Query 033230
Match_columns 124
No_of_seqs 107 out of 521
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 11:23:37 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033230.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033230hhsearch_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 2.8E-32 6.1E-37 205.1 9.2 96 6-106 26-121 (168)
2 KOG0871 Class 2 transcription 99.9 1.1E-27 2.3E-32 178.8 9.3 92 8-104 8-99 (156)
3 KOG0870 DNA polymerase epsilon 99.9 8.8E-27 1.9E-31 176.5 9.3 96 4-103 2-97 (172)
4 COG5150 Class 2 transcription 99.9 1.5E-22 3.3E-27 148.5 9.2 92 9-105 8-99 (148)
5 PF00808 CBFD_NFYB_HMF: Histon 99.8 2E-18 4.4E-23 111.7 7.4 64 12-81 2-65 (65)
6 COG2036 HHT1 Histones H3 and H 99.7 4.1E-17 8.9E-22 113.6 7.0 74 9-89 16-89 (91)
7 cd00076 H4 Histone H4, one of 99.4 1.8E-12 3.8E-17 89.3 8.4 70 12-88 13-82 (85)
8 PLN00035 histone H4; Provision 99.4 2.6E-12 5.7E-17 91.3 7.7 69 12-87 29-97 (103)
9 PTZ00015 histone H4; Provision 99.3 1.9E-11 4E-16 86.9 8.3 69 12-87 30-98 (102)
10 smart00417 H4 Histone H4. 99.2 4.3E-11 9.3E-16 80.6 6.2 62 12-80 13-74 (74)
11 smart00803 TAF TATA box bindin 99.2 1.1E-10 2.4E-15 76.5 7.4 64 12-82 2-65 (65)
12 smart00428 H3 Histone H3. 99.2 7.4E-11 1.6E-15 84.1 6.9 76 8-83 25-100 (105)
13 cd07981 TAF12 TATA Binding Pro 99.1 9.6E-10 2.1E-14 73.0 7.9 65 13-83 2-66 (72)
14 PF00125 Histone: Core histone 99.0 6.2E-10 1.3E-14 73.0 6.3 71 10-82 3-73 (75)
15 PLN00160 histone H3; Provision 98.8 6.4E-09 1.4E-13 73.3 5.8 74 8-82 17-90 (97)
16 PLN00161 histone H3; Provision 98.8 1.6E-08 3.4E-13 75.0 6.4 74 9-83 52-125 (135)
17 COG5208 HAP5 CCAAT-binding fac 98.7 7.1E-09 1.5E-13 82.8 3.2 79 6-90 103-181 (286)
18 PLN00121 histone H3; Provision 98.7 2.3E-08 4.9E-13 74.3 5.6 73 8-82 58-130 (136)
19 PTZ00018 histone H3; Provision 98.7 2.6E-08 5.7E-13 74.0 5.5 72 9-82 59-130 (136)
20 smart00576 BTP Bromodomain tra 98.7 1.6E-07 3.4E-12 62.9 8.0 66 15-87 9-74 (77)
21 cd07979 TAF9 TATA Binding Prot 98.5 4.7E-07 1E-11 65.4 7.9 84 16-106 5-89 (117)
22 cd00074 H2A Histone 2A; H2A is 98.5 6.4E-07 1.4E-11 64.8 6.8 68 10-83 18-85 (115)
23 KOG1657 CCAAT-binding factor, 98.2 1.4E-06 3E-11 69.9 4.8 73 11-89 73-145 (236)
24 cd08050 TAF6 TATA Binding Prot 98.2 8E-06 1.7E-10 68.0 7.8 67 14-87 1-67 (343)
25 PF15630 CENP-S: Kinetochore c 98.2 1.2E-05 2.5E-10 54.4 7.1 63 17-83 10-72 (76)
26 PF15511 CENP-T: Centromere ki 98.1 6.6E-06 1.4E-10 70.3 6.2 68 8-76 347-414 (414)
27 KOG1745 Histones H3 and H4 [Ch 98.1 1.9E-06 4E-11 64.2 2.4 76 8-85 59-134 (137)
28 KOG3467 Histone H4 [Chromatin 98.1 1.9E-05 4.2E-10 55.2 6.7 69 12-87 29-97 (103)
29 PF07524 Bromo_TP: Bromodomain 98.0 6E-05 1.3E-09 49.9 8.0 64 17-87 11-74 (77)
30 smart00427 H2B Histone H2B. 98.0 3.7E-05 8E-10 53.5 7.1 64 16-85 5-68 (89)
31 PF03847 TFIID_20kDa: Transcri 98.0 5.5E-05 1.2E-09 50.0 7.5 63 15-83 2-64 (68)
32 PF09415 CENP-X: CENP-S associ 97.9 2.3E-05 4.9E-10 52.4 4.5 66 14-83 1-67 (72)
33 cd08048 TAF11 TATA Binding Pro 97.9 8.5E-05 1.8E-09 51.1 7.1 66 12-84 16-84 (85)
34 PLN00158 histone H2B; Provisio 97.8 0.00014 3.1E-09 52.8 7.1 66 14-85 29-94 (116)
35 PTZ00463 histone H2B; Provisio 97.7 0.00017 3.7E-09 52.4 7.2 62 17-84 33-94 (117)
36 COG5262 HTA1 Histone H2A [Chro 97.6 0.00015 3.2E-09 53.1 5.4 68 10-83 24-91 (132)
37 PF04719 TAFII28: hTAFII28-lik 97.6 0.00035 7.6E-09 48.6 6.9 67 12-84 23-90 (90)
38 KOG1659 Class 2 transcription 97.6 0.00032 7E-09 55.7 7.3 77 12-94 13-89 (224)
39 PF02969 TAF: TATA box binding 97.5 0.00068 1.5E-08 44.7 7.5 64 12-82 3-66 (66)
40 smart00414 H2A Histone 2A. 97.3 0.0011 2.3E-08 47.4 6.3 68 10-83 7-74 (106)
41 COG5247 BUR6 Class 2 transcrip 97.2 0.0013 2.8E-08 47.1 6.1 79 12-96 23-101 (113)
42 PTZ00017 histone H2A; Provisio 97.0 0.0023 5E-08 47.6 5.7 68 10-83 25-92 (134)
43 KOG1142 Transcription initiati 96.9 0.0017 3.6E-08 52.9 5.1 66 12-83 154-219 (258)
44 PLN00154 histone H2A; Provisio 96.9 0.0037 8.1E-08 46.6 6.2 69 10-83 36-104 (136)
45 KOG1756 Histone 2A [Chromatin 96.8 0.0036 7.8E-08 46.3 5.9 69 9-83 24-92 (131)
46 PF02291 TFIID-31kDa: Transcri 96.8 0.0072 1.6E-07 44.5 7.3 93 8-107 6-101 (129)
47 KOG1744 Histone H2B [Chromatin 96.8 0.0055 1.2E-07 45.2 6.4 62 17-84 42-103 (127)
48 PLN00157 histone H2A; Provisio 96.7 0.0048 1E-07 45.8 5.6 68 10-83 24-91 (132)
49 PLN00153 histone H2A; Provisio 96.7 0.0053 1.1E-07 45.4 5.6 68 10-83 22-89 (129)
50 PLN00156 histone H2AX; Provisi 96.6 0.0066 1.4E-07 45.4 6.0 68 10-83 27-94 (139)
51 PF15510 CENP-W: Centromere ki 96.6 0.0048 1E-07 43.5 4.7 65 12-82 16-94 (102)
52 PF02269 TFIID-18kDa: Transcri 96.4 0.0037 8.1E-08 43.3 3.3 49 35-83 18-66 (93)
53 KOG3219 Transcription initiati 95.9 0.0076 1.6E-07 47.3 3.3 71 11-88 111-182 (195)
54 PTZ00252 histone H2A; Provisio 95.5 0.057 1.2E-06 40.2 6.2 69 9-83 22-92 (134)
55 KOG1658 DNA polymerase epsilon 95.3 0.015 3.2E-07 44.4 2.8 68 11-85 58-126 (162)
56 cd07978 TAF13 The TATA Binding 94.9 0.11 2.3E-06 36.1 6.0 47 36-83 20-66 (92)
57 KOG4336 TBP-associated transcr 94.4 0.34 7.5E-06 40.6 8.8 64 35-100 21-84 (323)
58 KOG3423 Transcription initiati 94.2 0.29 6.3E-06 37.9 7.4 69 12-87 86-168 (176)
59 TIGR03015 pepcterm_ATPase puta 93.7 0.23 5.1E-06 38.4 6.2 74 13-86 192-268 (269)
60 KOG2549 Transcription initiati 92.2 0.68 1.5E-05 41.6 7.5 67 14-87 13-79 (576)
61 PRK00411 cdc6 cell division co 90.7 1.2 2.6E-05 36.6 7.1 71 15-87 209-285 (394)
62 KOG2389 Predicted bromodomain 90.4 1.1 2.4E-05 38.1 6.8 89 12-107 29-120 (353)
63 KOG3334 Transcription initiati 88.9 3 6.5E-05 31.6 7.4 69 37-105 31-100 (148)
64 TIGR02928 orc1/cdc6 family rep 86.0 4 8.6E-05 33.0 7.2 76 16-93 202-283 (365)
65 PF09114 MotA_activ: Transcrip 85.2 0.75 1.6E-05 32.4 2.2 38 16-54 51-88 (96)
66 PF13654 AAA_32: AAA domain; P 83.2 5.3 0.00012 35.3 7.2 49 36-84 447-506 (509)
67 TIGR02902 spore_lonB ATP-depen 82.6 4.5 9.8E-05 35.6 6.6 66 16-86 266-334 (531)
68 PF08369 PCP_red: Proto-chloro 81.0 2.7 5.8E-05 25.4 3.3 42 38-80 2-44 (45)
69 COG1067 LonB Predicted ATP-dep 77.7 2.4 5.2E-05 38.7 3.3 30 56-85 371-400 (647)
70 PF13335 Mg_chelatase_2: Magne 77.3 10 0.00022 26.1 5.7 47 36-82 42-94 (96)
71 PF02861 Clp_N: Clp amino term 77.1 2.8 6E-05 24.6 2.5 26 60-85 1-26 (53)
72 COG5095 TAF6 Transcription ini 74.1 14 0.00031 31.8 6.8 54 34-87 20-73 (450)
73 TIGR00764 lon_rel lon-related 74.0 9.1 0.0002 34.5 5.9 50 36-85 330-392 (608)
74 PRK14987 gluconate operon tran 72.4 10 0.00022 29.9 5.3 48 1-58 1-52 (331)
75 PRK09862 putative ATP-dependen 70.6 18 0.00038 32.2 6.9 60 36-95 438-503 (506)
76 TIGR02030 BchI-ChlI magnesium 69.2 20 0.00044 29.9 6.7 48 34-81 252-306 (337)
77 PRK12402 replication factor C 68.1 21 0.00045 28.3 6.3 72 12-89 183-254 (337)
78 PF03540 TFIID_30kDa: Transcri 67.8 27 0.00059 21.8 5.9 48 12-66 2-49 (51)
79 KOG3901 Transcription initiati 66.6 19 0.00041 25.9 5.1 44 37-83 28-71 (109)
80 COG5162 Transcription initiati 66.6 38 0.00082 26.4 7.1 50 38-87 107-189 (197)
81 TIGR02442 Cob-chelat-sub cobal 66.2 21 0.00046 32.1 6.6 50 34-83 247-303 (633)
82 TIGR01128 holA DNA polymerase 65.9 31 0.00067 26.9 6.8 68 12-83 110-177 (302)
83 CHL00081 chlI Mg-protoporyphyr 65.3 17 0.00038 30.7 5.5 49 34-82 265-320 (350)
84 PRK09526 lacI lac repressor; R 65.1 18 0.00039 28.5 5.4 47 2-58 2-52 (342)
85 PRK00080 ruvB Holliday junctio 64.6 31 0.00068 27.9 6.8 72 13-88 180-254 (328)
86 KOG2680 DNA helicase TIP49, TB 63.5 22 0.00048 30.7 5.8 50 33-82 374-427 (454)
87 COG1224 TIP49 DNA helicase TIP 63.0 16 0.00035 32.0 4.9 48 34-81 378-429 (450)
88 PRK13406 bchD magnesium chelat 61.8 18 0.0004 32.5 5.3 49 34-82 193-248 (584)
89 cd08045 TAF4 TATA Binding Prot 61.4 31 0.00067 26.7 6.0 73 11-86 43-121 (212)
90 TIGR00635 ruvB Holliday juncti 61.0 31 0.00068 27.2 6.1 71 13-87 159-232 (305)
91 PF12010 DUF3502: Domain of un 60.5 9 0.00019 27.7 2.6 61 40-104 73-133 (134)
92 PRK07452 DNA polymerase III su 58.8 36 0.00078 27.3 6.1 66 18-87 135-202 (326)
93 COG4519 Uncharacterized protei 57.5 1.3 2.8E-05 30.8 -2.1 35 72-106 37-72 (95)
94 PRK13407 bchI magnesium chelat 57.3 33 0.00071 28.7 5.8 48 34-81 249-303 (334)
95 TIGR00368 Mg chelatase-related 57.2 28 0.0006 30.7 5.6 47 36-82 445-497 (499)
96 KOG1757 Histone 2A [Chromatin 57.2 17 0.00037 26.6 3.6 66 8-82 26-95 (131)
97 PF08823 PG_binding_2: Putativ 53.4 22 0.00048 23.5 3.4 32 75-106 19-56 (74)
98 TIGR02031 BchD-ChlD magnesium 52.8 46 0.001 29.8 6.3 49 34-82 201-256 (589)
99 COG1474 CDC6 Cdc6-related prot 52.7 23 0.00049 30.0 4.1 61 35-95 210-276 (366)
100 KOG0093 GTPase Rab3, small G p 50.5 3.5 7.5E-05 32.0 -1.0 73 39-111 106-183 (193)
101 PF04552 Sigma54_DBD: Sigma-54 50.4 24 0.00052 26.6 3.6 79 7-103 55-149 (160)
102 PF07647 SAM_2: SAM domain (St 50.1 22 0.00047 21.8 2.9 25 71-95 3-27 (66)
103 PRK13765 ATP-dependent proteas 50.1 28 0.00062 31.7 4.6 48 36-83 339-399 (637)
104 PF09123 DUF1931: Domain of un 49.4 36 0.00078 25.5 4.3 69 19-104 2-70 (138)
105 PRK02910 light-independent pro 49.3 37 0.0008 29.8 5.1 52 33-85 466-518 (519)
106 PRK07914 hypothetical protein; 49.2 42 0.00091 27.2 5.1 65 14-83 129-193 (320)
107 PRK05574 holA DNA polymerase I 48.6 63 0.0014 25.7 6.0 68 12-83 145-212 (340)
108 TIGR01242 26Sp45 26S proteasom 48.4 26 0.00056 28.9 3.8 31 53-83 332-362 (364)
109 smart00350 MCM minichromosome 48.1 49 0.0011 28.9 5.6 68 12-83 417-503 (509)
110 PTZ00361 26 proteosome regulat 48.0 26 0.00055 30.5 3.8 32 53-84 393-424 (438)
111 PF00531 Death: Death domain; 46.9 36 0.00079 21.4 3.6 30 68-97 54-83 (83)
112 COG5251 TAF40 Transcription in 46.5 25 0.00055 27.5 3.2 61 12-81 115-178 (199)
113 cd04752 Commd4 COMM_Domain con 46.1 76 0.0017 23.9 5.8 46 48-100 43-89 (174)
114 COG5248 TAF19 Transcription in 46.1 71 0.0015 23.4 5.3 47 35-83 26-72 (126)
115 COG1500 Predicted exosome subu 45.8 72 0.0016 25.9 5.8 85 16-107 70-157 (234)
116 PRK03992 proteasome-activating 45.3 31 0.00067 29.1 3.9 35 52-86 340-374 (389)
117 PF00536 SAM_1: SAM domain (St 44.7 28 0.0006 21.2 2.7 22 73-94 4-25 (64)
118 TIGR01278 DPOR_BchB light-inde 44.6 42 0.00092 29.4 4.7 52 34-85 460-511 (511)
119 cd00166 SAM Sterile alpha moti 44.5 20 0.00044 21.2 2.0 24 73-96 3-26 (63)
120 PF00356 LacI: Bacterial regul 44.5 48 0.001 19.9 3.6 33 10-51 8-40 (46)
121 PRK10014 DNA-binding transcrip 42.7 71 0.0015 25.1 5.4 46 3-58 4-53 (342)
122 PTZ00373 60S Acidic ribosomal 41.7 40 0.00087 24.3 3.5 28 60-87 8-35 (112)
123 COG2445 Uncharacterized conser 41.4 1.4E+02 0.0031 22.0 8.4 69 39-109 31-100 (138)
124 PF07499 RuvA_C: RuvA, C-termi 40.9 17 0.00037 21.7 1.2 14 75-88 4-17 (47)
125 PRK05932 RNA polymerase factor 40.5 79 0.0017 27.6 5.7 89 7-121 349-453 (455)
126 PF09339 HTH_IclR: IclR helix- 40.0 18 0.00039 21.5 1.3 18 9-26 26-43 (52)
127 TIGR00291 RNA_SBDS rRNA metabo 39.6 1.3E+02 0.0028 24.2 6.4 88 13-107 67-157 (231)
128 PRK06585 holA DNA polymerase I 39.4 83 0.0018 25.4 5.4 66 15-84 144-210 (343)
129 PF12627 PolyA_pol_RNAbd: Prob 39.0 13 0.00028 22.9 0.5 58 35-96 2-63 (64)
130 PTZ00454 26S protease regulato 38.9 45 0.00097 28.5 3.9 32 53-84 355-386 (398)
131 cd08779 Death_PIDD Death Domai 38.8 1.1E+02 0.0023 20.5 5.1 35 62-96 51-85 (86)
132 CHL00076 chlB photochlorophyll 38.6 64 0.0014 28.4 4.9 52 34-85 461-512 (513)
133 PRK10727 DNA-binding transcrip 36.8 90 0.002 24.7 5.2 38 11-58 11-48 (343)
134 smart00454 SAM Sterile alpha m 36.8 30 0.00065 20.6 1.9 26 71-96 3-28 (68)
135 COG1724 Predicted RNA binding 36.5 24 0.00053 23.3 1.5 17 71-87 6-22 (66)
136 PF05236 TAF4: Transcription i 36.4 62 0.0013 25.8 4.2 75 8-85 39-119 (264)
137 PF01934 DUF86: Protein of unk 36.2 1.4E+02 0.003 20.2 7.9 71 36-109 21-91 (119)
138 PLN00138 large subunit ribosom 36.2 56 0.0012 23.5 3.5 47 60-107 6-55 (113)
139 PF11625 DUF3253: Protein of u 35.9 1.1E+02 0.0023 21.0 4.7 36 64-99 17-52 (83)
140 cd05833 Ribosomal_P2 Ribosomal 35.7 58 0.0013 23.2 3.5 47 60-107 6-55 (109)
141 TIGR02639 ClpA ATP-dependent C 35.7 1.2E+02 0.0026 27.8 6.3 36 35-82 76-111 (731)
142 PHA03328 nuclear egress lamina 35.2 55 0.0012 27.7 3.8 78 11-103 232-309 (316)
143 PF13405 EF-hand_6: EF-hand do 35.1 47 0.001 17.5 2.3 26 60-85 5-31 (31)
144 PTZ00448 hypothetical protein; 33.9 1.6E+02 0.0036 25.5 6.5 95 7-108 67-166 (373)
145 PRK00440 rfc replication facto 33.0 1.1E+02 0.0023 23.9 5.0 66 13-84 161-226 (319)
146 PRK05907 hypothetical protein; 32.6 1E+02 0.0022 25.4 5.0 49 34-82 151-201 (311)
147 KOG0784 Isocitrate dehydrogena 32.3 19 0.00042 30.9 0.6 58 54-112 187-246 (375)
148 PF08393 DHC_N2: Dynein heavy 32.3 31 0.00067 28.6 1.9 70 37-120 246-317 (408)
149 smart00354 HTH_LACI helix_turn 32.3 75 0.0016 20.0 3.3 35 9-52 8-42 (70)
150 PF00403 HMA: Heavy-metal-asso 31.9 36 0.00078 20.4 1.7 16 72-87 47-62 (62)
151 PRK10865 protein disaggregatio 31.0 55 0.0012 30.7 3.5 38 36-85 5-42 (857)
152 CHL00095 clpC Clp protease ATP 30.8 73 0.0016 29.6 4.2 36 36-83 4-39 (821)
153 PF01922 SRP19: SRP19 protein; 30.1 39 0.00084 23.3 1.8 20 72-91 29-48 (95)
154 COG1239 ChlI Mg-chelatase subu 29.9 94 0.002 27.3 4.5 49 34-82 265-320 (423)
155 TIGR02397 dnaX_nterm DNA polym 29.9 1.3E+02 0.0027 24.1 5.0 63 15-82 178-240 (355)
156 PRK14971 DNA polymerase III su 29.7 1.2E+02 0.0026 27.5 5.2 73 12-89 179-251 (614)
157 TIGR01764 excise DNA binding d 29.7 57 0.0012 18.0 2.2 36 9-44 9-45 (49)
158 COG1508 RpoN DNA-directed RNA 29.3 2.1E+02 0.0046 25.3 6.5 82 7-105 336-433 (444)
159 PRK13760 putative RNA-associat 28.8 2.7E+02 0.0059 22.4 6.6 88 13-107 67-157 (231)
160 PRK08487 DNA polymerase III su 28.8 2.1E+02 0.0046 23.2 6.2 64 14-83 136-199 (328)
161 PRK10423 transcriptional repre 28.5 49 0.0011 25.7 2.3 37 11-57 8-44 (327)
162 PF02361 CbiQ: Cobalt transpor 28.4 77 0.0017 23.4 3.3 36 70-105 123-170 (224)
163 PRK14961 DNA polymerase III su 28.3 1.8E+02 0.0038 24.1 5.7 65 15-84 180-244 (363)
164 PF02718 Herpes_UL31: Herpesvi 28.3 74 0.0016 26.1 3.4 30 68-100 222-251 (258)
165 TIGR02639 ClpA ATP-dependent C 28.2 81 0.0018 28.9 4.0 33 37-81 1-33 (731)
166 COG1466 HolA DNA polymerase II 28.0 1.8E+02 0.0038 23.8 5.6 65 17-85 144-208 (334)
167 TIGR03346 chaperone_ClpB ATP-d 27.9 94 0.002 29.1 4.4 26 59-84 11-36 (852)
168 smart00027 EH Eps15 homology d 27.9 1.3E+02 0.0028 19.8 4.1 28 60-87 15-42 (96)
169 KOG1770 Translation initiation 27.8 26 0.00056 25.3 0.6 12 63-74 34-45 (112)
170 PF08681 DUF1778: Protein of u 27.6 14 0.00031 24.4 -0.7 18 34-51 3-20 (80)
171 PRK05629 hypothetical protein; 27.4 2E+02 0.0043 23.1 5.8 48 34-82 143-190 (318)
172 PRK00754 signal recognition pa 27.0 18 0.00039 25.3 -0.4 30 72-101 35-64 (95)
173 PRK14964 DNA polymerase III su 26.8 1.3E+02 0.0029 26.7 4.9 65 13-82 175-239 (491)
174 PRK09492 treR trehalose repres 26.4 86 0.0019 24.3 3.4 36 12-57 15-50 (315)
175 PF10440 WIYLD: Ubiquitin-bind 26.3 65 0.0014 21.1 2.2 35 78-114 15-51 (65)
176 TIGR01052 top6b DNA topoisomer 26.2 1.2E+02 0.0026 27.0 4.5 51 35-99 433-483 (488)
177 TIGR02395 rpoN_sigma RNA polym 26.2 1.7E+02 0.0037 25.3 5.4 80 7-103 324-419 (429)
178 PRK12469 RNA polymerase factor 25.9 1.8E+02 0.0039 25.8 5.5 80 7-103 375-469 (481)
179 PRK14958 DNA polymerase III su 25.8 1.8E+02 0.0038 25.7 5.5 70 13-87 178-247 (509)
180 PRK09111 DNA polymerase III su 25.5 1.8E+02 0.004 26.3 5.7 65 13-82 191-255 (598)
181 TIGR02454 CbiQ_TIGR cobalt ABC 25.4 1E+02 0.0023 22.7 3.5 38 70-107 112-160 (198)
182 KOG1528 Salt-sensitive 3'-phos 25.3 1.6E+02 0.0036 25.1 5.0 69 15-86 52-125 (351)
183 COG0017 AsnS Aspartyl/asparagi 25.3 2.8E+02 0.0061 24.5 6.6 77 42-121 235-338 (435)
184 TIGR02903 spore_lon_C ATP-depe 24.8 1.7E+02 0.0037 26.4 5.3 72 16-91 356-437 (615)
185 cd01392 HTH_LacI Helix-turn-he 24.4 1.5E+02 0.0032 16.9 3.4 35 9-52 5-39 (52)
186 PTZ00112 origin recognition co 24.1 1.5E+02 0.0033 29.2 5.1 20 69-88 991-1010(1164)
187 PRK14970 DNA polymerase III su 24.1 2.2E+02 0.0049 23.2 5.6 66 15-85 169-234 (367)
188 PRK11034 clpA ATP-dependent Cl 24.1 1E+02 0.0022 28.7 3.9 23 59-81 12-34 (758)
189 PF09660 DUF2397: Protein of u 23.7 1E+02 0.0023 27.1 3.7 41 69-109 28-70 (486)
190 PF13713 BRX_N: Transcription 23.5 1.3E+02 0.0028 17.8 3.0 21 46-66 7-27 (39)
191 PF01973 MAF_flag10: Protein o 23.5 49 0.0011 24.1 1.4 24 91-114 34-57 (170)
192 TIGR02677 conserved hypothetic 23.4 95 0.0021 27.6 3.4 40 69-109 29-69 (494)
193 PRK10339 DNA-binding transcrip 22.9 94 0.002 24.4 3.0 35 11-52 11-45 (327)
194 PF03484 B5: tRNA synthetase B 22.9 53 0.0011 20.9 1.3 18 70-87 17-34 (70)
195 PF10557 Cullin_Nedd8: Cullin 22.7 1.9E+02 0.004 18.3 3.9 16 69-84 39-54 (68)
196 COG1222 RPT1 ATP-dependent 26S 22.4 1E+02 0.0023 26.9 3.3 32 53-84 361-392 (406)
197 TIGR02849 spore_III_AD stage I 22.3 63 0.0014 22.9 1.7 37 36-74 36-72 (101)
198 PF10885 DUF2684: Protein of u 22.1 24 0.00053 24.4 -0.4 15 109-123 34-48 (89)
199 PF14194 Cys_rich_VLP: Cystein 21.9 33 0.00072 22.0 0.2 18 98-115 3-20 (56)
200 TIGR01481 ccpA catabolite cont 21.6 1.1E+02 0.0025 23.7 3.2 33 11-52 11-43 (329)
201 TIGR01241 FtsH_fam ATP-depende 21.5 1.4E+02 0.003 25.8 4.0 34 53-86 264-297 (495)
202 PF14434 Imm6: Immunity protei 21.1 3.3E+02 0.0071 19.6 6.4 39 55-94 25-65 (122)
203 cd00051 EFh EF-hand, calcium b 21.0 1.6E+02 0.0034 16.0 4.5 38 63-100 8-45 (63)
204 COG4987 CydC ABC-type transpor 21.0 1.8E+02 0.004 26.5 4.7 81 13-100 375-467 (573)
205 PF11539 DUF3228: Protein of u 20.6 82 0.0018 25.0 2.2 34 7-41 149-182 (197)
206 PF07928 Vps54: Vps54-like pro 20.2 34 0.00075 25.0 0.0 35 66-100 62-97 (135)
No 1
>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [Transcription]
Probab=99.97 E-value=2.8e-32 Score=205.11 Aligned_cols=96 Identities=27% Similarity=0.451 Sum_probs=91.0
Q ss_pred ccccccccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhhCC
Q 033230 6 VVPEAEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEID 85 (124)
Q Consensus 6 ~~~ed~~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~lg 85 (124)
+-.+|-.||+|+|.||||..||. +.+|||||++.+|+|++|||++||++|++.|.+++||||++|||+|||..||
T Consensus 26 ~reqDr~LPIANV~RIMK~~lP~-----naKIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIngdDllwAm~tLG 100 (168)
T KOG0869|consen 26 LREQDRFLPIANVSRIMKKALPA-----NAKISKDAKETVQECVSEFISFVTGEASEKCQREKRKTINGDDLLWAMSTLG 100 (168)
T ss_pred cchhhhhccHHHHHHHHHhcCCc-----ccccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCcccHHHHHHHHHHcC
Confidence 44567799999999999999995 8999999999999999999999999999999999999999999999999999
Q ss_pred CcccHHHHHHHHHHHHhhhch
Q 033230 86 FTEFVDPLRDSLDGQLTFRNW 106 (124)
Q Consensus 86 f~~~~~~l~~~l~~~~~~~~~ 106 (124)
|++|+++|+.||.+||++.+-
T Consensus 101 Fe~Y~eplkiyL~kYRe~e~e 121 (168)
T KOG0869|consen 101 FENYAEPLKIYLQKYRELEGE 121 (168)
T ss_pred cHhHHHHHHHHHHHHHHHhhh
Confidence 999999999999999997653
No 2
>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=99.95 E-value=1.1e-27 Score=178.79 Aligned_cols=92 Identities=29% Similarity=0.517 Sum_probs=87.9
Q ss_pred ccccccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhhCCCc
Q 033230 8 PEAEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFT 87 (124)
Q Consensus 8 ~ed~~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~lgf~ 87 (124)
.|++.||+|+|+++||+.||. +++|.+||+++|..||.+||+.||++||++|..+.||||+++||++||+.|||.
T Consensus 8 dde~sLPkAtv~KmIke~lP~-----d~rvakeareliincCvEFI~liSsEAneic~~e~KKTIa~EHV~KALe~LgF~ 82 (156)
T KOG0871|consen 8 DDELSLPKATVNKMIKEMLPK-----DVRVAKEARELIINCCVEFINLISSEANEICNKEAKKTIAPEHVIKALENLGFG 82 (156)
T ss_pred cccccCcHHHHHHHHHHhCCc-----ccccchHHHHHHHHHHHHHHHHHHHHHHHHHhHHhcccCCHHHHHHHHHHcchH
Confidence 478899999999999999994 899999999999999999999999999999999999999999999999999999
Q ss_pred ccHHHHHHHHHHHHhhh
Q 033230 88 EFVDPLRDSLDGQLTFR 104 (124)
Q Consensus 88 ~~~~~l~~~l~~~~~~~ 104 (124)
+|++.+.+.+++|+...
T Consensus 83 eYiee~~~vl~~~K~~~ 99 (156)
T KOG0871|consen 83 EYIEEAEEVLENCKEEA 99 (156)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 99999999999997643
No 3
>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription]
Probab=99.94 E-value=8.8e-27 Score=176.48 Aligned_cols=96 Identities=40% Similarity=0.698 Sum_probs=91.2
Q ss_pred ccccccccccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhh
Q 033230 4 EKVVPEAEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (124)
Q Consensus 4 ek~~~ed~~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~ 83 (124)
|...++|+.||+|+|.||+|++||+ +++.|||||+.+|+++|++|++||++.|+++|+.++||||+++||++||++
T Consensus 2 e~eri~dl~lP~AiI~rlvke~l~E----~~vsisKeA~~Ai~raAtVFv~~Lts~s~e~A~~q~rKt~sadDVl~aL~E 77 (172)
T KOG0870|consen 2 EDERIEDLNLPNAIITRLVKEVLPE----SNVSISKEARLAIARAATVFVIFLTSVSNEIAKDQKRKTISADDVLKALDE 77 (172)
T ss_pred cchhHHHhhccHHHHHHHHHHhCcc----ccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCcccHHHHHHHHHH
Confidence 4556789999999999999999997 369999999999999999999999999999999999999999999999999
Q ss_pred CCCcccHHHHHHHHHHHHhh
Q 033230 84 IDFTEFVDPLRDSLDGQLTF 103 (124)
Q Consensus 84 lgf~~~~~~l~~~l~~~~~~ 103 (124)
+||..|+++|+..|+.|+..
T Consensus 78 iefs~f~~plk~~Le~yk~~ 97 (172)
T KOG0870|consen 78 IEFSSFVNPLKSALEAYKKA 97 (172)
T ss_pred hchHHHhhHHHHHHHHHHHH
Confidence 99999999999999999865
No 4
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=99.88 E-value=1.5e-22 Score=148.46 Aligned_cols=92 Identities=29% Similarity=0.557 Sum_probs=88.4
Q ss_pred cccccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhhCCCcc
Q 033230 9 EAEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFTE 88 (124)
Q Consensus 9 ed~~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~lgf~~ 88 (124)
+.+.||+|||.+.+-+.||. +..++|||++.++.||.+||+.|+++|+++|..+.+|||+++||++||+.|||.+
T Consensus 8 De~sLPKATVqKMvS~iLp~-----dl~ftKearei~in~cieFi~~lsseAne~ce~EaKKTIa~EHviKALenLef~e 82 (148)
T COG5150 8 DENSLPKATVQKMVSSILPK-----DLVFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHVIKALENLEFEE 82 (148)
T ss_pred ccccCcHHHHHHHHHHhccc-----cccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHhccHHH
Confidence 67899999999999999995 8999999999999999999999999999999999999999999999999999999
Q ss_pred cHHHHHHHHHHHHhhhc
Q 033230 89 FVDPLRDSLDGQLTFRN 105 (124)
Q Consensus 89 ~~~~l~~~l~~~~~~~~ 105 (124)
|++.+.+.+.+|+..+.
T Consensus 83 yi~~~~e~~~n~k~~qK 99 (148)
T COG5150 83 YIESCMEEHENYKSYQK 99 (148)
T ss_pred HHHHHHHHHHHHHHHHh
Confidence 99999999999988764
No 5
>PF00808 CBFD_NFYB_HMF: Histone-like transcription factor (CBF/NF-Y) and archaeal histone; InterPro: IPR003958 The CCAAT-binding factor (CBF) is a mammalian transcription factor that binds to a CCAAT motif in the promoters of a wide variety of genes, including type I collagen and albumin. The factor is a heteromeric complex of A and B subunits, both of which are required for DNA-binding [, ]. The subunits can interact in the absence of DNA-binding, conserved regions in each being important in mediating this interaction. The A subunit can be split into 3 domains on the basis of sequence similarity, a non-conserved N-terminal 'A domain'; a highly-conserved central 'B domain' involved in DNA-binding; and a C-terminal 'C domain', which contains a number of glutamine and acidic residues involved in protein-protein interactions []. The A subunit shows striking similarity to the HAP3 subunit of the yeast CCAAT-binding heterotrimeric transcription factor [, ]. The Kluyveromyces lactis HAP3 protein has been predicted to contain a 4-cysteine zinc finger, which is thought to be present in similar HAP3 and CBF subunit A proteins, in which the third cysteine is replaced by a serine []. This domain is found in the CCAAT transcription factor and archaeal histones.; GO: 0043565 sequence-specific DNA binding, 0005622 intracellular; PDB: 1F1E_A 2BYM_D 2BYK_D 1HTA_A 1B67_A 1JFI_B 1KU5_B 1N1J_A 1BFM_A 1B6W_A ....
Probab=99.76 E-value=2e-18 Score=111.70 Aligned_cols=64 Identities=41% Similarity=0.619 Sum_probs=58.1
Q ss_pred ccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhh
Q 033230 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAI 81 (124)
Q Consensus 12 ~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL 81 (124)
.||.+.|.||||.. |+ ..+||+||..++++|+++||.||+.+|++.|.++|||||+++||..||
T Consensus 2 ~lP~a~vkri~k~~-~~-----~~~vs~ea~~~i~~a~e~Fi~~l~~~A~~~a~~~~rkti~~~Dv~~Av 65 (65)
T PF00808_consen 2 SLPLARVKRIMKSD-PD-----VMRVSKEAVEAIAKAAEEFIQYLAKEANEIAQRDKRKTITYEDVAKAV 65 (65)
T ss_dssp SS-HHHHHHHHHHT-ST-----TSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEE-HHHHHHHH
T ss_pred CCChHHHHHHhccC-CC-----ccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHC
Confidence 59999999999999 63 678999999999999999999999999999999999999999999986
No 6
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=99.70 E-value=4.1e-17 Score=113.64 Aligned_cols=74 Identities=23% Similarity=0.356 Sum_probs=69.8
Q ss_pred cccccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhhCCCcc
Q 033230 9 EAEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFTE 88 (124)
Q Consensus 9 ed~~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~lgf~~ 88 (124)
-+..||+++|.||||++.+ -+||.+|.+.+++++++|+..|+..|++.|.|+|||||+++||..|++.+|+..
T Consensus 16 ~~~~Lp~apv~Ri~r~~~~-------~Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~DI~la~~~~~~~~ 88 (91)
T COG2036 16 TDLLLPKAPVRRILRKAGA-------ERVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLALKRLGRRI 88 (91)
T ss_pred hhhhcCchHHHHHHHHHhH-------HHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHHHhcccc
Confidence 4678999999999999964 499999999999999999999999999999999999999999999999999876
Q ss_pred c
Q 033230 89 F 89 (124)
Q Consensus 89 ~ 89 (124)
|
T Consensus 89 ~ 89 (91)
T COG2036 89 Y 89 (91)
T ss_pred c
Confidence 5
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=99.40 E-value=1.8e-12 Score=89.35 Aligned_cols=70 Identities=17% Similarity=0.199 Sum_probs=66.4
Q ss_pred ccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhhCCCcc
Q 033230 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFTE 88 (124)
Q Consensus 12 ~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~lgf~~ 88 (124)
.||++.|.||++.. |..+||.|+.+.+.+..++|+..|..+|...|+++|||||+++||..||+..|-.-
T Consensus 13 gi~k~~I~RLarr~-------GvkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~alkr~g~~~ 82 (85)
T cd00076 13 GITKPAIRRLARRG-------GVKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTL 82 (85)
T ss_pred cCCHHHHHHHHHHc-------CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHCCCCc
Confidence 69999999999998 56899999999999999999999999999999999999999999999999999543
No 8
>PLN00035 histone H4; Provisional
Probab=99.36 E-value=2.6e-12 Score=91.32 Aligned_cols=69 Identities=19% Similarity=0.219 Sum_probs=65.6
Q ss_pred ccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhhCCCc
Q 033230 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFT 87 (124)
Q Consensus 12 ~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~lgf~ 87 (124)
.||+++|.||++.. |..+||.|+.+.+.+..++|+..|..+|...|++.+||||+++||..||+..|=.
T Consensus 29 ~ipk~~IrRLARr~-------GvkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr~g~~ 97 (103)
T PLN00035 29 GITKPAIRRLARRG-------GVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRT 97 (103)
T ss_pred cCCHHHHHHHHHHc-------CcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHcCCc
Confidence 59999999999998 5689999999999999999999999999999999999999999999999998853
No 9
>PTZ00015 histone H4; Provisional
Probab=99.29 E-value=1.9e-11 Score=86.85 Aligned_cols=69 Identities=17% Similarity=0.237 Sum_probs=65.8
Q ss_pred ccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhhCCCc
Q 033230 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFT 87 (124)
Q Consensus 12 ~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~lgf~ 87 (124)
.||+++|.||++.. |-.+||.|+.+.+.+..++|+..|..+|...|++.+||||+++||..||+..|-.
T Consensus 30 gI~k~~IrRLarr~-------GvkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~AlKr~g~~ 98 (102)
T PTZ00015 30 GITKGAIRRLARRG-------GVKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALKRQGRT 98 (102)
T ss_pred CCCHHHHHHHHHHc-------CCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhcCCC
Confidence 69999999999998 5789999999999999999999999999999999999999999999999998854
No 10
>smart00417 H4 Histone H4.
Probab=99.20 E-value=4.3e-11 Score=80.59 Aligned_cols=62 Identities=18% Similarity=0.209 Sum_probs=58.8
Q ss_pred ccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHh
Q 033230 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKA 80 (124)
Q Consensus 12 ~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~A 80 (124)
.||+++|.||++.. |-.+||.++.+.+.+..++|+..|..+|...|++.|||||+++||..|
T Consensus 13 gI~k~~IrRLaRr~-------GvkRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~~a 74 (74)
T smart00417 13 GITKPAIRRLARRG-------GVKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVYA 74 (74)
T ss_pred CCCHHHHHHHHHHc-------CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHheeC
Confidence 79999999999998 567999999999999999999999999999999999999999999754
No 11
>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=99.18 E-value=1.1e-10 Score=76.51 Aligned_cols=64 Identities=22% Similarity=0.254 Sum_probs=60.7
Q ss_pred ccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhh
Q 033230 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIE 82 (124)
Q Consensus 12 ~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~ 82 (124)
.+|+++|.||++.. |-.+||.|+...|.+-.+.++..|..+|...+.+.||||++++||-.||+
T Consensus 2 ~~p~~~i~ria~~~-------Gi~ris~~a~~~l~~~~e~rl~~i~~~A~k~~~hakRktlt~~DI~~Alk 65 (65)
T smart00803 2 WLPKETIKDVAESL-------GIGNLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSALR 65 (65)
T ss_pred CCCHHHHHHHHHHC-------CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCeecHHHHHHHhC
Confidence 58999999999998 45689999999999999999999999999999999999999999999984
No 12
>smart00428 H3 Histone H3.
Probab=99.18 E-value=7.4e-11 Score=84.14 Aligned_cols=76 Identities=21% Similarity=0.265 Sum_probs=68.9
Q ss_pred ccccccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhh
Q 033230 8 PEAEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (124)
Q Consensus 8 ~ed~~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~ 83 (124)
..++.+|+.+..|++++..++..++.+.+++.+|..+||++++.|+..+...|+..|.+.||+||.+.|+..|..-
T Consensus 25 st~lLI~k~pF~RLVREI~~~~~~~~~~R~~~~Al~aLQeasE~ylv~lfeda~~~a~HAkRvTl~~kDi~La~ri 100 (105)
T smart00428 25 STDLLIRKAPFQRLVREIAQKFTTGVDLRFQSSAIMALQEAAEAYLVGLFEDTNLLAIHAKRVTIMPKDIQLARRI 100 (105)
T ss_pred CcccccccccHHHHHHHHHHHcCCCCCceeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccCcHhhHHHHHHH
Confidence 3578899999999999999876643478999999999999999999999999999999999999999999888643
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=99.06 E-value=9.6e-10 Score=73.03 Aligned_cols=65 Identities=22% Similarity=0.236 Sum_probs=61.0
Q ss_pred cchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhh
Q 033230 13 LPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (124)
Q Consensus 13 LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~ 83 (124)
+|+..+..++|+.=| ..+++.||.++|++.+++|+.-++..|...|++.||+||.++||..+|+.
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 678889999999854 68999999999999999999999999999999999999999999999975
No 14
>PF00125 Histone: Core histone H2A/H2B/H3/H4 histone h2a signature histone h2b signature histone h3 signature histone h4 signature; InterPro: IPR007125 The core histones together with some other DNA binding proteins appear to form a superfamily defined by a common fold and distant sequence similarities [, ]. Some proteins contain local homology domains related to the histone fold [].; GO: 0003677 DNA binding; PDB: 2YFW_D 2YFV_B 1U35_H 2F8N_D 2PYO_D 2NQB_D 3AN2_C 3AZJ_C 3AV1_G 3AZM_G ....
Probab=99.05 E-value=6.2e-10 Score=73.02 Aligned_cols=71 Identities=18% Similarity=0.306 Sum_probs=63.9
Q ss_pred ccccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhh
Q 033230 10 AEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIE 82 (124)
Q Consensus 10 d~~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~ 82 (124)
....|+..|.|+.|+..++... ..+||++|..+|+..++.|+..|...|...|.+.||+||++.||..|++
T Consensus 3 ~~~~~~~~~~r~~r~i~~~~~~--~~ris~~a~~~L~~~~E~~~~~il~~A~~~a~~~kR~tI~~~DI~~A~r 73 (75)
T PF00125_consen 3 RRLIPKFPFSRLLREIGEEILS--KYRISSEALVALQSVLEYLLVEILEEAGNLARHAKRKTITPRDIQLAVR 73 (75)
T ss_dssp SHSSSHHHHHHHHHHHHHTTSS--SSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTBSEEGHHHHHHHHH
T ss_pred ccccCceEEeeeeehhhccccc--ccccccccchhhhhhhhhhhhhhhhHHHHHHhhcCCcEecHHHHHHHHh
Confidence 4578999999999999874321 2799999999999999999999999999999999999999999999975
No 15
>PLN00160 histone H3; Provisional
Probab=98.85 E-value=6.4e-09 Score=73.33 Aligned_cols=74 Identities=22% Similarity=0.150 Sum_probs=66.8
Q ss_pred ccccccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhh
Q 033230 8 PEAEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIE 82 (124)
Q Consensus 8 ~ed~~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~ 82 (124)
..++.+|+++..|++++..++.++ ++.+++.+|..+||++++.|+..+...|+..|.+.||.||.+.|+..|..
T Consensus 17 st~lLI~k~pF~RLVREI~~~~~~-~~~Rfq~~Al~ALQeAsEayLv~lfed~~lca~HakRVTl~~kD~~L~~r 90 (97)
T PLN00160 17 STDLLIRRLPFARLVREIQMEMSR-EAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTIMPKDMQLARR 90 (97)
T ss_pred chhhhhccccHHHHHHHHHHHcCC-CCcEeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcccccchhhHHHHHH
Confidence 356889999999999999876543 35899999999999999999999999999999999999999999988864
No 16
>PLN00161 histone H3; Provisional
Probab=98.78 E-value=1.6e-08 Score=75.02 Aligned_cols=74 Identities=23% Similarity=0.166 Sum_probs=67.0
Q ss_pred cccccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhh
Q 033230 9 EAEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (124)
Q Consensus 9 ed~~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~ 83 (124)
-++.+|+.+..|++++...+..+ .+.+++.+|..+||++++.|+..+...|+..|.+.||.||.+.|+..|..-
T Consensus 52 t~lLIpklPF~RLVREI~~~~~~-~~~Rfq~~Al~ALQEAsEayLV~lFeda~lcaiHAkRVTlm~kDm~La~ri 125 (135)
T PLN00161 52 TELLIRKLPFARLVREISNEMLR-EPFRWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMPKDMQLARRI 125 (135)
T ss_pred cccccccccHHHHHHHHHHhcCC-CCcEeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccchhhHHHHHHh
Confidence 46789999999999999876543 369999999999999999999999999999999999999999999888643
No 17
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=98.73 E-value=7.1e-09 Score=82.76 Aligned_cols=79 Identities=23% Similarity=0.386 Sum_probs=70.8
Q ss_pred ccccccccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhhCC
Q 033230 6 VVPEAEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEID 85 (124)
Q Consensus 6 ~~~ed~~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~lg 85 (124)
+...+..||.|.|.|+||-.= +--.||.||..++.+.++.||..||..|+-.|++++|+|+...||..|++..+
T Consensus 103 ~~~k~h~LPlARIkkvMKtde------dVkMisaEaPvlFak~~EiFI~ELTmRAW~~ae~NkRRtLQksDia~Av~kSe 176 (286)
T COG5208 103 ILLKDHNLPLARIKKVMKTDE------DVKMISAEAPVLFAKITEIFIEELTMRAWINAEENKRRTLQKSDIAAAVKKSE 176 (286)
T ss_pred HHHHhccCcHHHHHHHHhccc------chhheecccchHHHHHHHHHHHHHHHHHHHHHhHhhhhHHHHHHHHHHHHHHH
Confidence 445677899999999999872 23489999999999999999999999999999999999999999999999998
Q ss_pred CcccH
Q 033230 86 FTEFV 90 (124)
Q Consensus 86 f~~~~ 90 (124)
.-||+
T Consensus 177 MfDFL 181 (286)
T COG5208 177 MFDFL 181 (286)
T ss_pred HHhHH
Confidence 76664
No 18
>PLN00121 histone H3; Provisional
Probab=98.73 E-value=2.3e-08 Score=74.33 Aligned_cols=73 Identities=25% Similarity=0.275 Sum_probs=66.9
Q ss_pred ccccccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhh
Q 033230 8 PEAEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIE 82 (124)
Q Consensus 8 ~ed~~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~ 82 (124)
..++.+|+.+..|++++...+.. .+.+++.+|..+||++++.|+..+...++..|.+.||.||.+.|+..|..
T Consensus 58 st~lLI~k~pF~RLVREI~~~~~--~~~Rf~~~Al~ALQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~r 130 (136)
T PLN00121 58 STELLIRKLPFQRLVREIAQDFK--TDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
T ss_pred ccccccccccHHHHHHHHHHHhC--ccceeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcceecchhhHHHHHH
Confidence 35789999999999999988653 36899999999999999999999999999999999999999999988864
No 19
>PTZ00018 histone H3; Provisional
Probab=98.71 E-value=2.6e-08 Score=73.98 Aligned_cols=72 Identities=25% Similarity=0.277 Sum_probs=66.3
Q ss_pred cccccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhh
Q 033230 9 EAEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIE 82 (124)
Q Consensus 9 ed~~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~ 82 (124)
.++.+|+.+..|++++...+.. .+.+++.+|..+||++++.|+..+...++..|.+.||.||.+.|+..|..
T Consensus 59 t~lLI~k~pF~RLVREI~~~~~--~~~rf~~~al~aLQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~r 130 (136)
T PTZ00018 59 TELLIRKLPFQRLVREIAQDFK--TDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
T ss_pred chhccccccHHHHHHHHHHHcC--CcceeeHHHHHHHHHHHHHHHHHHhhhhHHHHHhhcceecchhhHHHHHH
Confidence 5789999999999999987653 36899999999999999999999999999999999999999999988864
No 20
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=98.67 E-value=1.6e-07 Score=62.86 Aligned_cols=66 Identities=21% Similarity=0.282 Sum_probs=59.5
Q ss_pred hhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhhCCCc
Q 033230 15 KTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFT 87 (124)
Q Consensus 15 ~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~lgf~ 87 (124)
+-.|.+|+|.+ |--+++.+|.+.|.+....|+..|+..+...|++.||+++++.||..||+++|+.
T Consensus 9 ~~~Vaqil~~~-------Gf~~~~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~~~Dv~~Al~~~gi~ 74 (77)
T smart00576 9 RIAVAQILESA-------GFDSFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPNLGDVVLALENLGIS 74 (77)
T ss_pred HHHHHHHHHHc-------CccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCcc
Confidence 34577777776 4468999999999999999999999999999999999999999999999999974
No 21
>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=98.54 E-value=4.7e-07 Score=65.39 Aligned_cols=84 Identities=19% Similarity=0.137 Sum_probs=70.5
Q ss_pred hHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhhCCCccc-HHHHH
Q 033230 16 TIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFTEF-VDPLR 94 (124)
Q Consensus 16 A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~lgf~~~-~~~l~ 94 (124)
..|.+|+|+. |..+++.++...|.+.+..++.-|..+|...|+++||+||+.+||..|++..+-..| -++-+
T Consensus 5 ~~v~~iLk~~-------Gv~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r~~~~f~~~p~~ 77 (117)
T cd07979 5 RVIAAILKSM-------GITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRVDYSFTSPPPR 77 (117)
T ss_pred HHHHHHHHHC-------CCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhccCCCCCCcH
Confidence 3577888876 457899999999999999999999999999999999999999999999988775444 44477
Q ss_pred HHHHHHHhhhch
Q 033230 95 DSLDGQLTFRNW 106 (124)
Q Consensus 95 ~~l~~~~~~~~~ 106 (124)
+.|-+....+|-
T Consensus 78 ~~l~~~a~~~N~ 89 (117)
T cd07979 78 DFLLELAREKNS 89 (117)
T ss_pred HHHHHHHHHhcc
Confidence 777776665554
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=98.46 E-value=6.4e-07 Score=64.79 Aligned_cols=68 Identities=13% Similarity=0.172 Sum_probs=62.5
Q ss_pred ccccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhh
Q 033230 10 AEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (124)
Q Consensus 10 d~~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~ 83 (124)
.+.||.+.|.|+||+.- ...|||.+|...|..+.+-+...|...|...|.+.+|++|+++||..|+..
T Consensus 18 gL~fPV~ri~R~Lk~~~------~a~RVs~~A~VyLaAvLEYL~aEIlelA~n~ak~~k~krItp~hi~lAi~n 85 (115)
T cd00074 18 GLQFPVGRIHRYLKKGR------YAERVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKKRITPRHLQLAVRN 85 (115)
T ss_pred CccCcHHHHHHHHHcCc------cccccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEcHHHHHHHHhc
Confidence 56899999999999853 258999999999999999999999999999999999999999999999865
No 23
>KOG1657 consensus CCAAT-binding factor, subunit C (HAP5) [Transcription]
Probab=98.25 E-value=1.4e-06 Score=69.86 Aligned_cols=73 Identities=22% Similarity=0.377 Sum_probs=65.8
Q ss_pred cccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhhCCCccc
Q 033230 11 EELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFTEF 89 (124)
Q Consensus 11 ~~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~lgf~~~ 89 (124)
..||++.|.+|||..= | --+|+.||...+.+||+.||..|+..|+..+.+.+|+|+...|+-.|+..-+-.+|
T Consensus 73 ~~lPlaRiKkimK~de-----d-v~mI~~Eapvl~aka~E~Fi~elt~~sw~~Tee~~rrtl~~sdia~av~~s~~fdF 145 (236)
T KOG1657|consen 73 HILPLARIKKIMKSDE-----D-VSMITAEAPVLFAKACELFITELTLRSWVHTEENKRRTLQKSDIAAAVTQSETFDF 145 (236)
T ss_pred ccCcHhhccccccccc-----c-ccccchhHHHHHHHHHHHHHHHHHHHhhhhhcccccccchHHHHHHHhccCCCccc
Confidence 3799999999999973 1 23899999999999999999999999999999999999999999999998885444
No 24
>cd08050 TAF6 TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and are involved in forming Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs functions such as serving as
Probab=98.16 E-value=8e-06 Score=67.98 Aligned_cols=67 Identities=15% Similarity=0.213 Sum_probs=60.4
Q ss_pred chhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhhCCCc
Q 033230 14 PKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFT 87 (124)
Q Consensus 14 P~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~lgf~ 87 (124)
|..+|.-+++.. |..++|+||..+|.+.++.++..|+.+|.+.+++.||||++++||-.||+.++.+
T Consensus 1 ~~~~i~~ia~~~-------Gi~~~~~~a~~~La~~~e~~~~~i~~~A~k~~~hskR~~l~~~Di~~Al~~~n~e 67 (343)
T cd08050 1 PQESIKLIAESL-------GIDSLSDEVAQLLAEDVEYRLREIIQEAAKFMRHSKRRKLTTSDVNHALRLRNVE 67 (343)
T ss_pred ChhHHHHHHHHc-------CCCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHHhCCC
Confidence 456677777776 4459999999999999999999999999999999999999999999999998875
No 25
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=98.15 E-value=1.2e-05 Score=54.40 Aligned_cols=63 Identities=21% Similarity=0.280 Sum_probs=53.1
Q ss_pred HHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhh
Q 033230 17 IVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (124)
Q Consensus 17 ~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~ 83 (124)
+|.||+.+...+ .++.+|+++..+|.+.+-.++..++..-...|+|+||+||+++||+...++
T Consensus 10 ~v~ki~ee~~~~----~~~~~s~~~i~al~ELv~~q~~~~a~DLe~FAkHA~R~tI~~dDV~Ll~Rr 72 (76)
T PF15630_consen 10 TVGKIVEEEAKE----KGVEVSPQFIAALTELVYKQLENLAKDLEAFAKHAGRSTINMDDVKLLARR 72 (76)
T ss_dssp HHHHHHHHCCCC----TTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHTTT
T ss_pred HHHHHHHHHHhc----cCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHHHhhc
Confidence 578888887532 478999999999999999999999999999999999999999999987654
No 26
>PF15511 CENP-T: Centromere kinetochore component CENP-T; PDB: 3B0D_T 3B0C_T 3VH5_T 3VH6_T.
Probab=98.10 E-value=6.6e-06 Score=70.25 Aligned_cols=68 Identities=24% Similarity=0.361 Sum_probs=48.4
Q ss_pred ccccccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhH
Q 033230 8 PEAEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAED 76 (124)
Q Consensus 8 ~ed~~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eD 76 (124)
++.-.||.+.|.|++...... +..++++|+|||..+|.+|...|-..|+..-..+|+|+|||||..+|
T Consensus 347 i~~P~lP~~~vK~la~~~ak~-s~~sK~kiskdal~aleqasdwfFeQl~dDL~aYA~HAgRKTIdesD 414 (414)
T PF15511_consen 347 IPYPSLPPGVVKKLAQHFAKS-SGGSKMKISKDALEALEQASDWFFEQLGDDLEAYAKHAGRKTIDESD 414 (414)
T ss_dssp -----S-HHHHHHHHHHHH--------S-B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHH
T ss_pred CCCCCCCccHHHHHHHHHHHh-hcccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCCCC
Confidence 344479999999998877653 22347999999999999999999999999999999999999999877
No 27
>KOG1745 consensus Histones H3 and H4 [Chromatin structure and dynamics]
Probab=98.09 E-value=1.9e-06 Score=64.16 Aligned_cols=76 Identities=22% Similarity=0.222 Sum_probs=66.7
Q ss_pred ccccccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhhCC
Q 033230 8 PEAEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEID 85 (124)
Q Consensus 8 ~ed~~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~lg 85 (124)
..|+.+++.+..|++++..++-. .+.++...|..+||++++.|+..|.-.+|..|.+.||.||-|.||..|..--|
T Consensus 59 stdLlI~K~PFqRlvrei~q~f~--~dLrfqs~Ai~ALQeA~EayLv~LfEdtnlcAihAkRVTimpkdiQlArrirg 134 (137)
T KOG1745|consen 59 STDLLIRKLPFQRLVREIAQDFK--TDLRFQSSAIAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRG 134 (137)
T ss_pred hhHHHhhcCcHHHHhHHHHhccc--ccceehHHHHHHHHHHHHHHHHHhccccchhhhccceeEecccceehhhhccc
Confidence 45788999999999997766433 27899999999999999999999999999999999999999999998875433
No 28
>KOG3467 consensus Histone H4 [Chromatin structure and dynamics]
Probab=98.05 E-value=1.9e-05 Score=55.18 Aligned_cols=69 Identities=19% Similarity=0.217 Sum_probs=62.8
Q ss_pred ccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhhCCCc
Q 033230 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFT 87 (124)
Q Consensus 12 ~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~lgf~ 87 (124)
.+.+-+|.||.+.. |--+|+.-.-+.+...+.+|+..+-+.|...+++.+||||++-||+-+|+..|..
T Consensus 29 gitKpaIRRlARr~-------GVkRi~G~~yeE~~~~~k~fl~n~i~~A~~yt~HAKRKTvT~~dvv~~LKR~G~~ 97 (103)
T KOG3467|consen 29 GITKPAIRRLARRG-------GVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRT 97 (103)
T ss_pred ccchHHHHHHHHhc-------CcchhchhhHHHHHHHHHHHHHHHHHHHHHHHhhhhhceeeHHHHHHHHHHcCce
Confidence 46788999999987 3568999999999999999999999999999999999999999999999999854
No 29
>PF07524 Bromo_TP: Bromodomain associated; InterPro: IPR006565 This bromodomain is found in eukaryotic transcription factors and PHD domain containing proteins (IPR001965 from INTERPRO). The tandem PHD finger-bromodomain is found in many chromatin-associated proteins. It is involved in gene silencing by the human co-repressor KRAB-associated protein 1 (KAP1). The tandem PHD finger-bromodomain of KAP1 has a distinct structure that joins the two protein modules. The first helix, alpha(Z), of an atypical bromodomain forms the central hydrophobic core that anchors the other three helices of the bromodomain on one side and the zinc binding PHD finger on the other []. The Rap1 GTPase-activating protein, Sipa1, is modulated by the cellular bromodomain protein, Brd4. Brd4 belongs to the BET family and is a multifunctional protein involved in transcription, replication, the signal transduction pathway, and cell cycle progression. All of these functions are linked to its association with acetylated chromatin. It has tandem bromodomains []. The dysregulation of the Brd4-associated pathways may play an important role in breast cancer progression []. Bovine papillomavirus type 1 E2 also binds to chromosomes in a complex with Brd4. Interaction with Brd4 is additionally important for E2-mediated transcriptional regulation [, ].
Probab=97.99 E-value=6e-05 Score=49.94 Aligned_cols=64 Identities=23% Similarity=0.283 Sum_probs=56.1
Q ss_pred HHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhhCCCc
Q 033230 17 IVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFT 87 (124)
Q Consensus 17 ~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~lgf~ 87 (124)
.|.++++.+ |=-.++..|.+.|...+..|+..|++.+...|.+.||...++.||..||+++|+.
T Consensus 11 ~va~il~~~-------GF~~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~~~gi~ 74 (77)
T PF07524_consen 11 SVAQILKHA-------GFDSASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPNLQDVEQALEEMGIS 74 (77)
T ss_pred HHHHHHHHc-------CccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCC
Confidence 455555554 2237899999999999999999999999999999999999999999999999984
No 30
>smart00427 H2B Histone H2B.
Probab=97.98 E-value=3.7e-05 Score=53.53 Aligned_cols=64 Identities=16% Similarity=0.249 Sum_probs=57.6
Q ss_pred hHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhhCC
Q 033230 16 TIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEID 85 (124)
Q Consensus 16 A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~lg 85 (124)
.-|.|+.|++-| +..||..|...++--......-|+.+|...+.-.+|+||++.+|..|.+-+=
T Consensus 5 ~Yi~kvLKqVhp------d~giS~kam~imnSfvnDiferIa~EAs~L~~~nkr~TltsreIqtAvrl~L 68 (89)
T smart00427 5 IYIYKVLKQVHP------DTGISSKAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRLIL 68 (89)
T ss_pred HHHHHHHHHhCC------CccccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHHc
Confidence 358999999987 5689999999999999999999999999999999999999999999986543
No 31
>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=97.97 E-value=5.5e-05 Score=50.02 Aligned_cols=63 Identities=22% Similarity=0.222 Sum_probs=51.4
Q ss_pred hhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhh
Q 033230 15 KTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (124)
Q Consensus 15 ~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~ 83 (124)
|..+..++++.=| +.++..|+.++|.+.|.+||.-++..|...|++.|-.|+...||.-.|++
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 4567888999855 68999999999999999999999999999999999999999999998874
No 32
>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=97.88 E-value=2.3e-05 Score=52.43 Aligned_cols=66 Identities=21% Similarity=0.381 Sum_probs=54.8
Q ss_pred chhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCc-cChhHHHHhhhh
Q 033230 14 PKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQT-INAEDVLKAIEE 83 (124)
Q Consensus 14 P~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKT-I~~eDVl~AL~~ 83 (124)
|+.+|.||++....+ .+.+||+||..++++....|+..-...|.+.+..+|..+ |..+|+-+.+-.
T Consensus 1 p~~li~rll~~~f~~----~~tkIs~dal~l~~eyl~iFV~EAv~Ra~~~a~~e~~~~~le~e~LEki~pq 67 (72)
T PF09415_consen 1 PPELIARLLHEHFKD----DKTKISKDALKLSAEYLRIFVREAVARAAEQAEAEGDEGFLEVEHLEKILPQ 67 (72)
T ss_dssp -CHHHHHHHCTTSSS----TT-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSEE-HHHHHHHCHC
T ss_pred ChHHHHHHHHHHhcC----CCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHHH
Confidence 899999999977653 479999999999999999999999999999999999999 999999876644
No 33
>cd08048 TAF11 TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypothes
Probab=97.86 E-value=8.5e-05 Score=51.09 Aligned_cols=66 Identities=18% Similarity=0.368 Sum_probs=60.4
Q ss_pred ccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC---CccChhHHHHhhhhC
Q 033230 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKR---QTINAEDVLKAIEEI 84 (124)
Q Consensus 12 ~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kR---KTI~~eDVl~AL~~l 84 (124)
.||++.|.|+|...++ ..++.+...++.-.+.+||..|..+|.++..+.+. ..|.|+||-.|...|
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 5999999999999974 57899999999999999999999999999998776 789999999998876
No 34
>PLN00158 histone H2B; Provisional
Probab=97.75 E-value=0.00014 Score=52.81 Aligned_cols=66 Identities=15% Similarity=0.222 Sum_probs=58.6
Q ss_pred chhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhhCC
Q 033230 14 PKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEID 85 (124)
Q Consensus 14 P~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~lg 85 (124)
-..-|.|++|++-| +..||..+...++--...+..-|+.+|...+.-.+|+||++.+|..|.+-+=
T Consensus 29 y~~YI~kVLKQVhP------d~gIS~kaM~ImnSfvnDiferIA~EAs~La~~nkr~TltsrEIqtAvrLvL 94 (116)
T PLN00158 29 YKIYIYKVLKQVHP------DTGISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVRLIL 94 (116)
T ss_pred HHHHHHHHHHHhCC------CCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHhc
Confidence 34569999999987 5679999999999989999999999999999999999999999999985543
No 35
>PTZ00463 histone H2B; Provisional
Probab=97.72 E-value=0.00017 Score=52.41 Aligned_cols=62 Identities=16% Similarity=0.300 Sum_probs=56.2
Q ss_pred HHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhhC
Q 033230 17 IVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEI 84 (124)
Q Consensus 17 ~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~l 84 (124)
-|.|++|++-| +..||..|...++--......-|+.+|...|.-.+|+||++.+|..|.+-+
T Consensus 33 YI~KVLKqVhP------d~gIS~kaM~ImnSfvnDifErIA~EAs~La~~nkr~TltsrEIQtAvrLl 94 (117)
T PTZ00463 33 YIFKVLKQVHP------DTGISRKSMNIMNSFLVDTFEKIATEASRLCKYTRRDTLSSREIQTAIRLV 94 (117)
T ss_pred HHHHHHHhhCC------CCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHhhc
Confidence 48999999987 567999999999988888888999999999999999999999999998544
No 36
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=97.61 E-value=0.00015 Score=53.15 Aligned_cols=68 Identities=15% Similarity=0.188 Sum_probs=60.8
Q ss_pred ccccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhh
Q 033230 10 AEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (124)
Q Consensus 10 d~~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~ 83 (124)
-+.+|.+.|.|+||..- ..+||+++|...+..|.+=.+..|+..|-..|...|+|.|.|.|+..|+..
T Consensus 24 gl~fpvgrvkr~lk~~~------~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~kkkri~PrHlqlAIrn 91 (132)
T COG5262 24 GLIFPVGRVKRLLKKGN------YRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRIIPRHLQLAIRN 91 (132)
T ss_pred CccccHHHHHHHHHcCc------cceeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhcCcceechHHHHHHhcC
Confidence 45799999999999542 379999999999999999888999999999999999999999999999854
No 37
>PF04719 TAFII28: hTAFII28-like protein conserved region; InterPro: IPR006809 The general transcription factor, TFIID, consists of the TATA-binding protein (TBP) associated with a series of TBP-associated factors (TAFs) that together participate in the assembly of the transcription preinitiation complex. The conserved region is found at the C terminus of most member proteins. The crystal structure of hTAFII28 with hTAFII18 shows that this region is involved in the binding of these two subunits. The conserved region contains four alpha helices and three loops arranged as in histone H3 [, ].; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005634 nucleus; PDB: 1BH9_B 1BH8_B.
Probab=97.59 E-value=0.00035 Score=48.64 Aligned_cols=67 Identities=16% Similarity=0.363 Sum_probs=51.5
Q ss_pred ccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC-ccChhHHHHhhhhC
Q 033230 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQ-TINAEDVLKAIEEI 84 (124)
Q Consensus 12 ~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRK-TI~~eDVl~AL~~l 84 (124)
.||++.|.|||...++ +..+|.....++.-.+..|+..|-.+|.++..+.+.. .|.|.|+-.|.+.|
T Consensus 23 ~~~k~~ikkli~~~~~------~qsv~~~v~i~v~g~aKvFVGEiVE~A~~Vq~~~~~~~pl~P~hlreA~rrL 90 (90)
T PF04719_consen 23 SFNKAAIKKLINQVLG------NQSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGETGPLQPDHLREAYRRL 90 (90)
T ss_dssp ---HHHHHHHHHHHHS-------S---HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SS--HHHHHHHHHHH
T ss_pred cCCHHHHHHHHHHHcC------CCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcHHHHHHHHhC
Confidence 6999999999999984 4789999999999999999999999999999976544 79999999998764
No 38
>KOG1659 consensus Class 2 transcription repressor NC2, alpha subunit (DRAP1) [Transcription]
Probab=97.57 E-value=0.00032 Score=55.74 Aligned_cols=77 Identities=12% Similarity=0.245 Sum_probs=68.3
Q ss_pred ccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhhCCCcccHH
Q 033230 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFTEFVD 91 (124)
Q Consensus 12 ~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~lgf~~~~~ 91 (124)
.+|.+.|.|||...=. --+|+.-....+.++.+.|+.-|-..+.+++...+-|||+++|+..|.+.-.-.+|+.
T Consensus 13 rfp~aRiKKIMQ~dEd------IGKvaqavPViisralElFl~~l~~~t~~~t~~~~aKt~s~~hlkq~v~~~~~FdFLk 86 (224)
T KOG1659|consen 13 RFPPARIKKIMQSDED------IGKVAQAVPVIISRALELFLESLLQKTLEITRSRGAKTVSSSHLKQAVESDPKFDFLK 86 (224)
T ss_pred cCCHHHHHHHHhhhhh------hhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhcCccccCHHHHHHHHhccchhHHHH
Confidence 6899999999988631 3489999999999999999999999999999999999999999999998888667766
Q ss_pred HHH
Q 033230 92 PLR 94 (124)
Q Consensus 92 ~l~ 94 (124)
.+-
T Consensus 87 ~~v 89 (224)
T KOG1659|consen 87 EVV 89 (224)
T ss_pred HHH
Confidence 643
No 39
>PF02969 TAF: TATA box binding protein associated factor (TAF); InterPro: IPR004823 The TATA box binding protein associated factor (TAF) is part of the transcription initiation factor TFIID multimeric protein complex. TFIID plays a central role in mediating promoter responses to various activators and repressors. It binds tightly to TAFII-250 and directly interacts with TAFII-40. TFIID is composed of TATA binding protein (TBP)and a number of TBP-associated factors (TAFS). TAF proteins adopt a histone-like fold.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus; PDB: 1TAF_B.
Probab=97.55 E-value=0.00068 Score=44.69 Aligned_cols=64 Identities=16% Similarity=0.232 Sum_probs=49.5
Q ss_pred ccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhh
Q 033230 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIE 82 (124)
Q Consensus 12 ~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~ 82 (124)
.+|..+|.-+.... |-..++.|+...|.+=++--|..|..+|.+...+.+|++++++||-.||+
T Consensus 3 ~~~~esvk~iAes~-------Gi~~l~de~a~~La~dveyrlreiiq~a~kfm~hskR~~Lt~~Di~~ALr 66 (66)
T PF02969_consen 3 VFSQESVKDIAESL-------GISNLSDEAAKALAEDVEYRLREIIQEALKFMRHSKRTKLTTDDINSALR 66 (66)
T ss_dssp ---HHHHHHHHHHT-------T---B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH-
T ss_pred cCCHHHHHHHHHHc-------CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhC
Confidence 46777877766665 34589999999999999999999999999999999999999999999985
No 40
>smart00414 H2A Histone 2A.
Probab=97.27 E-value=0.0011 Score=47.39 Aligned_cols=68 Identities=13% Similarity=0.194 Sum_probs=59.6
Q ss_pred ccccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhh
Q 033230 10 AEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (124)
Q Consensus 10 d~~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~ 83 (124)
.+.||.+.|.|+||+.-. ..+|+..|...+..+.+=+...|-..|-..|...+++.|+++|+..|+..
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 568999999999999732 46999999999998888888888888888899999999999999999865
No 41
>COG5247 BUR6 Class 2 transcription repressor NC2, alpha subunit (DRAP1 homolog) [Transcription]
Probab=97.21 E-value=0.0013 Score=47.15 Aligned_cols=79 Identities=9% Similarity=0.158 Sum_probs=68.2
Q ss_pred ccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhhCCCcccHH
Q 033230 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFTEFVD 91 (124)
Q Consensus 12 ~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~lgf~~~~~ 91 (124)
.+|.|.|.|||.-.-+ --+|+.-......++.+.|+..|-..+.+.|...+-|.|+.+++..|.+.-+=.+|+.
T Consensus 23 rFP~ar~KkIMQ~deD------iGKV~q~tPVIaskalE~Fl~~iv~~s~k~aR~~~skR~t~e~lk~a~~sdekFdFL~ 96 (113)
T COG5247 23 RFPIARLKKIMQLDED------IGKVGQSTPVIASKALEMFLTEIVGLSLKEARKKSSKRMTSEFLKRATESDEKFDFLK 96 (113)
T ss_pred cCCHHHHHHHHHhhhh------hhhhhhcchHHHHHHHHHHHHHHHHHHHHHHHhccchhhHHHHHHHHHhhhHHHHHHH
Confidence 6899999999987632 3489999999999999999999999999999999999999999999998877556666
Q ss_pred HHHHH
Q 033230 92 PLRDS 96 (124)
Q Consensus 92 ~l~~~ 96 (124)
.+..+
T Consensus 97 ~~~~~ 101 (113)
T COG5247 97 NMEQF 101 (113)
T ss_pred HHHHh
Confidence 55543
No 42
>PTZ00017 histone H2A; Provisional
Probab=96.95 E-value=0.0023 Score=47.57 Aligned_cols=68 Identities=18% Similarity=0.188 Sum_probs=59.8
Q ss_pred ccccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhh
Q 033230 10 AEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (124)
Q Consensus 10 d~~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~ 83 (124)
.+.||.+.|.|++|+.-- ..||+..|...|..+.+=+...|-..|-..|...+++-|+|+||..|+..
T Consensus 25 gL~FPVgRi~R~Lk~g~~------a~RV~a~A~VYLAAVLEYLtaEILELAgNaa~d~kk~RItPrHi~lAI~n 92 (134)
T PTZ00017 25 GLQFPVGRVHRYLKKGRY------AKRVGAGAPVYLAAVLEYLTAEVLELAGNAAKDNKKKRITPRHIQLAIRN 92 (134)
T ss_pred CcccchHHHHHHHhccch------hccccccchhhhHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHhhccC
Confidence 568999999999998632 46999999999999888888888888888999999999999999999853
No 43
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=96.92 E-value=0.0017 Score=52.92 Aligned_cols=66 Identities=18% Similarity=0.200 Sum_probs=59.2
Q ss_pred ccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhh
Q 033230 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (124)
Q Consensus 12 ~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~ 83 (124)
.|-+--+..+++.+- ++.++-+|+.+.|.+.|..||..|+..|...|++.|..||-+.||...||+
T Consensus 154 il~k~kl~dLvqqId------~~~~LD~dVedlLleiADdFV~sii~~sC~LAKHRKsdtlEvrDIqLhLEr 219 (258)
T KOG1142|consen 154 ILSKRKLDDLVQQID------GTTKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHRKSDTVEVRDIQLHLER 219 (258)
T ss_pred cccccchhHHHHhhc------CcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccchhheeeeeec
Confidence 355666778888883 478999999999999999999999999999999999999999999999975
No 44
>PLN00154 histone H2A; Provisional
Probab=96.87 E-value=0.0037 Score=46.60 Aligned_cols=69 Identities=16% Similarity=0.148 Sum_probs=57.4
Q ss_pred ccccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhh
Q 033230 10 AEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (124)
Q Consensus 10 d~~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~ 83 (124)
.+.||.+.|.|++|+.... ..||+..|...+....+=....|-..|-..|.+.+++-|+|.||..|+..
T Consensus 36 gL~FPVgRi~r~Lk~g~~~-----~~RVga~ApVYLAAVLEYLtAEVLELAGNaA~d~kk~RItPrHi~lAIrn 104 (136)
T PLN00154 36 GLQFPVGRIHRQLKQRVSA-----HGRVGATAAVYTAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRG 104 (136)
T ss_pred CccCchHHHHHHHHhhhhh-----ccccccchHHHHHHHHHHHHHHHHHHHHHHHHhhCCceecHHHhhhhccC
Confidence 5689999999999997421 46999999999988776666666667778888999999999999999854
No 45
>KOG1756 consensus Histone 2A [Chromatin structure and dynamics]
Probab=96.85 E-value=0.0036 Score=46.28 Aligned_cols=69 Identities=13% Similarity=0.186 Sum_probs=55.7
Q ss_pred cccccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhh
Q 033230 9 EAEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (124)
Q Consensus 9 ed~~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~ 83 (124)
..+.+|.+.|.|++|+.- ...+||.+|...+.-+.+=....|+..|-..|.++++.-|+|.||..|+..
T Consensus 24 agl~fPvgri~r~Lr~~~------~~~ri~~gapV~laavLeYL~Aeile~agnaardnkk~ri~PrH~~lAI~N 92 (131)
T KOG1756|consen 24 AGLQFPVGRIHRLLRKGR------YAQRVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRITPRHLQLAIRN 92 (131)
T ss_pred cccccCHHHHHHHHHccc------hhhhccCCChHHHHHHHHHHHHHHHHHhHHHhhhcCccccChHHHHHHHhC
Confidence 346899999999999942 268999999999996665555666666666777889999999999999863
No 46
>PF02291 TFIID-31kDa: Transcription initiation factor IID, 31kD subunit; InterPro: IPR003162 Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription []. TAFII-31 protein is a transcriptional coactivator of the p53 protein [].; GO: 0006352 transcription initiation, DNA-dependent; PDB: 1TAF_A.
Probab=96.81 E-value=0.0072 Score=44.55 Aligned_cols=93 Identities=22% Similarity=0.238 Sum_probs=46.5
Q ss_pred ccccccchh--HHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhh-hC
Q 033230 8 PEAEELPKT--IVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIE-EI 84 (124)
Q Consensus 8 ~ed~~LP~A--~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~-~l 84 (124)
.+...+|+. .|.-|+|+. |-......+...|.+-+-.|+.-|-..|...|.+.||++|+.+||..|++ .+
T Consensus 6 ~~~~~~PrDa~~i~~iL~~~-------Gv~~yeprVv~qLLEfayRYt~~vL~DA~~ya~hA~~~~i~~~DVrLAi~~r~ 78 (129)
T PF02291_consen 6 SQSKSLPRDARVIHLILKSM-------GVTEYEPRVVNQLLEFAYRYTSDVLEDAQVYADHAGRSTIDADDVRLAIQSRL 78 (129)
T ss_dssp -------HHHHHHHHHHHHT-------T---B-THHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHHHHT-
T ss_pred CCCccCChHHHHHHHHHHHc-------CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHH
Confidence 344467763 334444444 33356777888999999999999999999999999999999999999998 67
Q ss_pred CCcccHHHHHHHHHHHHhhhchh
Q 033230 85 DFTEFVDPLRDSLDGQLTFRNWI 107 (124)
Q Consensus 85 gf~~~~~~l~~~l~~~~~~~~~~ 107 (124)
++...-++-+++|-+.-..+|-+
T Consensus 79 ~~~f~~pppre~llelA~e~N~~ 101 (129)
T PF02291_consen 79 DHSFTQPPPREFLLELAREKNSI 101 (129)
T ss_dssp -----------------------
T ss_pred hhhccCCCChHHHHHHHHHhcCC
Confidence 78777788888888887777754
No 47
>KOG1744 consensus Histone H2B [Chromatin structure and dynamics]
Probab=96.77 E-value=0.0055 Score=45.21 Aligned_cols=62 Identities=18% Similarity=0.279 Sum_probs=55.4
Q ss_pred HHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhhC
Q 033230 17 IVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEI 84 (124)
Q Consensus 17 ~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~l 84 (124)
.|.|++|++-| +.-||.++...++--..++.-.|+.+|...+.-.||.||+..+|..|.+-+
T Consensus 42 yv~kvlk~Vhp------d~gis~~a~~vmnsf~ndife~iA~ea~rla~y~krstisSreiqta~rLl 103 (127)
T KOG1744|consen 42 YVYKVLKQVHP------DLGISSKAMGVMNSFVNDIFERIASEAGRLAHYNKRSTISSREIQTAVRLL 103 (127)
T ss_pred ehhhhhhcccC------CCCcCHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCcccHHHHHHHHHHh
Confidence 47789999977 355999999999999999999999999999999999999999999987543
No 48
>PLN00157 histone H2A; Provisional
Probab=96.69 E-value=0.0048 Score=45.80 Aligned_cols=68 Identities=13% Similarity=0.157 Sum_probs=58.3
Q ss_pred ccccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhh
Q 033230 10 AEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (124)
Q Consensus 10 d~~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~ 83 (124)
.+.||.+.|.|.+|+.-- ..||+..|...|.-+.+=....|-..|-..|...+++-|+|+||..|+..
T Consensus 24 gL~FPVgRi~R~Lk~g~~------a~RIg~~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~n 91 (132)
T PLN00157 24 GLQFPVGRIARYLKAGKY------ATRVGAGAPVYLAAVLEYLAAEVLELAGNAARDNKKSRIVPRHIQLAVRN 91 (132)
T ss_pred CcccchHHHHHHHhcCch------hhhcCCCcHhHHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHhhcccC
Confidence 568999999999999632 47999999999998877777777777888889999999999999999853
No 49
>PLN00153 histone H2A; Provisional
Probab=96.66 E-value=0.0053 Score=45.43 Aligned_cols=68 Identities=13% Similarity=0.157 Sum_probs=58.8
Q ss_pred ccccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhh
Q 033230 10 AEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (124)
Q Consensus 10 d~~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~ 83 (124)
.+.+|.+.|.|.+|+.-. ..||+..|...+.-+.+=....|-..|-..|...+++-|+|+||..|+..
T Consensus 22 gL~FpVgRi~R~Lr~g~~------a~Rvga~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~n 89 (129)
T PLN00153 22 GLQFPVGRIARYLKKGKY------AERIGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKNRIVPRHIQLAIRN 89 (129)
T ss_pred CcccchHHHHHHHhcCch------hhccCCCchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHhhccC
Confidence 578999999999998642 46999999999998887777777788888899999999999999999853
No 50
>PLN00156 histone H2AX; Provisional
Probab=96.62 E-value=0.0066 Score=45.43 Aligned_cols=68 Identities=13% Similarity=0.153 Sum_probs=57.3
Q ss_pred ccccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhh
Q 033230 10 AEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (124)
Q Consensus 10 d~~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~ 83 (124)
.+.+|.+.|.|.+|+.-- ..||+..|...|.-+.+=....|-..|-..|...+++-|+|+||..|+..
T Consensus 27 gL~FPVgRi~R~Lk~g~y------a~RVga~ApVYLAAVLEYLtaEVLELAgNaa~d~kk~RItPrHi~lAIrn 94 (139)
T PLN00156 27 GLQFPVGRIARFLKAGKY------AERVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRN 94 (139)
T ss_pred CcccchHHHHHHHhcCCh------hhccCCccHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHhhccC
Confidence 568999999999999732 46999999999988777666777777778888999999999999999853
No 51
>PF15510 CENP-W: Centromere kinetochore component W
Probab=96.57 E-value=0.0048 Score=43.48 Aligned_cols=65 Identities=26% Similarity=0.357 Sum_probs=53.2
Q ss_pred ccchhHHHHHHhccccCCCCCCcchhhHHHHHH--------------HHHHHHHHHHHHHHHHHHHHHhcCCCccChhHH
Q 033230 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLA--------------FCESARIFIHYLSATANDICKESKRQTINAEDV 77 (124)
Q Consensus 12 ~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~a--------------l~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDV 77 (124)
.-|++.+.|++|..-| ..++....-.+ +.-.+-.|++-|+-+|...|=+++-.||.++||
T Consensus 16 kaPrgfLkrv~Kr~Kp------hlRl~~~~Dllv~~~~f~~~~~~~~vhLncLLFvhrLAEEaRtnA~EnK~~~Ik~~Hv 89 (102)
T PF15510_consen 16 KAPRGFLKRVFKRQKP------HLRLETSGDLLVRFCPFSGWQWGGEVHLNCLLFVHRLAEEARTNACENKCGTIKKEHV 89 (102)
T ss_pred hCchHHHHHHHHhcCC------ceeecccccHHHhhcccccccccceeehhHHHHHHHHHHHHHHHHHHHhhccccHHHH
Confidence 4699999999998876 34554444333 566688999999999999999999999999999
Q ss_pred HHhhh
Q 033230 78 LKAIE 82 (124)
Q Consensus 78 l~AL~ 82 (124)
+.|-+
T Consensus 90 ~AaaK 94 (102)
T PF15510_consen 90 LAAAK 94 (102)
T ss_pred HHHHH
Confidence 99865
No 52
>PF02269 TFIID-18kDa: Transcription initiation factor IID, 18kD subunit; InterPro: IPR003195 This family includes the Spt3 yeast transcription factors and the 18 kDa subunit from human transcription initiation factor IID (TFIID-18). Determination of the crystal structure reveals an atypical histone fold [].; GO: 0006366 transcription from RNA polymerase II promoter; PDB: 1BH9_A 1BH8_A.
Probab=96.41 E-value=0.0037 Score=43.34 Aligned_cols=49 Identities=16% Similarity=0.196 Sum_probs=24.7
Q ss_pred chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhh
Q 033230 35 ISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (124)
Q Consensus 35 ~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~ 83 (124)
..-..|...++-+...+||..+...|...|...|+++|+.+|++-+|+.
T Consensus 18 ~~P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~rg~~~i~~eDl~F~lR~ 66 (93)
T PF02269_consen 18 EEPLPETVDLVEDIVREYIIELCQEAMEVAQRRGSKKIKVEDLLFLLRK 66 (93)
T ss_dssp SS--HHHHHHHHHHHHHHHHHHHHHHHC---------------------
T ss_pred CCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCcCcHHHHHHHHhc
Confidence 4568999999999999999999999999999999999999999999975
No 53
>KOG3219 consensus Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=95.94 E-value=0.0076 Score=47.35 Aligned_cols=71 Identities=14% Similarity=0.303 Sum_probs=61.8
Q ss_pred cccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC-ccChhHHHHhhhhCCCcc
Q 033230 11 EELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQ-TINAEDVLKAIEEIDFTE 88 (124)
Q Consensus 11 ~~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRK-TI~~eDVl~AL~~lgf~~ 88 (124)
..||+++|.|||..... .. ||.-+..+++-.+.+|+..|--+|.+++..-+.. .+.|.||-.|...|+...
T Consensus 111 s~f~Ka~iKkL~~~itg------~~-v~~nv~Ia~~GiaKvFVGEvVEeAl~V~~~~~e~~PLqP~HIREA~rrL~~qg 182 (195)
T KOG3219|consen 111 SAFPKAQIKKLMSSITG------QS-VSENVAIAMAGIAKVFVGEVVEEALDVREEWGESGPLQPKHIREAYRRLKLQG 182 (195)
T ss_pred hcCCHHHHHHHHHHHhC------Cc-cCcceeeeecchhhHhHHHHHHHHHHHHHHhccCCCCCcHHHHHHHHHHHhcC
Confidence 36999999999999974 23 8899999999999999999999999999976653 599999999999887654
No 54
>PTZ00252 histone H2A; Provisional
Probab=95.46 E-value=0.057 Score=40.21 Aligned_cols=69 Identities=9% Similarity=0.065 Sum_probs=50.1
Q ss_pred cccccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHh--cCCCccChhHHHHhhhh
Q 033230 9 EAEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKE--SKRQTINAEDVLKAIEE 83 (124)
Q Consensus 9 ed~~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~--~kRKTI~~eDVl~AL~~ 83 (124)
-.+.||.+.|.|.+++.-- ..||+..|...|.-+.+=....|-..|-..|.+ .+++-|+|+||..|+..
T Consensus 22 AGL~FPVgRi~R~Lr~g~y------a~RIga~ApVYLAAVLEYLtaEVLELAgnaa~d~~~kk~RItPrHi~lAIrN 92 (134)
T PTZ00252 22 AGLIFPVGRVGSLLRRGQY------ARRIGASGAVYMAAVLEYLTAELLELSVKAAAQQAKKPKRLTPRTVTLAVRH 92 (134)
T ss_pred cCccCchHHHHHHHHcCCc------ccccCCccHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccccHHHHHhhccC
Confidence 3578999999999998742 469999998888765544344444444444433 57788999999999853
No 55
>KOG1658 consensus DNA polymerase epsilon, subunit C [Replication, recombination and repair]
Probab=95.33 E-value=0.015 Score=44.38 Aligned_cols=68 Identities=29% Similarity=0.418 Sum_probs=56.9
Q ss_pred cccchhHHHHHHhccccCCCCCCcch-hhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhhCC
Q 033230 11 EELPKTIVRRVVKDKLHNCSPDTDIS-VHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEID 85 (124)
Q Consensus 11 ~~LP~A~I~RI~K~~Lp~~~~d~~~~-ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~lg 85 (124)
..||.+.|..++|-. .+.+ ..+|++-++.+++..||..|+..+...+...+|||+.-.|+-.|.+..+
T Consensus 58 ~rLpL~rik~vvkl~-------pdl~l~~dea~~l~a~aaelfi~~Ln~~~~~~~q~~k~kt~qr~d~D~ai~~~d 126 (162)
T KOG1658|consen 58 SRLPLARIKQVVKLD-------PDLTLLNDEASQLIAKAAELFIQELNDVAYTTAQLRKRKTEQRRDYDTAIEAVD 126 (162)
T ss_pred hhccHHHHHhhccCC-------cchhhhhhHHHHHHHHHHHHHHHHHHhccchhHHHHHhhhhhhhcccccccchH
Confidence 367888888888765 1454 4567899999999999999999999999999999999999888876654
No 56
>cd07978 TAF13 The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Several hy
Probab=94.94 E-value=0.11 Score=36.11 Aligned_cols=47 Identities=13% Similarity=0.232 Sum_probs=41.1
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhh
Q 033230 36 SVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (124)
Q Consensus 36 ~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~ 83 (124)
.-..|...++-+...+||..+..+|.+.|. .++.-++.||++-+|+.
T Consensus 20 ~P~~eTv~llE~iv~~~i~~l~~~a~~~A~-~r~~k~~~eD~~FliR~ 66 (92)
T cd07978 20 NPLPETVDLLEDIVVEYIIELCHKAAEVAQ-RRRGKVKVEDLIFLLRK 66 (92)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-cCCCCCCHHHHHHHHhc
Confidence 457899999999999999999999999998 44555699999999964
No 57
>KOG4336 consensus TBP-associated transcription factor Prodos [Transcription]
Probab=94.42 E-value=0.34 Score=40.61 Aligned_cols=64 Identities=20% Similarity=0.277 Sum_probs=57.8
Q ss_pred chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhhCCCcccHHHHHHHHHHH
Q 033230 35 ISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFTEFVDPLRDSLDGQ 100 (124)
Q Consensus 35 ~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~lgf~~~~~~l~~~l~~~ 100 (124)
-.|++-|.+.|.+....+|..|+..+...|...||.-.|.-||...|-++|+. ++.|..+++++
T Consensus 21 d~is~~aletlvell~~yi~eigrq~~n~celagRT~pT~~Dv~l~Li~mnI~--v~sL~~~~q~~ 84 (323)
T KOG4336|consen 21 DSISNAALETLVELLQSYIREIGRQLHNYCELAGRTIPTQGDVKLTLIEMNIK--VSSLYAYFQKQ 84 (323)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcHHHHHHHHHHhCCC--hhhhHHHHHhc
Confidence 46999999999999999999999999999999999999999999999999997 56666666654
No 58
>KOG3423 consensus Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=94.22 E-value=0.29 Score=37.87 Aligned_cols=69 Identities=16% Similarity=0.194 Sum_probs=55.1
Q ss_pred ccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC--------------CCccChhHH
Q 033230 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESK--------------RQTINAEDV 77 (124)
Q Consensus 12 ~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~k--------------RKTI~~eDV 77 (124)
.+|-+.+.-.++.+-= ...-.-.+.++.=++-.||+-|+..|.+.|+-.+ |-|++-+|+
T Consensus 86 ~IPDavt~~yL~~aGf-------~~~D~rv~RLvsLaAQKfvSDIa~DA~Q~~k~r~~~~~~~~k~~~kdkK~tLtmeDL 158 (176)
T KOG3423|consen 86 TIPDAVTDHYLKKAGF-------QTSDPRVKRLVSLAAQKFVSDIANDALQHSKIRTKTAIGKDKKQAKDKKYTLTMEDL 158 (176)
T ss_pred CCcHHHHHHHHHhcCC-------CcCcHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccccccccccccceeeeHHHH
Confidence 6888888888888721 2233445778899999999999999999998544 448999999
Q ss_pred HHhhhhCCCc
Q 033230 78 LKAIEEIDFT 87 (124)
Q Consensus 78 l~AL~~lgf~ 87 (124)
-.||++.|..
T Consensus 159 ~~AL~EyGin 168 (176)
T KOG3423|consen 159 SPALAEYGIN 168 (176)
T ss_pred HHHHHHhCcc
Confidence 9999999974
No 59
>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=93.71 E-value=0.23 Score=38.35 Aligned_cols=74 Identities=22% Similarity=0.248 Sum_probs=55.3
Q ss_pred cchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHH---HHHHHHHHHHHHHHhcCCCccChhHHHHhhhhCCC
Q 033230 13 LPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARI---FIHYLSATANDICKESKRQTINAEDVLKAIEEIDF 86 (124)
Q Consensus 13 LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~---FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~lgf 86 (124)
|...-+..++...+..........++.++...|.+.+.= .|+.+...|...+-..+.++|+.++|..++.++.+
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 333455555554443211112356899999999988875 79999999999999999999999999999998874
No 60
>KOG2549 consensus Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=92.19 E-value=0.68 Score=41.63 Aligned_cols=67 Identities=24% Similarity=0.328 Sum_probs=56.1
Q ss_pred chhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhhCCCc
Q 033230 14 PKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFT 87 (124)
Q Consensus 14 P~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~lgf~ 87 (124)
|+..+.- +-+.+ |-..+++|+..+|.+=.+.=|..|..+|.+.-.+.+|.+++.+||-.||.-+.-+
T Consensus 13 ~~Es~k~-vAEsl------Gi~nl~deaa~~La~dv~yrikEI~Q~aaKfm~hskR~kLtv~DV~~ALr~~nVe 79 (576)
T KOG2549|consen 13 PKESVKV-VAESL------GITNLNDEAALLLAEDVEYRIKEIVQDAAKFMVHSKRTKLTVDDVDYALRSLNVE 79 (576)
T ss_pred cHHHHHH-HHHHh------CccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcCcHHHHHHHHhhcccc
Confidence 4445444 44444 4567999999999999999999999999999999999999999999999987643
No 61
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=90.70 E-value=1.2 Score=36.58 Aligned_cols=71 Identities=18% Similarity=0.158 Sum_probs=49.6
Q ss_pred hhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHH------HHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhhCCCc
Q 033230 15 KTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESA------RIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFT 87 (124)
Q Consensus 15 ~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a------~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~lgf~ 87 (124)
..-+..|++..+...- ....++.++.+.+.+.+ --.+..+...|...|...++.+|+.+||..|++.+.-+
T Consensus 209 ~~e~~~il~~r~~~~~--~~~~~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~a~~~a~~~~~~~I~~~~v~~a~~~~~~~ 285 (394)
T PRK00411 209 ADEIFDILKDRVEEGF--YPGVVDDEVLDLIADLTAREHGDARVAIDLLRRAGLIAEREGSRKVTEEDVRKAYEKSEIV 285 (394)
T ss_pred HHHHHHHHHHHHHhhc--ccCCCCHhHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHHHH
Confidence 3455556555442100 02357888888887766 33455667888889999999999999999999988433
No 62
>KOG2389 consensus Predicted bromodomain transcription factor [Transcription]
Probab=90.44 E-value=1.1 Score=38.09 Aligned_cols=89 Identities=17% Similarity=0.198 Sum_probs=67.3
Q ss_pred ccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhhCCCc---c
Q 033230 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFT---E 88 (124)
Q Consensus 12 ~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~lgf~---~ 88 (124)
.|-+..|..|....- --....-|.+.|+.-+..||.-|+..|...+...||.-.+..||..||++|+.. .
T Consensus 29 sla~~avaQIcqslg-------~~~~~~sale~Ltd~~~qyvQ~lgk~a~~~~n~anR~epnl~Div~Al~dls~s~~~~ 101 (353)
T KOG2389|consen 29 SLARVAVAQICQSLG-------YSSTQNSALETLTDVLQQYVQNLGKTAHRYSNLANRTEPNLFDIVLALQDLSASLGAS 101 (353)
T ss_pred HHHHHHHHHHHHhcC-------CcccccHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCccHHHHHHHHHHhhhhcccc
Confidence 455667777776652 223344499999999999999999999999999999999999999999999864 3
Q ss_pred cHHHHHHHHHHHHhhhchh
Q 033230 89 FVDPLRDSLDGQLTFRNWI 107 (124)
Q Consensus 89 ~~~~l~~~l~~~~~~~~~~ 107 (124)
........|..=..+||.|
T Consensus 102 ~~~~~s~~L~ds~v~rdii 120 (353)
T KOG2389|consen 102 GSSGESHCLLDSKVLRDII 120 (353)
T ss_pred cccchhHHHhhhhhHHHHH
Confidence 3333455555546666654
No 63
>KOG3334 consensus Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=88.93 E-value=3 Score=31.57 Aligned_cols=69 Identities=26% Similarity=0.189 Sum_probs=53.2
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhhCCCcccHH-HHHHHHHHHHhhhc
Q 033230 37 VHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFTEFVD-PLRDSLDGQLTFRN 105 (124)
Q Consensus 37 ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~lgf~~~~~-~l~~~l~~~~~~~~ 105 (124)
...-...-|.+-+--++.-|-..|.-.+.+.++.||..+||..|++..+=-+|.+ +=+++|-+.-.-||
T Consensus 31 yEprVi~qlLefa~rYtt~vL~DA~vys~HA~ka~i~~eDVrlA~~~~~~~sf~~pPpRe~lL~lA~~rN 100 (148)
T KOG3334|consen 31 YEPRVINQLLEFAYRYTTTVLDDAKVYSSHAKKATIDAEDVRLAIQMRVDHSFTPPPPREFLLELAAERN 100 (148)
T ss_pred cChHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHhccccCCCCchHHHHHHHHhhc
Confidence 3444556677777778888889999999999999999999999999887655655 55666666555555
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=85.96 E-value=4 Score=33.03 Aligned_cols=76 Identities=14% Similarity=0.173 Sum_probs=48.7
Q ss_pred hHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHH------HHHHHHHHHHHHHHHhcCCCccChhHHHHhhhhCCCccc
Q 033230 16 TIVRRVVKDKLHNCSPDTDISVHKDALLAFCESAR------IFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFTEF 89 (124)
Q Consensus 16 A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~------~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~lgf~~~ 89 (124)
.-+..|++..+...- .+..+++|+...+.+.+. --+..+-..|...|..+++.+|+.+||..|++.+..+.+
T Consensus 202 ~e~~~il~~r~~~~~--~~~~~~~~~l~~i~~~~~~~~Gd~R~al~~l~~a~~~a~~~~~~~it~~~v~~a~~~~~~~~~ 279 (365)
T TIGR02928 202 EELRDILENRAEKAF--YDGVLDDGVIPLCAALAAQEHGDARKAIDLLRVAGEIAEREGAERVTEDHVEKAQEKIEKDRL 279 (365)
T ss_pred HHHHHHHHHHHHhhc--cCCCCChhHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHH
Confidence 445666655543100 023477787776655432 244556667788888899999999999999998865544
Q ss_pred HHHH
Q 033230 90 VDPL 93 (124)
Q Consensus 90 ~~~l 93 (124)
...+
T Consensus 280 ~~~i 283 (365)
T TIGR02928 280 LELI 283 (365)
T ss_pred HHHH
Confidence 4333
No 65
>PF09114 MotA_activ: Transcription factor MotA, activation domain; InterPro: IPR015198 Transcription factor MotA is required for the activation of middle promoters in Bacteriophage T4, in addition to phage T4 co-activator AsiA, and sigma-70-containing Escherichia coli RNA polymerase. Phage T4 middle promoters have the sigma70 -10 DNA element, but not the -35 element; instead, they have a MotA box at -30 to which the transcription factor MotA binds []. MotA and AsiA interact with the C-terminal of sigma70 (region 4), which normally binds the -35 element and the beta-flap, thereby diverting sigma70 away from host promoters that require -35 element-binding to phage T4 middle promoters. Transcription factor MotA has two domains: an N-terminal domain required for binding to sigma70, and a C-terminal domain required for binding to the -30 MotA box element in the phage T4 middle promoter. This entry represents the N-terminal (activation) domain of MotA factors that binds sigma70. The N-terminal domain adopts an almost completely alpha-helical topology, with five alpha-helices and a short, two-stranded, beta-ribbon. Four alpha helices (alpha1, alpha3, alpha4 and alpha5) are amphipathic and pack their hydrophobic surfaces around the central helix alpha2 [].; PDB: 1BJA_B 1I1S_A.
Probab=85.22 E-value=0.75 Score=32.39 Aligned_cols=38 Identities=13% Similarity=0.262 Sum_probs=32.9
Q ss_pred hHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHH
Q 033230 16 TIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIH 54 (124)
Q Consensus 16 A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~ 54 (124)
++|.+++|..|=+.|+|| ..++.++.+.|+++++.|-.
T Consensus 51 SNIGvLIKkglIEKSGDG-lv~T~~g~~Ii~~AA~l~a~ 88 (96)
T PF09114_consen 51 SNIGVLIKKGLIEKSGDG-LVITEEGMDIIIQAAELWAQ 88 (96)
T ss_dssp HHHHHHHHTTSEEEETTE-EEE-HHHHHHHHHHHHHHHH
T ss_pred HhHHHHHHcCcccccCCc-eEEechHHHHHHHHHHHHHh
Confidence 568889999998888887 99999999999999998854
No 66
>PF13654 AAA_32: AAA domain; PDB: 3K1J_B.
Probab=83.21 E-value=5.3 Score=35.34 Aligned_cols=49 Identities=27% Similarity=0.287 Sum_probs=36.1
Q ss_pred hhhHHHHHHHHHHHH-----------HHHHHHHHHHHHHHHhcCCCccChhHHHHhhhhC
Q 033230 36 SVHKDALLAFCESAR-----------IFIHYLSATANDICKESKRQTINAEDVLKAIEEI 84 (124)
Q Consensus 36 ~ISkdA~~al~~~a~-----------~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~l 84 (124)
-++.+|...|.+.+. .-|.-|-.+|+..|..+|+++|+++||..|++.-
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 356666666666554 2566777999999999999999999999999763
No 67
>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=82.62 E-value=4.5 Score=35.65 Aligned_cols=66 Identities=21% Similarity=0.256 Sum_probs=44.6
Q ss_pred hHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHH---HHHHHHHHHHHHHHHhcCCCccChhHHHHhhhhCCC
Q 033230 16 TIVRRVVKDKLHNCSPDTDISVHKDALLAFCESAR---IFIHYLSATANDICKESKRQTINAEDVLKAIEEIDF 86 (124)
Q Consensus 16 A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~---~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~lgf 86 (124)
.-+..|++..+.. .+..+++++.+.|.+.+. +.++ +...|..+|..++|++|+.+||.+++..-.+
T Consensus 266 eei~~Il~~~a~k----~~i~is~~al~~I~~y~~n~Rel~n-ll~~Aa~~A~~~~~~~It~~dI~~vl~~~~~ 334 (531)
T TIGR02902 266 EEIKEIAKNAAEK----IGINLEKHALELIVKYASNGREAVN-IVQLAAGIALGEGRKRILAEDIEWVAENGNY 334 (531)
T ss_pred HHHHHHHHHHHHH----cCCCcCHHHHHHHHHhhhhHHHHHH-HHHHHHHHHhhCCCcEEcHHHHHHHhCCccc
Confidence 3455556665542 246789999888776654 2333 3345556788889999999999999765444
No 68
>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=81.02 E-value=2.7 Score=25.42 Aligned_cols=42 Identities=21% Similarity=0.202 Sum_probs=25.4
Q ss_pred hHHHHHHHHHHHHHHH-HHHHHHHHHHHHhcCCCccChhHHHHh
Q 033230 38 HKDALLAFCESARIFI-HYLSATANDICKESKRQTINAEDVLKA 80 (124)
Q Consensus 38 SkdA~~al~~~a~~FI-~~lt~~A~~~a~~~kRKTI~~eDVl~A 80 (124)
+.||...|.+. =.|+ .-+=..+-..|.+.|...||.++|..|
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 34555555553 2233 334456667888999999999999876
No 69
>COG1067 LonB Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]
Probab=77.72 E-value=2.4 Score=38.71 Aligned_cols=30 Identities=37% Similarity=0.470 Sum_probs=26.4
Q ss_pred HHHHHHHHHHhcCCCccChhHHHHhhhhCC
Q 033230 56 LSATANDICKESKRQTINAEDVLKAIEEID 85 (124)
Q Consensus 56 lt~~A~~~a~~~kRKTI~~eDVl~AL~~lg 85 (124)
|-.+|..+|..+|++-|+++||.+|++.-.
T Consensus 371 lv~~A~~ia~~~~~~~I~ae~Ve~a~~~~~ 400 (647)
T COG1067 371 LVREAGDIAVSEGRKLITAEDVEEALQKRE 400 (647)
T ss_pred HHHHhhHHHhcCCcccCcHHHHHHHHHhhh
Confidence 335999999999999999999999998744
No 70
>PF13335 Mg_chelatase_2: Magnesium chelatase, subunit ChlI
Probab=77.30 E-value=10 Score=26.13 Aligned_cols=47 Identities=17% Similarity=0.226 Sum_probs=38.6
Q ss_pred hhhHHHHHHHHHHHHHH------HHHHHHHHHHHHHhcCCCccChhHHHHhhh
Q 033230 36 SVHKDALLAFCESARIF------IHYLSATANDICKESKRQTINAEDVLKAIE 82 (124)
Q Consensus 36 ~ISkdA~~al~~~a~~F------I~~lt~~A~~~a~~~kRKTI~~eDVl~AL~ 82 (124)
.+++++...|.+++..+ .+-|-.-|..+|.=++...|+.+||..||.
T Consensus 42 ~l~~~~~~~l~~~~~~~~lS~R~~~rilrvARTIADL~~~~~I~~~hi~EAl~ 94 (96)
T PF13335_consen 42 PLSSEAKKLLEQAAEKLNLSARGYHRILRVARTIADLEGSERITREHIAEALS 94 (96)
T ss_pred CCCHHHHHHHHHHHHHcCcCHHHHHHHHHHHHHHHhHcCCCCCCHHHHHHHHh
Confidence 46777777887777665 455668899999999999999999999984
No 71
>PF02861 Clp_N: Clp amino terminal domain; InterPro: IPR004176 This short domain is found in one or two copies at the amino terminus of ClpA and ClpB proteins from bacteria and eukaryotes. The function of these domains is uncertain but they may form a protein binding site []. The proteins are thought to be subunits of ATP-dependent proteases which act as chaperones to target the proteases to substrates.; GO: 0019538 protein metabolic process; PDB: 3FH2_A 3ZRJ_A 3ZRI_A 1QVR_C 3FES_C 2Y1R_F 3PXG_D 2Y1Q_A 3PXI_C 2K77_A ....
Probab=77.08 E-value=2.8 Score=24.61 Aligned_cols=26 Identities=31% Similarity=0.385 Sum_probs=21.0
Q ss_pred HHHHHHhcCCCccChhHHHHhhhhCC
Q 033230 60 ANDICKESKRQTINAEDVLKAIEEID 85 (124)
Q Consensus 60 A~~~a~~~kRKTI~~eDVl~AL~~lg 85 (124)
|.+.|...|...|+++|++.||=+-+
T Consensus 1 A~~~A~~~~~~~i~~eHlL~all~~~ 26 (53)
T PF02861_consen 1 AQELARERGHQYISPEHLLLALLEDP 26 (53)
T ss_dssp HHHHHHHTTBSSE-HHHHHHHHHHHT
T ss_pred CHHHHHHcCCCcccHHHHHHHHHhhh
Confidence 66889999999999999999965443
No 72
>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=74.11 E-value=14 Score=31.75 Aligned_cols=54 Identities=20% Similarity=0.265 Sum_probs=49.6
Q ss_pred cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhhCCCc
Q 033230 34 DISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFT 87 (124)
Q Consensus 34 ~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~lgf~ 87 (124)
-..|.+|+..++.--.+==|+.+-.+|.+.-.+.||..++.+||-.||..++.+
T Consensus 20 i~Ni~Dd~l~alamDlEYRI~ev~qea~KFmvhSKRtvLt~dDis~ALr~lNVe 73 (450)
T COG5095 20 ISNIDDDALRALAMDLEYRIKEVCQEASKFMVHSKRTVLTIDDISYALRSLNVE 73 (450)
T ss_pred CcccccHHHHHHHHhHHHHHHHHHHHHHHHhhcccceeeeHHhHHHHHHhcCCC
Confidence 457899999999998888899999999999999999999999999999998754
No 73
>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=73.96 E-value=9.1 Score=34.46 Aligned_cols=50 Identities=30% Similarity=0.287 Sum_probs=40.3
Q ss_pred hhhHHHHHHHHHHHH-------------HHHHHHHHHHHHHHHhcCCCccChhHHHHhhhhCC
Q 033230 36 SVHKDALLAFCESAR-------------IFIHYLSATANDICKESKRQTINAEDVLKAIEEID 85 (124)
Q Consensus 36 ~ISkdA~~al~~~a~-------------~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~lg 85 (124)
.++++|...|.+-++ -=+.-|-.+|..+|..+++.+|+++||..|++.-.
T Consensus 330 ~~s~~Av~~Li~~~~R~ag~r~~lsl~~R~L~~llR~A~~iA~~~~~~~I~~ehV~~Ai~~~~ 392 (608)
T TIGR00764 330 HFTRDAVEEIVREAQRRAGRKDHLTLRLRELGGLVRAAGDIAKSSGKVYVTAEHVLKAKKLAK 392 (608)
T ss_pred cCCHHHHHHHHHHHHHHHhcccccCCCHHHHHHHHHHHHHHHHhcCCceecHHHHHHHHHHHH
Confidence 688999888876544 34556678888999999999999999999987654
No 74
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=72.35 E-value=10 Score=29.87 Aligned_cols=48 Identities=15% Similarity=0.186 Sum_probs=36.4
Q ss_pred CCccccccccc----ccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHH
Q 033230 1 METEKVVPEAE----ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSA 58 (124)
Q Consensus 1 ~~~ek~~~ed~----~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~ 58 (124)
|...++++.|+ ..-++||.|++... .+||.+.+.-+.+++.+ +.|.-.
T Consensus 1 ~~~~~~ti~dIA~~agVS~~TVSrvLn~~---------~~vs~~tr~rV~~~a~e-lgY~pn 52 (331)
T PRK14987 1 MKKKRPVLQDVADRVGVTKMTVSRFLRNP---------EQVSVALRGKIAAALDE-LGYIPN 52 (331)
T ss_pred CCCCCCcHHHHHHHhCCCHHHhhhhhCCC---------CCCCHHHHHHHHHHHHH-hCCCcc
Confidence 45566666665 78899999998543 36999999999999998 556543
No 75
>PRK09862 putative ATP-dependent protease; Provisional
Probab=70.61 E-value=18 Score=32.16 Aligned_cols=60 Identities=12% Similarity=0.104 Sum_probs=45.7
Q ss_pred hhhHHHHHHHHHHHHHH------HHHHHHHHHHHHHhcCCCccChhHHHHhhhhCCCcccHHHHHH
Q 033230 36 SVHKDALLAFCESARIF------IHYLSATANDICKESKRQTINAEDVLKAIEEIDFTEFVDPLRD 95 (124)
Q Consensus 36 ~ISkdA~~al~~~a~~F------I~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~lgf~~~~~~l~~ 95 (124)
.+++++...+..+...+ .+.|...|..+|.=+||..|+++||..|+.=-+++..+-.++.
T Consensus 438 ~l~~~~~~~l~~~~~~~~lS~Ra~~rlLrvARTiADL~g~~~V~~~hv~eAl~yR~~~~~~~~~~~ 503 (506)
T PRK09862 438 KLESEDARWLEETLIHLGLSIRAWQRLLKVARTIADIDQSDIITRQHLQEAVSYRAIDRLLIHLQK 503 (506)
T ss_pred CCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHhhcccHHHHHHHH
Confidence 56777777777655444 5667788999999999999999999999987766655554443
No 76
>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=69.22 E-value=20 Score=29.95 Aligned_cols=48 Identities=15% Similarity=0.236 Sum_probs=39.1
Q ss_pred cchhhHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCccChhHHHHhh
Q 033230 34 DISVHKDALLAFCESARIFI-------HYLSATANDICKESKRQTINAEDVLKAI 81 (124)
Q Consensus 34 ~~~ISkdA~~al~~~a~~FI-------~~lt~~A~~~a~~~kRKTI~~eDVl~AL 81 (124)
.+.++++....+.+.+..+= .++...|...|.-+||..|+++||..+.
T Consensus 252 ~V~v~d~~~~~i~~l~~~~~~~s~Ra~i~l~raArA~Aal~GR~~V~~dDv~~~a 306 (337)
T TIGR02030 252 QVTIPYDVLVKVAELCAELDVDGLRGELTLNRAAKALAAFEGRTEVTVDDIRRVA 306 (337)
T ss_pred cCcCCHHHHHHHHHHHHHHCCCCCcHHHHHHHHHHHHHHHcCCCCCCHHHHHHHH
Confidence 58899999888888776653 3466778888999999999999999765
No 77
>PRK12402 replication factor C small subunit 2; Reviewed
Probab=68.15 E-value=21 Score=28.33 Aligned_cols=72 Identities=13% Similarity=0.056 Sum_probs=43.4
Q ss_pred ccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhhCCCccc
Q 033230 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFTEF 89 (124)
Q Consensus 12 ~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~lgf~~~ 89 (124)
.++...+..++++.+.. .+..++.++...|.+.+.-=+..+-......+. +..+|+.+||..++.....++-
T Consensus 183 ~~~~~~~~~~l~~~~~~----~~~~~~~~al~~l~~~~~gdlr~l~~~l~~~~~--~~~~It~~~v~~~~~~~~~~~~ 254 (337)
T PRK12402 183 APTDDELVDVLESIAEA----EGVDYDDDGLELIAYYAGGDLRKAILTLQTAAL--AAGEITMEAAYEALGDVGTDEV 254 (337)
T ss_pred CCCHHHHHHHHHHHHHH----cCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHH--cCCCCCHHHHHHHhCCCCCHHH
Confidence 34455666666665543 246789999888887763223333333333332 2347999999998876554433
No 78
>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=67.82 E-value=27 Score=21.85 Aligned_cols=48 Identities=17% Similarity=0.233 Sum_probs=35.5
Q ss_pred ccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 033230 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKE 66 (124)
Q Consensus 12 ~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~ 66 (124)
.+|-+.+.-.++.+.=+. .+ .-...+++=++..||..|+..|.+.|+-
T Consensus 2 ~IPD~v~~~yL~~~G~~~---~D----~rv~RLvSLaaQKFisdI~~dA~q~~k~ 49 (51)
T PF03540_consen 2 TIPDEVTDYYLERSGFQT---SD----PRVKRLVSLAAQKFISDIANDAMQYCKI 49 (51)
T ss_pred CCCHHHHHHHHHHCCCCC---CC----HhHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 478888888888873321 12 2345678888899999999999998863
No 79
>KOG3901 consensus Transcription initiation factor IID subunit [Transcription]
Probab=66.58 E-value=19 Score=25.94 Aligned_cols=44 Identities=18% Similarity=0.183 Sum_probs=36.4
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhh
Q 033230 37 VHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (124)
Q Consensus 37 ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~ 83 (124)
=-.|+.++|.....+||..++..|..+. +|-.+..||++-+|+.
T Consensus 28 P~~~tv~~Le~iV~~Yi~elt~~a~~~g---~rgk~~veD~~f~lRk 71 (109)
T KOG3901|consen 28 PYPETVDLLEDIVLEYITELTHAAMEIG---KRGKVKVEDFKFLLRK 71 (109)
T ss_pred ccHhHHHHHHHHHHHHHHHHHHHHHHhc---ccCceeHHHHHHHHHh
Confidence 3567888999999999999988888877 4556788999999864
No 80
>COG5162 Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=66.56 E-value=38 Score=26.45 Aligned_cols=50 Identities=18% Similarity=0.264 Sum_probs=37.4
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHH-h------------------c--------------CCCccChhHHHHhhhhC
Q 033230 38 HKDALLAFCESARIFIHYLSATANDICK-E------------------S--------------KRQTINAEDVLKAIEEI 84 (124)
Q Consensus 38 SkdA~~al~~~a~~FI~~lt~~A~~~a~-~------------------~--------------kRKTI~~eDVl~AL~~l 84 (124)
..-.+.++.-.+..||+-|+..|.+..+ + . ++-+++..|+-+||++.
T Consensus 107 D~rvKkLl~L~aqKFvsDiA~dayqYsrIr~~~sna~~t~~~a~~f~~gg~~~i~~~~~~~dr~K~vltv~DLs~Al~Ey 186 (197)
T COG5162 107 DQRVKKLLSLLAQKFVSDIAVDAYQYSRIRQGSSNAKATAQKAKRFAKGGASGIGSSGRRGDRKKPVLTVVDLSKALEEY 186 (197)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccchhhHHHHHHHHhcccccccccccccccCCceeeehHHHHHHHHh
Confidence 3456778888999999999977665432 0 1 45578899999999998
Q ss_pred CCc
Q 033230 85 DFT 87 (124)
Q Consensus 85 gf~ 87 (124)
|+.
T Consensus 187 Gin 189 (197)
T COG5162 187 GIN 189 (197)
T ss_pred ccc
Confidence 874
No 81
>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=66.17 E-value=21 Score=32.12 Aligned_cols=50 Identities=20% Similarity=0.218 Sum_probs=42.1
Q ss_pred cchhhHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCccChhHHHHhhhh
Q 033230 34 DISVHKDALLAFCESARIFI-------HYLSATANDICKESKRQTINAEDVLKAIEE 83 (124)
Q Consensus 34 ~~~ISkdA~~al~~~a~~FI-------~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~ 83 (124)
.+.|+.+....|.+.+..+- ..+...|..+|.=+||.+|+.+||..|++-
T Consensus 247 ~V~is~~~~~~l~~~~~~~~i~s~Ra~i~~~r~Ara~AaL~gr~~V~~~Dv~~A~~l 303 (633)
T TIGR02442 247 SVRISDSLIRFISELCIEFGVDGHRADIVMARAARALAALDGRRRVTAEDVREAAEL 303 (633)
T ss_pred CCCCCHHHHHHHHHHHHHhCCCCccHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHH
Confidence 57899999999998887762 456688888999999999999999988753
No 82
>TIGR01128 holA DNA polymerase III, delta subunit. subunit around DNA forming a DNA sliding clamp.
Probab=65.87 E-value=31 Score=26.93 Aligned_cols=68 Identities=15% Similarity=0.199 Sum_probs=49.5
Q ss_pred ccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhh
Q 033230 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (124)
Q Consensus 12 ~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~ 83 (124)
.++...+.+.+++.+.. .+..|+.++...|...+.-=...+..+-...+.-.+.++|+.+||...+..
T Consensus 110 ~~~~~~~~~~i~~~~~~----~g~~i~~~a~~~l~~~~~~d~~~l~~el~KL~~~~~~~~It~e~I~~~~~~ 177 (302)
T TIGR01128 110 TPKEQELPRWIQARLKK----LGLRIDPDAVQLLAELVEGNLLAIAQELEKLALYAPDGKITLEDVEEAVSD 177 (302)
T ss_pred CCCHHHHHHHHHHHHHH----cCCCCCHHHHHHHHHHhCcHHHHHHHHHHHHHhhCCCCCCCHHHHHHHHhh
Confidence 45567777777777653 257899999999988777656666666677666544558999999877653
No 83
>CHL00081 chlI Mg-protoporyphyrin IX chelatase
Probab=65.30 E-value=17 Score=30.68 Aligned_cols=49 Identities=12% Similarity=0.197 Sum_probs=41.5
Q ss_pred cchhhHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCccChhHHHHhhh
Q 033230 34 DISVHKDALLAFCESARIFI-------HYLSATANDICKESKRQTINAEDVLKAIE 82 (124)
Q Consensus 34 ~~~ISkdA~~al~~~a~~FI-------~~lt~~A~~~a~~~kRKTI~~eDVl~AL~ 82 (124)
.+.+|++....+.+.+...= .++...|.-.|.=+||..|+++||..+..
T Consensus 265 ~V~v~~~~~~yi~~l~~~~~~~s~Ra~i~l~raArA~Aal~GR~~V~pdDv~~~a~ 320 (350)
T CHL00081 265 KVEIDYDLRVKISQICSELDVDGLRGDIVTNRAAKALAAFEGRTEVTPKDIFKVIT 320 (350)
T ss_pred CCccCHHHHHHHHHHHHHHCCCCChHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 68899999999988888764 46678888889999999999999998753
No 84
>PRK09526 lacI lac repressor; Reviewed
Probab=65.11 E-value=18 Score=28.46 Aligned_cols=47 Identities=13% Similarity=0.123 Sum_probs=35.2
Q ss_pred Cccccccccc----ccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHH
Q 033230 2 ETEKVVPEAE----ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSA 58 (124)
Q Consensus 2 ~~ek~~~ed~----~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~ 58 (124)
...++++.|. ..-++||.|++... .+||.+.++-+.+++.+ +.|.-.
T Consensus 2 ~~~~~ti~dIA~~aGVS~~TVSrvLn~~---------~~vs~~tr~rV~~~a~e-lgY~pn 52 (342)
T PRK09526 2 KSKPVTLYDVARYAGVSYQTVSRVLNQA---------SHVSAKTREKVEAAMAE-LNYVPN 52 (342)
T ss_pred CCCCCcHHHHHHHhCCCHHHHHHHhcCC---------CCCCHHHHHHHHHHHHH-HCCCcC
Confidence 3344555554 67889999999653 35999999999999999 567544
No 85
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=64.61 E-value=31 Score=27.94 Aligned_cols=72 Identities=15% Similarity=0.209 Sum_probs=48.8
Q ss_pred cchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHH---HHHHHHHHHHHHHHHhcCCCccChhHHHHhhhhCCCcc
Q 033230 13 LPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESAR---IFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFTE 88 (124)
Q Consensus 13 LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~---~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~lgf~~ 88 (124)
++...+..+++..... .+..++.|+...|.+.+. -.+..+-..+.+.+...+.+.|+.++|..+++.++.+.
T Consensus 180 ~~~~e~~~il~~~~~~----~~~~~~~~~~~~ia~~~~G~pR~a~~~l~~~~~~a~~~~~~~I~~~~v~~~l~~~~~~~ 254 (328)
T PRK00080 180 YTVEELEKIVKRSARI----LGVEIDEEGALEIARRSRGTPRIANRLLRRVRDFAQVKGDGVITKEIADKALDMLGVDE 254 (328)
T ss_pred CCHHHHHHHHHHHHHH----cCCCcCHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCc
Confidence 4445555566555432 257888888888776662 23445555666777666777999999999999987653
No 86
>KOG2680 consensus DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=63.52 E-value=22 Score=30.73 Aligned_cols=50 Identities=18% Similarity=0.342 Sum_probs=42.2
Q ss_pred CcchhhHHHHHHHHHHHHH----HHHHHHHHHHHHHHhcCCCccChhHHHHhhh
Q 033230 33 TDISVHKDALLAFCESARI----FIHYLSATANDICKESKRQTINAEDVLKAIE 82 (124)
Q Consensus 33 ~~~~ISkdA~~al~~~a~~----FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~ 82 (124)
.++.++.||++.|.+.... |..+|-+.|+.+|.+.+-+++..+||-.+.+
T Consensus 374 Edv~m~~~A~d~Lt~i~~~tsLRYai~Lit~a~~~~~krk~~~v~~~di~r~y~ 427 (454)
T KOG2680|consen 374 EDVEMNPDALDLLTKIGEATSLRYAIHLITAASLVCLKRKGKVVEVDDIERVYR 427 (454)
T ss_pred hccccCHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHhcCceeehhHHHHHHH
Confidence 3688999999999876554 6677778899999999999999999999863
No 87
>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=62.97 E-value=16 Score=32.03 Aligned_cols=48 Identities=27% Similarity=0.309 Sum_probs=41.1
Q ss_pred cchhhHHHHHHHHHHHHH----HHHHHHHHHHHHHHhcCCCccChhHHHHhh
Q 033230 34 DISVHKDALLAFCESARI----FIHYLSATANDICKESKRQTINAEDVLKAI 81 (124)
Q Consensus 34 ~~~ISkdA~~al~~~a~~----FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL 81 (124)
+..+|+||.+.|....++ |..-|-.-|..+|+..|+++|..+||-.|-
T Consensus 378 ~i~l~~~Ale~L~~ig~etSLRYa~qLL~pa~iiA~~rg~~~V~~~dVe~a~ 429 (450)
T COG1224 378 DIELSDDALEYLTDIGEETSLRYAVQLLTPASIIAKRRGSKRVEVEDVERAK 429 (450)
T ss_pred ccccCHHHHHHHHhhchhhhHHHHHHhccHHHHHHHHhCCCeeehhHHHHHH
Confidence 688999999999877665 555666778999999999999999999984
No 88
>PRK13406 bchD magnesium chelatase subunit D; Provisional
Probab=61.80 E-value=18 Score=32.55 Aligned_cols=49 Identities=18% Similarity=0.231 Sum_probs=42.8
Q ss_pred cchhhHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCccChhHHHHhhh
Q 033230 34 DISVHKDALLAFCESARIFI-------HYLSATANDICKESKRQTINAEDVLKAIE 82 (124)
Q Consensus 34 ~~~ISkdA~~al~~~a~~FI-------~~lt~~A~~~a~~~kRKTI~~eDVl~AL~ 82 (124)
++.++.+....+.+.+..+- ..+...|..+|.=+||.+|+++||..|+.
T Consensus 193 ~v~v~~~~l~~i~~~~~~~gv~S~Ra~i~llraARa~AaL~Gr~~V~~~dv~~Aa~ 248 (584)
T PRK13406 193 AVGPPPEAIAALCAAAAALGIASLRAPLLALRAARAAAALAGRTAVEEEDLALAAR 248 (584)
T ss_pred cCCCCHHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 68899999998888887774 47788899999999999999999999974
No 89
>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=61.41 E-value=31 Score=26.74 Aligned_cols=73 Identities=11% Similarity=0.055 Sum_probs=55.6
Q ss_pred cccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhc------CCCccChhHHHHhhhhC
Q 033230 11 EELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKES------KRQTINAEDVLKAIEEI 84 (124)
Q Consensus 11 ~~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~------kRKTI~~eDVl~AL~~l 84 (124)
..|....+.+.|...+... |-..++.|....|.-|+.+++..|-......|.+- ...++-..||-.-|..|
T Consensus 43 ~fl~~~~l~~~~~~i~~~~---g~~~~~~d~~~lis~a~e~rlr~li~k~~~~s~hR~~~~~~~~r~~~~sdvr~qL~~l 119 (212)
T cd08045 43 SFLNPSPLAKKIRKIAKKH---GLKEVDEDVLDLISLALEERLRNLLEKLIEVSEHRVDSEKEDERYEITSDVRKQLRFL 119 (212)
T ss_pred hccCHHHHHHHHHHHHHHc---CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCceeecchHHHHHHHH
Confidence 4677777777777776542 11278999999999999999999999999988864 34566677887777666
Q ss_pred CC
Q 033230 85 DF 86 (124)
Q Consensus 85 gf 86 (124)
+-
T Consensus 120 ~~ 121 (212)
T cd08045 120 EQ 121 (212)
T ss_pred HH
Confidence 54
No 90
>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=61.00 E-value=31 Score=27.18 Aligned_cols=71 Identities=17% Similarity=0.223 Sum_probs=46.6
Q ss_pred cchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHH---HHHHHHHHHHHHHHHhcCCCccChhHHHHhhhhCCCc
Q 033230 13 LPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESAR---IFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFT 87 (124)
Q Consensus 13 LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~---~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~lgf~ 87 (124)
++...+..+++..... .+..++.++...|.+.+. -.+..+...+...+...+...|+.++|..++..++.+
T Consensus 159 l~~~e~~~il~~~~~~----~~~~~~~~al~~ia~~~~G~pR~~~~ll~~~~~~a~~~~~~~it~~~v~~~l~~l~~~ 232 (305)
T TIGR00635 159 YTVEELAEIVSRSAGL----LNVEIEPEAALEIARRSRGTPRIANRLLRRVRDFAQVRGQKIINRDIALKALEMLMID 232 (305)
T ss_pred CCHHHHHHHHHHHHHH----hCCCcCHHHHHHHHHHhCCCcchHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHhCCC
Confidence 3344455555554432 246788888877777543 2334555566677766666789999999999987654
No 91
>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=60.53 E-value=9 Score=27.71 Aligned_cols=61 Identities=8% Similarity=0.180 Sum_probs=38.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhhCCCcccHHHHHHHHHHHHhhh
Q 033230 40 DALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFTEFVDPLRDSLDGQLTFR 104 (124)
Q Consensus 40 dA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~lgf~~~~~~l~~~l~~~~~~~ 104 (124)
..+..|..|..+.-.|......-... ---.-......|+..|++..+.+++.++++|++..
T Consensus 73 ~Vk~Eiaa~~~v~~~Y~~~L~~G~vd----~e~~~~~~~~kLk~AGidkV~~E~QkQlda~~~~~ 133 (134)
T PF12010_consen 73 PVKNEIAACSNVWSEYYPPLETGLVD----PEEALPEFNEKLKAAGIDKVIAELQKQLDAFLAAN 133 (134)
T ss_pred hhHHHHHHHHHHHHHHHHHHHccCCC----HHHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHhc
Confidence 34555555555555554432211110 00124567888999999999999999999998754
No 92
>PRK07452 DNA polymerase III subunit delta; Validated
Probab=58.77 E-value=36 Score=27.26 Aligned_cols=66 Identities=12% Similarity=0.151 Sum_probs=48.9
Q ss_pred HHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHh--cCCCccChhHHHHhhhhCCCc
Q 033230 18 VRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKE--SKRQTINAEDVLKAIEEIDFT 87 (124)
Q Consensus 18 I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~--~kRKTI~~eDVl~AL~~lgf~ 87 (124)
+.+.|++.+.. .+..|+.+|...|...+.-=...+..+-.+.+.- .++.+|+.+||...+......
T Consensus 135 l~~~i~~~~~~----~g~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~~It~~~V~~~v~~~~~~ 202 (326)
T PRK07452 135 LKQLVERTAQE----LGVKLTPEAAELLAEAVGNDSRRLYNELEKLALYAENSTKPISAEEVKALVSNTTQN 202 (326)
T ss_pred HHHHHHHHHHH----cCCCCCHHHHHHHHHHhCccHHHHHHHHHHHHHhccCCCCccCHHHHHHHhccCcCc
Confidence 55555554432 2688999999999998887666777777777765 557889999999887766543
No 93
>COG4519 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=57.50 E-value=1.3 Score=30.84 Aligned_cols=35 Identities=31% Similarity=0.572 Sum_probs=24.7
Q ss_pred cChhHHHHhhhhCCCc-ccHHHHHHHHHHHHhhhch
Q 033230 72 INAEDVLKAIEEIDFT-EFVDPLRDSLDGQLTFRNW 106 (124)
Q Consensus 72 I~~eDVl~AL~~lgf~-~~~~~l~~~l~~~~~~~~~ 106 (124)
=+.+||++||..||.. .|+.+=....+.|-.+++|
T Consensus 37 RT~QDvikAlpglgi~l~FvQ~G~Rnn~GyYql~dW 72 (95)
T COG4519 37 RTAQDVIKALPGLGIVLEFVQEGARNNQGYYQLRDW 72 (95)
T ss_pred hHHHHHHHhCcCCCeEEEeeecccccCCCceEeeec
Confidence 3579999999999974 6766655555666555554
No 94
>PRK13407 bchI magnesium chelatase subunit I; Provisional
Probab=57.34 E-value=33 Score=28.71 Aligned_cols=48 Identities=6% Similarity=0.007 Sum_probs=39.6
Q ss_pred cchhhHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCccChhHHHHhh
Q 033230 34 DISVHKDALLAFCESARIFI-------HYLSATANDICKESKRQTINAEDVLKAI 81 (124)
Q Consensus 34 ~~~ISkdA~~al~~~a~~FI-------~~lt~~A~~~a~~~kRKTI~~eDVl~AL 81 (124)
.+.++++....+.+.+...= .++...|...|.-+||..|+++||..+.
T Consensus 249 ~V~v~~~~~~yi~~l~~~~~~~s~Ra~i~l~~aA~a~A~l~Gr~~V~~~Di~~~~ 303 (334)
T PRK13407 249 QLKTPNTVLHDCAALCIALGSDGLRGELTLLRAARALAAFEGAEAVGRSHLRSVA 303 (334)
T ss_pred CcccCHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHHcCCCeeCHHHHHHHH
Confidence 58899999998888877654 2377888889999999999999996654
No 95
>TIGR00368 Mg chelatase-related protein. The N-terminal end matches very strongly a pfam Mg_chelatase domain.
Probab=57.25 E-value=28 Score=30.75 Aligned_cols=47 Identities=17% Similarity=0.169 Sum_probs=40.4
Q ss_pred hhhHHHHHHHHHHHHHH------HHHHHHHHHHHHHhcCCCccChhHHHHhhh
Q 033230 36 SVHKDALLAFCESARIF------IHYLSATANDICKESKRQTINAEDVLKAIE 82 (124)
Q Consensus 36 ~ISkdA~~al~~~a~~F------I~~lt~~A~~~a~~~kRKTI~~eDVl~AL~ 82 (124)
.+++++...+.++...+ .+-|..-|..+|.=+++..|+.+||..|+.
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 45788889888887776 566778899999999999999999999984
No 96
>KOG1757 consensus Histone 2A [Chromatin structure and dynamics]
Probab=57.21 E-value=17 Score=26.65 Aligned_cols=66 Identities=18% Similarity=0.259 Sum_probs=47.3
Q ss_pred ccccccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhc----CCCccChhHHHHhhh
Q 033230 8 PEAEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKES----KRQTINAEDVLKAIE 82 (124)
Q Consensus 8 ~ed~~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~----kRKTI~~eDVl~AL~ 82 (124)
..-+.+|...|.|.+|.-... ..++..-+. +- ....+.|||.+-.+.|-.. +-|.|+|.|+..|++
T Consensus 26 raGlqFpVgRihr~LK~r~t~-----h~rVGataa--vy--~aaileYLTaEVLeLAgNasKdLKvKRitprHlqLAiR 95 (131)
T KOG1757|consen 26 RAGLQFPVGRIHRHLKTRTTS-----HGRVGATAA--VY--SAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 95 (131)
T ss_pred hcccccchHHHHHHHHHhccc-----ccccchHHH--HH--HHHHHHHHHHHHHHHcccccccceeeeccchhheeeec
Confidence 456789999999999998653 455554433 32 2345778998888887654 447799999988875
No 97
>PF08823 PG_binding_2: Putative peptidoglycan binding domain; InterPro: IPR014927 This entry may be a peptidoglycan binding domain.
Probab=53.37 E-value=22 Score=23.54 Aligned_cols=32 Identities=16% Similarity=0.328 Sum_probs=27.3
Q ss_pred hHHHHhhhhCCC------cccHHHHHHHHHHHHhhhch
Q 033230 75 EDVLKAIEEIDF------TEFVDPLRDSLDGQLTFRNW 106 (124)
Q Consensus 75 eDVl~AL~~lgf------~~~~~~l~~~l~~~~~~~~~ 106 (124)
+.|..+|..+|| +.+-+.+++.|..|.-..|+
T Consensus 19 ~evq~~L~~lGyy~g~~~g~~d~a~~~Al~~~~g~ENf 56 (74)
T PF08823_consen 19 REVQEALKRLGYYKGEADGVWDEATEDALRAWAGTENF 56 (74)
T ss_pred HHHHHHHHHcCCccCCCCCcccHHHHHHHHHHHHHhhH
Confidence 567889999999 67889999999999877775
No 98
>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=52.83 E-value=46 Score=29.83 Aligned_cols=49 Identities=14% Similarity=0.206 Sum_probs=38.7
Q ss_pred cchhhHHHHHHHHHHHHHH-------HHHHHHHHHHHHHhcCCCccChhHHHHhhh
Q 033230 34 DISVHKDALLAFCESARIF-------IHYLSATANDICKESKRQTINAEDVLKAIE 82 (124)
Q Consensus 34 ~~~ISkdA~~al~~~a~~F-------I~~lt~~A~~~a~~~kRKTI~~eDVl~AL~ 82 (124)
.+.|+.+....|.+.+..+ -.++...|...|.=+||.+|+++||..|..
T Consensus 201 ~V~i~~~~~~~l~~~~~~~gv~s~Ra~i~~~r~ArA~Aal~gr~~V~~~Dv~~a~~ 256 (589)
T TIGR02031 201 QVTISAEQVKELVLTAASLGISGHRADLFAVRAAKAHAALHGRTEVTEEDLKLAVE 256 (589)
T ss_pred CccCCHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHH
Confidence 5789999988877766543 224557788888899999999999999874
No 99
>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]
Probab=52.68 E-value=23 Score=29.99 Aligned_cols=61 Identities=16% Similarity=0.165 Sum_probs=43.6
Q ss_pred chhhHHHHHHHHHHH------HHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhhCCCcccHHHHHH
Q 033230 35 ISVHKDALLAFCESA------RIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFTEFVDPLRD 95 (124)
Q Consensus 35 ~~ISkdA~~al~~~a------~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~lgf~~~~~~l~~ 95 (124)
..++.++...+..-+ .-+...+...|-++|+.+++.+|+.+||..|-++.+..-+...++.
T Consensus 210 ~~~~~~vl~lia~~~a~~~GDAR~aidilr~A~eiAe~~~~~~v~~~~v~~a~~~~~~~~~~~~~~~ 276 (366)
T COG1474 210 GVIDDDVLKLIAALVAAESGDARKAIDILRRAGEIAEREGSRKVSEDHVREAQEEIERDVLEEVLKT 276 (366)
T ss_pred CCcCccHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHhhCCCCcCHHHHHHHHHHhhHHHHHHHHHc
Confidence 355566555554222 2344567788999999999999999999999877777666555443
No 100
>KOG0093 consensus GTPase Rab3, small G protein superfamily [Intracellular trafficking, secretion, and vesicular transport]
Probab=50.47 E-value=3.5 Score=32.03 Aligned_cols=73 Identities=12% Similarity=0.274 Sum_probs=45.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHH-----HHHHHHhcCCCccChhHHHHhhhhCCCcccHHHHHHHHHHHHhhhchheeee
Q 033230 39 KDALLAFCESARIFIHYLSAT-----ANDICKESKRQTINAEDVLKAIEEIDFTEFVDPLRDSLDGQLTFRNWIFIFC 111 (124)
Q Consensus 39 kdA~~al~~~a~~FI~~lt~~-----A~~~a~~~kRKTI~~eDVl~AL~~lgf~~~~~~l~~~l~~~~~~~~~~~~~~ 111 (124)
.++-.+++.-++..=.|--.. +-..|.-+..++|+.|.+..-.++|||+.|-...++-.+--..+..++-+.|
T Consensus 106 eeSf~svqdw~tqIktysw~naqvilvgnKCDmd~eRvis~e~g~~l~~~LGfefFEtSaK~NinVk~~Fe~lv~~Ic 183 (193)
T KOG0093|consen 106 EESFNSVQDWITQIKTYSWDNAQVILVGNKCDMDSERVISHERGRQLADQLGFEFFETSAKENINVKQVFERLVDIIC 183 (193)
T ss_pred HHHHHHHHHHHHHheeeeccCceEEEEecccCCccceeeeHHHHHHHHHHhChHHhhhcccccccHHHHHHHHHHHHH
Confidence 444555555554443331111 1234667888999999999999999998776666655544444555555544
No 101
>PF04552 Sigma54_DBD: Sigma-54, DNA binding domain; InterPro: IPR007634 This DNA-binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore, this region contains a putative helix-turn-helix motif. At the C terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins [].; PDB: 2AHQ_A 2O9L_A 2O8K_A.
Probab=50.37 E-value=24 Score=26.63 Aligned_cols=79 Identities=15% Similarity=0.214 Sum_probs=27.6
Q ss_pred cccccccchhHHHHHHhccccCCCC---------------CCcchhhHHHHH-HHHHHHHHHHHHHHHHHHHHHHhcCCC
Q 033230 7 VPEAEELPKTIVRRVVKDKLHNCSP---------------DTDISVHKDALL-AFCESARIFIHYLSATANDICKESKRQ 70 (124)
Q Consensus 7 ~~ed~~LP~A~I~RI~K~~Lp~~~~---------------d~~~~ISkdA~~-al~~~a~~FI~~lt~~A~~~a~~~kRK 70 (124)
..+++.+..+||.|+++..-=+++. +++..+|.++.. .|. .-+..+++.+
T Consensus 55 iA~~lgl~~STVSRav~~Ky~~t~~Gi~plk~fF~~~~~~~~~~~~S~~~ik~~i~--------------~lI~~Ed~~~ 120 (160)
T PF04552_consen 55 IADELGLHESTVSRAVKNKYIQTPRGIFPLKDFFSRSVSSGSGEEFSSEAIKARIK--------------ELIEEEDKKK 120 (160)
T ss_dssp ------------------------------S-----SS--SS-SS---TTH-HHHH--------------HHHTTS-TTS
T ss_pred HHHHhCCCHhHHHHHHcCceeecCCeeeeHHHhccccccCCCCcccHHHHHHHHHH--------------HHHHhcCCCC
Confidence 4578899999999999765432221 011123444332 222 2456677889
Q ss_pred ccChhHHHHhhhhCCCcccHHHHHHHHHHHHhh
Q 033230 71 TINAEDVLKAIEEIDFTEFVDPLRDSLDGQLTF 103 (124)
Q Consensus 71 TI~~eDVl~AL~~lgf~~~~~~l~~~l~~~~~~ 103 (124)
.+|-+.|...|+.-| +.--..-..+||+.
T Consensus 121 PlSD~~i~~~L~~~g----i~isRRTVaKYR~~ 149 (160)
T PF04552_consen 121 PLSDQEIAELLKEEG----IKISRRTVAKYREE 149 (160)
T ss_dssp ---HHHHHHHHTTTT----S---HHHHHHHHHH
T ss_pred CCCHHHHHHHHHHcC----CCccHHHHHHHHHH
Confidence 999999999999877 45667777888775
No 102
>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=50.12 E-value=22 Score=21.79 Aligned_cols=25 Identities=24% Similarity=0.522 Sum_probs=21.0
Q ss_pred ccChhHHHHhhhhCCCcccHHHHHH
Q 033230 71 TINAEDVLKAIEEIDFTEFVDPLRD 95 (124)
Q Consensus 71 TI~~eDVl~AL~~lgf~~~~~~l~~ 95 (124)
+=+++||..=|+.+||++|.+...+
T Consensus 3 ~w~~~~v~~WL~~~gl~~y~~~f~~ 27 (66)
T PF07647_consen 3 TWSPEDVAEWLKSLGLEQYADNFRE 27 (66)
T ss_dssp GHCHHHHHHHHHHTTCGGGHHHHHH
T ss_pred CCCHHHHHHHHHHCCcHHHHHHHHH
Confidence 3478999999999999999887764
No 103
>PRK13765 ATP-dependent protease Lon; Provisional
Probab=50.10 E-value=28 Score=31.75 Aligned_cols=48 Identities=25% Similarity=0.254 Sum_probs=38.1
Q ss_pred hhhHHHHHHHHHHHHHH-------------HHHHHHHHHHHHHhcCCCccChhHHHHhhhh
Q 033230 36 SVHKDALLAFCESARIF-------------IHYLSATANDICKESKRQTINAEDVLKAIEE 83 (124)
Q Consensus 36 ~ISkdA~~al~~~a~~F-------------I~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~ 83 (124)
.++++|...|.+-++.- +.-|-.+|..+|..++++.|+++||..|+..
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 57888887777765532 3337788999999999999999999999843
No 104
>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=49.39 E-value=36 Score=25.53 Aligned_cols=69 Identities=16% Similarity=0.212 Sum_probs=47.1
Q ss_pred HHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhhCCCcccHHHHHHHHH
Q 033230 19 RRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFTEFVDPLRDSLD 98 (124)
Q Consensus 19 ~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~lgf~~~~~~l~~~l~ 98 (124)
.|+.+.+. +.-|.|+-..-+....+.=+.-|.-.|...|+.+||-+|.+.|+=- -..+++.+.
T Consensus 2 e~lFR~aa-------~LdvdK~d~~r~~d~V~~Kl~DLl~va~~~Ak~ngRdvI~~~DLPI----------TkGlqesi~ 64 (138)
T PF09123_consen 2 ERLFRKAA-------GLDVDKNDAKRYSDFVEKKLYDLLLVAQENAKANGRDVIEPRDLPI----------TKGLQESIR 64 (138)
T ss_dssp HHHHHHHH-------S----HHHHHHHHHHHHHHHHHCCCCHHHHHHHTT-SEE-GGGS-------------HHHHHHHH
T ss_pred hHHHHHHh-------ccCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeeccccCCc----------cHHHHHHHH
Confidence 56777775 4667788888888888888888888999999999999999987532 245566666
Q ss_pred HHHhhh
Q 033230 99 GQLTFR 104 (124)
Q Consensus 99 ~~~~~~ 104 (124)
.|++..
T Consensus 65 ~Fr~ld 70 (138)
T PF09123_consen 65 EFRKLD 70 (138)
T ss_dssp HHHTTT
T ss_pred HHHHcc
Confidence 666553
No 105
>PRK02910 light-independent protochlorophyllide reductase subunit B; Provisional
Probab=49.27 E-value=37 Score=29.84 Aligned_cols=52 Identities=12% Similarity=0.165 Sum_probs=40.2
Q ss_pred CcchhhHHHHHHHHHHHHHHH-HHHHHHHHHHHHhcCCCccChhHHHHhhhhCC
Q 033230 33 TDISVHKDALLAFCESARIFI-HYLSATANDICKESKRQTINAEDVLKAIEEID 85 (124)
Q Consensus 33 ~~~~ISkdA~~al~~~a~~FI-~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~lg 85 (124)
+.+.++.||...|.+ .=-|+ .-+=..+-+.|++.|...|+.+.+..|-..+|
T Consensus 466 ~~~~w~~ea~~~l~~-~P~f~r~~~r~~~e~~a~~~g~~~it~~~~~~a~~~~~ 518 (519)
T PRK02910 466 SELVWTPEAEAELKK-IPFFVRGKVRRNTEKFARERGLPEITLEVLYDAKAHFG 518 (519)
T ss_pred CCCCCCHHHHHHHhh-CChhhHHHHHHHHHHHHHHcCCCeecHHHHHHHHHHhc
Confidence 367899999999965 33344 34456667788899999999999999977654
No 106
>PRK07914 hypothetical protein; Reviewed
Probab=49.20 E-value=42 Score=27.19 Aligned_cols=65 Identities=11% Similarity=0.196 Sum_probs=46.7
Q ss_pred chhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhh
Q 033230 14 PKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (124)
Q Consensus 14 P~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~ 83 (124)
+..-+.+.|++.+.. .+.+|+.+|...|.+.+..=...+..+-.+.+...| .+|+.+||...+..
T Consensus 129 ~~~~l~~wi~~~a~~----~g~~i~~~A~~~L~~~~g~dl~~l~~EleKL~~~~~-~~It~e~V~~~v~~ 193 (320)
T PRK07914 129 KAAERADFVRKEFRS----LRVKVDDDTVTALLDAVGSDLRELASACSQLVADTG-GAVDAAAVRRYHSG 193 (320)
T ss_pred CHHHHHHHHHHHHHH----cCCCCCHHHHHHHHHHHCccHHHHHHHHHHHhcCCC-CCcCHHHHHHHcCC
Confidence 455556666665543 267899999999999987666777777666665444 57999999887654
No 107
>PRK05574 holA DNA polymerase III subunit delta; Reviewed
Probab=48.55 E-value=63 Score=25.69 Aligned_cols=68 Identities=15% Similarity=0.182 Sum_probs=48.7
Q ss_pred ccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhh
Q 033230 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (124)
Q Consensus 12 ~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~ 83 (124)
.++...+.+.++..+.. .+..|+.+|...|.+.+..=...+..+-...+.-.+-+.|+.+||-..+..
T Consensus 145 ~~~~~~~~~~i~~~~~~----~g~~i~~~a~~~L~~~~~~d~~~l~~El~KL~l~~~~~~It~~~I~~~i~~ 212 (340)
T PRK05574 145 PPKEAELPQWIQQRLKQ----QGLQIDAAALQLLAERVEGNLLALAQELEKLALLYPDGKITLEDVEEAVPD 212 (340)
T ss_pred CCCHHHHHHHHHHHHHH----cCCCCCHHHHHHHHHHhCchHHHHHHHHHHHHhhcCCCCCCHHHHHHHHhh
Confidence 45666777777766653 257999999999998887766777777777776432223999998866544
No 108
>TIGR01242 26Sp45 26S proteasome subunit P45 family. Many proteins may score above the trusted cutoff because an internal
Probab=48.36 E-value=26 Score=28.89 Aligned_cols=31 Identities=19% Similarity=0.388 Sum_probs=26.6
Q ss_pred HHHHHHHHHHHHHhcCCCccChhHHHHhhhh
Q 033230 53 IHYLSATANDICKESKRQTINAEDVLKAIEE 83 (124)
Q Consensus 53 I~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~ 83 (124)
|..+..+|...|.+.++..|+.+|+..|++.
T Consensus 332 l~~l~~~A~~~a~~~~~~~i~~~d~~~a~~~ 362 (364)
T TIGR01242 332 LKAICTEAGMFAIREERDYVTMDDFIKAVEK 362 (364)
T ss_pred HHHHHHHHHHHHHHhCCCccCHHHHHHHHHH
Confidence 4466778888888999999999999999875
No 109
>smart00350 MCM minichromosome maintenance proteins.
Probab=48.11 E-value=49 Score=28.94 Aligned_cols=68 Identities=10% Similarity=0.124 Sum_probs=46.1
Q ss_pred ccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHH-------------------HHHHHHHHHHHHHhcCCCcc
Q 033230 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIF-------------------IHYLSATANDICKESKRQTI 72 (124)
Q Consensus 12 ~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~F-------------------I~~lt~~A~~~a~~~kRKTI 72 (124)
.++...+.+.+.-+=... .-.+|+++.+.|.+....- +..|-..|...|+-.+|.+|
T Consensus 417 ~~~~~~l~~yi~~ar~~~----~P~ls~~~~~~i~~~y~~~R~~~~~~~~~~~~~~t~R~l~sliRla~A~A~l~~r~~V 492 (509)
T smart00350 417 PISQEFLRKYIAYAREKI----KPKLSEEAAEKLVKAYVDLRKEDSQSEARSSIPITVRQLESIIRLSEAHAKMRLSDVV 492 (509)
T ss_pred cCCHHHHHHHHHHHHhcC----CCCCCHHHHHHHHHHHHHhcccccccccccccCcCHHHHHHHHHHHHHHHHHcCCCcc
Confidence 456666666654431100 1257899988886654442 24566778888999999999
Q ss_pred ChhHHHHhhhh
Q 033230 73 NAEDVLKAIEE 83 (124)
Q Consensus 73 ~~eDVl~AL~~ 83 (124)
+++||..|++-
T Consensus 493 ~~~Dv~~ai~l 503 (509)
T smart00350 493 EEADVEEAIRL 503 (509)
T ss_pred CHHHHHHHHHH
Confidence 99999999864
No 110
>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional
Probab=47.98 E-value=26 Score=30.52 Aligned_cols=32 Identities=22% Similarity=0.317 Sum_probs=27.9
Q ss_pred HHHHHHHHHHHHHhcCCCccChhHHHHhhhhC
Q 033230 53 IHYLSATANDICKESKRQTINAEDVLKAIEEI 84 (124)
Q Consensus 53 I~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~l 84 (124)
|..|..+|-..|.+++|..|+.+|+..|++..
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 55677889999999999999999999999874
No 111
>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=46.94 E-value=36 Score=21.40 Aligned_cols=30 Identities=10% Similarity=0.371 Sum_probs=24.4
Q ss_pred CCCccChhHHHHhhhhCCCcccHHHHHHHH
Q 033230 68 KRQTINAEDVLKAIEEIDFTEFVDPLRDSL 97 (124)
Q Consensus 68 kRKTI~~eDVl~AL~~lgf~~~~~~l~~~l 97 (124)
....-+..+++.||+++|..+.++.++..|
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 345667889999999999999988887764
No 112
>COG5251 TAF40 Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=46.50 E-value=25 Score=27.54 Aligned_cols=61 Identities=16% Similarity=0.134 Sum_probs=48.1
Q ss_pred ccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCc---cChhHHHHhh
Q 033230 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQT---INAEDVLKAI 81 (124)
Q Consensus 12 ~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKT---I~~eDVl~AL 81 (124)
.||++.|.+++..++. -.||...+.+|+-.+.+|+..|--.|..+-. ++.| +.+.|+-.|.
T Consensus 115 ~lnKt~VKKlastV~n-------QtVspNi~I~l~g~~KVfvGEiIElA~~Vq~--~w~~sgpl~p~h~reay 178 (199)
T COG5251 115 SLNKTQVKKLASTVAN-------QTVSPNIRIFLQGVGKVFVGEIIELAMIVQN--KWLTSGPLIPFHKREAY 178 (199)
T ss_pred CCCHHHHHHHHHHHhc-------cccCCCeeeeeechhHHHHHHHHHHHHHHHH--HhcccCCCChHHHHHHH
Confidence 6999999999999984 4577778888999999999998887766543 3333 7788887775
No 113
>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=46.13 E-value=76 Score=23.88 Aligned_cols=46 Identities=11% Similarity=0.333 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhhCCCc-ccHHHHHHHHHHH
Q 033230 48 SARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFT-EFVDPLRDSLDGQ 100 (124)
Q Consensus 48 ~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~lgf~-~~~~~l~~~l~~~ 100 (124)
++...+.||-..|. |.-++++++..-|+.+||+ +..+.+......+
T Consensus 43 ~~va~l~fiL~~A~-------k~n~~~~~l~~eL~~lglp~e~~~~l~~~~~~~ 89 (174)
T cd04752 43 ASIAVLSFILSSAA-------KYNVDGESLSSELQQLGLPKEHATSLCRSYEEK 89 (174)
T ss_pred HHHHHHHHHHHHHH-------HcCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHH
Confidence 55666777766554 3449999999999999997 4455554444444
No 114
>COG5248 TAF19 Transcription initiation factor TFIID, subunit TAF13 [Transcription]
Probab=46.08 E-value=71 Score=23.36 Aligned_cols=47 Identities=19% Similarity=0.263 Sum_probs=39.3
Q ss_pred chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhh
Q 033230 35 ISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (124)
Q Consensus 35 ~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~ 83 (124)
+.=..|..++|.+....+++.+-..|..+|. .|-.+..||..-||++
T Consensus 26 v~P~~dt~~~L~e~V~dY~~~~ctna~~~Aq--~rnK~k~eDfkfaLr~ 72 (126)
T COG5248 26 VAPRYDTAEALHEYVLDYMSILCTNAHNMAQ--VRNKTKTEDFKFALRR 72 (126)
T ss_pred CCcchhHHHHHHHHHHHHHHHHHHHHHHHHH--hcccchHHHHHHHHhh
Confidence 3446788999999999999999999999987 4556778999999865
No 115
>COG1500 Predicted exosome subunit [Translation, ribosomal structure and biogenesis]
Probab=45.82 E-value=72 Score=25.92 Aligned_cols=85 Identities=18% Similarity=0.196 Sum_probs=59.6
Q ss_pred hHHHHHHhccccCCCCCCcchhhHHHHHHHHHHH-HHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhhCCCc-ccHHHH
Q 033230 16 TIVRRVVKDKLHNCSPDTDISVHKDALLAFCESA-RIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFT-EFVDPL 93 (124)
Q Consensus 16 A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a-~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~lgf~-~~~~~l 93 (124)
+-+..|+++.|.. |...+|.+-+..+++.- ...|++|++.|.+ ...+....|.-|-.||++++|. ++..+.
T Consensus 70 td~~eI~~eIl~k----GeiQlTaeqR~~m~e~k~rqIi~~IsRn~Id---P~t~~P~Pp~rIe~Ameeakv~id~~K~a 142 (234)
T COG1500 70 TDPDEIAEEILKK----GEIQLTAEQRREMLEEKKRQIINIISRNAID---PQTKAPHPPARIEKAMEEAKVHIDPFKSA 142 (234)
T ss_pred CCHHHHHHHHHhc----CceeccHHHHHHHHHHHHHHHHHHHHHhccC---CCCCCCCCHHHHHHHHHhcCcccCCCCCH
Confidence 3467777777764 67899998877766654 4667788886655 5667789999999999999985 443333
Q ss_pred -HHHHHHHHhhhchh
Q 033230 94 -RDSLDGQLTFRNWI 107 (124)
Q Consensus 94 -~~~l~~~~~~~~~~ 107 (124)
+...+.-+.++-.+
T Consensus 143 e~Qv~evlK~l~~i~ 157 (234)
T COG1500 143 EEQVQEVLKALRPII 157 (234)
T ss_pred HHHHHHHHHHHhhcC
Confidence 44445556666554
No 116
>PRK03992 proteasome-activating nucleotidase; Provisional
Probab=45.32 E-value=31 Score=29.05 Aligned_cols=35 Identities=26% Similarity=0.286 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHHHHhcCCCccChhHHHHhhhhCCC
Q 033230 52 FIHYLSATANDICKESKRQTINAEDVLKAIEEIDF 86 (124)
Q Consensus 52 FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~lgf 86 (124)
=|.-+..+|...|.++++..|+.+|+..|++..-.
T Consensus 340 dl~~l~~eA~~~a~~~~~~~i~~~d~~~A~~~~~~ 374 (389)
T PRK03992 340 DLKAICTEAGMFAIRDDRTEVTMEDFLKAIEKVMG 374 (389)
T ss_pred HHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHhc
Confidence 34456677888888899999999999999987643
No 117
>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=44.68 E-value=28 Score=21.23 Aligned_cols=22 Identities=14% Similarity=0.430 Sum_probs=19.5
Q ss_pred ChhHHHHhhhhCCCcccHHHHH
Q 033230 73 NAEDVLKAIEEIDFTEFVDPLR 94 (124)
Q Consensus 73 ~~eDVl~AL~~lgf~~~~~~l~ 94 (124)
++++|..=|+.+|+++|.+...
T Consensus 4 ~~~~V~~WL~~~~l~~y~~~F~ 25 (64)
T PF00536_consen 4 SVEDVSEWLKSLGLEQYAENFE 25 (64)
T ss_dssp SHHHHHHHHHHTTGGGGHHHHH
T ss_pred CHHHHHHHHHHCCCHHHHHHHH
Confidence 6789999999999999998773
No 118
>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=44.64 E-value=42 Score=29.37 Aligned_cols=52 Identities=12% Similarity=0.115 Sum_probs=39.8
Q ss_pred cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhhCC
Q 033230 34 DISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEID 85 (124)
Q Consensus 34 ~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~lg 85 (124)
.+.+|.||...|.+.=--.=.-+=..+-+.|++.|...|+.+.+..|-+.+|
T Consensus 460 ~~~w~~ea~~~l~~~P~f~r~~~r~~~e~~a~~~g~~~it~~~~~~a~~~~~ 511 (511)
T TIGR01278 460 ELGWTAEAEAELKKVPFFVRGKVRRNTENFARERGYSVITLEVIYAAKEHFG 511 (511)
T ss_pred CCCcCHHHHHHHhhCChhhhHHHHHHHHHHHHHcCCCEEcHHHHHHHHHhcC
Confidence 5789999999996533222244556677788999999999999999977654
No 119
>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=44.54 E-value=20 Score=21.19 Aligned_cols=24 Identities=25% Similarity=0.566 Sum_probs=20.2
Q ss_pred ChhHHHHhhhhCCCcccHHHHHHH
Q 033230 73 NAEDVLKAIEEIDFTEFVDPLRDS 96 (124)
Q Consensus 73 ~~eDVl~AL~~lgf~~~~~~l~~~ 96 (124)
++++|..-|+.+|+++|.+..++.
T Consensus 3 ~~~~V~~wL~~~~~~~y~~~f~~~ 26 (63)
T cd00166 3 SPEDVAEWLESLGLGQYADNFREN 26 (63)
T ss_pred CHHHHHHHHHHcChHHHHHHHHHc
Confidence 678999999999999888887654
No 120
>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=44.51 E-value=48 Score=19.87 Aligned_cols=33 Identities=21% Similarity=0.229 Sum_probs=26.8
Q ss_pred ccccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHH
Q 033230 10 AEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARI 51 (124)
Q Consensus 10 d~~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~ 51 (124)
...+..+||.|++... -+||.+.++-+.+++.+
T Consensus 8 ~agvS~~TVSr~ln~~---------~~vs~~tr~rI~~~a~~ 40 (46)
T PF00356_consen 8 EAGVSKSTVSRVLNGP---------PRVSEETRERILEAAEE 40 (46)
T ss_dssp HHTSSHHHHHHHHTTC---------SSSTHHHHHHHHHHHHH
T ss_pred HHCcCHHHHHHHHhCC---------CCCCHHHHHHHHHHHHH
Confidence 4467889999999875 36899999999987765
No 121
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=42.72 E-value=71 Score=25.06 Aligned_cols=46 Identities=9% Similarity=0.073 Sum_probs=33.7
Q ss_pred ccccccccc----ccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHH
Q 033230 3 TEKVVPEAE----ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSA 58 (124)
Q Consensus 3 ~ek~~~ed~----~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~ 58 (124)
..++++.|+ ..-++||.|.+... -+||.+.++-+.+++.+- .|.-.
T Consensus 4 ~~~~Ti~dIA~~agVS~~TVSr~Ln~~---------~~vs~~tr~~V~~~a~el-gY~p~ 53 (342)
T PRK10014 4 AKKITIHDVALAAGVSVSTVSLVLSGK---------GRISTATGERVNQAIEEL-GFVRN 53 (342)
T ss_pred CCCCcHHHHHHHhCCCHHHHHHHHCCC---------CCCCHHHHHHHHHHHHHh-CCCcC
Confidence 345555554 68889999998643 359999999999998886 35443
No 122
>PTZ00373 60S Acidic ribosomal protein P2; Provisional
Probab=41.67 E-value=40 Score=24.26 Aligned_cols=28 Identities=11% Similarity=0.215 Sum_probs=24.4
Q ss_pred HHHHHHhcCCCccChhHHHHhhhhCCCc
Q 033230 60 ANDICKESKRQTINAEDVLKAIEEIDFT 87 (124)
Q Consensus 60 A~~~a~~~kRKTI~~eDVl~AL~~lgf~ 87 (124)
|.-.|.-.|+.++|.+||.+.|+..|.+
T Consensus 8 AYlL~~lgG~~~pTaddI~kIL~AaGve 35 (112)
T PTZ00373 8 AYLMCVLGGNENPTKKEVKNVLSAVNAD 35 (112)
T ss_pred HHHHHHHcCCCCCCHHHHHHHHHHcCCC
Confidence 5567778889999999999999999974
No 123
>COG2445 Uncharacterized conserved protein [Function unknown]
Probab=41.43 E-value=1.4e+02 Score=21.97 Aligned_cols=69 Identities=17% Similarity=0.168 Sum_probs=47.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-CCccChhHHHHhhhhCCCcccHHHHHHHHHHHHhhhchhee
Q 033230 39 KDALLAFCESARIFIHYLSATANDICKESK-RQTINAEDVLKAIEEIDFTEFVDPLRDSLDGQLTFRNWIFI 109 (124)
Q Consensus 39 kdA~~al~~~a~~FI~~lt~~A~~~a~~~k-RKTI~~eDVl~AL~~lgf~~~~~~l~~~l~~~~~~~~~~~~ 109 (124)
+--+.++.++...-|.-+.+-++..+...| |..=+..|++..|.+.|.=+ +...+.|...--+||++|-
T Consensus 31 ~~~~~av~~~lq~~ies~~Di~~~li~~~~~~~p~~y~d~~~~L~~~gvi~--~e~~e~L~~~~gfRN~lVH 100 (138)
T COG2445 31 KHERYAVERILQVAIESLIDIGNMLISKFGLRDPGTYDDCIDILVEEGVIP--EEEAEELKKMVGFRNILVH 100 (138)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHcCCCC--HHHHHHHHHHHHHHHHHHH
Confidence 334555555555556666666666666655 58889999999999988521 5555667777888888863
No 124
>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=40.93 E-value=17 Score=21.66 Aligned_cols=14 Identities=29% Similarity=0.643 Sum_probs=11.7
Q ss_pred hHHHHhhhhCCCcc
Q 033230 75 EDVLKAIEEIDFTE 88 (124)
Q Consensus 75 eDVl~AL~~lgf~~ 88 (124)
+|++.||..|||..
T Consensus 4 ~d~~~AL~~LGy~~ 17 (47)
T PF07499_consen 4 EDALEALISLGYSK 17 (47)
T ss_dssp HHHHHHHHHTTS-H
T ss_pred HHHHHHHHHcCCCH
Confidence 68999999999973
No 125
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=40.54 E-value=79 Score=27.61 Aligned_cols=89 Identities=12% Similarity=0.179 Sum_probs=58.9
Q ss_pred cccccccchhHHHHHHhccccCCCC----------------CCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q 033230 7 VPEAEELPKTIVRRVVKDKLHNCSP----------------DTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQ 70 (124)
Q Consensus 7 ~~ed~~LP~A~I~RI~K~~Lp~~~~----------------d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRK 70 (124)
..+.+.|-.+||.|+++..-=+++- +| --+|.++....- ..-+..+++++
T Consensus 349 vAe~lglheSTVSRav~~Kyv~tp~Gi~~lk~FFs~~~~~~~g-~~~S~~~Ik~~I-------------k~lI~~Ed~~~ 414 (455)
T PRK05932 349 IAEELGMHESTISRATTNKYMATPRGIFELKYFFSSAVSTDGG-GEASSTAIRALI-------------KKLIAAENPKK 414 (455)
T ss_pred HHHHhCCCccchhhhhcCceeecCCceEEHHHhcccccCCCCC-ccccHHHHHHHH-------------HHHHHhcCCCC
Confidence 4578889999999999765433321 11 113444432211 23456788899
Q ss_pred ccChhHHHHhhhhCCCcccHHHHHHHHHHHHhhhchheeeeccCCchhhhc
Q 033230 71 TINAEDVLKAIEEIDFTEFVDPLRDSLDGQLTFRNWIFIFCCNFPAFYFKR 121 (124)
Q Consensus 71 TI~~eDVl~AL~~lgf~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~ 121 (124)
.+|-+.|...|++-|+. ....-..+||+. .|.|.-+-+|
T Consensus 415 PlSD~~I~~~L~~~Gi~----IaRRTVaKYRe~--------L~Ip~s~~RK 453 (455)
T PRK05932 415 PLSDSKIAELLKEQGID----VARRTVAKYREA--------LNIPSSSQRK 453 (455)
T ss_pred CCCHHHHHHHHHHcCCC----eehHHHHHHHHH--------cCCCChHhcc
Confidence 99999999999998884 557777888875 4566555443
No 126
>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=40.05 E-value=18 Score=21.55 Aligned_cols=18 Identities=33% Similarity=0.527 Sum_probs=13.7
Q ss_pred cccccchhHHHHHHhccc
Q 033230 9 EAEELPKTIVRRVVKDKL 26 (124)
Q Consensus 9 ed~~LP~A~I~RI~K~~L 26 (124)
+...+|+++++|+++.-.
T Consensus 26 ~~~gl~~stv~r~L~tL~ 43 (52)
T PF09339_consen 26 RALGLPKSTVHRLLQTLV 43 (52)
T ss_dssp HHHTS-HHHHHHHHHHHH
T ss_pred HHHCcCHHHHHHHHHHHH
Confidence 456899999999998653
No 127
>TIGR00291 RNA_SBDS rRNA metabolism protein, SBDS family. This protein family, possibly universal in both archaea and eukaryotes, appears to be involved in (ribosomal) RNA metabolism. Mutations in the human ortholog are associated with Shwachman-Bodian-Diamond syndrome.
Probab=39.58 E-value=1.3e+02 Score=24.22 Aligned_cols=88 Identities=16% Similarity=0.179 Sum_probs=62.3
Q ss_pred cchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHH-HHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhhCCC--ccc
Q 033230 13 LPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCES-ARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDF--TEF 89 (124)
Q Consensus 13 LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~-a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~lgf--~~~ 89 (124)
+..+-+..+++..|.. |...+|.+=+..+.+. =.+.+.+|+..+.+ -+.++..++.-|-.||++++| +-+
T Consensus 67 FGT~d~~ei~~~IL~k----GeiQls~~eR~~~~e~k~~~Ii~~Ia~~~Vn---P~T~~P~p~~rIE~Am~e~~~~idp~ 139 (231)
T TIGR00291 67 FGTTDVDEVAEKIILK----GEIQLTAEQRREMLEKKRNQIINIISRNTIN---PQTKKPHPPTRIEKALEEAKVHIDIF 139 (231)
T ss_pred hCCCCHHHHHHHHHhc----CCccCCHHHHHHHHHHHHHHHHHHHHHhCcC---CCCCCCCCHHHHHHHHHhcCcCcCCC
Confidence 4555566777777754 6788888877666543 34555555543332 456777889999999999997 467
Q ss_pred HHHHHHHHHHHHhhhchh
Q 033230 90 VDPLRDSLDGQLTFRNWI 107 (124)
Q Consensus 90 ~~~l~~~l~~~~~~~~~~ 107 (124)
.+.=+..++--+.++..|
T Consensus 140 k~ak~Qa~~vik~L~~ii 157 (231)
T TIGR00291 140 KSVEEQVLEIVKALKQII 157 (231)
T ss_pred CCHHHHHHHHHHHHhhhC
Confidence 777778888888888766
No 128
>PRK06585 holA DNA polymerase III subunit delta; Reviewed
Probab=39.42 E-value=83 Score=25.42 Aligned_cols=66 Identities=12% Similarity=0.109 Sum_probs=44.9
Q ss_pred hhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHh-cCCCccChhHHHHhhhhC
Q 033230 15 KTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKE-SKRQTINAEDVLKAIEEI 84 (124)
Q Consensus 15 ~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~-~kRKTI~~eDVl~AL~~l 84 (124)
...+.+.+++.+.. .+.+|+.+|...|.+.+.-=...+..+-.+.+.- .+.++|+.+||...+...
T Consensus 144 ~~~l~~~i~~~~~~----~g~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~It~edV~~lv~~~ 210 (343)
T PRK06585 144 ERDLARLIDDELAE----AGLRITPDARALLVALLGGDRLASRNEIEKLALYAHGKGEITLDDVRAVVGDA 210 (343)
T ss_pred HHHHHHHHHHHHHH----CCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHhCCc
Confidence 34444445444432 2689999999999998886555666666666664 445789999997775443
No 129
>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=39.03 E-value=13 Score=22.86 Aligned_cols=58 Identities=17% Similarity=0.284 Sum_probs=27.4
Q ss_pred chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCc---cChhHHHHhhhhCCCccc-HHHHHHH
Q 033230 35 ISVHKDALLAFCESARIFIHYLSATANDICKESKRQT---INAEDVLKAIEEIDFTEF-VDPLRDS 96 (124)
Q Consensus 35 ~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKT---I~~eDVl~AL~~lgf~~~-~~~l~~~ 96 (124)
.+|.++...++.+++. .+..++.+ .-..+=.|. =.+...+..|.++|+-++ .|.+...
T Consensus 2 F~ie~~t~~ai~~~~~-~L~~is~E---Ri~~El~kil~~~~~~~~~~~l~~~gll~~ifP~l~~a 63 (64)
T PF12627_consen 2 FKIEPETEEAIKENAE-LLSKISKE---RIREELEKILSSPNPSRAFKLLDELGLLEYIFPELDAA 63 (64)
T ss_dssp -EE-HHHHHHHHHHGG-GGGGS-HH---HHHHHHHHHHTSTTHHHHHHHHHHTTCHHHHSTTHHT-
T ss_pred CccCHHHHHHHHHHHH-HHhcCCHH---HHHHHHHHHHcCCCHHHHHHHHHHcCCHHHHCcccccc
Confidence 4566666666666555 33333321 111111111 145667778888886544 4665543
No 130
>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional
Probab=38.86 E-value=45 Score=28.49 Aligned_cols=32 Identities=19% Similarity=0.172 Sum_probs=27.8
Q ss_pred HHHHHHHHHHHHHhcCCCccChhHHHHhhhhC
Q 033230 53 IHYLSATANDICKESKRQTINAEDVLKAIEEI 84 (124)
Q Consensus 53 I~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~l 84 (124)
|..|..+|...|.+++|..|+.+|+..|++..
T Consensus 355 I~~l~~eA~~~A~r~~~~~i~~~df~~A~~~v 386 (398)
T PTZ00454 355 IAAICQEAGMQAVRKNRYVILPKDFEKGYKTV 386 (398)
T ss_pred HHHHHHHHHHHHHHcCCCccCHHHHHHHHHHH
Confidence 56677888888999999999999999998764
No 131
>cd08779 Death_PIDD Death Domain of p53-induced protein with a death domain. Death domain (DD) found in PIDD (p53-induced protein with a death domain) and similar proteins. PIDD is a component of the PIDDosome complex, which is an oligomeric caspase-activating complex involved in caspase-2 activation and plays a role in mediating stress-induced apoptosis. The PIDDosome complex is composed of three components, PIDD, RAIDD and caspase-2, which interact through their DDs and DD-like domains. The DD of PIDD interacts with the DD of RAIDD, which also contains a Caspase Activation and Recruitment Domain (CARD) that interacts with the caspase-2 CARD. Autoproteolysis of PIDD determines the downstream signaling event, between pro-survival NF-kB or pro-death caspase-2 activation. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members
Probab=38.84 E-value=1.1e+02 Score=20.48 Aligned_cols=35 Identities=14% Similarity=0.211 Sum_probs=26.1
Q ss_pred HHHHhcCCCccChhHHHHhhhhCCCcccHHHHHHH
Q 033230 62 DICKESKRQTINAEDVLKAIEEIDFTEFVDPLRDS 96 (124)
Q Consensus 62 ~~a~~~kRKTI~~eDVl~AL~~lgf~~~~~~l~~~ 96 (124)
.....++...=+.+.+..||...|..+..+.+++.
T Consensus 51 ~W~~~~~~~~atv~~L~~AL~~~gr~dlae~l~~~ 85 (86)
T cd08779 51 SWAQRQAGDPDAVGKLVTALEESGRQDLADEVRAV 85 (86)
T ss_pred HHHHhcCCCchHHHHHHHHHHHcCHHHHHHHHHhh
Confidence 34455544444578899999999999999888764
No 132
>CHL00076 chlB photochlorophyllide reductase subunit B
Probab=38.60 E-value=64 Score=28.44 Aligned_cols=52 Identities=12% Similarity=0.167 Sum_probs=40.7
Q ss_pred cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhhCC
Q 033230 34 DISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEID 85 (124)
Q Consensus 34 ~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~lg 85 (124)
++.+|.||...|.+.=--.=.-+=..+-+.|+++|...||.+.+..|=.++|
T Consensus 461 ~~~w~~ea~~~l~~iP~f~r~~~r~~~e~~a~~~g~~~it~~~~~~a~~~~~ 512 (513)
T CHL00076 461 DLIWSPESQLELSKIPGFVRGKVKRNTEKFARQNGITNITVEVMYAAKEALS 512 (513)
T ss_pred CCCCCHHHHHHHHhCCHHhHHHHHHHHHHHHHHcCCCeEcHHHHHHHHHhhC
Confidence 5789999999999872222244456677788899999999999999977765
No 133
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=36.85 E-value=90 Score=24.65 Aligned_cols=38 Identities=16% Similarity=0.242 Sum_probs=29.5
Q ss_pred cccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHH
Q 033230 11 EELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSA 58 (124)
Q Consensus 11 ~~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~ 58 (124)
...-++||.|++... -+||.+.++-+.+++.+ +.|.-.
T Consensus 11 aGVS~~TVSrvLn~~---------~~Vs~~tr~rV~~~a~e-lgY~pn 48 (343)
T PRK10727 11 AGVSVATVSRVINNS---------PKASEASRLAVHSAMES-LSYHPN 48 (343)
T ss_pred hCCCHHHHHHHhCCC---------CCCCHHHHHHHHHHHHH-HCCCCC
Confidence 367789999999653 35999999999999998 455443
No 134
>smart00454 SAM Sterile alpha motif. Widespread domain in signalling and nuclear proteins. In EPH-related tyrosine kinases, appears to mediate cell-cell initiated signal transduction via the binding of SH2-containing proteins to a conserved tyrosine that is phosphorylated. In many cases mediates homodimerisation.
Probab=36.78 E-value=30 Score=20.55 Aligned_cols=26 Identities=23% Similarity=0.437 Sum_probs=20.7
Q ss_pred ccChhHHHHhhhhCCCcccHHHHHHH
Q 033230 71 TINAEDVLKAIEEIDFTEFVDPLRDS 96 (124)
Q Consensus 71 TI~~eDVl~AL~~lgf~~~~~~l~~~ 96 (124)
.-+.++|..-|+.+|+++|.+...+.
T Consensus 3 ~w~~~~v~~wL~~~g~~~y~~~f~~~ 28 (68)
T smart00454 3 QWSPESVADWLESIGLEQYADNFRKN 28 (68)
T ss_pred CCCHHHHHHHHHHCChHHHHHHHHHC
Confidence 34678899999999999888877654
No 135
>COG1724 Predicted RNA binding protein (dsRBD-like fold), HicA family [General function prediction only]
Probab=36.53 E-value=24 Score=23.30 Aligned_cols=17 Identities=35% Similarity=0.630 Sum_probs=15.2
Q ss_pred ccChhHHHHhhhhCCCc
Q 033230 71 TINAEDVLKAIEEIDFT 87 (124)
Q Consensus 71 TI~~eDVl~AL~~lgf~ 87 (124)
.+++.+|+++|+.+||.
T Consensus 6 ~~~~ke~ik~Le~~Gf~ 22 (66)
T COG1724 6 RMKAKEVIKALEKDGFQ 22 (66)
T ss_pred cCCHHHHHHHHHhCCcE
Confidence 47899999999999995
No 136
>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=36.41 E-value=62 Score=25.83 Aligned_cols=75 Identities=15% Similarity=0.098 Sum_probs=35.4
Q ss_pred ccccccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC------ccChhHHHHhh
Q 033230 8 PEAEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQ------TINAEDVLKAI 81 (124)
Q Consensus 8 ~ed~~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRK------TI~~eDVl~AL 81 (124)
.++..|....+.+-|....... |...+..|....|.-|+.+.+..|-..+..+|.+-..- +....||-..|
T Consensus 39 ~~~~fL~~~~L~~~i~~i~~~~---g~~~~~~d~l~llS~A~e~rLr~lie~~~~~s~hR~~~~~~~~~~~~~sdv~~ql 115 (264)
T PF05236_consen 39 KEEPFLNPSPLQKRIQKIAKKH---GLKSVDEDVLELLSLATEERLRNLIEKAIVLSRHRRDSSKSDPRYEIRSDVRKQL 115 (264)
T ss_dssp -----S-HHHHHHHHHHHHHCT---T--EE-TCHHHHHHHHHHHHHHHHHHHHH--------------------------
T ss_pred ccccccCHHHHHHHHHHHHHHc---CCcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccCCCcccccchHHHHHH
Confidence 3455677777777777776532 34679999999999999999999999999988763211 22355666666
Q ss_pred hhCC
Q 033230 82 EEID 85 (124)
Q Consensus 82 ~~lg 85 (124)
..|.
T Consensus 116 r~l~ 119 (264)
T PF05236_consen 116 RFLE 119 (264)
T ss_dssp ----
T ss_pred HHHH
Confidence 5554
No 137
>PF01934 DUF86: Protein of unknown function DUF86; InterPro: IPR008201 This entry describes prokaryotic proteins of unknown function.; PDB: 1YLM_A.
Probab=36.21 E-value=1.4e+02 Score=20.25 Aligned_cols=71 Identities=14% Similarity=0.141 Sum_probs=47.1
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhhCCCcccHHHHHHHHHHHHhhhchhee
Q 033230 36 SVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFTEFVDPLRDSLDGQLTFRNWIFI 109 (124)
Q Consensus 36 ~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~lgf~~~~~~l~~~l~~~~~~~~~~~~ 109 (124)
.=+.....++.+....-+..+..-+..++...|....... ++..|.+-|+-+ ......+.....+||.++-
T Consensus 21 ~~d~~~~~av~~~l~~~~e~~~di~~~i~~~~~~~~p~~~-~~~~L~~~~ii~--~~~~~~l~~~~g~RN~lvH 91 (119)
T PF01934_consen 21 LSDRMLQDAVERNLQLIIEAIIDIAKHIISEEGLGKPGSY-IFEILAEHGIIS--EEPAEPLRKMVGFRNRLVH 91 (119)
T ss_dssp T-SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----SSH-HHHHHHHTTSS---HHHHHHHHHHHTTHHHHHT
T ss_pred hcCHHHHHHHHHHHHHHHHHHhhhHHHHHHHhCCCCCccH-HHHHHHHcCCcc--chhHHHHHHHHHHHHHHcc
Confidence 3355666666666666666777777777777777776666 999999998643 4456777788888888763
No 138
>PLN00138 large subunit ribosomal protein LP2; Provisional
Probab=36.16 E-value=56 Score=23.47 Aligned_cols=47 Identities=15% Similarity=0.170 Sum_probs=33.9
Q ss_pred HHHHHHhcCCCccChhHHHHhhhhCCCc---ccHHHHHHHHHHHHhhhchh
Q 033230 60 ANDICKESKRQTINAEDVLKAIEEIDFT---EFVDPLRDSLDGQLTFRNWI 107 (124)
Q Consensus 60 A~~~a~~~kRKTI~~eDVl~AL~~lgf~---~~~~~l~~~l~~~~~~~~~~ 107 (124)
|.-.|.-.|..++|.+||.+.|+..|.+ +....+-..|+. +.+..+|
T Consensus 6 Ayll~~l~g~~~pta~dI~~IL~AaGvevd~~~~~~f~~~L~g-K~i~eLI 55 (113)
T PLN00138 6 AYLLAVLGGNTCPSAEDLKDILGSVGADADDDRIELLLSEVKG-KDITELI 55 (113)
T ss_pred HHHHHHhcCCCCCCHHHHHHHHHHcCCcccHHHHHHHHHHHcC-CCHHHHH
Confidence 5667888889999999999999999974 344444555544 5555555
No 139
>PF11625 DUF3253: Protein of unknown function (DUF3253); InterPro: IPR021660 This bacterial family of proteins has no known function. ; PDB: 2NS0_A.
Probab=35.94 E-value=1.1e+02 Score=20.98 Aligned_cols=36 Identities=19% Similarity=0.370 Sum_probs=25.0
Q ss_pred HHhcCCCccChhHHHHhhhhCCCcccHHHHHHHHHH
Q 033230 64 CKESKRQTINAEDVLKAIEEIDFTEFVDPLRDSLDG 99 (124)
Q Consensus 64 a~~~kRKTI~~eDVl~AL~~lgf~~~~~~l~~~l~~ 99 (124)
+.+..-|||-|.||..||..-++-++.+++.+.-..
T Consensus 17 ~~R~~~ktiCPSevARal~~~~WR~lm~~vR~~A~~ 52 (83)
T PF11625_consen 17 AARGPGKTICPSEVARALGPDDWRDLMPPVRAAARR 52 (83)
T ss_dssp HHS-TT--B-HHHHHHHH-TTS-GGGHHHHHHHHHH
T ss_pred HhcCCCCccCHHHHHHHHCchhhHHHHHHHHHHHHH
Confidence 345667999999999999888899999999887665
No 140
>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=35.69 E-value=58 Score=23.16 Aligned_cols=47 Identities=17% Similarity=0.215 Sum_probs=31.3
Q ss_pred HHHHHHhcCCCccChhHHHHhhhhCCCc--c-cHHHHHHHHHHHHhhhchh
Q 033230 60 ANDICKESKRQTINAEDVLKAIEEIDFT--E-FVDPLRDSLDGQLTFRNWI 107 (124)
Q Consensus 60 A~~~a~~~kRKTI~~eDVl~AL~~lgf~--~-~~~~l~~~l~~~~~~~~~~ 107 (124)
|.-.|.-.|+.+||.+||.+.|+..|.+ . ....+-..|+. +.+..+|
T Consensus 6 AylL~~l~g~~~pTa~dI~~IL~AaGveVe~~~~~lf~~~L~G-Kdi~eLI 55 (109)
T cd05833 6 AYLLAVLGGNASPSAADVKKILGSVGVEVDDEKLNKVISELEG-KDVEELI 55 (109)
T ss_pred HHHHHHHcCCCCCCHHHHHHHHHHcCCCccHHHHHHHHHHHcC-CCHHHHH
Confidence 4566777888899999999999999964 3 33333444433 4444443
No 141
>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA.
Probab=35.65 E-value=1.2e+02 Score=27.78 Aligned_cols=36 Identities=17% Similarity=0.053 Sum_probs=28.0
Q ss_pred chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhh
Q 033230 35 ISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIE 82 (124)
Q Consensus 35 ~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~ 82 (124)
...|..++..|.. |...|...|...|+.+|++.||-
T Consensus 76 ~~~S~~lk~vL~~------------A~~~A~~~g~~~I~teHLLLALl 111 (731)
T TIGR02639 76 PEQTVGVQRVLQR------------ALLHVKSAGKKEIGIGDILVALF 111 (731)
T ss_pred CCcCHHHHHHHHH------------HHHHHHHcCCCccCHHHHHHHHh
Confidence 4578888777774 45567777899999999998864
No 142
>PHA03328 nuclear egress lamina protein UL31; Provisional
Probab=35.24 E-value=55 Score=27.68 Aligned_cols=78 Identities=14% Similarity=0.210 Sum_probs=46.7
Q ss_pred cccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhhCCCcccH
Q 033230 11 EELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFTEFV 90 (124)
Q Consensus 11 ~~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~lgf~~~~ 90 (124)
+-||-.-|.+|+-. +| +.+|+-|... +.||..+...+--...++..-||+++||..++.+|+|++
T Consensus 232 lHL~~~~L~~Ll~n-~~------gY~i~adv~~------~~fvL~v~~~~~~~~~~~~~~~V~~~dIy~k~~dL~f~d-- 296 (316)
T PHA03328 232 LHLHYRLIDRLLTA-CP------GYRIIAHVWQ------TTFVLVVRRDAERQTTDADVPAVSAEDIYCKMCDLNFDG-- 296 (316)
T ss_pred ccchHHHHHHHHHh-CC------CCeEEEEEec------ceEEEEEeeCCCCCCccccccccCHHHHHHHHhCCCCCh--
Confidence 34454444444433 44 3555544321 345665654443345677888999999999999999985
Q ss_pred HHHHHHHHHHHhh
Q 033230 91 DPLRDSLDGQLTF 103 (124)
Q Consensus 91 ~~l~~~l~~~~~~ 103 (124)
+-+.++..-|..+
T Consensus 297 El~~Ey~kly~~f 309 (316)
T PHA03328 297 ELLLEYKRLYATF 309 (316)
T ss_pred HHHHHHHHHHHHH
Confidence 3344444444443
No 143
>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=35.08 E-value=47 Score=17.50 Aligned_cols=26 Identities=12% Similarity=0.181 Sum_probs=19.1
Q ss_pred HHHHHHhcCCCccChhHHHHhhh-hCC
Q 033230 60 ANDICKESKRQTINAEDVLKAIE-EID 85 (124)
Q Consensus 60 A~~~a~~~kRKTI~~eDVl~AL~-~lg 85 (124)
+....-.++.-+|+.+++..+|+ .+|
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 44455567778899999999998 576
No 144
>PTZ00448 hypothetical protein; Provisional
Probab=33.87 E-value=1.6e+02 Score=25.45 Aligned_cols=95 Identities=9% Similarity=0.095 Sum_probs=67.8
Q ss_pred ccccc--ccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHH-HHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhh
Q 033230 7 VPEAE--ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCE-SARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (124)
Q Consensus 7 ~~ed~--~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~-~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~ 83 (124)
..+|+ -+...-+..|++..|.. |...+|.+=+..+.+ --.+.+.+|+..+.+ -.-++..++.=|-.||++
T Consensus 67 ~~edL~kaFGTtD~~eI~k~IL~K----GElQlt~~ER~~~~E~k~r~Ii~~Ia~~~In---P~T~~P~P~~rIE~Am~e 139 (373)
T PTZ00448 67 NSDDLNTVFGTNSIDNICKTILSK----GEIQVSETERSYMLDKQFTDICHMLNRMTVN---PKNNLPLSVKIIESELKD 139 (373)
T ss_pred CHHHHHHHhCCCCHHHHHHHHHhc----CCcccCHHHHHHHHHHHHHHHHHHHHHhccC---CCCCCCCCHHHHHHHHHh
Confidence 34444 35556677788888864 678898888766554 345566666654433 466778999999999999
Q ss_pred CCCc--ccHHHHHHHHHHHHhhhchhe
Q 033230 84 IDFT--EFVDPLRDSLDGQLTFRNWIF 108 (124)
Q Consensus 84 lgf~--~~~~~l~~~l~~~~~~~~~~~ 108 (124)
.+|. -+.+.=+..++-.+.++.++-
T Consensus 140 ~~~~Vdp~Ksak~Qalevik~L~~iiP 166 (373)
T PTZ00448 140 SGFSVSLNKTTKEQALKAFDILKKRIP 166 (373)
T ss_pred cCcccCCCCCHHHHHHHHHHHHHHhCC
Confidence 9984 677777788888888887764
No 145
>PRK00440 rfc replication factor C small subunit; Reviewed
Probab=32.97 E-value=1.1e+02 Score=23.92 Aligned_cols=66 Identities=18% Similarity=0.134 Sum_probs=37.9
Q ss_pred cchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhhC
Q 033230 13 LPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEI 84 (124)
Q Consensus 13 LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~l 84 (124)
++..-+.++++..+.. .+..++.++...+.+.+.-=+..+-......+. . .++|+.+||..++...
T Consensus 161 l~~~ei~~~l~~~~~~----~~~~i~~~al~~l~~~~~gd~r~~~~~l~~~~~-~-~~~it~~~v~~~~~~~ 226 (319)
T PRK00440 161 LKKEAVAERLRYIAEN----EGIEITDDALEAIYYVSEGDMRKAINALQAAAA-T-GKEVTEEAVYKITGTA 226 (319)
T ss_pred CCHHHHHHHHHHHHHH----cCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHH-c-CCCCCHHHHHHHhCCC
Confidence 4455555666555532 146788888888877654322222222222222 2 3689999988887554
No 146
>PRK05907 hypothetical protein; Provisional
Probab=32.59 E-value=1e+02 Score=25.38 Aligned_cols=49 Identities=12% Similarity=0.144 Sum_probs=36.9
Q ss_pred cchhhHHHHHHHHHHH-HHHHHHHHHHHHHHHHh-cCCCccChhHHHHhhh
Q 033230 34 DISVHKDALLAFCESA-RIFIHYLSATANDICKE-SKRQTINAEDVLKAIE 82 (124)
Q Consensus 34 ~~~ISkdA~~al~~~a-~~FI~~lt~~A~~~a~~-~kRKTI~~eDVl~AL~ 82 (124)
+.+|+++|...+.+.. .-=+..+..+-.+.+.- .++++|+.+||.....
T Consensus 151 g~~i~~~a~~~L~~~~~~~nL~~l~~EleKL~ly~g~~~~It~e~V~~lv~ 201 (311)
T PRK05907 151 GISCSLGLASLFVSKFPQTGLFEILSEFQKLLCQMGKKESLEASDIQSFVV 201 (311)
T ss_pred CCCcCHHHHHHHHHHccCCCHHHHHHHHHHHHHhcCCCCeECHHHHHHHhc
Confidence 5789999988888866 34445666666666665 6688999999988743
No 147
>KOG0784 consensus Isocitrate dehydrogenase, gamma subunit [Amino acid transport and metabolism]
Probab=32.34 E-value=19 Score=30.95 Aligned_cols=58 Identities=17% Similarity=0.256 Sum_probs=44.0
Q ss_pred HHHHHHHHHHHHhcCCCccChhHHHHhhhhCCCcccHHHHHHHHHHH--Hhhhchheeeec
Q 033230 54 HYLSATANDICKESKRQTINAEDVLKAIEEIDFTEFVDPLRDSLDGQ--LTFRNWIFIFCC 112 (124)
Q Consensus 54 ~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~lgf~~~~~~l~~~l~~~--~~~~~~~~~~~~ 112 (124)
.-|+.-|.+.|...|||.+|+=|=-+ .-.||=+-|++.+++.-..| -++...|+--||
T Consensus 187 eRIaryAF~yA~k~gRKkVTaVHKAn-imKL~DGlFle~~~eva~~Yp~I~~e~miVDN~~ 246 (375)
T KOG0784|consen 187 ERIARYAFEYAKKNGRKKVTAVHKAN-IMKLGDGLFLESCQEVAKKYPDITFEEMIVDNAC 246 (375)
T ss_pred HHHHHHHHHHHHHhCCceEEEEeccC-ceecchhhHHHHHHHHHhcCCCccHHHhhHHHhH
Confidence 34667899999999999999977666 44677778999999988777 344555555554
No 148
>PF08393 DHC_N2: Dynein heavy chain, N-terminal region 2; InterPro: IPR013602 Dyneins are described as motor proteins of eukaryotic cells, as they can convert energy derived from the hydrolysis of ATP to force and movement along cytoskeletal polymers, such as microtubules. Dyneins generally contain one to three heavy chains, where each heavy chain consists of a C-terminal globular head, a flexible microtubule-binding stalk, and a flexible N-terminal tail known as the cargo-binding domain []. The two categories of dyneins are the axonemal dyneins, which produce the bending motions that propagate along cilia and flagella, and the cytosolic dyneins, which drive a variety of fundamental cellular processes including nuclear migration, organisation of the mitotic spindle, chromosome separation during mitosis, and the positioning and function of many intracellular organelles. Cytoplasmic dyneins contain several accessory subunits ranging from light to intermediate chains. This entry represents a region found C-terminal to the dynein heavy chain N-terminal region 1 (IPR013594 from INTERPRO) in many members of this family. No functions seem to have been attributed specifically to this region. ; PDB: 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A.
Probab=32.31 E-value=31 Score=28.60 Aligned_cols=70 Identities=23% Similarity=0.422 Sum_probs=34.2
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC--CccChhHHHHhhhhCCCcccHHHHHHHHHHHHhhhchheeeeccC
Q 033230 37 VHKDALLAFCESARIFIHYLSATANDICKESKR--QTINAEDVLKAIEEIDFTEFVDPLRDSLDGQLTFRNWIFIFCCNF 114 (124)
Q Consensus 37 ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kR--KTI~~eDVl~AL~~lgf~~~~~~l~~~l~~~~~~~~~~~~~~~~~ 114 (124)
++.|+. .+..+-..|...+.... +..+ ..+..+++...|+.+. +-++.++..|..|.+.++.. |
T Consensus 246 lp~e~~-~F~~i~~~~~~i~~~~~-----~~~~v~~~~~~~~~~~~l~~~~--~~l~~i~k~L~~~Le~kR~~------F 311 (408)
T PF08393_consen 246 LPKEAK-KFSSIDKEWRSIMKRAQ-----KDPNVLSVCSNPDLLEKLESIN--ESLEKIQKSLNDYLESKREA------F 311 (408)
T ss_dssp THHHHH-HHHHHHHHHHHHHHHHH-----CT-CCHHHCCSTTHHHHHHHHH--HHHHHHHHHHHHHHHHHHHH------S
T ss_pred HHHHHH-HHHHcChHHHHHHHHHH-----hCcchhHHhhHhhHHHHHHHHH--HHHHHHHHHHhHHHHHHHhh------c
Confidence 344443 45556666666555431 1111 1122355666665543 33344444444444444433 8
Q ss_pred Cchhhh
Q 033230 115 PAFYFK 120 (124)
Q Consensus 115 ~~~~~~ 120 (124)
|-|||-
T Consensus 312 PRfyFl 317 (408)
T PF08393_consen 312 PRFYFL 317 (408)
T ss_dssp CCHHHC
T ss_pred cceeec
Confidence 999994
No 149
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=32.26 E-value=75 Score=20.04 Aligned_cols=35 Identities=14% Similarity=0.144 Sum_probs=25.7
Q ss_pred cccccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHH
Q 033230 9 EAEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIF 52 (124)
Q Consensus 9 ed~~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~F 52 (124)
+...+..++|.|++... ..||.+.+..+.+++.++
T Consensus 8 ~~~gvS~~TVSr~ln~~---------~~v~~~t~~~i~~~~~~~ 42 (70)
T smart00354 8 RLAGVSKATVSRVLNGN---------GRVSEETREKVLAAMEEL 42 (70)
T ss_pred HHHCCCHHHHHHHHCCC---------CCCCHHHHHHHHHHHHHh
Confidence 34578889999988653 346888888888776664
No 150
>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=31.87 E-value=36 Score=20.44 Aligned_cols=16 Identities=25% Similarity=0.547 Sum_probs=13.6
Q ss_pred cChhHHHHhhhhCCCc
Q 033230 72 INAEDVLKAIEEIDFT 87 (124)
Q Consensus 72 I~~eDVl~AL~~lgf~ 87 (124)
+++++|..+++.+||+
T Consensus 47 ~~~~~i~~~i~~~Gy~ 62 (62)
T PF00403_consen 47 TSIEKIIEAIEKAGYE 62 (62)
T ss_dssp SCHHHHHHHHHHTTSE
T ss_pred CCHHHHHHHHHHhCcC
Confidence 6778999999999984
No 151
>PRK10865 protein disaggregation chaperone; Provisional
Probab=31.02 E-value=55 Score=30.73 Aligned_cols=38 Identities=16% Similarity=0.215 Sum_probs=30.6
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhhCC
Q 033230 36 SVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEID 85 (124)
Q Consensus 36 ~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~lg 85 (124)
++|.++..+|. .|...|..-+...|+++|++.||=.-+
T Consensus 5 ~~~~~~~~~l~------------~a~~~a~~~~~~~~~~~hll~~l~~~~ 42 (857)
T PRK10865 5 RLTNKFQLALA------------DAQSLALGHDNQFIEPLHLMSALLNQE 42 (857)
T ss_pred HhCHHHHHHHH------------HHHHHHHHcCCCcccHHHHHHHHHhCC
Confidence 56777777776 577889999999999999999985543
No 152
>CHL00095 clpC Clp protease ATP binding subunit
Probab=30.80 E-value=73 Score=29.61 Aligned_cols=36 Identities=8% Similarity=0.169 Sum_probs=29.5
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhh
Q 033230 36 SVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (124)
Q Consensus 36 ~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~ 83 (124)
++|+++..+|. .|...|..-+...|+++|++.||=.
T Consensus 4 rfT~~a~~vL~------------~A~~~A~~~~h~~V~~EHLLLaLL~ 39 (821)
T CHL00095 4 RFTEKAIKVIM------------LSQEEARRLGHNFVGTEQILLGLIG 39 (821)
T ss_pred hHhHHHHHHHH------------HHHHHHHHhCCCcCcHHHHHHHHHh
Confidence 56777777776 5788899999999999999998733
No 153
>PF01922 SRP19: SRP19 protein; InterPro: IPR002778 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the SRP19 subunit. The SRP19 protein is unstructured but forms a compact core domain and two extended RNA-binding loops upon binding the signal recognition particle (SRP) RNA [].; GO: 0008312 7S RNA binding, 0006614 SRP-dependent cotranslational protein targeting to membrane, 0048500 signal recognition particle; PDB: 3DLU_A 3DLV_B 2J37_B 1MFQ_B 3KTV_D 1RY1_B 1JID_A 1KVV_A 1KVN_A 3KTW_B ....
Probab=30.08 E-value=39 Score=23.29 Aligned_cols=20 Identities=15% Similarity=0.290 Sum_probs=15.6
Q ss_pred cChhHHHHhhhhCCCcccHH
Q 033230 72 INAEDVLKAIEEIDFTEFVD 91 (124)
Q Consensus 72 I~~eDVl~AL~~lgf~~~~~ 91 (124)
.+.++|..|++.|||..-++
T Consensus 29 P~~~EI~~a~~~Lgl~~~~E 48 (95)
T PF01922_consen 29 PTLEEIADACKKLGLPCVVE 48 (95)
T ss_dssp --HHHHHHHHHHTTSEEEEE
T ss_pred CCHHHHHHHHHHcCCCEEEc
Confidence 78899999999999986544
No 154
>COG1239 ChlI Mg-chelatase subunit ChlI [Coenzyme metabolism]
Probab=29.93 E-value=94 Score=27.32 Aligned_cols=49 Identities=18% Similarity=0.251 Sum_probs=41.4
Q ss_pred cchhhHHHHHHHHHHHHHHHH-------HHHHHHHHHHHhcCCCccChhHHHHhhh
Q 033230 34 DISVHKDALLAFCESARIFIH-------YLSATANDICKESKRQTINAEDVLKAIE 82 (124)
Q Consensus 34 ~~~ISkdA~~al~~~a~~FI~-------~lt~~A~~~a~~~kRKTI~~eDVl~AL~ 82 (124)
.+.++.++...+.+.|..+-. .+...|..+|.=.||.+++.+||-.|++
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 578899999999888877754 4678888899999999999999999874
No 155
>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau. This model represents the well-conserved first ~ 365 amino acids of the translation of the dnaX gene. The full-length product of the dnaX gene in the model bacterium E. coli is the DNA polymerase III tau subunit. A translational frameshift leads to early termination and a truncated protein subunit gamma, about 1/3 shorter than tau and present in roughly equal amounts. This frameshift mechanism is not necessarily universal for species with DNA polymerase III but appears conserved in the exterme thermophile Thermus thermophilis.
Probab=29.92 E-value=1.3e+02 Score=24.12 Aligned_cols=63 Identities=16% Similarity=0.128 Sum_probs=32.9
Q ss_pred hhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhh
Q 033230 15 KTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIE 82 (124)
Q Consensus 15 ~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~ 82 (124)
...+..++++.+.. .+..++.++...+.+.+.-=...+-.+....+.-.+ +.|+.+||..++.
T Consensus 178 ~~~l~~~l~~~~~~----~g~~i~~~a~~~l~~~~~g~~~~a~~~lekl~~~~~-~~it~~~v~~~~~ 240 (355)
T TIGR02397 178 LEDIVERLKKILDK----EGIKIEDEALELIARAADGSLRDALSLLDQLISFGN-GNITYEDVNELLG 240 (355)
T ss_pred HHHHHHHHHHHHHH----cCCCCCHHHHHHHHHHcCCChHHHHHHHHHHHhhcC-CCCCHHHHHHHhC
Confidence 44445555544431 145688888777776654333333333333333222 3488887766554
No 156
>PRK14971 DNA polymerase III subunits gamma and tau; Provisional
Probab=29.73 E-value=1.2e+02 Score=27.51 Aligned_cols=73 Identities=10% Similarity=0.129 Sum_probs=41.8
Q ss_pred ccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhhCCCccc
Q 033230 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFTEF 89 (124)
Q Consensus 12 ~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~lgf~~~ 89 (124)
.++..-+.+.++..+.. .+..++.++...|.+.+.-=+..+-++....+.-.|++ |+.++|...+.....+.+
T Consensus 179 ~ls~~ei~~~L~~ia~~----egi~i~~~al~~La~~s~gdlr~al~~Lekl~~y~~~~-It~~~V~~~l~~~~~~~i 251 (614)
T PRK14971 179 RIQVADIVNHLQYVASK----EGITAEPEALNVIAQKADGGMRDALSIFDQVVSFTGGN-ITYKSVIENLNILDYDYY 251 (614)
T ss_pred CCCHHHHHHHHHHHHHH----cCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhccCC-ccHHHHHHHhCCCCHHHH
Confidence 34455555555554432 14778888888877765543444444443433333444 888888877765554444
No 157
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=29.66 E-value=57 Score=18.05 Aligned_cols=36 Identities=14% Similarity=0.191 Sum_probs=23.0
Q ss_pred cccccchhHHHHHHhcc-ccCCCCCCcchhhHHHHHH
Q 033230 9 EAEELPKTIVRRVVKDK-LHNCSPDTDISVHKDALLA 44 (124)
Q Consensus 9 ed~~LP~A~I~RI~K~~-Lp~~~~d~~~~ISkdA~~a 44 (124)
+-+.++.++|.+++++. +|....++..+++++..+.
T Consensus 9 ~~lgis~~ti~~~~~~g~i~~~~~g~~~~~~~~~l~~ 45 (49)
T TIGR01764 9 EYLGVSKDTVYRLIHEGELPAYRVGRHYRIPREDVDE 45 (49)
T ss_pred HHHCCCHHHHHHHHHcCCCCeEEeCCeEEEeHHHHHH
Confidence 45689999999999887 3422112344666665544
No 158
>COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]
Probab=29.35 E-value=2.1e+02 Score=25.29 Aligned_cols=82 Identities=15% Similarity=0.217 Sum_probs=56.2
Q ss_pred cccccccchhHHHHHHhccccCCCC----------------CCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q 033230 7 VPEAEELPKTIVRRVVKDKLHNCSP----------------DTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQ 70 (124)
Q Consensus 7 ~~ed~~LP~A~I~RI~K~~Lp~~~~----------------d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRK 70 (124)
..+.+.+-.+||.|++++.--.++- .|+.--|+++...+. -.-++.++++|
T Consensus 336 vA~~i~~HESTISRai~nKy~~tprG~feLK~FFs~~i~s~~gg~~~S~~~Ik~~I-------------k~lI~~E~~~~ 402 (444)
T COG1508 336 VADEIGMHESTISRAITNKYLATPRGLFELKYFFSSSLASSEGGEASSTEAIKALI-------------KKLIEAEDKKK 402 (444)
T ss_pred HHHHhCccHHHHHHHHhcccccCCcceeeHHHHHHHhccCCCCCccccHHHHHHHH-------------HHHHhhccCCC
Confidence 4567788889999999887654431 011123333333222 23566788889
Q ss_pred ccChhHHHHhhhhCCCcccHHHHHHHHHHHHhhhc
Q 033230 71 TINAEDVLKAIEEIDFTEFVDPLRDSLDGQLTFRN 105 (124)
Q Consensus 71 TI~~eDVl~AL~~lgf~~~~~~l~~~l~~~~~~~~ 105 (124)
.+|-+.|..-|++-| ++..+....+||+.=|
T Consensus 403 pLSD~kIa~lLkekG----i~iARRTVAKYRe~L~ 433 (444)
T COG1508 403 PLSDSKIAELLKEKG----IDVARRTVAKYREELN 433 (444)
T ss_pred CCCHHHHHHHHHHcC----CchhHHhHHHHHHHcC
Confidence 999999999999988 5678888888887643
No 159
>PRK13760 putative RNA-associated protein; Provisional
Probab=28.81 E-value=2.7e+02 Score=22.42 Aligned_cols=88 Identities=15% Similarity=0.171 Sum_probs=61.1
Q ss_pred cchhHHHHHHhccccCCCCCCcchhhHHHHHHHHH-HHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhhCCCc--cc
Q 033230 13 LPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCE-SARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFT--EF 89 (124)
Q Consensus 13 LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~-~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~lgf~--~~ 89 (124)
+..+.+..+++..|-. |...+|.+=+..+.+ -=.+.+.+|+..+.+ -..++..++.=|-.||++++|. -+
T Consensus 67 FGT~d~~~i~~~IL~k----GeiQlt~~eR~~~~e~k~r~Ii~~Ia~~~vn---P~T~~P~p~~rIE~Am~e~~~~idp~ 139 (231)
T PRK13760 67 FGTTDPLEIAEEIIKK----GEIQLTAEQRREMLEEKRRQIINFIARNAIN---PQTGLPHPPQRIENAMEEARVHIDPF 139 (231)
T ss_pred hCCCCHHHHHHHHHhc----CCccCCHHHHHHHHHHHHHHHHHHHHHhccC---CCCCCCCCHHHHHHHHHhcCcccCCC
Confidence 4555566777777753 578888777655544 445566666654333 3567778999999999999974 67
Q ss_pred HHHHHHHHHHHHhhhchh
Q 033230 90 VDPLRDSLDGQLTFRNWI 107 (124)
Q Consensus 90 ~~~l~~~l~~~~~~~~~~ 107 (124)
.+.=+..++--+.++.+|
T Consensus 140 k~ak~Qa~~vik~L~~~i 157 (231)
T PRK13760 140 KSVEEQVKDIVKALRPII 157 (231)
T ss_pred CCHHHHHHHHHHHHHHhC
Confidence 777777777778887766
No 160
>PRK08487 DNA polymerase III subunit delta; Validated
Probab=28.80 E-value=2.1e+02 Score=23.19 Aligned_cols=64 Identities=6% Similarity=0.087 Sum_probs=43.2
Q ss_pred chhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhh
Q 033230 14 PKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (124)
Q Consensus 14 P~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~ 83 (124)
+..-+.+.+++.+.. .+.+|+.+|...|...+.-=...+..+-...+.=.+ +||.+||......
T Consensus 136 ~~~~l~~~i~~~~~~----~g~~i~~~a~~~L~~~~g~dl~~l~~ELeKL~ly~~--~It~edV~~~v~~ 199 (328)
T PRK08487 136 NAREALELLQERAKE----LGLDIDQNALNHLYFIHNEDLALAANELEKLAILNE--PITLKDIQELVFG 199 (328)
T ss_pred CHHHHHHHHHHHHHH----hCCCCCHHHHHHHHHHhCcHHHHHHHHHHHHHHhcC--CCCHHHHHHHhcc
Confidence 334455555555442 257899999999998877655666666666665443 7999999987643
No 161
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=28.49 E-value=49 Score=25.73 Aligned_cols=37 Identities=11% Similarity=0.158 Sum_probs=28.8
Q ss_pred cccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHH
Q 033230 11 EELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLS 57 (124)
Q Consensus 11 ~~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt 57 (124)
...-++||.|.+... -+||.+.++-+.+++.+- .|.-
T Consensus 8 agVS~~TVSrvLn~~---------~~vs~~tr~rV~~~a~~l-gY~p 44 (327)
T PRK10423 8 AGVSTSTVSHVINKD---------RFVSEAITAKVEAAIKEL-NYAP 44 (327)
T ss_pred hCCcHHHHHHHhCCC---------CCCCHHHHHHHHHHHHHH-CCCc
Confidence 456789999999653 359999999999998875 3443
No 162
>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=28.38 E-value=77 Score=23.42 Aligned_cols=36 Identities=14% Similarity=0.265 Sum_probs=29.7
Q ss_pred CccChhHHHHhhhhCCCcc------------cHHHHHHHHHHHHhhhc
Q 033230 70 QTINAEDVLKAIEEIDFTE------------FVDPLRDSLDGQLTFRN 105 (124)
Q Consensus 70 KTI~~eDVl~AL~~lgf~~------------~~~~l~~~l~~~~~~~~ 105 (124)
.|.+++|+..+++.+++.. |+|.+.+..++-++.++
T Consensus 123 ~tt~~~~l~~~l~~l~~P~~~~~~~i~l~~r~ip~l~~~~~~i~~A~~ 170 (224)
T PF02361_consen 123 LTTSPSDLISALRKLRLPYPKIALMISLTLRFIPLLLEEFKRIREAQR 170 (224)
T ss_pred HHCCHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4789999999999999887 78888888777766654
No 163
>PRK14961 DNA polymerase III subunits gamma and tau; Provisional
Probab=28.30 E-value=1.8e+02 Score=24.11 Aligned_cols=65 Identities=14% Similarity=0.058 Sum_probs=32.9
Q ss_pred hhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhhC
Q 033230 15 KTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEI 84 (124)
Q Consensus 15 ~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~l 84 (124)
...+...++..+.. .+..++.++...+.+.+.-=+-.+-......+. -++..|+.+||..++...
T Consensus 180 ~~el~~~L~~~~~~----~g~~i~~~al~~ia~~s~G~~R~al~~l~~~~~-~~~~~It~~~v~~~l~~~ 244 (363)
T PRK14961 180 EEKIFNFLKYILIK----ESIDTDEYALKLIAYHAHGSMRDALNLLEHAIN-LGKGNINIKNVTDMLGLL 244 (363)
T ss_pred HHHHHHHHHHHHHH----cCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHH-hcCCCCCHHHHHHHHCCC
Confidence 44444444443321 135678888777665543211111111111122 256789999998877533
No 164
>PF02718 Herpes_UL31: Herpesvirus UL31-like protein; InterPro: IPR021152 This is a family of Herpesvirus proteins, belong to the UL31 family, which including UL31, UL53, and the product of ORF69 in some strains. The proteins in this family have no known function.
Probab=28.27 E-value=74 Score=26.10 Aligned_cols=30 Identities=27% Similarity=0.531 Sum_probs=22.9
Q ss_pred CCCccChhHHHHhhhhCCCcccHHHHHHHHHHH
Q 033230 68 KRQTINAEDVLKAIEEIDFTEFVDPLRDSLDGQ 100 (124)
Q Consensus 68 kRKTI~~eDVl~AL~~lgf~~~~~~l~~~l~~~ 100 (124)
..-+|+++||..++.+|+|+ +++.+..++|
T Consensus 222 ~~~~I~~~~I~~ki~dld~~---dEl~~ey~k~ 251 (258)
T PF02718_consen 222 TSPKIDADDIYCKICDLDFP---DELKEEYEKY 251 (258)
T ss_pred CCcccCHHHHHHHHHcCCCC---hHHHHHHHHH
Confidence 47789999999999999998 4444444444
No 165
>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA.
Probab=28.24 E-value=81 Score=28.86 Aligned_cols=33 Identities=15% Similarity=0.231 Sum_probs=25.9
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhh
Q 033230 37 VHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAI 81 (124)
Q Consensus 37 ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL 81 (124)
+|+++..+|. .|...|..-+..-|+++|++.||
T Consensus 1 ~~~~a~~~L~------------~A~~~A~~~~h~~V~~EHLLlaL 33 (731)
T TIGR02639 1 ISEELERILD------------AALEEAKKRRHEFVTLEHILLAL 33 (731)
T ss_pred CCHHHHHHHH------------HHHHHHHHhCCCcCcHHHHHHHH
Confidence 3556666665 57788999999999999999886
No 166
>COG1466 HolA DNA polymerase III, delta subunit [DNA replication, recombination, and repair]
Probab=28.00 E-value=1.8e+02 Score=23.85 Aligned_cols=65 Identities=11% Similarity=0.201 Sum_probs=46.7
Q ss_pred HHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhhCC
Q 033230 17 IVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEID 85 (124)
Q Consensus 17 ~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~lg 85 (124)
.+.+.++..+.+ -+.+|++||.+.|..+..-=...+.++=...+.-.+-++|+.+||..++..-.
T Consensus 144 ~l~~~i~~~~~~----~~l~i~~~a~~~L~~~~~~nl~~i~~Ei~KL~l~~~~~~I~~~~V~~~v~~~~ 208 (334)
T COG1466 144 ELPQWIKKRAKE----LGLKIDQEAIQLLLEALGGNLLAIAQEIEKLALYAGDKEITLEDVEEVVSDVA 208 (334)
T ss_pred HHHHHHHHHHHH----cCCCCCHHHHHHHHHHhCCcHHHHHHHHHHHHHhCCCCcCCHHHHHHHHhccc
Confidence 344445444432 26899999999999988866666667777777655555999999999876654
No 167
>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB. Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family, ATPases associated with various cellular activities (pfam00004). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins.
Probab=27.93 E-value=94 Score=29.07 Aligned_cols=26 Identities=27% Similarity=0.381 Sum_probs=22.3
Q ss_pred HHHHHHHhcCCCccChhHHHHhhhhC
Q 033230 59 TANDICKESKRQTINAEDVLKAIEEI 84 (124)
Q Consensus 59 ~A~~~a~~~kRKTI~~eDVl~AL~~l 84 (124)
.|...|...+...|+++|++.||=.-
T Consensus 11 ~A~~~A~~~~h~~V~~EHLLlaLl~~ 36 (852)
T TIGR03346 11 AAQSLALGRDHQQIEPEHLLKALLDQ 36 (852)
T ss_pred HHHHHHHHcCCCcccHHHHHHHHHhC
Confidence 67889999999999999999986443
No 168
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=27.88 E-value=1.3e+02 Score=19.80 Aligned_cols=28 Identities=4% Similarity=0.014 Sum_probs=20.4
Q ss_pred HHHHHHhcCCCccChhHHHHhhhhCCCc
Q 033230 60 ANDICKESKRQTINAEDVLKAIEEIDFT 87 (124)
Q Consensus 60 A~~~a~~~kRKTI~~eDVl~AL~~lgf~ 87 (124)
+......++.-+|+.+++..+|..+|+.
T Consensus 15 ~F~~~D~d~~G~Is~~el~~~l~~~~~~ 42 (96)
T smart00027 15 IFRSLDKNQDGTVTGAQAKPILLKSGLP 42 (96)
T ss_pred HHHHhCCCCCCeEeHHHHHHHHHHcCCC
Confidence 4445556677788888888888887764
No 169
>KOG1770 consensus Translation initiation factor 1 (eIF-1/SUI1) [Translation, ribosomal structure and biogenesis]
Probab=27.78 E-value=26 Score=25.35 Aligned_cols=12 Identities=25% Similarity=0.443 Sum_probs=9.3
Q ss_pred HHHhcCCCccCh
Q 033230 63 ICKESKRQTINA 74 (124)
Q Consensus 63 ~a~~~kRKTI~~ 74 (124)
+-.++||||+|.
T Consensus 34 IQQRnGrKtlTt 45 (112)
T KOG1770|consen 34 IQQRNGRKTLTT 45 (112)
T ss_pred EEeeCCceEEEE
Confidence 345789999886
No 170
>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=27.59 E-value=14 Score=24.45 Aligned_cols=18 Identities=17% Similarity=0.182 Sum_probs=13.3
Q ss_pred cchhhHHHHHHHHHHHHH
Q 033230 34 DISVHKDALLAFCESARI 51 (124)
Q Consensus 34 ~~~ISkdA~~al~~~a~~ 51 (124)
++|++.+.+..|.++|..
T Consensus 3 ~iR~~~e~k~li~~AA~~ 20 (80)
T PF08681_consen 3 EIRVTPEEKELIERAAAL 20 (80)
T ss_dssp EEE--HHHHHHHHHHHHH
T ss_pred eEecCHHHHHHHHHHHHH
Confidence 478999999999998754
No 171
>PRK05629 hypothetical protein; Validated
Probab=27.39 E-value=2e+02 Score=23.15 Aligned_cols=48 Identities=13% Similarity=0.184 Sum_probs=36.5
Q ss_pred cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhh
Q 033230 34 DISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIE 82 (124)
Q Consensus 34 ~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~ 82 (124)
+.+|+.+|...|...+..=...+..+-.+.+... ..+|+.+||-..+.
T Consensus 143 g~~i~~~A~~~L~~~~g~dl~~l~~EleKL~~~~-~~~It~e~V~~~v~ 190 (318)
T PRK05629 143 GVRPTPDVVHALLEGVGSDLRELASAISQLVEDT-QGNVTVEKVRAYYV 190 (318)
T ss_pred CCCCCHHHHHHHHHHHCccHHHHHHHHHHHHhcC-CCCcCHHHHHHHhC
Confidence 5789999999998887766666666666666543 45799999987744
No 172
>PRK00754 signal recognition particle protein Srp19; Provisional
Probab=27.05 E-value=18 Score=25.26 Aligned_cols=30 Identities=17% Similarity=0.245 Sum_probs=22.1
Q ss_pred cChhHHHHhhhhCCCcccHHHHHHHHHHHH
Q 033230 72 INAEDVLKAIEEIDFTEFVDPLRDSLDGQL 101 (124)
Q Consensus 72 I~~eDVl~AL~~lgf~~~~~~l~~~l~~~~ 101 (124)
.+.++|..|++.||+...+++-+.+=..|-
T Consensus 35 P~~~EI~~a~~~lgl~~~~e~~K~yPr~~~ 64 (95)
T PRK00754 35 PRLEEIIEAAEKLGLNPEVEPDKAYPRSWW 64 (95)
T ss_pred CCHHHHHHHHHHcCCCeEEeeCCCCCchHh
Confidence 688999999999999876654444444443
No 173
>PRK14964 DNA polymerase III subunits gamma and tau; Provisional
Probab=26.77 E-value=1.3e+02 Score=26.65 Aligned_cols=65 Identities=12% Similarity=0.119 Sum_probs=37.7
Q ss_pred cchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhh
Q 033230 13 LPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIE 82 (124)
Q Consensus 13 LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~ 82 (124)
++...+...++..+.. .+..++.++...|.+.+.-=+..+-+.-.+.+...+ .+|+.+||...+.
T Consensus 175 l~~~el~~~L~~ia~~----Egi~i~~eAL~lIa~~s~GslR~alslLdqli~y~~-~~It~e~V~~llg 239 (491)
T PRK14964 175 IPTDKLVEHLVDIAKK----ENIEHDEESLKLIAENSSGSMRNALFLLEQAAIYSN-NKISEKSVRDLLG 239 (491)
T ss_pred ccHHHHHHHHHHHHHH----cCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhcC-CCCCHHHHHHHHc
Confidence 3444444444444332 257899999998887774333333333333333333 4799999987653
No 174
>PRK09492 treR trehalose repressor; Provisional
Probab=26.39 E-value=86 Score=24.26 Aligned_cols=36 Identities=14% Similarity=0.132 Sum_probs=28.4
Q ss_pred ccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHH
Q 033230 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLS 57 (124)
Q Consensus 12 ~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt 57 (124)
..-++||.|++... .+||.+.++-+.+++.+-= |.-
T Consensus 15 gVS~~TVSrvLn~~---------~~vs~~tr~rV~~~a~elg-Y~p 50 (315)
T PRK09492 15 GVGKSTVSRVLNNE---------SGVSEETRERVEAVINQHG-FSP 50 (315)
T ss_pred CCCHHHHhHHhCCC---------CCCCHHHHHHHHHHHHHHC-CCc
Confidence 68889999999753 3699999999999888743 443
No 175
>PF10440 WIYLD: Ubiquitin-binding WIYLD domain; InterPro: IPR018848 This entry represents a presumed domain which has been predicted to contain three alpha helices. It was named the WIYLD domain based on the pattern of the ost conserved residues []. This domain appears to be specific to plant SET-domain proteins. ; GO: 0018024 histone-lysine N-methyltransferase activity
Probab=26.25 E-value=65 Score=21.13 Aligned_cols=35 Identities=26% Similarity=0.382 Sum_probs=26.4
Q ss_pred HHhhhhCCCcc--cHHHHHHHHHHHHhhhchheeeeccC
Q 033230 78 LKAIEEIDFTE--FVDPLRDSLDGQLTFRNWIFIFCCNF 114 (124)
Q Consensus 78 l~AL~~lgf~~--~~~~l~~~l~~~~~~~~~~~~~~~~~ 114 (124)
+.||..|||+. -.+.|+.-|+-|- .||-+|=-.||
T Consensus 15 ~dam~~lG~~~~~v~~vl~~LL~lY~--~nW~lIEed~Y 51 (65)
T PF10440_consen 15 LDAMRQLGFSKKQVRPVLKNLLKLYD--GNWELIEEDNY 51 (65)
T ss_pred HHHHHHcCCCHHHHHHHHHHHHHHHc--CCchhhhcccH
Confidence 67888999974 6788888888884 56887765554
No 176
>TIGR01052 top6b DNA topoisomerase VI, B subunit. This model describes DNA topoisomerase VI, an archaeal type II DNA topoisomerase (DNA gyrase).
Probab=26.19 E-value=1.2e+02 Score=27.04 Aligned_cols=51 Identities=25% Similarity=0.316 Sum_probs=37.6
Q ss_pred chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhhCCCcccHHHHHHHHHH
Q 033230 35 ISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFTEFVDPLRDSLDG 99 (124)
Q Consensus 35 ~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~lgf~~~~~~l~~~l~~ 99 (124)
--|-+|.+.||++||..-=.||+..-...-..+++++ |..|++.+-..|..
T Consensus 433 ~ei~~ei~~al~~~~r~L~~~l~~~~~~~~~~~r~~~--------------~~~y~p~~a~~~~~ 483 (488)
T TIGR01052 433 PEIYNEIRLALMEVARRLRLYLSRKAREEEEIKRRKT--------------LEKYLPEIAKSLAY 483 (488)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------------HHHHHHHHHHHHHH
Confidence 3688999999999999999999987666555555444 44566666666554
No 177
>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., PubMed:15231786). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations
Probab=26.17 E-value=1.7e+02 Score=25.30 Aligned_cols=80 Identities=18% Similarity=0.227 Sum_probs=53.7
Q ss_pred cccccccchhHHHHHHhccccCCCC----------------CCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q 033230 7 VPEAEELPKTIVRRVVKDKLHNCSP----------------DTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQ 70 (124)
Q Consensus 7 ~~ed~~LP~A~I~RI~K~~Lp~~~~----------------d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRK 70 (124)
..+.+.+-.+||.|+++..-=+++- +++.-+|.++....- ..-+..+++++
T Consensus 324 iA~~lglheSTVSRav~~Kyi~tp~Gi~~lk~FFs~~~~~~~~g~~~S~~~Ik~~I-------------~~lI~~E~~~~ 390 (429)
T TIGR02395 324 VAEELGLHESTISRAINNKYLQTPRGVFELKYFFSRGVQTDSGEGEVSSTAIKALI-------------KELIAAEDKRK 390 (429)
T ss_pred HHHHhCCCccchhhhhcCceEecCCceEEHHHhcCCccCCCCCCCccCHHHHHHHH-------------HHHHHhcCCCC
Confidence 4577889999999999765433221 101114444432211 23456788899
Q ss_pred ccChhHHHHhhhhCCCcccHHHHHHHHHHHHhh
Q 033230 71 TINAEDVLKAIEEIDFTEFVDPLRDSLDGQLTF 103 (124)
Q Consensus 71 TI~~eDVl~AL~~lgf~~~~~~l~~~l~~~~~~ 103 (124)
.+|-+.|..-|+.-|+. -.+.-..+||+.
T Consensus 391 PlSD~~I~~~L~~~Gi~----IaRRTVaKYRe~ 419 (429)
T TIGR02395 391 PLSDQKIAELLKEKGIK----IARRTVAKYREE 419 (429)
T ss_pred CCCHHHHHHHHHhcCCC----eehHHHHHHHHH
Confidence 99999999999998864 557777888875
No 178
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=25.91 E-value=1.8e+02 Score=25.85 Aligned_cols=80 Identities=13% Similarity=0.081 Sum_probs=53.0
Q ss_pred cccccccchhHHHHHHhccccCCCC---------------CCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCc
Q 033230 7 VPEAEELPKTIVRRVVKDKLHNCSP---------------DTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQT 71 (124)
Q Consensus 7 ~~ed~~LP~A~I~RI~K~~Lp~~~~---------------d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKT 71 (124)
..+.+.+--+||.|+++..-=+++- +++--+|.++..... ..-+..++++|.
T Consensus 375 VAe~lglHeSTVSRa~~~KY~~tp~GifeLK~FFs~~v~~~~g~~~Ss~~Ik~~I-------------k~lI~~Ed~~kP 441 (481)
T PRK12469 375 VAEELGLHESTISRATGNKYMATPRGTFEFKHFFPRKLEAAGGGECSAAAVRALI-------------KEMIAAEQAGDP 441 (481)
T ss_pred HHHHhCCCcchhhHHhcCceeecCCceEeHHHhhccccCCCCCccccHHHHHHHH-------------HHHHHhcCCCCC
Confidence 4578889999999999765433321 011123433332222 224567888999
Q ss_pred cChhHHHHhhhhCCCcccHHHHHHHHHHHHhh
Q 033230 72 INAEDVLKAIEEIDFTEFVDPLRDSLDGQLTF 103 (124)
Q Consensus 72 I~~eDVl~AL~~lgf~~~~~~l~~~l~~~~~~ 103 (124)
+|-+.|..-|++-|+. ..+.-..+||+.
T Consensus 442 LSD~~I~~~L~~~GI~----IARRTVAKYRe~ 469 (481)
T PRK12469 442 LSDVALAEMLAGRGVL----IARRTVAKYREA 469 (481)
T ss_pred CCHHHHHHHHHhcCCC----eechhHHHHHHH
Confidence 9999999999998874 456677778775
No 179
>PRK14958 DNA polymerase III subunits gamma and tau; Provisional
Probab=25.82 E-value=1.8e+02 Score=25.72 Aligned_cols=70 Identities=13% Similarity=0.102 Sum_probs=38.2
Q ss_pred cchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhhCCCc
Q 033230 13 LPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFT 87 (124)
Q Consensus 13 LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~lgf~ 87 (124)
+|...+.+.++..+.. .+..+++++...|.+.+.-=+-.+-+.-.+.+ .-|...|+.+||...+....-+
T Consensus 178 l~~~~i~~~l~~il~~----egi~~~~~al~~ia~~s~GslR~al~lLdq~i-a~~~~~It~~~V~~~lg~~~~~ 247 (509)
T PRK14958 178 LPPLQIAAHCQHLLKE----ENVEFENAALDLLARAANGSVRDALSLLDQSI-AYGNGKVLIADVKTMLGTIEPL 247 (509)
T ss_pred CCHHHHHHHHHHHHHH----cCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHH-hcCCCCcCHHHHHHHHCCCCHH
Confidence 5555555555555432 25778888888887765421212211111112 2245679999998876554433
No 180
>PRK09111 DNA polymerase III subunits gamma and tau; Validated
Probab=25.47 E-value=1.8e+02 Score=26.29 Aligned_cols=65 Identities=11% Similarity=0.097 Sum_probs=40.2
Q ss_pred cchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhh
Q 033230 13 LPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIE 82 (124)
Q Consensus 13 LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~ 82 (124)
++..-+.+.++..+.. .+..++.++...|.+.+.--+..+.+...+.+.. +...|+.+||...+.
T Consensus 191 l~~~el~~~L~~i~~k----egi~i~~eAl~lIa~~a~Gdlr~al~~Ldkli~~-g~g~It~e~V~~llg 255 (598)
T PRK09111 191 IEADVLAAHLSRIAAK----EGVEVEDEALALIARAAEGSVRDGLSLLDQAIAH-GAGEVTAEAVRDMLG 255 (598)
T ss_pred CCHHHHHHHHHHHHHH----cCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHhh-cCCCcCHHHHHHHhC
Confidence 3344455555554432 2578999999888887765555555544443333 356799999987654
No 181
>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=25.42 E-value=1e+02 Score=22.69 Aligned_cols=38 Identities=16% Similarity=0.162 Sum_probs=30.0
Q ss_pred CccChhHHHHhhhhCCCc-----------ccHHHHHHHHHHHHhhhchh
Q 033230 70 QTINAEDVLKAIEEIDFT-----------EFVDPLRDSLDGQLTFRNWI 107 (124)
Q Consensus 70 KTI~~eDVl~AL~~lgf~-----------~~~~~l~~~l~~~~~~~~~~ 107 (124)
.|.+++|+..+|+.+|++ .|++.+.+..+.-++.|+.=
T Consensus 112 ~TT~~~~l~~~l~~l~~P~~~~~~~~l~~Rfip~l~~e~~~i~~Aq~aR 160 (198)
T TIGR02454 112 LTTPFPELLSALRRLGVPPLLVEILLLTYRYLFVLLEELRRMLLAQRSR 160 (198)
T ss_pred HcCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 477899999999999985 36788888887777666554
No 182
>KOG1528 consensus Salt-sensitive 3'-phosphoadenosine-5'-phosphatase HAL2/SAL1 [Nucleotide transport and metabolism; Inorganic ion transport and metabolism]
Probab=25.32 E-value=1.6e+02 Score=25.12 Aligned_cols=69 Identities=16% Similarity=0.174 Sum_probs=40.2
Q ss_pred hhHHHHHHhccccCCCCCCcchhhHHHHHHHHHH-HHHHHHHHHHHHHH---HHHhcCC-CccChhHHHHhhhhCCC
Q 033230 15 KTIVRRVVKDKLHNCSPDTDISVHKDALLAFCES-ARIFIHYLSATAND---ICKESKR-QTINAEDVLKAIEEIDF 86 (124)
Q Consensus 15 ~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~-a~~FI~~lt~~A~~---~a~~~kR-KTI~~eDVl~AL~~lgf 86 (124)
.|.|.-.+++.+|+.+ =..+..|-..-|.+. ++.++.-|+..-++ ....=+- ++.+.+||++|+..=+.
T Consensus 52 QAiVs~vL~~~f~~~p---~slVaEEds~~Lr~n~~~~~l~~i~~lvnetl~s~~sy~~~~~ls~~dvl~aID~G~s 125 (351)
T KOG1528|consen 52 QAIVSLVLEREFPDDP---LSLVAEEDSGFLRKNGSEGLLSRITKLVNETLASDESYGDNSPLSSDDVLKAIDRGNS 125 (351)
T ss_pred HHHHHHHHHHHcCCCC---cceEeeccchhhhhhhhHHHHHHHHHHHHHHhhhhhhccCCCCCCHHHHHHHHhcccc
Confidence 3778888899998532 113344443334333 44555555553333 2222223 78999999999976444
No 183
>COG0017 AsnS Aspartyl/asparaginyl-tRNA synthetases [Translation, ribosomal structure and biogenesis]
Probab=25.27 E-value=2.8e+02 Score=24.45 Aligned_cols=77 Identities=22% Similarity=0.402 Sum_probs=49.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhc-----------------CCCccChhHHHHhhhhCCCc------ccHHHHHHHHH
Q 033230 42 LLAFCESARIFIHYLSATANDICKES-----------------KRQTINAEDVLKAIEEIDFT------EFVDPLRDSLD 98 (124)
Q Consensus 42 ~~al~~~a~~FI~~lt~~A~~~a~~~-----------------kRKTI~~eDVl~AL~~lgf~------~~~~~l~~~l~ 98 (124)
..-+.+..+.+|.||.....+.|.++ .=+-|+.+|.+.-|++.|++ |+-.+.+.+|.
T Consensus 235 ~~d~m~l~E~~i~~i~~~v~e~~~~el~~l~~~~~~l~~~~~~pf~ritY~eAieiL~~~~~e~~~~GdDl~~e~Er~l~ 314 (435)
T COG0017 235 LNDVMDLAEELIKYLFKKVLEECADELEFLGRDNSELKRPESAPFPRITYKEAIEILEEKGFEKVEWGDDLGTEHERYLG 314 (435)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhHHHHHHhhccchhhcccccCCccEEEHHHHHHHHHhcCCcccCCCCccCCHHHHHHH
Confidence 34445566677777776666555442 23458889999999988883 44455555555
Q ss_pred HHHhhhchheeeeccCC----chhhhc
Q 033230 99 GQLTFRNWIFIFCCNFP----AFYFKR 121 (124)
Q Consensus 99 ~~~~~~~~~~~~~~~~~----~~~~~~ 121 (124)
+ +.... +.|--||| +||-+.
T Consensus 315 e-~~~~~--~vfv~~yP~~~kpFYm~~ 338 (435)
T COG0017 315 E-EYFKP--PVFVTNYPKEIKPFYMRP 338 (435)
T ss_pred H-HhCCC--cEEEEeCccccccccccc
Confidence 2 22223 56778999 899775
No 184
>TIGR02903 spore_lon_C ATP-dependent protease, Lon family. Members of this protein family resemble the widely distributed ATP-dependent protease La, also called Lon and LonA. It resembles even more closely LonB, which is a LonA paralog found in genomes if and only if the species is capable of endospore formation (as in Bacillus subtilis, Clostridium tetani, and select other members of the Firmicutes) and expressed specifically in the forespore compartment. Members of this family are restricted to a subset of spore-forming species, and are very likely to participate in the program of endospore formation. We propose the designation LonC.
Probab=24.83 E-value=1.7e+02 Score=26.43 Aligned_cols=72 Identities=14% Similarity=0.204 Sum_probs=43.4
Q ss_pred hHHHHHHhccccCCCCCCcchhhHHHHHHHHHHH---HHHHHHHHHHH-------HHHHHhcCCCccChhHHHHhhhhCC
Q 033230 16 TIVRRVVKDKLHNCSPDTDISVHKDALLAFCESA---RIFIHYLSATA-------NDICKESKRQTINAEDVLKAIEEID 85 (124)
Q Consensus 16 A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a---~~FI~~lt~~A-------~~~a~~~kRKTI~~eDVl~AL~~lg 85 (124)
.-+..|++..+.. .+..++.++..+|.+.+ ...++.|.... ...+...++.+|+.+||..+++.-.
T Consensus 356 edi~~Il~~~a~~----~~v~ls~eal~~L~~ys~~gRraln~L~~~~~~~~~~~~~~~~~~~~~~I~~edv~~~l~~~r 431 (615)
T TIGR02903 356 EDIALIVLNAAEK----INVHLAAGVEELIARYTIEGRKAVNILADVYGYALYRAAEAGKENDKVTITQDDVYEVIQISR 431 (615)
T ss_pred HHHHHHHHHHHHH----cCCCCCHHHHHHHHHCCCcHHHHHHHHHHHHHHHHHHHHHhccCCCCeeECHHHHHHHhCCCc
Confidence 4455555655542 13567888888887754 33344443221 1112334566899999999998887
Q ss_pred CcccHH
Q 033230 86 FTEFVD 91 (124)
Q Consensus 86 f~~~~~ 91 (124)
|..|..
T Consensus 432 ~~~~~~ 437 (615)
T TIGR02903 432 LSPYEK 437 (615)
T ss_pred Cccchh
Confidence 776543
No 185
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=24.38 E-value=1.5e+02 Score=16.93 Aligned_cols=35 Identities=20% Similarity=0.200 Sum_probs=25.0
Q ss_pred cccccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHH
Q 033230 9 EAEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIF 52 (124)
Q Consensus 9 ed~~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~F 52 (124)
+...+..++|.|+.+.. ..++.+....+.+++.++
T Consensus 5 ~~~gvs~~tvs~~l~g~---------~~vs~~~~~~i~~~~~~l 39 (52)
T cd01392 5 RAAGVSVATVSRVLNGK---------PRVSEETRERVLAAAEEL 39 (52)
T ss_pred HHHCcCHHHHHHHHcCC---------CCCCHHHHHHHHHHHHHh
Confidence 45678889999988754 257777777777666554
No 186
>PTZ00112 origin recognition complex 1 protein; Provisional
Probab=24.15 E-value=1.5e+02 Score=29.16 Aligned_cols=20 Identities=20% Similarity=0.189 Sum_probs=15.8
Q ss_pred CCccChhHHHHhhhhCCCcc
Q 033230 69 RQTINAEDVLKAIEEIDFTE 88 (124)
Q Consensus 69 RKTI~~eDVl~AL~~lgf~~ 88 (124)
..+|+.+||..|++.+..+.
T Consensus 991 gskVT~eHVrkAleeiE~sr 1010 (1164)
T PTZ00112 991 GQKIVPRDITEATNQLFDSP 1010 (1164)
T ss_pred CCccCHHHHHHHHHHHHhhh
Confidence 34899999999998884443
No 187
>PRK14970 DNA polymerase III subunits gamma and tau; Provisional
Probab=24.13 E-value=2.2e+02 Score=23.17 Aligned_cols=66 Identities=12% Similarity=0.120 Sum_probs=35.8
Q ss_pred hhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHhhhhCC
Q 033230 15 KTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEID 85 (124)
Q Consensus 15 ~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~lg 85 (124)
...+...+++.+.. .+..+++++...|.+.+.-=+..+-.+-...+.-.++. |+.+||...+....
T Consensus 169 ~~~l~~~l~~~~~~----~g~~i~~~al~~l~~~~~gdlr~~~~~lekl~~y~~~~-it~~~v~~~~~~~~ 234 (367)
T PRK14970 169 IKDIKEHLAGIAVK----EGIKFEDDALHIIAQKADGALRDALSIFDRVVTFCGKN-ITRQAVTENLNILD 234 (367)
T ss_pred HHHHHHHHHHHHHH----cCCCCCHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCCC-CCHHHHHHHhCCCC
Confidence 35555555443322 15678999888877654422233333333333333333 88888887766554
No 188
>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional
Probab=24.11 E-value=1e+02 Score=28.75 Aligned_cols=23 Identities=22% Similarity=0.312 Sum_probs=21.0
Q ss_pred HHHHHHHhcCCCccChhHHHHhh
Q 033230 59 TANDICKESKRQTINAEDVLKAI 81 (124)
Q Consensus 59 ~A~~~a~~~kRKTI~~eDVl~AL 81 (124)
.|...|..-+...|+++|++.||
T Consensus 12 ~a~~~a~~~~~~~~~~~h~l~~l 34 (758)
T PRK11034 12 MAFARAREHRHEFMTVEHLLLAL 34 (758)
T ss_pred HHHHHHHHcCCCcchHHHHHHHH
Confidence 68889999999999999999887
No 189
>PF09660 DUF2397: Protein of unknown function (DUF2397); InterPro: IPR013493 Proteins in this family are encoded within a conserved gene four-gene neighbourhood found sporadically in a phylogenetically broad range of bacteria including: Nocardia farcinica, Symbiobacterium thermophilum, Streptomyces avermitilis (Actinobacteria), Geobacillus kaustophilus (Firmicutes), Azoarcus sp. (strain EbN1) (Aromatoleum aromaticum (strain EbN1)) and Ralstonia solanacearum (Betaproteobacteria).
Probab=23.75 E-value=1e+02 Score=27.09 Aligned_cols=41 Identities=27% Similarity=0.486 Sum_probs=33.8
Q ss_pred CCccChhHHHHhhhhCC-Cccc-HHHHHHHHHHHHhhhchhee
Q 033230 69 RQTINAEDVLKAIEEID-FTEF-VDPLRDSLDGQLTFRNWIFI 109 (124)
Q Consensus 69 RKTI~~eDVl~AL~~lg-f~~~-~~~l~~~l~~~~~~~~~~~~ 109 (124)
+--+.++||+..|...+ |.+| .+.|+..|++-.+=.|++.+
T Consensus 28 ~~~L~~edV~~~L~~~~~~~~~t~e~l~~~L~qLv~WgNL~~~ 70 (486)
T PF09660_consen 28 RYWLRPEDVLARLRADGGFADYTIEQLQQDLDQLVEWGNLTAI 70 (486)
T ss_pred HhccCHHHHHHHHhhcCCcCCCCHHHHHHHHHHHHhcCCeeee
Confidence 44589999999998855 7889 89999999998887777654
No 190
>PF13713 BRX_N: Transcription factor BRX N-terminal domain
Probab=23.49 E-value=1.3e+02 Score=17.76 Aligned_cols=21 Identities=29% Similarity=0.581 Sum_probs=17.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHh
Q 033230 46 CESARIFIHYLSATANDICKE 66 (124)
Q Consensus 46 ~~~a~~FI~~lt~~A~~~a~~ 66 (124)
++++.++|.-||++-.+++.+
T Consensus 7 ~kaaKe~IKsLt~QlK~maek 27 (39)
T PF13713_consen 7 CKAAKEVIKSLTAQLKDMAEK 27 (39)
T ss_pred cHHHHHHHHHHHHHHHHHHHh
Confidence 467889999999999998875
No 191
>PF01973 MAF_flag10: Protein of unknown function DUF115; InterPro: IPR002826 The prokaryotic proteins in this family have no known function.
Probab=23.48 E-value=49 Score=24.14 Aligned_cols=24 Identities=21% Similarity=0.151 Sum_probs=21.8
Q ss_pred HHHHHHHHHHHhhhchheeeeccC
Q 033230 91 DPLRDSLDGQLTFRNWIFIFCCNF 114 (124)
Q Consensus 91 ~~l~~~l~~~~~~~~~~~~~~~~~ 114 (124)
|.|++.++.-|+.|+-.+++|||.
T Consensus 34 PSL~~~i~~lk~~~~~~~iia~~s 57 (170)
T PF01973_consen 34 PSLDKNIELLKENRNKAIIIAVNS 57 (170)
T ss_pred CCHHHHHHHHHhcccCcEEEEecH
Confidence 778888999999999999999985
No 192
>TIGR02677 conserved hypothetical protein TIGR02677. Members of this protein belong to a conserved gene four-gene neighborhood found sporadically in a phylogenetically broad range of bacteria: Nocardia farcinica, Symbiobacterium thermophilum, and Streptomyces avermitilis (Actinobacteria), Geobacillus kaustophilus (Firmicutes), Azoarcus sp. EbN1 and Ralstonia solanacearum (Betaproteobacteria).
Probab=23.44 E-value=95 Score=27.55 Aligned_cols=40 Identities=23% Similarity=0.382 Sum_probs=32.4
Q ss_pred CCccChhHHHHhhhhCC-CcccHHHHHHHHHHHHhhhchhee
Q 033230 69 RQTINAEDVLKAIEEID-FTEFVDPLRDSLDGQLTFRNWIFI 109 (124)
Q Consensus 69 RKTI~~eDVl~AL~~lg-f~~~~~~l~~~l~~~~~~~~~~~~ 109 (124)
+--+.++||+..|...| |.+|- .|+..|++--+-.|++.+
T Consensus 29 ~~~L~~~dV~~~L~~~~~~~dyt-~l~~~L~qLv~WgNL~~~ 69 (494)
T TIGR02677 29 RTYLRPDDVLAFLRQYLPVADLT-ELQQALDQLVKWGNLTAI 69 (494)
T ss_pred HHhcCHHHHHHHHHhCCCcccHH-HHHHHHHHHHhccCcccc
Confidence 44588999999998888 77775 899999988877777654
No 193
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=22.88 E-value=94 Score=24.36 Aligned_cols=35 Identities=20% Similarity=0.277 Sum_probs=28.2
Q ss_pred cccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHH
Q 033230 11 EELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIF 52 (124)
Q Consensus 11 ~~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~F 52 (124)
...-++||.|++... | ..+||.+.++-+.+++++.
T Consensus 11 agVS~~TVSrvln~~-~------~~~vs~~tr~rV~~~a~~l 45 (327)
T PRK10339 11 AGVSLATVSRVLNDD-P------TLNVKEETKHRILEIAEKL 45 (327)
T ss_pred hCCCHHhhhhhhcCC-C------CCCcCHHHHHHHHHHHHHh
Confidence 467789999999754 1 2469999999999998885
No 194
>PF03484 B5: tRNA synthetase B5 domain; InterPro: IPR005147 Domain B5 is found in phenylalanine-tRNA synthetase beta subunits. This domain has been shown to bind DNA through a winged helix-turn-helix motif []. Phenylalanine-tRNA synthetase may influence common cellular processes via DNA binding, in addition to its aminoacylation function.; GO: 0000287 magnesium ion binding, 0003723 RNA binding, 0005524 ATP binding, 0006432 phenylalanyl-tRNA aminoacylation; PDB: 2AKW_B 1B70_B 1B7Y_B 2ALY_B 2IY5_B 2AMC_B 3PCO_D 2CXI_C 1JJC_B 1EIY_B ....
Probab=22.86 E-value=53 Score=20.89 Aligned_cols=18 Identities=22% Similarity=0.599 Sum_probs=12.7
Q ss_pred CccChhHHHHhhhhCCCc
Q 033230 70 QTINAEDVLKAIEEIDFT 87 (124)
Q Consensus 70 KTI~~eDVl~AL~~lgf~ 87 (124)
..++.+++...|+.|||.
T Consensus 17 ~~i~~~~i~~~L~~lg~~ 34 (70)
T PF03484_consen 17 IDISPEEIIKILKRLGFK 34 (70)
T ss_dssp S---HHHHHHHHHHTT-E
T ss_pred CCCCHHHHHHHHHHCCCE
Confidence 378999999999999996
No 195
>PF10557 Cullin_Nedd8: Cullin protein neddylation domain; InterPro: IPR019559 This is the neddylation site of cullin proteins, which are a family of structurally related proteins containing an evolutionarily conserved cullin domain. With the exception of APC2, each member of the cullin family is modified by Nedd8 and several cullins function in Ubiquitin-dependent proteolysis, a process in which the 26S proteasome recognises and subsequently degrades a target protein tagged with K48-linked poly-ubiquitin chains. Cullins are molecular scaffolds responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like protein, which was originally found to be conjugated to Cdc53, a cullin component of the SCF (Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in Saccharomyces cerevisiae (Baker's yeast), and Nedd8 modification has now emerged as a regulatory pathway of fundamental importance for cell cycle control and for embryogenesis in metazoans. The only identified Nedd8 substrates are cullins. Neddylation results in covalent conjugation of a Nedd8 moiety onto a conserved cullin lysine residue []. ; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 3RTR_G 3TDU_D 1LDJ_A 3TDZ_D 1LDK_B 1U6G_A 3O6B_J 3O2P_E 4A0K_A 2HYE_C ....
Probab=22.73 E-value=1.9e+02 Score=18.27 Aligned_cols=16 Identities=31% Similarity=0.412 Sum_probs=8.7
Q ss_pred CCccChhHHHHhhhhC
Q 033230 69 RQTINAEDVLKAIEEI 84 (124)
Q Consensus 69 RKTI~~eDVl~AL~~l 84 (124)
+-+++..+|..+++.|
T Consensus 39 ~f~~~~~~ik~~Ie~L 54 (68)
T PF10557_consen 39 RFPPSVSDIKKRIESL 54 (68)
T ss_dssp TS---HHHHHHHHHHH
T ss_pred CcCCCHHHHHHHHHHH
Confidence 5566777777777655
No 196
>COG1222 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]
Probab=22.36 E-value=1e+02 Score=26.89 Aligned_cols=32 Identities=25% Similarity=0.465 Sum_probs=28.4
Q ss_pred HHHHHHHHHHHHHhcCCCccChhHHHHhhhhC
Q 033230 53 IHYLSATANDICKESKRQTINAEDVLKAIEEI 84 (124)
Q Consensus 53 I~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~l 84 (124)
|.-+..+|--.|.++.|..|+.+|..+|.+..
T Consensus 361 lkaictEAGm~AiR~~R~~Vt~~DF~~Av~KV 392 (406)
T COG1222 361 LKAICTEAGMFAIRERRDEVTMEDFLKAVEKV 392 (406)
T ss_pred HHHHHHHHhHHHHHhccCeecHHHHHHHHHHH
Confidence 56677899999999999999999999998764
No 197
>TIGR02849 spore_III_AD stage III sporulation protein AD. Members of this family are the uncharacterized protein SpoIIIAD, part of the spoIIIA operon that acts at sporulation stage III as part of a cascade of events leading to endospore formation. Note that the start sites of members of this family as annotated tend to be variable; quite a few members have apparent homologous protein-coding regions continuing upstream of the first available start codon. The length of the alignment has been set to try to detect all valid members of the family, even if annotation of the start site begins too far downstream.
Probab=22.33 E-value=63 Score=22.87 Aligned_cols=37 Identities=19% Similarity=0.360 Sum_probs=26.9
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCh
Q 033230 36 SVHKDALLAFCESARIFIHYLSATANDICKESKRQTINA 74 (124)
Q Consensus 36 ~ISkdA~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~ 74 (124)
.++..-...+-|... |.|++.-|.++|++.|-.+|..
T Consensus 36 ~i~~~Yi~~llKiiG--IaYIaef~s~iCkDAG~~aiAs 72 (101)
T TIGR02849 36 GLDSLYLATVLKIIG--IAYIAEFGSQICKDAGEKAIAS 72 (101)
T ss_pred CCChHHHHHHHHHHH--HHHHHHHHHHHHHHcChHHHHH
Confidence 345555555555433 7899999999999999888754
No 198
>PF10885 DUF2684: Protein of unknown function (DUF2684); InterPro: IPR020263 This entry contains proteins with no known function.
Probab=22.14 E-value=24 Score=24.41 Aligned_cols=15 Identities=40% Similarity=0.749 Sum_probs=11.9
Q ss_pred eeeccCCchhhhccC
Q 033230 109 IFCCNFPAFYFKRRN 123 (124)
Q Consensus 109 ~~~~~~~~~~~~~~~ 123 (124)
-||.+||.|+--+|+
T Consensus 34 q~f~~fP~fF~~~~i 48 (89)
T PF10885_consen 34 QFFTRFPVFFESRRI 48 (89)
T ss_pred hHhhcCceeeeeeee
Confidence 379999999877664
No 199
>PF14194 Cys_rich_VLP: Cysteine-rich VLP
Probab=21.86 E-value=33 Score=21.99 Aligned_cols=18 Identities=22% Similarity=0.527 Sum_probs=15.2
Q ss_pred HHHHhhhchheeeeccCC
Q 033230 98 DGQLTFRNWIFIFCCNFP 115 (124)
Q Consensus 98 ~~~~~~~~~~~~~~~~~~ 115 (124)
.+.+.++.+|-.-|||+-
T Consensus 3 ~q~r~~~~LV~~~C~Nyd 20 (56)
T PF14194_consen 3 RQRRRIRKLVRRECCNYD 20 (56)
T ss_pred HHHHHHHHHHHHHcccCC
Confidence 467888999999999985
No 200
>TIGR01481 ccpA catabolite control protein A. Catabolite control protein A is a LacI family global transcriptional regulator found in Gram-positive bacteria. CcpA is involved in repressing carbohydrate utilization genes [ex: alpha-amylase (amyE), acetyl-coenzyme A synthase (acsA)] and in activating genes involved in transporting excess carbon from the cell [ex: acetate kinase (ackA), alpha-acetolactate synthase (alsS)]. Additionally, disruption of CcpA in Bacillus megaterium, Staphylococcus xylosus, Lactobacillus casei and Lactocacillus pentosus also decreases growth rate, which suggests CcpA is involved in the regulation of other metabolic pathways.
Probab=21.55 E-value=1.1e+02 Score=23.73 Aligned_cols=33 Identities=18% Similarity=0.168 Sum_probs=26.7
Q ss_pred cccchhHHHHHHhccccCCCCCCcchhhHHHHHHHHHHHHHH
Q 033230 11 EELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIF 52 (124)
Q Consensus 11 ~~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA~~al~~~a~~F 52 (124)
..+-.+||.|++... .+||.+.++-+.+++++.
T Consensus 11 agvS~~TVSrvLn~~---------~~vs~~tr~rV~~~a~~l 43 (329)
T TIGR01481 11 AGVSMATVSRVVNGN---------PNVKPATRKKVLEVIKRL 43 (329)
T ss_pred hCCCHHHHHHHhCCC---------CCCCHHHHHHHHHHHHHH
Confidence 367789999998653 369999999999988874
No 201
>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=21.46 E-value=1.4e+02 Score=25.82 Aligned_cols=34 Identities=18% Similarity=0.241 Sum_probs=25.7
Q ss_pred HHHHHHHHHHHHHhcCCCccChhHHHHhhhhCCC
Q 033230 53 IHYLSATANDICKESKRQTINAEDVLKAIEEIDF 86 (124)
Q Consensus 53 I~~lt~~A~~~a~~~kRKTI~~eDVl~AL~~lgf 86 (124)
|..+..+|...|.+.+++.|+.+|+..|++..-+
T Consensus 264 l~~l~~eA~~~a~~~~~~~i~~~~l~~a~~~~~~ 297 (495)
T TIGR01241 264 LANLLNEAALLAARKNKTEITMNDIEEAIDRVIA 297 (495)
T ss_pred HHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhc
Confidence 3444456666677788899999999999997643
No 202
>PF14434 Imm6: Immunity protein Imm6
Probab=21.09 E-value=3.3e+02 Score=19.63 Aligned_cols=39 Identities=10% Similarity=0.197 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHh--cCCCccChhHHHHhhhhCCCcccHHHHH
Q 033230 55 YLSATANDICKE--SKRQTINAEDVLKAIEEIDFTEFVDPLR 94 (124)
Q Consensus 55 ~lt~~A~~~a~~--~kRKTI~~eDVl~AL~~lgf~~~~~~l~ 94 (124)
+...+|.+.|.. +| +.++|+++..-|+..++.+...-+.
T Consensus 25 ~~~~~aL~~cw~wle~-~~~~~D~LY~lldn~D~~gi~~~~~ 65 (122)
T PF14434_consen 25 EFVREALDACWKWLEG-KEVTGDELYSLLDNEDENGIFIFMQ 65 (122)
T ss_pred HHHHHHHHHHHHHHHc-CCCCHHHHHHHHhCcccccHHHHHH
Confidence 334888888885 55 8899999999999988876554444
No 203
>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=21.04 E-value=1.6e+02 Score=15.97 Aligned_cols=38 Identities=11% Similarity=0.173 Sum_probs=25.8
Q ss_pred HHHhcCCCccChhHHHHhhhhCCCcccHHHHHHHHHHH
Q 033230 63 ICKESKRQTINAEDVLKAIEEIDFTEFVDPLRDSLDGQ 100 (124)
Q Consensus 63 ~a~~~kRKTI~~eDVl~AL~~lgf~~~~~~l~~~l~~~ 100 (124)
....++.-.|+.+++..+++.++...-.+.+...++.+
T Consensus 8 ~~d~~~~g~l~~~e~~~~l~~~~~~~~~~~~~~~~~~~ 45 (63)
T cd00051 8 LFDKDGDGTISADELKAALKSLGEGLSEEEIDEMIREV 45 (63)
T ss_pred HhCCCCCCcCcHHHHHHHHHHhCCCCCHHHHHHHHHHh
Confidence 33445555788899999998888665555555555554
No 204
>COG4987 CydC ABC-type transport system involved in cytochrome bd biosynthesis, fused ATPase and permease components [Energy production and conversion / Posttranslational modification, protein turnover, chaperones]
Probab=20.98 E-value=1.8e+02 Score=26.55 Aligned_cols=81 Identities=10% Similarity=0.215 Sum_probs=50.5
Q ss_pred cchhHHHHHHhccccCCCCCCcchhhH-------H-----HHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChhHHHHh
Q 033230 13 LPKTIVRRVVKDKLHNCSPDTDISVHK-------D-----ALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKA 80 (124)
Q Consensus 13 LP~A~I~RI~K~~Lp~~~~d~~~~ISk-------d-----A~~al~~~a~~FI~~lt~~A~~~a~~~kRKTI~~eDVl~A 80 (124)
=-|+|+-.++-.+.+..+ |..+++. | +...+.+....|..-|-. =..=...+.|.|++..|
T Consensus 375 sGKSTllqLl~~~~~~~~--G~i~~~g~~~~~l~~~~~~e~i~vl~Qr~hlF~~Tlr~-----NL~lA~~~AsDEel~~a 447 (573)
T COG4987 375 SGKSTLLQLLAGAWDPQQ--GSITLNGVEIASLDEQALRETISVLTQRVHLFSGTLRD-----NLRLANPDASDEELWAA 447 (573)
T ss_pred CCHHHHHHHHHhccCCCC--CeeeECCcChhhCChhhHHHHHhhhccchHHHHHHHHH-----HHhhcCCCCCHHHHHHH
Confidence 357888888887776443 3333333 1 223334444444332221 22334566999999999
Q ss_pred hhhCCCcccHHHHHHHHHHH
Q 033230 81 IEEIDFTEFVDPLRDSLDGQ 100 (124)
Q Consensus 81 L~~lgf~~~~~~l~~~l~~~ 100 (124)
|+..|+++++...-+-|+-|
T Consensus 448 L~qvgL~~l~~~~p~gl~t~ 467 (573)
T COG4987 448 LQQVGLEKLLESAPDGLNTW 467 (573)
T ss_pred HHHcCHHHHHHhChhhhhch
Confidence 99999999998886655544
No 205
>PF11539 DUF3228: Protein of unknown function (DUF3228); InterPro: IPR021610 This family of proteins has no known function. ; PDB: 2PD0_B 4FBD_B.
Probab=20.59 E-value=82 Score=24.98 Aligned_cols=34 Identities=15% Similarity=0.276 Sum_probs=15.4
Q ss_pred cccccccchhHHHHHHhccccCCCCCCcchhhHHH
Q 033230 7 VPEAEELPKTIVRRVVKDKLHNCSPDTDISVHKDA 41 (124)
Q Consensus 7 ~~ed~~LP~A~I~RI~K~~Lp~~~~d~~~~ISkdA 41 (124)
..++.++|.++|+ +|+++|.-..+++++-+.+|+
T Consensus 149 Q~e~~E~PM~PIT-mmRNALG~eEGGSGVpLDRek 182 (197)
T PF11539_consen 149 QDEDYELPMQPIT-MMRNALGIEEGGSGVPLDREK 182 (197)
T ss_dssp ESSSS-----HHH-HHHTTS-CCCTS------HHH
T ss_pred cCCCCCCCCccHH-HHHHHhhhhcCCCCCcccHHH
Confidence 3477899999997 789999654444457777665
No 206
>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=20.17 E-value=34 Score=25.02 Aligned_cols=35 Identities=17% Similarity=0.335 Sum_probs=0.0
Q ss_pred hcCCCccChhHHHHhhhhCCC-cccHHHHHHHHHHH
Q 033230 66 ESKRQTINAEDVLKAIEEIDF-TEFVDPLRDSLDGQ 100 (124)
Q Consensus 66 ~~kRKTI~~eDVl~AL~~lgf-~~~~~~l~~~l~~~ 100 (124)
..|-||||+.|+--|-+.++| -.++|.++++++..
T Consensus 62 ~agLK~IT~KhLALasq~L~~~~~lip~i~~~~~~~ 97 (135)
T PF07928_consen 62 SAGLKTITAKHLALASQSLSFIISLIPYIREFFERH 97 (135)
T ss_dssp ------------------------------------
T ss_pred ccCcCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 467999999999999999997 47888888777765
Done!