Query 004519
Match_columns 747
No_of_seqs 389 out of 1847
Neff 8.9
Searched_HMMs 46136
Date Fri Mar 29 00:47:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/004519.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/004519hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03097 FHY3 Protein FAR-RED 100.0 7.9E-71 1.7E-75 628.1 42.4 475 178-674 71-623 (846)
2 cd06410 PB1_UP2 Uncharacterize 99.9 1.3E-23 2.8E-28 177.4 11.0 90 11-101 1-96 (97)
3 PF10551 MULE: MULE transposas 99.9 8.5E-22 1.8E-26 170.0 8.7 90 379-470 1-93 (93)
4 PF00872 Transposase_mut: Tran 99.8 1.2E-21 2.6E-26 212.1 5.6 227 280-555 112-350 (381)
5 PF03108 DBD_Tnp_Mut: MuDR fam 99.7 1.7E-16 3.7E-21 127.0 9.0 67 178-244 1-67 (67)
6 COG3328 Transposase and inacti 99.6 3.4E-14 7.3E-19 150.4 16.9 224 280-554 98-328 (379)
7 smart00575 ZnF_PMZ plant mutat 98.9 7.6E-10 1.6E-14 71.0 1.9 27 632-658 1-27 (28)
8 PF08731 AFT: Transcription fa 98.7 4.8E-08 1E-12 82.9 8.9 69 187-255 1-111 (111)
9 smart00666 PB1 PB1 domain. Pho 98.6 4.1E-07 8.8E-12 75.9 9.4 75 24-101 4-80 (81)
10 PF03101 FAR1: FAR1 DNA-bindin 98.5 2.8E-07 6E-12 78.8 6.5 61 195-256 1-90 (91)
11 PF04434 SWIM: SWIM zinc finge 98.1 2.4E-06 5.2E-11 60.4 2.8 30 627-656 10-39 (40)
12 cd05992 PB1 The PB1 domain is 98.0 5E-05 1.1E-09 63.2 9.3 74 25-101 4-80 (81)
13 cd06407 PB1_NLP A PB1 domain i 97.9 0.0001 2.2E-09 60.9 9.3 70 30-101 8-80 (82)
14 PF00564 PB1: PB1 domain; Int 97.9 8.6E-05 1.9E-09 62.3 8.7 76 26-103 6-83 (84)
15 cd06408 PB1_NoxR The PB1 domai 97.3 0.0013 2.8E-08 54.1 8.4 59 30-92 10-68 (86)
16 cd06396 PB1_NBR1 The PB1 domai 97.3 0.0012 2.7E-08 53.6 7.5 68 30-101 8-78 (81)
17 cd06406 PB1_P67 A PB1 domain i 97.0 0.0027 5.9E-08 51.3 7.1 66 25-94 6-71 (80)
18 cd06402 PB1_p62 The PB1 domain 97.0 0.0077 1.7E-07 49.9 9.5 69 31-102 14-85 (87)
19 cd06398 PB1_Joka2 The PB1 doma 96.9 0.0081 1.8E-07 50.7 9.7 74 26-102 5-87 (91)
20 cd06397 PB1_UP1 Uncharacterize 96.8 0.0065 1.4E-07 48.6 7.7 65 26-93 5-69 (82)
21 cd06404 PB1_aPKC PB1 domain is 96.8 0.0087 1.9E-07 48.6 8.1 63 29-93 7-70 (83)
22 cd06409 PB1_MUG70 The MUG70 pr 96.6 0.014 3.1E-07 48.3 8.1 71 30-102 9-84 (86)
23 cd06403 PB1_Par6 The PB1 domai 96.4 0.025 5.4E-07 45.3 8.3 72 27-102 5-78 (80)
24 cd06401 PB1_TFG The PB1 domain 95.9 0.056 1.2E-06 43.8 8.2 69 30-101 8-80 (81)
25 cd06405 PB1_Mekk2_3 The PB1 do 95.6 0.083 1.8E-06 41.6 7.5 69 27-102 6-77 (79)
26 PF00098 zf-CCHC: Zinc knuckle 95.5 0.0098 2.1E-07 33.7 1.6 18 729-746 1-18 (18)
27 cd06411 PB1_p51 The PB1 domain 95.3 0.078 1.7E-06 42.7 6.8 62 32-93 7-68 (78)
28 PF01610 DDE_Tnp_ISL3: Transpo 94.8 0.043 9.3E-07 56.3 5.4 94 375-474 1-97 (249)
29 PF15288 zf-CCHC_6: Zinc knuck 94.6 0.016 3.4E-07 40.0 1.1 18 729-746 2-21 (40)
30 PF13610 DDE_Tnp_IS240: DDE do 94.1 0.027 5.9E-07 52.2 1.9 80 373-456 2-81 (140)
31 PF06782 UPF0236: Uncharacteri 94.0 0.57 1.2E-05 52.6 12.4 132 412-554 235-377 (470)
32 PF04684 BAF1_ABF1: BAF1 / ABF 93.8 0.12 2.7E-06 55.3 6.2 57 182-238 23-80 (496)
33 PF03050 DDE_Tnp_IS66: Transpo 93.7 0.17 3.6E-06 52.7 7.3 146 266-475 6-156 (271)
34 PHA02517 putative transposase 93.5 2.8 6E-05 43.7 16.0 151 268-445 30-181 (277)
35 PF03106 WRKY: WRKY DNA -bindi 93.0 0.2 4.3E-06 38.6 4.7 40 215-254 20-59 (60)
36 cd06395 PB1_Map2k5 PB1 domain 90.3 0.59 1.3E-05 37.4 4.6 59 31-93 11-71 (91)
37 PF13696 zf-CCHC_2: Zinc knuck 88.7 0.24 5.2E-06 32.5 1.2 19 728-746 8-26 (32)
38 COG3316 Transposase and inacti 88.4 4.1 8.9E-05 40.0 10.0 121 290-459 32-152 (215)
39 PF04500 FLYWCH: FLYWCH zinc f 87.8 0.85 1.9E-05 35.1 4.2 46 204-253 14-62 (62)
40 cd06399 PB1_P40 The PB1 domain 86.7 2.2 4.9E-05 34.9 5.9 59 31-93 13-75 (92)
41 smart00774 WRKY DNA binding do 85.9 0.96 2.1E-05 34.6 3.3 38 216-253 21-59 (59)
42 PF13565 HTH_32: Homeodomain-l 83.4 2.7 5.9E-05 34.1 5.3 41 268-308 34-76 (77)
43 PF00665 rve: Integrase core d 81.8 3.6 7.7E-05 36.3 6.0 76 372-448 6-82 (120)
44 PF14392 zf-CCHC_4: Zinc knuck 81.8 0.59 1.3E-05 34.5 0.6 19 728-746 31-49 (49)
45 smart00343 ZnF_C2HC zinc finge 80.1 0.86 1.9E-05 28.5 0.9 16 730-745 1-16 (26)
46 cd01799 Hoil1_N Ubiquitin-like 76.6 7.5 0.00016 31.5 5.7 38 29-67 10-47 (75)
47 PRK14702 insertion element IS2 76.0 51 0.0011 34.0 13.1 143 266-443 10-162 (262)
48 PF02178 AT_hook: AT hook moti 75.0 1.4 3E-05 22.8 0.6 9 709-717 2-10 (13)
49 cd01794 DC_UbP_C dendritic cel 73.9 12 0.00027 29.8 6.2 42 26-67 3-44 (70)
50 PF04937 DUF659: Protein of un 73.8 31 0.00067 32.3 9.8 99 375-475 36-138 (153)
51 PF14560 Ubiquitin_2: Ubiquiti 72.7 10 0.00022 31.7 5.7 47 33-79 15-61 (87)
52 COG5431 Uncharacterized metal- 69.5 7 0.00015 33.2 3.8 45 622-668 42-91 (117)
53 cd01812 BAG1_N Ubiquitin-like 69.2 9.1 0.0002 30.3 4.6 41 26-67 5-45 (71)
54 cd01796 DDI1_N DNA damage indu 67.9 9.2 0.0002 30.5 4.3 38 30-67 8-45 (71)
55 PRK09409 IS2 transposase TnpB; 67.3 88 0.0019 33.0 12.8 142 268-444 51-202 (301)
56 cd01807 GDX_N ubiquitin-like d 66.6 12 0.00026 30.0 4.8 42 26-67 5-46 (74)
57 smart00384 AT_hook DNA binding 66.5 3.7 8.1E-05 25.4 1.2 12 708-719 1-12 (26)
58 PF11976 Rad60-SLD: Ubiquitin- 65.3 17 0.00038 28.8 5.5 42 26-67 5-47 (72)
59 cd01809 Scythe_N Ubiquitin-lik 64.0 16 0.00035 28.9 5.1 42 26-67 5-46 (72)
60 cd01803 Ubiquitin Ubiquitin. U 62.0 15 0.00033 29.4 4.7 41 27-67 6-46 (76)
61 cd01798 parkin_N amino-termina 61.9 16 0.00034 29.0 4.6 41 27-67 4-44 (70)
62 cd00196 UBQ Ubiquitin-like pro 61.2 18 0.0004 26.6 4.8 43 26-68 2-44 (69)
63 PRK12286 rpmF 50S ribosomal pr 60.0 8.8 0.00019 29.3 2.6 43 705-747 4-46 (57)
64 PF04800 ETC_C1_NDUFA4: ETC co 59.0 14 0.00031 31.8 3.9 29 183-215 51-79 (101)
65 PTZ00044 ubiquitin; Provisiona 58.1 21 0.00046 28.6 4.9 41 27-67 6-46 (76)
66 cd01800 SF3a120_C Ubiquitin-li 57.8 17 0.00038 29.3 4.2 39 29-67 5-43 (76)
67 COG4279 Uncharacterized conser 57.2 5.4 0.00012 39.7 1.3 23 632-657 125-147 (266)
68 cd01806 Nedd8 Nebb8-like ubiq 55.7 29 0.00062 27.7 5.2 41 27-67 6-46 (76)
69 PRK14892 putative transcriptio 53.2 12 0.00025 32.2 2.5 10 727-736 20-29 (99)
70 cd01805 RAD23_N Ubiquitin-like 53.0 34 0.00073 27.5 5.3 42 26-67 5-48 (77)
71 PF11470 TUG-UBL1: GLUT4 regul 52.9 25 0.00053 27.7 4.1 38 30-67 5-42 (65)
72 TIGR01031 rpmF_bact ribosomal 52.2 15 0.00033 27.7 2.7 43 705-747 2-45 (55)
73 KOG0695 Serine/threonine prote 51.0 48 0.001 34.7 6.9 66 27-94 20-86 (593)
74 smart00213 UBQ Ubiquitin homol 50.8 35 0.00076 25.9 4.8 40 27-67 6-45 (64)
75 cd01763 Sumo Small ubiquitin-r 49.8 35 0.00075 28.5 4.9 42 26-67 16-57 (87)
76 PRK09335 30S ribosomal protein 49.7 15 0.00032 30.9 2.5 27 705-736 2-28 (95)
77 PF00240 ubiquitin: Ubiquitin 47.4 40 0.00086 26.4 4.7 39 29-67 3-41 (69)
78 cd01769 UBL Ubiquitin-like dom 47.3 45 0.00099 25.7 5.1 41 27-67 3-43 (69)
79 PF13592 HTH_33: Winged helix- 46.7 31 0.00068 26.4 3.8 29 281-309 3-31 (60)
80 PF12762 DDE_Tnp_IS1595: ISXO2 46.4 51 0.0011 30.5 6.0 68 374-446 5-87 (151)
81 cd01810 ISG15_repeat2 ISG15 ub 46.3 40 0.00086 27.0 4.6 42 26-67 3-44 (74)
82 cd01793 Fubi Fubi ubiquitin-li 46.0 46 0.001 26.6 4.9 39 29-67 6-44 (74)
83 COG5179 TAF1 Transcription ini 46.0 11 0.00025 42.1 1.7 20 727-746 936-957 (968)
84 cd01789 Alp11_N Ubiquitin-like 44.5 51 0.0011 27.3 5.0 33 36-68 17-49 (84)
85 KOG3389 NADH:ubiquinone oxidor 44.5 19 0.00042 32.4 2.6 36 175-214 107-154 (178)
86 PLN00186 ribosomal protein S26 44.3 19 0.00042 31.0 2.4 27 705-736 2-28 (109)
87 cd01813 UBP_N UBP ubiquitin pr 44.0 39 0.00085 27.2 4.2 38 30-67 8-45 (74)
88 PTZ00172 40S ribosomal protein 43.8 20 0.00043 30.9 2.4 27 705-736 2-28 (108)
89 PF14201 DUF4318: Domain of un 43.6 37 0.00079 27.5 3.8 29 186-214 13-41 (74)
90 cd01802 AN1_N ubiquitin-like d 42.8 49 0.0011 28.7 4.9 42 26-67 32-73 (103)
91 COG4715 Uncharacterized conser 42.5 53 0.0012 36.9 6.1 44 616-661 51-100 (587)
92 PRK13130 H/ACA RNA-protein com 41.1 16 0.00034 27.7 1.3 20 727-747 4-23 (56)
93 PRK00766 hypothetical protein; 39.2 2.4E+02 0.0053 27.5 9.4 87 373-459 10-128 (194)
94 COG0333 RpmF Ribosomal protein 36.9 20 0.00043 27.2 1.3 43 705-747 4-46 (57)
95 cd01804 midnolin_N Ubiquitin-l 36.6 78 0.0017 25.7 4.9 39 29-67 9-47 (78)
96 PHA00689 hypothetical protein 34.7 18 0.0004 26.0 0.7 13 726-738 15-27 (62)
97 PF01498 HTH_Tnp_Tc3_2: Transp 32.5 37 0.0008 27.0 2.3 36 273-309 4-39 (72)
98 PF08766 DEK_C: DEK C terminal 32.2 81 0.0018 23.6 4.0 36 269-304 5-42 (54)
99 PF13917 zf-CCHC_3: Zinc knuck 31.0 26 0.00057 24.8 1.0 18 728-745 4-21 (42)
100 PF13276 HTH_21: HTH-like doma 29.6 1.1E+02 0.0024 23.2 4.5 41 269-309 6-47 (60)
101 PF01783 Ribosomal_L32p: Ribos 29.6 13 0.00029 28.2 -0.7 22 726-747 24-45 (56)
102 COG5082 AIR1 Arginine methyltr 28.4 28 0.00061 33.5 1.1 16 729-744 98-113 (190)
103 cd01791 Ubl5 UBL5 ubiquitin-li 27.5 1.2E+02 0.0026 24.3 4.5 37 31-67 11-47 (73)
104 PF13082 DUF3931: Protein of u 26.3 1.7E+02 0.0038 21.4 4.5 40 374-413 10-62 (66)
105 PF10045 DUF2280: Uncharacteri 25.9 75 0.0016 27.3 3.0 24 284-307 21-44 (104)
106 PF13877 RPAP3_C: Potential Mo 25.7 35 0.00075 28.9 1.1 34 496-529 5-38 (94)
107 PF01283 Ribosomal_S26e: Ribos 25.2 53 0.0011 28.8 2.1 27 705-736 2-28 (113)
108 PF13551 HTH_29: Winged helix- 24.8 1.4E+02 0.003 25.6 4.9 38 272-309 65-108 (112)
109 cd01792 ISG15_repeat1 ISG15 ub 24.6 2E+02 0.0043 23.4 5.4 39 28-66 9-47 (80)
110 PF08086 Toxin_17: Ergtoxin fa 24.2 8.9 0.00019 25.7 -2.1 11 734-744 24-34 (41)
111 cd01797 NIRF_N amino-terminal 24.1 1.4E+02 0.0029 24.4 4.3 38 30-67 9-48 (78)
112 KOG4027 Uncharacterized conser 23.9 92 0.002 28.9 3.4 36 377-412 70-108 (187)
113 PF08459 UvrC_HhH_N: UvrC Heli 23.8 1.6E+02 0.0035 27.7 5.2 45 411-455 51-101 (155)
114 PRK01110 rpmF 50S ribosomal pr 23.4 60 0.0013 25.1 1.9 37 705-741 4-42 (60)
115 cd01808 hPLIC_N Ubiquitin-like 22.0 1.7E+02 0.0036 23.0 4.4 36 30-66 9-44 (71)
116 PRK14890 putative Zn-ribbon RN 21.4 38 0.00083 25.9 0.5 19 728-747 36-54 (59)
117 PF01949 DUF99: Protein of unk 21.4 3.5E+02 0.0076 26.3 7.2 85 374-458 6-120 (187)
118 COG4416 Com Mu-like prophage p 21.3 37 0.00081 25.1 0.4 21 727-747 3-30 (60)
119 COG0484 DnaJ DnaJ-class molecu 21.1 94 0.002 33.6 3.5 22 726-747 140-165 (371)
120 PF09713 A_thal_3526: Plant pr 20.9 94 0.002 23.4 2.4 26 282-307 12-38 (54)
121 PF14847 Ras_bdg_2: Ras-bindin 20.7 3.8E+02 0.0082 23.3 6.5 76 26-101 5-83 (105)
122 PF03705 CheR_N: CheR methyltr 20.4 2.9E+02 0.0063 20.4 5.3 50 286-339 6-55 (57)
No 1
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=100.00 E-value=7.9e-71 Score=628.06 Aligned_cols=475 Identities=17% Similarity=0.234 Sum_probs=375.3
Q ss_pred CcccccCceeCCHHHHHHHHHHHHHhcCeeEEEeecCCe-------EEEEEeec--------------------------
Q 004519 178 NTITGVDQRFSSFSEFREALHKYSIAHGFAYRYKKNDSH-------RVTVKCKC-------------------------- 224 (747)
Q Consensus 178 ~~~~~vG~~F~s~~e~~~ai~~yai~~~f~~~~~rs~~~-------r~~~~C~~-------------------------- 224 (747)
+..|.+||+|+|.+|++++|+.||...||++|+.++.++ ..+++|.+
T Consensus 71 ~~~P~vGMeF~S~eeA~~FYn~YA~~~GFsVRi~~srrsk~~~~ii~r~fvCsreG~~~~~~~~~~~~~~~~~k~~~~~~ 150 (846)
T PLN03097 71 NLEPLSGMEFESHGEAYSFYQEYARSMGFNTAIQNSRRSKTSREFIDAKFACSRYGTKREYDKSFNRPRARQTKQDPENG 150 (846)
T ss_pred CccCcCCCeECCHHHHHHHHHHHHhhcCceEEeeceeccCCCCcEEEEEEEEcCCCCCcccccccccccccccccCcccc
Confidence 356899999999999999999999999999998644321 23566653
Q ss_pred --------CCCCeEEEEEEcCCcceEEEEecCCcccccCccccccccccchhHHHHHHHHhhhCCCCChHHHHHHHHHHh
Q 004519 225 --------QGCPWRIYASRLSTTQLVCIKKMNSKHTCEGASVKAGYRATRGWVGNIIKEKLKASPNYKPKDIADDIKREY 296 (747)
Q Consensus 225 --------~gC~w~i~a~~~~~~~~~~V~~~~~~Htc~~~~~~~~~~~s~~~i~~~~~~~~~~~~~~~~~~i~~~i~~~~ 296 (747)
+||+++|++.+. ..+.|.|+.++.+|||++.........+++....... .+....++. .++.+.
T Consensus 151 ~~rR~~tRtGC~A~m~Vk~~-~~gkW~V~~fv~eHNH~L~p~~~~~~~~r~~~~~~~~-~~~~~~~v~------~~~~d~ 222 (846)
T PLN03097 151 TGRRSCAKTDCKASMHVKRR-PDGKWVIHSFVKEHNHELLPAQAVSEQTRKMYAAMAR-QFAEYKNVV------GLKNDS 222 (846)
T ss_pred cccccccCCCCceEEEEEEc-CCCeEEEEEEecCCCCCCCCccccchhhhhhHHHHHh-hhhcccccc------ccchhh
Confidence 479999999885 4468999999999999987432210011111100000 000000000 000000
Q ss_pred CCccCHHHHHHHHHHHHHHHhcCHHHHhccHHHHHHHHHHhCCCCEEEEEecCCCceeEEEeehhchHHHHhhcCccEEE
Q 004519 297 GIQLNYSQAWRAKEIAREQLQGSYKDSYTLLPFFCEKIKETNPGSVVTFTTKEDSSFHRLFVSFHASISGFQQGCRPLLF 376 (747)
Q Consensus 297 g~~~~~~~~~r~k~~~~~~~~g~~~~~~~~L~~~~~~l~~~npg~~~~~~~~~~~~f~~lf~~~~~~~~~f~~~~~~vl~ 376 (747)
.++ .-+.+.+ .+. ....+.|..|+.++++.||+|+|.+++|++++++++||+++.|+..|.+ |++||.
T Consensus 223 ---~~~--~~~~r~~---~~~---~gD~~~ll~yf~~~q~~nP~Ffy~~qlDe~~~l~niFWaD~~sr~~Y~~-FGDvV~ 290 (846)
T PLN03097 223 ---KSS--FDKGRNL---GLE---AGDTKILLDFFTQMQNMNSNFFYAVDLGEDQRLKNLFWVDAKSRHDYGN-FSDVVS 290 (846)
T ss_pred ---cch--hhHHHhh---hcc---cchHHHHHHHHHHHHhhCCCceEEEEEccCCCeeeEEeccHHHHHHHHh-cCCEEE
Confidence 011 1111111 111 2345678999999999999999999999999999999999999999998 999999
Q ss_pred EeccccCCcccceEEEEEEecCCCCeEEEEEEEeecCCcccHHHHHHHHHhhcCCCCcEEEEecCcchhHHHHhhhccCc
Q 004519 377 LDTTPLNSKYQGTLLTATSADGDDGIFPVAFAVVDAETEDNWHWFLQELKSAVSTSQQITFIADFQNGLNKSLAEVFDNC 456 (747)
Q Consensus 377 iD~t~~~~~y~~~l~~a~g~d~~~~~~pla~a~v~~E~~e~~~wfl~~l~~~~~~~~~~~iisD~~~~l~~Ai~~vfP~a 456 (747)
+|+||++|+|++||+.++|+|+|++++++|+||+.+|+.++|.|+|++|+++|++..|.+||||++.+|.+||++|||++
T Consensus 291 fDTTY~tN~y~~Pfa~FvGvNhH~qtvlfGcaLl~dEt~eSf~WLf~tfl~aM~gk~P~tIiTDqd~am~~AI~~VfP~t 370 (846)
T PLN03097 291 FDTTYVRNKYKMPLALFVGVNQHYQFMLLGCALISDESAATYSWLMQTWLRAMGGQAPKVIITDQDKAMKSVISEVFPNA 370 (846)
T ss_pred EeceeeccccCcEEEEEEEecCCCCeEEEEEEEcccCchhhHHHHHHHHHHHhCCCCCceEEecCCHHHHHHHHHHCCCc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cchhhHHHHHHHHHhhhcccccHHHHHHHHHHHHHHhcC-CChhhHHHHHHH-HhccChhHHHHHhhc--CCCCcccccc
Q 004519 457 YHSYCLRHLAEKLNRDIKGQFSHEARRFMINDLYAAAYA-PKFEGFQCSIES-IKGISPDAYDWVTQS--EPEHWANTYF 532 (747)
Q Consensus 457 ~h~~C~~Hi~~n~~~~~~~~~~~~~~~~~~~~~~~~~~a-~~~~ef~~~~~~-l~~~~~~~~~~l~~~--~~~~Wa~a~~ 532 (747)
.|++|+|||++|+.+++...+.. .+.+...|..+++. .+++||+..|.. |.+++.+..+||..+ .+++|+++|+
T Consensus 371 ~Hr~C~wHI~~~~~e~L~~~~~~--~~~f~~~f~~cv~~s~t~eEFE~~W~~mi~ky~L~~n~WL~~LY~~RekWapaY~ 448 (846)
T PLN03097 371 HHCFFLWHILGKVSENLGQVIKQ--HENFMAKFEKCIYRSWTEEEFGKRWWKILDRFELKEDEWMQSLYEDRKQWVPTYM 448 (846)
T ss_pred eehhhHHHHHHHHHHHhhHHhhh--hhHHHHHHHHHHhCCCCHHHHHHHHHHHHHhhcccccHHHHHHHHhHhhhhHHHh
Confidence 99999999999999999876532 34788899999886 699999999966 567789999999999 6999999999
Q ss_pred CCCccccc-ccchhhhhhhhhhhh--ccCChhHHHHHHHHHHHHHHHHH-----------------HHhhhhcccCCCch
Q 004519 533 PGARYDHM-TSNFGQQFYSWVSEA--HELPITHMVDVLRGKMMETIYTR-----------------RVESNQWLTKLTPS 592 (747)
Q Consensus 533 ~~~~~~~~-ttN~~Es~n~~lk~~--r~~~i~~~l~~i~~~~~~~~~~~-----------------~~~~~~~~~~~tp~ 592 (747)
++.+++.| ||+++||+|+++++. +..+|..|++.+-.-+-.+..+. ...+++.+..|||.
T Consensus 449 k~~F~agm~sTqRSES~Ns~fk~yv~~~tsL~~Fv~qye~~l~~~~ekE~~aD~~s~~~~P~l~t~~piEkQAs~iYT~~ 528 (846)
T PLN03097 449 RDAFLAGMSTVQRSESINAFFDKYVHKKTTVQEFVKQYETILQDRYEEEAKADSDTWNKQPALKSPSPLEKSVSGVYTHA 528 (846)
T ss_pred cccccCCcccccccccHHHHHHHHhCcCCCHHHHHHHHHHHHHHHHHHHHHhhhhcccCCcccccccHHHHHHHHHhHHH
Confidence 99887655 779999999999984 77888888876543322222111 12345668899999
Q ss_pred HHHHHHHHHhhccceEEEEe----CCceEEEEc---ceeEEEeC----cCceeecCCcccCCCCcchHHHHHHHhcC--C
Q 004519 593 KEDKLQKETAIARSFQVLHL----QSSTFEVRG---ESADIVDV----DRWDCTCKTWHLTGLPCCHAIAVLEWIGR--S 659 (747)
Q Consensus 593 ~~~kl~~~~~~a~~~~v~~~----~~~~f~V~~---~~~~~V~l----~~~~CtC~~~~~~giPC~Halav~~~~~~--~ 659 (747)
+|++||+|+..+..|.+... ...+|.|.+ .+.|.|.. ...+|+|++|+..||||+|||.||...++ .
T Consensus 529 iF~kFQ~El~~~~~~~~~~~~~dg~~~~y~V~~~~~~~~~~V~~d~~~~~v~CsC~kFE~~GILCrHaLkVL~~~~v~~I 608 (846)
T PLN03097 529 VFKKFQVEVLGAVACHPKMESQDETSITFRVQDFEKNQDFTVTWNQTKLEVSCICRLFEYKGYLCRHALVVLQMCQLSAI 608 (846)
T ss_pred HHHHHHHHHHHhhheEEeeeccCCceEEEEEEEecCCCcEEEEEecCCCeEEeeccCeecCccchhhHHHHHhhcCcccC
Confidence 99999999999988877643 224688865 34566632 47899999999999999999999999985 5
Q ss_pred cccccccchhHHHHH
Q 004519 660 PYDYCSKYFTTESYR 674 (747)
Q Consensus 660 p~~yi~~~~t~~~~~ 674 (747)
|+.||.+|||+++-.
T Consensus 609 P~~YILkRWTKdAK~ 623 (846)
T PLN03097 609 PSQYILKRWTKDAKS 623 (846)
T ss_pred chhhhhhhchhhhhh
Confidence 999999999998753
No 2
>cd06410 PB1_UP2 Uncharacterized protein 2. The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions.
Probab=99.90 E-value=1.3e-23 Score=177.41 Aligned_cols=90 Identities=33% Similarity=0.672 Sum_probs=85.3
Q ss_pred EEeeCCEEEeCC-CCCEEEecCceeEEEecCCCChhhHHHHHHHHhcCCCCceEEEEEecCCCCc-ceeeeCcHHHHHHH
Q 004519 11 ICQSGGEFVTNK-DGSLSYNGGEAYAIDIDEETEFSGFKSEVAEMFNCSADTMSIKYFLPGNKKT-LISISKDKDFKRML 88 (747)
Q Consensus 11 ~~~~gG~~~~~~-~g~~~Y~gg~~~~~~v~~~~s~~~~~~~l~~~~~~~~~~~~~~y~lp~~~~~-l~~v~~D~dl~~m~ 88 (747)
+||+||+|+|++ ||+++|+||+|+++.|+|++||.||.++|+++++.+.+ +++||+||+++++ |++|++|+||.+|+
T Consensus 1 ~cs~GG~i~pr~~dg~l~Y~GG~tr~i~V~r~~s~~el~~kl~~~~~~~~~-~~lky~Lp~edld~Lisv~~DeDl~~M~ 79 (97)
T cd06410 1 LCSYGGRILPRPPDGQLRYVGGETRIVSVDRSISFKELVSKLSELFGAGVV-VTLKYQLPDEDLDALISVSNDEDLKNMM 79 (97)
T ss_pred CcccCCEEeCcCCCCCEEEcCCceEEEEEcCCCCHHHHHHHHHHHhCCCCc-eEEEEEcCCCCcceeEEecCcHHHHHHH
Confidence 599999999765 99999999999999999999999999999999998765 9999999999999 99999999999999
Q ss_pred hhcc----CcceEEEEE
Q 004519 89 NFLG----DTATVDVFI 101 (747)
Q Consensus 89 ~~~~----~~~~~~i~~ 101 (747)
++++ .+.+++||+
T Consensus 80 ~e~~~~~~~~~rirvfl 96 (97)
T cd06410 80 EEYDRLSGGSARLRVFL 96 (97)
T ss_pred HhhccccCCCceEEEEE
Confidence 9999 788999987
No 3
>PF10551 MULE: MULE transposase domain; InterPro: IPR018289 This entry represents a domain found in Mutator-like elements (MULE)-encoded tranposases, some of which also contain a zinc-finger motif [, ]. This domain is also found in a transposase for the insertion sequence element IS256 in transposon Tn4001 [].
Probab=99.86 E-value=8.5e-22 Score=170.01 Aligned_cols=90 Identities=39% Similarity=0.716 Sum_probs=86.8
Q ss_pred ccccCCcccceEEE---EEEecCCCCeEEEEEEEeecCCcccHHHHHHHHHhhcCCCCcEEEEecCcchhHHHHhhhccC
Q 004519 379 TTPLNSKYQGTLLT---ATSADGDDGIFPVAFAVVDAETEDNWHWFLQELKSAVSTSQQITFIADFQNGLNKSLAEVFDN 455 (747)
Q Consensus 379 ~t~~~~~y~~~l~~---a~g~d~~~~~~pla~a~v~~E~~e~~~wfl~~l~~~~~~~~~~~iisD~~~~l~~Ai~~vfP~ 455 (747)
|||++|+| ++++. ++|+|++|+.+|+||+++++|+.++|.|||+.+++.++.. |.+||||++.|+.+||+++||+
T Consensus 1 ~T~~tn~~-~~l~~~~~~~~~d~~~~~~~v~~~l~~~e~~~~~~~~l~~~~~~~~~~-p~~ii~D~~~~~~~Ai~~vfP~ 78 (93)
T PF10551_consen 1 GTYKTNKY-GPLLYLMIAVGIDGNGRGFPVAFALVSSESEESYEWFLEKLKEAMPQK-PKVIISDFDKALINAIKEVFPD 78 (93)
T ss_pred Cccccccc-cccceeceEEEEcCCCCEEEEEEEEEcCCChhhhHHHHHHhhhccccC-ceeeeccccHHHHHHHHHHCCC
Confidence 79999999 98886 9999999999999999999999999999999999999877 9999999999999999999999
Q ss_pred ccchhhHHHHHHHHH
Q 004519 456 CYHSYCLRHLAEKLN 470 (747)
Q Consensus 456 a~h~~C~~Hi~~n~~ 470 (747)
+.|++|.||+.+|++
T Consensus 79 ~~~~~C~~H~~~n~k 93 (93)
T PF10551_consen 79 ARHQLCLFHILRNIK 93 (93)
T ss_pred ceEehhHHHHHHhhC
Confidence 999999999999974
No 4
>PF00872 Transposase_mut: Transposase, Mutator family; InterPro: IPR001207 Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element. Transposases have been grouped into various families [, , ]. The mutator family of transposases consists of a number of elements that include, mutator from maize, IsT2 from Thiobacillus ferrooxidans, Is256 from Staphylococcus aureus, Is1201 from Lactobacillus helveticus, Is1081 from Mycobacterium bovis, IsRm3 from Rhizobium meliloti and others. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=99.84 E-value=1.2e-21 Score=212.07 Aligned_cols=227 Identities=22% Similarity=0.288 Sum_probs=182.9
Q ss_pred CCCCChHHHHHHHHHHhC-CccCHHHHHHHHHHHHHHHhcCHHHHhccHHHHHHHHHHhCCCCEEEEEecCCCceeEEEe
Q 004519 280 SPNYKPKDIADDIKREYG-IQLNYSQAWRAKEIAREQLQGSYKDSYTLLPFFCEKIKETNPGSVVTFTTKEDSSFHRLFV 358 (747)
Q Consensus 280 ~~~~~~~~i~~~i~~~~g-~~~~~~~~~r~k~~~~~~~~g~~~~~~~~L~~~~~~l~~~npg~~~~~~~~~~~~f~~lf~ 358 (747)
-.+++.++|.+.++.-+| ..+|-+++.|..+...+.+. .|..+-+.
T Consensus 112 ~~G~Str~i~~~l~~l~g~~~~S~s~vSri~~~~~~~~~-----------~w~~R~L~---------------------- 158 (381)
T PF00872_consen 112 LKGVSTRDIEEALEELYGEVAVSKSTVSRITKQLDEEVE-----------AWRNRPLE---------------------- 158 (381)
T ss_pred ccccccccccchhhhhhcccccCchhhhhhhhhhhhhHH-----------HHhhhccc----------------------
Confidence 357899999999999999 77998888886655544322 22111111
Q ss_pred ehhchHHHHhhcC-ccEEEEeccccCCccc-----ceEEEEEEecCCCCeEEEEEEEeecCCcccHHHHHHHHHhhcCCC
Q 004519 359 SFHASISGFQQGC-RPLLFLDTTPLNSKYQ-----GTLLTATSADGDDGIFPVAFAVVDAETEDNWHWFLQELKSAVSTS 432 (747)
Q Consensus 359 ~~~~~~~~f~~~~-~~vl~iD~t~~~~~y~-----~~l~~a~g~d~~~~~~pla~a~v~~E~~e~~~wfl~~l~~~~~~~ 432 (747)
+. -|+|+|||+|.+.+.+ ..+++|+|+|.+|+..+||+.+.+.|+.++|.-||+.|++. |..
T Consensus 159 -----------~~~y~~l~iD~~~~kvr~~~~~~~~~~~v~iGi~~dG~r~vLg~~~~~~Es~~~W~~~l~~L~~R-Gl~ 226 (381)
T PF00872_consen 159 -----------SEPYPYLWIDGTYFKVREDGRVVKKAVYVAIGIDEDGRREVLGFWVGDRESAASWREFLQDLKER-GLK 226 (381)
T ss_pred -----------cccccceeeeeeecccccccccccchhhhhhhhhcccccceeeeecccCCccCEeeecchhhhhc-ccc
Confidence 13 3799999999987654 45799999999999999999999999999999999999988 445
Q ss_pred CcEEEEecCcchhHHHHhhhccCccchhhHHHHHHHHHhhhcccccHHHHHHHHHHHHHHhcCCChhhHHHHHHHH----
Q 004519 433 QQITFIADFQNGLNKSLAEVFDNCYHSYCLRHLAEKLNRDIKGQFSHEARRFMINDLYAAAYAPKFEGFQCSIESI---- 508 (747)
Q Consensus 433 ~~~~iisD~~~~l~~Ai~~vfP~a~h~~C~~Hi~~n~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~ef~~~~~~l---- 508 (747)
.+..||+|+++||..||+++||++.++.|++|+++|+.++++... ++.+...++.+..+.+.++....++.+
T Consensus 227 ~~~lvv~Dg~~gl~~ai~~~fp~a~~QrC~vH~~RNv~~~v~~k~----~~~v~~~Lk~I~~a~~~e~a~~~l~~f~~~~ 302 (381)
T PF00872_consen 227 DILLVVSDGHKGLKEAIREVFPGAKWQRCVVHLMRNVLRKVPKKD----RKEVKADLKAIYQAPDKEEAREALEEFAEKW 302 (381)
T ss_pred ccceeeccccccccccccccccchhhhhheechhhhhcccccccc----chhhhhhccccccccccchhhhhhhhccccc
Confidence 699999999999999999999999999999999999999987653 345666677777777777777666554
Q ss_pred hccChhHHHHHhhcCCCCccccccCCCcc-cccccchhhhhhhhhhhh
Q 004519 509 KGISPDAYDWVTQSEPEHWANTYFPGARY-DHMTSNFGQQFYSWVSEA 555 (747)
Q Consensus 509 ~~~~~~~~~~l~~~~~~~Wa~a~~~~~~~-~~~ttN~~Es~n~~lk~~ 555 (747)
...+|.+.+++++...+.|+..-|+...+ ...|||.+|++|+.||+.
T Consensus 303 ~~kyp~~~~~l~~~~~~~~tf~~fP~~~~~~i~TTN~iEsln~~irrr 350 (381)
T PF00872_consen 303 EKKYPKAAKSLEENWDELLTFLDFPPEHRRSIRTTNAIESLNKEIRRR 350 (381)
T ss_pred ccccchhhhhhhhccccccceeeecchhccccchhhhccccccchhhh
Confidence 44679999999998888888766665544 567999999999999873
No 5
>PF03108 DBD_Tnp_Mut: MuDR family transposase; InterPro: IPR004332 The plant MuDR transposase domain is present in plant proteins that are presumed to be the transposases for Mutator transposable elements [, ]. The function of these proteins is unknown. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=99.68 E-value=1.7e-16 Score=127.01 Aligned_cols=67 Identities=42% Similarity=0.769 Sum_probs=65.0
Q ss_pred CcccccCceeCCHHHHHHHHHHHHHhcCeeEEEeecCCeEEEEEeecCCCCeEEEEEEcCCcceEEE
Q 004519 178 NTITGVDQRFSSFSEFREALHKYSIAHGFAYRYKKNDSHRVTVKCKCQGCPWRIYASRLSTTQLVCI 244 (747)
Q Consensus 178 ~~~~~vG~~F~s~~e~~~ai~~yai~~~f~~~~~rs~~~r~~~~C~~~gC~w~i~a~~~~~~~~~~V 244 (747)
||.+.+||+|+|++||++||..||++++|++++.+|++.|++++|...||||+|+|++.++++.|+|
T Consensus 1 n~~l~~G~~F~~~~e~k~av~~yai~~~~~~~v~ksd~~r~~~~C~~~~C~Wrv~as~~~~~~~~~I 67 (67)
T PF03108_consen 1 NPELEVGQTFPSKEEFKEAVREYAIKNGFEFKVKKSDKKRYRAKCKDKGCPWRVRASKRKRSDTFQI 67 (67)
T ss_pred CCccccCCEECCHHHHHHHHHHHHHhcCcEEEEeccCCEEEEEEEcCCCCCEEEEEEEcCCCCEEEC
Confidence 6789999999999999999999999999999999999999999999999999999999999999986
No 6
>COG3328 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=99.58 E-value=3.4e-14 Score=150.41 Aligned_cols=224 Identities=17% Similarity=0.202 Sum_probs=172.4
Q ss_pred CCCCChHHHHHHHHHHhCCccCHHHHHHHHHHHHHHHhcCHHHHhccHHHHHHHHHHhCCCCEEEEEecCCCceeEEEee
Q 004519 280 SPNYKPKDIADDIKREYGIQLNYSQAWRAKEIAREQLQGSYKDSYTLLPFFCEKIKETNPGSVVTFTTKEDSSFHRLFVS 359 (747)
Q Consensus 280 ~~~~~~~~i~~~i~~~~g~~~~~~~~~r~k~~~~~~~~g~~~~~~~~L~~~~~~l~~~npg~~~~~~~~~~~~f~~lf~~ 359 (747)
..+++++++...+++.++..++-....+.-....+. +.+++..-+
T Consensus 98 ~~gv~Tr~i~~~~~~~~~~~~s~~~iS~~~~~~~e~---------------v~~~~~r~l-------------------- 142 (379)
T COG3328 98 AKGVTTREIEALLEELYGHKVSPSVISVVTDRLDEK---------------VKAWQNRPL-------------------- 142 (379)
T ss_pred HcCCcHHHHHHHHHHhhCcccCHHHhhhHHHHHHHH---------------HHHHHhccc--------------------
Confidence 357899999999999998877776665554443332 222332211
Q ss_pred hhchHHHHhhcCccEEEEeccccCCc--ccceEEEEEEecCCCCeEEEEEEEeecCCcccHHHHHHHHHhhcCCCCcEEE
Q 004519 360 FHASISGFQQGCRPLLFLDTTPLNSK--YQGTLLTATSADGDDGIFPVAFAVVDAETEDNWHWFLQELKSAVSTSQQITF 437 (747)
Q Consensus 360 ~~~~~~~f~~~~~~vl~iD~t~~~~~--y~~~l~~a~g~d~~~~~~pla~a~v~~E~~e~~~wfl~~l~~~~~~~~~~~i 437 (747)
+..|++++|++|++-+ -+..+++|+|++.+|+...+++.+-+.|+ ..|.-||..|+.. |......+
T Consensus 143 ----------~~~~~v~~D~~~~k~r~v~~~~~~ia~Gv~~eG~reilg~~~~~~e~-~~w~~~l~~l~~r-gl~~v~l~ 210 (379)
T COG3328 143 ----------GDYPYVYLDAKYVKVRSVRNKAVYIAIGVTEEGRREILGIWVGVRES-KFWLSFLLDLKNR-GLSDVLLV 210 (379)
T ss_pred ----------cCceEEEEecceeehhhhhhheeeeeeccCcccchhhhceeeecccc-hhHHHHHHHHHhc-cccceeEE
Confidence 2567999999999887 34689999999999999999999999999 9999999999887 33456677
Q ss_pred EecCcchhHHHHhhhccCccchhhHHHHHHHHHhhhcccccHHHHHHHHHHHHHHhcCCChhhHHHHHHH----HhccCh
Q 004519 438 IADFQNGLNKSLAEVFDNCYHSYCLRHLAEKLNRDIKGQFSHEARRFMINDLYAAAYAPKFEGFQCSIES----IKGISP 513 (747)
Q Consensus 438 isD~~~~l~~Ai~~vfP~a~h~~C~~Hi~~n~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~ef~~~~~~----l~~~~~ 513 (747)
++|+.+||.+||.++||.+.++.|..|+.+|+..++... .++.+...+..+--+.+.++-...+.. +....|
T Consensus 211 v~Dg~~gl~~aI~~v~p~a~~Q~C~vH~~Rnll~~v~~k----~~d~i~~~~~~I~~a~~~e~~~~~~~~~~~~w~~~yP 286 (379)
T COG3328 211 VVDGLKGLPEAISAVFPQAAVQRCIVHLVRNLLDKVPRK----DQDAVLSDLRSIYIAPDAEEALLALLAFSELWGKRYP 286 (379)
T ss_pred ecchhhhhHHHHHHhccHhhhhhhhhHHHhhhhhhhhhh----hhHHHHhhhhhhhccCCcHHHHHHHHHHHHhhhhhcc
Confidence 789999999999999999999999999999999998764 344566666666666666666666544 455678
Q ss_pred hHHHHHhhcCCCCccccccC-CCcccccccchhhhhhhhhhh
Q 004519 514 DAYDWVTQSEPEHWANTYFP-GARYDHMTSNFGQQFYSWVSE 554 (747)
Q Consensus 514 ~~~~~l~~~~~~~Wa~a~~~-~~~~~~~ttN~~Es~n~~lk~ 554 (747)
....|+.+..-+.|...-|+ ..+-.+.|||..|++|+.++.
T Consensus 287 ~i~~~~~~~~~~~~~F~~fp~~~r~~i~ttN~IE~~n~~ir~ 328 (379)
T COG3328 287 AILKSWRNALEELLPFFAFPSEIRKIIYTTNAIESLNKLIRR 328 (379)
T ss_pred hHHHHHHHHHHHhcccccCcHHHHhHhhcchHHHHHHHHHHH
Confidence 88888888766666544444 444567899999999997774
No 7
>smart00575 ZnF_PMZ plant mutator transposase zinc finger.
Probab=98.88 E-value=7.6e-10 Score=70.99 Aligned_cols=27 Identities=41% Similarity=0.960 Sum_probs=24.9
Q ss_pred ceeecCCcccCCCCcchHHHHHHHhcC
Q 004519 632 WDCTCKTWHLTGLPCCHAIAVLEWIGR 658 (747)
Q Consensus 632 ~~CtC~~~~~~giPC~Halav~~~~~~ 658 (747)
.+|||++|+..||||+|+|+|+...++
T Consensus 1 ~~CsC~~~~~~gipC~H~i~v~~~~~~ 27 (28)
T smart00575 1 KTCSCRKFQLSGIPCRHALAAAIHIGL 27 (28)
T ss_pred CcccCCCcccCCccHHHHHHHHHHhCC
Confidence 479999999999999999999988775
No 8
>PF08731 AFT: Transcription factor AFT; InterPro: IPR014842 AFT (activator of iron transcription) is an iron regulated transcriptional activator that regulates the expression of genes involved in iron homeostasis. This entry includes the paralogous pair of transcription factors AFT1 and AFT2.
Probab=98.75 E-value=4.8e-08 Score=82.92 Aligned_cols=69 Identities=23% Similarity=0.406 Sum_probs=65.4
Q ss_pred eCCHHHHHHHHHHHHHhcCeeEEEeecCCeEEEEEeec------------------------------------------
Q 004519 187 FSSFSEFREALHKYSIAHGFAYRYKKNDSHRVTVKCKC------------------------------------------ 224 (747)
Q Consensus 187 F~s~~e~~~ai~~yai~~~f~~~~~rs~~~r~~~~C~~------------------------------------------ 224 (747)
|.+++|++.+|+.++...||++.+.||+++.+.++|..
T Consensus 1 F~~k~~ikpwlq~~~~~~Gi~iVIerSd~~ki~FkCk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~k~t~srk 80 (111)
T PF08731_consen 1 FDDKDEIKPWLQKIFYPQGIGIVIERSDKKKIVFKCKNGKRYRHKKKKKGQAQAQQKESTSGNKNKSSKKKKKKRTKSRK 80 (111)
T ss_pred CCchHHHHHHHHHHhhhcCceEEEEecCCceEEEEEecCCCcccccccccccccccccccccccccccccccCCcccccc
Confidence 88999999999999999999999999999999999984
Q ss_pred CCCCeEEEEEEcCCcceEEEEecCCcccccC
Q 004519 225 QGCPWRIYASRLSTTQLVCIKKMNSKHTCEG 255 (747)
Q Consensus 225 ~gC~w~i~a~~~~~~~~~~V~~~~~~Htc~~ 255 (747)
..|||+|+|+.....+.|.|..+++.|+|++
T Consensus 81 ~~CPFriRA~yS~k~k~W~lvvvnn~HnH~l 111 (111)
T PF08731_consen 81 NTCPFRIRANYSKKNKKWTLVVVNNEHNHPL 111 (111)
T ss_pred cCCCeEEEEEEEecCCeEEEEEecCCcCCCC
Confidence 2899999999999999999999999999974
No 9
>smart00666 PB1 PB1 domain. Phox and Bem1p domain, present in many eukaryotic cytoplasmic signalling proteins. The domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate.
Probab=98.56 E-value=4.1e-07 Score=75.89 Aligned_cols=75 Identities=21% Similarity=0.481 Sum_probs=65.1
Q ss_pred CCEEEecCceeEEEecCCCChhhHHHHHHHHhcCCCCceEEEEEecCCCCcceeeeCcHHHHHHHhhccCc--ceEEEEE
Q 004519 24 GSLSYNGGEAYAIDIDEETEFSGFKSEVAEMFNCSADTMSIKYFLPGNKKTLISISKDKDFKRMLNFLGDT--ATVDVFI 101 (747)
Q Consensus 24 g~~~Y~gg~~~~~~v~~~~s~~~~~~~l~~~~~~~~~~~~~~y~lp~~~~~l~~v~~D~dl~~m~~~~~~~--~~~~i~~ 101 (747)
.++.| ||+++.+.++++++|.+|.++|.+.+++..+.+.++|. .++.+++++.+|+||..|+++.... ..+.|++
T Consensus 4 vK~~~-~~~~~~~~~~~~~s~~dL~~~i~~~~~~~~~~~~l~Y~--Dedgd~v~l~sd~Dl~~a~~~~~~~~~~~l~l~v 80 (81)
T smart00666 4 VKLRY-GGETRRLSVPRDISFEDLRSKVAKRFGLDNQSFTLKYQ--DEDGDLVSLTSDEDLEEAIEEYDSLGSKKLRLHV 80 (81)
T ss_pred EEEEE-CCEEEEEEECCCCCHHHHHHHHHHHhCCCCCCeEEEEE--CCCCCEEEecCHHHHHHHHHHHHHcCCceEEEEe
Confidence 35677 89999999999999999999999999987788999999 5556799999999999999998863 4566664
No 10
>PF03101 FAR1: FAR1 DNA-binding domain; InterPro: IPR004330 Phytochrome A is the primary photoreceptor for mediating various far-red light-induced responses in higher plants. It has been found that the proteins governing this response, which include FAR-RED ELONGATED HYPOCOTYL3 (FHY3) and FAR-RED-IMPAIRED RESPONSE1 (FAR1), are a pair of homologous proteins sharing significant sequence homology to mutator-like transposases. These proteins appear to be novel transcription factors, which are essential for activating the expression of FHY1 and FHL (for FHY1-like) and related genes, whose products are required for light-induced phytochrome A nuclear accumulation and subsequent light responses in plants. The FRS (FAR1 Related Sequences) family of proteins share a similar domain structure to mutator-like transposases, including an N-terminal C2H2 zinc finger domain, a central putative core transposase domain, and a C-terminal SWIM motif (named after SWI2/SNF and MuDR transposases). It seems plausible that the FRS family represent transcription factors derived from mutator-like transposases [, ]. This entry represents a domain found in FAR1 and FRS proteins. It contains a WRKY like fold and is therefore most likely a zinc binding DNA-binding domain.
Probab=98.48 E-value=2.8e-07 Score=78.82 Aligned_cols=61 Identities=25% Similarity=0.371 Sum_probs=53.3
Q ss_pred HHHHHHHHhcCeeEEEeecCCe-------EEEEEeec----------------------CCCCeEEEEEEcCCcceEEEE
Q 004519 195 EALHKYSIAHGFAYRYKKNDSH-------RVTVKCKC----------------------QGCPWRIYASRLSTTQLVCIK 245 (747)
Q Consensus 195 ~ai~~yai~~~f~~~~~rs~~~-------r~~~~C~~----------------------~gC~w~i~a~~~~~~~~~~V~ 245 (747)
++|+.||...||.++..++.+. ++.++|.+ +||||+|.+.... .+.|.|+
T Consensus 1 ~fy~~yA~~~GF~vr~~~s~~~~~~~~~~~~~~~C~r~G~~~~~~~~~~~~~r~~~s~ktgC~a~i~v~~~~-~~~w~v~ 79 (91)
T PF03101_consen 1 DFYNSYARRHGFSVRKSSSRKSKKNGEIKRVTFVCSRGGKYKSKKKNEEKRRRNRPSKKTGCKARINVKRRK-DGKWRVT 79 (91)
T ss_pred CHHHHhcCcCCeEEEEeeeEeCCCCceEEEEEEEECCcccccccccccccccccccccccCCCEEEEEEEcc-CCEEEEE
Confidence 4799999999999999865443 78899985 4999999999988 7899999
Q ss_pred ecCCcccccCc
Q 004519 246 KMNSKHTCEGA 256 (747)
Q Consensus 246 ~~~~~Htc~~~ 256 (747)
.+..+|||++.
T Consensus 80 ~~~~~HNH~L~ 90 (91)
T PF03101_consen 80 SFVLEHNHPLC 90 (91)
T ss_pred ECcCCcCCCCC
Confidence 99999999864
No 11
>PF04434 SWIM: SWIM zinc finger; InterPro: IPR007527 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the SWIM (SWI2/SNF2 and MuDR) zinc-binding domain, which is found in a variety of prokaryotic and eukaryotic proteins, such as mitogen-activated protein kinase kinase kinase 1 (or MEKK1). It is also found in the related protein MEX (MEKK1-related protein X), a testis-expressed protein that acts as an E3 ubiquitin ligase through the action of E2 ubiquitin-conjugating enzymes in the proteasome degradation pathway; the SWIM domain is critical for MEX ubiquitination []. SWIM domains are also found in the homologous recombination protein Sws1 [], as well as in several hypothetical proteins. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=98.08 E-value=2.4e-06 Score=60.42 Aligned_cols=30 Identities=33% Similarity=0.774 Sum_probs=27.2
Q ss_pred EeCcCceeecCCcccCCCCcchHHHHHHHh
Q 004519 627 VDVDRWDCTCKTWHLTGLPCCHAIAVLEWI 656 (747)
Q Consensus 627 V~l~~~~CtC~~~~~~giPC~Halav~~~~ 656 (747)
+++...+|||..|+..|.||+|++|++...
T Consensus 10 ~~~~~~~CsC~~~~~~~~~CkHi~av~~~~ 39 (40)
T PF04434_consen 10 VSIEQASCSCPYFQFRGGPCKHIVAVLLAL 39 (40)
T ss_pred ccccccEeeCCCccccCCcchhHHHHHHhh
Confidence 667899999999999999999999998754
No 12
>cd05992 PB1 The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as a noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants.
Probab=97.98 E-value=5e-05 Score=63.19 Aligned_cols=74 Identities=23% Similarity=0.419 Sum_probs=59.2
Q ss_pred CEEEecCceeEEEec-CCCChhhHHHHHHHHhcCCCCceEEEEEecCCCCcceeeeCcHHHHHHHhhccC--cceEEEEE
Q 004519 25 SLSYNGGEAYAIDID-EETEFSGFKSEVAEMFNCSADTMSIKYFLPGNKKTLISISKDKDFKRMLNFLGD--TATVDVFI 101 (747)
Q Consensus 25 ~~~Y~gg~~~~~~v~-~~~s~~~~~~~l~~~~~~~~~~~~~~y~lp~~~~~l~~v~~D~dl~~m~~~~~~--~~~~~i~~ 101 (747)
++.|. |+++.+.+. +++||.+|.++|.+.+++....+.++|.-+. .++++|.+|+||..|++.... ...+.|++
T Consensus 4 K~~~~-~~~~~~~~~~~~~s~~~L~~~i~~~~~~~~~~~~l~y~D~e--~d~v~l~sd~Dl~~a~~~~~~~~~~~l~l~v 80 (81)
T cd05992 4 KVKYG-GEIRRFVVVSRSISFEDLRSKIAEKFGLDAVSFKLKYPDED--GDLVTISSDEDLEEAIEEARRSGSKKLRLFV 80 (81)
T ss_pred EEEec-CCCEEEEEecCCCCHHHHHHHHHHHhCCCCCcEEEEeeCCC--CCEEEeCCHHHHHHHHHHHhhcCCccEEEEe
Confidence 45666 557777777 9999999999999999986667788887544 379999999999999999874 45666664
No 13
>cd06407 PB1_NLP A PB1 domain is present in NIN like proteins (NLP), a key enzyme in a process of establishment of symbiosis betweeen legumes and nitrogen fixing bacteria (Rhizobium). The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes like osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-inte
Probab=97.89 E-value=0.0001 Score=60.90 Aligned_cols=70 Identities=17% Similarity=0.385 Sum_probs=60.3
Q ss_pred cCceeEEEecCCCChhhHHHHHHHHhcCCC-CceEEEEEecCCCCcceeeeCcHHHHHHHhhccC--cceEEEEE
Q 004519 30 GGEAYAIDIDEETEFSGFKSEVAEMFNCSA-DTMSIKYFLPGNKKTLISISKDKDFKRMLNFLGD--TATVDVFI 101 (747)
Q Consensus 30 gg~~~~~~v~~~~s~~~~~~~l~~~~~~~~-~~~~~~y~lp~~~~~l~~v~~D~dl~~m~~~~~~--~~~~~i~~ 101 (747)
||++..+.+..+++|.+|.++|.+.++++. +.+.++|.=.. .++++|++|+||+.-++++.. ...+.++|
T Consensus 8 ~~d~~r~~l~~~~~~~~L~~~i~~r~~~~~~~~f~LkY~Dde--gd~v~ltsd~DL~eai~i~~~~~~~~v~l~v 80 (82)
T cd06407 8 GEEKIRFRLPPSWGFTELKQEIAKRFKLDDMSAFDLKYLDDD--EEWVLLTCDADLEECIDVYRSSGSHTIRLLV 80 (82)
T ss_pred CCeEEEEEcCCCCCHHHHHHHHHHHhCCCCCCeeEEEEECCC--CCeEEeecHHHHHHHHHHHHHCCCCeEEEEe
Confidence 678999999999999999999999999875 78999999433 559999999999999988876 35677776
No 14
>PF00564 PB1: PB1 domain; InterPro: IPR000270 The Phox and Bem1p domain, is present in many eukaryotic cytoplasmic signalling proteins. The domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate.; GO: 0005515 protein binding; PDB: 1IPG_A 1IP9_A 2KFK_A 1WMH_A 1VD2_A 1WI0_A 1OEY_C 1PQS_A 1Q1O_A 1TZ1_A ....
Probab=97.85 E-value=8.6e-05 Score=62.27 Aligned_cols=76 Identities=22% Similarity=0.458 Sum_probs=62.0
Q ss_pred EEEecCceeEEEecCCCChhhHHHHHHHHhcCCCCceEEEEEecCCCCcceeeeCcHHHHHHHhhccCc--ceEEEEEec
Q 004519 26 LSYNGGEAYAIDIDEETEFSGFKSEVAEMFNCSADTMSIKYFLPGNKKTLISISKDKDFKRMLNFLGDT--ATVDVFIQS 103 (747)
Q Consensus 26 ~~Y~gg~~~~~~v~~~~s~~~~~~~l~~~~~~~~~~~~~~y~lp~~~~~l~~v~~D~dl~~m~~~~~~~--~~~~i~~~~ 103 (747)
+.|.|+..+.+.+.++++|.+|.++|.+.++.....+.++|.=.. .++++|.+|+||..|++..... ..+.++|..
T Consensus 6 ~~~~~~~~~~~~~~~~~s~~~L~~~i~~~~~~~~~~~~l~Y~D~d--gD~V~i~sd~Dl~~a~~~~~~~~~~~lrl~v~~ 83 (84)
T PF00564_consen 6 VRYGGDIRRIISLPSDVSFDDLRSKIREKFGLLDEDFQLKYKDED--GDLVTISSDEDLQEAIEQAKESGSKTLRLFVQD 83 (84)
T ss_dssp EEETTEEEEEEEECSTSHHHHHHHHHHHHHTTSTSSEEEEEEETT--SSEEEESSHHHHHHHHHHHHHCTTSCEEEEEEE
T ss_pred EEECCeeEEEEEcCCCCCHHHHHHHHHHHhCCCCccEEEEeeCCC--CCEEEeCCHHHHHHHHHHHHhcCCCcEEEEEEe
Confidence 566655555699999999999999999999987788999998533 3699999999999999888653 467777753
No 15
>cd06408 PB1_NoxR The PB1 domain is present in the Epichloe festucae NoxR protein (NADPH oxidase regulator), a key regulator of NADPH oxidase isoform, NoxA. NoxA is essential for growth control of the fungal endophyte in plant tissue in the process of symbiotic interaction between a fungi and its plant host. The Epichloe festucae p67(phox)-like regulator, NoxR, dispensable in culture but essential in plants for the symbiotic interaction. Plants infected with a noxR deletion mutant show severe stunting and premature senescence, whereas hyphae in the meristematic tissues show increased branching leading to increased fungal colonization of pseudostem and leaf blade tissue. The PB1 domain is a modular domain mediating specific protein-protein interactions which a play role in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is
Probab=97.34 E-value=0.0013 Score=54.13 Aligned_cols=59 Identities=17% Similarity=0.311 Sum_probs=52.0
Q ss_pred cCceeEEEecCCCChhhHHHHHHHHhcCCCCceEEEEEecCCCCcceeeeCcHHHHHHHhhcc
Q 004519 30 GGEAYAIDIDEETEFSGFKSEVAEMFNCSADTMSIKYFLPGNKKTLISISKDKDFKRMLNFLG 92 (747)
Q Consensus 30 gg~~~~~~v~~~~s~~~~~~~l~~~~~~~~~~~~~~y~lp~~~~~l~~v~~D~dl~~m~~~~~ 92 (747)
+|.++.|.|+.+++|.+|.++|.+.|++. +.++++|.=. .++++|+++.||+.-+.-..
T Consensus 10 ~~Dv~~i~v~~~i~f~dL~~kIrdkf~~~-~~~~iKykDE---GD~iti~sq~DLd~Ai~~a~ 68 (86)
T cd06408 10 QDDTRYIMIGPDTGFADFEDKIRDKFGFK-RRLKIKMKDD---GDMITMGDQDDLDMAIDTAR 68 (86)
T ss_pred cCcEEEEEcCCCCCHHHHHHHHHHHhCCC-CceEEEEEcC---CCCccccCHHHHHHHHHHHH
Confidence 47799999999999999999999999985 7899999966 35899999999999886554
No 16
>cd06396 PB1_NBR1 The PB1 domain is an essential part of NBR1 protein, next to BRCA1, a scaffold protein mediating specific protein-protein interaction with both titin protein kinase and with another scaffold protein p62. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The NBR1 protein contains a type I PB1 domain.
Probab=97.28 E-value=0.0012 Score=53.64 Aligned_cols=68 Identities=15% Similarity=0.335 Sum_probs=56.7
Q ss_pred cCceeEEEecC--CCChhhHHHHHHHHhcCCCCceEEEEEecCCCCcceeeeCcHHHHHHHhhccCcce-EEEEE
Q 004519 30 GGEAYAIDIDE--ETEFSGFKSEVAEMFNCSADTMSIKYFLPGNKKTLISISKDKDFKRMLNFLGDTAT-VDVFI 101 (747)
Q Consensus 30 gg~~~~~~v~~--~~s~~~~~~~l~~~~~~~~~~~~~~y~lp~~~~~l~~v~~D~dl~~m~~~~~~~~~-~~i~~ 101 (747)
||++..+.++. +++|.+|..+|...|+++ .+.+||. .++.+++.|++|.||+..++.+.+..+ +.+.|
T Consensus 8 ~~d~~rf~~~~~~~~~~~~L~~ev~~rf~l~--~f~lKYl--Dde~e~v~lssd~eLeE~~rl~~~~~~~l~~~v 78 (81)
T cd06396 8 NGESQSFLVSDSENTTWASVEAMVKVSFGLN--DIQIKYV--DEENEEVSVNSQGEYEEALKSAVRQGNLLQMNV 78 (81)
T ss_pred CCeEEEEEecCCCCCCHHHHHHHHHHHhCCC--cceeEEE--cCCCCEEEEEchhhHHHHHHHHHhCCCEEEEEE
Confidence 47777788887 999999999999999987 8999999 444459999999999999999988754 44444
No 17
>cd06406 PB1_P67 A PB1 domain is present in p67 proteins which forms a signaling complex with p40, a crucial step for activation of NADPH oxidase during phagocytosis. PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes . A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants. The p67 proteins contain
Probab=97.03 E-value=0.0027 Score=51.33 Aligned_cols=66 Identities=9% Similarity=0.239 Sum_probs=54.7
Q ss_pred CEEEecCceeEEEecCCCChhhHHHHHHHHhcCCCCceEEEEEecCCCCcceeeeCcHHHHHHHhhccCc
Q 004519 25 SLSYNGGEAYAIDIDEETEFSGFKSEVAEMFNCSADTMSIKYFLPGNKKTLISISKDKDFKRMLNFLGDT 94 (747)
Q Consensus 25 ~~~Y~gg~~~~~~v~~~~s~~~~~~~l~~~~~~~~~~~~~~y~lp~~~~~l~~v~~D~dl~~m~~~~~~~ 94 (747)
++.|.+ +-.|.|..+++|.+|.++|++.+.+..+.+++.|.-+.. ..++++ +|+||+.++....+.
T Consensus 6 KV~f~~--tIaIrvp~~~~y~~L~~ki~~kLkl~~e~i~LsYkde~s-~~~v~l-~d~dle~aws~~~~~ 71 (80)
T cd06406 6 KVHFKY--TVAIQVARGLSYATLLQKISSKLELPAEHITLSYKSEAS-GEDVIL-SDTNMEDVWSQAKDG 71 (80)
T ss_pred EEEEEE--EEEEEcCCCCCHHHHHHHHHHHhCCCchhcEEEeccCCC-CCccCc-ChHHHHHHHHhhcCC
Confidence 378887 888999999999999999999999988889999985432 235666 899999999776553
No 18
>cd06402 PB1_p62 The PB1 domain is an essential part of p62 scaffold protein (alias sequestosome 1,SQSTM) involved in cell signaling, receptor internalization, and protein turnover. The PB1 domain is a modular domain mediating specific protein-protein interaction which play roles in many critical cell processes. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants.
Probab=96.97 E-value=0.0077 Score=49.94 Aligned_cols=69 Identities=22% Similarity=0.351 Sum_probs=54.6
Q ss_pred CceeEEEecC--CCChhhHHHHHHHHh-cCCCCceEEEEEecCCCCcceeeeCcHHHHHHHhhccCcceEEEEEe
Q 004519 31 GEAYAIDIDE--ETEFSGFKSEVAEMF-NCSADTMSIKYFLPGNKKTLISISKDKDFKRMLNFLGDTATVDVFIQ 102 (747)
Q Consensus 31 g~~~~~~v~~--~~s~~~~~~~l~~~~-~~~~~~~~~~y~lp~~~~~l~~v~~D~dl~~m~~~~~~~~~~~i~~~ 102 (747)
-+.|-+.++. ..||.+|.+++.++| ++....++++|.=. +.+|++|++|++|..-++... -..+++|+-
T Consensus 14 ~EIRRf~l~~~~~~s~~~L~~~V~~~f~~l~~~~ftlky~De--eGDlvtIssdeEL~~A~~~~~-~~~~RlyI~ 85 (87)
T cd06402 14 AEIRRFAIDEDVSTSYEYLVEKVAAVFPSLRGKNFQLFWKDE--EGDLVAFSSDEELVMALGSLN-DDTFRIYIK 85 (87)
T ss_pred cceEEEEecCCCCcCHHHHHHHHHHHccccCCCcEEEEEECC--CCCEEeecCHHHHHHHHHcCC-CCcEEEEEE
Confidence 4667777765 679999999999999 55566899999843 345999999999999887765 456777764
No 19
>cd06398 PB1_Joka2 The PB1 domain is present in the Nicotiana plumbaginifolia Joka2 protein which interacts with sulfur stress inducible UP9 protein. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module
Probab=96.95 E-value=0.0081 Score=50.65 Aligned_cols=74 Identities=16% Similarity=0.446 Sum_probs=56.5
Q ss_pred EEEecCceeEEEecC-----CCChhhHHHHHHHHhcCCC-CceEEEEEecCCCCcceeeeCcHHHHHHHhhccC---cce
Q 004519 26 LSYNGGEAYAIDIDE-----ETEFSGFKSEVAEMFNCSA-DTMSIKYFLPGNKKTLISISKDKDFKRMLNFLGD---TAT 96 (747)
Q Consensus 26 ~~Y~gg~~~~~~v~~-----~~s~~~~~~~l~~~~~~~~-~~~~~~y~lp~~~~~l~~v~~D~dl~~m~~~~~~---~~~ 96 (747)
+.| ||.++-+.++. +++|.+|.+||.+.|++.. .++.++|. .++.+++.+.+|.||..-++.... ...
T Consensus 5 v~y-~~~~rRf~l~~~~~~~d~~~~~L~~kI~~~f~l~~~~~~~l~Y~--Dedgd~V~l~~D~DL~~a~~~~~~~~~~~~ 81 (91)
T cd06398 5 VKY-GGTLRRFTFPVAENQLDLNMDGLREKVEELFSLSPDADLSLTYT--DEDGDVVTLVDDNDLTDAIQYFCSGSRLNP 81 (91)
T ss_pred EEe-CCEEEEEEeccccccCCCCHHHHHHHHHHHhCCCCCCcEEEEEE--CCCCCEEEEccHHHHHHHHHHHhccCCCce
Confidence 445 56677777774 7999999999999999976 67899888 335569999999999999987522 245
Q ss_pred EEEEEe
Q 004519 97 VDVFIQ 102 (747)
Q Consensus 97 ~~i~~~ 102 (747)
+.|+|.
T Consensus 82 lrl~v~ 87 (91)
T cd06398 82 LRIDVT 87 (91)
T ss_pred EEEEEE
Confidence 566554
No 20
>cd06397 PB1_UP1 Uncharacterized protein 1. The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions.
Probab=96.85 E-value=0.0065 Score=48.58 Aligned_cols=65 Identities=14% Similarity=0.300 Sum_probs=54.9
Q ss_pred EEEecCceeEEEecCCCChhhHHHHHHHHhcCCCCceEEEEEecCCCCcceeeeCcHHHHHHHhhccC
Q 004519 26 LSYNGGEAYAIDIDEETEFSGFKSEVAEMFNCSADTMSIKYFLPGNKKTLISISKDKDFKRMLNFLGD 93 (747)
Q Consensus 26 ~~Y~gg~~~~~~v~~~~s~~~~~~~l~~~~~~~~~~~~~~y~lp~~~~~l~~v~~D~dl~~m~~~~~~ 93 (747)
+.| ||.+|-++.+..-+|..|.+||..++++....+.++|.=. +.+.|.+++|.||+..+.....
T Consensus 5 v~~-~g~~RRf~~~~~pt~~~L~~kl~~Lf~lp~~~~~vtYiDe--D~D~ITlssd~eL~d~~~~~~~ 69 (82)
T cd06397 5 SSF-LGDTRRIVFPDIPTWEALASKLENLYNLPEIKVGVTYIDN--DNDEITLSSNKELQDFYRLSHR 69 (82)
T ss_pred EEe-CCceEEEecCCCccHHHHHHHHHHHhCCChhHeEEEEEcC--CCCEEEecchHHHHHHHHhccc
Confidence 344 4677778888899999999999999999888899999944 4459999999999998887665
No 21
>cd06404 PB1_aPKC PB1 domain is an essential modular domain of the atypical protein kinase C (aPKC) which in complex with Par6 and Par3 proteins is crucial for establishment of apical-basal polarity of animal cells. PB1 domain is a modular domain mediating specific protein-protein interaction which play roles in many critical cell processes. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi,
Probab=96.78 E-value=0.0087 Score=48.56 Aligned_cols=63 Identities=14% Similarity=0.252 Sum_probs=52.8
Q ss_pred ecCceeEEEecCCCChhhHHHHHHHHhcCCC-CceEEEEEecCCCCcceeeeCcHHHHHHHhhccC
Q 004519 29 NGGEAYAIDIDEETEFSGFKSEVAEMFNCSA-DTMSIKYFLPGNKKTLISISKDKDFKRMLNFLGD 93 (747)
Q Consensus 29 ~gg~~~~~~v~~~~s~~~~~~~l~~~~~~~~-~~~~~~y~lp~~~~~l~~v~~D~dl~~m~~~~~~ 93 (747)
-+|....+.++..+||.+|.+++.+++.+.. +.+++||.=+ +.+++.|++|++|..-+..+.-
T Consensus 7 y~gdi~it~~d~~~s~e~L~~~v~~~c~~~~~q~ft~kw~DE--EGDp~tiSS~~EL~EA~rl~~~ 70 (83)
T cd06404 7 YNGDIMITSIDPSISLEELCNEVRDMCRFHNDQPFTLKWIDE--EGDPCTISSQMELEEAFRLYEL 70 (83)
T ss_pred ecCcEEEEEcCCCcCHHHHHHHHHHHhCCCCCCcEEEEEECC--CCCceeecCHHHHHHHHHHHHh
Confidence 3578888999999999999999999998765 4789999944 3449999999999998866654
No 22
>cd06409 PB1_MUG70 The MUG70 protein is a product of the meiotically up-regulated gene 70 which has a role in meiosis and harbors a PB1 domain. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domains depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic amino acid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is
Probab=96.56 E-value=0.014 Score=48.28 Aligned_cols=71 Identities=8% Similarity=0.262 Sum_probs=59.5
Q ss_pred cCceeEEEecCCCChhhHHHHHHHHhcCCC---CceEEEEEecCCCCcceeeeCcHHHHHHHhhccCc--ceEEEEEe
Q 004519 30 GGEAYAIDIDEETEFSGFKSEVAEMFNCSA---DTMSIKYFLPGNKKTLISISKDKDFKRMLNFLGDT--ATVDVFIQ 102 (747)
Q Consensus 30 gg~~~~~~v~~~~s~~~~~~~l~~~~~~~~---~~~~~~y~lp~~~~~l~~v~~D~dl~~m~~~~~~~--~~~~i~~~ 102 (747)
.|+++-+.+..++++.+|++.|...++.+. ..+.++|. .++.+.+.|.+|+||..-+++.... ..+.+++.
T Consensus 9 ~GrvhRf~~~~s~~~~~L~~~I~~Rl~~d~~~~~~~~L~Yl--DDEgD~VllT~D~DL~e~v~iar~~g~~~v~L~v~ 84 (86)
T cd06409 9 KGRVHRFRLRPSESLEELRTLISQRLGDDDFETHLYALSYV--DDEGDIVLITSDSDLVAAVLVARSAGLKKLDLHLH 84 (86)
T ss_pred CCCEEEEEecCCCCHHHHHHHHHHHhCCccccCCcccEEEE--cCCCCEEEEeccchHHHHHHHHHHcCCCEEEEEEe
Confidence 488888999999999999999999999886 57889998 4444599999999999999887664 56777764
No 23
>cd06403 PB1_Par6 The PB1 domain is an essential part of Par6 protein which in complex with Par3 and aPKC proteins is crucial for establishment of apical-basal polarity of animal cells. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants. The
Probab=96.42 E-value=0.025 Score=45.28 Aligned_cols=72 Identities=22% Similarity=0.351 Sum_probs=60.6
Q ss_pred EEecCceeEEEecCC--CChhhHHHHHHHHhcCCCCceEEEEEecCCCCcceeeeCcHHHHHHHhhccCcceEEEEEe
Q 004519 27 SYNGGEAYAIDIDEE--TEFSGFKSEVAEMFNCSADTMSIKYFLPGNKKTLISISKDKDFKRMLNFLGDTATVDVFIQ 102 (747)
Q Consensus 27 ~Y~gg~~~~~~v~~~--~s~~~~~~~l~~~~~~~~~~~~~~y~lp~~~~~l~~v~~D~dl~~m~~~~~~~~~~~i~~~ 102 (747)
++-|++.|-+.++++ -+|.+|-+.|..+.++...++.+.|.=| +.+|++|.||+++..-++-. -.-++|+|.
T Consensus 5 SkfdaEfRRFsl~r~~~~~f~ef~~ll~~lH~l~~~~f~i~Y~D~--~gDLLPInNDdNf~kAlssa--~plLRl~iq 78 (80)
T cd06403 5 SKFDAEFRRFSLDRNKPGKFEDFYKLLEHLHHIPNVDFLIGYTDP--HGDLLPINNDDNFLKALSSA--NPLLRIFIQ 78 (80)
T ss_pred cccCCeEEEEEeccccCcCHHHHHHHHHHHhCCCCCcEEEEEeCC--CCCEecccCcHHHHHHHHcC--CCceEEEEE
Confidence 456889999999996 8999999999999998888999999988 55699999999999988744 344666654
No 24
>cd06401 PB1_TFG The PB1 domain found in TFG protein, an oncogenic gene product and fusion partner to nerve growth factor tyrosine kinase receptor TrkA and to the tyrosine kinase ALK. The PB1 domain is a modular domain mediating specific protein-protein interaction in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The PB1 domains of TFG represent a type I/II PB1 domain. The physiological function of TFG remains unknown.
Probab=95.94 E-value=0.056 Score=43.83 Aligned_cols=69 Identities=19% Similarity=0.310 Sum_probs=53.6
Q ss_pred cCceeEEEecC-CCChhhHHHHHHHHhcCCC---CceEEEEEecCCCCcceeeeCcHHHHHHHhhccCcceEEEEE
Q 004519 30 GGEAYAIDIDE-ETEFSGFKSEVAEMFNCSA---DTMSIKYFLPGNKKTLISISKDKDFKRMLNFLGDTATVDVFI 101 (747)
Q Consensus 30 gg~~~~~~v~~-~~s~~~~~~~l~~~~~~~~---~~~~~~y~lp~~~~~l~~v~~D~dl~~m~~~~~~~~~~~i~~ 101 (747)
||.+|++.+.. .++|.+|.+.+..+|+... .++.+||.=+.+ +|+.|.+++||.--+... +...+.+|+
T Consensus 8 g~DiR~~~~~~~~~t~~~L~~~v~~~F~~~~~~~~~flIKYkD~dG--DlVTIts~~dL~~A~~~~-~~~~l~~~~ 80 (81)
T cd06401 8 GDDIRRIPIHNEDITYDELLLMMQRVFRGKLGSSDDVLIKYKDEDG--DLITIFDSSDLSFAIQCS-RILKLTLFV 80 (81)
T ss_pred CCeEEEEeccCccccHHHHHHHHHHHhccccCCcccEEEEEECCCC--CEEEeccHHHHHHHHhcC-cceEEEEec
Confidence 89999999997 5899999999999997543 578999985543 499999999998775443 344555553
No 25
>cd06405 PB1_Mekk2_3 The PB1 domain is present in the two mitogen-activated protein kinase kinases MEKK2 and MEKK3 which are two members of the signaling kinase cascade involved in angiogenesis and early cardiovascular development. The PB1 domain of MEKK2 (and/or MEKK3) interacts with the PB1 domain of another member of the kinase cascade Map2k5. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, f
Probab=95.56 E-value=0.083 Score=41.59 Aligned_cols=69 Identities=20% Similarity=0.455 Sum_probs=57.0
Q ss_pred EEecCceeEEEecCCCChhhHHHHHHHHhcCCCCceEEEEEecCCCCcceeeeCcHHHHHHHhhccCc---ceEEEEEe
Q 004519 27 SYNGGEAYAIDIDEETEFSGFKSEVAEMFNCSADTMSIKYFLPGNKKTLISISKDKDFKRMLNFLGDT---ATVDVFIQ 102 (747)
Q Consensus 27 ~Y~gg~~~~~~v~~~~s~~~~~~~l~~~~~~~~~~~~~~y~lp~~~~~l~~v~~D~dl~~m~~~~~~~---~~~~i~~~ 102 (747)
+|. |+.+++...|-+.|.|+.+|+...|| +.+.++|+... -+|++.+.+||++-++..+.+ .++.|++.
T Consensus 6 E~~-gEKRIi~f~RPvkf~dl~~kv~~afG---q~mdl~ytn~e---L~iPl~~Q~DLDkAie~ld~s~~~ksLRilL~ 77 (79)
T cd06405 6 EHN-GEKRIIQFPRPVKFKDLQQKVTTAFG---QPMDLHYTNNE---LLIPLKNQEDLDRAIELLDRSPHMKSLRILLS 77 (79)
T ss_pred Eec-CceEEEecCCCccHHHHHHHHHHHhC---CeeeEEEeccc---EEEeccCHHHHHHHHHHHccCccccceeEeEe
Confidence 444 88999999999999999999999996 58899999544 388999999999988776664 55666654
No 26
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=95.46 E-value=0.0098 Score=33.74 Aligned_cols=18 Identities=28% Similarity=0.733 Sum_probs=16.3
Q ss_pred eecCCCCCCCcCcCCCCC
Q 004519 729 LQCSKCKGLGHNKKTCKD 746 (747)
Q Consensus 729 ~~Cs~C~~~GHn~~tC~~ 746 (747)
++|-+|++.||.++.||+
T Consensus 1 ~~C~~C~~~GH~~~~Cp~ 18 (18)
T PF00098_consen 1 RKCFNCGEPGHIARDCPK 18 (18)
T ss_dssp SBCTTTSCSSSCGCTSSS
T ss_pred CcCcCCCCcCcccccCcc
Confidence 379999999999999985
No 27
>cd06411 PB1_p51 The PB1 domain is present in the p51 protein, a homolog of the p67 protein. p51 plays an important role in NADPH oxidase activation during phagosytosis. The PB1 domain is a modular domain mediating specific protein-protein interaction in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain mo
Probab=95.26 E-value=0.078 Score=42.71 Aligned_cols=62 Identities=16% Similarity=0.287 Sum_probs=55.2
Q ss_pred ceeEEEecCCCChhhHHHHHHHHhcCCCCceEEEEEecCCCCcceeeeCcHHHHHHHhhccC
Q 004519 32 EAYAIDIDEETEFSGFKSEVAEMFNCSADTMSIKYFLPGNKKTLISISKDKDFKRMLNFLGD 93 (747)
Q Consensus 32 ~~~~~~v~~~~s~~~~~~~l~~~~~~~~~~~~~~y~lp~~~~~l~~v~~D~dl~~m~~~~~~ 93 (747)
-|-.|.|.++.+|++|..+|++.+.+-.+..++.|.-|+++..+++++.|+|++.+..-..+
T Consensus 7 fTVai~v~~g~~y~~L~~~ls~kL~l~~~~~~LSY~~~~~~~~~v~l~~e~~me~aW~~v~~ 68 (78)
T cd06411 7 FTVALRAPRGADVSSLRALLSQALPQQAQRGQLSYRAPGEDGHWVPISGEESLQRAWQDVAD 68 (78)
T ss_pred EEEEEEccCCCCHHHHHHHHHHHhcCChhhcEEEecCCCCCccEeecCcchHHHHHHHhccC
Confidence 45678899999999999999999999899999999999888789999999999998866544
No 28
>PF01610 DDE_Tnp_ISL3: Transposase; InterPro: IPR002560 Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element. Transposases have been grouped into various families [, , ]. This family includes the IS204 [], IS1001 [], IS1096 [] and IS1165 [] transposases. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=94.77 E-value=0.043 Score=56.34 Aligned_cols=94 Identities=15% Similarity=0.182 Sum_probs=70.9
Q ss_pred EEEeccccCCcccceEEEEEEecC--CCCeEEEEEEEeecCCcccHHHHHHHH-HhhcCCCCcEEEEecCcchhHHHHhh
Q 004519 375 LFLDTTPLNSKYQGTLLTATSADG--DDGIFPVAFAVVDAETEDNWHWFLQEL-KSAVSTSQQITFIADFQNGLNKSLAE 451 (747)
Q Consensus 375 l~iD~t~~~~~y~~~l~~a~g~d~--~~~~~pla~a~v~~E~~e~~~wfl~~l-~~~~~~~~~~~iisD~~~~l~~Ai~~ 451 (747)
|+||-+.....++. ++.+.+|. +.+. .++++++-+.++..-||..+ -.. ......+|++|...+...|+++
T Consensus 1 lgiDE~~~~~g~~~--y~t~~~d~~~~~~~---il~i~~~r~~~~l~~~~~~~~~~~-~~~~v~~V~~Dm~~~y~~~~~~ 74 (249)
T PF01610_consen 1 LGIDEFAFRKGHRS--YVTVVVDLDTDTGR---ILDILPGRDKETLKDFFRSLYPEE-ERKNVKVVSMDMSPPYRSAIRE 74 (249)
T ss_pred CeEeeeeeecCCcc--eeEEEEECccCCce---EEEEcCCccHHHHHHHHHHhCccc-cccceEEEEcCCCccccccccc
Confidence 46777766543432 45555565 3322 24588899999999999877 333 3346789999999999999999
Q ss_pred hccCccchhhHHHHHHHHHhhhc
Q 004519 452 VFDNCYHSYCLRHLAEKLNRDIK 474 (747)
Q Consensus 452 vfP~a~h~~C~~Hi~~n~~~~~~ 474 (747)
.||+|.+..-.||+++++.+.+.
T Consensus 75 ~~P~A~iv~DrFHvvk~~~~al~ 97 (249)
T PF01610_consen 75 YFPNAQIVADRFHVVKLANRALD 97 (249)
T ss_pred cccccccccccchhhhhhhhcch
Confidence 99999999999999999987654
No 29
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=94.61 E-value=0.016 Score=39.98 Aligned_cols=18 Identities=33% Similarity=0.973 Sum_probs=16.1
Q ss_pred eecCCCCCCCcCc--CCCCC
Q 004519 729 LQCSKCKGLGHNK--KTCKD 746 (747)
Q Consensus 729 ~~Cs~C~~~GHn~--~tC~~ 746 (747)
++|++|++.||.+ ++||.
T Consensus 2 ~kC~~CG~~GH~~t~k~CP~ 21 (40)
T PF15288_consen 2 VKCKNCGAFGHMRTNKRCPM 21 (40)
T ss_pred ccccccccccccccCccCCC
Confidence 6899999999998 78885
No 30
>PF13610 DDE_Tnp_IS240: DDE domain
Probab=94.09 E-value=0.027 Score=52.17 Aligned_cols=80 Identities=11% Similarity=0.057 Sum_probs=67.5
Q ss_pred cEEEEeccccCCcccceEEEEEEecCCCCeEEEEEEEeecCCcccHHHHHHHHHhhcCCCCcEEEEecCcchhHHHHhhh
Q 004519 373 PLLFLDTTPLNSKYQGTLLTATSADGDDGIFPVAFAVVDAETEDNWHWFLQELKSAVSTSQQITFIADFQNGLNKSLAEV 452 (747)
Q Consensus 373 ~vl~iD~t~~~~~y~~~l~~a~g~d~~~~~~pla~a~v~~E~~e~~~wfl~~l~~~~~~~~~~~iisD~~~~l~~Ai~~v 452 (747)
+.+.+|-||.+-+= -..+.-.++|.+++ .|.+-|...-+...=..||..+.+..+ ..|..|+||+.++...|++++
T Consensus 2 ~~w~~DEt~iki~G-~~~yl~~aiD~~~~--~l~~~ls~~Rd~~aA~~Fl~~~l~~~~-~~p~~ivtDk~~aY~~A~~~l 77 (140)
T PF13610_consen 2 DSWHVDETYIKIKG-KWHYLWRAIDAEGN--ILDFYLSKRRDTAAAKRFLKRALKRHR-GEPRVIVTDKLPAYPAAIKEL 77 (140)
T ss_pred CEEEEeeEEEEECC-EEEEEEEeeccccc--chhhhhhhhcccccceeeccccceeec-cccceeecccCCccchhhhhc
Confidence 56889999976432 24455788999998 899999999999998999998888765 679999999999999999999
Q ss_pred ccCc
Q 004519 453 FDNC 456 (747)
Q Consensus 453 fP~a 456 (747)
++..
T Consensus 78 ~~~~ 81 (140)
T PF13610_consen 78 NPEG 81 (140)
T ss_pred cccc
Confidence 9974
No 31
>PF06782 UPF0236: Uncharacterised protein family (UPF0236); InterPro: IPR009620 This is a group of proteins of unknown function.
Probab=93.96 E-value=0.57 Score=52.62 Aligned_cols=132 Identities=10% Similarity=0.069 Sum_probs=86.1
Q ss_pred cCCcccHHHHHHHHHhhcCCC--CcEEEEecCcchhHHHHhhhccCccchhhHHHHHHHHHhhhcccccHHHHHHHHHHH
Q 004519 412 AETEDNWHWFLQELKSAVSTS--QQITFIADFQNGLNKSLAEVFDNCYHSYCLRHLAEKLNRDIKGQFSHEARRFMINDL 489 (747)
Q Consensus 412 ~E~~e~~~wfl~~l~~~~~~~--~~~~iisD~~~~l~~Ai~~vfP~a~h~~C~~Hi~~n~~~~~~~~~~~~~~~~~~~~~ 489 (747)
..+.+-|.-+++.+.+..... .-+++.+|+...+.+++. .||++.|.+..+|+.+.+.+.++.. + .+...+
T Consensus 235 ~~~~~~~~~v~~~i~~~Y~~~~~~~iiingDGa~WIk~~~~-~~~~~~~~LD~FHl~k~i~~~~~~~--~----~~~~~~ 307 (470)
T PF06782_consen 235 ESAEEFWEEVLDYIYNHYDLDKTTKIIINGDGASWIKEGAE-FFPKAEYFLDRFHLNKKIKQALSHD--P----ELKEKI 307 (470)
T ss_pred cchHHHHHHHHHHHHHhcCcccceEEEEeCCCcHHHHHHHH-hhcCceEEecHHHHHHHHHHHhhhC--h----HHHHHH
Confidence 455678888888887775433 257788999999988776 9999999999999999999888653 2 244545
Q ss_pred HHHhcCCChhhHHHHHHHHhccC---------hhHHHHHhhcCCCCccccccCCCcccccccchhhhhhhhhhh
Q 004519 490 YAAAYAPKFEGFQCSIESIKGIS---------PDAYDWVTQSEPEHWANTYFPGARYDHMTSNFGQQFYSWVSE 554 (747)
Q Consensus 490 ~~~~~a~~~~ef~~~~~~l~~~~---------~~~~~~l~~~~~~~Wa~a~~~~~~~~~~ttN~~Es~n~~lk~ 554 (747)
+++.+.....+++..++.+.... .++..||..+.... ..|-. +-+.......|+.+..+..
T Consensus 308 ~~al~~~d~~~l~~~L~~~~~~~~~~~~~~~i~~~~~Yl~~n~~~i--~~y~~--~~~~~g~g~ee~~~~~~s~ 377 (470)
T PF06782_consen 308 RKALKKGDKKKLETVLDTAESCAKDEEERKKIRKLRKYLLNNWDGI--KPYRE--REGLRGIGAEESVSHVLSY 377 (470)
T ss_pred HHHHHhcCHHHHHHHHHHHHHhhhchHHHHHHHHHHHHHHHCHHHh--hhhhh--ccCCCccchhhhhhhHHHH
Confidence 56666667777777776665432 13556666552111 11111 0222334456777766643
No 32
>PF04684 BAF1_ABF1: BAF1 / ABF1 chromatin reorganising factor; InterPro: IPR006774 ABF1 is a sequence-specific DNA binding protein involved in transcription activation, gene silencing and initiation of DNA replication. ABF1 is known to remodel chromatin, and it is proposed that it mediates its effects on transcription and gene expression by modifying local chromatin architecture []. These functions require a conserved stretch of 20 amino acids in the C-terminal region of ABF1 (amino acids 639 to 662 Saccharomyces cerevisiae (P14164 from SWISSPROT)) []. The N-terminal two thirds of the protein are necessary for DNA binding, and the N terminus (amino acids 9 to 91 in S. cerevisiae) is thought to contain a novel zinc-finger motif which may stabilise the protein structure [].; GO: 0003677 DNA binding, 0006338 chromatin remodeling, 0005634 nucleus
Probab=93.77 E-value=0.12 Score=55.26 Aligned_cols=57 Identities=16% Similarity=0.442 Sum_probs=51.4
Q ss_pred ccCceeCCHHHHHHHHHHHHHhcCeeEEEeecC-CeEEEEEeecCCCCeEEEEEEcCC
Q 004519 182 GVDQRFSSFSEFREALHKYSIAHGFAYRYKKND-SHRVTVKCKCQGCPWRIYASRLST 238 (747)
Q Consensus 182 ~vG~~F~s~~e~~~ai~~yai~~~f~~~~~rs~-~~r~~~~C~~~gC~w~i~a~~~~~ 238 (747)
.-+..|++.++-+++|+.|....+..|..+.|- .+.++|-|....|||+|..+..+.
T Consensus 23 ~~~~~f~tl~~wy~v~ndyefq~rcpiilknsh~nkhftfachlk~c~fkillsy~g~ 80 (496)
T PF04684_consen 23 AQARKFPTLEAWYNVINDYEFQSRCPIILKNSHRNKHFTFACHLKNCPFKILLSYCGN 80 (496)
T ss_pred ccccCCCcHHHHHHHHhhhhhhhcCceeecccccccceEEEeeccCCCceeeeeeccc
Confidence 346789999999999999999999999999885 578999999999999999998764
No 33
>PF03050 DDE_Tnp_IS66: Transposase IS66 family ; InterPro: IPR004291 Transposase proteins are necessary for efficient DNA transposition. This family includes the bacterial insertion sequence (IS) element, IS66, from Agrobacterium tumefaciens []. IS66 may cause genetic and structural variations of the T region and the vir region of the octopine Ti plasmids []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=93.75 E-value=0.17 Score=52.71 Aligned_cols=146 Identities=20% Similarity=0.207 Sum_probs=91.4
Q ss_pred chhHHHHHHHHhhhCCCCChHHHHHHHHHHhCCccCHHHHHHHHHHHHHHHhcCHHHHhccHHHHHHHHHHhCCCCEEEE
Q 004519 266 RGWVGNIIKEKLKASPNYKPKDIADDIKREYGIQLNYSQAWRAKEIAREQLQGSYKDSYTLLPFFCEKIKETNPGSVVTF 345 (747)
Q Consensus 266 ~~~i~~~~~~~~~~~~~~~~~~i~~~i~~~~g~~~~~~~~~r~k~~~~~~~~g~~~~~~~~L~~~~~~l~~~npg~~~~~ 345 (747)
.+++|-.+... -.-.++-..+.+.+.+. |+.+|..++.+.-.++.+.+.. .| +.|.+.-
T Consensus 6 ~~~~a~i~~l~--~~~~lp~~r~~~~~~~~-G~~is~~ti~~~~~~~~~~l~~----~~-------~~l~~~~------- 64 (271)
T PF03050_consen 6 PSLLALIAYLK--YVYHLPLYRIQQMLEDL-GITISRGTIANWIKRVAEALKP----LY-------EALKEEL------- 64 (271)
T ss_pred HHHHHHHHHHH--hcCCCCHHHHhhhhhcc-ceeeccchhHhHhhhhhhhhhh----hh-------hhhhhhc-------
Confidence 34444443332 23355666777777777 9999999888876555443221 11 2222211
Q ss_pred EecCCCceeEEEeehhchHHHHhhcCccEEEEeccccC----Ccc-cceEEEEEEecCCCCeEEEEEEEeecCCcccHHH
Q 004519 346 TTKEDSSFHRLFVSFHASISGFQQGCRPLLFLDTTPLN----SKY-QGTLLTATSADGDDGIFPVAFAVVDAETEDNWHW 420 (747)
Q Consensus 346 ~~~~~~~f~~lf~~~~~~~~~f~~~~~~vl~iD~t~~~----~~y-~~~l~~a~g~d~~~~~~pla~a~v~~E~~e~~~w 420 (747)
. -.+++.+|-|..+ ++. ++-+-++++-+ .+.|.+.++-+.+...-
T Consensus 65 ----------------------~--~~~~~~~DET~~~vl~~~~g~~~~~Wv~~~~~------~v~f~~~~sR~~~~~~~ 114 (271)
T PF03050_consen 65 ----------------------R--SSPVVHADETGWRVLDKGKGKKGYLWVFVSPE------VVLFFYAPSRSSKVIKE 114 (271)
T ss_pred ----------------------c--ccceeccCCceEEEeccccccceEEEeeeccc------eeeeeecccccccchhh
Confidence 1 2468888888766 333 33344444433 66677777777777766
Q ss_pred HHHHHHhhcCCCCcEEEEecCcchhHHHHhhhccCccchhhHHHHHHHHHhhhcc
Q 004519 421 FLQELKSAVSTSQQITFIADFQNGLNKSLAEVFDNCYHSYCLRHLAEKLNRDIKG 475 (747)
Q Consensus 421 fl~~l~~~~~~~~~~~iisD~~~~l~~Ai~~vfP~a~h~~C~~Hi~~n~~~~~~~ 475 (747)
+|.. -.-+++||+-.+-.. +..+.|+.|+.|+.+.|..-...
T Consensus 115 ~L~~--------~~GilvsD~y~~Y~~-----~~~~~hq~C~AH~~R~~~~~~~~ 156 (271)
T PF03050_consen 115 FLGD--------FSGILVSDGYSAYNK-----LAGITHQLCWAHLRRDFQDAAES 156 (271)
T ss_pred hhcc--------cceeeeccccccccc-----ccccccccccccccccccccccc
Confidence 6544 234899999887654 23889999999999999877654
No 34
>PHA02517 putative transposase OrfB; Reviewed
Probab=93.48 E-value=2.8 Score=43.67 Aligned_cols=151 Identities=17% Similarity=0.089 Sum_probs=84.4
Q ss_pred hHHHHHHHHhhh-CCCCChHHHHHHHHHHhCCccCHHHHHHHHHHHHHHHhcCHHHHhccHHHHHHHHHHhCCCCEEEEE
Q 004519 268 WVGNIIKEKLKA-SPNYKPKDIADDIKREYGIQLNYSQAWRAKEIAREQLQGSYKDSYTLLPFFCEKIKETNPGSVVTFT 346 (747)
Q Consensus 268 ~i~~~~~~~~~~-~~~~~~~~i~~~i~~~~g~~~~~~~~~r~k~~~~~~~~g~~~~~~~~L~~~~~~l~~~npg~~~~~~ 346 (747)
.+.+.+.+.... .+.+..+.|...|++. |+.++.++++|..... |-... .. ..-.....+-. .
T Consensus 30 ~l~~~I~~i~~~~~~~~G~r~I~~~L~~~-g~~vs~~tV~Rim~~~-----gl~~~-~~------~k~~~~~~~~~---~ 93 (277)
T PHA02517 30 WLKSEILRVYDENHQVYGVRKVWRQLNRE-GIRVARCTVGRLMKEL-----GLAGV-LR------GKKVRTTISRK---A 93 (277)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHHHhc-CcccCHHHHHHHHHHc-----CCceE-ec------CCCcCCCCCCC---C
Confidence 455566666554 5789999999998765 9999999988753321 11000 00 00000000000 0
Q ss_pred ecCCCceeEEEeehhchHHHHhhcCccEEEEeccccCCcccceEEEEEEecCCCCeEEEEEEEeecCCcccHHHHHHHHH
Q 004519 347 TKEDSSFHRLFVSFHASISGFQQGCRPLLFLDTTPLNSKYQGTLLTATSADGDDGIFPVAFAVVDAETEDNWHWFLQELK 426 (747)
Q Consensus 347 ~~~~~~f~~lf~~~~~~~~~f~~~~~~vl~iD~t~~~~~y~~~l~~a~g~d~~~~~~pla~a~v~~E~~e~~~wfl~~l~ 426 (747)
....+.+.+-|-+. .-..++..|.|+..... |..+.++.+|...+ +++|+.+...++.+...-+|+...
T Consensus 94 ~~~~n~~~r~f~~~---------~pn~~w~~D~t~~~~~~-g~~yl~~iiD~~sr-~i~~~~~~~~~~~~~~~~~l~~a~ 162 (277)
T PHA02517 94 VAAPDRVNRQFVAT---------RPNQLWVADFTYVSTWQ-GWVYVAFIIDVFAR-RIVGWRVSSSMDTDFVLDALEQAL 162 (277)
T ss_pred CCCCCcccCCCCCC---------CCCCeEEeceeEEEeCC-CCEEEEEecccCCC-eeeecccCCCCChHHHHHHHHHHH
Confidence 00011111112111 12358999999975443 56677777886554 577888888888776655555555
Q ss_pred hhcCCCCcEEEEecCcchh
Q 004519 427 SAVSTSQQITFIADFQNGL 445 (747)
Q Consensus 427 ~~~~~~~~~~iisD~~~~l 445 (747)
...+...+.+|.||+....
T Consensus 163 ~~~~~~~~~i~~sD~G~~y 181 (277)
T PHA02517 163 WARGRPGGLIHHSDKGSQY 181 (277)
T ss_pred HhcCCCcCcEeeccccccc
Confidence 4444334467779987643
No 35
>PF03106 WRKY: WRKY DNA -binding domain; InterPro: IPR003657 The WRKY domain is a 60 amino acid region that is defined by the conserved amino acid sequence WRKYGQK at its N-terminal end, together with a novel zinc-finger- like motif. The WRKY domain is found in one or two copies in a superfamily of plant transcription factors involved in the regulation of various physiological programs that are unique to plants, including pathogen defence, senescence, trichome development and the biosynthesis of secondary metabolites. The WRKY domain binds specifically to the DNA sequence motif (T)(T)TGAC(C/T), which is known as the W box. The invariant TGAC core of the W box is essential for function and WRKY binding []. Some proteins known to contain a WRKY domain include Arabidopsis thaliana ZAP1 (Zinc-dependent Activator Protein-1) and AtWRKY44/TTG2, a protein involved in trichome development and anthocyanin pigmentation; and wild oat ABF1-2, two proteins involved in the gibberelic acid-induced expression of the alpha-Amy2 gene. Structural studies indicate that this domain is a four-stranded beta-sheet with a zinc binding pocket, forming a novel zinc and DNA binding structure []. The WRKYGQK residues correspond to the most N-terminal beta-strand, which enables extensive hydrophobic interactions, contributing to the structural stability of the beta-sheet.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2AYD_A 1WJ2_A 2LEX_A.
Probab=93.00 E-value=0.2 Score=38.64 Aligned_cols=40 Identities=20% Similarity=0.375 Sum_probs=33.1
Q ss_pred CeEEEEEeecCCCCeEEEEEEcCCcceEEEEecCCccccc
Q 004519 215 SHRVTVKCKCQGCPWRIYASRLSTTQLVCIKKMNSKHTCE 254 (747)
Q Consensus 215 ~~r~~~~C~~~gC~w~i~a~~~~~~~~~~V~~~~~~Htc~ 254 (747)
..|-.++|+..+||++-.+.+..++....+.++.++|||+
T Consensus 20 ~pRsYYrCt~~~C~akK~Vqr~~~d~~~~~vtY~G~H~h~ 59 (60)
T PF03106_consen 20 YPRSYYRCTHPGCPAKKQVQRSADDPNIVIVTYEGEHNHP 59 (60)
T ss_dssp CEEEEEEEECTTEEEEEEEEEETTCCCEEEEEEES--SS-
T ss_pred eeeEeeeccccChhheeeEEEecCCCCEEEEEEeeeeCCC
Confidence 4577899999999999999998877788999999999996
No 36
>cd06395 PB1_Map2k5 PB1 domain is essential part of the mitogen-activated protein kinase kinase 5 (Map2k5, alias MEK5) one of the key member of the signaling kinases cascade which involved in angiogenesis and early cardiovascular development. The PB1 domain of Map2k5 interacts with the PB1 domain of another members of kinase cascade MEKK2 (or MEKK3). A canonical PB1-PB1 interaction, involving heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The Map2k5 protein contains a type I PB1 domain.
Probab=90.28 E-value=0.59 Score=37.38 Aligned_cols=59 Identities=17% Similarity=0.305 Sum_probs=43.8
Q ss_pred CceeEEEec--CCCChhhHHHHHHHHhcCCCCceEEEEEecCCCCcceeeeCcHHHHHHHhhccC
Q 004519 31 GEAYAIDID--EETEFSGFKSEVAEMFNCSADTMSIKYFLPGNKKTLISISKDKDFKRMLNFLGD 93 (747)
Q Consensus 31 g~~~~~~v~--~~~s~~~~~~~l~~~~~~~~~~~~~~y~lp~~~~~l~~v~~D~dl~~m~~~~~~ 93 (747)
|...| .|+ ..++|.++++.|...+.- .....|.|- .++.+-|.|.+|+.++.|++.+.+
T Consensus 11 g~vDw-~V~~~~~L~F~DvL~~I~~vlp~-aT~tAFeYE--DE~gDRITVRSDeEm~AMlsyy~~ 71 (91)
T cd06395 11 GAVDW-TVQSGPQLLFRDVLDVIGQVLPE-ATTTAFEYE--DEDGDRITVRSDEEMKAMLSYYCS 71 (91)
T ss_pred Ccccc-cccCcccccHHHHHHHHHHhccc-ccccceeec--cccCCeeEecchHHHHHHHHHHHH
Confidence 44444 444 579999999999999942 223456664 566668999999999999998754
No 37
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=88.66 E-value=0.24 Score=32.51 Aligned_cols=19 Identities=26% Similarity=0.693 Sum_probs=17.6
Q ss_pred eeecCCCCCCCcCcCCCCC
Q 004519 728 SLQCSKCKGLGHNKKTCKD 746 (747)
Q Consensus 728 ~~~Cs~C~~~GHn~~tC~~ 746 (747)
.+.|.+|++.||..+.||.
T Consensus 8 ~Y~C~~C~~~GH~i~dCP~ 26 (32)
T PF13696_consen 8 GYVCHRCGQKGHWIQDCPT 26 (32)
T ss_pred CCEeecCCCCCccHhHCCC
Confidence 4899999999999999996
No 38
>COG3316 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=88.40 E-value=4.1 Score=39.99 Aligned_cols=121 Identities=14% Similarity=0.166 Sum_probs=85.2
Q ss_pred HHHHHHhCCccCHHHHHHHHHHHHHHHhcCHHHHhccHHHHHHHHHHhCCCCEEEEEecCCCceeEEEeehhchHHHHhh
Q 004519 290 DDIKREYGIQLNYSQAWRAKEIAREQLQGSYKDSYTLLPFFCEKIKETNPGSVVTFTTKEDSSFHRLFVSFHASISGFQQ 369 (747)
Q Consensus 290 ~~i~~~~g~~~~~~~~~r~k~~~~~~~~g~~~~~~~~L~~~~~~l~~~npg~~~~~~~~~~~~f~~lf~~~~~~~~~f~~ 369 (747)
+.+..+.|+.+.+.++.|.=++.- |.+.+.+.+.++.
T Consensus 32 ~e~l~~rgi~v~h~Ti~rwv~k~~--------------~~~~~~~~~r~~~----------------------------- 68 (215)
T COG3316 32 EEMLAERGIEVDHETIHRWVQKYG--------------PLLARRLKRRKRK----------------------------- 68 (215)
T ss_pred HHHHHHcCcchhHHHHHHHHHHHh--------------HHHHHHhhhhccc-----------------------------
Confidence 346667899999999888644322 3344555555544
Q ss_pred cCccEEEEeccccCCcccceEEEEEEecCCCCeEEEEEEEeecCCcccHHHHHHHHHhhcCCCCcEEEEecCcchhHHHH
Q 004519 370 GCRPLLFLDTTPLNSKYQGTLLTATSADGDDGIFPVAFAVVDAETEDNWHWFLQELKSAVSTSQQITFIADFQNGLNKSL 449 (747)
Q Consensus 370 ~~~~vl~iD~t~~~~~y~~~l~~a~g~d~~~~~~pla~a~v~~E~~e~~~wfl~~l~~~~~~~~~~~iisD~~~~l~~Ai 449 (747)
-...+.+|-||.+-+-+.. +.-.++|.+| .++-+-|...-+...=.-||..+++.. ..|.+|+||+.+....|+
T Consensus 69 -~~~~w~vDEt~ikv~gkw~-ylyrAid~~g--~~Ld~~L~~rRn~~aAk~Fl~kllk~~--g~p~v~vtDka~s~~~A~ 142 (215)
T COG3316 69 -AGDSWRVDETYIKVNGKWH-YLYRAIDADG--LTLDVWLSKRRNALAAKAFLKKLLKKH--GEPRVFVTDKAPSYTAAL 142 (215)
T ss_pred -cccceeeeeeEEeeccEee-ehhhhhccCC--CeEEEEEEcccCcHHHHHHHHHHHHhc--CCCceEEecCccchHHHH
Confidence 2357888888875433222 2234556664 578888888888877788888887776 579999999999999999
Q ss_pred hhhccCccch
Q 004519 450 AEVFDNCYHS 459 (747)
Q Consensus 450 ~~vfP~a~h~ 459 (747)
+++-+.+.|+
T Consensus 143 ~~l~~~~ehr 152 (215)
T COG3316 143 RKLGSEVEHR 152 (215)
T ss_pred HhcCcchhee
Confidence 9998866554
No 39
>PF04500 FLYWCH: FLYWCH zinc finger domain; InterPro: IPR007588 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a potential FLYWCH Zn-finger domain found in a number of eukaryotic proteins. FLYWCH is a C2H2-type zinc finger characterised by five conserved hydrophobic residues, containing the conserved sequence motif: F/Y-X(n)-L-X(n)-F/Y-X(n)-WXCX(6-12)CX(17-22)HXH where X indicates any amino acid. This domain was first characterised in Drosophila Modifier of mdg4 proteins, Mod(mgd4), putative chromatin modulators involved in higher order chromatin domains. Mod(mdg4) proteins share a common N-terminal BTB/POZ domain, but differ in their C-terminal region, most containing C-terminal FLYWCH zinc finger motifs []. The FLYWCH domain in Mod(mdg4) proteins has a putative role in protein-protein interactions; for example, Mod(mdg4)-67.2 interacts with DNA-binding protein Su(Hw) via its FLYWCH domain. FLYWCH domains have been described in other proteins as well, including suppressor of killer of prune, Su(Kpn), which contains 4 terminal FLYWCH zinc finger motifs in a tandem array and a C-terminal glutathione SH-transferase (GST) domain []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2RPR_A.
Probab=87.77 E-value=0.85 Score=35.12 Aligned_cols=46 Identities=20% Similarity=0.480 Sum_probs=25.2
Q ss_pred cCeeEEEeecCCeEEEEEeecC---CCCeEEEEEEcCCcceEEEEecCCcccc
Q 004519 204 HGFAYRYKKNDSHRVTVKCKCQ---GCPWRIYASRLSTTQLVCIKKMNSKHTC 253 (747)
Q Consensus 204 ~~f~~~~~rs~~~r~~~~C~~~---gC~w~i~a~~~~~~~~~~V~~~~~~Htc 253 (747)
.|+.|...+.......+.|... +|+++|... .+ .-.|.....+|||
T Consensus 14 ~Gy~y~~~~~~~~~~~WrC~~~~~~~C~a~~~~~--~~--~~~~~~~~~~HnH 62 (62)
T PF04500_consen 14 DGYRYYFNKRNDGKTYWRCSRRRSHGCRARLITD--AG--DGRVVRTNGEHNH 62 (62)
T ss_dssp TTEEEEEEEE-SS-EEEEEGGGTTS----EEEEE------TTEEEE-S---SS
T ss_pred CCeEEECcCCCCCcEEEEeCCCCCCCCeEEEEEE--CC--CCEEEECCCccCC
Confidence 5777887777788899999864 899999988 22 2345555578887
No 40
>cd06399 PB1_P40 The PB1 domain is essential part of the p40 adaptor protein which plays an important role in activating phagocyte NADPH oxidase during phagocytosis. The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes , such as osteoclastogenesis, angiogenesis, early cardiovascular development and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The PB1 domain of p40 represents a type I PB1 domain which interacts with the PB1 domain of oxidase activator p67 w
Probab=86.69 E-value=2.2 Score=34.91 Aligned_cols=59 Identities=15% Similarity=0.239 Sum_probs=46.4
Q ss_pred CceeEEEecCCC----ChhhHHHHHHHHhcCCCCceEEEEEecCCCCcceeeeCcHHHHHHHhhccC
Q 004519 31 GEAYAIDIDEET----EFSGFKSEVAEMFNCSADTMSIKYFLPGNKKTLISISKDKDFKRMLNFLGD 93 (747)
Q Consensus 31 g~~~~~~v~~~~----s~~~~~~~l~~~~~~~~~~~~~~y~lp~~~~~l~~v~~D~dl~~m~~~~~~ 93 (747)
-.++-|.|..++ +|.+|+.-+...|. .+.+.+-|.=+..+ ||.|-+|+|+.-|+.....
T Consensus 13 ~~~rdi~vee~l~~~P~~kdLl~lmr~~f~--~~dIaLNYrD~EGD--LIRllddeDv~LMV~~~r~ 75 (92)
T cd06399 13 STIRDIAVEEDLSSTPLLKDLLELTRREFQ--REDIALNYRDAEGD--LIRLLSDEDVALMVRQSRG 75 (92)
T ss_pred ccccceEeecccccCccHHHHHHHHHHHhc--hhheeeeeecCCCC--EEEEcchhhHHHHHHHHhc
Confidence 455666666543 78999999999997 45899999965543 9999999999999987644
No 41
>smart00774 WRKY DNA binding domain. The WRKY domain is a DNA binding domain found in one or two copies in a superfamily of plant transcription factors. These transcription factors are involved in the regulation of various physiological programs that are unique to plants, including pathogen defense, senescence and trichome development. The domain is a 60 amino acid region that is defined by the conserved amino acid sequence WRKYGQK at its N-terminal end, together with a novel zinc-finger-like motif. It binds specifically to the DNA sequence motif (T)(T)TGAC(C/T), which is known as the W box. The invariant TGAC core is essential for function and WRKY binding.
Probab=85.89 E-value=0.96 Score=34.63 Aligned_cols=38 Identities=26% Similarity=0.412 Sum_probs=31.8
Q ss_pred eEEEEEeec-CCCCeEEEEEEcCCcceEEEEecCCcccc
Q 004519 216 HRVTVKCKC-QGCPWRIYASRLSTTQLVCIKKMNSKHTC 253 (747)
Q Consensus 216 ~r~~~~C~~-~gC~w~i~a~~~~~~~~~~V~~~~~~Htc 253 (747)
.|-.++|+. .||+++=.+.+..+++...+.++.++|||
T Consensus 21 pRsYYrCt~~~~C~a~K~Vq~~~~d~~~~~vtY~g~H~h 59 (59)
T smart00774 21 PRSYYRCTYSQGCPAKKQVQRSDDDPSVVEVTYEGEHTH 59 (59)
T ss_pred cceEEeccccCCCCCcccEEEECCCCCEEEEEEeeEeCC
Confidence 466789998 89999888887766667788899999997
No 42
>PF13565 HTH_32: Homeodomain-like domain
Probab=83.37 E-value=2.7 Score=34.05 Aligned_cols=41 Identities=24% Similarity=0.503 Sum_probs=34.3
Q ss_pred hHHHHHHHHhhhCCCCChHHHHHHHHHHhCCcc--CHHHHHHH
Q 004519 268 WVGNIIKEKLKASPNYKPKDIADDIKREYGIQL--NYSQAWRA 308 (747)
Q Consensus 268 ~i~~~~~~~~~~~~~~~~~~i~~~i~~~~g~~~--~~~~~~r~ 308 (747)
.+...+.+.+..+|.+++.+|++.|.+++|+.+ |.+++||.
T Consensus 34 e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~~~S~~tv~R~ 76 (77)
T PF13565_consen 34 EQRERIIALIEEHPRWTPREIAEYLEEEFGISVRVSRSTVYRI 76 (77)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCCccHhHHHHh
Confidence 344566677778999999999999999999876 99999874
No 43
>PF00665 rve: Integrase core domain; InterPro: IPR001584 Integrase comprises three domains capable of folding independently and whose three-dimensional structures are known. However, the manner in which the N-terminal, catalytic, and C-terminal domains interact in the holoenzyme remains obscure. Numerous studies indicate that the enzyme functions as a multimer, minimally a dimer. The integrase proteins from Human immunodeficiency virus 1 (HIV-1) and Avian sarcoma virus (ASV) have been studied most carefully with respect to the structural basis of catalysis. Although the active site of ASV integrase does not undergo significant conformational changes on binding the required metal cofactor, that of HIV-1 does. This active site-mediated conformational change in HIV-1 reorganises the catalytic core and C-terminal domains and appears to promote an interaction that is favourable for catalysis []. Retroviral integrase is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. The presence of retrovirus integrase-related gene sequences in eukaryotes is known. Bacterial transposases involved in the transposition of the insertion sequence also belong to this group. HIV integrase catalyses the incorporation of virally derived DNA into the human genome. This unique step in the virus life cycle provides a variety of points for intervention and hence is an attractive target for the development of new therapeutics for the treatment of AIDS []. Substrate recognition by the retroviral integrase enzyme is critical for retroviral integration. To catalyse this recombination event, integrase must recognise and act on two types of substrates, viral DNA and host DNA, yet the necessary interactions exhibit markedly different degrees of specificity [].; GO: 0015074 DNA integration; PDB: 3AO3_A 3OVN_A 3AO5_A 3AO4_A 3AO1_A 1C6V_D 3HPG_A 3HPH_A 3OYD_A 3OYF_B ....
Probab=81.78 E-value=3.6 Score=36.33 Aligned_cols=76 Identities=17% Similarity=0.113 Sum_probs=56.2
Q ss_pred ccEEEEeccccC-CcccceEEEEEEecCCCCeEEEEEEEeecCCcccHHHHHHHHHhhcCCCCcEEEEecCcchhHHH
Q 004519 372 RPLLFLDTTPLN-SKYQGTLLTATSADGDDGIFPVAFAVVDAETEDNWHWFLQELKSAVSTSQQITFIADFQNGLNKS 448 (747)
Q Consensus 372 ~~vl~iD~t~~~-~~y~~~l~~a~g~d~~~~~~pla~a~v~~E~~e~~~wfl~~l~~~~~~~~~~~iisD~~~~l~~A 448 (747)
...+.+|.++.. ...++..+..+.+|..-+ +.+++.+-..++.+.+..+|+......+...|.+|+||+.....+.
T Consensus 6 ~~~~~~D~~~~~~~~~~~~~~~~~~iD~~S~-~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~p~~i~tD~g~~f~~~ 82 (120)
T PF00665_consen 6 GERWQIDFTPMPIPDKGGRVYLLVFIDDYSR-FIYAFPVSSKETAEAALRALKRAIEKRGGRPPRVIRTDNGSEFTSH 82 (120)
T ss_dssp TTEEEEEEEEETGGCTT-CEEEEEEEETTTT-EEEEEEESSSSHHHHHHHHHHHHHHHHS-SE-SEEEEESCHHHHSH
T ss_pred CCEEEEeeEEEecCCCCccEEEEEEEECCCC-cEEEEEeecccccccccccccccccccccccceecccccccccccc
Confidence 458899999765 345568889999997655 5567777777788888888887777766555999999999877643
No 44
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=81.77 E-value=0.59 Score=34.45 Aligned_cols=19 Identities=32% Similarity=0.800 Sum_probs=17.3
Q ss_pred eeecCCCCCCCcCcCCCCC
Q 004519 728 SLQCSKCKGLGHNKKTCKD 746 (747)
Q Consensus 728 ~~~Cs~C~~~GHn~~tC~~ 746 (747)
...|++|+..||+.+.||.
T Consensus 31 p~~C~~C~~~gH~~~~C~k 49 (49)
T PF14392_consen 31 PRFCFHCGRIGHSDKECPK 49 (49)
T ss_pred ChhhcCCCCcCcCHhHcCC
Confidence 4789999999999999985
No 45
>smart00343 ZnF_C2HC zinc finger.
Probab=80.12 E-value=0.86 Score=28.49 Aligned_cols=16 Identities=31% Similarity=0.862 Sum_probs=14.8
Q ss_pred ecCCCCCCCcCcCCCC
Q 004519 730 QCSKCKGLGHNKKTCK 745 (747)
Q Consensus 730 ~Cs~C~~~GHn~~tC~ 745 (747)
+|.+|++.||..+.||
T Consensus 1 ~C~~CG~~GH~~~~C~ 16 (26)
T smart00343 1 KCYNCGKEGHIARDCP 16 (26)
T ss_pred CCccCCCCCcchhhCC
Confidence 4899999999999998
No 46
>cd01799 Hoil1_N Ubiquitin-like domain of HOIL1. HOIL1_N HOIL-1 (heme-oxidized IRP2 ubiquitin ligase-1) is an E3 ubiquitin-protein ligase that recognizes heme-oxidized IRP2 (iron regulatory protein2) and is thought to affect the turnover of oxidatively damaged proteins. Hoil-1 has an amino-terminal ubiquitin-like domain as well as an RBR signature consisting of two RING finger domains separated by an IBR/DRIL domain.
Probab=76.57 E-value=7.5 Score=31.53 Aligned_cols=38 Identities=5% Similarity=0.040 Sum_probs=34.2
Q ss_pred ecCceeEEEecCCCChhhHHHHHHHHhcCCCCceEEEEE
Q 004519 29 NGGEAYAIDIDEETEFSGFKSEVAEMFNCSADTMSIKYF 67 (747)
Q Consensus 29 ~gg~~~~~~v~~~~s~~~~~~~l~~~~~~~~~~~~~~y~ 67 (747)
.+|.+..+.|+.+++-.+++.+|.+..++..++.++ |.
T Consensus 10 ~~~~t~~l~v~~~~TV~~lK~kI~~~~gip~~~QrL-~~ 47 (75)
T cd01799 10 SHTVTIWLTVRPDMTVAQLKDKVFLDYGFPPAVQRW-VI 47 (75)
T ss_pred cCCCeEEEEECCCCcHHHHHHHHHHHHCcCHHHEEE-Ec
Confidence 357888899999999999999999999999988888 64
No 47
>PRK14702 insertion element IS2 transposase InsD; Provisional
Probab=76.03 E-value=51 Score=33.98 Aligned_cols=143 Identities=13% Similarity=0.078 Sum_probs=86.5
Q ss_pred chhHHHHHHHHhhhCCCCChHHHHHHHHHH---hCC-ccCHHHHHHHHHHH-HHHHhcCHHHHhccHHHHHHHHHHhCCC
Q 004519 266 RGWVGNIIKEKLKASPNYKPKDIADDIKRE---YGI-QLNYSQAWRAKEIA-REQLQGSYKDSYTLLPFFCEKIKETNPG 340 (747)
Q Consensus 266 ~~~i~~~~~~~~~~~~~~~~~~i~~~i~~~---~g~-~~~~~~~~r~k~~~-~~~~~g~~~~~~~~L~~~~~~l~~~npg 340 (747)
...+...|.+....++.+..+.|...|+++ .|+ .++..+++|....+ +..... ...+.
T Consensus 10 ~~~l~~~I~~~~~~~~~yG~rri~~~L~~~~~~~g~~~v~~krV~rlmr~~gL~~~~r-----------------~~~~~ 72 (262)
T PRK14702 10 DTDVLLRIHHVIGELPTYGYRRVWALLRRQAELDGMPAINAKRVYRLMRQNALLLERK-----------------PAVPP 72 (262)
T ss_pred hHHHHHHHHHHHHhCcccChHHHHHHHHhhhcccCccccCHHHHHHHHHHhCCccccC-----------------CCCCC
Confidence 344556667666778899999999999876 377 48998888854321 110000 00000
Q ss_pred CEEEEEecCCCceeEEEeehhchHHHHhhcCccEEEEeccccCCcccceEEEEEEecCCCCeEEEEEEEeec-CCcccHH
Q 004519 341 SVVTFTTKEDSSFHRLFVSFHASISGFQQGCRPLLFLDTTPLNSKYQGTLLTATSADGDDGIFPVAFAVVDA-ETEDNWH 419 (747)
Q Consensus 341 ~~~~~~~~~~~~f~~lf~~~~~~~~~f~~~~~~vl~iD~t~~~~~y~~~l~~a~g~d~~~~~~pla~a~v~~-E~~e~~~ 419 (747)
+. .+.... |. ...-..++..|-||.....++.++.++.+|...+ .+||+++-.. .+.+.-.
T Consensus 73 ~~-------~~~~~~-~~---------~~~pn~~W~~DiT~~~~~~g~~~Yl~~viD~~sR-~ivg~~is~~~~~~~~v~ 134 (262)
T PRK14702 73 SK-------RAHTGR-VA---------VKESNQRWCSDGFEFCCDNGERLRVTFALDCCDR-EALHWAVTTGGFNSETVQ 134 (262)
T ss_pred CC-------cCCCCc-cc---------cCCCCCEEEeeeEEEEecCCcEEEEEEEEecccc-eeeeEEeccCcCCHHHHH
Confidence 00 000000 10 1112358999999976544557888888997665 7899999874 5666666
Q ss_pred HHHHHHHhh-cC---CCCcEEEEecCcc
Q 004519 420 WFLQELKSA-VS---TSQQITFIADFQN 443 (747)
Q Consensus 420 wfl~~l~~~-~~---~~~~~~iisD~~~ 443 (747)
-+|+...+. .+ ...|.+|.||+..
T Consensus 135 ~~l~~A~~~~~~~~~~~~~~iihSD~Gs 162 (262)
T PRK14702 135 DVMLGAVERRFGNDLPSSPVEWLTDNGS 162 (262)
T ss_pred HHHHHHHHHHhcccCCCCCeEEEcCCCc
Confidence 666644333 22 2357899999976
No 48
>PF02178 AT_hook: AT hook motif; InterPro: IPR017956 AT hooks are DNA-binding motifs with a preference for A/T rich regions. These motifs are found in a variety of proteins, including the high mobility group (HMG) proteins [], in DNA-binding proteins from plants [] and in hBRG1 protein, a central ATPase of the human switching/sucrose non-fermenting (SWI/SNF) remodeling complex []. High mobility group (HMG) proteins are a family of relatively low molecular weight non-histone components in chromatin []. HMG-I and HMG-Y (HMGA) are proteins of about 100 amino acid residues which are produced by the alternative splicing of a single gene. HMG-I/Y proteins bind preferentially to the minor groove of AT-rich regions in double-stranded DNA in a non-sequence specific manner [, ]. It is suggested that these proteins could function in nucleosome phasing and in the 3' end processing of mRNA transcripts. They are also involved in the transcription regulation of genes containing, or in close proximity to, AT-rich regions. ; GO: 0003677 DNA binding; PDB: 2EZE_A 2EZD_A 2EZF_A 2EZG_A.
Probab=74.95 E-value=1.4 Score=22.79 Aligned_cols=9 Identities=44% Similarity=0.896 Sum_probs=3.5
Q ss_pred CCCCCCCCC
Q 004519 709 RPPGRPKMK 717 (747)
Q Consensus 709 r~~GRPkk~ 717 (747)
|++|||++.
T Consensus 2 r~RGRP~k~ 10 (13)
T PF02178_consen 2 RKRGRPRKN 10 (13)
T ss_dssp --SS--TT-
T ss_pred CcCCCCccc
Confidence 678999885
No 49
>cd01794 DC_UbP_C dendritic cell derived ubiquitin-like protein. DC_UbP (dendritic cell derived ubiquitin-like protein) is a ubiquitin-like protein from human dendritic cells that is expressed in the mitochondrion. The ubiquitin-like domain of this protein is found at the C-terminus and lacks the canonical gly-gly motif of ubiquitin required for ubiquitinization. DC_UbP is expressed in tumor cells but not in normal human adult tissue suggesting a role for DC_UbP in tumorogenesis.
Probab=73.90 E-value=12 Score=29.77 Aligned_cols=42 Identities=5% Similarity=0.102 Sum_probs=37.8
Q ss_pred EEEecCceeEEEecCCCChhhHHHHHHHHhcCCCCceEEEEE
Q 004519 26 LSYNGGEAYAIDIDEETEFSGFKSEVAEMFNCSADTMSIKYF 67 (747)
Q Consensus 26 ~~Y~gg~~~~~~v~~~~s~~~~~~~l~~~~~~~~~~~~~~y~ 67 (747)
++..+|++..+.|+.+.|-.++..+|.+..++...+.++.|-
T Consensus 3 vk~~~G~~~~l~v~~~~TV~~lK~~I~~~~gi~~~~q~Li~~ 44 (70)
T cd01794 3 VRLSTGKDVKLSVSSKDTVGQLKKQLQAAEGVDPCCQRWFFS 44 (70)
T ss_pred EEcCCCCEEEEEECCcChHHHHHHHHHHHhCCCHHHeEEEEC
Confidence 567789999999999999999999999999998888888775
No 50
>PF04937 DUF659: Protein of unknown function (DUF 659); InterPro: IPR007021 These are transposase-like proteins with no known function.
Probab=73.83 E-value=31 Score=32.35 Aligned_cols=99 Identities=15% Similarity=0.236 Sum_probs=64.9
Q ss_pred EEEeccccCCcccceEEEEEEecCCCCeEEEEEEEee-cCCcccHHHHHHHHHhhcCCCCcEEEEecCcchhHHH---Hh
Q 004519 375 LFLDTTPLNSKYQGTLLTATSADGDDGIFPVAFAVVD-AETEDNWHWFLQELKSAVSTSQQITFIADFQNGLNKS---LA 450 (747)
Q Consensus 375 l~iD~t~~~~~y~~~l~~a~g~d~~~~~~pla~a~v~-~E~~e~~~wfl~~l~~~~~~~~~~~iisD~~~~l~~A---i~ 450 (747)
|..||= ++..+.+|+.+...-+.|-.|.=..-.-+ ..+.+...-+|+...+.+|..+..-||||....+.+| +.
T Consensus 36 i~~DgW--td~~~~~lInf~v~~~~g~~Flksvd~s~~~~~a~~l~~ll~~vIeeVG~~nVvqVVTDn~~~~~~a~~~L~ 113 (153)
T PF04937_consen 36 IMSDGW--TDRKGRSLINFMVYCPEGTVFLKSVDASSIIKTAEYLFELLDEVIEEVGEENVVQVVTDNASNMKKAGKLLM 113 (153)
T ss_pred EEEecC--cCCCCCeEEEEEEEcccccEEEEEEecccccccHHHHHHHHHHHHHHhhhhhhhHHhccCchhHHHHHHHHH
Confidence 444443 23334455555555555554433322222 2455666677777777778777788999999988888 45
Q ss_pred hhccCccchhhHHHHHHHHHhhhcc
Q 004519 451 EVFDNCYHSYCLRHLAEKLNRDIKG 475 (747)
Q Consensus 451 ~vfP~a~h~~C~~Hi~~n~~~~~~~ 475 (747)
+-+|.....-|..|-+.-+.+.+.+
T Consensus 114 ~k~p~ifw~~CaaH~inLmledi~k 138 (153)
T PF04937_consen 114 EKYPHIFWTPCAAHCINLMLEDIGK 138 (153)
T ss_pred hcCCCEEEechHHHHHHHHHHHHhc
Confidence 5689999999999999888777654
No 51
>PF14560 Ubiquitin_2: Ubiquitin-like domain; PDB: 1WJN_A 2KJ6_A 2KJR_A 1V6E_A 1T0Y_A.
Probab=72.65 E-value=10 Score=31.66 Aligned_cols=47 Identities=6% Similarity=0.133 Sum_probs=34.9
Q ss_pred eeEEEecCCCChhhHHHHHHHHhcCCCCceEEEEEecCCCCcceeee
Q 004519 33 AYAIDIDEETEFSGFKSEVAEMFNCSADTMSIKYFLPGNKKTLISIS 79 (747)
Q Consensus 33 ~~~~~v~~~~s~~~~~~~l~~~~~~~~~~~~~~y~lp~~~~~l~~v~ 79 (747)
..-..++.+|+..+|..+|+.++|++...+++.|.-..++..+..+.
T Consensus 15 ~~ekr~~~~~Tv~eLK~kl~~~~Gi~~~~m~L~l~~~~~~~~~~~~~ 61 (87)
T PF14560_consen 15 SVEKRFPKSITVSELKQKLEKLTGIPPSDMRLQLKSDKDDSKIEELD 61 (87)
T ss_dssp EEEEEEETTSBHHHHHHHHHHHHTS-TTTEEEEEE-TSSSSEEEESS
T ss_pred eEEEEcCCCCCHHHHHHHHHHHhCCCcccEEEEEEecCCCccccccC
Confidence 34478889999999999999999999999999886333333344443
No 52
>COG5431 Uncharacterized metal-binding protein [Function unknown]
Probab=69.47 E-value=7 Score=33.18 Aligned_cols=45 Identities=29% Similarity=0.557 Sum_probs=28.8
Q ss_pred ceeEEEeCcCceeecCCcc----c-CCCCcchHHHHHHHhcCCcccccccch
Q 004519 622 ESADIVDVDRWDCTCKTWH----L-TGLPCCHAIAVLEWIGRSPYDYCSKYF 668 (747)
Q Consensus 622 ~~~~~V~l~~~~CtC~~~~----~-~giPC~Halav~~~~~~~p~~yi~~~~ 668 (747)
++.|+++.+ -|||..+- . -.-||.|++++-...-..-.+||+-++
T Consensus 42 ~rdYIl~~g--fCSCp~~~~svvl~Gk~~C~Hi~glk~A~~~gk~~~I~~y~ 91 (117)
T COG5431 42 ERDYILEGG--FCSCPDFLGSVVLKGKSPCAHIIGLKVAKITGKYDYIDAYY 91 (117)
T ss_pred ccceEEEcC--cccCHHHHhHhhhcCcccchhhhheeeeeecCcEEEEEEec
Confidence 457888877 89999876 2 234899998864333223445555443
No 53
>cd01812 BAG1_N Ubiquitin-like domain of BAG1. BAG1_N N-terminal ubiquitin-like (Ubl) domain of the BAG1 protein. This domain occurs together with the BAG domain and is closely related to the Ubl domain of a family of deubiquitinases that includes Rpn11, UBP6 (USP14), USP7 (HAUSP).
Probab=69.17 E-value=9.1 Score=30.29 Aligned_cols=41 Identities=15% Similarity=0.288 Sum_probs=35.8
Q ss_pred EEEecCceeEEEecCCCChhhHHHHHHHHhcCCCCceEEEEE
Q 004519 26 LSYNGGEAYAIDIDEETEFSGFKSEVAEMFNCSADTMSIKYF 67 (747)
Q Consensus 26 ~~Y~gg~~~~~~v~~~~s~~~~~~~l~~~~~~~~~~~~~~y~ 67 (747)
+.+. |++..+.|+.+.+..+|.++|.+..++..+..++.|.
T Consensus 5 vk~~-g~~~~i~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~ 45 (71)
T cd01812 5 VKHG-GESHDLSISSQATFGDLKKMLAPVTGVEPRDQKLIFK 45 (71)
T ss_pred EEEC-CEEEEEEECCCCcHHHHHHHHHHhhCCChHHeEEeeC
Confidence 4564 8888899999999999999999999998888888775
No 54
>cd01796 DDI1_N DNA damage inducible protein 1 ubiquitin-like domain. DDI1_N DDI1 (DNA damage inducible protein 1) has an amino-terminal ubiquitin-like domain, an retroviral protease-like (RVP-like) domain, and a UBA (ubiquitin-associated) domain. This CD represents the amino-terminal ubiquitin-like domain of DDI1.
Probab=67.89 E-value=9.2 Score=30.55 Aligned_cols=38 Identities=18% Similarity=0.349 Sum_probs=35.3
Q ss_pred cCceeEEEecCCCChhhHHHHHHHHhcCCCCceEEEEE
Q 004519 30 GGEAYAIDIDEETEFSGFKSEVAEMFNCSADTMSIKYF 67 (747)
Q Consensus 30 gg~~~~~~v~~~~s~~~~~~~l~~~~~~~~~~~~~~y~ 67 (747)
+|++..+.|+.+++..+|+.+|.+..|+..++.++.|-
T Consensus 8 ~g~~~~l~v~~~~TV~~lK~~I~~~~gip~~~q~Li~~ 45 (71)
T cd01796 8 SETTFSLDVDPDLELENFKALCEAESGIPASQQQLIYN 45 (71)
T ss_pred CCCEEEEEECCcCCHHHHHHHHHHHhCCCHHHeEEEEC
Confidence 79999999999999999999999999998888888875
No 55
>PRK09409 IS2 transposase TnpB; Reviewed
Probab=67.32 E-value=88 Score=32.97 Aligned_cols=142 Identities=14% Similarity=0.102 Sum_probs=85.8
Q ss_pred hHHHHHHHHhhhCCCCChHHHHHHHHHHh---CC-ccCHHHHHHHHHHH-HHHHhcCHHHHhccHHHHHHHHHHhCCCCE
Q 004519 268 WVGNIIKEKLKASPNYKPKDIADDIKREY---GI-QLNYSQAWRAKEIA-REQLQGSYKDSYTLLPFFCEKIKETNPGSV 342 (747)
Q Consensus 268 ~i~~~~~~~~~~~~~~~~~~i~~~i~~~~---g~-~~~~~~~~r~k~~~-~~~~~g~~~~~~~~L~~~~~~l~~~npg~~ 342 (747)
.+...|.+.....+.+..+.|...|+++. |+ .++..+++|..+.+ +.... ....+.+.
T Consensus 51 ~l~~~I~~i~~~~~~yG~Rri~~~L~~~g~~~g~~~v~~k~V~RlMr~~Gl~~~~-----------------~~~~~~~~ 113 (301)
T PRK09409 51 DVLLRIHHVIGELPTYGYRRVWALLRRQAELDGMPAINAKRVYRIMRQNALLLER-----------------KPAVPPSK 113 (301)
T ss_pred HHHHHHHHHHHhCccCCHHHHHHHHHhhhcccCccccCHHHHHHHHHHcCCcccc-----------------cCCCCCCC
Confidence 34555666666788999999999998762 66 58888888753321 11000 00000000
Q ss_pred EEEEecCCCceeEEEeehhchHHHHhhcCccEEEEeccccCCcccceEEEEEEecCCCCeEEEEEEEeec-CCcccHHHH
Q 004519 343 VTFTTKEDSSFHRLFVSFHASISGFQQGCRPLLFLDTTPLNSKYQGTLLTATSADGDDGIFPVAFAVVDA-ETEDNWHWF 421 (747)
Q Consensus 343 ~~~~~~~~~~f~~lf~~~~~~~~~f~~~~~~vl~iD~t~~~~~y~~~l~~a~g~d~~~~~~pla~a~v~~-E~~e~~~wf 421 (747)
..+... |. ...-..+++.|-||....-++.++.++.+|...+ .+||+++... .+.+.-.-+
T Consensus 114 -------~~~~~~-~~---------~~~pN~~W~tDiT~~~~~~g~~~Yl~~ViD~~sR-~ivg~~~s~~~~~~~~v~~~ 175 (301)
T PRK09409 114 -------RAHTGR-VA---------VKESNQRWCSDGFEFCCDNGERLRVTFALDCCDR-EALHWAVTTGGFNSETVQDV 175 (301)
T ss_pred -------CCCCCC-cC---------CCCCCCEEEeeeEEEEeCCCCEEEEEEEeecccc-eEEEEEeccCCCCHHHHHHH
Confidence 000000 10 1113459999999976544557888888998776 7899999876 566666666
Q ss_pred HHH-HHhhcC---CCCcEEEEecCcch
Q 004519 422 LQE-LKSAVS---TSQQITFIADFQNG 444 (747)
Q Consensus 422 l~~-l~~~~~---~~~~~~iisD~~~~ 444 (747)
|+. +....+ ...|.+|.||+...
T Consensus 176 l~~a~~~~~~~~~~~~~~iihSDrGsq 202 (301)
T PRK09409 176 MLGAVERRFGNDLPSSPVEWLTDNGSC 202 (301)
T ss_pred HHHHHHHHhccCCCCCCcEEecCCCcc
Confidence 664 333333 23478999999763
No 56
>cd01807 GDX_N ubiquitin-like domain of GDX. GDX contains an N-terminal ubiquitin-like domain as well as an uncharacterized c-terminal domain. The function of GDX is unknown.
Probab=66.60 E-value=12 Score=30.03 Aligned_cols=42 Identities=17% Similarity=0.306 Sum_probs=37.0
Q ss_pred EEEecCceeEEEecCCCChhhHHHHHHHHhcCCCCceEEEEE
Q 004519 26 LSYNGGEAYAIDIDEETEFSGFKSEVAEMFNCSADTMSIKYF 67 (747)
Q Consensus 26 ~~Y~gg~~~~~~v~~~~s~~~~~~~l~~~~~~~~~~~~~~y~ 67 (747)
++..+|++..+.|+.+.+..++.+.|++..|+..++.++-|.
T Consensus 5 vk~~~G~~~~l~v~~~~tV~~lK~~i~~~~gi~~~~q~L~~~ 46 (74)
T cd01807 5 VKLLQGRECSLQVSEKESVSTLKKLVSEHLNVPEEQQRLLFK 46 (74)
T ss_pred EEeCCCCEEEEEECCCCcHHHHHHHHHHHHCCCHHHeEEEEC
Confidence 456678888899999999999999999999998888888765
No 57
>smart00384 AT_hook DNA binding domain with preference for A/T rich regions. Small DNA-binding motif first described in the high mobility group non-histone chromosomal protein HMG-I(Y).
Probab=66.52 E-value=3.7 Score=25.41 Aligned_cols=12 Identities=33% Similarity=0.692 Sum_probs=9.6
Q ss_pred CCCCCCCCCCCC
Q 004519 708 RRPPGRPKMKQP 719 (747)
Q Consensus 708 ~r~~GRPkk~r~ 719 (747)
.|++|||+|...
T Consensus 1 kRkRGRPrK~~~ 12 (26)
T smart00384 1 KRKRGRPRKAPK 12 (26)
T ss_pred CCCCCCCCCCCC
Confidence 478999999754
No 58
>PF11976 Rad60-SLD: Ubiquitin-2 like Rad60 SUMO-like; InterPro: IPR022617 This entry includes small ubiquitin-related modifier (SUMO) proteins. SUMOs are small proteins that are covalently attached to lysines as post-translational modifications and are used to control multiple cellular process including signal transduction, nuclear transport and DNA replication and repair []. Unlike ubiquitin, they are not involved in protein degradation. This entry also contains the C-terminal Rad60 DNA repair protein SUMO-like domain.; PDB: 3RD2_A 2JXX_A 3RCZ_A 3GOE_A 3A4S_D 3A4R_B 2IO1_D 1U4A_A 2K1F_A 1WZ0_A ....
Probab=65.34 E-value=17 Score=28.80 Aligned_cols=42 Identities=10% Similarity=0.182 Sum_probs=36.7
Q ss_pred EEEecCceeEEEecCCCChhhHHHHHHHHhcCCC-CceEEEEE
Q 004519 26 LSYNGGEAYAIDIDEETEFSGFKSEVAEMFNCSA-DTMSIKYF 67 (747)
Q Consensus 26 ~~Y~gg~~~~~~v~~~~s~~~~~~~l~~~~~~~~-~~~~~~y~ 67 (747)
|.-.+|+...+.|.++.++..++++.++..+++. ++++|.|-
T Consensus 5 v~~~~~~~~~~~v~~~~~~~~l~~~~~~~~~i~~~~~~~l~fd 47 (72)
T PF11976_consen 5 VRSQDGKEIKFKVKPTTTVSKLIEKYCEKKGIPPEESIRLIFD 47 (72)
T ss_dssp EEETTSEEEEEEEETTSCCHHHHHHHHHHHTTTT-TTEEEEET
T ss_pred EEeCCCCEEEEEECCCCcHHHHHHHHHHhhCCCccceEEEEEC
Confidence 4556788888999999999999999999999988 78888875
No 59
>cd01809 Scythe_N Ubiquitin-like domain of Scythe protein. Scythe protein (also known as Bat3) is an apoptotic regulator that is highly conserved in eukaryotes and contains a ubiquitin-like domain near its N-terminus. Scythe binds reaper, a potent apoptotic inducer, and Scythe/Reaper are thought to signal apoptosis, in part through regulating the folding and activity of apoptotic signaling molecules.
Probab=64.03 E-value=16 Score=28.89 Aligned_cols=42 Identities=14% Similarity=0.243 Sum_probs=36.1
Q ss_pred EEEecCceeEEEecCCCChhhHHHHHHHHhcCCCCceEEEEE
Q 004519 26 LSYNGGEAYAIDIDEETEFSGFKSEVAEMFNCSADTMSIKYF 67 (747)
Q Consensus 26 ~~Y~gg~~~~~~v~~~~s~~~~~~~l~~~~~~~~~~~~~~y~ 67 (747)
+....|++..+.++.+.+..+|.++|.+..++..+..++.|.
T Consensus 5 vk~~~g~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~ 46 (72)
T cd01809 5 VKTLDSQTHTFTVEEEITVLDLKEKIAEEVGIPVEQQRLIYS 46 (72)
T ss_pred EEeCCCCEEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEEEC
Confidence 345567888899999999999999999999998888888873
No 60
>cd01803 Ubiquitin Ubiquitin. Ubiquitin (includes Ubq/RPL40e and Ubq/RPS27a fusions as well as homopolymeric multiubiquitin protein chains)
Probab=62.05 E-value=15 Score=29.35 Aligned_cols=41 Identities=7% Similarity=0.228 Sum_probs=35.4
Q ss_pred EEecCceeEEEecCCCChhhHHHHHHHHhcCCCCceEEEEE
Q 004519 27 SYNGGEAYAIDIDEETEFSGFKSEVAEMFNCSADTMSIKYF 67 (747)
Q Consensus 27 ~Y~gg~~~~~~v~~~~s~~~~~~~l~~~~~~~~~~~~~~y~ 67 (747)
+..+|++..+.|+.+.+-.+|..+|.+..++..+.+++.|-
T Consensus 6 ~~~~g~~~~~~v~~~~tV~~lK~~i~~~~g~~~~~q~L~~~ 46 (76)
T cd01803 6 KTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFA 46 (76)
T ss_pred EcCCCCEEEEEECCcCcHHHHHHHHHHHhCCCHHHeEEEEC
Confidence 44567888899999999999999999999998888888863
No 61
>cd01798 parkin_N amino-terminal ubiquitin-like of parkin protein. parkin_N parkin protein is a RING-type E3 ubiquitin ligase with an amino-terminal ubiquitin-like (Ubl) domain and an RBR signature consisting of two RING finger domains separated by an IBR/DRIL domain. Naturally occurring mutations in parkin are thought to cause the disease AR_JP (autosomal-recessive juvenile parkinsonism). Parkin binds the Rpn10 subunit of 26S proteasomes through its Ubl domain.
Probab=61.94 E-value=16 Score=28.96 Aligned_cols=41 Identities=20% Similarity=0.433 Sum_probs=36.3
Q ss_pred EEecCceeEEEecCCCChhhHHHHHHHHhcCCCCceEEEEE
Q 004519 27 SYNGGEAYAIDIDEETEFSGFKSEVAEMFNCSADTMSIKYF 67 (747)
Q Consensus 27 ~Y~gg~~~~~~v~~~~s~~~~~~~l~~~~~~~~~~~~~~y~ 67 (747)
...+|++..+.|+.+.+..++.+.|++..|++.++.++.|-
T Consensus 4 k~~~g~~~~~~v~~~~tV~~lK~~i~~~~gi~~~~q~Li~~ 44 (70)
T cd01798 4 RTNTGHTFPVEVDPDTDIKQLKEVVAKRQGVPPDQLRVIFA 44 (70)
T ss_pred EcCCCCEEEEEECCCChHHHHHHHHHHHHCCCHHHeEEEEC
Confidence 44578888899999999999999999999998888888765
No 62
>cd00196 UBQ Ubiquitin-like proteins. Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate.
Probab=61.17 E-value=18 Score=26.60 Aligned_cols=43 Identities=12% Similarity=0.182 Sum_probs=35.7
Q ss_pred EEEecCceeEEEecCCCChhhHHHHHHHHhcCCCCceEEEEEe
Q 004519 26 LSYNGGEAYAIDIDEETEFSGFKSEVAEMFNCSADTMSIKYFL 68 (747)
Q Consensus 26 ~~Y~gg~~~~~~v~~~~s~~~~~~~l~~~~~~~~~~~~~~y~l 68 (747)
+.+.+|....+.+..+.+..++++++++.++.+.+.+.+.+..
T Consensus 2 v~~~~~~~~~~~~~~~~tv~~l~~~i~~~~~~~~~~~~l~~~~ 44 (69)
T cd00196 2 VKLNDGKTVELLVPSGTTVADLKEKLAKKLGLPPEQQRLLVNG 44 (69)
T ss_pred eEecCCCEEEEEcCCCCcHHHHHHHHHHHHCcChHHeEEEECC
Confidence 3455788889999999999999999999998777777776654
No 63
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=60.01 E-value=8.8 Score=29.26 Aligned_cols=43 Identities=12% Similarity=0.324 Sum_probs=25.5
Q ss_pred CCCCCCCCCCCCCCCCccccccceeecCCCCCCCcCcCCCCCC
Q 004519 705 PPTRRPPGRPKMKQPESAEIIKRSLQCSKCKGLGHNKKTCKDS 747 (747)
Q Consensus 705 P~~~r~~GRPkk~r~~~~~~~kr~~~Cs~C~~~GHn~~tC~~~ 747 (747)
|..+..+.|..++|..-.........|+.||..-=.=+-||.|
T Consensus 4 PKrk~S~srr~~RRsh~~l~~~~l~~C~~CG~~~~~H~vC~~C 46 (57)
T PRK12286 4 PKRKTSKSRKRKRRAHFKLKAPGLVECPNCGEPKLPHRVCPSC 46 (57)
T ss_pred CcCcCChhhcchhcccccccCCcceECCCCCCccCCeEECCCC
Confidence 5666667777666654333334568899998753333445543
No 64
>PF04800 ETC_C1_NDUFA4: ETC complex I subunit conserved region; InterPro: IPR006885 This entry represents prokaryotic NADH-ubiquinone oxidoreductase subunits (1.6.5.3 from EC, 1.6.99.3 from EC) from complex I of the electron transport chain initially identified in Neurospora crassa as a 21 kDa protein [].; GO: 0016651 oxidoreductase activity, acting on NADH or NADPH, 0022900 electron transport chain, 0005743 mitochondrial inner membrane; PDB: 2JYA_A 2LJU_A.
Probab=59.00 E-value=14 Score=31.79 Aligned_cols=29 Identities=21% Similarity=0.400 Sum_probs=22.7
Q ss_pred cCceeCCHHHHHHHHHHHHHhcCeeEEEeecCC
Q 004519 183 VDQRFSSFSEFREALHKYSIAHGFAYRYKKNDS 215 (747)
Q Consensus 183 vG~~F~s~~e~~~ai~~yai~~~f~~~~~rs~~ 215 (747)
+.+.|+|+|++.. ||.++|..|.+.....
T Consensus 51 v~l~F~skE~Ai~----yaer~G~~Y~V~~p~~ 79 (101)
T PF04800_consen 51 VRLKFDSKEDAIA----YAERNGWDYEVEEPKK 79 (101)
T ss_dssp CEEEESSHHHHHH----HHHHCT-EEEEE-STT
T ss_pred eEeeeCCHHHHHH----HHHHcCCeEEEeCCCC
Confidence 7889999999865 8999999999875443
No 65
>PTZ00044 ubiquitin; Provisional
Probab=58.10 E-value=21 Score=28.64 Aligned_cols=41 Identities=10% Similarity=0.164 Sum_probs=36.1
Q ss_pred EEecCceeEEEecCCCChhhHHHHHHHHhcCCCCceEEEEE
Q 004519 27 SYNGGEAYAIDIDEETEFSGFKSEVAEMFNCSADTMSIKYF 67 (747)
Q Consensus 27 ~Y~gg~~~~~~v~~~~s~~~~~~~l~~~~~~~~~~~~~~y~ 67 (747)
+-.+|++..+.|+.+.+-.++..+|++..++..++.++.|.
T Consensus 6 k~~~G~~~~l~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~ 46 (76)
T PTZ00044 6 KTLTGKKQSFNFEPDNTVQQVKMALQEKEGIDVKQIRLIYS 46 (76)
T ss_pred EeCCCCEEEEEECCCCcHHHHHHHHHHHHCCCHHHeEEEEC
Confidence 34568888999999999999999999999998888888874
No 66
>cd01800 SF3a120_C Ubiquitin-like domain of Mammalian splicing factor SF3a_120. SF3a120_C Mammalian splicing factor SF3a consists of three subunits of 60, 66, and 120 kDa and functions early during pre-mRNA splicing by converting the U2 snRNP to its active form. The 120kDa subunit (SF3a120) has a carboxy-terminal ubiquitin-like domain and two SWAP (suppressor-of-white-apricot) domains, referred to collectively as the SURP module, at its amino-terminus.
Probab=57.80 E-value=17 Score=29.34 Aligned_cols=39 Identities=15% Similarity=0.192 Sum_probs=35.6
Q ss_pred ecCceeEEEecCCCChhhHHHHHHHHhcCCCCceEEEEE
Q 004519 29 NGGEAYAIDIDEETEFSGFKSEVAEMFNCSADTMSIKYF 67 (747)
Q Consensus 29 ~gg~~~~~~v~~~~s~~~~~~~l~~~~~~~~~~~~~~y~ 67 (747)
.+|++..+.|+.+.|-.+|.++|.+..++..+..++.|.
T Consensus 5 l~g~~~~l~v~~~~TV~~lK~~i~~~~gip~~~q~L~~~ 43 (76)
T cd01800 5 LNGQMLNFTLQLSDPVSVLKVKIHEETGMPAGKQKLQYE 43 (76)
T ss_pred cCCeEEEEEECCCCcHHHHHHHHHHHHCCCHHHEEEEEC
Confidence 368899999999999999999999999998888888876
No 67
>COG4279 Uncharacterized conserved protein [Function unknown]
Probab=57.19 E-value=5.4 Score=39.73 Aligned_cols=23 Identities=35% Similarity=0.751 Sum_probs=19.6
Q ss_pred ceeecCCcccCCCCcchHHHHHHHhc
Q 004519 632 WDCTCKTWHLTGLPCCHAIAVLEWIG 657 (747)
Q Consensus 632 ~~CtC~~~~~~giPC~Halav~~~~~ 657 (747)
..|||..|.. ||.|+-||....+
T Consensus 125 ~dCSCPD~an---PCKHi~AvyY~la 147 (266)
T COG4279 125 TDCSCPDYAN---PCKHIAAVYYLLA 147 (266)
T ss_pred cccCCCCccc---chHHHHHHHHHHH
Confidence 5799999875 9999999988765
No 68
>cd01806 Nedd8 Nebb8-like ubiquitin protein. Nedd8 (also known as Rub1) has a single conserved ubiquitin-like domain that is part of a protein modification pathway similar to that of ubiquitin. Nedd8 modifies a family of molecular scaffold proteins called cullins that are responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis.
Probab=55.66 E-value=29 Score=27.74 Aligned_cols=41 Identities=20% Similarity=0.233 Sum_probs=34.9
Q ss_pred EEecCceeEEEecCCCChhhHHHHHHHHhcCCCCceEEEEE
Q 004519 27 SYNGGEAYAIDIDEETEFSGFKSEVAEMFNCSADTMSIKYF 67 (747)
Q Consensus 27 ~Y~gg~~~~~~v~~~~s~~~~~~~l~~~~~~~~~~~~~~y~ 67 (747)
.-.+|++..+.|+.+.+-.+|..+|++..++..+.+++.|.
T Consensus 6 ~~~~g~~~~~~v~~~~tv~~lK~~i~~~~g~~~~~qrL~~~ 46 (76)
T cd01806 6 KTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYS 46 (76)
T ss_pred EeCCCCEEEEEECCCCCHHHHHHHHhHhhCCChhhEEEEEC
Confidence 33457777799999999999999999999998888888764
No 69
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=53.20 E-value=12 Score=32.20 Aligned_cols=10 Identities=20% Similarity=0.949 Sum_probs=7.6
Q ss_pred ceeecCCCCC
Q 004519 727 RSLQCSKCKG 736 (747)
Q Consensus 727 r~~~Cs~C~~ 736 (747)
....|.+|+.
T Consensus 20 t~f~CP~Cge 29 (99)
T PRK14892 20 KIFECPRCGK 29 (99)
T ss_pred cEeECCCCCC
Confidence 4688888883
No 70
>cd01805 RAD23_N Ubiquitin-like domain of RAD23. RAD23 belongs to a family of adaptor molecules having affinity for both the proteasome and ubiquitinylated proteins and thought to shuttle these ubiquitinylated proteins to the proteasome for destruction. RAD23 interacts with ubiquitin through its C-terminal ubiquitin-associated domains (UBA) and with the proteasome through its N-terminal ubiquitin-like domain (UBL).
Probab=53.02 E-value=34 Score=27.51 Aligned_cols=42 Identities=14% Similarity=0.381 Sum_probs=35.7
Q ss_pred EEEecCceeEEEecCCCChhhHHHHHHHHhcC--CCCceEEEEE
Q 004519 26 LSYNGGEAYAIDIDEETEFSGFKSEVAEMFNC--SADTMSIKYF 67 (747)
Q Consensus 26 ~~Y~gg~~~~~~v~~~~s~~~~~~~l~~~~~~--~~~~~~~~y~ 67 (747)
+...+|++..+.|+.+.+-.+|...|.+..++ ..+..++.|.
T Consensus 5 vk~~~g~~~~l~v~~~~TV~~lK~~i~~~~~i~~~~~~q~L~~~ 48 (77)
T cd01805 5 FKTLKQQTFPIEVDPDDTVAELKEKIEEEKGCDYPPEQQKLIYS 48 (77)
T ss_pred EEeCCCCEEEEEECCCCcHHHHHHHHHHhhCCCCChhHeEEEEC
Confidence 45667888899999999999999999999998 6777777764
No 71
>PF11470 TUG-UBL1: GLUT4 regulating protein TUG; InterPro: IPR021569 TUG is a GLUT4 regulating protein and functions to retain membrane vesicles containing GLUT4 intracellularly. TUG releases the GLUT4 containing vesicles to the cellular exocytic machinery in response to insulin stimulation which allows translocation to the plasma membrane []. TUG has an N-terminal ubiquitin-like domain (UBL1) which in similar proteins appears to participate in protein-protein interactions []. The region does have a area of negative electrostatic potential and increased backbone motility which leads to suggestions of a potential protein-protein interaction site []. ; PDB: 2AL3_A.
Probab=52.89 E-value=25 Score=27.67 Aligned_cols=38 Identities=11% Similarity=0.204 Sum_probs=27.0
Q ss_pred cCceeEEEecCCCChhhHHHHHHHHhcCCCCceEEEEE
Q 004519 30 GGEAYAIDIDEETEFSGFKSEVAEMFNCSADTMSIKYF 67 (747)
Q Consensus 30 gg~~~~~~v~~~~s~~~~~~~l~~~~~~~~~~~~~~y~ 67 (747)
+|++..+.|..+.+..+.+++.|..++++.++..++|.
T Consensus 5 ~~rr~~vkvtp~~~l~~VL~eac~k~~l~~~~~~L~h~ 42 (65)
T PF11470_consen 5 NFRRFKVKVTPNTTLNQVLEEACKKFGLDPSSYDLKHN 42 (65)
T ss_dssp TS-EEEE---TTSBHHHHHHHHHHHTT--GGG-EEEET
T ss_pred CCcEEEEEECCCCCHHHHHHHHHHHcCCCccceEEEEC
Confidence 57788899999999999999999999999886666665
No 72
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=52.22 E-value=15 Score=27.75 Aligned_cols=43 Identities=14% Similarity=0.398 Sum_probs=26.0
Q ss_pred CCCCCCCCCCCCCCCCcc-ccccceeecCCCCCCCcCcCCCCCC
Q 004519 705 PPTRRPPGRPKMKQPESA-EIIKRSLQCSKCKGLGHNKKTCKDS 747 (747)
Q Consensus 705 P~~~r~~GRPkk~r~~~~-~~~kr~~~Cs~C~~~GHn~~tC~~~ 747 (747)
|..+..+-|.+++|.... ........|+.||+.--.=+-||.|
T Consensus 2 PKrk~Sksr~~~RRah~~kl~~p~l~~C~~cG~~~~~H~vc~~c 45 (55)
T TIGR01031 2 PKRKTSKSRKRKRRSHDAKLTAPTLVVCPNCGEFKLPHRVCPSC 45 (55)
T ss_pred CCCcCCcccccchhcCcccccCCcceECCCCCCcccCeeECCcc
Confidence 455555666666655422 3334568899999865555566654
No 73
>KOG0695 consensus Serine/threonine protein kinase [Signal transduction mechanisms]
Probab=50.99 E-value=48 Score=34.74 Aligned_cols=66 Identities=15% Similarity=0.344 Sum_probs=51.6
Q ss_pred EEecCceeEEEecCCCChhhHHHHHHHHhcCCC-CceEEEEEecCCCCcceeeeCcHHHHHHHhhccCc
Q 004519 27 SYNGGEAYAIDIDEETEFSGFKSEVAEMFNCSA-DTMSIKYFLPGNKKTLISISKDKDFKRMLNFLGDT 94 (747)
Q Consensus 27 ~Y~gg~~~~~~v~~~~s~~~~~~~l~~~~~~~~-~~~~~~y~lp~~~~~l~~v~~D~dl~~m~~~~~~~ 94 (747)
.|-+|..-+.+++..++|.+|...+.+++.+.. +.+++||.- ++.++++|++.-.|+.-+..+...
T Consensus 20 a~y~g~i~i~~~~p~~~~e~~~~~vrd~c~~h~~q~~t~kwid--eegdp~tv~sqmeleea~r~~~~~ 86 (593)
T KOG0695|consen 20 AHYGGDIFITSVDPATTFEELCEEVRDMCRLHQQQPLTLKWID--EEGDPCTVSSQMELEEAFRLARQC 86 (593)
T ss_pred EeecCcEEEEeccCcccHHHHHHHHHHHHHHhhcCCceeEeec--CCCCcceechhhhHHHHHHHHHhc
Confidence 455677777888889999999999999996654 457999984 344588999999998888766543
No 74
>smart00213 UBQ Ubiquitin homologues. Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression
Probab=50.76 E-value=35 Score=25.92 Aligned_cols=40 Identities=13% Similarity=0.235 Sum_probs=32.6
Q ss_pred EEecCceeEEEecCCCChhhHHHHHHHHhcCCCCceEEEEE
Q 004519 27 SYNGGEAYAIDIDEETEFSGFKSEVAEMFNCSADTMSIKYF 67 (747)
Q Consensus 27 ~Y~gg~~~~~~v~~~~s~~~~~~~l~~~~~~~~~~~~~~y~ 67 (747)
+..+ .+..+.|+.+.+..+|..+|.+.+++..+.+++.|.
T Consensus 6 k~~~-~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~~~L~~~ 45 (64)
T smart00213 6 KTLD-GTITLEVKPSDTVSELKEKIAELTGIPVEQQRLIYK 45 (64)
T ss_pred EECC-ceEEEEECCCCcHHHHHHHHHHHHCCCHHHEEEEEC
Confidence 3444 466789999999999999999999988777777664
No 75
>cd01763 Sumo Small ubiquitin-related modifier (SUMO). Small ubiquitin-related modifier (SUMO) proteins are conjugated to numerous intracellular targets and serve to modulate protein interaction, localization, activity or stability. SUMO (also known as "Smt3" and "sentrin" in other organisms) is linked to several different pathways, including nucleocytoplasmic transport. Attachment of SUMO to targets proteins is stimulated by PIAS (Protein inhibitor of activated STATs) proteins which serve as E3-like ligases.
Probab=49.76 E-value=35 Score=28.47 Aligned_cols=42 Identities=10% Similarity=0.121 Sum_probs=37.1
Q ss_pred EEEecCceeEEEecCCCChhhHHHHHHHHhcCCCCceEEEEE
Q 004519 26 LSYNGGEAYAIDIDEETEFSGFKSEVAEMFNCSADTMSIKYF 67 (747)
Q Consensus 26 ~~Y~gg~~~~~~v~~~~s~~~~~~~l~~~~~~~~~~~~~~y~ 67 (747)
+....|.+..+.|.++.++..+++++++..+++.++.+|.|.
T Consensus 16 v~~~~g~~~~~~v~~~~~l~~l~~~y~~~~gi~~~~~rf~f~ 57 (87)
T cd01763 16 VKGQDGNEVFFKIKRSTPLKKLMEAYCQRQGLSMNSVRFLFD 57 (87)
T ss_pred EECCCCCEEEEEEcCCCHHHHHHHHHHHHhCCCccceEEEEC
Confidence 455567888899999999999999999999999988888886
No 76
>PRK09335 30S ribosomal protein S26e; Provisional
Probab=49.72 E-value=15 Score=30.93 Aligned_cols=27 Identities=30% Similarity=0.505 Sum_probs=19.5
Q ss_pred CCCCCCCCCCCCCCCCccccccceeecCCCCC
Q 004519 705 PPTRRPPGRPKMKQPESAEIIKRSLQCSKCKG 736 (747)
Q Consensus 705 P~~~r~~GRPkk~r~~~~~~~kr~~~Cs~C~~ 736 (747)
|.+||-.||-|+.|- .-..++|++|+.
T Consensus 2 ~kKRrn~GR~K~~rG-----hv~~V~C~nCgr 28 (95)
T PRK09335 2 PKKRENRGRRKGDKG-----HVGYVQCDNCGR 28 (95)
T ss_pred CcccccCCCCCCCCC-----CCccEEeCCCCC
Confidence 567778888887652 224689999986
No 77
>PF00240 ubiquitin: Ubiquitin family; InterPro: IPR000626 Ubiquitinylation is an ATP-dependent process that involves the action of at least three enzymes: a ubiquitin-activating enzyme (E1, IPR000011 from INTERPRO), a ubiquitin-conjugating enzyme (E2, IPR000608 from INTERPRO), and a ubiquitin ligase (E3, IPR000569 from INTERPRO, IPR003613 from INTERPRO), which work sequentially in a cascade. There are many different E3 ligases, which are responsible for the type of ubiquitin chain formed, the specificity of the target protein, and the regulation of the ubiquitinylation process []. Ubiquitinylation is an important regulatory tool that controls the concentration of key signalling proteins, such as those involved in cell cycle control, as well as removing misfolded, damaged or mutant proteins that could be harmful to the cell. Several ubiquitin-like molecules have been discovered, such as Ufm1 (IPR005375 from INTERPRO), SUMO1 (IPR003653 from INTERPRO), NEDD8, Rad23 (IPR004806 from INTERPRO), Elongin B and Parkin (IPR003977 from INTERPRO), the latter being involved in Parkinson's disease []. Ubiquitin is a protein of 76 amino acid residues, found in all eukaryotic cells and whose sequence is extremely well conserved from protozoan to vertebrates. Ubiquitin acts through its post-translational attachment (ubiquitinylation) to other proteins, where these modifications alter the function, location or trafficking of the protein, or targets it for destruction by the 26S proteasome []. The terminal glycine in the C-terminal 4-residue tail of ubiquitin can form an isopeptide bond with a lysine residue in the target protein, or with a lysine in another ubiquitin molecule to form a ubiquitin chain that attaches itself to a target protein. Ubiquitin has seven lysine residues, any one of which can be used to link ubiquitin molecules together, resulting in different structures that alter the target protein in different ways. It appears that Lys(11)-, Lys(29) and Lys(48)-linked poly-ubiquitin chains target the protein to the proteasome for degradation, while mono-ubiquitinylated and Lys(6)- or Lys(63)-linked poly-ubiquitin chains signal reversible modifications in protein activity, location or trafficking []. For example, Lys(63)-linked poly-ubiquitinylation is known to be involved in DNA damage tolerance, inflammatory response, protein trafficking and signal transduction through kinase activation []. In addition, the length of the ubiquitin chain alters the fate of the target protein. Regulatory proteins such as transcription factors and histones are frequent targets of ubquitinylation [].; GO: 0005515 protein binding; PDB: 2DZI_A 2XEW_E 3NOB_E 2KWU_B 2Y5B_F 3PHD_G 2KWV_B 2KOX_A 2XK5_B 3NHE_B ....
Probab=47.39 E-value=40 Score=26.37 Aligned_cols=39 Identities=15% Similarity=0.400 Sum_probs=34.9
Q ss_pred ecCceeEEEecCCCChhhHHHHHHHHhcCCCCceEEEEE
Q 004519 29 NGGEAYAIDIDEETEFSGFKSEVAEMFNCSADTMSIKYF 67 (747)
Q Consensus 29 ~gg~~~~~~v~~~~s~~~~~~~l~~~~~~~~~~~~~~y~ 67 (747)
..|++..+.|+.+.+..+|...|.+..++....+.+-|-
T Consensus 3 ~~g~~~~~~v~~~~tV~~lK~~i~~~~~~~~~~~~L~~~ 41 (69)
T PF00240_consen 3 LSGKTFTLEVDPDDTVADLKQKIAEETGIPPEQQRLIYN 41 (69)
T ss_dssp TTSEEEEEEEETTSBHHHHHHHHHHHHTSTGGGEEEEET
T ss_pred CCCcEEEEEECCCCCHHHhhhhcccccccccccceeeee
Confidence 357788899999999999999999999999888888874
No 78
>cd01769 UBL Ubiquitin-like domain of UBL. UBLs function by remodeling the surface of their target proteins, changing their target's half-life, enzymatic activity, protein-protein interactions, subcellular localization or other properties. At least 10 different ubiquitin-like modifications exist in mammals, and attachment of different ubls to a target leads to different biological consequences. Ubl-conjugation cascades are initiated by activating enzymes, which also coordinate the ubls with their downstream pathways.
Probab=47.32 E-value=45 Score=25.70 Aligned_cols=41 Identities=10% Similarity=0.292 Sum_probs=34.2
Q ss_pred EEecCceeEEEecCCCChhhHHHHHHHHhcCCCCceEEEEE
Q 004519 27 SYNGGEAYAIDIDEETEFSGFKSEVAEMFNCSADTMSIKYF 67 (747)
Q Consensus 27 ~Y~gg~~~~~~v~~~~s~~~~~~~l~~~~~~~~~~~~~~y~ 67 (747)
+..+|++..+.++.+.+..+|..+|.+.+++....+++.|.
T Consensus 3 ~~~~~~~~~~~~~~~~ti~~lK~~i~~~~~~~~~~~~l~~~ 43 (69)
T cd01769 3 KTLTGKTFELEVSPDDTVAELKAKIAAKEGVPPEQQRLIYA 43 (69)
T ss_pred EccCCCEEEEEECCCChHHHHHHHHHHHHCcChHHEEEEEC
Confidence 33467777888999999999999999999988888888653
No 79
>PF13592 HTH_33: Winged helix-turn helix
Probab=46.73 E-value=31 Score=26.44 Aligned_cols=29 Identities=28% Similarity=0.460 Sum_probs=25.0
Q ss_pred CCCChHHHHHHHHHHhCCccCHHHHHHHH
Q 004519 281 PNYKPKDIADDIKREYGIQLNYSQAWRAK 309 (747)
Q Consensus 281 ~~~~~~~i~~~i~~~~g~~~~~~~~~r~k 309 (747)
..++.++|++.|.++||+.++.+.+|+.-
T Consensus 3 ~~wt~~~i~~~I~~~fgv~ys~~~v~~lL 31 (60)
T PF13592_consen 3 GRWTLKEIAAYIEEEFGVKYSPSGVYRLL 31 (60)
T ss_pred CcccHHHHHHHHHHHHCCEEcHHHHHHHH
Confidence 45678999999999999999999888753
No 80
>PF12762 DDE_Tnp_IS1595: ISXO2-like transposase domain; InterPro: IPR024445 This domain probably functions as an integrase that is found in a wide variety of transposases, including ISXO2.
Probab=46.35 E-value=51 Score=30.54 Aligned_cols=68 Identities=18% Similarity=0.164 Sum_probs=42.0
Q ss_pred EEEEeccccCCcc--------------cceEEEEEEecCC-CCeEEEEEEEeecCCcccHHHHHHHHHhhcCCCCcEEEE
Q 004519 374 LLFLDTTPLNSKY--------------QGTLLTATSADGD-DGIFPVAFAVVDAETEDNWHWFLQELKSAVSTSQQITFI 438 (747)
Q Consensus 374 vl~iD~t~~~~~y--------------~~~l~~a~g~d~~-~~~~pla~a~v~~E~~e~~~wfl~~l~~~~~~~~~~~ii 438 (747)
+|-||.||..++- .....++++++-+ +..--+...++++.+.++..-+++.... +..+|+
T Consensus 5 ~VEiDEty~~~~~~~~~~~~~~~gr~~~~k~~V~~~ver~~~~~~~~~~~~v~~~~~~tl~~~i~~~i~-----~gs~i~ 79 (151)
T PF12762_consen 5 IVEIDETYFGGRKNKKPRRKGKRGRGSKNKVPVFGAVERNDGGTGRVFMFVVPDRSAETLKPIIQEHIE-----PGSTII 79 (151)
T ss_pred EEEeCcCEECCcccccccCCCCCCCcCCCCcEEEEEEeecccCCceEEEEeecccccchhHHHHHHhhh-----ccceee
Confidence 6777777764322 2234455555554 4444455556688888888777654433 356799
Q ss_pred ecCcchhH
Q 004519 439 ADFQNGLN 446 (747)
Q Consensus 439 sD~~~~l~ 446 (747)
||..++-.
T Consensus 80 TD~~~aY~ 87 (151)
T PF12762_consen 80 TDGWRAYN 87 (151)
T ss_pred ecchhhcC
Confidence 99988664
No 81
>cd01810 ISG15_repeat2 ISG15 ubiquitin-like protein, second repeat of 2. ISG15 is a ubiquitin-like protein containing two ubiquitin homology domains and becomes conjugated to a variety of proteins when cells are treated with type I interferon or lipopolysaccharide. Although ISG15 has properties similar to those of other ubiquitin-like molecules, it is a unique member of the ubiquitin-like superfamily, whose expression and conjugation to target proteins are tightly regulated by specific signaling pathways, indicating it may have specialized functions in the immune system.
Probab=46.33 E-value=40 Score=27.00 Aligned_cols=42 Identities=12% Similarity=0.220 Sum_probs=36.0
Q ss_pred EEEecCceeEEEecCCCChhhHHHHHHHHhcCCCCceEEEEE
Q 004519 26 LSYNGGEAYAIDIDEETEFSGFKSEVAEMFNCSADTMSIKYF 67 (747)
Q Consensus 26 ~~Y~gg~~~~~~v~~~~s~~~~~~~l~~~~~~~~~~~~~~y~ 67 (747)
++...|++..+.|+.+.|-.++.++|.+..++..++.++.|.
T Consensus 3 vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~gi~~~~q~L~~~ 44 (74)
T cd01810 3 VRNDKGRSSIYEVQLTQTVATLKQQVSQRERVQADQFWLSFE 44 (74)
T ss_pred EECCCCCEEEEEECCcChHHHHHHHHHHHhCCCHHHeEEEEC
Confidence 345568888999999999999999999999988888888764
No 82
>cd01793 Fubi Fubi ubiquitin-like protein. Fubi is a ubiquitin-like protein encoded by the fau gene which has an N-terminal ubiquitin-like domain (also referred to as FUBI) fused to the ribosomal protein S30. Fubi is thought to be a tumor suppressor protein and the FUBI domain may act as a substitute or an inhibitor of ubiquitin or one of ubiquitin's close relatives UCRP, FAT10, and Nedd8.
Probab=46.00 E-value=46 Score=26.63 Aligned_cols=39 Identities=10% Similarity=0.173 Sum_probs=34.4
Q ss_pred ecCceeEEEecCCCChhhHHHHHHHHhcCCCCceEEEEE
Q 004519 29 NGGEAYAIDIDEETEFSGFKSEVAEMFNCSADTMSIKYF 67 (747)
Q Consensus 29 ~gg~~~~~~v~~~~s~~~~~~~l~~~~~~~~~~~~~~y~ 67 (747)
.++++..+.|+.+.+-.++..+|.+..++..++.++.|.
T Consensus 6 k~~~~~~l~v~~~~tV~~lK~~i~~~~gip~~~q~Li~~ 44 (74)
T cd01793 6 RAQNTHTLEVTGQETVSDIKAHVAGLEGIDVEDQVLLLA 44 (74)
T ss_pred ECCCEEEEEECCcCcHHHHHHHHHhhhCCCHHHEEEEEC
Confidence 345778899999999999999999999998888888886
No 83
>COG5179 TAF1 Transcription initiation factor TFIID, subunit TAF1 [Transcription]
Probab=45.97 E-value=11 Score=42.09 Aligned_cols=20 Identities=35% Similarity=0.863 Sum_probs=16.4
Q ss_pred ceeecCCCCCCCcCc--CCCCC
Q 004519 727 RSLQCSKCKGLGHNK--KTCKD 746 (747)
Q Consensus 727 r~~~Cs~C~~~GHn~--~tC~~ 746 (747)
.+++|++||+.||-+ +.||.
T Consensus 936 Ttr~C~nCGQvGHmkTNK~CP~ 957 (968)
T COG5179 936 TTRTCGNCGQVGHMKTNKACPK 957 (968)
T ss_pred cceecccccccccccccccCcc
Confidence 479999999999965 46774
No 84
>cd01789 Alp11_N Ubiquitin-like domain of Alp11 tubulin-folding cofactor B. Alp11, also known as tubulin-folding cofactor B, is one of at least three proteins required for the proper folding of tubulins prior to their incorporation into microtubules. These cofactors are necessary for the biogenesis of microtubules and for cell viability. Alp11 has three domains including an N-terminal ubiquitin-like domain (represented by this CD) which executes the essential function, a central coiled-coil domain necessary for maintenance of cellular alpha-tubulin levels, and a C-terminal CLIP-170 domain is required for efficient binding to alpha-tubulin.
Probab=44.52 E-value=51 Score=27.31 Aligned_cols=33 Identities=12% Similarity=0.214 Sum_probs=29.3
Q ss_pred EEecCCCChhhHHHHHHHHhcCCCCceEEEEEe
Q 004519 36 IDIDEETEFSGFKSEVAEMFNCSADTMSIKYFL 68 (747)
Q Consensus 36 ~~v~~~~s~~~~~~~l~~~~~~~~~~~~~~y~l 68 (747)
..++.+|+..+|..+|...+|.+...+++.++-
T Consensus 17 kr~~~~~Tv~~lK~kl~~~~G~~~~~mrL~l~~ 49 (84)
T cd01789 17 KKYSRGLTIAELKKKLELVVGTPASSMRLQLFD 49 (84)
T ss_pred EecCCCCcHHHHHHHHHHHHCCCccceEEEEEc
Confidence 558889999999999999999999999997653
No 85
>KOG3389 consensus NADH:ubiquinone oxidoreductase, NDUFS4/18 kDa subunit [Energy production and conversion]
Probab=44.47 E-value=19 Score=32.40 Aligned_cols=36 Identities=22% Similarity=0.624 Sum_probs=27.3
Q ss_pred ccCCcccc----------cCc--eeCCHHHHHHHHHHHHHhcCeeEEEeecC
Q 004519 175 QWENTITG----------VDQ--RFSSFSEFREALHKYSIAHGFAYRYKKND 214 (747)
Q Consensus 175 ~~~~~~~~----------vG~--~F~s~~e~~~ai~~yai~~~f~~~~~rs~ 214 (747)
+||||.|+ ||| .|.++|+++. ||-++|.+|.+..-.
T Consensus 107 rWENPLMGWtsTaDPlsNvgm~L~F~tkEdA~s----FaEkngW~ydveep~ 154 (178)
T KOG3389|consen 107 RWENPLMGWTSTADPLSNVGMALAFDTKEDAKS----FAEKNGWDYDVEEPN 154 (178)
T ss_pred hccCccccccccCCcccccceeeeeccHHHHHH----HHHHcCCcccccCCC
Confidence 57777665 555 6999988764 788999999987543
No 86
>PLN00186 ribosomal protein S26; Provisional
Probab=44.32 E-value=19 Score=30.97 Aligned_cols=27 Identities=30% Similarity=0.548 Sum_probs=19.3
Q ss_pred CCCCCCCCCCCCCCCCccccccceeecCCCCC
Q 004519 705 PPTRRPPGRPKMKQPESAEIIKRSLQCSKCKG 736 (747)
Q Consensus 705 P~~~r~~GRPkk~r~~~~~~~kr~~~Cs~C~~ 736 (747)
|.+||-.||-|+.|- .-+.++|++|+.
T Consensus 2 ~kKRrN~GR~K~~rG-----hv~~V~C~nCgr 28 (109)
T PLN00186 2 TKKRRNGGRNKHGRG-----HVKRIRCSNCGK 28 (109)
T ss_pred CcccccCCCCCCCCC-----CCcceeeCCCcc
Confidence 567777888887652 224689999986
No 87
>cd01813 UBP_N UBP ubiquitin processing protease. The UBP (ubiquitin processing protease) domain (also referred to as USP which stands for "ubiquitin-specific protease") is present at in a large family of cysteine proteases that specifically cleave ubiquitin conjugates. This family includes Rpn11, UBP6 (USP14), USP7 (HAUSP). This domain is closely related to the amino-terminal ubiquitin-like domain of BAG1 (Bcl2-associated anthanogene1) protein and is found only in eukaryotes.
Probab=44.05 E-value=39 Score=27.21 Aligned_cols=38 Identities=13% Similarity=0.245 Sum_probs=34.2
Q ss_pred cCceeEEEecCCCChhhHHHHHHHHhcCCCCceEEEEE
Q 004519 30 GGEAYAIDIDEETEFSGFKSEVAEMFNCSADTMSIKYF 67 (747)
Q Consensus 30 gg~~~~~~v~~~~s~~~~~~~l~~~~~~~~~~~~~~y~ 67 (747)
+|++.-+.|+.+-+..+|.++|++..++..++.++-|.
T Consensus 8 ~g~~~~v~v~~~~Tv~~lK~~i~~~tgvp~~~QKLi~~ 45 (74)
T cd01813 8 GGQEYSVTTLSEDTVLDLKQFIKTLTGVLPERQKLLGL 45 (74)
T ss_pred CCEEEEEEECCCCCHHHHHHHHHHHHCCCHHHEEEEee
Confidence 46777789999999999999999999999999999993
No 88
>PTZ00172 40S ribosomal protein S26; Provisional
Probab=43.84 E-value=20 Score=30.89 Aligned_cols=27 Identities=30% Similarity=0.581 Sum_probs=19.4
Q ss_pred CCCCCCCCCCCCCCCCccccccceeecCCCCC
Q 004519 705 PPTRRPPGRPKMKQPESAEIIKRSLQCSKCKG 736 (747)
Q Consensus 705 P~~~r~~GRPkk~r~~~~~~~kr~~~Cs~C~~ 736 (747)
|.+||-.||-|+.|- .-+.++|++|+.
T Consensus 2 ~kKRrN~GR~K~~rG-----hv~~V~C~nCgr 28 (108)
T PTZ00172 2 TSKRRNNGRSKHGRG-----HVKPVRCSNCGR 28 (108)
T ss_pred CcccccCCCCCCCCC-----CCccEEeCCccc
Confidence 567778888887652 234689999986
No 89
>PF14201 DUF4318: Domain of unknown function (DUF4318)
Probab=43.61 E-value=37 Score=27.45 Aligned_cols=29 Identities=31% Similarity=0.542 Sum_probs=26.1
Q ss_pred eeCCHHHHHHHHHHHHHhcCeeEEEeecC
Q 004519 186 RFSSFSEFREALHKYSIAHGFAYRYKKND 214 (747)
Q Consensus 186 ~F~s~~e~~~ai~~yai~~~f~~~~~rs~ 214 (747)
.|||.+++-.+|..|+.+++-.+++.+.+
T Consensus 13 ~yPs~e~i~~aIE~YC~~~~~~l~Fisr~ 41 (74)
T PF14201_consen 13 KYPSKEEICEAIEKYCIKNGESLEFISRD 41 (74)
T ss_pred CCCCHHHHHHHHHHHHHHcCCceEEEecC
Confidence 58899999999999999999999987643
No 90
>cd01802 AN1_N ubiquitin-like domain of AN1. AN1 (also known as ANUBL1 and RSD-7) is ubiquitin-like protein with a testis-specific expression in rats that has an N-terminal ubiquitin-like domain and a C-terminal zinc-binding domain. Unlike ubiquitin polyproteins and most ubiquitin fusion proteins, the N-terminal ubiquitin-like domain of An1 does not undergo proteolytic processing. The function of AN1 is unknown.
Probab=42.78 E-value=49 Score=28.65 Aligned_cols=42 Identities=5% Similarity=0.138 Sum_probs=37.0
Q ss_pred EEEecCceeEEEecCCCChhhHHHHHHHHhcCCCCceEEEEE
Q 004519 26 LSYNGGEAYAIDIDEETEFSGFKSEVAEMFNCSADTMSIKYF 67 (747)
Q Consensus 26 ~~Y~gg~~~~~~v~~~~s~~~~~~~l~~~~~~~~~~~~~~y~ 67 (747)
++-.+|++..+.|+.+.|-.++.++|.+..++..++.++.|-
T Consensus 32 Vk~l~G~~~~leV~~~~TV~~lK~kI~~~~gip~~~QrLi~~ 73 (103)
T cd01802 32 IETLTGTCFELRVSPFETVISVKAKIQRLEGIPVAQQHLIWN 73 (103)
T ss_pred EEcCCCCEEEEEeCCCCcHHHHHHHHHHHhCCChHHEEEEEC
Confidence 355568899999999999999999999999998888898876
No 91
>COG4715 Uncharacterized conserved protein [Function unknown]
Probab=42.55 E-value=53 Score=36.93 Aligned_cols=44 Identities=27% Similarity=0.290 Sum_probs=31.1
Q ss_pred eEEEEcceeE--EEeC----cCceeecCCcccCCCCcchHHHHHHHhcCCcc
Q 004519 616 TFEVRGESAD--IVDV----DRWDCTCKTWHLTGLPCCHAIAVLEWIGRSPY 661 (747)
Q Consensus 616 ~f~V~~~~~~--~V~l----~~~~CtC~~~~~~giPC~Halav~~~~~~~p~ 661 (747)
.-+|.+.+.| .|.+ -+.+|||.. ...| -|.|+.||+...-..|+
T Consensus 51 ~A~V~Gs~~y~v~vtL~~~~~ss~CTCP~-~~~g-aCKH~VAvvl~~~~~p~ 100 (587)
T COG4715 51 RAVVEGSRRYRVRVTLEGGALSSICTCPY-GGSG-ACKHVVAVVLEYLDDPE 100 (587)
T ss_pred EEEEeccceeeEEEEeecCCcCceeeCCC-CCCc-chHHHHHHHHHHhhccc
Confidence 3467776655 4555 367999998 5555 59999999887654443
No 92
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=41.06 E-value=16 Score=27.74 Aligned_cols=20 Identities=25% Similarity=0.522 Sum_probs=16.3
Q ss_pred ceeecCCCCCCCcCcCCCCCC
Q 004519 727 RSLQCSKCKGLGHNKKTCKDS 747 (747)
Q Consensus 727 r~~~Cs~C~~~GHn~~tC~~~ 747 (747)
+.++|+.|+...= +..||.|
T Consensus 4 ~mr~C~~CgvYTL-k~~CP~C 23 (56)
T PRK13130 4 KIRKCPKCGVYTL-KEICPVC 23 (56)
T ss_pred cceECCCCCCEEc-cccCcCC
Confidence 5689999998776 8888875
No 93
>PRK00766 hypothetical protein; Provisional
Probab=39.17 E-value=2.4e+02 Score=27.54 Aligned_cols=87 Identities=15% Similarity=0.136 Sum_probs=51.5
Q ss_pred cEEEEe-ccccCCcccceEEEEEEecCCCCeEEEEEEEeecCCcccHHHHHHHHHhhcC---------------------
Q 004519 373 PLLFLD-TTPLNSKYQGTLLTATSADGDDGIFPVAFAVVDAETEDNWHWFLQELKSAVS--------------------- 430 (747)
Q Consensus 373 ~vl~iD-~t~~~~~y~~~l~~a~g~d~~~~~~pla~a~v~~E~~e~~~wfl~~l~~~~~--------------------- 430 (747)
.|++|| +.|..+.-+-.+++-+..-++.-+.-++|+-+.....|.=.-+.+.++....
T Consensus 10 rvlGidds~f~~~~~~~~~lvGvv~r~~~~idGv~~~~itvdG~DaT~~i~~mv~~~~~r~~i~~V~L~Git~agFNvvD 89 (194)
T PRK00766 10 RVLGIDDGTFLFKSSEKVILVGVVMRGGDWVDGVLSRWITVDGLDATEAIIEMVNSSRHKGQLRVIMLDGITYGGFNVVD 89 (194)
T ss_pred eEEEEecCccccCCCCCEEEEEEEEECCeEEeeEEEEEEEECCccHHHHHHHHHHhcccccceEEEEECCEeeeeeEEec
Confidence 388888 4454432233455555555555556677777766666666655555544110
Q ss_pred -------CCCcEEEEecCcc---hhHHHHhhhccCccch
Q 004519 431 -------TSQQITFIADFQN---GLNKSLAEVFDNCYHS 459 (747)
Q Consensus 431 -------~~~~~~iisD~~~---~l~~Ai~~vfP~a~h~ 459 (747)
..-|+++++...+ +|.+|+++.||+...+
T Consensus 90 ~~~l~~~tg~PVI~V~r~~p~~~~ie~AL~k~f~~~~~R 128 (194)
T PRK00766 90 IEELYRETGLPVIVVMRKKPDFEAIESALKKHFSDWEER 128 (194)
T ss_pred HHHHHHHHCCCEEEEEecCCCHHHHHHHHHHHCCCHHHH
Confidence 0136666644443 7889999999987654
No 94
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=36.89 E-value=20 Score=27.25 Aligned_cols=43 Identities=16% Similarity=0.371 Sum_probs=23.2
Q ss_pred CCCCCCCCCCCCCCCCccccccceeecCCCCCCCcCcCCCCCC
Q 004519 705 PPTRRPPGRPKMKQPESAEIIKRSLQCSKCKGLGHNKKTCKDS 747 (747)
Q Consensus 705 P~~~r~~GRPkk~r~~~~~~~kr~~~Cs~C~~~GHn~~tC~~~ 747 (747)
|..+..+-|..++|.--.-.......|+.||....--+.|+.|
T Consensus 4 PkrktSksrr~~RRsh~~l~~~~~~~c~~cG~~~l~Hrvc~~c 46 (57)
T COG0333 4 PKRKTSKSRRRMRRSHDALKAPTLSVCPNCGEYKLPHRVCLKC 46 (57)
T ss_pred CcccCChhhhhhhhhhHhhhCccceeccCCCCcccCceEcCCC
Confidence 3333344444444432122223368999999876666667654
No 95
>cd01804 midnolin_N Ubiquitin-like domain of midnolin. midnolin_N Midnolin (midbrain nucleolar protein) is expressed in the nucleolus and is thought to regulate genes involved in neurogenesis. Midnolin contains an amino-terminal ubiquitin-like domain.
Probab=36.59 E-value=78 Score=25.69 Aligned_cols=39 Identities=8% Similarity=0.336 Sum_probs=33.3
Q ss_pred ecCceeEEEecCCCChhhHHHHHHHHhcCCCCceEEEEE
Q 004519 29 NGGEAYAIDIDEETEFSGFKSEVAEMFNCSADTMSIKYF 67 (747)
Q Consensus 29 ~gg~~~~~~v~~~~s~~~~~~~l~~~~~~~~~~~~~~y~ 67 (747)
..|++..+.|+.+.|..+|..+|.+..++..+..++-|.
T Consensus 9 ~~G~~~~l~v~~~~TV~~LK~~I~~~~~~~~~~qrL~~~ 47 (78)
T cd01804 9 TTGTRFDLSVPPDETVEGLKKRISQRLKVPKERLALLHR 47 (78)
T ss_pred CCCCEEEEEECCcCHHHHHHHHHHHHhCCChHHEEEEEC
Confidence 346778899999999999999999999988877777665
No 96
>PHA00689 hypothetical protein
Probab=34.69 E-value=18 Score=25.99 Aligned_cols=13 Identities=31% Similarity=0.920 Sum_probs=10.8
Q ss_pred cceeecCCCCCCC
Q 004519 726 KRSLQCSKCKGLG 738 (747)
Q Consensus 726 kr~~~Cs~C~~~G 738 (747)
.|..+|.+|++.|
T Consensus 15 pravtckrcgktg 27 (62)
T PHA00689 15 PRAVTCKRCGKTG 27 (62)
T ss_pred cceeehhhccccC
Confidence 4779999998876
No 97
>PF01498 HTH_Tnp_Tc3_2: Transposase; InterPro: IPR002492 Transposase proteins are necessary for efficient DNA transposition. This family includes the amino-terminal region of Tc1, Tc1A, Tc1B and Tc2B transposases of Caenorhabditis elegans. The region encompasses the specific DNA binding and second DNA recognition domains as well as an amino-terminal region of the catalytic domain of Tc3 as described in []. Tc3 is a member of the Tc1/mariner family of transposable elements. This entry also includes histone-lysine N-methyltransferase SETMAR, which is a SET domain and mariner transposase fusion gene-containing protein. This histone methyltransferase has sequence-specific DNA-binding activity and recognises the 19-mer core of the 5'-terminal inverted repeats (TIRs) of the Hsmar1 element. This protein has DNA nicking activity, and has in vivo end joining activity and may mediate genomic integration of foreign DNA [, , , ]. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated, 0015074 DNA integration; PDB: 3K9K_B 3F2K_B 3K9J_B 1U78_A.
Probab=32.49 E-value=37 Score=26.95 Aligned_cols=36 Identities=22% Similarity=0.436 Sum_probs=16.0
Q ss_pred HHHHhhhCCCCChHHHHHHHHHHhCCccCHHHHHHHH
Q 004519 273 IKEKLKASPNYKPKDIADDIKREYGIQLNYSQAWRAK 309 (747)
Q Consensus 273 ~~~~~~~~~~~~~~~i~~~i~~~~g~~~~~~~~~r~k 309 (747)
|...++.+|..+..+|...+.+. |..+|..+++|.-
T Consensus 4 I~~~v~~~p~~s~~~i~~~l~~~-~~~vS~~TI~r~L 39 (72)
T PF01498_consen 4 IVRMVRRNPRISAREIAQELQEA-GISVSKSTIRRRL 39 (72)
T ss_dssp ------------HHHHHHHT----T--S-HHHHHHHH
T ss_pred HHHHHHHCCCCCHHHHHHHHHHc-cCCcCHHHHHHHH
Confidence 34556789999999999999988 9999999998864
No 98
>PF08766 DEK_C: DEK C terminal domain; InterPro: IPR014876 DEK is a chromatin associated protein that is linked with cancers and autoimmune disease. This domain is found at the C-terminal of DEK and is of clinical importance since it can reverse the characteristic abnormal DNA-mutagen sensitivity in fibroblasts from ataxia-telangiectasia (A-T) patients []. The structure of this domain shows it to be homologous to the E2F/DP transcription factor family []. This domain is also found in chitin synthase proteins like Q8TF96 from SWISSPROT, and in protein phosphatases such as Q6NN85 from SWISSPROT. ; PDB: 1Q1V_A.
Probab=32.18 E-value=81 Score=23.57 Aligned_cols=36 Identities=17% Similarity=0.447 Sum_probs=22.9
Q ss_pred HHHHHHHHhhh--CCCCChHHHHHHHHHHhCCccCHHH
Q 004519 269 VGNIIKEKLKA--SPNYKPKDIADDIKREYGIQLNYSQ 304 (747)
Q Consensus 269 i~~~~~~~~~~--~~~~~~~~i~~~i~~~~g~~~~~~~ 304 (747)
+...+.+.++. -..++.++|.+.+.+.+|+.++..+
T Consensus 5 i~~~i~~iL~~~dl~~vT~k~vr~~Le~~~~~dL~~~K 42 (54)
T PF08766_consen 5 IREAIREILREADLDTVTKKQVREQLEERFGVDLSSRK 42 (54)
T ss_dssp HHHHHHHHHTTS-GGG--HHHHHHHHHHH-SS--SHHH
T ss_pred HHHHHHHHHHhCCHhHhhHHHHHHHHHHHHCCCcHHHH
Confidence 45566666663 2467999999999999999998543
No 99
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=30.95 E-value=26 Score=24.83 Aligned_cols=18 Identities=33% Similarity=0.798 Sum_probs=16.3
Q ss_pred eeecCCCCCCCcCcCCCC
Q 004519 728 SLQCSKCKGLGHNKKTCK 745 (747)
Q Consensus 728 ~~~Cs~C~~~GHn~~tC~ 745 (747)
...|-+|++.||-.--||
T Consensus 4 ~~~CqkC~~~GH~tyeC~ 21 (42)
T PF13917_consen 4 RVRCQKCGQKGHWTYECP 21 (42)
T ss_pred CCcCcccCCCCcchhhCC
Confidence 368999999999999998
No 100
>PF13276 HTH_21: HTH-like domain
Probab=29.65 E-value=1.1e+02 Score=23.16 Aligned_cols=41 Identities=32% Similarity=0.509 Sum_probs=32.9
Q ss_pred HHHHHHHHhhhC-CCCChHHHHHHHHHHhCCccCHHHHHHHH
Q 004519 269 VGNIIKEKLKAS-PNYKPKDIADDIKREYGIQLNYSQAWRAK 309 (747)
Q Consensus 269 i~~~~~~~~~~~-~~~~~~~i~~~i~~~~g~~~~~~~~~r~k 309 (747)
+...+.+....+ +.+..+.|...|++++|+.++..+++|..
T Consensus 6 l~~~I~~i~~~~~~~yG~rri~~~L~~~~~~~v~~krV~RlM 47 (60)
T PF13276_consen 6 LRELIKEIFKESKPTYGYRRIWAELRREGGIRVSRKRVRRLM 47 (60)
T ss_pred HHHHHHHHHHHcCCCeehhHHHHHHhccCcccccHHHHHHHH
Confidence 445566666654 88999999999999999999999888753
No 101
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=29.61 E-value=13 Score=28.20 Aligned_cols=22 Identities=14% Similarity=0.483 Sum_probs=15.3
Q ss_pred cceeecCCCCCCCcCcCCCCCC
Q 004519 726 KRSLQCSKCKGLGHNKKTCKDS 747 (747)
Q Consensus 726 kr~~~Cs~C~~~GHn~~tC~~~ 747 (747)
.....|+.||..--.-+-|+.|
T Consensus 24 ~~l~~c~~cg~~~~~H~vc~~c 45 (56)
T PF01783_consen 24 PNLVKCPNCGEPKLPHRVCPSC 45 (56)
T ss_dssp TSEEESSSSSSEESTTSBCTTT
T ss_pred cceeeeccCCCEecccEeeCCC
Confidence 3678999999765444666654
No 102
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=28.37 E-value=28 Score=33.47 Aligned_cols=16 Identities=31% Similarity=0.875 Sum_probs=14.4
Q ss_pred eecCCCCCCCcCcCCC
Q 004519 729 LQCSKCKGLGHNKKTC 744 (747)
Q Consensus 729 ~~Cs~C~~~GHn~~tC 744 (747)
.+|.+||+.||-++-|
T Consensus 98 ~~C~~Cg~~GH~~~dC 113 (190)
T COG5082 98 KKCYNCGETGHLSRDC 113 (190)
T ss_pred cccccccccCcccccc
Confidence 5899999999999999
No 103
>cd01791 Ubl5 UBL5 ubiquitin-like modifier. UBL5 (also known as HUB1) is a ubiquitin-like modifier that is both widely expressed and highly phylogenetically conserved. At the C-terminal end of the ubiquitin-like fold of UBL5 is a di-tyrosine motif followed by a single variable residue instead of the characteristic di-glycine found in all other ubiquitin-like modifiers. ULB5 interacts with a cyclin-like kinase called CLK4 but not with other cyclin-like kinase family members.
Probab=27.50 E-value=1.2e+02 Score=24.34 Aligned_cols=37 Identities=11% Similarity=0.277 Sum_probs=33.2
Q ss_pred CceeEEEecCCCChhhHHHHHHHHhcCCCCceEEEEE
Q 004519 31 GEAYAIDIDEETEFSGFKSEVAEMFNCSADTMSIKYF 67 (747)
Q Consensus 31 g~~~~~~v~~~~s~~~~~~~l~~~~~~~~~~~~~~y~ 67 (747)
|+...+.|+.+-+-.+|..+|.+..+++.+..++.|.
T Consensus 11 Gk~~~~~v~~~~TV~~LK~~I~~~~~~~~~~qrLi~~ 47 (73)
T cd01791 11 GKKVRVKCNPDDTIGDLKKLIAAQTGTRPEKIVLKKW 47 (73)
T ss_pred CCEEEEEeCCCCcHHHHHHHHHHHhCCChHHEEEEeC
Confidence 6777789999999999999999999999999998876
No 104
>PF13082 DUF3931: Protein of unknown function (DUF3931)
Probab=26.31 E-value=1.7e+02 Score=21.43 Aligned_cols=40 Identities=10% Similarity=0.155 Sum_probs=26.0
Q ss_pred EEEEeccccC-Cc------------ccceEEEEEEecCCCCeEEEEEEEeecC
Q 004519 374 LLFLDTTPLN-SK------------YQGTLLTATSADGDDGIFPVAFAVVDAE 413 (747)
Q Consensus 374 vl~iD~t~~~-~~------------y~~~l~~a~g~d~~~~~~pla~a~v~~E 413 (747)
||.|||.-++ .. |...-++..|..++|+...+...+..+|
T Consensus 10 visidgkkkksdtysypklvvenktyefssfvlcgetpdgrrlvlthmistde 62 (66)
T PF13082_consen 10 VISIDGKKKKSDTYSYPKLVVENKTYEFSSFVLCGETPDGRRLVLTHMISTDE 62 (66)
T ss_pred EEEeccccccCCcccCceEEEeCceEEEEEEEEEccCCCCcEEEEEEEecchh
Confidence 7778876543 22 3344566778888888877777665554
No 105
>PF10045 DUF2280: Uncharacterized conserved protein (DUF2280); InterPro: IPR018738 This entry is represented by Burkholderia phage Bups phi1, Orf2.36. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=25.92 E-value=75 Score=27.31 Aligned_cols=24 Identities=29% Similarity=0.621 Sum_probs=20.9
Q ss_pred ChHHHHHHHHHHhCCccCHHHHHH
Q 004519 284 KPKDIADDIKREYGIQLNYSQAWR 307 (747)
Q Consensus 284 ~~~~i~~~i~~~~g~~~~~~~~~r 307 (747)
+|.++.+.++++||+.+|..|+-.
T Consensus 21 TPs~v~~aVk~eFgi~vsrQqve~ 44 (104)
T PF10045_consen 21 TPSEVAEAVKEEFGIDVSRQQVES 44 (104)
T ss_pred CHHHHHHHHHHHhCCccCHHHHHH
Confidence 789999999999999999876643
No 106
>PF13877 RPAP3_C: Potential Monad-binding region of RPAP3
Probab=25.69 E-value=35 Score=28.88 Aligned_cols=34 Identities=12% Similarity=0.269 Sum_probs=28.2
Q ss_pred CChhhHHHHHHHHhccChhHHHHHhhcCCCCccc
Q 004519 496 PKFEGFQCSIESIKGISPDAYDWVTQSEPEHWAN 529 (747)
Q Consensus 496 ~~~~ef~~~~~~l~~~~~~~~~~l~~~~~~~Wa~ 529 (747)
.+..||++.|..+.......++||..+.++....
T Consensus 5 ~~~~eF~~~w~~~~~~~~~~~~yL~~i~p~~l~~ 38 (94)
T PF13877_consen 5 KNSYEFERDWRRLKKDPEERYEYLKSIPPDSLPK 38 (94)
T ss_pred CCHHHHHHHHHHHcCCHHHHHHHHHhCChHHHHH
Confidence 4678999999999877778999999987776664
No 107
>PF01283 Ribosomal_S26e: Ribosomal protein S26e; InterPro: IPR000892 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic ribosomal proteins can be grouped on the basis of sequence similarities. One of these families, the S26E family, includes mammalian S26 []; Octopus S26 []; Drosophila S26 (DS31) []; plant cytoplasmic S26; and fungal S26 []. These proteins have 114 to 127 amino acids.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3U5G_a 3U5C_a 2XZM_5 2XZN_5.
Probab=25.24 E-value=53 Score=28.83 Aligned_cols=27 Identities=26% Similarity=0.532 Sum_probs=12.9
Q ss_pred CCCCCCCCCCCCCCCCccccccceeecCCCCC
Q 004519 705 PPTRRPPGRPKMKQPESAEIIKRSLQCSKCKG 736 (747)
Q Consensus 705 P~~~r~~GRPkk~r~~~~~~~kr~~~Cs~C~~ 736 (747)
|.+||-.||-|+.|- .-..++|.+|+.
T Consensus 2 ~~KRrN~Gr~KkgrG-----hv~~V~C~nCgr 28 (113)
T PF01283_consen 2 TKKRRNNGRSKKGRG-----HVQPVRCDNCGR 28 (113)
T ss_dssp ----TTTTSS-SSSS--------EEE-TTTB-
T ss_pred CcccccCCCCCCCCC-----CCcCEeeCcccc
Confidence 456777787776652 224689999975
No 108
>PF13551 HTH_29: Winged helix-turn helix
Probab=24.83 E-value=1.4e+02 Score=25.58 Aligned_cols=38 Identities=24% Similarity=0.441 Sum_probs=29.6
Q ss_pred HHHHHhhhCC-----CCChHHHHHHH-HHHhCCccCHHHHHHHH
Q 004519 272 IIKEKLKASP-----NYKPKDIADDI-KREYGIQLNYSQAWRAK 309 (747)
Q Consensus 272 ~~~~~~~~~~-----~~~~~~i~~~i-~~~~g~~~~~~~~~r~k 309 (747)
.+.+.+..+| .+++..|.+.+ ++.+|+.++.+.+++.-
T Consensus 65 ~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L 108 (112)
T PF13551_consen 65 QLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRIL 108 (112)
T ss_pred HHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHH
Confidence 5555566665 46789999876 88899999999998864
No 109
>cd01792 ISG15_repeat1 ISG15 ubiquitin-like protein, first repeat of 2. ISG15 is a ubiquitin-like protein containing two ubiquitin homology domains that becomes conjugated to a variety of proteins when cells are treated with type I interferon or lipopolysaccharide. Although ISG15 has properties similar to those of other ubiquitin-like molecules, it is a unique member of the ubiquitin-like superfamily, whose expression and conjugation to target proteins are tightly regulated by specific signaling pathways, indicating it may have specialized functions in the immune system.
Probab=24.62 E-value=2e+02 Score=23.37 Aligned_cols=39 Identities=15% Similarity=0.311 Sum_probs=32.5
Q ss_pred EecCceeEEEecCCCChhhHHHHHHHHhcCCCCceEEEE
Q 004519 28 YNGGEAYAIDIDEETEFSGFKSEVAEMFNCSADTMSIKY 66 (747)
Q Consensus 28 Y~gg~~~~~~v~~~~s~~~~~~~l~~~~~~~~~~~~~~y 66 (747)
-.+|++..+.|+.+.+-.+|.++|.+..++..+..++.+
T Consensus 9 ~~~G~~~~~~v~~~~TV~~lK~~I~~~~~i~~~~qrL~~ 47 (80)
T cd01792 9 MLGGNEFLVSLRDSMTVSELKQQIAQKIGVPAFQQRLAH 47 (80)
T ss_pred eCCCCEEEEEcCCCCcHHHHHHHHHHHhCCCHHHEEEEe
Confidence 345777778899999999999999999998888888743
No 110
>PF08086 Toxin_17: Ergtoxin family; InterPro: IPR012622 The Ergtoxin (ErgTx) family is a class of peptides from scorpion venom that specifically block ERG (ether-a-go-go-related gene) K+ channels of the nerve, heart and endocrine cells [, , ]. Peptides of the ErgTx family have from 42 to 47 amino acid residues cross-linked by four disulphide bridges. The four disulphide bridges have been assigned as C1-C4, C2-C6, C3-C7 and C5-C8 (see the schematic representation below) []. ErgTxs consist of a triple-stranded beta-sheet and an alpha-helix, as is typical of K+ channel scorpion toxins. There is a large hydrophobic patch on the surface of the toxin, surrounding a central lysine residue located near the beta-hairpin loop between the second and third strands of the beta-sheet. It has been postulated that this hydrophobic patch is likely to form part of the binding surface of the toxin []. Peptides of the ErgTx family possess a Knottin scaffold (see http://knottin.cbs.cnrs.fr). Some proteins known to belong to the ErgTx family are listed below: ErgTx1, ErgTx2 and ErgTx3 from Centruroides elegans (Bark scorpion). ErgTx1, ErgTx2, ErgTx3 and ErgTx4 from Centruroides exilicauda (Bark scorpion). ErgTx1, ErgTx2 and ErgTx3 from Centruroides gracilis (Slenderbrown scorpion) (Florida bark scorpion). ErgTx1, ErgTx2, ErgTx3 and ErgTx4 from Centruroides limpidus limpidus (Mexican scorpion). ErgTx1, ErgTx2, ErgTx3, ErgTx4, ErgTx5 and gamma-KTx 4.12 from Centruroides sculpturatus (Bark scorpion). ErgTx, ErgTx2, ErgTx3, ErgTx4 and ErgTx5 from Centruroides noxius (Mexican scorpion). ; GO: 0019870 potassium channel inhibitor activity, 0009405 pathogenesis, 0005576 extracellular region; PDB: 1NE5_A 1PX9_A.
Probab=24.21 E-value=8.9 Score=25.74 Aligned_cols=11 Identities=55% Similarity=1.123 Sum_probs=8.5
Q ss_pred CCCCCcCcCCC
Q 004519 734 CKGLGHNKKTC 744 (747)
Q Consensus 734 C~~~GHn~~tC 744 (747)
|+..|||..||
T Consensus 24 ckkag~~~gtc 34 (41)
T PF08086_consen 24 CKKAGHRGGTC 34 (41)
T ss_dssp HHHHTSS-EEE
T ss_pred HHHhCCCCcee
Confidence 67899999888
No 111
>cd01797 NIRF_N amino-terminal ubiquitin-like domain of Np95 and NIRF. NIRF_N This CD represents the amino-terminal ubiquitin-like domain of a family of nuclear proteins that includes Np95 and NIRF (Np95/ICBP90-like RING finger) protein. Both Np95 and NIRF have a domain architecture consisting of a ubiquitin-like domain, a PHD finger, a YDG/SRA domain, Rb-binding motifs and a RING finger domain. Both Np95 and NIRF are ubiquitin ligases that ubiquitinate PCNP (PEST-containing nuclear proteins). While Np95 is capable of binding histones, NIRF is involved in cell cycle regulation.
Probab=24.06 E-value=1.4e+02 Score=24.35 Aligned_cols=38 Identities=16% Similarity=0.406 Sum_probs=31.4
Q ss_pred cCce-eEE-EecCCCChhhHHHHHHHHhcCCCCceEEEEE
Q 004519 30 GGEA-YAI-DIDEETEFSGFKSEVAEMFNCSADTMSIKYF 67 (747)
Q Consensus 30 gg~~-~~~-~v~~~~s~~~~~~~l~~~~~~~~~~~~~~y~ 67 (747)
.|++ ..+ .++.+.|..+|.++|.+..++..++.++-|.
T Consensus 9 ~G~~~~~l~~v~~~~TV~~lK~~i~~~~gi~~~~QrLi~~ 48 (78)
T cd01797 9 DGKETRTVDSLSRLTKVEELREKIQELFNVEPECQRLFYR 48 (78)
T ss_pred CCCEEEEeeccCCcCcHHHHHHHHHHHhCCCHHHeEEEeC
Confidence 4554 456 4788999999999999999998888899885
No 112
>KOG4027 consensus Uncharacterized conserved protein [Function unknown]
Probab=23.92 E-value=92 Score=28.93 Aligned_cols=36 Identities=14% Similarity=0.171 Sum_probs=30.4
Q ss_pred Eecccc-CCcccce--EEEEEEecCCCCeEEEEEEEeec
Q 004519 377 LDTTPL-NSKYQGT--LLTATSADGDDGIFPVAFAVVDA 412 (747)
Q Consensus 377 iD~t~~-~~~y~~~--l~~a~g~d~~~~~~pla~a~v~~ 412 (747)
||.||+ ++.|++| ++...|.|+-|+-...|||.+.-
T Consensus 70 ievt~KstsPygWPqivl~vfg~d~~G~d~v~GYg~~hi 108 (187)
T KOG4027|consen 70 IEVTLKSTSPYGWPQIVLNVFGKDHSGKDCVTGYGMLHI 108 (187)
T ss_pred eEEEeccCCCCCCceEEEEEecCCcCCcceeeeeeeEec
Confidence 678886 7899987 67788999999999999998743
No 113
>PF08459 UvrC_HhH_N: UvrC Helix-hairpin-helix N-terminal; InterPro: IPR001162 During the process of Escherichia coli nucleotide excision repair, DNA damage recognition and processing are achieved by the action of the uvrA, uvrB, and uvrC gene products []. The UvrC proteins contain 4 conserved regions: a central region which interacts with UvrB (Uvr domain), a Helix hairpin Helix (HhH) domain important for 5 prime incision of damage DNA and the homology regions 1 and 2 of unknown function. UvrC homology region 2 is specific for UvrC proteins, whereas UvrC homology region 1 is also shared by few other nucleases. Proteins that contain the UvrC homology region 1, IPR000305 from INTERPRO, are listed below: Prokaryotic UvrC proteins. Bacteriophage T4 END2 protein. Small subunit of ribonucleotide reductase enzyme. T4 TEV1 protein. Endonuclease specific to the thymidylate synthase (td) gene splice junction. Found in putative intron-homing endonucleases encoded by group I introns of fungi and phage. Mycobacterium hypothetical protein Y002. Exonuclease by similarity. Bacillus subtilis hypothetical protein YURQ. ; GO: 0003677 DNA binding, 0004518 nuclease activity, 0006289 nucleotide-excision repair; PDB: 3C65_A 2NRZ_A 2NRR_A 2NRX_A 2NRV_A 2NRT_A 2NRW_A.
Probab=23.76 E-value=1.6e+02 Score=27.65 Aligned_cols=45 Identities=13% Similarity=0.121 Sum_probs=32.5
Q ss_pred ecCCcccHHHHHHHHHhhcCCC------CcEEEEecCcchhHHHHhhhccC
Q 004519 411 DAETEDNWHWFLQELKSAVSTS------QQITFIADFQNGLNKSLAEVFDN 455 (747)
Q Consensus 411 ~~E~~e~~~wfl~~l~~~~~~~------~~~~iisD~~~~l~~Ai~~vfP~ 455 (747)
+.+..++|..+-+.+.+.+... -|-.|+.|+.+|-.+|+.+++-.
T Consensus 51 ~~~~~dDy~~M~Evl~RR~~~~~~~~~~lPDLilIDGG~gQl~aa~~~l~~ 101 (155)
T PF08459_consen 51 TVDGGDDYAAMREVLTRRFKRLKEEKEPLPDLILIDGGKGQLNAAKEVLKE 101 (155)
T ss_dssp --STT-HHHHHHHHHHHHHCCCHHHT----SEEEESSSHHHHHHHHHHHHC
T ss_pred CCCCCcHHHHHHHHHHHHHhcccccCCCCCCEEEEcCCHHHHHHHHHHHHH
Confidence 3455688999988888876532 47889999999999999888653
No 114
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=23.44 E-value=60 Score=25.06 Aligned_cols=37 Identities=8% Similarity=0.069 Sum_probs=20.7
Q ss_pred CCCCCCCCCCCCCCCCccccccceeecCCCCCC--CcCc
Q 004519 705 PPTRRPPGRPKMKQPESAEIIKRSLQCSKCKGL--GHNK 741 (747)
Q Consensus 705 P~~~r~~GRPkk~r~~~~~~~kr~~~Cs~C~~~--GHn~ 741 (747)
|..+..+-|.+++|..-.........|+.|+.. -|..
T Consensus 4 PKrK~Sksr~~~RRa~~~~~~~~~~~c~~cg~~~~pH~v 42 (60)
T PRK01110 4 PKRKTSKSKRRMRRSHWKLTAPTLSVDKTTGEYHLPHHV 42 (60)
T ss_pred CcCccchhhchhhhhhhhccCCceeEcCCCCceecccee
Confidence 445555555555554322233346889999864 5543
No 115
>cd01808 hPLIC_N Ubiquitin-like domain of hPLIC-1 and hPLIC2. hPLIC-1 and hPLIC-2 (human homologs of the yeast ubiquitin-like Dsk2 protein) are type2 UBL's (ubiquitin-like) proteins that are thought to serve as adaptors that link the ubiquitination machinery to the proteasome. The hPLIC's have an N-terminal UBL domain that binds the S5a subunit of the proteasome and a C-terminal UBA (ubiquitin-associated) domain that binds a ubiquitylated protein.
Probab=21.99 E-value=1.7e+02 Score=23.05 Aligned_cols=36 Identities=19% Similarity=0.482 Sum_probs=30.1
Q ss_pred cCceeEEEecCCCChhhHHHHHHHHhcCCCCceEEEE
Q 004519 30 GGEAYAIDIDEETEFSGFKSEVAEMFNCSADTMSIKY 66 (747)
Q Consensus 30 gg~~~~~~v~~~~s~~~~~~~l~~~~~~~~~~~~~~y 66 (747)
.|.. .+.|+.+.|-.+|..+|.+..++..++.++.|
T Consensus 9 ~g~~-~l~v~~~~TV~~lK~~I~~~~~i~~~~~~Li~ 44 (71)
T cd01808 9 KDKE-EIEIAEDASVKDFKEAVSKKFKANQEQLVLIF 44 (71)
T ss_pred CCCE-EEEECCCChHHHHHHHHHHHhCCCHHHEEEEE
Confidence 3443 68999999999999999999998877788766
No 116
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=21.44 E-value=38 Score=25.87 Aligned_cols=19 Identities=26% Similarity=0.679 Sum_probs=13.3
Q ss_pred eeecCCCCCCCcCcCCCCCC
Q 004519 728 SLQCSKCKGLGHNKKTCKDS 747 (747)
Q Consensus 728 ~~~Cs~C~~~GHn~~tC~~~ 747 (747)
+.+|.+|++.|+. =+||+|
T Consensus 36 I~RC~~CRk~~~~-Y~CP~C 54 (59)
T PRK14890 36 IYRCEKCRKQSNP-YTCPKC 54 (59)
T ss_pred EeechhHHhcCCc-eECCCC
Confidence 5778888888744 457765
No 117
>PF01949 DUF99: Protein of unknown function DUF99; InterPro: IPR002802 The function of the archaebacterial proteins in this family is unknown.; PDB: 2QH9_A.
Probab=21.43 E-value=3.5e+02 Score=26.28 Aligned_cols=85 Identities=18% Similarity=0.264 Sum_probs=49.5
Q ss_pred EEEEeccccCCcccceEEEEEEecCCCCeEEEEEEEeecCCcccHHHHHHHHHhh--------c-CC-------------
Q 004519 374 LLFLDTTPLNSKYQGTLLTATSADGDDGIFPVAFAVVDAETEDNWHWFLQELKSA--------V-ST------------- 431 (747)
Q Consensus 374 vl~iD~t~~~~~y~~~l~~a~g~d~~~~~~pla~a~v~~E~~e~~~wfl~~l~~~--------~-~~------------- 431 (747)
+|+||-.|....-+..+++-+-..+++..--++|+.+.-...|.=.-+.+.++.. | .+
T Consensus 6 vlGidDs~f~~~~~~s~lvGvv~r~~~~idGv~~~~itvdG~DaT~~i~~m~~~~~r~~i~~v~LdGit~agFNiiD~~~ 85 (187)
T PF01949_consen 6 VLGIDDSPFPRSDGKSVLVGVVMRGDRRIDGVAFGRITVDGMDATEAIIEMVKRLFRPDIRVVMLDGITFAGFNIIDIER 85 (187)
T ss_dssp EEEEEEEE-SS----EEEEEEEEETT-EEEEEEEEEE-TT-S-HHHHHHHHHCCTTTTTEEEEEESSSEETTTEE--HHH
T ss_pred EEEEecCCCccCCCceEEEEEEEeCCeEEEEEEEEEEEECCchHHHHHHHHHHhcccCcceEEEECCEeEEeeEEecHHH
Confidence 7888877765544445666666667767777899988888888777777777651 0 00
Q ss_pred -----CCcEEEEecCcc---hhHHHHhhhccCccc
Q 004519 432 -----SQQITFIADFQN---GLNKSLAEVFDNCYH 458 (747)
Q Consensus 432 -----~~~~~iisD~~~---~l~~Ai~~vfP~a~h 458 (747)
.-|++.++-..+ +|.+|+++.||+...
T Consensus 86 l~~~tg~PVI~V~~~~p~~~~i~~AL~~hF~d~~~ 120 (187)
T PF01949_consen 86 LYEETGLPVIVVMRKEPNLEGIESALRKHFPDWEE 120 (187)
T ss_dssp HHHHH---EEEEESS---HHHHHHCCTT-STTHHH
T ss_pred HHHHHCCCEEEEEEeCCCHHHHHHHHHHhCCCHHH
Confidence 025555555544 688999999998764
No 118
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=21.32 E-value=37 Score=25.13 Aligned_cols=21 Identities=29% Similarity=0.808 Sum_probs=12.9
Q ss_pred ceeecCCCC-------CCCcCcCCCCCC
Q 004519 727 RSLQCSKCK-------GLGHNKKTCKDS 747 (747)
Q Consensus 727 r~~~Cs~C~-------~~GHn~~tC~~~ 747 (747)
++.+|..|+ ..||=...||.|
T Consensus 3 ~tiRC~~CnKlLa~a~~~~yle~KCPrC 30 (60)
T COG4416 3 QTIRCAKCNKLLAEAEGQAYLEKKCPRC 30 (60)
T ss_pred eeeehHHHhHHHHhcccceeeeecCCcc
Confidence 346677773 346667777765
No 119
>COG0484 DnaJ DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]
Probab=21.09 E-value=94 Score=33.56 Aligned_cols=22 Identities=41% Similarity=0.872 Sum_probs=15.3
Q ss_pred cceeecCCCCCCCcCcC----CCCCC
Q 004519 726 KRSLQCSKCKGLGHNKK----TCKDS 747 (747)
Q Consensus 726 kr~~~Cs~C~~~GHn~~----tC~~~ 747 (747)
.+...|+.|++.|=... ||+.|
T Consensus 140 ~~~~~C~~C~GsGak~gt~~~tC~tC 165 (371)
T COG0484 140 TRSVTCSTCHGSGAKPGTDPKTCPTC 165 (371)
T ss_pred ceeeECCcCCCCCCCCCCCCCcCCCC
Confidence 46788888877655444 77776
No 120
>PF09713 A_thal_3526: Plant protein 1589 of unknown function (A_thal_3526); InterPro: IPR006476 This plant-specific family of proteins are defined by an uncharacterised region 57 residues in length. It is found toward the N terminus of most proteins that contain it. Examples include at least several proteins from Arabidopsis thaliana (Mouse-ear cress) and Oryza sativa (Rice). The function of the proteins are unknown.
Probab=20.88 E-value=94 Score=23.43 Aligned_cols=26 Identities=12% Similarity=0.404 Sum_probs=18.9
Q ss_pred CCChHHHHHHHHHHhCCccCH-HHHHH
Q 004519 282 NYKPKDIADDIKREYGIQLNY-SQAWR 307 (747)
Q Consensus 282 ~~~~~~i~~~i~~~~g~~~~~-~~~~r 307 (747)
.++..+++..+.++.++.... ..+|+
T Consensus 12 yMsk~E~v~~L~~~a~I~P~~T~~VW~ 38 (54)
T PF09713_consen 12 YMSKEECVRALQKQANIEPVFTSTVWQ 38 (54)
T ss_pred cCCHHHHHHHHHHHcCCChHHHHHHHH
Confidence 467789999999998887654 34554
No 121
>PF14847 Ras_bdg_2: Ras-binding domain of Byr2; PDB: 1I35_A 1K8R_B.
Probab=20.68 E-value=3.8e+02 Score=23.33 Aligned_cols=76 Identities=11% Similarity=0.132 Sum_probs=45.9
Q ss_pred EEEecCceeEEEecCCCChhhHHHHHHHHhcCCCCc-eEEEEEecC-C-CCcceeeeCcHHHHHHHhhccCcceEEEEE
Q 004519 26 LSYNGGEAYAIDIDEETEFSGFKSEVAEMFNCSADT-MSIKYFLPG-N-KKTLISISKDKDFKRMLNFLGDTATVDVFI 101 (747)
Q Consensus 26 ~~Y~gg~~~~~~v~~~~s~~~~~~~l~~~~~~~~~~-~~~~y~lp~-~-~~~l~~v~~D~dl~~m~~~~~~~~~~~i~~ 101 (747)
+.+.||.++.+.|..=.+-.+.+.++...||+..+. -=.-|.+.+ + +......-.|.+|..+..-.++..+=++.+
T Consensus 5 ~I~~dG~tk~VNV~~c~~a~eI~~rvLKKfg~~~~~~~~~~~v~d~~~~~~~~~~~LsD~EL~~IC~s~~r~er~Rlil 83 (105)
T PF14847_consen 5 FILEDGSTKTVNVSGCFNAQEIKRRVLKKFGLPEHPRNYCFYVLDGESPDPSNCRPLSDVELVTICHSPDRPERNRLIL 83 (105)
T ss_dssp EEETTTEEEEEE--S--HHHHHHHHHHHHHTSS--CCCEEEEEE-S-----SSEEEE-SSHHHHHHHTT--SSS--EEE
T ss_pred EECCCCcEEEEEECCCCCHHHHHHHHHHHcCCccccccceEEEecccccccccceECcHHHHHHHHcCCCCccccceEE
Confidence 567899999999999889999999999999876521 234455554 2 222455557889988887777766555665
No 122
>PF03705 CheR_N: CheR methyltransferase, all-alpha domain; InterPro: IPR022641 CheR proteins are part of the chemotaxis signaling mechanism which methylates the chemotaxis receptor at specific glutamate residues. This entry refers to the N-terminal domain of the CherR-type MCP methyltransferases, which are found in bacteria, archaea and green plants. This entry is found in association with PF01739 from PFAM. Methyl transfer from the ubiquitous S-adenosyl-L-methionine (AdoMet) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms ranging from bacteria to plants and mammals. The reaction is catalysed by methyltransferases (Mtases) and modifies DNA, RNA, proteins and small molecules, such as catechol for regulatory purposes. The various aspects of the role of DNA methylation in prokaryotic restriction-modification systems and in a number of cellular processes in eukaryotes including gene regulation and differentiation is well documented. Three classes of DNA Mtases transfer the methyl group from AdoMet to the target base to form either N-6-methyladenine, or N-4-methylcytosine, or C-5- methylcytosine. In C-5-cytosine Mtases, ten conserved motifs are arranged in the same order []. Motif I (a glycine-rich or closely related consensus sequence; FAGxGG in M.HhaI []), shared by other AdoMet-Mtases [], is part of the cofactor binding site and motif IV (PCQ) is part of the catalytic site. In contrast, sequence comparison among N-6-adenine and N-4-cytosine Mtases indicated two of the conserved segments [], although more conserved segments may be present. One of them corresponds to motif I in C-5-cytosine Mtases, and the other is named (D/N/S)PP(Y/F). Crystal structures are known for a number of Mtases [, , , ]. The cofactor binding sites are almost identical and the essential catalytic amino acids coincide. The comparable protein folding and the existence of equivalent amino acids in similar secondary and tertiary positions indicate that many (if not all) AdoMet-Mtases have a common catalytic domain structure. This permits tertiary structure prediction of other DNA, RNA, protein, and small-molecule AdoMet-Mtases from their amino acid sequences []. Flagellated bacteria swim towards favourable chemicals and away from deleterious ones. Sensing of chemoeffector gradients involves chemotaxis receptors, transmembrane (TM) proteins that detect stimuli through their periplasmic domains and transduce the signals via their cytoplasmic domains []. Signalling outputs from these receptors are influenced both by the binding of the chemoeffector ligand to their periplasmic domains and by methylation of specific glutamate residues on their cytoplasmic domains. Methylation is catalysed by CheR, an S-adenosylmethionine-dependent methyltransferase [], which reversibly methylates specific glutamate residues within a coiled coil region, to form gamma-glutamyl methyl ester residues [, ]. The structure of the Salmonella typhimurium chemotaxis receptor methyltransferase CheR, bound to S-adenosylhomocysteine, has been determined to a resolution of 2.0 A []. The structure reveals CheR to be a two-domain protein, with a smaller N-terminal helical domain linked via a single polypeptide connection to a larger C-terminal alpha/beta domain. The C-terminal domain has the characteristics of a nucleotide-binding fold, with an insertion of a small anti-parallel beta-sheet subdomain. The S-adenosylhomocysteine-binding site is formed mainly by the large domain, with contributions from residues within the N-terminal domain and the linker region [].; PDB: 1AF7_A 1BC5_A.
Probab=20.45 E-value=2.9e+02 Score=20.44 Aligned_cols=50 Identities=14% Similarity=0.186 Sum_probs=22.0
Q ss_pred HHHHHHHHHHhCCccCHHHHHHHHHHHHHHHhcCHHHHhccHHHHHHHHHHhCC
Q 004519 286 KDIADDIKREYGIQLNYSQAWRAKEIAREQLQGSYKDSYTLLPFFCEKIKETNP 339 (747)
Q Consensus 286 ~~i~~~i~~~~g~~~~~~~~~r~k~~~~~~~~g~~~~~~~~L~~~~~~l~~~np 339 (747)
..+.+.|.+.+|+.++-.+-...+++....+. ...+..+..|++.| +++|
T Consensus 6 ~~~~~~i~~~~Gi~l~~~K~~~l~rRl~~rm~---~~~~~~~~~y~~~L-~~d~ 55 (57)
T PF03705_consen 6 ERFRELIYRRTGIDLSEYKRSLLERRLARRMR---ALGLPSFAEYYELL-RSDP 55 (57)
T ss_dssp HHHHHHHHHHH-----GGGHHHHHHHHHHHHH---HHT---HHHHHHHH-HH-T
T ss_pred HHHHHHHHHHHCCCCchhhHHHHHHHHHHHHH---HcCCCCHHHHHHHH-HhCC
Confidence 35678889999998876554444333333322 22344556666655 3344
Done!