Query psy13691
Match_columns 103
No_of_seqs 122 out of 567
Neff 6.3
Searched_HMMs 46136
Date Fri Aug 16 18:01:48 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13691.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13691hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0869|consensus 100.0 1.4E-35 3.1E-40 209.6 10.1 93 3-99 26-118 (168)
2 KOG0871|consensus 100.0 1.6E-30 3.5E-35 182.4 10.5 94 4-101 7-100 (156)
3 KOG0870|consensus 100.0 1.6E-28 3.5E-33 174.9 9.6 97 1-100 2-98 (172)
4 COG5150 Class 2 transcription 99.9 6.6E-26 1.4E-30 156.1 10.2 98 1-102 1-100 (148)
5 PF00808 CBFD_NFYB_HMF: Histon 99.8 8.3E-21 1.8E-25 116.7 7.9 64 9-77 2-65 (65)
6 COG2036 HHT1 Histones H3 and H 99.8 1.6E-18 3.6E-23 113.8 6.7 76 4-85 14-89 (91)
7 cd00076 H4 Histone H4, one of 99.4 2.9E-12 6.4E-17 83.2 8.2 71 9-85 13-83 (85)
8 PLN00035 histone H4; Provision 99.3 8E-12 1.7E-16 83.7 8.1 69 9-83 29-97 (103)
9 PTZ00015 histone H4; Provision 99.3 2.6E-11 5.7E-16 81.1 8.2 71 8-84 29-99 (102)
10 smart00428 H3 Histone H3. 99.2 4.8E-11 1E-15 80.3 6.9 76 4-79 24-100 (105)
11 smart00803 TAF TATA box bindin 99.2 2.3E-10 5E-15 70.8 7.7 64 9-78 2-65 (65)
12 smart00417 H4 Histone H4. 99.1 1.7E-10 3.7E-15 73.2 6.7 62 9-76 13-74 (74)
13 PF00125 Histone: Core histone 99.1 2.7E-10 5.8E-15 71.0 6.6 71 7-78 3-73 (75)
14 cd07981 TAF12 TATA Binding Pro 99.1 8.2E-10 1.8E-14 69.4 8.6 65 10-79 2-66 (72)
15 COG5208 HAP5 CCAAT-binding fac 99.1 1.3E-10 2.9E-15 87.0 4.9 77 6-88 106-183 (286)
16 PLN00160 histone H3; Provision 99.0 7.4E-10 1.6E-14 73.6 5.9 75 4-78 16-90 (97)
17 PLN00161 histone H3; Provision 99.0 1.7E-09 3.6E-14 75.6 6.7 75 4-78 50-124 (135)
18 PLN00121 histone H3; Provision 98.9 3.1E-09 6.6E-14 74.4 5.7 74 4-78 57-130 (136)
19 PTZ00018 histone H3; Provision 98.9 3.2E-09 7E-14 74.3 5.7 74 4-78 57-130 (136)
20 KOG1657|consensus 98.8 6.3E-09 1.4E-13 78.6 4.4 84 7-95 72-158 (236)
21 smart00576 BTP Bromodomain tra 98.7 1.9E-07 4.1E-12 59.1 8.5 66 12-83 9-74 (77)
22 cd00074 H2A Histone 2A; H2A is 98.6 1.3E-07 2.8E-12 64.5 7.0 72 7-83 18-90 (115)
23 KOG1659|consensus 98.3 3.4E-06 7.4E-11 62.9 7.6 79 8-91 12-90 (224)
24 KOG1745|consensus 98.2 6.4E-07 1.4E-11 62.7 2.1 77 4-81 58-134 (137)
25 cd07979 TAF9 TATA Binding Prot 98.2 8.8E-06 1.9E-10 55.5 7.6 67 14-86 6-72 (117)
26 PF15511 CENP-T: Centromere ki 98.2 3.2E-06 7E-11 68.2 6.4 68 5-72 347-414 (414)
27 cd08050 TAF6 TATA Binding Prot 98.1 1.4E-05 3E-10 63.0 8.3 67 11-83 1-67 (343)
28 smart00427 H2B Histone H2B. 98.1 2.2E-05 4.7E-10 51.5 7.7 63 13-80 5-67 (89)
29 PF09415 CENP-X: CENP-S associ 98.1 6.3E-06 1.4E-10 52.0 4.6 66 11-79 1-67 (72)
30 PF07524 Bromo_TP: Bromodomain 98.1 4.7E-05 1E-09 47.8 8.5 65 13-83 10-74 (77)
31 cd08048 TAF11 TATA Binding Pro 98.1 4.6E-05 1E-09 49.4 8.1 66 9-80 16-84 (85)
32 PF03847 TFIID_20kDa: Transcri 98.0 4.1E-05 8.9E-10 47.8 7.3 63 12-79 2-64 (68)
33 COG5247 BUR6 Class 2 transcrip 98.0 2.7E-05 5.9E-10 52.2 6.7 80 8-92 22-101 (113)
34 COG5262 HTA1 Histone H2A [Chro 98.0 1.8E-05 3.9E-10 54.3 5.8 67 7-78 24-90 (132)
35 PF15630 CENP-S: Kinetochore c 98.0 4.5E-05 9.8E-10 48.6 7.1 62 14-79 10-72 (76)
36 PLN00158 histone H2B; Provisio 97.9 7.6E-05 1.6E-09 51.0 7.7 65 11-80 29-93 (116)
37 PTZ00463 histone H2B; Provisio 97.9 9.2E-05 2E-09 50.6 7.7 62 14-80 33-94 (117)
38 KOG3467|consensus 97.9 9.4E-05 2E-09 48.5 7.2 68 10-83 30-97 (103)
39 smart00414 H2A Histone 2A. 97.7 0.00013 2.9E-09 49.1 6.5 68 7-79 7-74 (106)
40 PF02969 TAF: TATA box binding 97.7 0.00041 8.8E-09 43.1 8.0 64 9-78 3-66 (66)
41 PF04719 TAFII28: hTAFII28-lik 97.7 0.00034 7.4E-09 45.9 7.5 67 9-80 23-90 (90)
42 PLN00154 histone H2A; Provisio 97.6 0.00025 5.3E-09 49.8 6.4 69 7-79 36-104 (136)
43 PTZ00017 histone H2A; Provisio 97.5 0.00033 7.2E-09 49.0 5.7 67 7-78 25-91 (134)
44 KOG1756|consensus 97.5 0.00047 1E-08 47.9 6.0 68 6-78 24-91 (131)
45 PLN00153 histone H2A; Provisio 97.3 0.00081 1.8E-08 46.8 5.6 67 7-78 22-88 (129)
46 PLN00157 histone H2A; Provisio 97.3 0.00081 1.7E-08 47.0 5.5 67 7-78 24-90 (132)
47 PLN00156 histone H2AX; Provisi 97.2 0.0011 2.4E-08 46.6 6.1 67 7-78 27-93 (139)
48 KOG1142|consensus 97.2 0.001 2.3E-08 50.9 6.0 69 5-78 150-218 (258)
49 KOG1658|consensus 97.2 0.0003 6.6E-09 50.3 2.7 67 8-80 58-125 (162)
50 KOG1744|consensus 97.0 0.0036 7.8E-08 43.4 6.8 62 14-80 42-103 (127)
51 PF15510 CENP-W: Centromere ki 96.9 0.0024 5.1E-08 42.2 5.0 66 9-79 16-95 (102)
52 PF02269 TFIID-18kDa: Transcri 96.8 0.0019 4E-08 42.4 3.8 48 31-78 18-65 (93)
53 PTZ00252 histone H2A; Provisio 96.6 0.0088 1.9E-07 41.9 6.3 67 7-78 23-91 (134)
54 cd07978 TAF13 The TATA Binding 96.4 0.083 1.8E-06 34.6 9.4 78 13-96 6-87 (92)
55 KOG3219|consensus 96.3 0.0065 1.4E-07 44.9 4.3 71 8-84 111-182 (195)
56 PF02291 TFIID-31kDa: Transcri 95.3 0.15 3.2E-06 35.4 7.5 63 32-94 29-92 (129)
57 KOG4336|consensus 95.3 0.17 3.7E-06 39.9 8.5 65 32-98 22-86 (323)
58 KOG3423|consensus 94.0 0.52 1.1E-05 34.3 7.9 70 8-83 85-168 (176)
59 TIGR03015 pepcterm_ATPase puta 93.7 0.36 7.8E-06 35.5 6.9 52 31-82 214-268 (269)
60 PRK00411 cdc6 cell division co 93.1 0.99 2.1E-05 35.2 8.9 73 12-85 209-287 (394)
61 KOG2389|consensus 92.2 0.45 9.7E-06 38.1 5.8 69 9-83 29-97 (353)
62 KOG2549|consensus 91.8 1.1 2.5E-05 37.9 8.0 65 11-81 13-77 (576)
63 TIGR02928 orc1/cdc6 family rep 91.4 2.2 4.9E-05 32.7 8.9 78 12-90 201-284 (365)
64 KOG1757|consensus 88.0 1.1 2.4E-05 30.8 4.2 64 7-78 28-95 (131)
65 PF13654 AAA_32: AAA domain; P 87.2 4.3 9.3E-05 33.9 8.1 49 32-80 447-506 (509)
66 TIGR02902 spore_lonB ATP-depen 85.5 3.4 7.3E-05 34.5 6.6 68 12-82 265-334 (531)
67 PF13335 Mg_chelatase_2: Magne 83.8 5.8 0.00013 25.8 5.9 48 31-78 41-94 (96)
68 COG5095 TAF6 Transcription ini 83.3 4.9 0.00011 32.5 6.3 52 32-83 22-73 (450)
69 TIGR00764 lon_rel lon-related 83.1 7.5 0.00016 33.1 7.8 50 32-81 330-392 (608)
70 COG1067 LonB Predicted ATP-dep 82.8 1.7 3.8E-05 37.4 3.9 49 32-80 338-399 (647)
71 PF08369 PCP_red: Proto-chloro 81.1 3 6.5E-05 23.7 3.3 42 34-76 2-44 (45)
72 cd08045 TAF4 TATA Binding Prot 80.2 21 0.00045 26.2 8.4 77 6-84 41-123 (212)
73 PF02861 Clp_N: Clp amino term 79.6 2 4.3E-05 23.9 2.2 25 56-80 1-25 (53)
74 KOG3334|consensus 78.8 6 0.00013 28.2 4.9 55 33-87 31-85 (148)
75 PRK09862 putative ATP-dependen 77.9 14 0.0003 31.0 7.6 61 31-91 437-503 (506)
76 KOG2680|consensus 73.4 22 0.00047 29.0 7.3 49 30-78 375-427 (454)
77 COG1474 CDC6 Cdc6-related prot 72.4 29 0.00062 27.8 7.8 58 32-89 211-274 (366)
78 PF09114 MotA_activ: Transcrip 70.0 5.3 0.00012 26.4 2.6 38 13-50 51-88 (96)
79 cd04752 Commd4 COMM_Domain con 69.0 22 0.00048 25.3 6.0 49 44-99 43-92 (174)
80 TIGR00368 Mg chelatase-related 68.5 17 0.00036 30.4 5.9 47 32-78 445-497 (499)
81 COG5162 Transcription initiati 67.7 46 0.00099 24.4 8.0 69 9-83 88-189 (197)
82 PF12010 DUF3502: Domain of un 67.0 9 0.00019 26.2 3.5 63 35-101 72-134 (134)
83 PRK00080 ruvB Holliday junctio 66.9 34 0.00074 26.2 7.1 71 10-83 180-253 (328)
84 COG5251 TAF40 Transcription in 66.9 7 0.00015 28.8 3.0 62 9-78 115-179 (199)
85 PF03540 TFIID_30kDa: Transcri 66.0 25 0.00054 20.7 6.5 48 9-62 2-49 (51)
86 TIGR02442 Cob-chelat-sub cobal 64.6 35 0.00076 29.1 7.2 48 31-78 248-302 (633)
87 KOG3901|consensus 62.8 31 0.00067 23.3 5.3 45 31-78 26-70 (109)
88 TIGR02030 BchI-ChlI magnesium 62.7 50 0.0011 26.1 7.3 48 31-78 253-307 (337)
89 PRK13765 ATP-dependent proteas 62.7 16 0.00035 31.4 4.9 48 32-79 339-399 (637)
90 cd00166 SAM Sterile alpha moti 61.7 11 0.00024 21.2 2.7 23 69-91 3-25 (63)
91 PRK07452 DNA polymerase III su 61.4 37 0.0008 25.8 6.3 55 31-85 148-204 (326)
92 TIGR00635 ruvB Holliday juncti 61.0 39 0.00084 25.3 6.3 53 31-83 177-232 (305)
93 COG5248 TAF19 Transcription in 60.8 35 0.00075 23.4 5.3 46 31-78 26-71 (126)
94 PF07647 SAM_2: SAM domain (St 60.4 13 0.00028 21.6 2.9 24 68-91 4-27 (66)
95 PRK12402 replication factor C 60.2 45 0.00098 25.0 6.6 70 10-84 184-253 (337)
96 PF07499 RuvA_C: RuvA, C-termi 59.4 7 0.00015 22.0 1.5 14 71-84 4-17 (47)
97 PF05236 TAF4: Transcription i 59.2 17 0.00037 27.5 4.1 76 5-82 39-120 (264)
98 PF00356 LacI: Bacterial regul 58.6 27 0.00058 19.7 3.9 31 9-47 10-40 (46)
99 PF00536 SAM_1: SAM domain (St 57.7 15 0.00032 21.2 2.8 22 69-90 4-25 (64)
100 COG1224 TIP49 DNA helicase TIP 57.4 28 0.00062 28.7 5.2 65 31-98 379-447 (450)
101 PF09123 DUF1931: Domain of un 56.8 29 0.00062 24.5 4.5 53 16-74 2-54 (138)
102 CHL00081 chlI Mg-protoporyphyr 56.2 46 0.001 26.6 6.2 48 31-78 266-320 (350)
103 PRK13406 bchD magnesium chelat 56.2 31 0.00067 29.4 5.5 48 31-78 194-248 (584)
104 smart00350 MCM minichromosome 55.3 86 0.0019 25.9 7.8 68 9-80 417-504 (509)
105 TIGR01052 top6b DNA topoisomer 54.9 25 0.00053 29.5 4.6 51 32-96 434-484 (488)
106 PRK03992 proteasome-activating 54.8 20 0.00044 28.5 4.0 35 48-82 340-374 (389)
107 TIGR01242 26Sp45 26S proteasom 54.6 21 0.00045 27.9 3.9 32 48-79 331-362 (364)
108 PTZ00361 26 proteosome regulat 53.7 20 0.00044 29.4 3.9 32 49-80 393-424 (438)
109 smart00454 SAM Sterile alpha m 53.0 18 0.00039 20.4 2.7 25 68-92 4-28 (68)
110 PF00531 Death: Death domain; 52.4 44 0.00095 19.9 4.5 29 65-93 55-83 (83)
111 PF13405 EF-hand_6: EF-hand do 51.8 21 0.00046 17.8 2.5 26 56-81 5-31 (31)
112 PRK13407 bchI magnesium chelat 51.0 68 0.0015 25.3 6.4 47 31-77 250-303 (334)
113 TIGR01128 holA DNA polymerase 50.6 1E+02 0.0022 22.8 7.5 66 10-78 111-176 (302)
114 PF04552 Sigma54_DBD: Sigma-54 49.6 18 0.0004 25.7 2.7 80 4-100 55-150 (160)
115 TIGR02031 BchD-ChlD magnesium 48.4 87 0.0019 26.6 7.0 48 31-78 202-256 (589)
116 PF08681 DUF1778: Protein of u 48.4 28 0.00061 21.7 3.1 67 31-97 4-79 (80)
117 PTZ00454 26S protease regulato 47.8 30 0.00065 27.9 4.0 32 49-80 355-386 (398)
118 PLN00138 large subunit ribosom 47.2 58 0.0013 22.0 4.7 28 56-83 6-33 (113)
119 smart00027 EH Eps15 homology d 46.3 55 0.0012 20.4 4.4 28 56-83 15-42 (96)
120 COG1724 Predicted RNA binding 45.1 16 0.00034 22.7 1.5 17 67-83 6-22 (66)
121 PTZ00373 60S Acidic ribosomal 44.9 65 0.0014 21.8 4.7 28 56-83 8-35 (112)
122 PRK09526 lacI lac repressor; R 44.5 23 0.0005 26.5 2.7 37 9-54 16-52 (342)
123 PRK02910 light-independent pro 44.2 51 0.0011 27.4 4.9 51 30-81 467-518 (519)
124 COG1500 Predicted exosome subu 44.0 1E+02 0.0022 23.6 6.0 63 15-83 72-135 (234)
125 PF08823 PG_binding_2: Putativ 43.4 31 0.00067 21.5 2.7 29 71-99 19-53 (74)
126 PF09339 HTH_IclR: IclR helix- 43.1 17 0.00037 20.4 1.4 17 7-23 27-43 (52)
127 KOG1528|consensus 43.0 86 0.0019 25.2 5.7 68 12-81 52-124 (351)
128 PRK06585 holA DNA polymerase I 42.5 87 0.0019 24.0 5.7 48 31-78 160-208 (343)
129 PRK05574 holA DNA polymerase I 42.2 1.2E+02 0.0027 22.8 6.4 67 10-79 146-212 (340)
130 cd08779 Death_PIDD Death Domai 42.0 88 0.0019 19.7 5.9 33 60-92 53-85 (86)
131 smart00354 HTH_LACI helix_turn 41.3 56 0.0012 19.4 3.6 33 8-48 10-42 (70)
132 TIGR01278 DPOR_BchB light-inde 40.2 62 0.0013 26.8 4.8 51 30-81 460-511 (511)
133 KOG1658|consensus 39.6 34 0.00074 24.7 2.8 67 7-78 9-87 (162)
134 PF01922 SRP19: SRP19 protein; 39.3 19 0.00041 23.4 1.3 19 68-86 29-47 (95)
135 PRK14987 gluconate operon tran 38.5 29 0.00062 26.0 2.4 37 9-54 16-52 (331)
136 PF12668 DUF3791: Protein of u 38.0 80 0.0017 18.5 3.9 30 64-93 13-42 (62)
137 PRK07914 hypothetical protein; 37.9 1.1E+02 0.0023 23.5 5.6 64 11-78 129-192 (320)
138 TIGR02454 CbiQ_TIGR cobalt ABC 37.3 57 0.0012 22.9 3.7 36 66-101 112-158 (198)
139 COG1508 RpoN DNA-directed RNA 37.1 95 0.0021 25.9 5.3 79 6-101 338-433 (444)
140 PF00403 HMA: Heavy-metal-asso 36.2 27 0.00058 19.9 1.6 16 68-83 47-62 (62)
141 CHL00076 chlB photochlorophyll 36.0 88 0.0019 26.1 5.1 51 30-81 461-512 (513)
142 cd05833 Ribosomal_P2 Ribosomal 35.6 1.1E+02 0.0025 20.4 4.7 28 56-83 6-33 (109)
143 COG4018 Uncharacterized protei 35.6 64 0.0014 26.5 4.0 39 6-46 327-365 (505)
144 PF02361 CbiQ: Cobalt transpor 35.4 55 0.0012 23.0 3.4 64 31-100 94-169 (224)
145 COG1389 DNA topoisomerase VI, 35.2 33 0.00072 29.0 2.4 38 32-69 442-479 (538)
146 COG5340 Predicted transcriptio 34.9 76 0.0016 24.6 4.1 57 4-60 149-207 (269)
147 PF07928 Vps54: Vps54-like pro 34.8 13 0.00028 25.7 0.0 36 61-96 61-97 (135)
148 PRK14868 DNA topoisomerase VI 34.8 74 0.0016 28.4 4.6 36 32-67 633-668 (795)
149 PRK10423 transcriptional repre 34.5 48 0.001 24.5 3.0 36 9-53 9-44 (327)
150 KOG0785|consensus 34.4 1.4E+02 0.0029 24.2 5.6 66 33-99 164-229 (365)
151 PTZ00112 origin recognition co 34.1 1.5E+02 0.0032 27.7 6.3 51 32-86 955-1012(1164)
152 PF07580 Peptidase_M26_C: M26 33.4 91 0.002 27.7 4.9 62 29-90 590-653 (737)
153 PTZ00183 centrin; Provisional 33.3 1.4E+02 0.003 19.5 5.4 19 61-79 63-81 (158)
154 cd00823 TopoIIB_Trans TopoIIB_ 32.8 1.1E+02 0.0024 21.8 4.5 27 31-57 118-144 (151)
155 PRK14971 DNA polymerase III su 32.4 1.8E+02 0.004 24.9 6.5 71 10-85 180-251 (614)
156 PRK14867 DNA topoisomerase VI 31.7 97 0.0021 27.1 4.7 36 32-67 592-627 (659)
157 PF10113 Fibrillarin_2: Fibril 31.6 70 0.0015 26.9 3.7 40 4-46 325-364 (505)
158 PF14434 Imm6: Immunity protei 31.6 1.7E+02 0.0037 19.9 5.9 36 51-87 25-62 (122)
159 cd01392 HTH_LacI Helix-turn-he 30.6 88 0.0019 16.9 3.1 34 7-48 6-39 (52)
160 PF02718 Herpes_UL31: Herpesvi 30.4 62 0.0013 25.0 3.1 74 5-97 179-252 (258)
161 PF03477 ATP-cone: ATP cone do 30.1 61 0.0013 19.9 2.6 37 52-88 40-80 (90)
162 PRK10727 DNA-binding transcrip 30.0 50 0.0011 24.8 2.5 37 9-54 12-48 (343)
163 PRK06402 rpl12p 50S ribosomal 30.0 1.5E+02 0.0032 19.9 4.5 27 56-83 6-32 (106)
164 COG1239 ChlI Mg-chelatase subu 30.0 1.1E+02 0.0025 25.3 4.7 48 31-78 266-320 (423)
165 PRK00754 signal recognition pa 30.0 41 0.00089 22.0 1.8 21 68-88 35-55 (95)
166 PF03484 B5: tRNA synthetase B 29.8 33 0.00071 20.6 1.2 17 67-83 18-34 (70)
167 TIGR02639 ClpA ATP-dependent C 29.8 2E+02 0.0044 24.9 6.4 36 31-78 76-111 (731)
168 TIGR02639 ClpA ATP-dependent C 29.7 85 0.0018 27.2 4.1 23 55-77 11-33 (731)
169 smart00445 LINK Link (Hyaluron 29.6 74 0.0016 20.9 3.0 29 54-83 18-46 (94)
170 PF03979 Sigma70_r1_1: Sigma-7 29.4 91 0.002 19.3 3.3 34 61-94 15-49 (82)
171 CHL00095 clpC Clp protease ATP 29.2 78 0.0017 27.9 3.8 35 32-78 4-38 (821)
172 TIGR02903 spore_lon_C ATP-depe 29.1 1.4E+02 0.003 25.6 5.2 71 13-86 356-436 (615)
173 cd01102 Link_Domain The link d 29.1 73 0.0016 20.8 2.9 29 54-83 17-45 (92)
174 TIGR02849 spore_III_AD stage I 29.0 37 0.00081 22.6 1.5 38 31-70 35-72 (101)
175 PRK00440 rfc replication facto 29.0 2.4E+02 0.0052 20.8 6.6 65 10-80 161-226 (319)
176 COG1222 RPT1 ATP-dependent 26S 28.8 70 0.0015 26.3 3.2 50 31-80 338-392 (406)
177 PRK14961 DNA polymerase III su 28.8 2.5E+02 0.0055 21.9 6.4 49 31-80 196-244 (363)
178 KOG0784|consensus 28.6 43 0.00093 27.2 2.0 49 49-98 186-234 (375)
179 PRK14964 DNA polymerase III su 28.4 2.3E+02 0.0051 23.7 6.3 47 31-78 193-239 (491)
180 cd04411 Ribosomal_P1_P2_L12p R 28.1 1.6E+02 0.0035 19.5 4.4 27 56-83 6-32 (105)
181 TIGR01481 ccpA catabolite cont 27.9 77 0.0017 23.5 3.2 32 9-48 12-43 (329)
182 PF03130 HEAT_PBS: PBS lyase H 27.8 85 0.0018 15.3 3.0 23 73-95 5-27 (27)
183 PF11625 DUF3253: Protein of u 27.6 1.6E+02 0.0034 18.9 4.1 35 61-95 18-52 (83)
184 PF12627 PolyA_pol_RNAbd: Prob 27.4 12 0.00027 21.6 -1.0 58 31-92 2-63 (64)
185 PRK14970 DNA polymerase III su 27.1 2.8E+02 0.0061 21.4 6.4 50 31-81 185-234 (367)
186 TIGR01241 FtsH_fam ATP-depende 27.0 1.1E+02 0.0023 25.1 4.1 33 49-81 264-296 (495)
187 PRK05907 hypothetical protein; 26.9 1.9E+02 0.0041 22.5 5.3 53 31-83 152-207 (311)
188 cd00051 EFh EF-hand, calcium b 26.9 1E+02 0.0022 15.9 4.3 35 60-94 9-43 (63)
189 TIGR02397 dnaX_nterm DNA polym 26.8 2.8E+02 0.006 21.0 6.2 62 12-78 178-240 (355)
190 PF10728 DUF2520: Domain of un 26.8 2.1E+02 0.0045 19.4 5.3 47 13-63 14-63 (132)
191 PRK05629 hypothetical protein; 26.7 2.7E+02 0.0059 21.2 6.1 47 31-78 144-190 (318)
192 COG3267 ExeA Type II secretory 26.6 2.7E+02 0.0057 21.8 5.9 44 31-74 221-267 (269)
193 cd03521 Link_domain_KIAA0527_l 26.4 92 0.002 20.6 2.9 30 54-83 17-46 (95)
194 COG4987 CydC ABC-type transpor 26.4 2.2E+02 0.0048 24.6 5.9 78 11-94 376-465 (573)
195 KOG0482|consensus 26.3 91 0.002 27.1 3.6 42 58-101 667-708 (721)
196 PF13499 EF-hand_7: EF-hand do 25.6 1.3E+02 0.0029 16.8 4.0 37 55-91 4-40 (66)
197 PRK14975 bifunctional 3'-5' ex 25.3 3.6E+02 0.0078 22.6 7.0 70 7-83 161-240 (553)
198 PF01934 DUF86: Protein of unk 25.2 1.9E+02 0.0041 18.4 7.4 68 32-100 21-89 (119)
199 PF09239 Topo-VIb_trans: Topoi 25.2 72 0.0016 23.0 2.5 26 32-57 128-153 (160)
200 PF04218 CENP-B_N: CENP-B N-te 25.1 21 0.00046 20.5 -0.2 16 7-22 31-46 (53)
201 PF01418 HTH_6: Helix-turn-hel 25.0 92 0.002 18.9 2.7 32 56-90 37-68 (77)
202 cd03518 Link_domain_HAPLN_modu 25.0 1.1E+02 0.0024 20.1 3.2 29 54-83 17-45 (95)
203 cd04750 Commd2 COMM_Domain con 24.8 2.6E+02 0.0055 19.8 5.5 33 65-97 49-82 (166)
204 PRK08487 DNA polymerase III su 24.6 3E+02 0.0065 21.1 6.1 46 31-78 153-198 (328)
205 PRK03745 signal recognition pa 24.2 60 0.0013 21.6 1.8 17 68-84 32-48 (100)
206 COG1400 SEC65 Signal recogniti 24.2 53 0.0011 21.6 1.5 17 68-84 32-48 (93)
207 KOG0093|consensus 24.0 45 0.00097 24.4 1.2 52 35-86 106-162 (193)
208 smart00874 B5 tRNA synthetase 23.9 56 0.0012 19.2 1.5 17 67-83 18-34 (71)
209 COG1466 HolA DNA polymerase II 23.6 3E+02 0.0064 21.3 5.9 50 31-80 158-207 (334)
210 cd00454 Trunc_globin Truncated 23.5 1.4E+02 0.0029 19.0 3.4 30 72-101 84-114 (116)
211 PF13713 BRX_N: Transcription 23.3 1.5E+02 0.0032 16.4 3.1 21 42-62 7-27 (39)
212 PRK10339 DNA-binding transcrip 23.3 96 0.0021 23.1 3.0 34 9-48 12-45 (327)
213 PRK04184 DNA topoisomerase VI 23.2 68 0.0015 27.3 2.3 37 32-68 439-475 (535)
214 cd03515 Link_domain_TSG_6_like 23.1 1.4E+02 0.0031 19.5 3.4 29 54-83 17-45 (93)
215 PF05225 HTH_psq: helix-turn-h 23.0 66 0.0014 17.8 1.6 18 7-24 25-42 (45)
216 PRK07764 DNA polymerase III su 22.2 3.3E+02 0.0071 24.4 6.4 63 10-76 179-242 (824)
217 PRK05932 RNA polymerase factor 22.0 96 0.0021 25.6 2.9 78 6-100 351-444 (455)
218 PHA03328 nuclear egress lamina 21.8 1.4E+02 0.0031 23.8 3.7 67 6-84 230-296 (316)
219 PF06782 UPF0236: Uncharacteri 21.8 2.3E+02 0.005 23.4 5.1 54 31-87 116-170 (470)
220 COG4396 Mu-like prophage host- 21.4 85 0.0018 22.5 2.2 25 70-94 111-135 (170)
221 PF09077 Phage-MuB_C: Mu B tra 21.2 41 0.00089 21.3 0.5 26 54-80 53-78 (78)
222 cd00052 EH Eps15 homology doma 21.2 1.6E+02 0.0035 16.2 4.4 21 62-82 10-30 (67)
223 PF15605 Toxin_52: Putative to 21.1 2.7E+02 0.0058 18.7 5.1 37 11-52 58-94 (103)
224 cd03516 Link_domain_CD44_like 21.0 1.3E+02 0.0028 21.3 3.1 29 54-83 22-50 (144)
225 PRK11303 DNA-binding transcrip 21.0 1.6E+02 0.0034 21.8 3.7 35 9-48 11-45 (328)
226 PRK10703 DNA-binding transcrip 21.0 1.3E+02 0.0028 22.4 3.3 32 9-48 12-43 (341)
227 COG4519 Uncharacterized protei 21.0 41 0.00088 21.9 0.5 15 69-83 38-52 (95)
228 PRK09492 treR trehalose repres 21.0 1.2E+02 0.0026 22.3 3.0 32 9-48 15-46 (315)
229 PRK09111 DNA polymerase III su 20.4 4.1E+02 0.0088 22.8 6.4 47 31-78 209-255 (598)
230 KOG1775|consensus 20.4 73 0.0016 20.4 1.5 19 79-97 34-52 (84)
231 PRK14958 DNA polymerase III su 20.0 4.1E+02 0.009 22.2 6.3 68 10-82 178-246 (509)
No 1
>KOG0869|consensus
Probab=100.00 E-value=1.4e-35 Score=209.65 Aligned_cols=93 Identities=30% Similarity=0.393 Sum_probs=90.8
Q ss_pred CCccCCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCc
Q psy13691 3 ESLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGF 82 (103)
Q Consensus 3 ~~~~d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf 82 (103)
.+++|..||+|+|.||||..||.+ .+|||||++.+|+|+++||+|+|++|++.|..++||||+++||+|||..|||
T Consensus 26 ~reqDr~LPIANV~RIMK~~lP~n----aKIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIngdDllwAm~tLGF 101 (168)
T KOG0869|consen 26 LREQDRFLPIANVSRIMKKALPAN----AKISKDAKETVQECVSEFISFVTGEASEKCQREKRKTINGDDLLWAMSTLGF 101 (168)
T ss_pred cchhhhhccHHHHHHHHHhcCCcc----cccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCcccHHHHHHHHHHcCc
Confidence 478899999999999999999998 9999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHHHHHHHhc
Q psy13691 83 EVIIEILGKSYNAAVSI 99 (103)
Q Consensus 83 ~~~~~~l~~~l~~~k~~ 99 (103)
++|+++|+.||..||+.
T Consensus 102 e~Y~eplkiyL~kYRe~ 118 (168)
T KOG0869|consen 102 ENYAEPLKIYLQKYREL 118 (168)
T ss_pred HhHHHHHHHHHHHHHHH
Confidence 99999999999999985
No 2
>KOG0871|consensus
Probab=99.97 E-value=1.6e-30 Score=182.41 Aligned_cols=94 Identities=31% Similarity=0.450 Sum_probs=90.7
Q ss_pred CccCCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCch
Q psy13691 4 SLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFE 83 (103)
Q Consensus 4 ~~~d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~ 83 (103)
..+++.||+|+|++|||+.||.+ ++|.+||+++|..||.+||+.|+++||++|.++.||||++|||++||+.|||.
T Consensus 7 ~dde~sLPkAtv~KmIke~lP~d----~rvakeareliincCvEFI~liSsEAneic~~e~KKTIa~EHV~KALe~LgF~ 82 (156)
T KOG0871|consen 7 EDDELSLPKATVNKMIKEMLPKD----VRVAKEARELIINCCVEFINLISSEANEICNKEAKKTIAPEHVIKALENLGFG 82 (156)
T ss_pred ccccccCcHHHHHHHHHHhCCcc----cccchHHHHHHHHHHHHHHHHHHHHHHHHHhHHhcccCCHHHHHHHHHHcchH
Confidence 56799999999999999999988 99999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhccc
Q psy13691 84 VIIEILGKSYNAAVSIKV 101 (103)
Q Consensus 84 ~~~~~l~~~l~~~k~~~~ 101 (103)
+|++.+.+.+++||...+
T Consensus 83 eYiee~~~vl~~~K~~~~ 100 (156)
T KOG0871|consen 83 EYIEEAEEVLENCKEEAK 100 (156)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 999999999999997654
No 3
>KOG0870|consensus
Probab=99.95 E-value=1.6e-28 Score=174.93 Aligned_cols=97 Identities=38% Similarity=0.631 Sum_probs=93.2
Q ss_pred CCCCccCCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhc
Q psy13691 1 MAESLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQI 80 (103)
Q Consensus 1 m~~~~~d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~l 80 (103)
|+++++++.||+|+|.|++|+.||++ ++.|||||+.+|+++|++|++||++.|+++|..++||||+++||+.||+.+
T Consensus 2 e~eri~dl~lP~AiI~rlvke~l~E~---~vsisKeA~~Ai~raAtVFv~~Lts~s~e~A~~q~rKt~sadDVl~aL~Ei 78 (172)
T KOG0870|consen 2 EDERIEDLNLPNAIITRLVKEVLPES---NVSISKEARLAIARAATVFVIFLTSVSNEIAKDQKRKTISADDVLKALDEI 78 (172)
T ss_pred cchhHHHhhccHHHHHHHHHHhCccc---cccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCcccHHHHHHHHHHh
Confidence 67899999999999999999999986 489999999999999999999999999999999999999999999999999
Q ss_pred CchHHHHHHHHHHHHHHhcc
Q psy13691 81 GFEVIIEILGKSYNAAVSIK 100 (103)
Q Consensus 81 gf~~~~~~l~~~l~~~k~~~ 100 (103)
||.+|+.||+..|+.|+..+
T Consensus 79 efs~f~~plk~~Le~yk~~~ 98 (172)
T KOG0870|consen 79 EFSSFVNPLKSALEAYKKAV 98 (172)
T ss_pred chHHHhhHHHHHHHHHHHHH
Confidence 99999999999999999764
No 4
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=99.93 E-value=6.6e-26 Score=156.10 Aligned_cols=98 Identities=29% Similarity=0.344 Sum_probs=93.7
Q ss_pred CCC--CccCCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691 1 MAE--SLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK 78 (103)
Q Consensus 1 m~~--~~~d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~ 78 (103)
|++ ..++..||+|+|++++.+.||.+ ..++|||+++++.||-+||+.|+++||++|.++.+|||.++||++||+
T Consensus 1 Mn~~~~dDe~sLPKATVqKMvS~iLp~d----l~ftKearei~in~cieFi~~lsseAne~ce~EaKKTIa~EHviKALe 76 (148)
T COG5150 1 MNMEKNDDENSLPKATVQKMVSSILPKD----LVFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHVIKALE 76 (148)
T ss_pred CCCccccccccCcHHHHHHHHHHhcccc----ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHH
Confidence 555 56789999999999999999999 999999999999999999999999999999999999999999999999
Q ss_pred hcCchHHHHHHHHHHHHHHhcccc
Q psy13691 79 QIGFEVIIEILGKSYNAAVSIKVV 102 (103)
Q Consensus 79 ~lgf~~~~~~l~~~l~~~k~~~~~ 102 (103)
.|||.+|++.+.+.+.+|++.+++
T Consensus 77 nLef~eyi~~~~e~~~n~k~~qK~ 100 (148)
T COG5150 77 NLEFEEYIESCMEEHENYKSYQKQ 100 (148)
T ss_pred hccHHHHHHHHHHHHHHHHHHHhh
Confidence 999999999999999999998775
No 5
>PF00808 CBFD_NFYB_HMF: Histone-like transcription factor (CBF/NF-Y) and archaeal histone; InterPro: IPR003958 The CCAAT-binding factor (CBF) is a mammalian transcription factor that binds to a CCAAT motif in the promoters of a wide variety of genes, including type I collagen and albumin. The factor is a heteromeric complex of A and B subunits, both of which are required for DNA-binding [, ]. The subunits can interact in the absence of DNA-binding, conserved regions in each being important in mediating this interaction. The A subunit can be split into 3 domains on the basis of sequence similarity, a non-conserved N-terminal 'A domain'; a highly-conserved central 'B domain' involved in DNA-binding; and a C-terminal 'C domain', which contains a number of glutamine and acidic residues involved in protein-protein interactions []. The A subunit shows striking similarity to the HAP3 subunit of the yeast CCAAT-binding heterotrimeric transcription factor [, ]. The Kluyveromyces lactis HAP3 protein has been predicted to contain a 4-cysteine zinc finger, which is thought to be present in similar HAP3 and CBF subunit A proteins, in which the third cysteine is replaced by a serine []. This domain is found in the CCAAT transcription factor and archaeal histones.; GO: 0043565 sequence-specific DNA binding, 0005622 intracellular; PDB: 1F1E_A 2BYM_D 2BYK_D 1HTA_A 1B67_A 1JFI_B 1KU5_B 1N1J_A 1BFM_A 1B6W_A ....
Probab=99.84 E-value=8.3e-21 Score=116.67 Aligned_cols=64 Identities=41% Similarity=0.498 Sum_probs=58.7
Q ss_pred CCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhh
Q psy13691 9 NLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGV 77 (103)
Q Consensus 9 ~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al 77 (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 SLPLARVKRIMKSD-PDV----MRVSKEAVEAIAKAAEEFIQYLAKEANEIAQRDKRKTITYEDVAKAV 65 (65)
T ss_dssp SS-HHHHHHHHHHT-STT----SEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEE-HHHHHHHH
T ss_pred CCChHHHHHHhccC-CCc----cchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHC
Confidence 69999999999999 777 79999999999999999999999999999999999999999999986
No 6
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=99.76 E-value=1.6e-18 Score=113.76 Aligned_cols=76 Identities=24% Similarity=0.373 Sum_probs=72.0
Q ss_pred CccCCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCch
Q psy13691 4 SLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFE 83 (103)
Q Consensus 4 ~~~d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~ 83 (103)
+..+..||+++|.||||+..++ +||.+|.+.+++|.++|+..|+..|++.|.++|||||+++||..|++.+||.
T Consensus 14 ~~~~~~Lp~apv~Ri~r~~~~~------Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~DI~la~~~~~~~ 87 (91)
T COG2036 14 RSTDLLLPKAPVRRILRKAGAE------RVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLALKRLGRR 87 (91)
T ss_pred hhhhhhcCchHHHHHHHHHhHH------HhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHHHhccc
Confidence 5678899999999999999763 8999999999999999999999999999999999999999999999999997
Q ss_pred HH
Q psy13691 84 VI 85 (103)
Q Consensus 84 ~~ 85 (103)
.|
T Consensus 88 ~~ 89 (91)
T COG2036 88 IY 89 (91)
T ss_pred cc
Confidence 65
No 7
>cd00076 H4 Histone H4, one of the four histones, along with H2A, H2B and H3, which forms the eukaryotic nucleosome core; along with H3, it plays a central role in nucleosome formation; histones bind to DNA and wrap the genetic material into "beads on a string" in which DNA (the string) is wrapped around small blobs of histones (the beads) at regular intervals; play a role in the inheritance of specialized chromosome structures and the control of gene activity; defects in the establishment of proper chromosome structure by histones may activate or silence genes aberrantly and thus lead to disease; the sequence of histone H4 has remained almost invariant in more than 2 billion years of evolution
Probab=99.38 E-value=2.9e-12 Score=83.22 Aligned_cols=71 Identities=18% Similarity=0.287 Sum_probs=65.7
Q ss_pred CCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCchHH
Q psy13691 9 NLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFEVI 85 (103)
Q Consensus 9 ~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~~ 85 (103)
.||++.|.||++...- .+||.|+.+.+.++.++|+..+..+|...|+++|||||+++||..||+..|-.-|
T Consensus 13 gi~k~~I~RLarr~Gv------kRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~alkr~g~~~y 83 (85)
T cd00076 13 GITKPAIRRLARRGGV------KRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLY 83 (85)
T ss_pred cCCHHHHHHHHHHcCc------chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHCCCCcc
Confidence 5999999999999742 5899999999999999999999999999999999999999999999999885533
No 8
>PLN00035 histone H4; Provisional
Probab=99.33 E-value=8e-12 Score=83.73 Aligned_cols=69 Identities=19% Similarity=0.302 Sum_probs=64.5
Q ss_pred CCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCch
Q psy13691 9 NLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFE 83 (103)
Q Consensus 9 ~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~ 83 (103)
.||+++|.||++...- .+||.|+.+.+.+..++|+..|..+|...|++.+||||+++||..||+..|-.
T Consensus 29 ~ipk~~IrRLARr~Gv------kRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr~g~~ 97 (103)
T PLN00035 29 GITKPAIRRLARRGGV------KRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRT 97 (103)
T ss_pred cCCHHHHHHHHHHcCc------ccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHcCCc
Confidence 5999999999999842 58999999999999999999999999999999999999999999999987754
No 9
>PTZ00015 histone H4; Provisional
Probab=99.28 E-value=2.6e-11 Score=81.12 Aligned_cols=71 Identities=18% Similarity=0.279 Sum_probs=65.6
Q ss_pred CCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCchH
Q psy13691 8 LNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFEV 84 (103)
Q Consensus 8 ~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~ 84 (103)
..||++.|.||++...- .+||.|+.+.+.++.++|+..|..+|...|++++||||+++||..||+..|-.-
T Consensus 29 ~gI~k~~IrRLarr~Gv------kRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~AlKr~g~~~ 99 (102)
T PTZ00015 29 RGITKGAIRRLARRGGV------KRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALKRQGRTL 99 (102)
T ss_pred cCCCHHHHHHHHHHcCC------ccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhcCCCC
Confidence 46999999999999733 589999999999999999999999999999999999999999999999887643
No 10
>smart00428 H3 Histone H3.
Probab=99.21 E-value=4.8e-11 Score=80.27 Aligned_cols=76 Identities=21% Similarity=0.215 Sum_probs=68.1
Q ss_pred CccCCCCcHHHHHHHHHhhCCCCCc-ccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhh
Q psy13691 4 SLDDLNLPSAIIQRLIKEALPKDAE-GKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQ 79 (103)
Q Consensus 4 ~~~d~~LP~a~V~ri~K~~l~~~~~-~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~ 79 (103)
+..++.+|+.++.|++++..++... .+.+++.+|..+||++++.|+.-+...|+..|.+.||+||.++|+.-|..-
T Consensus 24 kst~lLI~k~pF~RLVREI~~~~~~~~~~R~~~~Al~aLQeasE~ylv~lfeda~~~a~HAkRvTl~~kDi~La~ri 100 (105)
T smart00428 24 KSTDLLIRKAPFQRLVREIAQKFTTGVDLRFQSSAIMALQEAAEAYLVGLFEDTNLLAIHAKRVTIMPKDIQLARRI 100 (105)
T ss_pred cCcccccccccHHHHHHHHHHHcCCCCCceeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccCcHhhHHHHHHH
Confidence 5678999999999999999876422 258999999999999999999999999999999999999999999888643
No 11
>smart00803 TAF TATA box binding protein associated factor. TAFs (TATA box binding protein associated factors) are part of the transcription initiation factor TFIID multimeric protein complex. TFIID is composed of the TATA box binding protein (TBP) and a number of TAFs. The TAFs provide binding sites for many different transcriptional activators and co-activators that modulate transcription initiation by Pol II. TAF proteins adopt a histone-like fold.
Probab=99.16 E-value=2.3e-10 Score=70.80 Aligned_cols=64 Identities=20% Similarity=0.230 Sum_probs=59.7
Q ss_pred CCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691 9 NLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK 78 (103)
Q Consensus 9 ~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~ 78 (103)
.||+++|.||.+...- -+||.|+...+.+-.+.|+..|..+|...+++.||||++++||-.||+
T Consensus 2 ~~p~~~i~ria~~~Gi------~ris~~a~~~l~~~~e~rl~~i~~~A~k~~~hakRktlt~~DI~~Alk 65 (65)
T smart00803 2 WLPKETIKDVAESLGI------GNLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSALR 65 (65)
T ss_pred CCCHHHHHHHHHHCCC------ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCeecHHHHHHHhC
Confidence 5899999999998732 479999999999999999999999999999999999999999999984
No 12
>smart00417 H4 Histone H4.
Probab=99.15 E-value=1.7e-10 Score=73.23 Aligned_cols=62 Identities=18% Similarity=0.275 Sum_probs=57.7
Q ss_pred CCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHh
Q psy13691 9 NLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEG 76 (103)
Q Consensus 9 ~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~A 76 (103)
.||++.|.||++...- -+||.++.+.+.+..++|+..+..+|...|++.|||||+++||..|
T Consensus 13 gI~k~~IrRLaRr~Gv------kRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~~a 74 (74)
T smart00417 13 GITKPAIRRLARRGGV------KRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVYA 74 (74)
T ss_pred CCCHHHHHHHHHHcCc------chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHheeC
Confidence 6999999999999743 5899999999999999999999999999999999999999999653
No 13
>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=99.12 E-value=2.7e-10 Score=71.00 Aligned_cols=71 Identities=21% Similarity=0.266 Sum_probs=63.4
Q ss_pred CCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691 7 DLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK 78 (103)
Q Consensus 7 d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~ 78 (103)
+..+|+..|.|+.|+..++. ....+||++|...|+.+++.|+.-|...|...|.+.||+||+++||..|++
T Consensus 3 ~~~~~~~~~~r~~r~i~~~~-~~~~ris~~a~~~L~~~~E~~~~~il~~A~~~a~~~kR~tI~~~DI~~A~r 73 (75)
T PF00125_consen 3 RRLIPKFPFSRLLREIGEEI-LSKYRISSEALVALQSVLEYLLVEILEEAGNLARHAKRKTITPRDIQLAVR 73 (75)
T ss_dssp SHSSSHHHHHHHHHHHHHTT-SSSSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTBSEEGHHHHHHHHH
T ss_pred ccccCceEEeeeeehhhccc-ccccccccccchhhhhhhhhhhhhhhhHHHHHHhhcCCcEecHHHHHHHHh
Confidence 45789999999999987763 111599999999999999999999999999999999999999999999975
No 14
>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=99.11 E-value=8.2e-10 Score=69.36 Aligned_cols=65 Identities=25% Similarity=0.281 Sum_probs=60.9
Q ss_pred CcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhh
Q psy13691 10 LPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQ 79 (103)
Q Consensus 10 LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~ 79 (103)
+|+..+..++|+.-|. .+++.||.++|++.++.|+.-++..|...|++.||+||.++||..+++.
T Consensus 2 ~~k~~l~~lv~~id~~-----~~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~~~tv~~~Di~l~l~r 66 (72)
T cd07981 2 LTKRKLQELLKEIDPR-----EQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQLHLER 66 (72)
T ss_pred CcHHHHHHHHHhhCCC-----CCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence 6888999999998653 7999999999999999999999999999999999999999999999975
No 15
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=99.08 E-value=1.3e-10 Score=86.99 Aligned_cols=77 Identities=30% Similarity=0.382 Sum_probs=70.5
Q ss_pred cCCCCcHHHHHHHHHhhCCCCCcccc-cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCchH
Q psy13691 6 DDLNLPSAIIQRLIKEALPKDAEGKI-NVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFEV 84 (103)
Q Consensus 6 ~d~~LP~a~V~ri~K~~l~~~~~~~~-~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~ 84 (103)
.+.+||.|+|.|+||.. ++ + .||.||..++.+.|+.||..||-.|+-.+++++|+|+-..||..|++..++.+
T Consensus 106 k~h~LPlARIkkvMKtd--ed----VkMisaEaPvlFak~~EiFI~ELTmRAW~~ae~NkRRtLQksDia~Av~kSeMfD 179 (286)
T COG5208 106 KDHNLPLARIKKVMKTD--ED----VKMISAEAPVLFAKITEIFIEELTMRAWINAEENKRRTLQKSDIAAAVKKSEMFD 179 (286)
T ss_pred HhccCcHHHHHHHHhcc--cc----hhheecccchHHHHHHHHHHHHHHHHHHHHHhHhhhhHHHHHHHHHHHHHHHHHh
Confidence 36789999999999986 44 5 59999999999999999999999999999999999999999999999999888
Q ss_pred HHHH
Q psy13691 85 IIEI 88 (103)
Q Consensus 85 ~~~~ 88 (103)
|+-.
T Consensus 180 FLid 183 (286)
T COG5208 180 FLID 183 (286)
T ss_pred HHhh
Confidence 8643
No 16
>PLN00160 histone H3; Provisional
Probab=99.02 E-value=7.4e-10 Score=73.55 Aligned_cols=75 Identities=19% Similarity=0.119 Sum_probs=66.9
Q ss_pred CccCCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691 4 SLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK 78 (103)
Q Consensus 4 ~~~d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~ 78 (103)
+..++.+|+.+..|++++..++-..++.+++.+|..+||++++.|+.-+...|+-.|.+.||.||.+.|+.-|..
T Consensus 16 kst~lLI~k~pF~RLVREI~~~~~~~~~Rfq~~Al~ALQeAsEayLv~lfed~~lca~HakRVTl~~kD~~L~~r 90 (97)
T PLN00160 16 KSTDLLIRRLPFARLVREIQMEMSREAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTIMPKDMQLARR 90 (97)
T ss_pred cchhhhhccccHHHHHHHHHHHcCCCCcEeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcccccchhhHHHHHH
Confidence 567889999999999999976432234899999999999999999999999999999999999999999988764
No 17
>PLN00161 histone H3; Provisional
Probab=98.98 E-value=1.7e-09 Score=75.55 Aligned_cols=75 Identities=19% Similarity=0.176 Sum_probs=67.1
Q ss_pred CccCCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691 4 SLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK 78 (103)
Q Consensus 4 ~~~d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~ 78 (103)
+..++.+|+.++.|++++...+....+.+++.+|..+||++++.|+.-+...|+-.|.+.||.||.+.|+.-|..
T Consensus 50 kst~lLIpklPF~RLVREI~~~~~~~~~Rfq~~Al~ALQEAsEayLV~lFeda~lcaiHAkRVTlm~kDm~La~r 124 (135)
T PLN00161 50 KSTELLIRKLPFARLVREISNEMLREPFRWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMPKDMQLARR 124 (135)
T ss_pred cccccccccccHHHHHHHHHHhcCCCCcEeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccchhhHHHHHH
Confidence 567889999999999999976532234899999999999999999999999999999999999999999988864
No 18
>PLN00121 histone H3; Provisional
Probab=98.91 E-value=3.1e-09 Score=74.39 Aligned_cols=74 Identities=19% Similarity=0.195 Sum_probs=67.2
Q ss_pred CccCCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691 4 SLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK 78 (103)
Q Consensus 4 ~~~d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~ 78 (103)
...++.+|+..+.|++++...+. ..+.+++.+|..+||++++.|+.-+...++-.|.+.||.||.+.|+.-+..
T Consensus 57 kst~lLI~k~pF~RLVREI~~~~-~~~~Rf~~~Al~ALQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~r 130 (136)
T PLN00121 57 KSTELLIRKLPFQRLVREIAQDF-KTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
T ss_pred cccccccccccHHHHHHHHHHHh-CccceeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcceecchhhHHHHHH
Confidence 56789999999999999998763 234899999999999999999999999999999999999999999988764
No 19
>PTZ00018 histone H3; Provisional
Probab=98.90 E-value=3.2e-09 Score=74.29 Aligned_cols=74 Identities=19% Similarity=0.195 Sum_probs=66.7
Q ss_pred CccCCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691 4 SLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK 78 (103)
Q Consensus 4 ~~~d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~ 78 (103)
+..++.+|+..+.|++++...+. ..+++++.+|..+||++++.|+.-|...++..|.+.||.||.+.|+.-|..
T Consensus 57 kst~lLI~k~pF~RLVREI~~~~-~~~~rf~~~al~aLQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~r 130 (136)
T PTZ00018 57 KSTELLIRKLPFQRLVREIAQDF-KTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
T ss_pred ccchhccccccHHHHHHHHHHHc-CCcceeeHHHHHHHHHHHHHHHHHHhhhhHHHHHhhcceecchhhHHHHHH
Confidence 56789999999999999997653 234899999999999999999999999999999999999999999988764
No 20
>KOG1657|consensus
Probab=98.79 E-value=6.3e-09 Score=78.59 Aligned_cols=84 Identities=24% Similarity=0.218 Sum_probs=69.7
Q ss_pred CCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCchHH-
Q psy13691 7 DLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFEVI- 85 (103)
Q Consensus 7 d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~~- 85 (103)
...||+++|.+|||..= +- -.|+.||..++.+||+.||..|+..|+..+.+.+|+|+...|+..|+..-+-.+|
T Consensus 72 ~~~lPlaRiKkimK~de-dv----~mI~~Eapvl~aka~E~Fi~elt~~sw~~Tee~~rrtl~~sdia~av~~s~~fdFL 146 (236)
T KOG1657|consen 72 NHILPLARIKKIMKSDE-DV----SMITAEAPVLFAKACELFITELTLRSWVHTEENKRRTLQKSDIAAAVTQSETFDFL 146 (236)
T ss_pred hccCcHhhccccccccc-cc----cccchhHHHHHHHHHHHHHHHHHHHhhhhhcccccccchHHHHHHHhccCCCccce
Confidence 45899999999999972 22 2799999999999999999999999999999999999999999999996555444
Q ss_pred --HHHHHHHHHH
Q psy13691 86 --IEILGKSYNA 95 (103)
Q Consensus 86 --~~~l~~~l~~ 95 (103)
+.|.+...+.
T Consensus 147 ~DivP~~~~~~~ 158 (236)
T KOG1657|consen 147 RDIVPRKILAEK 158 (236)
T ss_pred eccccchhcccc
Confidence 4444444433
No 21
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=98.70 E-value=1.9e-07 Score=59.06 Aligned_cols=66 Identities=15% Similarity=0.127 Sum_probs=59.2
Q ss_pred HHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCch
Q psy13691 12 SAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFE 83 (103)
Q Consensus 12 ~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~ 83 (103)
+-.|.+|++.+.= -+++.+|.+.|.+....|+..|+..+...|++.||++.++.||..||+++|+.
T Consensus 9 ~~~Vaqil~~~Gf------~~~~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~~~Dv~~Al~~~gi~ 74 (77)
T smart00576 9 RIAVAQILESAGF------DSFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPNLGDVVLALENLGIS 74 (77)
T ss_pred HHHHHHHHHHcCc------cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCcc
Confidence 3457788887632 37999999999999999999999999999999999999999999999999974
No 22
>cd00074 H2A Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins.
Probab=98.65 E-value=1.3e-07 Score=64.54 Aligned_cols=72 Identities=14% Similarity=0.165 Sum_probs=63.7
Q ss_pred CCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhh-cCch
Q psy13691 7 DLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQ-IGFE 83 (103)
Q Consensus 7 d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~-lgf~ 83 (103)
.+.||.++|.|+||+.-. . .|||.+|...|..+.+.+...|...|...|.+.+|++|+++||..|+.. -+|.
T Consensus 18 gL~fPV~ri~R~Lk~~~~-a----~RVs~~A~VyLaAvLEYL~aEIlelA~n~ak~~k~krItp~hi~lAi~nD~EL~ 90 (115)
T cd00074 18 GLQFPVGRIHRYLKKGRY-A----ERVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKKRITPRHLQLAVRNDEELN 90 (115)
T ss_pred CccCcHHHHHHHHHcCcc-c----cccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEcHHHHHHHHhccHHHH
Confidence 678999999999998422 1 6999999999999999999999999999999999999999999999974 3443
No 23
>KOG1659|consensus
Probab=98.30 E-value=3.4e-06 Score=62.89 Aligned_cols=79 Identities=19% Similarity=0.263 Sum_probs=70.1
Q ss_pred CCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCchHHHH
Q psy13691 8 LNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFEVIIE 87 (103)
Q Consensus 8 ~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~~~~ 87 (103)
-.||.++|.|||...=+-+ +|+.-....+.++.+.|+.-|-..+.+++...+-|||+++|+..+++.-.-.+|+.
T Consensus 12 trfp~aRiKKIMQ~dEdIG-----KvaqavPViisralElFl~~l~~~t~~~t~~~~aKt~s~~hlkq~v~~~~~FdFLk 86 (224)
T KOG1659|consen 12 TRFPPARIKKIMQSDEDIG-----KVAQAVPVIISRALELFLESLLQKTLEITRSRGAKTVSSSHLKQAVESDPKFDFLK 86 (224)
T ss_pred ccCCHHHHHHHHhhhhhhh-----hhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhcCccccCHHHHHHHHhccchhHHHH
Confidence 3689999999998863222 89999999999999999999999999999999999999999999999888888887
Q ss_pred HHHH
Q psy13691 88 ILGK 91 (103)
Q Consensus 88 ~l~~ 91 (103)
.+-.
T Consensus 87 ~~v~ 90 (224)
T KOG1659|consen 87 EVVE 90 (224)
T ss_pred HHHH
Confidence 7544
No 24
>KOG1745|consensus
Probab=98.22 E-value=6.4e-07 Score=62.71 Aligned_cols=77 Identities=19% Similarity=0.182 Sum_probs=66.4
Q ss_pred CccCCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcC
Q psy13691 4 SLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIG 81 (103)
Q Consensus 4 ~~~d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lg 81 (103)
+..|+.+++.+..|++++..++. ..+.++...|..+||++++.|+.-|.-.+|-.|.+.||.||-+.|+.-|..--|
T Consensus 58 kstdLlI~K~PFqRlvrei~q~f-~~dLrfqs~Ai~ALQeA~EayLv~LfEdtnlcAihAkRVTimpkdiQlArrirg 134 (137)
T KOG1745|consen 58 KSTDLLIRKLPFQRLVREIAQDF-KTDLRFQSSAIAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRG 134 (137)
T ss_pred hhhHHHhhcCcHHHHhHHHHhcc-cccceehHHHHHHHHHHHHHHHHHhccccchhhhccceeEecccceehhhhccc
Confidence 45788899999999999665543 123899999999999999999999999999999999999999999998876443
No 25
>cd07979 TAF9 TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. The TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Human TAF9 has a paralogue gene (TAF9L) whi
Probab=98.22 E-value=8.8e-06 Score=55.50 Aligned_cols=67 Identities=10% Similarity=0.012 Sum_probs=58.3
Q ss_pred HHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCchHHH
Q psy13691 14 IIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFEVII 86 (103)
Q Consensus 14 ~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~~~ 86 (103)
.|.+|+|+..- .+++.++...|.+.+..++.-+..+|...|+++||+||+.+||.-|++..+-..|.
T Consensus 6 ~v~~iLk~~Gv------~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r~~~~f~ 72 (117)
T cd07979 6 VIAAILKSMGI------TEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRVDYSFT 72 (117)
T ss_pred HHHHHHHHCCC------CccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhccCCC
Confidence 57788887621 47999999999999999999999999999999999999999999999976654443
No 26
>PF15511 CENP-T: Centromere kinetochore component CENP-T; PDB: 3B0D_T 3B0C_T 3VH5_T 3VH6_T.
Probab=98.22 E-value=3.2e-06 Score=68.17 Aligned_cols=68 Identities=24% Similarity=0.350 Sum_probs=47.7
Q ss_pred ccCCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhh
Q psy13691 5 LDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVD 72 (103)
Q Consensus 5 ~~d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eD 72 (103)
+.--.||.+.|.|++.........++++|++||..+|.+|...|-..|+..=--.|.++|||||..+|
T Consensus 347 i~~P~lP~~~vK~la~~~ak~s~~sK~kiskdal~aleqasdwfFeQl~dDL~aYA~HAgRKTIdesD 414 (414)
T PF15511_consen 347 IPYPSLPPGVVKKLAQHFAKSSGGSKMKISKDALEALEQASDWFFEQLGDDLEAYAKHAGRKTIDESD 414 (414)
T ss_dssp -----S-HHHHHHHHHHHH-------S-B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHH
T ss_pred CCCCCCCccHHHHHHHHHHHhhcccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCCCC
Confidence 34457999999999877755322345899999999999999999999999888899999999999876
No 27
>cd08050 TAF6 TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and are involved in forming Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs functions such as serving as
Probab=98.14 E-value=1.4e-05 Score=63.01 Aligned_cols=67 Identities=16% Similarity=0.190 Sum_probs=59.0
Q ss_pred cHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCch
Q psy13691 11 PSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFE 83 (103)
Q Consensus 11 P~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~ 83 (103)
|..+|.-|.++..- .++++||...+.+..+.++..+..+|...+++.||||++++||-.||+.++.+
T Consensus 1 ~~~~i~~ia~~~Gi------~~~~~~a~~~La~~~e~~~~~i~~~A~k~~~hskR~~l~~~Di~~Al~~~n~e 67 (343)
T cd08050 1 PQESIKLIAESLGI------DSLSDEVAQLLAEDVEYRLREIIQEAAKFMRHSKRRKLTTSDVNHALRLRNVE 67 (343)
T ss_pred ChhHHHHHHHHcCC------CcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHHhCCC
Confidence 45677777777622 38999999999999999999999999999999999999999999999976655
No 28
>smart00427 H2B Histone H2B.
Probab=98.13 E-value=2.2e-05 Score=51.47 Aligned_cols=63 Identities=19% Similarity=0.266 Sum_probs=57.8
Q ss_pred HHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhc
Q psy13691 13 AIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQI 80 (103)
Q Consensus 13 a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~l 80 (103)
.-|+|+.|+.-|+ .-||..+...+.--...+..-|+.+|...|...+|+||+.++|..|++-+
T Consensus 5 ~Yi~kvLKqVhpd-----~giS~kam~imnSfvnDiferIa~EAs~L~~~nkr~TltsreIqtAvrl~ 67 (89)
T smart00427 5 IYIYKVLKQVHPD-----TGISSKAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRLI 67 (89)
T ss_pred HHHHHHHHHhCCC-----ccccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHH
Confidence 3589999999987 58999999999999999999999999999999999999999999998754
No 29
>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=98.10 E-value=6.3e-06 Score=51.98 Aligned_cols=66 Identities=23% Similarity=0.308 Sum_probs=54.8
Q ss_pred cHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCC-cChhhHHHhhhh
Q psy13691 11 PSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKT-LSGVDVIEGVKQ 79 (103)
Q Consensus 11 P~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkT-I~~eDV~~Al~~ 79 (103)
|+.+|.||++....++ +.+||+||..++.+....|+..-...|.+.+..+|... |..+|+-+.+-.
T Consensus 1 p~~li~rll~~~f~~~---~tkIs~dal~l~~eyl~iFV~EAv~Ra~~~a~~e~~~~~le~e~LEki~pq 67 (72)
T PF09415_consen 1 PPELIARLLHEHFKDD---KTKISKDALKLSAEYLRIFVREAVARAAEQAEAEGDEGFLEVEHLEKILPQ 67 (72)
T ss_dssp -CHHHHHHHCTTSSST---T-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSEE-HHHHHHHCHC
T ss_pred ChHHHHHHHHHHhcCC---CCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHHH
Confidence 8899999999877543 38999999999999999999999999999999999999 999999887643
No 30
>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=98.09 E-value=4.7e-05 Score=47.79 Aligned_cols=65 Identities=15% Similarity=0.134 Sum_probs=56.9
Q ss_pred HHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCch
Q psy13691 13 AIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFE 83 (103)
Q Consensus 13 a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~ 83 (103)
-.|.+|.+...= -.++..|.+.|...+..|+..|++.+...|...||...++.||..||+++|+.
T Consensus 10 ~~va~il~~~GF------~~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~~~gi~ 74 (77)
T PF07524_consen 10 RSVAQILKHAGF------DSASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPNLQDVEQALEEMGIS 74 (77)
T ss_pred HHHHHHHHHcCc------cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCC
Confidence 346666666522 26999999999999999999999999999999999999999999999999984
No 31
>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=98.05 E-value=4.6e-05 Score=49.43 Aligned_cols=66 Identities=26% Similarity=0.377 Sum_probs=60.4
Q ss_pred CCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC---CCcChhhHHHhhhhc
Q psy13691 9 NLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNR---KTLSGVDVIEGVKQI 80 (103)
Q Consensus 9 ~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~R---kTI~~eDV~~Al~~l 80 (103)
.||++.|.|||...++ -.++.+...+|.-.+-+||.-|.-+|.++..+.+. ..|.|+||-+|...|
T Consensus 16 ~f~k~~iKr~~~~~~~------~~v~~~v~i~v~glaKvFVGeivE~A~~V~~~~~~~~~~Pl~P~HireA~rrl 84 (85)
T cd08048 16 SFPKAAIKRLIQSVTG------QSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGEANTGPLQPRHLREAYRRL 84 (85)
T ss_pred hccHHHHHHHHHHHcC------CCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCCCCCcHHHHHHHHHh
Confidence 5999999999999976 36999999999999999999999999999877665 889999999999876
No 32
>PF03847 TFIID_20kDa: Transcription initiation factor TFIID subunit A; InterPro: IPR003228 Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription [].; GO: 0006352 transcription initiation, DNA-dependent, 0005669 transcription factor TFIID complex; PDB: 1H3O_B.
Probab=98.03 E-value=4.1e-05 Score=47.75 Aligned_cols=63 Identities=22% Similarity=0.219 Sum_probs=51.2
Q ss_pred HHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhh
Q psy13691 12 SAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQ 79 (103)
Q Consensus 12 ~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~ 79 (103)
+..+..++++.-|. ..+.+|+.++|.+.|..||.-++..|...|++.|-.|+...||.-.|++
T Consensus 2 K~~l~~Lv~~iDp~-----~~ld~~vee~Ll~laddFv~~v~~~ac~lAKhR~s~tle~~Dv~~~Ler 64 (68)
T PF03847_consen 2 KRKLQELVKQIDPN-----EKLDPDVEELLLELADDFVDDVVSFACRLAKHRKSSTLEVKDVQLHLER 64 (68)
T ss_dssp HHHHHHHHHCC-SS---------HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHHH
T ss_pred hHHHHHHHHHcCCC-----CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCHHHHHHHHHh
Confidence 45678899998554 6999999999999999999999999999999999999999999998874
No 33
>COG5247 BUR6 Class 2 transcription repressor NC2, alpha subunit (DRAP1 homolog) [Transcription]
Probab=98.02 E-value=2.7e-05 Score=52.23 Aligned_cols=80 Identities=14% Similarity=0.143 Sum_probs=69.5
Q ss_pred CCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCchHHHH
Q psy13691 8 LNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFEVIIE 87 (103)
Q Consensus 8 ~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~~~~ 87 (103)
..+|.|.|.|||.-.-+- -+|+.-......++.+.|+..|-.++.+.++..+-|.++.+++..|.+.-+=.+|+.
T Consensus 22 trFP~ar~KkIMQ~deDi-----GKV~q~tPVIaskalE~Fl~~iv~~s~k~aR~~~skR~t~e~lk~a~~sdekFdFL~ 96 (113)
T COG5247 22 TRFPIARLKKIMQLDEDI-----GKVGQSTPVIASKALEMFLTEIVGLSLKEARKKSSKRMTSEFLKRATESDEKFDFLK 96 (113)
T ss_pred hcCCHHHHHHHHHhhhhh-----hhhhhcchHHHHHHHHHHHHHHHHHHHHHHHhccchhhHHHHHHHHHhhhHHHHHHH
Confidence 369999999999876332 289999999999999999999999999999999999999999999999877777776
Q ss_pred HHHHH
Q psy13691 88 ILGKS 92 (103)
Q Consensus 88 ~l~~~ 92 (103)
...++
T Consensus 97 ~~~~~ 101 (113)
T COG5247 97 NMEQF 101 (113)
T ss_pred HHHHh
Confidence 65543
No 34
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=98.01 E-value=1.8e-05 Score=54.34 Aligned_cols=67 Identities=12% Similarity=0.198 Sum_probs=60.4
Q ss_pred CCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691 7 DLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK 78 (103)
Q Consensus 7 d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~ 78 (103)
-+.+|.+.|.|+||.. ... +||+++|...+.-|.+-.+..++..|-..|...|+|.|.|.|+..|+.
T Consensus 24 gl~fpvgrvkr~lk~~-~~~----~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~kkkri~PrHlqlAIr 90 (132)
T COG5262 24 GLIFPVGRVKRLLKKG-NYR----MRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRIIPRHLQLAIR 90 (132)
T ss_pred CccccHHHHHHHHHcC-ccc----eeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhcCcceechHHHHHHhc
Confidence 5689999999999943 223 899999999999999999999999999999999999999999999986
No 35
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=97.99 E-value=4.5e-05 Score=48.56 Aligned_cols=62 Identities=18% Similarity=0.187 Sum_probs=51.2
Q ss_pred HHHHHHHhhC-CCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhh
Q psy13691 14 IIQRLIKEAL-PKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQ 79 (103)
Q Consensus 14 ~V~ri~K~~l-~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~ 79 (103)
.|.||+.+.. +.+ +.+|+.+..+|.+-+-.++..++..-..-|+++||+||+++||+-...+
T Consensus 10 ~v~ki~ee~~~~~~----~~~s~~~i~al~ELv~~q~~~~a~DLe~FAkHA~R~tI~~dDV~Ll~Rr 72 (76)
T PF15630_consen 10 TVGKIVEEEAKEKG----VEVSPQFIAALTELVYKQLENLAKDLEAFAKHAGRSTINMDDVKLLARR 72 (76)
T ss_dssp HHHHHHHHCCCCTT----SEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHTTT
T ss_pred HHHHHHHHHHhccC----CccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHHHhhc
Confidence 5788888874 334 8999999999999999999999998888999999999999999876653
No 36
>PLN00158 histone H2B; Provisional
Probab=97.93 E-value=7.6e-05 Score=51.01 Aligned_cols=65 Identities=17% Similarity=0.217 Sum_probs=58.9
Q ss_pred cHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhc
Q psy13691 11 PSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQI 80 (103)
Q Consensus 11 P~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~l 80 (103)
...-|+|+.|++-|+ ..||..+...|.-....+..-|+.+|...|...+|+||+..+|..|++-+
T Consensus 29 y~~YI~kVLKQVhPd-----~gIS~kaM~ImnSfvnDiferIA~EAs~La~~nkr~TltsrEIqtAvrLv 93 (116)
T PLN00158 29 YKIYIYKVLKQVHPD-----TGISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVRLI 93 (116)
T ss_pred HHHHHHHHHHHhCCC-----CCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHh
Confidence 345699999999987 58999999999999999999999999999999999999999999998644
No 37
>PTZ00463 histone H2B; Provisional
Probab=97.90 E-value=9.2e-05 Score=50.63 Aligned_cols=62 Identities=18% Similarity=0.239 Sum_probs=56.9
Q ss_pred HHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhc
Q psy13691 14 IIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQI 80 (103)
Q Consensus 14 ~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~l 80 (103)
-|+|+.|+.-|+ .-||..+...|+-.......-|+.+|...|...+|+||++.+|..|++-+
T Consensus 33 YI~KVLKqVhPd-----~gIS~kaM~ImnSfvnDifErIA~EAs~La~~nkr~TltsrEIQtAvrLl 94 (117)
T PTZ00463 33 YIFKVLKQVHPD-----TGISRKSMNIMNSFLVDTFEKIATEASRLCKYTRRDTLSSREIQTAIRLV 94 (117)
T ss_pred HHHHHHHhhCCC-----CCccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHhhc
Confidence 499999999987 57999999999998888889999999999999999999999999998644
No 38
>KOG3467|consensus
Probab=97.88 E-value=9.4e-05 Score=48.53 Aligned_cols=68 Identities=19% Similarity=0.302 Sum_probs=59.3
Q ss_pred CcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCch
Q psy13691 10 LPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFE 83 (103)
Q Consensus 10 LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~ 83 (103)
+.+-.|.||.+...- -+|+.-.-+.+..++.+|+..+-+.|...+.+.+||||++-||+-+|++.|.-
T Consensus 30 itKpaIRRlARr~GV------kRi~G~~yeE~~~~~k~fl~n~i~~A~~yt~HAKRKTvT~~dvv~~LKR~G~~ 97 (103)
T KOG3467|consen 30 ITKPAIRRLARRGGV------KRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRT 97 (103)
T ss_pred cchHHHHHHHHhcCc------chhchhhHHHHHHHHHHHHHHHHHHHHHHHhhhhhceeeHHHHHHHHHHcCce
Confidence 456678888887622 37888888999999999999999999999999999999999999999998753
No 39
>smart00414 H2A Histone 2A.
Probab=97.75 E-value=0.00013 Score=49.09 Aligned_cols=68 Identities=12% Similarity=0.198 Sum_probs=60.7
Q ss_pred CCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhh
Q psy13691 7 DLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQ 79 (103)
Q Consensus 7 d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~ 79 (103)
.+.||.+.|.|++|+.-- . .+|+..|...|.-+.+-+...+-..|-..|...+++.|+++|+..|+..
T Consensus 7 gL~fPVgRi~r~Lk~~~~-~----~Rv~~~A~VyLaAvLEYLtaEILeLagn~a~~~k~~rItp~hi~lAi~n 74 (106)
T smart00414 7 GLQFPVGRIHRLLRKGTY-A----KRVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKRRITPRHLQLAIRN 74 (106)
T ss_pred CccCchHHHHHHHHcCcc-c----cccccccHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchHHHhhhccC
Confidence 678999999999998632 2 5999999999999999999998888999999999999999999999874
No 40
>PF02969 TAF: TATA box binding protein associated factor (TAF); InterPro: IPR004823 The TATA box binding protein associated factor (TAF) is part of the transcription initiation factor TFIID multimeric protein complex. TFIID plays a central role in mediating promoter responses to various activators and repressors. It binds tightly to TAFII-250 and directly interacts with TAFII-40. TFIID is composed of TATA binding protein (TBP)and a number of TBP-associated factors (TAFS). TAF proteins adopt a histone-like fold.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus; PDB: 1TAF_B.
Probab=97.73 E-value=0.00041 Score=43.09 Aligned_cols=64 Identities=14% Similarity=0.208 Sum_probs=49.6
Q ss_pred CCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691 9 NLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK 78 (103)
Q Consensus 9 ~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~ 78 (103)
.+|..+|.-+.... +- ..++.|+...|.+=++.-|..|..+|.....+.+|++++++||-.||+
T Consensus 3 ~~~~esvk~iAes~-Gi-----~~l~de~a~~La~dveyrlreiiq~a~kfm~hskR~~Lt~~Di~~ALr 66 (66)
T PF02969_consen 3 VFSQESVKDIAESL-GI-----SNLSDEAAKALAEDVEYRLREIIQEALKFMRHSKRTKLTTDDINSALR 66 (66)
T ss_dssp ---HHHHHHHHHHT-T--------B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH-
T ss_pred cCCHHHHHHHHHHc-CC-----CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhC
Confidence 57888887766554 32 279999999999999999999999999999999999999999999985
No 41
>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=97.68 E-value=0.00034 Score=45.88 Aligned_cols=67 Identities=24% Similarity=0.355 Sum_probs=51.4
Q ss_pred CCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCC-CcChhhHHHhhhhc
Q psy13691 9 NLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRK-TLSGVDVIEGVKQI 80 (103)
Q Consensus 9 ~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~Rk-TI~~eDV~~Al~~l 80 (103)
.||++.|.|||...+++ -.++.....++.-.+..|+-.|-.+|.+++.+.+.. .|.|.|+-+|...|
T Consensus 23 ~~~k~~ikkli~~~~~~-----qsv~~~v~i~v~g~aKvFVGEiVE~A~~Vq~~~~~~~pl~P~hlreA~rrL 90 (90)
T PF04719_consen 23 SFNKAAIKKLINQVLGN-----QSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGETGPLQPDHLREAYRRL 90 (90)
T ss_dssp ---HHHHHHHHHHHHS------S---HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SS--HHHHHHHHHHH
T ss_pred cCCHHHHHHHHHHHcCC-----CCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcHHHHHHHHhC
Confidence 69999999999999873 479999999999999999999999999998765543 79999999998765
No 42
>PLN00154 histone H2A; Provisional
Probab=97.61 E-value=0.00025 Score=49.75 Aligned_cols=69 Identities=12% Similarity=0.149 Sum_probs=60.1
Q ss_pred CCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhh
Q psy13691 7 DLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQ 79 (103)
Q Consensus 7 d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~ 79 (103)
.+.||.++|.|++|+...-. .||+..|...+.-..+-+...+-..|-..|...+++-|+|.||..|+..
T Consensus 36 gL~FPVgRi~r~Lk~g~~~~----~RVga~ApVYLAAVLEYLtAEVLELAGNaA~d~kk~RItPrHi~lAIrn 104 (136)
T PLN00154 36 GLQFPVGRIHRQLKQRVSAH----GRVGATAAVYTAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRG 104 (136)
T ss_pred CccCchHHHHHHHHhhhhhc----cccccchHHHHHHHHHHHHHHHHHHHHHHHHhhCCceecHHHhhhhccC
Confidence 67899999999999975323 5999999999999888888888888888899999999999999999863
No 43
>PTZ00017 histone H2A; Provisional
Probab=97.49 E-value=0.00033 Score=49.01 Aligned_cols=67 Identities=12% Similarity=0.183 Sum_probs=60.3
Q ss_pred CCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691 7 DLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK 78 (103)
Q Consensus 7 d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~ 78 (103)
.+.||.+.|.|++|+.--. .||+..|...|.-+.+.+...|-..|-..|...+++-|+|+||..|+.
T Consensus 25 gL~FPVgRi~R~Lk~g~~a-----~RV~a~A~VYLAAVLEYLtaEILELAgNaa~d~kk~RItPrHi~lAI~ 91 (134)
T PTZ00017 25 GLQFPVGRVHRYLKKGRYA-----KRVGAGAPVYLAAVLEYLTAEVLELAGNAAKDNKKKRITPRHIQLAIR 91 (134)
T ss_pred CcccchHHHHHHHhccchh-----ccccccchhhhHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHhhcc
Confidence 5789999999999986322 599999999999999999999998999999999999999999999986
No 44
>KOG1756|consensus
Probab=97.45 E-value=0.00047 Score=47.87 Aligned_cols=68 Identities=12% Similarity=0.207 Sum_probs=57.0
Q ss_pred cCCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691 6 DDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK 78 (103)
Q Consensus 6 ~d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~ 78 (103)
..+.+|.+.|.|++|+. .. ..+|+.+|...+.-+.+.....++..|-..+..+++.-|+|+|+..|+.
T Consensus 24 agl~fPvgri~r~Lr~~--~~---~~ri~~gapV~laavLeYL~Aeile~agnaardnkk~ri~PrH~~lAI~ 91 (131)
T KOG1756|consen 24 AGLQFPVGRIHRLLRKG--RY---AQRVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRITPRHLQLAIR 91 (131)
T ss_pred cccccCHHHHHHHHHcc--ch---hhhccCCChHHHHHHHHHHHHHHHHHhHHHhhhcCccccChHHHHHHHh
Confidence 36789999999999993 22 2699999999999777766777777777778888999999999999997
No 45
>PLN00153 histone H2A; Provisional
Probab=97.28 E-value=0.00081 Score=46.80 Aligned_cols=67 Identities=10% Similarity=0.149 Sum_probs=59.7
Q ss_pred CCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691 7 DLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK 78 (103)
Q Consensus 7 d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~ 78 (103)
.+.||.+.|.|.+|+.--. .||+..|...+.-+.+.....+-..|-..|...+++-|+|+|+..|+.
T Consensus 22 gL~FpVgRi~R~Lr~g~~a-----~Rvga~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~ 88 (129)
T PLN00153 22 GLQFPVGRIARYLKKGKYA-----ERIGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKNRIVPRHIQLAIR 88 (129)
T ss_pred CcccchHHHHHHHhcCchh-----hccCCCchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHhhcc
Confidence 5789999999999985322 599999999999999988888888888889999999999999999986
No 46
>PLN00157 histone H2A; Provisional
Probab=97.26 E-value=0.00081 Score=46.98 Aligned_cols=67 Identities=13% Similarity=0.153 Sum_probs=59.4
Q ss_pred CCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691 7 DLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK 78 (103)
Q Consensus 7 d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~ 78 (103)
.+.||.+.|.|.+|+.-- . .||+..|...|.-+.+.....|-..|-..|...+++-|+++||..|+.
T Consensus 24 gL~FPVgRi~R~Lk~g~~-a----~RIg~~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~ 90 (132)
T PLN00157 24 GLQFPVGRIARYLKAGKY-A----TRVGAGAPVYLAAVLEYLAAEVLELAGNAARDNKKSRIVPRHIQLAVR 90 (132)
T ss_pred CcccchHHHHHHHhcCch-h----hhcCCCcHhHHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHhhccc
Confidence 578999999999998522 2 599999999999998888888888888889999999999999999986
No 47
>PLN00156 histone H2AX; Provisional
Probab=97.25 E-value=0.0011 Score=46.63 Aligned_cols=67 Identities=13% Similarity=0.155 Sum_probs=58.8
Q ss_pred CCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691 7 DLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK 78 (103)
Q Consensus 7 d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~ 78 (103)
.+.||.++|.|.+|+.-- . .||+..|...|.-+.+-....+-..|-..|...+++-|+|+|+..|+.
T Consensus 27 gL~FPVgRi~R~Lk~g~y-a----~RVga~ApVYLAAVLEYLtaEVLELAgNaa~d~kk~RItPrHi~lAIr 93 (139)
T PLN00156 27 GLQFPVGRIARFLKAGKY-A----ERVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR 93 (139)
T ss_pred CcccchHHHHHHHhcCCh-h----hccCCccHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHhhcc
Confidence 578999999999998622 2 599999999999998888888888888889999999999999999986
No 48
>KOG1142|consensus
Probab=97.20 E-value=0.001 Score=50.94 Aligned_cols=69 Identities=13% Similarity=0.137 Sum_probs=61.4
Q ss_pred ccCCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691 5 LDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK 78 (103)
Q Consensus 5 ~~d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~ 78 (103)
..+..|-+-.+..+++..-++ .++-+|+.++|.+.|..||..|+..|...|++.|..||-..||...||
T Consensus 150 ~~~~il~k~kl~dLvqqId~~-----~~LD~dVedlLleiADdFV~sii~~sC~LAKHRKsdtlEvrDIqLhLE 218 (258)
T KOG1142|consen 150 GNNPILSKRKLDDLVQQIDGT-----TKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHRKSDTVEVRDIQLHLE 218 (258)
T ss_pred CCCccccccchhHHHHhhcCc-----ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccchhheeeeee
Confidence 345566677888889988443 699999999999999999999999999999999999999999999998
No 49
>KOG1658|consensus
Probab=97.18 E-value=0.0003 Score=50.31 Aligned_cols=67 Identities=28% Similarity=0.368 Sum_probs=57.4
Q ss_pred CCCcHHHHHHHHHhhCCCCCccccc-ccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhc
Q psy13691 8 LNLPSAIIQRLIKEALPKDAEGKIN-VSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQI 80 (103)
Q Consensus 8 ~~LP~a~V~ri~K~~l~~~~~~~~~-iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~l 80 (103)
..||.++|..+||-. ++ .+ ..+|+..++.++++.||..|...++..+...+|||+.-.|+=.|.+.-
T Consensus 58 ~rLpL~rik~vvkl~--pd----l~l~~dea~~l~a~aaelfi~~Ln~~~~~~~q~~k~kt~qr~d~D~ai~~~ 125 (162)
T KOG1658|consen 58 SRLPLARIKQVVKLD--PD----LTLLNDEASQLIAKAAELFIQELNDVAYTTAQLRKRKTEQRRDYDTAIEAV 125 (162)
T ss_pred hhccHHHHHhhccCC--cc----hhhhhhHHHHHHHHHHHHHHHHHHhccchhHHHHHhhhhhhhcccccccch
Confidence 479999999999875 44 54 567889999999999999999999999999999999988887776543
No 50
>KOG1744|consensus
Probab=97.03 E-value=0.0036 Score=43.45 Aligned_cols=62 Identities=16% Similarity=0.274 Sum_probs=56.3
Q ss_pred HHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhc
Q psy13691 14 IIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQI 80 (103)
Q Consensus 14 ~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~l 80 (103)
.|+|+.|++-|+ .-|+.++...+.-....+...|+.+|+..+...||.||+..+|..|..-+
T Consensus 42 yv~kvlk~Vhpd-----~gis~~a~~vmnsf~ndife~iA~ea~rla~y~krstisSreiqta~rLl 103 (127)
T KOG1744|consen 42 YVYKVLKQVHPD-----LGISSKAMGVMNSFVNDIFERIASEAGRLAHYNKRSTISSREIQTAVRLL 103 (127)
T ss_pred ehhhhhhcccCC-----CCcCHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCcccHHHHHHHHHHh
Confidence 478899999886 46999999999999999999999999999999999999999999998643
No 51
>PF15510 CENP-W: Centromere kinetochore component W
Probab=96.94 E-value=0.0024 Score=42.22 Aligned_cols=66 Identities=23% Similarity=0.320 Sum_probs=54.0
Q ss_pred CCcHHHHHHHHHhhCCCCCcccccccHHHHHH--------------HHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHH
Q psy13691 9 NLPSAIIQRLIKEALPKDAEGKINVSKDVRLA--------------AGKAASLFILHLTTEALSIANEKNRKTLSGVDVI 74 (103)
Q Consensus 9 ~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~--------------l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~ 74 (103)
.-|++.+.|++|..=|. .++....-.+ +.-.|-.|++-|+-||...|=+++-.||.++||+
T Consensus 16 kaPrgfLkrv~Kr~Kph-----lRl~~~~Dllv~~~~f~~~~~~~~vhLncLLFvhrLAEEaRtnA~EnK~~~Ik~~Hv~ 90 (102)
T PF15510_consen 16 KAPRGFLKRVFKRQKPH-----LRLETSGDLLVRFCPFSGWQWGGEVHLNCLLFVHRLAEEARTNACENKCGTIKKEHVL 90 (102)
T ss_pred hCchHHHHHHHHhcCCc-----eeecccccHHHhhcccccccccceeehhHHHHHHHHHHHHHHHHHHHhhccccHHHHH
Confidence 46999999999987664 5665554444 5667889999999999998888899999999999
Q ss_pred Hhhhh
Q psy13691 75 EGVKQ 79 (103)
Q Consensus 75 ~Al~~ 79 (103)
.|-+.
T Consensus 91 AaaKv 95 (102)
T PF15510_consen 91 AAAKV 95 (102)
T ss_pred HHHHH
Confidence 98653
No 52
>PF02269 TFIID-18kDa: Transcription initiation factor IID, 18kD subunit; InterPro: IPR003195 This family includes the Spt3 yeast transcription factors and the 18 kDa subunit from human transcription initiation factor IID (TFIID-18). Determination of the crystal structure reveals an atypical histone fold [].; GO: 0006366 transcription from RNA polymerase II promoter; PDB: 1BH9_A 1BH8_A.
Probab=96.82 E-value=0.0019 Score=42.35 Aligned_cols=48 Identities=15% Similarity=0.183 Sum_probs=24.9
Q ss_pred ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691 31 INVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK 78 (103)
Q Consensus 31 ~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~ 78 (103)
-.-..|...+|-+....||..+...|..+|...|++.|+.+|++-+|+
T Consensus 18 ~~P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~rg~~~i~~eDl~F~lR 65 (93)
T PF02269_consen 18 EEPLPETVDLVEDIVREYIIELCQEAMEVAQRRGSKKIKVEDLLFLLR 65 (93)
T ss_dssp SS--HHHHHHHHHHHHHHHHHHHHHHHC--------------------
T ss_pred CCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCcCcHHHHHHHHh
Confidence 478899999999999999999999999999999999999999999997
No 53
>PTZ00252 histone H2A; Provisional
Probab=96.64 E-value=0.0088 Score=41.88 Aligned_cols=67 Identities=15% Similarity=0.161 Sum_probs=52.5
Q ss_pred CCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHh--CCCCCcChhhHHHhhh
Q psy13691 7 DLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANE--KNRKTLSGVDVIEGVK 78 (103)
Q Consensus 7 d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~--~~RkTI~~eDV~~Al~ 78 (103)
.+.||.+.|.|.+++.--. .||+.-|...|.-+.+-....+-..|-..|.. .+++-|+++||..|+.
T Consensus 23 GL~FPVgRi~R~Lr~g~ya-----~RIga~ApVYLAAVLEYLtaEVLELAgnaa~d~~~kk~RItPrHi~lAIr 91 (134)
T PTZ00252 23 GLIFPVGRVGSLLRRGQYA-----RRIGASGAVYMAAVLEYLTAELLELSVKAAAQQAKKPKRLTPRTVTLAVR 91 (134)
T ss_pred CccCchHHHHHHHHcCCcc-----cccCCccHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccccHHHHHhhcc
Confidence 5799999999999986332 59999999988887666555555556565643 5778899999999986
No 54
>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=96.38 E-value=0.083 Score=34.60 Aligned_cols=78 Identities=13% Similarity=0.071 Sum_probs=56.3
Q ss_pred HHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh----hcCchHHHHH
Q psy13691 13 AIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK----QIGFEVIIEI 88 (103)
Q Consensus 13 a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~----~lgf~~~~~~ 88 (103)
.-|..+|-...+. -.-..|...++-+....||..++.+|.+.|. .+|.-++.+|++-++. .++--.++-.
T Consensus 6 ~ei~~mmy~~GD~-----~~P~~eTv~llE~iv~~~i~~l~~~a~~~A~-~r~~k~~~eD~~FliR~D~~Kl~Rl~~lL~ 79 (92)
T cd07978 6 KEIRQMMYGFGDV-----QNPLPETVDLLEDIVVEYIIELCHKAAEVAQ-RRRGKVKVEDLIFLLRKDPKKLARLRELLS 79 (92)
T ss_pred HHHHHHHHHcCCC-----CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-cCCCCCCHHHHHHHHhcCHHHHHHHHHHHH
Confidence 3466777766443 3678899999999999999999999999998 4455569999999997 3333333333
Q ss_pred HHHHHHHH
Q psy13691 89 LGKSYNAA 96 (103)
Q Consensus 89 l~~~l~~~ 96 (103)
.+..+++.
T Consensus 80 ~k~~~k~a 87 (92)
T cd07978 80 MKDELKKA 87 (92)
T ss_pred HHHHHHHH
Confidence 44444433
No 55
>KOG3219|consensus
Probab=96.32 E-value=0.0065 Score=44.92 Aligned_cols=71 Identities=23% Similarity=0.347 Sum_probs=61.9
Q ss_pred CCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC-CCcChhhHHHhhhhcCchH
Q psy13691 8 LNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNR-KTLSGVDVIEGVKQIGFEV 84 (103)
Q Consensus 8 ~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~R-kTI~~eDV~~Al~~lgf~~ 84 (103)
..||++.|.|+|.+.... .|+.-+..++.-.+.+||-.|--+|.++|..-+. -.|.|.||-.|...|+...
T Consensus 111 s~f~Ka~iKkL~~~itg~------~v~~nv~Ia~~GiaKvFVGEvVEeAl~V~~~~~e~~PLqP~HIREA~rrL~~qg 182 (195)
T KOG3219|consen 111 SAFPKAQIKKLMSSITGQ------SVSENVAIAMAGIAKVFVGEVVEEALDVREEWGESGPLQPKHIREAYRRLKLQG 182 (195)
T ss_pred hcCCHHHHHHHHHHHhCC------ccCcceeeeecchhhHhHHHHHHHHHHHHHHhccCCCCCcHHHHHHHHHHHhcC
Confidence 479999999999999653 3999999999999999999999999999977654 4599999999999887643
No 56
>PF02291 TFIID-31kDa: Transcription initiation factor IID, 31kD subunit; InterPro: IPR003162 Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription []. TAFII-31 protein is a transcriptional coactivator of the p53 protein [].; GO: 0006352 transcription initiation, DNA-dependent; PDB: 1TAF_A.
Probab=95.28 E-value=0.15 Score=35.42 Aligned_cols=63 Identities=13% Similarity=0.035 Sum_probs=41.7
Q ss_pred cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh-hcCchHHHHHHHHHHH
Q psy13691 32 NVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK-QIGFEVIIEILGKSYN 94 (103)
Q Consensus 32 ~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~-~lgf~~~~~~l~~~l~ 94 (103)
.....+...|.+.+-.|+.-|-..|...|.+.||++|+.+||..|++ .+++.-.-++-++++-
T Consensus 29 ~yeprVv~qLLEfayRYt~~vL~DA~~ya~hA~~~~i~~~DVrLAi~~r~~~~f~~pppre~ll 92 (129)
T PF02291_consen 29 EYEPRVVNQLLEFAYRYTSDVLEDAQVYADHAGRSTIDADDVRLAIQSRLDHSFTQPPPREFLL 92 (129)
T ss_dssp -B-THHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHHHHT---------------
T ss_pred ccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHhhhccCCCChHHHH
Confidence 57788889999999999999999999999999999999999999999 5666655555555543
No 57
>KOG4336|consensus
Probab=95.27 E-value=0.17 Score=39.95 Aligned_cols=65 Identities=9% Similarity=0.045 Sum_probs=58.2
Q ss_pred cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCchHHHHHHHHHHHHHHh
Q psy13691 32 NVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFEVIIEILGKSYNAAVS 98 (103)
Q Consensus 32 ~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~~~~~l~~~l~~~k~ 98 (103)
.|++-|++.|.+....+|.-++.++...|...||...+.-||...|-++|+. +..|..+++.+-.
T Consensus 22 ~is~~aletlvell~~yi~eigrq~~n~celagRT~pT~~Dv~l~Li~mnI~--v~sL~~~~q~~~~ 86 (323)
T KOG4336|consen 22 SISNAALETLVELLQSYIREIGRQLHNYCELAGRTIPTQGDVKLTLIEMNIK--VSSLYAYFQKQEF 86 (323)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcHHHHHHHHHHhCCC--hhhhHHHHHhccc
Confidence 5999999999999999999999999999999999999999999999999997 4666666665543
No 58
>KOG3423|consensus
Probab=94.01 E-value=0.52 Score=34.33 Aligned_cols=70 Identities=20% Similarity=0.297 Sum_probs=55.5
Q ss_pred CCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC--------------CCCcChhhH
Q psy13691 8 LNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKN--------------RKTLSGVDV 73 (103)
Q Consensus 8 ~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~--------------RkTI~~eDV 73 (103)
..+|-+.+.-.++.+.=. ..-.-.+-++.=++..||.-|+..|.+.|+-.+ |-|++-+|+
T Consensus 85 P~IPDavt~~yL~~aGf~------~~D~rv~RLvsLaAQKfvSDIa~DA~Q~~k~r~~~~~~~~k~~~kdkK~tLtmeDL 158 (176)
T KOG3423|consen 85 PTIPDAVTDHYLKKAGFQ------TSDPRVKRLVSLAAQKFVSDIANDALQHSKIRTKTAIGKDKKQAKDKKYTLTMEDL 158 (176)
T ss_pred CCCcHHHHHHHHHhcCCC------cCcHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccccccccccccceeeeHHHH
Confidence 468888888888876321 234456788999999999999999999986433 458999999
Q ss_pred HHhhhhcCch
Q psy13691 74 IEGVKQIGFE 83 (103)
Q Consensus 74 ~~Al~~lgf~ 83 (103)
..||.+.|..
T Consensus 159 ~~AL~EyGin 168 (176)
T KOG3423|consen 159 SPALAEYGIN 168 (176)
T ss_pred HHHHHHhCcc
Confidence 9999999874
No 59
>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily. Members of this protein are marked as probable ATPases by the nucleotide binding P-loop motif GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of helicases, and extensive homology to ATPases of MSHA-type pilus systems and to GspA proteins associated with type II protein secretion systems.
Probab=93.67 E-value=0.36 Score=35.46 Aligned_cols=52 Identities=21% Similarity=0.154 Sum_probs=46.9
Q ss_pred ccccHHHHHHHHHHHHH---HHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCc
Q psy13691 31 INVSKDVRLAAGKAASL---FILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGF 82 (103)
Q Consensus 31 ~~iskda~~~l~~~~~~---Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf 82 (103)
..++.++...|.+.+.- .|+.++..|...+-..+.++|+.++|..++.++.|
T Consensus 214 ~~~~~~~~~~i~~~s~G~p~~i~~l~~~~~~~a~~~~~~~i~~~~v~~~~~~~~~ 268 (269)
T TIGR03015 214 PVFSEGAFDAIHRFSRGIPRLINILCDRLLLSAFLEEKREIGGEEVREVIAEIDF 268 (269)
T ss_pred CCcCHHHHHHHHHHcCCcccHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhhc
Confidence 46999999999999886 89999999999988889999999999999998764
No 60
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=93.15 E-value=0.99 Score=35.16 Aligned_cols=73 Identities=14% Similarity=0.090 Sum_probs=50.3
Q ss_pred HHHHHHHHHhhCCCCCcccccccHHHHHHHHHHH------HHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCchHH
Q psy13691 12 SAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAA------SLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFEVI 85 (103)
Q Consensus 12 ~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~------~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~~ 85 (103)
..-+..|++..+... -....++.++.+.+.+.+ -..+..+...|...|...++.+|+.+||..|++.+....+
T Consensus 209 ~~e~~~il~~r~~~~-~~~~~~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~a~~~a~~~~~~~I~~~~v~~a~~~~~~~~~ 287 (394)
T PRK00411 209 ADEIFDILKDRVEEG-FYPGVVDDEVLDLIADLTAREHGDARVAIDLLRRAGLIAEREGSRKVTEEDVRKAYEKSEIVHL 287 (394)
T ss_pred HHHHHHHHHHHHHhh-cccCCCCHhHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHHHHHH
Confidence 445555655543211 001358899988887766 3345566678888899999999999999999998854433
No 61
>KOG2389|consensus
Probab=92.21 E-value=0.45 Score=38.13 Aligned_cols=69 Identities=10% Similarity=0.128 Sum_probs=58.5
Q ss_pred CCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCch
Q psy13691 9 NLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFE 83 (103)
Q Consensus 9 ~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~ 83 (103)
.|-+..|..|+....-+ ....-|.+.|+.-+..||+-|+..|...+...||.-.+..||..||++|+..
T Consensus 29 sla~~avaQIcqslg~~------~~~~sale~Ltd~~~qyvQ~lgk~a~~~~n~anR~epnl~Div~Al~dls~s 97 (353)
T KOG2389|consen 29 SLARVAVAQICQSLGYS------STQNSALETLTDVLQQYVQNLGKTAHRYSNLANRTEPNLFDIVLALQDLSAS 97 (353)
T ss_pred HHHHHHHHHHHHhcCCc------ccccHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCccHHHHHHHHHHhhhh
Confidence 45667788888776332 3445599999999999999999999999999999999999999999988765
No 62
>KOG2549|consensus
Probab=91.85 E-value=1.1 Score=37.91 Aligned_cols=65 Identities=17% Similarity=0.237 Sum_probs=54.2
Q ss_pred cHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcC
Q psy13691 11 PSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIG 81 (103)
Q Consensus 11 P~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lg 81 (103)
|...+.-++ +++.- ..++.|+..+|..=.+.=|..++.+|.+.-.+.+|.+++.+||..||+.+.
T Consensus 13 ~~Es~k~vA-EslGi-----~nl~deaa~~La~dv~yrikEI~Q~aaKfm~hskR~kLtv~DV~~ALr~~n 77 (576)
T KOG2549|consen 13 PKESVKVVA-ESLGI-----TNLNDEAALLLAEDVEYRIKEIVQDAAKFMVHSKRTKLTVDDVDYALRSLN 77 (576)
T ss_pred cHHHHHHHH-HHhCc-----cccCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcCcHHHHHHHHhhcc
Confidence 345554444 44443 369999999999999999999999999999999999999999999999553
No 63
>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=91.40 E-value=2.2 Score=32.74 Aligned_cols=78 Identities=13% Similarity=0.102 Sum_probs=50.2
Q ss_pred HHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHH------HHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCchHH
Q psy13691 12 SAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAAS------LFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFEVI 85 (103)
Q Consensus 12 ~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~------~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~~ 85 (103)
..-+..|++..+... ..+..++.|+...+.+.+. -.+..+...|.+.|..+++.+|+.+||..|++.+..+.+
T Consensus 201 ~~e~~~il~~r~~~~-~~~~~~~~~~l~~i~~~~~~~~Gd~R~al~~l~~a~~~a~~~~~~~it~~~v~~a~~~~~~~~~ 279 (365)
T TIGR02928 201 AEELRDILENRAEKA-FYDGVLDDGVIPLCAALAAQEHGDARKAIDLLRVAGEIAEREGAERVTEDHVEKAQEKIEKDRL 279 (365)
T ss_pred HHHHHHHHHHHHHhh-ccCCCCChhHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHH
Confidence 344556665544210 0003588888777665442 244456667888888889999999999999998865555
Q ss_pred HHHHH
Q psy13691 86 IEILG 90 (103)
Q Consensus 86 ~~~l~ 90 (103)
...+.
T Consensus 280 ~~~i~ 284 (365)
T TIGR02928 280 LELIR 284 (365)
T ss_pred HHHHH
Confidence 44333
No 64
>KOG1757|consensus
Probab=88.04 E-value=1.1 Score=30.76 Aligned_cols=64 Identities=19% Similarity=0.260 Sum_probs=48.4
Q ss_pred CCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhC----CCCCcChhhHHHhhh
Q psy13691 7 DLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEK----NRKTLSGVDVIEGVK 78 (103)
Q Consensus 7 d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~----~RkTI~~eDV~~Al~ 78 (103)
-+.||..+|.|..|.-.... .++..-+..- ..-.+.|||.|-.+.|.+. +-|.|+|.|+..|+.
T Consensus 28 GlqFpVgRihr~LK~r~t~h----~rVGataavy----~aaileYLTaEVLeLAgNasKdLKvKRitprHlqLAiR 95 (131)
T KOG1757|consen 28 GLQFPVGRIHRHLKTRTTSH----GRVGATAAVY----SAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 95 (131)
T ss_pred ccccchHHHHHHHHHhcccc----cccchHHHHH----HHHHHHHHHHHHHHHcccccccceeeeccchhheeeec
Confidence 46899999999999987765 6776544433 2345789999888877654 457899999998876
No 65
>PF13654 AAA_32: AAA domain; PDB: 3K1J_B.
Probab=87.23 E-value=4.3 Score=33.93 Aligned_cols=49 Identities=12% Similarity=0.123 Sum_probs=38.5
Q ss_pred cccHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhc
Q psy13691 32 NVSKDVRLAAGKAASL-----------FILHLTTEALSIANEKNRKTLSGVDVIEGVKQI 80 (103)
Q Consensus 32 ~iskda~~~l~~~~~~-----------Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~l 80 (103)
.++.+|...|.+.+.. -|.-|-.+|+..|...+++.|+++||..|++.-
T Consensus 447 ~~~~~Av~~li~~~~R~~q~kLsl~~~~l~~ll~EA~~~A~~~~~~~I~~~~V~~Ai~~r 506 (509)
T PF13654_consen 447 PFDRSAVARLIEYSARLDQDKLSLRFSWLADLLREANYWARKEGAKVITAEHVEQAIEER 506 (509)
T ss_dssp -BBHHHHHHHHHHHHHCC-SEEE--HHHHHHHHHHHHHHHHHCT-SSB-HHHHHHHHHH-
T ss_pred CCCHHHHHHHHHHHHHHhCCEeCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHcc
Confidence 4788888887776653 567788999999999999999999999999753
No 66
>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=85.50 E-value=3.4 Score=34.47 Aligned_cols=68 Identities=24% Similarity=0.131 Sum_probs=45.9
Q ss_pred HHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHH--HHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCc
Q psy13691 12 SAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASL--FILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGF 82 (103)
Q Consensus 12 ~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~--Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf 82 (103)
..-+.+|++..+... ...+++++...|.+.+.. .+..+...|..+|..++|++|+.+||.+++..-.|
T Consensus 265 ~eei~~Il~~~a~k~---~i~is~~al~~I~~y~~n~Rel~nll~~Aa~~A~~~~~~~It~~dI~~vl~~~~~ 334 (531)
T TIGR02902 265 DEEIKEIAKNAAEKI---GINLEKHALELIVKYASNGREAVNIVQLAAGIALGEGRKRILAEDIEWVAENGNY 334 (531)
T ss_pred HHHHHHHHHHHHHHc---CCCcCHHHHHHHHHhhhhHHHHHHHHHHHHHHHhhCCCcEEcHHHHHHHhCCccc
Confidence 344555666655432 267999999988777652 22233345666788889999999999999765444
No 67
>PF13335 Mg_chelatase_2: Magnesium chelatase, subunit ChlI
Probab=83.84 E-value=5.8 Score=25.76 Aligned_cols=48 Identities=15% Similarity=0.183 Sum_probs=41.5
Q ss_pred ccccHHHHHHHHHHHHHH------HHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691 31 INVSKDVRLAAGKAASLF------ILHLTTEALSIANEKNRKTLSGVDVIEGVK 78 (103)
Q Consensus 31 ~~iskda~~~l~~~~~~F------i~~lt~~A~~~a~~~~RkTI~~eDV~~Al~ 78 (103)
..+++++..+|..++..| .+-|..-|..+|--++...|..+||..||.
T Consensus 41 ~~l~~~~~~~l~~~~~~~~lS~R~~~rilrvARTIADL~~~~~I~~~hi~EAl~ 94 (96)
T PF13335_consen 41 CPLSSEAKKLLEQAAEKLNLSARGYHRILRVARTIADLEGSERITREHIAEALS 94 (96)
T ss_pred cCCCHHHHHHHHHHHHHcCcCHHHHHHHHHHHHHHHhHcCCCCCCHHHHHHHHh
Confidence 468889999999888876 566778899999999999999999999984
No 68
>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=83.30 E-value=4.9 Score=32.47 Aligned_cols=52 Identities=19% Similarity=0.190 Sum_probs=48.7
Q ss_pred cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCch
Q psy13691 32 NVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFE 83 (103)
Q Consensus 32 ~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~ 83 (103)
.|.+|+..++..-.+-=|+.+..+|..--.+.||..++-+||..||..+..+
T Consensus 22 Ni~Dd~l~alamDlEYRI~ev~qea~KFmvhSKRtvLt~dDis~ALr~lNVe 73 (450)
T COG5095 22 NIDDDALRALAMDLEYRIKEVCQEASKFMVHSKRTVLTIDDISYALRSLNVE 73 (450)
T ss_pred ccccHHHHHHHHhHHHHHHHHHHHHHHHhhcccceeeeHHhHHHHHHhcCCC
Confidence 7999999999999999999999999999999999999999999999987654
No 69
>TIGR00764 lon_rel lon-related putative ATP-dependent protease. Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein.
Probab=83.14 E-value=7.5 Score=33.08 Aligned_cols=50 Identities=16% Similarity=0.103 Sum_probs=40.6
Q ss_pred cccHHHHHHHHHHHH-------------HHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcC
Q psy13691 32 NVSKDVRLAAGKAAS-------------LFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIG 81 (103)
Q Consensus 32 ~iskda~~~l~~~~~-------------~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lg 81 (103)
.++++|...|.+.++ .=+.-|-.+|..+|..+++.+|+.+||.+|++.-.
T Consensus 330 ~~s~~Av~~Li~~~~R~ag~r~~lsl~~R~L~~llR~A~~iA~~~~~~~I~~ehV~~Ai~~~~ 392 (608)
T TIGR00764 330 HFTRDAVEEIVREAQRRAGRKDHLTLRLRELGGLVRAAGDIAKSSGKVYVTAEHVLKAKKLAK 392 (608)
T ss_pred cCCHHHHHHHHHHHHHHHhcccccCCCHHHHHHHHHHHHHHHHhcCCceecHHHHHHHHHHHH
Confidence 589999988876554 34556778898899999999999999999987553
No 70
>COG1067 LonB Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]
Probab=82.78 E-value=1.7 Score=37.38 Aligned_cols=49 Identities=27% Similarity=0.238 Sum_probs=35.6
Q ss_pred cccHHHHHHHHHHHHHH-------------HHHHHHHHHHHHHhCCCCCcChhhHHHhhhhc
Q psy13691 32 NVSKDVRLAAGKAASLF-------------ILHLTTEALSIANEKNRKTLSGVDVIEGVKQI 80 (103)
Q Consensus 32 ~iskda~~~l~~~~~~F-------------i~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~l 80 (103)
-++++|..-|.+-+..- +.-|-.+|..+|..+|++-|+++||.+|++.-
T Consensus 338 ~~~~~Av~~li~~a~R~Ag~~~~Ltl~~rdl~~lv~~A~~ia~~~~~~~I~ae~Ve~a~~~~ 399 (647)
T COG1067 338 HLDKDAVEELIREAARRAGDQNKLTLRLRDLGNLVREAGDIAVSEGRKLITAEDVEEALQKR 399 (647)
T ss_pred CCCHHHHHHHHHHHHHhccccceeccCHHHHHHHHHHhhHHHhcCCcccCcHHHHHHHHHhh
Confidence 36666665555444322 23334489999999999999999999999873
No 71
>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=81.09 E-value=3 Score=23.68 Aligned_cols=42 Identities=12% Similarity=0.120 Sum_probs=26.9
Q ss_pred cHHHHHHHHHHHHHHHHHHHH-HHHHHHHhCCCCCcChhhHHHh
Q psy13691 34 SKDVRLAAGKAASLFILHLTT-EALSIANEKNRKTLSGVDVIEG 76 (103)
Q Consensus 34 skda~~~l~~~~~~Fi~~lt~-~A~~~a~~~~RkTI~~eDV~~A 76 (103)
+.||...|.+. =.|+.--.. .+-..|.+.|...|+.++|..|
T Consensus 2 ~~eA~~~L~~i-P~fvR~~~r~~~E~~Ar~~G~~~IT~e~v~~A 44 (45)
T PF08369_consen 2 TDEAEARLDRI-PFFVRKKLRDAAEKYARERGYDEITVEVVDAA 44 (45)
T ss_dssp -HHHHHHHCTS--HHHHHHHHHHHHHHHHHCT-SEE-HHHHHHH
T ss_pred CHHHHHHHHHC-CHHHHHHHHHHHHHHHHHcCCCeECHHHHHhh
Confidence 46677776665 446654444 4446789999999999998876
No 72
>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=80.25 E-value=21 Score=26.21 Aligned_cols=77 Identities=14% Similarity=0.104 Sum_probs=56.5
Q ss_pred cCCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhC------CCCCcChhhHHHhhhh
Q psy13691 6 DDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEK------NRKTLSGVDVIEGVKQ 79 (103)
Q Consensus 6 ~d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~------~RkTI~~eDV~~Al~~ 79 (103)
+...|....+.+.|...+...+ -..++.|...+|..||+.++..|-......|++- ...+.-..||-.-|..
T Consensus 41 ~~~fl~~~~l~~~~~~i~~~~g--~~~~~~d~~~lis~a~e~rlr~li~k~~~~s~hR~~~~~~~~r~~~~sdvr~qL~~ 118 (212)
T cd08045 41 DPSFLNPSPLAKKIRKIAKKHG--LKEVDEDVLDLISLALEERLRNLLEKLIEVSEHRVDSEKEDERYEITSDVRKQLRF 118 (212)
T ss_pred hhhccCHHHHHHHHHHHHHHcC--CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCceeecchHHHHHHH
Confidence 3456777777777777766541 1169999999999999999999999998888763 3355667788777765
Q ss_pred cCchH
Q psy13691 80 IGFEV 84 (103)
Q Consensus 80 lgf~~ 84 (103)
|+--+
T Consensus 119 l~~~e 123 (212)
T cd08045 119 LEQLE 123 (212)
T ss_pred HHHHH
Confidence 55443
No 73
>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=79.57 E-value=2 Score=23.92 Aligned_cols=25 Identities=16% Similarity=0.205 Sum_probs=20.1
Q ss_pred HHHHHHhCCCCCcChhhHHHhhhhc
Q psy13691 56 ALSIANEKNRKTLSGVDVIEGVKQI 80 (103)
Q Consensus 56 A~~~a~~~~RkTI~~eDV~~Al~~l 80 (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 5678999999999999999996443
No 74
>KOG3334|consensus
Probab=78.83 E-value=6 Score=28.16 Aligned_cols=55 Identities=11% Similarity=-0.010 Sum_probs=43.9
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCchHHHH
Q psy13691 33 VSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFEVIIE 87 (103)
Q Consensus 33 iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~~~~ 87 (103)
...-...-|.+.+--++.-+-..|.-.+.+.++.||..+||..|++..+=.+|..
T Consensus 31 yEprVi~qlLefa~rYtt~vL~DA~vys~HA~ka~i~~eDVrlA~~~~~~~sf~~ 85 (148)
T KOG3334|consen 31 YEPRVINQLLEFAYRYTTTVLDDAKVYSSHAKKATIDAEDVRLAIQMRVDHSFTP 85 (148)
T ss_pred cChHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHhccccCC
Confidence 4444555667777788888889999999999999999999999999666555544
No 75
>PRK09862 putative ATP-dependent protease; Provisional
Probab=77.88 E-value=14 Score=31.02 Aligned_cols=61 Identities=13% Similarity=0.076 Sum_probs=47.2
Q ss_pred ccccHHHHHHHHHHHHHH------HHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCchHHHHHHHH
Q psy13691 31 INVSKDVRLAAGKAASLF------ILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFEVIIEILGK 91 (103)
Q Consensus 31 ~~iskda~~~l~~~~~~F------i~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~~~~~l~~ 91 (103)
..++.++...+..+...+ .+.|..-|..+|--++|..|+++||..|+.--+++..+-.+..
T Consensus 437 ~~l~~~~~~~l~~~~~~~~lS~Ra~~rlLrvARTiADL~g~~~V~~~hv~eAl~yR~~~~~~~~~~~ 503 (506)
T PRK09862 437 CKLESEDARWLEETLIHLGLSIRAWQRLLKVARTIADIDQSDIITRQHLQEAVSYRAIDRLLIHLQK 503 (506)
T ss_pred hCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHhhcccHHHHHHHH
Confidence 467888888877765544 5677788889999999999999999999987666655544443
No 76
>KOG2680|consensus
Probab=73.43 E-value=22 Score=28.98 Aligned_cols=49 Identities=16% Similarity=0.190 Sum_probs=40.7
Q ss_pred cccccHHHHHHHHHHHHH----HHHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691 30 KINVSKDVRLAAGKAASL----FILHLTTEALSIANEKNRKTLSGVDVIEGVK 78 (103)
Q Consensus 30 ~~~iskda~~~l~~~~~~----Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~ 78 (103)
++.++.||++.|.+..+. |-.+|-+.|+.+|.+.|-+++..+||-.+.+
T Consensus 375 dv~m~~~A~d~Lt~i~~~tsLRYai~Lit~a~~~~~krk~~~v~~~di~r~y~ 427 (454)
T KOG2680|consen 375 DVEMNPDALDLLTKIGEATSLRYAIHLITAASLVCLKRKGKVVEVDDIERVYR 427 (454)
T ss_pred ccccCHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHhcCceeehhHHHHHHH
Confidence 488999999999876543 5556666788999999999999999999964
No 77
>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]
Probab=72.35 E-value=29 Score=27.76 Aligned_cols=58 Identities=21% Similarity=0.212 Sum_probs=42.5
Q ss_pred cccHHHHHHHHHHH------HHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCchHHHHHH
Q psy13691 32 NVSKDVRLAAGKAA------SLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFEVIIEIL 89 (103)
Q Consensus 32 ~iskda~~~l~~~~------~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~~~~~l 89 (103)
.++.++..++..-+ ..+...+...|-++|+.+++.+++.+||..|-+..+..-+...+
T Consensus 211 ~~~~~vl~lia~~~a~~~GDAR~aidilr~A~eiAe~~~~~~v~~~~v~~a~~~~~~~~~~~~~ 274 (366)
T COG1474 211 VIDDDVLKLIAALVAAESGDARKAIDILRRAGEIAEREGSRKVSEDHVREAQEEIERDVLEEVL 274 (366)
T ss_pred CcCccHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHhhCCCCcCHHHHHHHHHHhhHHHHHHHH
Confidence 56666666555322 23556677889999999999999999999997777766555543
No 78
>PF09114 MotA_activ: Transcription factor MotA, activation domain; InterPro: IPR015198 Transcription factor MotA is required for the activation of middle promoters in Bacteriophage T4, in addition to phage T4 co-activator AsiA, and sigma-70-containing Escherichia coli RNA polymerase. Phage T4 middle promoters have the sigma70 -10 DNA element, but not the -35 element; instead, they have a MotA box at -30 to which the transcription factor MotA binds []. MotA and AsiA interact with the C-terminal of sigma70 (region 4), which normally binds the -35 element and the beta-flap, thereby diverting sigma70 away from host promoters that require -35 element-binding to phage T4 middle promoters. Transcription factor MotA has two domains: an N-terminal domain required for binding to sigma70, and a C-terminal domain required for binding to the -30 MotA box element in the phage T4 middle promoter. This entry represents the N-terminal (activation) domain of MotA factors that binds sigma70. The N-terminal domain adopts an almost completely alpha-helical topology, with five alpha-helices and a short, two-stranded, beta-ribbon. Four alpha helices (alpha1, alpha3, alpha4 and alpha5) are amphipathic and pack their hydrophobic surfaces around the central helix alpha2 [].; PDB: 1BJA_B 1I1S_A.
Probab=69.99 E-value=5.3 Score=26.40 Aligned_cols=38 Identities=21% Similarity=0.180 Sum_probs=28.4
Q ss_pred HHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHH
Q psy13691 13 AIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFIL 50 (103)
Q Consensus 13 a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~ 50 (103)
++|.+++|..|=+..+....++.++.+.++++++.|-.
T Consensus 51 SNIGvLIKkglIEKSGDGlv~T~~g~~Ii~~AA~l~a~ 88 (96)
T PF09114_consen 51 SNIGVLIKKGLIEKSGDGLVITEEGMDIIIQAAELWAQ 88 (96)
T ss_dssp HHHHHHHHTTSEEEETTEEEE-HHHHHHHHHHHHHHHH
T ss_pred HhHHHHHHcCcccccCCceEEechHHHHHHHHHHHHHh
Confidence 56788999877543222288999999999999999854
No 79
>cd04752 Commd4 COMM_Domain containing protein 4. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=68.95 E-value=22 Score=25.32 Aligned_cols=49 Identities=18% Similarity=0.257 Sum_probs=36.1
Q ss_pred HHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCch-HHHHHHHHHHHHHHhc
Q psy13691 44 AASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFE-VIIEILGKSYNAAVSI 99 (103)
Q Consensus 44 ~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~-~~~~~l~~~l~~~k~~ 99 (103)
++...+.||-..|. |.-++++++..-|+.+||+ +.++.+...+..+++.
T Consensus 43 ~~va~l~fiL~~A~-------k~n~~~~~l~~eL~~lglp~e~~~~l~~~~~~~~~~ 92 (174)
T cd04752 43 ASIAVLSFILSSAA-------KYNVDGESLSSELQQLGLPKEHATSLCRSYEEKQSK 92 (174)
T ss_pred HHHHHHHHHHHHHH-------HcCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHH
Confidence 55666777776663 3459999999999999998 5667777776666653
No 80
>TIGR00368 Mg chelatase-related protein. The N-terminal end matches very strongly a pfam Mg_chelatase domain.
Probab=68.51 E-value=17 Score=30.38 Aligned_cols=47 Identities=19% Similarity=0.131 Sum_probs=41.3
Q ss_pred cccHHHHHHHHHHHHHH------HHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691 32 NVSKDVRLAAGKAASLF------ILHLTTEALSIANEKNRKTLSGVDVIEGVK 78 (103)
Q Consensus 32 ~iskda~~~l~~~~~~F------i~~lt~~A~~~a~~~~RkTI~~eDV~~Al~ 78 (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 56889999999998887 566778899999999999999999999984
No 81
>COG5162 Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=67.75 E-value=46 Score=24.41 Aligned_cols=69 Identities=14% Similarity=0.291 Sum_probs=47.1
Q ss_pred CCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHh-------------------C------
Q psy13691 9 NLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANE-------------------K------ 63 (103)
Q Consensus 9 ~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~-------------------~------ 63 (103)
.+|-+.+.=.+..+ + =.....-.+.++.-.+..||.-|+..|++..+= .
T Consensus 88 liPd~v~DYyl~k~---G---f~~~D~rvKkLl~L~aqKFvsDiA~dayqYsrIr~~~sna~~t~~~a~~f~~gg~~~i~ 161 (197)
T COG5162 88 LIPDSVTDYYLEKA---G---FVTSDQRVKKLLSLLAQKFVSDIAVDAYQYSRIRQGSSNAKATAQKAKRFAKGGASGIG 161 (197)
T ss_pred CccHHHHHHHHHhc---C---ceeccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccchhhHHHHHHHHhccccccc
Confidence 45555555444443 1 123445567888999999999999888765421 1
Q ss_pred --------CCCCcChhhHHHhhhhcCch
Q psy13691 64 --------NRKTLSGVDVIEGVKQIGFE 83 (103)
Q Consensus 64 --------~RkTI~~eDV~~Al~~lgf~ 83 (103)
++-+++..|+..||++.|+.
T Consensus 162 ~~~~~~dr~K~vltv~DLs~Al~EyGin 189 (197)
T COG5162 162 SSGRRGDRKKPVLTVVDLSKALEEYGIN 189 (197)
T ss_pred ccccccccCCceeeehHHHHHHHHhccc
Confidence 45678999999999988874
No 82
>PF12010 DUF3502: Domain of unknown function (DUF3502); InterPro: IPR022627 This domain is about 140 amino acids in length and is functionally uncharacterised. It is found in bacteria C-terminal to PF01547 from PFAM.
Probab=67.03 E-value=9 Score=26.18 Aligned_cols=63 Identities=13% Similarity=0.123 Sum_probs=42.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCchHHHHHHHHHHHHHHhccc
Q psy13691 35 KDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFEVIIEILGKSYNAAVSIKV 101 (103)
Q Consensus 35 kda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~~~~~l~~~l~~~k~~~~ 101 (103)
...+.-|..|..+.-.|......-.. ----.-..+...|+..|++..+.+++..+++|+..++
T Consensus 72 s~Vk~Eiaa~~~v~~~Y~~~L~~G~v----d~e~~~~~~~~kLk~AGidkV~~E~QkQlda~~~~~k 134 (134)
T PF12010_consen 72 SPVKNEIAACSNVWSEYYPPLETGLV----DPEEALPEFNEKLKAAGIDKVIAELQKQLDAFLAANK 134 (134)
T ss_pred chhHHHHHHHHHHHHHHHHHHHccCC----CHHHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHhcC
Confidence 34556667777766666554332211 0011245677888999999999999999999988653
No 83
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=66.93 E-value=34 Score=26.24 Aligned_cols=71 Identities=8% Similarity=0.130 Sum_probs=47.9
Q ss_pred CcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHH---HHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCch
Q psy13691 10 LPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASL---FILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFE 83 (103)
Q Consensus 10 LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~---Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~ 83 (103)
++...+..|++...... ++.++.|+...|.+.|.- .+..+...+.+.+...+.+.|+.+++..+++.++..
T Consensus 180 ~~~~e~~~il~~~~~~~---~~~~~~~~~~~ia~~~~G~pR~a~~~l~~~~~~a~~~~~~~I~~~~v~~~l~~~~~~ 253 (328)
T PRK00080 180 YTVEELEKIVKRSARIL---GVEIDEEGALEIARRSRGTPRIANRLLRRVRDFAQVKGDGVITKEIADKALDMLGVD 253 (328)
T ss_pred CCHHHHHHHHHHHHHHc---CCCcCHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCC
Confidence 34445555555443321 278999999888877743 344455556666766667789999999999987665
No 84
>COG5251 TAF40 Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=66.92 E-value=7 Score=28.77 Aligned_cols=62 Identities=15% Similarity=0.219 Sum_probs=49.6
Q ss_pred CCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCC---CcChhhHHHhhh
Q psy13691 9 NLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRK---TLSGVDVIEGVK 78 (103)
Q Consensus 9 ~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~Rk---TI~~eDV~~Al~ 78 (103)
.||++.|.+++...+.. .|+...+.+++-.+.+|+-.+--.|..+- +++. .+.+.|+-.|..
T Consensus 115 ~lnKt~VKKlastV~nQ------tVspNi~I~l~g~~KVfvGEiIElA~~Vq--~~w~~sgpl~p~h~reayr 179 (199)
T COG5251 115 SLNKTQVKKLASTVANQ------TVSPNIRIFLQGVGKVFVGEIIELAMIVQ--NKWLTSGPLIPFHKREAYR 179 (199)
T ss_pred CCCHHHHHHHHHHHhcc------ccCCCeeeeeechhHHHHHHHHHHHHHHH--HHhcccCCCChHHHHHHHH
Confidence 79999999999999865 48888899999999999998887775543 2333 488888887764
No 85
>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=65.99 E-value=25 Score=20.67 Aligned_cols=48 Identities=15% Similarity=0.235 Sum_probs=36.6
Q ss_pred CCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy13691 9 NLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANE 62 (103)
Q Consensus 9 ~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~ 62 (103)
.+|-+.+.-+++.+.=+. -..-..-++.=++..||.-++..|.+.|+-
T Consensus 2 ~IPD~v~~~yL~~~G~~~------~D~rv~RLvSLaaQKFisdI~~dA~q~~k~ 49 (51)
T PF03540_consen 2 TIPDEVTDYYLERSGFQT------SDPRVKRLVSLAAQKFISDIANDAMQYCKI 49 (51)
T ss_pred CCCHHHHHHHHHHCCCCC------CCHhHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 478888888888874321 223345688899999999999999998864
No 86
>TIGR02442 Cob-chelat-sub cobaltochelatase subunit. A number of genomes (actinobacteria, cyanobacteria, betaproteobacteria and pseudomonads) which apparently biosynthesize B12, encode a cobN gene but are demonstrably lacking cobS and cobT. These genomes do, however contain a homolog (modelled here) of the magnesium chelatase subunits BchI/BchD family. Aside from the cyanobacteria (which have a separate magnesium chelatase trimer), these species do not make chlorins, so do not have any use for a magnesium chelatase. Furthermore, in nearly all cases the members of this family are proximal to either CobN itself or other genes involved in cobalt transport or B12 biosynthesis.
Probab=64.62 E-value=35 Score=29.10 Aligned_cols=48 Identities=17% Similarity=0.218 Sum_probs=40.8
Q ss_pred ccccHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691 31 INVSKDVRLAAGKAASLFI-------LHLTTEALSIANEKNRKTLSGVDVIEGVK 78 (103)
Q Consensus 31 ~~iskda~~~l~~~~~~Fi-------~~lt~~A~~~a~~~~RkTI~~eDV~~Al~ 78 (103)
+.|+.+....+...+..+- .++..-|..+|--+||.+|+.+||..|++
T Consensus 248 V~is~~~~~~l~~~~~~~~i~s~Ra~i~~~r~Ara~AaL~gr~~V~~~Dv~~A~~ 302 (633)
T TIGR02442 248 VRISDSLIRFISELCIEFGVDGHRADIVMARAARALAALDGRRRVTAEDVREAAE 302 (633)
T ss_pred CCCCHHHHHHHHHHHHHhCCCCccHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHH
Confidence 7899999999999887762 45667777888999999999999999986
No 87
>KOG3901|consensus
Probab=62.84 E-value=31 Score=23.33 Aligned_cols=45 Identities=18% Similarity=0.116 Sum_probs=37.3
Q ss_pred ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691 31 INVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK 78 (103)
Q Consensus 31 ~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~ 78 (103)
..=-.|..+++-....+||..++..|..+. +|--+..||+.-+|+
T Consensus 26 ~nP~~~tv~~Le~iV~~Yi~elt~~a~~~g---~rgk~~veD~~f~lR 70 (109)
T KOG3901|consen 26 VNPYPETVDLLEDIVLEYITELTHAAMEIG---KRGKVKVEDFKFLLR 70 (109)
T ss_pred CCccHhHHHHHHHHHHHHHHHHHHHHHHhc---ccCceeHHHHHHHHH
Confidence 455678899999999999999977777765 566788999999987
No 88
>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=62.71 E-value=50 Score=26.13 Aligned_cols=48 Identities=17% Similarity=0.173 Sum_probs=38.2
Q ss_pred ccccHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691 31 INVSKDVRLAAGKAASLFI-------LHLTTEALSIANEKNRKTLSGVDVIEGVK 78 (103)
Q Consensus 31 ~~iskda~~~l~~~~~~Fi-------~~lt~~A~~~a~~~~RkTI~~eDV~~Al~ 78 (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 7899999888888766552 34556677788889999999999998765
No 89
>PRK13765 ATP-dependent protease Lon; Provisional
Probab=62.69 E-value=16 Score=31.43 Aligned_cols=48 Identities=19% Similarity=0.095 Sum_probs=38.8
Q ss_pred cccHHHHHHHHHHHHHH-------------HHHHHHHHHHHHHhCCCCCcChhhHHHhhhh
Q psy13691 32 NVSKDVRLAAGKAASLF-------------ILHLTTEALSIANEKNRKTLSGVDVIEGVKQ 79 (103)
Q Consensus 32 ~iskda~~~l~~~~~~F-------------i~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~ 79 (103)
.++.+|...|.+-++.- +.-|-.+|..+|..++++.|+.+||..|+..
T Consensus 339 ~f~~eAVa~LI~~~~R~ag~r~~lsl~~~~l~~l~r~a~~~a~~~~~~~i~~~~v~~a~~~ 399 (637)
T PRK13765 339 HFDRDAVEEIIREAKRRAGRKGHLTLKLRDLGGLVRVAGDIARSEGAELTTAEHVLEAKKI 399 (637)
T ss_pred CCCHHHHHHHHHHHHHHhCCccccccCHHHHHHHHHHHHHHHHhhccceecHHHHHHHHHh
Confidence 58899888887766633 3347788999999999999999999999743
No 90
>cd00166 SAM Sterile alpha motif.; Widespread domain in signalling and nuclear proteins. In EPH-related tyrosine kinases, appears to mediate cell-cell initiated signal transduction via the binding of SH2-containing proteins to a conserved tyrosine that is phosphorylated. In many cases mediates homodimerization.
Probab=61.69 E-value=11 Score=21.16 Aligned_cols=23 Identities=22% Similarity=0.270 Sum_probs=19.6
Q ss_pred ChhhHHHhhhhcCchHHHHHHHH
Q psy13691 69 SGVDVIEGVKQIGFEVIIEILGK 91 (103)
Q Consensus 69 ~~eDV~~Al~~lgf~~~~~~l~~ 91 (103)
++++|..-|+.+|+++|.+...+
T Consensus 3 ~~~~V~~wL~~~~~~~y~~~f~~ 25 (63)
T cd00166 3 SPEDVAEWLESLGLGQYADNFRE 25 (63)
T ss_pred CHHHHHHHHHHcChHHHHHHHHH
Confidence 67889999999999999887755
No 91
>PRK07452 DNA polymerase III subunit delta; Validated
Probab=61.39 E-value=37 Score=25.80 Aligned_cols=55 Identities=15% Similarity=0.061 Sum_probs=43.1
Q ss_pred ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHh--CCCCCcChhhHHHhhhhcCchHH
Q psy13691 31 INVSKDVRLAAGKAASLFILHLTTEALSIANE--KNRKTLSGVDVIEGVKQIGFEVI 85 (103)
Q Consensus 31 ~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~--~~RkTI~~eDV~~Al~~lgf~~~ 85 (103)
..|+.+|...|...+..=...+..+-...+.- .++.+|+.+||...+....+.-|
T Consensus 148 ~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~~It~~~V~~~v~~~~~~if 204 (326)
T PRK07452 148 VKLTPEAAELLAEAVGNDSRRLYNELEKLALYAENSTKPISAEEVKALVSNTTQNSL 204 (326)
T ss_pred CCCCHHHHHHHHHHhCccHHHHHHHHHHHHHhccCCCCccCHHHHHHHhccCcCcHH
Confidence 78999999999999887666666666676665 45788999999998876665433
No 92
>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=60.99 E-value=39 Score=25.28 Aligned_cols=53 Identities=8% Similarity=0.161 Sum_probs=39.1
Q ss_pred ccccHHHHHHHHHHHHH---HHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCch
Q psy13691 31 INVSKDVRLAAGKAASL---FILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFE 83 (103)
Q Consensus 31 ~~iskda~~~l~~~~~~---Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~ 83 (103)
..++.++...|.+.+.- ++..+...+...+...+...|+.++|..++..++++
T Consensus 177 ~~~~~~al~~ia~~~~G~pR~~~~ll~~~~~~a~~~~~~~it~~~v~~~l~~l~~~ 232 (305)
T TIGR00635 177 VEIEPEAALEIARRSRGTPRIANRLLRRVRDFAQVRGQKIINRDIALKALEMLMID 232 (305)
T ss_pred CCcCHHHHHHHHHHhCCCcchHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHhCCC
Confidence 67899999888876542 344555566666666666789999999999987654
No 93
>COG5248 TAF19 Transcription initiation factor TFIID, subunit TAF13 [Transcription]
Probab=60.85 E-value=35 Score=23.41 Aligned_cols=46 Identities=17% Similarity=0.096 Sum_probs=40.4
Q ss_pred ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691 31 INVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK 78 (103)
Q Consensus 31 ~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~ 78 (103)
+.=..|..+++.+...-+++.+...|..+|. .|..+..+|..-||+
T Consensus 26 v~P~~dt~~~L~e~V~dY~~~~ctna~~~Aq--~rnK~k~eDfkfaLr 71 (126)
T COG5248 26 VAPRYDTAEALHEYVLDYMSILCTNAHNMAQ--VRNKTKTEDFKFALR 71 (126)
T ss_pred CCcchhHHHHHHHHHHHHHHHHHHHHHHHHH--hcccchHHHHHHHHh
Confidence 5667889999999999999999999999988 466678899999997
No 94
>PF07647 SAM_2: SAM domain (Sterile alpha motif); InterPro: IPR011510 The sterile alpha motif (SAM) domain is a putative protein interaction module present in a wide variety of proteins [] involved in many biological processes. The SAM domain that spreads over around 70 residues is found in diverse eukaryotic organisms []. SAM domains have been shown to homo- and hetero-oligomerise, forming multiple self-association architectures and also binding to various non-SAM domain-containing proteins [], nevertheless with a low affinity constant []. SAM domains also appear to possess the ability to bind RNA []. Smaug, a protein that helps to establish a morphogen gradient in Drosophila embryos by repressing the translation of nanos (nos) mRNA, binds to the 3' untranslated region (UTR) of nos mRNA via two similar hairpin structures. The 3D crystal structure of the Smaug RNA-binding region shows a cluster of positively charged residues on the Smaug-SAM domain, which could be the RNA-binding surface. This electropositive potential is unique among all previously determined SAM-domain structures and is conserved among Smaug-SAM homologs. These results suggest that the SAM domain might have a primary role in RNA binding. Structural analyses show that the SAM domain is arranged in a small five-helix bundle with two large interfaces []. In the case of the SAM domain of EphB2, each of these interfaces is able to form dimers. The presence of these two distinct intermonomers binding surface suggest that SAM could form extended polymeric structures []. This entry represents a second domain related to the SAM domain. ; GO: 0005515 protein binding; PDB: 1B0X_A 1X9X_B 1OW5_A 1V38_A 3BS7_A 3BS5_A 3TAD_A 3TAC_B 2K60_A 2DL0_A ....
Probab=60.37 E-value=13 Score=21.60 Aligned_cols=24 Identities=29% Similarity=0.337 Sum_probs=20.1
Q ss_pred cChhhHHHhhhhcCchHHHHHHHH
Q psy13691 68 LSGVDVIEGVKQIGFEVIIEILGK 91 (103)
Q Consensus 68 I~~eDV~~Al~~lgf~~~~~~l~~ 91 (103)
=+++||..-|+.+||.+|.+....
T Consensus 4 w~~~~v~~WL~~~gl~~y~~~f~~ 27 (66)
T PF07647_consen 4 WSPEDVAEWLKSLGLEQYADNFRE 27 (66)
T ss_dssp HCHHHHHHHHHHTTCGGGHHHHHH
T ss_pred CCHHHHHHHHHHCCcHHHHHHHHH
Confidence 368899999999999999887654
No 95
>PRK12402 replication factor C small subunit 2; Reviewed
Probab=60.21 E-value=45 Score=25.02 Aligned_cols=70 Identities=7% Similarity=-0.017 Sum_probs=42.2
Q ss_pred CcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCchH
Q psy13691 10 LPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFEV 84 (103)
Q Consensus 10 LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~ 84 (103)
++...+.++++..+... ...++.++...|.+.+.-=+..+-......+. +..+|+.+||..++.....++
T Consensus 184 ~~~~~~~~~l~~~~~~~---~~~~~~~al~~l~~~~~gdlr~l~~~l~~~~~--~~~~It~~~v~~~~~~~~~~~ 253 (337)
T PRK12402 184 PTDDELVDVLESIAEAE---GVDYDDDGLELIAYYAGGDLRKAILTLQTAAL--AAGEITMEAAYEALGDVGTDE 253 (337)
T ss_pred CCHHHHHHHHHHHHHHc---CCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHH--cCCCCCHHHHHHHhCCCCCHH
Confidence 44555666666554432 16799999999888774333333333333332 234799999999887655443
No 96
>PF07499 RuvA_C: RuvA, C-terminal domain; InterPro: IPR011114 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. The domain represents the C-terminal domain III of RuvA. This domain plays a significant role in the ATP-dependent branch migration of the hetero-duplex through direct contact with RuvB []. Within the Holliday junction, this domain makes no interaction with the DNA.; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination, 0009379 Holliday junction helicase complex; PDB: 1HJP_A 1CUK_A 1C7Y_A 1IXS_A 1IXR_B 1BVS_E 2ZTC_A 2ZTD_B 2H5X_A.
Probab=59.40 E-value=7 Score=22.00 Aligned_cols=14 Identities=21% Similarity=0.541 Sum_probs=11.8
Q ss_pred hhHHHhhhhcCchH
Q psy13691 71 VDVIEGVKQIGFEV 84 (103)
Q Consensus 71 eDV~~Al~~lgf~~ 84 (103)
+|++.||..|||..
T Consensus 4 ~d~~~AL~~LGy~~ 17 (47)
T PF07499_consen 4 EDALEALISLGYSK 17 (47)
T ss_dssp HHHHHHHHHTTS-H
T ss_pred HHHHHHHHHcCCCH
Confidence 68999999999984
No 97
>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=59.23 E-value=17 Score=27.45 Aligned_cols=76 Identities=17% Similarity=0.155 Sum_probs=34.7
Q ss_pred ccCCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCC------CcChhhHHHhhh
Q psy13691 5 LDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRK------TLSGVDVIEGVK 78 (103)
Q Consensus 5 ~~d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~Rk------TI~~eDV~~Al~ 78 (103)
.++..|....+.+-|....... |...+..|...+|.-||++.+..|-..+..+|++-..- +....||-..|.
T Consensus 39 ~~~~fL~~~~L~~~i~~i~~~~--g~~~~~~d~l~llS~A~e~rLr~lie~~~~~s~hR~~~~~~~~~~~~~sdv~~qlr 116 (264)
T PF05236_consen 39 KEEPFLNPSPLQKRIQKIAKKH--GLKSVDEDVLELLSLATEERLRNLIEKAIVLSRHRRDSSKSDPRYEIRSDVRKQLR 116 (264)
T ss_dssp -----S-HHHHHHHHHHHHHCT--T--EE-TCHHHHHHHHHHHHHHHHHHHHH---------------------------
T ss_pred ccccccCHHHHHHHHHHHHHHc--CCcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccCCCcccccchHHHHHHH
Confidence 3455677777777776665433 22579999999999999999999999998888763111 223556666655
Q ss_pred hcCc
Q psy13691 79 QIGF 82 (103)
Q Consensus 79 ~lgf 82 (103)
.|.-
T Consensus 117 ~l~~ 120 (264)
T PF05236_consen 117 FLEQ 120 (264)
T ss_dssp ----
T ss_pred HHHH
Confidence 4443
No 98
>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=58.57 E-value=27 Score=19.73 Aligned_cols=31 Identities=19% Similarity=0.247 Sum_probs=25.8
Q ss_pred CCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHH
Q psy13691 9 NLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASL 47 (103)
Q Consensus 9 ~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~ 47 (103)
.+..++|.|++... -+||.+.++-+.+++.+
T Consensus 10 gvS~~TVSr~ln~~--------~~vs~~tr~rI~~~a~~ 40 (46)
T PF00356_consen 10 GVSKSTVSRVLNGP--------PRVSEETRERILEAAEE 40 (46)
T ss_dssp TSSHHHHHHHHTTC--------SSSTHHHHHHHHHHHHH
T ss_pred CcCHHHHHHHHhCC--------CCCCHHHHHHHHHHHHH
Confidence 56789999999764 36999999999998875
No 99
>PF00536 SAM_1: SAM domain (Sterile alpha motif); InterPro: IPR021129 The sterile alpha motif (SAM) domain is a putative protein interaction module present in a wide variety of proteins [] involved in many biological processes. The SAM domain that spreads over around 70 residues is found in diverse eukaryotic organisms []. SAM domains have been shown to homo- and hetero-oligomerise, forming multiple self-association architectures and also binding to various non-SAM domain-containing proteins [], nevertheless with a low affinity constant []. SAM domains also appear to possess the ability to bind RNA []. Smaug, a protein that helps to establish a morphogen gradient in Drosophila embryos by repressing the translation of nanos (nos) mRNA, binds to the 3' untranslated region (UTR) of nos mRNA via two similar hairpin structures. The 3D crystal structure of the Smaug RNA-binding region shows a cluster of positively charged residues on the Smaug-SAM domain, which could be the RNA-binding surface. This electropositive potential is unique among all previously determined SAM-domain structures and is conserved among Smaug-SAM homologs. These results suggest that the SAM domain might have a primary role in RNA binding. Structural analyses show that the SAM domain is arranged in a small five-helix bundle with two large interfaces []. In the case of the SAM domain of EphB2, each of these interfaces is able to form dimers. The presence of these two distinct intermonomers binding surface suggest that SAM could form extended polymeric structures []. This entry represents type 1 SAM domains. ; PDB: 2KIV_A 3HIL_B 3KKA_A 3K1R_B 3SEN_B 3SEI_B 1V85_A 2KE7_A 2EAM_A 1WWV_A ....
Probab=57.74 E-value=15 Score=21.23 Aligned_cols=22 Identities=36% Similarity=0.336 Sum_probs=19.3
Q ss_pred ChhhHHHhhhhcCchHHHHHHH
Q psy13691 69 SGVDVIEGVKQIGFEVIIEILG 90 (103)
Q Consensus 69 ~~eDV~~Al~~lgf~~~~~~l~ 90 (103)
++++|..-|+.+|+++|.+...
T Consensus 4 ~~~~V~~WL~~~~l~~y~~~F~ 25 (64)
T PF00536_consen 4 SVEDVSEWLKSLGLEQYAENFE 25 (64)
T ss_dssp SHHHHHHHHHHTTGGGGHHHHH
T ss_pred CHHHHHHHHHHCCCHHHHHHHH
Confidence 6789999999999999998763
No 100
>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=57.39 E-value=28 Score=28.74 Aligned_cols=65 Identities=18% Similarity=0.074 Sum_probs=46.1
Q ss_pred ccccHHHHHHHHHHHHH----HHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCchHHHHHHHHHHHHHHh
Q psy13691 31 INVSKDVRLAAGKAASL----FILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFEVIIEILGKSYNAAVS 98 (103)
Q Consensus 31 ~~iskda~~~l~~~~~~----Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~~~~~l~~~l~~~k~ 98 (103)
+.+++||.+.|.+-.++ |..-|-.-|+.+|+..|+++|..+||-.|-+ =|.|-. .--++++.|.+
T Consensus 379 i~l~~~Ale~L~~ig~etSLRYa~qLL~pa~iiA~~rg~~~V~~~dVe~a~~--lF~D~k-rSv~~v~~~~~ 447 (450)
T COG1224 379 IELSDDALEYLTDIGEETSLRYAVQLLTPASIIAKRRGSKRVEVEDVERAKE--LFLDVK-RSVEYVEKYEG 447 (450)
T ss_pred cccCHHHHHHHHhhchhhhHHHHHHhccHHHHHHHHhCCCeeehhHHHHHHH--HHhhHH-HHHHHHHHHHh
Confidence 88999999999876554 4444556688999999999999999999943 233322 22345555544
No 101
>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=56.84 E-value=29 Score=24.50 Aligned_cols=53 Identities=19% Similarity=0.179 Sum_probs=38.3
Q ss_pred HHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHH
Q psy13691 16 QRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVI 74 (103)
Q Consensus 16 ~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~ 74 (103)
.|+++.+.+ .-|.|+-..-+....+.=+.-|.--|...|+.+||.+|.+.|+=
T Consensus 2 e~lFR~aa~------LdvdK~d~~r~~d~V~~Kl~DLl~va~~~Ak~ngRdvI~~~DLP 54 (138)
T PF09123_consen 2 ERLFRKAAG------LDVDKNDAKRYSDFVEKKLYDLLLVAQENAKANGRDVIEPRDLP 54 (138)
T ss_dssp HHHHHHHHS----------HHHHHHHHHHHHHHHHHCCCCHHHHHHHTT-SEE-GGGS-
T ss_pred hHHHHHHhc------cCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeeccccCC
Confidence 567777755 44778888888888888888888889999999999999999863
No 102
>CHL00081 chlI Mg-protoporyphyrin IX chelatase
Probab=56.20 E-value=46 Score=26.60 Aligned_cols=48 Identities=15% Similarity=0.244 Sum_probs=40.1
Q ss_pred ccccHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691 31 INVSKDVRLAAGKAASLFI-------LHLTTEALSIANEKNRKTLSGVDVIEGVK 78 (103)
Q Consensus 31 ~~iskda~~~l~~~~~~Fi-------~~lt~~A~~~a~~~~RkTI~~eDV~~Al~ 78 (103)
+.|+++....+.+.|..+= .++...|.-.|--+||..++++||..+..
T Consensus 266 V~v~~~~~~yi~~l~~~~~~~s~Ra~i~l~raArA~Aal~GR~~V~pdDv~~~a~ 320 (350)
T CHL00081 266 VEIDYDLRVKISQICSELDVDGLRGDIVTNRAAKALAAFEGRTEVTPKDIFKVIT 320 (350)
T ss_pred CccCHHHHHHHHHHHHHHCCCCChHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 7899999998888887763 35666777788889999999999998875
No 103
>PRK13406 bchD magnesium chelatase subunit D; Provisional
Probab=56.16 E-value=31 Score=29.41 Aligned_cols=48 Identities=17% Similarity=0.084 Sum_probs=41.8
Q ss_pred ccccHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691 31 INVSKDVRLAAGKAASLFI-------LHLTTEALSIANEKNRKTLSGVDVIEGVK 78 (103)
Q Consensus 31 ~~iskda~~~l~~~~~~Fi-------~~lt~~A~~~a~~~~RkTI~~eDV~~Al~ 78 (103)
+.|+.+....+.+.|..|= .++..-|..+|--+||..|+.+||..|+.
T Consensus 194 v~v~~~~l~~i~~~~~~~gv~S~Ra~i~llraARa~AaL~Gr~~V~~~dv~~Aa~ 248 (584)
T PRK13406 194 VGPPPEAIAALCAAAAALGIASLRAPLLALRAARAAAALAGRTAVEEEDLALAAR 248 (584)
T ss_pred CCCCHHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 7899999998888777774 47778888899999999999999999986
No 104
>smart00350 MCM minichromosome maintenance proteins.
Probab=55.26 E-value=86 Score=25.93 Aligned_cols=68 Identities=13% Similarity=0.115 Sum_probs=47.1
Q ss_pred CCcHHHHHHHHHhhCC-CCCcccccccHHHHHHHHHHHHHH-------------------HHHHHHHHHHHHHhCCCCCc
Q psy13691 9 NLPSAIIQRLIKEALP-KDAEGKINVSKDVRLAAGKAASLF-------------------ILHLTTEALSIANEKNRKTL 68 (103)
Q Consensus 9 ~LP~a~V~ri~K~~l~-~~~~~~~~iskda~~~l~~~~~~F-------------------i~~lt~~A~~~a~~~~RkTI 68 (103)
.+|...+.+.+.-+=. -. -.+|+++.+.|.+..... +..|-..|.-.|+-.+|.++
T Consensus 417 ~~~~~~l~~yi~~ar~~~~----P~ls~~~~~~i~~~y~~~R~~~~~~~~~~~~~~t~R~l~sliRla~A~A~l~~r~~V 492 (509)
T smart00350 417 PISQEFLRKYIAYAREKIK----PKLSEEAAEKLVKAYVDLRKEDSQSEARSSIPITVRQLESIIRLSEAHAKMRLSDVV 492 (509)
T ss_pred cCCHHHHHHHHHHHHhcCC----CCCCHHHHHHHHHHHHHhcccccccccccccCcCHHHHHHHHHHHHHHHHHcCCCcc
Confidence 5677777777644421 01 258999998886654432 24555667778899999999
Q ss_pred ChhhHHHhhhhc
Q psy13691 69 SGVDVIEGVKQI 80 (103)
Q Consensus 69 ~~eDV~~Al~~l 80 (103)
+++||..|.+-+
T Consensus 493 ~~~Dv~~ai~l~ 504 (509)
T smart00350 493 EEADVEEAIRLL 504 (509)
T ss_pred CHHHHHHHHHHH
Confidence 999999998643
No 105
>TIGR01052 top6b DNA topoisomerase VI, B subunit. This model describes DNA topoisomerase VI, an archaeal type II DNA topoisomerase (DNA gyrase).
Probab=54.91 E-value=25 Score=29.50 Aligned_cols=51 Identities=27% Similarity=0.278 Sum_probs=37.4
Q ss_pred cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCchHHHHHHHHHHHHH
Q psy13691 32 NVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFEVIIEILGKSYNAA 96 (103)
Q Consensus 32 ~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~~~~~l~~~l~~~ 96 (103)
-|-+|.+.+|++||...=.||...-...-..+++++ |..|++.+...+...
T Consensus 434 ei~~ei~~al~~~~r~L~~~l~~~~~~~~~~~r~~~--------------~~~y~p~~a~~~~~~ 484 (488)
T TIGR01052 434 EIYNEIRLALMEVARRLRLYLSRKAREEEEIKRRKT--------------LEKYLPEIAKSLAYI 484 (488)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------------HHHHHHHHHHHHHHH
Confidence 588899999999999999999986655444444443 566777777666554
No 106
>PRK03992 proteasome-activating nucleotidase; Provisional
Probab=54.80 E-value=20 Score=28.51 Aligned_cols=35 Identities=17% Similarity=0.156 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCc
Q psy13691 48 FILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGF 82 (103)
Q Consensus 48 Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf 82 (103)
=|.-|..+|...|..++++.|+.+|+..|++..-.
T Consensus 340 dl~~l~~eA~~~a~~~~~~~i~~~d~~~A~~~~~~ 374 (389)
T PRK03992 340 DLKAICTEAGMFAIRDDRTEVTMEDFLKAIEKVMG 374 (389)
T ss_pred HHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHhc
Confidence 45567788888888899999999999999987643
No 107
>TIGR01242 26Sp45 26S proteasome subunit P45 family. Many proteins may score above the trusted cutoff because an internal
Probab=54.57 E-value=21 Score=27.94 Aligned_cols=32 Identities=25% Similarity=0.213 Sum_probs=27.4
Q ss_pred HHHHHHHHHHHHHHhCCCCCcChhhHHHhhhh
Q psy13691 48 FILHLTTEALSIANEKNRKTLSGVDVIEGVKQ 79 (103)
Q Consensus 48 Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~ 79 (103)
-|..+..+|...|...++..|+.+|+..|++.
T Consensus 331 dl~~l~~~A~~~a~~~~~~~i~~~d~~~a~~~ 362 (364)
T TIGR01242 331 DLKAICTEAGMFAIREERDYVTMDDFIKAVEK 362 (364)
T ss_pred HHHHHHHHHHHHHHHhCCCccCHHHHHHHHHH
Confidence 34567788888898999999999999999875
No 108
>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional
Probab=53.71 E-value=20 Score=29.41 Aligned_cols=32 Identities=22% Similarity=0.247 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHHHhCCCCCcChhhHHHhhhhc
Q psy13691 49 ILHLTTEALSIANEKNRKTLSGVDVIEGVKQI 80 (103)
Q Consensus 49 i~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~l 80 (103)
|..+..+|...|..++|..|+.+|+..|++..
T Consensus 393 I~~i~~eA~~~Alr~~r~~Vt~~D~~~A~~~v 424 (438)
T PTZ00361 393 IKAICTEAGLLALRERRMKVTQADFRKAKEKV 424 (438)
T ss_pred HHHHHHHHHHHHHHhcCCccCHHHHHHHHHHH
Confidence 55678889999999999999999999999864
No 109
>smart00454 SAM Sterile alpha motif. Widespread domain in signalling and nuclear proteins. In EPH-related tyrosine kinases, appears to mediate cell-cell initiated signal transduction via the binding of SH2-containing proteins to a conserved tyrosine that is phosphorylated. In many cases mediates homodimerisation.
Probab=53.03 E-value=18 Score=20.42 Aligned_cols=25 Identities=24% Similarity=0.284 Sum_probs=20.0
Q ss_pred cChhhHHHhhhhcCchHHHHHHHHH
Q psy13691 68 LSGVDVIEGVKQIGFEVIIEILGKS 92 (103)
Q Consensus 68 I~~eDV~~Al~~lgf~~~~~~l~~~ 92 (103)
-+.++|..-|+.+||++|.+...+.
T Consensus 4 w~~~~v~~wL~~~g~~~y~~~f~~~ 28 (68)
T smart00454 4 WSPESVADWLESIGLEQYADNFRKN 28 (68)
T ss_pred CCHHHHHHHHHHCChHHHHHHHHHC
Confidence 4678889999999999988876553
No 110
>PF00531 Death: Death domain; InterPro: IPR000488 The death domain (DD) is a homotypic protein interaction module composed of a bundle of six alpha-helices. DD is related in sequence and structure to the death effector domain (DED, see IPR001875 from INTERPRO) and the caspase recruitment domain (CARD, see IPR001315 from INTERPRO), which work in similar pathways and show similar interaction properties []. DD bind each other forming oligomers. Mammals have numerous and diverse DD-containing proteins []. Within these proteins, the DD domains can be found in combination with other domains, including: CARDs, DEDs, ankyrin repeats (IPR002110 from INTERPRO), caspase-like folds, kinase domains, leucine zippers (IPR002158 from INTERPRO), leucine-rich repeats (LRR) (IPR001611 from INTERPRO), TIR domains (IPR000157 from INTERPRO), and ZU5 domains (IPR000906 from INTERPRO) []. Some DD-containing proteins are involved in the regulation of apoptosis and inflammation through their activation of caspases and NF-kappaB, which typically involves interactions with TNF (tumour necrosis factor) cytokine receptors [, ]. In humans, eight of the over 30 known TNF receptors contain DD in their cytoplasmic tails; several of these TNF receptors use caspase activation as a signalling mechanism. The DD mediates self-association of these receptors, thus giving the signal to downstream events that lead to apoptosis. Other DD-containing proteins, such as ankyrin, MyD88 and pelle, are probably not directly involved in cell death signalling. DD-containing proteins also have links to innate immunity, communicating with Toll family receptors through bipartite adapter proteins such as MyD88 [].; GO: 0005515 protein binding, 0007165 signal transduction; PDB: 3OQ9_L 3EZQ_F 1E41_A 1E3Y_A 2GF5_A 2OF5_L 3EWV_E 3G5B_A 3MOP_L 2A9I_A ....
Probab=52.43 E-value=44 Score=19.88 Aligned_cols=29 Identities=14% Similarity=0.212 Sum_probs=24.0
Q ss_pred CCCcChhhHHHhhhhcCchHHHHHHHHHH
Q psy13691 65 RKTLSGVDVIEGVKQIGFEVIIEILGKSY 93 (103)
Q Consensus 65 RkTI~~eDV~~Al~~lgf~~~~~~l~~~l 93 (103)
...-+.++++.||+.+|..+-++.++..+
T Consensus 55 ~~~at~~~L~~aL~~~~~~d~~~~i~~~~ 83 (83)
T PF00531_consen 55 GPNATVDQLIQALRDIGRNDLAEKIEQML 83 (83)
T ss_dssp GSTSSHHHHHHHHHHTTHHHHHHHHHHH-
T ss_pred CCCCcHHHHHHHHHHCCcHHHHHHHHhhC
Confidence 45667889999999999999998887754
No 111
>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=51.84 E-value=21 Score=17.77 Aligned_cols=26 Identities=8% Similarity=0.172 Sum_probs=19.5
Q ss_pred HHHHHHhCCCCCcChhhHHHhhh-hcC
Q psy13691 56 ALSIANEKNRKTLSGVDVIEGVK-QIG 81 (103)
Q Consensus 56 A~~~a~~~~RkTI~~eDV~~Al~-~lg 81 (103)
+....-.++.-+|+.+++..+|+ .+|
T Consensus 5 ~F~~~D~d~dG~I~~~el~~~l~~~lG 31 (31)
T PF13405_consen 5 AFKMFDKDGDGFIDFEELRAILRKSLG 31 (31)
T ss_dssp HHHHH-TTSSSEEEHHHHHHHHHHHTT
T ss_pred HHHHHCCCCCCcCcHHHHHHHHHHhcC
Confidence 44555567788999999999998 576
No 112
>PRK13407 bchI magnesium chelatase subunit I; Provisional
Probab=50.98 E-value=68 Score=25.34 Aligned_cols=47 Identities=11% Similarity=0.049 Sum_probs=38.2
Q ss_pred ccccHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhCCCCCcChhhHHHhh
Q psy13691 31 INVSKDVRLAAGKAASLFI-------LHLTTEALSIANEKNRKTLSGVDVIEGV 77 (103)
Q Consensus 31 ~~iskda~~~l~~~~~~Fi-------~~lt~~A~~~a~~~~RkTI~~eDV~~Al 77 (103)
+.|+++....+.+.+..+= .+|...|.-.|.-+||..|+++||..+.
T Consensus 250 V~v~~~~~~yi~~l~~~~~~~s~Ra~i~l~~aA~a~A~l~Gr~~V~~~Di~~~~ 303 (334)
T PRK13407 250 LKTPNTVLHDCAALCIALGSDGLRGELTLLRAARALAAFEGAEAVGRSHLRSVA 303 (334)
T ss_pred cccCHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHHcCCCeeCHHHHHHHH
Confidence 7899999998888877654 2366777778999999999999997665
No 113
>TIGR01128 holA DNA polymerase III, delta subunit. subunit around DNA forming a DNA sliding clamp.
Probab=50.61 E-value=1e+02 Score=22.80 Aligned_cols=66 Identities=18% Similarity=0.116 Sum_probs=45.4
Q ss_pred CcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691 10 LPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK 78 (103)
Q Consensus 10 LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~ 78 (103)
++...+.+.+++.+... +..|+.++...|...+..=...+-.+-...+.-.+.++|+.+||...+.
T Consensus 111 ~~~~~~~~~i~~~~~~~---g~~i~~~a~~~l~~~~~~d~~~l~~el~KL~~~~~~~~It~e~I~~~~~ 176 (302)
T TIGR01128 111 PKEQELPRWIQARLKKL---GLRIDPDAVQLLAELVEGNLLAIAQELEKLALYAPDGKITLEDVEEAVS 176 (302)
T ss_pred CCHHHHHHHHHHHHHHc---CCCCCHHHHHHHHHHhCcHHHHHHHHHHHHHhhCCCCCCCHHHHHHHHh
Confidence 44555565665554432 2789999999998888765566666666666554445799999987766
No 114
>PF04552 Sigma54_DBD: Sigma-54, DNA binding domain; InterPro: IPR007634 This DNA-binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore, this region contains a putative helix-turn-helix motif. At the C terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins [].; PDB: 2AHQ_A 2O9L_A 2O8K_A.
Probab=49.56 E-value=18 Score=25.73 Aligned_cols=80 Identities=23% Similarity=0.249 Sum_probs=27.3
Q ss_pred CccCCCCcHHHHHHHHHhhCCCCCcc----------------cccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCC
Q psy13691 4 SLDDLNLPSAIIQRLIKEALPKDAEG----------------KINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKT 67 (103)
Q Consensus 4 ~~~d~~LP~a~V~ri~K~~l~~~~~~----------------~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkT 67 (103)
--+++.+..++|.|++++.-=..+.| ...+|.++... ....-+..+++.+.
T Consensus 55 iA~~lgl~~STVSRav~~Ky~~t~~Gi~plk~fF~~~~~~~~~~~~S~~~ik~-------------~i~~lI~~Ed~~~P 121 (160)
T PF04552_consen 55 IADELGLHESTVSRAVKNKYIQTPRGIFPLKDFFSRSVSSGSGEEFSSEAIKA-------------RIKELIEEEDKKKP 121 (160)
T ss_dssp ------------------------------S-----SS--SS-SS---TTH-H-------------HHHHHHTTS-TTS-
T ss_pred HHHHhCCCHhHHHHHHcCceeecCCeeeeHHHhccccccCCCCcccHHHHHHH-------------HHHHHHHhcCCCCC
Confidence 34678899999999997653222111 11133333221 11223566678899
Q ss_pred cChhhHHHhhhhcCchHHHHHHHHHHHHHHhcc
Q psy13691 68 LSGVDVIEGVKQIGFEVIIEILGKSYNAAVSIK 100 (103)
Q Consensus 68 I~~eDV~~Al~~lgf~~~~~~l~~~l~~~k~~~ 100 (103)
++.+.|...|+.-| +..-...+..||+..
T Consensus 122 lSD~~i~~~L~~~g----i~isRRTVaKYR~~L 150 (160)
T PF04552_consen 122 LSDQEIAELLKEEG----IKISRRTVAKYREEL 150 (160)
T ss_dssp --HHHHHHHHTTTT----S---HHHHHHHHHHH
T ss_pred CCHHHHHHHHHHcC----CCccHHHHHHHHHHc
Confidence 99999999999877 456677777888764
No 115
>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=48.42 E-value=87 Score=26.58 Aligned_cols=48 Identities=17% Similarity=0.094 Sum_probs=36.6
Q ss_pred ccccHHHHHHHHHHHHHH-------HHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691 31 INVSKDVRLAAGKAASLF-------ILHLTTEALSIANEKNRKTLSGVDVIEGVK 78 (103)
Q Consensus 31 ~~iskda~~~l~~~~~~F-------i~~lt~~A~~~a~~~~RkTI~~eDV~~Al~ 78 (103)
+.|+.+....|.+.+..+ -.++...|.-.|.-+||.+|+++||..|..
T Consensus 202 V~i~~~~~~~l~~~~~~~gv~s~Ra~i~~~r~ArA~Aal~gr~~V~~~Dv~~a~~ 256 (589)
T TIGR02031 202 VTISAEQVKELVLTAASLGISGHRADLFAVRAAKAHAALHGRTEVTEEDLKLAVE 256 (589)
T ss_pred ccCCHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHH
Confidence 789999887776665443 124456666778889999999999999975
No 116
>PF08681 DUF1778: Protein of unknown function (DUF1778); InterPro: IPR014795 This entry is represented by Vibrio phage ICP1, Orf50. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a family of uncharacterised proteins. The structure of one of the hypothetical proteins in this family has been solved and it forms a helix structure which may form interactions with DNA. ; PDB: 1Y9B_A.
Probab=48.40 E-value=28 Score=21.69 Aligned_cols=67 Identities=24% Similarity=0.159 Sum_probs=33.4
Q ss_pred ccccHHHHHHHHHHHH-------HHHHHHHHHHHHHH-HhCCCCCcChhhHHHhhhhcCch-HHHHHHHHHHHHHH
Q psy13691 31 INVSKDVRLAAGKAAS-------LFILHLTTEALSIA-NEKNRKTLSGVDVIEGVKQIGFE-VIIEILGKSYNAAV 97 (103)
Q Consensus 31 ~~iskda~~~l~~~~~-------~Fi~~lt~~A~~~a-~~~~RkTI~~eDV~~Al~~lgf~-~~~~~l~~~l~~~k 97 (103)
+|++.+.+..|.+++. .||.-.+.++.+.. .....-+++.+|--.-++.|+=+ .=-+.|+..+..|+
T Consensus 4 iR~~~e~k~li~~AA~~~G~sls~Fi~~aa~~~A~~~i~~~~~~~Ls~~~~~~f~~aLd~p~~p~~~L~~a~~~~~ 79 (80)
T PF08681_consen 4 IRVTPEEKELIERAAALSGVSLSDFILSAALEAAEEVIEEHERIRLSAEDFEAFMAALDNPPQPNERLKEAMRRYR 79 (80)
T ss_dssp EE--HHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH-HHHHHHHHHHHC----
T ss_pred EecCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhcceeEcCHHHHHHHHHHHhCCCCCCHHHHHHHHhcc
Confidence 7899999999999975 45555554444332 22334456666654444444332 23344455544444
No 117
>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional
Probab=47.83 E-value=30 Score=27.93 Aligned_cols=32 Identities=31% Similarity=0.265 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHHHhCCCCCcChhhHHHhhhhc
Q psy13691 49 ILHLTTEALSIANEKNRKTLSGVDVIEGVKQI 80 (103)
Q Consensus 49 i~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~l 80 (103)
|..|..+|...|...+|..|+.+|+..|++..
T Consensus 355 I~~l~~eA~~~A~r~~~~~i~~~df~~A~~~v 386 (398)
T PTZ00454 355 IAAICQEAGMQAVRKNRYVILPKDFEKGYKTV 386 (398)
T ss_pred HHHHHHHHHHHHHHcCCCccCHHHHHHHHHHH
Confidence 66788889999999999999999999998863
No 118
>PLN00138 large subunit ribosomal protein LP2; Provisional
Probab=47.24 E-value=58 Score=21.99 Aligned_cols=28 Identities=18% Similarity=0.143 Sum_probs=25.0
Q ss_pred HHHHHHhCCCCCcChhhHHHhhhhcCch
Q psy13691 56 ALSIANEKNRKTLSGVDVIEGVKQIGFE 83 (103)
Q Consensus 56 A~~~a~~~~RkTI~~eDV~~Al~~lgf~ 83 (103)
|+-.|.-.|...++.+||...|+..|.+
T Consensus 6 Ayll~~l~g~~~pta~dI~~IL~AaGve 33 (113)
T PLN00138 6 AYLLAVLGGNTCPSAEDLKDILGSVGAD 33 (113)
T ss_pred HHHHHHhcCCCCCCHHHHHHHHHHcCCc
Confidence 5678888899999999999999998876
No 119
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=46.29 E-value=55 Score=20.43 Aligned_cols=28 Identities=11% Similarity=0.185 Sum_probs=19.2
Q ss_pred HHHHHHhCCCCCcChhhHHHhhhhcCch
Q psy13691 56 ALSIANEKNRKTLSGVDVIEGVKQIGFE 83 (103)
Q Consensus 56 A~~~a~~~~RkTI~~eDV~~Al~~lgf~ 83 (103)
+....-.++...|+.+++..+|..+|+.
T Consensus 15 ~F~~~D~d~~G~Is~~el~~~l~~~~~~ 42 (96)
T smart00027 15 IFRSLDKNQDGTVTGAQAKPILLKSGLP 42 (96)
T ss_pred HHHHhCCCCCCeEeHHHHHHHHHHcCCC
Confidence 4445555666777777777777777765
No 120
>COG1724 Predicted RNA binding protein (dsRBD-like fold), HicA family [General function prediction only]
Probab=45.15 E-value=16 Score=22.71 Aligned_cols=17 Identities=24% Similarity=0.575 Sum_probs=15.2
Q ss_pred CcChhhHHHhhhhcCch
Q psy13691 67 TLSGVDVIEGVKQIGFE 83 (103)
Q Consensus 67 TI~~eDV~~Al~~lgf~ 83 (103)
.+++.+++++|+.+||.
T Consensus 6 ~~~~ke~ik~Le~~Gf~ 22 (66)
T COG1724 6 RMKAKEVIKALEKDGFQ 22 (66)
T ss_pred cCCHHHHHHHHHhCCcE
Confidence 47889999999999996
No 121
>PTZ00373 60S Acidic ribosomal protein P2; Provisional
Probab=44.90 E-value=65 Score=21.80 Aligned_cols=28 Identities=7% Similarity=0.041 Sum_probs=24.8
Q ss_pred HHHHHHhCCCCCcChhhHHHhhhhcCch
Q psy13691 56 ALSIANEKNRKTLSGVDVIEGVKQIGFE 83 (103)
Q Consensus 56 A~~~a~~~~RkTI~~eDV~~Al~~lgf~ 83 (103)
|+-.|.-.|..+++.+||...|+..|.+
T Consensus 8 AYlL~~lgG~~~pTaddI~kIL~AaGve 35 (112)
T PTZ00373 8 AYLMCVLGGNENPTKKEVKNVLSAVNAD 35 (112)
T ss_pred HHHHHHHcCCCCCCHHHHHHHHHHcCCC
Confidence 5667888899999999999999988876
No 122
>PRK09526 lacI lac repressor; Reviewed
Probab=44.52 E-value=23 Score=26.48 Aligned_cols=37 Identities=16% Similarity=0.208 Sum_probs=29.2
Q ss_pred CCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHH
Q psy13691 9 NLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTT 54 (103)
Q Consensus 9 ~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~ 54 (103)
..-+++|.|++... -+||.+.+.-+.+++.+ +.|.-.
T Consensus 16 GVS~~TVSrvLn~~--------~~vs~~tr~rV~~~a~e-lgY~pn 52 (342)
T PRK09526 16 GVSYQTVSRVLNQA--------SHVSAKTREKVEAAMAE-LNYVPN 52 (342)
T ss_pred CCCHHHHHHHhcCC--------CCCCHHHHHHHHHHHHH-HCCCcC
Confidence 55678999998642 36999999999999999 567544
No 123
>PRK02910 light-independent protochlorophyllide reductase subunit B; Provisional
Probab=44.15 E-value=51 Score=27.42 Aligned_cols=51 Identities=10% Similarity=0.141 Sum_probs=39.2
Q ss_pred cccccHHHHHHHHHHHHHHHHHHH-HHHHHHHHhCCCCCcChhhHHHhhhhcC
Q psy13691 30 KINVSKDVRLAAGKAASLFILHLT-TEALSIANEKNRKTLSGVDVIEGVKQIG 81 (103)
Q Consensus 30 ~~~iskda~~~l~~~~~~Fi~~lt-~~A~~~a~~~~RkTI~~eDV~~Al~~lg 81 (103)
.+.++.||...|.+ .=-|+.-=. ..+-+.|++.|...|+.+.+..|-..+|
T Consensus 467 ~~~w~~ea~~~l~~-~P~f~r~~~r~~~e~~a~~~g~~~it~~~~~~a~~~~~ 518 (519)
T PRK02910 467 ELVWTPEAEAELKK-IPFFVRGKVRRNTEKFARERGLPEITLEVLYDAKAHFG 518 (519)
T ss_pred CCCCCHHHHHHHhh-CChhhHHHHHHHHHHHHHHcCCCeecHHHHHHHHHHhc
Confidence 47899999999965 455655433 4445678999999999999999976654
No 124
>COG1500 Predicted exosome subunit [Translation, ribosomal structure and biogenesis]
Probab=43.97 E-value=1e+02 Score=23.61 Aligned_cols=63 Identities=11% Similarity=0.184 Sum_probs=45.7
Q ss_pred HHHHHHhhCCCCCcccccccHHHHHHHHHHHH-HHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCch
Q psy13691 15 IQRLIKEALPKDAEGKINVSKDVRLAAGKAAS-LFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFE 83 (103)
Q Consensus 15 V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~-~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~ 83 (103)
+..|+++.|..+ .+.++.+-+..|++.-. ..|+++++.|.+ -..+....+.-|-+||++++|.
T Consensus 72 ~~eI~~eIl~kG---eiQlTaeqR~~m~e~k~rqIi~~IsRn~Id---P~t~~P~Pp~rIe~Ameeakv~ 135 (234)
T COG1500 72 PDEIAEEILKKG---EIQLTAEQRREMLEEKKRQIINIISRNAID---PQTKAPHPPARIEKAMEEAKVH 135 (234)
T ss_pred HHHHHHHHHhcC---ceeccHHHHHHHHHHHHHHHHHHHHHhccC---CCCCCCCCHHHHHHHHHhcCcc
Confidence 555666665543 48999999988777765 455577775533 2455689999999999999997
No 125
>PF08823 PG_binding_2: Putative peptidoglycan binding domain; InterPro: IPR014927 This entry may be a peptidoglycan binding domain.
Probab=43.44 E-value=31 Score=21.48 Aligned_cols=29 Identities=24% Similarity=0.296 Sum_probs=22.8
Q ss_pred hhHHHhhhhcCc------hHHHHHHHHHHHHHHhc
Q psy13691 71 VDVIEGVKQIGF------EVIIEILGKSYNAAVSI 99 (103)
Q Consensus 71 eDV~~Al~~lgf------~~~~~~l~~~l~~~k~~ 99 (103)
+.|..+|..+|| +.+-+..++.+..|...
T Consensus 19 ~evq~~L~~lGyy~g~~~g~~d~a~~~Al~~~~g~ 53 (74)
T PF08823_consen 19 REVQEALKRLGYYKGEADGVWDEATEDALRAWAGT 53 (74)
T ss_pred HHHHHHHHHcCCccCCCCCcccHHHHHHHHHHHHH
Confidence 467889999999 56778888888877654
No 126
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=43.10 E-value=17 Score=20.42 Aligned_cols=17 Identities=29% Similarity=0.669 Sum_probs=13.1
Q ss_pred CCCCcHHHHHHHHHhhC
Q psy13691 7 DLNLPSAIIQRLIKEAL 23 (103)
Q Consensus 7 d~~LP~a~V~ri~K~~l 23 (103)
...+|+++++|+++.-.
T Consensus 27 ~~gl~~stv~r~L~tL~ 43 (52)
T PF09339_consen 27 ALGLPKSTVHRLLQTLV 43 (52)
T ss_dssp HHTS-HHHHHHHHHHHH
T ss_pred HHCcCHHHHHHHHHHHH
Confidence 45899999999998753
No 127
>KOG1528|consensus
Probab=43.04 E-value=86 Score=25.21 Aligned_cols=68 Identities=16% Similarity=0.175 Sum_probs=41.7
Q ss_pred HHHHHHHHHhhCCCCCcccccccHHHHHHHHHH-HHHHHHHHHHHHHH---HHHhCCC-CCcChhhHHHhhhhcC
Q psy13691 12 SAIIQRLIKEALPKDAEGKINVSKDVRLAAGKA-ASLFILHLTTEALS---IANEKNR-KTLSGVDVIEGVKQIG 81 (103)
Q Consensus 12 ~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~-~~~Fi~~lt~~A~~---~a~~~~R-kTI~~eDV~~Al~~lg 81 (103)
.|.|.-.+++.+|+++- ..+..|--.-+.+. ++.|+.-++..-|+ ....=+- ++++.+||++|++.-+
T Consensus 52 QAiVs~vL~~~f~~~p~--slVaEEds~~Lr~n~~~~~l~~i~~lvnetl~s~~sy~~~~~ls~~dvl~aID~G~ 124 (351)
T KOG1528|consen 52 QAIVSLVLEREFPDDPL--SLVAEEDSGFLRKNGSEGLLSRITKLVNETLASDESYGDNSPLSSDDVLKAIDRGN 124 (351)
T ss_pred HHHHHHHHHHHcCCCCc--ceEeeccchhhhhhhhHHHHHHHHHHHHHHhhhhhhccCCCCCCHHHHHHHHhccc
Confidence 46778888999998620 03455555445444 55666666663333 2222233 8899999999997543
No 128
>PRK06585 holA DNA polymerase III subunit delta; Reviewed
Probab=42.47 E-value=87 Score=23.97 Aligned_cols=48 Identities=17% Similarity=0.011 Sum_probs=36.4
Q ss_pred ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHh-CCCCCcChhhHHHhhh
Q psy13691 31 INVSKDVRLAAGKAASLFILHLTTEALSIANE-KNRKTLSGVDVIEGVK 78 (103)
Q Consensus 31 ~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~-~~RkTI~~eDV~~Al~ 78 (103)
.+|+.+|...|.+.+.-=...+..+-...+.- .+.++|+.+||...+.
T Consensus 160 ~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~It~edV~~lv~ 208 (343)
T PRK06585 160 LRITPDARALLVALLGGDRLASRNEIEKLALYAHGKGEITLDDVRAVVG 208 (343)
T ss_pred CCCCHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHhC
Confidence 78999999999998886555555555555554 3457899999988765
No 129
>PRK05574 holA DNA polymerase III subunit delta; Reviewed
Probab=42.15 E-value=1.2e+02 Score=22.78 Aligned_cols=67 Identities=16% Similarity=0.114 Sum_probs=45.2
Q ss_pred CcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhh
Q psy13691 10 LPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQ 79 (103)
Q Consensus 10 LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~ 79 (103)
++...+.+.++..+... ...|+.++...|.+.+..=...+..+-...+.-.+-+.|+.+||-..+..
T Consensus 146 ~~~~~~~~~i~~~~~~~---g~~i~~~a~~~L~~~~~~d~~~l~~El~KL~l~~~~~~It~~~I~~~i~~ 212 (340)
T PRK05574 146 PKEAELPQWIQQRLKQQ---GLQIDAAALQLLAERVEGNLLALAQELEKLALLYPDGKITLEDVEEAVPD 212 (340)
T ss_pred CCHHHHHHHHHHHHHHc---CCCCCHHHHHHHHHHhCchHHHHHHHHHHHHhhcCCCCCCHHHHHHHHhh
Confidence 44555555555544332 27899999999999888766677777777765432223999999877653
No 130
>cd08779 Death_PIDD Death Domain of p53-induced protein with a death domain. Death domain (DD) found in PIDD (p53-induced protein with a death domain) and similar proteins. PIDD is a component of the PIDDosome complex, which is an oligomeric caspase-activating complex involved in caspase-2 activation and plays a role in mediating stress-induced apoptosis. The PIDDosome complex is composed of three components, PIDD, RAIDD and caspase-2, which interact through their DDs and DD-like domains. The DD of PIDD interacts with the DD of RAIDD, which also contains a Caspase Activation and Recruitment Domain (CARD) that interacts with the caspase-2 CARD. Autoproteolysis of PIDD determines the downstream signaling event, between pro-survival NF-kB or pro-death caspase-2 activation. 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
Probab=41.95 E-value=88 Score=19.69 Aligned_cols=33 Identities=6% Similarity=0.074 Sum_probs=24.7
Q ss_pred HHhCCCCCcChhhHHHhhhhcCchHHHHHHHHH
Q psy13691 60 ANEKNRKTLSGVDVIEGVKQIGFEVIIEILGKS 92 (103)
Q Consensus 60 a~~~~RkTI~~eDV~~Al~~lgf~~~~~~l~~~ 92 (103)
....+...=+.+.+..||...|..+..+.+++.
T Consensus 53 ~~~~~~~~atv~~L~~AL~~~gr~dlae~l~~~ 85 (86)
T cd08779 53 AQRQAGDPDAVGKLVTALEESGRQDLADEVRAV 85 (86)
T ss_pred HHhcCCCchHHHHHHHHHHHcCHHHHHHHHHhh
Confidence 344444444578899999999999999888764
No 131
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=41.26 E-value=56 Score=19.43 Aligned_cols=33 Identities=18% Similarity=0.192 Sum_probs=26.2
Q ss_pred CCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHH
Q psy13691 8 LNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLF 48 (103)
Q Consensus 8 ~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~F 48 (103)
..+..++|.|++... ..|+.+.+..+.+++.++
T Consensus 10 ~gvS~~TVSr~ln~~--------~~v~~~t~~~i~~~~~~~ 42 (70)
T smart00354 10 AGVSKATVSRVLNGN--------GRVSEETREKVLAAMEEL 42 (70)
T ss_pred HCCCHHHHHHHHCCC--------CCCCHHHHHHHHHHHHHh
Confidence 467889999988543 358999999999988775
No 132
>TIGR01278 DPOR_BchB light-independent protochlorophyllide reductase, B subunit. This enzyme describes the B subunit of the dark form protochlorophyllide reductase, a nitrogenase-like enzyme. This subunit shows homology to the nitrogenase molybdenum-iron protein. It catalyzes a step in bacteriochlorophyll biosynthesis.
Probab=40.18 E-value=62 Score=26.82 Aligned_cols=51 Identities=10% Similarity=0.203 Sum_probs=38.5
Q ss_pred cccccHHHHHHHHHHHHHHHHH-HHHHHHHHHHhCCCCCcChhhHHHhhhhcC
Q psy13691 30 KINVSKDVRLAAGKAASLFILH-LTTEALSIANEKNRKTLSGVDVIEGVKQIG 81 (103)
Q Consensus 30 ~~~iskda~~~l~~~~~~Fi~~-lt~~A~~~a~~~~RkTI~~eDV~~Al~~lg 81 (103)
.+.++.||...|.+ .=-|+.- +=..+-+.|++.|...|+.+.+..|=+.+|
T Consensus 460 ~~~w~~ea~~~l~~-~P~f~r~~~r~~~e~~a~~~g~~~it~~~~~~a~~~~~ 511 (511)
T TIGR01278 460 ELGWTAEAEAELKK-VPFFVRGKVRRNTENFARERGYSVITLEVIYAAKEHFG 511 (511)
T ss_pred CCCcCHHHHHHHhh-CChhhhHHHHHHHHHHHHHcCCCEEcHHHHHHHHHhcC
Confidence 36899999999965 4445543 334455778999999999999999866654
No 133
>KOG1658|consensus
Probab=39.55 E-value=34 Score=24.68 Aligned_cols=67 Identities=15% Similarity=0.186 Sum_probs=47.5
Q ss_pred CCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHH-----------HHH-HhCCCCCcChhhHH
Q psy13691 7 DLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEAL-----------SIA-NEKNRKTLSGVDVI 74 (103)
Q Consensus 7 d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~-----------~~a-~~~~RkTI~~eDV~ 74 (103)
..-||.+-+.||-|+. |.. +.=+.++..+...+++.|+.-++..+. +.| +..---|+..++++
T Consensus 9 ~p~~p~ekvkkiak~d-Pey----~~te~~a~~etafatE~fvq~lv~~p~a~l~rLpL~rik~vvkl~pdl~l~~dea~ 83 (162)
T KOG1658|consen 9 SPKLPMEKVKKIAKND-PEY----MDTEDDAFVETAFATEQFVQVLVHLPQASLSRLPLARIKQVVKLDPDLTLLNDEAS 83 (162)
T ss_pred CccccHHHHHHhhcCC-chh----hhcccchHHHHHHHHHHHHhhhhhhhhhhhhhccHHHHHhhccCCcchhhhhhHHH
Confidence 4579999999999987 666 677888888999999999988887221 111 11223366677776
Q ss_pred Hhhh
Q psy13691 75 EGVK 78 (103)
Q Consensus 75 ~Al~ 78 (103)
.++.
T Consensus 84 ~l~a 87 (162)
T KOG1658|consen 84 QLIA 87 (162)
T ss_pred HHHH
Confidence 6654
No 134
>PF01922 SRP19: SRP19 protein; InterPro: IPR002778 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the SRP19 subunit. The SRP19 protein is unstructured but forms a compact core domain and two extended RNA-binding loops upon binding the signal recognition particle (SRP) RNA [].; GO: 0008312 7S RNA binding, 0006614 SRP-dependent cotranslational protein targeting to membrane, 0048500 signal recognition particle; PDB: 3DLU_A 3DLV_B 2J37_B 1MFQ_B 3KTV_D 1RY1_B 1JID_A 1KVV_A 1KVN_A 3KTW_B ....
Probab=39.26 E-value=19 Score=23.43 Aligned_cols=19 Identities=11% Similarity=0.403 Sum_probs=14.6
Q ss_pred cChhhHHHhhhhcCchHHH
Q psy13691 68 LSGVDVIEGVKQIGFEVII 86 (103)
Q Consensus 68 I~~eDV~~Al~~lgf~~~~ 86 (103)
.+.++|..|++.|||...+
T Consensus 29 P~~~EI~~a~~~Lgl~~~~ 47 (95)
T PF01922_consen 29 PTLEEIADACKKLGLPCVV 47 (95)
T ss_dssp --HHHHHHHHHHTTSEEEE
T ss_pred CCHHHHHHHHHHcCCCEEE
Confidence 7889999999999997543
No 135
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=38.55 E-value=29 Score=25.95 Aligned_cols=37 Identities=14% Similarity=0.172 Sum_probs=28.3
Q ss_pred CCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHH
Q psy13691 9 NLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTT 54 (103)
Q Consensus 9 ~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~ 54 (103)
..-+++|.|++.+. -+||.+.+.-+.+++.+ +.|.-.
T Consensus 16 gVS~~TVSrvLn~~--------~~vs~~tr~rV~~~a~e-lgY~pn 52 (331)
T PRK14987 16 GVTKMTVSRFLRNP--------EQVSVALRGKIAAALDE-LGYIPN 52 (331)
T ss_pred CCCHHHhhhhhCCC--------CCCCHHHHHHHHHHHHH-hCCCcc
Confidence 45678888888542 36999999999999998 556543
No 136
>PF12668 DUF3791: Protein of unknown function (DUF3791); InterPro: IPR024269 This entry represents proteins of unknown function.
Probab=37.99 E-value=80 Score=18.55 Aligned_cols=30 Identities=17% Similarity=0.063 Sum_probs=24.0
Q ss_pred CCCCcChhhHHHhhhhcCchHHHHHHHHHH
Q psy13691 64 NRKTLSGVDVIEGVKQIGFEVIIEILGKSY 93 (103)
Q Consensus 64 ~RkTI~~eDV~~Al~~lgf~~~~~~l~~~l 93 (103)
+|.-++++++.+-+++.|.-+|+.+.-+.+
T Consensus 13 ~~~~~s~~ea~~~~~~~~~~~~i~~~Yd~l 42 (62)
T PF12668_consen 13 KKLNISGEEAYNYFKRSGVIDYIIDCYDVL 42 (62)
T ss_pred HHHCcCHHHHHHHHHHcCcHHHHHHcchHH
Confidence 467799999999999999888887655444
No 137
>PRK07914 hypothetical protein; Reviewed
Probab=37.94 E-value=1.1e+02 Score=23.47 Aligned_cols=64 Identities=11% Similarity=0.099 Sum_probs=42.7
Q ss_pred cHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691 11 PSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK 78 (103)
Q Consensus 11 P~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~ 78 (103)
+...+.+.|++.+... ..+|+.||...|..++..=...+..+-...+...+ .+|+.+||...+.
T Consensus 129 ~~~~l~~wi~~~a~~~---g~~i~~~A~~~L~~~~g~dl~~l~~EleKL~~~~~-~~It~e~V~~~v~ 192 (320)
T PRK07914 129 KAAERADFVRKEFRSL---RVKVDDDTVTALLDAVGSDLRELASACSQLVADTG-GAVDAAAVRRYHS 192 (320)
T ss_pred CHHHHHHHHHHHHHHc---CCCCCHHHHHHHHHHHCccHHHHHHHHHHHhcCCC-CCcCHHHHHHHcC
Confidence 3444444444443321 27899999999999987656666666555554334 5799999998865
No 138
>TIGR02454 CbiQ_TIGR cobalt ABC transporter, permease protein CbiQ. This model represents the permease component of the cobalt-specific ABC transporter. This model finds permeases which are generally next to the other subunits of the complex (CbiN and CbiO) or the cobalamin biosynthesis protein CbiM which is a transmembrane protein which likely interacts with the complex in some manner. In genomes which possess all of these subunits the ATPase is most likely running in the direction of import (for the biosynthesis of coenzyme B12). In other genomes, this subunit may be involved in the export of cobalt and/or other closely related heavy metals.
Probab=37.31 E-value=57 Score=22.87 Aligned_cols=36 Identities=8% Similarity=0.124 Sum_probs=27.5
Q ss_pred CCcChhhHHHhhhhcCch-----------HHHHHHHHHHHHHHhccc
Q psy13691 66 KTLSGVDVIEGVKQIGFE-----------VIIEILGKSYNAAVSIKV 101 (103)
Q Consensus 66 kTI~~eDV~~Al~~lgf~-----------~~~~~l~~~l~~~k~~~~ 101 (103)
-|.++.|+..+|+.+|++ .|++.+.+..+.-+++++
T Consensus 112 ~TT~~~~l~~~l~~l~~P~~~~~~~~l~~Rfip~l~~e~~~i~~Aq~ 158 (198)
T TIGR02454 112 LTTPFPELLSALRRLGVPPLLVEILLLTYRYLFVLLEELRRMLLAQR 158 (198)
T ss_pred HcCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 467899999999999986 466777777776666553
No 139
>COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]
Probab=37.09 E-value=95 Score=25.89 Aligned_cols=79 Identities=20% Similarity=0.209 Sum_probs=52.7
Q ss_pred cCCCCcHHHHHHHHHhhCCCCCccc-----------------ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCc
Q psy13691 6 DDLNLPSAIIQRLIKEALPKDAEGK-----------------INVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTL 68 (103)
Q Consensus 6 ~d~~LP~a~V~ri~K~~l~~~~~~~-----------------~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI 68 (103)
+++.+--|+|.|++++..-..+-|- ---|+++.-.+.+ .-+..+++++.+
T Consensus 338 ~~i~~HESTISRai~nKy~~tprG~feLK~FFs~~i~s~~gg~~~S~~~Ik~~Ik-------------~lI~~E~~~~pL 404 (444)
T COG1508 338 DEIGMHESTISRAITNKYLATPRGLFELKYFFSSSLASSEGGEASSTEAIKALIK-------------KLIEAEDKKKPL 404 (444)
T ss_pred HHhCccHHHHHHHHhcccccCCcceeeHHHHHHHhccCCCCCccccHHHHHHHHH-------------HHHhhccCCCCC
Confidence 4567778999999988654443221 1233322222211 235677788899
Q ss_pred ChhhHHHhhhhcCchHHHHHHHHHHHHHHhccc
Q psy13691 69 SGVDVIEGVKQIGFEVIIEILGKSYNAAVSIKV 101 (103)
Q Consensus 69 ~~eDV~~Al~~lgf~~~~~~l~~~l~~~k~~~~ 101 (103)
+...|..-|++-|+ +.-...+..||+...
T Consensus 405 SD~kIa~lLkekGi----~iARRTVAKYRe~L~ 433 (444)
T COG1508 405 SDSKIAELLKEKGI----DVARRTVAKYREELN 433 (444)
T ss_pred CHHHHHHHHHHcCC----chhHHhHHHHHHHcC
Confidence 99999999999884 577888888988753
No 140
>PF00403 HMA: Heavy-metal-associated domain; InterPro: IPR006121 Proteins that transport heavy metals in micro-organisms and mammals share similarities in their sequences and structures. These proteins provide an important focus for research, some being involved in bacterial resistance to toxic metals, such as lead and cadmium, while others are involved in inherited human syndromes, such as Wilson's and Menke's diseases []. A conserved domain has been found in a number of these heavy metal transport or detoxification proteins []. The domain, which has been termed Heavy-Metal-Associated (HMA), contains two conserved cysteines that are probably involved in metal binding. Structure solution of the fourth HMA domain of the Menke's copper transporting ATPase shows a well-defined structure comprising a four-stranded antiparallel beta-sheet and two alpha helices packed in an alpha-beta sandwich fold []. This fold is common to other domains and is classified as "ferredoxin-like".; GO: 0046872 metal ion binding, 0030001 metal ion transport; PDB: 2VOY_A 1P6T_A 1KQK_A 2RML_A 1JWW_A 3K7R_F 1FES_A 1CC8_A 1FD8_A 2GGP_A ....
Probab=36.20 E-value=27 Score=19.87 Aligned_cols=16 Identities=31% Similarity=0.553 Sum_probs=13.4
Q ss_pred cChhhHHHhhhhcCch
Q psy13691 68 LSGVDVIEGVKQIGFE 83 (103)
Q Consensus 68 I~~eDV~~Al~~lgf~ 83 (103)
++.++|..+++.+||+
T Consensus 47 ~~~~~i~~~i~~~Gy~ 62 (62)
T PF00403_consen 47 TSIEKIIEAIEKAGYE 62 (62)
T ss_dssp SCHHHHHHHHHHTTSE
T ss_pred CCHHHHHHHHHHhCcC
Confidence 6678899999999884
No 141
>CHL00076 chlB photochlorophyllide reductase subunit B
Probab=36.02 E-value=88 Score=26.09 Aligned_cols=51 Identities=10% Similarity=0.082 Sum_probs=40.1
Q ss_pred cccccHHHHHHHHHHHHHHHHHHH-HHHHHHHHhCCCCCcChhhHHHhhhhcC
Q psy13691 30 KINVSKDVRLAAGKAASLFILHLT-TEALSIANEKNRKTLSGVDVIEGVKQIG 81 (103)
Q Consensus 30 ~~~iskda~~~l~~~~~~Fi~~lt-~~A~~~a~~~~RkTI~~eDV~~Al~~lg 81 (103)
.+.+|.||...|.+. =-|+.-=. ..+-..|++.|...|+.+.+..|=.++|
T Consensus 461 ~~~w~~ea~~~l~~i-P~f~r~~~r~~~e~~a~~~g~~~it~~~~~~a~~~~~ 512 (513)
T CHL00076 461 DLIWSPESQLELSKI-PGFVRGKVKRNTEKFARQNGITNITVEVMYAAKEALS 512 (513)
T ss_pred CCCCCHHHHHHHHhC-CHHhHHHHHHHHHHHHHHcCCCeEcHHHHHHHHHhhC
Confidence 378999999999998 55555333 4445678999999999999999977665
No 142
>cd05833 Ribosomal_P2 Ribosomal protein P2. This subfamily represents the eukaryotic large ribosomal protein P2. Eukaryotic P1 and P2 are functionally equivalent to the bacterial protein L7/L12, but are not homologous to L7/L12. P2 is located in the L12 stalk, with proteins P1, P0, L11, and 28S rRNA. P1 and P2 are the only proteins in the ribosome to occur as multimers, always appearing as sets of heterodimers. Recent data indicate that eukaryotes have four copies (two heterodimers), while most archaeal species contain six copies of L12p (three homodimers). Bacteria may have four or six copies of L7/L12 (two or three homodimers) depending on the species. Experiments using S. cerevisiae P1 and P2 indicate that P1 proteins are positioned more internally with limited reactivity in the C-terminal domains, while P2 proteins seem to be more externally located and are more likely to interact with other cellular components. In lower eukaryotes, P1 and P2 are further subdivided into P1A, P1B, P2
Probab=35.59 E-value=1.1e+02 Score=20.37 Aligned_cols=28 Identities=25% Similarity=0.224 Sum_probs=24.3
Q ss_pred HHHHHHhCCCCCcChhhHHHhhhhcCch
Q psy13691 56 ALSIANEKNRKTLSGVDVIEGVKQIGFE 83 (103)
Q Consensus 56 A~~~a~~~~RkTI~~eDV~~Al~~lgf~ 83 (103)
|+-.|.-.|+..+|.+||...|+..|.+
T Consensus 6 AylL~~l~g~~~pTa~dI~~IL~AaGve 33 (109)
T cd05833 6 AYLLAVLGGNASPSAADVKKILGSVGVE 33 (109)
T ss_pred HHHHHHHcCCCCCCHHHHHHHHHHcCCC
Confidence 5667888888899999999999988875
No 143
>COG4018 Uncharacterized protein conserved in archaea [Function unknown]
Probab=35.56 E-value=64 Score=26.54 Aligned_cols=39 Identities=23% Similarity=0.351 Sum_probs=31.0
Q ss_pred cCCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHH
Q psy13691 6 DDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAAS 46 (103)
Q Consensus 6 ~d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~ 46 (103)
..+.|| .|.+|||+-+..++..++-|.++-.++|..++.
T Consensus 327 GkFGLp--rVm~Imree~~sg~~t~vpi~k~~leaia~a~~ 365 (505)
T COG4018 327 GKFGLP--RVMAIMREELGSGYNTKVPIGKEELEAIARAAL 365 (505)
T ss_pred cccCcH--HHHHHHHHHHhcCCCCcCCcCHHHHHHHHHHHH
Confidence 345666 589999999887655667899999999988764
No 144
>PF02361 CbiQ: Cobalt transport protein; InterPro: IPR003339 Cobalt transport proteins are most often found in cobalamin (vitamin B12) biosynthesis operons. Salmonella typhimurium synthesizes cobalamin (vitamin B12) de novo under anaerobic conditions. Not all Salmonella and Pseudomonas cobalamin synthetic genes have apparent homologs in the other species suggesting that the cobalamin biosynthetic pathways differ between the two organisms [].; GO: 0015087 cobalt ion transmembrane transporter activity, 0006824 cobalt ion transport, 0009236 cobalamin biosynthetic process
Probab=35.40 E-value=55 Score=23.00 Aligned_cols=64 Identities=17% Similarity=0.155 Sum_probs=39.7
Q ss_pred ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCchH------------HHHHHHHHHHHHHh
Q psy13691 31 INVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFEV------------IIEILGKSYNAAVS 98 (103)
Q Consensus 31 ~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~------------~~~~l~~~l~~~k~ 98 (103)
..++.+. +..++..++..+..-..-.. =-.|.+++|+..+++.++++. |++.+.+..+.-++
T Consensus 94 ~~i~~~g---~~~~~~~~lr~~~~~~~~~~---~~~tt~~~~l~~~l~~l~~P~~~~~~~i~l~~r~ip~l~~~~~~i~~ 167 (224)
T PF02361_consen 94 FSITQEG---LIYAALLALRILAILLASLL---FILTTSPSDLISALRKLRLPYPKIALMISLTLRFIPLLLEEFKRIRE 167 (224)
T ss_pred hhhhHHH---HHHHHHHHHHHHHHHHHHHH---HHHHCCHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3455554 44444444444433332222 124788999999999999887 77888777776666
Q ss_pred cc
Q psy13691 99 IK 100 (103)
Q Consensus 99 ~~ 100 (103)
++
T Consensus 168 A~ 169 (224)
T PF02361_consen 168 AQ 169 (224)
T ss_pred HH
Confidence 54
No 145
>COG1389 DNA topoisomerase VI, subunit B [DNA replication, recombination, and repair]
Probab=35.18 E-value=33 Score=29.02 Aligned_cols=38 Identities=26% Similarity=0.399 Sum_probs=32.6
Q ss_pred cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcC
Q psy13691 32 NVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLS 69 (103)
Q Consensus 32 ~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~ 69 (103)
-|-+|.+.++++||.+.=.||.....+.-..+++++|.
T Consensus 442 eIe~Eir~Al~evaRkL~~yLsrk~r~~e~~~K~~~i~ 479 (538)
T COG1389 442 EIENEIRLALMEVARKLKLYLSRKRREMEERKKRKTIE 479 (538)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 47789999999999999999999998877777777653
No 146
>COG5340 Predicted transcriptional regulator [Transcription]
Probab=34.92 E-value=76 Score=24.55 Aligned_cols=57 Identities=19% Similarity=0.156 Sum_probs=45.9
Q ss_pred CccCCCCcHHHHHHHHHhhCCCCC--cccccccHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy13691 4 SLDDLNLPSAIIQRLIKEALPKDA--EGKINVSKDVRLAAGKAASLFILHLTTEALSIA 60 (103)
Q Consensus 4 ~~~d~~LP~a~V~ri~K~~l~~~~--~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a 60 (103)
.++.+..|.+++.|-++..+.... +|-.-+.+-.+.+...++++|..|+-..+|-.+
T Consensus 149 ~Ie~~~VpvttlaKTi~DC~~kP~YCGG~~~~akAl~aa~e~a~~e~t~Yl~R~~n~Aa 207 (269)
T COG5340 149 SIEGTVVPVTTLAKTIVDCADKPEYCGGIRELAKALVAADEQACSEATEYLQRLDNGAA 207 (269)
T ss_pred ceeeeeeehHHHHHHHHHHhcCccccCCHHHHHHHHHHhHHHHHHHHHHHHHhccchHH
Confidence 356667999999999999987521 344579999999999999999999988776544
No 147
>PF07928 Vps54: Vps54-like protein; InterPro: IPR012501 This family contains various proteins that are homologues of the yeast Vps54 protein, such as the rat homologue (Q9JMK8 from SWISSPROT), the human homologue (Q86YF7 from SWISSPROT), and the mouse homologue (Q8R3X1 from SWISSPROT). In yeast, Vps54 associates with Vps52 and Vps53 proteins to form a trimolecular complex that is involved in protein transport between Golgi, endosomal, and vacuolar compartments []. All Vps54 homologues contain a coiled coil region (not found in the region featured in this family) and multiple dileucine motifs []. ; GO: 0042147 retrograde transport, endosome to Golgi; PDB: 3N1E_B 3N1B_B.
Probab=34.84 E-value=13 Score=25.74 Aligned_cols=36 Identities=11% Similarity=0.222 Sum_probs=0.0
Q ss_pred HhCCCCCcChhhHHHhhhhcCch-HHHHHHHHHHHHH
Q psy13691 61 NEKNRKTLSGVDVIEGVKQIGFE-VIIEILGKSYNAA 96 (103)
Q Consensus 61 ~~~~RkTI~~eDV~~Al~~lgf~-~~~~~l~~~l~~~ 96 (103)
+..|-|+|++.|+.-|-+.|+|- .++|.++++++.+
T Consensus 61 ~~agLK~IT~KhLALasq~L~~~~~lip~i~~~~~~~ 97 (135)
T PF07928_consen 61 RSAGLKTITAKHLALASQSLSFIISLIPYIREFFERH 97 (135)
T ss_dssp -------------------------------------
T ss_pred hccCcCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 45689999999999999999995 6788888777765
No 148
>PRK14868 DNA topoisomerase VI subunit B; Provisional
Probab=34.78 E-value=74 Score=28.44 Aligned_cols=36 Identities=14% Similarity=0.163 Sum_probs=28.4
Q ss_pred cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCC
Q psy13691 32 NVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKT 67 (103)
Q Consensus 32 ~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkT 67 (103)
-|-+|.+.+|++||.+.=.||...-...-..+++++
T Consensus 633 EI~~EI~lAl~~~aR~Lk~yl~k~~~~~~~~~k~~~ 668 (795)
T PRK14868 633 EIEDEIELAIREAARELKSYLNKRRSMQKRREKQDV 668 (795)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 578889999999999999999987665555555544
No 149
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=34.45 E-value=48 Score=24.50 Aligned_cols=36 Identities=11% Similarity=0.111 Sum_probs=28.1
Q ss_pred CCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHH
Q psy13691 9 NLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLT 53 (103)
Q Consensus 9 ~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt 53 (103)
..-.+||.|.+... -+||.+.++-+.+++.+. .|.-
T Consensus 9 gVS~~TVSrvLn~~--------~~vs~~tr~rV~~~a~~l-gY~p 44 (327)
T PRK10423 9 GVSTSTVSHVINKD--------RFVSEAITAKVEAAIKEL-NYAP 44 (327)
T ss_pred CCcHHHHHHHhCCC--------CCCCHHHHHHHHHHHHHH-CCCc
Confidence 56689999999642 369999999999999875 4543
No 150
>KOG0785|consensus
Probab=34.42 E-value=1.4e+02 Score=24.22 Aligned_cols=66 Identities=14% Similarity=0.073 Sum_probs=48.5
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCchHHHHHHHHHHHHHHhc
Q psy13691 33 VSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFEVIIEILGKSYNAAVSI 99 (103)
Q Consensus 33 iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~~~~~l~~~l~~~k~~ 99 (103)
+-.-..+.|...++.--.-++.-|.++|+..+|+.++.-|=.+-|+..+ .-|++.+++.-+.|-+.
T Consensus 164 vvpGVvqsiK~IT~~AS~Ria~~AF~yAr~~~R~~vtvvHKaNImr~tD-GLFle~cre~a~~y~dI 229 (365)
T KOG0785|consen 164 VVPGVVQSIKLITEAASRRIAEYAFEYARQNGRKRVTVVHKANIMRMTD-GLFLECCREVAKKYPDI 229 (365)
T ss_pred ccccHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCceEEEehhhhhhhcc-hHHHHHHHHHhhhCCcc
Confidence 4444677777777777778888999999999999999888777775443 34667777666555443
No 151
>PTZ00112 origin recognition complex 1 protein; Provisional
Probab=34.10 E-value=1.5e+02 Score=27.69 Aligned_cols=51 Identities=10% Similarity=0.038 Sum_probs=29.3
Q ss_pred cccHHHHHHHHH-------HHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCchHHH
Q psy13691 32 NVSKDVRLAAGK-------AASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFEVII 86 (103)
Q Consensus 32 ~iskda~~~l~~-------~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~~~ 86 (103)
.++.++..++.+ =+...+..| ..|.++ .+..+|+.+||..|++.+..+...
T Consensus 955 VLdDdAIELIArkVAq~SGDARKALDIL-RrAgEi---kegskVT~eHVrkAleeiE~srI~ 1012 (1164)
T PTZ00112 955 IIDHTAIQLCARKVANVSGDIRKALQIC-RKAFEN---KRGQKIVPRDITEATNQLFDSPLT 1012 (1164)
T ss_pred CCCHHHHHHHHHhhhhcCCHHHHHHHHH-HHHHhh---cCCCccCHHHHHHHHHHHHhhhHH
Confidence 466666666654 122222222 334343 234489999999999988555433
No 152
>PF07580 Peptidase_M26_C: M26 IgA1-specific Metallo-endopeptidase C-terminal region; InterPro: IPR011505 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. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This entry represents metallopeptidases belonging to MEROPS peptidase family M26 (IgA1-specific metallopeptidase, clan MA). They are extracellular enzymes, which cleave mammalian IgA. They are only found in Gram-positive bacteria and are often found associated with IPR001899 from INTERPRO; they may be attached to the cell wall. This entry also contains the metallopeptidases ZmpB and ZmpC from Streptococcus pneumoniae. These metallopeptidases are thought to contribute to the inflammatory response to Streptococcal infection [, ].; GO: 0004222 metalloendopeptidase activity, 0008270 zinc ion binding, 0005576 extracellular region, 0005618 cell wall
Probab=33.40 E-value=91 Score=27.66 Aligned_cols=62 Identities=13% Similarity=0.097 Sum_probs=49.6
Q ss_pred ccccccHHHHHHHHHHH--HHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCchHHHHHHH
Q psy13691 29 GKINVSKDVRLAAGKAA--SLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFEVIIEILG 90 (103)
Q Consensus 29 ~~~~iskda~~~l~~~~--~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~~~~~l~ 90 (103)
|++.+-+-|-+++..-. .-||-|++.+=...|+.+|+.+++.+-|++.+-.=.|..+.+--|
T Consensus 590 G~~~Frr~afeLlg~~GYe~Gfv~Y~SNkyk~~A~~~g~~~l~D~~ii~Ki~~g~y~s~~~fKK 653 (737)
T PF07580_consen 590 GDLMFRRNAFELLGYYGYEDGFVPYASNKYKKEAKAEGKKILSDDYIIKKIFNGQYNSWEDFKK 653 (737)
T ss_pred ccchhhHHHHHHHHHhcccccchHhhhhhHHHHHHhcCCCcccHHHHHHHHhcCccCCHHHHHH
Confidence 55677777777776543 569999999999999999999999999999998888865544333
No 153
>PTZ00183 centrin; Provisional
Probab=33.32 E-value=1.4e+02 Score=19.45 Aligned_cols=19 Identities=0% Similarity=0.113 Sum_probs=11.4
Q ss_pred HhCCCCCcChhhHHHhhhh
Q psy13691 61 NEKNRKTLSGVDVIEGVKQ 79 (103)
Q Consensus 61 ~~~~RkTI~~eDV~~Al~~ 79 (103)
-.++...|+.++.+.++..
T Consensus 63 d~~~~g~i~~~eF~~~~~~ 81 (158)
T PTZ00183 63 DKDGSGKIDFEEFLDIMTK 81 (158)
T ss_pred CCCCCCcEeHHHHHHHHHH
Confidence 3455666777776666543
No 154
>cd00823 TopoIIB_Trans TopoIIB_Trans: Transducer domain, having a ribosomal S5 domain 2-like fold, of the type found in proteins of the type IIB family of DNA topoisomerases similar to Sulfolobus shibatae topoisomerase VI (topoVI). The sole representative of the Type IIB family is topo VI. Topo VI enzymes are heterotetramers found in archaea and plants. S. shibatae topoVI relaxes both positive and negative supercoils, and in addition has a strong decatenase activity. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes.
Probab=32.83 E-value=1.1e+02 Score=21.83 Aligned_cols=27 Identities=15% Similarity=0.206 Sum_probs=23.1
Q ss_pred ccccHHHHHHHHHHHHHHHHHHHHHHH
Q psy13691 31 INVSKDVRLAAGKAASLFILHLTTEAL 57 (103)
Q Consensus 31 ~~iskda~~~l~~~~~~Fi~~lt~~A~ 57 (103)
--|-+|.+.+|++||...=.||...-.
T Consensus 118 pEI~~EIrlAl~~~~R~L~~~l~kk~~ 144 (151)
T cd00823 118 PEIEEEIKLALQEVARKLKRYLSKKRK 144 (151)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 358889999999999999999987543
No 155
>PRK14971 DNA polymerase III subunits gamma and tau; Provisional
Probab=32.37 E-value=1.8e+02 Score=24.88 Aligned_cols=71 Identities=10% Similarity=0.053 Sum_probs=40.5
Q ss_pred CcHHHHHHHHHhhCC-CCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCchHH
Q psy13691 10 LPSAIIQRLIKEALP-KDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFEVI 85 (103)
Q Consensus 10 LP~a~V~ri~K~~l~-~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~~ 85 (103)
++..-+.+.++..+. .+ +.++.++...|.+.+.-=+..+-.+....+.-.+++ |+.++|...+.....+.+
T Consensus 180 ls~~ei~~~L~~ia~~eg----i~i~~~al~~La~~s~gdlr~al~~Lekl~~y~~~~-It~~~V~~~l~~~~~~~i 251 (614)
T PRK14971 180 IQVADIVNHLQYVASKEG----ITAEPEALNVIAQKADGGMRDALSIFDQVVSFTGGN-ITYKSVIENLNILDYDYY 251 (614)
T ss_pred CCHHHHHHHHHHHHHHcC----CCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhccCC-ccHHHHHHHhCCCCHHHH
Confidence 334444444444332 24 788999888887766544444444443433333444 888888877765554444
No 156
>PRK14867 DNA topoisomerase VI subunit B; Provisional
Probab=31.68 E-value=97 Score=27.09 Aligned_cols=36 Identities=17% Similarity=0.103 Sum_probs=27.8
Q ss_pred cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCC
Q psy13691 32 NVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKT 67 (103)
Q Consensus 32 ~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkT 67 (103)
-|-+|.+.+|++||...=.||...-...-..+++++
T Consensus 592 eI~~Ei~lAl~~~~r~L~~~l~~~~~~~~~~~k~~~ 627 (659)
T PRK14867 592 EIFNEIRQALMICARELEKYISRIRREKEEEQKRKY 627 (659)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 477899999999999999999986555444444544
No 157
>PF10113 Fibrillarin_2: Fibrillarin-like archaeal protein; InterPro: IPR016760 Members of this protein family are HmdC, whose gene regularly occurs in the context of genes for HmdA (5,10-methenyltetrahydromethanopterin hydrogenase) and the radical SAM protein HmdB involved in biosynthesis of the HmdA cofactor. Bioinformatics suggests this protein, a homologue of eukaryotic fibrillarin, may be involved in biosynthesis of the guanylyl pyridinol cofactor in HmdA.
Probab=31.63 E-value=70 Score=26.85 Aligned_cols=40 Identities=20% Similarity=0.319 Sum_probs=30.1
Q ss_pred CccCCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHH
Q psy13691 4 SLDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAAS 46 (103)
Q Consensus 4 ~~~d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~ 46 (103)
+...+.||+ |-||||+-+..+ .+...++++-..+|.+++.
T Consensus 325 rRg~FGLPR--V~~ImkeEv~~~-~~~~p~~k~~l~ala~a~k 364 (505)
T PF10113_consen 325 RRGNFGLPR--VMKIMKEEVANG-LTPVPAQKEELEALAKAVK 364 (505)
T ss_pred ccccCCcHH--HHHHHHHHHhcC-CCcccccHHHHHHHHHHHh
Confidence 345667775 899999988543 3456899999999998653
No 158
>PF14434 Imm6: Immunity protein Imm6
Probab=31.57 E-value=1.7e+02 Score=19.89 Aligned_cols=36 Identities=17% Similarity=0.166 Sum_probs=27.7
Q ss_pred HHHHHHHHHHHh--CCCCCcChhhHHHhhhhcCchHHHH
Q psy13691 51 HLTTEALSIANE--KNRKTLSGVDVIEGVKQIGFEVIIE 87 (103)
Q Consensus 51 ~lt~~A~~~a~~--~~RkTI~~eDV~~Al~~lgf~~~~~ 87 (103)
+...+|.+.|.+ +| +.++++++..-|+..++.+...
T Consensus 25 ~~~~~aL~~cw~wle~-~~~~~D~LY~lldn~D~~gi~~ 62 (122)
T PF14434_consen 25 EFVREALDACWKWLEG-KEVTGDELYSLLDNEDENGIFI 62 (122)
T ss_pred HHHHHHHHHHHHHHHc-CCCCHHHHHHHHhCcccccHHH
Confidence 344888888876 45 8999999999998877765443
No 159
>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=30.58 E-value=88 Score=16.90 Aligned_cols=34 Identities=21% Similarity=0.219 Sum_probs=24.4
Q ss_pred CCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHH
Q psy13691 7 DLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLF 48 (103)
Q Consensus 7 d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~F 48 (103)
...+..++|.|+.+.. ..++.+....+.+++.++
T Consensus 6 ~~gvs~~tvs~~l~g~--------~~vs~~~~~~i~~~~~~l 39 (52)
T cd01392 6 AAGVSVATVSRVLNGK--------PRVSEETRERVLAAAEEL 39 (52)
T ss_pred HHCcCHHHHHHHHcCC--------CCCCHHHHHHHHHHHHHh
Confidence 3467788899988653 358888888877776654
No 160
>PF02718 Herpes_UL31: Herpesvirus UL31-like protein; InterPro: IPR021152 This is a family of Herpesvirus proteins, belong to the UL31 family, which including UL31, UL53, and the product of ORF69 in some strains. The proteins in this family have no known function.
Probab=30.39 E-value=62 Score=25.02 Aligned_cols=74 Identities=20% Similarity=0.336 Sum_probs=44.3
Q ss_pred ccCCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCchH
Q psy13691 5 LDDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFEV 84 (103)
Q Consensus 5 ~~d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~ 84 (103)
.+++-||-.-|.+|+-+. |. .+|+-|... .-|+.-++... ..+..-+|.++||..++.+|+|++
T Consensus 179 ~~~lHl~~~~i~~ll~n~-~~-----Y~i~~dv~~------~~fvL~v~~~~----~~~~~~~I~~~~I~~ki~dld~~d 242 (258)
T PF02718_consen 179 GKSLHLHERCIRQLLDNC-PG-----YKISADVWQ------GTFVLVVRPDR----EEQTSPKIDADDIYCKICDLDFPD 242 (258)
T ss_pred CCCccchHHHHHHHHHhC-CC-----CeEEEEEec------CEEEEEEEeCC----CcCCCcccCHHHHHHHHHcCCCCh
Confidence 356778877777777666 54 355444321 12333333221 122477899999999999999984
Q ss_pred HHHHHHHHHHHHH
Q psy13691 85 IIEILGKSYNAAV 97 (103)
Q Consensus 85 ~~~~l~~~l~~~k 97 (103)
++....+.|.
T Consensus 243 ---El~~ey~k~~ 252 (258)
T PF02718_consen 243 ---ELKEEYEKYY 252 (258)
T ss_pred ---HHHHHHHHHH
Confidence 4444444443
No 161
>PF03477 ATP-cone: ATP cone domain; InterPro: IPR005144 The ATP-cone is an evolutionarily mobile, ATP-binding regulatory domain which is found in a variety of proteins including ribonucleotide reductases, phosphoglycerate kinases and transcriptional regulators []. In ribonucleotide reductase protein R1 (P28903 from SWISSPROT) from Escherichia coli this domain is located at the N terminus, and is composed mostly of helices []. It forms part of the allosteric effector region and contains the general allosteric activity site in a cleft located at the tip of the N-terminal region []. This site binds either ATP (activating) or dATP (inhibitory), with the base bound in a hydrophobic pocket and the phosphates bound to basic residues. Substrate binding to this site is thought to affect enzyme activity by altering the relative positions of the two subunits of ribonucleotide reductase.; PDB: 2XO4_A 1RLR_A 7R1R_B 5R1R_A 2XO5_B 2XAW_A 2R1R_C 2XAY_B 2X0X_C 2XAZ_A ....
Probab=30.14 E-value=61 Score=19.89 Aligned_cols=37 Identities=14% Similarity=0.241 Sum_probs=19.9
Q ss_pred HHHHHHHHHHhCCCCCcChhhHHHhhh----hcCchHHHHH
Q psy13691 52 LTTEALSIANEKNRKTLSGVDVIEGVK----QIGFEVIIEI 88 (103)
Q Consensus 52 lt~~A~~~a~~~~RkTI~~eDV~~Al~----~lgf~~~~~~ 88 (103)
|+.+........++..|+.++|...+. +.|+.++...
T Consensus 40 i~~~V~~~l~~~~~~~is~~eI~~~v~~~L~~~~~~~~a~~ 80 (90)
T PF03477_consen 40 IASEVENKLYDSGKEEISTEEIQDIVENALMEEGFYDVARA 80 (90)
T ss_dssp HHHHHHTC-ST----TEEHHHHHHHHHHHHHTSTTHHHHHH
T ss_pred HHHHHHHHHHhccCCCeeHHHHHHHHHHHHHcCChHHHHHH
Confidence 344455555666677899999877665 5565555443
No 162
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=30.01 E-value=50 Score=24.82 Aligned_cols=37 Identities=22% Similarity=0.248 Sum_probs=28.6
Q ss_pred CCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHH
Q psy13691 9 NLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTT 54 (103)
Q Consensus 9 ~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~ 54 (103)
..-.++|.|++... -+||.+.++-+.+++.+ +.|.-.
T Consensus 12 GVS~~TVSrvLn~~--------~~Vs~~tr~rV~~~a~e-lgY~pn 48 (343)
T PRK10727 12 GVSVATVSRVINNS--------PKASEASRLAVHSAMES-LSYHPN 48 (343)
T ss_pred CCCHHHHHHHhCCC--------CCCCHHHHHHHHHHHHH-HCCCCC
Confidence 56678999998542 36999999999999998 455443
No 163
>PRK06402 rpl12p 50S ribosomal protein L12P; Reviewed
Probab=30.00 E-value=1.5e+02 Score=19.91 Aligned_cols=27 Identities=11% Similarity=0.209 Sum_probs=21.5
Q ss_pred HHHHHHhCCCCCcChhhHHHhhhhcCch
Q psy13691 56 ALSIANEKNRKTLSGVDVIEGVKQIGFE 83 (103)
Q Consensus 56 A~~~a~~~~RkTI~~eDV~~Al~~lgf~ 83 (103)
|.-++...|+ .||.++|...|+..|.+
T Consensus 6 AaLLL~~~g~-~it~e~I~~IL~AAGve 32 (106)
T PRK06402 6 AALLLHSAGK-EINEDNLKKVLEAAGVE 32 (106)
T ss_pred HHHHHHhcCC-CCCHHHHHHHHHHcCCC
Confidence 4445666666 99999999999999886
No 164
>COG1239 ChlI Mg-chelatase subunit ChlI [Coenzyme metabolism]
Probab=29.99 E-value=1.1e+02 Score=25.28 Aligned_cols=48 Identities=13% Similarity=0.234 Sum_probs=40.7
Q ss_pred ccccHHHHHHHHHHHHHHHH-------HHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691 31 INVSKDVRLAAGKAASLFIL-------HLTTEALSIANEKNRKTLSGVDVIEGVK 78 (103)
Q Consensus 31 ~~iskda~~~l~~~~~~Fi~-------~lt~~A~~~a~~~~RkTI~~eDV~~Al~ 78 (103)
+.++.++...+...|..+-. .++..|..++.-.||.+++.+||-.|++
T Consensus 266 V~l~~~~~~~ia~~~~~~~v~g~radi~~~r~a~a~aa~~Gr~~v~~~Di~~a~~ 320 (423)
T COG1239 266 VELDDDAETKIAELCARLAVDGHRADIVVVRAAKALAALRGRTEVEEEDIREAAE 320 (423)
T ss_pred ccCcHHHHHHHHHHHHHhccCCCchhhHHHHHHHHHHHhcCceeeehhhHHHHHh
Confidence 78999999999988887753 4667777888899999999999999975
No 165
>PRK00754 signal recognition particle protein Srp19; Provisional
Probab=29.97 E-value=41 Score=22.03 Aligned_cols=21 Identities=19% Similarity=0.316 Sum_probs=17.4
Q ss_pred cChhhHHHhhhhcCchHHHHH
Q psy13691 68 LSGVDVIEGVKQIGFEVIIEI 88 (103)
Q Consensus 68 I~~eDV~~Al~~lgf~~~~~~ 88 (103)
.+.++|..|++.||+...+++
T Consensus 35 P~~~EI~~a~~~lgl~~~~e~ 55 (95)
T PRK00754 35 PRLEEIIEAAEKLGLNPEVEP 55 (95)
T ss_pred CCHHHHHHHHHHcCCCeEEee
Confidence 688999999999999865543
No 166
>PF03484 B5: tRNA synthetase B5 domain; InterPro: IPR005147 Domain B5 is found in phenylalanine-tRNA synthetase beta subunits. This domain has been shown to bind DNA through a winged helix-turn-helix motif []. Phenylalanine-tRNA synthetase may influence common cellular processes via DNA binding, in addition to its aminoacylation function.; GO: 0000287 magnesium ion binding, 0003723 RNA binding, 0005524 ATP binding, 0006432 phenylalanyl-tRNA aminoacylation; PDB: 2AKW_B 1B70_B 1B7Y_B 2ALY_B 2IY5_B 2AMC_B 3PCO_D 2CXI_C 1JJC_B 1EIY_B ....
Probab=29.78 E-value=33 Score=20.64 Aligned_cols=17 Identities=29% Similarity=0.630 Sum_probs=12.1
Q ss_pred CcChhhHHHhhhhcCch
Q psy13691 67 TLSGVDVIEGVKQIGFE 83 (103)
Q Consensus 67 TI~~eDV~~Al~~lgf~ 83 (103)
.++.+++...|+.|||.
T Consensus 18 ~i~~~~i~~~L~~lg~~ 34 (70)
T PF03484_consen 18 DISPEEIIKILKRLGFK 34 (70)
T ss_dssp ---HHHHHHHHHHTT-E
T ss_pred CCCHHHHHHHHHHCCCE
Confidence 78999999999999996
No 167
>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA.
Probab=29.76 E-value=2e+02 Score=24.94 Aligned_cols=36 Identities=14% Similarity=0.114 Sum_probs=27.1
Q ss_pred ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691 31 INVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK 78 (103)
Q Consensus 31 ~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~ 78 (103)
...|..++..|.. |...|...+...|+.+|++.||=
T Consensus 76 ~~~S~~lk~vL~~------------A~~~A~~~g~~~I~teHLLLALl 111 (731)
T TIGR02639 76 PEQTVGVQRVLQR------------ALLHVKSAGKKEIGIGDILVALF 111 (731)
T ss_pred CCcCHHHHHHHHH------------HHHHHHHcCCCccCHHHHHHHHh
Confidence 4577777777766 44456667899999999998864
No 168
>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA.
Probab=29.69 E-value=85 Score=27.20 Aligned_cols=23 Identities=13% Similarity=0.200 Sum_probs=19.1
Q ss_pred HHHHHHHhCCCCCcChhhHHHhh
Q psy13691 55 EALSIANEKNRKTLSGVDVIEGV 77 (103)
Q Consensus 55 ~A~~~a~~~~RkTI~~eDV~~Al 77 (103)
.|...|..-+..-|+++|++.||
T Consensus 11 ~A~~~A~~~~h~~V~~EHLLlaL 33 (731)
T TIGR02639 11 AALEEAKKRRHEFVTLEHILLAL 33 (731)
T ss_pred HHHHHHHHhCCCcCcHHHHHHHH
Confidence 46678888888999999998875
No 169
>smart00445 LINK Link (Hyaluronan-binding).
Probab=29.58 E-value=74 Score=20.85 Aligned_cols=29 Identities=14% Similarity=0.197 Sum_probs=26.2
Q ss_pred HHHHHHHHhCCCCCcChhhHHHhhhhcCch
Q psy13691 54 TEALSIANEKNRKTLSGVDVIEGVKQIGFE 83 (103)
Q Consensus 54 ~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~ 83 (103)
.+|.+.|...+-.--+++++..|-+. ||+
T Consensus 18 ~eA~~aC~~~ga~lAs~~QL~~Aw~~-Gld 46 (94)
T smart00445 18 AEAREACRAQGATLATVGQLYAAWQD-GFD 46 (94)
T ss_pred HHHHHHHHHcCCEeCCHHHHHHHHHh-chh
Confidence 68999999999999999999999886 876
No 170
>PF03979 Sigma70_r1_1: Sigma-70 factor, region 1.1; InterPro: IPR007127 The bacterial core RNA polymerase complex, which consists of five subunits, 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 []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. This entry represents Region 1.1 which modulates DNA binding by region 2 and 4 when sigma is unbound by the core RNA polymerase [, ]. Region 1.1 is also involved in promoter binding.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2K6X_A.
Probab=29.42 E-value=91 Score=19.30 Aligned_cols=34 Identities=9% Similarity=0.142 Sum_probs=19.0
Q ss_pred HhCCCCCcChhhHHHhhhhcCch-HHHHHHHHHHH
Q psy13691 61 NEKNRKTLSGVDVIEGVKQIGFE-VIIEILGKSYN 94 (103)
Q Consensus 61 ~~~~RkTI~~eDV~~Al~~lgf~-~~~~~l~~~l~ 94 (103)
...+|..||+++|..+|....++ +-++.+-..|+
T Consensus 15 ~gK~~G~lT~~eI~~~L~~~~~~~e~id~i~~~L~ 49 (82)
T PF03979_consen 15 KGKKKGYLTYDEINDALPEDDLDPEQIDEIYDTLE 49 (82)
T ss_dssp HHHHHSS-BHHHHHHH-S-S---HHHHHHHHHHHH
T ss_pred HHhhcCcCCHHHHHHHcCccCCCHHHHHHHHHHHH
Confidence 33456679999999999977775 44555555544
No 171
>CHL00095 clpC Clp protease ATP binding subunit
Probab=29.21 E-value=78 Score=27.87 Aligned_cols=35 Identities=6% Similarity=-0.004 Sum_probs=26.9
Q ss_pred cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691 32 NVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK 78 (103)
Q Consensus 32 ~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~ 78 (103)
++++++..+|. .|...|..-+...|+++|++.||=
T Consensus 4 rfT~~a~~vL~------------~A~~~A~~~~h~~V~~EHLLLaLL 38 (821)
T CHL00095 4 RFTEKAIKVIM------------LSQEEARRLGHNFVGTEQILLGLI 38 (821)
T ss_pred hHhHHHHHHHH------------HHHHHHHHhCCCcCcHHHHHHHHH
Confidence 45566666654 477788899999999999998873
No 172
>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=29.14 E-value=1.4e+02 Score=25.55 Aligned_cols=71 Identities=14% Similarity=0.097 Sum_probs=43.7
Q ss_pred HHHHHHHHhhCCCCCcccccccHHHHHHHHHHH---HHHHHHHHHHH----HH---HHHhCCCCCcChhhHHHhhhhcCc
Q psy13691 13 AIIQRLIKEALPKDAEGKINVSKDVRLAAGKAA---SLFILHLTTEA----LS---IANEKNRKTLSGVDVIEGVKQIGF 82 (103)
Q Consensus 13 a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~---~~Fi~~lt~~A----~~---~a~~~~RkTI~~eDV~~Al~~lgf 82 (103)
.-+..|++..+... ...++.++..+|.+++ ...++.|.... +. .+...++..|+.+||.++++.--|
T Consensus 356 edi~~Il~~~a~~~---~v~ls~eal~~L~~ys~~gRraln~L~~~~~~~~~~~~~~~~~~~~~~I~~edv~~~l~~~r~ 432 (615)
T TIGR02903 356 EDIALIVLNAAEKI---NVHLAAGVEELIARYTIEGRKAVNILADVYGYALYRAAEAGKENDKVTITQDDVYEVIQISRL 432 (615)
T ss_pred HHHHHHHHHHHHHc---CCCCCHHHHHHHHHCCCcHHHHHHHHHHHHHHHHHHHHHhccCCCCeeECHHHHHHHhCCCcC
Confidence 44556666655431 1568899998888765 34444443221 11 122345568999999999987777
Q ss_pred hHHH
Q psy13691 83 EVII 86 (103)
Q Consensus 83 ~~~~ 86 (103)
..|.
T Consensus 433 ~~~~ 436 (615)
T TIGR02903 433 SPYE 436 (615)
T ss_pred ccch
Confidence 6554
No 173
>cd01102 Link_Domain The link domain is a hyaluronan (HA)-binding domain. It functions to mediate adhesive interactions during inflammatory leukocyte homing and tumor metastasis. It is found in the CD44 receptor and in human TSG-6. TSG-6 is the protein product of the tumor necrosis factor-stimulated gene-6. TSG-6 has a strong anti-inflammatory effect in models of acute inflammation and autoimmune arthritis and plays an essential role in female fertility. This group also contains the link domains of the chondroitin sulfate proteoglycan core proteins (CSPG) including aggrecan, versican, neurocan, and brevican and the link domains of the vertebrate HAPLN (HA and proteoglycan binding link) protein family. In cartilage, aggrecan forms cartilage link protein stabilized aggregates with HA. These aggregates contribute to the tissue's load bearing properties. Aggregates in which other CSPGs substitute for aggregan might contribute to the structural integrity of many different tissues. Members of
Probab=29.06 E-value=73 Score=20.78 Aligned_cols=29 Identities=14% Similarity=0.204 Sum_probs=26.0
Q ss_pred HHHHHHHHhCCCCCcChhhHHHhhhhcCch
Q psy13691 54 TEALSIANEKNRKTLSGVDVIEGVKQIGFE 83 (103)
Q Consensus 54 ~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~ 83 (103)
.+|.+.|...|-.-=+++++..|-+. ||+
T Consensus 17 ~eA~~aC~~~ga~lAs~~QL~~Aw~~-G~~ 45 (92)
T cd01102 17 AEAALACKARGAHLATPGQLEAAWQD-GFD 45 (92)
T ss_pred HHHHHHHHHcCCEeCCHHHHHHHHHc-chh
Confidence 68999999999999999999999876 876
No 174
>TIGR02849 spore_III_AD stage III sporulation protein AD. Members of this family are the uncharacterized protein SpoIIIAD, part of the spoIIIA operon that acts at sporulation stage III as part of a cascade of events leading to endospore formation. Note that the start sites of members of this family as annotated tend to be variable; quite a few members have apparent homologous protein-coding regions continuing upstream of the first available start codon. The length of the alignment has been set to try to detect all valid members of the family, even if annotation of the start site begins too far downstream.
Probab=29.02 E-value=37 Score=22.59 Aligned_cols=38 Identities=11% Similarity=0.063 Sum_probs=29.8
Q ss_pred ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcCh
Q psy13691 31 INVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSG 70 (103)
Q Consensus 31 ~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~ 70 (103)
..++..-...+-|... |.|++.-+.++|++.|-.+|..
T Consensus 35 a~i~~~Yi~~llKiiG--IaYIaef~s~iCkDAG~~aiAs 72 (101)
T TIGR02849 35 AGLDSLYLATVLKIIG--IAYIAEFGSQICKDAGEKAIAS 72 (101)
T ss_pred cCCChHHHHHHHHHHH--HHHHHHHHHHHHHHcChHHHHH
Confidence 4566666777777654 7899999999999999888754
No 175
>PRK00440 rfc replication factor C small subunit; Reviewed
Probab=28.95 E-value=2.4e+02 Score=20.82 Aligned_cols=65 Identities=11% Similarity=0.012 Sum_probs=38.1
Q ss_pred CcHHHHHHHHHhhCCC-CCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhc
Q psy13691 10 LPSAIIQRLIKEALPK-DAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQI 80 (103)
Q Consensus 10 LP~a~V~ri~K~~l~~-~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~l 80 (103)
++...+.++++..+.. + ..++.++...+.+.+.-=+..+-..-...+.. .++|+.+||..++...
T Consensus 161 l~~~ei~~~l~~~~~~~~----~~i~~~al~~l~~~~~gd~r~~~~~l~~~~~~--~~~it~~~v~~~~~~~ 226 (319)
T PRK00440 161 LKKEAVAERLRYIAENEG----IEITDDALEAIYYVSEGDMRKAINALQAAAAT--GKEVTEEAVYKITGTA 226 (319)
T ss_pred CCHHHHHHHHHHHHHHcC----CCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHc--CCCCCHHHHHHHhCCC
Confidence 3445555555554432 3 67999999888887653333332222222222 3689999998887543
No 176
>COG1222 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]
Probab=28.79 E-value=70 Score=26.35 Aligned_cols=50 Identities=22% Similarity=0.312 Sum_probs=38.2
Q ss_pred ccccHHHH-HHHHHHHHHH----HHHHHHHHHHHHHhCCCCCcChhhHHHhhhhc
Q psy13691 31 INVSKDVR-LAAGKAASLF----ILHLTTEALSIANEKNRKTLSGVDVIEGVKQI 80 (103)
Q Consensus 31 ~~iskda~-~~l~~~~~~F----i~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~l 80 (103)
|++++|.- +.|.+.+..| |.-+..+|--.|..+.|..|+-+|...|.+..
T Consensus 338 M~l~~dvd~e~la~~~~g~sGAdlkaictEAGm~AiR~~R~~Vt~~DF~~Av~KV 392 (406)
T COG1222 338 MNLADDVDLELLARLTEGFSGADLKAICTEAGMFAIRERRDEVTMEDFLKAVEKV 392 (406)
T ss_pred ccCccCcCHHHHHHhcCCCchHHHHHHHHHHhHHHHHhccCeecHHHHHHHHHHH
Confidence 55555542 4555555444 67788999999999999999999999998753
No 177
>PRK14961 DNA polymerase III subunits gamma and tau; Provisional
Probab=28.76 E-value=2.5e+02 Score=21.94 Aligned_cols=49 Identities=8% Similarity=-0.069 Sum_probs=27.4
Q ss_pred ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhc
Q psy13691 31 INVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQI 80 (103)
Q Consensus 31 ~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~l 80 (103)
..++.++...+.+.+.-=+..+-......+. -++..|+.+||.+++...
T Consensus 196 ~~i~~~al~~ia~~s~G~~R~al~~l~~~~~-~~~~~It~~~v~~~l~~~ 244 (363)
T PRK14961 196 IDTDEYALKLIAYHAHGSMRDALNLLEHAIN-LGKGNINIKNVTDMLGLL 244 (363)
T ss_pred CCCCHHHHHHHHHHcCCCHHHHHHHHHHHHH-hcCCCCCHHHHHHHHCCC
Confidence 5788888887776553211111111111122 246789999998876533
No 178
>KOG0784|consensus
Probab=28.59 E-value=43 Score=27.22 Aligned_cols=49 Identities=14% Similarity=0.135 Sum_probs=37.7
Q ss_pred HHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCchHHHHHHHHHHHHHHh
Q psy13691 49 ILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFEVIIEILGKSYNAAVS 98 (103)
Q Consensus 49 i~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~~~~~l~~~l~~~k~ 98 (103)
..-++.-|.+.|.+.|||.+++-|=.+- -.||=.-|++.+++.-+.|-.
T Consensus 186 seRIaryAF~yA~k~gRKkVTaVHKAni-mKL~DGlFle~~~eva~~Yp~ 234 (375)
T KOG0784|consen 186 SERIARYAFEYAKKNGRKKVTAVHKANI-MKLGDGLFLESCQEVAKKYPD 234 (375)
T ss_pred hHHHHHHHHHHHHHhCCceEEEEeccCc-eecchhhHHHHHHHHHhcCCC
Confidence 3456777999999999999999887663 367777788888887765543
No 179
>PRK14964 DNA polymerase III subunits gamma and tau; Provisional
Probab=28.35 E-value=2.3e+02 Score=23.71 Aligned_cols=47 Identities=13% Similarity=-0.057 Sum_probs=30.3
Q ss_pred ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691 31 INVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK 78 (103)
Q Consensus 31 ~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~ 78 (103)
..++.++...|.+.+.-=+..+-+.-...+...+ .+|+.+||...+.
T Consensus 193 i~i~~eAL~lIa~~s~GslR~alslLdqli~y~~-~~It~e~V~~llg 239 (491)
T PRK14964 193 IEHDEESLKLIAENSSGSMRNALFLLEQAAIYSN-NKISEKSVRDLLG 239 (491)
T ss_pred CCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhcC-CCCCHHHHHHHHc
Confidence 7899999999888775433333333333333333 4799999987653
No 180
>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=28.08 E-value=1.6e+02 Score=19.50 Aligned_cols=27 Identities=19% Similarity=0.234 Sum_probs=21.0
Q ss_pred HHHHHHhCCCCCcChhhHHHhhhhcCch
Q psy13691 56 ALSIANEKNRKTLSGVDVIEGVKQIGFE 83 (103)
Q Consensus 56 A~~~a~~~~RkTI~~eDV~~Al~~lgf~ 83 (103)
|+-++...|.. ||.+||...|+..|.+
T Consensus 6 A~Lll~~~g~~-~ta~~I~~IL~aaGve 32 (105)
T cd04411 6 AYLLLHKGGKE-LTEDKIKELLSAAGAE 32 (105)
T ss_pred HHHHHHhcCCC-CCHHHHHHHHHHcCCC
Confidence 44556666655 9999999999988875
No 181
>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=27.94 E-value=77 Score=23.45 Aligned_cols=32 Identities=16% Similarity=0.186 Sum_probs=25.9
Q ss_pred CCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHH
Q psy13691 9 NLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLF 48 (103)
Q Consensus 9 ~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~F 48 (103)
.+-.++|.|++... -+||.+.++-+.+++++.
T Consensus 12 gvS~~TVSrvLn~~--------~~vs~~tr~rV~~~a~~l 43 (329)
T TIGR01481 12 GVSMATVSRVVNGN--------PNVKPATRKKVLEVIKRL 43 (329)
T ss_pred CCCHHHHHHHhCCC--------CCCCHHHHHHHHHHHHHH
Confidence 56678999998652 369999999999998874
No 182
>PF03130 HEAT_PBS: PBS lyase HEAT-like repeat; InterPro: IPR004155 These proteins contain a short bi-helical repeat that is related to HEAT. Cyanobacteria and red algae harvest light energy using macromolecular complexes known as phycobilisomes (PBS), peripherally attached to the photosynthetic membrane. The major components of PBS are the phycobiliproteins. These heterodimeric proteins are covalently attached to phycobilins: open-chain tetrapyrrole chromophores, which function as the photosynthetic light-harvesting pigments. Phycobiliproteins differ in sequence and in the nature and number of attached phycobilins to each of their subunits. These proteins include the lyase enzymes that specifically attach particular phycobilins to apophycobiliprotein subunits. The most comprehensively studied of these is the CpcE/Flyase P31967 from SWISSPROT, P31968 from SWISSPROT, which attaches phycocyanobilin (PCB) to the alpha subunit of apophycocyanin []. Similarly, MpeU/V attaches phycoerythrobilin to phycoerythrin II, while CpeY/Z is thought to be involved in phycoerythrobilin (PEB) attachment to phycoerythrin (PE) I (PEs I and II differ in sequence and in the number of attached molecules of PEB: PE I has five, PE II has six) []. All the reactions of the above lyases involve an apoprotein cysteine SH addition to a terminal delta 3,3'-double bond. Such a reaction is not possible in the case of phycoviolobilin (PVB), the phycobilin of alpha-phycoerythrocyanin (alpha-PEC). It is thought that in this case, PCB, not PVB, is first added to apo-alpha-PEC, and is then isomerized to PVB. The addition reaction has been shown to occur in the presence of either of the components of alpha-PEC-PVB lyase PecE or PecF (or both). The isomerisation reaction occurs only when both PecE and PecF components are present, i.e. the PecE/F phycobiliprotein lyase is also a phycobilin isomerase []. Another member of this family is the NblB protein, whose similarity to the phycobiliprotein lyases was previously noted []. This constitutively expressed protein is not known to have any lyase activity. It is thought to be involved in the coordination of PBS degradation with environmental nutrient limitation. It has been suggested that the similarity of NblB to the phycobiliprotein lyases is due to the ability to bind tetrapyrrole phycobilins via the common repeated motif [].; PDB: 1TE4_A.
Probab=27.76 E-value=85 Score=15.26 Aligned_cols=23 Identities=22% Similarity=0.169 Sum_probs=17.8
Q ss_pred HHHhhhhcCchHHHHHHHHHHHH
Q psy13691 73 VIEGVKQIGFEVIIEILGKSYNA 95 (103)
Q Consensus 73 V~~Al~~lgf~~~~~~l~~~l~~ 95 (103)
..++|-.+|-...+++|.+.++.
T Consensus 5 Aa~aLg~igd~~ai~~L~~~L~d 27 (27)
T PF03130_consen 5 AARALGQIGDPRAIPALIEALED 27 (27)
T ss_dssp HHHHHGGG-SHHHHHHHHHHHHH
T ss_pred HHHHHHHcCCHHHHHHHHHHhcC
Confidence 35788888989999999988763
No 183
>PF11625 DUF3253: Protein of unknown function (DUF3253); InterPro: IPR021660 This bacterial family of proteins has no known function. ; PDB: 2NS0_A.
Probab=27.62 E-value=1.6e+02 Score=18.95 Aligned_cols=35 Identities=9% Similarity=0.082 Sum_probs=23.4
Q ss_pred HhCCCCCcChhhHHHhhhhcCchHHHHHHHHHHHH
Q psy13691 61 NEKNRKTLSGVDVIEGVKQIGFEVIIEILGKSYNA 95 (103)
Q Consensus 61 ~~~~RkTI~~eDV~~Al~~lgf~~~~~~l~~~l~~ 95 (103)
....-|||-|.||..||..-++-++.+++....-.
T Consensus 18 ~R~~~ktiCPSevARal~~~~WR~lm~~vR~~A~~ 52 (83)
T PF11625_consen 18 ARGPGKTICPSEVARALGPDDWRDLMPPVRAAARR 52 (83)
T ss_dssp HS-TT--B-HHHHHHHH-TTS-GGGHHHHHHHHHH
T ss_pred hcCCCCccCHHHHHHHHCchhhHHHHHHHHHHHHH
Confidence 44557999999999999877898998888776544
No 184
>PF12627 PolyA_pol_RNAbd: Probable RNA and SrmB- binding site of polymerase A; PDB: 1OU5_B 3H38_A 3H3A_B 3H39_B 3H37_A 3AQN_A 3AQK_A 3AQM_B 3AQL_B 1MIY_A ....
Probab=27.37 E-value=12 Score=21.65 Aligned_cols=58 Identities=16% Similarity=0.217 Sum_probs=32.1
Q ss_pred ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCc---ChhhHHHhhhhcCchHHH-HHHHHH
Q psy13691 31 INVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTL---SGVDVIEGVKQIGFEVII-EILGKS 92 (103)
Q Consensus 31 ~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI---~~eDV~~Al~~lgf~~~~-~~l~~~ 92 (103)
.+|.++...+|.+++. .+..++.+ .-..+=.|.+ .+...+..|.++|+.+++ +.+..+
T Consensus 2 F~ie~~t~~ai~~~~~-~L~~is~E---Ri~~El~kil~~~~~~~~~~~l~~~gll~~ifP~l~~a 63 (64)
T PF12627_consen 2 FKIEPETEEAIKENAE-LLSKISKE---RIREELEKILSSPNPSRAFKLLDELGLLEYIFPELDAA 63 (64)
T ss_dssp -EE-HHHHHHHHHHGG-GGGGS-HH---HHHHHHHHHHTSTTHHHHHHHHHHTTCHHHHSTTHHT-
T ss_pred CccCHHHHHHHHHHHH-HHhcCCHH---HHHHHHHHHHcCCCHHHHHHHHHHcCCHHHHCcccccc
Confidence 5778888888888776 44444432 1111112222 456667777888987764 655443
No 185
>PRK14970 DNA polymerase III subunits gamma and tau; Provisional
Probab=27.14 E-value=2.8e+02 Score=21.39 Aligned_cols=50 Identities=10% Similarity=0.043 Sum_probs=28.7
Q ss_pred ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcC
Q psy13691 31 INVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIG 81 (103)
Q Consensus 31 ~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lg 81 (103)
+.+++++...+.+.+.-=+..+-.+-...+.-.++. |+.+||...+....
T Consensus 185 ~~i~~~al~~l~~~~~gdlr~~~~~lekl~~y~~~~-it~~~v~~~~~~~~ 234 (367)
T PRK14970 185 IKFEDDALHIIAQKADGALRDALSIFDRVVTFCGKN-ITRQAVTENLNILD 234 (367)
T ss_pred CCCCHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCCC-CCHHHHHHHhCCCC
Confidence 779999998877755432222223333333333333 88888877766443
No 186
>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=26.96 E-value=1.1e+02 Score=25.15 Aligned_cols=33 Identities=24% Similarity=0.357 Sum_probs=25.5
Q ss_pred HHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcC
Q psy13691 49 ILHLTTEALSIANEKNRKTLSGVDVIEGVKQIG 81 (103)
Q Consensus 49 i~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lg 81 (103)
|..+..+|...+...+++.|+.+|+..|++..-
T Consensus 264 l~~l~~eA~~~a~~~~~~~i~~~~l~~a~~~~~ 296 (495)
T TIGR01241 264 LANLLNEAALLAARKNKTEITMNDIEEAIDRVI 296 (495)
T ss_pred HHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHh
Confidence 445555666667777889999999999999753
No 187
>PRK05907 hypothetical protein; Provisional
Probab=26.92 E-value=1.9e+02 Score=22.50 Aligned_cols=53 Identities=11% Similarity=0.044 Sum_probs=38.5
Q ss_pred ccccHHHHHHHHHHH-HHHHHHHHHHHHHHHHh-CCCCCcChhhHHHhhh-hcCch
Q psy13691 31 INVSKDVRLAAGKAA-SLFILHLTTEALSIANE-KNRKTLSGVDVIEGVK-QIGFE 83 (103)
Q Consensus 31 ~~iskda~~~l~~~~-~~Fi~~lt~~A~~~a~~-~~RkTI~~eDV~~Al~-~lgf~ 83 (103)
.+|+++|...+.+.+ .-=+..+..+-...|.- ..+++|+.+||...+. .+++.
T Consensus 152 ~~i~~~a~~~L~~~~~~~nL~~l~~EleKL~ly~g~~~~It~e~V~~lv~~s~e~n 207 (311)
T PRK05907 152 ISCSLGLASLFVSKFPQTGLFEILSEFQKLLCQMGKKESLEASDIQSFVVKKEAAS 207 (311)
T ss_pred CCcCHHHHHHHHHHccCCCHHHHHHHHHHHHHhcCCCCeECHHHHHHHhcCccccc
Confidence 789999998888877 34444556666666665 5688999999998854 44444
No 188
>cd00051 EFh EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers.
Probab=26.90 E-value=1e+02 Score=15.90 Aligned_cols=35 Identities=14% Similarity=0.183 Sum_probs=20.1
Q ss_pred HHhCCCCCcChhhHHHhhhhcCchHHHHHHHHHHH
Q psy13691 60 ANEKNRKTLSGVDVIEGVKQIGFEVIIEILGKSYN 94 (103)
Q Consensus 60 a~~~~RkTI~~eDV~~Al~~lgf~~~~~~l~~~l~ 94 (103)
...++.-.|+.+++..+++.++...-.+.+...+.
T Consensus 9 ~d~~~~g~l~~~e~~~~l~~~~~~~~~~~~~~~~~ 43 (63)
T cd00051 9 FDKDGDGTISADELKAALKSLGEGLSEEEIDEMIR 43 (63)
T ss_pred hCCCCCCcCcHHHHHHHHHHhCCCCCHHHHHHHHH
Confidence 33445556777777777777765543343443333
No 189
>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau. This model represents the well-conserved first ~ 365 amino acids of the translation of the dnaX gene. The full-length product of the dnaX gene in the model bacterium E. coli is the DNA polymerase III tau subunit. A translational frameshift leads to early termination and a truncated protein subunit gamma, about 1/3 shorter than tau and present in roughly equal amounts. This frameshift mechanism is not necessarily universal for species with DNA polymerase III but appears conserved in the exterme thermophile Thermus thermophilis.
Probab=26.83 E-value=2.8e+02 Score=20.96 Aligned_cols=62 Identities=18% Similarity=0.058 Sum_probs=34.4
Q ss_pred HHHHHHHHHhhCCC-CCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691 12 SAIIQRLIKEALPK-DAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK 78 (103)
Q Consensus 12 ~a~V~ri~K~~l~~-~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~ 78 (103)
...+..+++..+.. + ..++.++...+.+.+.-=...+-.+....+...+ +.|+.+||..++.
T Consensus 178 ~~~l~~~l~~~~~~~g----~~i~~~a~~~l~~~~~g~~~~a~~~lekl~~~~~-~~it~~~v~~~~~ 240 (355)
T TIGR02397 178 LEDIVERLKKILDKEG----IKIEDEALELIARAADGSLRDALSLLDQLISFGN-GNITYEDVNELLG 240 (355)
T ss_pred HHHHHHHHHHHHHHcC----CCCCHHHHHHHHHHcCCChHHHHHHHHHHHhhcC-CCCCHHHHHHHhC
Confidence 44455555543322 3 6788888888777665433333333333333233 3488888876654
No 190
>PF10728 DUF2520: Domain of unknown function (DUF2520); InterPro: IPR018931 This presumed domain is found C-terminal to a Rossmann-like domain suggesting that these proteins are oxidoreductases. ; PDB: 3D1L_A 2I76_A 3DFU_A.
Probab=26.79 E-value=2.1e+02 Score=19.44 Aligned_cols=47 Identities=23% Similarity=0.277 Sum_probs=32.8
Q ss_pred HHHHHHHHhhCCCCCcccccccHHHHHHHHHHH---HHHHHHHHHHHHHHHHhC
Q psy13691 13 AIIQRLIKEALPKDAEGKINVSKDVRLAAGKAA---SLFILHLTTEALSIANEK 63 (103)
Q Consensus 13 a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~---~~Fi~~lt~~A~~~a~~~ 63 (103)
..+.++++...... ..|+.+-|....-++ ..|+..|...|.+.+...
T Consensus 14 ~~l~~l~~~lg~~~----~~i~~~~r~~yHaAav~asNf~~~L~~~a~~ll~~~ 63 (132)
T PF10728_consen 14 EVLQELAKELGGRP----FEIDSEQRALYHAAAVFASNFLVALYALAAELLEQA 63 (132)
T ss_dssp HHHHHHHHHTTSEE----EE--GGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHhCCce----EEeCHHhHHHHHHHHHHHHhhHHHHHHHHHHHHHHc
Confidence 34566676654433 789999998887775 478888888888887766
No 191
>PRK05629 hypothetical protein; Validated
Probab=26.66 E-value=2.7e+02 Score=21.19 Aligned_cols=47 Identities=11% Similarity=0.029 Sum_probs=34.7
Q ss_pred ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691 31 INVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK 78 (103)
Q Consensus 31 ~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~ 78 (103)
.+|+.+|...|...+..=...+..+--..+... ..+|+.+||...+.
T Consensus 144 ~~i~~~A~~~L~~~~g~dl~~l~~EleKL~~~~-~~~It~e~V~~~v~ 190 (318)
T PRK05629 144 VRPTPDVVHALLEGVGSDLRELASAISQLVEDT-QGNVTVEKVRAYYV 190 (318)
T ss_pred CCCCHHHHHHHHHHHCccHHHHHHHHHHHHhcC-CCCcCHHHHHHHhC
Confidence 789999999988888765555555555555443 45799999988754
No 192
>COG3267 ExeA Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]
Probab=26.56 E-value=2.7e+02 Score=21.80 Aligned_cols=44 Identities=25% Similarity=0.197 Sum_probs=39.3
Q ss_pred ccccHHHHHHHHHHHH---HHHHHHHHHHHHHHHhCCCCCcChhhHH
Q psy13691 31 INVSKDVRLAAGKAAS---LFILHLTTEALSIANEKNRKTLSGVDVI 74 (103)
Q Consensus 31 ~~iskda~~~l~~~~~---~Fi~~lt~~A~~~a~~~~RkTI~~eDV~ 74 (103)
-.++.+++.++..... --|+-+...|.+.|-..|+.+|+...+-
T Consensus 221 ~l~~~~a~~~i~~~sqg~P~lin~~~~~Al~~a~~a~~~~v~~a~~~ 267 (269)
T COG3267 221 PLFSDDALLLIHEASQGIPRLINNLATLALDAAYSAGEDGVSEAEIK 267 (269)
T ss_pred ccCChhHHHHHHHHhccchHHHHHHHHHHHHHHHHcCCCccchhhcc
Confidence 5899999999999988 7899999999999999999999876553
No 193
>cd03521 Link_domain_KIAA0527_like Link_domain_KIAA0527_like; this domain is found in the human protein KIAA0527. Sequence-wise, it is highly similar to the link domain. The link domain is a hyaluronan-binding (HA) domain. KIAA0527 contains a single link module. The KIAA0527 gene was originally cloned from human brain tissue.
Probab=26.39 E-value=92 Score=20.60 Aligned_cols=30 Identities=13% Similarity=0.078 Sum_probs=27.4
Q ss_pred HHHHHHHHhCCCCCcChhhHHHhhhhcCch
Q psy13691 54 TEALSIANEKNRKTLSGVDVIEGVKQIGFE 83 (103)
Q Consensus 54 ~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~ 83 (103)
.+|...|.+.+-.--+++.+..|-++.||+
T Consensus 17 ~eA~~AC~~~gA~lAs~~QL~~AW~~~Gld 46 (95)
T cd03521 17 RAARQSCASLGARLASAAELRRAVVECFFS 46 (95)
T ss_pred HHHHHHHHHcCCEeccHHHHHHHHHHhCcc
Confidence 578888999999999999999999998886
No 194
>COG4987 CydC ABC-type transport system involved in cytochrome bd biosynthesis, fused ATPase and permease components [Energy production and conversion / Posttranslational modification, protein turnover, chaperones]
Probab=26.38 E-value=2.2e+02 Score=24.59 Aligned_cols=78 Identities=17% Similarity=0.232 Sum_probs=46.8
Q ss_pred cHHHHHHHHHhhCCCCCcccccccH-------H-----HHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691 11 PSAIIQRLIKEALPKDAEGKINVSK-------D-----VRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK 78 (103)
Q Consensus 11 P~a~V~ri~K~~l~~~~~~~~~isk-------d-----a~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~ 78 (103)
-|++.-.++-.+.+.+ .|.++++. | +.-.+.+....|-.-|-. =..=...+.+.|++..||+
T Consensus 376 GKSTllqLl~~~~~~~-~G~i~~~g~~~~~l~~~~~~e~i~vl~Qr~hlF~~Tlr~-----NL~lA~~~AsDEel~~aL~ 449 (573)
T COG4987 376 GKSTLLQLLAGAWDPQ-QGSITLNGVEIASLDEQALRETISVLTQRVHLFSGTLRD-----NLRLANPDASDEELWAALQ 449 (573)
T ss_pred CHHHHHHHHHhccCCC-CCeeeECCcChhhCChhhHHHHHhhhccchHHHHHHHHH-----HHhhcCCCCCHHHHHHHHH
Confidence 3677778887776654 33333333 1 222334444444332221 1122345699999999999
Q ss_pred hcCchHHHHHHHHHHH
Q psy13691 79 QIGFEVIIEILGKSYN 94 (103)
Q Consensus 79 ~lgf~~~~~~l~~~l~ 94 (103)
..|+.++++..-+-+.
T Consensus 450 qvgL~~l~~~~p~gl~ 465 (573)
T COG4987 450 QVGLEKLLESAPDGLN 465 (573)
T ss_pred HcCHHHHHHhChhhhh
Confidence 9999999988754443
No 195
>KOG0482|consensus
Probab=26.33 E-value=91 Score=27.13 Aligned_cols=42 Identities=17% Similarity=0.247 Sum_probs=33.9
Q ss_pred HHHHhCCCCCcChhhHHHhhhhcCchHHHHHHHHHHHHHHhccc
Q psy13691 58 SIANEKNRKTLSGVDVIEGVKQIGFEVIIEILGKSYNAAVSIKV 101 (103)
Q Consensus 58 ~~a~~~~RkTI~~eDV~~Al~~lgf~~~~~~l~~~l~~~k~~~~ 101 (103)
+.+.+.||.+++..++.+....-||.. ..++..+++|-+..|
T Consensus 667 el~~e~g~~~v~~s~~~~r~~~kGfs~--~ql~~~i~ey~~lnV 708 (721)
T KOG0482|consen 667 ELAGEGGKRCVKLSNAEQRCVRKGFSE--AQLKKCIDEYAELNV 708 (721)
T ss_pred HHHhhcCCceeeHHHHHHHHHHcCCCH--HHHHHHHHHHHhcCe
Confidence 334477899999999999999999985 567788888887655
No 196
>PF13499 EF-hand_7: EF-hand domain pair; PDB: 1TCF_A 2TN4_A 1TN4_A 1A2X_A 2CT9_B 2OTG_B 2OS8_B 1SNL_A 3O4Y_A 3J04_E ....
Probab=25.58 E-value=1.3e+02 Score=16.82 Aligned_cols=37 Identities=16% Similarity=0.190 Sum_probs=25.1
Q ss_pred HHHHHHHhCCCCCcChhhHHHhhhhcCchHHHHHHHH
Q psy13691 55 EALSIANEKNRKTLSGVDVIEGVKQIGFEVIIEILGK 91 (103)
Q Consensus 55 ~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~~~~~l~~ 91 (103)
++....-.++.-.|+.+++..++..++....-..+..
T Consensus 4 ~~F~~~D~d~~G~i~~~el~~~~~~~~~~~~~~~~~~ 40 (66)
T PF13499_consen 4 EAFKKFDKDGDGYISKEELRRALKHLGRDMSDEESDE 40 (66)
T ss_dssp HHHHHHSTTSSSEEEHHHHHHHHHHTTSHSTHHHHHH
T ss_pred HHHHHHcCCccCCCCHHHHHHHHHHhcccccHHHHHH
Confidence 3455556677778899999999998887543333333
No 197
>PRK14975 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Probab=25.31 E-value=3.6e+02 Score=22.62 Aligned_cols=70 Identities=16% Similarity=0.104 Sum_probs=48.9
Q ss_pred CCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHH----------HHHHHHHHHHHHHHHhCCCCCcChhhHHHh
Q psy13691 7 DLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAAS----------LFILHLTTEALSIANEKNRKTLSGVDVIEG 76 (103)
Q Consensus 7 d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~----------~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~A 76 (103)
++++|.+.|---|... + +.+..+....+..-.. .-+.-|..+..+......=..=++.+|..+
T Consensus 161 ~~E~~~~~~l~~me~~---G----i~~D~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~~~g~~~~n~~S~~ql~~~ 233 (553)
T PRK14975 161 AAESAGALAAAEMELA---G----LPWDTDVHEALLAELLGPRPAAGGRPARLAELAAEIREALGRPRLNPDSPQQVLRA 233 (553)
T ss_pred HHHhhHHHHHHHHHHh---C----eEeCHHHHHHHHHHHhcccccccchHHHHHHHHHHHHHHhCCCCCCCCCHHHHHHH
Confidence 4577777777777664 4 8898888777666555 566677777666553321244578899999
Q ss_pred hhhcCch
Q psy13691 77 VKQIGFE 83 (103)
Q Consensus 77 l~~lgf~ 83 (103)
|+.+|+.
T Consensus 234 L~~~g~~ 240 (553)
T PRK14975 234 LRRAGIE 240 (553)
T ss_pred HHHCCCC
Confidence 9999885
No 198
>PF01934 DUF86: Protein of unknown function DUF86; InterPro: IPR008201 This entry describes prokaryotic proteins of unknown function.; PDB: 1YLM_A.
Probab=25.19 E-value=1.9e+02 Score=18.44 Aligned_cols=68 Identities=12% Similarity=-0.034 Sum_probs=42.2
Q ss_pred cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCch-HHHHHHHHHHHHHHhcc
Q psy13691 32 NVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFE-VIIEILGKSYNAAVSIK 100 (103)
Q Consensus 32 ~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~-~~~~~l~~~l~~~k~~~ 100 (103)
.=+.....++......-+.-+..-+..++...|....... ++..|.+-|+- .+...-...+..||+..
T Consensus 21 ~~d~~~~~av~~~l~~~~e~~~di~~~i~~~~~~~~p~~~-~~~~L~~~~ii~~~~~~~l~~~~g~RN~l 89 (119)
T PF01934_consen 21 LSDRMLQDAVERNLQLIIEAIIDIAKHIISEEGLGKPGSY-IFEILAEHGIISEEPAEPLRKMVGFRNRL 89 (119)
T ss_dssp T-SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----SSH-HHHHHHHTTSS-HHHHHHHHHHHTTHHHH
T ss_pred hcCHHHHHHHHHHHHHHHHHHhhhHHHHHHHhCCCCCccH-HHHHHHHcCCccchhHHHHHHHHHHHHHH
Confidence 3345566666666666666666777777777777766666 99999999974 44444455555666544
No 199
>PF09239 Topo-VIb_trans: Topoisomerase VI B subunit, transducer; InterPro: IPR015320 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils []. This entry represents subunit B of topoisomerase VI, an ATP-dependent type IIB enzyme. Members of this family adopt a structure consisting of a four-stranded beta-sheet backed by three alpha-helices, the last of which is over 50 amino acids long and extends from the body of the protein by several turns. This domain has been proposed to mediate intersubunit communication by structurally transducing signals from the ATP binding and hydrolysis domains to the DNA binding and cleavage domains of the gyrase holoenzyme []. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0006265 DNA topological change, 0005694 chromosome; PDB: 2ZBK_F 2HKJ_A 1Z5B_A 1Z5C_B 1MX0_F 1Z5A_A 1MU5_A 1Z59_A 2Q2E_B.
Probab=25.17 E-value=72 Score=23.03 Aligned_cols=26 Identities=23% Similarity=0.300 Sum_probs=23.0
Q ss_pred cccHHHHHHHHHHHHHHHHHHHHHHH
Q psy13691 32 NVSKDVRLAAGKAASLFILHLTTEAL 57 (103)
Q Consensus 32 ~iskda~~~l~~~~~~Fi~~lt~~A~ 57 (103)
-|-+|.+.+|++||...=.||.....
T Consensus 128 EI~~Ei~lAl~e~~R~L~~yl~rk~~ 153 (160)
T PF09239_consen 128 EIEKEIRLALQECARKLKKYLSRKRK 153 (160)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 57899999999999999999997653
No 200
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=25.12 E-value=21 Score=20.53 Aligned_cols=16 Identities=6% Similarity=0.418 Sum_probs=11.6
Q ss_pred CCCCcHHHHHHHHHhh
Q psy13691 7 DLNLPSAIIQRLIKEA 22 (103)
Q Consensus 7 d~~LP~a~V~ri~K~~ 22 (103)
++.+|.++|.+|+|+-
T Consensus 31 ~fgv~~sTv~~I~K~k 46 (53)
T PF04218_consen 31 EFGVSRSTVSTILKNK 46 (53)
T ss_dssp HHT--CCHHHHHHHCH
T ss_pred HhCCCHHHHHHHHHhH
Confidence 5789999999999863
No 201
>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=25.04 E-value=92 Score=18.88 Aligned_cols=32 Identities=19% Similarity=0.218 Sum_probs=22.2
Q ss_pred HHHHHHhCCCCCcChhhHHHhhhhcCchHHHHHHH
Q psy13691 56 ALSIANEKNRKTLSGVDVIEGVKQIGFEVIIEILG 90 (103)
Q Consensus 56 A~~~a~~~~RkTI~~eDV~~Al~~lgf~~~~~~l~ 90 (103)
..++|... -+++.=|.+-.+.|||.+|-+--.
T Consensus 37 i~elA~~~---~vS~sti~Rf~kkLG~~gf~efk~ 68 (77)
T PF01418_consen 37 ISELAEKA---GVSPSTIVRFCKKLGFSGFKEFKI 68 (77)
T ss_dssp HHHHHHHC---TS-HHHHHHHHHHCTTTCHHHHHH
T ss_pred HHHHHHHc---CCCHHHHHHHHHHhCCCCHHHHHH
Confidence 33455544 478888999999999998865433
No 202
>cd03518 Link_domain_HAPLN_module_1 Link_domain_HAPLN_module_1; this link domain is found in the first link module of proteins similar to the vertebrate HAPLN (hyaluronan/HA and proteoglycan binding link) protein family which includes cartilage link protein. The link domain is a HA-binding domain. HAPLNs contain two contiguous link modules. Both link modules of cartilage link protein are involved in interaction with HA. In cartilage, a chondroitin sulfate proteoglycan core protein (CSPG) aggrecan forms cartilage link protein stabilized aggregates with HA. These aggregates contribute to the tissue's load bearing properties. Aggregates with other CSPGs substituting for aggregan may contribute to the structural integrity of many different tissues. Members of the vertebrate HAPLN gene family are physically linked adjacent to CSPG genes.
Probab=24.99 E-value=1.1e+02 Score=20.13 Aligned_cols=29 Identities=17% Similarity=0.170 Sum_probs=25.7
Q ss_pred HHHHHHHHhCCCCCcChhhHHHhhhhcCch
Q psy13691 54 TEALSIANEKNRKTLSGVDVIEGVKQIGFE 83 (103)
Q Consensus 54 ~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~ 83 (103)
.+|.+.|...+-..=+.+++..|-+ .||+
T Consensus 17 ~eA~~aC~~~ga~lAs~~QL~~Aw~-~Gld 45 (95)
T cd03518 17 HEAQQACEEQDATLASFEQLYQAWT-EGLD 45 (95)
T ss_pred HHHHHHHHHcCCeeCCHHHHHHHHH-cCcc
Confidence 6899999999999999999999986 7775
No 203
>cd04750 Commd2 COMM_Domain containing protein 2. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=24.77 E-value=2.6e+02 Score=19.75 Aligned_cols=33 Identities=27% Similarity=0.401 Sum_probs=23.6
Q ss_pred CCCcChhhHHHhhhhcCchH-HHHHHHHHHHHHH
Q psy13691 65 RKTLSGVDVIEGVKQIGFEV-IIEILGKSYNAAV 97 (103)
Q Consensus 65 RkTI~~eDV~~Al~~lgf~~-~~~~l~~~l~~~k 97 (103)
|..++.+++..-|..+||++ ....+...+.+.+
T Consensus 49 K~~l~~~~~~~~L~~l~~~~e~~~~l~~~y~~~~ 82 (166)
T cd04750 49 KLKLSERDFQDSIEFLGFSDDLNEILLQLYESNR 82 (166)
T ss_pred hccCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHH
Confidence 34499999999999999974 4555555554443
No 204
>PRK08487 DNA polymerase III subunit delta; Validated
Probab=24.62 E-value=3e+02 Score=21.11 Aligned_cols=46 Identities=11% Similarity=-0.041 Sum_probs=34.5
Q ss_pred ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691 31 INVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK 78 (103)
Q Consensus 31 ~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~ 78 (103)
..|+.+|...|...+.-=...+..|=...+.-.+ +|+.+||...+.
T Consensus 153 ~~i~~~a~~~L~~~~g~dl~~l~~ELeKL~ly~~--~It~edV~~~v~ 198 (328)
T PRK08487 153 LDIDQNALNHLYFIHNEDLALAANELEKLAILNE--PITLKDIQELVF 198 (328)
T ss_pred CCCCHHHHHHHHHHhCcHHHHHHHHHHHHHHhcC--CCCHHHHHHHhc
Confidence 7899999999998877655555555555555433 799999999874
No 205
>PRK03745 signal recognition particle protein Srp19; Provisional
Probab=24.21 E-value=60 Score=21.55 Aligned_cols=17 Identities=18% Similarity=0.532 Sum_probs=15.4
Q ss_pred cChhhHHHhhhhcCchH
Q psy13691 68 LSGVDVIEGVKQIGFEV 84 (103)
Q Consensus 68 I~~eDV~~Al~~lgf~~ 84 (103)
-+.++|..|++.||+.-
T Consensus 32 P~~~EI~~a~~~lgl~~ 48 (100)
T PRK03745 32 PTLEEIVDAAEALGFKV 48 (100)
T ss_pred CCHHHHHHHHHHcCCCc
Confidence 68899999999999985
No 206
>COG1400 SEC65 Signal recognition particle 19 kDa protein [Intracellular trafficking and secretion]
Probab=24.20 E-value=53 Score=21.61 Aligned_cols=17 Identities=18% Similarity=0.387 Sum_probs=15.2
Q ss_pred cChhhHHHhhhhcCchH
Q psy13691 68 LSGVDVIEGVKQIGFEV 84 (103)
Q Consensus 68 I~~eDV~~Al~~lgf~~ 84 (103)
.+.++|..|+++|||.-
T Consensus 32 P~~~ei~~a~~~LGl~~ 48 (93)
T COG1400 32 PSLEEIAEALRELGLKP 48 (93)
T ss_pred CCHHHHHHHHHHcCCCe
Confidence 68899999999999974
No 207
>KOG0093|consensus
Probab=23.96 E-value=45 Score=24.38 Aligned_cols=52 Identities=10% Similarity=-0.010 Sum_probs=33.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHH-----HHHHHHhCCCCCcChhhHHHhhhhcCchHHH
Q psy13691 35 KDVRLAAGKAASLFILHLTTE-----ALSIANEKNRKTLSGVDVIEGVKQIGFEVII 86 (103)
Q Consensus 35 kda~~~l~~~~~~Fi~~lt~~-----A~~~a~~~~RkTI~~eDV~~Al~~lgf~~~~ 86 (103)
.+..-+++.-++..=+|--.- +-..|--+..++|+.|....-.++|||+-|-
T Consensus 106 eeSf~svqdw~tqIktysw~naqvilvgnKCDmd~eRvis~e~g~~l~~~LGfefFE 162 (193)
T KOG0093|consen 106 EESFNSVQDWITQIKTYSWDNAQVILVGNKCDMDSERVISHERGRQLADQLGFEFFE 162 (193)
T ss_pred HHHHHHHHHHHHHheeeeccCceEEEEecccCCccceeeeHHHHHHHHHHhChHHhh
Confidence 344455555554443331111 1234666788999999999999999996554
No 208
>smart00874 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits.
Probab=23.91 E-value=56 Score=19.19 Aligned_cols=17 Identities=41% Similarity=0.657 Sum_probs=15.3
Q ss_pred CcChhhHHHhhhhcCch
Q psy13691 67 TLSGVDVIEGVKQIGFE 83 (103)
Q Consensus 67 TI~~eDV~~Al~~lgf~ 83 (103)
.++++++...|+.|||.
T Consensus 18 ~i~~~ei~~~L~~lg~~ 34 (71)
T smart00874 18 DLSAEEIEEILKRLGFE 34 (71)
T ss_pred CCCHHHHHHHHHHCCCe
Confidence 58899999999999986
No 209
>COG1466 HolA DNA polymerase III, delta subunit [DNA replication, recombination, and repair]
Probab=23.60 E-value=3e+02 Score=21.28 Aligned_cols=50 Identities=18% Similarity=0.129 Sum_probs=39.5
Q ss_pred ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhc
Q psy13691 31 INVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQI 80 (103)
Q Consensus 31 ~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~l 80 (103)
++|++||.+.+..+..-=...+.++=...+--.+-++|+.+||..++-.-
T Consensus 158 l~i~~~a~~~L~~~~~~nl~~i~~Ei~KL~l~~~~~~I~~~~V~~~v~~~ 207 (334)
T COG1466 158 LKIDQEAIQLLLEALGGNLLAIAQEIEKLALYAGDKEITLEDVEEVVSDV 207 (334)
T ss_pred CCCCHHHHHHHHHHhCCcHHHHHHHHHHHHHhCCCCcCCHHHHHHHHhcc
Confidence 89999999999999886666666666666655555599999999988643
No 210
>cd00454 Trunc_globin Truncated hemoglobins (trHbs) are a family of oxygen-binding heme proteins found in cyanobacteria, eubacteria, unicellular eukaryotes, and plants. The truncated hemoglobins have a characteristic two-over-two alpha helical folding pattern that is distinct from the three-over-three pattern found in other globins. A subset of these have been demonstrated to form homodimers.
Probab=23.53 E-value=1.4e+02 Score=19.02 Aligned_cols=30 Identities=10% Similarity=0.117 Sum_probs=21.2
Q ss_pred hHHHhhhhcCch-HHHHHHHHHHHHHHhccc
Q psy13691 72 DVIEGVKQIGFE-VIIEILGKSYNAAVSIKV 101 (103)
Q Consensus 72 DV~~Al~~lgf~-~~~~~l~~~l~~~k~~~~ 101 (103)
++..||++++.+ +..+.+...++..+...|
T Consensus 84 ~l~~al~~~~~~~~~~~~~~~~~~~~~~~~v 114 (116)
T cd00454 84 LLRDALDELGVPAELADALLARAERIADHMV 114 (116)
T ss_pred HHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 456778888887 677777777777665543
No 211
>PF13713 BRX_N: Transcription factor BRX N-terminal domain
Probab=23.32 E-value=1.5e+02 Score=16.41 Aligned_cols=21 Identities=33% Similarity=0.289 Sum_probs=17.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHh
Q psy13691 42 GKAASLFILHLTTEALSIANE 62 (103)
Q Consensus 42 ~~~~~~Fi~~lt~~A~~~a~~ 62 (103)
.+++.+||.-||++-.+++.+
T Consensus 7 ~kaaKe~IKsLt~QlK~maek 27 (39)
T PF13713_consen 7 CKAAKEVIKSLTAQLKDMAEK 27 (39)
T ss_pred cHHHHHHHHHHHHHHHHHHHh
Confidence 367889999999999888865
No 212
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=23.28 E-value=96 Score=23.07 Aligned_cols=34 Identities=15% Similarity=0.290 Sum_probs=27.0
Q ss_pred CCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHH
Q psy13691 9 NLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLF 48 (103)
Q Consensus 9 ~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~F 48 (103)
..-+++|.|.+... ++ .+||.+.++-+.+++++.
T Consensus 12 gVS~~TVSrvln~~--~~----~~vs~~tr~rV~~~a~~l 45 (327)
T PRK10339 12 GVSLATVSRVLNDD--PT----LNVKEETKHRILEIAEKL 45 (327)
T ss_pred CCCHHhhhhhhcCC--CC----CCcCHHHHHHHHHHHHHh
Confidence 56688999999653 22 369999999999999885
No 213
>PRK04184 DNA topoisomerase VI subunit B; Validated
Probab=23.22 E-value=68 Score=27.26 Aligned_cols=37 Identities=24% Similarity=0.293 Sum_probs=29.3
Q ss_pred cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCc
Q psy13691 32 NVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTL 68 (103)
Q Consensus 32 ~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI 68 (103)
-|-+|.+.++++||...=.||...-...-..++++++
T Consensus 439 ei~~ei~~al~~~~r~L~~~l~~~~~~~~~~~k~~~~ 475 (535)
T PRK04184 439 EIEKEIRLALQEVARKLKKYLSRKRKEEEAKKKAKTF 475 (535)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5889999999999999999999877655555555543
No 214
>cd03515 Link_domain_TSG_6_like This is the extracellular link domain of the type found in human TSG-6. The link domain is a hyaluronan (HA)-binding domain. TSG-6 is the protein product of tumor necrosis factor-stimulated gene-6. TSG-6 is up-regulated in inflammatory lesions and in the ovary during ovulation. It has a strong anti-inflammatory and chondroprotective effect in models of acute inflammation and autoimmune arthritis and plays an essential role in female fertility. Also included in this group are the stabilins: stabilin-1 (FEEL-1, CLEVER-1) and stabilin-2 (FEEL-2). Stabilin-2 functions as the major liver and lymph node-scavenging receptor for HA and related glycosaminoglycans. Stabilin-2 is a scavenger receptor with a broad range of ligands including advanced glycation end (AGE) products, acetylated low density lipoprotein and procollagen peptides. In contrast, stabilin-1 does not bind HA, but binds acetylated low density lipoprotein and AGEs with lower affinity. As AGEs accum
Probab=23.12 E-value=1.4e+02 Score=19.52 Aligned_cols=29 Identities=17% Similarity=0.253 Sum_probs=25.8
Q ss_pred HHHHHHHHhCCCCCcChhhHHHhhhhcCch
Q psy13691 54 TEALSIANEKNRKTLSGVDVIEGVKQIGFE 83 (103)
Q Consensus 54 ~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~ 83 (103)
.+|.+.|...+-..=+.+++..|-+ .||+
T Consensus 17 ~eA~~aC~~~ga~lAs~~QL~~Aw~-~G~d 45 (93)
T cd03515 17 TEAKAACEAEGAHLATYSQLSAAQQ-LGFH 45 (93)
T ss_pred HHHHHHHHHcCCccCCHHHHHHHHH-cCcc
Confidence 6899999999999999999999987 5776
No 215
>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []. In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.
Probab=22.98 E-value=66 Score=17.84 Aligned_cols=18 Identities=11% Similarity=0.368 Sum_probs=13.0
Q ss_pred CCCCcHHHHHHHHHhhCC
Q psy13691 7 DLNLPSAIIQRLIKEALP 24 (103)
Q Consensus 7 d~~LP~a~V~ri~K~~l~ 24 (103)
.+.+|++++.+-++...|
T Consensus 25 ~ygVp~sTL~~r~~g~~~ 42 (45)
T PF05225_consen 25 KYGVPRSTLRRRLRGKPS 42 (45)
T ss_dssp HHT--HHHHHHHHHHTTT
T ss_pred HHCcCHHHHHHHHcCCCC
Confidence 468999999999988754
No 216
>PRK07764 DNA polymerase III subunits gamma and tau; Validated
Probab=22.24 E-value=3.3e+02 Score=24.42 Aligned_cols=63 Identities=6% Similarity=0.031 Sum_probs=33.6
Q ss_pred CcHHHHHHHHHhhCCC-CCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHh
Q psy13691 10 LPSAIIQRLIKEALPK-DAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEG 76 (103)
Q Consensus 10 LP~a~V~ri~K~~l~~-~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~A 76 (103)
|+...+.+.+++.+.. + +.+++++..+|.+.+.-=+..+-++..+.+...+...|+.+||...
T Consensus 179 l~~~~l~~~L~~il~~EG----v~id~eal~lLa~~sgGdlR~Al~eLEKLia~~~~~~IT~e~V~al 242 (824)
T PRK07764 179 VPPEVMRGYLERICAQEG----VPVEPGVLPLVIRAGGGSVRDSLSVLDQLLAGAGPEGVTYERAVAL 242 (824)
T ss_pred CCHHHHHHHHHHHHHHcC----CCCCHHHHHHHHHHcCCCHHHHHHHHHHHHhhcCCCCCCHHHHHHH
Confidence 4455666666655432 3 6788888777766654323333333333333334455777755443
No 217
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=22.01 E-value=96 Score=25.61 Aligned_cols=78 Identities=19% Similarity=0.233 Sum_probs=50.7
Q ss_pred cCCCCcHHHHHHHHHhhCCCCCcc----------cc------cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcC
Q psy13691 6 DDLNLPSAIIQRLIKEALPKDAEG----------KI------NVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLS 69 (103)
Q Consensus 6 ~d~~LP~a~V~ri~K~~l~~~~~~----------~~------~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~ 69 (103)
+++.|-.|||.|++++.-=..+-| .+ -+|.++.... -..-+..+++++.++
T Consensus 351 e~lglheSTVSRav~~Kyv~tp~Gi~~lk~FFs~~~~~~~g~~~S~~~Ik~~-------------Ik~lI~~Ed~~~PlS 417 (455)
T PRK05932 351 EELGMHESTISRATTNKYMATPRGIFELKYFFSSAVSTDGGGEASSTAIRAL-------------IKKLIAAENPKKPLS 417 (455)
T ss_pred HHhCCCccchhhhhcCceeecCCceEEHHHhcccccCCCCCccccHHHHHHH-------------HHHHHHhcCCCCCCC
Confidence 467888999999997643222211 01 1333332211 123356778899999
Q ss_pred hhhHHHhhhhcCchHHHHHHHHHHHHHHhcc
Q psy13691 70 GVDVIEGVKQIGFEVIIEILGKSYNAAVSIK 100 (103)
Q Consensus 70 ~eDV~~Al~~lgf~~~~~~l~~~l~~~k~~~ 100 (103)
.+.|...|+.-|+. .-...+..||+..
T Consensus 418 D~~I~~~L~~~Gi~----IaRRTVaKYRe~L 444 (455)
T PRK05932 418 DSKIAELLKEQGID----VARRTVAKYREAL 444 (455)
T ss_pred HHHHHHHHHHcCCC----eehHHHHHHHHHc
Confidence 99999999998884 5567777888764
No 218
>PHA03328 nuclear egress lamina protein UL31; Provisional
Probab=21.84 E-value=1.4e+02 Score=23.79 Aligned_cols=67 Identities=19% Similarity=0.322 Sum_probs=43.5
Q ss_pred cCCCCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCchH
Q psy13691 6 DDLNLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGFEV 84 (103)
Q Consensus 6 ~d~~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~~ 84 (103)
+++-||-.-|.+|+-+ +|. .+|+-|... .-||..+....--..-.+..-||+++||..++.+|+|++
T Consensus 230 ~slHL~~~~L~~Ll~n-~~g-----Y~i~adv~~------~~fvL~v~~~~~~~~~~~~~~~V~~~dIy~k~~dL~f~d 296 (316)
T PHA03328 230 KSLHLHYRLIDRLLTA-CPG-----YRIIAHVWQ------TTFVLVVRRDAERQTTDADVPAVSAEDIYCKMCDLNFDG 296 (316)
T ss_pred CcccchHHHHHHHHHh-CCC-----CeEEEEEec------ceEEEEEeeCCCCCCccccccccCHHHHHHHHhCCCCCh
Confidence 4566777777666655 453 455544332 235555554333234566788999999999999999985
No 219
>PF06782 UPF0236: Uncharacterised protein family (UPF0236); InterPro: IPR009620 This is a group of proteins of unknown function.
Probab=21.80 E-value=2.3e+02 Score=23.37 Aligned_cols=54 Identities=22% Similarity=0.191 Sum_probs=40.9
Q ss_pred ccccHHHHHHHHHHHHHHHHHHHHHHHH-HHHhCCCCCcChhhHHHhhhhcCchHHHH
Q psy13691 31 INVSKDVRLAAGKAASLFILHLTTEALS-IANEKNRKTLSGVDVIEGVKQIGFEVIIE 87 (103)
Q Consensus 31 ~~iskda~~~l~~~~~~Fi~~lt~~A~~-~a~~~~RkTI~~eDV~~Al~~lgf~~~~~ 87 (103)
.++|.+....+.+.|+. ..|= .|.+ +-...+...||.+-|.++++.+|+....+
T Consensus 116 ~R~S~~~~~~i~~~a~~-~sYr--~aa~~l~~~~~~~~iS~~tV~~~v~~~g~~~~~~ 170 (470)
T PF06782_consen 116 QRISPELKEKIVELATE-MSYR--KAAEILEELLGNVSISKQTVWNIVKEAGFEEIKE 170 (470)
T ss_pred cchhHHHHHHHHHHHhh-cCHH--HHHHHHhhccCCCccCHHHHHHHHHhccchhhhc
Confidence 69999999999888877 5553 3333 33455789999999999999999654433
No 220
>COG4396 Mu-like prophage host-nuclease inhibitor protein Gam [General function prediction only]
Probab=21.38 E-value=85 Score=22.49 Aligned_cols=25 Identities=20% Similarity=0.244 Sum_probs=20.0
Q ss_pred hhhHHHhhhhcCchHHHHHHHHHHH
Q psy13691 70 GVDVIEGVKQIGFEVIIEILGKSYN 94 (103)
Q Consensus 70 ~eDV~~Al~~lgf~~~~~~l~~~l~ 94 (103)
.+-|+.-|+++||+.|+..-++.-.
T Consensus 111 veaV~e~L~rmgf~rFiRTk~EinK 135 (170)
T COG4396 111 VEAVLEWLSRMGFARFIRTKKEINK 135 (170)
T ss_pred HHHHHHHHHHhhHHHHHHhHHHhcH
Confidence 4678888899999999988776543
No 221
>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=21.19 E-value=41 Score=21.35 Aligned_cols=26 Identities=12% Similarity=0.136 Sum_probs=17.5
Q ss_pred HHHHHHHHhCCCCCcChhhHHHhhhhc
Q psy13691 54 TEALSIANEKNRKTLSGVDVIEGVKQI 80 (103)
Q Consensus 54 ~~A~~~a~~~~RkTI~~eDV~~Al~~l 80 (103)
..|...|..+|.. |+.+||..|.++|
T Consensus 53 rlA~m~A~g~g~~-i~~~~i~~A~~~l 78 (78)
T PF09077_consen 53 RLAAMFAKGEGEA-ITADHIRAAWKEL 78 (78)
T ss_dssp GGGT-TT-TTS---SSHHHHHHHHTSS
T ss_pred HHHHHHhccCCCc-CCHHHHHHHHHhC
Confidence 4466677777776 9999999998764
No 222
>cd00052 EH Eps15 homology domain; found in proteins implicated in endocytosis, vesicle transport, and signal transduction. The alignment contains a pair of EF-hand motifs, typically one of them is canonical and binds to Ca2+, while the other may not bind to Ca2+. A hydrophobic binding pocket is formed by residues from both EF-hand motifs. The EH domain binds to proteins containing NPF (class I), [WF]W or SWG (class II), or H[TS]F (class III) sequence motifs.
Probab=21.16 E-value=1.6e+02 Score=16.19 Aligned_cols=21 Identities=14% Similarity=0.162 Sum_probs=13.1
Q ss_pred hCCCCCcChhhHHHhhhhcCc
Q psy13691 62 EKNRKTLSGVDVIEGVKQIGF 82 (103)
Q Consensus 62 ~~~RkTI~~eDV~~Al~~lgf 82 (103)
.++.-.|+.+++..++..+|+
T Consensus 10 ~~~~G~i~~~el~~~l~~~g~ 30 (67)
T cd00052 10 PDGDGLISGDEARPFLGKSGL 30 (67)
T ss_pred CCCCCcCcHHHHHHHHHHcCC
Confidence 344556666666666666665
No 223
>PF15605 Toxin_52: Putative toxin 52
Probab=21.14 E-value=2.7e+02 Score=18.68 Aligned_cols=37 Identities=16% Similarity=-0.006 Sum_probs=29.0
Q ss_pred cHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHHHHHH
Q psy13691 11 PSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLFILHL 52 (103)
Q Consensus 11 P~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~Fi~~l 52 (103)
-..++.|.++..|++. +.|...+..++..-.+-..+|
T Consensus 58 GL~n~~~~le~~L~np-----~l~~~~r~~lq~~l~ea~~~l 94 (103)
T PF15605_consen 58 GLVNRKRTLEGSLKNP-----NLSGRTRELLQSKLNEANNYL 94 (103)
T ss_pred HHHHHHHHHHHhcCCC-----CCchHHHHHHHHHHHHHHHHH
Confidence 3567889999999875 789999999988776655554
No 224
>cd03516 Link_domain_CD44_like This domain is a hyaluronan (HA)-binding domain. It is found in CD44 receptor and mediates adhesive interactions during inflammatory leukocyte homing and tumor metastasis. It also plays an important role in arteriogenesis. The functional HA-binding domain of CD44 is an extended domain comprised of a single link module flanked with N-and C- extensions. These extensions are essential for folding and for functional activity. This group also contains the cell surface retention sequence (CRS) binding protein-1 (CRSBP-1) and lymph vessel endothelial receptor-1 (LYVE-1). CRSBP-1 is a cell surface binding protein for the CRS motif of PDGF-BB (platelet-derived growth factor-BB) and is responsible for the cell surface retention of PDGF-BB in SSV-transformed cells. CRSBP-1 may play a role in autocrine regulation of cell growth mediated by CRS containing growth regulators. LYVE-1 is preferentially expressed on the lymphatic endothelium and is used as a molecular marke
Probab=21.02 E-value=1.3e+02 Score=21.30 Aligned_cols=29 Identities=31% Similarity=0.267 Sum_probs=25.7
Q ss_pred HHHHHHHHhCCCCCcChhhHHHhhhhcCch
Q psy13691 54 TEALSIANEKNRKTLSGVDVIEGVKQIGFE 83 (103)
Q Consensus 54 ~~A~~~a~~~~RkTI~~eDV~~Al~~lgf~ 83 (103)
.+|.+.|...|-..=+.+++..|.+. ||+
T Consensus 22 ~eA~~aC~~~ga~lAs~~QL~~Aw~~-Gld 50 (144)
T cd03516 22 TEAKEACRALGLTLASKAQVETALKF-GFE 50 (144)
T ss_pred HHHHHHHHHcCCeeCCHHHHHHHHHc-Chh
Confidence 68999999999999999999999874 886
No 225
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=21.02 E-value=1.6e+02 Score=21.78 Aligned_cols=35 Identities=11% Similarity=0.027 Sum_probs=26.4
Q ss_pred CCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHH
Q psy13691 9 NLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLF 48 (103)
Q Consensus 9 ~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~F 48 (103)
..-+++|.|++...- .. .+||.+.++.+.+++++.
T Consensus 11 GVS~~TVSrvLn~~~-~~----~~Vs~~tr~rV~~~a~el 45 (328)
T PRK11303 11 GVSRTTASYVINGKA-KQ----YRVSDKTVEKVMAVVREH 45 (328)
T ss_pred CCCHHHHHHHHcCCC-CC----CCcCHHHHHHHHHHHHHh
Confidence 556899999996541 11 269999999999998774
No 226
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=20.99 E-value=1.3e+02 Score=22.42 Aligned_cols=32 Identities=16% Similarity=0.210 Sum_probs=26.3
Q ss_pred CCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHH
Q psy13691 9 NLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLF 48 (103)
Q Consensus 9 ~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~F 48 (103)
..-+++|.|.++.. -+||++.+.-+.+++.+.
T Consensus 12 gVS~~TVSrvLn~~--------~~vs~~tr~~V~~~a~el 43 (341)
T PRK10703 12 GVSTTTVSHVINKT--------RFVAEETRNAVWAAIKEL 43 (341)
T ss_pred CCCHHHHHHHHcCC--------CCCCHHHHHHHHHHHHHH
Confidence 56789999999642 369999999999998875
No 227
>COG4519 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.98 E-value=41 Score=21.93 Aligned_cols=15 Identities=27% Similarity=0.512 Sum_probs=12.7
Q ss_pred ChhhHHHhhhhcCch
Q psy13691 69 SGVDVIEGVKQIGFE 83 (103)
Q Consensus 69 ~~eDV~~Al~~lgf~ 83 (103)
+.+||++||..||..
T Consensus 38 T~QDvikAlpglgi~ 52 (95)
T COG4519 38 TAQDVIKALPGLGIV 52 (95)
T ss_pred HHHHHHHhCcCCCeE
Confidence 468999999998874
No 228
>PRK09492 treR trehalose repressor; Provisional
Probab=20.98 E-value=1.2e+02 Score=22.30 Aligned_cols=32 Identities=13% Similarity=0.234 Sum_probs=26.0
Q ss_pred CCcHHHHHHHHHhhCCCCCcccccccHHHHHHHHHHHHHH
Q psy13691 9 NLPSAIIQRLIKEALPKDAEGKINVSKDVRLAAGKAASLF 48 (103)
Q Consensus 9 ~LP~a~V~ri~K~~l~~~~~~~~~iskda~~~l~~~~~~F 48 (103)
..-+++|.|++... -+||.+.++-+.+++++.
T Consensus 15 gVS~~TVSrvLn~~--------~~vs~~tr~rV~~~a~el 46 (315)
T PRK09492 15 GVGKSTVSRVLNNE--------SGVSEETRERVEAVINQH 46 (315)
T ss_pred CCCHHHHhHHhCCC--------CCCCHHHHHHHHHHHHHH
Confidence 56678899888642 379999999999998874
No 229
>PRK09111 DNA polymerase III subunits gamma and tau; Validated
Probab=20.41 E-value=4.1e+02 Score=22.82 Aligned_cols=47 Identities=9% Similarity=-0.030 Sum_probs=32.9
Q ss_pred ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhh
Q psy13691 31 INVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVK 78 (103)
Q Consensus 31 ~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~ 78 (103)
..++.++...|.+.+.--+..+.++..+.+.. +.+.|+.+||...+.
T Consensus 209 i~i~~eAl~lIa~~a~Gdlr~al~~Ldkli~~-g~g~It~e~V~~llg 255 (598)
T PRK09111 209 VEVEDEALALIARAAEGSVRDGLSLLDQAIAH-GAGEVTAEAVRDMLG 255 (598)
T ss_pred CCCCHHHHHHHHHHcCCCHHHHHHHHHHHHhh-cCCCcCHHHHHHHhC
Confidence 78999999998888776555555544443333 356799999987764
No 230
>KOG1775|consensus
Probab=20.40 E-value=73 Score=20.42 Aligned_cols=19 Identities=11% Similarity=0.296 Sum_probs=14.9
Q ss_pred hcCchHHHHHHHHHHHHHH
Q psy13691 79 QIGFEVIIEILGKSYNAAV 97 (103)
Q Consensus 79 ~lgf~~~~~~l~~~l~~~k 97 (103)
-+||++|+.-+-+-.-+|.
T Consensus 34 L~GFDd~VNmvLeDvtEye 52 (84)
T KOG1775|consen 34 LVGFDDFVNMVLEDVTEYE 52 (84)
T ss_pred EechHHHHHHHHHhhhhee
Confidence 5799999988877776664
No 231
>PRK14958 DNA polymerase III subunits gamma and tau; Provisional
Probab=20.05 E-value=4.1e+02 Score=22.16 Aligned_cols=68 Identities=13% Similarity=0.006 Sum_probs=36.4
Q ss_pred CcHHHHHHHHHhhCCC-CCcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChhhHHHhhhhcCc
Q psy13691 10 LPSAIIQRLIKEALPK-DAEGKINVSKDVRLAAGKAASLFILHLTTEALSIANEKNRKTLSGVDVIEGVKQIGF 82 (103)
Q Consensus 10 LP~a~V~ri~K~~l~~-~~~~~~~iskda~~~l~~~~~~Fi~~lt~~A~~~a~~~~RkTI~~eDV~~Al~~lgf 82 (103)
+|...+.+.++..+.. + +.+++++...|.+.+.-=+..+-+.--. +..-+...|+.+||...+....-
T Consensus 178 l~~~~i~~~l~~il~~eg----i~~~~~al~~ia~~s~GslR~al~lLdq-~ia~~~~~It~~~V~~~lg~~~~ 246 (509)
T PRK14958 178 LPPLQIAAHCQHLLKEEN----VEFENAALDLLARAANGSVRDALSLLDQ-SIAYGNGKVLIADVKTMLGTIEP 246 (509)
T ss_pred CCHHHHHHHHHHHHHHcC----CCCCHHHHHHHHHHcCCcHHHHHHHHHH-HHhcCCCCcCHHHHHHHHCCCCH
Confidence 4555554444433322 3 7889999888877664322222111111 11124567999998887654433
Done!