Query 033283
Match_columns 122
No_of_seqs 119 out of 610
Neff 5.7
Searched_HMMs 46136
Date Fri Mar 29 12:02:02 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033283.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033283hhsearch_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 2.1E-36 4.6E-41 225.1 11.9 109 11-119 9-120 (168)
2 KOG0871 Class 2 transcription 100.0 2.5E-28 5.5E-33 180.3 10.0 96 24-119 5-100 (156)
3 KOG0870 DNA polymerase epsilon 99.9 6.7E-26 1.4E-30 170.0 9.2 95 25-119 4-99 (172)
4 COG5150 Class 2 transcription 99.9 2E-23 4.4E-28 151.5 9.1 96 25-120 5-100 (148)
5 PF00808 CBFD_NFYB_HMF: Histon 99.8 7.3E-20 1.6E-24 117.7 7.4 64 31-95 2-65 (65)
6 COG2036 HHT1 Histones H3 and H 99.7 6.2E-18 1.3E-22 116.7 6.5 79 23-103 11-89 (91)
7 cd00076 H4 Histone H4, one of 99.3 7.3E-12 1.6E-16 85.5 8.2 71 31-103 13-83 (85)
8 PLN00035 histone H4; Provision 99.3 6.2E-12 1.4E-16 88.6 7.0 76 26-103 24-99 (103)
9 PTZ00015 histone H4; Provision 99.2 4.6E-11 1E-15 84.1 8.2 75 27-103 26-100 (102)
10 smart00803 TAF TATA box bindin 99.1 2.4E-10 5.2E-15 74.3 7.2 64 31-96 2-65 (65)
11 smart00428 H3 Histone H3. 99.1 1.6E-10 3.5E-15 81.7 6.7 73 25-97 23-100 (105)
12 smart00417 H4 Histone H4. 99.1 3.9E-10 8.4E-15 75.3 5.8 62 30-93 12-73 (74)
13 cd07981 TAF12 TATA Binding Pro 99.0 2.7E-09 5.8E-14 70.3 8.3 65 32-97 2-66 (72)
14 PF00125 Histone: Core histone 99.0 1.1E-09 2.3E-14 71.4 6.1 68 29-96 3-73 (75)
15 COG5208 HAP5 CCAAT-binding fac 99.0 2.8E-10 6E-15 89.8 3.9 76 28-104 106-181 (286)
16 PLN00160 histone H3; Provision 98.9 7.4E-09 1.6E-13 72.3 6.4 72 25-96 15-90 (97)
17 PLN00121 histone H3; Provision 98.8 6.3E-09 1.4E-13 76.6 5.7 71 26-96 57-130 (136)
18 PLN00161 histone H3; Provision 98.8 1.3E-08 2.9E-13 74.7 7.3 71 26-96 50-124 (135)
19 PTZ00018 histone H3; Provision 98.8 8.7E-09 1.9E-13 75.8 5.5 71 26-96 57-130 (136)
20 KOG1657 CCAAT-binding factor, 98.7 1.4E-08 3.1E-13 80.6 4.5 85 29-114 72-159 (236)
21 smart00576 BTP Bromodomain tra 98.6 2.5E-07 5.5E-12 61.4 8.0 66 34-101 9-74 (77)
22 cd00074 H2A Histone 2A; H2A is 98.5 2.8E-07 6E-12 66.1 6.8 68 29-97 18-85 (115)
23 cd07979 TAF9 TATA Binding Prot 98.3 4.5E-06 9.8E-11 59.8 8.4 80 35-116 5-85 (117)
24 PF15511 CENP-T: Centromere ki 98.2 2.5E-06 5.4E-11 72.3 5.9 68 23-90 343-414 (414)
25 KOG1745 Histones H3 and H4 [Ch 98.2 1.2E-06 2.6E-11 64.5 2.6 75 25-99 57-134 (137)
26 cd08050 TAF6 TATA Binding Prot 98.1 1.5E-05 3.2E-10 65.9 8.1 67 33-101 1-67 (343)
27 PF15630 CENP-S: Kinetochore c 98.1 1.6E-05 3.5E-10 53.2 6.2 62 36-97 10-72 (76)
28 COG5262 HTA1 Histone H2A [Chro 98.0 3.1E-05 6.7E-10 56.1 6.4 69 27-96 22-90 (132)
29 KOG1659 Class 2 transcription 97.9 3.2E-05 6.9E-10 60.8 6.7 78 29-107 11-88 (224)
30 PF07524 Bromo_TP: Bromodomain 97.9 0.00011 2.5E-09 48.2 8.3 64 36-101 11-74 (77)
31 smart00427 H2B Histone H2B. 97.9 7.5E-05 1.6E-09 51.5 7.3 62 36-98 6-67 (89)
32 cd08048 TAF11 TATA Binding Pro 97.9 0.00011 2.4E-09 50.1 8.0 66 31-98 16-84 (85)
33 PF03847 TFIID_20kDa: Transcri 97.8 0.00012 2.6E-09 48.0 7.0 63 34-97 2-64 (68)
34 PF09415 CENP-X: CENP-S associ 97.8 2.9E-05 6.2E-10 51.5 4.0 64 33-96 1-66 (72)
35 KOG3467 Histone H4 [Chromatin 97.7 0.00017 3.7E-09 49.9 7.0 68 32-101 30-97 (103)
36 KOG1142 Transcription initiati 97.7 0.00023 4.9E-09 57.4 8.1 98 5-103 124-228 (258)
37 KOG1658 DNA polymerase epsilon 97.7 2.8E-05 6.1E-10 58.4 2.6 69 27-97 55-124 (162)
38 PLN00158 histone H2B; Provisio 97.7 0.00027 5.8E-09 50.9 7.4 67 31-98 27-93 (116)
39 PTZ00463 histone H2B; Provisio 97.6 0.00031 6.7E-09 50.6 7.4 63 35-98 32-94 (117)
40 COG5247 BUR6 Class 2 transcrip 97.6 0.00017 3.8E-09 51.0 5.6 81 29-110 21-101 (113)
41 PLN00154 histone H2A; Provisio 97.6 0.00054 1.2E-08 50.6 8.4 70 28-97 35-104 (136)
42 PF04719 TAFII28: hTAFII28-lik 97.5 0.00047 1E-08 47.6 7.0 67 31-98 23-90 (90)
43 PF02969 TAF: TATA box binding 97.5 0.00073 1.6E-08 44.1 7.5 64 31-96 3-66 (66)
44 smart00414 H2A Histone 2A. 97.5 0.00042 9.1E-09 49.0 6.1 68 29-97 7-74 (106)
45 KOG1756 Histone 2A [Chromatin 97.3 0.00094 2E-08 48.8 6.3 69 27-96 23-91 (131)
46 PF15510 CENP-W: Centromere ki 97.2 0.00072 1.6E-08 47.1 4.7 67 30-97 15-95 (102)
47 PTZ00017 histone H2A; Provisio 97.1 0.0011 2.4E-08 48.8 5.4 68 28-96 24-91 (134)
48 PLN00156 histone H2AX; Provisi 96.9 0.0047 1E-07 45.8 7.3 67 29-96 27-93 (139)
49 PLN00153 histone H2A; Provisio 96.9 0.005 1.1E-07 45.1 7.3 69 28-97 21-89 (129)
50 PLN00157 histone H2A; Provisio 96.9 0.0024 5.1E-08 47.0 5.1 69 28-97 23-91 (132)
51 KOG1744 Histone H2B [Chromatin 96.8 0.0055 1.2E-07 44.8 6.7 71 24-98 33-103 (127)
52 PTZ00252 histone H2A; Provisio 96.5 0.015 3.1E-07 42.9 7.2 68 29-97 23-92 (134)
53 PF02269 TFIID-18kDa: Transcri 96.4 0.0056 1.2E-07 42.1 4.0 60 37-97 7-66 (93)
54 KOG3219 Transcription initiati 96.2 0.0076 1.6E-07 46.9 4.2 70 31-102 112-182 (195)
55 PF02291 TFIID-31kDa: Transcri 96.0 0.049 1.1E-06 39.8 7.4 86 28-115 7-95 (129)
56 cd07978 TAF13 The TATA Binding 95.4 0.16 3.4E-06 35.0 7.9 60 35-96 6-65 (92)
57 KOG4336 TBP-associated transcr 94.6 0.25 5.4E-06 41.0 8.3 74 37-114 11-84 (323)
58 KOG2389 Predicted bromodomain 94.2 0.11 2.4E-06 43.6 5.5 88 12-101 8-97 (353)
59 KOG3423 Transcription initiati 93.9 0.39 8.5E-06 36.8 7.5 69 31-101 86-168 (176)
60 TIGR03015 pepcterm_ATPase puta 93.5 0.31 6.8E-06 37.4 6.6 69 32-100 192-268 (269)
61 KOG2549 Transcription initiati 91.7 1 2.2E-05 40.1 8.0 66 33-100 13-78 (576)
62 PRK00411 cdc6 cell division co 90.9 1.4 3.1E-05 35.9 7.8 71 32-102 207-286 (394)
63 KOG1757 Histone 2A [Chromatin 87.5 1.1 2.3E-05 32.5 4.1 67 26-96 25-95 (131)
64 TIGR02928 orc1/cdc6 family rep 87.2 3.6 7.8E-05 33.1 7.5 72 34-105 201-281 (365)
65 cd08045 TAF4 TATA Binding Prot 84.4 8 0.00017 29.8 7.9 75 29-103 42-124 (212)
66 KOG3334 Transcription initiati 82.5 6.8 0.00015 29.4 6.5 64 51-114 31-95 (148)
67 TIGR00764 lon_rel lon-related 82.5 5.8 0.00013 35.4 7.2 49 50-98 330-391 (608)
68 PF13654 AAA_32: AAA domain; P 82.4 7 0.00015 34.3 7.6 49 50-98 447-506 (509)
69 COG5095 TAF6 Transcription ini 82.4 4.6 9.9E-05 34.4 6.1 53 49-101 21-73 (450)
70 TIGR02902 spore_lonB ATP-depen 80.9 4.7 0.0001 35.3 6.0 67 34-100 265-334 (531)
71 PF13335 Mg_chelatase_2: Magne 80.0 7.8 0.00017 26.4 5.8 48 49-96 41-94 (96)
72 KOG2680 DNA helicase TIP49, TB 76.9 13 0.00027 31.9 7.1 60 37-96 363-427 (454)
73 PF08369 PCP_red: Proto-chloro 74.6 4 8.8E-05 24.4 2.7 42 52-94 2-44 (45)
74 COG1067 LonB Predicted ATP-dep 73.0 3.4 7.4E-05 37.4 3.0 49 50-98 338-399 (647)
75 COG5162 Transcription initiati 69.6 38 0.00082 26.2 7.6 51 51-101 106-189 (197)
76 PRK09862 putative ATP-dependen 69.1 21 0.00045 31.5 6.9 60 49-108 437-502 (506)
77 PRK00080 ruvB Holliday junctio 66.6 29 0.00063 27.9 6.9 72 31-102 179-254 (328)
78 TIGR02442 Cob-chelat-sub cobal 65.3 27 0.00058 31.3 7.0 49 48-96 247-302 (633)
79 TIGR00635 ruvB Holliday juncti 64.8 47 0.001 26.0 7.7 70 32-101 159-232 (305)
80 TIGR02030 BchI-ChlI magnesium 64.5 34 0.00074 28.4 7.1 54 42-96 247-307 (337)
81 PF02861 Clp_N: Clp amino term 64.1 5.9 0.00013 23.0 1.9 25 74-98 1-25 (53)
82 TIGR00368 Mg chelatase-related 62.8 21 0.00045 31.3 5.7 47 50-96 445-497 (499)
83 PRK13406 bchD magnesium chelat 61.1 22 0.00048 31.8 5.7 59 36-96 183-248 (584)
84 PF09114 MotA_activ: Transcrip 60.3 16 0.00035 25.5 3.7 33 35-67 51-87 (96)
85 COG1222 RPT1 ATP-dependent 26S 60.1 15 0.00033 31.6 4.3 79 20-98 309-392 (406)
86 PRK12728 fliE flagellar hook-b 59.3 47 0.001 23.1 6.0 40 80-120 59-100 (102)
87 PF03540 TFIID_30kDa: Transcri 59.1 41 0.00088 20.8 6.4 48 31-80 2-49 (51)
88 TIGR01128 holA DNA polymerase 58.7 56 0.0012 25.3 7.1 66 31-96 110-176 (302)
89 CHL00081 chlI Mg-protoporyphyr 58.2 32 0.0007 28.8 5.9 54 42-96 260-320 (350)
90 PRK13765 ATP-dependent proteas 57.6 34 0.00073 31.0 6.2 48 50-97 339-399 (637)
91 PF02049 FliE: Flagellar hook- 56.6 59 0.0013 21.9 6.3 66 54-120 26-94 (96)
92 KOG3901 Transcription initiati 56.5 36 0.00079 24.3 5.0 47 47-96 24-70 (109)
93 PF05570 DUF765: Circovirus pr 56.4 11 0.00024 20.5 1.9 22 1-22 1-26 (29)
94 smart00350 MCM minichromosome 56.4 64 0.0014 28.0 7.6 68 30-97 416-503 (509)
95 COG1474 CDC6 Cdc6-related prot 56.3 54 0.0012 27.5 6.9 74 35-108 193-275 (366)
96 PF05236 TAF4: Transcription i 52.2 25 0.00055 27.9 4.2 74 27-100 39-120 (264)
97 PRK07452 DNA polymerase III su 51.5 44 0.00095 26.6 5.5 66 37-102 135-203 (326)
98 PTZ00361 26 proteosome regulat 51.4 20 0.00044 30.9 3.7 32 67-98 393-424 (438)
99 COG1224 TIP49 DNA helicase TIP 51.0 46 0.001 29.0 5.7 83 32-117 361-448 (450)
100 PRK12402 replication factor C 50.8 42 0.0009 26.4 5.2 68 32-101 184-252 (337)
101 TIGR01242 26Sp45 26S proteasom 50.6 23 0.00049 29.1 3.8 32 66-97 331-362 (364)
102 PRK03992 proteasome-activating 50.5 22 0.00048 29.7 3.7 36 65-100 339-374 (389)
103 TIGR02031 BchD-ChlD magnesium 50.1 64 0.0014 28.7 6.7 54 42-96 196-256 (589)
104 PF00356 LacI: Bacterial regul 49.6 44 0.00095 19.8 4.0 32 31-66 10-41 (46)
105 PF08681 DUF1778: Protein of u 49.5 15 0.00032 24.2 2.1 67 49-115 4-79 (80)
106 PRK00790 fliE flagellar hook-b 49.4 91 0.002 22.0 6.2 35 86-120 71-107 (109)
107 PF00531 Death: Death domain; 49.1 31 0.00068 21.6 3.6 30 82-111 54-83 (83)
108 PRK13407 bchI magnesium chelat 49.0 62 0.0013 26.9 6.1 53 42-95 244-303 (334)
109 PF08823 PG_binding_2: Putativ 48.8 29 0.00063 22.7 3.4 31 89-119 19-55 (74)
110 PRK05574 holA DNA polymerase I 47.6 63 0.0014 25.5 5.8 67 31-97 145-212 (340)
111 COG5624 TAF61 Transcription in 47.2 12 0.00027 32.6 1.8 76 31-106 383-461 (505)
112 PLN00138 large subunit ribosom 47.1 56 0.0012 23.2 4.9 39 74-112 6-44 (113)
113 PF07647 SAM_2: SAM domain (St 45.1 26 0.00056 21.3 2.6 24 86-109 4-27 (66)
114 PTZ00454 26S protease regulato 44.8 31 0.00067 29.3 3.8 33 66-98 354-386 (398)
115 PTZ00373 60S Acidic ribosomal 43.5 70 0.0015 22.8 4.9 38 74-111 8-45 (112)
116 TIGR01052 top6b DNA topoisomer 42.9 33 0.00071 30.2 3.7 44 42-85 426-469 (488)
117 PF12010 DUF3502: Domain of un 42.9 27 0.00058 25.0 2.7 61 52-118 71-133 (134)
118 COG5248 TAF19 Transcription in 41.9 85 0.0019 22.7 5.1 57 37-96 15-71 (126)
119 PF00536 SAM_1: SAM domain (St 40.9 31 0.00066 20.9 2.4 22 87-108 4-25 (64)
120 cd00166 SAM Sterile alpha moti 40.5 23 0.00049 20.8 1.8 23 87-109 3-25 (63)
121 PF09123 DUF1931: Domain of un 40.2 24 0.00053 26.2 2.2 53 37-91 1-53 (138)
122 COG5251 TAF40 Transcription in 39.8 50 0.0011 25.7 3.9 64 31-96 115-179 (199)
123 PTZ00183 centrin; Provisional 38.3 1.3E+02 0.0028 20.6 5.7 21 77-97 61-81 (158)
124 COG1724 Predicted RNA binding 37.4 22 0.00047 23.3 1.4 18 85-102 6-23 (66)
125 PRK06585 holA DNA polymerase I 37.3 94 0.002 24.9 5.4 63 34-96 144-208 (343)
126 PRK14975 bifunctional 3'-5' ex 37.2 2.2E+02 0.0048 25.1 8.0 70 29-101 161-240 (553)
127 PF07499 RuvA_C: RuvA, C-termi 37.1 21 0.00046 21.0 1.2 14 89-102 4-17 (47)
128 COG1466 HolA DNA polymerase II 37.1 84 0.0018 25.6 5.1 61 37-97 145-206 (334)
129 PRK00253 fliE flagellar hook-b 37.0 1.5E+02 0.0032 20.8 6.4 40 81-120 65-106 (108)
130 PRK01482 fliE flagellar hook-b 37.0 1.5E+02 0.0033 20.9 6.5 65 54-119 38-106 (108)
131 TIGR00205 fliE flagellar hook- 36.6 1.5E+02 0.0033 20.8 6.6 67 52-119 36-106 (108)
132 cd04752 Commd4 COMM_Domain con 36.0 1.8E+02 0.004 21.6 9.0 50 62-118 43-93 (174)
133 TIGR01278 DPOR_BchB light-inde 35.9 73 0.0016 27.7 4.8 51 48-99 460-511 (511)
134 cd05833 Ribosomal_P2 Ribosomal 35.3 1.1E+02 0.0025 21.4 4.9 28 74-101 6-33 (109)
135 PRK00732 fliE flagellar hook-b 34.3 1.6E+02 0.0035 20.5 6.2 35 86-120 64-100 (102)
136 PF12627 PolyA_pol_RNAbd: Prob 33.6 32 0.0007 20.8 1.7 58 48-109 1-62 (64)
137 cd00823 TopoIIB_Trans TopoIIB_ 33.6 88 0.0019 23.6 4.3 48 24-74 96-143 (151)
138 COG5340 Predicted transcriptio 32.5 77 0.0017 25.8 4.1 53 26-78 149-207 (269)
139 KOG1528 Salt-sensitive 3'-phos 32.5 1.3E+02 0.0028 25.5 5.4 74 24-98 43-123 (351)
140 PF13405 EF-hand_6: EF-hand do 32.5 48 0.001 17.3 2.1 26 74-99 5-31 (31)
141 COG1389 DNA topoisomerase VI, 32.3 37 0.00081 30.2 2.4 46 42-87 434-479 (538)
142 smart00454 SAM Sterile alpha m 31.5 36 0.00078 20.0 1.6 25 86-110 4-28 (68)
143 TIGR02454 CbiQ_TIGR cobalt ABC 31.4 68 0.0015 23.6 3.4 37 84-120 112-159 (198)
144 PRK03907 fliE flagellar hook-b 31.4 1.8E+02 0.0039 20.1 6.4 36 85-120 58-95 (97)
145 smart00027 EH Eps15 homology d 31.4 93 0.002 20.4 3.8 28 74-101 15-42 (96)
146 PF02361 CbiQ: Cobalt transpor 31.1 66 0.0014 23.7 3.3 58 59-119 101-170 (224)
147 KOG0785 Isocitrate dehydrogena 30.7 1.1E+02 0.0025 25.9 4.9 64 51-115 164-227 (365)
148 PRK07914 hypothetical protein; 30.6 1.3E+02 0.0028 24.2 5.1 63 33-96 129-192 (320)
149 COG3267 ExeA Type II secretory 30.4 1.5E+02 0.0032 24.4 5.4 56 37-92 209-267 (269)
150 smart00354 HTH_LACI helix_turn 30.3 1.2E+02 0.0025 19.0 4.0 33 30-66 10-42 (70)
151 PF09339 HTH_IclR: IclR helix- 29.9 31 0.00066 20.3 1.1 17 29-45 27-43 (52)
152 KOG1658 DNA polymerase epsilon 29.3 1.1E+02 0.0024 23.3 4.2 69 27-96 7-87 (162)
153 PRK09526 lacI lac repressor; R 28.8 67 0.0014 25.1 3.2 37 31-72 16-52 (342)
154 TIGR02903 spore_lon_C ATP-depe 27.9 1.2E+02 0.0027 27.1 5.0 71 34-104 355-436 (615)
155 COG3404 Methenyl tetrahydrofol 27.8 28 0.00061 27.5 0.8 14 2-16 16-29 (208)
156 PF10728 DUF2520: Domain of un 27.6 2E+02 0.0044 20.5 5.3 58 34-94 13-73 (132)
157 PRK00440 rfc replication facto 27.2 1.4E+02 0.0031 23.1 4.8 65 32-98 161-226 (319)
158 PF00403 HMA: Heavy-metal-asso 26.6 44 0.00094 19.9 1.4 16 86-101 47-62 (62)
159 COG1239 ChlI Mg-chelatase subu 26.5 1.3E+02 0.0029 26.2 4.7 49 48-96 265-320 (423)
160 PF11884 DUF3404: Domain of un 26.1 31 0.00067 28.1 0.8 19 50-68 155-173 (262)
161 PRK05629 hypothetical protein; 25.5 2.4E+02 0.0051 22.6 5.8 49 47-96 142-190 (318)
162 PF07928 Vps54: Vps54-like pro 25.0 24 0.00052 25.6 0.0 36 79-114 61-97 (135)
163 PRK04184 DNA topoisomerase VI 24.8 58 0.0013 29.0 2.3 55 42-96 431-487 (535)
164 PRK14987 gluconate operon tran 24.7 77 0.0017 24.7 2.8 37 31-72 16-52 (331)
165 PF09239 Topo-VIb_trans: Topoi 24.5 89 0.0019 23.8 3.0 33 42-74 120-152 (160)
166 KOG0729 26S proteasome regulat 24.3 66 0.0014 27.3 2.4 49 49-97 364-417 (435)
167 cd03521 Link_domain_KIAA0527_l 23.8 95 0.0021 21.7 2.8 31 72-102 17-47 (95)
168 cd00051 EFh EF-hand, calcium b 23.8 1.3E+02 0.0029 16.2 4.4 37 78-114 9-45 (63)
169 cd04411 Ribosomal_P1_P2_L12p R 23.4 2.3E+02 0.005 19.7 4.8 38 74-112 6-43 (105)
170 PF13413 HTH_25: Helix-turn-he 23.4 84 0.0018 19.6 2.3 32 88-119 23-56 (62)
171 PF06782 UPF0236: Uncharacteri 23.2 1.6E+02 0.0034 25.6 4.6 58 45-104 112-169 (470)
172 PF03792 PBC: PBC domain; Int 22.9 3E+02 0.0066 21.5 5.7 75 21-109 100-176 (191)
173 TIGR01241 FtsH_fam ATP-depende 22.9 1.2E+02 0.0026 26.0 3.9 33 67-99 264-296 (495)
174 CHL00076 chlB photochlorophyll 22.8 1.7E+02 0.0036 25.6 4.8 51 48-99 461-512 (513)
175 PF13713 BRX_N: Transcription 22.4 1.5E+02 0.0032 17.3 3.0 22 60-81 7-28 (39)
176 PRK02910 light-independent pro 22.4 1.6E+02 0.0035 25.6 4.6 52 47-99 466-518 (519)
177 TIGR03261 phnS2 putative 2-ami 22.2 2.4E+02 0.0052 22.3 5.3 60 60-119 260-330 (334)
178 PRK12729 fliE flagellar hook-b 21.6 2E+02 0.0042 21.1 4.2 40 81-120 85-126 (127)
179 PRK06402 rpl12p 50S ribosomal 21.3 2.4E+02 0.0053 19.8 4.5 37 74-111 6-42 (106)
180 COG3093 VapI Plasmid maintenan 20.6 56 0.0012 23.1 1.1 75 1-80 2-81 (104)
181 smart00445 LINK Link (Hyaluron 20.6 1.1E+02 0.0025 21.0 2.7 30 71-101 17-46 (94)
182 KOG0784 Isocitrate dehydrogena 20.3 60 0.0013 27.7 1.5 45 69-114 188-232 (375)
183 PRK14868 DNA topoisomerase VI 20.2 83 0.0018 29.6 2.4 59 24-85 610-668 (795)
No 1
>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [Transcription]
Probab=100.00 E-value=2.1e-36 Score=225.11 Aligned_cols=109 Identities=75% Similarity=1.186 Sum_probs=100.2
Q ss_pred CCCCCCCC---CCCCCCCccccccChhhHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCC
Q 033283 11 GGSHESGE---QSPRSNVREQDRYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTIN 87 (122)
Q Consensus 11 ~~~~~~~~---~~~~~~~~~~d~~LP~A~V~Ri~K~~lp~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~ 87 (122)
+|.|+.++ ++.+.+.++.|..||+|+|.||||..||.+.+|||||++.+|+|+.+||+|||.+|.+.|.+++||||+
T Consensus 9 ~~~~e~~g~~~~~~~~~~reqDr~LPIANV~RIMK~~lP~naKIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIn 88 (168)
T KOG0869|consen 9 GGGDENGGNSSPQSSLSLREQDRFLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASEKCQREKRKTIN 88 (168)
T ss_pred CccccCCcccCCccccccchhhhhccHHHHHHHHHhcCCcccccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCccc
Confidence 44555554 333458999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cchHHHHHHhcCCcccHHHHHHHHHHHHHHhc
Q 033283 88 GDDLLWAMATLGFEDYIDPLKIYLTRYREVIC 119 (122)
Q Consensus 88 ~eDV~~Al~~lgf~~~~~~l~~~l~~~re~~~ 119 (122)
.|||+|||..|||++|+++|+.||++|||+.+
T Consensus 89 gdDllwAm~tLGFe~Y~eplkiyL~kYRe~e~ 120 (168)
T KOG0869|consen 89 GDDLLWAMSTLGFENYAEPLKIYLQKYRELEG 120 (168)
T ss_pred HHHHHHHHHHcCcHhHHHHHHHHHHHHHHHhh
Confidence 99999999999999999999999999999754
No 2
>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=99.95 E-value=2.5e-28 Score=180.33 Aligned_cols=96 Identities=32% Similarity=0.621 Sum_probs=92.3
Q ss_pred CCccccccChhhHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHHhcCCccc
Q 033283 24 NVREQDRYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMATLGFEDY 103 (122)
Q Consensus 24 ~~~~~d~~LP~A~V~Ri~K~~lp~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~~ 103 (122)
+...|++.||+|+|++|||+.||.+++|.+|++++|.+||.+||+.|+++||++|.++.||||.++||++||+.|||.+|
T Consensus 5 ~~~dde~sLPkAtv~KmIke~lP~d~rvakeareliincCvEFI~liSsEAneic~~e~KKTIa~EHV~KALe~LgF~eY 84 (156)
T KOG0871|consen 5 GKEDDELSLPKATVNKMIKEMLPKDVRVAKEARELIINCCVEFINLISSEANEICNKEAKKTIAPEHVIKALENLGFGEY 84 (156)
T ss_pred ccccccccCcHHHHHHHHHHhCCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHhHHhcccCCHHHHHHHHHHcchHHH
Confidence 34678899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhc
Q 033283 104 IDPLKIYLTRYREVIC 119 (122)
Q Consensus 104 ~~~l~~~l~~~re~~~ 119 (122)
++.+...+++|+..+.
T Consensus 85 iee~~~vl~~~K~~~~ 100 (156)
T KOG0871|consen 85 IEEAEEVLENCKEEAK 100 (156)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 9999999999998765
No 3
>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription]
Probab=99.93 E-value=6.7e-26 Score=170.02 Aligned_cols=95 Identities=34% Similarity=0.582 Sum_probs=91.3
Q ss_pred CccccccChhhHHHHHHHhhCCCC-ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHHhcCCccc
Q 033283 25 VREQDRYLPIANISRIMKKALPAN-GKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMATLGFEDY 103 (122)
Q Consensus 25 ~~~~d~~LP~A~V~Ri~K~~lp~~-~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~~ 103 (122)
.+++|+.||+|+|.||+|+.||+. ..|||||+.+|+++|++||+||++.|+++|..++||||+++||++||++++|.+|
T Consensus 4 eri~dl~lP~AiI~rlvke~l~E~~vsisKeA~~Ai~raAtVFv~~Lts~s~e~A~~q~rKt~sadDVl~aL~Eiefs~f 83 (172)
T KOG0870|consen 4 ERIEDLNLPNAIITRLVKEVLPESNVSISKEARLAIARAATVFVIFLTSVSNEIAKDQKRKTISADDVLKALDEIEFSSF 83 (172)
T ss_pred hhHHHhhccHHHHHHHHHHhCccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCcccHHHHHHHHHHhchHHH
Confidence 467899999999999999999987 8999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhc
Q 033283 104 IDPLKIYLTRYREVIC 119 (122)
Q Consensus 104 ~~~l~~~l~~~re~~~ 119 (122)
+.+|+..|+.||...+
T Consensus 84 ~~plk~~Le~yk~~~k 99 (172)
T KOG0870|consen 84 VNPLKSALEAYKKAVK 99 (172)
T ss_pred hhHHHHHHHHHHHHHH
Confidence 9999999999997653
No 4
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=99.90 E-value=2e-23 Score=151.47 Aligned_cols=96 Identities=27% Similarity=0.481 Sum_probs=92.4
Q ss_pred CccccccChhhHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHHhcCCcccH
Q 033283 25 VREQDRYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMATLGFEDYI 104 (122)
Q Consensus 25 ~~~~d~~LP~A~V~Ri~K~~lp~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~~~ 104 (122)
...|+..||+|+|.++|.+.||.+..++|||++.+++||-+||+.|+++|++.|.++.+|||.++||++||++|||.+|+
T Consensus 5 ~~dDe~sLPKATVqKMvS~iLp~dl~ftKearei~in~cieFi~~lsseAne~ce~EaKKTIa~EHviKALenLef~eyi 84 (148)
T COG5150 5 KNDDENSLPKATVQKMVSSILPKDLVFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHVIKALENLEFEEYI 84 (148)
T ss_pred cccccccCcHHHHHHHHHHhccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHhccHHHHH
Confidence 35678999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHhcc
Q 033283 105 DPLKIYLTRYREVICV 120 (122)
Q Consensus 105 ~~l~~~l~~~re~~~~ 120 (122)
+.+.+...+|+..+++
T Consensus 85 ~~~~e~~~n~k~~qK~ 100 (148)
T COG5150 85 ESCMEEHENYKSYQKQ 100 (148)
T ss_pred HHHHHHHHHHHHHHhh
Confidence 9999999999998875
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=99.81 E-value=7.3e-20 Score=117.69 Aligned_cols=64 Identities=39% Similarity=0.639 Sum_probs=59.2
Q ss_pred cChhhHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHH
Q 033283 31 YLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAM 95 (122)
Q Consensus 31 ~LP~A~V~Ri~K~~lp~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al 95 (122)
.||+++|+||||.. |++.+||+||.++|++|+++||.||+.+|++.|.+++||||+++||..||
T Consensus 2 ~lP~a~vkri~k~~-~~~~~vs~ea~~~i~~a~e~Fi~~l~~~A~~~a~~~~rkti~~~Dv~~Av 65 (65)
T PF00808_consen 2 SLPLARVKRIMKSD-PDVMRVSKEAVEAIAKAAEEFIQYLAKEANEIAQRDKRKTITYEDVAKAV 65 (65)
T ss_dssp SS-HHHHHHHHHHT-STTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEE-HHHHHHHH
T ss_pred CCChHHHHHHhccC-CCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHC
Confidence 69999999999999 88889999999999999999999999999999999999999999999986
No 6
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=99.73 E-value=6.2e-18 Score=116.69 Aligned_cols=79 Identities=32% Similarity=0.498 Sum_probs=74.7
Q ss_pred CCCccccccChhhHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHHhcCCcc
Q 033283 23 SNVREQDRYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMATLGFED 102 (122)
Q Consensus 23 ~~~~~~d~~LP~A~V~Ri~K~~lp~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~ 102 (122)
...+..+..||+++|.||||+..++ +||.+|.+.++++.++|+..|+..|+++|.+.|||||+++||..|++.+||..
T Consensus 11 ~~~~~~~~~Lp~apv~Ri~r~~~~~--Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~DI~la~~~~~~~~ 88 (91)
T COG2036 11 RYQRSTDLLLPKAPVRRILRKAGAE--RVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLALKRLGRRI 88 (91)
T ss_pred hhhhhhhhhcCchHHHHHHHHHhHH--HhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHHHhcccc
Confidence 4557788999999999999999985 99999999999999999999999999999999999999999999999999976
Q ss_pred c
Q 033283 103 Y 103 (122)
Q Consensus 103 ~ 103 (122)
|
T Consensus 89 ~ 89 (91)
T COG2036 89 Y 89 (91)
T ss_pred c
Confidence 6
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=99.34 E-value=7.3e-12 Score=85.50 Aligned_cols=71 Identities=18% Similarity=0.320 Sum_probs=66.6
Q ss_pred cChhhHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHHhcCCccc
Q 033283 31 YLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMATLGFEDY 103 (122)
Q Consensus 31 ~LP~A~V~Ri~K~~lp~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~~ 103 (122)
.||++.|.||++... ..+||.|+.+.+.++.++|+..|..+|..+|++.+||||+++||..||+..|-.-|
T Consensus 13 gi~k~~I~RLarr~G--vkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~alkr~g~~~y 83 (85)
T cd00076 13 GITKPAIRRLARRGG--VKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLY 83 (85)
T ss_pred cCCHHHHHHHHHHcC--cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHCCCCcc
Confidence 599999999999986 47999999999999999999999999999999999999999999999999986544
No 8
>PLN00035 histone H4; Provisional
Probab=99.31 E-value=6.2e-12 Score=88.58 Aligned_cols=76 Identities=18% Similarity=0.284 Sum_probs=68.2
Q ss_pred ccccccChhhHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHHhcCCccc
Q 033283 26 REQDRYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMATLGFEDY 103 (122)
Q Consensus 26 ~~~d~~LP~A~V~Ri~K~~lp~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~~ 103 (122)
++.-..||+++|.||++... ..+||.|+.+.+.+..++|+..|+.+|..+|++.+||||+++||..||+..|-.-|
T Consensus 24 ~d~i~~ipk~~IrRLARr~G--vkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr~g~~ly 99 (103)
T PLN00035 24 RDNIQGITKPAIRRLARRGG--VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTLY 99 (103)
T ss_pred HhhhccCCHHHHHHHHHHcC--cccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHcCCcCC
Confidence 33344699999999999986 47999999999999999999999999999999999999999999999998875443
No 9
>PTZ00015 histone H4; Provisional
Probab=99.24 E-value=4.6e-11 Score=84.07 Aligned_cols=75 Identities=20% Similarity=0.343 Sum_probs=68.3
Q ss_pred cccccChhhHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHHhcCCccc
Q 033283 27 EQDRYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMATLGFEDY 103 (122)
Q Consensus 27 ~~d~~LP~A~V~Ri~K~~lp~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~~ 103 (122)
+-...||++.|.||++... ..+||.|+.+.+.++.++|+..|..+|..+|++.+||||+.+||..||+..|-.-|
T Consensus 26 ~~i~gI~k~~IrRLarr~G--vkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~AlKr~g~~~y 100 (102)
T PTZ00015 26 DNIRGITKGAIRRLARRGG--VKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALKRQGRTLY 100 (102)
T ss_pred hcccCCCHHHHHHHHHHcC--CccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhcCCCCC
Confidence 4445799999999999985 46999999999999999999999999999999999999999999999999886544
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=99.13 E-value=2.4e-10 Score=74.28 Aligned_cols=64 Identities=25% Similarity=0.285 Sum_probs=60.3
Q ss_pred cChhhHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHH
Q 033283 31 YLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMA 96 (122)
Q Consensus 31 ~LP~A~V~Ri~K~~lp~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~ 96 (122)
.||+++|.||++...- .+||.|+...|.+-.+.|+..|..+|.+++++.+||||+++||-.||+
T Consensus 2 ~~p~~~i~ria~~~Gi--~ris~~a~~~l~~~~e~rl~~i~~~A~k~~~hakRktlt~~DI~~Alk 65 (65)
T smart00803 2 WLPKETIKDVAESLGI--GNLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSALR 65 (65)
T ss_pred CCCHHHHHHHHHHCCC--ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCeecHHHHHHHhC
Confidence 5899999999998853 489999999999999999999999999999999999999999999974
No 11
>smart00428 H3 Histone H3.
Probab=99.13 E-value=1.6e-10 Score=81.69 Aligned_cols=73 Identities=16% Similarity=0.186 Sum_probs=66.8
Q ss_pred CccccccChhhHHHHHHHhhCCC-----CccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHHh
Q 033283 25 VREQDRYLPIANISRIMKKALPA-----NGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMAT 97 (122)
Q Consensus 25 ~~~~d~~LP~A~V~Ri~K~~lp~-----~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~~ 97 (122)
.+..++.+|+.++.|++++...+ +.+++.+|..+||++++.|+..+...|+..|.+.||+||.++|+.-|..-
T Consensus 23 Qkst~lLI~k~pF~RLVREI~~~~~~~~~~R~~~~Al~aLQeasE~ylv~lfeda~~~a~HAkRvTl~~kDi~La~ri 100 (105)
T smart00428 23 QKSTDLLIRKAPFQRLVREIAQKFTTGVDLRFQSSAIMALQEAAEAYLVGLFEDTNLLAIHAKRVTIMPKDIQLARRI 100 (105)
T ss_pred ccCcccccccccHHHHHHHHHHHcCCCCCceeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccCcHhhHHHHHHH
Confidence 36678999999999999998864 67999999999999999999999999999999999999999999887643
No 12
>smart00417 H4 Histone H4.
Probab=99.06 E-value=3.9e-10 Score=75.26 Aligned_cols=62 Identities=15% Similarity=0.295 Sum_probs=57.9
Q ss_pred ccChhhHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHH
Q 033283 30 RYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLW 93 (122)
Q Consensus 30 ~~LP~A~V~Ri~K~~lp~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~ 93 (122)
-.||++.|.||+|...- -+||.++.+.+.+..++|+..+..+|..+|++.+||||+++||.-
T Consensus 12 ~gI~k~~IrRLaRr~Gv--kRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~~ 73 (74)
T smart00417 12 QGITKPAIRRLARRGGV--KRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVY 73 (74)
T ss_pred cCCCHHHHHHHHHHcCc--chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHhee
Confidence 35999999999999853 689999999999999999999999999999999999999999964
No 13
>cd07981 TAF12 TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of the seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs function such as serving as activator-bind
Probab=99.01 E-value=2.7e-09 Score=70.31 Aligned_cols=65 Identities=17% Similarity=0.328 Sum_probs=61.4
Q ss_pred ChhhHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHHh
Q 033283 32 LPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMAT 97 (122)
Q Consensus 32 LP~A~V~Ri~K~~lp~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~~ 97 (122)
+++..+..++|+.=| +.+++.||.++|++.++.|+..++..|...|++.||+||..+||..+++.
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 678889999999876 68999999999999999999999999999999999999999999999985
No 14
>PF00125 Histone: Core histone H2A/H2B/H3/H4 histone h2a signature histone h2b signature histone h3 signature histone h4 signature; InterPro: IPR007125 The core histones together with some other DNA binding proteins appear to form a superfamily defined by a common fold and distant sequence similarities [, ]. Some proteins contain local homology domains related to the histone fold [].; GO: 0003677 DNA binding; PDB: 2YFW_D 2YFV_B 1U35_H 2F8N_D 2PYO_D 2NQB_D 3AN2_C 3AZJ_C 3AV1_G 3AZM_G ....
Probab=99.01 E-value=1.1e-09 Score=71.45 Aligned_cols=68 Identities=25% Similarity=0.336 Sum_probs=62.4
Q ss_pred cccChhhHHHHHHHhhCCC---CccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHH
Q 033283 29 DRYLPIANISRIMKKALPA---NGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMA 96 (122)
Q Consensus 29 d~~LP~A~V~Ri~K~~lp~---~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~ 96 (122)
+..+|+..|.|+.|+..++ ..+||++|...|+..++.|+..|...|...|.+.||+||+++||..|++
T Consensus 3 ~~~~~~~~~~r~~r~i~~~~~~~~ris~~a~~~L~~~~E~~~~~il~~A~~~a~~~kR~tI~~~DI~~A~r 73 (75)
T PF00125_consen 3 RRLIPKFPFSRLLREIGEEILSKYRISSEALVALQSVLEYLLVEILEEAGNLARHAKRKTITPRDIQLAVR 73 (75)
T ss_dssp SHSSSHHHHHHHHHHHHHTTSSSSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTBSEEGHHHHHHHHH
T ss_pred ccccCceEEeeeeehhhcccccccccccccchhhhhhhhhhhhhhhhHHHHHHhhcCCcEecHHHHHHHHh
Confidence 4578999999999988864 2699999999999999999999999999999999999999999999976
No 15
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=99.00 E-value=2.8e-10 Score=89.82 Aligned_cols=76 Identities=25% Similarity=0.335 Sum_probs=68.5
Q ss_pred ccccChhhHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHHhcCCcccH
Q 033283 28 QDRYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMATLGFEDYI 104 (122)
Q Consensus 28 ~d~~LP~A~V~Ri~K~~lp~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~~~ 104 (122)
.+..||+|+|+|+||-.-. .-.||.||-.++.+.|+.||..||..|+-.+++++|+|+...||..|+++-++.+|+
T Consensus 106 k~h~LPlARIkkvMKtded-VkMisaEaPvlFak~~EiFI~ELTmRAW~~ae~NkRRtLQksDia~Av~kSeMfDFL 181 (286)
T COG5208 106 KDHNLPLARIKKVMKTDED-VKMISAEAPVLFAKITEIFIEELTMRAWINAEENKRRTLQKSDIAAAVKKSEMFDFL 181 (286)
T ss_pred HhccCcHHHHHHHHhcccc-hhheecccchHHHHHHHHHHHHHHHHHHHHHhHhhhhHHHHHHHHHHHHHHHHHhHH
Confidence 3568999999999997632 335999999999999999999999999999999999999999999999998887775
No 16
>PLN00160 histone H3; Provisional
Probab=98.86 E-value=7.4e-09 Score=72.31 Aligned_cols=72 Identities=15% Similarity=0.107 Sum_probs=65.5
Q ss_pred CccccccChhhHHHHHHHhhCC----CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHH
Q 033283 25 VREQDRYLPIANISRIMKKALP----ANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMA 96 (122)
Q Consensus 25 ~~~~d~~LP~A~V~Ri~K~~lp----~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~ 96 (122)
.+..++.+|+.++.|++++... ++.+++.+|..+||++++.|+.-+...++..|.+.||.||.+.|+.-|..
T Consensus 15 Qkst~lLI~k~pF~RLVREI~~~~~~~~~Rfq~~Al~ALQeAsEayLv~lfed~~lca~HakRVTl~~kD~~L~~r 90 (97)
T PLN00160 15 QKSTDLLIRRLPFARLVREIQMEMSREAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTIMPKDMQLARR 90 (97)
T ss_pred ccchhhhhccccHHHHHHHHHHHcCCCCcEeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcccccchhhHHHHHH
Confidence 3567899999999999999864 35899999999999999999999999999999999999999999987754
No 17
>PLN00121 histone H3; Provisional
Probab=98.84 E-value=6.3e-09 Score=76.59 Aligned_cols=71 Identities=14% Similarity=0.171 Sum_probs=65.5
Q ss_pred ccccccChhhHHHHHHHhhCCC---CccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHH
Q 033283 26 REQDRYLPIANISRIMKKALPA---NGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMA 96 (122)
Q Consensus 26 ~~~d~~LP~A~V~Ri~K~~lp~---~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~ 96 (122)
+..++.+|+.++.|+|++...+ +.+++.+|..+||+++|.|+..|...++..+.+.+|.||.+.|+.-+..
T Consensus 57 kst~lLI~k~pF~RLVREI~~~~~~~~Rf~~~Al~ALQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~r 130 (136)
T PLN00121 57 KSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
T ss_pred cccccccccccHHHHHHHHHHHhCccceeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcceecchhhHHHHHH
Confidence 4568899999999999998865 6899999999999999999999999999999999999999999987753
No 18
>PLN00161 histone H3; Provisional
Probab=98.83 E-value=1.3e-08 Score=74.73 Aligned_cols=71 Identities=15% Similarity=0.192 Sum_probs=65.0
Q ss_pred ccccccChhhHHHHHHHhhCC----CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHH
Q 033283 26 REQDRYLPIANISRIMKKALP----ANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMA 96 (122)
Q Consensus 26 ~~~d~~LP~A~V~Ri~K~~lp----~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~ 96 (122)
+..++.+|+.++.|+|++... .+.+++.+|..+||++++.|+.-|...++..|.+.+|.||.+.|+.-|..
T Consensus 50 kst~lLIpklPF~RLVREI~~~~~~~~~Rfq~~Al~ALQEAsEayLV~lFeda~lcaiHAkRVTlm~kDm~La~r 124 (135)
T PLN00161 50 KSTELLIRKLPFARLVREISNEMLREPFRWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMPKDMQLARR 124 (135)
T ss_pred cccccccccccHHHHHHHHHHhcCCCCcEeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccchhhHHHHHH
Confidence 566889999999999999864 35899999999999999999999999999999999999999999987764
No 19
>PTZ00018 histone H3; Provisional
Probab=98.80 E-value=8.7e-09 Score=75.84 Aligned_cols=71 Identities=14% Similarity=0.175 Sum_probs=65.0
Q ss_pred ccccccChhhHHHHHHHhhCC---CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHH
Q 033283 26 REQDRYLPIANISRIMKKALP---ANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMA 96 (122)
Q Consensus 26 ~~~d~~LP~A~V~Ri~K~~lp---~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~ 96 (122)
+..++.+|+.++.|+|++... .+.+++.+|..+||+++|.|+..|...++..|.+.+|.||.+.|+.-+..
T Consensus 57 kst~lLI~k~pF~RLVREI~~~~~~~~rf~~~al~aLQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~r 130 (136)
T PTZ00018 57 KSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
T ss_pred ccchhccccccHHHHHHHHHHHcCCcceeeHHHHHHHHHHHHHHHHHHhhhhHHHHHhhcceecchhhHHHHHH
Confidence 456889999999999999874 36899999999999999999999999999999999999999999987754
No 20
>KOG1657 consensus CCAAT-binding factor, subunit C (HAP5) [Transcription]
Probab=98.71 E-value=1.4e-08 Score=80.59 Aligned_cols=85 Identities=27% Similarity=0.374 Sum_probs=71.4
Q ss_pred cccChhhHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHHh---cCCcccHH
Q 033283 29 DRYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMAT---LGFEDYID 105 (122)
Q Consensus 29 d~~LP~A~V~Ri~K~~lp~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~~---lgf~~~~~ 105 (122)
...||+++|++|||..- +.-.|+.||..++.+||+.||..|+..|+..++..+|+|+...|+..|+.. .+|.-.+-
T Consensus 72 ~~~lPlaRiKkimK~de-dv~mI~~Eapvl~aka~E~Fi~elt~~sw~~Tee~~rrtl~~sdia~av~~s~~fdFL~Div 150 (236)
T KOG1657|consen 72 NHILPLARIKKIMKSDE-DVSMITAEAPVLFAKACELFITELTLRSWVHTEENKRRTLQKSDIAAAVTQSETFDFLRDIV 150 (236)
T ss_pred hccCcHhhccccccccc-cccccchhHHHHHHHHHHHHHHHHHHHhhhhhcccccccchHHHHHHHhccCCCccceeccc
Confidence 35799999999999874 344799999999999999999999999999999999999999999999995 45544455
Q ss_pred HHHHHHHHH
Q 033283 106 PLKIYLTRY 114 (122)
Q Consensus 106 ~l~~~l~~~ 114 (122)
+.+...+.|
T Consensus 151 P~~~~~~~~ 159 (236)
T KOG1657|consen 151 PRKILAEKY 159 (236)
T ss_pred cchhccccc
Confidence 555555444
No 21
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=98.63 E-value=2.5e-07 Score=61.36 Aligned_cols=66 Identities=20% Similarity=0.265 Sum_probs=58.5
Q ss_pred hhHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHHhcCCc
Q 033283 34 IANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMATLGFE 101 (122)
Q Consensus 34 ~A~V~Ri~K~~lp~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~ 101 (122)
+-.|.+|+|...= -+++.+|++.|++..+.|+..|+..+..+|++.||++.+..||..||+++|+.
T Consensus 9 ~~~Vaqil~~~Gf--~~~~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~~~Dv~~Al~~~gi~ 74 (77)
T smart00576 9 RIAVAQILESAGF--DSFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPNLGDVVLALENLGIS 74 (77)
T ss_pred HHHHHHHHHHcCc--cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCcc
Confidence 3456677776642 48999999999999999999999999999999999999999999999999974
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=98.55 E-value=2.8e-07 Score=66.13 Aligned_cols=68 Identities=18% Similarity=0.238 Sum_probs=62.5
Q ss_pred cccChhhHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHHh
Q 033283 29 DRYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMAT 97 (122)
Q Consensus 29 d~~LP~A~V~Ri~K~~lp~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~~ 97 (122)
.+.||.+.|.|+||+.-- ..||+.+|...|..+.+-+...|...|...|++.+|++|+++||..|+..
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 589999999999998422 37999999999999999999999999999999999999999999999984
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=98.32 E-value=4.5e-06 Score=59.77 Aligned_cols=80 Identities=14% Similarity=0.157 Sum_probs=65.4
Q ss_pred hHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHHhcCCcccHH-HHHHHHHH
Q 033283 35 ANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMATLGFEDYID-PLKIYLTR 113 (122)
Q Consensus 35 A~V~Ri~K~~lp~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~~~~-~l~~~l~~ 113 (122)
..|.+|+|+.. ..+++.++...|.+.+..++.-|..+|...|++.||+||+.+||..|++...-..|.. +-+++|.+
T Consensus 5 ~~v~~iLk~~G--v~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r~~~~f~~~p~~~~l~~ 82 (117)
T cd07979 5 RVIAAILKSMG--ITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRVDYSFTSPPPRDFLLE 82 (117)
T ss_pred HHHHHHHHHCC--CCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhccCCCCCCcHHHHHH
Confidence 35778888763 3589999999999999999999999999999999999999999999999765544433 35666655
Q ss_pred HHH
Q 033283 114 YRE 116 (122)
Q Consensus 114 ~re 116 (122)
+-.
T Consensus 83 ~a~ 85 (117)
T cd07979 83 LAR 85 (117)
T ss_pred HHH
Confidence 444
No 24
>PF15511 CENP-T: Centromere kinetochore component CENP-T; PDB: 3B0D_T 3B0C_T 3VH5_T 3VH6_T.
Probab=98.21 E-value=2.5e-06 Score=72.28 Aligned_cols=68 Identities=22% Similarity=0.268 Sum_probs=48.2
Q ss_pred CCCccccccChhhHHHHHHHhhCC----CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcch
Q 033283 23 SNVREQDRYLPIANISRIMKKALP----ANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDD 90 (122)
Q Consensus 23 ~~~~~~d~~LP~A~V~Ri~K~~lp----~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eD 90 (122)
|-.++.--.||.+.|+|++..... .+++|++||..+|.+|...|-..|...-..+|+|.|||||..+|
T Consensus 343 Skhgi~~P~lP~~~vK~la~~~ak~s~~sK~kiskdal~aleqasdwfFeQl~dDL~aYA~HAgRKTIdesD 414 (414)
T PF15511_consen 343 SKHGIPYPSLPPGVVKKLAQHFAKSSGGSKMKISKDALEALEQASDWFFEQLGDDLEAYAKHAGRKTIDESD 414 (414)
T ss_dssp ---------S-HHHHHHHHHHHH-------S-B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHH
T ss_pred CCCCCCCCCCCccHHHHHHHHHHHhhcccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCCCC
Confidence 445666678999999999887754 46899999999999999999999999999999999999999876
No 25
>KOG1745 consensus Histones H3 and H4 [Chromatin structure and dynamics]
Probab=98.16 E-value=1.2e-06 Score=64.53 Aligned_cols=75 Identities=16% Similarity=0.195 Sum_probs=66.1
Q ss_pred CccccccChhhHHHHHHHhhCC---CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHHhcC
Q 033283 25 VREQDRYLPIANISRIMKKALP---ANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMATLG 99 (122)
Q Consensus 25 ~~~~d~~LP~A~V~Ri~K~~lp---~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~~lg 99 (122)
.+..|+.+++.+..|++++..+ .+.++...|..+||++++.|+.-|.-.+|-+|.+.||.||.+.||--|..-.|
T Consensus 57 QkstdLlI~K~PFqRlvrei~q~f~~dLrfqs~Ai~ALQeA~EayLv~LfEdtnlcAihAkRVTimpkdiQlArrirg 134 (137)
T KOG1745|consen 57 QKSTDLLIRKLPFQRLVREIAQDFKTDLRFQSSAIAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRG 134 (137)
T ss_pred HhhhHHHhhcCcHHHHhHHHHhcccccceehHHHHHHHHHHHHHHHHHhccccchhhhccceeEecccceehhhhccc
Confidence 3466889999999999995554 47799999999999999999999999999999999999999999988876443
No 26
>cd08050 TAF6 TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and are involved in forming Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs functions such as serving as
Probab=98.10 E-value=1.5e-05 Score=65.92 Aligned_cols=67 Identities=19% Similarity=0.206 Sum_probs=58.8
Q ss_pred hhhHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHHhcCCc
Q 033283 33 PIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMATLGFE 101 (122)
Q Consensus 33 P~A~V~Ri~K~~lp~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~ 101 (122)
|..+|+-|.+... -.++++||..+|.+.++.++..++.+|.+.+++.||||++.+||-.||+.++.+
T Consensus 1 ~~~~i~~ia~~~G--i~~~~~~a~~~La~~~e~~~~~i~~~A~k~~~hskR~~l~~~Di~~Al~~~n~e 67 (343)
T cd08050 1 PQESIKLIAESLG--IDSLSDEVAQLLAEDVEYRLREIIQEAAKFMRHSKRRKLTTSDVNHALRLRNVE 67 (343)
T ss_pred ChhHHHHHHHHcC--CCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHHhCCC
Confidence 4566777777663 249999999999999999999999999999999999999999999999976654
No 27
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=98.06 E-value=1.6e-05 Score=53.19 Aligned_cols=62 Identities=15% Similarity=0.195 Sum_probs=52.5
Q ss_pred HHHHHHHhhC-CCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHHh
Q 033283 36 NISRIMKKAL-PANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMAT 97 (122)
Q Consensus 36 ~V~Ri~K~~l-p~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~~ 97 (122)
+|.||+.+.. +.++.+|+++.-+|.+.+-.++..++..-...|++.||+||+.+||+-...+
T Consensus 10 ~v~ki~ee~~~~~~~~~s~~~i~al~ELv~~q~~~~a~DLe~FAkHA~R~tI~~dDV~Ll~Rr 72 (76)
T PF15630_consen 10 TVGKIVEEEAKEKGVEVSPQFIAALTELVYKQLENLAKDLEAFAKHAGRSTINMDDVKLLARR 72 (76)
T ss_dssp HHHHHHHHCCCCTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHTTT
T ss_pred HHHHHHHHHHhccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHHHhhc
Confidence 5788999885 4467899999999999999999999999999999999999999999876543
No 28
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=97.95 E-value=3.1e-05 Score=56.06 Aligned_cols=69 Identities=19% Similarity=0.252 Sum_probs=60.9
Q ss_pred cccccChhhHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHH
Q 033283 27 EQDRYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMA 96 (122)
Q Consensus 27 ~~d~~LP~A~V~Ri~K~~lp~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~ 96 (122)
...+.+|...|.|+||.. .-.+||+++|...++-|.+=.+..++.-|-..|...++|.|.|.|+-.|+.
T Consensus 22 ~agl~fpvgrvkr~lk~~-~~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~kkkri~PrHlqlAIr 90 (132)
T COG5262 22 KAGLIFPVGRVKRLLKKG-NYRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRIIPRHLQLAIR 90 (132)
T ss_pred hcCccccHHHHHHHHHcC-ccceeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhcCcceechHHHHHHhc
Confidence 345789999999999943 346899999999999999888888888888999999999999999999987
No 29
>KOG1659 consensus Class 2 transcription repressor NC2, alpha subunit (DRAP1) [Transcription]
Probab=97.93 E-value=3.2e-05 Score=60.80 Aligned_cols=78 Identities=18% Similarity=0.265 Sum_probs=69.8
Q ss_pred cccChhhHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHHhcCCcccHHHH
Q 033283 29 DRYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMATLGFEDYIDPL 107 (122)
Q Consensus 29 d~~LP~A~V~Ri~K~~lp~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~~~~~l 107 (122)
...+|.++|+|||...- +..+|..-.-..+.++.+.|+..|-..+.+++...+-|||+++|+.++++.-.-.+|+..+
T Consensus 11 ~trfp~aRiKKIMQ~dE-dIGKvaqavPViisralElFl~~l~~~t~~~t~~~~aKt~s~~hlkq~v~~~~~FdFLk~~ 88 (224)
T KOG1659|consen 11 KTRFPPARIKKIMQSDE-DIGKVAQAVPVIISRALELFLESLLQKTLEITRSRGAKTVSSSHLKQAVESDPKFDFLKEV 88 (224)
T ss_pred hccCCHHHHHHHHhhhh-hhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhcCccccCHHHHHHHHhccchhHHHHHH
Confidence 35799999999999775 3568999999999999999999999999999999999999999999999987777776653
No 30
>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=97.92 E-value=0.00011 Score=48.24 Aligned_cols=64 Identities=17% Similarity=0.264 Sum_probs=55.1
Q ss_pred HHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHHhcCCc
Q 033283 36 NISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMATLGFE 101 (122)
Q Consensus 36 ~V~Ri~K~~lp~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~ 101 (122)
.|.+|++... =-.++..|.+.|++.+..|+..|+..+...|++.+|...+..||..||+++|+.
T Consensus 11 ~va~il~~~G--F~~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~~~gi~ 74 (77)
T PF07524_consen 11 SVAQILKHAG--FDSASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPNLQDVEQALEEMGIS 74 (77)
T ss_pred HHHHHHHHcC--ccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCC
Confidence 3444454432 127999999999999999999999999999999999999999999999999984
No 31
>smart00427 H2B Histone H2B.
Probab=97.90 E-value=7.5e-05 Score=51.51 Aligned_cols=62 Identities=21% Similarity=0.350 Sum_probs=57.4
Q ss_pred HHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHHhc
Q 033283 36 NISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMATL 98 (122)
Q Consensus 36 ~V~Ri~K~~lp~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~~l 98 (122)
-|.|+.|+.-| +..||..+...|+-....+..-|+.+|...|...+|+||+..+|..|++-+
T Consensus 6 Yi~kvLKqVhp-d~giS~kam~imnSfvnDiferIa~EAs~L~~~nkr~TltsreIqtAvrl~ 67 (89)
T smart00427 6 YIYKVLKQVHP-DTGISSKAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRLI 67 (89)
T ss_pred HHHHHHHHhCC-CccccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHH
Confidence 58999999998 568999999999999999999999999999999999999999999998754
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=97.89 E-value=0.00011 Score=50.11 Aligned_cols=66 Identities=20% Similarity=0.213 Sum_probs=61.3
Q ss_pred cChhhHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC---CCCCcchHHHHHHhc
Q 033283 31 YLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKR---KTINGDDLLWAMATL 98 (122)
Q Consensus 31 ~LP~A~V~Ri~K~~lp~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~R---kTI~~eDV~~Al~~l 98 (122)
.||++.|+|||...++ ..++.+...+|.-.+.+||..|..+|.++..+.+. .-|.|+||-+|...|
T Consensus 16 ~f~k~~iKr~~~~~~~--~~v~~~v~i~v~glaKvFVGeivE~A~~V~~~~~~~~~~Pl~P~HireA~rrl 84 (85)
T cd08048 16 SFPKAAIKRLIQSVTG--QSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGEANTGPLQPRHLREAYRRL 84 (85)
T ss_pred hccHHHHHHHHHHHcC--CCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCCCCCcHHHHHHHHHh
Confidence 4999999999999986 79999999999999999999999999999988776 789999999998876
No 33
>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=97.82 E-value=0.00012 Score=47.97 Aligned_cols=63 Identities=21% Similarity=0.311 Sum_probs=51.3
Q ss_pred hhHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHHh
Q 033283 34 IANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMAT 97 (122)
Q Consensus 34 ~A~V~Ri~K~~lp~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~~ 97 (122)
+..+..+|++.=| +..+.+|+.++|.+.|..||.-++..|-..|++-|-.||...||.-.|++
T Consensus 2 K~~l~~Lv~~iDp-~~~ld~~vee~Ll~laddFv~~v~~~ac~lAKhR~s~tle~~Dv~~~Ler 64 (68)
T PF03847_consen 2 KRKLQELVKQIDP-NEKLDPDVEELLLELADDFVDDVVSFACRLAKHRKSSTLEVKDVQLHLER 64 (68)
T ss_dssp HHHHHHHHHCC-S-S----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHHH
T ss_pred hHHHHHHHHHcCC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCHHHHHHHHHh
Confidence 3467888998855 78999999999999999999999999999999999999999999999874
No 34
>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=97.81 E-value=2.9e-05 Score=51.47 Aligned_cols=64 Identities=20% Similarity=0.305 Sum_probs=53.6
Q ss_pred hhhHHHHHHHhhCC-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCC-CCcchHHHHHH
Q 033283 33 PIANISRIMKKALP-ANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKT-INGDDLLWAMA 96 (122)
Q Consensus 33 P~A~V~Ri~K~~lp-~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkT-I~~eDV~~Al~ 96 (122)
|..+|.||++.... ++.+|++||..++++....||..-...|.+.++.++... |..+|+-+.+-
T Consensus 1 p~~li~rll~~~f~~~~tkIs~dal~l~~eyl~iFV~EAv~Ra~~~a~~e~~~~~le~e~LEki~p 66 (72)
T PF09415_consen 1 PPELIARLLHEHFKDDKTKISKDALKLSAEYLRIFVREAVARAAEQAEAEGDEGFLEVEHLEKILP 66 (72)
T ss_dssp -CHHHHHHHCTTSSSTT-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSEE-HHHHHHHCH
T ss_pred ChHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHH
Confidence 88999999998774 467999999999999999999999999999999999988 99999987654
No 35
>KOG3467 consensus Histone H4 [Chromatin structure and dynamics]
Probab=97.74 E-value=0.00017 Score=49.89 Aligned_cols=68 Identities=19% Similarity=0.296 Sum_probs=60.8
Q ss_pred ChhhHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHHhcCCc
Q 033283 32 LPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMATLGFE 101 (122)
Q Consensus 32 LP~A~V~Ri~K~~lp~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~ 101 (122)
+-+-+|.||.+... .-+|+--.-+.+..++.+|+..+-..|..++++.+||||++-||+-+|+..|.-
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 56788999999774 357888888889999999999999999999999999999999999999998754
No 36
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=97.69 E-value=0.00023 Score=57.36 Aligned_cols=98 Identities=17% Similarity=0.325 Sum_probs=74.9
Q ss_pred CCCCCCCCCCCCCCCCCCC-CCc---cccccChhhHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 033283 5 APASPGGGSHESGEQSPRS-NVR---EQDRYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQR 80 (122)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~-~~~---~~d~~LP~A~V~Ri~K~~lp~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~ 80 (122)
+|-.++||+-..|+..|+. ... ..+..|=+-.+..+|++.- .+..|-+|+.++|.+.|..||..|+..|-..|++
T Consensus 124 ~P~~~~~g~~~g~~~sp~~s~s~~~~~~~~il~k~kl~dLvqqId-~~~~LD~dVedlLleiADdFV~sii~~sC~LAKH 202 (258)
T KOG1142|consen 124 APVIGSQGSVSGGGTSPAGSSSQDEPGNNPILSKRKLDDLVQQID-GTTKLDDDVEDLLLEIADDFVSSIIHRSCKLAKH 202 (258)
T ss_pred CCCCCCCCccCCCCCCCCcccccccCCCCccccccchhHHHHhhc-CcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3444444655555555543 222 2234577788889999984 3679999999999999999999999999999999
Q ss_pred cCCCCCCcchHHHHHHh---cCCccc
Q 033283 81 EKRKTINGDDLLWAMAT---LGFEDY 103 (122)
Q Consensus 81 ~~RkTI~~eDV~~Al~~---lgf~~~ 103 (122)
-+..||-..||...||+ +.|..|
T Consensus 203 RKsdtlEvrDIqLhLEr~~Nm~iPgf 228 (258)
T KOG1142|consen 203 RKSDTVEVRDIQLHLERNFNMEIPGF 228 (258)
T ss_pred cccCccchhheeeeeeccccccCCCc
Confidence 99999999999999993 444443
No 37
>KOG1658 consensus DNA polymerase epsilon, subunit C [Replication, recombination and repair]
Probab=97.68 E-value=2.8e-05 Score=58.45 Aligned_cols=69 Identities=25% Similarity=0.297 Sum_probs=60.5
Q ss_pred cccccChhhHHHHHHHhhCCCCcc-ccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHHh
Q 033283 27 EQDRYLPIANISRIMKKALPANGK-IAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMAT 97 (122)
Q Consensus 27 ~~d~~LP~A~V~Ri~K~~lp~~~~-iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~~ 97 (122)
..-..||++.|..+|| ++++.+ ...|++.++.++++.||..|...++..+...+|||+.-.|+-.|++.
T Consensus 55 a~l~rLpL~rik~vvk--l~pdl~l~~dea~~l~a~aaelfi~~Ln~~~~~~~q~~k~kt~qr~d~D~ai~~ 124 (162)
T KOG1658|consen 55 ASLSRLPLARIKQVVK--LDPDLTLLNDEASQLIAKAAELFIQELNDVAYTTAQLRKRKTEQRRDYDTAIEA 124 (162)
T ss_pred hhhhhccHHHHHhhcc--CCcchhhhhhHHHHHHHHHHHHHHHHHHhccchhHHHHHhhhhhhhcccccccc
Confidence 3446899999999999 556676 57788999999999999999999999999999999999998887764
No 38
>PLN00158 histone H2B; Provisional
Probab=97.67 E-value=0.00027 Score=50.88 Aligned_cols=67 Identities=16% Similarity=0.261 Sum_probs=60.1
Q ss_pred cChhhHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHHhc
Q 033283 31 YLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMATL 98 (122)
Q Consensus 31 ~LP~A~V~Ri~K~~lp~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~~l 98 (122)
+--..-|.|++|+.-| +..||..+...|+-....+..-|+.+|...|.-.+|+||+..+|..|++-+
T Consensus 27 esy~~YI~kVLKQVhP-d~gIS~kaM~ImnSfvnDiferIA~EAs~La~~nkr~TltsrEIqtAvrLv 93 (116)
T PLN00158 27 ETYKIYIYKVLKQVHP-DTGISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVRLI 93 (116)
T ss_pred ccHHHHHHHHHHHhCC-CCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHh
Confidence 3445669999999998 568999999999999999999999999999999999999999999998744
No 39
>PTZ00463 histone H2B; Provisional
Probab=97.64 E-value=0.00031 Score=50.59 Aligned_cols=63 Identities=19% Similarity=0.368 Sum_probs=57.6
Q ss_pred hHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHHhc
Q 033283 35 ANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMATL 98 (122)
Q Consensus 35 A~V~Ri~K~~lp~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~~l 98 (122)
.-|.|++|+.-| +..||..+...|+-.......-|+.+|...|.-.+|+||+..+|..|++-+
T Consensus 32 ~YI~KVLKqVhP-d~gIS~kaM~ImnSfvnDifErIA~EAs~La~~nkr~TltsrEIQtAvrLl 94 (117)
T PTZ00463 32 LYIFKVLKQVHP-DTGISRKSMNIMNSFLVDTFEKIATEASRLCKYTRRDTLSSREIQTAIRLV 94 (117)
T ss_pred HHHHHHHHhhCC-CCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHhhc
Confidence 359999999998 568999999999999999999999999999999999999999999998744
No 40
>COG5247 BUR6 Class 2 transcription repressor NC2, alpha subunit (DRAP1 homolog) [Transcription]
Probab=97.61 E-value=0.00017 Score=50.99 Aligned_cols=81 Identities=16% Similarity=0.281 Sum_probs=70.4
Q ss_pred cccChhhHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHHhcCCcccHHHHH
Q 033283 29 DRYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMATLGFEDYIDPLK 108 (122)
Q Consensus 29 d~~LP~A~V~Ri~K~~lp~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~~~~~l~ 108 (122)
-..+|.|.|.|||.-.- |..+|+.-.-....++.+.|+..|-.+..+.+...+-|.|+.+++..|.+.-+=.+|+..+.
T Consensus 21 ktrFP~ar~KkIMQ~de-DiGKV~q~tPVIaskalE~Fl~~iv~~s~k~aR~~~skR~t~e~lk~a~~sdekFdFL~~~~ 99 (113)
T COG5247 21 KTRFPIARLKKIMQLDE-DIGKVGQSTPVIASKALEMFLTEIVGLSLKEARKKSSKRMTSEFLKRATESDEKFDFLKNME 99 (113)
T ss_pred hhcCCHHHHHHHHHhhh-hhhhhhhcchHHHHHHHHHHHHHHHHHHHHHHHhccchhhHHHHHHHHHhhhHHHHHHHHHH
Confidence 35799999999999664 35689999999999999999999999999999999999999999999999776666766655
Q ss_pred HH
Q 033283 109 IY 110 (122)
Q Consensus 109 ~~ 110 (122)
.+
T Consensus 100 ~~ 101 (113)
T COG5247 100 QF 101 (113)
T ss_pred Hh
Confidence 44
No 41
>PLN00154 histone H2A; Provisional
Probab=97.61 E-value=0.00054 Score=50.56 Aligned_cols=70 Identities=19% Similarity=0.242 Sum_probs=58.3
Q ss_pred ccccChhhHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHHh
Q 033283 28 QDRYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMAT 97 (122)
Q Consensus 28 ~d~~LP~A~V~Ri~K~~lp~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~~ 97 (122)
..+.||.+.|.|++|+...-..||+..|...|.-..+=+...|-..|-..|...+++.|++.||..|+..
T Consensus 35 AgL~FPVgRi~r~Lk~g~~~~~RVga~ApVYLAAVLEYLtAEVLELAGNaA~d~kk~RItPrHi~lAIrn 104 (136)
T PLN00154 35 AGLQFPVGRIHRQLKQRVSAHGRVGATAAVYTAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRG 104 (136)
T ss_pred cCccCchHHHHHHHHhhhhhccccccchHHHHHHHHHHHHHHHHHHHHHHHHhhCCceecHHHhhhhccC
Confidence 3689999999999999763346999999988888776666666666778889999999999999999863
No 42
>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=97.54 E-value=0.00047 Score=47.55 Aligned_cols=67 Identities=21% Similarity=0.231 Sum_probs=52.1
Q ss_pred cChhhHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC-CCCCcchHHHHHHhc
Q 033283 31 YLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKR-KTINGDDLLWAMATL 98 (122)
Q Consensus 31 ~LP~A~V~Ri~K~~lp~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~R-kTI~~eDV~~Al~~l 98 (122)
.||++.|+|||...+. +..|+.....+|.=.+..||-.|-.+|.+++...+. .-|.|.|+-+|.+.|
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 5999999999999985 579999999999999999999999999999986665 379999999998765
No 43
>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=97.54 E-value=0.00073 Score=44.13 Aligned_cols=64 Identities=20% Similarity=0.235 Sum_probs=48.4
Q ss_pred cChhhHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHH
Q 033283 31 YLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMA 96 (122)
Q Consensus 31 ~LP~A~V~Ri~K~~lp~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~ 96 (122)
.+|..+|+-+... +. -..++.|+...|.+-++--|..|..+|.+...+.+|++++.+||-.||+
T Consensus 3 ~~~~esvk~iAes-~G-i~~l~de~a~~La~dveyrlreiiq~a~kfm~hskR~~Lt~~Di~~ALr 66 (66)
T PF02969_consen 3 VFSQESVKDIAES-LG-ISNLSDEAAKALAEDVEYRLREIIQEALKFMRHSKRTKLTTDDINSALR 66 (66)
T ss_dssp ---HHHHHHHHHH-TT----B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH-
T ss_pred cCCHHHHHHHHHH-cC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhC
Confidence 3677777655554 43 2379999999999999999999999999999999999999999999985
No 44
>smart00414 H2A Histone 2A.
Probab=97.46 E-value=0.00042 Score=49.03 Aligned_cols=68 Identities=15% Similarity=0.258 Sum_probs=59.1
Q ss_pred cccChhhHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHHh
Q 033283 29 DRYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMAT 97 (122)
Q Consensus 29 d~~LP~A~V~Ri~K~~lp~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~~ 97 (122)
.+.||.+.|.|+||+.-- ..||+..|...|.-+.+=+...+-..|...|...+++.|+++|+..|+..
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 478999999999998642 35999999999998888777777777888899999999999999999874
No 45
>KOG1756 consensus Histone 2A [Chromatin structure and dynamics]
Probab=97.29 E-value=0.00094 Score=48.84 Aligned_cols=69 Identities=16% Similarity=0.251 Sum_probs=55.8
Q ss_pred cccccChhhHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHH
Q 033283 27 EQDRYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMA 96 (122)
Q Consensus 27 ~~d~~LP~A~V~Ri~K~~lp~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~ 96 (122)
-..+.+|.+.|.|++|+. .--.+|+.+|...+.-+.+=....+...|-..+..++|.-|+++||..|+.
T Consensus 23 ~agl~fPvgri~r~Lr~~-~~~~ri~~gapV~laavLeYL~Aeile~agnaardnkk~ri~PrH~~lAI~ 91 (131)
T KOG1756|consen 23 RAGLQFPVGRIHRLLRKG-RYAQRVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRITPRHLQLAIR 91 (131)
T ss_pred hcccccCHHHHHHHHHcc-chhhhccCCChHHHHHHHHHHHHHHHHHhHHHhhhcCccccChHHHHHHHh
Confidence 345899999999999983 224689999999999766555555666666777888999999999999997
No 46
>PF15510 CENP-W: Centromere kinetochore component W
Probab=97.21 E-value=0.00072 Score=47.08 Aligned_cols=67 Identities=21% Similarity=0.257 Sum_probs=55.3
Q ss_pred ccChhhHHHHHHHhhCCCCccccHHHHHH--------------HHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHH
Q 033283 30 RYLPIANISRIMKKALPANGKIAKDAKET--------------VQECVSEFISFITSEASDKCQREKRKTINGDDLLWAM 95 (122)
Q Consensus 30 ~~LP~A~V~Ri~K~~lp~~~~iskdA~~a--------------l~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al 95 (122)
..-|++.+.|++|..-| ..++....-.+ +.--|-.|++-|+.||...|=+++-.||.++||+.|.
T Consensus 15 rkaPrgfLkrv~Kr~Kp-hlRl~~~~Dllv~~~~f~~~~~~~~vhLncLLFvhrLAEEaRtnA~EnK~~~Ik~~Hv~Aaa 93 (102)
T PF15510_consen 15 RKAPRGFLKRVFKRQKP-HLRLETSGDLLVRFCPFSGWQWGGEVHLNCLLFVHRLAEEARTNACENKCGTIKKEHVLAAA 93 (102)
T ss_pred HhCchHHHHHHHHhcCC-ceeecccccHHHhhcccccccccceeehhHHHHHHHHHHHHHHHHHHHhhccccHHHHHHHH
Confidence 35799999999998877 56665544344 6667889999999999998888899999999999997
Q ss_pred Hh
Q 033283 96 AT 97 (122)
Q Consensus 96 ~~ 97 (122)
+.
T Consensus 94 Kv 95 (102)
T PF15510_consen 94 KV 95 (102)
T ss_pred HH
Confidence 64
No 47
>PTZ00017 histone H2A; Provisional
Probab=97.13 E-value=0.0011 Score=48.80 Aligned_cols=68 Identities=15% Similarity=0.227 Sum_probs=59.6
Q ss_pred ccccChhhHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHH
Q 033283 28 QDRYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMA 96 (122)
Q Consensus 28 ~d~~LP~A~V~Ri~K~~lp~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~ 96 (122)
..+.||.+.|.|++|+.-- ..||+..|...|.-+.+-+...|-..|...|...+++-|+++||..|+.
T Consensus 24 agL~FPVgRi~R~Lk~g~~-a~RV~a~A~VYLAAVLEYLtaEILELAgNaa~d~kk~RItPrHi~lAI~ 91 (134)
T PTZ00017 24 AGLQFPVGRVHRYLKKGRY-AKRVGAGAPVYLAAVLEYLTAEVLELAGNAAKDNKKKRITPRHIQLAIR 91 (134)
T ss_pred CCcccchHHHHHHHhccch-hccccccchhhhHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHhhcc
Confidence 3689999999999998632 3599999999999988888888888888889999999999999999986
No 48
>PLN00156 histone H2AX; Provisional
Probab=96.95 E-value=0.0047 Score=45.78 Aligned_cols=67 Identities=13% Similarity=0.206 Sum_probs=56.6
Q ss_pred cccChhhHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHH
Q 033283 29 DRYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMA 96 (122)
Q Consensus 29 d~~LP~A~V~Ri~K~~lp~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~ 96 (122)
.+.||.+.|.|++|+.-- ..||+..|...|.-+.+=....|-..|...|...+++.|+++||..|+.
T Consensus 27 gL~FPVgRi~R~Lk~g~y-a~RVga~ApVYLAAVLEYLtaEVLELAgNaa~d~kk~RItPrHi~lAIr 93 (139)
T PLN00156 27 GLQFPVGRIARFLKAGKY-AERVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR 93 (139)
T ss_pred CcccchHHHHHHHhcCCh-hhccCCccHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHhhcc
Confidence 589999999999998643 3599999998888887666666666777788999999999999999986
No 49
>PLN00153 histone H2A; Provisional
Probab=96.94 E-value=0.005 Score=45.11 Aligned_cols=69 Identities=16% Similarity=0.219 Sum_probs=58.9
Q ss_pred ccccChhhHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHHh
Q 033283 28 QDRYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMAT 97 (122)
Q Consensus 28 ~d~~LP~A~V~Ri~K~~lp~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~~ 97 (122)
..+.||.+.|.|++|+.-- ..||+..|...|.-+.+=....|-..|...|...+++.|+++||..|+..
T Consensus 21 agL~FpVgRi~R~Lr~g~~-a~Rvga~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~n 89 (129)
T PLN00153 21 AGLQFPVGRIARYLKKGKY-AERIGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKNRIVPRHIQLAIRN 89 (129)
T ss_pred cCcccchHHHHHHHhcCch-hhccCCCchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHhhccC
Confidence 3689999999999998643 35999999999988877777777777788889999999999999999863
No 50
>PLN00157 histone H2A; Provisional
Probab=96.87 E-value=0.0024 Score=46.98 Aligned_cols=69 Identities=13% Similarity=0.187 Sum_probs=58.4
Q ss_pred ccccChhhHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHHh
Q 033283 28 QDRYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMAT 97 (122)
Q Consensus 28 ~d~~LP~A~V~Ri~K~~lp~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~~ 97 (122)
..+.||.+.|.|++|+.-- ..||+..|...|.-+.+-....|-..|...|...+++-|+++||..|+..
T Consensus 23 agL~FPVgRi~R~Lk~g~~-a~RIg~~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~n 91 (132)
T PLN00157 23 AGLQFPVGRIARYLKAGKY-ATRVGAGAPVYLAAVLEYLAAEVLELAGNAARDNKKSRIVPRHIQLAVRN 91 (132)
T ss_pred cCcccchHHHHHHHhcCch-hhhcCCCcHhHHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHhhcccC
Confidence 3589999999999998532 35999999999888877777777777788889999999999999999863
No 51
>KOG1744 consensus Histone H2B [Chromatin structure and dynamics]
Probab=96.82 E-value=0.0055 Score=44.76 Aligned_cols=71 Identities=23% Similarity=0.277 Sum_probs=60.7
Q ss_pred CCccccccChhhHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHHhc
Q 033283 24 NVREQDRYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMATL 98 (122)
Q Consensus 24 ~~~~~d~~LP~A~V~Ri~K~~lp~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~~l 98 (122)
..+.+.+..+ |.|++|+.-|+ .-|+.++...++-..-.+...|+.+|+..+.-.+|.||+-.+|..|..-|
T Consensus 33 ~~~~e~~s~y---v~kvlk~Vhpd-~gis~~a~~vmnsf~ndife~iA~ea~rla~y~krstisSreiqta~rLl 103 (127)
T KOG1744|consen 33 TRRKESYSEY---VYKVLKQVHPD-LGISSKAMGVMNSFVNDIFERIASEAGRLAHYNKRSTISSREIQTAVRLL 103 (127)
T ss_pred ccccCceeee---hhhhhhcccCC-CCcCHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCcccHHHHHHHHHHh
Confidence 4555555554 56689999886 66999999999999999999999999999999999999999999987643
No 52
>PTZ00252 histone H2A; Provisional
Probab=96.54 E-value=0.015 Score=42.94 Aligned_cols=68 Identities=7% Similarity=0.169 Sum_probs=49.0
Q ss_pred cccChhhHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHh--cCCCCCCcchHHHHHHh
Q 033283 29 DRYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQR--EKRKTINGDDLLWAMAT 97 (122)
Q Consensus 29 d~~LP~A~V~Ri~K~~lp~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~--~~RkTI~~eDV~~Al~~ 97 (122)
.+.||.+.|.|++|+.-- ..||+.-|-..|.-+.+=....|-..|...|.. .+++.|+++||..|+..
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 589999999999998754 358999888887776443333333334444433 56788999999999863
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=96.36 E-value=0.0056 Score=42.09 Aligned_cols=60 Identities=25% Similarity=0.310 Sum_probs=30.0
Q ss_pred HHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHHh
Q 033283 37 ISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMAT 97 (122)
Q Consensus 37 V~Ri~K~~lp~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~~ 97 (122)
|..+|..-. +.-.-..|...+|-+....||..+..+|...|...|+++|+.+|++-+|+.
T Consensus 7 I~~mMy~fG-D~~~P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~rg~~~i~~eDl~F~lR~ 66 (93)
T PF02269_consen 7 IRQMMYGFG-DVEEPLPETVDLVEDIVREYIIELCQEAMEVAQRRGSKKIKVEDLLFLLRK 66 (93)
T ss_dssp CHHHHHCTT-S-SS--HHHHHHHHHHHHHHHHHHHHHHHC---------------------
T ss_pred HHHHHHHcC-CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCcCcHHHHHHHHhc
Confidence 345555444 455789999999999999999999999999999999999999999999983
No 54
>KOG3219 consensus Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=96.17 E-value=0.0076 Score=46.91 Aligned_cols=70 Identities=14% Similarity=0.187 Sum_probs=62.3
Q ss_pred cChhhHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC-CCCCcchHHHHHHhcCCcc
Q 033283 31 YLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKR-KTINGDDLLWAMATLGFED 102 (122)
Q Consensus 31 ~LP~A~V~Ri~K~~lp~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~R-kTI~~eDV~~Al~~lgf~~ 102 (122)
.||++.|.|||.+... ..|+..+..+++=.+.+||-.|--+|.++|..-+. --|.|.||-.|...|....
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 5999999999999986 34999999999999999999999999999988776 4699999999999887643
No 55
>PF02291 TFIID-31kDa: Transcription initiation factor IID, 31kD subunit; InterPro: IPR003162 Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription []. TAFII-31 protein is a transcriptional coactivator of the p53 protein [].; GO: 0006352 transcription initiation, DNA-dependent; PDB: 1TAF_A.
Probab=95.96 E-value=0.049 Score=39.77 Aligned_cols=86 Identities=21% Similarity=0.214 Sum_probs=46.0
Q ss_pred ccccChhh--HHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHH-hcCCcccH
Q 033283 28 QDRYLPIA--NISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMA-TLGFEDYI 104 (122)
Q Consensus 28 ~d~~LP~A--~V~Ri~K~~lp~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~-~lgf~~~~ 104 (122)
..-.+|+. .|.-|+|+.. .......+...|.+.+-.|+.-|-..|..++.+.+|++|+.+||..|++ .+++.-..
T Consensus 7 ~~~~~PrDa~~i~~iL~~~G--v~~yeprVv~qLLEfayRYt~~vL~DA~~ya~hA~~~~i~~~DVrLAi~~r~~~~f~~ 84 (129)
T PF02291_consen 7 QSKSLPRDARVIHLILKSMG--VTEYEPRVVNQLLEFAYRYTSDVLEDAQVYADHAGRSTIDADDVRLAIQSRLDHSFTQ 84 (129)
T ss_dssp ------HHHHHHHHHHHHTT-----B-THHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHHHHT-------
T ss_pred CCccCChHHHHHHHHHHHcC--CcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHhhhccC
Confidence 34456663 2334444331 2256778888999999999999999999999999999999999999999 56776666
Q ss_pred HHHHHHHHHHH
Q 033283 105 DPLKIYLTRYR 115 (122)
Q Consensus 105 ~~l~~~l~~~r 115 (122)
++-+++|.+.-
T Consensus 85 pppre~llelA 95 (129)
T PF02291_consen 85 PPPREFLLELA 95 (129)
T ss_dssp -----------
T ss_pred CCChHHHHHHH
Confidence 66666665443
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=95.42 E-value=0.16 Score=34.99 Aligned_cols=60 Identities=17% Similarity=0.281 Sum_probs=49.9
Q ss_pred hHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHH
Q 033283 35 ANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMA 96 (122)
Q Consensus 35 A~V~Ri~K~~lp~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~ 96 (122)
.-|..+|.-.. ++-.-..|...+|-+...+||..++.+|.+.|. .++.-++.+|++-++.
T Consensus 6 ~ei~~mmy~~G-D~~~P~~eTv~llE~iv~~~i~~l~~~a~~~A~-~r~~k~~~eD~~FliR 65 (92)
T cd07978 6 KEIRQMMYGFG-DVQNPLPETVDLLEDIVVEYIIELCHKAAEVAQ-RRRGKVKVEDLIFLLR 65 (92)
T ss_pred HHHHHHHHHcC-CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-cCCCCCCHHHHHHHHh
Confidence 34677777665 355678999999999999999999999999998 4454569999999997
No 57
>KOG4336 consensus TBP-associated transcription factor Prodos [Transcription]
Probab=94.64 E-value=0.25 Score=41.03 Aligned_cols=74 Identities=19% Similarity=0.314 Sum_probs=60.7
Q ss_pred HHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHHhcCCcccHHHHHHHHHHH
Q 033283 37 ISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMATLGFEDYIDPLKIYLTRY 114 (122)
Q Consensus 37 V~Ri~K~~lp~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~~~~~l~~~l~~~ 114 (122)
|.-|.++.+= ..|++-|++.|.+.....|..+...+..+|+..||...+.-||...|-++|+. +..|..+++.+
T Consensus 11 V~~Ll~~~gf--d~is~~aletlvell~~yi~eigrq~~n~celagRT~pT~~Dv~l~Li~mnI~--v~sL~~~~q~~ 84 (323)
T KOG4336|consen 11 VSNLLKTKGF--DSISNAALETLVELLQSYIREIGRQLHNYCELAGRTIPTQGDVKLTLIEMNIK--VSSLYAYFQKQ 84 (323)
T ss_pred HHHHHHHhCc--hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcHHHHHHHHHHhCCC--hhhhHHHHHhc
Confidence 4444444432 25999999999999999999999999999999999999999999999999996 45555555544
No 58
>KOG2389 consensus Predicted bromodomain transcription factor [Transcription]
Probab=94.19 E-value=0.11 Score=43.61 Aligned_cols=88 Identities=18% Similarity=0.224 Sum_probs=65.9
Q ss_pred CCCCCCCCCCCCCCccccc--cChhhHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcc
Q 033283 12 GSHESGEQSPRSNVREQDR--YLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGD 89 (122)
Q Consensus 12 ~~~~~~~~~~~~~~~~~d~--~LP~A~V~Ri~K~~lp~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~e 89 (122)
|+-+++...-++.-...++ .|-+..|..|+....-+ ....-|.+.|+..+..||+.|+..|..++...||.-.+-.
T Consensus 8 ~~~q~~~~~~~~~~~~~~ya~sla~~avaQIcqslg~~--~~~~sale~Ltd~~~qyvQ~lgk~a~~~~n~anR~epnl~ 85 (353)
T KOG2389|consen 8 ENQQAEEESERSESEEAEYAFSLARVAVAQICQSLGYS--STQNSALETLTDVLQQYVQNLGKTAHRYSNLANRTEPNLF 85 (353)
T ss_pred hhhhhhhhcCccchhHHHHHHHHHHHHHHHHHHhcCCc--ccccHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCccHH
Confidence 4433333333344444444 57777888888765432 3444499999999999999999999999999999999999
Q ss_pred hHHHHHHhcCCc
Q 033283 90 DLLWAMATLGFE 101 (122)
Q Consensus 90 DV~~Al~~lgf~ 101 (122)
||+.||+.|+..
T Consensus 86 Div~Al~dls~s 97 (353)
T KOG2389|consen 86 DIVLALQDLSAS 97 (353)
T ss_pred HHHHHHHHhhhh
Confidence 999999987763
No 59
>KOG3423 consensus Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=93.93 E-value=0.39 Score=36.79 Aligned_cols=69 Identities=25% Similarity=0.244 Sum_probs=55.4
Q ss_pred cChhhHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC--------------CCCCCcchHHHHHH
Q 033283 31 YLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREK--------------RKTINGDDLLWAMA 96 (122)
Q Consensus 31 ~LP~A~V~Ri~K~~lp~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~--------------RkTI~~eDV~~Al~ 96 (122)
.||=+.+.-.++.+.= .....-.+-+|.-++..||.-|+..|.+.|+-.. |-|++-+|+..||+
T Consensus 86 ~IPDavt~~yL~~aGf--~~~D~rv~RLvsLaAQKfvSDIa~DA~Q~~k~r~~~~~~~~k~~~kdkK~tLtmeDL~~AL~ 163 (176)
T KOG3423|consen 86 TIPDAVTDHYLKKAGF--QTSDPRVKRLVSLAAQKFVSDIANDALQHSKIRTKTAIGKDKKQAKDKKYTLTMEDLSPALA 163 (176)
T ss_pred CCcHHHHHHHHHhcCC--CcCcHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccccccccccccceeeeHHHHHHHHH
Confidence 5888888888887641 2344556778999999999999999999996544 45899999999999
Q ss_pred hcCCc
Q 033283 97 TLGFE 101 (122)
Q Consensus 97 ~lgf~ 101 (122)
+.|+.
T Consensus 164 EyGin 168 (176)
T KOG3423|consen 164 EYGIN 168 (176)
T ss_pred HhCcc
Confidence 99874
No 60
>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily. Members of this protein are marked as probable ATPases by the nucleotide binding P-loop motif GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of helicases, and extensive homology to ATPases of MSHA-type pilus systems and to GspA proteins associated with type II protein secretion systems.
Probab=93.51 E-value=0.31 Score=37.43 Aligned_cols=69 Identities=13% Similarity=0.233 Sum_probs=54.8
Q ss_pred ChhhHHHHHHHhhCC-----CCccccHHHHHHHHHHHHH---HHHHHHHHHHHHHHhcCCCCCCcchHHHHHHhcCC
Q 033283 32 LPIANISRIMKKALP-----ANGKIAKDAKETVQECVSE---FISFITSEASDKCQREKRKTINGDDLLWAMATLGF 100 (122)
Q Consensus 32 LP~A~V~Ri~K~~lp-----~~~~iskdA~~al~~~a~~---FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~~lgf 100 (122)
|...-+..++...+. ....+++++...|.+.+.= .|+.++..+...+-..+.++|+.++|..++.++.|
T Consensus 192 l~~~e~~~~l~~~l~~~g~~~~~~~~~~~~~~i~~~s~G~p~~i~~l~~~~~~~a~~~~~~~i~~~~v~~~~~~~~~ 268 (269)
T TIGR03015 192 LDREETREYIEHRLERAGNRDAPVFSEGAFDAIHRFSRGIPRLINILCDRLLLSAFLEEKREIGGEEVREVIAEIDF 268 (269)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCCCcCHHHHHHHHHHcCCcccHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhhc
Confidence 444555555554431 2346999999999998875 79999999999988889999999999999999875
No 61
>KOG2549 consensus Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=91.67 E-value=1 Score=40.15 Aligned_cols=66 Identities=21% Similarity=0.292 Sum_probs=54.6
Q ss_pred hhhHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHHhcCC
Q 033283 33 PIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMATLGF 100 (122)
Q Consensus 33 P~A~V~Ri~K~~lp~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~~lgf 100 (122)
|.-.+ +.|-+.+. -..++.|+..+|.+=.+.=|..++.+|.+.-.+.+|.+++.+||..||+.+..
T Consensus 13 ~~Es~-k~vAEslG-i~nl~deaa~~La~dv~yrikEI~Q~aaKfm~hskR~kLtv~DV~~ALr~~nV 78 (576)
T KOG2549|consen 13 PKESV-KVVAESLG-ITNLNDEAALLLAEDVEYRIKEIVQDAAKFMVHSKRTKLTVDDVDYALRSLNV 78 (576)
T ss_pred cHHHH-HHHHHHhC-ccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcCcHHHHHHHHhhccc
Confidence 34444 44445553 34699999999999999999999999999999999999999999999995543
No 62
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=90.91 E-value=1.4 Score=35.89 Aligned_cols=71 Identities=13% Similarity=0.169 Sum_probs=51.2
Q ss_pred ChhhHHHHHHHhhCCC---CccccHHHHHHHHHHH------HHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHHhcCCcc
Q 033283 32 LPIANISRIMKKALPA---NGKIAKDAKETVQECV------SEFISFITSEASDKCQREKRKTINGDDLLWAMATLGFED 102 (122)
Q Consensus 32 LP~A~V~Ri~K~~lp~---~~~iskdA~~al~~~a------~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~ 102 (122)
+...-+..|++..+.. ...++.++.+.+.+.+ -..+..+...|.+.|...++.+|+.+||..|++.+....
T Consensus 207 y~~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~a~~~a~~~~~~~I~~~~v~~a~~~~~~~~ 286 (394)
T PRK00411 207 YTADEIFDILKDRVEEGFYPGVVDDEVLDLIADLTAREHGDARVAIDLLRRAGLIAEREGSRKVTEEDVRKAYEKSEIVH 286 (394)
T ss_pred CCHHHHHHHHHHHHHhhcccCCCCHhHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHHHHH
Confidence 3345566666655422 2358999988888877 334556667888889989999999999999999884333
No 63
>KOG1757 consensus Histone 2A [Chromatin structure and dynamics]
Probab=87.49 E-value=1.1 Score=32.53 Aligned_cols=67 Identities=18% Similarity=0.326 Sum_probs=51.2
Q ss_pred ccccccChhhHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC----CCCCcchHHHHHH
Q 033283 26 REQDRYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKR----KTINGDDLLWAMA 96 (122)
Q Consensus 26 ~~~d~~LP~A~V~Ri~K~~lp~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~R----kTI~~eDV~~Al~ 96 (122)
.-..+.+|.++|.|.+|.......++..-+..-. ...+.||+.|-.+.|.+..+ |.|++.|+-.|++
T Consensus 25 ~raGlqFpVgRihr~LK~r~t~h~rVGataavy~----aaileYLTaEVLeLAgNasKdLKvKRitprHlqLAiR 95 (131)
T KOG1757|consen 25 ARAGLQFPVGRIHRHLKTRTTSHGRVGATAAVYS----AAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 95 (131)
T ss_pred HhcccccchHHHHHHHHHhcccccccchHHHHHH----HHHHHHHHHHHHHHcccccccceeeeccchhheeeec
Confidence 3345899999999999999887888865443322 33567899988888876655 7899999988876
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=87.19 E-value=3.6 Score=33.08 Aligned_cols=72 Identities=10% Similarity=0.126 Sum_probs=49.0
Q ss_pred hhHHHHHHHhhCC---CCccccHHHHHHHHHHHH------HHHHHHHHHHHHHHHhcCCCCCCcchHHHHHHhcCCcccH
Q 033283 34 IANISRIMKKALP---ANGKIAKDAKETVQECVS------EFISFITSEASDKCQREKRKTINGDDLLWAMATLGFEDYI 104 (122)
Q Consensus 34 ~A~V~Ri~K~~lp---~~~~iskdA~~al~~~a~------~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~~~ 104 (122)
..-+..|++..+. ....++.|+...+.+.+. -.+..+...|.+.|...++.+|+.+||..|++.+....+.
T Consensus 201 ~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~R~al~~l~~a~~~a~~~~~~~it~~~v~~a~~~~~~~~~~ 280 (365)
T TIGR02928 201 AEELRDILENRAEKAFYDGVLDDGVIPLCAALAAQEHGDARKAIDLLRVAGEIAEREGAERVTEDHVEKAQEKIEKDRLL 280 (365)
T ss_pred HHHHHHHHHHHHHhhccCCCCChhHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHH
Confidence 4446666665543 123588888877766443 2344456677788888899999999999999988544444
Q ss_pred H
Q 033283 105 D 105 (122)
Q Consensus 105 ~ 105 (122)
.
T Consensus 281 ~ 281 (365)
T TIGR02928 281 E 281 (365)
T ss_pred H
Confidence 3
No 65
>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=84.42 E-value=8 Score=29.80 Aligned_cols=75 Identities=9% Similarity=0.151 Sum_probs=56.3
Q ss_pred cccChhhHHHHHHHhhCCCCc--cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhc------CCCCCCcchHHHHHHhcCC
Q 033283 29 DRYLPIANISRIMKKALPANG--KIAKDAKETVQECVSEFISFITSEASDKCQRE------KRKTINGDDLLWAMATLGF 100 (122)
Q Consensus 29 d~~LP~A~V~Ri~K~~lp~~~--~iskdA~~al~~~a~~FI~~la~~A~~~a~~~------~RkTI~~eDV~~Al~~lgf 100 (122)
...|....+.+.|...+.... .++.|...+|..||+.++..|-......|++- ...+....||-.-|..|+-
T Consensus 42 ~~fl~~~~l~~~~~~i~~~~g~~~~~~d~~~lis~a~e~rlr~li~k~~~~s~hR~~~~~~~~r~~~~sdvr~qL~~l~~ 121 (212)
T cd08045 42 PSFLNPSPLAKKIRKIAKKHGLKEVDEDVLDLISLALEERLRNLLEKLIEVSEHRVDSEKEDERYEITSDVRKQLRFLEQ 121 (212)
T ss_pred hhccCHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCceeecchHHHHHHHHHH
Confidence 356677777776666665433 69999999999999999999999988888764 3456777888877776655
Q ss_pred ccc
Q 033283 101 EDY 103 (122)
Q Consensus 101 ~~~ 103 (122)
-+.
T Consensus 122 ~ek 124 (212)
T cd08045 122 LER 124 (212)
T ss_pred HHH
Confidence 433
No 66
>KOG3334 consensus Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=82.52 E-value=6.8 Score=29.38 Aligned_cols=64 Identities=14% Similarity=0.207 Sum_probs=48.1
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHHhcCCcccHH-HHHHHHHHH
Q 033283 51 IAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMATLGFEDYID-PLKIYLTRY 114 (122)
Q Consensus 51 iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~~~~-~l~~~l~~~ 114 (122)
...-...-|-+.+=-++.-|-..|.-++.+.+|.||..+||..|++...=.+|.. +=+++|-++
T Consensus 31 yEprVi~qlLefa~rYtt~vL~DA~vys~HA~ka~i~~eDVrlA~~~~~~~sf~~pPpRe~lL~l 95 (148)
T KOG3334|consen 31 YEPRVINQLLEFAYRYTTTVLDDAKVYSSHAKKATIDAEDVRLAIQMRVDHSFTPPPPREFLLEL 95 (148)
T ss_pred cChHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHhccccCCCCchHHHHHH
Confidence 4455556667777777788888999999999999999999999999766656654 444444433
No 67
>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=82.46 E-value=5.8 Score=35.45 Aligned_cols=49 Identities=14% Similarity=0.160 Sum_probs=40.0
Q ss_pred cccHHHHHHHHHHHH-------------HHHHHHHHHHHHHHHhcCCCCCCcchHHHHHHhc
Q 033283 50 KIAKDAKETVQECVS-------------EFISFITSEASDKCQREKRKTINGDDLLWAMATL 98 (122)
Q Consensus 50 ~iskdA~~al~~~a~-------------~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~~l 98 (122)
.++++|...|.+.++ .=+.-|-.+|..+|..+++.+|+.+||.+|++.-
T Consensus 330 ~~s~~Av~~Li~~~~R~ag~r~~lsl~~R~L~~llR~A~~iA~~~~~~~I~~ehV~~Ai~~~ 391 (608)
T TIGR00764 330 HFTRDAVEEIVREAQRRAGRKDHLTLRLRELGGLVRAAGDIAKSSGKVYVTAEHVLKAKKLA 391 (608)
T ss_pred cCCHHHHHHHHHHHHHHHhcccccCCCHHHHHHHHHHHHHHHHhcCCceecHHHHHHHHHHH
Confidence 689999988876544 3455667788889989999999999999998854
No 68
>PF13654 AAA_32: AAA domain; PDB: 3K1J_B.
Probab=82.42 E-value=7 Score=34.32 Aligned_cols=49 Identities=16% Similarity=0.199 Sum_probs=38.8
Q ss_pred cccHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHhcCCCCCCcchHHHHHHhc
Q 033283 50 KIAKDAKETVQECVSE-----------FISFITSEASDKCQREKRKTINGDDLLWAMATL 98 (122)
Q Consensus 50 ~iskdA~~al~~~a~~-----------FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~~l 98 (122)
.++.+|+..|-+.+.. .|.-|-.+|+.+|...++++|+++||.+|++.-
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 5888888888777653 567778899999999999999999999999863
No 69
>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=82.37 E-value=4.6 Score=34.36 Aligned_cols=53 Identities=26% Similarity=0.290 Sum_probs=49.2
Q ss_pred ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHHhcCCc
Q 033283 49 GKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMATLGFE 101 (122)
Q Consensus 49 ~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~ 101 (122)
..|..|+..++..-.+-=|+.+..+|.+.-.+.||..++-+||..||..++.+
T Consensus 21 ~Ni~Dd~l~alamDlEYRI~ev~qea~KFmvhSKRtvLt~dDis~ALr~lNVe 73 (450)
T COG5095 21 SNIDDDALRALAMDLEYRIKEVCQEASKFMVHSKRTVLTIDDISYALRSLNVE 73 (450)
T ss_pred cccccHHHHHHHHhHHHHHHHHHHHHHHHhhcccceeeeHHhHHHHHHhcCCC
Confidence 47999999999999999999999999999999999999999999999987653
No 70
>TIGR02902 spore_lonB ATP-dependent protease LonB. Members of this protein are LonB, a paralog of the ATP-dependent protease La (LonA, TIGR00763). LonB proteins are found strictly, and almost universally, in endospore-forming bacteria. This protease was shown, in Bacillus subtilis, to be expressed specifically in the forespore, during sporulation, under control of sigma(F). The lonB gene, despite location immediately upstream of lonA, was shown to be monocistronic. LonB appears able to act on sigma(H) for post-translation control, but lonB mutation did not produce an obvious sporulation defect under the conditions tested. Note that additional paralogs of LonA and LonB occur in the Clostridium lineage and this model selects only one per species as the protein that corresponds to LonB in B. subtilis.
Probab=80.94 E-value=4.7 Score=35.31 Aligned_cols=67 Identities=24% Similarity=0.228 Sum_probs=45.3
Q ss_pred hhHHHHHHHhhCCC-CccccHHHHHHHHHHHHHH--HHHHHHHHHHHHHhcCCCCCCcchHHHHHHhcCC
Q 033283 34 IANISRIMKKALPA-NGKIAKDAKETVQECVSEF--ISFITSEASDKCQREKRKTINGDDLLWAMATLGF 100 (122)
Q Consensus 34 ~A~V~Ri~K~~lp~-~~~iskdA~~al~~~a~~F--I~~la~~A~~~a~~~~RkTI~~eDV~~Al~~lgf 100 (122)
..-+.+|++..+.. +..+++++...|.+.+... +..+...|...|..++|++|+.+||.+++..-.|
T Consensus 265 ~eei~~Il~~~a~k~~i~is~~al~~I~~y~~n~Rel~nll~~Aa~~A~~~~~~~It~~dI~~vl~~~~~ 334 (531)
T TIGR02902 265 DEEIKEIAKNAAEKIGINLEKHALELIVKYASNGREAVNIVQLAAGIALGEGRKRILAEDIEWVAENGNY 334 (531)
T ss_pred HHHHHHHHHHHHHHcCCCcCHHHHHHHHHhhhhHHHHHHHHHHHHHHHhhCCCcEEcHHHHHHHhCCccc
Confidence 34456666666542 4578999999887776521 2223344556777788999999999999764433
No 71
>PF13335 Mg_chelatase_2: Magnesium chelatase, subunit ChlI
Probab=80.02 E-value=7.8 Score=26.44 Aligned_cols=48 Identities=15% Similarity=0.197 Sum_probs=38.8
Q ss_pred ccccHHHHHHHHHHHHHH------HHHHHHHHHHHHHhcCCCCCCcchHHHHHH
Q 033283 49 GKIAKDAKETVQECVSEF------ISFITSEASDKCQREKRKTINGDDLLWAMA 96 (122)
Q Consensus 49 ~~iskdA~~al~~~a~~F------I~~la~~A~~~a~~~~RkTI~~eDV~~Al~ 96 (122)
..+++++...|.+++..+ ++-|..-|..+|--++...|..+||..||.
T Consensus 41 ~~l~~~~~~~l~~~~~~~~lS~R~~~rilrvARTIADL~~~~~I~~~hi~EAl~ 94 (96)
T PF13335_consen 41 CPLSSEAKKLLEQAAEKLNLSARGYHRILRVARTIADLEGSERITREHIAEALS 94 (96)
T ss_pred cCCCHHHHHHHHHHHHHcCcCHHHHHHHHHHHHHHHhHcCCCCCCHHHHHHHHh
Confidence 357778888888777665 445566789999999999999999999985
No 72
>KOG2680 consensus DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=76.94 E-value=13 Score=31.88 Aligned_cols=60 Identities=18% Similarity=0.279 Sum_probs=46.0
Q ss_pred HHHHHHhhCC-CCccccHHHHHHHHHHHHH----HHHHHHHHHHHHHHhcCCCCCCcchHHHHHH
Q 033283 37 ISRIMKKALP-ANGKIAKDAKETVQECVSE----FISFITSEASDKCQREKRKTINGDDLLWAMA 96 (122)
Q Consensus 37 V~Ri~K~~lp-~~~~iskdA~~al~~~a~~----FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~ 96 (122)
+..|.+-... +++.++.||++.|.+..+. +..+|-+.|+..|.+.+-+++..+||-.+.+
T Consensus 363 ~~~IL~iRc~EEdv~m~~~A~d~Lt~i~~~tsLRYai~Lit~a~~~~~krk~~~v~~~di~r~y~ 427 (454)
T KOG2680|consen 363 IKKILRIRCQEEDVEMNPDALDLLTKIGEATSLRYAIHLITAASLVCLKRKGKVVEVDDIERVYR 427 (454)
T ss_pred HHHHHHhhhhhhccccCHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHhcCceeehhHHHHHHH
Confidence 4444444333 3678999999999876553 5566667789999999999999999999976
No 73
>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=74.62 E-value=4 Score=24.38 Aligned_cols=42 Identities=12% Similarity=0.063 Sum_probs=28.0
Q ss_pred cHHHHHHHHHHHHHHHHHHHH-HHHHHHHhcCCCCCCcchHHHH
Q 033283 52 AKDAKETVQECVSEFISFITS-EASDKCQREKRKTINGDDLLWA 94 (122)
Q Consensus 52 skdA~~al~~~a~~FI~~la~-~A~~~a~~~~RkTI~~eDV~~A 94 (122)
+.||...|.+. -.|+.--.. .+-..|...|...|+.++|..|
T Consensus 2 ~~eA~~~L~~i-P~fvR~~~r~~~E~~Ar~~G~~~IT~e~v~~A 44 (45)
T PF08369_consen 2 TDEAEARLDRI-PFFVRKKLRDAAEKYARERGYDEITVEVVDAA 44 (45)
T ss_dssp -HHHHHHHCTS--HHHHHHHHHHHHHHHHHCT-SEE-HHHHHHH
T ss_pred CHHHHHHHHHC-CHHHHHHHHHHHHHHHHHcCCCeECHHHHHhh
Confidence 56777777775 667765444 3447889999999999998876
No 74
>COG1067 LonB Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]
Probab=73.04 E-value=3.4 Score=37.44 Aligned_cols=49 Identities=27% Similarity=0.268 Sum_probs=37.1
Q ss_pred cccHHHHHHHHHHHHH-------------HHHHHHHHHHHHHHhcCCCCCCcchHHHHHHhc
Q 033283 50 KIAKDAKETVQECVSE-------------FISFITSEASDKCQREKRKTINGDDLLWAMATL 98 (122)
Q Consensus 50 ~iskdA~~al~~~a~~-------------FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~~l 98 (122)
-++++|..-|.+-+.. -+.-|-.+|..+|..++++-|+++||.+|++.-
T Consensus 338 ~~~~~Av~~li~~a~R~Ag~~~~Ltl~~rdl~~lv~~A~~ia~~~~~~~I~ae~Ve~a~~~~ 399 (647)
T COG1067 338 HLDKDAVEELIREAARRAGDQNKLTLRLRDLGNLVREAGDIAVSEGRKLITAEDVEEALQKR 399 (647)
T ss_pred CCCHHHHHHHHHHHHHhccccceeccCHHHHHHHHHHhhHHHhcCCcccCcHHHHHHHHHhh
Confidence 4777777666655543 233344589999999999999999999999973
No 75
>COG5162 Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=69.57 E-value=38 Score=26.17 Aligned_cols=51 Identities=20% Similarity=0.221 Sum_probs=39.5
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHHHh---------------------------------cCCCCCCcchHHHHHHh
Q 033283 51 IAKDAKETVQECVSEFISFITSEASDKCQR---------------------------------EKRKTINGDDLLWAMAT 97 (122)
Q Consensus 51 iskdA~~al~~~a~~FI~~la~~A~~~a~~---------------------------------~~RkTI~~eDV~~Al~~ 97 (122)
...-.+-++.-.+..||.-|+..|+++.+- .++.+++-.|+..||++
T Consensus 106 ~D~rvKkLl~L~aqKFvsDiA~dayqYsrIr~~~sna~~t~~~a~~f~~gg~~~i~~~~~~~dr~K~vltv~DLs~Al~E 185 (197)
T COG5162 106 SDQRVKKLLSLLAQKFVSDIAVDAYQYSRIRQGSSNAKATAQKAKRFAKGGASGIGSSGRRGDRKKPVLTVVDLSKALEE 185 (197)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccchhhHHHHHHHHhcccccccccccccccCCceeeehHHHHHHHH
Confidence 344567788899999999999888765421 15567899999999999
Q ss_pred cCCc
Q 033283 98 LGFE 101 (122)
Q Consensus 98 lgf~ 101 (122)
.|+.
T Consensus 186 yGin 189 (197)
T COG5162 186 YGIN 189 (197)
T ss_pred hccc
Confidence 8873
No 76
>PRK09862 putative ATP-dependent protease; Provisional
Probab=69.11 E-value=21 Score=31.48 Aligned_cols=60 Identities=12% Similarity=0.119 Sum_probs=45.4
Q ss_pred ccccHHHHHHHHHHHHHH------HHHHHHHHHHHHHhcCCCCCCcchHHHHHHhcCCcccHHHHH
Q 033283 49 GKIAKDAKETVQECVSEF------ISFITSEASDKCQREKRKTINGDDLLWAMATLGFEDYIDPLK 108 (122)
Q Consensus 49 ~~iskdA~~al~~~a~~F------I~~la~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~~~~~l~ 108 (122)
..+++++...+.++...+ .+.|..-|..+|--+++..|+++||..|++=-+++..+-.+.
T Consensus 437 ~~l~~~~~~~l~~~~~~~~lS~Ra~~rlLrvARTiADL~g~~~V~~~hv~eAl~yR~~~~~~~~~~ 502 (506)
T PRK09862 437 CKLESEDARWLEETLIHLGLSIRAWQRLLKVARTIADIDQSDIITRQHLQEAVSYRAIDRLLIHLQ 502 (506)
T ss_pred hCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHhhcccHHHHHHH
Confidence 367888888777765444 566777889999999999999999999998666554444333
No 77
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=66.62 E-value=29 Score=27.92 Aligned_cols=72 Identities=13% Similarity=0.193 Sum_probs=50.1
Q ss_pred cChhhHHHHHHHhhCC-CCccccHHHHHHHHHHHHH---HHHHHHHHHHHHHHhcCCCCCCcchHHHHHHhcCCcc
Q 033283 31 YLPIANISRIMKKALP-ANGKIAKDAKETVQECVSE---FISFITSEASDKCQREKRKTINGDDLLWAMATLGFED 102 (122)
Q Consensus 31 ~LP~A~V~Ri~K~~lp-~~~~iskdA~~al~~~a~~---FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~ 102 (122)
.++...+..|++.... .++.++.|+...|.+.+.- .+..+-..+...+...+.+.|+.++|..+++.++...
T Consensus 179 ~~~~~e~~~il~~~~~~~~~~~~~~~~~~ia~~~~G~pR~a~~~l~~~~~~a~~~~~~~I~~~~v~~~l~~~~~~~ 254 (328)
T PRK00080 179 FYTVEELEKIVKRSARILGVEIDEEGALEIARRSRGTPRIANRLLRRVRDFAQVKGDGVITKEIADKALDMLGVDE 254 (328)
T ss_pred CCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCc
Confidence 3555666666665543 2567999998888877632 3444445566666666677899999999999877654
No 78
>TIGR02442 Cob-chelat-sub cobaltochelatase subunit. A number of genomes (actinobacteria, cyanobacteria, betaproteobacteria and pseudomonads) which apparently biosynthesize B12, encode a cobN gene but are demonstrably lacking cobS and cobT. These genomes do, however contain a homolog (modelled here) of the magnesium chelatase subunits BchI/BchD family. Aside from the cyanobacteria (which have a separate magnesium chelatase trimer), these species do not make chlorins, so do not have any use for a magnesium chelatase. Furthermore, in nearly all cases the members of this family are proximal to either CobN itself or other genes involved in cobalt transport or B12 biosynthesis.
Probab=65.32 E-value=27 Score=31.28 Aligned_cols=49 Identities=16% Similarity=0.188 Sum_probs=41.7
Q ss_pred CccccHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCCCCcchHHHHHH
Q 033283 48 NGKIAKDAKETVQECVSEFI-------SFITSEASDKCQREKRKTINGDDLLWAMA 96 (122)
Q Consensus 48 ~~~iskdA~~al~~~a~~FI-------~~la~~A~~~a~~~~RkTI~~eDV~~Al~ 96 (122)
.+.|+.+.+..|.+.+..+- .++...|..+|.-++|.+|+.+||..|++
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 57899999999998887762 45667788889999999999999999987
No 79
>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=64.84 E-value=47 Score=26.01 Aligned_cols=70 Identities=19% Similarity=0.204 Sum_probs=47.6
Q ss_pred ChhhHHHHHHHhhCC-CCccccHHHHHHHHHHHH---HHHHHHHHHHHHHHHhcCCCCCCcchHHHHHHhcCCc
Q 033283 32 LPIANISRIMKKALP-ANGKIAKDAKETVQECVS---EFISFITSEASDKCQREKRKTINGDDLLWAMATLGFE 101 (122)
Q Consensus 32 LP~A~V~Ri~K~~lp-~~~~iskdA~~al~~~a~---~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~ 101 (122)
++...+..+++.... .+..++.|+...|.+.+. -++..+...+...+...+...|+.++|..++..++++
T Consensus 159 l~~~e~~~il~~~~~~~~~~~~~~al~~ia~~~~G~pR~~~~ll~~~~~~a~~~~~~~it~~~v~~~l~~l~~~ 232 (305)
T TIGR00635 159 YTVEELAEIVSRSAGLLNVEIEPEAALEIARRSRGTPRIANRLLRRVRDFAQVRGQKIINRDIALKALEMLMID 232 (305)
T ss_pred CCHHHHHHHHHHHHHHhCCCcCHHHHHHHHHHhCCCcchHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHhCCC
Confidence 445556666665543 246789999888887653 2334445556666666666779999999999987654
No 80
>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I. This model represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria.
Probab=64.55 E-value=34 Score=28.40 Aligned_cols=54 Identities=22% Similarity=0.205 Sum_probs=41.7
Q ss_pred HhhCCCCccccHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCCCCcchHHHHHH
Q 033283 42 KKALPANGKIAKDAKETVQECVSEFI-------SFITSEASDKCQREKRKTINGDDLLWAMA 96 (122)
Q Consensus 42 K~~lp~~~~iskdA~~al~~~a~~FI-------~~la~~A~~~a~~~~RkTI~~eDV~~Al~ 96 (122)
++.++ .+.|+.+.+..+.+.+..+= .++...|...|.-+||..|+++||..+..
T Consensus 247 ~~~~~-~V~v~d~~~~~i~~l~~~~~~~s~Ra~i~l~raArA~Aal~GR~~V~~dDv~~~a~ 307 (337)
T TIGR02030 247 QNLLP-QVTIPYDVLVKVAELCAELDVDGLRGELTLNRAAKALAAFEGRTEVTVDDIRRVAV 307 (337)
T ss_pred HHHhc-cCcCCHHHHHHHHHHHHHHCCCCCcHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 34444 57889988888888766542 34667788889999999999999998876
No 81
>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=64.13 E-value=5.9 Score=22.98 Aligned_cols=25 Identities=20% Similarity=0.251 Sum_probs=20.0
Q ss_pred HHHHHHhcCCCCCCcchHHHHHHhc
Q 033283 74 ASDKCQREKRKTINGDDLLWAMATL 98 (122)
Q Consensus 74 A~~~a~~~~RkTI~~eDV~~Al~~l 98 (122)
|.+.|...+-..|+++|++.||=+-
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 5678889999999999999996543
No 82
>TIGR00368 Mg chelatase-related protein. The N-terminal end matches very strongly a pfam Mg_chelatase domain.
Probab=62.81 E-value=21 Score=31.31 Aligned_cols=47 Identities=15% Similarity=0.181 Sum_probs=40.5
Q ss_pred cccHHHHHHHHHHHHHH------HHHHHHHHHHHHHhcCCCCCCcchHHHHHH
Q 033283 50 KIAKDAKETVQECVSEF------ISFITSEASDKCQREKRKTINGDDLLWAMA 96 (122)
Q Consensus 50 ~iskdA~~al~~~a~~F------I~~la~~A~~~a~~~~RkTI~~eDV~~Al~ 96 (122)
.++++++..|.++...+ .+-+..-|..+|.-+++..|..+||..|++
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 56888999999888776 556677899999999999999999999985
No 83
>PRK13406 bchD magnesium chelatase subunit D; Provisional
Probab=61.12 E-value=22 Score=31.80 Aligned_cols=59 Identities=15% Similarity=0.142 Sum_probs=47.1
Q ss_pred HHHHHHHhhCCCCccccHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCCCCcchHHHHHH
Q 033283 36 NISRIMKKALPANGKIAKDAKETVQECVSEFI-------SFITSEASDKCQREKRKTINGDDLLWAMA 96 (122)
Q Consensus 36 ~V~Ri~K~~lp~~~~iskdA~~al~~~a~~FI-------~~la~~A~~~a~~~~RkTI~~eDV~~Al~ 96 (122)
.|.+.- +.++ ++.|+.+....+.+.|..|= .++...|..+|--++|.+|+.+||..|+.
T Consensus 183 ~I~~AR-~rl~-~v~v~~~~l~~i~~~~~~~gv~S~Ra~i~llraARa~AaL~Gr~~V~~~dv~~Aa~ 248 (584)
T PRK13406 183 DIAAAR-ARLP-AVGPPPEAIAALCAAAAALGIASLRAPLLALRAARAAAALAGRTAVEEEDLALAAR 248 (584)
T ss_pred HHHHHH-HHHc-cCCCCHHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 444333 3444 78899999998888877774 46778899999999999999999999987
No 84
>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=60.28 E-value=16 Score=25.47 Aligned_cols=33 Identities=18% Similarity=0.298 Sum_probs=26.4
Q ss_pred hHHHHHHHhhC----CCCccccHHHHHHHHHHHHHHH
Q 033283 35 ANISRIMKKAL----PANGKIAKDAKETVQECVSEFI 67 (122)
Q Consensus 35 A~V~Ri~K~~l----p~~~~iskdA~~al~~~a~~FI 67 (122)
++|.+++|..| .|+..++.++.+.|+++++.|-
T Consensus 51 SNIGvLIKkglIEKSGDGlv~T~~g~~Ii~~AA~l~a 87 (96)
T PF09114_consen 51 SNIGVLIKKGLIEKSGDGLVITEEGMDIIIQAAELWA 87 (96)
T ss_dssp HHHHHHHHTTSEEEETTEEEE-HHHHHHHHHHHHHHH
T ss_pred HhHHHHHHcCcccccCCceEEechHHHHHHHHHHHHH
Confidence 45777999877 3466899999999999999984
No 85
>COG1222 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]
Probab=60.07 E-value=15 Score=31.62 Aligned_cols=79 Identities=23% Similarity=0.228 Sum_probs=49.5
Q ss_pred CCCCCCccccccChhhHHHHHHHhhCCCCccccHHH-HHHHHHHHHHH----HHHHHHHHHHHHHhcCCCCCCcchHHHH
Q 033283 20 SPRSNVREQDRYLPIANISRIMKKALPANGKIAKDA-KETVQECVSEF----ISFITSEASDKCQREKRKTINGDDLLWA 94 (122)
Q Consensus 20 ~~~~~~~~~d~~LP~A~V~Ri~K~~lp~~~~iskdA-~~al~~~a~~F----I~~la~~A~~~a~~~~RkTI~~eDV~~A 94 (122)
.||-.-+.=++.||--.=++-|=+.--..|.+.+|. .+.|.+.++-| |.-++.+|-..|.++.|..|+.+|.++|
T Consensus 309 RPGR~DRkIEfplPd~~gR~~Il~IHtrkM~l~~dvd~e~la~~~~g~sGAdlkaictEAGm~AiR~~R~~Vt~~DF~~A 388 (406)
T COG1222 309 RPGRFDRKIEFPLPDEEGRAEILKIHTRKMNLADDVDLELLARLTEGFSGADLKAICTEAGMFAIRERRDEVTMEDFLKA 388 (406)
T ss_pred CCCcccceeecCCCCHHHHHHHHHHHhhhccCccCcCHHHHHHhcCCCchHHHHHHHHHHhHHHHHhccCeecHHHHHHH
Confidence 344455555566664332222211111234555544 34555555444 6788899999999999999999999999
Q ss_pred HHhc
Q 033283 95 MATL 98 (122)
Q Consensus 95 l~~l 98 (122)
.++.
T Consensus 389 v~KV 392 (406)
T COG1222 389 VEKV 392 (406)
T ss_pred HHHH
Confidence 8854
No 86
>PRK12728 fliE flagellar hook-basal body protein FliE; Provisional
Probab=59.34 E-value=47 Score=23.10 Aligned_cols=40 Identities=10% Similarity=0.211 Sum_probs=32.1
Q ss_pred hcCCCCCCcchHHHHHHh--cCCcccHHHHHHHHHHHHHHhcc
Q 033283 80 REKRKTINGDDLLWAMAT--LGFEDYIDPLKIYLTRYREVICV 120 (122)
Q Consensus 80 ~~~RkTI~~eDV~~Al~~--lgf~~~~~~l~~~l~~~re~~~~ 120 (122)
..|. +++..||.-|+++ +.|.-.+.--...++.|+|+++-
T Consensus 59 ~~G~-~~~lhevmiA~~kA~lslq~~vqVRNKlv~AYqEIMrM 100 (102)
T PRK12728 59 VKGE-IVDLHDVMIAAQKASISLQLTVQIRNKVVEAYQEIMRM 100 (102)
T ss_pred HcCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 3444 7899999999995 66667788888999999999874
No 87
>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=59.11 E-value=41 Score=20.84 Aligned_cols=48 Identities=19% Similarity=0.202 Sum_probs=35.8
Q ss_pred cChhhHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 033283 31 YLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQR 80 (122)
Q Consensus 31 ~LP~A~V~Ri~K~~lp~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~ 80 (122)
.+|-+.+.-+++.+.=+ .-..-..-+++=++..||..++..|.+.|+-
T Consensus 2 ~IPD~v~~~yL~~~G~~--~~D~rv~RLvSLaaQKFisdI~~dA~q~~k~ 49 (51)
T PF03540_consen 2 TIPDEVTDYYLERSGFQ--TSDPRVKRLVSLAAQKFISDIANDAMQYCKI 49 (51)
T ss_pred CCCHHHHHHHHHHCCCC--CCCHhHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 46777888888877521 1233445688899999999999999998863
No 88
>TIGR01128 holA DNA polymerase III, delta subunit. subunit around DNA forming a DNA sliding clamp.
Probab=58.74 E-value=56 Score=25.30 Aligned_cols=66 Identities=18% Similarity=0.118 Sum_probs=47.6
Q ss_pred cChhhHHHHHHHhhCCC-CccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHH
Q 033283 31 YLPIANISRIMKKALPA-NGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMA 96 (122)
Q Consensus 31 ~LP~A~V~Ri~K~~lp~-~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~ 96 (122)
.+....+.+.+++.+.. +..|+.++...|.+.+.-=+..+-.+-.+.+.-.+.++|+.+||...+.
T Consensus 110 ~~~~~~~~~~i~~~~~~~g~~i~~~a~~~l~~~~~~d~~~l~~el~KL~~~~~~~~It~e~I~~~~~ 176 (302)
T TIGR01128 110 TPKEQELPRWIQARLKKLGLRIDPDAVQLLAELVEGNLLAIAQELEKLALYAPDGKITLEDVEEAVS 176 (302)
T ss_pred CCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCcHHHHHHHHHHHHHhhCCCCCCCHHHHHHHHh
Confidence 45566677777666543 5689999999998887765566666666666554445799999988776
No 89
>CHL00081 chlI Mg-protoporyphyrin IX chelatase
Probab=58.22 E-value=32 Score=28.83 Aligned_cols=54 Identities=19% Similarity=0.245 Sum_probs=43.5
Q ss_pred HhhCCCCccccHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCCCCcchHHHHHH
Q 033283 42 KKALPANGKIAKDAKETVQECVSEFI-------SFITSEASDKCQREKRKTINGDDLLWAMA 96 (122)
Q Consensus 42 K~~lp~~~~iskdA~~al~~~a~~FI-------~~la~~A~~~a~~~~RkTI~~eDV~~Al~ 96 (122)
++.++ .+.|+.+.+..+.+.+..+= .++...|.-.|--+||..|+++||..+..
T Consensus 260 r~~~~-~V~v~~~~~~yi~~l~~~~~~~s~Ra~i~l~raArA~Aal~GR~~V~pdDv~~~a~ 320 (350)
T CHL00081 260 QNLLP-KVEIDYDLRVKISQICSELDVDGLRGDIVTNRAAKALAAFEGRTEVTPKDIFKVIT 320 (350)
T ss_pred HHhcC-CCccCHHHHHHHHHHHHHHCCCCChHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 44454 57899999998888887763 35667788889999999999999999876
No 90
>PRK13765 ATP-dependent protease Lon; Provisional
Probab=57.59 E-value=34 Score=31.05 Aligned_cols=48 Identities=17% Similarity=0.152 Sum_probs=39.1
Q ss_pred cccHHHHHHHHHHHHHH-------------HHHHHHHHHHHHHhcCCCCCCcchHHHHHHh
Q 033283 50 KIAKDAKETVQECVSEF-------------ISFITSEASDKCQREKRKTINGDDLLWAMAT 97 (122)
Q Consensus 50 ~iskdA~~al~~~a~~F-------------I~~la~~A~~~a~~~~RkTI~~eDV~~Al~~ 97 (122)
.++++|...|-+.++.- +.-|-.+|..+|...+++.|+.+||..|+..
T Consensus 339 ~f~~eAVa~LI~~~~R~ag~r~~lsl~~~~l~~l~r~a~~~a~~~~~~~i~~~~v~~a~~~ 399 (637)
T PRK13765 339 HFDRDAVEEIIREAKRRAGRKGHLTLKLRDLGGLVRVAGDIARSEGAELTTAEHVLEAKKI 399 (637)
T ss_pred CCCHHHHHHHHHHHHHHhCCccccccCHHHHHHHHHHHHHHHHhhccceecHHHHHHHHHh
Confidence 68999988887766633 3337788999999999999999999999843
No 91
>PF02049 FliE: Flagellar hook-basal body complex protein FliE; InterPro: IPR001624 Four genes from the major Bacillus subtilis chemotaxis locus have been shown to encode proteins that are similar to the Salmonella typhimurium FlgB, FlgC, FlgG and FliF proteins; a further gene product is similar to the Escherichia coli FliE protein []. All of these proteins are thought to form part of the hook-basal body complex of the bacterial flagella []. The FlgB, FlgC and FlgG proteins are components of the proximal and distal rods; FliF forms the M-ring that anchors the rod assembly to the membrane; but the role of FliE has not yet been determined []. The similarity between the proteins in these two organisms suggests that the structures of the M-ring and the rod may be similar []. Nevertheless, some differences in size and amino acid composition between some of the homologues suggest the basal body proteins may be organised slightly differently within B. subtilis []. From gel electrophoresis and autoradiography of 35S-labelled S. typhimurium hook-basal body complexes and the deduced number of sulphur-containing residues in FliE, the stoichiometry of the protein in the hook-basal body complex has been estimated to be about nine subunits []. FliE does not undergo cleavage of a signal peptide, nor does it show any similarity to the axial components like the rod or hook proteins, which are thought to be exported by the flagellum-specific export pathway []. On this evidence, it has been suggested that FliE may be in the vicinity of the MS ring, perhaps acting as an adaptor protein between ring and rod substructures [].; GO: 0003774 motor activity, 0005198 structural molecule activity, 0001539 ciliary or flagellar motility, 0009288 bacterial-type flagellum
Probab=56.55 E-value=59 Score=21.95 Aligned_cols=66 Identities=9% Similarity=0.179 Sum_probs=42.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH-HHHHhcCCCCCCcchHHHHHHh--cCCcccHHHHHHHHHHHHHHhcc
Q 033283 54 DAKETVQECVSEFISFITSEAS-DKCQREKRKTINGDDLLWAMAT--LGFEDYIDPLKIYLTRYREVICV 120 (122)
Q Consensus 54 dA~~al~~~a~~FI~~la~~A~-~~a~~~~RkTI~~eDV~~Al~~--lgf~~~~~~l~~~l~~~re~~~~ 120 (122)
++.+.|.++....-........ ...-..|. ..+..||+-|+++ +-|.-.+.--...++.|+|+++-
T Consensus 26 ~F~~~l~~al~~vn~~q~~a~~~~~~~~~G~-~~dl~~vmia~~kA~lslq~~vqVRnK~v~AYqEImrM 94 (96)
T PF02049_consen 26 SFSDVLKNALDEVNQTQQQADQMAQAFATGE-SVDLHEVMIAMQKASLSLQLAVQVRNKAVEAYQEIMRM 94 (96)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 3444455544444333332222 22233344 8899999999995 66667788888999999999874
No 92
>KOG3901 consensus Transcription initiation factor IID subunit [Transcription]
Probab=56.53 E-value=36 Score=24.26 Aligned_cols=47 Identities=17% Similarity=0.270 Sum_probs=38.2
Q ss_pred CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHH
Q 033283 47 ANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMA 96 (122)
Q Consensus 47 ~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~ 96 (122)
++..=-.|.++++...+.+||..++..|.++. +|-.+.-||+.-+|+
T Consensus 24 Dd~nP~~~tv~~Le~iV~~Yi~elt~~a~~~g---~rgk~~veD~~f~lR 70 (109)
T KOG3901|consen 24 DDVNPYPETVDLLEDIVLEYITELTHAAMEIG---KRGKVKVEDFKFLLR 70 (109)
T ss_pred CCCCccHhHHHHHHHHHHHHHHHHHHHHHHhc---ccCceeHHHHHHHHH
Confidence 34455678899999999999999988877766 455578899999987
No 93
>PF05570 DUF765: Circovirus protein of unknown function (DUF765); InterPro: IPR008484 This family consists of several short (27-30aa) porcine and bovine circovirus ORF6 proteins of unknown function.
Probab=56.41 E-value=11 Score=20.46 Aligned_cols=22 Identities=36% Similarity=0.611 Sum_probs=14.6
Q ss_pred CCCCCCCCCCC----CCCCCCCCCCC
Q 033283 1 MAAEAPASPGG----GSHESGEQSPR 22 (122)
Q Consensus 1 ~~~~~~~~~~~----~~~~~~~~~~~ 22 (122)
|||..|+||.- ++.-|.+.+||
T Consensus 1 masstpaspapsdils~~pqs~rppg 26 (29)
T PF05570_consen 1 MASSTPASPAPSDILSSKPQSKRPPG 26 (29)
T ss_pred CCcCCCCCCCcHHHHhcCccccCCCC
Confidence 89999999976 44444444443
No 94
>smart00350 MCM minichromosome maintenance proteins.
Probab=56.35 E-value=64 Score=28.03 Aligned_cols=68 Identities=10% Similarity=0.117 Sum_probs=48.4
Q ss_pred ccChhhHHHHHHHhhCC-CCccccHHHHHHHHHHHHHH-------------------HHHHHHHHHHHHHhcCCCCCCcc
Q 033283 30 RYLPIANISRIMKKALP-ANGKIAKDAKETVQECVSEF-------------------ISFITSEASDKCQREKRKTINGD 89 (122)
Q Consensus 30 ~~LP~A~V~Ri~K~~lp-~~~~iskdA~~al~~~a~~F-------------------I~~la~~A~~~a~~~~RkTI~~e 89 (122)
..++...+.+.+.-+-. -.-.+|+++.+.|.+..... +..|-..|.-.|+-..|.+|+++
T Consensus 416 ~~~~~~~l~~yi~~ar~~~~P~ls~~~~~~i~~~y~~~R~~~~~~~~~~~~~~t~R~l~sliRla~A~A~l~~r~~V~~~ 495 (509)
T smart00350 416 VPISQEFLRKYIAYAREKIKPKLSEEAAEKLVKAYVDLRKEDSQSEARSSIPITVRQLESIIRLSEAHAKMRLSDVVEEA 495 (509)
T ss_pred ccCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhcccccccccccccCcCHHHHHHHHHHHHHHHHHcCCCccCHH
Confidence 45777888877754421 01168999999887654442 24555677788899999999999
Q ss_pred hHHHHHHh
Q 033283 90 DLLWAMAT 97 (122)
Q Consensus 90 DV~~Al~~ 97 (122)
||..|++-
T Consensus 496 Dv~~ai~l 503 (509)
T smart00350 496 DVEEAIRL 503 (509)
T ss_pred HHHHHHHH
Confidence 99999864
No 95
>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]
Probab=56.35 E-value=54 Score=27.50 Aligned_cols=74 Identities=18% Similarity=0.215 Sum_probs=49.7
Q ss_pred hHHHHHHHhhCCC---CccccHHHHHHHHHHH------HHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHHhcCCcccHH
Q 033283 35 ANISRIMKKALPA---NGKIAKDAKETVQECV------SEFISFITSEASDKCQREKRKTINGDDLLWAMATLGFEDYID 105 (122)
Q Consensus 35 A~V~Ri~K~~lp~---~~~iskdA~~al~~~a------~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~~~~ 105 (122)
.-+.-|+++-... ...++.++...+..-+ ..+...+...|.++|+.+++.+++.+||..|-++.+..-+..
T Consensus 193 ~el~~Il~~R~~~~~~~~~~~~~vl~lia~~~a~~~GDAR~aidilr~A~eiAe~~~~~~v~~~~v~~a~~~~~~~~~~~ 272 (366)
T COG1474 193 EELYDILRERVEEGFSAGVIDDDVLKLIAALVAAESGDARKAIDILRRAGEIAEREGSRKVSEDHVREAQEEIERDVLEE 272 (366)
T ss_pred HHHHHHHHHHHHhhccCCCcCccHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHhhCCCCcCHHHHHHHHHHhhHHHHHH
Confidence 3455555554432 3467777766665332 234456667789999999999999999999977777665555
Q ss_pred HHH
Q 033283 106 PLK 108 (122)
Q Consensus 106 ~l~ 108 (122)
.++
T Consensus 273 ~~~ 275 (366)
T COG1474 273 VLK 275 (366)
T ss_pred HHH
Confidence 443
No 96
>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=52.21 E-value=25 Score=27.86 Aligned_cols=74 Identities=11% Similarity=0.106 Sum_probs=34.8
Q ss_pred cccccChhhHHHHHHHhhCCC--CccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC------CCCCcchHHHHHHhc
Q 033283 27 EQDRYLPIANISRIMKKALPA--NGKIAKDAKETVQECVSEFISFITSEASDKCQREKR------KTINGDDLLWAMATL 98 (122)
Q Consensus 27 ~~d~~LP~A~V~Ri~K~~lp~--~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~R------kTI~~eDV~~Al~~l 98 (122)
.++..|....+.+-|...... ...+..|...+|.-||++.+..|-..+..+|++-.. .+....||-..|..|
T Consensus 39 ~~~~fL~~~~L~~~i~~i~~~~g~~~~~~d~l~llS~A~e~rLr~lie~~~~~s~hR~~~~~~~~~~~~~sdv~~qlr~l 118 (264)
T PF05236_consen 39 KEEPFLNPSPLQKRIQKIAKKHGLKSVDEDVLELLSLATEERLRNLIEKAIVLSRHRRDSSKSDPRYEIRSDVRKQLRFL 118 (264)
T ss_dssp -----S-HHHHHHHHHHHHHCTT--EE-TCHHHHHHHHHHHHHHHHHHHHH-----------------------------
T ss_pred ccccccCHHHHHHHHHHHHHHcCCcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccCCCcccccchHHHHHHHHH
Confidence 445678887787777776643 346999999999999999999999998888765322 233456776666655
Q ss_pred CC
Q 033283 99 GF 100 (122)
Q Consensus 99 gf 100 (122)
+-
T Consensus 119 ~~ 120 (264)
T PF05236_consen 119 EQ 120 (264)
T ss_dssp --
T ss_pred HH
Confidence 44
No 97
>PRK07452 DNA polymerase III subunit delta; Validated
Probab=51.48 E-value=44 Score=26.60 Aligned_cols=66 Identities=12% Similarity=0.158 Sum_probs=48.3
Q ss_pred HHHHHHhhCC-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHh--cCCCCCCcchHHHHHHhcCCcc
Q 033283 37 ISRIMKKALP-ANGKIAKDAKETVQECVSEFISFITSEASDKCQR--EKRKTINGDDLLWAMATLGFED 102 (122)
Q Consensus 37 V~Ri~K~~lp-~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~--~~RkTI~~eDV~~Al~~lgf~~ 102 (122)
+.+.|++.+. .+..|+.+|...|.+.+.-=...+..+-.+.+.- .++.+|+.+||...+....+.-
T Consensus 135 l~~~i~~~~~~~g~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~~It~~~V~~~v~~~~~~i 203 (326)
T PRK07452 135 LKQLVERTAQELGVKLTPEAAELLAEAVGNDSRRLYNELEKLALYAENSTKPISAEEVKALVSNTTQNS 203 (326)
T ss_pred HHHHHHHHHHHcCCCCCHHHHHHHHHHhCccHHHHHHHHHHHHHhccCCCCccCHHHHHHHhccCcCcH
Confidence 4454544443 3568999999999999887666677777777765 4577899999999887666443
No 98
>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional
Probab=51.45 E-value=20 Score=30.91 Aligned_cols=32 Identities=28% Similarity=0.279 Sum_probs=28.4
Q ss_pred HHHHHHHHHHHHHhcCCCCCCcchHHHHHHhc
Q 033283 67 ISFITSEASDKCQREKRKTINGDDLLWAMATL 98 (122)
Q Consensus 67 I~~la~~A~~~a~~~~RkTI~~eDV~~Al~~l 98 (122)
|..|..+|...|.+.+|..|+.+|+..|++..
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 56778889999999999999999999999864
No 99
>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=51.03 E-value=46 Score=28.98 Aligned_cols=83 Identities=19% Similarity=0.242 Sum_probs=55.6
Q ss_pred ChhhHHHHHHHhhCC-CCccccHHHHHHHHHHHHH----HHHHHHHHHHHHHHhcCCCCCCcchHHHHHHhcCCcccHHH
Q 033283 32 LPIANISRIMKKALP-ANGKIAKDAKETVQECVSE----FISFITSEASDKCQREKRKTINGDDLLWAMATLGFEDYIDP 106 (122)
Q Consensus 32 LP~A~V~Ri~K~~lp-~~~~iskdA~~al~~~a~~----FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~~~~~ 106 (122)
.+..-|+-|++--.. .++.+++||.+.|++..++ +...|-.-|+.+|+..|+++|..+||-.|-+- |.+- ..
T Consensus 361 y~~~EireIi~iRa~ee~i~l~~~Ale~L~~ig~etSLRYa~qLL~pa~iiA~~rg~~~V~~~dVe~a~~l--F~D~-kr 437 (450)
T COG1224 361 YSREEIREIIRIRAKEEDIELSDDALEYLTDIGEETSLRYAVQLLTPASIIAKRRGSKRVEVEDVERAKEL--FLDV-KR 437 (450)
T ss_pred CCHHHHHHHHHHhhhhhccccCHHHHHHHHhhchhhhHHHHHHhccHHHHHHHHhCCCeeehhHHHHHHHH--HhhH-HH
Confidence 455556666665443 3678999999999887655 44445556889999999999999999998442 2222 22
Q ss_pred HHHHHHHHHHH
Q 033283 107 LKIYLTRYREV 117 (122)
Q Consensus 107 l~~~l~~~re~ 117 (122)
--++++.|++.
T Consensus 438 Sv~~v~~~~~~ 448 (450)
T COG1224 438 SVEYVEKYEGL 448 (450)
T ss_pred HHHHHHHHHhh
Confidence 23455555543
No 100
>PRK12402 replication factor C small subunit 2; Reviewed
Probab=50.81 E-value=42 Score=26.41 Aligned_cols=68 Identities=7% Similarity=0.011 Sum_probs=42.8
Q ss_pred ChhhHHHHHHHhhCC-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHHhcCCc
Q 033283 32 LPIANISRIMKKALP-ANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMATLGFE 101 (122)
Q Consensus 32 LP~A~V~Ri~K~~lp-~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~ 101 (122)
++...+.+++++.+. .+..++.++...|.+.+.-=+..+-......+. +..+|+.+||..++.....+
T Consensus 184 ~~~~~~~~~l~~~~~~~~~~~~~~al~~l~~~~~gdlr~l~~~l~~~~~--~~~~It~~~v~~~~~~~~~~ 252 (337)
T PRK12402 184 PTDDELVDVLESIAEAEGVDYDDDGLELIAYYAGGDLRKAILTLQTAAL--AAGEITMEAAYEALGDVGTD 252 (337)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHH--cCCCCCHHHHHHHhCCCCCH
Confidence 445566666666544 245799999999888874333333333333442 23479999999988765543
No 101
>TIGR01242 26Sp45 26S proteasome subunit P45 family. Many proteins may score above the trusted cutoff because an internal
Probab=50.56 E-value=23 Score=29.06 Aligned_cols=32 Identities=28% Similarity=0.288 Sum_probs=27.6
Q ss_pred HHHHHHHHHHHHHHhcCCCCCCcchHHHHHHh
Q 033283 66 FISFITSEASDKCQREKRKTINGDDLLWAMAT 97 (122)
Q Consensus 66 FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~~ 97 (122)
-|..+..+|...|...++..|+.+|+..|++.
T Consensus 331 dl~~l~~~A~~~a~~~~~~~i~~~d~~~a~~~ 362 (364)
T TIGR01242 331 DLKAICTEAGMFAIREERDYVTMDDFIKAVEK 362 (364)
T ss_pred HHHHHHHHHHHHHHHhCCCccCHHHHHHHHHH
Confidence 35577788888899999999999999999976
No 102
>PRK03992 proteasome-activating nucleotidase; Provisional
Probab=50.51 E-value=22 Score=29.71 Aligned_cols=36 Identities=22% Similarity=0.192 Sum_probs=29.6
Q ss_pred HHHHHHHHHHHHHHHhcCCCCCCcchHHHHHHhcCC
Q 033283 65 EFISFITSEASDKCQREKRKTINGDDLLWAMATLGF 100 (122)
Q Consensus 65 ~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~~lgf 100 (122)
-=|..|..+|...|.+++++.|+.+|+..|++..-.
T Consensus 339 adl~~l~~eA~~~a~~~~~~~i~~~d~~~A~~~~~~ 374 (389)
T PRK03992 339 ADLKAICTEAGMFAIRDDRTEVTMEDFLKAIEKVMG 374 (389)
T ss_pred HHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHhc
Confidence 345567788888888999999999999999997643
No 103
>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=50.10 E-value=64 Score=28.74 Aligned_cols=54 Identities=17% Similarity=0.244 Sum_probs=40.0
Q ss_pred HhhCCCCccccHHHHHHHHHHHHHH-------HHHHHHHHHHHHHhcCCCCCCcchHHHHHH
Q 033283 42 KKALPANGKIAKDAKETVQECVSEF-------ISFITSEASDKCQREKRKTINGDDLLWAMA 96 (122)
Q Consensus 42 K~~lp~~~~iskdA~~al~~~a~~F-------I~~la~~A~~~a~~~~RkTI~~eDV~~Al~ 96 (122)
++.++ .+.|+.+....|.+.+..+ -.++...|...|.-++|.+|+++||..|+.
T Consensus 196 r~~~~-~V~i~~~~~~~l~~~~~~~gv~s~Ra~i~~~r~ArA~Aal~gr~~V~~~Dv~~a~~ 256 (589)
T TIGR02031 196 RELLP-QVTISAEQVKELVLTAASLGISGHRADLFAVRAAKAHAALHGRTEVTEEDLKLAVE 256 (589)
T ss_pred HHhcC-CccCCHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHH
Confidence 33444 5788999887777666443 224556677888899999999999999987
No 104
>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=49.60 E-value=44 Score=19.85 Aligned_cols=32 Identities=16% Similarity=0.428 Sum_probs=26.2
Q ss_pred cChhhHHHHHHHhhCCCCccccHHHHHHHHHHHHHH
Q 033283 31 YLPIANISRIMKKALPANGKIAKDAKETVQECVSEF 66 (122)
Q Consensus 31 ~LP~A~V~Ri~K~~lp~~~~iskdA~~al~~~a~~F 66 (122)
.+-.++|.|++... .+||.+.++-+.+++++.
T Consensus 10 gvS~~TVSr~ln~~----~~vs~~tr~rI~~~a~~l 41 (46)
T PF00356_consen 10 GVSKSTVSRVLNGP----PRVSEETRERILEAAEEL 41 (46)
T ss_dssp TSSHHHHHHHHTTC----SSSTHHHHHHHHHHHHHH
T ss_pred CcCHHHHHHHHhCC----CCCCHHHHHHHHHHHHHH
Confidence 46788999998865 489999999999987763
No 105
>PF08681 DUF1778: Protein of unknown function (DUF1778); InterPro: IPR014795 This entry is represented by Vibrio phage ICP1, Orf50. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a family of uncharacterised proteins. The structure of one of the hypothetical proteins in this family has been solved and it forms a helix structure which may form interactions with DNA. ; PDB: 1Y9B_A.
Probab=49.45 E-value=15 Score=24.18 Aligned_cols=67 Identities=24% Similarity=0.338 Sum_probs=34.3
Q ss_pred ccccHHHHHHHHHHHH-------HHHHHHHHHHH-HHHHhcCCCCCCcchHHHHHHhcCCc-ccHHHHHHHHHHHH
Q 033283 49 GKIAKDAKETVQECVS-------EFISFITSEAS-DKCQREKRKTINGDDLLWAMATLGFE-DYIDPLKIYLTRYR 115 (122)
Q Consensus 49 ~~iskdA~~al~~~a~-------~FI~~la~~A~-~~a~~~~RkTI~~eDV~~Al~~lgf~-~~~~~l~~~l~~~r 115 (122)
+|++.+.+..|.+++. .||.-.+.++. +.-..+..-+++.+|.-.-++-|+=+ .=-+.|+..+..|+
T Consensus 4 iR~~~e~k~li~~AA~~~G~sls~Fi~~aa~~~A~~~i~~~~~~~Ls~~~~~~f~~aLd~p~~p~~~L~~a~~~~~ 79 (80)
T PF08681_consen 4 IRVTPEEKELIERAAALSGVSLSDFILSAALEAAEEVIEEHERIRLSAEDFEAFMAALDNPPQPNERLKEAMRRYR 79 (80)
T ss_dssp EE--HHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH-HHHHHHHHHHHC----
T ss_pred EecCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhcceeEcCHHHHHHHHHHHhCCCCCCHHHHHHHHhcc
Confidence 6899999999999975 45555444433 22233344566776655554444432 33444555555554
No 106
>PRK00790 fliE flagellar hook-basal body protein FliE; Reviewed
Probab=49.37 E-value=91 Score=22.03 Aligned_cols=35 Identities=9% Similarity=0.152 Sum_probs=29.1
Q ss_pred CCcchHHHHHHh--cCCcccHHHHHHHHHHHHHHhcc
Q 033283 86 INGDDLLWAMAT--LGFEDYIDPLKIYLTRYREVICV 120 (122)
Q Consensus 86 I~~eDV~~Al~~--lgf~~~~~~l~~~l~~~re~~~~ 120 (122)
++..||.-|+++ +.|.-.+.--...++.|+|+++-
T Consensus 71 ~dlhevmiA~~kA~lslq~~vqVRNKlVeAYqEIMrM 107 (109)
T PRK00790 71 ADTREVVDAVMQAEQALQTAVAIRDKVVEAYLEILRM 107 (109)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence 478899999995 66677788888999999999874
No 107
>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=49.13 E-value=31 Score=21.57 Aligned_cols=30 Identities=20% Similarity=0.333 Sum_probs=24.1
Q ss_pred CCCCCCcchHHHHHHhcCCcccHHHHHHHH
Q 033283 82 KRKTINGDDLLWAMATLGFEDYIDPLKIYL 111 (122)
Q Consensus 82 ~RkTI~~eDV~~Al~~lgf~~~~~~l~~~l 111 (122)
....-+.++++.||+++|..+.+..++..|
T Consensus 54 ~~~~at~~~L~~aL~~~~~~d~~~~i~~~~ 83 (83)
T PF00531_consen 54 EGPNATVDQLIQALRDIGRNDLAEKIEQML 83 (83)
T ss_dssp HGSTSSHHHHHHHHHHTTHHHHHHHHHHH-
T ss_pred cCCCCcHHHHHHHHHHCCcHHHHHHHHhhC
Confidence 344567889999999999999988887654
No 108
>PRK13407 bchI magnesium chelatase subunit I; Provisional
Probab=49.03 E-value=62 Score=26.86 Aligned_cols=53 Identities=11% Similarity=0.031 Sum_probs=41.0
Q ss_pred HhhCCCCccccHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCCCCcchHHHHH
Q 033283 42 KKALPANGKIAKDAKETVQECVSEFI-------SFITSEASDKCQREKRKTINGDDLLWAM 95 (122)
Q Consensus 42 K~~lp~~~~iskdA~~al~~~a~~FI-------~~la~~A~~~a~~~~RkTI~~eDV~~Al 95 (122)
++.++ .+.|+.+....+.+.+..+= .+|...|...|-.+||..|+++||..+.
T Consensus 244 ~~~~~-~V~v~~~~~~yi~~l~~~~~~~s~Ra~i~l~~aA~a~A~l~Gr~~V~~~Di~~~~ 303 (334)
T PRK13407 244 RARLP-QLKTPNTVLHDCAALCIALGSDGLRGELTLLRAARALAAFEGAEAVGRSHLRSVA 303 (334)
T ss_pred HHhcC-CcccCHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHHcCCCeeCHHHHHHHH
Confidence 34444 57889999888888877653 2366778888999999999999997665
No 109
>PF08823 PG_binding_2: Putative peptidoglycan binding domain; InterPro: IPR014927 This entry may be a peptidoglycan binding domain.
Probab=48.80 E-value=29 Score=22.75 Aligned_cols=31 Identities=13% Similarity=0.147 Sum_probs=25.7
Q ss_pred chHHHHHHhcCC------cccHHHHHHHHHHHHHHhc
Q 033283 89 DDLLWAMATLGF------EDYIDPLKIYLTRYREVIC 119 (122)
Q Consensus 89 eDV~~Al~~lgf------~~~~~~l~~~l~~~re~~~ 119 (122)
+.|..+|..||| ..+-+.++..|..|..+.+
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 457788999999 6788899999999887664
No 110
>PRK05574 holA DNA polymerase III subunit delta; Reviewed
Probab=47.64 E-value=63 Score=25.55 Aligned_cols=67 Identities=15% Similarity=0.058 Sum_probs=47.4
Q ss_pred cChhhHHHHHHHhhCCC-CccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHHh
Q 033283 31 YLPIANISRIMKKALPA-NGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMAT 97 (122)
Q Consensus 31 ~LP~A~V~Ri~K~~lp~-~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~~ 97 (122)
.+....+.+.|++.+.. +..|+.+|...|.+.+..=...+..+-...+.-.+-+.|+.+||-..+..
T Consensus 145 ~~~~~~~~~~i~~~~~~~g~~i~~~a~~~L~~~~~~d~~~l~~El~KL~l~~~~~~It~~~I~~~i~~ 212 (340)
T PRK05574 145 PPKEAELPQWIQQRLKQQGLQIDAAALQLLAERVEGNLLALAQELEKLALLYPDGKITLEDVEEAVPD 212 (340)
T ss_pred CCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCchHHHHHHHHHHHHhhcCCCCCCHHHHHHHHhh
Confidence 45566666666666643 56899999999999887766677777777765432223999999877663
No 111
>COG5624 TAF61 Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=47.20 E-value=12 Score=32.59 Aligned_cols=76 Identities=12% Similarity=0.187 Sum_probs=60.8
Q ss_pred cChhhHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHHh---cCCcccHHH
Q 033283 31 YLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMAT---LGFEDYIDP 106 (122)
Q Consensus 31 ~LP~A~V~Ri~K~~lp~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~~---lgf~~~~~~ 106 (122)
.+-+-.+.-+++..+....+|-.|.-+++-.-+-.|+.-++.-+-.++++-+-+||-..|+-.-|+. +-++.|+..
T Consensus 383 l~skrkL~el~~~~vd~eekie~eveelll~~ad~fve~vt~FsCrlakhrkSdtlevrD~qlhlErnwnIr~pGf~~d 461 (505)
T COG5624 383 LDSKRKLEELQHGGVDEEEKIENEVEELLLSRADGFVEPVTEFSCRLAKHRKSDTLEVRDGQLHLERNWNIRCPGFVDD 461 (505)
T ss_pred hhhhhhHHHHHhhccCcceeccchHHHHHHhhhcccccccchheeEeeccCCCCceeeccceeeeccccceecCcchHH
Confidence 4555566667777776667899999999999999999999998888999999999999999877773 334566543
No 112
>PLN00138 large subunit ribosomal protein LP2; Provisional
Probab=47.13 E-value=56 Score=23.22 Aligned_cols=39 Identities=15% Similarity=0.123 Sum_probs=29.6
Q ss_pred HHHHHHhcCCCCCCcchHHHHHHhcCCcccHHHHHHHHH
Q 033283 74 ASDKCQREKRKTINGDDLLWAMATLGFEDYIDPLKIYLT 112 (122)
Q Consensus 74 A~~~a~~~~RkTI~~eDV~~Al~~lgf~~~~~~l~~~l~ 112 (122)
|+-.|.-.+...++.+||.+.|+..|.+-=-..++.++.
T Consensus 6 Ayll~~l~g~~~pta~dI~~IL~AaGvevd~~~~~~f~~ 44 (113)
T PLN00138 6 AYLLAVLGGNTCPSAEDLKDILGSVGADADDDRIELLLS 44 (113)
T ss_pred HHHHHHhcCCCCCCHHHHHHHHHHcCCcccHHHHHHHHH
Confidence 678899999999999999999999887533333444443
No 113
>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=45.09 E-value=26 Score=21.28 Aligned_cols=24 Identities=25% Similarity=0.437 Sum_probs=19.8
Q ss_pred CCcchHHHHHHhcCCcccHHHHHH
Q 033283 86 INGDDLLWAMATLGFEDYIDPLKI 109 (122)
Q Consensus 86 I~~eDV~~Al~~lgf~~~~~~l~~ 109 (122)
=+++||..-|+.+||++|.+....
T Consensus 4 w~~~~v~~WL~~~gl~~y~~~f~~ 27 (66)
T PF07647_consen 4 WSPEDVAEWLKSLGLEQYADNFRE 27 (66)
T ss_dssp HCHHHHHHHHHHTTCGGGHHHHHH
T ss_pred CCHHHHHHHHHHCCcHHHHHHHHH
Confidence 367899999999999999887654
No 114
>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional
Probab=44.79 E-value=31 Score=29.26 Aligned_cols=33 Identities=27% Similarity=0.201 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHHHHhcCCCCCCcchHHHHHHhc
Q 033283 66 FISFITSEASDKCQREKRKTINGDDLLWAMATL 98 (122)
Q Consensus 66 FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~~l 98 (122)
=|..|..+|...|...+|..|+.+|+..|++..
T Consensus 354 DI~~l~~eA~~~A~r~~~~~i~~~df~~A~~~v 386 (398)
T PTZ00454 354 DIAAICQEAGMQAVRKNRYVILPKDFEKGYKTV 386 (398)
T ss_pred HHHHHHHHHHHHHHHcCCCccCHHHHHHHHHHH
Confidence 366788889999999999999999999998863
No 115
>PTZ00373 60S Acidic ribosomal protein P2; Provisional
Probab=43.53 E-value=70 Score=22.81 Aligned_cols=38 Identities=11% Similarity=0.078 Sum_probs=28.6
Q ss_pred HHHHHHhcCCCCCCcchHHHHHHhcCCcccHHHHHHHH
Q 033283 74 ASDKCQREKRKTINGDDLLWAMATLGFEDYIDPLKIYL 111 (122)
Q Consensus 74 A~~~a~~~~RkTI~~eDV~~Al~~lgf~~~~~~l~~~l 111 (122)
|+-.|...|+.+++.+||.+.|+..|.+-=-..++.++
T Consensus 8 AYlL~~lgG~~~pTaddI~kIL~AaGveVd~~~~~l~~ 45 (112)
T PTZ00373 8 AYLMCVLGGNENPTKKEVKNVLSAVNADVEDDVLDNFF 45 (112)
T ss_pred HHHHHHHcCCCCCCHHHHHHHHHHcCCCccHHHHHHHH
Confidence 67888999999999999999999888753333333333
No 116
>TIGR01052 top6b DNA topoisomerase VI, B subunit. This model describes DNA topoisomerase VI, an archaeal type II DNA topoisomerase (DNA gyrase).
Probab=42.89 E-value=33 Score=30.22 Aligned_cols=44 Identities=16% Similarity=0.295 Sum_probs=31.5
Q ss_pred HhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCC
Q 033283 42 KKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKT 85 (122)
Q Consensus 42 K~~lp~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkT 85 (122)
|+++.+.--|-+|.+.||++||...=.||...-...-...++++
T Consensus 426 Ke~ia~~~ei~~ei~~al~~~~r~L~~~l~~~~~~~~~~~r~~~ 469 (488)
T TIGR01052 426 KQSVADIPEIYNEIRLALMEVARRLRLYLSRKAREEEEIKRRKT 469 (488)
T ss_pred hhhhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44444444688899999999999999999986555444444443
No 117
>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=42.88 E-value=27 Score=25.02 Aligned_cols=61 Identities=10% Similarity=0.143 Sum_probs=40.8
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCC--CCcchHHHHHHhcCCcccHHHHHHHHHHHHHHh
Q 033283 52 AKDAKETVQECVSEFISFITSEASDKCQREKRKT--INGDDLLWAMATLGFEDYIDPLKIYLTRYREVI 118 (122)
Q Consensus 52 skdA~~al~~~a~~FI~~la~~A~~~a~~~~RkT--I~~eDV~~Al~~lgf~~~~~~l~~~l~~~re~~ 118 (122)
+...+.-|..|..+.-.|...... |-.- -.-.++...|+..|++..+.+++.-+++|+...
T Consensus 71 ~s~Vk~Eiaa~~~v~~~Y~~~L~~------G~vd~e~~~~~~~~kLk~AGidkV~~E~QkQlda~~~~~ 133 (134)
T PF12010_consen 71 PSPVKNEIAACSNVWSEYYPPLET------GLVDPEEALPEFNEKLKAAGIDKVIAELQKQLDAFLAAN 133 (134)
T ss_pred CchhHHHHHHHHHHHHHHHHHHHc------cCCCHHHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHhc
Confidence 345566666776666555443221 2111 123566778889999999999999999998764
No 118
>COG5248 TAF19 Transcription initiation factor TFIID, subunit TAF13 [Transcription]
Probab=41.85 E-value=85 Score=22.70 Aligned_cols=57 Identities=21% Similarity=0.291 Sum_probs=43.7
Q ss_pred HHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHH
Q 033283 37 ISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMA 96 (122)
Q Consensus 37 V~Ri~K~~lp~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~ 96 (122)
|.-+|..-. +...=..|...++.+.+.-+++.+...|...|.. |-.+..+|..-||+
T Consensus 15 ikslmYayG-Dvv~P~~dt~~~L~e~V~dY~~~~ctna~~~Aq~--rnK~k~eDfkfaLr 71 (126)
T COG5248 15 IKSLMYAYG-DVVAPRYDTAEALHEYVLDYMSILCTNAHNMAQV--RNKTKTEDFKFALR 71 (126)
T ss_pred HHHHHHHhC-CCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHh--cccchHHHHHHHHh
Confidence 344444333 4556678899999999999999999999988873 44467899999987
No 119
>PF00536 SAM_1: SAM domain (Sterile alpha motif); InterPro: IPR021129 The sterile alpha motif (SAM) domain is a putative protein interaction module present in a wide variety of proteins [] involved in many biological processes. The SAM domain that spreads over around 70 residues is found in diverse eukaryotic organisms []. SAM domains have been shown to homo- and hetero-oligomerise, forming multiple self-association architectures and also binding to various non-SAM domain-containing proteins [], nevertheless with a low affinity constant []. SAM domains also appear to possess the ability to bind RNA []. Smaug, a protein that helps to establish a morphogen gradient in Drosophila embryos by repressing the translation of nanos (nos) mRNA, binds to the 3' untranslated region (UTR) of nos mRNA via two similar hairpin structures. The 3D crystal structure of the Smaug RNA-binding region shows a cluster of positively charged residues on the Smaug-SAM domain, which could be the RNA-binding surface. This electropositive potential is unique among all previously determined SAM-domain structures and is conserved among Smaug-SAM homologs. These results suggest that the SAM domain might have a primary role in RNA binding. Structural analyses show that the SAM domain is arranged in a small five-helix bundle with two large interfaces []. In the case of the SAM domain of EphB2, each of these interfaces is able to form dimers. The presence of these two distinct intermonomers binding surface suggest that SAM could form extended polymeric structures []. This entry represents type 1 SAM domains. ; PDB: 2KIV_A 3HIL_B 3KKA_A 3K1R_B 3SEN_B 3SEI_B 1V85_A 2KE7_A 2EAM_A 1WWV_A ....
Probab=40.87 E-value=31 Score=20.85 Aligned_cols=22 Identities=23% Similarity=0.453 Sum_probs=19.1
Q ss_pred CcchHHHHHHhcCCcccHHHHH
Q 033283 87 NGDDLLWAMATLGFEDYIDPLK 108 (122)
Q Consensus 87 ~~eDV~~Al~~lgf~~~~~~l~ 108 (122)
++++|..-|+.+|+++|.+..+
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 5789999999999999988763
No 120
>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=40.54 E-value=23 Score=20.80 Aligned_cols=23 Identities=22% Similarity=0.424 Sum_probs=19.0
Q ss_pred CcchHHHHHHhcCCcccHHHHHH
Q 033283 87 NGDDLLWAMATLGFEDYIDPLKI 109 (122)
Q Consensus 87 ~~eDV~~Al~~lgf~~~~~~l~~ 109 (122)
+.++|..-|+.+|+++|.+..+.
T Consensus 3 ~~~~V~~wL~~~~~~~y~~~f~~ 25 (63)
T cd00166 3 SPEDVAEWLESLGLGQYADNFRE 25 (63)
T ss_pred CHHHHHHHHHHcChHHHHHHHHH
Confidence 56789999999999888887654
No 121
>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=40.19 E-value=24 Score=26.17 Aligned_cols=53 Identities=19% Similarity=0.260 Sum_probs=38.3
Q ss_pred HHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchH
Q 033283 37 ISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDL 91 (122)
Q Consensus 37 V~Ri~K~~lp~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV 91 (122)
+.|+.+.+.. .-|.|+-..-+....+.=+.-|.-.|...|+.+||.+|.+.|+
T Consensus 1 fe~lFR~aa~--LdvdK~d~~r~~d~V~~Kl~DLl~va~~~Ak~ngRdvI~~~DL 53 (138)
T PF09123_consen 1 FERLFRKAAG--LDVDKNDAKRYSDFVEKKLYDLLLVAQENAKANGRDVIEPRDL 53 (138)
T ss_dssp HHHHHHHHHS------HHHHHHHHHHHHHHHHHCCCCHHHHHHHTT-SEE-GGGS
T ss_pred ChHHHHHHhc--cCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeeccccC
Confidence 3577777763 5677777778888888877778888999999999999999986
No 122
>COG5251 TAF40 Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=39.83 E-value=50 Score=25.68 Aligned_cols=64 Identities=9% Similarity=-0.046 Sum_probs=48.9
Q ss_pred cChhhHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC-CCCCcchHHHHHH
Q 033283 31 YLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKR-KTINGDDLLWAMA 96 (122)
Q Consensus 31 ~LP~A~V~Ri~K~~lp~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~R-kTI~~eDV~~Al~ 96 (122)
.||++.|++++...+. -.|+...+.+|+-.+.+|+-.+--.|..+-.+-+- --+.+.|+-.|..
T Consensus 115 ~lnKt~VKKlastV~n--QtVspNi~I~l~g~~KVfvGEiIElA~~Vq~~w~~sgpl~p~h~reayr 179 (199)
T COG5251 115 SLNKTQVKKLASTVAN--QTVSPNIRIFLQGVGKVFVGEIIELAMIVQNKWLTSGPLIPFHKREAYR 179 (199)
T ss_pred CCCHHHHHHHHHHHhc--cccCCCeeeeeechhHHHHHHHHHHHHHHHHHhcccCCCChHHHHHHHH
Confidence 5999999999999984 57888888899999999998887776654332221 2477888887754
No 123
>PTZ00183 centrin; Provisional
Probab=38.32 E-value=1.3e+02 Score=20.55 Aligned_cols=21 Identities=14% Similarity=0.254 Sum_probs=12.5
Q ss_pred HHHhcCCCCCCcchHHHHHHh
Q 033283 77 KCQREKRKTINGDDLLWAMAT 97 (122)
Q Consensus 77 ~a~~~~RkTI~~eDV~~Al~~ 97 (122)
.+..++...|+.++.+.++..
T Consensus 61 ~~d~~~~g~i~~~eF~~~~~~ 81 (158)
T PTZ00183 61 DVDKDGSGKIDFEEFLDIMTK 81 (158)
T ss_pred HhCCCCCCcEeHHHHHHHHHH
Confidence 334455566777777666654
No 124
>COG1724 Predicted RNA binding protein (dsRBD-like fold), HicA family [General function prediction only]
Probab=37.42 E-value=22 Score=23.30 Aligned_cols=18 Identities=17% Similarity=0.381 Sum_probs=15.7
Q ss_pred CCCcchHHHHHHhcCCcc
Q 033283 85 TINGDDLLWAMATLGFED 102 (122)
Q Consensus 85 TI~~eDV~~Al~~lgf~~ 102 (122)
.+++.||+++|+.+||..
T Consensus 6 ~~~~ke~ik~Le~~Gf~~ 23 (66)
T COG1724 6 RMKAKEVIKALEKDGFQL 23 (66)
T ss_pred cCCHHHHHHHHHhCCcEE
Confidence 478899999999999963
No 125
>PRK06585 holA DNA polymerase III subunit delta; Reviewed
Probab=37.32 E-value=94 Score=24.93 Aligned_cols=63 Identities=16% Similarity=0.142 Sum_probs=43.0
Q ss_pred hhHHHHHHHhhCC-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHh-cCCCCCCcchHHHHHH
Q 033283 34 IANISRIMKKALP-ANGKIAKDAKETVQECVSEFISFITSEASDKCQR-EKRKTINGDDLLWAMA 96 (122)
Q Consensus 34 ~A~V~Ri~K~~lp-~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~-~~RkTI~~eDV~~Al~ 96 (122)
-..+.+.+++.+. .+.+|+.||...|.+.+.-=...+..+-.+.+.- .+.++|+.+||...+.
T Consensus 144 ~~~l~~~i~~~~~~~g~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~It~edV~~lv~ 208 (343)
T PRK06585 144 ERDLARLIDDELAEAGLRITPDARALLVALLGGDRLASRNEIEKLALYAHGKGEITLDDVRAVVG 208 (343)
T ss_pred HHHHHHHHHHHHHHCCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHhC
Confidence 3334444444443 3568999999999999886555666666666654 3456899999988766
No 126
>PRK14975 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Probab=37.23 E-value=2.2e+02 Score=25.06 Aligned_cols=70 Identities=16% Similarity=0.085 Sum_probs=45.6
Q ss_pred cccChhhHHHHHHHhhCCCCccccHHHHHHHHHHHH----------HHHHHHHHHHHHHHHhcCCCCCCcchHHHHHHhc
Q 033283 29 DRYLPIANISRIMKKALPANGKIAKDAKETVQECVS----------EFISFITSEASDKCQREKRKTINGDDLLWAMATL 98 (122)
Q Consensus 29 d~~LP~A~V~Ri~K~~lp~~~~iskdA~~al~~~a~----------~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~~l 98 (122)
++++|.+.|---|... ++.|..+....+..-.. .-+..|..+..+......=.-=++++|..+|+.+
T Consensus 161 ~~E~~~~~~l~~me~~---Gi~~D~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~~~g~~~~n~~S~~ql~~~L~~~ 237 (553)
T PRK14975 161 AAESAGALAAAEMELA---GLPWDTDVHEALLAELLGPRPAAGGRPARLAELAAEIREALGRPRLNPDSPQQVLRALRRA 237 (553)
T ss_pred HHHhhHHHHHHHHHHh---CeEeCHHHHHHHHHHHhcccccccchHHHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHC
Confidence 4566777776666654 47888887766665555 5566666666655422111234678999999988
Q ss_pred CCc
Q 033283 99 GFE 101 (122)
Q Consensus 99 gf~ 101 (122)
|+.
T Consensus 238 g~~ 240 (553)
T PRK14975 238 GIE 240 (553)
T ss_pred CCC
Confidence 884
No 127
>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=37.14 E-value=21 Score=21.04 Aligned_cols=14 Identities=36% Similarity=0.672 Sum_probs=11.6
Q ss_pred chHHHHHHhcCCcc
Q 033283 89 DDLLWAMATLGFED 102 (122)
Q Consensus 89 eDV~~Al~~lgf~~ 102 (122)
+|++.||..|||..
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 68999999999974
No 128
>COG1466 HolA DNA polymerase III, delta subunit [DNA replication, recombination, and repair]
Probab=37.13 E-value=84 Score=25.56 Aligned_cols=61 Identities=18% Similarity=0.150 Sum_probs=45.6
Q ss_pred HHHHHHhhCC-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHHh
Q 033283 37 ISRIMKKALP-ANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMAT 97 (122)
Q Consensus 37 V~Ri~K~~lp-~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~~ 97 (122)
+.+.++..+. .+.+|++||.+.+..+..-=...+..+=...+--.+-++|+.+||..++..
T Consensus 145 l~~~i~~~~~~~~l~i~~~a~~~L~~~~~~nl~~i~~Ei~KL~l~~~~~~I~~~~V~~~v~~ 206 (334)
T COG1466 145 LPQWIKKRAKELGLKIDQEAIQLLLEALGGNLLAIAQEIEKLALYAGDKEITLEDVEEVVSD 206 (334)
T ss_pred HHHHHHHHHHHcCCCCCHHHHHHHHHHhCCcHHHHHHHHHHHHHhCCCCcCCHHHHHHHHhc
Confidence 4444444443 257899999999999998767777777777776666569999999999874
No 129
>PRK00253 fliE flagellar hook-basal body protein FliE; Reviewed
Probab=36.97 E-value=1.5e+02 Score=20.80 Aligned_cols=40 Identities=15% Similarity=0.292 Sum_probs=32.8
Q ss_pred cCCCCCCcchHHHHHHh--cCCcccHHHHHHHHHHHHHHhcc
Q 033283 81 EKRKTINGDDLLWAMAT--LGFEDYIDPLKIYLTRYREVICV 120 (122)
Q Consensus 81 ~~RkTI~~eDV~~Al~~--lgf~~~~~~l~~~l~~~re~~~~ 120 (122)
.|.-.++..||.-|+++ +.|.-.+.--...++.|+|+++-
T Consensus 65 ~G~~~v~lhevmia~~kA~lslq~~~qVRNKlv~AYqEIMrM 106 (108)
T PRK00253 65 LGDPGVSLNDVMIALQKASVSFQAGIQVRNKLVAAYQEIMNM 106 (108)
T ss_pred cCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence 45557899999999995 66677788888999999999874
No 130
>PRK01482 fliE flagellar hook-basal body protein FliE; Reviewed
Probab=36.97 E-value=1.5e+02 Score=20.95 Aligned_cols=65 Identities=14% Similarity=0.162 Sum_probs=42.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH--HHhcCCCCCCcchHHHHHHh--cCCcccHHHHHHHHHHHHHHhc
Q 033283 54 DAKETVQECVSEFISFITSEASDK--CQREKRKTINGDDLLWAMAT--LGFEDYIDPLKIYLTRYREVIC 119 (122)
Q Consensus 54 dA~~al~~~a~~FI~~la~~A~~~--a~~~~RkTI~~eDV~~Al~~--lgf~~~~~~l~~~l~~~re~~~ 119 (122)
.+-+.|.++....-.-.. +|.+. ..-.+...+...||.-|+++ +.|.-.+.--...++.|+|+++
T Consensus 38 sF~d~L~~Al~~Vn~~Q~-~a~~~~~~~~~gg~~~dlhevmIA~qkA~lslql~vqVRNKlVeAYqEIMr 106 (108)
T PRK01482 38 TFKDTLLNAIDDVNNSQL-NVSKVTEQAILDPESVDVHDVTIAMAKANMNLSIAKAVVERSIKAYQDIIN 106 (108)
T ss_pred CHHHHHHHHHHHHHHHHH-HHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 345555555555433322 22222 22234556799999999995 5566778888899999999986
No 131
>TIGR00205 fliE flagellar hook-basal body complex protein FliE. fliE is a component of the flagellar hook-basal body complex located possibly at (MS-ring)-rod junction.
Probab=36.64 E-value=1.5e+02 Score=20.83 Aligned_cols=67 Identities=7% Similarity=0.150 Sum_probs=45.8
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHH--HhcCCCCCCcchHHHHHHh--cCCcccHHHHHHHHHHHHHHhc
Q 033283 52 AKDAKETVQECVSEFISFITSEASDKC--QREKRKTINGDDLLWAMAT--LGFEDYIDPLKIYLTRYREVIC 119 (122)
Q Consensus 52 skdA~~al~~~a~~FI~~la~~A~~~a--~~~~RkTI~~eDV~~Al~~--lgf~~~~~~l~~~l~~~re~~~ 119 (122)
...+.+.|.++....-.-... |.+.. -..|.+.++..||.-|+++ +-|.-.+.--...++.|+|+++
T Consensus 36 ~~sF~~~L~~ai~~vn~~q~~-a~~~~~~~~~G~~~~dlhevmia~~kA~lslq~~vqVRNKlveAYqEIMr 106 (108)
T TIGR00205 36 NDSFSDLLKNSITDLNKTQLA-SDKVTEQAALGPSSVDLHDVMIAMQKASMSMSILKEVRNKAVKAYQEIMR 106 (108)
T ss_pred CcCHHHHHHHHHHHHHHHHHH-HHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 445666666666654433322 33333 2356678999999999995 5556677888889999999986
No 132
>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=35.97 E-value=1.8e+02 Score=21.62 Aligned_cols=50 Identities=20% Similarity=0.307 Sum_probs=33.5
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHHhcCCc-ccHHHHHHHHHHHHHHh
Q 033283 62 CVSEFISFITSEASDKCQREKRKTINGDDLLWAMATLGFE-DYIDPLKIYLTRYREVI 118 (122)
Q Consensus 62 ~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~-~~~~~l~~~l~~~re~~ 118 (122)
.+...+.||-..|. |.-++++++..-|+.|||+ +..+.+......+++.+
T Consensus 43 ~~va~l~fiL~~A~-------k~n~~~~~l~~eL~~lglp~e~~~~l~~~~~~~~~~l 93 (174)
T cd04752 43 ASIAVLSFILSSAA-------KYNVDGESLSSELQQLGLPKEHATSLCRSYEEKQSKL 93 (174)
T ss_pred HHHHHHHHHHHHHH-------HcCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHH
Confidence 34445555555443 3349999999999999998 55666666666665544
No 133
>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=35.86 E-value=73 Score=27.70 Aligned_cols=51 Identities=12% Similarity=0.105 Sum_probs=39.7
Q ss_pred CccccHHHHHHHHHHHHHHHHHHHH-HHHHHHHhcCCCCCCcchHHHHHHhcC
Q 033283 48 NGKIAKDAKETVQECVSEFISFITS-EASDKCQREKRKTINGDDLLWAMATLG 99 (122)
Q Consensus 48 ~~~iskdA~~al~~~a~~FI~~la~-~A~~~a~~~~RkTI~~eDV~~Al~~lg 99 (122)
.+.++.||...|.+ .--|+.-=.. .+-+.|+..|...|+.+.+..|=+.+|
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 46899999999954 6667764443 445788999999999999999876654
No 134
>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=35.29 E-value=1.1e+02 Score=21.44 Aligned_cols=28 Identities=14% Similarity=0.076 Sum_probs=24.6
Q ss_pred HHHHHHhcCCCCCCcchHHHHHHhcCCc
Q 033283 74 ASDKCQREKRKTINGDDLLWAMATLGFE 101 (122)
Q Consensus 74 A~~~a~~~~RkTI~~eDV~~Al~~lgf~ 101 (122)
|+-.|...|+..++.+||.+.|+..|.+
T Consensus 6 AylL~~l~g~~~pTa~dI~~IL~AaGve 33 (109)
T cd05833 6 AYLLAVLGGNASPSAADVKKILGSVGVE 33 (109)
T ss_pred HHHHHHHcCCCCCCHHHHHHHHHHcCCC
Confidence 5778888899899999999999988864
No 135
>PRK00732 fliE flagellar hook-basal body protein FliE; Reviewed
Probab=34.29 E-value=1.6e+02 Score=20.49 Aligned_cols=35 Identities=17% Similarity=0.239 Sum_probs=29.2
Q ss_pred CCcchHHHHHHh--cCCcccHHHHHHHHHHHHHHhcc
Q 033283 86 INGDDLLWAMAT--LGFEDYIDPLKIYLTRYREVICV 120 (122)
Q Consensus 86 I~~eDV~~Al~~--lgf~~~~~~l~~~l~~~re~~~~ 120 (122)
++-.||.-|+++ +.|.-.+.--...++.|+|+++-
T Consensus 64 ~~l~~vmiA~~kA~lslq~~vqVRNKlveAYqEIMrM 100 (102)
T PRK00732 64 ANLMDVVTAVAETDVAVSTLVSVRDRVIQAYEEIMRM 100 (102)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 378899999995 66677788888999999999874
No 136
>PF12627 PolyA_pol_RNAbd: Probable RNA and SrmB- binding site of polymerase A; PDB: 1OU5_B 3H38_A 3H3A_B 3H39_B 3H37_A 3AQN_A 3AQK_A 3AQM_B 3AQL_B 1MIY_A ....
Probab=33.59 E-value=32 Score=20.81 Aligned_cols=58 Identities=26% Similarity=0.373 Sum_probs=31.1
Q ss_pred CccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCC---CcchHHHHHHhcCCcccH-HHHHH
Q 033283 48 NGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTI---NGDDLLWAMATLGFEDYI-DPLKI 109 (122)
Q Consensus 48 ~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI---~~eDV~~Al~~lgf~~~~-~~l~~ 109 (122)
+.+|.+++..+|.+++. .+..++.+-. ..+=.|.+ .+...+..|.++|+.+++ +.++.
T Consensus 1 gF~ie~~t~~ai~~~~~-~L~~is~ERi---~~El~kil~~~~~~~~~~~l~~~gll~~ifP~l~~ 62 (64)
T PF12627_consen 1 GFKIEPETEEAIKENAE-LLSKISKERI---REELEKILSSPNPSRAFKLLDELGLLEYIFPELDA 62 (64)
T ss_dssp T-EE-HHHHHHHHHHGG-GGGGS-HHHH---HHHHHHHHTSTTHHHHHHHHHHTTCHHHHSTTHHT
T ss_pred CCccCHHHHHHHHHHHH-HHhcCCHHHH---HHHHHHHHcCCCHHHHHHHHHHcCCHHHHCccccc
Confidence 35677888888888776 4555554321 11112222 455566677788876663 54443
No 137
>cd00823 TopoIIB_Trans TopoIIB_Trans: Transducer domain, having a ribosomal S5 domain 2-like fold, of the type found in proteins of the type IIB family of DNA topoisomerases similar to Sulfolobus shibatae topoisomerase VI (topoVI). The sole representative of the Type IIB family is topo VI. Topo VI enzymes are heterotetramers found in archaea and plants. S. shibatae topoVI relaxes both positive and negative supercoils, and in addition has a strong decatenase activity. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes.
Probab=33.59 E-value=88 Score=23.56 Aligned_cols=48 Identities=17% Similarity=0.281 Sum_probs=33.8
Q ss_pred CCccccccChhhHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHH
Q 033283 24 NVREQDRYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEA 74 (122)
Q Consensus 24 ~~~~~d~~LP~A~V~Ri~K~~lp~~~~iskdA~~al~~~a~~FI~~la~~A 74 (122)
.+.+-...+|-.... |+++.+.--|-+|.+.+|++||...=.||...-
T Consensus 96 ~Vhi~St~VPfts~~---KeaIadvpEI~~EIrlAl~~~~R~L~~~l~kk~ 143 (151)
T cd00823 96 LVHVASTKVPFTSEG---KEAIADIPEIEEEIKLALQEVARKLKRYLSKKR 143 (151)
T ss_pred EEEEeecCCCcCCcc---hhhhcCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334444555554443 455555456889999999999999999998753
No 138
>COG5340 Predicted transcriptional regulator [Transcription]
Probab=32.53 E-value=77 Score=25.80 Aligned_cols=53 Identities=9% Similarity=0.187 Sum_probs=43.0
Q ss_pred ccccccChhhHHHHHHHhhCCC-----Cc-cccHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033283 26 REQDRYLPIANISRIMKKALPA-----NG-KIAKDAKETVQECVSEFISFITSEASDKC 78 (122)
Q Consensus 26 ~~~d~~LP~A~V~Ri~K~~lp~-----~~-~iskdA~~al~~~a~~FI~~la~~A~~~a 78 (122)
.++.+..|.+++.|-+++++.. ++ -+.+-.+.+...++++|..|+-..+|-.+
T Consensus 149 ~Ie~~~VpvttlaKTi~DC~~kP~YCGG~~~~akAl~aa~e~a~~e~t~Yl~R~~n~Aa 207 (269)
T COG5340 149 SIEGTVVPVTTLAKTIVDCADKPEYCGGIRELAKALVAADEQACSEATEYLQRLDNGAA 207 (269)
T ss_pred ceeeeeeehHHHHHHHHHHhcCccccCCHHHHHHHHHHhHHHHHHHHHHHHHhccchHH
Confidence 4556679999999999999975 33 48888999999999999999887765443
No 139
>KOG1528 consensus Salt-sensitive 3'-phosphoadenosine-5'-phosphatase HAL2/SAL1 [Nucleotide transport and metabolism; Inorganic ion transport and metabolism]
Probab=32.52 E-value=1.3e+02 Score=25.52 Aligned_cols=74 Identities=18% Similarity=0.213 Sum_probs=45.0
Q ss_pred CCccccccChhhHHHHHHHhhCCCCc--cccHHHHHHHHHH-HHHHHHHHHHHHHH---HHHhcCC-CCCCcchHHHHHH
Q 033283 24 NVREQDRYLPIANISRIMKKALPANG--KIAKDAKETVQEC-VSEFISFITSEASD---KCQREKR-KTINGDDLLWAMA 96 (122)
Q Consensus 24 ~~~~~d~~LP~A~V~Ri~K~~lp~~~--~iskdA~~al~~~-a~~FI~~la~~A~~---~a~~~~R-kTI~~eDV~~Al~ 96 (122)
++...|+- --|.|.-.+++.+|+.- .|..|-..-+.+. ++.|+.-++..-|+ ....=+- +.++.+||++|+.
T Consensus 43 PVTvaDyG-~QAiVs~vL~~~f~~~p~slVaEEds~~Lr~n~~~~~l~~i~~lvnetl~s~~sy~~~~~ls~~dvl~aID 121 (351)
T KOG1528|consen 43 PVTVADYG-SQAIVSLVLEREFPDDPLSLVAEEDSGFLRKNGSEGLLSRITKLVNETLASDESYGDNSPLSSDDVLKAID 121 (351)
T ss_pred Ccchhhhh-HHHHHHHHHHHHcCCCCcceEeeccchhhhhhhhHHHHHHHHHHHHHHhhhhhhccCCCCCCHHHHHHHHh
Confidence 34444432 24678888899998643 4555555555544 55666666663332 2222233 7899999999987
Q ss_pred hc
Q 033283 97 TL 98 (122)
Q Consensus 97 ~l 98 (122)
.-
T Consensus 122 ~G 123 (351)
T KOG1528|consen 122 RG 123 (351)
T ss_pred cc
Confidence 54
No 140
>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=32.46 E-value=48 Score=17.29 Aligned_cols=26 Identities=19% Similarity=0.227 Sum_probs=19.0
Q ss_pred HHHHHHhcCCCCCCcchHHHHHH-hcC
Q 033283 74 ASDKCQREKRKTINGDDLLWAMA-TLG 99 (122)
Q Consensus 74 A~~~a~~~~RkTI~~eDV~~Al~-~lg 99 (122)
+.+..-.++.-+|+.+++..+|+ .||
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 34555666777899999999998 576
No 141
>COG1389 DNA topoisomerase VI, subunit B [DNA replication, recombination, and repair]
Probab=32.26 E-value=37 Score=30.21 Aligned_cols=46 Identities=20% Similarity=0.367 Sum_probs=35.8
Q ss_pred HhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCC
Q 033283 42 KKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTIN 87 (122)
Q Consensus 42 K~~lp~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~ 87 (122)
|++..+.--|-+|.+.|+++||.+.=.||.....+.=+.+++++|.
T Consensus 434 KqsIa~vpeIe~Eir~Al~evaRkL~~yLsrk~r~~e~~~K~~~i~ 479 (538)
T COG1389 434 KQSIADVPEIENEIRLALMEVARKLKLYLSRKRREMEERKKRKTIE 479 (538)
T ss_pred chhccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444444467899999999999999999999988777777666653
No 142
>smart00454 SAM Sterile alpha motif. Widespread domain in signalling and nuclear proteins. In EPH-related tyrosine kinases, appears to mediate cell-cell initiated signal transduction via the binding of SH2-containing proteins to a conserved tyrosine that is phosphorylated. In many cases mediates homodimerisation.
Probab=31.53 E-value=36 Score=20.04 Aligned_cols=25 Identities=16% Similarity=0.331 Sum_probs=19.1
Q ss_pred CCcchHHHHHHhcCCcccHHHHHHH
Q 033283 86 INGDDLLWAMATLGFEDYIDPLKIY 110 (122)
Q Consensus 86 I~~eDV~~Al~~lgf~~~~~~l~~~ 110 (122)
-+.++|..-|+.+||++|.......
T Consensus 4 w~~~~v~~wL~~~g~~~y~~~f~~~ 28 (68)
T smart00454 4 WSPESVADWLESIGLEQYADNFRKN 28 (68)
T ss_pred CCHHHHHHHHHHCChHHHHHHHHHC
Confidence 4567888889999988887776543
No 143
>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=31.45 E-value=68 Score=23.55 Aligned_cols=37 Identities=27% Similarity=0.123 Sum_probs=28.2
Q ss_pred CCCCcchHHHHHHhcCCcc-----------cHHHHHHHHHHHHHHhcc
Q 033283 84 KTINGDDLLWAMATLGFED-----------YIDPLKIYLTRYREVICV 120 (122)
Q Consensus 84 kTI~~eDV~~Al~~lgf~~-----------~~~~l~~~l~~~re~~~~ 120 (122)
.|.++.|+..+++.++++. |++.+.+..++-++.++.
T Consensus 112 ~TT~~~~l~~~l~~l~~P~~~~~~~~l~~Rfip~l~~e~~~i~~Aq~a 159 (198)
T TIGR02454 112 LTTPFPELLSALRRLGVPPLLVEILLLTYRYLFVLLEELRRMLLAQRS 159 (198)
T ss_pred HcCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4678899999999999864 667777777776666543
No 144
>PRK03907 fliE flagellar hook-basal body protein FliE; Reviewed
Probab=31.42 E-value=1.8e+02 Score=20.15 Aligned_cols=36 Identities=8% Similarity=0.146 Sum_probs=29.6
Q ss_pred CCCcchHHHHHHh--cCCcccHHHHHHHHHHHHHHhcc
Q 033283 85 TINGDDLLWAMAT--LGFEDYIDPLKIYLTRYREVICV 120 (122)
Q Consensus 85 TI~~eDV~~Al~~--lgf~~~~~~l~~~l~~~re~~~~ 120 (122)
..+..||+-|+++ +.|.-.+.--...++.|+|+++-
T Consensus 58 ~~dlhevmIA~~kA~ls~q~~vqVRNKlveAYqEIMrM 95 (97)
T PRK03907 58 VKDLHQAAIAIGKAETSMKLMLEVRNKAISAYKEILRT 95 (97)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence 4588889999995 66667788888999999999874
No 145
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=31.41 E-value=93 Score=20.36 Aligned_cols=28 Identities=11% Similarity=0.135 Sum_probs=20.1
Q ss_pred HHHHHHhcCCCCCCcchHHHHHHhcCCc
Q 033283 74 ASDKCQREKRKTINGDDLLWAMATLGFE 101 (122)
Q Consensus 74 A~~~a~~~~RkTI~~eDV~~Al~~lgf~ 101 (122)
+...+-.++.-.|+.++|..+|..+|+.
T Consensus 15 ~F~~~D~d~~G~Is~~el~~~l~~~~~~ 42 (96)
T smart00027 15 IFRSLDKNQDGTVTGAQAKPILLKSGLP 42 (96)
T ss_pred HHHHhCCCCCCeEeHHHHHHHHHHcCCC
Confidence 3455556667778888888888887764
No 146
>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=31.06 E-value=66 Score=23.66 Aligned_cols=58 Identities=17% Similarity=0.067 Sum_probs=38.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHHhcCCcc------------cHHHHHHHHHHHHHHhc
Q 033283 59 VQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMATLGFED------------YIDPLKIYLTRYREVIC 119 (122)
Q Consensus 59 l~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~------------~~~~l~~~l~~~re~~~ 119 (122)
+..++..++..+..-..-.. =-.|.+++|+..+++.+.++. |++.+.+.+++-++.++
T Consensus 101 ~~~~~~~~lr~~~~~~~~~~---~~~tt~~~~l~~~l~~l~~P~~~~~~~i~l~~r~ip~l~~~~~~i~~A~~ 170 (224)
T PF02361_consen 101 LIYAALLALRILAILLASLL---FILTTSPSDLISALRKLRLPYPKIALMISLTLRFIPLLLEEFKRIREAQR 170 (224)
T ss_pred HHHHHHHHHHHHHHHHHHHH---HHHHCCHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44444444444443332222 124789999999999999988 78888887777776654
No 147
>KOG0785 consensus Isocitrate dehydrogenase, alpha subunit [Amino acid transport and metabolism]
Probab=30.65 E-value=1.1e+02 Score=25.92 Aligned_cols=64 Identities=9% Similarity=0.063 Sum_probs=45.5
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHHhcCCcccHHHHHHHHHHHH
Q 033283 51 IAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMATLGFEDYIDPLKIYLTRYR 115 (122)
Q Consensus 51 iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~~~~~l~~~l~~~r 115 (122)
+-.-..+.|...++.-..-++.-|.++|+.++|+.++.-|=.+-|+.-+ .-|++.+++.-++|-
T Consensus 164 vvpGVvqsiK~IT~~AS~Ria~~AF~yAr~~~R~~vtvvHKaNImr~tD-GLFle~cre~a~~y~ 227 (365)
T KOG0785|consen 164 VVPGVVQSIKLITEAASRRIAEYAFEYARQNGRKRVTVVHKANIMRMTD-GLFLECCREVAKKYP 227 (365)
T ss_pred ccccHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCceEEEehhhhhhhcc-hHHHHHHHHHhhhCC
Confidence 3344667777777777778888899999999999999888766665432 346666666655443
No 148
>PRK07914 hypothetical protein; Reviewed
Probab=30.55 E-value=1.3e+02 Score=24.20 Aligned_cols=63 Identities=11% Similarity=0.139 Sum_probs=44.1
Q ss_pred hhhHHHHHHHhhCCC-CccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHH
Q 033283 33 PIANISRIMKKALPA-NGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMA 96 (122)
Q Consensus 33 P~A~V~Ri~K~~lp~-~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~ 96 (122)
+...+.+.|++.+.. +..|+.||...|.+++..=...+..+-.+.+-..+ .+|+.+||...+.
T Consensus 129 ~~~~l~~wi~~~a~~~g~~i~~~A~~~L~~~~g~dl~~l~~EleKL~~~~~-~~It~e~V~~~v~ 192 (320)
T PRK07914 129 KAAERADFVRKEFRSLRVKVDDDTVTALLDAVGSDLRELASACSQLVADTG-GAVDAAAVRRYHS 192 (320)
T ss_pred CHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHCccHHHHHHHHHHHhcCCC-CCcCHHHHHHHcC
Confidence 445555555555433 56899999999999987666666666666654334 5699999988866
No 149
>COG3267 ExeA Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]
Probab=30.45 E-value=1.5e+02 Score=24.38 Aligned_cols=56 Identities=13% Similarity=0.136 Sum_probs=45.2
Q ss_pred HHHHHHhhCCCCccccHHHHHHHHHHHH---HHHHHHHHHHHHHHHhcCCCCCCcchHH
Q 033283 37 ISRIMKKALPANGKIAKDAKETVQECVS---EFISFITSEASDKCQREKRKTINGDDLL 92 (122)
Q Consensus 37 V~Ri~K~~lp~~~~iskdA~~al~~~a~---~FI~~la~~A~~~a~~~~RkTI~~eDV~ 92 (122)
+.-.++.+..+.-.++.+++.++.+... .-|+.++..|.+.|-..++.+|+...+-
T Consensus 209 l~~~Le~a~~~~~l~~~~a~~~i~~~sqg~P~lin~~~~~Al~~a~~a~~~~v~~a~~~ 267 (269)
T COG3267 209 LRHRLEGAGLPEPLFSDDALLLIHEASQGIPRLINNLATLALDAAYSAGEDGVSEAEIK 267 (269)
T ss_pred HHHHHhccCCCcccCChhHHHHHHHHhccchHHHHHHHHHHHHHHHHcCCCccchhhcc
Confidence 3444555554455799999999999877 7899999999999999999999876553
No 150
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=30.33 E-value=1.2e+02 Score=18.96 Aligned_cols=33 Identities=24% Similarity=0.525 Sum_probs=25.2
Q ss_pred ccChhhHHHHHHHhhCCCCccccHHHHHHHHHHHHHH
Q 033283 30 RYLPIANISRIMKKALPANGKIAKDAKETVQECVSEF 66 (122)
Q Consensus 30 ~~LP~A~V~Ri~K~~lp~~~~iskdA~~al~~~a~~F 66 (122)
..+..++|.|++.. ...|+.+.+..+.+++.++
T Consensus 10 ~gvS~~TVSr~ln~----~~~v~~~t~~~i~~~~~~~ 42 (70)
T smart00354 10 AGVSKATVSRVLNG----NGRVSEETREKVLAAMEEL 42 (70)
T ss_pred HCCCHHHHHHHHCC----CCCCCHHHHHHHHHHHHHh
Confidence 34778889888763 3467899999998888775
No 151
>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=29.93 E-value=31 Score=20.34 Aligned_cols=17 Identities=18% Similarity=0.393 Sum_probs=12.8
Q ss_pred cccChhhHHHHHHHhhC
Q 033283 29 DRYLPIANISRIMKKAL 45 (122)
Q Consensus 29 d~~LP~A~V~Ri~K~~l 45 (122)
.+.+|++++.|+++.-.
T Consensus 27 ~~gl~~stv~r~L~tL~ 43 (52)
T PF09339_consen 27 ALGLPKSTVHRLLQTLV 43 (52)
T ss_dssp HHTS-HHHHHHHHHHHH
T ss_pred HHCcCHHHHHHHHHHHH
Confidence 36799999999998643
No 152
>KOG1658 consensus DNA polymerase epsilon, subunit C [Replication, recombination and repair]
Probab=29.29 E-value=1.1e+02 Score=23.29 Aligned_cols=69 Identities=17% Similarity=0.239 Sum_probs=47.0
Q ss_pred cccccChhhHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHH-----------HHH-HhcCCCCCCcchHHHH
Q 033283 27 EQDRYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEAS-----------DKC-QREKRKTINGDDLLWA 94 (122)
Q Consensus 27 ~~d~~LP~A~V~Ri~K~~lp~~~~iskdA~~al~~~a~~FI~~la~~A~-----------~~a-~~~~RkTI~~eDV~~A 94 (122)
+-..-||.+-+.||-|.. |..+.=+.++..+...+++.|+..++..+. +.| +..---|+..++++.+
T Consensus 7 e~~p~~p~ekvkkiak~d-Pey~~te~~a~~etafatE~fvq~lv~~p~a~l~rLpL~rik~vvkl~pdl~l~~dea~~l 85 (162)
T KOG1658|consen 7 ECSPKLPMEKVKKIAKND-PEYMDTEDDAFVETAFATEQFVQVLVHLPQASLSRLPLARIKQVVKLDPDLTLLNDEASQL 85 (162)
T ss_pred hhCccccHHHHHHhhcCC-chhhhcccchHHHHHHHHHHHHhhhhhhhhhhhhhccHHHHHhhccCCcchhhhhhHHHHH
Confidence 334569999999999977 445556778888999999999888887221 111 1222246777777776
Q ss_pred HH
Q 033283 95 MA 96 (122)
Q Consensus 95 l~ 96 (122)
+.
T Consensus 86 ~a 87 (162)
T KOG1658|consen 86 IA 87 (162)
T ss_pred HH
Confidence 65
No 153
>PRK09526 lacI lac repressor; Reviewed
Probab=28.84 E-value=67 Score=25.07 Aligned_cols=37 Identities=16% Similarity=0.501 Sum_probs=29.3
Q ss_pred cChhhHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHH
Q 033283 31 YLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITS 72 (122)
Q Consensus 31 ~LP~A~V~Ri~K~~lp~~~~iskdA~~al~~~a~~FI~~la~ 72 (122)
..-++||.|.+... .+||++.+.-+.+++++ +.|.-.
T Consensus 16 GVS~~TVSrvLn~~----~~vs~~tr~rV~~~a~e-lgY~pn 52 (342)
T PRK09526 16 GVSYQTVSRVLNQA----SHVSAKTREKVEAAMAE-LNYVPN 52 (342)
T ss_pred CCCHHHHHHHhcCC----CCCCHHHHHHHHHHHHH-HCCCcC
Confidence 45678999998743 47999999999999998 566544
No 154
>TIGR02903 spore_lon_C ATP-dependent protease, Lon family. Members of this protein family resemble the widely distributed ATP-dependent protease La, also called Lon and LonA. It resembles even more closely LonB, which is a LonA paralog found in genomes if and only if the species is capable of endospore formation (as in Bacillus subtilis, Clostridium tetani, and select other members of the Firmicutes) and expressed specifically in the forespore compartment. Members of this family are restricted to a subset of spore-forming species, and are very likely to participate in the program of endospore formation. We propose the designation LonC.
Probab=27.93 E-value=1.2e+02 Score=27.12 Aligned_cols=71 Identities=15% Similarity=0.194 Sum_probs=45.3
Q ss_pred hhHHHHHHHhhCCC-CccccHHHHHHHHHHH---HHHHHHHHHHH----HH---HHHhcCCCCCCcchHHHHHHhcCCcc
Q 033283 34 IANISRIMKKALPA-NGKIAKDAKETVQECV---SEFISFITSEA----SD---KCQREKRKTINGDDLLWAMATLGFED 102 (122)
Q Consensus 34 ~A~V~Ri~K~~lp~-~~~iskdA~~al~~~a---~~FI~~la~~A----~~---~a~~~~RkTI~~eDV~~Al~~lgf~~ 102 (122)
..-+..|++..+.. +..++.++..+|.+++ ...++.|.... +. .+...++.+|+.+||.++++.--|..
T Consensus 355 ~edi~~Il~~~a~~~~v~ls~eal~~L~~ys~~gRraln~L~~~~~~~~~~~~~~~~~~~~~~I~~edv~~~l~~~r~~~ 434 (615)
T TIGR02903 355 PEDIALIVLNAAEKINVHLAAGVEELIARYTIEGRKAVNILADVYGYALYRAAEAGKENDKVTITQDDVYEVIQISRLSP 434 (615)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHCCCcHHHHHHHHHHHHHHHHHHHHHhccCCCCeeECHHHHHHHhCCCcCcc
Confidence 35566777766543 3468999999988765 34444443321 11 12233456899999999999777765
Q ss_pred cH
Q 033283 103 YI 104 (122)
Q Consensus 103 ~~ 104 (122)
|.
T Consensus 435 ~~ 436 (615)
T TIGR02903 435 YE 436 (615)
T ss_pred ch
Confidence 54
No 155
>COG3404 Methenyl tetrahydrofolate cyclohydrolase [Amino acid transport and metabolism]
Probab=27.79 E-value=28 Score=27.45 Aligned_cols=14 Identities=57% Similarity=1.092 Sum_probs=8.5
Q ss_pred CCCCCCCCCCCCCCC
Q 033283 2 AAEAPASPGGGSHES 16 (122)
Q Consensus 2 ~~~~~~~~~~~~~~~ 16 (122)
+|+.| .|||||-..
T Consensus 16 as~~P-tPGGGsasA 29 (208)
T COG3404 16 ASEKP-TPGGGSASA 29 (208)
T ss_pred cCCCC-CCCCchHHH
Confidence 56665 477776543
No 156
>PF10728 DUF2520: Domain of unknown function (DUF2520); InterPro: IPR018931 This presumed domain is found C-terminal to a Rossmann-like domain suggesting that these proteins are oxidoreductases. ; PDB: 3D1L_A 2I76_A 3DFU_A.
Probab=27.62 E-value=2e+02 Score=20.53 Aligned_cols=58 Identities=12% Similarity=0.139 Sum_probs=38.1
Q ss_pred hhHHHHHHHhhCCCCccccHHHHHHHHHHHH---HHHHHHHHHHHHHHHhcCCCCCCcchHHHH
Q 033283 34 IANISRIMKKALPANGKIAKDAKETVQECVS---EFISFITSEASDKCQREKRKTINGDDLLWA 94 (122)
Q Consensus 34 ~A~V~Ri~K~~lp~~~~iskdA~~al~~~a~---~FI~~la~~A~~~a~~~~RkTI~~eDV~~A 94 (122)
...+.++++........|..+-|....-++. -|+.+|...|.+.+...| |..++..++
T Consensus 13 ~~~l~~l~~~lg~~~~~i~~~~r~~yHaAav~asNf~~~L~~~a~~ll~~~g---i~~~~a~~~ 73 (132)
T PF10728_consen 13 LEVLQELAKELGGRPFEIDSEQRALYHAAAVFASNFLVALYALAAELLEQAG---IDFEEALEA 73 (132)
T ss_dssp HHHHHHHHHHTTSEEEE--GGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----SHHH--HH
T ss_pred HHHHHHHHHHhCCceEEeCHHhHHHHHHHHHHHHhhHHHHHHHHHHHHHHcC---CCchhHHHH
Confidence 3456778887776667899999988887755 678888888888877663 455443333
No 157
>PRK00440 rfc replication factor C small subunit; Reviewed
Probab=27.24 E-value=1.4e+02 Score=23.09 Aligned_cols=65 Identities=11% Similarity=0.059 Sum_probs=38.7
Q ss_pred ChhhHHHHHHHhhCC-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHHhc
Q 033283 32 LPIANISRIMKKALP-ANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMATL 98 (122)
Q Consensus 32 LP~A~V~Ri~K~~lp-~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~~l 98 (122)
++...+.++++..+. .+..|+.++...+.+.+.-=+..+-.+-...+.. .++|+.+||..++...
T Consensus 161 l~~~ei~~~l~~~~~~~~~~i~~~al~~l~~~~~gd~r~~~~~l~~~~~~--~~~it~~~v~~~~~~~ 226 (319)
T PRK00440 161 LKKEAVAERLRYIAENEGIEITDDALEAIYYVSEGDMRKAINALQAAAAT--GKEVTEEAVYKITGTA 226 (319)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHc--CCCCCHHHHHHHhCCC
Confidence 445555555555443 2457999999988887653333333322233332 3679999988887543
No 158
>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=26.57 E-value=44 Score=19.90 Aligned_cols=16 Identities=19% Similarity=0.406 Sum_probs=13.4
Q ss_pred CCcchHHHHHHhcCCc
Q 033283 86 INGDDLLWAMATLGFE 101 (122)
Q Consensus 86 I~~eDV~~Al~~lgf~ 101 (122)
++.++|..+++++||+
T Consensus 47 ~~~~~i~~~i~~~Gy~ 62 (62)
T PF00403_consen 47 TSIEKIIEAIEKAGYE 62 (62)
T ss_dssp SCHHHHHHHHHHTTSE
T ss_pred CCHHHHHHHHHHhCcC
Confidence 6678899999999884
No 159
>COG1239 ChlI Mg-chelatase subunit ChlI [Coenzyme metabolism]
Probab=26.53 E-value=1.3e+02 Score=26.19 Aligned_cols=49 Identities=14% Similarity=0.210 Sum_probs=40.1
Q ss_pred CccccHHHHHHHHHHHHHHHH-------HHHHHHHHHHHhcCCCCCCcchHHHHHH
Q 033283 48 NGKIAKDAKETVQECVSEFIS-------FITSEASDKCQREKRKTINGDDLLWAMA 96 (122)
Q Consensus 48 ~~~iskdA~~al~~~a~~FI~-------~la~~A~~~a~~~~RkTI~~eDV~~Al~ 96 (122)
.+.++.++...+.+.|..+-. .++..|..++.-.||.+++.+||-.|++
T Consensus 265 ~V~l~~~~~~~ia~~~~~~~v~g~radi~~~r~a~a~aa~~Gr~~v~~~Di~~a~~ 320 (423)
T COG1239 265 EVELDDDAETKIAELCARLAVDGHRADIVVVRAAKALAALRGRTEVEEEDIREAAE 320 (423)
T ss_pred cccCcHHHHHHHHHHHHHhccCCCchhhHHHHHHHHHHHhcCceeeehhhHHHHHh
Confidence 467888888888888877643 3666777889999999999999999976
No 160
>PF11884 DUF3404: Domain of unknown function (DUF3404); InterPro: IPR021821 This domain is functionally uncharacterised. This domain is found in bacteria. This presumed domain is about 260 amino acids in length. This domain is found associated with PF02518 from PFAM, PF00512 from PFAM.
Probab=26.07 E-value=31 Score=28.14 Aligned_cols=19 Identities=11% Similarity=0.441 Sum_probs=15.7
Q ss_pred cccHHHHHHHHHHHHHHHH
Q 033283 50 KIAKDAKETVQECVSEFIS 68 (122)
Q Consensus 50 ~iskdA~~al~~~a~~FI~ 68 (122)
+++.|.++||..-..-|+.
T Consensus 155 ~ms~~~~~ALl~G~r~~l~ 173 (262)
T PF11884_consen 155 RMSDDGRDALLSGYRAFLE 173 (262)
T ss_pred cCCHHHHHHHHHhHHHHcc
Confidence 7889999999988777763
No 161
>PRK05629 hypothetical protein; Validated
Probab=25.50 E-value=2.4e+02 Score=22.57 Aligned_cols=49 Identities=10% Similarity=0.041 Sum_probs=36.3
Q ss_pred CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHH
Q 033283 47 ANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMA 96 (122)
Q Consensus 47 ~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~ 96 (122)
.+.+|+.+|...|...+..=...+..+-.+.+.-. ..+|+.+||...+.
T Consensus 142 ~g~~i~~~A~~~L~~~~g~dl~~l~~EleKL~~~~-~~~It~e~V~~~v~ 190 (318)
T PRK05629 142 HGVRPTPDVVHALLEGVGSDLRELASAISQLVEDT-QGNVTVEKVRAYYV 190 (318)
T ss_pred cCCCCCHHHHHHHHHHHCccHHHHHHHHHHHHhcC-CCCcCHHHHHHHhC
Confidence 35689999999988888765666666666666543 45799999988755
No 162
>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=24.96 E-value=24 Score=25.62 Aligned_cols=36 Identities=25% Similarity=0.332 Sum_probs=0.0
Q ss_pred HhcCCCCCCcchHHHHHHhcCCc-ccHHHHHHHHHHH
Q 033283 79 QREKRKTINGDDLLWAMATLGFE-DYIDPLKIYLTRY 114 (122)
Q Consensus 79 ~~~~RkTI~~eDV~~Al~~lgf~-~~~~~l~~~l~~~ 114 (122)
+..|-|+|++.|+--|-+.|+|- .+++.++.+++..
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 44578999999999999999995 7788888777765
No 163
>PRK04184 DNA topoisomerase VI subunit B; Validated
Probab=24.83 E-value=58 Score=29.05 Aligned_cols=55 Identities=18% Similarity=0.342 Sum_probs=37.4
Q ss_pred HhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCc--chHHHHHH
Q 033283 42 KKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTING--DDLLWAMA 96 (122)
Q Consensus 42 K~~lp~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~--eDV~~Al~ 96 (122)
|++..+.--|-+|.+.||++||...=.||...-...-...+++++.. .+|..+|.
T Consensus 431 Ke~ia~~~ei~~ei~~al~~~~r~L~~~l~~~~~~~~~~~k~~~~~~y~p~~a~~~~ 487 (535)
T PRK04184 431 KEAIADVPEIEKEIRLALQEVARKLKKYLSRKRKEEEAKKKAKTFEKYIPEIARKLA 487 (535)
T ss_pred hhhhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45555445688999999999999999999987665555555554432 34444444
No 164
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=24.70 E-value=77 Score=24.70 Aligned_cols=37 Identities=11% Similarity=0.357 Sum_probs=28.3
Q ss_pred cChhhHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHH
Q 033283 31 YLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITS 72 (122)
Q Consensus 31 ~LP~A~V~Ri~K~~lp~~~~iskdA~~al~~~a~~FI~~la~ 72 (122)
..-++||.|.+... .+||.+.+..+.+++++ +.|.-.
T Consensus 16 gVS~~TVSrvLn~~----~~vs~~tr~rV~~~a~e-lgY~pn 52 (331)
T PRK14987 16 GVTKMTVSRFLRNP----EQVSVALRGKIAAALDE-LGYIPN 52 (331)
T ss_pred CCCHHHhhhhhCCC----CCCCHHHHHHHHHHHHH-hCCCcc
Confidence 45678899988643 47999999999999988 456543
No 165
>PF09239 Topo-VIb_trans: Topoisomerase VI B subunit, transducer; InterPro: IPR015320 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils []. This entry represents subunit B of topoisomerase VI, an ATP-dependent type IIB enzyme. Members of this family adopt a structure consisting of a four-stranded beta-sheet backed by three alpha-helices, the last of which is over 50 amino acids long and extends from the body of the protein by several turns. This domain has been proposed to mediate intersubunit communication by structurally transducing signals from the ATP binding and hydrolysis domains to the DNA binding and cleavage domains of the gyrase holoenzyme []. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0006265 DNA topological change, 0005694 chromosome; PDB: 2ZBK_F 2HKJ_A 1Z5B_A 1Z5C_B 1MX0_F 1Z5A_A 1MU5_A 1Z59_A 2Q2E_B.
Probab=24.50 E-value=89 Score=23.76 Aligned_cols=33 Identities=21% Similarity=0.477 Sum_probs=25.0
Q ss_pred HhhCCCCccccHHHHHHHHHHHHHHHHHHHHHH
Q 033283 42 KKALPANGKIAKDAKETVQECVSEFISFITSEA 74 (122)
Q Consensus 42 K~~lp~~~~iskdA~~al~~~a~~FI~~la~~A 74 (122)
|++..+.--|-+|.+.+|++|+...=.||....
T Consensus 120 KeaIa~~pEI~~Ei~lAl~e~~R~L~~yl~rk~ 152 (160)
T PF09239_consen 120 KEAIADVPEIEKEIRLALQECARKLKKYLSRKR 152 (160)
T ss_dssp SSSB---HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hhhhcCcHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455544446889999999999999999998754
No 166
>KOG0729 consensus 26S proteasome regulatory complex, ATPase RPT1 [Posttranslational modification, protein turnover, chaperones]
Probab=24.28 E-value=66 Score=27.29 Aligned_cols=49 Identities=20% Similarity=0.196 Sum_probs=35.5
Q ss_pred ccccHHHHH-HHHHH----HHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHHh
Q 033283 49 GKIAKDAKE-TVQEC----VSEFISFITSEASDKCQREKRKTINGDDLLWAMAT 97 (122)
Q Consensus 49 ~~iskdA~~-al~~~----a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~~ 97 (122)
+.|-+|-+. +|.+. +..=|.-+..+|-..|.+..||+.+..|.+.|+++
T Consensus 364 msverdir~ellarlcpnstgaeirsvcteagmfairarrk~atekdfl~av~k 417 (435)
T KOG0729|consen 364 MSVERDIRFELLARLCPNSTGAEIRSVCTEAGMFAIRARRKVATEKDFLDAVNK 417 (435)
T ss_pred cccccchhHHHHHhhCCCCcchHHHHHHHHhhHHHHHHHhhhhhHHHHHHHHHH
Confidence 345555543 33332 23456677788999999999999999999999875
No 167
>cd03521 Link_domain_KIAA0527_like Link_domain_KIAA0527_like; this domain is found in the human protein KIAA0527. Sequence-wise, it is highly similar to the link domain. The link domain is a hyaluronan-binding (HA) domain. KIAA0527 contains a single link module. The KIAA0527 gene was originally cloned from human brain tissue.
Probab=23.84 E-value=95 Score=21.66 Aligned_cols=31 Identities=16% Similarity=0.200 Sum_probs=27.9
Q ss_pred HHHHHHHHhcCCCCCCcchHHHHHHhcCCcc
Q 033283 72 SEASDKCQREKRKTINGDDLLWAMATLGFED 102 (122)
Q Consensus 72 ~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~ 102 (122)
.+|...|...+-.--+++.+..|-++.||+.
T Consensus 17 ~eA~~AC~~~gA~lAs~~QL~~AW~~~Gld~ 47 (95)
T cd03521 17 RAARQSCASLGARLASAAELRRAVVECFFSA 47 (95)
T ss_pred HHHHHHHHHcCCEeccHHHHHHHHHHhCccc
Confidence 5788999999999999999999999988863
No 168
>cd00051 EFh EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers.
Probab=23.75 E-value=1.3e+02 Score=16.17 Aligned_cols=37 Identities=19% Similarity=0.224 Sum_probs=22.3
Q ss_pred HHhcCCCCCCcchHHHHHHhcCCcccHHHHHHHHHHH
Q 033283 78 CQREKRKTINGDDLLWAMATLGFEDYIDPLKIYLTRY 114 (122)
Q Consensus 78 a~~~~RkTI~~eDV~~Al~~lgf~~~~~~l~~~l~~~ 114 (122)
+..++.-.|+.+|+..+++.++...-...++..+..+
T Consensus 9 ~d~~~~g~l~~~e~~~~l~~~~~~~~~~~~~~~~~~~ 45 (63)
T cd00051 9 FDKDGDGTISADELKAALKSLGEGLSEEEIDEMIREV 45 (63)
T ss_pred hCCCCCCcCcHHHHHHHHHHhCCCCCHHHHHHHHHHh
Confidence 3444455678888888888777555444444444433
No 169
>cd04411 Ribosomal_P1_P2_L12p Ribosomal protein P1, P2, and L12p. Ribosomal proteins P1 and P2 are the eukaryotic proteins that are functionally equivalent to bacterial L7/L12. L12p is the archaeal homolog. Unlike other ribosomal proteins, the archaeal L12p and eukaryotic P1 and P2 do not share sequence similarity with their bacterial counterparts. They are part of the ribosomal stalk (called the L7/L12 stalk in bacteria), along with 28S rRNA and the proteins L11 and P0 in eukaryotes (23S rRNA, L11, and L10e in archaea). In bacterial ribosomes, L7/L12 homodimers bind the extended C-terminal helix of L10 to anchor the L7/L12 molecules to the ribosome. Eukaryotic P1/P2 heterodimers and archaeal L12p homodimers are believed to bind the L10 equivalent proteins, eukaryotic P0 and archaeal L10e, in a similar fashion. P1 and P2 (L12p, L7/L12) are the only proteins in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain
Probab=23.45 E-value=2.3e+02 Score=19.73 Aligned_cols=38 Identities=16% Similarity=0.212 Sum_probs=26.0
Q ss_pred HHHHHHhcCCCCCCcchHHHHHHhcCCcccHHHHHHHHH
Q 033283 74 ASDKCQREKRKTINGDDLLWAMATLGFEDYIDPLKIYLT 112 (122)
Q Consensus 74 A~~~a~~~~RkTI~~eDV~~Al~~lgf~~~~~~l~~~l~ 112 (122)
|+-++...|.. |+.+||.+.|+..|.+==-..++.++.
T Consensus 6 A~Lll~~~g~~-~ta~~I~~IL~aaGveVe~~~~~~~~~ 43 (105)
T cd04411 6 AYLLLHKGGKE-LTEDKIKELLSAAGAEIEPERVKLFLS 43 (105)
T ss_pred HHHHHHhcCCC-CCHHHHHHHHHHcCCCcCHHHHHHHHH
Confidence 56667777766 999999999998887533333344433
No 170
>PF13413 HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_A.
Probab=23.42 E-value=84 Score=19.60 Aligned_cols=32 Identities=22% Similarity=0.359 Sum_probs=24.6
Q ss_pred cchHHHHHHhcCCcccHHH--HHHHHHHHHHHhc
Q 033283 88 GDDLLWAMATLGFEDYIDP--LKIYLTRYREVIC 119 (122)
Q Consensus 88 ~eDV~~Al~~lgf~~~~~~--l~~~l~~~re~~~ 119 (122)
..+.++|||.-+|+.+-.+ ++.++..|-+..+
T Consensus 23 ~~~~l~aiE~~~~~~lp~~~y~rg~lr~Ya~~Lg 56 (62)
T PF13413_consen 23 SVSYLEAIENGDFDSLPSPVYARGYLRKYARFLG 56 (62)
T ss_dssp -HHHHHHHHCT-GCCSSSHHHHHHHHHHHHHHTT
T ss_pred CHHHHHHHHCcChhhCCcHHHHHHHHHHHHHHhC
Confidence 4577899999999988654 7999999987765
No 171
>PF06782 UPF0236: Uncharacterised protein family (UPF0236); InterPro: IPR009620 This is a group of proteins of unknown function.
Probab=23.24 E-value=1.6e+02 Score=25.58 Aligned_cols=58 Identities=21% Similarity=0.234 Sum_probs=42.3
Q ss_pred CCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHHhcCCcccH
Q 033283 45 LPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMATLGFEDYI 104 (122)
Q Consensus 45 lp~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~~~ 104 (122)
+++..++|.+++..+.+.+++ ..|=- .|..+-...+...|+.+-|.++++.+|+....
T Consensus 112 l~~~~R~S~~~~~~i~~~a~~-~sYr~-aa~~l~~~~~~~~iS~~tV~~~v~~~g~~~~~ 169 (470)
T PF06782_consen 112 LKKYQRISPELKEKIVELATE-MSYRK-AAEILEELLGNVSISKQTVWNIVKEAGFEEIK 169 (470)
T ss_pred CCcccchhHHHHHHHHHHHhh-cCHHH-HHHHHhhccCCCccCHHHHHHHHHhccchhhh
Confidence 345679999999999988877 44432 23333345577899999999999999965443
No 172
>PF03792 PBC: PBC domain; InterPro: IPR005542 Pbx proteins are members of the TALE (three-amino-acid loop extension) family of atypical homeodomain proteins, whose members are characterised by a three-residue insertion in the first helix of the homeodomain involved in their interaction with Hox proteins. Examination of Pbx1 has shown that, in addition to the homeodomain, a short 16-residue C-terminal tail is essential for maximal cooperative interactions with Hox partners as well as for maximal monomeric binding of Pbx1 to DNA. The PBX domain is a bipartite acidic domain [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0005634 nucleus
Probab=22.95 E-value=3e+02 Score=21.47 Aligned_cols=75 Identities=15% Similarity=0.258 Sum_probs=52.0
Q ss_pred CCCCCccccccChhhHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHHHHhc--
Q 033283 21 PRSNVREQDRYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKTINGDDLLWAMATL-- 98 (122)
Q Consensus 21 ~~~~~~~~d~~LP~A~V~Ri~K~~lp~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkTI~~eDV~~Al~~l-- 98 (122)
|.+++...|+.-=++.|+.+-...+ ....++|.+|..++..--. ....-+-|++.++-.-+...
T Consensus 100 ~~~~~d~~dYr~kL~~ir~~y~~el-----------~kye~ac~eF~~hV~~lLr---eQs~~RPIs~keiE~m~~~i~~ 165 (191)
T PF03792_consen 100 ADNSIDHSDYRAKLSQIRQIYHSEL-----------EKYEQACNEFTEHVMNLLR---EQSEFRPISPKEIERMVNIIHR 165 (191)
T ss_pred cccccchHHHHHHHHHHHHHHHHHH-----------HHHHHHhhhhHHHHHHHHH---HhcccCCCCHHHHHHHHHHHHH
Confidence 3456677788888888888887776 6777999999999887543 23344789999987766632
Q ss_pred CCcccHHHHHH
Q 033283 99 GFEDYIDPLKI 109 (122)
Q Consensus 99 gf~~~~~~l~~ 109 (122)
-|..+...||+
T Consensus 166 Kf~~iq~qLKQ 176 (191)
T PF03792_consen 166 KFSKIQMQLKQ 176 (191)
T ss_pred HHHHHHHHHHH
Confidence 34444444443
No 173
>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH. HflB(FtsH) is a pleiotropic protein required for correct cell division in bacteria. It has ATP-dependent zinc metalloprotease activity. It was formerly designated cell division protein FtsH.
Probab=22.87 E-value=1.2e+02 Score=26.02 Aligned_cols=33 Identities=18% Similarity=0.196 Sum_probs=25.7
Q ss_pred HHHHHHHHHHHHHhcCCCCCCcchHHHHHHhcC
Q 033283 67 ISFITSEASDKCQREKRKTINGDDLLWAMATLG 99 (122)
Q Consensus 67 I~~la~~A~~~a~~~~RkTI~~eDV~~Al~~lg 99 (122)
|..|..+|...+...+++.|+.+|+..|++..-
T Consensus 264 l~~l~~eA~~~a~~~~~~~i~~~~l~~a~~~~~ 296 (495)
T TIGR01241 264 LANLLNEAALLAARKNKTEITMNDIEEAIDRVI 296 (495)
T ss_pred HHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHh
Confidence 455556676667777888999999999999753
No 174
>CHL00076 chlB photochlorophyllide reductase subunit B
Probab=22.80 E-value=1.7e+02 Score=25.64 Aligned_cols=51 Identities=8% Similarity=0.053 Sum_probs=41.2
Q ss_pred CccccHHHHHHHHHHHHHHHHHHHH-HHHHHHHhcCCCCCCcchHHHHHHhcC
Q 033283 48 NGKIAKDAKETVQECVSEFISFITS-EASDKCQREKRKTINGDDLLWAMATLG 99 (122)
Q Consensus 48 ~~~iskdA~~al~~~a~~FI~~la~-~A~~~a~~~~RkTI~~eDV~~Al~~lg 99 (122)
.+.+|.||...|.+. --|+.-=.. .+.+.|+.+|...|+.+.+..|=.++|
T Consensus 461 ~~~w~~ea~~~l~~i-P~f~r~~~r~~~e~~a~~~g~~~it~~~~~~a~~~~~ 512 (513)
T CHL00076 461 DLIWSPESQLELSKI-PGFVRGKVKRNTEKFARQNGITNITVEVMYAAKEALS 512 (513)
T ss_pred CCCCCHHHHHHHHhC-CHHhHHHHHHHHHHHHHHcCCCeEcHHHHHHHHHhhC
Confidence 467999999999998 777764444 445788999999999999999977665
No 175
>PF13713 BRX_N: Transcription factor BRX N-terminal domain
Probab=22.37 E-value=1.5e+02 Score=17.34 Aligned_cols=22 Identities=18% Similarity=0.258 Sum_probs=17.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHhc
Q 033283 60 QECVSEFISFITSEASDKCQRE 81 (122)
Q Consensus 60 ~~~a~~FI~~la~~A~~~a~~~ 81 (122)
.+++.+||..||++-.+.+.+-
T Consensus 7 ~kaaKe~IKsLt~QlK~maekl 28 (39)
T PF13713_consen 7 CKAAKEVIKSLTAQLKDMAEKL 28 (39)
T ss_pred cHHHHHHHHHHHHHHHHHHHhC
Confidence 4678899999999888887653
No 176
>PRK02910 light-independent protochlorophyllide reductase subunit B; Provisional
Probab=22.37 E-value=1.6e+02 Score=25.64 Aligned_cols=52 Identities=13% Similarity=0.098 Sum_probs=40.9
Q ss_pred CCccccHHHHHHHHHHHHHHHHHHHH-HHHHHHHhcCCCCCCcchHHHHHHhcC
Q 033283 47 ANGKIAKDAKETVQECVSEFISFITS-EASDKCQREKRKTINGDDLLWAMATLG 99 (122)
Q Consensus 47 ~~~~iskdA~~al~~~a~~FI~~la~-~A~~~a~~~~RkTI~~eDV~~Al~~lg 99 (122)
+.+.++.||...|.+ .--|+.-=.. .+-+.|+..|...|+.+.+..|-..+|
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 457899999999954 6777765444 444788999999999999999977654
No 177
>TIGR03261 phnS2 putative 2-aminoethylphosphonate ABC transporter, periplasmic 2-aminoethylphosphonate-binding protein. This ABC transporter extracellular solute-binding protein is found in a number of genomes in operon-like contexts strongly suggesting a substrate specificity for 2-aminoethylphosphonate (2-AEP). The characterized PhnSTUV system is absent in the genomes in which this system is found. These genomes encode systems for the catabolism of 2-AEP, making the need for a 2-AEP-specific transporter likely.
Probab=22.17 E-value=2.4e+02 Score=22.32 Aligned_cols=60 Identities=5% Similarity=0.034 Sum_probs=36.6
Q ss_pred HHHHHHHHHHHHHHHH-HHHHhcCCCCCC----------cchHHHHHHhcCCcccHHHHHHHHHHHHHHhc
Q 033283 60 QECVSEFISFITSEAS-DKCQREKRKTIN----------GDDLLWAMATLGFEDYIDPLKIYLTRYREVIC 119 (122)
Q Consensus 60 ~~~a~~FI~~la~~A~-~~a~~~~RkTI~----------~eDV~~Al~~lgf~~~~~~l~~~l~~~re~~~ 119 (122)
.++|..||.|+.+.-. ..-.+.+...+. ++++...+-..++..+.+.....+++|.+..+
T Consensus 260 ~e~A~~fidfllS~e~Q~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~rw~~~~~ 330 (334)
T TIGR03261 260 NDAAKKLVDWSISDEAMELYAKNYAVVATPGVAKPDAGFPKNVEDLLIKNDFVWAAANRDKILEEWSKRYG 330 (334)
T ss_pred HHHHHHHHHHHcCHHHHHHHHhcCcccccCCcccCcccCCcchhhhcccCCHHHHHHhHHHHHHHHHHHhh
Confidence 3789999999976433 322222322221 12444444456666678888888999988765
No 178
>PRK12729 fliE flagellar hook-basal body protein FliE; Provisional
Probab=21.56 E-value=2e+02 Score=21.08 Aligned_cols=40 Identities=13% Similarity=0.167 Sum_probs=32.5
Q ss_pred cCCCCCCcchHHHHHHh--cCCcccHHHHHHHHHHHHHHhcc
Q 033283 81 EKRKTINGDDLLWAMAT--LGFEDYIDPLKIYLTRYREVICV 120 (122)
Q Consensus 81 ~~RkTI~~eDV~~Al~~--lgf~~~~~~l~~~l~~~re~~~~ 120 (122)
.|...++-.||+-|+++ +.|.-.+.--...++.|+|+++.
T Consensus 85 ~G~~~vdLhdVMIA~qKAslSlql~vQVRNKvVeAYqEIM~~ 126 (127)
T PRK12729 85 FDPNSVDAHDVMIASEKARVALTFTKTIADGVVRAYRELTSL 126 (127)
T ss_pred hCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 35567889999999995 55667788888999999999863
No 179
>PRK06402 rpl12p 50S ribosomal protein L12P; Reviewed
Probab=21.28 E-value=2.4e+02 Score=19.85 Aligned_cols=37 Identities=22% Similarity=0.179 Sum_probs=25.6
Q ss_pred HHHHHHhcCCCCCCcchHHHHHHhcCCcccHHHHHHHH
Q 033283 74 ASDKCQREKRKTINGDDLLWAMATLGFEDYIDPLKIYL 111 (122)
Q Consensus 74 A~~~a~~~~RkTI~~eDV~~Al~~lgf~~~~~~l~~~l 111 (122)
|+-++...|+ .|+.++|.+.|+..|.+-=...++.++
T Consensus 6 AaLLL~~~g~-~it~e~I~~IL~AAGveVee~~~k~~v 42 (106)
T PRK06402 6 AALLLHSAGK-EINEDNLKKVLEAAGVEVDEARVKALV 42 (106)
T ss_pred HHHHHHhcCC-CCCHHHHHHHHHHcCCCccHHHHHHHH
Confidence 4566666666 899999999999888753333333333
No 180
>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only]
Probab=20.60 E-value=56 Score=23.13 Aligned_cols=75 Identities=20% Similarity=0.177 Sum_probs=40.7
Q ss_pred CCCCCCCCCCC-CCCCCCCC-CCCCCCccccccChhhHHHHHHHhhCCCCccccHHHHHHHHHH---HHHHHHHHHHHHH
Q 033283 1 MAAEAPASPGG-GSHESGEQ-SPRSNVREQDRYLPIANISRIMKKALPANGKIAKDAKETVQEC---VSEFISFITSEAS 75 (122)
Q Consensus 1 ~~~~~~~~~~~-~~~~~~~~-~~~~~~~~~d~~LP~A~V~Ri~K~~lp~~~~iskdA~~al~~~---a~~FI~~la~~A~ 75 (122)
|....|.|||+ =..++..+ .-+...=.+-+.+|+.+|.+||... ..|+.|.-.-|.++ +.+|-..|=+ ++
T Consensus 2 ~~~~~P~~PGEiL~eeflep~glt~~~lA~~lgV~r~~is~ling~----~~iT~dmAlrL~k~fGtspefWlNlQ~-~y 76 (104)
T COG3093 2 MTMRKPAHPGEILREEFLEPLGLTQTELAEALGVTRNTISELINGR----RAITADMALRLAKVFGTSPEFWLNLQN-AY 76 (104)
T ss_pred CCCCCCCCchHHHHHHHhccccCCHHHHHHHhCCCHHHHHHHHcCC----cCCCHHHHHHHHHHhCCCHHHHHHHHH-HH
Confidence 34567888887 22333322 1111111223578999999999854 35777776666664 3445444433 34
Q ss_pred HHHHh
Q 033283 76 DKCQR 80 (122)
Q Consensus 76 ~~a~~ 80 (122)
+....
T Consensus 77 dL~~~ 81 (104)
T COG3093 77 DLWEA 81 (104)
T ss_pred HHHHH
Confidence 44433
No 181
>smart00445 LINK Link (Hyaluronan-binding).
Probab=20.58 E-value=1.1e+02 Score=21.03 Aligned_cols=30 Identities=23% Similarity=0.374 Sum_probs=26.1
Q ss_pred HHHHHHHHHhcCCCCCCcchHHHHHHhcCCc
Q 033283 71 TSEASDKCQREKRKTINGDDLLWAMATLGFE 101 (122)
Q Consensus 71 a~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~ 101 (122)
..+|.+.|+..+=..-+.+++..|-+. ||+
T Consensus 17 f~eA~~aC~~~ga~lAs~~QL~~Aw~~-Gld 46 (94)
T smart00445 17 FAEAREACRAQGATLATVGQLYAAWQD-GFD 46 (94)
T ss_pred HHHHHHHHHHcCCEeCCHHHHHHHHHh-chh
Confidence 367999999999999999999999886 775
No 182
>KOG0784 consensus Isocitrate dehydrogenase, gamma subunit [Amino acid transport and metabolism]
Probab=20.34 E-value=60 Score=27.75 Aligned_cols=45 Identities=16% Similarity=0.192 Sum_probs=33.7
Q ss_pred HHHHHHHHHHHhcCCCCCCcchHHHHHHhcCCcccHHHHHHHHHHH
Q 033283 69 FITSEASDKCQREKRKTINGDDLLWAMATLGFEDYIDPLKIYLTRY 114 (122)
Q Consensus 69 ~la~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~~~~~l~~~l~~~ 114 (122)
-++.-|.++|.+.+||.+++=|=-+ +..|+=.-|++.+++.-..|
T Consensus 188 RIaryAF~yA~k~gRKkVTaVHKAn-imKL~DGlFle~~~eva~~Y 232 (375)
T KOG0784|consen 188 RIARYAFEYAKKNGRKKVTAVHKAN-IMKLGDGLFLESCQEVAKKY 232 (375)
T ss_pred HHHHHHHHHHHHhCCceEEEEeccC-ceecchhhHHHHHHHHHhcC
Confidence 4556689999999999999877555 44666677888877766544
No 183
>PRK14868 DNA topoisomerase VI subunit B; Provisional
Probab=20.18 E-value=83 Score=29.55 Aligned_cols=59 Identities=22% Similarity=0.325 Sum_probs=40.6
Q ss_pred CCccccccChhhHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCC
Q 033283 24 NVREQDRYLPIANISRIMKKALPANGKIAKDAKETVQECVSEFISFITSEASDKCQREKRKT 85 (122)
Q Consensus 24 ~~~~~d~~LP~A~V~Ri~K~~lp~~~~iskdA~~al~~~a~~FI~~la~~A~~~a~~~~RkT 85 (122)
.+..-...+|-.... |+++.+.--|-+|.+.+|++||.+.=.||...-...-.++++++
T Consensus 610 ~VhvaST~VPfts~s---KeaIA~vpEI~~EI~lAl~~~aR~Lk~yl~k~~~~~~~~~k~~~ 668 (795)
T PRK14868 610 MVHVASTNVPFTSES---KDAIANVPEIEDEIELAIREAARELKSYLNKRRSMQKRREKQDV 668 (795)
T ss_pred EEEEeecCCCCCCcc---hhhhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444455566655443 45555444689999999999999999999986655545554444
Done!