Query 034139
Match_columns 103
No_of_seqs 121 out of 487
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 10:12:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034139.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034139hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00035 histone H4; Provision 100.0 1.5E-43 3.2E-48 237.5 10.5 103 1-103 1-103 (103)
2 PTZ00015 histone H4; Provision 100.0 1.5E-40 3.2E-45 222.8 10.4 101 1-101 1-102 (102)
3 cd00076 H4 Histone H4, one of 100.0 2.9E-35 6.3E-40 191.8 9.0 85 17-101 1-85 (85)
4 KOG3467 Histone H4 [Chromatin 100.0 1.7E-34 3.7E-39 188.5 8.8 103 1-103 1-103 (103)
5 smart00417 H4 Histone H4. 99.9 3.8E-28 8.2E-33 154.7 6.4 74 17-90 1-74 (74)
6 COG2036 HHT1 Histones H3 and H 99.9 1.9E-27 4.2E-32 156.6 7.3 90 12-101 2-91 (91)
7 smart00803 TAF TATA box bindin 99.9 7.1E-23 1.5E-27 127.5 8.0 64 29-92 2-65 (65)
8 PLN00163 histone H4; Provision 99.8 1.5E-20 3.4E-25 114.0 3.1 59 1-59 1-59 (59)
9 KOG0869 CCAAT-binding factor, 99.7 3.3E-17 7.3E-22 116.8 7.3 80 21-100 24-105 (168)
10 PF02969 TAF: TATA box binding 99.7 1.1E-16 2.5E-21 99.9 8.1 64 29-92 3-66 (66)
11 cd08050 TAF6 TATA Binding Prot 99.7 9.4E-17 2E-21 126.2 9.0 73 31-103 1-74 (343)
12 smart00428 H3 Histone H3. 99.7 2E-16 4.3E-21 106.7 7.1 82 16-97 16-104 (105)
13 cd07979 TAF9 TATA Binding Prot 99.6 1.7E-15 3.6E-20 103.8 8.2 68 33-102 5-72 (117)
14 PF00125 Histone: Core histone 99.6 4.8E-15 1E-19 92.9 7.7 67 27-93 3-74 (75)
15 PF00808 CBFD_NFYB_HMF: Histon 99.6 4.7E-14 1E-18 86.7 8.7 63 29-91 2-65 (65)
16 PLN00160 histone H3; Provision 99.5 1.5E-14 3.3E-19 96.3 6.5 80 17-96 9-94 (97)
17 PLN00121 histone H3; Provision 99.5 3E-14 6.5E-19 99.9 6.1 78 19-96 52-134 (136)
18 PLN00161 histone H3; Provision 99.5 7.6E-14 1.6E-18 97.6 7.7 77 20-96 46-128 (135)
19 cd07981 TAF12 TATA Binding Pro 99.5 2E-13 4.3E-18 86.2 8.4 65 30-94 2-67 (72)
20 PTZ00018 histone H3; Provision 99.5 6E-14 1.3E-18 98.4 6.4 78 19-96 52-134 (136)
21 KOG2549 Transcription initiati 99.5 1.2E-13 2.7E-18 113.9 8.8 74 30-103 12-86 (576)
22 PF15511 CENP-T: Centromere ki 99.5 7.3E-14 1.6E-18 112.5 7.3 70 17-86 337-414 (414)
23 smart00576 BTP Bromodomain tra 99.5 5.4E-13 1.2E-17 84.9 8.6 68 30-97 7-74 (77)
24 cd00074 H2A Histone 2A; H2A is 99.5 5.4E-13 1.2E-17 91.3 8.9 65 29-93 20-85 (115)
25 COG5095 TAF6 Transcription ini 99.4 1.3E-12 2.9E-17 102.9 8.2 74 29-102 5-79 (450)
26 KOG1745 Histones H3 and H4 [Ch 99.3 2E-12 4.4E-17 90.6 2.4 80 17-96 51-135 (137)
27 PF15630 CENP-S: Kinetochore c 99.2 6.1E-11 1.3E-15 75.9 7.5 61 34-94 10-73 (76)
28 PLN00153 histone H2A; Provisio 99.2 1.2E-10 2.5E-15 81.1 7.9 87 1-92 1-88 (129)
29 PLN00157 histone H2A; Provisio 99.1 2.3E-10 5.1E-15 79.9 7.8 87 1-92 1-90 (132)
30 PF02291 TFIID-31kDa: Transcri 99.1 3.9E-10 8.5E-15 78.6 7.9 67 28-94 9-77 (129)
31 PF07524 Bromo_TP: Bromodomain 99.0 6.4E-09 1.4E-13 65.7 8.7 66 32-97 9-74 (77)
32 KOG3334 Transcription initiati 99.0 4.8E-09 1E-13 74.1 8.8 69 26-94 8-78 (148)
33 KOG1756 Histone 2A [Chromatin 99.0 3.4E-09 7.5E-14 73.5 7.8 88 1-92 1-91 (131)
34 PLN00154 histone H2A; Provisio 99.0 5.6E-09 1.2E-13 73.2 8.6 64 29-92 38-103 (136)
35 PTZ00017 histone H2A; Provisio 98.9 7.7E-09 1.7E-13 72.5 8.1 64 29-92 27-91 (134)
36 KOG0871 Class 2 transcription 98.9 1.2E-08 2.5E-13 72.6 7.5 75 25-99 8-84 (156)
37 PLN00156 histone H2AX; Provisi 98.8 3.5E-08 7.7E-13 69.5 8.2 64 29-92 29-93 (139)
38 KOG0870 DNA polymerase epsilon 98.7 6.8E-08 1.5E-12 69.7 8.0 70 28-97 9-81 (172)
39 COG5262 HTA1 Histone H2A [Chro 98.7 6.7E-08 1.5E-12 66.5 7.2 86 4-92 4-90 (132)
40 PF03847 TFIID_20kDa: Transcri 98.5 7.8E-07 1.7E-11 55.7 8.1 63 32-94 2-65 (68)
41 smart00414 H2A Histone 2A. 98.5 6E-07 1.3E-11 60.7 6.6 64 29-92 9-73 (106)
42 COG5094 TAF9 Transcription ini 98.4 5.8E-07 1.3E-11 62.5 5.7 60 35-94 20-82 (145)
43 KOG1142 Transcription initiati 98.3 2.1E-06 4.6E-11 65.7 7.5 83 21-103 146-230 (258)
44 PTZ00252 histone H2A; Provisio 98.2 5.8E-06 1.3E-10 58.0 7.2 64 29-92 25-91 (134)
45 COG5150 Class 2 transcription 98.2 8E-06 1.7E-10 57.1 6.9 73 27-99 9-83 (148)
46 KOG4336 TBP-associated transcr 98.0 2.8E-05 6E-10 61.0 7.7 66 33-98 9-74 (323)
47 PTZ00463 histone H2B; Provisio 98.0 8E-05 1.7E-09 51.1 8.2 60 35-94 34-94 (117)
48 PLN00158 histone H2B; Provisio 98.0 7.9E-05 1.7E-09 51.1 8.1 61 34-94 32-93 (116)
49 smart00427 H2B Histone H2B. 97.9 7.8E-05 1.7E-09 49.1 7.6 60 35-94 7-67 (89)
50 PLN00155 histone H2A; Provisio 97.8 3.7E-05 8E-10 46.9 4.5 56 1-61 1-57 (58)
51 PF02269 TFIID-18kDa: Transcri 97.8 2.1E-05 4.6E-10 51.8 3.7 61 35-95 7-68 (93)
52 COG5208 HAP5 CCAAT-binding fac 97.8 5E-05 1.1E-09 57.6 5.3 67 27-93 107-174 (286)
53 cd08048 TAF11 TATA Binding Pro 97.8 0.00023 5.1E-09 46.3 7.5 66 29-94 16-84 (85)
54 KOG1757 Histone 2A [Chromatin 97.6 0.00013 2.9E-09 50.0 4.9 91 1-92 1-95 (131)
55 KOG3423 Transcription initiati 97.5 0.0012 2.7E-08 48.0 8.8 71 26-96 83-167 (176)
56 KOG2389 Predicted bromodomain 97.5 0.0003 6.5E-09 56.0 6.1 70 28-97 28-97 (353)
57 PF09415 CENP-X: CENP-S associ 97.5 0.0004 8.6E-09 43.9 5.3 61 31-91 1-65 (72)
58 cd07978 TAF13 The TATA Binding 97.4 0.0014 2.9E-08 43.2 7.5 61 33-94 6-67 (92)
59 KOG1657 CCAAT-binding factor, 97.3 0.00038 8.3E-09 52.9 4.7 68 27-94 72-140 (236)
60 KOG1659 Class 2 transcription 97.3 0.0011 2.3E-08 49.9 6.5 66 27-92 11-77 (224)
61 PF04719 TAFII28: hTAFII28-lik 97.2 0.0028 6.1E-08 41.7 7.4 66 29-94 23-90 (90)
62 PF03540 TFIID_30kDa: Transcri 97.0 0.0055 1.2E-07 36.5 6.5 49 28-76 1-49 (51)
63 KOG1744 Histone H2B [Chromatin 96.9 0.0042 9E-08 43.3 6.5 60 35-94 43-103 (127)
64 COG5247 BUR6 Class 2 transcrip 96.9 0.0086 1.9E-07 40.5 7.3 67 26-92 20-87 (113)
65 PF13654 AAA_32: AAA domain; P 95.9 0.045 9.7E-07 45.7 8.0 60 35-94 436-506 (509)
66 KOG3219 Transcription initiati 95.9 0.013 2.9E-07 43.5 4.1 68 28-95 111-179 (195)
67 cd08045 TAF4 TATA Binding Prot 95.6 0.084 1.8E-06 39.0 7.6 60 35-94 54-119 (212)
68 COG5162 Transcription initiati 95.1 0.24 5.1E-06 36.3 8.2 71 27-97 86-189 (197)
69 PF05236 TAF4: Transcription i 94.8 0.047 1E-06 41.6 4.3 66 29-94 43-118 (264)
70 KOG3901 Transcription initiati 94.3 0.17 3.7E-06 34.3 5.6 56 36-94 16-72 (109)
71 COG5248 TAF19 Transcription in 94.3 0.35 7.5E-06 33.2 7.1 59 34-94 14-73 (126)
72 TIGR02902 spore_lonB ATP-depen 93.0 0.45 9.8E-06 39.7 7.2 62 30-92 263-330 (531)
73 COG1067 LonB Predicted ATP-dep 92.9 0.53 1.1E-05 40.6 7.5 59 35-93 327-398 (647)
74 TIGR00764 lon_rel lon-related 92.9 0.68 1.5E-05 39.4 8.1 59 35-93 318-390 (608)
75 PRK07452 DNA polymerase III su 92.8 0.38 8.2E-06 36.9 6.0 61 35-96 139-201 (326)
76 KOG1658 DNA polymerase epsilon 92.3 0.098 2.1E-06 37.7 2.0 70 26-95 56-126 (162)
77 PF08369 PCP_red: Proto-chloro 91.3 0.58 1.3E-05 26.8 4.2 43 47-90 1-44 (45)
78 PRK06585 holA DNA polymerase I 91.3 0.66 1.4E-05 35.8 5.8 59 35-94 151-210 (343)
79 TIGR01128 holA DNA polymerase 90.1 1.5 3.3E-05 32.7 6.7 59 35-94 120-178 (302)
80 PRK05574 holA DNA polymerase I 90.0 1.4 3.1E-05 33.5 6.6 65 35-100 155-220 (340)
81 PRK00411 cdc6 cell division co 90.0 1.3 2.9E-05 34.5 6.6 65 30-94 207-282 (394)
82 PRK08487 DNA polymerase III su 89.7 1.3 2.9E-05 34.3 6.3 57 35-94 144-200 (328)
83 TIGR03015 pepcterm_ATPase puta 89.6 1.6 3.4E-05 32.1 6.4 69 27-95 189-267 (269)
84 PRK05907 hypothetical protein; 89.6 1.2 2.5E-05 34.9 5.9 59 35-94 143-203 (311)
85 PRK07914 hypothetical protein; 89.6 1.1 2.3E-05 34.7 5.7 58 35-94 137-194 (320)
86 COG5624 TAF61 Transcription in 88.8 0.11 2.5E-06 42.7 -0.2 96 7-102 360-459 (505)
87 PRK05629 hypothetical protein; 87.6 2.2 4.8E-05 32.9 6.2 58 35-94 135-192 (318)
88 cd08313 Death_TNFR1 Death doma 86.7 4.9 0.00011 25.6 6.5 66 28-96 7-72 (80)
89 PF12767 SAGA-Tad1: Transcript 86.3 2 4.3E-05 32.4 5.3 40 35-74 212-251 (252)
90 PF09123 DUF1931: Domain of un 85.6 0.64 1.4E-05 32.9 2.1 54 35-88 1-54 (138)
91 COG1466 HolA DNA polymerase II 84.7 3.6 7.8E-05 32.1 6.1 59 35-94 149-207 (334)
92 PRK13765 ATP-dependent proteas 84.6 3.8 8.3E-05 35.3 6.7 50 44-93 337-399 (637)
93 COG1224 TIP49 DNA helicase TIP 84.3 4.4 9.4E-05 33.5 6.5 49 46-94 380-432 (450)
94 PF13335 Mg_chelatase_2: Magne 82.2 11 0.00024 24.5 7.1 61 26-92 28-94 (96)
95 TIGR02928 orc1/cdc6 family rep 81.9 6.4 0.00014 30.3 6.5 65 30-94 199-274 (365)
96 PRK12402 replication factor C 80.2 5.2 0.00011 30.2 5.4 56 35-93 193-248 (337)
97 smart00350 MCM minichromosome 78.5 11 0.00023 31.3 7.1 66 29-94 417-504 (509)
98 TIGR02397 dnaX_nterm DNA polym 77.1 7.3 0.00016 29.8 5.4 56 35-92 185-240 (355)
99 PRK14964 DNA polymerase III su 76.6 6.8 0.00015 32.8 5.4 56 35-92 184-239 (491)
100 PRK00080 ruvB Holliday junctio 75.6 22 0.00047 27.4 7.7 72 29-101 179-257 (328)
101 PF00356 LacI: Bacterial regul 75.5 8.1 0.00017 22.0 4.0 32 29-62 10-41 (46)
102 PRK00440 rfc replication facto 75.4 9.8 0.00021 28.4 5.6 56 35-93 170-225 (319)
103 PF09288 UBA_3: Fungal ubiquit 74.9 4.1 8.9E-05 24.5 2.7 37 27-63 18-54 (55)
104 PRK14970 DNA polymerase III su 74.0 9.8 0.00021 29.7 5.5 56 35-92 176-231 (367)
105 PTZ00361 26 proteosome regulat 73.3 5.7 0.00012 32.7 4.2 34 61-94 391-424 (438)
106 PRK14955 DNA polymerase III su 72.1 13 0.00028 29.7 5.9 55 36-91 196-254 (397)
107 PRK09111 DNA polymerase III su 71.7 11 0.00023 32.3 5.5 56 35-92 200-255 (598)
108 COG1737 RpiR Transcriptional r 71.6 19 0.00041 27.4 6.4 64 29-94 47-127 (281)
109 PRK06645 DNA polymerase III su 70.1 13 0.00027 31.3 5.5 58 35-93 196-255 (507)
110 PF06971 Put_DNA-bind_N: Putat 69.8 7.6 0.00016 22.7 3.1 28 29-56 2-38 (50)
111 TIGR01278 DPOR_BchB light-inde 69.4 12 0.00027 31.0 5.4 50 45-95 461-511 (511)
112 COG5251 TAF40 Transcription in 68.5 4.2 9E-05 30.0 2.1 65 29-94 115-181 (199)
113 cd08784 Death_DRs Death Domain 67.9 27 0.00058 21.8 6.2 65 28-96 7-71 (79)
114 PRK13407 bchI magnesium chelat 65.6 32 0.00069 27.3 6.8 60 33-92 238-304 (334)
115 PRK14962 DNA polymerase III su 65.6 21 0.00045 29.6 5.9 63 29-93 175-241 (472)
116 TIGR00635 ruvB Holliday juncti 65.6 53 0.0011 24.6 7.8 66 29-95 158-230 (305)
117 PRK09087 hypothetical protein; 65.4 53 0.0011 24.2 7.9 58 35-94 162-222 (226)
118 PTZ00454 26S protease regulato 65.1 11 0.00023 30.6 4.1 34 61-94 353-386 (398)
119 PRK02910 light-independent pro 65.1 17 0.00037 30.3 5.4 51 44-95 467-518 (519)
120 PRK03992 proteasome-activating 64.5 12 0.00026 29.9 4.3 34 61-94 339-372 (389)
121 TIGR02030 BchI-ChlI magnesium 64.2 32 0.00069 27.3 6.5 48 45-92 253-307 (337)
122 TIGR01242 26Sp45 26S proteasom 64.1 12 0.00027 29.3 4.2 42 52-93 317-362 (364)
123 KOG3902 Histone acetyltransfer 64.0 40 0.00087 27.1 6.9 59 35-93 30-89 (352)
124 PF06160 EzrA: Septation ring 63.7 41 0.00089 28.4 7.4 74 20-93 428-521 (560)
125 TIGR02442 Cob-chelat-sub cobal 63.0 16 0.00035 31.2 4.9 49 45-93 248-303 (633)
126 TIGR03420 DnaA_homol_Hda DnaA 62.9 45 0.00097 23.6 6.6 50 41-92 174-226 (226)
127 PRK14963 DNA polymerase III su 61.9 21 0.00046 29.8 5.4 61 29-92 174-238 (504)
128 PF07766 LETM1: LETM1-like pro 61.8 41 0.00088 25.7 6.6 70 28-100 169-238 (268)
129 PRK14954 DNA polymerase III su 61.2 26 0.00057 30.2 5.9 63 29-92 185-255 (620)
130 PRK14961 DNA polymerase III su 60.2 27 0.00058 27.5 5.5 62 29-92 177-242 (363)
131 PF11705 RNA_pol_3_Rpc31: DNA- 59.4 6.3 0.00014 29.4 1.7 12 1-12 1-12 (233)
132 CHL00076 chlB photochlorophyll 59.3 27 0.0006 29.1 5.6 50 45-95 462-512 (513)
133 CHL00081 chlI Mg-protoporyphyr 58.0 68 0.0015 25.7 7.4 60 33-92 254-320 (350)
134 cd08315 Death_TRAILR_DR4_DR5 D 57.5 51 0.0011 21.4 5.9 65 28-96 15-79 (96)
135 TIGR00368 Mg chelatase-related 56.9 36 0.00078 28.5 5.9 47 46-92 445-497 (499)
136 cd08815 Death_TNFRSF25_DR3 Dea 56.7 50 0.0011 21.1 6.0 63 27-95 6-68 (77)
137 PRK13406 bchD magnesium chelat 56.7 62 0.0013 27.7 7.3 53 40-92 189-248 (584)
138 PRK14971 DNA polymerase III su 56.6 21 0.00046 30.5 4.6 63 29-93 179-245 (614)
139 PRK09862 putative ATP-dependen 55.7 42 0.00091 28.3 6.1 47 47-93 439-491 (506)
140 PRK04195 replication factor C 54.2 37 0.0008 27.8 5.5 55 35-92 169-223 (482)
141 PF00725 3HCDH: 3-hydroxyacyl- 53.9 30 0.00066 21.6 4.0 36 59-97 4-40 (97)
142 PRK08727 hypothetical protein; 53.3 62 0.0013 23.8 6.1 63 30-94 162-231 (233)
143 PRK08903 DnaA regulatory inact 52.5 84 0.0018 22.5 7.0 54 37-92 168-224 (227)
144 KOG2680 DNA helicase TIP49, TB 52.1 50 0.0011 27.1 5.8 49 46-94 377-429 (454)
145 TIGR01241 FtsH_fam ATP-depende 52.0 24 0.00053 28.9 4.1 43 52-94 249-295 (495)
146 COG1222 RPT1 ATP-dependent 26S 51.8 24 0.00053 29.0 4.0 34 61-94 359-392 (406)
147 PF04157 EAP30: EAP30/Vps36 fa 51.5 25 0.00054 25.9 3.8 16 80-95 131-146 (223)
148 TIGR02031 BchD-ChlD magnesium 50.8 49 0.0011 28.2 5.8 47 46-92 203-256 (589)
149 KOG1942 DNA helicase, TBP-inte 50.6 42 0.00091 27.4 5.1 49 45-93 385-437 (456)
150 PF00493 MCM: MCM2/3/5 family 50.5 16 0.00034 28.6 2.7 66 29-94 241-326 (331)
151 KOG0784 Isocitrate dehydrogena 50.3 8.1 0.00018 31.4 1.0 37 49-85 172-208 (375)
152 PRK06305 DNA polymerase III su 50.2 47 0.001 27.2 5.5 62 29-92 179-244 (451)
153 cd07064 AlkD_like_1 A new stru 49.8 30 0.00066 25.3 4.0 73 17-92 11-87 (208)
154 CHL00176 ftsH cell division pr 49.7 25 0.00055 30.3 4.0 33 62-94 391-423 (638)
155 cd08780 Death_TRADD Death Doma 49.6 73 0.0016 21.0 5.9 62 34-96 15-80 (90)
156 PRK14958 DNA polymerase III su 49.6 54 0.0012 27.4 5.8 63 29-93 177-243 (509)
157 TIGR02903 spore_lon_C ATP-depe 49.5 67 0.0014 27.5 6.5 65 31-96 354-432 (615)
158 KOG0480 DNA replication licens 49.5 89 0.0019 27.8 7.2 82 19-100 545-649 (764)
159 cd08316 Death_FAS_TNFRSF6 Deat 49.4 73 0.0016 20.9 5.9 64 28-95 16-80 (97)
160 PF02971 FTCD: Formiminotransf 49.4 50 0.0011 23.6 4.8 57 35-102 73-136 (145)
161 PRK14953 DNA polymerase III su 48.9 50 0.0011 27.5 5.5 56 35-92 187-242 (486)
162 PRK14950 DNA polymerase III su 48.9 46 0.001 28.1 5.4 62 30-93 179-244 (585)
163 PRK13531 regulatory ATPase Rav 48.8 1.2E+02 0.0027 25.6 7.8 63 29-91 206-281 (498)
164 PRK06893 DNA replication initi 48.6 1E+02 0.0022 22.5 6.7 50 41-92 176-228 (229)
165 PRK00149 dnaA chromosomal repl 48.4 77 0.0017 25.6 6.4 47 46-93 299-348 (450)
166 PRK14952 DNA polymerase III su 48.3 49 0.0011 28.3 5.5 62 29-91 176-241 (584)
167 COG0325 Predicted enzyme with 48.0 51 0.0011 25.2 5.0 40 60-100 4-54 (228)
168 PF12909 DUF3832: Protein of u 47.7 43 0.00094 21.8 4.0 34 48-81 35-68 (89)
169 smart00354 HTH_LACI helix_turn 46.2 48 0.001 19.8 3.9 33 29-63 11-43 (70)
170 cd01392 HTH_LacI Helix-turn-he 46.0 50 0.0011 18.0 3.9 32 29-62 8-39 (52)
171 PRK10733 hflB ATP-dependent me 45.9 33 0.00072 29.4 4.1 33 62-94 360-392 (644)
172 KOG0481 DNA replication licens 45.6 1E+02 0.0023 26.9 6.9 69 26-94 545-639 (729)
173 PRK11302 DNA-binding transcrip 45.4 1.1E+02 0.0024 22.7 6.5 64 29-94 45-125 (284)
174 PRK14957 DNA polymerase III su 45.3 59 0.0013 27.6 5.5 63 29-93 177-243 (546)
175 PTZ00111 DNA replication licen 44.8 83 0.0018 28.7 6.5 67 29-95 696-805 (915)
176 PRK08451 DNA polymerase III su 44.2 69 0.0015 27.2 5.7 62 28-91 174-239 (535)
177 PRK08084 DNA replication initi 42.9 1.3E+02 0.0029 22.0 7.4 59 32-92 169-234 (235)
178 TIGR00362 DnaA chromosomal rep 42.9 1.5E+02 0.0033 23.4 7.3 55 36-92 278-335 (405)
179 TIGR02639 ClpA ATP-dependent C 42.8 90 0.0019 27.1 6.3 54 45-98 367-434 (731)
180 PF02861 Clp_N: Clp amino term 42.7 35 0.00077 18.6 2.7 25 70-94 1-25 (53)
181 PF15510 CENP-W: Centromere ki 42.0 49 0.0011 22.0 3.6 65 29-93 16-95 (102)
182 PF06144 DNA_pol3_delta: DNA p 41.9 61 0.0013 21.9 4.3 39 35-74 133-171 (172)
183 PRK14959 DNA polymerase III su 41.4 75 0.0016 27.6 5.6 61 29-91 177-241 (624)
184 KOG0729 26S proteasome regulat 41.1 21 0.00046 28.8 2.1 33 62-94 386-418 (435)
185 PRK05896 DNA polymerase III su 41.0 86 0.0019 27.2 5.9 61 29-91 177-241 (605)
186 PRK06620 hypothetical protein; 40.6 1.4E+02 0.0031 21.7 7.1 55 35-91 156-213 (214)
187 PRK08691 DNA polymerase III su 40.1 89 0.0019 27.6 5.9 64 29-94 177-244 (709)
188 PRK05563 DNA polymerase III su 39.3 83 0.0018 26.6 5.5 54 36-91 188-241 (559)
189 CHL00206 ycf2 Ycf2; Provisiona 39.3 45 0.00097 33.1 4.2 34 61-94 1844-1877(2281)
190 COG4477 EzrA Negative regulato 39.0 1E+02 0.0022 26.6 5.9 44 20-63 431-484 (570)
191 PRK07764 DNA polymerase III su 38.9 85 0.0018 28.1 5.7 62 29-91 178-243 (824)
192 PF02042 RWP-RK: RWP-RK domain 38.3 34 0.00074 20.2 2.2 21 29-49 26-46 (52)
193 PF07830 PP2C_C: Protein serin 38.3 1.1E+02 0.0023 19.6 5.4 49 43-94 9-57 (81)
194 PRK06647 DNA polymerase III su 38.0 93 0.002 26.5 5.6 62 29-92 177-242 (563)
195 PRK14975 bifunctional 3'-5' ex 37.8 2.1E+02 0.0046 24.0 7.7 65 29-97 163-240 (553)
196 COG4130 Predicted sugar epimer 37.7 71 0.0015 24.8 4.4 66 29-95 48-128 (272)
197 PF13405 EF-hand_6: EF-hand do 37.2 57 0.0012 16.1 3.8 27 69-95 4-31 (31)
198 PRK14087 dnaA chromosomal repl 36.7 2E+02 0.0043 23.6 7.2 60 35-94 284-348 (450)
199 PRK14960 DNA polymerase III su 36.1 96 0.0021 27.5 5.4 64 28-93 175-242 (702)
200 PF02459 Adeno_terminal: Adeno 36.0 78 0.0017 27.2 4.7 38 58-95 448-485 (548)
201 COG3854 SpoIIIAA ncharacterize 35.9 23 0.00049 27.9 1.5 61 32-102 11-75 (308)
202 COG4401 AroH Chorismate mutase 35.8 41 0.00088 23.3 2.6 27 43-69 8-34 (125)
203 PRK14965 DNA polymerase III su 35.6 97 0.0021 26.3 5.3 61 29-91 177-241 (576)
204 KOG1957 DNA topoisomerase III 35.0 43 0.00092 28.5 3.0 23 76-98 135-164 (555)
205 TIGR03280 methan_mark_11 putat 34.9 64 0.0014 25.4 3.9 37 66-102 232-268 (292)
206 cd08318 Death_NMPP84 Death dom 34.1 1.2E+02 0.0026 19.0 5.9 60 33-96 19-78 (86)
207 PF14841 FliG_M: FliG middle d 33.0 1.1E+02 0.0023 18.9 4.1 42 28-69 34-76 (79)
208 PRK14969 DNA polymerase III su 33.0 1.2E+02 0.0026 25.5 5.4 62 29-92 177-242 (527)
209 COG1241 MCM2 Predicted ATPase 33.0 1.8E+02 0.0038 25.7 6.5 65 31-95 507-593 (682)
210 COG2255 RuvB Holliday junction 32.5 2.7E+02 0.0058 22.5 7.1 72 30-102 181-259 (332)
211 PF13779 DUF4175: Domain of un 32.3 86 0.0019 28.1 4.6 44 51-94 497-547 (820)
212 TIGR01481 ccpA catabolite cont 32.3 71 0.0015 23.7 3.7 29 29-59 12-40 (329)
213 PLN03025 replication factor C 31.8 1.2E+02 0.0025 23.3 4.9 53 35-90 167-219 (319)
214 PRK10339 DNA-binding transcrip 31.3 66 0.0014 24.0 3.4 34 29-62 12-45 (327)
215 PRK14086 dnaA chromosomal repl 31.0 2.8E+02 0.006 24.2 7.4 56 36-93 456-514 (617)
216 PF11753 DUF3310: Protein of u 31.0 1.2E+02 0.0026 18.0 4.8 33 59-92 24-56 (60)
217 PRK10703 DNA-binding transcrip 30.6 81 0.0018 23.6 3.8 32 29-62 12-43 (341)
218 cd05831 Ribosomal_P1 Ribosomal 30.3 1.1E+02 0.0024 20.3 3.9 35 23-58 11-45 (103)
219 KOG2202 U2 snRNP splicing fact 30.1 1.6E+02 0.0035 22.9 5.3 49 51-99 70-135 (260)
220 COG1474 CDC6 Cdc6-related prot 29.9 88 0.0019 25.1 4.0 48 44-91 209-262 (366)
221 KOG0785 Isocitrate dehydrogena 29.9 1.2E+02 0.0025 24.7 4.6 46 46-91 163-208 (365)
222 PRK14951 DNA polymerase III su 29.2 1.5E+02 0.0032 25.7 5.5 62 29-92 182-247 (618)
223 COG5665 NOT5 CCR4-NOT transcri 29.2 57 0.0012 27.2 2.8 37 29-65 144-180 (548)
224 cd08306 Death_FADD Fas-associa 29.2 1.5E+02 0.0033 18.6 5.4 60 34-97 15-75 (86)
225 TIGR00207 fliG flagellar motor 29.0 93 0.002 24.6 4.0 40 28-67 152-192 (338)
226 PF01706 FliG_C: FliG C-termin 28.9 1.7E+02 0.0036 19.0 5.5 62 27-93 25-93 (110)
227 PRK07194 fliG flagellar motor 28.6 1E+02 0.0023 24.3 4.2 39 28-66 149-188 (334)
228 PRK13342 recombination factor 28.6 1.5E+02 0.0032 23.7 5.1 65 28-94 149-219 (413)
229 PRK11557 putative DNA-binding 28.5 2.5E+02 0.0053 20.8 6.0 20 29-48 41-60 (278)
230 PRK11337 DNA-binding transcrip 28.5 2.5E+02 0.0055 20.9 6.5 27 29-56 57-83 (292)
231 PF14394 DUF4423: Domain of un 28.4 94 0.002 22.2 3.6 29 45-73 127-155 (171)
232 cd06863 PX_Atg24p The phosphoi 28.3 43 0.00094 22.1 1.7 26 45-70 78-103 (118)
233 PRK07133 DNA polymerase III su 28.1 1.7E+02 0.0036 26.0 5.6 62 28-91 175-240 (725)
234 cd08319 Death_RAIDD Death doma 27.4 1.7E+02 0.0037 18.6 5.2 64 34-101 15-81 (83)
235 PRK09526 lacI lac repressor; R 27.3 1.1E+02 0.0023 22.9 3.9 31 29-61 16-46 (342)
236 PRK10423 transcriptional repre 27.0 1.2E+02 0.0026 22.4 4.1 30 29-60 9-38 (327)
237 PF04695 Pex14_N: Peroxisomal 26.8 58 0.0013 22.4 2.2 19 79-97 32-50 (136)
238 COG0177 Nth Predicted EndoIII- 26.5 1.3E+02 0.0028 22.6 4.1 35 27-63 132-167 (211)
239 PRK10727 DNA-binding transcrip 26.2 1E+02 0.0022 23.2 3.6 31 29-61 12-42 (343)
240 cd04411 Ribosomal_P1_P2_L12p R 26.2 1.4E+02 0.0029 19.9 3.8 29 29-58 16-44 (105)
241 PF12392 DUF3656: Collagenase 25.7 51 0.0011 21.8 1.7 28 74-101 58-85 (122)
242 COG1239 ChlI Mg-chelatase subu 25.6 1.4E+02 0.0031 24.8 4.5 27 66-92 294-320 (423)
243 PRK06402 rpl12p 50S ribosomal 25.6 1.4E+02 0.003 20.1 3.8 33 26-59 13-45 (106)
244 PHA02943 hypothetical protein; 25.5 2.1E+02 0.0044 20.9 4.8 40 46-92 66-105 (165)
245 COG3267 ExeA Type II secretory 25.4 1.2E+02 0.0025 23.8 3.8 55 34-88 208-267 (269)
246 PRK07492 adenylosuccinate lyas 25.4 3.6E+02 0.0079 22.1 6.9 62 29-91 39-107 (435)
247 PF07599 DUF1563: Protein of u 25.4 1.4E+02 0.0029 16.8 4.1 26 55-80 18-43 (43)
248 KOG1067 Predicted RNA-binding 25.2 1.4E+02 0.0031 26.3 4.6 63 32-94 257-329 (760)
249 smart00481 POLIIIAc DNA polyme 25.0 58 0.0013 18.9 1.7 22 81-102 14-35 (67)
250 cd01670 Death Death Domain: a 24.9 1.6E+02 0.0034 17.3 6.1 60 33-96 11-70 (79)
251 KOG0726 26S proteasome regulat 24.8 73 0.0016 26.0 2.7 32 62-93 394-425 (440)
252 PRK11303 DNA-binding transcrip 24.7 1.3E+02 0.0028 22.3 3.9 33 29-61 11-44 (328)
253 PF11903 DUF3423: Protein of u 24.5 1.2E+02 0.0026 18.9 3.2 51 42-92 1-55 (72)
254 PRK09492 treR trehalose repres 24.3 1.2E+02 0.0026 22.3 3.7 32 29-62 15-46 (315)
255 PF10346 Con-6: Conidiation pr 24.3 84 0.0018 17.2 2.1 19 44-62 16-34 (36)
256 COG3097 Uncharacterized protei 24.2 23 0.0005 23.7 -0.2 14 76-89 17-30 (106)
257 COG4352 RPL13 Ribosomal protei 24.2 81 0.0018 21.5 2.4 31 37-67 74-110 (113)
258 PF07278 DUF1441: Protein of u 24.1 2.7E+02 0.0059 19.9 5.7 54 21-74 81-150 (152)
259 COG5466 Predicted small metal- 23.8 1.6E+02 0.0035 17.9 3.4 29 65-93 26-54 (59)
260 PRK10014 DNA-binding transcrip 23.8 1.4E+02 0.0029 22.3 3.9 29 29-59 17-45 (342)
261 PRK14700 recombination factor 23.7 3E+02 0.0066 21.8 5.9 67 28-94 37-115 (300)
262 PRK10401 DNA-binding transcrip 23.5 1.3E+02 0.0028 22.7 3.7 31 29-61 12-42 (346)
263 TIGR02417 fruct_sucro_rep D-fr 23.5 1.4E+02 0.003 22.2 3.9 33 29-61 10-43 (327)
264 cd05030 calgranulins Calgranul 23.3 1.4E+02 0.0031 18.5 3.4 21 72-92 13-37 (88)
265 cd07293 PX_SNX3 The phosphoino 23.3 1.2E+02 0.0026 20.5 3.2 27 43-69 79-105 (123)
266 cd06409 PB1_MUG70 The MUG70 pr 23.3 76 0.0017 20.5 2.1 17 67-83 64-80 (86)
267 TIGR02440 FadJ fatty oxidation 23.1 2.4E+02 0.0052 24.5 5.7 58 35-98 469-526 (699)
268 cd00862 ProRS_anticodon_zinc P 23.1 2.7E+02 0.0058 20.1 5.2 46 49-96 100-146 (202)
269 cd06456 M3A_DCP_Oligopeptidase 23.0 2.6E+02 0.0056 22.7 5.6 55 48-102 37-96 (422)
270 KOG0728 26S proteasome regulat 23.0 76 0.0016 25.5 2.4 34 60-93 354-387 (404)
271 TIGR01796 CM_mono_aroH monofun 22.7 1E+02 0.0022 21.2 2.7 26 43-68 6-31 (117)
272 cd02185 AroH Chorismate mutase 22.5 1E+02 0.0022 21.2 2.7 26 43-68 6-31 (117)
273 cd06864 PX_SNX4 The phosphoino 22.5 90 0.002 21.2 2.5 30 43-72 87-116 (129)
274 COG1223 Predicted ATPase (AAA+ 22.5 1.4E+02 0.003 24.1 3.7 29 65-93 326-354 (368)
275 PF13443 HTH_26: Cro/C1-type H 22.4 94 0.002 17.6 2.3 36 29-65 21-56 (63)
276 KOG0027 Calmodulin and related 22.3 2.5E+02 0.0055 18.8 8.5 33 66-98 86-118 (151)
277 PF08673 RsbU_N: Phosphoserine 22.2 1.4E+02 0.003 18.8 3.1 39 54-92 7-45 (77)
278 PF09077 Phage-MuB_C: Mu B tra 22.0 41 0.00089 21.4 0.6 62 29-93 11-77 (78)
279 PF01726 LexA_DNA_bind: LexA D 21.8 1.8E+02 0.0039 17.4 3.5 29 29-60 23-51 (65)
280 PF08672 APC2: Anaphase promot 21.6 1E+02 0.0023 18.4 2.4 41 26-69 8-48 (60)
281 COG4463 CtsR Transcriptional r 21.6 53 0.0011 23.5 1.2 38 55-92 4-47 (153)
282 TIGR03346 chaperone_ClpB ATP-d 21.4 4.1E+02 0.009 23.6 6.9 30 62-91 81-110 (852)
283 CHL00195 ycf46 Ycf46; Provisio 21.4 2.1E+02 0.0047 23.9 4.9 45 49-94 415-463 (489)
284 COG1609 PurR Transcriptional r 21.3 1.5E+02 0.0032 22.9 3.8 30 29-60 11-40 (333)
285 PF12146 Hydrolase_4: Putative 21.2 42 0.0009 20.8 0.5 19 84-102 32-50 (79)
286 PRK14101 bifunctional glucokin 21.1 4E+02 0.0086 22.7 6.6 20 29-48 385-404 (638)
287 PF05597 Phasin: Poly(hydroxya 21.1 2.2E+02 0.0049 19.7 4.3 16 82-97 91-106 (132)
288 COG0464 SpoVK ATPases of the A 20.9 1.4E+02 0.0031 24.3 3.7 46 49-94 433-483 (494)
289 PF01418 HTH_6: Helix-turn-hel 20.8 84 0.0018 19.1 1.9 20 29-48 45-64 (77)
290 PF06183 DinI: DinI-like famil 20.8 73 0.0016 19.4 1.6 24 48-71 2-25 (65)
291 PF07261 DnaB_2: Replication i 20.7 1.9E+02 0.0042 16.9 6.6 52 39-92 5-58 (77)
292 smart00027 EH Eps15 homology d 20.6 2.3E+02 0.0049 17.6 4.1 56 45-101 25-80 (96)
293 cd02191 FtsZ FtsZ is a GTPase 20.6 2.7E+02 0.0059 21.6 5.1 65 29-101 152-216 (303)
294 PF07498 Rho_N: Rho terminatio 20.6 1.5E+02 0.0033 16.2 2.8 30 29-58 4-33 (43)
295 KOG0731 AAA+-type ATPase conta 20.5 1.2E+02 0.0027 27.1 3.4 33 62-94 521-553 (774)
296 PRK11559 garR tartronate semia 20.3 3.7E+02 0.0081 20.0 6.0 56 34-92 147-208 (296)
297 TIGR02302 aProt_lowcomp conser 20.2 2.2E+02 0.0047 25.9 4.9 44 51-94 528-577 (851)
298 PF00531 Death: Death domain; 20.2 2E+02 0.0044 16.9 4.5 61 31-95 11-71 (83)
No 1
>PLN00035 histone H4; Provisional
Probab=100.00 E-value=1.5e-43 Score=237.48 Aligned_cols=103 Identities=100% Similarity=1.472 Sum_probs=101.9
Q ss_pred CCCCCCCCccCCCCCCcccchhhcccccCcchHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCc
Q 034139 1 MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRK 80 (103)
Q Consensus 1 ~~~~~~~~~~~~~~g~kr~~k~~r~~~~~ip~a~IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~Rk 80 (103)
|||+||||+|+|++|.|||+|+++|++.+||++||+|||+++|++|||++||+++++++++|+++|++||+.||+|++||
T Consensus 1 m~~~~k~~~g~g~~g~kr~~k~~~d~i~~ipk~~IrRLARr~GvkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RK 80 (103)
T PLN00035 1 MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRK 80 (103)
T ss_pred CCCCCCCCCCCCCCcchHHHHHHHhhhccCCHHHHHHHHHHcCcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eecHHHHHHHHHhcCCcccccCC
Q 034139 81 TVTAMDVVYALKRQGRTLYGFGG 103 (103)
Q Consensus 81 TI~~~DV~~Alkr~g~~lYgf~~ 103 (103)
||+++||.+||+++|.|||||++
T Consensus 81 TV~~~DV~~Alkr~g~~lyGf~~ 103 (103)
T PLN00035 81 TVTAMDVVYALKRQGRTLYGFGG 103 (103)
T ss_pred cCcHHHHHHHHHHcCCcCCCCCC
Confidence 99999999999999999999985
No 2
>PTZ00015 histone H4; Provisional
Probab=100.00 E-value=1.5e-40 Score=222.81 Aligned_cols=101 Identities=84% Similarity=1.223 Sum_probs=99.9
Q ss_pred CCCCCCCCccCC-CCCCcccchhhcccccCcchHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCC
Q 034139 1 MSGRGKGGKGLG-KGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARR 79 (103)
Q Consensus 1 ~~~~~~~~~~~~-~~g~kr~~k~~r~~~~~ip~a~IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~R 79 (103)
|||+||||+++| ++|.|||+|+++|++++||+++|+|||+++|++|||+++|+++++++++|+++|++||+.||+|++|
T Consensus 1 ~~~~~k~~~~~~~~g~~kr~rk~~r~~i~gI~k~~IrRLarr~GvkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~R 80 (102)
T PTZ00015 1 MSGMGKGKKSLGAKGGQKRQKKVLRDNIRGITKGAIRRLARRGGVKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARR 80 (102)
T ss_pred CCCcccCCCccccccchhhHHHHHhhcccCCCHHHHHHHHHHcCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 899999999999 8899999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ceecHHHHHHHHHhcCCccccc
Q 034139 80 KTVTAMDVVYALKRQGRTLYGF 101 (103)
Q Consensus 80 kTI~~~DV~~Alkr~g~~lYgf 101 (103)
|||+++||.+||+++|.|+|||
T Consensus 81 KTVt~~DV~~AlKr~g~~~ygf 102 (102)
T PTZ00015 81 KTVTAMDVVYALKRQGRTLYGF 102 (102)
T ss_pred CcccHHHHHHHHHhcCCCCCCC
Confidence 9999999999999999999999
No 3
>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=100.00 E-value=2.9e-35 Score=191.77 Aligned_cols=85 Identities=87% Similarity=1.288 Sum_probs=84.3
Q ss_pred cccchhhcccccCcchHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhcCC
Q 034139 17 KRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGR 96 (103)
Q Consensus 17 kr~~k~~r~~~~~ip~a~IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~g~ 96 (103)
|||+|+++|++.+||+++|+|||+++|++|||+++|+++++++++|+++|++||+.||+|++||||+++||.+||+++|.
T Consensus 1 kr~r~~~~~~~~gi~k~~I~RLarr~GvkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~alkr~g~ 80 (85)
T cd00076 1 KRHRKVLRDNIKGITKPAIRRLARRGGVKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKRQGR 80 (85)
T ss_pred CchhHHHHHhhccCCHHHHHHHHHHcCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHCCC
Confidence 69999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccc
Q 034139 97 TLYGF 101 (103)
Q Consensus 97 ~lYgf 101 (103)
|+|||
T Consensus 81 ~~ygf 85 (85)
T cd00076 81 TLYGY 85 (85)
T ss_pred CccCC
Confidence 99999
No 4
>KOG3467 consensus Histone H4 [Chromatin structure and dynamics]
Probab=100.00 E-value=1.7e-34 Score=188.47 Aligned_cols=103 Identities=98% Similarity=1.462 Sum_probs=101.6
Q ss_pred CCCCCCCCccCCCCCCcccchhhcccccCcchHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCc
Q 034139 1 MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRK 80 (103)
Q Consensus 1 ~~~~~~~~~~~~~~g~kr~~k~~r~~~~~ip~a~IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~Rk 80 (103)
||++||||||++|+|.|||||+++|++++|++++|+||||++|+.||+.-+|++.+.++..|+++++.+|..|++||+||
T Consensus 1 Ms~r~~g~KG~~KG~AKrHRK~LsDnIqgitKpaIRRlARr~GVkRi~G~~yeE~~~~~k~fl~n~i~~A~~yt~HAKRK 80 (103)
T KOG3467|consen 1 MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRK 80 (103)
T ss_pred CCCcCccccccccchHHHHHHHHHhhccccchHHHHHHHHhcCcchhchhhHHHHHHHHHHHHHHHHHHHHHHHhhhhhc
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eecHHHHHHHHHhcCCcccccCC
Q 034139 81 TVTAMDVVYALKRQGRTLYGFGG 103 (103)
Q Consensus 81 TI~~~DV~~Alkr~g~~lYgf~~ 103 (103)
|||+.||..+|+|+|..+|||..
T Consensus 81 TvT~~dvv~~LKR~G~~~~g~~~ 103 (103)
T KOG3467|consen 81 TVTAMDVVYALKRQGRTLYGFGG 103 (103)
T ss_pred eeeHHHHHHHHHHcCceeeccCC
Confidence 99999999999999999999963
No 5
>smart00417 H4 Histone H4.
Probab=99.95 E-value=3.8e-28 Score=154.68 Aligned_cols=74 Identities=92% Similarity=1.314 Sum_probs=72.2
Q ss_pred cccchhhcccccCcchHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHH
Q 034139 17 KRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYA 90 (103)
Q Consensus 17 kr~~k~~r~~~~~ip~a~IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~A 90 (103)
+||+|+++|++++||+++|+|||+++|++|||+++|+++++++++|+++|+.||+.||+|++||||+++||.+|
T Consensus 1 ~r~~~~~~d~i~gI~k~~IrRLaRr~GvkRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~~a 74 (74)
T smart00417 1 RRHKKVLRDNIQGITKPAIRRLARRGGVKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVYA 74 (74)
T ss_pred CchhHHHHhhhcCCCHHHHHHHHHHcCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHheeC
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999864
No 6
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=99.94 E-value=1.9e-27 Score=156.62 Aligned_cols=90 Identities=41% Similarity=0.602 Sum_probs=86.4
Q ss_pred CCCCCcccchhhcccccCcchHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHH
Q 034139 12 GKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYAL 91 (103)
Q Consensus 12 ~~~g~kr~~k~~r~~~~~ip~a~IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Al 91 (103)
|..|.+..+++|++++..||++||.||+|++|..|||++|.++|++++|+|+.+|+++|+.||.|+|||||+++||.+|+
T Consensus 2 ~~~~~~~~r~~~~~~~~~Lp~apv~Ri~r~~~~~Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~DI~la~ 81 (91)
T COG2036 2 GAVGLKEIRRYQRSTDLLLPKAPVRRILRKAGAERVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLAL 81 (91)
T ss_pred CcchHHHHHhhhhhhhhhcCchHHHHHHHHHhHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHH
Confidence 44678899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhcCCccccc
Q 034139 92 KRQGRTLYGF 101 (103)
Q Consensus 92 kr~g~~lYgf 101 (103)
+.+|+..|++
T Consensus 82 ~~~~~~~~~~ 91 (91)
T COG2036 82 KRLGRRIYGE 91 (91)
T ss_pred HHhccccccC
Confidence 9999998875
No 7
>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=99.89 E-value=7.1e-23 Score=127.45 Aligned_cols=64 Identities=20% Similarity=0.345 Sum_probs=62.5
Q ss_pred CcchHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHH
Q 034139 29 GITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALK 92 (103)
Q Consensus 29 ~ip~a~IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alk 92 (103)
.||+++|+|||++.|++|||++++++|++.+|+|+.+|+++|++|++|++||||+++||.+||+
T Consensus 2 ~~p~~~i~ria~~~Gi~ris~~a~~~l~~~~e~rl~~i~~~A~k~~~hakRktlt~~DI~~Alk 65 (65)
T smart00803 2 WLPKETIKDVAESLGIGNLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSALR 65 (65)
T ss_pred CCCHHHHHHHHHHCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCeecHHHHHHHhC
Confidence 4899999999999999999999999999999999999999999999999999999999999985
No 8
>PLN00163 histone H4; Provisional
Probab=99.81 E-value=1.5e-20 Score=113.99 Aligned_cols=59 Identities=98% Similarity=1.458 Sum_probs=56.8
Q ss_pred CCCCCCCCccCCCCCCcccchhhcccccCcchHHHHHHHHhcCccccchHHHHHHHHHH
Q 034139 1 MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVL 59 (103)
Q Consensus 1 ~~~~~~~~~~~~~~g~kr~~k~~r~~~~~ip~a~IkRiar~~G~~riS~da~~~l~~~~ 59 (103)
|+|+||||||+|++|.|||+|+++|++++|++++|+|||++.|++|||..+|++.+.++
T Consensus 1 m~g~gkggkglGkggaKRhrk~lrd~i~gItKpaIrRLARRgGVKRIs~~iY~e~R~vl 59 (59)
T PLN00163 1 MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRTVL 59 (59)
T ss_pred CCCCCCCCCccCCccchhHHHHHHHhhcccchHHHHHHHHhcCceeecchhhHhHhccC
Confidence 89999999999999999999999999999999999999999999999999999988753
No 9
>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [Transcription]
Probab=99.71 E-value=3.3e-17 Score=116.79 Aligned_cols=80 Identities=20% Similarity=0.278 Sum_probs=75.4
Q ss_pred hhhcccccCcchHHHHHHHHhcC--ccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhcCCcc
Q 034139 21 KVLRDNIQGITKPAIRRLARRGG--VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTL 98 (103)
Q Consensus 21 k~~r~~~~~ip~a~IkRiar~~G--~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~g~~l 98 (103)
...++.++.||+|+|-|||+++- -..||+||.+.+++|+.+|+..|+.+|..-|+..+||||+.+||.+||..+|++.
T Consensus 24 ~~~reqDr~LPIANV~RIMK~~lP~naKIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIngdDllwAm~tLGFe~ 103 (168)
T KOG0869|consen 24 LSLREQDRFLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASEKCQREKRKTINGDDLLWAMSTLGFEN 103 (168)
T ss_pred cccchhhhhccHHHHHHHHHhcCCcccccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCcccHHHHHHHHHHcCcHh
Confidence 45788999999999999999985 4789999999999999999999999999999999999999999999999999988
Q ss_pred cc
Q 034139 99 YG 100 (103)
Q Consensus 99 Yg 100 (103)
|-
T Consensus 104 Y~ 105 (168)
T KOG0869|consen 104 YA 105 (168)
T ss_pred HH
Confidence 84
No 10
>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=99.70 E-value=1.1e-16 Score=99.89 Aligned_cols=64 Identities=19% Similarity=0.351 Sum_probs=53.7
Q ss_pred CcchHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHH
Q 034139 29 GITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALK 92 (103)
Q Consensus 29 ~ip~a~IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alk 92 (103)
.+|..+|+.+|++.|+..+++++...|.+.+|+++.+|+++|.+|++|++|+++|++||..|||
T Consensus 3 ~~~~esvk~iAes~Gi~~l~de~a~~La~dveyrlreiiq~a~kfm~hskR~~Lt~~Di~~ALr 66 (66)
T PF02969_consen 3 VFSQESVKDIAESLGISNLSDEAAKALAEDVEYRLREIIQEALKFMRHSKRTKLTTDDINSALR 66 (66)
T ss_dssp ---HHHHHHHHHHTT---B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH-
T ss_pred cCCHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhC
Confidence 5899999999999999999999999999999999999999999999999999999999999996
No 11
>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=99.69 E-value=9.4e-17 Score=126.20 Aligned_cols=73 Identities=25% Similarity=0.446 Sum_probs=69.5
Q ss_pred chHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhcC-CcccccCC
Q 034139 31 TKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQG-RTLYGFGG 103 (103)
Q Consensus 31 p~a~IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~g-~~lYgf~~ 103 (103)
|..+|+-||++.|+.++|+||..+|.+.+|+++.+|+++|.+||+|++|+|++++||..||+..+ +|+|||.+
T Consensus 1 ~~~~i~~ia~~~Gi~~~~~~a~~~La~~~e~~~~~i~~~A~k~~~hskR~~l~~~Di~~Al~~~n~eplyG~~~ 74 (343)
T cd08050 1 PQESIKLIAESLGIDSLSDEVAQLLAEDVEYRLREIIQEAAKFMRHSKRRKLTTSDVNHALRLRNVEPLYGFSS 74 (343)
T ss_pred ChhHHHHHHHHcCCCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHHhCCCcccCCCC
Confidence 56899999999999999999999999999999999999999999999999999999999999665 89999964
No 12
>smart00428 H3 Histone H3.
Probab=99.67 E-value=2e-16 Score=106.70 Aligned_cols=82 Identities=21% Similarity=0.233 Sum_probs=73.8
Q ss_pred CcccchhhcccccCcchHHHHHHHHhcC-------ccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHH
Q 034139 16 AKRHRKVLRDNIQGITKPAIRRLARRGG-------VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVV 88 (103)
Q Consensus 16 ~kr~~k~~r~~~~~ip~a~IkRiar~~G-------~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~ 88 (103)
.+--+++|+++...||+.|+.|+++... .-||+++|..+|++++|.|+.++++||+.+|.|++|+||+++||.
T Consensus 16 LrEIr~yQkst~lLI~k~pF~RLVREI~~~~~~~~~~R~~~~Al~aLQeasE~ylv~lfeda~~~a~HAkRvTl~~kDi~ 95 (105)
T smart00428 16 LREIRKYQKSTDLLIRKAPFQRLVREIAQKFTTGVDLRFQSSAIMALQEAAEAYLVGLFEDTNLLAIHAKRVTIMPKDIQ 95 (105)
T ss_pred HHHHHHHccCcccccccccHHHHHHHHHHHcCCCCCceeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccCcHhhHH
Confidence 4456788999999999999999998764 349999999999999999999999999999999999999999999
Q ss_pred HHHHhcCCc
Q 034139 89 YALKRQGRT 97 (103)
Q Consensus 89 ~Alkr~g~~ 97 (103)
+|.+..|..
T Consensus 96 La~rir~~~ 104 (105)
T smart00428 96 LARRIRGER 104 (105)
T ss_pred HHHHHhccC
Confidence 999766654
No 13
>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=99.63 E-value=1.7e-15 Score=103.76 Aligned_cols=68 Identities=22% Similarity=0.351 Sum_probs=63.3
Q ss_pred HHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhcCCcccccC
Q 034139 33 PAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTLYGFG 102 (103)
Q Consensus 33 a~IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~g~~lYgf~ 102 (103)
..|.+|+++.|+.+++++|..+|.++++.|+.+|++||..||+||+|+||+++||.+|++..+. |.|.
T Consensus 5 ~~v~~iLk~~Gv~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r~~--~~f~ 72 (117)
T cd07979 5 RVIAAILKSMGITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRVD--YSFT 72 (117)
T ss_pred HHHHHHHHHCCCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhc--cCCC
Confidence 3589999999999999999999999999999999999999999999999999999999997665 5654
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=99.60 E-value=4.8e-15 Score=92.89 Aligned_cols=67 Identities=31% Similarity=0.376 Sum_probs=63.1
Q ss_pred ccCcchHHHHHHHHhcCc-----cccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHh
Q 034139 27 IQGITKPAIRRLARRGGV-----KRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKR 93 (103)
Q Consensus 27 ~~~ip~a~IkRiar~~G~-----~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr 93 (103)
...+|+.||.|+++..+. .+||.+|++.|+.++|+|+.+|+++|..+|.|++|+||+++||.+|++.
T Consensus 3 ~~~~~~~~~~r~~r~i~~~~~~~~ris~~a~~~L~~~~E~~~~~il~~A~~~a~~~kR~tI~~~DI~~A~r~ 74 (75)
T PF00125_consen 3 RRLIPKFPFSRLLREIGEEILSKYRISSEALVALQSVLEYLLVEILEEAGNLARHAKRKTITPRDIQLAVRI 74 (75)
T ss_dssp SHSSSHHHHHHHHHHHHHTTSSSSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTBSEEGHHHHHHHHHH
T ss_pred ccccCceEEeeeeehhhcccccccccccccchhhhhhhhhhhhhhhhHHHHHHhhcCCcEecHHHHHHHHhc
Confidence 457999999999999876 4999999999999999999999999999999999999999999999974
No 15
>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=99.55 E-value=4.7e-14 Score=86.74 Aligned_cols=63 Identities=22% Similarity=0.342 Sum_probs=57.7
Q ss_pred CcchHHHHHHHHhc-CccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHH
Q 034139 29 GITKPAIRRLARRG-GVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYAL 91 (103)
Q Consensus 29 ~ip~a~IkRiar~~-G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Al 91 (103)
.||.+.|+||++.. +..+||.|+...+.+++|.|+..|+.+|...|++.+||||+.+||..||
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 SLPLARVKRIMKSDPDVMRVSKEAVEAIAKAAEEFIQYLAKEANEIAQRDKRKTITYEDVAKAV 65 (65)
T ss_dssp SS-HHHHHHHHHHTSTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEE-HHHHHHHH
T ss_pred CCChHHHHHHhccCCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHC
Confidence 58999999999998 6789999999999999999999999999999999999999999999986
No 16
>PLN00160 histone H3; Provisional
Probab=99.54 E-value=1.5e-14 Score=96.31 Aligned_cols=80 Identities=19% Similarity=0.183 Sum_probs=72.8
Q ss_pred cccchhhcccccCcchHHHHHHHHhcC------ccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHH
Q 034139 17 KRHRKVLRDNIQGITKPAIRRLARRGG------VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYA 90 (103)
Q Consensus 17 kr~~k~~r~~~~~ip~a~IkRiar~~G------~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~A 90 (103)
+--+++|+++...||+.|+.|+++... .-|+.++|..+|+++.|.|+..+++|++.||.|++|.||++.|+.++
T Consensus 9 rEIR~yQkst~lLI~k~pF~RLVREI~~~~~~~~~Rfq~~Al~ALQeAsEayLv~lfed~~lca~HakRVTl~~kD~~L~ 88 (97)
T PLN00160 9 KEIKMYQKSTDLLIRRLPFARLVREIQMEMSREAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTIMPKDMQLA 88 (97)
T ss_pred HHHHHHccchhhhhccccHHHHHHHHHHHcCCCCcEeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcccccchhhHHHH
Confidence 445789999999999999999998763 37999999999999999999999999999999999999999999999
Q ss_pred HHhcCC
Q 034139 91 LKRQGR 96 (103)
Q Consensus 91 lkr~g~ 96 (103)
.+..|+
T Consensus 89 ~rirg~ 94 (97)
T PLN00160 89 RRIRGQ 94 (97)
T ss_pred HHhhcc
Confidence 976664
No 17
>PLN00121 histone H3; Provisional
Probab=99.51 E-value=3e-14 Score=99.89 Aligned_cols=78 Identities=22% Similarity=0.224 Sum_probs=71.1
Q ss_pred cchhhcccccCcchHHHHHHHHhcC-----ccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHh
Q 034139 19 HRKVLRDNIQGITKPAIRRLARRGG-----VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKR 93 (103)
Q Consensus 19 ~~k~~r~~~~~ip~a~IkRiar~~G-----~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr 93 (103)
.+++|+++...||+.|+.||++... .-||.++|+.+|+++.|.|+..+++|++.||.|++|.||++.||.++++.
T Consensus 52 Ir~yQkst~lLI~k~pF~RLVREI~~~~~~~~Rf~~~Al~ALQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~ri 131 (136)
T PLN00121 52 IRKYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRI 131 (136)
T ss_pred HHHhccccccccccccHHHHHHHHHHHhCccceeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcceecchhhHHHHHHh
Confidence 3577888888999999999998874 36999999999999999999999999999999999999999999999976
Q ss_pred cCC
Q 034139 94 QGR 96 (103)
Q Consensus 94 ~g~ 96 (103)
.|.
T Consensus 132 rg~ 134 (136)
T PLN00121 132 RGE 134 (136)
T ss_pred ccc
Confidence 665
No 18
>PLN00161 histone H3; Provisional
Probab=99.50 E-value=7.6e-14 Score=97.62 Aligned_cols=77 Identities=23% Similarity=0.207 Sum_probs=70.2
Q ss_pred chhhcccccCcchHHHHHHHHhcC------ccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHh
Q 034139 20 RKVLRDNIQGITKPAIRRLARRGG------VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKR 93 (103)
Q Consensus 20 ~k~~r~~~~~ip~a~IkRiar~~G------~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr 93 (103)
+++|+.+...||+.|+.|+++.+. .-||.++|+.+|+++.|.|+..+++|++.||.|++|.||.+.||.++.+.
T Consensus 46 R~yQkst~lLIpklPF~RLVREI~~~~~~~~~Rfq~~Al~ALQEAsEayLV~lFeda~lcaiHAkRVTlm~kDm~La~ri 125 (135)
T PLN00161 46 RKYQKSTELLIRKLPFARLVREISNEMLREPFRWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMPKDMQLARRI 125 (135)
T ss_pred HHHccccccccccccHHHHHHHHHHhcCCCCcEeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccchhhHHHHHHh
Confidence 678889998999999999988762 47999999999999999999999999999999999999999999999966
Q ss_pred cCC
Q 034139 94 QGR 96 (103)
Q Consensus 94 ~g~ 96 (103)
.|.
T Consensus 126 rg~ 128 (135)
T PLN00161 126 RGP 128 (135)
T ss_pred ccc
Confidence 554
No 19
>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=99.49 E-value=2e-13 Score=86.16 Aligned_cols=65 Identities=22% Similarity=0.331 Sum_probs=60.6
Q ss_pred cchHHHHHHHHhcC-ccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhc
Q 034139 30 ITKPAIRRLARRGG-VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 94 (103)
Q Consensus 30 ip~a~IkRiar~~G-~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~ 94 (103)
+++..+..+++... -.+++++|.+.|++.+++|+.+++.+|+.+|.|++|+||+++||.++++++
T Consensus 2 ~~k~~l~~lv~~id~~~~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~~~tv~~~Di~l~l~r~ 67 (72)
T cd07981 2 LTKRKLQELLKEIDPREQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQLHLERN 67 (72)
T ss_pred CcHHHHHHHHHhhCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHh
Confidence 57778888888874 489999999999999999999999999999999999999999999999976
No 20
>PTZ00018 histone H3; Provisional
Probab=99.49 E-value=6e-14 Score=98.36 Aligned_cols=78 Identities=21% Similarity=0.221 Sum_probs=71.1
Q ss_pred cchhhcccccCcchHHHHHHHHhcC-----ccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHh
Q 034139 19 HRKVLRDNIQGITKPAIRRLARRGG-----VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKR 93 (103)
Q Consensus 19 ~~k~~r~~~~~ip~a~IkRiar~~G-----~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr 93 (103)
.+++|+.+...||+.|+.||++... .-||..+|+.+|+++.|.|+..+++|++.||.|++|.||++.|+.++.+.
T Consensus 52 Ir~yQkst~lLI~k~pF~RLVREI~~~~~~~~rf~~~al~aLQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~ri 131 (136)
T PTZ00018 52 IRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRI 131 (136)
T ss_pred HHHHcccchhccccccHHHHHHHHHHHcCCcceeeHHHHHHHHHHHHHHHHHHhhhhHHHHHhhcceecchhhHHHHHHh
Confidence 3578888999999999999998874 36999999999999999999999999999999999999999999999976
Q ss_pred cCC
Q 034139 94 QGR 96 (103)
Q Consensus 94 ~g~ 96 (103)
.|.
T Consensus 132 rg~ 134 (136)
T PTZ00018 132 RGE 134 (136)
T ss_pred ccc
Confidence 664
No 21
>KOG2549 consensus Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=99.49 E-value=1.2e-13 Score=113.87 Aligned_cols=74 Identities=24% Similarity=0.425 Sum_probs=70.6
Q ss_pred cchHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhcC-CcccccCC
Q 034139 30 ITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQG-RTLYGFGG 103 (103)
Q Consensus 30 ip~a~IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~g-~~lYgf~~ 103 (103)
.|..+++-+|++.|++.+++|+...|.+.+++.+++|++||.+|+.|++|.+++.+||..||+-.+ +|+|||++
T Consensus 12 s~~Es~k~vAEslGi~nl~deaa~~La~dv~yrikEI~Q~aaKfm~hskR~kLtv~DV~~ALr~~nVep~yg~~s 86 (576)
T KOG2549|consen 12 SPKESVKVVAESLGITNLNDEAALLLAEDVEYRIKEIVQDAAKFMVHSKRTKLTVDDVDYALRSLNVEPLYGFGA 86 (576)
T ss_pred CcHHHHHHHHHHhCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcCcHHHHHHHHhhcccccccCccc
Confidence 459999999999999999999999999999999999999999999999999999999999999665 99999975
No 22
>PF15511 CENP-T: Centromere kinetochore component CENP-T; PDB: 3B0D_T 3B0C_T 3VH5_T 3VH6_T.
Probab=99.49 E-value=7.3e-14 Score=112.45 Aligned_cols=70 Identities=26% Similarity=0.351 Sum_probs=48.5
Q ss_pred cccchhhcccccC--cchHHHHHHHHhc------CccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHH
Q 034139 17 KRHRKVLRDNIQG--ITKPAIRRLARRG------GVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMD 86 (103)
Q Consensus 17 kr~~k~~r~~~~~--ip~a~IkRiar~~------G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~D 86 (103)
++.+|+.|..+.+ +|.++||++|.+. +-.+|+++++++|.+|++|||+++..|...||.|||||||+++|
T Consensus 337 ~k~~k~Skhgi~~P~lP~~~vK~la~~~ak~s~~sK~kiskdal~aleqasdwfFeQl~dDL~aYA~HAgRKTIdesD 414 (414)
T PF15511_consen 337 QKQKKVSKHGIPYPSLPPGVVKKLAQHFAKSSGGSKMKISKDALEALEQASDWFFEQLGDDLEAYAKHAGRKTIDESD 414 (414)
T ss_dssp ---------------S-HHHHHHHHHHHH-------S-B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHH
T ss_pred ccccCCCCCCCCCCCCCccHHHHHHHHHHHhhcccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCCCC
Confidence 3667888888875 9999999999776 34899999999999999999999999999999999999999998
No 23
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=99.46 E-value=5.4e-13 Score=84.90 Aligned_cols=68 Identities=24% Similarity=0.353 Sum_probs=63.8
Q ss_pred cchHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhcCCc
Q 034139 30 ITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRT 97 (103)
Q Consensus 30 ip~a~IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~g~~ 97 (103)
+-+-+|-+|++..|.++++++|.+.|.+.++.|+.+|++.+..||+|++|++++..||.+||+.+|..
T Consensus 7 ll~~~Vaqil~~~Gf~~~~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~~~Dv~~Al~~~gi~ 74 (77)
T smart00576 7 LLRIAVAQILESAGFDSFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPNLGDVVLALENLGIS 74 (77)
T ss_pred HHHHHHHHHHHHcCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCcc
Confidence 34567889999999999999999999999999999999999999999999999999999999998864
No 24
>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=99.46 E-value=5.4e-13 Score=91.30 Aligned_cols=65 Identities=15% Similarity=0.164 Sum_probs=62.4
Q ss_pred CcchHHHHHHHHh-cCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHh
Q 034139 29 GITKPAIRRLARR-GGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKR 93 (103)
Q Consensus 29 ~ip~a~IkRiar~-~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr 93 (103)
.||.+.|+|+++. .+..|||++|...|..++|++..+|++.|..+|+|.+|++|+++||.+|++.
T Consensus 20 ~fPV~ri~R~Lk~~~~a~RVs~~A~VyLaAvLEYL~aEIlelA~n~ak~~k~krItp~hi~lAi~n 85 (115)
T cd00074 20 QFPVGRIHRYLKKGRYAERVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKKRITPRHLQLAVRN 85 (115)
T ss_pred cCcHHHHHHHHHcCccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEcHHHHHHHHhc
Confidence 7999999999998 6789999999999999999999999999999999999999999999999964
No 25
>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=99.39 E-value=1.3e-12 Score=102.89 Aligned_cols=74 Identities=23% Similarity=0.380 Sum_probs=71.0
Q ss_pred CcchHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhcC-CcccccC
Q 034139 29 GITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQG-RTLYGFG 102 (103)
Q Consensus 29 ~ip~a~IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~g-~~lYgf~ 102 (103)
.+.+.+|+.+|++.|+.+|.+|+..+|...+|+++.+|+++|.+|+.|++|..+|.+||..||+.++ +|||||+
T Consensus 5 ~ws~et~KdvAeslGi~Ni~Dd~l~alamDlEYRI~ev~qea~KFmvhSKRtvLt~dDis~ALr~lNVePLyGyd 79 (450)
T COG5095 5 LWSKETLKDVAESLGISNIDDDALRALAMDLEYRIKEVCQEASKFMVHSKRTVLTIDDISYALRSLNVEPLYGYD 79 (450)
T ss_pred eecHHHHHHHHHHcCCcccccHHHHHHHHhHHHHHHHHHHHHHHHhhcccceeeeHHhHHHHHHhcCCCcccCCC
Confidence 4678999999999999999999999999999999999999999999999999999999999999775 9999997
No 26
>KOG1745 consensus Histones H3 and H4 [Chromatin structure and dynamics]
Probab=99.27 E-value=2e-12 Score=90.59 Aligned_cols=80 Identities=21% Similarity=0.240 Sum_probs=71.8
Q ss_pred cccchhhcccccCcchHHHHHHHHhcC-----ccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHH
Q 034139 17 KRHRKVLRDNIQGITKPAIRRLARRGG-----VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYAL 91 (103)
Q Consensus 17 kr~~k~~r~~~~~ip~a~IkRiar~~G-----~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Al 91 (103)
+--+++|+.++..|++.|+.|+++..- .-|+.++|+.+|+++.|.||..+++|++.||.||+|.||.+.||.+|.
T Consensus 51 ~eirkyQkstdLlI~K~PFqRlvrei~q~f~~dLrfqs~Ai~ALQeA~EayLv~LfEdtnlcAihAkRVTimpkdiQlAr 130 (137)
T KOG1745|consen 51 REIRKYQKSTDLLIRKLPFQRLVREIAQDFKTDLRFQSSAIAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 130 (137)
T ss_pred HHHHHHHhhhHHHhhcCcHHHHhHHHHhcccccceehHHHHHHHHHHHHHHHHHhccccchhhhccceeEecccceehhh
Confidence 334678999999999999999998431 478999999999999999999999999999999999999999999999
Q ss_pred HhcCC
Q 034139 92 KRQGR 96 (103)
Q Consensus 92 kr~g~ 96 (103)
+..|+
T Consensus 131 rirg~ 135 (137)
T KOG1745|consen 131 RIRGE 135 (137)
T ss_pred hcccC
Confidence 86664
No 27
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=99.23 E-value=6.1e-11 Score=75.86 Aligned_cols=61 Identities=20% Similarity=0.286 Sum_probs=51.8
Q ss_pred HHHHHHHhcC---ccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhc
Q 034139 34 AIRRLARRGG---VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 94 (103)
Q Consensus 34 ~IkRiar~~G---~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~ 94 (103)
+|-+|+++.+ -..+|+.++.+|.+.+..++..+..|...||+||||+||+.+||.+..+++
T Consensus 10 ~v~ki~ee~~~~~~~~~s~~~i~al~ELv~~q~~~~a~DLe~FAkHA~R~tI~~dDV~Ll~Rrn 73 (76)
T PF15630_consen 10 TVGKIVEEEAKEKGVEVSPQFIAALTELVYKQLENLAKDLEAFAKHAGRSTINMDDVKLLARRN 73 (76)
T ss_dssp HHHHHHHHCCCCTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHTTT-
T ss_pred HHHHHHHHHHhccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHHHhhcC
Confidence 5678887775 246999999999999999999999999999999999999999999999875
No 28
>PLN00153 histone H2A; Provisional
Probab=99.18 E-value=1.2e-10 Score=81.14 Aligned_cols=87 Identities=20% Similarity=0.287 Sum_probs=72.1
Q ss_pred CCCCCCCCccCCCCCCcccchhhcccccCcchHHHHHHHHhcC-ccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCC
Q 034139 1 MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGG-VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARR 79 (103)
Q Consensus 1 ~~~~~~~~~~~~~~g~kr~~k~~r~~~~~ip~a~IkRiar~~G-~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~R 79 (103)
|||+|||++...+..+++. +..+ .||..-|+|++++.. ..||++.|...|..++||...||++-|...|+..++
T Consensus 1 m~g~~~~~~~~~k~~srS~----ragL-~FpVgRi~R~Lr~g~~a~Rvga~A~VYLAAVLEYLtaEVLELAgnaa~d~kk 75 (129)
T PLN00153 1 MAGRGKGKTSGKKAVSRSA----KAGL-QFPVGRIARYLKKGKYAERIGAGAPVYLAAVLEYLTAEVLELAGNAARDNKK 75 (129)
T ss_pred CCCCCCCCccccCccCccc----ccCc-ccchHHHHHHHhcCchhhccCCCchHHHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 8999885433323333222 4444 799999999998754 689999999999999999999999999999999999
Q ss_pred ceecHHHHHHHHH
Q 034139 80 KTVTAMDVVYALK 92 (103)
Q Consensus 80 kTI~~~DV~~Alk 92 (103)
+-|++++|.+|++
T Consensus 76 ~RItPrHi~lAI~ 88 (129)
T PLN00153 76 NRIVPRHIQLAIR 88 (129)
T ss_pred CccChHHHHhhcc
Confidence 9999999999995
No 29
>PLN00157 histone H2A; Provisional
Probab=99.14 E-value=2.3e-10 Score=79.90 Aligned_cols=87 Identities=22% Similarity=0.321 Sum_probs=70.7
Q ss_pred CCCCCC--CCccCCCCCCcccchhhcccccCcchHHHHHHHHhcC-ccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Q 034139 1 MSGRGK--GGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGG-VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHA 77 (103)
Q Consensus 1 ~~~~~~--~~~~~~~~g~kr~~k~~r~~~~~ip~a~IkRiar~~G-~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha 77 (103)
|||||| |++...+...++ .+..+ .||..-|+|++++.. ..||++.|...|..++||...||++.|...|...
T Consensus 1 ms~~g~~~~~~~~~k~~srS----~ragL-~FPVgRi~R~Lk~g~~a~RIg~~A~VYLAAVLEYLtaEVLELAgnaa~d~ 75 (132)
T PLN00157 1 MSGRGKRKGGGGGKKATSRS----AKAGL-QFPVGRIARYLKAGKYATRVGAGAPVYLAAVLEYLAAEVLELAGNAARDN 75 (132)
T ss_pred CCCCCCCCCCccCcCCcCcc----cccCc-ccchHHHHHHHhcCchhhhcCCCcHhHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 899887 322222222222 24444 799999999998853 6899999999999999999999999999999999
Q ss_pred CCceecHHHHHHHHH
Q 034139 78 RRKTVTAMDVVYALK 92 (103)
Q Consensus 78 ~RkTI~~~DV~~Alk 92 (103)
+++-|++++|.+|++
T Consensus 76 kk~RItPrHi~lAI~ 90 (132)
T PLN00157 76 KKSRIVPRHIQLAVR 90 (132)
T ss_pred CCccccHHHHhhccc
Confidence 999999999999995
No 30
>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=99.11 E-value=3.9e-10 Score=78.55 Aligned_cols=67 Identities=22% Similarity=0.358 Sum_probs=53.7
Q ss_pred cCcchH--HHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhc
Q 034139 28 QGITKP--AIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 94 (103)
Q Consensus 28 ~~ip~a--~IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~ 94 (103)
..+|.. .|.-|+++.|+....+.+...|.+++..|+.+|++||..|++|++|++|+.+||.+|++..
T Consensus 9 ~~~PrDa~~i~~iL~~~Gv~~yeprVv~qLLEfayRYt~~vL~DA~~ya~hA~~~~i~~~DVrLAi~~r 77 (129)
T PF02291_consen 9 KSLPRDARVIHLILKSMGVTEYEPRVVNQLLEFAYRYTSDVLEDAQVYADHAGRSTIDADDVRLAIQSR 77 (129)
T ss_dssp ----HHHHHHHHHHHHTT---B-THHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHHHHT
T ss_pred ccCChHHHHHHHHHHHcCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHH
Confidence 356665 4889999999999999999999999999999999999999999999999999999999843
No 31
>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=98.98 E-value=6.4e-09 Score=65.74 Aligned_cols=66 Identities=24% Similarity=0.383 Sum_probs=62.1
Q ss_pred hHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhcCCc
Q 034139 32 KPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRT 97 (103)
Q Consensus 32 ~a~IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~g~~ 97 (103)
...|-.|+++.|...+++.|++.|.+.+..|+.+|.+.+..||+|++|...+..||..||+..|..
T Consensus 9 ~~~va~il~~~GF~~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~~~gi~ 74 (77)
T PF07524_consen 9 RRSVAQILKHAGFDSASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPNLQDVEQALEEMGIS 74 (77)
T ss_pred HHHHHHHHHHcCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCC
Confidence 456788999999999999999999999999999999999999999999999999999999998863
No 32
>KOG3334 consensus Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=98.97 E-value=4.8e-09 Score=74.12 Aligned_cols=69 Identities=23% Similarity=0.380 Sum_probs=63.2
Q ss_pred cccCcchHH--HHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhc
Q 034139 26 NIQGITKPA--IRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 94 (103)
Q Consensus 26 ~~~~ip~a~--IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~ 94 (103)
+...-|+.. |..|+++.|+.-..+.+...|.++...|...|++||..|++||++.||+++||.+|++-.
T Consensus 8 ~~~~~pkDa~~i~~iL~s~GI~eyEprVi~qlLefa~rYtt~vL~DA~vys~HA~ka~i~~eDVrlA~~~~ 78 (148)
T KOG3334|consen 8 GTKGVPKDARVIASILKSLGIQEYEPRVINQLLEFAYRYTTTVLDDAKVYSSHAKKATIDAEDVRLAIQMR 78 (148)
T ss_pred cccCCcHHHHHHHHHHHHcCccccChHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcHHHHHHHHHHH
Confidence 344567665 889999999999999999999999999999999999999999999999999999999854
No 33
>KOG1756 consensus Histone 2A [Chromatin structure and dynamics]
Probab=98.97 E-value=3.4e-09 Score=73.50 Aligned_cols=88 Identities=25% Similarity=0.322 Sum_probs=73.4
Q ss_pred CCCCCCCCccCCCCCCcccchhhcc--cccCcchHHHHHHHHhc-CccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Q 034139 1 MSGRGKGGKGLGKGGAKRHRKVLRD--NIQGITKPAIRRLARRG-GVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHA 77 (103)
Q Consensus 1 ~~~~~~~~~~~~~~g~kr~~k~~r~--~~~~ip~a~IkRiar~~-G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha 77 (103)
|||+||+|++..+ +..+.+++ .-..+|...|.|++|.. ...||+.++...|..++||...+|++-|-.+|+..
T Consensus 1 ~s~~~k~gk~~~~----~~~~~srs~~agl~fPvgri~r~Lr~~~~~~ri~~gapV~laavLeYL~Aeile~agnaardn 76 (131)
T KOG1756|consen 1 MSGRGKGGKAKPR----AKAKSSRSSRAGLQFPVGRIHRLLRKGRYAQRVGAGAPVYLAAVLEYLTAEILELAGNAARDN 76 (131)
T ss_pred CCccCCCCcccch----hhhhcchhhhcccccCHHHHHHHHHccchhhhccCCChHHHHHHHHHHHHHHHHHhHHHhhhc
Confidence 7889998877554 12222221 12279999999999993 47999999999999999999999999999999999
Q ss_pred CCceecHHHHHHHHH
Q 034139 78 RRKTVTAMDVVYALK 92 (103)
Q Consensus 78 ~RkTI~~~DV~~Alk 92 (103)
++..|++..|.+|++
T Consensus 77 kk~ri~PrH~~lAI~ 91 (131)
T KOG1756|consen 77 KKTRITPRHLQLAIR 91 (131)
T ss_pred CccccChHHHHHHHh
Confidence 999999999999996
No 34
>PLN00154 histone H2A; Provisional
Probab=98.96 E-value=5.6e-09 Score=73.23 Aligned_cols=64 Identities=16% Similarity=0.155 Sum_probs=61.0
Q ss_pred CcchHHHHHHHHhcC--ccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHH
Q 034139 29 GITKPAIRRLARRGG--VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALK 92 (103)
Q Consensus 29 ~ip~a~IkRiar~~G--~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alk 92 (103)
.||..-|+|++++.. ..||+..+...|..++||...||++-|-..|+..+++-|++.+|.+|++
T Consensus 38 ~FPVgRi~r~Lk~g~~~~~RVga~ApVYLAAVLEYLtAEVLELAGNaA~d~kk~RItPrHi~lAIr 103 (136)
T PLN00154 38 QFPVGRIHRQLKQRVSAHGRVGATAAVYTAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 103 (136)
T ss_pred cCchHHHHHHHHhhhhhccccccchHHHHHHHHHHHHHHHHHHHHHHHHhhCCceecHHHhhhhcc
Confidence 689999999999975 5799999999999999999999999999999999999999999999995
No 35
>PTZ00017 histone H2A; Provisional
Probab=98.92 E-value=7.7e-09 Score=72.49 Aligned_cols=64 Identities=17% Similarity=0.226 Sum_probs=60.6
Q ss_pred CcchHHHHHHHHhc-CccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHH
Q 034139 29 GITKPAIRRLARRG-GVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALK 92 (103)
Q Consensus 29 ~ip~a~IkRiar~~-G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alk 92 (103)
.||..-|+|++++. -..||++.|...|..++||+..||++-|...|+..+++-|++++|.+|++
T Consensus 27 ~FPVgRi~R~Lk~g~~a~RV~a~A~VYLAAVLEYLtaEILELAgNaa~d~kk~RItPrHi~lAI~ 91 (134)
T PTZ00017 27 QFPVGRVHRYLKKGRYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAAKDNKKKRITPRHIQLAIR 91 (134)
T ss_pred ccchHHHHHHHhccchhccccccchhhhHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHhhcc
Confidence 79999999999886 36899999999999999999999999999999999999999999999995
No 36
>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=98.86 E-value=1.2e-08 Score=72.56 Aligned_cols=75 Identities=17% Similarity=0.200 Sum_probs=69.2
Q ss_pred ccccCcchHHHHHHHHhcCc--cccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhcCCccc
Q 034139 25 DNIQGITKPAIRRLARRGGV--KRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTLY 99 (103)
Q Consensus 25 ~~~~~ip~a~IkRiar~~G~--~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~g~~lY 99 (103)
|..-.||+++|..|.+..-. .||..|+-+-+.++.-+|+.-|..+|+..|....+|||.+|.|..||+.+|+.-|
T Consensus 8 dde~sLPkAtv~KmIke~lP~d~rvakeareliincCvEFI~liSsEAneic~~e~KKTIa~EHV~KALe~LgF~eY 84 (156)
T KOG0871|consen 8 DDELSLPKATVNKMIKEMLPKDVRVAKEARELIINCCVEFINLISSEANEICNKEAKKTIAPEHVIKALENLGFGEY 84 (156)
T ss_pred cccccCcHHHHHHHHHHhCCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHhHHhcccCCHHHHHHHHHHcchHHH
Confidence 34458999999999999864 7999999999999999999999999999999999999999999999999998654
No 37
>PLN00156 histone H2AX; Provisional
Probab=98.80 E-value=3.5e-08 Score=69.48 Aligned_cols=64 Identities=14% Similarity=0.190 Sum_probs=60.4
Q ss_pred CcchHHHHHHHHhcC-ccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHH
Q 034139 29 GITKPAIRRLARRGG-VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALK 92 (103)
Q Consensus 29 ~ip~a~IkRiar~~G-~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alk 92 (103)
.||..-|+|++++.. ..||++.|...|..++||...||++.|-..|...+++-|++++|.+|++
T Consensus 29 ~FPVgRi~R~Lk~g~ya~RVga~ApVYLAAVLEYLtaEVLELAgNaa~d~kk~RItPrHi~lAIr 93 (139)
T PLN00156 29 QFPVGRIARFLKAGKYAERVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR 93 (139)
T ss_pred ccchHHHHHHHhcCChhhccCCccHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHhhcc
Confidence 699999999998863 5899999999999999999999999999999999999999999999995
No 38
>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription]
Probab=98.73 E-value=6.8e-08 Score=69.73 Aligned_cols=70 Identities=20% Similarity=0.155 Sum_probs=64.9
Q ss_pred cCcchHHHHHHHHhcCc---cccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhcCCc
Q 034139 28 QGITKPAIRRLARRGGV---KRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRT 97 (103)
Q Consensus 28 ~~ip~a~IkRiar~~G~---~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~g~~ 97 (103)
..||.+.|.||++..-. ..||.+|..++.....-|+-.++.-|..+|...+|||++++||..||..++++
T Consensus 9 l~lP~AiI~rlvke~l~E~~vsisKeA~~Ai~raAtVFv~~Lts~s~e~A~~q~rKt~sadDVl~aL~Eiefs 81 (172)
T KOG0870|consen 9 LNLPNAIITRLVKEVLPESNVSISKEARLAIARAATVFVIFLTSVSNEIAKDQKRKTISADDVLKALDEIEFS 81 (172)
T ss_pred hhccHHHHHHHHHHhCccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCcccHHHHHHHHHHhchH
Confidence 46999999999998854 45999999999999999999999999999999999999999999999998764
No 39
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=98.72 E-value=6.7e-08 Score=66.50 Aligned_cols=86 Identities=19% Similarity=0.213 Sum_probs=71.7
Q ss_pred CCCCCccCCCCCCcccchhhcccccCcchHHHHHHHHhc-CccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCcee
Q 034139 4 RGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRG-GVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTV 82 (103)
Q Consensus 4 ~~~~~~~~~~~g~kr~~k~~r~~~~~ip~a~IkRiar~~-G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI 82 (103)
.|||||. .+++..++-+-..-..+|..-|+||+++. +..||++++...+..++||.+.||++-|-..|...+.|.|
T Consensus 4 ~GKGgK~---a~~r~~~s~sa~agl~fpvgrvkr~lk~~~~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~kkkri 80 (132)
T COG5262 4 GGKGGKA---ADARVSQSRSAKAGLIFPVGRVKRLLKKGNYRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRI 80 (132)
T ss_pred CCcCccc---ccchhccchhhhcCccccHHHHHHHHHcCccceeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhcCccee
Confidence 4666663 44555544334444579999999999954 5799999999999999999999999999999999999999
Q ss_pred cHHHHHHHHH
Q 034139 83 TAMDVVYALK 92 (103)
Q Consensus 83 ~~~DV~~Alk 92 (103)
++..+.+|++
T Consensus 81 ~PrHlqlAIr 90 (132)
T COG5262 81 IPRHLQLAIR 90 (132)
T ss_pred chHHHHHHhc
Confidence 9999999996
No 40
>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=98.55 E-value=7.8e-07 Score=55.75 Aligned_cols=63 Identities=19% Similarity=0.273 Sum_probs=52.0
Q ss_pred hHHHHHHHHhcCc-cccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhc
Q 034139 32 KPAIRRLARRGGV-KRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 94 (103)
Q Consensus 32 ~a~IkRiar~~G~-~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~ 94 (103)
+..+..+++.... ..+.+++.+.|.+..++|+.+++..|...|+|-+-.||+..||.+.|+|.
T Consensus 2 K~~l~~Lv~~iDp~~~ld~~vee~Ll~laddFv~~v~~~ac~lAKhR~s~tle~~Dv~~~Ler~ 65 (68)
T PF03847_consen 2 KRKLQELVKQIDPNEKLDPDVEELLLELADDFVDDVVSFACRLAKHRKSSTLEVKDVQLHLERN 65 (68)
T ss_dssp HHHHHHHHHCC-SS----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHHHH
T ss_pred hHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCHHHHHHHHHhh
Confidence 5667888888864 88999999999999999999999999999999999999999999999875
No 41
>smart00414 H2A Histone 2A.
Probab=98.48 E-value=6e-07 Score=60.69 Aligned_cols=64 Identities=20% Similarity=0.263 Sum_probs=60.8
Q ss_pred CcchHHHHHHHHhcC-ccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHH
Q 034139 29 GITKPAIRRLARRGG-VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALK 92 (103)
Q Consensus 29 ~ip~a~IkRiar~~G-~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alk 92 (103)
.||..-|+|++++.. ..||++.|...|..++|++..+|++-|...|...+++.|+++|+.+|++
T Consensus 9 ~fPVgRi~r~Lk~~~~~~Rv~~~A~VyLaAvLEYLtaEILeLagn~a~~~k~~rItp~hi~lAi~ 73 (106)
T smart00414 9 QFPVGRIHRLLRKGTYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKRRITPRHLQLAIR 73 (106)
T ss_pred cCchHHHHHHHHcCccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchHHHhhhcc
Confidence 799999999998864 6899999999999999999999999999999999999999999999985
No 42
>COG5094 TAF9 Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=98.43 E-value=5.8e-07 Score=62.53 Aligned_cols=60 Identities=22% Similarity=0.336 Sum_probs=55.3
Q ss_pred HHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecH---HHHHHHHHhc
Q 034139 35 IRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTA---MDVVYALKRQ 94 (103)
Q Consensus 35 IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~---~DV~~Alkr~ 94 (103)
|+-|+++.|+...++.+.-+|.++...|..++++||..|++|+||-.+.. |||.+|+..+
T Consensus 20 ihliL~Slgi~~ye~~VplQLl~FAhRYTq~vl~Dalvya~htgrg~~a~l~veDvrLA~at~ 82 (145)
T COG5094 20 IHLILRSLGIEEYEPKVPLQLLEFAHRYTQDVLEDALVYAKHTGRGHIATLGVEDVRLALATK 82 (145)
T ss_pred HHHHHHhcCchhhCccchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHHHHHHH
Confidence 78899999999999999999999999999999999999999999985555 9999999743
No 43
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=98.34 E-value=2.1e-06 Score=65.73 Aligned_cols=83 Identities=16% Similarity=0.246 Sum_probs=73.3
Q ss_pred hhhcccccCcchHHHHHHHHhcC-ccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhc-CCcc
Q 034139 21 KVLRDNIQGITKPAIRRLARRGG-VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ-GRTL 98 (103)
Q Consensus 21 k~~r~~~~~ip~a~IkRiar~~G-~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~-g~~l 98 (103)
.....+.+.+.+..+..+++.+. -+.+.+||.+-|.++.+.|++.|+.-+..+|+|-+-.||.+.||.+.|+|. +..+
T Consensus 146 ~~~~~~~~il~k~kl~dLvqqId~~~~LD~dVedlLleiADdFV~sii~~sC~LAKHRKsdtlEvrDIqLhLEr~~Nm~i 225 (258)
T KOG1142|consen 146 QDEPGNNPILSKRKLDDLVQQIDGTTKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHRKSDTVEVRDIQLHLERNFNMEI 225 (258)
T ss_pred cccCCCCccccccchhHHHHhhcCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccchhheeeeeeccccccC
Confidence 34446677899999999999884 588999999999999999999999999999999999999999999999986 7777
Q ss_pred cccCC
Q 034139 99 YGFGG 103 (103)
Q Consensus 99 Ygf~~ 103 (103)
=||++
T Consensus 226 Pgf~s 230 (258)
T KOG1142|consen 226 PGFSS 230 (258)
T ss_pred CCccc
Confidence 67754
No 44
>PTZ00252 histone H2A; Provisional
Probab=98.24 E-value=5.8e-06 Score=57.97 Aligned_cols=64 Identities=20% Similarity=0.226 Sum_probs=58.5
Q ss_pred CcchHHHHHHHHhcC-ccccchHHHHHHHHHHHHHHHHHHHHHHHHHhh--CCCceecHHHHHHHHH
Q 034139 29 GITKPAIRRLARRGG-VKRISGLIYEETRGVLKIFLENVIRDAVTYTEH--ARRKTVTAMDVVYALK 92 (103)
Q Consensus 29 ~ip~a~IkRiar~~G-~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~h--a~RkTI~~~DV~~Alk 92 (103)
.||..-|.|++++.. ..||++.|...|..++||...||++.|...|+. .+++-|++++|.+|++
T Consensus 25 ~FPVgRi~R~Lr~g~ya~RIga~ApVYLAAVLEYLtaEVLELAgnaa~d~~~kk~RItPrHi~lAIr 91 (134)
T PTZ00252 25 IFPVGRVGSLLRRGQYARRIGASGAVYMAAVLEYLTAELLELSVKAAAQQAKKPKRLTPRTVTLAVR 91 (134)
T ss_pred cCchHHHHHHHHcCCcccccCCccHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccccHHHHHhhcc
Confidence 799999999998875 589999999999999999999999999999964 5667899999999995
No 45
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=98.18 E-value=8e-06 Score=57.06 Aligned_cols=73 Identities=15% Similarity=0.087 Sum_probs=65.6
Q ss_pred ccCcchHHHHHHHHhcCc--cccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhcCCccc
Q 034139 27 IQGITKPAIRRLARRGGV--KRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTLY 99 (103)
Q Consensus 27 ~~~ip~a~IkRiar~~G~--~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~g~~lY 99 (103)
...||+++|+.+.-++-. --++.++.+.+.++.-+|+-.+..+|++.|+....|||.++.|.-||+.+++.-|
T Consensus 9 e~sLPKATVqKMvS~iLp~dl~ftKearei~in~cieFi~~lsseAne~ce~EaKKTIa~EHviKALenLef~ey 83 (148)
T COG5150 9 ENSLPKATVQKMVSSILPKDLVFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHVIKALENLEFEEY 83 (148)
T ss_pred cccCcHHHHHHHHHHhccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHhccHHHH
Confidence 348999999999988753 4589999999999999999999999999999999999999999999999886544
No 46
>KOG4336 consensus TBP-associated transcription factor Prodos [Transcription]
Probab=98.02 E-value=2.8e-05 Score=61.03 Aligned_cols=66 Identities=24% Similarity=0.315 Sum_probs=61.2
Q ss_pred HHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhcCCcc
Q 034139 33 PAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTL 98 (103)
Q Consensus 33 a~IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~g~~l 98 (103)
..|.-|+...|..-|+.-+.+.|.+.+..|+.+|.+.+..+|+|+||.-.|.-||.+.|..+|+++
T Consensus 9 ~VV~~Ll~~~gfd~is~~aletlvell~~yi~eigrq~~n~celagRT~pT~~Dv~l~Li~mnI~v 74 (323)
T KOG4336|consen 9 PVVSNLLKTKGFDSISNAALETLVELLQSYIREIGRQLHNYCELAGRTIPTQGDVKLTLIEMNIKV 74 (323)
T ss_pred HHHHHHHHHhCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcHHHHHHHHHHhCCCh
Confidence 346678889999999999999999999999999999999999999999999999999999998753
No 47
>PTZ00463 histone H2B; Provisional
Probab=97.95 E-value=8e-05 Score=51.14 Aligned_cols=60 Identities=17% Similarity=0.168 Sum_probs=54.5
Q ss_pred HHHHHHhcCc-cccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhc
Q 034139 35 IRRLARRGGV-KRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 94 (103)
Q Consensus 35 IkRiar~~G~-~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~ 94 (103)
|.++++..-. .-||..+...+..++.+.++.|+.+|...|++.+|.||+..||..|.+..
T Consensus 34 I~KVLKqVhPd~gIS~kaM~ImnSfvnDifErIA~EAs~La~~nkr~TltsrEIQtAvrLl 94 (117)
T PTZ00463 34 IFKVLKQVHPDTGISRKSMNIMNSFLVDTFEKIATEASRLCKYTRRDTLSSREIQTAIRLV 94 (117)
T ss_pred HHHHHHhhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHhhc
Confidence 7788887753 56899999999999999999999999999999999999999999999754
No 48
>PLN00158 histone H2B; Provisional
Probab=97.95 E-value=7.9e-05 Score=51.12 Aligned_cols=61 Identities=15% Similarity=0.159 Sum_probs=55.1
Q ss_pred HHHHHHHhcCc-cccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhc
Q 034139 34 AIRRLARRGGV-KRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 94 (103)
Q Consensus 34 ~IkRiar~~G~-~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~ 94 (103)
-|.++++..-. .-||..+...+..++.+.++.|+.+|...+++.+|.||+..||..|.+..
T Consensus 32 YI~kVLKQVhPd~gIS~kaM~ImnSfvnDiferIA~EAs~La~~nkr~TltsrEIqtAvrLv 93 (116)
T PLN00158 32 YIYKVLKQVHPDTGISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVRLI 93 (116)
T ss_pred HHHHHHHHhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHh
Confidence 47888888753 56899999999999999999999999999999999999999999999754
No 49
>smart00427 H2B Histone H2B.
Probab=97.94 E-value=7.8e-05 Score=49.07 Aligned_cols=60 Identities=12% Similarity=0.166 Sum_probs=54.2
Q ss_pred HHHHHHhcCc-cccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhc
Q 034139 35 IRRLARRGGV-KRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 94 (103)
Q Consensus 35 IkRiar~~G~-~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~ 94 (103)
|.++++..-. .-||..+...+..++.+.++.|+.+|...++..+|.||+..||..|.+..
T Consensus 7 i~kvLKqVhpd~giS~kam~imnSfvnDiferIa~EAs~L~~~nkr~TltsreIqtAvrl~ 67 (89)
T smart00427 7 IYKVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRLI 67 (89)
T ss_pred HHHHHHHhCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHH
Confidence 6778877753 56999999999999999999999999999999999999999999999753
No 50
>PLN00155 histone H2A; Provisional
Probab=97.84 E-value=3.7e-05 Score=46.87 Aligned_cols=56 Identities=25% Similarity=0.318 Sum_probs=39.5
Q ss_pred CCCCCCCCccCCCCCCcccchhhcccccCcchHHHHHHHHhcC-ccccchHHHHHHHHHHHH
Q 034139 1 MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGG-VKRISGLIYEETRGVLKI 61 (103)
Q Consensus 1 ~~~~~~~~~~~~~~g~kr~~k~~r~~~~~ip~a~IkRiar~~G-~~riS~da~~~l~~~~e~ 61 (103)
|||+|||++...+... +..+..+ .||...|+|++++.. ..||+..+...|..++|+
T Consensus 1 msg~g~g~~~~~k~~s----rS~rAgL-~FPVgri~r~Lr~g~~a~Rvga~apVYlAAVLEY 57 (58)
T PLN00155 1 MAGRGKGKTSGKKAVS----RSAKAGL-QFPVGRIARYLKKGKYAERIGAGAPVYLAAVLEY 57 (58)
T ss_pred CCCCCCCCccccCccC----ccccccc-ccchHHHHHHHhcCChhhcccCCcHHHHHHHHHh
Confidence 8988885322222211 2223344 799999999998864 589999999999998886
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=97.84 E-value=2.1e-05 Score=51.76 Aligned_cols=61 Identities=13% Similarity=0.279 Sum_probs=30.6
Q ss_pred HHHHHHhcC-ccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhcC
Q 034139 35 IRRLARRGG-VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQG 95 (103)
Q Consensus 35 IkRiar~~G-~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~g 95 (103)
|..++--.| ...-.++.+..+.+++-+|+.+++..|..+|...|+++|+.+|+.++|++..
T Consensus 7 I~~mMy~fGD~~~P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~rg~~~i~~eDl~F~lR~D~ 68 (93)
T PF02269_consen 7 IRQMMYGFGDVEEPLPETVDLVEDIVREYIIELCQEAMEVAQRRGSKKIKVEDLLFLLRKDP 68 (93)
T ss_dssp CHHHHHCTTS-SS--HHHHHHHHHHHHHHHHHHHHHHHC-----------------------
T ss_pred HHHHHHHcCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCcCcHHHHHHHHhcCH
Confidence 455666666 4678889999999999999999999999999999999999999999998753
No 52
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=97.78 E-value=5e-05 Score=57.55 Aligned_cols=67 Identities=22% Similarity=0.294 Sum_probs=62.6
Q ss_pred ccCcchHHHHHHHHhc-CccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHh
Q 034139 27 IQGITKPAIRRLARRG-GVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKR 93 (103)
Q Consensus 27 ~~~ip~a~IkRiar~~-G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr 93 (103)
+..||.+.|+++++.- +++=||++|-.......|.|+++++-.|-..|+..+|.|+...||..|++.
T Consensus 107 ~h~LPlARIkkvMKtdedVkMisaEaPvlFak~~EiFI~ELTmRAW~~ae~NkRRtLQksDia~Av~k 174 (286)
T COG5208 107 DHNLPLARIKKVMKTDEDVKMISAEAPVLFAKITEIFIEELTMRAWINAEENKRRTLQKSDIAAAVKK 174 (286)
T ss_pred hccCcHHHHHHHHhcccchhheecccchHHHHHHHHHHHHHHHHHHHHHhHhhhhHHHHHHHHHHHHH
Confidence 3469999999999875 688999999999999999999999999999999999999999999999975
No 53
>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=97.75 E-value=0.00023 Score=46.28 Aligned_cols=66 Identities=20% Similarity=0.275 Sum_probs=61.0
Q ss_pred CcchHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCC---ceecHHHHHHHHHhc
Q 034139 29 GITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARR---KTVTAMDVVYALKRQ 94 (103)
Q Consensus 29 ~ip~a~IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~R---kTI~~~DV~~Alkr~ 94 (103)
.||++.|+||+....-..+++++...|.-....|+.+|++.|....+..+. .-|.+++|..|.+++
T Consensus 16 ~f~k~~iKr~~~~~~~~~v~~~v~i~v~glaKvFVGeivE~A~~V~~~~~~~~~~Pl~P~HireA~rrl 84 (85)
T cd08048 16 SFPKAAIKRLIQSVTGQSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGEANTGPLQPRHLREAYRRL 84 (85)
T ss_pred hccHHHHHHHHHHHcCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCCCCCcHHHHHHHHHh
Confidence 499999999999887789999999999999999999999999999998665 679999999999875
No 54
>KOG1757 consensus Histone 2A [Chromatin structure and dynamics]
Probab=97.61 E-value=0.00013 Score=49.99 Aligned_cols=91 Identities=20% Similarity=0.250 Sum_probs=70.7
Q ss_pred CCCCCCCCccCCCCCCcccchhhcccc--cCcchHHHHHHHHhc--CccccchHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 034139 1 MSGRGKGGKGLGKGGAKRHRKVLRDNI--QGITKPAIRRLARRG--GVKRISGLIYEETRGVLKIFLENVIRDAVTYTEH 76 (103)
Q Consensus 1 ~~~~~~~~~~~~~~g~kr~~k~~r~~~--~~ip~a~IkRiar~~--G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~h 76 (103)
|+|. +.||+.++..+.....+++... ..||...|+|.++.- +..||-+.+......++|+...++++-|-..+..
T Consensus 1 m~g~-~~gk~~~~~k~~~~k~vs~s~raGlqFpVgRihr~LK~r~t~h~rVGataavy~aaileYLTaEVLeLAgNasKd 79 (131)
T KOG1757|consen 1 MAGG-KAGKDSGKAKDSKAKAVSRSARAGLQFPVGRIHRHLKTRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKD 79 (131)
T ss_pred CCCc-cccCcccccchhhhhhhhHHHhcccccchHHHHHHHHHhcccccccchHHHHHHHHHHHHHHHHHHHHccccccc
Confidence 6754 6777666655332222222222 279999999999764 4689999999999999999999999999999998
Q ss_pred CCCceecHHHHHHHHH
Q 034139 77 ARRKTVTAMDVVYALK 92 (103)
Q Consensus 77 a~RkTI~~~DV~~Alk 92 (103)
=+=|.||+..+.+|++
T Consensus 80 LKvKRitprHlqLAiR 95 (131)
T KOG1757|consen 80 LKVKRITPRHLQLAIR 95 (131)
T ss_pred ceeeeccchhheeeec
Confidence 8888899999999885
No 55
>KOG3423 consensus Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=97.49 E-value=0.0012 Score=47.96 Aligned_cols=71 Identities=15% Similarity=0.192 Sum_probs=63.5
Q ss_pred cccCcchHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhC--------------CCceecHHHHHHHH
Q 034139 26 NIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHA--------------RRKTVTAMDVVYAL 91 (103)
Q Consensus 26 ~~~~ip~a~IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha--------------~RkTI~~~DV~~Al 91 (103)
--+.||.+-+.=+++++|+......+..-+.-+..+|+.+|+.||..+|+-. ++-|+|.+|+.-||
T Consensus 83 YtP~IPDavt~~yL~~aGf~~~D~rv~RLvsLaAQKfvSDIa~DA~Q~~k~r~~~~~~~~k~~~kdkK~tLtmeDL~~AL 162 (176)
T KOG3423|consen 83 YTPTIPDAVTDHYLKKAGFQTSDPRVKRLVSLAAQKFVSDIANDALQHSKIRTKTAIGKDKKQAKDKKYTLTMEDLSPAL 162 (176)
T ss_pred CCCCCcHHHHHHHHHhcCCCcCcHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccccccccccccceeeeHHHHHHHH
Confidence 3457999999999999999999999999999999999999999999999843 35589999999999
Q ss_pred HhcCC
Q 034139 92 KRQGR 96 (103)
Q Consensus 92 kr~g~ 96 (103)
+..|.
T Consensus 163 ~EyGi 167 (176)
T KOG3423|consen 163 AEYGI 167 (176)
T ss_pred HHhCc
Confidence 98775
No 56
>KOG2389 consensus Predicted bromodomain transcription factor [Transcription]
Probab=97.49 E-value=0.0003 Score=56.02 Aligned_cols=70 Identities=20% Similarity=0.317 Sum_probs=65.2
Q ss_pred cCcchHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhcCCc
Q 034139 28 QGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRT 97 (103)
Q Consensus 28 ~~ip~a~IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~g~~ 97 (103)
..+.+..|..|..+.|...+...+++.|.+++..|+.++.+.|--|+.++||.-...-||.+||+.++-.
T Consensus 28 ~sla~~avaQIcqslg~~~~~~sale~Ltd~~~qyvQ~lgk~a~~~~n~anR~epnl~Div~Al~dls~s 97 (353)
T KOG2389|consen 28 FSLARVAVAQICQSLGYSSTQNSALETLTDVLQQYVQNLGKTAHRYSNLANRTEPNLFDIVLALQDLSAS 97 (353)
T ss_pred HHHHHHHHHHHHHhcCCcccccHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCccHHHHHHHHHHhhhh
Confidence 3577888999999999999999999999999999999999999999999999999999999999987643
No 57
>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=97.46 E-value=0.0004 Score=43.92 Aligned_cols=61 Identities=18% Similarity=0.190 Sum_probs=50.6
Q ss_pred chHHHHHHHHhc---CccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCce-ecHHHHHHHH
Q 034139 31 TKPAIRRLARRG---GVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKT-VTAMDVVYAL 91 (103)
Q Consensus 31 p~a~IkRiar~~---G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkT-I~~~DV~~Al 91 (103)
|+..|.||++.. -..+||+||...+.+.++-|+.+.+..|+..++..+-.+ |+.+|++..+
T Consensus 1 p~~li~rll~~~f~~~~tkIs~dal~l~~eyl~iFV~EAv~Ra~~~a~~e~~~~~le~e~LEki~ 65 (72)
T PF09415_consen 1 PPELIARLLHEHFKDDKTKISKDALKLSAEYLRIFVREAVARAAEQAEAEGDEGFLEVEHLEKIL 65 (72)
T ss_dssp -CHHHHHHHCTTSSSTT-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSEE-HHHHHHHC
T ss_pred ChHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHH
Confidence 788999999843 258999999999999999999999999999999999988 9999998754
No 58
>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=97.40 E-value=0.0014 Score=43.23 Aligned_cols=61 Identities=15% Similarity=0.235 Sum_probs=51.9
Q ss_pred HHHHHHHHhcCc-cccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhc
Q 034139 33 PAIRRLARRGGV-KRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 94 (103)
Q Consensus 33 a~IkRiar~~G~-~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~ 94 (103)
.-|+.++--.|- ..-.++....|.+++-+|+.+++..|..+|. .+|..++.||+.++|++.
T Consensus 6 ~ei~~mmy~~GD~~~P~~eTv~llE~iv~~~i~~l~~~a~~~A~-~r~~k~~~eD~~FliR~D 67 (92)
T cd07978 6 KEIRQMMYGFGDVQNPLPETVDLLEDIVVEYIIELCHKAAEVAQ-RRRGKVKVEDLIFLLRKD 67 (92)
T ss_pred HHHHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-cCCCCCCHHHHHHHHhcC
Confidence 347778877774 5667899999999999999999999999998 666668999999999754
No 59
>KOG1657 consensus CCAAT-binding factor, subunit C (HAP5) [Transcription]
Probab=97.32 E-value=0.00038 Score=52.91 Aligned_cols=68 Identities=15% Similarity=0.197 Sum_probs=62.4
Q ss_pred ccCcchHHHHHHHHhc-CccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhc
Q 034139 27 IQGITKPAIRRLARRG-GVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 94 (103)
Q Consensus 27 ~~~ip~a~IkRiar~~-G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~ 94 (103)
+..||.+.||+|++.- .+.-|+.||...+..++|.|+.++...+-..++..+|+|+...|+..|+...
T Consensus 72 ~~~lPlaRiKkimK~dedv~mI~~Eapvl~aka~E~Fi~elt~~sw~~Tee~~rrtl~~sdia~av~~s 140 (236)
T KOG1657|consen 72 NHILPLARIKKIMKSDEDVSMITAEAPVLFAKACELFITELTLRSWVHTEENKRRTLQKSDIAAAVTQS 140 (236)
T ss_pred hccCcHhhccccccccccccccchhHHHHHHHHHHHHHHHHHHHhhhhhcccccccchHHHHHHHhccC
Confidence 3479999999999876 5688999999999999999999999999999999999999999999998654
No 60
>KOG1659 consensus Class 2 transcription repressor NC2, alpha subunit (DRAP1) [Transcription]
Probab=97.27 E-value=0.0011 Score=49.94 Aligned_cols=66 Identities=15% Similarity=0.290 Sum_probs=60.0
Q ss_pred ccCcchHHHHHHHHhc-CccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHH
Q 034139 27 IQGITKPAIRRLARRG-GVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALK 92 (103)
Q Consensus 27 ~~~ip~a~IkRiar~~-G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alk 92 (103)
.--||.+-|++||..- -+.+|...+-..+..+||-|++.|++.+.+.++--+-|||+++.+..|..
T Consensus 11 ~trfp~aRiKKIMQ~dEdIGKvaqavPViisralElFl~~l~~~t~~~t~~~~aKt~s~~hlkq~v~ 77 (224)
T KOG1659|consen 11 KTRFPPARIKKIMQSDEDIGKVAQAVPVIISRALELFLESLLQKTLEITRSRGAKTVSSSHLKQAVE 77 (224)
T ss_pred hccCCHHHHHHHHhhhhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhcCccccCHHHHHHHHh
Confidence 4469999999999764 36789999999999999999999999999999999999999999999985
No 61
>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=97.22 E-value=0.0028 Score=41.72 Aligned_cols=66 Identities=18% Similarity=0.252 Sum_probs=50.7
Q ss_pred CcchHHHHHHHHhcCc-cccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCc-eecHHHHHHHHHhc
Q 034139 29 GITKPAIRRLARRGGV-KRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRK-TVTAMDVVYALKRQ 94 (103)
Q Consensus 29 ~ip~a~IkRiar~~G~-~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~Rk-TI~~~DV~~Alkr~ 94 (103)
.||++.|++|+...-- ..+|+.+.-.+.-...-|+.||++.|...++.-+-. .|++.++..|.+++
T Consensus 23 ~~~k~~ikkli~~~~~~qsv~~~v~i~v~g~aKvFVGEiVE~A~~Vq~~~~~~~pl~P~hlreA~rrL 90 (90)
T PF04719_consen 23 SFNKAAIKKLINQVLGNQSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGETGPLQPDHLREAYRRL 90 (90)
T ss_dssp ---HHHHHHHHHHHHS-S---HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SS--HHHHHHHHHHH
T ss_pred cCCHHHHHHHHHHHcCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcHHHHHHHHhC
Confidence 5899999999998754 789999999999999999999999999999865544 69999999998874
No 62
>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=96.99 E-value=0.0055 Score=36.45 Aligned_cols=49 Identities=14% Similarity=0.203 Sum_probs=45.2
Q ss_pred cCcchHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 034139 28 QGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEH 76 (103)
Q Consensus 28 ~~ip~a~IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~h 76 (103)
+.||.+-+.-++++.|...-.+.+..-+.=+..+|+.+|+.||..||+.
T Consensus 1 P~IPD~v~~~yL~~~G~~~~D~rv~RLvSLaaQKFisdI~~dA~q~~k~ 49 (51)
T PF03540_consen 1 PTIPDEVTDYYLERSGFQTSDPRVKRLVSLAAQKFISDIANDAMQYCKI 49 (51)
T ss_pred CCCCHHHHHHHHHHCCCCCCCHhHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3589999999999999998888999999999999999999999999874
No 63
>KOG1744 consensus Histone H2B [Chromatin structure and dynamics]
Probab=96.94 E-value=0.0042 Score=43.30 Aligned_cols=60 Identities=12% Similarity=0.155 Sum_probs=51.6
Q ss_pred HHHHHHhcCc-cccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhc
Q 034139 35 IRRLARRGGV-KRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 94 (103)
Q Consensus 35 IkRiar~~G~-~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~ 94 (103)
|.|+++..-. .-||..+...+..++.++++.|+.+|..+++..+|-||+..+|..|.+.+
T Consensus 43 v~kvlk~Vhpd~gis~~a~~vmnsf~ndife~iA~ea~rla~y~krstisSreiqta~rLl 103 (127)
T KOG1744|consen 43 VYKVLKQVHPDLGISSKAMGVMNSFVNDIFERIASEAGRLAHYNKRSTISSREIQTAVRLL 103 (127)
T ss_pred hhhhhhcccCCCCcCHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCcccHHHHHHHHHHh
Confidence 4556666532 34899999999999999999999999999999999999999999998754
No 64
>COG5247 BUR6 Class 2 transcription repressor NC2, alpha subunit (DRAP1 homolog) [Transcription]
Probab=96.87 E-value=0.0086 Score=40.50 Aligned_cols=67 Identities=9% Similarity=0.134 Sum_probs=57.6
Q ss_pred cccCcchHHHHHHHHhc-CccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHH
Q 034139 26 NIQGITKPAIRRLARRG-GVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALK 92 (103)
Q Consensus 26 ~~~~ip~a~IkRiar~~-G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alk 92 (103)
...-+|.+-|++|+.-- .+..|+...-.....++|.|+.+|++.+.+.|+-..-|.+|.+-+..|..
T Consensus 20 ~ktrFP~ar~KkIMQ~deDiGKV~q~tPVIaskalE~Fl~~iv~~s~k~aR~~~skR~t~e~lk~a~~ 87 (113)
T COG5247 20 KKTRFPIARLKKIMQLDEDIGKVGQSTPVIASKALEMFLTEIVGLSLKEARKKSSKRMTSEFLKRATE 87 (113)
T ss_pred hhhcCCHHHHHHHHHhhhhhhhhhhcchHHHHHHHHHHHHHHHHHHHHHHHhccchhhHHHHHHHHHh
Confidence 34469999999999643 35678888888899999999999999999999988888899999988874
No 65
>PF13654 AAA_32: AAA domain; PDB: 3K1J_B.
Probab=95.94 E-value=0.045 Score=45.68 Aligned_cols=60 Identities=17% Similarity=0.252 Sum_probs=48.7
Q ss_pred HHHHHHhcCccccchHHHHHHHHHHHH-----------HHHHHHHHHHHHHhhCCCceecHHHHHHHHHhc
Q 034139 35 IRRLARRGGVKRISGLIYEETRGVLKI-----------FLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 94 (103)
Q Consensus 35 IkRiar~~G~~riS~da~~~l~~~~e~-----------~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~ 94 (103)
|..++++.+...++.+|+.+|.+.... .+.+|+.+|..+|+..+.++|+.+||..|++..
T Consensus 436 i~~~~~~~~L~~~~~~Av~~li~~~~R~~q~kLsl~~~~l~~ll~EA~~~A~~~~~~~I~~~~V~~Ai~~r 506 (509)
T PF13654_consen 436 IASICQKEGLPPFDRSAVARLIEYSARLDQDKLSLRFSWLADLLREANYWARKEGAKVITAEHVEQAIEER 506 (509)
T ss_dssp HHHHHHHHSS--BBHHHHHHHHHHHHHCC-SEEE--HHHHHHHHHHHHHHHHHCT-SSB-HHHHHHHHHH-
T ss_pred HHHHHHhCCCCCCCHHHHHHHHHHHHHHhCCEeCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHcc
Confidence 667778888999999999999987543 688999999999999999999999999999854
No 66
>KOG3219 consensus Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=95.87 E-value=0.013 Score=43.48 Aligned_cols=68 Identities=18% Similarity=0.252 Sum_probs=59.9
Q ss_pred cCcchHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCc-eecHHHHHHHHHhcC
Q 034139 28 QGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRK-TVTAMDVVYALKRQG 95 (103)
Q Consensus 28 ~~ip~a~IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~Rk-TI~~~DV~~Alkr~g 95 (103)
..||++.|++|+..+.-.-|++.+.-++.-+..-|+-+|+++|...++.-+-. -|.+.+|..|.+|+.
T Consensus 111 s~f~Ka~iKkL~~~itg~~v~~nv~Ia~~GiaKvFVGEvVEeAl~V~~~~~e~~PLqP~HIREA~rrL~ 179 (195)
T KOG3219|consen 111 SAFPKAQIKKLMSSITGQSVSENVAIAMAGIAKVFVGEVVEEALDVREEWGESGPLQPKHIREAYRRLK 179 (195)
T ss_pred hcCCHHHHHHHHHHHhCCccCcceeeeecchhhHhHHHHHHHHHHHHHHhccCCCCCcHHHHHHHHHHH
Confidence 36999999999999855559999999999999999999999999999876553 499999999999874
No 67
>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=95.61 E-value=0.084 Score=39.03 Aligned_cols=60 Identities=22% Similarity=0.317 Sum_probs=50.4
Q ss_pred HHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhC------CCceecHHHHHHHHHhc
Q 034139 35 IRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHA------RRKTVTAMDVVYALKRQ 94 (103)
Q Consensus 35 IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha------~RkTI~~~DV~~Alkr~ 94 (103)
|.+|+...|+..+++++++.|..+++.|+..|+..++.+|+|- .-.++..+||..-|+.+
T Consensus 54 ~~~i~~~~g~~~~~~d~~~lis~a~e~rlr~li~k~~~~s~hR~~~~~~~~r~~~~sdvr~qL~~l 119 (212)
T cd08045 54 IRKIAKKHGLKEVDEDVLDLISLALEERLRNLLEKLIEVSEHRVDSEKEDERYEITSDVRKQLRFL 119 (212)
T ss_pred HHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCceeecchHHHHHHHH
Confidence 5677777788889999999999999999999999999999984 33566778888777654
No 68
>COG5162 Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=95.07 E-value=0.24 Score=36.29 Aligned_cols=71 Identities=17% Similarity=0.218 Sum_probs=60.6
Q ss_pred ccCcchHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhh--------C---------------------
Q 034139 27 IQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEH--------A--------------------- 77 (103)
Q Consensus 27 ~~~ip~a~IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~h--------a--------------------- 77 (103)
-+.||.+.+.=.+...|.......+...|.-....|+.+|+.||-.|.+- +
T Consensus 86 ~PliPd~v~DYyl~k~Gf~~~D~rvKkLl~L~aqKFvsDiA~dayqYsrIr~~~sna~~t~~~a~~f~~gg~~~i~~~~~ 165 (197)
T COG5162 86 TPLIPDSVTDYYLEKAGFVTSDQRVKKLLSLLAQKFVSDIAVDAYQYSRIRQGSSNAKATAQKAKRFAKGGASGIGSSGR 165 (197)
T ss_pred CCCccHHHHHHHHHhcCceeccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccchhhHHHHHHHHhccccccccccc
Confidence 45789999999999999988888888999999999999999999988751 1
Q ss_pred ----CCceecHHHHHHHHHhcCCc
Q 034139 78 ----RRKTVTAMDVVYALKRQGRT 97 (103)
Q Consensus 78 ----~RkTI~~~DV~~Alkr~g~~ 97 (103)
++.++|..|+..||...|..
T Consensus 166 ~~dr~K~vltv~DLs~Al~EyGin 189 (197)
T COG5162 166 RGDRKKPVLTVVDLSKALEEYGIN 189 (197)
T ss_pred ccccCCceeeehHHHHHHHHhccc
Confidence 45579999999999987754
No 69
>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=94.84 E-value=0.047 Score=41.56 Aligned_cols=66 Identities=21% Similarity=0.251 Sum_probs=33.2
Q ss_pred CcchHH----HHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCc------eecHHHHHHHHHhc
Q 034139 29 GITKPA----IRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRK------TVTAMDVVYALKRQ 94 (103)
Q Consensus 29 ~ip~a~----IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~Rk------TI~~~DV~~Alkr~ 94 (103)
.|...+ |.+|++..|...+.+|+++.|.-++++++..|+++++..|+|--.- +...+||...|+.+
T Consensus 43 fL~~~~L~~~i~~i~~~~g~~~~~~d~l~llS~A~e~rLr~lie~~~~~s~hR~~~~~~~~~~~~~sdv~~qlr~l 118 (264)
T PF05236_consen 43 FLNPSPLQKRIQKIAKKHGLKSVDEDVLELLSLATEERLRNLIEKAIVLSRHRRDSSKSDPRYEIRSDVRKQLRFL 118 (264)
T ss_dssp -S-HHHHHHHHHHHHHCTT--EE-TCHHHHHHHHHHHHHHHHHHHHH-----------------------------
T ss_pred ccCHHHHHHHHHHHHHHcCCcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccCCCcccccchHHHHHHHHH
Confidence 455554 5667777788899999999999999999999999999999983221 23466777666543
No 70
>KOG3901 consensus Transcription initiation factor IID subunit [Transcription]
Probab=94.33 E-value=0.17 Score=34.29 Aligned_cols=56 Identities=13% Similarity=0.163 Sum_probs=41.1
Q ss_pred HHHHHhcC-ccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhc
Q 034139 36 RRLARRGG-VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 94 (103)
Q Consensus 36 kRiar~~G-~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~ 94 (103)
+.++=-.| ...=-++.++.|.+.+-+|+.+++..|.... +|-.+..||+.++|++-
T Consensus 16 ~~mmYgfGDd~nP~~~tv~~Le~iV~~Yi~elt~~a~~~g---~rgk~~veD~~f~lRkD 72 (109)
T KOG3901|consen 16 RSMMYGFGDDVNPYPETVDLLEDIVLEYITELTHAAMEIG---KRGKVKVEDFKFLLRKD 72 (109)
T ss_pred HHHHHhcCCCCCccHhHHHHHHHHHHHHHHHHHHHHHHhc---ccCceeHHHHHHHHHhC
Confidence 33333344 2333458889999999999999977776665 66669999999999863
No 71
>COG5248 TAF19 Transcription initiation factor TFIID, subunit TAF13 [Transcription]
Probab=94.31 E-value=0.35 Score=33.24 Aligned_cols=59 Identities=19% Similarity=0.173 Sum_probs=48.1
Q ss_pred HHHHHHHhcC-ccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhc
Q 034139 34 AIRRLARRGG-VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 94 (103)
Q Consensus 34 ~IkRiar~~G-~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~ 94 (103)
.|+.++=-.| +..=-.|.++.|-+.+..|+.+++-.|...|+ .|-.+..+|..+||++-
T Consensus 14 DikslmYayGDvv~P~~dt~~~L~e~V~dY~~~~ctna~~~Aq--~rnK~k~eDfkfaLr~D 73 (126)
T COG5248 14 DIKSLMYAYGDVVAPRYDTAEALHEYVLDYMSILCTNAHNMAQ--VRNKTKTEDFKFALRRD 73 (126)
T ss_pred HHHHHHHHhCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHH--hcccchHHHHHHHHhhC
Confidence 4666776666 33344688899999999999999999999998 56679999999999864
No 72
>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=93.04 E-value=0.45 Score=39.69 Aligned_cols=62 Identities=16% Similarity=0.167 Sum_probs=45.2
Q ss_pred cchHHHHHHHHh----cCccccchHHHHHHHHHHH--HHHHHHHHHHHHHHhhCCCceecHHHHHHHHH
Q 034139 30 ITKPAIRRLARR----GGVKRISGLIYEETRGVLK--IFLENVIRDAVTYTEHARRKTVTAMDVVYALK 92 (103)
Q Consensus 30 ip~a~IkRiar~----~G~~riS~da~~~l~~~~e--~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alk 92 (103)
++...+..|++. .++ .+++++++.|..... ..+..+++.|..+|...+|++|+.+||.+++.
T Consensus 263 L~~eei~~Il~~~a~k~~i-~is~~al~~I~~y~~n~Rel~nll~~Aa~~A~~~~~~~It~~dI~~vl~ 330 (531)
T TIGR02902 263 LLDEEIKEIAKNAAEKIGI-NLEKHALELIVKYASNGREAVNIVQLAAGIALGEGRKRILAEDIEWVAE 330 (531)
T ss_pred CCHHHHHHHHHHHHHHcCC-CcCHHHHHHHHHhhhhHHHHHHHHHHHHHHHhhCCCcEEcHHHHHHHhC
Confidence 344445555544 454 589999988765533 34567778888888888999999999999996
No 73
>COG1067 LonB Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]
Probab=92.88 E-value=0.53 Score=40.61 Aligned_cols=59 Identities=31% Similarity=0.326 Sum_probs=50.1
Q ss_pred HHHHHHhcCccccchHHHHHHHHHHHHH-------------HHHHHHHHHHHHhhCCCceecHHHHHHHHHh
Q 034139 35 IRRLARRGGVKRISGLIYEETRGVLKIF-------------LENVIRDAVTYTEHARRKTVTAMDVVYALKR 93 (103)
Q Consensus 35 IkRiar~~G~~riS~da~~~l~~~~e~~-------------~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr 93 (103)
++.+.+......++.+|++.|-..+..+ +..+++.|..+|.-++++-|+++||+.|++.
T Consensus 327 ~q~v~~d~~ip~~~~~Av~~li~~a~R~Ag~~~~Ltl~~rdl~~lv~~A~~ia~~~~~~~I~ae~Ve~a~~~ 398 (647)
T COG1067 327 VQELARDGNIPHLDKDAVEELIREAARRAGDQNKLTLRLRDLGNLVREAGDIAVSEGRKLITAEDVEEALQK 398 (647)
T ss_pred HHHHHhcCCCCCCCHHHHHHHHHHHHHhccccceeccCHHHHHHHHHHhhHHHhcCCcccCcHHHHHHHHHh
Confidence 4455566678889999999998887765 5678899999999999999999999999986
No 74
>TIGR00764 lon_rel lon-related putative ATP-dependent protease. Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein.
Probab=92.85 E-value=0.68 Score=39.41 Aligned_cols=59 Identities=20% Similarity=0.177 Sum_probs=46.7
Q ss_pred HHHHHHhcC-ccccchHHHHHHHHHHH-------------HHHHHHHHHHHHHHhhCCCceecHHHHHHHHHh
Q 034139 35 IRRLARRGG-VKRISGLIYEETRGVLK-------------IFLENVIRDAVTYTEHARRKTVTAMDVVYALKR 93 (103)
Q Consensus 35 IkRiar~~G-~~riS~da~~~l~~~~e-------------~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr 93 (103)
|.+.+++.| ...++++++++|.+... .-+..|++.|..+|+..+..+|+.+||..|++.
T Consensus 318 i~~~~~r~G~l~~~s~~Av~~Li~~~~R~ag~r~~lsl~~R~L~~llR~A~~iA~~~~~~~I~~ehV~~Ai~~ 390 (608)
T TIGR00764 318 VAQEVKKDGRIPHFTRDAVEEIVREAQRRAGRKDHLTLRLRELGGLVRAAGDIAKSSGKVYVTAEHVLKAKKL 390 (608)
T ss_pred HHHHHHHhCCCCcCCHHHHHHHHHHHHHHHhcccccCCCHHHHHHHHHHHHHHHHhcCCceecHHHHHHHHHH
Confidence 344445554 56899999999986533 567889999999999999999999999998773
No 75
>PRK07452 DNA polymerase III subunit delta; Validated
Probab=92.80 E-value=0.38 Score=36.88 Aligned_cols=61 Identities=15% Similarity=0.084 Sum_probs=51.9
Q ss_pred HHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhh--CCCceecHHHHHHHHHhcCC
Q 034139 35 IRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEH--ARRKTVTAMDVVYALKRQGR 96 (103)
Q Consensus 35 IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~h--a~RkTI~~~DV~~Alkr~g~ 96 (103)
|+..+++.|.. |+++|.+.|.+.+..=+..+.++..+.+-+ .+..+||.+||...+-....
T Consensus 139 i~~~~~~~g~~-i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~~It~~~V~~~v~~~~~ 201 (326)
T PRK07452 139 VERTAQELGVK-LTPEAAELLAEAVGNDSRRLYNELEKLALYAENSTKPISAEEVKALVSNTTQ 201 (326)
T ss_pred HHHHHHHcCCC-CCHHHHHHHHHHhCccHHHHHHHHHHHHHhccCCCCccCHHHHHHHhccCcC
Confidence 66777788875 999999999999999999999999999988 45788999999998754433
No 76
>KOG1658 consensus DNA polymerase epsilon, subunit C [Replication, recombination and repair]
Probab=92.25 E-value=0.098 Score=37.72 Aligned_cols=70 Identities=13% Similarity=0.154 Sum_probs=58.9
Q ss_pred cccCcchHHHHHHHHhcC-ccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhcC
Q 034139 26 NIQGITKPAIRRLARRGG-VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQG 95 (103)
Q Consensus 26 ~~~~ip~a~IkRiar~~G-~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~g 95 (103)
+...+|.+.|+.+++.-- ..=...++...+....+-|+.++..++..+++-.+|||+...|+..|++.-.
T Consensus 56 ~l~rLpL~rik~vvkl~pdl~l~~dea~~l~a~aaelfi~~Ln~~~~~~~q~~k~kt~qr~d~D~ai~~~d 126 (162)
T KOG1658|consen 56 SLSRLPLARIKQVVKLDPDLTLLNDEASQLIAKAAELFIQELNDVAYTTAQLRKRKTEQRRDYDTAIEAVD 126 (162)
T ss_pred hhhhccHHHHHhhccCCcchhhhhhHHHHHHHHHHHHHHHHHHhccchhHHHHHhhhhhhhcccccccchH
Confidence 445788999999887654 4445677888889999999999999999999999999999999999886543
No 77
>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=91.35 E-value=0.58 Score=26.79 Aligned_cols=43 Identities=16% Similarity=0.146 Sum_probs=26.8
Q ss_pred cchHHHHHHHHHHHHHHHHHHH-HHHHHHhhCCCceecHHHHHHH
Q 034139 47 ISGLIYEETRGVLKIFLENVIR-DAVTYTEHARRKTVTAMDVVYA 90 (103)
Q Consensus 47 iS~da~~~l~~~~e~~~~~I~~-dA~~~a~ha~RkTI~~~DV~~A 90 (103)
+++||...|.++ =.|+..-++ .+..||+..|...||.++|..|
T Consensus 1 W~~eA~~~L~~i-P~fvR~~~r~~~E~~Ar~~G~~~IT~e~v~~A 44 (45)
T PF08369_consen 1 WTDEAEARLDRI-PFFVRKKLRDAAEKYARERGYDEITVEVVDAA 44 (45)
T ss_dssp E-HHHHHHHCTS--HHHHHHHHHHHHHHHHHCT-SEE-HHHHHHH
T ss_pred CCHHHHHHHHHC-CHHHHHHHHHHHHHHHHHcCCCeECHHHHHhh
Confidence 355666666654 344544444 4557999999999999998765
No 78
>PRK06585 holA DNA polymerase III subunit delta; Reviewed
Probab=91.29 E-value=0.66 Score=35.85 Aligned_cols=59 Identities=14% Similarity=-0.022 Sum_probs=49.7
Q ss_pred HHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCC-CceecHHHHHHHHHhc
Q 034139 35 IRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHAR-RKTVTAMDVVYALKRQ 94 (103)
Q Consensus 35 IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~-RkTI~~~DV~~Alkr~ 94 (103)
|...++..|.. |+++|++.|.+.+..=+..+.++..+.+-+.+ ..+||.+||...+-..
T Consensus 151 i~~~~~~~g~~-i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~It~edV~~lv~~~ 210 (343)
T PRK06585 151 IDDELAEAGLR-ITPDARALLVALLGGDRLASRNEIEKLALYAHGKGEITLDDVRAVVGDA 210 (343)
T ss_pred HHHHHHHCCCC-CCHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHhCCc
Confidence 67777888874 99999999999999988888888888888754 5689999999887654
No 79
>TIGR01128 holA DNA polymerase III, delta subunit. subunit around DNA forming a DNA sliding clamp.
Probab=90.08 E-value=1.5 Score=32.71 Aligned_cols=59 Identities=17% Similarity=0.094 Sum_probs=47.0
Q ss_pred HHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhc
Q 034139 35 IRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 94 (103)
Q Consensus 35 IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~ 94 (103)
|+..+++.|+ .+++++.+.|.+.+..=+..+..+..+++-..+-++||.+||...+-..
T Consensus 120 i~~~~~~~g~-~i~~~a~~~l~~~~~~d~~~l~~el~KL~~~~~~~~It~e~I~~~~~~~ 178 (302)
T TIGR01128 120 IQARLKKLGL-RIDPDAVQLLAELVEGNLLAIAQELEKLALYAPDGKITLEDVEEAVSDS 178 (302)
T ss_pred HHHHHHHcCC-CCCHHHHHHHHHHhCcHHHHHHHHHHHHHhhCCCCCCCHHHHHHHHhhh
Confidence 5555666676 5999999999999988778887888887777665689999999887643
No 80
>PRK05574 holA DNA polymerase III subunit delta; Reviewed
Probab=89.97 E-value=1.4 Score=33.49 Aligned_cols=65 Identities=12% Similarity=0.093 Sum_probs=50.2
Q ss_pred HHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhcC-Ccccc
Q 034139 35 IRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQG-RTLYG 100 (103)
Q Consensus 35 IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~g-~~lYg 100 (103)
|+..+++.|+ .|++++.+.|.+.+..=+..+..+..+++-..+-+.||.+||...+-... ..+|.
T Consensus 155 i~~~~~~~g~-~i~~~a~~~L~~~~~~d~~~l~~El~KL~l~~~~~~It~~~I~~~i~~~~~~~~f~ 220 (340)
T PRK05574 155 IQQRLKQQGL-QIDAAALQLLAERVEGNLLALAQELEKLALLYPDGKITLEDVEEAVPDSARFDVFD 220 (340)
T ss_pred HHHHHHHcCC-CCCHHHHHHHHHHhCchHHHHHHHHHHHHhhcCCCCCCHHHHHHHHhhhhcCCHHH
Confidence 5666677787 49999999999999988888888888888776333399999998876543 34443
No 81
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=89.97 E-value=1.3 Score=34.48 Aligned_cols=65 Identities=17% Similarity=0.165 Sum_probs=47.9
Q ss_pred cchHHHHHHHHhc---C--ccccchHHHHHHHHHHH------HHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhc
Q 034139 30 ITKPAIRRLARRG---G--VKRISGLIYEETRGVLK------IFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 94 (103)
Q Consensus 30 ip~a~IkRiar~~---G--~~riS~da~~~l~~~~e------~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~ 94 (103)
++...+..|++.- + ..-+++++.+.+.+.+. .++-+++..|...|...++.+|+.+||..|+...
T Consensus 207 y~~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~a~~~a~~~~~~~I~~~~v~~a~~~~ 282 (394)
T PRK00411 207 YTADEIFDILKDRVEEGFYPGVVDDEVLDLIADLTAREHGDARVAIDLLRRAGLIAEREGSRKVTEEDVRKAYEKS 282 (394)
T ss_pred CCHHHHHHHHHHHHHhhcccCCCCHhHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHH
Confidence 4444455554321 2 23589999999988773 3455778888889988899999999999999865
No 82
>PRK08487 DNA polymerase III subunit delta; Validated
Probab=89.66 E-value=1.3 Score=34.29 Aligned_cols=57 Identities=11% Similarity=-0.010 Sum_probs=49.5
Q ss_pred HHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhc
Q 034139 35 IRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 94 (103)
Q Consensus 35 IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~ 94 (103)
|...++..|.. |+++|.+.|.+.+..=+..+..+..+.+-+.+ +||.+||....-..
T Consensus 144 i~~~~~~~g~~-i~~~a~~~L~~~~g~dl~~l~~ELeKL~ly~~--~It~edV~~~v~~~ 200 (328)
T PRK08487 144 LQERAKELGLD-IDQNALNHLYFIHNEDLALAANELEKLAILNE--PITLKDIQELVFGL 200 (328)
T ss_pred HHHHHHHhCCC-CCHHHHHHHHHHhCcHHHHHHHHHHHHHHhcC--CCCHHHHHHHhccc
Confidence 67777888875 99999999999999999999999999888866 69999999987543
No 83
>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=89.63 E-value=1.6 Score=32.08 Aligned_cols=69 Identities=7% Similarity=0.101 Sum_probs=51.6
Q ss_pred ccCcchHHHHHHH----HhcCc---cccchHHHHHHHHHHHH---HHHHHHHHHHHHHhhCCCceecHHHHHHHHHhcC
Q 034139 27 IQGITKPAIRRLA----RRGGV---KRISGLIYEETRGVLKI---FLENVIRDAVTYTEHARRKTVTAMDVVYALKRQG 95 (103)
Q Consensus 27 ~~~ip~a~IkRia----r~~G~---~riS~da~~~l~~~~e~---~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~g 95 (103)
+..++...+..++ +..|. ..+++++++.|.+...= ++..++..+...+--.+.++|+.+||..+++...
T Consensus 189 l~~l~~~e~~~~l~~~l~~~g~~~~~~~~~~~~~~i~~~s~G~p~~i~~l~~~~~~~a~~~~~~~i~~~~v~~~~~~~~ 267 (269)
T TIGR03015 189 LGPLDREETREYIEHRLERAGNRDAPVFSEGAFDAIHRFSRGIPRLINILCDRLLLSAFLEEKREIGGEEVREVIAEID 267 (269)
T ss_pred CCCCCHHHHHHHHHHHHHHcCCCCCCCcCHHHHHHHHHHcCCcccHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhh
Confidence 4456666655544 34442 46999999999988664 6888888888887777888999999999998643
No 84
>PRK05907 hypothetical protein; Provisional
Probab=89.62 E-value=1.2 Score=34.94 Aligned_cols=59 Identities=10% Similarity=0.076 Sum_probs=49.8
Q ss_pred HHHHHHhcCccccchHHHHHHHHHH-HHHHHHHHHHHHHHHhh-CCCceecHHHHHHHHHhc
Q 034139 35 IRRLARRGGVKRISGLIYEETRGVL-KIFLENVIRDAVTYTEH-ARRKTVTAMDVVYALKRQ 94 (103)
Q Consensus 35 IkRiar~~G~~riS~da~~~l~~~~-e~~~~~I~~dA~~~a~h-a~RkTI~~~DV~~Alkr~ 94 (103)
|...+++.|. .++++|.+.+.+.+ +.=+..+.++..+.+-+ ..+.+||.+||...+-..
T Consensus 143 i~~~~~~~g~-~i~~~a~~~L~~~~~~~nL~~l~~EleKL~ly~g~~~~It~e~V~~lv~~s 203 (311)
T PRK05907 143 LIQRAKELGI-SCSLGLASLFVSKFPQTGLFEILSEFQKLLCQMGKKESLEASDIQSFVVKK 203 (311)
T ss_pred HHHHHHHcCC-CcCHHHHHHHHHHccCCCHHHHHHHHHHHHHhcCCCCeECHHHHHHHhcCc
Confidence 6666777786 59999999999988 68888999999999988 558899999999887543
No 85
>PRK07914 hypothetical protein; Reviewed
Probab=89.57 E-value=1.1 Score=34.66 Aligned_cols=58 Identities=14% Similarity=0.036 Sum_probs=48.8
Q ss_pred HHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhc
Q 034139 35 IRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 94 (103)
Q Consensus 35 IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~ 94 (103)
|...+++.|.. |+++|.+.|.+.+..=+..+.++..+.+-+.+ .+||.+||...+...
T Consensus 137 i~~~a~~~g~~-i~~~A~~~L~~~~g~dl~~l~~EleKL~~~~~-~~It~e~V~~~v~~~ 194 (320)
T PRK07914 137 VRKEFRSLRVK-VDDDTVTALLDAVGSDLRELASACSQLVADTG-GAVDAAAVRRYHSGK 194 (320)
T ss_pred HHHHHHHcCCC-CCHHHHHHHHHHHCccHHHHHHHHHHHhcCCC-CCcCHHHHHHHcCCC
Confidence 77777888875 99999999999998888888888888876555 579999999987644
No 86
>COG5624 TAF61 Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=88.81 E-value=0.11 Score=42.70 Aligned_cols=96 Identities=21% Similarity=0.207 Sum_probs=74.3
Q ss_pred CCccCCCCCCcccchhhccc-ccCcchHHHHHHHHhc--CccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceec
Q 034139 7 GGKGLGKGGAKRHRKVLRDN-IQGITKPAIRRLARRG--GVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVT 83 (103)
Q Consensus 7 ~~~~~~~~g~kr~~k~~r~~-~~~ip~a~IkRiar~~--G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~ 83 (103)
+..|+.-+|--|---+-+|+ .+...+..++.+.+-+ +-+.|..|+-+.|.+....|.+.+..=+..+|.|-+-+||.
T Consensus 360 ~~~gl~Tpg~~k~p~ye~D~~~Rl~skrkL~el~~~~vd~eekie~eveelll~~ad~fve~vt~FsCrlakhrkSdtle 439 (505)
T COG5624 360 PDGGLATPGRDKGPLYERDDLWRLDSKRKLEELQHGGVDEEEKIENEVEELLLSRADGFVEPVTEFSCRLAKHRKSDTLE 439 (505)
T ss_pred CCcccCCCcccCCCchhcchhhhhhhhhhHHHHHhhccCcceeccchHHHHHHhhhcccccccchheeEeeccCCCCcee
Confidence 33445555533332444566 5677888888888765 34788899999999999999999999999999999999999
Q ss_pred HHHHHHHHHhc-CCcccccC
Q 034139 84 AMDVVYALKRQ-GRTLYGFG 102 (103)
Q Consensus 84 ~~DV~~Alkr~-g~~lYgf~ 102 (103)
+.|+.+-|++. ...+=||.
T Consensus 440 vrD~qlhlErnwnIr~pGf~ 459 (505)
T COG5624 440 VRDGQLHLERNWNIRCPGFV 459 (505)
T ss_pred eccceeeeccccceecCcch
Confidence 99999999987 55666774
No 87
>PRK05629 hypothetical protein; Validated
Probab=87.58 E-value=2.2 Score=32.86 Aligned_cols=58 Identities=12% Similarity=0.019 Sum_probs=47.9
Q ss_pred HHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhc
Q 034139 35 IRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 94 (103)
Q Consensus 35 IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~ 94 (103)
|...+++.|.. |+++|.+.|.+.+..=+..+.++..+.+-+.+ .+||.+||...+-..
T Consensus 135 i~~~~~~~g~~-i~~~A~~~L~~~~g~dl~~l~~EleKL~~~~~-~~It~e~V~~~v~~~ 192 (318)
T PRK05629 135 VTQEFKNHGVR-PTPDVVHALLEGVGSDLRELASAISQLVEDTQ-GNVTVEKVRAYYVGV 192 (318)
T ss_pred HHHHHHHcCCC-CCHHHHHHHHHHHCccHHHHHHHHHHHHhcCC-CCcCHHHHHHHhCCC
Confidence 67777888875 99999999999998888888888888776654 579999999887544
No 88
>cd08313 Death_TNFR1 Death domain of Tumor Necrosis Factor Receptor 1. Death Domain (DD) found in tumor necrosis factor receptor-1 (TNFR-1). TNFR-1 has many names including TNFRSF1A, CD120a, p55, p60, and TNFR60. It activates two major intracellular signaling pathways that lead to the activation of the transcription factor NF-kB and the induction of cell death. Upon binding of its ligand TNF, TNFR-1 trimerizes which leads to the recruitment of an adaptor protein named TNFR-associated death domain protein (TRADD) through a DD/DD interaction. Mutations in the TNFRSF1A gene causes TNFR-associated periodic syndrome (TRAPS), a rare disorder characterized recurrent fever, myalgia, abdominal pain, conjunctivitis and skin eruptions. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation a
Probab=86.69 E-value=4.9 Score=25.64 Aligned_cols=66 Identities=14% Similarity=0.095 Sum_probs=49.8
Q ss_pred cCcchHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhcCC
Q 034139 28 QGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGR 96 (103)
Q Consensus 28 ~~ip~a~IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~g~ 96 (103)
..+|...+++++|+.| +|+.-++.+...-...-+++.+-.....+..|+..-+.+++..||+..+.
T Consensus 7 d~v~~~~wk~~~R~LG---lse~~Id~ie~~~~~~~Eq~yqmL~~W~~~~g~~~At~~~L~~aLr~~~l 72 (80)
T cd08313 7 DEVPPRRWKEFVRRLG---LSDNEIERVELDHRRCRDAQYQMLKVWKERGPRPYATLQHLLSVLRDMEL 72 (80)
T ss_pred HhCCHHHHHHHHHHcC---CCHHHHHHHHHhCCChHHHHHHHHHHHHHhcCCCcchHHHHHHHHHHcCc
Confidence 4689999999999999 56777777665544444555666667777777777888999999987664
No 89
>PF12767 SAGA-Tad1: Transcriptional regulator of RNA polII, SAGA, subunit; InterPro: IPR024738 The yeast Spt-Ada-Gcn5-Acetyl (SAGA) transferase complex is a multifunctional coactivator involved in multiple cellular processes [], including regulation of transcription by RNA polymerase II [, ]. It is formed of five major modular subunits and shows a high degree of structural conservation to human TFTC and STAGA []. This entry represents Ada1 (known as Tada1 in higher eukaryotes), one of the subunits that constitute the SAGA core. It also functions as a component of the SALSA and SLIK complexes. ; GO: 0070461 SAGA-type complex
Probab=86.35 E-value=2 Score=32.42 Aligned_cols=40 Identities=18% Similarity=0.274 Sum_probs=35.0
Q ss_pred HHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHH
Q 034139 35 IRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYT 74 (103)
Q Consensus 35 IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a 74 (103)
+..+|...|..-||.+|++.|.-++|.|+++|+.-++..+
T Consensus 212 m~~ia~e~GL~gvs~~~a~ll~~ale~~LK~lI~s~l~~~ 251 (252)
T PF12767_consen 212 MEQIAWEHGLGGVSDDCANLLNLALEVHLKNLIKSCLDLV 251 (252)
T ss_pred HHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 5567777899899999999999999999999999887653
No 90
>PF09123 DUF1931: Domain of unknown function (DUF1931); InterPro: IPR015207 This entry represents a set of hypothetical bacterial proteins containing a core of six alpha-helices, where one central helix is surrounded by the other five. The exact function of this family has not, as yet, been determined []. ; PDB: 1WWS_A 1WWI_A 1R4V_A.
Probab=85.58 E-value=0.64 Score=32.89 Aligned_cols=54 Identities=13% Similarity=0.094 Sum_probs=42.5
Q ss_pred HHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHH
Q 034139 35 IRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVV 88 (103)
Q Consensus 35 IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~ 88 (103)
++++.|.++--.|.++=.+.+.++++.-+.+++.-|...|...||-+|...|+-
T Consensus 1 fe~lFR~aa~LdvdK~d~~r~~d~V~~Kl~DLl~va~~~Ak~ngRdvI~~~DLP 54 (138)
T PF09123_consen 1 FERLFRKAAGLDVDKNDAKRYSDFVEKKLYDLLLVAQENAKANGRDVIEPRDLP 54 (138)
T ss_dssp HHHHHHHHHS----HHHHHHHHHHHHHHHHHCCCCHHHHHHHTT-SEE-GGGS-
T ss_pred ChHHHHHHhccCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeeccccCC
Confidence 467888876566889999999999999999999999999999999999988863
No 91
>COG1466 HolA DNA polymerase III, delta subunit [DNA replication, recombination, and repair]
Probab=84.71 E-value=3.6 Score=32.09 Aligned_cols=59 Identities=19% Similarity=0.111 Sum_probs=51.1
Q ss_pred HHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhc
Q 034139 35 IRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 94 (103)
Q Consensus 35 IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~ 94 (103)
|...++..|. +|+++|.+.|.+.++.=+..|.++..+.+-..+=++|+.+||..++-..
T Consensus 149 i~~~~~~~~l-~i~~~a~~~L~~~~~~nl~~i~~Ei~KL~l~~~~~~I~~~~V~~~v~~~ 207 (334)
T COG1466 149 IKKRAKELGL-KIDQEAIQLLLEALGGNLLAIAQEIEKLALYAGDKEITLEDVEEVVSDV 207 (334)
T ss_pred HHHHHHHcCC-CCCHHHHHHHHHHhCCcHHHHHHHHHHHHHhCCCCcCCHHHHHHHHhcc
Confidence 5556667776 6999999999999999999999999999988777799999999998654
No 92
>PRK13765 ATP-dependent protease Lon; Provisional
Probab=84.62 E-value=3.8 Score=35.31 Aligned_cols=50 Identities=22% Similarity=0.061 Sum_probs=41.4
Q ss_pred ccccchHHHHHHHHHHH-------------HHHHHHHHHHHHHHhhCCCceecHHHHHHHHHh
Q 034139 44 VKRISGLIYEETRGVLK-------------IFLENVIRDAVTYTEHARRKTVTAMDVVYALKR 93 (103)
Q Consensus 44 ~~riS~da~~~l~~~~e-------------~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr 93 (103)
...++++|+.+|.+... .-+.+|+++|..+|+..+++.|+.+||..|+.+
T Consensus 337 l~~f~~eAVa~LI~~~~R~ag~r~~lsl~~~~l~~l~r~a~~~a~~~~~~~i~~~~v~~a~~~ 399 (637)
T PRK13765 337 IPHFDRDAVEEIIREAKRRAGRKGHLTLKLRDLGGLVRVAGDIARSEGAELTTAEHVLEAKKI 399 (637)
T ss_pred CCCCCHHHHHHHHHHHHHHhCCccccccCHHHHHHHHHHHHHHHHhhccceecHHHHHHHHHh
Confidence 45799999988887544 345569999999999999999999999988764
No 93
>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=84.25 E-value=4.4 Score=33.47 Aligned_cols=49 Identities=16% Similarity=0.066 Sum_probs=42.7
Q ss_pred ccchHHHHHHHHH----HHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhc
Q 034139 46 RISGLIYEETRGV----LKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 94 (103)
Q Consensus 46 riS~da~~~l~~~----~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~ 94 (103)
-+|++|++.|.+. .-.|..+++.-|...|+..|+++|..+||+.|-+.+
T Consensus 380 ~l~~~Ale~L~~ig~etSLRYa~qLL~pa~iiA~~rg~~~V~~~dVe~a~~lF 432 (450)
T COG1224 380 ELSDDALEYLTDIGEETSLRYAVQLLTPASIIAKRRGSKRVEVEDVERAKELF 432 (450)
T ss_pred ccCHHHHHHHHhhchhhhHHHHHHhccHHHHHHHHhCCCeeehhHHHHHHHHH
Confidence 4899999999976 446888999999999999999999999999987643
No 94
>PF13335 Mg_chelatase_2: Magnesium chelatase, subunit ChlI
Probab=82.21 E-value=11 Score=24.47 Aligned_cols=61 Identities=13% Similarity=0.132 Sum_probs=50.4
Q ss_pred cccCcchHHHHHHHHhcCccccchHHHHHHHHHHHHH------HHHHHHHHHHHHhhCCCceecHHHHHHHHH
Q 034139 26 NIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIF------LENVIRDAVTYTEHARRKTVTAMDVVYALK 92 (103)
Q Consensus 26 ~~~~ip~a~IkRiar~~G~~riS~da~~~l~~~~e~~------~~~I~~dA~~~a~ha~RkTI~~~DV~~Alk 92 (103)
.+..||...|.+.. .+++++...|..+++.+ +..|++-|-..|.-++...|+.+||..||.
T Consensus 28 ~Na~l~~~~l~~~~------~l~~~~~~~l~~~~~~~~lS~R~~~rilrvARTIADL~~~~~I~~~hi~EAl~ 94 (96)
T PF13335_consen 28 CNAQLPGEELRKYC------PLSSEAKKLLEQAAEKLNLSARGYHRILRVARTIADLEGSERITREHIAEALS 94 (96)
T ss_pred ccccCCHHHHHhHc------CCCHHHHHHHHHHHHHcCcCHHHHHHHHHHHHHHHhHcCCCCCCHHHHHHHHh
Confidence 34478877777764 48888888888887765 577888999999999999999999999984
No 95
>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=81.87 E-value=6.4 Score=30.30 Aligned_cols=65 Identities=12% Similarity=0.034 Sum_probs=46.0
Q ss_pred cchHHHHHHHHhcC-----ccccchHHHHHHHHHHH------HHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhc
Q 034139 30 ITKPAIRRLARRGG-----VKRISGLIYEETRGVLK------IFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 94 (103)
Q Consensus 30 ip~a~IkRiar~~G-----~~riS~da~~~l~~~~e------~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~ 94 (103)
++...+..|++.-- ..-+++++.+.+.+... ..+.+++..|...|.-.++.+|+.+||..|+...
T Consensus 199 ~~~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~R~al~~l~~a~~~a~~~~~~~it~~~v~~a~~~~ 274 (365)
T TIGR02928 199 YDAEELRDILENRAEKAFYDGVLDDGVIPLCAALAAQEHGDARKAIDLLRVAGEIAEREGAERVTEDHVEKAQEKI 274 (365)
T ss_pred CCHHHHHHHHHHHHHhhccCCCCChhHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHH
Confidence 44444666654321 13478888887777654 4566788888888888888999999999988654
No 96
>PRK12402 replication factor C small subunit 2; Reviewed
Probab=80.17 E-value=5.2 Score=30.23 Aligned_cols=56 Identities=18% Similarity=-0.019 Sum_probs=40.4
Q ss_pred HHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHh
Q 034139 35 IRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKR 93 (103)
Q Consensus 35 IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr 93 (103)
+++++++.|+. +++++.+.|.+...-=+.++...+..++. ...+||.+||..++..
T Consensus 193 l~~~~~~~~~~-~~~~al~~l~~~~~gdlr~l~~~l~~~~~--~~~~It~~~v~~~~~~ 248 (337)
T PRK12402 193 LESIAEAEGVD-YDDDGLELIAYYAGGDLRKAILTLQTAAL--AAGEITMEAAYEALGD 248 (337)
T ss_pred HHHHHHHcCCC-CCHHHHHHHHHHcCCCHHHHHHHHHHHHH--cCCCCCHHHHHHHhCC
Confidence 44455556764 99999999998876667777666666663 2347999999988754
No 97
>smart00350 MCM minichromosome maintenance proteins.
Probab=78.49 E-value=11 Score=31.35 Aligned_cols=66 Identities=20% Similarity=0.127 Sum_probs=48.7
Q ss_pred CcchHHHHHHH---HhcCccccchHHHHHHHHHHHH-------------------HHHHHHHHHHHHHhhCCCceecHHH
Q 034139 29 GITKPAIRRLA---RRGGVKRISGLIYEETRGVLKI-------------------FLENVIRDAVTYTEHARRKTVTAMD 86 (103)
Q Consensus 29 ~ip~a~IkRia---r~~G~~riS~da~~~l~~~~e~-------------------~~~~I~~dA~~~a~ha~RkTI~~~D 86 (103)
.++...+++.. |..-...+|+++.+.|.+...+ .++.+++-|..+|.-..|.+|+.+|
T Consensus 417 ~~~~~~l~~yi~~ar~~~~P~ls~~~~~~i~~~y~~~R~~~~~~~~~~~~~~t~R~l~sliRla~A~A~l~~r~~V~~~D 496 (509)
T smart00350 417 PISQEFLRKYIAYAREKIKPKLSEEAAEKLVKAYVDLRKEDSQSEARSSIPITVRQLESIIRLSEAHAKMRLSDVVEEAD 496 (509)
T ss_pred cCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhcccccccccccccCcCHHHHHHHHHHHHHHHHHcCCCccCHHH
Confidence 56777776554 4312245899998888765332 2367888899999999999999999
Q ss_pred HHHHHHhc
Q 034139 87 VVYALKRQ 94 (103)
Q Consensus 87 V~~Alkr~ 94 (103)
|..|++..
T Consensus 497 v~~ai~l~ 504 (509)
T smart00350 497 VEEAIRLL 504 (509)
T ss_pred HHHHHHHH
Confidence 99998754
No 98
>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=77.09 E-value=7.3 Score=29.78 Aligned_cols=56 Identities=14% Similarity=0.136 Sum_probs=38.7
Q ss_pred HHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHH
Q 034139 35 IRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALK 92 (103)
Q Consensus 35 IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alk 92 (103)
++.++++.|. .+++++++.+.+...--+..+.....+.+.+.++ .|+.+||..++.
T Consensus 185 l~~~~~~~g~-~i~~~a~~~l~~~~~g~~~~a~~~lekl~~~~~~-~it~~~v~~~~~ 240 (355)
T TIGR02397 185 LKKILDKEGI-KIEDEALELIARAADGSLRDALSLLDQLISFGNG-NITYEDVNELLG 240 (355)
T ss_pred HHHHHHHcCC-CCCHHHHHHHHHHcCCChHHHHHHHHHHHhhcCC-CCCHHHHHHHhC
Confidence 3344445675 5899999999888776666666666665555553 499999977664
No 99
>PRK14964 DNA polymerase III subunits gamma and tau; Provisional
Probab=76.56 E-value=6.8 Score=32.80 Aligned_cols=56 Identities=7% Similarity=-0.048 Sum_probs=42.1
Q ss_pred HHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHH
Q 034139 35 IRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALK 92 (103)
Q Consensus 35 IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alk 92 (103)
++++++..|+ .+++++++.|.+..+-=+..+.....+.+.+.+ .+||.+||...+-
T Consensus 184 L~~ia~~Egi-~i~~eAL~lIa~~s~GslR~alslLdqli~y~~-~~It~e~V~~llg 239 (491)
T PRK14964 184 LVDIAKKENI-EHDEESLKLIAENSSGSMRNALFLLEQAAIYSN-NKISEKSVRDLLG 239 (491)
T ss_pred HHHHHHHcCC-CCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhcC-CCCCHHHHHHHHc
Confidence 3445555565 599999999999887777777777767666766 4799999988763
No 100
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=75.58 E-value=22 Score=27.42 Aligned_cols=72 Identities=17% Similarity=0.107 Sum_probs=48.0
Q ss_pred CcchHHHHHHHHh----cCccccchHHHHHHHHHHHH---HHHHHHHHHHHHHhhCCCceecHHHHHHHHHhcCCccccc
Q 034139 29 GITKPAIRRLARR----GGVKRISGLIYEETRGVLKI---FLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTLYGF 101 (103)
Q Consensus 29 ~ip~a~IkRiar~----~G~~riS~da~~~l~~~~e~---~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~g~~lYgf 101 (103)
.++...+..|+++ .++ .+++++++.|.+...- .+..+++.+..++.-.+...|+.++|..++...+...+|.
T Consensus 179 ~~~~~e~~~il~~~~~~~~~-~~~~~~~~~ia~~~~G~pR~a~~~l~~~~~~a~~~~~~~I~~~~v~~~l~~~~~~~~~l 257 (328)
T PRK00080 179 FYTVEELEKIVKRSARILGV-EIDEEGALEIARRSRGTPRIANRLLRRVRDFAQVKGDGVITKEIADKALDMLGVDELGL 257 (328)
T ss_pred CCCHHHHHHHHHHHHHHcCC-CcCHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCcCCC
Confidence 4555555555543 333 5899999998876543 3555555566666555566899999999998776554443
No 101
>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=75.48 E-value=8.1 Score=22.01 Aligned_cols=32 Identities=19% Similarity=0.257 Sum_probs=26.2
Q ss_pred CcchHHHHHHHHhcCccccchHHHHHHHHHHHHH
Q 034139 29 GITKPAIRRLARRGGVKRISGLIYEETRGVLKIF 62 (103)
Q Consensus 29 ~ip~a~IkRiar~~G~~riS~da~~~l~~~~e~~ 62 (103)
+++.++|.|++... .+||++..+.+.++++++
T Consensus 10 gvS~~TVSr~ln~~--~~vs~~tr~rI~~~a~~l 41 (46)
T PF00356_consen 10 GVSKSTVSRVLNGP--PRVSEETRERILEAAEEL 41 (46)
T ss_dssp TSSHHHHHHHHTTC--SSSTHHHHHHHHHHHHHH
T ss_pred CcCHHHHHHHHhCC--CCCCHHHHHHHHHHHHHH
Confidence 67888899988755 689999999988887764
No 102
>PRK00440 rfc replication factor C small subunit; Reviewed
Probab=75.44 E-value=9.8 Score=28.45 Aligned_cols=56 Identities=20% Similarity=0.115 Sum_probs=40.8
Q ss_pred HHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHh
Q 034139 35 IRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKR 93 (103)
Q Consensus 35 IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr 93 (103)
++.+++..|+ .+++++++.+.+...--+..+......++.. ..+||.+||..++..
T Consensus 170 l~~~~~~~~~-~i~~~al~~l~~~~~gd~r~~~~~l~~~~~~--~~~it~~~v~~~~~~ 225 (319)
T PRK00440 170 LRYIAENEGI-EITDDALEAIYYVSEGDMRKAINALQAAAAT--GKEVTEEAVYKITGT 225 (319)
T ss_pred HHHHHHHcCC-CCCHHHHHHHHHHcCCCHHHHHHHHHHHHHc--CCCCCHHHHHHHhCC
Confidence 4455555666 4999999999988776777766666666655 367999999887743
No 103
>PF09288 UBA_3: Fungal ubiquitin-associated domain ; InterPro: IPR015368 This C-terminal domain is found in ubiquitin binding proteins, it adopts a structure consisting of a three alpha-helix bundle. This domain is predominantly found in fungi []. ; PDB: 1TTE_A.
Probab=74.89 E-value=4.1 Score=24.52 Aligned_cols=37 Identities=24% Similarity=0.415 Sum_probs=23.2
Q ss_pred ccCcchHHHHHHHHhcCccccchHHHHHHHHHHHHHH
Q 034139 27 IQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFL 63 (103)
Q Consensus 27 ~~~ip~a~IkRiar~~G~~riS~da~~~l~~~~e~~~ 63 (103)
..++|+..|-..+++.|++++.......-..++|+.+
T Consensus 18 ~mGF~~dkVvevlrrlgik~~n~~dn~t~~~ilEELL 54 (55)
T PF09288_consen 18 NMGFERDKVVEVLRRLGIKSMNGVDNETENKILEELL 54 (55)
T ss_dssp HHT--HHHHHHHHHHS--SS--SS--HHHHHHHHHHT
T ss_pred HcCCcHHHHHHHHHHhCCCCCCCccchhHHHHHHHHh
Confidence 3589999999999999999988766677777777654
No 104
>PRK14970 DNA polymerase III subunits gamma and tau; Provisional
Probab=73.96 E-value=9.8 Score=29.67 Aligned_cols=56 Identities=11% Similarity=0.075 Sum_probs=39.4
Q ss_pred HHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHH
Q 034139 35 IRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALK 92 (103)
Q Consensus 35 IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alk 92 (103)
+.+++++.|+ .+++++++.|.+.+.-=+..+.......+.+.+.. ||.+||..++.
T Consensus 176 l~~~~~~~g~-~i~~~al~~l~~~~~gdlr~~~~~lekl~~y~~~~-it~~~v~~~~~ 231 (367)
T PRK14970 176 LAGIAVKEGI-KFEDDALHIIAQKADGALRDALSIFDRVVTFCGKN-ITRQAVTENLN 231 (367)
T ss_pred HHHHHHHcCC-CCCHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCCC-CCHHHHHHHhC
Confidence 4455556676 49999999999877655566666666666555554 99999887764
No 105
>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional
Probab=73.30 E-value=5.7 Score=32.68 Aligned_cols=34 Identities=21% Similarity=0.155 Sum_probs=30.0
Q ss_pred HHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhc
Q 034139 61 IFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 94 (103)
Q Consensus 61 ~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~ 94 (103)
.-+..|+.+|...|...+|..|+.+|+..|+++.
T Consensus 391 AdI~~i~~eA~~~Alr~~r~~Vt~~D~~~A~~~v 424 (438)
T PTZ00361 391 ADIKAICTEAGLLALRERRMKVTQADFRKAKEKV 424 (438)
T ss_pred HHHHHHHHHHHHHHHHhcCCccCHHHHHHHHHHH
Confidence 3467889999999999999999999999999863
No 106
>PRK14955 DNA polymerase III subunits gamma and tau; Provisional
Probab=72.06 E-value=13 Score=29.70 Aligned_cols=55 Identities=5% Similarity=-0.031 Sum_probs=38.2
Q ss_pred HHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhh----CCCceecHHHHHHHH
Q 034139 36 RRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEH----ARRKTVTAMDVVYAL 91 (103)
Q Consensus 36 kRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~h----a~RkTI~~~DV~~Al 91 (103)
+++++..|. .|++++++.|.+.+.--+..+.....+.+-+ ...++|+.+||..++
T Consensus 196 ~~~~~~~g~-~i~~~al~~l~~~s~g~lr~a~~~L~kl~~~~~~~~~~~~It~~~v~~~v 254 (397)
T PRK14955 196 QGICEAEGI-SVDADALQLIGRKAQGSMRDAQSILDQVIAFSVESEGEGSIRYDKVAELL 254 (397)
T ss_pred HHHHHHcCC-CCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhccccCCCCccCHHHHHHHH
Confidence 333444454 4999999999988877666666655554433 456799999998765
No 107
>PRK09111 DNA polymerase III subunits gamma and tau; Validated
Probab=71.74 E-value=11 Score=32.34 Aligned_cols=56 Identities=18% Similarity=0.098 Sum_probs=42.0
Q ss_pred HHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHH
Q 034139 35 IRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALK 92 (103)
Q Consensus 35 IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alk 92 (103)
++++++..|+ .+++++.+.|.+...-.+..+.....+.+-+. ...|+.+||...+.
T Consensus 200 L~~i~~kegi-~i~~eAl~lIa~~a~Gdlr~al~~Ldkli~~g-~g~It~e~V~~llg 255 (598)
T PRK09111 200 LSRIAAKEGV-EVEDEALALIARAAEGSVRDGLSLLDQAIAHG-AGEVTAEAVRDMLG 255 (598)
T ss_pred HHHHHHHcCC-CCCHHHHHHHHHHcCCCHHHHHHHHHHHHhhc-CCCcCHHHHHHHhC
Confidence 3445555665 49999999999988888887777776666664 45799999998764
No 108
>COG1737 RpiR Transcriptional regulators [Transcription]
Probab=71.61 E-value=19 Score=27.43 Aligned_cols=64 Identities=17% Similarity=0.198 Sum_probs=43.7
Q ss_pred CcchHHHHHHHHhcCccccchHHHHHHHHHHHH-----------------HHHHHHHHHHHHHhhCCCceecHHHHHHHH
Q 034139 29 GITKPAIRRLARRGGVKRISGLIYEETRGVLKI-----------------FLENVIRDAVTYTEHARRKTVTAMDVVYAL 91 (103)
Q Consensus 29 ~ip~a~IkRiar~~G~~riS~da~~~l~~~~e~-----------------~~~~I~~dA~~~a~ha~RkTI~~~DV~~Al 91 (103)
+.+.++|-|++++.|..-++ |-...|++.+.. .+..++.......++ -...++.+++..|.
T Consensus 47 ~VS~aTv~Rf~~kLGf~Gf~-efk~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~-t~~~l~~~~l~~av 124 (281)
T COG1737 47 GVSPATVVRFARKLGFEGFS-EFKLALAQELAEGRAQLLREIAEDDGPESILEKLLAANIAALER-TLNLLDEEALERAV 124 (281)
T ss_pred CCCHHHHHHHHHHcCCCCHH-HHHHHHHHHHhhccchhhcccCCCCCHHHHHHHHHHHHHHHHHH-HHHhcCHHHHHHHH
Confidence 57889999999999976666 455555555532 556666666665544 44567888888888
Q ss_pred Hhc
Q 034139 92 KRQ 94 (103)
Q Consensus 92 kr~ 94 (103)
+.+
T Consensus 125 ~~L 127 (281)
T COG1737 125 ELL 127 (281)
T ss_pred HHH
Confidence 754
No 109
>PRK06645 DNA polymerase III subunits gamma and tau; Validated
Probab=70.08 E-value=13 Score=31.29 Aligned_cols=58 Identities=2% Similarity=-0.101 Sum_probs=41.1
Q ss_pred HHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCC--CceecHHHHHHHHHh
Q 034139 35 IRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHAR--RKTVTAMDVVYALKR 93 (103)
Q Consensus 35 IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~--RkTI~~~DV~~Alkr 93 (103)
++++++..|+ .+++++++.+.+..+--+.+++....+.+.+++ ...||.+||...+-.
T Consensus 196 L~~i~~~egi-~ie~eAL~~Ia~~s~GslR~al~~Ldkai~~~~~~~~~It~~~V~~llg~ 255 (507)
T PRK06645 196 LEYITKQENL-KTDIEALRIIAYKSEGSARDAVSILDQAASMSAKSDNIISPQVINQMLGL 255 (507)
T ss_pred HHHHHHHcCC-CCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhhccCCCCcCHHHHHHHHCC
Confidence 4455566675 489999999998877777777666666555543 347999999987643
No 110
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=69.84 E-value=7.6 Score=22.69 Aligned_cols=28 Identities=39% Similarity=0.553 Sum_probs=17.9
Q ss_pred CcchHHHHHHH---------HhcCccccchHHHHHHH
Q 034139 29 GITKPAIRRLA---------RRGGVKRISGLIYEETR 56 (103)
Q Consensus 29 ~ip~a~IkRia---------r~~G~~riS~da~~~l~ 56 (103)
.||.++|+|+. ...|+.+||..-+.++.
T Consensus 2 ~Ip~~ti~RL~~Y~r~L~~l~~~G~~~vSS~~La~~~ 38 (50)
T PF06971_consen 2 KIPKATIRRLPLYLRYLEQLKEEGVERVSSQELAEAL 38 (50)
T ss_dssp S-SHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHHHHHHHcCCeeECHHHHHHHH
Confidence 48899998876 45678888877665544
No 111
>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=69.38 E-value=12 Score=30.98 Aligned_cols=50 Identities=16% Similarity=0.155 Sum_probs=39.2
Q ss_pred cccchHHHHHHHHHHHHHH-HHHHHHHHHHHhhCCCceecHHHHHHHHHhcC
Q 034139 45 KRISGLIYEETRGVLKIFL-ENVIRDAVTYTEHARRKTVTAMDVVYALKRQG 95 (103)
Q Consensus 45 ~riS~da~~~l~~~~e~~~-~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~g 95 (103)
..|++||-.+|.++ =.|+ ..+=+.+.+||+..|...||.+.+..|-...|
T Consensus 461 ~~w~~ea~~~l~~~-P~f~r~~~r~~~e~~a~~~g~~~it~~~~~~a~~~~~ 511 (511)
T TIGR01278 461 LGWTAEAEAELKKV-PFFVRGKVRRNTENFARERGYSVITLEVIYAAKEHFG 511 (511)
T ss_pred CCcCHHHHHHHhhC-ChhhhHHHHHHHHHHHHHcCCCEEcHHHHHHHHHhcC
Confidence 46999999999764 3333 45556677899999999999999998876543
No 112
>COG5251 TAF40 Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=68.50 E-value=4.2 Score=30.04 Aligned_cols=65 Identities=18% Similarity=0.209 Sum_probs=55.2
Q ss_pred CcchHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCc--eecHHHHHHHHHhc
Q 034139 29 GITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRK--TVTAMDVVYALKRQ 94 (103)
Q Consensus 29 ~ip~a~IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~Rk--TI~~~DV~~Alkr~ 94 (103)
.||++.|+.+|-..--.-||+.+.-.|.-+..-|+.+|++-|.+.-+. -+. -+.+.|+..|.+..
T Consensus 115 ~lnKt~VKKlastV~nQtVspNi~I~l~g~~KVfvGEiIElA~~Vq~~-w~~sgpl~p~h~reayr~~ 181 (199)
T COG5251 115 SLNKTQVKKLASTVANQTVSPNIRIFLQGVGKVFVGEIIELAMIVQNK-WLTSGPLIPFHKREAYRYK 181 (199)
T ss_pred CCCHHHHHHHHHHHhccccCCCeeeeeechhHHHHHHHHHHHHHHHHH-hcccCCCChHHHHHHHHHH
Confidence 699999999999988788999999999999999999999999877643 222 38889999888753
No 113
>cd08784 Death_DRs Death Domain of Death Receptors. Death domain (DD) found in death receptor proteins. Death receptors are members of the tumor necrosis factor (TNF) receptor superfamily, characterized by having a cytoplasmic DD. Known members of the family are Fas (CD95/APO-1), TNF-receptor 1 (TNFR1/TNFRSF1A/p55/CD120a), TNF-related apoptosis-inducing ligand receptor 1 (TRAIL-R1 /DR4), and receptor 2 (TRAIL-R2/DR5/APO-2/KILLER), as well as Death Receptor 3 (DR3/APO-3/TRAMP/WSL-1/LARD). They are involved in apoptosis signaling pathways. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=67.91 E-value=27 Score=21.77 Aligned_cols=65 Identities=15% Similarity=0.090 Sum_probs=45.7
Q ss_pred cCcchHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhcCC
Q 034139 28 QGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGR 96 (103)
Q Consensus 28 ~~ip~a~IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~g~ 96 (103)
..+|....+.++|+.| +|+...+.+...-...-+++.+-....-+..|+ .-|.+.+..||+..|.
T Consensus 7 ~~v~~~~Wk~laR~LG---ls~~~I~~ie~~~~~~~eq~~~mL~~W~~k~G~-~At~~~L~~aL~~~~~ 71 (79)
T cd08784 7 EEVPFDQHKRFFRKLG---LSDNEIKVAELDNPQHRDRVYELLRIWRNKEGR-KATLNTLIKALKDLDQ 71 (79)
T ss_pred HHCCHHHHHHHHHHcC---CCHHHHHHHHHcCCchHHHHHHHHHHHHhccCc-CcHHHHHHHHHHHccc
Confidence 4678899999999999 455555555544333345555666677776676 5678999999988764
No 114
>PRK13407 bchI magnesium chelatase subunit I; Provisional
Probab=65.62 E-value=32 Score=27.30 Aligned_cols=60 Identities=8% Similarity=0.016 Sum_probs=43.6
Q ss_pred HHHHHHHHhcCccccchHHHHHHHHHHHHHHH-------HHHHHHHHHHhhCCCceecHHHHHHHHH
Q 034139 33 PAIRRLARRGGVKRISGLIYEETRGVLKIFLE-------NVIRDAVTYTEHARRKTVTAMDVVYALK 92 (103)
Q Consensus 33 a~IkRiar~~G~~riS~da~~~l~~~~e~~~~-------~I~~dA~~~a~ha~RkTI~~~DV~~Alk 92 (103)
..|...-+..---.|++++.+.+.+.+...=. .+++-|..+|-.+||..|+.+||..+..
T Consensus 238 ~~i~~a~~~~~~V~v~~~~~~yi~~l~~~~~~~s~Ra~i~l~~aA~a~A~l~Gr~~V~~~Di~~~~~ 304 (334)
T PRK13407 238 GRILGARARLPQLKTPNTVLHDCAALCIALGSDGLRGELTLLRAARALAAFEGAEAVGRSHLRSVAT 304 (334)
T ss_pred HHHHHHHHhcCCcccCHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHHcCCCeeCHHHHHHHHH
Confidence 44444444444456888888888887665431 2778889999999999999999976653
No 115
>PRK14962 DNA polymerase III subunits gamma and tau; Provisional
Probab=65.60 E-value=21 Score=29.59 Aligned_cols=63 Identities=14% Similarity=0.004 Sum_probs=37.8
Q ss_pred CcchHHHHHHH----HhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHh
Q 034139 29 GITKPAIRRLA----RRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKR 93 (103)
Q Consensus 29 ~ip~a~IkRia----r~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr 93 (103)
.++...+..++ +..|+ .+++++++.|.+...-=+..++.....++..++. .||.+||..++..
T Consensus 175 ~l~~~el~~~L~~i~~~egi-~i~~eal~~Ia~~s~GdlR~aln~Le~l~~~~~~-~It~e~V~~~l~~ 241 (472)
T PRK14962 175 NISDELIIKRLQEVAEAEGI-EIDREALSFIAKRASGGLRDALTMLEQVWKFSEG-KITLETVHEALGL 241 (472)
T ss_pred CccHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCC-CCCHHHHHHHHcC
Confidence 34445444444 34454 5999999999986553333333333333333333 3999999988854
No 116
>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=65.59 E-value=53 Score=24.60 Aligned_cols=66 Identities=14% Similarity=0.035 Sum_probs=43.2
Q ss_pred CcchHHHHHHHHh----cCccccchHHHHHHHHHHHH---HHHHHHHHHHHHHhhCCCceecHHHHHHHHHhcC
Q 034139 29 GITKPAIRRLARR----GGVKRISGLIYEETRGVLKI---FLENVIRDAVTYTEHARRKTVTAMDVVYALKRQG 95 (103)
Q Consensus 29 ~ip~a~IkRiar~----~G~~riS~da~~~l~~~~e~---~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~g 95 (103)
.++...+..++++ .++ .+++++++.+.+...- .+..++..+..++...+...|+.++|..++..+.
T Consensus 158 ~l~~~e~~~il~~~~~~~~~-~~~~~al~~ia~~~~G~pR~~~~ll~~~~~~a~~~~~~~it~~~v~~~l~~l~ 230 (305)
T TIGR00635 158 FYTVEELAEIVSRSAGLLNV-EIEPEAALEIARRSRGTPRIANRLLRRVRDFAQVRGQKIINRDIALKALEMLM 230 (305)
T ss_pred CCCHHHHHHHHHHHHHHhCC-CcCHHHHHHHHHHhCCCcchHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHhC
Confidence 3455555555543 333 5899999998886543 3345555555566555666799999999998743
No 117
>PRK09087 hypothetical protein; Validated
Probab=65.42 E-value=53 Score=24.24 Aligned_cols=58 Identities=9% Similarity=-0.066 Sum_probs=40.5
Q ss_pred HHHHHHhcCccccchHHHHHHHHHHHHHHHHHHH---HHHHHHhhCCCceecHHHHHHHHHhc
Q 034139 35 IRRLARRGGVKRISGLIYEETRGVLKIFLENVIR---DAVTYTEHARRKTVTAMDVVYALKRQ 94 (103)
Q Consensus 35 IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~---dA~~~a~ha~RkTI~~~DV~~Alkr~ 94 (103)
+++.++..|. .+++++++.|.+.+..=+..+.. ....++...+| .||...+..+|+..
T Consensus 162 L~~~~~~~~~-~l~~ev~~~La~~~~r~~~~l~~~l~~L~~~~~~~~~-~it~~~~~~~l~~~ 222 (226)
T PRK09087 162 IFKLFADRQL-YVDPHVVYYLVSRMERSLFAAQTIVDRLDRLALERKS-RITRALAAEVLNEM 222 (226)
T ss_pred HHHHHHHcCC-CCCHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhCC-CCCHHHHHHHHHhh
Confidence 4444555554 59999999999887766666654 44455555554 49999999999754
No 118
>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional
Probab=65.15 E-value=11 Score=30.57 Aligned_cols=34 Identities=12% Similarity=0.056 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhc
Q 034139 61 IFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 94 (103)
Q Consensus 61 ~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~ 94 (103)
.=+..|+.+|...|...+|..|+.+|+..|+++.
T Consensus 353 aDI~~l~~eA~~~A~r~~~~~i~~~df~~A~~~v 386 (398)
T PTZ00454 353 ADIAAICQEAGMQAVRKNRYVILPKDFEKGYKTV 386 (398)
T ss_pred HHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHHH
Confidence 3377889999999999999999999999999974
No 119
>PRK02910 light-independent protochlorophyllide reductase subunit B; Provisional
Probab=65.14 E-value=17 Score=30.27 Aligned_cols=51 Identities=14% Similarity=0.085 Sum_probs=39.8
Q ss_pred ccccchHHHHHHHHHHHHHH-HHHHHHHHHHHhhCCCceecHHHHHHHHHhcC
Q 034139 44 VKRISGLIYEETRGVLKIFL-ENVIRDAVTYTEHARRKTVTAMDVVYALKRQG 95 (103)
Q Consensus 44 ~~riS~da~~~l~~~~e~~~-~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~g 95 (103)
...|++||-.+|.++ =.|+ ..+=+.+.+||+..|...||.+.+..|-..+|
T Consensus 467 ~~~w~~ea~~~l~~~-P~f~r~~~r~~~e~~a~~~g~~~it~~~~~~a~~~~~ 518 (519)
T PRK02910 467 ELVWTPEAEAELKKI-PFFVRGKVRRNTEKFARERGLPEITLEVLYDAKAHFG 518 (519)
T ss_pred CCCCCHHHHHHHhhC-ChhhHHHHHHHHHHHHHHcCCCeecHHHHHHHHHHhc
Confidence 357999999999764 4444 44555667899999999999999999876654
No 120
>PRK03992 proteasome-activating nucleotidase; Provisional
Probab=64.48 E-value=12 Score=29.87 Aligned_cols=34 Identities=21% Similarity=0.253 Sum_probs=30.0
Q ss_pred HHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhc
Q 034139 61 IFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 94 (103)
Q Consensus 61 ~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~ 94 (103)
.-+..++.+|..+|-..++..|+.+|+..|+++.
T Consensus 339 adl~~l~~eA~~~a~~~~~~~i~~~d~~~A~~~~ 372 (389)
T PRK03992 339 ADLKAICTEAGMFAIRDDRTEVTMEDFLKAIEKV 372 (389)
T ss_pred HHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHH
Confidence 5567888889999989999999999999999865
No 121
>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=64.16 E-value=32 Score=27.30 Aligned_cols=48 Identities=15% Similarity=0.019 Sum_probs=35.9
Q ss_pred cccchHHHHHHHHHHHHHHH-------HHHHHHHHHHhhCCCceecHHHHHHHHH
Q 034139 45 KRISGLIYEETRGVLKIFLE-------NVIRDAVTYTEHARRKTVTAMDVVYALK 92 (103)
Q Consensus 45 ~riS~da~~~l~~~~e~~~~-------~I~~dA~~~a~ha~RkTI~~~DV~~Alk 92 (103)
-.|++++.+.+.+.+...=. .+++-|..+|--+||..|+++||..+..
T Consensus 253 V~v~d~~~~~i~~l~~~~~~~s~Ra~i~l~raArA~Aal~GR~~V~~dDv~~~a~ 307 (337)
T TIGR02030 253 VTIPYDVLVKVAELCAELDVDGLRGELTLNRAAKALAAFEGRTEVTVDDIRRVAV 307 (337)
T ss_pred CcCCHHHHHHHHHHHHHHCCCCCcHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 45788888877776554322 2556677888889999999999997765
No 122
>TIGR01242 26Sp45 26S proteasome subunit P45 family. Many proteins may score above the trusted cutoff because an internal
Probab=64.11 E-value=12 Score=29.26 Aligned_cols=42 Identities=19% Similarity=0.230 Sum_probs=32.9
Q ss_pred HHHHHHHHH----HHHHHHHHHHHHHHhhCCCceecHHHHHHHHHh
Q 034139 52 YEETRGVLK----IFLENVIRDAVTYTEHARRKTVTAMDVVYALKR 93 (103)
Q Consensus 52 ~~~l~~~~e----~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr 93 (103)
++.+.+..+ .-+..++.+|...|-..++..|+.+|+..|++.
T Consensus 317 ~~~la~~t~g~sg~dl~~l~~~A~~~a~~~~~~~i~~~d~~~a~~~ 362 (364)
T TIGR01242 317 LEAIAKMTEGASGADLKAICTEAGMFAIREERDYVTMDDFIKAVEK 362 (364)
T ss_pred HHHHHHHcCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHH
Confidence 445554443 346688888999998899999999999999975
No 123
>KOG3902 consensus Histone acetyltransferase PCAF/SAGA, subunit SUPT3H/SPT3 [Transcription]
Probab=64.00 E-value=40 Score=27.07 Aligned_cols=59 Identities=8% Similarity=0.150 Sum_probs=49.4
Q ss_pred HHHHHHhcC-ccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHh
Q 034139 35 IRRLARRGG-VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKR 93 (103)
Q Consensus 35 IkRiar~~G-~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr 93 (103)
|+.++=..| +..=+++...-+.+.+.--+-+++..|++.+...+-..||++|+.+.++.
T Consensus 30 iQqmmf~sGei~~P~pett~Lved~V~gqvie~l~qa~eia~lrgsr~Itpedliflir~ 89 (352)
T KOG3902|consen 30 IQQMMFQSGEIPDPLPETTNLVEDNVRGQVIESLVQANEIADLRGSRSITPEDLIFLIRH 89 (352)
T ss_pred HHHHHHHhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCccccChHHHHHHhhc
Confidence 556665555 56677788888888888888999999999999999999999999998863
No 124
>PF06160 EzrA: Septation ring formation regulator, EzrA ; InterPro: IPR010379 During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerises into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation [].; GO: 0000921 septin ring assembly, 0005940 septin ring, 0016021 integral to membrane
Probab=63.68 E-value=41 Score=28.38 Aligned_cols=74 Identities=16% Similarity=0.095 Sum_probs=52.8
Q ss_pred chhhcccccCcchHH----------HHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHH----------HHHHhhCCC
Q 034139 20 RKVLRDNIQGITKPA----------IRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDA----------VTYTEHARR 79 (103)
Q Consensus 20 ~k~~r~~~~~ip~a~----------IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA----------~~~a~ha~R 79 (103)
|++.+.++++||..- |.++.....-.+|.-+.+......+...+..+...+ ....++++|
T Consensus 428 R~lek~nLPGlp~~y~~~~~~~~~~i~~l~~~L~~~pinm~~v~~~l~~a~~~v~~L~~~t~~li~~A~L~E~~iQYaNR 507 (560)
T PF06160_consen 428 RRLEKSNLPGLPEDYLDYFFDVSDEIEELSDELNQVPINMDEVNKQLEEAEDDVETLEEKTEELIDNATLAEQLIQYANR 507 (560)
T ss_pred HHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHhcCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 567789999999873 667777777777777777766666555555443332 245567899
Q ss_pred ceecHHHHHHHHHh
Q 034139 80 KTVTAMDVVYALKR 93 (103)
Q Consensus 80 kTI~~~DV~~Alkr 93 (103)
---+-.+|..++.+
T Consensus 508 YR~~~~~v~~al~~ 521 (560)
T PF06160_consen 508 YRSDNPEVDEALTE 521 (560)
T ss_pred ccCCCHHHHHHHHH
Confidence 88888899998875
No 125
>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=63.00 E-value=16 Score=31.20 Aligned_cols=49 Identities=27% Similarity=0.125 Sum_probs=38.5
Q ss_pred cccchHHHHHHHHHHHHHH-------HHHHHHHHHHHhhCCCceecHHHHHHHHHh
Q 034139 45 KRISGLIYEETRGVLKIFL-------ENVIRDAVTYTEHARRKTVTAMDVVYALKR 93 (103)
Q Consensus 45 ~riS~da~~~l~~~~e~~~-------~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr 93 (103)
-.|++++.+.|.+....+- ..+++-|-.+|.-.+|.+|+.+||..|++.
T Consensus 248 V~is~~~~~~l~~~~~~~~i~s~Ra~i~~~r~Ara~AaL~gr~~V~~~Dv~~A~~l 303 (633)
T TIGR02442 248 VRISDSLIRFISELCIEFGVDGHRADIVMARAARALAALDGRRRVTAEDVREAAEL 303 (633)
T ss_pred CCCCHHHHHHHHHHHHHhCCCCccHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHH
Confidence 3578888888887765542 346677778888999999999999988863
No 126
>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda. Members of this protein family are Hda (Homologous to DnaA). These proteins are about half the length of DnaA and homologous over length of Hda. In the model species Escherichia coli, the initiation of DNA replication requires DnaA bound to ATP rather than ADP; Hda helps facilitate the conversion of DnaA-ATP to DnaA-ADP.
Probab=62.94 E-value=45 Score=23.62 Aligned_cols=50 Identities=14% Similarity=0.019 Sum_probs=36.1
Q ss_pred hcCccccchHHHHHHHHHHH---HHHHHHHHHHHHHHhhCCCceecHHHHHHHHH
Q 034139 41 RGGVKRISGLIYEETRGVLK---IFLENVIRDAVTYTEHARRKTVTAMDVVYALK 92 (103)
Q Consensus 41 ~~G~~riS~da~~~l~~~~e---~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alk 92 (103)
+.|+ .+++++...|..... ..+..+++++..++..++ ++|+.+.|...|+
T Consensus 174 ~~~~-~~~~~~l~~L~~~~~gn~r~L~~~l~~~~~~~~~~~-~~i~~~~~~~~~~ 226 (226)
T TIGR03420 174 RRGL-QLPDEVADYLLRHGSRDMGSLMALLDALDRASLAAK-RKITIPFVKEVLA 226 (226)
T ss_pred HcCC-CCCHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHhC-CCCCHHHHHHHhC
Confidence 3454 599999999998644 356666777777776655 5799999887763
No 127
>PRK14963 DNA polymerase III subunits gamma and tau; Provisional
Probab=61.91 E-value=21 Score=29.80 Aligned_cols=61 Identities=18% Similarity=0.064 Sum_probs=44.7
Q ss_pred CcchHHH----HHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHH
Q 034139 29 GITKPAI----RRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALK 92 (103)
Q Consensus 29 ~ip~a~I----kRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alk 92 (103)
.++...+ +++++..|+ .+++++++.+.+...--+..+......++.. ..+||.+||..++.
T Consensus 174 ~ls~~el~~~L~~i~~~egi-~i~~~Al~~ia~~s~GdlR~aln~Lekl~~~--~~~It~~~V~~~l~ 238 (504)
T PRK14963 174 RLTEEEIAGKLRRLLEAEGR-EAEPEALQLVARLADGAMRDAESLLERLLAL--GTPVTRKQVEEALG 238 (504)
T ss_pred CCCHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHHcCCCHHHHHHHHHHHHhc--CCCCCHHHHHHHHC
Confidence 4555554 455556676 4899999999998888888887777776655 33799999988764
No 128
>PF07766 LETM1: LETM1-like protein; InterPro: IPR011685 This is a group of mainly hypothetical eukaryotic proteins. Putative features found in LETM1, such as a transmembrane domain and a CK2 and PKC phosphorylation site [], are relatively conserved throughout the family. Deletion of LETM1 is thought to be involved in the development of Wolf-Hirschhorn syndrome in humans []. A member of this family, P91927 from SWISSPROT, is known to be expressed in the mitochondria of Drosophila melanogaster [], suggesting that this may be a group of mitochondrial proteins.; PDB: 3SKQ_A.
Probab=61.79 E-value=41 Score=25.72 Aligned_cols=70 Identities=17% Similarity=0.209 Sum_probs=50.1
Q ss_pred cCcchHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhcCCcccc
Q 034139 28 QGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTLYG 100 (103)
Q Consensus 28 ~~ip~a~IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~g~~lYg 100 (103)
..++...++.+++-.|+..+..+.. ++.-+..++..|..|=...... |=..++.+++..|+...|....|
T Consensus 169 d~Lsr~~L~~L~r~~~l~~~~~~~~--lr~rL~~~~~~l~~dD~~i~~e-Gv~~Ls~~EL~~Ac~~RGl~~~~ 238 (268)
T PF07766_consen 169 DNLSRPHLRALCRLLGLTPFGPSSL--LRRRLRKRLRYLKQDDRLIKRE-GVDSLSEEELQDACYERGLRSTG 238 (268)
T ss_dssp HHS-HHHHHHHHHHTT----SSHHH--HHHHHHHHHHHHHHHHHHHHHH--GGGS-HHHHHHHHHHTT---TT
T ss_pred ccCCHHHHHHHHHHhccCcCCchHH--HHHHHHHHHHHHHHHHHHHHHh-ccccCCHHHHHHHHHHhCCCcCC
Confidence 3577777888999888888876665 6788999999999888887776 77889999999999999876555
No 129
>PRK14954 DNA polymerase III subunits gamma and tau; Provisional
Probab=61.19 E-value=26 Score=30.16 Aligned_cols=63 Identities=13% Similarity=0.071 Sum_probs=44.3
Q ss_pred CcchHHHH----HHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhC----CCceecHHHHHHHHH
Q 034139 29 GITKPAIR----RLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHA----RRKTVTAMDVVYALK 92 (103)
Q Consensus 29 ~ip~a~Ik----Riar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha----~RkTI~~~DV~~Alk 92 (103)
.++...|. ++++..|. .|++++++.|.+...--+..+.....+.+.+. ..++|+.+||...+.
T Consensus 185 ~l~~~ei~~~L~~i~~~egi-~I~~eal~~La~~s~Gdlr~al~eLeKL~~y~~~~~~~~~It~~~V~~lv~ 255 (620)
T PRK14954 185 RIPLDEIQSQLQMICRAEGI-QIDADALQLIARKAQGSMRDAQSILDQVIAFSVGSEAEKVIAYQGVAELLN 255 (620)
T ss_pred CCCHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHHhCCCHHHHHHHHHHHHHhccccccCCccCHHHHHHHHc
Confidence 34444444 44444454 49999999999988877777777766666554 377899999977663
No 130
>PRK14961 DNA polymerase III subunits gamma and tau; Provisional
Probab=60.20 E-value=27 Score=27.52 Aligned_cols=62 Identities=6% Similarity=-0.045 Sum_probs=38.7
Q ss_pred CcchHHHH----HHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHH
Q 034139 29 GITKPAIR----RLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALK 92 (103)
Q Consensus 29 ~ip~a~Ik----Riar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alk 92 (103)
.++...+. .+++..|+ .+++++++.+.+...-=+..+...+...+.. ++..|+.+||..++.
T Consensus 177 ~l~~~el~~~L~~~~~~~g~-~i~~~al~~ia~~s~G~~R~al~~l~~~~~~-~~~~It~~~v~~~l~ 242 (363)
T PRK14961 177 IISEEKIFNFLKYILIKESI-DTDEYALKLIAYHAHGSMRDALNLLEHAINL-GKGNINIKNVTDMLG 242 (363)
T ss_pred CCCHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHHcCCCHHHHHHHHHHHHHh-cCCCCCHHHHHHHHC
Confidence 34444444 34445553 5899999988877655444444444444444 467799999988764
No 131
>PF11705 RNA_pol_3_Rpc31: DNA-directed RNA polymerase III subunit Rpc31; InterPro: IPR024661 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. RNA polymerase III contains seventeen subunits in yeasts and in human cells. Twelve of these are akin to RNA polymerase I or II and the other five are RNA polymerase III-specific, and form the functionally distinct groups: (i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31, Rpc34 and Rpc82 form a cluster of enzyme-specific subunits that contribute to transcription initiation in Saccharomyces cerevisiae and Homo sapiens. There is evidence that these subunits are anchored at or near the N-terminal Zn-fold of Rpc1, itself prolonged by a highly conserved but RNA polymerase III-specific domain []. This entry represents the Rpc31 subunit.
Probab=59.41 E-value=6.3 Score=29.41 Aligned_cols=12 Identities=67% Similarity=1.077 Sum_probs=8.8
Q ss_pred CCCCCCCCccCC
Q 034139 1 MSGRGKGGKGLG 12 (103)
Q Consensus 1 ~~~~~~~~~~~~ 12 (103)
|||||.|+++.+
T Consensus 1 MSgRGggrg~~~ 12 (233)
T PF11705_consen 1 MSGRGGGRGGRG 12 (233)
T ss_pred CCCCCCCCCCCC
Confidence 998888666555
No 132
>CHL00076 chlB photochlorophyllide reductase subunit B
Probab=59.30 E-value=27 Score=29.12 Aligned_cols=50 Identities=14% Similarity=0.022 Sum_probs=40.0
Q ss_pred cccchHHHHHHHHHHHHHH-HHHHHHHHHHHhhCCCceecHHHHHHHHHhcC
Q 034139 45 KRISGLIYEETRGVLKIFL-ENVIRDAVTYTEHARRKTVTAMDVVYALKRQG 95 (103)
Q Consensus 45 ~riS~da~~~l~~~~e~~~-~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~g 95 (103)
..||++|-..|.++ =.|+ ..+=..+.+||+..|...||.+.+..|-..+|
T Consensus 462 ~~w~~ea~~~l~~i-P~f~r~~~r~~~e~~a~~~g~~~it~~~~~~a~~~~~ 512 (513)
T CHL00076 462 LIWSPESQLELSKI-PGFVRGKVKRNTEKFARQNGITNITVEVMYAAKEALS 512 (513)
T ss_pred CCCCHHHHHHHHhC-CHHhHHHHHHHHHHHHHHcCCCeEcHHHHHHHHHhhC
Confidence 46999999999987 3333 45556677899999999999999998876654
No 133
>CHL00081 chlI Mg-protoporyphyrin IX chelatase
Probab=58.03 E-value=68 Score=25.69 Aligned_cols=60 Identities=13% Similarity=-0.015 Sum_probs=41.1
Q ss_pred HHHHHHHHhcCccccchHHHHHHHHHHHHHH-------HHHHHHHHHHHhhCCCceecHHHHHHHHH
Q 034139 33 PAIRRLARRGGVKRISGLIYEETRGVLKIFL-------ENVIRDAVTYTEHARRKTVTAMDVVYALK 92 (103)
Q Consensus 33 a~IkRiar~~G~~riS~da~~~l~~~~e~~~-------~~I~~dA~~~a~ha~RkTI~~~DV~~Alk 92 (103)
..|...-+..---.||+++.+.+.+.+...- ..+++-|-.+|--+||..|+++||..+..
T Consensus 254 ~~I~~ar~~~~~V~v~~~~~~yi~~l~~~~~~~s~Ra~i~l~raArA~Aal~GR~~V~pdDv~~~a~ 320 (350)
T CHL00081 254 SKIVAAQNLLPKVEIDYDLRVKISQICSELDVDGLRGDIVTNRAAKALAAFEGRTEVTPKDIFKVIT 320 (350)
T ss_pred HHHHHHHHhcCCCccCHHHHHHHHHHHHHHCCCCChHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 3343333333345578888888877766643 23456667788889999999999998875
No 134
>cd08315 Death_TRAILR_DR4_DR5 Death domain of Tumor necrosis factor-Related Apoptosis-Inducing Ligand Receptors. Death Domain (DD) found in Tumor necrosis factor-Related Apoptosis-Inducing Ligand (TRAIL) Receptors. In mammals, this family includes TRAILR1 (also called DR4 or TNFRSF10A) and TRAILR2 (also called DR5, TNFRSF10B, or KILLER). They function as receptors for the cytokine TRAIL and are involved in apoptosis signaling pathways. TRAIL preferentially induces apoptosis in cancer cells while exhibiting little toxicity in normal cells. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=57.45 E-value=51 Score=21.44 Aligned_cols=65 Identities=17% Similarity=0.215 Sum_probs=40.1
Q ss_pred cCcchHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhcCC
Q 034139 28 QGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGR 96 (103)
Q Consensus 28 ~~ip~a~IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~g~ 96 (103)
..+|...++++||+.| +|+.-.+.+...--.--+++.+-.....+..|+ .=|.+.+..||+..+.
T Consensus 15 ~~V~~~~Wk~laR~LG---Lse~~I~~i~~~~~~~~eq~~qmL~~W~~~~G~-~At~~~L~~aL~~~~~ 79 (96)
T cd08315 15 KEVPFDSWNRLMRQLG---LSENEIDVAKANERVTREQLYQMLLTWVNKTGR-KASVNTLLDALEAIGL 79 (96)
T ss_pred HHCCHHHHHHHHHHcC---CCHHHHHHHHHHCCCCHHHHHHHHHHHHHhhCC-CcHHHHHHHHHHHccc
Confidence 3578888999999998 455555555543222234445555555555555 4556777777776654
No 135
>TIGR00368 Mg chelatase-related protein. The N-terminal end matches very strongly a pfam Mg_chelatase domain.
Probab=56.89 E-value=36 Score=28.48 Aligned_cols=47 Identities=15% Similarity=0.285 Sum_probs=39.6
Q ss_pred ccchHHHHHHHHHHHHH------HHHHHHHHHHHHhhCCCceecHHHHHHHHH
Q 034139 46 RISGLIYEETRGVLKIF------LENVIRDAVTYTEHARRKTVTAMDVVYALK 92 (103)
Q Consensus 46 riS~da~~~l~~~~e~~------~~~I~~dA~~~a~ha~RkTI~~~DV~~Alk 92 (103)
.+++++.+.|.++++.+ ...|++-|-.+|.-+++..|+.+||..|+.
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 36777777777776665 678889999999999999999999999985
No 136
>cd08815 Death_TNFRSF25_DR3 Death domain of Tumor Necrosis Factor Receptor superfamily 25. Death Domain (DD) found in Tumor Necrosis Factor (TNF) receptor superfamily 25 (TNFRSF25), also known as TRAMP (TNF receptor-related apoptosis-mediating protein), LARD, APO-3, WSL-1, or DR3 (Death Receptor-3). TNFRSF25 is primarily expressed in T cells, is activated by binding to its ligand TL1A, and plays an important role in T-cell function. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=56.69 E-value=50 Score=21.11 Aligned_cols=63 Identities=14% Similarity=0.145 Sum_probs=36.5
Q ss_pred ccCcchHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhcC
Q 034139 27 IQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQG 95 (103)
Q Consensus 27 ~~~ip~a~IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~g 95 (103)
...+|.+..++++|+.|. |+..++.....-.-+-+..-+-.....+... -+.+++..||+..+
T Consensus 6 ~D~VP~~~wk~F~R~LGL---sdn~Ie~~E~~~~~~rda~y~ML~~W~~q~~---a~~n~Ll~aL~~m~ 68 (77)
T cd08815 6 MDAVPARRWKEFVRTLGL---REAEIEAVELEIGRFRDQQYEMLKRWRQQQP---AGLDAVYAALERMG 68 (77)
T ss_pred eccCChHHHHHHHHHcCC---cHhHHHHHHhcccchHHHHHHHHHHHHHcCC---CcHHHHHHHHHHHH
Confidence 347899999999999995 3443333322221122333333445554432 46777777777654
No 137
>PRK13406 bchD magnesium chelatase subunit D; Provisional
Probab=56.68 E-value=62 Score=27.72 Aligned_cols=53 Identities=15% Similarity=-0.014 Sum_probs=41.4
Q ss_pred HhcCccccchHHHHHHHHHHHHHH-------HHHHHHHHHHHhhCCCceecHHHHHHHHH
Q 034139 40 RRGGVKRISGLIYEETRGVLKIFL-------ENVIRDAVTYTEHARRKTVTAMDVVYALK 92 (103)
Q Consensus 40 r~~G~~riS~da~~~l~~~~e~~~-------~~I~~dA~~~a~ha~RkTI~~~DV~~Alk 92 (103)
++.+-..|+++.+..+.+.+..+- ..+++-|-.+|.-++|.+|+.+||..|+.
T Consensus 189 ~rl~~v~v~~~~l~~i~~~~~~~gv~S~Ra~i~llraARa~AaL~Gr~~V~~~dv~~Aa~ 248 (584)
T PRK13406 189 ARLPAVGPPPEAIAALCAAAAALGIASLRAPLLALRAARAAAALAGRTAVEEEDLALAAR 248 (584)
T ss_pred HHHccCCCCHHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 333455688888888777666654 35677788889999999999999999986
No 138
>PRK14971 DNA polymerase III subunits gamma and tau; Provisional
Probab=56.62 E-value=21 Score=30.53 Aligned_cols=63 Identities=11% Similarity=0.030 Sum_probs=43.1
Q ss_pred CcchHHH----HHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHh
Q 034139 29 GITKPAI----RRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKR 93 (103)
Q Consensus 29 ~ip~a~I----kRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr 93 (103)
.++...+ +++++..|+ .+++++++.|.+.+.--+..+.......+.+++.. |+.+||...+..
T Consensus 179 ~ls~~ei~~~L~~ia~~egi-~i~~~al~~La~~s~gdlr~al~~Lekl~~y~~~~-It~~~V~~~l~~ 245 (614)
T PRK14971 179 RIQVADIVNHLQYVASKEGI-TAEPEALNVIAQKADGGMRDALSIFDQVVSFTGGN-ITYKSVIENLNI 245 (614)
T ss_pred CCCHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhccCC-ccHHHHHHHhCC
Confidence 3444444 444456675 58999999999887776777777666666566655 888888776643
No 139
>PRK09862 putative ATP-dependent protease; Provisional
Probab=55.72 E-value=42 Score=28.27 Aligned_cols=47 Identities=11% Similarity=0.039 Sum_probs=35.1
Q ss_pred cchHHHHHHHHHHHHH------HHHHHHHHHHHHhhCCCceecHHHHHHHHHh
Q 034139 47 ISGLIYEETRGVLKIF------LENVIRDAVTYTEHARRKTVTAMDVVYALKR 93 (103)
Q Consensus 47 iS~da~~~l~~~~e~~------~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr 93 (103)
+++++...+......+ ...|++-|-.+|.-++|..|+.+||..|+.-
T Consensus 439 l~~~~~~~l~~~~~~~~lS~Ra~~rlLrvARTiADL~g~~~V~~~hv~eAl~y 491 (506)
T PRK09862 439 LESEDARWLEETLIHLGLSIRAWQRLLKVARTIADIDQSDIITRQHLQEAVSY 491 (506)
T ss_pred CCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHh
Confidence 5555555555544333 4567777888999999999999999999983
No 140
>PRK04195 replication factor C large subunit; Provisional
Probab=54.23 E-value=37 Score=27.82 Aligned_cols=55 Identities=20% Similarity=0.180 Sum_probs=40.8
Q ss_pred HHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHH
Q 034139 35 IRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALK 92 (103)
Q Consensus 35 IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alk 92 (103)
++++++..|+ .+++++++.|.+...--+..++.++..++. ++..|+.+||...+.
T Consensus 169 L~~i~~~egi-~i~~eaL~~Ia~~s~GDlR~ain~Lq~~a~--~~~~it~~~v~~~~~ 223 (482)
T PRK04195 169 LKRICRKEGI-ECDDEALKEIAERSGGDLRSAINDLQAIAE--GYGKLTLEDVKTLGR 223 (482)
T ss_pred HHHHHHHcCC-CCCHHHHHHHHHHcCCCHHHHHHHHHHHhc--CCCCCcHHHHHHhhc
Confidence 3445555566 489999999998887778888888777664 456799999987663
No 141
>PF00725 3HCDH: 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; InterPro: IPR006108 3-hydroxyacyl-CoA dehydrogenase (1.1.1.35 from EC) (HCDH) [] is an enzyme involved in fatty acid metabolism, it catalyzes the reduction of 3-hydroxyacyl-CoA to 3-oxoacyl-CoA. Most eukaryotic cells have 2 fatty-acid beta-oxidation systems, one located in mitochondria and the other in peroxisomes. In peroxisomes 3-hydroxyacyl-CoA dehydrogenase forms, with enoyl-CoA hydratase (ECH) and 3,2-trans-enoyl-CoA isomerase (ECI) a multifunctional enzyme where the N-terminal domain bears the hydratase/isomerase activities and the C-terminal domain the dehydrogenase activity. There are two mitochondrial enzymes: one which is monofunctional and the other which is, like its peroxisomal counterpart, multifunctional. In Escherichia coli (gene fadB) and Pseudomonas fragi (gene faoA) HCDH is part of a multifunctional enzyme which also contains an ECH/ECI domain as well as a 3-hydroxybutyryl-CoA epimerase domain []. There are two major region of similarities in the sequences of proteins of the HCDH family, the first one located in the N-terminal, corresponds to the NAD-binding site, the second one is located in the centre of the sequence. This represents the C-terminal domain which is also found in lambda crystallin. Some proteins include two copies of this domain.; GO: 0003857 3-hydroxyacyl-CoA dehydrogenase activity, 0016491 oxidoreductase activity, 0006631 fatty acid metabolic process, 0055114 oxidation-reduction process; PDB: 3MOG_A 2WTB_A 3ADP_A 3ADO_A 1WDL_B 2D3T_B 1WDK_A 1WDM_B 3K6J_A 1ZCJ_A ....
Probab=53.87 E-value=30 Score=21.58 Aligned_cols=36 Identities=17% Similarity=0.291 Sum_probs=26.7
Q ss_pred HHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHh-cCCc
Q 034139 59 LKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKR-QGRT 97 (103)
Q Consensus 59 ~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr-~g~~ 97 (103)
++..+.-++.+|..+.+.. ..+++||+.+++. .|+|
T Consensus 4 ~nRl~~~~~~ea~~l~~eg---vas~~~ID~~~~~~~G~p 40 (97)
T PF00725_consen 4 VNRLLAALLNEAARLVEEG---VASPEDIDRAMRYGLGFP 40 (97)
T ss_dssp HHHHHHHHHHHHHHHHHTT---SSSHHHHHHHHHHHHTHS
T ss_pred HHHHHHHHHHHHHHHHHHc---CCCHHHHHHHHHHhCCCC
Confidence 3445556677788888753 3689999999997 6776
No 142
>PRK08727 hypothetical protein; Validated
Probab=53.32 E-value=62 Score=23.78 Aligned_cols=63 Identities=14% Similarity=0.018 Sum_probs=40.2
Q ss_pred cchHHHHHHHHh----cCccccchHHHHHHHHHHHHHH---HHHHHHHHHHHhhCCCceecHHHHHHHHHhc
Q 034139 30 ITKPAIRRLARR----GGVKRISGLIYEETRGVLKIFL---ENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 94 (103)
Q Consensus 30 ip~a~IkRiar~----~G~~riS~da~~~l~~~~e~~~---~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~ 94 (103)
+.......|+++ -|+ .+++++.+.|.+...-=+ ..+++.+..++...+| .||.+.|...|...
T Consensus 162 ~~~e~~~~iL~~~a~~~~l-~l~~e~~~~La~~~~rd~r~~l~~L~~l~~~~~~~~~-~it~~~~~~~l~~~ 231 (233)
T PRK08727 162 LDDVARAAVLRERAQRRGL-ALDEAAIDWLLTHGERELAGLVALLDRLDRESLAAKR-RVTVPFLRRVLEEG 231 (233)
T ss_pred CCHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhCC-CCCHHHHHHHHhhc
Confidence 344444555543 354 599999999998866333 3335555544555555 69999999988654
No 143
>PRK08903 DnaA regulatory inactivator Hda; Validated
Probab=52.51 E-value=84 Score=22.49 Aligned_cols=54 Identities=13% Similarity=0.095 Sum_probs=37.5
Q ss_pred HHHHhcCccccchHHHHHHHHHHH---HHHHHHHHHHHHHHhhCCCceecHHHHHHHHH
Q 034139 37 RLARRGGVKRISGLIYEETRGVLK---IFLENVIRDAVTYTEHARRKTVTAMDVVYALK 92 (103)
Q Consensus 37 Riar~~G~~riS~da~~~l~~~~e---~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alk 92 (103)
+++...|+ .+++++++.|..... ..+..++++...++...+ ++||...|..+|.
T Consensus 168 ~~~~~~~v-~l~~~al~~L~~~~~gn~~~l~~~l~~l~~~~~~~~-~~i~~~~~~~~l~ 224 (227)
T PRK08903 168 AAAAERGL-QLADEVPDYLLTHFRRDMPSLMALLDALDRYSLEQK-RPVTLPLLREMLA 224 (227)
T ss_pred HHHHHcCC-CCCHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHhC-CCCCHHHHHHHHh
Confidence 33334454 699999999998755 334456666666666655 5899998888874
No 144
>KOG2680 consensus DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=52.14 E-value=50 Score=27.06 Aligned_cols=49 Identities=10% Similarity=0.023 Sum_probs=40.4
Q ss_pred ccchHHHHHHHHHHH----HHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhc
Q 034139 46 RISGLIYEETRGVLK----IFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 94 (103)
Q Consensus 46 riS~da~~~l~~~~e----~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~ 94 (103)
-+++||++.|...-+ .|.-.++.-|...|...+-++|..+||..+.+.+
T Consensus 377 ~m~~~A~d~Lt~i~~~tsLRYai~Lit~a~~~~~krk~~~v~~~di~r~y~LF 429 (454)
T KOG2680|consen 377 EMNPDALDLLTKIGEATSLRYAIHLITAASLVCLKRKGKVVEVDDIERVYRLF 429 (454)
T ss_pred ccCHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHhcCceeehhHHHHHHHHH
Confidence 489999999886633 5777888888888888888999999999998754
No 145
>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH. HflB(FtsH) is a pleiotropic protein required for correct cell division in bacteria. It has ATP-dependent zinc metalloprotease activity. It was formerly designated cell division protein FtsH.
Probab=52.00 E-value=24 Score=28.91 Aligned_cols=43 Identities=16% Similarity=0.200 Sum_probs=32.1
Q ss_pred HHHHHHHHH----HHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhc
Q 034139 52 YEETRGVLK----IFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 94 (103)
Q Consensus 52 ~~~l~~~~e----~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~ 94 (103)
.+.+.+.++ .-+..++++|...+...+++.|+.+|+..|+++.
T Consensus 249 l~~la~~t~G~sgadl~~l~~eA~~~a~~~~~~~i~~~~l~~a~~~~ 295 (495)
T TIGR01241 249 LKAVARRTPGFSGADLANLLNEAALLAARKNKTEITMNDIEEAIDRV 295 (495)
T ss_pred HHHHHHhCCCCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHH
Confidence 445554433 4467778888877777788899999999999875
No 146
>COG1222 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]
Probab=51.84 E-value=24 Score=29.01 Aligned_cols=34 Identities=24% Similarity=0.299 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhc
Q 034139 61 IFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 94 (103)
Q Consensus 61 ~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~ 94 (103)
.=+..|+.+|-.||-.+.|..||.+|...|.+..
T Consensus 359 AdlkaictEAGm~AiR~~R~~Vt~~DF~~Av~KV 392 (406)
T COG1222 359 ADLKAICTEAGMFAIRERRDEVTMEDFLKAVEKV 392 (406)
T ss_pred HHHHHHHHHHhHHHHHhccCeecHHHHHHHHHHH
Confidence 4478899999999999999999999999999864
No 147
>PF04157 EAP30: EAP30/Vps36 family; InterPro: IPR007286 EAP30 is a subunit of the ELL complex. The ELL is an 80kDa RNA polymerase II transcription factor. ELL interacts with three other proteins to form the complex known as ELL complex. The ELL complex is capable of increasing that catalytic rate of transcription elongation, but is unable to repress initiation of transcription by RNA polymerase II as is the case of ELL. EAP30 is thought to lead to the derepression of ELL's transcriptional inhibitory activity. ; PDB: 2ZME_A 3CUQ_A 1W7P_D 1U5T_B.
Probab=51.50 E-value=25 Score=25.92 Aligned_cols=16 Identities=19% Similarity=0.212 Sum_probs=11.6
Q ss_pred ceecHHHHHHHHHhcC
Q 034139 80 KTVTAMDVVYALKRQG 95 (103)
Q Consensus 80 kTI~~~DV~~Alkr~g 95 (103)
..|+++||..|++.+.
T Consensus 131 ~lISp~Di~~A~~~l~ 146 (223)
T PF04157_consen 131 ELISPEDILRACKLLE 146 (223)
T ss_dssp ST--HHHHHHHHHHHC
T ss_pred CCcCHHHHHHHHHHHH
Confidence 3799999999999763
No 148
>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=50.81 E-value=49 Score=28.16 Aligned_cols=47 Identities=21% Similarity=0.063 Sum_probs=34.9
Q ss_pred ccchHHHHHHHHHHHHHH-------HHHHHHHHHHHhhCCCceecHHHHHHHHH
Q 034139 46 RISGLIYEETRGVLKIFL-------ENVIRDAVTYTEHARRKTVTAMDVVYALK 92 (103)
Q Consensus 46 riS~da~~~l~~~~e~~~-------~~I~~dA~~~a~ha~RkTI~~~DV~~Alk 92 (103)
.|++++.+.+.+..-.+- ..+++-|..+|--.+|.+|+.+||..|..
T Consensus 203 ~i~~~~~~~l~~~~~~~gv~s~Ra~i~~~r~ArA~Aal~gr~~V~~~Dv~~a~~ 256 (589)
T TIGR02031 203 TISAEQVKELVLTAASLGISGHRADLFAVRAAKAHAALHGRTEVTEEDLKLAVE 256 (589)
T ss_pred cCCHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHH
Confidence 578888777776643332 23456677778889999999999999986
No 149
>KOG1942 consensus DNA helicase, TBP-interacting protein [Replication, recombination and repair]
Probab=50.57 E-value=42 Score=27.43 Aligned_cols=49 Identities=10% Similarity=0.079 Sum_probs=40.7
Q ss_pred cccchHHHHHHHHH----HHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHh
Q 034139 45 KRISGLIYEETRGV----LKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKR 93 (103)
Q Consensus 45 ~riS~da~~~l~~~----~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr 93 (103)
-.++++|++.|.+. .-.|.-+++--|..+|+-.||+.|..+||+.+-..
T Consensus 385 l~~~e~a~~~l~~~gt~tsLRy~vqLl~p~~~~ak~~g~~~i~v~dvee~~~L 437 (456)
T KOG1942|consen 385 LQVEEEALDLLAEIGTSTSLRYAVQLLTPASILAKTNGRKEISVEDVEEVTEL 437 (456)
T ss_pred ceecHHHHHHHHhhccchhHHHHHHhcCHHHHHHHHcCCceeecccHHHHHHH
Confidence 35889999988874 45677888888999999999999999999987543
No 150
>PF00493 MCM: MCM2/3/5 family This family extends the MCM domain of Prosite.; InterPro: IPR001208 MCM proteins are DNA-dependent ATPases required for the initiation of eukaryotic DNA replication [, , ]. In eukaryotes there is a family of six proteins, MCM2 to MCM7. They were first identified in yeast where most of them have a direct role in the initiation of chromosomal DNA replication by interacting directly with autonomously replicating sequences (ARS). They were thus called minichromosome maintenance proteins, MCM proteins []. This family is also present in the archebacteria in 1 to 4 copies. Methanocaldococcus jannaschii (Methanococcus jannaschii) has four members, MJ0363, MJ0961, MJ1489 and MJECL13. The "MCM motif" contains Walker-A and Walker-B type nucleotide binding motifs. The diagnostic sequence defining the MCMs is IDEFDKM. Only Mcm2 (aka Cdc19 or Nda1) has been subjected to mutational analysis in this region, and most mutations abolish its activity []. The presence of a putative ATP-binding domain implies that these proteins may be involved in an ATP-consuming step in the initiation of DNA replication in eukaryotes. The MCM proteins bind together in a large complex []. Within this complex, individual subunits associate with different affinities, and there is a tightly associated core of Mcm4 (Cdc21), Mcm6 (Mis5) and Mcm7 []. This core complex in human MCMs has been associated with helicase activity in vitro [], leading to the suggestion that the MCM proteins are the eukaryotic replicative helicase. Schizosaccharomyces pombe (Fission yeast) MCMs, like those in metazoans, are found in the nucleus throughout the cell cycle. This is in contrast to the Saccharomyces cerevisiae (Baker's yeast) in which MCM proteins move in and out of the nucleus during each cell cycle. The assembly of the MCM complex in S. pombe is required for MCM localisation, ensuring that only intact MCM complexes remain in the nucleus [].; GO: 0003677 DNA binding, 0005524 ATP binding, 0006260 DNA replication; PDB: 3F8T_A 3F9V_A.
Probab=50.53 E-value=16 Score=28.60 Aligned_cols=66 Identities=23% Similarity=0.134 Sum_probs=46.3
Q ss_pred CcchHHHHHHH---HhcCccccchHHHHHHHHHH------H-----------HHHHHHHHHHHHHHhhCCCceecHHHHH
Q 034139 29 GITKPAIRRLA---RRGGVKRISGLIYEETRGVL------K-----------IFLENVIRDAVTYTEHARRKTVTAMDVV 88 (103)
Q Consensus 29 ~ip~a~IkRia---r~~G~~riS~da~~~l~~~~------e-----------~~~~~I~~dA~~~a~ha~RkTI~~~DV~ 88 (103)
.+|...+++.. |..-...+|++|.+.|.+.- . ..++.+++-|...|+-.-|.+|+.+||.
T Consensus 241 ~~~~~~lr~yI~yar~~~~P~ls~ea~~~I~~~Yv~lR~~~~~~~~~~~iT~R~LeSLIRLseA~AKl~lr~~V~~~Dv~ 320 (331)
T PF00493_consen 241 PISEDLLRKYIAYARQNIHPVLSEEAKELIINYYVELRKESKSNNKSIPITIRQLESLIRLSEAHAKLRLRDEVTEEDVE 320 (331)
T ss_dssp TT-HCCCHHHHHHHHHHC--EE-HHCHHHHHHHHCCCCHCHHCHSS-B-SSCCCCCHHHHHHHHHHHCTTSSECSHHHHH
T ss_pred ccCHHHHHHHHHHHHhhcccccCHHHHHHHHHHHHHhcccccccccccccchhhHHHHHHHHHHHHHHhccCceeHHHHH
Confidence 56666666443 52223469999988887651 1 1347788999999999999999999999
Q ss_pred HHHHhc
Q 034139 89 YALKRQ 94 (103)
Q Consensus 89 ~Alkr~ 94 (103)
.|++..
T Consensus 321 ~Ai~L~ 326 (331)
T PF00493_consen 321 EAIRLF 326 (331)
T ss_dssp HHHHHH
T ss_pred HHHHHH
Confidence 998753
No 151
>KOG0784 consensus Isocitrate dehydrogenase, gamma subunit [Amino acid transport and metabolism]
Probab=50.28 E-value=8.1 Score=31.36 Aligned_cols=37 Identities=30% Similarity=0.322 Sum_probs=30.2
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHH
Q 034139 49 GLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAM 85 (103)
Q Consensus 49 ~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~ 85 (103)
+.+++.|.=+..+-.+.|++-|.+||...+||.||+-
T Consensus 172 pGVVEsLKVvT~~kseRIaryAF~yA~k~gRKkVTaV 208 (375)
T KOG0784|consen 172 PGVVESLKVVTRFKSERIARYAFEYAKKNGRKKVTAV 208 (375)
T ss_pred cchhheeeeehhhhhHHHHHHHHHHHHHhCCceEEEE
Confidence 4566666666777888999999999999999999863
No 152
>PRK06305 DNA polymerase III subunits gamma and tau; Validated
Probab=50.16 E-value=47 Score=27.24 Aligned_cols=62 Identities=15% Similarity=-0.030 Sum_probs=37.5
Q ss_pred CcchHHHHHHHH----hcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHH
Q 034139 29 GITKPAIRRLAR----RGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALK 92 (103)
Q Consensus 29 ~ip~a~IkRiar----~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alk 92 (103)
.++...+..+++ ..|+ .+++++++.|.+...-=+..+.......+...+ .+|+.+||..++-
T Consensus 179 ~l~~~el~~~L~~~~~~eg~-~i~~~al~~L~~~s~gdlr~a~~~Lekl~~~~~-~~It~~~V~~l~~ 244 (451)
T PRK06305 179 RIPEETIIDKLALIAKQEGI-ETSREALLPIARAAQGSLRDAESLYDYVVGLFP-KSLDPDSVAKALG 244 (451)
T ss_pred CCCHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhcc-CCcCHHHHHHHHC
Confidence 455555554443 3454 489999999888765555555554444433333 3489988876653
No 153
>cd07064 AlkD_like_1 A new structural DNA glycosylase containing HEAT-like repeats. This domain represents a new and uncharacterized structural superfamily of DNA glycosylases that form an alpha-alpha superhelix fold that are not belong to the identified five structural DNA glycosylase superfamilies (UDG, AAG/MNPG, MutM/Fpg and helix-hairpin-helix). DNA glycosylases removing alkylated base residues have been identified in all organisms investigated and may be universally present in nature. DNA glycosylases catalyze the first step in Base Excision Repair (BER) pathway by cleaving damaged DNA bases within double strand DNA to produce an abasic site. The resulting abasic site is further processed by AP endonuclease, phosphodiesterase, DNA polymerases, and DNA ligase functions to restore the DNA to an undamaged state. All glycosylase examined to date utilize a similar strategy for binding DNA and base flipping despite their structural diversity. The known structures for members of this fa
Probab=49.83 E-value=30 Score=25.26 Aligned_cols=73 Identities=19% Similarity=0.078 Sum_probs=38.4
Q ss_pred cccchhhcccccCcchHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHH----HHHHHhhCCCceecHHHHHHHHH
Q 034139 17 KRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRD----AVTYTEHARRKTVTAMDVVYALK 92 (103)
Q Consensus 17 kr~~k~~r~~~~~ip~a~IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~d----A~~~a~ha~RkTI~~~DV~~Alk 92 (103)
+|++|.... ..++|.+.++.+++..+.. ++.+..+++.+.++++.++-..+ |..+... .++.++.+|+....+
T Consensus 11 ~~y~k~~~~-f~Gv~~P~~R~lak~~~~~-~~~~~~~~~~~l~~~Lw~~~~~E~r~~al~~l~~-~~~~~~~~~~~~~~~ 87 (208)
T cd07064 11 KAYMKNQFP-FYGIKTPERRALSKPFLKE-SKLPDKEELWELVLELWQQPEREYQYVAIDLLRK-YKKFLTPEDLPLLEE 87 (208)
T ss_pred HHHHhcCCc-cCCCChHHHHHHHHHHHHH-cCCCcHHHHHHHHHHHHcchHHHHHHHHHHHHHH-HHhcCCHHHHHHHHH
Confidence 345555443 3499999999999988642 11111333333333333333222 2333332 455678888655443
No 154
>CHL00176 ftsH cell division protein; Validated
Probab=49.66 E-value=25 Score=30.30 Aligned_cols=33 Identities=24% Similarity=0.367 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHHHhhCCCceecHHHHHHHHHhc
Q 034139 62 FLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 94 (103)
Q Consensus 62 ~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~ 94 (103)
-+..++.+|...+...+++.|+.+|+..|+.+.
T Consensus 391 DL~~lvneAal~a~r~~~~~It~~dl~~Ai~rv 423 (638)
T CHL00176 391 DLANLLNEAAILTARRKKATITMKEIDTAIDRV 423 (638)
T ss_pred HHHHHHHHHHHHHHHhCCCCcCHHHHHHHHHHH
Confidence 567888888888777888999999999999875
No 155
>cd08780 Death_TRADD Death Domain of Tumor Necrosis Factor Receptor 1-Associated Death Domain protein. Death domain (DD) of TRADD (TNF Receptor 1-Associated Death Domain or TNFRSF1A-associated via death domain) protein. TRADD is a central signaling adaptor for TNF-receptor 1 (TNFR1), mediating activation of Nuclear Factor -kappaB (NF-kB) and c-Jun N-terminal kinase (JNK), as well as caspase-dependent apoptosis. It also carries important immunological roles including germinal center formation, DR3-mediated T-cell stimulation, and TNFalpha-mediated inflammatory responses. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into s
Probab=49.58 E-value=73 Score=20.96 Aligned_cols=62 Identities=13% Similarity=0.126 Sum_probs=44.2
Q ss_pred HHHHHHHhcC--ccccchHHHHHHHHHHH-H-HHHHHHHHHHHHHhhCCCceecHHHHHHHHHhcCC
Q 034139 34 AIRRLARRGG--VKRISGLIYEETRGVLK-I-FLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGR 96 (103)
Q Consensus 34 ~IkRiar~~G--~~riS~da~~~l~~~~e-~-~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~g~ 96 (103)
..++++|+.| ..-+++..++.|...-+ + .-+++-+-...+-+..|++ -|.+.+..||+..+.
T Consensus 15 ~WK~laR~Lg~~cral~d~~ID~I~~~y~r~gL~EqvyQ~L~~W~~~eg~~-Atv~~Lv~AL~~c~l 80 (90)
T cd08780 15 KWKPVGRSLQKNCRALRDPAIDNLAYEYDREGLYEQAYQLLRRFIQSEGKK-ATLQRLVQALEENGL 80 (90)
T ss_pred HHHHHHHHHcccccccchhHHHHHHhhcccccHHHHHHHHHHHHHHhcccc-chHHHHHHHHHHccc
Confidence 3677888887 34478888888874433 3 4555556666777777877 999999999987654
No 156
>PRK14958 DNA polymerase III subunits gamma and tau; Provisional
Probab=49.56 E-value=54 Score=27.45 Aligned_cols=63 Identities=11% Similarity=0.018 Sum_probs=39.8
Q ss_pred CcchHHH----HHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHh
Q 034139 29 GITKPAI----RRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKR 93 (103)
Q Consensus 29 ~ip~a~I----kRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr 93 (103)
.+|...| +.+++..|+ .++++++..+.+...-=+..+.......+-+ +...|+.+||...+-.
T Consensus 177 ~l~~~~i~~~l~~il~~egi-~~~~~al~~ia~~s~GslR~al~lLdq~ia~-~~~~It~~~V~~~lg~ 243 (509)
T PRK14958 177 QLPPLQIAAHCQHLLKEENV-EFENAALDLLARAANGSVRDALSLLDQSIAY-GNGKVLIADVKTMLGT 243 (509)
T ss_pred CCCHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHHcCCcHHHHHHHHHHHHhc-CCCCcCHHHHHHHHCC
Confidence 4555544 345666675 4899999988877655444444444333333 3556999999987643
No 157
>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=49.53 E-value=67 Score=27.50 Aligned_cols=65 Identities=17% Similarity=0.101 Sum_probs=39.3
Q ss_pred chHHHHHHHHh----cCccccchHHHHHHHHHHH--HHHHHHHHHHHHHH--------hhCCCceecHHHHHHHHHhcCC
Q 034139 31 TKPAIRRLARR----GGVKRISGLIYEETRGVLK--IFLENVIRDAVTYT--------EHARRKTVTAMDVVYALKRQGR 96 (103)
Q Consensus 31 p~a~IkRiar~----~G~~riS~da~~~l~~~~e--~~~~~I~~dA~~~a--------~ha~RkTI~~~DV~~Alkr~g~ 96 (103)
+...+..|+++ .++ .+++++.+.|.+..- .....+++++..++ +..+..+|+.+||..+++...+
T Consensus 354 s~edi~~Il~~~a~~~~v-~ls~eal~~L~~ys~~gRraln~L~~~~~~~~~~~~~~~~~~~~~~I~~edv~~~l~~~r~ 432 (615)
T TIGR02903 354 TPEDIALIVLNAAEKINV-HLAAGVEELIARYTIEGRKAVNILADVYGYALYRAAEAGKENDKVTITQDDVYEVIQISRL 432 (615)
T ss_pred CHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHCCCcHHHHHHHHHHHHHHHHHHHHHhccCCCCeeECHHHHHHHhCCCcC
Confidence 33445555544 343 488998888876421 22334555555443 2334568999999999986544
No 158
>KOG0480 consensus DNA replication licensing factor, MCM6 component [Replication, recombination and repair]
Probab=49.51 E-value=89 Score=27.78 Aligned_cols=82 Identities=22% Similarity=0.129 Sum_probs=57.9
Q ss_pred cchhhccccc--CcchHHHHHHHHhc--CccccchHHHHHHHHHHH-------------------HHHHHHHHHHHHHHh
Q 034139 19 HRKVLRDNIQ--GITKPAIRRLARRG--GVKRISGLIYEETRGVLK-------------------IFLENVIRDAVTYTE 75 (103)
Q Consensus 19 ~~k~~r~~~~--~ip~a~IkRiar~~--G~~riS~da~~~l~~~~e-------------------~~~~~I~~dA~~~a~ 75 (103)
|+.+...+.+ .+|..-|++.++=+ =-.++|.+|.+.|.+... .-|+.+++-+...|+
T Consensus 545 h~~i~~~~~~~~~~~~e~vrkYi~yAR~~~P~ls~ea~~~lve~Y~~lR~~~~~~~~~~s~~ITvRqLESlIRLsEA~Ar 624 (764)
T KOG0480|consen 545 HRGIDDATERVCVYTLEQVRKYIRYARNFKPKLSKEASEMLVEKYKGLRQRDAQGNNRSSYRITVRQLESLIRLSEARAR 624 (764)
T ss_pred hccccccccccccccHHHHHHHHHHHHhcCccccHHHHHHHHHHHHHHHHhhccccCcccccccHHHHHHHHHHHHHHHh
Confidence 3333334444 78888888655322 235788888888775422 235667888888999
Q ss_pred hCCCceecHHHHHHHHHhcCCcccc
Q 034139 76 HARRKTVTAMDVVYALKRQGRTLYG 100 (103)
Q Consensus 76 ha~RkTI~~~DV~~Alkr~g~~lYg 100 (103)
-.-|.-||.+||..|.+.+...+|.
T Consensus 625 ~~~~devt~~~v~ea~eLlk~Siv~ 649 (764)
T KOG0480|consen 625 VECRDEVTKEDVEEAVELLKKSIVR 649 (764)
T ss_pred hhhhhhccHHHHHHHHHHHHhhhee
Confidence 9999999999999999987766554
No 159
>cd08316 Death_FAS_TNFRSF6 Death domain of FAS or TNF receptor superfamily member 6. Death Domain (DD) found in the FS7-associated cell surface antigen (FAS). FAS, also known as TNFRSF6 (TNF receptor superfamily member 6), APT1, CD95, FAS1, or APO-1, together with FADD (Fas-associating via Death Domain) and caspase 8, is an integral part of the death inducing signalling complex (DISC), which plays an important role in the induction of apoptosis and is activated by binding of the ligand FasL to FAS. FAS also plays a critical role in self-tolerance by eliminating cell types (autoreactive T and B cells) that contribute to autoimmunity. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in sign
Probab=49.44 E-value=73 Score=20.90 Aligned_cols=64 Identities=11% Similarity=0.139 Sum_probs=41.6
Q ss_pred cCcchHHHHHHHHhcCccccchHHHHHHHHHH-HHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhcC
Q 034139 28 QGITKPAIRRLARRGGVKRISGLIYEETRGVL-KIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQG 95 (103)
Q Consensus 28 ~~ip~a~IkRiar~~G~~riS~da~~~l~~~~-e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~g 95 (103)
..+|...+++++|+.| +|+...+.+...- ...-++..+-...+.+-.|++ =+.+++..+|+..+
T Consensus 16 ~~~~~~~wK~faR~lg---lse~~Id~I~~~~~~d~~Eq~~qmL~~W~~~~G~~-a~~~~Li~aLr~~~ 80 (97)
T cd08316 16 DVMTLKDVKKFVRKSG---LSEPKIDEIKLDNPQDTAEQKVQLLRAWYQSHGKT-GAYRTLIKTLRKAK 80 (97)
T ss_pred HHcCHHHHHHHHHHcC---CCHHHHHHHHHcCCCChHHHHHHHHHHHHHHhCCC-chHHHHHHHHHHcc
Confidence 3578889999999999 5666666666432 334455555566666654443 23477777777654
No 160
>PF02971 FTCD: Formiminotransferase domain; InterPro: IPR013802 The formiminotransferase (FT) domain of formiminotransferase-cyclodeaminase (FTCD) forms a homodimer, with each protomer being comprised of two subdomains. The formiminotransferase domain has an N-terminal subdomain that is made up of a six-stranded mixed beta-pleated sheet and five alpha helices, which are arranged on the external surface of the beta sheet. This, in turn, faces the beta-sheet of the C-terminal subdomain to form a double beta-sheet layer. The two subdomains are separated by a short linker sequence, which is not thought to be any more flexible than the remainder of the molecule. The substrate is predicted to form a number of contacts with residues found in both the N-terminal and C-terminal subdomains []. In humans, deficiency of this enzyme results in a disease phenotype []. This entry represents the C-terminal subdomain of the formiminotransferase domain.; GO: 0005542 folic acid binding, 0016740 transferase activity, 0008152 metabolic process; PDB: 1QD1_B 2PFD_C.
Probab=49.39 E-value=50 Score=23.56 Aligned_cols=57 Identities=21% Similarity=0.309 Sum_probs=31.3
Q ss_pred HHHHHHhcCccccchHH-----HHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHH-HHHHHHhcC-CcccccC
Q 034139 35 IRRLARRGGVKRISGLI-----YEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMD-VVYALKRQG-RTLYGFG 102 (103)
Q Consensus 35 IkRiar~~G~~riS~da-----~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~D-V~~Alkr~g-~~lYgf~ 102 (103)
|++.|++.|+.-+..+. .++|.++.++|+. -+++.++..++ |.+|++++| ..+.-|+
T Consensus 73 v~~eA~~~Gv~v~gsElVGlvP~~Alldaa~yyl~-----------~e~~~~~~e~~~i~lav~~LGL~~l~pF~ 136 (145)
T PF02971_consen 73 VKREAARYGVPVVGSELVGLVPLDALLDAAEYYLQ-----------KENFFILPEEQKIRLAVKRLGLDSLSPFD 136 (145)
T ss_dssp HHHHHHCTT--EEEEEEES-B-HHHHHHHHHHHHH-----------HCT----SHHHHHHHHHHCCTTTSSS---
T ss_pred HHHHHHHhCCCccceEEEccccHHHHHHHHHHHhc-----------ccccccCChHHHHHHHHHHcCccccCCCC
Confidence 66777777765444444 5667777777765 34556677766 567788888 4555554
No 161
>PRK14953 DNA polymerase III subunits gamma and tau; Provisional
Probab=48.92 E-value=50 Score=27.46 Aligned_cols=56 Identities=9% Similarity=-0.047 Sum_probs=37.8
Q ss_pred HHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHH
Q 034139 35 IRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALK 92 (103)
Q Consensus 35 IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alk 92 (103)
+.++++..|+ .++++++..|.+..+-=+..+...+...+.++ ...||.+||..++-
T Consensus 187 L~~i~k~egi-~id~~al~~La~~s~G~lr~al~~Ldkl~~~~-~~~It~~~V~~~lg 242 (486)
T PRK14953 187 LKRICNEEKI-EYEEKALDLLAQASEGGMRDAASLLDQASTYG-EGKVTIKVVEEFLG 242 (486)
T ss_pred HHHHHHHcCC-CCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhc-CCCcCHHHHHHHhC
Confidence 4445556675 58999999988877665665555555554454 33599999887663
No 162
>PRK14950 DNA polymerase III subunits gamma and tau; Provisional
Probab=48.88 E-value=46 Score=28.13 Aligned_cols=62 Identities=8% Similarity=-0.020 Sum_probs=41.4
Q ss_pred cchHHHHH----HHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHh
Q 034139 30 ITKPAIRR----LARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKR 93 (103)
Q Consensus 30 ip~a~IkR----iar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr 93 (103)
++...+.. ++...|+ .++++++..|.+...--+..+.....+++.+. ..+|+.+||..++..
T Consensus 179 l~~~el~~~L~~~a~~egl-~i~~eal~~La~~s~Gdlr~al~~LekL~~y~-~~~It~e~V~~ll~~ 244 (585)
T PRK14950 179 HSVADMAAHLRKIAAAEGI-NLEPGALEAIARAATGSMRDAENLLQQLATTY-GGEISLSQVQSLLGI 244 (585)
T ss_pred CCHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhc-CCCCCHHHHHHHhcC
Confidence 44444443 4444465 48999999998887766666666666666553 447999998876644
No 163
>PRK13531 regulatory ATPase RavA; Provisional
Probab=48.81 E-value=1.2e+02 Score=25.64 Aligned_cols=63 Identities=13% Similarity=0.145 Sum_probs=43.3
Q ss_pred CcchHHHHHHHHhcCccccchHHHHHHHHHHHH-------------HHHHHHHHHHHHHhhCCCceecHHHHHHHH
Q 034139 29 GITKPAIRRLARRGGVKRISGLIYEETRGVLKI-------------FLENVIRDAVTYTEHARRKTVTAMDVVYAL 91 (103)
Q Consensus 29 ~ip~a~IkRiar~~G~~riS~da~~~l~~~~e~-------------~~~~I~~dA~~~a~ha~RkTI~~~DV~~Al 91 (103)
.|+...+..+-+.+---.|++++.+.+.+.... ....++.-|..+|=-.||..|+++||..+.
T Consensus 206 vis~eel~~lq~~v~~V~v~d~v~eyI~~L~~~lr~~r~~~~~SpR~~~~l~~~akA~A~l~GR~~V~p~Dv~ll~ 281 (498)
T PRK13531 206 QITDEEYQQWQKEIGKITLPDHVFELIFQLRQQLDALPNAPYVSDRRWKKAIRLLQASAFFSGRDAIAPIDLILLK 281 (498)
T ss_pred CCCHHHHHHHHHHhcceeCCHHHHHHHHHHHHHHhcCCCCCCcCcHHHHHHHHHHHHHHHHCCCCCCCHHHHHHhH
Confidence 355566666655555456777777777766542 233456667777888999999999999543
No 164
>PRK06893 DNA replication initiation factor; Validated
Probab=48.56 E-value=1e+02 Score=22.49 Aligned_cols=50 Identities=18% Similarity=0.003 Sum_probs=30.9
Q ss_pred hcCccccchHHHHHHHHHHH---HHHHHHHHHHHHHHhhCCCceecHHHHHHHHH
Q 034139 41 RGGVKRISGLIYEETRGVLK---IFLENVIRDAVTYTEHARRKTVTAMDVVYALK 92 (103)
Q Consensus 41 ~~G~~riS~da~~~l~~~~e---~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alk 92 (103)
.-+ -.+++++++.|.+.++ ..+..+++.....+-..+| .||...|..+|.
T Consensus 176 ~~~-l~l~~~v~~~L~~~~~~d~r~l~~~l~~l~~~~~~~~~-~it~~~v~~~L~ 228 (229)
T PRK06893 176 QRG-IELSDEVANFLLKRLDRDMHTLFDALDLLDKASLQAQR-KLTIPFVKEILG 228 (229)
T ss_pred HcC-CCCCHHHHHHHHHhccCCHHHHHHHHHHHHHHHHhcCC-CCCHHHHHHHhc
Confidence 334 3689999999987654 2333333333333334455 599999888763
No 165
>PRK00149 dnaA chromosomal replication initiation protein; Reviewed
Probab=48.40 E-value=77 Score=25.64 Aligned_cols=47 Identities=17% Similarity=0.146 Sum_probs=29.3
Q ss_pred ccchHHHHHHHHHHH---HHHHHHHHHHHHHHhhCCCceecHHHHHHHHHh
Q 034139 46 RISGLIYEETRGVLK---IFLENVIRDAVTYTEHARRKTVTAMDVVYALKR 93 (103)
Q Consensus 46 riS~da~~~l~~~~e---~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr 93 (103)
.+++++++.|.+.+. .-+..++.....++...+|. ||.+.+..+|+.
T Consensus 299 ~l~~e~l~~ia~~~~~~~R~l~~~l~~l~~~~~~~~~~-it~~~~~~~l~~ 348 (450)
T PRK00149 299 DLPDEVLEFIAKNITSNVRELEGALNRLIAYASLTGKP-ITLELAKEALKD 348 (450)
T ss_pred CCCHHHHHHHHcCcCCCHHHHHHHHHHHHHHHHhhCCC-CCHHHHHHHHHH
Confidence 488888888887544 22333444555555555543 777777777764
No 166
>PRK14952 DNA polymerase III subunits gamma and tau; Provisional
Probab=48.26 E-value=49 Score=28.34 Aligned_cols=62 Identities=13% Similarity=0.046 Sum_probs=39.7
Q ss_pred CcchHHH----HHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHH
Q 034139 29 GITKPAI----RRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYAL 91 (103)
Q Consensus 29 ~ip~a~I----kRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Al 91 (103)
.++...+ .++++..|+ .++++++..+.+...-=+.+++...-+++-..+...|+.+||...+
T Consensus 176 ~l~~~~i~~~L~~i~~~egi-~i~~~al~~Ia~~s~GdlR~aln~Ldql~~~~~~~~It~~~v~~ll 241 (584)
T PRK14952 176 LLPPRTMRALIARICEQEGV-VVDDAVYPLVIRAGGGSPRDTLSVLDQLLAGAADTHVTYQRALGLL 241 (584)
T ss_pred CCCHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHHcCCCHHHHHHHHHHHHhccCCCCcCHHHHHHHH
Confidence 4555544 445555665 4899999888776555455555555555545556678988887665
No 167
>COG0325 Predicted enzyme with a TIM-barrel fold [General function prediction only]
Probab=48.00 E-value=51 Score=25.16 Aligned_cols=40 Identities=35% Similarity=0.366 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHHHHHhhCCC-----------ceecHHHHHHHHHhcCCcccc
Q 034139 60 KIFLENVIRDAVTYTEHARR-----------KTVTAMDVVYALKRQGRTLYG 100 (103)
Q Consensus 60 e~~~~~I~~dA~~~a~ha~R-----------kTI~~~DV~~Alkr~g~~lYg 100 (103)
..-+..|.+.-...|++++| ||+.++||..|+ ..|...+|
T Consensus 4 ~~nl~~v~~~I~~a~~~a~R~~~~V~LvAVSK~~~~~~I~~~~-~aG~r~fG 54 (228)
T COG0325 4 KENLAAVRERIAAAAERAGRNPGSVTLVAVSKTVPAEDIREAY-EAGQRHFG 54 (228)
T ss_pred HHHHHHHHHHHHHHHHHcCCCCCcEEEEEEeCCCCHHHHHHHH-HcCChhhc
Confidence 34455666667777888888 689999999888 45655555
No 168
>PF12909 DUF3832: Protein of unknown function (DUF3832); InterPro: IPR024308 This domain found in bacteria and Acanthamoeba polyphaga mimivirus (APMV) L591 protein has no known function. In Q0AZ30 from SWISSPROT and other uncharacterised proteins this domain is found C-terminal, while the N terminus shows remote homology to the bacterial toxin/antitoxin 'addiction module' (PF12910 from PFAM).; PDB: 3K6Q_C.
Probab=47.75 E-value=43 Score=21.81 Aligned_cols=34 Identities=12% Similarity=0.113 Sum_probs=28.8
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCce
Q 034139 48 SGLIYEETRGVLKIFLENVIRDAVTYTEHARRKT 81 (103)
Q Consensus 48 S~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkT 81 (103)
-++|.++|.+.+-+|.++=..+.-.|..+-+|+.
T Consensus 35 ~eeA~~~lie~l~dYAedy~~~~~~~~~apnR~~ 68 (89)
T PF12909_consen 35 LEEAIEDLIEDLRDYAEDYMNRFPLFYNAPNRRH 68 (89)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHTHHHHHTSTTTGG
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccc
Confidence 3588888889999999999999999988888874
No 169
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=46.23 E-value=48 Score=19.83 Aligned_cols=33 Identities=21% Similarity=0.337 Sum_probs=24.7
Q ss_pred CcchHHHHHHHHhcCccccchHHHHHHHHHHHHHH
Q 034139 29 GITKPAIRRLARRGGVKRISGLIYEETRGVLKIFL 63 (103)
Q Consensus 29 ~ip~a~IkRiar~~G~~riS~da~~~l~~~~e~~~ 63 (103)
+++.++|.|++. |...|+++..+.+.++++++-
T Consensus 11 gvS~~TVSr~ln--~~~~v~~~t~~~i~~~~~~~g 43 (70)
T smart00354 11 GVSKATVSRVLN--GNGRVSEETREKVLAAMEELG 43 (70)
T ss_pred CCCHHHHHHHHC--CCCCCCHHHHHHHHHHHHHhC
Confidence 678888888885 456688888888877766653
No 170
>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=46.04 E-value=50 Score=18.00 Aligned_cols=32 Identities=19% Similarity=0.303 Sum_probs=22.7
Q ss_pred CcchHHHHHHHHhcCccccchHHHHHHHHHHHHH
Q 034139 29 GITKPAIRRLARRGGVKRISGLIYEETRGVLKIF 62 (103)
Q Consensus 29 ~ip~a~IkRiar~~G~~riS~da~~~l~~~~e~~ 62 (103)
+++.++|.++.+ |...++++....+.+++.++
T Consensus 8 gvs~~tvs~~l~--g~~~vs~~~~~~i~~~~~~l 39 (52)
T cd01392 8 GVSVATVSRVLN--GKPRVSEETRERVLAAAEEL 39 (52)
T ss_pred CcCHHHHHHHHc--CCCCCCHHHHHHHHHHHHHh
Confidence 678888888886 44467877777777665543
No 171
>PRK10733 hflB ATP-dependent metalloprotease; Reviewed
Probab=45.88 E-value=33 Score=29.42 Aligned_cols=33 Identities=15% Similarity=0.316 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHHHhhCCCceecHHHHHHHHHhc
Q 034139 62 FLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 94 (103)
Q Consensus 62 ~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~ 94 (103)
-+..++.+|...|...++..|+.+|+..|+.+.
T Consensus 360 dl~~l~~eAa~~a~r~~~~~i~~~d~~~a~~~v 392 (644)
T PRK10733 360 DLANLVNEAALFAARGNKRVVSMVEFEKAKDKI 392 (644)
T ss_pred HHHHHHHHHHHHHHHcCCCcccHHHHHHHHHHH
Confidence 678888899999999999999999999998754
No 172
>KOG0481 consensus DNA replication licensing factor, MCM5 component [Replication, recombination and repair]
Probab=45.60 E-value=1e+02 Score=26.94 Aligned_cols=69 Identities=23% Similarity=0.106 Sum_probs=50.0
Q ss_pred cccCcchHHHHHHH---HhcCccccchHHHHHHHHH-----------------------HHHHHHHHHHHHHHHHhhCCC
Q 034139 26 NIQGITKPAIRRLA---RRGGVKRISGLIYEETRGV-----------------------LKIFLENVIRDAVTYTEHARR 79 (103)
Q Consensus 26 ~~~~ip~a~IkRia---r~~G~~riS~da~~~l~~~-----------------------~e~~~~~I~~dA~~~a~ha~R 79 (103)
+...||...++|.. |.-...|+|++|.+.|... .-.-++-|++-+.-.|+..=-
T Consensus 545 ~~~ei~~~~~KryI~YcR~kc~PrLs~~AaekL~~~yV~~R~~~~q~e~~s~~rssIPITVRQLEAIiRI~ESLAKm~Ls 624 (729)
T KOG0481|consen 545 NEGEIPIEKLKRYIQYCRLKCGPRLSAEAAEKLSSRYVTMRKGVRQHEQDSDKRSSIPITVRQLEAIIRIAESLAKMELS 624 (729)
T ss_pred CCCcccHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHhHHHHHHHHhhhcccccCCCceeHHHHHHHHHHHHHHHhhcCC
Confidence 45579999999876 5556689999999888732 123455666666677776666
Q ss_pred ceecHHHHHHHHHhc
Q 034139 80 KTVTAMDVVYALKRQ 94 (103)
Q Consensus 80 kTI~~~DV~~Alkr~ 94 (103)
--.|..||+.|++.+
T Consensus 625 ~~ate~hV~EA~RLF 639 (729)
T KOG0481|consen 625 PFATEAHVEEALRLF 639 (729)
T ss_pred ccccHHHHHHHHHHH
Confidence 678888888888753
No 173
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=45.41 E-value=1.1e+02 Score=22.68 Aligned_cols=64 Identities=13% Similarity=0.205 Sum_probs=35.0
Q ss_pred CcchHHHHHHHHhcCccccchHHHHHHHHHH-----------------HHHHHHHHHHHHHHHhhCCCceecHHHHHHHH
Q 034139 29 GITKPAIRRLARRGGVKRISGLIYEETRGVL-----------------KIFLENVIRDAVTYTEHARRKTVTAMDVVYAL 91 (103)
Q Consensus 29 ~ip~a~IkRiar~~G~~riS~da~~~l~~~~-----------------e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Al 91 (103)
+.+.++|-|++++.|..-++ |-..+|++.+ +.++..+++...... ++-...++.+++..+.
T Consensus 45 ~vS~aTv~Rf~kklG~~gf~-e~k~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l-~~t~~~id~~~i~~~~ 122 (284)
T PRK11302 45 NVSEPTVNRFCRSLDTKGFP-DFKLHLAQSLANGTPYVNRNVEEDDSVEAYTGKIFESAMASL-DHARQSLDPSAINRAV 122 (284)
T ss_pred CCCHHHHHHHHHHcCCCCHH-HHHHHHHHHhhccccccccCCCCCCCHHHHHHHHHHHHHHHH-HHHHHhcCHHHHHHHH
Confidence 56888999999999976554 3333333322 122222222222222 2234457778887777
Q ss_pred Hhc
Q 034139 92 KRQ 94 (103)
Q Consensus 92 kr~ 94 (103)
+..
T Consensus 123 ~~i 125 (284)
T PRK11302 123 DLL 125 (284)
T ss_pred HHH
Confidence 753
No 174
>PRK14957 DNA polymerase III subunits gamma and tau; Provisional
Probab=45.28 E-value=59 Score=27.63 Aligned_cols=63 Identities=10% Similarity=-0.010 Sum_probs=39.0
Q ss_pred CcchHHHH----HHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHh
Q 034139 29 GITKPAIR----RLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKR 93 (103)
Q Consensus 29 ~ip~a~Ik----Riar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr 93 (103)
.++...|. ++++..|+ .++++++..+.+...-=+..++.....++.+.+ ..|+.+||..++..
T Consensus 177 ~Ls~~eI~~~L~~il~~egi-~~e~~Al~~Ia~~s~GdlR~alnlLek~i~~~~-~~It~~~V~~~l~~ 243 (546)
T PRK14957 177 HISQADIKDQLKIILAKENI-NSDEQSLEYIAYHAKGSLRDALSLLDQAISFCG-GELKQAQIKQMLGI 243 (546)
T ss_pred CCCHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhcc-CCCCHHHHHHHHcc
Confidence 45555544 44445565 589999999888766544444444443333434 56999999887643
No 175
>PTZ00111 DNA replication licensing factor MCM4; Provisional
Probab=44.75 E-value=83 Score=28.68 Aligned_cols=67 Identities=13% Similarity=0.076 Sum_probs=49.2
Q ss_pred CcchHHHHHHH---HhcCccccchHHHHHHHHH----------------------------------------HHHHHHH
Q 034139 29 GITKPAIRRLA---RRGGVKRISGLIYEETRGV----------------------------------------LKIFLEN 65 (103)
Q Consensus 29 ~ip~a~IkRia---r~~G~~riS~da~~~l~~~----------------------------------------~e~~~~~ 65 (103)
.||...+++.. |+---..+|++|.+.|.+. .-.-|+.
T Consensus 696 ~i~~~lLrkYI~YAR~~~~P~Ls~eA~~~i~~~Yv~mR~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~iT~RqLEs 775 (915)
T PTZ00111 696 KNDLDMLRMYIKFSKLHCFPKLSDEAKKVITREYVKMRQGNFQTSNLDELEHAQEDDDDDLYYQSSGTRMIYVSSRMISS 775 (915)
T ss_pred CCCHHHHHHHHHHHhccCCCCCCHHHHHHHHHHHHHHhhhhccccccccccccccccccccccccccCCcccccHHHHHH
Confidence 36777777554 5434467888888777542 2234667
Q ss_pred HHHHHHHHHhhCCCceecHHHHHHHHHhcC
Q 034139 66 VIRDAVTYTEHARRKTVTAMDVVYALKRQG 95 (103)
Q Consensus 66 I~~dA~~~a~ha~RkTI~~~DV~~Alkr~g 95 (103)
+++-|...|+-.=+.+|+.+||..|++...
T Consensus 776 LIRLsEA~AK~rLs~~Vt~~Dv~~Ai~L~~ 805 (915)
T PTZ00111 776 IIRISVSLARMRLSTVVTPADALQAVQIVK 805 (915)
T ss_pred HHHHHHHHhhhcCcCcccHHHHHHHHHHHH
Confidence 888888999999999999999999998653
No 176
>PRK08451 DNA polymerase III subunits gamma and tau; Validated
Probab=44.16 E-value=69 Score=27.21 Aligned_cols=62 Identities=15% Similarity=0.048 Sum_probs=38.4
Q ss_pred cCcchHHHH----HHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHH
Q 034139 28 QGITKPAIR----RLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYAL 91 (103)
Q Consensus 28 ~~ip~a~Ik----Riar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Al 91 (103)
..++...+. .+++..|+ .++++++..+.+...--+..+....-.++..+ +..||.+||...+
T Consensus 174 ~~Ls~~ei~~~L~~Il~~EGi-~i~~~Al~~Ia~~s~GdlR~alnlLdqai~~~-~~~It~~~V~~~l 239 (535)
T PRK08451 174 KQIPQNSIISHLKTILEKEGV-SYEPEALEILARSGNGSLRDTLTLLDQAIIYC-KNAITESKVADML 239 (535)
T ss_pred CCCCHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHHcCCcHHHHHHHHHHHHHhc-CCCCCHHHHHHHh
Confidence 345665544 44456675 58999999999876655555544444433333 3468888887654
No 177
>PRK08084 DNA replication initiation factor; Provisional
Probab=42.93 E-value=1.3e+02 Score=22.02 Aligned_cols=59 Identities=17% Similarity=-0.037 Sum_probs=33.8
Q ss_pred hHHHHHHHHh----cCccccchHHHHHHHHHHHHH---HHHHHHHHHHHHhhCCCceecHHHHHHHHH
Q 034139 32 KPAIRRLARR----GGVKRISGLIYEETRGVLKIF---LENVIRDAVTYTEHARRKTVTAMDVVYALK 92 (103)
Q Consensus 32 ~a~IkRiar~----~G~~riS~da~~~l~~~~e~~---~~~I~~dA~~~a~ha~RkTI~~~DV~~Alk 92 (103)
......++++ -|+ .+++++++.|.+.++-= +..+++.....+-..+|+ ||.+-|..+|.
T Consensus 169 ~~~~~~~l~~~a~~~~~-~l~~~v~~~L~~~~~~d~r~l~~~l~~l~~~~l~~~~~-it~~~~k~~l~ 234 (235)
T PRK08084 169 DEEKLQALQLRARLRGF-ELPEDVGRFLLKRLDREMRTLFMTLDQLDRASITAQRK-LTIPFVKEILK 234 (235)
T ss_pred HHHHHHHHHHHHHHcCC-CCCHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHhcCCC-CCHHHHHHHHc
Confidence 3444444443 354 59999999999776532 233333332233333444 88888887763
No 178
>TIGR00362 DnaA chromosomal replication initiator protein DnaA. DnaA is involved in DNA biosynthesis; initiation of chromosome replication and can also be transcription regulator. The C-terminal of the family hits the pfam bacterial DnaA (bac_dnaA) domain family. For a review, see Kaguni (2006).
Probab=42.89 E-value=1.5e+02 Score=23.43 Aligned_cols=55 Identities=18% Similarity=0.225 Sum_probs=29.5
Q ss_pred HHHHHhcCccccchHHHHHHHHHHHH---HHHHHHHHHHHHHhhCCCceecHHHHHHHHH
Q 034139 36 RRLARRGGVKRISGLIYEETRGVLKI---FLENVIRDAVTYTEHARRKTVTAMDVVYALK 92 (103)
Q Consensus 36 kRiar~~G~~riS~da~~~l~~~~e~---~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alk 92 (103)
+..++..+. .+++++++.|.+.+.. -++.++.....++...+| .||.+.+..+|+
T Consensus 278 ~~~~~~~~~-~l~~e~l~~ia~~~~~~~r~l~~~l~~l~~~a~~~~~-~it~~~~~~~L~ 335 (405)
T TIGR00362 278 QKKAEEEGL-ELPDEVLEFIAKNIRSNVRELEGALNRLLAYASLTGK-PITLELAKEALK 335 (405)
T ss_pred HHHHHHcCC-CCCHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHhCC-CCCHHHHHHHHH
Confidence 333333343 5888888888766442 233344444445544333 256666655554
No 179
>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA.
Probab=42.76 E-value=90 Score=27.12 Aligned_cols=54 Identities=13% Similarity=0.167 Sum_probs=39.1
Q ss_pred cccchHHHHHHHHHHHHHHHH---------HHHHHHHHHhh----CCCceecHHHHHHHHHhc-CCcc
Q 034139 45 KRISGLIYEETRGVLKIFLEN---------VIRDAVTYTEH----ARRKTVTAMDVVYALKRQ-GRTL 98 (103)
Q Consensus 45 ~riS~da~~~l~~~~e~~~~~---------I~~dA~~~a~h----a~RkTI~~~DV~~Alkr~-g~~l 98 (103)
-.+++++++.+.+....|+.+ ++.+|.....- ..+.+|+.+||..++... |.|+
T Consensus 367 v~i~~~al~~~~~ls~ryi~~r~~P~kai~lld~a~a~~~~~~~~~~~~~v~~~~i~~~i~~~tgiP~ 434 (731)
T TIGR02639 367 VKYSDEALEAAVELSARYINDRFLPDKAIDVIDEAGASFRLRPKAKKKANVSVKDIENVVAKMAHIPV 434 (731)
T ss_pred cccCHHHHHHHHHhhhcccccccCCHHHHHHHHHhhhhhhcCcccccccccCHHHHHHHHHHHhCCCh
Confidence 369999999999998888744 45555543321 124579999999999976 6764
No 180
>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=42.67 E-value=35 Score=18.62 Aligned_cols=25 Identities=12% Similarity=0.179 Sum_probs=18.8
Q ss_pred HHHHHhhCCCceecHHHHHHHHHhc
Q 034139 70 AVTYTEHARRKTVTAMDVVYALKRQ 94 (103)
Q Consensus 70 A~~~a~ha~RkTI~~~DV~~Alkr~ 94 (103)
|...|...+...|+++++.+||=..
T Consensus 1 A~~~A~~~~~~~i~~eHlL~all~~ 25 (53)
T PF02861_consen 1 AQELARERGHQYISPEHLLLALLED 25 (53)
T ss_dssp HHHHHHHTTBSSE-HHHHHHHHHHH
T ss_pred CHHHHHHcCCCcccHHHHHHHHHhh
Confidence 4567788888899999999997443
No 181
>PF15510 CENP-W: Centromere kinetochore component W
Probab=41.99 E-value=49 Score=22.04 Aligned_cols=65 Identities=20% Similarity=0.204 Sum_probs=45.3
Q ss_pred CcchHHHHHHHHhcCc-ccc--chHHHH------------HHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHh
Q 034139 29 GITKPAIRRLARRGGV-KRI--SGLIYE------------ETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKR 93 (103)
Q Consensus 29 ~ip~a~IkRiar~~G~-~ri--S~da~~------------~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr 93 (103)
.-|....+|++++--. -|+ +.|.+. .+--..--|+..++++|-..|=..+=.||..+.|..|.+.
T Consensus 16 kaPrgfLkrv~Kr~KphlRl~~~~Dllv~~~~f~~~~~~~~vhLncLLFvhrLAEEaRtnA~EnK~~~Ik~~Hv~AaaKv 95 (102)
T PF15510_consen 16 KAPRGFLKRVFKRQKPHLRLETSGDLLVRFCPFSGWQWGGEVHLNCLLFVHRLAEEARTNACENKCGTIKKEHVLAAAKV 95 (102)
T ss_pred hCchHHHHHHHHhcCCceeecccccHHHhhcccccccccceeehhHHHHHHHHHHHHHHHHHHHhhccccHHHHHHHHHH
Confidence 5688899999985432 233 223330 0111234588999999998888889999999999999874
No 182
>PF06144 DNA_pol3_delta: DNA polymerase III, delta subunit; InterPro: IPR010372 DNA polymerase III, delta subunit (2.7.7.7 from EC) is required for, along with delta' subunit, the assembly of the processivity factor beta(2) onto primed DNA in the DNA polymerase III holoenzyme-catalysed reaction []. The delta subunit is also known as HolA.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication, 0009360 DNA polymerase III complex; PDB: 3GLG_F 1XXH_A 1JQL_B 3GLF_F 1JQJ_C 3GLI_F.
Probab=41.89 E-value=61 Score=21.91 Aligned_cols=39 Identities=13% Similarity=0.076 Sum_probs=29.0
Q ss_pred HHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHH
Q 034139 35 IRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYT 74 (103)
Q Consensus 35 IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a 74 (103)
|+..+++.|. .+++++.+.|.+.+..=+..|.++..+.+
T Consensus 133 i~~~~~~~g~-~i~~~a~~~L~~~~~~d~~~l~~EleKL~ 171 (172)
T PF06144_consen 133 IKERAKKNGL-KIDPDAAQYLIERVGNDLSLLQNELEKLS 171 (172)
T ss_dssp HHHHHHHTT--EE-HHHHHHHHHHHTT-HHHHHHHHHHHH
T ss_pred HHHHHHHcCC-CCCHHHHHHHHHHhChHHHHHHHHHHHhc
Confidence 7777888887 59999999999988888887777766654
No 183
>PRK14959 DNA polymerase III subunits gamma and tau; Provisional
Probab=41.41 E-value=75 Score=27.59 Aligned_cols=61 Identities=8% Similarity=-0.063 Sum_probs=37.0
Q ss_pred CcchHHHHHH----HHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHH
Q 034139 29 GITKPAIRRL----ARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYAL 91 (103)
Q Consensus 29 ~ip~a~IkRi----ar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Al 91 (103)
.++...|..+ ++..|+ .|++++++.|.+...--+..++....+.+.. +..+|+.+||..++
T Consensus 177 pLs~~eL~~~L~~il~~egi-~id~eal~lIA~~s~GdlR~Al~lLeqll~~-g~~~It~d~V~~~l 241 (624)
T PRK14959 177 RLSEAGLEAHLTKVLGREGV-DYDPAAVRLIARRAAGSVRDSMSLLGQVLAL-GESRLTIDGARGVL 241 (624)
T ss_pred CCCHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHHcCCCHHHHHHHHHHHHHh-cCCCcCHHHHHHHh
Confidence 4445544433 334454 4899999998887665555555444444423 44579988876655
No 184
>KOG0729 consensus 26S proteasome regulatory complex, ATPase RPT1 [Posttranslational modification, protein turnover, chaperones]
Probab=41.12 E-value=21 Score=28.77 Aligned_cols=33 Identities=27% Similarity=0.338 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHHHhhCCCceecHHHHHHHHHhc
Q 034139 62 FLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 94 (103)
Q Consensus 62 ~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~ 94 (103)
-+..+.-+|-.||..+.||+.|..|..-|....
T Consensus 386 eirsvcteagmfairarrk~atekdfl~av~kv 418 (435)
T KOG0729|consen 386 EIRSVCTEAGMFAIRARRKVATEKDFLDAVNKV 418 (435)
T ss_pred HHHHHHHHhhHHHHHHHhhhhhHHHHHHHHHHH
Confidence 356788899999999999999999999998754
No 185
>PRK05896 DNA polymerase III subunits gamma and tau; Validated
Probab=40.99 E-value=86 Score=27.15 Aligned_cols=61 Identities=7% Similarity=0.129 Sum_probs=39.8
Q ss_pred CcchHHHHHHH----HhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHH
Q 034139 29 GITKPAIRRLA----RRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYAL 91 (103)
Q Consensus 29 ~ip~a~IkRia----r~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Al 91 (103)
.++...+..++ +..|+ .+++++...+.+...--+..+......++...+.. |+.+||..++
T Consensus 177 ~Ls~~eL~~~L~~il~kegi-~Is~eal~~La~lS~GdlR~AlnlLekL~~y~~~~-It~e~V~ell 241 (605)
T PRK05896 177 KLNNSELQELLKSIAKKEKI-KIEDNAIDKIADLADGSLRDGLSILDQLSTFKNSE-IDIEDINKTF 241 (605)
T ss_pred CCCHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHHcCCcHHHHHHHHHHHHhhcCCC-CCHHHHHHHh
Confidence 34454444333 34454 48999999988887766666666666666666643 8888877653
No 186
>PRK06620 hypothetical protein; Validated
Probab=40.60 E-value=1.4e+02 Score=21.71 Aligned_cols=55 Identities=18% Similarity=0.068 Sum_probs=31.6
Q ss_pred HHHHHHhcCccccchHHHHHHHHHHHHHHHHH---HHHHHHHHhhCCCceecHHHHHHHH
Q 034139 35 IRRLARRGGVKRISGLIYEETRGVLKIFLENV---IRDAVTYTEHARRKTVTAMDVVYAL 91 (103)
Q Consensus 35 IkRiar~~G~~riS~da~~~l~~~~e~~~~~I---~~dA~~~a~ha~RkTI~~~DV~~Al 91 (103)
+++.+...|+ .+++++++.|.+.+..=+..+ ++....++...+| .||.+.+..+|
T Consensus 156 l~k~~~~~~l-~l~~ev~~~L~~~~~~d~r~l~~~l~~l~~~~~~~~~-~it~~~~~~~l 213 (214)
T PRK06620 156 IFKHFSISSV-TISRQIIDFLLVNLPREYSKIIEILENINYFALISKR-KITISLVKEVL 213 (214)
T ss_pred HHHHHHHcCC-CCCHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHcCC-CCCHHHHHHHh
Confidence 3444444454 599999999987644322222 2222233444444 58888887776
No 187
>PRK08691 DNA polymerase III subunits gamma and tau; Validated
Probab=40.09 E-value=89 Score=27.64 Aligned_cols=64 Identities=6% Similarity=-0.060 Sum_probs=39.5
Q ss_pred CcchHH----HHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhc
Q 034139 29 GITKPA----IRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 94 (103)
Q Consensus 29 ~ip~a~----IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~ 94 (103)
.++... ++++++..|+ .++++++..|.+...-=+..++......+.+ +...|+.+||...+-..
T Consensus 177 ~Ls~eeI~~~L~~Il~kEgi-~id~eAL~~Ia~~A~GslRdAlnLLDqaia~-g~g~It~e~V~~lLG~~ 244 (709)
T PRK08691 177 NMTAQQVADHLAHVLDSEKI-AYEPPALQLLGRAAAGSMRDALSLLDQAIAL-GSGKVAENDVRQMIGAV 244 (709)
T ss_pred CCCHHHHHHHHHHHHHHcCC-CcCHHHHHHHHHHhCCCHHHHHHHHHHHHHh-cCCCcCHHHHHHHHccc
Confidence 444444 3455556665 4899999999988664444444443333333 24469999988877543
No 188
>PRK05563 DNA polymerase III subunits gamma and tau; Validated
Probab=39.35 E-value=83 Score=26.59 Aligned_cols=54 Identities=7% Similarity=-0.015 Sum_probs=31.4
Q ss_pred HHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHH
Q 034139 36 RRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYAL 91 (103)
Q Consensus 36 kRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Al 91 (103)
+.+++..|+ .++++++..+.....-=+..++.....+...+ ...|+.+||..++
T Consensus 188 ~~i~~~egi-~i~~~al~~ia~~s~G~~R~al~~Ldq~~~~~-~~~It~~~V~~vl 241 (559)
T PRK05563 188 KYILDKEGI-EYEDEALRLIARAAEGGMRDALSILDQAISFG-DGKVTYEDALEVT 241 (559)
T ss_pred HHHHHHcCC-CCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhc-cCCCCHHHHHHHh
Confidence 344445565 48899988888765543333333333332232 3468888887665
No 189
>CHL00206 ycf2 Ycf2; Provisional
Probab=39.31 E-value=45 Score=33.14 Aligned_cols=34 Identities=18% Similarity=0.221 Sum_probs=30.4
Q ss_pred HHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhc
Q 034139 61 IFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 94 (103)
Q Consensus 61 ~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~ 94 (103)
.=+..++.+|...|-..++..|+.+|+..|+.|+
T Consensus 1844 ADLanLvNEAaliAirq~ks~Id~~~I~~Al~Rq 1877 (2281)
T CHL00206 1844 RDLVALTNEALSISITQKKSIIDTNTIRSALHRQ 1877 (2281)
T ss_pred HHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHHH
Confidence 4467788889999999999999999999999987
No 190
>COG4477 EzrA Negative regulator of septation ring formation [Cell division and chromosome partitioning]
Probab=39.02 E-value=1e+02 Score=26.56 Aligned_cols=44 Identities=11% Similarity=0.098 Sum_probs=28.4
Q ss_pred chhhcccccCcchHHH----------HHHHHhcCccccchHHHHHHHHHHHHHH
Q 034139 20 RKVLRDNIQGITKPAI----------RRLARRGGVKRISGLIYEETRGVLKIFL 63 (103)
Q Consensus 20 ~k~~r~~~~~ip~a~I----------kRiar~~G~~riS~da~~~l~~~~e~~~ 63 (103)
|.+.+.++++||..-+ ..++...+-.+|.-+++..+.+..+.-+
T Consensus 431 R~mek~nLPGlPe~~l~l~~~~~~~i~~l~~eLse~pinm~~v~~~v~~a~~~m 484 (570)
T COG4477 431 RYMEKSNLPGLPETFLSLFFTAGHEIQDLMKELSEVPINMEAVSALVDIATEDM 484 (570)
T ss_pred HHHHHcCCCCCcHHHHHHHHhhhhHHHHHHHHHhhcCCcHHHHHHHHHHHHHHH
Confidence 4566899999998754 4445555556666666666665544433
No 191
>PRK07764 DNA polymerase III subunits gamma and tau; Validated
Probab=38.86 E-value=85 Score=28.06 Aligned_cols=62 Identities=15% Similarity=0.000 Sum_probs=39.1
Q ss_pred CcchHHHHHHHHh----cCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHH
Q 034139 29 GITKPAIRRLARR----GGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYAL 91 (103)
Q Consensus 29 ~ip~a~IkRiar~----~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Al 91 (103)
.++...+..++++ .|+ .++++++..|.....--+..++....+++-..+...||.+||...+
T Consensus 178 ~l~~~~l~~~L~~il~~EGv-~id~eal~lLa~~sgGdlR~Al~eLEKLia~~~~~~IT~e~V~all 243 (824)
T PRK07764 178 LVPPEVMRGYLERICAQEGV-PVEPGVLPLVIRAGGGSVRDSLSVLDQLLAGAGPEGVTYERAVALL 243 (824)
T ss_pred CCCHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHHcCCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHh
Confidence 4556665544443 465 4888988888877665555555555555555555668888776544
No 192
>PF02042 RWP-RK: RWP-RK domain; InterPro: IPR003035 This domain is named RWP-RK after a conserved motif at the C terminus of the domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [].
Probab=38.34 E-value=34 Score=20.17 Aligned_cols=21 Identities=29% Similarity=0.510 Sum_probs=18.1
Q ss_pred CcchHHHHHHHHhcCccccch
Q 034139 29 GITKPAIRRLARRGGVKRISG 49 (103)
Q Consensus 29 ~ip~a~IkRiar~~G~~riS~ 49 (103)
++....++|+.|+.|+.|+.-
T Consensus 26 gv~~T~LKr~CR~~GI~RWP~ 46 (52)
T PF02042_consen 26 GVSVTTLKRRCRRLGIPRWPY 46 (52)
T ss_pred CCCHHHHHHHHHHcCCCCCCc
Confidence 678888999999999998863
No 193
>PF07830 PP2C_C: Protein serine/threonine phosphatase 2C, C-terminal domain; InterPro: IPR012911 Protein phosphatase 2C (PP2C) is involved in regulating cellular responses to stress in various eukaryotes. It consists of two domains: an N-terminal catalytic domain and a C-terminal domain characteristic of mammalian PP2Cs. This domain consists of three antiparallel alpha helices, one of which packs against two corresponding alpha-helices of the N-terminal domain. The C-terminal domain does not seem to play a role in catalysis, but it may provide protein substrate specificity due to the cleft that is created between it and the catalytic domain []. ; GO: 0000287 magnesium ion binding, 0004721 phosphoprotein phosphatase activity, 0030145 manganese ion binding; PDB: 2P8E_A 3FXL_A 3FXO_A 1A6Q_A 3FXK_A 3FXM_A 3FXJ_A.
Probab=38.34 E-value=1.1e+02 Score=19.64 Aligned_cols=49 Identities=14% Similarity=0.255 Sum_probs=20.5
Q ss_pred CccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhc
Q 034139 43 GVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 94 (103)
Q Consensus 43 G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~ 94 (103)
|+.++|++|+..=.+ |+.++++.+++...-+...+ ..+...|...|...
T Consensus 9 gAPkvs~EAv~~E~e-Ld~~l~~rv~ei~~~~~~~~--~~~l~~V~~~L~~e 57 (81)
T PF07830_consen 9 GAPKVSEEAVKKEAE-LDKYLEQRVEEIIEKSSEEE--NPDLVYVMRTLASE 57 (81)
T ss_dssp TS----HHHHHHHHH-HHHHHHHHHHHHT------------HHHHHHHHHHT
T ss_pred CCCCCCHHHHHHHHH-HHHHHHHHHHHHHHHhcccC--CCCHHHHHHHHHhc
Confidence 677899999876544 66666666655544432222 23334444444433
No 194
>PRK06647 DNA polymerase III subunits gamma and tau; Validated
Probab=38.03 E-value=93 Score=26.46 Aligned_cols=62 Identities=3% Similarity=-0.107 Sum_probs=37.5
Q ss_pred CcchHHHHH----HHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHH
Q 034139 29 GITKPAIRR----LARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALK 92 (103)
Q Consensus 29 ~ip~a~IkR----iar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alk 92 (103)
.++...+.. +++..|+ .++++++..|.+...--+..+.....+.+-+.+ ..|+.+||..++.
T Consensus 177 ~l~~~el~~~L~~i~~~egi-~id~eAl~lLa~~s~GdlR~alslLdklis~~~-~~It~e~V~~llg 242 (563)
T PRK06647 177 LLSLEKIYNMLKKVCLEDQI-KYEDEALKWIAYKSTGSVRDAYTLFDQVVSFSD-SDITLEQIRSKMG 242 (563)
T ss_pred CCCHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHHcCCCHHHHHHHHHHHHhhcC-CCCCHHHHHHHhC
Confidence 355555543 3344464 488999999888765545544444444443444 3589888887653
No 195
>PRK14975 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Probab=37.80 E-value=2.1e+02 Score=24.03 Aligned_cols=65 Identities=15% Similarity=0.066 Sum_probs=48.4
Q ss_pred CcchHHHHHHHHhcCccccchHHHHHHHHHHH----------HHHHHHHHHHHHHHhhCCCc---eecHHHHHHHHHhcC
Q 034139 29 GITKPAIRRLARRGGVKRISGLIYEETRGVLK----------IFLENVIRDAVTYTEHARRK---TVTAMDVVYALKRQG 95 (103)
Q Consensus 29 ~ip~a~IkRiar~~G~~riS~da~~~l~~~~e----------~~~~~I~~dA~~~a~ha~Rk---TI~~~DV~~Alkr~g 95 (103)
+.|..+|-.-++..|+ .|..+..+++...++ ..+.++.+++...+ +.. --++.+|..+|++.|
T Consensus 163 E~~~~~~l~~me~~Gi-~~D~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~~~---g~~~~n~~S~~ql~~~L~~~g 238 (553)
T PRK14975 163 ESAGALAAAEMELAGL-PWDTDVHEALLAELLGPRPAAGGRPARLAELAAEIREAL---GRPRLNPDSPQQVLRALRRAG 238 (553)
T ss_pred HhhHHHHHHHHHHhCe-EeCHHHHHHHHHHHhcccccccchHHHHHHHHHHHHHHh---CCCCCCCCCHHHHHHHHHHCC
Confidence 5777888888888897 488888888887777 66777766665544 433 356789999998888
Q ss_pred Cc
Q 034139 96 RT 97 (103)
Q Consensus 96 ~~ 97 (103)
.+
T Consensus 239 ~~ 240 (553)
T PRK14975 239 IE 240 (553)
T ss_pred CC
Confidence 66
No 196
>COG4130 Predicted sugar epimerase [Carbohydrate transport and metabolism]
Probab=37.72 E-value=71 Score=24.75 Aligned_cols=66 Identities=20% Similarity=0.181 Sum_probs=42.8
Q ss_pred CcchHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCC--------------c-eecHHHHHHHHHh
Q 034139 29 GITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARR--------------K-TVTAMDVVYALKR 93 (103)
Q Consensus 29 ~ip~a~IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~R--------------k-TI~~~DV~~Alkr 93 (103)
+.|.+.|+-+|++.|+.-||=.|+....+..++...+ ++....||+-.|- - .+..+|+..||++
T Consensus 48 g~p~a~vka~Aek~Gl~IvSINAlypFn~wt~~~~a~-a~~la~yA~acGA~aLvlcPlNd~s~~~~~vr~~~lv~Alka 126 (272)
T COG4130 48 GTPAAEVKALAEKAGLTIVSINALYPFNEWTEERVAE-ARGLADYAAACGAKALVLCPLNDGSWPGTAVRREDLVEALKA 126 (272)
T ss_pred CCCHHHHHHHHHHcCcEEEEeeccccccccChHHHHH-HHHHHHHHHhcCCceEEEEeccCCCCCCcccchHHHHHHHHH
Confidence 6899999999999999888877765554443333322 2223333333232 2 3667899999998
Q ss_pred cC
Q 034139 94 QG 95 (103)
Q Consensus 94 ~g 95 (103)
+.
T Consensus 127 Lk 128 (272)
T COG4130 127 LK 128 (272)
T ss_pred hh
Confidence 64
No 197
>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=37.19 E-value=57 Score=16.14 Aligned_cols=27 Identities=11% Similarity=0.139 Sum_probs=19.3
Q ss_pred HHHHHHhhCCCceecHHHHHHHHH-hcC
Q 034139 69 DAVTYTEHARRKTVTAMDVVYALK-RQG 95 (103)
Q Consensus 69 dA~~~a~ha~RkTI~~~DV~~Alk-r~g 95 (103)
.+.......+--+|+.+|+..+|+ .+|
T Consensus 4 ~~F~~~D~d~dG~I~~~el~~~l~~~lG 31 (31)
T PF13405_consen 4 EAFKMFDKDGDGFIDFEELRAILRKSLG 31 (31)
T ss_dssp HHHHHH-TTSSSEEEHHHHHHHHHHHTT
T ss_pred HHHHHHCCCCCCcCcHHHHHHHHHHhcC
Confidence 344455666777899999999998 354
No 198
>PRK14087 dnaA chromosomal replication initiation protein; Provisional
Probab=36.75 E-value=2e+02 Score=23.64 Aligned_cols=60 Identities=7% Similarity=0.056 Sum_probs=35.1
Q ss_pred HHHHHHhcCc-cccchHHHHHHHHHHHHHH---HHHHHHHHHHHhhCC-CceecHHHHHHHHHhc
Q 034139 35 IRRLARRGGV-KRISGLIYEETRGVLKIFL---ENVIRDAVTYTEHAR-RKTVTAMDVVYALKRQ 94 (103)
Q Consensus 35 IkRiar~~G~-~riS~da~~~l~~~~e~~~---~~I~~dA~~~a~ha~-RkTI~~~DV~~Alkr~ 94 (103)
+++.++..|. ..+++++++.|.+.+.-=+ ..++..+..++...+ .+.|+.+.|..+++..
T Consensus 284 L~~~~~~~gl~~~l~~evl~~Ia~~~~gd~R~L~gaL~~l~~~a~~~~~~~~it~~~v~~~l~~~ 348 (450)
T PRK14087 284 IKKEIKNQNIKQEVTEEAINFISNYYSDDVRKIKGSVSRLNFWSQQNPEEKIITIEIVSDLFRDI 348 (450)
T ss_pred HHHHHHhcCCCCCCCHHHHHHHHHccCCCHHHHHHHHHHHHHHHhcccCCCCCCHHHHHHHHhhc
Confidence 4444444454 2699999999987655322 223333333333321 3568888888888754
No 199
>PRK14960 DNA polymerase III subunits gamma and tau; Provisional
Probab=36.08 E-value=96 Score=27.46 Aligned_cols=64 Identities=9% Similarity=-0.033 Sum_probs=40.2
Q ss_pred cCcchHHHH----HHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHh
Q 034139 28 QGITKPAIR----RLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKR 93 (103)
Q Consensus 28 ~~ip~a~Ik----Riar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr 93 (103)
..++...+. +|++.-|+ .++++++..|.+...-=+..++...-..+-+ +...|+.+||...+-.
T Consensus 175 kpLs~eEI~k~L~~Il~kEgI-~id~eAL~~IA~~S~GdLRdALnLLDQaIay-g~g~IT~edV~~lLG~ 242 (702)
T PRK14960 175 RPLAVDEITKHLGAILEKEQI-AADQDAIWQIAESAQGSLRDALSLTDQAIAY-GQGAVHHQDVKEMLGL 242 (702)
T ss_pred cCCCHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHHcCCCHHHHHHHHHHHHHh-cCCCcCHHHHHHHhcc
Confidence 345555544 44445565 5899999999887665555555444333333 3566999999887643
No 200
>PF02459 Adeno_terminal: Adenoviral DNA terminal protein; InterPro: IPR003391 The genome of adenovirus contains a protein covalently bound to the 5' end of each strand of the linear DNA molecule []. Since adenovirus DNA replication is initiated at the termini of the DNA molecule it has been proposed that the terminal protein serves as the primer for initiation of replication. However, the priming function now appears to reside in the precursor form of the terminal protein (pTP) found on the 5' ends of nascent DNA strands replicated in vitro [, ] and as a component of DNA-protein complexes isolated from virions of the protease-deficient adenovirus serotype 2 (Ad2) mutant tsl. The pTP is encoded by the leftward-transcribed strand of the viral genome and comprises part of a transcription unit that also encodes the single-strand DNA binding protein [].; GO: 0003677 DNA binding, 0006260 DNA replication
Probab=35.99 E-value=78 Score=27.17 Aligned_cols=38 Identities=16% Similarity=0.233 Sum_probs=33.7
Q ss_pred HHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhcC
Q 034139 58 VLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQG 95 (103)
Q Consensus 58 ~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~g 95 (103)
.+......|+.|....++++|+-.++++|++..|....
T Consensus 448 aF~~l~~RI~~Dl~~~verag~~~~~~ee~e~~l~dI~ 485 (548)
T PF02459_consen 448 AFSQLMRRISRDLLATVERAGRGELEEEEIEQFLADIA 485 (548)
T ss_pred HHHHHHHHHHHHHHHHHhccCcccCCHHHHHHHHHHhc
Confidence 46777889999999999999999999999999997654
No 201
>COG3854 SpoIIIAA ncharacterized protein conserved in bacteria [Function unknown]
Probab=35.91 E-value=23 Score=27.92 Aligned_cols=61 Identities=20% Similarity=0.243 Sum_probs=38.2
Q ss_pred hHHHHHHHHhcCccccchHHHHHHHHH---HHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhcC-CcccccC
Q 034139 32 KPAIRRLARRGGVKRISGLIYEETRGV---LKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQG-RTLYGFG 102 (103)
Q Consensus 32 ~a~IkRiar~~G~~riS~da~~~l~~~---~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~g-~~lYgf~ 102 (103)
..+|++++++. ++ ++.|+++ +..-++-++.--..|..|.+ ||.+|+..++.+++ ..+|+|+
T Consensus 11 Pe~i~~~l~~~-----p~--~~~l~Evri~v~Rp~e~~~~~~~vyl~~~~---vT~ed~~~~~~rls~ysiys~e 75 (308)
T COG3854 11 PEKIRQILKEI-----PD--RNNLEEVRIRVNRPLEAIFPGQPVYLSYIG---VTKEDLQKTLNRLSGYSIYSVE 75 (308)
T ss_pred hHHHHHHHHhC-----Cc--cccceeeEeecCCCceEecCCCceeccccc---ccHHHHHHHHHHhcccccccch
Confidence 35666666543 22 2233222 33334444444556777776 99999999999985 8889875
No 202
>COG4401 AroH Chorismate mutase [Amino acid transport and metabolism]
Probab=35.78 E-value=41 Score=23.27 Aligned_cols=27 Identities=22% Similarity=0.271 Sum_probs=24.2
Q ss_pred CccccchHHHHHHHHHHHHHHHHHHHH
Q 034139 43 GVKRISGLIYEETRGVLKIFLENVIRD 69 (103)
Q Consensus 43 G~~riS~da~~~l~~~~e~~~~~I~~d 69 (103)
|++-|+.+.-+++.+++++.+++|.++
T Consensus 8 GATTV~~nt~eeI~~at~eLl~~i~~~ 34 (125)
T COG4401 8 GATTVESNTEEEILDATKELLEEIEEE 34 (125)
T ss_pred cceeecCCCHHHHHHHHHHHHHHHHHh
Confidence 778899999999999999999998765
No 203
>PRK14965 DNA polymerase III subunits gamma and tau; Provisional
Probab=35.55 E-value=97 Score=26.28 Aligned_cols=61 Identities=16% Similarity=0.062 Sum_probs=35.8
Q ss_pred CcchHHHH----HHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHH
Q 034139 29 GITKPAIR----RLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYAL 91 (103)
Q Consensus 29 ~ip~a~Ik----Riar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Al 91 (103)
.++...|. .++++.|+ .++++++..+.+...-=+..++...-+...+.+ ..|+.+||...+
T Consensus 177 ~l~~~~i~~~L~~i~~~egi-~i~~~al~~la~~a~G~lr~al~~Ldqliay~g-~~It~edV~~ll 241 (576)
T PRK14965 177 RIPLQKIVDRLRYIADQEGI-SISDAALALVARKGDGSMRDSLSTLDQVLAFCG-DAVGDDDVAELL 241 (576)
T ss_pred CCCHHHHHHHHHHHHHHhCC-CCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhcc-CCCCHHHHHHHh
Confidence 45555444 34445565 488999998887766544444444433333333 248999887653
No 204
>KOG1957 consensus DNA topoisomerase III beta [Replication, recombination and repair]
Probab=34.99 E-value=43 Score=28.46 Aligned_cols=23 Identities=26% Similarity=0.317 Sum_probs=19.7
Q ss_pred hCCCce-------ecHHHHHHHHHhcCCcc
Q 034139 76 HARRKT-------VTAMDVVYALKRQGRTL 98 (103)
Q Consensus 76 ha~RkT-------I~~~DV~~Alkr~g~~l 98 (103)
|.+++| ||..||..||+-+|+|.
T Consensus 135 ~~~~~tyra~fsaitekdi~~am~~lg~p~ 164 (555)
T KOG1957|consen 135 RSDFKTYRAHFSAITEKDIKKAMRNLGEPD 164 (555)
T ss_pred cCcceEEeeeeccccHHHHHHHHHhcCCCC
Confidence 667665 89999999999999885
No 205
>TIGR03280 methan_mark_11 putative methanogenesis marker protein 11. Members of this protein family, to date, are found in a completed prokaryotic genome if and only if the species is one of the archaeal methanogens. The exact function is unknown, but likely is linked to methanogenesis or a process closely connected to it.
Probab=34.95 E-value=64 Score=25.45 Aligned_cols=37 Identities=14% Similarity=0.196 Sum_probs=31.6
Q ss_pred HHHHHHHHHhhCCCceecHHHHHHHHHhcCCcccccC
Q 034139 66 VIRDAVTYTEHARRKTVTAMDVVYALKRQGRTLYGFG 102 (103)
Q Consensus 66 I~~dA~~~a~ha~RkTI~~~DV~~Alkr~g~~lYgf~ 102 (103)
+.+....|...+++.-|+.+|....+++.|..+++|.
T Consensus 232 ~p~~L~~fg~~Ak~~vvt~eeA~~~a~~~gi~l~~~~ 268 (292)
T TIGR03280 232 PPKELKEYGNKAKREMVSIEEAERVAERNNIEIIEVT 268 (292)
T ss_pred CcHHHHHHHHHHHhceeCHHHHHHHHHHCCcEEEEeC
Confidence 3445678999999999999999999999998888763
No 206
>cd08318 Death_NMPP84 Death domain of Nuclear Matrix Protein P84. Death domain (DD) found in the Nuclear Matrix Protein P84 (also known as HPR1 or THOC1). HPR1/p84 resides in the nuclear matrix and is part of the THO complex, also called TREX (transcription/export) complex, which functions in mRNP biogenesis at the interface between transcription and export of mRNA from the nucleus. Mice lacking THOC1 have abnormal testis development and are sterile. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=34.06 E-value=1.2e+02 Score=19.02 Aligned_cols=60 Identities=12% Similarity=0.041 Sum_probs=38.8
Q ss_pred HHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhcCC
Q 034139 33 PAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGR 96 (103)
Q Consensus 33 a~IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~g~ 96 (103)
...+++|++.|. |++-++.+...-...-++..+-...+.+..+. .-|.+-+..||+..|.
T Consensus 19 ~~Wk~Lar~LGl---s~~dI~~i~~~~~~~~eq~~~mL~~W~~r~g~-~AT~~~L~~aL~~~~~ 78 (86)
T cd08318 19 EDWKTLAPHLEM---KDKEIRAIESDSEDIKMQAKQLLVAWQDREGS-QATPETLITALNAAGL 78 (86)
T ss_pred hhHHHHHHHcCC---CHHHHHHHHhcCCCHHHHHHHHHHHHHHhcCc-cccHHHHHHHHHHcCc
Confidence 346778888874 55555555544334445555556667777664 4678888889987764
No 207
>PF14841 FliG_M: FliG middle domain; PDB: 3HJL_A 3AJC_A 1LKV_X 3SOH_D 3USY_B 3USW_A.
Probab=33.01 E-value=1.1e+02 Score=18.91 Aligned_cols=42 Identities=24% Similarity=0.213 Sum_probs=28.6
Q ss_pred cCcchHHHHHHHHhc-CccccchHHHHHHHHHHHHHHHHHHHH
Q 034139 28 QGITKPAIRRLARRG-GVKRISGLIYEETRGVLKIFLENVIRD 69 (103)
Q Consensus 28 ~~ip~a~IkRiar~~-G~~riS~da~~~l~~~~e~~~~~I~~d 69 (103)
..||..-=..++++. ....+|+++...+.+.++.-+..+...
T Consensus 34 ~~lp~e~r~~v~~Ria~~~~v~~~~i~~ie~~L~~~l~~~~~~ 76 (79)
T PF14841_consen 34 SQLPEELRAEVVRRIARLESVSPEVIEEIEEVLEEKLEAVGSQ 76 (79)
T ss_dssp HTS-HHHHHHHHHHHHTCCCCSHHHHHHHHHHHHHHCHHHHHH
T ss_pred HHCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHhhccc
Confidence 356665444444444 357899999999999998887776543
No 208
>PRK14969 DNA polymerase III subunits gamma and tau; Provisional
Probab=32.96 E-value=1.2e+02 Score=25.46 Aligned_cols=62 Identities=10% Similarity=0.021 Sum_probs=37.8
Q ss_pred CcchHHHH----HHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHH
Q 034139 29 GITKPAIR----RLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALK 92 (103)
Q Consensus 29 ~ip~a~Ik----Riar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alk 92 (103)
.++...|. ++++..|+ .++++++..+.+...--+..++..+...+.+ +...|+.+||...+.
T Consensus 177 ~l~~~~i~~~L~~il~~egi-~~~~~al~~la~~s~Gslr~al~lldqai~~-~~~~I~~~~v~~~~~ 242 (527)
T PRK14969 177 QMPPPLIVSHLQHILEQENI-PFDATALQLLARAAAGSMRDALSLLDQAIAY-GGGTVNESEVRAMLG 242 (527)
T ss_pred CCCHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHHcCCCHHHHHHHHHHHHHh-cCCCcCHHHHHHHHC
Confidence 45555444 34444465 4888888888877665444444444433334 356799999887764
No 209
>COG1241 MCM2 Predicted ATPase involved in replication control, Cdc46/Mcm family [DNA replication, recombination, and repair]
Probab=32.96 E-value=1.8e+02 Score=25.72 Aligned_cols=65 Identities=22% Similarity=0.143 Sum_probs=45.0
Q ss_pred chHHHHHH---HHhcCccccchHHHHHHHHHHH-------------------HHHHHHHHHHHHHHhhCCCceecHHHHH
Q 034139 31 TKPAIRRL---ARRGGVKRISGLIYEETRGVLK-------------------IFLENVIRDAVTYTEHARRKTVTAMDVV 88 (103)
Q Consensus 31 p~a~IkRi---ar~~G~~riS~da~~~l~~~~e-------------------~~~~~I~~dA~~~a~ha~RkTI~~~DV~ 88 (103)
|...+++. ||+--...++++|.+.|.+... .-++.|++-|...|+-.-.-.|+.+||.
T Consensus 507 ~~~~lrkYI~YAR~~v~P~lt~ea~e~l~~~Yv~~Rk~~~~~~~~~~~piT~RqLEsiiRLaeA~Ak~rLS~~V~~eD~~ 586 (682)
T COG1241 507 DFELLRKYISYARKNVTPVLTEEAREELEDYYVEMRKKSALVEEKRTIPITARQLESIIRLAEAHAKMRLSDVVEEEDVD 586 (682)
T ss_pred cHHHHHHHHHHHhccCCcccCHHHHHHHHHHHHHhhhccccccccCcccccHHHHHHHHHHHHHHHhhhccCCCCHHHHH
Confidence 44445543 3443225788888777765432 2344588888888988888899999999
Q ss_pred HHHHhcC
Q 034139 89 YALKRQG 95 (103)
Q Consensus 89 ~Alkr~g 95 (103)
.|++...
T Consensus 587 eAi~lv~ 593 (682)
T COG1241 587 EAIRLVD 593 (682)
T ss_pred HHHHHHH
Confidence 9998654
No 210
>COG2255 RuvB Holliday junction resolvasome, helicase subunit [DNA replication, recombination, and repair]
Probab=32.45 E-value=2.7e+02 Score=22.48 Aligned_cols=72 Identities=14% Similarity=0.119 Sum_probs=52.8
Q ss_pred cchHHHHHHHHhc----CccccchHHHHHHHHHH---HHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhcCCcccccC
Q 034139 30 ITKPAIRRLARRG----GVKRISGLIYEETRGVL---KIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTLYGFG 102 (103)
Q Consensus 30 ip~a~IkRiar~~----G~~riS~da~~~l~~~~---e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~g~~lYgf~ 102 (103)
-...-+..|..+. ++ .+++++..++.... =...-.+++..-.||+-.+--+|+.+=+..||+.++..-.||+
T Consensus 181 Y~~~eL~~Iv~r~a~~l~i-~i~~~~a~eIA~rSRGTPRIAnRLLrRVRDfa~V~~~~~I~~~ia~~aL~~L~Vd~~GLd 259 (332)
T COG2255 181 YTVEELEEIVKRSAKILGI-EIDEEAALEIARRSRGTPRIANRLLRRVRDFAQVKGDGDIDRDIADKALKMLDVDELGLD 259 (332)
T ss_pred CCHHHHHHHHHHHHHHhCC-CCChHHHHHHHHhccCCcHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHhCccccccc
Confidence 3445555555443 44 48888888888653 2455566777788999888889999999999999987777876
No 211
>PF13779 DUF4175: Domain of unknown function (DUF4175)
Probab=32.32 E-value=86 Score=28.13 Aligned_cols=44 Identities=11% Similarity=0.282 Sum_probs=35.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhh-------CCCceecHHHHHHHHHhc
Q 034139 51 IYEETRGVLKIFLENVIRDAVTYTEH-------ARRKTVTAMDVVYALKRQ 94 (103)
Q Consensus 51 a~~~l~~~~e~~~~~I~~dA~~~a~h-------a~RkTI~~~DV~~Alkr~ 94 (103)
-.++|++++.+|+.++++.+...-.- .+..+++.+|+...|.+.
T Consensus 497 Lm~eLR~A~~~ym~~LAeq~~~~~~~~~~p~~~~~~~~~~~~dL~~mmd~i 547 (820)
T PF13779_consen 497 LMQELREAMQDYMQALAEQAQRNPQQQDQPPDQGNSQMMSQQDLQRMMDRI 547 (820)
T ss_pred HHHHHHHHHHHHHHHHHHHhHhCcccccCcccchhhhccCHHHHHHHHHHH
Confidence 34678889999999999998876543 356789999999988764
No 212
>TIGR01481 ccpA catabolite control protein A. Catabolite control protein A is a LacI family global transcriptional regulator found in Gram-positive bacteria. CcpA is involved in repressing carbohydrate utilization genes [ex: alpha-amylase (amyE), acetyl-coenzyme A synthase (acsA)] and in activating genes involved in transporting excess carbon from the cell [ex: acetate kinase (ackA), alpha-acetolactate synthase (alsS)]. Additionally, disruption of CcpA in Bacillus megaterium, Staphylococcus xylosus, Lactobacillus casei and Lactocacillus pentosus also decreases growth rate, which suggests CcpA is involved in the regulation of other metabolic pathways.
Probab=32.31 E-value=71 Score=23.69 Aligned_cols=29 Identities=10% Similarity=0.238 Sum_probs=15.8
Q ss_pred CcchHHHHHHHHhcCccccchHHHHHHHHHH
Q 034139 29 GITKPAIRRLARRGGVKRISGLIYEETRGVL 59 (103)
Q Consensus 29 ~ip~a~IkRiar~~G~~riS~da~~~l~~~~ 59 (103)
+++.++|-|++.. ..+||++..+.+.+++
T Consensus 12 gvS~~TVSrvLn~--~~~vs~~tr~rV~~~a 40 (329)
T TIGR01481 12 GVSMATVSRVVNG--NPNVKPATRKKVLEVI 40 (329)
T ss_pred CCCHHHHHHHhCC--CCCCCHHHHHHHHHHH
Confidence 4555666666543 2356666665555443
No 213
>PLN03025 replication factor C subunit; Provisional
Probab=31.77 E-value=1.2e+02 Score=23.31 Aligned_cols=53 Identities=8% Similarity=-0.090 Sum_probs=33.0
Q ss_pred HHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHH
Q 034139 35 IRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYA 90 (103)
Q Consensus 35 IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~A 90 (103)
++++++.-|+ .+++++++.+.+...-=+..++....... .+...|+.+||...
T Consensus 167 L~~i~~~egi-~i~~~~l~~i~~~~~gDlR~aln~Lq~~~--~~~~~i~~~~v~~~ 219 (319)
T PLN03025 167 LMKVVEAEKV-PYVPEGLEAIIFTADGDMRQALNNLQATH--SGFGFVNQENVFKV 219 (319)
T ss_pred HHHHHHHcCC-CCCHHHHHHHHHHcCCCHHHHHHHHHHHH--hcCCCCCHHHHHHH
Confidence 3455556676 48999999988776655555554444322 23446888887643
No 214
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=31.33 E-value=66 Score=24.01 Aligned_cols=34 Identities=6% Similarity=0.120 Sum_probs=21.0
Q ss_pred CcchHHHHHHHHhcCccccchHHHHHHHHHHHHH
Q 034139 29 GITKPAIRRLARRGGVKRISGLIYEETRGVLKIF 62 (103)
Q Consensus 29 ~ip~a~IkRiar~~G~~riS~da~~~l~~~~e~~ 62 (103)
++++++|.|.+....-.+||++..+.+.+++++.
T Consensus 12 gVS~~TVSrvln~~~~~~vs~~tr~rV~~~a~~l 45 (327)
T PRK10339 12 GVSLATVSRVLNDDPTLNVKEETKHRILEIAEKL 45 (327)
T ss_pred CCCHHhhhhhhcCCCCCCcCHHHHHHHHHHHHHh
Confidence 5666677777753321257777777777666554
No 215
>PRK14086 dnaA chromosomal replication initiation protein; Provisional
Probab=31.05 E-value=2.8e+02 Score=24.21 Aligned_cols=56 Identities=14% Similarity=0.102 Sum_probs=30.6
Q ss_pred HHHHHhcCccccchHHHHHHHHHHH---HHHHHHHHHHHHHHhhCCCceecHHHHHHHHHh
Q 034139 36 RRLARRGGVKRISGLIYEETRGVLK---IFLENVIRDAVTYTEHARRKTVTAMDVVYALKR 93 (103)
Q Consensus 36 kRiar~~G~~riS~da~~~l~~~~e---~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr 93 (103)
+..++.-|+ .+++++++.|.+-++ ..|+.++.....|+.-. ++.|+.+.+..+|+.
T Consensus 456 ~kka~~r~l-~l~~eVi~yLa~r~~rnvR~LegaL~rL~a~a~~~-~~~itl~la~~vL~~ 514 (617)
T PRK14086 456 RKKAVQEQL-NAPPEVLEFIASRISRNIRELEGALIRVTAFASLN-RQPVDLGLTEIVLRD 514 (617)
T ss_pred HHHHHhcCC-CCCHHHHHHHHHhccCCHHHHHHHHHHHHHHHHhh-CCCCCHHHHHHHHHH
Confidence 333344444 588888888887655 33333344444444332 344666666666653
No 216
>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=30.97 E-value=1.2e+02 Score=17.98 Aligned_cols=33 Identities=24% Similarity=0.171 Sum_probs=27.3
Q ss_pred HHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHH
Q 034139 59 LKIFLENVIRDAVTYTEHARRKTVTAMDVVYALK 92 (103)
Q Consensus 59 ~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alk 92 (103)
.+.++.-....|++|+-.+++| =..+|+.-|..
T Consensus 24 ~~~~~~f~~gnaiKY~~R~~~K-~~~eDl~KA~~ 56 (60)
T PF11753_consen 24 EEQFLGFCLGNAIKYLWRAGKK-NGIEDLKKAKW 56 (60)
T ss_pred chhhhhHHHHHHHHHHHHHccc-CcHHHHHHHHH
Confidence 4577777788899999999999 66999998864
No 217
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=30.61 E-value=81 Score=23.58 Aligned_cols=32 Identities=6% Similarity=0.235 Sum_probs=21.2
Q ss_pred CcchHHHHHHHHhcCccccchHHHHHHHHHHHHH
Q 034139 29 GITKPAIRRLARRGGVKRISGLIYEETRGVLKIF 62 (103)
Q Consensus 29 ~ip~a~IkRiar~~G~~riS~da~~~l~~~~e~~ 62 (103)
++++++|.|.+.. -.+||++..+.+.+++++.
T Consensus 12 gVS~~TVSrvLn~--~~~vs~~tr~~V~~~a~el 43 (341)
T PRK10703 12 GVSTTTVSHVINK--TRFVAEETRNAVWAAIKEL 43 (341)
T ss_pred CCCHHHHHHHHcC--CCCCCHHHHHHHHHHHHHH
Confidence 5677777777753 2367887777776665543
No 218
>cd05831 Ribosomal_P1 Ribosomal protein P1. This subfamily represents the eukaryotic large ribosomal protein P1. Eukaryotic P1 and P2 are functionally equivalent to the bacterial protein L7/L12, but are not homologous to L7/L12. P1 is located in the L12 stalk, with proteins P2, 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) and bacteria may have four or six copies (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, P2A, and
Probab=30.29 E-value=1.1e+02 Score=20.26 Aligned_cols=35 Identities=23% Similarity=0.180 Sum_probs=25.8
Q ss_pred hcccccCcchHHHHHHHHhcCccccchHHHHHHHHH
Q 034139 23 LRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGV 58 (103)
Q Consensus 23 ~r~~~~~ip~a~IkRiar~~G~~riS~da~~~l~~~ 58 (103)
+.|....++...|+.|++..|+. +.+.-...+.+.
T Consensus 11 L~d~~~~~Tae~I~~ilkAaGve-ve~~~~~~f~~~ 45 (103)
T cd05831 11 LHDDGIEITADNINALLKAAGVN-VEPYWPGLFAKA 45 (103)
T ss_pred HccCCCCCCHHHHHHHHHHcCCc-ccHHHHHHHHHH
Confidence 45566678999999999999974 665666655543
No 219
>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]
Probab=30.14 E-value=1.6e+02 Score=22.93 Aligned_cols=49 Identities=24% Similarity=0.216 Sum_probs=34.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHH-HHHhhCCC----------------ceecHHHHHHHHHhcCCccc
Q 034139 51 IYEETRGVLKIFLENVIRDAV-TYTEHARR----------------KTVTAMDVVYALKRQGRTLY 99 (103)
Q Consensus 51 a~~~l~~~~e~~~~~I~~dA~-~~a~ha~R----------------kTI~~~DV~~Alkr~g~~lY 99 (103)
-=++++...++|.++++.+.. +|.+-... +-=..+|...|+..++-+.|
T Consensus 70 ~de~~q~~~defyEd~f~E~~~kygEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~ 135 (260)
T KOG2202|consen 70 TDEELQRHEDEFYEDVFTELEDKYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWY 135 (260)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCccc
Confidence 345677788888888888887 77766555 22347888888887655444
No 220
>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]
Probab=29.90 E-value=88 Score=25.07 Aligned_cols=48 Identities=15% Similarity=0.079 Sum_probs=39.0
Q ss_pred ccccchHHHHHHHHHHH------HHHHHHHHHHHHHHhhCCCceecHHHHHHHH
Q 034139 44 VKRISGLIYEETRGVLK------IFLENVIRDAVTYTEHARRKTVTAMDVVYAL 91 (103)
Q Consensus 44 ~~riS~da~~~l~~~~e------~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Al 91 (103)
...+++++.+.+....- .+.-++++-|...|+..++.+|+.++|..|-
T Consensus 209 ~~~~~~~vl~lia~~~a~~~GDAR~aidilr~A~eiAe~~~~~~v~~~~v~~a~ 262 (366)
T COG1474 209 AGVIDDDVLKLIAALVAAESGDARKAIDILRRAGEIAEREGSRKVSEDHVREAQ 262 (366)
T ss_pred CCCcCccHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHhhCCCCcCHHHHHHHH
Confidence 46678888777764432 4667899999999999999999999999994
No 221
>KOG0785 consensus Isocitrate dehydrogenase, alpha subunit [Amino acid transport and metabolism]
Probab=29.89 E-value=1.2e+02 Score=24.67 Aligned_cols=46 Identities=13% Similarity=0.172 Sum_probs=37.0
Q ss_pred ccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHH
Q 034139 46 RISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYAL 91 (103)
Q Consensus 46 riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Al 91 (103)
.+-+.+++.+.-+.|.=...|++-|..||+..+|+.||.-.=.+.|
T Consensus 163 ~vvpGVvqsiK~IT~~AS~Ria~~AF~yAr~~~R~~vtvvHKaNIm 208 (365)
T KOG0785|consen 163 QVVPGVVQSIKLITEAASRRIAEYAFEYARQNGRKRVTVVHKANIM 208 (365)
T ss_pred eccccHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCceEEEehhhhh
Confidence 3556688889889999999999999999999999988854433333
No 222
>PRK14951 DNA polymerase III subunits gamma and tau; Provisional
Probab=29.25 E-value=1.5e+02 Score=25.71 Aligned_cols=62 Identities=5% Similarity=-0.051 Sum_probs=37.2
Q ss_pred CcchHHHH----HHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHH
Q 034139 29 GITKPAIR----RLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALK 92 (103)
Q Consensus 29 ~ip~a~Ik----Riar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alk 92 (103)
.++...|. +++...|+ .++++++..|.+...-=+..++...-+.+-+. ...|+.++|...|-
T Consensus 182 ~Ls~eei~~~L~~i~~~egi-~ie~~AL~~La~~s~GslR~al~lLdq~ia~~-~~~It~~~V~~~Lg 247 (618)
T PRK14951 182 PMAPETVLEHLTQVLAAENV-PAEPQALRLLARAARGSMRDALSLTDQAIAFG-SGQLQEAAVRQMLG 247 (618)
T ss_pred CCCHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhc-CCCcCHHHHHHHHc
Confidence 45555544 44455565 58899998888775544444444433333333 34689888887663
No 223
>COG5665 NOT5 CCR4-NOT transcriptional regulation complex, NOT5 subunit [Transcription]
Probab=29.24 E-value=57 Score=27.25 Aligned_cols=37 Identities=14% Similarity=0.183 Sum_probs=32.1
Q ss_pred CcchHHHHHHHHhcCccccchHHHHHHHHHHHHHHHH
Q 034139 29 GITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLEN 65 (103)
Q Consensus 29 ~ip~a~IkRiar~~G~~riS~da~~~l~~~~e~~~~~ 65 (103)
.+..+.+.-|+++.--..|++++++++++.+.+|++.
T Consensus 144 ~~h~~~le~i~~~l~n~~~~pe~v~~~q~di~yyve~ 180 (548)
T COG5665 144 EFHIANLENILKKLQNNEMDPEPVEEFQDDIKYYVEN 180 (548)
T ss_pred HHHHHHHHHHHHHHhccCCChhhHHHHHHHHHHHhhc
Confidence 4566778889999888899999999999999999863
No 224
>cd08306 Death_FADD Fas-associated Death Domain protein-protein interaction domain. Death domain (DD) found in FAS-associated via death domain (FADD). FADD is a component of the death-inducing signaling complex (DISC) and serves as an adaptor in the signaling pathway of death receptor proteins. It modulates apoptosis as well as non-apoptotic processes such as cell cycle progression, survival, innate immune signaling, and hematopoiesis. FADD contains an N-terminal DED and a C-terminal DD. Its DD interacts with the DD of the activated death receptor, FAS, and its DED recruits the initiator caspases, caspase-8 and -10, to the DISC complex via a homotypic interaction with the N-terminal DED of the caspase. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain),
Probab=29.15 E-value=1.5e+02 Score=18.61 Aligned_cols=60 Identities=22% Similarity=0.254 Sum_probs=38.9
Q ss_pred HHHHHHHhcCccccchHHHHHHHHHH-HHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhcCCc
Q 034139 34 AIRRLARRGGVKRISGLIYEETRGVL-KIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRT 97 (103)
Q Consensus 34 ~IkRiar~~G~~riS~da~~~l~~~~-e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~g~~ 97 (103)
..+.++|+.| +|+.-.+.+...- ...-+++.+-.....+..| +.-|.+-+..||+..+..
T Consensus 15 ~Wk~laR~LG---lse~~Id~i~~~~~~~~~eq~~~mL~~W~~~~g-~~At~~~L~~aL~~~~l~ 75 (86)
T cd08306 15 DWRKLARKLG---LSETKIESIEEAHPRNLREQVRQSLREWKKIKK-KEAKVADLIKALRDCQLN 75 (86)
T ss_pred hHHHHHHHcC---CCHHHHHHHHHHCCCCHHHHHHHHHHHHHHhHC-cchHHHHHHHHHHHcCcH
Confidence 4678888887 5666666665443 2223455555556676666 556788888888877654
No 225
>TIGR00207 fliG flagellar motor switch protein FliG. The fliG protein along with fliM and fliN interact to form the switch complex of the bacterial flagellar motor located at the base of the basal body. This complex interacts with chemotaxis proteins (eg CHEY). In addition the complex interacts with other components of the motor that determine the direction of flagellar rotation. The model contains putative members of the fliG family at scores of less than 100 from Agrobacterium radiobacter and Sinorhizobium meliloti as well as fliG-like genes from treponema pallidum and Borrelia burgdorferi. That is why the suggested cutoff is set at 20 but was set at 100 to construct the family.
Probab=29.02 E-value=93 Score=24.61 Aligned_cols=40 Identities=23% Similarity=0.155 Sum_probs=31.5
Q ss_pred cCcchHHHHHHHHhc-CccccchHHHHHHHHHHHHHHHHHH
Q 034139 28 QGITKPAIRRLARRG-GVKRISGLIYEETRGVLKIFLENVI 67 (103)
Q Consensus 28 ~~ip~a~IkRiar~~-G~~riS~da~~~l~~~~e~~~~~I~ 67 (103)
..||..-...|+.+. ....||+++.+++.+.+++++..+.
T Consensus 152 ~~Lp~~~~~ei~~ria~l~~vs~~~i~~ie~~L~~~~~~~~ 192 (338)
T TIGR00207 152 SLFPEEVQAEVARRIATMGRTSPEVVAEVERVLEGKLDSLN 192 (338)
T ss_pred HhCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhhc
Confidence 457877777766555 4689999999999999998887654
No 226
>PF01706 FliG_C: FliG C-terminal domain; InterPro: IPR023087 The flagellar motor switch in Escherichia coli and Salmonella typhimurium regulates the direction of flagellar rotation and hence controls swimming behaviour []. The switch is a complex apparatus that responds to signals transduced by the chemotaxis sensory signalling system during chemotactic behaviour []. CheY, the chemotaxis response regulator, is believed to act directly on the switch to induce tumbles in the swimming pattern, but no physical interactions of CheY and switch proteins have yet been demonstrated. The switch complex comprises at least three proteins - FliG, FliM and FliN. It has been shown that FliG interacts with FliM, FliM interacts with itself, and FliM interacts with FliN []. Several residues within the middle third of FliG appear to be strongly involved in the FliG-FliM interaction, with residues near the N- or C-termini being less important []. Such clustering suggests that FliG-FliM interaction plays a central role in switching. Analysis of the FliG, FliM and FliN sequences shows that none are especially hydrophobic or appear to be integral membrane proteins []. This result is consistent with other evidence suggesting that the proteins may be peripheral to the membrane, possibly mounted on the basal body M ring [, ]. FliG is present in about 25 copies per flagellum. This entry represents the C-terminal domain of FliG, the structure of which is known. This domain functions specifically in motor rotation [].; PDB: 3USY_B 3USW_A 3HJL_A 3AJC_A 1LKV_X 1QC7_B.
Probab=28.93 E-value=1.7e+02 Score=19.01 Aligned_cols=62 Identities=15% Similarity=0.144 Sum_probs=34.7
Q ss_pred ccCcchHHHHHHHHhcCc-------cccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHh
Q 034139 27 IQGITKPAIRRLARRGGV-------KRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKR 93 (103)
Q Consensus 27 ~~~ip~a~IkRiar~~G~-------~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr 93 (103)
+..+|...++++++.... .-.+++..+.+-..+.....+.+++-.... +. |+.+||..|-+.
T Consensus 25 l~~l~~~~l~~ll~~v~~~~la~ALkga~~e~~~~il~nms~r~a~~l~~e~~~~---g~--v~~~di~~Aq~~ 93 (110)
T PF01706_consen 25 LVRLDDRDLQKLLREVDPDDLALALKGASEELREKILSNMSKRAAEMLREEMEAL---GP--VRLSDIEEAQRE 93 (110)
T ss_dssp GGGS-HHHHHHHHTTS-HHHHHHHHCTS-HHHHHHHHTTS-HHHHHHHHHHHHHH----S----HHHHHHHHHH
T ss_pred HHcCCHHHHHHHHHHCCHhHHHHHHccCCHHHHHHHHHHcCHHHHHHHHHHHHhc---CC--CCHHHHHHHHHH
Confidence 446788888888888762 334555555555556666666555555443 33 678888777654
No 227
>PRK07194 fliG flagellar motor switch protein G; Reviewed
Probab=28.62 E-value=1e+02 Score=24.25 Aligned_cols=39 Identities=8% Similarity=0.096 Sum_probs=30.9
Q ss_pred cCcchHHHHHHHHhcC-ccccchHHHHHHHHHHHHHHHHH
Q 034139 28 QGITKPAIRRLARRGG-VKRISGLIYEETRGVLKIFLENV 66 (103)
Q Consensus 28 ~~ip~a~IkRiar~~G-~~riS~da~~~l~~~~e~~~~~I 66 (103)
..||..-+.+|+++.. ...||+++.+++.++++.++...
T Consensus 149 ~~Lpe~~~~~v~~ria~l~~Vs~e~~~~V~e~l~~~~~~~ 188 (334)
T PRK07194 149 KYLPEDRQDDILYRIAQLDDVDRDVVDELDELIERCLAVL 188 (334)
T ss_pred HhCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHhh
Confidence 4688888888887764 68999999999987777776653
No 228
>PRK13342 recombination factor protein RarA; Reviewed
Probab=28.62 E-value=1.5e+02 Score=23.75 Aligned_cols=65 Identities=11% Similarity=0.087 Sum_probs=37.9
Q ss_pred cCcchHHHHHHHHhc------CccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhc
Q 034139 28 QGITKPAIRRLARRG------GVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 94 (103)
Q Consensus 28 ~~ip~a~IkRiar~~------G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~ 94 (103)
..++...+..++++. |...+++++++.+.+...--+.++..-....+.. ...|+.+||..++...
T Consensus 149 ~~ls~e~i~~lL~~~l~~~~~~~i~i~~~al~~l~~~s~Gd~R~aln~Le~~~~~--~~~It~~~v~~~~~~~ 219 (413)
T PRK13342 149 KPLSEEDIEQLLKRALEDKERGLVELDDEALDALARLANGDARRALNLLELAALG--VDSITLELLEEALQKR 219 (413)
T ss_pred CCCCHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHhCCCCHHHHHHHHHHHHHc--cCCCCHHHHHHHHhhh
Confidence 345556666666553 2225888888888776443333333332222222 4569999999988753
No 229
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=28.49 E-value=2.5e+02 Score=20.81 Aligned_cols=20 Identities=20% Similarity=0.522 Sum_probs=16.3
Q ss_pred CcchHHHHHHHHhcCccccc
Q 034139 29 GITKPAIRRLARRGGVKRIS 48 (103)
Q Consensus 29 ~ip~a~IkRiar~~G~~riS 48 (103)
..+.++|-|++++.|..-++
T Consensus 41 ~vS~aTv~Rf~kklG~~Gf~ 60 (278)
T PRK11557 41 GVSQSSVVKFAQKLGYKGFP 60 (278)
T ss_pred CCCHHHHHHHHHHcCCCCHH
Confidence 56889999999999965554
No 230
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional
Probab=28.46 E-value=2.5e+02 Score=20.94 Aligned_cols=27 Identities=11% Similarity=0.245 Sum_probs=19.7
Q ss_pred CcchHHHHHHHHhcCccccchHHHHHHH
Q 034139 29 GITKPAIRRLARRGGVKRISGLIYEETR 56 (103)
Q Consensus 29 ~ip~a~IkRiar~~G~~riS~da~~~l~ 56 (103)
+.+.++|-|++++.|..-++ |-..+|.
T Consensus 57 ~vS~aTi~Rf~kkLGf~gf~-efk~~l~ 83 (292)
T PRK11337 57 AVSEAMIVKVAKKLGFSGFR-NLRSALE 83 (292)
T ss_pred CCChHHHHHHHHHcCCCCHH-HHHHHHH
Confidence 57889999999999976665 4444443
No 231
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=28.42 E-value=94 Score=22.17 Aligned_cols=29 Identities=21% Similarity=0.205 Sum_probs=25.4
Q ss_pred cccchHHHHHHHHHHHHHHHHHHHHHHHH
Q 034139 45 KRISGLIYEETRGVLKIFLENVIRDAVTY 73 (103)
Q Consensus 45 ~riS~da~~~l~~~~e~~~~~I~~dA~~~ 73 (103)
..||++.|+.+.+.+.+|-.+|..-+...
T Consensus 127 ~~vs~~~~~ki~~~i~~fRk~i~~i~~~~ 155 (171)
T PF14394_consen 127 MSVSREDYEKIKKEIREFRKKIIAIAEED 155 (171)
T ss_pred EEeCHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 56899999999999999999998776654
No 232
>cd06863 PX_Atg24p The phosphoinositide binding Phox Homology domain of yeast Atg24p, an autophagic degradation protein. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. The yeast Atg24p is a sorting nexin (SNX) which is involved in membrane fusion events at the vacuolar surface during pexophagy. This is facilitated via binding of Atg24p to phosphatidylinositol 3-phosphate (PI3P) through its PX domain. SNXs make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway.
Probab=28.26 E-value=43 Score=22.07 Aligned_cols=26 Identities=19% Similarity=0.212 Sum_probs=22.2
Q ss_pred cccchHHHHHHHHHHHHHHHHHHHHH
Q 034139 45 KRISGLIYEETRGVLKIFLENVIRDA 70 (103)
Q Consensus 45 ~riS~da~~~l~~~~e~~~~~I~~dA 70 (103)
.+++++..++=+..++.|+..|+..-
T Consensus 78 ~~~~~~~ie~Rr~~Le~fL~~i~~~p 103 (118)
T cd06863 78 DRFSPEFITRRAQSLQRFLRRISLHP 103 (118)
T ss_pred cCCCHHHHHHHHHHHHHHHHHHhcCc
Confidence 46889999999999999999987653
No 233
>PRK07133 DNA polymerase III subunits gamma and tau; Validated
Probab=28.14 E-value=1.7e+02 Score=26.03 Aligned_cols=62 Identities=10% Similarity=0.020 Sum_probs=37.1
Q ss_pred cCcchHHHHHHHH----hcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHH
Q 034139 28 QGITKPAIRRLAR----RGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYAL 91 (103)
Q Consensus 28 ~~ip~a~IkRiar----~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Al 91 (103)
..+|...|..+++ ..|+ .++++++..+.....-=+..++..+...+.+++. .|+.++|..++
T Consensus 175 ~~L~~eeI~~~L~~il~kegI-~id~eAl~~LA~lS~GslR~AlslLekl~~y~~~-~It~e~V~ell 240 (725)
T PRK07133 175 RRISEDEIVSRLEFILEKENI-SYEKNALKLIAKLSSGSLRDALSIAEQVSIFGNN-KITLKNVEELF 240 (725)
T ss_pred cCCCHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhccC-CCCHHHHHHHH
Confidence 3466666554443 4464 4788888888877655455555444444444433 38888887654
No 234
>cd08319 Death_RAIDD Death domain of RIP-associated ICH-1 homologous protein with a death domain. Death domain (DD) of RAIDD (RIP-associated ICH-1 homologous protein with a death domain), also known as CRADD (Caspase and RIP adaptor). RAIDD is an adaptor protein that together with the p53-inducible protein PIDD and caspase-2, forms the PIDDosome complex, which is required for caspase-2 activation and plays a role in mediating stress-induced apoptosis. RAIDD contains an N-terminal Caspase Activation and Recruitment Domain (CARD), which interacts with the caspase-2 CARD, and a C-terminal DD, which interacts with the DD of PIDD. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD, DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other pr
Probab=27.35 E-value=1.7e+02 Score=18.55 Aligned_cols=64 Identities=13% Similarity=0.129 Sum_probs=40.4
Q ss_pred HHHHHHHhcCccccchHHHHHHHHH-HHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhcC--Cccccc
Q 034139 34 AIRRLARRGGVKRISGLIYEETRGV-LKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQG--RTLYGF 101 (103)
Q Consensus 34 ~IkRiar~~G~~riS~da~~~l~~~-~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~g--~~lYgf 101 (103)
..+.+|++.| +|+.-++.+... -...-+++.+-....-+..| +.-|.+.+..||+..+ ..+|.|
T Consensus 15 ~W~~Lar~Lg---ls~~~I~~i~~~~p~~l~eQv~~mL~~W~~r~G-~~ATv~~L~~aL~~~~~~~~~~~~ 81 (83)
T cd08319 15 EWEQVLLDLG---LSQTDIYRCKENHPHNVQSQIVEALVKWRQRFG-KKATVQSLIQSLKAVEVDPSVLQF 81 (83)
T ss_pred hHHHHHHHcC---CCHHHHHHHHHhCCCCHHHHHHHHHHHHHHhcC-CCCcHHHHHHHHHHcCCCHHHHHh
Confidence 4566777776 445555555543 22333555556666776666 5677899999999765 455665
No 235
>PRK09526 lacI lac repressor; Reviewed
Probab=27.33 E-value=1.1e+02 Score=22.89 Aligned_cols=31 Identities=13% Similarity=0.293 Sum_probs=22.9
Q ss_pred CcchHHHHHHHHhcCccccchHHHHHHHHHHHH
Q 034139 29 GITKPAIRRLARRGGVKRISGLIYEETRGVLKI 61 (103)
Q Consensus 29 ~ip~a~IkRiar~~G~~riS~da~~~l~~~~e~ 61 (103)
++++++|.|.+.. ..+||++..+.+.+++++
T Consensus 16 GVS~~TVSrvLn~--~~~vs~~tr~rV~~~a~e 46 (342)
T PRK09526 16 GVSYQTVSRVLNQ--ASHVSAKTREKVEAAMAE 46 (342)
T ss_pred CCCHHHHHHHhcC--CCCCCHHHHHHHHHHHHH
Confidence 6778888888863 357888888887776654
No 236
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=27.02 E-value=1.2e+02 Score=22.37 Aligned_cols=30 Identities=13% Similarity=0.335 Sum_probs=18.3
Q ss_pred CcchHHHHHHHHhcCccccchHHHHHHHHHHH
Q 034139 29 GITKPAIRRLARRGGVKRISGLIYEETRGVLK 60 (103)
Q Consensus 29 ~ip~a~IkRiar~~G~~riS~da~~~l~~~~e 60 (103)
++++++|.|.+.. -.+||++..+.+.++++
T Consensus 9 gVS~~TVSrvLn~--~~~vs~~tr~rV~~~a~ 38 (327)
T PRK10423 9 GVSTSTVSHVINK--DRFVSEAITAKVEAAIK 38 (327)
T ss_pred CCcHHHHHHHhCC--CCCCCHHHHHHHHHHHH
Confidence 5666777777743 23577776666655543
No 237
>PF04695 Pex14_N: Peroxisomal membrane anchor protein (Pex14p) conserved region; InterPro: IPR006785 This conserved region defines a group of peroxisomal membrane anchor proteins which bind the PTS1 (peroxisomal targeting signal) receptor and are required for the import of PTS1-containing proteins into peroxisomes. Loss of functional Pex14p results in defects in both the PTS1 and PTS2-dependent import pathways. Deletion analysis of this conserved region implicates it in selective peroxisome degradation. In the majority of members this region is situated at the N terminus of the protein [, ].; GO: 0005777 peroxisome, 0016020 membrane; PDB: 2W85_A 2W84_A 3FF5_B.
Probab=26.80 E-value=58 Score=22.36 Aligned_cols=19 Identities=32% Similarity=0.365 Sum_probs=12.5
Q ss_pred CceecHHHHHHHHHhcCCc
Q 034139 79 RKTVTAMDVVYALKRQGRT 97 (103)
Q Consensus 79 RkTI~~~DV~~Alkr~g~~ 97 (103)
.|=++.+||..||++-+.+
T Consensus 32 sKGLt~~EI~~al~~a~~~ 50 (136)
T PF04695_consen 32 SKGLTEEEIDEALGRAGSP 50 (136)
T ss_dssp HCT--HHHHHHHHHHHT--
T ss_pred cCCCCHHHHHHHHHhcCCc
Confidence 3569999999999987643
No 238
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=26.51 E-value=1.3e+02 Score=22.63 Aligned_cols=35 Identities=26% Similarity=0.361 Sum_probs=23.0
Q ss_pred ccCcchHH-HHHHHHhcCccccchHHHHHHHHHHHHHH
Q 034139 27 IQGITKPA-IRRLARRGGVKRISGLIYEETRGVLKIFL 63 (103)
Q Consensus 27 ~~~ip~a~-IkRiar~~G~~riS~da~~~l~~~~e~~~ 63 (103)
...||..+ |.|++++.|... ..-.+++.+.+..++
T Consensus 132 ~p~i~VDTHV~Rvs~R~gl~~--~~~p~~ve~~L~~~i 167 (211)
T COG0177 132 IPAIAVDTHVHRVSNRLGLVP--GKTPEEVEEALMKLI 167 (211)
T ss_pred CCcccccchHHHHHHHhCCCC--CCCHHHHHHHHHHHC
Confidence 34677776 999999999754 344455555555544
No 239
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=26.23 E-value=1e+02 Score=23.18 Aligned_cols=31 Identities=10% Similarity=0.200 Sum_probs=18.9
Q ss_pred CcchHHHHHHHHhcCccccchHHHHHHHHHHHH
Q 034139 29 GITKPAIRRLARRGGVKRISGLIYEETRGVLKI 61 (103)
Q Consensus 29 ~ip~a~IkRiar~~G~~riS~da~~~l~~~~e~ 61 (103)
++++++|-|.+..- .+||++..+.+.+++++
T Consensus 12 GVS~~TVSrvLn~~--~~Vs~~tr~rV~~~a~e 42 (343)
T PRK10727 12 GVSVATVSRVINNS--PKASEASRLAVHSAMES 42 (343)
T ss_pred CCCHHHHHHHhCCC--CCCCHHHHHHHHHHHHH
Confidence 56666777766432 35777777666655443
No 240
>cd04411 Ribosomal_P1_P2_L12p Ribosomal protein P1, P2, and L12p. Ribosomal proteins P1 and P2 are the eukaryotic proteins that are functionally equivalent to bacterial L7/L12. L12p is the archaeal homolog. Unlike other ribosomal proteins, the archaeal L12p and eukaryotic P1 and P2 do not share sequence similarity with their bacterial counterparts. They are part of the ribosomal stalk (called the L7/L12 stalk in bacteria), along with 28S rRNA and the proteins L11 and P0 in eukaryotes (23S rRNA, L11, and L10e in archaea). In bacterial ribosomes, L7/L12 homodimers bind the extended C-terminal helix of L10 to anchor the L7/L12 molecules to the ribosome. Eukaryotic P1/P2 heterodimers and archaeal L12p homodimers are believed to bind the L10 equivalent proteins, eukaryotic P0 and archaeal L10e, in a similar fashion. P1 and P2 (L12p, L7/L12) are the only proteins in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain
Probab=26.22 E-value=1.4e+02 Score=19.92 Aligned_cols=29 Identities=17% Similarity=0.150 Sum_probs=24.4
Q ss_pred CcchHHHHHHHHhcCccccchHHHHHHHHH
Q 034139 29 GITKPAIRRLARRGGVKRISGLIYEETRGV 58 (103)
Q Consensus 29 ~ip~a~IkRiar~~G~~riS~da~~~l~~~ 58 (103)
.++...|+.|++..|+. |.++....+.+.
T Consensus 16 ~~ta~~I~~IL~aaGve-Ve~~~~~~~~~a 44 (105)
T cd04411 16 ELTEDKIKELLSAAGAE-IEPERVKLFLSA 44 (105)
T ss_pred CCCHHHHHHHHHHcCCC-cCHHHHHHHHHH
Confidence 47888999999999984 888888877776
No 241
>PF12392 DUF3656: Collagenase ; InterPro: IPR020988 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. The peptidases families associated with clan U- have an unknown catalytic mechanism as the protein fold of the active site domain and the active site residues have not been reported. This domain is found in a number of proteins belonging to the MEROPS peptidase family U32. Peptidase family U32 contains endopeptidases, including collagenase, from bacteria.
Probab=25.68 E-value=51 Score=21.82 Aligned_cols=28 Identities=18% Similarity=0.360 Sum_probs=24.1
Q ss_pred HhhCCCceecHHHHHHHHHhcCCccccc
Q 034139 74 TEHARRKTVTAMDVVYALKRQGRTLYGF 101 (103)
Q Consensus 74 a~ha~RkTI~~~DV~~Alkr~g~~lYgf 101 (103)
++.|..+.++.++|...|.+.|.+.|-+
T Consensus 58 ~e~A~~~p~~~e~i~~ql~KlG~T~F~~ 85 (122)
T PF12392_consen 58 PEPAKKRPLDEERIRKQLSKLGNTPFEL 85 (122)
T ss_pred chhhCCCccCHHHHHHHHHhhCCCcEEE
Confidence 5678899999999999999999876654
No 242
>COG1239 ChlI Mg-chelatase subunit ChlI [Coenzyme metabolism]
Probab=25.55 E-value=1.4e+02 Score=24.82 Aligned_cols=27 Identities=26% Similarity=0.259 Sum_probs=21.7
Q ss_pred HHHHHHHHHhhCCCceecHHHHHHHHH
Q 034139 66 VIRDAVTYTEHARRKTVTAMDVVYALK 92 (103)
Q Consensus 66 I~~dA~~~a~ha~RkTI~~~DV~~Alk 92 (103)
+++-+..+|.-.||.+|+.+||..|+.
T Consensus 294 ~~r~a~a~aa~~Gr~~v~~~Di~~a~~ 320 (423)
T COG1239 294 VVRAAKALAALRGRTEVEEEDIREAAE 320 (423)
T ss_pred HHHHHHHHHHhcCceeeehhhHHHHHh
Confidence 344556777789999999999998876
No 243
>PRK06402 rpl12p 50S ribosomal protein L12P; Reviewed
Probab=25.55 E-value=1.4e+02 Score=20.09 Aligned_cols=33 Identities=12% Similarity=0.219 Sum_probs=26.2
Q ss_pred cccCcchHHHHHHHHhcCccccchHHHHHHHHHH
Q 034139 26 NIQGITKPAIRRLARRGGVKRISGLIYEETRGVL 59 (103)
Q Consensus 26 ~~~~ip~a~IkRiar~~G~~riS~da~~~l~~~~ 59 (103)
.-..|+...|+.|++..|+. |.+.-...+.+.|
T Consensus 13 ~g~~it~e~I~~IL~AAGve-Vee~~~k~~v~aL 45 (106)
T PRK06402 13 AGKEINEDNLKKVLEAAGVE-VDEARVKALVAAL 45 (106)
T ss_pred cCCCCCHHHHHHHHHHcCCC-ccHHHHHHHHHHH
Confidence 33378889999999999975 8888877777663
No 244
>PHA02943 hypothetical protein; Provisional
Probab=25.45 E-value=2.1e+02 Score=20.88 Aligned_cols=40 Identities=13% Similarity=0.135 Sum_probs=28.9
Q ss_pred ccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHH
Q 034139 46 RISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALK 92 (103)
Q Consensus 46 riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alk 92 (103)
.+.+|+|..+ +.+++++.-.+-...++|-|++.|+...+.
T Consensus 66 ~l~~day~~~-------v~~~~Relwrlv~s~~~kfi~p~~l~~li~ 105 (165)
T PHA02943 66 CLDEDAYTNL-------VFEIKRELWRLVCNSRLKFITPSRLLRLIA 105 (165)
T ss_pred EEChHHHHHH-------HHHHHHHHHHHHHhccccccChHHHHHHHH
Confidence 4566666555 455666677888888999999999876653
No 245
>COG3267 ExeA Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]
Probab=25.44 E-value=1.2e+02 Score=23.82 Aligned_cols=55 Identities=13% Similarity=0.057 Sum_probs=43.9
Q ss_pred HHHHHHHhcC--ccccchHHHHHHHHHHH---HHHHHHHHHHHHHHhhCCCceecHHHHH
Q 034139 34 AIRRLARRGG--VKRISGLIYEETRGVLK---IFLENVIRDAVTYTEHARRKTVTAMDVV 88 (103)
Q Consensus 34 ~IkRiar~~G--~~riS~da~~~l~~~~e---~~~~~I~~dA~~~a~ha~RkTI~~~DV~ 88 (103)
.++-.++.+| ..=+|++++..+.+... .-+.+++..|...|-++++.+|+..-+.
T Consensus 208 yl~~~Le~a~~~~~l~~~~a~~~i~~~sqg~P~lin~~~~~Al~~a~~a~~~~v~~a~~~ 267 (269)
T COG3267 208 YLRHRLEGAGLPEPLFSDDALLLIHEASQGIPRLINNLATLALDAAYSAGEDGVSEAEIK 267 (269)
T ss_pred HHHHHHhccCCCcccCChhHHHHHHHHhccchHHHHHHHHHHHHHHHHcCCCccchhhcc
Confidence 3555555555 36689999999998877 6788999999999999999999877654
No 246
>PRK07492 adenylosuccinate lyase; Provisional
Probab=25.44 E-value=3.6e+02 Score=22.06 Aligned_cols=62 Identities=13% Similarity=0.184 Sum_probs=40.3
Q ss_pred CcchHHHHHHHHhcCccccchHHHHHHHH-------HHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHH
Q 034139 29 GITKPAIRRLARRGGVKRISGLIYEETRG-------VLKIFLENVIRDAVTYTEHARRKTVTAMDVVYAL 91 (103)
Q Consensus 29 ~ip~a~IkRiar~~G~~riS~da~~~l~~-------~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Al 91 (103)
.||......|.+.+....+..+.+.+... .++.++.+.+.++..|. |-|+.+-+..|-.+.|
T Consensus 39 ~ip~~aa~~i~~~~~~~~~d~~~~~~~~~~~~h~v~a~~~~L~~~~g~~~~~v-H~G~Ts~Di~dTa~~L 107 (435)
T PRK07492 39 VIPKEAAETIWEKGKDAEFDVARIDEIEAVTKHDVIAFLTHLAEFVGPDARFV-HQGMTSSDVLDTCLNV 107 (435)
T ss_pred CCCHHHHHHHHHhCcccCCCHHHHHHHHHHhCCChHHHHHHHHHHhhHhhhhh-cCCCChhhhHHHHHHH
Confidence 48999999998765432355555555543 46677777777666665 7788776666555554
No 247
>PF07599 DUF1563: Protein of unknown function (DUF1563); InterPro: IPR011457 This is a small family of short hypothetical proteins in Leptospira interrogans.
Probab=25.40 E-value=1.4e+02 Score=16.80 Aligned_cols=26 Identities=19% Similarity=0.280 Sum_probs=19.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhCCCc
Q 034139 55 TRGVLKIFLENVIRDAVTYTEHARRK 80 (103)
Q Consensus 55 l~~~~e~~~~~I~~dA~~~a~ha~Rk 80 (103)
....+|+|+.+++-|.+.-.-...||
T Consensus 18 Yatyve~~lkq~fld~~qki~k~~~k 43 (43)
T PF07599_consen 18 YATYVEYFLKQTFLDSMQKISKMDRK 43 (43)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhccC
Confidence 45678999999999887665555543
No 248
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=25.15 E-value=1.4e+02 Score=26.27 Aligned_cols=63 Identities=14% Similarity=0.076 Sum_probs=43.5
Q ss_pred hHHHHHHHHhcCccc--------cchHHHHHHHHHHHHHHHHHHHHHH--HHHhhCCCceecHHHHHHHHHhc
Q 034139 32 KPAIRRLARRGGVKR--------ISGLIYEETRGVLKIFLENVIRDAV--TYTEHARRKTVTAMDVVYALKRQ 94 (103)
Q Consensus 32 ~a~IkRiar~~G~~r--------iS~da~~~l~~~~e~~~~~I~~dA~--~~a~ha~RkTI~~~DV~~Alkr~ 94 (103)
...|.|+++..|..+ .+++.+..+.+...+.+..+++|-. ++.+..-=..|..+|++..-+..
T Consensus 257 i~~i~~L~k~~Gk~Kr~~~~~~~p~pel~K~v~~la~erl~~vftd~shdK~sR~eAvn~i~~~~e~~~~e~~ 329 (760)
T KOG1067|consen 257 IQGIERLAKKYGKQKREPQKLFLPDPELVKHVHKLAMERLYAVFTDYSHDKISRDEAVNKIRLDDEDKVKEEF 329 (760)
T ss_pred HHHHHHHHHHhCccccchhhhcCCCHHHHHHHHHHHHHHHHHHhcccccccchhhhHHhhhccchHHHHHhhc
Confidence 446899999999644 5677888888888888988888876 55544333345556665555444
No 249
>smart00481 POLIIIAc DNA polymerase alpha chain like domain. DNA polymerase alpha chain like domain, incl. family of hypothetical proteins
Probab=25.01 E-value=58 Score=18.90 Aligned_cols=22 Identities=14% Similarity=0.172 Sum_probs=17.3
Q ss_pred eecHHHHHHHHHhcCCcccccC
Q 034139 81 TVTAMDVVYALKRQGRTLYGFG 102 (103)
Q Consensus 81 TI~~~DV~~Alkr~g~~lYgf~ 102 (103)
+++++|+....+++|....|++
T Consensus 14 ~~~~~~~~~~a~~~g~~~v~iT 35 (67)
T smart00481 14 ALSPEELVKRAKELGLKAIAIT 35 (67)
T ss_pred cCCHHHHHHHHHHcCCCEEEEe
Confidence 5778888888888888777664
No 250
>cd01670 Death Death Domain: a protein-protein interaction domain. Death Domains (DDs) are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. Structural analysis of DD-DD complexes show that the domains interact with each other in many different ways. DD-containing proteins serve as adaptors in signaling pathways and they can recruit other proteins into signaling complexes. In mammals, they are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways. In invertebrates, they are involved in transcriptional regulation of zygotic patterning genes in insect embryogenesis, and are components of the ToII/NF-kappaB pathway, a conserved innate immune pathway in a
Probab=24.87 E-value=1.6e+02 Score=17.34 Aligned_cols=60 Identities=20% Similarity=0.225 Sum_probs=37.2
Q ss_pred HHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhcCC
Q 034139 33 PAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGR 96 (103)
Q Consensus 33 a~IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~g~ 96 (103)
...++++++.| +++.-++.+...-....+...+-.....+..+. .-|.+++..||+..+.
T Consensus 11 ~~W~~la~~Lg---l~~~~I~~i~~~~~~~~~~~~~mL~~W~~~~~~-~at~~~L~~aL~~~~~ 70 (79)
T cd01670 11 KDWKKLARKLG---LSDGEIDQIEEDNPRVREQAYQLLLKWEEREGD-NATVGNLIEALREIGR 70 (79)
T ss_pred hHHHHHHHHhC---CCHHHHHHHHHhCCCHHHHHHHHHHHHHhccCc-CcHHHHHHHHHHHcCH
Confidence 56788898888 566666666655433223333333333433333 7888999999987764
No 251
>KOG0726 consensus 26S proteasome regulatory complex, ATPase RPT2 [Posttranslational modification, protein turnover, chaperones]
Probab=24.78 E-value=73 Score=26.05 Aligned_cols=32 Identities=22% Similarity=0.173 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHHHhhCCCceecHHHHHHHHHh
Q 034139 62 FLENVIRDAVTYTEHARRKTVTAMDVVYALKR 93 (103)
Q Consensus 62 ~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr 93 (103)
=+..|+-+|-..|-.+.|++|+.+|...|.+.
T Consensus 394 dIkAictEaGllAlRerRm~vt~~DF~ka~e~ 425 (440)
T KOG0726|consen 394 DIKAICTEAGLLALRERRMKVTMEDFKKAKEK 425 (440)
T ss_pred cHHHHHHHHhHHHHHHHHhhccHHHHHHHHHH
Confidence 46778889999999999999999999998775
No 252
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=24.68 E-value=1.3e+02 Score=22.29 Aligned_cols=33 Identities=15% Similarity=0.232 Sum_probs=18.8
Q ss_pred CcchHHHHHHHHhcCc-cccchHHHHHHHHHHHH
Q 034139 29 GITKPAIRRLARRGGV-KRISGLIYEETRGVLKI 61 (103)
Q Consensus 29 ~ip~a~IkRiar~~G~-~riS~da~~~l~~~~e~ 61 (103)
++++++|.|.+..-+- .+||++..+.+.+++++
T Consensus 11 GVS~~TVSrvLn~~~~~~~Vs~~tr~rV~~~a~e 44 (328)
T PRK11303 11 GVSRTTASYVINGKAKQYRVSDKTVEKVMAVVRE 44 (328)
T ss_pred CCCHHHHHHHHcCCCCCCCcCHHHHHHHHHHHHH
Confidence 4566666666643321 25777766666655444
No 253
>PF11903 DUF3423: Protein of unknown function (DUF3423); InterPro: IPR021831 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 73 to 118 amino acids in length.
Probab=24.47 E-value=1.2e+02 Score=18.90 Aligned_cols=51 Identities=12% Similarity=0.034 Sum_probs=34.5
Q ss_pred cCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhh----CCCceecHHHHHHHHH
Q 034139 42 GGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEH----ARRKTVTAMDVVYALK 92 (103)
Q Consensus 42 ~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~h----a~RkTI~~~DV~~Alk 92 (103)
+++.||+++.++.++.........|...+.-+++- +.--+++.+.|...|-
T Consensus 1 ~~~vri~~~L~~~ar~~a~~~~RSi~~QiE~WariGr~~E~np~l~~~~I~~~l~ 55 (72)
T PF11903_consen 1 MGSVRISDELHDQARAEAAAESRSINGQIEHWARIGRAAEDNPDLSYSFIEEMLL 55 (72)
T ss_pred CCCeeeCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHH
Confidence 36678999999999988877777777766655542 1122466666666654
No 254
>PRK09492 treR trehalose repressor; Provisional
Probab=24.28 E-value=1.2e+02 Score=22.27 Aligned_cols=32 Identities=19% Similarity=0.293 Sum_probs=22.2
Q ss_pred CcchHHHHHHHHhcCccccchHHHHHHHHHHHHH
Q 034139 29 GITKPAIRRLARRGGVKRISGLIYEETRGVLKIF 62 (103)
Q Consensus 29 ~ip~a~IkRiar~~G~~riS~da~~~l~~~~e~~ 62 (103)
+++.++|.|.+.. ..+||++..+.+.+++++.
T Consensus 15 gVS~~TVSrvLn~--~~~vs~~tr~rV~~~a~el 46 (315)
T PRK09492 15 GVGKSTVSRVLNN--ESGVSEETRERVEAVINQH 46 (315)
T ss_pred CCCHHHHhHHhCC--CCCCCHHHHHHHHHHHHHH
Confidence 5677777777764 3468888887777665543
No 255
>PF10346 Con-6: Conidiation protein 6; InterPro: IPR018824 This entry represents a conserved region found in fungal conidiation-specific protein 6 []. This protein is expressed approximately 6 hours after the induction of development and is induced just prior to major constriction-chain growth [].
Probab=24.25 E-value=84 Score=17.23 Aligned_cols=19 Identities=16% Similarity=0.095 Sum_probs=15.9
Q ss_pred ccccchHHHHHHHHHHHHH
Q 034139 44 VKRISGLIYEETRGVLKIF 62 (103)
Q Consensus 44 ~~riS~da~~~l~~~~e~~ 62 (103)
-.++|+++.+..++.|++.
T Consensus 16 NPnvSeeaK~~A~~~Le~~ 34 (36)
T PF10346_consen 16 NPNVSEEAKQHAREKLEEM 34 (36)
T ss_pred CCCcCHHHHHHHHHHHHHc
Confidence 3689999999999988764
No 256
>COG3097 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.22 E-value=23 Score=23.75 Aligned_cols=14 Identities=43% Similarity=0.295 Sum_probs=10.7
Q ss_pred hCCCceecHHHHHH
Q 034139 76 HARRKTVTAMDVVY 89 (103)
Q Consensus 76 ha~RkTI~~~DV~~ 89 (103)
-|||||||..|=-.
T Consensus 17 lagrKTITIRD~SE 30 (106)
T COG3097 17 LAGRKTITIRDKSE 30 (106)
T ss_pred hCCCceEEEeccch
Confidence 47999999877443
No 257
>COG4352 RPL13 Ribosomal protein L13E [Translation, ribosomal structure and biogenesis]
Probab=24.16 E-value=81 Score=21.54 Aligned_cols=31 Identities=29% Similarity=0.348 Sum_probs=22.2
Q ss_pred HHHHhcCc------cccchHHHHHHHHHHHHHHHHHH
Q 034139 37 RLARRGGV------KRISGLIYEETRGVLKIFLENVI 67 (103)
Q Consensus 37 Riar~~G~------~riS~da~~~l~~~~e~~~~~I~ 67 (103)
+-|+..|+ ...+++.++++.+.++.|++.++
T Consensus 74 ~~AR~LGI~VD~RRr~~~~en~eal~k~ik~ll~~~~ 110 (113)
T COG4352 74 RKARTLGIAVDHRRRNRNPENFEALVKRIKELLEKII 110 (113)
T ss_pred HHHHhhCcceehhhccCCHHHHHHHHHHHHHHHhcCc
Confidence 34566663 56788888888888888877654
No 258
>PF07278 DUF1441: Protein of unknown function (DUF1441); InterPro: IPR009901 This entry is represented by Bacteriophage VT1-Sakai, H0025. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several hypothetical Enterobacterial proteins of around 160 residues in length. The function of this family is unknown.
Probab=24.12 E-value=2.7e+02 Score=19.86 Aligned_cols=54 Identities=11% Similarity=0.036 Sum_probs=37.3
Q ss_pred hhhcccccCcchHHHHHHHHhcC----------------ccccchHHHHHHHHHHHHHHHHHHHHHHHHH
Q 034139 21 KVLRDNIQGITKPAIRRLARRGG----------------VKRISGLIYEETRGVLKIFLENVIRDAVTYT 74 (103)
Q Consensus 21 k~~r~~~~~ip~a~IkRiar~~G----------------~~riS~da~~~l~~~~e~~~~~I~~dA~~~a 74 (103)
|+.+.+-..||.+-|.+.+-..- -.-++++++..+++.+.....++.......|
T Consensus 81 k~e~e~g~Lipa~eV~~~~s~~~Kav~q~LetlPD~LERd~gL~p~~v~~vQ~~iD~lR~~l~~~i~~~~ 150 (152)
T PF07278_consen 81 KFEKETGQLIPAEEVRREMSEMAKAVVQVLETLPDILERDAGLPPEQVARVQSVIDDLRDQLAERIQEAC 150 (152)
T ss_pred HHHHHHcccCcHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 44445556788777665442211 1237899999999999999998888777766
No 259
>COG5466 Predicted small metal-binding protein [Function unknown]
Probab=23.81 E-value=1.6e+02 Score=17.90 Aligned_cols=29 Identities=24% Similarity=0.320 Sum_probs=19.5
Q ss_pred HHHHHHHHHHhhCCCceecHHHHHHHHHh
Q 034139 65 NVIRDAVTYTEHARRKTVTAMDVVYALKR 93 (103)
Q Consensus 65 ~I~~dA~~~a~ha~RkTI~~~DV~~Alkr 93 (103)
+|.++...-++.++--|.-.||++..++.
T Consensus 26 Ev~~~iv~H~k~~Hg~t~I~ed~in~Ik~ 54 (59)
T COG5466 26 EVMRRIVEHAKEAHGETEIREDMINKIKS 54 (59)
T ss_pred HHHHHHHHHHHHhcCCccccHHHHHHHHH
Confidence 44455556666666678778888877764
No 260
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=23.76 E-value=1.4e+02 Score=22.30 Aligned_cols=29 Identities=17% Similarity=0.209 Sum_probs=19.7
Q ss_pred CcchHHHHHHHHhcCccccchHHHHHHHHHH
Q 034139 29 GITKPAIRRLARRGGVKRISGLIYEETRGVL 59 (103)
Q Consensus 29 ~ip~a~IkRiar~~G~~riS~da~~~l~~~~ 59 (103)
+++.++|.|.+.. -.+||++..+.+.+++
T Consensus 17 gVS~~TVSr~Ln~--~~~vs~~tr~~V~~~a 45 (342)
T PRK10014 17 GVSVSTVSLVLSG--KGRISTATGERVNQAI 45 (342)
T ss_pred CCCHHHHHHHHCC--CCCCCHHHHHHHHHHH
Confidence 5677777777753 3468888777665554
No 261
>PRK14700 recombination factor protein RarA; Provisional
Probab=23.72 E-value=3e+02 Score=21.78 Aligned_cols=67 Identities=9% Similarity=0.055 Sum_probs=40.9
Q ss_pred cCcchHHHHHHHHhcCc---------cccchHHHHHHHHHHH---HHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhc
Q 034139 28 QGITKPAIRRLARRGGV---------KRISGLIYEETRGVLK---IFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 94 (103)
Q Consensus 28 ~~ip~a~IkRiar~~G~---------~riS~da~~~l~~~~e---~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~ 94 (103)
..|+...|..+++++-. -.+++++.+.|.+... ..+-.+++-|+..+...+...||.++|..++.+.
T Consensus 37 ~~L~~~di~~il~ral~~~~~~~~~~~~i~~~al~~ia~~a~GDaR~aLN~LE~a~~~~~~~~~~~it~~~~~~~~~~~ 115 (300)
T PRK14700 37 KRLSLVATQKLIEKALSQDEVLAKHKFKIDDGLYNAMHNYNEGDCRKILNLLERMFLISTRGDEIYLNKELFDQAVGET 115 (300)
T ss_pred cCCCHHHHHHHHHHHHHhhhccCCcCCCcCHHHHHHHHHhcCCHHHHHHHHHHHHHhhccccCCCccCHHHHHHHHhHH
Confidence 35677777777766531 2588999998887633 2223344444433323333359999999998654
No 262
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=23.55 E-value=1.3e+02 Score=22.65 Aligned_cols=31 Identities=13% Similarity=0.179 Sum_probs=20.7
Q ss_pred CcchHHHHHHHHhcCccccchHHHHHHHHHHHH
Q 034139 29 GITKPAIRRLARRGGVKRISGLIYEETRGVLKI 61 (103)
Q Consensus 29 ~ip~a~IkRiar~~G~~riS~da~~~l~~~~e~ 61 (103)
++++++|.|.+... .+||++..+.+.+++++
T Consensus 12 GVS~~TVSrvLn~~--~~Vs~~tr~kV~~~a~e 42 (346)
T PRK10401 12 GVSVATVSRVLNNS--ALVSADTREAVMKAVSE 42 (346)
T ss_pred CCCHHHHHHHHCCC--CCCCHHHHHHHHHHHHH
Confidence 56777777777533 46787777777666544
No 263
>TIGR02417 fruct_sucro_rep D-fructose-responsive transcription factor. Members of this family belong the lacI helix-turn-helix family (pfam00356) of DNA-binding transcriptional regulators. All members are from the proteobacteria. Characterized members act as positive and negative transcriptional regulators of fructose and sucrose transport and metabolism. Sucrose is a disaccharide composed of fructose and glucose; D-fructose-1-phosphate rather than an intact sucrose moiety has been shown to act as the inducer.
Probab=23.50 E-value=1.4e+02 Score=22.15 Aligned_cols=33 Identities=21% Similarity=0.220 Sum_probs=18.8
Q ss_pred CcchHHHHHHHHhcCc-cccchHHHHHHHHHHHH
Q 034139 29 GITKPAIRRLARRGGV-KRISGLIYEETRGVLKI 61 (103)
Q Consensus 29 ~ip~a~IkRiar~~G~-~riS~da~~~l~~~~e~ 61 (103)
++++++|.|.+...+- .+||++..+.+.+++++
T Consensus 10 GVS~~TVSrvLn~~~~~~~vs~~tr~rV~~~a~~ 43 (327)
T TIGR02417 10 GVSKTTASYVINGKAKEYRISQETVERVMAVVRE 43 (327)
T ss_pred CCCHHHHHHHHcCCCCCCccCHHHHHHHHHHHHH
Confidence 4566666666654321 15777766666655444
No 264
>cd05030 calgranulins Calgranulins: S-100 domain found in proteins belonging to the Calgranulin subgroup of the S100 family of EF-hand calcium-modulated proteins, including S100A8, S100A9, and S100A12 . Note that the S-100 hierarchy, to which this Calgranulin group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. These proteins are expressed mainly in granulocytes, and are involved in inflammation, allergy, and neuritogenesis, as well as in host-parasite response. Calgranulins are modulated not only by calcium, but also by other metals such as zinc and copper. Structural data suggested that calgranulins may exist in multiple structural forms, homodimers, as well as hetero-oligomers. For example, the S100A8/S100A9 complex called calprotectin plays important roles in the regulation of inflammatory processes, wound repair, and regulating zinc-dependent enzymes as well as microbial growth.
Probab=23.32 E-value=1.4e+02 Score=18.50 Aligned_cols=21 Identities=14% Similarity=0.210 Sum_probs=14.0
Q ss_pred HHHhhCCCc----eecHHHHHHHHH
Q 034139 72 TYTEHARRK----TVTAMDVVYALK 92 (103)
Q Consensus 72 ~~a~ha~Rk----TI~~~DV~~Alk 92 (103)
.|.++++++ +|+.+|+...|.
T Consensus 13 ~f~~y~~~~~~~~~Is~~El~~ll~ 37 (88)
T cd05030 13 VFHQYSVRKGHPDTLYKKEFKQLVE 37 (88)
T ss_pred HHHHHhccCCCcccCCHHHHHHHHH
Confidence 344455443 788888888886
No 265
>cd07293 PX_SNX3 The phosphoinositide binding Phox Homology domain of Sorting Nexin 3. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. SNX3 associates with early endosomes through a PX domain-mediated interaction with phosphatidylinositol-3-phosphate (PI3P). It associates with the retromer complex, a membrane coat multimeric complex required for endosomal retrieval of lysosomal hydrolase receptors to the Golgi, and functions as a cargo-specific adaptor f
Probab=23.26 E-value=1.2e+02 Score=20.50 Aligned_cols=27 Identities=22% Similarity=0.210 Sum_probs=22.7
Q ss_pred CccccchHHHHHHHHHHHHHHHHHHHH
Q 034139 43 GVKRISGLIYEETRGVLKIFLENVIRD 69 (103)
Q Consensus 43 G~~riS~da~~~l~~~~e~~~~~I~~d 69 (103)
+..+++++..++=+..|+.|+..|+..
T Consensus 79 ~~~~~~~~fie~Rr~~Le~FL~~i~~h 105 (123)
T cd07293 79 DDGIFDDSFIEERKQGLEQFLNKVAGH 105 (123)
T ss_pred ccCCCCHHHHHHHHHHHHHHHHHHHcC
Confidence 345789999999999999999998654
No 266
>cd06409 PB1_MUG70 The MUG70 protein is a product of the meiotically up-regulated gene 70 which has a role in meiosis and harbors a PB1 domain. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domains depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic amino acid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is
Probab=23.26 E-value=76 Score=20.49 Aligned_cols=17 Identities=24% Similarity=0.178 Sum_probs=13.9
Q ss_pred HHHHHHHHhhCCCceec
Q 034139 67 IRDAVTYTEHARRKTVT 83 (103)
Q Consensus 67 ~~dA~~~a~ha~RkTI~ 83 (103)
+.+|+..|+.+++++|.
T Consensus 64 L~e~v~iar~~g~~~v~ 80 (86)
T cd06409 64 LVAAVLVARSAGLKKLD 80 (86)
T ss_pred HHHHHHHHHHcCCCEEE
Confidence 45688899999999875
No 267
>TIGR02440 FadJ fatty oxidation complex, alpha subunit FadJ. Members represent alpha subunit of multifunctional enzyme complex of the fatty acid degradation cycle. Plays a minor role in aerobic beta-oxidation of fatty acids. FadJI complex is necessary for anaerobic growth on short-chain acids with nitrate as an electron acceptor. Activities include: enoyl-CoA hydratase (EC 4.2.1.17),3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35), 3-hydroxybutyryl-CoA epimerase (EC 5.1.2.3). A representative is E. coli FadJ (aka YfcX). This model excludes the FadB of TIGR02437 equivalog.
Probab=23.12 E-value=2.4e+02 Score=24.51 Aligned_cols=58 Identities=16% Similarity=0.103 Sum_probs=34.7
Q ss_pred HHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhcCCcc
Q 034139 35 IRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTL 98 (103)
Q Consensus 35 IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~g~~l 98 (103)
+..++++.|-..|-- .+.=--++...+.-++.+|..+.++ | ++++||+.+++..|+|.
T Consensus 469 ~~~~~~~~gk~pv~v--~d~pGfi~nRl~~~~~~Ea~~l~~~-G---~~~~dID~a~~~~G~p~ 526 (699)
T TIGR02440 469 TVALAKKQGKTPIVV--ADKAGFYVNRILAPYMNEAARLLLE-G---EPVEHIDKALVKFGFPV 526 (699)
T ss_pred HHHHHHHcCCeEEEE--ccccchHHHHHHHHHHHHHHHHHHC-C---CCHHHHHHHHHHcCCCc
Confidence 445556666332211 1111233455566677778777764 4 48999999997667764
No 268
>cd00862 ProRS_anticodon_zinc ProRS Prolyl-anticodon binding domain, long version found predominantly in eukaryotes and archaea. ProRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only, and an additional C-terminal zinc-binding domain specific to this subfamily of aaRSs.
Probab=23.07 E-value=2.7e+02 Score=20.12 Aligned_cols=46 Identities=20% Similarity=0.272 Sum_probs=32.9
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCcee-cHHHHHHHHHhcCC
Q 034139 49 GLIYEETRGVLKIFLENVIRDAVTYTEHARRKTV-TAMDVVYALKRQGR 96 (103)
Q Consensus 49 ~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI-~~~DV~~Alkr~g~ 96 (103)
++..+.+.+.++.+-.++.+.|..+.+. ..++ +.+++..++...|+
T Consensus 100 ~el~~~i~~ll~~i~~~l~~~A~~~~~~--~~~~~~~~e~~~~~~~~~~ 146 (202)
T cd00862 100 AELVEKVPELLDEIQEDLYERALEFRDA--TRIVDTWEEFKEALNEKGI 146 (202)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhc--eEeeCCHHHHHHHHhcCCE
Confidence 3566777788888888999999988876 3333 46777777765444
No 269
>cd06456 M3A_DCP_Oligopeptidase_A Peptidase family M3 dipeptidyl carboxypeptidase (DCP; Dcp II; peptidyl dipeptidase; EC 3.4.15.5). This metal-binding M3A family also includes oligopeptidase A (OpdA; EC 3.4.24.70) enzyme. DCP cleaves dipeptides off the C-termini of various peptides and proteins, the smallest substrate being N-blocked tripeptides and unblocked tetrapeptides. DCP from E. coli is inhibited by the anti-hypertensive drug captopril, an inhibitor of the mammalian angiotensin converting enzyme (ACE, also called peptidyl dipeptidase A). Oligopeptidase A (OpdA) may play a specific role in the degradation of signal peptides after they are released from precursor forms of secreted proteins. It can also cleave N-acetyl-L-Ala.
Probab=22.98 E-value=2.6e+02 Score=22.75 Aligned_cols=55 Identities=11% Similarity=0.065 Sum_probs=30.0
Q ss_pred chHHHHHHHHHHHHHHHHHHHH----HHHHHh-hCCCceecHHHHHHHHHhcCCcccccC
Q 034139 48 SGLIYEETRGVLKIFLENVIRD----AVTYTE-HARRKTVTAMDVVYALKRQGRTLYGFG 102 (103)
Q Consensus 48 S~da~~~l~~~~e~~~~~I~~d----A~~~a~-ha~RkTI~~~DV~~Alkr~g~~lYgf~ 102 (103)
|++.+..+.+.+...+...+++ ...+++ ..+-.+|.+-|+....+......|.|+
T Consensus 37 sp~~v~~Fl~~l~~~~~p~~~~e~~~L~~~~~~~~~~~~l~~wD~~yy~~~~~~~~~~~d 96 (422)
T cd06456 37 SPEAVLEFLEDLAPKAKPQAKKELAELQAFAKEEGGEDELEPWDWAYYSEKLRKEKYDLD 96 (422)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHhcCCC
Confidence 4444444444444444443333 233333 233346999999998887666556553
No 270
>KOG0728 consensus 26S proteasome regulatory complex, ATPase RPT6 [Posttranslational modification, protein turnover, chaperones]
Probab=22.96 E-value=76 Score=25.47 Aligned_cols=34 Identities=26% Similarity=0.270 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHh
Q 034139 60 KIFLENVIRDAVTYTEHARRKTVTAMDVVYALKR 93 (103)
Q Consensus 60 e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr 93 (103)
-.-+..++-+|-.||-.+.|..||-||.++|.-.
T Consensus 354 gaevk~vcteagm~alrerrvhvtqedfemav~k 387 (404)
T KOG0728|consen 354 GAEVKGVCTEAGMYALRERRVHVTQEDFEMAVAK 387 (404)
T ss_pred cchhhhhhhhhhHHHHHHhhccccHHHHHHHHHH
Confidence 3346677888999999999999999999999753
No 271
>TIGR01796 CM_mono_aroH monofunctional chorismate mutase, gram positive type, clade 1. This model represents a family of monofunctional (non-fused) chorismate mutases from gram positive bacteria (Firmicutes) and cyanobacteria. Trusted members of the family are found in operons with other enzymes of the chorismate pathways, both up- and downstream of CM (Listeria, Bacillus, Oceanobacillus) or are the sole CM in the genome where the other members of the chorismate pathways are found elsewhere in the genome (Nostoc, Thermosynechococcus).
Probab=22.69 E-value=1e+02 Score=21.23 Aligned_cols=26 Identities=15% Similarity=0.208 Sum_probs=22.7
Q ss_pred CccccchHHHHHHHHHHHHHHHHHHH
Q 034139 43 GVKRISGLIYEETRGVLKIFLENVIR 68 (103)
Q Consensus 43 G~~riS~da~~~l~~~~e~~~~~I~~ 68 (103)
|+.-++++..+++.+++.+.+.+|++
T Consensus 6 GAtTv~~nt~e~I~~at~eLl~~ii~ 31 (117)
T TIGR01796 6 GATTVERNEAEEIGEAVAELLTELME 31 (117)
T ss_pred CceecCCCCHHHHHHHHHHHHHHHHH
Confidence 67789999999999999999988765
No 272
>cd02185 AroH Chorismate mutase (AroH) is one of at least five chorismate-utilizing enzymes present in microorganisms that catalyze the rearrangement of chorismate to prephenic acid, the first committed step in the biosynthesis of aromatic amino acids. In prokaryotes, chorismate mutase may be fused to prephenate dehydratase, prephenate dehydrogenase, or 3-deoxy-D-arabino-heptulosonat-7-phosphate (DAHP) as part of a bifunctional enzyme. The AroH domain forms a homotrimer with three-fold symmetry.
Probab=22.49 E-value=1e+02 Score=21.20 Aligned_cols=26 Identities=23% Similarity=0.305 Sum_probs=22.7
Q ss_pred CccccchHHHHHHHHHHHHHHHHHHH
Q 034139 43 GVKRISGLIYEETRGVLKIFLENVIR 68 (103)
Q Consensus 43 G~~riS~da~~~l~~~~e~~~~~I~~ 68 (103)
|+.-++++..+++.+++.+.+.+|++
T Consensus 6 GAtTv~~nt~e~I~~at~eLl~~i~~ 31 (117)
T cd02185 6 GATTVEENTAEEILEATRELLEEIIE 31 (117)
T ss_pred CceecCCCCHHHHHHHHHHHHHHHHH
Confidence 67789999999999999999988765
No 273
>cd06864 PX_SNX4 The phosphoinositide binding Phox Homology domain of Sorting Nexin 4. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. SNX4 is involved in recycling traffic from the sorting endosome (post-Golgi endosome) back to the late Golgi. It shows a similar domain architecture as SNX1-2, among others, containing a Bin/Amphiphysin/Rvs (BAR) domain, which detects membrane curvature, C-terminal to the PX domain. SNX4 is implicated in the regulation of
Probab=22.48 E-value=90 Score=21.19 Aligned_cols=30 Identities=20% Similarity=0.127 Sum_probs=23.9
Q ss_pred CccccchHHHHHHHHHHHHHHHHHHHHHHH
Q 034139 43 GVKRISGLIYEETRGVLKIFLENVIRDAVT 72 (103)
Q Consensus 43 G~~riS~da~~~l~~~~e~~~~~I~~dA~~ 72 (103)
+..+++++.+++=+..||.|+..|+.....
T Consensus 87 ~~~~~~~~fie~Rr~~Le~fL~~i~~~p~l 116 (129)
T cd06864 87 SSDTFDPDFVERRRAGLENFLLRVAGHPEL 116 (129)
T ss_pred cccCCCHHHHHHHHHHHHHHHHHHHcChhh
Confidence 345678899999999999999999765543
No 274
>COG1223 Predicted ATPase (AAA+ superfamily) [General function prediction only]
Probab=22.46 E-value=1.4e+02 Score=24.11 Aligned_cols=29 Identities=28% Similarity=0.362 Sum_probs=22.6
Q ss_pred HHHHHHHHHHhhCCCceecHHHHHHHHHh
Q 034139 65 NVIRDAVTYTEHARRKTVTAMDVVYALKR 93 (103)
Q Consensus 65 ~I~~dA~~~a~ha~RkTI~~~DV~~Alkr 93 (103)
.++.-|..-|..++|-.|+.+|++.|++.
T Consensus 326 kvlK~aLh~Ai~ed~e~v~~edie~al~k 354 (368)
T COG1223 326 KVLKTALHRAIAEDREKVEREDIEKALKK 354 (368)
T ss_pred HHHHHHHHHHHHhchhhhhHHHHHHHHHh
Confidence 34444666666789999999999999984
No 275
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=22.41 E-value=94 Score=17.59 Aligned_cols=36 Identities=19% Similarity=0.167 Sum_probs=18.7
Q ss_pred CcchHHHHHHHHhcCccccchHHHHHHHHHHHHHHHH
Q 034139 29 GITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLEN 65 (103)
Q Consensus 29 ~ip~a~IkRiar~~G~~riS~da~~~l~~~~e~~~~~ 65 (103)
+|+.++|.++...- ...++-+.+..|.+++.-=+.+
T Consensus 21 gis~~tl~~~~~~~-~~~~~~~~l~~ia~~l~~~~~e 56 (63)
T PF13443_consen 21 GISRSTLSRILNGK-PSNPSLDTLEKIAKALNCSPEE 56 (63)
T ss_dssp T--HHHHHHHHTTT------HHHHHHHHHHHT--HHH
T ss_pred CcCHHHHHHHHhcc-cccccHHHHHHHHHHcCCCHHH
Confidence 78888888888732 4577777777777766544433
No 276
>KOG0027 consensus Calmodulin and related proteins (EF-Hand superfamily) [Signal transduction mechanisms]
Probab=22.29 E-value=2.5e+02 Score=18.84 Aligned_cols=33 Identities=15% Similarity=0.239 Sum_probs=28.2
Q ss_pred HHHHHHHHHhhCCCceecHHHHHHHHHhcCCcc
Q 034139 66 VIRDAVTYTEHARRKTVTAMDVVYALKRQGRTL 98 (103)
Q Consensus 66 I~~dA~~~a~ha~RkTI~~~DV~~Alkr~g~~l 98 (103)
-+.+|-..-...+.=.|+++++...|...|.++
T Consensus 86 el~eaF~~fD~d~~G~Is~~el~~~l~~lg~~~ 118 (151)
T KOG0027|consen 86 ELKEAFRVFDKDGDGFISASELKKVLTSLGEKL 118 (151)
T ss_pred HHHHHHHHHccCCCCcCcHHHHHHHHHHhCCcC
Confidence 667788888888888999999999999998754
No 277
>PF08673 RsbU_N: Phosphoserine phosphatase RsbU, N-terminal domain; InterPro: IPR014787 The phosphoserine phosphatase RsbU acts as a positive regulator of the general stress-response factor of Gram-positive organisms, sigma-B. RsbU dephosphorylates rsbV in response to environmental stress conveyed from the rsbXST module. The phosphatase activity of RsbU is stimulated during the stress response by associating with the RsbT kinase. This association leads to the induction of sigmaB activity. The N-terminal domain forms a helix-swapped dimer that is otherwise similar to the KaiA domain dimer. Deletions in the N-terminal domain are deleterious to the activity of RsbU. The C-terminal domain of RsbU is similar to the catalytic domains of PP2C-type phosphatases [].; PDB: 2J6Y_D 2J6Z_A 2J70_A 1W53_A.
Probab=22.23 E-value=1.4e+02 Score=18.80 Aligned_cols=39 Identities=18% Similarity=0.151 Sum_probs=19.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHH
Q 034139 54 ETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALK 92 (103)
Q Consensus 54 ~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alk 92 (103)
.|.+.++.--+..+-.|..|.+..=.+.|.++||..--+
T Consensus 7 lL~~yl~~~~E~~L~~~~~~~r~~i~~~I~PEeIv~iH~ 45 (77)
T PF08673_consen 7 LLREYLETQDEQSLYQAQEFGRELIEKDISPEEIVEIHK 45 (77)
T ss_dssp HHHHHHHH--HHHHHHHHHHHHHHHHTT--HHHHHHHHH
T ss_pred HHHHHHhCCCHHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 344444444455555566666655445577777765433
No 278
>PF09077 Phage-MuB_C: Mu B transposition protein, C terminal ; InterPro: IPR009084 Bacteriophage Mu can integrate into the host bacterial genome and replicate via transposition. Mu requires the activity of four proteins for DNA transposition. Two of these proteins are the phage-encoded A and B transposition proteins, while the other two are host-specified accessory factors HU and IHF. These four proteins can form nucleoprotein complexes (transposomes), which enable strand transfer. The stable protein-DNA intermediate is subsequently disassembled prior to DNA replication by host proteins. The Mu B transposition protein is an ATP-dependent, DNA-binding protein required for target capture and immunity, as well as for activating transpososome function []. The C-terminal domain of the B transposition protein is believed to be involved in both DNA-binding and protein-protein contacts with the Mu A transposition protein. The structure of the C-terminal domain consists of four helices in an irregular array [].; GO: 0003677 DNA binding, 0006313 transposition, DNA-mediated; PDB: 1F6V_A.
Probab=21.98 E-value=41 Score=21.43 Aligned_cols=62 Identities=18% Similarity=0.171 Sum_probs=35.9
Q ss_pred CcchHHHHHHHHhcCccccchHHHHHHHHHHH-----HHHHHHHHHHHHHHhhCCCceecHHHHHHHHHh
Q 034139 29 GITKPAIRRLARRGGVKRISGLIYEETRGVLK-----IFLENVIRDAVTYTEHARRKTVTAMDVVYALKR 93 (103)
Q Consensus 29 ~ip~a~IkRiar~~G~~riS~da~~~l~~~~e-----~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr 93 (103)
.=+++.|+-|++.-|+ -.+++...|..+.+ .-+.+.++-|..+|.-++.. |+.++|..|.+.
T Consensus 11 k~~~~Di~Ai~~AWgI--~d~~~~~~l~~I~~k~GaLR~l~ktLrlA~m~A~g~g~~-i~~~~i~~A~~~ 77 (78)
T PF09077_consen 11 KPKKADIKAIAKAWGI--TDKEERKLLQSIAEKPGALRQLTKTLRLAAMFAKGEGEA-ITADHIRAAWKE 77 (78)
T ss_dssp S-SGGGTTHHHHSSSS--SSSHHHHHHHTTSSS-S-HHHHHHHHGGGT-TT-TTS---SSHHHHHHHHTS
T ss_pred CCCHHHHHHHHHHhCC--CCHHHHHHHHHHcccccHHHHHHHHHHHHHHHhccCCCc-CCHHHHHHHHHh
Confidence 3345556666666665 23455555554422 23455566788888777776 999999998754
No 279
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=21.79 E-value=1.8e+02 Score=17.44 Aligned_cols=29 Identities=28% Similarity=0.411 Sum_probs=16.7
Q ss_pred CcchHHHHHHHHhcCccccchHHHHHHHHHHH
Q 034139 29 GITKPAIRRLARRGGVKRISGLIYEETRGVLK 60 (103)
Q Consensus 29 ~ip~a~IkRiar~~G~~riS~da~~~l~~~~e 60 (103)
+.| ++++.|++..|+. |..++....+.||
T Consensus 23 G~~-Pt~rEIa~~~g~~--S~~tv~~~L~~Le 51 (65)
T PF01726_consen 23 GYP-PTVREIAEALGLK--STSTVQRHLKALE 51 (65)
T ss_dssp SS----HHHHHHHHTSS--SHHHHHHHHHHHH
T ss_pred CCC-CCHHHHHHHhCCC--ChHHHHHHHHHHH
Confidence 455 4788888888875 4555555444444
No 280
>PF08672 APC2: Anaphase promoting complex (APC) subunit 2; InterPro: IPR014786 The anaphase-promoting complex (APC) or cyclosome is a multi-subunit E3 protein ubiquitin ligase that regulates important events in mitosis such as the initiation of anaphase and exit from telophase. The APC, in conjunction with other enzymes, assembles multi-ubiquitin chains on a variety of regulatory proteins, thereby targeting them for proteolysis by the 26S proteasome. Anaphase is initiated when the APC triggers the destruction of securin, thereby allowing the protease, separase, to disrupt sister-chromatid cohesion. Securin ubiquitination by the APC is inhibited by cyclin-dependent kinase 1 (Cdk1)-dependent phosphorylation []. Forkhead Box M1 (FoxM1), which is a transcription factor that is over-expressed in many cancers, is degraded in late mitosis and early G1 phase by the APC/cyclosome (APC/C) E3 ubiquitin ligase []. The APC/C targets mitotic cyclins for destruction in mitosis and G1 phase and is then inactivated at S phase. It thereby generates alternating states of high and low cyclin-Cdk activity, which is required for the alternation of mitosis and DNA replication []. The APC/C is composed of at least 13 subunits that stay tightly associated throughout the cell cycle: APC1, APC2, APC4, APC5, APC9, APC11, CDC16, CDC23, CDC26, CDC27, DOC1, MND2 and SWM1[], []. In fission yeast the 13 subunits are known as: Apc1, Apc2, Nuc2, Apc4, Apc5, Cut9, Apc8, Apc10, Apc11, Hcn1, Apc13, Apc14 and Apc15 []. This entry represents a C-terminal domain found in APC subunit 2. ; PDB: 1LDD_A.
Probab=21.60 E-value=1e+02 Score=18.37 Aligned_cols=41 Identities=15% Similarity=0.193 Sum_probs=23.1
Q ss_pred cccCcchHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHH
Q 034139 26 NIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRD 69 (103)
Q Consensus 26 ~~~~ip~a~IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~d 69 (103)
|...+|..-|+-+++-. ..+++.++.-.+.++.|+.+..++
T Consensus 8 N~gsl~l~RIh~mLkmf---~~~~~~~~~s~~eL~~fL~~lv~e 48 (60)
T PF08672_consen 8 NLGSLPLDRIHSMLKMF---PKDPGGYDISLEELQEFLDRLVEE 48 (60)
T ss_dssp HH-SEEHHHHHHHHHHH----GGG--TT--HHHHHHHHHHHHHT
T ss_pred cCCCCCHHHHHHHHHhc---cCCCCCCCCCHHHHHHHHHHHHHC
Confidence 34468888899888876 123344555555666677665554
No 281
>COG4463 CtsR Transcriptional repressor of class III stress genes [Transcription]
Probab=21.56 E-value=53 Score=23.53 Aligned_cols=38 Identities=16% Similarity=0.424 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHHHHHH------HHHHhhCCCceecHHHHHHHHH
Q 034139 55 TRGVLKIFLENVIRDA------VTYTEHARRKTVTAMDVVYALK 92 (103)
Q Consensus 55 l~~~~e~~~~~I~~dA------~~~a~ha~RkTI~~~DV~~Alk 92 (103)
+.+.+|+|+++++.++ ++-++-|.+..+-++.|...++
T Consensus 4 ~SDiIE~YlK~ll~es~~~ivEIkRselAd~FqcVPSQINYVIk 47 (153)
T COG4463 4 TSDIIEAYLKELLEESTEEIVEIKRSELADQFQCVPSQINYVIK 47 (153)
T ss_pred hHHHHHHHHHHHHHhcccchhhhhHHHHhhhcccchhheeeeee
Confidence 4578899999999988 4566677778888888877776
No 282
>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB. Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family, ATPases associated with various cellular activities (pfam00004). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins.
Probab=21.44 E-value=4.1e+02 Score=23.64 Aligned_cols=30 Identities=13% Similarity=0.190 Sum_probs=25.2
Q ss_pred HHHHHHHHHHHHHhhCCCceecHHHHHHHH
Q 034139 62 FLENVIRDAVTYTEHARRKTVTAMDVVYAL 91 (103)
Q Consensus 62 ~~~~I~~dA~~~a~ha~RkTI~~~DV~~Al 91 (103)
-+..+++.|...+...+...|..+++.+||
T Consensus 81 ~~~~vLe~A~~~A~~~g~~~I~teHLLlAL 110 (852)
T TIGR03346 81 ELNRLLNLAEKLAQKRGDEFISSEHLLLAL 110 (852)
T ss_pred HHHHHHHHHHHHHHHcCCCcccHHHHHHHH
Confidence 456788888888888888899999999987
No 283
>CHL00195 ycf46 Ycf46; Provisional
Probab=21.42 E-value=2.1e+02 Score=23.89 Aligned_cols=45 Identities=20% Similarity=0.155 Sum_probs=29.9
Q ss_pred hHHHHHHHHHHHH----HHHHHHHHHHHHHhhCCCceecHHHHHHHHHhc
Q 034139 49 GLIYEETRGVLKI----FLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 94 (103)
Q Consensus 49 ~da~~~l~~~~e~----~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~ 94 (103)
+.-++.|.+..+- =++.++.+|...|-..+| .|+.+|+..|++..
T Consensus 415 ~~dl~~La~~T~GfSGAdI~~lv~eA~~~A~~~~~-~lt~~dl~~a~~~~ 463 (489)
T CHL00195 415 KYDIKKLSKLSNKFSGAEIEQSIIEAMYIAFYEKR-EFTTDDILLALKQF 463 (489)
T ss_pred ccCHHHHHhhcCCCCHHHHHHHHHHHHHHHHHcCC-CcCHHHHHHHHHhc
Confidence 3335555554333 356677778877766664 69999999999653
No 284
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=21.29 E-value=1.5e+02 Score=22.93 Aligned_cols=30 Identities=20% Similarity=0.316 Sum_probs=19.8
Q ss_pred CcchHHHHHHHHhcCccccchHHHHHHHHHHH
Q 034139 29 GITKPAIRRLARRGGVKRISGLIYEETRGVLK 60 (103)
Q Consensus 29 ~ip~a~IkRiar~~G~~riS~da~~~l~~~~e 60 (103)
++++++|-|.+...+ .||++..+.+.++++
T Consensus 11 GVS~sTVSrvln~~~--~Vs~eTr~kV~~a~~ 40 (333)
T COG1609 11 GVSKATVSRVLNGSP--YVSEETREKVLAAIK 40 (333)
T ss_pred CCCHHHHHHHHcCCC--CCCHHHHHHHHHHHH
Confidence 566667777766444 677777777776544
No 285
>PF12146 Hydrolase_4: Putative lysophospholipase; InterPro: IPR022742 This domain is found in bacteria and eukaryotes and is approximately 110 amino acids in length. Many members are annotated as being lysophospholipases, and others as alpha-beta hydrolase fold-containing proteins.
Probab=21.21 E-value=42 Score=20.77 Aligned_cols=19 Identities=16% Similarity=0.336 Sum_probs=12.4
Q ss_pred HHHHHHHHHhcCCcccccC
Q 034139 84 AMDVVYALKRQGRTLYGFG 102 (103)
Q Consensus 84 ~~DV~~Alkr~g~~lYgf~ 102 (103)
-+++...|..+|..+|+||
T Consensus 32 y~~~a~~L~~~G~~V~~~D 50 (79)
T PF12146_consen 32 YAHLAEFLAEQGYAVFAYD 50 (79)
T ss_pred HHHHHHHHHhCCCEEEEEC
Confidence 4556666667777777664
No 286
>PRK14101 bifunctional glucokinase/RpiR family transcriptional regulator; Provisional
Probab=21.14 E-value=4e+02 Score=22.68 Aligned_cols=20 Identities=25% Similarity=0.576 Sum_probs=16.3
Q ss_pred CcchHHHHHHHHhcCccccc
Q 034139 29 GITKPAIRRLARRGGVKRIS 48 (103)
Q Consensus 29 ~ip~a~IkRiar~~G~~riS 48 (103)
..+.++|-|++++.|..-++
T Consensus 385 ~vS~aTV~Rf~kkLGf~Gf~ 404 (638)
T PRK14101 385 DVSQPTVIRFCRSLGCQGLS 404 (638)
T ss_pred CCCHHHHHHHHHHhCCCCHH
Confidence 56889999999999976554
No 287
>PF05597 Phasin: Poly(hydroxyalcanoate) granule associated protein (phasin); InterPro: IPR008769 Polyhydroxyalkanoates (PHAs) are storage polyesters synthesised by various bacteria as intracellular carbon and energy reserve material. PHAs are accumulated as water-insoluble inclusions within the cells. This family consists of the phasins PhaF and PhaI which act as a transcriptional regulator of PHA biosynthesis genes. PhaF has been proposed to repress expression of the phaC1 gene and the phaIF operon.
Probab=21.08 E-value=2.2e+02 Score=19.67 Aligned_cols=16 Identities=31% Similarity=0.252 Sum_probs=12.3
Q ss_pred ecHHHHHHHHHhcCCc
Q 034139 82 VTAMDVVYALKRQGRT 97 (103)
Q Consensus 82 I~~~DV~~Alkr~g~~ 97 (103)
+-.+.|..||.++|.|
T Consensus 91 ~fd~rV~~aL~rLgvP 106 (132)
T PF05597_consen 91 AFDERVARALNRLGVP 106 (132)
T ss_pred HHHHHHHHHHHhcCCC
Confidence 4455688999998877
No 288
>COG0464 SpoVK ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]
Probab=20.94 E-value=1.4e+02 Score=24.25 Aligned_cols=46 Identities=24% Similarity=0.200 Sum_probs=34.9
Q ss_pred hHHHHHHHH----HHHHHHHHHHHHHHHHHhhCC-CceecHHHHHHHHHhc
Q 034139 49 GLIYEETRG----VLKIFLENVIRDAVTYTEHAR-RKTVTAMDVVYALKRQ 94 (103)
Q Consensus 49 ~da~~~l~~----~~e~~~~~I~~dA~~~a~ha~-RkTI~~~DV~~Alkr~ 94 (103)
+-.++.+.+ ..-.-+..++++|...+.... +..|+.+|+..|++..
T Consensus 433 ~~~~~~l~~~t~~~sgadi~~i~~ea~~~~~~~~~~~~~~~~~~~~a~~~~ 483 (494)
T COG0464 433 DVDLEELAEITEGYSGADIAALVREAALEALREARRREVTLDDFLDALKKI 483 (494)
T ss_pred hhhHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHhccCCccHHHHHHHHHhc
Confidence 334445554 344567888999999998888 7889999999999873
No 289
>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=20.78 E-value=84 Score=19.14 Aligned_cols=20 Identities=20% Similarity=0.479 Sum_probs=12.0
Q ss_pred CcchHHHHHHHHhcCccccc
Q 034139 29 GITKPAIRRLARRGGVKRIS 48 (103)
Q Consensus 29 ~ip~a~IkRiar~~G~~riS 48 (103)
+++.++|-|++++.|-.-++
T Consensus 45 ~vS~sti~Rf~kkLG~~gf~ 64 (77)
T PF01418_consen 45 GVSPSTIVRFCKKLGFSGFK 64 (77)
T ss_dssp TS-HHHHHHHHHHCTTTCHH
T ss_pred CCCHHHHHHHHHHhCCCCHH
Confidence 45666777777777764443
No 290
>PF06183 DinI: DinI-like family; InterPro: IPR010391 This family of short proteins includes DNA-damage-inducible protein I (DinI) and related proteins. The SOS response, a set of cellular phenomena exhibited by eubacteria, is initiated by various causes that include DNA damage-induced replication arrest, and is positively regulated by the co- protease activity of RecA. Escherichia coli DinI, a LexA-regulated SOS gene product, shuts off the initiation of the SOS response when overexpressed in vivo. Biochemical and genetic studies indicated that DinI physically interacts with RecA to inhibit its co-protease activity []. The structure of DinI is known [].; PDB: 1GHH_A.
Probab=20.78 E-value=73 Score=19.40 Aligned_cols=24 Identities=21% Similarity=0.037 Sum_probs=15.3
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHH
Q 034139 48 SGLIYEETRGVLKIFLENVIRDAV 71 (103)
Q Consensus 48 S~da~~~l~~~~e~~~~~I~~dA~ 71 (103)
++.++++|+..++.++..+.-|+.
T Consensus 2 p~ga~~AL~~EL~kRl~~~yPd~~ 25 (65)
T PF06183_consen 2 PAGALEALESELTKRLHRQYPDAE 25 (65)
T ss_dssp -TTHHHHHHHHHHHHHHHH-SS-E
T ss_pred CccHHHHHHHHHHHHHHHHCCCce
Confidence 556777777777777777766654
No 291
>PF07261 DnaB_2: Replication initiation and membrane attachment; InterPro: IPR006343 This entry represents a domain found in several bacterial replication initiation and membrane attachment proteins, DnaB and DnaD. The DnaD protein is a component of the PriA primosome. The PriA primosome functions to recruit the replication fork helicase onto the DNA []. Members, both chromosomal or phage-associated, are found in the Bacillus/Clostridium group of Gram-positive bacteria []. The DnaB protein is essential for both replication initiation and membrane attachment of the origin region of the chromosome and Plasmid pUB110 in Bacillus subtilis. It is known that there are two different classes (DnaBI and DnaBII) in the DnaB mutants; DnaBI is essential for both chromosome and pUB110 replication, whereas DnaBII is necessary only for chromosome replication []. This domain tends to be found towards the C terminus of DnaB and DnaD proteins and is alpha helical in nature.; PDB: 2I5U_A 2ZC2_A.
Probab=20.75 E-value=1.9e+02 Score=16.88 Aligned_cols=52 Identities=13% Similarity=0.098 Sum_probs=35.7
Q ss_pred HHhcCccccchHHHHHHHHHHH--HHHHHHHHHHHHHHhhCCCceecHHHHHHHHH
Q 034139 39 ARRGGVKRISGLIYEETRGVLK--IFLENVIRDAVTYTEHARRKTVTAMDVVYALK 92 (103)
Q Consensus 39 ar~~G~~riS~da~~~l~~~~e--~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alk 92 (103)
.+......+|+.-.+.|.+.++ .|-.+++..|+.+|--.+..+ ..=|...|+
T Consensus 5 ~e~~~~~~~s~~e~~~l~~~~~~~~~~~~~v~~ai~~~~~~~~~~--~~Yi~~Il~ 58 (77)
T PF07261_consen 5 YEKNFGRPPSPSEIEKLEKWIDDYGFSPEVVNEAIEYALENNKRS--FNYIEKILN 58 (77)
T ss_dssp HHCCCTSS--HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCT--S--HHHHHHHHH
T ss_pred HHHHcCCCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHcCCCC--HHHHHHHHH
Confidence 3444446789999999999999 999999999999998655544 444444443
No 292
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=20.62 E-value=2.3e+02 Score=17.60 Aligned_cols=56 Identities=9% Similarity=0.068 Sum_probs=34.6
Q ss_pred cccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhcCCccccc
Q 034139 45 KRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTLYGF 101 (103)
Q Consensus 45 ~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~g~~lYgf 101 (103)
..|+.+-+..+...+ .+-.+-+.+........+-.+|+.++...++.......+|+
T Consensus 25 G~Is~~el~~~l~~~-~~~~~ev~~i~~~~d~~~~g~I~~~eF~~~~~~~~~~~~g~ 80 (96)
T smart00027 25 GTVTGAQAKPILLKS-GLPQTLLAKIWNLADIDNDGELDKDEFALAMHLIYRKLNGY 80 (96)
T ss_pred CeEeHHHHHHHHHHc-CCCHHHHHHHHHHhcCCCCCCcCHHHHHHHHHHHHHHHcCC
Confidence 455544433333222 23455566666666666667788888888888777776776
No 293
>cd02191 FtsZ FtsZ is a GTPase that is similar to the eukaryotic tubulins and is essential for cell division in prokaryotes. FtsZ is capable of polymerizing in a GTP-driven process into structures similar to those formed by tubulin. FtsZ forms a ring-shaped septum at the site of bacterial cell division, which is required for constriction of cell membrane and cell envelope to yield two daughter cells.
Probab=20.61 E-value=2.7e+02 Score=21.58 Aligned_cols=65 Identities=15% Similarity=0.245 Sum_probs=42.6
Q ss_pred CcchHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhcCCccccc
Q 034139 29 GITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTLYGF 101 (103)
Q Consensus 29 ~ip~a~IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~g~~lYgf 101 (103)
.||...+.++..+.+ + .+++..+.+.+...+..|+ ...++.+--.++..||...|+.-|..+-||
T Consensus 152 v~dN~~L~~~~~~~~---~-~~af~~~N~~ia~~i~~it----~~i~~~g~invD~~dv~~~l~~~G~a~ig~ 216 (303)
T cd02191 152 VIPNEKLRQIGEKAS---L-EGAFDHADEVLVRAVGGLF----GAIEIEGEINVDFADVKNVMDGGGVAMVGY 216 (303)
T ss_pred EEehHHHHHHhhcCC---h-HHHHHHHHHHHHHHHHHHH----HhhccCCcccCCHHHHHHHhccCCeEEEEE
Confidence 456666666554422 3 2466666666666555555 444566788899999999998777766555
No 294
>PF07498 Rho_N: Rho termination factor, N-terminal domain; InterPro: IPR011112 The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It is thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers []. This domain is found to the N terminus of the RNA binding domain (IPR011113 from INTERPRO).; GO: 0006353 transcription termination, DNA-dependent; PDB: 1A8V_B 1PVO_A 1PV4_D 3ICE_A 1XPU_C 1XPO_D 1XPR_F 2A8V_B 2HT1_B 1A63_A ....
Probab=20.58 E-value=1.5e+02 Score=16.19 Aligned_cols=30 Identities=20% Similarity=0.231 Sum_probs=19.7
Q ss_pred CcchHHHHHHHHhcCccccchHHHHHHHHH
Q 034139 29 GITKPAIRRLARRGGVKRISGLIYEETRGV 58 (103)
Q Consensus 29 ~ip~a~IkRiar~~G~~riS~da~~~l~~~ 58 (103)
..|..-++.+|+..|+..++.--..+|...
T Consensus 4 ~~~~~eL~~iAk~lgI~~~~~~~K~eLI~~ 33 (43)
T PF07498_consen 4 SMTLSELREIAKELGIEGYSKMRKQELIFA 33 (43)
T ss_dssp CS-HHHHHHHHHCTT-TTGCCS-HHHHHHH
T ss_pred cCCHHHHHHHHHHcCCCCCCcCCHHHHHHH
Confidence 456777888999999887776666665543
No 295
>KOG0731 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]
Probab=20.46 E-value=1.2e+02 Score=27.10 Aligned_cols=33 Identities=21% Similarity=0.321 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHHHhhCCCceecHHHHHHHHHhc
Q 034139 62 FLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 94 (103)
Q Consensus 62 ~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~ 94 (103)
=+..|+.+|...|-..++..|+..|+..|++|.
T Consensus 521 dl~n~~neaa~~a~r~~~~~i~~~~~~~a~~Rv 553 (774)
T KOG0731|consen 521 DLANLCNEAALLAARKGLREIGTKDLEYAIERV 553 (774)
T ss_pred HHHhhhhHHHHHHHHhccCccchhhHHHHHHHH
Confidence 466777888888888899999999999999965
No 296
>PRK11559 garR tartronate semialdehyde reductase; Provisional
Probab=20.32 E-value=3.7e+02 Score=19.98 Aligned_cols=56 Identities=14% Similarity=0.095 Sum_probs=37.2
Q ss_pred HHHHHHHhcCc--ccc----chHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHH
Q 034139 34 AIRRLARRGGV--KRI----SGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALK 92 (103)
Q Consensus 34 ~IkRiar~~G~--~ri----S~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alk 92 (103)
.++.+++..|. ..+ +..+...+...+......++.++..+|++.| ++.++|..+++
T Consensus 147 ~~~~~l~~~~~~~~~~g~~g~a~~~Kl~~n~~~~~~~~~~~Ea~~l~~~~G---i~~~~~~~~l~ 208 (296)
T PRK11559 147 KYYDLMKAMAGSVVHTGDIGAGNVTKLANQVIVALNIAAMSEALVLATKAG---VNPDLVYQAIR 208 (296)
T ss_pred HHHHHHHHhcCCeEEeCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcC---CCHHHHHHHHh
Confidence 35566666652 222 3344444555555666667899999998876 88999988885
No 297
>TIGR02302 aProt_lowcomp conserved hypothetical protein TIGR02302. Members of this family are long (~850 residue) bacterial proteins from the alpha Proteobacteria. Each has 2-3 predicted transmembrane helices near the N-terminus and a long C-terminal region that includes stretches of Gln/Gly-rich low complexity sequence, predicted by TMHMM to be outside the membrane. In Bradyrhizobium japonicum, two tandem reading frames are together homologous the single members found in other species; the cutoffs scores are set low enough that the longer scores above the trusted cutoff and the shorter above the noise cutoff for this model.
Probab=20.20 E-value=2.2e+02 Score=25.86 Aligned_cols=44 Identities=7% Similarity=0.250 Sum_probs=33.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHh------hCCCceecHHHHHHHHHhc
Q 034139 51 IYEETRGVLKIFLENVIRDAVTYTE------HARRKTVTAMDVVYALKRQ 94 (103)
Q Consensus 51 a~~~l~~~~e~~~~~I~~dA~~~a~------ha~RkTI~~~DV~~Alkr~ 94 (103)
-.++|++++.+|+.++++.+..--. ..+-.+++.+|+..-|.+.
T Consensus 528 Lm~eLR~Am~~ym~~LAeq~~~~~~~~~~~~~~~~~~l~~~dLq~Mmd~i 577 (851)
T TIGR02302 528 LTDKLRAAMQTYMRQLAQQLRNNPQQLARPLDPNTKVLRQQDLQNMMDQI 577 (851)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhCcccccccCCccccccCHHHHHHHHHHH
Confidence 4567888999999999988885421 2345789999998888764
No 298
>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=20.19 E-value=2e+02 Score=16.88 Aligned_cols=61 Identities=20% Similarity=0.182 Sum_probs=29.8
Q ss_pred chHHHHHHHHhcCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCceecHHHHHHHHHhcC
Q 034139 31 TKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQG 95 (103)
Q Consensus 31 p~a~IkRiar~~G~~riS~da~~~l~~~~e~~~~~I~~dA~~~a~ha~RkTI~~~DV~~Alkr~g 95 (103)
+....+.+|+..| ++..-++.+...-...-....+-...+.+. ....-|..++..||+..+
T Consensus 11 ~~~~Wk~La~~Lg---~~~~~i~~i~~~~~~~~~~~~~~L~~W~~~-~~~~at~~~L~~aL~~~~ 71 (83)
T PF00531_consen 11 LGSDWKRLARKLG---LSESEIENIEEENPDLREQTYEMLQRWRQR-EGPNATVDQLIQALRDIG 71 (83)
T ss_dssp HSTCHHHHHHHTT---S-HHHHHHHHHHSTSHHHHHHHHHHHHHHH-HGSTSSHHHHHHHHHHTT
T ss_pred chhhHHHHHHHhC---cCHHHHHHHHHhCCChHHHHHHHHHHHHHh-cCCCCcHHHHHHHHHHCC
Confidence 3445677777776 444555555443221111111112222222 334567788888888765
Done!