Query 027605
Match_columns 221
No_of_seqs 131 out of 580
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 12:26:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027605.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027605hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0869 CCAAT-binding factor, 100.0 1.1E-35 2.4E-40 249.3 9.9 106 19-124 24-129 (168)
2 KOG0871 Class 2 transcription 99.9 1E-27 2.3E-32 199.5 10.5 101 19-119 4-104 (156)
3 KOG0870 DNA polymerase epsilon 99.9 1.1E-26 2.4E-31 196.1 9.7 108 18-125 1-109 (172)
4 COG5150 Class 2 transcription 99.9 2.1E-22 4.5E-27 165.2 10.2 99 22-120 6-104 (148)
5 PF00808 CBFD_NFYB_HMF: Histon 99.7 4.6E-18 9.9E-23 121.2 7.6 64 27-91 2-65 (65)
6 COG2036 HHT1 Histones H3 and H 99.6 1.7E-15 3.8E-20 117.4 6.4 78 21-100 13-90 (91)
7 cd00076 H4 Histone H4, one of 99.1 6.9E-10 1.5E-14 85.2 8.3 71 27-99 13-83 (85)
8 PLN00035 histone H4; Provision 99.0 1.3E-09 2.9E-14 86.5 8.4 71 26-98 28-98 (103)
9 PTZ00015 histone H4; Provision 98.9 3.7E-09 8E-14 83.8 8.3 75 23-99 26-100 (102)
10 smart00803 TAF TATA box bindin 98.8 1.6E-08 3.4E-13 73.7 7.5 64 27-92 2-65 (65)
11 cd07981 TAF12 TATA Binding Pro 98.7 9.6E-08 2.1E-12 70.4 8.3 66 28-94 2-67 (72)
12 smart00417 H4 Histone H4. 98.7 3.3E-08 7.2E-13 74.3 5.9 61 27-89 13-73 (74)
13 PF00125 Histone: Core histone 98.7 6.1E-08 1.3E-12 70.0 6.0 68 25-92 3-73 (75)
14 COG5208 HAP5 CCAAT-binding fac 98.6 3.6E-08 7.8E-13 88.1 4.2 78 24-103 106-184 (286)
15 smart00428 H3 Histone H3. 98.5 2.5E-07 5.4E-12 73.7 6.3 71 22-92 24-99 (105)
16 KOG1657 CCAAT-binding factor, 98.4 1.2E-07 2.6E-12 84.4 3.0 84 25-110 72-159 (236)
17 smart00576 BTP Bromodomain tra 98.2 1.1E-05 2.5E-10 59.7 8.3 66 30-97 9-74 (77)
18 cd00074 H2A Histone 2A; H2A is 98.0 1.5E-05 3.4E-10 64.2 6.8 69 24-93 17-85 (115)
19 PLN00121 histone H3; Provision 98.0 1.1E-05 2.4E-10 67.1 5.3 70 22-91 57-129 (136)
20 PLN00161 histone H3; Provision 98.0 2.7E-05 5.8E-10 64.8 7.1 70 22-91 50-123 (135)
21 PLN00160 histone H3; Provision 97.9 2.2E-05 4.8E-10 62.0 6.1 70 22-91 16-89 (97)
22 PTZ00018 histone H3; Provision 97.9 2E-05 4.3E-10 65.5 5.2 70 22-91 57-129 (136)
23 cd07979 TAF9 TATA Binding Prot 97.9 9.6E-05 2.1E-09 59.4 8.8 78 31-110 5-83 (117)
24 cd08050 TAF6 TATA Binding Prot 97.7 0.00011 2.4E-09 67.8 8.1 67 29-97 1-67 (343)
25 PF15511 CENP-T: Centromere ki 97.7 6.2E-05 1.4E-09 71.4 5.8 65 22-86 346-414 (414)
26 smart00427 H2B Histone H2B. 97.6 0.0003 6.5E-09 54.9 7.3 63 31-94 5-67 (89)
27 cd08048 TAF11 TATA Binding Pro 97.6 0.00045 9.8E-09 53.0 7.8 66 27-94 16-84 (85)
28 PF15630 CENP-S: Kinetochore c 97.6 0.00033 7.2E-09 52.9 6.9 62 32-93 10-72 (76)
29 PF09415 CENP-X: CENP-S associ 97.5 0.00018 3.8E-09 53.8 4.4 64 29-92 1-66 (72)
30 PF03847 TFIID_20kDa: Transcri 97.5 0.00064 1.4E-08 50.3 7.3 63 30-93 2-64 (68)
31 PF07524 Bromo_TP: Bromodomain 97.4 0.0011 2.4E-08 48.6 8.4 65 31-97 10-74 (77)
32 PLN00158 histone H2B; Provisio 97.3 0.001 2.2E-08 54.2 7.3 66 28-94 28-93 (116)
33 PTZ00463 histone H2B; Provisio 97.3 0.0013 2.7E-08 53.8 7.3 62 32-94 33-94 (117)
34 KOG3467 Histone H4 [Chromatin 97.2 0.0013 2.8E-08 52.0 7.0 68 28-97 30-97 (103)
35 PF04719 TAFII28: hTAFII28-lik 97.2 0.0016 3.5E-08 50.7 6.8 67 27-94 23-90 (90)
36 KOG1659 Class 2 transcription 97.1 0.00072 1.6E-08 60.2 5.2 82 26-108 12-93 (224)
37 COG5262 HTA1 Histone H2A [Chro 97.1 0.0011 2.4E-08 54.6 5.4 71 21-92 20-90 (132)
38 PF02969 TAF: TATA box binding 96.9 0.0061 1.3E-07 45.0 7.5 64 27-92 3-66 (66)
39 COG5247 BUR6 Class 2 transcrip 96.7 0.004 8.7E-08 50.3 5.4 81 23-104 19-99 (113)
40 KOG1658 DNA polymerase epsilon 96.4 0.0022 4.8E-08 54.8 2.8 66 26-93 58-124 (162)
41 PF15510 CENP-W: Centromere ki 96.4 0.0064 1.4E-07 48.3 4.8 67 26-93 15-95 (102)
42 smart00414 H2A Histone 2A. 96.3 0.013 2.8E-07 46.8 6.5 69 24-93 6-74 (106)
43 KOG1142 Transcription initiati 96.2 0.013 2.8E-07 53.5 6.4 69 23-92 150-218 (258)
44 KOG1745 Histones H3 and H4 [Ch 96.1 0.0035 7.7E-08 52.4 2.3 71 22-92 58-131 (137)
45 PLN00154 histone H2A; Provisio 95.9 0.025 5.4E-07 47.4 6.3 70 24-93 35-104 (136)
46 PTZ00017 histone H2A; Provisio 95.7 0.067 1.5E-06 44.6 8.1 68 24-92 24-91 (134)
47 PF02269 TFIID-18kDa: Transcri 95.5 0.018 3.9E-07 44.5 3.9 59 34-93 8-66 (93)
48 KOG1744 Histone H2B [Chromatin 95.4 0.056 1.2E-06 44.8 6.8 62 32-94 42-103 (127)
49 PLN00156 histone H2AX; Provisi 95.0 0.067 1.5E-06 44.9 6.0 68 24-92 26-93 (139)
50 PLN00157 histone H2A; Provisio 95.0 0.056 1.2E-06 45.0 5.5 68 24-92 23-90 (132)
51 KOG3219 Transcription initiati 95.0 0.029 6.3E-07 49.4 4.0 70 27-98 112-182 (195)
52 PLN00153 histone H2A; Provisio 95.0 0.063 1.4E-06 44.6 5.7 68 24-92 21-88 (129)
53 KOG1756 Histone 2A [Chromatin 95.0 0.069 1.5E-06 44.5 5.9 69 23-92 23-91 (131)
54 cd07978 TAF13 The TATA Binding 94.4 0.28 6.1E-06 38.1 7.7 60 32-93 7-66 (92)
55 PF02291 TFIID-31kDa: Transcri 93.4 0.37 8E-06 39.8 7.1 84 25-110 8-94 (129)
56 KOG3423 Transcription initiati 91.9 0.81 1.8E-05 39.9 7.5 69 27-97 86-168 (176)
57 PTZ00252 histone H2A; Provisio 91.6 0.63 1.4E-05 39.0 6.3 64 24-92 22-91 (134)
58 TIGR03015 pepcterm_ATPase puta 90.4 0.9 2E-05 38.7 6.4 71 27-97 191-269 (269)
59 KOG4336 TBP-associated transcr 87.3 3.3 7.1E-05 39.2 8.2 77 32-112 10-86 (323)
60 PRK00411 cdc6 cell division co 86.9 2.9 6.3E-05 37.9 7.6 71 29-99 208-287 (394)
61 KOG2549 Transcription initiati 86.7 2.7 5.8E-05 42.4 7.7 66 28-95 12-77 (576)
62 TIGR02928 orc1/cdc6 family rep 81.5 6.3 0.00014 35.3 7.3 72 30-101 201-281 (365)
63 cd08045 TAF4 TATA Binding Prot 80.2 7.2 0.00016 33.8 6.9 79 23-101 40-126 (212)
64 KOG2389 Predicted bromodomain 78.5 5.6 0.00012 38.1 6.1 71 25-97 27-97 (353)
65 KOG1757 Histone 2A [Chromatin 76.4 6.4 0.00014 32.7 5.2 66 23-92 26-95 (131)
66 PF13654 AAA_32: AAA domain; P 72.9 13 0.00028 36.8 7.2 61 32-94 435-506 (509)
67 TIGR00764 lon_rel lon-related 71.6 14 0.0003 37.1 7.2 50 46-95 330-392 (608)
68 KOG2680 DNA helicase TIP49, TB 71.1 17 0.00037 35.4 7.3 50 43-92 374-427 (454)
69 TIGR02902 spore_lonB ATP-depen 71.0 11 0.00024 37.0 6.3 66 30-96 265-334 (531)
70 KOG3334 Transcription initiati 70.1 34 0.00074 29.3 8.1 64 47-110 31-95 (148)
71 COG1067 LonB Predicted ATP-dep 69.9 4.1 8.8E-05 41.6 3.1 47 46-93 338-398 (647)
72 PF13335 Mg_chelatase_2: Magne 61.9 29 0.00063 26.8 5.8 48 45-92 41-94 (96)
73 COG5095 TAF6 Transcription ini 56.3 24 0.00052 34.2 5.4 64 31-96 9-72 (450)
74 TIGR00635 ruvB Holliday juncti 55.6 83 0.0018 27.5 8.3 70 28-97 159-232 (305)
75 PRK00080 ruvB Holliday junctio 54.9 60 0.0013 29.3 7.5 71 28-98 180-254 (328)
76 PF02861 Clp_N: Clp amino term 54.4 11 0.00023 24.6 2.0 26 70-95 1-26 (53)
77 COG5162 Transcription initiati 53.3 75 0.0016 28.1 7.5 52 46-97 105-189 (197)
78 PF03540 TFIID_30kDa: Transcri 51.8 85 0.0018 22.3 6.4 47 27-76 2-49 (51)
79 TIGR02442 Cob-chelat-sub cobal 50.1 53 0.0011 33.1 6.9 53 39-92 243-302 (633)
80 TIGR02030 BchI-ChlI magnesium 49.4 63 0.0014 30.2 6.9 54 38-92 247-307 (337)
81 PRK07452 DNA polymerase III su 46.8 78 0.0017 28.2 6.9 54 44-97 147-202 (326)
82 PF05236 TAF4: Transcription i 46.2 26 0.00055 31.3 3.7 75 23-97 39-121 (264)
83 PF08369 PCP_red: Proto-chloro 44.9 29 0.00063 23.6 3.0 42 48-90 2-44 (45)
84 PRK13765 ATP-dependent proteas 44.6 59 0.0013 33.2 6.3 48 46-93 339-399 (637)
85 cd04752 Commd4 COMM_Domain con 43.8 73 0.0016 26.9 5.9 50 58-114 43-93 (174)
86 KOG3901 Transcription initiati 43.6 63 0.0014 26.5 5.2 49 42-93 23-71 (109)
87 KOG2181 LIM domain binding pro 43.3 12 0.00026 35.9 1.2 25 162-194 312-337 (415)
88 PRK13406 bchD magnesium chelat 43.2 49 0.0011 33.4 5.5 59 32-92 183-248 (584)
89 COG1224 TIP49 DNA helicase TIP 42.1 49 0.0011 32.7 5.1 65 28-92 361-430 (450)
90 PRK09862 putative ATP-dependen 41.7 86 0.0019 31.2 6.9 58 45-102 437-500 (506)
91 COG5248 TAF19 Transcription in 41.6 67 0.0015 26.7 5.1 50 42-93 23-72 (126)
92 PRK12402 replication factor C 41.4 59 0.0013 28.5 5.2 70 27-98 183-253 (337)
93 PRK14975 bifunctional 3'-5' ex 40.8 1.6E+02 0.0034 29.2 8.5 93 24-119 160-272 (553)
94 PF00531 Death: Death domain; 39.8 39 0.00084 23.8 3.1 61 46-107 23-83 (83)
95 PF00356 LacI: Bacterial regul 38.6 74 0.0016 21.6 4.2 32 27-62 10-41 (46)
96 PF08681 DUF1778: Protein of u 38.4 25 0.00053 26.2 2.0 51 44-94 3-61 (80)
97 PF12010 DUF3502: Domain of un 38.3 25 0.00053 28.5 2.2 62 49-114 72-133 (134)
98 CHL00081 chlI Mg-protoporyphyr 37.9 1E+02 0.0022 29.3 6.4 55 37-92 259-320 (350)
99 TIGR01052 top6b DNA topoisomer 37.6 32 0.0007 34.2 3.2 58 38-109 426-483 (488)
100 TIGR01128 holA DNA polymerase 37.4 1.5E+02 0.0033 25.6 7.1 66 27-92 110-176 (302)
101 COG1474 CDC6 Cdc6-related prot 36.7 1.2E+02 0.0025 28.8 6.6 73 32-104 194-275 (366)
102 TIGR02031 BchD-ChlD magnesium 36.4 1.1E+02 0.0023 30.8 6.7 55 37-92 195-256 (589)
103 smart00350 MCM minichromosome 36.3 1.5E+02 0.0032 29.0 7.5 68 26-93 416-503 (509)
104 TIGR00368 Mg chelatase-related 36.1 83 0.0018 31.1 5.8 47 46-92 445-497 (499)
105 PRK13407 bchI magnesium chelat 33.8 1.2E+02 0.0025 28.5 6.1 53 38-91 244-303 (334)
106 PLN00138 large subunit ribosom 33.8 1.1E+02 0.0023 24.8 5.2 45 64-110 2-46 (113)
107 PRK12728 fliE flagellar hook-b 30.8 2E+02 0.0043 22.8 6.1 66 48-115 30-99 (102)
108 PF07647 SAM_2: SAM domain (St 30.8 49 0.0011 22.6 2.4 24 82-105 4-27 (66)
109 PTZ00361 26 proteosome regulat 30.4 60 0.0013 31.6 3.7 32 63-94 393-424 (438)
110 PRK09526 lacI lac repressor; R 30.3 29 0.00064 30.2 1.5 37 27-68 16-52 (342)
111 PTZ00373 60S Acidic ribosomal 30.1 1.4E+02 0.0031 24.2 5.3 43 64-108 4-46 (112)
112 PRK05574 holA DNA polymerase I 29.7 2E+02 0.0044 25.4 6.7 66 27-93 145-212 (340)
113 PF08823 PG_binding_2: Putativ 29.6 82 0.0018 23.5 3.6 33 85-117 19-57 (74)
114 PRK03992 proteasome-activating 29.0 69 0.0015 30.1 3.8 35 62-96 340-374 (389)
115 PF09114 MotA_activ: Transcrip 29.0 87 0.0019 25.1 3.7 32 31-62 51-86 (96)
116 TIGR01242 26Sp45 26S proteasom 28.8 69 0.0015 29.4 3.7 33 62-94 331-363 (364)
117 PLN02900 alanyl-tRNA synthetas 28.6 3.4E+02 0.0073 29.3 9.1 29 75-103 404-433 (936)
118 COG5251 TAF40 Transcription in 28.4 78 0.0017 28.1 3.7 62 27-92 115-179 (199)
119 PF02361 CbiQ: Cobalt transpor 28.1 80 0.0017 26.0 3.6 70 46-121 95-176 (224)
120 PF00536 SAM_1: SAM domain (St 27.4 57 0.0012 22.2 2.2 22 83-104 4-25 (64)
121 cd00166 SAM Sterile alpha moti 27.1 41 0.0009 22.1 1.5 24 83-106 3-26 (63)
122 PTZ00183 centrin; Provisional 27.0 2.4E+02 0.0052 21.5 6.0 20 77-96 29-48 (158)
123 PF07499 RuvA_C: RuvA, C-termi 26.7 41 0.00088 22.6 1.4 13 85-97 4-16 (47)
124 smart00354 HTH_LACI helix_turn 26.5 1.2E+02 0.0026 21.5 3.9 33 26-62 10-42 (70)
125 PRK07914 hypothetical protein; 25.7 1.6E+02 0.0034 26.6 5.3 62 30-92 130-192 (320)
126 COG1724 Predicted RNA binding 25.3 43 0.00093 25.2 1.4 17 81-97 6-22 (66)
127 PTZ00454 26S protease regulato 25.0 84 0.0018 30.0 3.6 32 63-94 355-386 (398)
128 PF12627 PolyA_pol_RNAbd: Prob 24.9 14 0.0003 25.4 -1.2 58 45-106 2-63 (64)
129 PRK14987 gluconate operon tran 24.4 40 0.00087 29.3 1.3 38 27-69 16-53 (331)
130 PRK06585 holA DNA polymerase I 24.3 1.6E+02 0.0035 26.4 5.2 49 44-92 159-208 (343)
131 cd05833 Ribosomal_P2 Ribosomal 24.0 2.1E+02 0.0045 23.0 5.2 31 65-97 3-33 (109)
132 PF14434 Imm6: Immunity protei 23.8 2.5E+02 0.0053 22.9 5.6 49 53-101 8-62 (122)
133 TIGR02454 CbiQ_TIGR cobalt ABC 23.5 1.2E+02 0.0026 25.0 3.8 38 80-117 112-160 (198)
134 COG1389 DNA topoisomerase VI, 23.4 58 0.0012 32.9 2.2 39 45-83 441-479 (538)
135 COG1222 RPT1 ATP-dependent 26S 23.1 1.2E+02 0.0026 29.9 4.3 75 20-94 313-392 (406)
136 KOG1792 Reticulon [Intracellul 23.1 1.8E+02 0.0039 26.2 5.1 56 40-95 110-166 (230)
137 cd00823 TopoIIB_Trans TopoIIB_ 23.0 1.3E+02 0.0028 25.9 4.0 34 38-71 111-144 (151)
138 PRK10423 transcriptional repre 22.5 59 0.0013 28.0 1.9 37 27-68 9-45 (327)
139 PF02049 FliE: Flagellar hook- 22.2 3.6E+02 0.0078 20.6 6.2 69 47-115 23-93 (96)
140 KOG1528 Salt-sensitive 3'-phos 22.2 1.9E+02 0.0041 27.9 5.2 79 16-95 39-124 (351)
141 smart00027 EH Eps15 homology d 21.9 1.5E+02 0.0032 21.9 3.8 28 70-97 15-42 (96)
142 PRK14868 DNA topoisomerase VI 21.4 88 0.0019 33.2 3.2 45 38-82 625-669 (795)
143 COG1466 HolA DNA polymerase II 21.0 2.5E+02 0.0055 25.6 5.8 50 44-93 157-206 (334)
144 TIGR03261 phnS2 putative 2-ami 20.9 2.2E+02 0.0047 25.3 5.2 61 56-116 260-331 (334)
145 PRK00440 rfc replication facto 20.8 2.4E+02 0.0053 24.4 5.4 65 28-94 161-226 (319)
146 PRK14971 DNA polymerase III su 20.6 2.2E+02 0.0047 28.9 5.7 64 28-92 180-244 (614)
147 PRK09492 treR trehalose repres 20.5 71 0.0015 27.4 2.0 37 27-68 15-51 (315)
148 TIGR02903 spore_lon_C ATP-depe 20.4 1.8E+02 0.004 29.3 5.1 72 30-101 355-437 (615)
149 smart00454 SAM Sterile alpha m 20.3 64 0.0014 21.3 1.4 25 82-106 4-28 (68)
150 KOG3468 NADH:ubiquinone oxidor 20.1 2.5E+02 0.0053 23.5 4.9 113 10-132 11-126 (128)
No 1
>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [Transcription]
Probab=100.00 E-value=1.1e-35 Score=249.27 Aligned_cols=106 Identities=81% Similarity=1.226 Sum_probs=100.6
Q ss_pred CCCCccccCCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHHhhcCCCc
Q 027605 19 ISDKEQDRFLPIANVSRIMKKSLPANAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAMTTLGFEN 98 (221)
Q Consensus 19 ~s~~eeD~~LPrAtV~RImK~aLP~n~kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~ALe~LGF~~ 98 (221)
.+.+++|++||+|+|.||||..||++.||||||++.||+|++|||+|||+||+++|.+++||||++|||||||..|||++
T Consensus 24 ~~~reqDr~LPIANV~RIMK~~lP~naKIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIngdDllwAm~tLGFe~ 103 (168)
T KOG0869|consen 24 LSLREQDRFLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASEKCQREKRKTINGDDLLWAMSTLGFEN 103 (168)
T ss_pred cccchhhhhccHHHHHHHHHhcCCcccccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCcccHHHHHHHHHHcCcHh
Confidence 46889999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred chHHHHHHHHHHHHHHhhhhhhhhhh
Q 027605 99 YVSPLKIYLNKYRETEGEKNSMARQE 124 (221)
Q Consensus 99 yv~~Lk~~Le~yRe~~k~Kks~~k~~ 124 (221)
|+++|+.||.+|||.+.++....+..
T Consensus 104 Y~eplkiyL~kYRe~e~e~~~~~~~~ 129 (168)
T KOG0869|consen 104 YAEPLKIYLQKYRELEGERGRSGKGG 129 (168)
T ss_pred HHHHHHHHHHHHHHHhhhcccccccC
Confidence 99999999999999988777655444
No 2
>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=99.95 E-value=1e-27 Score=199.53 Aligned_cols=101 Identities=30% Similarity=0.602 Sum_probs=95.6
Q ss_pred CCCCccccCCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHHhhcCCCc
Q 027605 19 ISDKEQDRFLPIANVSRIMKKSLPANAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAMTTLGFEN 98 (221)
Q Consensus 19 ~s~~eeD~~LPrAtV~RImK~aLP~n~kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~ALe~LGF~~ 98 (221)
+....+|+.||+|+|.+|||+.||.+++|.+|++++|.+||.+||++|+++||++|.++.||||++|||++||+.|||.+
T Consensus 4 ~~~~dde~sLPkAtv~KmIke~lP~d~rvakeareliincCvEFI~liSsEAneic~~e~KKTIa~EHV~KALe~LgF~e 83 (156)
T KOG0871|consen 4 DGKEDDELSLPKATVNKMIKEMLPKDVRVAKEARELIINCCVEFINLISSEANEICNKEAKKTIAPEHVIKALENLGFGE 83 (156)
T ss_pred CccccccccCcHHHHHHHHHHhCCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHhHHhcccCCHHHHHHHHHHcchHH
Confidence 34567899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred chHHHHHHHHHHHHHHhhhhh
Q 027605 99 YVSPLKIYLNKYRETEGEKNS 119 (221)
Q Consensus 99 yv~~Lk~~Le~yRe~~k~Kks 119 (221)
|++.+.+.|+.||...+.++.
T Consensus 84 Yiee~~~vl~~~K~~~~~~~~ 104 (156)
T KOG0871|consen 84 YIEEAEEVLENCKEEAKKRRR 104 (156)
T ss_pred HHHHHHHHHHHHHHHHHHhhh
Confidence 999999999999988776544
No 3
>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription]
Probab=99.94 E-value=1.1e-26 Score=196.15 Aligned_cols=108 Identities=31% Similarity=0.523 Sum_probs=102.6
Q ss_pred CCCCCccccCCchhHHHHHHhhcCCCC-cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHHhhcCC
Q 027605 18 NISDKEQDRFLPIANVSRIMKKSLPAN-AKISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAMTTLGF 96 (221)
Q Consensus 18 ~~s~~eeD~~LPrAtV~RImK~aLP~n-~kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~ALe~LGF 96 (221)
+++.+++|+.||+|+|.||+|+.||+. +.|+|||+.+|+++|++||+||++.|+++|+.++||||+++|||+||++|+|
T Consensus 1 qe~eri~dl~lP~AiI~rlvke~l~E~~vsisKeA~~Ai~raAtVFv~~Lts~s~e~A~~q~rKt~sadDVl~aL~Eief 80 (172)
T KOG0870|consen 1 QEDERIEDLNLPNAIITRLVKEVLPESNVSISKEARLAIARAATVFVIFLTSVSNEIAKDQKRKTISADDVLKALDEIEF 80 (172)
T ss_pred CcchhHHHhhccHHHHHHHHHHhCccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCcccHHHHHHHHHHhch
Confidence 367889999999999999999999987 9999999999999999999999999999999999999999999999999999
Q ss_pred CcchHHHHHHHHHHHHHHhhhhhhhhhhh
Q 027605 97 ENYVSPLKIYLNKYRETEGEKNSMARQED 125 (221)
Q Consensus 97 ~~yv~~Lk~~Le~yRe~~k~Kks~~k~~~ 125 (221)
..|+.+|+..|+.||...++|+..+..+.
T Consensus 81 s~f~~plk~~Le~yk~~~k~Kk~~~~~~~ 109 (172)
T KOG0870|consen 81 SSFVNPLKSALEAYKKAVKQKKLAKANKS 109 (172)
T ss_pred HHHhhHHHHHHHHHHHHHHHHHHhccccc
Confidence 99999999999999999999998765554
No 4
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=99.88 E-value=2.1e-22 Score=165.22 Aligned_cols=99 Identities=28% Similarity=0.509 Sum_probs=95.4
Q ss_pred CccccCCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHHhhcCCCcchH
Q 027605 22 KEQDRFLPIANVSRIMKKSLPANAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAMTTLGFENYVS 101 (221)
Q Consensus 22 ~eeD~~LPrAtV~RImK~aLP~n~kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~ALe~LGF~~yv~ 101 (221)
..++..||+|+|.+++.+.||.+..++|||++.+++||.+||+.|+++||++|..+.+|||.+|||++||+.|+|.+|++
T Consensus 6 ~dDe~sLPKATVqKMvS~iLp~dl~ftKearei~in~cieFi~~lsseAne~ce~EaKKTIa~EHviKALenLef~eyi~ 85 (148)
T COG5150 6 NDDENSLPKATVQKMVSSILPKDLVFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHVIKALENLEFEEYIE 85 (148)
T ss_pred ccccccCcHHHHHHHHHHhccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHhccHHHHHH
Confidence 46788999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHhhhhhh
Q 027605 102 PLKIYLNKYRETEGEKNSM 120 (221)
Q Consensus 102 ~Lk~~Le~yRe~~k~Kks~ 120 (221)
.+.+.++.|+..++.|.+.
T Consensus 86 ~~~e~~~n~k~~qK~ke~k 104 (148)
T COG5150 86 SCMEEHENYKSYQKQKESK 104 (148)
T ss_pred HHHHHHHHHHHHHhhchhh
Confidence 9999999999999888764
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=99.74 E-value=4.6e-18 Score=121.18 Aligned_cols=64 Identities=44% Similarity=0.659 Sum_probs=59.4
Q ss_pred CCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHH
Q 027605 27 FLPIANVSRIMKKSLPANAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAM 91 (221)
Q Consensus 27 ~LPrAtV~RImK~aLP~n~kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~AL 91 (221)
.||++.|.||||.. |+..+||+||.++|++|+++||.||+.+|++.|..++||||+++||..||
T Consensus 2 ~lP~a~vkri~k~~-~~~~~vs~ea~~~i~~a~e~Fi~~l~~~A~~~a~~~~rkti~~~Dv~~Av 65 (65)
T PF00808_consen 2 SLPLARVKRIMKSD-PDVMRVSKEAVEAIAKAAEEFIQYLAKEANEIAQRDKRKTITYEDVAKAV 65 (65)
T ss_dssp SS-HHHHHHHHHHT-STTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEE-HHHHHHHH
T ss_pred CCChHHHHHHhccC-CCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHC
Confidence 69999999999999 88899999999999999999999999999999999999999999999986
No 6
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=99.59 E-value=1.7e-15 Score=117.44 Aligned_cols=78 Identities=32% Similarity=0.508 Sum_probs=73.3
Q ss_pred CCccccCCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHHhhcCCCcch
Q 027605 21 DKEQDRFLPIANVSRIMKKSLPANAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAMTTLGFENYV 100 (221)
Q Consensus 21 ~~eeD~~LPrAtV~RImK~aLP~n~kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~ALe~LGF~~yv 100 (221)
.+..|..||+++|.||||+..++ +||.+|++.|++|+++|+..|+..|.+.|.++|||||+++||..|++.+||..|.
T Consensus 13 ~~~~~~~Lp~apv~Ri~r~~~~~--Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~DI~la~~~~~~~~~~ 90 (91)
T COG2036 13 QRSTDLLLPKAPVRRILRKAGAE--RVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLALKRLGRRIYG 90 (91)
T ss_pred hhhhhhhcCchHHHHHHHHHhHH--HhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHHHhcccccc
Confidence 34678899999999999999975 9999999999999999999999999999999999999999999999999997653
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=99.07 E-value=6.9e-10 Score=85.23 Aligned_cols=71 Identities=18% Similarity=0.317 Sum_probs=66.4
Q ss_pred CCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHHhhcCCCcc
Q 027605 27 FLPIANVSRIMKKSLPANAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAMTTLGFENY 99 (221)
Q Consensus 27 ~LPrAtV~RImK~aLP~n~kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~ALe~LGF~~y 99 (221)
.||++.|.||++... ..+||.|+.+.+.++..+|+..|..+|...|++.+||||+++||.-||++.|-.-|
T Consensus 13 gi~k~~I~RLarr~G--vkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~alkr~g~~~y 83 (85)
T cd00076 13 GITKPAIRRLARRGG--VKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLY 83 (85)
T ss_pred cCCHHHHHHHHHHcC--cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHCCCCcc
Confidence 499999999999995 67899999999999999999999999999999999999999999999999986543
No 8
>PLN00035 histone H4; Provisional
Probab=99.02 E-value=1.3e-09 Score=86.47 Aligned_cols=71 Identities=17% Similarity=0.254 Sum_probs=66.1
Q ss_pred cCCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHHhhcCCCc
Q 027605 26 RFLPIANVSRIMKKSLPANAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAMTTLGFEN 98 (221)
Q Consensus 26 ~~LPrAtV~RImK~aLP~n~kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~ALe~LGF~~ 98 (221)
..||++.|.||++..- ..+||.|+.+.+.+..++|+.-|..+|...|++.+||||+++||.-||++.|=.-
T Consensus 28 ~~ipk~~IrRLARr~G--vkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr~g~~l 98 (103)
T PLN00035 28 QGITKPAIRRLARRGG--VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTL 98 (103)
T ss_pred ccCCHHHHHHHHHHcC--cccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHcCCcC
Confidence 3599999999999995 5789999999999999999999999999999999999999999999999887543
No 9
>PTZ00015 histone H4; Provisional
Probab=98.95 E-value=3.7e-09 Score=83.80 Aligned_cols=75 Identities=19% Similarity=0.336 Sum_probs=68.0
Q ss_pred ccccCCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHHhhcCCCcc
Q 027605 23 EQDRFLPIANVSRIMKKSLPANAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAMTTLGFENY 99 (221)
Q Consensus 23 eeD~~LPrAtV~RImK~aLP~n~kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~ALe~LGF~~y 99 (221)
+-...||++.|.||++..- ..+||.|+.+.+.++..+|+..|..+|...|++.+||||+++||..||++.|-.-|
T Consensus 26 ~~i~gI~k~~IrRLarr~G--vkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~AlKr~g~~~y 100 (102)
T PTZ00015 26 DNIRGITKGAIRRLARRGG--VKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALKRQGRTLY 100 (102)
T ss_pred hcccCCCHHHHHHHHHHcC--CccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhcCCCCC
Confidence 3345799999999999995 57899999999999999999999999999999999999999999999999886443
No 10
>smart00803 TAF TATA box binding protein associated factor. TAFs (TATA box binding protein associated factors) are part of the transcription initiation factor TFIID multimeric protein complex. TFIID is composed of the TATA box binding protein (TBP) and a number of TAFs. The TAFs provide binding sites for many different transcriptional activators and co-activators that modulate transcription initiation by Pol II. TAF proteins adopt a histone-like fold.
Probab=98.83 E-value=1.6e-08 Score=73.74 Aligned_cols=64 Identities=25% Similarity=0.246 Sum_probs=60.2
Q ss_pred CCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHHh
Q 027605 27 FLPIANVSRIMKKSLPANAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAMT 92 (221)
Q Consensus 27 ~LPrAtV~RImK~aLP~n~kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~ALe 92 (221)
.||++.|.||++... -.+||.|+...|.+-++.|+.-|..+|...+++.+||||+++||-.||+
T Consensus 2 ~~p~~~i~ria~~~G--i~ris~~a~~~l~~~~e~rl~~i~~~A~k~~~hakRktlt~~DI~~Alk 65 (65)
T smart00803 2 WLPKETIKDVAESLG--IGNLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSALR 65 (65)
T ss_pred CCCHHHHHHHHHHCC--CccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCeecHHHHHHHhC
Confidence 589999999999984 4579999999999999999999999999999999999999999999985
No 11
>cd07981 TAF12 TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of the seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs function such as serving as activator-bind
Probab=98.70 E-value=9.6e-08 Score=70.36 Aligned_cols=66 Identities=15% Similarity=0.290 Sum_probs=62.1
Q ss_pred CchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHHhhc
Q 027605 28 LPIANVSRIMKKSLPANAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAMTTL 94 (221)
Q Consensus 28 LPrAtV~RImK~aLP~n~kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~ALe~L 94 (221)
|++..+..++|+.=| ..+|+.||.++|++.+.+|+.-|+..|...|++.+|+||.++||.-+|++.
T Consensus 2 ~~k~~l~~lv~~id~-~~~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~~~tv~~~Di~l~l~r~ 67 (72)
T cd07981 2 LTKRKLQELLKEIDP-REQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQLHLERN 67 (72)
T ss_pred CcHHHHHHHHHhhCC-CCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHh
Confidence 678889999999976 699999999999999999999999999999999999999999999999863
No 12
>smart00417 H4 Histone H4.
Probab=98.70 E-value=3.3e-08 Score=74.33 Aligned_cols=61 Identities=15% Similarity=0.290 Sum_probs=57.6
Q ss_pred CCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHH
Q 027605 27 FLPIANVSRIMKKSLPANAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLW 89 (221)
Q Consensus 27 ~LPrAtV~RImK~aLP~n~kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~ 89 (221)
.||++.|.||+|... --+||.|+.+.+.+...+|+..|..+|...|++.+||||+++||..
T Consensus 13 gI~k~~IrRLaRr~G--vkRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~~ 73 (74)
T smart00417 13 GITKPAIRRLARRGG--VKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVY 73 (74)
T ss_pred CCCHHHHHHHHHHcC--cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHhee
Confidence 599999999999984 5679999999999999999999999999999999999999999964
No 13
>PF00125 Histone: Core histone H2A/H2B/H3/H4 histone h2a signature histone h2b signature histone h3 signature histone h4 signature; InterPro: IPR007125 The core histones together with some other DNA binding proteins appear to form a superfamily defined by a common fold and distant sequence similarities [, ]. Some proteins contain local homology domains related to the histone fold [].; GO: 0003677 DNA binding; PDB: 2YFW_D 2YFV_B 1U35_H 2F8N_D 2PYO_D 2NQB_D 3AN2_C 3AZJ_C 3AV1_G 3AZM_G ....
Probab=98.66 E-value=6.1e-08 Score=69.97 Aligned_cols=68 Identities=28% Similarity=0.352 Sum_probs=62.0
Q ss_pred ccCCchhHHHHHHhhcCCC---CcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHHh
Q 027605 25 DRFLPIANVSRIMKKSLPA---NAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAMT 92 (221)
Q Consensus 25 D~~LPrAtV~RImK~aLP~---n~kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~ALe 92 (221)
+..+|+..|.|+.|+..++ ..+||++|..+|+..++.|+.-|..+|...|...+|+||+++||..|++
T Consensus 3 ~~~~~~~~~~r~~r~i~~~~~~~~ris~~a~~~L~~~~E~~~~~il~~A~~~a~~~kR~tI~~~DI~~A~r 73 (75)
T PF00125_consen 3 RRLIPKFPFSRLLREIGEEILSKYRISSEALVALQSVLEYLLVEILEEAGNLARHAKRKTITPRDIQLAVR 73 (75)
T ss_dssp SHSSSHHHHHHHHHHHHHTTSSSSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTBSEEGHHHHHHHHH
T ss_pred ccccCceEEeeeeehhhcccccccccccccchhhhhhhhhhhhhhhhHHHHHHhhcCCcEecHHHHHHHHh
Confidence 4568899999999988763 2699999999999999999999999999999999999999999999975
No 14
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=98.60 E-value=3.6e-08 Score=88.12 Aligned_cols=78 Identities=26% Similarity=0.365 Sum_probs=71.0
Q ss_pred cccCCchhHHHHHHhhcCCCCcc-cCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHHhhcCCCcchHH
Q 027605 24 QDRFLPIANVSRIMKKSLPANAK-ISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAMTTLGFENYVSP 102 (221)
Q Consensus 24 eD~~LPrAtV~RImK~aLP~n~k-ISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~ALe~LGF~~yv~~ 102 (221)
.+..||.|.|+|+||.. +++| ||.||-.++.+.|+.||.-||..|.-.+++++|+|+.-.||..|+++-++-+|+-.
T Consensus 106 k~h~LPlARIkkvMKtd--edVkMisaEaPvlFak~~EiFI~ELTmRAW~~ae~NkRRtLQksDia~Av~kSeMfDFLid 183 (286)
T COG5208 106 KDHNLPLARIKKVMKTD--EDVKMISAEAPVLFAKITEIFIEELTMRAWINAEENKRRTLQKSDIAAAVKKSEMFDFLID 183 (286)
T ss_pred HhccCcHHHHHHHHhcc--cchhheecccchHHHHHHHHHHHHHHHHHHHHHhHhhhhHHHHHHHHHHHHHHHHHhHHhh
Confidence 35679999999999966 5777 99999999999999999999999999999999999999999999999888777654
Q ss_pred H
Q 027605 103 L 103 (221)
Q Consensus 103 L 103 (221)
+
T Consensus 184 i 184 (286)
T COG5208 184 I 184 (286)
T ss_pred h
Confidence 4
No 15
>smart00428 H3 Histone H3.
Probab=98.51 E-value=2.5e-07 Score=73.69 Aligned_cols=71 Identities=18% Similarity=0.217 Sum_probs=64.7
Q ss_pred CccccCCchhHHHHHHhhcCCC-----CcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHHh
Q 027605 22 KEQDRFLPIANVSRIMKKSLPA-----NAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAMT 92 (221)
Q Consensus 22 ~eeD~~LPrAtV~RImK~aLP~-----n~kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~ALe 92 (221)
+..++.+|+....|++++...+ +.+++.+|.++||++++.|+.-|...|+..+.+.+|+||.++|+.-|..
T Consensus 24 kst~lLI~k~pF~RLVREI~~~~~~~~~~R~~~~Al~aLQeasE~ylv~lfeda~~~a~HAkRvTl~~kDi~La~r 99 (105)
T smart00428 24 KSTDLLIRKAPFQRLVREIAQKFTTGVDLRFQSSAIMALQEAAEAYLVGLFEDTNLLAIHAKRVTIMPKDIQLARR 99 (105)
T ss_pred cCcccccccccHHHHHHHHHHHcCCCCCceeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccCcHhhHHHHHH
Confidence 4567889999999999998753 6799999999999999999999999999999999999999999977753
No 16
>KOG1657 consensus CCAAT-binding factor, subunit C (HAP5) [Transcription]
Probab=98.43 E-value=1.2e-07 Score=84.40 Aligned_cols=84 Identities=29% Similarity=0.431 Sum_probs=72.3
Q ss_pred ccCCchhHHHHHHhhcCCCCc-ccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHHhh---cCCCcch
Q 027605 25 DRFLPIANVSRIMKKSLPANA-KISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAMTT---LGFENYV 100 (221)
Q Consensus 25 D~~LPrAtV~RImK~aLP~n~-kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~ALe~---LGF~~yv 100 (221)
...||++.|++|||.. +++ .|+.||..++.+||+.||..|+..|...++..+|+|+...|+..|+.. .+|.-.+
T Consensus 72 ~~~lPlaRiKkimK~d--edv~mI~~Eapvl~aka~E~Fi~elt~~sw~~Tee~~rrtl~~sdia~av~~s~~fdFL~Di 149 (236)
T KOG1657|consen 72 NHILPLARIKKIMKSD--EDVSMITAEAPVLFAKACELFITELTLRSWVHTEENKRRTLQKSDIAAAVTQSETFDFLRDI 149 (236)
T ss_pred hccCcHhhcccccccc--ccccccchhHHHHHHHHHHHHHHHHHHHhhhhhcccccccchHHHHHHHhccCCCccceecc
Confidence 3579999999999987 345 599999999999999999999999999999999999999999999984 4555555
Q ss_pred HHHHHHHHHH
Q 027605 101 SPLKIYLNKY 110 (221)
Q Consensus 101 ~~Lk~~Le~y 110 (221)
-+.+..+++|
T Consensus 150 vP~~~~~~~~ 159 (236)
T KOG1657|consen 150 VPRKILAEKY 159 (236)
T ss_pred ccchhccccc
Confidence 5666667666
No 17
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=98.18 E-value=1.1e-05 Score=59.68 Aligned_cols=66 Identities=20% Similarity=0.258 Sum_probs=58.9
Q ss_pred hhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHHhhcCCC
Q 027605 30 IANVSRIMKKSLPANAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAMTTLGFE 97 (221)
Q Consensus 30 rAtV~RImK~aLP~n~kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~ALe~LGF~ 97 (221)
+-.|.+|+|... --+++.+|++.|.+....|+.-|+..+...|+..+|++++.+||..||+++|+.
T Consensus 9 ~~~Vaqil~~~G--f~~~~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~~~Dv~~Al~~~gi~ 74 (77)
T smart00576 9 RIAVAQILESAG--FDSFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPNLGDVVLALENLGIS 74 (77)
T ss_pred HHHHHHHHHHcC--ccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCcc
Confidence 445677777763 358999999999999999999999999999999999999999999999999973
No 18
>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=98.03 E-value=1.5e-05 Score=64.23 Aligned_cols=69 Identities=16% Similarity=0.221 Sum_probs=62.9
Q ss_pred cccCCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHHhh
Q 027605 24 QDRFLPIANVSRIMKKSLPANAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAMTT 93 (221)
Q Consensus 24 eD~~LPrAtV~RImK~aLP~n~kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~ALe~ 93 (221)
-.+.||.+.|.|+||+.-- ..+|+.+|...|..+.+.+..-|...|...|+..+|++|+++||..|+..
T Consensus 17 agL~fPV~ri~R~Lk~~~~-a~RVs~~A~VyLaAvLEYL~aEIlelA~n~ak~~k~krItp~hi~lAi~n 85 (115)
T cd00074 17 AGLQFPVGRIHRYLKKGRY-AERVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKKRITPRHLQLAVRN 85 (115)
T ss_pred cCccCcHHHHHHHHHcCcc-ccccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEcHHHHHHHHhc
Confidence 3688999999999998432 48999999999999999999999999999999999999999999999874
No 19
>PLN00121 histone H3; Provisional
Probab=97.99 E-value=1.1e-05 Score=67.08 Aligned_cols=70 Identities=16% Similarity=0.190 Sum_probs=63.9
Q ss_pred CccccCCchhHHHHHHhhcCCC---CcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHH
Q 027605 22 KEQDRFLPIANVSRIMKKSLPA---NAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAM 91 (221)
Q Consensus 22 ~eeD~~LPrAtV~RImK~aLP~---n~kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~AL 91 (221)
+..|+.+|+....||+++...+ +.+++.+|.++||++++.|+--|-..++-.|.+.+|.||.+.|+.-++
T Consensus 57 kst~lLI~k~pF~RLVREI~~~~~~~~Rf~~~Al~ALQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~ 129 (136)
T PLN00121 57 KSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 129 (136)
T ss_pred cccccccccccHHHHHHHHHHHhCccceeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcceecchhhHHHHH
Confidence 4458889999999999998754 789999999999999999999999999999999999999999997665
No 20
>PLN00161 histone H3; Provisional
Probab=97.95 E-value=2.7e-05 Score=64.76 Aligned_cols=70 Identities=19% Similarity=0.218 Sum_probs=63.4
Q ss_pred CccccCCchhHHHHHHhhcCC----CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHH
Q 027605 22 KEQDRFLPIANVSRIMKKSLP----ANAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAM 91 (221)
Q Consensus 22 ~eeD~~LPrAtV~RImK~aLP----~n~kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~AL 91 (221)
+..++.+|+....|++++... .+.+++.+|.++||++++.|+--|-..++-.|.+.+|.||.+.|+.-|.
T Consensus 50 kst~lLIpklPF~RLVREI~~~~~~~~~Rfq~~Al~ALQEAsEayLV~lFeda~lcaiHAkRVTlm~kDm~La~ 123 (135)
T PLN00161 50 KSTELLIRKLPFARLVREISNEMLREPFRWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMPKDMQLAR 123 (135)
T ss_pred cccccccccccHHHHHHHHHHhcCCCCcEeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccchhhHHHHH
Confidence 456788999999999999863 4689999999999999999999999999999999999999999997775
No 21
>PLN00160 histone H3; Provisional
Probab=97.94 E-value=2.2e-05 Score=61.97 Aligned_cols=70 Identities=17% Similarity=0.127 Sum_probs=63.3
Q ss_pred CccccCCchhHHHHHHhhcCC----CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHH
Q 027605 22 KEQDRFLPIANVSRIMKKSLP----ANAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAM 91 (221)
Q Consensus 22 ~eeD~~LPrAtV~RImK~aLP----~n~kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~AL 91 (221)
+..++.+|+....|++++... ++.+++.+|.++||++++.|+--|-..++-.|.+.||.||.+.|+.-+.
T Consensus 16 kst~lLI~k~pF~RLVREI~~~~~~~~~Rfq~~Al~ALQeAsEayLv~lfed~~lca~HakRVTl~~kD~~L~~ 89 (97)
T PLN00160 16 KSTDLLIRRLPFARLVREIQMEMSREAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTIMPKDMQLAR 89 (97)
T ss_pred cchhhhhccccHHHHHHHHHHHcCCCCcEeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcccccchhhHHHHH
Confidence 356788999999999999864 3589999999999999999999999999999999999999999997665
No 22
>PTZ00018 histone H3; Provisional
Probab=97.89 E-value=2e-05 Score=65.53 Aligned_cols=70 Identities=16% Similarity=0.194 Sum_probs=63.5
Q ss_pred CccccCCchhHHHHHHhhcCC---CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHH
Q 027605 22 KEQDRFLPIANVSRIMKKSLP---ANAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAM 91 (221)
Q Consensus 22 ~eeD~~LPrAtV~RImK~aLP---~n~kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~AL 91 (221)
+..|+.+|+....||+++... .+.+++.+|.++||++++.|+--|-..++-.|.+.+|.||.+.|+.-+.
T Consensus 57 kst~lLI~k~pF~RLVREI~~~~~~~~rf~~~al~aLQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~ 129 (136)
T PTZ00018 57 KSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 129 (136)
T ss_pred ccchhccccccHHHHHHHHHHHcCCcceeeHHHHHHHHHHHHHHHHHHhhhhHHHHHhhcceecchhhHHHHH
Confidence 345888999999999999864 3689999999999999999999999999999999999999999997665
No 23
>cd07979 TAF9 TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. The TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Human TAF9 has a paralogue gene (TAF9L) whi
Probab=97.88 E-value=9.6e-05 Score=59.35 Aligned_cols=78 Identities=14% Similarity=0.173 Sum_probs=64.9
Q ss_pred hHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHHhhcCCCcchH-HHHHHHHH
Q 027605 31 ANVSRIMKKSLPANAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAMTTLGFENYVS-PLKIYLNK 109 (221)
Q Consensus 31 AtV~RImK~aLP~n~kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~ALe~LGF~~yv~-~Lk~~Le~ 109 (221)
..|.+|+|+.. ..+++.+++..|.+.+..++.-|..+|...|++.+|+||+++||.-|++...-..|.. +-+++|-+
T Consensus 5 ~~v~~iLk~~G--v~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r~~~~f~~~p~~~~l~~ 82 (117)
T cd07979 5 RVIAAILKSMG--ITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRVDYSFTSPPPRDFLLE 82 (117)
T ss_pred HHHHHHHHHCC--CCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhccCCCCCCcHHHHHH
Confidence 36788888873 4689999999999999999999999999999999999999999999999665544444 45666544
Q ss_pred H
Q 027605 110 Y 110 (221)
Q Consensus 110 y 110 (221)
.
T Consensus 83 ~ 83 (117)
T cd07979 83 L 83 (117)
T ss_pred H
Confidence 3
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=97.74 E-value=0.00011 Score=67.78 Aligned_cols=67 Identities=21% Similarity=0.201 Sum_probs=59.5
Q ss_pred chhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHHhhcCCC
Q 027605 29 PIANVSRIMKKSLPANAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAMTTLGFE 97 (221)
Q Consensus 29 PrAtV~RImK~aLP~n~kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~ALe~LGF~ 97 (221)
|..+|.-|+++.. -.++++||..+|.+.++.+|.-|..+|.+.+++.+||||+++||-.||+.++.+
T Consensus 1 ~~~~i~~ia~~~G--i~~~~~~a~~~La~~~e~~~~~i~~~A~k~~~hskR~~l~~~Di~~Al~~~n~e 67 (343)
T cd08050 1 PQESIKLIAESLG--IDSLSDEVAQLLAEDVEYRLREIIQEAAKFMRHSKRRKLTTSDVNHALRLRNVE 67 (343)
T ss_pred ChhHHHHHHHHcC--CCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHHhCCC
Confidence 4567777777773 349999999999999999999999999999999999999999999999976654
No 25
>PF15511 CENP-T: Centromere kinetochore component CENP-T; PDB: 3B0D_T 3B0C_T 3VH5_T 3VH6_T.
Probab=97.69 E-value=6.2e-05 Score=71.36 Aligned_cols=65 Identities=23% Similarity=0.277 Sum_probs=47.7
Q ss_pred CccccCCchhHHHHHHhhcCC----CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcch
Q 027605 22 KEQDRFLPIANVSRIMKKSLP----ANAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDD 86 (221)
Q Consensus 22 ~eeD~~LPrAtV~RImK~aLP----~n~kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeD 86 (221)
++.--.||.+.|+|++..... .+++|+|||..+|.+|...|-..|+..---+|++.|||||..+|
T Consensus 346 gi~~P~lP~~~vK~la~~~ak~s~~sK~kiskdal~aleqasdwfFeQl~dDL~aYA~HAgRKTIdesD 414 (414)
T PF15511_consen 346 GIPYPSLPPGVVKKLAQHFAKSSGGSKMKISKDALEALEQASDWFFEQLGDDLEAYAKHAGRKTIDESD 414 (414)
T ss_dssp ------S-HHHHHHHHHHHH-------S-B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHH
T ss_pred CCCCCCCCccHHHHHHHHHHHhhcccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCCCC
Confidence 455567999999998877653 57999999999999999999999999999999999999999876
No 26
>smart00427 H2B Histone H2B.
Probab=97.59 E-value=0.0003 Score=54.92 Aligned_cols=63 Identities=21% Similarity=0.347 Sum_probs=58.1
Q ss_pred hHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHHhhc
Q 027605 31 ANVSRIMKKSLPANAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAMTTL 94 (221)
Q Consensus 31 AtV~RImK~aLP~n~kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~ALe~L 94 (221)
.-|.|++|+.-| ++.||..+...|.--+..+..-|+.||...|...+|+||+..+|..|++-+
T Consensus 5 ~Yi~kvLKqVhp-d~giS~kam~imnSfvnDiferIa~EAs~L~~~nkr~TltsreIqtAvrl~ 67 (89)
T smart00427 5 IYIYKVLKQVHP-DTGISSKAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRLI 67 (89)
T ss_pred HHHHHHHHHhCC-CccccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHH
Confidence 358999999998 689999999999999999999999999999999999999999999998744
No 27
>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=97.56 E-value=0.00045 Score=53.03 Aligned_cols=66 Identities=20% Similarity=0.198 Sum_probs=61.5
Q ss_pred CCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC---CccCcchHHHHHhhc
Q 027605 27 FLPIANVSRIMKKSLPANAKISKEAKETVQECVSEFISFITGEASDKCQREKR---KTINGDDLLWAMTTL 94 (221)
Q Consensus 27 ~LPrAtV~RImK~aLP~n~kISkDAk~al~kcateFI~yLTseAneic~~ekR---KTIsaeDVl~ALe~L 94 (221)
.||++.|.|||...++ .+++.+...+|.-.+.+||--|.-+|.++..+.+. .-|.++||-+|.+.|
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 4999999999999984 89999999999999999999999999999998665 889999999999876
No 28
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=97.55 E-value=0.00033 Score=52.87 Aligned_cols=62 Identities=18% Similarity=0.222 Sum_probs=52.8
Q ss_pred HHHHHHhhcC-CCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHHhh
Q 027605 32 NVSRIMKKSL-PANAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAMTT 93 (221)
Q Consensus 32 tV~RImK~aL-P~n~kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~ALe~ 93 (221)
.|.||+.+.. +.++.+|+++..+|.+.+-.++.-++..---.|++.||+||+.+||+-..++
T Consensus 10 ~v~ki~ee~~~~~~~~~s~~~i~al~ELv~~q~~~~a~DLe~FAkHA~R~tI~~dDV~Ll~Rr 72 (76)
T PF15630_consen 10 TVGKIVEEEAKEKGVEVSPQFIAALTELVYKQLENLAKDLEAFAKHAGRSTINMDDVKLLARR 72 (76)
T ss_dssp HHHHHHHHCCCCTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHTTT
T ss_pred HHHHHHHHHHhccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHHHhhc
Confidence 5788888875 5688999999999999999999999999999999999999999999977654
No 29
>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=97.47 E-value=0.00018 Score=53.80 Aligned_cols=64 Identities=19% Similarity=0.303 Sum_probs=53.7
Q ss_pred chhHHHHHHhhcCC-CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCc-cCcchHHHHHh
Q 027605 29 PIANVSRIMKKSLP-ANAKISKEAKETVQECVSEFISFITGEASDKCQREKRKT-INGDDLLWAMT 92 (221)
Q Consensus 29 PrAtV~RImK~aLP-~n~kISkDAk~al~kcateFI~yLTseAneic~~ekRKT-IsaeDVl~ALe 92 (221)
|..+|.||++.... ++++|++||..++.+....||.--...|.+.++.++... |..+|+-+.+-
T Consensus 1 p~~li~rll~~~f~~~~tkIs~dal~l~~eyl~iFV~EAv~Ra~~~a~~e~~~~~le~e~LEki~p 66 (72)
T PF09415_consen 1 PPELIARLLHEHFKDDKTKISKDALKLSAEYLRIFVREAVARAAEQAEAEGDEGFLEVEHLEKILP 66 (72)
T ss_dssp -CHHHHHHHCTTSSSTT-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSEE-HHHHHHHCH
T ss_pred ChHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHH
Confidence 88999999997773 579999999999999999999999999999999999888 99999987654
No 30
>PF03847 TFIID_20kDa: Transcription initiation factor TFIID subunit A; InterPro: IPR003228 Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription [].; GO: 0006352 transcription initiation, DNA-dependent, 0005669 transcription factor TFIID complex; PDB: 1H3O_B.
Probab=97.46 E-value=0.00064 Score=50.26 Aligned_cols=63 Identities=17% Similarity=0.288 Sum_probs=51.6
Q ss_pred hhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHHhh
Q 027605 30 IANVSRIMKKSLPANAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAMTT 93 (221)
Q Consensus 30 rAtV~RImK~aLP~n~kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~ALe~ 93 (221)
+..+..+|++.=| +.++.+|+.++|.+.|.+||.-++..|-..|++.+-.||...||.-.|++
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 3567889999866 89999999999999999999999999999999999999999999998875
No 31
>PF07524 Bromo_TP: Bromodomain associated; InterPro: IPR006565 This bromodomain is found in eukaryotic transcription factors and PHD domain containing proteins (IPR001965 from INTERPRO). The tandem PHD finger-bromodomain is found in many chromatin-associated proteins. It is involved in gene silencing by the human co-repressor KRAB-associated protein 1 (KAP1). The tandem PHD finger-bromodomain of KAP1 has a distinct structure that joins the two protein modules. The first helix, alpha(Z), of an atypical bromodomain forms the central hydrophobic core that anchors the other three helices of the bromodomain on one side and the zinc binding PHD finger on the other []. The Rap1 GTPase-activating protein, Sipa1, is modulated by the cellular bromodomain protein, Brd4. Brd4 belongs to the BET family and is a multifunctional protein involved in transcription, replication, the signal transduction pathway, and cell cycle progression. All of these functions are linked to its association with acetylated chromatin. It has tandem bromodomains []. The dysregulation of the Brd4-associated pathways may play an important role in breast cancer progression []. Bovine papillomavirus type 1 E2 also binds to chromosomes in a complex with Brd4. Interaction with Brd4 is additionally important for E2-mediated transcriptional regulation [, ].
Probab=97.44 E-value=0.0011 Score=48.62 Aligned_cols=65 Identities=18% Similarity=0.249 Sum_probs=56.4
Q ss_pred hHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHHhhcCCC
Q 027605 31 ANVSRIMKKSLPANAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAMTTLGFE 97 (221)
Q Consensus 31 AtV~RImK~aLP~n~kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~ALe~LGF~ 97 (221)
-.|.+|++... =-.++..|.+.|.+.+..||..|+..+...|+..+|...+..||..||+++|+.
T Consensus 10 ~~va~il~~~G--F~~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~~~gi~ 74 (77)
T PF07524_consen 10 RSVAQILKHAG--FDSASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPNLQDVEQALEEMGIS 74 (77)
T ss_pred HHHHHHHHHcC--ccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCC
Confidence 34555555542 236999999999999999999999999999999999999999999999999984
No 32
>PLN00158 histone H2B; Provisional
Probab=97.30 E-value=0.001 Score=54.22 Aligned_cols=66 Identities=17% Similarity=0.275 Sum_probs=59.9
Q ss_pred CchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHHhhc
Q 027605 28 LPIANVSRIMKKSLPANAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAMTTL 94 (221)
Q Consensus 28 LPrAtV~RImK~aLP~n~kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~ALe~L 94 (221)
--..-|.|++|+.-| ++.||..+...|.--...+..-|+.||...|.-.+|+||+..+|..|++-+
T Consensus 28 sy~~YI~kVLKQVhP-d~gIS~kaM~ImnSfvnDiferIA~EAs~La~~nkr~TltsrEIqtAvrLv 93 (116)
T PLN00158 28 TYKIYIYKVLKQVHP-DTGISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVRLI 93 (116)
T ss_pred cHHHHHHHHHHHhCC-CCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHh
Confidence 345569999999998 688999999999999999999999999999999999999999999997744
No 33
>PTZ00463 histone H2B; Provisional
Probab=97.25 E-value=0.0013 Score=53.81 Aligned_cols=62 Identities=19% Similarity=0.377 Sum_probs=57.6
Q ss_pred HHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHHhhc
Q 027605 32 NVSRIMKKSLPANAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAMTTL 94 (221)
Q Consensus 32 tV~RImK~aLP~n~kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~ALe~L 94 (221)
-|.|++|+.-| ++.||..+...|.--......-|+.||...|.-.+|+||+..+|-.|++-+
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 49999999998 688999999999999999999999999999999999999999999997643
No 34
>KOG3467 consensus Histone H4 [Chromatin structure and dynamics]
Probab=97.24 E-value=0.0013 Score=51.95 Aligned_cols=68 Identities=19% Similarity=0.304 Sum_probs=60.2
Q ss_pred CchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHHhhcCCC
Q 027605 28 LPIANVSRIMKKSLPANAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAMTTLGFE 97 (221)
Q Consensus 28 LPrAtV~RImK~aLP~n~kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~ALe~LGF~ 97 (221)
+.+-.|.||.+..- .-+|+--.-+-+...+.+||.-+-..|...+++.+||||++.||+-+|++.|.-
T Consensus 30 itKpaIRRlARr~G--VkRi~G~~yeE~~~~~k~fl~n~i~~A~~yt~HAKRKTvT~~dvv~~LKR~G~~ 97 (103)
T KOG3467|consen 30 ITKPAIRRLARRGG--VKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRT 97 (103)
T ss_pred cchHHHHHHHHhcC--cchhchhhHHHHHHHHHHHHHHHHHHHHHHHhhhhhceeeHHHHHHHHHHcCce
Confidence 55678999999874 346888888889999999999999999999999999999999999999998754
No 35
>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=97.15 E-value=0.0016 Score=50.71 Aligned_cols=67 Identities=21% Similarity=0.216 Sum_probs=52.5
Q ss_pred CCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC-CccCcchHHHHHhhc
Q 027605 27 FLPIANVSRIMKKSLPANAKISKEAKETVQECVSEFISFITGEASDKCQREKR-KTINGDDLLWAMTTL 94 (221)
Q Consensus 27 ~LPrAtV~RImK~aLP~n~kISkDAk~al~kcateFI~yLTseAneic~~ekR-KTIsaeDVl~ALe~L 94 (221)
.||++.|.|||...+. +..|+.....+|.=.+.+||--|-.+|.+++.+.+. .-|.+.|+-+|.++|
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 5999999999999994 589999999999999999999999999999997544 489999999998875
No 36
>KOG1659 consensus Class 2 transcription repressor NC2, alpha subunit (DRAP1) [Transcription]
Probab=97.13 E-value=0.00072 Score=60.22 Aligned_cols=82 Identities=12% Similarity=0.171 Sum_probs=70.0
Q ss_pred cCCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHHhhcCCCcchHHHHH
Q 027605 26 RFLPIANVSRIMKKSLPANAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAMTTLGFENYVSPLKI 105 (221)
Q Consensus 26 ~~LPrAtV~RImK~aLP~n~kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~ALe~LGF~~yv~~Lk~ 105 (221)
-.||.+.|.|||...= +-.||..-+-..+.++.+.|+.-|...+.++++..+-|||+++|+..|++.-.--+|+..+-.
T Consensus 12 trfp~aRiKKIMQ~dE-dIGKvaqavPViisralElFl~~l~~~t~~~t~~~~aKt~s~~hlkq~v~~~~~FdFLk~~v~ 90 (224)
T KOG1659|consen 12 TRFPPARIKKIMQSDE-DIGKVAQAVPVIISRALELFLESLLQKTLEITRSRGAKTVSSSHLKQAVESDPKFDFLKEVVE 90 (224)
T ss_pred ccCCHHHHHHHHhhhh-hhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhcCccccCHHHHHHHHhccchhHHHHHHHH
Confidence 3699999999998763 245899999999999999999999999999999999999999999999997766667666444
Q ss_pred HHH
Q 027605 106 YLN 108 (221)
Q Consensus 106 ~Le 108 (221)
.+.
T Consensus 91 ~vp 93 (224)
T KOG1659|consen 91 KVP 93 (224)
T ss_pred hcC
Confidence 333
No 37
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=97.07 E-value=0.0011 Score=54.63 Aligned_cols=71 Identities=20% Similarity=0.251 Sum_probs=61.6
Q ss_pred CCccccCCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHHh
Q 027605 21 DKEQDRFLPIANVSRIMKKSLPANAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAMT 92 (221)
Q Consensus 21 ~~eeD~~LPrAtV~RImK~aLP~n~kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~ALe 92 (221)
..-.-+.+|...|.||||..- -.++|+++|...+.-|.+-.+.-|+.-|-..|...++|.|.+.|+-.|+.
T Consensus 20 sa~agl~fpvgrvkr~lk~~~-~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~kkkri~PrHlqlAIr 90 (132)
T COG5262 20 SAKAGLIFPVGRVKRLLKKGN-YRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRIIPRHLQLAIR 90 (132)
T ss_pred hhhcCccccHHHHHHHHHcCc-cceeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhcCcceechHHHHHHhc
Confidence 335667899999999999443 47999999999999998888888888888888999999999999999987
No 38
>PF02969 TAF: TATA box binding protein associated factor (TAF); InterPro: IPR004823 The TATA box binding protein associated factor (TAF) is part of the transcription initiation factor TFIID multimeric protein complex. TFIID plays a central role in mediating promoter responses to various activators and repressors. It binds tightly to TAFII-250 and directly interacts with TAFII-40. TFIID is composed of TATA binding protein (TBP)and a number of TBP-associated factors (TAFS). TAF proteins adopt a histone-like fold.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus; PDB: 1TAF_B.
Probab=96.90 E-value=0.0061 Score=45.03 Aligned_cols=64 Identities=23% Similarity=0.206 Sum_probs=49.4
Q ss_pred CCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHHh
Q 027605 27 FLPIANVSRIMKKSLPANAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAMT 92 (221)
Q Consensus 27 ~LPrAtV~RImK~aLP~n~kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~ALe 92 (221)
.+|..+|.-+..... -..++.|+...|.+-++--|..|..+|....++.+|++++++||-.||+
T Consensus 3 ~~~~esvk~iAes~G--i~~l~de~a~~La~dveyrlreiiq~a~kfm~hskR~~Lt~~Di~~ALr 66 (66)
T PF02969_consen 3 VFSQESVKDIAESLG--ISNLSDEAAKALAEDVEYRLREIIQEALKFMRHSKRTKLTTDDINSALR 66 (66)
T ss_dssp ---HHHHHHHHHHTT-----B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH-
T ss_pred cCCHHHHHHHHHHcC--CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhC
Confidence 367788876666552 3379999999999999999999999999999999999999999999985
No 39
>COG5247 BUR6 Class 2 transcription repressor NC2, alpha subunit (DRAP1 homolog) [Transcription]
Probab=96.66 E-value=0.004 Score=50.26 Aligned_cols=81 Identities=15% Similarity=0.255 Sum_probs=67.9
Q ss_pred ccccCCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHHhhcCCCcchHH
Q 027605 23 EQDRFLPIANVSRIMKKSLPANAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAMTTLGFENYVSP 102 (221)
Q Consensus 23 eeD~~LPrAtV~RImK~aLP~n~kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~ALe~LGF~~yv~~ 102 (221)
---..+|.|.|.|||.-.- +-.+|+.-.-....++.+.|+..|-.++.+.++..+-|.|+.+++..|.+.-+=-+|+..
T Consensus 19 ~~ktrFP~ar~KkIMQ~de-DiGKV~q~tPVIaskalE~Fl~~iv~~s~k~aR~~~skR~t~e~lk~a~~sdekFdFL~~ 97 (113)
T COG5247 19 KKKTRFPIARLKKIMQLDE-DIGKVGQSTPVIASKALEMFLTEIVGLSLKEARKKSSKRMTSEFLKRATESDEKFDFLKN 97 (113)
T ss_pred hhhhcCCHHHHHHHHHhhh-hhhhhhhcchHHHHHHHHHHHHHHHHHHHHHHHhccchhhHHHHHHHHHhhhHHHHHHHH
Confidence 3445799999999998653 245899999999999999999999999999999999999999999999986655555544
Q ss_pred HH
Q 027605 103 LK 104 (221)
Q Consensus 103 Lk 104 (221)
+.
T Consensus 98 ~~ 99 (113)
T COG5247 98 ME 99 (113)
T ss_pred HH
Confidence 43
No 40
>KOG1658 consensus DNA polymerase epsilon, subunit C [Replication, recombination and repair]
Probab=96.44 E-value=0.0022 Score=54.80 Aligned_cols=66 Identities=26% Similarity=0.342 Sum_probs=57.5
Q ss_pred cCCchhHHHHHHhhcCCCCcc-cCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHHhh
Q 027605 26 RFLPIANVSRIMKKSLPANAK-ISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAMTT 93 (221)
Q Consensus 26 ~~LPrAtV~RImK~aLP~n~k-ISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~ALe~ 93 (221)
..||++.|..+|| ++++.+ ..+|++.+|.+++..||..|...++..+...+|||+.--|+=.|++.
T Consensus 58 ~rLpL~rik~vvk--l~pdl~l~~dea~~l~a~aaelfi~~Ln~~~~~~~q~~k~kt~qr~d~D~ai~~ 124 (162)
T KOG1658|consen 58 SRLPLARIKQVVK--LDPDLTLLNDEASQLIAKAAELFIQELNDVAYTTAQLRKRKTEQRRDYDTAIEA 124 (162)
T ss_pred hhccHHHHHhhcc--CCcchhhhhhHHHHHHHHHHHHHHHHHHhccchhHHHHHhhhhhhhcccccccc
Confidence 5799999999999 667887 56788999999999999999999999999999999988777666553
No 41
>PF15510 CENP-W: Centromere kinetochore component W
Probab=96.37 E-value=0.0064 Score=48.29 Aligned_cols=67 Identities=21% Similarity=0.261 Sum_probs=56.6
Q ss_pred cCCchhHHHHHHhhcCCCCcccCHHHHHH--------------HHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHH
Q 027605 26 RFLPIANVSRIMKKSLPANAKISKEAKET--------------VQECVSEFISFITGEASDKCQREKRKTINGDDLLWAM 91 (221)
Q Consensus 26 ~~LPrAtV~RImK~aLP~n~kISkDAk~a--------------l~kcateFI~yLTseAneic~~ekRKTIsaeDVl~AL 91 (221)
..-|+..+.|++|..-| ..++....-.+ +.-.|-.||+-|+-||...|=+++-.||..+||+.|-
T Consensus 15 rkaPrgfLkrv~Kr~Kp-hlRl~~~~Dllv~~~~f~~~~~~~~vhLncLLFvhrLAEEaRtnA~EnK~~~Ik~~Hv~Aaa 93 (102)
T PF15510_consen 15 RKAPRGFLKRVFKRQKP-HLRLETSGDLLVRFCPFSGWQWGGEVHLNCLLFVHRLAEEARTNACENKCGTIKKEHVLAAA 93 (102)
T ss_pred HhCchHHHHHHHHhcCC-ceeecccccHHHhhcccccccccceeehhHHHHHHHHHHHHHHHHHHHhhccccHHHHHHHH
Confidence 45799999999998887 67766655555 6677899999999999988888899999999999986
Q ss_pred hh
Q 027605 92 TT 93 (221)
Q Consensus 92 e~ 93 (221)
+.
T Consensus 94 Kv 95 (102)
T PF15510_consen 94 KV 95 (102)
T ss_pred HH
Confidence 53
No 42
>smart00414 H2A Histone 2A.
Probab=96.35 E-value=0.013 Score=46.80 Aligned_cols=69 Identities=13% Similarity=0.239 Sum_probs=58.5
Q ss_pred cccCCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHHhh
Q 027605 24 QDRFLPIANVSRIMKKSLPANAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAMTT 93 (221)
Q Consensus 24 eD~~LPrAtV~RImK~aLP~n~kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~ALe~ 93 (221)
-.+.||.+.|.|+||+.-- ..+|+..|...|.-+.+-+...|-..|-..|...+++.|+++||..|+..
T Consensus 6 agL~fPVgRi~r~Lk~~~~-~~Rv~~~A~VyLaAvLEYLtaEILeLagn~a~~~k~~rItp~hi~lAi~n 74 (106)
T smart00414 6 AGLQFPVGRIHRLLRKGTY-AKRVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKRRITPRHLQLAIRN 74 (106)
T ss_pred CCccCchHHHHHHHHcCcc-ccccccccHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchHHHhhhccC
Confidence 3678999999999998743 46999999999988877777777767778888889999999999999875
No 43
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=96.17 E-value=0.013 Score=53.46 Aligned_cols=69 Identities=13% Similarity=0.264 Sum_probs=62.6
Q ss_pred ccccCCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHHh
Q 027605 23 EQDRFLPIANVSRIMKKSLPANAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAMT 92 (221)
Q Consensus 23 eeD~~LPrAtV~RImK~aLP~n~kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~ALe 92 (221)
..+.-|=+-.|.-+++++-+ +.+|.+|+.++|.+.|..||.-|+..|-..|++.|..||..-||.-.||
T Consensus 150 ~~~~il~k~kl~dLvqqId~-~~~LD~dVedlLleiADdFV~sii~~sC~LAKHRKsdtlEvrDIqLhLE 218 (258)
T KOG1142|consen 150 GNNPILSKRKLDDLVQQIDG-TTKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHRKSDTVEVRDIQLHLE 218 (258)
T ss_pred CCCccccccchhHHHHhhcC-cccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccchhheeeeee
Confidence 34456777888899999854 7899999999999999999999999999999999999999999999999
No 44
>KOG1745 consensus Histones H3 and H4 [Chromatin structure and dynamics]
Probab=96.12 E-value=0.0035 Score=52.41 Aligned_cols=71 Identities=17% Similarity=0.209 Sum_probs=60.7
Q ss_pred CccccCCchhHHHHHHhhcC---CCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHHh
Q 027605 22 KEQDRFLPIANVSRIMKKSL---PANAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAMT 92 (221)
Q Consensus 22 ~eeD~~LPrAtV~RImK~aL---P~n~kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~ALe 92 (221)
+..|+.+++....|++++.. -.+.++...|..+||++++-|+.-|--.+|-.+.+.||.||.+.|+--|..
T Consensus 58 kstdLlI~K~PFqRlvrei~q~f~~dLrfqs~Ai~ALQeA~EayLv~LfEdtnlcAihAkRVTimpkdiQlArr 131 (137)
T KOG1745|consen 58 KSTDLLIRKLPFQRLVREIAQDFKTDLRFQSSAIAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 131 (137)
T ss_pred hhhHHHhhcCcHHHHhHHHHhcccccceehHHHHHHHHHHHHHHHHHhccccchhhhccceeEecccceehhhh
Confidence 35677778888888888443 348899999999999999999999999999999999999999999977754
No 45
>PLN00154 histone H2A; Provisional
Probab=95.88 E-value=0.025 Score=47.37 Aligned_cols=70 Identities=16% Similarity=0.203 Sum_probs=56.1
Q ss_pred cccCCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHHhh
Q 027605 24 QDRFLPIANVSRIMKKSLPANAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAMTT 93 (221)
Q Consensus 24 eD~~LPrAtV~RImK~aLP~n~kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~ALe~ 93 (221)
-.+.||.+.|.|++|+-..-..+|+..|...|.-+.+=+..-|-..|-..|...+++-|++.||..|+..
T Consensus 35 AgL~FPVgRi~r~Lk~g~~~~~RVga~ApVYLAAVLEYLtAEVLELAGNaA~d~kk~RItPrHi~lAIrn 104 (136)
T PLN00154 35 AGLQFPVGRIHRQLKQRVSAHGRVGATAAVYTAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRG 104 (136)
T ss_pred cCccCchHHHHHHHHhhhhhccccccchHHHHHHHHHHHHHHHHHHHHHHHHhhCCceecHHHhhhhccC
Confidence 4789999999999999754357999999988887765444445555667788889999999999999863
No 46
>PTZ00017 histone H2A; Provisional
Probab=95.69 E-value=0.067 Score=44.63 Aligned_cols=68 Identities=16% Similarity=0.219 Sum_probs=58.6
Q ss_pred cccCCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHHh
Q 027605 24 QDRFLPIANVSRIMKKSLPANAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAMT 92 (221)
Q Consensus 24 eD~~LPrAtV~RImK~aLP~n~kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~ALe 92 (221)
-.+.||...|.|+||+.-- ..+|+..|...|.-+.+-+..-|-..|-..|...+++-|+++||..|+.
T Consensus 24 agL~FPVgRi~R~Lk~g~~-a~RV~a~A~VYLAAVLEYLtaEILELAgNaa~d~kk~RItPrHi~lAI~ 91 (134)
T PTZ00017 24 AGLQFPVGRVHRYLKKGRY-AKRVGAGAPVYLAAVLEYLTAEVLELAGNAAKDNKKKRITPRHIQLAIR 91 (134)
T ss_pred CCcccchHHHHHHHhccch-hccccccchhhhHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHhhcc
Confidence 4789999999999998643 4699999999999888777777777777888899999999999999986
No 47
>PF02269 TFIID-18kDa: Transcription initiation factor IID, 18kD subunit; InterPro: IPR003195 This family includes the Spt3 yeast transcription factors and the 18 kDa subunit from human transcription initiation factor IID (TFIID-18). Determination of the crystal structure reveals an atypical histone fold [].; GO: 0006366 transcription from RNA polymerase II promoter; PDB: 1BH9_A 1BH8_A.
Probab=95.54 E-value=0.018 Score=44.54 Aligned_cols=59 Identities=25% Similarity=0.306 Sum_probs=28.9
Q ss_pred HHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHHhh
Q 027605 34 SRIMKKSLPANAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAMTT 93 (221)
Q Consensus 34 ~RImK~aLP~n~kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~ALe~ 93 (221)
..+|-.- .+.-.-..|.+.+|-+.+.+||..|..+|.+.|...+++.|+.||++-+|++
T Consensus 8 ~~mMy~f-GD~~~P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~rg~~~i~~eDl~F~lR~ 66 (93)
T PF02269_consen 8 RQMMYGF-GDVEEPLPETVDLVEDIVREYIIELCQEAMEVAQRRGSKKIKVEDLLFLLRK 66 (93)
T ss_dssp HHHHHCT-TS-SS--HHHHHHHHHHHHHHHHHHHHHHHC---------------------
T ss_pred HHHHHHc-CCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCcCcHHHHHHHHhc
Confidence 3444443 3456788999999999999999999999999999999999999999999984
No 48
>KOG1744 consensus Histone H2B [Chromatin structure and dynamics]
Probab=95.45 E-value=0.056 Score=44.83 Aligned_cols=62 Identities=26% Similarity=0.341 Sum_probs=56.3
Q ss_pred HHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHHhhc
Q 027605 32 NVSRIMKKSLPANAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAMTTL 94 (221)
Q Consensus 32 tV~RImK~aLP~n~kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~ALe~L 94 (221)
.|.|++|+.-|+ .-|+.++...|.--..+++-.|+.+|...+.-.+|.||+..+|..|.+-|
T Consensus 42 yv~kvlk~Vhpd-~gis~~a~~vmnsf~ndife~iA~ea~rla~y~krstisSreiqta~rLl 103 (127)
T KOG1744|consen 42 YVYKVLKQVHPD-LGISSKAMGVMNSFVNDIFERIASEAGRLAHYNKRSTISSREIQTAVRLL 103 (127)
T ss_pred ehhhhhhcccCC-CCcCHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCcccHHHHHHHHHHh
Confidence 367799999986 77999999999999999999999999999999999999999999887643
No 49
>PLN00156 histone H2AX; Provisional
Probab=95.00 E-value=0.067 Score=44.93 Aligned_cols=68 Identities=12% Similarity=0.189 Sum_probs=55.5
Q ss_pred cccCCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHHh
Q 027605 24 QDRFLPIANVSRIMKKSLPANAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAMT 92 (221)
Q Consensus 24 eD~~LPrAtV~RImK~aLP~n~kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~ALe 92 (221)
-.+.||...|.|++|+.-- ..+|+..|...|.-+.+=.+.-|-..|-..|...+++-|+++||..|+.
T Consensus 26 AgL~FPVgRi~R~Lk~g~y-a~RVga~ApVYLAAVLEYLtaEVLELAgNaa~d~kk~RItPrHi~lAIr 93 (139)
T PLN00156 26 AGLQFPVGRIARFLKAGKY-AERVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR 93 (139)
T ss_pred cCcccchHHHHHHHhcCCh-hhccCCccHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHhhcc
Confidence 4688999999999998743 4689999998888876655555555666778888999999999999986
No 50
>PLN00157 histone H2A; Provisional
Probab=94.99 E-value=0.056 Score=45.02 Aligned_cols=68 Identities=12% Similarity=0.178 Sum_probs=56.9
Q ss_pred cccCCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHHh
Q 027605 24 QDRFLPIANVSRIMKKSLPANAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAMT 92 (221)
Q Consensus 24 eD~~LPrAtV~RImK~aLP~n~kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~ALe 92 (221)
-.+.||...|.|++|+.-- ..+|+..|...|.-+.+-.+.-|-..|-..|...+++-|+++||..|+.
T Consensus 23 agL~FPVgRi~R~Lk~g~~-a~RIg~~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~ 90 (132)
T PLN00157 23 AGLQFPVGRIARYLKAGKY-ATRVGAGAPVYLAAVLEYLAAEVLELAGNAARDNKKSRIVPRHIQLAVR 90 (132)
T ss_pred cCcccchHHHHHHHhcCch-hhhcCCCcHhHHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHhhccc
Confidence 4789999999999999643 4689999999888877666666666677788888999999999999986
No 51
>KOG3219 consensus Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=94.99 E-value=0.029 Score=49.39 Aligned_cols=70 Identities=14% Similarity=0.179 Sum_probs=62.0
Q ss_pred CCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC-CccCcchHHHHHhhcCCCc
Q 027605 27 FLPIANVSRIMKKSLPANAKISKEAKETVQECVSEFISFITGEASDKCQREKR-KTINGDDLLWAMTTLGFEN 98 (221)
Q Consensus 27 ~LPrAtV~RImK~aLP~n~kISkDAk~al~kcateFI~yLTseAneic~~ekR-KTIsaeDVl~ALe~LGF~~ 98 (221)
.||++.|.|||.+... -.|+.-+..+|+=.+.+||--|--+|.++|..-+. --|.+.||-+|..+|....
T Consensus 112 ~f~Ka~iKkL~~~itg--~~v~~nv~Ia~~GiaKvFVGEvVEeAl~V~~~~~e~~PLqP~HIREA~rrL~~qg 182 (195)
T KOG3219|consen 112 AFPKAQIKKLMSSITG--QSVSENVAIAMAGIAKVFVGEVVEEALDVREEWGESGPLQPKHIREAYRRLKLQG 182 (195)
T ss_pred cCCHHHHHHHHHHHhC--CccCcceeeeecchhhHhHHHHHHHHHHHHHHhccCCCCCcHHHHHHHHHHHhcC
Confidence 5999999999999984 44999999999999999999999999999998654 4699999999999887643
No 52
>PLN00153 histone H2A; Provisional
Probab=94.97 E-value=0.063 Score=44.58 Aligned_cols=68 Identities=15% Similarity=0.206 Sum_probs=57.6
Q ss_pred cccCCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHHh
Q 027605 24 QDRFLPIANVSRIMKKSLPANAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAMT 92 (221)
Q Consensus 24 eD~~LPrAtV~RImK~aLP~n~kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~ALe 92 (221)
-.+.||...|.|++|+.-. ..+|+..|...|.-+.+-.+.-|-..|-..|...+++-|+++||..|+.
T Consensus 21 agL~FpVgRi~R~Lr~g~~-a~Rvga~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~ 88 (129)
T PLN00153 21 AGLQFPVGRIARYLKKGKY-AERIGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKNRIVPRHIQLAIR 88 (129)
T ss_pred cCcccchHHHHHHHhcCch-hhccCCCchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHhhcc
Confidence 4789999999999998654 4689999999988887766666666677788888999999999999986
No 53
>KOG1756 consensus Histone 2A [Chromatin structure and dynamics]
Probab=94.96 E-value=0.069 Score=44.51 Aligned_cols=69 Identities=14% Similarity=0.232 Sum_probs=52.8
Q ss_pred ccccCCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHHh
Q 027605 23 EQDRFLPIANVSRIMKKSLPANAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAMT 92 (221)
Q Consensus 23 eeD~~LPrAtV~RImK~aLP~n~kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~ALe 92 (221)
-..+.+|...|.|++|+.= -..+|+.+|...|.-|.+=.+.-|+..|-..+..++|.-|++.||..|+.
T Consensus 23 ~agl~fPvgri~r~Lr~~~-~~~ri~~gapV~laavLeYL~Aeile~agnaardnkk~ri~PrH~~lAI~ 91 (131)
T KOG1756|consen 23 RAGLQFPVGRIHRLLRKGR-YAQRVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRITPRHLQLAIR 91 (131)
T ss_pred hcccccCHHHHHHHHHccc-hhhhccCCChHHHHHHHHHHHHHHHHHhHHHhhhcCccccChHHHHHHHh
Confidence 4567899999999999932 25789999999999654433444444444556677889999999999997
No 54
>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=94.37 E-value=0.28 Score=38.12 Aligned_cols=60 Identities=17% Similarity=0.276 Sum_probs=49.1
Q ss_pred HHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHHhh
Q 027605 32 NVSRIMKKSLPANAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAMTT 93 (221)
Q Consensus 32 tV~RImK~aLP~n~kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~ALe~ 93 (221)
-|..+|-.-. +.-.-..|.+.+|-+.+.+||.-|+.+|.+.|. .+|.-|+.||++-+|+.
T Consensus 7 ei~~mmy~~G-D~~~P~~eTv~llE~iv~~~i~~l~~~a~~~A~-~r~~k~~~eD~~FliR~ 66 (92)
T cd07978 7 EIRQMMYGFG-DVQNPLPETVDLLEDIVVEYIIELCHKAAEVAQ-RRRGKVKVEDLIFLLRK 66 (92)
T ss_pred HHHHHHHHcC-CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-cCCCCCCHHHHHHHHhc
Confidence 4666666554 345678999999999999999999999999998 44555699999999974
No 55
>PF02291 TFIID-31kDa: Transcription initiation factor IID, 31kD subunit; InterPro: IPR003162 Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription []. TAFII-31 protein is a transcriptional coactivator of the p53 protein [].; GO: 0006352 transcription initiation, DNA-dependent; PDB: 1TAF_A.
Probab=93.35 E-value=0.37 Score=39.76 Aligned_cols=84 Identities=19% Similarity=0.216 Sum_probs=47.5
Q ss_pred ccCCchh--HHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHHh-hcCCCcchH
Q 027605 25 DRFLPIA--NVSRIMKKSLPANAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAMT-TLGFENYVS 101 (221)
Q Consensus 25 D~~LPrA--tV~RImK~aLP~n~kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~ALe-~LGF~~yv~ 101 (221)
.-.+|+. .|.-|+|+.. -......+...|.+.+-.|+.-|-..|...+.+.+|++|+.+||--|++ ++++.-..+
T Consensus 8 ~~~~PrDa~~i~~iL~~~G--v~~yeprVv~qLLEfayRYt~~vL~DA~~ya~hA~~~~i~~~DVrLAi~~r~~~~f~~p 85 (129)
T PF02291_consen 8 SKSLPRDARVIHLILKSMG--VTEYEPRVVNQLLEFAYRYTSDVLEDAQVYADHAGRSTIDADDVRLAIQSRLDHSFTQP 85 (129)
T ss_dssp -----HHHHHHHHHHHHTT-----B-THHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHHHHT--------
T ss_pred CccCChHHHHHHHHHHHcC--CcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHhhhccCC
Confidence 3456763 3444555542 2357888999999999999999999999999999999999999999999 777777777
Q ss_pred HHHHHHHHH
Q 027605 102 PLKIYLNKY 110 (221)
Q Consensus 102 ~Lk~~Le~y 110 (221)
+-+++|-+.
T Consensus 86 ppre~llel 94 (129)
T PF02291_consen 86 PPREFLLEL 94 (129)
T ss_dssp ---------
T ss_pred CChHHHHHH
Confidence 766666543
No 56
>KOG3423 consensus Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=91.89 E-value=0.81 Score=39.88 Aligned_cols=69 Identities=22% Similarity=0.242 Sum_probs=57.3
Q ss_pred CCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC--------------CCccCcchHHHHHh
Q 027605 27 FLPIANVSRIMKKSLPANAKISKEAKETVQECVSEFISFITGEASDKCQREK--------------RKTINGDDLLWAMT 92 (221)
Q Consensus 27 ~LPrAtV~RImK~aLP~n~kISkDAk~al~kcateFI~yLTseAneic~~ek--------------RKTIsaeDVl~ALe 92 (221)
.||-+.+.-+++.+. -.....-.+-+|.-++..||+-|+..|.+.|+-.. |-|++-+|+-.||+
T Consensus 86 ~IPDavt~~yL~~aG--f~~~D~rv~RLvsLaAQKfvSDIa~DA~Q~~k~r~~~~~~~~k~~~kdkK~tLtmeDL~~AL~ 163 (176)
T KOG3423|consen 86 TIPDAVTDHYLKKAG--FQTSDPRVKRLVSLAAQKFVSDIANDALQHSKIRTKTAIGKDKKQAKDKKYTLTMEDLSPALA 163 (176)
T ss_pred CCcHHHHHHHHHhcC--CCcCcHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccccccccccccceeeeHHHHHHHHH
Confidence 588888888888874 23356677889999999999999999999998543 45899999999999
Q ss_pred hcCCC
Q 027605 93 TLGFE 97 (221)
Q Consensus 93 ~LGF~ 97 (221)
+.|..
T Consensus 164 EyGin 168 (176)
T KOG3423|consen 164 EYGIN 168 (176)
T ss_pred HhCcc
Confidence 98873
No 57
>PTZ00252 histone H2A; Provisional
Probab=91.56 E-value=0.63 Score=39.02 Aligned_cols=64 Identities=13% Similarity=0.277 Sum_probs=49.0
Q ss_pred cccCCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHH----Hh--cCCCccCcchHHHHHh
Q 027605 24 QDRFLPIANVSRIMKKSLPANAKISKEAKETVQECVSEFISFITGEASDKC----QR--EKRKTINGDDLLWAMT 92 (221)
Q Consensus 24 eD~~LPrAtV~RImK~aLP~n~kISkDAk~al~kcateFI~yLTseAneic----~~--ekRKTIsaeDVl~ALe 92 (221)
-.+.||...|.|++|+.-- ..+|+.-|-..|.-+. .||++|-.|.+ .+ .+++-|+++||..|+.
T Consensus 22 AGL~FPVgRi~R~Lr~g~y-a~RIga~ApVYLAAVL----EYLtaEVLELAgnaa~d~~~kk~RItPrHi~lAIr 91 (134)
T PTZ00252 22 AGLIFPVGRVGSLLRRGQY-ARRIGASGAVYMAAVL----EYLTAELLELSVKAAAQQAKKPKRLTPRTVTLAVR 91 (134)
T ss_pred cCccCchHHHHHHHHcCCc-ccccCCccHHHHHHHH----HHHHHHHHHHHHHHHHhccCCcccccHHHHHhhcc
Confidence 4689999999999998764 4689998888777654 45665555444 32 4778999999999986
No 58
>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily. Members of this protein are marked as probable ATPases by the nucleotide binding P-loop motif GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of helicases, and extensive homology to ATPases of MSHA-type pilus systems and to GspA proteins associated with type II protein secretion systems.
Probab=90.38 E-value=0.9 Score=38.70 Aligned_cols=71 Identities=14% Similarity=0.228 Sum_probs=55.4
Q ss_pred CCchhHHHHHHhhcC-----CCCcccCHHHHHHHHHHHHH---HHHHHHHHHHHHHHhcCCCccCcchHHHHHhhcCCC
Q 027605 27 FLPIANVSRIMKKSL-----PANAKISKEAKETVQECVSE---FISFITGEASDKCQREKRKTINGDDLLWAMTTLGFE 97 (221)
Q Consensus 27 ~LPrAtV~RImK~aL-----P~n~kISkDAk~al~kcate---FI~yLTseAneic~~ekRKTIsaeDVl~ALe~LGF~ 97 (221)
.|...-+..++...+ .....+++++.+.|.+.+.= .|+.+...+...+-..+.++|+.++|..++.++.|+
T Consensus 191 ~l~~~e~~~~l~~~l~~~g~~~~~~~~~~~~~~i~~~s~G~p~~i~~l~~~~~~~a~~~~~~~i~~~~v~~~~~~~~~~ 269 (269)
T TIGR03015 191 PLDREETREYIEHRLERAGNRDAPVFSEGAFDAIHRFSRGIPRLINILCDRLLLSAFLEEKREIGGEEVREVIAEIDFE 269 (269)
T ss_pred CCCHHHHHHHHHHHHHHcCCCCCCCcCHHHHHHHHHHcCCcccHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhhcC
Confidence 344555555554433 12356999999999998875 799999999988888899999999999999998753
No 59
>KOG4336 consensus TBP-associated transcription factor Prodos [Transcription]
Probab=87.29 E-value=3.3 Score=39.16 Aligned_cols=77 Identities=25% Similarity=0.299 Sum_probs=63.6
Q ss_pred HHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHHhhcCCCcchHHHHHHHHHHH
Q 027605 32 NVSRIMKKSLPANAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAMTTLGFENYVSPLKIYLNKYR 111 (221)
Q Consensus 32 tV~RImK~aLP~n~kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~ALe~LGF~~yv~~Lk~~Le~yR 111 (221)
.|.-|.++.+ =-.|++-|++.|.+....+|.-+...+.-.|+..+|...+.-||.-.|-++|+. +..|..+++++-
T Consensus 10 VV~~Ll~~~g--fd~is~~aletlvell~~yi~eigrq~~n~celagRT~pT~~Dv~l~Li~mnI~--v~sL~~~~q~~~ 85 (323)
T KOG4336|consen 10 VVSNLLKTKG--FDSISNAALETLVELLQSYIREIGRQLHNYCELAGRTIPTQGDVKLTLIEMNIK--VSSLYAYFQKQE 85 (323)
T ss_pred HHHHHHHHhC--chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcHHHHHHHHHHhCCC--hhhhHHHHHhcc
Confidence 3444444443 234999999999999999999999999999999999999999999999999997 566777666554
Q ss_pred H
Q 027605 112 E 112 (221)
Q Consensus 112 e 112 (221)
.
T Consensus 86 ~ 86 (323)
T KOG4336|consen 86 F 86 (323)
T ss_pred c
Confidence 4
No 60
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=86.94 E-value=2.9 Score=37.91 Aligned_cols=71 Identities=11% Similarity=0.146 Sum_probs=51.1
Q ss_pred chhHHHHHHhhcCCC---CcccCHHHHHHHHHHH------HHHHHHHHHHHHHHHHhcCCCccCcchHHHHHhhcCCCcc
Q 027605 29 PIANVSRIMKKSLPA---NAKISKEAKETVQECV------SEFISFITGEASDKCQREKRKTINGDDLLWAMTTLGFENY 99 (221)
Q Consensus 29 PrAtV~RImK~aLP~---n~kISkDAk~al~kca------teFI~yLTseAneic~~ekRKTIsaeDVl~ALe~LGF~~y 99 (221)
....+..|++..+.. ...++.++.+.+.+.+ -..+..+...|.+.|..+++.+|+.+||.+|++++....+
T Consensus 208 ~~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~a~~~a~~~~~~~I~~~~v~~a~~~~~~~~~ 287 (394)
T PRK00411 208 TADEIFDILKDRVEEGFYPGVVDDEVLDLIADLTAREHGDARVAIDLLRRAGLIAEREGSRKVTEEDVRKAYEKSEIVHL 287 (394)
T ss_pred CHHHHHHHHHHHHHhhcccCCCCHhHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHHHHHH
Confidence 345566666554421 2358999998888877 3345566678888898899999999999999998844333
No 61
>KOG2549 consensus Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=86.65 E-value=2.7 Score=42.44 Aligned_cols=66 Identities=23% Similarity=0.215 Sum_probs=55.2
Q ss_pred CchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHHhhcC
Q 027605 28 LPIANVSRIMKKSLPANAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAMTTLG 95 (221)
Q Consensus 28 LPrAtV~RImK~aLP~n~kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~ALe~LG 95 (221)
-|+..+.-+++... -..|++|+..+|.+-.+.=|.-|+.+|.+.-.+.+|.+++.+||-.||+-+.
T Consensus 12 s~~Es~k~vAEslG--i~nl~deaa~~La~dv~yrikEI~Q~aaKfm~hskR~kLtv~DV~~ALr~~n 77 (576)
T KOG2549|consen 12 SPKESVKVVAESLG--ITNLNDEAALLLAEDVEYRIKEIVQDAAKFMVHSKRTKLTVDDVDYALRSLN 77 (576)
T ss_pred CcHHHHHHHHHHhC--ccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcCcHHHHHHHHhhcc
Confidence 34556655555442 3459999999999999999999999999999999999999999999999554
No 62
>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=81.54 E-value=6.3 Score=35.27 Aligned_cols=72 Identities=8% Similarity=0.077 Sum_probs=48.7
Q ss_pred hhHHHHHHhhcCC---CCcccCHHHHHHHHHHHH------HHHHHHHHHHHHHHHhcCCCccCcchHHHHHhhcCCCcch
Q 027605 30 IANVSRIMKKSLP---ANAKISKEAKETVQECVS------EFISFITGEASDKCQREKRKTINGDDLLWAMTTLGFENYV 100 (221)
Q Consensus 30 rAtV~RImK~aLP---~n~kISkDAk~al~kcat------eFI~yLTseAneic~~ekRKTIsaeDVl~ALe~LGF~~yv 100 (221)
..-+..|++..+. ....+++|+...+.+.+. -.+..+...|.+.|..+++.+|+.+||..|++.+....+.
T Consensus 201 ~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~R~al~~l~~a~~~a~~~~~~~it~~~v~~a~~~~~~~~~~ 280 (365)
T TIGR02928 201 AEELRDILENRAEKAFYDGVLDDGVIPLCAALAAQEHGDARKAIDLLRVAGEIAEREGAERVTEDHVEKAQEKIEKDRLL 280 (365)
T ss_pred HHHHHHHHHHHHHhhccCCCCChhHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHH
Confidence 4446666655442 134588888877766442 2344455577788888899999999999999988544444
Q ss_pred H
Q 027605 101 S 101 (221)
Q Consensus 101 ~ 101 (221)
.
T Consensus 281 ~ 281 (365)
T TIGR02928 281 E 281 (365)
T ss_pred H
Confidence 3
No 63
>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=80.18 E-value=7.2 Score=33.79 Aligned_cols=79 Identities=8% Similarity=0.096 Sum_probs=57.7
Q ss_pred ccccCCchhHHHHHHhhcCCCC-c-ccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhc------CCCccCcchHHHHHhhc
Q 027605 23 EQDRFLPIANVSRIMKKSLPAN-A-KISKEAKETVQECVSEFISFITGEASDKCQRE------KRKTINGDDLLWAMTTL 94 (221)
Q Consensus 23 eeD~~LPrAtV~RImK~aLP~n-~-kISkDAk~al~kcateFI~yLTseAneic~~e------kRKTIsaeDVl~ALe~L 94 (221)
.+..+|....|.+.|...+... . .|+.|++.+|.-||.+++..|-......|++- ...++--.||-.-|..|
T Consensus 40 ~~~~fl~~~~l~~~~~~i~~~~g~~~~~~d~~~lis~a~e~rlr~li~k~~~~s~hR~~~~~~~~r~~~~sdvr~qL~~l 119 (212)
T cd08045 40 KDPSFLNPSPLAKKIRKIAKKHGLKEVDEDVLDLISLALEERLRNLLEKLIEVSEHRVDSEKEDERYEITSDVRKQLRFL 119 (212)
T ss_pred chhhccCHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCceeecchHHHHHHHH
Confidence 3445677777776666665432 2 69999999999999999999999998888864 34566678887777766
Q ss_pred CCCcchH
Q 027605 95 GFENYVS 101 (221)
Q Consensus 95 GF~~yv~ 101 (221)
+--+-.+
T Consensus 120 ~~~ek~e 126 (212)
T cd08045 120 EQLEREE 126 (212)
T ss_pred HHHHHHH
Confidence 5543333
No 64
>KOG2389 consensus Predicted bromodomain transcription factor [Transcription]
Probab=78.48 E-value=5.6 Score=38.09 Aligned_cols=71 Identities=17% Similarity=0.148 Sum_probs=59.9
Q ss_pred ccCCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHHhhcCCC
Q 027605 25 DRFLPIANVSRIMKKSLPANAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAMTTLGFE 97 (221)
Q Consensus 25 D~~LPrAtV~RImK~aLP~n~kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~ALe~LGF~ 97 (221)
.+.|-+..|.+|+...-=. ....-|.+.|+.-+..||+-|+..|...+...+|.-.+..||+.||+.|+..
T Consensus 27 a~sla~~avaQIcqslg~~--~~~~sale~Ltd~~~qyvQ~lgk~a~~~~n~anR~epnl~Div~Al~dls~s 97 (353)
T KOG2389|consen 27 AFSLARVAVAQICQSLGYS--STQNSALETLTDVLQQYVQNLGKTAHRYSNLANRTEPNLFDIVLALQDLSAS 97 (353)
T ss_pred HHHHHHHHHHHHHHhcCCc--ccccHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCccHHHHHHHHHHhhhh
Confidence 3467888889998766422 2344499999999999999999999999999999999999999999987763
No 65
>KOG1757 consensus Histone 2A [Chromatin structure and dynamics]
Probab=76.45 E-value=6.4 Score=32.66 Aligned_cols=66 Identities=17% Similarity=0.286 Sum_probs=50.7
Q ss_pred ccccCCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhc----CCCccCcchHHHHHh
Q 027605 23 EQDRFLPIANVSRIMKKSLPANAKISKEAKETVQECVSEFISFITGEASDKCQRE----KRKTINGDDLLWAMT 92 (221)
Q Consensus 23 eeD~~LPrAtV~RImK~aLP~n~kISkDAk~al~kcateFI~yLTseAneic~~e----kRKTIsaeDVl~ALe 92 (221)
..-+.||...|.|.+|.-.....+|..-+.... .-.+.|||+|-.+.+... +-|.|++.|+--|++
T Consensus 26 raGlqFpVgRihr~LK~r~t~h~rVGataavy~----aaileYLTaEVLeLAgNasKdLKvKRitprHlqLAiR 95 (131)
T KOG1757|consen 26 RAGLQFPVGRIHRHLKTRTTSHGRVGATAAVYS----AAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 95 (131)
T ss_pred hcccccchHHHHHHHHHhcccccccchHHHHHH----HHHHHHHHHHHHHHcccccccceeeeccchhheeeec
Confidence 456789999999999999887788875544332 345679999988888765 448899999887775
No 66
>PF13654 AAA_32: AAA domain; PDB: 3K1J_B.
Probab=72.86 E-value=13 Score=36.77 Aligned_cols=61 Identities=16% Similarity=0.168 Sum_probs=42.7
Q ss_pred HHHHHHhhcCCCCcccCHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHhcCCCccCcchHHHHHhhc
Q 027605 32 NVSRIMKKSLPANAKISKEAKETVQECVSE-----------FISFITGEASDKCQREKRKTINGDDLLWAMTTL 94 (221)
Q Consensus 32 tV~RImK~aLP~n~kISkDAk~al~kcate-----------FI~yLTseAneic~~ekRKTIsaeDVl~ALe~L 94 (221)
-|.+++++.- --.++.+|+..|.+.+.. -|.-|-.||+..|..++++.|+++||..|++.-
T Consensus 435 ~i~~~~~~~~--L~~~~~~Av~~li~~~~R~~q~kLsl~~~~l~~ll~EA~~~A~~~~~~~I~~~~V~~Ai~~r 506 (509)
T PF13654_consen 435 FIASICQKEG--LPPFDRSAVARLIEYSARLDQDKLSLRFSWLADLLREANYWARKEGAKVITAEHVEQAIEER 506 (509)
T ss_dssp HHHHHHHHHS--S--BBHHHHHHHHHHHHHCC-SEEE--HHHHHHHHHHHHHHHHHCT-SSB-HHHHHHHHHH-
T ss_pred HHHHHHHhCC--CCCCCHHHHHHHHHHHHHHhCCEeCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHcc
Confidence 3444454431 124888888888877653 566677899999999999999999999999863
No 67
>TIGR00764 lon_rel lon-related putative ATP-dependent protease. Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein.
Probab=71.63 E-value=14 Score=37.13 Aligned_cols=50 Identities=12% Similarity=0.140 Sum_probs=39.7
Q ss_pred ccCHHHHHHHHHHHHH-------------HHHHHHHHHHHHHHhcCCCccCcchHHHHHhhcC
Q 027605 46 KISKEAKETVQECVSE-------------FISFITGEASDKCQREKRKTINGDDLLWAMTTLG 95 (221)
Q Consensus 46 kISkDAk~al~kcate-------------FI~yLTseAneic~~ekRKTIsaeDVl~ALe~LG 95 (221)
.++++|++.|.+.++. =|.-|-.+|..+|..+++.+|+.+||.+|++.-.
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 6999999999865542 3444556788899889999999999999988553
No 68
>KOG2680 consensus DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=71.09 E-value=17 Score=35.35 Aligned_cols=50 Identities=16% Similarity=0.261 Sum_probs=41.8
Q ss_pred CCcccCHHHHHHHHHHHH----HHHHHHHHHHHHHHHhcCCCccCcchHHHHHh
Q 027605 43 ANAKISKEAKETVQECVS----EFISFITGEASDKCQREKRKTINGDDLLWAMT 92 (221)
Q Consensus 43 ~n~kISkDAk~al~kcat----eFI~yLTseAneic~~ekRKTIsaeDVl~ALe 92 (221)
+++.++.||++.|.+... -|-.+|-+.|+.+|.+.+-+++..+||-.+-+
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 578999999999987654 35566667888999999999999999998865
No 69
>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=71.02 E-value=11 Score=36.97 Aligned_cols=66 Identities=21% Similarity=0.305 Sum_probs=44.6
Q ss_pred hhHHHHHHhhcCC-CCcccCHHHHHHHHHHHH---HHHHHHHHHHHHHHHhcCCCccCcchHHHHHhhcCC
Q 027605 30 IANVSRIMKKSLP-ANAKISKEAKETVQECVS---EFISFITGEASDKCQREKRKTINGDDLLWAMTTLGF 96 (221)
Q Consensus 30 rAtV~RImK~aLP-~n~kISkDAk~al~kcat---eFI~yLTseAneic~~ekRKTIsaeDVl~ALe~LGF 96 (221)
..-+.+|++..+. .+..|++++.+.|.+.+. +.++.| ..|..+|..++|++|+.+||.+++..-.|
T Consensus 265 ~eei~~Il~~~a~k~~i~is~~al~~I~~y~~n~Rel~nll-~~Aa~~A~~~~~~~It~~dI~~vl~~~~~ 334 (531)
T TIGR02902 265 DEEIKEIAKNAAEKIGINLEKHALELIVKYASNGREAVNIV-QLAAGIALGEGRKRILAEDIEWVAENGNY 334 (531)
T ss_pred HHHHHHHHHHHHHHcCCCcCHHHHHHHHHhhhhHHHHHHHH-HHHHHHHhhCCCcEEcHHHHHHHhCCccc
Confidence 3445555555543 246799999998887765 333333 34556777788999999999999765433
No 70
>KOG3334 consensus Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=70.05 E-value=34 Score=29.31 Aligned_cols=64 Identities=14% Similarity=0.217 Sum_probs=51.0
Q ss_pred cCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHHhhcCCCcchH-HHHHHHHHH
Q 027605 47 ISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAMTTLGFENYVS-PLKIYLNKY 110 (221)
Q Consensus 47 ISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~ALe~LGF~~yv~-~Lk~~Le~y 110 (221)
...-+...|.+-+=-++.-|-..|.-.+.+.+|.+|.++||--|++...=..|.. +=+++|-++
T Consensus 31 yEprVi~qlLefa~rYtt~vL~DA~vys~HA~ka~i~~eDVrlA~~~~~~~sf~~pPpRe~lL~l 95 (148)
T KOG3334|consen 31 YEPRVINQLLEFAYRYTTTVLDDAKVYSSHAKKATIDAEDVRLAIQMRVDHSFTPPPPREFLLEL 95 (148)
T ss_pred cChHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHhccccCCCCchHHHHHH
Confidence 5666777788888888888889999999999999999999999999766666666 444454443
No 71
>COG1067 LonB Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]
Probab=69.92 E-value=4.1 Score=41.61 Aligned_cols=47 Identities=26% Similarity=0.340 Sum_probs=36.5
Q ss_pred ccCHHHHHHHHHHHH--------------HHHHHHHHHHHHHHHhcCCCccCcchHHHHHhh
Q 027605 46 KISKEAKETVQECVS--------------EFISFITGEASDKCQREKRKTINGDDLLWAMTT 93 (221)
Q Consensus 46 kISkDAk~al~kcat--------------eFI~yLTseAneic~~ekRKTIsaeDVl~ALe~ 93 (221)
.++++|..-|.+-+. .-...|. +|.++|..++++-|+++||.+|++.
T Consensus 338 ~~~~~Av~~li~~a~R~Ag~~~~Ltl~~rdl~~lv~-~A~~ia~~~~~~~I~ae~Ve~a~~~ 398 (647)
T COG1067 338 HLDKDAVEELIREAARRAGDQNKLTLRLRDLGNLVR-EAGDIAVSEGRKLITAEDVEEALQK 398 (647)
T ss_pred CCCHHHHHHHHHHHHHhccccceeccCHHHHHHHHH-HhhHHHhcCCcccCcHHHHHHHHHh
Confidence 377777666655443 3444444 9999999999999999999999987
No 72
>PF13335 Mg_chelatase_2: Magnesium chelatase, subunit ChlI
Probab=61.93 E-value=29 Score=26.75 Aligned_cols=48 Identities=19% Similarity=0.225 Sum_probs=38.5
Q ss_pred cccCHHHHHHHHHHHHHH------HHHHHHHHHHHHHhcCCCccCcchHHHHHh
Q 027605 45 AKISKEAKETVQECVSEF------ISFITGEASDKCQREKRKTINGDDLLWAMT 92 (221)
Q Consensus 45 ~kISkDAk~al~kcateF------I~yLTseAneic~~ekRKTIsaeDVl~ALe 92 (221)
..+++++..+|.+++..| ++-|..-|..+|--++...|..+||.+||.
T Consensus 41 ~~l~~~~~~~l~~~~~~~~lS~R~~~rilrvARTIADL~~~~~I~~~hi~EAl~ 94 (96)
T PF13335_consen 41 CPLSSEAKKLLEQAAEKLNLSARGYHRILRVARTIADLEGSERITREHIAEALS 94 (96)
T ss_pred cCCCHHHHHHHHHHHHHcCcCHHHHHHHHHHHHHHHhHcCCCCCCHHHHHHHHh
Confidence 346778888888877765 445566788999999999999999999984
No 73
>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=56.35 E-value=24 Score=34.20 Aligned_cols=64 Identities=22% Similarity=0.254 Sum_probs=52.8
Q ss_pred hHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHHhhcCC
Q 027605 31 ANVSRIMKKSLPANAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAMTTLGF 96 (221)
Q Consensus 31 AtV~RImK~aLP~n~kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~ALe~LGF 96 (221)
.+|.-+.. .|. -..|.+|+..+|.--.+-=|+-+..+|...-.+.||..++-+||-.||+.|..
T Consensus 9 et~KdvAe-slG-i~Ni~Dd~l~alamDlEYRI~ev~qea~KFmvhSKRtvLt~dDis~ALr~lNV 72 (450)
T COG5095 9 ETLKDVAE-SLG-ISNIDDDALRALAMDLEYRIKEVCQEASKFMVHSKRTVLTIDDISYALRSLNV 72 (450)
T ss_pred HHHHHHHH-HcC-CcccccHHHHHHHHhHHHHHHHHHHHHHHHhhcccceeeeHHhHHHHHHhcCC
Confidence 34444443 332 34699999999999999999999999999999999999999999999998764
No 74
>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=55.65 E-value=83 Score=27.53 Aligned_cols=70 Identities=21% Similarity=0.216 Sum_probs=46.3
Q ss_pred CchhHHHHHHhhcCC-CCcccCHHHHHHHHHHHHH---HHHHHHHHHHHHHHhcCCCccCcchHHHHHhhcCCC
Q 027605 28 LPIANVSRIMKKSLP-ANAKISKEAKETVQECVSE---FISFITGEASDKCQREKRKTINGDDLLWAMTTLGFE 97 (221)
Q Consensus 28 LPrAtV~RImK~aLP-~n~kISkDAk~al~kcate---FI~yLTseAneic~~ekRKTIsaeDVl~ALe~LGF~ 97 (221)
++...+..+++.... .+..++.|+...|.+.+.= ++.-+...+.+.+...+...|+.++|..++..++++
T Consensus 159 l~~~e~~~il~~~~~~~~~~~~~~al~~ia~~~~G~pR~~~~ll~~~~~~a~~~~~~~it~~~v~~~l~~l~~~ 232 (305)
T TIGR00635 159 YTVEELAEIVSRSAGLLNVEIEPEAALEIARRSRGTPRIANRLLRRVRDFAQVRGQKIINRDIALKALEMLMID 232 (305)
T ss_pred CCHHHHHHHHHHHHHHhCCCcCHHHHHHHHHHhCCCcchHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHhCCC
Confidence 444555555554432 2567999999888876532 233344455566655666789999999999997665
No 75
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=54.89 E-value=60 Score=29.28 Aligned_cols=71 Identities=15% Similarity=0.185 Sum_probs=48.4
Q ss_pred CchhHHHHHHhhcCC-CCcccCHHHHHHHHHHHHH---HHHHHHHHHHHHHHhcCCCccCcchHHHHHhhcCCCc
Q 027605 28 LPIANVSRIMKKSLP-ANAKISKEAKETVQECVSE---FISFITGEASDKCQREKRKTINGDDLLWAMTTLGFEN 98 (221)
Q Consensus 28 LPrAtV~RImK~aLP-~n~kISkDAk~al~kcate---FI~yLTseAneic~~ekRKTIsaeDVl~ALe~LGF~~ 98 (221)
++...+.+|++.... .++.++.|+...|.+.|.= .+..+-..+.+.+...+.+.|+.++|..+++.++...
T Consensus 180 ~~~~e~~~il~~~~~~~~~~~~~~~~~~ia~~~~G~pR~a~~~l~~~~~~a~~~~~~~I~~~~v~~~l~~~~~~~ 254 (328)
T PRK00080 180 YTVEELEKIVKRSARILGVEIDEEGALEIARRSRGTPRIANRLLRRVRDFAQVKGDGVITKEIADKALDMLGVDE 254 (328)
T ss_pred CCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCc
Confidence 445555556554432 2678999999888877732 2334444555666666677999999999999887654
No 76
>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=54.35 E-value=11 Score=24.65 Aligned_cols=26 Identities=19% Similarity=0.220 Sum_probs=21.1
Q ss_pred HHHHHHhcCCCccCcchHHHHHhhcC
Q 027605 70 ASDKCQREKRKTINGDDLLWAMTTLG 95 (221)
Q Consensus 70 Aneic~~ekRKTIsaeDVl~ALe~LG 95 (221)
|.+.|+..+...|+.+|++.||=+.+
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 56788999999999999999976544
No 77
>COG5162 Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=53.32 E-value=75 Score=28.11 Aligned_cols=52 Identities=19% Similarity=0.204 Sum_probs=40.4
Q ss_pred ccCHHHHHHHHHHHHHHHHHHHHHHHHHHHh-------------------c--------------CCCccCcchHHHHHh
Q 027605 46 KISKEAKETVQECVSEFISFITGEASDKCQR-------------------E--------------KRKTINGDDLLWAMT 92 (221)
Q Consensus 46 kISkDAk~al~kcateFI~yLTseAneic~~-------------------e--------------kRKTIsaeDVl~ALe 92 (221)
....-.+.+|.-.+..||+-|+..|.+..+= . ++.+++..|+-+||+
T Consensus 105 ~~D~rvKkLl~L~aqKFvsDiA~dayqYsrIr~~~sna~~t~~~a~~f~~gg~~~i~~~~~~~dr~K~vltv~DLs~Al~ 184 (197)
T COG5162 105 TSDQRVKKLLSLLAQKFVSDIAVDAYQYSRIRQGSSNAKATAQKAKRFAKGGASGIGSSGRRGDRKKPVLTVVDLSKALE 184 (197)
T ss_pred eccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccchhhHHHHHHHHhcccccccccccccccCCceeeehHHHHHHH
Confidence 3556678889999999999999887765431 1 566789999999999
Q ss_pred hcCCC
Q 027605 93 TLGFE 97 (221)
Q Consensus 93 ~LGF~ 97 (221)
+.|+.
T Consensus 185 EyGin 189 (197)
T COG5162 185 EYGIN 189 (197)
T ss_pred Hhccc
Confidence 98873
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=51.79 E-value=85 Score=22.34 Aligned_cols=47 Identities=21% Similarity=0.246 Sum_probs=37.5
Q ss_pred CCchhHHHHHHhhcCCCCcc-cCHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 027605 27 FLPIANVSRIMKKSLPANAK-ISKEAKETVQECVSEFISFITGEASDKCQR 76 (221)
Q Consensus 27 ~LPrAtV~RImK~aLP~n~k-ISkDAk~al~kcateFI~yLTseAneic~~ 76 (221)
.+|-+.+.-+++.+. .. -..-.+-+|.=++..||.-|+..|.+.|+-
T Consensus 2 ~IPD~v~~~yL~~~G---~~~~D~rv~RLvSLaaQKFisdI~~dA~q~~k~ 49 (51)
T PF03540_consen 2 TIPDEVTDYYLERSG---FQTSDPRVKRLVSLAAQKFISDIANDAMQYCKI 49 (51)
T ss_pred CCCHHHHHHHHHHCC---CCCCCHhHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 478888888998884 33 344566788889999999999999999864
No 79
>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=50.09 E-value=53 Score=33.06 Aligned_cols=53 Identities=21% Similarity=0.255 Sum_probs=43.1
Q ss_pred hcCCCCcccCHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCccCcchHHHHHh
Q 027605 39 KSLPANAKISKEAKETVQECVSEFI-------SFITGEASDKCQREKRKTINGDDLLWAMT 92 (221)
Q Consensus 39 ~aLP~n~kISkDAk~al~kcateFI-------~yLTseAneic~~ekRKTIsaeDVl~ALe 92 (221)
..+| .+.|+.++++.|.+.+..+- .++...|.-+|.-++|.+|+.+||..|++
T Consensus 243 ~~~~-~V~is~~~~~~l~~~~~~~~i~s~Ra~i~~~r~Ara~AaL~gr~~V~~~Dv~~A~~ 302 (633)
T TIGR02442 243 SLLP-SVRISDSLIRFISELCIEFGVDGHRADIVMARAARALAALDGRRRVTAEDVREAAE 302 (633)
T ss_pred HhCC-CCCCCHHHHHHHHHHHHHhCCCCccHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHH
Confidence 3443 68999999999999887762 45666777888889999999999999877
No 80
>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I. This model represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria.
Probab=49.36 E-value=63 Score=30.23 Aligned_cols=54 Identities=20% Similarity=0.203 Sum_probs=42.0
Q ss_pred hhcCCCCcccCHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCccCcchHHHHHh
Q 027605 38 KKSLPANAKISKEAKETVQECVSEFI-------SFITGEASDKCQREKRKTINGDDLLWAMT 92 (221)
Q Consensus 38 K~aLP~n~kISkDAk~al~kcateFI-------~yLTseAneic~~ekRKTIsaeDVl~ALe 92 (221)
++.+| .+.|+++.+..+.+.|..+= .++...|.-.|.-++|..|+++||..+..
T Consensus 247 ~~~~~-~V~v~d~~~~~i~~l~~~~~~~s~Ra~i~l~raArA~Aal~GR~~V~~dDv~~~a~ 307 (337)
T TIGR02030 247 QNLLP-QVTIPYDVLVKVAELCAELDVDGLRGELTLNRAAKALAAFEGRTEVTVDDIRRVAV 307 (337)
T ss_pred HHHhc-cCcCCHHHHHHHHHHHHHHCCCCCcHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 45565 78999999998888776652 34556677788889999999999998765
No 81
>PRK07452 DNA polymerase III subunit delta; Validated
Probab=46.84 E-value=78 Score=28.19 Aligned_cols=54 Identities=17% Similarity=0.155 Sum_probs=42.9
Q ss_pred CcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHh--cCCCccCcchHHHHHhhcCCC
Q 027605 44 NAKISKEAKETVQECVSEFISFITGEASDKCQR--EKRKTINGDDLLWAMTTLGFE 97 (221)
Q Consensus 44 n~kISkDAk~al~kcateFI~yLTseAneic~~--ekRKTIsaeDVl~ALe~LGF~ 97 (221)
+.+|+.+|...|.+++.-=...+..|-...|.- .++++|+.+||...+....+.
T Consensus 147 g~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~~It~~~V~~~v~~~~~~ 202 (326)
T PRK07452 147 GVKLTPEAAELLAEAVGNDSRRLYNELEKLALYAENSTKPISAEEVKALVSNTTQN 202 (326)
T ss_pred CCCCCHHHHHHHHHHhCccHHHHHHHHHHHHHhccCCCCccCHHHHHHHhccCcCc
Confidence 678999999999999887666777777777665 457889999999887765543
No 82
>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=46.24 E-value=26 Score=31.29 Aligned_cols=75 Identities=11% Similarity=0.087 Sum_probs=34.3
Q ss_pred ccccCCchhHHHHHHhhcCCC--CcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC------CccCcchHHHHHhhc
Q 027605 23 EQDRFLPIANVSRIMKKSLPA--NAKISKEAKETVQECVSEFISFITGEASDKCQREKR------KTINGDDLLWAMTTL 94 (221)
Q Consensus 23 eeD~~LPrAtV~RImK~aLP~--n~kISkDAk~al~kcateFI~yLTseAneic~~ekR------KTIsaeDVl~ALe~L 94 (221)
.++.+|....+.+.|...... ...|..|.+.+|.-||.+.|..|-..+..+|++-.. .+....||-..|..|
T Consensus 39 ~~~~fL~~~~L~~~i~~i~~~~g~~~~~~d~l~llS~A~e~rLr~lie~~~~~s~hR~~~~~~~~~~~~~sdv~~qlr~l 118 (264)
T PF05236_consen 39 KEEPFLNPSPLQKRIQKIAKKHGLKSVDEDVLELLSLATEERLRNLIEKAIVLSRHRRDSSKSDPRYEIRSDVRKQLRFL 118 (264)
T ss_dssp -----S-HHHHHHHHHHHHHCTT--EE-TCHHHHHHHHHHHHHHHHHHHHH-----------------------------
T ss_pred ccccccCHHHHHHHHHHHHHHcCCcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccCCCcccccchHHHHHHHHH
Confidence 456678887777777766532 356999999999999999999999999888875322 233467777777655
Q ss_pred CCC
Q 027605 95 GFE 97 (221)
Q Consensus 95 GF~ 97 (221)
.--
T Consensus 119 ~~~ 121 (264)
T PF05236_consen 119 EQL 121 (264)
T ss_dssp ---
T ss_pred HHH
Confidence 543
No 83
>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=44.92 E-value=29 Score=23.63 Aligned_cols=42 Identities=14% Similarity=0.099 Sum_probs=26.8
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHH-HHHHhcCCCccCcchHHHH
Q 027605 48 SKEAKETVQECVSEFISFITGEAS-DKCQREKRKTINGDDLLWA 90 (221)
Q Consensus 48 SkDAk~al~kcateFI~yLTseAn-eic~~ekRKTIsaeDVl~A 90 (221)
+.||...|.+. -.||.=-...+. +.|...|...|+.++|..|
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 45677777774 667764444444 6677889999999998876
No 84
>PRK13765 ATP-dependent protease Lon; Provisional
Probab=44.56 E-value=59 Score=33.24 Aligned_cols=48 Identities=15% Similarity=0.142 Sum_probs=39.0
Q ss_pred ccCHHHHHHHHHHHHHH-------------HHHHHHHHHHHHHhcCCCccCcchHHHHHhh
Q 027605 46 KISKEAKETVQECVSEF-------------ISFITGEASDKCQREKRKTINGDDLLWAMTT 93 (221)
Q Consensus 46 kISkDAk~al~kcateF-------------I~yLTseAneic~~ekRKTIsaeDVl~ALe~ 93 (221)
.++++|+..|.+.++.- |.-|-.+|..+|+.++++.|+.+||..|+..
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 69999998888866632 2236678999999999999999999999843
No 85
>cd04752 Commd4 COMM_Domain containing protein 4. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=43.77 E-value=73 Score=26.89 Aligned_cols=50 Identities=18% Similarity=0.288 Sum_probs=33.8
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHHhhcCCC-cchHHHHHHHHHHHHHH
Q 027605 58 CVSEFISFITGEASDKCQREKRKTINGDDLLWAMTTLGFE-NYVSPLKIYLNKYRETE 114 (221)
Q Consensus 58 cateFI~yLTseAneic~~ekRKTIsaeDVl~ALe~LGF~-~yv~~Lk~~Le~yRe~~ 114 (221)
.+.+.++||-.+|. |.-++.+++..-|+.|||+ +.++.+.....++|+..
T Consensus 43 ~~va~l~fiL~~A~-------k~n~~~~~l~~eL~~lglp~e~~~~l~~~~~~~~~~l 93 (174)
T cd04752 43 ASIAVLSFILSSAA-------KYNVDGESLSSELQQLGLPKEHATSLCRSYEEKQSKL 93 (174)
T ss_pred HHHHHHHHHHHHHH-------HcCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHH
Confidence 45566777776663 4559999999999999997 44444444444444443
No 86
>KOG3901 consensus Transcription initiation factor IID subunit [Transcription]
Probab=43.62 E-value=63 Score=26.45 Aligned_cols=49 Identities=18% Similarity=0.274 Sum_probs=39.9
Q ss_pred CCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHHhh
Q 027605 42 PANAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAMTT 93 (221)
Q Consensus 42 P~n~kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~ALe~ 93 (221)
.++..=-.|.+++|-..+.+||.-++..|.++. +|--+..||++-+|++
T Consensus 23 GDd~nP~~~tv~~Le~iV~~Yi~elt~~a~~~g---~rgk~~veD~~f~lRk 71 (109)
T KOG3901|consen 23 GDDVNPYPETVDLLEDIVLEYITELTHAAMEIG---KRGKVKVEDFKFLLRK 71 (109)
T ss_pred CCCCCccHhHHHHHHHHHHHHHHHHHHHHHHhc---ccCceeHHHHHHHHHh
Confidence 345556678999999999999999987777776 5666788999999983
No 87
>KOG2181 consensus LIM domain binding protein LDB1/NLI/CLIM [Transcription]
Probab=43.26 E-value=12 Score=35.94 Aligned_cols=25 Identities=36% Similarity=0.352 Sum_probs=17.4
Q ss_pred ccccCccccccCCCCCccceeccccc-ccccccc
Q 027605 162 GFYSLGAQVAPNSNGEGTRVMGYGEN-LGVEAFN 194 (221)
Q Consensus 162 ~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~ 194 (221)
-..||-.|| +.+|+-||+ +|-|.|-
T Consensus 312 p~~slssQ~--------pDVMVVGEPtlMGgEFG 337 (415)
T KOG2181|consen 312 PMTSLSSQM--------PDVMVVGEPTLMGGEFG 337 (415)
T ss_pred cchhhhhcC--------CceEEecCccccccccc
Confidence 467777776 568888888 5555563
No 88
>PRK13406 bchD magnesium chelatase subunit D; Provisional
Probab=43.19 E-value=49 Score=33.39 Aligned_cols=59 Identities=15% Similarity=0.186 Sum_probs=47.1
Q ss_pred HHHHHHhhcCCCCcccCHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCccCcchHHHHHh
Q 027605 32 NVSRIMKKSLPANAKISKEAKETVQECVSEFI-------SFITGEASDKCQREKRKTINGDDLLWAMT 92 (221)
Q Consensus 32 tV~RImK~aLP~n~kISkDAk~al~kcateFI-------~yLTseAneic~~ekRKTIsaeDVl~ALe 92 (221)
.|.+. ++.++ ++.|+.+.+..+.+.|..|= .++...|..+|--++|..|+.+||..|+.
T Consensus 183 ~I~~A-R~rl~-~v~v~~~~l~~i~~~~~~~gv~S~Ra~i~llraARa~AaL~Gr~~V~~~dv~~Aa~ 248 (584)
T PRK13406 183 DIAAA-RARLP-AVGPPPEAIAALCAAAAALGIASLRAPLLALRAARAAAALAGRTAVEEEDLALAAR 248 (584)
T ss_pred HHHHH-HHHHc-cCCCCHHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 34433 33454 89999999999888887773 46777888899999999999999999987
No 89
>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=42.13 E-value=49 Score=32.71 Aligned_cols=65 Identities=17% Similarity=0.200 Sum_probs=47.8
Q ss_pred CchhHHHHHHhhcC-CCCcccCHHHHHHHHHHHHH----HHHHHHHHHHHHHHhcCCCccCcchHHHHHh
Q 027605 28 LPIANVSRIMKKSL-PANAKISKEAKETVQECVSE----FISFITGEASDKCQREKRKTINGDDLLWAMT 92 (221)
Q Consensus 28 LPrAtV~RImK~aL-P~n~kISkDAk~al~kcate----FI~yLTseAneic~~ekRKTIsaeDVl~ALe 92 (221)
.++.-|.-|++--. -+++.+++||.+.|.+..++ |..-|-.-|+.+|+..++++|..+||-.|-+
T Consensus 361 y~~~EireIi~iRa~ee~i~l~~~Ale~L~~ig~etSLRYa~qLL~pa~iiA~~rg~~~V~~~dVe~a~~ 430 (450)
T COG1224 361 YSREEIREIIRIRAKEEDIELSDDALEYLTDIGEETSLRYAVQLLTPASIIAKRRGSKRVEVEDVERAKE 430 (450)
T ss_pred CCHHHHHHHHHHhhhhhccccCHHHHHHHHhhchhhhHHHHHHhccHHHHHHHHhCCCeeehhHHHHHHH
Confidence 34444555554322 24788999999999876654 4455666788999999999999999999843
No 90
>PRK09862 putative ATP-dependent protease; Provisional
Probab=41.74 E-value=86 Score=31.22 Aligned_cols=58 Identities=12% Similarity=0.117 Sum_probs=44.0
Q ss_pred cccCHHHHHHHHHHHHHH------HHHHHHHHHHHHHhcCCCccCcchHHHHHhhcCCCcchHH
Q 027605 45 AKISKEAKETVQECVSEF------ISFITGEASDKCQREKRKTINGDDLLWAMTTLGFENYVSP 102 (221)
Q Consensus 45 ~kISkDAk~al~kcateF------I~yLTseAneic~~ekRKTIsaeDVl~ALe~LGF~~yv~~ 102 (221)
+.+++++...+.++...+ .+.|..-|..+|--++|..|+.+||.+||+=-+++..+-.
T Consensus 437 ~~l~~~~~~~l~~~~~~~~lS~Ra~~rlLrvARTiADL~g~~~V~~~hv~eAl~yR~~~~~~~~ 500 (506)
T PRK09862 437 CKLESEDARWLEETLIHLGLSIRAWQRLLKVARTIADIDQSDIITRQHLQEAVSYRAIDRLLIH 500 (506)
T ss_pred hCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHhhcccHHHHH
Confidence 467888888777765544 5667778889999999999999999999985555544333
No 91
>COG5248 TAF19 Transcription initiation factor TFIID, subunit TAF13 [Transcription]
Probab=41.63 E-value=67 Score=26.66 Aligned_cols=50 Identities=18% Similarity=0.306 Sum_probs=42.5
Q ss_pred CCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHHhh
Q 027605 42 PANAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAMTT 93 (221)
Q Consensus 42 P~n~kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~ALe~ 93 (221)
.+.+.=-.|..++|.+.+..+++.+...|...|+ .|-.+..||+.-||++
T Consensus 23 GDvv~P~~dt~~~L~e~V~dY~~~~ctna~~~Aq--~rnK~k~eDfkfaLr~ 72 (126)
T COG5248 23 GDVVAPRYDTAEALHEYVLDYMSILCTNAHNMAQ--VRNKTKTEDFKFALRR 72 (126)
T ss_pred CCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHH--hcccchHHHHHHHHhh
Confidence 3456677899999999999999999999999988 4556778999999983
No 92
>PRK12402 replication factor C small subunit 2; Reviewed
Probab=41.44 E-value=59 Score=28.54 Aligned_cols=70 Identities=6% Similarity=-0.014 Sum_probs=43.8
Q ss_pred CCchhHHHHHHhhcCC-CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHHhhcCCCc
Q 027605 27 FLPIANVSRIMKKSLP-ANAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAMTTLGFEN 98 (221)
Q Consensus 27 ~LPrAtV~RImK~aLP-~n~kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~ALe~LGF~~ 98 (221)
.++...+.++++..+. .+..++.++.+.|.+.+.-=+..+-.+....|. ..++|+.+||..++.....++
T Consensus 183 ~~~~~~~~~~l~~~~~~~~~~~~~~al~~l~~~~~gdlr~l~~~l~~~~~--~~~~It~~~v~~~~~~~~~~~ 253 (337)
T PRK12402 183 APTDDELVDVLESIAEAEGVDYDDDGLELIAYYAGGDLRKAILTLQTAAL--AAGEITMEAAYEALGDVGTDE 253 (337)
T ss_pred CCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHH--cCCCCCHHHHHHHhCCCCCHH
Confidence 3455566666666543 356799999999988873333333333333332 234799999999888655443
No 93
>PRK14975 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Probab=40.78 E-value=1.6e+02 Score=29.23 Aligned_cols=93 Identities=14% Similarity=0.089 Sum_probs=60.5
Q ss_pred cccCCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHH----------HHHHHHHHHHHHHHHhcCCCccCcchHHHHHhh
Q 027605 24 QDRFLPIANVSRIMKKSLPANAKISKEAKETVQECVS----------EFISFITGEASDKCQREKRKTINGDDLLWAMTT 93 (221)
Q Consensus 24 eD~~LPrAtV~RImK~aLP~n~kISkDAk~al~kcat----------eFI~yLTseAneic~~ekRKTIsaeDVl~ALe~ 93 (221)
.++++|.+.|-.-|... ++.|..+....+..-.. .-+.-|..+..+......=..=++++|.++|++
T Consensus 160 ~~~E~~~~~~l~~me~~---Gi~~D~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~~~g~~~~n~~S~~ql~~~L~~ 236 (553)
T PRK14975 160 AAAESAGALAAAEMELA---GLPWDTDVHEALLAELLGPRPAAGGRPARLAELAAEIREALGRPRLNPDSPQQVLRALRR 236 (553)
T ss_pred HHHHhhHHHHHHHHHHh---CeEeCHHHHHHHHHHHhcccccccchHHHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHH
Confidence 34567777777777766 68899997776665555 555666666655542221133467899999999
Q ss_pred cCCC----------cchHHHHHHHHHHHHHHhhhhh
Q 027605 94 LGFE----------NYVSPLKIYLNKYRETEGEKNS 119 (221)
Q Consensus 94 LGF~----------~yv~~Lk~~Le~yRe~~k~Kks 119 (221)
+|+. .-..|+-..|-+||+..+....
T Consensus 237 ~g~~~~~t~~~~L~~~~hp~~~~ile~r~~~kl~st 272 (553)
T PRK14975 237 AGIELPSTRKWELREIDHPAVEPLLEYRKLSKLLSA 272 (553)
T ss_pred CCCCCCCCcHHHhccCCCchHHHHHHHHHHHHHHHH
Confidence 9984 1112445566788887776654
No 94
>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=39.76 E-value=39 Score=23.78 Aligned_cols=61 Identities=16% Similarity=0.230 Sum_probs=35.2
Q ss_pred ccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHHhhcCCCcchHHHHHHH
Q 027605 46 KISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAMTTLGFENYVSPLKIYL 107 (221)
Q Consensus 46 kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~ALe~LGF~~yv~~Lk~~L 107 (221)
.++.+-.+.|..+... ..--+.+....-.......-+.++++.||+++|..+.++.|+..|
T Consensus 23 g~~~~~i~~i~~~~~~-~~~~~~~~L~~W~~~~~~~at~~~L~~aL~~~~~~d~~~~i~~~~ 83 (83)
T PF00531_consen 23 GLSESEIENIEEENPD-LREQTYEMLQRWRQREGPNATVDQLIQALRDIGRNDLAEKIEQML 83 (83)
T ss_dssp TS-HHHHHHHHHHSTS-HHHHHHHHHHHHHHHHGSTSSHHHHHHHHHHTTHHHHHHHHHHH-
T ss_pred CcCHHHHHHHHHhCCC-hHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHCCcHHHHHHHHhhC
Confidence 4555555555554422 111222222222222455678889999999999999888887654
No 95
>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=38.64 E-value=74 Score=21.63 Aligned_cols=32 Identities=25% Similarity=0.460 Sum_probs=26.7
Q ss_pred CCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHH
Q 027605 27 FLPIANVSRIMKKSLPANAKISKEAKETVQECVSEF 62 (221)
Q Consensus 27 ~LPrAtV~RImK~aLP~n~kISkDAk~al~kcateF 62 (221)
.+-+++|.|++... -+|+.+.++-|.+++.+.
T Consensus 10 gvS~~TVSr~ln~~----~~vs~~tr~rI~~~a~~l 41 (46)
T PF00356_consen 10 GVSKSTVSRVLNGP----PRVSEETRERILEAAEEL 41 (46)
T ss_dssp TSSHHHHHHHHTTC----SSSTHHHHHHHHHHHHHH
T ss_pred CcCHHHHHHHHhCC----CCCCHHHHHHHHHHHHHH
Confidence 56789999999866 489999999999988763
No 96
>PF08681 DUF1778: Protein of unknown function (DUF1778); InterPro: IPR014795 This entry is represented by Vibrio phage ICP1, Orf50. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a family of uncharacterised proteins. The structure of one of the hypothetical proteins in this family has been solved and it forms a helix structure which may form interactions with DNA. ; PDB: 1Y9B_A.
Probab=38.39 E-value=25 Score=26.21 Aligned_cols=51 Identities=22% Similarity=0.376 Sum_probs=29.6
Q ss_pred CcccCHHHHHHHHHHHH-------HHHHHHHHHHHHH-HHhcCCCccCcchHHHHHhhc
Q 027605 44 NAKISKEAKETVQECVS-------EFISFITGEASDK-CQREKRKTINGDDLLWAMTTL 94 (221)
Q Consensus 44 n~kISkDAk~al~kcat-------eFI~yLTseAnei-c~~ekRKTIsaeDVl~ALe~L 94 (221)
+++|+.+.+++|.+++. .||.-.+.++.+. -..+..-+++.+|.-.-++.|
T Consensus 3 ~iR~~~e~k~li~~AA~~~G~sls~Fi~~aa~~~A~~~i~~~~~~~Ls~~~~~~f~~aL 61 (80)
T PF08681_consen 3 EIRVTPEEKELIERAAALSGVSLSDFILSAALEAAEEVIEEHERIRLSAEDFEAFMAAL 61 (80)
T ss_dssp EEE--HHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHH
T ss_pred eEecCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhcceeEcCHHHHHHHHHHH
Confidence 47899999999999874 5666555554433 223344566666644444433
No 97
>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=38.34 E-value=25 Score=28.46 Aligned_cols=62 Identities=8% Similarity=0.182 Sum_probs=42.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHHhhcCCCcchHHHHHHHHHHHHHH
Q 027605 49 KEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAMTTLGFENYVSPLKIYLNKYRETE 114 (221)
Q Consensus 49 kDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~ALe~LGF~~yv~~Lk~~Le~yRe~~ 114 (221)
..++.-|..|..+.-.|......-.. ----.-..++..|+..|++..+.+++..|++|++..
T Consensus 72 s~Vk~Eiaa~~~v~~~Y~~~L~~G~v----d~e~~~~~~~~kLk~AGidkV~~E~QkQlda~~~~~ 133 (134)
T PF12010_consen 72 SPVKNEIAACSNVWSEYYPPLETGLV----DPEEALPEFNEKLKAAGIDKVIAELQKQLDAFLAAN 133 (134)
T ss_pred chhHHHHHHHHHHHHHHHHHHHccCC----CHHHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHhc
Confidence 45556677777776666554332111 011124667888999999999999999999998754
No 98
>CHL00081 chlI Mg-protoporyphyrin IX chelatase
Probab=37.89 E-value=1e+02 Score=29.28 Aligned_cols=55 Identities=18% Similarity=0.251 Sum_probs=44.5
Q ss_pred HhhcCCCCcccCHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCccCcchHHHHHh
Q 027605 37 MKKSLPANAKISKEAKETVQECVSEFI-------SFITGEASDKCQREKRKTINGDDLLWAMT 92 (221)
Q Consensus 37 mK~aLP~n~kISkDAk~al~kcateFI-------~yLTseAneic~~ekRKTIsaeDVl~ALe 92 (221)
+++.++ .+.|+++.+..|.+.|..+= .++...|.-.|--++|..|+++||..+..
T Consensus 259 ar~~~~-~V~v~~~~~~yi~~l~~~~~~~s~Ra~i~l~raArA~Aal~GR~~V~pdDv~~~a~ 320 (350)
T CHL00081 259 AQNLLP-KVEIDYDLRVKISQICSELDVDGLRGDIVTNRAAKALAAFEGRTEVTPKDIFKVIT 320 (350)
T ss_pred HHHhcC-CCccCHHHHHHHHHHHHHHCCCCChHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 355565 79999999999999888763 35666777788889999999999998876
No 99
>TIGR01052 top6b DNA topoisomerase VI, B subunit. This model describes DNA topoisomerase VI, an archaeal type II DNA topoisomerase (DNA gyrase).
Probab=37.64 E-value=32 Score=34.17 Aligned_cols=58 Identities=21% Similarity=0.335 Sum_probs=40.0
Q ss_pred hhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHHhhcCCCcchHHHHHHHHH
Q 027605 38 KKSLPANAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAMTTLGFENYVSPLKIYLNK 109 (221)
Q Consensus 38 K~aLP~n~kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~ALe~LGF~~yv~~Lk~~Le~ 109 (221)
|+++-+.--|-+|.+.||++||.+.=.||...-...-+++++++ |..|++.+...|..
T Consensus 426 Ke~ia~~~ei~~ei~~al~~~~r~L~~~l~~~~~~~~~~~r~~~--------------~~~y~p~~a~~~~~ 483 (488)
T TIGR01052 426 KQSVADIPEIYNEIRLALMEVARRLRLYLSRKAREEEEIKRRKT--------------LEKYLPEIAKSLAY 483 (488)
T ss_pred hhhhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------------HHHHHHHHHHHHHH
Confidence 34443344588999999999999999999987665555555444 44566666655544
No 100
>TIGR01128 holA DNA polymerase III, delta subunit. subunit around DNA forming a DNA sliding clamp.
Probab=37.40 E-value=1.5e+02 Score=25.55 Aligned_cols=66 Identities=17% Similarity=0.116 Sum_probs=47.1
Q ss_pred CCchhHHHHHHhhcCC-CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHHh
Q 027605 27 FLPIANVSRIMKKSLP-ANAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAMT 92 (221)
Q Consensus 27 ~LPrAtV~RImK~aLP-~n~kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~ALe 92 (221)
.+....+.+++++.+. .+.+|++++...|.+.+.-=+..+-.+-...|.-.+.++|+.+||...+.
T Consensus 110 ~~~~~~~~~~i~~~~~~~g~~i~~~a~~~l~~~~~~d~~~l~~el~KL~~~~~~~~It~e~I~~~~~ 176 (302)
T TIGR01128 110 TPKEQELPRWIQARLKKLGLRIDPDAVQLLAELVEGNLLAIAQELEKLALYAPDGKITLEDVEEAVS 176 (302)
T ss_pred CCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCcHHHHHHHHHHHHHhhCCCCCCCHHHHHHHHh
Confidence 3455666666665553 35789999999998888766666666777766654445799999987765
No 101
>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]
Probab=36.68 E-value=1.2e+02 Score=28.79 Aligned_cols=73 Identities=15% Similarity=0.179 Sum_probs=49.0
Q ss_pred HHHHHHhhcCC---CCcccCHHHHHHHHHHHH------HHHHHHHHHHHHHHHhcCCCccCcchHHHHHhhcCCCcchHH
Q 027605 32 NVSRIMKKSLP---ANAKISKEAKETVQECVS------EFISFITGEASDKCQREKRKTINGDDLLWAMTTLGFENYVSP 102 (221)
Q Consensus 32 tV~RImK~aLP---~n~kISkDAk~al~kcat------eFI~yLTseAneic~~ekRKTIsaeDVl~ALe~LGF~~yv~~ 102 (221)
-|.-|+++-.. ....++.++..++..-+. .+..-|...|.++|+.+++.+|+.+||.+|-++.+..-+.+.
T Consensus 194 el~~Il~~R~~~~~~~~~~~~~vl~lia~~~a~~~GDAR~aidilr~A~eiAe~~~~~~v~~~~v~~a~~~~~~~~~~~~ 273 (366)
T COG1474 194 ELYDILRERVEEGFSAGVIDDDVLKLIAALVAAESGDARKAIDILRRAGEIAEREGSRKVSEDHVREAQEEIERDVLEEV 273 (366)
T ss_pred HHHHHHHHHHHhhccCCCcCccHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHhhCCCCcCHHHHHHHHHHhhHHHHHHH
Confidence 44445544332 245677777766663322 234556668889999999999999999999777777655554
Q ss_pred HH
Q 027605 103 LK 104 (221)
Q Consensus 103 Lk 104 (221)
++
T Consensus 274 ~~ 275 (366)
T COG1474 274 LK 275 (366)
T ss_pred HH
Confidence 43
No 102
>TIGR02031 BchD-ChlD magnesium chelatase ATPase subunit D. This model represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria. Unlike subunit I (TIGR02030), this subunit is not found in archaea.
Probab=36.39 E-value=1.1e+02 Score=30.77 Aligned_cols=55 Identities=20% Similarity=0.257 Sum_probs=40.7
Q ss_pred HhhcCCCCcccCHHHHHHHHHHHHHH-------HHHHHHHHHHHHHhcCCCccCcchHHHHHh
Q 027605 37 MKKSLPANAKISKEAKETVQECVSEF-------ISFITGEASDKCQREKRKTINGDDLLWAMT 92 (221)
Q Consensus 37 mK~aLP~n~kISkDAk~al~kcateF-------I~yLTseAneic~~ekRKTIsaeDVl~ALe 92 (221)
+++.+| .+.|+.+..+.|.+.|..+ -.++...|.-.|.-++|.+|+.+||..|+.
T Consensus 195 ar~~~~-~V~i~~~~~~~l~~~~~~~gv~s~Ra~i~~~r~ArA~Aal~gr~~V~~~Dv~~a~~ 256 (589)
T TIGR02031 195 ARELLP-QVTISAEQVKELVLTAASLGISGHRADLFAVRAAKAHAALHGRTEVTEEDLKLAVE 256 (589)
T ss_pred HHHhcC-CccCCHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHH
Confidence 344555 6899999988777776543 124445666777788999999999999976
No 103
>smart00350 MCM minichromosome maintenance proteins.
Probab=36.30 E-value=1.5e+02 Score=29.00 Aligned_cols=68 Identities=12% Similarity=0.120 Sum_probs=46.1
Q ss_pred cCCchhHHHHHHhhcCC-CCcccCHHHHHHHHHHHHHH-------------------HHHHHHHHHHHHHhcCCCccCcc
Q 027605 26 RFLPIANVSRIMKKSLP-ANAKISKEAKETVQECVSEF-------------------ISFITGEASDKCQREKRKTINGD 85 (221)
Q Consensus 26 ~~LPrAtV~RImK~aLP-~n~kISkDAk~al~kcateF-------------------I~yLTseAneic~~ekRKTIsae 85 (221)
..++...+.+.+.-+=- -.-+|++++.+.|.+...+. +..|-..|--.|+-..|.+|+.+
T Consensus 416 ~~~~~~~l~~yi~~ar~~~~P~ls~~~~~~i~~~y~~~R~~~~~~~~~~~~~~t~R~l~sliRla~A~A~l~~r~~V~~~ 495 (509)
T smart00350 416 VPISQEFLRKYIAYAREKIKPKLSEEAAEKLVKAYVDLRKEDSQSEARSSIPITVRQLESIIRLSEAHAKMRLSDVVEEA 495 (509)
T ss_pred ccCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhcccccccccccccCcCHHHHHHHHHHHHHHHHHcCCCccCHH
Confidence 45788888887744320 01258999999887654442 13444455667788899999999
Q ss_pred hHHHHHhh
Q 027605 86 DLLWAMTT 93 (221)
Q Consensus 86 DVl~ALe~ 93 (221)
||..|++-
T Consensus 496 Dv~~ai~l 503 (509)
T smart00350 496 DVEEAIRL 503 (509)
T ss_pred HHHHHHHH
Confidence 99998764
No 104
>TIGR00368 Mg chelatase-related protein. The N-terminal end matches very strongly a pfam Mg_chelatase domain.
Probab=36.08 E-value=83 Score=31.08 Aligned_cols=47 Identities=17% Similarity=0.188 Sum_probs=40.2
Q ss_pred ccCHHHHHHHHHHHHHH------HHHHHHHHHHHHHhcCCCccCcchHHHHHh
Q 027605 46 KISKEAKETVQECVSEF------ISFITGEASDKCQREKRKTINGDDLLWAMT 92 (221)
Q Consensus 46 kISkDAk~al~kcateF------I~yLTseAneic~~ekRKTIsaeDVl~ALe 92 (221)
.++++++..|.++...| ++-|..-|..+|--+++..|..+||.+||.
T Consensus 445 ~l~~~~~~~l~~a~~~~~lS~R~~~rilrvArTiAdL~g~~~i~~~hv~eA~~ 497 (499)
T TIGR00368 445 KLSAIDANDLEGALNKLGLSSRATHRILKVARTIADLKEEKNISREHLAEAIE 497 (499)
T ss_pred CCCHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHh
Confidence 46889999999888876 556667888899999999999999999985
No 105
>PRK13407 bchI magnesium chelatase subunit I; Provisional
Probab=33.80 E-value=1.2e+02 Score=28.48 Aligned_cols=53 Identities=11% Similarity=0.049 Sum_probs=42.2
Q ss_pred hhcCCCCcccCHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCccCcchHHHHH
Q 027605 38 KKSLPANAKISKEAKETVQECVSEFI-------SFITGEASDKCQREKRKTINGDDLLWAM 91 (221)
Q Consensus 38 K~aLP~n~kISkDAk~al~kcateFI-------~yLTseAneic~~ekRKTIsaeDVl~AL 91 (221)
++.++ .+.|+++....+.+.|..+= .+|...|.-.|--++|..|+++||..+.
T Consensus 244 ~~~~~-~V~v~~~~~~yi~~l~~~~~~~s~Ra~i~l~~aA~a~A~l~Gr~~V~~~Di~~~~ 303 (334)
T PRK13407 244 RARLP-QLKTPNTVLHDCAALCIALGSDGLRGELTLLRAARALAAFEGAEAVGRSHLRSVA 303 (334)
T ss_pred HHhcC-CcccCHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHHcCCCeeCHHHHHHHH
Confidence 44554 78999999999999887753 2366677788889999999999996654
No 106
>PLN00138 large subunit ribosomal protein LP2; Provisional
Probab=33.78 E-value=1.1e+02 Score=24.82 Aligned_cols=45 Identities=11% Similarity=0.096 Sum_probs=32.4
Q ss_pred HHHHHHHHHHHHhcCCCccCcchHHHHHhhcCCCcchHHHHHHHHHH
Q 027605 64 SFITGEASDKCQREKRKTINGDDLLWAMTTLGFENYVSPLKIYLNKY 110 (221)
Q Consensus 64 ~yLTseAneic~~ekRKTIsaeDVl~ALe~LGF~~yv~~Lk~~Le~y 110 (221)
.||+ |+-.|.-.++..|+.+||.+.|+..|.+---..+..+++..
T Consensus 2 kyva--Ayll~~l~g~~~pta~dI~~IL~AaGvevd~~~~~~f~~~L 46 (113)
T PLN00138 2 KVVA--AYLLAVLGGNTCPSAEDLKDILGSVGADADDDRIELLLSEV 46 (113)
T ss_pred hHHH--HHHHHHhcCCCCCCHHHHHHHHHHcCCcccHHHHHHHHHHH
Confidence 3555 66778888999999999999999998763333444444433
No 107
>PRK12728 fliE flagellar hook-basal body protein FliE; Provisional
Probab=30.81 E-value=2e+02 Score=22.77 Aligned_cols=66 Identities=14% Similarity=0.238 Sum_probs=44.4
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHh--cCCCccCcchHHHHHhh--cCCCcchHHHHHHHHHHHHHHh
Q 027605 48 SKEAKETVQECVSEFISFITGEASDKCQR--EKRKTINGDDLLWAMTT--LGFENYVSPLKIYLNKYRETEG 115 (221)
Q Consensus 48 SkDAk~al~kcateFI~yLTseAneic~~--ekRKTIsaeDVl~ALe~--LGF~~yv~~Lk~~Le~yRe~~k 115 (221)
...+.++|.++... +.-.-.+|.+...+ .| ++++..||+-|+++ |.|.-.+..-...++.|+|..+
T Consensus 30 ~~sF~~~L~~ai~~-vn~~q~~a~~~~~~~~~G-~~~~lhevmiA~~kA~lslq~~vqVRNKlv~AYqEIMr 99 (102)
T PRK12728 30 QKSFSDFLKEALNK-VNELQVEADNSTEKLVKG-EIVDLHDVMIAAQKASISLQLTVQIRNKVVEAYQEIMR 99 (102)
T ss_pred ccCHHHHHHHHHHH-HHHHHHHHHHHHHHHHcC-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 34577777777766 44444444433332 34 38899999999994 5556667777779999998754
No 108
>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=30.77 E-value=49 Score=22.63 Aligned_cols=24 Identities=21% Similarity=0.396 Sum_probs=20.2
Q ss_pred cCcchHHHHHhhcCCCcchHHHHH
Q 027605 82 INGDDLLWAMTTLGFENYVSPLKI 105 (221)
Q Consensus 82 IsaeDVl~ALe~LGF~~yv~~Lk~ 105 (221)
=+++||..=|+.+||++|.+....
T Consensus 4 w~~~~v~~WL~~~gl~~y~~~f~~ 27 (66)
T PF07647_consen 4 WSPEDVAEWLKSLGLEQYADNFRE 27 (66)
T ss_dssp HCHHHHHHHHHHTTCGGGHHHHHH
T ss_pred CCHHHHHHHHHHCCcHHHHHHHHH
Confidence 367899999999999999887764
No 109
>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional
Probab=30.38 E-value=60 Score=31.61 Aligned_cols=32 Identities=28% Similarity=0.251 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHHHhcCCCccCcchHHHHHhhc
Q 027605 63 ISFITGEASDKCQREKRKTINGDDLLWAMTTL 94 (221)
Q Consensus 63 I~yLTseAneic~~ekRKTIsaeDVl~ALe~L 94 (221)
|..|..+|...|.+++|..|+.+||..|+++.
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 56678889999999999999999999998864
No 110
>PRK09526 lacI lac repressor; Reviewed
Probab=30.26 E-value=29 Score=30.16 Aligned_cols=37 Identities=19% Similarity=0.499 Sum_probs=30.4
Q ss_pred CCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHH
Q 027605 27 FLPIANVSRIMKKSLPANAKISKEAKETVQECVSEFISFITG 68 (221)
Q Consensus 27 ~LPrAtV~RImK~aLP~n~kISkDAk~al~kcateFI~yLTs 68 (221)
..-++||.|++... .+||++.++-|.+++.+ +.|.-.
T Consensus 16 GVS~~TVSrvLn~~----~~vs~~tr~rV~~~a~e-lgY~pn 52 (342)
T PRK09526 16 GVSYQTVSRVLNQA----SHVSAKTREKVEAAMAE-LNYVPN 52 (342)
T ss_pred CCCHHHHHHHhcCC----CCCCHHHHHHHHHHHHH-HCCCcC
Confidence 57789999999753 46999999999999999 567544
No 111
>PTZ00373 60S Acidic ribosomal protein P2; Provisional
Probab=30.14 E-value=1.4e+02 Score=24.20 Aligned_cols=43 Identities=7% Similarity=0.127 Sum_probs=31.0
Q ss_pred HHHHHHHHHHHHhcCCCccCcchHHHHHhhcCCCcchHHHHHHHH
Q 027605 64 SFITGEASDKCQREKRKTINGDDLLWAMTTLGFENYVSPLKIYLN 108 (221)
Q Consensus 64 ~yLTseAneic~~ekRKTIsaeDVl~ALe~LGF~~yv~~Lk~~Le 108 (221)
.||+ |.-.|.-.++.+|+.+||.+.|+..|.+---..+..+++
T Consensus 4 kyva--AYlL~~lgG~~~pTaddI~kIL~AaGveVd~~~~~l~~~ 46 (112)
T PTZ00373 4 KYVA--AYLMCVLGGNENPTKKEVKNVLSAVNADVEDDVLDNFFK 46 (112)
T ss_pred HHHH--HHHHHHHcCCCCCCHHHHHHHHHHcCCCccHHHHHHHHH
Confidence 3555 666788889999999999999999988533333343433
No 112
>PRK05574 holA DNA polymerase III subunit delta; Reviewed
Probab=29.67 E-value=2e+02 Score=25.36 Aligned_cols=66 Identities=17% Similarity=0.090 Sum_probs=46.7
Q ss_pred CCchhHHHHHHhhcCC-CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhc-CCCccCcchHHHHHhh
Q 027605 27 FLPIANVSRIMKKSLP-ANAKISKEAKETVQECVSEFISFITGEASDKCQRE-KRKTINGDDLLWAMTT 93 (221)
Q Consensus 27 ~LPrAtV~RImK~aLP-~n~kISkDAk~al~kcateFI~yLTseAneic~~e-kRKTIsaeDVl~ALe~ 93 (221)
.++...+.+.|++.+- .+..|+.++...|.+.+..=+..+..|-...|.-. +++ |+.+||-..+..
T Consensus 145 ~~~~~~~~~~i~~~~~~~g~~i~~~a~~~L~~~~~~d~~~l~~El~KL~l~~~~~~-It~~~I~~~i~~ 212 (340)
T PRK05574 145 PPKEAELPQWIQQRLKQQGLQIDAAALQLLAERVEGNLLALAQELEKLALLYPDGK-ITLEDVEEAVPD 212 (340)
T ss_pred CCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCchHHHHHHHHHHHHhhcCCCC-CCHHHHHHHHhh
Confidence 3555555555555543 36789999999999998877777777777776643 334 999998776653
No 113
>PF08823 PG_binding_2: Putative peptidoglycan binding domain; InterPro: IPR014927 This entry may be a peptidoglycan binding domain.
Probab=29.58 E-value=82 Score=23.54 Aligned_cols=33 Identities=18% Similarity=0.225 Sum_probs=27.1
Q ss_pred chHHHHHhhcCC------CcchHHHHHHHHHHHHHHhhh
Q 027605 85 DDLLWAMTTLGF------ENYVSPLKIYLNKYRETEGEK 117 (221)
Q Consensus 85 eDVl~ALe~LGF------~~yv~~Lk~~Le~yRe~~k~K 117 (221)
+.|..+|.+||| ..+-+.++..|..|...++-.
T Consensus 19 ~evq~~L~~lGyy~g~~~g~~d~a~~~Al~~~~g~ENfE 57 (74)
T PF08823_consen 19 REVQEALKRLGYYKGEADGVWDEATEDALRAWAGTENFE 57 (74)
T ss_pred HHHHHHHHHcCCccCCCCCcccHHHHHHHHHHHHHhhHH
Confidence 467889999999 678889999999998776543
No 114
>PRK03992 proteasome-activating nucleotidase; Provisional
Probab=28.99 E-value=69 Score=30.08 Aligned_cols=35 Identities=23% Similarity=0.171 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHHHHhcCCCccCcchHHHHHhhcCC
Q 027605 62 FISFITGEASDKCQREKRKTINGDDLLWAMTTLGF 96 (221)
Q Consensus 62 FI~yLTseAneic~~ekRKTIsaeDVl~ALe~LGF 96 (221)
=|.-|..+|...|.+++++.|+.+|+..|++..-.
T Consensus 340 dl~~l~~eA~~~a~~~~~~~i~~~d~~~A~~~~~~ 374 (389)
T PRK03992 340 DLKAICTEAGMFAIRDDRTEVTMEDFLKAIEKVMG 374 (389)
T ss_pred HHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHhc
Confidence 35566778888888889999999999999987644
No 115
>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=28.96 E-value=87 Score=25.12 Aligned_cols=32 Identities=19% Similarity=0.357 Sum_probs=26.3
Q ss_pred hHHHHHHhhcC----CCCcccCHHHHHHHHHHHHHH
Q 027605 31 ANVSRIMKKSL----PANAKISKEAKETVQECVSEF 62 (221)
Q Consensus 31 AtV~RImK~aL----P~n~kISkDAk~al~kcateF 62 (221)
++|.+++|.-| .|+..++.++.+.|+++++.|
T Consensus 51 SNIGvLIKkglIEKSGDGlv~T~~g~~Ii~~AA~l~ 86 (96)
T PF09114_consen 51 SNIGVLIKKGLIEKSGDGLVITEEGMDIIIQAAELW 86 (96)
T ss_dssp HHHHHHHHTTSEEEETTEEEE-HHHHHHHHHHHHHH
T ss_pred HhHHHHHHcCcccccCCceEEechHHHHHHHHHHHH
Confidence 45777999887 356789999999999999998
No 116
>TIGR01242 26Sp45 26S proteasome subunit P45 family. Many proteins may score above the trusted cutoff because an internal
Probab=28.84 E-value=69 Score=29.38 Aligned_cols=33 Identities=27% Similarity=0.270 Sum_probs=27.9
Q ss_pred HHHHHHHHHHHHHHhcCCCccCcchHHHHHhhc
Q 027605 62 FISFITGEASDKCQREKRKTINGDDLLWAMTTL 94 (221)
Q Consensus 62 FI~yLTseAneic~~ekRKTIsaeDVl~ALe~L 94 (221)
-|..|..+|...|...++..|+.+|+..|++..
T Consensus 331 dl~~l~~~A~~~a~~~~~~~i~~~d~~~a~~~~ 363 (364)
T TIGR01242 331 DLKAICTEAGMFAIREERDYVTMDDFIKAVEKV 363 (364)
T ss_pred HHHHHHHHHHHHHHHhCCCccCHHHHHHHHHHh
Confidence 355677788888989999999999999999863
No 117
>PLN02900 alanyl-tRNA synthetase
Probab=28.65 E-value=3.4e+02 Score=29.33 Aligned_cols=29 Identities=17% Similarity=0.367 Sum_probs=22.6
Q ss_pred HhcCCCccCcchHHHHHhhcCCC-cchHHH
Q 027605 75 QREKRKTINGDDLLWAMTTLGFE-NYVSPL 103 (221)
Q Consensus 75 ~~ekRKTIsaeDVl~ALe~LGF~-~yv~~L 103 (221)
+.+++++|+++|++..-+..||+ ++...+
T Consensus 404 ~~~~~~~l~g~~af~LydTyGfP~dlt~~i 433 (936)
T PLN02900 404 KANGGPVLSGKDAFLLYDTYGFPVDLTELM 433 (936)
T ss_pred hhcCCCcCCHHHHHHHHhccCCCHHHHHHH
Confidence 33456789999999999999997 555544
No 118
>COG5251 TAF40 Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=28.39 E-value=78 Score=28.14 Aligned_cols=62 Identities=16% Similarity=-0.006 Sum_probs=46.5
Q ss_pred CCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC---ccCcchHHHHHh
Q 027605 27 FLPIANVSRIMKKSLPANAKISKEAKETVQECVSEFISFITGEASDKCQREKRK---TINGDDLLWAMT 92 (221)
Q Consensus 27 ~LPrAtV~RImK~aLP~n~kISkDAk~al~kcateFI~yLTseAneic~~ekRK---TIsaeDVl~ALe 92 (221)
.||++.|.+++...+ +-.|+...+.+|+-.+.+|+--|--.|..+- +++. -+.+.|+-.|..
T Consensus 115 ~lnKt~VKKlastV~--nQtVspNi~I~l~g~~KVfvGEiIElA~~Vq--~~w~~sgpl~p~h~reayr 179 (199)
T COG5251 115 SLNKTQVKKLASTVA--NQTVSPNIRIFLQGVGKVFVGEIIELAMIVQ--NKWLTSGPLIPFHKREAYR 179 (199)
T ss_pred CCCHHHHHHHHHHHh--ccccCCCeeeeeechhHHHHHHHHHHHHHHH--HHhcccCCCChHHHHHHHH
Confidence 599999999999998 5678888888999999999988776664332 2232 366777766643
No 119
>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=28.15 E-value=80 Score=25.96 Aligned_cols=70 Identities=14% Similarity=0.101 Sum_probs=45.2
Q ss_pred ccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHHhhcCCCc------------chHHHHHHHHHHHHH
Q 027605 46 KISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAMTTLGFEN------------YVSPLKIYLNKYRET 113 (221)
Q Consensus 46 kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~ALe~LGF~~------------yv~~Lk~~Le~yRe~ 113 (221)
.+..+. +..++..++..+..-..-.. =-.|.+.+|++.+|+.+.++. |++.+.+.+++-++.
T Consensus 95 ~i~~~g---~~~~~~~~lr~~~~~~~~~~---~~~tt~~~~l~~~l~~l~~P~~~~~~~i~l~~r~ip~l~~~~~~i~~A 168 (224)
T PF02361_consen 95 SITQEG---LIYAALLALRILAILLASLL---FILTTSPSDLISALRKLRLPYPKIALMISLTLRFIPLLLEEFKRIREA 168 (224)
T ss_pred hhhHHH---HHHHHHHHHHHHHHHHHHHH---HHHHCCHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455553 44555555544443333222 135789999999999999988 777777777777777
Q ss_pred Hhhhhhhh
Q 027605 114 EGEKNSMA 121 (221)
Q Consensus 114 ~k~Kks~~ 121 (221)
++.+-...
T Consensus 169 ~~~Rg~~~ 176 (224)
T PF02361_consen 169 QRLRGVGI 176 (224)
T ss_pred HHHcCCCc
Confidence 66665543
No 120
>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=27.35 E-value=57 Score=22.23 Aligned_cols=22 Identities=23% Similarity=0.433 Sum_probs=19.4
Q ss_pred CcchHHHHHhhcCCCcchHHHH
Q 027605 83 NGDDLLWAMTTLGFENYVSPLK 104 (221)
Q Consensus 83 saeDVl~ALe~LGF~~yv~~Lk 104 (221)
++++|..-|+.+|++.|++...
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 5789999999999999998774
No 121
>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=27.15 E-value=41 Score=22.11 Aligned_cols=24 Identities=17% Similarity=0.338 Sum_probs=19.8
Q ss_pred CcchHHHHHhhcCCCcchHHHHHH
Q 027605 83 NGDDLLWAMTTLGFENYVSPLKIY 106 (221)
Q Consensus 83 saeDVl~ALe~LGF~~yv~~Lk~~ 106 (221)
+.++|..-|+.+|+++|.+.++..
T Consensus 3 ~~~~V~~wL~~~~~~~y~~~f~~~ 26 (63)
T cd00166 3 SPEDVAEWLESLGLGQYADNFREN 26 (63)
T ss_pred CHHHHHHHHHHcChHHHHHHHHHc
Confidence 578999999999998888877653
No 122
>PTZ00183 centrin; Provisional
Probab=27.05 E-value=2.4e+02 Score=21.50 Aligned_cols=20 Identities=40% Similarity=0.592 Sum_probs=12.2
Q ss_pred cCCCccCcchHHHHHhhcCC
Q 027605 77 EKRKTINGDDLLWAMTTLGF 96 (221)
Q Consensus 77 ekRKTIsaeDVl~ALe~LGF 96 (221)
++.-+|+.+++..+|+.+|+
T Consensus 29 ~~~G~i~~~e~~~~l~~~g~ 48 (158)
T PTZ00183 29 DGSGTIDPKELKVAMRSLGF 48 (158)
T ss_pred CCCCcccHHHHHHHHHHhCC
Confidence 34556666666666666655
No 123
>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=26.70 E-value=41 Score=22.62 Aligned_cols=13 Identities=38% Similarity=0.716 Sum_probs=11.4
Q ss_pred chHHHHHhhcCCC
Q 027605 85 DDLLWAMTTLGFE 97 (221)
Q Consensus 85 eDVl~ALe~LGF~ 97 (221)
+|++.||..|||.
T Consensus 4 ~d~~~AL~~LGy~ 16 (47)
T PF07499_consen 4 EDALEALISLGYS 16 (47)
T ss_dssp HHHHHHHHHTTS-
T ss_pred HHHHHHHHHcCCC
Confidence 6899999999997
No 124
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=26.47 E-value=1.2e+02 Score=21.53 Aligned_cols=33 Identities=27% Similarity=0.445 Sum_probs=24.4
Q ss_pred cCCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHH
Q 027605 26 RFLPIANVSRIMKKSLPANAKISKEAKETVQECVSEF 62 (221)
Q Consensus 26 ~~LPrAtV~RImK~aLP~n~kISkDAk~al~kcateF 62 (221)
..+.+++|.|++... ..|+.+.++.|.+++.++
T Consensus 10 ~gvS~~TVSr~ln~~----~~v~~~t~~~i~~~~~~~ 42 (70)
T smart00354 10 AGVSKATVSRVLNGN----GRVSEETREKVLAAMEEL 42 (70)
T ss_pred HCCCHHHHHHHHCCC----CCCCHHHHHHHHHHHHHh
Confidence 457788888887643 457888888888877775
No 125
>PRK07914 hypothetical protein; Reviewed
Probab=25.71 E-value=1.6e+02 Score=26.63 Aligned_cols=62 Identities=8% Similarity=0.140 Sum_probs=41.4
Q ss_pred hhHHHHHHhhcCC-CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHHh
Q 027605 30 IANVSRIMKKSLP-ANAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAMT 92 (221)
Q Consensus 30 rAtV~RImK~aLP-~n~kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~ALe 92 (221)
...+.+.|++.+- .+.+|+.||...|.+++..=+..+..|-...+...+ .+|+.+||...+.
T Consensus 130 ~~~l~~wi~~~a~~~g~~i~~~A~~~L~~~~g~dl~~l~~EleKL~~~~~-~~It~e~V~~~v~ 192 (320)
T PRK07914 130 AAERADFVRKEFRSLRVKVDDDTVTALLDAVGSDLRELASACSQLVADTG-GAVDAAAVRRYHS 192 (320)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHCccHHHHHHHHHHHhcCCC-CCcCHHHHHHHcC
Confidence 4444444443332 257899999999999997666666666655554333 5799998877754
No 126
>COG1724 Predicted RNA binding protein (dsRBD-like fold), HicA family [General function prediction only]
Probab=25.35 E-value=43 Score=25.20 Aligned_cols=17 Identities=18% Similarity=0.480 Sum_probs=15.3
Q ss_pred ccCcchHHHHHhhcCCC
Q 027605 81 TINGDDLLWAMTTLGFE 97 (221)
Q Consensus 81 TIsaeDVl~ALe~LGF~ 97 (221)
.+++.+|+++|+.+||.
T Consensus 6 ~~~~ke~ik~Le~~Gf~ 22 (66)
T COG1724 6 RMKAKEVIKALEKDGFQ 22 (66)
T ss_pred cCCHHHHHHHHHhCCcE
Confidence 47889999999999995
No 127
>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional
Probab=24.97 E-value=84 Score=30.01 Aligned_cols=32 Identities=28% Similarity=0.247 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHHHhcCCCccCcchHHHHHhhc
Q 027605 63 ISFITGEASDKCQREKRKTINGDDLLWAMTTL 94 (221)
Q Consensus 63 I~yLTseAneic~~ekRKTIsaeDVl~ALe~L 94 (221)
|.-|..+|.-.|.+++|+.|+.+|+..|+++.
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 66778889999999999999999999998763
No 128
>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=24.95 E-value=14 Score=25.39 Aligned_cols=58 Identities=26% Similarity=0.389 Sum_probs=32.4
Q ss_pred cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcc---CcchHHHHHhhcCCCcch-HHHHHH
Q 027605 45 AKISKEAKETVQECVSEFISFITGEASDKCQREKRKTI---NGDDLLWAMTTLGFENYV-SPLKIY 106 (221)
Q Consensus 45 ~kISkDAk~al~kcateFI~yLTseAneic~~ekRKTI---saeDVl~ALe~LGF~~yv-~~Lk~~ 106 (221)
.+|.++...+|.+++. .+..|+.+ .-..+=.|.+ .+...+..|.++|+.+++ |.+...
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 4678888888888777 44555443 2222323333 345566677788876553 555543
No 129
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=24.42 E-value=40 Score=29.33 Aligned_cols=38 Identities=16% Similarity=0.359 Sum_probs=30.0
Q ss_pred CCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHH
Q 027605 27 FLPIANVSRIMKKSLPANAKISKEAKETVQECVSEFISFITGE 69 (221)
Q Consensus 27 ~LPrAtV~RImK~aLP~n~kISkDAk~al~kcateFI~yLTse 69 (221)
..-++||.|++... .+||.+.++-+.+++.+ +.|.-..
T Consensus 16 gVS~~TVSrvLn~~----~~vs~~tr~rV~~~a~e-lgY~pn~ 53 (331)
T PRK14987 16 GVTKMTVSRFLRNP----EQVSVALRGKIAAALDE-LGYIPNR 53 (331)
T ss_pred CCCHHHhhhhhCCC----CCCCHHHHHHHHHHHHH-hCCCccH
Confidence 56789999998643 47999999999999998 4665433
No 130
>PRK06585 holA DNA polymerase III subunit delta; Reviewed
Probab=24.25 E-value=1.6e+02 Score=26.44 Aligned_cols=49 Identities=12% Similarity=0.043 Sum_probs=36.8
Q ss_pred CcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHh-cCCCccCcchHHHHHh
Q 027605 44 NAKISKEAKETVQECVSEFISFITGEASDKCQR-EKRKTINGDDLLWAMT 92 (221)
Q Consensus 44 n~kISkDAk~al~kcateFI~yLTseAneic~~-ekRKTIsaeDVl~ALe 92 (221)
+.+|+.||...|.+++.-=...+..|-...+.- ..+++|+.+||...+.
T Consensus 159 g~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~It~edV~~lv~ 208 (343)
T PRK06585 159 GLRITPDARALLVALLGGDRLASRNEIEKLALYAHGKGEITLDDVRAVVG 208 (343)
T ss_pred CCCCCHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHhC
Confidence 678999999999999886555666666666554 3456899999977654
No 131
>cd05833 Ribosomal_P2 Ribosomal protein P2. This subfamily represents the eukaryotic large ribosomal protein P2. Eukaryotic P1 and P2 are functionally equivalent to the bacterial protein L7/L12, but are not homologous to L7/L12. P2 is located in the L12 stalk, with proteins P1, P0, L11, and 28S rRNA. P1 and P2 are the only proteins in the ribosome to occur as multimers, always appearing as sets of heterodimers. Recent data indicate that eukaryotes have four copies (two heterodimers), while most archaeal species contain six copies of L12p (three homodimers). Bacteria may have four or six copies of L7/L12 (two or three homodimers) depending on the species. Experiments using S. cerevisiae P1 and P2 indicate that P1 proteins are positioned more internally with limited reactivity in the C-terminal domains, while P2 proteins seem to be more externally located and are more likely to interact with other cellular components. In lower eukaryotes, P1 and P2 are further subdivided into P1A, P1B, P2
Probab=24.02 E-value=2.1e+02 Score=22.96 Aligned_cols=31 Identities=13% Similarity=0.146 Sum_probs=26.0
Q ss_pred HHHHHHHHHHHhcCCCccCcchHHHHHhhcCCC
Q 027605 65 FITGEASDKCQREKRKTINGDDLLWAMTTLGFE 97 (221)
Q Consensus 65 yLTseAneic~~ekRKTIsaeDVl~ALe~LGF~ 97 (221)
||+ |.-.|.-.++..||.+||.+.|+..|-+
T Consensus 3 yva--AylL~~l~g~~~pTa~dI~~IL~AaGve 33 (109)
T cd05833 3 YVA--AYLLAVLGGNASPSAADVKKILGSVGVE 33 (109)
T ss_pred HHH--HHHHHHHcCCCCCCHHHHHHHHHHcCCC
Confidence 555 5667778888899999999999998875
No 132
>PF14434 Imm6: Immunity protein Imm6
Probab=23.84 E-value=2.5e+02 Score=22.92 Aligned_cols=49 Identities=20% Similarity=0.287 Sum_probs=34.6
Q ss_pred HHHHHHHHHHH-----HHHHHHHHHHHHhc-CCCccCcchHHHHHhhcCCCcchH
Q 027605 53 ETVQECVSEFI-----SFITGEASDKCQRE-KRKTINGDDLLWAMTTLGFENYVS 101 (221)
Q Consensus 53 ~al~kcateFI-----~yLTseAneic~~e-kRKTIsaeDVl~ALe~LGF~~yv~ 101 (221)
..|.++...+| .++..+|.+.|.+- ..+.++++++..-|+..+|.+...
T Consensus 8 l~iae~~~~~I~~~~~~~~~~~aL~~cw~wle~~~~~~D~LY~lldn~D~~gi~~ 62 (122)
T PF14434_consen 8 LAIAEKLVDYIKKSEYGEFVREALDACWKWLEGKEVTGDELYSLLDNEDENGIFI 62 (122)
T ss_pred HHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHcCCCCHHHHHHHHhCcccccHHH
Confidence 34455555555 34448899999873 339999999999999877765443
No 133
>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=23.51 E-value=1.2e+02 Score=24.99 Aligned_cols=38 Identities=24% Similarity=0.205 Sum_probs=28.2
Q ss_pred CccCcchHHHHHhhcCCC-----------cchHHHHHHHHHHHHHHhhh
Q 027605 80 KTINGDDLLWAMTTLGFE-----------NYVSPLKIYLNKYRETEGEK 117 (221)
Q Consensus 80 KTIsaeDVl~ALe~LGF~-----------~yv~~Lk~~Le~yRe~~k~K 117 (221)
-|.+.+|++.+|++++++ .|++.+.+..++-++.++.+
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 467889999999999985 45666666666666666555
No 134
>COG1389 DNA topoisomerase VI, subunit B [DNA replication, recombination, and repair]
Probab=23.35 E-value=58 Score=32.94 Aligned_cols=39 Identities=23% Similarity=0.397 Sum_probs=33.3
Q ss_pred cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccC
Q 027605 45 AKISKEAKETVQECVSEFISFITGEASDKCQREKRKTIN 83 (221)
Q Consensus 45 ~kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIs 83 (221)
--|=+|.+.|+++||.+.=+||.....+.-+.+++++|.
T Consensus 441 peIe~Eir~Al~evaRkL~~yLsrk~r~~e~~~K~~~i~ 479 (538)
T COG1389 441 PEIENEIRLALMEVARKLKLYLSRKRREMEERKKRKTIE 479 (538)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 357799999999999999999999998887777777653
No 135
>COG1222 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]
Probab=23.13 E-value=1.2e+02 Score=29.85 Aligned_cols=75 Identities=20% Similarity=0.223 Sum_probs=48.0
Q ss_pred CCCccccCCchhHHHHHHhhcCCCCcccCHHH-HHHHHHHHHHH----HHHHHHHHHHHHHhcCCCccCcchHHHHHhhc
Q 027605 20 SDKEQDRFLPIANVSRIMKKSLPANAKISKEA-KETVQECVSEF----ISFITGEASDKCQREKRKTINGDDLLWAMTTL 94 (221)
Q Consensus 20 s~~eeD~~LPrAtV~RImK~aLP~n~kISkDA-k~al~kcateF----I~yLTseAneic~~ekRKTIsaeDVl~ALe~L 94 (221)
-.+.-++.||-.-=++-|=...-..|.+.+|. .+.|.+++.-| |.-|+.||--.|.++.|..|+-+|+++|.++.
T Consensus 313 ~DRkIEfplPd~~gR~~Il~IHtrkM~l~~dvd~e~la~~~~g~sGAdlkaictEAGm~AiR~~R~~Vt~~DF~~Av~KV 392 (406)
T COG1222 313 FDRKIEFPLPDEEGRAEILKIHTRKMNLADDVDLELLARLTEGFSGADLKAICTEAGMFAIRERRDEVTMEDFLKAVEKV 392 (406)
T ss_pred ccceeecCCCCHHHHHHHHHHHhhhccCccCcCHHHHHHhcCCCchHHHHHHHHHHhHHHHHhccCeecHHHHHHHHHHH
Confidence 34444556664433332222222345555544 23455555444 67788899999999999999999999998754
No 136
>KOG1792 consensus Reticulon [Intracellular trafficking, secretion, and vesicular transport]
Probab=23.07 E-value=1.8e+02 Score=26.23 Aligned_cols=56 Identities=20% Similarity=0.245 Sum_probs=47.0
Q ss_pred cCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHH-HHhcCCCccCcchHHHHHhhcC
Q 027605 40 SLPANAKISKEAKETVQECVSEFISFITGEASDK-CQREKRKTINGDDLLWAMTTLG 95 (221)
Q Consensus 40 aLP~n~kISkDAk~al~kcateFI~yLTseAnei-c~~ekRKTIsaeDVl~ALe~LG 95 (221)
-+|.++.|++|....+..++.+-|...+.+.+++ |.++-+.-+...=.+|.+.-+|
T Consensus 110 ~lp~~i~ipee~~~~~a~~~~~~in~~l~~l~~ia~~~d~~~~lk~~v~lw~lS~vG 166 (230)
T KOG1792|consen 110 YLPVEITIPEEFVLALASSLRVEINQALSELRDIALGRDLKDFLKVAVGLWILSYVG 166 (230)
T ss_pred cCCceeecCHHHHHHHHHHHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHHHH
Confidence 4666899999999999999999999999999999 5566666666666888888777
No 137
>cd00823 TopoIIB_Trans TopoIIB_Trans: Transducer domain, having a ribosomal S5 domain 2-like fold, of the type found in proteins of the type IIB family of DNA topoisomerases similar to Sulfolobus shibatae topoisomerase VI (topoVI). The sole representative of the Type IIB family is topo VI. Topo VI enzymes are heterotetramers found in archaea and plants. S. shibatae topoVI relaxes both positive and negative supercoils, and in addition has a strong decatenase activity. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes.
Probab=23.00 E-value=1.3e+02 Score=25.91 Aligned_cols=34 Identities=18% Similarity=0.336 Sum_probs=26.1
Q ss_pred hhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHH
Q 027605 38 KKSLPANAKISKEAKETVQECVSEFISFITGEAS 71 (221)
Q Consensus 38 K~aLP~n~kISkDAk~al~kcateFI~yLTseAn 71 (221)
|+++-+.--|-+|.+.+|++||.+.=.||...-.
T Consensus 111 KeaIadvpEI~~EIrlAl~~~~R~L~~~l~kk~~ 144 (151)
T cd00823 111 KEAIADIPEIEEEIKLALQEVARKLKRYLSKKRK 144 (151)
T ss_pred hhhhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4444344458899999999999999999986543
No 138
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=22.47 E-value=59 Score=28.01 Aligned_cols=37 Identities=16% Similarity=0.329 Sum_probs=29.0
Q ss_pred CCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHH
Q 027605 27 FLPIANVSRIMKKSLPANAKISKEAKETVQECVSEFISFITG 68 (221)
Q Consensus 27 ~LPrAtV~RImK~aLP~n~kISkDAk~al~kcateFI~yLTs 68 (221)
.+-++||.|++... -+||++.++-|.+++.+. .|.-.
T Consensus 9 gVS~~TVSrvLn~~----~~vs~~tr~rV~~~a~~l-gY~pn 45 (327)
T PRK10423 9 GVSTSTVSHVINKD----RFVSEAITAKVEAAIKEL-NYAPS 45 (327)
T ss_pred CCcHHHHHHHhCCC----CCCCHHHHHHHHHHHHHH-CCCcc
Confidence 45679999999753 469999999999999876 45443
No 139
>PF02049 FliE: Flagellar hook-basal body complex protein FliE; InterPro: IPR001624 Four genes from the major Bacillus subtilis chemotaxis locus have been shown to encode proteins that are similar to the Salmonella typhimurium FlgB, FlgC, FlgG and FliF proteins; a further gene product is similar to the Escherichia coli FliE protein []. All of these proteins are thought to form part of the hook-basal body complex of the bacterial flagella []. The FlgB, FlgC and FlgG proteins are components of the proximal and distal rods; FliF forms the M-ring that anchors the rod assembly to the membrane; but the role of FliE has not yet been determined []. The similarity between the proteins in these two organisms suggests that the structures of the M-ring and the rod may be similar []. Nevertheless, some differences in size and amino acid composition between some of the homologues suggest the basal body proteins may be organised slightly differently within B. subtilis []. From gel electrophoresis and autoradiography of 35S-labelled S. typhimurium hook-basal body complexes and the deduced number of sulphur-containing residues in FliE, the stoichiometry of the protein in the hook-basal body complex has been estimated to be about nine subunits []. FliE does not undergo cleavage of a signal peptide, nor does it show any similarity to the axial components like the rod or hook proteins, which are thought to be exported by the flagellum-specific export pathway []. On this evidence, it has been suggested that FliE may be in the vicinity of the MS ring, perhaps acting as an adaptor protein between ring and rod substructures [].; GO: 0003774 motor activity, 0005198 structural molecule activity, 0001539 ciliary or flagellar motility, 0009288 bacterial-type flagellum
Probab=22.23 E-value=3.6e+02 Score=20.56 Aligned_cols=69 Identities=10% Similarity=0.086 Sum_probs=44.6
Q ss_pred cCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHHh--hcCCCcchHHHHHHHHHHHHHHh
Q 027605 47 ISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAMT--TLGFENYVSPLKIYLNKYRETEG 115 (221)
Q Consensus 47 ISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~ALe--~LGF~~yv~~Lk~~Le~yRe~~k 115 (221)
=..++.+.|.++....-..........-.-..-+.++..||+-|++ ++-|.-.+..-...++.|+|..+
T Consensus 23 ~~~~F~~~l~~al~~vn~~q~~a~~~~~~~~~G~~~dl~~vmia~~kA~lslq~~vqVRnK~v~AYqEImr 93 (96)
T PF02049_consen 23 GGASFSDVLKNALDEVNQTQQQADQMAQAFATGESVDLHEVMIAMQKASLSLQLAVQVRNKAVEAYQEIMR 93 (96)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3455666777766666555443222222222233899999999999 45566777777789999998764
No 140
>KOG1528 consensus Salt-sensitive 3'-phosphoadenosine-5'-phosphatase HAL2/SAL1 [Nucleotide transport and metabolism; Inorganic ion transport and metabolism]
Probab=22.17 E-value=1.9e+02 Score=27.94 Aligned_cols=79 Identities=19% Similarity=0.212 Sum_probs=51.5
Q ss_pred CCCCCCCccccCCchhHHHHHHhhcCCCCc--ccCHHHHHHHHHH-HHHHHHHHHHHHHH-HHHhc--CC-CccCcchHH
Q 027605 16 SGNISDKEQDRFLPIANVSRIMKKSLPANA--KISKEAKETVQEC-VSEFISFITGEASD-KCQRE--KR-KTINGDDLL 88 (221)
Q Consensus 16 ~~~~s~~eeD~~LPrAtV~RImK~aLP~n~--kISkDAk~al~kc-ateFI~yLTseAne-ic~~e--kR-KTIsaeDVl 88 (221)
+|+.++...|+- -.|.|.-.+++.+|+.- .|..|-..-|.+. ++.|+.-|+..-|+ ++.++ +- +.++.+||+
T Consensus 39 ~D~SPVTvaDyG-~QAiVs~vL~~~f~~~p~slVaEEds~~Lr~n~~~~~l~~i~~lvnetl~s~~sy~~~~~ls~~dvl 117 (351)
T KOG1528|consen 39 SDKSPVTVADYG-SQAIVSLVLEREFPDDPLSLVAEEDSGFLRKNGSEGLLSRITKLVNETLASDESYGDNSPLSSDDVL 117 (351)
T ss_pred CCCCCcchhhhh-HHHHHHHHHHHHcCCCCcceEeeccchhhhhhhhHHHHHHHHHHHHHHhhhhhhccCCCCCCHHHHH
Confidence 444455666654 46889999999999654 4666555555554 55666667664444 22222 22 789999999
Q ss_pred HHHhhcC
Q 027605 89 WAMTTLG 95 (221)
Q Consensus 89 ~ALe~LG 95 (221)
+|++.-.
T Consensus 118 ~aID~G~ 124 (351)
T KOG1528|consen 118 KAIDRGN 124 (351)
T ss_pred HHHhccc
Confidence 9998543
No 141
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=21.92 E-value=1.5e+02 Score=21.93 Aligned_cols=28 Identities=11% Similarity=0.134 Sum_probs=21.7
Q ss_pred HHHHHHhcCCCccCcchHHHHHhhcCCC
Q 027605 70 ASDKCQREKRKTINGDDLLWAMTTLGFE 97 (221)
Q Consensus 70 Aneic~~ekRKTIsaeDVl~ALe~LGF~ 97 (221)
+.+.+-.++.-.|+.++|..+|+.+|+.
T Consensus 15 ~F~~~D~d~~G~Is~~el~~~l~~~~~~ 42 (96)
T smart00027 15 IFRSLDKNQDGTVTGAQAKPILLKSGLP 42 (96)
T ss_pred HHHHhCCCCCCeEeHHHHHHHHHHcCCC
Confidence 3355556777889999999999988875
No 142
>PRK14868 DNA topoisomerase VI subunit B; Provisional
Probab=21.40 E-value=88 Score=33.20 Aligned_cols=45 Identities=22% Similarity=0.375 Sum_probs=33.6
Q ss_pred hhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcc
Q 027605 38 KKSLPANAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTI 82 (221)
Q Consensus 38 K~aLP~n~kISkDAk~al~kcateFI~yLTseAneic~~ekRKTI 82 (221)
|+++-+.--|-+|.+.+|++||.+.=.||...-...-++++++++
T Consensus 625 KeaIA~vpEI~~EI~lAl~~~aR~Lk~yl~k~~~~~~~~~k~~~~ 669 (795)
T PRK14868 625 KDAIANVPEIEDEIELAIREAARELKSYLNKRRSMQKRREKQDVL 669 (795)
T ss_pred hhhhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344433345889999999999999999999877666666666554
No 143
>COG1466 HolA DNA polymerase III, delta subunit [DNA replication, recombination, and repair]
Probab=20.99 E-value=2.5e+02 Score=25.61 Aligned_cols=50 Identities=20% Similarity=0.155 Sum_probs=40.3
Q ss_pred CcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHHhh
Q 027605 44 NAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAMTT 93 (221)
Q Consensus 44 n~kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~ALe~ 93 (221)
+++|++||.+.|..+..-=...+..|=...|--..-++|+.+||..++-+
T Consensus 157 ~l~i~~~a~~~L~~~~~~nl~~i~~Ei~KL~l~~~~~~I~~~~V~~~v~~ 206 (334)
T COG1466 157 GLKIDQEAIQLLLEALGGNLLAIAQEIEKLALYAGDKEITLEDVEEVVSD 206 (334)
T ss_pred CCCCCHHHHHHHHHHhCCcHHHHHHHHHHHHHhCCCCcCCHHHHHHHHhc
Confidence 68999999999999998666777777777666655559999999988763
No 144
>TIGR03261 phnS2 putative 2-aminoethylphosphonate ABC transporter, periplasmic 2-aminoethylphosphonate-binding protein. This ABC transporter extracellular solute-binding protein is found in a number of genomes in operon-like contexts strongly suggesting a substrate specificity for 2-aminoethylphosphonate (2-AEP). The characterized PhnSTUV system is absent in the genomes in which this system is found. These genomes encode systems for the catabolism of 2-AEP, making the need for a 2-AEP-specific transporter likely.
Probab=20.90 E-value=2.2e+02 Score=25.34 Aligned_cols=61 Identities=5% Similarity=0.102 Sum_probs=37.9
Q ss_pred HHHHHHHHHHHHHHHH-HHHHhcCCCccC----------cchHHHHHhhcCCCcchHHHHHHHHHHHHHHhh
Q 027605 56 QECVSEFISFITGEAS-DKCQREKRKTIN----------GDDLLWAMTTLGFENYVSPLKIYLNKYRETEGE 116 (221)
Q Consensus 56 ~kcateFI~yLTseAn-eic~~ekRKTIs----------aeDVl~ALe~LGF~~yv~~Lk~~Le~yRe~~k~ 116 (221)
.++|..||.||.+.-. ..-.+.....+. ++++...+-.+++....+.....+++|.+..+.
T Consensus 260 ~e~A~~fidfllS~e~Q~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~rw~~~~~~ 331 (334)
T TIGR03261 260 NDAAKKLVDWSISDEAMELYAKNYAVVATPGVAKPDAGFPKNVEDLLIKNDFVWAAANRDKILEEWSKRYGA 331 (334)
T ss_pred HHHHHHHHHHHcCHHHHHHHHhcCcccccCCcccCcccCCcchhhhcccCCHHHHHHhHHHHHHHHHHHhhc
Confidence 3789999999976533 332222222111 124444455667777788888889998887764
No 145
>PRK00440 rfc replication factor C small subunit; Reviewed
Probab=20.81 E-value=2.4e+02 Score=24.38 Aligned_cols=65 Identities=11% Similarity=0.058 Sum_probs=39.1
Q ss_pred CchhHHHHHHhhcCC-CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHHhhc
Q 027605 28 LPIANVSRIMKKSLP-ANAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAMTTL 94 (221)
Q Consensus 28 LPrAtV~RImK~aLP-~n~kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~ALe~L 94 (221)
++...+.++++..+. .+..|+.++.+.+.+.+.--+..+-.+-...+.. .++|+.+||..++...
T Consensus 161 l~~~ei~~~l~~~~~~~~~~i~~~al~~l~~~~~gd~r~~~~~l~~~~~~--~~~it~~~v~~~~~~~ 226 (319)
T PRK00440 161 LKKEAVAERLRYIAENEGIEITDDALEAIYYVSEGDMRKAINALQAAAAT--GKEVTEEAVYKITGTA 226 (319)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHc--CCCCCHHHHHHHhCCC
Confidence 444555555554442 2567999999999887653333333222222222 4689999998887643
No 146
>PRK14971 DNA polymerase III subunits gamma and tau; Provisional
Probab=20.56 E-value=2.2e+02 Score=28.93 Aligned_cols=64 Identities=6% Similarity=0.012 Sum_probs=34.5
Q ss_pred CchhHHHHHHhhcCC-CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcchHHHHHh
Q 027605 28 LPIANVSRIMKKSLP-ANAKISKEAKETVQECVSEFISFITGEASDKCQREKRKTINGDDLLWAMT 92 (221)
Q Consensus 28 LPrAtV~RImK~aLP-~n~kISkDAk~al~kcateFI~yLTseAneic~~ekRKTIsaeDVl~ALe 92 (221)
|+...+.+.++..+- .++.+++++..+|.+.+.-=+..+-.+....+.-.+++ |+.++|.+.+.
T Consensus 180 ls~~ei~~~L~~ia~~egi~i~~~al~~La~~s~gdlr~al~~Lekl~~y~~~~-It~~~V~~~l~ 244 (614)
T PRK14971 180 IQVADIVNHLQYVASKEGITAEPEALNVIAQKADGGMRDALSIFDQVVSFTGGN-ITYKSVIENLN 244 (614)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhccCC-ccHHHHHHHhC
Confidence 445555555544332 26789999888887765543343333333333323333 66666665543
No 147
>PRK09492 treR trehalose repressor; Provisional
Probab=20.54 E-value=71 Score=27.41 Aligned_cols=37 Identities=22% Similarity=0.416 Sum_probs=29.3
Q ss_pred CCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHH
Q 027605 27 FLPIANVSRIMKKSLPANAKISKEAKETVQECVSEFISFITG 68 (221)
Q Consensus 27 ~LPrAtV~RImK~aLP~n~kISkDAk~al~kcateFI~yLTs 68 (221)
.+-++||.|++... .+||.+.++-|.+++.+. .|.-.
T Consensus 15 gVS~~TVSrvLn~~----~~vs~~tr~rV~~~a~el-gY~pn 51 (315)
T PRK09492 15 GVGKSTVSRVLNNE----SGVSEETRERVEAVINQH-GFSPS 51 (315)
T ss_pred CCCHHHHhHHhCCC----CCCCHHHHHHHHHHHHHH-CCCcC
Confidence 57789999999753 479999999999999885 35443
No 148
>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=20.39 E-value=1.8e+02 Score=29.29 Aligned_cols=72 Identities=11% Similarity=0.189 Sum_probs=44.6
Q ss_pred hhHHHHHHhhcCCC-CcccCHHHHHHHHHHH---HHHHHHHHHHH----HH---HHHhcCCCccCcchHHHHHhhcCCCc
Q 027605 30 IANVSRIMKKSLPA-NAKISKEAKETVQECV---SEFISFITGEA----SD---KCQREKRKTINGDDLLWAMTTLGFEN 98 (221)
Q Consensus 30 rAtV~RImK~aLP~-n~kISkDAk~al~kca---teFI~yLTseA----ne---ic~~ekRKTIsaeDVl~ALe~LGF~~ 98 (221)
..-+..|++..+.. +..++.++..+|.+++ ...+..|.... .. .+...++..|+.+||.++++.--|..
T Consensus 355 ~edi~~Il~~~a~~~~v~ls~eal~~L~~ys~~gRraln~L~~~~~~~~~~~~~~~~~~~~~~I~~edv~~~l~~~r~~~ 434 (615)
T TIGR02903 355 PEDIALIVLNAAEKINVHLAAGVEELIARYTIEGRKAVNILADVYGYALYRAAEAGKENDKVTITQDDVYEVIQISRLSP 434 (615)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHCCCcHHHHHHHHHHHHHHHHHHHHHhccCCCCeeECHHHHHHHhCCCcCcc
Confidence 34566666665532 3568999999998865 33444443221 11 12233556899999999998877765
Q ss_pred chH
Q 027605 99 YVS 101 (221)
Q Consensus 99 yv~ 101 (221)
|..
T Consensus 435 ~~~ 437 (615)
T TIGR02903 435 YEK 437 (615)
T ss_pred chh
Confidence 543
No 149
>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=20.30 E-value=64 Score=21.31 Aligned_cols=25 Identities=12% Similarity=0.283 Sum_probs=19.9
Q ss_pred cCcchHHHHHhhcCCCcchHHHHHH
Q 027605 82 INGDDLLWAMTTLGFENYVSPLKIY 106 (221)
Q Consensus 82 IsaeDVl~ALe~LGF~~yv~~Lk~~ 106 (221)
-+.++|..-|+.+||++|++.+.+.
T Consensus 4 w~~~~v~~wL~~~g~~~y~~~f~~~ 28 (68)
T smart00454 4 WSPESVADWLESIGLEQYADNFRKN 28 (68)
T ss_pred CCHHHHHHHHHHCChHHHHHHHHHC
Confidence 4678899999999998888776553
No 150
>KOG3468 consensus NADH:ubiquinone oxidoreductase, NDUFB7/B18 subunit [Energy production and conversion]
Probab=20.09 E-value=2.5e+02 Score=23.48 Aligned_cols=113 Identities=15% Similarity=0.195 Sum_probs=65.5
Q ss_pred CCCCCCCCCCCCCccccCCchhHHHHHHhhcCC--CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-CCccCcch
Q 027605 10 PIGSPTSGNISDKEQDRFLPIANVSRIMKKSLP--ANAKISKEAKETVQECVSEFISFITGEASDKCQREK-RKTINGDD 86 (221)
Q Consensus 10 ~~~sp~~~~~s~~eeD~~LPrAtV~RImK~aLP--~n~kISkDAk~al~kcateFI~yLTseAneic~~ek-RKTIsaeD 86 (221)
|..-|.-+.+.-=.-++.+|. .-.|-|...-- ...+|.-..++ =|+-..|.+.. |+.+. --....+|
T Consensus 11 p~v~P~pd~~PTFdP~~gf~~-Rk~r~MiATqeEM~~akl~l~~RD---yCAH~lI~l~k------Cr~~~fp~~~kC~~ 80 (128)
T KOG3468|consen 11 PEVAPRPDRPPTFDPQYGFPG-RKEREMIATQEEMEAAKLALGSRD---YCAHLLIPLNK------CRQDEFPFPWKCED 80 (128)
T ss_pred cccCCCCCCCCCCCcccCCCc-hhHHHHHhhHHHHHhhhcCcchHH---HHHHHHHHHHH------hhcccCCcchhccc
Confidence 444455555555556677887 33333332211 01223222222 36666655544 43321 11233444
Q ss_pred HHHHHhhcCCCcchHHHHHHHHHHHHHHhhhhhhhhhhhccCCCCC
Q 027605 87 LLWAMTTLGFENYVSPLKIYLNKYRETEGEKNSMARQEDQAANPNP 132 (221)
Q Consensus 87 Vl~ALe~LGF~~yv~~Lk~~Le~yRe~~k~Kks~~k~~~~~~~~~~ 132 (221)
=--+-+..++++|+..++++-.+=|-.+.+|+..+...++..+.++
T Consensus 81 erh~~dkCEyed~vmRmkefeRErrlLqrq~r~e~~Aa~~~~~~~~ 126 (128)
T KOG3468|consen 81 ERHVYDKCEYEDYVMRMKEFERERRLLQRQKRLEKNAAVPLIPKTA 126 (128)
T ss_pred cccchhhhhHHHHHHHHHHHHHHHHHHHHHHHHhhcccccccCCCC
Confidence 4445678889999999999998888888888888877777766654
Done!