Query 047516
Match_columns 214
No_of_seqs 148 out of 653
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 11:50:37 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/047516.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/047516hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0869 CCAAT-binding factor, 100.0 1.3E-37 2.8E-42 258.6 12.9 109 33-141 22-130 (168)
2 KOG0871 Class 2 transcription 99.9 9.7E-27 2.1E-31 192.1 12.2 114 38-151 7-124 (156)
3 KOG0870 DNA polymerase epsilon 99.9 3.8E-23 8.3E-28 173.4 9.7 98 36-133 3-101 (172)
4 COG5150 Class 2 transcription 99.9 2.1E-21 4.5E-26 157.8 11.8 113 39-151 7-123 (148)
5 COG2036 HHT1 Histones H3 and H 99.7 4.8E-18 1E-22 130.8 7.1 80 35-116 11-90 (91)
6 PF00808 CBFD_NFYB_HMF: Histon 99.7 9.9E-18 2.1E-22 119.2 8.1 64 43-107 2-65 (65)
7 cd00076 H4 Histone H4, one of 99.5 2.7E-13 5.8E-18 103.3 8.9 71 43-115 13-83 (85)
8 PLN00035 histone H4; Provision 99.4 6.8E-13 1.5E-17 104.4 8.9 77 37-115 23-99 (103)
9 PTZ00015 histone H4; Provision 99.4 1.5E-12 3.3E-17 102.3 8.8 77 37-115 24-100 (102)
10 smart00417 H4 Histone H4. 99.3 9.9E-12 2.1E-16 92.6 6.3 64 41-106 11-74 (74)
11 smart00803 TAF TATA box bindin 99.3 2.6E-11 5.7E-16 87.8 7.9 64 43-108 2-65 (65)
12 smart00428 H3 Histone H3. 99.2 3.6E-11 7.7E-16 94.9 7.1 75 37-111 23-102 (105)
13 PLN00160 histone H3; Provision 99.0 1E-09 2.2E-14 85.7 6.6 73 37-109 15-91 (97)
14 PLN00161 histone H3; Provision 99.0 1.7E-09 3.6E-14 88.9 7.7 73 37-109 49-125 (135)
15 PLN00121 histone H3; Provision 99.0 8.9E-10 1.9E-14 90.6 5.8 73 37-109 56-131 (136)
16 cd07981 TAF12 TATA Binding Pro 99.0 4.5E-09 9.7E-14 77.1 8.8 65 44-109 2-66 (72)
17 PTZ00018 histone H3; Provision 99.0 1.7E-09 3.6E-14 89.0 7.0 74 37-110 56-132 (136)
18 PF00125 Histone: Core histone 98.9 2E-09 4.3E-14 77.6 6.2 68 41-108 3-73 (75)
19 COG5208 HAP5 CCAAT-binding fac 98.7 9.3E-09 2E-13 90.9 4.6 77 40-118 106-183 (286)
20 KOG3467 Histone H4 [Chromatin 98.7 4.1E-08 9E-13 76.0 7.6 69 43-113 29-97 (103)
21 smart00576 BTP Bromodomain tra 98.6 2.4E-07 5.2E-12 68.4 8.7 66 46-113 9-74 (77)
22 cd00074 H2A Histone 2A; H2A is 98.5 7E-07 1.5E-11 71.5 8.9 69 39-108 16-84 (115)
23 cd07979 TAF9 TATA Binding Prot 98.5 8.4E-07 1.8E-11 70.8 9.2 75 47-123 5-80 (117)
24 KOG1657 CCAAT-binding factor, 98.5 2.2E-07 4.7E-12 82.4 5.2 84 41-126 72-159 (236)
25 KOG1745 Histones H3 and H4 [Ch 98.4 8.2E-08 1.8E-12 79.1 2.1 75 37-111 57-134 (137)
26 cd08050 TAF6 TATA Binding Prot 98.2 4.8E-06 1.1E-10 76.6 8.8 67 45-113 1-67 (343)
27 PF15630 CENP-S: Kinetochore c 97.9 3.5E-05 7.6E-10 57.7 6.9 62 48-109 10-72 (76)
28 PF15511 CENP-T: Centromere ki 97.9 1.6E-05 3.4E-10 75.2 6.3 63 40-102 348-414 (414)
29 PF07524 Bromo_TP: Bromodomain 97.9 9.2E-05 2E-09 54.2 8.9 64 48-113 11-74 (77)
30 PF02969 TAF: TATA box binding 97.8 0.00014 3E-09 53.2 8.0 64 43-108 3-66 (66)
31 COG5247 BUR6 Class 2 transcrip 97.8 0.0001 2.2E-09 58.7 7.3 76 40-116 20-95 (113)
32 PF03847 TFIID_20kDa: Transcri 97.7 0.00018 4E-09 52.7 7.7 63 46-109 2-64 (68)
33 smart00427 H2B Histone H2B. 97.7 0.00025 5.5E-09 54.8 7.9 62 48-110 6-67 (89)
34 KOG1142 Transcription initiati 97.6 0.00028 6E-09 63.7 8.1 69 40-109 151-219 (258)
35 KOG1659 Class 2 transcription 97.6 0.00023 5E-09 62.8 7.1 83 43-126 13-95 (224)
36 PLN00158 histone H2B; Provisio 97.6 0.00062 1.3E-08 55.0 8.8 67 43-110 27-93 (116)
37 COG5262 HTA1 Histone H2A [Chro 97.5 0.00029 6.4E-09 57.3 6.1 71 37-108 20-90 (132)
38 cd08048 TAF11 TATA Binding Pro 97.4 0.00097 2.1E-08 50.9 8.1 66 43-110 16-84 (85)
39 PF09415 CENP-X: CENP-S associ 97.4 0.00031 6.7E-09 52.1 5.2 64 45-108 1-66 (72)
40 PTZ00463 histone H2B; Provisio 97.4 0.00093 2E-08 54.0 7.9 62 48-110 33-94 (117)
41 smart00414 H2A Histone 2A. 97.3 0.00099 2.1E-08 52.8 6.6 68 40-108 6-73 (106)
42 PF04719 TAFII28: hTAFII28-lik 97.1 0.0027 5.9E-08 49.1 7.4 67 43-110 23-90 (90)
43 PLN00154 histone H2A; Provisio 97.1 0.0042 9.1E-08 51.5 8.8 70 39-108 34-103 (136)
44 PTZ00017 histone H2A; Provisio 96.9 0.0025 5.5E-08 52.6 6.1 68 40-108 24-91 (134)
45 PF02291 TFIID-31kDa: Transcri 96.7 0.0073 1.6E-07 49.4 7.5 81 43-125 10-93 (129)
46 PLN00156 histone H2AX; Provisi 96.7 0.012 2.5E-07 49.0 8.6 69 39-108 25-93 (139)
47 KOG1756 Histone 2A [Chromatin 96.6 0.009 1.9E-07 49.2 7.5 70 38-108 22-91 (131)
48 PLN00157 histone H2A; Provisio 96.6 0.0048 1E-07 50.9 5.8 68 40-108 23-90 (132)
49 PLN00153 histone H2A; Provisio 96.6 0.0053 1.2E-07 50.4 6.0 68 40-108 21-88 (129)
50 KOG1658 DNA polymerase epsilon 96.5 0.0017 3.7E-08 54.9 2.4 66 42-109 58-124 (162)
51 KOG1744 Histone H2B [Chromatin 96.4 0.015 3.3E-07 47.7 7.3 63 47-110 41-103 (127)
52 PF15510 CENP-W: Centromere ki 96.2 0.011 2.4E-07 46.4 5.4 67 42-109 15-95 (102)
53 PF02269 TFIID-18kDa: Transcri 95.8 0.012 2.5E-07 45.3 3.9 59 50-109 8-66 (93)
54 PTZ00252 histone H2A; Provisio 95.7 0.038 8.3E-07 45.7 6.7 70 38-108 20-91 (134)
55 KOG3219 Transcription initiati 95.6 0.017 3.8E-07 50.4 4.4 68 43-112 112-180 (195)
56 KOG4336 TBP-associated transcr 95.4 0.15 3.3E-06 47.4 10.3 66 61-128 21-86 (323)
57 cd07978 TAF13 The TATA Binding 94.8 0.25 5.4E-06 38.1 8.3 59 48-109 7-66 (92)
58 KOG2549 Transcription initiati 94.6 0.15 3.2E-06 50.8 8.2 65 44-110 12-76 (576)
59 KOG3423 Transcription initiati 93.7 0.4 8.7E-06 41.3 8.0 68 43-112 86-167 (176)
60 KOG3334 Transcription initiati 92.9 0.79 1.7E-05 38.6 8.4 75 50-126 20-95 (148)
61 TIGR03015 pepcterm_ATPase puta 90.5 1.1 2.3E-05 38.3 7.0 69 44-112 192-268 (269)
62 COG5095 TAF6 Transcription ini 89.4 1.5 3.2E-05 41.8 7.4 65 46-112 8-72 (450)
63 PRK00411 cdc6 cell division co 88.1 2.8 6E-05 38.1 8.2 71 45-115 208-287 (394)
64 KOG2389 Predicted bromodomain 87.9 1.6 3.5E-05 41.3 6.7 68 44-113 30-97 (353)
65 cd08045 TAF4 TATA Binding Prot 84.3 14 0.00029 32.0 10.1 78 40-117 41-126 (212)
66 TIGR02928 orc1/cdc6 family rep 84.2 4.2 9.1E-05 36.4 7.2 72 46-117 201-281 (365)
67 PF13654 AAA_32: AAA domain; P 83.8 5 0.00011 39.4 8.1 48 62-109 447-505 (509)
68 PF08369 PCP_red: Proto-chloro 76.6 4.2 9.1E-05 27.5 3.5 42 64-106 2-44 (45)
69 TIGR00764 lon_rel lon-related 76.4 11 0.00024 37.7 7.9 48 62-109 330-390 (608)
70 KOG2680 DNA helicase TIP49, TB 74.5 14 0.00031 35.4 7.7 49 59-107 374-426 (454)
71 TIGR02902 spore_lonB ATP-depen 74.0 9.3 0.0002 37.4 6.5 64 46-109 265-331 (531)
72 COG1067 LonB Predicted ATP-dep 73.2 3.6 7.8E-05 41.7 3.6 48 62-109 338-398 (647)
73 COG5162 Transcription initiati 73.1 21 0.00046 31.1 7.7 50 63-112 106-188 (197)
74 KOG1757 Histone 2A [Chromatin 72.9 4.9 0.00011 32.9 3.6 66 39-108 26-95 (131)
75 PF03540 TFIID_30kDa: Transcri 72.7 22 0.00048 25.0 6.4 48 43-92 2-49 (51)
76 PF13335 Mg_chelatase_2: Magne 69.2 22 0.00048 27.2 6.4 48 61-108 41-94 (96)
77 COG5094 TAF9 Transcription ini 69.0 38 0.00083 28.3 8.0 74 59-132 28-105 (145)
78 KOG3901 Transcription initiati 64.7 36 0.00079 27.4 6.9 50 57-109 22-71 (109)
79 TIGR00635 ruvB Holliday juncti 63.9 53 0.0012 28.7 8.6 72 44-115 159-234 (305)
80 COG5624 TAF61 Transcription in 62.0 3.5 7.7E-05 40.2 0.9 82 37-118 375-461 (505)
81 PLN03162 golden-2 like transcr 61.4 1.7E+02 0.0036 28.9 11.8 55 60-132 237-292 (526)
82 PRK00080 ruvB Holliday junctio 60.2 51 0.0011 29.7 8.0 72 44-115 180-255 (328)
83 PF05236 TAF4: Transcription i 57.1 17 0.00036 32.3 4.3 78 38-115 38-123 (264)
84 COG5248 TAF19 Transcription in 55.3 39 0.00084 27.7 5.6 50 58-109 23-72 (126)
85 COG1224 TIP49 DNA helicase TIP 54.4 36 0.00078 33.3 6.2 50 59-108 377-430 (450)
86 TIGR02442 Cob-chelat-sub cobal 54.0 43 0.00093 33.6 7.0 50 59-108 246-302 (633)
87 TIGR02030 BchI-ChlI magnesium 53.9 41 0.00089 31.3 6.4 54 54-108 247-307 (337)
88 PRK09862 putative ATP-dependen 52.2 60 0.0013 32.1 7.5 52 62-113 438-495 (506)
89 COG1474 CDC6 Cdc6-related prot 51.4 58 0.0012 30.7 7.0 71 47-117 193-272 (366)
90 PF09123 DUF1931: Domain of un 50.8 14 0.0003 30.9 2.6 69 49-129 1-69 (138)
91 smart00350 MCM minichromosome 48.6 80 0.0017 30.7 7.7 67 42-110 416-504 (509)
92 TIGR01128 holA DNA polymerase 48.5 1E+02 0.0022 26.6 7.7 66 44-109 111-177 (302)
93 PRK13406 bchD magnesium chelat 47.9 67 0.0014 32.3 7.2 52 56-108 190-248 (584)
94 PRK07452 DNA polymerase III su 47.9 55 0.0012 29.1 6.1 65 49-113 135-202 (326)
95 PF02861 Clp_N: Clp amino term 47.0 32 0.00069 22.2 3.4 26 86-111 1-26 (53)
96 PF09114 MotA_activ: Transcrip 46.9 27 0.00059 27.6 3.5 33 47-79 51-87 (96)
97 PRK12402 replication factor C 45.3 66 0.0014 28.2 6.1 71 44-116 184-255 (337)
98 PRK13765 ATP-dependent proteas 45.2 40 0.00088 34.2 5.3 47 62-108 339-398 (637)
99 CHL00081 chlI Mg-protoporyphyr 44.8 94 0.002 29.3 7.3 54 54-108 260-320 (350)
100 PF12627 PolyA_pol_RNAbd: Prob 43.3 13 0.00028 25.4 1.1 57 61-121 2-62 (64)
101 TIGR00368 Mg chelatase-related 43.2 67 0.0014 31.6 6.3 47 62-108 445-497 (499)
102 PF08681 DUF1778: Protein of u 42.5 21 0.00045 26.4 2.2 18 60-77 3-20 (80)
103 PRK13407 bchI magnesium chelat 40.5 1.3E+02 0.0029 27.9 7.6 49 59-107 248-303 (334)
104 TIGR02031 BchD-ChlD magnesium 40.2 1E+02 0.0023 30.7 7.3 54 54-108 196-256 (589)
105 PTZ00361 26 proteosome regulat 39.9 42 0.00091 32.5 4.3 33 77-109 391-423 (438)
106 PF00531 Death: Death domain; 39.7 53 0.0011 23.0 3.9 30 94-123 54-83 (83)
107 PF04552 Sigma54_DBD: Sigma-54 37.7 40 0.00086 28.4 3.4 40 89-132 113-152 (160)
108 PRK05574 holA DNA polymerase I 36.8 2.1E+02 0.0046 25.2 8.0 66 44-109 146-212 (340)
109 PF11753 DUF3310: Protein of u 36.4 1.1E+02 0.0024 21.5 5.1 41 66-108 14-56 (60)
110 KOG3535 Adaptor protein Disabl 36.2 26 0.00056 34.7 2.3 41 156-196 324-364 (557)
111 TIGR01242 26Sp45 26S proteasom 36.2 56 0.0012 29.9 4.4 33 77-109 330-362 (364)
112 PRK05932 RNA polymerase factor 36.0 93 0.002 30.3 6.0 78 40-131 351-445 (455)
113 PRK03992 proteasome-activating 35.8 57 0.0012 30.5 4.4 34 77-110 339-372 (389)
114 PF00356 LacI: Bacterial regul 35.7 84 0.0018 21.1 4.1 32 43-78 10-41 (46)
115 PRK06585 holA DNA polymerase I 35.2 1.1E+02 0.0024 27.4 6.1 50 60-109 159-209 (343)
116 PF07647 SAM_2: SAM domain (St 35.2 54 0.0012 22.3 3.2 24 98-121 4-27 (66)
117 PRK02910 light-independent pro 34.5 1.6E+02 0.0034 28.9 7.3 52 59-111 466-518 (519)
118 PRK07914 hypothetical protein; 33.0 1.1E+02 0.0025 27.4 5.8 63 45-108 129-192 (320)
119 PRK14975 bifunctional 3'-5' ex 31.8 3E+02 0.0065 27.2 8.9 90 40-132 160-269 (553)
120 PF13405 EF-hand_6: EF-hand do 31.4 59 0.0013 19.2 2.6 26 86-111 5-31 (31)
121 PTZ00454 26S protease regulato 31.4 73 0.0016 30.3 4.4 33 77-109 353-385 (398)
122 cd00166 SAM Sterile alpha moti 30.6 46 0.001 21.8 2.2 23 99-121 3-25 (63)
123 PF00536 SAM_1: SAM domain (St 30.6 64 0.0014 21.8 3.0 22 99-120 4-25 (64)
124 smart00027 EH Eps15 homology d 30.2 1.2E+02 0.0026 22.3 4.6 28 86-113 15-42 (96)
125 TIGR02395 rpoN_sigma RNA polym 29.9 1.3E+02 0.0028 29.0 5.9 75 40-131 326-421 (429)
126 COG1466 HolA DNA polymerase II 29.2 1.7E+02 0.0037 26.6 6.3 50 60-109 157-206 (334)
127 PRK14971 DNA polymerase III su 27.9 1.4E+02 0.0031 30.1 6.0 64 44-108 180-244 (614)
128 PLN00138 large subunit ribosom 27.8 1.8E+02 0.004 23.3 5.5 28 86-113 6-33 (113)
129 COG1724 Predicted RNA binding 27.8 47 0.001 24.6 1.9 17 97-113 6-22 (66)
130 PRK12469 RNA polymerase factor 27.6 1.5E+02 0.0033 29.3 6.0 78 40-131 377-471 (481)
131 cd04752 Commd4 COMM_Domain con 27.0 3.8E+02 0.0082 22.4 9.5 48 74-128 43-91 (174)
132 TIGR01278 DPOR_BchB light-inde 26.9 1.3E+02 0.0028 29.3 5.4 52 59-111 459-511 (511)
133 CHL00076 chlB photochlorophyll 26.8 1.4E+02 0.003 29.3 5.5 52 59-111 460-512 (513)
134 PF08823 PG_binding_2: Putativ 26.7 1.3E+02 0.0028 22.3 4.1 32 101-132 19-56 (74)
135 PF12010 DUF3502: Domain of un 26.7 66 0.0014 25.8 2.8 62 64-129 71-132 (134)
136 PLN03105 TCP24 transcription f 26.3 45 0.00098 30.8 2.0 14 182-195 290-303 (324)
137 PRK00440 rfc replication facto 26.2 1.6E+02 0.0035 25.5 5.3 65 44-110 161-226 (319)
138 PTZ00373 60S Acidic ribosomal 25.9 2.1E+02 0.0045 23.0 5.5 28 86-113 8-35 (112)
139 PRK05629 hypothetical protein; 25.7 2.3E+02 0.0051 25.3 6.5 48 60-108 143-190 (318)
140 PRK14700 recombination factor 25.3 4.7E+02 0.01 24.5 8.5 65 44-109 39-114 (300)
141 PRK05907 hypothetical protein; 25.0 1.8E+02 0.0039 26.7 5.7 73 60-132 151-233 (311)
142 PF07499 RuvA_C: RuvA, C-termi 24.7 57 0.0012 21.7 1.8 14 100-113 3-16 (47)
143 smart00454 SAM Sterile alpha m 24.6 65 0.0014 21.2 2.1 25 98-122 4-28 (68)
144 TIGR02639 ClpA ATP-dependent C 24.3 4.9E+02 0.011 26.6 9.1 68 46-113 347-433 (731)
145 cd00051 EFh EF-hand, calcium b 23.8 1.8E+02 0.0038 17.6 5.1 38 89-126 8-45 (63)
146 PTZ00184 calmodulin; Provision 23.4 2.9E+02 0.0062 20.6 5.7 40 84-123 87-126 (149)
147 TIGR01052 top6b DNA topoisomer 23.3 84 0.0018 31.1 3.4 52 61-126 433-484 (488)
148 PRK14964 DNA polymerase III su 23.1 1.7E+02 0.0038 28.8 5.5 47 60-107 192-238 (491)
149 KOG2296 Integral membrane prot 22.6 73 0.0016 32.8 2.8 44 105-148 529-576 (673)
150 TIGR02903 spore_lon_C ATP-depe 22.5 1.7E+02 0.0037 29.4 5.4 71 45-116 354-436 (615)
151 PRK09111 DNA polymerase III su 22.3 2.1E+02 0.0046 28.8 6.0 61 46-107 193-254 (598)
152 KOG0027 Calmodulin and related 22.2 4E+02 0.0087 21.1 8.2 80 44-123 41-127 (151)
153 COG5251 TAF40 Transcription in 22.0 1.3E+02 0.0029 26.4 3.9 63 43-107 115-178 (199)
154 PRK12728 fliE flagellar hook-b 21.6 4E+02 0.0087 20.9 7.1 39 92-131 59-99 (102)
155 COG1222 RPT1 ATP-dependent 26S 21.6 1.1E+02 0.0024 29.8 3.7 41 69-109 347-391 (406)
156 PRK08487 DNA polymerase III su 21.5 3.2E+02 0.0069 24.7 6.5 59 49-109 140-199 (328)
157 PF05930 Phage_AlpA: Prophage 21.4 52 0.0011 22.0 1.1 25 42-66 13-38 (51)
158 KOG2129 Uncharacterized conser 21.3 4E+02 0.0086 26.7 7.4 19 13-31 17-35 (552)
159 PTZ00186 heat shock 70 kDa pre 21.1 2.6E+02 0.0055 28.5 6.3 14 43-56 526-539 (657)
160 PF02361 CbiQ: Cobalt transpor 21.0 1.7E+02 0.0036 24.0 4.2 38 96-133 123-172 (224)
161 cd04750 Commd2 COMM_Domain con 21.0 5E+02 0.011 21.7 9.4 20 95-114 49-68 (166)
162 KOG1528 Salt-sensitive 3'-phos 20.9 2.4E+02 0.0053 26.9 5.7 64 46-109 52-122 (351)
163 COG1389 DNA topoisomerase VI, 20.6 1.1E+02 0.0023 30.8 3.5 37 62-98 442-478 (538)
164 PRK10339 DNA-binding transcrip 20.4 1.1E+02 0.0025 26.5 3.3 34 43-78 12-45 (327)
165 PRK09526 lacI lac repressor; R 20.3 1E+02 0.0022 26.8 3.0 38 43-85 16-53 (342)
166 PRK14961 DNA polymerase III su 20.3 2.8E+02 0.0061 25.5 6.0 63 45-108 179-242 (363)
No 1
>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [Transcription]
Probab=100.00 E-value=1.3e-37 Score=258.64 Aligned_cols=109 Identities=72% Similarity=1.142 Sum_probs=103.4
Q ss_pred CCCCCccccccCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHHHcCC
Q 047516 33 NNHNSKEQDRFLPIANVGRIMKKVIPGNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAITTLGF 112 (214)
Q Consensus 33 ~~~~~k~~Dl~LPkA~V~RImK~~LP~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~LGF 112 (214)
.....+++|++||+|+|.||||..||.+.+|+|||++.+|+|+.|||+|||++|++.|.+++||||++|||||||..|||
T Consensus 22 ~~~~~reqDr~LPIANV~RIMK~~lP~naKIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIngdDllwAm~tLGF 101 (168)
T KOG0869|consen 22 SSLSLREQDRFLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASEKCQREKRKTINGDDLLWAMSTLGF 101 (168)
T ss_pred cccccchhhhhccHHHHHHHHHhcCCcccccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCcccHHHHHHHHHHcCc
Confidence 44779999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcchHHHHHHHHHHHHHHhhhcCCchhhh
Q 047516 113 EDYVAPLKLYLSKYREIEGEKLNIPKQQR 141 (214)
Q Consensus 113 ~dyi~~Lk~~L~~yre~~~~K~~~~~~~~ 141 (214)
++|+++|+.||.+|||.++++....+...
T Consensus 102 e~Y~eplkiyL~kYRe~e~e~~~~~~~~~ 130 (168)
T KOG0869|consen 102 ENYAEPLKIYLQKYRELEGERGRSGKGGQ 130 (168)
T ss_pred HhHHHHHHHHHHHHHHHhhhcccccccCc
Confidence 99999999999999999999876665544
No 2
>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=99.94 E-value=9.7e-27 Score=192.10 Aligned_cols=114 Identities=29% Similarity=0.566 Sum_probs=99.9
Q ss_pred ccccccCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHHHcCCCcchH
Q 047516 38 KEQDRFLPIANVGRIMKKVIPGNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAITTLGFEDYVA 117 (214)
Q Consensus 38 k~~Dl~LPkA~V~RImK~~LP~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~LGF~dyi~ 117 (214)
..+|+.||+|+|.+|||+.||.++||.+||+++|.+||.+||+.|+++||++|..+.||||.+|||++||+.|||.+|++
T Consensus 7 ~dde~sLPkAtv~KmIke~lP~d~rvakeareliincCvEFI~liSsEAneic~~e~KKTIa~EHV~KALe~LgF~eYie 86 (156)
T KOG0871|consen 7 EDDELSLPKATVNKMIKEMLPKDVRVAKEARELIINCCVEFINLISSEANEICNKEAKKTIAPEHVIKALENLGFGEYIE 86 (156)
T ss_pred ccccccCcHHHHHHHHHHhCCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHhHHhcccCCHHHHHHHHHHcchHHHHH
Confidence 35788999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHhhh--cCCc--hhhhHHHHHHHHHH
Q 047516 118 PLKLYLSKYREIEGEK--LNIP--KQQRSEQRVQQQQQ 151 (214)
Q Consensus 118 ~Lk~~L~~yre~~~~K--~~~~--~~~~~E~~~~~q~~ 151 (214)
.+...|+.|+.....+ ++.+ +..-.|++|..|||
T Consensus 87 e~~~vl~~~K~~~~~~~~kssk~e~~Gi~eEEL~~qQq 124 (156)
T KOG0871|consen 87 EAEEVLENCKEEAKKRRRKSSKFEKSGIPEEELLRQQQ 124 (156)
T ss_pred HHHHHHHHHHHHHHHhhhhhhhHHhcCCCHHHHHHHHH
Confidence 9999999999865432 2111 13346777777666
No 3
>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription]
Probab=99.89 E-value=3.8e-23 Score=173.36 Aligned_cols=98 Identities=32% Similarity=0.550 Sum_probs=93.0
Q ss_pred CCccccccCchhHHHHHHhhcCCCC-cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHHHcCCCc
Q 047516 36 NSKEQDRFLPIANVGRIMKKVIPGN-GKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAITTLGFED 114 (214)
Q Consensus 36 ~~k~~Dl~LPkA~V~RImK~~LP~~-~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~LGF~d 114 (214)
..+.+|+.||.|+|.||+|+.||.. +.|+|||+.+|+++|++||+||++.|+++|...+||||+++||+.||++|+|..
T Consensus 3 ~eri~dl~lP~AiI~rlvke~l~E~~vsisKeA~~Ai~raAtVFv~~Lts~s~e~A~~q~rKt~sadDVl~aL~Eiefs~ 82 (172)
T KOG0870|consen 3 DERIEDLNLPNAIITRLVKEVLPESNVSISKEARLAIARAATVFVIFLTSVSNEIAKDQKRKTISADDVLKALDEIEFSS 82 (172)
T ss_pred chhHHHhhccHHHHHHHHHHhCccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCcccHHHHHHHHHHhchHH
Confidence 3467899999999999999999987 899999999999999999999999999999999999999999999999999999
Q ss_pred chHHHHHHHHHHHHHHhhh
Q 047516 115 YVAPLKLYLSKYREIEGEK 133 (214)
Q Consensus 115 yi~~Lk~~L~~yre~~~~K 133 (214)
|+.+|+..|+.|+.....|
T Consensus 83 f~~plk~~Le~yk~~~k~K 101 (172)
T KOG0870|consen 83 FVNPLKSALEAYKKAVKQK 101 (172)
T ss_pred HhhHHHHHHHHHHHHHHHH
Confidence 9999999999999876554
No 4
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=99.86 E-value=2.1e-21 Score=157.76 Aligned_cols=113 Identities=26% Similarity=0.448 Sum_probs=100.3
Q ss_pred cccccCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHHHcCCCcchHH
Q 047516 39 EQDRFLPIANVGRIMKKVIPGNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAITTLGFEDYVAP 118 (214)
Q Consensus 39 ~~Dl~LPkA~V~RImK~~LP~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~LGF~dyi~~ 118 (214)
.+++.||+|+|.++|-+.||.+..+++||++.+++||.+||+.|+++|++.|..+.+|||.+|||++||+.|||.+|++.
T Consensus 7 dDe~sLPKATVqKMvS~iLp~dl~ftKearei~in~cieFi~~lsseAne~ce~EaKKTIa~EHviKALenLef~eyi~~ 86 (148)
T COG5150 7 DDENSLPKATVQKMVSSILPKDLVFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHVIKALENLEFEEYIES 86 (148)
T ss_pred cccccCcHHHHHHHHHHhccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHhccHHHHHHH
Confidence 46788999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhhhcCCc----hhhhHHHHHHHHHH
Q 047516 119 LKLYLSKYREIEGEKLNIP----KQQRSEQRVQQQQQ 151 (214)
Q Consensus 119 Lk~~L~~yre~~~~K~~~~----~~~~~E~~~~~q~~ 151 (214)
+.+.+..|+..++.|-..- ...-++.+|.+||.
T Consensus 87 ~~e~~~n~k~~qK~ke~k~sKFk~SGls~eELlrQQe 123 (148)
T COG5150 87 CMEEHENYKSYQKQKESKISKFKDSGLSMEELLRQQE 123 (148)
T ss_pred HHHHHHHHHHHHhhchhhhhHHHhcCCCHHHHHHHHH
Confidence 9999999999876653322 22345667766654
No 5
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=99.74 E-value=4.8e-18 Score=130.76 Aligned_cols=80 Identities=31% Similarity=0.476 Sum_probs=74.6
Q ss_pred CCCccccccCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHHHcCCCc
Q 047516 35 HNSKEQDRFLPIANVGRIMKKVIPGNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAITTLGFED 114 (214)
Q Consensus 35 ~~~k~~Dl~LPkA~V~RImK~~LP~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~LGF~d 114 (214)
..++..++.||+++|.||||+..+ -|||.+|+++|++|+++|+..|+..|+++|.|+|||||+++||..|++.+||..
T Consensus 11 ~~~~~~~~~Lp~apv~Ri~r~~~~--~Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~DI~la~~~~~~~~ 88 (91)
T COG2036 11 RYQRSTDLLLPKAPVRRILRKAGA--ERVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLALKRLGRRI 88 (91)
T ss_pred hhhhhhhhhcCchHHHHHHHHHhH--HHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHHHhcccc
Confidence 346788999999999999999954 499999999999999999999999999999999999999999999999999986
Q ss_pred ch
Q 047516 115 YV 116 (214)
Q Consensus 115 yi 116 (214)
|.
T Consensus 89 ~~ 90 (91)
T COG2036 89 YG 90 (91)
T ss_pred cc
Confidence 63
No 6
>PF00808 CBFD_NFYB_HMF: Histone-like transcription factor (CBF/NF-Y) and archaeal histone; InterPro: IPR003958 The CCAAT-binding factor (CBF) is a mammalian transcription factor that binds to a CCAAT motif in the promoters of a wide variety of genes, including type I collagen and albumin. The factor is a heteromeric complex of A and B subunits, both of which are required for DNA-binding [, ]. The subunits can interact in the absence of DNA-binding, conserved regions in each being important in mediating this interaction. The A subunit can be split into 3 domains on the basis of sequence similarity, a non-conserved N-terminal 'A domain'; a highly-conserved central 'B domain' involved in DNA-binding; and a C-terminal 'C domain', which contains a number of glutamine and acidic residues involved in protein-protein interactions []. The A subunit shows striking similarity to the HAP3 subunit of the yeast CCAAT-binding heterotrimeric transcription factor [, ]. The Kluyveromyces lactis HAP3 protein has been predicted to contain a 4-cysteine zinc finger, which is thought to be present in similar HAP3 and CBF subunit A proteins, in which the third cysteine is replaced by a serine []. This domain is found in the CCAAT transcription factor and archaeal histones.; GO: 0043565 sequence-specific DNA binding, 0005622 intracellular; PDB: 1F1E_A 2BYM_D 2BYK_D 1HTA_A 1B67_A 1JFI_B 1KU5_B 1N1J_A 1BFM_A 1B6W_A ....
Probab=99.73 E-value=9.9e-18 Score=119.19 Aligned_cols=64 Identities=42% Similarity=0.630 Sum_probs=59.4
Q ss_pred cCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHH
Q 047516 43 FLPIANVGRIMKKVIPGNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAI 107 (214)
Q Consensus 43 ~LPkA~V~RImK~~LP~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~AL 107 (214)
.||++.|.||||.. |++.+||+||.++|++|+++||.||+.+|++.|.+++||||+++||..||
T Consensus 2 ~lP~a~vkri~k~~-~~~~~vs~ea~~~i~~a~e~Fi~~l~~~A~~~a~~~~rkti~~~Dv~~Av 65 (65)
T PF00808_consen 2 SLPLARVKRIMKSD-PDVMRVSKEAVEAIAKAAEEFIQYLAKEANEIAQRDKRKTITYEDVAKAV 65 (65)
T ss_dssp SS-HHHHHHHHHHT-STTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEE-HHHHHHHH
T ss_pred CCChHHHHHHhccC-CCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHC
Confidence 69999999999999 88999999999999999999999999999999999999999999999986
No 7
>cd00076 H4 Histone H4, one of the four histones, along with H2A, H2B and H3, which forms the eukaryotic nucleosome core; along with H3, it plays a central role in nucleosome formation; histones bind to DNA and wrap the genetic material into "beads on a string" in which DNA (the string) is wrapped around small blobs of histones (the beads) at regular intervals; play a role in the inheritance of specialized chromosome structures and the control of gene activity; defects in the establishment of proper chromosome structure by histones may activate or silence genes aberrantly and thus lead to disease; the sequence of histone H4 has remained almost invariant in more than 2 billion years of evolution
Probab=99.47 E-value=2.7e-13 Score=103.28 Aligned_cols=71 Identities=21% Similarity=0.357 Sum_probs=67.9
Q ss_pred cCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHHHcCCCcc
Q 047516 43 FLPIANVGRIMKKVIPGNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAITTLGFEDY 115 (214)
Q Consensus 43 ~LPkA~V~RImK~~LP~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~LGF~dy 115 (214)
.||++.|.||+|.. +..|||.|+.+.+.++.++|+..|..+|..+|+|++||||+++||..||+..|-.-|
T Consensus 13 gi~k~~I~RLarr~--GvkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~alkr~g~~~y 83 (85)
T cd00076 13 GITKPAIRRLARRG--GVKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLY 83 (85)
T ss_pred cCCHHHHHHHHHHc--CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHCCCCcc
Confidence 59999999999999 889999999999999999999999999999999999999999999999999986554
No 8
>PLN00035 histone H4; Provisional
Probab=99.43 E-value=6.8e-13 Score=104.38 Aligned_cols=77 Identities=19% Similarity=0.297 Sum_probs=70.1
Q ss_pred CccccccCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHHHcCCCcc
Q 047516 37 SKEQDRFLPIANVGRIMKKVIPGNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAITTLGFEDY 115 (214)
Q Consensus 37 ~k~~Dl~LPkA~V~RImK~~LP~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~LGF~dy 115 (214)
++.....||+++|.||+|.. +..|||.|+.+++.+..++|+..|+.+|..+|+|++||||+++||..||+.+|-.-|
T Consensus 23 ~~d~i~~ipk~~IrRLARr~--GvkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr~g~~ly 99 (103)
T PLN00035 23 LRDNIQGITKPAIRRLARRG--GVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTLY 99 (103)
T ss_pred HHhhhccCCHHHHHHHHHHc--CcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHcCCcCC
Confidence 34445569999999999999 889999999999999999999999999999999999999999999999998875444
No 9
>PTZ00015 histone H4; Provisional
Probab=99.39 E-value=1.5e-12 Score=102.26 Aligned_cols=77 Identities=22% Similarity=0.371 Sum_probs=70.9
Q ss_pred CccccccCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHHHcCCCcc
Q 047516 37 SKEQDRFLPIANVGRIMKKVIPGNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAITTLGFEDY 115 (214)
Q Consensus 37 ~k~~Dl~LPkA~V~RImK~~LP~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~LGF~dy 115 (214)
++.....||+++|.||+|.. +..|||.|+.+.+.++.++|+..|+.+|..+|+|++||||+++||..||+..|-.-|
T Consensus 24 ~r~~i~gI~k~~IrRLarr~--GvkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~AlKr~g~~~y 100 (102)
T PTZ00015 24 LRDNIRGITKGAIRRLARRG--GVKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALKRQGRTLY 100 (102)
T ss_pred HhhcccCCCHHHHHHHHHHc--CCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhcCCCCC
Confidence 34455679999999999999 889999999999999999999999999999999999999999999999999886544
No 10
>smart00417 H4 Histone H4.
Probab=99.27 E-value=9.9e-12 Score=92.60 Aligned_cols=64 Identities=19% Similarity=0.316 Sum_probs=60.5
Q ss_pred cccCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHH
Q 047516 41 DRFLPIANVGRIMKKVIPGNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWA 106 (214)
Q Consensus 41 Dl~LPkA~V~RImK~~LP~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~A 106 (214)
-..||+++|+||+|.. +..|||.++.+.+.+..++|+..|+.+|..+|+|++||||+++||..|
T Consensus 11 i~gI~k~~IrRLaRr~--GvkRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~~a 74 (74)
T smart00417 11 IQGITKPAIRRLARRG--GVKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVYA 74 (74)
T ss_pred hcCCCHHHHHHHHHHc--CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHheeC
Confidence 3469999999999999 889999999999999999999999999999999999999999999754
No 11
>smart00803 TAF TATA box binding protein associated factor. TAFs (TATA box binding protein associated factors) are part of the transcription initiation factor TFIID multimeric protein complex. TFIID is composed of the TATA box binding protein (TBP) and a number of TAFs. The TAFs provide binding sites for many different transcriptional activators and co-activators that modulate transcription initiation by Pol II. TAF proteins adopt a histone-like fold.
Probab=99.26 E-value=2.6e-11 Score=87.78 Aligned_cols=64 Identities=27% Similarity=0.347 Sum_probs=61.8
Q ss_pred cCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHH
Q 047516 43 FLPIANVGRIMKKVIPGNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAIT 108 (214)
Q Consensus 43 ~LPkA~V~RImK~~LP~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe 108 (214)
.||+++|+||++.. |..+||.|+..+|.+-++.|+..|..+|..+++|+|||||+++||..||+
T Consensus 2 ~~p~~~i~ria~~~--Gi~ris~~a~~~l~~~~e~rl~~i~~~A~k~~~hakRktlt~~DI~~Alk 65 (65)
T smart00803 2 WLPKETIKDVAESL--GIGNLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSALR 65 (65)
T ss_pred CCCHHHHHHHHHHC--CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCeecHHHHHHHhC
Confidence 68999999999999 88899999999999999999999999999999999999999999999984
No 12
>smart00428 H3 Histone H3.
Probab=99.21 E-value=3.6e-11 Score=94.90 Aligned_cols=75 Identities=20% Similarity=0.222 Sum_probs=68.6
Q ss_pred CccccccCchhHHHHHHhhcCCC-----CcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHHHcC
Q 047516 37 SKEQDRFLPIANVGRIMKKVIPG-----NGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAITTLG 111 (214)
Q Consensus 37 ~k~~Dl~LPkA~V~RImK~~LP~-----~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~LG 111 (214)
++.+++.||+.++.|++|+...+ +.||+.+|+++||++++.|+.-+...|+.+|.|+||+||+++||..|...-|
T Consensus 23 Qkst~lLI~k~pF~RLVREI~~~~~~~~~~R~~~~Al~aLQeasE~ylv~lfeda~~~a~HAkRvTl~~kDi~La~rir~ 102 (105)
T smart00428 23 QKSTDLLIRKAPFQRLVREIAQKFTTGVDLRFQSSAIMALQEAAEAYLVGLFEDTNLLAIHAKRVTIMPKDIQLARRIRG 102 (105)
T ss_pred ccCcccccccccHHHHHHHHHHHcCCCCCceeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccCcHhhHHHHHHHhc
Confidence 57899999999999999999542 7899999999999999999999999999999999999999999998875433
No 13
>PLN00160 histone H3; Provisional
Probab=98.99 E-value=1e-09 Score=85.69 Aligned_cols=73 Identities=16% Similarity=0.117 Sum_probs=67.2
Q ss_pred CccccccCchhHHHHHHhhcCC----CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHHH
Q 047516 37 SKEQDRFLPIANVGRIMKKVIP----GNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAITT 109 (214)
Q Consensus 37 ~k~~Dl~LPkA~V~RImK~~LP----~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~ 109 (214)
+++.++.||++++.|++|+... ++.|++.+|..+||++++.|+.-+...|+.+|.|+||.||++.|+..|...
T Consensus 15 Qkst~lLI~k~pF~RLVREI~~~~~~~~~Rfq~~Al~ALQeAsEayLv~lfed~~lca~HakRVTl~~kD~~L~~ri 91 (97)
T PLN00160 15 QKSTDLLIRRLPFARLVREIQMEMSREAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTIMPKDMQLARRI 91 (97)
T ss_pred ccchhhhhccccHHHHHHHHHHHcCCCCcEeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcccccchhhHHHHHHh
Confidence 5778999999999999999953 458999999999999999999999999999999999999999999888753
No 14
>PLN00161 histone H3; Provisional
Probab=98.98 E-value=1.7e-09 Score=88.85 Aligned_cols=73 Identities=16% Similarity=0.196 Sum_probs=67.6
Q ss_pred CccccccCchhHHHHHHhhcC----CCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHHH
Q 047516 37 SKEQDRFLPIANVGRIMKKVI----PGNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAITT 109 (214)
Q Consensus 37 ~k~~Dl~LPkA~V~RImK~~L----P~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~ 109 (214)
++..++.||+..+.||+|++. +.+.|++.+|+++||++++.|+.-|..+|+.+|.|+||.||++.||..|...
T Consensus 49 Qkst~lLIpklPF~RLVREI~~~~~~~~~Rfq~~Al~ALQEAsEayLV~lFeda~lcaiHAkRVTlm~kDm~La~ri 125 (135)
T PLN00161 49 QKSTELLIRKLPFARLVREISNEMLREPFRWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMPKDMQLARRI 125 (135)
T ss_pred ccccccccccccHHHHHHHHHHhcCCCCcEeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccchhhHHHHHHh
Confidence 588999999999999999984 3469999999999999999999999999999999999999999999988753
No 15
>PLN00121 histone H3; Provisional
Probab=98.97 E-value=8.9e-10 Score=90.57 Aligned_cols=73 Identities=16% Similarity=0.177 Sum_probs=67.7
Q ss_pred CccccccCchhHHHHHHhhcCC---CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHHH
Q 047516 37 SKEQDRFLPIANVGRIMKKVIP---GNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAITT 109 (214)
Q Consensus 37 ~k~~Dl~LPkA~V~RImK~~LP---~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~ 109 (214)
++.+++.||+..+.||++++.. .+.|++.+|+++||+++|.|+..|...++.+|.|+||.||++.||..++..
T Consensus 56 Qkst~lLI~k~pF~RLVREI~~~~~~~~Rf~~~Al~ALQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~ri 131 (136)
T PLN00121 56 QKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRI 131 (136)
T ss_pred ccccccccccccHHHHHHHHHHHhCccceeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcceecchhhHHHHHHh
Confidence 4778999999999999999964 378999999999999999999999999999999999999999999888743
No 16
>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=98.97 E-value=4.5e-09 Score=77.07 Aligned_cols=65 Identities=18% Similarity=0.343 Sum_probs=61.2
Q ss_pred CchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHHH
Q 047516 44 LPIANVGRIMKKVIPGNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAITT 109 (214)
Q Consensus 44 LPkA~V~RImK~~LP~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~ 109 (214)
|++..+..++|+.=| ..+|+.||.++|++.++.|+..|+..|..+|+|.||+||.++||..+|++
T Consensus 2 ~~k~~l~~lv~~id~-~~~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~~~tv~~~Di~l~l~r 66 (72)
T cd07981 2 LTKRKLQELLKEIDP-REQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQLHLER 66 (72)
T ss_pred CcHHHHHHHHHhhCC-CCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence 678889999999954 58999999999999999999999999999999999999999999999985
No 17
>PTZ00018 histone H3; Provisional
Probab=98.96 E-value=1.7e-09 Score=88.97 Aligned_cols=74 Identities=16% Similarity=0.165 Sum_probs=68.0
Q ss_pred CccccccCchhHHHHHHhhcCC---CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHHHc
Q 047516 37 SKEQDRFLPIANVGRIMKKVIP---GNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAITTL 110 (214)
Q Consensus 37 ~k~~Dl~LPkA~V~RImK~~LP---~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~L 110 (214)
++..|+.||+..+.||++++.. .+.|+..+|+++||++++.|+..|...++.+|.|+||.||++.|+..|...-
T Consensus 56 Qkst~lLI~k~pF~RLVREI~~~~~~~~rf~~~al~aLQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~rir 132 (136)
T PTZ00018 56 QKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIR 132 (136)
T ss_pred cccchhccccccHHHHHHHHHHHcCCcceeeHHHHHHHHHHHHHHHHHHhhhhHHHHHhhcceecchhhHHHHHHhc
Confidence 4788999999999999999953 4789999999999999999999999999999999999999999998887543
No 18
>PF00125 Histone: Core histone H2A/H2B/H3/H4 histone h2a signature histone h2b signature histone h3 signature histone h4 signature; InterPro: IPR007125 The core histones together with some other DNA binding proteins appear to form a superfamily defined by a common fold and distant sequence similarities [, ]. Some proteins contain local homology domains related to the histone fold [].; GO: 0003677 DNA binding; PDB: 2YFW_D 2YFV_B 1U35_H 2F8N_D 2PYO_D 2NQB_D 3AN2_C 3AZJ_C 3AV1_G 3AZM_G ....
Probab=98.95 E-value=2e-09 Score=77.62 Aligned_cols=68 Identities=25% Similarity=0.357 Sum_probs=62.4
Q ss_pred cccCchhHHHHHHhhcCCC---CcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHH
Q 047516 41 DRFLPIANVGRIMKKVIPG---NGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAIT 108 (214)
Q Consensus 41 Dl~LPkA~V~RImK~~LP~---~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe 108 (214)
+..+|+..|.|++|+..++ ..+|+++|..+|+..++.|+..|..+|..+|.+.||+||+++||..|++
T Consensus 3 ~~~~~~~~~~r~~r~i~~~~~~~~ris~~a~~~L~~~~E~~~~~il~~A~~~a~~~kR~tI~~~DI~~A~r 73 (75)
T PF00125_consen 3 RRLIPKFPFSRLLREIGEEILSKYRISSEALVALQSVLEYLLVEILEEAGNLARHAKRKTITPRDIQLAVR 73 (75)
T ss_dssp SHSSSHHHHHHHHHHHHHTTSSSSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTBSEEGHHHHHHHHH
T ss_pred ccccCceEEeeeeehhhcccccccccccccchhhhhhhhhhhhhhhhHHHHHHhhcCCcEecHHHHHHHHh
Confidence 4578999999999998543 2699999999999999999999999999999999999999999999985
No 19
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=98.74 E-value=9.3e-09 Score=90.92 Aligned_cols=77 Identities=27% Similarity=0.340 Sum_probs=70.7
Q ss_pred ccccCchhHHHHHHhhcCCCCcc-cCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHHHcCCCcchHH
Q 047516 40 QDRFLPIANVGRIMKKVIPGNGK-ISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAITTLGFEDYVAP 118 (214)
Q Consensus 40 ~Dl~LPkA~V~RImK~~LP~~~r-ISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~LGF~dyi~~ 118 (214)
.+..||.|+|+|+||-. ++++ ||.||-.++.+.++.||..||..|.-.|++.+|+|+-..||..|+++-++-||+-.
T Consensus 106 k~h~LPlARIkkvMKtd--edVkMisaEaPvlFak~~EiFI~ELTmRAW~~ae~NkRRtLQksDia~Av~kSeMfDFLid 183 (286)
T COG5208 106 KDHNLPLARIKKVMKTD--EDVKMISAEAPVLFAKITEIFIEELTMRAWINAEENKRRTLQKSDIAAAVKKSEMFDFLID 183 (286)
T ss_pred HhccCcHHHHHHHHhcc--cchhheecccchHHHHHHHHHHHHHHHHHHHHHhHhhhhHHHHHHHHHHHHHHHHHhHHhh
Confidence 45679999999999998 6776 99999999999999999999999999999999999999999999999888777643
No 20
>KOG3467 consensus Histone H4 [Chromatin structure and dynamics]
Probab=98.74 E-value=4.1e-08 Score=76.02 Aligned_cols=69 Identities=22% Similarity=0.311 Sum_probs=65.4
Q ss_pred cCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHHHcCCC
Q 047516 43 FLPIANVGRIMKKVIPGNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAITTLGFE 113 (214)
Q Consensus 43 ~LPkA~V~RImK~~LP~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~LGF~ 113 (214)
.+.+.+|+||++.. +..||+--..+.+..++.+||..+.+.|..+++|++||||++.||+.+|+++|--
T Consensus 29 gitKpaIRRlARr~--GVkRi~G~~yeE~~~~~k~fl~n~i~~A~~yt~HAKRKTvT~~dvv~~LKR~G~~ 97 (103)
T KOG3467|consen 29 GITKPAIRRLARRG--GVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRT 97 (103)
T ss_pred ccchHHHHHHHHhc--CcchhchhhHHHHHHHHHHHHHHHHHHHHHHHhhhhhceeeHHHHHHHHHHcCce
Confidence 47799999999999 7889999999999999999999999999999999999999999999999998854
No 21
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=98.63 E-value=2.4e-07 Score=68.36 Aligned_cols=66 Identities=21% Similarity=0.317 Sum_probs=60.7
Q ss_pred hhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHHHcCCC
Q 047516 46 IANVGRIMKKVIPGNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAITTLGFE 113 (214)
Q Consensus 46 kA~V~RImK~~LP~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~LGF~ 113 (214)
+-.|.+|+|.. |--+++.+|++.|.+.+..|+..|+..+..+|+++||++++..||..||+.+|+.
T Consensus 9 ~~~Vaqil~~~--Gf~~~~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~~~Dv~~Al~~~gi~ 74 (77)
T smart00576 9 RIAVAQILESA--GFDSFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPNLGDVVLALENLGIS 74 (77)
T ss_pred HHHHHHHHHHc--CccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCcc
Confidence 44677888887 6678999999999999999999999999999999999999999999999999974
No 22
>cd00074 H2A Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins.
Probab=98.51 E-value=7e-07 Score=71.53 Aligned_cols=69 Identities=16% Similarity=0.193 Sum_probs=63.6
Q ss_pred cccccCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHH
Q 047516 39 EQDRFLPIANVGRIMKKVIPGNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAIT 108 (214)
Q Consensus 39 ~~Dl~LPkA~V~RImK~~LP~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe 108 (214)
...+.||.+.|.|+||+.- ...||+.+|...|..+.+.+...|...|...|.+.+|++|+++||..|+.
T Consensus 16 ragL~fPV~ri~R~Lk~~~-~a~RVs~~A~VyLaAvLEYL~aEIlelA~n~ak~~k~krItp~hi~lAi~ 84 (115)
T cd00074 16 RAGLQFPVGRIHRYLKKGR-YAERVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKKRITPRHLQLAVR 84 (115)
T ss_pred ccCccCcHHHHHHHHHcCc-cccccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEcHHHHHHHHh
Confidence 3578899999999999842 35899999999999999999999999999999999999999999999985
No 23
>cd07979 TAF9 TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. The TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Human TAF9 has a paralogue gene (TAF9L) whi
Probab=98.50 E-value=8.4e-07 Score=70.85 Aligned_cols=75 Identities=17% Similarity=0.243 Sum_probs=63.8
Q ss_pred hHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHHHcCCCcchHH-HHHHH
Q 047516 47 ANVGRIMKKVIPGNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAITTLGFEDYVAP-LKLYL 123 (214)
Q Consensus 47 A~V~RImK~~LP~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~LGF~dyi~~-Lk~~L 123 (214)
..|.+|+|+. +..+++.++...|.+.+..++..|..+|..+|+|+||+||+.+||..|++..+-..|..+ -+++|
T Consensus 5 ~~v~~iLk~~--Gv~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r~~~~f~~~p~~~~l 80 (117)
T cd07979 5 RVIAAILKSM--GITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRVDYSFTSPPPRDFL 80 (117)
T ss_pred HHHHHHHHHC--CCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhccCCCCCCcHHHH
Confidence 3578899988 778999999999999999999999999999999999999999999999987655444432 44443
No 24
>KOG1657 consensus CCAAT-binding factor, subunit C (HAP5) [Transcription]
Probab=98.46 E-value=2.2e-07 Score=82.43 Aligned_cols=84 Identities=27% Similarity=0.396 Sum_probs=73.0
Q ss_pred cccCchhHHHHHHhhcCCCCc-ccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHHH---cCCCcch
Q 047516 41 DRFLPIANVGRIMKKVIPGNG-KISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAITT---LGFEDYV 116 (214)
Q Consensus 41 Dl~LPkA~V~RImK~~LP~~~-rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~---LGF~dyi 116 (214)
...||+++|++|||.. +++ .|+.||..++.+||+.||..|+..|...+...+|+|+...|+..|+.. .+|.-.+
T Consensus 72 ~~~lPlaRiKkimK~d--edv~mI~~Eapvl~aka~E~Fi~elt~~sw~~Tee~~rrtl~~sdia~av~~s~~fdFL~Di 149 (236)
T KOG1657|consen 72 NHILPLARIKKIMKSD--EDVSMITAEAPVLFAKACELFITELTLRSWVHTEENKRRTLQKSDIAAAVTQSETFDFLRDI 149 (236)
T ss_pred hccCcHhhcccccccc--ccccccchhHHHHHHHHHHHHHHHHHHHhhhhhcccccccchHHHHHHHhccCCCccceecc
Confidence 3459999999999999 454 599999999999999999999999999999999999999999999996 4555555
Q ss_pred HHHHHHHHHH
Q 047516 117 APLKLYLSKY 126 (214)
Q Consensus 117 ~~Lk~~L~~y 126 (214)
-+.+..+.+|
T Consensus 150 vP~~~~~~~~ 159 (236)
T KOG1657|consen 150 VPRKILAEKY 159 (236)
T ss_pred ccchhccccc
Confidence 5666777766
No 25
>KOG1745 consensus Histones H3 and H4 [Chromatin structure and dynamics]
Probab=98.45 E-value=8.2e-08 Score=79.10 Aligned_cols=75 Identities=19% Similarity=0.210 Sum_probs=68.1
Q ss_pred CccccccCchhHHHHHHhhcC---CCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHHHcC
Q 047516 37 SKEQDRFLPIANVGRIMKKVI---PGNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAITTLG 111 (214)
Q Consensus 37 ~k~~Dl~LPkA~V~RImK~~L---P~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~LG 111 (214)
++.+|+.|++.++.|++|+.. -.+.++...|+.+||++++.|+.-|...+|.+|.|+||.||++.||-.|...-|
T Consensus 57 QkstdLlI~K~PFqRlvrei~q~f~~dLrfqs~Ai~ALQeA~EayLv~LfEdtnlcAihAkRVTimpkdiQlArrirg 134 (137)
T KOG1745|consen 57 QKSTDLLIRKLPFQRLVREIAQDFKTDLRFQSSAIAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRG 134 (137)
T ss_pred HhhhHHHhhcCcHHHHhHHHHhcccccceehHHHHHHHHHHHHHHHHHhccccchhhhccceeEecccceehhhhccc
Confidence 678999999999999999554 358899999999999999999999999999999999999999999998876543
No 26
>cd08050 TAF6 TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and are involved in forming Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs functions such as serving as
Probab=98.23 E-value=4.8e-06 Score=76.60 Aligned_cols=67 Identities=19% Similarity=0.270 Sum_probs=60.7
Q ss_pred chhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHHHcCCC
Q 047516 45 PIANVGRIMKKVIPGNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAITTLGFE 113 (214)
Q Consensus 45 PkA~V~RImK~~LP~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~LGF~ 113 (214)
|..+|+-|++.. |..++++||..+|.+.++.++..|+.+|...++|.||||++++||-.||+.++.+
T Consensus 1 ~~~~i~~ia~~~--Gi~~~~~~a~~~La~~~e~~~~~i~~~A~k~~~hskR~~l~~~Di~~Al~~~n~e 67 (343)
T cd08050 1 PQESIKLIAESL--GIDSLSDEVAQLLAEDVEYRLREIIQEAAKFMRHSKRRKLTTSDVNHALRLRNVE 67 (343)
T ss_pred ChhHHHHHHHHc--CCCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHHhCCC
Confidence 456788888888 6679999999999999999999999999999999999999999999999975543
No 27
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=97.94 E-value=3.5e-05 Score=57.71 Aligned_cols=62 Identities=19% Similarity=0.221 Sum_probs=52.2
Q ss_pred HHHHHHhhcC-CCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHHH
Q 047516 48 NVGRIMKKVI-PGNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAITT 109 (214)
Q Consensus 48 ~V~RImK~~L-P~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~ 109 (214)
.|.||+.+.. +.++.+|+.+..+|.+.+-.++..++.+---.|+|+||+||+.+||+...++
T Consensus 10 ~v~ki~ee~~~~~~~~~s~~~i~al~ELv~~q~~~~a~DLe~FAkHA~R~tI~~dDV~Ll~Rr 72 (76)
T PF15630_consen 10 TVGKIVEEEAKEKGVEVSPQFIAALTELVYKQLENLAKDLEAFAKHAGRSTINMDDVKLLARR 72 (76)
T ss_dssp HHHHHHHHCCCCTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHTTT
T ss_pred HHHHHHHHHHhccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHHHhhc
Confidence 5778888873 5678899999999999999999999999999999999999999999987643
No 28
>PF15511 CENP-T: Centromere kinetochore component CENP-T; PDB: 3B0D_T 3B0C_T 3VH5_T 3VH6_T.
Probab=97.94 E-value=1.6e-05 Score=75.18 Aligned_cols=63 Identities=25% Similarity=0.304 Sum_probs=47.6
Q ss_pred ccccCchhHHHHHHhhcCC----CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHH
Q 047516 40 QDRFLPIANVGRIMKKVIP----GNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDD 102 (214)
Q Consensus 40 ~Dl~LPkA~V~RImK~~LP----~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eD 102 (214)
.--.||.+.|+||+..... ...+|++||+.+|.+|...|-.-|+..--.+|.|+|||||..+|
T Consensus 348 ~~P~lP~~~vK~la~~~ak~s~~sK~kiskdal~aleqasdwfFeQl~dDL~aYA~HAgRKTIdesD 414 (414)
T PF15511_consen 348 PYPSLPPGVVKKLAQHFAKSSGGSKMKISKDALEALEQASDWFFEQLGDDLEAYAKHAGRKTIDESD 414 (414)
T ss_dssp ----S-HHHHHHHHHHHH-------S-B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHH
T ss_pred CCCCCCccHHHHHHHHHHHhhcccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCCCC
Confidence 3345999999998766643 46899999999999999999999999999999999999999887
No 29
>PF07524 Bromo_TP: Bromodomain associated; InterPro: IPR006565 This bromodomain is found in eukaryotic transcription factors and PHD domain containing proteins (IPR001965 from INTERPRO). The tandem PHD finger-bromodomain is found in many chromatin-associated proteins. It is involved in gene silencing by the human co-repressor KRAB-associated protein 1 (KAP1). The tandem PHD finger-bromodomain of KAP1 has a distinct structure that joins the two protein modules. The first helix, alpha(Z), of an atypical bromodomain forms the central hydrophobic core that anchors the other three helices of the bromodomain on one side and the zinc binding PHD finger on the other []. The Rap1 GTPase-activating protein, Sipa1, is modulated by the cellular bromodomain protein, Brd4. Brd4 belongs to the BET family and is a multifunctional protein involved in transcription, replication, the signal transduction pathway, and cell cycle progression. All of these functions are linked to its association with acetylated chromatin. It has tandem bromodomains []. The dysregulation of the Brd4-associated pathways may play an important role in breast cancer progression []. Bovine papillomavirus type 1 E2 also binds to chromosomes in a complex with Brd4. Interaction with Brd4 is additionally important for E2-mediated transcriptional regulation [, ].
Probab=97.93 E-value=9.2e-05 Score=54.17 Aligned_cols=64 Identities=20% Similarity=0.310 Sum_probs=57.0
Q ss_pred HHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHHHcCCC
Q 047516 48 NVGRIMKKVIPGNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAITTLGFE 113 (214)
Q Consensus 48 ~V~RImK~~LP~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~LGF~ 113 (214)
.|.+|++.. |=-.++..|++.|.+.+..||..|+..+..+|++.+|...+..||..||+++|+.
T Consensus 11 ~va~il~~~--GF~~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~~~gi~ 74 (77)
T PF07524_consen 11 SVAQILKHA--GFDSASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPNLQDVEQALEEMGIS 74 (77)
T ss_pred HHHHHHHHc--CccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCC
Confidence 455666665 3347999999999999999999999999999999999999999999999999984
No 30
>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=97.81 E-value=0.00014 Score=53.24 Aligned_cols=64 Identities=23% Similarity=0.272 Sum_probs=51.1
Q ss_pred cCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHH
Q 047516 43 FLPIANVGRIMKKVIPGNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAIT 108 (214)
Q Consensus 43 ~LPkA~V~RImK~~LP~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe 108 (214)
.+|..+|.-+.... |-..++.|+..+|.+-++.-|..|..+|...+.|.+|++++.+||-.||+
T Consensus 3 ~~~~esvk~iAes~--Gi~~l~de~a~~La~dveyrlreiiq~a~kfm~hskR~~Lt~~Di~~ALr 66 (66)
T PF02969_consen 3 VFSQESVKDIAESL--GISNLSDEAAKALAEDVEYRLREIIQEALKFMRHSKRTKLTTDDINSALR 66 (66)
T ss_dssp ---HHHHHHHHHHT--T---B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH-
T ss_pred cCCHHHHHHHHHHc--CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhC
Confidence 47888888877777 66689999999999999999999999999999999999999999999985
No 31
>COG5247 BUR6 Class 2 transcription repressor NC2, alpha subunit (DRAP1 homolog) [Transcription]
Probab=97.78 E-value=0.0001 Score=58.65 Aligned_cols=76 Identities=16% Similarity=0.274 Sum_probs=65.4
Q ss_pred ccccCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHHHcCCCcch
Q 047516 40 QDRFLPIANVGRIMKKVIPGNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAITTLGFEDYV 116 (214)
Q Consensus 40 ~Dl~LPkA~V~RImK~~LP~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~LGF~dyi 116 (214)
--..+|+|.|.|||.-. .+..+|+.-.-..+.++.+.|+..|-..+.+.|+..+-|.|+.+++..|.+.-+=.||+
T Consensus 20 ~ktrFP~ar~KkIMQ~d-eDiGKV~q~tPVIaskalE~Fl~~iv~~s~k~aR~~~skR~t~e~lk~a~~sdekFdFL 95 (113)
T COG5247 20 KKTRFPIARLKKIMQLD-EDIGKVGQSTPVIASKALEMFLTEIVGLSLKEARKKSSKRMTSEFLKRATESDEKFDFL 95 (113)
T ss_pred hhhcCCHHHHHHHHHhh-hhhhhhhhcchHHHHHHHHHHHHHHHHHHHHHHHhccchhhHHHHHHHHHhhhHHHHHH
Confidence 33469999999999887 24578999999999999999999999999999999999999999999998764444444
No 32
>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=97.74 E-value=0.00018 Score=52.73 Aligned_cols=63 Identities=19% Similarity=0.274 Sum_probs=51.7
Q ss_pred hhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHHH
Q 047516 46 IANVGRIMKKVIPGNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAITT 109 (214)
Q Consensus 46 kA~V~RImK~~LP~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~ 109 (214)
+..+..+|++.= ++.++..|+.++|.+.|.+||..++..|...|+|-|-.||...||...|++
T Consensus 2 K~~l~~Lv~~iD-p~~~ld~~vee~Ll~laddFv~~v~~~ac~lAKhR~s~tle~~Dv~~~Ler 64 (68)
T PF03847_consen 2 KRKLQELVKQID-PNEKLDPDVEELLLELADDFVDDVVSFACRLAKHRKSSTLEVKDVQLHLER 64 (68)
T ss_dssp HHHHHHHHHCC--SS----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHHH
T ss_pred hHHHHHHHHHcC-CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCHHHHHHHHHh
Confidence 456788899984 478999999999999999999999999999999999999999999999875
No 33
>smart00427 H2B Histone H2B.
Probab=97.68 E-value=0.00025 Score=54.82 Aligned_cols=62 Identities=23% Similarity=0.363 Sum_probs=57.4
Q ss_pred HHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHHHc
Q 047516 48 NVGRIMKKVIPGNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAITTL 110 (214)
Q Consensus 48 ~V~RImK~~LP~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~L 110 (214)
-|+|++|++-| +..||..|...|.-.+..+..-|+.+|...|.-.+|+||+..+|..|.+.+
T Consensus 6 Yi~kvLKqVhp-d~giS~kam~imnSfvnDiferIa~EAs~L~~~nkr~TltsreIqtAvrl~ 67 (89)
T smart00427 6 YIYKVLKQVHP-DTGISSKAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRLI 67 (89)
T ss_pred HHHHHHHHhCC-CccccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHH
Confidence 48999999987 678999999999999999999999999999999999999999999998653
No 34
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=97.59 E-value=0.00028 Score=63.67 Aligned_cols=69 Identities=16% Similarity=0.345 Sum_probs=63.5
Q ss_pred ccccCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHHH
Q 047516 40 QDRFLPIANVGRIMKKVIPGNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAITT 109 (214)
Q Consensus 40 ~Dl~LPkA~V~RImK~~LP~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~ 109 (214)
.+..|-+-.|.-+|+++ ..+..|-+|+.++|.+.|..||..|+..|...|+|-|..||-+.||...||+
T Consensus 151 ~~~il~k~kl~dLvqqI-d~~~~LD~dVedlLleiADdFV~sii~~sC~LAKHRKsdtlEvrDIqLhLEr 219 (258)
T KOG1142|consen 151 NNPILSKRKLDDLVQQI-DGTTKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHRKSDTVEVRDIQLHLER 219 (258)
T ss_pred CCccccccchhHHHHhh-cCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccchhheeeeeec
Confidence 45568888899999999 3578999999999999999999999999999999999999999999999995
No 35
>KOG1659 consensus Class 2 transcription repressor NC2, alpha subunit (DRAP1) [Transcription]
Probab=97.57 E-value=0.00023 Score=62.76 Aligned_cols=83 Identities=13% Similarity=0.191 Sum_probs=71.9
Q ss_pred cCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHHHcCCCcchHHHHHH
Q 047516 43 FLPIANVGRIMKKVIPGNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAITTLGFEDYVAPLKLY 122 (214)
Q Consensus 43 ~LPkA~V~RImK~~LP~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~LGF~dyi~~Lk~~ 122 (214)
.||.++|.|||... -+..+|..-+-..+.++.+.|+..|...+.+++...+-|||+++|+..++..-.-.+|+..+-..
T Consensus 13 rfp~aRiKKIMQ~d-EdIGKvaqavPViisralElFl~~l~~~t~~~t~~~~aKt~s~~hlkq~v~~~~~FdFLk~~v~~ 91 (224)
T KOG1659|consen 13 RFPPARIKKIMQSD-EDIGKVAQAVPVIISRALELFLESLLQKTLEITRSRGAKTVSSSHLKQAVESDPKFDFLKEVVEK 91 (224)
T ss_pred cCCHHHHHHHHhhh-hhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhcCccccCHHHHHHHHhccchhHHHHHHHHh
Confidence 59999999999988 24578999999999999999999999999999999999999999999999887766776665544
Q ss_pred HHHH
Q 047516 123 LSKY 126 (214)
Q Consensus 123 L~~y 126 (214)
+..+
T Consensus 92 vpd~ 95 (224)
T KOG1659|consen 92 VPDR 95 (224)
T ss_pred cCCC
Confidence 4433
No 36
>PLN00158 histone H2B; Provisional
Probab=97.55 E-value=0.00062 Score=55.00 Aligned_cols=67 Identities=18% Similarity=0.257 Sum_probs=60.1
Q ss_pred cCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHHHc
Q 047516 43 FLPIANVGRIMKKVIPGNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAITTL 110 (214)
Q Consensus 43 ~LPkA~V~RImK~~LP~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~L 110 (214)
.--..-|+|++|++-| +..||..|...|.-.+..+..-|+.||...|.-.+|+||+..+|..|++.+
T Consensus 27 esy~~YI~kVLKQVhP-d~gIS~kaM~ImnSfvnDiferIA~EAs~La~~nkr~TltsrEIqtAvrLv 93 (116)
T PLN00158 27 ETYKIYIYKVLKQVHP-DTGISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVRLI 93 (116)
T ss_pred ccHHHHHHHHHHHhCC-CCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHh
Confidence 3445669999999987 678999999999999999999999999999999999999999999998653
No 37
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=97.47 E-value=0.00029 Score=57.32 Aligned_cols=71 Identities=20% Similarity=0.224 Sum_probs=63.4
Q ss_pred CccccccCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHH
Q 047516 37 SKEQDRFLPIANVGRIMKKVIPGNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAIT 108 (214)
Q Consensus 37 ~k~~Dl~LPkA~V~RImK~~LP~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe 108 (214)
.....+.+|...|.||||.. ...+||+++|..++.-|.+..+..|+.-|-..|...|+|.|++.|+-.|+.
T Consensus 20 sa~agl~fpvgrvkr~lk~~-~~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~kkkri~PrHlqlAIr 90 (132)
T COG5262 20 SAKAGLIFPVGRVKRLLKKG-NYRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRIIPRHLQLAIR 90 (132)
T ss_pred hhhcCccccHHHHHHHHHcC-ccceeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhcCcceechHHHHHHhc
Confidence 34466789999999999954 257899999999999999999999999999999999999999999999986
No 38
>cd08048 TAF11 TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypothes
Probab=97.42 E-value=0.00097 Score=50.86 Aligned_cols=66 Identities=18% Similarity=0.216 Sum_probs=60.7
Q ss_pred cCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC---CccChHHHHHHHHHc
Q 047516 43 FLPIANVGRIMKKVIPGNGKISKDAKETVQECVSEFISFVTGEASDKCQREKR---KTINGDDIIWAITTL 110 (214)
Q Consensus 43 ~LPkA~V~RImK~~LP~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kR---KTI~~eDVl~ALe~L 110 (214)
.||++.|.|||...+ +..++.+...+|.-.+.+||-.|..+|.++..+.+. .-|.++||..|.+.|
T Consensus 16 ~f~k~~iKr~~~~~~--~~~v~~~v~i~v~glaKvFVGeivE~A~~V~~~~~~~~~~Pl~P~HireA~rrl 84 (85)
T cd08048 16 SFPKAAIKRLIQSVT--GQSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGEANTGPLQPRHLREAYRRL 84 (85)
T ss_pred hccHHHHHHHHHHHc--CCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCCCCCcHHHHHHHHHh
Confidence 499999999999996 489999999999999999999999999999987665 899999999998876
No 39
>PF09415 CENP-X: CENP-S associating Centromere protein X; InterPro: IPR018552 Centromere protein X (CENP-X) is a component of the CENP-S complex. The CENP-S complex is composed of at least of CENP-S and CENP-X and is essential for the stable assembly of the outer kinetchore []. CENP-X is also a DNA-binding component of the Fanconi anemia (FA) core complex involved in DNA damage repair and genome maintenance. The FA complex is composed of CENPS, FANCA, FANCB, FANCC, FANCE, FANCF, FANCG, FANCL/PHF9, FANCM, FAAP24 and CENPX. Interacts with CENPS, FANCM and FAAP24 [, ].; PDB: 4DRB_L 4DRA_H 3V9R_D.
Probab=97.42 E-value=0.00031 Score=52.11 Aligned_cols=64 Identities=19% Similarity=0.288 Sum_probs=53.6
Q ss_pred chhHHHHHHhhcCC-CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCc-cChHHHHHHHH
Q 047516 45 PIANVGRIMKKVIP-GNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKT-INGDDIIWAIT 108 (214)
Q Consensus 45 PkA~V~RImK~~LP-~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKT-I~~eDVl~ALe 108 (214)
|..+|.||++.... +.+||++||..++.+....||..-...|...+..+|..+ |..+|+-+.+-
T Consensus 1 p~~li~rll~~~f~~~~tkIs~dal~l~~eyl~iFV~EAv~Ra~~~a~~e~~~~~le~e~LEki~p 66 (72)
T PF09415_consen 1 PPELIARLLHEHFKDDKTKISKDALKLSAEYLRIFVREAVARAAEQAEAEGDEGFLEVEHLEKILP 66 (72)
T ss_dssp -CHHHHHHHCTTSSSTT-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSEE-HHHHHHHCH
T ss_pred ChHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHH
Confidence 78899999998774 578999999999999999999999999999999999988 99999987653
No 40
>PTZ00463 histone H2B; Provisional
Probab=97.39 E-value=0.00093 Score=54.04 Aligned_cols=62 Identities=23% Similarity=0.381 Sum_probs=57.2
Q ss_pred HHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHHHc
Q 047516 48 NVGRIMKKVIPGNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAITTL 110 (214)
Q Consensus 48 ~V~RImK~~LP~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~L 110 (214)
-|+|++|++-| +..||..|...|.-.+.....-|+.||...|.-.+|.||+..+|..|++-+
T Consensus 33 YI~KVLKqVhP-d~gIS~kaM~ImnSfvnDifErIA~EAs~La~~nkr~TltsrEIQtAvrLl 94 (117)
T PTZ00463 33 YIFKVLKQVHP-DTGISRKSMNIMNSFLVDTFEKIATEASRLCKYTRRDTLSSREIQTAIRLV 94 (117)
T ss_pred HHHHHHHhhCC-CCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHhhc
Confidence 49999999987 677999999999999999999999999999999999999999999998654
No 41
>smart00414 H2A Histone 2A.
Probab=97.25 E-value=0.00099 Score=52.76 Aligned_cols=68 Identities=15% Similarity=0.218 Sum_probs=61.4
Q ss_pred ccccCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHH
Q 047516 40 QDRFLPIANVGRIMKKVIPGNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAIT 108 (214)
Q Consensus 40 ~Dl~LPkA~V~RImK~~LP~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe 108 (214)
-.+.||.+.|.|+||+.- -..||+..|...|.-+.+.+...|..-|...|...+++.|+++||..|+.
T Consensus 6 agL~fPVgRi~r~Lk~~~-~~~Rv~~~A~VyLaAvLEYLtaEILeLagn~a~~~k~~rItp~hi~lAi~ 73 (106)
T smart00414 6 AGLQFPVGRIHRLLRKGT-YAKRVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKRRITPRHLQLAIR 73 (106)
T ss_pred CCccCchHHHHHHHHcCc-cccccccccHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchHHHhhhcc
Confidence 467899999999999873 25699999999999999999999999999999999999999999999985
No 42
>PF04719 TAFII28: hTAFII28-like protein conserved region; InterPro: IPR006809 The general transcription factor, TFIID, consists of the TATA-binding protein (TBP) associated with a series of TBP-associated factors (TAFs) that together participate in the assembly of the transcription preinitiation complex. The conserved region is found at the C terminus of most member proteins. The crystal structure of hTAFII28 with hTAFII18 shows that this region is involved in the binding of these two subunits. The conserved region contains four alpha helices and three loops arranged as in histone H3 [, ].; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005634 nucleus; PDB: 1BH9_B 1BH8_B.
Probab=97.09 E-value=0.0027 Score=49.07 Aligned_cols=67 Identities=19% Similarity=0.255 Sum_probs=52.2
Q ss_pred cCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC-CccChHHHHHHHHHc
Q 047516 43 FLPIANVGRIMKKVIPGNGKISKDAKETVQECVSEFISFVTGEASDKCQREKR-KTINGDDIIWAITTL 110 (214)
Q Consensus 43 ~LPkA~V~RImK~~LP~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kR-KTI~~eDVl~ALe~L 110 (214)
.||++.|+|||...+ ++..|+.....+|.-.+..||-.|-.+|.+++...+. .-|.+.|+..|.++|
T Consensus 23 ~~~k~~ikkli~~~~-~~qsv~~~v~i~v~g~aKvFVGEiVE~A~~Vq~~~~~~~pl~P~hlreA~rrL 90 (90)
T PF04719_consen 23 SFNKAAIKKLINQVL-GNQSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGETGPLQPDHLREAYRRL 90 (90)
T ss_dssp ---HHHHHHHHHHHH-S-S---HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SS--HHHHHHHHHHH
T ss_pred cCCHHHHHHHHHHHc-CCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcHHHHHHHHhC
Confidence 499999999999997 4689999999999999999999999999999986654 489999999998765
No 43
>PLN00154 histone H2A; Provisional
Probab=97.07 E-value=0.0042 Score=51.48 Aligned_cols=70 Identities=17% Similarity=0.224 Sum_probs=62.0
Q ss_pred cccccCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHH
Q 047516 39 EQDRFLPIANVGRIMKKVIPGNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAIT 108 (214)
Q Consensus 39 ~~Dl~LPkA~V~RImK~~LP~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe 108 (214)
...+.||.+.|.|++|+...-..||+..|-..|.-+.+.+...|..-|-..|...+++-|++.||..|+.
T Consensus 34 rAgL~FPVgRi~r~Lk~g~~~~~RVga~ApVYLAAVLEYLtAEVLELAGNaA~d~kk~RItPrHi~lAIr 103 (136)
T PLN00154 34 RAGLQFPVGRIHRQLKQRVSAHGRVGATAAVYTAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 103 (136)
T ss_pred ccCccCchHHHHHHHHhhhhhccccccchHHHHHHHHHHHHHHHHHHHHHHHHhhCCceecHHHhhhhcc
Confidence 3578899999999999984335799999999999999888888888888899999999999999999984
No 44
>PTZ00017 histone H2A; Provisional
Probab=96.90 E-value=0.0025 Score=52.62 Aligned_cols=68 Identities=21% Similarity=0.204 Sum_probs=61.8
Q ss_pred ccccCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHH
Q 047516 40 QDRFLPIANVGRIMKKVIPGNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAIT 108 (214)
Q Consensus 40 ~Dl~LPkA~V~RImK~~LP~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe 108 (214)
..+.||.+.|.|+||+.- -..||+..|...|.-+.+.+...|..-|...|...+++-|+++||..|+.
T Consensus 24 agL~FPVgRi~R~Lk~g~-~a~RV~a~A~VYLAAVLEYLtaEILELAgNaa~d~kk~RItPrHi~lAI~ 91 (134)
T PTZ00017 24 AGLQFPVGRVHRYLKKGR-YAKRVGAGAPVYLAAVLEYLTAEVLELAGNAAKDNKKKRITPRHIQLAIR 91 (134)
T ss_pred CCcccchHHHHHHHhccc-hhccccccchhhhHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHhhcc
Confidence 578899999999999863 24699999999999999999999999999999999999999999999984
No 45
>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=96.74 E-value=0.0073 Score=49.40 Aligned_cols=81 Identities=23% Similarity=0.263 Sum_probs=48.8
Q ss_pred cCchh--HHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHH-HcCCCcchHHH
Q 047516 43 FLPIA--NVGRIMKKVIPGNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAIT-TLGFEDYVAPL 119 (214)
Q Consensus 43 ~LPkA--~V~RImK~~LP~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe-~LGF~dyi~~L 119 (214)
.+|+. .|.-|+|+. +.......+...|.+.+-.|+..|..+|..++.|++|++|+.+||..|++ ++++.-..++-
T Consensus 10 ~~PrDa~~i~~iL~~~--Gv~~yeprVv~qLLEfayRYt~~vL~DA~~ya~hA~~~~i~~~DVrLAi~~r~~~~f~~ppp 87 (129)
T PF02291_consen 10 SLPRDARVIHLILKSM--GVTEYEPRVVNQLLEFAYRYTSDVLEDAQVYADHAGRSTIDADDVRLAIQSRLDHSFTQPPP 87 (129)
T ss_dssp ---HHHHHHHHHHHHT--T---B-THHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHHHHT----------
T ss_pred cCChHHHHHHHHHHHc--CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHhhhccCCCC
Confidence 56663 345556666 55568888999999999999999999999999999999999999999999 46666555555
Q ss_pred HHHHHH
Q 047516 120 KLYLSK 125 (214)
Q Consensus 120 k~~L~~ 125 (214)
+++|-+
T Consensus 88 re~lle 93 (129)
T PF02291_consen 88 REFLLE 93 (129)
T ss_dssp ------
T ss_pred hHHHHH
Confidence 555543
No 46
>PLN00156 histone H2AX; Provisional
Probab=96.70 E-value=0.012 Score=49.01 Aligned_cols=69 Identities=14% Similarity=0.181 Sum_probs=61.2
Q ss_pred cccccCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHH
Q 047516 39 EQDRFLPIANVGRIMKKVIPGNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAIT 108 (214)
Q Consensus 39 ~~Dl~LPkA~V~RImK~~LP~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe 108 (214)
...+.||.+.|.|+||+.- -..||+..|...|.-+.+.....|..-|-..|...+++-|+++||..|+.
T Consensus 25 rAgL~FPVgRi~R~Lk~g~-ya~RVga~ApVYLAAVLEYLtaEVLELAgNaa~d~kk~RItPrHi~lAIr 93 (139)
T PLN00156 25 KAGLQFPVGRIARFLKAGK-YAERVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR 93 (139)
T ss_pred ccCcccchHHHHHHHhcCC-hhhccCCccHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHhhcc
Confidence 3578899999999999973 24699999999999999988888888888899999999999999999984
No 47
>KOG1756 consensus Histone 2A [Chromatin structure and dynamics]
Probab=96.65 E-value=0.009 Score=49.16 Aligned_cols=70 Identities=13% Similarity=0.200 Sum_probs=59.7
Q ss_pred ccccccCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHH
Q 047516 38 KEQDRFLPIANVGRIMKKVIPGNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAIT 108 (214)
Q Consensus 38 k~~Dl~LPkA~V~RImK~~LP~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe 108 (214)
....+.+|...|.|+||+. .-..||+.+|...|.-|.+..+..|+.-|-..+..+++.-|++.||..|+.
T Consensus 22 ~~agl~fPvgri~r~Lr~~-~~~~ri~~gapV~laavLeYL~Aeile~agnaardnkk~ri~PrH~~lAI~ 91 (131)
T KOG1756|consen 22 SRAGLQFPVGRIHRLLRKG-RYAQRVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRITPRHLQLAIR 91 (131)
T ss_pred hhcccccCHHHHHHHHHcc-chhhhccCCChHHHHHHHHHHHHHHHHHhHHHhhhcCccccChHHHHHHHh
Confidence 4467789999999999994 235789999999999887777777777777788899999999999999984
No 48
>PLN00157 histone H2A; Provisional
Probab=96.62 E-value=0.0048 Score=50.85 Aligned_cols=68 Identities=15% Similarity=0.162 Sum_probs=61.4
Q ss_pred ccccCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHH
Q 047516 40 QDRFLPIANVGRIMKKVIPGNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAIT 108 (214)
Q Consensus 40 ~Dl~LPkA~V~RImK~~LP~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe 108 (214)
..+.||.+.|.|++|+.- -..||+..|...|.-+.+.....|..-|...|...+++-|+++||..|+.
T Consensus 23 agL~FPVgRi~R~Lk~g~-~a~RIg~~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~ 90 (132)
T PLN00157 23 AGLQFPVGRIARYLKAGK-YATRVGAGAPVYLAAVLEYLAAEVLELAGNAARDNKKSRIVPRHIQLAVR 90 (132)
T ss_pred cCcccchHHHHHHHhcCc-hhhhcCCCcHhHHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHhhccc
Confidence 578899999999999963 24699999999999999999988888899999999999999999999984
No 49
>PLN00153 histone H2A; Provisional
Probab=96.62 E-value=0.0053 Score=50.43 Aligned_cols=68 Identities=19% Similarity=0.199 Sum_probs=61.6
Q ss_pred ccccCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHH
Q 047516 40 QDRFLPIANVGRIMKKVIPGNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAIT 108 (214)
Q Consensus 40 ~Dl~LPkA~V~RImK~~LP~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe 108 (214)
..+.||.+.|.|++|+.-- ..||+..|...|.-+.+..+..|..-|-..|...+++-|+++||..|+.
T Consensus 21 agL~FpVgRi~R~Lr~g~~-a~Rvga~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~ 88 (129)
T PLN00153 21 AGLQFPVGRIARYLKKGKY-AERIGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKNRIVPRHIQLAIR 88 (129)
T ss_pred cCcccchHHHHHHHhcCch-hhccCCCchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHhhcc
Confidence 5788999999999998732 4699999999999999999999999999999999999999999999984
No 50
>KOG1658 consensus DNA polymerase epsilon, subunit C [Replication, recombination and repair]
Probab=96.49 E-value=0.0017 Score=54.92 Aligned_cols=66 Identities=24% Similarity=0.264 Sum_probs=58.4
Q ss_pred ccCchhHHHHHHhhcCCCCccc-CHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHHH
Q 047516 42 RFLPIANVGRIMKKVIPGNGKI-SKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAITT 109 (214)
Q Consensus 42 l~LPkA~V~RImK~~LP~~~rI-SkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~ 109 (214)
..||.+.|..+||.. +++++ ..+++.+|.++++.||..|...|+..+...+|||+.-.|+-.|++.
T Consensus 58 ~rLpL~rik~vvkl~--pdl~l~~dea~~l~a~aaelfi~~Ln~~~~~~~q~~k~kt~qr~d~D~ai~~ 124 (162)
T KOG1658|consen 58 SRLPLARIKQVVKLD--PDLTLLNDEASQLIAKAAELFIQELNDVAYTTAQLRKRKTEQRRDYDTAIEA 124 (162)
T ss_pred hhccHHHHHhhccCC--cchhhhhhHHHHHHHHHHHHHHHHHHhccchhHHHHHhhhhhhhcccccccc
Confidence 469999999999987 67774 6679999999999999999999999999999999998888777653
No 51
>KOG1744 consensus Histone H2B [Chromatin structure and dynamics]
Probab=96.39 E-value=0.015 Score=47.70 Aligned_cols=63 Identities=27% Similarity=0.335 Sum_probs=57.0
Q ss_pred hHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHHHc
Q 047516 47 ANVGRIMKKVIPGNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAITTL 110 (214)
Q Consensus 47 A~V~RImK~~LP~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~L 110 (214)
..|+|++|+.-|+ .-|+.+++..|.-..-.+...|+.+|...+.-.||.||+..+|..|++-|
T Consensus 41 ~yv~kvlk~Vhpd-~gis~~a~~vmnsf~ndife~iA~ea~rla~y~krstisSreiqta~rLl 103 (127)
T KOG1744|consen 41 EYVYKVLKQVHPD-LGISSKAMGVMNSFVNDIFERIASEAGRLAHYNKRSTISSREIQTAVRLL 103 (127)
T ss_pred eehhhhhhcccCC-CCcCHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCcccHHHHHHHHHHh
Confidence 3467799999986 66999999999999999999999999999999999999999999988543
No 52
>PF15510 CENP-W: Centromere kinetochore component W
Probab=96.23 E-value=0.011 Score=46.41 Aligned_cols=67 Identities=19% Similarity=0.228 Sum_probs=54.7
Q ss_pred ccCchhHHHHHHhhcCCCCcccCHHHHHH--------------HHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHH
Q 047516 42 RFLPIANVGRIMKKVIPGNGKISKDAKET--------------VQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAI 107 (214)
Q Consensus 42 l~LPkA~V~RImK~~LP~~~rISkDA~ea--------------lqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~AL 107 (214)
+.-|++.++|++|..-| ..|+...+-.+ +.--|-.|++-|+.||-..|-+++-.||..+||+.|-
T Consensus 15 rkaPrgfLkrv~Kr~Kp-hlRl~~~~Dllv~~~~f~~~~~~~~vhLncLLFvhrLAEEaRtnA~EnK~~~Ik~~Hv~Aaa 93 (102)
T PF15510_consen 15 RKAPRGFLKRVFKRQKP-HLRLETSGDLLVRFCPFSGWQWGGEVHLNCLLFVHRLAEEARTNACENKCGTIKKEHVLAAA 93 (102)
T ss_pred HhCchHHHHHHHHhcCC-ceeecccccHHHhhcccccccccceeehhHHHHHHHHHHHHHHHHHHHhhccccHHHHHHHH
Confidence 35799999999998754 66765544444 5556789999999999999999999999999999997
Q ss_pred HH
Q 047516 108 TT 109 (214)
Q Consensus 108 e~ 109 (214)
+.
T Consensus 94 Kv 95 (102)
T PF15510_consen 94 KV 95 (102)
T ss_pred HH
Confidence 54
No 53
>PF02269 TFIID-18kDa: Transcription initiation factor IID, 18kD subunit; InterPro: IPR003195 This family includes the Spt3 yeast transcription factors and the 18 kDa subunit from human transcription initiation factor IID (TFIID-18). Determination of the crystal structure reveals an atypical histone fold [].; GO: 0006366 transcription from RNA polymerase II promoter; PDB: 1BH9_A 1BH8_A.
Probab=95.82 E-value=0.012 Score=45.29 Aligned_cols=59 Identities=20% Similarity=0.291 Sum_probs=28.7
Q ss_pred HHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHHH
Q 047516 50 GRIMKKVIPGNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAITT 109 (214)
Q Consensus 50 ~RImK~~LP~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~ 109 (214)
..+|-.- .+...-..|+..+|-+.+.+||..|..+|..+|...|+++|+.+|++.+|+.
T Consensus 8 ~~mMy~f-GD~~~P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~rg~~~i~~eDl~F~lR~ 66 (93)
T PF02269_consen 8 RQMMYGF-GDVEEPLPETVDLVEDIVREYIIELCQEAMEVAQRRGSKKIKVEDLLFLLRK 66 (93)
T ss_dssp HHHHHCT-TS-SS--HHHHHHHHHHHHHHHHHHHHHHHC---------------------
T ss_pred HHHHHHc-CCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCcCcHHHHHHHHhc
Confidence 3444444 3345689999999999999999999999999999999999999999999974
No 54
>PTZ00252 histone H2A; Provisional
Probab=95.71 E-value=0.038 Score=45.75 Aligned_cols=70 Identities=10% Similarity=0.197 Sum_probs=57.2
Q ss_pred ccccccCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHh--cCCCccChHHHHHHHH
Q 047516 38 KEQDRFLPIANVGRIMKKVIPGNGKISKDAKETVQECVSEFISFVTGEASDKCQR--EKRKTINGDDIIWAIT 108 (214)
Q Consensus 38 k~~Dl~LPkA~V~RImK~~LP~~~rISkDA~ealqeca~eFI~~LtseAne~a~~--~kRKTI~~eDVl~ALe 108 (214)
..-.+.||.+.|.|++|+.-- ..||+..|...|.-+.+.....|..-|...|.. .+++-|+++||..|+.
T Consensus 20 ~rAGL~FPVgRi~R~Lr~g~y-a~RIga~ApVYLAAVLEYLtaEVLELAgnaa~d~~~kk~RItPrHi~lAIr 91 (134)
T PTZ00252 20 AKAGLIFPVGRVGSLLRRGQY-ARRIGASGAVYMAAVLEYLTAELLELSVKAAAQQAKKPKRLTPRTVTLAVR 91 (134)
T ss_pred cccCccCchHHHHHHHHcCCc-ccccCCccHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccccHHHHHhhcc
Confidence 346789999999999998842 469999999999888777777777777777754 6788999999999984
No 55
>KOG3219 consensus Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=95.57 E-value=0.017 Score=50.37 Aligned_cols=68 Identities=18% Similarity=0.201 Sum_probs=59.6
Q ss_pred cCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC-CccChHHHHHHHHHcCC
Q 047516 43 FLPIANVGRIMKKVIPGNGKISKDAKETVQECVSEFISFVTGEASDKCQREKR-KTINGDDIIWAITTLGF 112 (214)
Q Consensus 43 ~LPkA~V~RImK~~LP~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kR-KTI~~eDVl~ALe~LGF 112 (214)
.||++.|.|||..... ..|+.-+..+|+-.+.+||-.|-.+|.++|..-+. --|.+.||..|..+|+.
T Consensus 112 ~f~Ka~iKkL~~~itg--~~v~~nv~Ia~~GiaKvFVGEvVEeAl~V~~~~~e~~PLqP~HIREA~rrL~~ 180 (195)
T KOG3219|consen 112 AFPKAQIKKLMSSITG--QSVSENVAIAMAGIAKVFVGEVVEEALDVREEWGESGPLQPKHIREAYRRLKL 180 (195)
T ss_pred cCCHHHHHHHHHHHhC--CccCcceeeeecchhhHhHHHHHHHHHHHHHHhccCCCCCcHHHHHHHHHHHh
Confidence 4999999999999963 33999999999999999999999999999987665 47999999999877654
No 56
>KOG4336 consensus TBP-associated transcription factor Prodos [Transcription]
Probab=95.45 E-value=0.15 Score=47.38 Aligned_cols=66 Identities=21% Similarity=0.315 Sum_probs=60.7
Q ss_pred cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHHHcCCCcchHHHHHHHHHHHH
Q 047516 61 GKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAITTLGFEDYVAPLKLYLSKYRE 128 (214)
Q Consensus 61 ~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~LGF~dyi~~Lk~~L~~yre 128 (214)
-.|++-|++.|.+....+|..++..+.-+|.++||-..+.-||..+|-.+|+. +..|..+++++..
T Consensus 21 d~is~~aletlvell~~yi~eigrq~~n~celagRT~pT~~Dv~l~Li~mnI~--v~sL~~~~q~~~~ 86 (323)
T KOG4336|consen 21 DSISNAALETLVELLQSYIREIGRQLHNYCELAGRTIPTQGDVKLTLIEMNIK--VSSLYAYFQKQEF 86 (323)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcHHHHHHHHHHhCCC--hhhhHHHHHhccc
Confidence 35999999999999999999999999999999999999999999999999997 7788888776655
No 57
>cd07978 TAF13 The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Several hy
Probab=94.82 E-value=0.25 Score=38.13 Aligned_cols=59 Identities=17% Similarity=0.353 Sum_probs=48.6
Q ss_pred HHHHHHhhcCCCCc-ccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHHH
Q 047516 48 NVGRIMKKVIPGNG-KISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAITT 109 (214)
Q Consensus 48 ~V~RImK~~LP~~~-rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~ 109 (214)
-|..+|-.. |+. .-..|...+|-+.+.+||..|+.+|..+|. .+|.-|+.||++.+|+.
T Consensus 7 ei~~mmy~~--GD~~~P~~eTv~llE~iv~~~i~~l~~~a~~~A~-~r~~k~~~eD~~FliR~ 66 (92)
T cd07978 7 EIRQMMYGF--GDVQNPLPETVDLLEDIVVEYIIELCHKAAEVAQ-RRRGKVKVEDLIFLLRK 66 (92)
T ss_pred HHHHHHHHc--CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-cCCCCCCHHHHHHHHhc
Confidence 356666665 444 578899999999999999999999999999 55555699999999963
No 58
>KOG2549 consensus Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=94.62 E-value=0.15 Score=50.77 Aligned_cols=65 Identities=22% Similarity=0.276 Sum_probs=57.8
Q ss_pred CchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHHHc
Q 047516 44 LPIANVGRIMKKVIPGNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAITTL 110 (214)
Q Consensus 44 LPkA~V~RImK~~LP~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~L 110 (214)
-|+..+.-+++.. |-..|+.||..+|.+-++.=|..|+.+|.++-.+.||.+++.+||..||+.+
T Consensus 12 s~~Es~k~vAEsl--Gi~nl~deaa~~La~dv~yrikEI~Q~aaKfm~hskR~kLtv~DV~~ALr~~ 76 (576)
T KOG2549|consen 12 SPKESVKVVAESL--GITNLNDEAALLLAEDVEYRIKEIVQDAAKFMVHSKRTKLTVDDVDYALRSL 76 (576)
T ss_pred CcHHHHHHHHHHh--CccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcCcHHHHHHHHhhc
Confidence 3466666666666 6777999999999999999999999999999999999999999999999964
No 59
>KOG3423 consensus Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=93.70 E-value=0.4 Score=41.30 Aligned_cols=68 Identities=22% Similarity=0.287 Sum_probs=55.9
Q ss_pred cCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhc--------------CCCccChHHHHHHHH
Q 047516 43 FLPIANVGRIMKKVIPGNGKISKDAKETVQECVSEFISFVTGEASDKCQRE--------------KRKTINGDDIIWAIT 108 (214)
Q Consensus 43 ~LPkA~V~RImK~~LP~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~--------------kRKTI~~eDVl~ALe 108 (214)
.||=+.+.-.++.+ +-.....-.+.+|.-+|-.||+.|+..|.++|+-. +|-|++-+|+-.||+
T Consensus 86 ~IPDavt~~yL~~a--Gf~~~D~rv~RLvsLaAQKfvSDIa~DA~Q~~k~r~~~~~~~~k~~~kdkK~tLtmeDL~~AL~ 163 (176)
T KOG3423|consen 86 TIPDAVTDHYLKKA--GFQTSDPRVKRLVSLAAQKFVSDIANDALQHSKIRTKTAIGKDKKQAKDKKYTLTMEDLSPALA 163 (176)
T ss_pred CCcHHHHHHHHHhc--CCCcCcHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccccccccccccceeeeHHHHHHHHH
Confidence 47888888888887 43345566788999999999999999999999743 345999999999999
Q ss_pred HcCC
Q 047516 109 TLGF 112 (214)
Q Consensus 109 ~LGF 112 (214)
+.|.
T Consensus 164 EyGi 167 (176)
T KOG3423|consen 164 EYGI 167 (176)
T ss_pred HhCc
Confidence 9886
No 60
>KOG3334 consensus Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=92.91 E-value=0.79 Score=38.62 Aligned_cols=75 Identities=19% Similarity=0.268 Sum_probs=56.7
Q ss_pred HHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHHHcCCCcchH-HHHHHHHHH
Q 047516 50 GRIMKKVIPGNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAITTLGFEDYVA-PLKLYLSKY 126 (214)
Q Consensus 50 ~RImK~~LP~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~LGF~dyi~-~Lk~~L~~y 126 (214)
.-|+|+. +.--...-...-|-+.+=.++.-|...|.-++.|+++.||.++||..|++..+--.|.. +=+++|-++
T Consensus 20 ~~iL~s~--GI~eyEprVi~qlLefa~rYtt~vL~DA~vys~HA~ka~i~~eDVrlA~~~~~~~sf~~pPpRe~lL~l 95 (148)
T KOG3334|consen 20 ASILKSL--GIQEYEPRVINQLLEFAYRYTTTVLDDAKVYSSHAKKATIDAEDVRLAIQMRVDHSFTPPPPREFLLEL 95 (148)
T ss_pred HHHHHHc--CccccChHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHhccccCCCCchHHHHHH
Confidence 3344444 44446667778888999999999999999999999999999999999999766555554 444554443
No 61
>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily. Members of this protein are marked as probable ATPases by the nucleotide binding P-loop motif GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of helicases, and extensive homology to ATPases of MSHA-type pilus systems and to GspA proteins associated with type II protein secretion systems.
Probab=90.51 E-value=1.1 Score=38.29 Aligned_cols=69 Identities=13% Similarity=0.224 Sum_probs=54.8
Q ss_pred CchhHHHHHHhhcCC-----CCcccCHHHHHHHHHHHHH---HHHHHHHHHHHHHHhcCCCccChHHHHHHHHHcCC
Q 047516 44 LPIANVGRIMKKVIP-----GNGKISKDAKETVQECVSE---FISFVTGEASDKCQREKRKTINGDDIIWAITTLGF 112 (214)
Q Consensus 44 LPkA~V~RImK~~LP-----~~~rISkDA~ealqeca~e---FI~~LtseAne~a~~~kRKTI~~eDVl~ALe~LGF 112 (214)
|...-+..++...+. ....++.++.+.|.+.+.- .|+.++..|...+-..+.++|+.++|..++..+.|
T Consensus 192 l~~~e~~~~l~~~l~~~g~~~~~~~~~~~~~~i~~~s~G~p~~i~~l~~~~~~~a~~~~~~~i~~~~v~~~~~~~~~ 268 (269)
T TIGR03015 192 LDREETREYIEHRLERAGNRDAPVFSEGAFDAIHRFSRGIPRLINILCDRLLLSAFLEEKREIGGEEVREVIAEIDF 268 (269)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCCCcCHHHHHHHHHHcCCcccHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhhc
Confidence 444556665554431 2346999999999998875 79999999999988889999999999999998875
No 62
>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=89.37 E-value=1.5 Score=41.75 Aligned_cols=65 Identities=25% Similarity=0.269 Sum_probs=56.2
Q ss_pred hhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHHHcCC
Q 047516 46 IANVGRIMKKVIPGNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAITTLGF 112 (214)
Q Consensus 46 kA~V~RImK~~LP~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~LGF 112 (214)
+.+|.-++..- +-..|.+|+..+|..-.+.=|..+..+|...-.|.||..++-+||-.||+.|..
T Consensus 8 ~et~KdvAesl--Gi~Ni~Dd~l~alamDlEYRI~ev~qea~KFmvhSKRtvLt~dDis~ALr~lNV 72 (450)
T COG5095 8 KETLKDVAESL--GISNIDDDALRALAMDLEYRIKEVCQEASKFMVHSKRTVLTIDDISYALRSLNV 72 (450)
T ss_pred HHHHHHHHHHc--CCcccccHHHHHHHHhHHHHHHHHHHHHHHHhhcccceeeeHHhHHHHHHhcCC
Confidence 44555554444 567899999999999999999999999999999999999999999999998754
No 63
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=88.12 E-value=2.8 Score=38.06 Aligned_cols=71 Identities=11% Similarity=0.147 Sum_probs=51.6
Q ss_pred chhHHHHHHhhcCCC---CcccCHHHHHHHHHHH------HHHHHHHHHHHHHHHHhcCCCccChHHHHHHHHHcCCCcc
Q 047516 45 PIANVGRIMKKVIPG---NGKISKDAKETVQECV------SEFISFVTGEASDKCQREKRKTINGDDIIWAITTLGFEDY 115 (214)
Q Consensus 45 PkA~V~RImK~~LP~---~~rISkDA~ealqeca------~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~LGF~dy 115 (214)
...-+..|++..+-. ...++.++.+.+.+.+ -..+..+...|.+.|...++.+|+.+||..|++.+....+
T Consensus 208 ~~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~a~~~a~~~~~~~I~~~~v~~a~~~~~~~~~ 287 (394)
T PRK00411 208 TADEIFDILKDRVEEGFYPGVVDDEVLDLIADLTAREHGDARVAIDLLRRAGLIAEREGSRKVTEEDVRKAYEKSEIVHL 287 (394)
T ss_pred CHHHHHHHHHHHHHhhcccCCCCHhHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHHHHHH
Confidence 345556665554321 2358999999988877 3455667788888999999999999999999998844333
No 64
>KOG2389 consensus Predicted bromodomain transcription factor [Transcription]
Probab=87.93 E-value=1.6 Score=41.29 Aligned_cols=68 Identities=21% Similarity=0.268 Sum_probs=57.7
Q ss_pred CchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHHHcCCC
Q 047516 44 LPIANVGRIMKKVIPGNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAITTLGFE 113 (214)
Q Consensus 44 LPkA~V~RImK~~LP~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~LGF~ 113 (214)
|-+..|..|.... +.-....-|++.|...+..||..|+..|..++...+|--.+..||+.||+.|+..
T Consensus 30 la~~avaQIcqsl--g~~~~~~sale~Ltd~~~qyvQ~lgk~a~~~~n~anR~epnl~Div~Al~dls~s 97 (353)
T KOG2389|consen 30 LARVAVAQICQSL--GYSSTQNSALETLTDVLQQYVQNLGKTAHRYSNLANRTEPNLFDIVLALQDLSAS 97 (353)
T ss_pred HHHHHHHHHHHhc--CCcccccHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCccHHHHHHHHHHhhhh
Confidence 5666677777666 3444555699999999999999999999999999999999999999999987753
No 65
>cd08045 TAF4 TATA Binding Protein (TBP) Associated Factor 4 (TAF4) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 4 (TAF4) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryote. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypotheses are
Probab=84.30 E-value=14 Score=31.96 Aligned_cols=78 Identities=9% Similarity=0.108 Sum_probs=59.0
Q ss_pred ccccCchhHHHHHHhhcCCC-Cc-ccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhc------CCCccChHHHHHHHHHcC
Q 047516 40 QDRFLPIANVGRIMKKVIPG-NG-KISKDAKETVQECVSEFISFVTGEASDKCQRE------KRKTINGDDIIWAITTLG 111 (214)
Q Consensus 40 ~Dl~LPkA~V~RImK~~LP~-~~-rISkDA~ealqeca~eFI~~LtseAne~a~~~------kRKTI~~eDVl~ALe~LG 111 (214)
...+|....|.+.|...+.. +. .|+.|++.+|.-||++++..|.......|++- .-.++.-.||...|..|+
T Consensus 41 ~~~fl~~~~l~~~~~~i~~~~g~~~~~~d~~~lis~a~e~rlr~li~k~~~~s~hR~~~~~~~~r~~~~sdvr~qL~~l~ 120 (212)
T cd08045 41 DPSFLNPSPLAKKIRKIAKKHGLKEVDEDVLDLISLALEERLRNLLEKLIEVSEHRVDSEKEDERYEITSDVRKQLRFLE 120 (212)
T ss_pred hhhccCHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCceeecchHHHHHHHHH
Confidence 44567777777777666432 22 79999999999999999999999999998764 446777888888887665
Q ss_pred CCcchH
Q 047516 112 FEDYVA 117 (214)
Q Consensus 112 F~dyi~ 117 (214)
--+..+
T Consensus 121 ~~ek~e 126 (212)
T cd08045 121 QLEREE 126 (212)
T ss_pred HHHHHH
Confidence 544443
No 66
>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=84.16 E-value=4.2 Score=36.41 Aligned_cols=72 Identities=10% Similarity=0.085 Sum_probs=50.2
Q ss_pred hhHHHHHHhhcCC---CCcccCHHHHHHHHHHHH------HHHHHHHHHHHHHHHhcCCCccChHHHHHHHHHcCCCcch
Q 047516 46 IANVGRIMKKVIP---GNGKISKDAKETVQECVS------EFISFVTGEASDKCQREKRKTINGDDIIWAITTLGFEDYV 116 (214)
Q Consensus 46 kA~V~RImK~~LP---~~~rISkDA~ealqeca~------eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~LGF~dyi 116 (214)
..-+..|++..+. ....+..++.+.+.+.+. ..+..+...|.+.|...++.+|+.+||..|++.+..+-+.
T Consensus 201 ~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~R~al~~l~~a~~~a~~~~~~~it~~~v~~a~~~~~~~~~~ 280 (365)
T TIGR02928 201 AEELRDILENRAEKAFYDGVLDDGVIPLCAALAAQEHGDARKAIDLLRVAGEIAEREGAERVTEDHVEKAQEKIEKDRLL 280 (365)
T ss_pred HHHHHHHHHHHHHhhccCCCCChhHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHH
Confidence 4446666665542 234588888887766543 3455566778888988899999999999999988544444
Q ss_pred H
Q 047516 117 A 117 (214)
Q Consensus 117 ~ 117 (214)
.
T Consensus 281 ~ 281 (365)
T TIGR02928 281 E 281 (365)
T ss_pred H
Confidence 3
No 67
>PF13654 AAA_32: AAA domain; PDB: 3K1J_B.
Probab=83.76 E-value=5 Score=39.43 Aligned_cols=48 Identities=19% Similarity=0.230 Sum_probs=38.9
Q ss_pred ccCHHHHHHHHHHHH-----------HHHHHHHHHHHHHHHhcCCCccChHHHHHHHHH
Q 047516 62 KISKDAKETVQECVS-----------EFISFVTGEASDKCQREKRKTINGDDIIWAITT 109 (214)
Q Consensus 62 rISkDA~ealqeca~-----------eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~ 109 (214)
-++.+|+..|.+.+. ..|..|..+|+.+|..+++++|+++||..|++.
T Consensus 447 ~~~~~Av~~li~~~~R~~q~kLsl~~~~l~~ll~EA~~~A~~~~~~~I~~~~V~~Ai~~ 505 (509)
T PF13654_consen 447 PFDRSAVARLIEYSARLDQDKLSLRFSWLADLLREANYWARKEGAKVITAEHVEQAIEE 505 (509)
T ss_dssp -BBHHHHHHHHHHHHHCC-SEEE--HHHHHHHHHHHHHHHHHCT-SSB-HHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHHhCCEeCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHc
Confidence 488888888877664 367788899999999999999999999999975
No 68
>PF08369 PCP_red: Proto-chlorophyllide reductase 57 kD subunit; InterPro: IPR013580 This domain is found in bacteria and plant chloroplast proteins. It often appears at the C-terminal of nitrogenase component 1 type oxidoreductases (IPR000510 from INTERPRO) and sometimes independently in bacterial proteins such as the proto-chlorophyllide reductase subunit B of the cyanobacterium Synechocystis. This domain is also associated with chlorophyllide reductase subunit Z, converts chlorophylls (Chl) into bacteriochlorophylls (BChl) by reducing ring B of the tetrapyrrole.; GO: 0016491 oxidoreductase activity, 0015979 photosynthesis, 0015995 chlorophyll biosynthetic process, 0055114 oxidation-reduction process; PDB: 2KRU_A 2L09_A.
Probab=76.56 E-value=4.2 Score=27.48 Aligned_cols=42 Identities=12% Similarity=0.124 Sum_probs=30.6
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHH-HHHhcCCCccChHHHHHH
Q 047516 64 SKDAKETVQECVSEFISFVTGEASD-KCQREKRKTINGDDIIWA 106 (214)
Q Consensus 64 SkDA~ealqeca~eFI~~LtseAne-~a~~~kRKTI~~eDVl~A 106 (214)
+.||...|.+. -.|+.--...+.+ +|...|...|+.++|..|
T Consensus 2 ~~eA~~~L~~i-P~fvR~~~r~~~E~~Ar~~G~~~IT~e~v~~A 44 (45)
T PF08369_consen 2 TDEAEARLDRI-PFFVRKKLRDAAEKYARERGYDEITVEVVDAA 44 (45)
T ss_dssp -HHHHHHHCTS--HHHHHHHHHHHHHHHHHCT-SEE-HHHHHHH
T ss_pred CHHHHHHHHHC-CHHHHHHHHHHHHHHHHHcCCCeECHHHHHhh
Confidence 57788888775 7788777766666 788999999999999876
No 69
>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=76.39 E-value=11 Score=37.67 Aligned_cols=48 Identities=13% Similarity=0.165 Sum_probs=39.8
Q ss_pred ccCHHHHHHHHHHHH-------------HHHHHHHHHHHHHHHhcCCCccChHHHHHHHHH
Q 047516 62 KISKDAKETVQECVS-------------EFISFVTGEASDKCQREKRKTINGDDIIWAITT 109 (214)
Q Consensus 62 rISkDA~ealqeca~-------------eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~ 109 (214)
.++++|+..|.+-++ .=|.-|..+|..+|..+++.+|+.+||..|++.
T Consensus 330 ~~s~~Av~~Li~~~~R~ag~r~~lsl~~R~L~~llR~A~~iA~~~~~~~I~~ehV~~Ai~~ 390 (608)
T TIGR00764 330 HFTRDAVEEIVREAQRRAGRKDHLTLRLRELGGLVRAAGDIAKSSGKVYVTAEHVLKAKKL 390 (608)
T ss_pred cCCHHHHHHHHHHHHHHHhcccccCCCHHHHHHHHHHHHHHHHhcCCceecHHHHHHHHHH
Confidence 689999999886544 346677788988999999999999999999854
No 70
>KOG2680 consensus DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=74.55 E-value=14 Score=35.42 Aligned_cols=49 Identities=20% Similarity=0.251 Sum_probs=41.8
Q ss_pred CCcccCHHHHHHHHHHHH----HHHHHHHHHHHHHHHhcCCCccChHHHHHHH
Q 047516 59 GNGKISKDAKETVQECVS----EFISFVTGEASDKCQREKRKTINGDDIIWAI 107 (214)
Q Consensus 59 ~~~rISkDA~ealqeca~----eFI~~LtseAne~a~~~kRKTI~~eDVl~AL 107 (214)
.++.++.||++.|.+..+ .|..+|...|+..|.+.|-+++..+||-.+.
T Consensus 374 Edv~m~~~A~d~Lt~i~~~tsLRYai~Lit~a~~~~~krk~~~v~~~di~r~y 426 (454)
T KOG2680|consen 374 EDVEMNPDALDLLTKIGEATSLRYAIHLITAASLVCLKRKGKVVEVDDIERVY 426 (454)
T ss_pred hccccCHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHhcCceeehhHHHHHH
Confidence 578899999999987654 4667777889999999999999999999884
No 71
>TIGR02902 spore_lonB ATP-dependent protease LonB. Members of this protein are LonB, a paralog of the ATP-dependent protease La (LonA, TIGR00763). LonB proteins are found strictly, and almost universally, in endospore-forming bacteria. This protease was shown, in Bacillus subtilis, to be expressed specifically in the forespore, during sporulation, under control of sigma(F). The lonB gene, despite location immediately upstream of lonA, was shown to be monocistronic. LonB appears able to act on sigma(H) for post-translation control, but lonB mutation did not produce an obvious sporulation defect under the conditions tested. Note that additional paralogs of LonA and LonB occur in the Clostridium lineage and this model selects only one per species as the protein that corresponds to LonB in B. subtilis.
Probab=73.98 E-value=9.3 Score=37.41 Aligned_cols=64 Identities=22% Similarity=0.193 Sum_probs=45.0
Q ss_pred hhHHHHHHhhcCC-CCcccCHHHHHHHHHHHHH--HHHHHHHHHHHHHHhcCCCccChHHHHHHHHH
Q 047516 46 IANVGRIMKKVIP-GNGKISKDAKETVQECVSE--FISFVTGEASDKCQREKRKTINGDDIIWAITT 109 (214)
Q Consensus 46 kA~V~RImK~~LP-~~~rISkDA~ealqeca~e--FI~~LtseAne~a~~~kRKTI~~eDVl~ALe~ 109 (214)
..-+.+|++..+. .+..|++++.++|.+.+.. .+..+...|..+|..++|++|+.+||.+++..
T Consensus 265 ~eei~~Il~~~a~k~~i~is~~al~~I~~y~~n~Rel~nll~~Aa~~A~~~~~~~It~~dI~~vl~~ 331 (531)
T TIGR02902 265 DEEIKEIAKNAAEKIGINLEKHALELIVKYASNGREAVNIVQLAAGIALGEGRKRILAEDIEWVAEN 331 (531)
T ss_pred HHHHHHHHHHHHHHcCCCcCHHHHHHHHHhhhhHHHHHHHHHHHHHHHhhCCCcEEcHHHHHHHhCC
Confidence 3445666666543 2467999999988777652 23344455667788889999999999999753
No 72
>COG1067 LonB Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]
Probab=73.17 E-value=3.6 Score=41.75 Aligned_cols=48 Identities=27% Similarity=0.293 Sum_probs=37.5
Q ss_pred ccCHHHHHHHHHHHHH-------------HHHHHHHHHHHHHHhcCCCccChHHHHHHHHH
Q 047516 62 KISKDAKETVQECVSE-------------FISFVTGEASDKCQREKRKTINGDDIIWAITT 109 (214)
Q Consensus 62 rISkDA~ealqeca~e-------------FI~~LtseAne~a~~~kRKTI~~eDVl~ALe~ 109 (214)
-++++|...|.+-+.. -|.-|-.+|.++|..++++-|+++||.+|++.
T Consensus 338 ~~~~~Av~~li~~a~R~Ag~~~~Ltl~~rdl~~lv~~A~~ia~~~~~~~I~ae~Ve~a~~~ 398 (647)
T COG1067 338 HLDKDAVEELIREAARRAGDQNKLTLRLRDLGNLVREAGDIAVSEGRKLITAEDVEEALQK 398 (647)
T ss_pred CCCHHHHHHHHHHHHHhccccceeccCHHHHHHHHHHhhHHHhcCCcccCcHHHHHHHHHh
Confidence 3777777777666543 24445559999999999999999999999965
No 73
>COG5162 Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=73.14 E-value=21 Score=31.08 Aligned_cols=50 Identities=18% Similarity=0.253 Sum_probs=39.8
Q ss_pred cCHHHHHHHHHHHHHHHHHHHHHHHHHHH-hc--------------------------------CCCccChHHHHHHHHH
Q 047516 63 ISKDAKETVQECVSEFISFVTGEASDKCQ-RE--------------------------------KRKTINGDDIIWAITT 109 (214)
Q Consensus 63 ISkDA~ealqeca~eFI~~LtseAne~a~-~~--------------------------------kRKTI~~eDVl~ALe~ 109 (214)
...-.+.+|.-.+-.||+.|+-.|.++.+ +. ++-+++..|+-.||++
T Consensus 106 ~D~rvKkLl~L~aqKFvsDiA~dayqYsrIr~~~sna~~t~~~a~~f~~gg~~~i~~~~~~~dr~K~vltv~DLs~Al~E 185 (197)
T COG5162 106 SDQRVKKLLSLLAQKFVSDIAVDAYQYSRIRQGSSNAKATAQKAKRFAKGGASGIGSSGRRGDRKKPVLTVVDLSKALEE 185 (197)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccchhhHHHHHHHHhcccccccccccccccCCceeeehHHHHHHHH
Confidence 45567889999999999999998887642 11 4568899999999998
Q ss_pred cCC
Q 047516 110 LGF 112 (214)
Q Consensus 110 LGF 112 (214)
.|+
T Consensus 186 yGi 188 (197)
T COG5162 186 YGI 188 (197)
T ss_pred hcc
Confidence 776
No 74
>KOG1757 consensus Histone 2A [Chromatin structure and dynamics]
Probab=72.94 E-value=4.9 Score=32.91 Aligned_cols=66 Identities=18% Similarity=0.298 Sum_probs=51.0
Q ss_pred cccccCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhc----CCCccChHHHHHHHH
Q 047516 39 EQDRFLPIANVGRIMKKVIPGNGKISKDAKETVQECVSEFISFVTGEASDKCQRE----KRKTINGDDIIWAIT 108 (214)
Q Consensus 39 ~~Dl~LPkA~V~RImK~~LP~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~----kRKTI~~eDVl~ALe 108 (214)
...+.||..+|.|.+|.......||..-+...+ ...+.||+.|-.+.|..+ +-|.|++.|+-.|++
T Consensus 26 raGlqFpVgRihr~LK~r~t~h~rVGataavy~----aaileYLTaEVLeLAgNasKdLKvKRitprHlqLAiR 95 (131)
T KOG1757|consen 26 RAGLQFPVGRIHRHLKTRTTSHGRVGATAAVYS----AAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 95 (131)
T ss_pred hcccccchHHHHHHHHHhcccccccchHHHHHH----HHHHHHHHHHHHHHcccccccceeeeccchhheeeec
Confidence 356789999999999999777888876555443 345678888888877654 457899999988875
No 75
>PF03540 TFIID_30kDa: Transcription initiation factor TFIID 23-30kDa subunit; InterPro: IPR003923 Transcription initiation factor TFIID is a multimeric protein complex that plays a central role in mediating promoter responses to various activators and repressors. The complex includes TATA binding protein (TBP) and various TBP-associated factors (TAFS). TFIID a bona fide RNA polymerase II-specific TATA-binding protein-associated factor (TAF) and is essential for viability []. TFIID acts to nucleate the transcription complex, recruiting the rest of the factors through a direct interaction with TFIIB. The TBP subunit of TFIID is sufficient for TATA-element binding and TFIIB interaction, and can support basal transcription. The protein belongs to the TAF2H family.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus
Probab=72.73 E-value=22 Score=24.98 Aligned_cols=48 Identities=19% Similarity=0.259 Sum_probs=36.7
Q ss_pred cCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 047516 43 FLPIANVGRIMKKVIPGNGKISKDAKETVQECVSEFISFVTGEASDKCQR 92 (214)
Q Consensus 43 ~LPkA~V~RImK~~LP~~~rISkDA~ealqeca~eFI~~LtseAne~a~~ 92 (214)
.||-+-+.-+++.+ |--.-..-.+-++.=++..||..|+..|..+|+-
T Consensus 2 ~IPD~v~~~yL~~~--G~~~~D~rv~RLvSLaaQKFisdI~~dA~q~~k~ 49 (51)
T PF03540_consen 2 TIPDEVTDYYLERS--GFQTSDPRVKRLVSLAAQKFISDIANDAMQYCKI 49 (51)
T ss_pred CCCHHHHHHHHHHC--CCCCCCHhHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 46778888888887 3222334466788899999999999999999863
No 76
>PF13335 Mg_chelatase_2: Magnesium chelatase, subunit ChlI
Probab=69.17 E-value=22 Score=27.21 Aligned_cols=48 Identities=17% Similarity=0.207 Sum_probs=39.8
Q ss_pred cccCHHHHHHHHHHHHHH------HHHHHHHHHHHHHhcCCCccChHHHHHHHH
Q 047516 61 GKISKDAKETVQECVSEF------ISFVTGEASDKCQREKRKTINGDDIIWAIT 108 (214)
Q Consensus 61 ~rISkDA~ealqeca~eF------I~~LtseAne~a~~~kRKTI~~eDVl~ALe 108 (214)
..+++++..+|..++..| +.-|..-|-++|.-++...|..+||..||.
T Consensus 41 ~~l~~~~~~~l~~~~~~~~lS~R~~~rilrvARTIADL~~~~~I~~~hi~EAl~ 94 (96)
T PF13335_consen 41 CPLSSEAKKLLEQAAEKLNLSARGYHRILRVARTIADLEGSERITREHIAEALS 94 (96)
T ss_pred cCCCHHHHHHHHHHHHHcCcCHHHHHHHHHHHHHHHhHcCCCCCCHHHHHHHHh
Confidence 357888888888887765 455667789999999999999999999983
No 77
>COG5094 TAF9 Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=68.99 E-value=38 Score=28.29 Aligned_cols=74 Identities=19% Similarity=0.177 Sum_probs=53.9
Q ss_pred CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCh---HHHHHHHHH-cCCCcchHHHHHHHHHHHHHHhh
Q 047516 59 GNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTING---DDIIWAITT-LGFEDYVAPLKLYLSKYREIEGE 132 (214)
Q Consensus 59 ~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~---eDVl~ALe~-LGF~dyi~~Lk~~L~~yre~~~~ 132 (214)
+.-....-+..-|.+.|-.|-.-|...|.-++++.||--++. |||..|+.. .|..---++=++||-+.-.++..
T Consensus 28 gi~~ye~~VplQLl~FAhRYTq~vl~Dalvya~htgrg~~a~l~veDvrLA~at~v~~~F~pppPke~llela~erN~ 105 (145)
T COG5094 28 GIEEYEPKVPLQLLEFAHRYTQDVLEDALVYAKHTGRGHIATLGVEDVRLALATKVGRHFVPPPPKEYLLELATERNS 105 (145)
T ss_pred CchhhCccchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHHHHHHHhcCCcCCCChHHHHHHHHHHhcC
Confidence 344466667777888899999999999999999999975555 999999985 45443344566666655544443
No 78
>KOG3901 consensus Transcription initiation factor IID subunit [Transcription]
Probab=64.66 E-value=36 Score=27.45 Aligned_cols=50 Identities=16% Similarity=0.236 Sum_probs=41.1
Q ss_pred CCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHHH
Q 047516 57 IPGNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAITT 109 (214)
Q Consensus 57 LP~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~ 109 (214)
..++..=-.|.+++|-..+.+||..++..|.++. +|--+..||++.+|++
T Consensus 22 fGDd~nP~~~tv~~Le~iV~~Yi~elt~~a~~~g---~rgk~~veD~~f~lRk 71 (109)
T KOG3901|consen 22 FGDDVNPYPETVDLLEDIVLEYITELTHAAMEIG---KRGKVKVEDFKFLLRK 71 (109)
T ss_pred cCCCCCccHhHHHHHHHHHHHHHHHHHHHHHHhc---ccCceeHHHHHHHHHh
Confidence 3455566788999999999999999988887776 6667888999999974
No 79
>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=63.93 E-value=53 Score=28.69 Aligned_cols=72 Identities=17% Similarity=0.169 Sum_probs=49.6
Q ss_pred CchhHHHHHHhhcCC-CCcccCHHHHHHHHHHHH---HHHHHHHHHHHHHHHhcCCCccChHHHHHHHHHcCCCcc
Q 047516 44 LPIANVGRIMKKVIP-GNGKISKDAKETVQECVS---EFISFVTGEASDKCQREKRKTINGDDIIWAITTLGFEDY 115 (214)
Q Consensus 44 LPkA~V~RImK~~LP-~~~rISkDA~ealqeca~---eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~LGF~dy 115 (214)
++...+..+++..+. .+..++.++.+.|.+.+. .++..+...+...+...+...|+.++|..++..++++.+
T Consensus 159 l~~~e~~~il~~~~~~~~~~~~~~al~~ia~~~~G~pR~~~~ll~~~~~~a~~~~~~~it~~~v~~~l~~l~~~~~ 234 (305)
T TIGR00635 159 YTVEELAEIVSRSAGLLNVEIEPEAALEIARRSRGTPRIANRLLRRVRDFAQVRGQKIINRDIALKALEMLMIDEL 234 (305)
T ss_pred CCHHHHHHHHHHHHHHhCCCcCHHHHHHHHHHhCCCcchHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHhCCCCC
Confidence 445556666655432 256799999988888763 244555556666776666678999999999998766543
No 80
>COG5624 TAF61 Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=62.02 E-value=3.5 Score=40.20 Aligned_cols=82 Identities=15% Similarity=0.177 Sum_probs=67.3
Q ss_pred Ccccc--ccCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHHH---cC
Q 047516 37 SKEQD--RFLPIANVGRIMKKVIPGNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAITT---LG 111 (214)
Q Consensus 37 ~k~~D--l~LPkA~V~RImK~~LP~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~---LG 111 (214)
.+.+| +.+-+-.+.-+++..+.+..+|-.|.-+++-..|..|+.-++.-|..+|+|-+-+||-+.|+-.-|++ +-
T Consensus 375 ye~D~~~Rl~skrkL~el~~~~vd~eekie~eveelll~~ad~fve~vt~FsCrlakhrkSdtlevrD~qlhlErnwnIr 454 (505)
T COG5624 375 YERDDLWRLDSKRKLEELQHGGVDEEEKIENEVEELLLSRADGFVEPVTEFSCRLAKHRKSDTLEVRDGQLHLERNWNIR 454 (505)
T ss_pred hhcchhhhhhhhhhHHHHHhhccCcceeccchHHHHHHhhhcccccccchheeEeeccCCCCceeeccceeeecccccee
Confidence 34444 34677777888888887788999999999999999999999999999999999999999999888875 33
Q ss_pred CCcchHH
Q 047516 112 FEDYVAP 118 (214)
Q Consensus 112 F~dyi~~ 118 (214)
++.|+..
T Consensus 455 ~pGf~~d 461 (505)
T COG5624 455 CPGFVDD 461 (505)
T ss_pred cCcchHH
Confidence 4555543
No 81
>PLN03162 golden-2 like transcription factor; Provisional
Probab=61.40 E-value=1.7e+02 Score=28.87 Aligned_cols=55 Identities=13% Similarity=0.126 Sum_probs=33.8
Q ss_pred CcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHHHcCCCcc-hHHHHHHHHHHHHHHhh
Q 047516 60 NGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAITTLGFEDY-VAPLKLYLSKYREIEGE 132 (214)
Q Consensus 60 ~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~LGF~dy-i~~Lk~~L~~yre~~~~ 132 (214)
-++++.|.-..+.+++... |-..-++.-|+.. +++... +..++.+|++||-..+.
T Consensus 237 RLrWTpELH~rFVeAV~qL---------------G~dKATPK~ILel---MnV~GLTRenVKSHLQKYRl~rk~ 292 (526)
T PLN03162 237 KVDWTPELHRRFVHAVEQL---------------GVEKAFPSRILEL---MGVQCLTRHNIASHLQKYRSHRRH 292 (526)
T ss_pred cccCCHHHHHHHHHHHHHh---------------CcCccchHHHHHH---cCCCCcCHHHHHHHHHHHHHhccc
Confidence 4678887666555544332 1122345555554 455544 67899999999987654
No 82
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=60.24 E-value=51 Score=29.66 Aligned_cols=72 Identities=13% Similarity=0.142 Sum_probs=51.3
Q ss_pred CchhHHHHHHhhcCC-CCcccCHHHHHHHHHHHH---HHHHHHHHHHHHHHHhcCCCccChHHHHHHHHHcCCCcc
Q 047516 44 LPIANVGRIMKKVIP-GNGKISKDAKETVQECVS---EFISFVTGEASDKCQREKRKTINGDDIIWAITTLGFEDY 115 (214)
Q Consensus 44 LPkA~V~RImK~~LP-~~~rISkDA~ealqeca~---eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~LGF~dy 115 (214)
++...+..|++..+. .++.++.|+...|.+.+. ..+..+...+.++|...+...|+.++|..+++.++....
T Consensus 180 ~~~~e~~~il~~~~~~~~~~~~~~~~~~ia~~~~G~pR~a~~~l~~~~~~a~~~~~~~I~~~~v~~~l~~~~~~~~ 255 (328)
T PRK00080 180 YTVEELEKIVKRSARILGVEIDEEGALEIARRSRGTPRIANRLLRRVRDFAQVKGDGVITKEIADKALDMLGVDEL 255 (328)
T ss_pred CCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCcC
Confidence 455666666665532 357799999988887773 345555556666776667779999999999998876643
No 83
>PF05236 TAF4: Transcription initiation factor TFIID component TAF4 family; InterPro: IPR007900 Accurate transcription initiation at protein-coding genes by RNA polymerase II requires the assembly of a multiprotein complex around the mRNA start site. Transcription factor TFIID is one of the general factors involved in this process. Yeast TFIID comprises the TATA binding protein and 14 TBP-associated factors (TAFIIs), nine of which contain histone-fold domains (IPR007124 from INTERPRO). The C-terminal region of the TFIID-specific yeast TAF4 (yTAF4) containing the HFD shares strong sequence similarity with Drosophila (d)TAF4 and human TAF4. A structure/function analysis of yTAF4 demonstrates that the HFD, a short conserved C-terminal domain (CCTD), and the region separating them are all required for yTAF4 function. This region of similarity is found in Transcription initiation factor TFIID component TAF4 []. ; GO: 0006352 transcription initiation, DNA-dependent, 0005669 transcription factor TFIID complex; PDB: 1H3O_C.
Probab=57.12 E-value=17 Score=32.32 Aligned_cols=78 Identities=13% Similarity=0.144 Sum_probs=34.2
Q ss_pred ccccccCchhHHHHHHhhcCC--CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC------CccChHHHHHHHHH
Q 047516 38 KEQDRFLPIANVGRIMKKVIP--GNGKISKDAKETVQECVSEFISFVTGEASDKCQREKR------KTINGDDIIWAITT 109 (214)
Q Consensus 38 k~~Dl~LPkA~V~RImK~~LP--~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kR------KTI~~eDVl~ALe~ 109 (214)
..++.+|-...+.+-|..... +...|..|.+.+|.-||+++|..|...+..+|++--. .+....||-..|..
T Consensus 38 ~~~~~fL~~~~L~~~i~~i~~~~g~~~~~~d~l~llS~A~e~rLr~lie~~~~~s~hR~~~~~~~~~~~~~sdv~~qlr~ 117 (264)
T PF05236_consen 38 EKEEPFLNPSPLQKRIQKIAKKHGLKSVDEDVLELLSLATEERLRNLIEKAIVLSRHRRDSSKSDPRYEIRSDVRKQLRF 117 (264)
T ss_dssp ------S-HHHHHHHHHHHHHCTT--EE-TCHHHHHHHHHHHHHHHHHHHHH----------------------------
T ss_pred cccccccCHHHHHHHHHHHHHHcCCcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccCCCcccccchHHHHHHHH
Confidence 345667888777777766642 3457999999999999999999999999998876321 23346777777766
Q ss_pred cCCCcc
Q 047516 110 LGFEDY 115 (214)
Q Consensus 110 LGF~dy 115 (214)
|.-.+-
T Consensus 118 l~~~e~ 123 (264)
T PF05236_consen 118 LEQLEK 123 (264)
T ss_dssp ------
T ss_pred HHHHHH
Confidence 554433
No 84
>COG5248 TAF19 Transcription initiation factor TFIID, subunit TAF13 [Transcription]
Probab=55.34 E-value=39 Score=27.68 Aligned_cols=50 Identities=20% Similarity=0.286 Sum_probs=42.6
Q ss_pred CCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHHH
Q 047516 58 PGNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAITT 109 (214)
Q Consensus 58 P~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~ 109 (214)
.+.+.=..|..++|.+.+..|++.+...|...|. .|-.+..||+..||++
T Consensus 23 GDvv~P~~dt~~~L~e~V~dY~~~~ctna~~~Aq--~rnK~k~eDfkfaLr~ 72 (126)
T COG5248 23 GDVVAPRYDTAEALHEYVLDYMSILCTNAHNMAQ--VRNKTKTEDFKFALRR 72 (126)
T ss_pred CCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHH--hcccchHHHHHHHHhh
Confidence 3555677899999999999999999999999888 5666778999999984
No 85
>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=54.44 E-value=36 Score=33.25 Aligned_cols=50 Identities=22% Similarity=0.191 Sum_probs=41.7
Q ss_pred CCcccCHHHHHHHHHHHHH----HHHHHHHHHHHHHHhcCCCccChHHHHHHHH
Q 047516 59 GNGKISKDAKETVQECVSE----FISFVTGEASDKCQREKRKTINGDDIIWAIT 108 (214)
Q Consensus 59 ~~~rISkDA~ealqeca~e----FI~~LtseAne~a~~~kRKTI~~eDVl~ALe 108 (214)
.++.+++||++.|....++ |..-|..-|..+|...|+++|..+||-.|-+
T Consensus 377 e~i~l~~~Ale~L~~ig~etSLRYa~qLL~pa~iiA~~rg~~~V~~~dVe~a~~ 430 (450)
T COG1224 377 EDIELSDDALEYLTDIGEETSLRYAVQLLTPASIIAKRRGSKRVEVEDVERAKE 430 (450)
T ss_pred hccccCHHHHHHHHhhchhhhHHHHHHhccHHHHHHHHhCCCeeehhHHHHHHH
Confidence 4678999999999876543 5566667799999999999999999999853
No 86
>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=54.05 E-value=43 Score=33.57 Aligned_cols=50 Identities=18% Similarity=0.176 Sum_probs=42.2
Q ss_pred CCcccCHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCccChHHHHHHHH
Q 047516 59 GNGKISKDAKETVQECVSEFI-------SFVTGEASDKCQREKRKTINGDDIIWAIT 108 (214)
Q Consensus 59 ~~~rISkDA~ealqeca~eFI-------~~LtseAne~a~~~kRKTI~~eDVl~ALe 108 (214)
..+.|+.++++.|...+..+- .++...|-.+|.-++|.+|+.+||..|++
T Consensus 246 ~~V~is~~~~~~l~~~~~~~~i~s~Ra~i~~~r~Ara~AaL~gr~~V~~~Dv~~A~~ 302 (633)
T TIGR02442 246 PSVRISDSLIRFISELCIEFGVDGHRADIVMARAARALAALDGRRRVTAEDVREAAE 302 (633)
T ss_pred CCCCCCHHHHHHHHHHHHHhCCCCccHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHH
Confidence 468899999999999887763 45667777889999999999999999985
No 87
>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=53.86 E-value=41 Score=31.30 Aligned_cols=54 Identities=20% Similarity=0.154 Sum_probs=41.9
Q ss_pred hhcCCCCcccCHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCccChHHHHHHHH
Q 047516 54 KKVIPGNGKISKDAKETVQECVSEFI-------SFVTGEASDKCQREKRKTINGDDIIWAIT 108 (214)
Q Consensus 54 K~~LP~~~rISkDA~ealqeca~eFI-------~~LtseAne~a~~~kRKTI~~eDVl~ALe 108 (214)
++.+ ..+.|+.+.+..+.+.+..+= .++...|-..|.-+||..|+++||..+..
T Consensus 247 ~~~~-~~V~v~d~~~~~i~~l~~~~~~~s~Ra~i~l~raArA~Aal~GR~~V~~dDv~~~a~ 307 (337)
T TIGR02030 247 QNLL-PQVTIPYDVLVKVAELCAELDVDGLRGELTLNRAAKALAAFEGRTEVTVDDIRRVAV 307 (337)
T ss_pred HHHh-ccCcCCHHHHHHHHHHHHHHCCCCCcHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 3344 478899999998888776653 24666777789999999999999998764
No 88
>PRK09862 putative ATP-dependent protease; Provisional
Probab=52.17 E-value=60 Score=32.14 Aligned_cols=52 Identities=10% Similarity=0.120 Sum_probs=40.7
Q ss_pred ccCHHHHHHHHHHHHHH------HHHHHHHHHHHHHhcCCCccChHHHHHHHHHcCCC
Q 047516 62 KISKDAKETVQECVSEF------ISFVTGEASDKCQREKRKTINGDDIIWAITTLGFE 113 (214)
Q Consensus 62 rISkDA~ealqeca~eF------I~~LtseAne~a~~~kRKTI~~eDVl~ALe~LGF~ 113 (214)
.++.++...+..++..+ ...|..-|-++|.-++|..|+.+||..|+.--+++
T Consensus 438 ~l~~~~~~~l~~~~~~~~lS~Ra~~rlLrvARTiADL~g~~~V~~~hv~eAl~yR~~~ 495 (506)
T PRK09862 438 KLESEDARWLEETLIHLGLSIRAWQRLLKVARTIADIDQSDIITRQHLQEAVSYRAID 495 (506)
T ss_pred CCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHhhccc
Confidence 57788888777765544 55677788899999999999999999999644433
No 89
>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]
Probab=51.42 E-value=58 Score=30.66 Aligned_cols=71 Identities=14% Similarity=0.173 Sum_probs=50.3
Q ss_pred hHHHHHHhhcCC---CCcccCHHHHHHHHHHH------HHHHHHHHHHHHHHHHhcCCCccChHHHHHHHHHcCCCcchH
Q 047516 47 ANVGRIMKKVIP---GNGKISKDAKETVQECV------SEFISFVTGEASDKCQREKRKTINGDDIIWAITTLGFEDYVA 117 (214)
Q Consensus 47 A~V~RImK~~LP---~~~rISkDA~ealqeca------~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~LGF~dyi~ 117 (214)
.-|+-|++.-.. ....++.++.+++..-+ ..+...|...|.++|+.+++.+|+.+||..|-+..+..-+.+
T Consensus 193 ~el~~Il~~R~~~~~~~~~~~~~vl~lia~~~a~~~GDAR~aidilr~A~eiAe~~~~~~v~~~~v~~a~~~~~~~~~~~ 272 (366)
T COG1474 193 EELYDILRERVEEGFSAGVIDDDVLKLIAALVAAESGDARKAIDILRRAGEIAEREGSRKVSEDHVREAQEEIERDVLEE 272 (366)
T ss_pred HHHHHHHHHHHHhhccCCCcCccHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHhhCCCCcCHHHHHHHHHHhhHHHHHH
Confidence 445555554432 24568888877776443 345678888999999999999999999999966665544433
No 90
>PF09123 DUF1931: Domain of unknown function (DUF1931); InterPro: IPR015207 This entry represents a set of hypothetical bacterial proteins containing a core of six alpha-helices, where one central helix is surrounded by the other five. The exact function of this family has not, as yet, been determined []. ; PDB: 1WWS_A 1WWI_A 1R4V_A.
Probab=50.81 E-value=14 Score=30.92 Aligned_cols=69 Identities=14% Similarity=0.240 Sum_probs=49.3
Q ss_pred HHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHHHcCCCcchHHHHHHHHHHHH
Q 047516 49 VGRIMKKVIPGNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAITTLGFEDYVAPLKLYLSKYRE 128 (214)
Q Consensus 49 V~RImK~~LP~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~LGF~dyi~~Lk~~L~~yre 128 (214)
+.|++|.+ .+.-|.|+-..-+...++.=+..|.-.|...|+.++|.+|..-|+=-. ..+++.+..||+
T Consensus 1 fe~lFR~a--a~LdvdK~d~~r~~d~V~~Kl~DLl~va~~~Ak~ngRdvI~~~DLPIT----------kGlqesi~~Fr~ 68 (138)
T PF09123_consen 1 FERLFRKA--AGLDVDKNDAKRYSDFVEKKLYDLLLVAQENAKANGRDVIEPRDLPIT----------KGLQESIREFRK 68 (138)
T ss_dssp HHHHHHHH--HS----HHHHHHHHHHHHHHHHHCCCCHHHHHHHTT-SEE-GGGS-------------HHHHHHHHHHHT
T ss_pred ChHHHHHH--hccCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeeccccCCcc----------HHHHHHHHHHHH
Confidence 35788888 467788888888899999999999999999999999999999886433 355667777776
Q ss_pred H
Q 047516 129 I 129 (214)
Q Consensus 129 ~ 129 (214)
.
T Consensus 69 l 69 (138)
T PF09123_consen 69 L 69 (138)
T ss_dssp T
T ss_pred c
Confidence 5
No 91
>smart00350 MCM minichromosome maintenance proteins.
Probab=48.60 E-value=80 Score=30.71 Aligned_cols=67 Identities=12% Similarity=0.141 Sum_probs=48.0
Q ss_pred ccCchhHHHHHHhhcCCCC---cccCHHHHHHHHHHHHHH-------------------HHHHHHHHHHHHHhcCCCccC
Q 047516 42 RFLPIANVGRIMKKVIPGN---GKISKDAKETVQECVSEF-------------------ISFVTGEASDKCQREKRKTIN 99 (214)
Q Consensus 42 l~LPkA~V~RImK~~LP~~---~rISkDA~ealqeca~eF-------------------I~~LtseAne~a~~~kRKTI~ 99 (214)
..++...+++.+.-+ .. -+|++++.+.|.+...+. +..|...|--.|+-..|.+|+
T Consensus 416 ~~~~~~~l~~yi~~a--r~~~~P~ls~~~~~~i~~~y~~~R~~~~~~~~~~~~~~t~R~l~sliRla~A~A~l~~r~~V~ 493 (509)
T smart00350 416 VPISQEFLRKYIAYA--REKIKPKLSEEAAEKLVKAYVDLRKEDSQSEARSSIPITVRQLESIIRLSEAHAKMRLSDVVE 493 (509)
T ss_pred ccCCHHHHHHHHHHH--HhcCCCCCCHHHHHHHHHHHHHhcccccccccccccCcCHHHHHHHHHHHHHHHHHcCCCccC
Confidence 357777777776444 21 258999999887655432 245566677788999999999
Q ss_pred hHHHHHHHHHc
Q 047516 100 GDDIIWAITTL 110 (214)
Q Consensus 100 ~eDVl~ALe~L 110 (214)
.+||..|++-+
T Consensus 494 ~~Dv~~ai~l~ 504 (509)
T smart00350 494 EADVEEAIRLL 504 (509)
T ss_pred HHHHHHHHHHH
Confidence 99999998643
No 92
>TIGR01128 holA DNA polymerase III, delta subunit. subunit around DNA forming a DNA sliding clamp.
Probab=48.46 E-value=1e+02 Score=26.64 Aligned_cols=66 Identities=15% Similarity=0.090 Sum_probs=46.4
Q ss_pred CchhHHHHHHhhcCC-CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHHH
Q 047516 44 LPIANVGRIMKKVIP-GNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAITT 109 (214)
Q Consensus 44 LPkA~V~RImK~~LP-~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~ 109 (214)
+....+.+++++.+. .+..|+.+|...|.+.+..=+..+-.+-...|.-.+.++|+.+||...+..
T Consensus 111 ~~~~~~~~~i~~~~~~~g~~i~~~a~~~l~~~~~~d~~~l~~el~KL~~~~~~~~It~e~I~~~~~~ 177 (302)
T TIGR01128 111 PKEQELPRWIQARLKKLGLRIDPDAVQLLAELVEGNLLAIAQELEKLALYAPDGKITLEDVEEAVSD 177 (302)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCcHHHHHHHHHHHHHhhCCCCCCCHHHHHHHHhh
Confidence 455566666666543 367899999999988887655566666666665544457999999887763
No 93
>PRK13406 bchD magnesium chelatase subunit D; Provisional
Probab=47.94 E-value=67 Score=32.29 Aligned_cols=52 Identities=10% Similarity=0.059 Sum_probs=44.7
Q ss_pred cCCCCcccCHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCccChHHHHHHHH
Q 047516 56 VIPGNGKISKDAKETVQECVSEFI-------SFVTGEASDKCQREKRKTINGDDIIWAIT 108 (214)
Q Consensus 56 ~LP~~~rISkDA~ealqeca~eFI-------~~LtseAne~a~~~kRKTI~~eDVl~ALe 108 (214)
.+ +++.|+.+.+..+.++|..|- .++...|-.+|.-+||..|+.+||..|+.
T Consensus 190 rl-~~v~v~~~~l~~i~~~~~~~gv~S~Ra~i~llraARa~AaL~Gr~~V~~~dv~~Aa~ 248 (584)
T PRK13406 190 RL-PAVGPPPEAIAALCAAAAALGIASLRAPLLALRAARAAAALAGRTAVEEEDLALAAR 248 (584)
T ss_pred HH-ccCCCCHHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 44 478999999999888888774 47788899999999999999999999985
No 94
>PRK07452 DNA polymerase III subunit delta; Validated
Probab=47.87 E-value=55 Score=29.09 Aligned_cols=65 Identities=12% Similarity=0.142 Sum_probs=46.6
Q ss_pred HHHHHhhcCC-CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHh--cCCCccChHHHHHHHHHcCCC
Q 047516 49 VGRIMKKVIP-GNGKISKDAKETVQECVSEFISFVTGEASDKCQR--EKRKTINGDDIIWAITTLGFE 113 (214)
Q Consensus 49 V~RImK~~LP-~~~rISkDA~ealqeca~eFI~~LtseAne~a~~--~kRKTI~~eDVl~ALe~LGF~ 113 (214)
+.+.|++.+- .+..|+.+|...|.+++..=+..+..+-...|.- .++.+|+.+||...+....+.
T Consensus 135 l~~~i~~~~~~~g~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~~It~~~V~~~v~~~~~~ 202 (326)
T PRK07452 135 LKQLVERTAQELGVKLTPEAAELLAEAVGNDSRRLYNELEKLALYAENSTKPISAEEVKALVSNTTQN 202 (326)
T ss_pred HHHHHHHHHHHcCCCCCHHHHHHHHHHhCccHHHHHHHHHHHHHhccCCCCccCHHHHHHHhccCcCc
Confidence 4444444322 3678999999999999887666666666666664 457899999999988766543
No 95
>PF02861 Clp_N: Clp amino terminal domain; InterPro: IPR004176 This short domain is found in one or two copies at the amino terminus of ClpA and ClpB proteins from bacteria and eukaryotes. The function of these domains is uncertain but they may form a protein binding site []. The proteins are thought to be subunits of ATP-dependent proteases which act as chaperones to target the proteases to substrates.; GO: 0019538 protein metabolic process; PDB: 3FH2_A 3ZRJ_A 3ZRI_A 1QVR_C 3FES_C 2Y1R_F 3PXG_D 2Y1Q_A 3PXI_C 2K77_A ....
Probab=46.99 E-value=32 Score=22.17 Aligned_cols=26 Identities=12% Similarity=0.189 Sum_probs=20.6
Q ss_pred HHHHHHhcCCCccChHHHHHHHHHcC
Q 047516 86 ASDKCQREKRKTINGDDIIWAITTLG 111 (214)
Q Consensus 86 Ane~a~~~kRKTI~~eDVl~ALe~LG 111 (214)
|.+.|...+...|+.+|++.||=..+
T Consensus 1 A~~~A~~~~~~~i~~eHlL~all~~~ 26 (53)
T PF02861_consen 1 AQELARERGHQYISPEHLLLALLEDP 26 (53)
T ss_dssp HHHHHHHTTBSSE-HHHHHHHHHHHT
T ss_pred CHHHHHHcCCCcccHHHHHHHHHhhh
Confidence 56788999999999999999975433
No 96
>PF09114 MotA_activ: Transcription factor MotA, activation domain; InterPro: IPR015198 Transcription factor MotA is required for the activation of middle promoters in Bacteriophage T4, in addition to phage T4 co-activator AsiA, and sigma-70-containing Escherichia coli RNA polymerase. Phage T4 middle promoters have the sigma70 -10 DNA element, but not the -35 element; instead, they have a MotA box at -30 to which the transcription factor MotA binds []. MotA and AsiA interact with the C-terminal of sigma70 (region 4), which normally binds the -35 element and the beta-flap, thereby diverting sigma70 away from host promoters that require -35 element-binding to phage T4 middle promoters. Transcription factor MotA has two domains: an N-terminal domain required for binding to sigma70, and a C-terminal domain required for binding to the -30 MotA box element in the phage T4 middle promoter. This entry represents the N-terminal (activation) domain of MotA factors that binds sigma70. The N-terminal domain adopts an almost completely alpha-helical topology, with five alpha-helices and a short, two-stranded, beta-ribbon. Four alpha helices (alpha1, alpha3, alpha4 and alpha5) are amphipathic and pack their hydrophobic surfaces around the central helix alpha2 [].; PDB: 1BJA_B 1I1S_A.
Probab=46.86 E-value=27 Score=27.56 Aligned_cols=33 Identities=15% Similarity=0.314 Sum_probs=26.4
Q ss_pred hHHHHHHhhcC----CCCcccCHHHHHHHHHHHHHHH
Q 047516 47 ANVGRIMKKVI----PGNGKISKDAKETVQECVSEFI 79 (214)
Q Consensus 47 A~V~RImK~~L----P~~~rISkDA~ealqeca~eFI 79 (214)
++|.+|+|..| .++..++.++.+.|+++++.|-
T Consensus 51 SNIGvLIKkglIEKSGDGlv~T~~g~~Ii~~AA~l~a 87 (96)
T PF09114_consen 51 SNIGVLIKKGLIEKSGDGLVITEEGMDIIIQAAELWA 87 (96)
T ss_dssp HHHHHHHHTTSEEEETTEEEE-HHHHHHHHHHHHHHH
T ss_pred HhHHHHHHcCcccccCCceEEechHHHHHHHHHHHHH
Confidence 45777898886 3567899999999999999984
No 97
>PRK12402 replication factor C small subunit 2; Reviewed
Probab=45.35 E-value=66 Score=28.21 Aligned_cols=71 Identities=7% Similarity=0.022 Sum_probs=43.2
Q ss_pred CchhHHHHHHhhcCC-CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHHHcCCCcch
Q 047516 44 LPIANVGRIMKKVIP-GNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAITTLGFEDYV 116 (214)
Q Consensus 44 LPkA~V~RImK~~LP-~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~LGF~dyi 116 (214)
++...+.++++..+. .+..++.++.+.|.+.+.-=+..+.......|. +..+|+.+||..++.....++.+
T Consensus 184 ~~~~~~~~~l~~~~~~~~~~~~~~al~~l~~~~~gdlr~l~~~l~~~~~--~~~~It~~~v~~~~~~~~~~~~i 255 (337)
T PRK12402 184 PTDDELVDVLESIAEAEGVDYDDDGLELIAYYAGGDLRKAILTLQTAAL--AAGEITMEAAYEALGDVGTDEVI 255 (337)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHH--cCCCCCHHHHHHHhCCCCCHHHH
Confidence 344556666665443 356799999999988873333333333333342 23479999999988765544433
No 98
>PRK13765 ATP-dependent protease Lon; Provisional
Probab=45.24 E-value=40 Score=34.21 Aligned_cols=47 Identities=15% Similarity=0.143 Sum_probs=38.9
Q ss_pred ccCHHHHHHHHHHHHH-------------HHHHHHHHHHHHHHhcCCCccChHHHHHHHH
Q 047516 62 KISKDAKETVQECVSE-------------FISFVTGEASDKCQREKRKTINGDDIIWAIT 108 (214)
Q Consensus 62 rISkDA~ealqeca~e-------------FI~~LtseAne~a~~~kRKTI~~eDVl~ALe 108 (214)
.++++|+..|.+-++. =|.-|..+|..+|+.++++.|+.+||..|+.
T Consensus 339 ~f~~eAVa~LI~~~~R~ag~r~~lsl~~~~l~~l~r~a~~~a~~~~~~~i~~~~v~~a~~ 398 (637)
T PRK13765 339 HFDRDAVEEIIREAKRRAGRKGHLTLKLRDLGGLVRVAGDIARSEGAELTTAEHVLEAKK 398 (637)
T ss_pred CCCHHHHHHHHHHHHHHhCCccccccCHHHHHHHHHHHHHHHHhhccceecHHHHHHHHH
Confidence 5899998888876652 2344788899999999999999999999984
No 99
>CHL00081 chlI Mg-protoporyphyrin IX chelatase
Probab=44.80 E-value=94 Score=29.29 Aligned_cols=54 Identities=20% Similarity=0.225 Sum_probs=43.7
Q ss_pred hhcCCCCcccCHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCccChHHHHHHHH
Q 047516 54 KKVIPGNGKISKDAKETVQECVSEFI-------SFVTGEASDKCQREKRKTINGDDIIWAIT 108 (214)
Q Consensus 54 K~~LP~~~rISkDA~ealqeca~eFI-------~~LtseAne~a~~~kRKTI~~eDVl~ALe 108 (214)
++.+ ..+.|+.+.+..|.+.|..+= .++...|--.|--+||..|+++||..+..
T Consensus 260 r~~~-~~V~v~~~~~~yi~~l~~~~~~~s~Ra~i~l~raArA~Aal~GR~~V~pdDv~~~a~ 320 (350)
T CHL00081 260 QNLL-PKVEIDYDLRVKISQICSELDVDGLRGDIVTNRAAKALAAFEGRTEVTPKDIFKVIT 320 (350)
T ss_pred HHhc-CCCccCHHHHHHHHHHHHHHCCCCChHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 3444 468899999999999887764 35667777889999999999999998874
No 100
>PF12627 PolyA_pol_RNAbd: Probable RNA and SrmB- binding site of polymerase A; PDB: 1OU5_B 3H38_A 3H3A_B 3H39_B 3H37_A 3AQN_A 3AQK_A 3AQM_B 3AQL_B 1MIY_A ....
Probab=43.31 E-value=13 Score=25.42 Aligned_cols=57 Identities=23% Similarity=0.331 Sum_probs=29.8
Q ss_pred cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCc---cChHHHHHHHHHcCCCcch-HHHHH
Q 047516 61 GKISKDAKETVQECVSEFISFVTGEASDKCQREKRKT---INGDDIIWAITTLGFEDYV-APLKL 121 (214)
Q Consensus 61 ~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKT---I~~eDVl~ALe~LGF~dyi-~~Lk~ 121 (214)
.+|.+++..+|.+++. .+..|+.+-. ..+=.|. =.+...+..|.++|+-+++ +.+..
T Consensus 2 F~ie~~t~~ai~~~~~-~L~~is~ERi---~~El~kil~~~~~~~~~~~l~~~gll~~ifP~l~~ 62 (64)
T PF12627_consen 2 FKIEPETEEAIKENAE-LLSKISKERI---REELEKILSSPNPSRAFKLLDELGLLEYIFPELDA 62 (64)
T ss_dssp -EE-HHHHHHHHHHGG-GGGGS-HHHH---HHHHHHHHTSTTHHHHHHHHHHTTCHHHHSTTHHT
T ss_pred CccCHHHHHHHHHHHH-HHhcCCHHHH---HHHHHHHHcCCCHHHHHHHHHHcCCHHHHCccccc
Confidence 4677777777777766 4444444321 1111111 1456667777788876663 55543
No 101
>TIGR00368 Mg chelatase-related protein. The N-terminal end matches very strongly a pfam Mg_chelatase domain.
Probab=43.15 E-value=67 Score=31.58 Aligned_cols=47 Identities=15% Similarity=0.179 Sum_probs=40.5
Q ss_pred ccCHHHHHHHHHHHHHH------HHHHHHHHHHHHHhcCCCccChHHHHHHHH
Q 047516 62 KISKDAKETVQECVSEF------ISFVTGEASDKCQREKRKTINGDDIIWAIT 108 (214)
Q Consensus 62 rISkDA~ealqeca~eF------I~~LtseAne~a~~~kRKTI~~eDVl~ALe 108 (214)
.+++++...|.+++..| ..-|..-|.++|.-+++..|..+||..|+.
T Consensus 445 ~l~~~~~~~l~~a~~~~~lS~R~~~rilrvArTiAdL~g~~~i~~~hv~eA~~ 497 (499)
T TIGR00368 445 KLSAIDANDLEGALNKLGLSSRATHRILKVARTIADLKEEKNISREHLAEAIE 497 (499)
T ss_pred CCCHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHh
Confidence 46888999999888776 566777899999999999999999999984
No 102
>PF08681 DUF1778: Protein of unknown function (DUF1778); InterPro: IPR014795 This entry is represented by Vibrio phage ICP1, Orf50. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a family of uncharacterised proteins. The structure of one of the hypothetical proteins in this family has been solved and it forms a helix structure which may form interactions with DNA. ; PDB: 1Y9B_A.
Probab=42.55 E-value=21 Score=26.39 Aligned_cols=18 Identities=11% Similarity=0.287 Sum_probs=13.4
Q ss_pred CcccCHHHHHHHHHHHHH
Q 047516 60 NGKISKDAKETVQECVSE 77 (214)
Q Consensus 60 ~~rISkDA~ealqeca~e 77 (214)
++||+.+.++.|.++|..
T Consensus 3 ~iR~~~e~k~li~~AA~~ 20 (80)
T PF08681_consen 3 EIRVTPEEKELIERAAAL 20 (80)
T ss_dssp EEE--HHHHHHHHHHHHH
T ss_pred eEecCHHHHHHHHHHHHH
Confidence 468999999999999853
No 103
>PRK13407 bchI magnesium chelatase subunit I; Provisional
Probab=40.48 E-value=1.3e+02 Score=27.94 Aligned_cols=49 Identities=6% Similarity=-0.089 Sum_probs=40.6
Q ss_pred CCcccCHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCccChHHHHHHH
Q 047516 59 GNGKISKDAKETVQECVSEFI-------SFVTGEASDKCQREKRKTINGDDIIWAI 107 (214)
Q Consensus 59 ~~~rISkDA~ealqeca~eFI-------~~LtseAne~a~~~kRKTI~~eDVl~AL 107 (214)
..+.|+.+.+..+.+.+..+= .+|...|...|--+||..|+++||..+.
T Consensus 248 ~~V~v~~~~~~yi~~l~~~~~~~s~Ra~i~l~~aA~a~A~l~Gr~~V~~~Di~~~~ 303 (334)
T PRK13407 248 PQLKTPNTVLHDCAALCIALGSDGLRGELTLLRAARALAAFEGAEAVGRSHLRSVA 303 (334)
T ss_pred CCcccCHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHHcCCCeeCHHHHHHHH
Confidence 478899999999999887664 2377778889999999999999997665
No 104
>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=40.20 E-value=1e+02 Score=30.70 Aligned_cols=54 Identities=15% Similarity=0.259 Sum_probs=39.9
Q ss_pred hhcCCCCcccCHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCccChHHHHHHHH
Q 047516 54 KKVIPGNGKISKDAKETVQECVSEFI-------SFVTGEASDKCQREKRKTINGDDIIWAIT 108 (214)
Q Consensus 54 K~~LP~~~rISkDA~ealqeca~eFI-------~~LtseAne~a~~~kRKTI~~eDVl~ALe 108 (214)
++.++ .+.|+.+.++.|.+.+..+- .++...|-..|.-++|.+|+.+||..|+.
T Consensus 196 r~~~~-~V~i~~~~~~~l~~~~~~~gv~s~Ra~i~~~r~ArA~Aal~gr~~V~~~Dv~~a~~ 256 (589)
T TIGR02031 196 RELLP-QVTISAEQVKELVLTAASLGISGHRADLFAVRAAKAHAALHGRTEVTEEDLKLAVE 256 (589)
T ss_pred HHhcC-CccCCHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHH
Confidence 33343 67899999888777765432 24455666788889999999999999974
No 105
>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional
Probab=39.89 E-value=42 Score=32.47 Aligned_cols=33 Identities=24% Similarity=0.152 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHHHHHhcCCCccChHHHHHHHHH
Q 047516 77 EFISFVTGEASDKCQREKRKTINGDDIIWAITT 109 (214)
Q Consensus 77 eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~ 109 (214)
.-|..|..+|...|.+.+|..|+.+||..|++.
T Consensus 391 AdI~~i~~eA~~~Alr~~r~~Vt~~D~~~A~~~ 423 (438)
T PTZ00361 391 ADIKAICTEAGLLALRERRMKVTQADFRKAKEK 423 (438)
T ss_pred HHHHHHHHHHHHHHHHhcCCccCHHHHHHHHHH
Confidence 336678888999999999999999999999865
No 106
>PF00531 Death: Death domain; InterPro: IPR000488 The death domain (DD) is a homotypic protein interaction module composed of a bundle of six alpha-helices. DD is related in sequence and structure to the death effector domain (DED, see IPR001875 from INTERPRO) and the caspase recruitment domain (CARD, see IPR001315 from INTERPRO), which work in similar pathways and show similar interaction properties []. DD bind each other forming oligomers. Mammals have numerous and diverse DD-containing proteins []. Within these proteins, the DD domains can be found in combination with other domains, including: CARDs, DEDs, ankyrin repeats (IPR002110 from INTERPRO), caspase-like folds, kinase domains, leucine zippers (IPR002158 from INTERPRO), leucine-rich repeats (LRR) (IPR001611 from INTERPRO), TIR domains (IPR000157 from INTERPRO), and ZU5 domains (IPR000906 from INTERPRO) []. Some DD-containing proteins are involved in the regulation of apoptosis and inflammation through their activation of caspases and NF-kappaB, which typically involves interactions with TNF (tumour necrosis factor) cytokine receptors [, ]. In humans, eight of the over 30 known TNF receptors contain DD in their cytoplasmic tails; several of these TNF receptors use caspase activation as a signalling mechanism. The DD mediates self-association of these receptors, thus giving the signal to downstream events that lead to apoptosis. Other DD-containing proteins, such as ankyrin, MyD88 and pelle, are probably not directly involved in cell death signalling. DD-containing proteins also have links to innate immunity, communicating with Toll family receptors through bipartite adapter proteins such as MyD88 [].; GO: 0005515 protein binding, 0007165 signal transduction; PDB: 3OQ9_L 3EZQ_F 1E41_A 1E3Y_A 2GF5_A 2OF5_L 3EWV_E 3G5B_A 3MOP_L 2A9I_A ....
Probab=39.75 E-value=53 Score=22.99 Aligned_cols=30 Identities=20% Similarity=0.320 Sum_probs=24.3
Q ss_pred CCCccChHHHHHHHHHcCCCcchHHHHHHH
Q 047516 94 KRKTINGDDIIWAITTLGFEDYVAPLKLYL 123 (214)
Q Consensus 94 kRKTI~~eDVl~ALe~LGF~dyi~~Lk~~L 123 (214)
....-+..+++.||+.+|..+-++.++.+|
T Consensus 54 ~~~~at~~~L~~aL~~~~~~d~~~~i~~~~ 83 (83)
T PF00531_consen 54 EGPNATVDQLIQALRDIGRNDLAEKIEQML 83 (83)
T ss_dssp HGSTSSHHHHHHHHHHTTHHHHHHHHHHH-
T ss_pred cCCCCcHHHHHHHHHHCCcHHHHHHHHhhC
Confidence 345667889999999999999988887664
No 107
>PF04552 Sigma54_DBD: Sigma-54, DNA binding domain; InterPro: IPR007634 This DNA-binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore, this region contains a putative helix-turn-helix motif. At the C terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins [].; PDB: 2AHQ_A 2O9L_A 2O8K_A.
Probab=37.72 E-value=40 Score=28.41 Aligned_cols=40 Identities=23% Similarity=0.317 Sum_probs=26.4
Q ss_pred HHHhcCCCccChHHHHHHHHHcCCCcchHHHHHHHHHHHHHHhh
Q 047516 89 KCQREKRKTINGDDIIWAITTLGFEDYVAPLKLYLSKYREIEGE 132 (214)
Q Consensus 89 ~a~~~kRKTI~~eDVl~ALe~LGF~dyi~~Lk~~L~~yre~~~~ 132 (214)
+..+++.+-++-+.|...|+.-| +..-..-+.+||+..+-
T Consensus 113 I~~Ed~~~PlSD~~i~~~L~~~g----i~isRRTVaKYR~~L~I 152 (160)
T PF04552_consen 113 IEEEDKKKPLSDQEIAELLKEEG----IKISRRTVAKYREELGI 152 (160)
T ss_dssp HTTS-TTS---HHHHHHHHTTTT----S---HHHHHHHHHHHT-
T ss_pred HHhcCCCCCCCHHHHHHHHHHcC----CCccHHHHHHHHHHcCC
Confidence 45567889999999999998777 45777888999997653
No 108
>PRK05574 holA DNA polymerase III subunit delta; Reviewed
Probab=36.84 E-value=2.1e+02 Score=25.17 Aligned_cols=66 Identities=14% Similarity=0.048 Sum_probs=46.4
Q ss_pred CchhHHHHHHhhcCC-CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHHH
Q 047516 44 LPIANVGRIMKKVIP-GNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAITT 109 (214)
Q Consensus 44 LPkA~V~RImK~~LP-~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~ 109 (214)
+....+.+.|+..+- .+..|+.+|...|.+.+..=+..+..+....|.-.+-+.|+.+||-..+..
T Consensus 146 ~~~~~~~~~i~~~~~~~g~~i~~~a~~~L~~~~~~d~~~l~~El~KL~l~~~~~~It~~~I~~~i~~ 212 (340)
T PRK05574 146 PKEAELPQWIQQRLKQQGLQIDAAALQLLAERVEGNLLALAQELEKLALLYPDGKITLEDVEEAVPD 212 (340)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCchHHHHHHHHHHHHhhcCCCCCCHHHHHHHHhh
Confidence 555566666655543 367899999999999988766677777777665432222999999877664
No 109
>PF11753 DUF3310: Protein of unknwon function (DUF3310); InterPro: IPR021739 This entry is represented by Bacteriophage T7, Gp1.7. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=36.38 E-value=1.1e+02 Score=21.54 Aligned_cols=41 Identities=22% Similarity=0.217 Sum_probs=32.4
Q ss_pred HHHHHHHHH--HHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHH
Q 047516 66 DAKETVQEC--VSEFISFVTGEASDKCQREKRKTINGDDIIWAIT 108 (214)
Q Consensus 66 DA~ealqec--a~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe 108 (214)
|+.+.| +. ...|+.|....|..++-+.++|.- .+|+.+|..
T Consensus 14 e~id~~-~~~~~~~~~~f~~gnaiKY~~R~~~K~~-~eDl~KA~~ 56 (60)
T PF11753_consen 14 ECIDFI-EQFTEEQFLGFCLGNAIKYLWRAGKKNG-IEDLKKAKW 56 (60)
T ss_pred cHHHHH-HHhcchhhhhHHHHHHHHHHHHHcccCc-HHHHHHHHH
Confidence 455555 44 458999999999999999999944 899999874
No 110
>KOG3535 consensus Adaptor protein Disabled [Signal transduction mechanisms]
Probab=36.24 E-value=26 Score=34.66 Aligned_cols=41 Identities=27% Similarity=0.401 Sum_probs=26.0
Q ss_pred hccccCCCCCcccccCCCCCCCCcccCCCCCCCcccCCCch
Q 047516 156 HEHEQQLPYSSVYSSTNLMSQSPFMATDHHHQSFPLPFSPN 196 (214)
Q Consensus 156 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 196 (214)
+-+-...|.-.++.-|+|+.-.----.-|||++|++-.++|
T Consensus 324 ~~~~~~~p~~~~~s~tqP~a~~qng~~~~~qq~f~~~~~~n 364 (557)
T KOG3535|consen 324 HAHSTPAPGTNGFSDTQPFASAQNGQARHHQQPFQLLLQHN 364 (557)
T ss_pred hhcccCCCccCCCCCCCchhhcCCCccccccCCcceeccCC
Confidence 33455556666777777765333333567889999877776
No 111
>TIGR01242 26Sp45 26S proteasome subunit P45 family. Many proteins may score above the trusted cutoff because an internal
Probab=36.21 E-value=56 Score=29.91 Aligned_cols=33 Identities=27% Similarity=0.260 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHHHHHhcCCCccChHHHHHHHHH
Q 047516 77 EFISFVTGEASDKCQREKRKTINGDDIIWAITT 109 (214)
Q Consensus 77 eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~ 109 (214)
.-|..|..+|...|...+|..|+.+|+..|++.
T Consensus 330 ~dl~~l~~~A~~~a~~~~~~~i~~~d~~~a~~~ 362 (364)
T TIGR01242 330 ADLKAICTEAGMFAIREERDYVTMDDFIKAVEK 362 (364)
T ss_pred HHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHH
Confidence 345677888989999999999999999999975
No 112
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=35.98 E-value=93 Score=30.27 Aligned_cols=78 Identities=14% Similarity=0.257 Sum_probs=51.9
Q ss_pred ccccCchhHHHHHHhhcC---CCCc---------ccCHH-----HHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHH
Q 047516 40 QDRFLPIANVGRIMKKVI---PGNG---------KISKD-----AKETVQECVSEFISFVTGEASDKCQREKRKTINGDD 102 (214)
Q Consensus 40 ~Dl~LPkA~V~RImK~~L---P~~~---------rISkD-----A~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eD 102 (214)
+++.|-.+||.|+++... |.++ .++.+ +.+.|......+ +..+++++-++-+.
T Consensus 351 e~lglheSTVSRav~~Kyv~tp~Gi~~lk~FFs~~~~~~~g~~~S~~~Ik~~Ik~l----------I~~Ed~~~PlSD~~ 420 (455)
T PRK05932 351 EELGMHESTISRATTNKYMATPRGIFELKYFFSSAVSTDGGGEASSTAIRALIKKL----------IAAENPKKPLSDSK 420 (455)
T ss_pred HHhCCCccchhhhhcCceeecCCceEEHHHhcccccCCCCCccccHHHHHHHHHHH----------HHhcCCCCCCCHHH
Confidence 456788899999998762 3211 11111 222233333332 55678889999999
Q ss_pred HHHHHHHcCCCcchHHHHHHHHHHHHHHh
Q 047516 103 IIWAITTLGFEDYVAPLKLYLSKYREIEG 131 (214)
Q Consensus 103 Vl~ALe~LGF~dyi~~Lk~~L~~yre~~~ 131 (214)
|...|+.-|+. .....+.+||+..+
T Consensus 421 I~~~L~~~Gi~----IaRRTVaKYRe~L~ 445 (455)
T PRK05932 421 IAELLKEQGID----VARRTVAKYREALN 445 (455)
T ss_pred HHHHHHHcCCC----eehHHHHHHHHHcC
Confidence 99999999985 56788889999754
No 113
>PRK03992 proteasome-activating nucleotidase; Provisional
Probab=35.76 E-value=57 Score=30.52 Aligned_cols=34 Identities=21% Similarity=0.246 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHHHHHhcCCCccChHHHHHHHHHc
Q 047516 77 EFISFVTGEASDKCQREKRKTINGDDIIWAITTL 110 (214)
Q Consensus 77 eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~L 110 (214)
.=|..|..+|...|.+++++.|+.+|+..|++..
T Consensus 339 adl~~l~~eA~~~a~~~~~~~i~~~d~~~A~~~~ 372 (389)
T PRK03992 339 ADLKAICTEAGMFAIRDDRTEVTMEDFLKAIEKV 372 (389)
T ss_pred HHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHH
Confidence 4466778888889999999999999999999764
No 114
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=35.73 E-value=84 Score=21.10 Aligned_cols=32 Identities=19% Similarity=0.390 Sum_probs=26.4
Q ss_pred cCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHH
Q 047516 43 FLPIANVGRIMKKVIPGNGKISKDAKETVQECVSEF 78 (214)
Q Consensus 43 ~LPkA~V~RImK~~LP~~~rISkDA~ealqeca~eF 78 (214)
.+.+++|.|++... .+|+.+.++-+.+++++.
T Consensus 10 gvS~~TVSr~ln~~----~~vs~~tr~rI~~~a~~l 41 (46)
T PF00356_consen 10 GVSKSTVSRVLNGP----PRVSEETRERILEAAEEL 41 (46)
T ss_dssp TSSHHHHHHHHTTC----SSSTHHHHHHHHHHHHHH
T ss_pred CcCHHHHHHHHhCC----CCCCHHHHHHHHHHHHHH
Confidence 46789999998876 589999999998887763
No 115
>PRK06585 holA DNA polymerase III subunit delta; Reviewed
Probab=35.22 E-value=1.1e+02 Score=27.45 Aligned_cols=50 Identities=14% Similarity=0.057 Sum_probs=37.4
Q ss_pred CcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHh-cCCCccChHHHHHHHHH
Q 047516 60 NGKISKDAKETVQECVSEFISFVTGEASDKCQR-EKRKTINGDDIIWAITT 109 (214)
Q Consensus 60 ~~rISkDA~ealqeca~eFI~~LtseAne~a~~-~kRKTI~~eDVl~ALe~ 109 (214)
+.+|+.+|...|.+++.-=...+..+--..+.- .++++|+.+||...+..
T Consensus 159 g~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~It~edV~~lv~~ 209 (343)
T PRK06585 159 GLRITPDARALLVALLGGDRLASRNEIEKLALYAHGKGEITLDDVRAVVGD 209 (343)
T ss_pred CCCCCHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHhCC
Confidence 778999999999999886555555555555554 34578999999877653
No 116
>PF07647 SAM_2: SAM domain (Sterile alpha motif); InterPro: IPR011510 The sterile alpha motif (SAM) domain is a putative protein interaction module present in a wide variety of proteins [] involved in many biological processes. The SAM domain that spreads over around 70 residues is found in diverse eukaryotic organisms []. SAM domains have been shown to homo- and hetero-oligomerise, forming multiple self-association architectures and also binding to various non-SAM domain-containing proteins [], nevertheless with a low affinity constant []. SAM domains also appear to possess the ability to bind RNA []. Smaug, a protein that helps to establish a morphogen gradient in Drosophila embryos by repressing the translation of nanos (nos) mRNA, binds to the 3' untranslated region (UTR) of nos mRNA via two similar hairpin structures. The 3D crystal structure of the Smaug RNA-binding region shows a cluster of positively charged residues on the Smaug-SAM domain, which could be the RNA-binding surface. This electropositive potential is unique among all previously determined SAM-domain structures and is conserved among Smaug-SAM homologs. These results suggest that the SAM domain might have a primary role in RNA binding. Structural analyses show that the SAM domain is arranged in a small five-helix bundle with two large interfaces []. In the case of the SAM domain of EphB2, each of these interfaces is able to form dimers. The presence of these two distinct intermonomers binding surface suggest that SAM could form extended polymeric structures []. This entry represents a second domain related to the SAM domain. ; GO: 0005515 protein binding; PDB: 1B0X_A 1X9X_B 1OW5_A 1V38_A 3BS7_A 3BS5_A 3TAD_A 3TAC_B 2K60_A 2DL0_A ....
Probab=35.17 E-value=54 Score=22.29 Aligned_cols=24 Identities=21% Similarity=0.410 Sum_probs=20.4
Q ss_pred cChHHHHHHHHHcCCCcchHHHHH
Q 047516 98 INGDDIIWAITTLGFEDYVAPLKL 121 (214)
Q Consensus 98 I~~eDVl~ALe~LGF~dyi~~Lk~ 121 (214)
=+.+||..-|+.+||.+|++....
T Consensus 4 w~~~~v~~WL~~~gl~~y~~~f~~ 27 (66)
T PF07647_consen 4 WSPEDVAEWLKSLGLEQYADNFRE 27 (66)
T ss_dssp HCHHHHHHHHHHTTCGGGHHHHHH
T ss_pred CCHHHHHHHHHHCCcHHHHHHHHH
Confidence 367899999999999999987663
No 117
>PRK02910 light-independent protochlorophyllide reductase subunit B; Provisional
Probab=34.48 E-value=1.6e+02 Score=28.90 Aligned_cols=52 Identities=10% Similarity=0.082 Sum_probs=42.5
Q ss_pred CCcccCHHHHHHHHHHHHHHHHHHHHHHHH-HHHhcCCCccChHHHHHHHHHcC
Q 047516 59 GNGKISKDAKETVQECVSEFISFVTGEASD-KCQREKRKTINGDDIIWAITTLG 111 (214)
Q Consensus 59 ~~~rISkDA~ealqeca~eFI~~LtseAne-~a~~~kRKTI~~eDVl~ALe~LG 111 (214)
+.+.++.||...|.+ .--|+.--...+.+ +|+..|...|+.+.|..|-..+|
T Consensus 466 ~~~~w~~ea~~~l~~-~P~f~r~~~r~~~e~~a~~~g~~~it~~~~~~a~~~~~ 518 (519)
T PRK02910 466 SELVWTPEAEAELKK-IPFFVRGKVRRNTEKFARERGLPEITLEVLYDAKAHFG 518 (519)
T ss_pred CCCCCCHHHHHHHhh-CChhhHHHHHHHHHHHHHHcCCCeecHHHHHHHHHHhc
Confidence 567899999999954 77888766665555 78999999999999999977654
No 118
>PRK07914 hypothetical protein; Reviewed
Probab=33.02 E-value=1.1e+02 Score=27.40 Aligned_cols=63 Identities=10% Similarity=0.086 Sum_probs=42.6
Q ss_pred chhHHHHHHhhcCC-CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHH
Q 047516 45 PIANVGRIMKKVIP-GNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAIT 108 (214)
Q Consensus 45 PkA~V~RImK~~LP-~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe 108 (214)
+...+.+.|++.+- .+..|+.+|...|.+++..=+..+..|--..+-..+ .+|+.+||...+.
T Consensus 129 ~~~~l~~wi~~~a~~~g~~i~~~A~~~L~~~~g~dl~~l~~EleKL~~~~~-~~It~e~V~~~v~ 192 (320)
T PRK07914 129 KAAERADFVRKEFRSLRVKVDDDTVTALLDAVGSDLRELASACSQLVADTG-GAVDAAAVRRYHS 192 (320)
T ss_pred CHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHCccHHHHHHHHHHHhcCCC-CCcCHHHHHHHcC
Confidence 34444444444432 267899999999999997656666666555554333 5799999987765
No 119
>PRK14975 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Probab=31.81 E-value=3e+02 Score=27.18 Aligned_cols=90 Identities=14% Similarity=0.101 Sum_probs=55.4
Q ss_pred ccccCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHH----------HHHHHHHHHHHHHHHhcCCCccChHHHHHHHHH
Q 047516 40 QDRFLPIANVGRIMKKVIPGNGKISKDAKETVQECVS----------EFISFVTGEASDKCQREKRKTINGDDIIWAITT 109 (214)
Q Consensus 40 ~Dl~LPkA~V~RImK~~LP~~~rISkDA~ealqeca~----------eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~ 109 (214)
.++++|.+.|---|... ++.|..+....+..-.. .-+..|..+..+.+-...=.-=++.+|..+|+.
T Consensus 160 ~~~E~~~~~~l~~me~~---Gi~~D~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~~~g~~~~n~~S~~ql~~~L~~ 236 (553)
T PRK14975 160 AAAESAGALAAAEMELA---GLPWDTDVHEALLAELLGPRPAAGGRPARLAELAAEIREALGRPRLNPDSPQQVLRALRR 236 (553)
T ss_pred HHHHhhHHHHHHHHHHh---CeEeCHHHHHHHHHHHhcccccccchHHHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHH
Confidence 34456777776666666 78898887777665555 556666666655442211123467899999999
Q ss_pred cCCC----------cchHHHHHHHHHHHHHHhh
Q 047516 110 LGFE----------DYVAPLKLYLSKYREIEGE 132 (214)
Q Consensus 110 LGF~----------dyi~~Lk~~L~~yre~~~~ 132 (214)
+|+. .-.-++-..+-+||+..+.
T Consensus 237 ~g~~~~~t~~~~L~~~~hp~~~~ile~r~~~kl 269 (553)
T PRK14975 237 AGIELPSTRKWELREIDHPAVEPLLEYRKLSKL 269 (553)
T ss_pred CCCCCCCCcHHHhccCCCchHHHHHHHHHHHHH
Confidence 9885 0011334455677776544
No 120
>PF13405 EF-hand_6: EF-hand domain; PDB: 2AMI_A 3QRX_A 1W7J_B 1OE9_B 1W7I_B 1KFU_S 1KFX_S 2BL0_B 1Y1X_B 3MSE_B ....
Probab=31.45 E-value=59 Score=19.20 Aligned_cols=26 Identities=15% Similarity=0.215 Sum_probs=20.3
Q ss_pred HHHHHHhcCCCccChHHHHHHHH-HcC
Q 047516 86 ASDKCQREKRKTINGDDIIWAIT-TLG 111 (214)
Q Consensus 86 Ane~a~~~kRKTI~~eDVl~ALe-~LG 111 (214)
+......++.-+|+.+++..+|+ .||
T Consensus 5 ~F~~~D~d~dG~I~~~el~~~l~~~lG 31 (31)
T PF13405_consen 5 AFKMFDKDGDGFIDFEELRAILRKSLG 31 (31)
T ss_dssp HHHHH-TTSSSEEEHHHHHHHHHHHTT
T ss_pred HHHHHCCCCCCcCcHHHHHHHHHHhcC
Confidence 44566777888999999999998 576
No 121
>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional
Probab=31.41 E-value=73 Score=30.29 Aligned_cols=33 Identities=24% Similarity=0.153 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHHHHHhcCCCccChHHHHHHHHH
Q 047516 77 EFISFVTGEASDKCQREKRKTINGDDIIWAITT 109 (214)
Q Consensus 77 eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~ 109 (214)
.=|..|..+|...|.+.+|..|+.+|+..|++.
T Consensus 353 aDI~~l~~eA~~~A~r~~~~~i~~~df~~A~~~ 385 (398)
T PTZ00454 353 ADIAAICQEAGMQAVRKNRYVILPKDFEKGYKT 385 (398)
T ss_pred HHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHH
Confidence 336778889999999999999999999999865
No 122
>cd00166 SAM Sterile alpha motif.; Widespread domain in signalling and nuclear proteins. In EPH-related tyrosine kinases, appears to mediate cell-cell initiated signal transduction via the binding of SH2-containing proteins to a conserved tyrosine that is phosphorylated. In many cases mediates homodimerization.
Probab=30.58 E-value=46 Score=21.79 Aligned_cols=23 Identities=17% Similarity=0.387 Sum_probs=19.5
Q ss_pred ChHHHHHHHHHcCCCcchHHHHH
Q 047516 99 NGDDIIWAITTLGFEDYVAPLKL 121 (214)
Q Consensus 99 ~~eDVl~ALe~LGF~dyi~~Lk~ 121 (214)
+.++|..-|+.+|+++|++.++.
T Consensus 3 ~~~~V~~wL~~~~~~~y~~~f~~ 25 (63)
T cd00166 3 SPEDVAEWLESLGLGQYADNFRE 25 (63)
T ss_pred CHHHHHHHHHHcChHHHHHHHHH
Confidence 57899999999999888887754
No 123
>PF00536 SAM_1: SAM domain (Sterile alpha motif); InterPro: IPR021129 The sterile alpha motif (SAM) domain is a putative protein interaction module present in a wide variety of proteins [] involved in many biological processes. The SAM domain that spreads over around 70 residues is found in diverse eukaryotic organisms []. SAM domains have been shown to homo- and hetero-oligomerise, forming multiple self-association architectures and also binding to various non-SAM domain-containing proteins [], nevertheless with a low affinity constant []. SAM domains also appear to possess the ability to bind RNA []. Smaug, a protein that helps to establish a morphogen gradient in Drosophila embryos by repressing the translation of nanos (nos) mRNA, binds to the 3' untranslated region (UTR) of nos mRNA via two similar hairpin structures. The 3D crystal structure of the Smaug RNA-binding region shows a cluster of positively charged residues on the Smaug-SAM domain, which could be the RNA-binding surface. This electropositive potential is unique among all previously determined SAM-domain structures and is conserved among Smaug-SAM homologs. These results suggest that the SAM domain might have a primary role in RNA binding. Structural analyses show that the SAM domain is arranged in a small five-helix bundle with two large interfaces []. In the case of the SAM domain of EphB2, each of these interfaces is able to form dimers. The presence of these two distinct intermonomers binding surface suggest that SAM could form extended polymeric structures []. This entry represents type 1 SAM domains. ; PDB: 2KIV_A 3HIL_B 3KKA_A 3K1R_B 3SEN_B 3SEI_B 1V85_A 2KE7_A 2EAM_A 1WWV_A ....
Probab=30.55 E-value=64 Score=21.82 Aligned_cols=22 Identities=23% Similarity=0.457 Sum_probs=19.4
Q ss_pred ChHHHHHHHHHcCCCcchHHHH
Q 047516 99 NGDDIIWAITTLGFEDYVAPLK 120 (214)
Q Consensus 99 ~~eDVl~ALe~LGF~dyi~~Lk 120 (214)
++++|..-|+.+|++.|++...
T Consensus 4 ~~~~V~~WL~~~~l~~y~~~F~ 25 (64)
T PF00536_consen 4 SVEDVSEWLKSLGLEQYAENFE 25 (64)
T ss_dssp SHHHHHHHHHHTTGGGGHHHHH
T ss_pred CHHHHHHHHHHCCCHHHHHHHH
Confidence 5789999999999999998774
No 124
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=30.16 E-value=1.2e+02 Score=22.27 Aligned_cols=28 Identities=11% Similarity=0.139 Sum_probs=23.0
Q ss_pred HHHHHHhcCCCccChHHHHHHHHHcCCC
Q 047516 86 ASDKCQREKRKTINGDDIIWAITTLGFE 113 (214)
Q Consensus 86 Ane~a~~~kRKTI~~eDVl~ALe~LGF~ 113 (214)
+...+..++.-.|+.++|..+|..+|+.
T Consensus 15 ~F~~~D~d~~G~Is~~el~~~l~~~~~~ 42 (96)
T smart00027 15 IFRSLDKNQDGTVTGAQAKPILLKSGLP 42 (96)
T ss_pred HHHHhCCCCCCeEeHHHHHHHHHHcCCC
Confidence 4456667788899999999999998875
No 125
>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., PubMed:15231786). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations
Probab=29.87 E-value=1.3e+02 Score=29.03 Aligned_cols=75 Identities=20% Similarity=0.329 Sum_probs=51.7
Q ss_pred ccccCchhHHHHHHhhc---CCCCc------------------ccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcc
Q 047516 40 QDRFLPIANVGRIMKKV---IPGNG------------------KISKDAKETVQECVSEFISFVTGEASDKCQREKRKTI 98 (214)
Q Consensus 40 ~Dl~LPkA~V~RImK~~---LP~~~------------------rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI 98 (214)
+++.|-.+||.|+++.. .|.++ -+|. +.+.....+. +...++++-+
T Consensus 326 ~~lglheSTVSRav~~Kyi~tp~Gi~~lk~FFs~~~~~~~~g~~~S~---~~Ik~~I~~l----------I~~E~~~~Pl 392 (429)
T TIGR02395 326 EELGLHESTISRAINNKYLQTPRGVFELKYFFSRGVQTDSGEGEVSS---TAIKALIKEL----------IAAEDKRKPL 392 (429)
T ss_pred HHhCCCccchhhhhcCceEecCCceEEHHHhcCCccCCCCCCCccCH---HHHHHHHHHH----------HHhcCCCCCC
Confidence 45678899999999876 23111 1233 2233333332 4567889999
Q ss_pred ChHHHHHHHHHcCCCcchHHHHHHHHHHHHHHh
Q 047516 99 NGDDIIWAITTLGFEDYVAPLKLYLSKYREIEG 131 (214)
Q Consensus 99 ~~eDVl~ALe~LGF~dyi~~Lk~~L~~yre~~~ 131 (214)
+-+.|...|+.-|+. ....-+.+||+..+
T Consensus 393 SD~~I~~~L~~~Gi~----IaRRTVaKYRe~L~ 421 (429)
T TIGR02395 393 SDQKIAELLKEKGIK----IARRTVAKYREELG 421 (429)
T ss_pred CHHHHHHHHHhcCCC----eehHHHHHHHHHcC
Confidence 999999999999864 56788889999754
No 126
>COG1466 HolA DNA polymerase III, delta subunit [DNA replication, recombination, and repair]
Probab=29.23 E-value=1.7e+02 Score=26.59 Aligned_cols=50 Identities=16% Similarity=0.141 Sum_probs=39.0
Q ss_pred CcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHHH
Q 047516 60 NGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAITT 109 (214)
Q Consensus 60 ~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~ 109 (214)
+.+|+.||.+.|.++..-=+..+..+=...|--.+-++|+.+||..++-.
T Consensus 157 ~l~i~~~a~~~L~~~~~~nl~~i~~Ei~KL~l~~~~~~I~~~~V~~~v~~ 206 (334)
T COG1466 157 GLKIDQEAIQLLLEALGGNLLAIAQEIEKLALYAGDKEITLEDVEEVVSD 206 (334)
T ss_pred CCCCCHHHHHHHHHHhCCcHHHHHHHHHHHHHhCCCCcCCHHHHHHHHhc
Confidence 68899999999999998666666666666555444449999999988764
No 127
>PRK14971 DNA polymerase III subunits gamma and tau; Provisional
Probab=27.93 E-value=1.4e+02 Score=30.07 Aligned_cols=64 Identities=8% Similarity=0.015 Sum_probs=34.5
Q ss_pred CchhHHHHHHhhcCC-CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHH
Q 047516 44 LPIANVGRIMKKVIP-GNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAIT 108 (214)
Q Consensus 44 LPkA~V~RImK~~LP-~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe 108 (214)
|+...+.+.++..+- .++.++.++..+|.+.+.-=+..+-.+.-..+.-.+++ |+.++|...+.
T Consensus 180 ls~~ei~~~L~~ia~~egi~i~~~al~~La~~s~gdlr~al~~Lekl~~y~~~~-It~~~V~~~l~ 244 (614)
T PRK14971 180 IQVADIVNHLQYVASKEGITAEPEALNVIAQKADGGMRDALSIFDQVVSFTGGN-ITYKSVIENLN 244 (614)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhccCC-ccHHHHHHHhC
Confidence 444445545544322 25778999888887766443333333333333333433 77777665543
No 128
>PLN00138 large subunit ribosomal protein LP2; Provisional
Probab=27.82 E-value=1.8e+02 Score=23.27 Aligned_cols=28 Identities=11% Similarity=0.028 Sum_probs=24.9
Q ss_pred HHHHHHhcCCCccChHHHHHHHHHcCCC
Q 047516 86 ASDKCQREKRKTINGDDIIWAITTLGFE 113 (214)
Q Consensus 86 Ane~a~~~kRKTI~~eDVl~ALe~LGF~ 113 (214)
|+-.|.-.+...++.+||...|+..|.+
T Consensus 6 Ayll~~l~g~~~pta~dI~~IL~AaGve 33 (113)
T PLN00138 6 AYLLAVLGGNTCPSAEDLKDILGSVGAD 33 (113)
T ss_pred HHHHHHhcCCCCCCHHHHHHHHHHcCCc
Confidence 5668888899999999999999998875
No 129
>COG1724 Predicted RNA binding protein (dsRBD-like fold), HicA family [General function prediction only]
Probab=27.76 E-value=47 Score=24.65 Aligned_cols=17 Identities=24% Similarity=0.528 Sum_probs=15.3
Q ss_pred ccChHHHHHHHHHcCCC
Q 047516 97 TINGDDIIWAITTLGFE 113 (214)
Q Consensus 97 TI~~eDVl~ALe~LGF~ 113 (214)
-+++.+|+++|+.+||.
T Consensus 6 ~~~~ke~ik~Le~~Gf~ 22 (66)
T COG1724 6 RMKAKEVIKALEKDGFQ 22 (66)
T ss_pred cCCHHHHHHHHHhCCcE
Confidence 47899999999999996
No 130
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=27.60 E-value=1.5e+02 Score=29.27 Aligned_cols=78 Identities=14% Similarity=0.180 Sum_probs=51.8
Q ss_pred ccccCchhHHHHHHhhcC---CCCc---------ccCHH-----HHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHH
Q 047516 40 QDRFLPIANVGRIMKKVI---PGNG---------KISKD-----AKETVQECVSEFISFVTGEASDKCQREKRKTINGDD 102 (214)
Q Consensus 40 ~Dl~LPkA~V~RImK~~L---P~~~---------rISkD-----A~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eD 102 (214)
+++.|-.+||.|+++... |.++ .|+.+ +.++|.....++ +...+++|-++-+.
T Consensus 377 e~lglHeSTVSRa~~~KY~~tp~GifeLK~FFs~~v~~~~g~~~Ss~~Ik~~Ik~l----------I~~Ed~~kPLSD~~ 446 (481)
T PRK12469 377 EELGLHESTISRATGNKYMATPRGTFEFKHFFPRKLEAAGGGECSAAAVRALIKEM----------IAAEQAGDPLSDVA 446 (481)
T ss_pred HHhCCCcchhhHHhcCceeecCCceEeHHHhhccccCCCCCccccHHHHHHHHHHH----------HHhcCCCCCCCHHH
Confidence 456788899999998762 3221 11111 222233222222 45678899999999
Q ss_pred HHHHHHHcCCCcchHHHHHHHHHHHHHHh
Q 047516 103 IIWAITTLGFEDYVAPLKLYLSKYREIEG 131 (214)
Q Consensus 103 Vl~ALe~LGF~dyi~~Lk~~L~~yre~~~ 131 (214)
|...|+.-|+. ....-+.+||+..+
T Consensus 447 I~~~L~~~GI~----IARRTVAKYRe~L~ 471 (481)
T PRK12469 447 LAEMLAGRGVL----IARRTVAKYREAMK 471 (481)
T ss_pred HHHHHHhcCCC----eechhHHHHHHHcC
Confidence 99999998885 56778889999764
No 131
>cd04752 Commd4 COMM_Domain containing protein 4. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=26.98 E-value=3.8e+02 Score=22.44 Aligned_cols=48 Identities=15% Similarity=0.293 Sum_probs=31.2
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHHHcCCCc-chHHHHHHHHHHHH
Q 047516 74 CVSEFISFVTGEASDKCQREKRKTINGDDIIWAITTLGFED-YVAPLKLYLSKYRE 128 (214)
Q Consensus 74 ca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~LGF~d-yi~~Lk~~L~~yre 128 (214)
.+.+.+.||...|. |.-++.+++..-|+.|||+. .++.+...+.++|+
T Consensus 43 ~~va~l~fiL~~A~-------k~n~~~~~l~~eL~~lglp~e~~~~l~~~~~~~~~ 91 (174)
T cd04752 43 ASIAVLSFILSSAA-------KYNVDGESLSSELQQLGLPKEHATSLCRSYEEKQS 91 (174)
T ss_pred HHHHHHHHHHHHHH-------HcCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHH
Confidence 44555666666553 45599999999999999974 34444444444443
No 132
>TIGR01278 DPOR_BchB light-independent protochlorophyllide reductase, B subunit. This enzyme describes the B subunit of the dark form protochlorophyllide reductase, a nitrogenase-like enzyme. This subunit shows homology to the nitrogenase molybdenum-iron protein. It catalyzes a step in bacteriochlorophyll biosynthesis.
Probab=26.90 E-value=1.3e+02 Score=29.33 Aligned_cols=52 Identities=15% Similarity=0.124 Sum_probs=41.6
Q ss_pred CCcccCHHHHHHHHHHHHHHHHHHHHHHHH-HHHhcCCCccChHHHHHHHHHcC
Q 047516 59 GNGKISKDAKETVQECVSEFISFVTGEASD-KCQREKRKTINGDDIIWAITTLG 111 (214)
Q Consensus 59 ~~~rISkDA~ealqeca~eFI~~LtseAne-~a~~~kRKTI~~eDVl~ALe~LG 111 (214)
+.+.++.||...|. -.--|+.-=...+.+ .|+..|...|+.+.|..|-..+|
T Consensus 459 ~~~~w~~ea~~~l~-~~P~f~r~~~r~~~e~~a~~~g~~~it~~~~~~a~~~~~ 511 (511)
T TIGR01278 459 GELGWTAEAEAELK-KVPFFVRGKVRRNTENFARERGYSVITLEVIYAAKEHFG 511 (511)
T ss_pred CCCCcCHHHHHHHh-hCChhhhHHHHHHHHHHHHHcCCCEEcHHHHHHHHHhcC
Confidence 35689999999995 477788765555555 78999999999999999976654
No 133
>CHL00076 chlB photochlorophyllide reductase subunit B
Probab=26.79 E-value=1.4e+02 Score=29.34 Aligned_cols=52 Identities=10% Similarity=0.059 Sum_probs=42.9
Q ss_pred CCcccCHHHHHHHHHHHHHHHHHHHHHHHH-HHHhcCCCccChHHHHHHHHHcC
Q 047516 59 GNGKISKDAKETVQECVSEFISFVTGEASD-KCQREKRKTINGDDIIWAITTLG 111 (214)
Q Consensus 59 ~~~rISkDA~ealqeca~eFI~~LtseAne-~a~~~kRKTI~~eDVl~ALe~LG 111 (214)
+...++.||...|.+. --|+.--...+.+ +|+..|...|+.|.|..|-..+|
T Consensus 460 ~~~~w~~ea~~~l~~i-P~f~r~~~r~~~e~~a~~~g~~~it~~~~~~a~~~~~ 512 (513)
T CHL00076 460 SDLIWSPESQLELSKI-PGFVRGKVKRNTEKFARQNGITNITVEVMYAAKEALS 512 (513)
T ss_pred CCCCCCHHHHHHHHhC-CHHhHHHHHHHHHHHHHHcCCCeEcHHHHHHHHHhhC
Confidence 3567999999999988 7787765555555 78999999999999999977766
No 134
>PF08823 PG_binding_2: Putative peptidoglycan binding domain; InterPro: IPR014927 This entry may be a peptidoglycan binding domain.
Probab=26.74 E-value=1.3e+02 Score=22.27 Aligned_cols=32 Identities=16% Similarity=0.181 Sum_probs=26.1
Q ss_pred HHHHHHHHHcCC------CcchHHHHHHHHHHHHHHhh
Q 047516 101 DDIIWAITTLGF------EDYVAPLKLYLSKYREIEGE 132 (214)
Q Consensus 101 eDVl~ALe~LGF------~dyi~~Lk~~L~~yre~~~~ 132 (214)
+.|..+|..||| ..+-+.++..|..|...++-
T Consensus 19 ~evq~~L~~lGyy~g~~~g~~d~a~~~Al~~~~g~ENf 56 (74)
T PF08823_consen 19 REVQEALKRLGYYKGEADGVWDEATEDALRAWAGTENF 56 (74)
T ss_pred HHHHHHHHHcCCccCCCCCcccHHHHHHHHHHHHHhhH
Confidence 457788999999 77888899999999877543
No 135
>PF12010 DUF3502: Domain of unknown function (DUF3502); InterPro: IPR022627 This domain is about 140 amino acids in length and is functionally uncharacterised. It is found in bacteria C-terminal to PF01547 from PFAM.
Probab=26.71 E-value=66 Score=25.82 Aligned_cols=62 Identities=10% Similarity=0.161 Sum_probs=41.2
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHHHcCCCcchHHHHHHHHHHHHH
Q 047516 64 SKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAITTLGFEDYVAPLKLYLSKYREI 129 (214)
Q Consensus 64 SkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~LGF~dyi~~Lk~~L~~yre~ 129 (214)
+..++..|..|..+.-.|...-..-.. ----....++..|+..|++..+.++...|++|+..
T Consensus 71 ~s~Vk~Eiaa~~~v~~~Y~~~L~~G~v----d~e~~~~~~~~kLk~AGidkV~~E~QkQlda~~~~ 132 (134)
T PF12010_consen 71 PSPVKNEIAACSNVWSEYYPPLETGLV----DPEEALPEFNEKLKAAGIDKVIAELQKQLDAFLAA 132 (134)
T ss_pred CchhHHHHHHHHHHHHHHHHHHHccCC----CHHHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHh
Confidence 445667777777776666544221111 01112456778888999999999999999999764
No 136
>PLN03105 TCP24 transcription factor TCP24 (TEOSINTE BRANCHED1, CYCLOIDEA, AND PCF FAMILY 24); Provisional
Probab=26.27 E-value=45 Score=30.81 Aligned_cols=14 Identities=36% Similarity=0.733 Sum_probs=11.0
Q ss_pred CCCCCCCcccCCCc
Q 047516 182 TDHHHQSFPLPFSP 195 (214)
Q Consensus 182 ~~~~~~~~~~~~~~ 195 (214)
-||||+-||-.|+-
T Consensus 290 ~~hh~hq~p~~fdg 303 (324)
T PLN03105 290 LDHHNHQLPETFDG 303 (324)
T ss_pred cccccccCCCCcCc
Confidence 38888889988863
No 137
>PRK00440 rfc replication factor C small subunit; Reviewed
Probab=26.20 E-value=1.6e+02 Score=25.50 Aligned_cols=65 Identities=12% Similarity=0.077 Sum_probs=38.6
Q ss_pred CchhHHHHHHhhcCC-CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHHHc
Q 047516 44 LPIANVGRIMKKVIP-GNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAITTL 110 (214)
Q Consensus 44 LPkA~V~RImK~~LP-~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~L 110 (214)
++...+.++++..+. .++.|+.++.+.|.+.+.--+..+-.+--..+.. .++|+.+||..++...
T Consensus 161 l~~~ei~~~l~~~~~~~~~~i~~~al~~l~~~~~gd~r~~~~~l~~~~~~--~~~it~~~v~~~~~~~ 226 (319)
T PRK00440 161 LKKEAVAERLRYIAENEGIEITDDALEAIYYVSEGDMRKAINALQAAAAT--GKEVTEEAVYKITGTA 226 (319)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHc--CCCCCHHHHHHHhCCC
Confidence 344555555554432 2567999999999887653333332222222322 4689999998887543
No 138
>PTZ00373 60S Acidic ribosomal protein P2; Provisional
Probab=25.95 E-value=2.1e+02 Score=23.04 Aligned_cols=28 Identities=7% Similarity=0.098 Sum_probs=24.5
Q ss_pred HHHHHHhcCCCccChHHHHHHHHHcCCC
Q 047516 86 ASDKCQREKRKTINGDDIIWAITTLGFE 113 (214)
Q Consensus 86 Ane~a~~~kRKTI~~eDVl~ALe~LGF~ 113 (214)
|+-.|.-.|..+|+.+||...|+..|.+
T Consensus 8 AYlL~~lgG~~~pTaddI~kIL~AaGve 35 (112)
T PTZ00373 8 AYLMCVLGGNENPTKKEVKNVLSAVNAD 35 (112)
T ss_pred HHHHHHHcCCCCCCHHHHHHHHHHcCCC
Confidence 5668888899999999999999998864
No 139
>PRK05629 hypothetical protein; Validated
Probab=25.67 E-value=2.3e+02 Score=25.33 Aligned_cols=48 Identities=8% Similarity=0.038 Sum_probs=35.3
Q ss_pred CcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHH
Q 047516 60 NGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAIT 108 (214)
Q Consensus 60 ~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe 108 (214)
+.+|+.+|...|.+++..=+..+..|--..|.-. ..+|+.+||...+.
T Consensus 143 g~~i~~~A~~~L~~~~g~dl~~l~~EleKL~~~~-~~~It~e~V~~~v~ 190 (318)
T PRK05629 143 GVRPTPDVVHALLEGVGSDLRELASAISQLVEDT-QGNVTVEKVRAYYV 190 (318)
T ss_pred CCCCCHHHHHHHHHHHCccHHHHHHHHHHHHhcC-CCCcCHHHHHHHhC
Confidence 6789999999999888765555555555555433 45799999988755
No 140
>PRK14700 recombination factor protein RarA; Provisional
Probab=25.30 E-value=4.7e+02 Score=24.46 Aligned_cols=65 Identities=11% Similarity=0.138 Sum_probs=44.9
Q ss_pred CchhHHHHHHhhcCCC-------CcccCHHHHHHHHHHH----HHHHHHHHHHHHHHHHhcCCCccChHHHHHHHHH
Q 047516 44 LPIANVGRIMKKVIPG-------NGKISKDAKETVQECV----SEFISFVTGEASDKCQREKRKTINGDDIIWAITT 109 (214)
Q Consensus 44 LPkA~V~RImK~~LP~-------~~rISkDA~ealqeca----~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~ 109 (214)
|-...|.+|+++++.+ .+.|+.||+..|.+.| ..+++.|=. |...+...+...|+.++|..++..
T Consensus 39 L~~~di~~il~ral~~~~~~~~~~~~i~~~al~~ia~~a~GDaR~aLN~LE~-a~~~~~~~~~~~it~~~~~~~~~~ 114 (300)
T PRK14700 39 LSLVATQKLIEKALSQDEVLAKHKFKIDDGLYNAMHNYNEGDCRKILNLLER-MFLISTRGDEIYLNKELFDQAVGE 114 (300)
T ss_pred CCHHHHHHHHHHHHHhhhccCCcCCCcCHHHHHHHHHhcCCHHHHHHHHHHH-HHhhccccCCCccCHHHHHHHHhH
Confidence 6677788888888752 3579999999999976 455555433 333333333346999999999874
No 141
>PRK05907 hypothetical protein; Provisional
Probab=25.04 E-value=1.8e+02 Score=26.71 Aligned_cols=73 Identities=10% Similarity=-0.069 Sum_probs=47.1
Q ss_pred CcccCHHHHHHHHHHH-HHHHHHHHHHHHHHHHh-cCCCccChHHHHHHHHH-cCCCcc--hH-----HHHHHHHHHHHH
Q 047516 60 NGKISKDAKETVQECV-SEFISFVTGEASDKCQR-EKRKTINGDDIIWAITT-LGFEDY--VA-----PLKLYLSKYREI 129 (214)
Q Consensus 60 ~~rISkDA~ealqeca-~eFI~~LtseAne~a~~-~kRKTI~~eDVl~ALe~-LGF~dy--i~-----~Lk~~L~~yre~ 129 (214)
+..|+++|...|.+.+ .-=+..+..|--..|.- ..+++|+.+||...+.. +.+.=| ++ .....+.-|++.
T Consensus 151 g~~i~~~a~~~L~~~~~~~nL~~l~~EleKL~ly~g~~~~It~e~V~~lv~~s~e~nIF~L~dai~~~~~~~Al~il~~L 230 (311)
T PRK05907 151 GISCSLGLASLFVSKFPQTGLFEILSEFQKLLCQMGKKESLEASDIQSFVVKKEAASLWKLRDALLRRDRVEGHSLLRSL 230 (311)
T ss_pred CCCcCHHHHHHHHHHccCCCHHHHHHHHHHHHHhcCCCCeECHHHHHHHhcCcccccHHHHHHHHHccCHHHHHHHHHHH
Confidence 6789999999988877 33344555555555554 56899999999988653 454432 22 233455566665
Q ss_pred Hhh
Q 047516 130 EGE 132 (214)
Q Consensus 130 ~~~ 132 (214)
...
T Consensus 231 l~~ 233 (311)
T PRK05907 231 LSD 233 (311)
T ss_pred HHh
Confidence 443
No 142
>PF07499 RuvA_C: RuvA, C-terminal domain; InterPro: IPR011114 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. The domain represents the C-terminal domain III of RuvA. This domain plays a significant role in the ATP-dependent branch migration of the hetero-duplex through direct contact with RuvB []. Within the Holliday junction, this domain makes no interaction with the DNA.; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination, 0009379 Holliday junction helicase complex; PDB: 1HJP_A 1CUK_A 1C7Y_A 1IXS_A 1IXR_B 1BVS_E 2ZTC_A 2ZTD_B 2H5X_A.
Probab=24.72 E-value=57 Score=21.66 Aligned_cols=14 Identities=29% Similarity=0.541 Sum_probs=11.8
Q ss_pred hHHHHHHHHHcCCC
Q 047516 100 GDDIIWAITTLGFE 113 (214)
Q Consensus 100 ~eDVl~ALe~LGF~ 113 (214)
.+|++.||..|||.
T Consensus 3 ~~d~~~AL~~LGy~ 16 (47)
T PF07499_consen 3 LEDALEALISLGYS 16 (47)
T ss_dssp HHHHHHHHHHTTS-
T ss_pred HHHHHHHHHHcCCC
Confidence 37999999999997
No 143
>smart00454 SAM Sterile alpha motif. Widespread domain in signalling and nuclear proteins. In EPH-related tyrosine kinases, appears to mediate cell-cell initiated signal transduction via the binding of SH2-containing proteins to a conserved tyrosine that is phosphorylated. In many cases mediates homodimerisation.
Probab=24.60 E-value=65 Score=21.19 Aligned_cols=25 Identities=12% Similarity=0.298 Sum_probs=20.2
Q ss_pred cChHHHHHHHHHcCCCcchHHHHHH
Q 047516 98 INGDDIIWAITTLGFEDYVAPLKLY 122 (214)
Q Consensus 98 I~~eDVl~ALe~LGF~dyi~~Lk~~ 122 (214)
-+.++|..-|+.+||++|++.+...
T Consensus 4 w~~~~v~~wL~~~g~~~y~~~f~~~ 28 (68)
T smart00454 4 WSPESVADWLESIGLEQYADNFRKN 28 (68)
T ss_pred CCHHHHHHHHHHCChHHHHHHHHHC
Confidence 4678899999999999888776543
No 144
>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA.
Probab=24.29 E-value=4.9e+02 Score=26.58 Aligned_cols=68 Identities=21% Similarity=0.253 Sum_probs=44.8
Q ss_pred hhHHHHHHhhcCC-----CCcccCHHHHHHHHHHHHHHHHH--HH-------HHHHHHHHh----cCCCccChHHHHHHH
Q 047516 46 IANVGRIMKKVIP-----GNGKISKDAKETVQECVSEFISF--VT-------GEASDKCQR----EKRKTINGDDIIWAI 107 (214)
Q Consensus 46 kA~V~RImK~~LP-----~~~rISkDA~ealqeca~eFI~~--Lt-------seAne~a~~----~kRKTI~~eDVl~AL 107 (214)
......|++..++ -++.|+.+|..++.+.+..||.. +- .+|...+.- ..+.+|+.+||..++
T Consensus 347 ~~~~~~il~~~~~~~e~~~~v~i~~~al~~~~~ls~ryi~~r~~P~kai~lld~a~a~~~~~~~~~~~~~v~~~~i~~~i 426 (731)
T TIGR02639 347 IEETVKILKGLKEKYEEFHHVKYSDEALEAAVELSARYINDRFLPDKAIDVIDEAGASFRLRPKAKKKANVSVKDIENVV 426 (731)
T ss_pred HHHHHHHHHHHHHHHHhccCcccCHHHHHHHHHhhhcccccccCCHHHHHHHHHhhhhhhcCcccccccccCHHHHHHHH
Confidence 3444555654433 24689999999999999998844 33 333332211 125679999999999
Q ss_pred HHc-CCC
Q 047516 108 TTL-GFE 113 (214)
Q Consensus 108 e~L-GF~ 113 (214)
..+ |.+
T Consensus 427 ~~~tgiP 433 (731)
T TIGR02639 427 AKMAHIP 433 (731)
T ss_pred HHHhCCC
Confidence 975 665
No 145
>cd00051 EFh EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers.
Probab=23.82 E-value=1.8e+02 Score=17.59 Aligned_cols=38 Identities=16% Similarity=0.184 Sum_probs=25.3
Q ss_pred HHHhcCCCccChHHHHHHHHHcCCCcchHHHHHHHHHH
Q 047516 89 KCQREKRKTINGDDIIWAITTLGFEDYVAPLKLYLSKY 126 (214)
Q Consensus 89 ~a~~~kRKTI~~eDVl~ALe~LGF~dyi~~Lk~~L~~y 126 (214)
.+...+.-.|+.+|+..+|+.++...-.+.+...+..+
T Consensus 8 ~~d~~~~g~l~~~e~~~~l~~~~~~~~~~~~~~~~~~~ 45 (63)
T cd00051 8 LFDKDGDGTISADELKAALKSLGEGLSEEEIDEMIREV 45 (63)
T ss_pred HhCCCCCCcCcHHHHHHHHHHhCCCCCHHHHHHHHHHh
Confidence 44455566789999999999888655555555444433
No 146
>PTZ00184 calmodulin; Provisional
Probab=23.37 E-value=2.9e+02 Score=20.61 Aligned_cols=40 Identities=18% Similarity=0.152 Sum_probs=26.9
Q ss_pred HHHHHHHHhcCCCccChHHHHHHHHHcCCCcchHHHHHHH
Q 047516 84 GEASDKCQREKRKTINGDDIIWAITTLGFEDYVAPLKLYL 123 (214)
Q Consensus 84 seAne~a~~~kRKTI~~eDVl~ALe~LGF~dyi~~Lk~~L 123 (214)
..+...+..+++-.|+.+|+..+|..+|+.--...++..+
T Consensus 87 ~~~F~~~D~~~~g~i~~~e~~~~l~~~~~~~~~~~~~~~~ 126 (149)
T PTZ00184 87 KEAFKVFDRDGNGFISAAELRHVMTNLGEKLTDEEVDEMI 126 (149)
T ss_pred HHHHHhhCCCCCCeEeHHHHHHHHHHHCCCCCHHHHHHHH
Confidence 3444555667778899999999999888754334444433
No 147
>TIGR01052 top6b DNA topoisomerase VI, B subunit. This model describes DNA topoisomerase VI, an archaeal type II DNA topoisomerase (DNA gyrase).
Probab=23.35 E-value=84 Score=31.11 Aligned_cols=52 Identities=17% Similarity=0.313 Sum_probs=36.7
Q ss_pred cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHHHcCCCcchHHHHHHHHHH
Q 047516 61 GKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAITTLGFEDYVAPLKLYLSKY 126 (214)
Q Consensus 61 ~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~LGF~dyi~~Lk~~L~~y 126 (214)
--|-+|.+.||++||...=.||...-...-...++++ |..|++.+-..|..+
T Consensus 433 ~ei~~ei~~al~~~~r~L~~~l~~~~~~~~~~~r~~~--------------~~~y~p~~a~~~~~~ 484 (488)
T TIGR01052 433 PEIYNEIRLALMEVARRLRLYLSRKAREEEEIKRRKT--------------LEKYLPEIAKSLAYI 484 (488)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------------HHHHHHHHHHHHHHH
Confidence 3578888999999999999999987665555555444 344666666555543
No 148
>PRK14964 DNA polymerase III subunits gamma and tau; Provisional
Probab=23.07 E-value=1.7e+02 Score=28.82 Aligned_cols=47 Identities=9% Similarity=-0.038 Sum_probs=29.7
Q ss_pred CcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHH
Q 047516 60 NGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAI 107 (214)
Q Consensus 60 ~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~AL 107 (214)
++.|+.+|..+|.+.+.-=+..+.+.--..+...+ .+|+.+||...|
T Consensus 192 gi~i~~eAL~lIa~~s~GslR~alslLdqli~y~~-~~It~e~V~~ll 238 (491)
T PRK14964 192 NIEHDEESLKLIAENSSGSMRNALFLLEQAAIYSN-NKISEKSVRDLL 238 (491)
T ss_pred CCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhcC-CCCCHHHHHHHH
Confidence 67899999999988774333333333333333333 479998887654
No 149
>KOG2296 consensus Integral membrane protein [General function prediction only]
Probab=22.63 E-value=73 Score=32.79 Aligned_cols=44 Identities=20% Similarity=0.351 Sum_probs=22.5
Q ss_pred HHHHHcCCCcchHHHHHH---HHHHHH-HHhhhcCCchhhhHHHHHHH
Q 047516 105 WAITTLGFEDYVAPLKLY---LSKYRE-IEGEKLNIPKQQRSEQRVQQ 148 (214)
Q Consensus 105 ~ALe~LGF~dyi~~Lk~~---L~~yre-~~~~K~~~~~~~~~E~~~~~ 148 (214)
.||..+||++|.+.-+.. +++=|+ ..++|++...+...|.|..+
T Consensus 529 ~~ln~~GFdqF~~n~emt~dlinegk~li~kEkrsrkr~ee~e~r~r~ 576 (673)
T KOG2296|consen 529 RALNTDGFDQFSENSEMTMDLINEGKGLISKEKRSRKRGEEREARTRK 576 (673)
T ss_pred eeccccchhhhhccchhHHHHHHHhHHHHHHHHHHHhhhhhHHHHHHH
Confidence 356778999887533322 233333 23445544444444444444
No 150
>TIGR02903 spore_lon_C ATP-dependent protease, Lon family. Members of this protein family resemble the widely distributed ATP-dependent protease La, also called Lon and LonA. It resembles even more closely LonB, which is a LonA paralog found in genomes if and only if the species is capable of endospore formation (as in Bacillus subtilis, Clostridium tetani, and select other members of the Firmicutes) and expressed specifically in the forespore compartment. Members of this family are restricted to a subset of spore-forming species, and are very likely to participate in the program of endospore formation. We propose the designation LonC.
Probab=22.52 E-value=1.7e+02 Score=29.42 Aligned_cols=71 Identities=13% Similarity=0.181 Sum_probs=45.4
Q ss_pred chhHHHHHHhhcCCC-CcccCHHHHHHHHHHH---HHHHHHHHHHHHHH--------HHhcCCCccChHHHHHHHHHcCC
Q 047516 45 PIANVGRIMKKVIPG-NGKISKDAKETVQECV---SEFISFVTGEASDK--------CQREKRKTINGDDIIWAITTLGF 112 (214)
Q Consensus 45 PkA~V~RImK~~LP~-~~rISkDA~ealqeca---~eFI~~LtseAne~--------a~~~kRKTI~~eDVl~ALe~LGF 112 (214)
...-+..|++..+.. +..++.++.++|.+++ ...++.|... ..+ +...++.+|+.+||..++..--|
T Consensus 354 s~edi~~Il~~~a~~~~v~ls~eal~~L~~ys~~gRraln~L~~~-~~~~~~~~~~~~~~~~~~~I~~edv~~~l~~~r~ 432 (615)
T TIGR02903 354 TPEDIALIVLNAAEKINVHLAAGVEELIARYTIEGRKAVNILADV-YGYALYRAAEAGKENDKVTITQDDVYEVIQISRL 432 (615)
T ss_pred CHHHHHHHHHHHHHHcCCCCCHHHHHHHHHCCCcHHHHHHHHHHH-HHHHHHHHHHhccCCCCeeECHHHHHHHhCCCcC
Confidence 345566677666542 3568999999998865 3444444322 222 22334569999999999987776
Q ss_pred Ccch
Q 047516 113 EDYV 116 (214)
Q Consensus 113 ~dyi 116 (214)
..|.
T Consensus 433 ~~~~ 436 (615)
T TIGR02903 433 SPYE 436 (615)
T ss_pred ccch
Confidence 6554
No 151
>PRK09111 DNA polymerase III subunits gamma and tau; Validated
Probab=22.31 E-value=2.1e+02 Score=28.83 Aligned_cols=61 Identities=2% Similarity=0.000 Sum_probs=37.3
Q ss_pred hhHHHHHHhhcCC-CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHH
Q 047516 46 IANVGRIMKKVIP-GNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAI 107 (214)
Q Consensus 46 kA~V~RImK~~LP-~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~AL 107 (214)
...+.+.++..+. .+..|+.++..+|.+.+.--+..+.++.-..+.. +.+.|+.+||...+
T Consensus 193 ~~el~~~L~~i~~kegi~i~~eAl~lIa~~a~Gdlr~al~~Ldkli~~-g~g~It~e~V~~ll 254 (598)
T PRK09111 193 ADVLAAHLSRIAAKEGVEVEDEALALIARAAEGSVRDGLSLLDQAIAH-GAGEVTAEAVRDML 254 (598)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHhh-cCCCcCHHHHHHHh
Confidence 3344444444332 3678999999999888765555555544343333 34579988887654
No 152
>KOG0027 consensus Calmodulin and related proteins (EF-Hand superfamily) [Signal transduction mechanisms]
Probab=22.17 E-value=4e+02 Score=21.05 Aligned_cols=80 Identities=16% Similarity=0.115 Sum_probs=48.0
Q ss_pred CchhHHHHHHhhcC-CCCcccCHHHHHHHHHHHHHHHHH------HHHHHHHHHHhcCCCccChHHHHHHHHHcCCCcch
Q 047516 44 LPIANVGRIMKKVI-PGNGKISKDAKETVQECVSEFISF------VTGEASDKCQREKRKTINGDDIIWAITTLGFEDYV 116 (214)
Q Consensus 44 LPkA~V~RImK~~L-P~~~rISkDA~ealqeca~eFI~~------LtseAne~a~~~kRKTI~~eDVl~ALe~LGF~dyi 116 (214)
....-+..++++.= .++..|+-+-...|..-....... -..+|-.+...++.-.|+++++...|..+|...-.
T Consensus 41 ~t~~el~~~~~~~D~dg~g~I~~~eF~~l~~~~~~~~~~~~~~~~el~eaF~~fD~d~~G~Is~~el~~~l~~lg~~~~~ 120 (151)
T KOG0027|consen 41 PTEEELRDLIKEIDLDGDGTIDFEEFLDLMEKLGEEKTDEEASSEELKEAFRVFDKDGDGFISASELKKVLTSLGEKLTD 120 (151)
T ss_pred CCHHHHHHHHHHhCCCCCCeEcHHHHHHHHHhhhcccccccccHHHHHHHHHHHccCCCCcCcHHHHHHHHHHhCCcCCH
Confidence 44555666666552 234566554333332222221111 34677788888899999999999999999987664
Q ss_pred HHHHHHH
Q 047516 117 APLKLYL 123 (214)
Q Consensus 117 ~~Lk~~L 123 (214)
++++.-+
T Consensus 121 ~e~~~mi 127 (151)
T KOG0027|consen 121 EECKEMI 127 (151)
T ss_pred HHHHHHH
Confidence 4444433
No 153
>COG5251 TAF40 Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=22.04 E-value=1.3e+02 Score=26.37 Aligned_cols=63 Identities=14% Similarity=-0.016 Sum_probs=44.2
Q ss_pred cCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC-CccChHHHHHHH
Q 047516 43 FLPIANVGRIMKKVIPGNGKISKDAKETVQECVSEFISFVTGEASDKCQREKR-KTINGDDIIWAI 107 (214)
Q Consensus 43 ~LPkA~V~RImK~~LP~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kR-KTI~~eDVl~AL 107 (214)
.||++.|.+++-.++ +-.|+...+.+|+-.+.+|+-.+-.-|..+-.+=+- --+.+.|+..|.
T Consensus 115 ~lnKt~VKKlastV~--nQtVspNi~I~l~g~~KVfvGEiIElA~~Vq~~w~~sgpl~p~h~reay 178 (199)
T COG5251 115 SLNKTQVKKLASTVA--NQTVSPNIRIFLQGVGKVFVGEIIELAMIVQNKWLTSGPLIPFHKREAY 178 (199)
T ss_pred CCCHHHHHHHHHHHh--ccccCCCeeeeeechhHHHHHHHHHHHHHHHHHhcccCCCChHHHHHHH
Confidence 499999999999995 456777777788888999987777766544332211 245666666553
No 154
>PRK12728 fliE flagellar hook-basal body protein FliE; Provisional
Probab=21.63 E-value=4e+02 Score=20.85 Aligned_cols=39 Identities=15% Similarity=0.189 Sum_probs=29.4
Q ss_pred hcCCCccChHHHHHHHHH--cCCCcchHHHHHHHHHHHHHHh
Q 047516 92 REKRKTINGDDIIWAITT--LGFEDYVAPLKLYLSKYREIEG 131 (214)
Q Consensus 92 ~~kRKTI~~eDVl~ALe~--LGF~dyi~~Lk~~L~~yre~~~ 131 (214)
..|. ++...||.-|+.+ +.|.-.+..=...++.|.|+.+
T Consensus 59 ~~G~-~~~lhevmiA~~kA~lslq~~vqVRNKlv~AYqEIMr 99 (102)
T PRK12728 59 VKGE-IVDLHDVMIAAQKASISLQLTVQIRNKVVEAYQEIMR 99 (102)
T ss_pred HcCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3454 8899999999996 5566666666688889998754
No 155
>COG1222 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]
Probab=21.62 E-value=1.1e+02 Score=29.79 Aligned_cols=41 Identities=22% Similarity=0.322 Sum_probs=33.0
Q ss_pred HHHHHHHHHH----HHHHHHHHHHHHHhcCCCccChHHHHHHHHH
Q 047516 69 ETVQECVSEF----ISFVTGEASDKCQREKRKTINGDDIIWAITT 109 (214)
Q Consensus 69 ealqeca~eF----I~~LtseAne~a~~~kRKTI~~eDVl~ALe~ 109 (214)
+.|.+++..| |.-|..||--.|.++.|..|+-+|++.|.++
T Consensus 347 e~la~~~~g~sGAdlkaictEAGm~AiR~~R~~Vt~~DF~~Av~K 391 (406)
T COG1222 347 ELLARLTEGFSGADLKAICTEAGMFAIRERRDEVTMEDFLKAVEK 391 (406)
T ss_pred HHHHHhcCCCchHHHHHHHHHHhHHHHHhccCeecHHHHHHHHHH
Confidence 4455544443 7788899999999999999999999999764
No 156
>PRK08487 DNA polymerase III subunit delta; Validated
Probab=21.49 E-value=3.2e+02 Score=24.68 Aligned_cols=59 Identities=12% Similarity=0.023 Sum_probs=38.9
Q ss_pred HHHHHhhcCC-CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHHH
Q 047516 49 VGRIMKKVIP-GNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAITT 109 (214)
Q Consensus 49 V~RImK~~LP-~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe~ 109 (214)
+.+.|++.+- .+..|+.+|...|...+.-=...+..|--..+.=.+ +|+.+||...+..
T Consensus 140 l~~~i~~~~~~~g~~i~~~a~~~L~~~~g~dl~~l~~ELeKL~ly~~--~It~edV~~~v~~ 199 (328)
T PRK08487 140 ALELLQERAKELGLDIDQNALNHLYFIHNEDLALAANELEKLAILNE--PITLKDIQELVFG 199 (328)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHHHhCcHHHHHHHHHHHHHHhcC--CCCHHHHHHHhcc
Confidence 3444443332 267899999999999887555555555444444333 7999999998753
No 157
>PF05930 Phage_AlpA: Prophage CP4-57 regulatory protein (AlpA); InterPro: IPR010260 This entry is represents phage P4, Orf88. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. In Escherichia coli phage P4 Orf 88 is similar to AlpA of the CP4-57 cryptic prophage []. AlpA acts as a positive transcriptional regulator of slpA, a gene linked to alpA and necessary for suppression of lon mutants [, ]. The sequence of slpA suggests that it encodes an integrase gene closely related to phage P4 int and that both alpA and slpA are part of a cryptic P4-like prophage. Increase in alpA expression increases SlpA synthesis. Increased SlpA leads, in turn, to the excision and loss of the cryptic prophage. ; PDB: 1Z4H_A.
Probab=21.35 E-value=52 Score=22.01 Aligned_cols=25 Identities=16% Similarity=0.159 Sum_probs=16.3
Q ss_pred ccCchhHHHHHHhhc-CCCCcccCHH
Q 047516 42 RFLPIANVGRIMKKV-IPGNGKISKD 66 (214)
Q Consensus 42 l~LPkA~V~RImK~~-LP~~~rISkD 66 (214)
+.+-+++|+|+||.. +|..++|+.-
T Consensus 13 ~g~s~~ti~~~~k~g~FP~pvklg~r 38 (51)
T PF05930_consen 13 LGVSRSTIYRLIKDGKFPKPVKLGGR 38 (51)
T ss_dssp HSS-HHHHHHHHHHHH---SEESSS-
T ss_pred HCCCHHHHHHHHhcccCCCCEEECCC
Confidence 357889999999876 8888888753
No 158
>KOG2129 consensus Uncharacterized conserved protein H4 [Function unknown]
Probab=21.25 E-value=4e+02 Score=26.70 Aligned_cols=19 Identities=26% Similarity=0.424 Sum_probs=13.9
Q ss_pred CCCCCCCCCCccCCCCCCC
Q 047516 13 PDGGSPESPCVKSSGSNSN 31 (214)
Q Consensus 13 ~~~~~p~~~~~~~~~~~~~ 31 (214)
.+.|..+|+|.+.+++.++
T Consensus 17 ~as~~meSscss~ss~~GG 35 (552)
T KOG2129|consen 17 DASGRMESSCSSHSSHSGG 35 (552)
T ss_pred cccccccCCcccccCCCCC
Confidence 3557789999998865553
No 159
>PTZ00186 heat shock 70 kDa precursor protein; Provisional
Probab=21.06 E-value=2.6e+02 Score=28.49 Aligned_cols=14 Identities=7% Similarity=0.211 Sum_probs=10.7
Q ss_pred cCchhHHHHHHhhc
Q 047516 43 FLPIANVGRIMKKV 56 (214)
Q Consensus 43 ~LPkA~V~RImK~~ 56 (214)
.|....|.|+++++
T Consensus 526 ~ls~~~i~~~~~~~ 539 (657)
T PTZ00186 526 GLSKEQIEQMIRDS 539 (657)
T ss_pred cCCHHHHHHHHHHH
Confidence 47777888888777
No 160
>PF02361 CbiQ: Cobalt transport protein; InterPro: IPR003339 Cobalt transport proteins are most often found in cobalamin (vitamin B12) biosynthesis operons. Salmonella typhimurium synthesizes cobalamin (vitamin B12) de novo under anaerobic conditions. Not all Salmonella and Pseudomonas cobalamin synthetic genes have apparent homologs in the other species suggesting that the cobalamin biosynthetic pathways differ between the two organisms [].; GO: 0015087 cobalt ion transmembrane transporter activity, 0006824 cobalt ion transport, 0009236 cobalamin biosynthetic process
Probab=20.98 E-value=1.7e+02 Score=24.02 Aligned_cols=38 Identities=21% Similarity=0.259 Sum_probs=30.3
Q ss_pred CccChHHHHHHHHHcCCCc------------chHHHHHHHHHHHHHHhhh
Q 047516 96 KTINGDDIIWAITTLGFED------------YVAPLKLYLSKYREIEGEK 133 (214)
Q Consensus 96 KTI~~eDVl~ALe~LGF~d------------yi~~Lk~~L~~yre~~~~K 133 (214)
.|.+.+|++.+|+.++++. |++.+.+.+++-++.++.+
T Consensus 123 ~tt~~~~l~~~l~~l~~P~~~~~~~i~l~~r~ip~l~~~~~~i~~A~~~R 172 (224)
T PF02361_consen 123 LTTSPSDLISALRKLRLPYPKIALMISLTLRFIPLLLEEFKRIREAQRLR 172 (224)
T ss_pred HHCCHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 4788999999999999988 7777777777777665553
No 161
>cd04750 Commd2 COMM_Domain containing protein 2. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=20.95 E-value=5e+02 Score=21.67 Aligned_cols=20 Identities=30% Similarity=0.454 Sum_probs=17.3
Q ss_pred CCccChHHHHHHHHHcCCCc
Q 047516 95 RKTINGDDIIWAITTLGFED 114 (214)
Q Consensus 95 RKTI~~eDVl~ALe~LGF~d 114 (214)
|.-++.+++...|..|||++
T Consensus 49 K~~l~~~~~~~~L~~l~~~~ 68 (166)
T cd04750 49 KLKLSERDFQDSIEFLGFSD 68 (166)
T ss_pred hccCCHHHHHHHHHHcCCCH
Confidence 44599999999999999985
No 162
>KOG1528 consensus Salt-sensitive 3'-phosphoadenosine-5'-phosphatase HAL2/SAL1 [Nucleotide transport and metabolism; Inorganic ion transport and metabolism]
Probab=20.88 E-value=2.4e+02 Score=26.89 Aligned_cols=64 Identities=16% Similarity=0.275 Sum_probs=42.7
Q ss_pred hhHHHHHHhhcCCCCc--ccCHHHHHHHHHH-HHHHHHHHHHHHHH-HHHhc--CC-CccChHHHHHHHHH
Q 047516 46 IANVGRIMKKVIPGNG--KISKDAKETVQEC-VSEFISFVTGEASD-KCQRE--KR-KTINGDDIIWAITT 109 (214)
Q Consensus 46 kA~V~RImK~~LP~~~--rISkDA~ealqec-a~eFI~~LtseAne-~a~~~--kR-KTI~~eDVl~ALe~ 109 (214)
-|.|.-++++.+|++- .|..|--.-|.+. ++.|+.-|+.--++ ++..+ +- ..++.+||++|++.
T Consensus 52 QAiVs~vL~~~f~~~p~slVaEEds~~Lr~n~~~~~l~~i~~lvnetl~s~~sy~~~~~ls~~dvl~aID~ 122 (351)
T KOG1528|consen 52 QAIVSLVLEREFPDDPLSLVAEEDSGFLRKNGSEGLLSRITKLVNETLASDESYGDNSPLSSDDVLKAIDR 122 (351)
T ss_pred HHHHHHHHHHHcCCCCcceEeeccchhhhhhhhHHHHHHHHHHHHHHhhhhhhccCCCCCCHHHHHHHHhc
Confidence 4678888899998654 5665555555554 56677777764444 22222 23 78999999999974
No 163
>COG1389 DNA topoisomerase VI, subunit B [DNA replication, recombination, and repair]
Probab=20.60 E-value=1.1e+02 Score=30.78 Aligned_cols=37 Identities=22% Similarity=0.390 Sum_probs=32.5
Q ss_pred ccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcc
Q 047516 62 KISKDAKETVQECVSEFISFVTGEASDKCQREKRKTI 98 (214)
Q Consensus 62 rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI 98 (214)
-|=+|.+.|+++||.+.=.||.....+.-...++++|
T Consensus 442 eIe~Eir~Al~evaRkL~~yLsrk~r~~e~~~K~~~i 478 (538)
T COG1389 442 EIENEIRLALMEVARKLKLYLSRKRREMEERKKRKTI 478 (538)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4778999999999999999999999888777777776
No 164
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=20.45 E-value=1.1e+02 Score=26.51 Aligned_cols=34 Identities=15% Similarity=0.290 Sum_probs=28.3
Q ss_pred cCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHH
Q 047516 43 FLPIANVGRIMKKVIPGNGKISKDAKETVQECVSEF 78 (214)
Q Consensus 43 ~LPkA~V~RImK~~LP~~~rISkDA~ealqeca~eF 78 (214)
.+-+++|.|++... +..+||.+.++-+.+++++.
T Consensus 12 gVS~~TVSrvln~~--~~~~vs~~tr~rV~~~a~~l 45 (327)
T PRK10339 12 GVSLATVSRVLNDD--PTLNVKEETKHRILEIAEKL 45 (327)
T ss_pred CCCHHhhhhhhcCC--CCCCcCHHHHHHHHHHHHHh
Confidence 46789999999765 33579999999999999886
No 165
>PRK09526 lacI lac repressor; Reviewed
Probab=20.30 E-value=1e+02 Score=26.81 Aligned_cols=38 Identities=18% Similarity=0.455 Sum_probs=30.2
Q ss_pred cCchhHHHHHHhhcCCCCcccCHHHHHHHHHHHHHHHHHHHHH
Q 047516 43 FLPIANVGRIMKKVIPGNGKISKDAKETVQECVSEFISFVTGE 85 (214)
Q Consensus 43 ~LPkA~V~RImK~~LP~~~rISkDA~ealqeca~eFI~~Ltse 85 (214)
..-+++|.|++... .+||.+.++-+.+++++ +.|.-..
T Consensus 16 GVS~~TVSrvLn~~----~~vs~~tr~rV~~~a~e-lgY~pn~ 53 (342)
T PRK09526 16 GVSYQTVSRVLNQA----SHVSAKTREKVEAAMAE-LNYVPNR 53 (342)
T ss_pred CCCHHHHHHHhcCC----CCCCHHHHHHHHHHHHH-HCCCcCH
Confidence 46788999998754 47999999999999999 4565443
No 166
>PRK14961 DNA polymerase III subunits gamma and tau; Provisional
Probab=20.28 E-value=2.8e+02 Score=25.52 Aligned_cols=63 Identities=6% Similarity=-0.047 Sum_probs=32.7
Q ss_pred chhHHHHHHhhcCC-CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHHHHH
Q 047516 45 PIANVGRIMKKVIP-GNGKISKDAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDIIWAIT 108 (214)
Q Consensus 45 PkA~V~RImK~~LP-~~~rISkDA~ealqeca~eFI~~LtseAne~a~~~kRKTI~~eDVl~ALe 108 (214)
+...+..+++..+. .+..++.++...|.+.+.-=+..+-...-..+.- ++..|+.+||..++.
T Consensus 179 ~~~el~~~L~~~~~~~g~~i~~~al~~ia~~s~G~~R~al~~l~~~~~~-~~~~It~~~v~~~l~ 242 (363)
T PRK14961 179 SEEKIFNFLKYILIKESIDTDEYALKLIAYHAHGSMRDALNLLEHAINL-GKGNINIKNVTDMLG 242 (363)
T ss_pred CHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHh-cCCCCCHHHHHHHHC
Confidence 34444444444322 2567899988887776532111111111111222 467788898887654
Done!