Query 033083
Match_columns 128
No_of_seqs 139 out of 370
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 09:37:02 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033083.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033083hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00463 histone H2B; Provisio 100.0 2.9E-46 6.3E-51 277.5 9.1 80 48-127 19-98 (117)
2 PLN00158 histone H2B; Provisio 100.0 6.8E-46 1.5E-50 275.2 8.1 79 49-127 19-97 (116)
3 smart00427 H2B Histone H2B. 100.0 1.9E-43 4.1E-48 252.0 7.6 71 57-127 1-71 (89)
4 KOG1744 Histone H2B [Chromatin 100.0 1.2E-38 2.5E-43 239.7 7.8 79 49-127 29-107 (127)
5 PF00125 Histone: Core histone 99.6 1.8E-16 4E-21 105.3 4.6 69 54-122 2-74 (75)
6 cd07981 TAF12 TATA Binding Pro 98.3 2.9E-06 6.3E-11 57.5 7.6 60 63-122 7-66 (72)
7 PF00808 CBFD_NFYB_HMF: Histon 98.3 2.1E-06 4.6E-11 56.1 6.4 58 62-120 7-65 (65)
8 COG2036 HHT1 Histones H3 and H 98.1 1.3E-05 2.8E-10 57.7 6.0 62 63-125 25-86 (91)
9 PF03847 TFIID_20kDa: Transcri 97.7 0.00017 3.8E-09 49.0 6.1 59 63-121 5-63 (68)
10 smart00803 TAF TATA box bindin 97.5 0.00039 8.5E-09 46.7 6.3 59 62-121 7-65 (65)
11 cd00074 H2A Histone 2A; H2A is 97.5 0.00032 6.8E-09 52.2 6.3 61 61-121 24-84 (115)
12 PLN00035 histone H4; Provision 97.4 0.00074 1.6E-08 49.7 7.2 60 62-122 34-93 (103)
13 cd00076 H4 Histone H4, one of 97.4 0.001 2.2E-08 47.2 7.1 60 62-122 18-77 (85)
14 PTZ00015 histone H4; Provision 97.3 0.00087 1.9E-08 49.2 6.0 62 60-122 33-94 (102)
15 smart00428 H3 Histone H3. 97.2 0.0026 5.6E-08 46.8 7.6 69 55-123 31-101 (105)
16 cd07979 TAF9 TATA Binding Prot 97.0 0.0051 1.1E-07 45.4 8.2 65 60-125 4-68 (117)
17 KOG0869 CCAAT-binding factor, 96.7 0.0057 1.2E-07 48.5 6.6 59 63-121 38-97 (168)
18 smart00417 H4 Histone H4. 96.6 0.0045 9.7E-08 43.0 4.9 55 62-117 18-72 (74)
19 KOG0871 Class 2 transcription 96.2 0.019 4.2E-07 45.1 6.7 62 62-123 17-79 (156)
20 KOG1142 Transcription initiati 96.2 0.0093 2E-07 50.1 5.3 66 62-127 159-228 (258)
21 smart00414 H2A Histone 2A. 95.8 0.028 6E-07 41.2 5.6 61 61-121 13-73 (106)
22 PLN00157 histone H2A; Provisio 95.8 0.02 4.3E-07 43.9 5.0 65 57-121 25-90 (132)
23 PTZ00017 histone H2A; Provisio 95.7 0.026 5.6E-07 43.3 5.1 61 61-121 31-91 (134)
24 PLN00156 histone H2AX; Provisi 95.6 0.033 7.1E-07 43.1 5.5 64 58-121 29-93 (139)
25 smart00576 BTP Bromodomain tra 95.6 0.096 2.1E-06 35.5 7.1 47 76-122 24-70 (77)
26 PF02969 TAF: TATA box binding 95.5 0.055 1.2E-06 36.8 5.9 46 76-121 21-66 (66)
27 cd08050 TAF6 TATA Binding Prot 95.5 0.042 9.2E-07 46.6 6.4 49 75-123 16-64 (343)
28 PLN00153 histone H2A; Provisio 95.5 0.036 7.7E-07 42.4 5.3 65 57-121 23-88 (129)
29 PF15510 CENP-W: Centromere ki 94.6 0.069 1.5E-06 39.3 4.6 64 60-125 19-98 (102)
30 PTZ00252 histone H2A; Provisio 94.4 0.13 2.8E-06 39.6 5.8 66 56-121 23-91 (134)
31 KOG0870 DNA polymerase epsilon 94.1 0.27 5.8E-06 39.3 7.1 63 61-123 14-78 (172)
32 PLN00154 histone H2A; Provisio 94.0 0.15 3.3E-06 39.3 5.5 61 61-121 42-103 (136)
33 COG5262 HTA1 Histone H2A [Chro 93.7 0.17 3.7E-06 38.8 5.2 60 62-121 31-90 (132)
34 PLN00121 histone H3; Provision 93.7 0.31 6.8E-06 37.5 6.7 66 57-122 66-131 (136)
35 PTZ00018 histone H3; Provision 93.1 0.43 9.2E-06 36.8 6.6 66 57-122 66-131 (136)
36 PF15630 CENP-S: Kinetochore c 92.5 0.38 8.2E-06 33.4 5.1 58 63-120 11-70 (76)
37 PF07524 Bromo_TP: Bromodomain 91.9 1.4 3E-05 29.4 7.2 63 60-122 5-70 (77)
38 KOG1756 Histone 2A [Chromatin 91.3 0.67 1.4E-05 35.7 5.7 60 62-121 32-91 (131)
39 PLN00161 histone H3; Provision 89.8 2 4.3E-05 33.2 7.2 66 57-122 59-125 (135)
40 PF15511 CENP-T: Centromere ki 88.6 1.1 2.4E-05 39.2 5.7 55 61-115 355-414 (414)
41 PLN00160 histone H3; Provision 87.2 3.9 8.4E-05 29.8 6.9 66 57-122 25-91 (97)
42 PF02291 TFIID-31kDa: Transcri 86.9 1.8 4E-05 32.7 5.3 60 61-124 16-78 (129)
43 KOG2549 Transcription initiati 85.8 2.1 4.6E-05 39.8 6.0 48 76-123 29-76 (576)
44 PF02269 TFIID-18kDa: Transcri 84.8 1.2 2.7E-05 31.4 3.3 46 76-121 20-65 (93)
45 cd08048 TAF11 TATA Binding Pro 84.7 7.5 0.00016 27.4 7.2 60 63-123 22-84 (85)
46 cd07978 TAF13 The TATA Binding 80.7 7.1 0.00015 27.8 5.9 45 76-121 21-65 (92)
47 TIGR02442 Cob-chelat-sub cobal 78.8 7.9 0.00017 35.4 7.0 59 68-126 242-307 (633)
48 PRK09522 bifunctional glutamin 78.3 4.4 9.6E-05 36.7 5.2 59 69-127 168-229 (531)
49 COG1466 HolA DNA polymerase II 75.5 10 0.00023 31.5 6.3 64 57-122 143-206 (334)
50 PF14687 DUF4460: Domain of un 74.2 4.2 9.1E-05 29.9 3.3 37 58-94 10-54 (112)
51 TIGR01128 holA DNA polymerase 73.1 19 0.00041 28.4 6.9 63 57-121 114-176 (302)
52 smart00350 MCM minichromosome 72.8 17 0.00037 32.3 7.3 66 57-124 421-505 (509)
53 PF04719 TAFII28: hTAFII28-lik 72.3 25 0.00054 25.2 6.8 62 62-123 28-90 (90)
54 PRK07452 DNA polymerase III su 72.1 15 0.00032 29.8 6.3 61 59-121 135-197 (326)
55 PRK08487 DNA polymerase III su 71.9 14 0.0003 30.6 6.2 59 59-121 140-198 (328)
56 COG5095 TAF6 Transcription ini 70.8 4.9 0.00011 35.9 3.4 60 64-123 8-70 (450)
57 PRK05574 holA DNA polymerase I 70.6 21 0.00046 28.7 6.8 63 57-121 149-211 (340)
58 KOG3334 Transcription initiati 68.8 18 0.00039 28.4 5.8 58 66-123 18-78 (148)
59 PRK14607 bifunctional glutamin 68.6 9 0.0002 34.4 4.7 58 69-127 167-224 (534)
60 smart00271 DnaJ DnaJ molecular 64.4 17 0.00036 22.1 4.0 17 61-77 20-36 (60)
61 PRK06585 holA DNA polymerase I 63.9 21 0.00046 29.2 5.7 62 58-121 146-208 (343)
62 TIGR03015 pepcterm_ATPase puta 63.3 40 0.00087 26.0 6.9 67 57-123 195-266 (269)
63 PF00725 3HCDH: 3-hydroxyacyl- 62.6 18 0.0004 24.3 4.3 34 87-123 3-36 (97)
64 COG5208 HAP5 CCAAT-binding fac 61.1 14 0.0003 31.3 4.2 58 63-121 115-173 (286)
65 cd06257 DnaJ DnaJ domain or J- 59.7 21 0.00047 21.2 3.9 17 61-77 19-35 (55)
66 PRK05907 hypothetical protein; 58.7 23 0.00051 29.8 5.2 59 59-120 139-200 (311)
67 PRK07914 hypothetical protein; 58.6 29 0.00062 28.5 5.6 58 60-120 134-191 (320)
68 KOG0568 Molecular chaperone (D 57.0 23 0.00049 30.6 4.8 48 63-115 68-117 (342)
69 PF09415 CENP-X: CENP-S associ 55.7 29 0.00062 23.8 4.3 56 63-118 5-63 (72)
70 KOG1745 Histones H3 and H4 [Ch 54.3 16 0.00035 28.3 3.2 49 71-123 81-133 (137)
71 PF03477 ATP-cone: ATP cone do 53.0 26 0.00056 23.3 3.7 58 56-124 10-69 (90)
72 PRK09333 30S ribosomal protein 51.3 30 0.00066 27.0 4.3 50 56-105 94-149 (150)
73 PRK05629 hypothetical protein; 51.0 54 0.0012 26.8 6.0 60 58-120 130-189 (318)
74 PF00226 DnaJ: DnaJ domain; I 50.7 49 0.0011 20.5 4.6 40 60-99 18-58 (64)
75 COG5150 Class 2 transcription 50.6 48 0.001 25.9 5.3 50 73-122 28-77 (148)
76 TIGR00764 lon_rel lon-related 48.6 88 0.0019 28.8 7.5 66 57-122 312-390 (608)
77 TIGR02030 BchI-ChlI magnesium 48.0 41 0.00089 28.7 5.0 25 101-125 287-311 (337)
78 cd07353 harmonin_N N-terminal 47.3 15 0.00033 26.0 1.9 29 56-92 18-46 (79)
79 TIGR02031 BchD-ChlD magnesium 45.0 79 0.0017 28.9 6.6 58 68-125 196-260 (589)
80 PRK03992 proteasome-activating 44.8 35 0.00075 29.2 4.1 43 85-127 334-376 (389)
81 cd00043 CYCLIN Cyclin box fold 43.4 75 0.0016 19.3 5.1 62 58-119 4-71 (88)
82 CHL00081 chlI Mg-protoporyphyr 43.3 78 0.0017 27.4 6.1 27 99-125 298-324 (350)
83 PF13335 Mg_chelatase_2: Magne 41.7 55 0.0012 23.0 4.1 48 75-122 42-95 (96)
84 PF05674 DUF816: Baculovirus p 41.0 1.1E+02 0.0024 24.6 6.2 56 57-112 93-169 (171)
85 PLN03213 repressor of silencin 40.6 24 0.00051 33.4 2.6 23 73-95 183-205 (759)
86 PRK05637 anthranilate synthase 40.4 23 0.0005 27.9 2.3 24 69-92 183-206 (208)
87 PF13148 DUF3987: Protein of u 38.7 1.4E+02 0.003 24.5 6.6 68 56-123 261-360 (378)
88 KOG1657 CCAAT-binding factor, 38.7 59 0.0013 26.9 4.5 56 64-121 81-138 (236)
89 PF11945 WASH_WAHD: WAHD domai 38.1 41 0.00088 28.7 3.5 22 79-100 25-46 (297)
90 PRK13406 bchD magnesium chelat 37.7 88 0.0019 28.9 5.8 32 94-125 221-252 (584)
91 KOG0240 Kinesin (SMY1 subfamil 37.7 33 0.00071 32.4 3.0 41 57-97 65-126 (607)
92 PF13654 AAA_32: AAA domain; P 37.7 50 0.0011 29.9 4.2 63 57-121 430-504 (509)
93 KOG1757 Histone 2A [Chromatin 37.2 40 0.00087 25.9 3.0 56 62-121 35-95 (131)
94 PRK00464 nrdR transcriptional 37.2 85 0.0018 24.3 4.9 16 109-124 101-116 (154)
95 COG2238 RPS19A Ribosomal prote 37.1 44 0.00095 26.3 3.2 38 60-97 95-141 (147)
96 PF07587 PSD1: Protein of unkn 36.9 1.2E+02 0.0026 24.7 6.0 24 76-99 197-221 (266)
97 PF05798 Phage_FRD3: Bacteriop 36.7 17 0.00036 25.6 0.8 18 61-78 12-29 (75)
98 PF11841 DUF3361: Domain of un 35.5 36 0.00077 26.8 2.6 59 60-119 57-121 (160)
99 PRK00411 cdc6 cell division co 34.7 2.6E+02 0.0057 23.0 8.3 57 67-123 220-282 (394)
100 TIGR01242 26Sp45 26S proteasom 32.4 66 0.0014 26.9 3.8 41 84-124 324-364 (364)
101 TIGR00888 guaA_Nterm GMP synth 32.4 38 0.00083 25.5 2.2 23 68-90 161-183 (188)
102 PRK13407 bchI magnesium chelat 32.1 1.4E+02 0.003 25.6 5.8 31 95-125 278-308 (334)
103 PHA03102 Small T antigen; Revi 31.7 82 0.0018 24.4 4.0 36 64-103 29-64 (153)
104 PRK10733 hflB ATP-dependent me 31.4 75 0.0016 29.3 4.3 41 86-126 355-395 (644)
105 TIGR01241 FtsH_fam ATP-depende 31.4 1.5E+02 0.0033 26.0 6.0 40 87-126 259-298 (495)
106 PLN02347 GMP synthetase 31.3 38 0.00083 30.9 2.4 25 68-92 179-203 (536)
107 KOG4336 TBP-associated transcr 31.2 2E+02 0.0043 25.4 6.5 58 64-122 12-69 (323)
108 PF00493 MCM: MCM2/3/5 family 31.2 39 0.00084 28.4 2.3 66 56-123 244-326 (331)
109 PTZ00361 26 proteosome regulat 31.1 66 0.0014 28.6 3.8 43 83-125 384-426 (438)
110 smart00385 CYCLIN domain prese 28.7 1.2E+02 0.0027 18.2 3.8 55 62-116 2-62 (83)
111 TIGR02397 dnaX_nterm DNA polym 27.9 1.8E+02 0.0038 23.5 5.5 60 59-121 181-240 (355)
112 TIGR00368 Mg chelatase-related 27.7 1.4E+02 0.0031 26.9 5.4 49 74-122 444-498 (499)
113 TIGR03543 divI1A_rptt_fam DivI 27.1 85 0.0018 25.2 3.4 27 88-120 16-43 (178)
114 PF03008 DUF234: Archaea bacte 26.3 89 0.0019 21.6 3.1 25 81-105 25-49 (100)
115 PF04157 EAP30: EAP30/Vps36 fa 26.2 1.7E+02 0.0036 23.1 5.0 69 56-124 56-146 (223)
116 PRK08293 3-hydroxybutyryl-CoA 25.5 1.4E+02 0.0031 23.9 4.6 37 85-124 189-225 (287)
117 cd07347 harmonin_N_like N-term 24.9 1.1E+02 0.0024 21.4 3.3 33 60-100 21-53 (78)
118 PF14374 Ribos_L4_asso_C: 60S 24.5 9.8 0.00021 26.8 -2.1 11 111-121 19-29 (80)
119 PRK08857 para-aminobenzoate sy 24.1 51 0.0011 25.2 1.7 21 69-89 171-191 (193)
120 PRK00074 guaA GMP synthase; Re 23.6 63 0.0014 29.0 2.3 23 69-91 167-189 (511)
121 smart00339 FH FORKHEAD. FORKHE 23.4 1E+02 0.0023 21.5 3.0 31 56-97 3-33 (89)
122 PRK15361 pathogenicity island 23.4 49 0.0011 27.1 1.5 45 76-120 24-74 (195)
123 PLN02545 3-hydroxybutyryl-CoA 22.9 1.8E+02 0.0039 23.3 4.7 35 86-123 188-222 (295)
124 PF08118 MDM31_MDM32: Yeast mi 22.7 1E+02 0.0023 28.4 3.6 45 82-126 453-498 (503)
125 PTZ00454 26S protease regulato 22.5 1.3E+02 0.0029 26.2 4.1 40 87-126 350-389 (398)
126 TIGR02928 orc1/cdc6 family rep 22.5 4.2E+02 0.0092 21.5 8.3 63 61-123 206-274 (365)
127 PF09193 CholecysA-Rec_N: Chol 22.3 31 0.00068 22.4 0.1 13 112-124 35-47 (47)
128 PRK14970 DNA polymerase III su 22.1 2.6E+02 0.0056 23.1 5.6 60 59-121 172-231 (367)
129 CHL00176 ftsH cell division pr 21.8 1.2E+02 0.0026 28.3 3.8 35 92-126 392-426 (638)
130 PRK07819 3-hydroxybutyryl-CoA 21.8 2E+02 0.0043 23.5 4.7 33 87-122 192-224 (286)
131 PF08546 ApbA_C: Ketopantoate 21.7 2.3E+02 0.0051 19.6 4.6 38 85-123 33-70 (125)
132 PRK05808 3-hydroxybutyryl-CoA 21.7 2E+02 0.0043 22.9 4.7 35 86-123 187-221 (282)
133 cd05133 RasGAP_IQGAP1 IQGAP1 i 21.4 1.3E+02 0.0029 26.2 3.8 65 60-124 213-298 (360)
134 PF01090 Ribosomal_S19e: Ribos 21.3 1.4E+02 0.003 23.1 3.5 37 58-94 92-138 (139)
135 PRK13765 ATP-dependent proteas 21.3 3.1E+02 0.0068 25.7 6.4 65 57-121 318-398 (637)
136 PF14081 DUF4262: Domain of un 21.0 74 0.0016 23.0 1.9 29 68-96 30-58 (125)
137 cd05131 RasGAP_IQGAP2 IQGAP2 i 20.5 1.4E+02 0.0031 25.5 3.8 65 60-124 213-298 (339)
138 PF13843 DDE_Tnp_1_7: Transpos 20.4 2.1E+02 0.0046 23.6 4.8 44 81-124 3-50 (351)
139 PF15469 Sec5: Exocyst complex 20.4 1.8E+02 0.0039 21.9 4.0 36 78-124 131-166 (182)
140 PF03428 RP-C: Replication pro 20.1 80 0.0017 24.9 2.1 28 62-89 27-54 (177)
141 PF08221 HTH_9: RNA polymerase 20.0 2.1E+02 0.0045 18.5 3.7 34 86-121 5-38 (62)
No 1
>PTZ00463 histone H2B; Provisional
Probab=100.00 E-value=2.9e-46 Score=277.49 Aligned_cols=80 Identities=65% Similarity=1.009 Sum_probs=76.8
Q ss_pred ccccccccchhhHHHHHHHhhhccCCCCcchhhHHHHHhHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHHhhcCCC
Q 033083 48 KKKRAKKSIETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLVLPAS 127 (128)
Q Consensus 48 ~kk~~kkr~esys~YIyKVLKQVhPd~gISskAM~IMnSfVnDiFErIA~EAs~La~~nkk~TltsREIQtAVRLlLPGE 127 (128)
+++++++|.|+|++||||||||||||+|||++||+||||||||||||||.||++|++||+++|||+||||||||||||||
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 35567778999999999999999999999999999999999999999999999999999999999999999999999998
No 2
>PLN00158 histone H2B; Provisional
Probab=100.00 E-value=6.8e-46 Score=275.23 Aligned_cols=79 Identities=80% Similarity=1.140 Sum_probs=76.1
Q ss_pred cccccccchhhHHHHHHHhhhccCCCCcchhhHHHHHhHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHHhhcCCC
Q 033083 49 KKRAKKSIETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLVLPAS 127 (128)
Q Consensus 49 kk~~kkr~esys~YIyKVLKQVhPd~gISskAM~IMnSfVnDiFErIA~EAs~La~~nkk~TltsREIQtAVRLlLPGE 127 (128)
++++++|.|+|++||||||||||||+|||++||+||||||||||||||.||++|++||+++|||+||||||||||||||
T Consensus 19 kk~~~kr~esy~~YI~kVLKQVhPd~gIS~kaM~ImnSfvnDiferIA~EAs~La~~nkr~TltsrEIqtAvrLvLpgE 97 (116)
T PLN00158 19 KKGSKSKTETYKIYIYKVLKQVHPDTGISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVRLILPGE 97 (116)
T ss_pred ccccccccccHHHHHHHHHHHhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHhccHH
Confidence 4566678899999999999999999999999999999999999999999999999999999999999999999999997
No 3
>smart00427 H2B Histone H2B.
Probab=100.00 E-value=1.9e-43 Score=252.05 Aligned_cols=71 Identities=79% Similarity=1.169 Sum_probs=70.3
Q ss_pred hhhHHHHHHHhhhccCCCCcchhhHHHHHhHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHHhhcCCC
Q 033083 57 ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLVLPAS 127 (128)
Q Consensus 57 esys~YIyKVLKQVhPd~gISskAM~IMnSfVnDiFErIA~EAs~La~~nkk~TltsREIQtAVRLlLPGE 127 (128)
|+|++||||||||||||+|||++||+||||||||||||||.||++|++||+|+|||+||||||||||||||
T Consensus 1 esy~~Yi~kvLKqVhpd~giS~kam~imnSfvnDiferIa~EAs~L~~~nkr~TltsreIqtAvrl~Lpge 71 (89)
T smart00427 1 ETYAIYIYKVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRLILPGE 71 (89)
T ss_pred CcHHHHHHHHHHHhCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHHccHH
Confidence 68999999999999999999999999999999999999999999999999999999999999999999997
No 4
>KOG1744 consensus Histone H2B [Chromatin structure and dynamics]
Probab=100.00 E-value=1.2e-38 Score=239.67 Aligned_cols=79 Identities=70% Similarity=1.090 Sum_probs=76.6
Q ss_pred cccccccchhhHHHHHHHhhhccCCCCcchhhHHHHHhHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHHhhcCCC
Q 033083 49 KKRAKKSIETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLVLPAS 127 (128)
Q Consensus 49 kk~~kkr~esys~YIyKVLKQVhPd~gISskAM~IMnSfVnDiFErIA~EAs~La~~nkk~TltsREIQtAVRLlLPGE 127 (128)
+++..++.|+|+.||||||||||||+|||+++|+||||||||||||||+||++|++||+++|||||||||||||+||||
T Consensus 29 k~~~~~~~e~~s~yv~kvlk~Vhpd~gis~~a~~vmnsf~ndife~iA~ea~rla~y~krstisSreiqta~rLllPge 107 (127)
T KOG1744|consen 29 KKRSTRRKESYSEYVYKVLKQVHPDLGISSKAMGVMNSFVNDIFERIASEAGRLAHYNKRSTISSREIQTAVRLLLPGE 107 (127)
T ss_pred ccCcccccCceeeehhhhhhcccCCCCcCHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCcccHHHHHHHHHHhCchH
Confidence 5566888999999999999999999999999999999999999999999999999999999999999999999999997
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=99.64 E-value=1.8e-16 Score=105.31 Aligned_cols=69 Identities=32% Similarity=0.418 Sum_probs=65.8
Q ss_pred ccchhhHHHHHHHhhhccCC----CCcchhhHHHHHhHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHHh
Q 033083 54 KSIETYKIYIFKVLKQVHPD----IGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRL 122 (128)
Q Consensus 54 kr~esys~YIyKVLKQVhPd----~gISskAM~IMnSfVnDiFErIA~EAs~La~~nkk~TltsREIQtAVRL 122 (128)
++...+..||+||+++++++ ..||+.||.+|+++++|+|.+|.++|..++.+++|.||+++|||.|+|+
T Consensus 2 ~~~~~~~~~~~r~~r~i~~~~~~~~ris~~a~~~L~~~~E~~~~~il~~A~~~a~~~kR~tI~~~DI~~A~r~ 74 (75)
T PF00125_consen 2 TRRLIPKFPFSRLLREIGEEILSKYRISSEALVALQSVLEYLLVEILEEAGNLARHAKRKTITPRDIQLAVRI 74 (75)
T ss_dssp HSHSSSHHHHHHHHHHHHHTTSSSSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTBSEEGHHHHHHHHHH
T ss_pred cccccCceEEeeeeehhhcccccccccccccchhhhhhhhhhhhhhhhHHHHHHhhcCCcEecHHHHHHHHhc
Confidence 34678999999999999999 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=98.35 E-value=2.9e-06 Score=57.49 Aligned_cols=60 Identities=18% Similarity=0.398 Sum_probs=57.1
Q ss_pred HHHHhhhccCCCCcchhhHHHHHhHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHHh
Q 033083 63 IFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRL 122 (128)
Q Consensus 63 IyKVLKQVhPd~gISskAM~IMnSfVnDiFErIA~EAs~La~~nkk~TltsREIQtAVRL 122 (128)
+...++++.|...++..+...|-.+.+|+.+.|+..|..||.+.++.||..+|||-+++-
T Consensus 7 l~~lv~~id~~~~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~~~tv~~~Di~l~l~r 66 (72)
T cd07981 7 LQELLKEIDPREQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQLHLER 66 (72)
T ss_pred HHHHHHhhCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence 567899999999999999999999999999999999999999999999999999998864
No 7
>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=98.33 E-value=2.1e-06 Score=56.10 Aligned_cols=58 Identities=28% Similarity=0.469 Sum_probs=52.4
Q ss_pred HHHHHhhhccCCC-CcchhhHHHHHhHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHH
Q 033083 62 YIFKVLKQVHPDI-GISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAV 120 (128)
Q Consensus 62 YIyKVLKQVhPd~-gISskAM~IMnSfVnDiFErIA~EAs~La~~nkk~TltsREIQtAV 120 (128)
=|.|++|+. ||. .||..|...|+.....+.+.|+.+|...+..++|+||+.+||..||
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 378999998 775 5999999999999999999999999999999999999999999986
No 8
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=98.05 E-value=1.3e-05 Score=57.68 Aligned_cols=62 Identities=21% Similarity=0.398 Sum_probs=58.6
Q ss_pred HHHHhhhccCCCCcchhhHHHHHhHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHHhhcC
Q 033083 63 IFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLVLP 125 (128)
Q Consensus 63 IyKVLKQVhPd~gISskAM~IMnSfVnDiFErIA~EAs~La~~nkk~TltsREIQtAVRLlLP 125 (128)
|-|++|++.++ .||..|...|+..+..+++-|+.+|..+|.+-+|.||+..||+-|++.+..
T Consensus 25 v~Ri~r~~~~~-Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~DI~la~~~~~~ 86 (91)
T COG2036 25 VRRILRKAGAE-RVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLALKRLGR 86 (91)
T ss_pred HHHHHHHHhHH-HhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHHHhcc
Confidence 77888998888 999999999999999999999999999999999999999999999998754
No 9
>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=97.66 E-value=0.00017 Score=49.03 Aligned_cols=59 Identities=19% Similarity=0.391 Sum_probs=48.6
Q ss_pred HHHHhhhccCCCCcchhhHHHHHhHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHH
Q 033083 63 IFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVR 121 (128)
Q Consensus 63 IyKVLKQVhPd~gISskAM~IMnSfVnDiFErIA~EAs~La~~nkk~TltsREIQtAVR 121 (128)
+-..++||-|+..|...+..+|-.+.+|+.+.+.+-|++||++.+..||..+|||....
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 56789999999999999999999999999999999999999999999999999997654
No 10
>smart00803 TAF TATA box binding protein associated factor. TAFs (TATA box binding protein associated factors) are part of the transcription initiation factor TFIID multimeric protein complex. TFIID is composed of the TATA box binding protein (TBP) and a number of TAFs. The TAFs provide binding sites for many different transcriptional activators and co-activators that modulate transcription initiation by Pol II. TAF proteins adopt a histone-like fold.
Probab=97.53 E-value=0.00039 Score=46.67 Aligned_cols=59 Identities=24% Similarity=0.350 Sum_probs=51.5
Q ss_pred HHHHHhhhccCCCCcchhhHHHHHhHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHH
Q 033083 62 YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVR 121 (128)
Q Consensus 62 YIyKVLKQVhPd~gISskAM~IMnSfVnDiFErIA~EAs~La~~nkk~TltsREIQtAVR 121 (128)
.|.+++++..=+ .||..+..-|-..+.+..+.|+.+|..++++.+|.|||..||--|++
T Consensus 7 ~i~ria~~~Gi~-ris~~a~~~l~~~~e~rl~~i~~~A~k~~~hakRktlt~~DI~~Alk 65 (65)
T smart00803 7 TIKDVAESLGIG-NLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSALR 65 (65)
T ss_pred HHHHHHHHCCCc-cccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCeecHHHHHHHhC
Confidence 477788876422 58999999999999999999999999999999999999999988864
No 11
>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=97.52 E-value=0.00032 Score=52.16 Aligned_cols=61 Identities=28% Similarity=0.252 Sum_probs=55.2
Q ss_pred HHHHHHhhhccCCCCcchhhHHHHHhHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHH
Q 033083 61 IYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVR 121 (128)
Q Consensus 61 ~YIyKVLKQVhPd~gISskAM~IMnSfVnDiFErIA~EAs~La~~nkk~TltsREIQtAVR 121 (128)
.=|+|.|++-.--..||..|.--|-..+..+...|.+.|.+.++.+++.+||.|+|+.|++
T Consensus 24 ~ri~R~Lk~~~~a~RVs~~A~VyLaAvLEYL~aEIlelA~n~ak~~k~krItp~hi~lAi~ 84 (115)
T cd00074 24 GRIHRYLKKGRYAERVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKKRITPRHLQLAVR 84 (115)
T ss_pred HHHHHHHHcCccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEcHHHHHHHHh
Confidence 3489999985555789999999999999999999999999999999999999999999997
No 12
>PLN00035 histone H4; Provisional
Probab=97.43 E-value=0.00074 Score=49.68 Aligned_cols=60 Identities=13% Similarity=0.153 Sum_probs=54.1
Q ss_pred HHHHHhhhccCCCCcchhhHHHHHhHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHHh
Q 033083 62 YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRL 122 (128)
Q Consensus 62 YIyKVLKQVhPd~gISskAM~IMnSfVnDiFErIA~EAs~La~~nkk~TltsREIQtAVRL 122 (128)
-|.|+++.-- --.||..+..-+...+.++++.|+.+|..++.+.+|.||+..||--|++.
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 3788888764 45699999999999999999999999999999999999999999999874
No 13
>cd00076 H4 Histone H4, one of the four histones, along with H2A, H2B and H3, which forms the eukaryotic nucleosome core; along with H3, it plays a central role in nucleosome formation; histones bind to DNA and wrap the genetic material into "beads on a string" in which DNA (the string) is wrapped around small blobs of histones (the beads) at regular intervals; play a role in the inheritance of specialized chromosome structures and the control of gene activity; defects in the establishment of proper chromosome structure by histones may activate or silence genes aberrantly and thus lead to disease; the sequence of histone H4 has remained almost invariant in more than 2 billion years of evolution
Probab=97.37 E-value=0.001 Score=47.23 Aligned_cols=60 Identities=15% Similarity=0.199 Sum_probs=52.8
Q ss_pred HHHHHhhhccCCCCcchhhHHHHHhHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHHh
Q 033083 62 YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRL 122 (128)
Q Consensus 62 YIyKVLKQVhPd~gISskAM~IMnSfVnDiFErIA~EAs~La~~nkk~TltsREIQtAVRL 122 (128)
-|.|+++.-- -..||..+..-+...+..+|+.|+.+|..++.+.+|.|||..||--|++.
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 4777777653 45699999999999999999999999999999999999999999998873
No 14
>PTZ00015 histone H4; Provisional
Probab=97.27 E-value=0.00087 Score=49.18 Aligned_cols=62 Identities=15% Similarity=0.248 Sum_probs=54.0
Q ss_pred HHHHHHHhhhccCCCCcchhhHHHHHhHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHHh
Q 033083 60 KIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRL 122 (128)
Q Consensus 60 s~YIyKVLKQVhPd~gISskAM~IMnSfVnDiFErIA~EAs~La~~nkk~TltsREIQtAVRL 122 (128)
..-|.|+++.-- --.||..+..-+..+++++++.|+.+|..++.+.+|.|+|..||--|++.
T Consensus 33 k~~IrRLarr~G-vkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~AlKr 94 (102)
T PTZ00015 33 KGAIRRLARRGG-VKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALKR 94 (102)
T ss_pred HHHHHHHHHHcC-CccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHh
Confidence 345888888642 34599999999999999999999999999999999999999999988864
No 15
>smart00428 H3 Histone H3.
Probab=97.17 E-value=0.0026 Score=46.81 Aligned_cols=69 Identities=19% Similarity=0.253 Sum_probs=62.9
Q ss_pred cchhhHHHHHHHhhhccC--CCCcchhhHHHHHhHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHHhh
Q 033083 55 SIETYKIYIFKVLKQVHP--DIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLV 123 (128)
Q Consensus 55 r~esys~YIyKVLKQVhP--d~gISskAM~IMnSfVnDiFErIA~EAs~La~~nkk~TltsREIQtAVRLl 123 (128)
++-.|+..+..+..+..+ |.-+++.|+..|.....+..-.+..+|..++.+.+|.||..+|||-|.||-
T Consensus 31 ~k~pF~RLVREI~~~~~~~~~~R~~~~Al~aLQeasE~ylv~lfeda~~~a~HAkRvTl~~kDi~La~rir 101 (105)
T smart00428 31 RKAPFQRLVREIAQKFTTGVDLRFQSSAIMALQEAAEAYLVGLFEDTNLLAIHAKRVTIMPKDIQLARRIR 101 (105)
T ss_pred ccccHHHHHHHHHHHcCCCCCceeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccCcHhhHHHHHHHh
Confidence 356788888888888888 889999999999999999999999999999999999999999999999863
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=97.04 E-value=0.0051 Score=45.38 Aligned_cols=65 Identities=12% Similarity=0.156 Sum_probs=56.9
Q ss_pred HHHHHHHhhhccCCCCcchhhHHHHHhHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHHhhcC
Q 033083 60 KIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLVLP 125 (128)
Q Consensus 60 s~YIyKVLKQVhPd~gISskAM~IMnSfVnDiFErIA~EAs~La~~nkk~TltsREIQtAVRLlLP 125 (128)
...|.++|+.-+ ....+..+..-|.-|+....+.|+.+|..++.+.+|.||+..||.-|+...+.
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 356888888752 34688999999999999999999999999999999999999999999987664
No 17
>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [Transcription]
Probab=96.72 E-value=0.0057 Score=48.50 Aligned_cols=59 Identities=20% Similarity=0.318 Sum_probs=55.1
Q ss_pred HHHHhhhccCCCC-cchhhHHHHHhHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHH
Q 033083 63 IFKVLKQVHPDIG-ISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVR 121 (128)
Q Consensus 63 IyKVLKQVhPd~g-ISskAM~IMnSfVnDiFErIA~EAs~La~~nkk~TltsREIQtAVR 121 (128)
|-|+.|+.-|..+ ||..|-.+|.-.|..+.-=|+.||+..|+.-+|+||+-.||-.|+-
T Consensus 38 V~RIMK~~lP~naKIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIngdDllwAm~ 97 (168)
T KOG0869|consen 38 VSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASEKCQREKRKTINGDDLLWAMS 97 (168)
T ss_pred HHHHHHhcCCcccccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCcccHHHHHHHHH
Confidence 7789999988755 9999999999999999999999999999999999999999999875
No 18
>smart00417 H4 Histone H4.
Probab=96.64 E-value=0.0045 Score=43.04 Aligned_cols=55 Identities=13% Similarity=0.189 Sum_probs=47.2
Q ss_pred HHHHHhhhccCCCCcchhhHHHHHhHHHHHHHHHHHHHhhHHhhCCCCCCChhHHH
Q 033083 62 YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQ 117 (128)
Q Consensus 62 YIyKVLKQVhPd~gISskAM~IMnSfVnDiFErIA~EAs~La~~nkk~TltsREIQ 117 (128)
-|.|+++.-- --.||..+..-+..++.++++.|+.+|..++.+.++.|+++.||-
T Consensus 18 ~IrRLaRr~G-vkRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~ 72 (74)
T smart00417 18 AIRRLARRGG-VKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVV 72 (74)
T ss_pred HHHHHHHHcC-cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHhe
Confidence 3777777641 234899999999999999999999999999999999999999984
No 19
>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=96.23 E-value=0.019 Score=45.14 Aligned_cols=62 Identities=18% Similarity=0.334 Sum_probs=57.5
Q ss_pred HHHHHhhhccC-CCCcchhhHHHHHhHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHHhh
Q 033083 62 YIFKVLKQVHP-DIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLV 123 (128)
Q Consensus 62 YIyKVLKQVhP-d~gISskAM~IMnSfVnDiFErIA~EAs~La~~nkk~TltsREIQtAVRLl 123 (128)
-|.+++|.+-| |..+...|-++++..--.+...|+.||..+|.-..++||....|+.|+.-|
T Consensus 17 tv~KmIke~lP~d~rvakeareliincCvEFI~liSsEAneic~~e~KKTIa~EHV~KALe~L 79 (156)
T KOG0871|consen 17 TVNKMIKEMLPKDVRVAKEARELIINCCVEFINLISSEANEICNKEAKKTIAPEHVIKALENL 79 (156)
T ss_pred HHHHHHHHhCCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHhHHhcccCCHHHHHHHHHHc
Confidence 38899999999 999999999999998889999999999999999999999999999998643
No 20
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=96.23 E-value=0.0093 Score=50.08 Aligned_cols=66 Identities=15% Similarity=0.322 Sum_probs=59.0
Q ss_pred HHHHHhhhccCCCCcchhhHHHHHhHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHH----hhcCCC
Q 033083 62 YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVR----LVLPAS 127 (128)
Q Consensus 62 YIyKVLKQVhPd~gISskAM~IMnSfVnDiFErIA~EAs~La~~nkk~TltsREIQtAVR----LlLPGE 127 (128)
-|...|+||.+++.|....-++|--+..|+.+.|..-+++||.+.+..||-.||||-.+. +-|||.
T Consensus 159 kl~dLvqqId~~~~LD~dVedlLleiADdFV~sii~~sC~LAKHRKsdtlEvrDIqLhLEr~~Nm~iPgf 228 (258)
T KOG1142|consen 159 KLDDLVQQIDGTTKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHRKSDTVEVRDIQLHLERNFNMEIPGF 228 (258)
T ss_pred chhHHHHhhcCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccchhheeeeeeccccccCCCc
Confidence 378889999999999999999999999999999999999999999999999999997653 345554
No 21
>smart00414 H2A Histone 2A.
Probab=95.80 E-value=0.028 Score=41.24 Aligned_cols=61 Identities=25% Similarity=0.260 Sum_probs=46.8
Q ss_pred HHHHHHhhhccCCCCcchhhHHHHHhHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHH
Q 033083 61 IYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVR 121 (128)
Q Consensus 61 ~YIyKVLKQVhPd~gISskAM~IMnSfVnDiFErIA~EAs~La~~nkk~TltsREIQtAVR 121 (128)
..|+|.|+.-+--..|++-|.--|-..+..+...|-+-|..-++.+++..||+|+||.|++
T Consensus 13 gRi~r~Lk~~~~~~Rv~~~A~VyLaAvLEYLtaEILeLagn~a~~~k~~rItp~hi~lAi~ 73 (106)
T smart00414 13 GRIHRLLRKGTYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKRRITPRHLQLAIR 73 (106)
T ss_pred HHHHHHHHcCccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchHHHhhhcc
Confidence 4689999887655678887776666666555555555666777889999999999999986
No 22
>PLN00157 histone H2A; Provisional
Probab=95.80 E-value=0.02 Score=43.89 Aligned_cols=65 Identities=26% Similarity=0.234 Sum_probs=53.3
Q ss_pred hhhH-HHHHHHhhhccCCCCcchhhHHHHHhHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHH
Q 033083 57 ETYK-IYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVR 121 (128)
Q Consensus 57 esys-~YIyKVLKQVhPd~gISskAM~IMnSfVnDiFErIA~EAs~La~~nkk~TltsREIQtAVR 121 (128)
-.|. .=|+|.|++-+--..|++.|.--|-..+..+...|-+-|.+-++.+++.-||.|.||.||+
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 3443 3499999997766789988888777777777777777788888999999999999999997
No 23
>PTZ00017 histone H2A; Provisional
Probab=95.67 E-value=0.026 Score=43.35 Aligned_cols=61 Identities=25% Similarity=0.244 Sum_probs=48.8
Q ss_pred HHHHHHhhhccCCCCcchhhHHHHHhHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHH
Q 033083 61 IYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVR 121 (128)
Q Consensus 61 ~YIyKVLKQVhPd~gISskAM~IMnSfVnDiFErIA~EAs~La~~nkk~TltsREIQtAVR 121 (128)
.=|+|.|+.-+--..|++-|.--|-..+..++..|-+-|.+-++.|++.-||.|+||.|++
T Consensus 31 gRi~R~Lk~g~~a~RV~a~A~VYLAAVLEYLtaEILELAgNaa~d~kk~RItPrHi~lAI~ 91 (134)
T PTZ00017 31 GRVHRYLKKGRYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAAKDNKKKRITPRHIQLAIR 91 (134)
T ss_pred HHHHHHHhccchhccccccchhhhHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHhhcc
Confidence 3488999887656678888777666666666666666777788999999999999999997
No 24
>PLN00156 histone H2AX; Provisional
Probab=95.60 E-value=0.033 Score=43.10 Aligned_cols=64 Identities=27% Similarity=0.247 Sum_probs=53.8
Q ss_pred hhH-HHHHHHhhhccCCCCcchhhHHHHHhHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHH
Q 033083 58 TYK-IYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVR 121 (128)
Q Consensus 58 sys-~YIyKVLKQVhPd~gISskAM~IMnSfVnDiFErIA~EAs~La~~nkk~TltsREIQtAVR 121 (128)
.|. .=|+|.|+.-+--..|++-|.--|-..+..+...|-+-|.+-++.|++.-|++|.||.|||
T Consensus 29 ~FPVgRi~R~Lk~g~ya~RVga~ApVYLAAVLEYLtaEVLELAgNaa~d~kk~RItPrHi~lAIr 93 (139)
T PLN00156 29 QFPVGRIARFLKAGKYAERVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR 93 (139)
T ss_pred ccchHHHHHHHhcCChhhccCCccHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHhhcc
Confidence 454 3489999987666789998888888888888888888888888999999999999999997
No 25
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=95.55 E-value=0.096 Score=35.51 Aligned_cols=47 Identities=11% Similarity=0.205 Sum_probs=41.8
Q ss_pred cchhhHHHHHhHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHHh
Q 033083 76 ISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRL 122 (128)
Q Consensus 76 ISskAM~IMnSfVnDiFErIA~EAs~La~~nkk~TltsREIQtAVRL 122 (128)
++..|++.|-.++.+.+..|+.++.+++...+|.+.+..||.-|+.-
T Consensus 24 ~~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~~~Dv~~Al~~ 70 (77)
T smart00576 24 FQESALETLTDILQSYIQELGRTAHSYAELAGRTEPNLGDVVLALEN 70 (77)
T ss_pred cCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence 66678888888888889999999999999999999999999988754
No 26
>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=95.54 E-value=0.055 Score=36.78 Aligned_cols=46 Identities=24% Similarity=0.389 Sum_probs=35.8
Q ss_pred cchhhHHHHHhHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHH
Q 033083 76 ISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVR 121 (128)
Q Consensus 76 ISskAM~IMnSfVnDiFErIA~EAs~La~~nkk~TltsREIQtAVR 121 (128)
++..+-..|-.=|..-+..|..+|.+++++.+|.+||..||..|.|
T Consensus 21 l~de~a~~La~dveyrlreiiq~a~kfm~hskR~~Lt~~Di~~ALr 66 (66)
T PF02969_consen 21 LSDEAAKALAEDVEYRLREIIQEALKFMRHSKRTKLTTDDINSALR 66 (66)
T ss_dssp B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH-
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhC
Confidence 4556666666667777888999999999999999999999999976
No 27
>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=95.52 E-value=0.042 Score=46.56 Aligned_cols=49 Identities=20% Similarity=0.388 Sum_probs=45.6
Q ss_pred CcchhhHHHHHhHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHHhh
Q 033083 75 GISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLV 123 (128)
Q Consensus 75 gISskAM~IMnSfVnDiFErIA~EAs~La~~nkk~TltsREIQtAVRLl 123 (128)
.+|..|...+..-+.+....|+.||.++++..+|.||+..||.-|++..
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 5788899999999999999999999999999999999999999999863
No 28
>PLN00153 histone H2A; Provisional
Probab=95.48 E-value=0.036 Score=42.37 Aligned_cols=65 Identities=26% Similarity=0.229 Sum_probs=53.0
Q ss_pred hhhH-HHHHHHhhhccCCCCcchhhHHHHHhHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHH
Q 033083 57 ETYK-IYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVR 121 (128)
Q Consensus 57 esys-~YIyKVLKQVhPd~gISskAM~IMnSfVnDiFErIA~EAs~La~~nkk~TltsREIQtAVR 121 (128)
-.|. .=|+|.|++-+.-..|++-|.--|-..+..+...|-+-|.+-++.|++.-||+|.||.||+
T Consensus 23 L~FpVgRi~R~Lr~g~~a~Rvga~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~ 88 (129)
T PLN00153 23 LQFPVGRIARYLKKGKYAERIGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKNRIVPRHIQLAIR 88 (129)
T ss_pred cccchHHHHHHHhcCchhhccCCCchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHhhcc
Confidence 3443 3489999987666788888888777777777777777778888999999999999999997
No 29
>PF15510 CENP-W: Centromere kinetochore component W
Probab=94.64 E-value=0.069 Score=39.34 Aligned_cols=64 Identities=23% Similarity=0.393 Sum_probs=51.9
Q ss_pred HHHHHHHhhhccCCCCcch--hhH--------------HHHHhHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHHhh
Q 033083 60 KIYIFKVLKQVHPDIGISS--KAM--------------GIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLV 123 (128)
Q Consensus 60 s~YIyKVLKQVhPd~gISs--kAM--------------~IMnSfVnDiFErIA~EAs~La~~nkk~TltsREIQtAVRLl 123 (128)
..++.||+|+--|.+.+-. ..| -=+|.++ +..|+|+|+--=+.-|+..||-...|+.|...+
T Consensus 19 rgfLkrv~Kr~KphlRl~~~~Dllv~~~~f~~~~~~~~vhLncLL--FvhrLAEEaRtnA~EnK~~~Ik~~Hv~AaaKvi 96 (102)
T PF15510_consen 19 RGFLKRVFKRQKPHLRLETSGDLLVRFCPFSGWQWGGEVHLNCLL--FVHRLAEEARTNACENKCGTIKKEHVLAAAKVI 96 (102)
T ss_pred hHHHHHHHHhcCCceeecccccHHHhhcccccccccceeehhHHH--HHHHHHHHHHHHHHHHhhccccHHHHHHHHHHH
Confidence 4678999998888876643 333 3356665 678999999999999999999999999999988
Q ss_pred cC
Q 033083 124 LP 125 (128)
Q Consensus 124 LP 125 (128)
|-
T Consensus 97 LK 98 (102)
T PF15510_consen 97 LK 98 (102)
T ss_pred HH
Confidence 74
No 30
>PTZ00252 histone H2A; Provisional
Probab=94.37 E-value=0.13 Score=39.63 Aligned_cols=66 Identities=17% Similarity=0.137 Sum_probs=47.1
Q ss_pred chhhH-HHHHHHhhhccCCCCcchhhHHHHHhHHHHHHHHHHHHHhhHHh--hCCCCCCChhHHHHHHH
Q 033083 56 IETYK-IYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLAR--YNKKPTITSREIQTAVR 121 (128)
Q Consensus 56 ~esys-~YIyKVLKQVhPd~gISskAM~IMnSfVnDiFErIA~EAs~La~--~nkk~TltsREIQtAVR 121 (128)
.-.|. .-|+|.|++-+-.-.|++-|.--|-..+..++..|-+-|.+-++ .|++.-|+.|.||-|||
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 34454 35889999887777888888775555555555555555555553 47889999999999997
No 31
>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription]
Probab=94.07 E-value=0.27 Score=39.33 Aligned_cols=63 Identities=21% Similarity=0.293 Sum_probs=48.0
Q ss_pred HHHHHHhhhccCC--CCcchhhHHHHHhHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHHhh
Q 033083 61 IYIFKVLKQVHPD--IGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLV 123 (128)
Q Consensus 61 ~YIyKVLKQVhPd--~gISskAM~IMnSfVnDiFErIA~EAs~La~~nkk~TltsREIQtAVRLl 123 (128)
.-|-|+.|.|-|+ ..||..|...|-.--.=+..-+..-+..+|+-++|+||+..||-.|++-+
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 4577888888777 47999888777654333334466667789999999999999999998754
No 32
>PLN00154 histone H2A; Provisional
Probab=94.02 E-value=0.15 Score=39.32 Aligned_cols=61 Identities=21% Similarity=0.181 Sum_probs=42.6
Q ss_pred HHHHHHhhhcc-CCCCcchhhHHHHHhHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHH
Q 033083 61 IYIFKVLKQVH-PDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVR 121 (128)
Q Consensus 61 ~YIyKVLKQVh-Pd~gISskAM~IMnSfVnDiFErIA~EAs~La~~nkk~TltsREIQtAVR 121 (128)
.-|.|.||+.. -...|++.|.--|-..+..+--.|-+-|.+-++.+++.-||.|.||.|||
T Consensus 42 gRi~r~Lk~g~~~~~RVga~ApVYLAAVLEYLtAEVLELAGNaA~d~kk~RItPrHi~lAIr 103 (136)
T PLN00154 42 GRIHRQLKQRVSAHGRVGATAAVYTAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 103 (136)
T ss_pred HHHHHHHHhhhhhccccccchHHHHHHHHHHHHHHHHHHHHHHHHhhCCceecHHHhhhhcc
Confidence 45889999874 34567777766444444444444444455567889999999999999997
No 33
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=93.68 E-value=0.17 Score=38.78 Aligned_cols=60 Identities=25% Similarity=0.298 Sum_probs=51.1
Q ss_pred HHHHHhhhccCCCCcchhhHHHHHhHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHH
Q 033083 62 YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVR 121 (128)
Q Consensus 62 YIyKVLKQVhPd~gISskAM~IMnSfVnDiFErIA~EAs~La~~nkk~TltsREIQtAVR 121 (128)
-|.|+||.-.-.+.|+++|.--+...+..+.-.|-+-|.+.++-|++.-|+.|.||-|+|
T Consensus 31 rvkr~lk~~~~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~kkkri~PrHlqlAIr 90 (132)
T COG5262 31 RVKRLLKKGNYRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRIIPRHLQLAIR 90 (132)
T ss_pred HHHHHHHcCccceeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhcCcceechHHHHHHhc
Confidence 488999966667889999988777777777777777788888999999999999999987
No 34
>PLN00121 histone H3; Provisional
Probab=93.67 E-value=0.31 Score=37.47 Aligned_cols=66 Identities=18% Similarity=0.237 Sum_probs=53.5
Q ss_pred hhhHHHHHHHhhhccCCCCcchhhHHHHHhHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHHh
Q 033083 57 ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRL 122 (128)
Q Consensus 57 esys~YIyKVLKQVhPd~gISskAM~IMnSfVnDiFErIA~EAs~La~~nkk~TltsREIQtAVRL 122 (128)
-.|...+..+.....+++-+.+.|+.-|.--..+.+-.+-+++...+.+.+|-||..+|||-+.||
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 456777777777777888899999988876666666666667888999999999999999999875
No 35
>PTZ00018 histone H3; Provisional
Probab=93.13 E-value=0.43 Score=36.76 Aligned_cols=66 Identities=18% Similarity=0.237 Sum_probs=53.0
Q ss_pred hhhHHHHHHHhhhccCCCCcchhhHHHHHhHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHHh
Q 033083 57 ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRL 122 (128)
Q Consensus 57 esys~YIyKVLKQVhPd~gISskAM~IMnSfVnDiFErIA~EAs~La~~nkk~TltsREIQtAVRL 122 (128)
-.|...+..|..+..+++-+.+.|+..|.--..+.+-.+-+++...+.+.+|-||..+|||-+.||
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 456666777776767888999999988876666666666667888899999999999999999875
No 36
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=92.55 E-value=0.38 Score=33.42 Aligned_cols=58 Identities=14% Similarity=0.314 Sum_probs=46.5
Q ss_pred HHHHhhhc--cCCCCcchhhHHHHHhHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHH
Q 033083 63 IFKVLKQV--HPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAV 120 (128)
Q Consensus 63 IyKVLKQV--hPd~gISskAM~IMnSfVnDiFErIA~EAs~La~~nkk~TltsREIQtAV 120 (128)
+-++..++ ..+..+|.+.++.|--++.+..+.++.+---+|++-+|+||+..|+.=.+
T Consensus 11 v~ki~ee~~~~~~~~~s~~~i~al~ELv~~q~~~~a~DLe~FAkHA~R~tI~~dDV~Ll~ 70 (76)
T PF15630_consen 11 VGKIVEEEAKEKGVEVSPQFIAALTELVYKQLENLAKDLEAFAKHAGRSTINMDDVKLLA 70 (76)
T ss_dssp HHHHHHHCCCCTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHT
T ss_pred HHHHHHHHHhccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHHHh
Confidence 44555665 45677999999999999999999999999999999999999999976443
No 37
>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=91.88 E-value=1.4 Score=29.43 Aligned_cols=63 Identities=13% Similarity=0.252 Sum_probs=49.3
Q ss_pred HHHHHHHhhhccCCC---CcchhhHHHHHhHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHHh
Q 033083 60 KIYIFKVLKQVHPDI---GISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRL 122 (128)
Q Consensus 60 s~YIyKVLKQVhPd~---gISskAM~IMnSfVnDiFErIA~EAs~La~~nkk~TltsREIQtAVRL 122 (128)
...+.++.-|+.-.. +++..|++++..++.+.+..|+..+...+...+|...+..||..|..-
T Consensus 5 ~~~l~~~va~il~~~GF~~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~~ 70 (77)
T PF07524_consen 5 RSLLRRSVAQILKHAGFDSASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPNLQDVEQALEE 70 (77)
T ss_pred HHHHHHHHHHHHHHcCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence 333344444443333 477889999999999999999999999999999999999999988753
No 38
>KOG1756 consensus Histone 2A [Chromatin structure and dynamics]
Probab=91.29 E-value=0.67 Score=35.70 Aligned_cols=60 Identities=25% Similarity=0.306 Sum_probs=43.2
Q ss_pred HHHHHhhhccCCCCcchhhHHHHHhHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHH
Q 033083 62 YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVR 121 (128)
Q Consensus 62 YIyKVLKQVhPd~gISskAM~IMnSfVnDiFErIA~EAs~La~~nkk~TltsREIQtAVR 121 (128)
-|.|.||.-+--..||+-|--.|--.+..+--.|-+-|..-++-|++.-|++|.||-|++
T Consensus 32 ri~r~Lr~~~~~~ri~~gapV~laavLeYL~Aeile~agnaardnkk~ri~PrH~~lAI~ 91 (131)
T KOG1756|consen 32 RIHRLLRKGRYAQRVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRITPRHLQLAIR 91 (131)
T ss_pred HHHHHHHccchhhhccCCChHHHHHHHHHHHHHHHHHhHHHhhhcCccccChHHHHHHHh
Confidence 588999997667788888766544433333333333445556889999999999999997
No 39
>PLN00161 histone H3; Provisional
Probab=89.83 E-value=2 Score=33.19 Aligned_cols=66 Identities=15% Similarity=0.210 Sum_probs=49.7
Q ss_pred hhhHHHHHHHhhhccC-CCCcchhhHHHHHhHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHHh
Q 033083 57 ETYKIYIFKVLKQVHP-DIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRL 122 (128)
Q Consensus 57 esys~YIyKVLKQVhP-d~gISskAM~IMnSfVnDiFErIA~EAs~La~~nkk~TltsREIQtAVRL 122 (128)
-.|+..+..|..+..+ |+-+.+.|+.-|..-..+.+-.+-+++.-.+.+-+|-||..+|||-|.||
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 4566666666655544 57889999888876655555555567778889999999999999999885
No 40
>PF15511 CENP-T: Centromere kinetochore component CENP-T; PDB: 3B0D_T 3B0C_T 3VH5_T 3VH6_T.
Probab=88.59 E-value=1.1 Score=39.20 Aligned_cols=55 Identities=18% Similarity=0.252 Sum_probs=41.1
Q ss_pred HHHHHHhhhc-----cCCCCcchhhHHHHHhHHHHHHHHHHHHHhhHHhhCCCCCCChhH
Q 033083 61 IYIFKVLKQV-----HPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSRE 115 (128)
Q Consensus 61 ~YIyKVLKQV-----hPd~gISskAM~IMnSfVnDiFErIA~EAs~La~~nkk~TltsRE 115 (128)
.+|.+++... +-.+.||..||..+....+.+||.|+..-.-.|.+-+|+||...|
T Consensus 355 ~~vK~la~~~ak~s~~sK~kiskdal~aleqasdwfFeQl~dDL~aYA~HAgRKTIdesD 414 (414)
T PF15511_consen 355 GVVKKLAQHFAKSSGGSKMKISKDALEALEQASDWFFEQLGDDLEAYAKHAGRKTIDESD 414 (414)
T ss_dssp HHHHHHHHHHH-------S-B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHH
T ss_pred cHHHHHHHHHHHhhcccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCCCC
Confidence 3455555544 345789999999999999999999999999999999999998654
No 41
>PLN00160 histone H3; Provisional
Probab=87.15 E-value=3.9 Score=29.85 Aligned_cols=66 Identities=14% Similarity=0.142 Sum_probs=47.5
Q ss_pred hhhHHHHHHHhhhccC-CCCcchhhHHHHHhHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHHh
Q 033083 57 ETYKIYIFKVLKQVHP-DIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRL 122 (128)
Q Consensus 57 esys~YIyKVLKQVhP-d~gISskAM~IMnSfVnDiFErIA~EAs~La~~nkk~TltsREIQtAVRL 122 (128)
-.|...+..+...... +.-+.+.|+.-|.--..+.+-.+=+.+.-.+.+.+|-||..+|||-+.||
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 4455555555544433 37788888888776555555555557777889999999999999999874
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=86.88 E-value=1.8 Score=32.72 Aligned_cols=60 Identities=18% Similarity=0.309 Sum_probs=41.1
Q ss_pred HHHHHHhhhccCCCCcch---hhHHHHHhHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHHhhc
Q 033083 61 IYIFKVLKQVHPDIGISS---KAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLVL 124 (128)
Q Consensus 61 ~YIyKVLKQVhPd~gISs---kAM~IMnSfVnDiFErIA~EAs~La~~nkk~TltsREIQtAVRLlL 124 (128)
..|.-+|+. +||+. +....|-.|+.-..-.|-.+|..++.+.++.+|+..||+-|+...+
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 345555554 56654 5666666676666677778899999999999999999999998543
No 43
>KOG2549 consensus Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=85.82 E-value=2.1 Score=39.76 Aligned_cols=48 Identities=15% Similarity=0.293 Sum_probs=43.3
Q ss_pred cchhhHHHHHhHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHHhh
Q 033083 76 ISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLV 123 (128)
Q Consensus 76 ISskAM~IMnSfVnDiFErIA~EAs~La~~nkk~TltsREIQtAVRLl 123 (128)
|+.++-.+|---|..=.+.|+.+|+++.+..+|.+||.+||.-|.|.+
T Consensus 29 l~deaa~~La~dv~yrikEI~Q~aaKfm~hskR~kLtv~DV~~ALr~~ 76 (576)
T KOG2549|consen 29 LNDEAALLLAEDVEYRIKEIVQDAAKFMVHSKRTKLTVDDVDYALRSL 76 (576)
T ss_pred cCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcCcHHHHHHHHhhc
Confidence 667888888888888889999999999999999999999999999864
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=84.84 E-value=1.2 Score=31.45 Aligned_cols=46 Identities=15% Similarity=0.265 Sum_probs=23.0
Q ss_pred cchhhHHHHHhHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHH
Q 033083 76 ISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVR 121 (128)
Q Consensus 76 ISskAM~IMnSfVnDiFErIA~EAs~La~~nkk~TltsREIQtAVR 121 (128)
-+.++..+|..+|.+-.-.+..+|..+|...++..|+..||-.++|
T Consensus 20 P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~rg~~~i~~eDl~F~lR 65 (93)
T PF02269_consen 20 PLPETVDLVEDIVREYIIELCQEAMEVAQRRGSKKIKVEDLLFLLR 65 (93)
T ss_dssp --HHHHHHHHHHHHHHHHHHHHHHHC--------------------
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCcCcHHHHHHHHh
Confidence 5668999999999999999999999999999999999999988877
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=84.69 E-value=7.5 Score=27.38 Aligned_cols=60 Identities=13% Similarity=0.203 Sum_probs=46.8
Q ss_pred HHHHhhhccCCCCcchhhHHHHHhHHHHHHHHHHHHHhhHHhhCCC---CCCChhHHHHHHHhh
Q 033083 63 IFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKK---PTITSREIQTAVRLV 123 (128)
Q Consensus 63 IyKVLKQVhPd~gISskAM~IMnSfVnDiFErIA~EAs~La~~nkk---~TltsREIQtAVRLl 123 (128)
|.|++.++-. ..++.....+|..+-.-+.-.|.++|..+..-... ..|.++.|+.|+|.+
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 6667777654 67777777777777666777888899988776554 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=80.74 E-value=7.1 Score=27.79 Aligned_cols=45 Identities=9% Similarity=0.295 Sum_probs=39.3
Q ss_pred cchhhHHHHHhHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHH
Q 033083 76 ISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVR 121 (128)
Q Consensus 76 ISskAM~IMnSfVnDiFErIA~EAs~La~~nkk~TltsREIQtAVR 121 (128)
-..++..+|..+|.+..-.|..+|..+|. .++.-++..||-.++|
T Consensus 21 P~~eTv~llE~iv~~~i~~l~~~a~~~A~-~r~~k~~~eD~~FliR 65 (92)
T cd07978 21 PLPETVDLLEDIVVEYIIELCHKAAEVAQ-RRRGKVKVEDLIFLLR 65 (92)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHH-cCCCCCCHHHHHHHHh
Confidence 45689999999999999999999999998 5555669999998887
No 47
>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=78.81 E-value=7.9 Score=35.40 Aligned_cols=59 Identities=22% Similarity=0.396 Sum_probs=44.3
Q ss_pred hhccCCCCcchhhHHHHHhHHHHH-------HHHHHHHHhhHHhhCCCCCCChhHHHHHHHhhcCC
Q 033083 68 KQVHPDIGISSKAMGIMNSFINDI-------FEKLAQEASRLARYNKKPTITSREIQTAVRLVLPA 126 (128)
Q Consensus 68 KQVhPd~gISskAM~IMnSfVnDi-------FErIA~EAs~La~~nkk~TltsREIQtAVRLlLPG 126 (128)
++..++..|+...+..+..+...+ ...+..-|--+|..+.+.+++..||+.|++|+|+.
T Consensus 242 r~~~~~V~is~~~~~~l~~~~~~~~i~s~Ra~i~~~r~Ara~AaL~gr~~V~~~Dv~~A~~lvL~h 307 (633)
T TIGR02442 242 RSLLPSVRISDSLIRFISELCIEFGVDGHRADIVMARAARALAALDGRRRVTAEDVREAAELVLPH 307 (633)
T ss_pred HHhCCCCCCCHHHHHHHHHHHHHhCCCCccHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHHHhhh
Confidence 345677888888887776666443 12344445568899999999999999999999963
No 48
>PRK09522 bifunctional glutamine amidotransferase/anthranilate phosphoribosyltransferase; Provisional
Probab=78.33 E-value=4.4 Score=36.65 Aligned_cols=59 Identities=15% Similarity=0.250 Sum_probs=41.5
Q ss_pred hccCCCCcchhhHHHHHhHHHHHHHHHHHH---HhhHHhhCCCCCCChhHHHHHHHhhcCCC
Q 033083 69 QVHPDIGISSKAMGIMNSFINDIFEKLAQE---ASRLARYNKKPTITSREIQTAVRLVLPAS 127 (128)
Q Consensus 69 QVhPd~gISskAM~IMnSfVnDiFErIA~E---As~La~~nkk~TltsREIQtAVRLlLPGE 127 (128)
|-||+.-.|...+.||.+|++-.+...-.+ ..-|-+......||..|...++..+|-|+
T Consensus 168 QFHPEs~~T~~G~~il~NFl~~~~~~~~~~~~~~~~l~~~~~~~~Lt~eea~~~~~~il~g~ 229 (531)
T PRK09522 168 QFHPESILTTQGARLLEQTLAWAQQKLEPTNTLQPILEKLYQAQTLSQQESHQLFSAVVRGE 229 (531)
T ss_pred EecCccccCcchHHHHHHHHHHHhhcCCCCCCHHHHHHHhhcCCCCCHHHHHHHHHHHHcCC
Confidence 779999999999999999985433210000 01122222456999999999999999886
No 49
>COG1466 HolA DNA polymerase III, delta subunit [DNA replication, recombination, and repair]
Probab=75.48 E-value=10 Score=31.51 Aligned_cols=64 Identities=22% Similarity=0.292 Sum_probs=55.3
Q ss_pred hhhHHHHHHHhhhccCCCCcchhhHHHHHhHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHHh
Q 033083 57 ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRL 122 (128)
Q Consensus 57 esys~YIyKVLKQVhPd~gISskAM~IMnSfVnDiFErIA~EAs~La~~nkk~TltsREIQtAVRL 122 (128)
+..-.+|-+.+++. ++.|+..|+..+..-++.=+--|+.|-.+|+.|..-.+||..+|+..|--
T Consensus 143 ~~l~~~i~~~~~~~--~l~i~~~a~~~L~~~~~~nl~~i~~Ei~KL~l~~~~~~I~~~~V~~~v~~ 206 (334)
T COG1466 143 AELPQWIKKRAKEL--GLKIDQEAIQLLLEALGGNLLAIAQEIEKLALYAGDKEITLEDVEEVVSD 206 (334)
T ss_pred HHHHHHHHHHHHHc--CCCCCHHHHHHHHHHhCCcHHHHHHHHHHHHHhCCCCcCCHHHHHHHHhc
Confidence 34566788888876 48899999999999998888889999999999999889999999998753
No 50
>PF14687 DUF4460: Domain of unknown function (DUF4460)
Probab=74.16 E-value=4.2 Score=29.91 Aligned_cols=37 Identities=16% Similarity=0.428 Sum_probs=30.5
Q ss_pred hhHHHHHHHhhhccCCCC--------cchhhHHHHHhHHHHHHHH
Q 033083 58 TYKIYIFKVLKQVHPDIG--------ISSKAMGIMNSFINDIFEK 94 (128)
Q Consensus 58 sys~YIyKVLKQVhPd~g--------ISskAM~IMnSfVnDiFEr 94 (128)
.....+...+..||||+= +-.+++.++|+++.++..+
T Consensus 10 ~l~~aLr~Fy~~VHPDlF~~~P~~k~~Ne~SLk~Ln~~Ld~l~~~ 54 (112)
T PF14687_consen 10 DLRSALRPFYFAVHPDLFGQHPEEKQVNEESLKLLNSYLDSLKKR 54 (112)
T ss_pred HHHHHHHHHHHHhCCcccccChHHHHhhHHHHHHHHHHHHHHhcc
Confidence 456778888899999942 6678999999999888875
No 51
>TIGR01128 holA DNA polymerase III, delta subunit. subunit around DNA forming a DNA sliding clamp.
Probab=73.14 E-value=19 Score=28.37 Aligned_cols=63 Identities=24% Similarity=0.378 Sum_probs=49.7
Q ss_pred hhhHHHHHHHhhhccCCCCcchhhHHHHHhHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHH
Q 033083 57 ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVR 121 (128)
Q Consensus 57 esys~YIyKVLKQVhPd~gISskAM~IMnSfVnDiFErIA~EAs~La~~nkk~TltsREIQtAVR 121 (128)
.....||...+++. +..|+..+...+-+.++.=...+..|.-+|+.|....+||..+|+..+.
T Consensus 114 ~~~~~~i~~~~~~~--g~~i~~~a~~~l~~~~~~d~~~l~~el~KL~~~~~~~~It~e~I~~~~~ 176 (302)
T TIGR01128 114 QELPRWIQARLKKL--GLRIDPDAVQLLAELVEGNLLAIAQELEKLALYAPDGKITLEDVEEAVS 176 (302)
T ss_pred HHHHHHHHHHHHHc--CCCCCHHHHHHHHHHhCcHHHHHHHHHHHHHhhCCCCCCCHHHHHHHHh
Confidence 34556777777765 5779999999888888755667899999999997666899999987654
No 52
>smart00350 MCM minichromosome maintenance proteins.
Probab=72.79 E-value=17 Score=32.26 Aligned_cols=66 Identities=18% Similarity=0.286 Sum_probs=46.8
Q ss_pred hhhHHHHHHHhhhccCCCCcchhhHHHHHhHHHHHH-------------------HHHHHHHhhHHhhCCCCCCChhHHH
Q 033083 57 ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIF-------------------EKLAQEASRLARYNKKPTITSREIQ 117 (128)
Q Consensus 57 esys~YIyKVLKQVhPd~gISskAM~IMnSfVnDiF-------------------ErIA~EAs~La~~nkk~TltsREIQ 117 (128)
+....||.-+=..++|. ||..++.++..|..++= |-|..=|--+|+...+.+++..|+.
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 44566765553337776 68888887777765543 3333444457888999999999999
Q ss_pred HHHHhhc
Q 033083 118 TAVRLVL 124 (128)
Q Consensus 118 tAVRLlL 124 (128)
.|++|+.
T Consensus 499 ~ai~l~~ 505 (509)
T smart00350 499 EAIRLLR 505 (509)
T ss_pred HHHHHHH
Confidence 9999984
No 53
>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=72.32 E-value=25 Score=25.17 Aligned_cols=62 Identities=15% Similarity=0.201 Sum_probs=38.9
Q ss_pred HHHHHhhhccCCCCcchhhHHHHHhHHHHHHHHHHHHHhhHHhh-CCCCCCChhHHHHHHHhh
Q 033083 62 YIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARY-NKKPTITSREIQTAVRLV 123 (128)
Q Consensus 62 YIyKVLKQVhPd~gISskAM~IMnSfVnDiFErIA~EAs~La~~-nkk~TltsREIQtAVRLl 123 (128)
=|.|+..++-.+..+|....-+|..+-.=+.-.|.++|..+..- +.-..|...+|..|.|-|
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 38888888886688888777777665555555566667665543 444599999999999854
No 54
>PRK07452 DNA polymerase III subunit delta; Validated
Probab=72.13 E-value=15 Score=29.80 Aligned_cols=61 Identities=18% Similarity=0.342 Sum_probs=49.7
Q ss_pred hHHHHHHHhhhccCCCCcchhhHHHHHhHHHHHHHHHHHHHhhHHhh--CCCCCCChhHHHHHHH
Q 033083 59 YKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARY--NKKPTITSREIQTAVR 121 (128)
Q Consensus 59 ys~YIyKVLKQVhPd~gISskAM~IMnSfVnDiFErIA~EAs~La~~--nkk~TltsREIQtAVR 121 (128)
...||...+++- +..|+..|...+-..+..=+-++..|.-+|+.| ....+||..+|+..|-
T Consensus 135 l~~~i~~~~~~~--g~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~~It~~~V~~~v~ 197 (326)
T PRK07452 135 LKQLVERTAQEL--GVKLTPEAAELLAEAVGNDSRRLYNELEKLALYAENSTKPISAEEVKALVS 197 (326)
T ss_pred HHHHHHHHHHHc--CCCCCHHHHHHHHHHhCccHHHHHHHHHHHHHhccCCCCccCHHHHHHHhc
Confidence 445666666554 577999999999988887778999999999999 5678999999998764
No 55
>PRK08487 DNA polymerase III subunit delta; Validated
Probab=71.93 E-value=14 Score=30.56 Aligned_cols=59 Identities=24% Similarity=0.236 Sum_probs=50.4
Q ss_pred hHHHHHHHhhhccCCCCcchhhHHHHHhHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHH
Q 033083 59 YKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVR 121 (128)
Q Consensus 59 ys~YIyKVLKQVhPd~gISskAM~IMnSfVnDiFErIA~EAs~La~~nkk~TltsREIQtAVR 121 (128)
...+|...+++- +..|+..|+..+...+..=+..|..|--+|+.|.+ +||..+|+..|-
T Consensus 140 l~~~i~~~~~~~--g~~i~~~a~~~L~~~~g~dl~~l~~ELeKL~ly~~--~It~edV~~~v~ 198 (328)
T PRK08487 140 ALELLQERAKEL--GLDIDQNALNHLYFIHNEDLALAANELEKLAILNE--PITLKDIQELVF 198 (328)
T ss_pred HHHHHHHHHHHh--CCCCCHHHHHHHHHHhCcHHHHHHHHHHHHHHhcC--CCCHHHHHHHhc
Confidence 456788888875 47799999999999888888899999999999965 799999998763
No 56
>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=70.79 E-value=4.9 Score=35.86 Aligned_cols=60 Identities=27% Similarity=0.340 Sum_probs=47.0
Q ss_pred HHHhhhccCCCCcchhhHHHHHhHHHHHHH---HHHHHHhhHHhhCCCCCCChhHHHHHHHhh
Q 033083 64 FKVLKQVHPDIGISSKAMGIMNSFINDIFE---KLAQEASRLARYNKKPTITSREIQTAVRLV 123 (128)
Q Consensus 64 yKVLKQVhPd~gISskAM~IMnSfVnDiFE---rIA~EAs~La~~nkk~TltsREIQtAVRLl 123 (128)
.--||.|-.-.||+.=.=+.+.-+-.|+=- .|..||+++....+|..||..||..|.|-+
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 455777777789887655555555555544 468899999999999999999999999854
No 57
>PRK05574 holA DNA polymerase III subunit delta; Reviewed
Probab=70.57 E-value=21 Score=28.66 Aligned_cols=63 Identities=25% Similarity=0.304 Sum_probs=50.0
Q ss_pred hhhHHHHHHHhhhccCCCCcchhhHHHHHhHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHH
Q 033083 57 ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVR 121 (128)
Q Consensus 57 esys~YIyKVLKQVhPd~gISskAM~IMnSfVnDiFErIA~EAs~La~~nkk~TltsREIQtAVR 121 (128)
.....||...+++. +..|+..|+..|-..++.=+..+..|.-+|+.|.....||..+|+..+-
T Consensus 149 ~~~~~~i~~~~~~~--g~~i~~~a~~~L~~~~~~d~~~l~~El~KL~l~~~~~~It~~~I~~~i~ 211 (340)
T PRK05574 149 AELPQWIQQRLKQQ--GLQIDAAALQLLAERVEGNLLALAQELEKLALLYPDGKITLEDVEEAVP 211 (340)
T ss_pred HHHHHHHHHHHHHc--CCCCCHHHHHHHHHHhCchHHHHHHHHHHHHhhcCCCCCCHHHHHHHHh
Confidence 44667777777764 4679999999988888777778999999999997444499999987654
No 58
>KOG3334 consensus Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=68.78 E-value=18 Score=28.45 Aligned_cols=58 Identities=17% Similarity=0.334 Sum_probs=40.8
Q ss_pred HhhhccCCCCcch---hhHHHHHhHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHHhh
Q 033083 66 VLKQVHPDIGISS---KAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLV 123 (128)
Q Consensus 66 VLKQVhPd~gISs---kAM~IMnSfVnDiFErIA~EAs~La~~nkk~TltsREIQtAVRLl 123 (128)
|+.++-.++||.. +-+.-|=-|-.--.-.|-..|.-++.+.++.||+..||+.|++..
T Consensus 18 ~i~~iL~s~GI~eyEprVi~qlLefa~rYtt~vL~DA~vys~HA~ka~i~~eDVrlA~~~~ 78 (148)
T KOG3334|consen 18 VIASILKSLGIQEYEPRVINQLLEFAYRYTTTVLDDAKVYSSHAKKATIDAEDVRLAIQMR 78 (148)
T ss_pred HHHHHHHHcCccccChHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcHHHHHHHHHHH
Confidence 3344444567755 344444444444556778889999999999999999999998754
No 59
>PRK14607 bifunctional glutamine amidotransferase/anthranilate phosphoribosyltransferase; Provisional
Probab=68.59 E-value=9 Score=34.43 Aligned_cols=58 Identities=17% Similarity=0.271 Sum_probs=41.5
Q ss_pred hccCCCCcchhhHHHHHhHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHHhhcCCC
Q 033083 69 QVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLVLPAS 127 (128)
Q Consensus 69 QVhPd~gISskAM~IMnSfVnDiFErIA~EAs~La~~nkk~TltsREIQtAVRLlLPGE 127 (128)
|-||+...+.....|++.|++-..+.+.- ..-|-..-....||..|+..+++.+|=|+
T Consensus 167 QFHPE~~~t~~g~~i~~nFl~~~~~~~~~-~~~i~~l~~g~~Lt~~ea~~~~~~il~g~ 224 (534)
T PRK14607 167 QFHPESILTEEGKRILKNFLNYQREEIDI-KSYLKKLVEGEDLSFEEAEDVMEDITDGN 224 (534)
T ss_pred EeCCCCCCChhHHHHHHHHHHHhhccCCH-HHHHHHhccCCCCCHHHHHHHHHHHHcCC
Confidence 78999877888889999998754332211 11233333456999999999999999876
No 60
>smart00271 DnaJ DnaJ molecular chaperone homology domain.
Probab=64.40 E-value=17 Score=22.15 Aligned_cols=17 Identities=24% Similarity=0.165 Sum_probs=13.0
Q ss_pred HHHHHHhhhccCCCCcc
Q 033083 61 IYIFKVLKQVHPDIGIS 77 (128)
Q Consensus 61 ~YIyKVLKQVhPd~gIS 77 (128)
.-.++..++.|||..-.
T Consensus 20 ~ay~~l~~~~HPD~~~~ 36 (60)
T smart00271 20 KAYRKLALKYHPDKNPG 36 (60)
T ss_pred HHHHHHHHHHCcCCCCC
Confidence 33567789999998874
No 61
>PRK06585 holA DNA polymerase III subunit delta; Reviewed
Probab=63.92 E-value=21 Score=29.18 Aligned_cols=62 Identities=19% Similarity=0.227 Sum_probs=49.9
Q ss_pred hhHHHHHHHhhhccCCCCcchhhHHHHHhHHHHHHHHHHHHHhhHHhhCC-CCCCChhHHHHHHH
Q 033083 58 TYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNK-KPTITSREIQTAVR 121 (128)
Q Consensus 58 sys~YIyKVLKQVhPd~gISskAM~IMnSfVnDiFErIA~EAs~La~~nk-k~TltsREIQtAVR 121 (128)
....||.+.+++- +..|+..|+..+-..+..=+..+..|--+|+.|.. ..+||..+|+..|-
T Consensus 146 ~l~~~i~~~~~~~--g~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~It~edV~~lv~ 208 (343)
T PRK06585 146 DLARLIDDELAEA--GLRITPDARALLVALLGGDRLASRNEIEKLALYAHGKGEITLDDVRAVVG 208 (343)
T ss_pred HHHHHHHHHHHHC--CCCCCHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHhC
Confidence 3456677777665 47799999999888888888899999999999954 56899999987653
No 62
>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=63.27 E-value=40 Score=26.02 Aligned_cols=67 Identities=18% Similarity=0.201 Sum_probs=49.6
Q ss_pred hhhHHHHHHHhhhccC--CCCcchhhHHHHHhHHHH---HHHHHHHHHhhHHhhCCCCCCChhHHHHHHHhh
Q 033083 57 ETYKIYIFKVLKQVHP--DIGISSKAMGIMNSFIND---IFEKLAQEASRLARYNKKPTITSREIQTAVRLV 123 (128)
Q Consensus 57 esys~YIyKVLKQVhP--d~gISskAM~IMnSfVnD---iFErIA~EAs~La~~nkk~TltsREIQtAVRLl 123 (128)
+....|+...|.+... +..+|.+++..+-....- .+..++..+...+..++..+|+...|..+++-+
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 356888888777666554 455666777666777888999999999998764
No 63
>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=62.60 E-value=18 Score=24.25 Aligned_cols=34 Identities=26% Similarity=0.431 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHHhh
Q 033083 87 FINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLV 123 (128)
Q Consensus 87 fVnDiFErIA~EAs~La~~nkk~TltsREIQtAVRLl 123 (128)
++|.|+-.+..||.+|+.-. ..|.+||.++++..
T Consensus 3 i~nRl~~~~~~ea~~l~~eg---vas~~~ID~~~~~~ 36 (97)
T PF00725_consen 3 IVNRLLAALLNEAARLVEEG---VASPEDIDRAMRYG 36 (97)
T ss_dssp THHHHHHHHHHHHHHHHHTT---SSSHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHc---CCCHHHHHHHHHHh
Confidence 57888899999999999865 46899999999873
No 64
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=61.10 E-value=14 Score=31.33 Aligned_cols=58 Identities=34% Similarity=0.352 Sum_probs=40.7
Q ss_pred HHHHhhhccCCCCcchhhHHHHHhHHHHHH-HHHHHHHhhHHhhCCCCCCChhHHHHHHH
Q 033083 63 IFKVLKQVHPDIGISSKAMGIMNSFINDIF-EKLAQEASRLARYNKKPTITSREIQTAVR 121 (128)
Q Consensus 63 IyKVLKQVhPd~gISskAM~IMnSfVnDiF-ErIA~EAs~La~~nkk~TltsREIQtAVR 121 (128)
|.||.|-------||++|= |+=+.+..|| +.|.-.|...+.-|+|+||---||-.||.
T Consensus 115 IkkvMKtdedVkMisaEaP-vlFak~~EiFI~ELTmRAW~~ae~NkRRtLQksDia~Av~ 173 (286)
T COG5208 115 IKKVMKTDEDVKMISAEAP-VLFAKITEIFIEELTMRAWINAEENKRRTLQKSDIAAAVK 173 (286)
T ss_pred HHHHHhcccchhheecccc-hHHHHHHHHHHHHHHHHHHHHHhHhhhhHHHHHHHHHHHH
Confidence 4455543221124777764 4445555555 67888899999999999999999999986
No 65
>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=59.74 E-value=21 Score=21.18 Aligned_cols=17 Identities=24% Similarity=0.167 Sum_probs=13.4
Q ss_pred HHHHHHhhhccCCCCcc
Q 033083 61 IYIFKVLKQVHPDIGIS 77 (128)
Q Consensus 61 ~YIyKVLKQVhPd~gIS 77 (128)
.-.+++.++.|||..-+
T Consensus 19 ~~y~~l~~~~HPD~~~~ 35 (55)
T cd06257 19 KAYRKLALKYHPDKNPD 35 (55)
T ss_pred HHHHHHHHHHCcCCCCC
Confidence 33567889999999876
No 66
>PRK05907 hypothetical protein; Provisional
Probab=58.73 E-value=23 Score=29.78 Aligned_cols=59 Identities=20% Similarity=0.277 Sum_probs=45.0
Q ss_pred hHHHHHHHhhhccCCCCcchhhHHHHHhHH--HHHHHHHHHHHhhHHhh-CCCCCCChhHHHHHH
Q 033083 59 YKIYIFKVLKQVHPDIGISSKAMGIMNSFI--NDIFEKLAQEASRLARY-NKKPTITSREIQTAV 120 (128)
Q Consensus 59 ys~YIyKVLKQVhPd~gISskAM~IMnSfV--nDiFErIA~EAs~La~~-nkk~TltsREIQtAV 120 (128)
...||-+.+++- +..|+..|+..+..-+ +|++ .|..|--+|+.| ....+||..+|+..|
T Consensus 139 L~~Wi~~~~~~~--g~~i~~~a~~~L~~~~~~~nL~-~l~~EleKL~ly~g~~~~It~e~V~~lv 200 (311)
T PRK05907 139 IAQLLIQRAKEL--GISCSLGLASLFVSKFPQTGLF-EILSEFQKLLCQMGKKESLEASDIQSFV 200 (311)
T ss_pred HHHHHHHHHHHc--CCCcCHHHHHHHHHHccCCCHH-HHHHHHHHHHHhcCCCCeECHHHHHHHh
Confidence 355566555554 3679999988777755 4554 899999999999 668899999998765
No 67
>PRK07914 hypothetical protein; Reviewed
Probab=58.59 E-value=29 Score=28.55 Aligned_cols=58 Identities=9% Similarity=0.179 Sum_probs=46.3
Q ss_pred HHHHHHHhhhccCCCCcchhhHHHHHhHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHH
Q 033083 60 KIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAV 120 (128)
Q Consensus 60 s~YIyKVLKQVhPd~gISskAM~IMnSfVnDiFErIA~EAs~La~~nkk~TltsREIQtAV 120 (128)
..+|-..+++- +..|+..|+..|-..+.+=+..|..|.-+|+.|.. .+||..+|+.-|
T Consensus 134 ~~wi~~~a~~~--g~~i~~~A~~~L~~~~g~dl~~l~~EleKL~~~~~-~~It~e~V~~~v 191 (320)
T PRK07914 134 ADFVRKEFRSL--RVKVDDDTVTALLDAVGSDLRELASACSQLVADTG-GAVDAAAVRRYH 191 (320)
T ss_pred HHHHHHHHHHc--CCCCCHHHHHHHHHHHCccHHHHHHHHHHHhcCCC-CCcCHHHHHHHc
Confidence 55666666654 46699999999999997677889999999987755 579999988765
No 68
>KOG0568 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=57.04 E-value=23 Score=30.60 Aligned_cols=48 Identities=38% Similarity=0.596 Sum_probs=29.1
Q ss_pred HHHHhhhccCCCCcchhhHHHHHhH--HHHHHHHHHHHHhhHHhhCCCCCCChhH
Q 033083 63 IFKVLKQVHPDIGISSKAMGIMNSF--INDIFEKLAQEASRLARYNKKPTITSRE 115 (128)
Q Consensus 63 IyKVLKQVhPd~gISskAM~IMnSf--VnDiFErIA~EAs~La~~nkk~TltsRE 115 (128)
+..+.||||||.|-.. |-+ ..| |..-|.++-.| .++..|.++.+...|
T Consensus 68 f~~lakq~hpdsgs~~-ada--a~f~qideafrkvlq~--~~~ktn~~qn~~ede 117 (342)
T KOG0568|consen 68 FHDLAKQVHPDSGSEE-ADA--ARFIQIDEAFRKVLQE--KFAKTNARQNIGEDE 117 (342)
T ss_pred HHHHHHHcCCCCCCcc-ccH--HHHHHHHHHHHHHHHH--HHHHhhhccccccch
Confidence 5778899999998432 111 122 34445555444 356677777777655
No 69
>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=55.71 E-value=29 Score=23.75 Aligned_cols=56 Identities=13% Similarity=0.217 Sum_probs=30.6
Q ss_pred HHHHhhhc--cCCCCcchhhHHHHHhHHHHHHHHHHHHHhhHHhhCCCCC-CChhHHHH
Q 033083 63 IFKVLKQV--HPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPT-ITSREIQT 118 (128)
Q Consensus 63 IyKVLKQV--hPd~gISskAM~IMnSfVnDiFErIA~EAs~La~~nkk~T-ltsREIQt 118 (128)
|-|+|..- ++.+.||..|+..+.-+++=+..--...|...++-.+... |...+++.
T Consensus 5 i~rll~~~f~~~~tkIs~dal~l~~eyl~iFV~EAv~Ra~~~a~~e~~~~~le~e~LEk 63 (72)
T PF09415_consen 5 IARLLHEHFKDDKTKISKDALKLSAEYLRIFVREAVARAAEQAEAEGDEGFLEVEHLEK 63 (72)
T ss_dssp HHHHHCTTSSSTT-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSEE-HHHHHH
T ss_pred HHHHHHHHhcCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHH
Confidence 56777753 4678899998876555443222223333334455566666 88888775
No 70
>KOG1745 consensus Histones H3 and H4 [Chromatin structure and dynamics]
Probab=54.26 E-value=16 Score=28.30 Aligned_cols=49 Identities=27% Similarity=0.417 Sum_probs=32.0
Q ss_pred cCCCCcchhhHHHHHh----HHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHHhh
Q 033083 71 HPDIGISSKAMGIMNS----FINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLV 123 (128)
Q Consensus 71 hPd~gISskAM~IMnS----fVnDiFErIA~EAs~La~~nkk~TltsREIQtAVRLl 123 (128)
-+|+-+-|-|+.-+-- |+-++||- ..-.+.+.++-||-..|||-|.|+-
T Consensus 81 ~~dLrfqs~Ai~ALQeA~EayLv~LfEd----tnlcAihAkRVTimpkdiQlArrir 133 (137)
T KOG1745|consen 81 KTDLRFQSSAIAALQEAAEAYLVGLFED----TNLCAIHAKRVTIMPKDIQLARRIR 133 (137)
T ss_pred cccceehHHHHHHHHHHHHHHHHHhccc----cchhhhccceeEecccceehhhhcc
Confidence 5566666665554432 33344443 2345667899999999999999953
No 71
>PF03477 ATP-cone: ATP cone domain; InterPro: IPR005144 The ATP-cone is an evolutionarily mobile, ATP-binding regulatory domain which is found in a variety of proteins including ribonucleotide reductases, phosphoglycerate kinases and transcriptional regulators []. In ribonucleotide reductase protein R1 (P28903 from SWISSPROT) from Escherichia coli this domain is located at the N terminus, and is composed mostly of helices []. It forms part of the allosteric effector region and contains the general allosteric activity site in a cleft located at the tip of the N-terminal region []. This site binds either ATP (activating) or dATP (inhibitory), with the base bound in a hydrophobic pocket and the phosphates bound to basic residues. Substrate binding to this site is thought to affect enzyme activity by altering the relative positions of the two subunits of ribonucleotide reductase.; PDB: 2XO4_A 1RLR_A 7R1R_B 5R1R_A 2XO5_B 2XAW_A 2R1R_C 2XAY_B 2X0X_C 2XAZ_A ....
Probab=53.01 E-value=26 Score=23.35 Aligned_cols=58 Identities=22% Similarity=0.272 Sum_probs=29.7
Q ss_pred chhhHHH-HHHHhhhcc-CCCCcchhhHHHHHhHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHHhhc
Q 033083 56 IETYKIY-IFKVLKQVH-PDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLVL 124 (128)
Q Consensus 56 ~esys~Y-IyKVLKQVh-Pd~gISskAM~IMnSfVnDiFErIA~EAs~La~~nkk~TltsREIQtAVRLlL 124 (128)
.+.|..+ |.+.|.... ...+++.. .-+.|+.+...-..-..+..+|..|||..|...|
T Consensus 10 ~e~F~~~KI~~~i~~a~~~~~~~~~~-----------~~~~i~~~V~~~l~~~~~~~is~~eI~~~v~~~L 69 (90)
T PF03477_consen 10 VEPFDREKIVRAIEKACEASRELSEE-----------DAEEIASEVENKLYDSGKEEISTEEIQDIVENAL 69 (90)
T ss_dssp EEES-HHHHHHHHHTTCTTTSTTTST------------HHHHHHHHHTC-ST----TEEHHHHHHHHHHHH
T ss_pred EeeecHHHHHHHHHHHHHhcccccHH-----------HHHHHHHHHHHHHHhccCCCeeHHHHHHHHHHHH
Confidence 4666655 667777666 33344432 1223333333322223334899999999997665
No 72
>PRK09333 30S ribosomal protein S19e; Provisional
Probab=51.30 E-value=30 Score=27.04 Aligned_cols=50 Identities=18% Similarity=0.315 Sum_probs=37.8
Q ss_pred chhhHHHHHHHhhhc-----cC-CCCcchhhHHHHHhHHHHHHHHHHHHHhhHHhh
Q 033083 56 IETYKIYIFKVLKQV-----HP-DIGISSKAMGIMNSFINDIFEKLAQEASRLARY 105 (128)
Q Consensus 56 ~esys~YIyKVLKQV-----hP-d~gISskAM~IMnSfVnDiFErIA~EAs~La~~ 105 (128)
..+--.|+.+.|-+. +| +--||+++.+.||.+-.+|+..+..|--.|.+|
T Consensus 94 sg~iiR~~LqqLE~~glVek~~~GR~lT~~G~~~LD~iA~~i~~~~~~~~p~l~~y 149 (150)
T PRK09333 94 SGSIIRKILQQLEKAGLVEKTKKGRVITPKGRSLLDNLAAEVKKELAEERPELEKY 149 (150)
T ss_pred ccHHHHHHHHHHHHCCCeeeCCCCCEeCHHHHHHHHHHHHHHHHHHHhhCcccccc
Confidence 344577888877764 33 233999999999999999999998776666665
No 73
>PRK05629 hypothetical protein; Validated
Probab=50.96 E-value=54 Score=26.84 Aligned_cols=60 Identities=10% Similarity=0.123 Sum_probs=45.7
Q ss_pred hhHHHHHHHhhhccCCCCcchhhHHHHHhHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHH
Q 033083 58 TYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAV 120 (128)
Q Consensus 58 sys~YIyKVLKQVhPd~gISskAM~IMnSfVnDiFErIA~EAs~La~~nkk~TltsREIQtAV 120 (128)
....+|.+.+++- +..|+..|+..+-..+..=+..|..|--+|+-|.+ .+||..+|+.-|
T Consensus 130 ~l~~wi~~~~~~~--g~~i~~~A~~~L~~~~g~dl~~l~~EleKL~~~~~-~~It~e~V~~~v 189 (318)
T PRK05629 130 ERPGWVTQEFKNH--GVRPTPDVVHALLEGVGSDLRELASAISQLVEDTQ-GNVTVEKVRAYY 189 (318)
T ss_pred HHHHHHHHHHHHc--CCCCCHHHHHHHHHHHCccHHHHHHHHHHHHhcCC-CCcCHHHHHHHh
Confidence 3456777777774 57799999977766665455679999999998864 579999998754
No 74
>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=50.74 E-value=49 Score=20.45 Aligned_cols=40 Identities=25% Similarity=0.215 Sum_probs=20.9
Q ss_pred HHHHHHHhhhccCCCC-cchhhHHHHHhHHHHHHHHHHHHH
Q 033083 60 KIYIFKVLKQVHPDIG-ISSKAMGIMNSFINDIFEKLAQEA 99 (128)
Q Consensus 60 s~YIyKVLKQVhPd~g-ISskAM~IMnSfVnDiFErIA~EA 99 (128)
..-..+++++.|||.. -....-.-.-..|+..|+-|..+.
T Consensus 18 k~~y~~l~~~~HPD~~~~~~~~~~~~~~~i~~Ay~~L~~~~ 58 (64)
T PF00226_consen 18 KKAYRRLSKQYHPDKNSGDEAEAEEKFARINEAYEILSDPE 58 (64)
T ss_dssp HHHHHHHHHHTSTTTGTSTHHHHHHHHHHHHHHHHHHHSHH
T ss_pred HHHHHhhhhccccccchhhhhhhhHHHHHHHHHHHHhCCHH
Confidence 3446788899999974 333111122223445555554443
No 75
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=50.59 E-value=48 Score=25.92 Aligned_cols=50 Identities=20% Similarity=0.210 Sum_probs=42.8
Q ss_pred CCCcchhhHHHHHhHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHHh
Q 033083 73 DIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRL 122 (128)
Q Consensus 73 d~gISskAM~IMnSfVnDiFErIA~EAs~La~~nkk~TltsREIQtAVRL 122 (128)
|+-....|-.|+-..--.+..-+..||...|.--.+.||....|..|+.-
T Consensus 28 dl~ftKearei~in~cieFi~~lsseAne~ce~EaKKTIa~EHviKALen 77 (148)
T COG5150 28 DLVFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHVIKALEN 77 (148)
T ss_pred cccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHh
Confidence 57788889888766666777889999999999999999999999998753
No 76
>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=48.64 E-value=88 Score=28.83 Aligned_cols=66 Identities=14% Similarity=0.126 Sum_probs=39.5
Q ss_pred hhhHHHHHHHhhhccCCCCcchhhHHHHHhHHH-------------HHHHHHHHHHhhHHhhCCCCCCChhHHHHHHHh
Q 033083 57 ETYKIYIFKVLKQVHPDIGISSKAMGIMNSFIN-------------DIFEKLAQEASRLARYNKKPTITSREIQTAVRL 122 (128)
Q Consensus 57 esys~YIyKVLKQVhPd~gISskAM~IMnSfVn-------------DiFErIA~EAs~La~~nkk~TltsREIQtAVRL 122 (128)
+.|..||.+.+++...--.+|..|+.-+-.+.. .-++.|..+|..+|+..+..+|+.++|+.|+.+
T Consensus 312 ~~~~~~i~~~~~r~G~l~~~s~~Av~~Li~~~~R~ag~r~~lsl~~R~L~~llR~A~~iA~~~~~~~I~~ehV~~Ai~~ 390 (608)
T TIGR00764 312 DKLVQFVAQEVKKDGRIPHFTRDAVEEIVREAQRRAGRKDHLTLRLRELGGLVRAAGDIAKSSGKVYVTAEHVLKAKKL 390 (608)
T ss_pred HHHHHHHHHHHHHhCCCCcCCHHHHHHHHHHHHHHHhcccccCCCHHHHHHHHHHHHHHHHhcCCceecHHHHHHHHHH
Confidence 345556665555441122677777665432211 334556677766777777778888888887653
No 77
>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=48.01 E-value=41 Score=28.73 Aligned_cols=25 Identities=24% Similarity=0.408 Sum_probs=23.0
Q ss_pred hHHhhCCCCCCChhHHHHHHHhhcC
Q 033083 101 RLARYNKKPTITSREIQTAVRLVLP 125 (128)
Q Consensus 101 ~La~~nkk~TltsREIQtAVRLlLP 125 (128)
-+|-.++|..++..||+.+++++|+
T Consensus 287 A~Aal~GR~~V~~dDv~~~a~~vL~ 311 (337)
T TIGR02030 287 ALAAFEGRTEVTVDDIRRVAVLALR 311 (337)
T ss_pred HHHHHcCCCCCCHHHHHHHHHHHHH
Confidence 3788899999999999999999986
No 78
>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=47.26 E-value=15 Score=26.04 Aligned_cols=29 Identities=24% Similarity=0.485 Sum_probs=21.4
Q ss_pred chhhHHHHHHHhhhccCCCCcchhhHHHHHhHHHHHH
Q 033083 56 IETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIF 92 (128)
Q Consensus 56 ~esys~YIyKVLKQVhPd~gISskAM~IMnSfVnDiF 92 (128)
.|.=..|+|-||++-|.-++| .-||+|+=
T Consensus 18 ~EaEkd~lY~~Lr~YHqSm~l--------p~li~Dlk 46 (79)
T cd07353 18 NEAEKDYLYDVLRMYHQSMNL--------PVLVGDLK 46 (79)
T ss_pred cHHHHHHHHHHHHHHHhccCH--------HHHHHHHH
Confidence 356689999999999954433 45888873
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=44.97 E-value=79 Score=28.92 Aligned_cols=58 Identities=19% Similarity=0.233 Sum_probs=37.2
Q ss_pred hhccCCCCcchhhHHHHHhHHHHHH-------HHHHHHHhhHHhhCCCCCCChhHHHHHHHhhcC
Q 033083 68 KQVHPDIGISSKAMGIMNSFINDIF-------EKLAQEASRLARYNKKPTITSREIQTAVRLVLP 125 (128)
Q Consensus 68 KQVhPd~gISskAM~IMnSfVnDiF-------ErIA~EAs~La~~nkk~TltsREIQtAVRLlLP 125 (128)
++..++..||...+.-+..++..+- ..+..-|--+|..+.+.+++..||+.|++|||+
T Consensus 196 r~~~~~V~i~~~~~~~l~~~~~~~gv~s~Ra~i~~~r~ArA~Aal~gr~~V~~~Dv~~a~~lvl~ 260 (589)
T TIGR02031 196 RELLPQVTISAEQVKELVLTAASLGISGHRADLFAVRAAKAHAALHGRTEVTEEDLKLAVELVLL 260 (589)
T ss_pred HHhcCCccCCHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhh
Confidence 4456677777765543333321110 112222334788899999999999999999995
No 80
>PRK03992 proteasome-activating nucleotidase; Provisional
Probab=44.77 E-value=35 Score=29.23 Aligned_cols=43 Identities=14% Similarity=0.195 Sum_probs=36.7
Q ss_pred HhHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHHhhcCCC
Q 033083 85 NSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLVLPAS 127 (128)
Q Consensus 85 nSfVnDiFErIA~EAs~La~~nkk~TltsREIQtAVRLlLPGE 127 (128)
+.|...-++.|+.||+.++-..++..||..||+.|+.-+.|+.
T Consensus 334 ~g~sgadl~~l~~eA~~~a~~~~~~~i~~~d~~~A~~~~~~~~ 376 (389)
T PRK03992 334 EGASGADLKAICTEAGMFAIRDDRTEVTMEDFLKAIEKVMGKE 376 (389)
T ss_pred CCCCHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHhccc
Confidence 4566566778999999999888889999999999999998864
No 81
>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=43.44 E-value=75 Score=19.32 Aligned_cols=62 Identities=15% Similarity=0.063 Sum_probs=41.3
Q ss_pred hhHHHHHHHhhhccCCCCcchhhHHHHHhHHH------HHHHHHHHHHhhHHhhCCCCCCChhHHHHH
Q 033083 58 TYKIYIFKVLKQVHPDIGISSKAMGIMNSFIN------DIFEKLAQEASRLARYNKKPTITSREIQTA 119 (128)
Q Consensus 58 sys~YIyKVLKQVhPd~gISskAM~IMnSfVn------DiFErIA~EAs~La~~nkk~TltsREIQtA 119 (128)
..-.||.++.....-+..+-.-|+.+++.|+. .-+..||.-+.-||..-.....+.+|+...
T Consensus 4 ~~~~~l~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~ 71 (88)
T cd00043 4 TPLDFLRRVAKALGLSPETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEEIPPWLKDLVHV 71 (88)
T ss_pred hHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHcCCCCCHHHHhHH
Confidence 44567777777776666666678888888866 335677777777776644446666666443
No 82
>CHL00081 chlI Mg-protoporyphyrin IX chelatase
Probab=43.30 E-value=78 Score=27.41 Aligned_cols=27 Identities=26% Similarity=0.474 Sum_probs=23.9
Q ss_pred HhhHHhhCCCCCCChhHHHHHHHhhcC
Q 033083 99 ASRLARYNKKPTITSREIQTAVRLVLP 125 (128)
Q Consensus 99 As~La~~nkk~TltsREIQtAVRLlLP 125 (128)
|--+|-.++|..++..||+.+++++|+
T Consensus 298 ArA~Aal~GR~~V~pdDv~~~a~~vL~ 324 (350)
T CHL00081 298 AKALAAFEGRTEVTPKDIFKVITLCLR 324 (350)
T ss_pred HHHHHHHcCCCCCCHHHHHHHHHHHHH
Confidence 334888999999999999999999986
No 83
>PF13335 Mg_chelatase_2: Magnesium chelatase, subunit ChlI
Probab=41.66 E-value=55 Score=23.03 Aligned_cols=48 Identities=19% Similarity=0.262 Sum_probs=34.6
Q ss_pred CcchhhHHHHHhHHHH------HHHHHHHHHhhHHhhCCCCCCChhHHHHHHHh
Q 033083 75 GISSKAMGIMNSFIND------IFEKLAQEASRLARYNKKPTITSREIQTAVRL 122 (128)
Q Consensus 75 gISskAM~IMnSfVnD------iFErIA~EAs~La~~nkk~TltsREIQtAVRL 122 (128)
.++..+..+|+..++. =+.||..-|--+|.......|+..+|..|+.+
T Consensus 42 ~l~~~~~~~l~~~~~~~~lS~R~~~rilrvARTIADL~~~~~I~~~hi~EAl~y 95 (96)
T PF13335_consen 42 PLSSEAKKLLEQAAEKLNLSARGYHRILRVARTIADLEGSERITREHIAEALSY 95 (96)
T ss_pred CCCHHHHHHHHHHHHHcCcCHHHHHHHHHHHHHHHhHcCCCCCCHHHHHHHHhC
Confidence 3444444444444432 25688888889999999999999999999853
No 84
>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=41.03 E-value=1.1e+02 Score=24.59 Aligned_cols=56 Identities=30% Similarity=0.443 Sum_probs=44.7
Q ss_pred hhhHHHHHHHh---hhccCCCCcchhhHHH------------------HHhHHHHHHHHHHHHHhhHHhhCCCCCCC
Q 033083 57 ETYKIYIFKVL---KQVHPDIGISSKAMGI------------------MNSFINDIFEKLAQEASRLARYNKKPTIT 112 (128)
Q Consensus 57 esys~YIyKVL---KQVhPd~gISskAM~I------------------MnSfVnDiFErIA~EAs~La~~nkk~Tlt 112 (128)
-+|..+|--.| ..+.||+.=|.++|-- |-+|+..|.-+|--|+..+..|++++++.
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 34555555444 4569999999999852 66899999999999999999999999874
No 85
>PLN03213 repressor of silencing 3; Provisional
Probab=40.65 E-value=24 Score=33.37 Aligned_cols=23 Identities=35% Similarity=0.668 Sum_probs=19.4
Q ss_pred CCCcchhhHHHHHhHHHHHHHHH
Q 033083 73 DIGISSKAMGIMNSFINDIFEKL 95 (128)
Q Consensus 73 d~gISskAM~IMnSfVnDiFErI 95 (128)
+.|+-.+-.+||||.||-+||+=
T Consensus 183 ~~g~~~eE~niMNSVMNKLFEke 205 (759)
T PLN03213 183 NVGRNEAEVNVMNSVMNKLFEKN 205 (759)
T ss_pred cccccHHHHHHHHHHHHHHHhhh
Confidence 35677788999999999999973
No 86
>PRK05637 anthranilate synthase component II; Provisional
Probab=40.38 E-value=23 Score=27.94 Aligned_cols=24 Identities=21% Similarity=0.411 Sum_probs=21.6
Q ss_pred hccCCCCcchhhHHHHHhHHHHHH
Q 033083 69 QVHPDIGISSKAMGIMNSFINDIF 92 (128)
Q Consensus 69 QVhPd~gISskAM~IMnSfVnDiF 92 (128)
|-||+.-.|...+.|+++|+...+
T Consensus 183 QfHPE~~~T~~G~~il~nfl~~~~ 206 (208)
T PRK05637 183 QFHPESVLSPTGPIILSRCVEQLL 206 (208)
T ss_pred EeCCccCcCCCHHHHHHHHHHHHh
Confidence 789999999999999999987654
No 87
>PF13148 DUF3987: Protein of unknown function (DUF3987)
Probab=38.75 E-value=1.4e+02 Score=24.49 Aligned_cols=68 Identities=26% Similarity=0.410 Sum_probs=47.2
Q ss_pred chhhHHHHHHHhhhcc-------CCCCcchhhHHHHHhHHHHHHHHH----------------HHHHhhHHh----h---
Q 033083 56 IETYKIYIFKVLKQVH-------PDIGISSKAMGIMNSFINDIFEKL----------------AQEASRLAR----Y--- 105 (128)
Q Consensus 56 ~esys~YIyKVLKQVh-------Pd~gISskAM~IMnSfVnDiFErI----------------A~EAs~La~----~--- 105 (128)
.+.|...|..++.... ..+.+|..|..+++.|.+.+..++ ..-+.|||- .
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 3566677788877765 336688999998888776665555 334444432 2
Q ss_pred --CCCCCCChhHHHHHHHhh
Q 033083 106 --NKKPTITSREIQTAVRLV 123 (128)
Q Consensus 106 --nkk~TltsREIQtAVRLl 123 (128)
....+|+...++.|++|+
T Consensus 341 ~~~~~~~I~~~~~~~Ai~l~ 360 (378)
T PF13148_consen 341 GSPPSTEISAETMERAIRLV 360 (378)
T ss_pred CCCCCCEECHHHHHHHHHHH
Confidence 367789999999999875
No 88
>KOG1657 consensus CCAAT-binding factor, subunit C (HAP5) [Transcription]
Probab=38.69 E-value=59 Score=26.90 Aligned_cols=56 Identities=23% Similarity=0.334 Sum_probs=38.6
Q ss_pred HHHhhhccCCCC-cchhhHHHHHhHHHHHH-HHHHHHHhhHHhhCCCCCCChhHHHHHHH
Q 033083 64 FKVLKQVHPDIG-ISSKAMGIMNSFINDIF-EKLAQEASRLARYNKKPTITSREIQTAVR 121 (128)
Q Consensus 64 yKVLKQVhPd~g-ISskAM~IMnSfVnDiF-ErIA~EAs~La~~nkk~TltsREIQtAVR 121 (128)
.++.|+ ++|+. |+.+|--++. +.+.+| +.++..+..-+.-++|.||.--+|..||.
T Consensus 81 KkimK~-dedv~mI~~Eapvl~a-ka~E~Fi~elt~~sw~~Tee~~rrtl~~sdia~av~ 138 (236)
T KOG1657|consen 81 KKIMKS-DEDVSMITAEAPVLFA-KACELFITELTLRSWVHTEENKRRTLQKSDIAAAVT 138 (236)
T ss_pred cccccc-cccccccchhHHHHHH-HHHHHHHHHHHHHhhhhhcccccccchHHHHHHHhc
Confidence 334443 55654 7877765544 444444 55666677788889999999999998885
No 89
>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=38.07 E-value=41 Score=28.70 Aligned_cols=22 Identities=23% Similarity=0.522 Sum_probs=17.7
Q ss_pred hhHHHHHhHHHHHHHHHHHHHh
Q 033083 79 KAMGIMNSFINDIFEKLAQEAS 100 (128)
Q Consensus 79 kAM~IMnSfVnDiFErIA~EAs 100 (128)
.+..-|+..+||||+||.....
T Consensus 25 ~aL~~L~~v~~diF~rI~~Rv~ 46 (297)
T PF11945_consen 25 DALEYLDKVSNDIFSRISARVE 46 (297)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 5777889999999999876443
No 90
>PRK13406 bchD magnesium chelatase subunit D; Provisional
Probab=37.72 E-value=88 Score=28.89 Aligned_cols=32 Identities=22% Similarity=0.290 Sum_probs=27.2
Q ss_pred HHHHHHhhHHhhCCCCCCChhHHHHHHHhhcC
Q 033083 94 KLAQEASRLARYNKKPTITSREIQTAVRLVLP 125 (128)
Q Consensus 94 rIA~EAs~La~~nkk~TltsREIQtAVRLlLP 125 (128)
+|..-|--+|..+.+..++..||+.|+.|+|+
T Consensus 221 ~llraARa~AaL~Gr~~V~~~dv~~Aa~lvL~ 252 (584)
T PRK13406 221 LALRAARAAAALAGRTAVEEEDLALAARLVLA 252 (584)
T ss_pred HHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHH
Confidence 34555556899999999999999999999985
No 91
>KOG0240 consensus Kinesin (SMY1 subfamily) [Cytoskeleton]
Probab=37.71 E-value=33 Score=32.37 Aligned_cols=41 Identities=24% Similarity=0.480 Sum_probs=29.9
Q ss_pred hhhHHHHHHHhhhccCC-------------------CC--cchhhHHHHHhHHHHHHHHHHH
Q 033083 57 ETYKIYIFKVLKQVHPD-------------------IG--ISSKAMGIMNSFINDIFEKLAQ 97 (128)
Q Consensus 57 esys~YIyKVLKQVhPd-------------------~g--ISskAM~IMnSfVnDiFErIA~ 97 (128)
+-|.--++-|+++|.-+ .| ....-|+||..+++|||++|-.
T Consensus 65 ~Vy~~~a~~Iv~dVL~GYNGTvfaYGqT~sGKTytm~G~~~d~~~~GIipRi~~diF~~Iys 126 (607)
T KOG0240|consen 65 DVYEFAAKPIVDDVLLGYNGTVFAYGQTGSGKTYTMEGIGHDPEEMGIIPRILNDIFDHIYS 126 (607)
T ss_pred HHHHHHHHHHHHHHhcccceeEEEecCCCCCcceeecccCCChhhcCcHHHHHHHHHHHHhc
Confidence 45777788899988322 11 2224689999999999999965
No 92
>PF13654 AAA_32: AAA domain; PDB: 3K1J_B.
Probab=37.69 E-value=50 Score=29.95 Aligned_cols=63 Identities=17% Similarity=0.244 Sum_probs=41.1
Q ss_pred hhhHHHHHHHhhhccCCCCcchhhHHHHHhH------------HHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHH
Q 033083 57 ETYKIYIFKVLKQVHPDIGISSKAMGIMNSF------------INDIFEKLAQEASRLARYNKKPTITSREIQTAVR 121 (128)
Q Consensus 57 esys~YIyKVLKQVhPd~gISskAM~IMnSf------------VnDiFErIA~EAs~La~~nkk~TltsREIQtAVR 121 (128)
..|..||..+..+-+ -..++..|+.-|--+ +.+| ..|..||..+|+.+++..|+..+|+.|+.
T Consensus 430 ~~~~~~i~~~~~~~~-L~~~~~~Av~~li~~~~R~~q~kLsl~~~~l-~~ll~EA~~~A~~~~~~~I~~~~V~~Ai~ 504 (509)
T PF13654_consen 430 RQYARFIASICQKEG-LPPFDRSAVARLIEYSARLDQDKLSLRFSWL-ADLLREANYWARKEGAKVITAEHVEQAIE 504 (509)
T ss_dssp HHHHHHHHHHHHHHS-S--BBHHHHHHHHHHHHHCC-SEEE--HHHH-HHHHHHHHHHHHHCT-SSB-HHHHHHHHH
T ss_pred HHHHHHHHHHHHhCC-CCCCCHHHHHHHHHHHHHHhCCEeCCCHHHH-HHHHHHHHHHHHHhCCCccCHHHHHHHHH
Confidence 456677776666542 235666666544321 2233 55669999999999999999999999986
No 93
>KOG1757 consensus Histone 2A [Chromatin structure and dynamics]
Probab=37.22 E-value=40 Score=25.86 Aligned_cols=56 Identities=32% Similarity=0.377 Sum_probs=38.0
Q ss_pred HHHHHhhhccCCCC-cchhhHHHHHhHHHHHHHHHHHHHhhHHhhC----CCCCCChhHHHHHHH
Q 033083 62 YIFKVLKQVHPDIG-ISSKAMGIMNSFINDIFEKLAQEASRLARYN----KKPTITSREIQTAVR 121 (128)
Q Consensus 62 YIyKVLKQVhPd~g-ISskAM~IMnSfVnDiFErIA~EAs~La~~n----kk~TltsREIQtAVR 121 (128)
-|+|-||+.....+ +-..+.- +..-|+|-+..|...|+-.. +-.-||.|.+|-|+|
T Consensus 35 Rihr~LK~r~t~h~rVGataav----y~aaileYLTaEVLeLAgNasKdLKvKRitprHlqLAiR 95 (131)
T KOG1757|consen 35 RIHRHLKTRTTSHGRVGATAAV----YSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 95 (131)
T ss_pred HHHHHHHHhcccccccchHHHH----HHHHHHHHHHHHHHHHcccccccceeeeccchhheeeec
Confidence 38888888644333 3333322 44567888888888888553 345799999998887
No 94
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=37.21 E-value=85 Score=24.33 Aligned_cols=16 Identities=31% Similarity=0.281 Sum_probs=13.8
Q ss_pred CCCChhHHHHHHHhhc
Q 033083 109 PTITSREIQTAVRLVL 124 (128)
Q Consensus 109 ~TltsREIQtAVRLlL 124 (128)
..++..|||..|.-.|
T Consensus 101 ~~IsveEIqDiVE~~L 116 (154)
T PRK00464 101 REVPSKEIGELVMEEL 116 (154)
T ss_pred CCCCHHHHHHHHHHHH
Confidence 5799999999998665
No 95
>COG2238 RPS19A Ribosomal protein S19E (S16A) [Translation, ribosomal structure and biogenesis]
Probab=37.06 E-value=44 Score=26.31 Aligned_cols=38 Identities=26% Similarity=0.394 Sum_probs=29.7
Q ss_pred HHHHHHHhhhc--------cC-CCCcchhhHHHHHhHHHHHHHHHHH
Q 033083 60 KIYIFKVLKQV--------HP-DIGISSKAMGIMNSFINDIFEKLAQ 97 (128)
Q Consensus 60 s~YIyKVLKQV--------hP-d~gISskAM~IMnSfVnDiFErIA~ 97 (128)
..-|.+||.|. +| +-.||.+.+++|+.+..+|++.++.
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 34466666653 66 5669999999999999999998876
No 96
>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=36.89 E-value=1.2e+02 Score=24.73 Aligned_cols=24 Identities=25% Similarity=0.394 Sum_probs=18.7
Q ss_pred cchhhHHHHHh-HHHHHHHHHHHHH
Q 033083 76 ISSKAMGIMNS-FINDIFEKLAQEA 99 (128)
Q Consensus 76 ISskAM~IMnS-fVnDiFErIA~EA 99 (128)
...+|+.+||+ ||++..+..+...
T Consensus 197 t~~QAL~LmNg~~v~~~a~~~a~r~ 221 (266)
T PF07587_consen 197 TPLQALFLMNGPFVNEAARAFANRL 221 (266)
T ss_pred CHHHHHHHhCcHHHHHHHHHHHHHH
Confidence 33689999999 8888887777643
No 97
>PF05798 Phage_FRD3: Bacteriophage FRD3 protein; InterPro: IPR008765 This is a group of proteins of unknown function from bacteriophage T2 and related phage.
Probab=36.66 E-value=17 Score=25.60 Aligned_cols=18 Identities=28% Similarity=0.527 Sum_probs=16.4
Q ss_pred HHHHHHhhhccCCCCcch
Q 033083 61 IYIFKVLKQVHPDIGISS 78 (128)
Q Consensus 61 ~YIyKVLKQVhPd~gISs 78 (128)
-||+.|++..||.++|.+
T Consensus 12 EY~eEvIRNRyPelsi~s 29 (75)
T PF05798_consen 12 EYTEEVIRNRYPELSITS 29 (75)
T ss_pred HhHHHHHHccCCceEEEE
Confidence 599999999999999875
No 98
>PF11841 DUF3361: Domain of unknown function (DUF3361)
Probab=35.50 E-value=36 Score=26.80 Aligned_cols=59 Identities=24% Similarity=0.446 Sum_probs=41.4
Q ss_pred HHHHHHHhhhccC---CCCcchhhHHHHHhHH---HHHHHHHHHHHhhHHhhCCCCCCChhHHHHH
Q 033083 60 KIYIFKVLKQVHP---DIGISSKAMGIMNSFI---NDIFEKLAQEASRLARYNKKPTITSREIQTA 119 (128)
Q Consensus 60 s~YIyKVLKQVhP---d~gISskAM~IMnSfV---nDiFErIA~EAs~La~~nkk~TltsREIQtA 119 (128)
..||.||.--|.- |..|-..|++|+.|+| .+.|..|+.|.. +-+...+---+..|||+-
T Consensus 57 ~~FI~Kia~~Vn~~~~d~~i~q~sLaILEs~Vl~S~~ly~~V~~evt-~~~Li~hLq~~~~~iq~n 121 (160)
T PF11841_consen 57 DSFIKKIASYVNSSAMDASILQRSLAILESIVLNSPKLYQLVEQEVT-LESLIRHLQVSNQEIQTN 121 (160)
T ss_pred HHHHHHHHHHHccccccchHHHHHHHHHHHHHhCCHHHHHHHhccCC-HHHHHHHHHcCCHHHHHH
Confidence 5678888887743 5667778999999999 478888888764 222222223388888873
No 99
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=34.71 E-value=2.6e+02 Score=23.02 Aligned_cols=57 Identities=9% Similarity=0.116 Sum_probs=36.2
Q ss_pred hhhccCCCCcchhhHHHHHhHHHH----H--HHHHHHHHhhHHhhCCCCCCChhHHHHHHHhh
Q 033083 67 LKQVHPDIGISSKAMGIMNSFIND----I--FEKLAQEASRLARYNKKPTITSREIQTAVRLV 123 (128)
Q Consensus 67 LKQVhPd~gISskAM~IMnSfVnD----i--FErIA~EAs~La~~nkk~TltsREIQtAVRLl 123 (128)
++..+.+..++..++..+-.++.- + .-.+...|..++...+..+||..+|..|+..+
T Consensus 220 ~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~a~~~a~~~~~~~I~~~~v~~a~~~~ 282 (394)
T PRK00411 220 VEEGFYPGVVDDEVLDLIADLTAREHGDARVAIDLLRRAGLIAEREGSRKVTEEDVRKAYEKS 282 (394)
T ss_pred HHhhcccCCCCHhHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHH
Confidence 333333445777777766555511 1 11234566667777788899999999998765
No 100
>TIGR01242 26Sp45 26S proteasome subunit P45 family. Many proteins may score above the trusted cutoff because an internal
Probab=32.39 E-value=66 Score=26.86 Aligned_cols=41 Identities=20% Similarity=0.192 Sum_probs=32.8
Q ss_pred HHhHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHHhhc
Q 033083 84 MNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLVL 124 (128)
Q Consensus 84 MnSfVnDiFErIA~EAs~La~~nkk~TltsREIQtAVRLlL 124 (128)
.+-|...-+..|..||...|....+..||..||+.|++-++
T Consensus 324 t~g~sg~dl~~l~~~A~~~a~~~~~~~i~~~d~~~a~~~~~ 364 (364)
T TIGR01242 324 TEGASGADLKAICTEAGMFAIREERDYVTMDDFIKAVEKVL 364 (364)
T ss_pred cCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHHhC
Confidence 34455444457899999999888999999999999998764
No 101
>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=32.36 E-value=38 Score=25.51 Aligned_cols=23 Identities=22% Similarity=0.510 Sum_probs=19.1
Q ss_pred hhccCCCCcchhhHHHHHhHHHH
Q 033083 68 KQVHPDIGISSKAMGIMNSFIND 90 (128)
Q Consensus 68 KQVhPd~gISskAM~IMnSfVnD 90 (128)
=|-||+...+..++.|+.+|+++
T Consensus 161 ~QfHPE~~~~~~g~~i~~~f~~~ 183 (188)
T TIGR00888 161 VQFHPEVTHTEYGNELLENFVYD 183 (188)
T ss_pred EeeCCccCCChhhHHHHHHHHHH
Confidence 37799998877889999999765
No 102
>PRK13407 bchI magnesium chelatase subunit I; Provisional
Probab=32.05 E-value=1.4e+02 Score=25.55 Aligned_cols=31 Identities=16% Similarity=0.339 Sum_probs=27.4
Q ss_pred HHHHHhhHHhhCCCCCCChhHHHHHHHhhcC
Q 033083 95 LAQEASRLARYNKKPTITSREIQTAVRLVLP 125 (128)
Q Consensus 95 IA~EAs~La~~nkk~TltsREIQtAVRLlLP 125 (128)
+..-|.-+|-.++|..++..||+.++.++|.
T Consensus 278 l~~aA~a~A~l~Gr~~V~~~Di~~~~~~vl~ 308 (334)
T PRK13407 278 LLRAARALAAFEGAEAVGRSHLRSVATMALS 308 (334)
T ss_pred HHHHHHHHHHHcCCCeeCHHHHHHHHHHhhh
Confidence 6666777899999999999999999999885
No 103
>PHA03102 Small T antigen; Reviewed
Probab=31.69 E-value=82 Score=24.43 Aligned_cols=36 Identities=22% Similarity=0.426 Sum_probs=26.2
Q ss_pred HHHhhhccCCCCcchhhHHHHHhHHHHHHHHHHHHHhhHH
Q 033083 64 FKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLA 103 (128)
Q Consensus 64 yKVLKQVhPd~gISskAM~IMnSfVnDiFErIA~EAs~La 103 (128)
.+..++.|||-|-+...|. -||..|+.|..+..++.
T Consensus 29 r~la~~~HPDkgg~~e~~k----~in~Ay~~L~d~~~r~~ 64 (153)
T PHA03102 29 LRKCLEFHPDKGGDEEKMK----ELNTLYKKFRESVKSLR 64 (153)
T ss_pred HHHHHHHCcCCCchhHHHH----HHHHHHHHHhhHHHhcc
Confidence 4556888999987766554 56778888887776655
No 104
>PRK10733 hflB ATP-dependent metalloprotease; Reviewed
Probab=31.40 E-value=75 Score=29.28 Aligned_cols=41 Identities=20% Similarity=0.244 Sum_probs=34.0
Q ss_pred hHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHHhhcCC
Q 033083 86 SFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLVLPA 126 (128)
Q Consensus 86 SfVnDiFErIA~EAs~La~~nkk~TltsREIQtAVRLlLPG 126 (128)
-|..-=+..|..||+.++...++..||-.|+..|+..+.+|
T Consensus 355 G~sgadl~~l~~eAa~~a~r~~~~~i~~~d~~~a~~~v~~g 395 (644)
T PRK10733 355 GFSGADLANLVNEAALFAARGNKRVVSMVEFEKAKDKIMMG 395 (644)
T ss_pred CCCHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHHHHhcc
Confidence 34444566788999999999999999999999999888776
No 105
>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=31.37 E-value=1.5e+02 Score=26.01 Aligned_cols=40 Identities=30% Similarity=0.378 Sum_probs=31.0
Q ss_pred HHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHHhhcCC
Q 033083 87 FINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLVLPA 126 (128)
Q Consensus 87 fVnDiFErIA~EAs~La~~nkk~TltsREIQtAVRLlLPG 126 (128)
|..-=++.|..||..++...++..||..+|+.|+..++.|
T Consensus 259 ~sgadl~~l~~eA~~~a~~~~~~~i~~~~l~~a~~~~~~~ 298 (495)
T TIGR01241 259 FSGADLANLLNEAALLAARKNKTEITMNDIEEAIDRVIAG 298 (495)
T ss_pred CCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhcc
Confidence 3433345677788888777788899999999999988765
No 106
>PLN02347 GMP synthetase
Probab=31.27 E-value=38 Score=30.88 Aligned_cols=25 Identities=32% Similarity=0.553 Sum_probs=21.2
Q ss_pred hhccCCCCcchhhHHHHHhHHHHHH
Q 033083 68 KQVHPDIGISSKAMGIMNSFINDIF 92 (128)
Q Consensus 68 KQVhPd~gISskAM~IMnSfVnDiF 92 (128)
=|-||+...|...+.||.+|+.+|.
T Consensus 179 vQFHPE~~~t~~G~~iL~NFl~~ic 203 (536)
T PLN02347 179 LQYHPEVTHSPKGMETLRHFLFDVC 203 (536)
T ss_pred EEccCCCCccchHHHHHHHHHHHHh
Confidence 3779999999999999999986654
No 107
>KOG4336 consensus TBP-associated transcription factor Prodos [Transcription]
Probab=31.17 E-value=2e+02 Score=25.37 Aligned_cols=58 Identities=12% Similarity=0.184 Sum_probs=46.3
Q ss_pred HHHhhhccCCCCcchhhHHHHHhHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHHh
Q 033083 64 FKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRL 122 (128)
Q Consensus 64 yKVLKQVhPd~gISskAM~IMnSfVnDiFErIA~EAs~La~~nkk~TltsREIQtAVRL 122 (128)
--+|+++.=|. ||.-|..-|--++.--|.+|+.++..++...+|.--|-.||.-....
T Consensus 12 ~~Ll~~~gfd~-is~~aletlvell~~yi~eigrq~~n~celagRT~pT~~Dv~l~Li~ 69 (323)
T KOG4336|consen 12 SNLLKTKGFDS-ISNAALETLVELLQSYIREIGRQLHNYCELAGRTIPTQGDVKLTLIE 69 (323)
T ss_pred HHHHHHhCchH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcHHHHHHHHHH
Confidence 33444444333 88888888888999999999999999999999999999998766553
No 108
>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=31.16 E-value=39 Score=28.36 Aligned_cols=66 Identities=20% Similarity=0.392 Sum_probs=42.0
Q ss_pred chhhHHHHHHHhhhccCCCCcchhhHHHHHhHHHHH-----------------HHHHHHHHhhHHhhCCCCCCChhHHHH
Q 033083 56 IETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDI-----------------FEKLAQEASRLARYNKKPTITSREIQT 118 (128)
Q Consensus 56 ~esys~YIyKVLKQVhPd~gISskAM~IMnSfVnDi-----------------FErIA~EAs~La~~nkk~TltsREIQt 118 (128)
.+.+..||.-+=.+++| .||.+|..++-.|--++ +|-|-.=|--+|+..-+.+++..|++.
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 35567788777568888 57777777664443211 122333333567778888999999999
Q ss_pred HHHhh
Q 033083 119 AVRLV 123 (128)
Q Consensus 119 AVRLl 123 (128)
|++|+
T Consensus 322 Ai~L~ 326 (331)
T PF00493_consen 322 AIRLF 326 (331)
T ss_dssp HHHHH
T ss_pred HHHHH
Confidence 99987
No 109
>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional
Probab=31.09 E-value=66 Score=28.64 Aligned_cols=43 Identities=19% Similarity=0.205 Sum_probs=35.8
Q ss_pred HHHhHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHHhhcC
Q 033083 83 IMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLVLP 125 (128)
Q Consensus 83 IMnSfVnDiFErIA~EAs~La~~nkk~TltsREIQtAVRLlLP 125 (128)
..+-|.-.-+..|+.||..+|...++..||..|+..|+.-++-
T Consensus 384 ~t~g~sgAdI~~i~~eA~~~Alr~~r~~Vt~~D~~~A~~~v~~ 426 (438)
T PTZ00361 384 AKDELSGADIKAICTEAGLLALRERRMKVTQADFRKAKEKVLY 426 (438)
T ss_pred hcCCCCHHHHHHHHHHHHHHHHHhcCCccCHHHHHHHHHHHHh
Confidence 3345566667789999999999999999999999999998764
No 110
>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=28.72 E-value=1.2e+02 Score=18.16 Aligned_cols=55 Identities=20% Similarity=0.259 Sum_probs=27.5
Q ss_pred HHHHHhhhccCCCCcchhhHHHHHhHHHH------HHHHHHHHHhhHHhhCCCCCCChhHH
Q 033083 62 YIFKVLKQVHPDIGISSKAMGIMNSFIND------IFEKLAQEASRLARYNKKPTITSREI 116 (128)
Q Consensus 62 YIyKVLKQVhPd~gISskAM~IMnSfVnD------iFErIA~EAs~La~~nkk~TltsREI 116 (128)
||.++....+-+..+-.-|+.+++.|+.+ -++.||.-+.-||........+..+|
T Consensus 2 ~l~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~ 62 (83)
T smart00385 2 FLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLAAKTEEIPPWTKEL 62 (83)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhcccCCHHHHHHHHHHHHHHHhcCCCCchhH
Confidence 34455554444444444566666655542 34556666666665433333344444
No 111
>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=27.91 E-value=1.8e+02 Score=23.50 Aligned_cols=60 Identities=13% Similarity=0.207 Sum_probs=42.9
Q ss_pred hHHHHHHHhhhccCCCCcchhhHHHHHhHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHH
Q 033083 59 YKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVR 121 (128)
Q Consensus 59 ys~YIyKVLKQVhPd~gISskAM~IMnSfVnDiFErIA~EAs~La~~nkk~TltsREIQtAVR 121 (128)
...||..++++- +..|+..++..+-.+++.-+.++..+.-+|+.|... .||..+|+..+.
T Consensus 181 l~~~l~~~~~~~--g~~i~~~a~~~l~~~~~g~~~~a~~~lekl~~~~~~-~it~~~v~~~~~ 240 (355)
T TIGR02397 181 IVERLKKILDKE--GIKIEDEALELIARAADGSLRDALSLLDQLISFGNG-NITYEDVNELLG 240 (355)
T ss_pred HHHHHHHHHHHc--CCCCCHHHHHHHHHHcCCChHHHHHHHHHHHhhcCC-CCCHHHHHHHhC
Confidence 445666666653 467888888777777766667788888888888764 599888877653
No 112
>TIGR00368 Mg chelatase-related protein. The N-terminal end matches very strongly a pfam Mg_chelatase domain.
Probab=27.75 E-value=1.4e+02 Score=26.90 Aligned_cols=49 Identities=12% Similarity=0.245 Sum_probs=41.9
Q ss_pred CCcchhhHHHHHhHHHHH------HHHHHHHHhhHHhhCCCCCCChhHHHHHHHh
Q 033083 74 IGISSKAMGIMNSFINDI------FEKLAQEASRLARYNKKPTITSREIQTAVRL 122 (128)
Q Consensus 74 ~gISskAM~IMnSfVnDi------FErIA~EAs~La~~nkk~TltsREIQtAVRL 122 (128)
..++..+..+|+..++.+ ++||..-|--+|.......|+..+|+.|+.+
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 356788888888777664 7899999999999999999999999999864
No 113
>TIGR03543 divI1A_rptt_fam DivIVA domain repeat protein. Members of this protein family contain two full and two partial repeats of a domain found at the N-terminus of Bacillus subtilis cell-division initiation protein DivIVA. The portion repeated four times in these proteins includes the motif GYxxxxVD.
Probab=27.12 E-value=85 Score=25.21 Aligned_cols=27 Identities=19% Similarity=0.470 Sum_probs=20.2
Q ss_pred HHHHHHHHHHHHhhHHhhCCCCC-CChhHHHHHH
Q 033083 88 INDIFEKLAQEASRLARYNKKPT-ITSREIQTAV 120 (128)
Q Consensus 88 VnDiFErIA~EAs~La~~nkk~T-ltsREIQtAV 120 (128)
|+++|+|++. .|..... ||++||+.++
T Consensus 16 VD~fl~r~~~------~~e~~~~~lt~~~VR~~~ 43 (178)
T TIGR03543 16 VDAFLERARA------AYDNEGGNLTSHDIRNVA 43 (178)
T ss_pred HHHHHHHHHH------HHcCCCCCCCHHHHHHhh
Confidence 6778888743 4566565 9999999875
No 114
>PF03008 DUF234: Archaea bacterial proteins of unknown function; InterPro: IPR004256 This represents a C-terminal domain of unknown function, usually fused to a prokaryotic putative DEXX-box ATPase domain (IPR011579 from INTERPRO) [].
Probab=26.33 E-value=89 Score=21.63 Aligned_cols=25 Identities=20% Similarity=0.262 Sum_probs=19.9
Q ss_pred HHHHHhHHHHHHHHHHHHHhhHHhh
Q 033083 81 MGIMNSFINDIFEKLAQEASRLARY 105 (128)
Q Consensus 81 M~IMnSfVnDiFErIA~EAs~La~~ 105 (128)
..-+++|+..+||.|+.|.......
T Consensus 25 ~~~l~~y~g~~fE~i~r~~l~~~~~ 49 (100)
T PF03008_consen 25 KPELNQYMGFAFEEICREYLRRLNR 49 (100)
T ss_pred HHHHHHHhhHHHHHHHHHHHHHhhc
Confidence 3457899999999999998775543
No 115
>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=26.17 E-value=1.7e+02 Score=23.13 Aligned_cols=69 Identities=19% Similarity=0.224 Sum_probs=35.5
Q ss_pred chhhHHHHHHHhhhccCCCCcchh----hHHHHHhHHHHHHHHHHHHHhh--------------HHhhCCCC----CCCh
Q 033083 56 IETYKIYIFKVLKQVHPDIGISSK----AMGIMNSFINDIFEKLAQEASR--------------LARYNKKP----TITS 113 (128)
Q Consensus 56 ~esys~YIyKVLKQVhPd~gISsk----AM~IMnSfVnDiFErIA~EAs~--------------La~~nkk~----Tlts 113 (128)
...|...|..++.++--|--.|.+ .+.-.+.|-..+=.+|++-+.. ++.||+.. .||.
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 345666777777776555444444 1112233333333333332222 23455555 8999
Q ss_pred hHHHHHHHhhc
Q 033083 114 REIQTAVRLVL 124 (128)
Q Consensus 114 REIQtAVRLlL 124 (128)
.||..|+.++-
T Consensus 136 ~Di~~A~~~l~ 146 (223)
T PF04157_consen 136 EDILRACKLLE 146 (223)
T ss_dssp HHHHHHHHHHC
T ss_pred HHHHHHHHHHH
Confidence 99999999874
No 116
>PRK08293 3-hydroxybutyryl-CoA dehydrogenase; Validated
Probab=25.50 E-value=1.4e+02 Score=23.92 Aligned_cols=37 Identities=11% Similarity=0.097 Sum_probs=30.0
Q ss_pred HhHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHHhhc
Q 033083 85 NSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLVL 124 (128)
Q Consensus 85 nSfVnDiFErIA~EAs~La~~nkk~TltsREIQtAVRLlL 124 (128)
..++|-|+--+..||.+|+.-. ..|..||.+|+++-|
T Consensus 189 gfi~nRi~~~~~~ea~~l~~~g---~a~~~~iD~a~~~~~ 225 (287)
T PRK08293 189 GYILNSLLVPFLSAALALWAKG---VADPETIDKTWMIAT 225 (287)
T ss_pred CHhHHHHHHHHHHHHHHHHHcC---CCCHHHHHHHHHhcc
Confidence 3567788888999999998765 678999999987644
No 117
>cd07347 harmonin_N_like N-terminal protein-binding module of harmonin and similar domains. This domain is found in harmonin, and similar proteins such as delphilin, and whirlin. These are postsynaptic density-95/discs-large/ZO-1 (PDZ) domain-containing scaffold proteins. Harmonin and whirlin are organizers of the Usher protein network of the inner ear and the retina, delphilin is found at the cerebellar parallel fiber-Purkinje cell synapses. This harmonin_N_like domain is found in either one or two copies. Harmonin contains a single copy, which is found at its N-terminus and binds specifically to a short internal peptide fragment of the cadherin 23 cytoplasmic domain; cadherin 23 is a component of the Usher protein network. Whirlin contains two copies of the harmonin_N_like domain; the first of these has been assayed for interaction with the cytoplasmic domain of cadherin 23 and no interaction could be detected.
Probab=24.94 E-value=1.1e+02 Score=21.37 Aligned_cols=33 Identities=15% Similarity=0.381 Sum_probs=24.9
Q ss_pred HHHHHHHhhhccCCCCcchhhHHHHHhHHHHHHHHHHHHHh
Q 033083 60 KIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEAS 100 (128)
Q Consensus 60 s~YIyKVLKQVhPd~gISskAM~IMnSfVnDiFErIA~EAs 100 (128)
..+++..|++-|-+.+ ++.||.|+|+=|-+.|-
T Consensus 21 r~~~~~~L~~Y~~~~~--------Vd~LV~~L~~vLdtPaK 53 (78)
T cd07347 21 REQVTRALERYHQERN--------VDDLVRDLYLVLDTPAK 53 (78)
T ss_pred HHHHHHHHHHHHhcCC--------HHHHHHHHHHHcCcHhH
Confidence 5678888998875443 46799999998877665
No 118
>PF14374 Ribos_L4_asso_C: 60S ribosomal protein L4 C-terminal domain; PDB: 3O5H_D 3IZS_D 3O58_D 3IZR_D 4A17_C 4A1C_C 4A1E_C 4A1A_C.
Probab=24.48 E-value=9.8 Score=26.82 Aligned_cols=11 Identities=55% Similarity=0.752 Sum_probs=9.5
Q ss_pred CChhHHHHHHH
Q 033083 111 ITSREIQTAVR 121 (128)
Q Consensus 111 ltsREIQtAVR 121 (128)
|.|.|||++||
T Consensus 19 InSdEIQsvlr 29 (80)
T PF14374_consen 19 INSDEIQSVLR 29 (80)
T ss_dssp HHSHHHHCCCH
T ss_pred hccHHHHHHHh
Confidence 67899999887
No 119
>PRK08857 para-aminobenzoate synthase component II; Provisional
Probab=24.12 E-value=51 Score=25.19 Aligned_cols=21 Identities=19% Similarity=0.442 Sum_probs=18.7
Q ss_pred hccCCCCcchhhHHHHHhHHH
Q 033083 69 QVHPDIGISSKAMGIMNSFIN 89 (128)
Q Consensus 69 QVhPd~gISskAM~IMnSfVn 89 (128)
|-||+..++.....|+..|++
T Consensus 171 QfHPE~~~t~~g~~i~~nFl~ 191 (193)
T PRK08857 171 QFHPESIKTEQGHQLLANFLA 191 (193)
T ss_pred eeCCCcCCCcchHHHHHHHHh
Confidence 679999899999999999975
No 120
>PRK00074 guaA GMP synthase; Reviewed
Probab=23.56 E-value=63 Score=29.01 Aligned_cols=23 Identities=26% Similarity=0.629 Sum_probs=20.1
Q ss_pred hccCCCCcchhhHHHHHhHHHHH
Q 033083 69 QVHPDIGISSKAMGIMNSFINDI 91 (128)
Q Consensus 69 QVhPd~gISskAM~IMnSfVnDi 91 (128)
|-||+..-+...+.|+.+|+.+|
T Consensus 167 QFHPE~~~t~~G~~il~nFl~~i 189 (511)
T PRK00074 167 QFHPEVTHTPQGKKLLENFVFDI 189 (511)
T ss_pred eCCCCcCCchhHHHHHHHHHHHh
Confidence 77999998889999999998655
No 121
>smart00339 FH FORKHEAD. FORKHEAD, also known as a "winged helix"
Probab=23.40 E-value=1e+02 Score=21.48 Aligned_cols=31 Identities=16% Similarity=0.299 Sum_probs=22.7
Q ss_pred chhhHHHHHHHhhhccCCCCcchhhHHHHHhHHHHHHHHHHH
Q 033083 56 IETYKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQ 97 (128)
Q Consensus 56 ~esys~YIyKVLKQVhPd~gISskAM~IMnSfVnDiFErIA~ 97 (128)
.-||+.-|..+|.. .|+-.++- ++||+-|..
T Consensus 3 ~~sY~~lI~~ai~~-sp~~~ltl----------~~Iy~~I~~ 33 (89)
T smart00339 3 PYSYIALIAMAILS-SPDKRLTL----------SEIYKWIED 33 (89)
T ss_pred CCCHHHHHHHHHHh-CCCCCeeH----------HHHHHHHHH
Confidence 45799999999988 57777663 567776664
No 122
>PRK15361 pathogenicity island 2 effector protein SseD; Provisional
Probab=23.39 E-value=49 Score=27.15 Aligned_cols=45 Identities=33% Similarity=0.434 Sum_probs=34.0
Q ss_pred cchhhHHHHHhH--HHHHHHHHHHHHhhH----HhhCCCCCCChhHHHHHH
Q 033083 76 ISSKAMGIMNSF--INDIFEKLAQEASRL----ARYNKKPTITSREIQTAV 120 (128)
Q Consensus 76 ISskAM~IMnSf--VnDiFErIA~EAs~L----a~~nkk~TltsREIQtAV 120 (128)
-|+.+|++|.-| ++||...+..-+-+| -.||.++-.-.++||.+.
T Consensus 24 ~~~~~md~~s~l~~fddii~kL~eLfKKLRDvl~~YnqkqQ~l~w~iQv~a 74 (195)
T PRK15361 24 PSGEGMGTESMLLLFDDIWMKLMELAKKLRDIMRSYNVEKQRLSWELQVNV 74 (195)
T ss_pred CCcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 467889887666 488888888877765 468888888888888653
No 123
>PLN02545 3-hydroxybutyryl-CoA dehydrogenase
Probab=22.89 E-value=1.8e+02 Score=23.35 Aligned_cols=35 Identities=20% Similarity=0.225 Sum_probs=29.0
Q ss_pred hHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHHhh
Q 033083 86 SFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLV 123 (128)
Q Consensus 86 SfVnDiFErIA~EAs~La~~nkk~TltsREIQtAVRLl 123 (128)
.++|.|+-.+..||.+|..-. ..+..||.+++++-
T Consensus 188 ~i~nri~~~~~~ea~~~~~~g---v~~~~~iD~~~~~g 222 (295)
T PLN02545 188 FIVNRILMPMINEAFYALYTG---VASKEDIDTGMKLG 222 (295)
T ss_pred HHHHHHHHHHHHHHHHHHHcC---CCCHHHHHHHHHhc
Confidence 467888899999999988765 36799999999854
No 124
>PF08118 MDM31_MDM32: Yeast mitochondrial distribution and morphology (MDM) proteins ; InterPro: IPR012571 Proteins in this family are yeast mitochondrial inner membrane proteins MDM31 and MDM32. These proteins are required for the maintenance of mitochondrial morphology, and the stability of mitochondrial DNA [].; GO: 0007005 mitochondrion organization, 0005743 mitochondrial inner membrane
Probab=22.72 E-value=1e+02 Score=28.45 Aligned_cols=45 Identities=20% Similarity=0.376 Sum_probs=33.9
Q ss_pred HHHHhHHHHHHHHHHHHHhhH-HhhCCCCCCChhHHHHHHHhhcCC
Q 033083 82 GIMNSFINDIFEKLAQEASRL-ARYNKKPTITSREIQTAVRLVLPA 126 (128)
Q Consensus 82 ~IMnSfVnDiFErIA~EAs~L-a~~nkk~TltsREIQtAVRLlLPG 126 (128)
.+|+.++.+++|-+|.-...= .|..+-..++.+=+|-|+.+||.|
T Consensus 453 gLmDdiS~evYdafa~~V~d~~~R~~R~kkVg~WSlql~~Q~ll~g 498 (503)
T PF08118_consen 453 GLMDDISAEVYDAFAKYVADEEARIRRLKKVGFWSLQLAAQLLLLG 498 (503)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHhhceeeehhHHHHHHHHHHHh
Confidence 578888888888887766633 233333679999999999999977
No 125
>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional
Probab=22.49 E-value=1.3e+02 Score=26.17 Aligned_cols=40 Identities=15% Similarity=0.171 Sum_probs=33.4
Q ss_pred HHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHHhhcCC
Q 033083 87 FINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLVLPA 126 (128)
Q Consensus 87 fVnDiFErIA~EAs~La~~nkk~TltsREIQtAVRLlLPG 126 (128)
|.-.-+..|+.||...+-...+..|+..|+..|++.+..+
T Consensus 350 ~sgaDI~~l~~eA~~~A~r~~~~~i~~~df~~A~~~v~~~ 389 (398)
T PTZ00454 350 ISAADIAAICQEAGMQAVRKNRYVILPKDFEKGYKTVVRK 389 (398)
T ss_pred CCHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHHHHhc
Confidence 4444466799999999999999999999999999987654
No 126
>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=22.46 E-value=4.2e+02 Score=21.46 Aligned_cols=63 Identities=11% Similarity=0.089 Sum_probs=36.6
Q ss_pred HHHHHHhhhccCCCCcchhhHHHHHhHHH----HH--HHHHHHHHhhHHhhCCCCCCChhHHHHHHHhh
Q 033083 61 IYIFKVLKQVHPDIGISSKAMGIMNSFIN----DI--FEKLAQEASRLARYNKKPTITSREIQTAVRLV 123 (128)
Q Consensus 61 ~YIyKVLKQVhPd~gISskAM~IMnSfVn----Di--FErIA~EAs~La~~nkk~TltsREIQtAVRLl 123 (128)
.++...+.....+..++..++..+..++. |+ .-.+...|..++..+++.+||..+|+.|+..+
T Consensus 206 ~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~R~al~~l~~a~~~a~~~~~~~it~~~v~~a~~~~ 274 (365)
T TIGR02928 206 DILENRAEKAFYDGVLDDGVIPLCAALAAQEHGDARKAIDLLRVAGEIAEREGAERVTEDHVEKAQEKI 274 (365)
T ss_pred HHHHHHHHhhccCCCCChhHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHH
Confidence 33433344333344466666655443331 21 11244556667777788899999999998765
No 127
>PF09193 CholecysA-Rec_N: Cholecystokinin A receptor, N-terminal; InterPro: IPR015276 This entry represents the extracellular N-terminal domain of the cholecystokinin A receptor. This domain adopts a tertiary structure consisting of a few helical turns and a disulphide-cross linked loop. It is required for interaction of the cholecystokinin A receptor with its corresponding hormonal ligand []. ; PDB: 1D6G_A.
Probab=22.30 E-value=31 Score=22.37 Aligned_cols=13 Identities=46% Similarity=0.654 Sum_probs=9.4
Q ss_pred ChhHHHHHHHhhc
Q 033083 112 TSREIQTAVRLVL 124 (128)
Q Consensus 112 tsREIQtAVRLlL 124 (128)
.++|.|-||+++|
T Consensus 35 pske~qpaVqILL 47 (47)
T PF09193_consen 35 PSKEWQPAVQILL 47 (47)
T ss_dssp S-SSHHHHHHS--
T ss_pred ChhHHhhhHhhhC
Confidence 7899999999986
No 128
>PRK14970 DNA polymerase III subunits gamma and tau; Provisional
Probab=22.14 E-value=2.6e+02 Score=23.14 Aligned_cols=60 Identities=13% Similarity=0.165 Sum_probs=45.4
Q ss_pred hHHHHHHHhhhccCCCCcchhhHHHHHhHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHH
Q 033083 59 YKIYIFKVLKQVHPDIGISSKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVR 121 (128)
Q Consensus 59 ys~YIyKVLKQVhPd~gISskAM~IMnSfVnDiFErIA~EAs~La~~nkk~TltsREIQtAVR 121 (128)
...+|.+++++- +..|+..++..+-...+.=+.++..+.-+|+.|.... ||..+|+..|-
T Consensus 172 l~~~l~~~~~~~--g~~i~~~al~~l~~~~~gdlr~~~~~lekl~~y~~~~-it~~~v~~~~~ 231 (367)
T PRK14970 172 IKEHLAGIAVKE--GIKFEDDALHIIAQKADGALRDALSIFDRVVTFCGKN-ITRQAVTENLN 231 (367)
T ss_pred HHHHHHHHHHHc--CCCCCHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCCC-CCHHHHHHHhC
Confidence 344666666653 4568999999888888877888888999999887655 88888876654
No 129
>CHL00176 ftsH cell division protein; Validated
Probab=21.84 E-value=1.2e+02 Score=28.32 Aligned_cols=35 Identities=40% Similarity=0.491 Sum_probs=28.5
Q ss_pred HHHHHHHHhhHHhhCCCCCCChhHHHHHHHhhcCC
Q 033083 92 FEKLAQEASRLARYNKKPTITSREIQTAVRLVLPA 126 (128)
Q Consensus 92 FErIA~EAs~La~~nkk~TltsREIQtAVRLlLPG 126 (128)
.+.+..||..++...++..||..||+.|++-++-|
T Consensus 392 L~~lvneAal~a~r~~~~~It~~dl~~Ai~rv~~g 426 (638)
T CHL00176 392 LANLLNEAAILTARRKKATITMKEIDTAIDRVIAG 426 (638)
T ss_pred HHHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHhh
Confidence 44777888888877888899999999999877544
No 130
>PRK07819 3-hydroxybutyryl-CoA dehydrogenase; Validated
Probab=21.82 E-value=2e+02 Score=23.52 Aligned_cols=33 Identities=21% Similarity=0.286 Sum_probs=27.8
Q ss_pred HHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHHh
Q 033083 87 FINDIFEKLAQEASRLARYNKKPTITSREIQTAVRL 122 (128)
Q Consensus 87 fVnDiFErIA~EAs~La~~nkk~TltsREIQtAVRL 122 (128)
++|.|+..+..||.+|..-+ ..|..||.+++++
T Consensus 192 i~nRi~~~~~~Ea~~ll~eG---v~~~~dID~~~~~ 224 (286)
T PRK07819 192 VVNALLVPYLLSAIRMVESG---FATAEDIDKAMVL 224 (286)
T ss_pred HHHHHHHHHHHHHHHHHHhC---CCCHHHHHHHHHh
Confidence 45789999999999999766 3679999999975
No 131
>PF08546 ApbA_C: Ketopantoate reductase PanE/ApbA C terminal; InterPro: IPR013752 This is the C-terminal domain of 2-dehydropantoate 2-reductases also known as ketopantoate reductases, 1.1.1.169 from EC. The reaction catalysed by this enzyme is: (R)-pantoate + NADP(+) = 2-dehydropantoate + NADPH. AbpA catalyses the NADPH reduction of ketopantoic acid to pantoic acid in the alternative pyrimidine biosynthetic (APB) pathway []. ApbA and PanE are allelic []. ApbA, the ketopantoate reductase enzyme is required for the synthesis of thiamine via the APB biosynthetic pathway []. ; GO: 0016491 oxidoreductase activity, 0050661 NADP binding, 0055114 oxidation-reduction process; PDB: 1YJQ_A 1KS9_A 2OFP_A 1YON_A 2EW2_B 3EGO_B 3HN2_D 3GHY_B 3G17_E 3HWR_B ....
Probab=21.72 E-value=2.3e+02 Score=19.56 Aligned_cols=38 Identities=18% Similarity=0.317 Sum_probs=28.3
Q ss_pred HhHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHHhh
Q 033083 85 NSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLV 123 (128)
Q Consensus 85 nSfVnDiFErIA~EAs~La~~nkk~TltsREIQtAVRLl 123 (128)
|.-..+++..|..|+..+++..+-. |+..++...+.-+
T Consensus 33 ~~~~~~~~~~l~~E~~~va~a~G~~-l~~~~~~~~~~~~ 70 (125)
T PF08546_consen 33 NPEARELIRALMREVIAVARALGIP-LDPDDLEEAIERL 70 (125)
T ss_dssp SHHHHHHHHHHHHHHHHHHHHTTSS---HHHHHHHHHHH
T ss_pred ChhHHHHHHHHHHHHHHHHHHhhcc-CcHHHHHHHHHHH
Confidence 4567899999999999999988855 8777676666543
No 132
>PRK05808 3-hydroxybutyryl-CoA dehydrogenase; Validated
Probab=21.69 E-value=2e+02 Score=22.92 Aligned_cols=35 Identities=20% Similarity=0.232 Sum_probs=28.6
Q ss_pred hHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHHhh
Q 033083 86 SFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLV 123 (128)
Q Consensus 86 SfVnDiFErIA~EAs~La~~nkk~TltsREIQtAVRLl 123 (128)
-++|.||-.+..||.+|..-+ ..|..||..++++=
T Consensus 187 ~i~~Ri~~~~~~ea~~~~~~g---v~~~~diD~~~~~g 221 (282)
T PRK05808 187 FVVNRILIPMINEAIFVLAEG---VATAEDIDEGMKLG 221 (282)
T ss_pred hHHHHHHHHHHHHHHHHHHhC---CCCHHHHHHHHHhC
Confidence 355889999999999998765 36699999999863
No 133
>cd05133 RasGAP_IQGAP1 IQGAP1 is a homodimeric protein that is widely expressed among vertebrate cell types from early embryogenesis. Mammalian IQGAP1 protein is the best characterized member of the IQGAP family, and contains several protein-interacting domains. Human IQGAP1 is most similar to mouse Iqgap1 (94% identity) and has 62% identity to human IQGAP2. IQGAP1 binds and cross-links actin filaments in vitro and has been implicated in Ca2+/calmodulin signaling, E-cadherin-dependent cell adhesion, cell motility, and invasion. Yeast IQGAP homologues have a role in the recruitment of actin filaments, are components of the spindle pole body, and are required for actomyosin ring assembly and cytokinesis. Furthermore, IQGAP1 over-expression has also been detected in gastric and colorectal carcinomas and gastric cancer cell lines.
Probab=21.35 E-value=1.3e+02 Score=26.24 Aligned_cols=65 Identities=20% Similarity=0.264 Sum_probs=43.6
Q ss_pred HHHHHHHhhhccCCCCcch--hhHHHHHhHHHHHHHHHHHH------------HhhHHhh------CC-CCCCChhHHHH
Q 033083 60 KIYIFKVLKQVHPDIGISS--KAMGIMNSFINDIFEKLAQE------------ASRLARY------NK-KPTITSREIQT 118 (128)
Q Consensus 60 s~YIyKVLKQVhPd~gISs--kAM~IMnSfVnDiFErIA~E------------As~La~~------nk-k~TltsREIQt 118 (128)
=..|.|||.|+--....+. .-|.-||.||.+.++++-.= -..+-.| ++ .-+||-.||-.
T Consensus 213 L~~iaKvLQ~lan~~~f~~~e~~m~pLN~fI~~~~~~~~~fl~~~~~V~d~ee~~~~dey~dl~~~~kP~l~Is~~eI~~ 292 (360)
T cd05133 213 LGSIAKMLQHAASNKMFLGDNAHLSIINEYLSQSYQKFRRFFQSACEVPELQDKFNVDEYSDLVTLTKPVIYISIGEIIN 292 (360)
T ss_pred HHHHHHHHHHHHcCCCCCCCccHHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHhcChhHHHHHHhccCCeEEeeHHHHHH
Confidence 5679999999976554443 38999999998888877542 2222223 22 24567888877
Q ss_pred HHHhhc
Q 033083 119 AVRLVL 124 (128)
Q Consensus 119 AVRLlL 124 (128)
=-+||+
T Consensus 293 ~H~Ll~ 298 (360)
T cd05133 293 THTLLL 298 (360)
T ss_pred HHHHHH
Confidence 777664
No 134
>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=21.35 E-value=1.4e+02 Score=23.10 Aligned_cols=37 Identities=19% Similarity=0.316 Sum_probs=26.6
Q ss_pred hhHHHHHHHhhhc--------cCCCC--cchhhHHHHHhHHHHHHHH
Q 033083 58 TYKIYIFKVLKQV--------HPDIG--ISSKAMGIMNSFINDIFEK 94 (128)
Q Consensus 58 sys~YIyKVLKQV--------hPd~g--ISskAM~IMnSfVnDiFEr 94 (128)
....-|..+|.|- +|+-| ||++++..||.+..+|++.
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 3455677777764 65554 9999999999998888764
No 135
>PRK13765 ATP-dependent protease Lon; Provisional
Probab=21.34 E-value=3.1e+02 Score=25.73 Aligned_cols=65 Identities=15% Similarity=0.078 Sum_probs=36.7
Q ss_pred hhhHHHHHHHhhhcc---CCCCcchhhHHHHHhHHH-------------HHHHHHHHHHhhHHhhCCCCCCChhHHHHHH
Q 033083 57 ETYKIYIFKVLKQVH---PDIGISSKAMGIMNSFIN-------------DIFEKLAQEASRLARYNKKPTITSREIQTAV 120 (128)
Q Consensus 57 esys~YIyKVLKQVh---Pd~gISskAM~IMnSfVn-------------DiFErIA~EAs~La~~nkk~TltsREIQtAV 120 (128)
+.+..|+..+-+++. +-..|+..|+.-+-..-. .-+..|..||..+|+...+..++..+|..|+
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 334688877654332211 1122356667777777777777777777665
Q ss_pred H
Q 033083 121 R 121 (128)
Q Consensus 121 R 121 (128)
+
T Consensus 398 ~ 398 (637)
T PRK13765 398 K 398 (637)
T ss_pred H
Confidence 4
No 136
>PF14081 DUF4262: Domain of unknown function (DUF4262)
Probab=20.99 E-value=74 Score=22.97 Aligned_cols=29 Identities=14% Similarity=0.345 Sum_probs=23.3
Q ss_pred hhccCCCCcchhhHHHHHhHHHHHHHHHH
Q 033083 68 KQVHPDIGISSKAMGIMNSFINDIFEKLA 96 (128)
Q Consensus 68 KQVhPd~gISskAM~IMnSfVnDiFErIA 96 (128)
..-||++-|..=...++.+++|++.++|.
T Consensus 30 ~~g~PEliv~GL~~~~a~~lLn~l~~~v~ 58 (125)
T PF14081_consen 30 EHGHPELIVFGLPPETAHSLLNELADRVR 58 (125)
T ss_pred cCCCCCEEEECCCHHHHHHHHHHHHHHHh
Confidence 34589987777677888999999999886
No 137
>cd05131 RasGAP_IQGAP2 IQGAP2 is a member of the IQGAP family that contains a calponin-homology (CH) domain which binds F-actin, IQGAP-specific repeat, a single WW domain, four IQ motifs which mediate interactions with calmodulin, and a Ras-GTPase-activating protein (GAP)-related domain that binds Rho family GTPases. IQGAP2 and IQGAP3 play important roles in the regulation of the cytoskeleton for axon outgrowth in hippocampal neurons and are thought to stay in a common regulatory pathway. The results of RNA interference studies indicated that IQGAP3 partially compensates functions of IQGAP2, but has lesser ability than IQGAP2 to promote axon outgrowth in hippocampal neuron. Morevover, IQGAP2 is required for the cadherin-mediated cell-to-cell adhesion in Xenopus laevis embryos.
Probab=20.53 E-value=1.4e+02 Score=25.53 Aligned_cols=65 Identities=22% Similarity=0.279 Sum_probs=41.9
Q ss_pred HHHHHHHhhhccCCCCcchh--hHHHHHhHHHHHHHHHHHHH------------hhHHhh------CC-CCCCChhHHHH
Q 033083 60 KIYIFKVLKQVHPDIGISSK--AMGIMNSFINDIFEKLAQEA------------SRLARY------NK-KPTITSREIQT 118 (128)
Q Consensus 60 s~YIyKVLKQVhPd~gISsk--AM~IMnSfVnDiFErIA~EA------------s~La~~------nk-k~TltsREIQt 118 (128)
-..|.|||-|+--....+.+ -|.-||.|+...++++-.=- ..+-.| ++ .-+|+..||-.
T Consensus 213 L~~iaKvLq~lan~~~F~~~e~~m~pLN~fi~~~~~~~~~fl~~l~~V~d~e~~~~~d~Y~dl~~~~kP~l~I~~~ei~~ 292 (339)
T cd05131 213 LGSVAKVLQHAASNKLFEGENDHLSSMNSYLSQTYQKFRKFFQAACDVPEPEEKFNVDEYSDLVTLSKPVIYISIEEIIN 292 (339)
T ss_pred HHHHHHHHHHHHCCCCCCCcChHHHhHHHHHHHHHHHHHHHHHHHhcCCCHHHHcChhHHHHHHhccCCeEEeeHHHHHH
Confidence 46799999999755444433 59999999987777764322 222223 22 25668888877
Q ss_pred HHHhhc
Q 033083 119 AVRLVL 124 (128)
Q Consensus 119 AVRLlL 124 (128)
=-+||+
T Consensus 293 ih~ll~ 298 (339)
T cd05131 293 THSLLL 298 (339)
T ss_pred HHHHHH
Confidence 666653
No 138
>PF13843 DDE_Tnp_1_7: Transposase IS4
Probab=20.45 E-value=2.1e+02 Score=23.65 Aligned_cols=44 Identities=23% Similarity=0.508 Sum_probs=33.6
Q ss_pred HHHHHhHH-HHHHHHHHHHHhhHHhh---CCCCCCChhHHHHHHHhhc
Q 033083 81 MGIMNSFI-NDIFEKLAQEASRLARY---NKKPTITSREIQTAVRLVL 124 (128)
Q Consensus 81 M~IMnSfV-nDiFErIA~EAs~La~~---nkk~TltsREIQtAVRLlL 124 (128)
+++.+.|+ .+|++.|+.+.-.-+.. ++...+|..||..=+-|++
T Consensus 3 ~~~F~~~f~~~~~~~iv~~TN~~~~~~~~~~~~~~t~~Ei~~f~Gl~i 50 (351)
T PF13843_consen 3 LDLFQLFFPDEIIQQIVEETNRYAKQKFKKKWKPVTAEEIKAFFGLLI 50 (351)
T ss_pred HHHHHHHCCHHHHHHHHHHHHHHHHHhccccCCCCCHHHHHHHHHHHH
Confidence 45666666 48999999888775554 6778999999998777654
No 139
>PF15469 Sec5: Exocyst complex component Sec5
Probab=20.45 E-value=1.8e+02 Score=21.88 Aligned_cols=36 Identities=25% Similarity=0.406 Sum_probs=22.3
Q ss_pred hhhHHHHHhHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHHhhc
Q 033083 78 SKAMGIMNSFINDIFEKLAQEASRLARYNKKPTITSREIQTAVRLVL 124 (128)
Q Consensus 78 skAM~IMnSfVnDiFErIA~EAs~La~~nkk~TltsREIQtAVRLlL 124 (128)
.+.-.||++|-++++++|..-- .+..++...|++||
T Consensus 131 ~eve~ii~~~r~~l~~~L~~~~-----------~s~~~~~~~i~~Ll 166 (182)
T PF15469_consen 131 SEVEKIIEEFREKLWEKLLSPP-----------SSQEEFLKLIRKLL 166 (182)
T ss_pred HHHHHHHHHHHHHHHHHHhCCC-----------CCHHHHHHHHHHHH
Confidence 4445667777777777765432 55666666666654
No 140
>PF03428 RP-C: Replication protein C N-terminal domain; InterPro: IPR005090 Proteins in this group have homology with the RepC protein of Agrobacterium Ri and Ti plasmids []. They may be involved in plasmid replication and stabilisation functions.
Probab=20.11 E-value=80 Score=24.93 Aligned_cols=28 Identities=21% Similarity=0.726 Sum_probs=25.0
Q ss_pred HHHHHhhhccCCCCcchhhHHHHHhHHH
Q 033083 62 YIFKVLKQVHPDIGISSKAMGIMNSFIN 89 (128)
Q Consensus 62 YIyKVLKQVhPd~gISskAM~IMnSfVn 89 (128)
=+++.|++.-|.+|||..++.+|+-++.
T Consensus 27 ~ll~~l~~a~~~lgl~~~~l~vL~aLls 54 (177)
T PF03428_consen 27 QLLRALKEARPALGLSDRALAVLDALLS 54 (177)
T ss_pred HHHHHHHHHHHhcCCChhHHHHHHHHHH
Confidence 3889999999999999999999988874
No 141
>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=20.04 E-value=2.1e+02 Score=18.50 Aligned_cols=34 Identities=18% Similarity=0.267 Sum_probs=18.3
Q ss_pred hHHHHHHHHHHHHHhhHHhhCCCCCCChhHHHHHHH
Q 033083 86 SFINDIFEKLAQEASRLARYNKKPTITSREIQTAVR 121 (128)
Q Consensus 86 SfVnDiFErIA~EAs~La~~nkk~TltsREIQtAVR 121 (128)
.++.|.|-.++.......-.+++ +|-++|....+
T Consensus 5 ~ii~~~fG~~~~~V~~~Ll~~G~--ltl~~i~~~t~ 38 (62)
T PF08221_consen 5 LIIEEHFGEIVAKVGEVLLSRGR--LTLREIVRRTG 38 (62)
T ss_dssp HHHHHHHHHHHHHHHHHHHHC-S--EEHHHHHHHHT
T ss_pred HHHHHHcChHHHHHHHHHHHcCC--cCHHHHHHHhC
Confidence 35677777777776664444443 33445444433
Done!