Query psy12711
Match_columns 639
No_of_seqs 303 out of 946
Neff 4.2
Searched_HMMs 46136
Date Fri Aug 16 17:44:38 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12711.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12711hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4392|consensus 100.0 1.8E-29 3.8E-34 226.9 12.5 110 75-187 1-111 (117)
2 cd06926 RNAP_II_RPB11 RPB11 su 100.0 4.7E-28 1E-32 213.2 12.0 92 87-181 2-93 (93)
3 PF13656 RNA_pol_L_2: RNA poly 99.9 9.9E-28 2.1E-32 204.5 8.4 77 105-181 1-77 (77)
4 cd07029 RNAP_I_III_AC19 AC19 s 99.9 3E-27 6.4E-32 205.2 10.6 80 102-181 6-85 (85)
5 cd06927 RNAP_L L subunit of Ar 99.9 1.7E-26 3.6E-31 199.7 10.3 77 102-178 6-82 (83)
6 PRK01146 DNA-directed RNA poly 99.9 1.7E-26 3.8E-31 200.4 10.4 76 103-178 9-84 (85)
7 cd07027 RNAP_RPB11_like RPB11 99.9 1.9E-26 4.2E-31 199.3 10.5 77 102-178 6-82 (83)
8 KOG3438|consensus 99.9 1.9E-25 4E-30 198.1 10.2 87 103-189 14-100 (105)
9 COG1761 RPB11 DNA-directed RNA 99.9 1.1E-24 2.3E-29 194.1 13.2 95 90-188 3-97 (99)
10 PF01582 TIR: TIR domain; Int 99.9 2.8E-23 6.1E-28 190.8 8.8 134 388-542 1-141 (141)
11 smart00255 TIR Toll - interleu 99.8 7E-21 1.5E-25 171.6 12.6 137 385-545 1-139 (140)
12 cd00460 RNAP_RPB11_RPB3 RPB11 99.8 9.4E-20 2E-24 157.9 9.8 75 102-177 6-86 (86)
13 cd08312 Death_MyD88 Death doma 99.7 1.5E-18 3.3E-23 148.6 5.4 76 252-337 1-79 (79)
14 cd08802 Death_UNC5B Death doma 99.6 4.8E-16 1E-20 135.3 5.2 79 248-335 1-81 (84)
15 PF13676 TIR_2: TIR domain; PD 99.6 6.8E-16 1.5E-20 133.6 1.9 102 388-497 1-102 (102)
16 cd08799 Death_UNC5C Death doma 99.5 1E-14 2.2E-19 127.0 5.1 77 248-333 1-79 (84)
17 cd08782 Death_DAPK1 Death doma 99.5 1.3E-14 2.7E-19 125.8 5.1 72 252-334 2-79 (82)
18 cd08781 Death_UNC5-like Death 99.4 1.1E-13 2.3E-18 119.9 5.7 78 248-334 1-80 (83)
19 cd08310 Death_NFkB-like Death 99.4 3.8E-13 8.3E-18 113.9 4.4 67 252-334 1-69 (72)
20 PF01193 RNA_pol_L: RNA polyme 99.4 4.9E-13 1.1E-17 110.4 4.6 65 107-175 1-66 (66)
21 PLN03194 putative disease resi 99.3 4.5E-12 9.8E-17 124.7 11.0 101 383-492 24-126 (187)
22 cd08793 Death_IRAK4 Death doma 99.1 2.2E-11 4.9E-16 109.2 3.6 72 243-330 1-86 (100)
23 cd08311 Death_p75NR Death doma 99.1 3.2E-11 6.9E-16 103.6 4.1 72 253-336 2-76 (77)
24 cd08800 Death_UNC5A Death doma 99.1 1.9E-10 4.1E-15 100.4 6.2 79 248-335 1-81 (84)
25 cd08309 Death_IRAK Death domai 99.0 4.1E-10 8.9E-15 99.8 4.2 77 243-333 1-91 (95)
26 cd08801 Death_UNC5D Death doma 98.7 2.4E-08 5.2E-13 88.7 6.4 80 248-336 1-82 (98)
27 cd08803 Death_ank3 Death domai 98.6 1.8E-08 3.8E-13 88.0 3.1 61 272-335 14-82 (84)
28 PF00531 Death: Death domain; 98.5 8.4E-08 1.8E-12 80.3 2.7 65 273-340 12-83 (83)
29 cd08797 Death_NFkB1_p105 Death 98.4 4.3E-07 9.3E-12 78.3 4.8 70 252-334 1-72 (76)
30 cd08777 Death_RIP1 Death Domai 98.4 2.3E-07 5.1E-12 81.2 2.8 65 272-338 12-85 (86)
31 smart00005 DEATH DEATH domain, 98.3 7E-07 1.5E-11 76.2 4.9 78 250-338 2-87 (88)
32 cd08804 Death_ank2 Death domai 98.3 5E-07 1.1E-11 78.7 2.8 60 272-334 14-81 (84)
33 cd08798 Death_NFkB2_p100 Death 98.2 1.5E-06 3.3E-11 75.0 4.9 70 252-334 1-72 (76)
34 PLN03210 Resistant to P. syrin 98.0 1.7E-05 3.7E-10 96.1 10.4 103 383-491 10-114 (1153)
35 cd01670 Death Death Domain: a 97.9 1.1E-05 2.5E-10 67.3 3.9 61 273-336 10-77 (79)
36 cd08318 Death_NMPP84 Death dom 97.9 1.8E-05 4E-10 69.1 5.2 61 273-336 18-85 (86)
37 cd08317 Death_ank Death domain 97.9 1.3E-05 2.8E-10 69.4 3.6 61 273-336 15-83 (84)
38 cd08307 Death_Pelle Death doma 97.8 3.1E-05 6.8E-10 69.7 5.3 76 243-334 1-84 (97)
39 KOG3678|consensus 97.7 0.00054 1.2E-08 76.2 14.2 136 383-525 610-762 (832)
40 KOG1480|consensus 97.4 0.00015 3.2E-09 83.8 4.8 78 248-334 815-894 (909)
41 cd08783 Death_MALT1 Death doma 97.4 0.00036 7.8E-09 62.8 6.1 76 246-334 2-91 (97)
42 PF08937 DUF1863: MTH538 TIR-l 97.3 0.00078 1.7E-08 62.1 7.3 89 386-480 1-107 (130)
43 cd08779 Death_PIDD Death Domai 97.0 0.00045 9.7E-09 60.6 3.0 66 273-340 13-86 (86)
44 cd08805 Death_ank1 Death domai 97.0 0.00061 1.3E-08 59.9 3.1 60 272-334 14-81 (84)
45 cd08796 Death_IRAK-M Death dom 96.9 0.0011 2.3E-08 59.1 4.1 71 245-328 3-80 (89)
46 cd08306 Death_FADD Fas-associa 96.7 0.0012 2.6E-08 57.8 3.1 64 272-338 12-83 (86)
47 cd08308 Death_Tube Death domai 96.7 0.0015 3.3E-08 61.5 3.7 79 243-334 2-99 (125)
48 PF08357 SEFIR: SEFIR domain; 96.1 0.048 1E-06 50.8 10.2 62 388-449 3-70 (150)
49 cd08784 Death_DRs Death Domain 95.9 0.007 1.5E-07 52.2 3.2 62 273-337 11-79 (79)
50 cd08315 Death_TRAILR_DR4_DR5 D 95.7 0.013 2.7E-07 52.7 4.3 65 274-341 20-91 (96)
51 cd08795 Death_IRAK2 Death doma 95.1 0.018 4E-07 51.4 3.2 69 245-328 3-79 (88)
52 cd08316 Death_FAS_TNFRSF6 Deat 94.8 0.044 9.5E-07 49.6 4.6 68 273-343 20-95 (97)
53 cd08319 Death_RAIDD Death doma 94.7 0.044 9.6E-07 48.2 4.3 53 273-328 13-73 (83)
54 cd08794 Death_IRAK1 Death doma 94.7 0.018 3.8E-07 50.8 1.8 53 271-329 21-76 (84)
55 cd08313 Death_TNFR1 Death doma 94.2 0.051 1.1E-06 47.6 3.6 66 270-337 8-80 (80)
56 PF10137 TIR-like: Predicted n 93.7 0.41 8.8E-06 45.1 8.9 107 388-500 2-121 (125)
57 cd08780 Death_TRADD Death Doma 91.8 0.13 2.9E-06 46.1 2.7 64 271-337 11-88 (90)
58 cd06928 RNAP_alpha_NTD N-termi 86.3 1.1 2.3E-05 45.7 4.9 45 131-175 163-213 (215)
59 PRK14979 DNA-directed RNA poly 86.2 2.4 5.3E-05 42.9 7.4 51 129-183 138-188 (195)
60 cd07028 RNAP_RPB3_like RPB3 su 85.7 1.6 3.5E-05 44.5 5.9 52 127-179 160-211 (212)
61 smart00662 RPOLD RNA polymeras 84.2 1.6 3.4E-05 44.6 5.0 46 131-176 162-223 (224)
62 TIGR02027 rpoA DNA-directed RN 83.2 2.5 5.4E-05 45.1 6.2 49 131-179 154-208 (297)
63 CHL00013 rpoA RNA polymerase a 79.6 3.3 7.2E-05 45.0 5.7 48 131-178 170-222 (327)
64 PRK05182 DNA-directed RNA poly 78.6 4 8.6E-05 44.0 5.8 49 131-179 171-225 (310)
65 PRK00783 DNA-directed RNA poly 75.7 3.1 6.7E-05 43.2 4.0 27 103-129 9-35 (263)
66 cd07028 RNAP_RPB3_like RPB3 su 68.7 4.7 0.0001 41.2 3.3 27 103-129 9-35 (212)
67 cd07031 RNAP_II_RPB3 RPB3 subu 68.6 8.8 0.00019 40.4 5.4 40 144-183 225-264 (265)
68 cd07030 RNAP_D D subunit of Ar 67.0 5 0.00011 41.6 3.2 27 103-129 9-35 (259)
69 cd06928 RNAP_alpha_NTD N-termi 63.7 9.2 0.0002 39.0 4.3 39 103-141 7-50 (215)
70 PRK05182 DNA-directed RNA poly 58.4 14 0.00031 39.8 4.8 38 103-140 17-59 (310)
71 smart00662 RPOLD RNA polymeras 55.5 13 0.00027 38.1 3.7 33 107-139 2-35 (224)
72 cd08815 Death_TNFRSF25_DR3 Dea 54.2 19 0.00042 31.8 4.0 54 273-331 11-71 (77)
73 COG4916 Uncharacterized protei 53.5 15 0.00033 39.3 3.8 78 383-462 175-259 (329)
74 PRK00783 DNA-directed RNA poly 52.9 26 0.00057 36.4 5.6 41 143-183 221-261 (263)
75 PRK14979 DNA-directed RNA poly 51.9 17 0.00036 37.0 3.8 45 103-148 12-60 (195)
76 cd08304 DD_superfamily The Dea 49.0 14 0.0003 31.3 2.3 56 273-334 10-67 (69)
77 cd07031 RNAP_II_RPB3 RPB3 subu 46.9 17 0.00037 38.3 3.1 33 103-135 9-42 (265)
78 cd07032 RNAP_I_II_AC40 AC40 su 45.6 37 0.0008 36.6 5.4 38 142-179 253-290 (291)
79 COG0202 RpoA DNA-directed RNA 43.6 23 0.00049 38.5 3.5 36 103-138 17-53 (317)
80 cd07030 RNAP_D D subunit of Ar 43.2 47 0.001 34.5 5.6 37 144-180 222-258 (259)
81 PF14786 Death_2: Tube Death d 37.4 39 0.00085 32.9 3.6 41 293-334 71-111 (137)
82 PF05014 Nuc_deoxyrib_tr: Nucl 35.4 1.9E+02 0.004 25.9 7.5 72 393-465 9-88 (113)
83 cd00860 ThrRS_anticodon ThrRS 34.2 1.6E+02 0.0036 24.4 6.6 62 385-450 1-63 (91)
84 CHL00013 rpoA RNA polymerase a 33.8 31 0.00068 37.6 2.7 39 103-141 18-61 (327)
85 COG4271 Predicted nucleotide-b 31.0 1.4E+02 0.003 31.2 6.5 61 387-450 84-146 (233)
86 PRK13789 phosphoribosylamine-- 30.6 69 0.0015 35.7 4.8 86 203-288 3-96 (426)
87 TIGR02027 rpoA DNA-directed RN 28.7 42 0.00092 36.0 2.6 30 112-141 11-41 (297)
88 cd04905 ACT_CM-PDT C-terminal 20.6 4.9E+02 0.011 21.7 7.1 67 106-174 3-70 (80)
No 1
>KOG4392|consensus
Probab=99.96 E-value=1.8e-29 Score=226.95 Aligned_cols=110 Identities=30% Similarity=0.449 Sum_probs=106.7
Q ss_pred cccccchhccccCCC-CceeEeecCCccCCCCeEEEEEccCCcchHHHHHHHHhcCCCeeEEeecCCCCCCCceEEEEEe
Q psy12711 75 SLCINYMESKQLENS-SPVWELRDNTLNVKPNCRTFVFEKEGHTFGSVITHILQSYPEVDFAGYSVPHPADFQIFIRIQV 153 (639)
Q Consensus 75 ~~~~~~~e~~~l~~~-~Kv~~~~dt~~~~~~N~~tf~i~gEDHTLGNlLR~~Llkdp~V~FAGY~IPHPLe~~i~LrIQT 153 (639)
||.+.+||+|.|.+| +||++..||+ .+|++.|+|++|||||||+|+.+|++||+|.||||++|||++.++.|||||
T Consensus 1 MNaP~~fE~fll~eg~kKvtin~DtK---vpNA~~fTiekEDHTLGNii~~qLl~D~~vLFagYkvpHPl~~~~~LRiqt 77 (117)
T KOG4392|consen 1 MNAPPAFESFLLFEGEKKITINKDTK---VPNAALFTIEKEDHTLGNIIKSQLLKDPRVLFAGYKVPHPLEHKIILRVQT 77 (117)
T ss_pred CCCchhhhhheeccCCceeEEecCCC---CCceEEEEEecccchHHHHHHHHHccCccceEeeecCCCcccccEEEEEec
Confidence 799999999999777 6699999999 499999999999999999999999999999999999999999999999999
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy12711 154 KDGYDSIDILKKGIKELESACDRITETFNDAMQC 187 (639)
Q Consensus 154 ~~~~~P~eaLk~Al~~L~~~~~~L~~~F~~ai~~ 187 (639)
+.+++|.++|.+|+.+++..++.+...|+.+++.
T Consensus 78 t~d~~p~~al~~a~~~l~~el~~l~~~f~~~~~~ 111 (117)
T KOG4392|consen 78 TEDCSPADALTNAITDLIEELSLLENRFKAEAAL 111 (117)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 9999999999999999999999999999999987
No 2
>cd06926 RNAP_II_RPB11 RPB11 subunit of Eukaryotic RNA polymerase II. The eukaryotic RPB11 subunit of RNA polymerase (RNAP) II is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP II is responsible for the synthesis of mRNA precursor. The RPB11 subunit heterodimerizes with the RPB3 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association.
Probab=99.95 E-value=4.7e-28 Score=213.23 Aligned_cols=92 Identities=37% Similarity=0.590 Sum_probs=88.2
Q ss_pred CCCCceeEeecCCccCCCCeEEEEEccCCcchHHHHHHHHhcCCCeeEEeecCCCCCCCceEEEEEeCCCCCHHHHHHHH
Q psy12711 87 ENSSPVWELRDNTLNVKPNCRTFVFEKEGHTFGSVITHILQSYPEVDFAGYSVPHPADFQIFIRIQVKDGYDSIDILKKG 166 (639)
Q Consensus 87 ~~~~Kv~~~~dt~~~~~~N~~tf~i~gEDHTLGNlLR~~Llkdp~V~FAGY~IPHPLe~~i~LrIQT~~~~~P~eaLk~A 166 (639)
++.+||++..|++ .+|+++|+|.||||||||+||+.|+++|+|.||||+||||++++++|||||+++.+|.+||++|
T Consensus 2 ~~~~kv~~~~d~k---~~n~~~~~i~~EdHTLgNlLr~~L~~~~~V~fagY~vpHPl~~~~~l~i~t~~~~~p~~al~~a 78 (93)
T cd06926 2 EGEKKITEKKDTK---VPNAATFTINKEDHTLGNLLRMQLLKDPNVLFAGYKVPHPLEHKIELRIQTDGSITPKEALKNA 78 (93)
T ss_pred CCccceEEeecCC---CCcEEEEEEeCCCchHHHHHHHHHhcCCCeeEEeeccCCCCCCceEEEEEeCCCCCHHHHHHHH
Confidence 3458999999988 5999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHH
Q psy12711 167 IKELESACDRITETF 181 (639)
Q Consensus 167 l~~L~~~~~~L~~~F 181 (639)
+++|.++|+.+++.|
T Consensus 79 ~~~l~~~~~~~~~~f 93 (93)
T cd06926 79 ITDLISELSLLKEEF 93 (93)
T ss_pred HHHHHHHHHHHHhhC
Confidence 999999999999876
No 3
>PF13656 RNA_pol_L_2: RNA polymerase Rpb3/Rpb11 dimerisation domain; PDB: 2Y0S_L 1I3Q_K 4A3D_K 2JA8_K 3GTP_K 1R9T_K 3PO2_K 4A3J_K 3HOX_K 2JA7_K ....
Probab=99.94 E-value=9.9e-28 Score=204.46 Aligned_cols=77 Identities=40% Similarity=0.714 Sum_probs=72.8
Q ss_pred CeEEEEEccCCcchHHHHHHHHhcCCCeeEEeecCCCCCCCceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q psy12711 105 NCRTFVFEKEGHTFGSVITHILQSYPEVDFAGYSVPHPADFQIFIRIQVKDGYDSIDILKKGIKELESACDRITETF 181 (639)
Q Consensus 105 N~~tf~i~gEDHTLGNlLR~~Llkdp~V~FAGY~IPHPLe~~i~LrIQT~~~~~P~eaLk~Al~~L~~~~~~L~~~F 181 (639)
|+++|+|.||||||||+||+.|+++|+|+||||+||||++++++|||||+++++|++||++|+++|.++|++|+++|
T Consensus 1 n~~~f~i~~EDHTlgNlLr~~L~~~p~V~fagY~vpHPl~~~i~l~Iqt~~~~~p~~~l~~a~~~l~~~~~~l~~~F 77 (77)
T PF13656_consen 1 NEITFTIYGEDHTLGNLLRYELLKDPDVEFAGYRVPHPLENKINLRIQTKGGITPIEALKKALEDLIKICEELKKEF 77 (77)
T ss_dssp TEEEEEEES--HHHHHHHHHCCTTSTTEEEEEEEESETTSSEEEEEEEESTTS-HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CeEEEEEeCCCccHHHHHHHHHhhCCCeEEEEeccCCCCCCceEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHhhC
Confidence 78999999999999999999999999999999999999999999999999999999999999999999999999988
No 4
>cd07029 RNAP_I_III_AC19 AC19 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III. The eukaryotic AC19 subunit of RNA polymerase (RNAP) I and RNAP III is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP I is responsible for the synthesis of ribosomal RNA precursor, while RNAP III functions in the synthesis of 5S and tRNA. The AC19 subunit is the equivalent of the RPB11 subunit of RNAP II. The RPB11 subunit heterodimerizes with the RPB3 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association. The homology of AC19 to RPB11 suggests a similar function. The AC19 subunit is likely to ass
Probab=99.94 E-value=3e-27 Score=205.20 Aligned_cols=80 Identities=46% Similarity=0.891 Sum_probs=77.8
Q ss_pred CCCCeEEEEEccCCcchHHHHHHHHhcCCCeeEEeecCCCCCCCceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q psy12711 102 VKPNCRTFVFEKEGHTFGSVITHILQSYPEVDFAGYSVPHPADFQIFIRIQVKDGYDSIDILKKGIKELESACDRITETF 181 (639)
Q Consensus 102 ~~~N~~tf~i~gEDHTLGNlLR~~Llkdp~V~FAGY~IPHPLe~~i~LrIQT~~~~~P~eaLk~Al~~L~~~~~~L~~~F 181 (639)
..+|+++|+|+||||||||+||++|+++|+|+||||+||||++++++|||||+++.+|.+||++|+++|.+.|+++.++|
T Consensus 6 ~~~n~~~~~i~~EdHTLgNlLr~~L~~~p~V~fagY~vpHPl~~~~~lriqT~~~~~p~~al~~a~~~l~~~~~~~~~~f 85 (85)
T cd07029 6 TDESCATFVFYGEDHTLGNSLRYVIMKNPEVEFCGYSIPHPSENKINLRIQTKGGEPAVDVLKKGLEDLEQICDHILSTF 85 (85)
T ss_pred CCCCeEEEEEeCCCcchHHHHHHHHhhCCCceEEeecccCCCCCccEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHhcC
Confidence 36999999999999999999999999999999999999999999999999999999999999999999999999999876
No 5
>cd06927 RNAP_L L subunit of Archaeal RNA polymerase. The archaeal L subunit of RNA polymerase (RNAP) is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. A single distinct RNAP complex is found in archaea, which may be responsible for the synthesis of all RNAs. The archaeal RNAP harbors homologues of all eukaryotic RNAP II subunits with two exceptions (RPB8 and RPB9). The 12 archaeal subunits are designated by letters and can be divided into three functional groups that are engaged in: (I) catalysis (A'/A", B'/B" or B); (II) assembly (L, N, D and P); and (III) auxiliary functions (F, E, H and K). The assembly of the two largest archaeal RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of the archaeal D/L heterodimer.
Probab=99.94 E-value=1.7e-26 Score=199.73 Aligned_cols=77 Identities=26% Similarity=0.413 Sum_probs=74.7
Q ss_pred CCCCeEEEEEccCCcchHHHHHHHHhcCCCeeEEeecCCCCCCCceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHH
Q psy12711 102 VKPNCRTFVFEKEGHTFGSVITHILQSYPEVDFAGYSVPHPADFQIFIRIQVKDGYDSIDILKKGIKELESACDRIT 178 (639)
Q Consensus 102 ~~~N~~tf~i~gEDHTLGNlLR~~Llkdp~V~FAGY~IPHPLe~~i~LrIQT~~~~~P~eaLk~Al~~L~~~~~~L~ 178 (639)
.++|+++|+|.||||||||+||++|+++|+|.||||+||||++++++|||||+++.+|.+||++|+++|++.|++|+
T Consensus 6 ~~~n~~~~~i~~EDHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~lrIqT~~~~~p~~al~~a~~~l~~~~~~~~ 82 (83)
T cd06927 6 KEDNELELEIEGEDHTLLNLLKEELLRDPGVKVASYDIEHPLLSNPVLKIKTDGGVDPLEALKEAAKRLIDLCEEFL 82 (83)
T ss_pred cCCCEEEEEEeCCCchHHHHHHHHHhcCCCeEEEEeecCCCCCCccEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHh
Confidence 36899999999999999999999999999999999999999999999999999999999999999999999999986
No 6
>PRK01146 DNA-directed RNA polymerase subunit L; Provisional
Probab=99.94 E-value=1.7e-26 Score=200.40 Aligned_cols=76 Identities=26% Similarity=0.436 Sum_probs=74.4
Q ss_pred CCCeEEEEEccCCcchHHHHHHHHhcCCCeeEEeecCCCCCCCceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHH
Q psy12711 103 KPNCRTFVFEKEGHTFGSVITHILQSYPEVDFAGYSVPHPADFQIFIRIQVKDGYDSIDILKKGIKELESACDRIT 178 (639)
Q Consensus 103 ~~N~~tf~i~gEDHTLGNlLR~~Llkdp~V~FAGY~IPHPLe~~i~LrIQT~~~~~P~eaLk~Al~~L~~~~~~L~ 178 (639)
++|+++|+|.||||||||+||++|+++|+|+||||+||||++++++|||||+++.+|.+||++|+++|++.|++|+
T Consensus 9 ~~n~~~~~i~~EDHTlgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~lrIqt~~~~~p~~al~~a~~~L~~~~~~~~ 84 (85)
T PRK01146 9 EDNELELEIEGEDHTLMNLLKEELLEDPGVEAASYDIDHPLISNPVLKIKTDGGIDPLEALKEAAKRIIDLCDEFL 84 (85)
T ss_pred CCCEEEEEEeCCCchHHHHHHHHHhcCCCeeEEEeecCCCCCCccEEEEEECCCCCHHHHHHHHHHHHHHHHHHHh
Confidence 6899999999999999999999999999999999999999999999999999999999999999999999999986
No 7
>cd07027 RNAP_RPB11_like RPB11 subunit of RNA polymerase. The eukaryotic RPB11 subunit of RNA polymerase (RNAP), as well as its archaeal (L subunit) and bacterial (alpha subunit) counterparts, is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The assembly of the two largest eukaryotic RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of RPB3/RPB11 heterodimer subunits. This is also true for the archaeal (D/
Probab=99.94 E-value=1.9e-26 Score=199.30 Aligned_cols=77 Identities=34% Similarity=0.503 Sum_probs=74.6
Q ss_pred CCCCeEEEEEccCCcchHHHHHHHHhcCCCeeEEeecCCCCCCCceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHH
Q psy12711 102 VKPNCRTFVFEKEGHTFGSVITHILQSYPEVDFAGYSVPHPADFQIFIRIQVKDGYDSIDILKKGIKELESACDRIT 178 (639)
Q Consensus 102 ~~~N~~tf~i~gEDHTLGNlLR~~Llkdp~V~FAGY~IPHPLe~~i~LrIQT~~~~~P~eaLk~Al~~L~~~~~~L~ 178 (639)
.++|+++|+|+||||||||+||++|+++|+|+||||+||||++++++|||||+++.+|.+||++|+++|.++|+++.
T Consensus 6 ~~~n~~~~~i~~EdHTLgNlLr~~L~~~~~V~fAgY~vpHPl~~~~~lrI~T~~~~~P~~al~~a~~~l~~~~~~l~ 82 (83)
T cd07027 6 KEKNSVTVEMENEDHTLGNLLREELLKDDQVDFARYYIKHPVIDKIQIRIQTKSGIKPKDALKRAVNKLSKLYEHLG 82 (83)
T ss_pred cCCCEEEEEEeCCCchHHHHHHHHHhcCCCeeEEEEecCCCCCCccEEEEEECCCCCHHHHHHHHHHHHHHHHHHhc
Confidence 46899999999999999999999999999999999999999999999999999989999999999999999999885
No 8
>KOG3438|consensus
Probab=99.92 E-value=1.9e-25 Score=198.13 Aligned_cols=87 Identities=36% Similarity=0.736 Sum_probs=84.4
Q ss_pred CCCeEEEEEccCCcchHHHHHHHHhcCCCeeEEeecCCCCCCCceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12711 103 KPNCRTFVFEKEGHTFGSVITHILQSYPEVDFAGYSVPHPADFQIFIRIQVKDGYDSIDILKKGIKELESACDRITETFN 182 (639)
Q Consensus 103 ~~N~~tf~i~gEDHTLGNlLR~~Llkdp~V~FAGY~IPHPLe~~i~LrIQT~~~~~P~eaLk~Al~~L~~~~~~L~~~F~ 182 (639)
+.++.+|++.+|||||||.||+.|+++|+|+||||.||||++++++|||||.++..++++|++||++|...|+++..+|+
T Consensus 14 d~~~~Tf~~~eEDHTlgNalR~vI~k~peVefcGYtIPHPse~k~niRIQt~~~~~A~evl~kgl~el~~~c~~v~~kF~ 93 (105)
T KOG3438|consen 14 DLSSATFQLREEDHTLGNALRYVIMKNPEVEFCGYTIPHPSEDKINIRIQTRDGDPAVEVLKKGLEELMQLCDHVRSKFE 93 (105)
T ss_pred CCCceEEEEEecCcchhHHHHHHHhcCCceEEEeccCCCCchhhheEEEEecCCCcchHHHHHHHHHHHHHHHHHHHHHH
Confidence 78999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhcc
Q psy12711 183 DAMQCKV 189 (639)
Q Consensus 183 ~ai~~k~ 189 (639)
+++++.+
T Consensus 94 ~~i~~~k 100 (105)
T KOG3438|consen 94 EEIEEYK 100 (105)
T ss_pred HHHHHhh
Confidence 9998654
No 9
>COG1761 RPB11 DNA-directed RNA polymerase, subunit L [Transcription]
Probab=99.92 E-value=1.1e-24 Score=194.09 Aligned_cols=95 Identities=26% Similarity=0.400 Sum_probs=87.4
Q ss_pred CceeEeecCCccCCCCeEEEEEccCCcchHHHHHHHHhcCCCeeEEeecCCCCCCCceEEEEEeCCCCCHHHHHHHHHHH
Q psy12711 90 SPVWELRDNTLNVKPNCRTFVFEKEGHTFGSVITHILQSYPEVDFAGYSVPHPADFQIFIRIQVKDGYDSIDILKKGIKE 169 (639)
Q Consensus 90 ~Kv~~~~dt~~~~~~N~~tf~i~gEDHTLGNlLR~~Llkdp~V~FAGY~IPHPLe~~i~LrIQT~~~~~P~eaLk~Al~~ 169 (639)
.++++..+++ ++|+++|++.||||||||+|++.|+++++|+||||+||||+.+++.|||||+++++|.+||++|++.
T Consensus 3 ~~~~l~ii~~---~~n~~~i~i~gEdHTL~NlL~~~L~~d~~V~~a~Y~i~HP~~~~~~i~Ikt~~~~dp~~aL~~A~~~ 79 (99)
T COG1761 3 PEMELRIIKK---DDNSLELEIEGEDHTLGNLLREELLKDEDVEFAAYSIPHPLIDNPKIRIKTKGGVDPKEALKRAARK 79 (99)
T ss_pred CceEEEEecc---CCCEEEEEEecCCchHHHHHHHHHhCCCCeeEEEEeCCCCCCCCceEEEEECCCCCHHHHHHHHHHH
Confidence 3455555554 6999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhhc
Q psy12711 170 LESACDRITETFNDAMQCK 188 (639)
Q Consensus 170 L~~~~~~L~~~F~~ai~~k 188 (639)
+++.|++|.++| ++++.+
T Consensus 80 i~~~~~~l~~~~-~~~e~~ 97 (99)
T COG1761 80 ILKDLEELLDQF-EEFEKK 97 (99)
T ss_pred HHHHHHHHHHHH-HHHHhh
Confidence 999999999998 887754
No 10
>PF01582 TIR: TIR domain; InterPro: IPR000157 In Drosophila melanogaster the Toll protein is involved in establishment of dorso-ventral polarity in the embryo. In addition, members of the Toll family play a key role in innate antibacterial and antifungal immunity in insects as well as in mammals. These proteins are type-I transmembrane receptors that share an intracellular 200 residue domain with the interleukin-1 receptor (IL-1R), the Toll/IL-1R homologous region (TIR). The similarity between Toll-like receptors (LTRs) and IL-1R is not restricted to sequence homology since these proteins also share a similar signalling pathway. They both induce the activation of a Rel type transcription factor via an adaptor protein and a protein kinase []. Interestingly, MyD88, a cytoplasmic adaptor protein found in mammals, contains a TIR domain associated to a DEATH domain (see IPR000488 from INTERPRO) [, , ]. Besides the mammalian and Drosophila melanogaster proteins, a TIR domain is also found in a number of plant proteins implicated in host defence []. As MyD88, these proteins are cytoplasmic. Site directed mutagenesis and deletion analysis have shown that the TIR domain is essential for Toll and IL-1R activities. Sequence analysis have revealed the presence of three highly conserved regions among the different members of the family: box 1 (FDAFISY), box 2 (GYKLC-RD-PG), and box 3 (a conserved W surrounded by basic residues). It has been proposed that boxes 1 and 2 are involved in the binding of proteins involved in signalling, whereas box 3 is primarily involved in directing localization of receptor, perhaps through interactions with cytoskeletal elements [].; GO: 0005515 protein binding, 0007165 signal transduction, 0005622 intracellular; PDB: 3J0A_A 2J67_B 3JRN_A 1FYV_A 1O77_D 1FYX_A 1FYW_A 3OZI_B 1T3G_B 2JS7_A ....
Probab=99.89 E-value=2.8e-23 Score=190.79 Aligned_cols=134 Identities=18% Similarity=0.310 Sum_probs=101.2
Q ss_pred eEEEecc-CCHHH-HHHHHHhhhcC--CceEEEecCCCCCCcchHHHHHHHHHhcceEEEEecccccCChhhHHHHHHHH
Q psy12711 388 ALLLYDE-ADFDL-AKQFNTQLNKM--GFTVCDKDNSFLTGQFEHSAFIQVMDRCTCVIVLMSTHFMNNSLLHSLTQYAE 463 (639)
Q Consensus 388 AFVsYS~-kD~dF-V~eLv~~LE~~--gykLCLh~RDflpG~~i~e~I~~aIerSRR~IvVLSpnFL~SeWc~fe~~~A~ 463 (639)
|||||+. +|.+| +.+|.+.||+. ||++|+++||+.||..+.++|.++|++||++|+|+|++|++|+||.+|+..|+
T Consensus 1 vfisy~~~~d~~~~~~~L~~~Le~~~~g~~~c~~~rD~~~G~~~~~~i~~~i~~Sr~~I~VlS~~y~~s~wc~~el~~a~ 80 (141)
T PF01582_consen 1 VFISYSGKDDREWFVSHLLPELEERPYGYKLCLDERDFLPGESILDNIQEAIERSRRTIVVLSRNYLSSEWCLFELQEAL 80 (141)
T ss_dssp EEEEE-GHHGHHHHHHCHHHHHHCTSSTS-EEEHHHCTSSSSCHHHHHHHHHHTEEEEEEEESHHHHHHTHHHHHHHHHH
T ss_pred cEEEeCCCCcHHHHHHHHHHHHHhCCCCeEEEEechhhcccccccchhhHhhhhceeeEEEeecccccccchhhhhhhhh
Confidence 8999999 89888 58899999955 99999999999999989999999999999999999999999999999999999
Q ss_pred HHhhhhcCCCcEEEEEeccCCCCcccchhhhhhcccccccchhhHHHHHHHHhccCCCCCccCCCCc---chhHHHHHHH
Q psy12711 464 AKHIDHTIHSKIIPILCSDDYFSVGFLQYCVKLKLNHYASNMEQFWDRLYYSLKGVGKGVPEWDFAS---NMEQFWDRLY 540 (639)
Q Consensus 464 ~l~l~~r~~~kLIpIlye~~~~~P~~Lr~~~~ld~~~~~~~~~wFW~RLr~aL~~~~~~~p~W~~~s---~~~~FW~KLr 540 (639)
......+ +.++|+|++.+.. +..+... ..++..++ ..++.+|+++. ....||++|+
T Consensus 81 ~~~~~~~-~~~~Il~v~~~v~--~~~~~~~----------------~~~~~~~~--~~~~~~w~~~~~~~~~~~fW~~l~ 139 (141)
T PF01582_consen 81 ERLLEEG-RDKLILPVFYDVS--PSDVRPD----------------QSLRFLLR--FLTYLRWPDDDSREDRSWFWKKLR 139 (141)
T ss_dssp HHHHCST-CTTEEEEESSSS---CHHCHTH----------------HHHHHHHH--CTHCEETSSSGGGGGHHHHHHHHH
T ss_pred hhccccc-cccceeeEeccCC--hhhcChh----------------hhHHHHHH--hhhheeCCCCCCccHHHHHHHHHh
Confidence 9877754 3566666665432 2233300 11111111 23345888753 4578999999
Q ss_pred Hh
Q psy12711 541 YS 542 (639)
Q Consensus 541 ~a 542 (639)
++
T Consensus 140 ~~ 141 (141)
T PF01582_consen 140 YH 141 (141)
T ss_dssp HH
T ss_pred cC
Confidence 85
No 11
>smart00255 TIR Toll - interleukin 1 - resistance.
Probab=99.85 E-value=7e-21 Score=171.62 Aligned_cols=137 Identities=18% Similarity=0.318 Sum_probs=101.6
Q ss_pred ccceEEEeccCCHHHHHHHHHhhhc--CCceEEEecCCCCCCcchHHHHHHHHHhcceEEEEecccccCChhhHHHHHHH
Q psy12711 385 HYDALLLYDEADFDLAKQFNTQLNK--MGFTVCDKDNSFLTGQFEHSAFIQVMDRCTCVIVLMSTHFMNNSLLHSLTQYA 462 (639)
Q Consensus 385 ~YDAFVsYS~kD~dFV~eLv~~LE~--~gykLCLh~RDflpG~~i~e~I~~aIerSRR~IvVLSpnFL~SeWc~fe~~~A 462 (639)
.||||||||++ .+...++++.|++ .++++|++.||+.+|....+.|.++|++|+++|+|+||+|++|+||.+|+..|
T Consensus 1 ~~dvFISys~~-~~~~~~~v~~L~~~l~~~~~~v~~d~~~~~~~~~~~i~~~i~~s~~~i~vlS~~~~~S~w~~~E~~~a 79 (140)
T smart00255 1 EYDVFISYSGK-EDVRNEFLSHLLEKLRGYGLCVFIDDFEPGGGDLEEIDEAIEKSRIAIVVLSPNYAESEWCLDELVAA 79 (140)
T ss_pred CCeEEEECCCC-HHHHHHHHHHHHHHhhcCCcEEEecCcccccchHHHHHHHHHHCcEEEEEECcccccChhHHHHHHHH
Confidence 49999999997 2224666777772 46789999999999965556889999999999999999999999999999999
Q ss_pred HHHhhhhcCCCcEEEEEeccCCCCcccchhhhhhcccccccchhhHHHHHHHHhccCCCCCccCCCCcchhHHHHHHHHh
Q psy12711 463 EAKHIDHTIHSKIIPILCSDDYFSVGFLQYCVKLKLNHYASNMEQFWDRLYYSLKGVGKGVPEWDFASNMEQFWDRLYYS 542 (639)
Q Consensus 463 ~~l~l~~r~~~kLIpIlye~~~~~P~~Lr~~~~ld~~~~~~~~~wFW~RLr~aL~~~~~~~p~W~~~s~~~~FW~KLr~a 542 (639)
.....+.+ +.+||||+++.+...+..+. ..|+.+++. ++.+|+++... .||++|+++
T Consensus 80 ~~~~~~~~-~~~iIPI~~~~~~~~~~~~~------------------~~l~~~~~~---~~~~w~~~~~~-~fW~~~~~~ 136 (140)
T smart00255 80 LENALEEG-GLRVIPIFYEVIPSDVRKQP------------------GKFRKVLKK---NYLKWPEDEKE-RFWKKALYA 136 (140)
T ss_pred HHHHHHcC-CCeEEEEEEecChHHHHhcc------------------cHHHHHHHH---HHhhcCCchhH-HHHHHHHHH
Confidence 88766544 58999999987621000010 123333321 14588863332 799999999
Q ss_pred hcC
Q psy12711 543 LKG 545 (639)
Q Consensus 543 L~d 545 (639)
|++
T Consensus 137 l~~ 139 (140)
T smart00255 137 VPS 139 (140)
T ss_pred hcc
Confidence 986
No 12
>cd00460 RNAP_RPB11_RPB3 RPB11 and RPB3 subunits of RNA polymerase. The eukaryotic RPB11 and RPB3 subunits of RNA polymerase (RNAP), as well as their archaeal (L and D subunits) and bacterial (alpha subunit) counterparts, are involved in the assembly of RNAP, a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The assembly of the two largest eukaryotic RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of RPB3/RPB11 heterodimer subunits. This is also true for the
Probab=99.81 E-value=9.4e-20 Score=157.94 Aligned_cols=75 Identities=28% Similarity=0.525 Sum_probs=71.7
Q ss_pred CCCCeEEEEEccCCcchHHHHHHHHhcCCCeeEEeecCCCCC------CCceEEEEEeCCCCCHHHHHHHHHHHHHHHHH
Q psy12711 102 VKPNCRTFVFEKEGHTFGSVITHILQSYPEVDFAGYSVPHPA------DFQIFIRIQVKDGYDSIDILKKGIKELESACD 175 (639)
Q Consensus 102 ~~~N~~tf~i~gEDHTLGNlLR~~Llkdp~V~FAGY~IPHPL------e~~i~LrIQT~~~~~P~eaLk~Al~~L~~~~~ 175 (639)
.++|+++|+|.||||||||+||+.|++ +.|.||||+||||+ .+++.|+|+|+|+++|.+||.+|++.|.+.|+
T Consensus 6 ~~~~~~~~~~~~edhTl~n~L~~~l~~-~pV~~a~Y~v~hp~~~~~~~~d~~~~~VeT~Gs~~P~~al~~Ai~~L~~~~~ 84 (86)
T cd00460 6 KEKNYVDFVLENEDHTLGNSLRRILLK-SPVEFAAYYVEHPVKLQRTDEDKFILRIETVGSIPPEEALRRAVEILRKKLE 84 (86)
T ss_pred CCCCEEEEEEeCCCchHHHHHHHHHhC-CCceEEEEEeCCCccCCCCCCCeEEEEEEECCCCCHHHHHHHHHHHHHHHHh
Confidence 368999999999999999999999999 99999999999999 99999999999999999999999999999987
Q ss_pred HH
Q psy12711 176 RI 177 (639)
Q Consensus 176 ~L 177 (639)
.|
T Consensus 85 ~~ 86 (86)
T cd00460 85 HL 86 (86)
T ss_pred hC
Confidence 54
No 13
>cd08312 Death_MyD88 Death domain of Myeloid Differentation primary response protein MyD88. Death Domain (DD) of Myeloid Differentiation primary response protein 88 (MyD88). MyD88 is an adaptor protein involved in interleukin-1 receptor (IL-1R)- and Toll-like receptor (TLR)-induced activation of nuclear factor-kappaB (NF-kB) and mitogen activated protein kinase pathways that lead to the induction of proinflammatory cytokines. It is a key component in the signaling pathway of pathogen recognition in the innate immune system. MyD88 contains an N-terminal DD and a C-terminal Toll/IL-1 Receptor (TIR) homology domain that mediates interaction with TLRs and IL-1R. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and
Probab=99.74 E-value=1.5e-18 Score=148.60 Aligned_cols=76 Identities=22% Similarity=0.290 Sum_probs=70.3
Q ss_pred hHHHHHhccCCcccccCCCCccCchHHHHHHcCCCCC---CCCCccchHHHHHHHhhccCCCCCCcccHHHHHHHHhhcc
Q psy12711 252 TRQVLNDKLCDIKQLMSPENYQRDYRGLADLMDIKAP---PNPNCEDLMKKMFEDWTKSSTLDRSVFNIATFLHFLECID 328 (639)
Q Consensus 252 tR~~Ls~~LNp~k~l~s~~g~~rDWRgLAelmgf~~~---~~e~~~~Pt~~vLe~W~~r~~~~~~~aTvg~Ll~~Le~id 328 (639)
||++||.+|||++.+ .+|||+||+.|||++. .+++.++||+.||+.|+.|++ ++|||+|.++|++|+
T Consensus 1 ~R~~L~~~Ldp~~~~------g~DWr~LA~~Lg~~~~~I~~f~~~~sPt~~lL~~W~~r~~----~atv~~L~~~L~~~~ 70 (79)
T cd08312 1 VRRRLSLFLNPPRVV------AADWTALAEEMGFEYLEIRNFETKPSPTEKVLEDWETRPD----GATVGNLLELLEKLE 70 (79)
T ss_pred CHHHHHHHcCCCCCc------ccCHHHHHHHcCCCHHHHHHHccCCChHHHHHHHHHhcCC----CCcHHHHHHHHHHcC
Confidence 699999999999876 8999999999999985 678889999999999999973 589999999999999
Q ss_pred cchhhhhch
Q psy12711 329 RFDVYDDCI 337 (639)
Q Consensus 329 R~DVldD~~ 337 (639)
|+||++|++
T Consensus 71 R~Dv~~d~~ 79 (79)
T cd08312 71 RRDVLHELG 79 (79)
T ss_pred hHHHHHhcC
Confidence 999999984
No 14
>cd08802 Death_UNC5B Death domain found in Uncoordinated-5B. Death Domain (DD) found in Uncoordinated-5B (UNC5B). UNC5B is part of the UNC-5 homolog family. It is a receptor for the secreted netrin-1 and plays a role in axonal guidance, angiogenesis, and apoptosis. UNC5B signaling is involved in the netrin-1-induced proliferation and migration of renal proximal tubular cells. It is also required for vascular patterning during embryonic development, and its activation inhibits sprouting angiogenesis. UNC5 proteins are transmembrane proteins with an extracellular domain consisting of two immunoglobulin repeats, two thrombospondin type-I modules and an intracellular region containing a ZU-5 domain, UPA domain and a DD. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activatio
Probab=99.61 E-value=4.8e-16 Score=135.28 Aligned_cols=79 Identities=14% Similarity=0.116 Sum_probs=71.1
Q ss_pred cChhhHHHHHhccCCcccccCCCCccCchHHHHHHcCCC-CC-CCCCccchHHHHHHHhhccCCCCCCcccHHHHHHHHh
Q psy12711 248 IRPKTRQVLNDKLCDIKQLMSPENYQRDYRGLADLMDIK-AP-PNPNCEDLMKKMFEDWTKSSTLDRSVFNIATFLHFLE 325 (639)
Q Consensus 248 L~~~tR~~Ls~~LNp~k~l~s~~g~~rDWRgLAelmgf~-~~-~~e~~~~Pt~~vLe~W~~r~~~~~~~aTvg~Ll~~Le 325 (639)
|.+.+|++|+.+|||+... ++|||.|||.|||+ |. .++..++||+.||+.|+.|+. .++||++|+++|+
T Consensus 1 ~p~~vR~kLc~~Ld~p~~~------g~DW~~LAekL~ld~yl~~f~~~psPT~~LLd~WE~~~~---~~~~v~~L~~~L~ 71 (84)
T cd08802 1 IPLSIRQKICNSLDAPNSR------GNDWRLLAQKLSMDRYLNYFATKASPTGVILDLWEARHQ---DDGDLNSLASALE 71 (84)
T ss_pred CChhHHHHHHHHhCCCCCC------CCcHHHHHHHcCchhHHHHHHcCCCcHHHHHHHHHhcCC---CcccHHHHHHHHH
Confidence 4678999999999999876 89999999999999 55 678899999999999999963 2689999999999
Q ss_pred hcccchhhhh
Q psy12711 326 CIDRFDVYDD 335 (639)
Q Consensus 326 ~idR~DVldD 335 (639)
+|+|.||+..
T Consensus 72 ~mgR~D~~~~ 81 (84)
T cd08802 72 EMGKSEMLVV 81 (84)
T ss_pred HcCcchHHHH
Confidence 9999999964
No 15
>PF13676 TIR_2: TIR domain; PDB: 3H16_B 3UB4_A 2Y92_A 3UB3_A 3UB2_A.
Probab=99.57 E-value=6.8e-16 Score=133.57 Aligned_cols=102 Identities=20% Similarity=0.265 Sum_probs=83.3
Q ss_pred eEEEeccCCHHHHHHHHHhhhcCCceEEEecCCCCCCcchHHHHHHHHHhcceEEEEecccccCChhhHHHHHHHHHHhh
Q psy12711 388 ALLLYDEADFDLAKQFNTQLNKMGFTVCDKDNSFLTGQFEHSAFIQVMDRCTCVIVLMSTHFMNNSLLHSLTQYAEAKHI 467 (639)
Q Consensus 388 AFVsYS~kD~dFV~eLv~~LE~~gykLCLh~RDflpG~~i~e~I~~aIerSRR~IvVLSpnFL~SeWc~fe~~~A~~l~l 467 (639)
+||||+.+|.+||..|...|+..|+++++.. |..+|....+.|.+++++|+.+|+++|++|++|+||.+|+..|..
T Consensus 1 VFIS~~~~D~~~a~~l~~~L~~~g~~v~~d~-~~~~g~~~~~~i~~~i~~s~~~i~~~S~~~~~s~~~~~E~~~a~~--- 76 (102)
T PF13676_consen 1 VFISYSSEDREFAERLAERLESAGIRVFLDR-DIPPGEDWREEIERAIERSDCVIVLLSPNYLKSPWCRFELGAAWK--- 76 (102)
T ss_dssp EEEEEEGGGCCCHHHHHHHHHHTT--EE-GG-EE-TTS-HHCCCHHCCTTEEEEEEEEEHHHHCTHHHHHHHHHHHC---
T ss_pred eEEEecCCcHHHHHHHHHHHhhcCCEEEEEE-eCCCCCCHHHHHHHHHHhCCEEEEEECcccccChHHHHHHHHHHH---
Confidence 6999999999999999999999999999886 999998777888899999999999999999999999999998843
Q ss_pred hhcCCCcEEEEEeccCCCCcccchhhhhhc
Q psy12711 468 DHTIHSKIIPILCSDDYFSVGFLQYCVKLK 497 (639)
Q Consensus 468 ~~r~~~kLIpIlye~~~~~P~~Lr~~~~ld 497 (639)
. +++||||++++++ +|+.|+.+.++|
T Consensus 77 -~--~~~iipv~~~~~~-~p~~l~~~~~id 102 (102)
T PF13676_consen 77 -R--GKPIIPVRLDPCE-LPGPLRGLQYID 102 (102)
T ss_dssp -T--SESEEEEECSGGG-S-GGGGGS--EE
T ss_pred -C--CCEEEEEEECCcC-CCHHHHhccCCC
Confidence 2 3579999998876 577888776654
No 16
>cd08799 Death_UNC5C Death domain found in Uncoordinated-5C. Death Domain (DD) found in Uncoordinated-5C (UNC5C). UNC5C is part of the UNC-5 homolog family. It is a receptor for the secreted netrin-1 and plays a role in axonal guidance, angiogenesis, and apoptosis. UNC5C plays a critical role in the development of spinal accesory motor neurons. Methylation of the UNC5C gene is associated with early stages of colorectal carcinogenesis. UNC5 proteins are transmembrane proteins with an extracellular domain consisting of two immunoglobulin repeats, two thrombospondin type-I modules and an intracellular region containing a ZU-5 domain, UPA domain and a DD. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN.
Probab=99.52 E-value=1e-14 Score=127.04 Aligned_cols=77 Identities=18% Similarity=0.167 Sum_probs=68.7
Q ss_pred cChhhHHHHHhccCCcccccCCCCccCchHHHHHHcCCC-CC-CCCCccchHHHHHHHhhccCCCCCCcccHHHHHHHHh
Q psy12711 248 IRPKTRQVLNDKLCDIKQLMSPENYQRDYRGLADLMDIK-AP-PNPNCEDLMKKMFEDWTKSSTLDRSVFNIATFLHFLE 325 (639)
Q Consensus 248 L~~~tR~~Ls~~LNp~k~l~s~~g~~rDWRgLAelmgf~-~~-~~e~~~~Pt~~vLe~W~~r~~~~~~~aTvg~Ll~~Le 325 (639)
|.+.+|++|+.+|||+... ++|||.||+.|||+ |. .+++..+||..||+.|+.|+. .++|||.|+++|+
T Consensus 1 ~p~~~R~kLc~lLd~p~~~------g~DWr~LAekLgl~~~l~~f~~~~SPT~~LLd~WEar~~---~~~tv~~L~~~L~ 71 (84)
T cd08799 1 IPLSIRQKLCGSLDAPQTR------GNDWRMLAHKLNLDRYLNYFATKSSPTGVILDLWEAQHF---PDGNLSRLAAVLE 71 (84)
T ss_pred CChHHHHHHHHHcCCCCCC------CCCHHHHHHHcCCHHHHHHHHcCCChHHHHHHHHHhccC---CCCcHHHHHHHHH
Confidence 4678999999999999876 89999999999999 54 677899999999999999842 2689999999999
Q ss_pred hcccchhh
Q psy12711 326 CIDRFDVY 333 (639)
Q Consensus 326 ~idR~DVl 333 (639)
+|+|.|.+
T Consensus 72 emgR~d~~ 79 (84)
T cd08799 72 EMGRHETV 79 (84)
T ss_pred HcCCccch
Confidence 99999986
No 17
>cd08782 Death_DAPK1 Death domain found in death-associated protein kinase 1. Death domain (DD) found in death-associated protein kinase 1 (DAPK1). DAPK1 is composed of several functional domains, including a kinase domain, a CaM regulatory domain, ankyrin repeats, a cytoskeletal binding domain and a C-terminal DD. It plays important roles in a diverse range of signal transduction pathways including apoptosis, growth factor signalling, and autophagy. Loss of DAPK1 expression, usually because of DNA methylation, is implicated in many tumor types. DAPK1 is highly abundant in the brain and has also been associated with neurodegeneration. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as ad
Probab=99.51 E-value=1.3e-14 Score=125.76 Aligned_cols=72 Identities=21% Similarity=0.254 Sum_probs=63.6
Q ss_pred hHHHHHhccCCcccccCCCCccCchHHHHHHcCCCCC--CCCCc----cchHHHHHHHhhccCCCCCCcccHHHHHHHHh
Q psy12711 252 TRQVLNDKLCDIKQLMSPENYQRDYRGLADLMDIKAP--PNPNC----EDLMKKMFEDWTKSSTLDRSVFNIATFLHFLE 325 (639)
Q Consensus 252 tR~~Ls~~LNp~k~l~s~~g~~rDWRgLAelmgf~~~--~~e~~----~~Pt~~vLe~W~~r~~~~~~~aTvg~Ll~~Le 325 (639)
+|++|+.+|||+... .+|||.||+.|||.+. .+... .+||+.||++|++++ .+|||+|+++|+
T Consensus 2 ~R~~L~~lLdpp~~~------g~DW~~LA~~Lg~~~~~~~~~~~~~~~~sPT~~LL~~W~~~~-----~~tvg~L~~~L~ 70 (82)
T cd08782 2 TRRKLSRLLDPPDPM------GRDWCLLAVNLGLTDLVPQLDTNSSSLPSPTDALLQEWATAP-----PSTIGTLIDKLR 70 (82)
T ss_pred HHHHHHHHcCCCCCC------CCCHHHHHHHcCChhhHHHHHhcCCCCCCcHHHHHHHHhcCC-----cccHHHHHHHHH
Confidence 799999999998755 8999999999998876 23332 799999999999986 489999999999
Q ss_pred hcccchhhh
Q psy12711 326 CIDRFDVYD 334 (639)
Q Consensus 326 ~idR~DVld 334 (639)
+|+|.||++
T Consensus 71 ~~gR~Da~~ 79 (82)
T cd08782 71 ELGREDAAD 79 (82)
T ss_pred HcCcHHHHH
Confidence 999999987
No 18
>cd08781 Death_UNC5-like Death domain found in Uncoordinated-5 homolog family. Death Domain (DD) found in Uncoordinated-5 (UNC-5) homolog family, which includes Unc5A, B, C and D in vertebrates. UNC5 proteins are receptors for secreted netrins (netrin-1, -3 and -4) that are involved in diverse processes like axonal guidance, neuronal migration, blood vessel patterning, and apoptosis. They are transmembrane proteins with an extracellular domain consisting of two immunoglobulin repeats, two thrombospondin type-I modules and an intracellular region containing a ZU-5 domain, UPA domain and a DD. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit
Probab=99.44 E-value=1.1e-13 Score=119.93 Aligned_cols=78 Identities=17% Similarity=0.150 Sum_probs=68.2
Q ss_pred cChhhHHHHHhccCCcccccCCCCccCchHHHHHHcCCCCC--CCCCccchHHHHHHHhhccCCCCCCcccHHHHHHHHh
Q psy12711 248 IRPKTRQVLNDKLCDIKQLMSPENYQRDYRGLADLMDIKAP--PNPNCEDLMKKMFEDWTKSSTLDRSVFNIATFLHFLE 325 (639)
Q Consensus 248 L~~~tR~~Ls~~LNp~k~l~s~~g~~rDWRgLAelmgf~~~--~~e~~~~Pt~~vLe~W~~r~~~~~~~aTvg~Ll~~Le 325 (639)
|.+.+|++|+.+|||.... .+|||+||+.||++.. .++...+||+.||+.|+.++. .++||++|.++|+
T Consensus 1 lp~~~r~~Lc~~LD~~~~~------g~dWr~LA~~Lgl~~~i~~~~~~~SPT~~LL~~We~~~~---~~~tv~~L~~~L~ 71 (83)
T cd08781 1 LPYSIRQKLCSSLDPPNPR------GNDWRLLAKKLSVDRYLNYFATKPSPTGVILDLWEARHR---DDGALNDLAQILE 71 (83)
T ss_pred CCHHHHHHHHHHcCCCCCC------CCCHHHHHHHhCcHHHHHHHcCCCChHHHHHHHHHhcCC---CcchHHHHHHHHH
Confidence 4678999999999999765 8999999999999842 456788999999999999853 2689999999999
Q ss_pred hcccchhhh
Q psy12711 326 CIDRFDVYD 334 (639)
Q Consensus 326 ~idR~DVld 334 (639)
+|+|.|+++
T Consensus 72 ~mgr~da~~ 80 (83)
T cd08781 72 EMGRTDAVN 80 (83)
T ss_pred HcCcHHHHH
Confidence 999999985
No 19
>cd08310 Death_NFkB-like Death domain of Nuclear Factor-KappaB precursor proteins. Death Domain (DD) of Nuclear Factor-KappaB (NF-kB) precursor proteins. The NF-kB family of transcription factors play a central role in cardiovascular growth, stress response, and inflammation by controlling the expression of a network of different genes. There are five NF-kB proteins, all containing an N-terminal REL Homology Domain (RHD). Two of these, NF-kB1 and NF-kB2 are produced from the processing of the precursor proteins p105 and p100, respectively. In addition to RHD, p105 and p100 contain ANK repeats and a C-terminal DD. NF-kBs are regulated by the Inhibitor of NF-kB (IkB) Kinase (IKK) complex through classical and non-canonical pathways, which differ in the IKK subunits involved and downstream targets. IKKs facilitate the release of NF-kB dimers from an inactive state, allowing them to migrate to the nucleus where they regulate gene transcription. The precursor proteins p105 and p100 function
Probab=99.37 E-value=3.8e-13 Score=113.91 Aligned_cols=67 Identities=21% Similarity=0.224 Sum_probs=61.7
Q ss_pred hHHHHHhccCCcccccCCCCccCchHHHHHHcCCCCC--CCCCccchHHHHHHHhhccCCCCCCcccHHHHHHHHhhccc
Q psy12711 252 TRQVLNDKLCDIKQLMSPENYQRDYRGLADLMDIKAP--PNPNCEDLMKKMFEDWTKSSTLDRSVFNIATFLHFLECIDR 329 (639)
Q Consensus 252 tR~~Ls~~LNp~k~l~s~~g~~rDWRgLAelmgf~~~--~~e~~~~Pt~~vLe~W~~r~~~~~~~aTvg~Ll~~Le~idR 329 (639)
+|++|+.+||| ..|||.||+.|||.+. .+++.++||+.+|+.|+.++ +||++|+++|+.|+|
T Consensus 1 ~r~~L~~lLd~----------~~dWr~LA~~L~~~~~i~~~~~~~sPt~~LL~~we~~~------~tv~~L~~~L~~mgr 64 (72)
T cd08310 1 TRERLCKLLDD----------GCDWRELAQLLDLGHLVNFIRLSPSPTKMLLDYFEMQG------GTLERLRDALEVLGE 64 (72)
T ss_pred CHHHHHHHhCC----------CCCHHHHHHHcCcHHHHHHHhcCCCHHHHHHHHHHhCC------CCHHHHHHHHHHcCc
Confidence 68999999998 5899999999999986 56789999999999999974 799999999999999
Q ss_pred chhhh
Q psy12711 330 FDVYD 334 (639)
Q Consensus 330 ~DVld 334 (639)
.|++.
T Consensus 65 ~dav~ 69 (72)
T cd08310 65 TEAVE 69 (72)
T ss_pred HHHHH
Confidence 99986
No 20
>PF01193 RNA_pol_L: RNA polymerase Rpb3/Rpb11 dimerisation domain; InterPro: IPR011261 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. RNA polymerase (RNAP) II, which is responsible for all mRNA synthesis in eukaryotes, consists of 12 subunits. Subunits Rpb3 and Rpb11 form a heterodimer that is functionally analogous to the archaeal RNAP D/L heterodimer, and to the prokaryotic RNAP alpha subunit (RpoA) homodimer. In each case, they play a key role in RNAP assembly by forming a platform on which the catalytic subunits (eukaryotic Rpb1/Rpb2, and prokaryotic beta/beta') can interact []. These different subunits share regions of homology required for dimerisation. In eukaryotic Rpb11 and archaeal L subunits, the dimerisation domain consists of a contiguous Rpb11-like domain, whereas in eukaryotic Rpb3, archaeal D and bacterial RpoA subunits (IPR011263 from INTERPRO), the dimerisation domain consists of the Rpb11-like domain interrupted by an insert domain. In the prokaryotic alpha subunit, this dimerisation domain is the N-terminal domain [].; GO: 0003899 DNA-directed RNA polymerase activity, 0046983 protein dimerization activity, 0006351 transcription, DNA-dependent; PDB: 1HQM_B 1YNJ_A 1YNN_A 1I6V_A 2GHO_A 3HKZ_V 2PMZ_X 2PA8_L 3GTK_C 1TWH_C ....
Probab=99.37 E-value=4.9e-13 Score=110.45 Aligned_cols=65 Identities=31% Similarity=0.509 Sum_probs=61.4
Q ss_pred EEEEEccCCcchHHHHHHHHhcC-CCeeEEeecCCCCCCCceEEEEEeCCCCCHHHHHHHHHHHHHHHHH
Q psy12711 107 RTFVFEKEGHTFGSVITHILQSY-PEVDFAGYSVPHPADFQIFIRIQVKDGYDSIDILKKGIKELESACD 175 (639)
Q Consensus 107 ~tf~i~gEDHTLGNlLR~~Llkd-p~V~FAGY~IPHPLe~~i~LrIQT~~~~~P~eaLk~Al~~L~~~~~ 175 (639)
++|.+.|||||+||+||..|+++ |+|.+++ ||.++++.|+|+|+|+.+|.+||++|++.|.+.|+
T Consensus 1 i~~~~~g~~~tl~N~LRr~ll~~vp~~ai~~----~~~~~~~~~~IeT~g~~~p~~~l~~A~~~l~~~~~ 66 (66)
T PF01193_consen 1 IEFLLKGEDHTLGNALRRILLSEVPGVAIDG----HPNEDKFVFRIETDGSLTPKEALLKAIKILKEKLN 66 (66)
T ss_dssp EEEEEESHHHHHHHHHHHHHHSSSEEEEEEE----SSEEEEEEEEEEEBSSS-HHHHHHHHHHHHHHHHC
T ss_pred CEeEEcCCchHHHHHHHHHHHhcCCCceEEe----cCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHhcC
Confidence 57999999999999999999999 9999999 99999999999999999999999999999998874
No 21
>PLN03194 putative disease resistance protein; Provisional
Probab=99.35 E-value=4.5e-12 Score=124.70 Aligned_cols=101 Identities=12% Similarity=0.222 Sum_probs=89.2
Q ss_pred CCccceEEEeccCCH--HHHHHHHHhhhcCCceEEEecCCCCCCcchHHHHHHHHHhcceEEEEecccccCChhhHHHHH
Q psy12711 383 LAHYDALLLYDEADF--DLAKQFNTQLNKMGFTVCDKDNSFLTGQFEHSAFIQVMDRCTCVIVLMSTHFMNNSLLHSLTQ 460 (639)
Q Consensus 383 ~k~YDAFVsYS~kD~--dFV~eLv~~LE~~gykLCLh~RDflpG~~i~e~I~~aIerSRR~IvVLSpnFL~SeWc~fe~~ 460 (639)
...||+||||..+|. .||..|...|+..|++.++.+.++.+|..+...|..+|+.||..|+|+|++|..|.||--|+.
T Consensus 24 ~~~yDVFISFrG~DtR~~FvshL~~aL~~~GI~vF~D~~el~~G~~i~~~L~~AIeeSri~IvVfS~~Ya~S~WCLdEL~ 103 (187)
T PLN03194 24 AKPCDVFINHRGIDTKRTIATLLYDHLSRLNLRPFLDNKNMKPGDKLFDKINSAIRNCKVGVAVFSPRYCESYFCLHELA 103 (187)
T ss_pred CCCCcEEEeCCCccccccHHHHHHHHHHHCCCEEEEcCccccCCCcHHHHHHHHHHhCeEEEEEECCCcccchhHHHHHH
Confidence 578999999999996 799999999999999999999999999888889999999999999999999999999999987
Q ss_pred HHHHHhhhhcCCCcEEEEEeccCCCCcccchh
Q psy12711 461 YAEAKHIDHTIHSKIIPILCSDDYFSVGFLQY 492 (639)
Q Consensus 461 ~A~~l~l~~r~~~kLIpIlye~~~~~P~~Lr~ 492 (639)
.+... +.+||||+|+- .|.+++.
T Consensus 104 ~I~e~------~~~ViPIFY~V---dPsdVr~ 126 (187)
T PLN03194 104 LIMES------KKRVIPIFCDV---KPSQLRV 126 (187)
T ss_pred HHHHc------CCEEEEEEecC---CHHHhhc
Confidence 76432 25799999853 4666664
No 22
>cd08793 Death_IRAK4 Death domain of Interleukin-1 Receptor-Associated Kinase 4. Death Domain (DD) of Interleukin-1 Receptor-Associated Kinase 4 (IRAK4). IRAKs are essential components of innate immunity and inflammation in mammals and other vertebrates. They are involved in signal transduction pathways involving IL-1 and IL-18 receptors, Toll-like receptors, nuclear factor-kappaB, and mitogen-activated protein kinases. IRAKs contain an N-terminal DD domain and a C-terminal kinase domain. IRAK4 is an active kinase that is also involved in T-cell receptor signaling pathways, implying that it may function in acquired immunity and not just in innate immunity. It is known as the master IRAK member because its absence strongly impairs TLR- and IL-1-mediated signaling and innate immune defenses, while the absence of other IRAK proteins only shows slight effects. IRAK4-deficient patients have impaired inflammatory responses and recurrent life-threatening infections. DDs are protein-protein int
Probab=99.14 E-value=2.2e-11 Score=109.24 Aligned_cols=72 Identities=11% Similarity=0.121 Sum_probs=63.0
Q ss_pred ccccccChhhHHHHHhccCCcccccCCCCccCchHHHHHHc-------CCCCC---CCCC----ccchHHHHHHHhhccC
Q psy12711 243 IPIEAIRPKTRQVLNDKLCDIKQLMSPENYQRDYRGLADLM-------DIKAP---PNPN----CEDLMKKMFEDWTKSS 308 (639)
Q Consensus 243 vPL~aL~~~tR~~Ls~~LNp~k~l~s~~g~~rDWRgLAelm-------gf~~~---~~e~----~~~Pt~~vLe~W~~r~ 308 (639)
+|+++|++.+|++||.+|||.+ +|+.||+.| ||+++ .+|. ..+||.++|++|++.
T Consensus 1 t~ir~L~~~vrkkL~~~LDp~~----------~W~~LA~~i~~~~~~~~y~~~ei~~ie~~~~~g~SPT~~LL~dWgt~- 69 (100)
T cd08793 1 TYVRNLNYGLLRQLSDFLDPQE----------GWKKIAVAIKKPSGDPRYSQFHIRRFEALVQQGKSPTCELLFDWGTT- 69 (100)
T ss_pred ChHHHcCHHHHHHHHHHhCCcc----------cHHHHHHHHhcccCCCCCCHHHHHHHHHHHHcCCChHHHHHHHHccC-
Confidence 5789999999999999999984 999999999 78874 4565 689999999999763
Q ss_pred CCCCCcccHHHHHHHHhhcccc
Q psy12711 309 TLDRSVFNIATFLHFLECIDRF 330 (639)
Q Consensus 309 ~~~~~~aTvg~Ll~~Le~idR~ 330 (639)
++|||+|+++|.+++=+
T Consensus 70 -----N~TV~~L~~lL~k~~l~ 86 (100)
T cd08793 70 -----NCTVGDLVDLLIQNEFF 86 (100)
T ss_pred -----CCcHHHHHHHHHHcccH
Confidence 58999999999988754
No 23
>cd08311 Death_p75NR Death domain of p75 Neurotophin Receptor. Death Domain (DD) found in p75 neurotrophin receptor (p75NTR, NGFR, TNFRSF16). p75NTR binds members of the neurotrophin (NT) family including nerve growth factor (NGF), brain-derived neurotrophic factor (BDNF), and NT3, among others. It contains an NT-binding extracellular region that bears four cysteine-rich repeats, a transmembrane domain, and an intracellular DD. p75NTR plays roles in the immune, vascular, and nervous systems, and has been shown to promote cell death or survival, and to induce neurite outgrowth or collapse depending on its ligands and co-receptors. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptor
Probab=99.14 E-value=3.2e-11 Score=103.57 Aligned_cols=72 Identities=18% Similarity=0.260 Sum_probs=60.2
Q ss_pred HHHHHhccCCcccccCCCCccCchHHHHHHcCCCCC---CCCCccchHHHHHHHhhccCCCCCCcccHHHHHHHHhhccc
Q psy12711 253 RQVLNDKLCDIKQLMSPENYQRDYRGLADLMDIKAP---PNPNCEDLMKKMFEDWTKSSTLDRSVFNIATFLHFLECIDR 329 (639)
Q Consensus 253 R~~Ls~~LNp~k~l~s~~g~~rDWRgLAelmgf~~~---~~e~~~~Pt~~vLe~W~~r~~~~~~~aTvg~Ll~~Le~idR 329 (639)
++.+..+||-- +.++||+.||+.|||++. .+++..+|+.++|..|+.|. +||++.|+..|.+|+|
T Consensus 2 ~~~v~~ll~~~-------nlG~dW~~LA~~LG~~~~~I~~i~~~~~p~~~lL~~W~~r~-----~ATv~~L~~aL~~i~R 69 (77)
T cd08311 2 QEEVEKLLESG-------RPGRDWRSLAGELGYEDEAIDTFGREESPVRTLLADWSAQE-----GATLDALCTALRRIQR 69 (77)
T ss_pred hHHHHHHHhCC-------CCccCHHHHHHHcCCCHHHHHHHHcChhHHHHHHHHHHHCc-----CchHHHHHHHHHHcCh
Confidence 34455666533 347999999999999986 45566799999999999986 5999999999999999
Q ss_pred chhhhhc
Q psy12711 330 FDVYDDC 336 (639)
Q Consensus 330 ~DVldD~ 336 (639)
.||++++
T Consensus 70 ~Di~~~L 76 (77)
T cd08311 70 EDIAESL 76 (77)
T ss_pred HHHHHhc
Confidence 9999976
No 24
>cd08800 Death_UNC5A Death domain found in Uncoordinated-5A. Death Domain (DD) found in Uncoordinated-5A (UNC5A). UNC5A is part of the UNC-5 homolog family. It is a receptor for the secreted netrin-1 and plays a critical role in neuronal development and differentiation, as well as axon-guidance. It also plays a role in regulating apoptosis in non-neuronal cells as a downstream target of p53. UNC5 proteins are transmembrane proteins with an extracellular domain consisting of two immunoglobulin repeats, two thrombospondin type-I modules and an intracellular region containing a ZU-5 domain, UPA domain and a DD. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathway
Probab=99.07 E-value=1.9e-10 Score=100.41 Aligned_cols=79 Identities=15% Similarity=0.045 Sum_probs=68.2
Q ss_pred cChhhHHHHHhccCCcccccCCCCccCchHHHHHHcCCCCC--CCCCccchHHHHHHHhhccCCCCCCcccHHHHHHHHh
Q psy12711 248 IRPKTRQVLNDKLCDIKQLMSPENYQRDYRGLADLMDIKAP--PNPNCEDLMKKMFEDWTKSSTLDRSVFNIATFLHFLE 325 (639)
Q Consensus 248 L~~~tR~~Ls~~LNp~k~l~s~~g~~rDWRgLAelmgf~~~--~~e~~~~Pt~~vLe~W~~r~~~~~~~aTvg~Ll~~Le 325 (639)
+...+|++|+..|+++..- .+|||.||.-+|++.. -+.+.++||..+|+.|+.++-+ +.||+.|...|+
T Consensus 1 ip~~iR~kLc~lLD~p~~~------G~DWr~LA~kL~ld~~~~~f~~~pSPT~~LLd~WEa~~~~---~g~l~~L~~~l~ 71 (84)
T cd08800 1 IPFLIRQKIISSLDAPCPN------GADWRLLAQKLKLDSHLSFFASKSSPTAVILNLWEAQHFP---NGNLNQLAAVVA 71 (84)
T ss_pred CChHHHHHHHHHcCCCCCC------CCcHHHHHHHcCCccHHHHHHcCCChHHHHHHHHHhccCC---CCcHHHHHHHHH
Confidence 4578999999999988644 7999999999999986 4567889999999999987432 568999999999
Q ss_pred hcccchhhhh
Q psy12711 326 CIDRFDVYDD 335 (639)
Q Consensus 326 ~idR~DVldD 335 (639)
.|+|-|+++-
T Consensus 72 emGR~da~~~ 81 (84)
T cd08800 72 EIGKQDAMLF 81 (84)
T ss_pred HhCchHHHHH
Confidence 9999999864
No 25
>cd08309 Death_IRAK Death domain of Interleukin-1 Receptor-Associated Kinases. Death Domains (DDs) found in Interleukin-1 (IL-1) Receptor-Associated Kinases (IRAK1-4) and similar proteins. IRAKs are essential components of innate immunity and inflammation in mammals and other vertebrates. All four types are involved in signal transduction involving IL-1 and IL-18 receptors, Toll-like receptors, nuclear factor-kappaB, and mitogen-activated protein kinase pathways. IRAK1 and IRAK4 are active kinases while IRAK2 and IRAK-M (also called IRAK3) are inactive. In general, IRAKs are expressed ubiquitously, except for IRAK-M which is detected only in macrophages. The insect homologs, Pelle and Tube, are important components of the Toll pathway, which functions in establishing dorsoventral polarity in embryos and also in the innate immune response. Most members have an N-terminal DD followed by a kinase domain. In general, DDs are protein-protein interaction domains found in a variety of domain a
Probab=98.97 E-value=4.1e-10 Score=99.80 Aligned_cols=77 Identities=13% Similarity=0.223 Sum_probs=65.5
Q ss_pred ccccccChhhHHHHHhccCCcccccCCCCccCchHHHHHHcC-------CCCC---CCCCcc----chHHHHHHHhhccC
Q psy12711 243 IPIEAIRPKTRQVLNDKLCDIKQLMSPENYQRDYRGLADLMD-------IKAP---PNPNCE----DLMKKMFEDWTKSS 308 (639)
Q Consensus 243 vPL~aL~~~tR~~Ls~~LNp~k~l~s~~g~~rDWRgLAelmg-------f~~~---~~e~~~----~Pt~~vLe~W~~r~ 308 (639)
+++..|++.+|++|+.+|||.. ..||+.||+.++ +++. .++.+. +||..+|++|+.++
T Consensus 1 ~~i~~Lp~~~~~~L~~~LD~~~--------~~~W~~LA~~i~~~~~~~~~~~~~i~~~e~~~~~g~SPt~~LL~~W~~~~ 72 (95)
T cd08309 1 TYIRQLPYSVLARLCKVLDPLE--------LKGWRQLASLIPKGLGGPRYDLTDVRQIESMKQRGRSPTRELLWDWGTQN 72 (95)
T ss_pred CcceeCCHHHHHHHHHHhCCcc--------cCChHHHHHHhccccccCCcCHHHHHHHHHHhhcCCChHHHHHHHHHhcC
Confidence 4678899999999999999872 699999999999 8874 334334 99999999998874
Q ss_pred CCCCCcccHHHHHHHHhhcccchhh
Q psy12711 309 TLDRSVFNIATFLHFLECIDRFDVY 333 (639)
Q Consensus 309 ~~~~~~aTvg~Ll~~Le~idR~DVl 333 (639)
+|||+|+++|.+|+-+-..
T Consensus 73 ------~Tv~~L~~~L~~~~l~~A~ 91 (95)
T cd08309 73 ------ATVQDLVQVLVQLELYRAA 91 (95)
T ss_pred ------CCHHHHHHHHHHcccHHHH
Confidence 7999999999999987544
No 26
>cd08801 Death_UNC5D Death domain found in Uncoordinated-5D. Death Domain (DD) found in Uncoordinated-5D (UNC5D). UNC5D is part of the UNC-5 homolog family. It is a receptor for the secreted netrin-1 and plays a role in axonal guidance, angiogenesis, and apoptosis. UNC5 proteins are transmembrane proteins with an extracellular domain consisting of two immunoglobulin repeats, two thrombospondin type-I modules and an intracellular region containing a ZU-5 domain, UPA domain and a DD. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=98.71 E-value=2.4e-08 Score=88.69 Aligned_cols=80 Identities=15% Similarity=0.090 Sum_probs=67.5
Q ss_pred cChhhHHHHHhccCCcccccCCCCccCchHHHHHHcCCCCC--CCCCccchHHHHHHHhhccCCCCCCcccHHHHHHHHh
Q psy12711 248 IRPKTRQVLNDKLCDIKQLMSPENYQRDYRGLADLMDIKAP--PNPNCEDLMKKMFEDWTKSSTLDRSVFNIATFLHFLE 325 (639)
Q Consensus 248 L~~~tR~~Ls~~LNp~k~l~s~~g~~rDWRgLAelmgf~~~--~~e~~~~Pt~~vLe~W~~r~~~~~~~aTvg~Ll~~Le 325 (639)
|.+.+|++|+..|++.+.- ..|||+||+-++++.. -+.+..+||..+|+.|++++- .+.++..|...|+
T Consensus 1 iP~~iRqklC~~LD~p~~k------g~DWR~LA~kL~iDRyl~yFatk~SPT~viLdLWEa~~~---~~g~L~~La~ale 71 (98)
T cd08801 1 IPYSIRQRICATFDTPNAK------GKDWQMLAQKNSIDRNLSYFATQSSPSAVILSLWEARHQ---HDGDLDSLACALE 71 (98)
T ss_pred CchhHHHHHHHHcCCCCCC------CccHHHHHHHhcchhHHHHHhcCCChHHHHHHHHHHhcC---CCCCHHHHHHHHH
Confidence 4567999999999988755 7999999999999763 235678999999999999963 3568999999999
Q ss_pred hcccchhhhhc
Q psy12711 326 CIDRFDVYDDC 336 (639)
Q Consensus 326 ~idR~DVldD~ 336 (639)
.|+|-|++..+
T Consensus 72 eiGr~~~~~~~ 82 (98)
T cd08801 72 EIGRTHSKQST 82 (98)
T ss_pred HhCcchhhHHh
Confidence 99999988543
No 27
>cd08803 Death_ank3 Death domain of Ankyrin-3. Death Domain (DD) of the human protein ankyrin-3 (ANK-3) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-3, also called anykyrin-G (for general or giant), is found in neurons and at least one splice variant has been shown to be essential for propagation of action potentials as a binding partner to neurofascin and voltage-gated sodium channels. It is required for maintaining axo-dendritic polarity, and may be a genetic risk factor associated with bipolar disorder. ANK-3 may also play roles in other cell types. Mutations affecting ANK-3 pathways for Na channel localization are associated with Brugada syndrome, a potentially fata arrythmia. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by se
Probab=98.63 E-value=1.8e-08 Score=88.04 Aligned_cols=61 Identities=15% Similarity=0.231 Sum_probs=52.6
Q ss_pred ccCchHHHHHHcCCCCCC-----CCCccchH---HHHHHHhhccCCCCCCcccHHHHHHHHhhcccchhhhh
Q psy12711 272 YQRDYRGLADLMDIKAPP-----NPNCEDLM---KKMFEDWTKSSTLDRSVFNIATFLHFLECIDRFDVYDD 335 (639)
Q Consensus 272 ~~rDWRgLAelmgf~~~~-----~e~~~~Pt---~~vLe~W~~r~~~~~~~aTvg~Ll~~Le~idR~DVldD 335 (639)
..+||+.||..|||++.. .++.+|++ ..+|..|+.+.+ +.||++.|+..|.+|+|.||++=
T Consensus 14 LG~dW~~LA~eLg~s~~dI~~i~~e~p~~~~~q~~~lL~~W~~r~g---~~At~~~L~~aL~~i~R~DIv~~ 82 (84)
T cd08803 14 LGLSWTELARELNFSVDEINQIRVENPNSLIAQSFMLLKKWVTRDG---KNATTDALTSVLTKINRIDIVTL 82 (84)
T ss_pred hhccHHHHHHHcCCCHHHHHHHHHhCCCCHHHHHHHHHHHHHHhhC---CCcHHHHHHHHHHHCCcHHHHHh
Confidence 379999999999999862 34467788 899999999974 58999999999999999999863
No 28
>PF00531 Death: Death domain; InterPro: IPR000488 The death domain (DD) is a homotypic protein interaction module composed of a bundle of six alpha-helices. DD is related in sequence and structure to the death effector domain (DED, see IPR001875 from INTERPRO) and the caspase recruitment domain (CARD, see IPR001315 from INTERPRO), which work in similar pathways and show similar interaction properties []. DD bind each other forming oligomers. Mammals have numerous and diverse DD-containing proteins []. Within these proteins, the DD domains can be found in combination with other domains, including: CARDs, DEDs, ankyrin repeats (IPR002110 from INTERPRO), caspase-like folds, kinase domains, leucine zippers (IPR002158 from INTERPRO), leucine-rich repeats (LRR) (IPR001611 from INTERPRO), TIR domains (IPR000157 from INTERPRO), and ZU5 domains (IPR000906 from INTERPRO) []. Some DD-containing proteins are involved in the regulation of apoptosis and inflammation through their activation of caspases and NF-kappaB, which typically involves interactions with TNF (tumour necrosis factor) cytokine receptors [, ]. In humans, eight of the over 30 known TNF receptors contain DD in their cytoplasmic tails; several of these TNF receptors use caspase activation as a signalling mechanism. The DD mediates self-association of these receptors, thus giving the signal to downstream events that lead to apoptosis. Other DD-containing proteins, such as ankyrin, MyD88 and pelle, are probably not directly involved in cell death signalling. DD-containing proteins also have links to innate immunity, communicating with Toll family receptors through bipartite adapter proteins such as MyD88 [].; GO: 0005515 protein binding, 0007165 signal transduction; PDB: 3OQ9_L 3EZQ_F 1E41_A 1E3Y_A 2GF5_A 2OF5_L 3EWV_E 3G5B_A 3MOP_L 2A9I_A ....
Probab=98.46 E-value=8.4e-08 Score=80.35 Aligned_cols=65 Identities=17% Similarity=0.361 Sum_probs=54.0
Q ss_pred cCchHHHHHHcCCCCC-------CCCCccchHHHHHHHhhccCCCCCCcccHHHHHHHHhhcccchhhhhchHHH
Q psy12711 273 QRDYRGLADLMDIKAP-------PNPNCEDLMKKMFEDWTKSSTLDRSVFNIATFLHFLECIDRFDVYDDCIGFI 340 (639)
Q Consensus 273 ~rDWRgLAelmgf~~~-------~~e~~~~Pt~~vLe~W~~r~~~~~~~aTvg~Ll~~Le~idR~DVldD~~~~i 340 (639)
..||+.||..+||+.. ..+...+|+..||..|..+.+ ..||+++|...|..|+|.|+++.++..+
T Consensus 12 ~~~Wk~La~~Lg~~~~~i~~i~~~~~~~~~~~~~~L~~W~~~~~---~~at~~~L~~aL~~~~~~d~~~~i~~~~ 83 (83)
T PF00531_consen 12 GSDWKRLARKLGLSESEIENIEEENPDLREQTYEMLQRWRQREG---PNATVDQLIQALRDIGRNDLAEKIEQML 83 (83)
T ss_dssp STCHHHHHHHTTS-HHHHHHHHHHSTSHHHHHHHHHHHHHHHHG---STSSHHHHHHHHHHTTHHHHHHHHHHH-
T ss_pred hhhHHHHHHHhCcCHHHHHHHHHhCCChHHHHHHHHHHHHHhcC---CCCcHHHHHHHHHHCCcHHHHHHHHhhC
Confidence 7999999999999875 122245899999999999943 4799999999999999999999988754
No 29
>cd08797 Death_NFkB1_p105 Death domain of the Nuclear Factor-KappaB1 precursor protein p105. Death Domain (DD) of the Nuclear Factor-KappaB1 (NF-kB1) precursor protein p105. The NF-kB family of transcription factors play a central role in cardiovascular growth, stress response, and inflammation by controlling the expression of a network of different genes. There are five NF-kB proteins, all containing an N-terminal REL Homology Domain (RHD). NF-kB1 (or p50) is produced from the processing of the precursor protein p105, which contains ANK repeats and a C-terminal DD in addition to the RHD. It is regulated by the classical (or canonical) NF-kB pathway. In the cytosol, p50 forms an inactive complex with RelA (or p65) and the Inhibitor of NF-kB (IkB). Activation is triggered by the phosphorylation and degradation of IkB, resulting in the active DNA-binding p50-RelA dimer to migrate to the nucleus. The classical pathway regulates the majority of genes activated by NF-kB including those encod
Probab=98.37 E-value=4.3e-07 Score=78.33 Aligned_cols=70 Identities=13% Similarity=0.167 Sum_probs=60.9
Q ss_pred hHHHHHhccCCcccccCCCCccCchHHHHHHcCCCCC--CCCCccchHHHHHHHhhccCCCCCCcccHHHHHHHHhhccc
Q psy12711 252 TRQVLNDKLCDIKQLMSPENYQRDYRGLADLMDIKAP--PNPNCEDLMKKMFEDWTKSSTLDRSVFNIATFLHFLECIDR 329 (639)
Q Consensus 252 tR~~Ls~~LNp~k~l~s~~g~~rDWRgLAelmgf~~~--~~e~~~~Pt~~vLe~W~~r~~~~~~~aTvg~Ll~~Le~idR 329 (639)
+|++|...|++... .-|||.||+.+|+.+. -+...++||+.+|+.|+..+ .||..|.+.|+.|+|
T Consensus 1 ~rqkLc~~Ld~p~~-------~g~Wr~LA~kL~l~~l~~~f~~~pSPt~~LLd~~E~~~------G~l~~L~~aL~~mG~ 67 (76)
T cd08797 1 VKQQLYKLLESPDP-------DKNWETLAQKLGLGILNNAFRLSPSPSKTLLDNYEVSG------GTVRELLAALKRMGY 67 (76)
T ss_pred ChhHHHHHhCCCCC-------CCCHHHHHHHHCchhHHHHHhCCCCcHHHHHHHHhcCC------CCHHHHHHHHHHhCc
Confidence 68999999997653 2479999999999986 46788999999999999954 589999999999999
Q ss_pred chhhh
Q psy12711 330 FDVYD 334 (639)
Q Consensus 330 ~DVld 334 (639)
.|.+.
T Consensus 68 ~eav~ 72 (76)
T cd08797 68 TEAIE 72 (76)
T ss_pred HHHHH
Confidence 99876
No 30
>cd08777 Death_RIP1 Death Domain of Receptor-Interacting Protein 1. Death domain (DD) found in Receptor-Interacting Protein 1 (RIP1) and related proteins. RIP kinases serve as essential sensors of cellular stress. Vertebrates contain several types containing a homologous N-terminal kinase domain and varying C-terminal domains. RIP1 harbors a C-terminal DD, which binds death receptors (DRs) including TNF receptor 1, Fas, TNF-related apoptosis-inducing ligand receptor 1 (TRAILR1), and TRAILR2. It also interacts with other DD-containing adaptor proteins such as TRADD and FADD. RIP1 plays a crucial role in determining a cell's fate, between survival or death, following exposure to stress signals. It is important in the signaling of NF-kappaB and MAPKs, and it links DR-associated signaling to reactive oxygen species (ROS) production. Abnormal RIP1 function may result in ROS accumulation affecting inflammatory responses, innate immunity, stress responses, and cell survival. In general, DDs ar
Probab=98.35 E-value=2.3e-07 Score=81.21 Aligned_cols=65 Identities=11% Similarity=0.167 Sum_probs=53.5
Q ss_pred ccCchHHHHHHcCCCCCC---CC--C----ccchHHHHHHHhhccCCCCCCcccHHHHHHHHhhcccchhhhhchH
Q psy12711 272 YQRDYRGLADLMDIKAPP---NP--N----CEDLMKKMFEDWTKSSTLDRSVFNIATFLHFLECIDRFDVYDDCIG 338 (639)
Q Consensus 272 ~~rDWRgLAelmgf~~~~---~e--~----~~~Pt~~vLe~W~~r~~~~~~~aTvg~Ll~~Le~idR~DVldD~~~ 338 (639)
+.+||+.||..|||++.. ++ . ..+++..+|..|..+.+ .+.|||+.|+..|+.++|.||+.|+..
T Consensus 12 lG~~Wk~lar~LG~s~~eI~~ie~~~~r~~~~eq~~~mL~~W~~r~g--~~~ATv~~L~~aL~~~~r~di~~~l~~ 85 (86)
T cd08777 12 LGKKWKRCARKLGFTESEIEEIDHDYERDGLKEKVHQMLHKWKMKEG--SKGATVGKLAQALEGCIKPDLLVSLIQ 85 (86)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHhcccCCHHHHHHHHHHHHHHccC--CCCcHHHHHHHHHHHcchhhHHHHHHh
Confidence 479999999999999852 22 1 13459999999999864 247999999999999999999999753
No 31
>smart00005 DEATH DEATH domain, found in proteins involved in cell death (apoptosis). Alpha-helical domain present in a variety of proteins with apoptotic functions. Some (but not all) of these domains form homotypic and heterotypic dimers.
Probab=98.32 E-value=7e-07 Score=76.17 Aligned_cols=78 Identities=19% Similarity=0.214 Sum_probs=63.4
Q ss_pred hhhHHHHHhccCCcccccCCCCccCchHHHHHHcCCCCCCC--------CCccchHHHHHHHhhccCCCCCCcccHHHHH
Q psy12711 250 PKTRQVLNDKLCDIKQLMSPENYQRDYRGLADLMDIKAPPN--------PNCEDLMKKMFEDWTKSSTLDRSVFNIATFL 321 (639)
Q Consensus 250 ~~tR~~Ls~~LNp~k~l~s~~g~~rDWRgLAelmgf~~~~~--------e~~~~Pt~~vLe~W~~r~~~~~~~aTvg~Ll 321 (639)
..+++.+..++|.. + ..||+.||..+||+...+ .+..+|+..+|..|..+.+ ..||++.|.
T Consensus 2 ~~~~~~~~~l~~~~--~------g~~W~~la~~Lg~~~~~i~~i~~~~~~~~~~~~~~lL~~W~~~~g---~~at~~~L~ 70 (88)
T smart00005 2 ELTREKLAKLLDHP--L------GLDWRELARKLGLSEADIDQIRTEAPRDLAEQSVQLLRLWEQREG---KNATLGTLL 70 (88)
T ss_pred hhHHHHHHHHHcCc--c------chHHHHHHHHcCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHccc---hhhHHHHHH
Confidence 45788888888764 2 699999999999975411 1234799999999999875 369999999
Q ss_pred HHHhhcccchhhhhchH
Q psy12711 322 HFLECIDRFDVYDDCIG 338 (639)
Q Consensus 322 ~~Le~idR~DVldD~~~ 338 (639)
..|..++|.|+.+.++.
T Consensus 71 ~aL~~~~~~d~a~~i~~ 87 (88)
T smart00005 71 EALRKMGRDDAVELLRS 87 (88)
T ss_pred HHHHHcChHHHHHHHhc
Confidence 99999999999997753
No 32
>cd08804 Death_ank2 Death domain of Ankyrin-2. Death Domain (DD) of Ankyrin-2 (ANK-2) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-2, also called ankyrin-B (for broadly expressed), is required for proper function of the Na/Ca ion exchanger-1 in cardiomyocytes, and is thought to function in linking integral membrane proteins to the underlying cytoskeleton. Human ANK-2 is associated with "Ankyrin-B syndrome", an atypical arrythmia disorder with risk of sudden cardiac death. It also plays key roles in the brain and striated muscle. Loss of ANK-2 is associated with significant nervous system defects and sarcomere disorganization. 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
Probab=98.26 E-value=5e-07 Score=78.70 Aligned_cols=60 Identities=15% Similarity=0.264 Sum_probs=51.8
Q ss_pred ccCchHHHHHHcCCCCCC--------CCCccchHHHHHHHhhccCCCCCCcccHHHHHHHHhhcccchhhh
Q psy12711 272 YQRDYRGLADLMDIKAPP--------NPNCEDLMKKMFEDWTKSSTLDRSVFNIATFLHFLECIDRFDVYD 334 (639)
Q Consensus 272 ~~rDWRgLAelmgf~~~~--------~e~~~~Pt~~vLe~W~~r~~~~~~~aTvg~Ll~~Le~idR~DVld 334 (639)
+.+||+.||..|||++.. ..+..+|+..+|..|+.|.+ +.||++.|...|.+|+|.||+.
T Consensus 14 LG~dWk~LAr~Lg~se~dI~~i~~~~~~~~~eq~~~mL~~W~~r~g---~~At~~~L~~aL~~i~r~Div~ 81 (84)
T cd08804 14 LGFSWTELARELDFTEEQIHQIRIENPNSLQDQSHALLKYWLERDG---KHATDTNLMKCLTKINRMDIVH 81 (84)
T ss_pred HhhhHHHHHHHcCCCHHHHHHHHHHCcccHHHHHHHHHHHHHHccC---CCchHHHHHHHHHHcChHHHHH
Confidence 378999999999999852 23456899999999999964 5899999999999999999975
No 33
>cd08798 Death_NFkB2_p100 Death domain of the Nuclear Factor-KappaB2 precursor protein p100. Death Domain (DD) of the Nuclear Factor-KappaB2 (NF-kB2) precursor protein p100. The NF-kB family of transcription factors play a central role in cardiovascular growth, stress response, and inflammation by controlling the expression of a network of different genes. There are five NF-kB proteins, all containing an N-terminal REL Homology Domain (RHD). NF-kB2 (or p52) is produced from the processing of the precursor protein p100, which contains ANK repeats and a C-terminal DD in addition to the RHD. It is regulated by the non-canonical NF-kB pathway. The p100 precursor is cytosolic and interacts with RelB. Upon phosphorylation by IKKalpha, p100 is processed to its 52kDa active, DNA binding form and the p52/RelB complex is translocated into the nucleus. The non-canonical pathway plays a role in adaptive immunity and lymphorganogenesis. In general, DDs are protein-protein interaction domains found i
Probab=98.22 E-value=1.5e-06 Score=74.99 Aligned_cols=70 Identities=11% Similarity=0.114 Sum_probs=60.1
Q ss_pred hHHHHHhccCCcccccCCCCccCchHHHHHHcCCCCC--CCCCccchHHHHHHHhhccCCCCCCcccHHHHHHHHhhccc
Q psy12711 252 TRQVLNDKLCDIKQLMSPENYQRDYRGLADLMDIKAP--PNPNCEDLMKKMFEDWTKSSTLDRSVFNIATFLHFLECIDR 329 (639)
Q Consensus 252 tR~~Ls~~LNp~k~l~s~~g~~rDWRgLAelmgf~~~--~~e~~~~Pt~~vLe~W~~r~~~~~~~aTvg~Ll~~Le~idR 329 (639)
|.++|...||.... ..|||.||+-+|+... -+...++||..+|+.|+.++ .+|..|.+.|+.|+|
T Consensus 1 ~~qkLc~~Ld~p~~-------g~dW~~LA~kL~l~~l~~~f~~~~SPt~~LLd~yE~~~------G~l~~L~~aL~~mG~ 67 (76)
T cd08798 1 TLQRLEQLLNDTQT-------DVPWMELAERLGLQSLVDTYKPTQSPPGSLLRSYELAG------GPLQGLIEALQDMGL 67 (76)
T ss_pred CHHHHHHHhcCCCC-------CCCHHHHHHHHCcchHHHHHhCCCCchHHHHHHhhccC------CCHHHHHHHHHHhCh
Confidence 46888888885532 5899999999999886 46778999999999999985 489999999999999
Q ss_pred chhhh
Q psy12711 330 FDVYD 334 (639)
Q Consensus 330 ~DVld 334 (639)
-|.+.
T Consensus 68 ~eav~ 72 (76)
T cd08798 68 REGVR 72 (76)
T ss_pred HHHHH
Confidence 98875
No 34
>PLN03210 Resistant to P. syringae 6; Provisional
Probab=98.03 E-value=1.7e-05 Score=96.12 Aligned_cols=103 Identities=14% Similarity=0.165 Sum_probs=83.9
Q ss_pred CCccceEEEeccCC--HHHHHHHHHhhhcCCceEEEecCCCCCCcchHHHHHHHHHhcceEEEEecccccCChhhHHHHH
Q psy12711 383 LAHYDALLLYDEAD--FDLAKQFNTQLNKMGFTVCDKDNSFLTGQFEHSAFIQVMDRCTCVIVLMSTHFMNNSLLHSLTQ 460 (639)
Q Consensus 383 ~k~YDAFVsYS~kD--~dFV~eLv~~LE~~gykLCLh~RDflpG~~i~e~I~~aIerSRR~IvVLSpnFL~SeWc~fe~~ 460 (639)
...||+|+||..+| ..|+.+|...|.+.|+..+. +-+...|..+...+.++|+.||=-|+|+|++|-.|.||--|+.
T Consensus 10 ~~~~~vf~sfrg~d~r~~f~~hl~~~l~~~~i~~f~-d~~~~~g~~~~~~l~~~i~~s~~~ivv~s~~ya~s~wcl~el~ 88 (1153)
T PLN03210 10 NWVYDVFPSFSGEDVRITFLSHFLKELDRKLIIAFK-DNEIERSQSLDPELKQAIRDSRIAVVVFSKNYASSSWCLNELL 88 (1153)
T ss_pred CCCCcEEeeCCCcccccCHHHHHHHHHHHCCCeEEc-cCCccCCCcccHHHHHHHHhCeEEEEEecCCcccchHHHHHHH
Confidence 45899999999998 56999999999999999998 4578889888889999999999999999999999999977764
Q ss_pred HHHHHhhhhcCCCcEEEEEeccCCCCcccch
Q psy12711 461 YAEAKHIDHTIHSKIIPILCSDDYFSVGFLQ 491 (639)
Q Consensus 461 ~A~~l~l~~r~~~kLIpIlye~~~~~P~~Lr 491 (639)
.-... -+.+ ...+|||+|+- .|.+++
T Consensus 89 ~i~~~-~~~~-~~~v~pvfy~v---~p~~v~ 114 (1153)
T PLN03210 89 EIVRC-KEEL-GQLVIPVFYGL---DPSHVR 114 (1153)
T ss_pred HHHHh-hhhc-CceEEEEEecc---cHHHHh
Confidence 43222 1333 46899999964 344554
No 35
>cd01670 Death Death Domain: a protein-protein interaction domain. Death Domains (DDs) are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. Structural analysis of DD-DD complexes show that the domains interact with each other in many different ways. DD-containing proteins serve as adaptors in signaling pathways and they can recruit other proteins into signaling complexes. In mammals, they are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways. In invertebrates, they are involved in transcriptional regulation of zygotic patterning genes in insect embryogenesis, and are components of the ToII/NF-kappaB pathway, a conserved innate immune pathway in a
Probab=97.89 E-value=1.1e-05 Score=67.29 Aligned_cols=61 Identities=16% Similarity=0.311 Sum_probs=50.9
Q ss_pred cCchHHHHHHcCCCCC-------CCCCccchHHHHHHHhhccCCCCCCcccHHHHHHHHhhcccchhhhhc
Q psy12711 273 QRDYRGLADLMDIKAP-------PNPNCEDLMKKMFEDWTKSSTLDRSVFNIATFLHFLECIDRFDVYDDC 336 (639)
Q Consensus 273 ~rDWRgLAelmgf~~~-------~~e~~~~Pt~~vLe~W~~r~~~~~~~aTvg~Ll~~Le~idR~DVldD~ 336 (639)
..||+.||..+||+.. ..+...+|+.+||..|..+.+ ..||++.|...|..++|.|+++++
T Consensus 10 g~~W~~la~~Lgl~~~~I~~i~~~~~~~~~~~~~mL~~W~~~~~---~~at~~~L~~aL~~~~~~~~a~~~ 77 (79)
T cd01670 10 GKDWKKLARKLGLSDGEIDQIEEDNPRVREQAYQLLLKWEEREG---DNATVGNLIEALREIGRRDDAAKL 77 (79)
T ss_pred hhHHHHHHHHhCCCHHHHHHHHHhCCCHHHHHHHHHHHHHhccC---cCcHHHHHHHHHHHcCHHHHHHHh
Confidence 4899999999999864 222346899999999999875 379999999999999997777665
No 36
>cd08318 Death_NMPP84 Death domain of Nuclear Matrix Protein P84. Death domain (DD) found in the Nuclear Matrix Protein P84 (also known as HPR1 or THOC1). HPR1/p84 resides in the nuclear matrix and is part of the THO complex, also called TREX (transcription/export) complex, which functions in mRNP biogenesis at the interface between transcription and export of mRNA from the nucleus. Mice lacking THOC1 have abnormal testis development and are sterile. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=97.89 E-value=1.8e-05 Score=69.07 Aligned_cols=61 Identities=15% Similarity=0.260 Sum_probs=52.0
Q ss_pred cCchHHHHHHcCCCCC-------CCCCccchHHHHHHHhhccCCCCCCcccHHHHHHHHhhcccchhhhhc
Q psy12711 273 QRDYRGLADLMDIKAP-------PNPNCEDLMKKMFEDWTKSSTLDRSVFNIATFLHFLECIDRFDVYDDC 336 (639)
Q Consensus 273 ~rDWRgLAelmgf~~~-------~~e~~~~Pt~~vLe~W~~r~~~~~~~aTvg~Ll~~Le~idR~DVldD~ 336 (639)
.+||+.||-.+||+.. ..+........+|..|..|.+ ..||++.|...|..++|.||.|.+
T Consensus 18 G~~Wk~Lar~LGls~~dI~~i~~~~~~~~eq~~~mL~~W~~r~g---~~AT~~~L~~aL~~~~~~diae~l 85 (86)
T cd08318 18 GEDWKTLAPHLEMKDKEIRAIESDSEDIKMQAKQLLVAWQDREG---SQATPETLITALNAAGLNEIAESL 85 (86)
T ss_pred hhhHHHHHHHcCCCHHHHHHHHhcCCCHHHHHHHHHHHHHHhcC---ccccHHHHHHHHHHcCcHHHHHhh
Confidence 7999999999999864 223445688999999999975 479999999999999999999864
No 37
>cd08317 Death_ank Death domain associated with Ankyrins. Death Domain (DD) associated with Ankyrins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. Ankyrins function as adaptor proteins and they interact, through ANK repeats, with structurally diverse membrane proteins, including ion channels/pumps, calcium release channels, and cell adhesion molecules. They play critical roles in the proper expression and membrane localization of these proteins. In mammals, this family includes ankyrin-R for restricted (or ANK1), ankyrin-B for broadly expressed (or ANK2) and ankyrin-G for general or giant (or ANK3). They are expressed in different combinations in many tissues and play non-overlapping functions. 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-associati
Probab=97.85 E-value=1.3e-05 Score=69.40 Aligned_cols=61 Identities=21% Similarity=0.347 Sum_probs=50.8
Q ss_pred cCchHHHHHHcCCCCCC-------CCC-ccchHHHHHHHhhccCCCCCCcccHHHHHHHHhhcccchhhhhc
Q psy12711 273 QRDYRGLADLMDIKAPP-------NPN-CEDLMKKMFEDWTKSSTLDRSVFNIATFLHFLECIDRFDVYDDC 336 (639)
Q Consensus 273 ~rDWRgLAelmgf~~~~-------~e~-~~~Pt~~vLe~W~~r~~~~~~~aTvg~Ll~~Le~idR~DVldD~ 336 (639)
.+||..||..|||+... +++ ..+....+|..|..|.+ ..||++.|.+.|..|+|-||++-+
T Consensus 15 G~dW~~LAr~Lg~~~~dI~~i~~~~~~~~~eq~~~mL~~W~~r~g---~~at~~~L~~AL~~i~r~Di~~~~ 83 (84)
T cd08317 15 GSDWPQLARELGVSETDIDLIKAENPNSLAQQAQAMLKLWLEREG---KKATGNSLEKALKKIGRDDIVEKC 83 (84)
T ss_pred hhHHHHHHHHcCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHhcC---CcchHHHHHHHHHHcChHHHHHHh
Confidence 69999999999999741 121 23568899999999975 479999999999999999999865
No 38
>cd08307 Death_Pelle Death domain of the protein kinase Pelle. Death domain (DD) of the protein kinase Pelle from Drosophila melanogaster and simlar proteins. In Drosophila, interaction between the DDs of Tube and Pelle is an important component of the Toll pathway, which functions in establishing dorsoventral polarity in embryos and in mediating innate immune responses to pathogens. Tube and Pelle transmit the signal from the Toll receptor to the Dorsal/Cactus complex. Pelle also functions in photoreceptor axon targeting. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=97.80 E-value=3.1e-05 Score=69.68 Aligned_cols=76 Identities=16% Similarity=0.133 Sum_probs=60.2
Q ss_pred ccccccChhhHHHHHhccCCcccccCCCCccCchHHHHHHcC-CCCCCC---C----CccchHHHHHHHhhccCCCCCCc
Q psy12711 243 IPIEAIRPKTRQVLNDKLCDIKQLMSPENYQRDYRGLADLMD-IKAPPN---P----NCEDLMKKMFEDWTKSSTLDRSV 314 (639)
Q Consensus 243 vPL~aL~~~tR~~Ls~~LNp~k~l~s~~g~~rDWRgLAelmg-f~~~~~---e----~~~~Pt~~vLe~W~~r~~~~~~~ 314 (639)
+++.-|++..|++|+.+|+|. ..|+.||+.+. ++...+ + ...+||..+|..|..++
T Consensus 1 ~yIr~Lp~~~~~~Lc~lLD~~----------~~W~~LA~~i~~ys~~~v~~i~~~~~~g~SPt~eLL~~WG~~n------ 64 (97)
T cd08307 1 MYIYDIPFTERKQLCALLDTD----------NVWEELAFVMMGYSNDDVEGIQRCCLRGRSPTEELLDIWGNKN------ 64 (97)
T ss_pred CCcccCCHHHHHHHHHHhCCc----------CcHHHHHHHHhcCCHHHHHHHHHHHcCCCChHHHHHHHHhhcC------
Confidence 466788999999999999887 47999999986 443311 1 45789999999997765
Q ss_pred ccHHHHHHHHhhcccchhhh
Q psy12711 315 FNIATFLHFLECIDRFDVYD 334 (639)
Q Consensus 315 aTvg~Ll~~Le~idR~DVld 334 (639)
.||++|..+|.+++=+-...
T Consensus 65 ~Tv~~L~~~L~k~kl~~Am~ 84 (97)
T cd08307 65 HTITELFVLLYREKLFRAMR 84 (97)
T ss_pred CCHHHHHHHHHHhchHHHHH
Confidence 69999999999987654433
No 39
>KOG3678|consensus
Probab=97.71 E-value=0.00054 Score=76.18 Aligned_cols=136 Identities=13% Similarity=0.243 Sum_probs=92.2
Q ss_pred CCccceEEEeccCCHHHHHHHHHh-hhcCCceEEEecCCCCCCcchHHHHHHHHHhcceEEEEecccccCC--------h
Q psy12711 383 LAHYDALLLYDEADFDLAKQFNTQ-LNKMGFTVCDKDNSFLTGQFEHSAFIQVMDRCTCVIVLMSTHFMNN--------S 453 (639)
Q Consensus 383 ~k~YDAFVsYS~kD~dFV~eLv~~-LE~~gykLCLh~RDflpG~~i~e~I~~aIerSRR~IvVLSpnFL~S--------e 453 (639)
.++.|+||||-..--.-...|+.. |.-.||++++.---+..|.|. +.+++.|...|.+|+||||+-|.- +
T Consensus 610 skq~DVFISYRRstGnQLASLiKV~LQL~GyrVFIDVdKL~AGKFd-ssLlkni~aAkhFiLVLtP~sLDr~lnD~nCeD 688 (832)
T KOG3678|consen 610 SKQIDVFISYRRSTGNQLASLIKVLLQLRGYRVFIDVDKLYAGKFD-SSLLKNIQAAKHFILVLTPNSLDRLLNDDNCED 688 (832)
T ss_pred cCCcceEEEeeccccHHHHHHHHHHHHhcCceEEEehhhhhccccc-HHHHHHHHhhheeEEEeCcchHHHHhccccHHH
Confidence 578999999976554444445554 446899999999889999877 567889999999999999998762 3
Q ss_pred hhHHHHHHHHHHhhhhcCCCcEEEEEec------cCCCCcccchhhhhhcccccc-cchhhHHHHHHHHhccC-CCCCcc
Q psy12711 454 LLHSLTQYAEAKHIDHTIHSKIIPILCS------DDYFSVGFLQYCVKLKLNHYA-SNMEQFWDRLYYSLKGV-GKGVPE 525 (639)
Q Consensus 454 Wc~fe~~~A~~l~l~~r~~~kLIpIlye------~~~~~P~~Lr~~~~ld~~~~~-~~~~wFW~RLr~aL~~~-~~~~p~ 525 (639)
|-+-|+.-|... ++-||||+-. +.+.+|.+++.+++.+-.+|. .|.+..-.++-.-|++. +++.|.
T Consensus 689 WVHKEl~~Afe~------~KNIiPI~D~aFE~Pt~ed~iPnDirmi~kyNGvKWvHdYQdA~maKvvRFitGe~nRttpt 762 (832)
T KOG3678|consen 689 WVHKELKCAFEH------QKNIIPIFDTAFEFPTKEDQIPNDIRMITKYNGVKWVHDYQDACMAKVVRFITGELNRTTPT 762 (832)
T ss_pred HHHHHHHHHHHh------cCCeeeeecccccCCCchhcCcHHHHHHHhccCeeeehhhHHHHHHHHHHHHhccccCCCCC
Confidence 666666655543 3569999943 122467788877766544432 23344555544444332 444433
No 40
>KOG1480|consensus
Probab=97.39 E-value=0.00015 Score=83.81 Aligned_cols=78 Identities=17% Similarity=0.136 Sum_probs=64.9
Q ss_pred cChhhHHHHHhccCCcccccCCCCccCchHHHHHHcCCCC-CC-CCCccchHHHHHHHhhccCCCCCCcccHHHHHHHHh
Q psy12711 248 IRPKTRQVLNDKLCDIKQLMSPENYQRDYRGLADLMDIKA-PP-NPNCEDLMKKMFEDWTKSSTLDRSVFNIATFLHFLE 325 (639)
Q Consensus 248 L~~~tR~~Ls~~LNp~k~l~s~~g~~rDWRgLAelmgf~~-~~-~e~~~~Pt~~vLe~W~~r~~~~~~~aTvg~Ll~~Le 325 (639)
|.+..|++|+.-|++.+-- ..|||+||..+.++. ++ +-+..+||.-+|++|++|.-+ ++++..|..-||
T Consensus 815 IP~~IRQkicssLD~Pn~r------G~DWRmLAqKL~lDRyLsyFATk~SPTavILdLWEA~~~~---dGdL~~LA~aLe 885 (909)
T KOG1480|consen 815 IPFSIRQKICSSLDAPNER------GSDWRMLAQKLHLDRYLSYFATKPSPTAVILDLWEARHQP---DGDLSSLAAALE 885 (909)
T ss_pred cchhHHHHHHhhcCCcccc------CccHHHHHHHhhhhhhhHhhccCCCCchhhHHHHHhhcCC---CCCHHHHHHHHH
Confidence 4567899999999988754 899999999999875 33 456789999999999999532 568999999999
Q ss_pred hcccchhhh
Q psy12711 326 CIDRFDVYD 334 (639)
Q Consensus 326 ~idR~DVld 334 (639)
.|+|-|-+-
T Consensus 886 emGr~da~l 894 (909)
T KOG1480|consen 886 EMGRPDAVL 894 (909)
T ss_pred HhCCCceEE
Confidence 999998543
No 41
>cd08783 Death_MALT1 Death domain similar to that found in Mucosa-associated lymphoid tissue-lymphoma-translocation gene 1. Death domain (DD) similar to that found in Malt1 (mucosa-associated lymphoid tissue-lymphoma-translocation gene 1). Malt1, together with Bcl10 (B-cell lymphoma 10), are the integral components of the CBM signalosome. They associate with CARD9 to form M-CBM (CBM complex in myeloid immune cells) and with CARMA1 to form L-CBM (CBM complex in lymphoid immune cells), to mediate activation of NF-kB and MAPK by ITAM-coupled receptors expressed on immune cells. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins
Probab=97.39 E-value=0.00036 Score=62.76 Aligned_cols=76 Identities=12% Similarity=0.204 Sum_probs=59.4
Q ss_pred cccChhhHHHHHhccCCcccccCCCCccCchHHHHHHcCCCCC--------------CCCCccchHHHHHHHhhccCCCC
Q psy12711 246 EAIRPKTRQVLNDKLCDIKQLMSPENYQRDYRGLADLMDIKAP--------------PNPNCEDLMKKMFEDWTKSSTLD 311 (639)
Q Consensus 246 ~aL~~~tR~~Ls~~LNp~k~l~s~~g~~rDWRgLAelmgf~~~--------------~~e~~~~Pt~~vLe~W~~r~~~~ 311 (639)
..|+....++|+.+|+...- .+.||.|||.+|-... ..+..-+|++.+|..|..|+
T Consensus 2 ~~L~e~~l~~L~~lLD~~~~-------~~gWr~LAe~lg~~~~fr~S~~el~~cslkvl~p~gSPsk~LL~~~~~rg--- 71 (97)
T cd08783 2 NRLREPLLRRLSELLDRAAD-------GKGWRKLAELAGSRGRFRLSCLDLEQCSLKVLEPEGSPSRSLLKLLGERG--- 71 (97)
T ss_pred CcccHHHHHHHHHHHhCCCc-------cCCHHHHHHHHccCCccccCHHHHHHHHHHHhcCCCCchHHHHHHHHHcC---
Confidence 45778889999999965531 4789999999997431 12334589999999999986
Q ss_pred CCcccHHHHHHHHhhcccchhhh
Q psy12711 312 RSVFNIATFLHFLECIDRFDVYD 334 (639)
Q Consensus 312 ~~~aTvg~Ll~~Le~idR~DVld 334 (639)
.||++|+++|+.|+--..++
T Consensus 72 ---~Tv~~Ll~~L~~Mgh~eAl~ 91 (97)
T cd08783 72 ---CTVTELSEFLQAMEHTEALQ 91 (97)
T ss_pred ---CcHHHHHHHHHHhhhHHHHH
Confidence 59999999999998665544
No 42
>PF08937 DUF1863: MTH538 TIR-like domain (DUF1863); InterPro: IPR015032 This protein adopts the flavodoxin fold, that is, five parallel beta-strands and four helical segments. The structure is a three-layer sandwich with alpha-1 and alpha-4 on one side of the beta-sheet, and alpha-2 and alpha-3 on the other side. Probable role in signal transduction as a phosphorylation-independent conformational switch protein []. This domain is similar to the TIR domain [].; PDB: 3HYN_A.
Probab=97.27 E-value=0.00078 Score=62.09 Aligned_cols=89 Identities=18% Similarity=0.279 Sum_probs=46.7
Q ss_pred cceEEEeccCCHH-HHHHHHHhhhc-------CCceE--EE-------ecCCCC-CCcchHHHHHHHHHhcceEEEEecc
Q psy12711 386 YDALLLYDEADFD-LAKQFNTQLNK-------MGFTV--CD-------KDNSFL-TGQFEHSAFIQVMDRCTCVIVLMST 447 (639)
Q Consensus 386 YDAFVsYS~kD~d-FV~eLv~~LE~-------~gykL--CL-------h~RDfl-pG~~i~e~I~~aIerSRR~IvVLSp 447 (639)
|.+||||+..|.+ +++.|...++. .++.+ .- ..+|-. ....+...|-+.|..|..+||++++
T Consensus 1 ~~vFIS~~~~d~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ik~~I~~~i~~s~~~IVLig~ 80 (130)
T PF08937_consen 1 YKVFISYSHDDDDWYYDQLKEWLENSYEIPRDKNFDFRFYDVSKWEPIRSRDDDSSSEYIKRKIRERIKNSSVTIVLIGP 80 (130)
T ss_dssp ----------THH-HHHHHHHHHHH-------TTSS--BT---TTT---TTS---TTTTHHHHHHHHHHTEEEEEEE--T
T ss_pred CCccccccccCcHHHHHHHHHHhccccccccccccccCcccccccCcccCccccchHHHHHHHHHHHHhcCCEEEEEeCC
Confidence 6799999999999 67877766663 12221 11 122222 2246677888899999999999999
Q ss_pred cccCChhhHHHHHHHHHHhhhhcCCCcEEEEEe
Q psy12711 448 HFMNNSLLHSLTQYAEAKHIDHTIHSKIIPILC 480 (639)
Q Consensus 448 nFL~SeWc~fe~~~A~~l~l~~r~~~kLIpIly 480 (639)
+--.|.|..+|...|... ...||.|.+
T Consensus 81 ~T~~s~wV~~EI~~A~~~------~~~Ii~V~~ 107 (130)
T PF08937_consen 81 NTAKSKWVNWEIEYALKK------GKPIIGVYL 107 (130)
T ss_dssp T----HHHHHHHHHHTTT---------EEEEET
T ss_pred CcccCcHHHHHHHHHHHC------CCCEEEEEC
Confidence 999999999999876542 256888875
No 43
>cd08779 Death_PIDD Death Domain of p53-induced protein with a death domain. Death domain (DD) found in PIDD (p53-induced protein with a death domain) and similar proteins. PIDD is a component of the PIDDosome complex, which is an oligomeric caspase-activating complex involved in caspase-2 activation and plays a role in mediating stress-induced apoptosis. The PIDDosome complex is composed of three components, PIDD, RAIDD and caspase-2, which interact through their DDs and DD-like domains. The DD of PIDD interacts with the DD of RAIDD, which also contains a Caspase Activation and Recruitment Domain (CARD) that interacts with the caspase-2 CARD. Autoproteolysis of PIDD determines the downstream signaling event, between pro-survival NF-kB or pro-death caspase-2 activation. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members
Probab=97.04 E-value=0.00045 Score=60.58 Aligned_cols=66 Identities=14% Similarity=0.222 Sum_probs=51.9
Q ss_pred cCchHHHHHHcCCCCCCC-----CCcc---chHHHHHHHhhccCCCCCCcccHHHHHHHHhhcccchhhhhchHHH
Q psy12711 273 QRDYRGLADLMDIKAPPN-----PNCE---DLMKKMFEDWTKSSTLDRSVFNIATFLHFLECIDRFDVYDDCIGFI 340 (639)
Q Consensus 273 ~rDWRgLAelmgf~~~~~-----e~~~---~Pt~~vLe~W~~r~~~~~~~aTvg~Ll~~Le~idR~DVldD~~~~i 340 (639)
.+||+.||-.+|++...+ .+.. .-...+|..|..+.+ +..|||+.|..-|..++|-|+.+.+++.+
T Consensus 13 G~~Wk~lar~LGlse~~Id~Ie~~~~~dl~eq~~~mL~~W~~~~~--~~~atv~~L~~AL~~~gr~dlae~l~~~~ 86 (86)
T cd08779 13 GLDWQAIGLHLGLSYRELQRIKYNNRDDLDEQIFDMLFSWAQRQA--GDPDAVGKLVTALEESGRQDLADEVRAVL 86 (86)
T ss_pred hHHHHHHHHHcCCCHHHHHHHHHHCccCHHHHHHHHHHHHHHhcC--CCchHHHHHHHHHHHcCHHHHHHHHHhhC
Confidence 789999999999997521 1222 345677888998753 24689999999999999999999988753
No 44
>cd08805 Death_ank1 Death domain of Ankyrin-1. Death Domain (DD) of the human protein ankyrin-1 (ANK-1) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-1, also called ankyrin-R (for restricted), is found in brain, muscle, and erythrocytes and is thought to function in linking integral membrane proteins to the underlying cytoskeleton. It plays a critical nonredundant role in erythroid development and is associated with hereditary spherocytosis (HS), a common disorder of the red cell membrane. The small alternatively-spliced variant, sANK-1, found in striated muscle and concentrated in the sarcoplasmic reticulum (SR) binds obscurin and titin, which facilitates the anchoring of the network SR to the contractile apparatus. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common featur
Probab=96.96 E-value=0.00061 Score=59.95 Aligned_cols=60 Identities=17% Similarity=0.294 Sum_probs=49.4
Q ss_pred ccCchHHHHHHcCCCCC-------CCCC-ccchHHHHHHHhhccCCCCCCcccHHHHHHHHhhcccchhhh
Q psy12711 272 YQRDYRGLADLMDIKAP-------PNPN-CEDLMKKMFEDWTKSSTLDRSVFNIATFLHFLECIDRFDVYD 334 (639)
Q Consensus 272 ~~rDWRgLAelmgf~~~-------~~e~-~~~Pt~~vLe~W~~r~~~~~~~aTvg~Ll~~Le~idR~DVld 334 (639)
+.+||+.||-.+||+-. .+++ ..+-...+|..|..+.+ +.||+..|..-|..++|-||+.
T Consensus 14 LG~dW~~Lar~L~vs~~dI~~I~~e~p~~l~~Q~~~~L~~W~~r~g---~~At~~~L~~AL~~i~R~div~ 81 (84)
T cd08805 14 LGLSWAELARELQFSVEDINRIRVENPNSLLEQSTALLNLWVDREG---ENAKMSPLYPALYSIDRLTIVN 81 (84)
T ss_pred hcchHHHHHHHcCCCHHHHHHHHHhCCCCHHHHHHHHHHHHHHhcC---ccchHHHHHHHHHHCChHHHHH
Confidence 37999999999999863 2222 33466789999999864 5899999999999999999985
No 45
>cd08796 Death_IRAK-M Death domain of Interleukin 1 Receptor Associated Kinase-M. Death Domain (DD) of Interleukin-1 Receptor-Associated Kinase M (IRAK-M). IRAKs are essential components of innate immunity and inflammation in mammals and other vertebrates. They are involved in signal transduction pathways involving IL-1 and IL-18 receptors, Toll-like receptors(TLRs), nuclear factor-kappaB (NF-kB), and mitogen-activated protein kinases (MAPKs). IRAKs contain an N-terminal DD domain and a C-terminal kinase domain. IRAK-M, also called IRAK-3, is an inactive kinase present only in macrophages in an inducible manner. It is a negative regulator of TLR signaling and it contributes to the attenuation of NF-kB activation. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitme
Probab=96.88 E-value=0.0011 Score=59.13 Aligned_cols=71 Identities=13% Similarity=0.130 Sum_probs=54.7
Q ss_pred ccccChhhHHHHHhccCCcccccCCCCccCchHHHHHHcCCCCCC---CC----CccchHHHHHHHhhccCCCCCCcccH
Q psy12711 245 IEAIRPKTRQVLNDKLCDIKQLMSPENYQRDYRGLADLMDIKAPP---NP----NCEDLMKKMFEDWTKSSTLDRSVFNI 317 (639)
Q Consensus 245 L~aL~~~tR~~Ls~~LNp~k~l~s~~g~~rDWRgLAelmgf~~~~---~e----~~~~Pt~~vLe~W~~r~~~~~~~aTv 317 (639)
|--|...++++|+..|+.-. -.-+|+.||+.++..... +| ...+||+.+|..|..++ .||
T Consensus 3 ly~lP~~v~~~lc~~LDs~~-------~~~~W~~lA~~i~~~~~~vr~ie~~~~~G~SPT~eLL~~Wg~~n------~TV 69 (89)
T cd08796 3 LFDLPPVLLGSLCALLDSGV-------GGLGWRTLAERLSSSWLEVRHIEKYVVQGKSGTRELLWSWAQKN------KTV 69 (89)
T ss_pred hhhCCHHHHHHHHHHhcCCC-------ccccHHHHHHHHhccHHHHHHHHHHHHcCCCcHHHHHHHHHccC------CCH
Confidence 34567889999999996432 136999999999965332 22 24679999999997765 699
Q ss_pred HHHHHHHhhcc
Q psy12711 318 ATFLHFLECID 328 (639)
Q Consensus 318 g~Ll~~Le~id 328 (639)
++|.++|.++.
T Consensus 70 ~eL~~~L~~~~ 80 (89)
T cd08796 70 GDLLQVLDEMG 80 (89)
T ss_pred HHHHHHHHHcC
Confidence 99999998876
No 46
>cd08306 Death_FADD Fas-associated Death Domain protein-protein interaction domain. Death domain (DD) found in FAS-associated via death domain (FADD). FADD is a component of the death-inducing signaling complex (DISC) and serves as an adaptor in the signaling pathway of death receptor proteins. It modulates apoptosis as well as non-apoptotic processes such as cell cycle progression, survival, innate immune signaling, and hematopoiesis. FADD contains an N-terminal DED and a C-terminal DD. Its DD interacts with the DD of the activated death receptor, FAS, and its DED recruits the initiator caspases, caspase-8 and -10, to the DISC complex via a homotypic interaction with the N-terminal DED of the caspase. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain),
Probab=96.72 E-value=0.0012 Score=57.82 Aligned_cols=64 Identities=20% Similarity=0.302 Sum_probs=50.6
Q ss_pred ccCchHHHHHHcCCCCCC-------CC-CccchHHHHHHHhhccCCCCCCcccHHHHHHHHhhcccchhhhhchH
Q psy12711 272 YQRDYRGLADLMDIKAPP-------NP-NCEDLMKKMFEDWTKSSTLDRSVFNIATFLHFLECIDRFDVYDDCIG 338 (639)
Q Consensus 272 ~~rDWRgLAelmgf~~~~-------~e-~~~~Pt~~vLe~W~~r~~~~~~~aTvg~Ll~~Le~idR~DVldD~~~ 338 (639)
..+||+.||-.+||+... ++ +..++..++|..|..+.+ +.||++.|++-|..+++.+|.|-++.
T Consensus 12 lG~~Wk~laR~LGlse~~Id~i~~~~~~~~~eq~~~mL~~W~~~~g---~~At~~~L~~aL~~~~l~~~ad~i~~ 83 (86)
T cd08306 12 VGRDWRKLARKLGLSETKIESIEEAHPRNLREQVRQSLREWKKIKK---KEAKVADLIKALRDCQLNLVADLVEE 83 (86)
T ss_pred HhhhHHHHHHHcCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHhHC---cchHHHHHHHHHHHcCcHHHHHHHHH
Confidence 379999999999998641 11 223588999999999865 58999999999999999666655443
No 47
>cd08308 Death_Tube Death domain of Tube. Death domains (DDs) similar to the DD in the protein Tube from Drosophila melanogaster. In Drosophila, interaction between the DDs of Tube and Pelle is an important component of the Toll pathway, which functions in establishing dorsoventral polarity in embryos and also in mediating innate immune response to pathogens. Tube and Pelle transmit the signal from the Toll receptor to the Dorsal/Cactus complex. Some members of this subfamily contain a C-terminal kinase domain, like Pelle, in addition to the DD. Tube has no counterpart in vertebrates. It contains an N-terminal DD and a C-terminal region with five copies of the Tube repeat, an 8-amino acid motif. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (D
Probab=96.68 E-value=0.0015 Score=61.48 Aligned_cols=79 Identities=15% Similarity=0.206 Sum_probs=57.8
Q ss_pred ccccccChhhHHHHHhccCCcccccCCCCccCchHHHHHH-----------cCCCCC---CCC-----CccchHHHHHHH
Q psy12711 243 IPIEAIRPKTRQVLNDKLCDIKQLMSPENYQRDYRGLADL-----------MDIKAP---PNP-----NCEDLMKKMFED 303 (639)
Q Consensus 243 vPL~aL~~~tR~~Ls~~LNp~k~l~s~~g~~rDWRgLAel-----------mgf~~~---~~e-----~~~~Pt~~vLe~ 303 (639)
+.++-|....|++|+..|||. ..|+.||.. +.++.. .++ ...+||..+|++
T Consensus 2 TeIR~Lp~~~~~~L~~iLD~~----------d~Wk~L~~~Ip~~~~~~~~~~~Y~~~hv~~ie~~~~~~grSpte~LL~e 71 (125)
T cd08308 2 TEIRKLPPADLYRLVNILDIN----------DGWKKLMAIIPSDDDDFNNLAKYNAEHFKLIEQAANKQRRSCSEILLDE 71 (125)
T ss_pred cchhcCCHHHHHHHHHHcCcc----------ccHHHHHHhcCCcccccccccccCHHHHHHHHHHHHhcCCChHHHHHHH
Confidence 457788999999999999886 479999994 233222 122 245899999999
Q ss_pred hhccCCCCCCcccHHHHHHHHhhcccchhhh
Q psy12711 304 WTKSSTLDRSVFNIATFLHFLECIDRFDVYD 334 (639)
Q Consensus 304 W~~r~~~~~~~aTvg~Ll~~Le~idR~DVld 334 (639)
|...+ +...|||+|+.+|-+.+=+-..|
T Consensus 72 WGT~g---~~r~Tv~~L~~LL~k~~L~~Aa~ 99 (125)
T cd08308 72 WGTSG---KVRPTLGVLLQLLVKAELFRAAD 99 (125)
T ss_pred HhhcC---CCCCcHHHHHHHHHHhhHHHHHH
Confidence 95433 24579999999998877654433
No 48
>PF08357 SEFIR: SEFIR domain; InterPro: IPR013568 This domain is found in IL17 receptors (IL17Rs, e.g. Q60943 from SWISSPROT) and SEF proteins (e.g. Q8QHJ9 from SWISSPROT). The latter are feedback inhibitors of FGF signalling and are also thought to be receptors. Due to its similarity to the TIR domain (IPR000157 from INTERPRO), the SEFIR region is thought to be involved in homotypic interactions with other SEFIR/TIR-domain-containing proteins. Thus, SEFs and IL17Rs may be involved in TOLL/IL1R-like signalling pathways [].
Probab=96.14 E-value=0.048 Score=50.79 Aligned_cols=62 Identities=11% Similarity=0.101 Sum_probs=47.4
Q ss_pred eEEEeccCCHHH---HHHHHHhhhcC-CceEEEecCCCCC--CcchHHHHHHHHHhcceEEEEecccc
Q psy12711 388 ALLLYDEADFDL---AKQFNTQLNKM-GFTVCDKDNSFLT--GQFEHSAFIQVMDRCTCVIVLMSTHF 449 (639)
Q Consensus 388 AFVsYS~kD~dF---V~eLv~~LE~~-gykLCLh~RDflp--G~~i~e~I~~aIerSRR~IvVLSpnF 449 (639)
+||+||+.+.+. |..|+..|++. |+.+++---|... +.-...=+.+.++++.++|+|.||.+
T Consensus 3 VfI~Ys~d~~~h~~~V~~la~~L~~~~g~~V~lD~~~~~~i~~~g~~~W~~~~~~~ad~Vliv~S~~~ 70 (150)
T PF08357_consen 3 VFISYSHDSEEHKEWVLALAEFLRQNCGIDVILDQWELNEIARQGPPRWMERQIREADKVLIVCSPGY 70 (150)
T ss_pred EEEEeCCCCHHHHHHHHHHHHHHHhccCCceeecHHhhcccccCCHHHHHHHHHhcCCEEEEEeccch
Confidence 799999977655 78888999966 9999998888733 42223334556899999999999644
No 49
>cd08784 Death_DRs Death Domain of Death Receptors. Death domain (DD) found in death receptor proteins. Death receptors are members of the tumor necrosis factor (TNF) receptor superfamily, characterized by having a cytoplasmic DD. Known members of the family are Fas (CD95/APO-1), TNF-receptor 1 (TNFR1/TNFRSF1A/p55/CD120a), TNF-related apoptosis-inducing ligand receptor 1 (TRAIL-R1 /DR4), and receptor 2 (TRAIL-R2/DR5/APO-2/KILLER), as well as Death Receptor 3 (DR3/APO-3/TRAMP/WSL-1/LARD). They are involved in apoptosis signaling pathways. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=95.90 E-value=0.007 Score=52.22 Aligned_cols=62 Identities=11% Similarity=0.205 Sum_probs=51.1
Q ss_pred cCchHHHHHHcCCCCCC-------CCCccchHHHHHHHhhccCCCCCCcccHHHHHHHHhhcccchhhhhch
Q psy12711 273 QRDYRGLADLMDIKAPP-------NPNCEDLMKKMFEDWTKSSTLDRSVFNIATFLHFLECIDRFDVYDDCI 337 (639)
Q Consensus 273 ~rDWRgLAelmgf~~~~-------~e~~~~Pt~~vLe~W~~r~~~~~~~aTvg~Ll~~Le~idR~DVldD~~ 337 (639)
.++|..||-.|||+... .+...+....+|..|..+.+ ..||+..|+..|..++..++.|+++
T Consensus 11 ~~~Wk~laR~LGls~~~I~~ie~~~~~~~eq~~~mL~~W~~k~G---~~At~~~L~~aL~~~~~~~~Ae~i~ 79 (79)
T cd08784 11 FDQHKRFFRKLGLSDNEIKVAELDNPQHRDRVYELLRIWRNKEG---RKATLNTLIKALKDLDQRRTAEKIE 79 (79)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHcCCchHHHHHHHHHHHHhccC---cCcHHHHHHHHHHHcccHhHHHHcC
Confidence 57899999999998742 22234567899999999875 4899999999999999999988764
No 50
>cd08315 Death_TRAILR_DR4_DR5 Death domain of Tumor necrosis factor-Related Apoptosis-Inducing Ligand Receptors. Death Domain (DD) found in Tumor necrosis factor-Related Apoptosis-Inducing Ligand (TRAIL) Receptors. In mammals, this family includes TRAILR1 (also called DR4 or TNFRSF10A) and TRAILR2 (also called DR5, TNFRSF10B, or KILLER). They function as receptors for the cytokine TRAIL and are involved in apoptosis signaling pathways. TRAIL preferentially induces apoptosis in cancer cells while exhibiting little toxicity in normal cells. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=95.74 E-value=0.013 Score=52.69 Aligned_cols=65 Identities=12% Similarity=0.168 Sum_probs=53.9
Q ss_pred CchHHHHHHcCCCCC-------CCCCccchHHHHHHHhhccCCCCCCcccHHHHHHHHhhcccchhhhhchHHHH
Q psy12711 274 RDYRGLADLMDIKAP-------PNPNCEDLMKKMFEDWTKSSTLDRSVFNIATFLHFLECIDRFDVYDDCIGFIE 341 (639)
Q Consensus 274 rDWRgLAelmgf~~~-------~~e~~~~Pt~~vLe~W~~r~~~~~~~aTvg~Ll~~Le~idR~DVldD~~~~ie 341 (639)
++|..||-.+|++.. ..+...+-..++|..|..+.+ +.||++.|+.-|..|+.-++.|.++..+-
T Consensus 20 ~~Wk~laR~LGLse~~I~~i~~~~~~~~eq~~qmL~~W~~~~G---~~At~~~L~~aL~~~~~~~~Ae~I~~~l~ 91 (96)
T cd08315 20 DSWNRLMRQLGLSENEIDVAKANERVTREQLYQMLLTWVNKTG---RKASVNTLLDALEAIGLRLAKESIQDELI 91 (96)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHhhC---CCcHHHHHHHHHHHcccccHHHHHHHHHH
Confidence 899999999999874 222235677899999999875 58999999999999999999998876543
No 51
>cd08795 Death_IRAK2 Death domain of Interleukin 1 Receptor Associated Kinase-2. Death Domain (DD) of Interleukin-1 Receptor-Associated Kinase 1 (IRAK1). IRAKs are essential components of innate immunity and inflammation in mammals and other vertebrates. They are involved in signal transduction pathways involving IL-1 and IL-18 receptors, Toll-like receptors (TLRs), nuclear factor-kappaB (NF-kB), and mitogen-activated protein kinases (MAPKs). IRAKs contain an N-terminal DD domain and a C-terminal kinase domain. IRAK2 is an essential component of several signaling pathways, including NF-kappaB and the IL-1 signaling pathways. It is an inactive kinase that participates in septic shock mediated by TLR4 and TLR9. It plays a redundant role with IRAK1 in early NF-kB and MAPK responses, and remains present at later stages whereas IRAK1 disappears. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-as
Probab=95.11 E-value=0.018 Score=51.36 Aligned_cols=69 Identities=7% Similarity=0.139 Sum_probs=51.9
Q ss_pred ccccChhhHHHHHhccCCcccccCCCCccCchHHHHHHcCCCCC----CCC----CccchHHHHHHHhhccCCCCCCccc
Q psy12711 245 IEAIRPKTRQVLNDKLCDIKQLMSPENYQRDYRGLADLMDIKAP----PNP----NCEDLMKKMFEDWTKSSTLDRSVFN 316 (639)
Q Consensus 245 L~aL~~~tR~~Ls~~LNp~k~l~s~~g~~rDWRgLAelmgf~~~----~~e----~~~~Pt~~vLe~W~~r~~~~~~~aT 316 (639)
+--|...+++.|+..|+.-. ..||.+.|.. +++.. -+| ...+||+.+|..|..++ .|
T Consensus 3 iy~lP~~v~~~lc~~lDsl~--------~w~~~~~a~~-~~~~q~~vr~ie~~~~~G~SpT~eLL~~Wg~~N------~T 67 (88)
T cd08795 3 VYQLPAWVLDDFCRNMDALS--------DWDWMRFASY-VITDQTQLRKIKSMEWTGVSITRELMWWWGMRL------AT 67 (88)
T ss_pred hhhCCHHHHHHHHHHHcccc--------hHHHHHHHHH-hcccHHHHHHHHHHHHcCCChHHHHHHHHHcCC------CC
Confidence 45577889999999997655 3688888875 33432 122 23689999999997765 69
Q ss_pred HHHHHHHHhhcc
Q psy12711 317 IATFLHFLECID 328 (639)
Q Consensus 317 vg~Ll~~Le~id 328 (639)
|++|.++|+++.
T Consensus 68 V~~L~~lL~~~~ 79 (88)
T cd08795 68 VQQLVDLLQRLE 79 (88)
T ss_pred HHHHHHHHHHCc
Confidence 999999998875
No 52
>cd08316 Death_FAS_TNFRSF6 Death domain of FAS or TNF receptor superfamily member 6. Death Domain (DD) found in the FS7-associated cell surface antigen (FAS). FAS, also known as TNFRSF6 (TNF receptor superfamily member 6), APT1, CD95, FAS1, or APO-1, together with FADD (Fas-associating via Death Domain) and caspase 8, is an integral part of the death inducing signalling complex (DISC), which plays an important role in the induction of apoptosis and is activated by binding of the ligand FasL to FAS. FAS also plays a critical role in self-tolerance by eliminating cell types (autoreactive T and B cells) that contribute to autoimmunity. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in sign
Probab=94.77 E-value=0.044 Score=49.59 Aligned_cols=68 Identities=18% Similarity=0.275 Sum_probs=57.5
Q ss_pred cCchHHHHHHcCCCCCC-------CC-CccchHHHHHHHhhccCCCCCCcccHHHHHHHHhhcccchhhhhchHHHHHh
Q psy12711 273 QRDYRGLADLMDIKAPP-------NP-NCEDLMKKMFEDWTKSSTLDRSVFNIATFLHFLECIDRFDVYDDCIGFIEED 343 (639)
Q Consensus 273 ~rDWRgLAelmgf~~~~-------~e-~~~~Pt~~vLe~W~~r~~~~~~~aTvg~Ll~~Le~idR~DVldD~~~~ieeD 343 (639)
.+||+.+|-.+|++... ++ +..+...++|..|..+.+ ..|+...|+..|..++-.++.|.++..+.+|
T Consensus 20 ~~~wK~faR~lglse~~Id~I~~~~~~d~~Eq~~qmL~~W~~~~G---~~a~~~~Li~aLr~~~l~~~Ad~I~~~l~~~ 95 (97)
T cd08316 20 LKDVKKFVRKSGLSEPKIDEIKLDNPQDTAEQKVQLLRAWYQSHG---KTGAYRTLIKTLRKAKLCTKADKIQDIIEAD 95 (97)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHcCCCChHHHHHHHHHHHHHHhC---CCchHHHHHHHHHHccchhHHHHHHHHHHhc
Confidence 48999999999999752 22 234678899999999864 5788999999999999999999999998876
No 53
>cd08319 Death_RAIDD Death domain of RIP-associated ICH-1 homologous protein with a death domain. Death domain (DD) of RAIDD (RIP-associated ICH-1 homologous protein with a death domain), also known as CRADD (Caspase and RIP adaptor). RAIDD is an adaptor protein that together with the p53-inducible protein PIDD and caspase-2, forms the PIDDosome complex, which is required for caspase-2 activation and plays a role in mediating stress-induced apoptosis. RAIDD contains an N-terminal Caspase Activation and Recruitment Domain (CARD), which interacts with the caspase-2 CARD, and a C-terminal DD, which interacts with the DD of PIDD. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD, DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other pr
Probab=94.66 E-value=0.044 Score=48.23 Aligned_cols=53 Identities=4% Similarity=0.167 Sum_probs=41.5
Q ss_pred cCchHHHHHHcCCCCCCC-----CCccc---hHHHHHHHhhccCCCCCCcccHHHHHHHHhhcc
Q psy12711 273 QRDYRGLADLMDIKAPPN-----PNCED---LMKKMFEDWTKSSTLDRSVFNIATFLHFLECID 328 (639)
Q Consensus 273 ~rDWRgLAelmgf~~~~~-----e~~~~---Pt~~vLe~W~~r~~~~~~~aTvg~Ll~~Le~id 328 (639)
.+||+.||-.+||+...+ .+..| -...+|-.|..|.+ +.||++.|..-|+.++
T Consensus 13 G~~W~~Lar~Lgls~~~I~~i~~~~p~~l~eQv~~mL~~W~~r~G---~~ATv~~L~~aL~~~~ 73 (83)
T cd08319 13 GPEWEQVLLDLGLSQTDIYRCKENHPHNVQSQIVEALVKWRQRFG---KKATVQSLIQSLKAVE 73 (83)
T ss_pred hhhHHHHHHHcCCCHHHHHHHHHhCCCCHHHHHHHHHHHHHHhcC---CCCcHHHHHHHHHHcC
Confidence 689999999999997521 12223 34568889999975 5899999999998887
No 54
>cd08794 Death_IRAK1 Death domain of Interleukin 1 Receptor Associated Kinase-1. Death Domain (DD) of Interleukin-1 Receptor-Associated Kinase 1 (IRAK1). IRAKs are essential components of innate immunity and inflammation in mammals and other vertebrates. They are involved in signal transduction pathways involving IL-1 and IL-18 receptors, Toll-like receptors, nuclear factor-kappaB (NF-kB), and mitogen-activated protein kinases (MAPKs). IRAKs contain an N-terminal DD domain and a C-terminal kinase domain. IRAK1 is an active kinase and also plays adaptor functions. It binds to the MyD88-IRAK4 complex via its DD, which facilitates its phosphorylation by IRAK4, activating it for further auto-phosphorylation. Hyper-phosphorylated IRAK1 forms a cytosolic complex with TRAF6, leading to the activation of NF-kB and MAPK pathways. IRAK1 is involved in autoimmunity and may be associated with lupus pathogenesis. DDs are protein-protein interaction domains found in a variety of domain architectures.
Probab=94.66 E-value=0.018 Score=50.81 Aligned_cols=53 Identities=11% Similarity=0.101 Sum_probs=41.5
Q ss_pred CccCchHHHHHHcCCCCC---CCCCccchHHHHHHHhhccCCCCCCcccHHHHHHHHhhccc
Q psy12711 271 NYQRDYRGLADLMDIKAP---PNPNCEDLMKKMFEDWTKSSTLDRSVFNIATFLHFLECIDR 329 (639)
Q Consensus 271 g~~rDWRgLAelmgf~~~---~~e~~~~Pt~~vLe~W~~r~~~~~~~aTvg~Ll~~Le~idR 329 (639)
....||+++|+.+==+.. -.|....+|+.|+-.|..|+ +|||+|+.+|+.|+=
T Consensus 21 ls~~dW~~fAS~ii~dqtelR~~E~~~s~T~elmw~W~~Rn------~tV~~Ll~iL~~L~l 76 (84)
T cd08794 21 LSDLDWTRFASEIIKDQTELRLLEQSGRRTDWVMWRWENRN------GRVGELLDILERLQL 76 (84)
T ss_pred cccccHHHHHHHHhccHHHHHHHHHcCCcHHHHHHHHHhcc------cHHHHHHHHHHHhhh
Confidence 347899999998643322 23455689999999999987 699999999998864
No 55
>cd08313 Death_TNFR1 Death domain of Tumor Necrosis Factor Receptor 1. Death Domain (DD) found in tumor necrosis factor receptor-1 (TNFR-1). TNFR-1 has many names including TNFRSF1A, CD120a, p55, p60, and TNFR60. It activates two major intracellular signaling pathways that lead to the activation of the transcription factor NF-kB and the induction of cell death. Upon binding of its ligand TNF, TNFR-1 trimerizes which leads to the recruitment of an adaptor protein named TNFR-associated death domain protein (TRADD) through a DD/DD interaction. Mutations in the TNFRSF1A gene causes TNFR-associated periodic syndrome (TRAPS), a rare disorder characterized recurrent fever, myalgia, abdominal pain, conjunctivitis and skin eruptions. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation a
Probab=94.18 E-value=0.051 Score=47.59 Aligned_cols=66 Identities=14% Similarity=0.285 Sum_probs=51.3
Q ss_pred CCccCchHHHHHHcCCCCC-------CCCCccchHHHHHHHhhccCCCCCCcccHHHHHHHHhhcccchhhhhch
Q psy12711 270 ENYQRDYRGLADLMDIKAP-------PNPNCEDLMKKMFEDWTKSSTLDRSVFNIATFLHFLECIDRFDVYDDCI 337 (639)
Q Consensus 270 ~g~~rDWRgLAelmgf~~~-------~~e~~~~Pt~~vLe~W~~r~~~~~~~aTvg~Ll~~Le~idR~DVldD~~ 337 (639)
+--.++|+.+|--+|++-. .+++..+...++|..|..+.+. ..||++.|+.-|..|+--++.|.++
T Consensus 8 ~v~~~~wk~~~R~LGlse~~Id~ie~~~~~~~Eq~yqmL~~W~~~~g~--~~At~~~L~~aLr~~~l~~~ae~I~ 80 (80)
T cd08313 8 EVPPRRWKEFVRRLGLSDNEIERVELDHRRCRDAQYQMLKVWKERGPR--PYATLQHLLSVLRDMELVGCAEDIE 80 (80)
T ss_pred hCCHHHHHHHHHHcCCCHHHHHHHHHhCCChHHHHHHHHHHHHHhcCC--CcchHHHHHHHHHHcCcHHHHHHhC
Confidence 3346899999999999864 2234445667899999998641 2799999999999999888887653
No 56
>PF10137 TIR-like: Predicted nucleotide-binding protein containing TIR-like domain; InterPro: IPR019302 This entry represents a TIR-like domain found in a family of prokaryotic predicted nucleotide-binding proteins. Their exact function has not, as yet, been defined.
Probab=93.73 E-value=0.41 Score=45.14 Aligned_cols=107 Identities=13% Similarity=0.064 Sum_probs=77.2
Q ss_pred eEEEeccCCHHHHHHHHHhhhcCCceEEEecCCCCCCcchHHHHHHHHHhcceEEEEecccccCCh----h---h-----
Q psy12711 388 ALLLYDEADFDLAKQFNTQLNKMGFTVCDKDNSFLTGQFEHSAFIQVMDRCTCVIVLMSTHFMNNS----L---L----- 455 (639)
Q Consensus 388 AFVsYS~kD~dFV~eLv~~LE~~gykLCLh~RDflpG~~i~e~I~~aIerSRR~IvVLSpnFL~Se----W---c----- 455 (639)
+||.|+ +|.+++.++...|+..|+..-+-......|..+.+.+.+.+.+|.--|+|+||+=+-.. + .
T Consensus 2 VFIvhg-~~~~~~~~v~~~L~~~~~ep~i~~~~~~~g~tiie~le~~~~~~~faIvl~TpDD~~~~~~~~~~~~~~aR~N 80 (125)
T PF10137_consen 2 VFIVHG-RDLAAAEAVERFLEKLGLEPIIWHEQPNLGQTIIEKLEEAADSVDFAIVLFTPDDIGYSRGEEEDLQPRARQN 80 (125)
T ss_pred EEEEeC-CCHHHHHHHHHHHHhCCCceEEeecCCCCCCchHHHHHHHhccCCEEEEEEcccccccccCCccccccccccc
Confidence 799999 99999999999999889887777777789988889999999999999999999654421 1 1
Q ss_pred -HHHHHHHHHHhhhhcCCCcEEEEEeccCCCCcccchhhhhhcccc
Q psy12711 456 -HSLTQYAEAKHIDHTIHSKIIPILCSDDYFSVGFLQYCVKLKLNH 500 (639)
Q Consensus 456 -~fe~~~A~~l~l~~r~~~kLIpIlye~~~~~P~~Lr~~~~ld~~~ 500 (639)
-||+-++... ++ ++|++.+.-+.. ..|++|.=+++++|..
T Consensus 81 VifE~G~f~g~-LG---r~rv~~l~~~~v-~~PSDl~Gi~~~~~~~ 121 (125)
T PF10137_consen 81 VIFELGLFIGK-LG---RERVFILVKGGV-ELPSDLSGITYIRFDD 121 (125)
T ss_pred eeehhhHHHhh-cC---cceEEEEEcCCc-cCCcccCCeEEEEcCC
Confidence 2455444432 12 245666653322 3788888777776653
No 57
>cd08780 Death_TRADD Death Domain of Tumor Necrosis Factor Receptor 1-Associated Death Domain protein. Death domain (DD) of TRADD (TNF Receptor 1-Associated Death Domain or TNFRSF1A-associated via death domain) protein. TRADD is a central signaling adaptor for TNF-receptor 1 (TNFR1), mediating activation of Nuclear Factor -kappaB (NF-kB) and c-Jun N-terminal kinase (JNK), as well as caspase-dependent apoptosis. It also carries important immunological roles including germinal center formation, DR3-mediated T-cell stimulation, and TNFalpha-mediated inflammatory responses. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into s
Probab=91.77 E-value=0.13 Score=46.10 Aligned_cols=64 Identities=8% Similarity=0.167 Sum_probs=48.6
Q ss_pred CccCchHHHHHHcC-----CCCCCCC-----Cc----cchHHHHHHHhhccCCCCCCcccHHHHHHHHhhcccchhhhhc
Q psy12711 271 NYQRDYRGLADLMD-----IKAPPNP-----NC----EDLMKKMFEDWTKSSTLDRSVFNIATFLHFLECIDRFDVYDDC 336 (639)
Q Consensus 271 g~~rDWRgLAelmg-----f~~~~~e-----~~----~~Pt~~vLe~W~~r~~~~~~~aTvg~Ll~~Le~idR~DVldD~ 336 (639)
++.+||+-+|-.+| ++...++ .. ..-+.++|..|....+ ..||+++|..-|+...=-++.+|+
T Consensus 11 nvGr~WK~laR~Lg~~cral~d~~ID~I~~~y~r~gL~EqvyQ~L~~W~~~eg---~~Atv~~Lv~AL~~c~l~~lAe~l 87 (90)
T cd08780 11 SVGKKWKPVGRSLQKNCRALRDPAIDNLAYEYDREGLYEQAYQLLRRFIQSEG---KKATLQRLVQALEENGLTSLAEDL 87 (90)
T ss_pred HHhHHHHHHHHHHcccccccchhHHHHHHhhcccccHHHHHHHHHHHHHHhcc---ccchHHHHHHHHHHccchHHHHHH
Confidence 44799999999999 7654221 12 2245789999998754 569999999999998887777766
Q ss_pred h
Q psy12711 337 I 337 (639)
Q Consensus 337 ~ 337 (639)
.
T Consensus 88 ~ 88 (90)
T cd08780 88 L 88 (90)
T ss_pred h
Confidence 4
No 58
>cd06928 RNAP_alpha_NTD N-terminal domain of the Alpha subunit of Bacterial RNA polymerase. The bacterial alpha subunit of RNA polymerase (RNAP) consists of two independently folded domains: an amino-terminal domain (alphaNTD) and a carboxy-terminal domain (alphaCTD). AlphaCTD is not required for RNAP assembly but interacts with transcription activators. AlphaNTD is essential in vivo and in vitro for RNAP assembly and basal transcription. It is similar to the eukaryotic RPB3/AC40/archaeal D subunit, and contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and the other is an inserted beta sheet subdomain. The alphaNTDs of plant plastid RNAP (PEP) are also included in this subfamily. PEP is largely responsible for the transcription of photosynthetic genes and is closely related to the multi-subunit bacterial RNAP, which is a large multi-subunit complex responsible for the synthesis of all bacterial RNAs. The bac
Probab=86.27 E-value=1.1 Score=45.65 Aligned_cols=45 Identities=18% Similarity=0.169 Sum_probs=38.2
Q ss_pred CeeEEeecCCC------CCCCceEEEEEeCCCCCHHHHHHHHHHHHHHHHH
Q psy12711 131 EVDFAGYSVPH------PADFQIFIRIQVKDGYDSIDILKKGIKELESACD 175 (639)
Q Consensus 131 ~V~FAGY~IPH------PLe~~i~LrIQT~~~~~P~eaLk~Al~~L~~~~~ 175 (639)
=|.-+.|.|.. .-.+++.|.|.|+|+++|.+||..|++.|.+.+.
T Consensus 163 PV~~vny~v~~~~~~~~~~~e~L~leI~TnGsi~P~~Al~~A~~il~~~~~ 213 (215)
T cd06928 163 PVRKVNYSVESTRVGQRTDYEKLILEIWTNGSISPEEALAQAAKILINHFS 213 (215)
T ss_pred CeEEEEEEEEEeecCCCCCceeEEEEEEECCCCCHHHHHHHHHHHHHHHhh
Confidence 47778888753 3457899999999999999999999999998865
No 59
>PRK14979 DNA-directed RNA polymerase subunit D; Provisional
Probab=86.23 E-value=2.4 Score=42.93 Aligned_cols=51 Identities=16% Similarity=0.320 Sum_probs=40.7
Q ss_pred CCCeeEEeecCCCCCCCceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12711 129 YPEVDFAGYSVPHPADFQIFIRIQVKDGYDSIDILKKGIKELESACDRITETFND 183 (639)
Q Consensus 129 dp~V~FAGY~IPHPLe~~i~LrIQT~~~~~P~eaLk~Al~~L~~~~~~L~~~F~~ 183 (639)
.| |. |.|+... .++..|.|.|+|+++|.+||..|++-|.+.++.|.+....
T Consensus 138 ~p-vd-a~y~~~~--~dkl~leIeTdGsi~P~~al~~Aa~iL~~~l~~~~~~l~~ 188 (195)
T PRK14979 138 QP-CN-AVYKQIS--NDEVEFKVESFGQMDAEDILRSALEILKNKAEKFLQELEG 188 (195)
T ss_pred cc-ee-eEEecCC--CcEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 55 55 4454322 4999999999999999999999999999998888766543
No 60
>cd07028 RNAP_RPB3_like RPB3 subunit of RNA polymerase. The eukaryotic RPB3 subunit of RNA polymerase (RNAP), as well as its archaeal (D subunit) and bacterial (alpha subunit) counterparts, is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar to the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and
Probab=85.68 E-value=1.6 Score=44.47 Aligned_cols=52 Identities=12% Similarity=0.178 Sum_probs=45.5
Q ss_pred hcCCCeeEEeecCCCCCCCceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHH
Q psy12711 127 QSYPEVDFAGYSVPHPADFQIFIRIQVKDGYDSIDILKKGIKELESACDRITE 179 (639)
Q Consensus 127 lkdp~V~FAGY~IPHPLe~~i~LrIQT~~~~~P~eaLk~Al~~L~~~~~~L~~ 179 (639)
.+-.=|.-|.|++. |-.++..|.|.|+|.++|.+||.+|++-|.+.++.|.+
T Consensus 160 Ak~sPV~~v~y~~~-~~~d~li~~VeT~Gsi~p~~~l~~A~~iL~~~~~~~~~ 211 (212)
T cd07028 160 AKFGPVAAIEFRYD-PVADTYIMNVESVGSLPPDQVVVEAIKTLQKKVASILL 211 (212)
T ss_pred CEeCCceEEEEEEE-ccCCEEEEEEEecCCcCHHHHHHHHHHHHHHHHHHHhh
Confidence 46677888899964 36799999999999999999999999999999988865
No 61
>smart00662 RPOLD RNA polymerases D. DNA-directed RNA polymerase subunit D and bacterial alpha chain
Probab=84.20 E-value=1.6 Score=44.63 Aligned_cols=46 Identities=15% Similarity=0.242 Sum_probs=37.7
Q ss_pred CeeEEeecCCCCC----------------CCceEEEEEeCCCCCHHHHHHHHHHHHHHHHHH
Q psy12711 131 EVDFAGYSVPHPA----------------DFQIFIRIQVKDGYDSIDILKKGIKELESACDR 176 (639)
Q Consensus 131 ~V~FAGY~IPHPL----------------e~~i~LrIQT~~~~~P~eaLk~Al~~L~~~~~~ 176 (639)
.|+.+.|.+.-|- .+++.|.|.|+|..+|.+||.+|++-|.+.++.
T Consensus 162 pv~~v~~~~~~~~~~~~~~~~~~c~~~~~~d~l~f~IeT~G~i~p~~al~~A~~iL~~k~~~ 223 (224)
T smart00662 162 PVDRVAYQVECPRVVQRTDCCRECDEGEEYDKLIFDVETNGSLKPEEAVLEAAKILKEKLEA 223 (224)
T ss_pred hhhheeeeccCCccceecccchhhhccCCCCEEEEEEEecCCcCHHHHHHHHHHHHHHHHhh
Confidence 3555566666654 578999999999999999999999999988754
No 62
>TIGR02027 rpoA DNA-directed RNA polymerase, alpha subunit, bacterial and chloroplast-type. This family consists of the bacterial (and chloroplast) DNA-directed RNA polymerase alpha subunit, encoded by the rpoA gene. The RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. The amino terminal domain is involved in dimerizing and assembling the other RNA polymerase subunits into a transcriptionally active enzyme. The carboxy-terminal domain contains determinants for interaction with DNA and with transcriptional activator proteins.
Probab=83.20 E-value=2.5 Score=45.15 Aligned_cols=49 Identities=14% Similarity=0.168 Sum_probs=40.3
Q ss_pred CeeEEeecCCC------CCCCceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHH
Q psy12711 131 EVDFAGYSVPH------PADFQIFIRIQVKDGYDSIDILKKGIKELESACDRITE 179 (639)
Q Consensus 131 ~V~FAGY~IPH------PLe~~i~LrIQT~~~~~P~eaLk~Al~~L~~~~~~L~~ 179 (639)
-|.-+.|.|.. ...++..|.|.|+|.++|.+||.+|++-|.+.+..|.+
T Consensus 154 PV~~Vny~ve~~rv~~~~~~d~li~eIeT~Gsi~P~~al~~A~~iL~~~~~~~~~ 208 (297)
T TIGR02027 154 PVLKVNYEVENTRVGQRTDYDKLILEIETNGSITPKDAIAEAAKILIEHLEPFVN 208 (297)
T ss_pred CeEEEEEEEeeeeccCCccccEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 46667777753 23468999999999999999999999999999887743
No 63
>CHL00013 rpoA RNA polymerase alpha subunit
Probab=79.63 E-value=3.3 Score=44.98 Aligned_cols=48 Identities=15% Similarity=0.169 Sum_probs=40.6
Q ss_pred CeeEEeecCCC-----CCCCceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHH
Q psy12711 131 EVDFAGYSVPH-----PADFQIFIRIQVKDGYDSIDILKKGIKELESACDRIT 178 (639)
Q Consensus 131 ~V~FAGY~IPH-----PLe~~i~LrIQT~~~~~P~eaLk~Al~~L~~~~~~L~ 178 (639)
=|.-+.|.|.. ...+++.|-|.|+|.++|.+||..|++-|.+.+..|.
T Consensus 170 PV~kVny~Ve~~~~~~~~~e~L~lEI~TnGsi~P~~Al~~Aa~il~~~~~~~~ 222 (327)
T CHL00013 170 PVRNVNYSIHSYGNGNEKQEILFLEIWTNGSITPKEALHEASRNLIDLFIPFL 222 (327)
T ss_pred CeeEEEEEEEEcccCCcccceEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHh
Confidence 47777888865 1257899999999999999999999999999987764
No 64
>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional
Probab=78.58 E-value=4 Score=43.95 Aligned_cols=49 Identities=12% Similarity=0.167 Sum_probs=40.1
Q ss_pred CeeEEeecCCCC------CCCceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHH
Q psy12711 131 EVDFAGYSVPHP------ADFQIFIRIQVKDGYDSIDILKKGIKELESACDRITE 179 (639)
Q Consensus 131 ~V~FAGY~IPHP------Le~~i~LrIQT~~~~~P~eaLk~Al~~L~~~~~~L~~ 179 (639)
-|.-+.|.|.-. -.+++.|.|.|+|.++|.+||..|++-|.+.+..|.+
T Consensus 171 PV~~vny~ve~~~~~~~~~~e~L~leI~TnGsi~P~eAl~~A~~iL~~~l~~f~~ 225 (310)
T PRK05182 171 PVKKVNYTVENTRVGQRTDYDKLILEVETDGSITPEEALALAAKILVEQLSVFVD 225 (310)
T ss_pred CccceEEEecccccCCCCcceEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHhC
Confidence 466677876542 1468999999999999999999999999999877644
No 65
>PRK00783 DNA-directed RNA polymerase subunit D; Provisional
Probab=75.71 E-value=3.1 Score=43.16 Aligned_cols=27 Identities=19% Similarity=0.251 Sum_probs=24.4
Q ss_pred CCCeEEEEEccCCcchHHHHHHHHhcC
Q psy12711 103 KPNCRTFVFEKEGHTFGSVITHILQSY 129 (639)
Q Consensus 103 ~~N~~tf~i~gEDHTLGNlLR~~Llkd 129 (639)
+++.++|.+.|-|+||||+||-.|+..
T Consensus 9 ~~~~~~f~~~g~~~t~~NalRRvlls~ 35 (263)
T PRK00783 9 DDRSARFVVEGVTPAFANAIRRAMIAD 35 (263)
T ss_pred CCcEEEEEEeCCCHHHHHHHHHHHHHc
Confidence 368899999999999999999999964
No 66
>cd07028 RNAP_RPB3_like RPB3 subunit of RNA polymerase. The eukaryotic RPB3 subunit of RNA polymerase (RNAP), as well as its archaeal (D subunit) and bacterial (alpha subunit) counterparts, is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar to the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and
Probab=68.71 E-value=4.7 Score=41.21 Aligned_cols=27 Identities=4% Similarity=0.188 Sum_probs=24.9
Q ss_pred CCCeEEEEEccCCcchHHHHHHHHhcC
Q psy12711 103 KPNCRTFVFEKEGHTFGSVITHILQSY 129 (639)
Q Consensus 103 ~~N~~tf~i~gEDHTLGNlLR~~Llkd 129 (639)
+++.++|.+.|-|+|+||+||-.|+..
T Consensus 9 ~~~~~~f~l~g~~~t~aNaLRRiLLse 35 (212)
T cd07028 9 DKDNVDFILSGVDLAMANALRRVMIAE 35 (212)
T ss_pred CCCEEEEEEEccChhHHHHHHHHHHHc
Confidence 578999999999999999999999875
No 67
>cd07031 RNAP_II_RPB3 RPB3 subunit of Eukaryotic RNA polymerase II. The eukaryotic RPB3 subunit of RNA polymerase (RNAP) II is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP II is responsible for the synthesis of mRNA precursor. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization, and the other is an inserted beta sheet subdomain. The RPB3 subunit heterodimerizes with the RPB11 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association.
Probab=68.56 E-value=8.8 Score=40.40 Aligned_cols=40 Identities=8% Similarity=0.220 Sum_probs=36.4
Q ss_pred CCceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12711 144 DFQIFIRIQVKDGYDSIDILKKGIKELESACDRITETFND 183 (639)
Q Consensus 144 e~~i~LrIQT~~~~~P~eaLk~Al~~L~~~~~~L~~~F~~ 183 (639)
.+.+.|.|.|+|...|.++|.+|++-|.+.++.|.+.+..
T Consensus 225 ~~~fiF~VES~Gsl~p~~Iv~~Al~iL~~K~~~l~~~l~~ 264 (265)
T cd07031 225 PDKFYFNVESTGALPPEQIVLSGLEILKKKLADLQLQLSE 264 (265)
T ss_pred CCEEEEEEEecCCCCHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 5779999999999999999999999999999999887653
No 68
>cd07030 RNAP_D D subunit of Archaeal RNA polymerase. The D subunit of archaeal RNA polymerase (RNAP) is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. A single distinct RNAP complex is found in archaea, which may be responsible for the synthesis of all RNAs. The archaeal RNAP harbors homologues of all eukaryotic RNAP II subunits with two exceptions (RPB8 and RPB9). The 12 archaeal subunits are designated by letters and can be divided into three functional groups that are engaged in: (I) catalysis (A'/A", B'/B" or B); (II) assembly (L, N, D and P); and (III) auxiliary functions (F, E, H and K). The D subunit is equivalent to the RPB3 subunit of eukaryotic RNAP II. It contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit w
Probab=67.02 E-value=5 Score=41.57 Aligned_cols=27 Identities=22% Similarity=0.278 Sum_probs=24.4
Q ss_pred CCCeEEEEEccCCcchHHHHHHHHhcC
Q psy12711 103 KPNCRTFVFEKEGHTFGSVITHILQSY 129 (639)
Q Consensus 103 ~~N~~tf~i~gEDHTLGNlLR~~Llkd 129 (639)
+++.++|.++|-|+|+||+||-.|+..
T Consensus 9 ~~~~~~f~~~g~~~s~~NalRRills~ 35 (259)
T cd07030 9 DDDRARFVLEGVPPAFANAIRRAIISE 35 (259)
T ss_pred CCCEEEEEEeCCCHHHHHHHHHHHHhc
Confidence 468899999999999999999999854
No 69
>cd06928 RNAP_alpha_NTD N-terminal domain of the Alpha subunit of Bacterial RNA polymerase. The bacterial alpha subunit of RNA polymerase (RNAP) consists of two independently folded domains: an amino-terminal domain (alphaNTD) and a carboxy-terminal domain (alphaCTD). AlphaCTD is not required for RNAP assembly but interacts with transcription activators. AlphaNTD is essential in vivo and in vitro for RNAP assembly and basal transcription. It is similar to the eukaryotic RPB3/AC40/archaeal D subunit, and contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and the other is an inserted beta sheet subdomain. The alphaNTDs of plant plastid RNAP (PEP) are also included in this subfamily. PEP is largely responsible for the transcription of photosynthetic genes and is closely related to the multi-subunit bacterial RNAP, which is a large multi-subunit complex responsible for the synthesis of all bacterial RNAs. The bac
Probab=63.67 E-value=9.2 Score=39.01 Aligned_cols=39 Identities=23% Similarity=0.454 Sum_probs=30.5
Q ss_pred CCCeEEEEE----ccCCcchHHHHHHHHhcC-CCeeEEeecCCC
Q psy12711 103 KPNCRTFVF----EKEGHTFGSVITHILQSY-PEVDFAGYSVPH 141 (639)
Q Consensus 103 ~~N~~tf~i----~gEDHTLGNlLR~~Llkd-p~V~FAGY~IPH 141 (639)
+.+.+.|.+ .|.++||||+||-.|+.. |+...-+-+|.+
T Consensus 7 ~~~~~~F~i~pl~~g~~~tlgNaLRRvLLs~ipg~aI~~v~I~~ 50 (215)
T cd06928 7 RENYGRFVIEPLERGQGTTLGNALRRVLLSSLPGAAITAVKIEG 50 (215)
T ss_pred CCcEEEEEEEcCCCCchhHHHHHHHHHHHhcCCeEEEEEEEEcc
Confidence 468899999 789999999999988866 666555555543
No 70
>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional
Probab=58.42 E-value=14 Score=39.79 Aligned_cols=38 Identities=26% Similarity=0.437 Sum_probs=31.0
Q ss_pred CCCeEEEEEc----cCCcchHHHHHHHHhcC-CCeeEEeecCC
Q psy12711 103 KPNCRTFVFE----KEGHTFGSVITHILQSY-PEVDFAGYSVP 140 (639)
Q Consensus 103 ~~N~~tf~i~----gEDHTLGNlLR~~Llkd-p~V~FAGY~IP 140 (639)
+++.+.|.+. |.++|+||+||-.|+.. |+....+-+|.
T Consensus 17 ~~~~~~F~i~Ple~G~g~tlgNaLRRvLLs~ipg~aI~~VkI~ 59 (310)
T PRK05182 17 DDNYGKFVLEPLERGFGTTLGNALRRVLLSSLPGAAVTSVKID 59 (310)
T ss_pred CCcEEEEEEeccCCCchhHHHHHHHHHHHhcCCeeEEEEEEEc
Confidence 4789999997 99999999999988876 66666665653
No 71
>smart00662 RPOLD RNA polymerases D. DNA-directed RNA polymerase subunit D and bacterial alpha chain
Probab=55.53 E-value=13 Score=38.11 Aligned_cols=33 Identities=24% Similarity=0.426 Sum_probs=25.4
Q ss_pred EEEEEccCCcchHHHHHHHHhcC-CCeeEEeecC
Q psy12711 107 RTFVFEKEGHTFGSVITHILQSY-PEVDFAGYSV 139 (639)
Q Consensus 107 ~tf~i~gEDHTLGNlLR~~Llkd-p~V~FAGY~I 139 (639)
+.|++.+-+||+||+||-.|+.. |+...-+.+|
T Consensus 2 ~~f~l~~~~~t~~NaLRRilLs~vp~~aI~~V~I 35 (224)
T smart00662 2 AKFVLEPYGLTLANALRRVLLSSVPGMAVTEVEI 35 (224)
T ss_pred eEEEEEcCCchHHHHHHHHHHHcCccceEEEEEE
Confidence 58999999999999999998865 5544444333
No 72
>cd08815 Death_TNFRSF25_DR3 Death domain of Tumor Necrosis Factor Receptor superfamily 25. Death Domain (DD) found in Tumor Necrosis Factor (TNF) receptor superfamily 25 (TNFRSF25), also known as TRAMP (TNF receptor-related apoptosis-mediating protein), LARD, APO-3, WSL-1, or DR3 (Death Receptor-3). TNFRSF25 is primarily expressed in T cells, is activated by binding to its ligand TL1A, and plays an important role in T-cell function. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=54.24 E-value=19 Score=31.81 Aligned_cols=54 Identities=11% Similarity=0.241 Sum_probs=43.2
Q ss_pred cCchHHHHHHcCCCCCCC-------CCccchHHHHHHHhhccCCCCCCcccHHHHHHHHhhcccch
Q psy12711 273 QRDYRGLADLMDIKAPPN-------PNCEDLMKKMFEDWTKSSTLDRSVFNIATFLHFLECIDRFD 331 (639)
Q Consensus 273 ~rDWRgLAelmgf~~~~~-------e~~~~Pt~~vLe~W~~r~~~~~~~aTvg~Ll~~Le~idR~D 331 (639)
++-|.-+.-.+|++--.+ -++.|+--.||..|..+. .|++..|+..|+.|+=--
T Consensus 11 ~~~wk~F~R~LGLsdn~Ie~~E~~~~~~rda~y~ML~~W~~q~-----~a~~n~Ll~aL~~m~l~g 71 (77)
T cd08815 11 ARRWKEFVRTLGLREAEIEAVELEIGRFRDQQYEMLKRWRQQQ-----PAGLDAVYAALERMGLAG 71 (77)
T ss_pred hHHHHHHHHHcCCcHhHHHHHHhcccchHHHHHHHHHHHHHcC-----CCcHHHHHHHHHHHHHHH
Confidence 467999999999986422 246788899999999886 389999999998887433
No 73
>COG4916 Uncharacterized protein containing a TIR (Toll-Interleukin 1-resistance) domain [Function unknown]
Probab=53.49 E-value=15 Score=39.27 Aligned_cols=78 Identities=15% Similarity=0.046 Sum_probs=55.6
Q ss_pred CCccceEEEeccCCHHHHHHHHHhhh-cCCceEEEecCC----CCCCcchHHHHHHHH--HhcceEEEEecccccCChhh
Q psy12711 383 LAHYDALLLYDEADFDLAKQFNTQLN-KMGFTVCDKDNS----FLTGQFEHSAFIQVM--DRCTCVIVLMSTHFMNNSLL 455 (639)
Q Consensus 383 ~k~YDAFVsYS~kD~dFV~eLv~~LE-~~gykLCLh~RD----flpG~~i~e~I~~aI--erSRR~IvVLSpnFL~SeWc 455 (639)
.+.||.=+|++.+-+..|++...+++ .-+=..-..+=| +.||+ .+.+.+-+ ++|+-++|.+..+|..-.||
T Consensus 175 ~~~~DiG~SFaGEAR~LVEqV~~E~~~~~~p~~~FYD~~~~~~L~~~s--L~~~L~~~Y~~rC~~~~VF~~~~Y~~K~~c 252 (329)
T COG4916 175 EKPVDSGISFAGEARNLVEQVQTEHSGLDIPTRRFYDLLVAHPLYPGS--LVSTLDPGYDIRCVVTTVFNTGSYICKSTC 252 (329)
T ss_pred ccccceeeEeehhhhhHHHHHHHhhhcccCCceeeeechhhccccCcc--HHHhcccccCceEEEEEEEeCCceEEeeee
Confidence 67899999999999999998888888 222122222222 22332 23344444 78999999999999999999
Q ss_pred HHHHHHH
Q psy12711 456 HSLTQYA 462 (639)
Q Consensus 456 ~fe~~~A 462 (639)
++|....
T Consensus 253 ~~E~~~~ 259 (329)
T COG4916 253 HIEGLEG 259 (329)
T ss_pred ccchhhc
Confidence 9987643
No 74
>PRK00783 DNA-directed RNA polymerase subunit D; Provisional
Probab=52.90 E-value=26 Score=36.38 Aligned_cols=41 Identities=15% Similarity=0.325 Sum_probs=37.0
Q ss_pred CCCceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12711 143 ADFQIFIRIQVKDGYDSIDILKKGIKELESACDRITETFND 183 (639)
Q Consensus 143 Le~~i~LrIQT~~~~~P~eaLk~Al~~L~~~~~~L~~~F~~ 183 (639)
..++..+.|.|+|..+|.+++..|++-|.+.++.|.++.++
T Consensus 221 ~~~~~if~vEs~G~l~p~~iv~~A~~~l~~k~~~~~~~~~~ 261 (263)
T PRK00783 221 DENKFIFTVESDGSLPVEEILLEALKILKRKADELIEALEE 261 (263)
T ss_pred cCCeEEEEeccCCCCCHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 45778899999999999999999999999999999888765
No 75
>PRK14979 DNA-directed RNA polymerase subunit D; Provisional
Probab=51.88 E-value=17 Score=37.03 Aligned_cols=45 Identities=16% Similarity=0.152 Sum_probs=32.6
Q ss_pred CCCeEEEEEccCCcchHHHHHHHHhcC-CCeeEEeecC---CCCCCCceE
Q psy12711 103 KPNCRTFVFEKEGHTFGSVITHILQSY-PEVDFAGYSV---PHPADFQIF 148 (639)
Q Consensus 103 ~~N~~tf~i~gEDHTLGNlLR~~Llkd-p~V~FAGY~I---PHPLe~~i~ 148 (639)
.++.++|.+. -|.||||+||-.|+.. |+...-+-+| -|++.+++.
T Consensus 12 ~~~~~~f~l~-~~~tlgNaLRRvLLssipg~AI~~V~I~~Nts~~~DEiv 60 (195)
T PRK14979 12 IGEEFKFSLK-APISFSSALRRIMISEVPTYAIENVYFYENSSSMYDEIL 60 (195)
T ss_pred CCcEEEEEEE-cCccHHHHHHHHHHhcCcceeEEEEEEecCcccccchhe
Confidence 4889999999 9999999999998865 5554444333 345555444
No 76
>cd08304 DD_superfamily The Death Domain Superfamily of protein-protein interaction domains. The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. 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. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer.
Probab=49.00 E-value=14 Score=31.27 Aligned_cols=56 Identities=5% Similarity=0.083 Sum_probs=42.1
Q ss_pred cCchHHHHHHcC--CCCCCCCCccchHHHHHHHhhccCCCCCCcccHHHHHHHHhhcccchhhh
Q psy12711 273 QRDYRGLADLMD--IKAPPNPNCEDLMKKMFEDWTKSSTLDRSVFNIATFLHFLECIDRFDVYD 334 (639)
Q Consensus 273 ~rDWRgLAelmg--f~~~~~e~~~~Pt~~vLe~W~~r~~~~~~~aTvg~Ll~~Le~idR~DVld 334 (639)
..+|-.++..+- |+....|.-. |...+|..|.++.+ =++-.+.++|+.+...|..+
T Consensus 10 ~~~~~~l~~~l~~~~~~~~~e~i~-~a~~ll~~l~~~~~-----~a~~~~~~vL~~~~~~~la~ 67 (69)
T cd08304 10 LEVLQQLKTALKSRIPPDQVEQIS-AANELLNILESQYN-----HTLQLLFALFEDLGLHNLAR 67 (69)
T ss_pred HhHHHHHHHHHHccCCHHHHHHhh-HHHHHHHHHHHhCc-----chHHHHHHHHHHcCCHhHHh
Confidence 357888888777 6544444333 89999999999863 47889999999999887654
No 77
>cd07031 RNAP_II_RPB3 RPB3 subunit of Eukaryotic RNA polymerase II. The eukaryotic RPB3 subunit of RNA polymerase (RNAP) II is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP II is responsible for the synthesis of mRNA precursor. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization, and the other is an inserted beta sheet subdomain. The RPB3 subunit heterodimerizes with the RPB11 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association.
Probab=46.92 E-value=17 Score=38.31 Aligned_cols=33 Identities=9% Similarity=0.292 Sum_probs=26.7
Q ss_pred CCCeEEEEEccCCcchHHHHHHHHhcC-CCeeEE
Q psy12711 103 KPNCRTFVFEKEGHTFGSVITHILQSY-PEVDFA 135 (639)
Q Consensus 103 ~~N~~tf~i~gEDHTLGNlLR~~Llkd-p~V~FA 135 (639)
+++.++|.+.+=|+|+||+||-.|+.. |....-
T Consensus 9 ~~~~~~F~l~~~~~s~aNALRRillsevPt~AI~ 42 (265)
T cd07031 9 TDDKVKFILENTDLSVANSLRRVMIAEVPTLAID 42 (265)
T ss_pred CCCEEEEEEEcCcHHHHHHHHHHHHHcCccceEE
Confidence 468899999999999999999998854 544333
No 78
>cd07032 RNAP_I_II_AC40 AC40 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III. The eukaryotic AC40 subunit of RNA polymerase (RNAP) I and RNAP III is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP I is responsible for the synthesis of ribosomal RNA precursor, while RNAP III functions in the synthesis of 5S and tRNA. The AC40 subunit is the equivalent of the RPB3 subunit of RNAP II. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and the other is an inserted beta sheet subdomain. The RPB3 subun
Probab=45.63 E-value=37 Score=36.57 Aligned_cols=38 Identities=16% Similarity=0.262 Sum_probs=34.2
Q ss_pred CCCCceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHH
Q psy12711 142 PADFQIFIRIQVKDGYDSIDILKKGIKELESACDRITE 179 (639)
Q Consensus 142 PLe~~i~LrIQT~~~~~P~eaLk~Al~~L~~~~~~L~~ 179 (639)
.-.+.+.+.|.|+|...|.+++.+|++-|.+.|+.|.+
T Consensus 253 ~~~d~fiF~VES~G~l~p~~i~~~Ai~iL~~K~~~l~~ 290 (291)
T cd07032 253 RVRDHFIFSIESTGALPPDVLFLEAIKILKEKCRKLLE 290 (291)
T ss_pred EeCCEEEEEEeCCCCCCHHHHHHHHHHHHHHHHHHHhh
Confidence 34566999999999999999999999999999998875
No 79
>COG0202 RpoA DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription]
Probab=43.61 E-value=23 Score=38.49 Aligned_cols=36 Identities=17% Similarity=0.146 Sum_probs=28.0
Q ss_pred CCCeEEEEEccCCcchHHHHHHHHhcC-CCeeEEeec
Q psy12711 103 KPNCRTFVFEKEGHTFGSVITHILQSY-PEVDFAGYS 138 (639)
Q Consensus 103 ~~N~~tf~i~gEDHTLGNlLR~~Llkd-p~V~FAGY~ 138 (639)
..-.++|...|-+|||||+||-.|+.. |+...-+-.
T Consensus 17 ~~~~ieplerG~g~tlgNALRRvLLSsiPg~Av~~V~ 53 (317)
T COG0202 17 AKFVIEPLERGFGVTLGNALRRVLLSSIPGAAVTAVE 53 (317)
T ss_pred ccEEEEEeeeCCcchhHHHHHHHHHHcCccceEEEEE
Confidence 467899999999999999999998865 554443333
No 80
>cd07030 RNAP_D D subunit of Archaeal RNA polymerase. The D subunit of archaeal RNA polymerase (RNAP) is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. A single distinct RNAP complex is found in archaea, which may be responsible for the synthesis of all RNAs. The archaeal RNAP harbors homologues of all eukaryotic RNAP II subunits with two exceptions (RPB8 and RPB9). The 12 archaeal subunits are designated by letters and can be divided into three functional groups that are engaged in: (I) catalysis (A'/A", B'/B" or B); (II) assembly (L, N, D and P); and (III) auxiliary functions (F, E, H and K). The D subunit is equivalent to the RPB3 subunit of eukaryotic RNAP II. It contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit w
Probab=43.18 E-value=47 Score=34.48 Aligned_cols=37 Identities=14% Similarity=0.322 Sum_probs=33.0
Q ss_pred CCceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q psy12711 144 DFQIFIRIQVKDGYDSIDILKKGIKELESACDRITET 180 (639)
Q Consensus 144 e~~i~LrIQT~~~~~P~eaLk~Al~~L~~~~~~L~~~ 180 (639)
.+...+.|.|+|..+|.++++.|++-|.+.++.|.++
T Consensus 222 ~~~~if~vEs~Gsl~p~~il~~A~~~l~~k~~~~~~~ 258 (259)
T cd07030 222 EDRFIFEVESDGSLPPKEILLEALRILKEKADELIEA 258 (259)
T ss_pred CCEEEEEEeCCCCCCHHHHHHHHHHHHHHHHHHHHhh
Confidence 4557899999999999999999999999999888764
No 81
>PF14786 Death_2: Tube Death domain; PDB: 1D2Z_B.
Probab=37.43 E-value=39 Score=32.88 Aligned_cols=41 Identities=15% Similarity=0.305 Sum_probs=27.0
Q ss_pred ccchHHHHHHHhhccCCCCCCcccHHHHHHHHhhcccchhhh
Q psy12711 293 CEDLMKKMFEDWTKSSTLDRSVFNIATFLHFLECIDRFDVYD 334 (639)
Q Consensus 293 ~~~Pt~~vLe~W~~r~~~~~~~aTvg~Ll~~Le~idR~DVld 334 (639)
..+++.-+|++|...+- -....|||+|+.+|-+-|=|--.|
T Consensus 71 ~~s~s~illdEWgTSGr-~~eRPTl~~Ll~LLvkael~rAAD 111 (137)
T PF14786_consen 71 NRSCSEILLDEWGTSGR-KNERPTLGHLLQLLVKAELFRAAD 111 (137)
T ss_dssp TS-HHHHHHHHHHT-SS-TTTS-BHHHHHHHHHHTT-HHHHH
T ss_pred CCcHHHHHHHHhhccCc-ccCCCcHHHHHHHHHHHHHHHHHH
Confidence 34588999999988542 112579999999998877654333
No 82
>PF05014 Nuc_deoxyrib_tr: Nucleoside 2-deoxyribosyltransferase; InterPro: IPR007710 Nucleoside 2-deoxyribosyltransferase (2.4.2.6 from EC) catalyses the cleavage of the glycosidic bonds of 2-deoxyribonucleosides. Nucleoside 2-deoxyribosyltransferases can be divided into two groups based on their substrate specificity: class I enzymes are specific for the transfer of deoxyribose between two purines, while class II enzymes will transfer the deoxyribose between either purines or pyrimidines. The structure of the class I [] and class II [] enzymes are very similar. In class I enzymes, the purine base shields the active site from solvent, which the smaller pyrimidine base cannot do, while in class II enzymes the active site is shielded by a loop (residues 48-62). Both classes of enzymes are found in various Lactobacillus species and participate in nucleoside recycling in these microorganisms. This entry represents both classes of enzymes.; GO: 0050144 nucleoside deoxyribosyltransferase activity, 0070694 deoxyribonucleoside 5'-monophosphate N-glycosidase activity, 0009159 deoxyribonucleoside monophosphate catabolic process; PDB: 1S2L_A 1S2D_C 1S2I_A 1S3F_B 1S2G_C 2A0K_A 2F67_A 2F64_B 2F62_A 2F2T_A ....
Probab=35.37 E-value=1.9e+02 Score=25.94 Aligned_cols=72 Identities=18% Similarity=0.130 Sum_probs=49.3
Q ss_pred ccCCHHHHHHHHHhhhcCCceEEEecC-CCC---CC----cchHHHHHHHHHhcceEEEEecccccCChhhHHHHHHHHH
Q psy12711 393 DEADFDLAKQFNTQLNKMGFTVCDKDN-SFL---TG----QFEHSAFIQVMDRCTCVIVLMSTHFMNNSLLHSLTQYAEA 464 (639)
Q Consensus 393 S~kD~dFV~eLv~~LE~~gykLCLh~R-Dfl---pG----~~i~e~I~~aIerSRR~IvVLSpnFL~SeWc~fe~~~A~~ 464 (639)
+.....++.++...|++.|+.+....+ +.. .+ ..+.+.-.+.|++|.-+|+++...- .+.=..||+-+|.+
T Consensus 9 ~~~~~~~~~~~~~~L~~~g~~v~~P~~~~~~~~~~~~~~~~~i~~~d~~~i~~~D~via~l~~~~-~d~Gt~~ElG~A~a 87 (113)
T PF05014_consen 9 SEEQKARVERLREALEKNGFEVYSPQDNDENDEEDSQEWAREIFERDLEGIRECDIVIANLDGFR-PDSGTAFELGYAYA 87 (113)
T ss_dssp SHHHHHHHHHHHHHHHTTTTEEEGGCTCSSS--TTSHHCHHHHHHHHHHHHHHSSEEEEEECSSS---HHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHhCCCEEEeccccccccccccchHHHHHHHHHHHHHHHCCEEEEECCCCC-CCCcHHHHHHHHHH
Confidence 345566788899999999998887763 332 11 2344444567899999999998754 33335688888876
Q ss_pred H
Q psy12711 465 K 465 (639)
Q Consensus 465 l 465 (639)
+
T Consensus 88 l 88 (113)
T PF05014_consen 88 L 88 (113)
T ss_dssp T
T ss_pred C
Confidence 6
No 83
>cd00860 ThrRS_anticodon ThrRS Threonyl-anticodon binding domain. ThrRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only.
Probab=34.22 E-value=1.6e+02 Score=24.37 Aligned_cols=62 Identities=13% Similarity=0.124 Sum_probs=38.9
Q ss_pred ccceEEEec-cCCHHHHHHHHHhhhcCCceEEEecCCCCCCcchHHHHHHHHHhcceEEEEeccccc
Q psy12711 385 HYDALLLYD-EADFDLAKQFNTQLNKMGFTVCDKDNSFLTGQFEHSAFIQVMDRCTCVIVLMSTHFM 450 (639)
Q Consensus 385 ~YDAFVsYS-~kD~dFV~eLv~~LE~~gykLCLh~RDflpG~~i~e~I~~aIerSRR~IvVLSpnFL 450 (639)
.||++|... ..+.+.+.++...|...|+++-+..|+-.+|. .+-.|-..-=+.++++.++.+
T Consensus 1 p~~v~ii~~~~~~~~~a~~~~~~Lr~~g~~v~~d~~~~~~~~----~~~~a~~~g~~~~iiig~~e~ 63 (91)
T cd00860 1 PVQVVVIPVTDEHLDYAKEVAKKLSDAGIRVEVDLRNEKLGK----KIREAQLQKIPYILVVGDKEV 63 (91)
T ss_pred CeEEEEEeeCchHHHHHHHHHHHHHHCCCEEEEECCCCCHHH----HHHHHHHcCCCEEEEECcchh
Confidence 367666665 44556678888999988999988777655552 333444344445555555543
No 84
>CHL00013 rpoA RNA polymerase alpha subunit
Probab=33.84 E-value=31 Score=37.64 Aligned_cols=39 Identities=10% Similarity=0.149 Sum_probs=31.0
Q ss_pred CCCeEEEEEc----cCCcchHHHHHHHHhcC-CCeeEEeecCCC
Q psy12711 103 KPNCRTFVFE----KEGHTFGSVITHILQSY-PEVDFAGYSVPH 141 (639)
Q Consensus 103 ~~N~~tf~i~----gEDHTLGNlLR~~Llkd-p~V~FAGY~IPH 141 (639)
..+...|.+. |..|||||+||-.|+.. |+..+.+-+|.+
T Consensus 18 ~~~y~~F~i~Pl~~G~g~TlGNaLRRvLLssi~g~aIt~vkI~g 61 (327)
T CHL00013 18 RLYYGRFILSPLMKGQADTIGIALRRALLGEIEGTCITRAKIEG 61 (327)
T ss_pred CCcEEEEEEECCCCCchhhhHHHHHHHHHhcCCceEEEEEEECC
Confidence 4778888885 67789999999999876 777777777654
No 85
>COG4271 Predicted nucleotide-binding protein containing TIR -like domain [Transcription]
Probab=30.95 E-value=1.4e+02 Score=31.21 Aligned_cols=61 Identities=10% Similarity=-0.014 Sum_probs=45.2
Q ss_pred ceEEEeccCCHHHHHHHHHhhhcCCceEEEecCCCCCC--cchHHHHHHHHHhcceEEEEeccccc
Q psy12711 387 DALLLYDEADFDLAKQFNTQLNKMGFTVCDKDNSFLTG--QFEHSAFIQVMDRCTCVIVLMSTHFM 450 (639)
Q Consensus 387 DAFVsYS~kD~dFV~eLv~~LE~~gykLCLh~RDflpG--~~i~e~I~~aIerSRR~IvVLSpnFL 450 (639)
-+||.|++.-.. .-....| .+.+++|...-|-.++ ..+.+.+-+.|+.+.--|++++|+=-
T Consensus 84 kvFvv~ghd~iA--rael~al-lrd~~l~~vi~d~~~~~g~~ile~lek~i~~v~FAi~latPDDk 146 (233)
T COG4271 84 KVFVVSGHDAIA--RAELEAL-LRDWKLEPVILDGLFSEGQTILESLEKYIAEVKFAIVLATPDDK 146 (233)
T ss_pred eEEEEeccHHHH--HHHHHHH-hhccccceEEecCcccccHHHHHHHHHHhhhceEEEEEecCccc
Confidence 899999876522 1112222 3568899888887776 56778878888999999999999976
No 86
>PRK13789 phosphoribosylamine--glycine ligase; Provisional
Probab=30.62 E-value=69 Score=35.74 Aligned_cols=86 Identities=17% Similarity=0.082 Sum_probs=46.4
Q ss_pred cccEEEEeecccccccccccC-CCCCCccccccc--CC-CCC---ccccccccChhhHHHHHhccCCcccccCCC-CccC
Q psy12711 203 KNLRVLVIGSQKHSMMQCRNM-DSNHDVEKYRYE--DS-MDY---IKIPIEAIRPKTRQVLNDKLCDIKQLMSPE-NYQR 274 (639)
Q Consensus 203 ~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~--~~-~d~---~~vPL~aL~~~tR~~Ls~~LNp~k~l~s~~-g~~r 274 (639)
+.|+||||||.-...--|.-. .|.+-+.-|.+- .. ..+ ..+++...+...-..++.-.++.-++++++ +...
T Consensus 3 ~~~kvLviG~g~rehal~~~~~~~~~~~~~~~~pgn~g~~~~~~~~~~~~~~~d~~~l~~~a~~~~iD~Vv~g~E~~l~~ 82 (426)
T PRK13789 3 VKLKVLLIGSGGRESAIAFALRKSNLLSELKVFPGNGGFPDDELLPADSFSILDKSSVQSFLKSNPFDLIVVGPEDPLVA 82 (426)
T ss_pred CCcEEEEECCCHHHHHHHHHHHhCCCCCEEEEECCchHHhccccccccCcCcCCHHHHHHHHHHcCCCEEEECCchHHHH
Confidence 569999999864332222222 233333444443 11 111 224566677777667777777877776654 3333
Q ss_pred chHHHHHHcCCCCC
Q psy12711 275 DYRGLADLMDIKAP 288 (639)
Q Consensus 275 DWRgLAelmgf~~~ 288 (639)
.-..+++.+|+.+.
T Consensus 83 glad~~~~~Gip~~ 96 (426)
T PRK13789 83 GFADWAAELGIPCF 96 (426)
T ss_pred HHHHHHHHcCCCcC
Confidence 33333445888653
No 87
>TIGR02027 rpoA DNA-directed RNA polymerase, alpha subunit, bacterial and chloroplast-type. This family consists of the bacterial (and chloroplast) DNA-directed RNA polymerase alpha subunit, encoded by the rpoA gene. The RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. The amino terminal domain is involved in dimerizing and assembling the other RNA polymerase subunits into a transcriptionally active enzyme. The carboxy-terminal domain contains determinants for interaction with DNA and with transcriptional activator proteins.
Probab=28.72 E-value=42 Score=36.00 Aligned_cols=30 Identities=20% Similarity=0.330 Sum_probs=23.5
Q ss_pred ccCCcchHHHHHHHHhcC-CCeeEEeecCCC
Q psy12711 112 EKEGHTFGSVITHILQSY-PEVDFAGYSVPH 141 (639)
Q Consensus 112 ~gEDHTLGNlLR~~Llkd-p~V~FAGY~IPH 141 (639)
.|.+|||||+||-.|+.. |++...+-+|..
T Consensus 11 ~g~g~TlGNaLRRvLLs~i~g~aI~~vkI~g 41 (297)
T TIGR02027 11 RGFGITLGNALRRVLLSSIPGAAITAVKIDG 41 (297)
T ss_pred CCchhHHHHHHHHHHHhcCCceEEEEEEEcc
Confidence 378999999999998876 777666666643
No 88
>cd04905 ACT_CM-PDT C-terminal ACT domain of the bifunctional chorismate mutase-prephenate dehydratase (CM-PDT) enzyme and the prephenate dehydratase (PDT) enzyme. The C-terminal ACT domain of the bifunctional chorismate mutase-prephenate dehydratase (CM-PDT) enzyme and the prephenate dehydratase (PDT) enzyme, found in plants, fungi, bacteria, and archaea. The P-protein of E. coli (CM-PDT, PheA) catalyzes the conversion of chorismate to prephenate and then the decarboxylation and dehydration to form phenylpyruvate. These are the first two steps in the biosynthesis of L-Phe and L-Tyr via the shikimate pathway in microorganisms and plants. The E. coli P-protein (CM-PDT) has three domains with an N-terminal domain with chorismate mutase activity, a middle domain with prephenate dehydratase activity, and an ACT regulatory C-terminal domain. The prephenate dehydratase enzyme has a PDT and ACT domain. The ACT domain is essential to bring about the negative allosteric regulation by L-Phe bindi
Probab=20.60 E-value=4.9e+02 Score=21.71 Aligned_cols=67 Identities=10% Similarity=0.099 Sum_probs=36.2
Q ss_pred eEEEEEccCCcchHHHHHHHHhcCCCeeEEeecCCCCC-CCceEEEEEeCCCCCHHHHHHHHHHHHHHHH
Q psy12711 106 CRTFVFEKEGHTFGSVITHILQSYPEVDFAGYSVPHPA-DFQIFIRIQVKDGYDSIDILKKGIKELESAC 174 (639)
Q Consensus 106 ~~tf~i~gEDHTLGNlLR~~Llkdp~V~FAGY~IPHPL-e~~i~LrIQT~~~~~P~eaLk~Al~~L~~~~ 174 (639)
++.|++.++-=+|..+|...-..+=++.--. ..|++- .....++|.+++..+ .+.++++++.|...+
T Consensus 3 sl~~~~~d~~G~L~~il~~f~~~~ini~~i~-s~p~~~~~~~~~f~vd~~~~~~-~~~~~~~l~~l~~~~ 70 (80)
T cd04905 3 SIVFTLPNKPGALYDVLGVFAERGINLTKIE-SRPSKGGLWEYVFFIDFEGHIE-DPNVAEALEELKRLT 70 (80)
T ss_pred EEEEEECCCCCHHHHHHHHHHHCCcCEEEEE-EEEcCCCCceEEEEEEEECCCC-CHHHHHHHHHHHHhC
Confidence 4566665543444444443333333333222 334432 456889999987533 467777777776543
Done!