~ 320 (350)
T CHL00081 265 KVEIDYDLRVKISQICSELDVDGLRGDIVTNRAAKALAAFEGRTEVTPKDIFKVIT 320 (350)
T ss_pred CCccCHHHHHHHHHHHHHHCCCCChHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 58899999998888887763 35667777788889999999999998865
No 97
>COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]
Probab=46.23 E-value=1e+02 Score=27.93 Aligned_cols=87 Identities=14% Similarity=0.240 Sum_probs=62.2
Q ss_pred cchhhccCchhHHHHHHhccccCCCCCC-----------------cccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcC
Q 032293 6 VVPEAEELPKTIVRRVVKDKLHNCSPDT-----------------DISVHKDALLAFCESARIFIHYLSATANDICKESK 68 (143)
Q Consensus 6 ~~~Ed~~LP~a~V~RI~K~~Lp~~~~~~-----------------~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~k 68 (143)
.+++.+.+--|||.|+++.....++ -| +---|++++-.+. -.-+...++
T Consensus 335 dvA~~i~~HESTISRai~nKy~~tp-rG~feLK~FFs~~i~s~~gg~~~S~~~Ik~~I-------------k~lI~~E~~ 400 (444)
T COG1508 335 DVADEIGMHESTISRAITNKYLATP-RGLFELKYFFSSSLASSEGGEASSTEAIKALI-------------KKLIEAEDK 400 (444)
T ss_pred HHHHHhCccHHHHHHHHhcccccCC-cceeeHHHHHHHhccCCCCCccccHHHHHHHH-------------HHHHhhccC
Confidence 4567888999999999999876654 11 1123332322221 124667788
Q ss_pred CCCCChHHHHHHHhhcCcccchHHHHHHHHHHHHHhhccccC
Q 032293 69 RQTINAEDVLKAIEEIDFTEFVDPLRDSLDEFRQKNAGKRAG 110 (143)
Q Consensus 69 RKTIs~eDVl~AL~~lgF~~yi~~l~~~l~~~ke~~~~Kk~~ 110 (143)
++.+|-..|..-|++-| ++.-+..+..||+...--.+.
T Consensus 401 ~~pLSD~kIa~lLkekG----i~iARRTVAKYRe~L~I~sS~ 438 (444)
T COG1508 401 KKPLSDSKIAELLKEKG----IDVARRTVAKYREELNIPSSS 438 (444)
T ss_pred CCCCCHHHHHHHHHHcC----CchhHHhHHHHHHHcCCCchh
Confidence 89999999999999887 678899999999998765544
No 98
>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=45.89 E-value=20 Score=21.75 Aligned_cols=24 Identities=25% Similarity=0.529 Sum_probs=20.2
Q ss_pred CChHHHHHHHhhcCcccchHHHHH
Q 032293 72 INAEDVLKAIEEIDFTEFVDPLRD 95 (143)
Q Consensus 72 Is~eDVl~AL~~lgF~~yi~~l~~ 95 (143)
-++++|..-|..+|++.|++.+..
T Consensus 2 w~~~~V~~wL~~~~~~~y~~~f~~ 25 (63)
T cd00166 2 WSPEDVAEWLESLGLGQYADNFRE 25 (63)
T ss_pred CCHHHHHHHHHHcChHHHHHHHHH
Confidence 367899999999999999888755
No 99
>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=45.11 E-value=30 Score=21.63 Aligned_cols=22 Identities=14% Similarity=0.430 Sum_probs=19.6
Q ss_pred ChHHHHHHHhhcCcccchHHHH
Q 032293 73 NAEDVLKAIEEIDFTEFVDPLR 94 (143)
Q Consensus 73 s~eDVl~AL~~lgF~~yi~~l~ 94 (143)
++++|..-|+.+|++.|++...
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 6789999999999999998773
No 100
>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=43.26 E-value=28 Score=25.82 Aligned_cols=61 Identities=10% Similarity=0.221 Sum_probs=41.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHhhcCcccchHHHHHHHHHHHHHh
Q 032293 40 DALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFTEFVDPLRDSLDEFRQKN 104 (143)
Q Consensus 40 dA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~lgF~~yi~~l~~~l~~~ke~~ 104 (143)
....-|..|..+.-.|......-... ---.-..++..|+..|++..+.+++..|++|+..+
T Consensus 73 ~Vk~Eiaa~~~v~~~Y~~~L~~G~vd----~e~~~~~~~~kLk~AGidkV~~E~QkQlda~~~~~ 133 (134)
T PF12010_consen 73 PVKNEIAACSNVWSEYYPPLETGLVD----PEEALPEFNEKLKAAGIDKVIAELQKQLDAFLAAN 133 (134)
T ss_pred hhHHHHHHHHHHHHHHHHHHHccCCC----HHHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHhc
Confidence 34555666666666665543333221 11124567888899999999999999999998754
No 101
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=42.63 E-value=71 Score=28.67 Aligned_cols=85 Identities=13% Similarity=0.201 Sum_probs=58.6
Q ss_pred cchhhccCchhHHHHHHhccccCCCCCC----------------cccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCC
Q 032293 6 VVPEAEELPKTIVRRVVKDKLHNCSPDT----------------DISVHKDALLAFCESARIFIHYLSATANDICKESKR 69 (143)
Q Consensus 6 ~~~Ed~~LP~a~V~RI~K~~Lp~~~~~~----------------~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kR 69 (143)
.+++.+.|..|||.|+++...=+++- | +--+|.+++... -..-|...+++
T Consensus 348 dvAe~lglheSTVSRav~~Kyv~tp~-Gi~~lk~FFs~~~~~~~g~~~S~~~Ik~~-------------Ik~lI~~Ed~~ 413 (455)
T PRK05932 348 DIAEELGMHESTISRATTNKYMATPR-GIFELKYFFSSAVSTDGGGEASSTAIRAL-------------IKKLIAAENPK 413 (455)
T ss_pred HHHHHhCCCccchhhhhcCceeecCC-ceEEHHHhcccccCCCCCccccHHHHHHH-------------HHHHHHhcCCC
Confidence 45788899999999999876544431 1 011333332211 12246678889
Q ss_pred CCCChHHHHHHHhhcCcccchHHHHHHHHHHHHHhhccc
Q 032293 70 QTINAEDVLKAIEEIDFTEFVDPLRDSLDEFRQKNAGKR 108 (143)
Q Consensus 70 KTIs~eDVl~AL~~lgF~~yi~~l~~~l~~~ke~~~~Kk 108 (143)
+.+|-+.|...|+.-|+ ..-+..+..||+...--.
T Consensus 414 ~PlSD~~I~~~L~~~Gi----~IaRRTVaKYRe~L~Ip~ 448 (455)
T PRK05932 414 KPLSDSKIAELLKEQGI----DVARRTVAKYREALNIPS 448 (455)
T ss_pred CCCCHHHHHHHHHHcCC----CeehHHHHHHHHHcCCCC
Confidence 99999999999999887 445788899999875433
No 102
>PF00531 Death: Death domain; InterPro: IPR000488 The death domain (DD) is a homotypic protein interaction module composed of a bundle of six alpha-helices. DD is related in sequence and structure to the death effector domain (DED, see IPR001875 from INTERPRO) and the caspase recruitment domain (CARD, see IPR001315 from INTERPRO), which work in similar pathways and show similar interaction properties []. DD bind each other forming oligomers. Mammals have numerous and diverse DD-containing proteins []. Within these proteins, the DD domains can be found in combination with other domains, including: CARDs, DEDs, ankyrin repeats (IPR002110 from INTERPRO), caspase-like folds, kinase domains, leucine zippers (IPR002158 from INTERPRO), leucine-rich repeats (LRR) (IPR001611 from INTERPRO), TIR domains (IPR000157 from INTERPRO), and ZU5 domains (IPR000906 from INTERPRO) []. Some DD-containing proteins are involved in the regulation of apoptosis and inflammation through their activation of caspases and NF-kappaB, which typically involves interactions with TNF (tumour necrosis factor) cytokine receptors [, ]. In humans, eight of the over 30 known TNF receptors contain DD in their cytoplasmic tails; several of these TNF receptors use caspase activation as a signalling mechanism. The DD mediates self-association of these receptors, thus giving the signal to downstream events that lead to apoptosis. Other DD-containing proteins, such as ankyrin, MyD88 and pelle, are probably not directly involved in cell death signalling. DD-containing proteins also have links to innate immunity, communicating with Toll family receptors through bipartite adapter proteins such as MyD88 [].; GO: 0005515 protein binding, 0007165 signal transduction; PDB: 3OQ9_L 3EZQ_F 1E41_A 1E3Y_A 2GF5_A 2OF5_L 3EWV_E 3G5B_A 3MOP_L 2A9I_A ....
Probab=42.34 E-value=57 Score=21.02 Aligned_cols=29 Identities=10% Similarity=0.370 Sum_probs=24.0
Q ss_pred CCCCChHHHHHHHhhcCcccchHHHHHHH
Q 032293 69 RQTINAEDVLKAIEEIDFTEFVDPLRDSL 97 (143)
Q Consensus 69 RKTIs~eDVl~AL~~lgF~~yi~~l~~~l 97 (143)
...-+..+++.||..+|..+-+..|+..|
T Consensus 55 ~~~at~~~L~~aL~~~~~~d~~~~i~~~~ 83 (83)
T PF00531_consen 55 GPNATVDQLIQALRDIGRNDLAEKIEQML 83 (83)
T ss_dssp GSTSSHHHHHHHHHHTTHHHHHHHHHHH-
T ss_pred CCCCcHHHHHHHHHHCCcHHHHHHHHhhC
Confidence 45667889999999999999988887754
No 103
>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=42.19 E-value=17 Score=22.25 Aligned_cols=19 Identities=32% Similarity=0.504 Sum_probs=14.2
Q ss_pred hhhccCchhHHHHHHhccc
Q 032293 8 PEAEELPKTIVRRVVKDKL 26 (143)
Q Consensus 8 ~Ed~~LP~a~V~RI~K~~L 26 (143)
.+.+.+|+++++|++..-.
T Consensus 25 a~~~gl~~stv~r~L~tL~ 43 (52)
T PF09339_consen 25 ARALGLPKSTVHRLLQTLV 43 (52)
T ss_dssp HHHHTS-HHHHHHHHHHHH
T ss_pred HHHHCcCHHHHHHHHHHHH
Confidence 4567899999999997643
No 104
>PRK13407 bchI magnesium chelatase subunit I; Provisional
Probab=40.65 E-value=94 Score=26.70 Aligned_cols=48 Identities=6% Similarity=0.007 Sum_probs=39.0
Q ss_pred cccccHHHHHHHHHHHHHHH-------HHHHHHHHHHhHhcCCCCCChHHHHHHH
Q 032293 34 DISVHKDALLAFCESARIFI-------HYLSATANDICKESKRQTINAEDVLKAI 81 (143)
Q Consensus 34 ~~~IskdA~~al~~~a~~FI-------~~lt~~A~~~a~~~kRKTIs~eDVl~AL 81 (143)
.+.|+.+....+.+.|..+= .+|...|.-.|--+||-.|+++||..+.
T Consensus 249 ~V~v~~~~~~yi~~l~~~~~~~s~Ra~i~l~~aA~a~A~l~Gr~~V~~~Di~~~~ 303 (334)
T PRK13407 249 QLKTPNTVLHDCAALCIALGSDGLRGELTLLRAARALAAFEGAEAVGRSHLRSVA 303 (334)
T ss_pred CcccCHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHHcCCCeeCHHHHHHHH
Confidence 58899999998888877653 2366778888889999999999997665
No 105
>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=40.04 E-value=63 Score=29.12 Aligned_cols=48 Identities=27% Similarity=0.309 Sum_probs=40.1
Q ss_pred cccccHHHHHHHHHHHHH----HHHHHHHHHHHHhHhcCCCCCChHHHHHHH
Q 032293 34 DISVHKDALLAFCESARI----FIHYLSATANDICKESKRQTINAEDVLKAI 81 (143)
Q Consensus 34 ~~~IskdA~~al~~~a~~----FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL 81 (143)
++.++.||.+.|..-.++ |..-|-.-|+.+|...|+++|..+||-.|-
T Consensus 378 ~i~l~~~Ale~L~~ig~etSLRYa~qLL~pa~iiA~~rg~~~V~~~dVe~a~ 429 (450)
T COG1224 378 DIELSDDALEYLTDIGEETSLRYAVQLLTPASIIAKRRGSKRVEVEDVERAK 429 (450)
T ss_pred ccccCHHHHHHHHhhchhhhHHHHHHhccHHHHHHHHhCCCeeehhHHHHHH
Confidence 688999999999865543 555566678999999999999999999984
No 106
>PRK13765 ATP-dependent protease Lon; Provisional
Probab=39.91 E-value=53 Score=30.82 Aligned_cols=47 Identities=26% Similarity=0.279 Sum_probs=37.6
Q ss_pred cccHHHHHHHHHHHHHH-------------HHHHHHHHHHHhHhcCCCCCChHHHHHHHh
Q 032293 36 SVHKDALLAFCESARIF-------------IHYLSATANDICKESKRQTINAEDVLKAIE 82 (143)
Q Consensus 36 ~IskdA~~al~~~a~~F-------------I~~lt~~A~~~a~~~kRKTIs~eDVl~AL~ 82 (143)
.|+.+|...|.+-++-- |.-|-.+|+.+|...+++.|+++||..|+.
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 58888888877765532 333677899999999999999999999984
No 107
>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]
Probab=39.62 E-value=50 Score=28.68 Aligned_cols=59 Identities=17% Similarity=0.156 Sum_probs=42.0
Q ss_pred ccccHHHHHHHHHHH------HHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHhhcCcccchHHH
Q 032293 35 ISVHKDALLAFCESA------RIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFTEFVDPL 93 (143)
Q Consensus 35 ~~IskdA~~al~~~a------~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~lgF~~yi~~l 93 (143)
-.++.++..++..-+ .-+...|...|-++|..+++.+|+.+||..|-+..+..-+...+
T Consensus 210 ~~~~~~vl~lia~~~a~~~GDAR~aidilr~A~eiAe~~~~~~v~~~~v~~a~~~~~~~~~~~~~ 274 (366)
T COG1474 210 GVIDDDVLKLIAALVAAESGDARKAIDILRRAGEIAEREGSRKVSEDHVREAQEEIERDVLEEVL 274 (366)
T ss_pred CCcCccHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHhhCCCCcCHHHHHHHHHHhhHHHHHHHH
Confidence 356666665555221 23455677889999999999999999999997777666555444
No 108
>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=39.61 E-value=1.1e+02 Score=28.29 Aligned_cols=49 Identities=14% Similarity=0.206 Sum_probs=37.4
Q ss_pred cccccHHHHHHHHHHHHHH-------HHHHHHHHHHHhHhcCCCCCChHHHHHHHh
Q 032293 34 DISVHKDALLAFCESARIF-------IHYLSATANDICKESKRQTINAEDVLKAIE 82 (143)
Q Consensus 34 ~~~IskdA~~al~~~a~~F-------I~~lt~~A~~~a~~~kRKTIs~eDVl~AL~ 82 (143)
.+.|+.+....|...|..+ -.++...|.-+|.=++|.+|+++||..|+.
T Consensus 201 ~V~i~~~~~~~l~~~~~~~gv~s~Ra~i~~~r~ArA~Aal~gr~~V~~~Dv~~a~~ 256 (589)
T TIGR02031 201 QVTISAEQVKELVLTAASLGISGHRADLFAVRAAKAHAALHGRTEVTEEDLKLAVE 256 (589)
T ss_pred CccCCHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHH
Confidence 5889999987777666443 124456666778889999999999999985
No 109
>PRK07914 hypothetical protein; Reviewed
Probab=39.10 E-value=75 Score=26.44 Aligned_cols=64 Identities=11% Similarity=0.203 Sum_probs=44.7
Q ss_pred chhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHh
Q 032293 14 PKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIE 82 (143)
Q Consensus 14 P~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~ 82 (143)
+..-+.+.|.+.+-. .+..|+.+|...|..++..=+..|..+-...+...+ .+|+.+||...+.
T Consensus 129 ~~~~l~~wi~~~a~~----~g~~i~~~A~~~L~~~~g~dl~~l~~EleKL~~~~~-~~It~e~V~~~v~ 192 (320)
T PRK07914 129 KAAERADFVRKEFRS----LRVKVDDDTVTALLDAVGSDLRELASACSQLVADTG-GAVDAAAVRRYHS 192 (320)
T ss_pred CHHHHHHHHHHHHHH----cCCCCCHHHHHHHHHHHCccHHHHHHHHHHHhcCCC-CCcCHHHHHHHcC
Confidence 455556666655542 257899999999999887656666666656554333 5799999988765
No 110
>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=38.90 E-value=53 Score=24.97 Aligned_cols=38 Identities=13% Similarity=0.218 Sum_probs=32.3
Q ss_pred CCCChHHHHHHHhhcCcc-----------cchHHHHHHHHHHHHHhhcc
Q 032293 70 QTINAEDVLKAIEEIDFT-----------EFVDPLRDSLDEFRQKNAGK 107 (143)
Q Consensus 70 KTIs~eDVl~AL~~lgF~-----------~yi~~l~~~l~~~ke~~~~K 107 (143)
-|.++.|++.+|+.+|++ .|++.+.+..+.-++.++.|
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 478899999999999986 38888888888888888777
No 111
>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=36.61 E-value=33 Score=20.91 Aligned_cols=26 Identities=23% Similarity=0.437 Sum_probs=20.8
Q ss_pred CCChHHHHHHHhhcCcccchHHHHHH
Q 032293 71 TINAEDVLKAIEEIDFTEFVDPLRDS 96 (143)
Q Consensus 71 TIs~eDVl~AL~~lgF~~yi~~l~~~ 96 (143)
.-+.++|..-|..+||+.|++.+...
T Consensus 3 ~w~~~~v~~wL~~~g~~~y~~~f~~~ 28 (68)
T smart00454 3 QWSPESVADWLESIGLEQYADNFRKN 28 (68)
T ss_pred CCCHHHHHHHHHHCChHHHHHHHHHC
Confidence 34678899999999999988877553
No 112
>TIGR01242 26Sp45 26S proteasome subunit P45 family. Many proteins may score above the trusted cutoff because an internal
Probab=35.37 E-value=59 Score=27.54 Aligned_cols=32 Identities=19% Similarity=0.330 Sum_probs=26.5
Q ss_pred HHHHHHHHHHHHhHhcCCCCCChHHHHHHHhh
Q 032293 52 FIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (143)
Q Consensus 52 FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~ 83 (143)
-|..|..+|...|...++..|+.+|+..|+..
T Consensus 331 dl~~l~~~A~~~a~~~~~~~i~~~d~~~a~~~ 362 (364)
T TIGR01242 331 DLKAICTEAGMFAIREERDYVTMDDFIKAVEK 362 (364)
T ss_pred HHHHHHHHHHHHHHHhCCCccCHHHHHHHHHH
Confidence 34566777888888889999999999999875
No 113
>PRK05574 holA DNA polymerase III subunit delta; Reviewed
Probab=34.73 E-value=1.5e+02 Score=24.22 Aligned_cols=67 Identities=15% Similarity=0.199 Sum_probs=46.8
Q ss_pred cCchhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhc-CCCCCChHHHHHHHhh
Q 032293 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKES-KRQTINAEDVLKAIEE 83 (143)
Q Consensus 12 ~LP~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~-kRKTIs~eDVl~AL~~ 83 (143)
.++...+.+.|+..+.. -+..|+.+|...|.+.+.-=+..+..+-..+|.-. +++ |+.+||-..+..
T Consensus 145 ~~~~~~~~~~i~~~~~~----~g~~i~~~a~~~L~~~~~~d~~~l~~El~KL~l~~~~~~-It~~~I~~~i~~ 212 (340)
T PRK05574 145 PPKEAELPQWIQQRLKQ----QGLQIDAAALQLLAERVEGNLLALAQELEKLALLYPDGK-ITLEDVEEAVPD 212 (340)
T ss_pred CCCHHHHHHHHHHHHHH----cCCCCCHHHHHHHHHHhCchHHHHHHHHHHHHhhcCCCC-CCHHHHHHHHhh
Confidence 45566666666666643 25789999999999888765666677777766533 333 999998776653
No 114
>PRK03992 proteasome-activating nucleotidase; Provisional
Probab=34.17 E-value=64 Score=27.92 Aligned_cols=35 Identities=26% Similarity=0.286 Sum_probs=27.4
Q ss_pred HHHHHHHHHHHHhHhcCCCCCChHHHHHHHhhcCc
Q 032293 52 FIHYLSATANDICKESKRQTINAEDVLKAIEEIDF 86 (143)
Q Consensus 52 FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~lgF 86 (143)
=|..|..+|...|...++..|+.+|+..|+...-.
T Consensus 340 dl~~l~~eA~~~a~~~~~~~i~~~d~~~A~~~~~~ 374 (389)
T PRK03992 340 DLKAICTEAGMFAIRDDRTEVTMEDFLKAIEKVMG 374 (389)
T ss_pred HHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHhc
Confidence 34556677777887888999999999999987543
No 115
>COG1724 Predicted RNA binding protein (dsRBD-like fold), HicA family [General function prediction only]
Probab=34.01 E-value=32 Score=23.28 Aligned_cols=17 Identities=35% Similarity=0.630 Sum_probs=15.4
Q ss_pred CCChHHHHHHHhhcCcc
Q 032293 71 TINAEDVLKAIEEIDFT 87 (143)
Q Consensus 71 TIs~eDVl~AL~~lgF~ 87 (143)
.+++.+|+++|+.+||.
T Consensus 6 ~~~~ke~ik~Le~~Gf~ 22 (66)
T COG1724 6 RMKAKEVIKALEKDGFQ 22 (66)
T ss_pred cCCHHHHHHHHHhCCcE
Confidence 57899999999999995
No 116
>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional
Probab=33.25 E-value=64 Score=28.84 Aligned_cols=32 Identities=22% Similarity=0.317 Sum_probs=27.4
Q ss_pred HHHHHHHHHHHhHhcCCCCCChHHHHHHHhhc
Q 032293 53 IHYLSATANDICKESKRQTINAEDVLKAIEEI 84 (143)
Q Consensus 53 I~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~l 84 (143)
|..|..+|-..|...+|..|+.+||..|++..
T Consensus 393 I~~i~~eA~~~Alr~~r~~Vt~~D~~~A~~~v 424 (438)
T PTZ00361 393 IKAICTEAGLLALRERRMKVTQADFRKAKEKV 424 (438)
T ss_pred HHHHHHHHHHHHHHhcCCccCHHHHHHHHHHH
Confidence 55677788889999999999999999999863
No 117
>PF08823 PG_binding_2: Putative peptidoglycan binding domain; InterPro: IPR014927 This entry may be a peptidoglycan binding domain.
Probab=32.49 E-value=91 Score=21.10 Aligned_cols=31 Identities=13% Similarity=0.355 Sum_probs=25.4
Q ss_pred HHHHHHHhhcCc------ccchHHHHHHHHHHHHHhh
Q 032293 75 EDVLKAIEEIDF------TEFVDPLRDSLDEFRQKNA 105 (143)
Q Consensus 75 eDVl~AL~~lgF------~~yi~~l~~~l~~~ke~~~ 105 (143)
..|..+|..||| +.|-..++..|..|.....
T Consensus 19 ~evq~~L~~lGyy~g~~~g~~d~a~~~Al~~~~g~EN 55 (74)
T PF08823_consen 19 REVQEALKRLGYYKGEADGVWDEATEDALRAWAGTEN 55 (74)
T ss_pred HHHHHHHHHcCCccCCCCCcccHHHHHHHHHHHHHhh
Confidence 467889999999 6788888999988877654
No 118
>PLN00138 large subunit ribosomal protein LP2; Provisional
Probab=32.16 E-value=1.3e+02 Score=22.04 Aligned_cols=28 Identities=14% Similarity=0.079 Sum_probs=24.5
Q ss_pred HHHHhHhcCCCCCChHHHHHHHhhcCcc
Q 032293 60 ANDICKESKRQTINAEDVLKAIEEIDFT 87 (143)
Q Consensus 60 A~~~a~~~kRKTIs~eDVl~AL~~lgF~ 87 (143)
|+-.|.-.+..++|.+||...|+..|.+
T Consensus 6 Ayll~~l~g~~~pta~dI~~IL~AaGve 33 (113)
T PLN00138 6 AYLLAVLGGNTCPSAEDLKDILGSVGAD 33 (113)
T ss_pred HHHHHHhcCCCCCCHHHHHHHHHHcCCc
Confidence 6677888888999999999999998865
No 119
>COG5248 TAF19 Transcription initiation factor TFIID, subunit TAF13 [Transcription]
Probab=31.87 E-value=1.7e+02 Score=21.90 Aligned_cols=47 Identities=19% Similarity=0.263 Sum_probs=39.8
Q ss_pred ccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHhh
Q 032293 35 ISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (143)
Q Consensus 35 ~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~ 83 (143)
+.-..|...+|.+...-+++.+-..|..+|. .|-.+..+|..-||+.
T Consensus 26 v~P~~dt~~~L~e~V~dY~~~~ctna~~~Aq--~rnK~k~eDfkfaLr~ 72 (126)
T COG5248 26 VAPRYDTAEALHEYVLDYMSILCTNAHNMAQ--VRNKTKTEDFKFALRR 72 (126)
T ss_pred CCcchhHHHHHHHHHHHHHHHHHHHHHHHHH--hcccchHHHHHHHHhh
Confidence 4556788999999999999999999999987 5566778999999984
No 120
>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=31.54 E-value=76 Score=24.13 Aligned_cols=42 Identities=17% Similarity=0.358 Sum_probs=34.1
Q ss_pred CCCChHHHHHHHhhcCccc------------chHHHHHHHHHHHHHhhccccCc
Q 032293 70 QTINAEDVLKAIEEIDFTE------------FVDPLRDSLDEFRQKNAGKRAGT 111 (143)
Q Consensus 70 KTIs~eDVl~AL~~lgF~~------------yi~~l~~~l~~~ke~~~~Kk~~~ 111 (143)
.|.++.|++.+|+.+++.. |++.+.+.+..-++.++.|-...
T Consensus 123 ~tt~~~~l~~~l~~l~~P~~~~~~~i~l~~r~ip~l~~~~~~i~~A~~~Rg~~~ 176 (224)
T PF02361_consen 123 LTTSPSDLISALRKLRLPYPKIALMISLTLRFIPLLLEEFKRIREAQRLRGVGI 176 (224)
T ss_pred HHCCHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCc
Confidence 5889999999999999887 88888888877777777665543
No 121
>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., PubMed:15231786). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations
Probab=31.42 E-value=1.5e+02 Score=26.42 Aligned_cols=87 Identities=17% Similarity=0.267 Sum_probs=58.9
Q ss_pred cchhhccCchhHHHHHHhccccCCCC----------------CCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCC
Q 032293 6 VVPEAEELPKTIVRRVVKDKLHNCSP----------------DTDISVHKDALLAFCESARIFIHYLSATANDICKESKR 69 (143)
Q Consensus 6 ~~~Ed~~LP~a~V~RI~K~~Lp~~~~----------------~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kR 69 (143)
.+++.+.+..|||.|+++...=+++- +++--+|.+++... -..-|...+++
T Consensus 323 diA~~lglheSTVSRav~~Kyi~tp~Gi~~lk~FFs~~~~~~~~g~~~S~~~Ik~~-------------I~~lI~~E~~~ 389 (429)
T TIGR02395 323 EVAEELGLHESTISRAINNKYLQTPRGVFELKYFFSRGVQTDSGEGEVSSTAIKAL-------------IKELIAAEDKR 389 (429)
T ss_pred HHHHHhCCCccchhhhhcCceEecCCceEEHHHhcCCccCCCCCCCccCHHHHHHH-------------HHHHHHhcCCC
Confidence 45788899999999999876544431 00011344332211 12246678889
Q ss_pred CCCChHHHHHHHhhcCcccchHHHHHHHHHHHHHhhcccc
Q 032293 70 QTINAEDVLKAIEEIDFTEFVDPLRDSLDEFRQKNAGKRA 109 (143)
Q Consensus 70 KTIs~eDVl~AL~~lgF~~yi~~l~~~l~~~ke~~~~Kk~ 109 (143)
+.+|-+.|...|+.-|+ ..-+..+..||+...--.+
T Consensus 390 ~PlSD~~I~~~L~~~Gi----~IaRRTVaKYRe~L~Ip~s 425 (429)
T TIGR02395 390 KPLSDQKIAELLKEKGI----KIARRTVAKYREELGIPSS 425 (429)
T ss_pred CCCCHHHHHHHHHhcCC----CeehHHHHHHHHHcCCCcc
Confidence 99999999999999885 4557888899998765433
No 122
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=31.21 E-value=1.4e+02 Score=27.15 Aligned_cols=85 Identities=13% Similarity=0.101 Sum_probs=57.6
Q ss_pred cchhhccCchhHHHHHHhccccCCCC---------------CCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCC
Q 032293 6 VVPEAEELPKTIVRRVVKDKLHNCSP---------------DTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQ 70 (143)
Q Consensus 6 ~~~Ed~~LP~a~V~RI~K~~Lp~~~~---------------~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRK 70 (143)
.+++.+.|.-+||.|++....=+++- +++--+|.+++..+- ..-|...++++
T Consensus 374 dVAe~lglHeSTVSRa~~~KY~~tp~GifeLK~FFs~~v~~~~g~~~Ss~~Ik~~I-------------k~lI~~Ed~~k 440 (481)
T PRK12469 374 DVAEELGLHESTISRATGNKYMATPRGTFEFKHFFPRKLEAAGGGECSAAAVRALI-------------KEMIAAEQAGD 440 (481)
T ss_pred HHHHHhCCCcchhhHHhcCceeecCCceEeHHHhhccccCCCCCccccHHHHHHHH-------------HHHHHhcCCCC
Confidence 45788899999999999877544431 001113333322211 12466778899
Q ss_pred CCChHHHHHHHhhcCcccchHHHHHHHHHHHHHhhcc
Q 032293 71 TINAEDVLKAIEEIDFTEFVDPLRDSLDEFRQKNAGK 107 (143)
Q Consensus 71 TIs~eDVl~AL~~lgF~~yi~~l~~~l~~~ke~~~~K 107 (143)
.+|-+.|..-|+.-|+ ..-+..+..||+...--
T Consensus 441 PLSD~~I~~~L~~~GI----~IARRTVAKYRe~L~Ip 473 (481)
T PRK12469 441 PLSDVALAEMLAGRGV----LIARRTVAKYREAMKIP 473 (481)
T ss_pred CCCHHHHHHHHHhcCC----CeechhHHHHHHHcCCC
Confidence 9999999999998887 34577888999987543
No 123
>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=30.86 E-value=96 Score=19.00 Aligned_cols=35 Identities=20% Similarity=0.223 Sum_probs=27.6
Q ss_pred hhhccCchhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHH
Q 032293 8 PEAEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARI 51 (143)
Q Consensus 8 ~Ed~~LP~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~ 51 (143)
.....+..++|.|++... -.||.+.+.-+.+++.+
T Consensus 6 A~~agvS~~TVSr~ln~~---------~~vs~~tr~rI~~~a~~ 40 (46)
T PF00356_consen 6 AREAGVSKSTVSRVLNGP---------PRVSEETRERILEAAEE 40 (46)
T ss_dssp HHHHTSSHHHHHHHHTTC---------SSSTHHHHHHHHHHHHH
T ss_pred HHHHCcCHHHHHHHHhCC---------CCCCHHHHHHHHHHHHH
Confidence 345578889999999875 26899999999887765
No 124
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=30.59 E-value=65 Score=18.30 Aligned_cols=38 Identities=13% Similarity=0.228 Sum_probs=23.7
Q ss_pred hhhccCchhHHHHHHhcc-ccCCCCCCcccccHHHHHHH
Q 032293 8 PEAEELPKTIVRRVVKDK-LHNCSPDTDISVHKDALLAF 45 (143)
Q Consensus 8 ~Ed~~LP~a~V~RI~K~~-Lp~~~~~~~~~IskdA~~al 45 (143)
.+-+.+++++|++++++. +|....++..++.++....+
T Consensus 8 a~~lgis~~ti~~~~~~g~i~~~~~g~~~~~~~~~l~~~ 46 (49)
T TIGR01764 8 AEYLGVSKDTVYRLIHEGELPAYRVGRHYRIPREDVDEY 46 (49)
T ss_pred HHHHCCCHHHHHHHHHcCCCCeEEeCCeEEEeHHHHHHH
Confidence 356789999999999887 44211123446666555443
No 125
>PRK02910 light-independent protochlorophyllide reductase subunit B; Provisional
Probab=30.18 E-value=1.1e+02 Score=27.63 Aligned_cols=52 Identities=12% Similarity=0.136 Sum_probs=40.0
Q ss_pred CcccccHHHHHHHHHHHHHHHHHHH-HHHHHHhHhcCCCCCChHHHHHHHhhcC
Q 032293 33 TDISVHKDALLAFCESARIFIHYLS-ATANDICKESKRQTINAEDVLKAIEEID 85 (143)
Q Consensus 33 ~~~~IskdA~~al~~~a~~FI~~lt-~~A~~~a~~~kRKTIs~eDVl~AL~~lg 85 (143)
+.+.++.||...|.+ .=-|+.-=. ..+-..|+..|...|+.+.|..|-..+|
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 367899999999965 555665333 4445589999999999999999977654
No 126
>PF14434 Imm6: Immunity protein Imm6
Probab=29.77 E-value=2.3e+02 Score=20.93 Aligned_cols=47 Identities=17% Similarity=0.274 Sum_probs=32.8
Q ss_pred HHHHHHHHHHH-----HHHHHHHHHHhHh--cCCCCCChHHHHHHHhhcCcccch
Q 032293 43 LAFCESARIFI-----HYLSATANDICKE--SKRQTINAEDVLKAIEEIDFTEFV 90 (143)
Q Consensus 43 ~al~~~a~~FI-----~~lt~~A~~~a~~--~kRKTIs~eDVl~AL~~lgF~~yi 90 (143)
..|.++...+| .++..+|.+.|.. +| +.++|+++..-|.+.+|.+..
T Consensus 8 l~iae~~~~~I~~~~~~~~~~~aL~~cw~wle~-~~~~~D~LY~lldn~D~~gi~ 61 (122)
T PF14434_consen 8 LAIAEKLVDYIKKSEYGEFVREALDACWKWLEG-KEVTGDELYSLLDNEDENGIF 61 (122)
T ss_pred HHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHc-CCCCHHHHHHHHhCcccccHH
Confidence 34444444444 3444888888864 44 899999999999987776544
No 127
>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=29.75 E-value=18 Score=27.26 Aligned_cols=36 Identities=17% Similarity=0.351 Sum_probs=0.0
Q ss_pred HhcCCCCCChHHHHHHHhhcCcc-cchHHHHHHHHHH
Q 032293 65 KESKRQTINAEDVLKAIEEIDFT-EFVDPLRDSLDEF 100 (143)
Q Consensus 65 ~~~kRKTIs~eDVl~AL~~lgF~-~yi~~l~~~l~~~ 100 (143)
+..|-||||+.|+.-|-+.|+|- .++|.++.+++.+
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 34678999999999999999974 7889999888776
No 128
>PTZ00373 60S Acidic ribosomal protein P2; Provisional
Probab=29.35 E-value=1.7e+02 Score=21.53 Aligned_cols=28 Identities=11% Similarity=0.215 Sum_probs=24.2
Q ss_pred HHHHhHhcCCCCCChHHHHHHHhhcCcc
Q 032293 60 ANDICKESKRQTINAEDVLKAIEEIDFT 87 (143)
Q Consensus 60 A~~~a~~~kRKTIs~eDVl~AL~~lgF~ 87 (143)
|+-.|.-.|..+||.+||...|+..|.+
T Consensus 8 AYlL~~lgG~~~pTaddI~kIL~AaGve 35 (112)
T PTZ00373 8 AYLMCVLGGNENPTKKEVKNVLSAVNAD 35 (112)
T ss_pred HHHHHHHcCCCCCCHHHHHHHHHHcCCC
Confidence 5677778889999999999999988864
No 129
>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=28.93 E-value=49 Score=20.35 Aligned_cols=16 Identities=25% Similarity=0.547 Sum_probs=13.9
Q ss_pred CChHHHHHHHhhcCcc
Q 032293 72 INAEDVLKAIEEIDFT 87 (143)
Q Consensus 72 Is~eDVl~AL~~lgF~ 87 (143)
++.++|..+|+.+||.
T Consensus 47 ~~~~~i~~~i~~~Gy~ 62 (62)
T PF00403_consen 47 TSIEKIIEAIEKAGYE 62 (62)
T ss_dssp SCHHHHHHHHHHTTSE
T ss_pred CCHHHHHHHHHHhCcC
Confidence 6779999999999984
No 130
>COG1500 Predicted exosome subunit [Translation, ribosomal structure and biogenesis]
Probab=28.85 E-value=2.2e+02 Score=23.74 Aligned_cols=73 Identities=18% Similarity=0.207 Sum_probs=52.6
Q ss_pred chhHHHHHHhccccCCCCCCcccccHHHHHHHHHHH-HHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHhhcCcc-cchH
Q 032293 14 PKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESA-RIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFT-EFVD 91 (143)
Q Consensus 14 P~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a-~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~lgF~-~yi~ 91 (143)
--+-+..|+.+.|.. |.+.++.+-+..|++.- ...|++|+..|.+ -..+....+.-|-.||++++|. ++..
T Consensus 68 gTtd~~eI~~eIl~k----GeiQlTaeqR~~m~e~k~rqIi~~IsRn~Id---P~t~~P~Pp~rIe~Ameeakv~id~~K 140 (234)
T COG1500 68 GTTDPDEIAEEILKK----GEIQLTAEQRREMLEEKKRQIINIISRNAID---PQTKAPHPPARIEKAMEEAKVHIDPFK 140 (234)
T ss_pred CCCCHHHHHHHHHhc----CceeccHHHHHHHHHHHHHHHHHHHHHhccC---CCCCCCCCHHHHHHHHHhcCcccCCCC
Confidence 334467777777754 67899999887776655 4566688876554 3456789999999999999997 4444
Q ss_pred HH
Q 032293 92 PL 93 (143)
Q Consensus 92 ~l 93 (143)
+.
T Consensus 141 ~a 142 (234)
T COG1500 141 SA 142 (234)
T ss_pred CH
Confidence 44
No 131
>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=28.71 E-value=66 Score=17.33 Aligned_cols=26 Identities=12% Similarity=0.181 Sum_probs=18.7
Q ss_pred HHHHhHhcCCCCCChHHHHHHHh-hcC
Q 032293 60 ANDICKESKRQTINAEDVLKAIE-EID 85 (143)
Q Consensus 60 A~~~a~~~kRKTIs~eDVl~AL~-~lg 85 (143)
+....-.++--+|+.+++..+|. .||
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 34445566777899999999998 576
No 132
>PRK06585 holA DNA polymerase III subunit delta; Reviewed
Probab=28.62 E-value=1.9e+02 Score=23.97 Aligned_cols=63 Identities=13% Similarity=0.098 Sum_probs=42.2
Q ss_pred hHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHh-cCCCCCChHHHHHHHh
Q 032293 16 TIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKE-SKRQTINAEDVLKAIE 82 (143)
Q Consensus 16 a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~-~kRKTIs~eDVl~AL~ 82 (143)
..+.+.|.+.+.. .+.+|+.+|...|.+++.-=...+..+-..++.- .+..+|+.+||...+.
T Consensus 145 ~~l~~~i~~~~~~----~g~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~It~edV~~lv~ 208 (343)
T PRK06585 145 RDLARLIDDELAE----AGLRITPDARALLVALLGGDRLASRNEIEKLALYAHGKGEITLDDVRAVVG 208 (343)
T ss_pred HHHHHHHHHHHHH----CCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHhC
Confidence 3444444444432 2689999999999998876555555555555553 4457899999977755
No 133
>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional
Probab=27.75 E-value=94 Score=27.28 Aligned_cols=32 Identities=19% Similarity=0.172 Sum_probs=27.1
Q ss_pred HHHHHHHHHHHhHhcCCCCCChHHHHHHHhhc
Q 032293 53 IHYLSATANDICKESKRQTINAEDVLKAIEEI 84 (143)
Q Consensus 53 I~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~l 84 (143)
|..|..+|...|...+|..|+.+|+..|+...
T Consensus 355 I~~l~~eA~~~A~r~~~~~i~~~df~~A~~~v 386 (398)
T PTZ00454 355 IAAICQEAGMQAVRKNRYVILPKDFEKGYKTV 386 (398)
T ss_pred HHHHHHHHHHHHHHcCCCccCHHHHHHHHHHH
Confidence 56677788888888899999999999998753
No 134
>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=27.10 Aligned_cols=51 Identities=14% Similarity=0.231 Sum_probs=39.2
Q ss_pred cccccHHHHHHHHHHHHHHHH-HHHHHHHHHhHhcCCCCCChHHHHHHHhhcC
Q 032293 34 DISVHKDALLAFCESARIFIH-YLSATANDICKESKRQTINAEDVLKAIEEID 85 (143)
Q Consensus 34 ~~~IskdA~~al~~~a~~FI~-~lt~~A~~~a~~~kRKTIs~eDVl~AL~~lg 85 (143)
.+.++.||...|.+ .=-|+. -+=..+-..|+.+|...|+.+.|..|=..+|
T Consensus 460 ~~~w~~ea~~~l~~-~P~f~r~~~r~~~e~~a~~~g~~~it~~~~~~a~~~~~ 511 (511)
T TIGR01278 460 ELGWTAEAEAELKK-VPFFVRGKVRRNTENFARERGYSVITLEVIYAAKEHFG 511 (511)
T ss_pred CCCcCHHHHHHHhh-CChhhhHHHHHHHHHHHHHcCCCEEcHHHHHHHHHhcC
Confidence 57899999999964 445555 3344455589999999999999999976654
No 135
>smart00350 MCM minichromosome maintenance proteins.
Probab=26.68 E-value=1.9e+02 Score=26.01 Aligned_cols=69 Identities=10% Similarity=0.114 Sum_probs=43.0
Q ss_pred cCchhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHH-------------------HHHHHHHHHHHHhHhcCCCCC
Q 032293 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARI-------------------FIHYLSATANDICKESKRQTI 72 (143)
Q Consensus 12 ~LP~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~-------------------FI~~lt~~A~~~a~~~kRKTI 72 (143)
.++...+.+.+.-+=... .-.||.++...|.+.... .+..|...|.-.|.-.+|.+|
T Consensus 417 ~~~~~~l~~yi~~ar~~~----~P~ls~~~~~~i~~~y~~~R~~~~~~~~~~~~~~t~R~l~sliRla~A~A~l~~r~~V 492 (509)
T smart00350 417 PISQEFLRKYIAYAREKI----KPKLSEEAAEKLVKAYVDLRKEDSQSEARSSIPITVRQLESIIRLSEAHAKMRLSDVV 492 (509)
T ss_pred cCCHHHHHHHHHHHHhcC----CCCCCHHHHHHHHHHHHHhcccccccccccccCcCHHHHHHHHHHHHHHHHHcCCCcc
Confidence 355555555553331000 114788888877654433 224455666677888899999
Q ss_pred ChHHHHHHHhhc
Q 032293 73 NAEDVLKAIEEI 84 (143)
Q Consensus 73 s~eDVl~AL~~l 84 (143)
+++||..|++-+
T Consensus 493 ~~~Dv~~ai~l~ 504 (509)
T smart00350 493 EEADVEEAIRLL 504 (509)
T ss_pred CHHHHHHHHHHH
Confidence 999999998644
No 136
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=25.90 E-value=1.6e+02 Score=19.86 Aligned_cols=28 Identities=4% Similarity=0.014 Sum_probs=19.4
Q ss_pred HHHHhHhcCCCCCChHHHHHHHhhcCcc
Q 032293 60 ANDICKESKRQTINAEDVLKAIEEIDFT 87 (143)
Q Consensus 60 A~~~a~~~kRKTIs~eDVl~AL~~lgF~ 87 (143)
+...+-.++.-+|+.++|..+|..+|+.
T Consensus 15 ~F~~~D~d~~G~Is~~el~~~l~~~~~~ 42 (96)
T smart00027 15 IFRSLDKNQDGTVTGAQAKPILLKSGLP 42 (96)
T ss_pred HHHHhCCCCCCeEeHHHHHHHHHHcCCC
Confidence 3444555666778888888888877764
No 137
>cd05833 Ribosomal_P2 Ribosomal protein P2. This subfamily represents the eukaryotic large ribosomal protein P2. Eukaryotic P1 and P2 are functionally equivalent to the bacterial protein L7/L12, but are not homologous to L7/L12. P2 is located in the L12 stalk, with proteins P1, P0, L11, and 28S rRNA. P1 and P2 are the only proteins in the ribosome to occur as multimers, always appearing as sets of heterodimers. Recent data indicate that eukaryotes have four copies (two heterodimers), while most archaeal species contain six copies of L12p (three homodimers). Bacteria may have four or six copies of L7/L12 (two or three homodimers) depending on the species. Experiments using S. cerevisiae P1 and P2 indicate that P1 proteins are positioned more internally with limited reactivity in the C-terminal domains, while P2 proteins seem to be more externally located and are more likely to interact with other cellular components. In lower eukaryotes, P1 and P2 are further subdivided into P1A, P1B, P2
Probab=24.60 E-value=2.2e+02 Score=20.66 Aligned_cols=28 Identities=18% Similarity=0.136 Sum_probs=23.8
Q ss_pred HHHHhHhcCCCCCChHHHHHHHhhcCcc
Q 032293 60 ANDICKESKRQTINAEDVLKAIEEIDFT 87 (143)
Q Consensus 60 A~~~a~~~kRKTIs~eDVl~AL~~lgF~ 87 (143)
|+-.|.-.|..+||.+||...|+..|.+
T Consensus 6 AylL~~l~g~~~pTa~dI~~IL~AaGve 33 (109)
T cd05833 6 AYLLAVLGGNASPSAADVKKILGSVGVE 33 (109)
T ss_pred HHHHHHHcCCCCCCHHHHHHHHHHcCCC
Confidence 5667777888899999999999988864
No 138
>PRK00440 rfc replication factor C small subunit; Reviewed
Probab=24.07 E-value=2.2e+02 Score=22.78 Aligned_cols=66 Identities=18% Similarity=0.126 Sum_probs=39.2
Q ss_pred CchhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHhhc
Q 032293 13 LPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEI 84 (143)
Q Consensus 13 LP~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~~l 84 (143)
++..-+.+++...+.. .++.|+.++...|.+.+.-=+..+-......+.. .++|+.+||..++...
T Consensus 161 l~~~ei~~~l~~~~~~----~~~~i~~~al~~l~~~~~gd~r~~~~~l~~~~~~--~~~it~~~v~~~~~~~ 226 (319)
T PRK00440 161 LKKEAVAERLRYIAEN----EGIEITDDALEAIYYVSEGDMRKAINALQAAAAT--GKEVTEEAVYKITGTA 226 (319)
T ss_pred CCHHHHHHHHHHHHHH----cCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHc--CCCCCHHHHHHHhCCC
Confidence 4445555566555532 1467899998888877653333322222223322 3689999999887543
No 139
>PF03484 B5: tRNA synthetase B5 domain; InterPro: IPR005147 Domain B5 is found in phenylalanine-tRNA synthetase beta subunits. This domain has been shown to bind DNA through a winged helix-turn-helix motif []. Phenylalanine-tRNA synthetase may influence common cellular processes via DNA binding, in addition to its aminoacylation function.; GO: 0000287 magnesium ion binding, 0003723 RNA binding, 0005524 ATP binding, 0006432 phenylalanyl-tRNA aminoacylation; PDB: 2AKW_B 1B70_B 1B7Y_B 2ALY_B 2IY5_B 2AMC_B 3PCO_D 2CXI_C 1JJC_B 1EIY_B ....
Probab=22.98 E-value=59 Score=21.20 Aligned_cols=19 Identities=21% Similarity=0.534 Sum_probs=13.2
Q ss_pred CCCChHHHHHHHhhcCccc
Q 032293 70 QTINAEDVLKAIEEIDFTE 88 (143)
Q Consensus 70 KTIs~eDVl~AL~~lgF~~ 88 (143)
..++.++|...|+.|||.-
T Consensus 17 ~~i~~~~i~~~L~~lg~~~ 35 (70)
T PF03484_consen 17 IDISPEEIIKILKRLGFKV 35 (70)
T ss_dssp S---HHHHHHHHHHTT-EE
T ss_pred CCCCHHHHHHHHHHCCCEE
Confidence 3789999999999999973
No 140
>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=22.87 E-value=63 Score=24.84 Aligned_cols=52 Identities=17% Similarity=0.257 Sum_probs=38.9
Q ss_pred HHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHH
Q 032293 19 RRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDV 77 (143)
Q Consensus 19 ~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDV 77 (143)
.|+++.+. +.-|-|+-..-+....+.=+.-|.--|...|..+||-+|.+.|+
T Consensus 2 e~lFR~aa-------~LdvdK~d~~r~~d~V~~Kl~DLl~va~~~Ak~ngRdvI~~~DL 53 (138)
T PF09123_consen 2 ERLFRKAA-------GLDVDKNDAKRYSDFVEKKLYDLLLVAQENAKANGRDVIEPRDL 53 (138)
T ss_dssp HHHHHHHH-------S----HHHHHHHHHHHHHHHHHCCCCHHHHHHHTT-SEE-GGGS
T ss_pred hHHHHHHh-------ccCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeeccccC
Confidence 57777776 46677888888888888888888889999999999999999885
No 141
>PRK14971 DNA polymerase III subunits gamma and tau; Provisional
Probab=21.57 E-value=2.3e+02 Score=26.39 Aligned_cols=65 Identities=9% Similarity=0.080 Sum_probs=34.9
Q ss_pred CchhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHh
Q 032293 13 LPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIE 82 (143)
Q Consensus 13 LP~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~ 82 (143)
|+..-+.+.++..+.. .++.++.++..+|...+.-=+..+-......+.-.++. |+.++|...+.
T Consensus 180 ls~~ei~~~L~~ia~~----egi~i~~~al~~La~~s~gdlr~al~~Lekl~~y~~~~-It~~~V~~~l~ 244 (614)
T PRK14971 180 IQVADIVNHLQYVASK----EGITAEPEALNVIAQKADGGMRDALSIFDQVVSFTGGN-ITYKSVIENLN 244 (614)
T ss_pred CCHHHHHHHHHHHHHH----cCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhccCC-ccHHHHHHHhC
Confidence 4445555555554432 14778888888877765433333333333333222333 77777766554
No 142
>PF03979 Sigma70_r1_1: Sigma-70 factor, region 1.1; InterPro: IPR007127 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. This entry represents Region 1.1 which modulates DNA binding by region 2 and 4 when sigma is unbound by the core RNA polymerase [, ]. Region 1.1 is also involved in promoter binding.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2K6X_A.
Probab=21.45 E-value=1.2e+02 Score=20.37 Aligned_cols=44 Identities=23% Similarity=0.320 Sum_probs=23.4
Q ss_pred HhHhcCCCCCChHHHHHHHhhcCcc-cchHHHHHHHHHHHHHhhc
Q 032293 63 ICKESKRQTINAEDVLKAIEEIDFT-EFVDPLRDSLDEFRQKNAG 106 (143)
Q Consensus 63 ~a~~~kRKTIs~eDVl~AL~~lgF~-~yi~~l~~~l~~~ke~~~~ 106 (143)
+....+|..||+++|..+|....|+ +-++.+-..|+..--.+..
T Consensus 13 i~~gK~~G~lT~~eI~~~L~~~~~~~e~id~i~~~L~~~gI~Vvd 57 (82)
T PF03979_consen 13 IEKGKKKGYLTYDEINDALPEDDLDPEQIDEIYDTLEDEGIEVVD 57 (82)
T ss_dssp HHHHHHHSS-BHHHHHHH-S-S---HHHHHHHHHHHHTT----B-
T ss_pred HHHHhhcCcCCHHHHHHHcCccCCCHHHHHHHHHHHHHCCCEEec
Confidence 3334455689999999999988775 5667777777665554444
No 143
>PRK08487 DNA polymerase III subunit delta; Validated
Probab=21.40 E-value=2.8e+02 Score=23.12 Aligned_cols=64 Identities=6% Similarity=0.079 Sum_probs=41.5
Q ss_pred CchhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHh
Q 032293 13 LPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIE 82 (143)
Q Consensus 13 LP~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~ 82 (143)
++..-+.+.|.+.+-. .+..|+.+|...|...+.-=...+..+-...+.=.+ +||.+||...+.
T Consensus 135 ~~~~~l~~~i~~~~~~----~g~~i~~~a~~~L~~~~g~dl~~l~~ELeKL~ly~~--~It~edV~~~v~ 198 (328)
T PRK08487 135 PNAREALELLQERAKE----LGLDIDQNALNHLYFIHNEDLALAANELEKLAILNE--PITLKDIQELVF 198 (328)
T ss_pred CCHHHHHHHHHHHHHH----hCCCCCHHHHHHHHHHhCcHHHHHHHHHHHHHHhcC--CCCHHHHHHHhc
Confidence 3334445555555432 257899999999988877555555555555554433 799999998874
No 144
>PF13713 BRX_N: Transcription factor BRX N-terminal domain
Probab=21.05 E-value=1.5e+02 Score=17.98 Aligned_cols=21 Identities=29% Similarity=0.581 Sum_probs=17.7
Q ss_pred HHHHHHHHHHHHHHHHHHhHh
Q 032293 46 CESARIFIHYLSATANDICKE 66 (143)
Q Consensus 46 ~~~a~~FI~~lt~~A~~~a~~ 66 (143)
.+++.+||-.||++-.+++.+
T Consensus 7 ~kaaKe~IKsLt~QlK~maek 27 (39)
T PF13713_consen 7 CKAAKEVIKSLTAQLKDMAEK 27 (39)
T ss_pred cHHHHHHHHHHHHHHHHHHHh
Confidence 467889999999999988864
No 145
>PF12668 DUF3791: Protein of unknown function (DUF3791); InterPro: IPR024269 This entry represents proteins of unknown function.
Probab=21.00 E-value=1e+02 Score=19.75 Aligned_cols=30 Identities=17% Similarity=0.295 Sum_probs=24.1
Q ss_pred CCCCCChHHHHHHHhhcCcccchHHHHHHH
Q 032293 68 KRQTINAEDVLKAIEEIDFTEFVDPLRDSL 97 (143)
Q Consensus 68 kRKTIs~eDVl~AL~~lgF~~yi~~l~~~l 97 (143)
.|.-|++.+++.-+.+.|.-+|+.+.-..|
T Consensus 13 ~~~~~s~~ea~~~~~~~~~~~~i~~~Yd~l 42 (62)
T PF12668_consen 13 KKLNISGEEAYNYFKRSGVIDYIIDCYDVL 42 (62)
T ss_pred HHHCcCHHHHHHHHHHcCcHHHHHHcchHH
Confidence 467799999999999999777887765544
No 146
>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA.
Probab=20.87 E-value=3.3e+02 Score=25.68 Aligned_cols=37 Identities=16% Similarity=0.083 Sum_probs=27.5
Q ss_pred cccccHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCCCCCChHHHHHHHh
Q 032293 34 DISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIE 82 (143)
Q Consensus 34 ~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTIs~eDVl~AL~ 82 (143)
...+|..++.+|..| ...|...+...|+.+|++.||=
T Consensus 75 ~~~~S~~lk~vL~~A------------~~~A~~~g~~~I~teHLLLALl 111 (731)
T TIGR02639 75 DPEQTVGVQRVLQRA------------LLHVKSAGKKEIGIGDILVALF 111 (731)
T ss_pred CCCcCHHHHHHHHHH------------HHHHHHcCCCccCHHHHHHHHh
Confidence 345777777777653 4456667889999999999874
No 147
>CHL00076 chlB photochlorophyllide reductase subunit B
Probab=20.70 E-value=2.2e+02 Score=25.84 Aligned_cols=51 Identities=14% Similarity=0.215 Sum_probs=40.3
Q ss_pred cccccHHHHHHHHHHHHHHHHH-HHHHHHHHhHhcCCCCCChHHHHHHHhhcC
Q 032293 34 DISVHKDALLAFCESARIFIHY-LSATANDICKESKRQTINAEDVLKAIEEID 85 (143)
Q Consensus 34 ~~~IskdA~~al~~~a~~FI~~-lt~~A~~~a~~~kRKTIs~eDVl~AL~~lg 85 (143)
.+.++.||...|.+. =-|+.- +=..+-..|+.+|...||.+.|..|=..+|
T Consensus 461 ~~~w~~ea~~~l~~i-P~f~r~~~r~~~e~~a~~~g~~~it~~~~~~a~~~~~ 512 (513)
T CHL00076 461 DLIWSPESQLELSKI-PGFVRGKVKRNTEKFARQNGITNITVEVMYAAKEALS 512 (513)
T ss_pred CCCCCHHHHHHHHhC-CHHhHHHHHHHHHHHHHHcCCCeEcHHHHHHHHHhhC
Confidence 578999999999987 555543 334455589999999999999999976665
No 148
>PRK12728 fliE flagellar hook-basal body protein FliE; Provisional
Probab=20.61 E-value=3.3e+02 Score=19.50 Aligned_cols=91 Identities=13% Similarity=0.070 Sum_probs=54.1
Q ss_pred ccCchhHHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHH--hHhcCCCCCChHHHHHHHhhcC--c
Q 032293 11 EELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDI--CKESKRQTINAEDVLKAIEEID--F 86 (143)
Q Consensus 11 ~~LP~a~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~--a~~~kRKTIs~eDVl~AL~~lg--F 86 (143)
..+|.+.|.-.-....+..-. ...-...+-.+|..+... ++..-..|... +-..|. +++..||+-|++..+ |
T Consensus 5 ~~~~~~~~~~~~~~~~~~~~~--~~~~~~sF~~~L~~ai~~-vn~~q~~a~~~~~~~~~G~-~~~lhevmiA~~kA~lsl 80 (102)
T PRK12728 5 EISPNQKVFDQNGSNKTNKNN--PAEAQKSFSDFLKEALNK-VNELQVEADNSTEKLVKGE-IVDLHDVMIAAQKASISL 80 (102)
T ss_pred cccCCcccccccccccCcccC--CCCCccCHHHHHHHHHHH-HHHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHHHHHHH
Confidence 345666655554444432100 011233466677666666 44444444442 234454 899999999999654 6
Q ss_pred ccchHHHHHHHHHHHHHhh
Q 032293 87 TEFVDPLRDSLDEFRQKNA 105 (143)
Q Consensus 87 ~~yi~~l~~~l~~~ke~~~ 105 (143)
.-.+..-...++.|++..+
T Consensus 81 q~~vqVRNKlv~AYqEIMr 99 (102)
T PRK12728 81 QLTVQIRNKVVEAYQEIMR 99 (102)
T ss_pred HHHHHHHHHHHHHHHHHHh
Confidence 6667777888999998753
No 149
>COG1466 HolA DNA polymerase III, delta subunit [DNA replication, recombination, and repair]
Probab=20.30 E-value=3.7e+02 Score=22.53 Aligned_cols=62 Identities=11% Similarity=0.223 Sum_probs=44.6
Q ss_pred HHHHHHhccccCCCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHHhH-hcCCCCCChHHHHHHHhh
Q 032293 17 IVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICK-ESKRQTINAEDVLKAIEE 83 (143)
Q Consensus 17 ~V~RI~K~~Lp~~~~~~~~~IskdA~~al~~~a~~FI~~lt~~A~~~a~-~~kRKTIs~eDVl~AL~~ 83 (143)
.+.+.|+..+-. -+++|+.+|...|..+..-=...+.++=+..+- ..++ +|+.+||..++-.
T Consensus 144 ~l~~~i~~~~~~----~~l~i~~~a~~~L~~~~~~nl~~i~~Ei~KL~l~~~~~-~I~~~~V~~~v~~ 206 (334)
T COG1466 144 ELPQWIKKRAKE----LGLKIDQEAIQLLLEALGGNLLAIAQEIEKLALYAGDK-EITLEDVEEVVSD 206 (334)
T ss_pred HHHHHHHHHHHH----cCCCCCHHHHHHHHHHhCCcHHHHHHHHHHHHHhCCCC-cCCHHHHHHHHhc
Confidence 445555555432 268999999999999888656666666666554 4555 9999999998875
No 150
>KOG0093 consensus GTPase Rab3, small G protein superfamily [Intracellular trafficking, secretion, and vesicular transport]
Probab=20.04 E-value=54 Score=26.15 Aligned_cols=55 Identities=13% Similarity=0.210 Sum_probs=37.1
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHH-----HHHhHhcCCCCCChHHHHHHHhhcCcccchHH
Q 032293 38 HKDALLAFCESARIFIHYLSATA-----NDICKESKRQTINAEDVLKAIEEIDFTEFVDP 92 (143)
Q Consensus 38 skdA~~al~~~a~~FI~~lt~~A-----~~~a~~~kRKTIs~eDVl~AL~~lgF~~yi~~ 92 (143)
..++..+++.-++..-+|--..| -..|.-+.-++|+.+.+..-.++|||+-|-..
T Consensus 105 NeeSf~svqdw~tqIktysw~naqvilvgnKCDmd~eRvis~e~g~~l~~~LGfefFEtS 164 (193)
T KOG0093|consen 105 NEESFNSVQDWITQIKTYSWDNAQVILVGNKCDMDSERVISHERGRQLADQLGFEFFETS 164 (193)
T ss_pred CHHHHHHHHHHHHHheeeeccCceEEEEecccCCccceeeeHHHHHHHHHHhChHHhhhc
Confidence 45566667766666555521111 12466677899999999999999999766543
No 151
>PF03130 HEAT_PBS: PBS lyase HEAT-like repeat; InterPro: IPR004155 These proteins contain a short bi-helical repeat that is related to HEAT. Cyanobacteria and red algae harvest light energy using macromolecular complexes known as phycobilisomes (PBS), peripherally attached to the photosynthetic membrane. The major components of PBS are the phycobiliproteins. These heterodimeric proteins are covalently attached to phycobilins: open-chain tetrapyrrole chromophores, which function as the photosynthetic light-harvesting pigments. Phycobiliproteins differ in sequence and in the nature and number of attached phycobilins to each of their subunits. These proteins include the lyase enzymes that specifically attach particular phycobilins to apophycobiliprotein subunits. The most comprehensively studied of these is the CpcE/Flyase P31967 from SWISSPROT, P31968 from SWISSPROT, which attaches phycocyanobilin (PCB) to the alpha subunit of apophycocyanin []. Similarly, MpeU/V attaches phycoerythrobilin to phycoerythrin II, while CpeY/Z is thought to be involved in phycoerythrobilin (PEB) attachment to phycoerythrin (PE) I (PEs I and II differ in sequence and in the number of attached molecules of PEB: PE I has five, PE II has six) []. All the reactions of the above lyases involve an apoprotein cysteine SH addition to a terminal delta 3,3'-double bond. Such a reaction is not possible in the case of phycoviolobilin (PVB), the phycobilin of alpha-phycoerythrocyanin (alpha-PEC). It is thought that in this case, PCB, not PVB, is first added to apo-alpha-PEC, and is then isomerized to PVB. The addition reaction has been shown to occur in the presence of either of the components of alpha-PEC-PVB lyase PecE or PecF (or both). The isomerisation reaction occurs only when both PecE and PecF components are present, i.e. the PecE/F phycobiliprotein lyase is also a phycobilin isomerase []. Another member of this family is the NblB protein, whose similarity to the phycobiliprotein lyases was previously noted []. This constitutively expressed protein is not known to have any lyase activity. It is thought to be involved in the coordination of PBS degradation with environmental nutrient limitation. It has been suggested that the similarity of NblB to the phycobiliprotein lyases is due to the ability to bind tetrapyrrole phycobilins via the common repeated motif [].; PDB: 1TE4_A.
Probab=20.02 E-value=1.2e+02 Score=16.05 Aligned_cols=23 Identities=17% Similarity=0.335 Sum_probs=17.6
Q ss_pred HHHHHhhcCcccchHHHHHHHHH
Q 032293 77 VLKAIEEIDFTEFVDPLRDSLDE 99 (143)
Q Consensus 77 Vl~AL~~lgF~~yi~~l~~~l~~ 99 (143)
...+|-.+|-...+++|...|+.
T Consensus 5 Aa~aLg~igd~~ai~~L~~~L~d 27 (27)
T PF03130_consen 5 AARALGQIGDPRAIPALIEALED 27 (27)
T ss_dssp HHHHHGGG-SHHHHHHHHHHHHH
T ss_pred HHHHHHHcCCHHHHHHHHHHhcC
Confidence 46788888888999999888763
Done!