Query psy17761
Match_columns 92
No_of_seqs 100 out of 253
Neff 4.3
Searched_HMMs 46136
Date Fri Aug 16 22:11:51 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17761.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17761hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00076 H4 Histone H4, one of 100.0 1.2E-28 2.5E-33 164.5 6.6 72 13-86 7-81 (85)
2 PTZ00015 histone H4; Provision 99.9 2.3E-27 4.9E-32 163.0 7.2 72 13-85 24-98 (102)
3 PLN00035 histone H4; Provision 99.9 2.4E-27 5.3E-32 163.2 6.6 71 13-84 23-96 (103)
4 KOG3467|consensus 99.9 4.5E-27 9.8E-32 160.4 5.7 74 13-87 23-99 (103)
5 smart00417 H4 Histone H4. 99.9 6.4E-26 1.4E-30 148.2 4.5 65 13-78 7-74 (74)
6 smart00803 TAF TATA box bindin 99.8 1.9E-19 4.1E-24 114.3 5.9 60 20-80 5-65 (65)
7 COG2036 HHT1 Histones H3 and H 99.8 1.2E-18 2.6E-23 117.7 6.0 66 21-87 23-89 (91)
8 PF15511 CENP-T: Centromere ki 99.4 8E-14 1.7E-18 113.0 4.5 64 9-74 343-414 (414)
9 cd07979 TAF9 TATA Binding Prot 99.4 5.7E-13 1.2E-17 92.5 6.6 60 23-83 8-67 (117)
10 smart00576 BTP Bromodomain tra 99.4 2.1E-12 4.5E-17 83.2 7.0 62 23-85 13-74 (77)
11 cd07981 TAF12 TATA Binding Pro 99.3 4E-12 8.6E-17 81.4 6.8 62 21-83 5-68 (72)
12 cd08050 TAF6 TATA Binding Prot 99.1 4.3E-10 9.4E-15 89.0 7.2 65 22-87 4-69 (343)
13 PF00125 Histone: Core histone 99.0 5.3E-10 1.1E-14 70.1 5.2 60 21-81 9-74 (75)
14 PLN00163 histone H4; Provision 98.9 2.3E-10 5E-15 72.5 0.4 34 13-46 23-59 (59)
15 PF00808 CBFD_NFYB_HMF: Histon 98.8 3.4E-08 7.4E-13 61.0 6.1 57 22-79 7-65 (65)
16 PF07524 Bromo_TP: Bromodomain 98.7 6.9E-08 1.5E-12 61.5 7.1 61 24-85 14-74 (77)
17 PF02969 TAF: TATA box binding 98.6 1.2E-07 2.7E-12 60.7 6.4 60 20-80 6-66 (66)
18 smart00428 H3 Histone H3. 98.6 9.8E-08 2.1E-12 66.1 5.8 51 33-84 53-103 (105)
19 cd00074 H2A Histone 2A; H2A is 98.6 1.1E-07 2.5E-12 66.4 5.5 58 23-81 27-85 (115)
20 PF15630 CENP-S: Kinetochore c 98.5 1.8E-07 3.9E-12 61.3 4.5 48 33-81 25-72 (76)
21 PF02291 TFIID-31kDa: Transcri 98.3 3.3E-06 7.1E-11 60.1 6.3 61 20-81 12-76 (129)
22 KOG0869|consensus 97.9 2.4E-05 5.2E-10 58.2 5.7 63 22-85 38-102 (168)
23 KOG3334|consensus 97.7 0.00015 3.3E-09 53.2 6.4 62 21-83 18-79 (148)
24 PLN00161 histone H3; Provision 97.5 0.00028 6E-09 51.1 5.7 55 32-87 77-131 (135)
25 PLN00160 histone H3; Provision 97.4 0.00045 9.8E-09 47.4 5.1 51 32-83 43-93 (97)
26 PF03847 TFIID_20kDa: Transcri 97.4 0.00065 1.4E-08 43.5 5.4 51 31-82 15-65 (68)
27 COG5094 TAF9 Transcription ini 97.3 0.00073 1.6E-08 49.1 6.2 67 16-82 10-82 (145)
28 PTZ00018 histone H3; Provision 97.2 0.00076 1.6E-08 48.7 5.2 50 33-83 84-133 (136)
29 PLN00121 histone H3; Provision 97.2 0.00093 2E-08 48.3 5.2 50 33-83 84-133 (136)
30 KOG2549|consensus 97.1 0.0017 3.7E-08 55.9 6.7 66 20-86 14-80 (576)
31 KOG4336|consensus 97.0 0.0027 5.8E-08 51.5 6.5 62 25-87 14-75 (323)
32 PF02269 TFIID-18kDa: Transcri 96.8 0.0017 3.7E-08 43.4 3.8 52 31-83 17-68 (93)
33 KOG1142|consensus 96.7 0.0023 5E-08 50.5 4.5 66 16-82 153-220 (258)
34 smart00427 H2B Histone H2B. 96.4 0.012 2.5E-07 40.0 5.6 49 32-81 18-66 (89)
35 smart00414 H2A Histone 2A. 96.3 0.012 2.6E-07 40.6 5.1 58 23-81 15-74 (106)
36 PLN00158 histone H2B; Provisio 95.5 0.045 9.7E-07 38.8 5.5 49 32-81 44-92 (116)
37 PTZ00463 histone H2B; Provisio 95.3 0.054 1.2E-06 38.5 5.4 49 32-81 45-93 (117)
38 KOG0870|consensus 95.2 0.062 1.4E-06 40.4 5.6 60 23-83 16-79 (172)
39 PTZ00017 histone H2A; Provisio 95.2 0.045 9.7E-07 39.6 4.7 57 23-80 33-91 (134)
40 PLN00157 histone H2A; Provisio 94.3 0.092 2E-06 37.9 4.5 58 22-80 31-90 (132)
41 KOG1745|consensus 93.6 0.061 1.3E-06 39.1 2.5 52 33-85 85-136 (137)
42 cd07978 TAF13 The TATA Binding 93.5 0.33 7.1E-06 32.6 5.7 49 31-81 18-66 (92)
43 PLN00156 histone H2AX; Provisi 93.5 0.2 4.4E-06 36.4 5.1 65 12-80 27-93 (139)
44 PLN00153 histone H2A; Provisio 93.4 0.19 4.1E-06 36.1 4.8 65 12-80 22-88 (129)
45 COG5095 TAF6 Transcription ini 93.1 0.25 5.4E-06 41.2 5.6 64 22-86 10-74 (450)
46 KOG3423|consensus 93.1 0.4 8.6E-06 36.2 6.2 61 25-85 95-168 (176)
47 KOG0871|consensus 92.4 0.37 7.9E-06 35.8 5.1 70 17-87 11-84 (156)
48 PLN00154 histone H2A; Provisio 92.3 0.36 7.8E-06 35.1 5.0 58 22-80 43-103 (136)
49 KOG2389|consensus 91.7 0.37 8.1E-06 39.7 4.9 49 36-85 49-97 (353)
50 KOG1744|consensus 91.6 0.61 1.3E-05 33.6 5.4 48 33-81 55-102 (127)
51 PTZ00252 histone H2A; Provisio 91.5 0.55 1.2E-05 34.1 5.1 66 11-80 22-91 (134)
52 COG5208 HAP5 CCAAT-binding fac 89.3 0.59 1.3E-05 37.1 4.0 60 22-82 114-175 (286)
53 KOG1756|consensus 87.8 1.7 3.6E-05 31.6 5.2 66 11-80 24-91 (131)
54 KOG1657|consensus 87.7 1 2.2E-05 35.0 4.4 61 21-82 78-140 (236)
55 cd08045 TAF4 TATA Binding Prot 84.9 4.3 9.3E-05 30.2 6.3 57 24-81 56-118 (212)
56 cd08048 TAF11 TATA Binding Pro 83.6 6.3 0.00014 26.1 6.1 62 20-82 19-84 (85)
57 PF09415 CENP-X: CENP-S associ 83.1 2.4 5.1E-05 27.3 3.8 48 31-79 17-65 (72)
58 PF03540 TFIID_30kDa: Transcri 82.3 4.6 0.0001 24.8 4.7 39 25-63 11-49 (51)
59 KOG1659|consensus 81.0 5.1 0.00011 31.4 5.5 57 23-80 19-77 (224)
60 PF05236 TAF4: Transcription i 76.0 4.4 9.6E-05 31.0 3.9 54 27-81 58-117 (264)
61 PF04719 TAFII28: hTAFII28-lik 73.5 12 0.00026 25.1 5.1 61 20-81 26-89 (90)
62 TIGR00764 lon_rel lon-related 73.5 13 0.00028 32.1 6.4 50 31-81 328-390 (608)
63 KOG3901|consensus 73.3 9.5 0.00021 26.9 4.7 43 39-82 29-72 (109)
64 COG5162 Transcription initiati 69.7 20 0.00043 27.4 6.0 61 26-86 98-190 (197)
65 TIGR02902 spore_lonB ATP-depen 69.5 6.3 0.00014 33.2 3.6 53 33-86 282-336 (531)
66 COG5262 HTA1 Histone H2A [Chro 66.3 18 0.00038 26.2 4.9 64 12-79 24-89 (132)
67 PRK00411 cdc6 cell division co 63.0 26 0.00057 27.1 5.8 50 33-83 228-283 (394)
68 COG5248 TAF19 Transcription in 61.0 26 0.00057 25.1 4.9 42 38-82 32-73 (126)
69 COG1067 LonB Predicted ATP-dep 60.5 23 0.00049 31.3 5.5 57 25-82 329-399 (647)
70 PF13335 Mg_chelatase_2: Magne 58.0 35 0.00076 22.5 4.9 28 51-79 66-93 (96)
71 COG5150 Class 2 transcription 56.7 19 0.00042 26.4 3.7 51 36-87 33-83 (148)
72 smart00350 MCM minichromosome 53.2 17 0.00037 30.3 3.4 31 50-81 473-503 (509)
73 PF13654 AAA_32: AAA domain; P 52.6 21 0.00045 30.4 3.9 34 49-83 474-507 (509)
74 TIGR03015 pepcterm_ATPase puta 52.0 44 0.00096 24.2 5.1 49 33-82 215-266 (269)
75 PF02579 Nitro_FeMo-Co: Dinitr 48.3 5.5 0.00012 24.7 -0.1 31 19-50 63-93 (94)
76 PF12767 SAGA-Tad1: Transcript 48.1 43 0.00094 25.4 4.7 34 28-61 218-251 (252)
77 PF08369 PCP_red: Proto-chloro 47.6 25 0.00055 20.5 2.7 29 47-76 13-42 (45)
78 PF12558 DUF3744: ATP-binding 45.9 14 0.00029 23.5 1.4 18 9-30 6-23 (74)
79 cd00852 NifB NifB belongs to a 42.3 12 0.00027 24.2 0.8 31 19-49 75-105 (106)
80 COG4401 AroH Chorismate mutase 39.9 32 0.00069 24.8 2.6 31 27-57 5-35 (125)
81 KOG0400|consensus 39.5 32 0.00069 25.4 2.7 45 8-64 55-102 (151)
82 PF00493 MCM: MCM2/3/5 family 39.1 21 0.00046 28.1 1.8 30 50-80 295-324 (331)
83 cd00851 MTH1175 This uncharact 38.6 15 0.00033 23.0 0.8 30 19-49 73-102 (103)
84 COG1963 Uncharacterized protei 37.7 12 0.00026 27.8 0.2 54 21-92 81-136 (153)
85 cd00853 NifX NifX belongs to a 36.6 17 0.00036 23.5 0.7 30 19-48 71-100 (102)
86 KOG3219|consensus 36.4 40 0.00087 25.9 2.9 66 20-86 115-185 (195)
87 TIGR02663 nifX nitrogen fixati 35.9 31 0.00067 23.1 2.0 34 19-52 73-106 (119)
88 TIGR00368 Mg chelatase-related 35.8 92 0.002 26.4 5.2 29 51-80 469-497 (499)
89 TIGR02928 orc1/cdc6 family rep 35.1 1.4E+02 0.0031 22.7 5.8 31 51-82 244-274 (365)
90 cd03412 CbiK_N Anaerobic cobal 34.7 46 0.00099 22.7 2.7 38 12-50 52-97 (127)
91 PRK07452 DNA polymerase III su 34.6 68 0.0015 24.4 3.9 49 33-82 149-199 (326)
92 PRK10733 hflB ATP-dependent me 34.4 84 0.0018 27.2 4.8 57 23-83 541-597 (644)
93 PF01296 Galanin: Galanin; In 34.0 18 0.0004 20.0 0.5 9 5-13 20-28 (29)
94 KOG1658|consensus 33.8 27 0.00058 26.2 1.5 43 37-80 81-123 (162)
95 PRK09862 putative ATP-dependen 33.7 98 0.0021 26.5 5.1 28 53-81 464-491 (506)
96 PF01024 Colicin: Colicin pore 33.3 73 0.0016 24.2 3.8 49 36-87 20-68 (187)
97 TIGR02442 Cob-chelat-sub cobal 32.8 1E+02 0.0023 26.5 5.1 48 33-81 249-303 (633)
98 PF06798 PrkA: PrkA serine pro 32.6 1.4E+02 0.0031 23.1 5.5 55 26-82 181-237 (254)
99 PTZ00361 26 proteosome regulat 31.9 60 0.0013 27.1 3.4 32 50-82 393-424 (438)
100 TIGR02030 BchI-ChlI magnesium 29.6 90 0.002 25.0 4.0 46 34-80 255-307 (337)
101 PRK13765 ATP-dependent proteas 29.5 1.2E+02 0.0026 26.6 5.0 31 50-81 369-399 (637)
102 PRK03992 proteasome-activating 28.8 81 0.0018 25.3 3.6 35 48-83 339-373 (389)
103 PF11815 DUF3336: Domain of un 28.4 1.9E+02 0.0041 20.4 5.1 41 41-85 105-145 (145)
104 PF03885 DUF327: Protein of un 28.2 1.1E+02 0.0024 21.6 3.9 36 31-66 60-95 (147)
105 PRK13406 bchD magnesium chelat 28.1 1.1E+02 0.0025 26.5 4.6 49 32-81 194-249 (584)
106 COG5247 BUR6 Class 2 transcrip 27.6 1.7E+02 0.0038 20.7 4.7 47 31-78 39-85 (113)
107 cd05030 calgranulins Calgranul 27.6 82 0.0018 20.0 2.9 24 59-83 13-40 (88)
108 cd07293 PX_SNX3 The phosphoino 27.5 1.4E+02 0.003 20.6 4.2 43 15-57 63-106 (123)
109 PF14394 DUF4423: Domain of un 26.9 99 0.0021 22.4 3.5 27 33-59 128-154 (171)
110 PF07261 DnaB_2: Replication i 26.1 1.5E+02 0.0033 17.6 4.2 40 31-70 10-51 (77)
111 cd00082 HisKA Histidine Kinase 25.3 1E+02 0.0022 16.0 2.7 19 10-28 12-31 (65)
112 PTZ00454 26S protease regulato 25.2 97 0.0021 25.3 3.5 32 50-82 355-386 (398)
113 TIGR01242 26Sp45 26S proteasom 25.2 1E+02 0.0022 24.2 3.5 33 49-82 331-363 (364)
114 cd02001 TPP_ComE_PpyrDC Thiami 24.6 1.2E+02 0.0025 21.2 3.4 43 7-50 95-142 (157)
115 CHL00176 ftsH cell division pr 24.3 96 0.0021 27.2 3.5 32 50-82 392-423 (638)
116 PRK07914 hypothetical protein; 24.1 1.5E+02 0.0032 22.9 4.2 49 32-82 146-194 (320)
117 PTZ00111 DNA replication licen 24.0 1.7E+02 0.0037 27.2 5.1 31 49-80 772-802 (915)
118 KOG2994|consensus 23.6 53 0.0012 26.7 1.7 36 5-52 141-180 (297)
119 cd08641 DNA_pol_gammaA Pol gam 23.1 93 0.002 26.5 3.1 33 34-66 17-49 (425)
120 KOG1257|consensus 23.0 71 0.0015 28.3 2.4 34 31-74 229-262 (582)
121 PF05046 Img2: Mitochondrial l 22.5 52 0.0011 21.5 1.2 52 31-83 31-86 (87)
122 PRK08487 DNA polymerase III su 22.3 2.2E+02 0.0048 22.0 4.9 48 32-82 153-200 (328)
123 cd00562 NifX_NifB This CD repr 22.2 38 0.00083 21.0 0.5 15 20-34 72-86 (102)
124 KOG0784|consensus 22.2 44 0.00095 28.0 1.0 33 38-70 174-206 (375)
125 PF09744 Jnk-SapK_ap_N: JNK_SA 21.8 1E+02 0.0022 22.5 2.8 26 33-58 3-28 (158)
126 cd06409 PB1_MUG70 The MUG70 pr 21.8 57 0.0012 21.7 1.3 17 54-70 64-80 (86)
127 COG2045 Phosphosulfolactate ph 21.3 83 0.0018 24.7 2.3 60 19-81 143-210 (230)
128 COG4854 Predicted membrane pro 20.9 88 0.0019 22.5 2.2 35 44-79 46-82 (126)
129 COG3684 LacD Tagatose-1,6-bisp 20.7 3E+02 0.0065 22.6 5.4 60 21-87 115-200 (306)
130 PLN00155 histone H2A; Provisio 20.5 84 0.0018 19.8 1.8 33 12-47 22-56 (58)
No 1
>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=99.95 E-value=1.2e-28 Score=164.46 Aligned_cols=72 Identities=40% Similarity=0.553 Sum_probs=66.3
Q ss_pred ccCCCCC--CchhHHhhhcc-cccchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccchhHHHHHHhhCCCC
Q psy17761 13 LRTPVSG--PPSVVWRVEVE-SSVFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMDSRLRAKTSRPHP 86 (92)
Q Consensus 13 ~~~~v~~--~~aIRrlar~G-akRIS~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt~~~DV~~alkr~g~~~ 86 (92)
++.++.| +|+|++|+++| ++|||+++|+|++++|++|+++|++||++||+||+||||+ ++||++|||+|| +|
T Consensus 7 ~~~~~~gi~k~~I~RLarr~GvkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt-~~DV~~alkr~g-~~ 81 (85)
T cd00076 7 LRDNIKGITKPAIRRLARRGGVKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVT-AMDVVYALKRQG-RT 81 (85)
T ss_pred HHHhhccCCHHHHHHHHHHcCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCc-HHHHHHHHHHCC-CC
Confidence 4455555 48999999996 9999999999999999999999999999999999999999 999999999999 44
No 2
>PTZ00015 histone H4; Provisional
Probab=99.94 E-value=2.3e-27 Score=163.05 Aligned_cols=72 Identities=36% Similarity=0.473 Sum_probs=66.6
Q ss_pred ccCCCCCC--chhHHhhhcc-cccchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccchhHHHHHHhhCCC
Q psy17761 13 LRTPVSGP--PSVVWRVEVE-SSVFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMDSRLRAKTSRPH 85 (92)
Q Consensus 13 ~~~~v~~~--~aIRrlar~G-akRIS~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt~~~DV~~alkr~g~~ 85 (92)
++.++.+. |+|++|+++| |+|||+++|+|++++|++|+++|++||++||+||+||||+ ++||++|||+||+.
T Consensus 24 ~r~~i~gI~k~~IrRLarr~GvkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt-~~DV~~AlKr~g~~ 98 (102)
T PTZ00015 24 LRDNIRGITKGAIRRLARRGGVKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVT-AMDVVYALKRQGRT 98 (102)
T ss_pred HhhcccCCCHHHHHHHHHHcCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccc-HHHHHHHHHhcCCC
Confidence 45555663 8999999996 9999999999999999999999999999999999999999 99999999999984
No 3
>PLN00035 histone H4; Provisional
Probab=99.94 E-value=2.4e-27 Score=163.24 Aligned_cols=71 Identities=48% Similarity=0.672 Sum_probs=66.4
Q ss_pred ccCCCCC--CchhHHhhhcc-cccchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccchhHHHHHHhhCC
Q psy17761 13 LRTPVSG--PPSVVWRVEVE-SSVFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMDSRLRAKTSRP 84 (92)
Q Consensus 13 ~~~~v~~--~~aIRrlar~G-akRIS~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt~~~DV~~alkr~g~ 84 (92)
++.++.+ .|+|+||+++| |+|||+++|+|++++|++|+++|++||++||+||+||||+ ++||++|||++|+
T Consensus 23 ~~d~i~~ipk~~IrRLARr~GvkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~-~~DV~~Alkr~g~ 96 (103)
T PLN00035 23 LRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVT-AMDVVYALKRQGR 96 (103)
T ss_pred HHhhhccCCHHHHHHHHHHcCcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCc-HHHHHHHHHHcCC
Confidence 5556665 38999999996 9999999999999999999999999999999999999999 9999999999998
No 4
>KOG3467|consensus
Probab=99.94 E-value=4.5e-27 Score=160.39 Aligned_cols=74 Identities=49% Similarity=0.635 Sum_probs=69.4
Q ss_pred ccCCCCC--CchhHHhhhcc-cccchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccchhHHHHHHhhCCCCc
Q psy17761 13 LRTPVSG--PPSVVWRVEVE-SSVFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMDSRLRAKTSRPHPC 87 (92)
Q Consensus 13 ~~~~v~~--~~aIRrlar~G-akRIS~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt~~~DV~~alkr~g~~~~ 87 (92)
|+.+|+| +|+||+|+++| ++||++.+|+|++.++++|+|+++.+|++||+||+||||| +|||+|+|||||+-.+
T Consensus 23 LsDnIqgitKpaIRRlARr~GVkRi~G~~yeE~~~~~k~fl~n~i~~A~~yt~HAKRKTvT-~~dvv~~LKR~G~~~~ 99 (103)
T KOG3467|consen 23 LRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVT-AMDVVYALKRQGRTLY 99 (103)
T ss_pred HHhhccccchHHHHHHHHhcCcchhchhhHHHHHHHHHHHHHHHHHHHHHHHhhhhhceee-HHHHHHHHHHcCceee
Confidence 6677887 59999999997 9999999999999999999999999999999999999999 9999999999997544
No 5
>smart00417 H4 Histone H4.
Probab=99.92 E-value=6.4e-26 Score=148.19 Aligned_cols=65 Identities=46% Similarity=0.672 Sum_probs=59.5
Q ss_pred ccCCCCC--CchhHHhhhcc-cccchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccchhHHHH
Q psy17761 13 LRTPVSG--PPSVVWRVEVE-SSVFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMDSRLR 78 (92)
Q Consensus 13 ~~~~v~~--~~aIRrlar~G-akRIS~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt~~~DV~~a 78 (92)
++.++.| +|+|++|+++| |+|||+++|+|++++|++|+++|++||++||+||+||||+ ++||+||
T Consensus 7 ~~d~i~gI~k~~IrRLaRr~GvkRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~-~~DV~~a 74 (74)
T smart00417 7 LRDNIQGITKPAIRRLARRGGVKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVT-AMDVVYA 74 (74)
T ss_pred HHhhhcCCCHHHHHHHHHHcCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccc-HHHheeC
Confidence 4455556 38999999996 9999999999999999999999999999999999999999 9999875
No 6
>smart00803 TAF TATA box binding protein associated factor. TAFs (TATA box binding protein associated factors) are part of the transcription initiation factor TFIID multimeric protein complex. TFIID is composed of the TATA box binding protein (TBP) and a number of TAFs. The TAFs provide binding sites for many different transcriptional activators and co-activators that modulate transcription initiation by Pol II. TAF proteins adopt a histone-like fold.
Probab=99.79 E-value=1.9e-19 Score=114.28 Aligned_cols=60 Identities=13% Similarity=0.128 Sum_probs=57.6
Q ss_pred CchhHHhhhc-ccccchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccchhHHHHHH
Q psy17761 20 PPSVVWRVEV-ESSVFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMDSRLRAK 80 (92)
Q Consensus 20 ~~aIRrlar~-GakRIS~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt~~~DV~~alk 80 (92)
+++|++++++ |++|||+++|+++++.+|.|+++|+++|+.|++|++|||++ ++||.+|||
T Consensus 5 ~~~i~ria~~~Gi~ris~~a~~~l~~~~e~rl~~i~~~A~k~~~hakRktlt-~~DI~~Alk 65 (65)
T smart00803 5 KETIKDVAESLGIGNLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLT-TSDIDSALR 65 (65)
T ss_pred HHHHHHHHHHCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCeec-HHHHHHHhC
Confidence 4889999988 59999999999999999999999999999999999999999 999999986
No 7
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=99.76 E-value=1.2e-18 Score=117.73 Aligned_cols=66 Identities=26% Similarity=0.241 Sum_probs=59.5
Q ss_pred chhHHhhh-cccccchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccchhHHHHHHhhCCCCc
Q psy17761 21 PSVVWRVE-VESSVFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMDSRLRAKTSRPHPC 87 (92)
Q Consensus 21 ~aIRrlar-~GakRIS~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt~~~DV~~alkr~g~~~~ 87 (92)
+.|+||.+ .|.+|||+++++++.+++++|+++|.++|+.||+|||||||+ ++||.+|++++|.+.+
T Consensus 23 apv~Ri~r~~~~~Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~-~~DI~la~~~~~~~~~ 89 (91)
T COG2036 23 APVRRILRKAGAERVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVK-AEDIKLALKRLGRRIY 89 (91)
T ss_pred hHHHHHHHHHhHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeec-HHHHHHHHHHhccccc
Confidence 45555555 579999999999999999999999999999999999999999 9999999999997643
No 8
>PF15511 CENP-T: Centromere kinetochore component CENP-T; PDB: 3B0D_T 3B0C_T 3VH5_T 3VH6_T.
Probab=99.44 E-value=8e-14 Score=112.96 Aligned_cols=64 Identities=25% Similarity=0.259 Sum_probs=43.2
Q ss_pred CcCCccCCCCCCch-hHHhhhccc-------ccchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccchh
Q psy17761 9 DAHGLRTPVSGPPS-VVWRVEVES-------SVFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMD 74 (92)
Q Consensus 9 ~~hg~~~~v~~~~a-IRrlar~Ga-------kRIS~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt~~~D 74 (92)
.+|||.|| ++|++ |++++..-+ .+||.++|++|.++++||+|++..|.-+||+|||||||. .+|
T Consensus 343 Skhgi~~P-~lP~~~vK~la~~~ak~s~~sK~kiskdal~aleqasdwfFeQl~dDL~aYA~HAgRKTId-esD 414 (414)
T PF15511_consen 343 SKHGIPYP-SLPPGVVKKLAQHFAKSSGGSKMKISKDALEALEQASDWFFEQLGDDLEAYAKHAGRKTID-ESD 414 (414)
T ss_dssp ----------S-HHHHHHHHHHHH-------S-B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE--HHH
T ss_pred CCCCCCCC-CCCccHHHHHHHHHHHhhcccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCC-CCC
Confidence 46999999 88744 555555433 499999999999999999999999999999999999999 887
No 9
>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=99.41 E-value=5.7e-13 Score=92.54 Aligned_cols=60 Identities=13% Similarity=0.125 Sum_probs=57.2
Q ss_pred hHHhhhcccccchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccchhHHHHHHhhC
Q psy17761 23 VVWRVEVESSVFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMDSRLRAKTSR 83 (92)
Q Consensus 23 IRrlar~GakRIS~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt~~~DV~~alkr~g 83 (92)
.++|+..|++++++++...+.+.+..|.++|++||..|++|||||||+ ++||.+|++..+
T Consensus 8 ~~iLk~~Gv~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~-~eDV~lAi~~r~ 67 (117)
T cd07979 8 AAILKSMGITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANID-ADDVKLAIQSRV 67 (117)
T ss_pred HHHHHHCCCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCC-HHHHHHHHHHHh
Confidence 478888899999999999999999999999999999999999999999 999999998865
No 10
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=99.37 E-value=2.1e-12 Score=83.16 Aligned_cols=62 Identities=16% Similarity=0.088 Sum_probs=58.6
Q ss_pred hHHhhhcccccchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccchhHHHHHHhhCCC
Q psy17761 23 VVWRVEVESSVFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMDSRLRAKTSRPH 85 (92)
Q Consensus 23 IRrlar~GakRIS~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt~~~DV~~alkr~g~~ 85 (92)
-++++..|++++++.+-+.+.++++.|+.++++.+..|++||||++++ ..||.+||+.+|.+
T Consensus 13 aqil~~~Gf~~~~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~-~~Dv~~Al~~~gi~ 74 (77)
T smart00576 13 AQILESAGFDSFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPN-LGDVVLALENLGIS 74 (77)
T ss_pred HHHHHHcCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCC-HHHHHHHHHHhCcc
Confidence 467778899999999999999999999999999999999999999999 99999999999864
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=99.34 E-value=4e-12 Score=81.43 Aligned_cols=62 Identities=15% Similarity=0.106 Sum_probs=54.7
Q ss_pred chhHHhhhcc--cccchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccchhHHHHHHhhC
Q psy17761 21 PSVVWRVEVE--SSVFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMDSRLRAKTSR 83 (92)
Q Consensus 21 ~aIRrlar~G--akRIS~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt~~~DV~~alkr~g 83 (92)
..+.-|.+.. -.|+++++.+++.+++++|+++|+.+|+.+|+|+|||||+ +.||.++|+|.-
T Consensus 5 ~~l~~lv~~id~~~~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~~~tv~-~~Di~l~l~r~~ 68 (72)
T cd07981 5 RKLQELLKEIDPREQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLE-VKDVQLHLERNW 68 (72)
T ss_pred HHHHHHHHhhCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCC-HHHHHHHHHHhc
Confidence 3444455543 5799999999999999999999999999999999999999 999999999864
No 12
>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=99.06 E-value=4.3e-10 Score=88.98 Aligned_cols=65 Identities=17% Similarity=0.197 Sum_probs=59.4
Q ss_pred hhHHhhhc-ccccchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccchhHHHHHHhhCCCCc
Q psy17761 22 SVVWRVEV-ESSVFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMDSRLRAKTSRPHPC 87 (92)
Q Consensus 22 aIRrlar~-GakRIS~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt~~~DV~~alkr~g~~~~ 87 (92)
+|+.+++. |++|+|+++..++...++.++.+|+++|+.+++|++|||++ ++||.+||+..+..|.
T Consensus 4 ~i~~ia~~~Gi~~~~~~a~~~La~~~e~~~~~i~~~A~k~~~hskR~~l~-~~Di~~Al~~~n~epl 69 (343)
T cd08050 4 SIKLIAESLGIDSLSDEVAQLLAEDVEYRLREIIQEAAKFMRHSKRRKLT-TSDVNHALRLRNVEPL 69 (343)
T ss_pred HHHHHHHHcCCCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCC-HHHHHHHHHHhCCCcc
Confidence 45555555 89999999999999999999999999999999999999999 9999999999877764
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=99.03 E-value=5.3e-10 Score=70.07 Aligned_cols=60 Identities=20% Similarity=0.181 Sum_probs=54.0
Q ss_pred chhHHhhhcc-c-----ccchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccchhHHHHHHh
Q psy17761 21 PSVVWRVEVE-S-----SVFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMDSRLRAKT 81 (92)
Q Consensus 21 ~aIRrlar~G-a-----kRIS~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt~~~DV~~alkr 81 (92)
+.|.++.+.- . .|||.++++.+..++|.|+.+|+.+|..+|.|++|+|++ +.||.+|++.
T Consensus 9 ~~~~r~~r~i~~~~~~~~ris~~a~~~L~~~~E~~~~~il~~A~~~a~~~kR~tI~-~~DI~~A~r~ 74 (75)
T PF00125_consen 9 FPFSRLLREIGEEILSKYRISSEALVALQSVLEYLLVEILEEAGNLARHAKRKTIT-PRDIQLAVRI 74 (75)
T ss_dssp HHHHHHHHHHHHTTSSSSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTBSEEG-HHHHHHHHHH
T ss_pred eEEeeeeehhhcccccccccccccchhhhhhhhhhhhhhhhHHHHHHhhcCCcEec-HHHHHHHHhc
Confidence 5677776663 2 399999999999999999999999999999999999999 9999999874
No 14
>PLN00163 histone H4; Provisional
Probab=98.92 E-value=2.3e-10 Score=72.50 Aligned_cols=34 Identities=41% Similarity=0.619 Sum_probs=29.1
Q ss_pred ccCCCCC--CchhHHhhhcc-cccchhhHHHHHHHHH
Q psy17761 13 LRTPVSG--PPSVVWRVEVE-SSVFAGLIYEETRGVL 46 (92)
Q Consensus 13 ~~~~v~~--~~aIRrlar~G-akRIS~~iy~elr~vL 46 (92)
++.++.+ +||||+||++| |||||+++|+|+|++|
T Consensus 23 lrd~i~gItKpaIrRLARRgGVKRIs~~iY~e~R~vl 59 (59)
T PLN00163 23 LRDNIQGITKPAIRRLARRGGVKRISGLIYEETRTVL 59 (59)
T ss_pred HHHhhcccchHHHHHHHHhcCceeecchhhHhHhccC
Confidence 4555566 49999999997 9999999999999875
No 15
>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=98.75 E-value=3.4e-08 Score=61.04 Aligned_cols=57 Identities=12% Similarity=0.046 Sum_probs=49.6
Q ss_pred hhHHhhhc--ccccchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccchhHHHHH
Q psy17761 22 SVVWRVEV--ESSVFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMDSRLRA 79 (92)
Q Consensus 22 aIRrlar~--GakRIS~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt~~~DV~~al 79 (92)
-|+++.+. +..+||.++.+.+..+.+.|++.+..+|...|++.+||||+ .+||..|+
T Consensus 7 ~vkri~k~~~~~~~vs~ea~~~i~~a~e~Fi~~l~~~A~~~a~~~~rkti~-~~Dv~~Av 65 (65)
T PF00808_consen 7 RVKRIMKSDPDVMRVSKEAVEAIAKAAEEFIQYLAKEANEIAQRDKRKTIT-YEDVAKAV 65 (65)
T ss_dssp HHHHHHHHTSTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEE--HHHHHHHH
T ss_pred HHHHHhccCCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccC-HHHHHHHC
Confidence 45666555 48899999999999999999999999999999999999999 99999875
No 16
>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=98.72 E-value=6.9e-08 Score=61.52 Aligned_cols=61 Identities=15% Similarity=0.072 Sum_probs=57.6
Q ss_pred HHhhhcccccchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccchhHHHHHHhhCCC
Q psy17761 24 VWRVEVESSVFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMDSRLRAKTSRPH 85 (92)
Q Consensus 24 Rrlar~GakRIS~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt~~~DV~~alkr~g~~ 85 (92)
.++...|.+.+++.+-+.+.+++..|++++.+.+..|++|++|.... ..||.++|+..|.+
T Consensus 14 ~il~~~GF~~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~-~~Dv~~al~~~gi~ 74 (77)
T PF07524_consen 14 QILKHAGFDSASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPN-LQDVEQALEEMGIS 74 (77)
T ss_pred HHHHHcCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCC-HHHHHHHHHHhCCC
Confidence 46777899999999999999999999999999999999999999999 99999999999975
No 17
>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=98.64 E-value=1.2e-07 Score=60.72 Aligned_cols=60 Identities=20% Similarity=0.147 Sum_probs=50.1
Q ss_pred CchhHHhhhc-ccccchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccchhHHHHHH
Q psy17761 20 PPSVVWRVEV-ESSVFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMDSRLRAK 80 (92)
Q Consensus 20 ~~aIRrlar~-GakRIS~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt~~~DV~~alk 80 (92)
+-+|+-++.. |+.-+++++...+.+-++..+.+|+.+|..+..|++|++.+ ++||-.|||
T Consensus 6 ~esvk~iAes~Gi~~l~de~a~~La~dveyrlreiiq~a~kfm~hskR~~Lt-~~Di~~ALr 66 (66)
T PF02969_consen 6 QESVKDIAESLGISNLSDEAAKALAEDVEYRLREIIQEALKFMRHSKRTKLT-TDDINSALR 66 (66)
T ss_dssp HHHHHHHHHHTT---B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB--HHHHHHHH-
T ss_pred HHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCC-HHHHHHHhC
Confidence 4578888888 89999999999999999999999999999999999999999 999999996
No 18
>smart00428 H3 Histone H3.
Probab=98.62 E-value=9.8e-08 Score=66.05 Aligned_cols=51 Identities=20% Similarity=0.135 Sum_probs=47.8
Q ss_pred cchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccchhHHHHHHhhCC
Q psy17761 33 VFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMDSRLRAKTSRP 84 (92)
Q Consensus 33 RIS~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt~~~DV~~alkr~g~ 84 (92)
|+++++.+++.++.|.|+.++.+||...|.||+|+|++ +.|+.++.+--|.
T Consensus 53 R~~~~Al~aLQeasE~ylv~lfeda~~~a~HAkRvTl~-~kDi~La~rir~~ 103 (105)
T smart00428 53 RFQSSAIMALQEAAEAYLVGLFEDTNLLAIHAKRVTIM-PKDIQLARRIRGE 103 (105)
T ss_pred eeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccCc-HhhHHHHHHHhcc
Confidence 99999999999999999999999999999999999999 9999999854443
No 19
>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=98.59 E-value=1.1e-07 Score=66.41 Aligned_cols=58 Identities=12% Similarity=-0.003 Sum_probs=52.3
Q ss_pred hHHhhh-cccccchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccchhHHHHHHh
Q psy17761 23 VVWRVE-VESSVFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMDSRLRAKT 81 (92)
Q Consensus 23 IRrlar-~GakRIS~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt~~~DV~~alkr 81 (92)
-|+|++ ++++|||+++...+..+||.+..+|++-|..++++++||+|+ ++||.+|.+.
T Consensus 27 ~R~Lk~~~~a~RVs~~A~VyLaAvLEYL~aEIlelA~n~ak~~k~krIt-p~hi~lAi~n 85 (115)
T cd00074 27 HRYLKKGRYAERVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKKRIT-PRHLQLAVRN 85 (115)
T ss_pred HHHHHcCccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEc-HHHHHHHHhc
Confidence 355554 459999999999999999999999999999999999999999 9999999864
No 20
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=98.51 E-value=1.8e-07 Score=61.28 Aligned_cols=48 Identities=23% Similarity=0.263 Sum_probs=42.0
Q ss_pred cchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccchhHHHHHHh
Q psy17761 33 VFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMDSRLRAKT 81 (92)
Q Consensus 33 RIS~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt~~~DV~~alkr 81 (92)
.+|..+...+.+..=.+++.+++|...+|+||||+||+ .+||.+.++|
T Consensus 25 ~~s~~~i~al~ELv~~q~~~~a~DLe~FAkHA~R~tI~-~dDV~Ll~Rr 72 (76)
T PF15630_consen 25 EVSPQFIAALTELVYKQLENLAKDLEAFAKHAGRSTIN-MDDVKLLARR 72 (76)
T ss_dssp EE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE--HHHHHHHTTT
T ss_pred ccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeec-HHHHHHHhhc
Confidence 58889999999999999999999999999999999999 9999998865
No 21
>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=98.25 E-value=3.3e-06 Score=60.11 Aligned_cols=61 Identities=20% Similarity=0.202 Sum_probs=49.5
Q ss_pred CchhH----HhhhcccccchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccchhHHHHHHh
Q psy17761 20 PPSVV----WRVEVESSVFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMDSRLRAKT 81 (92)
Q Consensus 20 ~~aIR----rlar~GakRIS~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt~~~DV~~alkr 81 (92)
|.+.| +|+..|+.--..-+..-+-+..-.|..+|+.||..|++||+|++++ .+||.+|.+-
T Consensus 12 PrDa~~i~~iL~~~Gv~~yeprVv~qLLEfayRYt~~vL~DA~~ya~hA~~~~i~-~~DVrLAi~~ 76 (129)
T PF02291_consen 12 PRDARVIHLILKSMGVTEYEPRVVNQLLEFAYRYTSDVLEDAQVYADHAGRSTID-ADDVRLAIQS 76 (129)
T ss_dssp -HHHHHHHHHHHHTT---B-THHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB--HHHHHHHHHH
T ss_pred ChHHHHHHHHHHHcCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccCC-hHHHHHHHHH
Confidence 45555 7888899988899999999999999999999999999999999999 9999999983
No 22
>KOG0869|consensus
Probab=97.93 E-value=2.4e-05 Score=58.21 Aligned_cols=63 Identities=13% Similarity=-0.052 Sum_probs=57.0
Q ss_pred hhHHhhhcc--cccchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccchhHHHHHHhhCCC
Q psy17761 22 SVVWRVEVE--SSVFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMDSRLRAKTSRPH 85 (92)
Q Consensus 22 aIRrlar~G--akRIS~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt~~~DV~~alkr~g~~ 85 (92)
-.|++++.= --.||.|+.+-+.+..-+|+.=|--+|-.-|...+||||+ .+|+..||..+|..
T Consensus 38 V~RIMK~~lP~naKIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIn-gdDllwAm~tLGFe 102 (168)
T KOG0869|consen 38 VSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASEKCQREKRKTIN-GDDLLWAMSTLGFE 102 (168)
T ss_pred HHHHHHhcCCcccccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCccc-HHHHHHHHHHcCcH
Confidence 357777663 5589999999999999999999999999999999999999 99999999999954
No 23
>KOG3334|consensus
Probab=97.68 E-value=0.00015 Score=53.15 Aligned_cols=62 Identities=18% Similarity=0.116 Sum_probs=53.5
Q ss_pred chhHHhhhcccccchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccchhHHHHHHhhC
Q psy17761 21 PSVVWRVEVESSVFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMDSRLRAKTSR 83 (92)
Q Consensus 21 ~aIRrlar~GakRIS~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt~~~DV~~alkr~g 83 (92)
.-.-+|+..|++=-..-+..-+-++.=-|-..|+.||--|++||++.||. ++||++|+....
T Consensus 18 ~i~~iL~s~GI~eyEprVi~qlLefa~rYtt~vL~DA~vys~HA~ka~i~-~eDVrlA~~~~~ 79 (148)
T KOG3334|consen 18 VIASILKSLGIQEYEPRVINQLLEFAYRYTTTVLDDAKVYSSHAKKATID-AEDVRLAIQMRV 79 (148)
T ss_pred HHHHHHHHcCccccChHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCc-HHHHHHHHHHHh
Confidence 33457788898877777777888888889999999999999999999999 999999998754
No 24
>PLN00161 histone H3; Provisional
Probab=97.51 E-value=0.00028 Score=51.05 Aligned_cols=55 Identities=18% Similarity=0.085 Sum_probs=50.0
Q ss_pred ccchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccchhHHHHHHhhCCCCc
Q psy17761 32 SVFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMDSRLRAKTSRPHPC 87 (92)
Q Consensus 32 kRIS~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt~~~DV~~alkr~g~~~~ 87 (92)
=|+..++...+.++.|.||-++..|+...|-||+|-|+. .-|+.++.+--|..++
T Consensus 77 ~Rfq~~Al~ALQEAsEayLV~lFeda~lcaiHAkRVTlm-~kDm~La~rirg~~~~ 131 (135)
T PLN00161 77 FRWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIM-PKDMQLARRIRGPIYG 131 (135)
T ss_pred cEeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccc-hhhHHHHHHhcccccc
Confidence 488899999999999999999999999999999999999 9999999866666554
No 25
>PLN00160 histone H3; Provisional
Probab=97.37 E-value=0.00045 Score=47.37 Aligned_cols=51 Identities=18% Similarity=0.123 Sum_probs=47.0
Q ss_pred ccchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccchhHHHHHHhhC
Q psy17761 32 SVFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMDSRLRAKTSR 83 (92)
Q Consensus 32 kRIS~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt~~~DV~~alkr~g 83 (92)
=|+.+++...+.++.|.||-++..|+...|-||+|-|+. +-|+.++.+--|
T Consensus 43 ~Rfq~~Al~ALQeAsEayLv~lfed~~lca~HakRVTl~-~kD~~L~~rirg 93 (97)
T PLN00160 43 YRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTIM-PKDMQLARRIRG 93 (97)
T ss_pred cEeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcccccc-hhhHHHHHHhhc
Confidence 589999999999999999999999999999999999999 999999874433
No 26
>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=97.36 E-value=0.00065 Score=43.53 Aligned_cols=51 Identities=16% Similarity=0.124 Sum_probs=43.0
Q ss_pred cccchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccchhHHHHHHhh
Q psy17761 31 SSVFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMDSRLRAKTS 82 (92)
Q Consensus 31 akRIS~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt~~~DV~~alkr~ 82 (92)
-..+-+++.+-+-++..+|+++|+..|+.+|+|-+=.|+. ..||.+.|+|.
T Consensus 15 ~~~ld~~vee~Ll~laddFv~~v~~~ac~lAKhR~s~tle-~~Dv~~~Ler~ 65 (68)
T PF03847_consen 15 NEKLDPDVEELLLELADDFVDDVVSFACRLAKHRKSSTLE-VKDVQLHLERN 65 (68)
T ss_dssp S----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE--HHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCC-HHHHHHHHHhh
Confidence 5678899999999999999999999999999999999999 99999999984
No 27
>COG5094 TAF9 Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=97.35 E-value=0.00073 Score=49.11 Aligned_cols=67 Identities=22% Similarity=0.229 Sum_probs=56.0
Q ss_pred CCCCCchhH----HhhhcccccchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccc--cchhHHHHHHhh
Q psy17761 16 PVSGPPSVV----WRVEVESSVFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGH--QRMDSRLRAKTS 82 (92)
Q Consensus 16 ~v~~~~aIR----rlar~GakRIS~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt--~~~DV~~alkr~ 82 (92)
-||||-++| +|+..|++--+..+--.+-+..-.|-.++++||.-|++|+||-.+. .++||.+|+..+
T Consensus 10 sv~gPrDvrlihliL~Slgi~~ye~~VplQLl~FAhRYTq~vl~Dalvya~htgrg~~a~l~veDvrLA~at~ 82 (145)
T COG5094 10 SVSGPRDVRLIHLILRSLGIEEYEPKVPLQLLEFAHRYTQDVLEDALVYAKHTGRGHIATLGVEDVRLALATK 82 (145)
T ss_pred cccCCcchhHHHHHHHhcCchhhCccchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHHHHHHH
Confidence 388988887 4577788888888877888888889999999999999999997666 159999999763
No 28
>PTZ00018 histone H3; Provisional
Probab=97.22 E-value=0.00076 Score=48.74 Aligned_cols=50 Identities=20% Similarity=0.129 Sum_probs=46.6
Q ss_pred cchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccchhHHHHHHhhC
Q psy17761 33 VFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMDSRLRAKTSR 83 (92)
Q Consensus 33 RIS~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt~~~DV~~alkr~g 83 (92)
|+..++.+.+.++.|.||-.+..|+...|-||+|-|+. .-|+.++.+--|
T Consensus 84 rf~~~al~aLQeaaE~yLv~lfed~~lca~HakRVTl~-~kD~~L~~rirg 133 (136)
T PTZ00018 84 RFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIM-PKDIQLARRIRG 133 (136)
T ss_pred eeeHHHHHHHHHHHHHHHHHHhhhhHHHHHhhcceecc-hhhHHHHHHhcc
Confidence 88999999999999999999999999999999999999 999999975444
No 29
>PLN00121 histone H3; Provisional
Probab=97.17 E-value=0.00093 Score=48.27 Aligned_cols=50 Identities=20% Similarity=0.129 Sum_probs=46.5
Q ss_pred cchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccchhHHHHHHhhC
Q psy17761 33 VFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMDSRLRAKTSR 83 (92)
Q Consensus 33 RIS~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt~~~DV~~alkr~g 83 (92)
|+..++...+.++.|.||-++..|+...|-||+|-|+. +-|+.++.+--|
T Consensus 84 Rf~~~Al~ALQeaaE~yLv~lfed~~lca~HakRVTl~-~kD~~L~~rirg 133 (136)
T PLN00121 84 RFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIM-PKDIQLARRIRG 133 (136)
T ss_pred eeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcceecc-hhhHHHHHHhcc
Confidence 89999999999999999999999999999999999999 999999984444
No 30
>KOG2549|consensus
Probab=97.08 E-value=0.0017 Score=55.88 Aligned_cols=66 Identities=15% Similarity=0.096 Sum_probs=60.0
Q ss_pred CchhHHhhhc-ccccchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccchhHHHHHHhhCCCC
Q psy17761 20 PPSVVWRVEV-ESSVFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMDSRLRAKTSRPHP 86 (92)
Q Consensus 20 ~~aIRrlar~-GakRIS~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt~~~DV~~alkr~g~~~ 86 (92)
+-+++-+|.. |.+=|+.++-..+..-++..+++|++||.++..|++|.+.+ .+||.+||+-.+.-|
T Consensus 14 ~Es~k~vAEslGi~nl~deaa~~La~dv~yrikEI~Q~aaKfm~hskR~kLt-v~DV~~ALr~~nVep 80 (576)
T KOG2549|consen 14 KESVKVVAESLGITNLNDEAALLLAEDVEYRIKEIVQDAAKFMVHSKRTKLT-VDDVDYALRSLNVEP 80 (576)
T ss_pred HHHHHHHHHHhCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcCc-HHHHHHHHhhccccc
Confidence 5677888887 89999999999999999999999999999999999999999 999999998765443
No 31
>KOG4336|consensus
Probab=96.95 E-value=0.0027 Score=51.45 Aligned_cols=62 Identities=13% Similarity=0.040 Sum_probs=57.1
Q ss_pred HhhhcccccchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccchhHHHHHHhhCCCCc
Q psy17761 25 WRVEVESSVFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMDSRLRAKTSRPHPC 87 (92)
Q Consensus 25 rlar~GakRIS~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt~~~DV~~alkr~g~~~~ 87 (92)
.|+..|..=||..+-+++.+.+..|+.+|.|.+-.||+|+||--.+ .-||.+.|.++|.+=-
T Consensus 14 Ll~~~gfd~is~~aletlvell~~yi~eigrq~~n~celagRT~pT-~~Dv~l~Li~mnI~v~ 75 (323)
T KOG4336|consen 14 LLKTKGFDSISNAALETLVELLQSYIREIGRQLHNYCELAGRTIPT-QGDVKLTLIEMNIKVS 75 (323)
T ss_pred HHHHhCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCc-HHHHHHHHHHhCCChh
Confidence 5677798899999999999999999999999999999999999888 9999999999997643
No 32
>PF02269 TFIID-18kDa: Transcription initiation factor IID, 18kD subunit; InterPro: IPR003195 This family includes the Spt3 yeast transcription factors and the 18 kDa subunit from human transcription initiation factor IID (TFIID-18). Determination of the crystal structure reveals an atypical histone fold [].; GO: 0006366 transcription from RNA polymerase II promoter; PDB: 1BH9_A 1BH8_A.
Probab=96.83 E-value=0.0017 Score=43.40 Aligned_cols=52 Identities=4% Similarity=-0.026 Sum_probs=22.9
Q ss_pred cccchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccchhHHHHHHhhC
Q psy17761 31 SSVFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMDSRLRAKTSR 83 (92)
Q Consensus 31 akRIS~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt~~~DV~~alkr~g 83 (92)
++.-+.+...-+-+++.+|+.+++..|..+|...|+++++ .+|+.+++++-.
T Consensus 17 ~~~P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~rg~~~i~-~eDl~F~lR~D~ 68 (93)
T PF02269_consen 17 VEEPLPETVDLVEDIVREYIIELCQEAMEVAQRRGSKKIK-VEDLLFLLRKDP 68 (93)
T ss_dssp -SS--HHHHHHHHHHHHHHHHHHHHHHHC------------------------
T ss_pred CCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCcCc-HHHHHHHHhcCH
Confidence 6666777777888889999999999999999999999999 999999997643
No 33
>KOG1142|consensus
Probab=96.74 E-value=0.0023 Score=50.50 Aligned_cols=66 Identities=12% Similarity=0.133 Sum_probs=55.2
Q ss_pred CCCCCchhHHhhhc--ccccchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccchhHHHHHHhh
Q psy17761 16 PVSGPPSVVWRVEV--ESSVFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMDSRLRAKTS 82 (92)
Q Consensus 16 ~v~~~~aIRrlar~--GakRIS~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt~~~DV~~alkr~ 82 (92)
|+.++.-+.-|.+. |-+-|-+++-+-|-++..+|++.|+.-++.+|+|.+-.||. +-||.+.|||-
T Consensus 153 ~il~k~kl~dLvqqId~~~~LD~dVedlLleiADdFV~sii~~sC~LAKHRKsdtlE-vrDIqLhLEr~ 220 (258)
T KOG1142|consen 153 PILSKRKLDDLVQQIDGTTKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHRKSDTVE-VRDIQLHLERN 220 (258)
T ss_pred ccccccchhHHHHhhcCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccc-hhheeeeeecc
Confidence 34445555555554 45677888999999999999999999999999999999999 99999999983
No 34
>smart00427 H2B Histone H2B.
Probab=96.41 E-value=0.012 Score=39.97 Aligned_cols=49 Identities=10% Similarity=0.114 Sum_probs=45.3
Q ss_pred ccchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccchhHHHHHHh
Q psy17761 32 SVFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMDSRLRAKT 81 (92)
Q Consensus 32 kRIS~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt~~~DV~~alkr 81 (92)
..||..+..-+...+.+.+|.|+.+|...+...+|+|++ ..+|..|.+-
T Consensus 18 ~giS~kam~imnSfvnDiferIa~EAs~L~~~nkr~Tlt-sreIqtAvrl 66 (89)
T smart00427 18 TGISSKAMSIMNSFVNDIFERIAAEASKLARYNKKSTLS-SREIQTAVRL 66 (89)
T ss_pred ccccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCC-HHHHHHHHHH
Confidence 478999999999999999999999999999999999999 9999988753
No 35
>smart00414 H2A Histone 2A.
Probab=96.26 E-value=0.012 Score=40.63 Aligned_cols=58 Identities=12% Similarity=0.016 Sum_probs=50.3
Q ss_pred hHHhhhcc--cccchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccchhHHHHHHh
Q psy17761 23 VVWRVEVE--SSVFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMDSRLRAKT 81 (92)
Q Consensus 23 IRrlar~G--akRIS~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt~~~DV~~alkr 81 (92)
|.++-+.| ++|||+.+..-+..+||.+..+|+.-|..++...+++-|+ +.++.+|...
T Consensus 15 i~r~Lk~~~~~~Rv~~~A~VyLaAvLEYLtaEILeLagn~a~~~k~~rIt-p~hi~lAi~n 74 (106)
T smart00414 15 IHRLLRKGTYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKRRIT-PRHLQLAIRN 74 (106)
T ss_pred HHHHHHcCccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccc-hHHHhhhccC
Confidence 44444554 9999999888899999999999999999999999999999 9999988743
No 36
>PLN00158 histone H2B; Provisional
Probab=95.51 E-value=0.045 Score=38.84 Aligned_cols=49 Identities=10% Similarity=0.116 Sum_probs=44.3
Q ss_pred ccchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccchhHHHHHHh
Q psy17761 32 SVFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMDSRLRAKT 81 (92)
Q Consensus 32 kRIS~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt~~~DV~~alkr 81 (92)
-.||..++.-+...+.+.+|.|+.+|...+.+.+|+|++ ..+|..|.+-
T Consensus 44 ~gIS~kaM~ImnSfvnDiferIA~EAs~La~~nkr~Tlt-srEIqtAvrL 92 (116)
T PLN00158 44 TGISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVT-SREIQTAVRL 92 (116)
T ss_pred CCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCC-HHHHHHHHHH
Confidence 367888888899999999999999999999999999999 9999888753
No 37
>PTZ00463 histone H2B; Provisional
Probab=95.32 E-value=0.054 Score=38.49 Aligned_cols=49 Identities=10% Similarity=0.062 Sum_probs=44.4
Q ss_pred ccchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccchhHHHHHHh
Q psy17761 32 SVFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMDSRLRAKT 81 (92)
Q Consensus 32 kRIS~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt~~~DV~~alkr 81 (92)
..||..++.-+...+.+.+|.|+.+|...+.+.+|+|++ ..||..|.+-
T Consensus 45 ~gIS~kaM~ImnSfvnDifErIA~EAs~La~~nkr~Tlt-srEIQtAvrL 93 (117)
T PTZ00463 45 TGISRKSMNIMNSFLVDTFEKIATEASRLCKYTRRDTLS-SREIQTAIRL 93 (117)
T ss_pred CCccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCC-HHHHHHHHhh
Confidence 368888888999999999999999999999999999999 9999888753
No 38
>KOG0870|consensus
Probab=95.17 E-value=0.062 Score=40.37 Aligned_cols=60 Identities=10% Similarity=-0.068 Sum_probs=50.7
Q ss_pred hHHhhhcc-c---ccchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccchhHHHHHHhhC
Q psy17761 23 VVWRVEVE-S---SVFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMDSRLRAKTSR 83 (92)
Q Consensus 23 IRrlar~G-a---kRIS~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt~~~DV~~alkr~g 83 (92)
|+||.+.- - -=||.++-..+......|+-.+.--|-..|.-++|||++ +.||+-||...+
T Consensus 16 I~rlvke~l~E~~vsisKeA~~Ai~raAtVFv~~Lts~s~e~A~~q~rKt~s-adDVl~aL~Eie 79 (172)
T KOG0870|consen 16 ITRLVKEVLPESNVSISKEARLAIARAATVFVIFLTSVSNEIAKDQKRKTIS-ADDVLKALDEIE 79 (172)
T ss_pred HHHHHHHhCccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccc-HHHHHHHHHHhc
Confidence 45555543 2 347888889999999999999999999999999999999 999999998876
No 39
>PTZ00017 histone H2A; Provisional
Probab=95.16 E-value=0.045 Score=39.55 Aligned_cols=57 Identities=12% Similarity=0.012 Sum_probs=50.5
Q ss_pred hHHhhhcc--cccchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccchhHHHHHH
Q psy17761 23 VVWRVEVE--SSVFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMDSRLRAK 80 (92)
Q Consensus 23 IRrlar~G--akRIS~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt~~~DV~~alk 80 (92)
|.++-+.| ++||++.+..-+..+||.+..+|+.-|..++...+++-|+ +.++.+|+.
T Consensus 33 i~R~Lk~g~~a~RV~a~A~VYLAAVLEYLtaEILELAgNaa~d~kk~RIt-PrHi~lAI~ 91 (134)
T PTZ00017 33 VHRYLKKGRYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAAKDNKKKRIT-PRHIQLAIR 91 (134)
T ss_pred HHHHHhccchhccccccchhhhHHHHHHHHHHHHHHHHHHHHhcCCCeec-HHHHHhhcc
Confidence 55555555 9999998888899999999999999999999999999999 999999874
No 40
>PLN00157 histone H2A; Provisional
Probab=94.30 E-value=0.092 Score=37.87 Aligned_cols=58 Identities=12% Similarity=0.040 Sum_probs=50.9
Q ss_pred hhHHhhhcc--cccchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccchhHHHHHH
Q psy17761 22 SVVWRVEVE--SSVFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMDSRLRAK 80 (92)
Q Consensus 22 aIRrlar~G--akRIS~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt~~~DV~~alk 80 (92)
=|.++-+.| ++|||+.+-.-+..+||....+|+.-|...+...+++-|+ +.++.+|+.
T Consensus 31 Ri~R~Lk~g~~a~RIg~~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RIt-PrHi~lAI~ 90 (132)
T PLN00157 31 RIARYLKAGKYATRVGAGAPVYLAAVLEYLAAEVLELAGNAARDNKKSRIV-PRHIQLAVR 90 (132)
T ss_pred HHHHHHhcCchhhhcCCCcHhHHHHHHHHHHHHHHHHHHHHHHhcCCcccc-HHHHhhccc
Confidence 455666666 9999999888899999999999999999999999999999 999888874
No 41
>KOG1745|consensus
Probab=93.59 E-value=0.061 Score=39.11 Aligned_cols=52 Identities=19% Similarity=0.146 Sum_probs=48.1
Q ss_pred cchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccchhHHHHHHhhCCC
Q psy17761 33 VFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMDSRLRAKTSRPH 85 (92)
Q Consensus 33 RIS~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt~~~DV~~alkr~g~~ 85 (92)
|+-+++...+.++.|.||-.+-.|+--.|-||+|-||. +-|+-+|.+--|.|
T Consensus 85 rfqs~Ai~ALQeA~EayLv~LfEdtnlcAihAkRVTim-pkdiQlArrirg~~ 136 (137)
T KOG1745|consen 85 RFQSSAIAALQEAAEAYLVGLFEDTNLCAIHAKRVTIM-PKDIQLARRIRGER 136 (137)
T ss_pred eehHHHHHHHHHHHHHHHHHhccccchhhhccceeEec-ccceehhhhcccCC
Confidence 88899999999999999999999999999999999999 99999998765543
No 42
>cd07978 TAF13 The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Several hy
Probab=93.47 E-value=0.33 Score=32.59 Aligned_cols=49 Identities=6% Similarity=-0.052 Sum_probs=39.1
Q ss_pred cccchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccchhHHHHHHh
Q psy17761 31 SSVFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMDSRLRAKT 81 (92)
Q Consensus 31 akRIS~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt~~~DV~~alkr 81 (92)
+..=+.+...-+-+++.+|+.+++..|...|. .+|.=++ .+|+.+++++
T Consensus 18 ~~~P~~eTv~llE~iv~~~i~~l~~~a~~~A~-~r~~k~~-~eD~~FliR~ 66 (92)
T cd07978 18 VQNPLPETVDLLEDIVVEYIIELCHKAAEVAQ-RRRGKVK-VEDLIFLLRK 66 (92)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-cCCCCCC-HHHHHHHHhc
Confidence 55556666677778888999999999999998 5555568 9999999954
No 43
>PLN00156 histone H2AX; Provisional
Probab=93.47 E-value=0.2 Score=36.44 Aligned_cols=65 Identities=17% Similarity=0.135 Sum_probs=52.9
Q ss_pred CccCCCCCCchhHHhhhcc--cccchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccchhHHHHHH
Q psy17761 12 GLRTPVSGPPSVVWRVEVE--SSVFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMDSRLRAK 80 (92)
Q Consensus 12 g~~~~v~~~~aIRrlar~G--akRIS~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt~~~DV~~alk 80 (92)
||--||+ =|.++-+.| ++||++.+..-+..+||....+|+.-|..-+...+++-|+ +..+.+|.+
T Consensus 27 gL~FPVg---Ri~R~Lk~g~ya~RVga~ApVYLAAVLEYLtaEVLELAgNaa~d~kk~RIt-PrHi~lAIr 93 (139)
T PLN00156 27 GLQFPVG---RIARFLKAGKYAERVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIV-PRHIQLAVR 93 (139)
T ss_pred CcccchH---HHHHHHhcCChhhccCCccHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCc-HHHHHhhcc
Confidence 4555532 244444555 9999999888899999999999999999999999999999 999888874
No 44
>PLN00153 histone H2A; Provisional
Probab=93.44 E-value=0.19 Score=36.12 Aligned_cols=65 Identities=17% Similarity=0.121 Sum_probs=53.2
Q ss_pred CccCCCCCCchhHHhhhcc--cccchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccchhHHHHHH
Q psy17761 12 GLRTPVSGPPSVVWRVEVE--SSVFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMDSRLRAK 80 (92)
Q Consensus 12 g~~~~v~~~~aIRrlar~G--akRIS~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt~~~DV~~alk 80 (92)
||--|| +=|.++-+.| ++||++.+-.-+..+||....+|+.-|...+...+++-|+ +..+.+|.+
T Consensus 22 gL~FpV---gRi~R~Lr~g~~a~Rvga~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RIt-PrHi~lAI~ 88 (129)
T PLN00153 22 GLQFPV---GRIARYLKKGKYAERIGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKNRIV-PRHIQLAIR 88 (129)
T ss_pred Ccccch---HHHHHHHhcCchhhccCCCchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccC-hHHHHhhcc
Confidence 455553 2355555665 9999998888899999999999999999999999999999 998888874
No 45
>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=93.10 E-value=0.25 Score=41.23 Aligned_cols=64 Identities=16% Similarity=0.068 Sum_probs=55.3
Q ss_pred hhHHhhhc-ccccchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccchhHHHHHHhhCCCC
Q psy17761 22 SVVWRVEV-ESSVFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMDSRLRAKTSRPHP 86 (92)
Q Consensus 22 aIRrlar~-GakRIS~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt~~~DV~~alkr~g~~~ 86 (92)
.+.-.|.. |..-|..|+...+.-=+|..+.+|+.+|+.+--|.+|.-.+ ..||-+||+..+-.|
T Consensus 10 t~KdvAeslGi~Ni~Dd~l~alamDlEYRI~ev~qea~KFmvhSKRtvLt-~dDis~ALr~lNVeP 74 (450)
T COG5095 10 TLKDVAESLGISNIDDDALRALAMDLEYRIKEVCQEASKFMVHSKRTVLT-IDDISYALRSLNVEP 74 (450)
T ss_pred HHHHHHHHcCCcccccHHHHHHHHhHHHHHHHHHHHHHHHhhcccceeee-HHhHHHHHHhcCCCc
Confidence 44445554 78889999999999999999999999999999999999888 999999998875444
No 46
>KOG3423|consensus
Probab=93.05 E-value=0.4 Score=36.22 Aligned_cols=61 Identities=5% Similarity=-0.068 Sum_probs=47.0
Q ss_pred HhhhcccccchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcC-------------CcccccchhHHHHHHhhCCC
Q psy17761 25 WRVEVESSVFAGLIYEETRGVLKVVLENVIRDAVTYPRHAK-------------RQTGHQRMDSRLRAKTSRPH 85 (92)
Q Consensus 25 rlar~GakRIS~~iy~elr~vLe~fle~IirdavtyaeHA~-------------RKTVt~~~DV~~alkr~g~~ 85 (92)
.|.++|+.-.-.-+..-+.-+-..|+.+|+.||..|++-.. ||.+-+.+|..-||+..|.|
T Consensus 95 yL~~aGf~~~D~rv~RLvsLaAQKfvSDIa~DA~Q~~k~r~~~~~~~~k~~~kdkK~tLtmeDL~~AL~EyGin 168 (176)
T KOG3423|consen 95 YLKKAGFQTSDPRVKRLVSLAAQKFVSDIANDALQHSKIRTKTAIGKDKKQAKDKKYTLTMEDLSPALAEYGIN 168 (176)
T ss_pred HHHhcCCCcCcHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccccccccccccceeeeHHHHHHHHHHhCcc
Confidence 58899976555555555666778999999999999987543 34333499999999999976
No 47
>KOG0871|consensus
Probab=92.36 E-value=0.37 Score=35.79 Aligned_cols=70 Identities=10% Similarity=-0.110 Sum_probs=59.0
Q ss_pred CCCC-chhHHhhhcccc---cchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccchhHHHHHHhhCCCCc
Q psy17761 17 VSGP-PSVVWRVEVESS---VFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMDSRLRAKTSRPHPC 87 (92)
Q Consensus 17 v~~~-~aIRrlar~Gak---RIS~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt~~~DV~~alkr~g~~~~ 87 (92)
+++| ..|-.+.+--.. ||..++-+-+...--+|+--|..+|-..|+-..+|||. .+-|.-||+.+|.+-+
T Consensus 11 ~sLPkAtv~KmIke~lP~d~rvakeareliincCvEFI~liSsEAneic~~e~KKTIa-~EHV~KALe~LgF~eY 84 (156)
T KOG0871|consen 11 LSLPKATVNKMIKEMLPKDVRVAKEARELIINCCVEFINLISSEANEICNKEAKKTIA-PEHVIKALENLGFGEY 84 (156)
T ss_pred ccCcHHHHHHHHHHhCCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHhHHhcccCC-HHHHHHHHHHcchHHH
Confidence 3554 556666665432 88889999999999999999999999999999999999 9999999999997643
No 48
>PLN00154 histone H2A; Provisional
Probab=92.34 E-value=0.36 Score=35.07 Aligned_cols=58 Identities=10% Similarity=0.040 Sum_probs=50.3
Q ss_pred hhHHhhhcc---cccchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccchhHHHHHH
Q psy17761 22 SVVWRVEVE---SSVFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMDSRLRAK 80 (92)
Q Consensus 22 aIRrlar~G---akRIS~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt~~~DV~~alk 80 (92)
=|.++-+.| ..|||..+-.-+..+||....+|++-|..++...+++-|+ +.++.+|.+
T Consensus 43 Ri~r~Lk~g~~~~~RVga~ApVYLAAVLEYLtAEVLELAGNaA~d~kk~RIt-PrHi~lAIr 103 (136)
T PLN00154 43 RIHRQLKQRVSAHGRVGATAAVYTAAILEYLTAEVLELAGNASKDLKVKRIT-PRHLQLAIR 103 (136)
T ss_pred HHHHHHHhhhhhccccccchHHHHHHHHHHHHHHHHHHHHHHHHhhCCceec-HHHhhhhcc
Confidence 355556665 5799999888899999999999999999999999999999 999988874
No 49
>KOG2389|consensus
Probab=91.67 E-value=0.37 Score=39.72 Aligned_cols=49 Identities=20% Similarity=0.201 Sum_probs=44.5
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccchhHHHHHHhhCCC
Q psy17761 36 GLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMDSRLRAKTSRPH 85 (92)
Q Consensus 36 ~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt~~~DV~~alkr~g~~ 85 (92)
..+-+-|.+++..|+.++.+.|-.|+++|+|--.. .-||+.||+-++.+
T Consensus 49 ~sale~Ltd~~~qyvQ~lgk~a~~~~n~anR~epn-l~Div~Al~dls~s 97 (353)
T KOG2389|consen 49 NSALETLTDVLQQYVQNLGKTAHRYSNLANRTEPN-LFDIVLALQDLSAS 97 (353)
T ss_pred cHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCcc-HHHHHHHHHHhhhh
Confidence 34678899999999999999999999999999888 99999999988754
No 50
>KOG1744|consensus
Probab=91.60 E-value=0.61 Score=33.58 Aligned_cols=48 Identities=10% Similarity=0.075 Sum_probs=42.8
Q ss_pred cchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccchhHHHHHHh
Q psy17761 33 VFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMDSRLRAKT 81 (92)
Q Consensus 33 RIS~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt~~~DV~~alkr 81 (92)
-||..+..-++..+.+++|.|+-+|-.++++-+|.||+ ..++..+.+-
T Consensus 55 gis~~a~~vmnsf~ndife~iA~ea~rla~y~krstis-Sreiqta~rL 102 (127)
T KOG1744|consen 55 GISSKAMGVMNSFVNDIFERIASEAGRLAHYNKRSTIS-SREIQTAVRL 102 (127)
T ss_pred CcCHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCccc-HHHHHHHHHH
Confidence 37888889999999999999999999999999999999 8888877643
No 51
>PTZ00252 histone H2A; Provisional
Probab=91.49 E-value=0.55 Score=34.07 Aligned_cols=66 Identities=15% Similarity=0.059 Sum_probs=50.3
Q ss_pred CCccCCCCCCchhHHhhhcc--cccchhhHHHHHHHHHHHHHHHHHHHHHhhhhh--cCCcccccchhHHHHHH
Q psy17761 11 HGLRTPVSGPPSVVWRVEVE--SSVFAGLIYEETRGVLKVVLENVIRDAVTYPRH--AKRQTGHQRMDSRLRAK 80 (92)
Q Consensus 11 hg~~~~v~~~~aIRrlar~G--akRIS~~iy~elr~vLe~fle~IirdavtyaeH--A~RKTVt~~~DV~~alk 80 (92)
=||-.||+ =|.++-+.| ++||++.+-.-+..+||....+|+.-|..-+.. .+++-|+ +..+.+|.+
T Consensus 22 AGL~FPVg---Ri~R~Lr~g~ya~RIga~ApVYLAAVLEYLtaEVLELAgnaa~d~~~kk~RIt-PrHi~lAIr 91 (134)
T PTZ00252 22 AGLIFPVG---RVGSLLRRGQYARRIGASGAVYMAAVLEYLTAELLELSVKAAAQQAKKPKRLT-PRTVTLAVR 91 (134)
T ss_pred cCccCchH---HHHHHHHcCCcccccCCccHHHHHHHHHHHHHHHHHHHHHHHHhccCCccccc-HHHHHhhcc
Confidence 35666642 244444555 999998877779999999999999999998854 4667788 888888874
No 52
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=89.30 E-value=0.59 Score=37.09 Aligned_cols=60 Identities=13% Similarity=0.095 Sum_probs=53.4
Q ss_pred hhHHhhhc--ccccchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccchhHHHHHHhh
Q psy17761 22 SVVWRVEV--ESSVFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMDSRLRAKTS 82 (92)
Q Consensus 22 aIRrlar~--GakRIS~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt~~~DV~~alkr~ 82 (92)
-|+++-+- +||=||+.+---..++-|.|++++--.|-..||..+|.|.. .+|+-.|+++.
T Consensus 114 RIkkvMKtdedVkMisaEaPvlFak~~EiFI~ELTmRAW~~ae~NkRRtLQ-ksDia~Av~kS 175 (286)
T COG5208 114 RIKKVMKTDEDVKMISAEAPVLFAKITEIFIEELTMRAWINAEENKRRTLQ-KSDIAAAVKKS 175 (286)
T ss_pred HHHHHHhcccchhheecccchHHHHHHHHHHHHHHHHHHHHHhHhhhhHHH-HHHHHHHHHHH
Confidence 35555555 49999999988899999999999999999999999999999 99999999885
No 53
>KOG1756|consensus
Probab=87.83 E-value=1.7 Score=31.56 Aligned_cols=66 Identities=15% Similarity=0.106 Sum_probs=53.8
Q ss_pred CCccCCCCCCchhHHhhhcc--cccchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccchhHHHHHH
Q psy17761 11 HGLRTPVSGPPSVVWRVEVE--SSVFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMDSRLRAK 80 (92)
Q Consensus 11 hg~~~~v~~~~aIRrlar~G--akRIS~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt~~~DV~~alk 80 (92)
-||-.||+ .|-++-+.| +.|||.++-.-+..+|+....+|..-|-..+.-.+++-|+ +.-+.+|+.
T Consensus 24 agl~fPvg---ri~r~Lr~~~~~~ri~~gapV~laavLeYL~Aeile~agnaardnkk~ri~-PrH~~lAI~ 91 (131)
T KOG1756|consen 24 AGLQFPVG---RIHRLLRKGRYAQRVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIT-PRHLQLAIR 91 (131)
T ss_pred cccccCHH---HHHHHHHccchhhhccCCChHHHHHHHHHHHHHHHHHhHHHhhhcCccccC-hHHHHHHHh
Confidence 35666744 565665656 9999999888899999999899999888888888888899 888888875
No 54
>KOG1657|consensus
Probab=87.72 E-value=1 Score=34.97 Aligned_cols=61 Identities=10% Similarity=0.022 Sum_probs=56.0
Q ss_pred chhHHhhhcc--cccchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccchhHHHHHHhh
Q psy17761 21 PSVVWRVEVE--SSVFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMDSRLRAKTS 82 (92)
Q Consensus 21 ~aIRrlar~G--akRIS~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt~~~DV~~alkr~ 82 (92)
..|+++.+.- +.-|+.++---+.++.|.|++.+--.+-.+|+-.+|+|+. ..|+--++.+.
T Consensus 78 aRiKkimK~dedv~mI~~Eapvl~aka~E~Fi~elt~~sw~~Tee~~rrtl~-~sdia~av~~s 140 (236)
T KOG1657|consen 78 ARIKKIMKSDEDVSMITAEAPVLFAKACELFITELTLRSWVHTEENKRRTLQ-KSDIAAAVTQS 140 (236)
T ss_pred hhccccccccccccccchhHHHHHHHHHHHHHHHHHHHhhhhhcccccccch-HHHHHHHhccC
Confidence 6788888885 9999999999999999999999999999999999999999 99999888765
No 55
>cd08045 TAF4 TATA Binding Protein (TBP) Associated Factor 4 (TAF4) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 4 (TAF4) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryote. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypotheses are
Probab=84.89 E-value=4.3 Score=30.17 Aligned_cols=57 Identities=11% Similarity=0.040 Sum_probs=44.6
Q ss_pred HHhhhcccccchhhHHHHHHHHHHHHHHHHHHHHHhhhhhc------CCcccccchhHHHHHHh
Q psy17761 24 VWRVEVESSVFAGLIYEETRGVLKVVLENVIRDAVTYPRHA------KRQTGHQRMDSRLRAKT 81 (92)
Q Consensus 24 Rrlar~GakRIS~~iy~elr~vLe~fle~IirdavtyaeHA------~RKTVt~~~DV~~alkr 81 (92)
++.+..|.+-|++++++-+-.+++.+|..|+.+++..++|- ...++- .+||.--|+.
T Consensus 56 ~i~~~~g~~~~~~d~~~lis~a~e~rlr~li~k~~~~s~hR~~~~~~~~r~~~-~sdvr~qL~~ 118 (212)
T cd08045 56 KIAKKHGLKEVDEDVLDLISLALEERLRNLLEKLIEVSEHRVDSEKEDERYEI-TSDVRKQLRF 118 (212)
T ss_pred HHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCceee-cchHHHHHHH
Confidence 44555577799999999999999999999999999999994 223444 5677665544
No 56
>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=83.62 E-value=6.3 Score=26.07 Aligned_cols=62 Identities=8% Similarity=0.050 Sum_probs=51.5
Q ss_pred CchhHHhhhcc-cccchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCC---cccccchhHHHHHHhh
Q psy17761 20 PPSVVWRVEVE-SSVFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKR---QTGHQRMDSRLRAKTS 82 (92)
Q Consensus 20 ~~aIRrlar~G-akRIS~~iy~elr~vLe~fle~IirdavtyaeHA~R---KTVt~~~DV~~alkr~ 82 (92)
++.|+++...= -..+|.++...+.++.|.|+-+|+..|.+..+.-+. +=+. +..+..|.+++
T Consensus 19 k~~iKr~~~~~~~~~v~~~v~i~v~glaKvFVGeivE~A~~V~~~~~~~~~~Pl~-P~HireA~rrl 84 (85)
T cd08048 19 KAAIKRLIQSVTGQSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGEANTGPLQ-PRHLREAYRRL 84 (85)
T ss_pred HHHHHHHHHHHcCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCCCCC-cHHHHHHHHHh
Confidence 46788887763 478999999999999999999999999988877554 5666 88888888775
No 57
>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=83.08 E-value=2.4 Score=27.35 Aligned_cols=48 Identities=4% Similarity=-0.042 Sum_probs=38.5
Q ss_pred cccchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcc-cccchhHHHHH
Q psy17761 31 SSVFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKRQT-GHQRMDSRLRA 79 (92)
Q Consensus 31 akRIS~~iy~elr~vLe~fle~IirdavtyaeHA~RKT-Vt~~~DV~~al 79 (92)
-.|||+++-.-+.++++.|..+-+.-|+.-++-.+-.+ |. .+|+.-.+
T Consensus 17 ~tkIs~dal~l~~eyl~iFV~EAv~Ra~~~a~~e~~~~~le-~e~LEki~ 65 (72)
T PF09415_consen 17 KTKISKDALKLSAEYLRIFVREAVARAAEQAEAEGDEGFLE-VEHLEKIL 65 (72)
T ss_dssp T-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSEE--HHHHHHHC
T ss_pred CCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCC-HHHHHHHH
Confidence 56999999999999999999999999998888888888 88 88876543
No 58
>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=82.31 E-value=4.6 Score=24.79 Aligned_cols=39 Identities=8% Similarity=0.033 Sum_probs=27.8
Q ss_pred HhhhcccccchhhHHHHHHHHHHHHHHHHHHHHHhhhhh
Q psy17761 25 WRVEVESSVFAGLIYEETRGVLKVVLENVIRDAVTYPRH 63 (92)
Q Consensus 25 rlar~GakRIS~~iy~elr~vLe~fle~IirdavtyaeH 63 (92)
.|.++|++=--.-+..-+.-+...|+++|+.||..|++.
T Consensus 11 yL~~~G~~~~D~rv~RLvSLaaQKFisdI~~dA~q~~k~ 49 (51)
T PF03540_consen 11 YLERSGFQTSDPRVKRLVSLAAQKFISDIANDAMQYCKI 49 (51)
T ss_pred HHHHCCCCCCCHhHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 577778553233344445666789999999999999875
No 59
>KOG1659|consensus
Probab=81.01 E-value=5.1 Score=31.37 Aligned_cols=57 Identities=11% Similarity=0.099 Sum_probs=46.8
Q ss_pred hHHhhhcc--cccchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccchhHHHHHH
Q psy17761 23 VVWRVEVE--SSVFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMDSRLRAK 80 (92)
Q Consensus 23 IRrlar~G--akRIS~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt~~~DV~~alk 80 (92)
|.++-..- +-+|+..+-.-+-++||-|++.++..+...|.--+-|||+ ++=++.+..
T Consensus 19 iKKIMQ~dEdIGKvaqavPViisralElFl~~l~~~t~~~t~~~~aKt~s-~~hlkq~v~ 77 (224)
T KOG1659|consen 19 IKKIMQSDEDIGKVAQAVPVIISRALELFLESLLQKTLEITRSRGAKTVS-SSHLKQAVE 77 (224)
T ss_pred HHHHHhhhhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhcCccccC-HHHHHHHHh
Confidence 44444443 7788888888899999999999999999999999999999 877666653
No 60
>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=75.96 E-value=4.4 Score=30.97 Aligned_cols=54 Identities=20% Similarity=0.209 Sum_probs=26.6
Q ss_pred hhcccccchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccc------cchhHHHHHHh
Q psy17761 27 VEVESSVFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGH------QRMDSRLRAKT 81 (92)
Q Consensus 27 ar~GakRIS~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt------~~~DV~~alkr 81 (92)
.+.|..-+.+|+++-+--+.+.+|.+||.+++..++| ++.+.. ..+||.-.|+.
T Consensus 58 ~~~g~~~~~~d~l~llS~A~e~rLr~lie~~~~~s~h-R~~~~~~~~~~~~~sdv~~qlr~ 117 (264)
T PF05236_consen 58 KKHGLKSVDEDVLELLSLATEERLRNLIEKAIVLSRH-RRDSSKSDPRYEIRSDVRKQLRF 117 (264)
T ss_dssp HCTT--EE-TCHHHHHHHHHHHHHHHHHHHHH-----------------------------
T ss_pred HHcCCcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHh-hhcccCCCcccccchHHHHHHHH
Confidence 3446889999999999999999999999999999999 344332 25566555543
No 61
>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=73.54 E-value=12 Score=25.14 Aligned_cols=61 Identities=8% Similarity=0.046 Sum_probs=43.4
Q ss_pred CchhHHhhhcc--cccchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCc-ccccchhHHHHHHh
Q psy17761 20 PPSVVWRVEVE--SSVFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKRQ-TGHQRMDSRLRAKT 81 (92)
Q Consensus 20 ~~aIRrlar~G--akRIS~~iy~elr~vLe~fle~IirdavtyaeHA~RK-TVt~~~DV~~alkr 81 (92)
++.|++|.+.- -.-||..+--.+.++-|.|+-+|+..|.+..+.-+-. -+. +..+..|.+|
T Consensus 26 k~~ikkli~~~~~~qsv~~~v~i~v~g~aKvFVGEiVE~A~~Vq~~~~~~~pl~-P~hlreA~rr 89 (90)
T PF04719_consen 26 KAAIKKLINQVLGNQSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGETGPLQ-PDHLREAYRR 89 (90)
T ss_dssp HHHHHHHHHHHHS-S---HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SS---HHHHHHHHHH
T ss_pred HHHHHHHHHHHcCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCC-cHHHHHHHHh
Confidence 57999999985 2588999999999999999999999998887743221 445 6667776665
No 62
>TIGR00764 lon_rel lon-related putative ATP-dependent protease. Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein.
Probab=73.45 E-value=13 Score=32.10 Aligned_cols=50 Identities=14% Similarity=-0.007 Sum_probs=39.8
Q ss_pred cccchhhHHHHHHHHHH-------------HHHHHHHHHHHhhhhhcCCcccccchhHHHHHHh
Q psy17761 31 SSVFAGLIYEETRGVLK-------------VVLENVIRDAVTYPRHAKRQTGHQRMDSRLRAKT 81 (92)
Q Consensus 31 akRIS~~iy~elr~vLe-------------~fle~IirdavtyaeHA~RKTVt~~~DV~~alkr 81 (92)
...+|.++.+++-+... .-++++++.|-.+|+..+.++|+ .+||..|++.
T Consensus 328 l~~~s~~Av~~Li~~~~R~ag~r~~lsl~~R~L~~llR~A~~iA~~~~~~~I~-~ehV~~Ai~~ 390 (608)
T TIGR00764 328 IPHFTRDAVEEIVREAQRRAGRKDHLTLRLRELGGLVRAAGDIAKSSGKVYVT-AEHVLKAKKL 390 (608)
T ss_pred CCcCCHHHHHHHHHHHHHHHhcccccCCCHHHHHHHHHHHHHHHHhcCCceec-HHHHHHHHHH
Confidence 56788888877754433 45678999998889888999999 9999988764
No 63
>KOG3901|consensus
Probab=73.33 E-value=9.5 Score=26.91 Aligned_cols=43 Identities=16% Similarity=0.165 Sum_probs=27.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhhhcC-CcccccchhHHHHHHhh
Q psy17761 39 YEETRGVLKVVLENVIRDAVTYPRHAK-RQTGHQRMDSRLRAKTS 82 (92)
Q Consensus 39 y~elr~vLe~fle~IirdavtyaeHA~-RKTVt~~~DV~~alkr~ 82 (92)
|.++.++|+++.-+-+.+...-|.-+| |--+. .+|+.|+|++-
T Consensus 29 ~~~tv~~Le~iV~~Yi~elt~~a~~~g~rgk~~-veD~~f~lRkD 72 (109)
T KOG3901|consen 29 YPETVDLLEDIVLEYITELTHAAMEIGKRGKVK-VEDFKFLLRKD 72 (109)
T ss_pred cHhHHHHHHHHHHHHHHHHHHHHHHhcccCcee-HHHHHHHHHhC
Confidence 456666666666665555544444444 44566 99999999763
No 64
>COG5162 Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=69.65 E-value=20 Score=27.39 Aligned_cols=61 Identities=8% Similarity=-0.045 Sum_probs=45.0
Q ss_pred hhhcccccchhhHHHHHHHHHHHHHHHHHHHHHhhhhhc------------------C--------------Ccccccch
Q psy17761 26 RVEVESSVFAGLIYEETRGVLKVVLENVIRDAVTYPRHA------------------K--------------RQTGHQRM 73 (92)
Q Consensus 26 lar~GakRIS~~iy~elr~vLe~fle~IirdavtyaeHA------------------~--------------RKTVt~~~ 73 (92)
|-.+|++-.-.-+..-+.-....|..+|+.||..|.+-. | -|+|-++.
T Consensus 98 l~k~Gf~~~D~rvKkLl~L~aqKFvsDiA~dayqYsrIr~~~sna~~t~~~a~~f~~gg~~~i~~~~~~~dr~K~vltv~ 177 (197)
T COG5162 98 LEKAGFVTSDQRVKKLLSLLAQKFVSDIAVDAYQYSRIRQGSSNAKATAQKAKRFAKGGASGIGSSGRRGDRKKPVLTVV 177 (197)
T ss_pred HHhcCceeccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccchhhHHHHHHHHhcccccccccccccccCCceeeeh
Confidence 667776555555566666677899999999999885431 1 56666699
Q ss_pred hHHHHHHhhCCCC
Q psy17761 74 DSRLRAKTSRPHP 86 (92)
Q Consensus 74 DV~~alkr~g~~~ 86 (92)
|..-||...|.|-
T Consensus 178 DLs~Al~EyGini 190 (197)
T COG5162 178 DLSKALEEYGINI 190 (197)
T ss_pred HHHHHHHHhcccc
Confidence 9999999998763
No 65
>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=69.46 E-value=6.3 Score=33.18 Aligned_cols=53 Identities=15% Similarity=0.006 Sum_probs=37.2
Q ss_pred cchhhHHHHHHHHHH--HHHHHHHHHHHhhhhhcCCcccccchhHHHHHHhhCCCC
Q psy17761 33 VFAGLIYEETRGVLK--VVLENVIRDAVTYPRHAKRQTGHQRMDSRLRAKTSRPHP 86 (92)
Q Consensus 33 RIS~~iy~elr~vLe--~fle~IirdavtyaeHA~RKTVt~~~DV~~alkr~g~~~ 86 (92)
.+++++++.+...-. ..+.++++.|..++...+|++|+ .+||..++.....+|
T Consensus 282 ~is~~al~~I~~y~~n~Rel~nll~~Aa~~A~~~~~~~It-~~dI~~vl~~~~~~~ 336 (531)
T TIGR02902 282 NLEKHALELIVKYASNGREAVNIVQLAAGIALGEGRKRIL-AEDIEWVAENGNYHP 336 (531)
T ss_pred CcCHHHHHHHHHhhhhHHHHHHHHHHHHHHHhhCCCcEEc-HHHHHHHhCCccccc
Confidence 355666655443322 23456788888888888999999 999999998666555
No 66
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=66.27 E-value=18 Score=26.23 Aligned_cols=64 Identities=17% Similarity=0.064 Sum_probs=50.4
Q ss_pred CccCCCCCCchhHHhhhcc--cccchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccchhHHHHH
Q psy17761 12 GLRTPVSGPPSVVWRVEVE--SSVFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMDSRLRA 79 (92)
Q Consensus 12 g~~~~v~~~~aIRrlar~G--akRIS~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt~~~DV~~al 79 (92)
|+-.|| +-|+++-+.| ..||++++--.+..+|+....+|+.-|-..|.--+.|-|+ +--+-+|.
T Consensus 24 gl~fpv---grvkr~lk~~~~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~kkkri~-PrHlqlAI 89 (132)
T COG5262 24 GLIFPV---GRVKRLLKKGNYRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRII-PRHLQLAI 89 (132)
T ss_pred CccccH---HHHHHHHHcCccceeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhcCcceec-hHHHHHHh
Confidence 455553 3466666655 8999999999999999999999999998888888888888 66665554
No 67
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=63.04 E-value=26 Score=27.11 Aligned_cols=50 Identities=14% Similarity=0.083 Sum_probs=36.2
Q ss_pred cchhhHHHHHHHHHHH------HHHHHHHHHHhhhhhcCCcccccchhHHHHHHhhC
Q psy17761 33 VFAGLIYEETRGVLKV------VLENVIRDAVTYPRHAKRQTGHQRMDSRLRAKTSR 83 (92)
Q Consensus 33 RIS~~iy~elr~vLe~------fle~IirdavtyaeHA~RKTVt~~~DV~~alkr~g 83 (92)
-+++++.+.+.+.... ++-++++.|..+|+..++++|+ .+||..|+++..
T Consensus 228 ~~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~a~~~a~~~~~~~I~-~~~v~~a~~~~~ 283 (394)
T PRK00411 228 VVDDEVLDLIADLTAREHGDARVAIDLLRRAGLIAEREGSRKVT-EEDVRKAYEKSE 283 (394)
T ss_pred CCCHhHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCCCcC-HHHHHHHHHHHH
Confidence 3566666666555422 2335778888888888999999 999999998763
No 68
>COG5248 TAF19 Transcription initiation factor TFIID, subunit TAF13 [Transcription]
Probab=60.95 E-value=26 Score=25.13 Aligned_cols=42 Identities=10% Similarity=0.067 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccchhHHHHHHhh
Q psy17761 38 IYEETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMDSRLRAKTS 82 (92)
Q Consensus 38 iy~elr~vLe~fle~IirdavtyaeHA~RKTVt~~~DV~~alkr~ 82 (92)
..+.+-++.-.|+..+.-.|-..|. .|.-++ .+|..+||++-
T Consensus 32 t~~~L~e~V~dY~~~~ctna~~~Aq--~rnK~k-~eDfkfaLr~D 73 (126)
T COG5248 32 TAEALHEYVLDYMSILCTNAHNMAQ--VRNKTK-TEDFKFALRRD 73 (126)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH--hcccch-HHHHHHHHhhC
Confidence 3445555566666666666666665 566778 99999999873
No 69
>COG1067 LonB Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]
Probab=60.46 E-value=23 Score=31.27 Aligned_cols=57 Identities=11% Similarity=-0.097 Sum_probs=45.6
Q ss_pred Hhhhcc-cccchhhHHHHHHHHHHHHHHH-------------HHHHHHhhhhhcCCcccccchhHHHHHHhh
Q psy17761 25 WRVEVE-SSVFAGLIYEETRGVLKVVLEN-------------VIRDAVTYPRHAKRQTGHQRMDSRLRAKTS 82 (92)
Q Consensus 25 rlar~G-akRIS~~iy~elr~vLe~fle~-------------IirdavtyaeHA~RKTVt~~~DV~~alkr~ 82 (92)
.+++.| ..=++.++++++-..+..+.++ +++.|-.+|+-.+++=++ ++||..|+++.
T Consensus 329 ~v~~d~~ip~~~~~Av~~li~~a~R~Ag~~~~Ltl~~rdl~~lv~~A~~ia~~~~~~~I~-ae~Ve~a~~~~ 399 (647)
T COG1067 329 ELARDGNIPHLDKDAVEELIREAARRAGDQNKLTLRLRDLGNLVREAGDIAVSEGRKLIT-AEDVEEALQKR 399 (647)
T ss_pred HHHhcCCCCCCCHHHHHHHHHHHHHhccccceeccCHHHHHHHHHHhhHHHhcCCcccCc-HHHHHHHHHhh
Confidence 445553 6667778888888877776554 888898999999999999 99999999874
No 70
>PF13335 Mg_chelatase_2: Magnesium chelatase, subunit ChlI
Probab=57.97 E-value=35 Score=22.54 Aligned_cols=28 Identities=14% Similarity=0.005 Sum_probs=25.8
Q ss_pred HHHHHHHHhhhhhcCCcccccchhHHHHH
Q psy17761 51 ENVIRDAVTYPRHAKRQTGHQRMDSRLRA 79 (92)
Q Consensus 51 e~IirdavtyaeHA~RKTVt~~~DV~~al 79 (92)
..|++-|-|.|+-++...|+ .+||..|+
T Consensus 66 ~rilrvARTIADL~~~~~I~-~~hi~EAl 93 (96)
T PF13335_consen 66 HRILRVARTIADLEGSERIT-REHIAEAL 93 (96)
T ss_pred HHHHHHHHHHHhHcCCCCCC-HHHHHHHH
Confidence 34999999999999999999 99999887
No 71
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=56.68 E-value=19 Score=26.43 Aligned_cols=51 Identities=6% Similarity=-0.190 Sum_probs=41.3
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccchhHHHHHHhhCCCCc
Q psy17761 36 GLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMDSRLRAKTSRPHPC 87 (92)
Q Consensus 36 ~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt~~~DV~~alkr~g~~~~ 87 (92)
.++-+-+..+--+|+-.+--.|-..|+-...|||. .+-|.-||+.++.+-+
T Consensus 33 Kearei~in~cieFi~~lsseAne~ce~EaKKTIa-~EHviKALenLef~ey 83 (148)
T COG5150 33 KEAREIFINACIEFINMLSSEANEACEEEAKKTIA-YEHVIKALENLEFEEY 83 (148)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccc-HHHHHHHHHhccHHHH
Confidence 34444455555678888999999999999999999 9999999999886643
No 72
>smart00350 MCM minichromosome maintenance proteins.
Probab=53.17 E-value=17 Score=30.30 Aligned_cols=31 Identities=16% Similarity=0.128 Sum_probs=28.2
Q ss_pred HHHHHHHHHhhhhhcCCcccccchhHHHHHHh
Q psy17761 50 LENVIRDAVTYPRHAKRQTGHQRMDSRLRAKT 81 (92)
Q Consensus 50 le~IirdavtyaeHA~RKTVt~~~DV~~alkr 81 (92)
++.++|=|.++|.-..|.+|+ .+||..|.+-
T Consensus 473 l~sliRla~A~A~l~~r~~V~-~~Dv~~ai~l 503 (509)
T smart00350 473 LESIIRLSEAHAKMRLSDVVE-EADVEEAIRL 503 (509)
T ss_pred HHHHHHHHHHHHHHcCCCccC-HHHHHHHHHH
Confidence 478999999999999999999 9999998753
No 73
>PF13654 AAA_32: AAA domain; PDB: 3K1J_B.
Probab=52.61 E-value=21 Score=30.36 Aligned_cols=34 Identities=15% Similarity=0.182 Sum_probs=27.5
Q ss_pred HHHHHHHHHHhhhhhcCCcccccchhHHHHHHhhC
Q psy17761 49 VLENVIRDAVTYPRHAKRQTGHQRMDSRLRAKTSR 83 (92)
Q Consensus 49 fle~IirdavtyaeHA~RKTVt~~~DV~~alkr~g 83 (92)
.+.+++++|-.+|...+.++|+ ++||..|++...
T Consensus 474 ~l~~ll~EA~~~A~~~~~~~I~-~~~V~~Ai~~r~ 507 (509)
T PF13654_consen 474 WLADLLREANYWARKEGAKVIT-AEHVEQAIEERR 507 (509)
T ss_dssp HHHHHHHHHHHHHHHCT-SSB--HHHHHHHHHH--
T ss_pred HHHHHHHHHHHHHHHhCCCccC-HHHHHHHHHccc
Confidence 4678999999999999999999 999999998653
No 74
>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=52.00 E-value=44 Score=24.21 Aligned_cols=49 Identities=6% Similarity=0.003 Sum_probs=33.0
Q ss_pred cchhhHHHHHHHHHHH---HHHHHHHHHHhhhhhcCCcccccchhHHHHHHhh
Q psy17761 33 VFAGLIYEETRGVLKV---VLENVIRDAVTYPRHAKRQTGHQRMDSRLRAKTS 82 (92)
Q Consensus 33 RIS~~iy~elr~vLe~---fle~IirdavtyaeHA~RKTVt~~~DV~~alkr~ 82 (92)
.+|+++.+.+.+...- .+..++..+...+--.+.++|+ .+||..+++..
T Consensus 215 ~~~~~~~~~i~~~s~G~p~~i~~l~~~~~~~a~~~~~~~i~-~~~v~~~~~~~ 266 (269)
T TIGR03015 215 VFSEGAFDAIHRFSRGIPRLINILCDRLLLSAFLEEKREIG-GEEVREVIAEI 266 (269)
T ss_pred CcCHHHHHHHHHHcCCcccHHHHHHHHHHHHHHHcCCCCCC-HHHHHHHHHHh
Confidence 4666666666555543 4555666666655556778999 99999988763
No 75
>PF02579 Nitro_FeMo-Co: Dinitrogenase iron-molybdenum cofactor; InterPro: IPR003731 This entry represents several Nif (B, X and Y) proteins, which are involved in the biosynthesis of the iron-molybdenum cofactor (FeMo-co) found in the dinitrogenase enzyme of the nitrogenase complex in nitrogen-fixing bacteria. The nitrogenase complex catalyses the reduction of atmospheric dinitrogen to ammonia, and is composed of an iron metalloprotein (dinitrogenase reductase; homodimer of NifH; IPR000392 from INTERPRO) and a Fe-Mo metalloprotein (dinitrogenase; heterotetramer of NifD and NifK; IPR000318 from INTERPRO). The pathway for the synthesis of the Fe-Mo cofactor involves several proteins, including NifB, NifE, NifH, NifN, NifQ, NifV and NifX. NifB appears to be an iron-sulphur source for FeMo-co biosynthesis, while NifX may be associated with the mature FeMo-co, in particular with the addition of homocitrate during the last step of biosynthesis []. The NifX protein shows sequence similarity with the C terminus of NifB [], as well as to the conserved protein MTH1175 from the archaeon Methanobacterium thermoautotrophicum, which displays a ribonuclease H-like motif of three layers, alpha/beta/alpha, with a single mixed beta-sheet [].; PDB: 2QTD_A 2KLA_A 1EO1_A 1P90_A 1RDU_A 2YX6_D 1O13_A 1T3V_A 2RE2_B 2WFB_A.
Probab=48.33 E-value=5.5 Score=24.67 Aligned_cols=31 Identities=19% Similarity=0.182 Sum_probs=19.9
Q ss_pred CCchhHHhhhcccccchhhHHHHHHHHHHHHH
Q psy17761 19 GPPSVVWRVEVESSVFAGLIYEETRGVLKVVL 50 (92)
Q Consensus 19 ~~~aIRrlar~GakRIS~~iy~elr~vLe~fl 50 (92)
|+++.+.|.+.|++-+.. .-..+.++|+.|+
T Consensus 63 G~~~~~~L~~~gI~v~~~-~~~~i~~~l~~~~ 93 (94)
T PF02579_consen 63 GEGAFRALKEAGIKVYQG-AGGDIEEALEAYL 93 (94)
T ss_dssp CHHHHHHHHHTTSEEEES-TSSBHHHHHHHHH
T ss_pred CHHHHHHHHHCCCEEEEc-CCCCHHHHHHHHh
Confidence 357788888888776664 4444555555554
No 76
>PF12767 SAGA-Tad1: Transcriptional regulator of RNA polII, SAGA, subunit; InterPro: IPR024738 The yeast Spt-Ada-Gcn5-Acetyl (SAGA) transferase complex is a multifunctional coactivator involved in multiple cellular processes [], including regulation of transcription by RNA polymerase II [, ]. It is formed of five major modular subunits and shows a high degree of structural conservation to human TFTC and STAGA []. This entry represents Ada1 (known as Tada1 in higher eukaryotes), one of the subunits that constitute the SAGA core. It also functions as a component of the SALSA and SLIK complexes. ; GO: 0070461 SAGA-type complex
Probab=48.07 E-value=43 Score=25.35 Aligned_cols=34 Identities=18% Similarity=0.078 Sum_probs=30.2
Q ss_pred hcccccchhhHHHHHHHHHHHHHHHHHHHHHhhh
Q psy17761 28 EVESSVFAGLIYEETRGVLKVVLENVIRDAVTYP 61 (92)
Q Consensus 28 r~GakRIS~~iy~elr~vLe~fle~Iirdavtya 61 (92)
..|..-||.++.+-+.-+|+.||.+||+.+++.+
T Consensus 218 e~GL~gvs~~~a~ll~~ale~~LK~lI~s~l~~~ 251 (252)
T PF12767_consen 218 EHGLGGVSDDCANLLNLALEVHLKNLIKSCLDLV 251 (252)
T ss_pred HcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 3467789999999999999999999999998765
No 77
>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=47.55 E-value=25 Score=20.52 Aligned_cols=29 Identities=17% Similarity=0.131 Sum_probs=19.4
Q ss_pred HHHHHHHHHHH-HhhhhhcCCcccccchhHH
Q psy17761 47 KVVLENVIRDA-VTYPRHAKRQTGHQRMDSR 76 (92)
Q Consensus 47 e~fle~Iirda-vtyaeHA~RKTVt~~~DV~ 76 (92)
=.|+...+++. -.||...|.+.|| .+.+.
T Consensus 13 P~fvR~~~r~~~E~~Ar~~G~~~IT-~e~v~ 42 (45)
T PF08369_consen 13 PFFVRKKLRDAAEKYARERGYDEIT-VEVVD 42 (45)
T ss_dssp -HHHHHHHHHHHHHHHHHCT-SEE--HHHHH
T ss_pred CHHHHHHHHHHHHHHHHHcCCCeEC-HHHHH
Confidence 34666777776 4799999999999 76553
No 78
>PF12558 DUF3744: ATP-binding cassette cobalt transporter; InterPro: IPR022216 This domain family is found in bacteria, and is approximately 70 amino acids in length. The family is found in association with PF00005 from PFAM. There is a conserved REP sequence motif. There is a single completely conserved residue P that may be functionally important. The proteins in this family are frequently annotated as ABC Cobalt transporters however there is little accompanying literature to confirm this. ; GO: 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances
Probab=45.93 E-value=14 Score=23.51 Aligned_cols=18 Identities=17% Similarity=0.248 Sum_probs=13.3
Q ss_pred CcCCccCCCCCCchhHHhhhcc
Q psy17761 9 DAHGLRTPVSGPPSVVWRVEVE 30 (92)
Q Consensus 9 ~~hg~~~~v~~~~aIRrlar~G 30 (92)
.+||||+| -=|--|+.+|
T Consensus 6 ~~~GIREP----LYitALk~ag 23 (74)
T PF12558_consen 6 EQNGIREP----LYITALKYAG 23 (74)
T ss_pred hhcCCCcc----HHHHHHHHcC
Confidence 47999999 3455677788
No 79
>cd00852 NifB NifB belongs to a family of iron-molybdenum cluster-binding proteins that includes NifX, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme as part of nitrogen fixation in bacteria. This domain is sometimes found fused to a N-terminal domain (the Radical SAM domain) in nifB-like proteins.
Probab=42.26 E-value=12 Score=24.22 Aligned_cols=31 Identities=16% Similarity=-0.021 Sum_probs=19.8
Q ss_pred CCchhHHhhhcccccchhhHHHHHHHHHHHH
Q psy17761 19 GPPSVVWRVEVESSVFAGLIYEETRGVLKVV 49 (92)
Q Consensus 19 ~~~aIRrlar~GakRIS~~iy~elr~vLe~f 49 (92)
|+.|..+|.++|++-+....-..+.++|+.|
T Consensus 75 G~~a~~~L~~~GI~v~~~~~~~~v~eal~~~ 105 (106)
T cd00852 75 GDEPKEKLEEAGIEVIEAYAGEYIEEALLEL 105 (106)
T ss_pred CccHHHHHHHCCCEEEEecCcCcHHHHHHHh
Confidence 4688888888887766433222456666655
No 80
>COG4401 AroH Chorismate mutase [Amino acid transport and metabolism]
Probab=39.88 E-value=32 Score=24.77 Aligned_cols=31 Identities=16% Similarity=0.104 Sum_probs=26.7
Q ss_pred hhcccccchhhHHHHHHHHHHHHHHHHHHHH
Q psy17761 27 VEVESSVFAGLIYEETRGVLKVVLENVIRDA 57 (92)
Q Consensus 27 ar~GakRIS~~iy~elr~vLe~fle~Iirda 57 (92)
+=+||.=||+..-+|++++.++.|+.|..+-
T Consensus 5 aIRGATTV~~nt~eeI~~at~eLl~~i~~~N 35 (125)
T COG4401 5 AIRGATTVESNTEEEILDATKELLEEIEEEN 35 (125)
T ss_pred eeccceeecCCCHHHHHHHHHHHHHHHHHhc
Confidence 3468999999999999999999999988764
No 81
>KOG0400|consensus
Probab=39.47 E-value=32 Score=25.43 Aligned_cols=45 Identities=22% Similarity=0.347 Sum_probs=33.2
Q ss_pred CCcCCccCC--CCCCchhHHhhhcc-cccchhhHHHHHHHHHHHHHHHHHHHHHhhhhhc
Q psy17761 8 NDAHGLRTP--VSGPPSVVWRVEVE-SSVFAGLIYEETRGVLKVVLENVIRDAVTYPRHA 64 (92)
Q Consensus 8 ~~~hg~~~~--v~~~~aIRrlar~G-akRIS~~iy~elr~vLe~fle~IirdavtyaeHA 64 (92)
-|+|||--- |.|---.|+|++-| +.-|-+|.|. +++.|++.-+|-
T Consensus 55 RDshGi~q~r~v~G~kI~Rilk~~Gl~PeiPeDLy~------------likkAv~iRkHL 102 (151)
T KOG0400|consen 55 RDSHGIGQVRFVTGNKILRILKSNGLAPEIPEDLYH------------LIKKAVAIRKHL 102 (151)
T ss_pred ecccCcchhheechhHHHHHHHHcCCCCCCcHHHHH------------HHHHHHHHHHHH
Confidence 478997543 67778889999999 8889888764 556666666663
No 82
>PF00493 MCM: MCM2/3/5 family This family extends the MCM domain of Prosite.; InterPro: IPR001208 MCM proteins are DNA-dependent ATPases required for the initiation of eukaryotic DNA replication [, , ]. In eukaryotes there is a family of six proteins, MCM2 to MCM7. They were first identified in yeast where most of them have a direct role in the initiation of chromosomal DNA replication by interacting directly with autonomously replicating sequences (ARS). They were thus called minichromosome maintenance proteins, MCM proteins []. This family is also present in the archebacteria in 1 to 4 copies. Methanocaldococcus jannaschii (Methanococcus jannaschii) has four members, MJ0363, MJ0961, MJ1489 and MJECL13. The "MCM motif" contains Walker-A and Walker-B type nucleotide binding motifs. The diagnostic sequence defining the MCMs is IDEFDKM. Only Mcm2 (aka Cdc19 or Nda1) has been subjected to mutational analysis in this region, and most mutations abolish its activity []. The presence of a putative ATP-binding domain implies that these proteins may be involved in an ATP-consuming step in the initiation of DNA replication in eukaryotes. The MCM proteins bind together in a large complex []. Within this complex, individual subunits associate with different affinities, and there is a tightly associated core of Mcm4 (Cdc21), Mcm6 (Mis5) and Mcm7 []. This core complex in human MCMs has been associated with helicase activity in vitro [], leading to the suggestion that the MCM proteins are the eukaryotic replicative helicase. Schizosaccharomyces pombe (Fission yeast) MCMs, like those in metazoans, are found in the nucleus throughout the cell cycle. This is in contrast to the Saccharomyces cerevisiae (Baker's yeast) in which MCM proteins move in and out of the nucleus during each cell cycle. The assembly of the MCM complex in S. pombe is required for MCM localisation, ensuring that only intact MCM complexes remain in the nucleus [].; GO: 0003677 DNA binding, 0005524 ATP binding, 0006260 DNA replication; PDB: 3F8T_A 3F9V_A.
Probab=39.15 E-value=21 Score=28.09 Aligned_cols=30 Identities=20% Similarity=0.157 Sum_probs=27.5
Q ss_pred HHHHHHHHHhhhhhcCCcccccchhHHHHHH
Q psy17761 50 LENVIRDAVTYPRHAKRQTGHQRMDSRLRAK 80 (92)
Q Consensus 50 le~IirdavtyaeHA~RKTVt~~~DV~~alk 80 (92)
||.++|=|...|+-.-|.+|+ .+||..|.+
T Consensus 295 LeSLIRLseA~AKl~lr~~V~-~~Dv~~Ai~ 324 (331)
T PF00493_consen 295 LESLIRLSEAHAKLRLRDEVT-EEDVEEAIR 324 (331)
T ss_dssp CCHHHHHHHHHHHCTTSSECS-HHHHHHHHH
T ss_pred HHHHHHHHHHHHHHhccCcee-HHHHHHHHH
Confidence 477999999999999999999 999999875
No 83
>cd00851 MTH1175 This uncharacterized conserved protein belongs to a family of iron-molybdenum cluster-binding proteins that includes NifX, NifB, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme. This domain is a predicted small-molecule-binding domain (SMBD) with an alpha/beta fold that is present either as a stand-alone domain (e.g. NifX and NifY) or fused to another conserved domain (e.g. NifB) however, its function is still undetermined.The SCOP database suggests that this domain is most similar to structures within the ribonuclease H superfamily. This conserved domain is represented in two of the three major divisions of life (bacteria and archaea).
Probab=38.58 E-value=15 Score=22.98 Aligned_cols=30 Identities=13% Similarity=0.227 Sum_probs=18.5
Q ss_pred CCchhHHhhhcccccchhhHHHHHHHHHHHH
Q psy17761 19 GPPSVVWRVEVESSVFAGLIYEETRGVLKVV 49 (92)
Q Consensus 19 ~~~aIRrlar~GakRIS~~iy~elr~vLe~f 49 (92)
|+++...|..+|++=+...- ..+.++|+.|
T Consensus 73 G~~~~~~l~~~gI~v~~~~~-~~i~~vl~~~ 102 (103)
T cd00851 73 GPRALNKLRNAGIKVYKGAE-GTVEEAIEAL 102 (103)
T ss_pred CcCHHHHHHHCCCEEEEcCC-CCHHHHHHhh
Confidence 45777788888866554433 4555666555
No 84
>COG1963 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=37.65 E-value=12 Score=27.81 Aligned_cols=54 Identities=15% Similarity=0.226 Sum_probs=29.3
Q ss_pred chhHHhhhc-ccccchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccchhHHHHHHh-hCCCCcccccC
Q psy17761 21 PSVVWRVEV-ESSVFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMDSRLRAKT-SRPHPCTVLAG 92 (92)
Q Consensus 21 ~aIRrlar~-GakRIS~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt~~~DV~~alkr-~g~~~~~~~~~ 92 (92)
-+|-.+..+ |+.|-|+.=.+-+ ....+++.++....++-. ||. .|++|++|++|
T Consensus 81 faiIvm~DA~GVRr~aG~QA~iL----N~l~~~~~~e~~~~~~~~--------------lKellGH~p~eV~~G 136 (153)
T COG1963 81 FAIIVMYDATGVRRSAGVQARIL----NQLIEELVNEKKDFDKKR--------------LKELLGHTPLEVFAG 136 (153)
T ss_pred HHHHHhhhhhhHHHhccchHHHH----HHHHHHHHHhhccCCHHH--------------HHHHhCCChHHHHHH
Confidence 344444444 6888777644433 444444444333222211 444 69999999876
No 85
>cd00853 NifX NifX belongs to a family of iron-molybdenum cluster-binding proteins that includes NifB, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme. The protein is part of the nitrogen fixation gene cluster in nitrogen-fixing bacteria and has sequence similarity to other members of the cluster.
Probab=36.56 E-value=17 Score=23.52 Aligned_cols=30 Identities=17% Similarity=0.046 Sum_probs=18.4
Q ss_pred CCchhHHhhhcccccchhhHHHHHHHHHHH
Q psy17761 19 GPPSVVWRVEVESSVFAGLIYEETRGVLKV 48 (92)
Q Consensus 19 ~~~aIRrlar~GakRIS~~iy~elr~vLe~ 48 (92)
|+.+..+|+++|++=+.......+.++|+.
T Consensus 71 G~~a~~~L~~~GI~v~~~~~~~~v~eal~~ 100 (102)
T cd00853 71 GGPAAARLVRAGIHPIKVPEGEPIAELLEE 100 (102)
T ss_pred ChhHHHHHHHcCCEEEEcCCCCcHHHHHHh
Confidence 468889999999776643322334445544
No 86
>KOG3219|consensus
Probab=36.44 E-value=40 Score=25.88 Aligned_cols=66 Identities=14% Similarity=0.083 Sum_probs=51.1
Q ss_pred CchhHHhhhc--ccccchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccchhHHHHHHhh---CCCC
Q psy17761 20 PPSVVWRVEV--ESSVFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMDSRLRAKTS---RPHP 86 (92)
Q Consensus 20 ~~aIRrlar~--GakRIS~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt~~~DV~~alkr~---g~~~ 86 (92)
+..|.+|... |-. ||.-+--.+.++-|.|.-+|+..|....+--+-.-=-++..|.-|.+|+ |+.|
T Consensus 115 Ka~iKkL~~~itg~~-v~~nv~Ia~~GiaKvFVGEvVEeAl~V~~~~~e~~PLqP~HIREA~rrL~~qgk~~ 185 (195)
T KOG3219|consen 115 KAQIKKLMSSITGQS-VSENVAIAMAGIAKVFVGEVVEEALDVREEWGESGPLQPKHIREAYRRLKLQGKLP 185 (195)
T ss_pred HHHHHHHHHHHhCCc-cCcceeeeecchhhHhHHHHHHHHHHHHHHhccCCCCCcHHHHHHHHHHHhcCCCC
Confidence 4789999776 544 8999999999999999999999999888875532111588888887775 4544
No 87
>TIGR02663 nifX nitrogen fixation protein NifX. Members of this family are NifX proteins encoded within operons for nitrogen fixation in a number of bacteria. NifX, NafY, and the C-terminal region of NifB all belong to the Pfam family pfam02579 and are involved in MoFe cofactor biosynthesis. NifX is a nitrogenase accessory protein with a role in expression of the MoFe cofactor.
Probab=35.94 E-value=31 Score=23.13 Aligned_cols=34 Identities=15% Similarity=0.044 Sum_probs=21.2
Q ss_pred CCchhHHhhhcccccchhhHHHHHHHHHHHHHHH
Q psy17761 19 GPPSVVWRVEVESSVFAGLIYEETRGVLKVVLEN 52 (92)
Q Consensus 19 ~~~aIRrlar~GakRIS~~iy~elr~vLe~fle~ 52 (92)
|++|..+|.++|++=+.......+.++|+.+.+.
T Consensus 73 G~~a~~~L~~~gI~~~~~~~~~~v~eal~~l~~~ 106 (119)
T TIGR02663 73 GGPAAAKVVAAKIHPIKVNEPESISELLERLQKM 106 (119)
T ss_pred CccHHHHHHHcCCeeEecCCCccHHHHHHHHHHH
Confidence 3678888999886666444344455555555443
No 88
>TIGR00368 Mg chelatase-related protein. The N-terminal end matches very strongly a pfam Mg_chelatase domain.
Probab=35.84 E-value=92 Score=26.38 Aligned_cols=29 Identities=10% Similarity=0.032 Sum_probs=26.3
Q ss_pred HHHHHHHHhhhhhcCCcccccchhHHHHHH
Q psy17761 51 ENVIRDAVTYPRHAKRQTGHQRMDSRLRAK 80 (92)
Q Consensus 51 e~IirdavtyaeHA~RKTVt~~~DV~~alk 80 (92)
..|+|-|-|+|+-++++.|+ .+||..|+.
T Consensus 469 ~rilrvArTiAdL~g~~~i~-~~hv~eA~~ 497 (499)
T TIGR00368 469 HRILKVARTIADLKEEKNIS-REHLAEAIE 497 (499)
T ss_pred HHHHHHHHHHHhhcCCCCCC-HHHHHHHHh
Confidence 34999999999999999999 999999883
No 89
>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=35.15 E-value=1.4e+02 Score=22.73 Aligned_cols=31 Identities=6% Similarity=-0.046 Sum_probs=24.4
Q ss_pred HHHHHHHHhhhhhcCCcccccchhHHHHHHhh
Q psy17761 51 ENVIRDAVTYPRHAKRQTGHQRMDSRLRAKTS 82 (92)
Q Consensus 51 e~IirdavtyaeHA~RKTVt~~~DV~~alkr~ 82 (92)
-++++.|..+|.-.++.+|+ .+||..|+...
T Consensus 244 l~~l~~a~~~a~~~~~~~it-~~~v~~a~~~~ 274 (365)
T TIGR02928 244 IDLLRVAGEIAEREGAERVT-EDHVEKAQEKI 274 (365)
T ss_pred HHHHHHHHHHHHHcCCCCCC-HHHHHHHHHHH
Confidence 34677777778777888999 99999887664
No 90
>cd03412 CbiK_N Anaerobic cobalamin biosynthetic cobalt chelatase (CbiK), N-terminal domain. CbiK is part of the cobalt-early path for cobalamin biosynthesis. It catalyzes the insertion of cobalt into the oxidized form of precorrin-2, factor II (sirohydrochlorin), the second step of the anaerobic branch of vitamin B12 biosynthesis. CbiK belongs to the class II family of chelatases and is a homomeric enzyme that does not require ATP for its enzymatic activity.
Probab=34.74 E-value=46 Score=22.71 Aligned_cols=38 Identities=11% Similarity=0.119 Sum_probs=28.8
Q ss_pred CccCCCCCCchhHHhhhccccc--------chhhHHHHHHHHHHHHH
Q psy17761 12 GLRTPVSGPPSVVWRVEVESSV--------FAGLIYEETRGVLKVVL 50 (92)
Q Consensus 12 g~~~~v~~~~aIRrlar~GakR--------IS~~iy~elr~vLe~fl 50 (92)
|+..| +.+-++..|...|+++ +.+.-|+.+...++.|-
T Consensus 52 ~~~~p-~~~eaL~~l~~~G~~~V~V~Pl~l~~G~e~~di~~~v~~~~ 97 (127)
T cd03412 52 GIEVD-TPEEALAKLAADGYTEVIVQSLHIIPGEEYEKLKREVDAFK 97 (127)
T ss_pred CCCCC-CHHHHHHHHHHCCCCEEEEEeCeeECcHHHHHHHHHHHHHh
Confidence 45567 6678999999999998 55666777777777654
No 91
>PRK07452 DNA polymerase III subunit delta; Validated
Probab=34.64 E-value=68 Score=24.39 Aligned_cols=49 Identities=2% Similarity=-0.133 Sum_probs=34.5
Q ss_pred cchhhHHHHHHHHHHHHHHHHHHHHHhhhhh--cCCcccccchhHHHHHHhh
Q psy17761 33 VFAGLIYEETRGVLKVVLENVIRDAVTYPRH--AKRQTGHQRMDSRLRAKTS 82 (92)
Q Consensus 33 RIS~~iy~elr~vLe~fle~IirdavtyaeH--A~RKTVt~~~DV~~alkr~ 82 (92)
.|+.++.+.+...+..=+..+..+.-..+-+ .+.++|+ .+||...+-.+
T Consensus 149 ~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~~It-~~~V~~~v~~~ 199 (326)
T PRK07452 149 KLTPEAAELLAEAVGNDSRRLYNELEKLALYAENSTKPIS-AEEVKALVSNT 199 (326)
T ss_pred CCCHHHHHHHHHHhCccHHHHHHHHHHHHHhccCCCCccC-HHHHHHHhccC
Confidence 4888888888777766666665555555555 3477899 99998776543
No 92
>PRK10733 hflB ATP-dependent metalloprotease; Reviewed
Probab=34.45 E-value=84 Score=27.20 Aligned_cols=57 Identities=9% Similarity=-0.028 Sum_probs=45.6
Q ss_pred hHHhhhcccccchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccchhHHHHHHhhC
Q psy17761 23 VVWRVEVESSVFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMDSRLRAKTSR 83 (92)
Q Consensus 23 IRrlar~GakRIS~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt~~~DV~~alkr~g 83 (92)
.......-+++|=..+|++.+++|+..-+.+-+-|-.+.++ +|++ .+||...++..+
T Consensus 541 ~~~~id~ev~~il~~~~~~a~~iL~~~~~~l~~la~~Lle~---etl~-~~ei~~i~~~~~ 597 (644)
T PRK10733 541 TARIIDQEVKALIERNYNRARQLLTDNMDILHAMKDALMKY---ETID-APQIDDLMARRD 597 (644)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHh---ceeC-HHHHHHHHhcCC
Confidence 33444555888999999999999999988877777777766 8999 999999998654
No 93
>PF01296 Galanin: Galanin; InterPro: IPR008174 Galanin is a peptide hormone that controls various biological activities []. Galanin-like immuno-reactivity has been found in the central and peripheral nervous systems of mammals, with high concentrations demonstrated in discrete regions of the central nervous system, including the median eminence, hypothalamus, arcuate nucleus, septum, neuro-intermediate lobe of the pituitary, and the spinal cord. Its localisation within neurosecretory granules suggests that galanin may function as a neurotransmitter, and it has been shown to coexist with a variety of other peptide and amine neurotransmitters within individual neurons []. Although the precise physiological role of galanin is uncertain, it has a number of pharmacological properties: it stimulates food intake, when injected into the third ventricle of rats; it increases levels of plasma growth hormone and prolactin, and decreases dopamine levels in the median eminence []; and infusion into humans results in hyperglycemia and glucose intolerance, and inhibits pancreatic release of insulin, somatostatin and pancreatic peptide. Galanin also modulates smooth muscle contractility within the gastro-intestinal and genito-urinary tracts, all such activities suggesting that the hormone may play an important role in the nervous modulation of endocrine and smooth muscle function []. Galanin is a 29 amino acid peptide processed from a larger precursor protein. Except in human, galanin is C-terminally amidated. Its sequence is highly conserved and the first 14 residues are identical in all currently known sequences.; GO: 0005179 hormone activity, 0005576 extracellular region
Probab=33.96 E-value=18 Score=19.98 Aligned_cols=9 Identities=56% Similarity=1.066 Sum_probs=7.7
Q ss_pred CCcCCcCCc
Q psy17761 5 GTFNDAHGL 13 (92)
Q Consensus 5 ~~~~~~hg~ 13 (92)
.+|+|+|||
T Consensus 20 RSf~DK~Gl 28 (29)
T PF01296_consen 20 RSFGDKHGL 28 (29)
T ss_pred cccccccCC
Confidence 479999997
No 94
>KOG1658|consensus
Probab=33.78 E-value=27 Score=26.19 Aligned_cols=43 Identities=16% Similarity=0.094 Sum_probs=35.9
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccchhHHHHHH
Q psy17761 37 LIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMDSRLRAK 80 (92)
Q Consensus 37 ~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt~~~DV~~alk 80 (92)
+|..-+....+.|+..+-+++-+++.-.+|||+. .-|+-.|.+
T Consensus 81 ea~~l~a~aaelfi~~Ln~~~~~~~q~~k~kt~q-r~d~D~ai~ 123 (162)
T KOG1658|consen 81 EASQLIAKAAELFIQELNDVAYTTAQLRKRKTEQ-RRDYDTAIE 123 (162)
T ss_pred HHHHHHHHHHHHHHHHHHhccchhHHHHHhhhhh-hhccccccc
Confidence 4666677888999999999999999999999998 777665543
No 95
>PRK09862 putative ATP-dependent protease; Provisional
Probab=33.72 E-value=98 Score=26.46 Aligned_cols=28 Identities=11% Similarity=-0.006 Sum_probs=25.9
Q ss_pred HHHHHHhhhhhcCCcccccchhHHHHHHh
Q psy17761 53 VIRDAVTYPRHAKRQTGHQRMDSRLRAKT 81 (92)
Q Consensus 53 IirdavtyaeHA~RKTVt~~~DV~~alkr 81 (92)
++|-|-|.|.-++|..|+ .+||..|+.=
T Consensus 464 lLrvARTiADL~g~~~V~-~~hv~eAl~y 491 (506)
T PRK09862 464 LLKVARTIADIDQSDIIT-RQHLQEAVSY 491 (506)
T ss_pred HHHHHHHHHHHcCCCCCC-HHHHHHHHHh
Confidence 888999999999999999 9999999953
No 96
>PF01024 Colicin: Colicin pore forming domain; InterPro: IPR000293 Colicins are plasmid-encoded polypeptide toxins produced by and active against Escherichia coli and closely related bacteria. Colicins are released into the environment to reduce competition from other bacterial strains. Colicins bind to outer membrane receptors, using them to translocate to the cytoplasm or cytoplasmic membrane, where they exert their cytotoxic effect, including depolarisation of the cytoplasmic membrane, DNase activity, RNase activity, or inhibition of murein synthesis. Channel-forming colicins (colicins A, B, E1, Ia, Ib, and N) are transmembrane proteins that depolarize the cytoplasmic membrane, leading to dissipation of cellular energy []. These colicins contain at least three domains: an N-terminal translocation domain responsible for movement across the outer membrane and periplasmic space; a central domain responsible for receptor recognition; and a C-terminal cytotoxic domain responsible for channel formation in the cytoplasmic membrane []. This entry represents the C-terminal cytotoxic domain, which has a globin-like fold with additional helices at either end.; GO: 0019835 cytolysis, 0050829 defense response to Gram-negative bacterium, 0016021 integral to membrane; PDB: 2I88_A 1CII_A 1RH1_A 1COL_B 1A87_A 3FEW_X.
Probab=33.32 E-value=73 Score=24.21 Aligned_cols=49 Identities=12% Similarity=-0.007 Sum_probs=31.9
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccchhHHHHHHhhCCCCc
Q psy17761 36 GLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMDSRLRAKTSRPHPC 87 (92)
Q Consensus 36 ~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt~~~DV~~alkr~g~~~~ 87 (92)
.++|+++- +.|.++--+-|-..|+-++=||+.+.+|-.-++.+...||.
T Consensus 20 ~~~~~~is---e~~G~Ky~~~A~elA~~~kGKkIRs~~dAl~s~eK~~~n~~ 68 (187)
T PF01024_consen 20 ADFYKKIS---EKYGEKYKKLAKELAEDAKGKKIRSVDDALKSFEKYKSNLN 68 (187)
T ss_dssp HHHHHHHH---HHH-HHHHHHHHHHHHHHHTGC---HHHHHHHHHHHHTHTT
T ss_pred HHHHHHHH---HHHHHHHHHHHHHHHHHhcccccCCHHHHHHHHHHHHhchh
Confidence 44565554 55666655555666666768999999999999998877775
No 97
>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=32.77 E-value=1e+02 Score=26.54 Aligned_cols=48 Identities=13% Similarity=-0.054 Sum_probs=35.4
Q ss_pred cchhhHHHHHHHHHHHHH-------HHHHHHHHhhhhhcCCcccccchhHHHHHHh
Q psy17761 33 VFAGLIYEETRGVLKVVL-------ENVIRDAVTYPRHAKRQTGHQRMDSRLRAKT 81 (92)
Q Consensus 33 RIS~~iy~elr~vLe~fl-------e~IirdavtyaeHA~RKTVt~~~DV~~alkr 81 (92)
.||+.+.+.+..+...+- ..+++-|-++|.-.+|.+|+ .+||..|++-
T Consensus 249 ~is~~~~~~l~~~~~~~~i~s~Ra~i~~~r~Ara~AaL~gr~~V~-~~Dv~~A~~l 303 (633)
T TIGR02442 249 RISDSLIRFISELCIEFGVDGHRADIVMARAARALAALDGRRRVT-AEDVREAAEL 303 (633)
T ss_pred CCCHHHHHHHHHHHHHhCCCCccHHHHHHHHHHHHHHHcCCCcCC-HHHHHHHHHH
Confidence 456666666665555442 23778888999999999999 9999877654
No 98
>PF06798 PrkA: PrkA serine protein kinase C-terminal domain; InterPro: IPR010650 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. This entry is found at the C terminus of PrkA proteins - bacterial and archaeal serine kinases approximately 630 residues in length. PrkA possesses the A-motif of nucleotide-binding proteins and exhibits distant homology to eukaryotic protein kinases []. Note that many of these are hypothetical.
Probab=32.61 E-value=1.4e+02 Score=23.14 Aligned_cols=55 Identities=15% Similarity=0.079 Sum_probs=39.2
Q ss_pred hhhcccccchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccc--cchhHHHHHHhh
Q psy17761 26 RVEVESSVFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGH--QRMDSRLRAKTS 82 (92)
Q Consensus 26 lar~GakRIS~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt--~~~DV~~alkr~ 82 (92)
+.+.| +.++-+.|+-|+.+++.+|..=.++++.++. ...||.. +..++...+.++
T Consensus 181 ~~~~g-~~~~~~~~e~Lr~~iEkkL~~d~~~~~~~~t-~~~k~~d~e~~~~~~~~i~rL 237 (254)
T PF06798_consen 181 LAREG-KKFDYTSYERLREAIEKKLFSDVKDLIKIIT-ESSKTPDKEQQRKIDEVIERL 237 (254)
T ss_pred HHcCC-CCCChhhhHHHHHHHHHHHHHHHHHHHHhcc-hhccCCCHHHHHHHHHHHHHH
Confidence 44445 6777899999999999999988899998876 2334443 344565666555
No 99
>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional
Probab=31.87 E-value=60 Score=27.11 Aligned_cols=32 Identities=13% Similarity=0.129 Sum_probs=28.0
Q ss_pred HHHHHHHHHhhhhhcCCcccccchhHHHHHHhh
Q psy17761 50 LENVIRDAVTYPRHAKRQTGHQRMDSRLRAKTS 82 (92)
Q Consensus 50 le~IirdavtyaeHA~RKTVt~~~DV~~alkr~ 82 (92)
+..|+++|...|...+|..|+ .+|+..|+.+.
T Consensus 393 I~~i~~eA~~~Alr~~r~~Vt-~~D~~~A~~~v 424 (438)
T PTZ00361 393 IKAICTEAGLLALRERRMKVT-QADFRKAKEKV 424 (438)
T ss_pred HHHHHHHHHHHHHHhcCCccC-HHHHHHHHHHH
Confidence 566888898889999999999 99999998874
No 100
>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=29.64 E-value=90 Score=25.04 Aligned_cols=46 Identities=13% Similarity=-0.055 Sum_probs=33.0
Q ss_pred chhhHHHHHHHHHHHHHH-------HHHHHHHhhhhhcCCcccccchhHHHHHH
Q psy17761 34 FAGLIYEETRGVLKVVLE-------NVIRDAVTYPRHAKRQTGHQRMDSRLRAK 80 (92)
Q Consensus 34 IS~~iy~elr~vLe~fle-------~IirdavtyaeHA~RKTVt~~~DV~~alk 80 (92)
||+.+.+.+..+...+-. ..++-|-++|--.||..|+ .+||..++.
T Consensus 255 v~d~~~~~i~~l~~~~~~~s~Ra~i~l~raArA~Aal~GR~~V~-~dDv~~~a~ 307 (337)
T TIGR02030 255 IPYDVLVKVAELCAELDVDGLRGELTLNRAAKALAAFEGRTEVT-VDDIRRVAV 307 (337)
T ss_pred CCHHHHHHHHHHHHHHCCCCCcHHHHHHHHHHHHHHHcCCCCCC-HHHHHHHHH
Confidence 556666656555544332 1667778899999999999 999997664
No 101
>PRK13765 ATP-dependent protease Lon; Provisional
Probab=29.48 E-value=1.2e+02 Score=26.63 Aligned_cols=31 Identities=16% Similarity=0.048 Sum_probs=27.0
Q ss_pred HHHHHHHHHhhhhhcCCcccccchhHHHHHHh
Q psy17761 50 LENVIRDAVTYPRHAKRQTGHQRMDSRLRAKT 81 (92)
Q Consensus 50 le~IirdavtyaeHA~RKTVt~~~DV~~alkr 81 (92)
+.++++.|..+|...+++.|+ .+||..|+++
T Consensus 369 l~~l~r~a~~~a~~~~~~~i~-~~~v~~a~~~ 399 (637)
T PRK13765 369 LGGLVRVAGDIARSEGAELTT-AEHVLEAKKI 399 (637)
T ss_pred HHHHHHHHHHHHHhhccceec-HHHHHHHHHh
Confidence 445899999999999999999 9999988765
No 102
>PRK03992 proteasome-activating nucleotidase; Provisional
Probab=28.81 E-value=81 Score=25.33 Aligned_cols=35 Identities=11% Similarity=0.012 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHhhhhhcCCcccccchhHHHHHHhhC
Q psy17761 48 VVLENVIRDAVTYPRHAKRQTGHQRMDSRLRAKTSR 83 (92)
Q Consensus 48 ~fle~IirdavtyaeHA~RKTVt~~~DV~~alkr~g 83 (92)
.-++.++++|...|-..+++.|+ .+|+..|+++..
T Consensus 339 adl~~l~~eA~~~a~~~~~~~i~-~~d~~~A~~~~~ 373 (389)
T PRK03992 339 ADLKAICTEAGMFAIRDDRTEVT-MEDFLKAIEKVM 373 (389)
T ss_pred HHHHHHHHHHHHHHHHcCCCCcC-HHHHHHHHHHHh
Confidence 45667888888888888999999 999999999864
No 103
>PF11815 DUF3336: Domain of unknown function (DUF3336); InterPro: IPR021771 This family of proteins is characterised by an N-terminal domain that is found adjacent to the patatin/phospholipase A2-related domain (see PF01734 from PFAM). The family of proteins, which contain these two domains, have been characterised in Saccharomyces cerevisiae (Baker's yeast) as a bifunctional enzyme with triacylglycerol lipase and lysophosphatidic acid acyltransferase or lysophosphatidylethanolamine acyltransferase activity. They are generally involved in triacylglycerol mobilisation and localized to lipid particles [, ].
Probab=28.36 E-value=1.9e+02 Score=20.43 Aligned_cols=41 Identities=10% Similarity=0.080 Sum_probs=29.6
Q ss_pred HHHHHHHHHHHHHHHHHHhhhhhcCCcccccchhHHHHHHhhCCC
Q psy17761 41 ETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMDSRLRAKTSRPH 85 (92)
Q Consensus 41 elr~vLe~fle~IirdavtyaeHA~RKTVt~~~DV~~alkr~g~~ 85 (92)
=+..++++|+++|....-..+++ .+++ .+.-.--+++..+|
T Consensus 105 GTK~lIe~Yi~ev~~~L~~l~~~---~~~~-~~~kl~ff~~~~~n 145 (145)
T PF11815_consen 105 GTKRLIEEYIDEVVRCLEYLAES---PELS-DEEKLSFFQETRHN 145 (145)
T ss_pred cchHHHHHHHHHHHHHHHHHHhC---cCCC-HHHHHHHHHHHhcC
Confidence 37888999999998888778877 6777 66555555555443
No 104
>PF03885 DUF327: Protein of unknown function (DUF327); InterPro: IPR005585 The proteins in this family are around 140-170 residues in length. The proteins contain many conserved residues, with the most conserved motifs found in the central and C-terminal region. The function of these proteins is unknown. ; PDB: 2P61_A 2QUP_A.
Probab=28.23 E-value=1.1e+02 Score=21.59 Aligned_cols=36 Identities=8% Similarity=0.104 Sum_probs=23.6
Q ss_pred cccchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCC
Q psy17761 31 SSVFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKR 66 (92)
Q Consensus 31 akRIS~~iy~elr~vLe~fle~IirdavtyaeHA~R 66 (92)
++..+-.-...-++.++.|+..+++.+..+-+..++
T Consensus 60 ~~~~t~~~l~~YK~~Vk~Fl~~~v~~~~~l~~~~~~ 95 (147)
T PF03885_consen 60 AESPTLENLKRYKELVKQFLKEVVKNGYKLEEESSW 95 (147)
T ss_dssp HHH--HHHHHHHHHHHHHHHHHHHHHHHHHHT----
T ss_pred hhCCCHHHHHHHHHHHHHHHHHHHHHHheeehcccC
Confidence 444444555666788999999999999998887776
No 105
>PRK13406 bchD magnesium chelatase subunit D; Provisional
Probab=28.13 E-value=1.1e+02 Score=26.46 Aligned_cols=49 Identities=14% Similarity=-0.074 Sum_probs=38.6
Q ss_pred ccchhhHHHHHHHHHHHHH-------HHHHHHHHhhhhhcCCcccccchhHHHHHHh
Q psy17761 32 SVFAGLIYEETRGVLKVVL-------ENVIRDAVTYPRHAKRQTGHQRMDSRLRAKT 81 (92)
Q Consensus 32 kRIS~~iy~elr~vLe~fl-------e~IirdavtyaeHA~RKTVt~~~DV~~alkr 81 (92)
-.|++.+.+.+..+...+. ..+++-|-++|.-+||.+|+ .+||..|+.-
T Consensus 194 v~v~~~~l~~i~~~~~~~gv~S~Ra~i~llraARa~AaL~Gr~~V~-~~dv~~Aa~l 249 (584)
T PRK13406 194 VGPPPEAIAALCAAAAALGIASLRAPLLALRAARAAAALAGRTAVE-EEDLALAARL 249 (584)
T ss_pred CCCCHHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHHHHcCCCCCC-HHHHHHHHHH
Confidence 4577777777666666654 24888899999999999999 9999888754
No 106
>COG5247 BUR6 Class 2 transcription repressor NC2, alpha subunit (DRAP1 homolog) [Transcription]
Probab=27.63 E-value=1.7e+02 Score=20.67 Aligned_cols=47 Identities=6% Similarity=-0.051 Sum_probs=36.4
Q ss_pred cccchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccchhHHHH
Q psy17761 31 SSVFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMDSRLR 78 (92)
Q Consensus 31 akRIS~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt~~~DV~~a 78 (92)
+-.|+...-.-.-++||-|+..|+..+...|.-.+-|-++ ++=+..|
T Consensus 39 iGKV~q~tPVIaskalE~Fl~~iv~~s~k~aR~~~skR~t-~e~lk~a 85 (113)
T COG5247 39 IGKVGQSTPVIASKALEMFLTEIVGLSLKEARKKSSKRMT-SEFLKRA 85 (113)
T ss_pred hhhhhhcchHHHHHHHHHHHHHHHHHHHHHHHhccchhhH-HHHHHHH
Confidence 5567777667778999999999999999998877777677 5544443
No 107
>cd05030 calgranulins Calgranulins: S-100 domain found in proteins belonging to the Calgranulin subgroup of the S100 family of EF-hand calcium-modulated proteins, including S100A8, S100A9, and S100A12 . Note that the S-100 hierarchy, to which this Calgranulin group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. These proteins are expressed mainly in granulocytes, and are involved in inflammation, allergy, and neuritogenesis, as well as in host-parasite response. Calgranulins are modulated not only by calcium, but also by other metals such as zinc and copper. Structural data suggested that calgranulins may exist in multiple structural forms, homodimers, as well as hetero-oligomers. For example, the S100A8/S100A9 complex called calprotectin plays important roles in the regulation of inflammatory processes, wound repair, and regulating zinc-dependent enzymes as well as microbial growth.
Probab=27.61 E-value=82 Score=19.96 Aligned_cols=24 Identities=8% Similarity=0.062 Sum_probs=16.0
Q ss_pred hhhhhcCCc----ccccchhHHHHHHhhC
Q psy17761 59 TYPRHAKRQ----TGHQRMDSRLRAKTSR 83 (92)
Q Consensus 59 tyaeHA~RK----TVt~~~DV~~alkr~g 83 (92)
.|-++|+++ +++ ..|+...|++..
T Consensus 13 ~f~~y~~~~~~~~~Is-~~El~~ll~~~~ 40 (88)
T cd05030 13 VFHQYSVRKGHPDTLY-KKEFKQLVEKEL 40 (88)
T ss_pred HHHHHhccCCCcccCC-HHHHHHHHHHHh
Confidence 344555554 788 888888887543
No 108
>cd07293 PX_SNX3 The phosphoinositide binding Phox Homology domain of Sorting Nexin 3. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. SNX3 associates with early endosomes through a PX domain-mediated interaction with phosphatidylinositol-3-phosphate (PI3P). It associates with the retromer complex, a membrane coat multimeric complex required for endosomal retrieval of lysosomal hydrolase receptors to the Golgi, and functions as a cargo-specific adaptor f
Probab=27.49 E-value=1.4e+02 Score=20.56 Aligned_cols=43 Identities=19% Similarity=0.196 Sum_probs=29.5
Q ss_pred CCCCCCchhHHhhhcc-cccchhhHHHHHHHHHHHHHHHHHHHH
Q psy17761 15 TPVSGPPSVVWRVEVE-SSVFAGLIYEETRGVLKVVLENVIRDA 57 (92)
Q Consensus 15 ~~v~~~~aIRrlar~G-akRIS~~iy~elr~vLe~fle~Iirda 57 (92)
.|++++..+.-+...| .-+.+++.-++=|..|+.||..|+..-
T Consensus 63 PpLP~K~~~~~~~~~~~~~~~~~~fie~Rr~~Le~FL~~i~~hP 106 (123)
T cd07293 63 PPLPGKALFRQLPFRGDDGIFDDSFIEERKQGLEQFLNKVAGHP 106 (123)
T ss_pred CCCCCCchhhhcccccccCCCCHHHHHHHHHHHHHHHHHHHcCc
Confidence 3344445444333333 457899999999999999999987643
No 109
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=26.95 E-value=99 Score=22.40 Aligned_cols=27 Identities=15% Similarity=0.137 Sum_probs=23.3
Q ss_pred cchhhHHHHHHHHHHHHHHHHHHHHHh
Q psy17761 33 VFAGLIYEETRGVLKVVLENVIRDAVT 59 (92)
Q Consensus 33 RIS~~iy~elr~vLe~fle~Iirdavt 59 (92)
-||...|+++.+.+++|-.+|+.-+-.
T Consensus 128 ~vs~~~~~ki~~~i~~fRk~i~~i~~~ 154 (171)
T PF14394_consen 128 SVSREDYEKIKKEIREFRKKIIAIAEE 154 (171)
T ss_pred EeCHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 588999999999999999998866543
No 110
>PF07261 DnaB_2: Replication initiation and membrane attachment; InterPro: IPR006343 This entry represents a domain found in several bacterial replication initiation and membrane attachment proteins, DnaB and DnaD. The DnaD protein is a component of the PriA primosome. The PriA primosome functions to recruit the replication fork helicase onto the DNA []. Members, both chromosomal or phage-associated, are found in the Bacillus/Clostridium group of Gram-positive bacteria []. The DnaB protein is essential for both replication initiation and membrane attachment of the origin region of the chromosome and Plasmid pUB110 in Bacillus subtilis. It is known that there are two different classes (DnaBI and DnaBII) in the DnaB mutants; DnaBI is essential for both chromosome and pUB110 replication, whereas DnaBII is necessary only for chromosome replication []. This domain tends to be found towards the C terminus of DnaB and DnaD proteins and is alpha helical in nature.; PDB: 2I5U_A 2ZC2_A.
Probab=26.10 E-value=1.5e+02 Score=17.58 Aligned_cols=40 Identities=10% Similarity=0.091 Sum_probs=30.1
Q ss_pred cccchhhHHHHHHHHHH--HHHHHHHHHHHhhhhhcCCcccc
Q psy17761 31 SSVFAGLIYEETRGVLK--VVLENVIRDAVTYPRHAKRQTGH 70 (92)
Q Consensus 31 akRIS~~iy~elr~vLe--~fle~IirdavtyaeHA~RKTVt 70 (92)
..-+|+...+.+...++ .|-.+++..|+.||--.+.+++.
T Consensus 10 ~~~~s~~e~~~l~~~~~~~~~~~~~v~~ai~~~~~~~~~~~~ 51 (77)
T PF07261_consen 10 GRPPSPSEIEKLEKWIDDYGFSPEVVNEAIEYALENNKRSFN 51 (77)
T ss_dssp TSS--HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCT--SHH
T ss_pred CCCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHcCCCCHH
Confidence 45678888899999999 99999999999999865555544
No 111
>cd00082 HisKA Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via trans-autophosphorylation by the catalytic domain of the histidine kinase. They subsequently transfer the phosphoryl group to the Asp acceptor residue of a response regulator protein. Two-component signalling systems, consisting of a histidine protein kinase that senses a signal input and a response regulator that mediates the output, are ancient and evolutionarily conserved signaling mechanisms in prokaryotes and eukaryotes.
Probab=25.34 E-value=1e+02 Score=15.96 Aligned_cols=19 Identities=32% Similarity=0.431 Sum_probs=11.0
Q ss_pred cCCccCCCCCC-chhHHhhh
Q psy17761 10 AHGLRTPVSGP-PSVVWRVE 28 (92)
Q Consensus 10 ~hg~~~~v~~~-~aIRrlar 28 (92)
.|-|++|+++. .++..+.+
T Consensus 12 ~hel~~pl~~i~~~~~~l~~ 31 (65)
T cd00082 12 SHELRTPLTAIRGALELLEE 31 (65)
T ss_pred hHHhcchHHHHHHHHHHHHh
Confidence 57788886653 33344444
No 112
>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional
Probab=25.20 E-value=97 Score=25.35 Aligned_cols=32 Identities=16% Similarity=0.011 Sum_probs=28.1
Q ss_pred HHHHHHHHHhhhhhcCCcccccchhHHHHHHhh
Q psy17761 50 LENVIRDAVTYPRHAKRQTGHQRMDSRLRAKTS 82 (92)
Q Consensus 50 le~IirdavtyaeHA~RKTVt~~~DV~~alkr~ 82 (92)
++.++++|.-.|-..+|+.|+ .+|+..|+++.
T Consensus 355 I~~l~~eA~~~A~r~~~~~i~-~~df~~A~~~v 386 (398)
T PTZ00454 355 IAAICQEAGMQAVRKNRYVIL-PKDFEKGYKTV 386 (398)
T ss_pred HHHHHHHHHHHHHHcCCCccC-HHHHHHHHHHH
Confidence 567888888888888999999 99999999985
No 113
>TIGR01242 26Sp45 26S proteasome subunit P45 family. Many proteins may score above the trusted cutoff because an internal
Probab=25.19 E-value=1e+02 Score=24.20 Aligned_cols=33 Identities=12% Similarity=0.027 Sum_probs=26.9
Q ss_pred HHHHHHHHHHhhhhhcCCcccccchhHHHHHHhh
Q psy17761 49 VLENVIRDAVTYPRHAKRQTGHQRMDSRLRAKTS 82 (92)
Q Consensus 49 fle~IirdavtyaeHA~RKTVt~~~DV~~alkr~ 82 (92)
-+..++++|...|-..+|+.|+ .+|+..|+++.
T Consensus 331 dl~~l~~~A~~~a~~~~~~~i~-~~d~~~a~~~~ 363 (364)
T TIGR01242 331 DLKAICTEAGMFAIREERDYVT-MDDFIKAVEKV 363 (364)
T ss_pred HHHHHHHHHHHHHHHhCCCccC-HHHHHHHHHHh
Confidence 4556788888777788999999 99999998763
No 114
>cd02001 TPP_ComE_PpyrDC Thiamine pyrophosphate (TPP) family, ComE and PpyrDC subfamily, TPP-binding module; composed of proteins similar to sulfopyruvate decarboxylase beta subunit (ComE) and phosphonopyruvate decarboxylase (Ppyr decarboxylase). Methanococcus jannaschii sulfopyruvate decarboxylase (ComDE) is a dodecamer of six alpha (D) subunits and six (E) beta subunits which, catalyzes the decarboxylation of sulfopyruvic acid to sulfoacetaldehyde in the coenzyme M pathway. Ppyr decarboxylase is a homotrimeric enzyme which functions in the biosynthesis of C-P compounds such as bialaphos tripeptide in Streptomyces hygroscopicus. Ppyr decarboxylase and ComDE require TPP and divalent metal cation cofactors.
Probab=24.55 E-value=1.2e+02 Score=21.25 Aligned_cols=43 Identities=19% Similarity=0.080 Sum_probs=26.4
Q ss_pred cCCcCCc----cCCCCCCchhHHhhhc-ccccchhhHHHHHHHHHHHHH
Q psy17761 7 FNDAHGL----RTPVSGPPSVVWRVEV-ESSVFAGLIYEETRGVLKVVL 50 (92)
Q Consensus 7 ~~~~hg~----~~~v~~~~aIRrlar~-GakRIS~~iy~elr~vLe~fl 50 (92)
||+.||+ +++ ..+|++-.++++ |++-+.-+-.+|+.+++++.+
T Consensus 95 nN~~~g~~~~~~~~-~~~~d~~~lA~a~G~~~~~v~~~~el~~al~~a~ 142 (157)
T cd02001 95 DNRAYGSTGGQPTP-SSNVNLEAWAAACGYLVLSAPLLGGLGSEFAGLL 142 (157)
T ss_pred eCccccccCCcCCC-CCCCCHHHHHHHCCCceEEcCCHHHHHHHHHHHH
Confidence 5666663 233 336889999988 644322233777777766655
No 115
>CHL00176 ftsH cell division protein; Validated
Probab=24.34 E-value=96 Score=27.16 Aligned_cols=32 Identities=16% Similarity=0.151 Sum_probs=0.0
Q ss_pred HHHHHHHHHhhhhhcCCcccccchhHHHHHHhh
Q psy17761 50 LENVIRDAVTYPRHAKRQTGHQRMDSRLRAKTS 82 (92)
Q Consensus 50 le~IirdavtyaeHA~RKTVt~~~DV~~alkr~ 82 (92)
+++++++|...+...+++.|+ .+|+..|+.+.
T Consensus 392 L~~lvneAal~a~r~~~~~It-~~dl~~Ai~rv 423 (638)
T CHL00176 392 LANLLNEAAILTARRKKATIT-MKEIDTAIDRV 423 (638)
T ss_pred HHHHHHHHHHHHHHhCCCCcC-HHHHHHHHHHH
No 116
>PRK07914 hypothetical protein; Reviewed
Probab=24.11 E-value=1.5e+02 Score=22.88 Aligned_cols=49 Identities=4% Similarity=-0.128 Sum_probs=32.1
Q ss_pred ccchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccchhHHHHHHhh
Q psy17761 32 SVFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMDSRLRAKTS 82 (92)
Q Consensus 32 kRIS~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt~~~DV~~alkr~ 82 (92)
..|+.++.+.+...+..=+..+..+.-..+-+.+ ++|+ .+||...+..+
T Consensus 146 ~~i~~~A~~~L~~~~g~dl~~l~~EleKL~~~~~-~~It-~e~V~~~v~~~ 194 (320)
T PRK07914 146 VKVDDDTVTALLDAVGSDLRELASACSQLVADTG-GAVD-AAAVRRYHSGK 194 (320)
T ss_pred CCCCHHHHHHHHHHHCccHHHHHHHHHHHhcCCC-CCcC-HHHHHHHcCCC
Confidence 3588888888887776555555555544443434 6799 88888776543
No 117
>PTZ00111 DNA replication licensing factor MCM4; Provisional
Probab=23.97 E-value=1.7e+02 Score=27.22 Aligned_cols=31 Identities=16% Similarity=0.196 Sum_probs=27.7
Q ss_pred HHHHHHHHHHhhhhhcCCcccccchhHHHHHH
Q psy17761 49 VLENVIRDAVTYPRHAKRQTGHQRMDSRLRAK 80 (92)
Q Consensus 49 fle~IirdavtyaeHA~RKTVt~~~DV~~alk 80 (92)
-||.+||=|.+.|+-.=+.+|+ .+||..|.+
T Consensus 772 qLEsLIRLsEA~AK~rLs~~Vt-~~Dv~~Ai~ 802 (915)
T PTZ00111 772 MISSIIRISVSLARMRLSTVVT-PADALQAVQ 802 (915)
T ss_pred HHHHHHHHHHHHhhhcCcCccc-HHHHHHHHH
Confidence 5788999999999999999999 999888764
No 118
>KOG2994|consensus
Probab=23.59 E-value=53 Score=26.69 Aligned_cols=36 Identities=33% Similarity=0.443 Sum_probs=26.9
Q ss_pred CCcCCcCCc----cCCCCCCchhHHhhhcccccchhhHHHHHHHHHHHHHHH
Q psy17761 5 GTFNDAHGL----RTPVSGPPSVVWRVEVESSVFAGLIYEETRGVLKVVLEN 52 (92)
Q Consensus 5 ~~~~~~hg~----~~~v~~~~aIRrlar~GakRIS~~iy~elr~vLe~fle~ 52 (92)
|.+|.+||| ..+|..|||.. .||+|+..-++.|..-
T Consensus 141 Hn~nQAhGLsFSV~~gvp~PPSLk------------NIYkEl~~Di~df~~P 180 (297)
T KOG2994|consen 141 HNPNQAHGLSFSVQPGVPPPPSLK------------NIYKELSSDIEDFVIP 180 (297)
T ss_pred CCCcccceeeeecCCCCCCCchHH------------HHHHHHhccccccccC
Confidence 788999995 55677788864 4688888777776543
No 119
>cd08641 DNA_pol_gammaA Pol gammaA is a family A polymerase that is responsible for DNA replication and repair in mitochondria. DNA polymerase gamma (Pol gamma), 5'-3' polymerase domain (Pol gammaA). Pol gammaA is a family A polymerase that is responsible for DNA replication and repair in mitochondria. Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified into six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaeota polymerase II (class D), human polymerase beta (class X), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerases are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I, mitochondrial polymerase gammaA, and several bacteriophage polymerases including those from odd-nu
Probab=23.07 E-value=93 Score=26.54 Aligned_cols=33 Identities=30% Similarity=0.301 Sum_probs=28.4
Q ss_pred chhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCC
Q psy17761 34 FAGLIYEETRGVLKVVLENVIRDAVTYPRHAKR 66 (92)
Q Consensus 34 IS~~iy~elr~vLe~fle~IirdavtyaeHA~R 66 (92)
=|++.|++++.-++.-|..++.|++.+.+.|+|
T Consensus 17 ~~e~~y~~~~~~~~~~l~~~~~~~~~~~~~a~~ 49 (425)
T cd08641 17 TAEETYQELQQEVKESLMQLAEDACQLDPQAKR 49 (425)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 367899999999999999999999988666643
No 120
>KOG1257|consensus
Probab=22.95 E-value=71 Score=28.27 Aligned_cols=34 Identities=26% Similarity=0.220 Sum_probs=24.5
Q ss_pred cccchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccchh
Q psy17761 31 SSVFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMD 74 (92)
Q Consensus 31 akRIS~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt~~~D 74 (92)
-+|+.++-|+|+ +.+|++.+.+. =|.+|+-|-+|
T Consensus 229 ~~R~~g~eYd~~---~dEFm~Av~~~-------yG~~~lIqFED 262 (582)
T KOG1257|consen 229 QRRVRGKEYDEF---LDEFMEAVVQR-------YGPNTLIQFED 262 (582)
T ss_pred cccccccHHHHH---HHHHHHHHHHH-------hCcceEEEehh
Confidence 369999999886 67888876543 26666666776
No 121
>PF05046 Img2: Mitochondrial large subunit ribosomal protein (Img2); InterPro: IPR007740 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family of proteins has been identified as part of the mitochondrial large ribosomal subunit in Saccharomyces cerevisiae [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome
Probab=22.45 E-value=52 Score=21.46 Aligned_cols=52 Identities=10% Similarity=-0.074 Sum_probs=30.6
Q ss_pred cccchhhHHHHHHHHHHHHHHHHHH--HHHhhhhhcCCcccc--cchhHHHHHHhhC
Q psy17761 31 SSVFAGLIYEETRGVLKVVLENVIR--DAVTYPRHAKRQTGH--QRMDSRLRAKTSR 83 (92)
Q Consensus 31 akRIS~~iy~elr~vLe~fle~Iir--davtyaeHA~RKTVt--~~~DV~~alkr~g 83 (92)
+++|.+|+ .++++-|+.+|+.... +.+..-+.++.=-|+ +..+|..-|...|
T Consensus 31 IrkI~GD~-~aL~~dL~~~l~~~~~~~~~~~V~~~~g~i~IkG~~~~~Vk~wL~~~G 86 (87)
T PF05046_consen 31 IRKIEGDI-WALKKDLRKFLGEKPKKKIDVRVNELTGHIEIKGDHVEEVKKWLLEKG 86 (87)
T ss_pred EEeecCCH-HHHHHHHHHHhhhhcCCCcceEEeecCCEEEEcCccHHHHHHHHHHCc
Confidence 78999996 5677778888877665 333444444333333 3444555554443
No 122
>PRK08487 DNA polymerase III subunit delta; Validated
Probab=22.25 E-value=2.2e+02 Score=22.02 Aligned_cols=48 Identities=4% Similarity=-0.254 Sum_probs=33.1
Q ss_pred ccchhhHHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccchhHHHHHHhh
Q psy17761 32 SVFAGLIYEETRGVLKVVLENVIRDAVTYPRHAKRQTGHQRMDSRLRAKTS 82 (92)
Q Consensus 32 kRIS~~iy~elr~vLe~fle~IirdavtyaeHA~RKTVt~~~DV~~alkr~ 82 (92)
..|+.++.+.+...+..=+..+..+.-..+-+.+ +|| .+||...+...
T Consensus 153 ~~i~~~a~~~L~~~~g~dl~~l~~ELeKL~ly~~--~It-~edV~~~v~~~ 200 (328)
T PRK08487 153 LDIDQNALNHLYFIHNEDLALAANELEKLAILNE--PIT-LKDIQELVFGL 200 (328)
T ss_pred CCCCHHHHHHHHHHhCcHHHHHHHHHHHHHHhcC--CCC-HHHHHHHhccc
Confidence 3588888888888777666666655555444544 688 88888766443
No 123
>cd00562 NifX_NifB This CD represents a family of iron-molybdenum cluster-binding proteins that includes NifB, NifX, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme. This domain is a predicted small-molecule-binding domain (SMBD) with an alpha/beta fold that is present either as a stand-alone domain (e.g. NifX and NifY) or fused to another conserved domain (e.g. NifB) however, its function is still undetermined.The SCOP database suggests that this domain is most similar to structures within the ribonuclease H superfamily. This conserved domain is represented in two of the three major divisions of life (bacteria and archaea).
Probab=22.19 E-value=38 Score=21.02 Aligned_cols=15 Identities=7% Similarity=-0.075 Sum_probs=8.6
Q ss_pred CchhHHhhhcccccc
Q psy17761 20 PPSVVWRVEVESSVF 34 (92)
Q Consensus 20 ~~aIRrlar~GakRI 34 (92)
+++..+|.++|++-+
T Consensus 72 ~~a~~~l~~~gI~v~ 86 (102)
T cd00562 72 GPAAAKLEAAGIKPI 86 (102)
T ss_pred ccHHHHHHHcCCEEE
Confidence 456666666665543
No 124
>KOG0784|consensus
Probab=22.19 E-value=44 Score=28.03 Aligned_cols=33 Identities=21% Similarity=0.286 Sum_probs=25.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhhcCCcccc
Q psy17761 38 IYEETRGVLKVVLENVIRDAVTYPRHAKRQTGH 70 (92)
Q Consensus 38 iy~elr~vLe~fle~IirdavtyaeHA~RKTVt 70 (92)
+.|.+.=+-+.--|.|+|-|..||.-.+||-||
T Consensus 174 VVEsLKVvT~~kseRIaryAF~yA~k~gRKkVT 206 (375)
T KOG0784|consen 174 VVESLKVVTRFKSERIARYAFEYAKKNGRKKVT 206 (375)
T ss_pred hhheeeeehhhhhHHHHHHHHHHHHHhCCceEE
Confidence 344444444556788999999999999999998
No 125
>PF09744 Jnk-SapK_ap_N: JNK_SAPK-associated protein-1; InterPro: IPR019143 This entry represents the N-terminal 200 residues of a set of proteins conserved from yeasts to humans. Most of the proteins in this entry have a RhoGEF domain (IPR000219 from INTERPRO) at their C-terminal end.
Probab=21.85 E-value=1e+02 Score=22.48 Aligned_cols=26 Identities=15% Similarity=0.134 Sum_probs=22.6
Q ss_pred cchhhHHHHHHHHHHHHHHHHHHHHH
Q psy17761 33 VFAGLIYEETRGVLKVVLENVIRDAV 58 (92)
Q Consensus 33 RIS~~iy~elr~vLe~fle~Iirdav 58 (92)
-|++.||.|+-.++..|...++...+
T Consensus 3 ~lA~~Ig~EfE~lId~~G~e~v~~Lm 28 (158)
T PF09744_consen 3 DLASSIGKEFERLIDRYGEEAVKGLM 28 (158)
T ss_pred HHHHHHHHHHHHHHHHhChhHHHHHH
Confidence 47889999999999999999877765
No 126
>cd06409 PB1_MUG70 The MUG70 protein is a product of the meiotically up-regulated gene 70 which has a role in meiosis and harbors a PB1 domain. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domains depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic amino acid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is
Probab=21.80 E-value=57 Score=21.69 Aligned_cols=17 Identities=24% Similarity=0.108 Sum_probs=15.1
Q ss_pred HHHHHhhhhhcCCcccc
Q psy17761 54 IRDAVTYPRHAKRQTGH 70 (92)
Q Consensus 54 irdavtyaeHA~RKTVt 70 (92)
+.+|+..+..+++|||+
T Consensus 64 L~e~v~iar~~g~~~v~ 80 (86)
T cd06409 64 LVAAVLVARSAGLKKLD 80 (86)
T ss_pred HHHHHHHHHHcCCCEEE
Confidence 57889999999999987
No 127
>COG2045 Phosphosulfolactate phosphohydrolase and related enzymes [Coenzyme metabolism / General function prediction only]
Probab=21.31 E-value=83 Score=24.68 Aligned_cols=60 Identities=17% Similarity=0.061 Sum_probs=36.1
Q ss_pred CCchhHHhhhcc--cccchhhHHHH--HHHHHHHHHHHHHHHHHhhhhhcCCcccccc----hhHHHHHHh
Q psy17761 19 GPPSVVWRVEVE--SSVFAGLIYEE--TRGVLKVVLENVIRDAVTYPRHAKRQTGHQR----MDSRLRAKT 81 (92)
Q Consensus 19 ~~~aIRrlar~G--akRIS~~iy~e--lr~vLe~fle~IirdavtyaeHA~RKTVt~~----~DV~~alkr 81 (92)
|++|+-=..-+| ++.+.+..-++ .+.++-+--+.-..+++.++.|++| .. . +||.|++|.
T Consensus 143 g~~alED~~~AG~I~~~l~g~~~~~~~~aa~~~~~~~~~~~~~~~~ss~~~r--L~-~lg~~eDveyc~~~ 210 (230)
T COG2045 143 GRFALEDFLCAGAIAHYLEGENGDGVAAAAVYMERTREDLEEAIKGSSHGKR--LL-ELGFEEDVEYCAKE 210 (230)
T ss_pred CCccHHHHHHHHHHHHHHhccCcchHHHHHHHHHHhcccHHHHHhhcchhhh--HH-hcchhhhhHHHHhh
Confidence 456666666666 44444443122 2222223333467778888999877 66 5 999999986
No 128
>COG4854 Predicted membrane protein [Function unknown]
Probab=20.92 E-value=88 Score=22.54 Aligned_cols=35 Identities=17% Similarity=0.241 Sum_probs=25.0
Q ss_pred HHHHHHHHHHHHHH--HhhhhhcCCcccccchhHHHHH
Q psy17761 44 GVLKVVLENVIRDA--VTYPRHAKRQTGHQRMDSRLRA 79 (92)
Q Consensus 44 ~vLe~fle~Iirda--vtyaeHA~RKTVt~~~DV~~al 79 (92)
-..+..+++|++|= ....|.|.|+|+. .--+.+|+
T Consensus 46 ~l~k~Rv~~vvEDER~lrvse~aSr~Tiq-V~~is~Al 82 (126)
T COG4854 46 SLVKRRVDEVVEDERTLRVSERASRRTIQ-VFSISAAL 82 (126)
T ss_pred HHHHHHHHHHhhhHHHHHHHHhhhheeEE-EEEehHHH
Confidence 34566677777775 5678999999998 65555544
No 129
>COG3684 LacD Tagatose-1,6-bisphosphate aldolase [Carbohydrate transport and metabolism]
Probab=20.68 E-value=3e+02 Score=22.60 Aligned_cols=60 Identities=17% Similarity=-0.023 Sum_probs=42.5
Q ss_pred chhHHhhhcccc--------cchhhHHHHHHHHHHHHHHHHHHHHH-----------hh-------hhhcCCcccccchh
Q psy17761 21 PSVVWRVEVESS--------VFAGLIYEETRGVLKVVLENVIRDAV-----------TY-------PRHAKRQTGHQRMD 74 (92)
Q Consensus 21 ~aIRrlar~Gak--------RIS~~iy~elr~vLe~fle~Iirdav-----------ty-------aeHA~RKTVt~~~D 74 (92)
-+-+++++.|++ |+-++ |+.+.=..|+|.+..++. +| .++|+||-.+
T Consensus 115 isa~riK~~G~~avK~Lvy~~~D~~---e~neqk~a~ierigsec~aedi~f~lE~ltyd~~~~d~~eyak~kp~k---- 187 (306)
T COG3684 115 ISAKRIKEDGGDAVKFLVYYRSDED---EINEQKLAYIERIGSECHAEDLPFFLEPLTYDPRIGDKEEYAKRKPQK---- 187 (306)
T ss_pred hCHHHHHHhcccceEEEEEEcCCch---HHhHHHHHHHHHHHHHhhhcCCceeEeeeecCCCCCChHHHHhhchHH----
Confidence 677888998854 66666 777777788888877764 22 5668888666
Q ss_pred HHHHHHhhCCCCc
Q psy17761 75 SRLRAKTSRPHPC 87 (92)
Q Consensus 75 V~~alkr~g~~~~ 87 (92)
|.-++|-++--..
T Consensus 188 V~~a~k~fsd~Ga 200 (306)
T COG3684 188 VIEAMKEFSDSGA 200 (306)
T ss_pred HHHHHHHhccCCC
Confidence 7788887764333
No 130
>PLN00155 histone H2A; Provisional
Probab=20.50 E-value=84 Score=19.80 Aligned_cols=33 Identities=18% Similarity=0.174 Sum_probs=22.0
Q ss_pred CccCCCCCCchhHHhhhcc--cccchhhHHHHHHHHHH
Q psy17761 12 GLRTPVSGPPSVVWRVEVE--SSVFAGLIYEETRGVLK 47 (92)
Q Consensus 12 g~~~~v~~~~aIRrlar~G--akRIS~~iy~elr~vLe 47 (92)
||.-||+ =|.++-+.| ++||+..+---+..+||
T Consensus 22 gL~FPVg---ri~r~Lr~g~~a~Rvga~apVYlAAVLE 56 (58)
T PLN00155 22 GLQFPVG---RIARYLKKGKYAERIGAGAPVYLAAVLE 56 (58)
T ss_pred ccccchH---HHHHHHhcCChhhcccCCcHHHHHHHHH
Confidence 5555532 356666777 99999875555777766
Done!