Query 032404
Match_columns 141
No_of_seqs 136 out of 361
Neff 4.2
Searched_HMMs 46136
Date Fri Mar 29 13:39:22 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032404.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032404hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00158 histone H2B; Provisio 100.0 1.8E-55 4E-60 330.2 11.0 99 43-141 18-116 (116)
2 PTZ00463 histone H2B; Provisio 100.0 5.6E-55 1.2E-59 327.8 11.2 98 43-140 19-116 (117)
3 smart00427 H2B Histone H2B. 100.0 1.1E-52 2.5E-57 303.0 10.3 89 52-140 1-89 (89)
4 KOG1744 Histone H2B [Chromatin 100.0 1.1E-46 2.4E-51 286.3 9.2 99 43-141 28-126 (127)
5 PF00125 Histone: Core histone 99.6 8.5E-16 1.8E-20 103.8 5.4 68 50-117 3-74 (75)
6 cd07981 TAF12 TATA Binding Pro 98.5 1E-06 2.2E-11 60.6 8.2 61 58-118 7-67 (72)
7 COG2036 HHT1 Histones H3 and H 98.3 2.3E-06 5E-11 62.3 6.5 63 58-121 25-87 (91)
8 PF00808 CBFD_NFYB_HMF: Histon 98.3 4.6E-06 1E-10 55.4 6.9 58 57-115 7-65 (65)
9 smart00803 TAF TATA box bindin 97.9 7.3E-05 1.6E-09 50.9 6.8 59 57-116 7-65 (65)
10 cd00074 H2A Histone 2A; H2A is 97.8 8.2E-05 1.8E-09 56.0 6.5 65 52-116 19-84 (115)
11 PLN00035 histone H4; Provision 97.8 0.00015 3.2E-09 54.1 7.6 60 57-117 34-93 (103)
12 cd00076 H4 Histone H4, one of 97.7 0.00021 4.6E-09 51.4 7.4 60 57-117 18-77 (85)
13 PF03847 TFIID_20kDa: Transcri 97.7 0.00018 3.9E-09 49.6 6.7 59 58-116 5-63 (68)
14 PTZ00015 histone H4; Provision 97.7 0.00025 5.3E-09 52.7 7.6 61 56-117 34-94 (102)
15 smart00428 H3 Histone H3. 97.5 0.00068 1.5E-08 50.5 8.0 68 51-118 32-101 (105)
16 cd07979 TAF9 TATA Binding Prot 97.3 0.0018 4E-08 48.4 8.3 65 55-120 4-68 (117)
17 smart00417 H4 Histone H4. 97.3 0.0008 1.7E-08 47.3 5.4 56 57-113 18-73 (74)
18 KOG0869 CCAAT-binding factor, 96.8 0.0047 1E-07 49.5 7.0 61 58-118 38-99 (168)
19 PLN00156 histone H2AX; Provisi 96.6 0.0075 1.6E-07 47.2 6.2 70 53-124 29-99 (139)
20 KOG0871 Class 2 transcription 96.5 0.013 2.7E-07 46.7 7.2 66 57-122 17-83 (156)
21 KOG1142 Transcription initiati 96.5 0.0045 9.7E-08 52.6 4.8 67 56-122 158-228 (258)
22 smart00414 H2A Histone 2A. 96.4 0.0095 2.1E-07 44.3 5.5 70 53-124 9-79 (106)
23 PF02969 TAF: TATA box binding 96.3 0.018 4E-07 39.6 6.2 47 70-116 20-66 (66)
24 PLN00157 histone H2A; Provisio 96.3 0.0077 1.7E-07 46.7 4.8 65 52-116 25-90 (132)
25 PTZ00017 histone H2A; Provisio 96.3 0.0093 2E-07 46.3 5.1 65 52-116 26-91 (134)
26 cd08050 TAF6 TATA Binding Prot 96.2 0.015 3.2E-07 50.2 6.7 49 70-118 16-64 (343)
27 PLN00153 histone H2A; Provisio 96.0 0.013 2.9E-07 45.2 5.0 71 52-124 23-94 (129)
28 smart00576 BTP Bromodomain tra 95.8 0.088 1.9E-06 36.2 7.7 60 57-117 11-70 (77)
29 PTZ00252 histone H2A; Provisio 95.5 0.038 8.3E-07 43.0 5.6 66 51-116 23-91 (134)
30 PLN00154 histone H2A; Provisio 95.4 0.044 9.6E-07 42.8 5.7 71 53-125 38-110 (136)
31 COG5262 HTA1 Histone H2A [Chro 95.4 0.037 8.1E-07 42.8 5.1 67 57-125 31-97 (132)
32 PLN00121 histone H3; Provision 95.2 0.1 2.2E-06 40.7 7.1 66 52-117 66-131 (136)
33 PF15510 CENP-W: Centromere ki 95.0 0.041 9E-07 40.9 4.2 65 54-120 18-98 (102)
34 PTZ00018 histone H3; Provision 94.9 0.13 2.8E-06 40.1 7.0 66 52-117 66-131 (136)
35 KOG0870 DNA polymerase epsilon 94.7 0.19 4.1E-06 40.6 7.6 63 56-118 14-78 (172)
36 PF15630 CENP-S: Kinetochore c 94.5 0.14 3.1E-06 36.0 5.8 59 58-116 11-71 (76)
37 KOG1756 Histone 2A [Chromatin 93.8 0.18 3.8E-06 39.3 5.5 67 57-125 32-98 (131)
38 PLN00161 histone H3; Provision 93.3 0.54 1.2E-05 36.7 7.5 66 52-117 59-125 (135)
39 PLN00160 histone H3; Provision 92.0 1.1 2.3E-05 33.2 7.3 66 52-117 25-91 (97)
40 PF15511 CENP-T: Centromere ki 92.0 0.45 9.9E-06 42.3 6.2 54 57-110 356-414 (414)
41 PF07524 Bromo_TP: Bromodomain 91.9 1.7 3.7E-05 29.4 7.8 48 69-116 22-69 (77)
42 PF02291 TFIID-31kDa: Transcri 89.9 1.1 2.4E-05 34.4 5.8 60 56-119 16-78 (129)
43 KOG2549 Transcription initiati 88.8 1.6 3.5E-05 41.0 7.1 50 69-118 27-76 (576)
44 PF02269 TFIID-18kDa: Transcri 87.0 0.9 2E-05 32.6 3.5 47 70-116 19-65 (93)
45 cd08048 TAF11 TATA Binding Pro 85.4 7.2 0.00016 27.8 7.4 60 58-118 22-84 (85)
46 cd07978 TAF13 The TATA Binding 85.2 4 8.8E-05 29.4 6.1 51 66-117 15-66 (92)
47 KOG3334 Transcription initiati 82.9 5 0.00011 31.9 6.2 59 57-119 18-79 (148)
48 PF04719 TAFII28: hTAFII28-lik 79.7 15 0.00032 26.7 7.3 62 57-118 28-90 (90)
49 PF14687 DUF4460: Domain of un 78.8 2.8 6.1E-05 31.3 3.5 38 52-89 9-54 (112)
50 TIGR02442 Cob-chelat-sub cobal 74.9 13 0.00028 34.6 7.3 61 63-123 242-309 (633)
51 COG5208 HAP5 CCAAT-binding fac 73.3 5.5 0.00012 34.0 4.2 47 70-116 127-173 (286)
52 PF09415 CENP-X: CENP-S associ 70.5 7.4 0.00016 27.0 3.6 57 58-114 5-64 (72)
53 COG5095 TAF6 Transcription ini 69.8 5 0.00011 36.2 3.3 60 59-118 8-70 (450)
54 KOG1745 Histones H3 and H4 [Ch 69.1 5.9 0.00013 31.1 3.2 53 62-118 77-133 (137)
55 TIGR01128 holA DNA polymerase 68.9 31 0.00066 27.7 7.4 66 52-119 114-179 (302)
56 smart00350 MCM minichromosome 68.6 30 0.00064 31.3 8.0 66 52-119 421-505 (509)
57 COG1466 HolA DNA polymerase II 67.6 23 0.0005 30.0 6.8 67 52-120 143-209 (334)
58 PRK07452 DNA polymerase III su 66.6 27 0.00058 28.9 6.8 62 54-117 135-198 (326)
59 PRK09333 30S ribosomal protein 66.3 15 0.00033 29.1 5.0 49 52-100 95-149 (150)
60 PRK09522 bifunctional glutamin 66.2 9.5 0.00021 35.1 4.4 61 64-124 168-231 (531)
61 PRK05574 holA DNA polymerase I 62.8 43 0.00092 27.4 7.3 66 52-119 149-214 (340)
62 PRK08487 DNA polymerase III su 61.1 34 0.00075 28.8 6.6 63 54-120 140-202 (328)
63 TIGR03015 pepcterm_ATPase puta 60.1 57 0.0012 25.7 7.3 67 52-118 195-266 (269)
64 KOG1757 Histone 2A [Chromatin 58.4 14 0.0003 28.6 3.4 60 53-116 30-95 (131)
65 PRK14607 bifunctional glutamin 57.8 14 0.00031 33.7 4.0 60 64-124 167-226 (534)
66 COG5150 Class 2 transcription 57.7 36 0.00078 26.9 5.7 51 68-118 28-78 (148)
67 smart00271 DnaJ DnaJ molecular 56.2 34 0.00074 21.1 4.5 18 55-72 19-36 (60)
68 PRK06585 holA DNA polymerase I 55.3 48 0.001 27.6 6.5 65 53-119 146-211 (343)
69 cd06257 DnaJ DnaJ domain or J- 53.6 36 0.00079 20.5 4.2 18 55-72 18-35 (55)
70 PF05674 DUF816: Baculovirus p 53.0 65 0.0014 26.2 6.6 56 52-107 93-169 (171)
71 PRK05907 hypothetical protein; 49.3 53 0.0012 28.1 5.9 61 54-116 139-201 (311)
72 TIGR02030 BchI-ChlI magnesium 49.2 45 0.00098 28.9 5.6 61 63-123 247-314 (337)
73 PF00725 3HCDH: 3-hydroxyacyl- 48.7 36 0.00077 23.2 4.0 33 82-117 3-35 (97)
74 TIGR00764 lon_rel lon-related 48.3 1.2E+02 0.0027 28.4 8.5 65 53-117 313-390 (608)
75 KOG0568 Molecular chaperone (D 45.8 41 0.0009 29.3 4.7 51 57-110 67-117 (342)
76 COG2238 RPS19A Ribosomal prote 45.5 29 0.00062 27.6 3.4 38 55-92 95-141 (147)
77 PRK07914 hypothetical protein; 45.5 70 0.0015 26.8 6.0 59 55-116 134-192 (320)
78 PRK00411 cdc6 cell division co 43.4 2E+02 0.0043 24.2 9.2 63 58-120 216-284 (394)
79 TIGR02031 BchD-ChlD magnesium 43.3 53 0.0012 30.5 5.3 62 62-123 195-263 (589)
80 PF00226 DnaJ: DnaJ domain; I 41.7 88 0.0019 19.6 5.0 17 54-70 17-33 (64)
81 PRK05629 hypothetical protein; 40.8 1.2E+02 0.0026 25.2 6.7 62 52-116 129-190 (318)
82 COG2511 GatE Archaeal Glu-tRNA 40.4 1.1E+02 0.0023 29.5 6.9 71 68-138 466-552 (631)
83 KOG4336 TBP-associated transcr 37.8 1.5E+02 0.0032 26.4 6.9 59 59-118 12-70 (323)
84 PRK13406 bchD magnesium chelat 36.8 85 0.0018 29.5 5.6 57 67-123 192-255 (584)
85 cd07353 harmonin_N N-terminal 36.3 34 0.00073 24.5 2.3 49 51-120 18-66 (79)
86 PF05258 DUF721: Protein of un 35.1 63 0.0014 21.2 3.4 25 105-129 19-43 (89)
87 CHL00081 chlI Mg-protoporyphyr 34.8 1.2E+02 0.0027 26.6 6.0 61 63-123 260-327 (350)
88 PRK03992 proteasome-activating 33.8 67 0.0015 28.0 4.2 43 80-122 334-376 (389)
89 PF13148 DUF3987: Protein of u 33.3 2.4E+02 0.0051 23.6 7.3 75 51-127 261-367 (378)
90 PF11945 WASH_WAHD: WAHD domai 32.4 60 0.0013 28.1 3.7 23 74-96 25-47 (297)
91 cd00043 CYCLIN Cyclin box fold 31.2 1.3E+02 0.0029 18.5 5.7 65 53-117 4-74 (88)
92 KOG2643 Ca2+ binding protein, 30.7 2.2E+02 0.0047 26.7 7.1 74 51-128 352-427 (489)
93 PF13335 Mg_chelatase_2: Magne 30.4 1.3E+02 0.0029 21.4 4.7 47 70-116 42-94 (96)
94 PRK13407 bchI magnesium chelat 30.3 2.2E+02 0.0048 24.7 6.8 58 64-123 245-311 (334)
95 KOG0240 Kinesin (SMY1 subfamil 29.7 54 0.0012 31.4 3.1 42 52-93 65-127 (607)
96 KOG3467 Histone H4 [Chromatin 29.5 1.4E+02 0.003 22.3 4.7 37 80-116 56-92 (103)
97 PLN03213 repressor of silencin 29.5 50 0.0011 31.6 2.9 22 69-90 184-205 (759)
98 PF04157 EAP30: EAP30/Vps36 fa 29.4 1.1E+02 0.0024 24.6 4.6 70 51-120 56-147 (223)
99 PF08221 HTH_9: RNA polymerase 28.9 1.7E+02 0.0037 19.1 4.8 44 81-128 5-48 (62)
100 TIGR02928 orc1/cdc6 family rep 28.5 3.4E+02 0.0074 22.4 8.8 64 56-119 206-275 (365)
101 TIGR01241 FtsH_fam ATP-depende 28.2 1.5E+02 0.0032 26.5 5.6 51 87-137 264-325 (495)
102 PRK00464 nrdR transcriptional 28.1 1.4E+02 0.0031 23.4 4.8 16 104-119 101-116 (154)
103 TIGR02397 dnaX_nterm DNA polym 28.1 2E+02 0.0044 23.6 6.0 63 53-118 180-242 (355)
104 PF05798 Phage_FRD3: Bacteriop 27.9 28 0.0006 24.7 0.7 18 56-73 12-29 (75)
105 PRK05637 anthranilate synthase 27.2 49 0.0011 26.6 2.1 24 64-87 183-206 (208)
106 PF00493 MCM: MCM2/3/5 family 26.7 49 0.0011 28.2 2.2 66 51-118 244-326 (331)
107 PF13654 AAA_32: AAA domain; P 26.7 94 0.002 28.7 4.1 64 52-116 430-504 (509)
108 PHA03102 Small T antigen; Revi 26.4 1.3E+02 0.0028 23.6 4.4 37 58-98 28-64 (153)
109 CHL00176 ftsH cell division pr 25.2 1.5E+02 0.0033 28.1 5.3 50 87-136 392-451 (638)
110 KOG1657 CCAAT-binding factor, 25.0 1.4E+02 0.003 25.1 4.5 58 58-116 80-138 (236)
111 PRK13765 ATP-dependent proteas 24.8 3.1E+02 0.0068 26.1 7.3 65 52-116 318-398 (637)
112 PRK10733 hflB ATP-dependent me 24.6 1.8E+02 0.0039 27.3 5.6 40 82-121 356-395 (644)
113 PTZ00361 26 proteosome regulat 24.6 1.1E+02 0.0023 27.8 4.0 42 79-120 385-426 (438)
114 TIGR00888 guaA_Nterm GMP synth 23.2 71 0.0015 24.5 2.3 22 64-85 162-183 (188)
115 PF01090 Ribosomal_S19e: Ribos 23.2 1.5E+02 0.0032 23.2 4.1 37 53-89 92-138 (139)
116 TIGR01242 26Sp45 26S proteasom 22.4 1.1E+02 0.0024 26.0 3.5 40 80-119 325-364 (364)
117 PLN02347 GMP synthetase 22.2 72 0.0016 29.6 2.5 24 64-87 180-203 (536)
118 PF14606 Lipase_GDSL_3: GDSL-l 21.7 58 0.0013 26.2 1.6 77 56-132 81-173 (178)
119 PRK14970 DNA polymerase III su 21.3 3.2E+02 0.0069 23.0 6.1 62 54-118 172-233 (367)
120 PHA02564 V virion protein; Pro 21.2 3.9E+02 0.0085 20.8 6.1 54 55-119 85-140 (141)
121 PF07587 PSD1: Protein of unkn 20.4 3.4E+02 0.0074 22.5 6.0 24 71-94 197-221 (266)
122 TIGR00368 Mg chelatase-related 20.4 2.7E+02 0.0059 25.5 5.8 49 69-117 444-498 (499)
123 COG2960 Uncharacterized protei 20.4 1.2E+02 0.0026 22.9 2.9 42 85-128 14-55 (103)
124 smart00385 CYCLIN domain prese 20.1 2.2E+02 0.0048 17.3 4.1 59 57-115 2-66 (83)
No 1
>PLN00158 histone H2B; Provisional
Probab=100.00 E-value=1.8e-55 Score=330.16 Aligned_cols=99 Identities=84% Similarity=1.164 Sum_probs=95.4
Q ss_pred ccccccccchhHHHHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCchH
Q 032404 43 KKKRTKKSIETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLPGE 122 (141)
Q Consensus 43 ~kk~~k~r~esy~~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLlLPGE 122 (141)
+++++++|.|+|++||||||||||||+|||++||+||||||||||||||.||++|++||+|+|||+||||+|||||||||
T Consensus 18 ~kk~~~kr~esy~~YI~kVLKQVhPd~gIS~kaM~ImnSfvnDiferIA~EAs~La~~nkr~TltsrEIqtAvrLvLpgE 97 (116)
T PLN00158 18 KKKGSKSKTETYKIYIYKVLKQVHPDTGISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVRLILPGE 97 (116)
T ss_pred cccccccccccHHHHHHHHHHHhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHhccHH
Confidence 45567778999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhHHHhhhhhhhcccCC
Q 032404 123 LAKHAVSEGTKAVTKFTSS 141 (141)
Q Consensus 123 LaKhAvseGtkAV~ky~ss 141 (141)
|+||||+||++||++|+++
T Consensus 98 LaKhAvsEGtkAv~k~~~~ 116 (116)
T PLN00158 98 LAKHAVSEGTKAVTKFTSA 116 (116)
T ss_pred HHHHHHHHHHHHHHHhhcC
Confidence 9999999999999999985
No 2
>PTZ00463 histone H2B; Provisional
Probab=100.00 E-value=5.6e-55 Score=327.77 Aligned_cols=98 Identities=72% Similarity=1.067 Sum_probs=94.7
Q ss_pred ccccccccchhHHHHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCchH
Q 032404 43 KKKRTKKSIETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLPGE 122 (141)
Q Consensus 43 ~kk~~k~r~esy~~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLlLPGE 122 (141)
+++++++|.|+|++||||||||||||+|||++||+||||||||||||||.||++|++||+++|||+||||||||||||||
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 45667778999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhHHHhhhhhhhcccC
Q 032404 123 LAKHAVSEGTKAVTKFTS 140 (141)
Q Consensus 123 LaKhAvseGtkAV~ky~s 140 (141)
|+||||+|||+||++|++
T Consensus 99 LaKhAvsEGtkAv~k~~~ 116 (117)
T PTZ00463 99 LAKHAVSEGTKAVTKFTS 116 (117)
T ss_pred HHHhhhhHHHHHHHHhhc
Confidence 999999999999999986
No 3
>smart00427 H2B Histone H2B.
Probab=100.00 E-value=1.1e-52 Score=302.98 Aligned_cols=89 Identities=82% Similarity=1.187 Sum_probs=87.8
Q ss_pred hhHHHHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCchHHHHhHHHhh
Q 032404 52 ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLPGELAKHAVSEG 131 (141)
Q Consensus 52 esy~~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLlLPGELaKhAvseG 131 (141)
|+|++||||||||||||+|||++||+||||||||||||||.||++|++||+|+|||+||||+||||+|||||+||||+||
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 032404 132 TKAVTKFTS 140 (141)
Q Consensus 132 tkAV~ky~s 140 (141)
||||+||++
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=1.1e-46 Score=286.35 Aligned_cols=99 Identities=75% Similarity=1.106 Sum_probs=95.9
Q ss_pred ccccccccchhHHHHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCchH
Q 032404 43 KKKRTKKSIETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLPGE 122 (141)
Q Consensus 43 ~kk~~k~r~esy~~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLlLPGE 122 (141)
+|++..++.++|+.||||||||||||+|||+++|.|||||||||||+||.||++|++||+|+||++||||+||||+||||
T Consensus 28 gk~~~~~~~e~~s~yv~kvlk~Vhpd~gis~~a~~vmnsf~ndife~iA~ea~rla~y~krstisSreiqta~rLllPge 107 (127)
T KOG1744|consen 28 GKKRSTRRKESYSEYVYKVLKQVHPDLGISSKAMGVMNSFVNDIFERIASEAGRLAHYNKRSTISSREIQTAVRLLLPGE 107 (127)
T ss_pred cccCcccccCceeeehhhhhhcccCCCCcCHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCcccHHHHHHHHHHhCchH
Confidence 46677888999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhHHHhhhhhhhcccCC
Q 032404 123 LAKHAVSEGTKAVTKFTSS 141 (141)
Q Consensus 123 LaKhAvseGtkAV~ky~ss 141 (141)
|++||++||++||++|+++
T Consensus 108 l~khA~seGtkav~ky~~s 126 (127)
T KOG1744|consen 108 LAKHAVSEGTKAVTKYTSS 126 (127)
T ss_pred HhhhhhcccchhheeeccC
Confidence 9999999999999999875
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=8.5e-16 Score=103.84 Aligned_cols=68 Identities=31% Similarity=0.417 Sum_probs=65.2
Q ss_pred cchhHHHHHHHHhhhhcCC----CCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHh
Q 032404 50 SIETYKIYIFKVLKQVHPD----IGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRL 117 (141)
Q Consensus 50 r~esy~~YIyKVLKQVhpd----~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrL 117 (141)
+...+..||+|++++++++ ..||++||.+|+++++|+|.+|.++|..++.+++|.||+++|||.|+|+
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 4567899999999999999 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=1e-06 Score=60.59 Aligned_cols=61 Identities=16% Similarity=0.373 Sum_probs=58.0
Q ss_pred HHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhh
Q 032404 58 IFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLV 118 (141)
Q Consensus 58 IyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLl 118 (141)
+...++++.|+..++..+...|-.+++|+.+.|+.+|..||.+.++.||..+|||-+++-.
T Consensus 7 l~~lv~~id~~~~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~~~tv~~~Di~l~l~r~ 67 (72)
T cd07981 7 LQELLKEIDPREQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQLHLERN 67 (72)
T ss_pred HHHHHHhhCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHh
Confidence 6678999999999999999999999999999999999999999999999999999998754
No 7
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=98.30 E-value=2.3e-06 Score=62.30 Aligned_cols=63 Identities=19% Similarity=0.380 Sum_probs=59.3
Q ss_pred HHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCch
Q 032404 58 IFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLPG 121 (141)
Q Consensus 58 IyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLlLPG 121 (141)
|-|++|++.++ .||..|...|+..+..+++.|+.+|+.+|.+.+|+||+.+||+-|.+.+...
T Consensus 25 v~Ri~r~~~~~-Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~DI~la~~~~~~~ 87 (91)
T COG2036 25 VRRILRKAGAE-RVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLALKRLGRR 87 (91)
T ss_pred HHHHHHHHhHH-HhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHHHhccc
Confidence 78889998888 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=98.26 E-value=4.6e-06 Score=55.39 Aligned_cols=58 Identities=26% Similarity=0.458 Sum_probs=52.6
Q ss_pred HHHHHhhhhcCC-CCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHH
Q 032404 57 YIFKVLKQVHPD-IGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAV 115 (141)
Q Consensus 57 YIyKVLKQVhpd-~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAV 115 (141)
-|.|++|+. || ..||.+|...|......+.+.|+.+|...+..++|+||+.+||..||
T Consensus 7 ~vkri~k~~-~~~~~vs~ea~~~i~~a~e~Fi~~l~~~A~~~a~~~~rkti~~~Dv~~Av 65 (65)
T PF00808_consen 7 RVKRIMKSD-PDVMRVSKEAVEAIAKAAEEFIQYLAKEANEIAQRDKRKTITYEDVAKAV 65 (65)
T ss_dssp HHHHHHHHT-STTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEE-HHHHHHHH
T ss_pred HHHHHhccC-CCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHC
Confidence 488999999 76 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=97.86 E-value=7.3e-05 Score=50.88 Aligned_cols=59 Identities=22% Similarity=0.317 Sum_probs=52.4
Q ss_pred HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHH
Q 032404 57 YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVR 116 (141)
Q Consensus 57 YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVr 116 (141)
.|.+++++..= ..||..+..-|-..+.+..+.|+.+|..++++.+|+|||..||..|++
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 47778877643 378999999999999999999999999999999999999999988864
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=8.2e-05 Score=56.03 Aligned_cols=65 Identities=25% Similarity=0.277 Sum_probs=58.7
Q ss_pred hhHHH-HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHH
Q 032404 52 ETYKI-YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVR 116 (141)
Q Consensus 52 esy~~-YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVr 116 (141)
-.|.. =|+|.|++-.--..||..|..-|...+.++...|.+.|...++.+++++||.|+|+.|++
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 599999986666899999999999999999999999999999999999999999999998
No 11
>PLN00035 histone H4; Provisional
Probab=97.77 E-value=0.00015 Score=54.05 Aligned_cols=60 Identities=12% Similarity=0.145 Sum_probs=54.7
Q ss_pred HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHh
Q 032404 57 YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRL 117 (141)
Q Consensus 57 YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrL 117 (141)
-|.|+++.-- -..||..+..-|...++++++.|+.+|..++.+.+|+||+..||..|++.
T Consensus 34 ~IrRLARr~G-vkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr 93 (103)
T PLN00035 34 AIRRLARRGG-VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKR 93 (103)
T ss_pred HHHHHHHHcC-cccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHH
Confidence 4788888764 46899999999999999999999999999999999999999999999874
No 12
>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=97.71 E-value=0.00021 Score=51.37 Aligned_cols=60 Identities=13% Similarity=0.191 Sum_probs=53.7
Q ss_pred HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHh
Q 032404 57 YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRL 117 (141)
Q Consensus 57 YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrL 117 (141)
-|.|+++.-- -..||..+..-+...++.+++.|+.+|..++.+.+|+||+..||..|++.
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 5778887653 46899999999999999999999999999999999999999999998873
No 13
>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=97.70 E-value=0.00018 Score=49.62 Aligned_cols=59 Identities=17% Similarity=0.383 Sum_probs=48.9
Q ss_pred HHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHH
Q 032404 58 IFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVR 116 (141)
Q Consensus 58 IyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVr 116 (141)
+...++||-|+..+...+..+|-.+.+|+.+.+..-|++||++.+-.||..+|||...+
T Consensus 5 l~~Lv~~iDp~~~ld~~vee~Ll~laddFv~~v~~~ac~lAKhR~s~tle~~Dv~~~Le 63 (68)
T PF03847_consen 5 LQELVKQIDPNEKLDPDVEELLLELADDFVDDVVSFACRLAKHRKSSTLEVKDVQLHLE 63 (68)
T ss_dssp HHHHHHCC-SS----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHH
T ss_pred HHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCHHHHHHHHH
Confidence 66789999999999999999999999999999999999999999999999999998764
No 14
>PTZ00015 histone H4; Provisional
Probab=97.67 E-value=0.00025 Score=52.72 Aligned_cols=61 Identities=15% Similarity=0.239 Sum_probs=54.3
Q ss_pred HHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHh
Q 032404 56 IYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRL 117 (141)
Q Consensus 56 ~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrL 117 (141)
.-|.|+++.- --..||..+..-+..+++++++.|+.+|..++.|.+|+||+..||..|++.
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 4588888764 236899999999999999999999999999999999999999999998864
No 15
>smart00428 H3 Histone H3.
Probab=97.51 E-value=0.00068 Score=50.52 Aligned_cols=68 Identities=19% Similarity=0.262 Sum_probs=62.5
Q ss_pred chhHHHHHHHHhhhhcC--CCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhh
Q 032404 51 IETYKIYIFKVLKQVHP--DIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLV 118 (141)
Q Consensus 51 ~esy~~YIyKVLKQVhp--d~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLl 118 (141)
+-.|+..|..+..+..+ |..+++.|+.-|.....+.+-.+.++|..++.+.+|.||..+|||-|.||-
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 45788888888888888 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=97.32 E-value=0.0018 Score=48.44 Aligned_cols=65 Identities=11% Similarity=0.149 Sum_probs=57.8
Q ss_pred HHHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCc
Q 032404 55 KIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLP 120 (141)
Q Consensus 55 ~~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLlLP 120 (141)
...|.++||... ...++..+...|..|+....+.|+.+|..++.+.+|+||+..||..|+...+.
T Consensus 4 ~~~v~~iLk~~G-v~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r~~ 68 (117)
T cd07979 4 ARVIAAILKSMG-ITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRVD 68 (117)
T ss_pred HHHHHHHHHHCC-CCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhc
Confidence 356888998752 35779999999999999999999999999999999999999999999988774
No 17
>smart00417 H4 Histone H4.
Probab=97.25 E-value=0.0008 Score=47.34 Aligned_cols=56 Identities=11% Similarity=0.166 Sum_probs=48.7
Q ss_pred HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHH
Q 032404 57 YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQT 113 (141)
Q Consensus 57 YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqt 113 (141)
-|.|+++.- ---.||..+..-+..+++++++.|+.+|..++.+.+|+|++..||..
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 477887764 22578999999999999999999999999999999999999999853
No 18
>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [Transcription]
Probab=96.84 E-value=0.0047 Score=49.52 Aligned_cols=61 Identities=18% Similarity=0.306 Sum_probs=56.2
Q ss_pred HHHHhhhhcCC-CCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhh
Q 032404 58 IFKVLKQVHPD-IGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLV 118 (141)
Q Consensus 58 IyKVLKQVhpd-~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLl 118 (141)
|-|+.|+.-|. ..||.+|-..|.-.|..+.-=|..||+..++..+|+||+..||..|+--|
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 78899988776 68999999999999999999999999999999999999999999998643
No 19
>PLN00156 histone H2AX; Provisional
Probab=96.57 E-value=0.0075 Score=47.18 Aligned_cols=70 Identities=26% Similarity=0.276 Sum_probs=60.5
Q ss_pred hHHH-HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCchHHH
Q 032404 53 TYKI-YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLPGELA 124 (141)
Q Consensus 53 sy~~-YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLlLPGELa 124 (141)
.|.. -|+|.|+.-+--..|+..|.--|-..+.++...|-+-|..-++.+++.-|+.|.||.||+ -..||.
T Consensus 29 ~FPVgRi~R~Lk~g~ya~RVga~ApVYLAAVLEYLtaEVLELAgNaa~d~kk~RItPrHi~lAIr--nDeEL~ 99 (139)
T PLN00156 29 QFPVGRIARFLKAGKYAERVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR--NDEELS 99 (139)
T ss_pred ccchHHHHHHHhcCChhhccCCccHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHhhcc--CcHHHH
Confidence 4654 699999998777899999999999999999999999999999999999999999999998 334443
No 20
>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=96.51 E-value=0.013 Score=46.66 Aligned_cols=66 Identities=18% Similarity=0.318 Sum_probs=59.6
Q ss_pred HHHHHhhhhcC-CCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCchH
Q 032404 57 YIFKVLKQVHP-DIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLPGE 122 (141)
Q Consensus 57 YIyKVLKQVhp-d~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLlLPGE 122 (141)
-|.|++|.+-| |..+..+|..+++..--.+..-|+.||.+++....|+||....|+.|..-|==||
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 9999999999998888889999999999999999999999999999998654343
No 21
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=96.46 E-value=0.0045 Score=52.63 Aligned_cols=67 Identities=18% Similarity=0.336 Sum_probs=60.0
Q ss_pred HHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHH----hhCchH
Q 032404 56 IYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVR----LVLPGE 122 (141)
Q Consensus 56 ~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVr----LlLPGE 122 (141)
.-+...++||.+++.|..+.-++|-.+..|+.+.|..-+++||++.+..||-.|||+..+. +-|||.
T Consensus 158 ~kl~dLvqqId~~~~LD~dVedlLleiADdFV~sii~~sC~LAKHRKsdtlEvrDIqLhLEr~~Nm~iPgf 228 (258)
T KOG1142|consen 158 RKLDDLVQQIDGTTKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHRKSDTVEVRDIQLHLERNFNMEIPGF 228 (258)
T ss_pred cchhHHHHhhcCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccchhheeeeeeccccccCCCc
Confidence 3488899999999999999999999999999999999999999999999999999998764 345554
No 22
>smart00414 H2A Histone 2A.
Probab=96.38 E-value=0.0095 Score=44.27 Aligned_cols=70 Identities=23% Similarity=0.292 Sum_probs=57.2
Q ss_pred hHHH-HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCchHHH
Q 032404 53 TYKI-YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLPGELA 124 (141)
Q Consensus 53 sy~~-YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLlLPGELa 124 (141)
.|.. .|+|.|+.-.--..|+.-|.--|-..+..+...|-+-|..-++.+++.-||.|+||.|++- -.||.
T Consensus 9 ~fPVgRi~r~Lk~~~~~~Rv~~~A~VyLaAvLEYLtaEILeLagn~a~~~k~~rItp~hi~lAi~n--D~EL~ 79 (106)
T smart00414 9 QFPVGRIHRLLRKGTYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKRRITPRHLQLAIRN--DEELN 79 (106)
T ss_pred cCchHHHHHHHHcCccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchHHHhhhccC--CHHHH
Confidence 3443 6999999877677999999888888888888888888888889999999999999999983 44443
No 23
>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=96.30 E-value=0.018 Score=39.58 Aligned_cols=47 Identities=21% Similarity=0.374 Sum_probs=38.7
Q ss_pred CcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHH
Q 032404 70 GISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVR 116 (141)
Q Consensus 70 gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVr 116 (141)
.++.++-..|-.=++.-+..|..+|.+++++.+|.+||..||..|.|
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 45788888888888888999999999999999999999999999876
No 24
>PLN00157 histone H2A; Provisional
Probab=96.29 E-value=0.0077 Score=46.72 Aligned_cols=65 Identities=25% Similarity=0.266 Sum_probs=58.2
Q ss_pred hhHHH-HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHH
Q 032404 52 ETYKI-YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVR 116 (141)
Q Consensus 52 esy~~-YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVr 116 (141)
-.|.. -|+|.|++-+-...|+..|.--|-..+..+...|-+-|..-++.+++.-|+.|.||.|++
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 45554 699999998777899999999999999999999999999999999999999999999998
No 25
>PTZ00017 histone H2A; Provisional
Probab=96.25 E-value=0.0093 Score=46.34 Aligned_cols=65 Identities=22% Similarity=0.270 Sum_probs=56.8
Q ss_pred hhHHH-HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHH
Q 032404 52 ETYKI-YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVR 116 (141)
Q Consensus 52 esy~~-YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVr 116 (141)
-.|.. -|+|.|++-+.-..|+..|.--|-..+..++..|-+-|..-++.+++.-||.|.||.|++
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 34554 699999987777799999988888888888888888899999999999999999999998
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=96.23 E-value=0.015 Score=50.16 Aligned_cols=49 Identities=18% Similarity=0.379 Sum_probs=46.6
Q ss_pred CcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhh
Q 032404 70 GISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLV 118 (141)
Q Consensus 70 gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLl 118 (141)
.+|.+|...|..-+.+....|+.||.+++++.+|+||+..||..|++..
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 6799999999999999999999999999999999999999999999863
No 27
>PLN00153 histone H2A; Provisional
Probab=96.05 E-value=0.013 Score=45.21 Aligned_cols=71 Identities=25% Similarity=0.256 Sum_probs=60.6
Q ss_pred hhHHH-HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCchHHH
Q 032404 52 ETYKI-YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLPGELA 124 (141)
Q Consensus 52 esy~~-YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLlLPGELa 124 (141)
-.|.. -|+|.|++-+.-..|+..|.--|-..+..+...|-+-|..-++.|++.-|+.|.||.||+ -..||.
T Consensus 23 L~FpVgRi~R~Lr~g~~a~Rvga~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~--nDeEL~ 94 (129)
T PLN00153 23 LQFPVGRIARYLKKGKYAERIGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKNRIVPRHIQLAIR--NDEELG 94 (129)
T ss_pred cccchHHHHHHHhcCchhhccCCCchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHhhcc--CcHHHH
Confidence 45554 699999987777899999999999999999999999999999999999999999999998 334443
No 28
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=95.77 E-value=0.088 Score=36.24 Aligned_cols=60 Identities=8% Similarity=0.155 Sum_probs=48.7
Q ss_pred HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHh
Q 032404 57 YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRL 117 (141)
Q Consensus 57 YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrL 117 (141)
.|-++|+..-= -+++..|++.|-.++.+.+..|+.++..++.+.+|.+.+..||..|+.-
T Consensus 11 ~Vaqil~~~Gf-~~~~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~~~Dv~~Al~~ 70 (77)
T smart00576 11 AVAQILESAGF-DSFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPNLGDVVLALEN 70 (77)
T ss_pred HHHHHHHHcCc-cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence 34444544311 3568889999999999999999999999999999999999999988764
No 29
>PTZ00252 histone H2A; Provisional
Probab=95.50 E-value=0.038 Score=43.03 Aligned_cols=66 Identities=18% Similarity=0.184 Sum_probs=55.2
Q ss_pred chhHHH-HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhh--cCCCCcChHHHHHHHH
Q 032404 51 IETYKI-YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARY--NKKPTITSREIQTAVR 116 (141)
Q Consensus 51 ~esy~~-YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~--nkk~TltsreIqtAVr 116 (141)
.-.|.. -|+|.|++-+-...|+.-|.--|-..+..++..|-+-|..-++- |++.-|+.|.||.||+
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 345654 69999999888889999999888888888888888888877743 8889999999999998
No 30
>PLN00154 histone H2A; Provisional
Probab=95.40 E-value=0.044 Score=42.76 Aligned_cols=71 Identities=20% Similarity=0.213 Sum_probs=56.9
Q ss_pred hHHH-HHHHHhhhhc-CCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCchHHHH
Q 032404 53 TYKI-YIFKVLKQVH-PDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLPGELAK 125 (141)
Q Consensus 53 sy~~-YIyKVLKQVh-pd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLlLPGELaK 125 (141)
.|-. -|.|.||+-. -...|+..|.--|-..+..+.-.|-+-|..-++.+++.-||.|.||.|++ =-.||.+
T Consensus 38 ~FPVgRi~r~Lk~g~~~~~RVga~ApVYLAAVLEYLtAEVLELAGNaA~d~kk~RItPrHi~lAIr--nDeEL~~ 110 (136)
T PLN00154 38 QFPVGRIHRQLKQRVSAHGRVGATAAVYTAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR--GDEELDT 110 (136)
T ss_pred cCchHHHHHHHHhhhhhccccccchHHHHHHHHHHHHHHHHHHHHHHHHhhCCceecHHHhhhhcc--CcHHHHH
Confidence 4544 6999999975 45689998988888888888888888888888999999999999999998 3345443
No 31
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=95.36 E-value=0.037 Score=42.76 Aligned_cols=67 Identities=25% Similarity=0.290 Sum_probs=58.3
Q ss_pred HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCchHHHH
Q 032404 57 YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLPGELAK 125 (141)
Q Consensus 57 YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLlLPGELaK 125 (141)
-|.|+||.-.-.+.|+++|.--+.-.+..+.-.|.+-|..-++-++++-|+.|.||-|+| =..||-+
T Consensus 31 rvkr~lk~~~~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~kkkri~PrHlqlAIr--nD~EL~~ 97 (132)
T COG5262 31 RVKRLLKKGNYRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRIIPRHLQLAIR--NDEELNK 97 (132)
T ss_pred HHHHHHHcCccceeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhcCcceechHHHHHHhc--CcHHHHH
Confidence 599999977777999999999888899999999999999999999999999999999998 3445433
No 32
>PLN00121 histone H3; Provisional
Probab=95.19 E-value=0.1 Score=40.67 Aligned_cols=66 Identities=18% Similarity=0.241 Sum_probs=55.7
Q ss_pred hhHHHHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHh
Q 032404 52 ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRL 117 (141)
Q Consensus 52 esy~~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrL 117 (141)
-.|...|..|.....++..+.+.|+.-|..-..+.+-.+-+++.-.+.+.+|-||..+|||-+.||
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 457777777777777889999999998887777777777778899999999999999999999875
No 33
>PF15510 CENP-W: Centromere kinetochore component W
Probab=95.01 E-value=0.041 Score=40.88 Aligned_cols=65 Identities=23% Similarity=0.369 Sum_probs=53.3
Q ss_pred HHHHHHHHhhhhcCCCCc--chHHH--------------HHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHh
Q 032404 54 YKIYIFKVLKQVHPDIGI--SSKAM--------------GIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRL 117 (141)
Q Consensus 54 y~~YIyKVLKQVhpd~gI--SskAm--------------~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrL 117 (141)
-..++.||+|+--|.+.+ +.+.| --||-++ +..|+|+||---+.-||+.||....|+.|.+.
T Consensus 18 PrgfLkrv~Kr~KphlRl~~~~Dllv~~~~f~~~~~~~~vhLncLL--FvhrLAEEaRtnA~EnK~~~Ik~~Hv~AaaKv 95 (102)
T PF15510_consen 18 PRGFLKRVFKRQKPHLRLETSGDLLVRFCPFSGWQWGGEVHLNCLL--FVHRLAEEARTNACENKCGTIKKEHVLAAAKV 95 (102)
T ss_pred chHHHHHHHHhcCCceeecccccHHHhhcccccccccceeehhHHH--HHHHHHHHHHHHHHHHhhccccHHHHHHHHHH
Confidence 346789999998888766 44445 3456665 67899999999999999999999999999998
Q ss_pred hCc
Q 032404 118 VLP 120 (141)
Q Consensus 118 lLP 120 (141)
+|-
T Consensus 96 iLK 98 (102)
T PF15510_consen 96 ILK 98 (102)
T ss_pred HHH
Confidence 874
No 34
>PTZ00018 histone H3; Provisional
Probab=94.94 E-value=0.13 Score=40.11 Aligned_cols=66 Identities=18% Similarity=0.241 Sum_probs=55.4
Q ss_pred hhHHHHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHh
Q 032404 52 ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRL 117 (141)
Q Consensus 52 esy~~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrL 117 (141)
-.|...|..|..+..++..+.+.|+.-|..-..+.+-.+-+++.-.+.+.+|-||..+|||-|.||
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 356777777777777889999999998887777777777778899999999999999999999875
No 35
>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription]
Probab=94.69 E-value=0.19 Score=40.63 Aligned_cols=63 Identities=22% Similarity=0.299 Sum_probs=49.9
Q ss_pred HHHHHHhhhhcCC--CCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhh
Q 032404 56 IYIFKVLKQVHPD--IGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLV 118 (141)
Q Consensus 56 ~YIyKVLKQVhpd--~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLl 118 (141)
.-|-|+.|.+-|+ .+||.+|...|-.-..=+..-+..-|..+|+-++|+||+..||-.|.+-+
T Consensus 14 AiI~rlvke~l~E~~vsisKeA~~Ai~raAtVFv~~Lts~s~e~A~~q~rKt~sadDVl~aL~Ei 78 (172)
T KOG0870|consen 14 AIITRLVKEVLPESNVSISKEARLAIARAATVFVIFLTSVSNEIAKDQKRKTISADDVLKALDEI 78 (172)
T ss_pred HHHHHHHHHhCccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCcccHHHHHHHHHHh
Confidence 4577888888776 58999998877665444445566667779999999999999999999865
No 36
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=94.52 E-value=0.14 Score=35.97 Aligned_cols=59 Identities=15% Similarity=0.330 Sum_probs=47.9
Q ss_pred HHHHhhhh--cCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHH
Q 032404 58 IFKVLKQV--HPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVR 116 (141)
Q Consensus 58 IyKVLKQV--hpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVr 116 (141)
|-++..++ ..+..+|.+.++-|..++.+..+.++.+---++++.+|+||+..|+.-.+|
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 456788999999999999999999999999999999999999999875544
No 37
>KOG1756 consensus Histone 2A [Chromatin structure and dynamics]
Probab=93.77 E-value=0.18 Score=39.27 Aligned_cols=67 Identities=25% Similarity=0.298 Sum_probs=54.6
Q ss_pred HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCchHHHH
Q 032404 57 YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLPGELAK 125 (141)
Q Consensus 57 YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLlLPGELaK 125 (141)
-|.|+||.-..-..||..|-..|.-.+..+--.|.+-|..-++-|++.-|++|.||-|++ =..||.+
T Consensus 32 ri~r~Lr~~~~~~ri~~gapV~laavLeYL~Aeile~agnaardnkk~ri~PrH~~lAI~--NDeEL~~ 98 (131)
T KOG1756|consen 32 RIHRLLRKGRYAQRVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRITPRHLQLAIR--NDEELNK 98 (131)
T ss_pred HHHHHHHccchhhhccCCChHHHHHHHHHHHHHHHHHhHHHhhhcCccccChHHHHHHHh--CcHHHHH
Confidence 699999997777899999988777777777777777777778899999999999999998 3344443
No 38
>PLN00161 histone H3; Provisional
Probab=93.33 E-value=0.54 Score=36.72 Aligned_cols=66 Identities=15% Similarity=0.208 Sum_probs=52.3
Q ss_pred hhHHHHHHHHhhhhcC-CCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHh
Q 032404 52 ETYKIYIFKVLKQVHP-DIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRL 117 (141)
Q Consensus 52 esy~~YIyKVLKQVhp-d~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrL 117 (141)
-.|+..|..|..+..+ |+.+.+.|+.-|..-..+.+-.+-+++.-.+.+.+|-||..+|||-|.||
T Consensus 59 lPF~RLVREI~~~~~~~~~Rfq~~Al~ALQEAsEayLV~lFeda~lcaiHAkRVTlm~kDm~La~ri 125 (135)
T PLN00161 59 LPFARLVREISNEMLREPFRWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMPKDMQLARRI 125 (135)
T ss_pred ccHHHHHHHHHHhcCCCCcEeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccchhhHHHHHHh
Confidence 3566666666655544 68899999888877776666666678888999999999999999999875
No 39
>PLN00160 histone H3; Provisional
Probab=92.04 E-value=1.1 Score=33.18 Aligned_cols=66 Identities=15% Similarity=0.148 Sum_probs=50.5
Q ss_pred hhHHHHHHHHhhhhcC-CCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHh
Q 032404 52 ETYKIYIFKVLKQVHP-DIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRL 117 (141)
Q Consensus 52 esy~~YIyKVLKQVhp-d~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrL 117 (141)
-.|+.-+..+.-.... +..+.+.|+.-|..-..+.+-.+-+++.-.+.+.+|-||..+|||-|.|+
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 4566666666554433 37889999888877666666666668888899999999999999999874
No 40
>PF15511 CENP-T: Centromere kinetochore component CENP-T; PDB: 3B0D_T 3B0C_T 3VH5_T 3VH6_T.
Probab=91.95 E-value=0.45 Score=42.27 Aligned_cols=54 Identities=19% Similarity=0.282 Sum_probs=41.7
Q ss_pred HHHHHhhhhc-----CCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHH
Q 032404 57 YIFKVLKQVH-----PDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSRE 110 (141)
Q Consensus 57 YIyKVLKQVh-----pd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~Tltsre 110 (141)
+|.+++.... -.+.||.+||..+....+.+||.|+..=.-.+.+.+|+||...|
T Consensus 356 ~vK~la~~~ak~s~~sK~kiskdal~aleqasdwfFeQl~dDL~aYA~HAgRKTIdesD 414 (414)
T PF15511_consen 356 VVKKLAQHFAKSSGGSKMKISKDALEALEQASDWFFEQLGDDLEAYAKHAGRKTIDESD 414 (414)
T ss_dssp HHHHHHHHHH-------S-B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHH
T ss_pred HHHHHHHHHHHhhcccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCCCC
Confidence 5555555543 45899999999999999999999999999999999999998765
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=91.92 E-value=1.7 Score=29.45 Aligned_cols=48 Identities=13% Similarity=0.269 Sum_probs=44.4
Q ss_pred CCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHH
Q 032404 69 IGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVR 116 (141)
Q Consensus 69 ~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVr 116 (141)
.+++..|+++|..++.+.+..|+..+...+....|...+..||..|..
T Consensus 22 ~~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~ 69 (77)
T PF07524_consen 22 DSASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPNLQDVEQALE 69 (77)
T ss_pred cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 467899999999999999999999999999999999999999998875
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=89.86 E-value=1.1 Score=34.43 Aligned_cols=60 Identities=17% Similarity=0.303 Sum_probs=44.4
Q ss_pred HHHHHHhhhhcCCCCcc---hHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhC
Q 032404 56 IYIFKVLKQVHPDIGIS---SKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVL 119 (141)
Q Consensus 56 ~YIyKVLKQVhpd~gIS---skAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLlL 119 (141)
..|.-+|+. +||+ .+....|-.|+.-..-.|-.+|..++.+.++.+|+..||+.|+..-+
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 456666654 5664 56667777777777788889999999999999999999999998654
No 43
>KOG2549 consensus Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=88.84 E-value=1.6 Score=41.02 Aligned_cols=50 Identities=12% Similarity=0.271 Sum_probs=45.7
Q ss_pred CCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhh
Q 032404 69 IGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLV 118 (141)
Q Consensus 69 ~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLl 118 (141)
..|+.++-.+|---|..=.+.|+.+|+++.++.+|.+||..||.-|.|.+
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 44678999999888999999999999999999999999999999999864
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=86.96 E-value=0.9 Score=32.63 Aligned_cols=47 Identities=13% Similarity=0.244 Sum_probs=23.6
Q ss_pred CcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHH
Q 032404 70 GISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVR 116 (141)
Q Consensus 70 gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVr 116 (141)
--+.++..+|..+|.+-.-.+..+|..++....+..|+..||..++|
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 45678999999999999999999999999999999999999999887
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=85.36 E-value=7.2 Score=27.85 Aligned_cols=60 Identities=12% Similarity=0.196 Sum_probs=49.8
Q ss_pred HHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCC---CCcChHHHHHHHHhh
Q 032404 58 IFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKK---PTITSREIQTAVRLV 118 (141)
Q Consensus 58 IyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk---~TltsreIqtAVrLl 118 (141)
|.|++.++-. .+++..-..+|..+-.-+.-.|.++|..+..-... ..|.++.|..|.|.+
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 7777777754 78888888888888888888999999998877554 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=85.15 E-value=4 Score=29.44 Aligned_cols=51 Identities=8% Similarity=0.281 Sum_probs=42.3
Q ss_pred cCCC-CcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHh
Q 032404 66 HPDI-GISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRL 117 (141)
Q Consensus 66 hpd~-gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrL 117 (141)
+-|. .-..++..+|..+|.+..-.|..+|..++. .++.-++..||..++|-
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 55556699999999873
No 47
>KOG3334 consensus Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=82.92 E-value=5 Score=31.88 Aligned_cols=59 Identities=19% Similarity=0.356 Sum_probs=42.5
Q ss_pred HHHHHhhhhcCCCCcch---HHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhC
Q 032404 57 YIFKVLKQVHPDIGISS---KAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVL 119 (141)
Q Consensus 57 YIyKVLKQVhpd~gISs---kAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLlL 119 (141)
-|.-+|+ ++||.. +-++.|=.|..--.-.|-..|.-++.+.++.||+..||+.|+....
T Consensus 18 ~i~~iL~----s~GI~eyEprVi~qlLefa~rYtt~vL~DA~vys~HA~ka~i~~eDVrlA~~~~~ 79 (148)
T KOG3334|consen 18 VIASILK----SLGIQEYEPRVINQLLEFAYRYTTTVLDDAKVYSSHAKKATIDAEDVRLAIQMRV 79 (148)
T ss_pred HHHHHHH----HcCccccChHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHh
Confidence 3444554 467754 3344444454555567889999999999999999999999998653
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=79.71 E-value=15 Score=26.70 Aligned_cols=62 Identities=13% Similarity=0.161 Sum_probs=44.6
Q ss_pred HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcC-CCCcChHHHHHHHHhh
Q 032404 57 YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNK-KPTITSREIQTAVRLV 118 (141)
Q Consensus 57 YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nk-k~TltsreIqtAVrLl 118 (141)
-|.|+..++-.+.++|....-+|..+-.=+.-.|.++|..+..-.. -..|....|..|.|-|
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 4899999998778999988888888888888888888888776433 3489999999998854
No 49
>PF14687 DUF4460: Domain of unknown function (DUF4460)
Probab=78.84 E-value=2.8 Score=31.28 Aligned_cols=38 Identities=16% Similarity=0.449 Sum_probs=31.2
Q ss_pred hhHHHHHHHHhhhhcCCC--------CcchHHHHHHHHHHHHHHHH
Q 032404 52 ETYKIYIFKVLKQVHPDI--------GISSKAMGIMNSFINDIFEK 89 (141)
Q Consensus 52 esy~~YIyKVLKQVhpd~--------gISskAm~ImnSfvnDifer 89 (141)
-.....+......||||+ .+-.+++.+||+++..+..+
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 345678888899999993 46788999999999888775
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=74.90 E-value=13 Score=34.65 Aligned_cols=61 Identities=20% Similarity=0.362 Sum_probs=47.8
Q ss_pred hhhcCCCCcchHHHHHHHHHHHHH-------HHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCchHH
Q 032404 63 KQVHPDIGISSKAMGIMNSFINDI-------FEKLAQESSRLARYNKKPTITSREIQTAVRLVLPGEL 123 (141)
Q Consensus 63 KQVhpd~gISskAm~ImnSfvnDi-------ferIA~EAs~La~~nkk~TltsreIqtAVrLlLPGEL 123 (141)
++..++..|+...+..+..+...+ ...+..=|--+|..+.+.+++..||+.|++|+|+.-+
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 345678889999888877777554 2344455556889999999999999999999998655
No 51
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=73.34 E-value=5.5 Score=34.04 Aligned_cols=47 Identities=26% Similarity=0.259 Sum_probs=36.6
Q ss_pred CcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHH
Q 032404 70 GISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVR 116 (141)
Q Consensus 70 gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVr 116 (141)
-||.+|--+..-+-.-+.+.+.-.|...+..|+|+||.--||-.||.
T Consensus 127 MisaEaPvlFak~~EiFI~ELTmRAW~~ae~NkRRtLQksDia~Av~ 173 (286)
T COG5208 127 MISAEAPVLFAKITEIFIEELTMRAWINAEENKRRTLQKSDIAAAVK 173 (286)
T ss_pred heecccchHHHHHHHHHHHHHHHHHHHHHhHhhhhHHHHHHHHHHHH
Confidence 46777654444333344478889999999999999999999999986
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=70.51 E-value=7.4 Score=27.00 Aligned_cols=57 Identities=11% Similarity=0.201 Sum_probs=35.1
Q ss_pred HHHHhhhh--cCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCC-cChHHHHHH
Q 032404 58 IFKVLKQV--HPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPT-ITSREIQTA 114 (141)
Q Consensus 58 IyKVLKQV--hpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~T-ltsreIqtA 114 (141)
|-|+|..- ++++.||.+|+..+.-+++=+-..-...|...++-..... |...+++.-
T Consensus 5 i~rll~~~f~~~~tkIs~dal~l~~eyl~iFV~EAv~Ra~~~a~~e~~~~~le~e~LEki 64 (72)
T PF09415_consen 5 IARLLHEHFKDDKTKISKDALKLSAEYLRIFVREAVARAAEQAEAEGDEGFLEVEHLEKI 64 (72)
T ss_dssp HHHHHCTTSSSTT-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSEE-HHHHHHH
T ss_pred HHHHHHHHhcCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHH
Confidence 66777754 4669999999887666654444444455555566666666 888888763
No 53
>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=69.85 E-value=5 Score=36.17 Aligned_cols=60 Identities=25% Similarity=0.382 Sum_probs=46.3
Q ss_pred HHHhhhhcCCCCcchHHHHHHHHHHHHH---HHHHHHHHhHHhhhcCCCCcChHHHHHHHHhh
Q 032404 59 FKVLKQVHPDIGISSKAMGIMNSFINDI---FEKLAQESSRLARYNKKPTITSREIQTAVRLV 118 (141)
Q Consensus 59 yKVLKQVhpd~gISskAm~ImnSfvnDi---ferIA~EAs~La~~nkk~TltsreIqtAVrLl 118 (141)
.--||.|-...||+.=.=+.+.-+..|+ ...|..||+++..++||..||..||..|.|-+
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 3456777777888765555555555555 45568999999999999999999999999965
No 54
>KOG1745 consensus Histones H3 and H4 [Chromatin structure and dynamics]
Probab=69.14 E-value=5.9 Score=31.06 Aligned_cols=53 Identities=25% Similarity=0.413 Sum_probs=37.4
Q ss_pred hhhhcCCCCcchHHHHHHHH----HHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhh
Q 032404 62 LKQVHPDIGISSKAMGIMNS----FINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLV 118 (141)
Q Consensus 62 LKQVhpd~gISskAm~ImnS----fvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLl 118 (141)
.....+|+.+.+.|+.-|-- |+.++|| ...-.+.+.+|-||-..|||-|.|+-
T Consensus 77 ~q~f~~dLrfqs~Ai~ALQeA~EayLv~LfE----dtnlcAihAkRVTimpkdiQlArrir 133 (137)
T KOG1745|consen 77 AQDFKTDLRFQSSAIAALQEAAEAYLVGLFE----DTNLCAIHAKRVTIMPKDIQLARRIR 133 (137)
T ss_pred HhcccccceehHHHHHHHHHHHHHHHHHhcc----ccchhhhccceeEecccceehhhhcc
Confidence 33446778888777665543 4444554 34466778999999999999999953
No 55
>TIGR01128 holA DNA polymerase III, delta subunit. subunit around DNA forming a DNA sliding clamp.
Probab=68.93 E-value=31 Score=27.71 Aligned_cols=66 Identities=23% Similarity=0.325 Sum_probs=51.8
Q ss_pred hhHHHHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhC
Q 032404 52 ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVL 119 (141)
Q Consensus 52 esy~~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLlL 119 (141)
.....||...+++. +..|+.++...|.+.++.=...+..|.-+|+.|....+||..+|+.-+.-..
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 34556777777764 5789999999988888766678999999999997666899999987765443
No 56
>smart00350 MCM minichromosome maintenance proteins.
Probab=68.56 E-value=30 Score=31.32 Aligned_cols=66 Identities=20% Similarity=0.291 Sum_probs=48.0
Q ss_pred hhHHHHHHHHhhhhcCCCCcchHHHHHHHHHHHHHH-------------------HHHHHHHhHHhhhcCCCCcChHHHH
Q 032404 52 ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIF-------------------EKLAQESSRLARYNKKPTITSREIQ 112 (141)
Q Consensus 52 esy~~YIyKVLKQVhpd~gISskAm~ImnSfvnDif-------------------erIA~EAs~La~~nkk~TltsreIq 112 (141)
+....||.-+=..++|. ||..+..++..+..++= +-|..-|--+|+..-+.+++..|+.
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 79999888877776653 3344445557888899999999999
Q ss_pred HHHHhhC
Q 032404 113 TAVRLVL 119 (141)
Q Consensus 113 tAVrLlL 119 (141)
.|++|+.
T Consensus 499 ~ai~l~~ 505 (509)
T smart00350 499 EAIRLLR 505 (509)
T ss_pred HHHHHHH
Confidence 9999874
No 57
>COG1466 HolA DNA polymerase III, delta subunit [DNA replication, recombination, and repair]
Probab=67.63 E-value=23 Score=30.01 Aligned_cols=67 Identities=22% Similarity=0.283 Sum_probs=57.5
Q ss_pred hhHHHHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCc
Q 032404 52 ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLP 120 (141)
Q Consensus 52 esy~~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLlLP 120 (141)
+..-.+|-+.+++. .+.|+.+|+..|..-++.=+--|..|--+|+-|..-.+||..+|+..|--...
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 34566777777775 47899999999999999999999999999999999889999999999866554
No 58
>PRK07452 DNA polymerase III subunit delta; Validated
Probab=66.57 E-value=27 Score=28.87 Aligned_cols=62 Identities=18% Similarity=0.316 Sum_probs=50.5
Q ss_pred HHHHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhh--cCCCCcChHHHHHHHHh
Q 032404 54 YKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARY--NKKPTITSREIQTAVRL 117 (141)
Q Consensus 54 y~~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~--nkk~TltsreIqtAVrL 117 (141)
...||...+++- +..|+..|...|...+..=+..+..|--+|+-| ....+||..+|+..|--
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 455666666554 467999999999998888888999999999999 56789999999987653
No 59
>PRK09333 30S ribosomal protein S19e; Provisional
Probab=66.25 E-value=15 Score=29.08 Aligned_cols=49 Identities=18% Similarity=0.337 Sum_probs=37.1
Q ss_pred hhHHHHHHHHhhhh-----cC-CCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhh
Q 032404 52 ETYKIYIFKVLKQV-----HP-DIGISSKAMGIMNSFINDIFEKLAQESSRLARY 100 (141)
Q Consensus 52 esy~~YIyKVLKQV-----hp-d~gISskAm~ImnSfvnDiferIA~EAs~La~~ 100 (141)
.+.-.|+.+.|-+. +| +--||+++.+.||.+-.+|+..+..|--.|.+|
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 44466777777654 22 356899999999999999999998776666655
No 60
>PRK09522 bifunctional glutamine amidotransferase/anthranilate phosphoribosyltransferase; Provisional
Probab=66.19 E-value=9.5 Score=35.13 Aligned_cols=61 Identities=20% Similarity=0.315 Sum_probs=42.0
Q ss_pred hhcCCCCcchHHHHHHHHHHHHHHHHHHHH---HhHHhhhcCCCCcChHHHHHHHHhhCchHHH
Q 032404 64 QVHPDIGISSKAMGIMNSFINDIFEKLAQE---SSRLARYNKKPTITSREIQTAVRLVLPGELA 124 (141)
Q Consensus 64 QVhpd~gISskAm~ImnSfvnDiferIA~E---As~La~~nkk~TltsreIqtAVrLlLPGELa 124 (141)
|-||+.-.|...+.||.+|++-.+...-.+ ..-|-+....+.||..|...++..+|-|+..
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 679999999999999999985433211000 0112222245799999999999999988743
No 61
>PRK05574 holA DNA polymerase III subunit delta; Reviewed
Probab=62.83 E-value=43 Score=27.44 Aligned_cols=66 Identities=24% Similarity=0.255 Sum_probs=51.5
Q ss_pred hhHHHHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhC
Q 032404 52 ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVL 119 (141)
Q Consensus 52 esy~~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLlL 119 (141)
..+..||...+++. +..|+..|...|-..++.=+..+..|.-+|+.|.....||..+|+..+--..
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 44666777777764 4679999999999888877789999999999997434499999987665433
No 62
>PRK08487 DNA polymerase III subunit delta; Validated
Probab=61.13 E-value=34 Score=28.76 Aligned_cols=63 Identities=22% Similarity=0.182 Sum_probs=52.4
Q ss_pred HHHHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCc
Q 032404 54 YKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLP 120 (141)
Q Consensus 54 y~~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLlLP 120 (141)
...+|...+++. +..|+..|+..+.+.+..=+..|..|--+|+-|.. +||..+|+..|--...
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 456788777775 47899999999999988888899999999999965 7999999998754443
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=60.07 E-value=57 Score=25.68 Aligned_cols=67 Identities=18% Similarity=0.197 Sum_probs=49.1
Q ss_pred hhHHHHHHHHhhhhcC--CCCcchHHHHHHHHHHHH---HHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhh
Q 032404 52 ETYKIYIFKVLKQVHP--DIGISSKAMGIMNSFIND---IFEKLAQESSRLARYNKKPTITSREIQTAVRLV 118 (141)
Q Consensus 52 esy~~YIyKVLKQVhp--d~gISskAm~ImnSfvnD---iferIA~EAs~La~~nkk~TltsreIqtAVrLl 118 (141)
+....|+...|.+... +..+|.+++..+-....- ....++.++...+..++..+|+...|..+++-+
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 345566666666667788999999999998753
No 64
>KOG1757 consensus Histone 2A [Chromatin structure and dynamics]
Probab=58.41 E-value=14 Score=28.63 Aligned_cols=60 Identities=28% Similarity=0.304 Sum_probs=39.3
Q ss_pred hHHH-HHHHHhhhhcCC-CCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhc----CCCCcChHHHHHHHH
Q 032404 53 TYKI-YIFKVLKQVHPD-IGISSKAMGIMNSFINDIFEKLAQESSRLARYN----KKPTITSREIQTAVR 116 (141)
Q Consensus 53 sy~~-YIyKVLKQVhpd-~gISskAm~ImnSfvnDiferIA~EAs~La~~n----kk~TltsreIqtAVr 116 (141)
.|-. -|+|-||+.... ..+-..+.--+. .|+|-+..|..+|+-.. |-+-||.|.+|-|+|
T Consensus 30 qFpVgRihr~LK~r~t~h~rVGataavy~a----aileYLTaEVLeLAgNasKdLKvKRitprHlqLAiR 95 (131)
T KOG1757|consen 30 QFPVGRIHRHLKTRTTSHGRVGATAAVYSA----AILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 95 (131)
T ss_pred ccchHHHHHHHHHhcccccccchHHHHHHH----HHHHHHHHHHHHHcccccccceeeeccchhheeeec
Confidence 4444 488999986544 344444444333 45667777777777543 446799999999988
No 65
>PRK14607 bifunctional glutamine amidotransferase/anthranilate phosphoribosyltransferase; Provisional
Probab=57.77 E-value=14 Score=33.72 Aligned_cols=60 Identities=18% Similarity=0.295 Sum_probs=42.4
Q ss_pred hhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCchHHH
Q 032404 64 QVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLPGELA 124 (141)
Q Consensus 64 QVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLlLPGELa 124 (141)
|-||+...+.....|++.|++-..+.+.- ..-|-+......||..|+..+++.+|-|+..
T Consensus 167 QFHPE~~~t~~g~~i~~nFl~~~~~~~~~-~~~i~~l~~g~~Lt~~ea~~~~~~il~g~~~ 226 (534)
T PRK14607 167 QFHPESILTEEGKRILKNFLNYQREEIDI-KSYLKKLVEGEDLSFEEAEDVMEDITDGNAT 226 (534)
T ss_pred EeCCCCCCChhHHHHHHHHHHHhhccCCH-HHHHHHhccCCCCCHHHHHHHHHHHHcCCCC
Confidence 77999777888889999998754332211 1123333445699999999999999988643
No 66
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=57.72 E-value=36 Score=26.88 Aligned_cols=51 Identities=18% Similarity=0.209 Sum_probs=43.9
Q ss_pred CCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhh
Q 032404 68 DIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLV 118 (141)
Q Consensus 68 d~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLl 118 (141)
|+....+|..|+-.---.+..-+..||...+....++||....|..|..-|
T Consensus 28 dl~ftKearei~in~cieFi~~lsseAne~ce~EaKKTIa~EHviKALenL 78 (148)
T COG5150 28 DLVFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHVIKALENL 78 (148)
T ss_pred cccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHhc
Confidence 578899999986655556778899999999999999999999999998754
No 67
>smart00271 DnaJ DnaJ molecular chaperone homology domain.
Probab=56.16 E-value=34 Score=21.05 Aligned_cols=18 Identities=28% Similarity=0.215 Sum_probs=13.7
Q ss_pred HHHHHHHhhhhcCCCCcc
Q 032404 55 KIYIFKVLKQVHPDIGIS 72 (141)
Q Consensus 55 ~~YIyKVLKQVhpd~gIS 72 (141)
..-.+++.++.|||..-.
T Consensus 19 k~ay~~l~~~~HPD~~~~ 36 (60)
T smart00271 19 KKAYRKLALKYHPDKNPG 36 (60)
T ss_pred HHHHHHHHHHHCcCCCCC
Confidence 344677889999998764
No 68
>PRK06585 holA DNA polymerase III subunit delta; Reviewed
Probab=55.29 E-value=48 Score=27.64 Aligned_cols=65 Identities=18% Similarity=0.180 Sum_probs=51.8
Q ss_pred hHHHHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcC-CCCcChHHHHHHHHhhC
Q 032404 53 TYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNK-KPTITSREIQTAVRLVL 119 (141)
Q Consensus 53 sy~~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nk-k~TltsreIqtAVrLlL 119 (141)
....+|.+.+++. +..|+..|...|...+..=+..+..|--+|+.|.. ..+||..||+..|--..
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 47899999999999998888899999999999953 46899999988765443
No 69
>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=53.58 E-value=36 Score=20.47 Aligned_cols=18 Identities=28% Similarity=0.217 Sum_probs=14.0
Q ss_pred HHHHHHHhhhhcCCCCcc
Q 032404 55 KIYIFKVLKQVHPDIGIS 72 (141)
Q Consensus 55 ~~YIyKVLKQVhpd~gIS 72 (141)
..-.+++.++.|||..-+
T Consensus 18 k~~y~~l~~~~HPD~~~~ 35 (55)
T cd06257 18 KKAYRKLALKYHPDKNPD 35 (55)
T ss_pred HHHHHHHHHHHCcCCCCC
Confidence 344678889999998776
No 70
>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=52.99 E-value=65 Score=26.22 Aligned_cols=56 Identities=30% Similarity=0.448 Sum_probs=44.7
Q ss_pred hhHHHHHHHH---hhhhcCCCCcchHHHHH------------------HHHHHHHHHHHHHHHHhHHhhhcCCCCcC
Q 032404 52 ETYKIYIFKV---LKQVHPDIGISSKAMGI------------------MNSFINDIFEKLAQESSRLARYNKKPTIT 107 (141)
Q Consensus 52 esy~~YIyKV---LKQVhpd~gISskAm~I------------------mnSfvnDiferIA~EAs~La~~nkk~Tlt 107 (141)
.+|..+|--. |..+.||+.=|.+||-- |-+|+..|.-+|--|+..+..|++++++.
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 3455555444 44569999999999853 67899999999999999999999999874
No 71
>PRK05907 hypothetical protein; Provisional
Probab=49.33 E-value=53 Score=28.09 Aligned_cols=61 Identities=18% Similarity=0.166 Sum_probs=46.1
Q ss_pred HHHHHHHHhhhhcCCCCcchHHHHHHHHHH-HHHHHHHHHHHhHHhhh-cCCCCcChHHHHHHHH
Q 032404 54 YKIYIFKVLKQVHPDIGISSKAMGIMNSFI-NDIFEKLAQESSRLARY-NKKPTITSREIQTAVR 116 (141)
Q Consensus 54 y~~YIyKVLKQVhpd~gISskAm~ImnSfv-nDiferIA~EAs~La~~-nkk~TltsreIqtAVr 116 (141)
...||-+.+++- +..|+..|...+..-+ ..=+..|..|--+|+.| ..+.+||..+|+..|-
T Consensus 139 L~~Wi~~~~~~~--g~~i~~~a~~~L~~~~~~~nL~~l~~EleKL~ly~g~~~~It~e~V~~lv~ 201 (311)
T PRK05907 139 IAQLLIQRAKEL--GISCSLGLASLFVSKFPQTGLFEILSEFQKLLCQMGKKESLEASDIQSFVV 201 (311)
T ss_pred HHHHHHHHHHHc--CCCcCHHHHHHHHHHccCCCHHHHHHHHHHHHHhcCCCCeECHHHHHHHhc
Confidence 345566666553 3679999988877766 23344999999999999 6688999999988754
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=49.21 E-value=45 Score=28.94 Aligned_cols=61 Identities=16% Similarity=0.312 Sum_probs=41.5
Q ss_pred hhhcCCCCcchHHHHHHHHHHHHHHH---H----HHHHHhHHhhhcCCCCcChHHHHHHHHhhCchHH
Q 032404 63 KQVHPDIGISSKAMGIMNSFINDIFE---K----LAQESSRLARYNKKPTITSREIQTAVRLVLPGEL 123 (141)
Q Consensus 63 KQVhpd~gISskAm~ImnSfvnDife---r----IA~EAs~La~~nkk~TltsreIqtAVrLlLPGEL 123 (141)
++.-++..|+...+.-+..++..+=. | +..=|--+|-.+.|..++..||+.+++++|+.-+
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 44557777777766655555544321 0 1222334788899999999999999999998654
No 73
>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=48.67 E-value=36 Score=23.21 Aligned_cols=33 Identities=24% Similarity=0.464 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHh
Q 032404 82 FINDIFEKLAQESSRLARYNKKPTITSREIQTAVRL 117 (141)
Q Consensus 82 fvnDiferIA~EAs~La~~nkk~TltsreIqtAVrL 117 (141)
++|.|+--+..||.+|+.-. -.|.+||..+++.
T Consensus 3 i~nRl~~~~~~ea~~l~~eg---vas~~~ID~~~~~ 35 (97)
T PF00725_consen 3 IVNRLLAALLNEAARLVEEG---VASPEDIDRAMRY 35 (97)
T ss_dssp THHHHHHHHHHHHHHHHHTT---SSSHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHc---CCCHHHHHHHHHH
Confidence 57888999999999999854 3689999999997
No 74
>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=48.32 E-value=1.2e+02 Score=28.36 Aligned_cols=65 Identities=12% Similarity=0.108 Sum_probs=36.2
Q ss_pred hHHHHHHHHhhhhcCCCCcchHHHHHHHHHHH-------------HHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHh
Q 032404 53 TYKIYIFKVLKQVHPDIGISSKAMGIMNSFIN-------------DIFEKLAQESSRLARYNKKPTITSREIQTAVRL 117 (141)
Q Consensus 53 sy~~YIyKVLKQVhpd~gISskAm~ImnSfvn-------------DiferIA~EAs~La~~nkk~TltsreIqtAVrL 117 (141)
.|..||.+.+++-..--.+|..|+.-+-.+.. .-+..|..+|..+++.....+|+.++|+.|++.
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 35555555554431112677777665433221 234455666666666666667777777776553
No 75
>KOG0568 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=45.77 E-value=41 Score=29.31 Aligned_cols=51 Identities=33% Similarity=0.422 Sum_probs=27.5
Q ss_pred HHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHH
Q 032404 57 YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSRE 110 (141)
Q Consensus 57 YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~Tltsre 110 (141)
-++.+.||||||.|-.. |-+-----|..-|.++-.|- ++..|.++.|...|
T Consensus 67 af~~lakq~hpdsgs~~-adaa~f~qideafrkvlq~~--~~ktn~~qn~~ede 117 (342)
T KOG0568|consen 67 AFHDLAKQVHPDSGSEE-ADAARFIQIDEAFRKVLQEK--FAKTNARQNIGEDE 117 (342)
T ss_pred HHHHHHHHcCCCCCCcc-ccHHHHHHHHHHHHHHHHHH--HHHhhhccccccch
Confidence 46788999999987532 11100011234445444442 45666666665544
No 76
>COG2238 RPS19A Ribosomal protein S19E (S16A) [Translation, ribosomal structure and biogenesis]
Probab=45.53 E-value=29 Score=27.64 Aligned_cols=38 Identities=26% Similarity=0.394 Sum_probs=30.6
Q ss_pred HHHHHHHhhhh--------cC-CCCcchHHHHHHHHHHHHHHHHHHH
Q 032404 55 KIYIFKVLKQV--------HP-DIGISSKAMGIMNSFINDIFEKLAQ 92 (141)
Q Consensus 55 ~~YIyKVLKQV--------hp-d~gISskAm~ImnSfvnDiferIA~ 92 (141)
..-|.+||.|. +| .-.||.+.+++|+.+..+|++.++.
T Consensus 95 gsI~RkilqqLE~~G~V~k~~~GR~ltp~GrsllD~~a~ei~eel~~ 141 (147)
T COG2238 95 GSIIRKVLQQLEKAGLVEKTPKGRVLTPKGRSLLDRIATEIKEELEE 141 (147)
T ss_pred chHHHHHHHHHHHCCceeecCCCceeCccchhHHHHHHHHHHHHhcc
Confidence 44566777664 56 5789999999999999999998876
No 77
>PRK07914 hypothetical protein; Reviewed
Probab=45.51 E-value=70 Score=26.77 Aligned_cols=59 Identities=8% Similarity=0.173 Sum_probs=46.7
Q ss_pred HHHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHH
Q 032404 55 KIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVR 116 (141)
Q Consensus 55 ~~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVr 116 (141)
..+|-..+++- +..|+..|+..|...+.+=+..|..|--+|+.|.. .+||..+|+.-|-
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 45666666654 46799999999999997777889999999987755 5799999887754
No 78
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=43.40 E-value=2e+02 Score=24.17 Aligned_cols=63 Identities=6% Similarity=0.059 Sum_probs=41.2
Q ss_pred HHHHhhhhcCCCCcchHHHHHHHHHHHH----H--HHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCc
Q 032404 58 IFKVLKQVHPDIGISSKAMGIMNSFIND----I--FEKLAQESSRLARYNKKPTITSREIQTAVRLVLP 120 (141)
Q Consensus 58 IyKVLKQVhpd~gISskAm~ImnSfvnD----i--ferIA~EAs~La~~nkk~TltsreIqtAVrLlLP 120 (141)
+..-++..+.+..++..++..+-.++.. + .-.+...|..++......+|+..+|..|+..+.+
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 3333443333456788888777665521 1 1234567777777777889999999999987744
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=43.25 E-value=53 Score=30.52 Aligned_cols=62 Identities=16% Similarity=0.192 Sum_probs=41.6
Q ss_pred hhhhcCCCCcchHHHHHHHHHHHHHH-------HHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCchHH
Q 032404 62 LKQVHPDIGISSKAMGIMNSFINDIF-------EKLAQESSRLARYNKKPTITSREIQTAVRLVLPGEL 123 (141)
Q Consensus 62 LKQVhpd~gISskAm~ImnSfvnDif-------erIA~EAs~La~~nkk~TltsreIqtAVrLlLPGEL 123 (141)
.++..++..||...+.-+..++..+- ..+..-|--+|..+.|.+++..||+.|++|+|+.-+
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 112233334788899999999999999999997544
No 80
>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=41.71 E-value=88 Score=19.60 Aligned_cols=17 Identities=35% Similarity=0.356 Sum_probs=12.8
Q ss_pred HHHHHHHHhhhhcCCCC
Q 032404 54 YKIYIFKVLKQVHPDIG 70 (141)
Q Consensus 54 y~~YIyKVLKQVhpd~g 70 (141)
-..-..++.++.|||..
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 81
>PRK05629 hypothetical protein; Validated
Probab=40.75 E-value=1.2e+02 Score=25.23 Aligned_cols=62 Identities=10% Similarity=0.105 Sum_probs=46.9
Q ss_pred hhHHHHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHH
Q 032404 52 ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVR 116 (141)
Q Consensus 52 esy~~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVr 116 (141)
.....+|.+.+++- +..|+..|...|...+.+=+..+..|--+|+-|.. .+||..+|+.-|-
T Consensus 129 ~~l~~wi~~~~~~~--g~~i~~~A~~~L~~~~g~dl~~l~~EleKL~~~~~-~~It~e~V~~~v~ 190 (318)
T PRK05629 129 RERPGWVTQEFKNH--GVRPTPDVVHALLEGVGSDLRELASAISQLVEDTQ-GNVTVEKVRAYYV 190 (318)
T ss_pred HHHHHHHHHHHHHc--CCCCCHHHHHHHHHHHCccHHHHHHHHHHHHhcCC-CCcCHHHHHHHhC
Confidence 33456777777774 46799999987777665556679999999988764 5799999987643
No 82
>COG2511 GatE Archaeal Glu-tRNAGln amidotransferase subunit E (contains GAD domain) [Translation, ribosomal structure and biogenesis]
Probab=40.42 E-value=1.1e+02 Score=29.45 Aligned_cols=71 Identities=28% Similarity=0.377 Sum_probs=54.2
Q ss_pred CCCcchH-HHHHHHHHHHHHHHHHHH------H-HhHHhhh--------cCCCCcChHHHHHHHHhhCchHHHHhHHHhh
Q 032404 68 DIGISSK-AMGIMNSFINDIFEKLAQ------E-SSRLARY--------NKKPTITSREIQTAVRLVLPGELAKHAVSEG 131 (141)
Q Consensus 68 d~gISsk-Am~ImnSfvnDiferIA~------E-As~La~~--------nkk~TltsreIqtAVrLlLPGELaKhAvseG 131 (141)
+.|+|.+ |-.+..+..-|.||.+.+ . |+-|... ..-.-|+.+.|...++++.-|+++|.|+.|-
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 3577744 677888899999999988 2 3333321 2223379999999999999999999999999
Q ss_pred hhhhhcc
Q 032404 132 TKAVTKF 138 (141)
Q Consensus 132 tkAV~ky 138 (141)
.+++...
T Consensus 546 l~~l~~~ 552 (631)
T COG2511 546 LKALAEN 552 (631)
T ss_pred HHHHHhC
Confidence 9988754
No 83
>KOG4336 consensus TBP-associated transcription factor Prodos [Transcription]
Probab=37.77 E-value=1.5e+02 Score=26.40 Aligned_cols=59 Identities=12% Similarity=0.197 Sum_probs=47.9
Q ss_pred HHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhh
Q 032404 59 FKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLV 118 (141)
Q Consensus 59 yKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLl 118 (141)
--+|+++.=| .||.-|..-|-.++.--|.+|+.++..++...+|.--|..||......+
T Consensus 12 ~~Ll~~~gfd-~is~~aletlvell~~yi~eigrq~~n~celagRT~pT~~Dv~l~Li~m 70 (323)
T KOG4336|consen 12 SNLLKTKGFD-SISNAALETLVELLQSYIREIGRQLHNYCELAGRTIPTQGDVKLTLIEM 70 (323)
T ss_pred HHHHHHhCch-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcHHHHHHHHHHh
Confidence 3344444433 3899999999999999999999999999999999999999998776543
No 84
>PRK13406 bchD magnesium chelatase subunit D; Provisional
Probab=36.83 E-value=85 Score=29.45 Aligned_cols=57 Identities=16% Similarity=0.225 Sum_probs=42.1
Q ss_pred CCCCcchHHHHHHHHHHHHHH-------HHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCchHH
Q 032404 67 PDIGISSKAMGIMNSFINDIF-------EKLAQESSRLARYNKKPTITSREIQTAVRLVLPGEL 123 (141)
Q Consensus 67 pd~gISskAm~ImnSfvnDif-------erIA~EAs~La~~nkk~TltsreIqtAVrLlLPGEL 123 (141)
++..|+...+.-++.++..+- .+|..=|--+|-.+.+..|+..||+.|+.++|+.-+
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 466677776665555544432 355666667899999999999999999999998644
No 85
>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=36.26 E-value=34 Score=24.50 Aligned_cols=49 Identities=29% Similarity=0.526 Sum_probs=31.1
Q ss_pred chhHHHHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCc
Q 032404 51 IETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLP 120 (141)
Q Consensus 51 ~esy~~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLlLP 120 (141)
.|.=..|+|-||++-|..++| .-||+|+= .+..|-.+|- +-.|+|-++|
T Consensus 18 ~EaEkd~lY~~Lr~YHqSm~l--------p~li~Dlk-~VIN~P~R~p------------Lfd~IR~lip 66 (79)
T cd07353 18 NEAEKDYLYDVLRMYHQSMNL--------PVLVGDLK-LVINEPSRLP------------LFDAIRPLIP 66 (79)
T ss_pred cHHHHHHHHHHHHHHHhccCH--------HHHHHHHH-HHhCCccccc------------hHHHHHhhcc
Confidence 356678999999999975544 34788863 3334444433 3346666666
No 86
>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=35.07 E-value=63 Score=21.15 Aligned_cols=25 Identities=20% Similarity=0.308 Sum_probs=19.6
Q ss_pred CcChHHHHHHHHhhCchHHHHhHHH
Q 032404 105 TITSREIQTAVRLVLPGELAKHAVS 129 (141)
Q Consensus 105 TltsreIqtAVrLlLPGELaKhAvs 129 (141)
.+...+++....-++|++|+.|.-.
T Consensus 19 ~~~~~~l~~~w~~ivg~~l~~~~~~ 43 (89)
T PF05258_consen 19 ALQLARLQQNWKQIVGPELAQHTRP 43 (89)
T ss_pred hHHHHHHHHHHHHHhCHHHHccEEE
Confidence 4455678889999999999988643
No 87
>CHL00081 chlI Mg-protoporyphyrin IX chelatase
Probab=34.85 E-value=1.2e+02 Score=26.63 Aligned_cols=61 Identities=15% Similarity=0.269 Sum_probs=41.5
Q ss_pred hhhcCCCCcchHHHHHHHHHHHHHHH-------HHHHHHhHHhhhcCCCCcChHHHHHHHHhhCchHH
Q 032404 63 KQVHPDIGISSKAMGIMNSFINDIFE-------KLAQESSRLARYNKKPTITSREIQTAVRLVLPGEL 123 (141)
Q Consensus 63 KQVhpd~gISskAm~ImnSfvnDife-------rIA~EAs~La~~nkk~TltsreIqtAVrLlLPGEL 123 (141)
++.-++..||...+.-+..++...=. -+..-|--+|-.+.|..++..||+.+++++|+.-+
T Consensus 260 r~~~~~V~v~~~~~~yi~~l~~~~~~~s~Ra~i~l~raArA~Aal~GR~~V~pdDv~~~a~~vL~HR~ 327 (350)
T CHL00081 260 QNLLPKVEIDYDLRVKISQICSELDVDGLRGDIVTNRAAKALAAFEGRTEVTPKDIFKVITLCLRHRL 327 (350)
T ss_pred HHhcCCCccCHHHHHHHHHHHHHHCCCCChHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHhC
Confidence 34456677777766655555544311 12233344888999999999999999999998655
No 88
>PRK03992 proteasome-activating nucleotidase; Provisional
Probab=33.81 E-value=67 Score=27.97 Aligned_cols=43 Identities=14% Similarity=0.206 Sum_probs=36.0
Q ss_pred HHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCchH
Q 032404 80 NSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLPGE 122 (141)
Q Consensus 80 nSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLlLPGE 122 (141)
+.|...-++.|+.||..++-...+..|+..||+.|+..+.|+.
T Consensus 334 ~g~sgadl~~l~~eA~~~a~~~~~~~i~~~d~~~A~~~~~~~~ 376 (389)
T PRK03992 334 EGASGADLKAICTEAGMFAIRDDRTEVTMEDFLKAIEKVMGKE 376 (389)
T ss_pred CCCCHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHhccc
Confidence 4455566678999999998888888999999999999998853
No 89
>PF13148 DUF3987: Protein of unknown function (DUF3987)
Probab=33.35 E-value=2.4e+02 Score=23.55 Aligned_cols=75 Identities=25% Similarity=0.366 Sum_probs=49.8
Q ss_pred chhHHHHHHHHhhhhc-------CCCCcchHHHHHHHHHHHHHHHHH----------------HHHHhHHhh--------
Q 032404 51 IETYKIYIFKVLKQVH-------PDIGISSKAMGIMNSFINDIFEKL----------------AQESSRLAR-------- 99 (141)
Q Consensus 51 ~esy~~YIyKVLKQVh-------pd~gISskAm~ImnSfvnDiferI----------------A~EAs~La~-------- 99 (141)
.+.|...|..++.... ..+.+|.+|..+++.|.+.+..++ ..-+.+||-
T Consensus 261 ~~~~~~~i~~l~~~~~~~~~~~~~~l~ls~eA~~~~~~~~~~~~~~~~~~~~~~~~~~~~~K~~~~~~RlA~ilh~~~~~ 340 (378)
T PF13148_consen 261 LEAYHERIKELLDWPPEDGSDEPIVLELSDEAKELFREWYNELENELRQPGGDLAMRSFASKAAEQALRLALILHLFESG 340 (378)
T ss_pred HHHHHHHHHHHHhhhhcccCCCCeEEecCHHHHHHHHHHHHHHHHHhhccCCChHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 3567777888887765 226789999888877766555554 344445442
Q ss_pred -hcCCCCcChHHHHHHHHhhCchHHHHhH
Q 032404 100 -YNKKPTITSREIQTAVRLVLPGELAKHA 127 (141)
Q Consensus 100 -~nkk~TltsreIqtAVrLlLPGELaKhA 127 (141)
.....+|+...++.|++|+ .-+..|+
T Consensus 341 ~~~~~~~I~~~~~~~Ai~l~--~~~~~~~ 367 (378)
T PF13148_consen 341 GSPPSTEISAETMERAIRLV--EYFLEHA 367 (378)
T ss_pred CCCCCCEECHHHHHHHHHHH--HHHHHHH
Confidence 1366789999999999865 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=32.40 E-value=60 Score=28.09 Aligned_cols=23 Identities=26% Similarity=0.551 Sum_probs=18.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhH
Q 032404 74 KAMGIMNSFINDIFEKLAQESSR 96 (141)
Q Consensus 74 kAm~ImnSfvnDiferIA~EAs~ 96 (141)
.+..-|+..+||||.||.....+
T Consensus 25 ~aL~~L~~v~~diF~rI~~Rv~~ 47 (297)
T PF11945_consen 25 DALEYLDKVSNDIFSRISARVER 47 (297)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 56777999999999998765543
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=31.23 E-value=1.3e+02 Score=18.54 Aligned_cols=65 Identities=12% Similarity=0.048 Sum_probs=44.5
Q ss_pred hHHHHHHHHhhhhcCCCCcchHHHHHHHHHHH------HHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHh
Q 032404 53 TYKIYIFKVLKQVHPDIGISSKAMGIMNSFIN------DIFEKLAQESSRLARYNKKPTITSREIQTAVRL 117 (141)
Q Consensus 53 sy~~YIyKVLKQVhpd~gISskAm~ImnSfvn------DiferIA~EAs~La~~nkk~TltsreIqtAVrL 117 (141)
..-.||.++.....-+..+-.-|+.+++.|+. .-+..||.-+.-||..-.....+.+|+......
T Consensus 4 ~~~~~l~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~ 74 (88)
T cd00043 4 TPLDFLRRVAKALGLSPETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEEIPPWLKDLVHVTGY 74 (88)
T ss_pred hHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHcCCCCCHHHHhHHhCC
Confidence 34567788887776666666777888887766 345677787877777654457777777655543
No 92
>KOG2643 consensus Ca2+ binding protein, contains EF-hand motifs [Inorganic ion transport and metabolism]
Probab=30.72 E-value=2.2e+02 Score=26.72 Aligned_cols=74 Identities=22% Similarity=0.330 Sum_probs=51.5
Q ss_pred chhHHHHHHHHhhhhcC-CCCcchHHHHHHHHHHHHHHH-HHHHHHhHHhhhcCCCCcChHHHHHHHHhhCchHHHHhHH
Q 032404 51 IETYKIYIFKVLKQVHP-DIGISSKAMGIMNSFINDIFE-KLAQESSRLARYNKKPTITSREIQTAVRLVLPGELAKHAV 128 (141)
Q Consensus 51 ~esy~~YIyKVLKQVhp-d~gISskAm~ImnSfvnDife-rIA~EAs~La~~nkk~TltsreIqtAVrLlLPGELaKhAv 128 (141)
.+.+..|..||.+.--- +-|||-+=-.-...|+|+|=+ -||--...+ -...|+..++|-|++.+.--||..|-+
T Consensus 352 ~~~k~~~lkrvk~kf~~~~~gISl~Ef~~Ff~Fl~~l~dfd~Al~fy~~----Ag~~i~~~~f~raa~~vtGveLSdhVv 427 (489)
T KOG2643|consen 352 SKKKHKYLKRVKEKFKDDGKGISLQEFKAFFRFLNNLNDFDIALRFYHM----AGASIDEKTFQRAAKVVTGVELSDHVV 427 (489)
T ss_pred hHhHHHHHHHHHHhccCCCCCcCHHHHHHHHHHHhhhhHHHHHHHHHHH----cCCCCCHHHHHHHHHHhcCccccccee
Confidence 45566677777766533 589998777767777776643 222222222 337899999999999999999998843
No 93
>PF13335 Mg_chelatase_2: Magnesium chelatase, subunit ChlI
Probab=30.42 E-value=1.3e+02 Score=21.36 Aligned_cols=47 Identities=17% Similarity=0.258 Sum_probs=34.8
Q ss_pred CcchHHHHHHHHHHHH------HHHHHHHHHhHHhhhcCCCCcChHHHHHHHH
Q 032404 70 GISSKAMGIMNSFIND------IFEKLAQESSRLARYNKKPTITSREIQTAVR 116 (141)
Q Consensus 70 gISskAm~ImnSfvnD------iferIA~EAs~La~~nkk~TltsreIqtAVr 116 (141)
.++..+..+|+..++. =+.||..=|-.+|.......|+..+|..|+.
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 4455555555444433 2568888899999999999999999999975
No 94
>PRK13407 bchI magnesium chelatase subunit I; Provisional
Probab=30.27 E-value=2.2e+02 Score=24.73 Aligned_cols=58 Identities=10% Similarity=0.226 Sum_probs=41.1
Q ss_pred hhcCCCCcchHHHHHHHHHHH---------HHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCchHH
Q 032404 64 QVHPDIGISSKAMGIMNSFIN---------DIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLPGEL 123 (141)
Q Consensus 64 QVhpd~gISskAm~ImnSfvn---------DiferIA~EAs~La~~nkk~TltsreIqtAVrLlLPGEL 123 (141)
+.-++..|+...+.-+..++. +|+ +..-|.-+|-.+.|..++..||+.++.++|..-+
T Consensus 245 ~~~~~V~v~~~~~~yi~~l~~~~~~~s~Ra~i~--l~~aA~a~A~l~Gr~~V~~~Di~~~~~~vl~hR~ 311 (334)
T PRK13407 245 ARLPQLKTPNTVLHDCAALCIALGSDGLRGELT--LLRAARALAAFEGAEAVGRSHLRSVATMALSHRL 311 (334)
T ss_pred HhcCCcccCHHHHHHHHHHHHHHCCCCchHHHH--HHHHHHHHHHHcCCCeeCHHHHHHHHHHhhhhhc
Confidence 334555666655554444443 233 6667777899999999999999999999998655
No 95
>KOG0240 consensus Kinesin (SMY1 subfamily) [Cytoskeleton]
Probab=29.72 E-value=54 Score=31.36 Aligned_cols=42 Identities=26% Similarity=0.502 Sum_probs=31.0
Q ss_pred hhHHHHHHHHhhhhcCC-------------------CCc--chHHHHHHHHHHHHHHHHHHHH
Q 032404 52 ETYKIYIFKVLKQVHPD-------------------IGI--SSKAMGIMNSFINDIFEKLAQE 93 (141)
Q Consensus 52 esy~~YIyKVLKQVhpd-------------------~gI--SskAm~ImnSfvnDiferIA~E 93 (141)
+-|.-.++-|+++|--+ .|+ ...-|+||..+++|||++|-.-
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 45777889999998332 122 2346899999999999999653
No 96
>KOG3467 consensus Histone H4 [Chromatin structure and dynamics]
Probab=29.52 E-value=1.4e+02 Score=22.28 Aligned_cols=37 Identities=14% Similarity=0.313 Sum_probs=27.1
Q ss_pred HHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHH
Q 032404 80 NSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVR 116 (141)
Q Consensus 80 nSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVr 116 (141)
|.....++|.+-..|.--+.+.+|+|+|.-||.-+.+
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 3444444555666778888899999999999877654
No 97
>PLN03213 repressor of silencing 3; Provisional
Probab=29.50 E-value=50 Score=31.61 Aligned_cols=22 Identities=36% Similarity=0.665 Sum_probs=19.1
Q ss_pred CCcchHHHHHHHHHHHHHHHHH
Q 032404 69 IGISSKAMGIMNSFINDIFEKL 90 (141)
Q Consensus 69 ~gISskAm~ImnSfvnDiferI 90 (141)
.|+-.+-++||||.||-|||+=
T Consensus 184 ~g~~~eE~niMNSVMNKLFEke 205 (759)
T PLN03213 184 VGRNEAEVNVMNSVMNKLFEKN 205 (759)
T ss_pred ccccHHHHHHHHHHHHHHHhhh
Confidence 5677788999999999999974
No 98
>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=29.40 E-value=1.1e+02 Score=24.57 Aligned_cols=70 Identities=19% Similarity=0.210 Sum_probs=38.4
Q ss_pred chhHHHHHHHHhhhhcCCCCcchH----HHHHHHHHHHHHHHHHHHHHhH--------------HhhhcCCC----CcCh
Q 032404 51 IETYKIYIFKVLKQVHPDIGISSK----AMGIMNSFINDIFEKLAQESSR--------------LARYNKKP----TITS 108 (141)
Q Consensus 51 ~esy~~YIyKVLKQVhpd~gISsk----Am~ImnSfvnDiferIA~EAs~--------------La~~nkk~----Tlts 108 (141)
...|...|..++.++--|-..|.+ .+.-.+.|-..+-.+|++-+.. ++.||+.+ .|+.
T Consensus 56 ~~~~r~~f~~~~~~lGvdp~~s~~~~s~~l~~~~~f~~ELa~qi~e~c~~~~~~~GGii~L~dl~~~~nr~R~g~~lISp 135 (223)
T PF04157_consen 56 DPEFRSQFQSMCASLGVDPLASSKFWSESLKGSGDFYYELAVQIAEVCLATRSKNGGIISLSDLYCRYNRARGGSELISP 135 (223)
T ss_dssp SHHHHHHHHHHHHHHT--CHCCTTCCCCCCSCHHHHHHHHHHHHHHHHHHHCCTTTSEEEHHHHHHHHHHCTTTSST--H
T ss_pred CchHHHHHHHHHHHcCCCcccchhhhhhccccchhHHHHHHHHHHHHHHHHHhcCCCEEEHHHHHHHHHHhcccCCCcCH
Confidence 456777788888877666554544 1112234444444444443332 23455555 8899
Q ss_pred HHHHHHHHhhCc
Q 032404 109 REIQTAVRLVLP 120 (141)
Q Consensus 109 reIqtAVrLlLP 120 (141)
.||..|+.++=+
T Consensus 136 ~Di~~A~~~l~~ 147 (223)
T PF04157_consen 136 EDILRACKLLEV 147 (223)
T ss_dssp HHHHHHHHHHCC
T ss_pred HHHHHHHHHHHH
Confidence 999999998744
No 99
>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=28.85 E-value=1.7e+02 Score=19.14 Aligned_cols=44 Identities=20% Similarity=0.256 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCchHHHHhHH
Q 032404 81 SFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLPGELAKHAV 128 (141)
Q Consensus 81 SfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLlLPGELaKhAv 128 (141)
.+++|.|-.++.......-... .+|.++|....+ ||-..-|+|.
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 566788888888 7766666664
No 100
>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=28.50 E-value=3.4e+02 Score=22.43 Aligned_cols=64 Identities=9% Similarity=0.066 Sum_probs=39.6
Q ss_pred HHHHHHhhhhcCCCCcchHHHHHHHHHHH----HH--HHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhC
Q 032404 56 IYIFKVLKQVHPDIGISSKAMGIMNSFIN----DI--FEKLAQESSRLARYNKKPTITSREIQTAVRLVL 119 (141)
Q Consensus 56 ~YIyKVLKQVhpd~gISskAm~ImnSfvn----Di--ferIA~EAs~La~~nkk~TltsreIqtAVrLlL 119 (141)
.++...++....+..++.+++..+..++. |+ .-.+...|..++..+++.+||..+|+.|+..+.
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 34444444333444577777765544442 21 123555667777777788999999999988763
No 101
>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=28.23 E-value=1.5e+02 Score=26.51 Aligned_cols=51 Identities=29% Similarity=0.350 Sum_probs=36.4
Q ss_pred HHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCch-----------HHHHhHHHhhhhhhhc
Q 032404 87 FEKLAQESSRLARYNKKPTITSREIQTAVRLVLPG-----------ELAKHAVSEGTKAVTK 137 (141)
Q Consensus 87 ferIA~EAs~La~~nkk~TltsreIqtAVrLlLPG-----------ELaKhAvseGtkAV~k 137 (141)
++.|..||..++....+..|+..+++.|+..+++| +.-..|+-|.-.||..
T Consensus 264 l~~l~~eA~~~a~~~~~~~i~~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~A~hEaGhAlv~ 325 (495)
T TIGR01241 264 LANLLNEAALLAARKNKTEITMNDIEEAIDRVIAGPEKKSRVISEKEKKLVAYHEAGHALVG 325 (495)
T ss_pred HHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhcccccccccccHHHHHHHHHHHHhHHHHH
Confidence 45677788777777777899999999999977543 3344566666666543
No 102
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=28.14 E-value=1.4e+02 Score=23.44 Aligned_cols=16 Identities=31% Similarity=0.281 Sum_probs=13.8
Q ss_pred CCcChHHHHHHHHhhC
Q 032404 104 PTITSREIQTAVRLVL 119 (141)
Q Consensus 104 ~TltsreIqtAVrLlL 119 (141)
..++..|||..|...|
T Consensus 101 ~~IsveEIqDiVE~~L 116 (154)
T PRK00464 101 REVPSKEIGELVMEEL 116 (154)
T ss_pred CCCCHHHHHHHHHHHH
Confidence 5799999999998655
No 103
>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=28.09 E-value=2e+02 Score=23.62 Aligned_cols=63 Identities=16% Similarity=0.229 Sum_probs=45.7
Q ss_pred hHHHHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhh
Q 032404 53 TYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLV 118 (141)
Q Consensus 53 sy~~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLl 118 (141)
....||...+++- +..|+..++..+-...+.-+.++..+.-+|+.|.. ..||..+|+..+...
T Consensus 180 ~l~~~l~~~~~~~--g~~i~~~a~~~l~~~~~g~~~~a~~~lekl~~~~~-~~it~~~v~~~~~~~ 242 (355)
T TIGR02397 180 DIVERLKKILDKE--GIKIEDEALELIARAADGSLRDALSLLDQLISFGN-GNITYEDVNELLGLV 242 (355)
T ss_pred HHHHHHHHHHHHc--CCCCCHHHHHHHHHHcCCChHHHHHHHHHHHhhcC-CCCCHHHHHHHhCCC
Confidence 3445666666653 46789899888777777667788888888888876 459999998776543
No 104
>PF05798 Phage_FRD3: Bacteriophage FRD3 protein; InterPro: IPR008765 This is a group of proteins of unknown function from bacteriophage T2 and related phage.
Probab=27.91 E-value=28 Score=24.71 Aligned_cols=18 Identities=28% Similarity=0.527 Sum_probs=15.8
Q ss_pred HHHHHHhhhhcCCCCcch
Q 032404 56 IYIFKVLKQVHPDIGISS 73 (141)
Q Consensus 56 ~YIyKVLKQVhpd~gISs 73 (141)
.||+.|+++.||.++|.+
T Consensus 12 EY~eEvIRNRyPelsi~s 29 (75)
T PF05798_consen 12 EYTEEVIRNRYPELSITS 29 (75)
T ss_pred HhHHHHHHccCCceEEEE
Confidence 599999999999998853
No 105
>PRK05637 anthranilate synthase component II; Provisional
Probab=27.20 E-value=49 Score=26.56 Aligned_cols=24 Identities=21% Similarity=0.411 Sum_probs=21.4
Q ss_pred hhcCCCCcchHHHHHHHHHHHHHH
Q 032404 64 QVHPDIGISSKAMGIMNSFINDIF 87 (141)
Q Consensus 64 QVhpd~gISskAm~ImnSfvnDif 87 (141)
|-||+.-.|.....|+++|+..++
T Consensus 183 QfHPE~~~T~~G~~il~nfl~~~~ 206 (208)
T PRK05637 183 QFHPESVLSPTGPIILSRCVEQLL 206 (208)
T ss_pred EeCCccCcCCCHHHHHHHHHHHHh
Confidence 679999999999999999997654
No 106
>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=26.74 E-value=49 Score=28.22 Aligned_cols=66 Identities=21% Similarity=0.398 Sum_probs=43.8
Q ss_pred chhHHHHHHHHhhhhcCCCCcchHHHHHHHHHHHHH-----------------HHHHHHHHhHHhhhcCCCCcChHHHHH
Q 032404 51 IETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDI-----------------FEKLAQESSRLARYNKKPTITSREIQT 113 (141)
Q Consensus 51 ~esy~~YIyKVLKQVhpd~gISskAm~ImnSfvnDi-----------------ferIA~EAs~La~~nkk~TltsreIqt 113 (141)
.+.+..||.-+=.+++| .+|.+|..++-.|-.++ +|-|-.=|--+|+..=+.+++..|++.
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 68888877765553222 233444455567777788999999999
Q ss_pred HHHhh
Q 032404 114 AVRLV 118 (141)
Q Consensus 114 AVrLl 118 (141)
|++|+
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 107
>PF13654 AAA_32: AAA domain; PDB: 3K1J_B.
Probab=26.68 E-value=94 Score=28.66 Aligned_cols=64 Identities=16% Similarity=0.214 Sum_probs=42.5
Q ss_pred hhHHHHHHHHhhhhcCCCCcchHHHHHHHHHH-----------HHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHH
Q 032404 52 ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFI-----------NDIFEKLAQESSRLARYNKKPTITSREIQTAVR 116 (141)
Q Consensus 52 esy~~YIyKVLKQVhpd~gISskAm~ImnSfv-----------nDiferIA~EAs~La~~nkk~TltsreIqtAVr 116 (141)
..|..||-.+..+-+ -..++..|+.-|-.+. -.-+..|..||..+|+.+.+..|+..+|+.|+.
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 2366777766543221 123456779999999999999999999999986
No 108
>PHA03102 Small T antigen; Reviewed
Probab=26.38 E-value=1.3e+02 Score=23.64 Aligned_cols=37 Identities=22% Similarity=0.398 Sum_probs=26.4
Q ss_pred HHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHh
Q 032404 58 IFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLA 98 (141)
Q Consensus 58 IyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La 98 (141)
..+..++.|||-+-+.+.|. -||..|+.|..+..++.
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 34566888999987766554 56677788877766655
No 109
>CHL00176 ftsH cell division protein; Validated
Probab=25.24 E-value=1.5e+02 Score=28.05 Aligned_cols=50 Identities=34% Similarity=0.379 Sum_probs=36.2
Q ss_pred HHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCch----------HHHHhHHHhhhhhhh
Q 032404 87 FEKLAQESSRLARYNKKPTITSREIQTAVRLVLPG----------ELAKHAVSEGTKAVT 136 (141)
Q Consensus 87 ferIA~EAs~La~~nkk~TltsreIqtAVrLlLPG----------ELaKhAvseGtkAV~ 136 (141)
++.+..||..++....+..||..||+.|++-++-| +.-..|+-|.-.||.
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 45777788887777778899999999999876433 444556666655654
No 110
>KOG1657 consensus CCAAT-binding factor, subunit C (HAP5) [Transcription]
Probab=24.98 E-value=1.4e+02 Score=25.09 Aligned_cols=58 Identities=24% Similarity=0.267 Sum_probs=41.3
Q ss_pred HHHHhhhhcCCC-CcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHH
Q 032404 58 IFKVLKQVHPDI-GISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVR 116 (141)
Q Consensus 58 IyKVLKQVhpd~-gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVr 116 (141)
|.++.|+ ++|+ .|+.+|.-++.-...-+.+.++..+..-+.-++|+||.--+|..||.
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 3344443 4453 68888877665555555566666678888889999999999999985
No 111
>PRK13765 ATP-dependent protease Lon; Provisional
Probab=24.85 E-value=3.1e+02 Score=26.13 Aligned_cols=65 Identities=14% Similarity=0.072 Sum_probs=33.1
Q ss_pred hhHHHHHHHHhhhhc---CCCCcchHHHHHHHHHHHH-------------HHHHHHHHHhHHhhhcCCCCcChHHHHHHH
Q 032404 52 ETYKIYIFKVLKQVH---PDIGISSKAMGIMNSFIND-------------IFEKLAQESSRLARYNKKPTITSREIQTAV 115 (141)
Q Consensus 52 esy~~YIyKVLKQVh---pd~gISskAm~ImnSfvnD-------------iferIA~EAs~La~~nkk~TltsreIqtAV 115 (141)
+.+..|+..+-+++. +-..++..|+.-|-....- -+..|..||..+++...+..++.++|..|+
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 455555544444442 3347788776543322211 112245556666666666666666666555
Q ss_pred H
Q 032404 116 R 116 (141)
Q Consensus 116 r 116 (141)
+
T Consensus 398 ~ 398 (637)
T PRK13765 398 K 398 (637)
T ss_pred H
Confidence 3
No 112
>PRK10733 hflB ATP-dependent metalloprotease; Reviewed
Probab=24.60 E-value=1.8e+02 Score=27.29 Aligned_cols=40 Identities=20% Similarity=0.287 Sum_probs=32.4
Q ss_pred HHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCch
Q 032404 82 FINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLPG 121 (141)
Q Consensus 82 fvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLlLPG 121 (141)
|.--=+..|..||..++....+..|+-.|+..|...+++|
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 3333556788899999988889999999999999877665
No 113
>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional
Probab=24.59 E-value=1.1e+02 Score=27.79 Aligned_cols=42 Identities=17% Similarity=0.206 Sum_probs=35.0
Q ss_pred HHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCc
Q 032404 79 MNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLP 120 (141)
Q Consensus 79 mnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLlLP 120 (141)
.+.|.-.-+..|+.||..+|....+..|+..|+..|+.-++.
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 344555557789999999999988999999999999998765
No 114
>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=23.24 E-value=71 Score=24.46 Aligned_cols=22 Identities=23% Similarity=0.558 Sum_probs=18.6
Q ss_pred hhcCCCCcchHHHHHHHHHHHH
Q 032404 64 QVHPDIGISSKAMGIMNSFIND 85 (141)
Q Consensus 64 QVhpd~gISskAm~ImnSfvnD 85 (141)
|-||+..-+..++.|+.+|+++
T Consensus 162 QfHPE~~~~~~g~~i~~~f~~~ 183 (188)
T TIGR00888 162 QFHPEVTHTEYGNELLENFVYD 183 (188)
T ss_pred eeCCccCCChhhHHHHHHHHHH
Confidence 6799988877889999999875
No 115
>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=23.23 E-value=1.5e+02 Score=23.20 Aligned_cols=37 Identities=16% Similarity=0.266 Sum_probs=27.0
Q ss_pred hHHHHHHHHhhhh--------cCC--CCcchHHHHHHHHHHHHHHHH
Q 032404 53 TYKIYIFKVLKQV--------HPD--IGISSKAMGIMNSFINDIFEK 89 (141)
Q Consensus 53 sy~~YIyKVLKQV--------hpd--~gISskAm~ImnSfvnDifer 89 (141)
....-|.++|.|. +|+ -.||+++++.||.+..+|++.
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 3455677788765 544 358999999999999888864
No 116
>TIGR01242 26Sp45 26S proteasome subunit P45 family. Many proteins may score above the trusted cutoff because an internal
Probab=22.38 E-value=1.1e+02 Score=26.04 Aligned_cols=40 Identities=18% Similarity=0.191 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhC
Q 032404 80 NSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVL 119 (141)
Q Consensus 80 nSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLlL 119 (141)
+.|...-+..|..||...+-...+..|+..||+.|++-++
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 3454444457888999888888888999999999998654
No 117
>PLN02347 GMP synthetase
Probab=22.16 E-value=72 Score=29.60 Aligned_cols=24 Identities=33% Similarity=0.605 Sum_probs=20.7
Q ss_pred hhcCCCCcchHHHHHHHHHHHHHH
Q 032404 64 QVHPDIGISSKAMGIMNSFINDIF 87 (141)
Q Consensus 64 QVhpd~gISskAm~ImnSfvnDif 87 (141)
|-||+..-|...+.||.+|+.+|.
T Consensus 180 QFHPE~~~t~~G~~iL~NFl~~ic 203 (536)
T PLN02347 180 QYHPEVTHSPKGMETLRHFLFDVC 203 (536)
T ss_pred EccCCCCccchHHHHHHHHHHHHh
Confidence 779999999999999999987654
No 118
>PF14606 Lipase_GDSL_3: GDSL-like Lipase/Acylhydrolase family; PDB: 3SKV_B.
Probab=21.71 E-value=58 Score=26.18 Aligned_cols=77 Identities=18% Similarity=0.295 Sum_probs=30.2
Q ss_pred HHHHHHhhhhcCCCCc---c-------------hHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhC
Q 032404 56 IYIFKVLKQVHPDIGI---S-------------SKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVL 119 (141)
Q Consensus 56 ~YIyKVLKQVhpd~gI---S-------------skAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLlL 119 (141)
.++.+.|+..||++.| | ...+.-+|..+++.|+.+-.+--.=..|-....|-..+-...|..+=
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 3678889999999765 2 33456678888888888765544444443333433334456777777
Q ss_pred chHHHHhHHHhhh
Q 032404 120 PGELAKHAVSEGT 132 (141)
Q Consensus 120 PGELaKhAvseGt 132 (141)
|++|+-.-+.++.
T Consensus 161 P~DlG~~~~a~~l 173 (178)
T PF14606_consen 161 PNDLGMMRMADAL 173 (178)
T ss_dssp -------------
T ss_pred ccccccccccccc
Confidence 8877765555543
No 119
>PRK14970 DNA polymerase III subunits gamma and tau; Provisional
Probab=21.31 E-value=3.2e+02 Score=23.03 Aligned_cols=62 Identities=13% Similarity=0.181 Sum_probs=47.3
Q ss_pred HHHHHHHHhhhhcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhh
Q 032404 54 YKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLV 118 (141)
Q Consensus 54 y~~YIyKVLKQVhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLl 118 (141)
...+|.+++++- +..|+.+++..+-...+.=+.++..+--+|+.|.... ||..+|+..+...
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 4568999999988888877888888999999886654 9998888777643
No 120
>PHA02564 V virion protein; Provisional
Probab=21.25 E-value=3.9e+02 Score=20.82 Aligned_cols=54 Identities=22% Similarity=0.367 Sum_probs=33.4
Q ss_pred HHHHHHHhhh--hcCCCCcchHHHHHHHHHHHHHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhC
Q 032404 55 KIYIFKVLKQ--VHPDIGISSKAMGIMNSFINDIFEKLAQESSRLARYNKKPTITSREIQTAVRLVL 119 (141)
Q Consensus 55 ~~YIyKVLKQ--Vhpd~gISskAm~ImnSfvnDiferIA~EAs~La~~nkk~TltsreIqtAVrLlL 119 (141)
..||-.|-+. |-||..|...=- +|..+|.-|. .+-|.....+..+|..|++++|
T Consensus 85 ~aYi~~Vs~~~GV~~~~~idl~d~-~l~~l~~Aii----------~~EnG~~pys~~~i~~~~~~~~ 140 (141)
T PHA02564 85 RAYATAVANAMGVPPQAGLHLDQD-TLAALVTAII----------RHENGQQPYSAEQIAQGVREVL 140 (141)
T ss_pred HHHHHHHHHHHCCCCCCcCcCCcH-HHHHHHHHHH----------HHhcCCCCCCHHHHHHHHHHhh
Confidence 3466655554 456655542111 5555554332 2345678999999999999876
No 121
>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=20.43 E-value=3.4e+02 Score=22.48 Aligned_cols=24 Identities=25% Similarity=0.382 Sum_probs=18.4
Q ss_pred cchHHHHHHHH-HHHHHHHHHHHHH
Q 032404 71 ISSKAMGIMNS-FINDIFEKLAQES 94 (141)
Q Consensus 71 ISskAm~ImnS-fvnDiferIA~EA 94 (141)
...+|+.+||+ |+++..+..+...
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 8887777666654
No 122
>TIGR00368 Mg chelatase-related protein. The N-terminal end matches very strongly a pfam Mg_chelatase domain.
Probab=20.42 E-value=2.7e+02 Score=25.54 Aligned_cols=49 Identities=10% Similarity=0.236 Sum_probs=42.1
Q ss_pred CCcchHHHHHHHHHHHHH------HHHHHHHHhHHhhhcCCCCcChHHHHHHHHh
Q 032404 69 IGISSKAMGIMNSFINDI------FEKLAQESSRLARYNKKPTITSREIQTAVRL 117 (141)
Q Consensus 69 ~gISskAm~ImnSfvnDi------ferIA~EAs~La~~nkk~TltsreIqtAVrL 117 (141)
..++..+..+|+..++.+ ++||..=|-.+|.......|+..+|+.|+.+
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 356888888888877664 7899999999999999999999999999864
No 123
>COG2960 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.40 E-value=1.2e+02 Score=22.88 Aligned_cols=42 Identities=26% Similarity=0.281 Sum_probs=25.7
Q ss_pred HHHHHHHHHHhHHhhhcCCCCcChHHHHHHHHhhCchHHHHhHH
Q 032404 85 DIFEKLAQESSRLARYNKKPTITSREIQTAVRLVLPGELAKHAV 128 (141)
Q Consensus 85 DiferIA~EAs~La~~nkk~TltsreIqtAVrLlLPGELaKhAv 128 (141)
+.|+.|+...+.++. +-.---.+||++++|.++-+.|.+.=+
T Consensus 14 ~~~e~~~~ql~e~~a--~~~~~~~~evE~~~r~~~q~~lnkLDl 55 (103)
T COG2960 14 NRFEDIAAQLSEDAA--GAAQEVRAEVEKAFRAQLQRQLNKLDL 55 (103)
T ss_pred HHHHHHHHHHHHHcc--ccchhhHHHHHHHHHHHHHHHHhhhhh
Confidence 334444444444333 112345689999999999999887643
No 124
>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=20.09 E-value=2.2e+02 Score=17.31 Aligned_cols=59 Identities=15% Similarity=0.169 Sum_probs=31.7
Q ss_pred HHHHHhhhhcCCCCcchHHHHHHHHHHH------HHHHHHHHHHhHHhhhcCCCCcChHHHHHHH
Q 032404 57 YIFKVLKQVHPDIGISSKAMGIMNSFIN------DIFEKLAQESSRLARYNKKPTITSREIQTAV 115 (141)
Q Consensus 57 YIyKVLKQVhpd~gISskAm~ImnSfvn------DiferIA~EAs~La~~nkk~TltsreIqtAV 115 (141)
||.++....+-+..+-.-|+.+++.++. .-+..||.-+.-||........+..++....
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
Done!