Query 032845
Match_columns 132
No_of_seqs 113 out of 532
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 06:38:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032845.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032845hhsearch_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 2.2E-33 4.7E-38 213.0 11.2 97 7-108 27-123 (168)
2 KOG0871 Class 2 transcription 100.0 1.7E-28 3.6E-33 184.7 10.0 95 9-108 9-103 (156)
3 KOG0870 DNA polymerase epsilon 99.9 1.9E-27 4.1E-32 181.7 10.9 102 6-111 4-105 (172)
4 COG5150 Class 2 transcription 99.9 5E-24 1.1E-28 157.5 9.6 101 9-115 8-108 (148)
5 PF00808 CBFD_NFYB_HMF: Histon 99.8 2.2E-18 4.7E-23 112.7 8.0 64 12-81 2-65 (65)
6 COG2036 HHT1 Histones H3 and H 99.7 2.1E-17 4.6E-22 116.1 7.2 79 4-89 10-89 (91)
7 cd00076 H4 Histone H4, one of 99.4 1.6E-12 3.4E-17 90.5 8.6 78 5-89 5-83 (85)
8 PLN00035 histone H4; Provision 99.4 3.2E-12 6.9E-17 91.8 8.3 76 5-87 21-97 (103)
9 PTZ00015 histone H4; Provision 99.3 1.7E-11 3.7E-16 87.8 8.5 78 5-89 22-100 (102)
10 smart00417 H4 Histone H4. 99.2 5.9E-11 1.3E-15 80.7 6.1 70 4-80 4-74 (74)
11 smart00428 H3 Histone H3. 99.1 2E-10 4.3E-15 82.7 7.4 76 9-84 26-101 (105)
12 smart00803 TAF TATA box bindin 99.1 4.2E-10 9.1E-15 74.5 7.6 64 12-82 2-65 (65)
13 cd07981 TAF12 TATA Binding Pro 99.0 2.2E-09 4.7E-14 72.0 8.4 66 13-84 2-67 (72)
14 PF00125 Histone: Core histone 99.0 1.3E-09 2.8E-14 72.3 7.2 71 10-82 3-73 (75)
15 PLN00160 histone H3; Provision 98.8 1.7E-08 3.6E-13 71.9 6.3 74 9-83 18-91 (97)
16 COG5208 HAP5 CCAAT-binding fac 98.7 6.5E-09 1.4E-13 83.7 3.6 79 6-91 103-182 (286)
17 PLN00161 histone H3; Provision 98.7 3.9E-08 8.4E-13 73.6 6.8 74 9-83 52-125 (135)
18 PLN00121 histone H3; Provision 98.7 4.2E-08 9.2E-13 73.6 6.0 72 9-82 59-130 (136)
19 PTZ00018 histone H3; Provision 98.7 4.7E-08 1E-12 73.3 6.1 73 9-83 59-131 (136)
20 smart00576 BTP Bromodomain tra 98.6 5.7E-07 1.2E-11 60.7 8.5 66 15-87 9-74 (77)
21 cd00074 H2A Histone 2A; H2A is 98.5 6E-07 1.3E-11 65.6 7.0 68 10-83 18-85 (115)
22 KOG1657 CCAAT-binding factor, 98.3 6.3E-07 1.4E-11 72.6 4.8 73 11-90 73-146 (236)
23 cd07979 TAF9 TATA Binding Prot 98.3 4.7E-06 1E-10 60.8 8.8 81 16-103 5-86 (117)
24 KOG3467 Histone H4 [Chromatin 98.2 1.1E-05 2.3E-10 56.9 7.1 77 4-87 20-97 (103)
25 PF15630 CENP-S: Kinetochore c 98.1 2.1E-05 4.4E-10 53.7 7.0 63 17-83 10-72 (76)
26 cd08050 TAF6 TATA Binding Prot 98.1 1.8E-05 3.8E-10 66.7 8.2 67 14-87 1-67 (343)
27 PF15511 CENP-T: Centromere ki 98.1 1.1E-05 2.4E-10 69.7 6.8 65 11-76 350-414 (414)
28 smart00427 H2B Histone H2B. 98.0 3.8E-05 8.1E-10 54.0 7.7 67 16-88 5-71 (89)
29 PF07524 Bromo_TP: Bromodomain 98.0 8.2E-05 1.8E-09 49.8 8.4 52 36-87 23-74 (77)
30 KOG1745 Histones H3 and H4 [Ch 97.9 5.6E-06 1.2E-10 62.2 2.6 76 8-85 59-134 (137)
31 PF03847 TFIID_20kDa: Transcri 97.9 0.00011 2.5E-09 49.0 8.0 63 15-83 2-64 (68)
32 PF09415 CENP-X: CENP-S associ 97.8 3.8E-05 8.2E-10 51.9 5.0 65 14-82 1-66 (72)
33 PLN00158 histone H2B; Provisio 97.8 0.00013 2.9E-09 53.5 7.7 68 15-88 30-97 (116)
34 PTZ00463 histone H2B; Provisio 97.8 0.00015 3.2E-09 53.3 7.6 66 17-88 33-98 (117)
35 KOG1659 Class 2 transcription 97.8 0.00013 2.8E-09 58.5 7.8 75 12-93 13-88 (224)
36 cd08048 TAF11 TATA Binding Pro 97.8 0.00019 4.2E-09 49.8 7.6 66 12-84 16-84 (85)
37 COG5262 HTA1 Histone H2A [Chro 97.6 0.00019 4E-09 53.1 5.6 67 11-83 25-91 (132)
38 PF04719 TAFII28: hTAFII28-lik 97.5 0.0008 1.7E-08 47.3 7.8 67 12-84 23-90 (90)
39 PF02969 TAF: TATA box binding 97.5 0.0012 2.7E-08 43.8 8.0 64 12-82 3-66 (66)
40 COG5247 BUR6 Class 2 transcrip 97.4 0.00075 1.6E-08 48.7 6.8 77 11-94 22-99 (113)
41 smart00414 H2A Histone 2A. 97.3 0.00086 1.9E-08 48.3 6.1 68 10-83 7-74 (106)
42 PTZ00017 histone H2A; Provisio 97.0 0.002 4.2E-08 48.4 5.7 68 10-83 25-92 (134)
43 PLN00154 histone H2A; Provisio 97.0 0.0028 6.2E-08 47.7 6.2 69 10-83 36-104 (136)
44 KOG1744 Histone H2B [Chromatin 96.9 0.004 8.7E-08 46.4 6.8 62 17-84 42-103 (127)
45 KOG1756 Histone 2A [Chromatin 96.9 0.003 6.4E-08 47.1 6.1 68 10-83 25-92 (131)
46 PF15510 CENP-W: Centromere ki 96.8 0.003 6.6E-08 44.9 4.9 66 12-83 16-95 (102)
47 PLN00153 histone H2A; Provisio 96.7 0.0038 8.3E-08 46.6 5.5 68 10-83 22-89 (129)
48 PLN00157 histone H2A; Provisio 96.7 0.0036 7.9E-08 46.9 5.4 68 10-83 24-91 (132)
49 PLN00156 histone H2AX; Provisi 96.7 0.005 1.1E-07 46.5 5.9 68 10-83 27-94 (139)
50 KOG1142 Transcription initiati 96.4 0.0058 1.3E-07 50.3 4.8 66 12-83 154-219 (258)
51 PF02269 TFIID-18kDa: Transcri 96.2 0.0053 1.1E-07 43.0 3.3 49 35-83 18-66 (93)
52 PF02291 TFIID-31kDa: Transcri 96.0 0.047 1E-06 40.6 7.5 68 36-103 29-97 (129)
53 KOG1658 DNA polymerase epsilon 95.9 0.0054 1.2E-07 47.2 2.4 70 11-87 58-128 (162)
54 PTZ00252 histone H2A; Provisio 95.6 0.044 9.5E-07 41.2 6.1 64 10-83 23-92 (134)
55 KOG3219 Transcription initiati 95.5 0.018 3.8E-07 45.8 3.9 71 11-88 111-182 (195)
56 cd07978 TAF13 The TATA Binding 94.8 0.14 3E-06 36.0 6.3 72 17-97 7-78 (92)
57 KOG4336 TBP-associated transcr 94.3 0.46 1E-05 40.3 9.2 65 36-102 22-86 (323)
58 KOG3423 Transcription initiati 93.4 0.6 1.3E-05 36.5 7.9 69 12-87 86-168 (176)
59 TIGR03015 pepcterm_ATPase puta 93.1 0.43 9.4E-06 37.3 6.9 74 13-86 192-268 (269)
60 KOG3334 Transcription initiati 92.2 0.8 1.7E-05 34.9 6.9 81 37-121 31-112 (148)
61 KOG2549 Transcription initiati 91.1 1.2 2.7E-05 40.4 8.0 67 14-87 13-79 (576)
62 PRK00411 cdc6 cell division co 90.3 1.8 4E-05 35.9 8.0 71 15-87 209-285 (394)
63 KOG2389 Predicted bromodomain 86.8 1.6 3.4E-05 37.6 5.3 69 12-87 29-97 (353)
64 TIGR02928 orc1/cdc6 family rep 84.1 6.6 0.00014 32.1 7.8 74 16-91 202-281 (365)
65 TIGR02902 spore_lonB ATP-depen 81.4 5.8 0.00013 35.4 6.9 66 16-86 266-334 (531)
66 PF13654 AAA_32: AAA domain; P 80.3 6.5 0.00014 35.2 6.8 49 36-84 447-506 (509)
67 PF08369 PCP_red: Proto-chloro 78.1 4.6 0.0001 24.6 3.7 42 38-80 2-44 (45)
68 TIGR00764 lon_rel lon-related 76.2 13 0.00029 33.8 7.7 50 36-85 330-392 (608)
69 COG1067 LonB Predicted ATP-dep 75.5 3.9 8.5E-05 37.8 4.1 49 36-85 338-400 (647)
70 cd04752 Commd4 COMM_Domain con 74.9 21 0.00045 27.3 7.4 60 48-114 43-103 (174)
71 COG5095 TAF6 Transcription ini 73.3 9.9 0.00021 33.0 5.7 53 35-87 21-73 (450)
72 PF13335 Mg_chelatase_2: Magne 73.1 17 0.00038 25.2 6.1 47 36-82 42-94 (96)
73 PF09114 MotA_activ: Transcrip 72.0 3.7 7.9E-05 29.2 2.4 38 16-54 51-88 (96)
74 PF02861 Clp_N: Clp amino term 71.2 8.3 0.00018 22.7 3.6 26 60-85 1-26 (53)
75 COG5162 Transcription initiati 69.2 34 0.00074 26.9 7.4 51 37-87 106-189 (197)
76 PRK09862 putative ATP-dependen 66.9 27 0.00059 31.4 7.3 61 35-95 437-503 (506)
77 KOG3901 Transcription initiati 65.9 23 0.0005 25.7 5.5 46 35-83 26-71 (109)
78 cd08045 TAF4 TATA Binding Prot 65.8 27 0.00059 27.3 6.5 76 11-90 43-125 (212)
79 PF12010 DUF3502: Domain of un 65.8 7.8 0.00017 28.3 3.2 61 40-104 73-133 (134)
80 TIGR02030 BchI-ChlI magnesium 65.0 23 0.00049 30.0 6.2 49 34-82 252-307 (337)
81 CHL00081 chlI Mg-protoporyphyr 63.8 23 0.0005 30.3 6.1 49 34-82 265-320 (350)
82 PRK00080 ruvB Holliday junctio 63.2 45 0.00097 27.3 7.6 72 13-88 180-254 (328)
83 KOG2680 DNA helicase TIP49, TB 62.9 28 0.0006 30.5 6.3 72 11-82 340-427 (454)
84 TIGR01128 holA DNA polymerase 61.8 57 0.0012 25.7 7.7 69 12-84 110-178 (302)
85 TIGR02442 Cob-chelat-sub cobal 61.7 28 0.00061 31.7 6.6 50 34-83 247-303 (633)
86 TIGR00635 ruvB Holliday juncti 59.7 44 0.00095 26.7 6.8 71 13-87 159-232 (305)
87 PF07647 SAM_2: SAM domain (St 58.4 17 0.00038 22.5 3.4 25 71-95 3-27 (66)
88 PRK13406 bchD magnesium chelat 58.2 29 0.00062 31.7 6.0 50 34-83 193-249 (584)
89 PRK12402 replication factor C 58.0 39 0.00084 27.1 6.2 71 12-88 183-253 (337)
90 PRK07452 DNA polymerase III su 57.6 41 0.00089 27.3 6.3 66 18-87 135-202 (326)
91 KOG1757 Histone 2A [Chromatin 56.9 15 0.00032 27.2 3.2 66 8-82 26-95 (131)
92 PF07733 DNA_pol3_alpha: Bacte 56.5 4.3 9.3E-05 35.5 0.4 46 78-129 31-76 (426)
93 PF03540 TFIID_30kDa: Transcri 56.3 49 0.0011 20.9 5.9 48 12-66 2-49 (51)
94 PRK13407 bchI magnesium chelat 55.8 45 0.00098 28.2 6.4 48 34-81 249-303 (334)
95 COG5248 TAF19 Transcription in 53.8 53 0.0011 24.2 5.7 48 34-83 25-72 (126)
96 COG1224 TIP49 DNA helicase TIP 53.7 33 0.00071 30.4 5.3 49 33-81 377-429 (450)
97 PF04552 Sigma54_DBD: Sigma-54 53.2 23 0.0005 27.0 3.9 84 5-106 53-152 (160)
98 cd00166 SAM Sterile alpha moti 52.5 17 0.00036 21.8 2.6 24 73-96 3-26 (63)
99 PF00536 SAM_1: SAM domain (St 52.3 23 0.00049 21.9 3.2 23 73-95 4-26 (64)
100 PF09123 DUF1931: Domain of un 51.6 22 0.00047 26.9 3.5 69 18-103 1-69 (138)
101 TIGR00368 Mg chelatase-related 51.3 44 0.00096 29.8 5.9 47 36-82 445-497 (499)
102 TIGR02031 BchD-ChlD magnesium 49.4 67 0.0014 29.2 6.9 50 34-83 201-257 (589)
103 PF07499 RuvA_C: RuvA, C-termi 48.8 14 0.0003 22.3 1.7 15 74-88 3-17 (47)
104 PRK13765 ATP-dependent proteas 48.1 37 0.00081 31.3 5.1 48 36-83 339-399 (637)
105 COG5251 TAF40 Transcription in 47.7 30 0.00064 27.4 3.8 64 12-82 115-179 (199)
106 PF12627 PolyA_pol_RNAbd: Prob 47.3 11 0.00023 23.5 1.1 58 35-96 2-63 (64)
107 COG1474 CDC6 Cdc6-related prot 47.3 92 0.002 26.6 7.1 61 35-95 210-276 (366)
108 PRK05574 holA DNA polymerase I 46.9 1.3E+02 0.0029 24.1 7.7 68 12-84 145-213 (340)
109 PF13405 EF-hand_6: EF-hand do 45.6 32 0.0007 18.3 2.8 26 60-85 5-31 (31)
110 PF00531 Death: Death domain; 44.9 51 0.0011 20.9 4.1 29 69-97 55-83 (83)
111 PF02361 CbiQ: Cobalt transpor 43.0 56 0.0012 24.5 4.7 61 35-101 94-166 (224)
112 PF00356 LacI: Bacterial regul 43.0 44 0.00096 20.2 3.4 35 8-51 6-40 (46)
113 PTZ00361 26 proteosome regulat 42.9 40 0.00087 29.6 4.3 32 53-84 393-424 (438)
114 smart00454 SAM Sterile alpha m 42.8 27 0.00059 21.0 2.5 26 71-96 3-28 (68)
115 PRK05898 dnaE DNA polymerase I 42.8 12 0.00025 36.4 1.0 46 78-129 262-307 (971)
116 TIGR01242 26Sp45 26S proteasom 42.8 43 0.00093 27.9 4.3 33 52-84 331-363 (364)
117 PRK07914 hypothetical protein; 41.7 70 0.0015 26.2 5.4 65 14-83 129-193 (320)
118 PRK03992 proteasome-activating 41.6 45 0.00097 28.4 4.3 35 52-86 340-374 (389)
119 PRK06826 dnaE DNA polymerase I 40.7 42 0.0009 33.2 4.4 46 78-129 326-371 (1151)
120 COG1724 Predicted RNA binding 40.7 24 0.00051 23.6 2.0 17 71-87 6-22 (66)
121 PF05236 TAF4: Transcription i 40.0 55 0.0012 26.4 4.4 75 9-86 40-120 (264)
122 PF09339 HTH_IclR: IclR helix- 39.9 19 0.00042 21.6 1.4 19 8-26 25-43 (52)
123 PRK02910 light-independent pro 39.3 70 0.0015 28.4 5.3 52 33-85 466-518 (519)
124 PRK05932 RNA polymerase factor 39.0 75 0.0016 28.1 5.4 88 5-110 347-450 (455)
125 smart00350 MCM minichromosome 38.8 94 0.002 27.5 6.0 69 12-84 417-504 (509)
126 TIGR02454 CbiQ_TIGR cobalt ABC 38.6 67 0.0014 24.0 4.5 35 70-104 112-157 (198)
127 COG1500 Predicted exosome subu 36.5 1.3E+02 0.0029 24.6 6.1 72 16-94 70-143 (234)
128 TIGR00594 polc DNA-directed DN 35.9 17 0.00037 35.3 1.0 46 78-129 330-375 (1022)
129 PF08823 PG_binding_2: Putativ 35.8 62 0.0013 21.6 3.5 30 74-103 18-53 (74)
130 PTZ00454 26S protease regulato 35.4 65 0.0014 27.8 4.4 32 53-84 355-386 (398)
131 TIGR01343 hacA_fam homoaconita 35.1 58 0.0012 28.7 4.0 29 100-132 75-104 (412)
132 PF00403 HMA: Heavy-metal-asso 34.6 39 0.00085 20.5 2.2 16 72-87 47-62 (62)
133 PRK09526 lacI lac repressor; R 34.2 60 0.0013 25.8 3.8 38 11-58 15-52 (342)
134 TIGR01278 DPOR_BchB light-inde 34.2 90 0.0019 27.7 5.2 51 34-85 460-511 (511)
135 smart00027 EH Eps15 homology d 34.1 1.1E+02 0.0024 20.4 4.6 28 60-87 15-42 (96)
136 PRK05673 dnaE DNA polymerase I 33.7 19 0.00041 35.4 0.9 46 78-129 326-371 (1135)
137 TIGR00170 leuC 3-isopropylmala 33.6 45 0.00097 29.8 3.2 19 113-132 96-114 (465)
138 KOG3537 Adaptor protein NUMB [ 33.3 25 0.00054 31.7 1.5 14 117-130 121-134 (543)
139 PRK06585 holA DNA polymerase I 32.9 1.5E+02 0.0033 24.2 6.1 65 15-83 144-209 (343)
140 PRK07135 dnaE DNA polymerase I 32.9 23 0.00051 34.3 1.4 46 78-129 260-305 (973)
141 KOG1528 Salt-sensitive 3'-phos 32.8 1.2E+02 0.0026 26.1 5.5 70 15-87 52-126 (351)
142 COG1508 RpoN DNA-directed RNA 32.7 1.9E+02 0.0042 25.8 6.9 88 6-110 335-438 (444)
143 PRK00440 rfc replication facto 31.8 1.5E+02 0.0032 23.4 5.7 67 13-85 161-227 (319)
144 PRK06920 dnaE DNA polymerase I 31.7 21 0.00045 35.1 0.8 46 78-129 311-356 (1107)
145 PRK07374 dnaE DNA polymerase I 31.6 21 0.00046 35.2 0.9 46 78-129 337-382 (1170)
146 PRK05807 hypothetical protein; 31.0 75 0.0016 23.3 3.6 20 84-103 96-115 (136)
147 PRK09532 DNA polymerase III su 30.9 23 0.0005 33.9 1.0 46 78-129 335-380 (874)
148 PRK07279 dnaE DNA polymerase I 30.7 22 0.00047 34.8 0.8 46 78-129 268-313 (1034)
149 TIGR02395 rpoN_sigma RNA polym 30.7 1.4E+02 0.0031 26.1 5.7 88 5-109 322-425 (429)
150 PRK14971 DNA polymerase III su 30.0 1.5E+02 0.0032 27.2 6.0 73 12-89 179-251 (614)
151 PF05385 Adeno_E4: Mastadenovi 29.5 77 0.0017 23.1 3.3 44 74-127 29-79 (109)
152 CHL00076 chlB photochlorophyll 29.2 1.3E+02 0.0028 26.8 5.4 51 34-85 461-512 (513)
153 PRK12469 RNA polymerase factor 29.1 1.6E+02 0.0036 26.3 5.9 89 5-110 373-476 (481)
154 PF08681 DUF1778: Protein of u 28.2 15 0.00033 24.6 -0.5 18 34-51 3-20 (80)
155 PF03484 B5: tRNA synthetase B 27.8 48 0.001 21.3 1.8 18 70-87 17-34 (70)
156 COG5094 TAF9 Transcription ini 27.8 2.7E+02 0.0058 21.0 6.5 82 36-121 31-116 (145)
157 smart00354 HTH_LACI helix_turn 27.5 1.1E+02 0.0023 19.5 3.4 36 8-52 7-42 (70)
158 COG2812 DnaX DNA polymerase II 27.3 2E+02 0.0042 26.2 6.1 71 12-87 177-247 (515)
159 COG1239 ChlI Mg-chelatase subu 27.3 1.2E+02 0.0026 27.0 4.6 50 34-83 265-321 (423)
160 COG1466 HolA DNA polymerase II 27.0 2.4E+02 0.0053 23.3 6.3 67 17-87 144-210 (334)
161 TIGR01764 excise DNA binding d 26.9 69 0.0015 17.9 2.3 37 8-44 8-45 (49)
162 smart00445 LINK Link (Hyaluron 26.9 98 0.0021 21.8 3.4 30 57-87 17-46 (94)
163 PF14434 Imm6: Immunity protei 26.3 2.6E+02 0.0056 20.4 6.7 39 55-94 25-65 (122)
164 cd00607 RNase_Sa RNase_Sa. Rib 26.3 50 0.0011 23.5 1.8 11 116-126 61-71 (95)
165 TIGR02639 ClpA ATP-dependent C 26.3 2.4E+02 0.0051 26.2 6.7 38 34-83 75-112 (731)
166 TIGR02903 spore_lon_C ATP-depe 26.2 1.7E+02 0.0038 26.7 5.7 72 16-91 356-437 (615)
167 TIGR02397 dnaX_nterm DNA polym 26.1 2E+02 0.0044 23.2 5.6 62 15-81 178-239 (355)
168 cd01102 Link_Domain The link d 26.1 96 0.0021 21.7 3.2 30 57-87 16-45 (92)
169 KOG3557 Epidermal growth facto 25.9 57 0.0012 30.7 2.5 33 87-119 281-315 (721)
170 PRK14964 DNA polymerase III su 25.6 1.9E+02 0.004 26.0 5.7 67 13-84 175-241 (491)
171 PRK10423 transcriptional repre 25.5 41 0.00089 26.5 1.4 40 8-57 5-44 (327)
172 PTZ00373 60S Acidic ribosomal 25.4 2.4E+02 0.0052 20.5 5.3 28 60-87 8-35 (112)
173 PF13499 EF-hand_7: EF-hand do 25.2 1.6E+02 0.0035 17.6 4.6 41 59-99 4-44 (66)
174 PLN00138 large subunit ribosom 24.8 2.5E+02 0.0054 20.3 5.3 28 60-87 6-33 (113)
175 KOG1792 Reticulon [Intracellul 24.6 3E+02 0.0065 22.3 6.2 52 34-85 114-166 (230)
176 PHA03328 nuclear egress lamina 24.6 1.1E+02 0.0025 26.1 3.9 37 52-88 260-296 (316)
177 TIGR01052 top6b DNA topoisomer 24.4 1.4E+02 0.0031 26.9 4.7 50 36-99 434-483 (488)
178 PRK05907 hypothetical protein; 24.2 2.4E+02 0.0051 23.5 5.8 49 34-82 151-201 (311)
179 TIGR02573 LcrG_PcrG type III s 24.2 1.5E+02 0.0032 21.0 3.8 34 91-124 49-82 (90)
180 cd01392 HTH_LacI Helix-turn-he 24.0 1.6E+02 0.0034 17.0 3.7 37 7-52 3-39 (52)
181 PF01972 SDH_sah: Serine dehyd 23.9 2.6E+02 0.0056 23.7 5.8 109 11-124 159-283 (285)
182 cd01585 AcnA_Bact Aconitase ca 23.8 39 0.00084 29.4 1.0 31 98-132 47-77 (380)
183 PF02718 Herpes_UL31: Herpesvi 23.8 1.3E+02 0.0028 25.0 4.0 32 68-102 222-253 (258)
184 PF07928 Vps54: Vps54-like pro 23.8 26 0.00057 25.9 0.0 36 65-100 61-97 (135)
185 cd00051 EFh EF-hand, calcium b 23.4 1.4E+02 0.0031 16.3 5.0 37 63-99 8-44 (63)
186 PRK08487 DNA polymerase III su 23.2 3.6E+02 0.0078 22.1 6.7 62 15-82 137-198 (328)
187 PRK14961 DNA polymerase III su 23.2 2.7E+02 0.0059 23.3 6.0 47 34-85 195-245 (363)
188 cd03521 Link_domain_KIAA0527_l 23.0 1.4E+02 0.0031 21.2 3.6 31 57-87 16-46 (95)
189 cd05833 Ribosomal_P2 Ribosomal 22.9 1.4E+02 0.003 21.4 3.7 28 60-87 6-33 (109)
190 TIGR02083 LEU2 3-isopropylmala 22.9 95 0.0021 27.4 3.3 31 99-132 76-107 (419)
191 cd03518 Link_domain_HAPLN_modu 22.8 1.4E+02 0.0031 21.0 3.6 30 57-87 16-45 (95)
192 PRK05672 dnaE2 error-prone DNA 22.8 38 0.00082 33.1 0.9 45 78-129 320-364 (1046)
193 COG4519 Uncharacterized protei 22.7 38 0.00083 23.8 0.6 19 73-91 38-57 (95)
194 PRK14958 DNA polymerase III su 22.5 2.5E+02 0.0054 25.1 5.9 72 12-88 177-248 (509)
195 PRK09111 DNA polymerase III su 22.5 2.4E+02 0.0053 25.8 5.9 65 13-82 191-255 (598)
196 PF10714 LEA_6: Late embryogen 22.4 72 0.0016 21.9 1.9 25 97-121 26-50 (79)
197 cd01582 Homoaconitase Homoacon 22.3 59 0.0013 28.2 1.9 30 99-132 47-76 (363)
198 PF11753 DUF3310: Protein of u 22.2 2.2E+02 0.0047 18.0 4.9 42 40-83 14-57 (60)
199 smart00874 B5 tRNA synthetase 22.1 82 0.0018 19.8 2.1 17 71-87 18-34 (71)
200 PF00543 P-II: Nitrogen regula 22.1 64 0.0014 22.1 1.7 17 73-89 9-25 (102)
201 PRK05629 hypothetical protein; 21.8 3.2E+02 0.007 22.2 6.1 48 34-82 143-190 (318)
202 PF01418 HTH_6: Helix-turn-hel 21.8 1.1E+02 0.0024 19.8 2.8 32 58-92 35-66 (77)
203 cd01581 AcnB Aconitate hydrata 21.5 1.3E+02 0.0028 26.8 3.8 17 112-132 86-102 (436)
204 COG1222 RPT1 ATP-dependent 26S 21.3 1.2E+02 0.0026 26.8 3.6 32 53-84 361-392 (406)
205 cd03515 Link_domain_TSG_6_like 21.2 1.8E+02 0.0038 20.5 3.8 30 57-87 16-45 (93)
206 PTZ00448 hypothetical protein; 21.1 5.7E+02 0.012 22.4 7.6 90 12-108 74-166 (373)
207 TIGR02849 spore_III_AD stage I 20.8 69 0.0015 22.9 1.7 38 35-74 35-72 (101)
208 PF11075 DUF2780: Protein of u 20.4 1.4E+02 0.0031 22.9 3.4 30 71-100 118-152 (163)
209 CHL00095 clpC Clp protease ATP 20.1 1.7E+02 0.0037 27.6 4.5 36 36-83 4-39 (821)
210 PLN03239 histone acetyltransfe 20.1 76 0.0016 27.5 2.1 35 69-103 293-333 (351)
211 TIGR02639 ClpA ATP-dependent C 20.1 1.6E+02 0.0035 27.3 4.3 23 59-81 11-33 (731)
212 PF11625 DUF3253: Protein of u 20.0 2.6E+02 0.0055 19.3 4.3 38 64-101 17-54 (83)
No 1
>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [Transcription]
Probab=100.00 E-value=2.2e-33 Score=212.96 Aligned_cols=97 Identities=27% Similarity=0.439 Sum_probs=90.4
Q ss_pred chhhcccchhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHCCC
Q 032845 7 VPEAEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDF 86 (132)
Q Consensus 7 ~~Ed~~LP~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~lgf 86 (132)
..+|-.||+|+|.||||+.||. +.+|||||++.+|+|+++||+|||++|++.|..++|||||++||||||..|||
T Consensus 27 reqDr~LPIANV~RIMK~~lP~-----naKIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIngdDllwAm~tLGF 101 (168)
T KOG0869|consen 27 REQDRFLPIANVSRIMKKALPA-----NAKISKDAKETVQECVSEFISFVTGEASEKCQREKRKTINGDDLLWAMSTLGF 101 (168)
T ss_pred chhhhhccHHHHHHHHHhcCCc-----ccccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCcccHHHHHHHHHHcCc
Confidence 3346799999999999999995 89999999999999999999999999999999999999999999999999999
Q ss_pred cccHHHHHHHHHHHHHHhhhhh
Q 032845 87 TEFVDPLRDSLDAKQIVSQKVV 108 (132)
Q Consensus 87 ~~y~~~l~~~l~~~k~~~q~~~ 108 (132)
++|+++|+.||.+||+...-+.
T Consensus 102 e~Y~eplkiyL~kYRe~e~e~~ 123 (168)
T KOG0869|consen 102 ENYAEPLKIYLQKYRELEGERG 123 (168)
T ss_pred HhHHHHHHHHHHHHHHHhhhcc
Confidence 9999999999999998644433
No 2
>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=99.95 E-value=1.7e-28 Score=184.70 Aligned_cols=95 Identities=29% Similarity=0.518 Sum_probs=90.3
Q ss_pred hhcccchhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHCCCcc
Q 032845 9 EAEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFTE 88 (132)
Q Consensus 9 Ed~~LP~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~lgf~~ 88 (132)
+++.||+|+|+++||+.||. +++|.+||+++|.+||.+||++|+++||++|..+.||||+++||++||+.|||.+
T Consensus 9 de~sLPkAtv~KmIke~lP~-----d~rvakeareliincCvEFI~liSsEAneic~~e~KKTIa~EHV~KALe~LgF~e 83 (156)
T KOG0871|consen 9 DELSLPKATVNKMIKEMLPK-----DVRVAKEARELIINCCVEFINLISSEANEICNKEAKKTIAPEHVIKALENLGFGE 83 (156)
T ss_pred ccccCcHHHHHHHHHHhCCc-----ccccchHHHHHHHHHHHHHHHHHHHHHHHHHhHHhcccCCHHHHHHHHHHcchHH
Confidence 67899999999999999995 8999999999999999999999999999999999999999999999999999999
Q ss_pred cHHHHHHHHHHHHHHhhhhh
Q 032845 89 FVDPLRDSLDAKQIVSQKVV 108 (132)
Q Consensus 89 y~~~l~~~l~~~k~~~q~~~ 108 (132)
|++.+.+.|++|+....+++
T Consensus 84 Yiee~~~vl~~~K~~~~~~~ 103 (156)
T KOG0871|consen 84 YIEEAEEVLENCKEEAKKRR 103 (156)
T ss_pred HHHHHHHHHHHHHHHHHHhh
Confidence 99999999999997666544
No 3
>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription]
Probab=99.95 E-value=1.9e-27 Score=181.71 Aligned_cols=102 Identities=37% Similarity=0.659 Sum_probs=95.4
Q ss_pred cchhhcccchhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHCC
Q 032845 6 VVPEAEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEID 85 (132)
Q Consensus 6 ~~~Ed~~LP~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~lg 85 (132)
..++++.||+|+|.||+|+.||+ +++.|||||+.+|+++|++|++|||+.|+++|+.++||||+++||++||+++|
T Consensus 4 eri~dl~lP~AiI~rlvke~l~E----~~vsisKeA~~Ai~raAtVFv~~Lts~s~e~A~~q~rKt~sadDVl~aL~Eie 79 (172)
T KOG0870|consen 4 ERIEDLNLPNAIITRLVKEVLPE----SNVSISKEARLAIARAATVFVIFLTSVSNEIAKDQKRKTISADDVLKALDEIE 79 (172)
T ss_pred hhHHHhhccHHHHHHHHHHhCcc----ccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCcccHHHHHHHHHHhc
Confidence 34579999999999999999996 46999999999999999999999999999999999999999999999999999
Q ss_pred CcccHHHHHHHHHHHHHHhhhhhhcC
Q 032845 86 FTEFVDPLRDSLDAKQIVSQKVVASN 111 (132)
Q Consensus 86 f~~y~~~l~~~l~~~k~~~q~~~~~~ 111 (132)
|.+|+++|+..|+.|+..++.++..+
T Consensus 80 fs~f~~plk~~Le~yk~~~k~Kk~~~ 105 (172)
T KOG0870|consen 80 FSSFVNPLKSALEAYKKAVKQKKLAK 105 (172)
T ss_pred hHHHhhHHHHHHHHHHHHHHHHHHhc
Confidence 99999999999999998887776543
No 4
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=99.91 E-value=5e-24 Score=157.53 Aligned_cols=101 Identities=31% Similarity=0.490 Sum_probs=93.1
Q ss_pred hhcccchhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHCCCcc
Q 032845 9 EAEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFTE 88 (132)
Q Consensus 9 Ed~~LP~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~lgf~~ 88 (132)
+.+.||+|+|.+++.+.||. +..++|||++.+++||.+||+.|+++||++|..+.+|||+++||++||+.|||.+
T Consensus 8 De~sLPKATVqKMvS~iLp~-----dl~ftKearei~in~cieFi~~lsseAne~ce~EaKKTIa~EHviKALenLef~e 82 (148)
T COG5150 8 DENSLPKATVQKMVSSILPK-----DLVFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHVIKALENLEFEE 82 (148)
T ss_pred ccccCcHHHHHHHHHHhccc-----cccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHhccHHH
Confidence 56799999999999999996 8899999999999999999999999999999999999999999999999999999
Q ss_pred cHHHHHHHHHHHHHHhhhhhhcCCCcc
Q 032845 89 FVDPLRDSLDAKQIVSQKVVASNPLFF 115 (132)
Q Consensus 89 y~~~l~~~l~~~k~~~q~~~~~~~~~~ 115 (132)
|++.+.+.+.+|+. .|+.+.++.-.+
T Consensus 83 yi~~~~e~~~n~k~-~qK~ke~k~sKF 108 (148)
T COG5150 83 YIESCMEEHENYKS-YQKQKESKISKF 108 (148)
T ss_pred HHHHHHHHHHHHHH-HHhhchhhhhHH
Confidence 99999999999994 566666655444
No 5
>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=99.77 E-value=2.2e-18 Score=112.72 Aligned_cols=64 Identities=41% Similarity=0.619 Sum_probs=58.2
Q ss_pred ccchhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHH
Q 032845 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAI 81 (132)
Q Consensus 12 ~LP~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL 81 (132)
.||.+.|.||||.. |+ ..+||+||..+|++|+++||.||+.+|++.|.+++||||+++||..||
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-PD-----VMRVSKEAVEAIAKAAEEFIQYLAKEANEIAQRDKRKTITYEDVAKAV 65 (65)
T ss_dssp SS-HHHHHHHHHHT-ST-----TSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEE-HHHHHHHH
T ss_pred CCChHHHHHHhccC-CC-----ccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHC
Confidence 59999999999999 74 679999999999999999999999999999999999999999999986
No 6
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=99.71 E-value=2.1e-17 Score=116.14 Aligned_cols=79 Identities=22% Similarity=0.333 Sum_probs=72.3
Q ss_pred cccchh-hcccchhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHH
Q 032845 4 EKVVPE-AEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIE 82 (132)
Q Consensus 4 ek~~~E-d~~LP~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~ 82 (132)
+++... +..||+++|.||||++.+ -+||.+|.+.|++++++|+..|+..|+++|.++|||||+++||..|++
T Consensus 10 r~~~~~~~~~Lp~apv~Ri~r~~~~-------~Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~DI~la~~ 82 (91)
T COG2036 10 RRYQRSTDLLLPKAPVRRILRKAGA-------ERVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLALK 82 (91)
T ss_pred HhhhhhhhhhcCchHHHHHHHHHhH-------HHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHH
Confidence 444444 569999999999999985 399999999999999999999999999999999999999999999999
Q ss_pred HCCCccc
Q 032845 83 EIDFTEF 89 (132)
Q Consensus 83 ~lgf~~y 89 (132)
.+|+..|
T Consensus 83 ~~~~~~~ 89 (91)
T COG2036 83 RLGRRIY 89 (91)
T ss_pred Hhccccc
Confidence 9999865
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=99.41 E-value=1.6e-12 Score=90.46 Aligned_cols=78 Identities=18% Similarity=0.217 Sum_probs=70.8
Q ss_pred ccchhhc-ccchhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 032845 5 KVVPEAE-ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (132)
Q Consensus 5 k~~~Ed~-~LP~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~ 83 (132)
|+..+.. .||++.|.||++... ..+||.|+.+.+.+...+|+..|..+|..+|++++||||+++||..||+.
T Consensus 5 ~~~~~~~~gi~k~~I~RLarr~G-------vkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~alkr 77 (85)
T cd00076 5 KVLRDNIKGITKPAIRRLARRGG-------VKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKR 77 (85)
T ss_pred HHHHHhhccCCHHHHHHHHHHcC-------cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHH
Confidence 5566665 699999999999983 67999999999999999999999999999999999999999999999999
Q ss_pred CCCccc
Q 032845 84 IDFTEF 89 (132)
Q Consensus 84 lgf~~y 89 (132)
.|-.-|
T Consensus 78 ~g~~~y 83 (85)
T cd00076 78 QGRTLY 83 (85)
T ss_pred CCCCcc
Confidence 996533
No 8
>PLN00035 histone H4; Provisional
Probab=99.37 E-value=3.2e-12 Score=91.75 Aligned_cols=76 Identities=20% Similarity=0.216 Sum_probs=69.6
Q ss_pred ccchhhc-ccchhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 032845 5 KVVPEAE-ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (132)
Q Consensus 5 k~~~Ed~-~LP~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~ 83 (132)
|++.+.. .||+++|.||++..- ..+||.|+.+.+.+..++|+..|..+|..+|++++||||+++||..||+.
T Consensus 21 k~~~d~i~~ipk~~IrRLARr~G-------vkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr 93 (103)
T PLN00035 21 KVLRDNIQGITKPAIRRLARRGG-------VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKR 93 (103)
T ss_pred HHHHhhhccCCHHHHHHHHHHcC-------cccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHH
Confidence 4556665 699999999999983 57999999999999999999999999999999999999999999999999
Q ss_pred CCCc
Q 032845 84 IDFT 87 (132)
Q Consensus 84 lgf~ 87 (132)
.|-.
T Consensus 94 ~g~~ 97 (103)
T PLN00035 94 QGRT 97 (103)
T ss_pred cCCc
Confidence 8854
No 9
>PTZ00015 histone H4; Provisional
Probab=99.29 E-value=1.7e-11 Score=87.83 Aligned_cols=78 Identities=18% Similarity=0.236 Sum_probs=69.8
Q ss_pred ccchhhc-ccchhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 032845 5 KVVPEAE-ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (132)
Q Consensus 5 k~~~Ed~-~LP~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~ 83 (132)
|+..+.. .||++.|.||++..- ..+||.|+.+.+.+..++|+..|..+|..+|++++||||+++||..||+.
T Consensus 22 k~~r~~i~gI~k~~IrRLarr~G-------vkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~AlKr 94 (102)
T PTZ00015 22 KVLRDNIRGITKGAIRRLARRGG-------VKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALKR 94 (102)
T ss_pred HHHhhcccCCCHHHHHHHHHHcC-------CccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHh
Confidence 4444544 799999999999983 67999999999999999999999999999999999999999999999999
Q ss_pred CCCccc
Q 032845 84 IDFTEF 89 (132)
Q Consensus 84 lgf~~y 89 (132)
.|-.-|
T Consensus 95 ~g~~~y 100 (102)
T PTZ00015 95 QGRTLY 100 (102)
T ss_pred cCCCCC
Confidence 886533
No 10
>smart00417 H4 Histone H4.
Probab=99.18 E-value=5.9e-11 Score=80.66 Aligned_cols=70 Identities=19% Similarity=0.209 Sum_probs=63.2
Q ss_pred cccchhhc-ccchhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHH
Q 032845 4 EKVVPEAE-ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKA 80 (132)
Q Consensus 4 ek~~~Ed~-~LP~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~A 80 (132)
.|++.+.. .||++.|.||++.+. .-+||.|+.+.+.+...+|+..|..+|..+|++++||||+++||..|
T Consensus 4 ~~~~~d~i~gI~k~~IrRLaRr~G-------vkRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~~a 74 (74)
T smart00417 4 KKVLRDNIQGITKPAIRRLARRGG-------VKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVYA 74 (74)
T ss_pred hHHHHhhhcCCCHHHHHHHHHHcC-------cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHheeC
Confidence 35666665 799999999999983 56999999999999999999999999999999999999999999643
No 11
>smart00428 H3 Histone H3.
Probab=99.13 E-value=2e-10 Score=82.72 Aligned_cols=76 Identities=21% Similarity=0.253 Sum_probs=68.5
Q ss_pred hhcccchhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHC
Q 032845 9 EAEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEI 84 (132)
Q Consensus 9 Ed~~LP~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~l 84 (132)
.++.+|+.+..|++++...+..++.+.+++.+|..+||++++.|+.-+...|+..|.+.||+||.+.|+..|..--
T Consensus 26 t~lLI~k~pF~RLVREI~~~~~~~~~~R~~~~Al~aLQeasE~ylv~lfeda~~~a~HAkRvTl~~kDi~La~rir 101 (105)
T smart00428 26 TDLLIRKAPFQRLVREIAQKFTTGVDLRFQSSAIMALQEAAEAYLVGLFEDTNLLAIHAKRVTIMPKDIQLARRIR 101 (105)
T ss_pred cccccccccHHHHHHHHHHHcCCCCCceeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccCcHhhHHHHHHHh
Confidence 4678999999999999998765434789999999999999999999999999999999999999999998886543
No 12
>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=99.11 E-value=4.2e-10 Score=74.47 Aligned_cols=64 Identities=22% Similarity=0.237 Sum_probs=60.2
Q ss_pred ccchhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHH
Q 032845 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIE 82 (132)
Q Consensus 12 ~LP~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~ 82 (132)
.||+++|.||++... --+||.|+...|.+-.+.|+.-|..+|...+++.+|||++++||-.||+
T Consensus 2 ~~p~~~i~ria~~~G-------i~ris~~a~~~l~~~~e~rl~~i~~~A~k~~~hakRktlt~~DI~~Alk 65 (65)
T smart00803 2 WLPKETIKDVAESLG-------IGNLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSALR 65 (65)
T ss_pred CCCHHHHHHHHHHCC-------CccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCeecHHHHHHHhC
Confidence 589999999999873 4589999999999999999999999999999999999999999999985
No 13
>cd07981 TAF12 TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of the seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs function such as serving as activator-bind
Probab=99.03 E-value=2.2e-09 Score=72.02 Aligned_cols=66 Identities=21% Similarity=0.218 Sum_probs=61.8
Q ss_pred cchhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHC
Q 032845 13 LPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEI 84 (132)
Q Consensus 13 LP~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~l 84 (132)
+++..+..++++.-| ..+++.||.++|++.+..|+.-++..|..+|++.||+||.++||..+|+..
T Consensus 2 ~~k~~l~~lv~~id~------~~~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~~~tv~~~Di~l~l~r~ 67 (72)
T cd07981 2 LTKRKLQELLKEIDP------REQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQLHLERN 67 (72)
T ss_pred CcHHHHHHHHHhhCC------CCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHh
Confidence 678889999999865 689999999999999999999999999999999999999999999999864
No 14
>PF00125 Histone: Core histone H2A/H2B/H3/H4 histone h2a signature histone h2b signature histone h3 signature histone h4 signature; InterPro: IPR007125 The core histones together with some other DNA binding proteins appear to form a superfamily defined by a common fold and distant sequence similarities [, ]. Some proteins contain local homology domains related to the histone fold [].; GO: 0003677 DNA binding; PDB: 2YFW_D 2YFV_B 1U35_H 2F8N_D 2PYO_D 2NQB_D 3AN2_C 3AZJ_C 3AV1_G 3AZM_G ....
Probab=99.02 E-value=1.3e-09 Score=72.29 Aligned_cols=71 Identities=18% Similarity=0.306 Sum_probs=63.9
Q ss_pred hcccchhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHH
Q 032845 10 AEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIE 82 (132)
Q Consensus 10 d~~LP~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~ 82 (132)
...+|+..|.|+.|+..++... ..+||++|..+|+..++.|+.-|...|...|.+.||+||++.||..|++
T Consensus 3 ~~~~~~~~~~r~~r~i~~~~~~--~~ris~~a~~~L~~~~E~~~~~il~~A~~~a~~~kR~tI~~~DI~~A~r 73 (75)
T PF00125_consen 3 RRLIPKFPFSRLLREIGEEILS--KYRISSEALVALQSVLEYLLVEILEEAGNLARHAKRKTITPRDIQLAVR 73 (75)
T ss_dssp SHSSSHHHHHHHHHHHHHTTSS--SSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTBSEEGHHHHHHHHH
T ss_pred ccccCceEEeeeeehhhccccc--ccccccccchhhhhhhhhhhhhhhhHHHHHHhhcCCcEecHHHHHHHHh
Confidence 4578999999999999874221 2799999999999999999999999999999999999999999999986
No 15
>PLN00160 histone H3; Provisional
Probab=98.79 E-value=1.7e-08 Score=71.86 Aligned_cols=74 Identities=22% Similarity=0.136 Sum_probs=66.4
Q ss_pred hhcccchhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 032845 9 EAEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (132)
Q Consensus 9 Ed~~LP~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~ 83 (132)
.++.+|+++..|++++...+..+ .+.+++.+|..+||++++.|+.-+...|+-.|.+.||.||.+.|+..|..-
T Consensus 18 t~lLI~k~pF~RLVREI~~~~~~-~~~Rfq~~Al~ALQeAsEayLv~lfed~~lca~HakRVTl~~kD~~L~~ri 91 (97)
T PLN00160 18 TDLLIRRLPFARLVREIQMEMSR-EAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTIMPKDMQLARRI 91 (97)
T ss_pred hhhhhccccHHHHHHHHHHHcCC-CCcEeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcccccchhhHHHHHHh
Confidence 46789999999999999875432 358999999999999999999999999999999999999999999888643
No 16
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=98.75 E-value=6.5e-09 Score=83.70 Aligned_cols=79 Identities=24% Similarity=0.423 Sum_probs=71.4
Q ss_pred cchhhcccchhHHHHHHhhhccCCCCCCcc-hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHC
Q 032845 6 VVPEAEELPKTIVRRVVKDKLHNCSPDTDI-SVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEI 84 (132)
Q Consensus 6 ~~~Ed~~LP~a~V~RimK~~Lp~~~~d~~~-~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~l 84 (132)
++.-++.||.|.|.|+||-.= ++ .||.||..++.+.++.||..||..|.-.|++++|+|+-..||-.|++..
T Consensus 103 ~~~k~h~LPlARIkkvMKtde-------dVkMisaEaPvlFak~~EiFI~ELTmRAW~~ae~NkRRtLQksDia~Av~kS 175 (286)
T COG5208 103 ILLKDHNLPLARIKKVMKTDE-------DVKMISAEAPVLFAKITEIFIEELTMRAWINAEENKRRTLQKSDIAAAVKKS 175 (286)
T ss_pred HHHHhccCcHHHHHHHHhccc-------chhheecccchHHHHHHHHHHHHHHHHHHHHHhHhhhhHHHHHHHHHHHHHH
Confidence 555677899999999998763 44 8999999999999999999999999999999999999999999999999
Q ss_pred CCcccHH
Q 032845 85 DFTEFVD 91 (132)
Q Consensus 85 gf~~y~~ 91 (132)
+..+|+-
T Consensus 176 eMfDFLi 182 (286)
T COG5208 176 EMFDFLI 182 (286)
T ss_pred HHHhHHh
Confidence 9777653
No 17
>PLN00161 histone H3; Provisional
Probab=98.72 E-value=3.9e-08 Score=73.65 Aligned_cols=74 Identities=23% Similarity=0.166 Sum_probs=66.5
Q ss_pred hhcccchhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 032845 9 EAEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (132)
Q Consensus 9 Ed~~LP~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~ 83 (132)
-++.+|+.++.|++++...+..+ .+++++.+|..+||++++.|+.-+...|+-.|.+.+|.||.+.|+..|..-
T Consensus 52 t~lLIpklPF~RLVREI~~~~~~-~~~Rfq~~Al~ALQEAsEayLV~lFeda~lcaiHAkRVTlm~kDm~La~ri 125 (135)
T PLN00161 52 TELLIRKLPFARLVREISNEMLR-EPFRWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMPKDMQLARRI 125 (135)
T ss_pred cccccccccHHHHHHHHHHhcCC-CCcEeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccchhhHHHHHHh
Confidence 36789999999999999876542 369999999999999999999999999999999999999999999888643
No 18
>PLN00121 histone H3; Provisional
Probab=98.68 E-value=4.2e-08 Score=73.57 Aligned_cols=72 Identities=25% Similarity=0.277 Sum_probs=66.3
Q ss_pred hhcccchhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHH
Q 032845 9 EAEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIE 82 (132)
Q Consensus 9 Ed~~LP~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~ 82 (132)
.++.+|+..+.|++++...++. .+++++.+|..+||++++.|+.-+...|+..|.+.+|.||.+.|+..|..
T Consensus 59 t~lLI~k~pF~RLVREI~~~~~--~~~Rf~~~Al~ALQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~r 130 (136)
T PLN00121 59 TELLIRKLPFQRLVREIAQDFK--TDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
T ss_pred cccccccccHHHHHHHHHHHhC--ccceeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcceecchhhHHHHHH
Confidence 4789999999999999987653 36899999999999999999999999999999999999999999988864
No 19
>PTZ00018 histone H3; Provisional
Probab=98.68 E-value=4.7e-08 Score=73.34 Aligned_cols=73 Identities=25% Similarity=0.261 Sum_probs=66.4
Q ss_pred hhcccchhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 032845 9 EAEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (132)
Q Consensus 9 Ed~~LP~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~ 83 (132)
.++.+|+..+.|++++...++. .+++++.+|..+||++++.|+.-+...++..|.+.+|.||.+.|+..|..-
T Consensus 59 t~lLI~k~pF~RLVREI~~~~~--~~~rf~~~al~aLQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~ri 131 (136)
T PTZ00018 59 TELLIRKLPFQRLVREIAQDFK--TDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRI 131 (136)
T ss_pred chhccccccHHHHHHHHHHHcC--CcceeeHHHHHHHHHHHHHHHHHHhhhhHHHHHhhcceecchhhHHHHHHh
Confidence 4789999999999999987643 368999999999999999999999999999999999999999999888643
No 20
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=98.57 E-value=5.7e-07 Score=60.73 Aligned_cols=66 Identities=21% Similarity=0.266 Sum_probs=58.8
Q ss_pred hhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHCCCc
Q 032845 15 KTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFT 87 (132)
Q Consensus 15 ~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~lgf~ 87 (132)
+-.|.+|++.+. --+++.+|.+.|.+....|+..|+..+..+|++.||+++++.||..||+++|+.
T Consensus 9 ~~~Vaqil~~~G-------f~~~~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~~~Dv~~Al~~~gi~ 74 (77)
T smart00576 9 RIAVAQILESAG-------FDSFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPNLGDVVLALENLGIS 74 (77)
T ss_pred HHHHHHHHHHcC-------ccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCcc
Confidence 345677777662 348999999999999999999999999999999999999999999999999974
No 21
>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=98.47 E-value=6e-07 Score=65.58 Aligned_cols=68 Identities=13% Similarity=0.170 Sum_probs=62.2
Q ss_pred hcccchhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 032845 10 AEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (132)
Q Consensus 10 d~~LP~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~ 83 (132)
-+.||.+.|.|+||+.-. ..+||.+|...|..+.+-+...|...|...|.+.+|++|+++||..|+..
T Consensus 18 gL~fPV~ri~R~Lk~~~~------a~RVs~~A~VyLaAvLEYL~aEIlelA~n~ak~~k~krItp~hi~lAi~n 85 (115)
T cd00074 18 GLQFPVGRIHRYLKKGRY------AERVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKKRITPRHLQLAVRN 85 (115)
T ss_pred CccCcHHHHHHHHHcCcc------ccccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEcHHHHHHHHhc
Confidence 468999999999998532 57999999999999999999999999999999999999999999999875
No 22
>KOG1657 consensus CCAAT-binding factor, subunit C (HAP5) [Transcription]
Probab=98.34 E-value=6.3e-07 Score=72.58 Aligned_cols=73 Identities=22% Similarity=0.421 Sum_probs=66.5
Q ss_pred cccchhHHHHHHhhhccCCCCCCcc-hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHCCCccc
Q 032845 11 EELPKTIVRRVVKDKLHNCSPDTDI-SVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFTEF 89 (132)
Q Consensus 11 ~~LP~a~V~RimK~~Lp~~~~d~~~-~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~lgf~~y 89 (132)
..||++.|.+|||..= ++ +|+.||..++.++|+.||..|+..|+..+...+|+|+...|+-.|+..-+-.+|
T Consensus 73 ~~lPlaRiKkimK~de-------dv~mI~~Eapvl~aka~E~Fi~elt~~sw~~Tee~~rrtl~~sdia~av~~s~~fdF 145 (236)
T KOG1657|consen 73 HILPLARIKKIMKSDE-------DVSMITAEAPVLFAKACELFITELTLRSWVHTEENKRRTLQKSDIAAAVTQSETFDF 145 (236)
T ss_pred ccCcHhhccccccccc-------cccccchhHHHHHHHHHHHHHHHHHHHhhhhhcccccccchHHHHHHHhccCCCccc
Confidence 4799999999999872 33 999999999999999999999999999999999999999999999999885554
Q ss_pred H
Q 032845 90 V 90 (132)
Q Consensus 90 ~ 90 (132)
+
T Consensus 146 L 146 (236)
T KOG1657|consen 146 L 146 (236)
T ss_pred e
Confidence 4
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=98.33 E-value=4.7e-06 Score=60.78 Aligned_cols=81 Identities=19% Similarity=0.143 Sum_probs=67.7
Q ss_pred hHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHCCCcccHHH-HH
Q 032845 16 TIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFTEFVDP-LR 94 (132)
Q Consensus 16 a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~lgf~~y~~~-l~ 94 (132)
..|.+|+|+. |..+++.++...|.+.+..+..-|..+|..+|+++||+||+++||.-|++..+-..|.++ -+
T Consensus 5 ~~v~~iLk~~-------Gv~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r~~~~f~~~p~~ 77 (117)
T cd07979 5 RVIAAILKSM-------GITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRVDYSFTSPPPR 77 (117)
T ss_pred HHHHHHHHHC-------CCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhccCCCCCCcH
Confidence 3577777776 246899999999999999999999999999999999999999999999998887666644 56
Q ss_pred HHHHHHHHH
Q 032845 95 DSLDAKQIV 103 (132)
Q Consensus 95 ~~l~~~k~~ 103 (132)
++|-+.-..
T Consensus 78 ~~l~~~a~~ 86 (117)
T cd07979 78 DFLLELARE 86 (117)
T ss_pred HHHHHHHHH
Confidence 666655533
No 24
>KOG3467 consensus Histone H4 [Chromatin structure and dynamics]
Probab=98.15 E-value=1.1e-05 Score=56.88 Aligned_cols=77 Identities=19% Similarity=0.213 Sum_probs=67.8
Q ss_pred cccchhhc-ccchhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHH
Q 032845 4 EKVVPEAE-ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIE 82 (132)
Q Consensus 4 ek~~~Ed~-~LP~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~ 82 (132)
.|+++++. .+.+-+|.||.+..- --+|+--.-+-+...+.+|+..+-+.|..++++++||||++-||+-+|+
T Consensus 20 RK~LsDnIqgitKpaIRRlARr~G-------VkRi~G~~yeE~~~~~k~fl~n~i~~A~~yt~HAKRKTvT~~dvv~~LK 92 (103)
T KOG3467|consen 20 RKVLRDNIQGITKPAIRRLARRGG-------VKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALK 92 (103)
T ss_pred HHHHHhhccccchHHHHHHHHhcC-------cchhchhhHHHHHHHHHHHHHHHHHHHHHHHhhhhhceeeHHHHHHHHH
Confidence 46677776 578889999998873 3488888888999999999999999999999999999999999999999
Q ss_pred HCCCc
Q 032845 83 EIDFT 87 (132)
Q Consensus 83 ~lgf~ 87 (132)
..|..
T Consensus 93 R~G~~ 97 (103)
T KOG3467|consen 93 RQGRT 97 (103)
T ss_pred HcCce
Confidence 99854
No 25
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=98.07 E-value=2.1e-05 Score=53.69 Aligned_cols=63 Identities=21% Similarity=0.289 Sum_probs=52.6
Q ss_pred HHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 032845 17 IVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (132)
Q Consensus 17 ~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~ 83 (132)
+|.||+.+... +.++.+|+.+..+|.+.+-.++..++..--..|+|+||+||+++||+-..++
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 TVGKIVEEEAK----EKGVEVSPQFIAALTELVYKQLENLAKDLEAFAKHAGRSTINMDDVKLLARR 72 (76)
T ss_dssp HHHHHHHHCCC----CTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHTTT
T ss_pred HHHHHHHHHHh----ccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHHHhhc
Confidence 57888888753 2479999999999999999999999999999999999999999999977654
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=98.07 E-value=1.8e-05 Score=66.67 Aligned_cols=67 Identities=15% Similarity=0.213 Sum_probs=59.5
Q ss_pred chhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHCCCc
Q 032845 14 PKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFT 87 (132)
Q Consensus 14 P~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~lgf~ 87 (132)
|..+|.-+++.. |.-++|+||..+|.+.++.++..|+.+|...+.+.||||++++||-.||+.++.+
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 456666677665 2349999999999999999999999999999999999999999999999998876
No 27
>PF15511 CENP-T: Centromere kinetochore component CENP-T; PDB: 3B0D_T 3B0C_T 3VH5_T 3VH6_T.
Probab=98.06 E-value=1.1e-05 Score=69.69 Aligned_cols=65 Identities=25% Similarity=0.404 Sum_probs=48.0
Q ss_pred cccchhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHH
Q 032845 11 EELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAED 76 (132)
Q Consensus 11 ~~LP~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eD 76 (132)
-.||.+.|+|++...... +...+++|+|||..+|.+|...|...|+..--.+|+|+|||||..+|
T Consensus 350 P~lP~~~vK~la~~~ak~-s~~sK~kiskdal~aleqasdwfFeQl~dDL~aYA~HAgRKTIdesD 414 (414)
T PF15511_consen 350 PSLPPGVVKKLAQHFAKS-SGGSKMKISKDALEALEQASDWFFEQLGDDLEAYAKHAGRKTIDESD 414 (414)
T ss_dssp --S-HHHHHHHHHHHH--------S-B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHH
T ss_pred CCCCccHHHHHHHHHHHh-hcccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCCCC
Confidence 368999999988777531 11236899999999999999999999999999999999999999887
No 28
>smart00427 H2B Histone H2B.
Probab=98.01 E-value=3.8e-05 Score=54.00 Aligned_cols=67 Identities=16% Similarity=0.231 Sum_probs=59.6
Q ss_pred hHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHCCCcc
Q 032845 16 TIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFTE 88 (132)
Q Consensus 16 a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~lgf~~ 88 (132)
.-|.|+.|+.-| +..||..|...+.--...+..-|+.+|...+.-.+|+||++.+|..|.+-+==++
T Consensus 5 ~Yi~kvLKqVhp------d~giS~kam~imnSfvnDiferIa~EAs~L~~~nkr~TltsreIqtAvrl~Lpge 71 (89)
T smart00427 5 IYIYKVLKQVHP------DTGISSKAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRLILPGE 71 (89)
T ss_pred HHHHHHHHHhCC------CccccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHHccHH
Confidence 358999999988 5789999999999999999999999999999999999999999999987664333
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=97.97 E-value=8.2e-05 Score=49.80 Aligned_cols=52 Identities=25% Similarity=0.341 Sum_probs=50.4
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHCCCc
Q 032845 36 SVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFT 87 (132)
Q Consensus 36 ~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~lgf~ 87 (132)
.++..|.+.|...+..|+..|++.+..+|.+.+|...+..||..||+++|+.
T Consensus 23 ~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~~~gi~ 74 (77)
T PF07524_consen 23 SASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPNLQDVEQALEEMGIS 74 (77)
T ss_pred ccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCC
Confidence 7999999999999999999999999999999999999999999999999984
No 30
>KOG1745 consensus Histones H3 and H4 [Chromatin structure and dynamics]
Probab=97.94 E-value=5.6e-06 Score=62.20 Aligned_cols=76 Identities=22% Similarity=0.222 Sum_probs=66.2
Q ss_pred hhhcccchhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHCC
Q 032845 8 PEAEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEID 85 (132)
Q Consensus 8 ~Ed~~LP~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~lg 85 (132)
..|+.+++.+..|++++..+.-. .++++.++|..+||++++.|+.-|.-.+|-.|.+.||.||-+.||--|..--|
T Consensus 59 stdLlI~K~PFqRlvrei~q~f~--~dLrfqs~Ai~ALQeA~EayLv~LfEdtnlcAihAkRVTimpkdiQlArrirg 134 (137)
T KOG1745|consen 59 STDLLIRKLPFQRLVREIAQDFK--TDLRFQSSAIAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRG 134 (137)
T ss_pred hhHHHhhcCcHHHHhHHHHhccc--ccceehHHHHHHHHHHHHHHHHHhccccchhhhccceeEecccceehhhhccc
Confidence 35788999999999997665422 27899999999999999999999999999999999999999999988876443
No 31
>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=97.89 E-value=0.00011 Score=48.97 Aligned_cols=63 Identities=22% Similarity=0.222 Sum_probs=51.5
Q ss_pred hhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 032845 15 KTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (132)
Q Consensus 15 ~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~ 83 (132)
+..+..++++.-| +..+..|+.++|.+.|..||.-+++.|-..|++-|-.|+...||.-.|++
T Consensus 2 K~~l~~Lv~~iDp------~~~ld~~vee~Ll~laddFv~~v~~~ac~lAKhR~s~tle~~Dv~~~Ler 64 (68)
T PF03847_consen 2 KRKLQELVKQIDP------NEKLDPDVEELLLELADDFVDDVVSFACRLAKHRKSSTLEVKDVQLHLER 64 (68)
T ss_dssp HHHHHHHHHCC-S------S----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHHH
T ss_pred hHHHHHHHHHcCC------CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCHHHHHHHHHh
Confidence 4567888999865 68999999999999999999999999999999999999999999998875
No 32
>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=97.84 E-value=3.8e-05 Score=51.86 Aligned_cols=65 Identities=22% Similarity=0.378 Sum_probs=54.0
Q ss_pred chhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCc-cCHHHHHHHHH
Q 032845 14 PKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQT-INAEDVLKAIE 82 (132)
Q Consensus 14 P~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKT-I~~eDVl~AL~ 82 (132)
|+.+|.||++....+ .+++||+||..++++....|+..-...|.+.+..++..+ |..+|+-+.+-
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 PPELIARLLHEHFKD----DKTKISKDALKLSAEYLRIFVREAVARAAEQAEAEGDEGFLEVEHLEKILP 66 (72)
T ss_dssp -CHHHHHHHCTTSSS----TT-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSEE-HHHHHHHCH
T ss_pred ChHHHHHHHHHHhcC----CCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHH
Confidence 889999999987753 579999999999999999999999999999999999888 99999877543
No 33
>PLN00158 histone H2B; Provisional
Probab=97.80 E-value=0.00013 Score=53.46 Aligned_cols=68 Identities=16% Similarity=0.224 Sum_probs=60.4
Q ss_pred hhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHCCCcc
Q 032845 15 KTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFTE 88 (132)
Q Consensus 15 ~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~lgf~~ 88 (132)
..-|.|+.|++-| +..||..|...|.--...+..-|+.+|...+.-.+|+||++.+|..|++-+==++
T Consensus 30 ~~YI~kVLKQVhP------d~gIS~kaM~ImnSfvnDiferIA~EAs~La~~nkr~TltsrEIqtAvrLvLpgE 97 (116)
T PLN00158 30 KIYIYKVLKQVHP------DTGISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVRLILPGE 97 (116)
T ss_pred HHHHHHHHHHhCC------CCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHhccHH
Confidence 3569999999988 5779999999999999999999999999999999999999999999987664333
No 34
>PTZ00463 histone H2B; Provisional
Probab=97.78 E-value=0.00015 Score=53.25 Aligned_cols=66 Identities=17% Similarity=0.256 Sum_probs=59.0
Q ss_pred HHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHCCCcc
Q 032845 17 IVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFTE 88 (132)
Q Consensus 17 ~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~lgf~~ 88 (132)
-|.|++|+.-| +..||..|...|+--......-|+.+|...|.-.+|+||++.+|..|++-+==++
T Consensus 33 YI~KVLKqVhP------d~gIS~kaM~ImnSfvnDifErIA~EAs~La~~nkr~TltsrEIQtAvrLlLpGE 98 (117)
T PTZ00463 33 YIFKVLKQVHP------DTGISRKSMNIMNSFLVDTFEKIATEASRLCKYTRRDTLSSREIQTAIRLVLPGE 98 (117)
T ss_pred HHHHHHHhhCC------CCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHhhcccHH
Confidence 48999999988 5779999999999999999999999999999999999999999999987664333
No 35
>KOG1659 consensus Class 2 transcription repressor NC2, alpha subunit (DRAP1) [Transcription]
Probab=97.77 E-value=0.00013 Score=58.51 Aligned_cols=75 Identities=15% Similarity=0.334 Sum_probs=68.0
Q ss_pred ccchhHHHHHHhhhccCCCCCCcc-hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHCCCcccH
Q 032845 12 ELPKTIVRRVVKDKLHNCSPDTDI-SVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFTEFV 90 (132)
Q Consensus 12 ~LP~a~V~RimK~~Lp~~~~d~~~-~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~lgf~~y~ 90 (132)
.||.+.|.|||...= ++ +|+.-....+.++.+.|+.-|-..+.+++...+-||||++|+..++..-.-.+|+
T Consensus 13 rfp~aRiKKIMQ~dE-------dIGKvaqavPViisralElFl~~l~~~t~~~t~~~~aKt~s~~hlkq~v~~~~~FdFL 85 (224)
T KOG1659|consen 13 RFPPARIKKIMQSDE-------DIGKVAQAVPVIISRALELFLESLLQKTLEITRSRGAKTVSSSHLKQAVESDPKFDFL 85 (224)
T ss_pred cCCHHHHHHHHhhhh-------hhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhcCccccCHHHHHHHHhccchhHHH
Confidence 699999999997652 44 8999999999999999999999999999999999999999999999998877777
Q ss_pred HHH
Q 032845 91 DPL 93 (132)
Q Consensus 91 ~~l 93 (132)
..+
T Consensus 86 k~~ 88 (224)
T KOG1659|consen 86 KEV 88 (224)
T ss_pred HHH
Confidence 663
No 36
>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=97.76 E-value=0.00019 Score=49.78 Aligned_cols=66 Identities=18% Similarity=0.368 Sum_probs=60.5
Q ss_pred ccchhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC---CccCHHHHHHHHHHC
Q 032845 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKR---QTINAEDVLKAIEEI 84 (132)
Q Consensus 12 ~LP~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kR---KTI~~eDVl~AL~~l 84 (132)
.||++.|.|+|...++ ..++.+...+|.-.+.+||--|..+|.++..+.+. ..|.|+||-.|.+.|
T Consensus 16 ~f~k~~iKr~~~~~~~-------~~v~~~v~i~v~glaKvFVGeivE~A~~V~~~~~~~~~~Pl~P~HireA~rrl 84 (85)
T cd08048 16 SFPKAAIKRLIQSVTG-------QSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGEANTGPLQPRHLREAYRRL 84 (85)
T ss_pred hccHHHHHHHHHHHcC-------CCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCCCCCcHHHHHHHHHh
Confidence 5999999999999983 67999999999999999999999999999987665 789999999999876
No 37
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=97.58 E-value=0.00019 Score=53.07 Aligned_cols=67 Identities=15% Similarity=0.188 Sum_probs=59.2
Q ss_pred cccchhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 032845 11 EELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (132)
Q Consensus 11 ~~LP~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~ 83 (132)
+.+|...|.|+||..- ..+||+++|...+.-|.+=.+..|+.-|-..|...++|.|.|.|+-.|+..
T Consensus 25 l~fpvgrvkr~lk~~~------~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~kkkri~PrHlqlAIrn 91 (132)
T COG5262 25 LIFPVGRVKRLLKKGN------YRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRIIPRHLQLAIRN 91 (132)
T ss_pred ccccHHHHHHHHHcCc------cceeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhcCcceechHHHHHHhcC
Confidence 5799999999999542 379999999999999988888888888888899999999999999999864
No 38
>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=97.49 E-value=0.0008 Score=47.30 Aligned_cols=67 Identities=16% Similarity=0.363 Sum_probs=51.5
Q ss_pred ccchhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC-ccCHHHHHHHHHHC
Q 032845 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQ-TINAEDVLKAIEEI 84 (132)
Q Consensus 12 ~LP~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRK-TI~~eDVl~AL~~l 84 (132)
.||++.|.|||...++ +..+|.....++.-.+..|+-.|-.+|.++....+.. .|.|.|+-.|.+.|
T Consensus 23 ~~~k~~ikkli~~~~~------~qsv~~~v~i~v~g~aKvFVGEiVE~A~~Vq~~~~~~~pl~P~hlreA~rrL 90 (90)
T PF04719_consen 23 SFNKAAIKKLINQVLG------NQSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGETGPLQPDHLREAYRRL 90 (90)
T ss_dssp ---HHHHHHHHHHHHS-------S---HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SS--HHHHHHHHHHH
T ss_pred cCCHHHHHHHHHHHcC------CCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcHHHHHHHHhC
Confidence 6999999999999984 4789999999999999999999999999999865533 79999999998765
No 39
>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=97.46 E-value=0.0012 Score=43.84 Aligned_cols=64 Identities=16% Similarity=0.232 Sum_probs=48.9
Q ss_pred ccchhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHH
Q 032845 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIE 82 (132)
Q Consensus 12 ~LP~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~ 82 (132)
.+|..+|.-+.... |-..++.|+...|.+=++--|..|..+|.....+.+|++++++||-.||+
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 46777877666544 23389999999999999999999999999999999999999999999985
No 40
>COG5247 BUR6 Class 2 transcription repressor NC2, alpha subunit (DRAP1 homolog) [Transcription]
Probab=97.40 E-value=0.00075 Score=48.74 Aligned_cols=77 Identities=12% Similarity=0.241 Sum_probs=66.3
Q ss_pred cccchhHHHHHHhhhccCCCCCCcc-hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHCCCccc
Q 032845 11 EELPKTIVRRVVKDKLHNCSPDTDI-SVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFTEF 89 (132)
Q Consensus 11 ~~LP~a~V~RimK~~Lp~~~~d~~~-~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~lgf~~y 89 (132)
..+|.|.|.|||.-.- ++ +|+.-......++.+.|+..|-..+-+.|...+-|.|+.+++..|.+.-.=.+|
T Consensus 22 trFP~ar~KkIMQ~de-------DiGKV~q~tPVIaskalE~Fl~~iv~~s~k~aR~~~skR~t~e~lk~a~~sdekFdF 94 (113)
T COG5247 22 TRFPIARLKKIMQLDE-------DIGKVGQSTPVIASKALEMFLTEIVGLSLKEARKKSSKRMTSEFLKRATESDEKFDF 94 (113)
T ss_pred hcCCHHHHHHHHHhhh-------hhhhhhhcchHHHHHHHHHHHHHHHHHHHHHHHhccchhhHHHHHHHHHhhhHHHHH
Confidence 4799999999996542 44 899999999999999999999999999999999999999999999887665556
Q ss_pred HHHHH
Q 032845 90 VDPLR 94 (132)
Q Consensus 90 ~~~l~ 94 (132)
+..+.
T Consensus 95 L~~~~ 99 (113)
T COG5247 95 LKNME 99 (113)
T ss_pred HHHHH
Confidence 54443
No 41
>smart00414 H2A Histone 2A.
Probab=97.29 E-value=0.00086 Score=48.34 Aligned_cols=68 Identities=13% Similarity=0.194 Sum_probs=59.1
Q ss_pred hcccchhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 032845 10 AEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (132)
Q Consensus 10 d~~LP~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~ 83 (132)
.+.||.+.|.|+||+.-- ..+|+..|...|.-+.+=+...|-..|-..|...+++.|+++|+..|+..
T Consensus 7 gL~fPVgRi~r~Lk~~~~------~~Rv~~~A~VyLaAvLEYLtaEILeLagn~a~~~k~~rItp~hi~lAi~n 74 (106)
T smart00414 7 GLQFPVGRIHRLLRKGTY------AKRVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKRRITPRHLQLAIRN 74 (106)
T ss_pred CccCchHHHHHHHHcCcc------ccccccccHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchHHHhhhccC
Confidence 478999999999998742 46999999999998887777777777888899999999999999999876
No 42
>PTZ00017 histone H2A; Provisional
Probab=96.99 E-value=0.002 Score=48.42 Aligned_cols=68 Identities=18% Similarity=0.188 Sum_probs=58.8
Q ss_pred hcccchhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 032845 10 AEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (132)
Q Consensus 10 d~~LP~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~ 83 (132)
-+.||.+.|.|+||+.-- ..+|+..|...|.-+.+-+...|...|-..|.+.+++-|+|.||..|+..
T Consensus 25 gL~FPVgRi~R~Lk~g~~------a~RV~a~A~VYLAAVLEYLtaEILELAgNaa~d~kk~RItPrHi~lAI~n 92 (134)
T PTZ00017 25 GLQFPVGRVHRYLKKGRY------AKRVGAGAPVYLAAVLEYLTAEVLELAGNAAKDNKKKRITPRHIQLAIRN 92 (134)
T ss_pred CcccchHHHHHHHhccch------hccccccchhhhHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHhhccC
Confidence 478999999999998642 46999999999998888777777778888889999999999999999854
No 43
>PLN00154 histone H2A; Provisional
Probab=96.95 E-value=0.0028 Score=47.66 Aligned_cols=69 Identities=16% Similarity=0.148 Sum_probs=55.6
Q ss_pred hcccchhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 032845 10 AEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (132)
Q Consensus 10 d~~LP~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~ 83 (132)
-+.||.+.|.|++|+.... ..+|+..|...|.-..+=+...|...|-..|.+.+++-|++.||..|+..
T Consensus 36 gL~FPVgRi~r~Lk~g~~~-----~~RVga~ApVYLAAVLEYLtAEVLELAGNaA~d~kk~RItPrHi~lAIrn 104 (136)
T PLN00154 36 GLQFPVGRIHRQLKQRVSA-----HGRVGATAAVYTAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRG 104 (136)
T ss_pred CccCchHHHHHHHHhhhhh-----ccccccchHHHHHHHHHHHHHHHHHHHHHHHHhhCCceecHHHhhhhccC
Confidence 4789999999999997521 46999999999887765555555556667788899999999999999864
No 44
>KOG1744 consensus Histone H2B [Chromatin structure and dynamics]
Probab=96.93 E-value=0.004 Score=46.36 Aligned_cols=62 Identities=18% Similarity=0.279 Sum_probs=56.2
Q ss_pred HHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHC
Q 032845 17 IVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEI 84 (132)
Q Consensus 17 ~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~l 84 (132)
.|.|++|++-| +..||..|..++.--...++..|+++|...+.-.+|.||+..+|..|.+-+
T Consensus 42 yv~kvlk~Vhp------d~gis~~a~~vmnsf~ndife~iA~ea~rla~y~krstisSreiqta~rLl 103 (127)
T KOG1744|consen 42 YVYKVLKQVHP------DLGISSKAMGVMNSFVNDIFERIASEAGRLAHYNKRSTISSREIQTAVRLL 103 (127)
T ss_pred ehhhhhhcccC------CCCcCHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCcccHHHHHHHHHHh
Confidence 46778999887 466999999999999999999999999999999999999999999997755
No 45
>KOG1756 consensus Histone 2A [Chromatin structure and dynamics]
Probab=96.92 E-value=0.003 Score=47.14 Aligned_cols=68 Identities=13% Similarity=0.189 Sum_probs=51.8
Q ss_pred hcccchhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 032845 10 AEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (132)
Q Consensus 10 d~~LP~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~ 83 (132)
.+.+|.+.|.|++|+.= -..+|+.+|...+.-+.+=....|+..|-..+..+++.-|+|.||..|+..
T Consensus 25 gl~fPvgri~r~Lr~~~------~~~ri~~gapV~laavLeYL~Aeile~agnaardnkk~ri~PrH~~lAI~N 92 (131)
T KOG1756|consen 25 GLQFPVGRIHRLLRKGR------YAQRVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRITPRHLQLAIRN 92 (131)
T ss_pred ccccCHHHHHHHHHccc------hhhhccCCChHHHHHHHHHHHHHHHHHhHHHhhhcCccccChHHHHHHHhC
Confidence 46899999999999942 257999999999995544333444444445566778888999999999874
No 46
>PF15510 CENP-W: Centromere kinetochore component W
Probab=96.79 E-value=0.003 Score=44.85 Aligned_cols=66 Identities=26% Similarity=0.342 Sum_probs=54.8
Q ss_pred ccchhHHHHHHhhhccCCCCCCcchhhHHHHHH--------------HHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHH
Q 032845 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLA--------------FCESARIFIHYLSATANDICKESKRQTINAEDV 77 (132)
Q Consensus 12 ~LP~a~V~RimK~~Lp~~~~d~~~~ISkDA~~a--------------l~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDV 77 (132)
.-|++.+.|++|..-| ..++....-.+ +.-.|-.|++-|+-||...|=.++=.||.++||
T Consensus 16 kaPrgfLkrv~Kr~Kp------hlRl~~~~Dllv~~~~f~~~~~~~~vhLncLLFvhrLAEEaRtnA~EnK~~~Ik~~Hv 89 (102)
T PF15510_consen 16 KAPRGFLKRVFKRQKP------HLRLETSGDLLVRFCPFSGWQWGGEVHLNCLLFVHRLAEEARTNACENKCGTIKKEHV 89 (102)
T ss_pred hCchHHHHHHHHhcCC------ceeecccccHHHhhcccccccccceeehhHHHHHHHHHHHHHHHHHHHhhccccHHHH
Confidence 5799999999998877 45665554444 566788999999999999999999999999999
Q ss_pred HHHHHH
Q 032845 78 LKAIEE 83 (132)
Q Consensus 78 l~AL~~ 83 (132)
+.|-+.
T Consensus 90 ~AaaKv 95 (102)
T PF15510_consen 90 LAAAKV 95 (102)
T ss_pred HHHHHH
Confidence 998654
No 47
>PLN00153 histone H2A; Provisional
Probab=96.75 E-value=0.0038 Score=46.60 Aligned_cols=68 Identities=13% Similarity=0.157 Sum_probs=57.6
Q ss_pred hcccchhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 032845 10 AEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (132)
Q Consensus 10 d~~LP~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~ 83 (132)
-+.||.+.|.|++|+.-. ..+|+..|...|.-+.+=....|...|-..|...+++-|+|.||..|+..
T Consensus 22 gL~FpVgRi~R~Lr~g~~------a~Rvga~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~n 89 (129)
T PLN00153 22 GLQFPVGRIARYLKKGKY------AERIGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKNRIVPRHIQLAIRN 89 (129)
T ss_pred CcccchHHHHHHHhcCch------hhccCCCchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHhhccC
Confidence 478999999999998643 46999999999988877777777777777888899999999999999854
No 48
>PLN00157 histone H2A; Provisional
Probab=96.75 E-value=0.0036 Score=46.88 Aligned_cols=68 Identities=13% Similarity=0.157 Sum_probs=57.1
Q ss_pred hcccchhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 032845 10 AEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (132)
Q Consensus 10 d~~LP~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~ 83 (132)
-+.||.+.|.|++|+.-- ..+|+..|...|.-+.+=....|...|-..|...+++-|++.||..|+..
T Consensus 24 gL~FPVgRi~R~Lk~g~~------a~RIg~~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~n 91 (132)
T PLN00157 24 GLQFPVGRIARYLKAGKY------ATRVGAGAPVYLAAVLEYLAAEVLELAGNAARDNKKSRIVPRHIQLAVRN 91 (132)
T ss_pred CcccchHHHHHHHhcCch------hhhcCCCcHhHHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHhhcccC
Confidence 468999999999999632 46999999999988777666666777777888899999999999999854
No 49
>PLN00156 histone H2AX; Provisional
Probab=96.71 E-value=0.005 Score=46.52 Aligned_cols=68 Identities=13% Similarity=0.153 Sum_probs=55.9
Q ss_pred hcccchhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 032845 10 AEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (132)
Q Consensus 10 d~~LP~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~ 83 (132)
-+.||.+.|.|++++.-- ..+|+..|...|.-+.+=....|...|-..|...+++-|+|.||..|+..
T Consensus 27 gL~FPVgRi~R~Lk~g~y------a~RVga~ApVYLAAVLEYLtaEVLELAgNaa~d~kk~RItPrHi~lAIrn 94 (139)
T PLN00156 27 GLQFPVGRIARFLKAGKY------AERVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRN 94 (139)
T ss_pred CcccchHHHHHHHhcCCh------hhccCCccHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHhhccC
Confidence 468999999999998632 46999999999988776666666666667788889999999999999854
No 50
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=96.37 E-value=0.0058 Score=50.27 Aligned_cols=66 Identities=18% Similarity=0.200 Sum_probs=59.0
Q ss_pred ccchhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 032845 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (132)
Q Consensus 12 ~LP~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~ 83 (132)
.|=+-.+..++++.- ++..+-+|+.++|.+.|..||..|+..|-..|++-|..||-+.||...|++
T Consensus 154 il~k~kl~dLvqqId------~~~~LD~dVedlLleiADdFV~sii~~sC~LAKHRKsdtlEvrDIqLhLEr 219 (258)
T KOG1142|consen 154 ILSKRKLDDLVQQID------GTTKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHRKSDTVEVRDIQLHLER 219 (258)
T ss_pred cccccchhHHHHhhc------CcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccchhheeeeeec
Confidence 345566778888884 478999999999999999999999999999999999999999999999986
No 51
>PF02269 TFIID-18kDa: Transcription initiation factor IID, 18kD subunit; InterPro: IPR003195 This family includes the Spt3 yeast transcription factors and the 18 kDa subunit from human transcription initiation factor IID (TFIID-18). Determination of the crystal structure reveals an atypical histone fold [].; GO: 0006366 transcription from RNA polymerase II promoter; PDB: 1BH9_A 1BH8_A.
Probab=96.23 E-value=0.0053 Score=43.01 Aligned_cols=49 Identities=16% Similarity=0.196 Sum_probs=24.8
Q ss_pred chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 032845 35 ISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (132)
Q Consensus 35 ~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~ 83 (132)
-.-..|+..+|-+...+||..+...|...|...|+++|+.+|++-+|+.
T Consensus 18 ~~P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~rg~~~i~~eDl~F~lR~ 66 (93)
T PF02269_consen 18 EEPLPETVDLVEDIVREYIIELCQEAMEVAQRRGSKKIKVEDLLFLLRK 66 (93)
T ss_dssp SS--HHHHHHHHHHHHHHHHHHHHHHHC---------------------
T ss_pred CCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCcCcHHHHHHHHhc
Confidence 4678999999999999999999999999999999999999999999985
No 52
>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=95.98 E-value=0.047 Score=40.63 Aligned_cols=68 Identities=22% Similarity=0.168 Sum_probs=41.0
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHH-HCCCcccHHHHHHHHHHHHHH
Q 032845 36 SVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIE-EIDFTEFVDPLRDSLDAKQIV 103 (132)
Q Consensus 36 ~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~-~lgf~~y~~~l~~~l~~~k~~ 103 (132)
.....+...|.+-+--|+.-|-..|..+|.+.+|++|+.+||..|++ .+++....++-+++|-+.-..
T Consensus 29 ~yeprVv~qLLEfayRYt~~vL~DA~~ya~hA~~~~i~~~DVrLAi~~r~~~~f~~pppre~llelA~e 97 (129)
T PF02291_consen 29 EYEPRVVNQLLEFAYRYTSDVLEDAQVYADHAGRSTIDADDVRLAIQSRLDHSFTQPPPREFLLELARE 97 (129)
T ss_dssp -B-THHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHHHHT--------------------
T ss_pred ccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHhhhccCCCChHHHHHHHHH
Confidence 56677888899999999999999999999999999999999999999 556666666667777665533
No 53
>KOG1658 consensus DNA polymerase epsilon, subunit C [Replication, recombination and repair]
Probab=95.94 E-value=0.0054 Score=47.16 Aligned_cols=70 Identities=29% Similarity=0.360 Sum_probs=58.3
Q ss_pred cccchhHHHHHHhhhccCCCCCCcc-hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHCCCc
Q 032845 11 EELPKTIVRRVVKDKLHNCSPDTDI-SVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFT 87 (132)
Q Consensus 11 ~~LP~a~V~RimK~~Lp~~~~d~~~-~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~lgf~ 87 (132)
..||.+.|..+||.. .++ ....+++.++.+++..||..|+..|+..+...+|||+.-.|+-.|.+..+=.
T Consensus 58 ~rLpL~rik~vvkl~-------pdl~l~~dea~~l~a~aaelfi~~Ln~~~~~~~q~~k~kt~qr~d~D~ai~~~de~ 128 (162)
T KOG1658|consen 58 SRLPLARIKQVVKLD-------PDLTLLNDEASQLIAKAAELFIQELNDVAYTTAQLRKRKTEQRRDYDTAIEAVDEF 128 (162)
T ss_pred hhccHHHHHhhccCC-------cchhhhhhHHHHHHHHHHHHHHHHHHhccchhHHHHHhhhhhhhcccccccchHHH
Confidence 478999999999754 256 4556789999999999999999999999999999999998888777665533
No 54
>PTZ00252 histone H2A; Provisional
Probab=95.61 E-value=0.044 Score=41.20 Aligned_cols=64 Identities=13% Similarity=0.174 Sum_probs=48.8
Q ss_pred hcccchhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHH----Hh--cCCCccCHHHHHHHHHH
Q 032845 10 AEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDIC----KE--SKRQTINAEDVLKAIEE 83 (132)
Q Consensus 10 d~~LP~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a----~~--~kRKTI~~eDVl~AL~~ 83 (132)
-+.||.+.|.|++++.-- ..+|+..|...|.-+. .||++|-.+.+ .+ .+++-|+++||..|+..
T Consensus 23 GL~FPVgRi~R~Lr~g~y------a~RIga~ApVYLAAVL----EYLtaEVLELAgnaa~d~~~kk~RItPrHi~lAIrN 92 (134)
T PTZ00252 23 GLIFPVGRVGSLLRRGQY------ARRIGASGAVYMAAVL----EYLTAELLELSVKAAAQQAKKPKRLTPRTVTLAVRH 92 (134)
T ss_pred CccCchHHHHHHHHcCCc------ccccCCccHHHHHHHH----HHHHHHHHHHHHHHHHhccCCcccccHHHHHhhccC
Confidence 478999999999998743 4699999998887654 45665555544 32 46788999999999854
No 55
>KOG3219 consensus Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=95.53 E-value=0.018 Score=45.75 Aligned_cols=71 Identities=15% Similarity=0.303 Sum_probs=61.3
Q ss_pred cccchhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC-CccCHHHHHHHHHHCCCcc
Q 032845 11 EELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKR-QTINAEDVLKAIEEIDFTE 88 (132)
Q Consensus 11 ~~LP~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kR-KTI~~eDVl~AL~~lgf~~ 88 (132)
..||++.|.|||..... -.|+.-+..+++-.+.+|+-.|--+|.+++..-+. -.+-|.||-.|...|+..+
T Consensus 111 s~f~Ka~iKkL~~~itg-------~~v~~nv~Ia~~GiaKvFVGEvVEeAl~V~~~~~e~~PLqP~HIREA~rrL~~qg 182 (195)
T KOG3219|consen 111 SAFPKAQIKKLMSSITG-------QSVSENVAIAMAGIAKVFVGEVVEEALDVREEWGESGPLQPKHIREAYRRLKLQG 182 (195)
T ss_pred hcCCHHHHHHHHHHHhC-------CccCcceeeeecchhhHhHHHHHHHHHHHHHHhccCCCCCcHHHHHHHHHHHhcC
Confidence 36999999999999984 23999999999999999999999999999987654 3599999999988887654
No 56
>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=94.80 E-value=0.14 Score=35.95 Aligned_cols=72 Identities=14% Similarity=0.170 Sum_probs=52.0
Q ss_pred HHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHCCCcccHHHHHHH
Q 032845 17 IVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFTEFVDPLRDS 96 (132)
Q Consensus 17 ~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~lgf~~y~~~l~~~ 96 (132)
-|..+|-.-.. .-.-..|...+|-+...+||.-++.+|.+.|. .++.-++.+|++-+|+.= .-.+.-++++
T Consensus 7 ei~~mmy~~GD------~~~P~~eTv~llE~iv~~~i~~l~~~a~~~A~-~r~~k~~~eD~~FliR~D--~~Kl~Rl~~l 77 (92)
T cd07978 7 EIRQMMYGFGD------VQNPLPETVDLLEDIVVEYIIELCHKAAEVAQ-RRRGKVKVEDLIFLLRKD--PKKLARLREL 77 (92)
T ss_pred HHHHHHHHcCC------CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-cCCCCCCHHHHHHHHhcC--HHHHHHHHHH
Confidence 35556655431 23567899999999999999999999999998 444456999999999642 2244445554
Q ss_pred H
Q 032845 97 L 97 (132)
Q Consensus 97 l 97 (132)
|
T Consensus 78 L 78 (92)
T cd07978 78 L 78 (92)
T ss_pred H
Confidence 4
No 57
>KOG4336 consensus TBP-associated transcription factor Prodos [Transcription]
Probab=94.26 E-value=0.46 Score=40.25 Aligned_cols=65 Identities=18% Similarity=0.303 Sum_probs=58.4
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHCCCcccHHHHHHHHHHHHH
Q 032845 36 SVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFTEFVDPLRDSLDAKQI 102 (132)
Q Consensus 36 ~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~lgf~~y~~~l~~~l~~~k~ 102 (132)
.|++-|.+-|.+....+|.-|...+.-+|+..||...|.-||..+|-++|+. ++.|..+++.+-.
T Consensus 22 ~is~~aletlvell~~yi~eigrq~~n~celagRT~pT~~Dv~l~Li~mnI~--v~sL~~~~q~~~~ 86 (323)
T KOG4336|consen 22 SISNAALETLVELLQSYIREIGRQLHNYCELAGRTIPTQGDVKLTLIEMNIK--VSSLYAYFQKQEF 86 (323)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcHHHHHHHHHHhCCC--hhhhHHHHHhccc
Confidence 6999999999999999999999999999999999999999999999999997 5666666665543
No 58
>KOG3423 consensus Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=93.40 E-value=0.6 Score=36.49 Aligned_cols=69 Identities=17% Similarity=0.222 Sum_probs=55.0
Q ss_pred ccchhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhc--------------CCCccCHHHH
Q 032845 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKES--------------KRQTINAEDV 77 (132)
Q Consensus 12 ~LP~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~--------------kRKTI~~eDV 77 (132)
.||-+.+.-.++.+.=+ ..-.-.+-+|.=++..||+-|+..|.+.|+-. +|-|++-+|+
T Consensus 86 ~IPDavt~~yL~~aGf~-------~~D~rv~RLvsLaAQKfvSDIa~DA~Q~~k~r~~~~~~~~k~~~kdkK~tLtmeDL 158 (176)
T KOG3423|consen 86 TIPDAVTDHYLKKAGFQ-------TSDPRVKRLVSLAAQKFVSDIANDALQHSKIRTKTAIGKDKKQAKDKKYTLTMEDL 158 (176)
T ss_pred CCcHHHHHHHHHhcCCC-------cCcHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccccccccccccceeeeHHHH
Confidence 68888888888877422 22334567889999999999999999999633 3558999999
Q ss_pred HHHHHHCCCc
Q 032845 78 LKAIEEIDFT 87 (132)
Q Consensus 78 l~AL~~lgf~ 87 (132)
-.||.+.|..
T Consensus 159 ~~AL~EyGin 168 (176)
T KOG3423|consen 159 SPALAEYGIN 168 (176)
T ss_pred HHHHHHhCcc
Confidence 9999999975
No 59
>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=93.08 E-value=0.43 Score=37.29 Aligned_cols=74 Identities=22% Similarity=0.248 Sum_probs=55.4
Q ss_pred cchhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHH---HHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHCCC
Q 032845 13 LPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARI---FIHYLSATANDICKESKRQTINAEDVLKAIEEIDF 86 (132)
Q Consensus 13 LP~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~---FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~lgf 86 (132)
|...-+..++...+..........++.++...|.+.+.- .|+.+...|...+-..+.++|+.++|-.++.++.|
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 334455555554442111112356899999999998875 79999999999988889999999999999999874
No 60
>KOG3334 consensus Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=92.19 E-value=0.8 Score=34.94 Aligned_cols=81 Identities=25% Similarity=0.179 Sum_probs=59.5
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHCCCcccHH-HHHHHHHHHHHHhhhhhhcCCCcc
Q 032845 37 VHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFTEFVD-PLRDSLDAKQIVSQKVVASNPLFF 115 (132)
Q Consensus 37 ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~lgf~~y~~-~l~~~l~~~k~~~q~~~~~~~~~~ 115 (132)
...-....|.+-+--+..-|-..|.-++.++++.||.++||..|++...--+|.+ +=+++|-++-.... ++|+-+
T Consensus 31 yEprVi~qlLefa~rYtt~vL~DA~vys~HA~ka~i~~eDVrlA~~~~~~~sf~~pPpRe~lL~lA~~rN----~~pLp~ 106 (148)
T KOG3334|consen 31 YEPRVINQLLEFAYRYTTTVLDDAKVYSSHAKKATIDAEDVRLAIQMRVDHSFTPPPPREFLLELAAERN----SKPLPQ 106 (148)
T ss_pred cChHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHhccccCCCCchHHHHHHHHhhc----cCCCCc
Confidence 3344455566677777778889999999999999999999999999998877776 44555555543322 677777
Q ss_pred cCCCCc
Q 032845 116 FRGNHV 121 (132)
Q Consensus 116 ~~g~~~ 121 (132)
-+|+-+
T Consensus 107 i~~~~g 112 (148)
T KOG3334|consen 107 IRAGPG 112 (148)
T ss_pred ccCCCC
Confidence 666543
No 61
>KOG2549 consensus Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=91.07 E-value=1.2 Score=40.44 Aligned_cols=67 Identities=25% Similarity=0.355 Sum_probs=56.3
Q ss_pred chhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHCCCc
Q 032845 14 PKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFT 87 (132)
Q Consensus 14 P~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~lgf~ 87 (132)
|+-.+. .|-+.+ |-..++.||..+|.+=.+.=|..|+.+|.+.-.+.+|.+++.+||-.||+.+..+
T Consensus 13 ~~Es~k-~vAEsl------Gi~nl~deaa~~La~dv~yrikEI~Q~aaKfm~hskR~kLtv~DV~~ALr~~nVe 79 (576)
T KOG2549|consen 13 PKESVK-VVAESL------GITNLNDEAALLLAEDVEYRIKEIVQDAAKFMVHSKRTKLTVDDVDYALRSLNVE 79 (576)
T ss_pred cHHHHH-HHHHHh------CccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcCcHHHHHHHHhhcccc
Confidence 444544 444555 2457999999999999999999999999999999999999999999999988755
No 62
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=90.26 E-value=1.8 Score=35.89 Aligned_cols=71 Identities=18% Similarity=0.158 Sum_probs=49.1
Q ss_pred hhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHH------HHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHCCCc
Q 032845 15 KTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESA------RIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFT 87 (132)
Q Consensus 15 ~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a------~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~lgf~ 87 (132)
..-+..+++..+...- ....++.++.+.+.+.+ .-.+..+...|...|...++.+|+.+||..|++.+...
T Consensus 209 ~~e~~~il~~r~~~~~--~~~~~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~a~~~a~~~~~~~I~~~~v~~a~~~~~~~ 285 (394)
T PRK00411 209 ADEIFDILKDRVEEGF--YPGVVDDEVLDLIADLTAREHGDARVAIDLLRRAGLIAEREGSRKVTEEDVRKAYEKSEIV 285 (394)
T ss_pred HHHHHHHHHHHHHhhc--ccCCCCHhHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHHHH
Confidence 3445555555442100 02357889988888777 33455666888888988999999999999999987443
No 63
>KOG2389 consensus Predicted bromodomain transcription factor [Transcription]
Probab=86.75 E-value=1.6 Score=37.63 Aligned_cols=69 Identities=17% Similarity=0.259 Sum_probs=57.3
Q ss_pred ccchhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHCCCc
Q 032845 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFT 87 (132)
Q Consensus 12 ~LP~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~lgf~ 87 (132)
.|-+..|..|....-- -....-|.+.|+.-+..||.-++..|..++...||.-.+..||+.||++|+..
T Consensus 29 sla~~avaQIcqslg~-------~~~~~sale~Ltd~~~qyvQ~lgk~a~~~~n~anR~epnl~Div~Al~dls~s 97 (353)
T KOG2389|consen 29 SLARVAVAQICQSLGY-------SSTQNSALETLTDVLQQYVQNLGKTAHRYSNLANRTEPNLFDIVLALQDLSAS 97 (353)
T ss_pred HHHHHHHHHHHHhcCC-------cccccHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCccHHHHHHHHHHhhhh
Confidence 5666778888755421 12333499999999999999999999999999999999999999999999865
No 64
>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=84.13 E-value=6.6 Score=32.13 Aligned_cols=74 Identities=15% Similarity=0.175 Sum_probs=47.1
Q ss_pred hHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHH------HHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHCCCccc
Q 032845 16 TIVRRVVKDKLHNCSPDTDISVHKDALLAFCESAR------IFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFTEF 89 (132)
Q Consensus 16 a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~------~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~lgf~~y 89 (132)
.-+..|++..+...- .+..++.++...+.+.+. -.+..+...|...|...++.+|+.+||..|++.+..+.+
T Consensus 202 ~e~~~il~~r~~~~~--~~~~~~~~~l~~i~~~~~~~~Gd~R~al~~l~~a~~~a~~~~~~~it~~~v~~a~~~~~~~~~ 279 (365)
T TIGR02928 202 EELRDILENRAEKAF--YDGVLDDGVIPLCAALAAQEHGDARKAIDLLRVAGEIAEREGAERVTEDHVEKAQEKIEKDRL 279 (365)
T ss_pred HHHHHHHHHHHHhhc--cCCCCChhHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHH
Confidence 445566655442100 023477887777665442 234445667778888888999999999999988855444
Q ss_pred HH
Q 032845 90 VD 91 (132)
Q Consensus 90 ~~ 91 (132)
..
T Consensus 280 ~~ 281 (365)
T TIGR02928 280 LE 281 (365)
T ss_pred HH
Confidence 43
No 65
>TIGR02902 spore_lonB ATP-dependent protease LonB. Members of this protein are LonB, a paralog of the ATP-dependent protease La (LonA, TIGR00763). LonB proteins are found strictly, and almost universally, in endospore-forming bacteria. This protease was shown, in Bacillus subtilis, to be expressed specifically in the forespore, during sporulation, under control of sigma(F). The lonB gene, despite location immediately upstream of lonA, was shown to be monocistronic. LonB appears able to act on sigma(H) for post-translation control, but lonB mutation did not produce an obvious sporulation defect under the conditions tested. Note that additional paralogs of LonA and LonB occur in the Clostridium lineage and this model selects only one per species as the protein that corresponds to LonB in B. subtilis.
Probab=81.37 E-value=5.8 Score=35.35 Aligned_cols=66 Identities=21% Similarity=0.256 Sum_probs=44.2
Q ss_pred hHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHH---HHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHCCC
Q 032845 16 TIVRRVVKDKLHNCSPDTDISVHKDALLAFCESAR---IFIHYLSATANDICKESKRQTINAEDVLKAIEEIDF 86 (132)
Q Consensus 16 a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~---~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~lgf 86 (132)
.-+..|++..+.. .++.+++++.+.|.+.+. +.++ +...|..+|..++|++|+.+||.+++..-.|
T Consensus 266 eei~~Il~~~a~k----~~i~is~~al~~I~~y~~n~Rel~n-ll~~Aa~~A~~~~~~~It~~dI~~vl~~~~~ 334 (531)
T TIGR02902 266 EEIKEIAKNAAEK----IGINLEKHALELIVKYASNGREAVN-IVQLAAGIALGEGRKRILAEDIEWVAENGNY 334 (531)
T ss_pred HHHHHHHHHHHHH----cCCCcCHHHHHHHHHhhhhHHHHHH-HHHHHHHHHhhCCCcEEcHHHHHHHhCCccc
Confidence 3344555555532 247889999988877665 2333 3345556777888999999999999764433
No 66
>PF13654 AAA_32: AAA domain; PDB: 3K1J_B.
Probab=80.28 E-value=6.5 Score=35.20 Aligned_cols=49 Identities=27% Similarity=0.283 Sum_probs=37.8
Q ss_pred hhhHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHC
Q 032845 36 SVHKDALLAFCESARI-----------FIHYLSATANDICKESKRQTINAEDVLKAIEEI 84 (132)
Q Consensus 36 ~ISkDA~~al~~~a~~-----------FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~l 84 (132)
-++.+|...|.+.+.- -|.-|-.+|+.+|...++++|+++||..|++.-
T Consensus 447 ~~~~~Av~~li~~~~R~~q~kLsl~~~~l~~ll~EA~~~A~~~~~~~I~~~~V~~Ai~~r 506 (509)
T PF13654_consen 447 PFDRSAVARLIEYSARLDQDKLSLRFSWLADLLREANYWARKEGAKVITAEHVEQAIEER 506 (509)
T ss_dssp -BBHHHHHHHHHHHHHCC-SEEE--HHHHHHHHHHHHHHHHHCT-SSB-HHHHHHHHHH-
T ss_pred CCCHHHHHHHHHHHHHHhCCEeCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHcc
Confidence 4778887777776643 566777999999999999999999999999864
No 67
>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=78.13 E-value=4.6 Score=24.60 Aligned_cols=42 Identities=21% Similarity=0.202 Sum_probs=26.1
Q ss_pred hHHHHHHHHHHHHHHHH-HHHHHHHHHHHhcCCCccCHHHHHHH
Q 032845 38 HKDALLAFCESARIFIH-YLSATANDICKESKRQTINAEDVLKA 80 (132)
Q Consensus 38 SkDA~~al~~~a~~FI~-~ltseA~~~a~~~kRKTI~~eDVl~A 80 (132)
+.||...|.+. =.|+- .+-..+-..|...|...||.++|..|
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 45666666664 33443 33355666788999999999999876
No 68
>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=76.18 E-value=13 Score=33.79 Aligned_cols=50 Identities=30% Similarity=0.287 Sum_probs=40.2
Q ss_pred hhhHHHHHHHHHHHH-------------HHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHCC
Q 032845 36 SVHKDALLAFCESAR-------------IFIHYLSATANDICKESKRQTINAEDVLKAIEEID 85 (132)
Q Consensus 36 ~ISkDA~~al~~~a~-------------~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~lg 85 (132)
.++.+|...|.+.++ -=+.-|-.+|+.+|..++..+|+.+||..|++.-.
T Consensus 330 ~~s~~Av~~Li~~~~R~ag~r~~lsl~~R~L~~llR~A~~iA~~~~~~~I~~ehV~~Ai~~~~ 392 (608)
T TIGR00764 330 HFTRDAVEEIVREAQRRAGRKDHLTLRLRELGGLVRAAGDIAKSSGKVYVTAEHVLKAKKLAK 392 (608)
T ss_pred cCCHHHHHHHHHHHHHHHhcccccCCCHHHHHHHHHHHHHHHHhcCCceecHHHHHHHHHHHH
Confidence 689999888876554 23555667888899888999999999999988654
No 69
>COG1067 LonB Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]
Probab=75.47 E-value=3.9 Score=37.78 Aligned_cols=49 Identities=29% Similarity=0.345 Sum_probs=36.4
Q ss_pred hhhHHHHHHHHHHHH--------------HHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHCC
Q 032845 36 SVHKDALLAFCESAR--------------IFIHYLSATANDICKESKRQTINAEDVLKAIEEID 85 (132)
Q Consensus 36 ~ISkDA~~al~~~a~--------------~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~lg 85 (132)
-++++|..-|.+-+. .-...| .+|..+|..++++-|+++||.+|++.-.
T Consensus 338 ~~~~~Av~~li~~a~R~Ag~~~~Ltl~~rdl~~lv-~~A~~ia~~~~~~~I~ae~Ve~a~~~~~ 400 (647)
T COG1067 338 HLDKDAVEELIREAARRAGDQNKLTLRLRDLGNLV-REAGDIAVSEGRKLITAEDVEEALQKRE 400 (647)
T ss_pred CCCHHHHHHHHHHHHHhccccceeccCHHHHHHHH-HHhhHHHhcCCcccCcHHHHHHHHHhhh
Confidence 466666665555443 333344 4999999999999999999999999843
No 70
>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=74.89 E-value=21 Score=27.27 Aligned_cols=60 Identities=17% Similarity=0.310 Sum_probs=40.9
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHCCCc-ccHHHHHHHHHHHHHHhhhhhhcCCCc
Q 032845 48 SARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFT-EFVDPLRDSLDAKQIVSQKVVASNPLF 114 (132)
Q Consensus 48 ~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~lgf~-~y~~~l~~~l~~~k~~~q~~~~~~~~~ 114 (132)
.+...+.||-..|. |.-++++++..-|+.+||+ +..+.+...+..+++..+..-.++.+.
T Consensus 43 ~~va~l~fiL~~A~-------k~n~~~~~l~~eL~~lglp~e~~~~l~~~~~~~~~~l~~~l~~~~l~ 103 (174)
T cd04752 43 ASIAVLSFILSSAA-------KYNVDGESLSSELQQLGLPKEHATSLCRSYEEKQSKLQESLRANSLR 103 (174)
T ss_pred HHHHHHHHHHHHHH-------HcCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Confidence 55666777776554 4449999999999999998 577777777776665544433333333
No 71
>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=73.32 E-value=9.9 Score=33.02 Aligned_cols=53 Identities=21% Similarity=0.294 Sum_probs=49.1
Q ss_pred chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHCCCc
Q 032845 35 ISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFT 87 (132)
Q Consensus 35 ~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~lgf~ 87 (132)
-.|..|+..++.--.+==|..+..+|...-.+.||..++.+||-.||+.++.+
T Consensus 21 ~Ni~Dd~l~alamDlEYRI~ev~qea~KFmvhSKRtvLt~dDis~ALr~lNVe 73 (450)
T COG5095 21 SNIDDDALRALAMDLEYRIKEVCQEASKFMVHSKRTVLTIDDISYALRSLNVE 73 (450)
T ss_pred cccccHHHHHHHHhHHHHHHHHHHHHHHHhhcccceeeeHHhHHHHHHhcCCC
Confidence 47899999999998888899999999999999999999999999999999765
No 72
>PF13335 Mg_chelatase_2: Magnesium chelatase, subunit ChlI
Probab=73.09 E-value=17 Score=25.19 Aligned_cols=47 Identities=17% Similarity=0.226 Sum_probs=39.6
Q ss_pred hhhHHHHHHHHHHHHHH------HHHHHHHHHHHHHhcCCCccCHHHHHHHHH
Q 032845 36 SVHKDALLAFCESARIF------IHYLSATANDICKESKRQTINAEDVLKAIE 82 (132)
Q Consensus 36 ~ISkDA~~al~~~a~~F------I~~ltseA~~~a~~~kRKTI~~eDVl~AL~ 82 (132)
.+++++..+|.+++..| ++-|..-|..+|.=++...|+.+||..||.
T Consensus 42 ~l~~~~~~~l~~~~~~~~lS~R~~~rilrvARTIADL~~~~~I~~~hi~EAl~ 94 (96)
T PF13335_consen 42 PLSSEAKKLLEQAAEKLNLSARGYHRILRVARTIADLEGSERITREHIAEALS 94 (96)
T ss_pred CCCHHHHHHHHHHHHHcCcCHHHHHHHHHHHHHHHhHcCCCCCCHHHHHHHHh
Confidence 47788888888887766 455667899999999999999999999984
No 73
>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=71.97 E-value=3.7 Score=29.21 Aligned_cols=38 Identities=13% Similarity=0.262 Sum_probs=31.2
Q ss_pred hHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHH
Q 032845 16 TIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIH 54 (132)
Q Consensus 16 a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~ 54 (132)
++|.+++|..|=+-+.|| ..++.++.+.|+++++.|-.
T Consensus 51 SNIGvLIKkglIEKSGDG-lv~T~~g~~Ii~~AA~l~a~ 88 (96)
T PF09114_consen 51 SNIGVLIKKGLIEKSGDG-LVITEEGMDIIIQAAELWAQ 88 (96)
T ss_dssp HHHHHHHHTTSEEEETTE-EEE-HHHHHHHHHHHHHHHH
T ss_pred HhHHHHHHcCcccccCCc-eEEechHHHHHHHHHHHHHh
Confidence 568889999987666665 89999999999999998854
No 74
>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=71.20 E-value=8.3 Score=22.73 Aligned_cols=26 Identities=31% Similarity=0.385 Sum_probs=21.0
Q ss_pred HHHHHHhcCCCccCHHHHHHHHHHCC
Q 032845 60 ANDICKESKRQTINAEDVLKAIEEID 85 (132)
Q Consensus 60 A~~~a~~~kRKTI~~eDVl~AL~~lg 85 (132)
|.+.|...+...|+++|++.||=.-+
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 56789999999999999999965544
No 75
>COG5162 Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=69.20 E-value=34 Score=26.94 Aligned_cols=51 Identities=18% Similarity=0.251 Sum_probs=39.1
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHH-hc--------------------------------CCCccCHHHHHHHHHH
Q 032845 37 VHKDALLAFCESARIFIHYLSATANDICK-ES--------------------------------KRQTINAEDVLKAIEE 83 (132)
Q Consensus 37 ISkDA~~al~~~a~~FI~~ltseA~~~a~-~~--------------------------------kRKTI~~eDVl~AL~~ 83 (132)
...-.+-+|.-.+..||+-|+..|.++.+ +. ++-+++..|+-+||++
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 34456778888999999999988877652 11 4557889999999999
Q ss_pred CCCc
Q 032845 84 IDFT 87 (132)
Q Consensus 84 lgf~ 87 (132)
.|+.
T Consensus 186 yGin 189 (197)
T COG5162 186 YGIN 189 (197)
T ss_pred hccc
Confidence 8875
No 76
>PRK09862 putative ATP-dependent protease; Provisional
Probab=66.93 E-value=27 Score=31.36 Aligned_cols=61 Identities=11% Similarity=0.096 Sum_probs=47.1
Q ss_pred chhhHHHHHHHHHHHHHH------HHHHHHHHHHHHHhcCCCccCHHHHHHHHHHCCCcccHHHHHH
Q 032845 35 ISVHKDALLAFCESARIF------IHYLSATANDICKESKRQTINAEDVLKAIEEIDFTEFVDPLRD 95 (132)
Q Consensus 35 ~~ISkDA~~al~~~a~~F------I~~ltseA~~~a~~~kRKTI~~eDVl~AL~~lgf~~y~~~l~~ 95 (132)
..++.++...+.++...+ .+.|..-|..+|.=+++..|+++||..|+.--+++..+-.++.
T Consensus 437 ~~l~~~~~~~l~~~~~~~~lS~Ra~~rlLrvARTiADL~g~~~V~~~hv~eAl~yR~~~~~~~~~~~ 503 (506)
T PRK09862 437 CKLESEDARWLEETLIHLGLSIRAWQRLLKVARTIADIDQSDIITRQHLQEAVSYRAIDRLLIHLQK 503 (506)
T ss_pred hCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHhhcccHHHHHHHH
Confidence 467778888777765544 5667788889999999999999999999987777655555443
No 77
>KOG3901 consensus Transcription initiation factor IID subunit [Transcription]
Probab=65.95 E-value=23 Score=25.75 Aligned_cols=46 Identities=17% Similarity=0.204 Sum_probs=38.1
Q ss_pred chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 032845 35 ISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (132)
Q Consensus 35 ~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~ 83 (132)
..=-.|++++|-..+.+||..++..|..+. +|--+..+|++-+|+.
T Consensus 26 ~nP~~~tv~~Le~iV~~Yi~elt~~a~~~g---~rgk~~veD~~f~lRk 71 (109)
T KOG3901|consen 26 VNPYPETVDLLEDIVLEYITELTHAAMEIG---KRGKVKVEDFKFLLRK 71 (109)
T ss_pred CCccHhHHHHHHHHHHHHHHHHHHHHHHhc---ccCceeHHHHHHHHHh
Confidence 345568899999999999999988888877 5666888999999875
No 78
>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=65.83 E-value=27 Score=27.33 Aligned_cols=76 Identities=12% Similarity=0.089 Sum_probs=58.0
Q ss_pred cccchhHHHHHHhhhccCCCCCCcc-hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhc------CCCccCHHHHHHHHHH
Q 032845 11 EELPKTIVRRVVKDKLHNCSPDTDI-SVHKDALLAFCESARIFIHYLSATANDICKES------KRQTINAEDVLKAIEE 83 (132)
Q Consensus 11 ~~LP~a~V~RimK~~Lp~~~~d~~~-~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~------kRKTI~~eDVl~AL~~ 83 (132)
..|....+.+.|...+.. .+. .++.|...+|.-|+..++..|-......|++- .-.++-..||-..|..
T Consensus 43 ~fl~~~~l~~~~~~i~~~----~g~~~~~~d~~~lis~a~e~rlr~li~k~~~~s~hR~~~~~~~~r~~~~sdvr~qL~~ 118 (212)
T cd08045 43 SFLNPSPLAKKIRKIAKK----HGLKEVDEDVLDLISLALEERLRNLLEKLIEVSEHRVDSEKEDERYEITSDVRKQLRF 118 (212)
T ss_pred hccCHHHHHHHHHHHHHH----cCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCceeecchHHHHHHH
Confidence 467777777777777654 123 79999999999999999999999999998763 3456667788877776
Q ss_pred CCCcccH
Q 032845 84 IDFTEFV 90 (132)
Q Consensus 84 lgf~~y~ 90 (132)
|+--+..
T Consensus 119 l~~~ek~ 125 (212)
T cd08045 119 LEQLERE 125 (212)
T ss_pred HHHHHHH
Confidence 6654433
No 79
>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=65.79 E-value=7.8 Score=28.34 Aligned_cols=61 Identities=8% Similarity=0.165 Sum_probs=39.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHCCCcccHHHHHHHHHHHHHHh
Q 032845 40 DALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFTEFVDPLRDSLDAKQIVS 104 (132)
Q Consensus 40 DA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~lgf~~y~~~l~~~l~~~k~~~ 104 (132)
..+.-|..|..+.-.|...-..-... ---.-......|+..|++..+.+++..+++|.+..
T Consensus 73 ~Vk~Eiaa~~~v~~~Y~~~L~~G~vd----~e~~~~~~~~kLk~AGidkV~~E~QkQlda~~~~~ 133 (134)
T PF12010_consen 73 PVKNEIAACSNVWSEYYPPLETGLVD----PEEALPEFNEKLKAAGIDKVIAELQKQLDAFLAAN 133 (134)
T ss_pred hhHHHHHHHHHHHHHHHHHHHccCCC----HHHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHhc
Confidence 34455555555555554432222110 01224667889999999999999999999998654
No 80
>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=64.97 E-value=23 Score=30.01 Aligned_cols=49 Identities=14% Similarity=0.219 Sum_probs=39.3
Q ss_pred cchhhHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCccCHHHHHHHHH
Q 032845 34 DISVHKDALLAFCESARIFI-------HYLSATANDICKESKRQTINAEDVLKAIE 82 (132)
Q Consensus 34 ~~~ISkDA~~al~~~a~~FI-------~~ltseA~~~a~~~kRKTI~~eDVl~AL~ 82 (132)
.+.|+.+....+.+.+..+= .++...|...|--+||..|+++||..+..
T Consensus 252 ~V~v~d~~~~~i~~l~~~~~~~s~Ra~i~l~raArA~Aal~GR~~V~~dDv~~~a~ 307 (337)
T TIGR02030 252 QVTIPYDVLVKVAELCAELDVDGLRGELTLNRAAKALAAFEGRTEVTVDDIRRVAV 307 (337)
T ss_pred cCcCCHHHHHHHHHHHHHHCCCCCcHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 68899999998888777653 24557777888889999999999997753
No 81
>CHL00081 chlI Mg-protoporyphyrin IX chelatase
Probab=63.83 E-value=23 Score=30.26 Aligned_cols=49 Identities=12% Similarity=0.197 Sum_probs=41.3
Q ss_pred cchhhHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCccCHHHHHHHHH
Q 032845 34 DISVHKDALLAFCESARIFI-------HYLSATANDICKESKRQTINAEDVLKAIE 82 (132)
Q Consensus 34 ~~~ISkDA~~al~~~a~~FI-------~~ltseA~~~a~~~kRKTI~~eDVl~AL~ 82 (132)
.+.+|.+....+.+.+..+= .++...|...|-=+||..|+++||..+..
T Consensus 265 ~V~v~~~~~~yi~~l~~~~~~~s~Ra~i~l~raArA~Aal~GR~~V~pdDv~~~a~ 320 (350)
T CHL00081 265 KVEIDYDLRVKISQICSELDVDGLRGDIVTNRAAKALAAFEGRTEVTPKDIFKVIT 320 (350)
T ss_pred CCccCHHHHHHHHHHHHHHCCCCChHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 68999999999999888864 36667788888889999999999998753
No 82
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=63.24 E-value=45 Score=27.33 Aligned_cols=72 Identities=15% Similarity=0.200 Sum_probs=49.0
Q ss_pred cchhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHH---HHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHCCCcc
Q 032845 13 LPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARI---FIHYLSATANDICKESKRQTINAEDVLKAIEEIDFTE 88 (132)
Q Consensus 13 LP~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~---FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~lgf~~ 88 (132)
++...+..+++..... .++.++.|+...|.+.+.- .+..+...+...+...+...|+.++|..+++.++.+.
T Consensus 180 ~~~~e~~~il~~~~~~----~~~~~~~~~~~~ia~~~~G~pR~a~~~l~~~~~~a~~~~~~~I~~~~v~~~l~~~~~~~ 254 (328)
T PRK00080 180 YTVEELEKIVKRSARI----LGVEIDEEGALEIARRSRGTPRIANRLLRRVRDFAQVKGDGVITKEIADKALDMLGVDE 254 (328)
T ss_pred CCHHHHHHHHHHHHHH----cCCCcCHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCc
Confidence 4445555555555432 2578999998888776632 3444555566666666677899999999999987663
No 83
>KOG2680 consensus DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=62.94 E-value=28 Score=30.47 Aligned_cols=72 Identities=15% Similarity=0.317 Sum_probs=52.1
Q ss_pred cccchhHHHHHHhhhccCCC------------CCCcchhhHHHHHHHHHHHHH----HHHHHHHHHHHHHHhcCCCccCH
Q 032845 11 EELPKTIVRRVVKDKLHNCS------------PDTDISVHKDALLAFCESARI----FIHYLSATANDICKESKRQTINA 74 (132)
Q Consensus 11 ~~LP~a~V~RimK~~Lp~~~------------~d~~~~ISkDA~~al~~~a~~----FI~~ltseA~~~a~~~kRKTI~~ 74 (132)
..+|...+.|++==...+|. ...++.++.||++.|.+.... |-.+|-+.|+..|.+.+-+++..
T Consensus 340 hGiP~D~lDR~lII~t~py~~~d~~~IL~iRc~EEdv~m~~~A~d~Lt~i~~~tsLRYai~Lit~a~~~~~krk~~~v~~ 419 (454)
T KOG2680|consen 340 HGIPIDLLDRMLIISTQPYTEEDIKKILRIRCQEEDVEMNPDALDLLTKIGEATSLRYAIHLITAASLVCLKRKGKVVEV 419 (454)
T ss_pred CCCcHHHhhhhheeecccCcHHHHHHHHHhhhhhhccccCHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHhcCceeeh
Confidence 45777777766522211122 124789999999999876543 56667778999999999999999
Q ss_pred HHHHHHHH
Q 032845 75 EDVLKAIE 82 (132)
Q Consensus 75 eDVl~AL~ 82 (132)
+||-.+.+
T Consensus 420 ~di~r~y~ 427 (454)
T KOG2680|consen 420 DDIERVYR 427 (454)
T ss_pred hHHHHHHH
Confidence 99999864
No 84
>TIGR01128 holA DNA polymerase III, delta subunit. subunit around DNA forming a DNA sliding clamp.
Probab=61.77 E-value=57 Score=25.71 Aligned_cols=69 Identities=14% Similarity=0.188 Sum_probs=48.6
Q ss_pred ccchhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHC
Q 032845 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEI 84 (132)
Q Consensus 12 ~LP~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~l 84 (132)
.+....+.+.+++.+.. .++.|+.+|...|...+.-=...+..+-...+.-.+.++|+.+||...+...
T Consensus 110 ~~~~~~~~~~i~~~~~~----~g~~i~~~a~~~l~~~~~~d~~~l~~el~KL~~~~~~~~It~e~I~~~~~~~ 178 (302)
T TIGR01128 110 TPKEQELPRWIQARLKK----LGLRIDPDAVQLLAELVEGNLLAIAQELEKLALYAPDGKITLEDVEEAVSDS 178 (302)
T ss_pred CCCHHHHHHHHHHHHHH----cCCCCCHHHHHHHHHHhCcHHHHHHHHHHHHHhhCCCCCCCHHHHHHHHhhh
Confidence 45566777777776653 3678999999999888765556666666666654444479999998776543
No 85
>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=61.68 E-value=28 Score=31.72 Aligned_cols=50 Identities=20% Similarity=0.218 Sum_probs=42.0
Q ss_pred cchhhHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 032845 34 DISVHKDALLAFCESARIFI-------HYLSATANDICKESKRQTINAEDVLKAIEE 83 (132)
Q Consensus 34 ~~~ISkDA~~al~~~a~~FI-------~~ltseA~~~a~~~kRKTI~~eDVl~AL~~ 83 (132)
.+.|+.++...|.+.+..+- .++...|..+|.=++|.+|+.+||..|+.-
T Consensus 247 ~V~is~~~~~~l~~~~~~~~i~s~Ra~i~~~r~Ara~AaL~gr~~V~~~Dv~~A~~l 303 (633)
T TIGR02442 247 SVRISDSLIRFISELCIEFGVDGHRADIVMARAARALAALDGRRRVTAEDVREAAEL 303 (633)
T ss_pred CCCCCHHHHHHHHHHHHHhCCCCccHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHH
Confidence 58899999999999887763 456677888888899999999999888754
No 86
>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=59.70 E-value=44 Score=26.67 Aligned_cols=71 Identities=17% Similarity=0.213 Sum_probs=46.5
Q ss_pred cchhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHH---HHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHCCCc
Q 032845 13 LPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARI---FIHYLSATANDICKESKRQTINAEDVLKAIEEIDFT 87 (132)
Q Consensus 13 LP~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~---FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~lgf~ 87 (132)
++...+..+++..... .++.++.++...|.+.+.- ++..+...+...+...+...|+.++|..++..++++
T Consensus 159 l~~~e~~~il~~~~~~----~~~~~~~~al~~ia~~~~G~pR~~~~ll~~~~~~a~~~~~~~it~~~v~~~l~~l~~~ 232 (305)
T TIGR00635 159 YTVEELAEIVSRSAGL----LNVEIEPEAALEIARRSRGTPRIANRLLRRVRDFAQVRGQKIINRDIALKALEMLMID 232 (305)
T ss_pred CCHHHHHHHHHHHHHH----hCCCcCHHHHHHHHHHhCCCcchHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHhCCC
Confidence 3344455555554432 2567888988888776532 334444556666665666789999999999997655
No 87
>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=58.37 E-value=17 Score=22.50 Aligned_cols=25 Identities=24% Similarity=0.522 Sum_probs=21.5
Q ss_pred ccCHHHHHHHHHHCCCcccHHHHHH
Q 032845 71 TINAEDVLKAIEEIDFTEFVDPLRD 95 (132)
Q Consensus 71 TI~~eDVl~AL~~lgf~~y~~~l~~ 95 (132)
+=++++|..-|+.+||.+|.+....
T Consensus 3 ~w~~~~v~~WL~~~gl~~y~~~f~~ 27 (66)
T PF07647_consen 3 TWSPEDVAEWLKSLGLEQYADNFRE 27 (66)
T ss_dssp GHCHHHHHHHHHHTTCGGGHHHHHH
T ss_pred CCCHHHHHHHHHHCCcHHHHHHHHH
Confidence 3478999999999999999988765
No 88
>PRK13406 bchD magnesium chelatase subunit D; Provisional
Probab=58.18 E-value=29 Score=31.67 Aligned_cols=50 Identities=18% Similarity=0.208 Sum_probs=43.4
Q ss_pred cchhhHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 032845 34 DISVHKDALLAFCESARIFI-------HYLSATANDICKESKRQTINAEDVLKAIEE 83 (132)
Q Consensus 34 ~~~ISkDA~~al~~~a~~FI-------~~ltseA~~~a~~~kRKTI~~eDVl~AL~~ 83 (132)
++.++.+....+.+.+..|- .++...|..+|-=++|.+|+++||..|+.-
T Consensus 193 ~v~v~~~~l~~i~~~~~~~gv~S~Ra~i~llraARa~AaL~Gr~~V~~~dv~~Aa~l 249 (584)
T PRK13406 193 AVGPPPEAIAALCAAAAALGIASLRAPLLALRAARAAAALAGRTAVEEEDLALAARL 249 (584)
T ss_pred cCCCCHHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence 68899999999888888875 477888999999999999999999999753
No 89
>PRK12402 replication factor C small subunit 2; Reviewed
Probab=57.98 E-value=39 Score=27.07 Aligned_cols=71 Identities=13% Similarity=0.056 Sum_probs=43.6
Q ss_pred ccchhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHCCCcc
Q 032845 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFTE 88 (132)
Q Consensus 12 ~LP~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~lgf~~ 88 (132)
.++...+..+++..+.. .++.++.++...|.+.+.-=+..+.......+. +..+|+.+||..++.....++
T Consensus 183 ~~~~~~~~~~l~~~~~~----~~~~~~~~al~~l~~~~~gdlr~l~~~l~~~~~--~~~~It~~~v~~~~~~~~~~~ 253 (337)
T PRK12402 183 APTDDELVDVLESIAEA----EGVDYDDDGLELIAYYAGGDLRKAILTLQTAAL--AAGEITMEAAYEALGDVGTDE 253 (337)
T ss_pred CCCHHHHHHHHHHHHHH----cCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHH--cCCCCCHHHHHHHhCCCCCHH
Confidence 34455666666666542 256799999988888763222333333333332 234799999999888655443
No 90
>PRK07452 DNA polymerase III subunit delta; Validated
Probab=57.59 E-value=41 Score=27.27 Aligned_cols=66 Identities=12% Similarity=0.151 Sum_probs=48.3
Q ss_pred HHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHh--cCCCccCHHHHHHHHHHCCCc
Q 032845 18 VRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKE--SKRQTINAEDVLKAIEEIDFT 87 (132)
Q Consensus 18 V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~--~kRKTI~~eDVl~AL~~lgf~ 87 (132)
+.+.|++.+-. .+..|+.+|...|.+.+.-=...+..+-...+.- .+..+|+.+||...+....+.
T Consensus 135 l~~~i~~~~~~----~g~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~~It~~~V~~~v~~~~~~ 202 (326)
T PRK07452 135 LKQLVERTAQE----LGVKLTPEAAELLAEAVGNDSRRLYNELEKLALYAENSTKPISAEEVKALVSNTTQN 202 (326)
T ss_pred HHHHHHHHHHH----cCCCCCHHHHHHHHHHhCccHHHHHHHHHHHHHhccCCCCccCHHHHHHHhccCcCc
Confidence 44555544432 2689999999999998887666667777777765 457889999999887776644
No 91
>KOG1757 consensus Histone 2A [Chromatin structure and dynamics]
Probab=56.88 E-value=15 Score=27.24 Aligned_cols=66 Identities=17% Similarity=0.223 Sum_probs=48.5
Q ss_pred hhhcccchhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC----CCccCHHHHHHHHH
Q 032845 8 PEAEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESK----RQTINAEDVLKAIE 82 (132)
Q Consensus 8 ~Ed~~LP~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~k----RKTI~~eDVl~AL~ 82 (132)
+.-+.||.+.|.|..|.-... ..++..-|.... +..+.|||.|-.+.|.+.. -|.|+|.|+..|++
T Consensus 26 raGlqFpVgRihr~LK~r~t~-----h~rVGataavy~----aaileYLTaEVLeLAgNasKdLKvKRitprHlqLAiR 95 (131)
T KOG1757|consen 26 RAGLQFPVGRIHRHLKTRTTS-----HGRVGATAAVYS----AAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 95 (131)
T ss_pred hcccccchHHHHHHHHHhccc-----ccccchHHHHHH----HHHHHHHHHHHHHHcccccccceeeeccchhheeeec
Confidence 445789999999999998753 566665544332 3457899999998886654 46799999887764
No 92
>PF07733 DNA_pol3_alpha: Bacterial DNA polymerase III alpha subunit; InterPro: IPR011708 This is a conserved region found in the the DNA polymerase III alpha subunit, (2.7.7.7 from EC). DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. This DNA polymerase also exhibits 3' to 5' exonuclease activity. The alpha chain is the DNA polymerase.; GO: 0008408 3'-5' exonuclease activity, 0006260 DNA replication, 0005737 cytoplasm; PDB: 3F2C_A 3F2B_A 3F2D_A 2HPM_A 2HPI_A 3E0D_A 2HQA_A 2HNH_A.
Probab=56.53 E-value=4.3 Score=35.53 Aligned_cols=46 Identities=13% Similarity=0.177 Sum_probs=33.3
Q ss_pred HHHHHHCCCcccHHHHHHHHHHHHHHhhhhhhcCCCcccCCCCcceeeeEee
Q 032845 78 LKAIEEIDFTEFVDPLRDSLDAKQIVSQKVVASNPLFFFRGNHVRRIICHCI 129 (132)
Q Consensus 78 l~AL~~lgf~~y~~~l~~~l~~~k~~~q~~~~~~~~~~~~g~~~~~~~~~~~ 129 (132)
+..+..+||.+|.-.+...++.-|+ ..-+.+||||..+--.+|+|+
T Consensus 31 l~~i~~~~~~~yfLi~~d~v~~a~~------~~i~~g~GRGS~~gSlv~y~l 76 (426)
T PF07733_consen 31 LEVIKKLGFADYFLIVWDLVNWARK------NGILVGPGRGSAAGSLVAYLL 76 (426)
T ss_dssp HHHHHHCT-HHHHHHHHHHHHHHHH------TT--BES-EGGGGG-HHHHHT
T ss_pred HHHHHhCCCcHhHhHHHHHHHHHHh------cCCccccCCCchHHHHHHHHh
Confidence 6678889999999888887776664 355678999999988888875
No 93
>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=56.35 E-value=49 Score=20.90 Aligned_cols=48 Identities=19% Similarity=0.243 Sum_probs=35.7
Q ss_pred ccchhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 032845 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKE 66 (132)
Q Consensus 12 ~LP~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~ 66 (132)
.+|-+.+.-.++.+.=++ .+.++ .-++.=++..||.-|+..|.+.|+-
T Consensus 2 ~IPD~v~~~yL~~~G~~~---~D~rv----~RLvSLaaQKFisdI~~dA~q~~k~ 49 (51)
T PF03540_consen 2 TIPDEVTDYYLERSGFQT---SDPRV----KRLVSLAAQKFISDIANDAMQYCKI 49 (51)
T ss_pred CCCHHHHHHHHHHCCCCC---CCHhH----HHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 368888888888775331 13333 5678888999999999999999863
No 94
>PRK13407 bchI magnesium chelatase subunit I; Provisional
Probab=55.80 E-value=45 Score=28.21 Aligned_cols=48 Identities=6% Similarity=0.007 Sum_probs=39.8
Q ss_pred cchhhHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCccCHHHHHHHH
Q 032845 34 DISVHKDALLAFCESARIFI-------HYLSATANDICKESKRQTINAEDVLKAI 81 (132)
Q Consensus 34 ~~~ISkDA~~al~~~a~~FI-------~~ltseA~~~a~~~kRKTI~~eDVl~AL 81 (132)
.+.++.+....+.+.+..+= .++...|...|--+||..|+++||..+.
T Consensus 249 ~V~v~~~~~~yi~~l~~~~~~~s~Ra~i~l~~aA~a~A~l~Gr~~V~~~Di~~~~ 303 (334)
T PRK13407 249 QLKTPNTVLHDCAALCIALGSDGLRGELTLLRAARALAAFEGAEAVGRSHLRSVA 303 (334)
T ss_pred CcccCHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHHcCCCeeCHHHHHHHH
Confidence 68899999999998887764 2366778888999999999999996654
No 95
>COG5248 TAF19 Transcription initiation factor TFIID, subunit TAF13 [Transcription]
Probab=53.78 E-value=53 Score=24.23 Aligned_cols=48 Identities=19% Similarity=0.238 Sum_probs=41.1
Q ss_pred cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 032845 34 DISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (132)
Q Consensus 34 ~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~ 83 (132)
.+.=..|..++|.+.+.-+++.+...|...|. .|-.+..+|..-||++
T Consensus 25 vv~P~~dt~~~L~e~V~dY~~~~ctna~~~Aq--~rnK~k~eDfkfaLr~ 72 (126)
T COG5248 25 VVAPRYDTAEALHEYVLDYMSILCTNAHNMAQ--VRNKTKTEDFKFALRR 72 (126)
T ss_pred CCCcchhHHHHHHHHHHHHHHHHHHHHHHHHH--hcccchHHHHHHHHhh
Confidence 34567889999999999999999999999997 4566788999999975
No 96
>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=53.72 E-value=33 Score=30.44 Aligned_cols=49 Identities=27% Similarity=0.302 Sum_probs=41.0
Q ss_pred CcchhhHHHHHHHHHHHHH----HHHHHHHHHHHHHHhcCCCccCHHHHHHHH
Q 032845 33 TDISVHKDALLAFCESARI----FIHYLSATANDICKESKRQTINAEDVLKAI 81 (132)
Q Consensus 33 ~~~~ISkDA~~al~~~a~~----FI~~ltseA~~~a~~~kRKTI~~eDVl~AL 81 (132)
.++.+|+||.+.|....++ |..-|-+-|+.+|+..|+++|..+||-.|-
T Consensus 377 e~i~l~~~Ale~L~~ig~etSLRYa~qLL~pa~iiA~~rg~~~V~~~dVe~a~ 429 (450)
T COG1224 377 EDIELSDDALEYLTDIGEETSLRYAVQLLTPASIIAKRRGSKRVEVEDVERAK 429 (450)
T ss_pred hccccCHHHHHHHHhhchhhhHHHHHHhccHHHHHHHHhCCCeeehhHHHHHH
Confidence 4789999999999877655 445556678999999999999999999984
No 97
>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=53.22 E-value=23 Score=27.03 Aligned_cols=84 Identities=17% Similarity=0.206 Sum_probs=29.3
Q ss_pred ccchhhcccchhHHHHHHhhhccCCCC---------------CCcchhhHHHHH-HHHHHHHHHHHHHHHHHHHHHHhcC
Q 032845 5 KVVPEAEELPKTIVRRVVKDKLHNCSP---------------DTDISVHKDALL-AFCESARIFIHYLSATANDICKESK 68 (132)
Q Consensus 5 k~~~Ed~~LP~a~V~RimK~~Lp~~~~---------------d~~~~ISkDA~~-al~~~a~~FI~~ltseA~~~a~~~k 68 (132)
+-+.+.+.+..+||.|+++..-=.++. +.+..+|.++.. .|.+ -+...++
T Consensus 53 ~~iA~~lgl~~STVSRav~~Ky~~t~~Gi~plk~fF~~~~~~~~~~~~S~~~ik~~i~~--------------lI~~Ed~ 118 (160)
T PF04552_consen 53 KDIADELGLHESTVSRAVKNKYIQTPRGIFPLKDFFSRSVSSGSGEEFSSEAIKARIKE--------------LIEEEDK 118 (160)
T ss_dssp --------------------------------S-----SS--SS-SS---TTH-HHHHH--------------HHTTS-T
T ss_pred HHHHHHhCCCHhHHHHHHcCceeecCCeeeeHHHhccccccCCCCcccHHHHHHHHHHH--------------HHHhcCC
Confidence 346788899999999999875433321 011123444332 3322 3455678
Q ss_pred CCccCHHHHHHHHHHCCCcccHHHHHHHHHHHHHHhhh
Q 032845 69 RQTINAEDVLKAIEEIDFTEFVDPLRDSLDAKQIVSQK 106 (132)
Q Consensus 69 RKTI~~eDVl~AL~~lgf~~y~~~l~~~l~~~k~~~q~ 106 (132)
.+.+|-+.|...|+.-| +..-..-..+||+....
T Consensus 119 ~~PlSD~~i~~~L~~~g----i~isRRTVaKYR~~L~I 152 (160)
T PF04552_consen 119 KKPLSDQEIAELLKEEG----IKISRRTVAKYREELGI 152 (160)
T ss_dssp TS---HHHHHHHHTTTT----S---HHHHHHHHHHHT-
T ss_pred CCCCCHHHHHHHHHHcC----CCccHHHHHHHHHHcCC
Confidence 89999999999999887 45667888899976654
No 98
>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=52.52 E-value=17 Score=21.82 Aligned_cols=24 Identities=25% Similarity=0.566 Sum_probs=20.7
Q ss_pred CHHHHHHHHHHCCCcccHHHHHHH
Q 032845 73 NAEDVLKAIEEIDFTEFVDPLRDS 96 (132)
Q Consensus 73 ~~eDVl~AL~~lgf~~y~~~l~~~ 96 (132)
++++|..-|+.+|+++|.+.+.+.
T Consensus 3 ~~~~V~~wL~~~~~~~y~~~f~~~ 26 (63)
T cd00166 3 SPEDVAEWLESLGLGQYADNFREN 26 (63)
T ss_pred CHHHHHHHHHHcChHHHHHHHHHc
Confidence 678999999999999998887654
No 99
>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=52.30 E-value=23 Score=21.88 Aligned_cols=23 Identities=13% Similarity=0.419 Sum_probs=20.2
Q ss_pred CHHHHHHHHHHCCCcccHHHHHH
Q 032845 73 NAEDVLKAIEEIDFTEFVDPLRD 95 (132)
Q Consensus 73 ~~eDVl~AL~~lgf~~y~~~l~~ 95 (132)
++++|..-|+.+|+++|.+....
T Consensus 4 ~~~~V~~WL~~~~l~~y~~~F~~ 26 (64)
T PF00536_consen 4 SVEDVSEWLKSLGLEQYAENFEK 26 (64)
T ss_dssp SHHHHHHHHHHTTGGGGHHHHHH
T ss_pred CHHHHHHHHHHCCCHHHHHHHHc
Confidence 68999999999999999988743
No 100
>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=51.65 E-value=22 Score=26.93 Aligned_cols=69 Identities=16% Similarity=0.224 Sum_probs=47.1
Q ss_pred HHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHCCCcccHHHHHHHH
Q 032845 18 VRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFTEFVDPLRDSL 97 (132)
Q Consensus 18 V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~lgf~~y~~~l~~~l 97 (132)
+.|+++.+. +.-|.|+-..-+...++.=+.-|.-.|...|+.++|-+|.+.|+=-. ..+++.+
T Consensus 1 fe~lFR~aa-------~LdvdK~d~~r~~d~V~~Kl~DLl~va~~~Ak~ngRdvI~~~DLPIT----------kGlqesi 63 (138)
T PF09123_consen 1 FERLFRKAA-------GLDVDKNDAKRYSDFVEKKLYDLLLVAQENAKANGRDVIEPRDLPIT----------KGLQESI 63 (138)
T ss_dssp HHHHHHHHH-------S----HHHHHHHHHHHHHHHHHCCCCHHHHHHHTT-SEE-GGGS-------------HHHHHHH
T ss_pred ChHHHHHHh-------ccCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeeccccCCcc----------HHHHHHH
Confidence 357788876 46777888888888888888888888999999999999999775322 4555666
Q ss_pred HHHHHH
Q 032845 98 DAKQIV 103 (132)
Q Consensus 98 ~~~k~~ 103 (132)
..|++.
T Consensus 64 ~~Fr~l 69 (138)
T PF09123_consen 64 REFRKL 69 (138)
T ss_dssp HHHHTT
T ss_pred HHHHHc
Confidence 666643
No 101
>TIGR00368 Mg chelatase-related protein. The N-terminal end matches very strongly a pfam Mg_chelatase domain.
Probab=51.26 E-value=44 Score=29.83 Aligned_cols=47 Identities=17% Similarity=0.169 Sum_probs=40.8
Q ss_pred hhhHHHHHHHHHHHHHH------HHHHHHHHHHHHHhcCCCccCHHHHHHHHH
Q 032845 36 SVHKDALLAFCESARIF------IHYLSATANDICKESKRQTINAEDVLKAIE 82 (132)
Q Consensus 36 ~ISkDA~~al~~~a~~F------I~~ltseA~~~a~~~kRKTI~~eDVl~AL~ 82 (132)
.+++++..+|.++...| .+-|..-|..+|.=+++..|+.+||..|+.
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 46889999999988887 566778899999999999999999999985
No 102
>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=49.42 E-value=67 Score=29.16 Aligned_cols=50 Identities=14% Similarity=0.179 Sum_probs=38.6
Q ss_pred cchhhHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 032845 34 DISVHKDALLAFCESARIFI-------HYLSATANDICKESKRQTINAEDVLKAIEE 83 (132)
Q Consensus 34 ~~~ISkDA~~al~~~a~~FI-------~~ltseA~~~a~~~kRKTI~~eDVl~AL~~ 83 (132)
.+.|+.+....|.+.+..+- .++...|...|.=++|.+|+++||..|..-
T Consensus 201 ~V~i~~~~~~~l~~~~~~~gv~s~Ra~i~~~r~ArA~Aal~gr~~V~~~Dv~~a~~l 257 (589)
T TIGR02031 201 QVTISAEQVKELVLTAASLGISGHRADLFAVRAAKAHAALHGRTEVTEEDLKLAVEL 257 (589)
T ss_pred CccCCHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHH
Confidence 68899999888877765542 244566777788899999999999998753
No 103
>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=48.78 E-value=14 Score=22.31 Aligned_cols=15 Identities=27% Similarity=0.574 Sum_probs=12.3
Q ss_pred HHHHHHHHHHCCCcc
Q 032845 74 AEDVLKAIEEIDFTE 88 (132)
Q Consensus 74 ~eDVl~AL~~lgf~~ 88 (132)
.+|++.||..|||..
T Consensus 3 ~~d~~~AL~~LGy~~ 17 (47)
T PF07499_consen 3 LEDALEALISLGYSK 17 (47)
T ss_dssp HHHHHHHHHHTTS-H
T ss_pred HHHHHHHHHHcCCCH
Confidence 379999999999984
No 104
>PRK13765 ATP-dependent protease Lon; Provisional
Probab=48.15 E-value=37 Score=31.32 Aligned_cols=48 Identities=25% Similarity=0.254 Sum_probs=38.7
Q ss_pred hhhHHHHHHHHHHHHHH-------------HHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 032845 36 SVHKDALLAFCESARIF-------------IHYLSATANDICKESKRQTINAEDVLKAIEE 83 (132)
Q Consensus 36 ~ISkDA~~al~~~a~~F-------------I~~ltseA~~~a~~~kRKTI~~eDVl~AL~~ 83 (132)
.++.+|...|-+.++-- +.-|-.+|..+|...+++.|+++||..|+..
T Consensus 339 ~f~~eAVa~LI~~~~R~ag~r~~lsl~~~~l~~l~r~a~~~a~~~~~~~i~~~~v~~a~~~ 399 (637)
T PRK13765 339 HFDRDAVEEIIREAKRRAGRKGHLTLKLRDLGGLVRVAGDIARSEGAELTTAEHVLEAKKI 399 (637)
T ss_pred CCCHHHHHHHHHHHHHHhCCccccccCHHHHHHHHHHHHHHHHhhccceecHHHHHHHHHh
Confidence 68999988887766632 2336788999999999999999999999843
No 105
>COG5251 TAF40 Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=47.72 E-value=30 Score=27.43 Aligned_cols=64 Identities=13% Similarity=0.089 Sum_probs=48.3
Q ss_pred ccchhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-CCccCHHHHHHHHH
Q 032845 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESK-RQTINAEDVLKAIE 82 (132)
Q Consensus 12 ~LP~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~k-RKTI~~eDVl~AL~ 82 (132)
.||++.|.+++...+. -.||...+.+|+-.+.+|+-.|---|..+-..-+ --.+.+.|+-.|..
T Consensus 115 ~lnKt~VKKlastV~n-------QtVspNi~I~l~g~~KVfvGEiIElA~~Vq~~w~~sgpl~p~h~reayr 179 (199)
T COG5251 115 SLNKTQVKKLASTVAN-------QTVSPNIRIFLQGVGKVFVGEIIELAMIVQNKWLTSGPLIPFHKREAYR 179 (199)
T ss_pred CCCHHHHHHHHHHHhc-------cccCCCeeeeeechhHHHHHHHHHHHHHHHHHhcccCCCChHHHHHHHH
Confidence 6999999999999984 5678888889999999999888777765543211 12377888777643
No 106
>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=47.32 E-value=11 Score=23.49 Aligned_cols=58 Identities=17% Similarity=0.301 Sum_probs=30.6
Q ss_pred chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCc---cCHHHHHHHHHHCCCcccH-HHHHHH
Q 032845 35 ISVHKDALLAFCESARIFIHYLSATANDICKESKRQT---INAEDVLKAIEEIDFTEFV-DPLRDS 96 (132)
Q Consensus 35 ~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKT---I~~eDVl~AL~~lgf~~y~-~~l~~~ 96 (132)
++|.+++..+|.+++. .+..++.+ .-..+=.|. =++...+..|.++|+-+++ |.+..+
T Consensus 2 F~ie~~t~~ai~~~~~-~L~~is~E---Ri~~El~kil~~~~~~~~~~~l~~~gll~~ifP~l~~a 63 (64)
T PF12627_consen 2 FKIEPETEEAIKENAE-LLSKISKE---RIREELEKILSSPNPSRAFKLLDELGLLEYIFPELDAA 63 (64)
T ss_dssp -EE-HHHHHHHHHHGG-GGGGS-HH---HHHHHHHHHHTSTTHHHHHHHHHHTTCHHHHSTTHHT-
T ss_pred CccCHHHHHHHHHHHH-HHhcCCHH---HHHHHHHHHHcCCCHHHHHHHHHHcCCHHHHCcccccc
Confidence 5677777777777665 34444322 111111111 1567778888888976653 666543
No 107
>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]
Probab=47.28 E-value=92 Score=26.62 Aligned_cols=61 Identities=16% Similarity=0.165 Sum_probs=43.3
Q ss_pred chhhHHHHHHHHHHH------HHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHCCCcccHHHHHH
Q 032845 35 ISVHKDALLAFCESA------RIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFTEFVDPLRD 95 (132)
Q Consensus 35 ~~ISkDA~~al~~~a------~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~lgf~~y~~~l~~ 95 (132)
-.++.++..++..-+ .-+..-+...|-++|+.+++.+|+.+||..|-++.+..-+...+..
T Consensus 210 ~~~~~~vl~lia~~~a~~~GDAR~aidilr~A~eiAe~~~~~~v~~~~v~~a~~~~~~~~~~~~~~~ 276 (366)
T COG1474 210 GVIDDDVLKLIAALVAAESGDARKAIDILRRAGEIAEREGSRKVSEDHVREAQEEIERDVLEEVLKT 276 (366)
T ss_pred CCcCccHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHhhCCCCcCHHHHHHHHHHhhHHHHHHHHHc
Confidence 356666655555322 2344567788999999999999999999999777776655555433
No 108
>PRK05574 holA DNA polymerase III subunit delta; Reviewed
Probab=46.88 E-value=1.3e+02 Score=24.13 Aligned_cols=68 Identities=15% Similarity=0.187 Sum_probs=48.3
Q ss_pred ccchhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhc-CCCccCHHHHHHHHHHC
Q 032845 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKES-KRQTINAEDVLKAIEEI 84 (132)
Q Consensus 12 ~LP~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~-kRKTI~~eDVl~AL~~l 84 (132)
.++...+.+.+++.+-. .++.|+.+|...|.+.+..=...+..+-...+.-. +++ |+.+||-..+..-
T Consensus 145 ~~~~~~~~~~i~~~~~~----~g~~i~~~a~~~L~~~~~~d~~~l~~El~KL~l~~~~~~-It~~~I~~~i~~~ 213 (340)
T PRK05574 145 PPKEAELPQWIQQRLKQ----QGLQIDAAALQLLAERVEGNLLALAQELEKLALLYPDGK-ITLEDVEEAVPDS 213 (340)
T ss_pred CCCHHHHHHHHHHHHHH----cCCCCCHHHHHHHHHHhCchHHHHHHHHHHHHhhcCCCC-CCHHHHHHHHhhh
Confidence 45566666667666643 36799999999999988766667777777776543 333 9999987765543
No 109
>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=45.63 E-value=32 Score=18.33 Aligned_cols=26 Identities=12% Similarity=0.181 Sum_probs=19.7
Q ss_pred HHHHHHhcCCCccCHHHHHHHHH-HCC
Q 032845 60 ANDICKESKRQTINAEDVLKAIE-EID 85 (132)
Q Consensus 60 A~~~a~~~kRKTI~~eDVl~AL~-~lg 85 (132)
+....-.++--+|+.+++..+|+ .+|
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 34455667788999999999999 676
No 110
>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=44.89 E-value=51 Score=20.93 Aligned_cols=29 Identities=10% Similarity=0.370 Sum_probs=23.9
Q ss_pred CCccCHHHHHHHHHHCCCcccHHHHHHHH
Q 032845 69 RQTINAEDVLKAIEEIDFTEFVDPLRDSL 97 (132)
Q Consensus 69 RKTI~~eDVl~AL~~lgf~~y~~~l~~~l 97 (132)
...-+.++++.||+.+|..+-++.++..|
T Consensus 55 ~~~at~~~L~~aL~~~~~~d~~~~i~~~~ 83 (83)
T PF00531_consen 55 GPNATVDQLIQALRDIGRNDLAEKIEQML 83 (83)
T ss_dssp GSTSSHHHHHHHHHHTTHHHHHHHHHHH-
T ss_pred CCCCcHHHHHHHHHHCCcHHHHHHHHhhC
Confidence 45667889999999999999988887754
No 111
>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=43.01 E-value=56 Score=24.48 Aligned_cols=61 Identities=13% Similarity=0.242 Sum_probs=36.1
Q ss_pred chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHCCCcc------------cHHHHHHHHHHHH
Q 032845 35 ISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFTE------------FVDPLRDSLDAKQ 101 (132)
Q Consensus 35 ~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~lgf~~------------y~~~l~~~l~~~k 101 (132)
..++.+. +..++..++..+..-..-.. ==.|.+++|+..+|+.+++.. |++.+.+.+++-+
T Consensus 94 ~~i~~~g---~~~~~~~~lr~~~~~~~~~~---~~~tt~~~~l~~~l~~l~~P~~~~~~~i~l~~r~ip~l~~~~~~i~ 166 (224)
T PF02361_consen 94 FSITQEG---LIYAALLALRILAILLASLL---FILTTSPSDLISALRKLRLPYPKIALMISLTLRFIPLLLEEFKRIR 166 (224)
T ss_pred hhhhHHH---HHHHHHHHHHHHHHHHHHHH---HHHHCCHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3455554 34444444444433332222 124789999999999999876 6666666555554
No 112
>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=43.01 E-value=44 Score=20.22 Aligned_cols=35 Identities=20% Similarity=0.223 Sum_probs=28.0
Q ss_pred hhhcccchhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHH
Q 032845 8 PEAEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARI 51 (132)
Q Consensus 8 ~Ed~~LP~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~ 51 (132)
.+...+..++|.|++... -.||.+.++-+.+++.+
T Consensus 6 A~~agvS~~TVSr~ln~~---------~~vs~~tr~rI~~~a~~ 40 (46)
T PF00356_consen 6 AREAGVSKSTVSRVLNGP---------PRVSEETRERILEAAEE 40 (46)
T ss_dssp HHHHTSSHHHHHHHHTTC---------SSSTHHHHHHHHHHHHH
T ss_pred HHHHCcCHHHHHHHHhCC---------CCCCHHHHHHHHHHHHH
Confidence 345578899999999654 36999999999988865
No 113
>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional
Probab=42.91 E-value=40 Score=29.65 Aligned_cols=32 Identities=22% Similarity=0.317 Sum_probs=27.4
Q ss_pred HHHHHHHHHHHHHhcCCCccCHHHHHHHHHHC
Q 032845 53 IHYLSATANDICKESKRQTINAEDVLKAIEEI 84 (132)
Q Consensus 53 I~~ltseA~~~a~~~kRKTI~~eDVl~AL~~l 84 (132)
|..|..+|-..|.+.+|..|+.+|+..|++..
T Consensus 393 I~~i~~eA~~~Alr~~r~~Vt~~D~~~A~~~v 424 (438)
T PTZ00361 393 IKAICTEAGLLALRERRMKVTQADFRKAKEKV 424 (438)
T ss_pred HHHHHHHHHHHHHHhcCCccCHHHHHHHHHHH
Confidence 55677888899999999999999999998763
No 114
>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=42.82 E-value=27 Score=20.96 Aligned_cols=26 Identities=23% Similarity=0.437 Sum_probs=21.2
Q ss_pred ccCHHHHHHHHHHCCCcccHHHHHHH
Q 032845 71 TINAEDVLKAIEEIDFTEFVDPLRDS 96 (132)
Q Consensus 71 TI~~eDVl~AL~~lgf~~y~~~l~~~ 96 (132)
.-+.++|..-|+.+||++|.+.+.+.
T Consensus 3 ~w~~~~v~~wL~~~g~~~y~~~f~~~ 28 (68)
T smart00454 3 QWSPESVADWLESIGLEQYADNFRKN 28 (68)
T ss_pred CCCHHHHHHHHHHCChHHHHHHHHHC
Confidence 34678999999999999988887654
No 115
>PRK05898 dnaE DNA polymerase III DnaE; Validated
Probab=42.77 E-value=12 Score=36.39 Aligned_cols=46 Identities=17% Similarity=0.170 Sum_probs=36.5
Q ss_pred HHHHHHCCCcccHHHHHHHHHHHHHHhhhhhhcCCCcccCCCCcceeeeEee
Q 032845 78 LKAIEEIDFTEFVDPLRDSLDAKQIVSQKVVASNPLFFFRGNHVRRIICHCI 129 (132)
Q Consensus 78 l~AL~~lgf~~y~~~l~~~l~~~k~~~q~~~~~~~~~~~~g~~~~~~~~~~~ 129 (132)
+..+.++||.+|.-.++++++--|+ ..=+-|||||.+.--.+|+|.
T Consensus 262 L~vI~~~gf~~YFLIV~D~i~~Ar~------~gI~vGpGRGSAAGSLVaY~L 307 (971)
T PRK05898 262 LDIINEKQFDDYFLIVYDFINFAKS------NGIIIGPGRGSAAGSLIAYLL 307 (971)
T ss_pred HHHHHhCCCcHHHHHHHHHHHHHHH------CCceeCCCCccHHHHHHHHHh
Confidence 6778899999999999998776553 134568999999888888775
No 116
>TIGR01242 26Sp45 26S proteasome subunit P45 family. Many proteins may score above the trusted cutoff because an internal
Probab=42.77 E-value=43 Score=27.92 Aligned_cols=33 Identities=18% Similarity=0.351 Sum_probs=27.3
Q ss_pred HHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHC
Q 032845 52 FIHYLSATANDICKESKRQTINAEDVLKAIEEI 84 (132)
Q Consensus 52 FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~l 84 (132)
-|..+..+|...|...++..|+.+|+..|++..
T Consensus 331 dl~~l~~~A~~~a~~~~~~~i~~~d~~~a~~~~ 363 (364)
T TIGR01242 331 DLKAICTEAGMFAIREERDYVTMDDFIKAVEKV 363 (364)
T ss_pred HHHHHHHHHHHHHHHhCCCccCHHHHHHHHHHh
Confidence 345667788888888899999999999998763
No 117
>PRK07914 hypothetical protein; Reviewed
Probab=41.74 E-value=70 Score=26.18 Aligned_cols=65 Identities=11% Similarity=0.196 Sum_probs=45.6
Q ss_pred chhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 032845 14 PKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (132)
Q Consensus 14 P~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~ 83 (132)
+...+.+.|++.+-. .+..|+.+|...|.+.+..=+..+.++-...+...+ .+|+.+||-..+..
T Consensus 129 ~~~~l~~wi~~~a~~----~g~~i~~~A~~~L~~~~g~dl~~l~~EleKL~~~~~-~~It~e~V~~~v~~ 193 (320)
T PRK07914 129 KAAERADFVRKEFRS----LRVKVDDDTVTALLDAVGSDLRELASACSQLVADTG-GAVDAAAVRRYHSG 193 (320)
T ss_pred CHHHHHHHHHHHHHH----cCCCCCHHHHHHHHHHHCccHHHHHHHHHHHhcCCC-CCcCHHHHHHHcCC
Confidence 455556666555542 367899999999999987666666666666654333 57999998877553
No 118
>PRK03992 proteasome-activating nucleotidase; Provisional
Probab=41.63 E-value=45 Score=28.41 Aligned_cols=35 Identities=26% Similarity=0.286 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHCCC
Q 032845 52 FIHYLSATANDICKESKRQTINAEDVLKAIEEIDF 86 (132)
Q Consensus 52 FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~lgf 86 (132)
=|..+..+|...|.+.++..|+.+|+..|++..-.
T Consensus 340 dl~~l~~eA~~~a~~~~~~~i~~~d~~~A~~~~~~ 374 (389)
T PRK03992 340 DLKAICTEAGMFAIRDDRTEVTMEDFLKAIEKVMG 374 (389)
T ss_pred HHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHhc
Confidence 34556777888888889999999999999887643
No 119
>PRK06826 dnaE DNA polymerase III DnaE; Reviewed
Probab=40.69 E-value=42 Score=33.22 Aligned_cols=46 Identities=11% Similarity=0.148 Sum_probs=36.4
Q ss_pred HHHHHHCCCcccHHHHHHHHHHHHHHhhhhhhcCCCcccCCCCcceeeeEee
Q 032845 78 LKAIEEIDFTEFVDPLRDSLDAKQIVSQKVVASNPLFFFRGNHVRRIICHCI 129 (132)
Q Consensus 78 l~AL~~lgf~~y~~~l~~~l~~~k~~~q~~~~~~~~~~~~g~~~~~~~~~~~ 129 (132)
+..+..+||++|.=.++++++--|+ ..=+-|||||.+.--.+|+|+
T Consensus 326 L~vI~~mgf~~YFLIV~D~i~~Ak~------~gI~vGpGRGSaAGSLVaY~L 371 (1151)
T PRK06826 326 LSVIKQMGYVDYFLIVWDFIRFARE------NGIMVGPGRGSAAGSLVAYTL 371 (1151)
T ss_pred HHHHHHCCCCccHHHHHHHHHHHHH------CCCeeCCCcccHHHHHHHHHh
Confidence 6778899999999999997765553 255778999998877777764
No 120
>COG1724 Predicted RNA binding protein (dsRBD-like fold), HicA family [General function prediction only]
Probab=40.68 E-value=24 Score=23.58 Aligned_cols=17 Identities=35% Similarity=0.630 Sum_probs=15.4
Q ss_pred ccCHHHHHHHHHHCCCc
Q 032845 71 TINAEDVLKAIEEIDFT 87 (132)
Q Consensus 71 TI~~eDVl~AL~~lgf~ 87 (132)
.+++.+|+++|+.+||.
T Consensus 6 ~~~~ke~ik~Le~~Gf~ 22 (66)
T COG1724 6 RMKAKEVIKALEKDGFQ 22 (66)
T ss_pred cCCHHHHHHHHHhCCcE
Confidence 47899999999999996
No 121
>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=39.95 E-value=55 Score=26.43 Aligned_cols=75 Identities=15% Similarity=0.095 Sum_probs=36.0
Q ss_pred hhcccchhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC------CccCHHHHHHHHH
Q 032845 9 EAEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKR------QTINAEDVLKAIE 82 (132)
Q Consensus 9 Ed~~LP~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kR------KTI~~eDVl~AL~ 82 (132)
++..|....+.+-|.+..... +...+..|...+|.-|+.+.+..|-..+..+|++-.. .+....||-..|.
T Consensus 40 ~~~fL~~~~L~~~i~~i~~~~---g~~~~~~d~l~llS~A~e~rLr~lie~~~~~s~hR~~~~~~~~~~~~~sdv~~qlr 116 (264)
T PF05236_consen 40 EEPFLNPSPLQKRIQKIAKKH---GLKSVDEDVLELLSLATEERLRNLIEKAIVLSRHRRDSSKSDPRYEIRSDVRKQLR 116 (264)
T ss_dssp ----S-HHHHHHHHHHHHHCT---T--EE-TCHHHHHHHHHHHHHHHHHHHHH---------------------------
T ss_pred cccccCHHHHHHHHHHHHHHc---CCcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccCCCcccccchHHHHHHH
Confidence 456777788888887776531 2468999999999999999999999999999875321 1233566766666
Q ss_pred HCCC
Q 032845 83 EIDF 86 (132)
Q Consensus 83 ~lgf 86 (132)
.|.-
T Consensus 117 ~l~~ 120 (264)
T PF05236_consen 117 FLEQ 120 (264)
T ss_dssp ----
T ss_pred HHHH
Confidence 5554
No 122
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=39.85 E-value=19 Score=21.64 Aligned_cols=19 Identities=32% Similarity=0.504 Sum_probs=14.2
Q ss_pred hhhcccchhHHHHHHhhhc
Q 032845 8 PEAEELPKTIVRRVVKDKL 26 (132)
Q Consensus 8 ~Ed~~LP~a~V~RimK~~L 26 (132)
.+.+.+|++++.|+++.-.
T Consensus 25 a~~~gl~~stv~r~L~tL~ 43 (52)
T PF09339_consen 25 ARALGLPKSTVHRLLQTLV 43 (52)
T ss_dssp HHHHTS-HHHHHHHHHHHH
T ss_pred HHHHCcCHHHHHHHHHHHH
Confidence 4567899999999997643
No 123
>PRK02910 light-independent protochlorophyllide reductase subunit B; Provisional
Probab=39.29 E-value=70 Score=28.44 Aligned_cols=52 Identities=12% Similarity=0.178 Sum_probs=39.8
Q ss_pred CcchhhHHHHHHHHHHHHHHHH-HHHHHHHHHHHhcCCCccCHHHHHHHHHHCC
Q 032845 33 TDISVHKDALLAFCESARIFIH-YLSATANDICKESKRQTINAEDVLKAIEEID 85 (132)
Q Consensus 33 ~~~~ISkDA~~al~~~a~~FI~-~ltseA~~~a~~~kRKTI~~eDVl~AL~~lg 85 (132)
+.+.++.||...|.+ .=-|+. -+=..+-+.|...|...|+.+.+..|-..+|
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 467899999999965 444444 3445566678899999999999999977654
No 124
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=39.05 E-value=75 Score=28.08 Aligned_cols=88 Identities=13% Similarity=0.143 Sum_probs=59.0
Q ss_pred ccchhhcccchhHHHHHHhhhccCCCC---------------CCcchhhHHHHH-HHHHHHHHHHHHHHHHHHHHHHhcC
Q 032845 5 KVVPEAEELPKTIVRRVVKDKLHNCSP---------------DTDISVHKDALL-AFCESARIFIHYLSATANDICKESK 68 (132)
Q Consensus 5 k~~~Ed~~LP~a~V~RimK~~Lp~~~~---------------d~~~~ISkDA~~-al~~~a~~FI~~ltseA~~~a~~~k 68 (132)
|-+.+.+.|-.+||.|+++...=+++- +++--+|.+++. .|. .-+...++
T Consensus 347 kdvAe~lglheSTVSRav~~Kyv~tp~Gi~~lk~FFs~~~~~~~g~~~S~~~Ik~~Ik--------------~lI~~Ed~ 412 (455)
T PRK05932 347 KDIAEELGMHESTISRATTNKYMATPRGIFELKYFFSSAVSTDGGGEASSTAIRALIK--------------KLIAAENP 412 (455)
T ss_pred HHHHHHhCCCccchhhhhcCceeecCCceEEHHHhcccccCCCCCccccHHHHHHHHH--------------HHHHhcCC
Confidence 346788899999999999776544331 000113444432 222 24556788
Q ss_pred CCccCHHHHHHHHHHCCCcccHHHHHHHHHHHHHHhhhhhhc
Q 032845 69 RQTINAEDVLKAIEEIDFTEFVDPLRDSLDAKQIVSQKVVAS 110 (132)
Q Consensus 69 RKTI~~eDVl~AL~~lgf~~y~~~l~~~l~~~k~~~q~~~~~ 110 (132)
++.+|-+.|...|+.-|+. .-..-..+||+....-.++
T Consensus 413 ~~PlSD~~I~~~L~~~Gi~----IaRRTVaKYRe~L~Ip~s~ 450 (455)
T PRK05932 413 KKPLSDSKIAELLKEQGID----VARRTVAKYREALNIPSSS 450 (455)
T ss_pred CCCCCHHHHHHHHHHcCCC----eehHHHHHHHHHcCCCChH
Confidence 8999999999999999984 5577888999866554333
No 125
>smart00350 MCM minichromosome maintenance proteins.
Probab=38.82 E-value=94 Score=27.50 Aligned_cols=69 Identities=10% Similarity=0.138 Sum_probs=44.6
Q ss_pred ccchhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHH-------------------HHHHHHHHHHHHHhcCCCcc
Q 032845 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIF-------------------IHYLSATANDICKESKRQTI 72 (132)
Q Consensus 12 ~LP~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~F-------------------I~~ltseA~~~a~~~kRKTI 72 (132)
.++...+.+.+.-+=.. -...+|+++.+.|.+..... +..|...|...|.-..|.+|
T Consensus 417 ~~~~~~l~~yi~~ar~~----~~P~ls~~~~~~i~~~y~~~R~~~~~~~~~~~~~~t~R~l~sliRla~A~A~l~~r~~V 492 (509)
T smart00350 417 PISQEFLRKYIAYAREK----IKPKLSEEAAEKLVKAYVDLRKEDSQSEARSSIPITVRQLESIIRLSEAHAKMRLSDVV 492 (509)
T ss_pred cCCHHHHHHHHHHHHhc----CCCCCCHHHHHHHHHHHHHhcccccccccccccCcCHHHHHHHHHHHHHHHHHcCCCcc
Confidence 35555566555333100 01258999988887654442 24455667777888999999
Q ss_pred CHHHHHHHHHHC
Q 032845 73 NAEDVLKAIEEI 84 (132)
Q Consensus 73 ~~eDVl~AL~~l 84 (132)
+++||..|++-+
T Consensus 493 ~~~Dv~~ai~l~ 504 (509)
T smart00350 493 EEADVEEAIRLL 504 (509)
T ss_pred CHHHHHHHHHHH
Confidence 999999997653
No 126
>TIGR02454 CbiQ_TIGR cobalt ABC transporter, permease protein CbiQ. This model represents the permease component of the cobalt-specific ABC transporter. This model finds permeases which are generally next to the other subunits of the complex (CbiN and CbiO) or the cobalamin biosynthesis protein CbiM which is a transmembrane protein which likely interacts with the complex in some manner. In genomes which possess all of these subunits the ATPase is most likely running in the direction of import (for the biosynthesis of coenzyme B12). In other genomes, this subunit may be involved in the export of cobalt and/or other closely related heavy metals.
Probab=38.57 E-value=67 Score=24.03 Aligned_cols=35 Identities=14% Similarity=0.214 Sum_probs=25.8
Q ss_pred CccCHHHHHHHHHHCCCcc-----------cHHHHHHHHHHHHHHh
Q 032845 70 QTINAEDVLKAIEEIDFTE-----------FVDPLRDSLDAKQIVS 104 (132)
Q Consensus 70 KTI~~eDVl~AL~~lgf~~-----------y~~~l~~~l~~~k~~~ 104 (132)
-|.++.|+..+|+.+|++. |++.+.+..++-++.+
T Consensus 112 ~TT~~~~l~~~l~~l~~P~~~~~~~~l~~Rfip~l~~e~~~i~~Aq 157 (198)
T TIGR02454 112 LTTPFPELLSALRRLGVPPLLVEILLLTYRYLFVLLEELRRMLLAQ 157 (198)
T ss_pred HcCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4678999999999999873 6666666665555433
No 127
>COG1500 Predicted exosome subunit [Translation, ribosomal structure and biogenesis]
Probab=36.54 E-value=1.3e+02 Score=24.63 Aligned_cols=72 Identities=17% Similarity=0.210 Sum_probs=51.3
Q ss_pred hHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHH-HHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHCCCc-ccHHHH
Q 032845 16 TIVRRVVKDKLHNCSPDTDISVHKDALLAFCESAR-IFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFT-EFVDPL 93 (132)
Q Consensus 16 a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~-~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~lgf~-~y~~~l 93 (132)
+.+..|+++.|.. |.+.+|.+-+..|++.-. ..|++|+..|.+ -..+....+.-|-+||++++|. ++....
T Consensus 70 td~~eI~~eIl~k----GeiQlTaeqR~~m~e~k~rqIi~~IsRn~Id---P~t~~P~Pp~rIe~Ameeakv~id~~K~a 142 (234)
T COG1500 70 TDPDEIAEEILKK----GEIQLTAEQRREMLEEKKRQIINIISRNAID---PQTKAPHPPARIEKAMEEAKVHIDPFKSA 142 (234)
T ss_pred CCHHHHHHHHHhc----CceeccHHHHHHHHHHHHHHHHHHHHHhccC---CCCCCCCCHHHHHHHHHhcCcccCCCCCH
Confidence 3466666666653 678999999887777664 555677765543 3456789999999999999997 444444
Q ss_pred H
Q 032845 94 R 94 (132)
Q Consensus 94 ~ 94 (132)
+
T Consensus 143 e 143 (234)
T COG1500 143 E 143 (234)
T ss_pred H
Confidence 3
No 128
>TIGR00594 polc DNA-directed DNA polymerase III (polc). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=35.86 E-value=17 Score=35.26 Aligned_cols=46 Identities=15% Similarity=0.191 Sum_probs=36.7
Q ss_pred HHHHHHCCCcccHHHHHHHHHHHHHHhhhhhhcCCCcccCCCCcceeeeEee
Q 032845 78 LKAIEEIDFTEFVDPLRDSLDAKQIVSQKVVASNPLFFFRGNHVRRIICHCI 129 (132)
Q Consensus 78 l~AL~~lgf~~y~~~l~~~l~~~k~~~q~~~~~~~~~~~~g~~~~~~~~~~~ 129 (132)
|..+..+||.+|.=.++++++--|+ ..=+-|||||.+.--.+|+|+
T Consensus 330 L~vI~~~gf~~YFLIV~D~v~~Ar~------~gI~vGpGRGSaAgSlVaY~L 375 (1022)
T TIGR00594 330 LDVINSMGFPGYFLIVWDFIKWAKD------HGIPVGPGRGSAAGSLVAYAL 375 (1022)
T ss_pred HHHHHhCCCchhHHHHHHHHHHHHH------CCCeeCCCCChHHHHHHHHHh
Confidence 6788899999999999987765442 145678999999888888875
No 129
>PF08823 PG_binding_2: Putative peptidoglycan binding domain; InterPro: IPR014927 This entry may be a peptidoglycan binding domain.
Probab=35.80 E-value=62 Score=21.59 Aligned_cols=30 Identities=20% Similarity=0.299 Sum_probs=23.9
Q ss_pred HHHHHHHHHHCCC------cccHHHHHHHHHHHHHH
Q 032845 74 AEDVLKAIEEIDF------TEFVDPLRDSLDAKQIV 103 (132)
Q Consensus 74 ~eDVl~AL~~lgf------~~y~~~l~~~l~~~k~~ 103 (132)
+..|..+|..||| +.|-+..++.|..|...
T Consensus 18 ~~evq~~L~~lGyy~g~~~g~~d~a~~~Al~~~~g~ 53 (74)
T PF08823_consen 18 AREVQEALKRLGYYKGEADGVWDEATEDALRAWAGT 53 (74)
T ss_pred HHHHHHHHHHcCCccCCCCCcccHHHHHHHHHHHHH
Confidence 3568889999999 56888888888888743
No 130
>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional
Probab=35.36 E-value=65 Score=27.83 Aligned_cols=32 Identities=19% Similarity=0.172 Sum_probs=27.4
Q ss_pred HHHHHHHHHHHHHhcCCCccCHHHHHHHHHHC
Q 032845 53 IHYLSATANDICKESKRQTINAEDVLKAIEEI 84 (132)
Q Consensus 53 I~~ltseA~~~a~~~kRKTI~~eDVl~AL~~l 84 (132)
|..|..+|...|...+|..|+.+|+..|++..
T Consensus 355 I~~l~~eA~~~A~r~~~~~i~~~df~~A~~~v 386 (398)
T PTZ00454 355 IAAICQEAGMQAVRKNRYVILPKDFEKGYKTV 386 (398)
T ss_pred HHHHHHHHHHHHHHcCCCccCHHHHHHHHHHH
Confidence 56677888888889999999999999998764
No 131
>TIGR01343 hacA_fam homoaconitate hydratase family protein. This model represents a subfamily of proteins consisting of aconitase, homoaconitase, 3-isopropylmalate dehydratase, and uncharacterized proteins. The majority of the members of this family have been designated as 3-isopropylmalate dehydratase large subunit (LeuC) in microbial genome annotation, but the only characterized member is Thermus thermophilus homoaconitase, an enzyme of a non-aspartate pathway of Lys biosynthesis.
Probab=35.11 E-value=58 Score=28.67 Aligned_cols=29 Identities=28% Similarity=0.448 Sum_probs=16.8
Q ss_pred HHHHhhhhhhcCCC-cccCCCCcceeeeEeeecC
Q 032845 100 KQIVSQKVVASNPL-FFFRGNHVRRIICHCIILE 132 (132)
Q Consensus 100 ~k~~~q~~~~~~~~-~~~~g~~~~~~~~~~~~~~ 132 (132)
++....-.+..... +.+-| .||||.+.+|
T Consensus 75 ~~~~r~fa~~~gi~~~~~~g----~GI~H~v~~E 104 (412)
T TIGR01343 75 QKLAREFVKKTGIKHFFDVG----EGICHQVLPE 104 (412)
T ss_pred HHHHHHHHHHcCCceeecCC----CCEEEEEchh
Confidence 33333333344444 55555 4999999876
No 132
>PF00403 HMA: Heavy-metal-associated domain; InterPro: IPR006121 Proteins that transport heavy metals in micro-organisms and mammals share similarities in their sequences and structures. These proteins provide an important focus for research, some being involved in bacterial resistance to toxic metals, such as lead and cadmium, while others are involved in inherited human syndromes, such as Wilson's and Menke's diseases []. A conserved domain has been found in a number of these heavy metal transport or detoxification proteins []. The domain, which has been termed Heavy-Metal-Associated (HMA), contains two conserved cysteines that are probably involved in metal binding. Structure solution of the fourth HMA domain of the Menke's copper transporting ATPase shows a well-defined structure comprising a four-stranded antiparallel beta-sheet and two alpha helices packed in an alpha-beta sandwich fold []. This fold is common to other domains and is classified as "ferredoxin-like".; GO: 0046872 metal ion binding, 0030001 metal ion transport; PDB: 2VOY_A 1P6T_A 1KQK_A 2RML_A 1JWW_A 3K7R_F 1FES_A 1CC8_A 1FD8_A 2GGP_A ....
Probab=34.61 E-value=39 Score=20.51 Aligned_cols=16 Identities=25% Similarity=0.547 Sum_probs=14.0
Q ss_pred cCHHHHHHHHHHCCCc
Q 032845 72 INAEDVLKAIEEIDFT 87 (132)
Q Consensus 72 I~~eDVl~AL~~lgf~ 87 (132)
++.++|..+++.+||+
T Consensus 47 ~~~~~i~~~i~~~Gy~ 62 (62)
T PF00403_consen 47 TSIEKIIEAIEKAGYE 62 (62)
T ss_dssp SCHHHHHHHHHHTTSE
T ss_pred CCHHHHHHHHHHhCcC
Confidence 6779999999999984
No 133
>PRK09526 lacI lac repressor; Reviewed
Probab=34.23 E-value=60 Score=25.79 Aligned_cols=38 Identities=13% Similarity=0.156 Sum_probs=30.2
Q ss_pred cccchhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHH
Q 032845 11 EELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSA 58 (132)
Q Consensus 11 ~~LP~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~lts 58 (132)
...-++||.|++... -.||.+.++-+.+++.+ +.|.-.
T Consensus 15 aGVS~~TVSrvLn~~---------~~vs~~tr~rV~~~a~e-lgY~pn 52 (342)
T PRK09526 15 AGVSYQTVSRVLNQA---------SHVSAKTREKVEAAMAE-LNYVPN 52 (342)
T ss_pred hCCCHHHHHHHhcCC---------CCCCHHHHHHHHHHHHH-HCCCcC
Confidence 478899999999542 36999999999999988 556543
No 134
>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=34.22 E-value=90 Score=27.67 Aligned_cols=51 Identities=14% Similarity=0.231 Sum_probs=38.9
Q ss_pred cchhhHHHHHHHHHHHHHHHH-HHHHHHHHHHHhcCCCccCHHHHHHHHHHCC
Q 032845 34 DISVHKDALLAFCESARIFIH-YLSATANDICKESKRQTINAEDVLKAIEEID 85 (132)
Q Consensus 34 ~~~ISkDA~~al~~~a~~FI~-~ltseA~~~a~~~kRKTI~~eDVl~AL~~lg 85 (132)
.+.+|.||...|.+ .=-|+. -+=..+-+.|...|...|+.+.+..|=..+|
T Consensus 460 ~~~w~~ea~~~l~~-~P~f~r~~~r~~~e~~a~~~g~~~it~~~~~~a~~~~~ 511 (511)
T TIGR01278 460 ELGWTAEAEAELKK-VPFFVRGKVRRNTENFARERGYSVITLEVIYAAKEHFG 511 (511)
T ss_pred CCCcCHHHHHHHhh-CChhhhHHHHHHHHHHHHHcCCCEEcHHHHHHHHHhcC
Confidence 57899999999965 334443 4445566678999999999999999876654
No 135
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=34.10 E-value=1.1e+02 Score=20.40 Aligned_cols=28 Identities=4% Similarity=0.014 Sum_probs=19.1
Q ss_pred HHHHHHhcCCCccCHHHHHHHHHHCCCc
Q 032845 60 ANDICKESKRQTINAEDVLKAIEEIDFT 87 (132)
Q Consensus 60 A~~~a~~~kRKTI~~eDVl~AL~~lgf~ 87 (132)
+......++..+|+.+++..+|..+|+.
T Consensus 15 ~F~~~D~d~~G~Is~~el~~~l~~~~~~ 42 (96)
T smart00027 15 IFRSLDKNQDGTVTGAQAKPILLKSGLP 42 (96)
T ss_pred HHHHhCCCCCCeEeHHHHHHHHHHcCCC
Confidence 3444555666778888888888777765
No 136
>PRK05673 dnaE DNA polymerase III subunit alpha; Validated
Probab=33.68 E-value=19 Score=35.45 Aligned_cols=46 Identities=15% Similarity=0.185 Sum_probs=36.0
Q ss_pred HHHHHHCCCcccHHHHHHHHHHHHHHhhhhhhcCCCcccCCCCcceeeeEee
Q 032845 78 LKAIEEIDFTEFVDPLRDSLDAKQIVSQKVVASNPLFFFRGNHVRRIICHCI 129 (132)
Q Consensus 78 l~AL~~lgf~~y~~~l~~~l~~~k~~~q~~~~~~~~~~~~g~~~~~~~~~~~ 129 (132)
+..+.++||++|.=.++.+++--|+ ..=+-|||||.+.--.+|.|+
T Consensus 326 L~vI~~mgf~~YFLIV~D~i~~Ak~------~gI~vGpGRGSaAGSLVaY~L 371 (1135)
T PRK05673 326 LDVIIQMGFPGYFLIVADFIQWAKD------NGIPVGPGRGSGAGSLVAYAL 371 (1135)
T ss_pred HHHHHhCCCCccHHHHHHHHHHHHH------CCCeeCCCCchHHHHHHHHHh
Confidence 6778899999999999998775442 145678999998877777764
No 137
>TIGR00170 leuC 3-isopropylmalate dehydratase, large subunit. Several pairs of archaeal proteins resemble the leuC and leuD pair in length and sequence but even more closely resemble the respective domains of homoaconitase, and their identity is uncertain. These homologs are now described by a separate model of subfamily (rather than equivalog) homology type, and the priors and cutoffs for this model have been changed to focus this equivalog family more narrowly.
Probab=33.62 E-value=45 Score=29.75 Aligned_cols=19 Identities=26% Similarity=0.186 Sum_probs=13.5
Q ss_pred CcccCCCCcceeeeEeeecC
Q 032845 113 LFFFRGNHVRRIICHCIILE 132 (132)
Q Consensus 113 ~~~~~g~~~~~~~~~~~~~~ 132 (132)
.+.+- +.++.||||.+.+|
T Consensus 96 ~~~~v-~~p~~GI~Hqv~~E 114 (465)
T TIGR00170 96 RLFDL-HSVDQGIVHVMGPE 114 (465)
T ss_pred eeecc-CCCCCCEeCeEccc
Confidence 34443 35778999999887
No 138
>KOG3537 consensus Adaptor protein NUMB [Signal transduction mechanisms]
Probab=33.35 E-value=25 Score=31.70 Aligned_cols=14 Identities=36% Similarity=0.816 Sum_probs=11.7
Q ss_pred CCCCcceeeeEeee
Q 032845 117 RGNHVRRIICHCII 130 (132)
Q Consensus 117 ~g~~~~~~~~~~~~ 130 (132)
|-+-.||-||||.+
T Consensus 121 RDGttRRW~CH~Fl 134 (543)
T KOG3537|consen 121 RDGTTRRWMCHGFL 134 (543)
T ss_pred ecCCcceeeeeeee
Confidence 55778999999975
No 139
>PRK06585 holA DNA polymerase III subunit delta; Reviewed
Probab=32.95 E-value=1.5e+02 Score=24.16 Aligned_cols=65 Identities=12% Similarity=0.115 Sum_probs=43.2
Q ss_pred hhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHh-cCCCccCHHHHHHHHHH
Q 032845 15 KTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKE-SKRQTINAEDVLKAIEE 83 (132)
Q Consensus 15 ~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~-~kRKTI~~eDVl~AL~~ 83 (132)
...+.+.+.+.+-. .+.+|+.+|...|.+.+.-=...+..+-...+.- .+.++|+.+||...+..
T Consensus 144 ~~~l~~~i~~~~~~----~g~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~It~edV~~lv~~ 209 (343)
T PRK06585 144 ERDLARLIDDELAE----AGLRITPDARALLVALLGGDRLASRNEIEKLALYAHGKGEITLDDVRAVVGD 209 (343)
T ss_pred HHHHHHHHHHHHHH----CCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHhCC
Confidence 33444444444432 3689999999999998876555566666666554 44568999999776543
No 140
>PRK07135 dnaE DNA polymerase III DnaE; Validated
Probab=32.89 E-value=23 Score=34.34 Aligned_cols=46 Identities=11% Similarity=0.147 Sum_probs=36.0
Q ss_pred HHHHHHCCCcccHHHHHHHHHHHHHHhhhhhhcCCCcccCCCCcceeeeEee
Q 032845 78 LKAIEEIDFTEFVDPLRDSLDAKQIVSQKVVASNPLFFFRGNHVRRIICHCI 129 (132)
Q Consensus 78 l~AL~~lgf~~y~~~l~~~l~~~k~~~q~~~~~~~~~~~~g~~~~~~~~~~~ 129 (132)
+..+..+||.+|.=.+..+.+--|+ ..=+-|||||.+.--.+|.|.
T Consensus 260 L~vI~~~gf~~YFLIV~D~v~~Ak~------~gI~vGpGRGSaAGSLVaY~L 305 (973)
T PRK07135 260 YSVIKKLKFSNYFLIIWDFIKWARK------NKISIGPGRGSASGSLVSYLL 305 (973)
T ss_pred HHHHHhCCCchhHHHHHHHHHHHHH------CCceeCCCCcchHHHHHHHHh
Confidence 6778899999999999887765442 245678999999888777775
No 141
>KOG1528 consensus Salt-sensitive 3'-phosphoadenosine-5'-phosphatase HAL2/SAL1 [Nucleotide transport and metabolism; Inorganic ion transport and metabolism]
Probab=32.77 E-value=1.2e+02 Score=26.13 Aligned_cols=70 Identities=16% Similarity=0.171 Sum_probs=40.7
Q ss_pred hhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHH-HHHHHHHHHHHHHH---HHHhcCC-CccCHHHHHHHHHHCCCc
Q 032845 15 KTIVRRVVKDKLHNCSPDTDISVHKDALLAFCES-ARIFIHYLSATAND---ICKESKR-QTINAEDVLKAIEEIDFT 87 (132)
Q Consensus 15 ~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~-a~~FI~~ltseA~~---~a~~~kR-KTI~~eDVl~AL~~lgf~ 87 (132)
.|.|.-.+++.+|+.+ --.+..|-...|.+. ++.|+.-|+..-|+ ....=+- ++.+.+||++|+..=+.+
T Consensus 52 QAiVs~vL~~~f~~~p---~slVaEEds~~Lr~n~~~~~l~~i~~lvnetl~s~~sy~~~~~ls~~dvl~aID~G~s~ 126 (351)
T KOG1528|consen 52 QAIVSLVLEREFPDDP---LSLVAEEDSGFLRKNGSEGLLSRITKLVNETLASDESYGDNSPLSSDDVLKAIDRGNSE 126 (351)
T ss_pred HHHHHHHHHHHcCCCC---cceEeeccchhhhhhhhHHHHHHHHHHHHHHhhhhhhccCCCCCCHHHHHHHHhccccc
Confidence 3788888999998622 113333333334333 45555555553333 2222222 789999999998765443
No 142
>COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]
Probab=32.67 E-value=1.9e+02 Score=25.82 Aligned_cols=88 Identities=14% Similarity=0.183 Sum_probs=59.9
Q ss_pred cchhhcccchhHHHHHHhhhccCCCCC----------------CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 032845 6 VVPEAEELPKTIVRRVVKDKLHNCSPD----------------TDISVHKDALLAFCESARIFIHYLSATANDICKESKR 69 (132)
Q Consensus 6 ~~~Ed~~LP~a~V~RimK~~Lp~~~~d----------------~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kR 69 (132)
.+.+.+.+--+||.|++++..-.++-+ |+---|++++-.+-+ .-++..+++
T Consensus 335 dvA~~i~~HESTISRai~nKy~~tprG~feLK~FFs~~i~s~~gg~~~S~~~Ik~~Ik-------------~lI~~E~~~ 401 (444)
T COG1508 335 DVADEIGMHESTISRAITNKYLATPRGLFELKYFFSSSLASSEGGEASSTEAIKALIK-------------KLIEAEDKK 401 (444)
T ss_pred HHHHHhCccHHHHHHHHhcccccCCcceeeHHHHHHHhccCCCCCccccHHHHHHHHH-------------HHHhhccCC
Confidence 456788899999999999887665411 111233322222211 235567788
Q ss_pred CccCHHHHHHHHHHCCCcccHHHHHHHHHHHHHHhhhhhhc
Q 032845 70 QTINAEDVLKAIEEIDFTEFVDPLRDSLDAKQIVSQKVVAS 110 (132)
Q Consensus 70 KTI~~eDVl~AL~~lgf~~y~~~l~~~l~~~k~~~q~~~~~ 110 (132)
+.+|-+.|..-|++-| ++.-.....+||+.....+++
T Consensus 402 ~pLSD~kIa~lLkekG----i~iARRTVAKYRe~L~I~sS~ 438 (444)
T COG1508 402 KPLSDSKIAELLKEKG----IDVARRTVAKYREELNIPSSS 438 (444)
T ss_pred CCCCHHHHHHHHHHcC----CchhHHhHHHHHHHcCCCchh
Confidence 8999999999999988 467888899999876654443
No 143
>PRK00440 rfc replication factor C small subunit; Reviewed
Probab=31.77 E-value=1.5e+02 Score=23.42 Aligned_cols=67 Identities=18% Similarity=0.123 Sum_probs=39.4
Q ss_pred cchhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHCC
Q 032845 13 LPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEID 85 (132)
Q Consensus 13 LP~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~lg 85 (132)
++...+.++++..+.. .++.++.++...+.+.+.--+..+-.+-...+.. .++|+.+||..++....
T Consensus 161 l~~~ei~~~l~~~~~~----~~~~i~~~al~~l~~~~~gd~r~~~~~l~~~~~~--~~~it~~~v~~~~~~~~ 227 (319)
T PRK00440 161 LKKEAVAERLRYIAEN----EGIEITDDALEAIYYVSEGDMRKAINALQAAAAT--GKEVTEEAVYKITGTAR 227 (319)
T ss_pred CCHHHHHHHHHHHHHH----cCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHc--CCCCCHHHHHHHhCCCC
Confidence 4455555666555532 2567899998888877643332222222222222 36899999988876543
No 144
>PRK06920 dnaE DNA polymerase III DnaE; Reviewed
Probab=31.65 E-value=21 Score=35.11 Aligned_cols=46 Identities=13% Similarity=0.140 Sum_probs=35.6
Q ss_pred HHHHHHCCCcccHHHHHHHHHHHHHHhhhhhhcCCCcccCCCCcceeeeEee
Q 032845 78 LKAIEEIDFTEFVDPLRDSLDAKQIVSQKVVASNPLFFFRGNHVRRIICHCI 129 (132)
Q Consensus 78 l~AL~~lgf~~y~~~l~~~l~~~k~~~q~~~~~~~~~~~~g~~~~~~~~~~~ 129 (132)
+..+.++||.+|.=.++++.+--|+ ..=+-|||||.+.--.+|+|.
T Consensus 311 L~vI~~mGf~~YFLIV~D~i~~Ak~------~gI~VGPGRGSaAGSLVaY~L 356 (1107)
T PRK06920 311 LNVISRMGFSDYFLIVWDFMKYAHE------NHILTGPGRGSAAGSLVSYVL 356 (1107)
T ss_pred HHHHHHCCCCcchHHHHHHHHHHHH------CCCEeCCCcchHHHHHHHHHh
Confidence 5678899999999999987765543 245678999998877777764
No 145
>PRK07374 dnaE DNA polymerase III subunit alpha; Validated
Probab=31.57 E-value=21 Score=35.23 Aligned_cols=46 Identities=20% Similarity=0.268 Sum_probs=35.8
Q ss_pred HHHHHHCCCcccHHHHHHHHHHHHHHhhhhhhcCCCcccCCCCcceeeeEee
Q 032845 78 LKAIEEIDFTEFVDPLRDSLDAKQIVSQKVVASNPLFFFRGNHVRRIICHCI 129 (132)
Q Consensus 78 l~AL~~lgf~~y~~~l~~~l~~~k~~~q~~~~~~~~~~~~g~~~~~~~~~~~ 129 (132)
+..+..+||++|.=.++++++--|+ ..=+-|||||.+.--.+|.|+
T Consensus 337 L~vI~~mgf~~YFLIV~D~i~~Ak~------~gI~vGPGRGSaAGSLVaY~L 382 (1170)
T PRK07374 337 LKIIEQMGFPTYFLVVWDYIRFARE------QGIPVGPGRGSAAGSLVAYAL 382 (1170)
T ss_pred HHHHHHCCCCccHHHHHHHHHHHHH------CCCeeCCCCchHHHHHHHHHh
Confidence 6678899999999999997765552 145778999998877777764
No 146
>PRK05807 hypothetical protein; Provisional
Probab=30.99 E-value=75 Score=23.31 Aligned_cols=20 Identities=20% Similarity=0.132 Sum_probs=15.4
Q ss_pred CCCcccHHHHHHHHHHHHHH
Q 032845 84 IDFTEFVDPLRDSLDAKQIV 103 (132)
Q Consensus 84 lgf~~y~~~l~~~l~~~k~~ 103 (132)
.||.+|.+.|..++++=.+.
T Consensus 96 ~~~~~~~~~l~~~~~~s~~~ 115 (136)
T PRK05807 96 NNNGNFEDRLSKFLKDSEER 115 (136)
T ss_pred CCCcCHHHHHHHHHHHHHHH
Confidence 48889988888888766543
No 147
>PRK09532 DNA polymerase III subunit alpha; Reviewed
Probab=30.89 E-value=23 Score=33.88 Aligned_cols=46 Identities=17% Similarity=0.337 Sum_probs=35.5
Q ss_pred HHHHHHCCCcccHHHHHHHHHHHHHHhhhhhhcCCCcccCCCCcceeeeEee
Q 032845 78 LKAIEEIDFTEFVDPLRDSLDAKQIVSQKVVASNPLFFFRGNHVRRIICHCI 129 (132)
Q Consensus 78 l~AL~~lgf~~y~~~l~~~l~~~k~~~q~~~~~~~~~~~~g~~~~~~~~~~~ 129 (132)
+..+..+||.+|.=.++++++--|+ ..=+-|||||...--.+|.|+
T Consensus 335 L~vI~~~gf~~YFLIV~D~v~~Ar~------~gi~VGpGRGSAAGSLVaY~L 380 (874)
T PRK09532 335 LKMLQQMGFSTYFLVVWDYIKYARD------NNIPVGPGRGSAAGSLVAYCL 380 (874)
T ss_pred HHHHHHCCCchhHHHHHHHHHHHHh------CCceecCCcccHHHHHHHHHh
Confidence 6678899999999998887765553 145678999998877777764
No 148
>PRK07279 dnaE DNA polymerase III DnaE; Reviewed
Probab=30.71 E-value=22 Score=34.81 Aligned_cols=46 Identities=15% Similarity=0.237 Sum_probs=35.1
Q ss_pred HHHHHHCCCcccHHHHHHHHHHHHHHhhhhhhcCCCcccCCCCcceeeeEee
Q 032845 78 LKAIEEIDFTEFVDPLRDSLDAKQIVSQKVVASNPLFFFRGNHVRRIICHCI 129 (132)
Q Consensus 78 l~AL~~lgf~~y~~~l~~~l~~~k~~~q~~~~~~~~~~~~g~~~~~~~~~~~ 129 (132)
+..+.++||.+|.=.++++.+--|+ ..=+-|||||.+.--.+|.|.
T Consensus 268 L~vI~~mgf~~YFLIV~D~i~~Ak~------~gI~vGPGRGSaAGSLVaY~L 313 (1034)
T PRK07279 268 LSVIHDMGFDDYFLIVWDLLRFGRS------QGYYMGMGRGSAAGSLVAYAL 313 (1034)
T ss_pred HHHHHHCCCchhhHHHHHHHHHHHh------CCceeCCCCchHHHHHHHHHh
Confidence 6678899999999999987765442 134668999998877777664
No 149
>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=30.65 E-value=1.4e+02 Score=26.13 Aligned_cols=88 Identities=15% Similarity=0.175 Sum_probs=58.3
Q ss_pred ccchhhcccchhHHHHHHhhhccCCCCC---------C-------cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q 032845 5 KVVPEAEELPKTIVRRVVKDKLHNCSPD---------T-------DISVHKDALLAFCESARIFIHYLSATANDICKESK 68 (132)
Q Consensus 5 k~~~Ed~~LP~a~V~RimK~~Lp~~~~d---------~-------~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~k 68 (132)
|-+.+.+.+-.+||.|+++..-=+++.+ . +--+|.+++. ... ..-+...++
T Consensus 322 kdiA~~lglheSTVSRav~~Kyi~tp~Gi~~lk~FFs~~~~~~~~g~~~S~~~Ik---~~I----------~~lI~~E~~ 388 (429)
T TIGR02395 322 REVAEELGLHESTISRAINNKYLQTPRGVFELKYFFSRGVQTDSGEGEVSSTAIK---ALI----------KELIAAEDK 388 (429)
T ss_pred HHHHHHhCCCccchhhhhcCceEecCCceEEHHHhcCCccCCCCCCCccCHHHHH---HHH----------HHHHHhcCC
Confidence 3467888999999999997764433310 0 0114444422 111 124556788
Q ss_pred CCccCHHHHHHHHHHCCCcccHHHHHHHHHHHHHHhhhhhh
Q 032845 69 RQTINAEDVLKAIEEIDFTEFVDPLRDSLDAKQIVSQKVVA 109 (132)
Q Consensus 69 RKTI~~eDVl~AL~~lgf~~y~~~l~~~l~~~k~~~q~~~~ 109 (132)
++.+|-+.|...|+.-|+. .-..-..+||+....-.+
T Consensus 389 ~~PlSD~~I~~~L~~~Gi~----IaRRTVaKYRe~L~Ip~s 425 (429)
T TIGR02395 389 RKPLSDQKIAELLKEKGIK----IARRTVAKYREELGIPSS 425 (429)
T ss_pred CCCCCHHHHHHHHHhcCCC----eehHHHHHHHHHcCCCcc
Confidence 9999999999999999874 557788899986654333
No 150
>PRK14971 DNA polymerase III subunits gamma and tau; Provisional
Probab=30.02 E-value=1.5e+02 Score=27.19 Aligned_cols=73 Identities=10% Similarity=0.129 Sum_probs=40.4
Q ss_pred ccchhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHCCCccc
Q 032845 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFTEF 89 (132)
Q Consensus 12 ~LP~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~lgf~~y 89 (132)
.++..-+.+.+++.+.. .++.++.++..+|.+.+.-=+..+-.+....+.-.+++ |+.++|...+.....+.|
T Consensus 179 ~ls~~ei~~~L~~ia~~----egi~i~~~al~~La~~s~gdlr~al~~Lekl~~y~~~~-It~~~V~~~l~~~~~~~i 251 (614)
T PRK14971 179 RIQVADIVNHLQYVASK----EGITAEPEALNVIAQKADGGMRDALSIFDQVVSFTGGN-ITYKSVIENLNILDYDYY 251 (614)
T ss_pred CCCHHHHHHHHHHHHHH----cCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhccCC-ccHHHHHHHhCCCCHHHH
Confidence 34455555555554432 25788888888887765443333334333333323333 888887776665444433
No 151
>PF05385 Adeno_E4: Mastadenovirus early E4 13 kDa protein; InterPro: IPR008680 This family consists of Homo sapiens and simian mastadenovirus early E4 13 kDa proteins. Human adenovirus 9 (HAdV-9) is unique in eliciting exclusively estrogen-dependent mammary tumours in Rattus spp. and in not requiring viral E1 region transforming genes for tumorigenicity. E4 codes for an oncoprotein essential for tumourigenesis by Ad9 [].
Probab=29.50 E-value=77 Score=23.11 Aligned_cols=44 Identities=30% Similarity=0.396 Sum_probs=22.5
Q ss_pred HHHHHHHHHHCCCc------ccHHHHHHHHH-HHHHHhhhhhhcCCCcccCCCCcceeeeE
Q 032845 74 AEDVLKAIEEIDFT------EFVDPLRDSLD-AKQIVSQKVVASNPLFFFRGNHVRRIICH 127 (132)
Q Consensus 74 ~eDVl~AL~~lgf~------~y~~~l~~~l~-~~k~~~q~~~~~~~~~~~~g~~~~~~~~~ 127 (132)
..||+.++..-|+. ..+..|.+-|- .|..+.|+ |+++.||++|+
T Consensus 29 ~~Dv~r~ir~~g~~ispeAe~lL~~LrEWLy~a~~tER~r----------r~drRr~~~c~ 79 (109)
T PF05385_consen 29 VVDVIRAIRRDGVFISPEAERLLTGLREWLYFALMTERQR----------RRDRRRREVCW 79 (109)
T ss_pred HHHHHHHHHHcCeeECHHHHHHHHHHHHHHHHHHHHHHHH----------Hhcccccchhh
Confidence 35677777666653 12223333222 33334444 44667788885
No 152
>CHL00076 chlB photochlorophyllide reductase subunit B
Probab=29.20 E-value=1.3e+02 Score=26.81 Aligned_cols=51 Identities=14% Similarity=0.227 Sum_probs=40.1
Q ss_pred cchhhHHHHHHHHHHHHHHHH-HHHHHHHHHHHhcCCCccCHHHHHHHHHHCC
Q 032845 34 DISVHKDALLAFCESARIFIH-YLSATANDICKESKRQTINAEDVLKAIEEID 85 (132)
Q Consensus 34 ~~~ISkDA~~al~~~a~~FI~-~ltseA~~~a~~~kRKTI~~eDVl~AL~~lg 85 (132)
++.+|.||...|.+. =-|+. -+=..+-+.|...|...||.+.+..|=..+|
T Consensus 461 ~~~w~~ea~~~l~~i-P~f~r~~~r~~~e~~a~~~g~~~it~~~~~~a~~~~~ 512 (513)
T CHL00076 461 DLIWSPESQLELSKI-PGFVRGKVKRNTEKFARQNGITNITVEVMYAAKEALS 512 (513)
T ss_pred CCCCCHHHHHHHHhC-CHHhHHHHHHHHHHHHHHcCCCeEcHHHHHHHHHhhC
Confidence 578999999999987 34443 3445566678899999999999999977665
No 153
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=29.05 E-value=1.6e+02 Score=26.35 Aligned_cols=89 Identities=12% Similarity=0.075 Sum_probs=58.3
Q ss_pred ccchhhcccchhHHHHHHhhhccCCCC---------------CCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 032845 5 KVVPEAEELPKTIVRRVVKDKLHNCSP---------------DTDISVHKDALLAFCESARIFIHYLSATANDICKESKR 69 (132)
Q Consensus 5 k~~~Ed~~LP~a~V~RimK~~Lp~~~~---------------d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kR 69 (132)
|-+.+.+.+-.+||.|+++...=.++- +++--+|.+++..+- ..-+...+++
T Consensus 373 kdVAe~lglHeSTVSRa~~~KY~~tp~GifeLK~FFs~~v~~~~g~~~Ss~~Ik~~I-------------k~lI~~Ed~~ 439 (481)
T PRK12469 373 RDVAEELGLHESTISRATGNKYMATPRGTFEFKHFFPRKLEAAGGGECSAAAVRALI-------------KEMIAAEQAG 439 (481)
T ss_pred HHHHHHhCCCcchhhHHhcCceeecCCceEeHHHhhccccCCCCCccccHHHHHHHH-------------HHHHHhcCCC
Confidence 345788899999999999776544331 011123333322211 1134567889
Q ss_pred CccCHHHHHHHHHHCCCcccHHHHHHHHHHHHHHhhhhhhc
Q 032845 70 QTINAEDVLKAIEEIDFTEFVDPLRDSLDAKQIVSQKVVAS 110 (132)
Q Consensus 70 KTI~~eDVl~AL~~lgf~~y~~~l~~~l~~~k~~~q~~~~~ 110 (132)
|.+|-+.|..-|+.-|+. .-..-..+||+....-.++
T Consensus 440 kPLSD~~I~~~L~~~GI~----IARRTVAKYRe~L~IpsS~ 476 (481)
T PRK12469 440 DPLSDVALAEMLAGRGVL----IARRTVAKYREAMKIPPAE 476 (481)
T ss_pred CCCCHHHHHHHHHhcCCC----eechhHHHHHHHcCCCChh
Confidence 999999999999998884 5577788999866554333
No 154
>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=28.22 E-value=15 Score=24.60 Aligned_cols=18 Identities=17% Similarity=0.182 Sum_probs=13.6
Q ss_pred cchhhHHHHHHHHHHHHH
Q 032845 34 DISVHKDALLAFCESARI 51 (132)
Q Consensus 34 ~~~ISkDA~~al~~~a~~ 51 (132)
+++++.+.+.+|.++|..
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 478999999999999754
No 155
>PF03484 B5: tRNA synthetase B5 domain; InterPro: IPR005147 Domain B5 is found in phenylalanine-tRNA synthetase beta subunits. This domain has been shown to bind DNA through a winged helix-turn-helix motif []. Phenylalanine-tRNA synthetase may influence common cellular processes via DNA binding, in addition to its aminoacylation function.; GO: 0000287 magnesium ion binding, 0003723 RNA binding, 0005524 ATP binding, 0006432 phenylalanyl-tRNA aminoacylation; PDB: 2AKW_B 1B70_B 1B7Y_B 2ALY_B 2IY5_B 2AMC_B 3PCO_D 2CXI_C 1JJC_B 1EIY_B ....
Probab=27.81 E-value=48 Score=21.32 Aligned_cols=18 Identities=22% Similarity=0.599 Sum_probs=12.8
Q ss_pred CccCHHHHHHHHHHCCCc
Q 032845 70 QTINAEDVLKAIEEIDFT 87 (132)
Q Consensus 70 KTI~~eDVl~AL~~lgf~ 87 (132)
..++.+++...|+.|||.
T Consensus 17 ~~i~~~~i~~~L~~lg~~ 34 (70)
T PF03484_consen 17 IDISPEEIIKILKRLGFK 34 (70)
T ss_dssp S---HHHHHHHHHHTT-E
T ss_pred CCCCHHHHHHHHHHCCCE
Confidence 378999999999999997
No 156
>COG5094 TAF9 Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=27.80 E-value=2.7e+02 Score=21.02 Aligned_cols=82 Identities=23% Similarity=0.152 Sum_probs=55.3
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCH---HHHHHHHHHCCCcccHHHH-HHHHHHHHHHhhhhhhcC
Q 032845 36 SVHKDALLAFCESARIFIHYLSATANDICKESKRQTINA---EDVLKAIEEIDFTEFVDPL-RDSLDAKQIVSQKVVASN 111 (132)
Q Consensus 36 ~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~---eDVl~AL~~lgf~~y~~~l-~~~l~~~k~~~q~~~~~~ 111 (132)
..+.....-|.+-|--+-.-+-..|.-++++.||--+++ +||..|+..-==-+|+++- +++|-+.--. +-+|
T Consensus 31 ~ye~~VplQLl~FAhRYTq~vl~Dalvya~htgrg~~a~l~veDvrLA~at~v~~~F~pppPke~llela~e----rN~K 106 (145)
T COG5094 31 EYEPKVPLQLLEFAHRYTQDVLEDALVYAKHTGRGHIATLGVEDVRLALATKVGRHFVPPPPKEYLLELATE----RNSK 106 (145)
T ss_pred hhCccchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHHHHHHHhcCCcCCCChHHHHHHHHHH----hcCC
Confidence 344445556667777777778888999999998876555 9999999875555677543 6665554433 3466
Q ss_pred CCcccCCCCc
Q 032845 112 PLFFFRGNHV 121 (132)
Q Consensus 112 ~~~~~~g~~~ 121 (132)
|+-+--|.-+
T Consensus 107 pLpq~~g~~g 116 (145)
T COG5094 107 PLPQPDGENG 116 (145)
T ss_pred CCCccCCccc
Confidence 7666555443
No 157
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=27.50 E-value=1.1e+02 Score=19.53 Aligned_cols=36 Identities=14% Similarity=0.143 Sum_probs=27.7
Q ss_pred hhhcccchhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHH
Q 032845 8 PEAEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIF 52 (132)
Q Consensus 8 ~Ed~~LP~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~F 52 (132)
.....+..++|.|++... -.|+.+.+..+.+++.++
T Consensus 7 A~~~gvS~~TVSr~ln~~---------~~v~~~t~~~i~~~~~~~ 42 (70)
T smart00354 7 ARLAGVSKATVSRVLNGN---------GRVSEETREKVLAAMEEL 42 (70)
T ss_pred HHHHCCCHHHHHHHHCCC---------CCCCHHHHHHHHHHHHHh
Confidence 345678899999988543 347899999999888775
No 158
>COG2812 DnaX DNA polymerase III, gamma/tau subunits [DNA replication, recombination, and repair]
Probab=27.30 E-value=2e+02 Score=26.17 Aligned_cols=71 Identities=15% Similarity=0.131 Sum_probs=45.1
Q ss_pred ccchhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHCCCc
Q 032845 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFT 87 (132)
Q Consensus 12 ~LP~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~lgf~ 87 (132)
.||...|.+.++..+.+ .++.+..+|...|.+++.-=.---.+--.+ +..-+-..|+.++|...|..+...
T Consensus 177 ri~~~~I~~~L~~i~~~----E~I~~e~~aL~~ia~~a~Gs~RDalslLDq-~i~~~~~~It~~~v~~~lG~~~~~ 247 (515)
T COG2812 177 RLDLEEIAKHLAAILDK----EGINIEEDALSLIARAAEGSLRDALSLLDQ-AIAFGEGEITLESVRDMLGLTDIE 247 (515)
T ss_pred CCCHHHHHHHHHHHHHh----cCCccCHHHHHHHHHHcCCChhhHHHHHHH-HHHccCCcccHHHHHHHhCCCCHH
Confidence 68888888888888864 468999999999988775422222121112 222222677877777666666544
No 159
>COG1239 ChlI Mg-chelatase subunit ChlI [Coenzyme metabolism]
Probab=27.26 E-value=1.2e+02 Score=27.00 Aligned_cols=50 Identities=18% Similarity=0.227 Sum_probs=41.8
Q ss_pred cchhhHHHHHHHHHHHHHHHH-------HHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 032845 34 DISVHKDALLAFCESARIFIH-------YLSATANDICKESKRQTINAEDVLKAIEE 83 (132)
Q Consensus 34 ~~~ISkDA~~al~~~a~~FI~-------~ltseA~~~a~~~kRKTI~~eDVl~AL~~ 83 (132)
.+.++.++...+.+.|..+-. .+...|..++.=.||.+++.+||-.|+.-
T Consensus 265 ~V~l~~~~~~~ia~~~~~~~v~g~radi~~~r~a~a~aa~~Gr~~v~~~Di~~a~~l 321 (423)
T COG1239 265 EVELDDDAETKIAELCARLAVDGHRADIVVVRAAKALAALRGRTEVEEEDIREAAEL 321 (423)
T ss_pred cccCcHHHHHHHHHHHHHhccCCCchhhHHHHHHHHHHHhcCceeeehhhHHHHHhh
Confidence 688999999999998887754 46677888888899999999999988654
No 160
>COG1466 HolA DNA polymerase III, delta subunit [DNA replication, recombination, and repair]
Probab=26.97 E-value=2.4e+02 Score=23.28 Aligned_cols=67 Identities=10% Similarity=0.165 Sum_probs=47.2
Q ss_pred HHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHCCCc
Q 032845 17 IVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFT 87 (132)
Q Consensus 17 ~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~lgf~ 87 (132)
.+.+.++..+-+ .+++|++||.+.|..+..-=...+.++=...+--.+-++|+.+||..++-+-.-.
T Consensus 144 ~l~~~i~~~~~~----~~l~i~~~a~~~L~~~~~~nl~~i~~Ei~KL~l~~~~~~I~~~~V~~~v~~~~~~ 210 (334)
T COG1466 144 ELPQWIKKRAKE----LGLKIDQEAIQLLLEALGGNLLAIAQEIEKLALYAGDKEITLEDVEEVVSDVAEF 210 (334)
T ss_pred HHHHHHHHHHHH----cCCCCCHHHHHHHHHHhCCcHHHHHHHHHHHHHhCCCCcCCHHHHHHHHhccccC
Confidence 344555554432 3689999999999999886666666666666654444499999999988765543
No 161
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=26.91 E-value=69 Score=17.89 Aligned_cols=37 Identities=14% Similarity=0.188 Sum_probs=22.9
Q ss_pred hhhcccchhHHHHHHhhh-ccCCCCCCcchhhHHHHHH
Q 032845 8 PEAEELPKTIVRRVVKDK-LHNCSPDTDISVHKDALLA 44 (132)
Q Consensus 8 ~Ed~~LP~a~V~RimK~~-Lp~~~~d~~~~ISkDA~~a 44 (132)
.+-+.++.++|.+++++. +|....++..++.++..+.
T Consensus 8 a~~lgis~~ti~~~~~~g~i~~~~~g~~~~~~~~~l~~ 45 (49)
T TIGR01764 8 AEYLGVSKDTVYRLIHEGELPAYRVGRHYRIPREDVDE 45 (49)
T ss_pred HHHHCCCHHHHHHHHHcCCCCeEEeCCeEEEeHHHHHH
Confidence 355689999999999887 4422112234565555443
No 162
>smart00445 LINK Link (Hyaluronan-binding).
Probab=26.89 E-value=98 Score=21.80 Aligned_cols=30 Identities=17% Similarity=0.323 Sum_probs=27.1
Q ss_pred HHHHHHHHHhcCCCccCHHHHHHHHHHCCCc
Q 032845 57 SATANDICKESKRQTINAEDVLKAIEEIDFT 87 (132)
Q Consensus 57 tseA~~~a~~~kRKTI~~eDVl~AL~~lgf~ 87 (132)
.++|.+.|...+=.--|.+++..|.+. ||+
T Consensus 17 f~eA~~aC~~~ga~lAs~~QL~~Aw~~-Gld 46 (94)
T smart00445 17 FAEAREACRAQGATLATVGQLYAAWQD-GFD 46 (94)
T ss_pred HHHHHHHHHHcCCEeCCHHHHHHHHHh-chh
Confidence 478999999999999999999999886 887
No 163
>PF14434 Imm6: Immunity protein Imm6
Probab=26.35 E-value=2.6e+02 Score=20.36 Aligned_cols=39 Identities=10% Similarity=0.197 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHh--cCCCccCHHHHHHHHHHCCCcccHHHHH
Q 032845 55 YLSATANDICKE--SKRQTINAEDVLKAIEEIDFTEFVDPLR 94 (132)
Q Consensus 55 ~ltseA~~~a~~--~kRKTI~~eDVl~AL~~lgf~~y~~~l~ 94 (132)
+...+|.+.|.. ++ +.++++++..-|++.++.+...-+.
T Consensus 25 ~~~~~aL~~cw~wle~-~~~~~D~LY~lldn~D~~gi~~~~~ 65 (122)
T PF14434_consen 25 EFVREALDACWKWLEG-KEVTGDELYSLLDNEDENGIFIFMQ 65 (122)
T ss_pred HHHHHHHHHHHHHHHc-CCCCHHHHHHHHhCcccccHHHHHH
Confidence 333888888875 44 8899999999999988876554443
No 164
>cd00607 RNase_Sa RNase_Sa. Ribonucleases first isolated from Streptomyces aureofaciens. In general, ribonucleases cleave phosphodiester bonds in RNA and are essential for both non-specific RNA degradation and for numerous forms of RNA processing. RNAse Sa is a guanylate specific endoribonuclease which belongs to the superfamily of microbial ribonucleases. Typical of this sub-family, the enzyme hydrolyses the phosphodiester bonds of RNA at the 3' oxygen end of guanosine residues to yield oligonucleotides with the guanosine-2',3'-cyclophosphate at the 3' end and the hydroxyl group at the 5' end. The terminal guanosine-2,3'-cyclophosphate is hydrolysed by guanyl RNAses to give guanosine-3'-phosphate.
Probab=26.33 E-value=50 Score=23.47 Aligned_cols=11 Identities=45% Similarity=0.878 Sum_probs=9.4
Q ss_pred cCCCCcceeee
Q 032845 116 FRGNHVRRIIC 126 (132)
Q Consensus 116 ~~g~~~~~~~~ 126 (132)
.+.+|.|||+|
T Consensus 61 ~~~RGarRIV~ 71 (95)
T cd00607 61 SRDRGARRIVC 71 (95)
T ss_pred CCCCCCCeEEE
Confidence 37789999998
No 165
>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA.
Probab=26.32 E-value=2.4e+02 Score=26.20 Aligned_cols=38 Identities=16% Similarity=0.120 Sum_probs=28.3
Q ss_pred cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 032845 34 DISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (132)
Q Consensus 34 ~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~ 83 (132)
....|..++.+|..+. ..|...+...|+.+|++.||-.
T Consensus 75 ~~~~S~~lk~vL~~A~------------~~A~~~g~~~I~teHLLLALl~ 112 (731)
T TIGR02639 75 DPEQTVGVQRVLQRAL------------LHVKSAGKKEIGIGDILVALFD 112 (731)
T ss_pred CCCcCHHHHHHHHHHH------------HHHHHcCCCccCHHHHHHHHhc
Confidence 3567888888777643 4566678899999999988753
No 166
>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=26.17 E-value=1.7e+02 Score=26.65 Aligned_cols=72 Identities=14% Similarity=0.204 Sum_probs=43.6
Q ss_pred hHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHH---HHHHHHHHHHH-------HHHHHhcCCCccCHHHHHHHHHHCC
Q 032845 16 TIVRRVVKDKLHNCSPDTDISVHKDALLAFCESA---RIFIHYLSATA-------NDICKESKRQTINAEDVLKAIEEID 85 (132)
Q Consensus 16 a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a---~~FI~~ltseA-------~~~a~~~kRKTI~~eDVl~AL~~lg 85 (132)
.-+..|++..+.. .++.++.++..+|.+++ ...++.|.... ...+...++.+|+.+||..+++.--
T Consensus 356 edi~~Il~~~a~~----~~v~ls~eal~~L~~ys~~gRraln~L~~~~~~~~~~~~~~~~~~~~~~I~~edv~~~l~~~r 431 (615)
T TIGR02903 356 EDIALIVLNAAEK----INVHLAAGVEELIARYTIEGRKAVNILADVYGYALYRAAEAGKENDKVTITQDDVYEVIQISR 431 (615)
T ss_pred HHHHHHHHHHHHH----cCCCCCHHHHHHHHHCCCcHHHHHHHHHHHHHHHHHHHHHhccCCCCeeECHHHHHHHhCCCc
Confidence 4455555555532 13568888888888754 33444443221 1112334556899999999999887
Q ss_pred CcccHH
Q 032845 86 FTEFVD 91 (132)
Q Consensus 86 f~~y~~ 91 (132)
|..|..
T Consensus 432 ~~~~~~ 437 (615)
T TIGR02903 432 LSPYEK 437 (615)
T ss_pred Cccchh
Confidence 776553
No 167
>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau. This model represents the well-conserved first ~ 365 amino acids of the translation of the dnaX gene. The full-length product of the dnaX gene in the model bacterium E. coli is the DNA polymerase III tau subunit. A translational frameshift leads to early termination and a truncated protein subunit gamma, about 1/3 shorter than tau and present in roughly equal amounts. This frameshift mechanism is not necessarily universal for species with DNA polymerase III but appears conserved in the exterme thermophile Thermus thermophilis.
Probab=26.14 E-value=2e+02 Score=23.20 Aligned_cols=62 Identities=16% Similarity=0.134 Sum_probs=31.5
Q ss_pred hhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHH
Q 032845 15 KTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAI 81 (132)
Q Consensus 15 ~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL 81 (132)
...+..++++.+.. .++.++.++...|.+.+.--...+-.+....+.-.+ +.|+.+||..++
T Consensus 178 ~~~l~~~l~~~~~~----~g~~i~~~a~~~l~~~~~g~~~~a~~~lekl~~~~~-~~it~~~v~~~~ 239 (355)
T TIGR02397 178 LEDIVERLKKILDK----EGIKIEDEALELIARAADGSLRDALSLLDQLISFGN-GNITYEDVNELL 239 (355)
T ss_pred HHHHHHHHHHHHHH----cCCCCCHHHHHHHHHHcCCChHHHHHHHHHHHhhcC-CCCCHHHHHHHh
Confidence 34444455443321 146788888877776654333333333333332222 347777765554
No 168
>cd01102 Link_Domain The link domain is a hyaluronan (HA)-binding domain. It functions to mediate adhesive interactions during inflammatory leukocyte homing and tumor metastasis. It is found in the CD44 receptor and in human TSG-6. TSG-6 is the protein product of the tumor necrosis factor-stimulated gene-6. TSG-6 has a strong anti-inflammatory effect in models of acute inflammation and autoimmune arthritis and plays an essential role in female fertility. This group also contains the link domains of the chondroitin sulfate proteoglycan core proteins (CSPG) including aggrecan, versican, neurocan, and brevican and the link domains of the vertebrate HAPLN (HA and proteoglycan binding link) protein family. In cartilage, aggrecan forms cartilage link protein stabilized aggregates with HA. These aggregates contribute to the tissue's load bearing properties. Aggregates in which other CSPGs substitute for aggregan might contribute to the structural integrity of many different tissues. Members of
Probab=26.11 E-value=96 Score=21.73 Aligned_cols=30 Identities=20% Similarity=0.227 Sum_probs=26.7
Q ss_pred HHHHHHHHHhcCCCccCHHHHHHHHHHCCCc
Q 032845 57 SATANDICKESKRQTINAEDVLKAIEEIDFT 87 (132)
Q Consensus 57 tseA~~~a~~~kRKTI~~eDVl~AL~~lgf~ 87 (132)
..+|.+.|...+=.--|.+++..|.+. ||+
T Consensus 16 f~eA~~aC~~~ga~lAs~~QL~~Aw~~-G~~ 45 (92)
T cd01102 16 FAEAALACKARGAHLATPGQLEAAWQD-GFD 45 (92)
T ss_pred HHHHHHHHHHcCCEeCCHHHHHHHHHc-chh
Confidence 378999999999999999999999886 887
No 169
>KOG3557 consensus Epidermal growth factor receptor kinase substrate [Signal transduction mechanisms]
Probab=25.85 E-value=57 Score=30.67 Aligned_cols=33 Identities=21% Similarity=0.153 Sum_probs=27.7
Q ss_pred cccHHHHHHHHHHHHHHhhhhh--hcCCCcccCCC
Q 032845 87 TEFVDPLRDSLDAKQIVSQKVV--ASNPLFFFRGN 119 (132)
Q Consensus 87 ~~y~~~l~~~l~~~k~~~q~~~--~~~~~~~~~g~ 119 (132)
+.|+.-|+..-+.+|+..|+++ .++.+.++.|-
T Consensus 281 E~FvaRLQkAAeA~reLe~Rkr~~K~~k~~pgeG~ 315 (721)
T KOG3557|consen 281 ESFVARLQKAAEAARELEQRKRGRKSKKRAPGEGL 315 (721)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhcccccCCCCCCce
Confidence 4599999999999999999988 67777777773
No 170
>PRK14964 DNA polymerase III subunits gamma and tau; Provisional
Probab=25.56 E-value=1.9e+02 Score=25.99 Aligned_cols=67 Identities=12% Similarity=0.116 Sum_probs=38.9
Q ss_pred cchhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHC
Q 032845 13 LPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEI 84 (132)
Q Consensus 13 LP~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~l 84 (132)
++...+...++..+.. .++.++.+|..+|.+.+.-=+..+-+.-.+.+...+ .+|+.+||...|...
T Consensus 175 l~~~el~~~L~~ia~~----Egi~i~~eAL~lIa~~s~GslR~alslLdqli~y~~-~~It~e~V~~llg~~ 241 (491)
T PRK14964 175 IPTDKLVEHLVDIAKK----ENIEHDEESLKLIAENSSGSMRNALFLLEQAAIYSN-NKISEKSVRDLLGCV 241 (491)
T ss_pred ccHHHHHHHHHHHHHH----cCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhcC-CCCCHHHHHHHHccC
Confidence 4444444444444421 257899999999888774333333333333333333 479999998765433
No 171
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=25.45 E-value=41 Score=26.50 Aligned_cols=40 Identities=10% Similarity=0.142 Sum_probs=30.6
Q ss_pred hhhcccchhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHH
Q 032845 8 PEAEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLS 57 (132)
Q Consensus 8 ~Ed~~LP~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~lt 57 (132)
.+....-++||.|.+... -.||.+.++-+.+++.+. .|.-
T Consensus 5 A~~agVS~~TVSrvLn~~---------~~vs~~tr~rV~~~a~~l-gY~p 44 (327)
T PRK10423 5 ARLAGVSTSTVSHVINKD---------RFVSEAITAKVEAAIKEL-NYAP 44 (327)
T ss_pred HHHhCCcHHHHHHHhCCC---------CCCCHHHHHHHHHHHHHH-CCCc
Confidence 344567789999999543 369999999999999875 3543
No 172
>PTZ00373 60S Acidic ribosomal protein P2; Provisional
Probab=25.36 E-value=2.4e+02 Score=20.45 Aligned_cols=28 Identities=11% Similarity=0.215 Sum_probs=24.4
Q ss_pred HHHHHHhcCCCccCHHHHHHHHHHCCCc
Q 032845 60 ANDICKESKRQTINAEDVLKAIEEIDFT 87 (132)
Q Consensus 60 A~~~a~~~kRKTI~~eDVl~AL~~lgf~ 87 (132)
|.-.|.-.+..++|.+||.+.|+..|.+
T Consensus 8 AYlL~~lgG~~~pTaddI~kIL~AaGve 35 (112)
T PTZ00373 8 AYLMCVLGGNENPTKKEVKNVLSAVNAD 35 (112)
T ss_pred HHHHHHHcCCCCCCHHHHHHHHHHcCCC
Confidence 5566777889999999999999999976
No 173
>PF13499 EF-hand_7: EF-hand domain pair; PDB: 1TCF_A 2TN4_A 1TN4_A 1A2X_A 2CT9_B 2OTG_B 2OS8_B 1SNL_A 3O4Y_A 3J04_E ....
Probab=25.20 E-value=1.6e+02 Score=17.64 Aligned_cols=41 Identities=12% Similarity=0.124 Sum_probs=30.1
Q ss_pred HHHHHHHhcCCCccCHHHHHHHHHHCCCcccHHHHHHHHHH
Q 032845 59 TANDICKESKRQTINAEDVLKAIEEIDFTEFVDPLRDSLDA 99 (132)
Q Consensus 59 eA~~~a~~~kRKTI~~eDVl~AL~~lgf~~y~~~l~~~l~~ 99 (132)
++....-.++.-.|+.+++..++..++....-..+.+.++.
T Consensus 4 ~~F~~~D~d~~G~i~~~el~~~~~~~~~~~~~~~~~~~~~~ 44 (66)
T PF13499_consen 4 EAFKKFDKDGDGYISKEELRRALKHLGRDMSDEESDEMIDQ 44 (66)
T ss_dssp HHHHHHSTTSSSEEEHHHHHHHHHHTTSHSTHHHHHHHHHH
T ss_pred HHHHHHcCCccCCCCHHHHHHHHHHhcccccHHHHHHHHHH
Confidence 34556667778889999999999999987655555555444
No 174
>PLN00138 large subunit ribosomal protein LP2; Provisional
Probab=24.75 E-value=2.5e+02 Score=20.29 Aligned_cols=28 Identities=14% Similarity=0.079 Sum_probs=24.4
Q ss_pred HHHHHHhcCCCccCHHHHHHHHHHCCCc
Q 032845 60 ANDICKESKRQTINAEDVLKAIEEIDFT 87 (132)
Q Consensus 60 A~~~a~~~kRKTI~~eDVl~AL~~lgf~ 87 (132)
|.-.|.-.+...+|.+||.+.|+..|.+
T Consensus 6 Ayll~~l~g~~~pta~dI~~IL~AaGve 33 (113)
T PLN00138 6 AYLLAVLGGNTCPSAEDLKDILGSVGAD 33 (113)
T ss_pred HHHHHHhcCCCCCCHHHHHHHHHHcCCc
Confidence 5667777888999999999999999976
No 175
>KOG1792 consensus Reticulon [Intracellular trafficking, secretion, and vesicular transport]
Probab=24.63 E-value=3e+02 Score=22.28 Aligned_cols=52 Identities=17% Similarity=0.232 Sum_probs=42.9
Q ss_pred cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHH-hcCCCccCHHHHHHHHHHCC
Q 032845 34 DISVHKDALLAFCESARIFIHYLSATANDICK-ESKRQTINAEDVLKAIEEID 85 (132)
Q Consensus 34 ~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~-~~kRKTI~~eDVl~AL~~lg 85 (132)
++.++++....+..++..-++..+++.++++- ++-+.-+...=.++.+..+|
T Consensus 114 ~i~ipee~~~~~a~~~~~~in~~l~~l~~ia~~~d~~~~lk~~v~lw~lS~vG 166 (230)
T KOG1792|consen 114 EITIPEEFVLALASSLRVEINQALSELRDIALGRDLKDFLKVAVGLWILSYVG 166 (230)
T ss_pred eeecCHHHHHHHHHHHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHHHH
Confidence 78999999999999999999999999999954 45455555555788888877
No 176
>PHA03328 nuclear egress lamina protein UL31; Provisional
Probab=24.55 E-value=1.1e+02 Score=26.11 Aligned_cols=37 Identities=16% Similarity=0.357 Sum_probs=26.5
Q ss_pred HHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHCCCcc
Q 032845 52 FIHYLSATANDICKESKRQTINAEDVLKAIEEIDFTE 88 (132)
Q Consensus 52 FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~lgf~~ 88 (132)
|+..+...+--....+..-||+++||.-++.+|+|++
T Consensus 260 fvL~v~~~~~~~~~~~~~~~V~~~dIy~k~~dL~f~d 296 (316)
T PHA03328 260 FVLVVRRDAERQTTDADVPAVSAEDIYCKMCDLNFDG 296 (316)
T ss_pred EEEEEeeCCCCCCccccccccCHHHHHHHHhCCCCCh
Confidence 4444443332234566788999999999999999984
No 177
>TIGR01052 top6b DNA topoisomerase VI, B subunit. This model describes DNA topoisomerase VI, an archaeal type II DNA topoisomerase (DNA gyrase).
Probab=24.44 E-value=1.4e+02 Score=26.85 Aligned_cols=50 Identities=26% Similarity=0.351 Sum_probs=36.8
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHCCCcccHHHHHHHHHH
Q 032845 36 SVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFTEFVDPLRDSLDA 99 (132)
Q Consensus 36 ~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~lgf~~y~~~l~~~l~~ 99 (132)
-|-+|.+.||++||...=.||+..-...-...++++ |..|++.+...|..
T Consensus 434 ei~~ei~~al~~~~r~L~~~l~~~~~~~~~~~r~~~--------------~~~y~p~~a~~~~~ 483 (488)
T TIGR01052 434 EIYNEIRLALMEVARRLRLYLSRKAREEEEIKRRKT--------------LEKYLPEIAKSLAY 483 (488)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------------HHHHHHHHHHHHHH
Confidence 688899999999999999999986666555554444 44566666655544
No 178
>PRK05907 hypothetical protein; Provisional
Probab=24.24 E-value=2.4e+02 Score=23.52 Aligned_cols=49 Identities=12% Similarity=0.144 Sum_probs=36.2
Q ss_pred cchhhHHHHHHHHHHH-HHHHHHHHHHHHHHHHh-cCCCccCHHHHHHHHH
Q 032845 34 DISVHKDALLAFCESA-RIFIHYLSATANDICKE-SKRQTINAEDVLKAIE 82 (132)
Q Consensus 34 ~~~ISkDA~~al~~~a-~~FI~~ltseA~~~a~~-~kRKTI~~eDVl~AL~ 82 (132)
+.+|+.+|...|.+.+ .-=+..+..+-...+.- ..+++|+.+||-..+.
T Consensus 151 g~~i~~~a~~~L~~~~~~~nL~~l~~EleKL~ly~g~~~~It~e~V~~lv~ 201 (311)
T PRK05907 151 GISCSLGLASLFVSKFPQTGLFEILSEFQKLLCQMGKKESLEASDIQSFVV 201 (311)
T ss_pred CCCcCHHHHHHHHHHccCCCHHHHHHHHHHHHHhcCCCCeECHHHHHHHhc
Confidence 5789999988888876 33444566666666554 6689999999988743
No 179
>TIGR02573 LcrG_PcrG type III secretion protein LcrG. This protein is found in type III secretion operons, along with LcrR, H and V. Also known as PcrG in Pseudomonas, the protein is believed to make a 1:1 complex with PcrV (LcrV). Mutants of LcrG cause premature secretion of effector proteins into the medium.
Probab=24.16 E-value=1.5e+02 Score=20.95 Aligned_cols=34 Identities=15% Similarity=0.073 Sum_probs=26.6
Q ss_pred HHHHHHHHHHHHHhhhhhhcCCCcccCCCCccee
Q 032845 91 DPLRDSLDAKQIVSQKVVASNPLFFFRGNHVRRI 124 (132)
Q Consensus 91 ~~l~~~l~~~k~~~q~~~~~~~~~~~~g~~~~~~ 124 (132)
+.++..-++.-...|+.+++.|.-+..|..+||.
T Consensus 49 e~~~~AEqELL~EiqRrr~~qp~~~~~GkR~RRP 82 (90)
T TIGR02573 49 ELMQHAEQELLEEVQRRRSQQPQQGEQGKRPRRP 82 (90)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCCCCcCCCCCCCC
Confidence 4445555666678889999999999999999985
No 180
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=24.03 E-value=1.6e+02 Score=17.00 Aligned_cols=37 Identities=19% Similarity=0.220 Sum_probs=26.7
Q ss_pred chhhcccchhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHH
Q 032845 7 VPEAEELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIF 52 (132)
Q Consensus 7 ~~Ed~~LP~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~F 52 (132)
+.+...+..++|.++.+.. ..++.+....+.+.+.++
T Consensus 3 lA~~~gvs~~tvs~~l~g~---------~~vs~~~~~~i~~~~~~l 39 (52)
T cd01392 3 IARAAGVSVATVSRVLNGK---------PRVSEETRERVLAAAEEL 39 (52)
T ss_pred HHHHHCcCHHHHHHHHcCC---------CCCCHHHHHHHHHHHHHh
Confidence 3456678889999988643 257888887777776654
No 181
>PF01972 SDH_sah: Serine dehydrogenase proteinase; InterPro: IPR002825 This family of archaebacterial proteins, formerly known as DUF114, has been found to be a serine dehydrogenase proteinase distantly related to ClpP proteinases that belong to the serine proteinase superfamily. The family belong to MEROPS peptidase family S49; they are mostly unassigned peptidases but include the archaean signal peptide peptidase 1 []. The family has a catalytic triad of Ser, Asp, His residues, which shows an altered residue ordering compared with the ClpP proteinases but similar to that of the carboxypeptidase clan []. ; GO: 0016021 integral to membrane
Probab=23.89 E-value=2.6e+02 Score=23.65 Aligned_cols=109 Identities=17% Similarity=0.203 Sum_probs=67.8
Q ss_pred cccchhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHH------HHHHHHHHh--cCCCc----cCHHHHH
Q 032845 11 EELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLS------ATANDICKE--SKRQT----INAEDVL 78 (132)
Q Consensus 11 ~~LP~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~lt------seA~~~a~~--~kRKT----I~~eDVl 78 (132)
...|.+.+-+.+.+.-+..-.|....+..-|+-++.++- .|+..+- ..|.++++. .|+-| |++++
T Consensus 159 ~~~pA~sil~~~~~K~~~~i~D~tlIladia~KAi~q~~-~~v~~lL~~~~~~eka~~ia~~L~~g~~tHdypi~~ee-- 235 (285)
T PF01972_consen 159 GQYPAASILKAVEQKPPDEIDDQTLILADIAEKAIRQVR-EFVKELLKDKMDEEKAEEIAEKLSSGKWTHDYPITVEE-- 235 (285)
T ss_pred cCCChHHHHHHHHhccccccCHHHHHHHHHHHHHHHHHH-HHHHHHHHcCCCHHHHHHHHHHhcCCCCCCCCCCCHHH--
Confidence 357877777777655433222223345556666666554 3555544 356667664 44444 66654
Q ss_pred HHHHHCCCc---ccHHHHHHHHHHHHHHhhhhhh-cCCCcccCCCCccee
Q 032845 79 KAIEEIDFT---EFVDPLRDSLDAKQIVSQKVVA-SNPLFFFRGNHVRRI 124 (132)
Q Consensus 79 ~AL~~lgf~---~y~~~l~~~l~~~k~~~q~~~~-~~~~~~~~g~~~~~~ 124 (132)
+++||+. +.=+++-+.++-|..-.+.++. +=-|.|.++...+|+
T Consensus 236 --a~~lGL~V~t~~p~ei~~lm~lypq~~~~~~~v~y~p~p~~~~~~~~~ 283 (285)
T PF01972_consen 236 --AKELGLPVSTDMPEEIYELMDLYPQPVQRRPSVEYIPVPYKREEQERN 283 (285)
T ss_pred --HHHcCCCcCCCCcHHHHHHHHhCccccCCCCCceeecCCCCCcccccC
Confidence 3678986 5667888888899977777665 666777777666653
No 182
>cd01585 AcnA_Bact Aconitase catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle. Bacterial Aconitase-like catalytic domain. Aconitase (aconitate hydratase or citrate hydrolyase) catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle. Cis-aconitate is formed as an intermediate product during the course of the reaction. This distinct subfamily is found only in bacteria and Archaea. Its exact characteristics are not known.
Probab=23.81 E-value=39 Score=29.41 Aligned_cols=31 Identities=26% Similarity=0.360 Sum_probs=16.8
Q ss_pred HHHHHHhhhhhhcCCCcccCCCCcceeeeEeeecC
Q 032845 98 DAKQIVSQKVVASNPLFFFRGNHVRRIICHCIILE 132 (132)
Q Consensus 98 ~~~k~~~q~~~~~~~~~~~~g~~~~~~~~~~~~~~ 132 (132)
+.|+....-.+.....+.+.| .||||.+.+|
T Consensus 47 ~~~~~lr~~a~~~gi~~~~~g----~GI~H~v~~E 77 (380)
T cd01585 47 DDHRFLQTVAARYGIYFSRPG----NGICHQVHLE 77 (380)
T ss_pred HHHHHHHHHHHHcCCEEECCC----CCeeeeecHh
Confidence 344433333333444444333 4999998876
No 183
>PF02718 Herpes_UL31: Herpesvirus UL31-like protein; InterPro: IPR021152 This is a family of Herpesvirus proteins, belong to the UL31 family, which including UL31, UL53, and the product of ORF69 in some strains. The proteins in this family have no known function.
Probab=23.79 E-value=1.3e+02 Score=24.99 Aligned_cols=32 Identities=25% Similarity=0.475 Sum_probs=24.3
Q ss_pred CCCccCHHHHHHHHHHCCCcccHHHHHHHHHHHHH
Q 032845 68 KRQTINAEDVLKAIEEIDFTEFVDPLRDSLDAKQI 102 (132)
Q Consensus 68 kRKTI~~eDVl~AL~~lgf~~y~~~l~~~l~~~k~ 102 (132)
..-+|+++||..++.+|+|+ +++.+..++|..
T Consensus 222 ~~~~I~~~~I~~ki~dld~~---dEl~~ey~k~~~ 253 (258)
T PF02718_consen 222 TSPKIDADDIYCKICDLDFP---DELKEEYEKYYA 253 (258)
T ss_pred CCcccCHHHHHHHHHcCCCC---hHHHHHHHHHHH
Confidence 37789999999999999998 455554555443
No 184
>PF07928 Vps54: Vps54-like protein; InterPro: IPR012501 This family contains various proteins that are homologues of the yeast Vps54 protein, such as the rat homologue (Q9JMK8 from SWISSPROT), the human homologue (Q86YF7 from SWISSPROT), and the mouse homologue (Q8R3X1 from SWISSPROT). In yeast, Vps54 associates with Vps52 and Vps53 proteins to form a trimolecular complex that is involved in protein transport between Golgi, endosomal, and vacuolar compartments []. All Vps54 homologues contain a coiled coil region (not found in the region featured in this family) and multiple dileucine motifs []. ; GO: 0042147 retrograde transport, endosome to Golgi; PDB: 3N1E_B 3N1B_B.
Probab=23.77 E-value=26 Score=25.92 Aligned_cols=36 Identities=17% Similarity=0.349 Sum_probs=0.0
Q ss_pred HhcCCCccCHHHHHHHHHHCCCc-ccHHHHHHHHHHH
Q 032845 65 KESKRQTINAEDVLKAIEEIDFT-EFVDPLRDSLDAK 100 (132)
Q Consensus 65 ~~~kRKTI~~eDVl~AL~~lgf~-~y~~~l~~~l~~~ 100 (132)
+..|=||||+.|+--|-+.|+|- .++|.++++++..
T Consensus 61 ~~agLK~IT~KhLALasq~L~~~~~lip~i~~~~~~~ 97 (135)
T PF07928_consen 61 RSAGLKTITAKHLALASQSLSFIISLIPYIREFFERH 97 (135)
T ss_dssp -------------------------------------
T ss_pred hccCcCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 34589999999999999999985 6888888877766
No 185
>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=23.36 E-value=1.4e+02 Score=16.35 Aligned_cols=37 Identities=11% Similarity=0.198 Sum_probs=25.0
Q ss_pred HHHhcCCCccCHHHHHHHHHHCCCcccHHHHHHHHHH
Q 032845 63 ICKESKRQTINAEDVLKAIEEIDFTEFVDPLRDSLDA 99 (132)
Q Consensus 63 ~a~~~kRKTI~~eDVl~AL~~lgf~~y~~~l~~~l~~ 99 (132)
....++.-.|+.+++..+++.++...-.+.+...+..
T Consensus 8 ~~d~~~~g~l~~~e~~~~l~~~~~~~~~~~~~~~~~~ 44 (63)
T cd00051 8 LFDKDGDGTISADELKAALKSLGEGLSEEEIDEMIRE 44 (63)
T ss_pred HhCCCCCCcCcHHHHHHHHHHhCCCCCHHHHHHHHHH
Confidence 3344555678999999999998866555555554443
No 186
>PRK08487 DNA polymerase III subunit delta; Validated
Probab=23.20 E-value=3.6e+02 Score=22.10 Aligned_cols=62 Identities=6% Similarity=0.099 Sum_probs=40.6
Q ss_pred hhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHH
Q 032845 15 KTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIE 82 (132)
Q Consensus 15 ~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~ 82 (132)
..-+.+.+++.+.. .+..|+.+|...|...+.-=...+..|-...+.=.+ +||.+||...+.
T Consensus 137 ~~~l~~~i~~~~~~----~g~~i~~~a~~~L~~~~g~dl~~l~~ELeKL~ly~~--~It~edV~~~v~ 198 (328)
T PRK08487 137 AREALELLQERAKE----LGLDIDQNALNHLYFIHNEDLALAANELEKLAILNE--PITLKDIQELVF 198 (328)
T ss_pred HHHHHHHHHHHHHH----hCCCCCHHHHHHHHHHhCcHHHHHHHHHHHHHHhcC--CCCHHHHHHHhc
Confidence 34445555554432 367899999999998877555555555555554433 799999988763
No 187
>PRK14961 DNA polymerase III subunits gamma and tau; Provisional
Probab=23.18 E-value=2.7e+02 Score=23.28 Aligned_cols=47 Identities=17% Similarity=0.169 Sum_probs=28.0
Q ss_pred cchhhHHHHHHHHHHHH----HHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHCC
Q 032845 34 DISVHKDALLAFCESAR----IFIHYLSATANDICKESKRQTINAEDVLKAIEEID 85 (132)
Q Consensus 34 ~~~ISkDA~~al~~~a~----~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~lg 85 (132)
++.++.++...+.+.+. .-++.+-. .+.- ++..|+.+||.+++....
T Consensus 195 g~~i~~~al~~ia~~s~G~~R~al~~l~~----~~~~-~~~~It~~~v~~~l~~~~ 245 (363)
T PRK14961 195 SIDTDEYALKLIAYHAHGSMRDALNLLEH----AINL-GKGNINIKNVTDMLGLLN 245 (363)
T ss_pred CCCCCHHHHHHHHHHcCCCHHHHHHHHHH----HHHh-cCCCCCHHHHHHHHCCCC
Confidence 45688888877766543 22222222 1222 467799999988776443
No 188
>cd03521 Link_domain_KIAA0527_like Link_domain_KIAA0527_like; this domain is found in the human protein KIAA0527. Sequence-wise, it is highly similar to the link domain. The link domain is a hyaluronan-binding (HA) domain. KIAA0527 contains a single link module. The KIAA0527 gene was originally cloned from human brain tissue.
Probab=23.02 E-value=1.4e+02 Score=21.18 Aligned_cols=31 Identities=19% Similarity=0.270 Sum_probs=28.5
Q ss_pred HHHHHHHHHhcCCCccCHHHHHHHHHHCCCc
Q 032845 57 SATANDICKESKRQTINAEDVLKAIEEIDFT 87 (132)
Q Consensus 57 tseA~~~a~~~kRKTI~~eDVl~AL~~lgf~ 87 (132)
..+|.+.|...+-.--++..+..|-++.||+
T Consensus 16 f~eA~~AC~~~gA~lAs~~QL~~AW~~~Gld 46 (95)
T cd03521 16 LRAARQSCASLGARLASAAELRRAVVECFFS 46 (95)
T ss_pred HHHHHHHHHHcCCEeccHHHHHHHHHHhCcc
Confidence 3689999999999999999999999998887
No 189
>cd05833 Ribosomal_P2 Ribosomal protein P2. This subfamily represents the eukaryotic large ribosomal protein P2. Eukaryotic P1 and P2 are functionally equivalent to the bacterial protein L7/L12, but are not homologous to L7/L12. P2 is located in the L12 stalk, with proteins P1, P0, L11, and 28S rRNA. P1 and P2 are the only proteins in the ribosome to occur as multimers, always appearing as sets of heterodimers. Recent data indicate that eukaryotes have four copies (two heterodimers), while most archaeal species contain six copies of L12p (three homodimers). Bacteria may have four or six copies of L7/L12 (two or three homodimers) depending on the species. Experiments using S. cerevisiae P1 and P2 indicate that P1 proteins are positioned more internally with limited reactivity in the C-terminal domains, while P2 proteins seem to be more externally located and are more likely to interact with other cellular components. In lower eukaryotes, P1 and P2 are further subdivided into P1A, P1B, P2
Probab=22.93 E-value=1.4e+02 Score=21.42 Aligned_cols=28 Identities=18% Similarity=0.136 Sum_probs=23.9
Q ss_pred HHHHHHhcCCCccCHHHHHHHHHHCCCc
Q 032845 60 ANDICKESKRQTINAEDVLKAIEEIDFT 87 (132)
Q Consensus 60 A~~~a~~~kRKTI~~eDVl~AL~~lgf~ 87 (132)
|.-.|.-.+..++|.+||.+.|+..|.+
T Consensus 6 AylL~~l~g~~~pTa~dI~~IL~AaGve 33 (109)
T cd05833 6 AYLLAVLGGNASPSAADVKKILGSVGVE 33 (109)
T ss_pred HHHHHHHcCCCCCCHHHHHHHHHHcCCC
Confidence 4556777788899999999999999975
No 190
>TIGR02083 LEU2 3-isopropylmalate dehydratase, large subunit. This model along with TIGR00170 describe clades which consist only of LeuC sequences. Here, the genes from Pyrococcus furiosus, Clostridium acetobutylicum, Thermotoga maritima and others are gene clustered with related genes from the leucine biosynthesis pathway.
Probab=22.91 E-value=95 Score=27.44 Aligned_cols=31 Identities=19% Similarity=0.184 Sum_probs=18.0
Q ss_pred HHHHHhhhhhhcCCC-cccCCCCcceeeeEeeecC
Q 032845 99 AKQIVSQKVVASNPL-FFFRGNHVRRIICHCIILE 132 (132)
Q Consensus 99 ~~k~~~q~~~~~~~~-~~~~g~~~~~~~~~~~~~~ 132 (132)
.++....-.+..... +++.| +.||||.+..|
T Consensus 76 ~~~~~r~fa~~~gi~~f~d~g---~~GI~H~v~~E 107 (419)
T TIGR02083 76 QCKMMREFAREQGIEKFFEIG---NMGIEHALLPE 107 (419)
T ss_pred HHHHHHHHHHHcCCcceecCC---Ccceeeeeccc
Confidence 334333444445554 55554 34999999876
No 191
>cd03518 Link_domain_HAPLN_module_1 Link_domain_HAPLN_module_1; this link domain is found in the first link module of proteins similar to the vertebrate HAPLN (hyaluronan/HA and proteoglycan binding link) protein family which includes cartilage link protein. The link domain is a HA-binding domain. HAPLNs contain two contiguous link modules. Both link modules of cartilage link protein are involved in interaction with HA. In cartilage, a chondroitin sulfate proteoglycan core protein (CSPG) aggrecan forms cartilage link protein stabilized aggregates with HA. These aggregates contribute to the tissue's load bearing properties. Aggregates with other CSPGs substituting for aggregan may contribute to the structural integrity of many different tissues. Members of the vertebrate HAPLN gene family are physically linked adjacent to CSPG genes.
Probab=22.81 E-value=1.4e+02 Score=21.04 Aligned_cols=30 Identities=17% Similarity=0.225 Sum_probs=26.7
Q ss_pred HHHHHHHHHhcCCCccCHHHHHHHHHHCCCc
Q 032845 57 SATANDICKESKRQTINAEDVLKAIEEIDFT 87 (132)
Q Consensus 57 tseA~~~a~~~kRKTI~~eDVl~AL~~lgf~ 87 (132)
.++|.+.|...+-..=|.+++..|.+ .||+
T Consensus 16 f~eA~~aC~~~ga~lAs~~QL~~Aw~-~Gld 45 (95)
T cd03518 16 FHEAQQACEEQDATLASFEQLYQAWT-EGLD 45 (95)
T ss_pred HHHHHHHHHHcCCeeCCHHHHHHHHH-cCcc
Confidence 47899999999999999999999987 8887
No 192
>PRK05672 dnaE2 error-prone DNA polymerase; Validated
Probab=22.77 E-value=38 Score=33.10 Aligned_cols=45 Identities=18% Similarity=0.335 Sum_probs=34.3
Q ss_pred HHHHHHCCCcccHHHHHHHHHHHHHHhhhhhhcCCCcccCCCCcceeeeEee
Q 032845 78 LKAIEEIDFTEFVDPLRDSLDAKQIVSQKVVASNPLFFFRGNHVRRIICHCI 129 (132)
Q Consensus 78 l~AL~~lgf~~y~~~l~~~l~~~k~~~q~~~~~~~~~~~~g~~~~~~~~~~~ 129 (132)
+..+.++||.+|.=.++++.+--| ....+.||||.+.--.+|.|+
T Consensus 320 L~vI~~~gf~~YFLIV~D~i~~Ak-------~~gi~vpGRGSaAGSLVaY~L 364 (1046)
T PRK05672 320 LALIAELGYEGYFLTVHDIVRFAR-------SQGILCQGRGSAANSAVCYAL 364 (1046)
T ss_pred HHHHHHCCCCccHHHHHHHHHHHH-------HCCceeCCCChHHHHHHHHHh
Confidence 667888999999998888776544 234556999998877777775
No 193
>COG4519 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.73 E-value=38 Score=23.77 Aligned_cols=19 Identities=42% Similarity=0.726 Sum_probs=15.3
Q ss_pred CHHHHHHHHHHCCCc-ccHH
Q 032845 73 NAEDVLKAIEEIDFT-EFVD 91 (132)
Q Consensus 73 ~~eDVl~AL~~lgf~-~y~~ 91 (132)
+.+||++||..||.. +|+.
T Consensus 38 T~QDvikAlpglgi~l~FvQ 57 (95)
T COG4519 38 TAQDVIKALPGLGIVLEFVQ 57 (95)
T ss_pred HHHHHHHhCcCCCeEEEeee
Confidence 579999999999975 5554
No 194
>PRK14958 DNA polymerase III subunits gamma and tau; Provisional
Probab=22.48 E-value=2.5e+02 Score=25.07 Aligned_cols=72 Identities=13% Similarity=0.094 Sum_probs=39.3
Q ss_pred ccchhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHCCCcc
Q 032845 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFTE 88 (132)
Q Consensus 12 ~LP~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~lgf~~ 88 (132)
.+|...+.+.++..+.. .++.++.+|...|.+.+.-=+-.+-+.-.+.+ .-+...|+.+||...+....-+.
T Consensus 177 ~l~~~~i~~~l~~il~~----egi~~~~~al~~ia~~s~GslR~al~lLdq~i-a~~~~~It~~~V~~~lg~~~~~~ 248 (509)
T PRK14958 177 QLPPLQIAAHCQHLLKE----ENVEFENAALDLLARAANGSVRDALSLLDQSI-AYGNGKVLIADVKTMLGTIEPLL 248 (509)
T ss_pred CCCHHHHHHHHHHHHHH----cCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHH-hcCCCCcCHHHHHHHHCCCCHHH
Confidence 35555555555555532 25788999988887765421111111111111 12456788888887765554433
No 195
>PRK09111 DNA polymerase III subunits gamma and tau; Validated
Probab=22.47 E-value=2.4e+02 Score=25.81 Aligned_cols=65 Identities=11% Similarity=0.097 Sum_probs=40.7
Q ss_pred cchhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHH
Q 032845 13 LPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIE 82 (132)
Q Consensus 13 LP~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~ 82 (132)
++..-+.+.+++.+.. .++.++.++...|.+.+.--+..+.++..+.+.. +...|+.+||...+.
T Consensus 191 l~~~el~~~L~~i~~k----egi~i~~eAl~lIa~~a~Gdlr~al~~Ldkli~~-g~g~It~e~V~~llg 255 (598)
T PRK09111 191 IEADVLAAHLSRIAAK----EGVEVEDEALALIARAAEGSVRDGLSLLDQAIAH-GAGEVTAEAVRDMLG 255 (598)
T ss_pred CCHHHHHHHHHHHHHH----cCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHhh-cCCCcCHHHHHHHhC
Confidence 4444555555554432 2578999999988887765555555554444333 345799999887654
No 196
>PF10714 LEA_6: Late embryogenesis abundant protein 18; InterPro: IPR018930 This is a family of late embryogenesis-abundant proteins There is high accumulation of this protein in dry seeds, and in the roots of full-grown plants in response to dehydration and ABA (abscisic acid application) treatments []. This LEA protein disappears after germination. It accumulates in growing regions of well irrigated hypocotyls and meristems suggesting a role in seedling growth resumption on rehydration []. As a group the LEA proteins are highly hydrophilic, contain a high percentage of glycine residues, lack Cys and Trp residues and do not coagulate upon exposure to high temperature, and for these reasons are considered to be members of a group of proteins called hydrophilins []. Expression of the protein is negatively regulated during etiolating growth, particularly in roots, in contrast to its expression patterns during normal growth [].
Probab=22.44 E-value=72 Score=21.91 Aligned_cols=25 Identities=12% Similarity=-0.081 Sum_probs=17.9
Q ss_pred HHHHHHHhhhhhhcCCCcccCCCCc
Q 032845 97 LDAKQIVSQKVVASNPLFFFRGNHV 121 (132)
Q Consensus 97 l~~~k~~~q~~~~~~~~~~~~g~~~ 121 (132)
|+.||..-=-...-.+|.++||+|.
T Consensus 26 LEDYK~~gYGt~GH~~pkpg~Ggg~ 50 (79)
T PF10714_consen 26 LEDYKRKGYGTEGHQEPKPGRGGGA 50 (79)
T ss_pred HHHHhhhccccccccCCCCCCCCCc
Confidence 7788844333455788889999875
No 197
>cd01582 Homoaconitase Homoaconitase and other uncharacterized proteins of the Aconitase family. Homoaconitase catalytic domain. Homoaconitase and other uncharacterized proteins of the Aconitase family. Homoaconitase is part of an unusual lysine biosynthesis pathway found only in filamentous fungi, in which lysine is synthesized via the alpha-aminoadipate pathway. In this pathway, homoaconitase catalyzes the conversion of cis-homoaconitic acid into homoisocitric acid. The reaction mechanism is believed to be similar to that of other aconitases.
Probab=22.35 E-value=59 Score=28.17 Aligned_cols=30 Identities=23% Similarity=0.235 Sum_probs=17.6
Q ss_pred HHHHHhhhhhhcCCCcccCCCCcceeeeEeeecC
Q 032845 99 AKQIVSQKVVASNPLFFFRGNHVRRIICHCIILE 132 (132)
Q Consensus 99 ~~k~~~q~~~~~~~~~~~~g~~~~~~~~~~~~~~ 132 (132)
.++....-.+.....+.+.| .||||.+.+|
T Consensus 47 ~~~~lr~~ak~~gi~~~~~g----~GI~Hqv~~E 76 (363)
T cd01582 47 KYKNIESFAKKHGIDFYPAG----RGIGHQIMIE 76 (363)
T ss_pred HHHHHHHHHHHhCCeEECCC----CCEEEEeccc
Confidence 34433333344444555555 4999999886
No 198
>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=22.18 E-value=2.2e+02 Score=18.03 Aligned_cols=42 Identities=17% Similarity=0.141 Sum_probs=32.4
Q ss_pred HHHHHHHHH--HHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 032845 40 DALLAFCES--ARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (132)
Q Consensus 40 DA~~al~~~--a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~ 83 (132)
+..+++ +. ...|..|....|..++-+.++|. ..+|+.+|..=
T Consensus 14 e~id~~-~~~~~~~~~~f~~gnaiKY~~R~~~K~-~~eDl~KA~~Y 57 (60)
T PF11753_consen 14 ECIDFI-EQFTEEQFLGFCLGNAIKYLWRAGKKN-GIEDLKKAKWY 57 (60)
T ss_pred cHHHHH-HHhcchhhhhHHHHHHHHHHHHHcccC-cHHHHHHHHHH
Confidence 455555 44 44899999999999999999994 48888888653
No 199
>smart00874 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits.
Probab=22.11 E-value=82 Score=19.78 Aligned_cols=17 Identities=18% Similarity=0.536 Sum_probs=15.6
Q ss_pred ccCHHHHHHHHHHCCCc
Q 032845 71 TINAEDVLKAIEEIDFT 87 (132)
Q Consensus 71 TI~~eDVl~AL~~lgf~ 87 (132)
.++++++...|+.|||.
T Consensus 18 ~i~~~ei~~~L~~lg~~ 34 (71)
T smart00874 18 DLSAEEIEEILKRLGFE 34 (71)
T ss_pred CCCHHHHHHHHHHCCCe
Confidence 58999999999999996
No 200
>PF00543 P-II: Nitrogen regulatory protein P-II members of this family.; InterPro: IPR002187 In Gram-negative bacteria, the activity and concentration of glutamine synthetase (GS) is regulated in response to nitrogen source availability. PII, a tetrameric protein encoded by the glnB gene, is a component of the adenylation cascade involved in the regulation of GS activity []. In nitrogen-limiting conditions, when the ratio of glutamine to 2-ketoglutarate decreases, P-II is uridylylated on a tyrosine residue to form P-II-UMP. P-II-UMP allows the deadenylation of GS, thus activating the enzyme. Conversely, in nitrogen excess, P-II-UMP is deuridylated and then promotes the adenylation of GS. P-II also indirectly controls the transcription of the GS gene (glnA) by preventing NR-II (ntrB) to phosphorylate NR-I (ntrC) which is the transcriptional activator of glnA. Once P-II is uridylylated, these events are reversed. P-II is a protein of about 110 amino acid residues extremely well conserved. The tyrosine which is uridylated is located in the central part of the protein. In cyanobacteria, P-II seems to be phosphorylated on a serine residue rather than being uridylated. In methanogenic archaebacteria, the nitrogenase iron protein gene (nifH) is followed by two open reading frames highly similar to the eubacterial P-II protein []. These proteins could be involved in the regulation of nitrogen fixation. In the red alga, Porphyra purpurea, there is a glnB homologue encoded in the chloroplast genome. Other proteins highly similar to glnB are: Bacillus subtilis protein nrgB []. Escherichia coli hypothetical protein ybaI []. ; GO: 0030234 enzyme regulator activity, 0006808 regulation of nitrogen utilization; PDB: 1V3S_B 1V3R_C 2XZW_A 2XUL_A 2V5H_J 2XG8_C 2JJ4_F 1QY7_C 4AFF_A 2XBP_A ....
Probab=22.09 E-value=64 Score=22.08 Aligned_cols=17 Identities=24% Similarity=0.448 Sum_probs=14.2
Q ss_pred CHHHHHHHHHHCCCccc
Q 032845 73 NAEDVLKAIEEIDFTEF 89 (132)
Q Consensus 73 ~~eDVl~AL~~lgf~~y 89 (132)
..++|..||+++||.++
T Consensus 9 ~~~~v~~aL~~~G~~g~ 25 (102)
T PF00543_consen 9 KLEEVIEALREAGVPGM 25 (102)
T ss_dssp GHHHHHHHHHHTTGSCE
T ss_pred HHHHHHHHHHHCCCCeE
Confidence 46899999999998764
No 201
>PRK05629 hypothetical protein; Validated
Probab=21.82 E-value=3.2e+02 Score=22.19 Aligned_cols=48 Identities=13% Similarity=0.184 Sum_probs=35.7
Q ss_pred cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHH
Q 032845 34 DISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIE 82 (132)
Q Consensus 34 ~~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~ 82 (132)
+.+|+.+|...|.+.+..=...+..+-...+.-. ..+|+.+||-..+.
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 6789999999998888765666666666666543 45799999987644
No 202
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []. Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=21.81 E-value=1.1e+02 Score=19.82 Aligned_cols=32 Identities=6% Similarity=0.368 Sum_probs=22.3
Q ss_pred HHHHHHHHhcCCCccCHHHHHHHHHHCCCcccHHH
Q 032845 58 ATANDICKESKRQTINAEDVLKAIEEIDFTEFVDP 92 (132)
Q Consensus 58 seA~~~a~~~kRKTI~~eDVl~AL~~lgf~~y~~~ 92 (132)
....++|+.. -|++.=|..-.+.|||.+|.+-
T Consensus 35 ~si~elA~~~---~vS~sti~Rf~kkLG~~gf~ef 66 (77)
T PF01418_consen 35 MSISELAEKA---GVSPSTIVRFCKKLGFSGFKEF 66 (77)
T ss_dssp --HHHHHHHC---TS-HHHHHHHHHHCTTTCHHHH
T ss_pred ccHHHHHHHc---CCCHHHHHHHHHHhCCCCHHHH
Confidence 3344555443 4889999999999999998763
No 203
>cd01581 AcnB Aconitate hydratase B catalyses the formation of cis-aconitate from citrate as part of the TCA cycle. Aconitase B catalytic domain. Aconitate hydratase B catalyses the formation of cis-aconitate from citrate as part of the TCA cycle. Aconitase has an active (4FE-4S) and an inactive (3FE-4S) form. The active cluster is part of the catalytic site that interconverts citrate, cis-aconitase and isocitrate. The domain architecture of aconitase B is different from other aconitases in that the catalytic domain is normally found at C-terminus for other aconitases, but it is at N-terminus for B family. It also has a HEAT domain before domain 4 which plays a role in protein-protein interaction. This alignment is the core domain including domains 1,2 and 3.
Probab=21.49 E-value=1.3e+02 Score=26.78 Aligned_cols=17 Identities=12% Similarity=0.083 Sum_probs=10.9
Q ss_pred CCcccCCCCcceeeeEeeecC
Q 032845 112 PLFFFRGNHVRRIICHCIILE 132 (132)
Q Consensus 112 ~~~~~~g~~~~~~~~~~~~~~ 132 (132)
..+.+.| .||||-+..|
T Consensus 86 i~~~~~g----~GI~Hqv~~e 102 (436)
T cd01581 86 GVALRPG----DGVIHSWLNR 102 (436)
T ss_pred CcEECCC----CCeeeeeehh
Confidence 3455555 4899988644
No 204
>COG1222 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]
Probab=21.32 E-value=1.2e+02 Score=26.77 Aligned_cols=32 Identities=25% Similarity=0.465 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHHHhcCCCccCHHHHHHHHHHC
Q 032845 53 IHYLSATANDICKESKRQTINAEDVLKAIEEI 84 (132)
Q Consensus 53 I~~ltseA~~~a~~~kRKTI~~eDVl~AL~~l 84 (132)
|.-+..+|--.|.++.|..|+-+|.++|.+..
T Consensus 361 lkaictEAGm~AiR~~R~~Vt~~DF~~Av~KV 392 (406)
T COG1222 361 LKAICTEAGMFAIRERRDEVTMEDFLKAVEKV 392 (406)
T ss_pred HHHHHHHHhHHHHHhccCeecHHHHHHHHHHH
Confidence 66788899999999999999999999997654
No 205
>cd03515 Link_domain_TSG_6_like This is the extracellular link domain of the type found in human TSG-6. The link domain is a hyaluronan (HA)-binding domain. TSG-6 is the protein product of tumor necrosis factor-stimulated gene-6. TSG-6 is up-regulated in inflammatory lesions and in the ovary during ovulation. It has a strong anti-inflammatory and chondroprotective effect in models of acute inflammation and autoimmune arthritis and plays an essential role in female fertility. Also included in this group are the stabilins: stabilin-1 (FEEL-1, CLEVER-1) and stabilin-2 (FEEL-2). Stabilin-2 functions as the major liver and lymph node-scavenging receptor for HA and related glycosaminoglycans. Stabilin-2 is a scavenger receptor with a broad range of ligands including advanced glycation end (AGE) products, acetylated low density lipoprotein and procollagen peptides. In contrast, stabilin-1 does not bind HA, but binds acetylated low density lipoprotein and AGEs with lower affinity. As AGEs accum
Probab=21.24 E-value=1.8e+02 Score=20.52 Aligned_cols=30 Identities=13% Similarity=0.241 Sum_probs=26.7
Q ss_pred HHHHHHHHHhcCCCccCHHHHHHHHHHCCCc
Q 032845 57 SATANDICKESKRQTINAEDVLKAIEEIDFT 87 (132)
Q Consensus 57 tseA~~~a~~~kRKTI~~eDVl~AL~~lgf~ 87 (132)
.++|.+.|...+-..=|.+++..|.+ .||+
T Consensus 16 f~eA~~aC~~~ga~lAs~~QL~~Aw~-~G~d 45 (93)
T cd03515 16 YTEAKAACEAEGAHLATYSQLSAAQQ-LGFH 45 (93)
T ss_pred HHHHHHHHHHcCCccCCHHHHHHHHH-cCcc
Confidence 47899999999999999999999988 5887
No 206
>PTZ00448 hypothetical protein; Provisional
Probab=21.12 E-value=5.7e+02 Score=22.44 Aligned_cols=90 Identities=11% Similarity=0.162 Sum_probs=61.8
Q ss_pred ccchhHHHHHHhhhccCCCCCCcchhhHHHHHHHHHHH-HHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHCCCc--c
Q 032845 12 ELPKTIVRRVVKDKLHNCSPDTDISVHKDALLAFCESA-RIFIHYLSATANDICKESKRQTINAEDVLKAIEEIDFT--E 88 (132)
Q Consensus 12 ~LP~a~V~RimK~~Lp~~~~d~~~~ISkDA~~al~~~a-~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~lgf~--~ 88 (132)
.|....+..|++..|-. |.+.+|.+=+..+.+.- ...+.+|+..+. .-.-++..++.=|-.||++++|. -
T Consensus 74 aFGTtD~~eI~k~IL~K----GElQlt~~ER~~~~E~k~r~Ii~~Ia~~~I---nP~T~~P~P~~rIE~Am~e~~~~Vdp 146 (373)
T PTZ00448 74 VFGTNSIDNICKTILSK----GEIQVSETERSYMLDKQFTDICHMLNRMTV---NPKNNLPLSVKIIESELKDSGFSVSL 146 (373)
T ss_pred HhCCCCHHHHHHHHHhc----CCcccCHHHHHHHHHHHHHHHHHHHHHhcc---CCCCCCCCCHHHHHHHHHhcCcccCC
Confidence 35566677888888864 68899988877666543 455555554322 23567789999999999999986 4
Q ss_pred cHHHHHHHHHHHHHHhhhhh
Q 032845 89 FVDPLRDSLDAKQIVSQKVV 108 (132)
Q Consensus 89 y~~~l~~~l~~~k~~~q~~~ 108 (132)
+.+.=++.++..+...+..|
T Consensus 147 ~Ksak~Qalevik~L~~iiP 166 (373)
T PTZ00448 147 NKTTKEQALKAFDILKKRIP 166 (373)
T ss_pred CCCHHHHHHHHHHHHHHhCC
Confidence 66666666777776654443
No 207
>TIGR02849 spore_III_AD stage III sporulation protein AD. Members of this family are the uncharacterized protein SpoIIIAD, part of the spoIIIA operon that acts at sporulation stage III as part of a cascade of events leading to endospore formation. Note that the start sites of members of this family as annotated tend to be variable; quite a few members have apparent homologous protein-coding regions continuing upstream of the first available start codon. The length of the alignment has been set to try to detect all valid members of the family, even if annotation of the start site begins too far downstream.
Probab=20.76 E-value=69 Score=22.89 Aligned_cols=38 Identities=18% Similarity=0.343 Sum_probs=28.4
Q ss_pred chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCH
Q 032845 35 ISVHKDALLAFCESARIFIHYLSATANDICKESKRQTINA 74 (132)
Q Consensus 35 ~~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~ 74 (132)
..++..-...+-|... |.|++.-|.++|++.|-.+|..
T Consensus 35 a~i~~~Yi~~llKiiG--IaYIaef~s~iCkDAG~~aiAs 72 (101)
T TIGR02849 35 AGLDSLYLATVLKIIG--IAYIAEFGSQICKDAGEKAIAS 72 (101)
T ss_pred cCCChHHHHHHHHHHH--HHHHHHHHHHHHHHcChHHHHH
Confidence 3455555666666554 6899999999999999888754
No 208
>PF11075 DUF2780: Protein of unknown function VcgC/VcgE (DUF2780); InterPro: IPR021302 This is a bacterial family of uncharacterised proteins.
Probab=20.38 E-value=1.4e+02 Score=22.90 Aligned_cols=30 Identities=23% Similarity=0.296 Sum_probs=24.4
Q ss_pred ccCHHHHHHHHHHCCCc-----ccHHHHHHHHHHH
Q 032845 71 TINAEDVLKAIEEIDFT-----EFVDPLRDSLDAK 100 (132)
Q Consensus 71 TI~~eDVl~AL~~lgf~-----~y~~~l~~~l~~~ 100 (132)
-=+..+|..+++.||++ .|+|.+..||..-
T Consensus 118 ~~~~~~v~~~F~~LGld~~mi~~f~pii~~yL~~q 152 (163)
T PF11075_consen 118 LGNMADVNSAFSALGLDPSMISQFVPIILSYLQSQ 152 (163)
T ss_pred cccHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhh
Confidence 34678999999999998 4888888887753
No 209
>CHL00095 clpC Clp protease ATP binding subunit
Probab=20.15 E-value=1.7e+02 Score=27.58 Aligned_cols=36 Identities=8% Similarity=0.169 Sum_probs=27.9
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHH
Q 032845 36 SVHKDALLAFCESARIFIHYLSATANDICKESKRQTINAEDVLKAIEE 83 (132)
Q Consensus 36 ~ISkDA~~al~~~a~~FI~~ltseA~~~a~~~kRKTI~~eDVl~AL~~ 83 (132)
++|+++..+|. .|...|..-+...|+++|++.||=.
T Consensus 4 rfT~~a~~vL~------------~A~~~A~~~~h~~V~~EHLLLaLL~ 39 (821)
T CHL00095 4 RFTEKAIKVIM------------LSQEEARRLGHNFVGTEQILLGLIG 39 (821)
T ss_pred hHhHHHHHHHH------------HHHHHHHHhCCCcCcHHHHHHHHHh
Confidence 45666666665 4668888888999999999998743
No 210
>PLN03239 histone acetyltransferase; Provisional
Probab=20.11 E-value=76 Score=27.51 Aligned_cols=35 Identities=20% Similarity=0.368 Sum_probs=24.1
Q ss_pred CCccCHHHHHHHHHHCCCcccHHH------HHHHHHHHHHH
Q 032845 69 RQTINAEDVLKAIEEIDFTEFVDP------LRDSLDAKQIV 103 (132)
Q Consensus 69 RKTI~~eDVl~AL~~lgf~~y~~~------l~~~l~~~k~~ 103 (132)
..-|..+||+.+|+.||+-.|... -...++++.+.
T Consensus 293 ~Tgi~~~DIi~tL~~l~~l~~~~g~~~i~~~~~~l~~~~~~ 333 (351)
T PLN03239 293 KTSIMAEDIVFALNQLGILKFINGIYFIAAEKGLLEELAEK 333 (351)
T ss_pred HhCCCHHHHHHHHHHCCcEEEECCeEEEEeCHHHHHHHHHH
Confidence 445999999999999996544322 34556666543
No 211
>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA.
Probab=20.11 E-value=1.6e+02 Score=27.29 Aligned_cols=23 Identities=22% Similarity=0.351 Sum_probs=19.7
Q ss_pred HHHHHHHhcCCCccCHHHHHHHH
Q 032845 59 TANDICKESKRQTINAEDVLKAI 81 (132)
Q Consensus 59 eA~~~a~~~kRKTI~~eDVl~AL 81 (132)
.|...|..-+..-|+++|++.||
T Consensus 11 ~A~~~A~~~~h~~V~~EHLLlaL 33 (731)
T TIGR02639 11 AALEEAKKRRHEFVTLEHILLAL 33 (731)
T ss_pred HHHHHHHHhCCCcCcHHHHHHHH
Confidence 46678888888999999999987
No 212
>PF11625 DUF3253: Protein of unknown function (DUF3253); InterPro: IPR021660 This bacterial family of proteins has no known function. ; PDB: 2NS0_A.
Probab=20.00 E-value=2.6e+02 Score=19.31 Aligned_cols=38 Identities=18% Similarity=0.334 Sum_probs=24.6
Q ss_pred HHhcCCCccCHHHHHHHHHHCCCcccHHHHHHHHHHHH
Q 032845 64 CKESKRQTINAEDVLKAIEEIDFTEFVDPLRDSLDAKQ 101 (132)
Q Consensus 64 a~~~kRKTI~~eDVl~AL~~lgf~~y~~~l~~~l~~~k 101 (132)
+...--|||-|.||-.||.--++-++.+.+......-.
T Consensus 17 ~~R~~~ktiCPSevARal~~~~WR~lm~~vR~~A~~L~ 54 (83)
T PF11625_consen 17 AARGPGKTICPSEVARALGPDDWRDLMPPVRAAARRLA 54 (83)
T ss_dssp HHS-TT--B-HHHHHHHH-TTS-GGGHHHHHHHHHHHH
T ss_pred HhcCCCCccCHHHHHHHHCchhhHHHHHHHHHHHHHHH
Confidence 34556799999999999987778888888877655444
Done!