Query 033999
Match_columns 106
No_of_seqs 105 out of 162
Neff 5.3
Searched_HMMs 46136
Date Fri Mar 29 08:39:55 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033999.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033999hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3463 Transcription initiati 100.0 3.5E-55 7.6E-60 302.9 12.5 106 1-106 1-107 (109)
2 COG5123 TOA2 Transcription ini 100.0 7.2E-44 1.6E-48 245.6 12.2 103 2-104 3-112 (113)
3 PF02751 TFIIA_gamma_C: Transc 100.0 4.2E-29 9.1E-34 154.1 6.2 50 52-101 1-52 (52)
4 PF02268 TFIIA_gamma_N: Transc 99.9 3.2E-26 6.9E-31 139.8 5.6 48 3-50 2-49 (49)
5 PF10925 DUF2680: Protein of u 93.2 0.33 7E-06 30.4 5.0 33 17-49 21-53 (59)
6 cd01709 RT_like_1 RT_like_1: A 88.7 0.43 9.3E-06 39.4 3.0 65 26-102 87-162 (346)
7 PF11848 DUF3368: Domain of un 87.1 1.9 4.1E-05 25.5 4.4 35 5-40 11-46 (48)
8 PF09925 DUF2157: Predicted me 86.1 0.74 1.6E-05 32.6 2.7 24 20-43 1-24 (145)
9 cd01646 RT_Bac_retron_I RT_Bac 86.0 1.2 2.6E-05 31.4 3.8 39 27-76 58-96 (158)
10 cd03487 RT_Bac_retron_II RT_Ba 85.8 2.3 4.9E-05 31.5 5.3 46 26-81 107-152 (214)
11 COG3937 Uncharacterized conser 79.9 8.2 0.00018 27.1 5.8 36 11-46 21-56 (108)
12 cd01651 RT_G2_intron RT_G2_int 79.0 3.1 6.6E-05 30.0 3.6 51 26-76 130-180 (226)
13 PF09677 TrbI_Ftype: Type-F co 72.6 11 0.00023 26.2 4.9 40 15-54 37-79 (111)
14 PRK10753 transcriptional regul 68.3 23 0.00049 23.2 5.5 42 18-61 5-46 (90)
15 PRK10664 transcriptional regul 67.3 23 0.00051 23.3 5.4 41 19-61 6-46 (90)
16 PF15606 Toxin_55: Putative to 67.0 6.6 0.00014 26.0 2.6 22 15-36 40-61 (77)
17 cd00304 RT_like RT_like: Rever 66.9 12 0.00026 23.5 3.9 41 25-76 14-54 (98)
18 TIGR02744 TrbI_Ftype type-F co 64.7 23 0.00051 24.9 5.2 38 16-53 39-79 (112)
19 PRK00285 ihfA integration host 64.3 22 0.00047 23.4 4.9 44 15-60 4-47 (99)
20 smart00411 BHL bacterial (prok 63.4 25 0.00054 22.3 4.9 42 17-60 4-45 (90)
21 PF06702 DUF1193: Protein of u 61.3 8.2 0.00018 30.2 2.6 46 6-51 150-204 (221)
22 PF00078 RVT_1: Reverse transc 60.8 12 0.00025 26.3 3.2 42 25-76 128-169 (214)
23 cd08332 CARD_CASP2 Caspase act 58.4 16 0.00035 24.1 3.4 25 16-40 22-46 (90)
24 PF00349 Hexokinase_1: Hexokin 57.9 19 0.00041 27.2 4.1 41 15-55 2-42 (206)
25 PF00619 CARD: Caspase recruit 57.3 20 0.00044 22.3 3.6 25 15-39 17-41 (85)
26 PF14848 HU-DNA_bdg: DNA-bindi 56.2 32 0.00069 23.8 4.7 37 15-51 30-67 (124)
27 PF14277 DUF4364: Domain of un 54.0 11 0.00025 27.6 2.3 38 15-52 35-85 (163)
28 cd08048 TAF11 TATA Binding Pro 53.9 21 0.00046 23.6 3.4 37 1-37 6-42 (85)
29 KOG3219 Transcription initiati 53.4 9.1 0.0002 29.4 1.7 34 1-34 102-135 (195)
30 cd00591 HU_IHF Integration hos 53.3 54 0.0012 20.5 5.3 41 18-60 4-44 (87)
31 cd08330 CARD_ASC_NALP1 Caspase 52.2 21 0.00045 23.2 3.1 25 15-39 16-40 (82)
32 cd01648 TERT TERT: Telomerase 52.1 18 0.00038 24.5 2.9 47 25-79 22-68 (119)
33 PF13742 tRNA_anti_2: OB-fold 51.3 55 0.0012 21.7 5.1 45 39-83 5-51 (99)
34 PRK00199 ihfB integration host 50.8 67 0.0014 20.8 5.9 42 18-61 5-47 (94)
35 PF04719 TAFII28: hTAFII28-lik 50.5 32 0.00068 23.2 3.8 42 2-44 14-56 (90)
36 PF15658 Latrotoxin_C: Latroto 49.9 21 0.00045 25.8 3.0 41 10-50 86-126 (127)
37 TIGR00987 himA integration hos 48.8 57 0.0012 21.3 4.9 42 17-60 5-46 (96)
38 TIGR01837 PHA_granule_1 poly(h 48.6 81 0.0018 21.8 5.8 33 14-46 22-54 (118)
39 PF14490 HHH_4: Helix-hairpin- 48.4 40 0.00087 22.0 4.1 35 16-51 8-42 (94)
40 cd08325 CARD_CASP1-like Caspas 48.3 49 0.0011 21.4 4.4 26 15-40 17-42 (83)
41 PF09851 SHOCT: Short C-termin 48.0 43 0.00094 17.9 3.6 22 17-38 5-26 (31)
42 KOG0375 Serine-threonine phosp 45.3 35 0.00077 29.2 4.1 40 21-64 53-97 (517)
43 PF14929 TAF1_subA: TAF RNA Po 45.0 23 0.0005 31.0 3.1 41 11-51 320-365 (547)
44 PF05186 Dpy-30: Dpy-30 motif; 43.8 28 0.00061 20.1 2.4 27 6-32 4-30 (42)
45 PF09693 Phage_XkdX: Phage unc 42.2 29 0.00063 19.7 2.3 21 17-37 15-35 (40)
46 PF02982 Scytalone_dh: Scytalo 40.4 44 0.00095 25.0 3.5 31 55-85 110-145 (160)
47 smart00114 CARD Caspase recrui 40.3 39 0.00084 21.6 3.0 23 17-39 23-45 (88)
48 TIGR03319 YmdA_YtgF conserved 40.2 65 0.0014 27.8 5.0 44 4-51 252-295 (514)
49 cd01721 Sm_D3 The eukaryotic S 39.5 68 0.0015 20.0 3.9 29 53-84 17-45 (70)
50 PF10335 DUF294_C: Putative nu 39.5 86 0.0019 22.0 4.9 36 18-53 66-101 (145)
51 cd08323 CARD_APAF1 Caspase act 39.4 39 0.00085 22.3 2.9 29 16-44 16-47 (86)
52 PF03492 Methyltransf_7: SAM d 39.3 24 0.00052 28.5 2.2 24 11-34 198-221 (334)
53 PF00681 Plectin: Plectin repe 37.3 60 0.0013 18.5 3.2 20 20-39 24-43 (45)
54 TIGR01669 phage_XkdX phage unc 37.2 37 0.00081 19.9 2.3 22 17-38 20-41 (45)
55 PF08638 Med14: Mediator compl 36.6 1.1E+02 0.0024 22.9 5.3 53 23-79 131-183 (195)
56 PF12960 DUF3849: Protein of u 36.3 1E+02 0.0022 22.2 4.8 49 5-53 17-71 (133)
57 cd01671 CARD Caspase activatio 36.2 62 0.0014 19.8 3.4 26 15-40 14-39 (80)
58 cd04446 DEP_DEPDC4 DEP (Dishev 36.2 49 0.0011 22.5 3.0 38 4-41 21-64 (95)
59 TIGR00988 hip integration host 36.2 1.2E+02 0.0026 19.5 5.9 42 18-61 5-47 (94)
60 cd04437 DEP_Epac DEP (Dishevel 35.9 30 0.00066 24.6 2.0 62 4-71 24-87 (125)
61 PF12713 DUF3806: Domain of un 35.1 1.1E+02 0.0024 19.9 4.6 41 18-59 4-45 (87)
62 cd04440 DEP_2_P-Rex DEP (Dishe 35.0 38 0.00082 23.0 2.3 61 5-71 32-93 (93)
63 PRK00111 hypothetical protein; 34.9 63 0.0014 24.4 3.7 58 14-74 67-127 (180)
64 PF13833 EF-hand_8: EF-hand do 34.6 78 0.0017 17.8 3.4 28 15-43 9-36 (54)
65 cd08329 CARD_BIRC2_BIRC3 Caspa 34.4 59 0.0013 21.6 3.2 22 18-39 27-48 (94)
66 PF09862 DUF2089: Protein of u 34.3 46 0.001 23.4 2.7 22 17-39 92-113 (113)
67 COG0776 HimA Bacterial nucleoi 34.2 1.5E+02 0.0032 20.1 5.9 38 21-60 9-46 (94)
68 PF10474 DUF2451: Protein of u 34.1 1.2E+02 0.0026 23.3 5.3 46 15-61 103-151 (234)
69 PF00216 Bac_DNA_binding: Bact 34.1 97 0.0021 19.4 4.1 30 22-51 9-38 (90)
70 TIGR02742 TrbC_Ftype type-F co 33.8 63 0.0014 23.0 3.4 27 14-40 102-128 (130)
71 cd01733 LSm10 The eukaryotic S 33.7 99 0.0021 19.9 4.1 31 53-86 26-56 (78)
72 PRK03195 hypothetical protein; 33.6 69 0.0015 24.2 3.8 58 14-74 73-133 (186)
73 COG3093 VapI Plasmid maintenan 33.6 55 0.0012 22.8 3.0 33 18-50 38-71 (104)
74 PF03048 Herpes_UL92: UL92 fam 33.5 1.1E+02 0.0023 23.5 4.8 32 16-47 104-135 (192)
75 cd08326 CARD_CASP9 Caspase act 33.5 68 0.0015 21.0 3.3 24 16-39 18-41 (84)
76 PF14802 TMEM192: TMEM192 fami 33.1 1.1E+02 0.0023 23.9 4.9 43 2-44 90-155 (236)
77 PF06256 Nucleo_LEF-12: Nucleo 32.9 67 0.0015 24.6 3.6 43 8-50 11-90 (185)
78 PF07527 Hairy_orange: Hairy O 32.9 96 0.0021 17.5 4.7 35 13-47 8-42 (43)
79 COG2405 Predicted nucleic acid 32.3 55 0.0012 24.3 3.0 25 18-42 130-155 (157)
80 KOG0037 Ca2+-binding protein, 32.3 52 0.0011 25.8 3.0 28 15-44 145-172 (221)
81 KOG3456 NADH:ubiquinone oxidor 31.4 33 0.00071 24.4 1.6 12 94-105 78-89 (120)
82 PF07565 Band_3_cyto: Band 3 c 31.2 56 0.0012 25.8 3.0 31 10-40 41-71 (257)
83 PRK10449 heat-inducible protei 30.6 89 0.0019 22.0 3.8 42 38-81 98-139 (140)
84 PF01756 ACOX: Acyl-CoA oxidas 30.6 1.4E+02 0.003 21.6 4.9 34 15-48 92-125 (187)
85 COG5026 Hexokinase [Carbohydra 30.1 1E+02 0.0022 26.7 4.6 41 12-52 13-53 (466)
86 cd01723 LSm4 The eukaryotic Sm 30.1 56 0.0012 20.7 2.4 28 53-83 18-45 (76)
87 PF12297 EVC2_like: Ellis van 29.6 2.2E+02 0.0047 24.5 6.4 43 4-46 297-339 (429)
88 COG2306 Predicted RNA-binding 29.4 1.5E+02 0.0032 22.7 4.9 31 18-48 126-156 (183)
89 PF08360 TetR_C_5: QacR-like p 27.8 1.7E+02 0.0037 20.4 4.8 45 10-54 32-79 (131)
90 TIGR02009 PGMB-YQAB-SF beta-ph 27.6 1.5E+02 0.0032 20.4 4.5 44 6-49 37-82 (185)
91 PLN02668 indole-3-acetate carb 27.6 69 0.0015 26.8 3.1 22 14-35 257-278 (386)
92 TIGR01425 SRP54_euk signal rec 27.6 1.4E+02 0.003 25.4 5.0 37 11-47 4-40 (429)
93 PF08784 RPA_C: Replication pr 27.5 52 0.0011 21.5 2.0 16 14-29 80-95 (102)
94 cd01130 VirB11-like_ATPase Typ 27.2 63 0.0014 23.2 2.5 21 20-40 1-21 (186)
95 cd08785 CARD_CARD9-like Caspas 26.9 98 0.0021 20.5 3.2 24 17-40 19-42 (86)
96 PF13443 HTH_26: Cro/C1-type H 26.9 1.4E+02 0.0029 17.3 3.7 45 2-49 12-58 (63)
97 PRK00106 hypothetical protein; 26.7 1.5E+02 0.0032 26.0 5.0 44 4-51 273-316 (535)
98 cd03715 RT_ZFREV_like RT_ZFREV 26.5 46 0.00099 24.3 1.7 20 13-32 14-33 (210)
99 PF14237 DUF4339: Domain of un 26.4 42 0.00092 19.0 1.2 16 17-32 16-31 (45)
100 PRK08132 FAD-dependent oxidore 25.8 2.5E+02 0.0055 23.5 6.2 57 41-103 127-184 (547)
101 KOG3438 DNA-directed RNA polym 25.8 1.5E+02 0.0033 20.7 4.1 31 10-47 68-98 (105)
102 cd01720 Sm_D2 The eukaryotic S 25.7 86 0.0019 20.7 2.8 26 53-81 21-46 (87)
103 PTZ00150 phosphoglucomutase-2- 25.4 1.2E+02 0.0026 26.3 4.3 31 13-43 436-477 (584)
104 COG0330 HflC Membrane protease 25.2 1.1E+02 0.0024 23.5 3.7 41 18-85 129-169 (291)
105 TIGR02148 Fibro_Slime fibro-sl 25.2 44 0.00094 22.7 1.3 25 61-85 19-43 (90)
106 COG5251 TAF40 Transcription in 25.2 36 0.00078 26.1 1.0 35 1-35 105-139 (199)
107 COG1542 Uncharacterized conser 24.9 52 0.0011 29.0 2.0 27 7-33 54-80 (593)
108 cd07367 CarBb CarBb is the B s 24.8 36 0.00078 26.5 0.9 44 8-51 151-207 (268)
109 PF12550 GCR1_C: Transcription 24.6 1.5E+02 0.0033 18.8 3.8 29 13-41 52-80 (81)
110 PRK00286 xseA exodeoxyribonucl 24.3 2.1E+02 0.0047 23.5 5.5 40 40-80 10-50 (438)
111 PF08004 DUF1699: Protein of u 24.3 47 0.001 24.1 1.4 28 12-39 103-130 (131)
112 PF09687 PRESAN: Plasmodium RE 24.2 2.1E+02 0.0045 18.5 5.2 41 11-51 44-84 (129)
113 COG3877 Uncharacterized protei 24.1 85 0.0018 22.3 2.6 20 20-39 102-121 (122)
114 PF14793 DUF4478: Domain of un 24.1 49 0.0011 23.4 1.4 12 3-14 30-41 (112)
115 PF01423 LSM: LSM domain ; In 23.9 1.7E+02 0.0037 17.4 4.1 30 54-86 16-45 (67)
116 TIGR02525 plasmid_TraJ plasmid 23.9 73 0.0016 26.3 2.6 26 13-38 342-367 (372)
117 COG0541 Ffh Signal recognition 23.9 1.8E+02 0.0039 25.1 5.0 39 10-48 3-41 (451)
118 PF11833 DUF3353: Protein of u 23.8 2.3E+02 0.0051 21.3 5.2 49 15-63 8-56 (194)
119 COG2137 OraA Uncharacterized p 23.8 1.3E+02 0.0028 22.4 3.7 35 16-51 87-121 (174)
120 PRK08486 single-stranded DNA-b 23.7 1.9E+02 0.0041 21.6 4.6 37 46-82 60-104 (182)
121 PF02885 Glycos_trans_3N: Glyc 23.6 1.5E+02 0.0033 18.0 3.5 25 16-40 2-26 (66)
122 cd01650 RT_nLTR_like RT_nLTR: 23.5 1.2E+02 0.0026 21.6 3.4 70 25-100 109-191 (220)
123 TIGR01420 pilT_fam pilus retra 23.5 91 0.002 24.9 3.0 26 13-38 313-338 (343)
124 PF05258 DUF721: Protein of un 22.9 1.7E+02 0.0036 17.8 3.6 40 16-55 2-43 (89)
125 TIGR01201 HU_rel DNA-binding p 22.8 2E+02 0.0044 20.4 4.5 38 14-51 31-68 (145)
126 COG2445 Uncharacterized conser 22.6 1.3E+02 0.0027 21.7 3.3 21 17-37 68-88 (138)
127 PF10689 DUF2496: Protein of u 22.5 1.8E+02 0.004 17.3 3.9 25 15-39 10-34 (44)
128 PRK03839 putative kinase; Prov 22.4 2.8E+02 0.006 19.4 5.1 58 9-66 13-77 (180)
129 PRK13358 protocatechuate 4,5-d 22.4 55 0.0012 25.2 1.5 41 11-51 154-207 (269)
130 PF15467 SGIII: Secretogranin- 22.2 2.3E+02 0.005 24.2 5.2 43 11-53 291-333 (453)
131 PF05609 LAP1C: Lamina-associa 22.0 68 0.0015 27.7 2.1 42 30-71 332-380 (465)
132 smart00049 DEP Domain found in 22.0 87 0.0019 19.2 2.2 35 5-41 15-49 (77)
133 PF10815 ComZ: ComZ; InterPro 22.0 2.1E+02 0.0046 17.8 5.2 35 15-49 13-48 (56)
134 PF14763 HPS3_C: Hermansky-Pud 21.9 16 0.00034 30.4 -1.6 41 28-68 3-44 (353)
135 cd08324 CARD_NOD1_CARD4 Caspas 21.8 89 0.0019 21.1 2.2 22 17-38 18-39 (85)
136 PF13730 HTH_36: Helix-turn-he 21.7 1.1E+02 0.0023 17.4 2.4 16 14-29 40-55 (55)
137 KOG1369 Hexokinase [Carbohydra 21.6 5.2E+02 0.011 22.4 7.4 71 13-83 24-99 (474)
138 PTZ00059 dynein light chain; P 21.5 1.7E+02 0.0036 19.2 3.5 18 28-45 34-51 (90)
139 KOG3430 Dynein light chain typ 21.5 2.3E+02 0.0049 19.3 4.2 18 29-46 35-52 (90)
140 PF08535 KorB: KorB domain; I 21.3 2.4E+02 0.0052 18.1 4.8 30 15-44 28-57 (93)
141 PF01003 Flavi_capsid: Flavivi 21.1 1.2E+02 0.0027 21.2 3.0 39 11-51 50-88 (117)
142 PF14076 DUF4258: Domain of un 20.9 1.5E+02 0.0034 17.4 3.1 22 18-40 5-26 (73)
143 PF00502 Phycobilisome: Phycob 20.9 1.6E+02 0.0034 21.1 3.6 43 5-47 110-155 (157)
144 PF11630 DUF3254: Protein of u 20.8 2E+02 0.0043 19.9 3.9 31 8-38 69-99 (100)
145 KOG4603 TBP-1 interacting prot 20.7 72 0.0016 24.5 1.8 23 12-34 38-60 (201)
146 PF11769 DUF3313: Protein of u 20.6 1.7E+02 0.0036 21.4 3.7 25 28-52 68-92 (201)
147 cd07366 3MGA_Dioxygenase Subun 20.6 85 0.0018 25.6 2.4 41 8-51 217-265 (328)
148 PF00436 SSB: Single-strand bi 20.5 2.3E+02 0.005 17.8 4.0 25 47-71 60-86 (104)
149 PF04840 Vps16_C: Vps16, C-ter 20.4 96 0.0021 25.0 2.6 34 7-42 171-204 (319)
150 PF13812 PPR_3: Pentatricopept 20.3 98 0.0021 15.2 1.8 10 18-27 22-31 (34)
151 cd04371 DEP DEP domain, named 20.1 1.1E+02 0.0023 18.7 2.3 35 5-41 23-57 (81)
152 PF05596 Taeniidae_ag: Taeniid 20.0 2.5E+02 0.0053 17.8 4.3 22 4-25 20-41 (64)
No 1
>KOG3463 consensus Transcription initiation factor IIA, gamma subunit [Transcription]
Probab=100.00 E-value=3.5e-55 Score=302.86 Aligned_cols=106 Identities=57% Similarity=0.925 Sum_probs=103.3
Q ss_pred ChhhHHHHhhhHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHhhcccceEEeeeCccceeeCcEEEEEEcCe
Q 033999 1 MATFELYRRSTIGMCLTETLDEMVQNGTLTPELAIQVLVQFDKSMTEALETQVKSKVSIKGHLHTYRFCDNVWTFILQDA 80 (106)
Q Consensus 1 m~~y~lYR~stlG~aL~dtLdeli~~~~I~p~la~kIl~~FDk~i~~~L~~~vk~k~~~KG~L~tYr~cDnVWtf~lkn~ 80 (106)
|+||||||+||||.+|++|||||+++|.|||+||++||++||+||+++|++++++|++|||+|+|||||||||||+++|+
T Consensus 1 m~~YelYR~ttlG~~L~~tLDe~v~~g~itp~la~~VL~~FDKSi~~al~~~vk~kmsfkg~L~tYr~CDnVWTFil~~~ 80 (109)
T KOG3463|consen 1 MSYYELYRRTTLGNALQKTLDELVSDGVITPSLAKKVLEQFDKSINEALNDKVKNKMSFKGKLDTYRFCDNVWTFILKDV 80 (109)
T ss_pred CcHHHHHHHhhHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhcccceeeeeccceeeeccceeeEEEcCe
Confidence 78999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEecceEee-eCeEEEEEecCCCCCC
Q 033999 81 LFKSEELQET-VGRVKIVACDSKLLSQ 106 (106)
Q Consensus 81 ~~k~~~~~~~-~~~lKIVAcd~~~~~~ 106 (106)
+|+.+++..+ +|+||||||||+.+|+
T Consensus 81 ~~r~~~e~~~~vdkvkIVACdg~~~~~ 107 (109)
T KOG3463|consen 81 EFREDNESFKTVDKVKIVACDGKDSGA 107 (109)
T ss_pred EEecccccccccceEEEEEecCccccc
Confidence 9999999985 9999999999998764
No 2
>COG5123 TOA2 Transcription initiation factor IIA, gamma subunit [Transcription]
Probab=100.00 E-value=7.2e-44 Score=245.55 Aligned_cols=103 Identities=42% Similarity=0.768 Sum_probs=98.9
Q ss_pred hhhHHHHhhhHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHhhcccceEEeeeCccceeeCcEEEEEEcCeE
Q 033999 2 ATFELYRRSTIGMCLTETLDEMVQNGTLTPELAIQVLVQFDKSMTEALETQVKSKVSIKGHLHTYRFCDNVWTFILQDAL 81 (106)
Q Consensus 2 ~~y~lYR~stlG~aL~dtLdeli~~~~I~p~la~kIl~~FDk~i~~~L~~~vk~k~~~KG~L~tYr~cDnVWtf~lkn~~ 81 (106)
.||||||+|+||..|.|+|||+|++|+|+|+|||+||+.||+++.++|++.|+++++|||+|++|+|||+||||+++|+.
T Consensus 3 ~yYElYRrs~ig~~L~dalD~lis~g~isp~lam~vLetFDksv~e~l~~~v~s~ltfKG~lDtY~fcD~VWtFi~kn~~ 82 (113)
T COG5123 3 GYYELYRRSMIGKVLEDALDELISAGVISPNLAMHVLETFDKSVPEVLNKSVTSSLTFKGKLDTYNFCDGVWTFITKNFV 82 (113)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHhcCCcCHHHHHHHHHHhhhHHHHHHHhhhheeeEEeecccccccccceeEEEecCeE
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEecc------eE-eeeCeEEEEEecCCCC
Q 033999 82 FKSEE------LQ-ETVGRVKIVACDSKLL 104 (106)
Q Consensus 82 ~k~~~------~~-~~~~~lKIVAcd~~~~ 104 (106)
|++++ +. |.++++.||||.++..
T Consensus 83 ~s~~n~~~~a~e~~i~~~k~rIvaca~r~s 112 (113)
T COG5123 83 MSLNNEYFNAGEVNIVACKARIVACAGRRS 112 (113)
T ss_pred EEeccccccccccceEeeeeeEEeeccccC
Confidence 99997 43 8889999999999864
No 3
>PF02751 TFIIA_gamma_C: Transcription initiation factor IIA, gamma subunit; InterPro: IPR015871 Transcription factor IIA (TFIIA) is one of several factors that form part of a transcription pre-initiation complex along with RNA polymerase II, the TATA-box-binding protein (TBP) and TBP-associated factors, on the TATA-box sequence upstream of the initiation start site. After initiation, some components of the pre-initiation complex (including TFIIA) remain attached and re-initiate a subsequent round of transcription. TFIIA binds to TBP to stabilise TBP binding to the TATA element. TFIIA also inhibits the cytokine HMGB1 (high mobility group 1 protein) binding to TBP [], and can dissociate HMGB1 already bound to TBP/TATA-box. Human and Drosophila TFIIA have three subunits: two large subunits, LN/alpha and LC/beta, derived from the same gene, and a small subunit, S/gamma. Yeast TFIIA has two subunits: a large TOA1 subunit that shows sequence similarity to the N-terminal of LN/alpha and the C-terminal of LC/beta, and a small subunit, TOA2 that is highly homologous with S/gamma. The conserved regions of the large and small subunits of TFIIA combine to form two domains: a four-helix bundle (helical domain) composed of two helices from each of the N-terminal regions of TOA1 and TOA2 in yeast; and a beta-barrel (beta-barrel domain) composed of beta-sheets from the C-terminal regions of TOA1 and TOA2 []. This entry represents the beta-barrel domain found at the C-terminal of the gamma subunit of transcription factor TFIIA. ; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005672 transcription factor TFIIA complex; PDB: 1NVP_D 1RM1_B 1YTF_D 1NH2_D.
Probab=99.96 E-value=4.2e-29 Score=154.12 Aligned_cols=50 Identities=64% Similarity=1.082 Sum_probs=45.0
Q ss_pred hcccceEEeeeCccceeeCcEEEEEEcCeEEEe--cceEeeeCeEEEEEecC
Q 033999 52 QVKSKVSIKGHLHTYRFCDNVWTFILQDALFKS--EELQETVGRVKIVACDS 101 (106)
Q Consensus 52 ~vk~k~~~KG~L~tYr~cDnVWtf~lkn~~~k~--~~~~~~~~~lKIVAcd~ 101 (106)
+|++|++|||||+|||||||||||+++|++|++ +++.+++|++|||||||
T Consensus 1 ~vk~k~~fKG~L~tYrfcDnVWTFi~kn~~fk~~~~~~~~~~dkvKIVACd~ 52 (52)
T PF02751_consen 1 KVKNKLSFKGHLDTYRFCDNVWTFILKNVEFKMEDNNETVKVDKVKIVACDS 52 (52)
T ss_dssp T---EEEEEEEEEEEEEETTEEEEEEEEEEEEEE-SSEEEEEEEEEEEEEES
T ss_pred CcceeEEEEEeeeEEEeeCcEEEEEEcCEEEEEecCCcEEEcCeEEEEEcCC
Confidence 589999999999999999999999999999999 57799999999999996
No 4
>PF02268 TFIIA_gamma_N: Transcription initiation factor IIA, gamma subunit, helical domain; InterPro: IPR015872 Transcription factor IIA (TFIIA) is one of several factors that form part of a transcription pre-initiation complex along with RNA polymerase II, the TATA-box-binding protein (TBP) and TBP-associated factors, on the TATA-box sequence upstream of the initiation start site. After initiation, some components of the pre-initiation complex (including TFIIA) remain attached and re-initiate a subsequent round of transcription. TFIIA binds to TBP to stabilise TBP binding to the TATA element. TFIIA also inhibits the cytokine HMGB1 (high mobility group 1 protein) binding to TBP [], and can dissociate HMGB1 already bound to TBP/TATA-box. Human and Drosophila TFIIA have three subunits: two large subunits, LN/alpha and LC/beta, derived from the same gene, and a small subunit, S/gamma. Yeast TFIIA has two subunits: a large TOA1 subunit that shows sequence similarity to the N-terminal of LN/alpha and the C-terminal of LC/beta, and a small subunit, TOA2 that is highly homologous with S/gamma. The conserved regions of the large and small subunits of TFIIA combine to form two domains: a four-helix bundle (helical domain) composed of two helices from each of the N-terminal regions of TOA1 and TOA2 in yeast; and a beta-barrel (beta-barrel domain) composed of beta-sheets from the C-terminal regions of TOA1 and TOA2 []. This entry represents the alpha-helical domain found at the N-terminal of the gamma subunit of transcription factor TFIIA.; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005672 transcription factor TFIIA complex; PDB: 1NVP_D 1RM1_B 1YTF_D 1NH2_D.
Probab=99.93 E-value=3.2e-26 Score=139.76 Aligned_cols=48 Identities=63% Similarity=1.032 Sum_probs=44.4
Q ss_pred hhHHHHhhhHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHH
Q 033999 3 TFELYRRSTIGMCLTETLDEMVQNGTLTPELAIQVLVQFDKSMTEALE 50 (106)
Q Consensus 3 ~y~lYR~stlG~aL~dtLdeli~~~~I~p~la~kIl~~FDk~i~~~L~ 50 (106)
|||+||+||||.||+|||||||++|.|+|+||++||++||++|+++|+
T Consensus 2 ~yelYR~stlG~aL~dtLDeli~~~~I~p~La~kVL~~FDksi~~~L~ 49 (49)
T PF02268_consen 2 YYELYRRSTLGIALTDTLDELIQEGKITPQLAMKVLEQFDKSINEALS 49 (49)
T ss_dssp --CGGGCSHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHHHHHH
T ss_pred cHHHHHcchHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHhC
Confidence 599999999999999999999999999999999999999999999985
No 5
>PF10925 DUF2680: Protein of unknown function (DUF2680); InterPro: IPR024485 Members in this family of proteins are annotated as YckD however currently no function is known.
Probab=93.17 E-value=0.33 Score=30.42 Aligned_cols=33 Identities=21% Similarity=0.284 Sum_probs=29.0
Q ss_pred HHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHH
Q 033999 17 TETLDEMVQNGTLTPELAIQVLVQFDKSMTEAL 49 (106)
Q Consensus 17 ~dtLdeli~~~~I~p~la~kIl~~FDk~i~~~L 49 (106)
...+|..+..|.||++.|..|.+.+|.-....-
T Consensus 21 K~~idk~Ve~G~iTqeqAd~ik~~id~~~~~~~ 53 (59)
T PF10925_consen 21 KQIIDKYVEAGVITQEQADAIKKHIDQRQEYMQ 53 (59)
T ss_pred HHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHH
Confidence 467899999999999999999999998776543
No 6
>cd01709 RT_like_1 RT_like_1: A subfamily of reverse transcriptases (RTs). An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.
Probab=88.71 E-value=0.43 Score=39.42 Aligned_cols=65 Identities=20% Similarity=0.258 Sum_probs=45.6
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHhhcccceEEeeeCccceeeCcEEEEEEcC-eEE----Eec------ceEeeeCeE
Q 033999 26 NGTLTPELAIQVLVQFDKSMTEALETQVKSKVSIKGHLHTYRFCDNVWTFILQD-ALF----KSE------ELQETVGRV 94 (106)
Q Consensus 26 ~~~I~p~la~kIl~~FDk~i~~~L~~~vk~k~~~KG~L~tYr~cDnVWtf~lkn-~~~----k~~------~~~~~~~~l 94 (106)
.|.|||=+|+-+|..||..|++... | ..-||+.||+|-+ -.. -.. .+. +-.++.+|=
T Consensus 87 GgviSplLaNiyL~~lD~~v~~~~~----------g-~~l~RYaDD~vi~-~~~~~a~~aw~~i~~fl~~lGLelN~eKT 154 (346)
T cd01709 87 SHALSDVFGELVLFCLDFAVNQATD----------G-GLLYRLHDDLWFW-GQPETCAKAWKAIQEFAKVMGLELNKEKT 154 (346)
T ss_pred CchhhHHHHHHHHHHHHHHHHhcCC----------C-ceEEEEcCeEEEE-cCHHHHHHHHHHHHHHHHHcCceeccccc
Confidence 4689999999999999999988632 2 4569999999988 221 000 000 225666788
Q ss_pred EEEEecCC
Q 033999 95 KIVACDSK 102 (106)
Q Consensus 95 KIVAcd~~ 102 (106)
+||-|...
T Consensus 155 ~iV~~~~~ 162 (346)
T cd01709 155 GSVYLSDD 162 (346)
T ss_pred eEEEeccC
Confidence 88877654
No 7
>PF11848 DUF3368: Domain of unknown function (DUF3368); InterPro: IPR021799 This domain is functionally uncharacterised. This domain is found in bacteria and archaea. This presumed domain is about 50 amino acids in length.
Probab=87.07 E-value=1.9 Score=25.46 Aligned_cols=35 Identities=29% Similarity=0.430 Sum_probs=28.1
Q ss_pred HHHHhhhHHHHHHHHHHHHHHCC-CCCHHHHHHHHHH
Q 033999 5 ELYRRSTIGMCLTETLDEMVQNG-TLTPELAIQVLVQ 40 (106)
Q Consensus 5 ~lYR~stlG~aL~dtLdeli~~~-~I~p~la~kIl~~ 40 (106)
+.+|+.-|- .....||+|.+.| .|+|++..++|+.
T Consensus 11 ~Ak~~GlI~-~~~~~l~~l~~~g~~is~~l~~~~L~~ 46 (48)
T PF11848_consen 11 LAKRRGLIS-EVKPLLDRLQQAGFRISPKLIEEILRR 46 (48)
T ss_pred HHHHcCChh-hHHHHHHHHHHcCcccCHHHHHHHHHH
Confidence 345555555 7888999999998 8999999999874
No 8
>PF09925 DUF2157: Predicted membrane protein (DUF2157); InterPro: IPR018677 This family of various hypothetical prokaryotic proteins has no known function.
Probab=86.08 E-value=0.74 Score=32.57 Aligned_cols=24 Identities=38% Similarity=0.620 Sum_probs=22.4
Q ss_pred HHHHHHCCCCCHHHHHHHHHHHHH
Q 033999 20 LDEMVQNGTLTPELAIQVLVQFDK 43 (106)
Q Consensus 20 Ldeli~~~~I~p~la~kIl~~FDk 43 (106)
|++++++|.|+|+++.++++.++.
T Consensus 1 l~~w~~~GlI~~~q~~~i~~~~~~ 24 (145)
T PF09925_consen 1 LDRWVEQGLITPEQAEAILAFYGE 24 (145)
T ss_pred CHhHHHCCCCCHHHHHHHHHHhhc
Confidence 689999999999999999999983
No 9
>cd01646 RT_Bac_retron_I RT_Bac_retron_I: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.
Probab=86.01 E-value=1.2 Score=31.42 Aligned_cols=39 Identities=18% Similarity=0.194 Sum_probs=33.8
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHhhcccceEEeeeCccceeeCcEEEEE
Q 033999 27 GTLTPELAIQVLVQFDKSMTEALETQVKSKVSIKGHLHTYRFCDNVWTFI 76 (106)
Q Consensus 27 ~~I~p~la~kIl~~FDk~i~~~L~~~vk~k~~~KG~L~tYr~cDnVWtf~ 76 (106)
..++|=|++.+|..||..+.+. .+.+...||+||++-+.
T Consensus 58 ~~lS~~L~~~~l~~~d~~i~~~-----------~~~~~~~RY~DD~~i~~ 96 (158)
T cd01646 58 PLTSRFLANIYLNDVDHELKSK-----------LKGVDYVRYVDDIRIFA 96 (158)
T ss_pred cchHHHHHHHHHHHHHHHHHhc-----------cCCceEEEecCcEEEEc
Confidence 3799999999999999999876 45677899999999876
No 10
>cd03487 RT_Bac_retron_II RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.
Probab=85.82 E-value=2.3 Score=31.51 Aligned_cols=46 Identities=22% Similarity=0.420 Sum_probs=35.2
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHhhcccceEEeeeCccceeeCcEEEEEEcCeE
Q 033999 26 NGTLTPELAIQVLVQFDKSMTEALETQVKSKVSIKGHLHTYRFCDNVWTFILQDAL 81 (106)
Q Consensus 26 ~~~I~p~la~kIl~~FDk~i~~~L~~~vk~k~~~KG~L~tYr~cDnVWtf~lkn~~ 81 (106)
...+||-|++-+|..||+.+.+..... .+..+||+||+ +|..++..
T Consensus 107 G~~lSp~Lanl~l~~~d~~l~~~~~~~---------~~~~~RYaDD~-~i~~~~~~ 152 (214)
T cd03487 107 GAPTSPALSNLVFRKLDERLSKLAKSN---------GLTYTRYADDI-TFSSNKKL 152 (214)
T ss_pred CCcccHHHHHHHHHHHHHHHHHHHHHc---------CCeEEEEeccE-EEEccccc
Confidence 358999999999999999998765321 13457999996 67777654
No 11
>COG3937 Uncharacterized conserved protein [Function unknown]
Probab=79.91 E-value=8.2 Score=27.13 Aligned_cols=36 Identities=19% Similarity=0.274 Sum_probs=29.4
Q ss_pred hHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHH
Q 033999 11 TIGMCLTETLDEMVQNGTLTPELAIQVLVQFDKSMT 46 (106)
Q Consensus 11 tlG~aL~dtLdeli~~~~I~p~la~kIl~~FDk~i~ 46 (106)
-++.-+++..|||+..|.|+++.|-+++..-=+.+.
T Consensus 21 ~~~ek~~klvDelVkkGeln~eEak~~vddl~~q~k 56 (108)
T COG3937 21 ETAEKVQKLVDELVKKGELNAEEAKRFVDDLLRQAK 56 (108)
T ss_pred HHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHH
Confidence 466778999999999999999999998876544443
No 12
>cd01651 RT_G2_intron RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).
Probab=79.03 E-value=3.1 Score=29.95 Aligned_cols=51 Identities=24% Similarity=0.275 Sum_probs=37.4
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHhhcccceEEeeeCccceeeCcEEEEE
Q 033999 26 NGTLTPELAIQVLVQFDKSMTEALETQVKSKVSIKGHLHTYRFCDNVWTFI 76 (106)
Q Consensus 26 ~~~I~p~la~kIl~~FDk~i~~~L~~~vk~k~~~KG~L~tYr~cDnVWtf~ 76 (106)
...++|=|++-++..+|+.+.+.+.+.-.....-.+.+...||.||+.-+.
T Consensus 130 G~~lSp~L~~~~l~~ld~~l~~~~~~~~~~~~~~~~~~~~~rY~DD~~i~~ 180 (226)
T cd01651 130 GGVISPLLANIYLHELDKFVEEKLKEYYDTSDPKFRRLRYVRYADDFVIGV 180 (226)
T ss_pred CccHHHHHHHHHHHHHHHHHHHhhhhcccccccccCceEEEEecCceEEec
Confidence 446789999999999999999988653222222234577799999987663
No 13
>PF09677 TrbI_Ftype: Type-F conjugative transfer system protein (TrbI_Ftype); InterPro: IPR014115 This entry represents TrbI, an essential component of the F-type conjugative transfer system for plasmid DNA transfer that has been shown to be localized to the periplasm [, ].
Probab=72.62 E-value=11 Score=26.23 Aligned_cols=40 Identities=30% Similarity=0.394 Sum_probs=34.0
Q ss_pred HHHHHHHHHHH---CCCCCHHHHHHHHHHHHHHHHHHHHhhcc
Q 033999 15 CLTETLDEMVQ---NGTLTPELAIQVLVQFDKSMTEALETQVK 54 (106)
Q Consensus 15 aL~dtLdeli~---~~~I~p~la~kIl~~FDk~i~~~L~~~vk 54 (106)
-|..++|++++ ...++|+....-...|.++++..|.+.-.
T Consensus 37 dl~~tv~~f~~~~a~~~lt~~q~~a~t~~F~~aL~~~L~~~~~ 79 (111)
T PF09677_consen 37 DLKGTVDEFVQQLARSSLTPEQVEALTQRFMQALEASLAEYQA 79 (111)
T ss_pred eHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46778888876 34899999999999999999999999643
No 14
>PRK10753 transcriptional regulator HU subunit alpha; Provisional
Probab=68.29 E-value=23 Score=23.25 Aligned_cols=42 Identities=21% Similarity=0.288 Sum_probs=32.0
Q ss_pred HHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHhhcccceEEee
Q 033999 18 ETLDEMVQNGTLTPELAIQVLVQFDKSMTEALETQVKSKVSIKG 61 (106)
Q Consensus 18 dtLdeli~~~~I~p~la~kIl~~FDk~i~~~L~~~vk~k~~~KG 61 (106)
|.++++-+...+|...+..+++.|-..|.++|.+. .++.|.|
T Consensus 5 eli~~ia~~~~~s~~~~~~~v~~~~~~i~~~L~~g--~~V~i~g 46 (90)
T PRK10753 5 QLIDVIADKAELSKTQAKAALESTLAAITESLKEG--DAVQLVG 46 (90)
T ss_pred HHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHcC--CeEEEcC
Confidence 34445555567999999999999999999999763 3466654
No 15
>PRK10664 transcriptional regulator HU subunit beta; Provisional
Probab=67.29 E-value=23 Score=23.27 Aligned_cols=41 Identities=22% Similarity=0.316 Sum_probs=31.3
Q ss_pred HHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHhhcccceEEee
Q 033999 19 TLDEMVQNGTLTPELAIQVLVQFDKSMTEALETQVKSKVSIKG 61 (106)
Q Consensus 19 tLdeli~~~~I~p~la~kIl~~FDk~i~~~L~~~vk~k~~~KG 61 (106)
.++++-+...+|+..+.++++.|=.+|.++|.+. .++.|.|
T Consensus 6 li~~ia~~~~~s~~~~~~~v~~~~~~i~~~L~~~--~~v~l~g 46 (90)
T PRK10664 6 LIDKIAAGADISKAAAGRALDAIIASVTESLKEG--DDVALVG 46 (90)
T ss_pred HHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHhCC--CEEEECC
Confidence 3444444567999999999999999999999873 3466654
No 16
>PF15606 Toxin_55: Putative toxin 55
Probab=67.05 E-value=6.6 Score=25.99 Aligned_cols=22 Identities=18% Similarity=0.329 Sum_probs=18.1
Q ss_pred HHHHHHHHHHHCCCCCHHHHHH
Q 033999 15 CLTETLDEMVQNGTLTPELAIQ 36 (106)
Q Consensus 15 aL~dtLdeli~~~~I~p~la~k 36 (106)
.-=|.|+|||..|.|++..+.+
T Consensus 40 drCd~Lqelid~g~~~~k~~K~ 61 (77)
T PF15606_consen 40 DRCDVLQELIDCGDISAKQAKS 61 (77)
T ss_pred cHHHHHHHHHHccCcCHHHHHH
Confidence 3458999999999999988643
No 17
>cd00304 RT_like RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.
Probab=66.89 E-value=12 Score=23.50 Aligned_cols=41 Identities=17% Similarity=0.306 Sum_probs=32.0
Q ss_pred HCCCCCHHHHHHHHHHHHHHHHHHHHhhcccceEEeeeCccceeeCcEEEEE
Q 033999 25 QNGTLTPELAIQVLVQFDKSMTEALETQVKSKVSIKGHLHTYRFCDNVWTFI 76 (106)
Q Consensus 25 ~~~~I~p~la~kIl~~FDk~i~~~L~~~vk~k~~~KG~L~tYr~cDnVWtf~ 76 (106)
+...++|-+++..+..+|..+.+. .+.....|+.|+++.+.
T Consensus 14 qG~~~Sp~l~~~~~~~l~~~~~~~-----------~~~~~~~~Y~DD~~i~~ 54 (98)
T cd00304 14 QGSPLSPALANLYMEKLEAPILKQ-----------LLDITLIRYVDDLVVIA 54 (98)
T ss_pred CCCchHHHHHHHHHHHHHHHHHHh-----------cCCceEEEeeCcEEEEe
Confidence 445789999999999999888771 12356789999998664
No 18
>TIGR02744 TrbI_Ftype type-F conjugative transfer system protein TrbI. This protein is an essential component of the F-type conjugative transfer sytem for plasmid DNA transfer and has been shown to be localized to the periplasm.
Probab=64.74 E-value=23 Score=24.86 Aligned_cols=38 Identities=18% Similarity=0.304 Sum_probs=31.7
Q ss_pred HHHHHHHHHH---CCCCCHHHHHHHHHHHHHHHHHHHHhhc
Q 033999 16 LTETLDEMVQ---NGTLTPELAIQVLVQFDKSMTEALETQV 53 (106)
Q Consensus 16 L~dtLdeli~---~~~I~p~la~kIl~~FDk~i~~~L~~~v 53 (106)
+..|||++++ +..+|++...+.+..|..+++.+|...-
T Consensus 39 mk~tld~F~~q~~~~~lte~q~~~~~~rF~~~L~~~L~~yq 79 (112)
T TIGR02744 39 MKQTLDAFFDSASQKKLSEAQQKALLGRFNALLEAELQAWQ 79 (112)
T ss_pred cHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4556666655 6789999999999999999999999853
No 19
>PRK00285 ihfA integration host factor subunit alpha; Reviewed
Probab=64.29 E-value=22 Score=23.41 Aligned_cols=44 Identities=16% Similarity=0.252 Sum_probs=34.8
Q ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHhhcccceEEe
Q 033999 15 CLTETLDEMVQNGTLTPELAIQVLVQFDKSMTEALETQVKSKVSIK 60 (106)
Q Consensus 15 aL~dtLdeli~~~~I~p~la~kIl~~FDk~i~~~L~~~vk~k~~~K 60 (106)
...|.++++-....++...+..++..|=..|.+.|++. .++.+.
T Consensus 4 tk~el~~~ia~~~~~s~~~v~~vl~~~~~~i~~~L~~g--~~V~l~ 47 (99)
T PRK00285 4 TKADLAEALFEKVGLSKREAKELVELFFEEIRDALENG--EQVKLS 47 (99)
T ss_pred CHHHHHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHHcC--CeEEEc
Confidence 45566777777788999999999999999999999873 234444
No 20
>smart00411 BHL bacterial (prokaryotic) histone like domain.
Probab=63.40 E-value=25 Score=22.28 Aligned_cols=42 Identities=26% Similarity=0.374 Sum_probs=32.8
Q ss_pred HHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHhhcccceEEe
Q 033999 17 TETLDEMVQNGTLTPELAIQVLVQFDKSMTEALETQVKSKVSIK 60 (106)
Q Consensus 17 ~dtLdeli~~~~I~p~la~kIl~~FDk~i~~~L~~~vk~k~~~K 60 (106)
.|..+++-+..-+++..+..+++.|-..|.+.|.+. .++.+.
T Consensus 4 ~eli~~ia~~~~~~~~~v~~vl~~l~~~i~~~L~~g--~~V~i~ 45 (90)
T smart00411 4 SELIDAIAEKAGLSKKDAKAAVDAFLEIITEALKKG--EKVELR 45 (90)
T ss_pred HHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHhCC--CeEEEe
Confidence 455566666777999999999999999999999883 244443
No 21
>PF06702 DUF1193: Protein of unknown function (DUF1193); InterPro: IPR009581 This family is baesd on the C terminus of several hypothetical eukaryotic proteins of unknown function. Proteins in this entry contain two conserved motifs: DRHHYE and QCC, as well as a number of conserved cysteine residues.
Probab=61.28 E-value=8.2 Score=30.15 Aligned_cols=46 Identities=30% Similarity=0.434 Sum_probs=41.4
Q ss_pred HHHhhhH---------HHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHh
Q 033999 6 LYRRSTI---------GMCLTETLDEMVQNGTLTPELAIQVLVQFDKSMTEALET 51 (106)
Q Consensus 6 lYR~stl---------G~aL~dtLdeli~~~~I~p~la~kIl~~FDk~i~~~L~~ 51 (106)
+.|+||. |..|.++|.|......+.|-|.+.-+.--|+-+..+|+.
T Consensus 150 ~iRrST~~rL~~l~~~~~~Ls~~m~~s~~~D~l~PvL~e~Hl~AldrRL~~Vl~~ 204 (221)
T PF06702_consen 150 RIRRSTWERLQLLSKGGYRLSDLMRESLSRDPLAPVLTEPHLEALDRRLDKVLRT 204 (221)
T ss_pred hccccHHHHHHHhccCCCcHHHHHHHHhccCccCccCcHHHHHHHHHHHHHHHHH
Confidence 5688887 888999999999999999999999999999999888866
No 22
>PF00078 RVT_1: Reverse transcriptase (RNA-dependent DNA polymerase); InterPro: IPR000477 The use of an RNA template to produce DNA, for integration into the host genome and exploitation of a host cell, is a strategy employed in the replication of retroid elements, such as the retroviruses and bacterial retrons. The enzyme catalysing polymerisation is an RNA-directed DNA-polymerase, or reverse trancriptase (RT) (2.7.7.49 from EC). Reverse transcriptase occurs in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. Retroviral reverse transcriptase is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. The discovery of retroelements in the prokaryotes raises intriguing questions concerning their roles in bacteria and the origin and evolution of reverse transcriptases and whether the bacterial reverse transcriptases are older than eukaryotic reverse transcriptases [].; GO: 0003723 RNA binding, 0003964 RNA-directed DNA polymerase activity, 0006278 RNA-dependent DNA replication; PDB: 1MU2_B 3RWE_C 3DU6_B 3DU5_A 3KYL_A 2WOM_B 1DTQ_A 2OPS_A 3FFI_A 1VRU_B ....
Probab=60.79 E-value=12 Score=26.30 Aligned_cols=42 Identities=21% Similarity=0.385 Sum_probs=33.4
Q ss_pred HCCCCCHHHHHHHHHHHHHHHHHHHHhhcccceEEeeeCccceeeCcEEEEE
Q 033999 25 QNGTLTPELAIQVLVQFDKSMTEALETQVKSKVSIKGHLHTYRFCDNVWTFI 76 (106)
Q Consensus 25 ~~~~I~p~la~kIl~~FDk~i~~~L~~~vk~k~~~KG~L~tYr~cDnVWtf~ 76 (106)
+...++|-++...+..+|+.+...+ .......|++||+.-+.
T Consensus 128 qG~~~S~~l~~~~l~~l~~~~~~~~----------~~~~~~~rY~DD~~i~~ 169 (214)
T PF00078_consen 128 QGSPLSPLLFNIYLDDLDRELQQEL----------NPDISYLRYADDILIIS 169 (214)
T ss_dssp TTSTCHHHHHHHHHHHHHHHHHHHS-----------TTSEEEEETTEEEEEE
T ss_pred ccccccchhhccccccccccccccc----------cccccceEeccccEEEE
Confidence 4457899999999999999988877 55566789999987543
No 23
>cd08332 CARD_CASP2 Caspase activation and recruitment domain of Caspase-2. Caspase activation and recruitment domain (CARD) similar to that found in caspase-2. Caspases are aspartate-specific cysteine proteases with functions in apoptosis and immune signaling. Caspase-2 (also known as ICH1, NEDD2, or CASP2) is one of the most evolutionarily conserved caspases, and plays a role in apoptosis, DNA damage response, cell cycle regulation, and tumor suppression. It is localized in the nucleus and exhibits properties of both an initiator and an effector caspase. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and
Probab=58.41 E-value=16 Score=24.13 Aligned_cols=25 Identities=28% Similarity=0.410 Sum_probs=21.7
Q ss_pred HHHHHHHHHHCCCCCHHHHHHHHHH
Q 033999 16 LTETLDEMVQNGTLTPELAIQVLVQ 40 (106)
Q Consensus 16 L~dtLdeli~~~~I~p~la~kIl~~ 40 (106)
..+.+|.|++.|.||++....|...
T Consensus 22 ~~~v~~~L~~~gvlt~~~~~~I~~~ 46 (90)
T cd08332 22 LDELLIHLLQKDILTDSMAESIMAK 46 (90)
T ss_pred HHHHHHHHHHcCCCCHHHHHHHHcC
Confidence 4678999999999999999988753
No 24
>PF00349 Hexokinase_1: Hexokinase; InterPro: IPR022672 Hexokinase is an important enzyme that catalyses the ATP-dependent conversion of aldo- and keto-hexose sugars to the hexose-6-phosphate (H6P). The enzyme can catalyse this reaction on glucose, fructose, sorbitol and glucosamine, and as such is the first step in a number of metabolic pathways []. The addition of a phosphate group to the sugar acts to trap it in a cell, since the negatively charged phosphate cannot easily traverse the plasma membrane. The enzyme is widely distributed in eukaryotes. There are three isozymes of hexokinase in yeast (PI, PII and glucokinase): isozymes PI and PII phosphorylate both aldo- and keto-sugars; glucokinase is specific for aldo-hexoses. All three isozymes contain two domains []. Structural studies of yeast hexokinase reveal a well-defined catalytic pocket that binds ATP and hexose, allowing easy transfer of the phosphate from ATP to the sugar []. Vertebrates contain four hexokinase isozymes, designated I to IV, where types I to III contain a duplication of the two-domain yeast-type hexokinases. Both the N- and C-terminal halves bind hexose and H6P, though in types I an III only the C-terminal half supports catalysis, while both halves support catalysis in type II. The N-terminal half is the regulatory region. Type IV hexokinase is similar to the yeast enzyme in containing only the two domains, and is sometimes incorrectly referred to as glucokinase. The different vertebrate isozymes differ in their catalysis, localisation and regulation, thereby contributing to the different patterns of glucose metabolism in different tissues []. Whereas types I to III can phosphorylate a variety of hexose sugars and are inhibited by glucose-6-phosphate (G6P), type IV is specific for glucose and shows no G6P inhibition. Type I enzyme may have a catabolic function, producing H6P for energy production in glycolysis; it is bound to the mitochondrial membrane, which enables the coordination of glycolysis with the TCA cycle. Types II and III enzyme may have anabolic functions, providing H6P for glycogen or lipid synthesis. Type IV enzyme is found in the liver and pancreatic beta-cells, where it is controlled by insulin (activation) and glucagon (inhibition). In pancreatic beta-cells, type IV enzyme acts as a glucose sensor to modify insulin secretion. Mutations in type IV hexokinase have been associated with diabetes mellitus. Hexokinase (2.7.1.1 from EC), a fructose and glucose phosphorylating enzyme, contains two structurally similar domains represented by this family and PF03727 from PFAM. Some hexokinases have two copies of each of these domains. This entry represents the N-terminal domain.; GO: 0005524 ATP binding, 0016773 phosphotransferase activity, alcohol group as acceptor, 0005975 carbohydrate metabolic process; PDB: 3O1W_A 3O6W_A 3O4W_B 3O08_B 3O80_A 3O5B_A 3O8M_A 3O1B_A 1BG3_A 4DHY_A ....
Probab=57.89 E-value=19 Score=27.19 Aligned_cols=41 Identities=22% Similarity=0.272 Sum_probs=35.4
Q ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHhhccc
Q 033999 15 CLTETLDEMVQNGTLTPELAIQVLVQFDKSMTEALETQVKS 55 (106)
Q Consensus 15 aL~dtLdeli~~~~I~p~la~kIl~~FDk~i~~~L~~~vk~ 55 (106)
-+.++++++.+.-.++++....|...|-..|..-|++.-.+
T Consensus 2 ~~~~~v~~~~~~f~~s~~~L~~i~~~f~~em~~gL~~~~~~ 42 (206)
T PF00349_consen 2 DLQQAVQKLLQQFTLSDEQLQEISDRFLEEMEKGLAKSSSS 42 (206)
T ss_dssp HHHHHHHHHHGGGS--HHHHHHHHHHHHHHHHHHHSTTTGC
T ss_pred hHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHccCCCC
Confidence 47889999999999999999999999999999999986554
No 25
>PF00619 CARD: Caspase recruitment domain; InterPro: IPR001315 The caspase recruitment domain domain (CARD) is a homotypic protein interaction module composed of a bundle of six alpha-helices. CARD is related in sequence and structure to the death domain (DD, see IPR000488 from INTERPRO) and the death effector domain (DED, see IPR001875 from INTERPRO), which work in similar pathways and show similar interaction properties []. The CARD domain typically associates with other CARD-containing proteins, forming either dimers or trimers. CARD domains can be found in isolation, or in combination with other domains. Domains associated with CARD include: NACHT (IPR007111 from INTERPRO) (in Nal1 and Bir1), NB-ARC (IPR002182 from INTERPRO) (in Apaf-1), pyrin/dapin domains (IPR004020 from INTERPRO) (in Nal1), leucine-rich repeats () (in Nal1), WD repeats (IPR001680 from INTERPRO) (in Apaf1), Src homology domains (IPR001452 from INTERPRO), PDZ (IPR001478 from INTERPRO), RING, kinase and DD domains []. CARD-containing proteins are involved in apoptosis through their regulation of caspases that contain CARDs in their N-terminal pro-domains, including human caspases 1, 2, 9, 11 and 12 []. CARD-containing proteins are also involved in inflammation through their regulation of NF-kappaB []. The mechanisms by which CARDs activate caspases and NF-kappaB involve the assembly of multi-protein complexes, which can facilitate dimerisation or serve as scaffolds on which proteases and kinases are assembled and activated.; GO: 0005515 protein binding, 0042981 regulation of apoptosis, 0005622 intracellular; PDB: 2NSN_A 2NZ7_B 2DBD_A 4E9M_C 2B1W_A 3YGS_P 2KN6_A 3CRD_A 1DGN_A 3KAT_A ....
Probab=57.34 E-value=20 Score=22.32 Aligned_cols=25 Identities=28% Similarity=0.364 Sum_probs=23.2
Q ss_pred HHHHHHHHHHHCCCCCHHHHHHHHH
Q 033999 15 CLTETLDEMVQNGTLTPELAIQVLV 39 (106)
Q Consensus 15 aL~dtLdeli~~~~I~p~la~kIl~ 39 (106)
.+...||.|++.|.||++-...|..
T Consensus 17 ~~~~ild~L~~~~vlt~~e~e~I~~ 41 (85)
T PF00619_consen 17 DLDDILDHLLSRGVLTEEEYEEIRS 41 (85)
T ss_dssp HHHHHHHHHHHTTSSSHHHHHHHHT
T ss_pred cHHHHHHHHHHCCCCCHHHHHHHHc
Confidence 4889999999999999999999987
No 26
>PF14848 HU-DNA_bdg: DNA-binding domain
Probab=56.16 E-value=32 Score=23.81 Aligned_cols=37 Identities=30% Similarity=0.333 Sum_probs=33.2
Q ss_pred HHHHHHHHHHHC-CCCCHHHHHHHHHHHHHHHHHHHHh
Q 033999 15 CLTETLDEMVQN-GTLTPELAIQVLVQFDKSMTEALET 51 (106)
Q Consensus 15 aL~dtLdeli~~-~~I~p~la~kIl~~FDk~i~~~L~~ 51 (106)
.|.|..+++... -.+++.-..-||..|.+.|.+.|.+
T Consensus 30 tl~~Ia~~i~~~~s~~t~~di~~vl~~~~~~~~~~l~~ 67 (124)
T PF14848_consen 30 TLEDIAEEIAKEGSTLTRADIEAVLNALKDEMIEALMN 67 (124)
T ss_pred CHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHhC
Confidence 577888899865 5999999999999999999999988
No 27
>PF14277 DUF4364: Domain of unknown function (DUF4364)
Probab=53.97 E-value=11 Score=27.64 Aligned_cols=38 Identities=26% Similarity=0.472 Sum_probs=30.6
Q ss_pred HHHHHHHHHHHCCCCCHH-------------HHHHHHHHHHHHHHHHHHhh
Q 033999 15 CLTETLDEMVQNGTLTPE-------------LAIQVLVQFDKSMTEALETQ 52 (106)
Q Consensus 15 aL~dtLdeli~~~~I~p~-------------la~kIl~~FDk~i~~~L~~~ 52 (106)
.|+++|+||+++|.|..+ ...++++.|..-|+....+.
T Consensus 35 ~lqq~l~eL~es~~i~~~~~~~~~~~y~iTe~G~~tl~~F~~~Ip~~i~~~ 85 (163)
T PF14277_consen 35 TLQQALSELVESGLITLETDSDNKTRYSITEKGKETLEFFENRIPESIRED 85 (163)
T ss_pred HHHHHHHHHHHCCCEEEeeccCCCcEEEECHhhHHHHHHHHHhCCHHHHHH
Confidence 589999999999998854 35788999988877776653
No 28
>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=53.86 E-value=21 Score=23.63 Aligned_cols=37 Identities=24% Similarity=0.443 Sum_probs=27.8
Q ss_pred ChhhHHHHhhhHHHHHHHHHHHHHHCCCCCHHHHHHH
Q 033999 1 MATFELYRRSTIGMCLTETLDEMVQNGTLTPELAIQV 37 (106)
Q Consensus 1 m~~y~lYR~stlG~aL~dtLdeli~~~~I~p~la~kI 37 (106)
|..|+.||++++=.+=..-|-.-+.++.++++.+.-|
T Consensus 6 ~~Rye~~Rra~f~k~~iKr~~~~~~~~~v~~~v~i~v 42 (85)
T cd08048 6 MNRYEMFRRSSFPKAAIKRLIQSVTGQSVSQNVVIAV 42 (85)
T ss_pred HHHHHHHHHhhccHHHHHHHHHHHcCCCCCchHHHHH
Confidence 3569999999887777666666677788888776543
No 29
>KOG3219 consensus Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=53.36 E-value=9.1 Score=29.42 Aligned_cols=34 Identities=18% Similarity=0.401 Sum_probs=28.6
Q ss_pred ChhhHHHHhhhHHHHHHHHHHHHHHCCCCCHHHH
Q 033999 1 MATFELYRRSTIGMCLTETLDEMVQNGTLTPELA 34 (106)
Q Consensus 1 m~~y~lYR~stlG~aL~dtLdeli~~~~I~p~la 34 (106)
|+-||.||+|.+-+|-..-|-.=|..+.+++..+
T Consensus 102 l~RYEvfRrs~f~Ka~iKkL~~~itg~~v~~nv~ 135 (195)
T KOG3219|consen 102 LSRYEVFRRSAFPKAQIKKLMSSITGQSVSENVA 135 (195)
T ss_pred HHHHHHHHHhcCCHHHHHHHHHHHhCCccCccee
Confidence 4569999999999999998888888888887654
No 30
>cd00591 HU_IHF Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and higher-order nucleoprotein complex assembly. The dimer subunits associate to form a compact globular core from which two beta ribbon arms (one from each subunit) protrude. The beta arms track and bind the DNA minor groove. Despite sequence and structural similarity, IHF and HU can be distinguished by their different DNA substrate preferences.
Probab=53.27 E-value=54 Score=20.50 Aligned_cols=41 Identities=24% Similarity=0.285 Sum_probs=30.9
Q ss_pred HHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHhhcccceEEe
Q 033999 18 ETLDEMVQNGTLTPELAIQVLVQFDKSMTEALETQVKSKVSIK 60 (106)
Q Consensus 18 dtLdeli~~~~I~p~la~kIl~~FDk~i~~~L~~~vk~k~~~K 60 (106)
|..+++-+..-+++..+..++..|-..|.+.|.+.- ++.+.
T Consensus 4 ~l~~~ia~~~~~~~~~v~~vl~~~~~~i~~~L~~g~--~V~l~ 44 (87)
T cd00591 4 ELIEAIAEKTGLSKKDAEAAVDAFLDVITEALAKGE--KVELP 44 (87)
T ss_pred HHHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHhCCC--eEEEe
Confidence 344555555679999999999999999999998732 44444
No 31
>cd08330 CARD_ASC_NALP1 Caspase activation and recruitment domain found in Human ASC, NALP1, and similar proteins. Caspase activation and recruitment domain (CARD) similar to those found in human ASC (Apoptosis-associated speck-like protein containing a CARD) and NALP1 (CARD7, NLRP1). ASC, an adaptor molecule, and NALP1, a member of the Nod-like receptor (NLR) family, are involved in the assembly of the 'inflammasome', a multiprotein platform, which is responsible for caspase-1 activation and regulation of IL-1beta maturation. In general, CARDs are death domains (DDs) associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They se
Probab=52.22 E-value=21 Score=23.22 Aligned_cols=25 Identities=20% Similarity=0.194 Sum_probs=21.9
Q ss_pred HHHHHHHHHHHCCCCCHHHHHHHHH
Q 033999 15 CLTETLDEMVQNGTLTPELAIQVLV 39 (106)
Q Consensus 15 aL~dtLdeli~~~~I~p~la~kIl~ 39 (106)
.....||.|+++|.|+++....|..
T Consensus 16 ~v~~ilD~L~~~~Vit~e~~~~I~a 40 (82)
T cd08330 16 NVDPILDKLHGKKVITQEQYSEVRA 40 (82)
T ss_pred hHHHHHHHHHHCCCCCHHHHHHHHc
Confidence 3577899999999999999988875
No 32
>cd01648 TERT TERT: Telomerase reverse transcriptase (TERT). Telomerase is a ribonucleoprotein (RNP) that synthesizes telomeric DNA repeats. The telomerase RNA subunit provides the template for synthesis of these repeats. The catalytic subunit of RNP is known as telomerase reverse transcriptase (TERT). The reverse transcriptase (RT) domain is located in the C-terminal region of the TERT polypeptide. Single amino acid substitutions in this region lead to telomere shortening and senescence. Telomerase is an enzyme that, in certain cells, maintains the physical ends of chromosomes (telomeres) during replication. In somatic cells, replication of the lagging strand requires the continual presence of an RNA primer approximately 200 nucleotides upstream, which is complementary to the template strand. Since there is a region of DNA less than 200 base pairs from the end of the chromosome where this is not possible, the chromosome is continually shortened. However, a surplus of repetitive DNA at
Probab=52.06 E-value=18 Score=24.50 Aligned_cols=47 Identities=17% Similarity=0.232 Sum_probs=32.9
Q ss_pred HCCCCCHHHHHHHHHHHHHHHHHHHHhhcccceEEeeeCccceeeCcEEEEEEcC
Q 033999 25 QNGTLTPELAIQVLVQFDKSMTEALETQVKSKVSIKGHLHTYRFCDNVWTFILQD 79 (106)
Q Consensus 25 ~~~~I~p~la~kIl~~FDk~i~~~L~~~vk~k~~~KG~L~tYr~cDnVWtf~lkn 79 (106)
|...+||-|++-++..+|+.+.+.+.. -.+.....||.||+ .+...+
T Consensus 22 QG~~lSp~L~nl~l~~l~~~~~~~~~~-------~~~~~~~~rYaDD~-li~~~~ 68 (119)
T cd01648 22 QGSPLSSLLCSLYYADLENKYLSFLDV-------IDKDSLLLRLVDDF-LLITTS 68 (119)
T ss_pred CCcchHHHHHHHHHHHHHHHHHhhccc-------CCCCceEEEEeCcE-EEEeCC
Confidence 455789999999999999988776511 11333457999995 555543
No 33
>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain
Probab=51.29 E-value=55 Score=21.66 Aligned_cols=45 Identities=16% Similarity=0.262 Sum_probs=34.5
Q ss_pred HHHHHHHHHHHHhhcc-cceEEeeeCcccee-eCcEEEEEEcCeEEE
Q 033999 39 VQFDKSMTEALETQVK-SKVSIKGHLHTYRF-CDNVWTFILQDALFK 83 (106)
Q Consensus 39 ~~FDk~i~~~L~~~vk-~k~~~KG~L~tYr~-cDnVWtf~lkn~~~k 83 (106)
.++-..|.+.|.+... ..+-++|.+..++. --+-|-|.|+|-.-+
T Consensus 5 s~l~~~ik~~le~~~~~~~vwV~GEIs~~~~~~~gh~YftLkD~~a~ 51 (99)
T PF13742_consen 5 SELNNYIKDLLERDPPLPNVWVEGEISNLKRHSSGHVYFTLKDEEAS 51 (99)
T ss_pred HHHHHHHHHHHhcCCCcCCEEEEEEEeecEECCCceEEEEEEcCCcE
Confidence 3455566667766544 78899999999999 789999999995433
No 34
>PRK00199 ihfB integration host factor subunit beta; Reviewed
Probab=50.79 E-value=67 Score=20.83 Aligned_cols=42 Identities=17% Similarity=0.352 Sum_probs=31.5
Q ss_pred HHHHHHHHC-CCCCHHHHHHHHHHHHHHHHHHHHhhcccceEEee
Q 033999 18 ETLDEMVQN-GTLTPELAIQVLVQFDKSMTEALETQVKSKVSIKG 61 (106)
Q Consensus 18 dtLdeli~~-~~I~p~la~kIl~~FDk~i~~~L~~~vk~k~~~KG 61 (106)
|.++.+.+. ..++...+.++++.|=..|.++|++. .++++.|
T Consensus 5 eli~~ia~~~~~~s~~~~~~vv~~~~~~i~~~L~~g--~~V~l~g 47 (94)
T PRK00199 5 ELIERLAARNPHLSAKDVENAVKEILEEMSDALARG--DRIEIRG 47 (94)
T ss_pred HHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHcC--CeEEEcC
Confidence 444555543 57999999999999999999999773 3455653
No 35
>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=50.52 E-value=32 Score=23.19 Aligned_cols=42 Identities=17% Similarity=0.443 Sum_probs=19.2
Q ss_pred hhhHHHHhhhHHHH-HHHHHHHHHHCCCCCHHHHHHHHHHHHHH
Q 033999 2 ATFELYRRSTIGMC-LTETLDEMVQNGTLTPELAIQVLVQFDKS 44 (106)
Q Consensus 2 ~~y~lYR~stlG~a-L~dtLdeli~~~~I~p~la~kIl~~FDk~ 44 (106)
.-||.||+|.+-.+ ..........++.+++..+. ++.-+=|.
T Consensus 14 ~Rye~fRRs~~~k~~ikkli~~~~~~qsv~~~v~i-~v~g~aKv 56 (90)
T PF04719_consen 14 DRYEAFRRSSFNKAAIKKLINQVLGNQSVSQNVVI-AVAGIAKV 56 (90)
T ss_dssp HHHHHHHH----HHHHHHHHHHHHS-S---HHHHH-HHHHHHHH
T ss_pred HHHHHHHHccCCHHHHHHHHHHHcCCCCCChhHHH-HHHHHHHH
Confidence 45999999998774 34444444433677777663 34434333
No 36
>PF15658 Latrotoxin_C: Latrotoxin C-terminal domain
Probab=49.94 E-value=21 Score=25.76 Aligned_cols=41 Identities=17% Similarity=0.296 Sum_probs=32.8
Q ss_pred hhHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHH
Q 033999 10 STIGMCLTETLDEMVQNGTLTPELAIQVLVQFDKSMTEALE 50 (106)
Q Consensus 10 stlG~aL~dtLdeli~~~~I~p~la~kIl~~FDk~i~~~L~ 50 (106)
+.|-.-|-..+++-..+|.++|++..+.|.+|-..+..+|+
T Consensus 86 neIs~~L~Sy~e~a~p~~~Ls~kq~~kfl~~f~~~~~~~ln 126 (127)
T PF15658_consen 86 NEISKILCSYAEKACPGSKLSPKQFDKFLAEFNSHLDVVLN 126 (127)
T ss_pred hHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHhccccccc
Confidence 45666677777777777999999999999999887776654
No 37
>TIGR00987 himA integration host factor, alpha subunit. This protein forms a site-specific DNA-binding heterodimer with the integration host factor beta subunit. It is closely related to the DNA-binding protein HU.
Probab=48.79 E-value=57 Score=21.33 Aligned_cols=42 Identities=19% Similarity=0.236 Sum_probs=31.3
Q ss_pred HHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHhhcccceEEe
Q 033999 17 TETLDEMVQNGTLTPELAIQVLVQFDKSMTEALETQVKSKVSIK 60 (106)
Q Consensus 17 ~dtLdeli~~~~I~p~la~kIl~~FDk~i~~~L~~~vk~k~~~K 60 (106)
.|..+++-....+|...+..++..|=..|.+.|.+. .++.|.
T Consensus 5 ~eli~~ia~~~~~s~~~v~~vv~~~~~~i~~~L~~g--~~V~l~ 46 (96)
T TIGR00987 5 AEMSEYLFDELGLSKREAKELVELFFEEIRRALENG--EQVKLS 46 (96)
T ss_pred HHHHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHHcC--CeEEec
Confidence 344455555567999999999999999999999773 234444
No 38
>TIGR01837 PHA_granule_1 poly(hydroxyalkanoate) granule-associated protein. This model describes a domain found in some proteins associated with polyhydroxyalkanoate (PHA) granules in a subset of species that have PHA inclusion granules. Included are two tandem proteins of Pseudomonas oleovorans, PhaI and PhaF, and their homologs in related species. PhaF proteins have a low-complexity C-terminal region with repeats similar to AAAKP.
Probab=48.63 E-value=81 Score=21.81 Aligned_cols=33 Identities=9% Similarity=0.081 Sum_probs=25.3
Q ss_pred HHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHH
Q 033999 14 MCLTETLDEMVQNGTLTPELAIQVLVQFDKSMT 46 (106)
Q Consensus 14 ~aL~dtLdeli~~~~I~p~la~kIl~~FDk~i~ 46 (106)
.-..+.+|+|+..|.++++.+...+...=..+.
T Consensus 22 ek~~k~~~~LVkkGe~~~ee~k~~~~e~~~~~~ 54 (118)
T TIGR01837 22 EEGSKFFNRLVKEGELAEKRGQKRFDESVDAAR 54 (118)
T ss_pred HHHHHHHHHHHHhccccHHHHHHHHHHHHHHHH
Confidence 445788999999999999999887655544443
No 39
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=48.45 E-value=40 Score=22.04 Aligned_cols=35 Identities=23% Similarity=0.398 Sum_probs=23.6
Q ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHh
Q 033999 16 LTETLDEMVQNGTLTPELAIQVLVQFDKSMTEALET 51 (106)
Q Consensus 16 L~dtLdeli~~~~I~p~la~kIl~~FDk~i~~~L~~ 51 (106)
+.+++..|.+ --|++.++++|.+.|-....+.|++
T Consensus 8 ~~~~~~~L~~-~gl~~~~a~kl~~~yg~~ai~~l~~ 42 (94)
T PF14490_consen 8 LRELMAFLQE-YGLSPKLAMKLYKKYGDDAIEILKE 42 (94)
T ss_dssp -HHHHHHHHH-TT--HHHHHHHHHHH-TTHHHHHHH
T ss_pred HHHHHHHHHH-cCCCHHHHHHHHHHHhHHHHHHHHH
Confidence 4455555555 4599999999999998877777776
No 40
>cd08325 CARD_CASP1-like Caspase activation and recruitment domain found in Caspase-1 and related proteins. Caspase activation and recruitment domain (CARD) similar to those found in Caspase-1 (CASP1, ICE) and related proteins, including CARD-only proteins such as ICEBERG or CARD18, INCA (CARD17), CARD16 (COP1, PSEUDO-ICE), CARD8 (DACAR, NDPP1, TUCAN), and CARD12 (NLRC4), as well as ICE-like caspases such as CASP12, CASP5 (ICH-3) and CASP4 (TX, ICH-2). Caspases are aspartate-specific cysteine proteases with functions in apoptosis and immune signaling. CASP1 plays a central role in the cellular response to a wide variety of microbial and non-microbial stimuli, being activated by the inflammasome or the pyroptosome. CARD8 binds itself and the initiator caspase-9, interfering with the binding of APAF-1 and suppressing caspase-9 activation. CARD12 is a Nod-like receptor (NLR) that plays an important role in the innate immune response to Gram-negative bacteria. Caspase-4 (CASP4), -5 (CASP5),
Probab=48.30 E-value=49 Score=21.45 Aligned_cols=26 Identities=15% Similarity=0.307 Sum_probs=23.8
Q ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHH
Q 033999 15 CLTETLDEMVQNGTLTPELAIQVLVQ 40 (106)
Q Consensus 15 aL~dtLdeli~~~~I~p~la~kIl~~ 40 (106)
.+...||+|++.+.|+.+-...|..+
T Consensus 17 ~i~~llD~Ll~~~Vl~~~E~e~i~~~ 42 (83)
T cd08325 17 VINGLLDDLLEKNVLNEEEMEKIKEE 42 (83)
T ss_pred hHHHHHHHHHHcCCCCHHHHHHHHhc
Confidence 57889999999999999999999884
No 41
>PF09851 SHOCT: Short C-terminal domain; InterPro: IPR018649 This family of hypothetical prokaryotic proteins has no known function.
Probab=48.04 E-value=43 Score=17.89 Aligned_cols=22 Identities=27% Similarity=0.290 Sum_probs=17.4
Q ss_pred HHHHHHHHHCCCCCHHHHHHHH
Q 033999 17 TETLDEMVQNGTLTPELAIQVL 38 (106)
Q Consensus 17 ~dtLdeli~~~~I~p~la~kIl 38 (106)
...|++|..+|.||++-..+..
T Consensus 5 L~~L~~l~~~G~IseeEy~~~k 26 (31)
T PF09851_consen 5 LEKLKELYDKGEISEEEYEQKK 26 (31)
T ss_pred HHHHHHHHHcCCCCHHHHHHHH
Confidence 3579999999999998665543
No 42
>KOG0375 consensus Serine-threonine phosphatase 2B, catalytic subunit [General function prediction only]
Probab=45.26 E-value=35 Score=29.22 Aligned_cols=40 Identities=20% Similarity=0.498 Sum_probs=31.8
Q ss_pred HHHHHCCCCCHHHHHHHHHHHHHHHHHHHHh-----hcccceEEeeeCc
Q 033999 21 DEMVQNGTLTPELAIQVLVQFDKSMTEALET-----QVKSKVSIKGHLH 64 (106)
Q Consensus 21 deli~~~~I~p~la~kIl~~FDk~i~~~L~~-----~vk~k~~~KG~L~ 64 (106)
+.++.+|+|++++|.+|+.+= ...|++ .|...+++.|.++
T Consensus 53 ~Hf~~EGrl~ee~alrIi~~~----a~llr~Eknmi~v~APiTVCGDIH 97 (517)
T KOG0375|consen 53 NHFIKEGRLEEEQALRIINEG----AALLRQEKNMIEVEAPITVCGDIH 97 (517)
T ss_pred HHHHhhcchhHHHHHHHHHHH----HHHHhcCCceEeccCCeeEecccc
Confidence 578999999999999999764 344554 4788899988764
No 43
>PF14929 TAF1_subA: TAF RNA Polymerase I subunit A
Probab=45.05 E-value=23 Score=30.95 Aligned_cols=41 Identities=29% Similarity=0.383 Sum_probs=32.6
Q ss_pred hHHHHHHHHHHHHHHC-----CCCCHHHHHHHHHHHHHHHHHHHHh
Q 033999 11 TIGMCLTETLDEMVQN-----GTLTPELAIQVLVQFDKSMTEALET 51 (106)
Q Consensus 11 tlG~aL~dtLdeli~~-----~~I~p~la~kIl~~FDk~i~~~L~~ 51 (106)
.+|.-|.|+|+|+... ..++-.++-++|+.||+..+.+|.+
T Consensus 320 l~~~~l~eal~~~e~~c~~~~~~lpi~~~~~lle~~d~~~~~~l~~ 365 (547)
T PF14929_consen 320 LIGGRLKEALNELEKFCISSTCALPIRLRAHLLEYFDQNNSSVLSS 365 (547)
T ss_pred eccccHHHHHHHHHHhccCCCccchHHHHHHHHHHhCcccHHHHHH
Confidence 5788999999999984 3788899999999999644444443
No 44
>PF05186 Dpy-30: Dpy-30 motif; InterPro: IPR007858 This motif is about 40 residues long and is probably formed of two alpha-helices. It is found in the Dpy-30 proteins, hence the motifs name. Dpy-30 from Caenorhabditis elegans is an essential component of dosage compensation machinery and loss of dpy-30 activity results in XX-specific lethality; in XO animals, Dpy-30 is required for developmental processes other than dosage compensation []. In yeast, the homologue of DPY-30, Saf19p, functions as part of the Set1 complex that is necessary for the methylation of histone H3 at lysine residue 4; Set1 is a key part of epigenetic developmental control []. There is also a human homologue of Dpy-30 []. This Dpy-30 region may be a dimerisation motif analogous that found in the cAMP-dependent protein kinase regulator, type II PKA, R subunit IPR003117 from INTERPRO.; PDB: 3G36_D.
Probab=43.83 E-value=28 Score=20.11 Aligned_cols=27 Identities=33% Similarity=0.489 Sum_probs=21.4
Q ss_pred HHHhhhHHHHHHHHHHHHHHCCCCCHH
Q 033999 6 LYRRSTIGMCLTETLDEMVQNGTLTPE 32 (106)
Q Consensus 6 lYR~stlG~aL~dtLdeli~~~~I~p~ 32 (106)
-|=..++|..|.++|.|+..+.--+|-
T Consensus 4 ~YL~~~v~p~L~~gL~~l~~~rP~DPi 30 (42)
T PF05186_consen 4 QYLKETVGPVLTEGLAELAKERPEDPI 30 (42)
T ss_dssp HHHHHHTHHHHHHHHHHHHHH--SSHH
T ss_pred HHHHHHhHHHHHHHHHHHHHHCCCChH
Confidence 477789999999999999998776663
No 45
>PF09693 Phage_XkdX: Phage uncharacterised protein (Phage_XkdX); InterPro: IPR010022 This entry is represented by Bacteriophage 69, Orf86. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry identifies a family of small (about 50 amino acid) phage proteins, found in at least 12 different phage and prophage regions of Gram-positive bacteria. In a number of these phage, the gene for this protein is found near the holin and endolysin genes.
Probab=42.16 E-value=29 Score=19.73 Aligned_cols=21 Identities=24% Similarity=0.357 Sum_probs=18.2
Q ss_pred HHHHHHHHHCCCCCHHHHHHH
Q 033999 17 TETLDEMVQNGTLTPELAIQV 37 (106)
Q Consensus 17 ~dtLdeli~~~~I~p~la~kI 37 (106)
.+-+..++..|.|||++...|
T Consensus 15 ~~~v~~~V~~g~IT~eey~eI 35 (40)
T PF09693_consen 15 KEDVKNFVEAGWITKEEYKEI 35 (40)
T ss_pred HHHHHHHhhcCeECHHHHHHh
Confidence 466889999999999998876
No 46
>PF02982 Scytalone_dh: Scytalone dehydratase; InterPro: IPR004235 Scytalone dehydratase is a member of the group of enzymes involved in fungal melanin biosynthesis. It was first identified in a phytopathogenic fungus, Magnaporthe grisea (Rice blast fungus), which causes rice blast disease. Scytalone dehydratase is a molecular target of inhibitor design efforts aimed at protecting rice plants from fungal disease [, ].; GO: 0030411 scytalone dehydratase activity, 0006582 melanin metabolic process; PDB: 4STD_A 3STD_A 6STD_A 7STD_C 1STD_A 5STD_C 1IDP_B 2STD_A.
Probab=40.37 E-value=44 Score=25.00 Aligned_cols=31 Identities=35% Similarity=0.571 Sum_probs=24.3
Q ss_pred cceEEeee-----CccceeeCcEEEEEEcCeEEEec
Q 033999 55 SKVSIKGH-----LHTYRFCDNVWTFILQDALFKSE 85 (106)
Q Consensus 55 ~k~~~KG~-----L~tYr~cDnVWtf~lkn~~~k~~ 85 (106)
.++..||| -+.|+-.|+||.|---.|.++-.
T Consensus 110 ~~V~~kGh~h~~~~h~Y~KvdG~WK~agl~P~v~w~ 145 (160)
T PF02982_consen 110 TEVKAKGHGHGTNTHWYRKVDGVWKFAGLKPEVRWN 145 (160)
T ss_dssp -SEEEEEEEEEEEEEEEEEETTEEEEEEEEEEEEEE
T ss_pred cEEEeeeccceeEEEEEEEeCCEEEEeeeccceeEe
Confidence 45666775 56899999999999888888754
No 47
>smart00114 CARD Caspase recruitment domain. Motif contained in proteins involved in apoptotic signalling. Mediates homodimerisation. Structure consists of six antiparallel helices arranged in a topology homologue to the DEATH and the DED domain.
Probab=40.28 E-value=39 Score=21.60 Aligned_cols=23 Identities=22% Similarity=0.216 Sum_probs=20.9
Q ss_pred HHHHHHHHHCCCCCHHHHHHHHH
Q 033999 17 TETLDEMVQNGTLTPELAIQVLV 39 (106)
Q Consensus 17 ~dtLdeli~~~~I~p~la~kIl~ 39 (106)
.+.||.|+++|.|+++-...|-.
T Consensus 23 ~~vld~L~~~~Vlt~~e~e~i~~ 45 (88)
T smart00114 23 DGLLDYLVEKNVLTEKEIEAIKA 45 (88)
T ss_pred hHHHHHHHHcCCCCHHHHHHHHc
Confidence 47999999999999999998876
No 48
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=40.17 E-value=65 Score=27.78 Aligned_cols=44 Identities=20% Similarity=0.427 Sum_probs=30.0
Q ss_pred hHHHHhhhHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHh
Q 033999 4 FELYRRSTIGMCLTETLDEMVQNGTLTPELAIQVLVQFDKSMTEALET 51 (106)
Q Consensus 4 y~lYR~stlG~aL~dtLdeli~~~~I~p~la~kIl~~FDk~i~~~L~~ 51 (106)
|.-+|+-.- .-||..|+.+|+|.|.-...+.++--+-|.+.+.+
T Consensus 252 fdp~rreia----~~~l~~li~dgrihp~riee~~~~~~~~~~~~i~~ 295 (514)
T TIGR03319 252 FDPVRREIA----RMALEKLIQDGRIHPARIEEMVEKATKEVDNAIRE 295 (514)
T ss_pred CchHHHHHH----HHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 555665433 34778899999999998877776655555554443
No 49
>cd01721 Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D3 heterodimerizes with subunit B and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=39.55 E-value=68 Score=20.02 Aligned_cols=29 Identities=17% Similarity=0.228 Sum_probs=22.6
Q ss_pred cccceEEeeeCccceeeCcEEEEEEcCeEEEe
Q 033999 53 VKSKVSIKGHLHTYRFCDNVWTFILQDALFKS 84 (106)
Q Consensus 53 vk~k~~~KG~L~tYr~cDnVWtf~lkn~~~k~ 84 (106)
.|+...++|.| ..||+-+.+.++|++...
T Consensus 17 Lk~g~~~~G~L---~~~D~~MNl~L~~~~~~~ 45 (70)
T cd01721 17 LKTGEVYRGKL---IEAEDNMNCQLKDVTVTA 45 (70)
T ss_pred ECCCcEEEEEE---EEEcCCceeEEEEEEEEC
Confidence 35666777887 468999999999997643
No 50
>PF10335 DUF294_C: Putative nucleotidyltransferase substrate binding domain; InterPro: IPR018821 This entry is found associated with presumed nucleotidyltransferase domains and seems to be distantly related to other helical substrate binding domains.
Probab=39.49 E-value=86 Score=22.00 Aligned_cols=36 Identities=25% Similarity=0.437 Sum_probs=31.4
Q ss_pred HHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHhhc
Q 033999 18 ETLDEMVQNGTLTPELAIQVLVQFDKSMTEALETQV 53 (106)
Q Consensus 18 dtLdeli~~~~I~p~la~kIl~~FDk~i~~~L~~~v 53 (106)
+=|+.+.+.|.|+++.+..+.+-|+-.+.--|...+
T Consensus 66 eRl~~L~~~g~l~~~~~~~l~~A~~~l~~lRl~~q~ 101 (145)
T PF10335_consen 66 ERLEALAEAGVLSPDDAEDLIEAFEFLLGLRLRHQL 101 (145)
T ss_pred HHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 457889999999999999999999999888877644
No 51
>cd08323 CARD_APAF1 Caspase activation and recruitment domain similar to that found in Apoptotic Protease-Activating Factor 1. Caspase activation and recruitment domain (CARD) similar to that found in apoptotic protease-activating factor 1 (APAF-1), which is an activator of caspase-9. APAF-1 contains WD-40 repeats, a CARD, and an ATPase domain. Upon stimulation, APAF-1, together with caspase-9, forms the heptameric 'apoptosome', which leads to the processing and activation of caspase-9, starting a caspase cascade which leads to apoptosis. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effect
Probab=39.40 E-value=39 Score=22.33 Aligned_cols=29 Identities=24% Similarity=0.342 Sum_probs=23.5
Q ss_pred HHHHHHHHHHCCCCCHHHHHHHHHH---HHHH
Q 033999 16 LTETLDEMVQNGTLTPELAIQVLVQ---FDKS 44 (106)
Q Consensus 16 L~dtLdeli~~~~I~p~la~kIl~~---FDk~ 44 (106)
..+.+|-|+++|.||++-...|..+ .|++
T Consensus 16 v~~ild~L~~~gvlt~~~~e~I~~~~t~~~qa 47 (86)
T cd08323 16 TSYIMDHMISDGVLTLDEEEKVKSKATQKEKA 47 (86)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHcCCChHHHH
Confidence 3568999999999999999888753 5554
No 52
>PF03492 Methyltransf_7: SAM dependent carboxyl methyltransferase; InterPro: IPR005299 This family of plant methyltransferases contains enzymes that act on a variety of substrates including salicylic acid, jasmonic acid and 7-Methylxanthine. Caffeine is synthesized through sequential three-step methylation of xanthine derivatives at positions 7-N, 3-N, and 1-N. The protein 7-methylxanthine methyltransferase (designated as CaMXMT) catalyses the second step to produce theobromine [].; GO: 0008168 methyltransferase activity; PDB: 2EFJ_A 1M6E_X 2EG5_C 3B5I_B.
Probab=39.34 E-value=24 Score=28.49 Aligned_cols=24 Identities=25% Similarity=0.378 Sum_probs=20.2
Q ss_pred hHHHHHHHHHHHHHHCCCCCHHHH
Q 033999 11 TIGMCLTETLDEMVQNGTLTPELA 34 (106)
Q Consensus 11 tlG~aL~dtLdeli~~~~I~p~la 34 (106)
.+...|.++|.||+.+|.|+++-.
T Consensus 198 ~~~~~l~~~l~dMv~eGlI~~ek~ 221 (334)
T PF03492_consen 198 MLWDLLADALRDMVAEGLISEEKV 221 (334)
T ss_dssp CHHHHHHHHHHHHHHTTSS-HCCC
T ss_pred hHHHHHHHHHHHHHHcCCcCHHHh
Confidence 567899999999999999998754
No 53
>PF00681 Plectin: Plectin repeat; InterPro: IPR001101 Plectin may have a role in cross-linking intermediate filaments, in inter-linking intermediate filaments with microtubules and microfilaments and in anchoring intermediate filaments to the plasma and nuclear membranes. Plectin is recruited into hemidesmosomes, multiprotein complexes that facilitate adhesion of epithelia to the basement membrane, thereby providing linkage between the intracellular keratin filaments to the laminins of the extracellular matrix. Plectin binds to hemidesmosomes through association of its actin-binding domain with the first pair of fibronectin type III repeats and a small part of the connecting segment of the integrin-beta4 subunit, the latter (integrin-alpha6,beta4) acting as a receptor for the extracellular matrix component laminin-5. The plectin repeat is also seen in the cell adhesion junction plaque proteins, desmoplakin, envoplakin, and bullous pemphigoid antigen. The domains in plakins show considerable sequence homology. The N terminus consists of a plakin domain containing a number of subdomains with high alpha-helical content, while the central coiled-coil domain is composed of heptad repeats involved in the dimerisation of plakin, and the C terminus contains one or more homologous repeat sequences referred to plectin repeats []. This entry represents the plectin repeats found in the C terminus of plakin proteins.; GO: 0005856 cytoskeleton; PDB: 1LM7_A 1LM5_A.
Probab=37.27 E-value=60 Score=18.53 Aligned_cols=20 Identities=25% Similarity=0.489 Sum_probs=16.3
Q ss_pred HHHHHHCCCCCHHHHHHHHH
Q 033999 20 LDEMVQNGTLTPELAIQVLV 39 (106)
Q Consensus 20 Ldeli~~~~I~p~la~kIl~ 39 (106)
++|=++.|.|+++++.++++
T Consensus 24 v~~A~~~glId~~~~~~L~e 43 (45)
T PF00681_consen 24 VEEAIQRGLIDSDTAQKLLE 43 (45)
T ss_dssp HHHHHHTTSS-HHHHHHHHH
T ss_pred HHHHHHCCCcCHHHHHHHHc
Confidence 56778899999999999886
No 54
>TIGR01669 phage_XkdX phage uncharacterized protein, XkdX family. This model represents a family of small (about 50 amino acid) phage proteins, found in at least 12 different phage and prophage regions of Gram-positive bacteria. In a number of these phage, the gene for this protein is found near the holin and endolysin genes.
Probab=37.15 E-value=37 Score=19.93 Aligned_cols=22 Identities=18% Similarity=0.256 Sum_probs=18.2
Q ss_pred HHHHHHHHHCCCCCHHHHHHHH
Q 033999 17 TETLDEMVQNGTLTPELAIQVL 38 (106)
Q Consensus 17 ~dtLdeli~~~~I~p~la~kIl 38 (106)
.+=+.+++..|.|||++...|-
T Consensus 20 ~e~v~~~V~~~~IT~eey~eIT 41 (45)
T TIGR01669 20 NEDVNKFVEKKLITREQYKVIT 41 (45)
T ss_pred HHHHHHHhhcCccCHHHHHHHh
Confidence 3458899999999999988773
No 55
>PF08638 Med14: Mediator complex subunit MED14; InterPro: IPR013947 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Saccharomyces cerevisiae (Baker's yeast) RGR1 mediator complex subunit affects chromatin structure, transcriptional regulation of diverse genes, and sporulation. It is required for glucose repression, HO repression, RME1 repression and sporulation [, ]. This subunit is also found in higher eukaryotes and MED14 is the agreed unified nomenclature for this subunit []. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=36.55 E-value=1.1e+02 Score=22.86 Aligned_cols=53 Identities=19% Similarity=0.317 Sum_probs=40.3
Q ss_pred HHHCCCCCHHHHHHHHHHHHHHHHHHHHhhcccceEEeeeCccceeeCcEEEEEEcC
Q 033999 23 MVQNGTLTPELAIQVLVQFDKSMTEALETQVKSKVSIKGHLHTYRFCDNVWTFILQD 79 (106)
Q Consensus 23 li~~~~I~p~la~kIl~~FDk~i~~~L~~~vk~k~~~KG~L~tYr~cDnVWtf~lkn 79 (106)
++....|+|+...+.|...+..|.--|.-. -.+.-.+..|+.-|+-=||.+.|
T Consensus 131 ~~~~~~l~~~e~l~~l~~ln~~i~~RL~~~----~~iP~~~~~~~I~dGrv~f~V~~ 183 (195)
T PF08638_consen 131 FIPPPPLSPEEILKTLRRLNTLIRIRLALH----EDIPKQFRNYSIKDGRVTFTVPG 183 (195)
T ss_pred cCCCCCCCHHHHHHHHHHHHHHHHHHHHhc----ccCCcccceEEEECCEEEEEECC
Confidence 455578999999999999999999887631 13334457888888888887766
No 56
>PF12960 DUF3849: Protein of unknown function (DUF3849); InterPro: IPR024383 This domain is found in a family of uncharacterised proteins found by clustering human gut metagenomic sequences [].
Probab=36.26 E-value=1e+02 Score=22.25 Aligned_cols=49 Identities=18% Similarity=0.351 Sum_probs=33.5
Q ss_pred HHHHhh-----hHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHH-HHHHHHHhhc
Q 033999 5 ELYRRS-----TIGMCLTETLDEMVQNGTLTPELAIQVLVQFDK-SMTEALETQV 53 (106)
Q Consensus 5 ~lYR~s-----tlG~aL~dtLdeli~~~~I~p~la~kIl~~FDk-~i~~~L~~~v 53 (106)
.+||.| .+=.+..+++.+--....++++-+..|+++|-- -+.-+|++-|
T Consensus 17 ~~~raS~~aN~~Ck~aIE~aI~~~~~~~~L~~~a~~~vie~fG~eR~~~VLAnTI 71 (133)
T PF12960_consen 17 AQYRASRKANIACKEAIEQAIREHFDGNRLDPDAVKEVIEKFGYERVAYVLANTI 71 (133)
T ss_pred HHHHHHHHhhHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456666 355566666666666779999999999999853 3445565543
No 57
>cd01671 CARD Caspase activation and recruitment domain: a protein-protein interaction domain. Caspase activation and recruitment domains (CARDs) are death domains (DDs) found associated with caspases. Caspases are aspartate-specific cysteine proteases with functions in apoptosis, immune signaling, inflammation, and host-defense mechanisms. In addition to caspases, proteins containing CARDs include adaptor proteins such as RAIDD, CARD9, and RIG-I-like helicases, which can form mutliprotein complexes and play important roles in mediating the signals to induce immune and inflammatory responses. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=36.22 E-value=62 Score=19.81 Aligned_cols=26 Identities=23% Similarity=0.372 Sum_probs=22.8
Q ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHH
Q 033999 15 CLTETLDEMVQNGTLTPELAIQVLVQ 40 (106)
Q Consensus 15 aL~dtLdeli~~~~I~p~la~kIl~~ 40 (106)
.....||.|++.|.|+++-...|...
T Consensus 14 ~~~~il~~L~~~~vlt~~e~~~i~~~ 39 (80)
T cd01671 14 DVEDVLDHLLSDGVLTEEEYEKIRSE 39 (80)
T ss_pred cHHHHHHHHHHcCCCCHHHHHHHHcC
Confidence 66789999999999999999888764
No 58
>cd04446 DEP_DEPDC4 DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in DEPDC4-like proteins. DEPDC4 is a DEP domain containing protein of unknown function.
Probab=36.22 E-value=49 Score=22.48 Aligned_cols=38 Identities=8% Similarity=0.164 Sum_probs=30.8
Q ss_pred hHHHHhhhHHHHHHHHHHHHHHCC------CCCHHHHHHHHHHH
Q 033999 4 FELYRRSTIGMCLTETLDEMVQNG------TLTPELAIQVLVQF 41 (106)
Q Consensus 4 y~lYR~stlG~aL~dtLdeli~~~------~I~p~la~kIl~~F 41 (106)
+..|+.+-+|..+.|-|-+....+ .+|-+.|-++.+.+
T Consensus 21 lk~y~~CF~GsEaVDwL~~~l~~n~~f~~~~~tR~~Av~l~q~L 64 (95)
T cd04446 21 LKSYHDCFLGSEAVDVVLAHLMQNKYFGDVDVPRAKAVRLCQAL 64 (95)
T ss_pred ceecccccchHHHHHHHHHHHhhccccCcccCCHHHHHHHHHHH
Confidence 467999999999999887766444 78999999888766
No 59
>TIGR00988 hip integration host factor, beta subunit. This protein forms a site-specific DNA-binding heterodimer with the homologous integration host factor alpha subunit. It is closely related to the DNA-binding protein HU.
Probab=36.21 E-value=1.2e+02 Score=19.52 Aligned_cols=42 Identities=17% Similarity=0.323 Sum_probs=30.6
Q ss_pred HHHHHHHHC-CCCCHHHHHHHHHHHHHHHHHHHHhhcccceEEee
Q 033999 18 ETLDEMVQN-GTLTPELAIQVLVQFDKSMTEALETQVKSKVSIKG 61 (106)
Q Consensus 18 dtLdeli~~-~~I~p~la~kIl~~FDk~i~~~L~~~vk~k~~~KG 61 (106)
|.++.+.+. ..+++..+..++..|=..|.+.|.+ ..++.|.|
T Consensus 5 eli~~i~~~~~~~s~~~v~~vv~~~~~~i~~~L~~--g~~V~l~g 47 (94)
T TIGR00988 5 ELIERIATQQSHLPAKDVEDAVKTMLEHMASALAQ--GDRIEIRG 47 (94)
T ss_pred HHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHc--CCeEEEcC
Confidence 344444443 4799999999999999999999977 23455553
No 60
>cd04437 DEP_Epac DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in Epac-like proteins. Epac (exchange proteins directly activated by cAMP) proteins are GEFs (guanine-nucleotide-exchange factors) for the small GTPases, Rap1 and Rap2. They are directly regulated by cyclic AMP, a second messenger that plays a role in the control of diverse cellular processes, such as cell adhesion and insulin secretion. Epac-like proteins share a common domain architecture, containing RasGEF, DEP and CAP-effector (cAMP binding) domains. The DEP domain is involved in membrane localization.
Probab=35.90 E-value=30 Score=24.55 Aligned_cols=62 Identities=19% Similarity=0.404 Sum_probs=43.2
Q ss_pred hHHHHhhhHHHHHHHHHHHHHHCCC--CCHHHHHHHHHHHHHHHHHHHHhhcccceEEeeeCccceeeCc
Q 033999 4 FELYRRSTIGMCLTETLDEMVQNGT--LTPELAIQVLVQFDKSMTEALETQVKSKVSIKGHLHTYRFCDN 71 (106)
Q Consensus 4 y~lYR~stlG~aL~dtLdeli~~~~--I~p~la~kIl~~FDk~i~~~L~~~vk~k~~~KG~L~tYr~cDn 71 (106)
...|+++-+|..|.| =|++.+. .+.+.|-.+.+.. +.+-+-.+|..+-.|+-.-.-|||.++
T Consensus 24 ~~~y~~cF~GsElVd---WLl~~~~~v~sR~eAv~lgq~L---l~~gvi~HV~~~h~F~D~~~fYrF~~d 87 (125)
T cd04437 24 LRTYRQCCVGTELVD---WLLQQSPCVQSRSQAVGMWQVL---LEEGVLLHVDQELHFQDKYQFYRFSDD 87 (125)
T ss_pred CEECCcccccHHHHH---HHHHcCCCCCCHHHHHHHHHHH---HhCCCeEEeCCcCccccCCeeEEECCc
Confidence 356899999976655 4666654 4888888776543 344444478889999955478998765
No 61
>PF12713 DUF3806: Domain of unknown function (DUF3806); InterPro: IPR024266 This entry represents a domain found at the C terminus of a family of bacterial proteins, whose function is unknown. In two related Bacteroides species the gene for members of this family lies immediately upstream from a putative ATP binding component of an ATP transporter and a putative histidinol phosphatase. The structure of this domain is strikingly similar to the N-terminal structure of 1ma7, whose C-terminal domain is a phage integrase.; PDB: 3HLZ_A.
Probab=35.12 E-value=1.1e+02 Score=19.89 Aligned_cols=41 Identities=15% Similarity=0.295 Sum_probs=32.1
Q ss_pred HHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHhhc-ccceEE
Q 033999 18 ETLDEMVQNGTLTPELAIQVLVQFDKSMTEALETQV-KSKVSI 59 (106)
Q Consensus 18 dtLdeli~~~~I~p~la~kIl~~FDk~i~~~L~~~v-k~k~~~ 59 (106)
++|+.++.++.++|+..+. ++.|=-++-+.|.+.+ ...+..
T Consensus 4 ~~lq~~id~~~~~~~d~~~-~~alGialG~~L~~e~~g~eW~~ 45 (87)
T PF12713_consen 4 EKLQRVIDSGEISPDDKDE-WQALGIALGDLLANEVDGMEWVT 45 (87)
T ss_dssp HHHHHHHHTT-S-TT-HHH-HHHHHHHHHHHHHHHSTT-EEEE
T ss_pred HHHHHHHHhCCCCCCcHHH-HHHHHHHHHHHHHhhcCCCeEEE
Confidence 6899999999999999998 9999999999999977 555443
No 62
>cd04440 DEP_2_P-Rex DEP (Dishevelled, Egl-10, and Pleckstrin) domain 2 found in P-Rex-like proteins. The P-Rex family is the guanine-nucleotide exchange factor (GEF) for the small GTPase Rac that contains an N-terminal RhoGEF domain, two DEP and PDZ domains. Rac-GEF activity is stimulated by phosphatidylinositol (3,4,5)-trisphosphate (PtdIns(3,4,5)P3), a lipid second messenger, and the G beta-gamma subunits of heterotrimeric G proteins. The DEP domains are not involved in mediating these stimuli, but may be of importance for basal and stimulated levels Rac-GEF activity.
Probab=35.05 E-value=38 Score=22.96 Aligned_cols=61 Identities=21% Similarity=0.238 Sum_probs=41.3
Q ss_pred HHHHhhhHHHHHHHHHHHHHHCC-CCCHHHHHHHHHHHHHHHHHHHHhhcccceEEeeeCccceeeCc
Q 033999 5 ELYRRSTIGMCLTETLDEMVQNG-TLTPELAIQVLVQFDKSMTEALETQVKSKVSIKGHLHTYRFCDN 71 (106)
Q Consensus 5 ~lYR~stlG~aL~dtLdeli~~~-~I~p~la~kIl~~FDk~i~~~L~~~vk~k~~~KG~L~tYr~cDn 71 (106)
..|+++-+|..|.|=| ++.| ..|.+.|-.+.+. -+..-+-.+|..+-.|+-.-.-|||+.+
T Consensus 32 ~~y~~cFvGsElVdWL---i~~g~~~tR~eAv~~gq~---Ll~~gii~HV~~~h~F~D~~lfYrF~~d 93 (93)
T cd04440 32 KTYKSVVPASKLVDWL---LAQGDCRTREEAVILGVG---LCNNGFMHHVLEKSEFKDEPLLFRFYAD 93 (93)
T ss_pred EEcccccchhHHHHHH---HHcCCCCCHHHHHHHHHH---HHhCCCEEecCCCcCcCCcCeEEEEecC
Confidence 4689999998877664 4544 5577777765542 1222333478999999955568999864
No 63
>PRK00111 hypothetical protein; Provisional
Probab=34.87 E-value=63 Score=24.39 Aligned_cols=58 Identities=22% Similarity=0.374 Sum_probs=42.0
Q ss_pred HHHHHHHHHHHHCCCCCHHHH-HHHHHHHHHHHHHHHHhhcccceEEe-eeCccceeeCc-EEE
Q 033999 14 MCLTETLDEMVQNGTLTPELA-IQVLVQFDKSMTEALETQVKSKVSIK-GHLHTYRFCDN-VWT 74 (106)
Q Consensus 14 ~aL~dtLdeli~~~~I~p~la-~kIl~~FDk~i~~~L~~~vk~k~~~K-G~L~tYr~cDn-VWt 74 (106)
.+|.++|++++++.-..+.+. -.|+...+..+-+.++++.+. ..|+ |.| |=.||+ +|.
T Consensus 67 qsLg~iL~~l~~~~Gw~~~l~~~~V~~~W~eIVG~~IA~hT~p-~~ikdgvL--~V~~sSsAWA 127 (180)
T PRK00111 67 ESLGSVLNKEIQRRGWGKDIAGGWVTSHWDELVGAKIAQHTKV-EMIKDKKL--FITCDSTAWA 127 (180)
T ss_pred ccHHHHHHHHHHhcCchhhhhHHHHHHHhHHHHCHHHHhhcCc-eEEECCEE--EEEeCCHHHH
Confidence 467888888888887777555 579999999999999886544 4555 555 555555 663
No 64
>PF13833 EF-hand_8: EF-hand domain pair; PDB: 3KF9_A 1TTX_A 1WLZ_A 1ALV_A 1NX3_A 1ALW_A 1NX2_A 1NX1_A 1NX0_A 1DF0_A ....
Probab=34.64 E-value=78 Score=17.79 Aligned_cols=28 Identities=18% Similarity=0.221 Sum_probs=19.5
Q ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHHHH
Q 033999 15 CLTETLDEMVQNGTLTPELAIQVLVQFDK 43 (106)
Q Consensus 15 aL~dtLdeli~~~~I~p~la~kIl~~FDk 43 (106)
.|..+| .....+.++++.+..++..||.
T Consensus 9 ~~~~~l-~~~g~~~~s~~e~~~l~~~~D~ 36 (54)
T PF13833_consen 9 EFRRAL-SKLGIKDLSEEEVDRLFREFDT 36 (54)
T ss_dssp HHHHHH-HHTTSSSSCHHHHHHHHHHHTT
T ss_pred HHHHHH-HHhCCCCCCHHHHHHHHHhccc
Confidence 455666 3332223999999999999985
No 65
>cd08329 CARD_BIRC2_BIRC3 Caspase activation and recruitment domain found in Baculoviral IAP repeat-containing proteins, BIRC2 (c-IAP1) and BIRC3 (c-IAP2). Caspase activation and recruitment domain (CARD) similar to those found in Baculoviral IAP repeat (BIR)-containing protein 2 (BIRC2) or cellular Inhibitor of Apoptosis Protein 1 (c-IAP1), and BIRC3 (or c-IAP2). IAPs are anti-apoptotic proteins that contain at least one BIR domain. Most IAPs also contain a C-terminal RING domain. In addition, both BIRC2 and BIRC3 contain a CARD. BIRC2 and BIRC3, through their binding with TRAF (TNF receptor-associated factor) 2, are recruited to TNFR-1/2 signaling complexes, where they regulate caspase-8 activity. They also play important roles in pro-survival NF-kB signaling pathways. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation and host-defense mechanisms. DDs are protein-protein interac
Probab=34.42 E-value=59 Score=21.64 Aligned_cols=22 Identities=14% Similarity=0.129 Sum_probs=19.5
Q ss_pred HHHHHHHHCCCCCHHHHHHHHH
Q 033999 18 ETLDEMVQNGTLTPELAIQVLV 39 (106)
Q Consensus 18 dtLdeli~~~~I~p~la~kIl~ 39 (106)
..||.|++.|.|+++-...|-.
T Consensus 27 ~ilD~Ll~~~Vlt~ee~e~I~~ 48 (94)
T cd08329 27 PILDSLLSANVITEQEYDVIKQ 48 (94)
T ss_pred HHHHHHHHcCCCCHHHHHHHHc
Confidence 5799999999999998888864
No 66
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=34.26 E-value=46 Score=23.36 Aligned_cols=22 Identities=32% Similarity=0.598 Sum_probs=16.3
Q ss_pred HHHHHHHHHCCCCCHHHHHHHHH
Q 033999 17 TETLDEMVQNGTLTPELAIQVLV 39 (106)
Q Consensus 17 ~dtLdeli~~~~I~p~la~kIl~ 39 (106)
.+.|+. +.+|.||++-|.++|.
T Consensus 92 ~~IL~~-L~~GeIs~eeA~~~Lk 113 (113)
T PF09862_consen 92 KEILDK-LEKGEISVEEALEILK 113 (113)
T ss_pred HHHHHH-HHcCCCCHHHHHHHhC
Confidence 344554 4599999999999873
No 67
>COG0776 HimA Bacterial nucleoid DNA-binding protein [DNA replication, recombination, and repair]
Probab=34.17 E-value=1.5e+02 Score=20.05 Aligned_cols=38 Identities=24% Similarity=0.369 Sum_probs=28.4
Q ss_pred HHHHHCCCCCHHHHHHHHHHHHHHHHHHHHhhcccceEEe
Q 033999 21 DEMVQNGTLTPELAIQVLVQFDKSMTEALETQVKSKVSIK 60 (106)
Q Consensus 21 deli~~~~I~p~la~kIl~~FDk~i~~~L~~~vk~k~~~K 60 (106)
+.+-+...|+...+..+++.|=..|.++|.+ ..++++.
T Consensus 9 ~~ia~~~~l~k~~a~~~v~~~~~~i~~aL~~--G~~V~l~ 46 (94)
T COG0776 9 DAIAEKAGLSKKDAEEAVDAFLEEITEALAK--GERVELR 46 (94)
T ss_pred HHHHHHcCCCHHHHHHHHHHHHHHHHHHHHc--CCeEEEe
Confidence 3334444499999999999999999999987 3444444
No 68
>PF10474 DUF2451: Protein of unknown function C-terminus (DUF2451); InterPro: IPR019514 This protein is found in eukaryotes but its function is not known. The N-terminal domain of some members is PF10475 from PFAM (DUF2450).
Probab=34.08 E-value=1.2e+02 Score=23.32 Aligned_cols=46 Identities=28% Similarity=0.357 Sum_probs=36.5
Q ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHh---hcccceEEee
Q 033999 15 CLTETLDEMVQNGTLTPELAIQVLVQFDKSMTEALET---QVKSKVSIKG 61 (106)
Q Consensus 15 aL~dtLdeli~~~~I~p~la~kIl~~FDk~i~~~L~~---~vk~k~~~KG 61 (106)
.+..-||++...+.|+++.-..+|+..=..+.++|=+ ++ .||+=.|
T Consensus 103 ~f~~rL~~i~~~~~i~~~~~~~lw~~~i~~~~~~Lveg~s~v-kKCs~eG 151 (234)
T PF10474_consen 103 QFSERLDEISKQGPIPPEVQNVLWDRLIFFAFETLVEGYSRV-KKCSNEG 151 (234)
T ss_pred HHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHhc-cCCChhh
Confidence 3677889999999999999999999999999888755 24 3555544
No 69
>PF00216 Bac_DNA_binding: Bacterial DNA-binding protein; InterPro: IPR000119 Bacteria synthesise a set of small, usually basic proteins of about 90 residues that bind DNA and are known as histone-like proteins [, ]. Examples include the HU protein in Escherichia coli is a dimer of closely related alpha and beta chains and in other bacteria can be a dimer of identical chains. HU-type proteins have been found in a variety of eubacteria, cyanobacteria and archaebacteria, and are also encoded in the chloroplast genome of some algae []. The integration host factor (IHF), a dimer of closely related chains which seem to function in genetic recombination as well as in translational and transcriptional control [] is found in enterobacteria and viral proteins include the African Swine fever virus protein A104R (or LMW5-AR) []. The exact function of these proteins is not yet clear but they are capable of wrapping DNA and stabilising it from denaturation under extreme environmental conditions. The structure is known for one of these proteins []. The protein exists as a dimer and two "beta-arms" function as the non-specific binding site for bacterial DNA. ; GO: 0003677 DNA binding; PDB: 3C4I_B 2O97_A 1MUL_A 1P78_A 1P51_C 1P71_B 2HT0_A 1OWG_A 2IIF_A 1OUZ_A ....
Probab=34.08 E-value=97 Score=19.38 Aligned_cols=30 Identities=20% Similarity=0.197 Sum_probs=24.9
Q ss_pred HHHHCCCCCHHHHHHHHHHHHHHHHHHHHh
Q 033999 22 EMVQNGTLTPELAIQVLVQFDKSMTEALET 51 (106)
Q Consensus 22 eli~~~~I~p~la~kIl~~FDk~i~~~L~~ 51 (106)
++-+..-+++..+..|+..|-..|.+.|.+
T Consensus 9 ~ia~~~~~s~~~v~~vl~~~~~~i~~~L~~ 38 (90)
T PF00216_consen 9 RIAEKTGLSKKDVEAVLDALFDVIKEALKE 38 (90)
T ss_dssp HHHHHHTSSHHHHHHHHHHHHHHHHHHHHT
T ss_pred HHHHhcCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 333343489999999999999999999977
No 70
>TIGR02742 TrbC_Ftype type-F conjugative transfer system pilin assembly protein TrbC. This protein is an essential component of the F-type conjugative pilus assembly system for the transfer of plasmid DNA. The N-terminal portion of these proteins are heterogeneous and are not covered by this model.
Probab=33.82 E-value=63 Score=22.97 Aligned_cols=27 Identities=30% Similarity=0.432 Sum_probs=22.9
Q ss_pred HHHHHHHHHHHHCCCCCHHHHHHHHHH
Q 033999 14 MCLTETLDEMVQNGTLTPELAIQVLVQ 40 (106)
Q Consensus 14 ~aL~dtLdeli~~~~I~p~la~kIl~~ 40 (106)
.+|.+||+++-++|...+..|.+.|+.
T Consensus 102 vsl~~ALe~ia~~g~~~~~~A~~~L~~ 128 (130)
T TIGR02742 102 VSLKGALEKMAQDGDSPQIVAQQLLER 128 (130)
T ss_pred ccHHHHHHHHHHhCCCcHHHHHHHHHh
Confidence 478999999999998877788888864
No 71
>cd01733 LSm10 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm10 is an SmD1-like protein which is thought to bind U7 snRNA along with LSm11 and five other Sm subunits to form a 7-member ring structure. LSm10 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.
Probab=33.69 E-value=99 Score=19.86 Aligned_cols=31 Identities=10% Similarity=0.263 Sum_probs=24.6
Q ss_pred cccceEEeeeCccceeeCcEEEEEEcCeEEEecc
Q 033999 53 VKSKVSIKGHLHTYRFCDNVWTFILQDALFKSEE 86 (106)
Q Consensus 53 vk~k~~~KG~L~tYr~cDnVWtf~lkn~~~k~~~ 86 (106)
.|+...++|.| ..||+-..+.|+|+++...+
T Consensus 26 LKng~~~~G~L---~~vD~~MNl~L~~~~~~~~~ 56 (78)
T cd01733 26 LRNETTVTGRI---ASVDAFMNIRLAKVTIIDRN 56 (78)
T ss_pred ECCCCEEEEEE---EEEcCCceeEEEEEEEEcCC
Confidence 46667778888 56899999999999977543
No 72
>PRK03195 hypothetical protein; Provisional
Probab=33.64 E-value=69 Score=24.22 Aligned_cols=58 Identities=16% Similarity=0.277 Sum_probs=42.2
Q ss_pred HHHHHHHHHHHHCCCCCHHHH-HHHHHHHHHHHHHHHHhhcccceEEe-eeCccceeeCc-EEE
Q 033999 14 MCLTETLDEMVQNGTLTPELA-IQVLVQFDKSMTEALETQVKSKVSIK-GHLHTYRFCDN-VWT 74 (106)
Q Consensus 14 ~aL~dtLdeli~~~~I~p~la-~kIl~~FDk~i~~~L~~~vk~k~~~K-G~L~tYr~cDn-VWt 74 (106)
++|.++|++|+++.-....++ -.|+......+-+.++.+.+. ..|+ |.| |=.|++ +|.
T Consensus 73 q~Lg~il~~l~~~~gW~~~l~~~~V~~~W~~IVG~~IA~ht~P-~~i~~gvL--~V~~~SsaWA 133 (186)
T PRK03195 73 QPLGALARDLAKKRGWSAKVAEGTVLGQWSAVVGEQIAAHATP-TALNDGVL--SVSAESTAWA 133 (186)
T ss_pred ccHHHHHHHHHHhcCchhhhhHhHHHHHhHHHHCHHHHhhcce-eEEECCEE--EEEeCCHHHH
Confidence 468899999998888876665 579999999999999886654 3444 555 445554 663
No 73
>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only]
Probab=33.58 E-value=55 Score=22.78 Aligned_cols=33 Identities=21% Similarity=0.369 Sum_probs=27.3
Q ss_pred HHHHHHHHCC-CCCHHHHHHHHHHHHHHHHHHHH
Q 033999 18 ETLDEMVQNG-TLTPELAIQVLVQFDKSMTEALE 50 (106)
Q Consensus 18 dtLdeli~~~-~I~p~la~kIl~~FDk~i~~~L~ 50 (106)
.++.++|+.+ .||++.|.++-..|+.+..--|+
T Consensus 38 ~~is~ling~~~iT~dmAlrL~k~fGtspefWlN 71 (104)
T COG3093 38 NTISELINGRRAITADMALRLAKVFGTSPEFWLN 71 (104)
T ss_pred HHHHHHHcCCcCCCHHHHHHHHHHhCCCHHHHHH
Confidence 4678899988 89999999999999887765543
No 74
>PF03048 Herpes_UL92: UL92 family; InterPro: IPR004289 Members of this family are functionally uncharacterised proteins from herpesviruses. The N terminus of these proteins contain 6 conserved cysteines and histidines that might form a zinc binding domain.
Probab=33.48 E-value=1.1e+02 Score=23.49 Aligned_cols=32 Identities=16% Similarity=0.397 Sum_probs=29.6
Q ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHH
Q 033999 16 LTETLDEMVQNGTLTPELAIQVLVQFDKSMTE 47 (106)
Q Consensus 16 L~dtLdeli~~~~I~p~la~kIl~~FDk~i~~ 47 (106)
+.+..++.+.+|.+.|+....|-..|.++...
T Consensus 104 ~~~V~~~i~~~g~l~~~i~~~I~~TF~~c~~~ 135 (192)
T PF03048_consen 104 YAEVKQAIFEDGELKPHIEDLIYFTFNHCFHV 135 (192)
T ss_pred HHHHHHHHHcCCcccHhHHHHHHHHHHHHHHh
Confidence 89999999999999999999999999987654
No 75
>cd08326 CARD_CASP9 Caspase activation and recruitment domain of Caspase-9. Caspase activation and recruitment domain (CARD) similar to that found in caspase-9 (CASP9, MCH6, APAF3), which interacts with the CARD of apoptotic protease-activating factor 1 (APAF-1). Caspases are aspartate-specific cysteine proteases with functions in apoptosis and immune signaling. Initiator caspases are the first to be activated following death- or inflammation-inducing signals. Caspase-9 is the initiator caspase associated with the intrinsic or mitochondrial pathway of apoptosis, induced by many pro-apoptotic signals. Together with APAF-1, it forms the heptameric 'apoptosome' in response to the release of cytochrome c from mitochondria. Activated caspase-9 cleaves and activates downstream effector caspases, like caspase-3, caspase-6, and caspase-7, resulting in apoptosis. In general, CARDs are death domains (DDs) associated with caspases. They are known to be important in the signaling pathways for apopt
Probab=33.45 E-value=68 Score=20.99 Aligned_cols=24 Identities=17% Similarity=0.380 Sum_probs=21.1
Q ss_pred HHHHHHHHHHCCCCCHHHHHHHHH
Q 033999 16 LTETLDEMVQNGTLTPELAIQVLV 39 (106)
Q Consensus 16 L~dtLdeli~~~~I~p~la~kIl~ 39 (106)
..+.+|.|+++|.+|++....|..
T Consensus 18 ~~~v~~~L~~~~Vlt~~~~e~I~~ 41 (84)
T cd08326 18 PKYLWDHLLSRGVFTPDMIEEIQA 41 (84)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHc
Confidence 357899999999999999988875
No 76
>PF14802 TMEM192: TMEM192 family
Probab=33.13 E-value=1.1e+02 Score=23.94 Aligned_cols=43 Identities=19% Similarity=0.419 Sum_probs=31.3
Q ss_pred hhhHHHHhh-----------hHHHHHHHHHHHHHHCCC------------CCHHHHHHHHHHHHHH
Q 033999 2 ATFELYRRS-----------TIGMCLTETLDEMVQNGT------------LTPELAIQVLVQFDKS 44 (106)
Q Consensus 2 ~~y~lYR~s-----------tlG~aL~dtLdeli~~~~------------I~p~la~kIl~~FDk~ 44 (106)
+|+++||.+ ++|.|.-=++..+..... ++|++...|+-..--.
T Consensus 90 GY~~fyr~t~~~rr~Pl~ivS~gna~LLlv~~~~~~~~~~~~~~~c~~~~ls~~~~l~i~~~lE~~ 155 (236)
T PF14802_consen 90 GYLDFYRKTKRLRRLPLQIVSLGNAVLLLVQAWQHHYFGPDFAEYCSVAPLSPQLYLQILCSLELL 155 (236)
T ss_pred CHHHHHHHHHHHhcchHHHHHHHHHHHHHHHHHHHhcccccchhhcccccCcHHHHHHHHHHHHHH
Confidence 678999987 577777666666665554 9999999888744433
No 77
>PF06256 Nucleo_LEF-12: Nucleopolyhedrovirus LEF-12 protein; InterPro: IPR009365 This family consists of several Nucleopolyhedrovirus late expression factor-12 (LEF-12) proteins. The function of this family is unknown [,].
Probab=32.95 E-value=67 Score=24.56 Aligned_cols=43 Identities=30% Similarity=0.397 Sum_probs=35.2
Q ss_pred HhhhHHHHHHHHHHHHHHCCCCCHHHH-----------------------------------HHHHH--HHHHHHHHHHH
Q 033999 8 RRSTIGMCLTETLDEMVQNGTLTPELA-----------------------------------IQVLV--QFDKSMTEALE 50 (106)
Q Consensus 8 R~stlG~aL~dtLdeli~~~~I~p~la-----------------------------------~kIl~--~FDk~i~~~L~ 50 (106)
+-.++-.-...|||+|++.|.|+++=+ .++|+ .|+.++.+.+.
T Consensus 11 ~v~~~~~~~~~~ld~M~~~geit~~Da~sLClaDDTAAWvCGRi~~cnfVSFRi~~~~F~~~~~~L~~f~FeEsl~Q~~~ 90 (185)
T PF06256_consen 11 YVQDFADMMKRTLDEMVEHGEITRADADSLCLADDTAAWVCGRIETCNFVSFRIKSAQFQHPSRALEHFGFEESLEQRLL 90 (185)
T ss_pred HHHHHHHHHHHHHHHHHHcCCcchhhhcceeecccchHHhcCCccCCceEEEEEEHhhhcCchHHHHHhCcHHHHHHHhc
Confidence 344566778899999999999999865 56788 78999999885
No 78
>PF07527 Hairy_orange: Hairy Orange; InterPro: IPR003650 This domain confers specificity among members of the Hairy/E(SPL) family. HES-2 (hairy and enhancer of split 2) is a transcription factor, and the hairy protein is a pair-rule protein that regulates embryonic segmentation and adult bristle patterning. These proteins are transcriptional repressors of genes that require the BHLH protein for their transcription.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DB7_A.
Probab=32.92 E-value=96 Score=17.46 Aligned_cols=35 Identities=14% Similarity=0.327 Sum_probs=27.8
Q ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHH
Q 033999 13 GMCLTETLDEMVQNGTLTPELAIQVLVQFDKSMTE 47 (106)
Q Consensus 13 G~aL~dtLdeli~~~~I~p~la~kIl~~FDk~i~~ 47 (106)
...+.++..=|-...-++|++..+++..+...+++
T Consensus 8 ~~C~~Ev~~fL~~~~~~~~~~~~rLl~HL~~~~~~ 42 (43)
T PF07527_consen 8 SECLNEVSRFLSSVEGVDPGVRARLLSHLQSCLNQ 42 (43)
T ss_dssp HHHHHHHHHHHHHTS---THHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHhcC
Confidence 35788888888888889999999999999998875
No 79
>COG2405 Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]
Probab=32.34 E-value=55 Score=24.35 Aligned_cols=25 Identities=20% Similarity=0.530 Sum_probs=21.7
Q ss_pred HHHHHHHHCC-CCCHHHHHHHHHHHH
Q 033999 18 ETLDEMVQNG-TLTPELAIQVLVQFD 42 (106)
Q Consensus 18 dtLdeli~~~-~I~p~la~kIl~~FD 42 (106)
-.|||||+.| ++|.++.+.||..-+
T Consensus 130 pild~LI~~GF~iS~~~~eeiL~~~~ 155 (157)
T COG2405 130 PILDELIEKGFRISRSILEEILRKLQ 155 (157)
T ss_pred HHHHHHHHhcCcccHHHHHHHHHHhc
Confidence 5899999998 999999999987654
No 80
>KOG0037 consensus Ca2+-binding protein, EF-Hand protein superfamily [Signal transduction mechanisms]
Probab=32.32 E-value=52 Score=25.78 Aligned_cols=28 Identities=18% Similarity=0.368 Sum_probs=23.8
Q ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHHHHH
Q 033999 15 CLTETLDEMVQNGTLTPELAIQVLVQFDKS 44 (106)
Q Consensus 15 aL~dtLdeli~~~~I~p~la~kIl~~FDk~ 44 (106)
.|.+||.+| .-+|+|++.+.++.+||+.
T Consensus 145 EL~~Al~~~--Gy~Lspq~~~~lv~kyd~~ 172 (221)
T KOG0037|consen 145 ELRQALTQL--GYRLSPQFYNLLVRKYDRF 172 (221)
T ss_pred HHHHHHHHc--CcCCCHHHHHHHHHHhccc
Confidence 588888776 4499999999999999965
No 81
>KOG3456 consensus NADH:ubiquinone oxidoreductase, NDUFS6/13 kDa subunit [Energy production and conversion]
Probab=31.43 E-value=33 Score=24.36 Aligned_cols=12 Identities=33% Similarity=0.592 Sum_probs=9.4
Q ss_pred EEEEEecCCCCC
Q 033999 94 VKIVACDSKLLS 105 (106)
Q Consensus 94 lKIVAcd~~~~~ 105 (106)
=+|||||+..++
T Consensus 78 ~RVV~CdGg~~a 89 (120)
T KOG3456|consen 78 GRVVACDGGTPA 89 (120)
T ss_pred ceEEEecCCCCC
Confidence 479999998643
No 82
>PF07565 Band_3_cyto: Band 3 cytoplasmic domain; InterPro: IPR013769 Bicarbonate (HCO3 -) transport mechanisms are the principal regulators of pH in animal cells. Such transport also plays a vital role in acid-base movements in the stomach, pancreas, intestine, kidney, reproductive organs and the central nervous system. Functional studies have suggested four different HCO3 - transport modes. Anion exchanger proteins exchange HCO3 - for Cl- in a reversible, electroneutral manner []. Na+/HCO3 - co-transport proteins mediate the coupled movement of Na+ and HCO3 - across plasma membranes, often in an electrogenic manner []. Na- driven Cl-/HCO3 - exchange and K+/HCO3 - exchange activities have also been detected in certain cell types, although the molecular identities of the proteins responsible remain to be determined. Sequence analysis of the two families of HCO3 - transporters that have been cloned to date (the anion exchangers and Na+/HCO3 - co-transporters) reveals that they are homologous. This is not entirely unexpected, given that they both transport HCO3 - and are inhibited by a class of pharmacological agents called disulphonic stilbenes []. They share around ~25-30% sequence identity, which is distributed along their entire sequence length, and have similar predicted membrane topologies, suggesting they have ~10 transmembrane (TM) domains.; GO: 0008509 anion transmembrane transporter activity, 0006820 anion transport, 0016021 integral to membrane; PDB: 1HYN_Q.
Probab=31.25 E-value=56 Score=25.75 Aligned_cols=31 Identities=32% Similarity=0.406 Sum_probs=24.9
Q ss_pred hhHHHHHHHHHHHHHHCCCCCHHHHHHHHHH
Q 033999 10 STIGMCLTETLDEMVQNGTLTPELAIQVLVQ 40 (106)
Q Consensus 10 stlG~aL~dtLdeli~~~~I~p~la~kIl~~ 40 (106)
+++.......+|+|+.++.|+|+...+|++-
T Consensus 41 ~tl~~I~~~vvd~~v~~~~l~~~~r~~V~~a 71 (257)
T PF07565_consen 41 KTLPEIADKVVDQMVSEGQLRPEDRDKVLRA 71 (257)
T ss_dssp -SHHHHHHHHHHHHHHTTSS-GGGHHHHHHH
T ss_pred cCHHHHHHHHHHHHHhhcCCCHHHHHHHHHH
Confidence 4677777889999999999999998888754
No 83
>PRK10449 heat-inducible protein; Provisional
Probab=30.59 E-value=89 Score=22.02 Aligned_cols=42 Identities=19% Similarity=0.347 Sum_probs=30.3
Q ss_pred HHHHHHHHHHHHHhhcccceEEeeeCccceeeCcEEEEEEcCeE
Q 033999 38 LVQFDKSMTEALETQVKSKVSIKGHLHTYRFCDNVWTFILQDAL 81 (106)
Q Consensus 38 l~~FDk~i~~~L~~~vk~k~~~KG~L~tYr~cDnVWtf~lkn~~ 81 (106)
+++.++.+.++|++. .+..+.|.--+.+--+..++|..+|+.
T Consensus 98 ~~~~E~~~~~~L~~~--~~~~~~g~~L~L~~~~~~l~f~~~~~~ 139 (140)
T PRK10449 98 LNELDNTISEMLKKG--AQVDLTANQLTLATAKQTLMYKLADLV 139 (140)
T ss_pred HHHHHHHHHHHHhcC--ceEEEcCCEEEEEcCCcEEEEEEhhhc
Confidence 457788888899774 444566654466777889999988863
No 84
>PF01756 ACOX: Acyl-CoA oxidase; InterPro: IPR002655 Acyl-CoA oxidase (ACO) acts on CoA derivatives of fatty acids with chain lengths from 8 to 18. It catalyses the first and rate-determining step of the peroxisomal beta-oxidation of fatty acids []. Acyl-CoA oxidase is a homodimer and the polypeptide chain of the subunit is folded into the N-terminal alpha-domain, beta-domain, and C-terminal alpha-domain []. Functional differences between the peroxisomal acyl-CoA oxidases and the mitochondrial acyl-CoA dehydrogenases are attributed to structural differences in the FAD environments []. Experimental data indicate that, in the pumpkin, the expression pattern of ACOX is very similar to that of the glyoxysomal enzyme 3-ketoacyl-CoA thiolase []. In humans, defects in ACOX1 are the cause of pseudoneonatal adrenoleukodystrophy, also known as peroxisomal acyl-CoA oxidase deficiency. Pseudo-NALD is a peroxisomal single-enzyme disorder. Clinical features include mental retardation, leukodystrophy, seizures, mild hepatomegaly and hearing deficit. Pseudo-NALD is characterised by increased plasma levels of very-long chain fatty acids due to a decrease in, or absence of, peroxisome acyl-CoA oxidase activity, despite the peroxisomes being intact and functioning. This entry represents the Acyl-CoA oxidase C-terminal.; GO: 0003997 acyl-CoA oxidase activity, 0006635 fatty acid beta-oxidation, 0055114 oxidation-reduction process, 0005777 peroxisome; PDB: 2FON_A 1IS2_B 2DDH_A 1W07_B.
Probab=30.57 E-value=1.4e+02 Score=21.60 Aligned_cols=34 Identities=18% Similarity=0.324 Sum_probs=27.0
Q ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHH
Q 033999 15 CLTETLDEMVQNGTLTPELAIQVLVQFDKSMTEA 48 (106)
Q Consensus 15 aL~dtLdeli~~~~I~p~la~kIl~~FDk~i~~~ 48 (106)
.+.+-+.++++.|.|+|+.+..|-+..++.+.+.
T Consensus 92 ~i~~~~g~fl~~g~ls~~~~~~l~~~i~~l~~~l 125 (187)
T PF01756_consen 92 IIEENAGDFLEHGYLSPEQIKALRKAIEELCAEL 125 (187)
T ss_dssp HHHHTHHHHHHTTSS-HHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhCCcCCHHHHHHHHHHHHHHHHHH
Confidence 4456678899999999999999998888777654
No 85
>COG5026 Hexokinase [Carbohydrate transport and metabolism]
Probab=30.09 E-value=1e+02 Score=26.73 Aligned_cols=41 Identities=20% Similarity=0.341 Sum_probs=36.7
Q ss_pred HHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHhh
Q 033999 12 IGMCLTETLDEMVQNGTLTPELAIQVLVQFDKSMTEALETQ 52 (106)
Q Consensus 12 lG~aL~dtLdeli~~~~I~p~la~kIl~~FDk~i~~~L~~~ 52 (106)
+-.+|+++++|++..-.++.+..++|-..|+..+...|+.+
T Consensus 13 ~~~~l~~~~~~~~~~~~~p~e~l~~v~~~Fieel~kgL~~~ 53 (466)
T COG5026 13 VEAALEQAVEELVESFTVPTEDLREVVKAFIEELEKGLQPK 53 (466)
T ss_pred ccHHHHHHHHHHhhcccCCHHHHHHHHHHHHHHHHhccCCC
Confidence 34689999999999999999999999999999998888744
No 86
>cd01723 LSm4 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm4 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=30.05 E-value=56 Score=20.69 Aligned_cols=28 Identities=29% Similarity=0.502 Sum_probs=23.0
Q ss_pred cccceEEeeeCccceeeCcEEEEEEcCeEEE
Q 033999 53 VKSKVSIKGHLHTYRFCDNVWTFILQDALFK 83 (106)
Q Consensus 53 vk~k~~~KG~L~tYr~cDnVWtf~lkn~~~k 83 (106)
.++...+.|.| ..||+-+.+.++|++..
T Consensus 18 Lkng~~~~G~L---~~~D~~mNi~L~~~~~~ 45 (76)
T cd01723 18 LKNGETYNGHL---VNCDNWMNIHLREVICT 45 (76)
T ss_pred ECCCCEEEEEE---EEEcCCCceEEEeEEEE
Confidence 36777788888 46899999999999775
No 87
>PF12297 EVC2_like: Ellis van Creveld protein 2 like protein; InterPro: IPR022076 This family of proteins is found in eukaryotes. Proteins in this family are typically between 571 and 1310 amino acids in length. There are two conserved sequence motifs: LPA and ELH. EVC2 is implicated in Ellis van Creveld chondrodysplastic dwarfism in humans. Mutations in this protein can give rise to this congenital condition. LIMBIN is a protein which shares around 80% sequence homology with EVC2 and it is implicated in a similar condition in bovine chondrodysplastic dwarfism.
Probab=29.64 E-value=2.2e+02 Score=24.51 Aligned_cols=43 Identities=23% Similarity=0.429 Sum_probs=37.5
Q ss_pred hHHHHhhhHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHH
Q 033999 4 FELYRRSTIGMCLTETLDEMVQNGTLTPELAIQVLVQFDKSMT 46 (106)
Q Consensus 4 y~lYR~stlG~aL~dtLdeli~~~~I~p~la~kIl~~FDk~i~ 46 (106)
+.++|+..+=.-...-|++.+..|.+.|+.|..++..|-+...
T Consensus 297 la~~~R~eLh~if~~qi~~ai~~GeL~~e~Ak~Ll~~y~~~Q~ 339 (429)
T PF12297_consen 297 LAVFRRVELHEIFFEQIKSAIFKGELKPEAAKSLLQDYSKIQE 339 (429)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHH
Confidence 5677888888888899999999999999999999999876543
No 88
>COG2306 Predicted RNA-binding protein, associated with RNAses E/G family [General function prediction only]
Probab=29.36 E-value=1.5e+02 Score=22.68 Aligned_cols=31 Identities=19% Similarity=0.297 Sum_probs=23.1
Q ss_pred HHHHHHHHCCCCCHHHHHHHHHHHHHHHHHH
Q 033999 18 ETLDEMVQNGTLTPELAIQVLVQFDKSMTEA 48 (106)
Q Consensus 18 dtLdeli~~~~I~p~la~kIl~~FDk~i~~~ 48 (106)
|-|..-++.|.|||+++++-...-++.+.++
T Consensus 126 DEL~~Al~~GlIT~~qf~~Ay~~a~aVe~el 156 (183)
T COG2306 126 DELEDALRYGLITPEQFEKAYRTANAVEAEL 156 (183)
T ss_pred HHHHHHHHcCCCCHHHHHHHHHHHHHHHHHH
Confidence 3455556899999999998888776666554
No 89
>PF08360 TetR_C_5: QacR-like protein, C-terminal region; InterPro: IPR013571 This entry represents the C-terminal domain found in the multidrug-binding transcription regulator QacR (P23217 from SWISSPROT) from Staphylococcus aureus, which is a member of the TetR (tetracycline-resistance) transcriptional regulator family of proteins. QacR is able to bind various environmental agents, which include a number of cationic lipophilic compounds, and thus regulate the transcription of QacA (P23215 from SWISSPROT), a multidrug efflux pump []. The C-terminal region of QacR contains a multifaceted, expansive drug-binding pocket, which is composed of several separate, but linked, binding sites []. The C-terminal domains of QacR and TetR share a multi-helical, interlocking structure.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2G0E_E 1JUM_A 1RPW_D 1QVT_B 2HQ5_D 1JT0_B 2DTZ_E 1JUP_D 1JT6_D 1JUS_E ....
Probab=27.75 E-value=1.7e+02 Score=20.45 Aligned_cols=45 Identities=18% Similarity=0.251 Sum_probs=32.8
Q ss_pred hhHHHHHHHHHHHHHHCCCCCHHHHHHH---HHHHHHHHHHHHHhhcc
Q 033999 10 STIGMCLTETLDEMVQNGTLTPELAIQV---LVQFDKSMTEALETQVK 54 (106)
Q Consensus 10 stlG~aL~dtLdeli~~~~I~p~la~kI---l~~FDk~i~~~L~~~vk 54 (106)
..+=.-|..|.+|+..+..-+|+...++ ...|...+.+.|++-+.
T Consensus 32 ~~i~~pl~~a~~EF~~~~~~~~ev~~~l~~i~~~~~~~~~~ileeGI~ 79 (131)
T PF08360_consen 32 DDIQTPLSKAGEEFYSNQSKNPEVLEKLNEIRRKYLEFFQKILEEGID 79 (131)
T ss_dssp HSSSGGGHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred HHhccHHHHHHHHHHHcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344557889999999999999998888 45555566666666443
No 90
>TIGR02009 PGMB-YQAB-SF beta-phosphoglucomutase family hydrolase. All of these are members of the larger Haloacid dehalogenase (HAD) subfamily IA and include the "variant 3" glu-asp version of the third conserved HAD domain (TIGR01509).
Probab=27.64 E-value=1.5e+02 Score=20.36 Aligned_cols=44 Identities=20% Similarity=0.197 Sum_probs=32.8
Q ss_pred HHHhhhHHHHHHHHHHHHHHCC--CCCHHHHHHHHHHHHHHHHHHH
Q 033999 6 LYRRSTIGMCLTETLDEMVQNG--TLTPELAIQVLVQFDKSMTEAL 49 (106)
Q Consensus 6 lYR~stlG~aL~dtLdeli~~~--~I~p~la~kIl~~FDk~i~~~L 49 (106)
-|+....|....+.+.++.... .++++...++.+.|.+.+.+.+
T Consensus 37 ~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 82 (185)
T TIGR02009 37 QYNTSLGGLSREDILRAILKLRKPGLSLETIHQLAERKNELYRELL 82 (185)
T ss_pred HHHHHcCCCCHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHH
Confidence 4566778888888899888764 5788888888877776665554
No 91
>PLN02668 indole-3-acetate carboxyl methyltransferase
Probab=27.63 E-value=69 Score=26.81 Aligned_cols=22 Identities=27% Similarity=0.410 Sum_probs=18.8
Q ss_pred HHHHHHHHHHHHCCCCCHHHHH
Q 033999 14 MCLTETLDEMVQNGTLTPELAI 35 (106)
Q Consensus 14 ~aL~dtLdeli~~~~I~p~la~ 35 (106)
..|.++|++|+.+|.|+++-..
T Consensus 257 ~~l~~al~dlv~eGlI~eek~d 278 (386)
T PLN02668 257 THFQDAWDDLVQEGLVTSEKRD 278 (386)
T ss_pred HHHHHHHHHHHHcCCCCHHHHh
Confidence 3489999999999999998654
No 92
>TIGR01425 SRP54_euk signal recognition particle protein SRP54. This model represents examples from the eukaryotic cytosol of the signal recognition particle protein component, SRP54. This GTP-binding protein is a component of the eukaryotic signal recognition particle, along with several other protein subunits and a 7S RNA. Some species, including Arabidopsis, have several closely related forms. The extreme C-terminal region is glycine-rich and lower in complexity, poorly conserved between species, and excluded from this model.
Probab=27.61 E-value=1.4e+02 Score=25.36 Aligned_cols=37 Identities=19% Similarity=0.307 Sum_probs=31.9
Q ss_pred hHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHH
Q 033999 11 TIGMCLTETLDEMVQNGTLTPELAIQVLVQFDKSMTE 47 (106)
Q Consensus 11 tlG~aL~dtLdeli~~~~I~p~la~kIl~~FDk~i~~ 47 (106)
+||..|..++.-+-..+.|+++-....+++.-++.-+
T Consensus 4 ~L~~~l~~~~~~l~~~~~l~e~~i~~~l~ei~~aLle 40 (429)
T TIGR01425 4 DLGSSITSALRSMSNATVIDEEVLNAMLKEICTALLE 40 (429)
T ss_pred HHHHHHHHHHHHHhCCCccCHHHHHHHHHHHHHHHHH
Confidence 6899999999999999999999988888887666544
No 93
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=27.46 E-value=52 Score=21.47 Aligned_cols=16 Identities=19% Similarity=0.324 Sum_probs=13.6
Q ss_pred HHHHHHHHHHHHCCCC
Q 033999 14 MCLTETLDEMVQNGTL 29 (106)
Q Consensus 14 ~aL~dtLdeli~~~~I 29 (106)
..+.++|++|+.+|.|
T Consensus 80 ~~v~~al~~L~~eG~I 95 (102)
T PF08784_consen 80 NEVRKALDFLSNEGHI 95 (102)
T ss_dssp HHHHHHHHHHHHTTSE
T ss_pred HHHHHHHHHHHhCCeE
Confidence 4578899999999987
No 94
>cd01130 VirB11-like_ATPase Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to plant cells. The pilus is a fibrous cell surface organelle, which mediates adhesion between bacteria during conjugative transfer or between bacteria and host eukaryotic cells during infection. VirB11- related ATPases include the archaeal flagella biosynthesis protein and the pilus assembly proteins CpaF/TadA and TrbB. This alignment contains the C-terminal domain, which is the ATPase.
Probab=27.16 E-value=63 Score=23.19 Aligned_cols=21 Identities=29% Similarity=0.575 Sum_probs=17.2
Q ss_pred HHHHHHCCCCCHHHHHHHHHH
Q 033999 20 LDEMVQNGTLTPELAIQVLVQ 40 (106)
Q Consensus 20 Ldeli~~~~I~p~la~kIl~~ 40 (106)
||+|++.|-++|+++..+...
T Consensus 1 ~~~l~~~g~~~~~~~~~l~~~ 21 (186)
T cd01130 1 LDDLIAQGTFSPLQAAYLWLA 21 (186)
T ss_pred CHHHHHcCCCCHHHHHHHHHH
Confidence 689999999999987766543
No 95
>cd08785 CARD_CARD9-like Caspase activation and recruitment domain of CARD9 and related proteins. Caspase activation and recruitment domain (CARD) found in CARD9, CARD14 (CARMA2), CARD10 (CARMA3), CARD11 (CARMA1) and BCL10. BCL10 (B-cell lymphoma 10), together with Malt1 (mucosa-associated lymphoid tissue-lymphoma-translocation gene 1), are integral components of the CBM signalosome. They associate with CARD9 to form M-CBM (CBM complex in myeloid immune cells), and with CARD11 to form L-CBM (CBM complex in lymphoid immune cells), which mediates activation of NF-kB and MAPK by ITAM-coupled receptors expressed on immune cells. BCL10/Malt1 also associates with CARD10, which is more widely expressed and is not restricted to hematopoietic cells, to play a role in GPCR-induced NF-kB activation. CARD14 has also been shown to associate with BCL10. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inf
Probab=26.90 E-value=98 Score=20.47 Aligned_cols=24 Identities=17% Similarity=0.048 Sum_probs=21.2
Q ss_pred HHHHHHHHHCCCCCHHHHHHHHHH
Q 033999 17 TETLDEMVQNGTLTPELAIQVLVQ 40 (106)
Q Consensus 17 ~dtLdeli~~~~I~p~la~kIl~~ 40 (106)
.+.+|-|.+.|.++++-++.|..+
T Consensus 19 ~~l~d~L~q~~VLt~~d~EeI~~~ 42 (86)
T cd08785 19 SRLTPYLRQCKVLDEQDEEEVLSS 42 (86)
T ss_pred HHHHHHHHhcCCCCHHHHHHHhCC
Confidence 457899999999999999999873
No 96
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=26.90 E-value=1.4e+02 Score=17.31 Aligned_cols=45 Identities=16% Similarity=0.195 Sum_probs=27.9
Q ss_pred hhhHHHHhhhHHHHHHHHHHHHHHCC--CCCHHHHHHHHHHHHHHHHHHH
Q 033999 2 ATFELYRRSTIGMCLTETLDEMVQNG--TLTPELAIQVLVQFDKSMTEAL 49 (106)
Q Consensus 2 ~~y~lYR~stlG~aL~dtLdeli~~~--~I~p~la~kIl~~FDk~i~~~L 49 (106)
+.++|-|.+-+.. .+|..+.+.+ .++.+...+|-.-|+-.+.+.+
T Consensus 12 t~~~La~~~gis~---~tl~~~~~~~~~~~~~~~l~~ia~~l~~~~~el~ 58 (63)
T PF13443_consen 12 TQKDLARKTGISR---STLSRILNGKPSNPSLDTLEKIAKALNCSPEELF 58 (63)
T ss_dssp -HHHHHHHHT--H---HHHHHHHTTT-----HHHHHHHHHHHT--HHHCT
T ss_pred CHHHHHHHHCcCH---HHHHHHHhcccccccHHHHHHHHHHcCCCHHHHh
Confidence 3456666665554 5788888877 7899999999998888877654
No 97
>PRK00106 hypothetical protein; Provisional
Probab=26.71 E-value=1.5e+02 Score=26.04 Aligned_cols=44 Identities=18% Similarity=0.379 Sum_probs=28.8
Q ss_pred hHHHHhhhHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHh
Q 033999 4 FELYRRSTIGMCLTETLDEMVQNGTLTPELAIQVLVQFDKSMTEALET 51 (106)
Q Consensus 4 y~lYR~stlG~aL~dtLdeli~~~~I~p~la~kIl~~FDk~i~~~L~~ 51 (106)
|.-+|+-.- .-||..|+.+|+|.|.=...+.++--+-|.+.+.+
T Consensus 273 fdpvRReiA----r~~le~Li~dgrIhp~rIEe~v~k~~~e~~~~i~~ 316 (535)
T PRK00106 273 FDPIRREIA----RMTLESLIKDGRIHPARIEELVEKNRLEMDNRIRE 316 (535)
T ss_pred CChHHHHHH----HHHHHHHHHcCCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 455555432 45788999999999987766665555544444433
No 98
>cd03715 RT_ZFREV_like RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the intact endogenous retrovirus ZFERV from zebrafish and to Moloney murine leukemia virus RT. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs. Phylogenetic analysis suggests that ZFERV belongs to a distinct group of retroviruses.
Probab=26.51 E-value=46 Score=24.34 Aligned_cols=20 Identities=25% Similarity=0.458 Sum_probs=17.2
Q ss_pred HHHHHHHHHHHHHCCCCCHH
Q 033999 13 GMCLTETLDEMVQNGTLTPE 32 (106)
Q Consensus 13 G~aL~dtLdeli~~~~I~p~ 32 (106)
=.++.+.+++|+++|.|.|.
T Consensus 14 ~~~~~~~v~~ll~~G~I~~~ 33 (210)
T cd03715 14 REGITPHIQELLEAGILVPC 33 (210)
T ss_pred HHHHHHHHHHHHHCCCeECC
Confidence 35788999999999999875
No 99
>PF14237 DUF4339: Domain of unknown function (DUF4339)
Probab=26.40 E-value=42 Score=18.99 Aligned_cols=16 Identities=25% Similarity=0.713 Sum_probs=13.0
Q ss_pred HHHHHHHHHCCCCCHH
Q 033999 17 TETLDEMVQNGTLTPE 32 (106)
Q Consensus 17 ~dtLdeli~~~~I~p~ 32 (106)
.+.|.+|+++|.|+++
T Consensus 16 ~~el~~l~~~g~i~~~ 31 (45)
T PF14237_consen 16 LEELRQLISSGEIDPD 31 (45)
T ss_pred HHHHHHHHHcCCCCCC
Confidence 4678889999999875
No 100
>PRK08132 FAD-dependent oxidoreductase; Provisional
Probab=25.78 E-value=2.5e+02 Score=23.49 Aligned_cols=57 Identities=14% Similarity=0.194 Sum_probs=32.3
Q ss_pred HHHHHHHHHHhhcccceEEeeeCccceeeCcEEEEEEcCeEEEecc-eEeeeCeEEEEEecCCC
Q 033999 41 FDKSMTEALETQVKSKVSIKGHLHTYRFCDNVWTFILQDALFKSEE-LQETVGRVKIVACDSKL 103 (106)
Q Consensus 41 FDk~i~~~L~~~vk~k~~~KG~L~tYr~cDnVWtf~lkn~~~k~~~-~~~~~~~lKIVAcd~~~ 103 (106)
+++.+.+.+.+.-.-++.+.-.+..+...++-|+..+++. ++ .++.++.| |+|||..
T Consensus 127 le~~L~~~~~~~~~v~v~~~~~v~~i~~~~~~v~v~~~~~----~g~~~i~ad~v--VgADG~~ 184 (547)
T PRK08132 127 VEGYLVERAQALPNIDLRWKNKVTGLEQHDDGVTLTVETP----DGPYTLEADWV--IACDGAR 184 (547)
T ss_pred HHHHHHHHHHhCCCcEEEeCCEEEEEEEcCCEEEEEEECC----CCcEEEEeCEE--EECCCCC
Confidence 3444555554322223334445666777777777655431 22 36788865 8999864
No 101
>KOG3438 consensus DNA-directed RNA polymerase, subunit L [Transcription]
Probab=25.78 E-value=1.5e+02 Score=20.68 Aligned_cols=31 Identities=26% Similarity=0.397 Sum_probs=25.0
Q ss_pred hhHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHH
Q 033999 10 STIGMCLTETLDEMVQNGTLTPELAIQVLVQFDKSMTE 47 (106)
Q Consensus 10 stlG~aL~dtLdeli~~~~I~p~la~kIl~~FDk~i~~ 47 (106)
.+-=..|.++|+||.+ +-..|...|+++|.+
T Consensus 68 ~~A~evl~kgl~el~~-------~c~~v~~kF~~~i~~ 98 (105)
T KOG3438|consen 68 DPAVEVLKKGLEELMQ-------LCDHVRSKFEEEIEE 98 (105)
T ss_pred CcchHHHHHHHHHHHH-------HHHHHHHHHHHHHHH
Confidence 3444678999999986 788899999999875
No 102
>cd01720 Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D2 heterodimerizes with subunit D1 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing D2, D3, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=25.66 E-value=86 Score=20.74 Aligned_cols=26 Identities=12% Similarity=0.324 Sum_probs=20.7
Q ss_pred cccceEEeeeCccceeeCcEEEEEEcCeE
Q 033999 53 VKSKVSIKGHLHTYRFCDNVWTFILQDAL 81 (106)
Q Consensus 53 vk~k~~~KG~L~tYr~cDnVWtf~lkn~~ 81 (106)
.++...+.|.| +-+|..|.++|.|++
T Consensus 21 lr~~r~~~G~L---~~fD~hmNlvL~d~~ 46 (87)
T cd01720 21 CRNNKKLLGRV---KAFDRHCNMVLENVK 46 (87)
T ss_pred EcCCCEEEEEE---EEecCccEEEEcceE
Confidence 35667788888 567899999999974
No 103
>PTZ00150 phosphoglucomutase-2-like protein; Provisional
Probab=25.38 E-value=1.2e+02 Score=26.25 Aligned_cols=31 Identities=16% Similarity=0.336 Sum_probs=20.0
Q ss_pred HHHHHHHHHHHHHCCC-----------CCHHHHHHHHHHHHH
Q 033999 13 GMCLTETLDEMVQNGT-----------LTPELAIQVLVQFDK 43 (106)
Q Consensus 13 G~aL~dtLdeli~~~~-----------I~p~la~kIl~~FDk 43 (106)
|.+|.+.|+|+-++-- ..++...+++..+..
T Consensus 436 g~sL~e~l~~l~~~~G~~~~~~~~~~~~~~~~~~~~~~~l~~ 477 (584)
T PTZ00150 436 GKTLVEHLESLYKQYGYHFTNNSYYICYDPSRIVSIFNDIRN 477 (584)
T ss_pred CCCHHHHHHHHHHHHCCCccceeeEecCCHHHHHHHHHHHhc
Confidence 6778888888765431 245666677776654
No 104
>COG0330 HflC Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]
Probab=25.25 E-value=1.1e+02 Score=23.46 Aligned_cols=41 Identities=22% Similarity=0.370 Sum_probs=25.8
Q ss_pred HHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHhhcccceEEeeeCccceeeCcEEEEEEcCeEEEec
Q 033999 18 ETLDEMVQNGTLTPELAIQVLVQFDKSMTEALETQVKSKVSIKGHLHTYRFCDNVWTFILQDALFKSE 85 (106)
Q Consensus 18 dtLdeli~~~~I~p~la~kIl~~FDk~i~~~L~~~vk~k~~~KG~L~tYr~cDnVWtf~lkn~~~k~~ 85 (106)
-+|||+++++. ..+...|.+.-|..+.. |-+.+.|+.++.-
T Consensus 129 ~~~~e~~~~~~--~~i~~~i~~~l~~~~~~-------------------------~Gi~V~~V~i~~i 169 (291)
T COG0330 129 MTLDELLTERR--AEINAKIREILDEAADP-------------------------WGIKVVDVEIKDI 169 (291)
T ss_pred ccHHHHhhCch--HHHHHHHHHHHHHhhhh-------------------------cCcEEEEEEEeec
Confidence 56777777776 44444544444444433 8888888888753
No 105
>TIGR02148 Fibro_Slime fibro-slime domain. This model represents a conserved region of about 90 amino acids, shared in at least 4 distinct large putative proteins from the slime mold Dictyostelium discoideum and 10 proteins from the rumen bacterium Fibrobacter succinogenes, and in no other species so far. We propose here the name fibro-slime domain
Probab=25.21 E-value=44 Score=22.71 Aligned_cols=25 Identities=28% Similarity=0.551 Sum_probs=16.7
Q ss_pred eeCccceeeCcEEEEEEcCeEEEec
Q 033999 61 GHLHTYRFCDNVWTFILQDALFKSE 85 (106)
Q Consensus 61 G~L~tYr~cDnVWtf~lkn~~~k~~ 85 (106)
|.--+++=-|+||.|+=.-..+.+.
T Consensus 19 ~e~F~F~GDDDvWVFIn~kLv~DlG 43 (90)
T TIGR02148 19 GQYFEFRGDDDVWVFINNKLVVDIG 43 (90)
T ss_pred CcEEEEEcCCeEEEEECCEEEEEcc
Confidence 3343445579999999666666655
No 106
>COG5251 TAF40 Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=25.16 E-value=36 Score=26.06 Aligned_cols=35 Identities=26% Similarity=0.550 Sum_probs=30.4
Q ss_pred ChhhHHHHhhhHHHHHHHHHHHHHHCCCCCHHHHH
Q 033999 1 MATFELYRRSTIGMCLTETLDEMVQNGTLTPELAI 35 (106)
Q Consensus 1 m~~y~lYR~stlG~aL~dtLdeli~~~~I~p~la~ 35 (106)
|.-||.+|++++-++=..-|..=|-.+-++|..+-
T Consensus 105 ~~RyEvFrrt~lnKt~VKKlastV~nQtVspNi~I 139 (199)
T COG5251 105 TNRYEVFRRTSLNKTQVKKLASTVANQTVSPNIRI 139 (199)
T ss_pred HHHHHHHHhcCCCHHHHHHHHHHHhccccCCCeee
Confidence 34699999999999999999999999999998653
No 107
>COG1542 Uncharacterized conserved protein [Function unknown]
Probab=24.90 E-value=52 Score=28.98 Aligned_cols=27 Identities=30% Similarity=0.487 Sum_probs=23.3
Q ss_pred HHhhhHHHHHHHHHHHHHHCCCCCHHH
Q 033999 7 YRRSTIGMCLTETLDEMVQNGTLTPEL 33 (106)
Q Consensus 7 YR~stlG~aL~dtLdeli~~~~I~p~l 33 (106)
|--|--|.+|.+++.|||..|.|+|+-
T Consensus 54 ~~lT~aGk~l~elv~d~Id~~~ipPee 80 (593)
T COG1542 54 YILTEAGKKLMELVADMIDLGKIPPEE 80 (593)
T ss_pred eeehHhHHHHHHHHHHHHhhccCChhh
Confidence 444667999999999999999999874
No 108
>cd07367 CarBb CarBb is the B subunit of the Class III Extradiol ring-cleavage dioxygenase, 2-aminophenol 1,6-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 2-aminophenyl-2,3-diol. CarBb is the B subunit of 2-aminophenol 1,6-dioxygenase (CarB), which catalyzes the oxidization and subsequent ring-opening of 2-aminophenyl-2,3-diol. It is a key enzyme in the carbazole degradation pathway isolated from bacterial strains with carbazole degradation ability. The enzyme is a heterotetramer composed of two A and two B subunits. CarB belongs to the class III extradiol dioxygenase family, a group of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Although the enzyme was originally isolated as a meta-cleavage enzyme for 2'-aminobiphenyl-2,3-diol involved in carbazole degradation, it has also shown high specificity for 2,3-dihydroxybiphenyl.
Probab=24.84 E-value=36 Score=26.53 Aligned_cols=44 Identities=25% Similarity=0.363 Sum_probs=33.2
Q ss_pred HhhhHHHHHHHHHHH---------HHHCCCCCHHH----HHHHHHHHHHHHHHHHHh
Q 033999 8 RRSTIGMCLTETLDE---------MVQNGTLTPEL----AIQVLVQFDKSMTEALET 51 (106)
Q Consensus 8 R~stlG~aL~dtLde---------li~~~~I~p~l----a~kIl~~FDk~i~~~L~~ 51 (106)
|.-.+|++|.+++++ +|-+|-+|-++ ...+-.+||+.+.+.|.+
T Consensus 151 ~~~~lG~al~~~i~~~~~~d~rV~iiaSGgLSH~l~~~~~~~~~~efD~~i~~~l~~ 207 (268)
T cd07367 151 RCWALGKVLAQYVEKRRPAGERVAVIAAGGLSHWLGVPRHGEVNEAFDRMFLDLLEG 207 (268)
T ss_pred HHHHHHHHHHHHHHhcCCCCCcEEEEEcccccCCCCCCcccccCHHHHHHHHHHHHc
Confidence 334699999999888 55667777666 223457999999999877
No 109
>PF12550 GCR1_C: Transcriptional activator of glycolytic enzymes; InterPro: IPR022210 This domain family is found in eukaryotes, and is approximately 80 amino acids in length. This family is activates the transcription of glycolytic enzymes.
Probab=24.55 E-value=1.5e+02 Score=18.83 Aligned_cols=29 Identities=14% Similarity=0.337 Sum_probs=23.7
Q ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHHHHH
Q 033999 13 GMCLTETLDEMVQNGTLTPELAIQVLVQF 41 (106)
Q Consensus 13 G~aL~dtLdeli~~~~I~p~la~kIl~~F 41 (106)
-.++.+.+..+....-++++.|-.+++.+
T Consensus 52 RK~Ii~~I~~l~~~~g~~~~~ai~~le~~ 80 (81)
T PF12550_consen 52 RKVIIDFIERLANERGISEEEAIEILEEI 80 (81)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHhc
Confidence 46778888888888889999998888765
No 110
>PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed
Probab=24.32 E-value=2.1e+02 Score=23.50 Aligned_cols=40 Identities=20% Similarity=0.498 Sum_probs=30.8
Q ss_pred HHHHHHHHHHHhhcccceEEeeeCccceee-CcEEEEEEcCe
Q 033999 40 QFDKSMTEALETQVKSKVSIKGHLHTYRFC-DNVWTFILQDA 80 (106)
Q Consensus 40 ~FDk~i~~~L~~~vk~k~~~KG~L~tYr~c-DnVWtf~lkn~ 80 (106)
++-..|...|... -..+.++|.+..++.- -+-|.|.|||-
T Consensus 10 el~~~ik~~le~~-~~~v~v~gEis~~~~~~sGH~Yf~Lkd~ 50 (438)
T PRK00286 10 ELNRYVKSLLERD-LGQVWVRGEISNFTRHSSGHWYFTLKDE 50 (438)
T ss_pred HHHHHHHHHHHhh-CCcEEEEEEeCCCeeCCCCeEEEEEEcC
Confidence 4445566666665 6788999999999876 57899999985
No 111
>PF08004 DUF1699: Protein of unknown function (DUF1699); InterPro: IPR012546 This family contains many archaeal proteins which have very conserved sequences.
Probab=24.25 E-value=47 Score=24.05 Aligned_cols=28 Identities=18% Similarity=0.331 Sum_probs=20.6
Q ss_pred HHHHHHHHHHHHHHCCCCCHHHHHHHHH
Q 033999 12 IGMCLTETLDEMVQNGTLTPELAIQVLV 39 (106)
Q Consensus 12 lG~aL~dtLdeli~~~~I~p~la~kIl~ 39 (106)
=|.+-.++.+++-.+.+++|++...|+.
T Consensus 103 eG~s~eei~~ki~~e~kl~pd~i~yi~~ 130 (131)
T PF08004_consen 103 EGKSEEEIAEKISRETKLSPDMIKYILK 130 (131)
T ss_pred cCCCHHHHHHHHHHhhcCCHHHHHHHhc
Confidence 3667777777777777888887777664
No 112
>PF09687 PRESAN: Plasmodium RESA N-terminal; InterPro: IPR019111 The short, four-helical domain first identified in the Plasmodium export proteins PHISTa and PHISTc [] has been extended to become this six-helical PRESAC domain identified in the P. falciparum-specific RESA-type (Ring-infected erythrocyte surface antigen) proteins in association with the DnaJ domain. Overall, at least 67 proteins have been detected in P. falciparum with complete copies of the PRESAC domain. No versions of this domain were detected in other apicomplexan genera, suggesting that the domain was 'invented' after the divergence of the lineage leading to the genus Plasmodium undergoing a dramatic proliferation only in P. falciparum. A secondary structure-prediction derived from the multiple alignment of the PRESAC family reveals that it is composed of an all-helical fold with six conserved helical segments. There is some evidence it might localise to membranes [].
Probab=24.23 E-value=2.1e+02 Score=18.54 Aligned_cols=41 Identities=12% Similarity=0.161 Sum_probs=36.6
Q ss_pred hHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHh
Q 033999 11 TIGMCLTETLDEMVQNGTLTPELAIQVLVQFDKSMTEALET 51 (106)
Q Consensus 11 tlG~aL~dtLdeli~~~~I~p~la~kIl~~FDk~i~~~L~~ 51 (106)
.+-.-|-..+++|.....||++...++|.+.-..|...|.+
T Consensus 44 ~m~~~L~~~~~~la~~~~ip~~~~~k~W~~c~~~i~~~l~~ 84 (129)
T PF09687_consen 44 DMINKLWKYFEELAKKYNIPEEYKKKIWKECYEEITKELKK 84 (129)
T ss_pred HHHHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHHHHHH
Confidence 35567888999999999999999999999999999988876
No 113
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.06 E-value=85 Score=22.34 Aligned_cols=20 Identities=30% Similarity=0.592 Sum_probs=16.1
Q ss_pred HHHHHHCCCCCHHHHHHHHH
Q 033999 20 LDEMVQNGTLTPELAIQVLV 39 (106)
Q Consensus 20 Ldeli~~~~I~p~la~kIl~ 39 (106)
+-++++.|.|+|+-|.++|.
T Consensus 102 i~~qle~Gei~peeA~~~L~ 121 (122)
T COG3877 102 IIDQLEKGEISPEEAIKMLN 121 (122)
T ss_pred HHHHHHcCCCCHHHHHHHhc
Confidence 34456789999999999885
No 114
>PF14793 DUF4478: Domain of unknown function (DUF4478); PDB: 2PMB_D 3GH1_D 3BQ9_B.
Probab=24.05 E-value=49 Score=23.37 Aligned_cols=12 Identities=17% Similarity=0.725 Sum_probs=9.4
Q ss_pred hhHHHHhhhHHH
Q 033999 3 TFELYRRSTIGM 14 (106)
Q Consensus 3 ~y~lYR~stlG~ 14 (106)
.|+|||++++..
T Consensus 30 ly~LfR~CsLAV 41 (112)
T PF14793_consen 30 LYQLFRNCSLAV 41 (112)
T ss_dssp HHHHHHHHHHHH
T ss_pred HHHHHHhhHHHH
Confidence 589999998753
No 115
>PF01423 LSM: LSM domain ; InterPro: IPR001163 This family is found in Lsm (like-Sm) proteins and in bacterial Lsm-related Hfq proteins. In each case, the domain adopts a core structure consisting of an open beta-barrel with an SH3-like topology. Lsm (like-Sm) proteins have diverse functions, and are thought to be important modulators of RNA biogenesis and function [, ]. The Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6) []. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker []. In other snRNPs, certain Sm proteins are replaced with different Lsm proteins, such as with U7 snRNPs, in which the D1 and D2 Sm proteins are replaced with U7-specific Lsm10 and Lsm11 proteins, where Lsm11 plays a role in histone U7-specific RNA processing []. Lsm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Lsm proteins. The pleiotropic translational regulator Hfq (host factor Q) is a bacterial Lsm-like protein, which modulates the structure of numerous RNA molecules by binding preferentially to A/U-rich sequences in RNA []. Hfq forms an Lsm-like fold, however, unlike the heptameric Sm proteins, Hfq forms a homo-hexameric ring.; PDB: 1D3B_K 2Y9D_D 2Y9A_D 2Y9C_R 3VRI_C 2Y9B_K 3QUI_D 3M4G_H 3INZ_E 1U1S_C ....
Probab=23.94 E-value=1.7e+02 Score=17.38 Aligned_cols=30 Identities=20% Similarity=0.263 Sum_probs=23.9
Q ss_pred ccceEEeeeCccceeeCcEEEEEEcCeEEEecc
Q 033999 54 KSKVSIKGHLHTYRFCDNVWTFILQDALFKSEE 86 (106)
Q Consensus 54 k~k~~~KG~L~tYr~cDnVWtf~lkn~~~k~~~ 86 (106)
++...+.|.| ..+|+-|...++|+.....+
T Consensus 16 ~~g~~~~G~L---~~~D~~~Nl~L~~~~~~~~~ 45 (67)
T PF01423_consen 16 KNGRTYRGTL---VSFDQFMNLVLSDVTETIKN 45 (67)
T ss_dssp TTSEEEEEEE---EEEETTEEEEEEEEEEEETT
T ss_pred eCCEEEEEEE---EEeechheEEeeeEEEEECC
Confidence 4566677877 45688999999999998775
No 116
>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ. Members of this protein family are predicted ATPases associated with plasmid transfer loci in bacteria. This family is most similar to the DotB ATPase of a type-IV secretion-like system of obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii (TIGR02524).
Probab=23.91 E-value=73 Score=26.31 Aligned_cols=26 Identities=19% Similarity=0.213 Sum_probs=22.7
Q ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHH
Q 033999 13 GMCLTETLDEMVQNGTLTPELAIQVL 38 (106)
Q Consensus 13 G~aL~dtLdeli~~~~I~p~la~kIl 38 (106)
|.++.+.+.+|+.+|.|+++.+.+++
T Consensus 342 ~~~~~~~~~~l~~~g~i~~~~~~~~~ 367 (372)
T TIGR02525 342 QRRIADQAWAMHQEGRIDEREAAEVI 367 (372)
T ss_pred CCCHHHHHHHHHHcCCCCHHHHHHHh
Confidence 56777888999999999999998876
No 117
>COG0541 Ffh Signal recognition particle GTPase [Intracellular trafficking and secretion]
Probab=23.90 E-value=1.8e+02 Score=25.12 Aligned_cols=39 Identities=18% Similarity=0.317 Sum_probs=33.0
Q ss_pred hhHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHH
Q 033999 10 STIGMCLTETLDEMVQNGTLTPELAIQVLVQFDKSMTEA 48 (106)
Q Consensus 10 stlG~aL~dtLdeli~~~~I~p~la~kIl~~FDk~i~~~ 48 (106)
.+||..|.++|.-+...+.|+++....++.+-.+|.-++
T Consensus 3 e~L~~~l~~~l~kl~g~~~i~E~~i~e~~reir~ALLeA 41 (451)
T COG0541 3 ESLSDRLSNALKKLRGKGRITEKDVKEALREIRRALLEA 41 (451)
T ss_pred HHHHHHHHHHHHHhhCCCcCCHHHHHHHHHHHHHHHHhc
Confidence 368999999999999999999999888887777666554
No 118
>PF11833 DUF3353: Protein of unknown function (DUF3353); InterPro: IPR021788 This family of proteins are functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 205 to 258 amino acids in length.
Probab=23.85 E-value=2.3e+02 Score=21.33 Aligned_cols=49 Identities=10% Similarity=0.177 Sum_probs=40.8
Q ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHhhcccceEEeeeC
Q 033999 15 CLTETLDEMVQNGTLTPELAIQVLVQFDKSMTEALETQVKSKVSIKGHL 63 (106)
Q Consensus 15 aL~dtLdeli~~~~I~p~la~kIl~~FDk~i~~~L~~~vk~k~~~KG~L 63 (106)
..++|=+.++++..=.++...+|=.-||+.+.+-|+.|.+.|++++-.+
T Consensus 8 EIq~Arn~ll~~y~gd~~~~~~IEaAYD~ILM~rL~~Rq~Gki~v~~~i 56 (194)
T PF11833_consen 8 EIQAARNRLLAQYAGDEKSREAIEAAYDAILMERLRQRQKGKIKVPERI 56 (194)
T ss_pred HHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHcCCCCccHHH
Confidence 3566777788888888999999999999999999999998888665443
No 119
>COG2137 OraA Uncharacterized protein conserved in bacteria [General function prediction only]
Probab=23.80 E-value=1.3e+02 Score=22.40 Aligned_cols=35 Identities=17% Similarity=0.208 Sum_probs=26.8
Q ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHh
Q 033999 16 LTETLDEMVQNGTLTPELAIQVLVQFDKSMTEALET 51 (106)
Q Consensus 16 L~dtLdeli~~~~I~p~la~kIl~~FDk~i~~~L~~ 51 (106)
=.-...+|.+.| |+++....+|+.+|..--.....
T Consensus 87 ~~rl~qeL~qkG-i~~~~Ie~aL~~~~~~~~~~~a~ 121 (174)
T COG2137 87 PARLKQELKQKG-IDDEIIEEALELIDEEDEQERAR 121 (174)
T ss_pred hHHHHHHHHHcC-CCHHHHHHHHhccchHHHHHHHH
Confidence 345678999999 99999999999777665444333
No 120
>PRK08486 single-stranded DNA-binding protein; Provisional
Probab=23.67 E-value=1.9e+02 Score=21.61 Aligned_cols=37 Identities=24% Similarity=0.259 Sum_probs=27.5
Q ss_pred HHHHHhhc--ccceEEeeeCccceeeCc------EEEEEEcCeEE
Q 033999 46 TEALETQV--KSKVSIKGHLHTYRFCDN------VWTFILQDALF 82 (106)
Q Consensus 46 ~~~L~~~v--k~k~~~KG~L~tYr~cDn------VWtf~lkn~~~ 82 (106)
.+.+.+++ .+++.+.|.|.+-++.|. .|.+++..+.|
T Consensus 60 AE~~~~~l~KG~~V~VeGrL~~~~y~dkdG~~r~~~eI~a~~v~~ 104 (182)
T PRK08486 60 AEIANQYLSKGSKVLIEGRLTFESWMDQNGQKRSKHTITAESMQM 104 (182)
T ss_pred HHHHHHHcCCCCEEEEEEEEEeCcEECCCCcEEEEEEEEEeEEEE
Confidence 45566643 589999999988888775 77777777765
No 121
>PF02885 Glycos_trans_3N: Glycosyl transferase family, helical bundle domain Prosite entry for Thymidine and pyrimidine-nucleoside phosphorylases; InterPro: IPR017459 The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates (2.4.1.- from EC) and related proteins into distinct sequence based families has been described []. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'. The glycosyl transferase family includes anthranilate phosphoribosyltransferase (TrpD, 2.4.2.18 from EC) and thymidine phosphorylase (2.4.2.2 from EC). All these proteins can transfer a phosphorylated ribose substrate. Thymidine phosphorylase (2.4.2.2 from EC) catalyses the reversible phosphorolysis of thymidine, deoxyuridine and their analogues to their respective bases and 2-deoxyribose 1-phosphate. This enzyme regulates the availability of thymidine and is therefore essential to nucleic acid metabolism. This N-terminal domain is found in various family 3 glycosyl transferases, including anthranilate phosphoribosyltransferase (TrpD, 2.4.2.18 from EC) and thymidine phosphorylase (2.4.2.2 from EC). All these proteins can transfer a phosphorylated ribose substrate. Thymidine phosphorylase catalyses the reversible phosphorolysis of thymidine, deoxyuridine and their analogues to their respective bases and 2-deoxyribose 1-phosphate. This enzyme regulates the availability of thymidine and is therefore essential to nucleic acid metabolism.; PDB: 2DSJ_B 2ELC_B 2BPQ_A 1ZVW_B 3QR9_B 1V8G_B 2WK5_C 2J0F_C 2WK6_B 1UOU_A ....
Probab=23.61 E-value=1.5e+02 Score=17.96 Aligned_cols=25 Identities=20% Similarity=0.234 Sum_probs=13.3
Q ss_pred HHHHHHHHHHCCCCCHHHHHHHHHH
Q 033999 16 LTETLDEMVQNGTLTPELAIQVLVQ 40 (106)
Q Consensus 16 L~dtLdeli~~~~I~p~la~kIl~~ 40 (106)
+.+.|..+.+...+|++.+..++..
T Consensus 2 ~~~~l~~l~~g~~Ls~~e~~~~~~~ 26 (66)
T PF02885_consen 2 IKEILKKLRDGEDLSREEAKAAFDA 26 (66)
T ss_dssp HHHHHHHHHTT----HHHHHHHHHH
T ss_pred HHHHHHHHHcCCCCCHHHHHHHHHH
Confidence 4566777777777777766665543
No 122
>cd01650 RT_nLTR_like RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.
Probab=23.55 E-value=1.2e+02 Score=21.57 Aligned_cols=70 Identities=13% Similarity=0.124 Sum_probs=44.2
Q ss_pred HCCCCCHHHHHHHHHHHHHHHHHHHHhhcccceEEeeeCccceeeCcEEEEEEcCeE--EE--ec---------ceEeee
Q 033999 25 QNGTLTPELAIQVLVQFDKSMTEALETQVKSKVSIKGHLHTYRFCDNVWTFILQDAL--FK--SE---------ELQETV 91 (106)
Q Consensus 25 ~~~~I~p~la~kIl~~FDk~i~~~L~~~vk~k~~~KG~L~tYr~cDnVWtf~lkn~~--~k--~~---------~~~~~~ 91 (106)
|...++|-|+.-.+..+|..+.+... ...-...+...+|.||+=. ..++.. +. .+ +-.++.
T Consensus 109 QG~~lSp~l~~l~~~~l~~~~~~~~~-----~~~~~~~~~~~~yaDD~~i-~~~~~~~~~~~~~~~~~~~~~~~gl~in~ 182 (220)
T cd01650 109 QGDPLSPLLFNLALDDLLRLLNKEEE-----IKLGGPGITHLAYADDIVL-FSEGKSRKLQELLQRLQEWSKESGLKINP 182 (220)
T ss_pred cCCcccHHHHHHHHHHHHHHHHhhcc-----ccCCCCccceEEeccceee-eccCCHHHHHHHHHHHHHHHHHcCCEECh
Confidence 45579999999999999998876654 1112234667889998754 344443 11 00 124666
Q ss_pred CeEEEEEec
Q 033999 92 GRVKIVACD 100 (106)
Q Consensus 92 ~~lKIVAcd 100 (106)
+|-+++...
T Consensus 183 ~Kt~~~~~~ 191 (220)
T cd01650 183 SKSKVMLIG 191 (220)
T ss_pred hheEEEEec
Confidence 777776554
No 123
>TIGR01420 pilT_fam pilus retraction protein PilT. This model represents the PilT subfamily of proteins related to GspE, a protein involved in type II secretion (also called the General Secretion Pathway). PilT is an apparent cytosolic ATPase associated with type IV pilus systems. It is not required for pilin biogenesis, but is required for twitching motility and social gliding behaviors, shown in some species, powered by pilus retraction. Members of this family may be found in some species that type IV pili but have related structures for DNA uptake and natural transformation.
Probab=23.46 E-value=91 Score=24.94 Aligned_cols=26 Identities=19% Similarity=0.277 Sum_probs=22.4
Q ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHH
Q 033999 13 GMCLTETLDEMVQNGTLTPELAIQVL 38 (106)
Q Consensus 13 G~aL~dtLdeli~~~~I~p~la~kIl 38 (106)
|.+|.+.+.+++.+|.|+++-+.++.
T Consensus 313 ~~t~~~~~~~~~~~g~~~~~~~~~~~ 338 (343)
T TIGR01420 313 MQTFDQHLAQLYRKGLITLEDALEAA 338 (343)
T ss_pred ChhHHHHHHHHHHcCCCCHHHHHHhc
Confidence 47899999999999999999887754
No 124
>PF05258 DUF721: Protein of unknown function (DUF721); InterPro: IPR007922 This family contains several actinomycete proteins of unknown function, and related sequences from other species.
Probab=22.90 E-value=1.7e+02 Score=17.84 Aligned_cols=40 Identities=10% Similarity=0.214 Sum_probs=26.2
Q ss_pred HHHHHHHHHHCCC-C-CHHHHHHHHHHHHHHHHHHHHhhccc
Q 033999 16 LTETLDEMVQNGT-L-TPELAIQVLVQFDKSMTEALETQVKS 55 (106)
Q Consensus 16 L~dtLdeli~~~~-I-~p~la~kIl~~FDk~i~~~L~~~vk~ 55 (106)
|.+.|++++.... . ......++...+...+...++++.+.
T Consensus 2 l~~~L~~~~~~~~~~~~~~~~~~l~~~w~~ivg~~l~~~~~~ 43 (89)
T PF05258_consen 2 LGDLLEELLKKSGLKKRALQLARLQQNWKQIVGPELAQHTRP 43 (89)
T ss_pred HHHHHHHHHhhhhHHHhhHHHHHHHHHHHHHhCHHHHccEEE
Confidence 4566666664433 3 45556777888888888888876543
No 125
>TIGR01201 HU_rel DNA-binding protein, histone-like, putative. This model describes a set of proteins related to but longer than DNA-binding protein HU. Its distinctive domain architecture compared to HU and related histone-like DNA-binding proteins justifies the designation as superfamily. Members include, so far, one from Bacteroides fragilis, a gut bacterium, and ten from Porphyromonas gingivalis, an oral anaerobe.
Probab=22.83 E-value=2e+02 Score=20.37 Aligned_cols=38 Identities=11% Similarity=0.229 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHh
Q 033999 14 MCLTETLDEMVQNGTLTPELAIQVLVQFDKSMTEALET 51 (106)
Q Consensus 14 ~aL~dtLdeli~~~~I~p~la~kIl~~FDk~i~~~L~~ 51 (106)
+.+.+..+.+-+...+|+..+..||+.+=..|.+.|++
T Consensus 31 mt~~el~~~Ia~~s~~s~~dv~~vl~~l~~~i~~~L~~ 68 (145)
T TIGR01201 31 IDFEEIAELIAEESSLSPGDVKGIIDRLAYVLRRELAN 68 (145)
T ss_pred cCHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHhC
Confidence 34555555566667799999999999999999999987
No 126
>COG2445 Uncharacterized conserved protein [Function unknown]
Probab=22.61 E-value=1.3e+02 Score=21.65 Aligned_cols=21 Identities=24% Similarity=0.458 Sum_probs=16.6
Q ss_pred HHHHHHHHHCCCCCHHHHHHH
Q 033999 17 TETLDEMVQNGTLTPELAIQV 37 (106)
Q Consensus 17 ~dtLdeli~~~~I~p~la~kI 37 (106)
.+.++.|.++|.|+++.+..+
T Consensus 68 ~d~~~~L~~~gvi~~e~~e~L 88 (138)
T COG2445 68 DDCIDILVEEGVIPEEEAEEL 88 (138)
T ss_pred HHHHHHHHHcCCCCHHHHHHH
Confidence 467888999999999877543
No 127
>PF10689 DUF2496: Protein of unknown function (DUF2496); InterPro: IPR019630 This family consists of proteins from Gammaproteobacteria species. Many members are annotated as being like the Escherichia coli protein; YbaM.
Probab=22.47 E-value=1.8e+02 Score=17.27 Aligned_cols=25 Identities=24% Similarity=0.332 Sum_probs=20.0
Q ss_pred HHHHHHHHHHHCCCCCHHHHHHHHH
Q 033999 15 CLTETLDEMVQNGTLTPELAIQVLV 39 (106)
Q Consensus 15 aL~dtLdeli~~~~I~p~la~kIl~ 39 (106)
.|.--|-.|.+++.|.|+.+.+-|+
T Consensus 10 kLAVDLI~LLE~n~i~p~~aL~ALe 34 (44)
T PF10689_consen 10 KLAVDLIYLLESNEIDPETALAALE 34 (44)
T ss_pred HHHHHHHHHHHhcCCCHHHHHHHHH
Confidence 4555677899999999999987665
No 128
>PRK03839 putative kinase; Provisional
Probab=22.43 E-value=2.8e+02 Score=19.37 Aligned_cols=58 Identities=24% Similarity=0.294 Sum_probs=28.7
Q ss_pred hhhHHHHHHHHH-------HHHHHCCCCCHHHHHHHHHHHHHHHHHHHHhhcccceEEeeeCccc
Q 033999 9 RSTIGMCLTETL-------DEMVQNGTLTPELAIQVLVQFDKSMTEALETQVKSKVSIKGHLHTY 66 (106)
Q Consensus 9 ~stlG~aL~dtL-------deli~~~~I~p~la~kIl~~FDk~i~~~L~~~vk~k~~~KG~L~tY 66 (106)
.||+|..|.+.| |+++....+........-..|+..-..+.+..-...+-+-|.+...
T Consensus 13 KsT~~~~La~~~~~~~id~d~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~vIidG~~~~l 77 (180)
T PRK03839 13 KTTVSKLLAEKLGYEYVDLTEFALKKGIGEEKDDEMEIDFDKLAYFIEEEFKEKNVVLDGHLSHL 77 (180)
T ss_pred HHHHHHHHHHHhCCcEEehhhhhhhcCCcccCChhhhcCHHHHHHHHHHhccCCCEEEEeccccc
Confidence 488999998884 7777654333221111122344333333222123346667765443
No 129
>PRK13358 protocatechuate 4,5-dioxygenase subunit beta; Provisional
Probab=22.41 E-value=55 Score=25.25 Aligned_cols=41 Identities=22% Similarity=0.426 Sum_probs=30.0
Q ss_pred hHHHHHHHHHHH---------HHHCCCCCHHHH----HHHHHHHHHHHHHHHHh
Q 033999 11 TIGMCLTETLDE---------MVQNGTLTPELA----IQVLVQFDKSMTEALET 51 (106)
Q Consensus 11 tlG~aL~dtLde---------li~~~~I~p~la----~kIl~~FDk~i~~~L~~ 51 (106)
.+|.+|.+++++ +|-+|-+|-.+. .-.-++||+.+.+.+.+
T Consensus 154 ~lG~al~~~~~~~~~~~~rvlvIaSGdlSH~l~~~~~~~~~~~fD~~~~~~i~~ 207 (269)
T PRK13358 154 ALGEVIRQAVEKDRPADERVAVIGTGGLSHWLGVPEHGEVNEDFDRMVMDALVS 207 (269)
T ss_pred HHHHHHHHHHHhhCCCCCcEEEEecCCccCCCCCccccccHHHHHHHHHHHHHc
Confidence 499999999987 455565554433 33467999999999876
No 130
>PF15467 SGIII: Secretogranin-3
Probab=22.21 E-value=2.3e+02 Score=24.21 Aligned_cols=43 Identities=28% Similarity=0.390 Sum_probs=37.3
Q ss_pred hHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHhhc
Q 033999 11 TIGMCLTETLDEMVQNGTLTPELAIQVLVQFDKSMTEALETQV 53 (106)
Q Consensus 11 tlG~aL~dtLdeli~~~~I~p~la~kIl~~FDk~i~~~L~~~v 53 (106)
||=.+|.|-.--|+.-|-|||+-.---|++.|.-|.-.-++++
T Consensus 291 TIMKTLIDFVKMMVKYGTItPEEGVsYLENLD~mIAlQtknKL 333 (453)
T PF15467_consen 291 TIMKTLIDFVKMMVKYGTITPEEGVSYLENLDAMIALQTKNKL 333 (453)
T ss_pred HHHHHHHHHHHHHHHhcCcChhhhhHHHHhHHHHHHHHHhhhh
Confidence 6788899999999999999999999999999998876555544
No 131
>PF05609 LAP1C: Lamina-associated polypeptide 1C (LAP1C); InterPro: IPR008662 This entry contains Rattus norvegicus LAP1C proteins and several uncharacterised highly related sequences from both Mus sp. and humans. Lamina-associated polypeptide 1s (LAP1s), also known as Torsin-1A-interacting protein 1, are type 2 integral membrane proteins with a single membrane-spanning region of the inner nuclear membrane []. LAP1s bind to both A- and B-type lamins and have a putative role in the membrane attachment and assembly of the nuclear lamina [].
Probab=22.05 E-value=68 Score=27.69 Aligned_cols=42 Identities=24% Similarity=0.454 Sum_probs=29.8
Q ss_pred CHHHHHHHHHHHHHHHHHHHHhhcccceE-----E--eeeCccceeeCc
Q 033999 30 TPELAIQVLVQFDKSMTEALETQVKSKVS-----I--KGHLHTYRFCDN 71 (106)
Q Consensus 30 ~p~la~kIl~~FDk~i~~~L~~~vk~k~~-----~--KG~L~tYr~cDn 71 (106)
....+..|...+|..+..+|.+..+.-+. + ...|.-|+||||
T Consensus 332 ~~~dsd~vK~~vD~~l~~~f~~~~~aavv~~~e~lpp~stlify~YCD~ 380 (465)
T PF05609_consen 332 AHQDSDQVKLEVDNELSSGFENGQKAAVVHRFESLPPGSTLIFYKYCDH 380 (465)
T ss_pred cccChHHHHHHHHHHHHHHhhCCCeeEEeehhhhCCCchhHHHHHhccC
Confidence 34567788899999999999873322221 1 245889999998
No 132
>smart00049 DEP Domain found in Dishevelled, Egl-10, and Pleckstrin. Domain of unknown function present in signalling proteins that contain PH, rasGEF, rhoGEF, rhoGAP, RGS, PDZ domains. DEP domain in Drosophila dishevelled is essential to rescue planar polarity defects and induce JNK signalling (Cell 94, 109-118).
Probab=22.03 E-value=87 Score=19.15 Aligned_cols=35 Identities=17% Similarity=0.191 Sum_probs=26.5
Q ss_pred HHHHhhhHHHHHHHHHHHHHHCCCCCHHHHHHHHHHH
Q 033999 5 ELYRRSTIGMCLTETLDEMVQNGTLTPELAIQVLVQF 41 (106)
Q Consensus 5 ~lYR~stlG~aL~dtLdeli~~~~I~p~la~kIl~~F 41 (106)
..|+.+-.|..+.+-|-+... ..+++.|..+.+.+
T Consensus 15 ~~~~~~F~G~e~v~wL~~~~~--~~~r~eA~~l~~~l 49 (77)
T smart00049 15 KTYPNCFTGSELVDWLMDNLE--IIDREEAVHLGQLL 49 (77)
T ss_pred EECcceeEcHHHHHHHHHcCC--cCCHHHHHHHHHHH
Confidence 467888889888887776664 57888888877665
No 133
>PF10815 ComZ: ComZ; InterPro: IPR024558 ComZ, which contains a leucine zipper motif, negatively regulates transcription of the ComG operon [].
Probab=22.02 E-value=2.1e+02 Score=17.81 Aligned_cols=35 Identities=29% Similarity=0.414 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHCC-CCCHHHHHHHHHHHHHHHHHHH
Q 033999 15 CLTETLDEMVQNG-TLTPELAIQVLVQFDKSMTEAL 49 (106)
Q Consensus 15 aL~dtLdeli~~~-~I~p~la~kIl~~FDk~i~~~L 49 (106)
.|-++=.+|-..| .+|++...-+++-|=++|+++-
T Consensus 13 ~lPEak~~L~k~GIeLsme~~qP~m~L~~~VM~eAY 48 (56)
T PF10815_consen 13 YLPEAKEELDKKGIELSMEMLQPLMQLLTKVMNEAY 48 (56)
T ss_pred HhHHHHHHHHHcCccCCHHHHHHHHHHHHHHHHHHH
Confidence 4667778888888 7999999999999999999985
No 134
>PF14763 HPS3_C: Hermansky-Pudlak syndrome 3, C-terminal
Probab=21.86 E-value=16 Score=30.39 Aligned_cols=41 Identities=32% Similarity=0.463 Sum_probs=34.8
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHhhcccceEEe-eeCcccee
Q 033999 28 TLTPELAIQVLVQFDKSMTEALETQVKSKVSIK-GHLHTYRF 68 (106)
Q Consensus 28 ~I~p~la~kIl~~FDk~i~~~L~~~vk~k~~~K-G~L~tYr~ 68 (106)
.|+|..|+++|++-|.++..++-.-.+.-+-.| |+|.+|++
T Consensus 3 n~~p~~a~~~L~~l~~~~~sv~~tltkA~mal~mgdl~~y~~ 44 (353)
T PF14763_consen 3 NIDPLTALQYLQKLEDSGPSVLLTLTKAAMALKMGDLDMYRN 44 (353)
T ss_pred CCCHHHHHHHHHHhhccCccHHHHHHHHHHHHhhCCHHHHHH
Confidence 489999999999999887777766677777788 99999986
No 135
>cd08324 CARD_NOD1_CARD4 Caspase activation and recruitment domain similar to that found in NOD1. Caspase activation and recruitment domain (CARD) found in human NOD1 (CARD4) and similar proteins. NOD1 is a member of the Nod-like receptor (NLR) family, which plays a central role in the innate immune response. NLRs typically contain an N-terminal effector domain, a central nucleotide-binding domain and a C-terminal ligand-binding region of several leucine-rich repeats (LRRs). In NOD1, as well as NOD2, the N-terminal effector domain is a CARD. Nod1-CARD has been shown to interact with the CARD domain of the downstream effector RICK (RIP2, CARDIAK), a serine/threonine kinase. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form hom
Probab=21.84 E-value=89 Score=21.07 Aligned_cols=22 Identities=23% Similarity=0.215 Sum_probs=18.1
Q ss_pred HHHHHHHHHCCCCCHHHHHHHH
Q 033999 17 TETLDEMVQNGTLTPELAIQVL 38 (106)
Q Consensus 17 ~dtLdeli~~~~I~p~la~kIl 38 (106)
.-.||.|.++|.|+.+.+..|-
T Consensus 18 ~plLD~Ll~n~~it~E~y~~V~ 39 (85)
T cd08324 18 QCLVDNLLKNDYFSTEDAEIVC 39 (85)
T ss_pred HHHHHHHhccCCccHHHHHHHH
Confidence 3469999999999998886664
No 136
>PF13730 HTH_36: Helix-turn-helix domain
Probab=21.67 E-value=1.1e+02 Score=17.40 Aligned_cols=16 Identities=13% Similarity=0.397 Sum_probs=12.6
Q ss_pred HHHHHHHHHHHHCCCC
Q 033999 14 MCLTETLDEMVQNGTL 29 (106)
Q Consensus 14 ~aL~dtLdeli~~~~I 29 (106)
.+...+|++|++.|.|
T Consensus 40 ~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 40 RTVQRAIKELEEKGLI 55 (55)
T ss_pred HHHHHHHHHHHHCcCC
Confidence 3567889999988875
No 137
>KOG1369 consensus Hexokinase [Carbohydrate transport and metabolism]
Probab=21.58 E-value=5.2e+02 Score=22.43 Aligned_cols=71 Identities=18% Similarity=0.146 Sum_probs=50.8
Q ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHhh-----cccceEEeeeCccceeeCcEEEEEEcCeEEE
Q 033999 13 GMCLTETLDEMVQNGTLTPELAIQVLVQFDKSMTEALETQ-----VKSKVSIKGHLHTYRFCDNVWTFILQDALFK 83 (106)
Q Consensus 13 G~aL~dtLdeli~~~~I~p~la~kIl~~FDk~i~~~L~~~-----vk~k~~~KG~L~tYr~cDnVWtf~lkn~~~k 83 (106)
-.++...|+++.+...++.+...+|...|...|..-|++. ++-..++...+++=+=-..+-.+-+-.-.|+
T Consensus 24 ~~~~~~~l~~~~~~f~l~~~~L~~v~~~~~~em~~gL~~~~~g~~~~mlpt~V~~lP~G~E~G~~lalDLGGTn~R 99 (474)
T KOG1369|consen 24 LAAVSRQLEELLALFQLPDEQLREVVDAFREEMERGLAKKTHGSAVKMLPTYVPDLPDGTEKGKFLALDLGGTNFR 99 (474)
T ss_pred hhhHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHhhhhccCCCcccccchhhcccCCCCCcCCCEEEEecCCCceE
Confidence 3567889999999999999999999999999999999953 3444566666665333334444444444443
No 138
>PTZ00059 dynein light chain; Provisional
Probab=21.52 E-value=1.7e+02 Score=19.21 Aligned_cols=18 Identities=22% Similarity=0.442 Sum_probs=13.9
Q ss_pred CCCHHHHHHHHHHHHHHH
Q 033999 28 TLTPELAIQVLVQFDKSM 45 (106)
Q Consensus 28 ~I~p~la~kIl~~FDk~i 45 (106)
....++|..|.++||+.-
T Consensus 34 ~~~kdiA~~IK~~fD~~y 51 (90)
T PTZ00059 34 NIEKDIAAYIKKEFDKKY 51 (90)
T ss_pred CchHHHHHHHHHHHHhhc
Confidence 446889999999999543
No 139
>KOG3430 consensus Dynein light chain type 1 [Cytoskeleton]
Probab=21.49 E-value=2.3e+02 Score=19.31 Aligned_cols=18 Identities=22% Similarity=0.396 Sum_probs=14.5
Q ss_pred CCHHHHHHHHHHHHHHHH
Q 033999 29 LTPELAIQVLVQFDKSMT 46 (106)
Q Consensus 29 I~p~la~kIl~~FDk~i~ 46 (106)
++.++|.-|.++||+..-
T Consensus 35 ~~k~iA~~iKkefDkkyG 52 (90)
T KOG3430|consen 35 IEKDIAAFIKKEFDKKYG 52 (90)
T ss_pred ChHHHHHHHHHHHhhhcC
Confidence 888888888888887544
No 140
>PF08535 KorB: KorB domain; InterPro: IPR013741 This entry contains several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon []. This domain includes the DNA-binding HTH motif []. ; PDB: 1R71_C.
Probab=21.25 E-value=2.4e+02 Score=18.10 Aligned_cols=30 Identities=23% Similarity=0.369 Sum_probs=18.5
Q ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHHHHH
Q 033999 15 CLTETLDEMVQNGTLTPELAIQVLVQFDKS 44 (106)
Q Consensus 15 aL~dtLdeli~~~~I~p~la~kIl~~FDk~ 44 (106)
.|-+.+.+|+.+|.|+.-.+...|..+.+.
T Consensus 28 ~lP~~i~~~v~~g~~~~~~a~~~L~~~~~~ 57 (93)
T PF08535_consen 28 DLPEEIKELVRSGRISDIRALYELRKLAEK 57 (93)
T ss_dssp S--HHHHHHHHTTS---HHHHHHHHHHHHH
T ss_pred cCCHHHHHHHHcCCCchHHHHHHHHHHHHh
Confidence 477889999999999877777556555443
No 141
>PF01003 Flavi_capsid: Flavivirus capsid protein C; InterPro: IPR001122 Flaviruses are small, enveloped RNA viruses that use arthropods such as mosquitoes for transmission to their vertebrate hosts, and include Yellow fever virus, West Nile virus, Tick-borne encephalitis virus, Japanese encephalitis virus, and Dengue virus 2 []. Flaviviruses consist of three structural proteins: the core nucleocapsid protein C, and the envelope glycoproteins M (IPR000069 from INTERPRO) and E. The virion of these viruses is a nucleocapsid covered by a lipoprotein envelope, where the nucleocapsid is a complex of capsid protein C and mRNA. The capsid protein C is a dimeric alpha-helical protein, and its interaction with RNA is critical for the production of viable virus particles [].; GO: 0005198 structural molecule activity, 0019028 viral capsid; PDB: 3C6E_C 3C5X_C 1R6R_B 1SFK_B.
Probab=21.06 E-value=1.2e+02 Score=21.24 Aligned_cols=39 Identities=28% Similarity=0.320 Sum_probs=27.5
Q ss_pred hHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHh
Q 033999 11 TIGMCLTETLDEMVQNGTLTPELAIQVLVQFDKSMTEALET 51 (106)
Q Consensus 11 tlG~aL~dtLdeli~~~~I~p~la~kIl~~FDk~i~~~L~~ 51 (106)
-.|.+.+-+|-.+=. .+++++|+++|..|-+.+..-|+-
T Consensus 50 ft~~k~T~~lk~rWr--~v~k~~a~kvL~~fKk~vg~Ll~~ 88 (117)
T PF01003_consen 50 FTGIKPTPGLKKRWR--TVDKSQAIKVLKKFKKEVGNLLNG 88 (117)
T ss_dssp HCT----HHHHHHHT--TS-CHHHHHHHHHHHHHHHHHHHH
T ss_pred HHcCCCCHHHHHHHh--cCCHHHHHHHHHHHHHHHHHHHHH
Confidence 456666777666654 689999999999999999988765
No 142
>PF14076 DUF4258: Domain of unknown function (DUF4258)
Probab=20.95 E-value=1.5e+02 Score=17.40 Aligned_cols=22 Identities=18% Similarity=0.259 Sum_probs=17.0
Q ss_pred HHHHHHHHCCCCCHHHHHHHHHH
Q 033999 18 ETLDEMVQNGTLTPELAIQVLVQ 40 (106)
Q Consensus 18 dtLdeli~~~~I~p~la~kIl~~ 40 (106)
.|++.|.+.| |+.+....+|..
T Consensus 5 Ha~~rm~eR~-Is~~~I~~~l~~ 26 (73)
T PF14076_consen 5 HARERMQERG-ISEEDIEDALEN 26 (73)
T ss_pred HHHHHHHhCC-CCHHHHHHHHhc
Confidence 5778888777 898888887754
No 143
>PF00502 Phycobilisome: Phycobilisome protein; InterPro: IPR012128 Cyanobacteria and red algae harvest light through water-soluble complexes, called phycobilisomes, which are attached to the outer face of the thylakoid membrane []. These complexes are capable of transferring the absorbed energy to the photosynthetic reaction centre with greater than 95% efficiency. Phycobilisomes contain various photosynthetic light harvesting proteins known as biliproteins, and linker proteins which help assemble the structure. The two main structural elements of the complex are a core located near the photosynthetic reaction centre, and rods attached to this core. Allophycocyanin is the major component of the core, while the rods contain phycocyanins, phycoerythrins and linker proteins. The rod biliproteins harvest photons, with the excitation energy being passed through the rods into the allophycocyanin in the core. Other core biliproteins subsequently pass this energy to chlorophyll within the thylakoid membrane. This entry represents the alpha and beta subunits found in biliproteins from cyanobacteria and red algae. Structural studies indicate that the basic structural unit of most biliproteins is a heterodimer composed of these alpha and beta subunits [, , , ]. The full protein is a ring-like trimer assembly of these heterodimers. Each subunit of the heterodimer has eight helices and binds chromophores through thioester bonds formed at particular cysteine residues. These chromophores, also known as bilins, are open-chain tetrapyrroles whose number and type vary with the particular biliprotein eg R-phyocerythrin binds five phycoerythrobilins per heterodimer, while allophycocyanin binds two phycocyanobilins per heterodimer.; GO: 0015979 photosynthesis, 0030089 phycobilisome; PDB: 2VML_I 2VJR_A 1KTP_B 3L0F_B 1JBO_B 3KVS_B 1PHN_B 3BRP_B 2C7K_B 2C7L_B ....
Probab=20.92 E-value=1.6e+02 Score=21.12 Aligned_cols=43 Identities=26% Similarity=0.374 Sum_probs=31.1
Q ss_pred HHHHhhhHH-HHHHHHHHHHHHC--CCCCHHHHHHHHHHHHHHHHH
Q 033999 5 ELYRRSTIG-MCLTETLDEMVQN--GTLTPELAIQVLVQFDKSMTE 47 (106)
Q Consensus 5 ~lYR~stlG-~aL~dtLdeli~~--~~I~p~la~kIl~~FDk~i~~ 47 (106)
++|+.--+= .+..++|..|... ..++++.+..+-.-||..|+.
T Consensus 110 ei~~al~vp~~~~v~al~~lk~~~~~~l~~e~~~~~~~yfD~~i~~ 155 (157)
T PF00502_consen 110 EIYRALGVPIDAYVEALQCLKEAALQLLSPEAAAEIAPYFDYLINA 155 (157)
T ss_dssp HHHHHHT--HHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHcCCchHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHHH
Confidence 566653322 2456777777776 778899999999999998864
No 144
>PF11630 DUF3254: Protein of unknown function (DUF3254); InterPro: IPR024509 Anti-lipopolysaccharide factor binds to bacterial LPS and may specifically inhibit the LPS-mediated activation of the hemolymph coagulation. It has a strong antibacterial effect, especially on the growth of Gram-negative bacteria [,]. This entry also includes the antibacterial protein Scygonadin, which has antibacterial activity against the Gram-positive bacterium Micrococcus luteus [].; PDB: 2JOB_A.
Probab=20.80 E-value=2e+02 Score=19.91 Aligned_cols=31 Identities=23% Similarity=0.240 Sum_probs=22.9
Q ss_pred HhhhHHHHHHHHHHHHHHCCCCCHHHHHHHH
Q 033999 8 RRSTIGMCLTETLDEMVQNGTLTPELAIQVL 38 (106)
Q Consensus 8 R~stlG~aL~dtLdeli~~~~I~p~la~kIl 38 (106)
|...++.|..|=...-++.|.||.+.|..-|
T Consensus 69 ~sg~~~~a~rDFv~kA~~~gLiT~eeA~~wL 99 (100)
T PF11630_consen 69 RSGVVRKATRDFVRKAFQAGLITEEEAQPWL 99 (100)
T ss_dssp HHHHHHHHHHHHHHHHHHHT-S-HHHHHHHH
T ss_pred CcchhhHHHHHHHHHHHHcCCccHHHHHHhh
Confidence 4456788888888888899999999987654
No 145
>KOG4603 consensus TBP-1 interacting protein [Signal transduction mechanisms]
Probab=20.74 E-value=72 Score=24.52 Aligned_cols=23 Identities=22% Similarity=0.398 Sum_probs=19.1
Q ss_pred HHHHHHHHHHHHHHCCCCCHHHH
Q 033999 12 IGMCLTETLDEMVQNGTLTPELA 34 (106)
Q Consensus 12 lG~aL~dtLdeli~~~~I~p~la 34 (106)
=|.+.+.|||.|-++|+|.....
T Consensus 38 gktavqk~Ld~La~~Gki~~K~Y 60 (201)
T KOG4603|consen 38 GKTAVQKTLDQLAQQGKIKEKMY 60 (201)
T ss_pred cchHHHHHHHHHHHcCchhHHhc
Confidence 35678999999999999987654
No 146
>PF11769 DUF3313: Protein of unknown function (DUF3313); InterPro: IPR021747 This a bacterial family of proteins which are annotated as putative lipoproteins.
Probab=20.60 E-value=1.7e+02 Score=21.38 Aligned_cols=25 Identities=28% Similarity=0.343 Sum_probs=23.5
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHhh
Q 033999 28 TLTPELAIQVLVQFDKSMTEALETQ 52 (106)
Q Consensus 28 ~I~p~la~kIl~~FDk~i~~~L~~~ 52 (106)
.|+++-..++...|++++.+.|+++
T Consensus 68 ~l~~~~~~~l~~~~~~~l~~~l~~~ 92 (201)
T PF11769_consen 68 GLSDADLQQLANYFDRALCEALSKR 92 (201)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHhc
Confidence 4899999999999999999999996
No 147
>cd07366 3MGA_Dioxygenase Subunit B of the Class III Extradiol ring-cleavage dioxygenase, 3-O-Methylgallate Dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 3-O-Methylgallate. 3-O-Methylgallate Dioxygenase catalyzes the oxidization and subsequent ring-opening of 3-O-Methylgallate (3MGA) between carbons 2 and 3. 3-O-Methylgallate Dioxygenase is a key enzyme in the syringate degradation pathway, in which the syringate is first converted to 3-O-Methylgallate by O-demethylase. This enzyme is a member of the class III extradiol dioxygenase family, a group of enzymes which uses a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. LigAB-like enzymes are usually composed of two subunits, designated A and B, which form a tetramer composed of two copies of each subunit. This model represents the catalytic subunit, B.
Probab=20.59 E-value=85 Score=25.56 Aligned_cols=41 Identities=20% Similarity=0.383 Sum_probs=32.5
Q ss_pred HhhhHHHHHHHHHHHH--------HHCCCCCHHHHHHHHHHHHHHHHHHHHh
Q 033999 8 RRSTIGMCLTETLDEM--------VQNGTLTPELAIQVLVQFDKSMTEALET 51 (106)
Q Consensus 8 R~stlG~aL~dtLdel--------i~~~~I~p~la~kIl~~FDk~i~~~L~~ 51 (106)
|.-.+|.+|.++++++ |-+|-+|-.+ +-.+||+.+.+.|.+
T Consensus 217 r~y~lG~aL~~ai~~~~~d~rV~IIaSGgLSH~l---~~~eFD~~~l~~l~~ 265 (328)
T cd07366 217 RCFEFGRAVARAIRSWPGDARVGVIASGGLSHFV---IDEEFDRRILDALRN 265 (328)
T ss_pred HHHHHHHHHHHHHHhcCCCCCEEEEEeCccccCC---ChHHHHHHHHHHHHc
Confidence 4447999999999876 3456677777 449999999999977
No 148
>PF00436 SSB: Single-strand binding protein family; InterPro: IPR000424 The Escherichia coli single-strand binding protein [] (gene ssb), also known as the helix-destabilising protein, is a protein of 177 amino acids. It binds tightly, as a homotetramer, to single-stranded DNA (ss-DNA) and plays an important role in DNA replication, recombination and repair. Closely related variants of SSB are encoded in the genome of a variety of large self-transmissible plasmids. SSB has also been characterised in bacteria such as Proteus mirabilis or Serratia marcescens. Eukaryotic mitochondrial proteins that bind ss-DNA and are probably involved in mitochondrial DNA replication are structurally and evolutionary related to prokaryotic SSB.; GO: 0003697 single-stranded DNA binding; PDB: 3UDG_B 1SE8_A 2CWA_A 3ULL_B 1S3O_A 2DUD_A 3AFP_A 3AFQ_A 3VDY_A 3EIV_C ....
Probab=20.54 E-value=2.3e+02 Score=17.80 Aligned_cols=25 Identities=24% Similarity=0.393 Sum_probs=17.1
Q ss_pred HHHHhh--cccceEEeeeCccceeeCc
Q 033999 47 EALETQ--VKSKVSIKGHLHTYRFCDN 71 (106)
Q Consensus 47 ~~L~~~--vk~k~~~KG~L~tYr~cDn 71 (106)
+.+.++ ..+.+.+.|.|.++.+.|+
T Consensus 60 ~~~~~~l~kG~~V~V~G~l~~~~~~~~ 86 (104)
T PF00436_consen 60 ENVAEYLKKGDRVYVEGRLRTRTYEDK 86 (104)
T ss_dssp HHHHHH--TT-EEEEEEEEEEEEEEST
T ss_pred cccceEEcCCCEEEEEEEEEeeEEECC
Confidence 344443 4688999999998887664
No 149
>PF04840 Vps16_C: Vps16, C-terminal region; InterPro: IPR006925 This protein forms part of the Class C vacuolar protein sorting (Vps) complex. Vps16 is essential for vacuolar protein sorting, which is essential for viability in plants, but not yeast []. The Class C Vps complex is required for SNARE-mediated membrane fusion at the lysosome-like yeast vacuole. It is thought to play essential roles in membrane docking and fusion at the Golgi-to-endosome and endosome-to-vacuole stages of transport []. The role of VPS16 in this complex is not known.; GO: 0006886 intracellular protein transport, 0005737 cytoplasm
Probab=20.41 E-value=96 Score=24.95 Aligned_cols=34 Identities=21% Similarity=0.489 Sum_probs=27.7
Q ss_pred HHhhhHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHH
Q 033999 7 YRRSTIGMCLTETLDEMVQNGTLTPELAIQVLVQFD 42 (106)
Q Consensus 7 YR~stlG~aL~dtLdeli~~~~I~p~la~kIl~~FD 42 (106)
|-.+-+|.+|.+|+-.++..|.. ..|.++-.+|-
T Consensus 171 ~~~~f~~~Sl~~Ti~~li~~~~~--k~A~kl~k~Fk 204 (319)
T PF04840_consen 171 YNTNFVGLSLNDTIRKLIEMGQE--KQAEKLKKEFK 204 (319)
T ss_pred hccchhcCCHHHHHHHHHHCCCH--HHHHHHHHHcC
Confidence 33456899999999999999974 67888888883
No 150
>PF13812 PPR_3: Pentatricopeptide repeat domain
Probab=20.32 E-value=98 Score=15.19 Aligned_cols=10 Identities=40% Similarity=0.743 Sum_probs=4.4
Q ss_pred HHHHHHHHCC
Q 033999 18 ETLDEMVQNG 27 (106)
Q Consensus 18 dtLdeli~~~ 27 (106)
+.+++|.+.|
T Consensus 22 ~~~~~M~~~g 31 (34)
T PF13812_consen 22 QLFDEMKEQG 31 (34)
T ss_pred HHHHHHHHhC
Confidence 3444444433
No 151
>cd04371 DEP DEP domain, named after Dishevelled, Egl-10, and Pleckstrin, where this domain was first discovered. The function of this domain is still not clear, but it is believed to be important for the membrane association of the signaling proteins in which it is present. New studies show that the DEP domain of Sst2, a yeast RGS protein is necessary and sufficient for receptor interaction.
Probab=20.05 E-value=1.1e+02 Score=18.72 Aligned_cols=35 Identities=20% Similarity=0.227 Sum_probs=27.0
Q ss_pred HHHHhhhHHHHHHHHHHHHHHCCCCCHHHHHHHHHHH
Q 033999 5 ELYRRSTIGMCLTETLDEMVQNGTLTPELAIQVLVQF 41 (106)
Q Consensus 5 ~lYR~stlG~aL~dtLdeli~~~~I~p~la~kIl~~F 41 (106)
..|+++-.|..+.+-|-+.... .+.+.|..+.+.+
T Consensus 23 ~~~~~~F~G~e~v~WL~~~~~~--~~r~ea~~~~~~l 57 (81)
T cd04371 23 KTYPNCFTGSELVDWLLDNLEA--ITREEAVELGQAL 57 (81)
T ss_pred EECCceeEcHHHHHHHHHhCCC--CCHHHHHHHHHHH
Confidence 3577888899888888777654 8888888887765
No 152
>PF05596 Taeniidae_ag: Taeniidae antigen; InterPro: IPR008860 This family consists of several antigen proteins from Taenia and Echinococcus (tapeworm) species.
Probab=20.04 E-value=2.5e+02 Score=17.78 Aligned_cols=22 Identities=5% Similarity=0.212 Sum_probs=19.8
Q ss_pred hHHHHhhhHHHHHHHHHHHHHH
Q 033999 4 FELYRRSTIGMCLTETLDEMVQ 25 (106)
Q Consensus 4 y~lYR~stlG~aL~dtLdeli~ 25 (106)
..+|++-|||.-+.+-..|+..
T Consensus 20 ~~FF~~DPlGqkIa~l~kdw~~ 41 (64)
T PF05596_consen 20 RNFFYEDPLGQKIAQLAKDWNE 41 (64)
T ss_pred HHHhccCchHHHHHHHHHHHHH
Confidence 5688999999999999999987
Done!