Query 032181
Match_columns 146
No_of_seqs 151 out of 376
Neff 4.2
Searched_HMMs 46136
Date Fri Mar 29 10:41:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032181.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032181hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00463 histone H2B; Provisio 100.0 1.5E-54 3.3E-59 327.2 11.2 98 48-145 19-116 (117)
2 PLN00158 histone H2B; Provisio 100.0 1.5E-54 3.3E-59 327.0 10.9 98 49-146 19-116 (116)
3 smart00427 H2B Histone H2B. 100.0 2E-52 4.3E-57 303.4 10.2 89 57-145 1-89 (89)
4 KOG1744 Histone H2B [Chromatin 100.0 5E-46 1.1E-50 284.4 9.2 98 49-146 29-126 (127)
5 PF00125 Histone: Core histone 99.6 8.6E-16 1.9E-20 104.4 5.7 68 55-122 3-74 (75)
6 cd07981 TAF12 TATA Binding Pro 98.5 1.1E-06 2.3E-11 60.8 8.2 62 63-124 7-68 (72)
7 COG2036 HHT1 Histones H3 and H 98.3 2.5E-06 5.4E-11 62.5 6.6 64 62-126 24-87 (91)
8 PF00808 CBFD_NFYB_HMF: Histon 98.3 4.2E-06 9.2E-11 55.9 7.0 59 61-120 6-65 (65)
9 smart00803 TAF TATA box bindin 97.9 6.8E-05 1.5E-09 51.3 6.8 59 62-121 7-65 (65)
10 cd00074 H2A Histone 2A; H2A is 97.8 8.1E-05 1.7E-09 56.4 6.5 65 57-121 19-84 (115)
11 PLN00035 histone H4; Provision 97.8 0.00014 2.9E-09 54.6 7.6 61 62-123 34-94 (103)
12 PF03847 TFIID_20kDa: Transcri 97.7 0.00016 3.5E-09 50.1 6.8 60 62-121 4-63 (68)
13 cd00076 H4 Histone H4, one of 97.7 0.0002 4.3E-09 51.8 7.4 60 62-122 18-77 (85)
14 PTZ00015 histone H4; Provision 97.7 0.00026 5.6E-09 52.9 7.6 61 61-122 34-94 (102)
15 smart00428 H3 Histone H3. 97.5 0.00072 1.6E-08 50.7 8.1 68 56-123 32-101 (105)
16 cd07979 TAF9 TATA Binding Prot 97.3 0.002 4.4E-08 48.5 8.3 65 60-125 4-68 (117)
17 smart00417 H4 Histone H4. 97.2 0.00087 1.9E-08 47.4 5.5 56 62-118 18-73 (74)
18 KOG0869 CCAAT-binding factor, 96.8 0.006 1.3E-07 49.2 7.0 61 63-123 38-99 (168)
19 KOG0871 Class 2 transcription 96.6 0.01 2.2E-07 47.5 7.2 66 62-127 17-83 (156)
20 KOG1142 Transcription initiati 96.5 0.0044 9.5E-08 53.0 4.8 68 60-127 157-228 (258)
21 smart00414 H2A Histone 2A. 96.4 0.0088 1.9E-07 44.7 5.6 65 58-122 9-74 (106)
22 PLN00156 histone H2AX; Provisi 96.4 0.011 2.4E-07 46.5 6.3 65 57-121 28-93 (139)
23 PLN00157 histone H2A; Provisio 96.4 0.0068 1.5E-07 47.3 4.8 65 57-121 25-90 (132)
24 PF02969 TAF: TATA box binding 96.4 0.017 3.6E-07 40.0 6.3 47 75-121 20-66 (66)
25 PTZ00017 histone H2A; Provisio 96.3 0.0083 1.8E-07 46.9 5.1 65 57-121 26-91 (134)
26 cd08050 TAF6 TATA Binding Prot 96.2 0.015 3.3E-07 50.4 6.8 49 75-123 16-64 (343)
27 PLN00153 histone H2A; Provisio 96.1 0.012 2.5E-07 45.8 5.1 65 57-121 23-88 (129)
28 smart00576 BTP Bromodomain tra 95.7 0.097 2.1E-06 36.2 7.6 60 62-122 11-70 (77)
29 PTZ00252 histone H2A; Provisio 95.6 0.034 7.4E-07 43.6 5.7 66 56-121 23-91 (134)
30 COG5262 HTA1 Histone H2A [Chro 95.6 0.029 6.3E-07 43.6 5.1 60 62-121 31-90 (132)
31 PLN00154 histone H2A; Provisio 95.5 0.037 8E-07 43.5 5.7 65 57-121 37-103 (136)
32 PLN00121 histone H3; Provision 95.3 0.092 2E-06 41.2 7.1 66 57-122 66-131 (136)
33 KOG0870 DNA polymerase epsilon 95.1 0.13 2.8E-06 41.8 7.6 65 60-124 13-79 (172)
34 PTZ00018 histone H3; Provision 95.0 0.12 2.5E-06 40.6 7.0 66 57-122 66-131 (136)
35 PF15510 CENP-W: Centromere ki 94.9 0.05 1.1E-06 40.7 4.4 64 60-125 19-98 (102)
36 PF15630 CENP-S: Kinetochore c 94.6 0.14 3.1E-06 36.2 5.9 59 63-121 11-71 (76)
37 KOG1756 Histone 2A [Chromatin 94.0 0.15 3.2E-06 40.0 5.5 60 62-121 32-91 (131)
38 PLN00161 histone H3; Provision 93.5 0.5 1.1E-05 37.1 7.6 67 57-123 59-126 (135)
39 PLN00160 histone H3; Provision 92.2 0.97 2.1E-05 33.6 7.3 66 57-122 25-91 (97)
40 PF15511 CENP-T: Centromere ki 92.0 0.43 9.3E-06 42.7 6.2 55 61-115 355-414 (414)
41 PF07524 Bromo_TP: Bromodomain 91.6 1.8 3.8E-05 29.6 7.6 49 74-122 22-70 (77)
42 PF02291 TFIID-31kDa: Transcri 91.1 0.72 1.6E-05 35.6 5.8 60 61-124 16-78 (129)
43 KOG2549 Transcription initiati 89.2 1.4 3.1E-05 41.6 7.1 50 74-123 27-76 (576)
44 PF02269 TFIID-18kDa: Transcri 87.2 0.87 1.9E-05 32.9 3.5 47 75-121 19-65 (93)
45 cd08048 TAF11 TATA Binding Pro 86.3 5.9 0.00013 28.4 7.4 60 63-123 22-84 (85)
46 cd07978 TAF13 The TATA Binding 84.8 4.3 9.2E-05 29.5 6.2 51 71-122 15-66 (92)
47 KOG3334 Transcription initiati 84.3 4 8.6E-05 32.6 6.2 57 68-124 20-79 (148)
48 PF04719 TAFII28: hTAFII28-lik 80.3 13 0.00029 27.1 7.3 62 62-123 28-90 (90)
49 PF14687 DUF4460: Domain of un 79.1 2.6 5.6E-05 31.7 3.4 38 57-94 9-54 (112)
50 TIGR02442 Cob-chelat-sub cobal 76.0 12 0.00025 35.2 7.4 61 68-128 242-309 (633)
51 COG5095 TAF6 Transcription ini 72.9 4 8.7E-05 37.0 3.4 60 64-123 8-70 (450)
52 PF09415 CENP-X: CENP-S associ 71.6 7.4 0.00016 27.2 3.9 58 62-119 4-64 (72)
53 TIGR01128 holA DNA polymerase 70.1 26 0.00057 28.3 7.3 66 57-124 114-179 (302)
54 COG5208 HAP5 CCAAT-binding fac 69.9 7.5 0.00016 33.4 4.2 58 63-121 115-173 (286)
55 PRK09522 bifunctional glutamin 69.5 7.8 0.00017 35.9 4.6 61 69-129 168-231 (531)
56 smart00350 MCM minichromosome 69.0 28 0.00061 31.7 8.0 66 57-124 421-505 (509)
57 COG1466 HolA DNA polymerase II 68.7 20 0.00044 30.5 6.7 67 57-125 143-209 (334)
58 KOG1745 Histones H3 and H4 [Ch 68.4 6.2 0.00014 31.1 3.2 54 66-123 76-133 (137)
59 PRK07452 DNA polymerase III su 68.4 22 0.00048 29.5 6.7 62 59-122 135-198 (326)
60 PRK05574 holA DNA polymerase I 64.3 35 0.00077 28.1 7.1 66 57-124 149-214 (340)
61 PRK08487 DNA polymerase III su 63.1 30 0.00064 29.3 6.6 63 59-125 140-202 (328)
62 PRK14607 bifunctional glutamin 62.0 12 0.00026 34.5 4.3 59 69-128 167-225 (534)
63 TIGR03015 pepcterm_ATPase puta 61.7 49 0.0011 26.2 7.3 67 57-123 195-266 (269)
64 COG5150 Class 2 transcription 59.9 32 0.00069 27.4 5.7 51 73-123 28-78 (148)
65 KOG1757 Histone 2A [Chromatin 59.9 12 0.00026 29.2 3.3 61 57-121 29-95 (131)
66 PRK09333 30S ribosomal protein 57.2 30 0.00065 27.6 5.3 49 57-105 95-149 (150)
67 smart00271 DnaJ DnaJ molecular 56.6 32 0.0007 21.3 4.4 18 60-77 19-36 (60)
68 PF05674 DUF816: Baculovirus p 56.4 52 0.0011 27.0 6.5 56 57-112 93-169 (171)
69 PRK06585 holA DNA polymerase I 56.4 43 0.00093 28.1 6.4 65 58-124 146-211 (343)
70 cd06257 DnaJ DnaJ domain or J- 53.6 35 0.00076 20.7 4.2 18 60-77 18-35 (55)
71 PRK05907 hypothetical protein; 52.2 44 0.00095 28.8 5.9 60 59-121 139-201 (311)
72 TIGR02030 BchI-ChlI magnesium 50.5 41 0.00088 29.4 5.5 61 68-128 247-314 (337)
73 TIGR00764 lon_rel lon-related 48.8 1E+02 0.0022 29.1 8.1 65 58-122 313-390 (608)
74 PRK00411 cdc6 cell division co 48.3 1.7E+02 0.0037 24.8 9.0 63 63-125 216-284 (394)
75 PF00725 3HCDH: 3-hydroxyacyl- 48.0 37 0.0008 23.3 4.0 35 87-124 3-37 (97)
76 KOG0568 Molecular chaperone (D 47.9 36 0.00078 29.8 4.7 49 62-115 67-117 (342)
77 PRK07914 hypothetical protein; 47.7 60 0.0013 27.3 5.9 59 60-121 134-192 (320)
78 COG2238 RPS19A Ribosomal prote 47.7 25 0.00055 28.1 3.5 39 59-97 94-141 (147)
79 TIGR02031 BchD-ChlD magnesium 45.6 45 0.00099 31.1 5.3 62 67-128 195-263 (589)
80 COG2511 GatE Archaeal Glu-tRNA 44.1 90 0.0019 30.1 7.0 71 73-143 466-552 (631)
81 PRK05629 hypothetical protein; 42.7 1E+02 0.0023 25.8 6.7 61 58-121 130-190 (318)
82 PF00226 DnaJ: DnaJ domain; I 42.5 86 0.0019 19.8 5.0 17 59-75 17-33 (64)
83 PRK13406 bchD magnesium chelat 38.1 76 0.0016 30.0 5.6 57 72-128 192-255 (584)
84 PF01090 Ribosomal_S19e: Ribos 37.7 81 0.0018 24.8 4.9 37 58-94 92-138 (139)
85 KOG4336 TBP-associated transcr 37.1 1.5E+02 0.0033 26.5 7.0 59 64-123 12-70 (323)
86 CHL00081 chlI Mg-protoporyphyr 36.5 1.1E+02 0.0023 27.2 6.0 60 69-128 261-327 (350)
87 PF05258 DUF721: Protein of un 35.7 61 0.0013 21.3 3.5 25 110-134 19-43 (89)
88 PRK03992 proteasome-activating 34.2 66 0.0014 28.2 4.3 43 85-127 334-376 (389)
89 PF13148 DUF3987: Protein of u 33.9 2.2E+02 0.0048 23.9 7.3 74 57-132 262-367 (378)
90 PF11945 WASH_WAHD: WAHD domai 33.4 57 0.0012 28.4 3.7 23 79-101 25-47 (297)
91 cd00043 CYCLIN Cyclin box fold 33.3 1.2E+02 0.0027 18.8 5.7 65 58-122 4-74 (88)
92 PRK13407 bchI magnesium chelat 32.5 1.9E+02 0.0041 25.3 6.8 56 71-128 247-311 (334)
93 KOG2643 Ca2+ binding protein, 31.4 2E+02 0.0044 27.1 7.1 74 56-132 352-426 (489)
94 TIGR02928 orc1/cdc6 family rep 31.2 3.1E+02 0.0067 22.8 8.7 64 61-124 206-275 (365)
95 PF13335 Mg_chelatase_2: Magne 31.1 1.2E+02 0.0027 21.6 4.6 47 75-121 42-94 (96)
96 PF08221 HTH_9: RNA polymerase 30.1 1.7E+02 0.0036 19.4 5.1 44 86-133 5-48 (62)
97 PF04157 EAP30: EAP30/Vps36 fa 29.9 94 0.002 25.1 4.3 71 55-125 55-147 (223)
98 KOG3467 Histone H4 [Chromatin 29.7 1.4E+02 0.003 22.4 4.7 37 85-121 56-92 (103)
99 PF05798 Phage_FRD3: Bacteriop 29.5 26 0.00055 25.1 0.8 18 61-78 12-29 (75)
100 TIGR02397 dnaX_nterm DNA polym 29.1 1.8E+02 0.0039 24.1 5.9 62 59-123 181-242 (355)
101 PRK00464 nrdR transcriptional 29.1 1.3E+02 0.0029 23.7 4.9 16 109-124 101-116 (154)
102 PRK05637 anthranilate synthase 28.2 46 0.00099 26.9 2.2 24 69-92 183-206 (208)
103 PF00493 MCM: MCM2/3/5 family 28.1 48 0.001 28.4 2.4 66 56-123 244-326 (331)
104 cd07353 harmonin_N N-terminal 28.1 52 0.0011 23.7 2.2 28 57-92 19-46 (79)
105 PLN03213 repressor of silencin 28.0 55 0.0012 31.5 2.9 22 74-95 184-205 (759)
106 KOG0240 Kinesin (SMY1 subfamil 27.7 59 0.0013 31.3 3.0 42 57-98 65-127 (607)
107 PF13654 AAA_32: AAA domain; P 27.1 93 0.002 28.9 4.2 64 57-121 430-504 (509)
108 TIGR01241 FtsH_fam ATP-depende 26.5 1.7E+02 0.0036 26.4 5.6 50 92-141 264-324 (495)
109 PHA03102 Small T antigen; Revi 26.0 1.3E+02 0.0028 23.8 4.3 37 63-103 28-64 (153)
110 KOG1657 CCAAT-binding factor, 25.1 1.4E+02 0.003 25.2 4.6 58 63-121 80-138 (236)
111 PF04444 Dioxygenase_N: Catech 24.9 1.3E+02 0.0029 21.0 3.7 35 79-124 3-37 (74)
112 PTZ00361 26 proteosome regulat 24.5 1.1E+02 0.0023 27.9 4.0 42 84-125 385-426 (438)
113 CHL00176 ftsH cell division pr 24.4 1.6E+02 0.0035 28.1 5.3 50 92-141 392-451 (638)
114 PF07587 PSD1: Protein of unkn 24.2 2.6E+02 0.0056 23.4 6.0 24 76-99 197-221 (266)
115 PRK10733 hflB ATP-dependent me 24.0 1.1E+02 0.0025 28.8 4.2 40 87-126 356-395 (644)
116 TIGR00888 guaA_Nterm GMP synth 23.5 70 0.0015 24.7 2.4 22 69-90 162-183 (188)
117 TIGR01242 26Sp45 26S proteasom 23.4 1E+02 0.0022 26.4 3.5 40 85-124 325-364 (364)
118 PLN02347 GMP synthetase 23.4 66 0.0014 30.0 2.5 24 69-92 180-203 (536)
119 PF14606 Lipase_GDSL_3: GDSL-l 22.6 49 0.0011 26.8 1.3 77 61-137 81-173 (178)
120 PTZ00095 40S ribosomal protein 22.5 2.2E+02 0.0047 23.3 5.0 38 59-96 118-166 (169)
121 PRK14970 DNA polymerase III su 22.4 2.8E+02 0.006 23.5 6.0 62 59-123 172-233 (367)
122 PRK13765 ATP-dependent proteas 22.1 3.7E+02 0.0079 25.8 7.2 65 57-121 318-398 (637)
123 smart00385 CYCLIN domain prese 21.0 2.1E+02 0.0046 17.5 4.2 59 62-120 2-66 (83)
124 TIGR00368 Mg chelatase-related 20.7 2.6E+02 0.0057 25.8 5.8 49 74-122 444-498 (499)
No 1
>PTZ00463 histone H2B; Provisional
Probab=100.00 E-value=1.5e-54 Score=327.20 Aligned_cols=98 Identities=73% Similarity=1.069 Sum_probs=94.3
Q ss_pred ccccccccchhHHHHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCchH
Q 032181 48 KKKRAKKSIETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLVLPGE 127 (146)
Q Consensus 48 ~kk~~kkr~esy~~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsrEIqtAVrLlLPGE 127 (146)
+++++++|.|+|++||||||||||||+|||++||+||||||||||||||.||++|++||+++|||+||||||||||||||
T Consensus 19 ~kk~~~kr~esy~~YI~KVLKqVhPd~gIS~kaM~ImnSfvnDifErIA~EAs~La~~nkr~TltsrEIQtAvrLlLpGE 98 (117)
T PTZ00463 19 KKKRKKSRYDSYGLYIFKVLKQVHPDTGISRKSMNIMNSFLVDTFEKIATEASRLCKYTRRDTLSSREIQTAIRLVLPGE 98 (117)
T ss_pred cccccccccchHHHHHHHHHHhhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHhhcccHH
Confidence 34566778899999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhHHHhhhhhhhcccC
Q 032181 128 LAKHAVSEGTKAVTKFTS 145 (146)
Q Consensus 128 LaKhAvseGtkAV~ky~s 145 (146)
|+||||+|||+||++|++
T Consensus 99 LaKhAvsEGtkAv~k~~~ 116 (117)
T PTZ00463 99 LAKHAVSEGTKAVTKFTS 116 (117)
T ss_pred HHHhhhhHHHHHHHHhhc
Confidence 999999999999999986
No 2
>PLN00158 histone H2B; Provisional
Probab=100.00 E-value=1.5e-54 Score=327.01 Aligned_cols=98 Identities=85% Similarity=1.168 Sum_probs=94.4
Q ss_pred cccccccchhHHHHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCchHH
Q 032181 49 KKRAKKSIETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLVLPGEL 128 (146)
Q Consensus 49 kk~~kkr~esy~~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsrEIqtAVrLlLPGEL 128 (146)
++++++|.|+|++||||||||||||+|||++||+||||||||||||||.||++|++||+++|||+||||+||||||||||
T Consensus 19 kk~~~kr~esy~~YI~kVLKQVhPd~gIS~kaM~ImnSfvnDiferIA~EAs~La~~nkr~TltsrEIqtAvrLvLpgEL 98 (116)
T PLN00158 19 KKGSKSKTETYKIYIYKVLKQVHPDTGISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVRLILPGEL 98 (116)
T ss_pred ccccccccccHHHHHHHHHHHhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHhccHHH
Confidence 44566678999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhHHHhhhhhhhcccCC
Q 032181 129 AKHAVSEGTKAVTKFTSS 146 (146)
Q Consensus 129 aKhAvseGtkAV~ky~ss 146 (146)
+||||+||++||++|+++
T Consensus 99 aKhAvsEGtkAv~k~~~~ 116 (116)
T PLN00158 99 AKHAVSEGTKAVTKFTSA 116 (116)
T ss_pred HHHHHHHHHHHHHHhhcC
Confidence 999999999999999986
No 3
>smart00427 H2B Histone H2B.
Probab=100.00 E-value=2e-52 Score=303.39 Aligned_cols=89 Identities=83% Similarity=1.192 Sum_probs=87.8
Q ss_pred hhHHHHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCchHHHHhHHHhh
Q 032181 57 ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLVLPGELAKHAVSEG 136 (146)
Q Consensus 57 esy~~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsrEIqtAVrLlLPGELaKhAvseG 136 (146)
|+|++||||||||||||+|||++||+||||||||||||||.||++|++||+|+|||+||||+||||+|||||+||||+||
T Consensus 1 esy~~Yi~kvLKqVhpd~giS~kam~imnSfvnDiferIa~EAs~L~~~nkr~TltsreIqtAvrl~LpgeLakhAvsEg 80 (89)
T smart00427 1 ETYAIYIYKVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRLILPGELAKHAVSEG 80 (89)
T ss_pred CcHHHHHHHHHHHhCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHHccHHHHHHHHHHH
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhcccC
Q 032181 137 TKAVTKFTS 145 (146)
Q Consensus 137 tkAV~ky~s 145 (146)
||||++|++
T Consensus 81 tkAv~k~~~ 89 (89)
T smart00427 81 TKAVTKYSS 89 (89)
T ss_pred HHHHHhhcC
Confidence 999999985
No 4
>KOG1744 consensus Histone H2B [Chromatin structure and dynamics]
Probab=100.00 E-value=5e-46 Score=284.38 Aligned_cols=98 Identities=77% Similarity=1.125 Sum_probs=94.8
Q ss_pred cccccccchhHHHHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCchHH
Q 032181 49 KKRAKKSIETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLVLPGEL 128 (146)
Q Consensus 49 kk~~kkr~esy~~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsrEIqtAVrLlLPGEL 128 (146)
+++..++.++|+.||||||||||||+|||+++|+|||||||||||+||.||++|++||+|+||++||||+||||+|||||
T Consensus 29 k~~~~~~~e~~s~yv~kvlk~Vhpd~gis~~a~~vmnsf~ndife~iA~ea~rla~y~krstisSreiqta~rLllPgel 108 (127)
T KOG1744|consen 29 KKRSTRRKESYSEYVYKVLKQVHPDLGISSKAMGVMNSFVNDIFERIASEAGRLAHYNKRSTISSREIQTAVRLLLPGEL 108 (127)
T ss_pred ccCcccccCceeeehhhhhhcccCCCCcCHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCcccHHHHHHHHHHhCchHH
Confidence 55667889999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhHHHhhhhhhhcccCC
Q 032181 129 AKHAVSEGTKAVTKFTSS 146 (146)
Q Consensus 129 aKhAvseGtkAV~ky~ss 146 (146)
++||++|||+||++|+++
T Consensus 109 ~khA~seGtkav~ky~~s 126 (127)
T KOG1744|consen 109 AKHAVSEGTKAVTKYTSS 126 (127)
T ss_pred hhhhhcccchhheeeccC
Confidence 999999999999999875
No 5
>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=99.61 E-value=8.6e-16 Score=104.40 Aligned_cols=68 Identities=32% Similarity=0.424 Sum_probs=65.2
Q ss_pred cchhHHHHHHHHhhhhcCC----CCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHh
Q 032181 55 SIETYKIYIFKVLKQVHPD----IGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRL 122 (146)
Q Consensus 55 r~esy~~YIyKVLKQVhpd----~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsrEIqtAVrL 122 (146)
+...|..||+||+++++++ ..||++||.+|+++++|+|.+|.++|..++.+++|.||+++|||.|+|+
T Consensus 3 ~~~~~~~~~~r~~r~i~~~~~~~~ris~~a~~~L~~~~E~~~~~il~~A~~~a~~~kR~tI~~~DI~~A~r~ 74 (75)
T PF00125_consen 3 RRLIPKFPFSRLLREIGEEILSKYRISSEALVALQSVLEYLLVEILEEAGNLARHAKRKTITPRDIQLAVRI 74 (75)
T ss_dssp SHSSSHHHHHHHHHHHHHTTSSSSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTBSEEGHHHHHHHHHH
T ss_pred ccccCceEEeeeeehhhcccccccccccccchhhhhhhhhhhhhhhhHHHHHHhhcCCcEecHHHHHHHHhc
Confidence 4577899999999999999 8999999999999999999999999999999999999999999999986
No 6
>cd07981 TAF12 TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of the seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs function such as serving as activator-bind
Probab=98.49 E-value=1.1e-06 Score=60.83 Aligned_cols=62 Identities=18% Similarity=0.370 Sum_probs=58.4
Q ss_pred HHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhC
Q 032181 63 IFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLVL 124 (146)
Q Consensus 63 IyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsrEIqtAVrLlL 124 (146)
+...++++.|...++..+...|-.+++|+.+.|+.+|..||.+.++.||..+|||-+++-.+
T Consensus 7 l~~lv~~id~~~~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~~~tv~~~Di~l~l~r~~ 68 (72)
T cd07981 7 LQELLKEIDPREQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQLHLERNW 68 (72)
T ss_pred HHHHHHhhCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhc
Confidence 66789999999999999999999999999999999999999999999999999999987543
No 7
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=98.29 E-value=2.5e-06 Score=62.47 Aligned_cols=64 Identities=20% Similarity=0.364 Sum_probs=59.8
Q ss_pred HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCch
Q 032181 62 YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLVLPG 126 (146)
Q Consensus 62 YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsrEIqtAVrLlLPG 126 (146)
=|-|++|++.++ .||..|...|+..+..+++.|+.+|+.++.+.+|+||+.+||+.|.+.+...
T Consensus 24 pv~Ri~r~~~~~-Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~DI~la~~~~~~~ 87 (91)
T COG2036 24 PVRRILRKAGAE-RVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLALKRLGRR 87 (91)
T ss_pred HHHHHHHHHhHH-HhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHHHhccc
Confidence 378899999888 9999999999999999999999999999999999999999999999987653
No 8
>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=98.28 E-value=4.2e-06 Score=55.87 Aligned_cols=59 Identities=27% Similarity=0.453 Sum_probs=52.9
Q ss_pred HHHHHHhhhhcCC-CCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHH
Q 032181 61 IYIFKVLKQVHPD-IGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAV 120 (146)
Q Consensus 61 ~YIyKVLKQVhpd-~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsrEIqtAV 120 (146)
.-|.|++|+. || ..||.+|...|+.....+.+.|+.+|...+..++|+||+.+||..||
T Consensus 6 a~vkri~k~~-~~~~~vs~ea~~~i~~a~e~Fi~~l~~~A~~~a~~~~rkti~~~Dv~~Av 65 (65)
T PF00808_consen 6 ARVKRIMKSD-PDVMRVSKEAVEAIAKAAEEFIQYLAKEANEIAQRDKRKTITYEDVAKAV 65 (65)
T ss_dssp HHHHHHHHHT-STTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEE-HHHHHHHH
T ss_pred HHHHHHhccC-CCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHC
Confidence 3488999999 66 56999999999999999999999999999999999999999999986
No 9
>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=97.87 E-value=6.8e-05 Score=51.33 Aligned_cols=59 Identities=24% Similarity=0.324 Sum_probs=52.4
Q ss_pred HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHH
Q 032181 62 YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVR 121 (146)
Q Consensus 62 YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsrEIqtAVr 121 (146)
.|.+++++..= ..||..+..-|-..+.+..+.|+.+|..++++.+|+|||..||..|++
T Consensus 7 ~i~ria~~~Gi-~ris~~a~~~l~~~~e~rl~~i~~~A~k~~~hakRktlt~~DI~~Alk 65 (65)
T smart00803 7 TIKDVAESLGI-GNLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSALR 65 (65)
T ss_pred HHHHHHHHCCC-ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCeecHHHHHHHhC
Confidence 47788887643 478999999999999999999999999999999999999999988864
No 10
>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=97.78 E-value=8.1e-05 Score=56.40 Aligned_cols=65 Identities=26% Similarity=0.284 Sum_probs=58.9
Q ss_pred hhHHH-HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHH
Q 032181 57 ETYKI-YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVR 121 (146)
Q Consensus 57 esy~~-YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsrEIqtAVr 121 (146)
-.|.. =|+|.|++-.--..||..|.--|...+.++...|.+.|.+.++.+++++||.|+|+.|++
T Consensus 19 L~fPV~ri~R~Lk~~~~a~RVs~~A~VyLaAvLEYL~aEIlelA~n~ak~~k~krItp~hi~lAi~ 84 (115)
T cd00074 19 LQFPVGRIHRYLKKGRYAERVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKKRITPRHLQLAVR 84 (115)
T ss_pred ccCcHHHHHHHHHcCccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEcHHHHHHHHh
Confidence 34544 699999986666899999999999999999999999999999999999999999999998
No 11
>PLN00035 histone H4; Provisional
Probab=97.78 E-value=0.00014 Score=54.56 Aligned_cols=61 Identities=13% Similarity=0.142 Sum_probs=55.4
Q ss_pred HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhh
Q 032181 62 YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLV 123 (146)
Q Consensus 62 YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsrEIqtAVrLl 123 (146)
-|.|+++.-- -..||..+..-|...++++++.|+.+|..++.+.+|+||+..||..|++..
T Consensus 34 ~IrRLARr~G-vkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr~ 94 (103)
T PLN00035 34 AIRRLARRGG-VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 94 (103)
T ss_pred HHHHHHHHcC-cccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHc
Confidence 4888888764 578999999999999999999999999999999999999999999998753
No 12
>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=97.72 E-value=0.00016 Score=50.11 Aligned_cols=60 Identities=18% Similarity=0.372 Sum_probs=49.3
Q ss_pred HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHH
Q 032181 62 YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVR 121 (146)
Q Consensus 62 YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsrEIqtAVr 121 (146)
-+...++||-|+..+...+..+|-.+.+|+.+.+.+.|.+||++.+..||..+|||...+
T Consensus 4 ~l~~Lv~~iDp~~~ld~~vee~Ll~laddFv~~v~~~ac~lAKhR~s~tle~~Dv~~~Le 63 (68)
T PF03847_consen 4 KLQELVKQIDPNEKLDPDVEELLLELADDFVDDVVSFACRLAKHRKSSTLEVKDVQLHLE 63 (68)
T ss_dssp HHHHHHHCC-SS----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHH
T ss_pred HHHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCHHHHHHHHH
Confidence 366789999999999999999999999999999999999999999999999999998765
No 13
>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=97.72 E-value=0.0002 Score=51.82 Aligned_cols=60 Identities=15% Similarity=0.199 Sum_probs=54.0
Q ss_pred HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHh
Q 032181 62 YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRL 122 (146)
Q Consensus 62 YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsrEIqtAVrL 122 (146)
-|.|+++.-- -..||..+..-+...++.+++.|+.+|..++.+.+|+|||..||..|++.
T Consensus 18 ~I~RLarr~G-vkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~alkr 77 (85)
T cd00076 18 AIRRLARRGG-VKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKR 77 (85)
T ss_pred HHHHHHHHcC-cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHH
Confidence 5788887653 47899999999999999999999999999999999999999999998874
No 14
>PTZ00015 histone H4; Provisional
Probab=97.66 E-value=0.00026 Score=52.90 Aligned_cols=61 Identities=13% Similarity=0.233 Sum_probs=54.7
Q ss_pred HHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHh
Q 032181 61 IYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRL 122 (146)
Q Consensus 61 ~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsrEIqtAVrL 122 (146)
.-|.|+++.- --..||..+..-+..+++++++.|+.+|..++.|.+|+|||..||..|++.
T Consensus 34 ~~IrRLarr~-GvkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~AlKr 94 (102)
T PTZ00015 34 GAIRRLARRG-GVKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALKR 94 (102)
T ss_pred HHHHHHHHHc-CCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHh
Confidence 4588888864 346799999999999999999999999999999999999999999998864
No 15
>smart00428 H3 Histone H3.
Probab=97.50 E-value=0.00072 Score=50.68 Aligned_cols=68 Identities=19% Similarity=0.257 Sum_probs=62.6
Q ss_pred chhHHHHHHHHhhhhcC--CCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhh
Q 032181 56 IETYKIYIFKVLKQVHP--DIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLV 123 (146)
Q Consensus 56 ~esy~~YIyKVLKQVhp--d~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsrEIqtAVrLl 123 (146)
+-.|+..+..+..+..+ |..+++.|+..|.....+.+-.+..+|..++.+.+|.||..+|||-|.||-
T Consensus 32 k~pF~RLVREI~~~~~~~~~~R~~~~Al~aLQeasE~ylv~lfeda~~~a~HAkRvTl~~kDi~La~rir 101 (105)
T smart00428 32 KAPFQRLVREIAQKFTTGVDLRFQSSAIMALQEAAEAYLVGLFEDTNLLAIHAKRVTIMPKDIQLARRIR 101 (105)
T ss_pred cccHHHHHHHHHHHcCCCCCceeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccCcHhhHHHHHHHh
Confidence 46788889989888888 899999999999999999999999999999999999999999999998863
No 16
>cd07979 TAF9 TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. The TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Human TAF9 has a paralogue gene (TAF9L) whi
Probab=97.29 E-value=0.002 Score=48.51 Aligned_cols=65 Identities=12% Similarity=0.155 Sum_probs=57.6
Q ss_pred HHHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCc
Q 032181 60 KIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLVLP 125 (146)
Q Consensus 60 ~~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsrEIqtAVrLlLP 125 (146)
...|.++|+.- -...++.++...|..|+....+.|..+|..++.+.+|+||+..||..|+...+.
T Consensus 4 ~~~v~~iLk~~-Gv~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r~~ 68 (117)
T cd07979 4 ARVIAAILKSM-GITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRVD 68 (117)
T ss_pred HHHHHHHHHHC-CCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhc
Confidence 35688899875 235679999999999999999999999999999999999999999999988774
No 17
>smart00417 H4 Histone H4.
Probab=97.23 E-value=0.00087 Score=47.43 Aligned_cols=56 Identities=13% Similarity=0.173 Sum_probs=48.9
Q ss_pred HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHH
Q 032181 62 YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQT 118 (146)
Q Consensus 62 YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsrEIqt 118 (146)
-|.|+++.- ---.||..+..-+..+++++++.|+.+|..++.+.+|+|++..||..
T Consensus 18 ~IrRLaRr~-GvkRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~~ 73 (74)
T smart00417 18 AIRRLARRG-GVKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVY 73 (74)
T ss_pred HHHHHHHHc-CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHhee
Confidence 477888764 23678999999999999999999999999999999999999999853
No 18
>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [Transcription]
Probab=96.76 E-value=0.006 Score=49.21 Aligned_cols=61 Identities=20% Similarity=0.313 Sum_probs=56.1
Q ss_pred HHHHhhhhcCC-CCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhh
Q 032181 63 IFKVLKQVHPD-IGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLV 123 (146)
Q Consensus 63 IyKVLKQVhpd-~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsrEIqtAVrLl 123 (146)
|-|+.|+.-|. ..||..|-..|.-.|..+.-=|..||+..++..+|+||+..||..|+--|
T Consensus 38 V~RIMK~~lP~naKIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIngdDllwAm~tL 99 (168)
T KOG0869|consen 38 VSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASEKCQREKRKTINGDDLLWAMSTL 99 (168)
T ss_pred HHHHHHhcCCcccccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCcccHHHHHHHHHHc
Confidence 78889988776 67999999999999999999999999999999999999999999998644
No 19
>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=96.60 E-value=0.01 Score=47.49 Aligned_cols=66 Identities=20% Similarity=0.324 Sum_probs=59.4
Q ss_pred HHHHHhhhhcC-CCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCchH
Q 032181 62 YIFKVLKQVHP-DIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLVLPGE 127 (146)
Q Consensus 62 YIyKVLKQVhp-d~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsrEIqtAVrLlLPGE 127 (146)
-|.|++|.+-| |+.+..+|.++++..--.+..-|+.||.+++....|+||....|+-|..-|==||
T Consensus 17 tv~KmIke~lP~d~rvakeareliincCvEFI~liSsEAneic~~e~KKTIa~EHV~KALe~LgF~e 83 (156)
T KOG0871|consen 17 TVNKMIKEMLPKDVRVAKEARELIINCCVEFINLISSEANEICNKEAKKTIAPEHVIKALENLGFGE 83 (156)
T ss_pred HHHHHHHHhCCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHhHHhcccCCHHHHHHHHHHcchHH
Confidence 48899999999 9999999999988888889999999999999999999999999999997653343
No 20
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=96.47 E-value=0.0044 Score=52.99 Aligned_cols=68 Identities=18% Similarity=0.317 Sum_probs=60.7
Q ss_pred HHHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHh----hCchH
Q 032181 60 KIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRL----VLPGE 127 (146)
Q Consensus 60 ~~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsrEIqtAVrL----lLPGE 127 (146)
..-|...++||.+++.|..+.-++|-.+..|+.+.|..-++.||++.+..||-.|||+..+.- -|||.
T Consensus 157 k~kl~dLvqqId~~~~LD~dVedlLleiADdFV~sii~~sC~LAKHRKsdtlEvrDIqLhLEr~~Nm~iPgf 228 (258)
T KOG1142|consen 157 KRKLDDLVQQIDGTTKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHRKSDTVEVRDIQLHLERNFNMEIPGF 228 (258)
T ss_pred ccchhHHHHhhcCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccchhheeeeeeccccccCCCc
Confidence 344888999999999999999999999999999999999999999999999999999987653 34654
No 21
>smart00414 H2A Histone 2A.
Probab=96.42 E-value=0.0088 Score=44.73 Aligned_cols=65 Identities=23% Similarity=0.291 Sum_probs=55.2
Q ss_pred hHHH-HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHh
Q 032181 58 TYKI-YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRL 122 (146)
Q Consensus 58 sy~~-YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsrEIqtAVrL 122 (146)
.|.. .|+|.|+.-+--..|+..|.--|-..+..+...|-+-|..-++.+++.-||.|+||.|++-
T Consensus 9 ~fPVgRi~r~Lk~~~~~~Rv~~~A~VyLaAvLEYLtaEILeLagn~a~~~k~~rItp~hi~lAi~n 74 (106)
T smart00414 9 QFPVGRIHRLLRKGTYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKRRITPRHLQLAIRN 74 (106)
T ss_pred cCchHHHHHHHHcCccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchHHHhhhccC
Confidence 4443 7999999987677999989888888888888888888888889999999999999999983
No 22
>PLN00156 histone H2AX; Provisional
Probab=96.40 E-value=0.011 Score=46.47 Aligned_cols=65 Identities=26% Similarity=0.268 Sum_probs=58.6
Q ss_pred hhHHH-HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHH
Q 032181 57 ETYKI-YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVR 121 (146)
Q Consensus 57 esy~~-YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsrEIqtAVr 121 (146)
-.|.. -|+|.|+.-+-...|+..|.-.|-..+.++...|-+-|..-++.+++.-|++|.||.|++
T Consensus 28 L~FPVgRi~R~Lk~g~ya~RVga~ApVYLAAVLEYLtaEVLELAgNaa~d~kk~RItPrHi~lAIr 93 (139)
T PLN00156 28 LQFPVGRIARFLKAGKYAERVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR 93 (139)
T ss_pred cccchHHHHHHHhcCChhhccCCccHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHhhcc
Confidence 35655 699999998777899999999999999999999999999999999999999999999997
No 23
>PLN00157 histone H2A; Provisional
Probab=96.36 E-value=0.0068 Score=47.30 Aligned_cols=65 Identities=26% Similarity=0.273 Sum_probs=58.4
Q ss_pred hhHHH-HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHH
Q 032181 57 ETYKI-YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVR 121 (146)
Q Consensus 57 esy~~-YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsrEIqtAVr 121 (146)
-.|.. -|+|.|++-+-...|+..|.--|-..+..+...|-+-|..-++.+++.-|+.|.||.|++
T Consensus 25 L~FPVgRi~R~Lk~g~~a~RIg~~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~ 90 (132)
T PLN00157 25 LQFPVGRIARYLKAGKYATRVGAGAPVYLAAVLEYLAAEVLELAGNAARDNKKSRIVPRHIQLAVR 90 (132)
T ss_pred cccchHHHHHHHhcCchhhhcCCCcHhHHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHhhccc
Confidence 45654 699999998777899999999999999999999999999999999999999999999997
No 24
>PF02969 TAF: TATA box binding protein associated factor (TAF); InterPro: IPR004823 The TATA box binding protein associated factor (TAF) is part of the transcription initiation factor TFIID multimeric protein complex. TFIID plays a central role in mediating promoter responses to various activators and repressors. It binds tightly to TAFII-250 and directly interacts with TAFII-40. TFIID is composed of TATA binding protein (TBP)and a number of TBP-associated factors (TAFS). TAF proteins adopt a histone-like fold.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus; PDB: 1TAF_B.
Probab=96.36 E-value=0.017 Score=40.04 Aligned_cols=47 Identities=23% Similarity=0.383 Sum_probs=38.5
Q ss_pred CcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHH
Q 032181 75 GISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVR 121 (146)
Q Consensus 75 gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsrEIqtAVr 121 (146)
.++.++-..|-.=++.-+..|..+|.+++++.+|.+||..||..|.|
T Consensus 20 ~l~de~a~~La~dveyrlreiiq~a~kfm~hskR~~Lt~~Di~~ALr 66 (66)
T PF02969_consen 20 NLSDEAAKALAEDVEYRLREIIQEALKFMRHSKRTKLTTDDINSALR 66 (66)
T ss_dssp -B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH-
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhC
Confidence 45778888888888888999999999999999999999999999875
No 25
>PTZ00017 histone H2A; Provisional
Probab=96.32 E-value=0.0083 Score=46.89 Aligned_cols=65 Identities=23% Similarity=0.277 Sum_probs=56.9
Q ss_pred hhHHH-HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHH
Q 032181 57 ETYKI-YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVR 121 (146)
Q Consensus 57 esy~~-YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsrEIqtAVr 121 (146)
-.|.. -|+|.|++-+--..|+..|.--|-..+..++..|-+-|..-++.+++.-||.|.||.|++
T Consensus 26 L~FPVgRi~R~Lk~g~~a~RV~a~A~VYLAAVLEYLtaEILELAgNaa~d~kk~RItPrHi~lAI~ 91 (134)
T PTZ00017 26 LQFPVGRVHRYLKKGRYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAAKDNKKKRITPRHIQLAIR 91 (134)
T ss_pred cccchHHHHHHHhccchhccccccchhhhHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHhhcc
Confidence 44554 699999988777799999988888888888888888899999999999999999999998
No 26
>cd08050 TAF6 TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and are involved in forming Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs functions such as serving as
Probab=96.21 E-value=0.015 Score=50.36 Aligned_cols=49 Identities=20% Similarity=0.388 Sum_probs=46.4
Q ss_pred CcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhh
Q 032181 75 GISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLV 123 (146)
Q Consensus 75 gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsrEIqtAVrLl 123 (146)
.+|.+|...|..-+.+....|+.||.+++++.+|+||+..||..|++..
T Consensus 16 ~~~~~a~~~La~~~e~~~~~i~~~A~k~~~hskR~~l~~~Di~~Al~~~ 64 (343)
T cd08050 16 SLSDEVAQLLAEDVEYRLREIIQEAAKFMRHSKRRKLTTSDVNHALRLR 64 (343)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHHh
Confidence 6789999999999999999999999999999999999999999999864
No 27
>PLN00153 histone H2A; Provisional
Probab=96.13 E-value=0.012 Score=45.81 Aligned_cols=65 Identities=26% Similarity=0.268 Sum_probs=58.4
Q ss_pred hhHHH-HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHH
Q 032181 57 ETYKI-YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVR 121 (146)
Q Consensus 57 esy~~-YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsrEIqtAVr 121 (146)
-.|.. -|+|.|++-+.-..|+..|.--|-..+..+...|-+-|..-++.|++.-|++|.||.|++
T Consensus 23 L~FpVgRi~R~Lr~g~~a~Rvga~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~ 88 (129)
T PLN00153 23 LQFPVGRIARYLKKGKYAERIGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKNRIVPRHIQLAIR 88 (129)
T ss_pred cccchHHHHHHHhcCchhhccCCCchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHhhcc
Confidence 45654 699999998777899999999999999999999999999999999999999999999997
No 28
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=95.65 E-value=0.097 Score=36.22 Aligned_cols=60 Identities=10% Similarity=0.158 Sum_probs=48.3
Q ss_pred HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHh
Q 032181 62 YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRL 122 (146)
Q Consensus 62 YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsrEIqtAVrL 122 (146)
.|-++|+..- =-+++..|++.|-.++.+.+..|+.++..++.+.+|.+.+..||..|+.-
T Consensus 11 ~Vaqil~~~G-f~~~~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~~~Dv~~Al~~ 70 (77)
T smart00576 11 AVAQILESAG-FDSFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPNLGDVVLALEN 70 (77)
T ss_pred HHHHHHHHcC-ccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence 3444444331 13467889999999999999999999999999999999999999988764
No 29
>PTZ00252 histone H2A; Provisional
Probab=95.60 E-value=0.034 Score=43.58 Aligned_cols=66 Identities=17% Similarity=0.178 Sum_probs=55.7
Q ss_pred chhHHH-HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhh--cCCCCcChHHHHHHHH
Q 032181 56 IETYKI-YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARY--NKKPTITSREIQTAVR 121 (146)
Q Consensus 56 ~esy~~-YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~--nkk~TltsrEIqtAVr 121 (146)
.-.|.. -|+|.|++-+-...|++.|.-.|-..+.+++..|-+-|..-++- |++.-|+.|.||.||+
T Consensus 23 GL~FPVgRi~R~Lr~g~ya~RIga~ApVYLAAVLEYLtaEVLELAgnaa~d~~~kk~RItPrHi~lAIr 91 (134)
T PTZ00252 23 GLIFPVGRVGSLLRRGQYARRIGASGAVYMAAVLEYLTAELLELSVKAAAQQAKKPKRLTPRTVTLAVR 91 (134)
T ss_pred CccCchHHHHHHHHcCCcccccCCccHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccccHHHHHhhcc
Confidence 355665 69999999888889999998888888888888888888887754 8889999999999997
No 30
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=95.56 E-value=0.029 Score=43.61 Aligned_cols=60 Identities=25% Similarity=0.298 Sum_probs=55.5
Q ss_pred HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHH
Q 032181 62 YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVR 121 (146)
Q Consensus 62 YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsrEIqtAVr 121 (146)
-|.|+||.-.-.+.|+++|.--+.-.+..+.-.|.+-|.+-++-++++-|++|.||-|+|
T Consensus 31 rvkr~lk~~~~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~kkkri~PrHlqlAIr 90 (132)
T COG5262 31 RVKRLLKKGNYRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRIIPRHLQLAIR 90 (132)
T ss_pred HHHHHHHcCccceeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhcCcceechHHHHHHhc
Confidence 599999977777999999998888889999999999999999999999999999999998
No 31
>PLN00154 histone H2A; Provisional
Probab=95.54 E-value=0.037 Score=43.45 Aligned_cols=65 Identities=20% Similarity=0.217 Sum_probs=54.6
Q ss_pred hhHHH-HHHHHhhhhc-CCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHH
Q 032181 57 ETYKI-YIFKVLKQVH-PDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVR 121 (146)
Q Consensus 57 esy~~-YIyKVLKQVh-pd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsrEIqtAVr 121 (146)
-.|-. -|+|.||+-. -...|++.|.-.|-..+..+.-.|-+-|.+-++.+++.-||.|.||.|++
T Consensus 37 L~FPVgRi~r~Lk~g~~~~~RVga~ApVYLAAVLEYLtAEVLELAGNaA~d~kk~RItPrHi~lAIr 103 (136)
T PLN00154 37 LQFPVGRIHRQLKQRVSAHGRVGATAAVYTAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 103 (136)
T ss_pred ccCchHHHHHHHHhhhhhccccccchHHHHHHHHHHHHHHHHHHHHHHHHhhCCceecHHHhhhhcc
Confidence 34544 6999999975 45689998988888888888888888888889999999999999999998
No 32
>PLN00121 histone H3; Provisional
Probab=95.28 E-value=0.092 Score=41.16 Aligned_cols=66 Identities=18% Similarity=0.237 Sum_probs=56.1
Q ss_pred hhHHHHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHh
Q 032181 57 ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRL 122 (146)
Q Consensus 57 esy~~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsrEIqtAVrL 122 (146)
-.|...|..|.....++..+.+.|+.-|..-..+.+-.+-+++.-.+.|.+|-||..+|||-+.||
T Consensus 66 ~pF~RLVREI~~~~~~~~Rf~~~Al~ALQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~ri 131 (136)
T PLN00121 66 LPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRI 131 (136)
T ss_pred ccHHHHHHHHHHHhCccceeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcceecchhhHHHHHHh
Confidence 457777777887778889999999988887777777777778899999999999999999999875
No 33
>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription]
Probab=95.06 E-value=0.13 Score=41.82 Aligned_cols=65 Identities=20% Similarity=0.274 Sum_probs=50.9
Q ss_pred HHHHHHHhhhhcCC--CCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhC
Q 032181 60 KIYIFKVLKQVHPD--IGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLVL 124 (146)
Q Consensus 60 ~~YIyKVLKQVhpd--~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsrEIqtAVrLlL 124 (146)
..-|-|+.|.+-|+ .+||.+|...|-.-..=+..-+..-|..+|+-++|+||+..||..|++-+=
T Consensus 13 ~AiI~rlvke~l~E~~vsisKeA~~Ai~raAtVFv~~Lts~s~e~A~~q~rKt~sadDVl~aL~Eie 79 (172)
T KOG0870|consen 13 NAIITRLVKEVLPESNVSISKEARLAIARAATVFVIFLTSVSNEIAKDQKRKTISADDVLKALDEIE 79 (172)
T ss_pred HHHHHHHHHHhCccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCcccHHHHHHHHHHhc
Confidence 34577888888776 689999988776644444445667777899999999999999999998653
No 34
>PTZ00018 histone H3; Provisional
Probab=95.03 E-value=0.12 Score=40.59 Aligned_cols=66 Identities=18% Similarity=0.237 Sum_probs=55.7
Q ss_pred hhHHHHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHh
Q 032181 57 ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRL 122 (146)
Q Consensus 57 esy~~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsrEIqtAVrL 122 (146)
-.|...+..|..+..++..+.+.|+.-|..-..+.+-.+-+++.-.+.+.+|-||..+|||-+.||
T Consensus 66 ~pF~RLVREI~~~~~~~~rf~~~al~aLQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~ri 131 (136)
T PTZ00018 66 LPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRI 131 (136)
T ss_pred ccHHHHHHHHHHHcCCcceeeHHHHHHHHHHHHHHHHHHhhhhHHHHHhhcceecchhhHHHHHHh
Confidence 456777777777777889999999998887777777777778899999999999999999999875
No 35
>PF15510 CENP-W: Centromere kinetochore component W
Probab=94.89 E-value=0.05 Score=40.68 Aligned_cols=64 Identities=25% Similarity=0.398 Sum_probs=52.8
Q ss_pred HHHHHHHhhhhcCCCCc--chHHH--------------HHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhh
Q 032181 60 KIYIFKVLKQVHPDIGI--SSKAM--------------GIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLV 123 (146)
Q Consensus 60 ~~YIyKVLKQVhpd~gI--SskAm--------------~ImnSfvnDiferIA~EAs~La~~nkk~TltsrEIqtAVrLl 123 (146)
..++.||+|+--|.+.+ +.+.| --||-++ +..|+|+||-.-+.-|++.||....|+.|.+.+
T Consensus 19 rgfLkrv~Kr~KphlRl~~~~Dllv~~~~f~~~~~~~~vhLncLL--FvhrLAEEaRtnA~EnK~~~Ik~~Hv~AaaKvi 96 (102)
T PF15510_consen 19 RGFLKRVFKRQKPHLRLETSGDLLVRFCPFSGWQWGGEVHLNCLL--FVHRLAEEARTNACENKCGTIKKEHVLAAAKVI 96 (102)
T ss_pred hHHHHHHHHhcCCceeecccccHHHhhcccccccccceeehhHHH--HHHHHHHHHHHHHHHHhhccccHHHHHHHHHHH
Confidence 46789999998888776 44444 3356665 678999999999999999999999999999988
Q ss_pred Cc
Q 032181 124 LP 125 (146)
Q Consensus 124 LP 125 (146)
|-
T Consensus 97 LK 98 (102)
T PF15510_consen 97 LK 98 (102)
T ss_pred HH
Confidence 74
No 36
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=94.56 E-value=0.14 Score=36.18 Aligned_cols=59 Identities=15% Similarity=0.335 Sum_probs=47.9
Q ss_pred HHHHhhhh--cCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHH
Q 032181 63 IFKVLKQV--HPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVR 121 (146)
Q Consensus 63 IyKVLKQV--hpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsrEIqtAVr 121 (146)
|-++..++ ..++.+|.+.+.-|..++.+..+.++.+---++++.+|+||+..|+.-.+|
T Consensus 11 v~ki~ee~~~~~~~~~s~~~i~al~ELv~~q~~~~a~DLe~FAkHA~R~tI~~dDV~Ll~R 71 (76)
T PF15630_consen 11 VGKIVEEEAKEKGVEVSPQFIAALTELVYKQLENLAKDLEAFAKHAGRSTINMDDVKLLAR 71 (76)
T ss_dssp HHHHHHHCCCCTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHTT
T ss_pred HHHHHHHHHhccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHHHhh
Confidence 45566666 466788999999999999999999999999999999999999999875544
No 37
>KOG1756 consensus Histone 2A [Chromatin structure and dynamics]
Probab=94.04 E-value=0.15 Score=39.95 Aligned_cols=60 Identities=25% Similarity=0.306 Sum_probs=52.6
Q ss_pred HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHH
Q 032181 62 YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVR 121 (146)
Q Consensus 62 YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsrEIqtAVr 121 (146)
-|.|+|+.-+.-..||..|--.|.-.+..+--.|.+-|..-++-|++.-|++|.||-|++
T Consensus 32 ri~r~Lr~~~~~~ri~~gapV~laavLeYL~Aeile~agnaardnkk~ri~PrH~~lAI~ 91 (131)
T KOG1756|consen 32 RIHRLLRKGRYAQRVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRITPRHLQLAIR 91 (131)
T ss_pred HHHHHHHccchhhhccCCChHHHHHHHHHHHHHHHHHhHHHhhhcCccccChHHHHHHHh
Confidence 699999997778999999988888777777777777778888999999999999999998
No 38
>PLN00161 histone H3; Provisional
Probab=93.48 E-value=0.5 Score=37.14 Aligned_cols=67 Identities=15% Similarity=0.197 Sum_probs=53.1
Q ss_pred hhHHHHHHHHhhhhcC-CCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhh
Q 032181 57 ETYKIYIFKVLKQVHP-DIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLV 123 (146)
Q Consensus 57 esy~~YIyKVLKQVhp-d~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsrEIqtAVrLl 123 (146)
-.|+.-+..|..+..+ |+.+.+.|+.-|..-..+.+-.+-+++.-.+.+.+|-||..+|||-|.||-
T Consensus 59 lPF~RLVREI~~~~~~~~~Rfq~~Al~ALQEAsEayLV~lFeda~lcaiHAkRVTlm~kDm~La~rir 126 (135)
T PLN00161 59 LPFARLVREISNEMLREPFRWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMPKDMQLARRIR 126 (135)
T ss_pred ccHHHHHHHHHHhcCCCCcEeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccchhhHHHHHHhc
Confidence 4566666666666554 688999998888777766666666788889999999999999999998763
No 39
>PLN00160 histone H3; Provisional
Probab=92.23 E-value=0.97 Score=33.59 Aligned_cols=66 Identities=14% Similarity=0.142 Sum_probs=50.8
Q ss_pred hhHHHHHHHHhhhhcC-CCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHh
Q 032181 57 ETYKIYIFKVLKQVHP-DIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRL 122 (146)
Q Consensus 57 esy~~YIyKVLKQVhp-d~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsrEIqtAVrL 122 (146)
-.|..-+..+.-.... +..+.+.|+.-|..-..+.+-.+-+++.-.+.+.+|-||..+|||-+.|+
T Consensus 25 ~pF~RLVREI~~~~~~~~~Rfq~~Al~ALQeAsEayLv~lfed~~lca~HakRVTl~~kD~~L~~ri 91 (97)
T PLN00160 25 LPFARLVREIQMEMSREAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTIMPKDMQLARRI 91 (97)
T ss_pred ccHHHHHHHHHHHcCCCCcEeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcccccchhhHHHHHHh
Confidence 4566666666555433 48889999888877666666666668888999999999999999999874
No 40
>PF15511 CENP-T: Centromere kinetochore component CENP-T; PDB: 3B0D_T 3B0C_T 3VH5_T 3VH6_T.
Probab=92.05 E-value=0.43 Score=42.69 Aligned_cols=55 Identities=18% Similarity=0.256 Sum_probs=42.1
Q ss_pred HHHHHHhhhhc-----CCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHH
Q 032181 61 IYIFKVLKQVH-----PDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSRE 115 (146)
Q Consensus 61 ~YIyKVLKQVh-----pd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsrE 115 (146)
.+|.+++.... -.+.||.+||..+......+||.|+..=.-.+.+.+|+||...|
T Consensus 355 ~~vK~la~~~ak~s~~sK~kiskdal~aleqasdwfFeQl~dDL~aYA~HAgRKTIdesD 414 (414)
T PF15511_consen 355 GVVKKLAQHFAKSSGGSKMKISKDALEALEQASDWFFEQLGDDLEAYAKHAGRKTIDESD 414 (414)
T ss_dssp HHHHHHHHHHH-------S-B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHH
T ss_pred cHHHHHHHHHHHhhcccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCCCC
Confidence 35555555543 46899999999999999999999999999999999999998765
No 41
>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=91.63 E-value=1.8 Score=29.58 Aligned_cols=49 Identities=14% Similarity=0.253 Sum_probs=44.5
Q ss_pred CCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHh
Q 032181 74 IGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRL 122 (146)
Q Consensus 74 ~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsrEIqtAVrL 122 (146)
.+++..|+++|-.++.+.+..|+..+...+....|...+..||..|..-
T Consensus 22 ~~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~~ 70 (77)
T PF07524_consen 22 DSASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPNLQDVEQALEE 70 (77)
T ss_pred cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence 4578899999999999999999999999999999999999999988753
No 42
>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=91.13 E-value=0.72 Score=35.63 Aligned_cols=60 Identities=18% Similarity=0.310 Sum_probs=44.4
Q ss_pred HHHHHHhhhhcCCCCcc---hHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhC
Q 032181 61 IYIFKVLKQVHPDIGIS---SKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLVL 124 (146)
Q Consensus 61 ~YIyKVLKQVhpd~gIS---skAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsrEIqtAVrLlL 124 (146)
..|.-+|+. +||+ .+....|-.|+.-..-.|-.+|..++.+.++.+|+..||+.|+...+
T Consensus 16 ~~i~~iL~~----~Gv~~yeprVv~qLLEfayRYt~~vL~DA~~ya~hA~~~~i~~~DVrLAi~~r~ 78 (129)
T PF02291_consen 16 RVIHLILKS----MGVTEYEPRVVNQLLEFAYRYTSDVLEDAQVYADHAGRSTIDADDVRLAIQSRL 78 (129)
T ss_dssp HHHHHHHHH----TT---B-THHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHHHHT-
T ss_pred HHHHHHHHH----cCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHH
Confidence 446666654 6774 46677777777777788889999999999999999999999998654
No 43
>KOG2549 consensus Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=89.17 E-value=1.4 Score=41.59 Aligned_cols=50 Identities=14% Similarity=0.280 Sum_probs=45.4
Q ss_pred CCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhh
Q 032181 74 IGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLV 123 (146)
Q Consensus 74 ~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsrEIqtAVrLl 123 (146)
..|+.++-.+|-.-|..=.+.|+.+|+++.++.+|.+||..||.-|.|.+
T Consensus 27 ~nl~deaa~~La~dv~yrikEI~Q~aaKfm~hskR~kLtv~DV~~ALr~~ 76 (576)
T KOG2549|consen 27 TNLNDEAALLLAEDVEYRIKEIVQDAAKFMVHSKRTKLTVDDVDYALRSL 76 (576)
T ss_pred cccCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcCcHHHHHHHHhhc
Confidence 44678999998888889999999999999999999999999999999864
No 44
>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=87.18 E-value=0.87 Score=32.91 Aligned_cols=47 Identities=15% Similarity=0.253 Sum_probs=23.5
Q ss_pred CcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHH
Q 032181 75 GISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVR 121 (146)
Q Consensus 75 gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsrEIqtAVr 121 (146)
--+.++..+|..+|.+-.-.+..+|..++...++..|+..||..++|
T Consensus 19 ~P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~rg~~~i~~eDl~F~lR 65 (93)
T PF02269_consen 19 EPLPETVDLVEDIVREYIIELCQEAMEVAQRRGSKKIKVEDLLFLLR 65 (93)
T ss_dssp S--HHHHHHHHHHHHHHHHHHHHHHHC--------------------
T ss_pred CCcHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCcCcHHHHHHHHh
Confidence 44678999999999999999999999999999999999999999887
No 45
>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=86.33 E-value=5.9 Score=28.44 Aligned_cols=60 Identities=13% Similarity=0.203 Sum_probs=49.9
Q ss_pred HHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCC---CCcChHHHHHHHHhh
Q 032181 63 IFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKK---PTITSREIQTAVRLV 123 (146)
Q Consensus 63 IyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk---~TltsrEIqtAVrLl 123 (146)
|.|++.++-. .+++.....+|..+-.-+.-.|.++|..+..-... ..|.++.|..|+|.+
T Consensus 22 iKr~~~~~~~-~~v~~~v~i~v~glaKvFVGeivE~A~~V~~~~~~~~~~Pl~P~HireA~rrl 84 (85)
T cd08048 22 IKRLIQSVTG-QSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGEANTGPLQPRHLREAYRRL 84 (85)
T ss_pred HHHHHHHHcC-CCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCCCCCcHHHHHHHHHh
Confidence 7777777755 78888888888888777888999999998877554 899999999999976
No 46
>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=84.82 E-value=4.3 Score=29.50 Aligned_cols=51 Identities=10% Similarity=0.289 Sum_probs=42.0
Q ss_pred cCCC-CcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHh
Q 032181 71 HPDI-GISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRL 122 (146)
Q Consensus 71 hpd~-gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsrEIqtAVrL 122 (146)
+-|. .-..++..+|..+|.+..-.|..+|..++. .++.-++..||..++|-
T Consensus 15 ~GD~~~P~~eTv~llE~iv~~~i~~l~~~a~~~A~-~r~~k~~~eD~~FliR~ 66 (92)
T cd07978 15 FGDVQNPLPETVDLLEDIVVEYIIELCHKAAEVAQ-RRRGKVKVEDLIFLLRK 66 (92)
T ss_pred cCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-cCCCCCCHHHHHHHHhc
Confidence 3443 346789999999999999999999999998 55555699999999873
No 47
>KOG3334 consensus Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=84.29 E-value=4 Score=32.63 Aligned_cols=57 Identities=16% Similarity=0.314 Sum_probs=42.1
Q ss_pred hhhcCCCCcch---HHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhC
Q 032181 68 KQVHPDIGISS---KAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLVL 124 (146)
Q Consensus 68 KQVhpd~gISs---kAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsrEIqtAVrLlL 124 (146)
.++-.++||.. +-+..|=.|..--.-.|-..|.-++.|.++.||+..||+.|+....
T Consensus 20 ~~iL~s~GI~eyEprVi~qlLefa~rYtt~vL~DA~vys~HA~ka~i~~eDVrlA~~~~~ 79 (148)
T KOG3334|consen 20 ASILKSLGIQEYEPRVINQLLEFAYRYTTTVLDDAKVYSSHAKKATIDAEDVRLAIQMRV 79 (148)
T ss_pred HHHHHHcCccccChHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHh
Confidence 33334567754 4444455555555567889999999999999999999999998654
No 48
>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=80.35 E-value=13 Score=27.08 Aligned_cols=62 Identities=15% Similarity=0.168 Sum_probs=44.4
Q ss_pred HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcC-CCCcChHHHHHHHHhh
Q 032181 62 YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNK-KPTITSREIQTAVRLV 123 (146)
Q Consensus 62 YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nk-k~TltsrEIqtAVrLl 123 (146)
-|.|+..++-.+.++|....-+|..+-.=+.-.|.++|..+..-.. -..|....|..|.|-|
T Consensus 28 ~ikkli~~~~~~qsv~~~v~i~v~g~aKvFVGEiVE~A~~Vq~~~~~~~pl~P~hlreA~rrL 90 (90)
T PF04719_consen 28 AIKKLINQVLGNQSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGETGPLQPDHLREAYRRL 90 (90)
T ss_dssp HHHHHHHHHHS-S---HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SS--HHHHHHHHHHH
T ss_pred HHHHHHHHHcCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcHHHHHHHHhC
Confidence 5899999998778999988888888887777888888888776433 3489999999998854
No 49
>PF14687 DUF4460: Domain of unknown function (DUF4460)
Probab=79.10 E-value=2.6 Score=31.65 Aligned_cols=38 Identities=16% Similarity=0.449 Sum_probs=30.9
Q ss_pred hhHHHHHHHHhhhhcCCC--------CcchHHHHHHHHHHHHHHHH
Q 032181 57 ETYKIYIFKVLKQVHPDI--------GISSKAMGIMNSFINDIFEK 94 (146)
Q Consensus 57 esy~~YIyKVLKQVhpd~--------gISskAm~ImnSfvnDifer 94 (146)
-....++......||||+ .+-.+++.+||+++..+..+
T Consensus 9 ~~l~~aLr~Fy~~VHPDlF~~~P~~k~~Ne~SLk~Ln~~Ld~l~~~ 54 (112)
T PF14687_consen 9 PDLRSALRPFYFAVHPDLFGQHPEEKQVNEESLKLLNSYLDSLKKR 54 (112)
T ss_pred HHHHHHHHHHHHHhCCcccccChHHHHhhHHHHHHHHHHHHHHhcc
Confidence 345678888999999993 35678899999999888774
No 50
>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=76.02 E-value=12 Score=35.16 Aligned_cols=61 Identities=21% Similarity=0.370 Sum_probs=47.6
Q ss_pred hhhcCCCCcchHHHHHHHHHHHHH-------HHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCchHH
Q 032181 68 KQVHPDIGISSKAMGIMNSFINDI-------FEKLAQEASRLARYNKKPTITSREIQTAVRLVLPGEL 128 (146)
Q Consensus 68 KQVhpd~gISskAm~ImnSfvnDi-------ferIA~EAs~La~~nkk~TltsrEIqtAVrLlLPGEL 128 (146)
++..++..|+...+..+..+...+ ...+..-|--+|..+.+.+++..||+.|++|+|+.-+
T Consensus 242 r~~~~~V~is~~~~~~l~~~~~~~~i~s~Ra~i~~~r~Ara~AaL~gr~~V~~~Dv~~A~~lvL~hR~ 309 (633)
T TIGR02442 242 RSLLPSVRISDSLIRFISELCIEFGVDGHRADIVMARAARALAALDGRRRVTAEDVREAAELVLPHRR 309 (633)
T ss_pred HHhCCCCCCCHHHHHHHHHHHHHhCCCCccHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHHHhhhhc
Confidence 345688899998888877777553 2334455556889999999999999999999998655
No 51
>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=72.87 E-value=4 Score=36.98 Aligned_cols=60 Identities=27% Similarity=0.389 Sum_probs=45.9
Q ss_pred HHHhhhhcCCCCcchHHHHHHHHHHHHH---HHHHHHHHhHHhhhcCCCCcChHHHHHHHHhh
Q 032181 64 FKVLKQVHPDIGISSKAMGIMNSFINDI---FEKLAQEASRLARYNKKPTITSREIQTAVRLV 123 (146)
Q Consensus 64 yKVLKQVhpd~gISskAm~ImnSfvnDi---ferIA~EAs~La~~nkk~TltsrEIqtAVrLl 123 (146)
.--||.|-.-.||+.=.=+.+.-+..|+ ...|..||+++..++||..||..||..|.|-+
T Consensus 8 ~et~KdvAeslGi~Ni~Dd~l~alamDlEYRI~ev~qea~KFmvhSKRtvLt~dDis~ALr~l 70 (450)
T COG5095 8 KETLKDVAESLGISNIDDDALRALAMDLEYRIKEVCQEASKFMVHSKRTVLTIDDISYALRSL 70 (450)
T ss_pred HHHHHHHHHHcCCcccccHHHHHHHHhHHHHHHHHHHHHHHHhhcccceeeeHHhHHHHHHhc
Confidence 4456777777888864444444444444 45578999999999999999999999999965
No 52
>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=71.62 E-value=7.4 Score=27.16 Aligned_cols=58 Identities=12% Similarity=0.205 Sum_probs=35.8
Q ss_pred HHHHHhhhh--cCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCC-cChHHHHHH
Q 032181 62 YIFKVLKQV--HPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPT-ITSREIQTA 119 (146)
Q Consensus 62 YIyKVLKQV--hpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~T-ltsrEIqtA 119 (146)
-|-|+|..- ++++.||..|+..+.-+++=+-..-...|...++-..... |...+++.-
T Consensus 4 li~rll~~~f~~~~tkIs~dal~l~~eyl~iFV~EAv~Ra~~~a~~e~~~~~le~e~LEki 64 (72)
T PF09415_consen 4 LIARLLHEHFKDDKTKISKDALKLSAEYLRIFVREAVARAAEQAEAEGDEGFLEVEHLEKI 64 (72)
T ss_dssp HHHHHHCTTSSSTT-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSEE-HHHHHHH
T ss_pred HHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHH
Confidence 366777754 4669999999888666664444444455555666666666 888888763
No 53
>TIGR01128 holA DNA polymerase III, delta subunit. subunit around DNA forming a DNA sliding clamp.
Probab=70.07 E-value=26 Score=28.25 Aligned_cols=66 Identities=23% Similarity=0.330 Sum_probs=51.2
Q ss_pred hhHHHHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhC
Q 032181 57 ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLVL 124 (146)
Q Consensus 57 esy~~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsrEIqtAVrLlL 124 (146)
.....||...+++. +..|+.++...|.+.+..=...+..|.-+|+.|....+||..+|+.-+.-..
T Consensus 114 ~~~~~~i~~~~~~~--g~~i~~~a~~~l~~~~~~d~~~l~~el~KL~~~~~~~~It~e~I~~~~~~~~ 179 (302)
T TIGR01128 114 QELPRWIQARLKKL--GLRIDPDAVQLLAELVEGNLLAIAQELEKLALYAPDGKITLEDVEEAVSDSA 179 (302)
T ss_pred HHHHHHHHHHHHHc--CCCCCHHHHHHHHHHhCcHHHHHHHHHHHHHhhCCCCCCCHHHHHHHHhhhh
Confidence 34455777777764 5789999999988888765668999999999997666899999987765443
No 54
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=69.91 E-value=7.5 Score=33.44 Aligned_cols=58 Identities=33% Similarity=0.281 Sum_probs=40.3
Q ss_pred HHHHhhhhcCCCCcchHHHHHHHHHHHHH-HHHHHHHHhHHhhhcCCCCcChHHHHHHHH
Q 032181 63 IFKVLKQVHPDIGISSKAMGIMNSFINDI-FEKLAQEASRLARYNKKPTITSREIQTAVR 121 (146)
Q Consensus 63 IyKVLKQVhpd~gISskAm~ImnSfvnDi-ferIA~EAs~La~~nkk~TltsrEIqtAVr 121 (146)
|.||.|-------||.+|--+ =+.+..| .+.+.-.|-..+..|+|+||.--||-.||.
T Consensus 115 IkkvMKtdedVkMisaEaPvl-Fak~~EiFI~ELTmRAW~~ae~NkRRtLQksDia~Av~ 173 (286)
T COG5208 115 IKKVMKTDEDVKMISAEAPVL-FAKITEIFIEELTMRAWINAEENKRRTLQKSDIAAAVK 173 (286)
T ss_pred HHHHHhcccchhheecccchH-HHHHHHHHHHHHHHHHHHHHhHhhhhHHHHHHHHHHHH
Confidence 444544322113567777444 3444444 477888999999999999999999999986
No 55
>PRK09522 bifunctional glutamine amidotransferase/anthranilate phosphoribosyltransferase; Provisional
Probab=69.53 E-value=7.8 Score=35.90 Aligned_cols=61 Identities=20% Similarity=0.313 Sum_probs=42.2
Q ss_pred hhcCCCCcchHHHHHHHHHHHHHHHHHHHH---HhHHhhhcCCCCcChHHHHHHHHhhCchHHH
Q 032181 69 QVHPDIGISSKAMGIMNSFINDIFEKLAQE---ASRLARYNKKPTITSREIQTAVRLVLPGELA 129 (146)
Q Consensus 69 QVhpd~gISskAm~ImnSfvnDiferIA~E---As~La~~nkk~TltsrEIqtAVrLlLPGELa 129 (146)
|-||+.-.|...+.||.+|++-.+...-.+ ..-|-+....+.||..|...++..+|-|+..
T Consensus 168 QFHPEs~~T~~G~~il~NFl~~~~~~~~~~~~~~~~l~~~~~~~~Lt~eea~~~~~~il~g~~~ 231 (531)
T PRK09522 168 QFHPESILTTQGARLLEQTLAWAQQKLEPTNTLQPILEKLYQAQTLSQQESHQLFSAVVRGELK 231 (531)
T ss_pred EecCccccCcchHHHHHHHHHHHhhcCCCCCCHHHHHHHhhcCCCCCHHHHHHHHHHHHcCCCC
Confidence 679999999999999999985432211000 0112222345799999999999999988743
No 56
>smart00350 MCM minichromosome maintenance proteins.
Probab=68.95 E-value=28 Score=31.67 Aligned_cols=66 Identities=18% Similarity=0.286 Sum_probs=47.8
Q ss_pred hhHHHHHHHHhhhhcCCCCcchHHHHHHHHHHHHHH-------------------HHHHHHHhHHhhhcCCCCcChHHHH
Q 032181 57 ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIF-------------------EKLAQEASRLARYNKKPTITSREIQ 117 (146)
Q Consensus 57 esy~~YIyKVLKQVhpd~gISskAm~ImnSfvnDif-------------------erIA~EAs~La~~nkk~TltsrEIq 117 (146)
+....||.-+=..++|. ||..++.++..|..++= +-|..-|--+|+..-+.+++..|+.
T Consensus 421 ~~l~~yi~~ar~~~~P~--ls~~~~~~i~~~y~~~R~~~~~~~~~~~~~~t~R~l~sliRla~A~A~l~~r~~V~~~Dv~ 498 (509)
T smart00350 421 EFLRKYIAYAREKIKPK--LSEEAAEKLVKAYVDLRKEDSQSEARSSIPITVRQLESIIRLSEAHAKMRLSDVVEEADVE 498 (509)
T ss_pred HHHHHHHHHHHhcCCCC--CCHHHHHHHHHHHHHhcccccccccccccCcCHHHHHHHHHHHHHHHHHcCCCccCHHHHH
Confidence 44566775554337786 78889888877766543 3344445567888999999999999
Q ss_pred HHHHhhC
Q 032181 118 TAVRLVL 124 (146)
Q Consensus 118 tAVrLlL 124 (146)
.|++|+.
T Consensus 499 ~ai~l~~ 505 (509)
T smart00350 499 EAIRLLR 505 (509)
T ss_pred HHHHHHH
Confidence 9999974
No 57
>COG1466 HolA DNA polymerase III, delta subunit [DNA replication, recombination, and repair]
Probab=68.67 E-value=20 Score=30.51 Aligned_cols=67 Identities=22% Similarity=0.288 Sum_probs=57.0
Q ss_pred hhHHHHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCc
Q 032181 57 ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLVLP 125 (146)
Q Consensus 57 esy~~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsrEIqtAVrLlLP 125 (146)
+..-.+|-+.+++. .+.|+.+|+..|..-++.=+--|..|-.+|+.|..-.+||..+|+..|--...
T Consensus 143 ~~l~~~i~~~~~~~--~l~i~~~a~~~L~~~~~~nl~~i~~Ei~KL~l~~~~~~I~~~~V~~~v~~~~~ 209 (334)
T COG1466 143 AELPQWIKKRAKEL--GLKIDQEAIQLLLEALGGNLLAIAQEIEKLALYAGDKEITLEDVEEVVSDVAE 209 (334)
T ss_pred HHHHHHHHHHHHHc--CCCCCHHHHHHHHHHhCCcHHHHHHHHHHHHHhCCCCcCCHHHHHHHHhcccc
Confidence 34556777777775 48899999999999998888899999999999999889999999999876554
No 58
>KOG1745 consensus Histones H3 and H4 [Chromatin structure and dynamics]
Probab=68.40 E-value=6.2 Score=31.13 Aligned_cols=54 Identities=24% Similarity=0.419 Sum_probs=37.9
Q ss_pred HhhhhcCCCCcchHHHHHHHH----HHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhh
Q 032181 66 VLKQVHPDIGISSKAMGIMNS----FINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLV 123 (146)
Q Consensus 66 VLKQVhpd~gISskAm~ImnS----fvnDiferIA~EAs~La~~nkk~TltsrEIqtAVrLl 123 (146)
+.....+|+.+.+.|+.-|-- |+.++|| ...-.+.+.++-||-..|||-|.++-
T Consensus 76 i~q~f~~dLrfqs~Ai~ALQeA~EayLv~LfE----dtnlcAihAkRVTimpkdiQlArrir 133 (137)
T KOG1745|consen 76 IAQDFKTDLRFQSSAIAALQEAAEAYLVGLFE----DTNLCAIHAKRVTIMPKDIQLARRIR 133 (137)
T ss_pred HHhcccccceehHHHHHHHHHHHHHHHHHhcc----ccchhhhccceeEecccceehhhhcc
Confidence 333446788888877665443 4444554 34466788999999999999999964
No 59
>PRK07452 DNA polymerase III subunit delta; Validated
Probab=68.39 E-value=22 Score=29.53 Aligned_cols=62 Identities=18% Similarity=0.321 Sum_probs=50.2
Q ss_pred HHHHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhh--cCCCCcChHHHHHHHHh
Q 032181 59 YKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARY--NKKPTITSREIQTAVRL 122 (146)
Q Consensus 59 y~~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~--nkk~TltsrEIqtAVrL 122 (146)
...||...+++- +..|+..|...|...+..=+..+..|--+|+.| ....+||..+|+..|.-
T Consensus 135 l~~~i~~~~~~~--g~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~~It~~~V~~~v~~ 198 (326)
T PRK07452 135 LKQLVERTAQEL--GVKLTPEAAELLAEAVGNDSRRLYNELEKLALYAENSTKPISAEEVKALVSN 198 (326)
T ss_pred HHHHHHHHHHHc--CCCCCHHHHHHHHHHhCccHHHHHHHHHHHHHhccCCCCccCHHHHHHHhcc
Confidence 445666666554 477999999999998887778999999999999 56789999999987653
No 60
>PRK05574 holA DNA polymerase III subunit delta; Reviewed
Probab=64.32 E-value=35 Score=28.09 Aligned_cols=66 Identities=24% Similarity=0.259 Sum_probs=51.1
Q ss_pred hhHHHHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhC
Q 032181 57 ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLVL 124 (146)
Q Consensus 57 esy~~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsrEIqtAVrLlL 124 (146)
..+..||...+++. +..|+..|...|-..+..=+..+..|.-+|+.|.....||..+|+..+--..
T Consensus 149 ~~~~~~i~~~~~~~--g~~i~~~a~~~L~~~~~~d~~~l~~El~KL~l~~~~~~It~~~I~~~i~~~~ 214 (340)
T PRK05574 149 AELPQWIQQRLKQQ--GLQIDAAALQLLAERVEGNLLALAQELEKLALLYPDGKITLEDVEEAVPDSA 214 (340)
T ss_pred HHHHHHHHHHHHHc--CCCCCHHHHHHHHHHhCchHHHHHHHHHHHHhhcCCCCCCHHHHHHHHhhhh
Confidence 34566777777764 4679999999998888777778999999999997434499999987765433
No 61
>PRK08487 DNA polymerase III subunit delta; Validated
Probab=63.10 E-value=30 Score=29.34 Aligned_cols=63 Identities=22% Similarity=0.187 Sum_probs=52.3
Q ss_pred HHHHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCc
Q 032181 59 YKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLVLP 125 (146)
Q Consensus 59 y~~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsrEIqtAVrLlLP 125 (146)
...+|...+++. +..|+..|+..+.+.+..=+..|..|--+|+-|.. +||..+|+..|--...
T Consensus 140 l~~~i~~~~~~~--g~~i~~~a~~~L~~~~g~dl~~l~~ELeKL~ly~~--~It~edV~~~v~~~~e 202 (328)
T PRK08487 140 ALELLQERAKEL--GLDIDQNALNHLYFIHNEDLALAANELEKLAILNE--PITLKDIQELVFGLGS 202 (328)
T ss_pred HHHHHHHHHHHh--CCCCCHHHHHHHHHHhCcHHHHHHHHHHHHHHhcC--CCCHHHHHHHhccccc
Confidence 355788888775 47899999999999988888899999999999965 7999999998755443
No 62
>PRK14607 bifunctional glutamine amidotransferase/anthranilate phosphoribosyltransferase; Provisional
Probab=61.99 E-value=12 Score=34.47 Aligned_cols=59 Identities=19% Similarity=0.294 Sum_probs=42.2
Q ss_pred hhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCchHH
Q 032181 69 QVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLVLPGEL 128 (146)
Q Consensus 69 QVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsrEIqtAVrLlLPGEL 128 (146)
|-||+...+.....|+++|++-..+.+.- ..-|-+......||..|+..+++.+|-|+.
T Consensus 167 QFHPE~~~t~~g~~i~~nFl~~~~~~~~~-~~~i~~l~~g~~Lt~~ea~~~~~~il~g~~ 225 (534)
T PRK14607 167 QFHPESILTEEGKRILKNFLNYQREEIDI-KSYLKKLVEGEDLSFEEAEDVMEDITDGNA 225 (534)
T ss_pred EeCCCCCCChhHHHHHHHHHHHhhccCCH-HHHHHHhccCCCCCHHHHHHHHHHHHcCCC
Confidence 77999777888889999998754332211 112333345569999999999999998764
No 63
>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=61.73 E-value=49 Score=26.23 Aligned_cols=67 Identities=18% Similarity=0.201 Sum_probs=49.2
Q ss_pred hhHHHHHHHHhhhhcC--CCCcchHHHHHHHHHHHH---HHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhh
Q 032181 57 ETYKIYIFKVLKQVHP--DIGISSKAMGIMNSFIND---IFEKLAQEASRLARYNKKPTITSREIQTAVRLV 123 (146)
Q Consensus 57 esy~~YIyKVLKQVhp--d~gISskAm~ImnSfvnD---iferIA~EAs~La~~nkk~TltsrEIqtAVrLl 123 (146)
+....|+...|.+... +..+|.+++..+.....- ....++..+...+..++..+|+...|..+++-+
T Consensus 195 ~e~~~~l~~~l~~~g~~~~~~~~~~~~~~i~~~s~G~p~~i~~l~~~~~~~a~~~~~~~i~~~~v~~~~~~~ 266 (269)
T TIGR03015 195 EETREYIEHRLERAGNRDAPVFSEGAFDAIHRFSRGIPRLINILCDRLLLSAFLEEKREIGGEEVREVIAEI 266 (269)
T ss_pred HHHHHHHHHHHHHcCCCCCCCcCHHHHHHHHHHcCCcccHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHh
Confidence 5567788888887643 356898888877766554 345566666666667788999999999998754
No 64
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=59.90 E-value=32 Score=27.35 Aligned_cols=51 Identities=20% Similarity=0.217 Sum_probs=43.7
Q ss_pred CCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhh
Q 032181 73 DIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLV 123 (146)
Q Consensus 73 d~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsrEIqtAVrLl 123 (146)
|+....+|..|+-.---.+..-+..||...+....++||....|..|..-|
T Consensus 28 dl~ftKearei~in~cieFi~~lsseAne~ce~EaKKTIa~EHviKALenL 78 (148)
T COG5150 28 DLVFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHVIKALENL 78 (148)
T ss_pred cccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHhc
Confidence 578899999886555556777899999999999999999999999998754
No 65
>KOG1757 consensus Histone 2A [Chromatin structure and dynamics]
Probab=59.89 E-value=12 Score=29.15 Aligned_cols=61 Identities=28% Similarity=0.290 Sum_probs=39.6
Q ss_pred hhHHH-HHHHHhhhhcCC-CCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhc----CCCCcChHHHHHHHH
Q 032181 57 ETYKI-YIFKVLKQVHPD-IGISSKAMGIMNSFINDIFEKLAQEASRLARYN----KKPTITSREIQTAVR 121 (146)
Q Consensus 57 esy~~-YIyKVLKQVhpd-~gISskAm~ImnSfvnDiferIA~EAs~La~~n----kk~TltsrEIqtAVr 121 (146)
..|-. -|+|-||+.... ..+-..+.--+- .|+|-+..|..+|+-.. +-+-||.|.+|-|+|
T Consensus 29 lqFpVgRihr~LK~r~t~h~rVGataavy~a----aileYLTaEVLeLAgNasKdLKvKRitprHlqLAiR 95 (131)
T KOG1757|consen 29 LQFPVGRIHRHLKTRTTSHGRVGATAAVYSA----AILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 95 (131)
T ss_pred cccchHHHHHHHHHhcccccccchHHHHHHH----HHHHHHHHHHHHHcccccccceeeeccchhheeeec
Confidence 34544 588999986443 344444444333 45666777777776543 446799999999988
No 66
>PRK09333 30S ribosomal protein S19e; Provisional
Probab=57.25 E-value=30 Score=27.59 Aligned_cols=49 Identities=18% Similarity=0.334 Sum_probs=35.5
Q ss_pred hhHHHHHHHHhhhh-----cC-CCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhh
Q 032181 57 ETYKIYIFKVLKQV-----HP-DIGISSKAMGIMNSFINDIFEKLAQEASRLARY 105 (146)
Q Consensus 57 esy~~YIyKVLKQV-----hp-d~gISskAm~ImnSfvnDiferIA~EAs~La~~ 105 (146)
.+.-.|+.+.|-+. +| .--||+++.+.||.+-.+|+..+..+--.|.+|
T Consensus 95 g~iiR~~LqqLE~~glVek~~~GR~lT~~G~~~LD~iA~~i~~~~~~~~p~l~~y 149 (150)
T PRK09333 95 GSIIRKILQQLEKAGLVEKTKKGRVITPKGRSLLDNLAAEVKKELAEERPELEKY 149 (150)
T ss_pred cHHHHHHHHHHHHCCCeeeCCCCCEeCHHHHHHHHHHHHHHHHHHHhhCcccccc
Confidence 34456666666554 22 355899999999999999999998776666554
No 67
>smart00271 DnaJ DnaJ molecular chaperone homology domain.
Probab=56.57 E-value=32 Score=21.32 Aligned_cols=18 Identities=28% Similarity=0.215 Sum_probs=13.8
Q ss_pred HHHHHHHhhhhcCCCCcc
Q 032181 60 KIYIFKVLKQVHPDIGIS 77 (146)
Q Consensus 60 ~~YIyKVLKQVhpd~gIS 77 (146)
..-.+++.++.|||....
T Consensus 19 k~ay~~l~~~~HPD~~~~ 36 (60)
T smart00271 19 KKAYRKLALKYHPDKNPG 36 (60)
T ss_pred HHHHHHHHHHHCcCCCCC
Confidence 344677889999998774
No 68
>PF05674 DUF816: Baculovirus protein of unknown function (DUF816); InterPro: IPR008534 This entry is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf106. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family includes proteins that are about 200 amino acids in length. The proteins are all from baculoviruses. This family includes ORF107 from Orgyia pseudotsugata multicapsid polyhedrosis virus (OpMNPV) and a variety of other numbered ORF proteins, such as ORF52 Q91F03 from SWISSPROT, ORF140 Q9YMI8 from SWISSPROT from other baculoviruses. The function of these proteins is unknown.
Probab=56.41 E-value=52 Score=26.95 Aligned_cols=56 Identities=30% Similarity=0.443 Sum_probs=44.7
Q ss_pred hhHHHHHHHHh---hhhcCCCCcchHHHHH------------------HHHHHHHHHHHHHHHHhHHhhhcCCCCcC
Q 032181 57 ETYKIYIFKVL---KQVHPDIGISSKAMGI------------------MNSFINDIFEKLAQEASRLARYNKKPTIT 112 (146)
Q Consensus 57 esy~~YIyKVL---KQVhpd~gISskAm~I------------------mnSfvnDiferIA~EAs~La~~nkk~Tlt 112 (146)
-+|..+|--.| ..+.||+.=|.+||-- |-+|+..|.-+|--|+..+..|++++++.
T Consensus 93 ~~yk~~~e~alkrL~~inpdlksSP~amLqhYnecle~ld~p~~deHhlitfaKei~tKifietv~~~s~~n~s~i~ 169 (171)
T PF05674_consen 93 PNYKSFIETALKRLDKINPDLKSSPRAMLQHYNECLENLDNPKNDEHHLITFAKEIATKIFIETVDLMSNNNKSPIE 169 (171)
T ss_pred hhhHHHHHHHHHHHhcCCCccccCHHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHHHHHHHHHHhcCCCCCcc
Confidence 34555554444 4569999999999853 67899999999999999999999999875
No 69
>PRK06585 holA DNA polymerase III subunit delta; Reviewed
Probab=56.40 E-value=43 Score=28.11 Aligned_cols=65 Identities=18% Similarity=0.186 Sum_probs=51.5
Q ss_pred hHHHHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcC-CCCcChHHHHHHHHhhC
Q 032181 58 TYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNK-KPTITSREIQTAVRLVL 124 (146)
Q Consensus 58 sy~~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nk-k~TltsrEIqtAVrLlL 124 (146)
....+|.+.+++. +..|+..|+..|...+..=+..+..|--+|+.|.. ..+||..||+..|--..
T Consensus 146 ~l~~~i~~~~~~~--g~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~It~edV~~lv~~~~ 211 (343)
T PRK06585 146 DLARLIDDELAEA--GLRITPDARALLVALLGGDRLASRNEIEKLALYAHGKGEITLDDVRAVVGDAS 211 (343)
T ss_pred HHHHHHHHHHHHC--CCCCCHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHhCCcc
Confidence 3455677777664 47799999999998888888899999999999953 46899999988765443
No 70
>cd06257 DnaJ DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification.
Probab=53.63 E-value=35 Score=20.69 Aligned_cols=18 Identities=28% Similarity=0.217 Sum_probs=14.1
Q ss_pred HHHHHHHhhhhcCCCCcc
Q 032181 60 KIYIFKVLKQVHPDIGIS 77 (146)
Q Consensus 60 ~~YIyKVLKQVhpd~gIS 77 (146)
..-.+++.++.|||..-+
T Consensus 18 k~~y~~l~~~~HPD~~~~ 35 (55)
T cd06257 18 KKAYRKLALKYHPDKNPD 35 (55)
T ss_pred HHHHHHHHHHHCcCCCCC
Confidence 344678889999998876
No 71
>PRK05907 hypothetical protein; Provisional
Probab=52.24 E-value=44 Score=28.78 Aligned_cols=60 Identities=20% Similarity=0.261 Sum_probs=46.0
Q ss_pred HHHHHHHHhhhhcCCCCcchHHHHHHHHHH--HHHHHHHHHHHhHHhhh-cCCCCcChHHHHHHHH
Q 032181 59 YKIYIFKVLKQVHPDIGISSKAMGIMNSFI--NDIFEKLAQEASRLARY-NKKPTITSREIQTAVR 121 (146)
Q Consensus 59 y~~YIyKVLKQVhpd~gISskAm~ImnSfv--nDiferIA~EAs~La~~-nkk~TltsrEIqtAVr 121 (146)
...||-+.+++- +..|+..|+..+..-+ +|++ .|..|--+|+.| ..+.+||..+|+..|-
T Consensus 139 L~~Wi~~~~~~~--g~~i~~~a~~~L~~~~~~~nL~-~l~~EleKL~ly~g~~~~It~e~V~~lv~ 201 (311)
T PRK05907 139 IAQLLIQRAKEL--GISCSLGLASLFVSKFPQTGLF-EILSEFQKLLCQMGKKESLEASDIQSFVV 201 (311)
T ss_pred HHHHHHHHHHHc--CCCcCHHHHHHHHHHccCCCHH-HHHHHHHHHHHhcCCCCeECHHHHHHHhc
Confidence 345566655553 3679999988877765 4555 899999999999 6688999999988764
No 72
>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=50.51 E-value=41 Score=29.42 Aligned_cols=61 Identities=18% Similarity=0.305 Sum_probs=41.1
Q ss_pred hhhcCCCCcchHHHHHHHHHHHHHHH-------HHHHHHhHHhhhcCCCCcChHHHHHHHHhhCchHH
Q 032181 68 KQVHPDIGISSKAMGIMNSFINDIFE-------KLAQEASRLARYNKKPTITSREIQTAVRLVLPGEL 128 (146)
Q Consensus 68 KQVhpd~gISskAm~ImnSfvnDife-------rIA~EAs~La~~nkk~TltsrEIqtAVrLlLPGEL 128 (146)
++.-++..||...+.-+..++..+=. -+..-|--+|-.+.|..++..||+.+++++|+.-+
T Consensus 247 ~~~~~~V~v~d~~~~~i~~l~~~~~~~s~Ra~i~l~raArA~Aal~GR~~V~~dDv~~~a~~vL~HR~ 314 (337)
T TIGR02030 247 QNLLPQVTIPYDVLVKVAELCAELDVDGLRGELTLNRAAKALAAFEGRTEVTVDDIRRVAVLALRHRL 314 (337)
T ss_pred HHHhccCcCCHHHHHHHHHHHHHHCCCCCcHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHhC
Confidence 34456777777666655555543321 02233334788899999999999999999997544
No 73
>TIGR00764 lon_rel lon-related putative ATP-dependent protease. Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein.
Probab=48.84 E-value=1e+02 Score=29.11 Aligned_cols=65 Identities=14% Similarity=0.114 Sum_probs=37.4
Q ss_pred hHHHHHHHHhhhhcCCCCcchHHHHHHHHHHH-------------HHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHh
Q 032181 58 TYKIYIFKVLKQVHPDIGISSKAMGIMNSFIN-------------DIFEKLAQEASRLARYNKKPTITSREIQTAVRL 122 (146)
Q Consensus 58 sy~~YIyKVLKQVhpd~gISskAm~ImnSfvn-------------DiferIA~EAs~La~~nkk~TltsrEIqtAVrL 122 (146)
.|..||.+.+++-..--.+|..|+.-+-.+.. .-+..|..+|..+++.....+|+.++|+.|++.
T Consensus 313 ~~~~~i~~~~~r~G~l~~~s~~Av~~Li~~~~R~ag~r~~lsl~~R~L~~llR~A~~iA~~~~~~~I~~ehV~~Ai~~ 390 (608)
T TIGR00764 313 KLVQFVAQEVKKDGRIPHFTRDAVEEIVREAQRRAGRKDHLTLRLRELGGLVRAAGDIAKSSGKVYVTAEHVLKAKKL 390 (608)
T ss_pred HHHHHHHHHHHHhCCCCcCCHHHHHHHHHHHHHHHhcccccCCCHHHHHHHHHHHHHHHHhcCCceecHHHHHHHHHH
Confidence 35555555554431122678877665433221 234556666666666666677777777777654
No 74
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=48.32 E-value=1.7e+02 Score=24.75 Aligned_cols=63 Identities=8% Similarity=0.066 Sum_probs=41.4
Q ss_pred HHHHhhhhcCCCCcchHHHHHHHHHHHH----H--HHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCc
Q 032181 63 IFKVLKQVHPDIGISSKAMGIMNSFIND----I--FEKLAQEASRLARYNKKPTITSREIQTAVRLVLP 125 (146)
Q Consensus 63 IyKVLKQVhpd~gISskAm~ImnSfvnD----i--ferIA~EAs~La~~nkk~TltsrEIqtAVrLlLP 125 (146)
+..-++..+.+..++..++..+-.++.. + .-.+...|..++......+||..+|..|+..+.+
T Consensus 216 l~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~a~~~a~~~~~~~I~~~~v~~a~~~~~~ 284 (394)
T PRK00411 216 LKDRVEEGFYPGVVDDEVLDLIADLTAREHGDARVAIDLLRRAGLIAEREGSRKVTEEDVRKAYEKSEI 284 (394)
T ss_pred HHHHHHhhcccCCCCHhHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHHH
Confidence 3333343333456888888777666521 1 1234567777777777889999999999987744
No 75
>PF00725 3HCDH: 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; InterPro: IPR006108 3-hydroxyacyl-CoA dehydrogenase (1.1.1.35 from EC) (HCDH) [] is an enzyme involved in fatty acid metabolism, it catalyzes the reduction of 3-hydroxyacyl-CoA to 3-oxoacyl-CoA. Most eukaryotic cells have 2 fatty-acid beta-oxidation systems, one located in mitochondria and the other in peroxisomes. In peroxisomes 3-hydroxyacyl-CoA dehydrogenase forms, with enoyl-CoA hydratase (ECH) and 3,2-trans-enoyl-CoA isomerase (ECI) a multifunctional enzyme where the N-terminal domain bears the hydratase/isomerase activities and the C-terminal domain the dehydrogenase activity. There are two mitochondrial enzymes: one which is monofunctional and the other which is, like its peroxisomal counterpart, multifunctional. In Escherichia coli (gene fadB) and Pseudomonas fragi (gene faoA) HCDH is part of a multifunctional enzyme which also contains an ECH/ECI domain as well as a 3-hydroxybutyryl-CoA epimerase domain []. There are two major region of similarities in the sequences of proteins of the HCDH family, the first one located in the N-terminal, corresponds to the NAD-binding site, the second one is located in the centre of the sequence. This represents the C-terminal domain which is also found in lambda crystallin. Some proteins include two copies of this domain.; GO: 0003857 3-hydroxyacyl-CoA dehydrogenase activity, 0016491 oxidoreductase activity, 0006631 fatty acid metabolic process, 0055114 oxidation-reduction process; PDB: 3MOG_A 2WTB_A 3ADP_A 3ADO_A 1WDL_B 2D3T_B 1WDK_A 1WDM_B 3K6J_A 1ZCJ_A ....
Probab=48.05 E-value=37 Score=23.29 Aligned_cols=35 Identities=29% Similarity=0.456 Sum_probs=29.4
Q ss_pred HHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhC
Q 032181 87 FINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLVL 124 (146)
Q Consensus 87 fvnDiferIA~EAs~La~~nkk~TltsrEIqtAVrLlL 124 (146)
++|.|+--+..||.+|+.-. ..|.+||..+++.-|
T Consensus 3 i~nRl~~~~~~ea~~l~~eg---vas~~~ID~~~~~~~ 37 (97)
T PF00725_consen 3 IVNRLLAALLNEAARLVEEG---VASPEDIDRAMRYGL 37 (97)
T ss_dssp THHHHHHHHHHHHHHHHHTT---SSSHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHc---CCCHHHHHHHHHHhC
Confidence 47888899999999999954 368999999999833
No 76
>KOG0568 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=47.92 E-value=36 Score=29.84 Aligned_cols=49 Identities=37% Similarity=0.548 Sum_probs=28.0
Q ss_pred HHHHHhhhhcCCCCcchHHHHHHHHH--HHHHHHHHHHHHhHHhhhcCCCCcChHH
Q 032181 62 YIFKVLKQVHPDIGISSKAMGIMNSF--INDIFEKLAQEASRLARYNKKPTITSRE 115 (146)
Q Consensus 62 YIyKVLKQVhpd~gISskAm~ImnSf--vnDiferIA~EAs~La~~nkk~TltsrE 115 (146)
-++.+.||||||.|--. |-+ ..| |..-|.++-.|- ++..|-++.|...|
T Consensus 67 af~~lakq~hpdsgs~~-ada--a~f~qideafrkvlq~~--~~ktn~~qn~~ede 117 (342)
T KOG0568|consen 67 AFHDLAKQVHPDSGSEE-ADA--ARFIQIDEAFRKVLQEK--FAKTNARQNIGEDE 117 (342)
T ss_pred HHHHHHHHcCCCCCCcc-ccH--HHHHHHHHHHHHHHHHH--HHHhhhccccccch
Confidence 46788999999988532 111 112 234455454442 45666667776554
No 77
>PRK07914 hypothetical protein; Reviewed
Probab=47.71 E-value=60 Score=27.34 Aligned_cols=59 Identities=8% Similarity=0.175 Sum_probs=46.4
Q ss_pred HHHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHH
Q 032181 60 KIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVR 121 (146)
Q Consensus 60 ~~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsrEIqtAVr 121 (146)
..+|-..+++- +..|+..|+..|...+.+=+..|..|--+|+.|.. .+||..+|+.-|-
T Consensus 134 ~~wi~~~a~~~--g~~i~~~A~~~L~~~~g~dl~~l~~EleKL~~~~~-~~It~e~V~~~v~ 192 (320)
T PRK07914 134 ADFVRKEFRSL--RVKVDDDTVTALLDAVGSDLRELASACSQLVADTG-GAVDAAAVRRYHS 192 (320)
T ss_pred HHHHHHHHHHc--CCCCCHHHHHHHHHHHCccHHHHHHHHHHHhcCCC-CCcCHHHHHHHcC
Confidence 44666666654 46799999999999996667789999999987755 5799999887754
No 78
>COG2238 RPS19A Ribosomal protein S19E (S16A) [Translation, ribosomal structure and biogenesis]
Probab=47.70 E-value=25 Score=28.09 Aligned_cols=39 Identities=26% Similarity=0.368 Sum_probs=31.6
Q ss_pred HHHHHHHHhhhh--------cC-CCCcchHHHHHHHHHHHHHHHHHHH
Q 032181 59 YKIYIFKVLKQV--------HP-DIGISSKAMGIMNSFINDIFEKLAQ 97 (146)
Q Consensus 59 y~~YIyKVLKQV--------hp-d~gISskAm~ImnSfvnDiferIA~ 97 (146)
+.+-|.+||.|. +| .-.||.+.+++|+.+..+|++.+..
T Consensus 94 sgsI~RkilqqLE~~G~V~k~~~GR~ltp~GrsllD~~a~ei~eel~~ 141 (147)
T COG2238 94 SGSIIRKVLQQLEKAGLVEKTPKGRVLTPKGRSLLDRIATEIKEELEE 141 (147)
T ss_pred CchHHHHHHHHHHHCCceeecCCCceeCccchhHHHHHHHHHHHHhcc
Confidence 345677777764 56 5779999999999999999998876
No 79
>TIGR02031 BchD-ChlD magnesium chelatase ATPase subunit D. This model represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria. Unlike subunit I (TIGR02030), this subunit is not found in archaea.
Probab=45.62 E-value=45 Score=31.14 Aligned_cols=62 Identities=18% Similarity=0.199 Sum_probs=41.7
Q ss_pred hhhhcCCCCcchHHHHHHHHHHHHHH-------HHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCchHH
Q 032181 67 LKQVHPDIGISSKAMGIMNSFINDIF-------EKLAQEASRLARYNKKPTITSREIQTAVRLVLPGEL 128 (146)
Q Consensus 67 LKQVhpd~gISskAm~ImnSfvnDif-------erIA~EAs~La~~nkk~TltsrEIqtAVrLlLPGEL 128 (146)
.++..++..||...+.-+..++..+- ..+..-|--+|..+.+.+++..||+.|++|+|+.-+
T Consensus 195 ar~~~~~V~i~~~~~~~l~~~~~~~gv~s~Ra~i~~~r~ArA~Aal~gr~~V~~~Dv~~a~~lvl~hR~ 263 (589)
T TIGR02031 195 ARELLPQVTISAEQVKELVLTAASLGISGHRADLFAVRAAKAHAALHGRTEVTEEDLKLAVELVLLPRA 263 (589)
T ss_pred HHHhcCCccCCHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhhhc
Confidence 34556777888877655444442221 112233444788899999999999999999997543
No 80
>COG2511 GatE Archaeal Glu-tRNAGln amidotransferase subunit E (contains GAD domain) [Translation, ribosomal structure and biogenesis]
Probab=44.06 E-value=90 Score=30.14 Aligned_cols=71 Identities=30% Similarity=0.389 Sum_probs=54.5
Q ss_pred CCCcchH-HHHHHHHHHHHHHHHHHH------H-HhHHhhh------cCC--CCcChHHHHHHHHhhCchHHHHhHHHhh
Q 032181 73 DIGISSK-AMGIMNSFINDIFEKLAQ------E-ASRLARY------NKK--PTITSREIQTAVRLVLPGELAKHAVSEG 136 (146)
Q Consensus 73 d~gISsk-Am~ImnSfvnDiferIA~------E-As~La~~------nkk--~TltsrEIqtAVrLlLPGELaKhAvseG 136 (146)
+.|+|.+ |-.+..+..-|.||.+.+ . |+-|... ... .-|+.+.|...++++.-|+++|.|+.|-
T Consensus 466 eygLs~~LA~~~~~~~~~~~FEel~e~~v~p~~~A~~L~~~~~~L~reg~~i~~l~~~~i~~~~~~~~~g~iake~iee~ 545 (631)
T COG2511 466 EYGLSKELAEQLASDPRVDLFEELVEKGVDPTLIASTLVNTLPELRREGVEIDNLDDEHIEELLRLVSEGKIAKEAIEEI 545 (631)
T ss_pred HhCCCHHHHHHHHhhhhHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcCCccccCCHHHHHHHHHHHhcccchHHHHHHH
Confidence 3677754 677888889999999988 2 3333321 222 3389999999999999999999999999
Q ss_pred hhhhhcc
Q 032181 137 TKAVTKF 143 (146)
Q Consensus 137 tkAV~ky 143 (146)
.+++...
T Consensus 546 l~~l~~~ 552 (631)
T COG2511 546 LKALAEN 552 (631)
T ss_pred HHHHHhC
Confidence 9988754
No 81
>PRK05629 hypothetical protein; Validated
Probab=42.73 E-value=1e+02 Score=25.79 Aligned_cols=61 Identities=10% Similarity=0.110 Sum_probs=46.2
Q ss_pred hHHHHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHH
Q 032181 58 TYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVR 121 (146)
Q Consensus 58 sy~~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsrEIqtAVr 121 (146)
....+|...+++- +..|+..|...|...+.+=+..+..|--+|+-|.. .+||..+|+.-|-
T Consensus 130 ~l~~wi~~~~~~~--g~~i~~~A~~~L~~~~g~dl~~l~~EleKL~~~~~-~~It~e~V~~~v~ 190 (318)
T PRK05629 130 ERPGWVTQEFKNH--GVRPTPDVVHALLEGVGSDLRELASAISQLVEDTQ-GNVTVEKVRAYYV 190 (318)
T ss_pred HHHHHHHHHHHHc--CCCCCHHHHHHHHHHHCccHHHHHHHHHHHHhcCC-CCcCHHHHHHHhC
Confidence 3456777777764 46799999977777665556679999999988864 5799999987643
No 82
>PF00226 DnaJ: DnaJ domain; InterPro: IPR001623 The prokaryotic heat shock protein DnaJ interacts with the chaperone hsp70-like DnaK protein []. Structurally, the DnaJ protein consists of an N-terminal conserved domain (called 'J' domain) of about 70 amino acids, a glycine-rich region ('G' domain') of about 30 residues, a central domain containing four repeats of a CXXCXGXG motif ('CRR' domain) and a C-terminal region of 120 to 170 residues. Such a structure is shown in the following schematic representation: +------------+-+-------+-----+-----------+--------------------------------+ | N-terminal | | Gly-R | | CXXCXGXG | C-terminal | +------------+-+-------+-----+-----------+--------------------------------+ It is thought that the 'J' domain of DnaJ mediates the interaction with the dnaK protein and consists of four helices, the second of which has a charged surface that includes at least one pair of basic residues that are essential for interaction with the ATPase domain of Hsp70. The J- and CRR-domains are found in many prokaryotic and eukaryotic proteins [], either together or separately. In yeast, J-domains have been classified into 3 groups; the class III proteins are functionally distinct and do not appear to act as molecular chaperones []. ; GO: 0031072 heat shock protein binding; PDB: 2GUZ_C 2L6L_A 1HDJ_A 2EJ7_A 1FPO_C 2CUG_A 2QSA_A 2OCH_A 3BVO_B 3APQ_A ....
Probab=42.52 E-value=86 Score=19.76 Aligned_cols=17 Identities=35% Similarity=0.356 Sum_probs=12.8
Q ss_pred HHHHHHHHhhhhcCCCC
Q 032181 59 YKIYIFKVLKQVHPDIG 75 (146)
Q Consensus 59 y~~YIyKVLKQVhpd~g 75 (146)
-..-..++.++.|||..
T Consensus 17 ik~~y~~l~~~~HPD~~ 33 (64)
T PF00226_consen 17 IKKAYRRLSKQYHPDKN 33 (64)
T ss_dssp HHHHHHHHHHHTSTTTG
T ss_pred HHHHHHhhhhccccccc
Confidence 34456788999999973
No 83
>PRK13406 bchD magnesium chelatase subunit D; Provisional
Probab=38.11 E-value=76 Score=29.95 Aligned_cols=57 Identities=18% Similarity=0.233 Sum_probs=41.4
Q ss_pred CCCCcchHHHHHHHHHHHHHH-------HHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCchHH
Q 032181 72 PDIGISSKAMGIMNSFINDIF-------EKLAQEASRLARYNKKPTITSREIQTAVRLVLPGEL 128 (146)
Q Consensus 72 pd~gISskAm~ImnSfvnDif-------erIA~EAs~La~~nkk~TltsrEIqtAVrLlLPGEL 128 (146)
++..|+...+.-++.++..+- .+|..=|--+|-.+.+..++..||+.|+.++|+.-+
T Consensus 192 ~~v~v~~~~l~~i~~~~~~~gv~S~Ra~i~llraARa~AaL~Gr~~V~~~dv~~Aa~lvL~hR~ 255 (584)
T PRK13406 192 PAVGPPPEAIAALCAAAAALGIASLRAPLLALRAARAAAALAGRTAVEEEDLALAARLVLAPRA 255 (584)
T ss_pred ccCCCCHHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHhhc
Confidence 456667666665554444332 345666667899999999999999999999997544
No 84
>PF01090 Ribosomal_S19e: Ribosomal protein S19e; InterPro: IPR001266 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 includes a number of eukaryotic and archaebacterial ribosomal proteins; mammalian S19, Drosophila S19, Ascaris lumbricoides S19g (ALEP-1) and S19s, yeast YS16 (RP55A and RP55B), Aspergillus S16 and Haloarcula marismortui HS12.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZ6_S 3U5G_T 3U5C_T 3O30_M 3O2Z_M 3IZB_S 2XZN_T 2XZM_T 2V7F_A.
Probab=37.72 E-value=81 Score=24.84 Aligned_cols=37 Identities=16% Similarity=0.266 Sum_probs=27.7
Q ss_pred hHHHHHHHHhhhh--------cCC--CCcchHHHHHHHHHHHHHHHH
Q 032181 58 TYKIYIFKVLKQV--------HPD--IGISSKAMGIMNSFINDIFEK 94 (146)
Q Consensus 58 sy~~YIyKVLKQV--------hpd--~gISskAm~ImnSfvnDifer 94 (146)
....-|.++|.|. +|+ -.||+++++.||.+..+|++.
T Consensus 92 asg~iiR~~LqqLE~~glv~k~~~~GR~lT~~G~~~lD~iA~~v~~~ 138 (139)
T PF01090_consen 92 ASGSIIRKILQQLEKAGLVEKDPKGGRRLTPKGQRDLDRIAGQVAKE 138 (139)
T ss_dssp CHHHHHHHHHHHHHHTTSEEEETTTEEEE-HHHHHHHHHHHHHHHHH
T ss_pred CCcHHHHHHHHHHHHCCCEEecCCCCCEECHHHHHHHHHHHHHHHHc
Confidence 4556788888875 544 358999999999999888864
No 85
>KOG4336 consensus TBP-associated transcription factor Prodos [Transcription]
Probab=37.07 E-value=1.5e+02 Score=26.48 Aligned_cols=59 Identities=12% Similarity=0.189 Sum_probs=47.7
Q ss_pred HHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhh
Q 032181 64 FKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLV 123 (146)
Q Consensus 64 yKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsrEIqtAVrLl 123 (146)
--+|+++.=|. ||.-|..-|-.++.--|.+|+.++-.++.+.+|.--|..||......+
T Consensus 12 ~~Ll~~~gfd~-is~~aletlvell~~yi~eigrq~~n~celagRT~pT~~Dv~l~Li~m 70 (323)
T KOG4336|consen 12 SNLLKTKGFDS-ISNAALETLVELLQSYIREIGRQLHNYCELAGRTIPTQGDVKLTLIEM 70 (323)
T ss_pred HHHHHHhCchH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcHHHHHHHHHHh
Confidence 33444444433 888899999999999999999999999999999999999998776543
No 86
>CHL00081 chlI Mg-protoporyphyrin IX chelatase
Probab=36.52 E-value=1.1e+02 Score=27.18 Aligned_cols=60 Identities=17% Similarity=0.273 Sum_probs=40.9
Q ss_pred hhcCCCCcchHHHHHHHHHHHHHHH-------HHHHHHhHHhhhcCCCCcChHHHHHHHHhhCchHH
Q 032181 69 QVHPDIGISSKAMGIMNSFINDIFE-------KLAQEASRLARYNKKPTITSREIQTAVRLVLPGEL 128 (146)
Q Consensus 69 QVhpd~gISskAm~ImnSfvnDife-------rIA~EAs~La~~nkk~TltsrEIqtAVrLlLPGEL 128 (146)
+.-++..||...+.-+..++...=. -+..-|--+|-.+.|..++..||+.+++++|+.-+
T Consensus 261 ~~~~~V~v~~~~~~yi~~l~~~~~~~s~Ra~i~l~raArA~Aal~GR~~V~pdDv~~~a~~vL~HR~ 327 (350)
T CHL00081 261 NLLPKVEIDYDLRVKISQICSELDVDGLRGDIVTNRAAKALAAFEGRTEVTPKDIFKVITLCLRHRL 327 (350)
T ss_pred HhcCCCccCHHHHHHHHHHHHHHCCCCChHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHhC
Confidence 4446677777666655555543211 12233444888999999999999999999997554
No 87
>PF05258 DUF721: Protein of unknown function (DUF721); InterPro: IPR007922 This family contains several actinomycete proteins of unknown function, and related sequences from other species.
Probab=35.66 E-value=61 Score=21.33 Aligned_cols=25 Identities=20% Similarity=0.308 Sum_probs=19.8
Q ss_pred CcChHHHHHHHHhhCchHHHHhHHH
Q 032181 110 TITSREIQTAVRLVLPGELAKHAVS 134 (146)
Q Consensus 110 TltsrEIqtAVrLlLPGELaKhAvs 134 (146)
.+...+++....-++|++|+.|.-.
T Consensus 19 ~~~~~~l~~~w~~ivg~~l~~~~~~ 43 (89)
T PF05258_consen 19 ALQLARLQQNWKQIVGPELAQHTRP 43 (89)
T ss_pred hHHHHHHHHHHHHHhCHHHHccEEE
Confidence 4456678889999999999998643
No 88
>PRK03992 proteasome-activating nucleotidase; Provisional
Probab=34.24 E-value=66 Score=28.17 Aligned_cols=43 Identities=16% Similarity=0.216 Sum_probs=35.9
Q ss_pred HHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCchH
Q 032181 85 NSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLVLPGE 127 (146)
Q Consensus 85 nSfvnDiferIA~EAs~La~~nkk~TltsrEIqtAVrLlLPGE 127 (146)
+.|...-++.|+.||..++-...+..|+..||+.|+..+.|+.
T Consensus 334 ~g~sgadl~~l~~eA~~~a~~~~~~~i~~~d~~~A~~~~~~~~ 376 (389)
T PRK03992 334 EGASGADLKAICTEAGMFAIRDDRTEVTMEDFLKAIEKVMGKE 376 (389)
T ss_pred CCCCHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHhccc
Confidence 4455556678999999998888889999999999999998853
No 89
>PF13148 DUF3987: Protein of unknown function (DUF3987)
Probab=33.86 E-value=2.2e+02 Score=23.87 Aligned_cols=74 Identities=27% Similarity=0.395 Sum_probs=49.1
Q ss_pred hhHHHHHHHHhhhhc-------CCCCcchHHHHHHHHHHHHHHHHH----------------HHHHhHHhh----h----
Q 032181 57 ETYKIYIFKVLKQVH-------PDIGISSKAMGIMNSFINDIFEKL----------------AQEASRLAR----Y---- 105 (146)
Q Consensus 57 esy~~YIyKVLKQVh-------pd~gISskAm~ImnSfvnDiferI----------------A~EAs~La~----~---- 105 (146)
+.|...|..++.... ..+.+|.+|..+++.|.+.+..++ ..-+.+||- .
T Consensus 262 ~~~~~~i~~l~~~~~~~~~~~~~~l~ls~eA~~~~~~~~~~~~~~~~~~~~~~~~~~~~~K~~~~~~RlA~ilh~~~~~~ 341 (378)
T PF13148_consen 262 EAYHERIKELLDWPPEDGSDEPIVLELSDEAKELFREWYNELENELRQPGGDLAMRSFASKAAEQALRLALILHLFESGG 341 (378)
T ss_pred HHHHHHHHHHHhhhhcccCCCCeEEecCHHHHHHHHHHHHHHHHHhhccCCChHHHHHHHHHHHHHHHHHHHHHHHhccC
Confidence 567777888887765 236779999888777666555544 344444442 2
Q ss_pred -cCCCCcChHHHHHHHHhhCchHHHHhH
Q 032181 106 -NKKPTITSREIQTAVRLVLPGELAKHA 132 (146)
Q Consensus 106 -nkk~TltsrEIqtAVrLlLPGELaKhA 132 (146)
....+|+...++.|++|+ .-+..|+
T Consensus 342 ~~~~~~I~~~~~~~Ai~l~--~~~~~~~ 367 (378)
T PF13148_consen 342 SPPSTEISAETMERAIRLV--EYFLEHA 367 (378)
T ss_pred CCCCCEECHHHHHHHHHHH--HHHHHHH
Confidence 367889999999999865 3444444
No 90
>PF11945 WASH_WAHD: WAHD domain of WASH complex; InterPro: IPR021854 This entry represents a component of the WASH complex. The WASH complex is present at the surface of endosomes and recruits and activates the Arp2/3 complex to induce actin polymerisation. The WASH complex plays a key role in the fission of tubules that serve as transport intermediates during endosome sorting []. The WASH complex's subunit structure: F-actin-capping protein subunit alpha (CAPZA1, CAPZA2 or CAPZA3), F-actin-capping protein subunit beta (CAPZB), WASH (WASH1, WASH2P, WASH3P, WASH4P, WASH5P or WASH6P), FAM21 (FAM21A, FAM21B or FAM21C), KIAA1033, KIAA0196 (strumpellin) and CCDC53. This entry represents the WASH subunit of the WASH complex. WASH genes duplicated to multiple chromosomal ends during primate evolution, with highest copy number reached in humans, whose WASH repertoires probably vary extensively among individuals []. It is therefore difficult to determine which gene is functional or not. The telomeric region of chromosome 9p is paralogous to the pericentromeric regions of chromosome 9 as well as to 2q. Paralogous regions contain 7 transcriptional units. Duplicated WASH genes are also present in the Xq/Yq pseudoautosomal region, as well as on chromosome 1 and 15. The chromosome 16 copy seems to be a pseudogene.
Probab=33.43 E-value=57 Score=28.42 Aligned_cols=23 Identities=26% Similarity=0.567 Sum_probs=18.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhH
Q 032181 79 KAMGIMNSFINDIFEKLAQEASR 101 (146)
Q Consensus 79 kAm~ImnSfvnDiferIA~EAs~ 101 (146)
.++.-|+..+||||.||.....+
T Consensus 25 ~aL~~L~~v~~diF~rI~~Rv~~ 47 (297)
T PF11945_consen 25 DALEYLDKVSNDIFSRISARVER 47 (297)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 57788999999999998765543
No 91
>cd00043 CYCLIN Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain.
Probab=33.26 E-value=1.2e+02 Score=18.81 Aligned_cols=65 Identities=14% Similarity=0.055 Sum_probs=44.7
Q ss_pred hHHHHHHHHhhhhcCCCCcchHHHHHHHHHHH------HHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHh
Q 032181 58 TYKIYIFKVLKQVHPDIGISSKAMGIMNSFIN------DIFEKLAQEASRLARYNKKPTITSREIQTAVRL 122 (146)
Q Consensus 58 sy~~YIyKVLKQVhpd~gISskAm~ImnSfvn------DiferIA~EAs~La~~nkk~TltsrEIqtAVrL 122 (146)
..-.||.++.....-+..+-.-|+.+++.|+. .-+..||.-+.-|+..-.....+.+|+......
T Consensus 4 ~~~~~l~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~ 74 (88)
T cd00043 4 TPLDFLRRVAKALGLSPETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEEIPPWLKDLVHVTGY 74 (88)
T ss_pred hHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHcCCCCCHHHHhHHhCC
Confidence 34567888887776666666777888887765 345677777877877654457777777655543
No 92
>PRK13407 bchI magnesium chelatase subunit I; Provisional
Probab=32.49 E-value=1.9e+02 Score=25.31 Aligned_cols=56 Identities=13% Similarity=0.255 Sum_probs=40.4
Q ss_pred cCCCCcchHHHHHHHHHHH---------HHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCchHH
Q 032181 71 HPDIGISSKAMGIMNSFIN---------DIFEKLAQEASRLARYNKKPTITSREIQTAVRLVLPGEL 128 (146)
Q Consensus 71 hpd~gISskAm~ImnSfvn---------DiferIA~EAs~La~~nkk~TltsrEIqtAVrLlLPGEL 128 (146)
-++..||...+.-+..++. +|+ +..-|.-+|-.+.|..++..||+.++.++|..-+
T Consensus 247 ~~~V~v~~~~~~yi~~l~~~~~~~s~Ra~i~--l~~aA~a~A~l~Gr~~V~~~Di~~~~~~vl~hR~ 311 (334)
T PRK13407 247 LPQLKTPNTVLHDCAALCIALGSDGLRGELT--LLRAARALAAFEGAEAVGRSHLRSVATMALSHRL 311 (334)
T ss_pred cCCcccCHHHHHHHHHHHHHHCCCCchHHHH--HHHHHHHHHHHcCCCeeCHHHHHHHHHHhhhhhc
Confidence 4555666655554444443 333 6677777899999999999999999999997655
No 93
>KOG2643 consensus Ca2+ binding protein, contains EF-hand motifs [Inorganic ion transport and metabolism]
Probab=31.43 E-value=2e+02 Score=27.06 Aligned_cols=74 Identities=22% Similarity=0.297 Sum_probs=50.8
Q ss_pred chhHHHHHHHHhhhhcC-CCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCchHHHHhH
Q 032181 56 IETYKIYIFKVLKQVHP-DIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLVLPGELAKHA 132 (146)
Q Consensus 56 ~esy~~YIyKVLKQVhp-d~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsrEIqtAVrLlLPGELaKhA 132 (146)
.+.+..|..||.+.--- +-|||-+=-.-...|+|+|=+ -.-|..+=. +-...|+..++|.|++.+.--||..|-
T Consensus 352 ~~~k~~~lkrvk~kf~~~~~gISl~Ef~~Ff~Fl~~l~d--fd~Al~fy~-~Ag~~i~~~~f~raa~~vtGveLSdhV 426 (489)
T KOG2643|consen 352 SKKKHKYLKRVKEKFKDDGKGISLQEFKAFFRFLNNLND--FDIALRFYH-MAGASIDEKTFQRAAKVVTGVELSDHV 426 (489)
T ss_pred hHhHHHHHHHHHHhccCCCCCcCHHHHHHHHHHHhhhhH--HHHHHHHHH-HcCCCCCHHHHHHHHHHhcCcccccce
Confidence 45566677777766533 689998776667777776533 122222222 223789999999999999999999884
No 94
>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=31.24 E-value=3.1e+02 Score=22.82 Aligned_cols=64 Identities=11% Similarity=0.073 Sum_probs=39.6
Q ss_pred HHHHHHhhhhcCCCCcchHHHHHHHHHHH----HH--HHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhC
Q 032181 61 IYIFKVLKQVHPDIGISSKAMGIMNSFIN----DI--FEKLAQEASRLARYNKKPTITSREIQTAVRLVL 124 (146)
Q Consensus 61 ~YIyKVLKQVhpd~gISskAm~ImnSfvn----Di--ferIA~EAs~La~~nkk~TltsrEIqtAVrLlL 124 (146)
.++...+.....+..++.+++..+..++. |+ .-.+...|..++..+++.+||..+|+.|+..+.
T Consensus 206 ~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~R~al~~l~~a~~~a~~~~~~~it~~~v~~a~~~~~ 275 (365)
T TIGR02928 206 DILENRAEKAFYDGVLDDGVIPLCAALAAQEHGDARKAIDLLRVAGEIAEREGAERVTEDHVEKAQEKIE 275 (365)
T ss_pred HHHHHHHHhhccCCCCChhHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHH
Confidence 34444444333344577777665544442 21 123555677777777788999999999988763
No 95
>PF13335 Mg_chelatase_2: Magnesium chelatase, subunit ChlI
Probab=31.05 E-value=1.2e+02 Score=21.64 Aligned_cols=47 Identities=19% Similarity=0.268 Sum_probs=34.3
Q ss_pred CcchHHHHHHHHHHHH------HHHHHHHHHhHHhhhcCCCCcChHHHHHHHH
Q 032181 75 GISSKAMGIMNSFIND------IFEKLAQEASRLARYNKKPTITSREIQTAVR 121 (146)
Q Consensus 75 gISskAm~ImnSfvnD------iferIA~EAs~La~~nkk~TltsrEIqtAVr 121 (146)
.++..+..+|+..++. =+.||..=|-.+|.......|+..+|..|+.
T Consensus 42 ~l~~~~~~~l~~~~~~~~lS~R~~~rilrvARTIADL~~~~~I~~~hi~EAl~ 94 (96)
T PF13335_consen 42 PLSSEAKKLLEQAAEKLNLSARGYHRILRVARTIADLEGSERITREHIAEALS 94 (96)
T ss_pred CCCHHHHHHHHHHHHHcCcCHHHHHHHHHHHHHHHhHcCCCCCCHHHHHHHHh
Confidence 3444444444444432 2568888889999999999999999999975
No 96
>PF08221 HTH_9: RNA polymerase III subunit RPC82 helix-turn-helix domain; InterPro: IPR013197 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae (Baker's yeast) RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In S. cerevisiae, the enzyme is composed of 15 subunits, ranging from 10 kDa to about 160 kDa []. This region is probably a DNA-binding helix-turn-helix.; PDB: 2XV4_S 2XUB_A.
Probab=30.15 E-value=1.7e+02 Score=19.35 Aligned_cols=44 Identities=20% Similarity=0.265 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCchHHHHhHH
Q 032181 86 SFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLVLPGELAKHAV 133 (146)
Q Consensus 86 SfvnDiferIA~EAs~La~~nkk~TltsrEIqtAVrLlLPGELaKhAv 133 (146)
.+++|.|-.++.......-... .+|-++|...++ ||-..-|+|+
T Consensus 5 ~ii~~~fG~~~~~V~~~Ll~~G--~ltl~~i~~~t~--l~~~~Vk~~L 48 (62)
T PF08221_consen 5 LIIEEHFGEIVAKVGEVLLSRG--RLTLREIVRRTG--LSPKQVKKAL 48 (62)
T ss_dssp HHHHHHHHHHHHHHHHHHHHC---SEEHHHHHHHHT----HHHHHHHH
T ss_pred HHHHHHcChHHHHHHHHHHHcC--CcCHHHHHHHhC--CCHHHHHHHH
Confidence 4678888888888777554443 566888988888 6766666664
No 97
>PF04157 EAP30: EAP30/Vps36 family; InterPro: IPR007286 EAP30 is a subunit of the ELL complex. The ELL is an 80kDa RNA polymerase II transcription factor. ELL interacts with three other proteins to form the complex known as ELL complex. The ELL complex is capable of increasing that catalytic rate of transcription elongation, but is unable to repress initiation of transcription by RNA polymerase II as is the case of ELL. EAP30 is thought to lead to the derepression of ELL's transcriptional inhibitory activity. ; PDB: 2ZME_A 3CUQ_A 1W7P_D 1U5T_B.
Probab=29.94 E-value=94 Score=25.12 Aligned_cols=71 Identities=20% Similarity=0.219 Sum_probs=39.4
Q ss_pred cchhHHHHHHHHhhhhcCCCCcchH----HHHHHHHHHHHHHHHHHHHHhH--------------HhhhcCCC----CcC
Q 032181 55 SIETYKIYIFKVLKQVHPDIGISSK----AMGIMNSFINDIFEKLAQEASR--------------LARYNKKP----TIT 112 (146)
Q Consensus 55 r~esy~~YIyKVLKQVhpd~gISsk----Am~ImnSfvnDiferIA~EAs~--------------La~~nkk~----Tlt 112 (146)
....|...|..++.++--|-..|.+ .+.=.+.|-..+-.+|++-+.. ++.||+.+ .||
T Consensus 55 ~~~~~r~~f~~~~~~lGvdp~~s~~~~s~~l~~~~~f~~ELa~qi~e~c~~~~~~~GGii~L~dl~~~~nr~R~g~~lIS 134 (223)
T PF04157_consen 55 SDPEFRSQFQSMCASLGVDPLASSKFWSESLKGSGDFYYELAVQIAEVCLATRSKNGGIISLSDLYCRYNRARGGSELIS 134 (223)
T ss_dssp CSHHHHHHHHHHHHHHT--CHCCTTCCCCCCSCHHHHHHHHHHHHHHHHHHHCCTTTSEEEHHHHHHHHHHCTTTSST--
T ss_pred CCchHHHHHHHHHHHcCCCcccchhhhhhccccchhHHHHHHHHHHHHHHHHHhcCCCEEEHHHHHHHHHHhcccCCCcC
Confidence 3456777888888887666555554 1112334444444444443332 23456665 889
Q ss_pred hHHHHHHHHhhCc
Q 032181 113 SREIQTAVRLVLP 125 (146)
Q Consensus 113 srEIqtAVrLlLP 125 (146)
..||..|+.++=+
T Consensus 135 p~Di~~A~~~l~~ 147 (223)
T PF04157_consen 135 PEDILRACKLLEV 147 (223)
T ss_dssp HHHHHHHHHHHCC
T ss_pred HHHHHHHHHHHHH
Confidence 9999999998744
No 98
>KOG3467 consensus Histone H4 [Chromatin structure and dynamics]
Probab=29.66 E-value=1.4e+02 Score=22.41 Aligned_cols=37 Identities=16% Similarity=0.325 Sum_probs=27.0
Q ss_pred HHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHH
Q 032181 85 NSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVR 121 (146)
Q Consensus 85 nSfvnDiferIA~EAs~La~~nkk~TltsrEIqtAVr 121 (146)
|.....++|.+-..|..-+.+.+|+|+|+-||.-+.+
T Consensus 56 ~~~~k~fl~n~i~~A~~yt~HAKRKTvT~~dvv~~LK 92 (103)
T KOG3467|consen 56 RGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALK 92 (103)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhhhceeeHHHHHHHHH
Confidence 3344444555666778888899999999999877654
No 99
>PF05798 Phage_FRD3: Bacteriophage FRD3 protein; InterPro: IPR008765 This is a group of proteins of unknown function from bacteriophage T2 and related phage.
Probab=29.54 E-value=26 Score=25.05 Aligned_cols=18 Identities=28% Similarity=0.527 Sum_probs=16.0
Q ss_pred HHHHHHhhhhcCCCCcch
Q 032181 61 IYIFKVLKQVHPDIGISS 78 (146)
Q Consensus 61 ~YIyKVLKQVhpd~gISs 78 (146)
.||+.|++..||.++|.+
T Consensus 12 EY~eEvIRNRyPelsi~s 29 (75)
T PF05798_consen 12 EYTEEVIRNRYPELSITS 29 (75)
T ss_pred HhHHHHHHccCCceEEEE
Confidence 599999999999998854
No 100
>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau. This model represents the well-conserved first ~ 365 amino acids of the translation of the dnaX gene. The full-length product of the dnaX gene in the model bacterium E. coli is the DNA polymerase III tau subunit. A translational frameshift leads to early termination and a truncated protein subunit gamma, about 1/3 shorter than tau and present in roughly equal amounts. This frameshift mechanism is not necessarily universal for species with DNA polymerase III but appears conserved in the exterme thermophile Thermus thermophilis.
Probab=29.12 E-value=1.8e+02 Score=24.09 Aligned_cols=62 Identities=16% Similarity=0.237 Sum_probs=45.2
Q ss_pred HHHHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhh
Q 032181 59 YKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLV 123 (146)
Q Consensus 59 y~~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsrEIqtAVrLl 123 (146)
...||..++++- +..|+..++..+-.+.+.-+.++..+.-+|+.|.. ..||..+|+..+...
T Consensus 181 l~~~l~~~~~~~--g~~i~~~a~~~l~~~~~g~~~~a~~~lekl~~~~~-~~it~~~v~~~~~~~ 242 (355)
T TIGR02397 181 IVERLKKILDKE--GIKIEDEALELIARAADGSLRDALSLLDQLISFGN-GNITYEDVNELLGLV 242 (355)
T ss_pred HHHHHHHHHHHc--CCCCCHHHHHHHHHHcCCChHHHHHHHHHHHhhcC-CCCCHHHHHHHhCCC
Confidence 445666666653 46789899888777776667788888888888876 459999988776543
No 101
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=29.10 E-value=1.3e+02 Score=23.73 Aligned_cols=16 Identities=31% Similarity=0.281 Sum_probs=13.9
Q ss_pred CCcChHHHHHHHHhhC
Q 032181 109 PTITSREIQTAVRLVL 124 (146)
Q Consensus 109 ~TltsrEIqtAVrLlL 124 (146)
..++..|||..|...|
T Consensus 101 ~~IsveEIqDiVE~~L 116 (154)
T PRK00464 101 REVPSKEIGELVMEEL 116 (154)
T ss_pred CCCCHHHHHHHHHHHH
Confidence 5799999999998665
No 102
>PRK05637 anthranilate synthase component II; Provisional
Probab=28.20 E-value=46 Score=26.88 Aligned_cols=24 Identities=21% Similarity=0.411 Sum_probs=21.5
Q ss_pred hhcCCCCcchHHHHHHHHHHHHHH
Q 032181 69 QVHPDIGISSKAMGIMNSFINDIF 92 (146)
Q Consensus 69 QVhpd~gISskAm~ImnSfvnDif 92 (146)
|-||+.-.|.....|+++|+..++
T Consensus 183 QfHPE~~~T~~G~~il~nfl~~~~ 206 (208)
T PRK05637 183 QFHPESVLSPTGPIILSRCVEQLL 206 (208)
T ss_pred EeCCccCcCCCHHHHHHHHHHHHh
Confidence 679999999999999999997664
No 103
>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=28.12 E-value=48 Score=28.43 Aligned_cols=66 Identities=20% Similarity=0.368 Sum_probs=44.0
Q ss_pred chhHHHHHHHHhhhhcCCCCcchHHHHHHHHHHHH-----------------HHHHHHHHHhHHhhhcCCCCcChHHHHH
Q 032181 56 IETYKIYIFKVLKQVHPDIGISSKAMGIMNSFIND-----------------IFEKLAQEASRLARYNKKPTITSREIQT 118 (146)
Q Consensus 56 ~esy~~YIyKVLKQVhpd~gISskAm~ImnSfvnD-----------------iferIA~EAs~La~~nkk~TltsrEIqt 118 (146)
.+.+..||.-+=.+++| .+|.+|..++-.|-.+ .+|-|-.=|--+|+..=+.+++..|++.
T Consensus 244 ~~~lr~yI~yar~~~~P--~ls~ea~~~I~~~Yv~lR~~~~~~~~~~~iT~R~LeSLIRLseA~AKl~lr~~V~~~Dv~~ 321 (331)
T PF00493_consen 244 EDLLRKYIAYARQNIHP--VLSEEAKELIINYYVELRKESKSNNKSIPITIRQLESLIRLSEAHAKLRLRDEVTEEDVEE 321 (331)
T ss_dssp HCCCHHHHHHHHHHC----EE-HHCHHHHHHHHCCCCHCHHCHSS-B-SSCCCCCHHHHHHHHHHHCTTSSECSHHHHHH
T ss_pred HHHHHHHHHHHHhhccc--ccCHHHHHHHHHHHHHhcccccccccccccchhhHHHHHHHHHHHHHHhccCceeHHHHHH
Confidence 35567788877568888 6888887776555322 1234444455567777788999999999
Q ss_pred HHHhh
Q 032181 119 AVRLV 123 (146)
Q Consensus 119 AVrLl 123 (146)
|++|+
T Consensus 322 Ai~L~ 326 (331)
T PF00493_consen 322 AIRLF 326 (331)
T ss_dssp HHHHH
T ss_pred HHHHH
Confidence 99986
No 104
>cd07353 harmonin_N N-terminal protein-binding module of harmonin. Harmonin is a postsynaptic density-95/discs-large/ZO-1 (PDZ) domain-containing scaffold protein, which organizes the Usher protein network of the inner ear and the retina. Harmonin contains a single copy of this domain, which is found at the N-terminus of all three harmonin isoform classes (a, b and c), and which preceeds the first PDZ protein-binding domain, PDZ1. This harmonin_N domain binds specifically to a short internal peptide fragment of the cadherin 23 cytoplasmic domain; cadherin 23 is a component of the Usher protein network.
Probab=28.09 E-value=52 Score=23.69 Aligned_cols=28 Identities=25% Similarity=0.535 Sum_probs=21.0
Q ss_pred hhHHHHHHHHhhhhcCCCCcchHHHHHHHHHHHHHH
Q 032181 57 ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIF 92 (146)
Q Consensus 57 esy~~YIyKVLKQVhpd~gISskAm~ImnSfvnDif 92 (146)
|.=..|+|-||++-|..++| .-||+|+=
T Consensus 19 EaEkd~lY~~Lr~YHqSm~l--------p~li~Dlk 46 (79)
T cd07353 19 EAEKDYLYDVLRMYHQSMNL--------PVLVGDLK 46 (79)
T ss_pred HHHHHHHHHHHHHHHhccCH--------HHHHHHHH
Confidence 56678999999999965443 45778764
No 105
>PLN03213 repressor of silencing 3; Provisional
Probab=28.02 E-value=55 Score=31.55 Aligned_cols=22 Identities=36% Similarity=0.665 Sum_probs=19.0
Q ss_pred CCcchHHHHHHHHHHHHHHHHH
Q 032181 74 IGISSKAMGIMNSFINDIFEKL 95 (146)
Q Consensus 74 ~gISskAm~ImnSfvnDiferI 95 (146)
.|+-.+-++||||.||-|||+=
T Consensus 184 ~g~~~eE~niMNSVMNKLFEke 205 (759)
T PLN03213 184 VGRNEAEVNVMNSVMNKLFEKN 205 (759)
T ss_pred ccccHHHHHHHHHHHHHHHhhh
Confidence 5677778999999999999974
No 106
>KOG0240 consensus Kinesin (SMY1 subfamily) [Cytoskeleton]
Probab=27.67 E-value=59 Score=31.28 Aligned_cols=42 Identities=26% Similarity=0.502 Sum_probs=30.4
Q ss_pred hhHHHHHHHHhhhhcCC-------------------CCc--chHHHHHHHHHHHHHHHHHHHH
Q 032181 57 ETYKIYIFKVLKQVHPD-------------------IGI--SSKAMGIMNSFINDIFEKLAQE 98 (146)
Q Consensus 57 esy~~YIyKVLKQVhpd-------------------~gI--SskAm~ImnSfvnDiferIA~E 98 (146)
+-|.-.++-|+++|--+ .|+ ...-|+||..+++|||++|-.-
T Consensus 65 ~Vy~~~a~~Iv~dVL~GYNGTvfaYGqT~sGKTytm~G~~~d~~~~GIipRi~~diF~~Iys~ 127 (607)
T KOG0240|consen 65 DVYEFAAKPIVDDVLLGYNGTVFAYGQTGSGKTYTMEGIGHDPEEMGIIPRILNDIFDHIYSM 127 (607)
T ss_pred HHHHHHHHHHHHHHhcccceeEEEecCCCCCcceeecccCCChhhcCcHHHHHHHHHHHHhcC
Confidence 45777788999988332 122 2246899999999999999653
No 107
>PF13654 AAA_32: AAA domain; PDB: 3K1J_B.
Probab=27.08 E-value=93 Score=28.88 Aligned_cols=64 Identities=17% Similarity=0.221 Sum_probs=42.2
Q ss_pred hhHHHHHHHHhhhhcCCCCcchHHHHHHHHHH-----------HHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHH
Q 032181 57 ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFI-----------NDIFEKLAQEASRLARYNKKPTITSREIQTAVR 121 (146)
Q Consensus 57 esy~~YIyKVLKQVhpd~gISskAm~ImnSfv-----------nDiferIA~EAs~La~~nkk~TltsrEIqtAVr 121 (146)
..|..||-.+..+-+ -..++..|+.-|-.+. -.-+..|..||..+|+.+.+..|+..+|+.|+.
T Consensus 430 ~~~~~~i~~~~~~~~-L~~~~~~Av~~li~~~~R~~q~kLsl~~~~l~~ll~EA~~~A~~~~~~~I~~~~V~~Ai~ 504 (509)
T PF13654_consen 430 RQYARFIASICQKEG-LPPFDRSAVARLIEYSARLDQDKLSLRFSWLADLLREANYWARKEGAKVITAEHVEQAIE 504 (509)
T ss_dssp HHHHHHHHHHHHHHS-S--BBHHHHHHHHHHHHHCC-SEEE--HHHHHHHHHHHHHHHHHCT-SSB-HHHHHHHHH
T ss_pred HHHHHHHHHHHHhCC-CCCCCHHHHHHHHHHHHHHhCCEeCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHH
Confidence 457777777766552 2456777765543221 123356779999999999999999999999986
No 108
>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH. HflB(FtsH) is a pleiotropic protein required for correct cell division in bacteria. It has ATP-dependent zinc metalloprotease activity. It was formerly designated cell division protein FtsH.
Probab=26.54 E-value=1.7e+02 Score=26.40 Aligned_cols=50 Identities=32% Similarity=0.373 Sum_probs=35.7
Q ss_pred HHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCch-----------HHHHhHHHhhhhhhh
Q 032181 92 FEKLAQEASRLARYNKKPTITSREIQTAVRLVLPG-----------ELAKHAVSEGTKAVT 141 (146)
Q Consensus 92 ferIA~EAs~La~~nkk~TltsrEIqtAVrLlLPG-----------ELaKhAvseGtkAV~ 141 (146)
++.|..||..++...++..|+..+++.|+..+++| +.-..|+-|.-.||.
T Consensus 264 l~~l~~eA~~~a~~~~~~~i~~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~A~hEaGhAlv 324 (495)
T TIGR01241 264 LANLLNEAALLAARKNKTEITMNDIEEAIDRVIAGPEKKSRVISEKEKKLVAYHEAGHALV 324 (495)
T ss_pred HHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhcccccccccccHHHHHHHHHHHHhHHHH
Confidence 45677788877777777899999999999977543 233456565556654
No 109
>PHA03102 Small T antigen; Reviewed
Probab=26.02 E-value=1.3e+02 Score=23.81 Aligned_cols=37 Identities=22% Similarity=0.408 Sum_probs=26.1
Q ss_pred HHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHh
Q 032181 63 IFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLA 103 (146)
Q Consensus 63 IyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La 103 (146)
.++..++.|||-+-+.+.|. -||..|+.|..+..++.
T Consensus 28 Yr~la~~~HPDkgg~~e~~k----~in~Ay~~L~d~~~r~~ 64 (153)
T PHA03102 28 YLRKCLEFHPDKGGDEEKMK----ELNTLYKKFRESVKSLR 64 (153)
T ss_pred HHHHHHHHCcCCCchhHHHH----HHHHHHHHHhhHHHhcc
Confidence 34666888999987766554 46677777777666655
No 110
>KOG1657 consensus CCAAT-binding factor, subunit C (HAP5) [Transcription]
Probab=25.08 E-value=1.4e+02 Score=25.24 Aligned_cols=58 Identities=22% Similarity=0.232 Sum_probs=39.8
Q ss_pred HHHHhhhhcCC-CCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHH
Q 032181 63 IFKVLKQVHPD-IGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVR 121 (146)
Q Consensus 63 IyKVLKQVhpd-~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsrEIqtAVr 121 (146)
|.++.|+ ++| -.|+.+|.-++.-...-+.+.++..+-.-+.-++|+||.--||..||.
T Consensus 80 iKkimK~-dedv~mI~~Eapvl~aka~E~Fi~elt~~sw~~Tee~~rrtl~~sdia~av~ 138 (236)
T KOG1657|consen 80 IKKIMKS-DEDVSMITAEAPVLFAKACELFITELTLRSWVHTEENKRRTLQKSDIAAAVT 138 (236)
T ss_pred ccccccc-cccccccchhHHHHHHHHHHHHHHHHHHHhhhhhcccccccchHHHHHHHhc
Confidence 3444443 344 368888866655444444455666677778889999999999999985
No 111
>PF04444 Dioxygenase_N: Catechol dioxygenase N terminus; InterPro: IPR007535 This domain is the N-terminal region of catechol, chlorocatechol or hydroxyquinol 1,2-dioxygenase proteins. This region is always found adjacent to the dioxygenase domain (IPR000627 from INTERPRO). Dioxygenases catalyse the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms. Cleavage of aromatic rings is one of the most important functions of dioxygenases, which play key roles in the degradation of aromatic compounds. The substrates of ring-cleavage dioxygenases can be classified into two groups according to the mode of scission of the aromatic ring. Intradiol enzymes use a non-haem Fe(III) to cleave the aromatic ring between two hydroxyl groups (ortho-cleavage), whereas extradiol enzymes (IPR000486 from INTERPRO) use a non-haem Fe(II) to cleave the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon (meta-cleavage) []. These two subfamilies differ in sequence, structural fold, iron ligands, and the orientation of second sphere active site amino acid residues. Enzymes that belong to the intradiol family include catechol 1,2-dioxygenase (1,2-CTD) (1.13.11.1 from EC); protocatechuate 3,4-dioxygenase (3,4-PCD) (1.13.11.3 from EC); and chlorocatechol 1,2-dioxygenase (1.13.11.1 from EC) [].; GO: 0005506 iron ion binding, 0018576 catechol 1,2-dioxygenase activity, 0009712 catechol-containing compound metabolic process, 0055114 oxidation-reduction process; PDB: 3O6R_B 1S9A_A 3O6J_A 3O5U_B 3O32_B 3HHY_A 3HHX_A 3HJS_A 3HJQ_A 3HKP_A ....
Probab=24.86 E-value=1.3e+02 Score=21.00 Aligned_cols=35 Identities=17% Similarity=0.298 Sum_probs=25.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhC
Q 032181 79 KAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLVL 124 (146)
Q Consensus 79 kAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsrEIqtAVrLlL 124 (146)
+.-.||.++|.+++.=| +..-||..|...|+..|-
T Consensus 3 R~~~i~~~lv~~lh~~i-----------~e~~lT~~E~~~av~~L~ 37 (74)
T PF04444_consen 3 RLKEIMARLVRHLHDFI-----------REVDLTEDEWWAAVDFLN 37 (74)
T ss_dssp HHHHHHHHHHHHHHHHH-----------HHCT--HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHH-----------HHhCCCHHHHHHHHHHHH
Confidence 34578888888887755 336799999999998775
No 112
>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional
Probab=24.51 E-value=1.1e+02 Score=27.93 Aligned_cols=42 Identities=19% Similarity=0.216 Sum_probs=34.9
Q ss_pred HHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCc
Q 032181 84 MNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLVLP 125 (146)
Q Consensus 84 mnSfvnDiferIA~EAs~La~~nkk~TltsrEIqtAVrLlLP 125 (146)
.+.|.-.-+..|+.||..+|....+..||..|+..|+.-++.
T Consensus 385 t~g~sgAdI~~i~~eA~~~Alr~~r~~Vt~~D~~~A~~~v~~ 426 (438)
T PTZ00361 385 KDELSGADIKAICTEAGLLALRERRMKVTQADFRKAKEKVLY 426 (438)
T ss_pred cCCCCHHHHHHHHHHHHHHHHHhcCCccCHHHHHHHHHHHHh
Confidence 344555557789999999999998999999999999998864
No 113
>CHL00176 ftsH cell division protein; Validated
Probab=24.35 E-value=1.6e+02 Score=28.09 Aligned_cols=50 Identities=36% Similarity=0.387 Sum_probs=35.9
Q ss_pred HHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCch----------HHHHhHHHhhhhhhh
Q 032181 92 FEKLAQEASRLARYNKKPTITSREIQTAVRLVLPG----------ELAKHAVSEGTKAVT 141 (146)
Q Consensus 92 ferIA~EAs~La~~nkk~TltsrEIqtAVrLlLPG----------ELaKhAvseGtkAV~ 141 (146)
++.+..||..++....+..||..||+.|++-++-| +.-..|+-|.-.||.
T Consensus 392 L~~lvneAal~a~r~~~~~It~~dl~~Ai~rv~~g~~~~~~~~~~~~~~vA~hEaGhA~v 451 (638)
T CHL00176 392 LANLLNEAAILTARRKKATITMKEIDTAIDRVIAGLEGTPLEDSKNKRLIAYHEVGHAIV 451 (638)
T ss_pred HHHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhhhccCccccHHHHHHHHHHhhhhHHH
Confidence 34677888888777778899999999999876433 444456656555554
No 114
>PF07587 PSD1: Protein of unknown function (DUF1553); InterPro: IPR022655 The function is not known. It is found associated with IPR011444 from INTERPRO It is also found associated with the Planctomycete cytochrome C domain IPR011429 from INTERPRO.
Probab=24.22 E-value=2.6e+02 Score=23.36 Aligned_cols=24 Identities=25% Similarity=0.394 Sum_probs=18.1
Q ss_pred cchHHHHHHHH-HHHHHHHHHHHHH
Q 032181 76 ISSKAMGIMNS-FINDIFEKLAQEA 99 (146)
Q Consensus 76 ISskAm~ImnS-fvnDiferIA~EA 99 (146)
...+|+-+||+ |+++.....+...
T Consensus 197 t~~QAL~LmNg~~v~~~a~~~a~r~ 221 (266)
T PF07587_consen 197 TPLQALFLMNGPFVNEAARAFANRL 221 (266)
T ss_pred CHHHHHHHhCcHHHHHHHHHHHHHH
Confidence 34799999999 8877777666643
No 115
>PRK10733 hflB ATP-dependent metalloprotease; Reviewed
Probab=24.03 E-value=1.1e+02 Score=28.81 Aligned_cols=40 Identities=23% Similarity=0.297 Sum_probs=32.3
Q ss_pred HHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCch
Q 032181 87 FINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLVLPG 126 (146)
Q Consensus 87 fvnDiferIA~EAs~La~~nkk~TltsrEIqtAVrLlLPG 126 (146)
|.--=+..|..||..++....+..|+-.|+..|...+++|
T Consensus 356 ~sgadl~~l~~eAa~~a~r~~~~~i~~~d~~~a~~~v~~g 395 (644)
T PRK10733 356 FSGADLANLVNEAALFAARGNKRVVSMVEFEKAKDKIMMG 395 (644)
T ss_pred CCHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHHHHhcc
Confidence 3333456788999999988899999999999999877665
No 116
>TIGR00888 guaA_Nterm GMP synthase (glutamine-hydrolyzing), N-terminal domain or A subunit. separate polypeptide chains in most of the Archaea. This N-terminal region would be the smaller subunit.
Probab=23.52 E-value=70 Score=24.65 Aligned_cols=22 Identities=23% Similarity=0.558 Sum_probs=18.6
Q ss_pred hhcCCCCcchHHHHHHHHHHHH
Q 032181 69 QVHPDIGISSKAMGIMNSFIND 90 (146)
Q Consensus 69 QVhpd~gISskAm~ImnSfvnD 90 (146)
|-||+..-+..++.|+.+|+++
T Consensus 162 QfHPE~~~~~~g~~i~~~f~~~ 183 (188)
T TIGR00888 162 QFHPEVTHTEYGNELLENFVYD 183 (188)
T ss_pred eeCCccCCChhhHHHHHHHHHH
Confidence 6799988877889999999865
No 117
>TIGR01242 26Sp45 26S proteasome subunit P45 family. Many proteins may score above the trusted cutoff because an internal
Probab=23.42 E-value=1e+02 Score=26.38 Aligned_cols=40 Identities=20% Similarity=0.202 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhC
Q 032181 85 NSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLVL 124 (146)
Q Consensus 85 nSfvnDiferIA~EAs~La~~nkk~TltsrEIqtAVrLlL 124 (146)
+.|...-+..|..||...+-...+..|+..||+.|++-++
T Consensus 325 ~g~sg~dl~~l~~~A~~~a~~~~~~~i~~~d~~~a~~~~~ 364 (364)
T TIGR01242 325 EGASGADLKAICTEAGMFAIREERDYVTMDDFIKAVEKVL 364 (364)
T ss_pred CCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHHhC
Confidence 3444434457888999988888888999999999998764
No 118
>PLN02347 GMP synthetase
Probab=23.37 E-value=66 Score=30.02 Aligned_cols=24 Identities=33% Similarity=0.605 Sum_probs=20.7
Q ss_pred hhcCCCCcchHHHHHHHHHHHHHH
Q 032181 69 QVHPDIGISSKAMGIMNSFINDIF 92 (146)
Q Consensus 69 QVhpd~gISskAm~ImnSfvnDif 92 (146)
|-||+..-|...+.||.+|+.+|.
T Consensus 180 QFHPE~~~t~~G~~iL~NFl~~ic 203 (536)
T PLN02347 180 QYHPEVTHSPKGMETLRHFLFDVC 203 (536)
T ss_pred EccCCCCccchHHHHHHHHHHHHh
Confidence 679999999999999999987654
No 119
>PF14606 Lipase_GDSL_3: GDSL-like Lipase/Acylhydrolase family; PDB: 3SKV_B.
Probab=22.59 E-value=49 Score=26.78 Aligned_cols=77 Identities=18% Similarity=0.295 Sum_probs=30.1
Q ss_pred HHHHHHhhhhcCCCCc---c-------------hHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhC
Q 032181 61 IYIFKVLKQVHPDIGI---S-------------SKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLVL 124 (146)
Q Consensus 61 ~YIyKVLKQVhpd~gI---S-------------skAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsrEIqtAVrLlL 124 (146)
.++.+.|+..||++.| | ...+.-+|..++++|+.+-.+--.=..|-....|-..+-...|..+=
T Consensus 81 ~~fv~~iR~~hP~tPIllv~~~~~~~~~~~~~~~~~~~~~~~~~r~~v~~l~~~g~~nl~~l~g~~llg~d~e~tvDgvH 160 (178)
T PF14606_consen 81 DGFVKTIREAHPDTPILLVSPIPYPAGYFDNSRGETVEEFREALREAVEQLRKEGDKNLYYLDGEELLGDDHEATVDGVH 160 (178)
T ss_dssp HHHHHHHHTT-SSS-EEEEE----TTTTS--TTS--HHHHHHHHHHHHHHHHHTT-TTEEEE-HHHCS------------
T ss_pred HHHHHHHHHhCCCCCEEEEecCCccccccCchHHHHHHHHHHHHHHHHHHHHHcCCCcEEEeCchhhcCccccccccccc
Confidence 3678888999999776 2 23456678888888888755444433433333433333456777777
Q ss_pred chHHHHhHHHhhh
Q 032181 125 PGELAKHAVSEGT 137 (146)
Q Consensus 125 PGELaKhAvseGt 137 (146)
|++|+-.-+.++.
T Consensus 161 P~DlG~~~~a~~l 173 (178)
T PF14606_consen 161 PNDLGMMRMADAL 173 (178)
T ss_dssp -------------
T ss_pred ccccccccccccc
Confidence 8888766655544
No 120
>PTZ00095 40S ribosomal protein S19; Provisional
Probab=22.50 E-value=2.2e+02 Score=23.26 Aligned_cols=38 Identities=13% Similarity=0.153 Sum_probs=28.7
Q ss_pred HHHHHHHHhhhh--------cC---CCCcchHHHHHHHHHHHHHHHHHH
Q 032181 59 YKIYIFKVLKQV--------HP---DIGISSKAMGIMNSFINDIFEKLA 96 (146)
Q Consensus 59 y~~YIyKVLKQV--------hp---d~gISskAm~ImnSfvnDiferIA 96 (146)
-..-|.++|.|. +| .-.||++.++.||.+..+|++++-
T Consensus 118 Sg~iiR~~LQqLE~~glVek~~~~~GR~lT~~Gr~~LD~iA~~v~~~l~ 166 (169)
T PTZ00095 118 SGKILRWICQQLEKLGLVEQGPKKKGRRLTRKGCNFANAFARQVTIRKF 166 (169)
T ss_pred chHHHHHHHHHHHHCCCEEecCCCCCCEECHhHHHHHHHHHHHHHHHHh
Confidence 345677777764 33 456899999999999999887763
No 121
>PRK14970 DNA polymerase III subunits gamma and tau; Provisional
Probab=22.44 E-value=2.8e+02 Score=23.52 Aligned_cols=62 Identities=13% Similarity=0.184 Sum_probs=47.0
Q ss_pred HHHHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhh
Q 032181 59 YKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLV 123 (146)
Q Consensus 59 y~~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsrEIqtAVrLl 123 (146)
...+|.+++++- +..|+.+++..+-...+.=+.++..+--+|+.|.... ||..+|+..+...
T Consensus 172 l~~~l~~~~~~~--g~~i~~~al~~l~~~~~gdlr~~~~~lekl~~y~~~~-it~~~v~~~~~~~ 233 (367)
T PRK14970 172 IKEHLAGIAVKE--GIKFEDDALHIIAQKADGALRDALSIFDRVVTFCGKN-ITRQAVTENLNIL 233 (367)
T ss_pred HHHHHHHHHHHc--CCCCCHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCCC-CCHHHHHHHhCCC
Confidence 344666666553 4668999999988888877888888989999887654 9998888776543
No 122
>PRK13765 ATP-dependent protease Lon; Provisional
Probab=22.05 E-value=3.7e+02 Score=25.85 Aligned_cols=65 Identities=15% Similarity=0.078 Sum_probs=34.5
Q ss_pred hhHHHHHHHHhhhhc---CCCCcchHHHHHHHHHHHH-------------HHHHHHHHHhHHhhhcCCCCcChHHHHHHH
Q 032181 57 ETYKIYIFKVLKQVH---PDIGISSKAMGIMNSFIND-------------IFEKLAQEASRLARYNKKPTITSREIQTAV 120 (146)
Q Consensus 57 esy~~YIyKVLKQVh---pd~gISskAm~ImnSfvnD-------------iferIA~EAs~La~~nkk~TltsrEIqtAV 120 (146)
+.+..|+..+-+++. +-..|+..|+.-|-..... -+..|..||..+++...+..++.++|..|+
T Consensus 318 e~~~~~~~~iaqe~~~~G~l~~f~~eAVa~LI~~~~R~ag~r~~lsl~~~~l~~l~r~a~~~a~~~~~~~i~~~~v~~a~ 397 (637)
T PRK13765 318 ENRRKLVRFVAQEVKRDGKIPHFDRDAVEEIIREAKRRAGRKGHLTLKLRDLGGLVRVAGDIARSEGAELTTAEHVLEAK 397 (637)
T ss_pred HHHHHHHHHHHHHhhhccCCCCCCHHHHHHHHHHHHHHhCCccccccCHHHHHHHHHHHHHHHHhhccceecHHHHHHHH
Confidence 445555544444442 3347888876543332211 122255566666666666666666666665
Q ss_pred H
Q 032181 121 R 121 (146)
Q Consensus 121 r 121 (146)
+
T Consensus 398 ~ 398 (637)
T PRK13765 398 K 398 (637)
T ss_pred H
Confidence 4
No 123
>smart00385 CYCLIN domain present in cyclins, TFIIB and Retinoblastoma. A helical domain present in cyclins and TFIIB (twice) and Retinoblastoma (once). A protein recognition domain functioning in cell-cycle and transcription control.
Probab=21.04 E-value=2.1e+02 Score=17.50 Aligned_cols=59 Identities=17% Similarity=0.177 Sum_probs=31.9
Q ss_pred HHHHHhhhhcCCCCcchHHHHHHHHHHH------HHHHHHHHHHhHHhhhcCCCCcChHHHHHHH
Q 032181 62 YIFKVLKQVHPDIGISSKAMGIMNSFIN------DIFEKLAQEASRLARYNKKPTITSREIQTAV 120 (146)
Q Consensus 62 YIyKVLKQVhpd~gISskAm~ImnSfvn------DiferIA~EAs~La~~nkk~TltsrEIqtAV 120 (146)
||.++....+-+..+-.-|+.+++.++. .-+..||.-+.-|+........+..++....
T Consensus 2 ~l~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~ 66 (83)
T smart00385 2 FLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLAAKTEEIPPWTKELVHYT 66 (83)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhcccCCHHHHHHHHHHHHHHHhcCCCCchhHhHhh
Confidence 4555555554444455555666655554 2355666666666665443344555554443
No 124
>TIGR00368 Mg chelatase-related protein. The N-terminal end matches very strongly a pfam Mg_chelatase domain.
Probab=20.69 E-value=2.6e+02 Score=25.82 Aligned_cols=49 Identities=12% Similarity=0.245 Sum_probs=41.8
Q ss_pred CCcchHHHHHHHHHHHHH------HHHHHHHHhHHhhhcCCCCcChHHHHHHHHh
Q 032181 74 IGISSKAMGIMNSFINDI------FEKLAQEASRLARYNKKPTITSREIQTAVRL 122 (146)
Q Consensus 74 ~gISskAm~ImnSfvnDi------ferIA~EAs~La~~nkk~TltsrEIqtAVrL 122 (146)
..++.++..+|+..++.+ ++||..=|-.+|.......|+..+|+.|+.+
T Consensus 444 ~~l~~~~~~~l~~a~~~~~lS~R~~~rilrvArTiAdL~g~~~i~~~hv~eA~~~ 498 (499)
T TIGR00368 444 CKLSAIDANDLEGALNKLGLSSRATHRILKVARTIADLKEEKNISREHLAEAIEY 498 (499)
T ss_pred cCCCHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHhc
Confidence 456888888888777664 7899999999999999999999999999864
Done!