Query 003638
Match_columns 806
No_of_seqs 434 out of 1823
Neff 8.4
Searched_HMMs 46136
Date Fri Mar 29 03:12:26 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/003638.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/003638hhsearch_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 4.6E-69 1E-73 625.6 42.8 473 237-732 73-623 (846)
2 cd06410 PB1_UP2 Uncharacterize 99.9 2.7E-25 5.8E-30 192.2 11.5 90 50-140 1-96 (97)
3 PF10551 MULE: MULE transposas 99.8 5.7E-21 1.2E-25 168.2 8.8 90 436-528 1-93 (93)
4 PF00872 Transposase_mut: Tran 99.8 8.2E-20 1.8E-24 201.7 4.3 241 337-627 112-368 (381)
5 PF03108 DBD_Tnp_Mut: MuDR fam 99.6 4.9E-16 1.1E-20 127.3 8.8 67 235-301 1-67 (67)
6 COG3328 Transposase and inacti 99.4 3.4E-12 7.3E-17 138.1 17.2 237 337-625 98-345 (379)
7 smart00575 ZnF_PMZ plant mutat 98.8 1.2E-09 2.5E-14 72.1 1.5 28 690-717 1-28 (28)
8 PF08731 AFT: Transcription fa 98.8 4.6E-08 9.9E-13 85.2 9.2 69 244-312 1-111 (111)
9 smart00666 PB1 PB1 domain. Pho 98.5 5.3E-07 1.2E-11 76.8 9.9 75 63-140 4-80 (81)
10 PF03101 FAR1: FAR1 DNA-bindin 98.5 2.4E-07 5.2E-12 80.9 6.4 61 252-313 1-90 (91)
11 cd05992 PB1 The PB1 domain is 98.1 2.8E-05 6E-10 66.2 9.8 74 64-140 4-80 (81)
12 PF04434 SWIM: SWIM zinc finge 97.9 4.5E-06 9.8E-11 60.5 2.1 30 685-714 10-39 (40)
13 cd06407 PB1_NLP A PB1 domain i 97.9 9E-05 1.9E-09 62.7 9.3 73 65-140 5-80 (82)
14 PF00564 PB1: PB1 domain; Int 97.9 5.7E-05 1.2E-09 64.8 8.3 75 65-141 6-82 (84)
15 cd06408 PB1_NoxR The PB1 domai 97.5 0.00038 8.2E-09 58.7 7.0 62 65-131 7-68 (86)
16 cd06406 PB1_P67 A PB1 domain i 97.4 0.0006 1.3E-08 56.5 7.0 67 64-134 6-72 (80)
17 cd06398 PB1_Joka2 The PB1 doma 97.0 0.0079 1.7E-07 52.0 10.0 74 65-141 5-87 (91)
18 cd06396 PB1_NBR1 The PB1 domai 96.7 0.012 2.7E-07 49.1 8.9 69 69-141 8-79 (81)
19 cd06402 PB1_p62 The PB1 domain 96.3 0.026 5.5E-07 48.1 8.2 64 75-141 21-85 (87)
20 cd06397 PB1_UP1 Uncharacterize 96.2 0.035 7.6E-07 45.7 8.2 65 65-132 5-69 (82)
21 cd06404 PB1_aPKC PB1 domain is 96.2 0.033 7.2E-07 46.4 8.1 63 69-133 8-71 (83)
22 cd06405 PB1_Mekk2_3 The PB1 do 96.0 0.063 1.4E-06 43.4 8.5 66 70-141 9-77 (79)
23 cd06411 PB1_p51 The PB1 domain 96.0 0.033 7.1E-07 46.0 7.1 63 72-134 8-70 (78)
24 cd06403 PB1_Par6 The PB1 domai 95.3 0.16 3.5E-06 41.8 8.8 70 67-140 6-77 (80)
25 cd06409 PB1_MUG70 The MUG70 pr 95.1 0.11 2.5E-06 44.1 7.8 70 69-140 9-83 (86)
26 PF00098 zf-CCHC: Zinc knuckle 95.0 0.015 3.4E-07 33.9 1.6 18 787-804 1-18 (18)
27 cd06401 PB1_TFG The PB1 domain 95.0 0.096 2.1E-06 43.6 6.8 60 69-130 8-71 (81)
28 PF03106 WRKY: WRKY DNA -bindi 93.5 0.17 3.6E-06 40.1 5.1 40 272-311 20-59 (60)
29 PF01610 DDE_Tnp_ISL3: Transpo 93.5 0.1 2.3E-06 54.5 5.3 93 432-531 1-96 (249)
30 PF06782 UPF0236: Uncharacteri 93.3 1.5 3.2E-05 50.3 14.6 92 469-567 235-327 (470)
31 PF15288 zf-CCHC_6: Zinc knuck 93.3 0.04 8.7E-07 39.1 1.1 19 786-804 1-21 (40)
32 PF13610 DDE_Tnp_IS240: DDE do 93.1 0.042 9.2E-07 52.0 1.4 81 429-514 1-81 (140)
33 PF03050 DDE_Tnp_IS66: Transpo 92.6 0.28 6.1E-06 52.0 7.1 131 339-532 20-155 (271)
34 PF04684 BAF1_ABF1: BAF1 / ABF 90.3 0.62 1.3E-05 51.2 6.5 56 240-295 24-80 (496)
35 cd01799 Hoil1_N Ubiquitin-like 88.6 1.2 2.6E-05 37.1 5.8 64 69-140 11-74 (75)
36 PF04500 FLYWCH: FLYWCH zinc f 88.1 0.9 1.9E-05 35.8 4.6 46 261-310 14-62 (62)
37 PF13696 zf-CCHC_2: Zinc knuck 87.3 0.35 7.7E-06 32.7 1.4 20 785-804 7-26 (32)
38 smart00774 WRKY DNA binding do 87.2 0.82 1.8E-05 35.9 3.6 39 272-310 20-59 (59)
39 PF13565 HTH_32: Homeodomain-l 81.9 2.7 5.9E-05 34.8 4.9 38 328-365 37-76 (77)
40 COG3316 Transposase and inacti 80.9 15 0.00032 37.0 10.3 121 347-517 32-152 (215)
41 PF00665 rve: Integrase core d 79.8 6.9 0.00015 35.2 7.3 76 428-505 5-81 (120)
42 cd01812 BAG1_N Ubiquitin-like 77.7 4.6 9.9E-05 32.8 4.9 41 65-106 5-45 (71)
43 PHA02517 putative transposase 76.9 9 0.00019 40.6 8.1 149 325-503 30-181 (277)
44 smart00343 ZnF_C2HC zinc finge 76.5 1.4 3.1E-05 28.3 1.2 17 788-804 1-17 (26)
45 cd06399 PB1_P40 The PB1 domain 76.0 11 0.00024 31.9 6.4 60 70-133 13-76 (92)
46 PF14560 Ubiquitin_2: Ubiquiti 75.3 5.8 0.00013 33.9 5.0 35 72-106 15-49 (87)
47 cd01807 GDX_N ubiquitin-like d 74.2 7.4 0.00016 32.1 5.2 42 65-106 5-46 (74)
48 PF11976 Rad60-SLD: Ubiquitin- 73.9 9.1 0.0002 31.2 5.7 42 65-106 5-47 (72)
49 PF11470 TUG-UBL1: GLUT4 regul 73.8 6.2 0.00013 31.8 4.4 38 69-106 5-42 (65)
50 COG5431 Uncharacterized metal- 73.0 7.2 0.00016 34.0 4.8 50 675-726 36-91 (117)
51 cd00196 UBQ Ubiquitin-like pro 72.7 8.5 0.00018 29.1 5.1 43 65-107 2-44 (69)
52 PF14392 zf-CCHC_4: Zinc knuck 72.4 1.5 3.3E-05 33.1 0.6 19 786-804 31-49 (49)
53 cd01796 DDI1_N DNA damage indu 72.3 7.3 0.00016 31.9 4.7 38 69-106 8-45 (71)
54 cd01809 Scythe_N Ubiquitin-lik 71.0 10 0.00022 30.7 5.4 41 65-105 5-45 (72)
55 cd01798 parkin_N amino-termina 70.8 9.3 0.0002 31.1 5.0 42 65-106 3-44 (70)
56 cd01794 DC_UbP_C dendritic cel 70.2 9.3 0.0002 31.3 4.8 54 65-125 3-56 (70)
57 PF02178 AT_hook: AT hook moti 66.0 2.6 5.7E-05 22.5 0.5 9 767-775 2-10 (13)
58 cd01803 Ubiquitin Ubiquitin. U 65.7 13 0.00029 30.4 5.1 41 65-105 5-45 (76)
59 PRK14702 insertion element IS2 65.0 1.1E+02 0.0024 32.1 13.0 147 323-503 10-164 (262)
60 cd01800 SF3a120_C Ubiquitin-li 63.7 13 0.00029 30.8 4.6 38 69-106 6-43 (76)
61 PTZ00044 ubiquitin; Provisiona 62.6 18 0.00039 29.8 5.2 41 66-106 6-46 (76)
62 cd01806 Nedd8 Nebb8-like ubiq 61.3 22 0.00047 29.1 5.6 41 66-106 6-46 (76)
63 cd01805 RAD23_N Ubiquitin-like 60.1 24 0.00051 29.1 5.6 41 65-105 5-47 (77)
64 smart00213 UBQ Ubiquitin homol 60.1 22 0.00047 27.8 5.2 40 66-106 6-45 (64)
65 cd01793 Fubi Fubi ubiquitin-li 57.6 25 0.00054 28.9 5.2 41 66-106 4-44 (74)
66 COG4279 Uncharacterized conser 56.7 4.3 9.3E-05 41.3 0.5 23 690-715 125-147 (266)
67 PRK09409 IS2 transposase TnpB; 56.2 2.4E+02 0.0051 30.3 13.8 145 325-503 51-203 (301)
68 cd01769 UBL Ubiquitin-like dom 56.0 30 0.00064 27.4 5.4 41 66-106 3-43 (69)
69 cd01789 Alp11_N Ubiquitin-like 55.7 28 0.0006 29.6 5.3 32 74-105 16-47 (84)
70 COG4715 Uncharacterized conser 55.6 24 0.00051 40.4 6.1 42 674-717 51-98 (587)
71 cd01813 UBP_N UBP ubiquitin pr 53.9 25 0.00054 29.1 4.6 38 69-106 8-45 (74)
72 smart00384 AT_hook DNA binding 53.8 8 0.00017 24.7 1.2 13 766-778 1-13 (26)
73 cd01763 Sumo Small ubiquitin-r 53.5 29 0.00063 29.7 5.1 42 65-106 16-57 (87)
74 cd01810 ISG15_repeat2 ISG15 ub 52.7 30 0.00065 28.4 4.9 41 65-105 3-43 (74)
75 cd06395 PB1_Map2k5 PB1 domain 50.9 44 0.00094 27.8 5.2 56 74-132 16-71 (91)
76 PF13592 HTH_33: Winged helix- 50.5 24 0.00052 27.8 3.8 30 337-366 2-31 (60)
77 PF00240 ubiquitin: Ubiquitin 48.7 40 0.00088 27.0 5.1 37 69-105 4-40 (69)
78 cd01802 AN1_N ubiquitin-like d 47.4 41 0.0009 29.8 5.2 41 66-106 33-73 (103)
79 cd01804 midnolin_N Ubiquitin-l 42.5 60 0.0013 27.0 5.3 39 68-106 9-47 (78)
80 COG5179 TAF1 Transcription ini 41.9 15 0.00033 42.0 1.9 20 785-804 936-957 (968)
81 PF11543 UN_NPL4: Nuclear pore 40.0 43 0.00093 28.2 3.9 32 72-103 15-46 (80)
82 PF05741 zf-nanos: Nanos RNA b 38.0 14 0.0003 28.7 0.6 20 785-804 32-54 (55)
83 KOG3069 Peroxisomal NUDIX hydr 36.9 13 0.00028 37.6 0.4 33 6-38 41-73 (246)
84 PF14201 DUF4318: Domain of un 35.8 59 0.0013 27.0 4.0 30 243-272 13-42 (74)
85 PRK13907 rnhA ribonuclease H; 34.9 3.2E+02 0.007 24.8 9.5 78 431-511 3-81 (128)
86 PRK09335 30S ribosomal protein 33.7 36 0.00079 29.4 2.5 27 763-794 2-28 (95)
87 PF04937 DUF659: Protein of un 33.7 2.8E+02 0.0061 26.5 8.9 62 470-532 73-137 (153)
88 cd01791 Ubl5 UBL5 ubiquitin-li 32.8 93 0.002 25.6 4.8 37 70-106 11-47 (73)
89 PF01498 HTH_Tnp_Tc3_2: Transp 32.4 41 0.0009 27.3 2.7 36 330-366 4-39 (72)
90 PHA00689 hypothetical protein 32.3 26 0.00055 26.0 1.2 15 783-797 14-28 (62)
91 COG5082 AIR1 Arginine methyltr 30.5 26 0.00056 34.5 1.3 16 787-802 98-113 (190)
92 PRK12286 rpmF 50S ribosomal pr 30.1 53 0.0011 25.7 2.7 34 763-796 4-37 (57)
93 PF13917 zf-CCHC_3: Zinc knuck 29.2 31 0.00068 25.2 1.2 18 786-803 4-21 (42)
94 cd01797 NIRF_N amino-terminal 28.9 1.1E+02 0.0025 25.4 4.8 39 68-106 8-48 (78)
95 PF13276 HTH_21: HTH-like doma 28.3 1.2E+02 0.0026 23.6 4.6 41 326-366 6-47 (60)
96 PLN00186 ribosomal protein S26 27.9 50 0.0011 29.2 2.5 27 763-794 2-28 (109)
97 KOG1769 Ubiquitin-like protein 27.9 1.4E+02 0.003 26.2 5.0 38 68-105 28-65 (99)
98 PF08766 DEK_C: DEK C terminal 27.0 1.2E+02 0.0025 23.3 4.1 36 326-361 5-42 (54)
99 PTZ00172 40S ribosomal protein 26.9 54 0.0012 29.1 2.5 27 763-794 2-28 (108)
100 PRK14892 putative transcriptio 26.4 53 0.0012 28.9 2.4 9 785-793 20-28 (99)
101 PF14847 Ras_bdg_2: Ras-bindin 26.0 2.7E+02 0.0059 24.8 6.8 76 65-140 5-83 (105)
102 PF12762 DDE_Tnp_IS1595: ISXO2 25.6 1.7E+02 0.0037 27.5 6.1 69 430-504 4-87 (151)
103 PF13877 RPAP3_C: Potential Mo 25.2 65 0.0014 27.8 2.8 34 554-587 5-38 (94)
104 KOG3389 NADH:ubiquinone oxidor 25.1 58 0.0013 30.2 2.4 28 240-271 125-154 (178)
105 cd01808 hPLIC_N Ubiquitin-like 24.9 1.5E+02 0.0033 23.9 4.8 36 69-105 9-44 (71)
106 cd01768 RA RA (Ras-associating 24.9 4.1E+02 0.0089 22.2 8.7 31 68-98 10-40 (87)
107 cd01792 ISG15_repeat1 ISG15 ub 24.7 1.4E+02 0.003 24.9 4.6 38 67-104 9-46 (80)
108 PF00788 RA: Ras association ( 22.7 4.6E+02 0.0099 21.9 8.8 69 72-141 18-89 (93)
109 TIGR01031 rpmF_bact ribosomal 21.9 1E+02 0.0022 24.0 2.9 39 765-803 4-43 (55)
110 PF04800 ETC_C1_NDUFA4: ETC co 21.6 1.2E+02 0.0026 26.9 3.6 31 239-273 50-80 (101)
111 PF08459 UvrC_HhH_N: UvrC Heli 21.2 3.3E+02 0.0071 26.2 6.9 65 431-513 32-101 (155)
112 PF13551 HTH_29: Winged helix- 21.0 1.6E+02 0.0035 25.7 4.6 38 329-366 65-108 (112)
113 cd01760 RBD Ubiquitin-like dom 20.5 2.6E+02 0.0056 23.0 5.2 37 70-106 9-45 (72)
114 KOG0695 Serine/threonine prote 20.4 2.6E+02 0.0057 30.1 6.5 65 67-133 21-86 (593)
No 1
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=100.00 E-value=4.6e-69 Score=625.59 Aligned_cols=473 Identities=17% Similarity=0.255 Sum_probs=377.5
Q ss_pred ccccCcccCCHHHHHHHHHHHHHHcCeEEEEeecCce-------EEEEEeec----------------------------
Q 003638 237 ITGVGQRFSSVHEFRELLRKYAIAHQFAFKYKKNDSH-------RVTVKCKA---------------------------- 281 (806)
Q Consensus 237 ~~~vG~~F~s~ee~~~a~~~yAi~~gf~~~~~ks~~~-------r~~~~C~~---------------------------- 281 (806)
.+.+||+|+|.+|++++|+.||...||++|+.++.++ ..+++|++
T Consensus 73 ~P~vGMeF~S~eeA~~FYn~YA~~~GFsVRi~~srrsk~~~~ii~r~fvCsreG~~~~~~~~~~~~~~~~~k~~~~~~~~ 152 (846)
T PLN03097 73 EPLSGMEFESHGEAYSFYQEYARSMGFNTAIQNSRRSKTSREFIDAKFACSRYGTKREYDKSFNRPRARQTKQDPENGTG 152 (846)
T ss_pred cCcCCCeECCHHHHHHHHHHHHhhcCceEEeeceeccCCCCcEEEEEEEEcCCCCCcccccccccccccccccCcccccc
Confidence 4679999999999999999999999999998755322 23567754
Q ss_pred ------CCCCeEEEEEEeCCCceEEEEecCCCccccCcccccccccchhhHHHHHHHHHhcCCCCChHHHHHHHHHHhCc
Q 003638 282 ------EGCPWRIHASRLSTTQLICIKKMNPTHTCEGAVVTNGNQATRSWVASIIKEKLKVFPNYKPKDIVNDIKQEYGI 355 (806)
Q Consensus 282 ------~gCpwri~as~~~~~~~~~I~~~~~~HnC~~~~~~~~~~~~~~~ia~~i~~~i~~~~~~~~~~I~~~l~~~~g~ 355 (806)
+|||++|.+.+. ..+.|.|+.+..+|||++.........++....... ..+....++.. +..+.
T Consensus 153 rR~~tRtGC~A~m~Vk~~-~~gkW~V~~fv~eHNH~L~p~~~~~~~~r~~~~~~~-~~~~~~~~v~~------~~~d~-- 222 (846)
T PLN03097 153 RRSCAKTDCKASMHVKRR-PDGKWVIHSFVKEHNHELLPAQAVSEQTRKMYAAMA-RQFAEYKNVVG------LKNDS-- 222 (846)
T ss_pred cccccCCCCceEEEEEEc-CCCeEEEEEEecCCCCCCCCccccchhhhhhHHHHH-hhhhccccccc------cchhh--
Confidence 379999999874 557899999999999999754321111111110000 00000000000 00000
Q ss_pred cccHHHHHHHHHHHHHHHhcChHHHhccHHHHHHHHHHhCCCcEEEEEecCCCceeEEEEEccccHHHHhhcCCceEEec
Q 003638 356 QLNYFQAWRGKEIAKEQLQGSYKEAYNQLPLFCERIMETNPGSLATFTTKEDSSFHRLFVSFHASLYGFIQGCRPLLFLD 435 (806)
Q Consensus 356 ~~s~~~~~rak~~~~~~~~g~~~~~~~~L~~~~~~l~~~NPg~~~~~~~~~~~~f~~lF~a~~~s~~~f~~~~~~vi~lD 435 (806)
....-+.|.+ + + ..+..+.|..|+.+++.+||+|+|.+++|++++++++|||++.|+..|. +|+|||.+|
T Consensus 223 ---~~~~~~~r~~--~-~---~~gD~~~ll~yf~~~q~~nP~Ffy~~qlDe~~~l~niFWaD~~sr~~Y~-~FGDvV~fD 292 (846)
T PLN03097 223 ---KSSFDKGRNL--G-L---EAGDTKILLDFFTQMQNMNSNFFYAVDLGEDQRLKNLFWVDAKSRHDYG-NFSDVVSFD 292 (846)
T ss_pred ---cchhhHHHhh--h-c---ccchHHHHHHHHHHHHhhCCCceEEEEEccCCCeeeEEeccHHHHHHHH-hcCCEEEEe
Confidence 0001111111 1 1 1235678999999999999999999999999999999999999999999 799999999
Q ss_pred cccccccccceEEEEeeecCCCCeeeEEEEEecCCCchhHHHHHHHHHHHccCCCCCeEEEecCchhHHHHHHhhccccc
Q 003638 436 SVPLKSKYQGTLLAATAADGDDGVFPVAFAVVDAETNDDWHWFLLQLKSALSTATCPITFVADKQKGLRESIAEIFKGSF 515 (806)
Q Consensus 436 ~T~~~~~y~~~ll~a~g~d~~~~~~plafa~v~~E~~esw~wfl~~lk~~~~~~~~p~~iisD~~~~l~~Ai~~vfP~a~ 515 (806)
+||++|+|++||+.++|+|+|+|++++|+||+.+|+.|+|.|+|++|+++|++. .|.+||||++.+|.+||++|||++.
T Consensus 293 TTY~tN~y~~Pfa~FvGvNhH~qtvlfGcaLl~dEt~eSf~WLf~tfl~aM~gk-~P~tIiTDqd~am~~AI~~VfP~t~ 371 (846)
T PLN03097 293 TTYVRNKYKMPLALFVGVNQHYQFMLLGCALISDESAATYSWLMQTWLRAMGGQ-APKVIITDQDKAMKSVISEVFPNAH 371 (846)
T ss_pred ceeeccccCcEEEEEEEecCCCCeEEEEEEEcccCchhhHHHHHHHHHHHhCCC-CCceEEecCCHHHHHHHHHHCCCce
Confidence 999999999999999999999999999999999999999999999999999998 8999999999999999999999999
Q ss_pred ccchHHHHHHHHHHHhcccccHHHHHHHHHHHHHHhc-CCCHHHHHHHHHH-HHhccHHHHHHHHh--ccCCCccccccC
Q 003638 516 HGYCLRYLTEQLVKDLKGQFSHEVKRLMIEDFYAAAY-APTPEEFERSIES-IKSISLEAYNWILQ--SEYLNWANAFFQ 591 (806)
Q Consensus 516 h~~C~~Hi~~n~~~~~~~~~~~~~~~~~~~~~~~~~~-a~t~~eF~~~~~~-l~~~~~~~~~~l~~--~~~~~W~~a~~~ 591 (806)
|++|.|||++|+.++++..+.. .+.+...|..+++ +.+++||+..|.. |.+++++.++||.. ..+++|+++|++
T Consensus 372 Hr~C~wHI~~~~~e~L~~~~~~--~~~f~~~f~~cv~~s~t~eEFE~~W~~mi~ky~L~~n~WL~~LY~~RekWapaY~k 449 (846)
T PLN03097 372 HCFFLWHILGKVSENLGQVIKQ--HENFMAKFEKCIYRSWTEEEFGKRWWKILDRFELKEDEWMQSLYEDRKQWVPTYMR 449 (846)
T ss_pred ehhhHHHHHHHHHHHhhHHhhh--hhHHHHHHHHHHhCCCCHHHHHHHHHHHHHhhcccccHHHHHHHHhHhhhhHHHhc
Confidence 9999999999999999765432 3568888999887 4799999999988 56889999999999 699999999999
Q ss_pred CCccccc-ccchhHhhhHHhhh--CCCCCHHHHHHHHHHHHHHHHHHHHH-----------------hhhhcccCCchhH
Q 003638 592 GARYNHM-TSNFGELFYSWASD--ANELPITQMVDVIRGKIMELIYTRRT-----------------DSNQWLTRLTPSM 651 (806)
Q Consensus 592 ~~~~~~~-ttN~~Es~n~~lk~--~r~~~i~~l~~~i~~~~~~~~~~r~~-----------------~~~~~~~~~tp~~ 651 (806)
+.+++.| ||+++||+|++|++ .+..+|..|++.....+..+..+..+ ..++.+..|||.+
T Consensus 450 ~~F~agm~sTqRSES~Ns~fk~yv~~~tsL~~Fv~qye~~l~~~~ekE~~aD~~s~~~~P~l~t~~piEkQAs~iYT~~i 529 (846)
T PLN03097 450 DAFLAGMSTVQRSESINAFFDKYVHKKTTVQEFVKQYETILQDRYEEEAKADSDTWNKQPALKSPSPLEKSVSGVYTHAV 529 (846)
T ss_pred ccccCCcccccccccHHHHHHHHhCcCCCHHHHHHHHHHHHHHHHHHHHHhhhhcccCCcccccccHHHHHHHHHhHHHH
Confidence 9998766 67899999999998 57788888887665544433322211 2356688999999
Q ss_pred HHHHHHHHhcccceEEEEeC-C---eEEEEec---ceeEEe--eC--cCcccccccccccCCcccchhHHhhhcCCC--c
Q 003638 652 EEKLEKESLKVRSLQVLLSA-G---RTFEVRG---DSIEVV--DI--DHWDCSCKGWQLTGLPCCHAIAVLSCIGCS--P 718 (806)
Q Consensus 652 ~~kl~~~~~~a~~~~v~~~~-~---~~f~V~~---~~~~~V--dl--~~~~CsC~~~~~~GiPC~H~lav~~~~~~~--~ 718 (806)
|++||+|+..+..|.+...+ + .+|.|.+ ...|.| |. ...+|+|++|+..||||+|||.|+...++. |
T Consensus 530 F~kFQ~El~~~~~~~~~~~~~dg~~~~y~V~~~~~~~~~~V~~d~~~~~v~CsC~kFE~~GILCrHaLkVL~~~~v~~IP 609 (846)
T PLN03097 530 FKKFQVEVLGAVACHPKMESQDETSITFRVQDFEKNQDFTVTWNQTKLEVSCICRLFEYKGYLCRHALVVLQMCQLSAIP 609 (846)
T ss_pred HHHHHHHHHHhhheEEeeeccCCceEEEEEEEecCCCcEEEEEecCCCeEEeeccCeecCccchhhHHHHHhhcCcccCc
Confidence 99999999999888876532 2 3588864 345766 32 477999999999999999999999999995 9
Q ss_pred ccccccchhhhHhh
Q 003638 719 YDYCSRYFMTESYR 732 (806)
Q Consensus 719 ~~yv~~~yt~~~~~ 732 (806)
..||.++||+++-.
T Consensus 610 ~~YILkRWTKdAK~ 623 (846)
T PLN03097 610 SQYILKRWTKDAKS 623 (846)
T ss_pred hhhhhhhchhhhhh
Confidence 99999999988653
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=99.92 E-value=2.7e-25 Score=192.17 Aligned_cols=90 Identities=34% Similarity=0.688 Sum_probs=84.8
Q ss_pred EEeeCCEEEecC-CCCEEEecCceEEEEecCCCChHHHHHHHHHHcCCCCccEEEEEEcCCC-CceeEEEeChHHHHHHH
Q 003638 50 ICQLGGEFETDK-DGSLSYKGGDAHAIDVDEQMKFNDFKTEVAEMFNCSFNAILLKYFLPGN-KKTLITISNDKDLQRMI 127 (806)
Q Consensus 50 ~c~~gG~~~~~~-~g~~~Y~Gg~~~~i~v~~~~s~~e~~~~l~~~~~~~~~~~~~~y~l~~~-~~~l~~~~~D~dl~~M~ 127 (806)
||||||+|+|++ ||+++|+||+||+|.|+|++||+||++||+++++++.. +++|||||++ +++|++|++|+||.+|+
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 699999999887 99999999999999999999999999999999988766 9999999988 57899999999999999
Q ss_pred HhcC----CCCeEEEEE
Q 003638 128 KFNG----DSATTDVFV 140 (806)
Q Consensus 128 ~~~~----~~~~v~iyv 140 (806)
++++ ....++||+
T Consensus 80 ~e~~~~~~~~~rirvfl 96 (97)
T cd06410 80 EEYDRLSGGSARLRVFL 96 (97)
T ss_pred HhhccccCCCceEEEEE
Confidence 9999 778888886
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=99.84 E-value=5.7e-21 Score=168.24 Aligned_cols=90 Identities=36% Similarity=0.636 Sum_probs=86.5
Q ss_pred cccccccccceEEE---EeeecCCCCeeeEEEEEecCCCchhHHHHHHHHHHHccCCCCCeEEEecCchhHHHHHHhhcc
Q 003638 436 SVPLKSKYQGTLLA---ATAADGDDGVFPVAFAVVDAETNDDWHWFLLQLKSALSTATCPITFVADKQKGLRESIAEIFK 512 (806)
Q Consensus 436 ~T~~~~~y~~~ll~---a~g~d~~~~~~plafa~v~~E~~esw~wfl~~lk~~~~~~~~p~~iisD~~~~l~~Ai~~vfP 512 (806)
|||++|+| ++++. ++|+|++|+.+|+||+++++|+.++|.|||+.+++.+... |.+||||++.|+.+||+++||
T Consensus 1 ~T~~tn~~-~~l~~~~~~~~~d~~~~~~~v~~~l~~~e~~~~~~~~l~~~~~~~~~~--p~~ii~D~~~~~~~Ai~~vfP 77 (93)
T PF10551_consen 1 GTYKTNKY-GPLLYLMIAVGIDGNGRGFPVAFALVSSESEESYEWFLEKLKEAMPQK--PKVIISDFDKALINAIKEVFP 77 (93)
T ss_pred Cccccccc-cccceeceEEEEcCCCCEEEEEEEEEcCCChhhhHHHHHHhhhccccC--ceeeeccccHHHHHHHHHHCC
Confidence 69999999 98886 9999999999999999999999999999999999999884 999999999999999999999
Q ss_pred cccccchHHHHHHHHH
Q 003638 513 GSFHGYCLRYLTEQLV 528 (806)
Q Consensus 513 ~a~h~~C~~Hi~~n~~ 528 (806)
++.|++|.||+.+|++
T Consensus 78 ~~~~~~C~~H~~~n~k 93 (93)
T PF10551_consen 78 DARHQLCLFHILRNIK 93 (93)
T ss_pred CceEehhHHHHHHhhC
Confidence 9999999999999974
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=99.78 E-value=8.2e-20 Score=201.66 Aligned_cols=241 Identities=20% Similarity=0.225 Sum_probs=189.0
Q ss_pred CCCCChHHHHHHHHHHhC-ccccHHHHHHHHHHHHHHHhcChHHHhccHHHHHHHHHHhCCCcEEEEEecCCCceeEEEE
Q 003638 337 FPNYKPKDIVNDIKQEYG-IQLNYFQAWRGKEIAKEQLQGSYKEAYNQLPLFCERIMETNPGSLATFTTKEDSSFHRLFV 415 (806)
Q Consensus 337 ~~~~~~~~I~~~l~~~~g-~~~s~~~~~rak~~~~~~~~g~~~~~~~~L~~~~~~l~~~NPg~~~~~~~~~~~~f~~lF~ 415 (806)
-.+++.++|.+.+..-+| ..+|-+++.|..+...+.+. .|..+-.
T Consensus 112 ~~G~Str~i~~~l~~l~g~~~~S~s~vSri~~~~~~~~~-----------~w~~R~L----------------------- 157 (381)
T PF00872_consen 112 LKGVSTRDIEEALEELYGEVAVSKSTVSRITKQLDEEVE-----------AWRNRPL----------------------- 157 (381)
T ss_pred ccccccccccchhhhhhcccccCchhhhhhhhhhhhhHH-----------HHhhhcc-----------------------
Confidence 357899999999999999 78999999887655444332 1111110
Q ss_pred EccccHHHHhhcC-CceEEecccccccccc-----ceEEEEeeecCCCCeeeEEEEEecCCCchhHHHHHHHHHHHccCC
Q 003638 416 SFHASLYGFIQGC-RPLLFLDSVPLKSKYQ-----GTLLAATAADGDDGVFPVAFAVVDAETNDDWHWFLLQLKSALSTA 489 (806)
Q Consensus 416 a~~~s~~~f~~~~-~~vi~lD~T~~~~~y~-----~~ll~a~g~d~~~~~~plafa~v~~E~~esw~wfl~~lk~~~~~~ 489 (806)
... .++|++|++|.+-+.+ ..+++++|+|.+|+..+||+.+.+.|+.++|.-||+.|++..-..
T Consensus 158 ----------~~~~y~~l~iD~~~~kvr~~~~~~~~~~~v~iGi~~dG~r~vLg~~~~~~Es~~~W~~~l~~L~~RGl~~ 227 (381)
T PF00872_consen 158 ----------ESEPYPYLWIDGTYFKVREDGRVVKKAVYVAIGIDEDGRREVLGFWVGDRESAASWREFLQDLKERGLKD 227 (381)
T ss_pred ----------ccccccceeeeeeecccccccccccchhhhhhhhhcccccceeeeecccCCccCEeeecchhhhhccccc
Confidence 134 5899999999986643 468999999999999999999999999999999999999886554
Q ss_pred CCCeEEEecCchhHHHHHHhhcccccccchHHHHHHHHHHHhcccccHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHH--
Q 003638 490 TCPITFVADKQKGLRESIAEIFKGSFHGYCLRYLTEQLVKDLKGQFSHEVKRLMIEDFYAAAYAPTPEEFERSIESIK-- 567 (806)
Q Consensus 490 ~~p~~iisD~~~~l~~Ai~~vfP~a~h~~C~~Hi~~n~~~~~~~~~~~~~~~~~~~~~~~~~~a~t~~eF~~~~~~l~-- 567 (806)
|..||+|+++||.+||.++||++.++.|.+|+++|+.+++... .++.+...++.+.++.+.++....++.+.
T Consensus 228 --~~lvv~Dg~~gl~~ai~~~fp~a~~QrC~vH~~RNv~~~v~~k----~~~~v~~~Lk~I~~a~~~e~a~~~l~~f~~~ 301 (381)
T PF00872_consen 228 --ILLVVSDGHKGLKEAIREVFPGAKWQRCVVHLMRNVLRKVPKK----DRKEVKADLKAIYQAPDKEEAREALEEFAEK 301 (381)
T ss_pred --cceeeccccccccccccccccchhhhhheechhhhhccccccc----cchhhhhhccccccccccchhhhhhhhcccc
Confidence 7999999999999999999999999999999999999998543 34566677788888888888777777654
Q ss_pred --hccHHHHHHHHhccCCCccccccCCCcc-cccccchhHhhhHHhhhC----CCCCHHHHHHHHHH
Q 003638 568 --SISLEAYNWILQSEYLNWANAFFQGARY-NHMTSNFGELFYSWASDA----NELPITQMVDVIRG 627 (806)
Q Consensus 568 --~~~~~~~~~l~~~~~~~W~~a~~~~~~~-~~~ttN~~Es~n~~lk~~----r~~~i~~l~~~i~~ 627 (806)
..+|++.+++.+...+.|+..-|+...+ ...|||.+||+|+.||+. ...|-.+.+..+..
T Consensus 302 ~~~kyp~~~~~l~~~~~~~~tf~~fP~~~~~~i~TTN~iEsln~~irrr~~~~~~Fp~~~s~lr~~~ 368 (381)
T PF00872_consen 302 WEKKYPKAAKSLEENWDELLTFLDFPPEHRRSIRTTNAIESLNKEIRRRTKVVGIFPNEESALRLVY 368 (381)
T ss_pred cccccchhhhhhhhccccccceeeecchhccccchhhhccccccchhhhccccccCCCHHHHHHHHH
Confidence 5688999999987777777654554444 466999999999999973 33454444443333
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=99.65 E-value=4.9e-16 Score=127.25 Aligned_cols=67 Identities=46% Similarity=0.823 Sum_probs=64.7
Q ss_pred CcccccCcccCCHHHHHHHHHHHHHHcCeEEEEeecCceEEEEEeecCCCCeEEEEEEeCCCceEEE
Q 003638 235 NTITGVGQRFSSVHEFRELLRKYAIAHQFAFKYKKNDSHRVTVKCKAEGCPWRIHASRLSTTQLICI 301 (806)
Q Consensus 235 ~~~~~vG~~F~s~ee~~~a~~~yAi~~gf~~~~~ks~~~r~~~~C~~~gCpwri~as~~~~~~~~~I 301 (806)
|+.+.+||+|+|++||+.||..||++++|++++.+|+++|++++|...||||+|+|++.++++.|+|
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 5678999999999999999999999999999999999999999999999999999999999999986
No 6
>COG3328 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=99.42 E-value=3.4e-12 Score=138.15 Aligned_cols=237 Identities=18% Similarity=0.158 Sum_probs=176.1
Q ss_pred CCCCChHHHHHHHHHHhCccccHHHHHHHHHHHHHHHhcChHHHhccHHHHHHHHHHhCCCcEEEEEecCCCceeEEEEE
Q 003638 337 FPNYKPKDIVNDIKQEYGIQLNYFQAWRGKEIAKEQLQGSYKEAYNQLPLFCERIMETNPGSLATFTTKEDSSFHRLFVS 416 (806)
Q Consensus 337 ~~~~~~~~I~~~l~~~~g~~~s~~~~~rak~~~~~~~~g~~~~~~~~L~~~~~~l~~~NPg~~~~~~~~~~~~f~~lF~a 416 (806)
..+++++++.+.+++.++..++-..+.+.-...++.+ ..++..-
T Consensus 98 ~~gv~Tr~i~~~~~~~~~~~~s~~~iS~~~~~~~e~v---------------~~~~~r~--------------------- 141 (379)
T COG3328 98 AKGVTTREIEALLEELYGHKVSPSVISVVTDRLDEKV---------------KAWQNRP--------------------- 141 (379)
T ss_pred HcCCcHHHHHHHHHHhhCcccCHHHhhhHHHHHHHHH---------------HHHHhcc---------------------
Confidence 4578999999999999988777777766544444333 2222211
Q ss_pred ccccHHHHhhcCCceEEecccccccc--ccceEEEEeeecCCCCeeeEEEEEecCCCchhHHHHHHHHHHHccCCCCCeE
Q 003638 417 FHASLYGFIQGCRPLLFLDSVPLKSK--YQGTLLAATAADGDDGVFPVAFAVVDAETNDDWHWFLLQLKSALSTATCPIT 494 (806)
Q Consensus 417 ~~~s~~~f~~~~~~vi~lD~T~~~~~--y~~~ll~a~g~d~~~~~~plafa~v~~E~~esw~wfl~~lk~~~~~~~~p~~ 494 (806)
. +..+++++|++|++-+ -+..+++|+|++.+|+-..+++.+-..|+ ..|.-||..|+...-.. -..
T Consensus 142 --------l-~~~~~v~~D~~~~k~r~v~~~~~~ia~Gv~~eG~reilg~~~~~~e~-~~w~~~l~~l~~rgl~~--v~l 209 (379)
T COG3328 142 --------L-GDYPYVYLDAKYVKVRSVRNKAVYIAIGVTEEGRREILGIWVGVRES-KFWLSFLLDLKNRGLSD--VLL 209 (379)
T ss_pred --------c-cCceEEEEecceeehhhhhhheeeeeeccCcccchhhhceeeecccc-hhHHHHHHHHHhccccc--eeE
Confidence 1 3568999999999887 45589999999999999999999999999 99999999999884433 266
Q ss_pred EEecCchhHHHHHHhhcccccccchHHHHHHHHHHHhcccccHHHHHHHHHHHHHHhcCCCHHHHHHHHHH----HHhcc
Q 003638 495 FVADKQKGLRESIAEIFKGSFHGYCLRYLTEQLVKDLKGQFSHEVKRLMIEDFYAAAYAPTPEEFERSIES----IKSIS 570 (806)
Q Consensus 495 iisD~~~~l~~Ai~~vfP~a~h~~C~~Hi~~n~~~~~~~~~~~~~~~~~~~~~~~~~~a~t~~eF~~~~~~----l~~~~ 570 (806)
+++|+.+|+.+||..+||.+.++.|..|+.+|+..+...+ .++.+...+..+-.+.+.++-...|.. +....
T Consensus 210 ~v~Dg~~gl~~aI~~v~p~a~~Q~C~vH~~Rnll~~v~~k----~~d~i~~~~~~I~~a~~~e~~~~~~~~~~~~w~~~y 285 (379)
T COG3328 210 VVVDGLKGLPEAISAVFPQAAVQRCIVHLVRNLLDKVPRK----DQDAVLSDLRSIYIAPDAEEALLALLAFSELWGKRY 285 (379)
T ss_pred EecchhhhhHHHHHHhccHhhhhhhhhHHHhhhhhhhhhh----hhHHHHhhhhhhhccCCcHHHHHHHHHHHHhhhhhc
Confidence 7779999999999999999999999999999999988542 235556666666677777776666655 44567
Q ss_pred HHHHHHHHhccCCCccc-cccCCCcccccccchhHhhhHHhhhC----CCCCHHHHHHHH
Q 003638 571 LEAYNWILQSEYLNWAN-AFFQGARYNHMTSNFGELFYSWASDA----NELPITQMVDVI 625 (806)
Q Consensus 571 ~~~~~~l~~~~~~~W~~-a~~~~~~~~~~ttN~~Es~n~~lk~~----r~~~i~~l~~~i 625 (806)
|....|+.+..-+.|.. +|.+..+-...|||..|++|+.++.. ..+|-...+..+
T Consensus 286 P~i~~~~~~~~~~~~~F~~fp~~~r~~i~ttN~IE~~n~~ir~~~~~~~~fpn~~sv~k~ 345 (379)
T COG3328 286 PAILKSWRNALEELLPFFAFPSEIRKIIYTTNAIESLNKLIRRRTKVVGIFPNEESVEKL 345 (379)
T ss_pred chHHHHHHHHHHHhcccccCcHHHHhHhhcchHHHHHHHHHHHHHhhhccCCCHHHHHHH
Confidence 88888887755555543 33334444577999999999977742 234444444433
No 7
>smart00575 ZnF_PMZ plant mutator transposase zinc finger.
Probab=98.83 E-value=1.2e-09 Score=72.10 Aligned_cols=28 Identities=50% Similarity=0.977 Sum_probs=25.5
Q ss_pred cccccccccccCCcccchhHHhhhcCCC
Q 003638 690 WDCSCKGWQLTGLPCCHAIAVLSCIGCS 717 (806)
Q Consensus 690 ~~CsC~~~~~~GiPC~H~lav~~~~~~~ 717 (806)
.+|||++|+..||||+|+|+|+...+++
T Consensus 1 ~~CsC~~~~~~gipC~H~i~v~~~~~~~ 28 (28)
T smart00575 1 KTCSCRKFQLSGIPCRHALAAAIHIGLS 28 (28)
T ss_pred CcccCCCcccCCccHHHHHHHHHHhCCC
Confidence 4799999999999999999999988763
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=4.6e-08 Score=85.17 Aligned_cols=69 Identities=22% Similarity=0.413 Sum_probs=65.4
Q ss_pred cCCHHHHHHHHHHHHHHcCeEEEEeecCceEEEEEeec------------------------------------------
Q 003638 244 FSSVHEFRELLRKYAIAHQFAFKYKKNDSHRVTVKCKA------------------------------------------ 281 (806)
Q Consensus 244 F~s~ee~~~a~~~yAi~~gf~~~~~ks~~~r~~~~C~~------------------------------------------ 281 (806)
|.+++|++.+|+..+...||++.+.+|+.+.+.|+|..
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 88999999999999999999999999999999999973
Q ss_pred CCCCeEEEEEEeCCCceEEEEecCCCccccC
Q 003638 282 EGCPWRIHASRLSTTQLICIKKMNPTHTCEG 312 (806)
Q Consensus 282 ~gCpwri~as~~~~~~~~~I~~~~~~HnC~~ 312 (806)
.+|||+|+|..+...+.|.|..+++.|+|++
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 2699999999999999999999999999974
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=98.55 E-value=5.3e-07 Score=76.84 Aligned_cols=75 Identities=25% Similarity=0.486 Sum_probs=65.0
Q ss_pred CCEEEecCceEEEEecCCCChHHHHHHHHHHcCCCCccEEEEEEcCCCCceeEEEeChHHHHHHHHhcCCC--CeEEEEE
Q 003638 63 GSLSYKGGDAHAIDVDEQMKFNDFKTEVAEMFNCSFNAILLKYFLPGNKKTLITISNDKDLQRMIKFNGDS--ATTDVFV 140 (806)
Q Consensus 63 g~~~Y~Gg~~~~i~v~~~~s~~e~~~~l~~~~~~~~~~~~~~y~l~~~~~~l~~~~~D~dl~~M~~~~~~~--~~v~iyv 140 (806)
.+++| ||+++.+.+++++||.||+++|.+.|++....++++|. .+...+++|.+|+|+..|+++.... ....|+|
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 46788 89999999999999999999999999988789999998 4445599999999999999988763 4567765
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=98.49 E-value=2.4e-07 Score=80.90 Aligned_cols=61 Identities=23% Similarity=0.369 Sum_probs=53.7
Q ss_pred HHHHHHHHHcCeEEEEeecCce-------EEEEEeec----------------------CCCCeEEEEEEeCCCceEEEE
Q 003638 252 ELLRKYAIAHQFAFKYKKNDSH-------RVTVKCKA----------------------EGCPWRIHASRLSTTQLICIK 302 (806)
Q Consensus 252 ~a~~~yAi~~gf~~~~~ks~~~-------r~~~~C~~----------------------~gCpwri~as~~~~~~~~~I~ 302 (806)
++|+.||...||.++..++.+. ++.++|++ +||||+|.+...+ ++.|.|.
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 4799999999999999876543 68899985 4899999999888 8899999
Q ss_pred ecCCCccccCc
Q 003638 303 KMNPTHTCEGA 313 (806)
Q Consensus 303 ~~~~~HnC~~~ 313 (806)
.+..+|||++.
T Consensus 80 ~~~~~HNH~L~ 90 (91)
T PF03101_consen 80 SFVLEHNHPLC 90 (91)
T ss_pred ECcCCcCCCCC
Confidence 99999999975
No 11
>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=98.07 E-value=2.8e-05 Score=66.17 Aligned_cols=74 Identities=30% Similarity=0.474 Sum_probs=59.6
Q ss_pred CEEEecCceEEEEec-CCCChHHHHHHHHHHcCCCCccEEEEEEcCCCCceeEEEeChHHHHHHHHhcCC--CCeEEEEE
Q 003638 64 SLSYKGGDAHAIDVD-EQMKFNDFKTEVAEMFNCSFNAILLKYFLPGNKKTLITISNDKDLQRMIKFNGD--SATTDVFV 140 (806)
Q Consensus 64 ~~~Y~Gg~~~~i~v~-~~~s~~e~~~~l~~~~~~~~~~~~~~y~l~~~~~~l~~~~~D~dl~~M~~~~~~--~~~v~iyv 140 (806)
+++|.| +.+.+.++ +++||.+|.++|.+.|++....+.++|. .+...+++|.+|+||+.|++.... ...+.|++
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 KVKYGG-EIRRFVVVSRSISFEDLRSKIAEKFGLDAVSFKLKYP--DEDGDLVTISSDEDLEEAIEEARRSGSKKLRLFV 80 (81)
T ss_pred EEEecC-CCEEEEEecCCCCHHHHHHHHHHHhCCCCCcEEEEee--CCCCCEEEeCCHHHHHHHHHHHhhcCCccEEEEe
Confidence 466765 46666666 9999999999999999887667888884 555589999999999999999884 45677775
No 12
>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=97.95 E-value=4.5e-06 Score=60.53 Aligned_cols=30 Identities=43% Similarity=0.835 Sum_probs=27.3
Q ss_pred eeCcCcccccccccccCCcccchhHHhhhc
Q 003638 685 VDIDHWDCSCKGWQLTGLPCCHAIAVLSCI 714 (806)
Q Consensus 685 Vdl~~~~CsC~~~~~~GiPC~H~lav~~~~ 714 (806)
+++...+|||..|+..|.||+|++|++...
T Consensus 10 ~~~~~~~CsC~~~~~~~~~CkHi~av~~~~ 39 (40)
T PF04434_consen 10 VSIEQASCSCPYFQFRGGPCKHIVAVLLAL 39 (40)
T ss_pred ccccccEeeCCCccccCCcchhHHHHHHhh
Confidence 667889999999999999999999998764
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=9e-05 Score=62.70 Aligned_cols=73 Identities=25% Similarity=0.417 Sum_probs=62.8
Q ss_pred EEEecCceEEEEecCCCChHHHHHHHHHHcCCCC-ccEEEEEEcCCCCceeEEEeChHHHHHHHHhcCCC--CeEEEEE
Q 003638 65 LSYKGGDAHAIDVDEQMKFNDFKTEVAEMFNCSF-NAILLKYFLPGNKKTLITISNDKDLQRMIKFNGDS--ATTDVFV 140 (806)
Q Consensus 65 ~~Y~Gg~~~~i~v~~~~s~~e~~~~l~~~~~~~~-~~~~~~y~l~~~~~~l~~~~~D~dl~~M~~~~~~~--~~v~iyv 140 (806)
+.| ||+...+.++.+++|.+|.+++.+.|+++. +.+.++|. .+..-.++|++|.||+.-++.+... ..|.+||
T Consensus 5 ~~~-~~d~~r~~l~~~~~~~~L~~~i~~r~~~~~~~~f~LkY~--Ddegd~v~ltsd~DL~eai~i~~~~~~~~v~l~v 80 (82)
T cd06407 5 ATY-GEEKIRFRLPPSWGFTELKQEIAKRFKLDDMSAFDLKYL--DDDEEWVLLTCDADLEECIDVYRSSGSHTIRLLV 80 (82)
T ss_pred EEe-CCeEEEEEcCCCCCHHHHHHHHHHHhCCCCCCeeEEEEE--CCCCCeEEeecHHHHHHHHHHHHHCCCCeEEEEe
Confidence 445 778999999999999999999999999876 79999994 5558899999999999998877664 5788887
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=97.89 E-value=5.7e-05 Score=64.76 Aligned_cols=75 Identities=31% Similarity=0.476 Sum_probs=62.3
Q ss_pred EEEecCceEEEEecCCCChHHHHHHHHHHcCCCCccEEEEEEcCCCCceeEEEeChHHHHHHHHhcCC--CCeEEEEEE
Q 003638 65 LSYKGGDAHAIDVDEQMKFNDFKTEVAEMFNCSFNAILLKYFLPGNKKTLITISNDKDLQRMIKFNGD--SATTDVFVI 141 (806)
Q Consensus 65 ~~Y~Gg~~~~i~v~~~~s~~e~~~~l~~~~~~~~~~~~~~y~l~~~~~~l~~~~~D~dl~~M~~~~~~--~~~v~iyv~ 141 (806)
++|.|+..+.+.+++++||.+|..+|.+.|+.....+.++|. .+..-+|+|++|+||..|++.... ...+.++|.
T Consensus 6 ~~~~~~~~~~~~~~~~~s~~~L~~~i~~~~~~~~~~~~l~Y~--D~dgD~V~i~sd~Dl~~a~~~~~~~~~~~lrl~v~ 82 (84)
T PF00564_consen 6 VRYGGDIRRIISLPSDVSFDDLRSKIREKFGLLDEDFQLKYK--DEDGDLVTISSDEDLQEAIEQAKESGSKTLRLFVQ 82 (84)
T ss_dssp EEETTEEEEEEEECSTSHHHHHHHHHHHHHTTSTSSEEEEEE--ETTSSEEEESSHHHHHHHHHHHHHCTTSCEEEEEE
T ss_pred EEECCeeEEEEEcCCCCCHHHHHHHHHHHhCCCCccEEEEee--CCCCCEEEeCCHHHHHHHHHHHHhcCCCcEEEEEE
Confidence 556555555699999999999999999999988789999995 444589999999999999998754 347888885
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=97.48 E-value=0.00038 Score=58.73 Aligned_cols=62 Identities=19% Similarity=0.348 Sum_probs=53.3
Q ss_pred EEEecCceEEEEecCCCChHHHHHHHHHHcCCCCccEEEEEEcCCCCceeEEEeChHHHHHHHHhcC
Q 003638 65 LSYKGGDAHAIDVDEQMKFNDFKTEVAEMFNCSFNAILLKYFLPGNKKTLITISNDKDLQRMIKFNG 131 (806)
Q Consensus 65 ~~Y~Gg~~~~i~v~~~~s~~e~~~~l~~~~~~~~~~~~~~y~l~~~~~~l~~~~~D~dl~~M~~~~~ 131 (806)
++| +|+++.|.|+.+++|.||..+|.++|++. +.++++|. .+ ..+++|+++.||+.-+.-..
T Consensus 7 v~~-~~Dv~~i~v~~~i~f~dL~~kIrdkf~~~-~~~~iKyk--DE-GD~iti~sq~DLd~Ai~~a~ 68 (86)
T cd06408 7 VHA-QDDTRYIMIGPDTGFADFEDKIRDKFGFK-RRLKIKMK--DD-GDMITMGDQDDLDMAIDTAR 68 (86)
T ss_pred EEe-cCcEEEEEcCCCCCHHHHHHHHHHHhCCC-CceEEEEE--cC-CCCccccCHHHHHHHHHHHH
Confidence 444 56799999999999999999999999985 79999995 44 78999999999998776554
No 16
>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=97.39 E-value=0.0006 Score=56.49 Aligned_cols=67 Identities=13% Similarity=0.239 Sum_probs=56.7
Q ss_pred CEEEecCceEEEEecCCCChHHHHHHHHHHcCCCCccEEEEEEcCCCCceeEEEeChHHHHHHHHhcCCCC
Q 003638 64 SLSYKGGDAHAIDVDEQMKFNDFKTEVAEMFNCSFNAILLKYFLPGNKKTLITISNDKDLQRMIKFNGDSA 134 (806)
Q Consensus 64 ~~~Y~Gg~~~~i~v~~~~s~~e~~~~l~~~~~~~~~~~~~~y~l~~~~~~l~~~~~D~dl~~M~~~~~~~~ 134 (806)
+|+|.+ +-.|.|+.+++|++|..||++.|.+..+.++|.|.= .....++++ +|+|++.++....++.
T Consensus 6 KV~f~~--tIaIrvp~~~~y~~L~~ki~~kLkl~~e~i~LsYkd-e~s~~~v~l-~d~dle~aws~~~~~~ 72 (80)
T cd06406 6 KVHFKY--TVAIQVARGLSYATLLQKISSKLELPAEHITLSYKS-EASGEDVIL-SDTNMEDVWSQAKDGC 72 (80)
T ss_pred EEEEEE--EEEEEcCCCCCHHHHHHHHHHHhCCCchhcEEEecc-CCCCCccCc-ChHHHHHHHHhhcCCe
Confidence 478887 999999999999999999999999988899999952 223456777 8999999999887664
No 17
>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=96.97 E-value=0.0079 Score=51.97 Aligned_cols=74 Identities=20% Similarity=0.394 Sum_probs=59.2
Q ss_pred EEEecCceEEEEecC-----CCChHHHHHHHHHHcCCCC-ccEEEEEEcCCCCceeEEEeChHHHHHHHHhcCC---CCe
Q 003638 65 LSYKGGDAHAIDVDE-----QMKFNDFKTEVAEMFNCSF-NAILLKYFLPGNKKTLITISNDKDLQRMIKFNGD---SAT 135 (806)
Q Consensus 65 ~~Y~Gg~~~~i~v~~-----~~s~~e~~~~l~~~~~~~~-~~~~~~y~l~~~~~~l~~~~~D~dl~~M~~~~~~---~~~ 135 (806)
+.| ||+.+-+.++. +++|.+|..|+.+.|++.. ..+.++|. .+....++|.+|+||..-++.... ...
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 456 66777777774 6999999999999999987 58999994 556789999999999998887522 245
Q ss_pred EEEEEE
Q 003638 136 TDVFVI 141 (806)
Q Consensus 136 v~iyv~ 141 (806)
+.|+|.
T Consensus 82 lrl~v~ 87 (91)
T cd06398 82 LRIDVT 87 (91)
T ss_pred EEEEEE
Confidence 777774
No 18
>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=96.72 E-value=0.012 Score=49.12 Aligned_cols=69 Identities=13% Similarity=0.273 Sum_probs=57.5
Q ss_pred cCceEEEEecC--CCChHHHHHHHHHHcCCCCccEEEEEEcCCCCceeEEEeChHHHHHHHHhcCCCC-eEEEEEE
Q 003638 69 GGDAHAIDVDE--QMKFNDFKTEVAEMFNCSFNAILLKYFLPGNKKTLITISNDKDLQRMIKFNGDSA-TTDVFVI 141 (806)
Q Consensus 69 Gg~~~~i~v~~--~~s~~e~~~~l~~~~~~~~~~~~~~y~l~~~~~~l~~~~~D~dl~~M~~~~~~~~-~v~iyv~ 141 (806)
||++..+.++. +++|.+|..++.+.|+++ .+.+||- .+..-.+.|++|.||+..++.....+ .+.+.|.
T Consensus 8 ~~d~~rf~~~~~~~~~~~~L~~ev~~rf~l~--~f~lKYl--Dde~e~v~lssd~eLeE~~rl~~~~~~~l~~~v~ 79 (81)
T cd06396 8 NGESQSFLVSDSENTTWASVEAMVKVSFGLN--DIQIKYV--DEENEEVSVNSQGEYEEALKSAVRQGNLLQMNVY 79 (81)
T ss_pred CCeEEEEEecCCCCCCHHHHHHHHHHHhCCC--cceeEEE--cCCCCEEEEEchhhHHHHHHHHHhCCCEEEEEEe
Confidence 56677778877 889999999999999988 8999993 55678899999999999999877764 5677663
No 19
>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=96.25 E-value=0.026 Score=48.10 Aligned_cols=64 Identities=19% Similarity=0.267 Sum_probs=53.3
Q ss_pred EEecCCCChHHHHHHHHHHc-CCCCccEEEEEEcCCCCceeEEEeChHHHHHHHHhcCCCCeEEEEEE
Q 003638 75 IDVDEQMKFNDFKTEVAEMF-NCSFNAILLKYFLPGNKKTLITISNDKDLQRMIKFNGDSATTDVFVI 141 (806)
Q Consensus 75 i~v~~~~s~~e~~~~l~~~~-~~~~~~~~~~y~l~~~~~~l~~~~~D~dl~~M~~~~~~~~~v~iyv~ 141 (806)
++.+..+||.+|..++.++| ++....++++|. .+..-||+|++|++|..-+.... .+.+.+||.
T Consensus 21 l~~~~~~s~~~L~~~V~~~f~~l~~~~ftlky~--DeeGDlvtIssdeEL~~A~~~~~-~~~~RlyI~ 85 (87)
T cd06402 21 IDEDVSTSYEYLVEKVAAVFPSLRGKNFQLFWK--DEEGDLVAFSSDEELVMALGSLN-DDTFRIYIK 85 (87)
T ss_pred ecCCCCcCHHHHHHHHHHHccccCCCcEEEEEE--CCCCCEEeecCHHHHHHHHHcCC-CCcEEEEEE
Confidence 55566779999999999998 454569999994 66678999999999999888877 567899984
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=96.17 E-value=0.035 Score=45.68 Aligned_cols=65 Identities=20% Similarity=0.360 Sum_probs=53.5
Q ss_pred EEEecCceEEEEecCCCChHHHHHHHHHHcCCCCccEEEEEEcCCCCceeEEEeChHHHHHHHHhcCC
Q 003638 65 LSYKGGDAHAIDVDEQMKFNDFKTEVAEMFNCSFNAILLKYFLPGNKKTLITISNDKDLQRMIKFNGD 132 (806)
Q Consensus 65 ~~Y~Gg~~~~i~v~~~~s~~e~~~~l~~~~~~~~~~~~~~y~l~~~~~~l~~~~~D~dl~~M~~~~~~ 132 (806)
+.| ||.+|-+..+..-||.+|.+||...|++...++.+.|. .+..-.|+|++|+||+.-+.....
T Consensus 5 v~~-~g~~RRf~~~~~pt~~~L~~kl~~Lf~lp~~~~~vtYi--DeD~D~ITlssd~eL~d~~~~~~~ 69 (82)
T cd06397 5 SSF-LGDTRRIVFPDIPTWEALASKLENLYNLPEIKVGVTYI--DNDNDEITLSSNKELQDFYRLSHR 69 (82)
T ss_pred EEe-CCceEEEecCCCccHHHHHHHHHHHhCCChhHeEEEEE--cCCCCEEEecchHHHHHHHHhccc
Confidence 445 45666677899999999999999999998888999994 444588999999999997775544
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=96.16 E-value=0.033 Score=46.45 Aligned_cols=63 Identities=19% Similarity=0.333 Sum_probs=52.5
Q ss_pred cCceEEEEecCCCChHHHHHHHHHHcCCCCc-cEEEEEEcCCCCceeEEEeChHHHHHHHHhcCCC
Q 003638 69 GGDAHAIDVDEQMKFNDFKTEVAEMFNCSFN-AILLKYFLPGNKKTLITISNDKDLQRMIKFNGDS 133 (806)
Q Consensus 69 Gg~~~~i~v~~~~s~~e~~~~l~~~~~~~~~-~~~~~y~l~~~~~~l~~~~~D~dl~~M~~~~~~~ 133 (806)
+|+..++.++.++||.+|..++.+++.+... .+++||. .+.--++++++|++|+.-+..+..+
T Consensus 8 ~gdi~it~~d~~~s~e~L~~~v~~~c~~~~~q~ft~kw~--DEEGDp~tiSS~~EL~EA~rl~~~n 71 (83)
T cd06404 8 NGDIMITSIDPSISLEELCNEVRDMCRFHNDQPFTLKWI--DEEGDPCTISSQMELEEAFRLYELN 71 (83)
T ss_pred cCcEEEEEcCCCcCHHHHHHHHHHHhCCCCCCcEEEEEE--CCCCCceeecCHHHHHHHHHHHHhc
Confidence 5677888999999999999999999988774 8999994 5566789999999999766655443
No 22
>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=95.97 E-value=0.063 Score=43.39 Aligned_cols=66 Identities=26% Similarity=0.478 Sum_probs=54.8
Q ss_pred CceEEEEecCCCChHHHHHHHHHHcCCCCccEEEEEEcCCCCceeEEEeChHHHHHHHHhcCCC---CeEEEEEE
Q 003638 70 GDAHAIDVDEQMKFNDFKTEVAEMFNCSFNAILLKYFLPGNKKTLITISNDKDLQRMIKFNGDS---ATTDVFVI 141 (806)
Q Consensus 70 g~~~~i~v~~~~s~~e~~~~l~~~~~~~~~~~~~~y~l~~~~~~l~~~~~D~dl~~M~~~~~~~---~~v~iyv~ 141 (806)
|+.++|..+|-+.|.|+..|+.+.|| +++.+.|+. ..-+|||.+-+||++-++..+.+ .+..|++.
T Consensus 9 gEKRIi~f~RPvkf~dl~~kv~~afG---q~mdl~ytn---~eL~iPl~~Q~DLDkAie~ld~s~~~ksLRilL~ 77 (79)
T cd06405 9 GEKRIIQFPRPVKFKDLQQKVTTAFG---QPMDLHYTN---NELLIPLKNQEDLDRAIELLDRSPHMKSLRILLS 77 (79)
T ss_pred CceEEEecCCCccHHHHHHHHHHHhC---CeeeEEEec---ccEEEeccCHHHHHHHHHHHccCccccceeEeEe
Confidence 68899999999999999999999986 678899963 34899999999999977765554 55677663
No 23
>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=95.96 E-value=0.033 Score=46.02 Aligned_cols=63 Identities=17% Similarity=0.242 Sum_probs=56.6
Q ss_pred eEEEEecCCCChHHHHHHHHHHcCCCCccEEEEEEcCCCCceeEEEeChHHHHHHHHhcCCCC
Q 003638 72 AHAIDVDEQMKFNDFKTEVAEMFNCSFNAILLKYFLPGNKKTLITISNDKDLQRMIKFNGDSA 134 (806)
Q Consensus 72 ~~~i~v~~~~s~~e~~~~l~~~~~~~~~~~~~~y~l~~~~~~l~~~~~D~dl~~M~~~~~~~~ 134 (806)
|-.|.|+++.+|++|..+|+++|..-.+..+|.|.-|++...+++++.|++++.+.....++.
T Consensus 8 TVai~v~~g~~y~~L~~~ls~kL~l~~~~~~LSY~~~~~~~~~v~l~~e~~me~aW~~v~~~~ 70 (78)
T cd06411 8 TVALRAPRGADVSSLRALLSQALPQQAQRGQLSYRAPGEDGHWVPISGEESLQRAWQDVADGP 70 (78)
T ss_pred EEEEEccCCCCHHHHHHHHHHHhcCChhhcEEEecCCCCCccEeecCcchHHHHHHHhccCCc
Confidence 668999999999999999999999999999999987777768999999999999988776653
No 24
>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=95.31 E-value=0.16 Score=41.80 Aligned_cols=70 Identities=19% Similarity=0.340 Sum_probs=57.5
Q ss_pred EecCceEEEEecCC--CChHHHHHHHHHHcCCCCccEEEEEEcCCCCceeEEEeChHHHHHHHHhcCCCCeEEEEE
Q 003638 67 YKGGDAHAIDVDEQ--MKFNDFKTEVAEMFNCSFNAILLKYFLPGNKKTLITISNDKDLQRMIKFNGDSATTDVFV 140 (806)
Q Consensus 67 Y~Gg~~~~i~v~~~--~s~~e~~~~l~~~~~~~~~~~~~~y~l~~~~~~l~~~~~D~dl~~M~~~~~~~~~v~iyv 140 (806)
+-|++.|-.+++++ .||.||-+.|....++...++.++|.=| ..-|+||.+|+.+..-+.-. ..-..|||
T Consensus 6 kfdaEfRRFsl~r~~~~~f~ef~~ll~~lH~l~~~~f~i~Y~D~--~gDLLPInNDdNf~kAlssa--~plLRl~i 77 (80)
T cd06403 6 KFDAEFRRFSLDRNKPGKFEDFYKLLEHLHHIPNVDFLIGYTDP--HGDLLPINNDDNFLKALSSA--NPLLRIFI 77 (80)
T ss_pred ccCCeEEEEEeccccCcCHHHHHHHHHHHhCCCCCcEEEEEeCC--CCCEecccCcHHHHHHHHcC--CCceEEEE
Confidence 44678888888887 8999999999999999888999999755 56799999999999988733 33467776
No 25
>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=95.14 E-value=0.11 Score=44.10 Aligned_cols=70 Identities=14% Similarity=0.298 Sum_probs=58.8
Q ss_pred cCceEEEEecCCCChHHHHHHHHHHcCCCC---ccEEEEEEcCCCCceeEEEeChHHHHHHHHhcCCC--CeEEEEE
Q 003638 69 GGDAHAIDVDEQMKFNDFKTEVAEMFNCSF---NAILLKYFLPGNKKTLITISNDKDLQRMIKFNGDS--ATTDVFV 140 (806)
Q Consensus 69 Gg~~~~i~v~~~~s~~e~~~~l~~~~~~~~---~~~~~~y~l~~~~~~l~~~~~D~dl~~M~~~~~~~--~~v~iyv 140 (806)
.|+++-+.+..+.++.+|++.+...+|.+. ..+.|+|. .+..-.+.|++|.||...+++.... ..++++|
T Consensus 9 ~GrvhRf~~~~s~~~~~L~~~I~~Rl~~d~~~~~~~~L~Yl--DDEgD~VllT~D~DL~e~v~iar~~g~~~v~L~v 83 (86)
T cd06409 9 KGRVHRFRLRPSESLEELRTLISQRLGDDDFETHLYALSYV--DDEGDIVLITSDSDLVAAVLVARSAGLKKLDLHL 83 (86)
T ss_pred CCCEEEEEecCCCCHHHHHHHHHHHhCCccccCCcccEEEE--cCCCCEEEEeccchHHHHHHHHHHcCCCEEEEEE
Confidence 577888888878999999999999999987 58889993 5556788999999999999877655 5688887
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=95.02 E-value=0.015 Score=33.94 Aligned_cols=18 Identities=28% Similarity=0.693 Sum_probs=16.3
Q ss_pred EeCCCCCCCCCCcCcCCC
Q 003638 787 LQCSKCKGLGHNKSTCKE 804 (806)
Q Consensus 787 ~~Cs~C~~~GHn~~tC~~ 804 (806)
++|-+|++.||-.+.||+
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
>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=95.01 E-value=0.096 Score=43.60 Aligned_cols=60 Identities=23% Similarity=0.469 Sum_probs=49.3
Q ss_pred cCceEEEEecC-CCChHHHHHHHHHHcCCCC---ccEEEEEEcCCCCceeEEEeChHHHHHHHHhc
Q 003638 69 GGDAHAIDVDE-QMKFNDFKTEVAEMFNCSF---NAILLKYFLPGNKKTLITISNDKDLQRMIKFN 130 (806)
Q Consensus 69 Gg~~~~i~v~~-~~s~~e~~~~l~~~~~~~~---~~~~~~y~l~~~~~~l~~~~~D~dl~~M~~~~ 130 (806)
||+.|.+.++. .+||.||+..+...|+... .++.+||. .+...|++|.+++||.--+...
T Consensus 8 g~DiR~~~~~~~~~t~~~L~~~v~~~F~~~~~~~~~flIKYk--D~dGDlVTIts~~dL~~A~~~~ 71 (81)
T cd06401 8 GDDIRRIPIHNEDITYDELLLMMQRVFRGKLGSSDDVLIKYK--DEDGDLITIFDSSDLSFAIQCS 71 (81)
T ss_pred CCeEEEEeccCccccHHHHHHHHHHHhccccCCcccEEEEEE--CCCCCEEEeccHHHHHHHHhcC
Confidence 88999999986 4899999999998887443 48999994 5567899999999998765544
No 28
>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=93.52 E-value=0.17 Score=40.11 Aligned_cols=40 Identities=23% Similarity=0.380 Sum_probs=33.3
Q ss_pred ceEEEEEeecCCCCeEEEEEEeCCCceEEEEecCCCcccc
Q 003638 272 SHRVTVKCKAEGCPWRIHASRLSTTQLICIKKMNPTHTCE 311 (806)
Q Consensus 272 ~~r~~~~C~~~gCpwri~as~~~~~~~~~I~~~~~~HnC~ 311 (806)
-.|..++|+..+||++-.+.+..++....++++.++|||+
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 4577899999999999999998878888899999999996
No 29
>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=93.49 E-value=0.1 Score=54.46 Aligned_cols=93 Identities=14% Similarity=0.110 Sum_probs=67.4
Q ss_pred EEeccccccccccceEEEEeeecC--CCCeeeEEEEEecCCCchhHHHHHHHH-HHHccCCCCCeEEEecCchhHHHHHH
Q 003638 432 LFLDSVPLKSKYQGTLLAATAADG--DDGVFPVAFAVVDAETNDDWHWFLLQL-KSALSTATCPITFVADKQKGLRESIA 508 (806)
Q Consensus 432 i~lD~T~~~~~y~~~ll~a~g~d~--~~~~~plafa~v~~E~~esw~wfl~~l-k~~~~~~~~p~~iisD~~~~l~~Ai~ 508 (806)
|+||=+.....+.. +..+.+|. +++. -+.++++-+.++..-||..+ -..... ...+|++|...+..+|++
T Consensus 1 lgiDE~~~~~g~~~--y~t~~~d~~~~~~~---il~i~~~r~~~~l~~~~~~~~~~~~~~--~v~~V~~Dm~~~y~~~~~ 73 (249)
T PF01610_consen 1 LGIDEFAFRKGHRS--YVTVVVDLDTDTGR---ILDILPGRDKETLKDFFRSLYPEEERK--NVKVVSMDMSPPYRSAIR 73 (249)
T ss_pred CeEeeeeeecCCcc--eeEEEEECccCCce---EEEEcCCccHHHHHHHHHHhCcccccc--ceEEEEcCCCcccccccc
Confidence 35565554433332 33444454 3333 24588889999988888876 333222 369999999999999999
Q ss_pred hhcccccccchHHHHHHHHHHHh
Q 003638 509 EIFKGSFHGYCLRYLTEQLVKDL 531 (806)
Q Consensus 509 ~vfP~a~h~~C~~Hi~~n~~~~~ 531 (806)
+.||+|.+..-.|||++++.+.+
T Consensus 74 ~~~P~A~iv~DrFHvvk~~~~al 96 (249)
T PF01610_consen 74 EYFPNAQIVADRFHVVKLANRAL 96 (249)
T ss_pred ccccccccccccchhhhhhhhcc
Confidence 99999999999999999988866
No 30
>PF06782 UPF0236: Uncharacterised protein family (UPF0236); InterPro: IPR009620 This is a group of proteins of unknown function.
Probab=93.33 E-value=1.5 Score=50.35 Aligned_cols=92 Identities=13% Similarity=0.123 Sum_probs=68.7
Q ss_pred CCCchhHHHHHHHHHHHccCCCC-CeEEEecCchhHHHHHHhhcccccccchHHHHHHHHHHHhcccccHHHHHHHHHHH
Q 003638 469 AETNDDWHWFLLQLKSALSTATC-PITFVADKQKGLRESIAEIFKGSFHGYCLRYLTEQLVKDLKGQFSHEVKRLMIEDF 547 (806)
Q Consensus 469 ~E~~esw~wfl~~lk~~~~~~~~-p~~iisD~~~~l~~Ai~~vfP~a~h~~C~~Hi~~n~~~~~~~~~~~~~~~~~~~~~ 547 (806)
..+.+-|.-+.+.+.+....... -.++.+|+...+.+++. .||.+.|.+..+|+.+.+.+.++.. .+ +.+.+
T Consensus 235 ~~~~~~~~~v~~~i~~~Y~~~~~~~iiingDGa~WIk~~~~-~~~~~~~~LD~FHl~k~i~~~~~~~--~~----~~~~~ 307 (470)
T PF06782_consen 235 ESAEEFWEEVLDYIYNHYDLDKTTKIIINGDGASWIKEGAE-FFPKAEYFLDRFHLNKKIKQALSHD--PE----LKEKI 307 (470)
T ss_pred cchHHHHHHHHHHHHHhcCcccceEEEEeCCCcHHHHHHHH-hhcCceEEecHHHHHHHHHHHhhhC--hH----HHHHH
Confidence 45677899888888877654422 37788999999988776 9999999999999999999988542 12 33444
Q ss_pred HHHhcCCCHHHHHHHHHHHH
Q 003638 548 YAAAYAPTPEEFERSIESIK 567 (806)
Q Consensus 548 ~~~~~a~t~~eF~~~~~~l~ 567 (806)
+++.+.....+++..++.+.
T Consensus 308 ~~al~~~d~~~l~~~L~~~~ 327 (470)
T PF06782_consen 308 RKALKKGDKKKLETVLDTAE 327 (470)
T ss_pred HHHHHhcCHHHHHHHHHHHH
Confidence 55556667777777776655
No 31
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=93.30 E-value=0.04 Score=39.12 Aligned_cols=19 Identities=26% Similarity=0.912 Sum_probs=16.4
Q ss_pred eEeCCCCCCCCCCc--CcCCC
Q 003638 786 QLQCSKCKGLGHNK--STCKE 804 (806)
Q Consensus 786 ~~~Cs~C~~~GHn~--~tC~~ 804 (806)
+++|++|++.||.+ ++||.
T Consensus 1 k~kC~~CG~~GH~~t~k~CP~ 21 (40)
T PF15288_consen 1 KVKCKNCGAFGHMRTNKRCPM 21 (40)
T ss_pred CccccccccccccccCccCCC
Confidence 36899999999998 77875
No 32
>PF13610 DDE_Tnp_IS240: DDE domain
Probab=93.08 E-value=0.042 Score=51.97 Aligned_cols=81 Identities=17% Similarity=0.111 Sum_probs=67.0
Q ss_pred CceEEeccccccccccceEEEEeeecCCCCeeeEEEEEecCCCchhHHHHHHHHHHHccCCCCCeEEEecCchhHHHHHH
Q 003638 429 RPLLFLDSVPLKSKYQGTLLAATAADGDDGVFPVAFAVVDAETNDDWHWFLLQLKSALSTATCPITFVADKQKGLRESIA 508 (806)
Q Consensus 429 ~~vi~lD~T~~~~~y~~~ll~a~g~d~~~~~~plafa~v~~E~~esw~wfl~~lk~~~~~~~~p~~iisD~~~~l~~Ai~ 508 (806)
++.+.+|-||.+-+-+ ..+...++|.+++ .|++-|...-+...=..||..+.+.... .|..|+||+.++...|++
T Consensus 1 ~~~w~~DEt~iki~G~-~~yl~~aiD~~~~--~l~~~ls~~Rd~~aA~~Fl~~~l~~~~~--~p~~ivtDk~~aY~~A~~ 75 (140)
T PF13610_consen 1 GDSWHVDETYIKIKGK-WHYLWRAIDAEGN--ILDFYLSKRRDTAAAKRFLKRALKRHRG--EPRVIVTDKLPAYPAAIK 75 (140)
T ss_pred CCEEEEeeEEEEECCE-EEEEEEeeccccc--chhhhhhhhcccccceeeccccceeecc--ccceeecccCCccchhhh
Confidence 3678999999874433 3444678899999 8899999999999888999888877763 489999999999999999
Q ss_pred hhcccc
Q 003638 509 EIFKGS 514 (806)
Q Consensus 509 ~vfP~a 514 (806)
++++..
T Consensus 76 ~l~~~~ 81 (140)
T PF13610_consen 76 ELNPEG 81 (140)
T ss_pred hccccc
Confidence 999874
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=92.63 E-value=0.28 Score=51.97 Aligned_cols=131 Identities=17% Similarity=0.185 Sum_probs=82.0
Q ss_pred CCChHHHHHHHHHHhCccccHHHHHHHHHHHHHHHhcChHHHhccHHHHHHHHHHhCCCcEEEEEecCCCceeEEEEEcc
Q 003638 339 NYKPKDIVNDIKQEYGIQLNYFQAWRGKEIAKEQLQGSYKEAYNQLPLFCERIMETNPGSLATFTTKEDSSFHRLFVSFH 418 (806)
Q Consensus 339 ~~~~~~I~~~l~~~~g~~~s~~~~~rak~~~~~~~~g~~~~~~~~L~~~~~~l~~~NPg~~~~~~~~~~~~f~~lF~a~~ 418 (806)
.++...+.+.+.+. |+.+|.+.+.+.-..+.+.+.. ..+.+.+.
T Consensus 20 ~lp~~r~~~~~~~~-G~~is~~ti~~~~~~~~~~l~~-----------~~~~l~~~------------------------ 63 (271)
T PF03050_consen 20 HLPLYRIQQMLEDL-GITISRGTIANWIKRVAEALKP-----------LYEALKEE------------------------ 63 (271)
T ss_pred CCCHHHHhhhhhcc-ceeeccchhHhHhhhhhhhhhh-----------hhhhhhhh------------------------
Confidence 44455566666666 9999999998876544433221 11222211
Q ss_pred ccHHHHhhcCCceEEecccccc----cccc-ceEEEEeeecCCCCeeeEEEEEecCCCchhHHHHHHHHHHHccCCCCCe
Q 003638 419 ASLYGFIQGCRPLLFLDSVPLK----SKYQ-GTLLAATAADGDDGVFPVAFAVVDAETNDDWHWFLLQLKSALSTATCPI 493 (806)
Q Consensus 419 ~s~~~f~~~~~~vi~lD~T~~~----~~y~-~~ll~a~g~d~~~~~~plafa~v~~E~~esw~wfl~~lk~~~~~~~~p~ 493 (806)
. --.+|+.+|-|... ++.. +-+-++.+-+ .+.|.+.++-+.+...-+|.. . .-
T Consensus 64 ------~-~~~~~~~~DET~~~vl~~~~g~~~~~Wv~~~~~------~v~f~~~~sR~~~~~~~~L~~-------~--~G 121 (271)
T PF03050_consen 64 ------L-RSSPVVHADETGWRVLDKGKGKKGYLWVFVSPE------VVLFFYAPSRSSKVIKEFLGD-------F--SG 121 (271)
T ss_pred ------c-cccceeccCCceEEEeccccccceEEEeeeccc------eeeeeecccccccchhhhhcc-------c--ce
Confidence 1 13578888888866 4433 3333333333 556666666666655555433 2 36
Q ss_pred EEEecCchhHHHHHHhhcccccccchHHHHHHHHHHHhc
Q 003638 494 TFVADKQKGLRESIAEIFKGSFHGYCLRYLTEQLVKDLK 532 (806)
Q Consensus 494 ~iisD~~~~l~~Ai~~vfP~a~h~~C~~Hi~~n~~~~~~ 532 (806)
+++||+-.+-.. +....|+.|+.|+.+.|.+...
T Consensus 122 ilvsD~y~~Y~~-----~~~~~hq~C~AH~~R~~~~~~~ 155 (271)
T PF03050_consen 122 ILVSDGYSAYNK-----LAGITHQLCWAHLRRDFQDAAE 155 (271)
T ss_pred eeeccccccccc-----cccccccccccccccccccccc
Confidence 899999888754 3378999999999999988774
No 34
>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=90.30 E-value=0.62 Score=51.17 Aligned_cols=56 Identities=16% Similarity=0.471 Sum_probs=50.4
Q ss_pred cCcccCCHHHHHHHHHHHHHHcCeEEEEeecC-ceEEEEEeecCCCCeEEEEEEeCC
Q 003638 240 VGQRFSSVHEFRELLRKYAIAHQFAFKYKKND-SHRVTVKCKAEGCPWRIHASRLST 295 (806)
Q Consensus 240 vG~~F~s~ee~~~a~~~yAi~~gf~~~~~ks~-~~r~~~~C~~~gCpwri~as~~~~ 295 (806)
.+..|++.++-+.+|+.|..+.+..|..+.|. .+.++|.|....|||+|..+..+.
T Consensus 24 ~~~~f~tl~~wy~v~ndyefq~rcpiilknsh~nkhftfachlk~c~fkillsy~g~ 80 (496)
T PF04684_consen 24 QARKFPTLEAWYNVINDYEFQSRCPIILKNSHRNKHFTFACHLKNCPFKILLSYCGN 80 (496)
T ss_pred cccCCCcHHHHHHHHhhhhhhhcCceeecccccccceEEEeeccCCCceeeeeeccc
Confidence 47789999999999999999999999999885 467999999999999999887654
No 35
>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=88.64 E-value=1.2 Score=37.08 Aligned_cols=64 Identities=8% Similarity=0.038 Sum_probs=45.9
Q ss_pred cCceEEEEecCCCChHHHHHHHHHHcCCCCccEEEEEEcCCCCceeEEEeChHHHHHHHHhcCCCCeEEEEE
Q 003638 69 GGDAHAIDVDEQMKFNDFKTEVAEMFNCSFNAILLKYFLPGNKKTLITISNDKDLQRMIKFNGDSATTDVFV 140 (806)
Q Consensus 69 Gg~~~~i~v~~~~s~~e~~~~l~~~~~~~~~~~~~~y~l~~~~~~l~~~~~D~dl~~M~~~~~~~~~v~iyv 140 (806)
+|.+..|.|+.++|-.+++.+|.+..|+.+....| |.-.. +.+|+....-...-.++..+.+|+
T Consensus 11 ~~~t~~l~v~~~~TV~~lK~kI~~~~gip~~~QrL-~~G~~-------L~dD~~tL~~ygi~~~g~~~~l~~ 74 (75)
T cd01799 11 HTVTIWLTVRPDMTVAQLKDKVFLDYGFPPAVQRW-VIGQR-------LARDQETLYSHGIRTNGDSAFLYI 74 (75)
T ss_pred CCCeEEEEECCCCcHHHHHHHHHHHHCcCHHHEEE-EcCCe-------eCCCcCCHHHcCCCCCCCEEEEEe
Confidence 57788899999999999999999999999999988 73211 344433333333333456777775
No 36
>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=88.13 E-value=0.9 Score=35.82 Aligned_cols=46 Identities=15% Similarity=0.361 Sum_probs=25.4
Q ss_pred cCeEEEEeecCceEEEEEeecC---CCCeEEEEEEeCCCceEEEEecCCCccc
Q 003638 261 HQFAFKYKKNDSHRVTVKCKAE---GCPWRIHASRLSTTQLICIKKMNPTHTC 310 (806)
Q Consensus 261 ~gf~~~~~ks~~~r~~~~C~~~---gCpwri~as~~~~~~~~~I~~~~~~HnC 310 (806)
.|+.|...+........+|+.. +|+++|... .+.-.|.....+|||
T Consensus 14 ~Gy~y~~~~~~~~~~~WrC~~~~~~~C~a~~~~~----~~~~~~~~~~~~HnH 62 (62)
T PF04500_consen 14 DGYRYYFNKRNDGKTYWRCSRRRSHGCRARLITD----AGDGRVVRTNGEHNH 62 (62)
T ss_dssp TTEEEEEEEE-SS-EEEEEGGGTTS----EEEEE------TTEEEE-S---SS
T ss_pred CCeEEECcCCCCCcEEEEeCCCCCCCCeEEEEEE----CCCCEEEECCCccCC
Confidence 4777888777788889999864 899999987 223345666688987
No 37
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=87.33 E-value=0.35 Score=32.69 Aligned_cols=20 Identities=25% Similarity=0.597 Sum_probs=18.0
Q ss_pred ceEeCCCCCCCCCCcCcCCC
Q 003638 785 RQLQCSKCKGLGHNKSTCKE 804 (806)
Q Consensus 785 ~~~~Cs~C~~~GHn~~tC~~ 804 (806)
..+.|.+|++.||-.+.||.
T Consensus 7 ~~Y~C~~C~~~GH~i~dCP~ 26 (32)
T PF13696_consen 7 PGYVCHRCGQKGHWIQDCPT 26 (32)
T ss_pred CCCEeecCCCCCccHhHCCC
Confidence 35799999999999999996
No 38
>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=87.21 E-value=0.82 Score=35.93 Aligned_cols=39 Identities=21% Similarity=0.348 Sum_probs=32.2
Q ss_pred ceEEEEEeec-CCCCeEEEEEEeCCCceEEEEecCCCccc
Q 003638 272 SHRVTVKCKA-EGCPWRIHASRLSTTQLICIKKMNPTHTC 310 (806)
Q Consensus 272 ~~r~~~~C~~-~gCpwri~as~~~~~~~~~I~~~~~~HnC 310 (806)
-.|..++|+. .|||++=.+.+..++....+.++.++|||
T Consensus 20 ~pRsYYrCt~~~~C~a~K~Vq~~~~d~~~~~vtY~g~H~h 59 (59)
T smart00774 20 FPRSYYRCTYSQGCPAKKQVQRSDDDPSVVEVTYEGEHTH 59 (59)
T ss_pred CcceEEeccccCCCCCcccEEEECCCCCEEEEEEeeEeCC
Confidence 3466789998 89999888877766667778889999998
No 39
>PF13565 HTH_32: Homeodomain-like domain
Probab=81.88 E-value=2.7 Score=34.84 Aligned_cols=38 Identities=21% Similarity=0.480 Sum_probs=33.3
Q ss_pred HHHHHHHhcCCCCChHHHHHHHHHHhCccc--cHHHHHHH
Q 003638 328 SIIKEKLKVFPNYKPKDIVNDIKQEYGIQL--NYFQAWRG 365 (806)
Q Consensus 328 ~~i~~~i~~~~~~~~~~I~~~l~~~~g~~~--s~~~~~ra 365 (806)
..|.+.+..+|.+++.+|.+.|.+++|+.+ |.+.+||.
T Consensus 37 ~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~~~S~~tv~R~ 76 (77)
T PF13565_consen 37 ERIIALIEEHPRWTPREIAEYLEEEFGISVRVSRSTVYRI 76 (77)
T ss_pred HHHHHHHHhCCCCCHHHHHHHHHHHhCCCCCccHhHHHHh
Confidence 566677788999999999999999999876 99999884
No 40
>COG3316 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=80.92 E-value=15 Score=37.02 Aligned_cols=121 Identities=17% Similarity=0.151 Sum_probs=82.5
Q ss_pred HHHHHHhCccccHHHHHHHHHHHHHHHhcChHHHhccHHHHHHHHHHhCCCcEEEEEecCCCceeEEEEEccccHHHHhh
Q 003638 347 NDIKQEYGIQLNYFQAWRGKEIAKEQLQGSYKEAYNQLPLFCERIMETNPGSLATFTTKEDSSFHRLFVSFHASLYGFIQ 426 (806)
Q Consensus 347 ~~l~~~~g~~~s~~~~~rak~~~~~~~~g~~~~~~~~L~~~~~~l~~~NPg~~~~~~~~~~~~f~~lF~a~~~s~~~f~~ 426 (806)
+.+..+.|+.+.+.++.|.-++.- |.+...+.+.++.
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 345667899999998888644322 2233444444322
Q ss_pred cCCceEEeccccccccccceEEEEeeecCCCCeeeEEEEEecCCCchhHHHHHHHHHHHccCCCCCeEEEecCchhHHHH
Q 003638 427 GCRPLLFLDSVPLKSKYQGTLLAATAADGDDGVFPVAFAVVDAETNDDWHWFLLQLKSALSTATCPITFVADKQKGLRES 506 (806)
Q Consensus 427 ~~~~vi~lD~T~~~~~y~~~ll~a~g~d~~~~~~plafa~v~~E~~esw~wfl~~lk~~~~~~~~p~~iisD~~~~l~~A 506 (806)
-++.+.+|-||.+-+-++. +.--++|.+| .++.+-+...-+...=.-||..+.+.. + .|.+|+||+.+....|
T Consensus 69 -~~~~w~vDEt~ikv~gkw~-ylyrAid~~g--~~Ld~~L~~rRn~~aAk~Fl~kllk~~-g--~p~v~vtDka~s~~~A 141 (215)
T COG3316 69 -AGDSWRVDETYIKVNGKWH-YLYRAIDADG--LTLDVWLSKRRNALAAKAFLKKLLKKH-G--EPRVFVTDKAPSYTAA 141 (215)
T ss_pred -cccceeeeeeEEeeccEee-ehhhhhccCC--CeEEEEEEcccCcHHHHHHHHHHHHhc-C--CCceEEecCccchHHH
Confidence 3467888888876443332 2234556664 467888888888887788888877776 3 4899999999999999
Q ss_pred HHhhccccccc
Q 003638 507 IAEIFKGSFHG 517 (806)
Q Consensus 507 i~~vfP~a~h~ 517 (806)
+.++-+...|+
T Consensus 142 ~~~l~~~~ehr 152 (215)
T COG3316 142 LRKLGSEVEHR 152 (215)
T ss_pred HHhcCcchhee
Confidence 99998755554
No 41
>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=79.82 E-value=6.9 Score=35.18 Aligned_cols=76 Identities=16% Similarity=0.080 Sum_probs=54.2
Q ss_pred CCceEEecccccc-ccccceEEEEeeecCCCCeeeEEEEEecCCCchhHHHHHHHHHHHccCCCCCeEEEecCchhHHH
Q 003638 428 CRPLLFLDSVPLK-SKYQGTLLAATAADGDDGVFPVAFAVVDAETNDDWHWFLLQLKSALSTATCPITFVADKQKGLRE 505 (806)
Q Consensus 428 ~~~vi~lD~T~~~-~~y~~~ll~a~g~d~~~~~~plafa~v~~E~~esw~wfl~~lk~~~~~~~~p~~iisD~~~~l~~ 505 (806)
-..++.+|.++.. ...++..+..+.+|..-+. .+++.+...++.+.+..+|.......+.. .|.+|++|+..+..+
T Consensus 5 p~~~~~~D~~~~~~~~~~~~~~~~~~iD~~S~~-~~~~~~~~~~~~~~~~~~l~~~~~~~~~~-~p~~i~tD~g~~f~~ 81 (120)
T PF00665_consen 5 PGERWQIDFTPMPIPDKGGRVYLLVFIDDYSRF-IYAFPVSSKETAEAALRALKRAIEKRGGR-PPRVIRTDNGSEFTS 81 (120)
T ss_dssp TTTEEEEEEEEETGGCTT-CEEEEEEEETTTTE-EEEEEESSSSHHHHHHHHHHHHHHHHS-S-E-SEEEEESCHHHHS
T ss_pred CCCEEEEeeEEEecCCCCccEEEEEEEECCCCc-EEEEEeecccccccccccccccccccccc-cceeccccccccccc
Confidence 4568899999665 3455588888899988775 45777777777777777777655555443 289999999998864
No 42
>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=77.72 E-value=4.6 Score=32.81 Aligned_cols=41 Identities=20% Similarity=0.318 Sum_probs=36.4
Q ss_pred EEEecCceEEEEecCCCChHHHHHHHHHHcCCCCccEEEEEE
Q 003638 65 LSYKGGDAHAIDVDEQMKFNDFKTEVAEMFNCSFNAILLKYF 106 (806)
Q Consensus 65 ~~Y~Gg~~~~i~v~~~~s~~e~~~~l~~~~~~~~~~~~~~y~ 106 (806)
+++. |++..+.|+.+.|..+|+.+|.+..|+.+...+|.|.
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 5664 8888899999999999999999999999888888874
No 43
>PHA02517 putative transposase OrfB; Reviewed
Probab=76.92 E-value=9 Score=40.59 Aligned_cols=149 Identities=19% Similarity=0.138 Sum_probs=82.8
Q ss_pred hHHHHHHHHHhc-CCCCChHHHHHHHHHHhCccccHHHHHHHHHHHHHHHhcChHHHhccHHHHHHHHHHhCCCcEEEEE
Q 003638 325 WVASIIKEKLKV-FPNYKPKDIVNDIKQEYGIQLNYFQAWRGKEIAKEQLQGSYKEAYNQLPLFCERIMETNPGSLATFT 403 (806)
Q Consensus 325 ~ia~~i~~~i~~-~~~~~~~~I~~~l~~~~g~~~s~~~~~rak~~~~~~~~g~~~~~~~~L~~~~~~l~~~NPg~~~~~~ 403 (806)
.+.+.|.+.+.. .+.+..+.|...|.+. |+.++.++++|..+. .|-.... . ..-.....+-. .
T Consensus 30 ~l~~~I~~i~~~~~~~~G~r~I~~~L~~~-g~~vs~~tV~Rim~~-----~gl~~~~-~------~k~~~~~~~~~---~ 93 (277)
T PHA02517 30 WLKSEILRVYDENHQVYGVRKVWRQLNRE-GIRVARCTVGRLMKE-----LGLAGVL-R------GKKVRTTISRK---A 93 (277)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHHHhc-CcccCHHHHHHHHHH-----cCCceEe-c------CCCcCCCCCCC---C
Confidence 455566666554 5789999999998765 999999999986432 1210000 0 00000000000 0
Q ss_pred ecCCCceeEEEEEccccHHHHhhcCCceEEeccccccccccceEEEEeeecCCCCeeeEEEEEecCCCchhHHHHHHHHH
Q 003638 404 TKEDSSFHRLFVSFHASLYGFIQGCRPLLFLDSVPLKSKYQGTLLAATAADGDDGVFPVAFAVVDAETNDDWHWFLLQLK 483 (806)
Q Consensus 404 ~~~~~~f~~lF~a~~~s~~~f~~~~~~vi~lD~T~~~~~y~~~ll~a~g~d~~~~~~plafa~v~~E~~esw~wfl~~lk 483 (806)
....+.+.+-|-+. .-..++..|.|+..... +..+.++.+|...+ +.+|+.+...++.+.. +..|+
T Consensus 94 ~~~~n~~~r~f~~~---------~pn~~w~~D~t~~~~~~-g~~yl~~iiD~~sr-~i~~~~~~~~~~~~~~---~~~l~ 159 (277)
T PHA02517 94 VAAPDRVNRQFVAT---------RPNQLWVADFTYVSTWQ-GWVYVAFIIDVFAR-RIVGWRVSSSMDTDFV---LDALE 159 (277)
T ss_pred CCCCCcccCCCCCC---------CCCCeEEeceeEEEeCC-CCEEEEEecccCCC-eeeecccCCCCChHHH---HHHHH
Confidence 00011111112111 24568999999976543 55677777888776 4678888877777754 44454
Q ss_pred HHccCCCCC--eEEEecCchhH
Q 003638 484 SALSTATCP--ITFVADKQKGL 503 (806)
Q Consensus 484 ~~~~~~~~p--~~iisD~~~~l 503 (806)
.++...+.| .+|.||+....
T Consensus 160 ~a~~~~~~~~~~i~~sD~G~~y 181 (277)
T PHA02517 160 QALWARGRPGGLIHHSDKGSQY 181 (277)
T ss_pred HHHHhcCCCcCcEeeccccccc
Confidence 444333223 56779986654
No 44
>smart00343 ZnF_C2HC zinc finger.
Probab=76.54 E-value=1.4 Score=28.28 Aligned_cols=17 Identities=29% Similarity=0.778 Sum_probs=15.3
Q ss_pred eCCCCCCCCCCcCcCCC
Q 003638 788 QCSKCKGLGHNKSTCKE 804 (806)
Q Consensus 788 ~Cs~C~~~GHn~~tC~~ 804 (806)
.|.+|++.||..+.||.
T Consensus 1 ~C~~CG~~GH~~~~C~~ 17 (26)
T smart00343 1 KCYNCGKEGHIARDCPK 17 (26)
T ss_pred CCccCCCCCcchhhCCc
Confidence 48999999999999984
No 45
>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=76.05 E-value=11 Score=31.87 Aligned_cols=60 Identities=22% Similarity=0.311 Sum_probs=45.8
Q ss_pred CceEEEEecCCC----ChHHHHHHHHHHcCCCCccEEEEEEcCCCCceeEEEeChHHHHHHHHhcCCC
Q 003638 70 GDAHAIDVDEQM----KFNDFKTEVAEMFNCSFNAILLKYFLPGNKKTLITISNDKDLQRMIKFNGDS 133 (806)
Q Consensus 70 g~~~~i~v~~~~----s~~e~~~~l~~~~~~~~~~~~~~y~l~~~~~~l~~~~~D~dl~~M~~~~~~~ 133 (806)
-.++-|.|..++ +|.||+..+...|+ ...+.|-|.=+ .--||-|-+|+|+.-|++-....
T Consensus 13 ~~~rdi~vee~l~~~P~~kdLl~lmr~~f~--~~dIaLNYrD~--EGDLIRllddeDv~LMV~~~r~~ 76 (92)
T cd06399 13 STIRDIAVEEDLSSTPLLKDLLELTRREFQ--REDIALNYRDA--EGDLIRLLSDEDVALMVRQSRGL 76 (92)
T ss_pred ccccceEeecccccCccHHHHHHHHHHHhc--hhheeeeeecC--CCCEEEEcchhhHHHHHHHHhcC
Confidence 344555554444 79999999999865 67899999622 34689999999999999987654
No 46
>PF14560 Ubiquitin_2: Ubiquitin-like domain; PDB: 1WJN_A 2KJ6_A 2KJR_A 1V6E_A 1T0Y_A.
Probab=75.29 E-value=5.8 Score=33.93 Aligned_cols=35 Identities=6% Similarity=0.124 Sum_probs=30.9
Q ss_pred eEEEEecCCCChHHHHHHHHHHcCCCCccEEEEEE
Q 003638 72 AHAIDVDEQMKFNDFKTEVAEMFNCSFNAILLKYF 106 (806)
Q Consensus 72 ~~~i~v~~~~s~~e~~~~l~~~~~~~~~~~~~~y~ 106 (806)
...+.+++++|..||+.+|...+|+.+..+.|.|.
T Consensus 15 ~~ekr~~~~~Tv~eLK~kl~~~~Gi~~~~m~L~l~ 49 (87)
T PF14560_consen 15 SVEKRFPKSITVSELKQKLEKLTGIPPSDMRLQLK 49 (87)
T ss_dssp EEEEEEETTSBHHHHHHHHHHHHTS-TTTEEEEEE
T ss_pred eEEEEcCCCCCHHHHHHHHHHHhCCCcccEEEEEE
Confidence 34588999999999999999999999999999885
No 47
>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=74.19 E-value=7.4 Score=32.07 Aligned_cols=42 Identities=19% Similarity=0.229 Sum_probs=37.4
Q ss_pred EEEecCceEEEEecCCCChHHHHHHHHHHcCCCCccEEEEEE
Q 003638 65 LSYKGGDAHAIDVDEQMKFNDFKTEVAEMFNCSFNAILLKYF 106 (806)
Q Consensus 65 ~~Y~Gg~~~~i~v~~~~s~~e~~~~l~~~~~~~~~~~~~~y~ 106 (806)
++..+|.+..+.|+.+.|..+|+.+|.+..|+...+..|-|.
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 456688888999999999999999999999998888888773
No 48
>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=73.90 E-value=9.1 Score=31.21 Aligned_cols=42 Identities=12% Similarity=0.107 Sum_probs=37.3
Q ss_pred EEEecCceEEEEecCCCChHHHHHHHHHHcCCCC-ccEEEEEE
Q 003638 65 LSYKGGDAHAIDVDEQMKFNDFKTEVAEMFNCSF-NAILLKYF 106 (806)
Q Consensus 65 ~~Y~Gg~~~~i~v~~~~s~~e~~~~l~~~~~~~~-~~~~~~y~ 106 (806)
|.-.+|....+.|.++.++..|+.+.++..|++. +++.|.|.
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 4556778778999999999999999999999999 89999983
No 49
>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=73.78 E-value=6.2 Score=31.82 Aligned_cols=38 Identities=16% Similarity=0.098 Sum_probs=27.4
Q ss_pred cCceEEEEecCCCChHHHHHHHHHHcCCCCccEEEEEE
Q 003638 69 GGDAHAIDVDEQMKFNDFKTEVAEMFNCSFNAILLKYF 106 (806)
Q Consensus 69 Gg~~~~i~v~~~~s~~e~~~~l~~~~~~~~~~~~~~y~ 106 (806)
+|+...|.|..+++..+++.+.|.+||++...+.|+|.
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 45667799999999999999999999999998888873
No 50
>COG5431 Uncharacterized metal-binding protein [Function unknown]
Probab=73.00 E-value=7.2 Score=33.97 Aligned_cols=50 Identities=28% Similarity=0.561 Sum_probs=31.5
Q ss_pred EEEec-ceeEEeeCcCccccccccc----cc-CCcccchhHHhhhcCCCcccccccch
Q 003638 675 FEVRG-DSIEVVDIDHWDCSCKGWQ----LT-GLPCCHAIAVLSCIGCSPYDYCSRYF 726 (806)
Q Consensus 675 f~V~~-~~~~~Vdl~~~~CsC~~~~----~~-GiPC~H~lav~~~~~~~~~~yv~~~y 726 (806)
|.+-| ++.|+++.+ .|||..|- .. .-||.|++++=...--.-.++|+-+|
T Consensus 36 fVyvG~~rdYIl~~g--fCSCp~~~~svvl~Gk~~C~Hi~glk~A~~~gk~~~I~~y~ 91 (117)
T COG5431 36 FVYVGKERDYILEGG--FCSCPDFLGSVVLKGKSPCAHIIGLKVAKITGKYDYIDAYY 91 (117)
T ss_pred EEEEccccceEEEcC--cccCHHHHhHhhhcCcccchhhhheeeeeecCcEEEEEEec
Confidence 44455 458999877 99999887 22 35899999864333323345554443
No 51
>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=72.67 E-value=8.5 Score=29.14 Aligned_cols=43 Identities=14% Similarity=0.087 Sum_probs=36.2
Q ss_pred EEEecCceEEEEecCCCChHHHHHHHHHHcCCCCccEEEEEEc
Q 003638 65 LSYKGGDAHAIDVDEQMKFNDFKTEVAEMFNCSFNAILLKYFL 107 (806)
Q Consensus 65 ~~Y~Gg~~~~i~v~~~~s~~e~~~~l~~~~~~~~~~~~~~y~l 107 (806)
+++.+|....+.++.+.|..+|+.++.+.+|.....+.+.+-.
T Consensus 2 v~~~~~~~~~~~~~~~~tv~~l~~~i~~~~~~~~~~~~l~~~~ 44 (69)
T cd00196 2 VKLNDGKTVELLVPSGTTVADLKEKLAKKLGLPPEQQRLLVNG 44 (69)
T ss_pred eEecCCCEEEEEcCCCCcHHHHHHHHHHHHCcChHHeEEEECC
Confidence 4556888899999999999999999999998777778877643
No 52
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=72.38 E-value=1.5 Score=33.14 Aligned_cols=19 Identities=26% Similarity=0.747 Sum_probs=17.1
Q ss_pred eEeCCCCCCCCCCcCcCCC
Q 003638 786 QLQCSKCKGLGHNKSTCKE 804 (806)
Q Consensus 786 ~~~Cs~C~~~GHn~~tC~~ 804 (806)
...|+.|+..||+.+.||.
T Consensus 31 p~~C~~C~~~gH~~~~C~k 49 (49)
T PF14392_consen 31 PRFCFHCGRIGHSDKECPK 49 (49)
T ss_pred ChhhcCCCCcCcCHhHcCC
Confidence 4689999999999999984
No 53
>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=72.26 E-value=7.3 Score=31.92 Aligned_cols=38 Identities=18% Similarity=0.271 Sum_probs=35.1
Q ss_pred cCceEEEEecCCCChHHHHHHHHHHcCCCCccEEEEEE
Q 003638 69 GGDAHAIDVDEQMKFNDFKTEVAEMFNCSFNAILLKYF 106 (806)
Q Consensus 69 Gg~~~~i~v~~~~s~~e~~~~l~~~~~~~~~~~~~~y~ 106 (806)
||++..+.|+.++|..+|+.++.+..|+...+..|-|.
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 88999999999999999999999999998888888873
No 54
>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=71.02 E-value=10 Score=30.72 Aligned_cols=41 Identities=22% Similarity=0.350 Sum_probs=36.3
Q ss_pred EEEecCceEEEEecCCCChHHHHHHHHHHcCCCCccEEEEE
Q 003638 65 LSYKGGDAHAIDVDEQMKFNDFKTEVAEMFNCSFNAILLKY 105 (806)
Q Consensus 65 ~~Y~Gg~~~~i~v~~~~s~~e~~~~l~~~~~~~~~~~~~~y 105 (806)
++...|++..+.++.+.|..+|+.+|.+..|+.....+|.|
T Consensus 5 vk~~~g~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~ 45 (72)
T cd01809 5 VKTLDSQTHTFTVEEEITVLDLKEKIAEEVGIPVEQQRLIY 45 (72)
T ss_pred EEeCCCCEEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEEE
Confidence 44566788899999999999999999999999888888888
No 55
>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=70.78 E-value=9.3 Score=31.05 Aligned_cols=42 Identities=14% Similarity=0.256 Sum_probs=37.1
Q ss_pred EEEecCceEEEEecCCCChHHHHHHHHHHcCCCCccEEEEEE
Q 003638 65 LSYKGGDAHAIDVDEQMKFNDFKTEVAEMFNCSFNAILLKYF 106 (806)
Q Consensus 65 ~~Y~Gg~~~~i~v~~~~s~~e~~~~l~~~~~~~~~~~~~~y~ 106 (806)
++..+|++..+.|+.+.|..+|+.+|.+..|+...+..|-|.
T Consensus 3 vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~gi~~~~q~Li~~ 44 (70)
T cd01798 3 VRTNTGHTFPVEVDPDTDIKQLKEVVAKRQGVPPDQLRVIFA 44 (70)
T ss_pred EEcCCCCEEEEEECCCChHHHHHHHHHHHHCCCHHHeEEEEC
Confidence 345678899999999999999999999999999989888773
No 56
>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=70.21 E-value=9.3 Score=31.26 Aligned_cols=54 Identities=9% Similarity=0.079 Sum_probs=43.3
Q ss_pred EEEecCceEEEEecCCCChHHHHHHHHHHcCCCCccEEEEEEcCCCCceeEEEeChHHHHH
Q 003638 65 LSYKGGDAHAIDVDEQMKFNDFKTEVAEMFNCSFNAILLKYFLPGNKKTLITISNDKDLQR 125 (806)
Q Consensus 65 ~~Y~Gg~~~~i~v~~~~s~~e~~~~l~~~~~~~~~~~~~~y~l~~~~~~l~~~~~D~dl~~ 125 (806)
++..+|++..+.|+...|-.+++.++.+..|+...+.+|-|- -.++.||..+..
T Consensus 3 vk~~~G~~~~l~v~~~~TV~~lK~~I~~~~gi~~~~q~Li~~-------G~~L~D~~~l~~ 56 (70)
T cd01794 3 VRLSTGKDVKLSVSSKDTVGQLKKQLQAAEGVDPCCQRWFFS-------GKLLTDKTRLQE 56 (70)
T ss_pred EEcCCCCEEEEEECCcChHHHHHHHHHHHhCCCHHHeEEEEC-------CeECCCCCCHHH
Confidence 667799999999999999999999999999988888888773 223555555543
No 57
>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=66.00 E-value=2.6 Score=22.50 Aligned_cols=9 Identities=44% Similarity=0.844 Sum_probs=3.5
Q ss_pred CCCCCCCcc
Q 003638 767 RPPGRPTTK 775 (806)
Q Consensus 767 r~~GRPkkk 775 (806)
|++|||++.
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 678999875
No 58
>cd01803 Ubiquitin Ubiquitin. Ubiquitin (includes Ubq/RPL40e and Ubq/RPS27a fusions as well as homopolymeric multiubiquitin protein chains)
Probab=65.67 E-value=13 Score=30.40 Aligned_cols=41 Identities=10% Similarity=0.178 Sum_probs=35.9
Q ss_pred EEEecCceEEEEecCCCChHHHHHHHHHHcCCCCccEEEEE
Q 003638 65 LSYKGGDAHAIDVDEQMKFNDFKTEVAEMFNCSFNAILLKY 105 (806)
Q Consensus 65 ~~Y~Gg~~~~i~v~~~~s~~e~~~~l~~~~~~~~~~~~~~y 105 (806)
++..+|++..+.|+.+.|-.+|+.+|.+..++......|.|
T Consensus 5 v~~~~g~~~~~~v~~~~tV~~lK~~i~~~~g~~~~~q~L~~ 45 (76)
T cd01803 5 VKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIF 45 (76)
T ss_pred EEcCCCCEEEEEECCcCcHHHHHHHHHHHhCCCHHHeEEEE
Confidence 44556888889999999999999999999999888888887
No 59
>PRK14702 insertion element IS2 transposase InsD; Provisional
Probab=65.00 E-value=1.1e+02 Score=32.07 Aligned_cols=147 Identities=14% Similarity=0.141 Sum_probs=87.9
Q ss_pred hhhHHHHHHHHHhcCCCCChHHHHHHHHHH---hCc-cccHHHHHHHHHHHHHHHhcChHHHhccHHHHHHHHHHhCCCc
Q 003638 323 RSWVASIIKEKLKVFPNYKPKDIVNDIKQE---YGI-QLNYFQAWRGKEIAKEQLQGSYKEAYNQLPLFCERIMETNPGS 398 (806)
Q Consensus 323 ~~~ia~~i~~~i~~~~~~~~~~I~~~l~~~---~g~-~~s~~~~~rak~~~~~~~~g~~~~~~~~L~~~~~~l~~~NPg~ 398 (806)
...+...|.+.+..++.+..+.|...|.++ .|+ .++..+++|..+.+ |-. ...+...+.+
T Consensus 10 ~~~l~~~I~~~~~~~~~yG~rri~~~L~~~~~~~g~~~v~~krV~rlmr~~-----gL~-----------~~~r~~~~~~ 73 (262)
T PRK14702 10 DTDVLLRIHHVIGELPTYGYRRVWALLRRQAELDGMPAINAKRVYRLMRQN-----ALL-----------LERKPAVPPS 73 (262)
T ss_pred hHHHHHHHHHHHHhCcccChHHHHHHHHhhhcccCccccCHHHHHHHHHHh-----CCc-----------cccCCCCCCC
Confidence 345566777777778999999999999875 377 48999998875321 100 0000000000
Q ss_pred EEEEEecCCCceeEEEEEccccHHHHhhcCCceEEeccccccccccceEEEEeeecCCCCeeeEEEEEecC-CCchhHHH
Q 003638 399 LATFTTKEDSSFHRLFVSFHASLYGFIQGCRPLLFLDSVPLKSKYQGTLLAATAADGDDGVFPVAFAVVDA-ETNDDWHW 477 (806)
Q Consensus 399 ~~~~~~~~~~~f~~lF~a~~~s~~~f~~~~~~vi~lD~T~~~~~y~~~ll~a~g~d~~~~~~plafa~v~~-E~~esw~w 477 (806)
. .+.... |. ...-..++..|-||....-++.++.++.+|...+ .++||++... .+.+.-.-
T Consensus 74 ~-------~~~~~~-~~---------~~~pn~~W~~DiT~~~~~~g~~~Yl~~viD~~sR-~ivg~~is~~~~~~~~v~~ 135 (262)
T PRK14702 74 K-------RAHTGR-VA---------VKESNQRWCSDGFEFCCDNGERLRVTFALDCCDR-EALHWAVTTGGFNSETVQD 135 (262)
T ss_pred C-------cCCCCc-cc---------cCCCCCEEEeeeEEEEecCCcEEEEEEEEecccc-eeeeEEeccCcCCHHHHHH
Confidence 0 000000 10 1123469999999976544456888888998887 6789999874 56665555
Q ss_pred HHHH-HHHHcc--CCCCCeEEEecCchhH
Q 003638 478 FLLQ-LKSALS--TATCPITFVADKQKGL 503 (806)
Q Consensus 478 fl~~-lk~~~~--~~~~p~~iisD~~~~l 503 (806)
+|+. +....+ ....|.+|.||+-...
T Consensus 136 ~l~~A~~~~~~~~~~~~~~iihSD~Gsqy 164 (262)
T PRK14702 136 VMLGAVERRFGNDLPSSPVEWLTDNGSCY 164 (262)
T ss_pred HHHHHHHHHhcccCCCCCeEEEcCCCccc
Confidence 5554 333322 1224788999985543
No 60
>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=63.71 E-value=13 Score=30.78 Aligned_cols=38 Identities=13% Similarity=0.105 Sum_probs=35.1
Q ss_pred cCceEEEEecCCCChHHHHHHHHHHcCCCCccEEEEEE
Q 003638 69 GGDAHAIDVDEQMKFNDFKTEVAEMFNCSFNAILLKYF 106 (806)
Q Consensus 69 Gg~~~~i~v~~~~s~~e~~~~l~~~~~~~~~~~~~~y~ 106 (806)
+|++..++|+.+.|-.+|+.+|.+..|+.....+|.|.
T Consensus 6 ~g~~~~l~v~~~~TV~~lK~~i~~~~gip~~~q~L~~~ 43 (76)
T cd01800 6 NGQMLNFTLQLSDPVSVLKVKIHEETGMPAGKQKLQYE 43 (76)
T ss_pred CCeEEEEEECCCCcHHHHHHHHHHHHCCCHHHEEEEEC
Confidence 68888999999999999999999999998889999884
No 61
>PTZ00044 ubiquitin; Provisional
Probab=62.61 E-value=18 Score=29.81 Aligned_cols=41 Identities=15% Similarity=0.179 Sum_probs=36.3
Q ss_pred EEecCceEEEEecCCCChHHHHHHHHHHcCCCCccEEEEEE
Q 003638 66 SYKGGDAHAIDVDEQMKFNDFKTEVAEMFNCSFNAILLKYF 106 (806)
Q Consensus 66 ~Y~Gg~~~~i~v~~~~s~~e~~~~l~~~~~~~~~~~~~~y~ 106 (806)
+-..|.+..+.|+.+.|-.+|+.+|++..|+.....+|.|.
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 34567888999999999999999999999999989999883
No 62
>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=61.30 E-value=22 Score=29.11 Aligned_cols=41 Identities=22% Similarity=0.166 Sum_probs=35.2
Q ss_pred EEecCceEEEEecCCCChHHHHHHHHHHcCCCCccEEEEEE
Q 003638 66 SYKGGDAHAIDVDEQMKFNDFKTEVAEMFNCSFNAILLKYF 106 (806)
Q Consensus 66 ~Y~Gg~~~~i~v~~~~s~~e~~~~l~~~~~~~~~~~~~~y~ 106 (806)
+-.+|++..+.|+.+.|-.+|+.+|++..++.....+|.|.
T Consensus 6 ~~~~g~~~~~~v~~~~tv~~lK~~i~~~~g~~~~~qrL~~~ 46 (76)
T cd01806 6 KTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYS 46 (76)
T ss_pred EeCCCCEEEEEECCCCCHHHHHHHHhHhhCCChhhEEEEEC
Confidence 33467777899999999999999999999998888888873
No 63
>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=60.10 E-value=24 Score=29.11 Aligned_cols=41 Identities=20% Similarity=0.287 Sum_probs=35.9
Q ss_pred EEEecCceEEEEecCCCChHHHHHHHHHHcCC--CCccEEEEE
Q 003638 65 LSYKGGDAHAIDVDEQMKFNDFKTEVAEMFNC--SFNAILLKY 105 (806)
Q Consensus 65 ~~Y~Gg~~~~i~v~~~~s~~e~~~~l~~~~~~--~~~~~~~~y 105 (806)
++..+|++..++|+.+.|-.+|+.+|.+..|+ ......+.|
T Consensus 5 vk~~~g~~~~l~v~~~~TV~~lK~~i~~~~~i~~~~~~q~L~~ 47 (77)
T cd01805 5 FKTLKQQTFPIEVDPDDTVAELKEKIEEEKGCDYPPEQQKLIY 47 (77)
T ss_pred EEeCCCCEEEEEECCCCcHHHHHHHHHHhhCCCCChhHeEEEE
Confidence 55678889999999999999999999999888 777778877
No 64
>smart00213 UBQ Ubiquitin homologues. Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression
Probab=60.10 E-value=22 Score=27.77 Aligned_cols=40 Identities=15% Similarity=0.202 Sum_probs=33.1
Q ss_pred EEecCceEEEEecCCCChHHHHHHHHHHcCCCCccEEEEEE
Q 003638 66 SYKGGDAHAIDVDEQMKFNDFKTEVAEMFNCSFNAILLKYF 106 (806)
Q Consensus 66 ~Y~Gg~~~~i~v~~~~s~~e~~~~l~~~~~~~~~~~~~~y~ 106 (806)
+..+ .+..+.|+.+.|..+|+.+|.+.+++......|.|.
T Consensus 6 k~~~-~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~~~L~~~ 45 (64)
T smart00213 6 KTLD-GTITLEVKPSDTVSELKEKIAELTGIPVEQQRLIYK 45 (64)
T ss_pred EECC-ceEEEEECCCCcHHHHHHHHHHHHCCCHHHEEEEEC
Confidence 3344 466799999999999999999999998888888773
No 65
>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=57.62 E-value=25 Score=28.91 Aligned_cols=41 Identities=20% Similarity=0.257 Sum_probs=35.4
Q ss_pred EEecCceEEEEecCCCChHHHHHHHHHHcCCCCccEEEEEE
Q 003638 66 SYKGGDAHAIDVDEQMKFNDFKTEVAEMFNCSFNAILLKYF 106 (806)
Q Consensus 66 ~Y~Gg~~~~i~v~~~~s~~e~~~~l~~~~~~~~~~~~~~y~ 106 (806)
.-.++++..+.|+.+.|-.+|+.+|.+..|+...+..|-|.
T Consensus 4 ~vk~~~~~~l~v~~~~tV~~lK~~i~~~~gip~~~q~Li~~ 44 (74)
T cd01793 4 FVRAQNTHTLEVTGQETVSDIKAHVAGLEGIDVEDQVLLLA 44 (74)
T ss_pred EEECCCEEEEEECCcCcHHHHHHHHHhhhCCCHHHEEEEEC
Confidence 33456788899999999999999999999998888888883
No 66
>COG4279 Uncharacterized conserved protein [Function unknown]
Probab=56.69 E-value=4.3 Score=41.29 Aligned_cols=23 Identities=39% Similarity=0.771 Sum_probs=19.3
Q ss_pred cccccccccccCCcccchhHHhhhcC
Q 003638 690 WDCSCKGWQLTGLPCCHAIAVLSCIG 715 (806)
Q Consensus 690 ~~CsC~~~~~~GiPC~H~lav~~~~~ 715 (806)
..|||..|. .||.|+-||....+
T Consensus 125 ~dCSCPD~a---nPCKHi~AvyY~la 147 (266)
T COG4279 125 TDCSCPDYA---NPCKHIAAVYYLLA 147 (266)
T ss_pred cccCCCCcc---cchHHHHHHHHHHH
Confidence 479999887 59999999987764
No 67
>PRK09409 IS2 transposase TnpB; Reviewed
Probab=56.16 E-value=2.4e+02 Score=30.34 Aligned_cols=145 Identities=14% Similarity=0.149 Sum_probs=87.2
Q ss_pred hHHHHHHHHHhcCCCCChHHHHHHHHHHh---Cc-cccHHHHHHHHHHHHHHHhcChHHHhccHHHHHHHHHHhCCCcEE
Q 003638 325 WVASIIKEKLKVFPNYKPKDIVNDIKQEY---GI-QLNYFQAWRGKEIAKEQLQGSYKEAYNQLPLFCERIMETNPGSLA 400 (806)
Q Consensus 325 ~ia~~i~~~i~~~~~~~~~~I~~~l~~~~---g~-~~s~~~~~rak~~~~~~~~g~~~~~~~~L~~~~~~l~~~NPg~~~ 400 (806)
.+...|.+.....+.+..+.|...|.++. |+ .++..+++|..+. .|-.. ......+.+.
T Consensus 51 ~l~~~I~~i~~~~~~yG~Rri~~~L~~~g~~~g~~~v~~k~V~RlMr~-----~Gl~~-----------~~~~~~~~~~- 113 (301)
T PRK09409 51 DVLLRIHHVIGELPTYGYRRVWALLRRQAELDGMPAINAKRVYRIMRQ-----NALLL-----------ERKPAVPPSK- 113 (301)
T ss_pred HHHHHHHHHHHhCccCCHHHHHHHHHhhhcccCccccCHHHHHHHHHH-----cCCcc-----------cccCCCCCCC-
Confidence 34556666666779999999999998762 66 5888888886432 11100 0000000000
Q ss_pred EEEecCCCceeEEEEEccccHHHHhhcCCceEEeccccccccccceEEEEeeecCCCCeeeEEEEEecC-CCchhHHHHH
Q 003638 401 TFTTKEDSSFHRLFVSFHASLYGFIQGCRPLLFLDSVPLKSKYQGTLLAATAADGDDGVFPVAFAVVDA-ETNDDWHWFL 479 (806)
Q Consensus 401 ~~~~~~~~~f~~lF~a~~~s~~~f~~~~~~vi~lD~T~~~~~y~~~ll~a~g~d~~~~~~plafa~v~~-E~~esw~wfl 479 (806)
..+... |. ...-..++..|-||....-++.++.++.+|...+ .+|||++... .+.+.-.-+|
T Consensus 114 ------~~~~~~-~~---------~~~pN~~W~tDiT~~~~~~g~~~Yl~~ViD~~sR-~ivg~~~s~~~~~~~~v~~~l 176 (301)
T PRK09409 114 ------RAHTGR-VA---------VKESNQRWCSDGFEFCCDNGERLRVTFALDCCDR-EALHWAVTTGGFNSETVQDVM 176 (301)
T ss_pred ------CCCCCC-cC---------CCCCCCEEEeeeEEEEeCCCCEEEEEEEeecccc-eEEEEEeccCCCCHHHHHHHH
Confidence 000000 10 1134579999999976544556888888999887 6789999875 5666655566
Q ss_pred HH-HHHHccC--CCCCeEEEecCchhH
Q 003638 480 LQ-LKSALST--ATCPITFVADKQKGL 503 (806)
Q Consensus 480 ~~-lk~~~~~--~~~p~~iisD~~~~l 503 (806)
+. +....+. ...|.+|-||+-...
T Consensus 177 ~~a~~~~~~~~~~~~~~iihSDrGsqy 203 (301)
T PRK09409 177 LGAVERRFGNDLPSSPVEWLTDNGSCY 203 (301)
T ss_pred HHHHHHHhccCCCCCCcEEecCCCccc
Confidence 54 4444322 224688999986543
No 68
>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=56.00 E-value=30 Score=27.42 Aligned_cols=41 Identities=15% Similarity=0.166 Sum_probs=34.6
Q ss_pred EEecCceEEEEecCCCChHHHHHHHHHHcCCCCccEEEEEE
Q 003638 66 SYKGGDAHAIDVDEQMKFNDFKTEVAEMFNCSFNAILLKYF 106 (806)
Q Consensus 66 ~Y~Gg~~~~i~v~~~~s~~e~~~~l~~~~~~~~~~~~~~y~ 106 (806)
+..+|....+.++.+.|..+|+.++.+.+++....+.|.|.
T Consensus 3 ~~~~~~~~~~~~~~~~ti~~lK~~i~~~~~~~~~~~~l~~~ 43 (69)
T cd01769 3 KTLTGKTFELEVSPDDTVAELKAKIAAKEGVPPEQQRLIYA 43 (69)
T ss_pred EccCCCEEEEEECCCChHHHHHHHHHHHHCcChHHEEEEEC
Confidence 44467777889999999999999999999988888888663
No 69
>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=55.75 E-value=28 Score=29.58 Aligned_cols=32 Identities=6% Similarity=0.174 Sum_probs=29.2
Q ss_pred EEEecCCCChHHHHHHHHHHcCCCCccEEEEE
Q 003638 74 AIDVDEQMKFNDFKTEVAEMFNCSFNAILLKY 105 (806)
Q Consensus 74 ~i~v~~~~s~~e~~~~l~~~~~~~~~~~~~~y 105 (806)
...++.++|..+|+.+|..++|+.+..+.|.|
T Consensus 16 ekr~~~~~Tv~~lK~kl~~~~G~~~~~mrL~l 47 (84)
T cd01789 16 EKKYSRGLTIAELKKKLELVVGTPASSMRLQL 47 (84)
T ss_pred eEecCCCCcHHHHHHHHHHHHCCCccceEEEE
Confidence 36699999999999999999999999999975
No 70
>COG4715 Uncharacterized conserved protein [Function unknown]
Probab=55.58 E-value=24 Score=40.39 Aligned_cols=42 Identities=24% Similarity=0.237 Sum_probs=30.9
Q ss_pred EEEEecceeEE--eeC----cCcccccccccccCCcccchhHHhhhcCCC
Q 003638 674 TFEVRGDSIEV--VDI----DHWDCSCKGWQLTGLPCCHAIAVLSCIGCS 717 (806)
Q Consensus 674 ~f~V~~~~~~~--Vdl----~~~~CsC~~~~~~GiPC~H~lav~~~~~~~ 717 (806)
.-+|.|++.|. |.+ -+.+|||.. ...| -|.|+.||+...-..
T Consensus 51 ~A~V~Gs~~y~v~vtL~~~~~ss~CTCP~-~~~g-aCKH~VAvvl~~~~~ 98 (587)
T COG4715 51 RAVVEGSRRYRVRVTLEGGALSSICTCPY-GGSG-ACKHVVAVVLEYLDD 98 (587)
T ss_pred EEEEeccceeeEEEEeecCCcCceeeCCC-CCCc-chHHHHHHHHHHhhc
Confidence 46788887654 444 366999998 5555 699999998876543
No 71
>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=53.88 E-value=25 Score=29.06 Aligned_cols=38 Identities=13% Similarity=0.073 Sum_probs=34.3
Q ss_pred cCceEEEEecCCCChHHHHHHHHHHcCCCCccEEEEEE
Q 003638 69 GGDAHAIDVDEQMKFNDFKTEVAEMFNCSFNAILLKYF 106 (806)
Q Consensus 69 Gg~~~~i~v~~~~s~~e~~~~l~~~~~~~~~~~~~~y~ 106 (806)
+|.+..++|+.+.|..+|+.+|++..++.+...+|-|.
T Consensus 8 ~g~~~~v~v~~~~Tv~~lK~~i~~~tgvp~~~QKLi~~ 45 (74)
T cd01813 8 GGQEYSVTTLSEDTVLDLKQFIKTLTGVLPERQKLLGL 45 (74)
T ss_pred CCEEEEEEECCCCCHHHHHHHHHHHHCCCHHHEEEEee
Confidence 56677799999999999999999999999999999993
No 72
>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=53.81 E-value=8 Score=24.75 Aligned_cols=13 Identities=31% Similarity=0.557 Sum_probs=10.0
Q ss_pred CCCCCCCCccCCC
Q 003638 766 RRPPGRPTTKKIG 778 (806)
Q Consensus 766 ~r~~GRPkkkR~~ 778 (806)
.|++|||+|....
T Consensus 1 kRkRGRPrK~~~~ 13 (26)
T smart00384 1 KRKRGRPRKAPKD 13 (26)
T ss_pred CCCCCCCCCCCCc
Confidence 4789999987653
No 73
>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=53.54 E-value=29 Score=29.66 Aligned_cols=42 Identities=7% Similarity=0.146 Sum_probs=36.7
Q ss_pred EEEecCceEEEEecCCCChHHHHHHHHHHcCCCCccEEEEEE
Q 003638 65 LSYKGGDAHAIDVDEQMKFNDFKTEVAEMFNCSFNAILLKYF 106 (806)
Q Consensus 65 ~~Y~Gg~~~~i~v~~~~s~~e~~~~l~~~~~~~~~~~~~~y~ 106 (806)
|...-|.+..+.|.++.++..|+.++++..|+...+.+|.|.
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 445557777899999999999999999999999999999984
No 74
>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=52.70 E-value=30 Score=28.41 Aligned_cols=41 Identities=12% Similarity=0.210 Sum_probs=35.7
Q ss_pred EEEecCceEEEEecCCCChHHHHHHHHHHcCCCCccEEEEE
Q 003638 65 LSYKGGDAHAIDVDEQMKFNDFKTEVAEMFNCSFNAILLKY 105 (806)
Q Consensus 65 ~~Y~Gg~~~~i~v~~~~s~~e~~~~l~~~~~~~~~~~~~~y 105 (806)
++...|.+..+.|+.+.|-.+|+.+|.+..|+...+..|-|
T Consensus 3 vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~gi~~~~q~L~~ 43 (74)
T cd01810 3 VRNDKGRSSIYEVQLTQTVATLKQQVSQRERVQADQFWLSF 43 (74)
T ss_pred EECCCCCEEEEEECCcChHHHHHHHHHHHhCCCHHHeEEEE
Confidence 44566788899999999999999999999998888888876
No 75
>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=50.89 E-value=44 Score=27.85 Aligned_cols=56 Identities=14% Similarity=0.362 Sum_probs=41.8
Q ss_pred EEEecCCCChHHHHHHHHHHcCCCCccEEEEEEcCCCCceeEEEeChHHHHHHHHhcCC
Q 003638 74 AIDVDEQMKFNDFKTEVAEMFNCSFNAILLKYFLPGNKKTLITISNDKDLQRMIKFNGD 132 (806)
Q Consensus 74 ~i~v~~~~s~~e~~~~l~~~~~~~~~~~~~~y~l~~~~~~l~~~~~D~dl~~M~~~~~~ 132 (806)
.+.....++|.|++.-+.+.+. +...-.|.| ..+..-=|+|.+|+.++-|+....+
T Consensus 16 ~V~~~~~L~F~DvL~~I~~vlp-~aT~tAFeY--EDE~gDRITVRSDeEm~AMlsyy~~ 71 (91)
T cd06395 16 TVQSGPQLLFRDVLDVIGQVLP-EATTTAFEY--EDEDGDRITVRSDEEMKAMLSYYCS 71 (91)
T ss_pred cccCcccccHHHHHHHHHHhcc-cccccceee--ccccCCeeEecchHHHHHHHHHHHH
Confidence 3555577999999999999872 233445667 4555677999999999999986543
No 76
>PF13592 HTH_33: Winged helix-turn helix
Probab=50.51 E-value=24 Score=27.80 Aligned_cols=30 Identities=20% Similarity=0.285 Sum_probs=26.3
Q ss_pred CCCCChHHHHHHHHHHhCccccHHHHHHHH
Q 003638 337 FPNYKPKDIVNDIKQEYGIQLNYFQAWRGK 366 (806)
Q Consensus 337 ~~~~~~~~I~~~l~~~~g~~~s~~~~~rak 366 (806)
+..++.++|++.|.+.||+.+|.+.+|+..
T Consensus 2 ~~~wt~~~i~~~I~~~fgv~ys~~~v~~lL 31 (60)
T PF13592_consen 2 GGRWTLKEIAAYIEEEFGVKYSPSGVYRLL 31 (60)
T ss_pred CCcccHHHHHHHHHHHHCCEEcHHHHHHHH
Confidence 456788999999999999999999998864
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=48.66 E-value=40 Score=26.95 Aligned_cols=37 Identities=24% Similarity=0.341 Sum_probs=34.5
Q ss_pred cCceEEEEecCCCChHHHHHHHHHHcCCCCccEEEEE
Q 003638 69 GGDAHAIDVDEQMKFNDFKTEVAEMFNCSFNAILLKY 105 (806)
Q Consensus 69 Gg~~~~i~v~~~~s~~e~~~~l~~~~~~~~~~~~~~y 105 (806)
.|.+..+.|+.+.|..+|+.+|.+..|+.+....|-|
T Consensus 4 ~g~~~~~~v~~~~tV~~lK~~i~~~~~~~~~~~~L~~ 40 (69)
T PF00240_consen 4 SGKTFTLEVDPDDTVADLKQKIAEETGIPPEQQRLIY 40 (69)
T ss_dssp TSEEEEEEEETTSBHHHHHHHHHHHHTSTGGGEEEEE
T ss_pred CCcEEEEEECCCCCHHHhhhhcccccccccccceeee
Confidence 5778889999999999999999999999999999998
No 78
>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=47.37 E-value=41 Score=29.83 Aligned_cols=41 Identities=10% Similarity=0.059 Sum_probs=36.2
Q ss_pred EEecCceEEEEecCCCChHHHHHHHHHHcCCCCccEEEEEE
Q 003638 66 SYKGGDAHAIDVDEQMKFNDFKTEVAEMFNCSFNAILLKYF 106 (806)
Q Consensus 66 ~Y~Gg~~~~i~v~~~~s~~e~~~~l~~~~~~~~~~~~~~y~ 106 (806)
+-.+|++..+.|+...|-.+|+.+|.+..|+.....+|.|.
T Consensus 33 k~l~G~~~~leV~~~~TV~~lK~kI~~~~gip~~~QrLi~~ 73 (103)
T cd01802 33 ETLTGTCFELRVSPFETVISVKAKIQRLEGIPVAQQHLIWN 73 (103)
T ss_pred EcCCCCEEEEEeCCCCcHHHHHHHHHHHhCCChHHEEEEEC
Confidence 44568888999999999999999999999998888888873
No 79
>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=42.54 E-value=60 Score=27.03 Aligned_cols=39 Identities=10% Similarity=0.159 Sum_probs=33.6
Q ss_pred ecCceEEEEecCCCChHHHHHHHHHHcCCCCccEEEEEE
Q 003638 68 KGGDAHAIDVDEQMKFNDFKTEVAEMFNCSFNAILLKYF 106 (806)
Q Consensus 68 ~Gg~~~~i~v~~~~s~~e~~~~l~~~~~~~~~~~~~~y~ 106 (806)
..|.+..|+|+.+.|..||+.++.+..++.....+|-|.
T Consensus 9 ~~G~~~~l~v~~~~TV~~LK~~I~~~~~~~~~~qrL~~~ 47 (78)
T cd01804 9 TTGTRFDLSVPPDETVEGLKKRISQRLKVPKERLALLHR 47 (78)
T ss_pred CCCCEEEEEECCcCHHHHHHHHHHHHhCCChHHEEEEEC
Confidence 356778899999999999999999998988888887764
No 80
>COG5179 TAF1 Transcription initiation factor TFIID, subunit TAF1 [Transcription]
Probab=41.86 E-value=15 Score=41.99 Aligned_cols=20 Identities=30% Similarity=0.798 Sum_probs=16.7
Q ss_pred ceEeCCCCCCCCCCc--CcCCC
Q 003638 785 RQLQCSKCKGLGHNK--STCKE 804 (806)
Q Consensus 785 ~~~~Cs~C~~~GHn~--~tC~~ 804 (806)
++++|++|+|.||-+ +.||.
T Consensus 936 Ttr~C~nCGQvGHmkTNK~CP~ 957 (968)
T COG5179 936 TTRTCGNCGQVGHMKTNKACPK 957 (968)
T ss_pred cceecccccccccccccccCcc
Confidence 589999999999966 46775
No 81
>PF11543 UN_NPL4: Nuclear pore localisation protein NPL4; InterPro: IPR024682 Npl4, along with Ufd1, forms the heterodimer adaptor complex UN, which is involved in the recruitment of p97, an AAA ATPase, for tasks involving the ubiquitin pathway. Npl4 has a N-terminal ubiquitin-like domain which has within its structure a beta-grasp fold with a helical insert []. This entry represents the ubiquitin-like domain.; PDB: 2PJH_A 1WF9_A.
Probab=39.99 E-value=43 Score=28.22 Aligned_cols=32 Identities=19% Similarity=0.300 Sum_probs=22.0
Q ss_pred eEEEEecCCCChHHHHHHHHHHcCCCCccEEE
Q 003638 72 AHAIDVDEQMKFNDFKTEVAEMFNCSFNAILL 103 (806)
Q Consensus 72 ~~~i~v~~~~s~~e~~~~l~~~~~~~~~~~~~ 103 (806)
+.-|.++.+-++.+|..++.+.+++...++.+
T Consensus 15 ~~Rie~~~~~t~~~L~~kI~~~l~~~~~~~~L 46 (80)
T PF11543_consen 15 MKRIEVSPSSTLSDLKEKISEQLSIPDSSQSL 46 (80)
T ss_dssp EEEEEE-TTSBHHHHHHHHHHHS---TTT---
T ss_pred CEEEEcCCcccHHHHHHHHHHHcCCCCcceEE
Confidence 66689999999999999999998876554443
No 82
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=37.98 E-value=14 Score=28.67 Aligned_cols=20 Identities=30% Similarity=0.757 Sum_probs=8.7
Q ss_pred ceEeCCCCCCCC---CCcCcCCC
Q 003638 785 RQLQCSKCKGLG---HNKSTCKE 804 (806)
Q Consensus 785 ~~~~Cs~C~~~G---Hn~~tC~~ 804 (806)
|.+.|..|+..| |+.+-||.
T Consensus 32 r~y~Cp~CgAtGd~AHT~~yCP~ 54 (55)
T PF05741_consen 32 RKYVCPICGATGDNAHTIKYCPK 54 (55)
T ss_dssp GG---TTT---GGG---GGG-TT
T ss_pred hcCcCCCCcCcCccccccccCcC
Confidence 567999999755 88888885
No 83
>KOG3069 consensus Peroxisomal NUDIX hydrolase [Replication, recombination and repair]
Probab=36.94 E-value=13 Score=37.64 Aligned_cols=33 Identities=18% Similarity=0.051 Sum_probs=29.0
Q ss_pred chhhhhhhhcccCCCCeEEEEEEeehhhHHHHH
Q 003638 6 PRLFRVLCDLVNGEGPIITTKFEVFEASLLQFY 38 (806)
Q Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 38 (806)
+|-++|||+|++|--+++.+.+++|+.-|.++.
T Consensus 41 ~~~~aVlI~L~~~~~~~l~vLltkRSr~Lrshs 73 (246)
T KOG3069|consen 41 NRKAAVLIPLVQVGSGELSVLLTKRSRTLRSHS 73 (246)
T ss_pred CCCccEEEEEEEcCCCceEEEEEeccccccccC
Confidence 588999999999988889999999998876654
No 84
>PF14201 DUF4318: Domain of unknown function (DUF4318)
Probab=35.78 E-value=59 Score=26.97 Aligned_cols=30 Identities=23% Similarity=0.456 Sum_probs=27.0
Q ss_pred ccCCHHHHHHHHHHHHHHcCeEEEEeecCc
Q 003638 243 RFSSVHEFRELLRKYAIAHQFAFKYKKNDS 272 (806)
Q Consensus 243 ~F~s~ee~~~a~~~yAi~~gf~~~~~ks~~ 272 (806)
.+||.+++-.+|.+|+.+++-.+++.+.+.
T Consensus 13 ~yPs~e~i~~aIE~YC~~~~~~l~Fisr~~ 42 (74)
T PF14201_consen 13 KYPSKEEICEAIEKYCIKNGESLEFISRDK 42 (74)
T ss_pred CCCCHHHHHHHHHHHHHHcCCceEEEecCC
Confidence 588999999999999999999999987654
No 85
>PRK13907 rnhA ribonuclease H; Provisional
Probab=34.91 E-value=3.2e+02 Score=24.76 Aligned_cols=78 Identities=10% Similarity=0.128 Sum_probs=43.2
Q ss_pred eEEeccccccccccceEEEEeeecCCCCeeeEEEE-EecCCCchhHHHHHHHHHHHccCCCCCeEEEecCchhHHHHHHh
Q 003638 431 LLFLDSVPLKSKYQGTLLAATAADGDDGVFPVAFA-VVDAETNDDWHWFLLQLKSALSTATCPITFVADKQKGLRESIAE 509 (806)
Q Consensus 431 vi~lD~T~~~~~y~~~ll~a~g~d~~~~~~plafa-~v~~E~~esw~wfl~~lk~~~~~~~~p~~iisD~~~~l~~Ai~~ 509 (806)
.|.+||.+..+.-.+-.-.++ .|..+... +++. -..+.+..-+.-++..|+.+......+..|-||. +.+.+++..
T Consensus 3 ~iy~DGa~~~~~g~~G~G~vi-~~~~~~~~-~~~~~~~~tn~~AE~~All~aL~~a~~~g~~~v~i~sDS-~~vi~~~~~ 79 (128)
T PRK13907 3 EVYIDGASKGNPGPSGAGVFI-KGVQPAVQ-LSLPLGTMSNHEAEYHALLAALKYCTEHNYNIVSFRTDS-QLVERAVEK 79 (128)
T ss_pred EEEEeeCCCCCCCccEEEEEE-EECCeeEE-EEecccccCCcHHHHHHHHHHHHHHHhCCCCEEEEEech-HHHHHHHhH
Confidence 478899887654333222222 45544432 3321 1234455557777777777754432457788887 555666665
Q ss_pred hc
Q 003638 510 IF 511 (806)
Q Consensus 510 vf 511 (806)
.+
T Consensus 80 ~~ 81 (128)
T PRK13907 80 EY 81 (128)
T ss_pred HH
Confidence 44
No 86
>PRK09335 30S ribosomal protein S26e; Provisional
Probab=33.73 E-value=36 Score=29.41 Aligned_cols=27 Identities=30% Similarity=0.495 Sum_probs=17.7
Q ss_pred CCCCCCCCCCCccCCCCCCCCCceEeCCCCCC
Q 003638 763 PPTRRPPGRPTTKKIGTQDVMKRQLQCSKCKG 794 (806)
Q Consensus 763 P~~~r~~GRPkkkR~~~~~~~k~~~~Cs~C~~ 794 (806)
|.++|..||-|+-|- .-..++|++|+.
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 445666777765432 235789999985
No 87
>PF04937 DUF659: Protein of unknown function (DUF 659); InterPro: IPR007021 These are transposase-like proteins with no known function.
Probab=33.65 E-value=2.8e+02 Score=26.52 Aligned_cols=62 Identities=13% Similarity=0.204 Sum_probs=43.6
Q ss_pred CCchhHHHHHHHHHHHccCCCCCeEEEecCchhHHHHH---HhhcccccccchHHHHHHHHHHHhc
Q 003638 470 ETNDDWHWFLLQLKSALSTATCPITFVADKQKGLRESI---AEIFKGSFHGYCLRYLTEQLVKDLK 532 (806)
Q Consensus 470 E~~esw~wfl~~lk~~~~~~~~p~~iisD~~~~l~~Ai---~~vfP~a~h~~C~~Hi~~n~~~~~~ 532 (806)
.+.+...-+|+...+.++.. .-..||||....+.+|- .+-+|......|..|-+.-+.+.+.
T Consensus 73 ~~a~~l~~ll~~vIeeVG~~-nVvqVVTDn~~~~~~a~~~L~~k~p~ifw~~CaaH~inLmledi~ 137 (153)
T PF04937_consen 73 KTAEYLFELLDEVIEEVGEE-NVVQVVTDNASNMKKAGKLLMEKYPHIFWTPCAAHCINLMLEDIG 137 (153)
T ss_pred ccHHHHHHHHHHHHHHhhhh-hhhHHhccCchhHHHHHHHHHhcCCCEEEechHHHHHHHHHHHHh
Confidence 34555555555555555444 34678999999888884 4448888889999999988777764
No 88
>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=32.83 E-value=93 Score=25.63 Aligned_cols=37 Identities=19% Similarity=0.265 Sum_probs=33.3
Q ss_pred CceEEEEecCCCChHHHHHHHHHHcCCCCccEEEEEE
Q 003638 70 GDAHAIDVDEQMKFNDFKTEVAEMFNCSFNAILLKYF 106 (806)
Q Consensus 70 g~~~~i~v~~~~s~~e~~~~l~~~~~~~~~~~~~~y~ 106 (806)
|....+.|+.+.|-.||+.+|.+..++.+...+|-|.
T Consensus 11 Gk~~~~~v~~~~TV~~LK~~I~~~~~~~~~~qrLi~~ 47 (73)
T cd01791 11 GKKVRVKCNPDDTIGDLKKLIAAQTGTRPEKIVLKKW 47 (73)
T ss_pred CCEEEEEeCCCCcHHHHHHHHHHHhCCChHHEEEEeC
Confidence 6677789999999999999999999999999999885
No 89
>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=32.44 E-value=41 Score=27.32 Aligned_cols=36 Identities=17% Similarity=0.326 Sum_probs=16.4
Q ss_pred HHHHHhcCCCCChHHHHHHHHHHhCccccHHHHHHHH
Q 003638 330 IKEKLKVFPNYKPKDIVNDIKQEYGIQLNYFQAWRGK 366 (806)
Q Consensus 330 i~~~i~~~~~~~~~~I~~~l~~~~g~~~s~~~~~rak 366 (806)
|...++.+|..+..+|...+.+. |..+|...+++.-
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 44566789999999999999988 9999999999864
No 90
>PHA00689 hypothetical protein
Probab=32.34 E-value=26 Score=26.02 Aligned_cols=15 Identities=27% Similarity=0.682 Sum_probs=12.0
Q ss_pred CCceEeCCCCCCCCC
Q 003638 783 MKRQLQCSKCKGLGH 797 (806)
Q Consensus 783 ~k~~~~Cs~C~~~GH 797 (806)
..|.++|.+|++.|-
T Consensus 14 epravtckrcgktgl 28 (62)
T PHA00689 14 EPRAVTCKRCGKTGL 28 (62)
T ss_pred CcceeehhhccccCc
Confidence 347899999998873
No 91
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=30.49 E-value=26 Score=34.48 Aligned_cols=16 Identities=31% Similarity=0.814 Sum_probs=14.0
Q ss_pred EeCCCCCCCCCCcCcC
Q 003638 787 LQCSKCKGLGHNKSTC 802 (806)
Q Consensus 787 ~~Cs~C~~~GHn~~tC 802 (806)
.+|.+|++.||-++-|
T Consensus 98 ~~C~~Cg~~GH~~~dC 113 (190)
T COG5082 98 KKCYNCGETGHLSRDC 113 (190)
T ss_pred cccccccccCcccccc
Confidence 5888999999998888
No 92
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=30.15 E-value=53 Score=25.74 Aligned_cols=34 Identities=12% Similarity=0.284 Sum_probs=20.3
Q ss_pred CCCCCCCCCCCccCCCCCCCCCceEeCCCCCCCC
Q 003638 763 PPTRRPPGRPTTKKIGTQDVMKRQLQCSKCKGLG 796 (806)
Q Consensus 763 P~~~r~~GRPkkkR~~~~~~~k~~~~Cs~C~~~G 796 (806)
|..+..+.|..++|............|+.|+..-
T Consensus 4 PKrk~S~srr~~RRsh~~l~~~~l~~C~~CG~~~ 37 (57)
T PRK12286 4 PKRKTSKSRKRKRRAHFKLKAPGLVECPNCGEPK 37 (57)
T ss_pred CcCcCChhhcchhcccccccCCcceECCCCCCcc
Confidence 4445556666666655333344567899998543
No 93
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=29.17 E-value=31 Score=25.17 Aligned_cols=18 Identities=33% Similarity=0.833 Sum_probs=16.5
Q ss_pred eEeCCCCCCCCCCcCcCC
Q 003638 786 QLQCSKCKGLGHNKSTCK 803 (806)
Q Consensus 786 ~~~Cs~C~~~GHn~~tC~ 803 (806)
...|.+|++.||-..-||
T Consensus 4 ~~~CqkC~~~GH~tyeC~ 21 (42)
T PF13917_consen 4 RVRCQKCGQKGHWTYECP 21 (42)
T ss_pred CCcCcccCCCCcchhhCC
Confidence 468999999999999998
No 94
>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=28.87 E-value=1.1e+02 Score=25.41 Aligned_cols=39 Identities=21% Similarity=0.404 Sum_probs=32.3
Q ss_pred ecCce-EEEE-ecCCCChHHHHHHHHHHcCCCCccEEEEEE
Q 003638 68 KGGDA-HAID-VDEQMKFNDFKTEVAEMFNCSFNAILLKYF 106 (806)
Q Consensus 68 ~Gg~~-~~i~-v~~~~s~~e~~~~l~~~~~~~~~~~~~~y~ 106 (806)
..|.+ ..++ ++.+.|-.+|+.+|.+..|+...+.+|-|.
T Consensus 8 ~~G~~~~~l~~v~~~~TV~~lK~~i~~~~gi~~~~QrLi~~ 48 (78)
T cd01797 8 MDGKETRTVDSLSRLTKVEELREKIQELFNVEPECQRLFYR 48 (78)
T ss_pred CCCCEEEEeeccCCcCcHHHHHHHHHHHhCCCHHHeEEEeC
Confidence 34554 4674 788899999999999999999889999884
No 95
>PF13276 HTH_21: HTH-like domain
Probab=28.33 E-value=1.2e+02 Score=23.60 Aligned_cols=41 Identities=27% Similarity=0.379 Sum_probs=33.7
Q ss_pred HHHHHHHHHhcC-CCCChHHHHHHHHHHhCccccHHHHHHHH
Q 003638 326 VASIIKEKLKVF-PNYKPKDIVNDIKQEYGIQLNYFQAWRGK 366 (806)
Q Consensus 326 ia~~i~~~i~~~-~~~~~~~I~~~l~~~~g~~~s~~~~~rak 366 (806)
+...|.+.+..+ +.+....|...|.++.|+.+|..+++|..
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 455666666654 88999999999999999999999998865
No 96
>PLN00186 ribosomal protein S26; Provisional
Probab=27.93 E-value=50 Score=29.25 Aligned_cols=27 Identities=26% Similarity=0.533 Sum_probs=17.5
Q ss_pred CCCCCCCCCCCccCCCCCCCCCceEeCCCCCC
Q 003638 763 PPTRRPPGRPTTKKIGTQDVMKRQLQCSKCKG 794 (806)
Q Consensus 763 P~~~r~~GRPkkkR~~~~~~~k~~~~Cs~C~~ 794 (806)
|.++|..||-|+-|- .-..++|++|+.
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 445666777765332 235789999985
No 97
>KOG1769 consensus Ubiquitin-like proteins [Posttranslational modification, protein turnover, chaperones]
Probab=27.86 E-value=1.4e+02 Score=26.25 Aligned_cols=38 Identities=11% Similarity=0.250 Sum_probs=34.2
Q ss_pred ecCceEEEEecCCCChHHHHHHHHHHcCCCCccEEEEE
Q 003638 68 KGGDAHAIDVDEQMKFNDFKTEVAEMFNCSFNAILLKY 105 (806)
Q Consensus 68 ~Gg~~~~i~v~~~~s~~e~~~~l~~~~~~~~~~~~~~y 105 (806)
.+|.+....|.+++.+.-|+..-|+.-|++.+++.|.|
T Consensus 28 qd~~~~~Fkikr~t~LkKLM~aYc~r~Gl~~~s~RFlF 65 (99)
T KOG1769|consen 28 QDGSVVVFKIKRHTPLKKLMKAYCERQGLSMNSLRFLF 65 (99)
T ss_pred CCCCEEEEEeecCChHHHHHHHHHHHcCCccceEEEEE
Confidence 45667779999999999999999999999999999988
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=26.97 E-value=1.2e+02 Score=23.35 Aligned_cols=36 Identities=17% Similarity=0.360 Sum_probs=22.3
Q ss_pred HHHHHHHHHhc-C-CCCChHHHHHHHHHHhCccccHHH
Q 003638 326 VASIIKEKLKV-F-PNYKPKDIVNDIKQEYGIQLNYFQ 361 (806)
Q Consensus 326 ia~~i~~~i~~-~-~~~~~~~I~~~l~~~~g~~~s~~~ 361 (806)
+...+.+.++. + .+++.++|...+.+.+|+.++..+
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 44566666663 2 468999999999999999988543
No 99
>PTZ00172 40S ribosomal protein S26; Provisional
Probab=26.92 E-value=54 Score=29.06 Aligned_cols=27 Identities=26% Similarity=0.538 Sum_probs=17.6
Q ss_pred CCCCCCCCCCCccCCCCCCCCCceEeCCCCCC
Q 003638 763 PPTRRPPGRPTTKKIGTQDVMKRQLQCSKCKG 794 (806)
Q Consensus 763 P~~~r~~GRPkkkR~~~~~~~k~~~~Cs~C~~ 794 (806)
|.++|..||-|+-|- .-..++|++|+.
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 445666777765332 235789999985
No 100
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=26.40 E-value=53 Score=28.91 Aligned_cols=9 Identities=22% Similarity=1.091 Sum_probs=6.6
Q ss_pred ceEeCCCCC
Q 003638 785 RQLQCSKCK 793 (806)
Q Consensus 785 ~~~~Cs~C~ 793 (806)
+...|.+|+
T Consensus 20 t~f~CP~Cg 28 (99)
T PRK14892 20 KIFECPRCG 28 (99)
T ss_pred cEeECCCCC
Confidence 567788887
No 101
>PF14847 Ras_bdg_2: Ras-binding domain of Byr2; PDB: 1I35_A 1K8R_B.
Probab=26.02 E-value=2.7e+02 Score=24.81 Aligned_cols=76 Identities=13% Similarity=0.202 Sum_probs=45.0
Q ss_pred EEEecCceEEEEecCCCChHHHHHHHHHHcCCCCcc-EEEEEEcCCC--CceeEEEeChHHHHHHHHhcCCCCeEEEEE
Q 003638 65 LSYKGGDAHAIDVDEQMKFNDFKTEVAEMFNCSFNA-ILLKYFLPGN--KKTLITISNDKDLQRMIKFNGDSATTDVFV 140 (806)
Q Consensus 65 ~~Y~Gg~~~~i~v~~~~s~~e~~~~l~~~~~~~~~~-~~~~y~l~~~--~~~l~~~~~D~dl~~M~~~~~~~~~v~iyv 140 (806)
+-+.+|.++.|.|..=.+-.|++.++..+||+..+. --..|.+-+. ...-+-.-.|.+|..+....+....=++-+
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 457889999999999899999999999999987631 2233445441 333444445778888888777776556666
No 102
>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=25.58 E-value=1.7e+02 Score=27.49 Aligned_cols=69 Identities=12% Similarity=0.145 Sum_probs=40.4
Q ss_pred ceEEeccccccccc--------------cceEEEEeeecCC-CCeeeEEEEEecCCCchhHHHHHHHHHHHccCCCCCeE
Q 003638 430 PLLFLDSVPLKSKY--------------QGTLLAATAADGD-DGVFPVAFAVVDAETNDDWHWFLLQLKSALSTATCPIT 494 (806)
Q Consensus 430 ~vi~lD~T~~~~~y--------------~~~ll~a~g~d~~-~~~~plafa~v~~E~~esw~wfl~~lk~~~~~~~~p~~ 494 (806)
.+|-+|-||..++- .....++++++-+ ++.--+...++.+.+.++..-+++.. +.. ..+
T Consensus 4 G~VEiDEty~~~~~~~~~~~~~~~gr~~~~k~~V~~~ver~~~~~~~~~~~~v~~~~~~tl~~~i~~~---i~~---gs~ 77 (151)
T PF12762_consen 4 GIVEIDETYFGGRKNKKPRRKGKRGRGSKNKVPVFGAVERNDGGTGRVFMFVVPDRSAETLKPIIQEH---IEP---GST 77 (151)
T ss_pred CEEEeCcCEECCcccccccCCCCCCCcCCCCcEEEEEEeecccCCceEEEEeecccccchhHHHHHHh---hhc---cce
Confidence 36777777764322 2234445555554 44444455566778887776555432 221 278
Q ss_pred EEecCchhHH
Q 003638 495 FVADKQKGLR 504 (806)
Q Consensus 495 iisD~~~~l~ 504 (806)
|+||...+-.
T Consensus 78 i~TD~~~aY~ 87 (151)
T PF12762_consen 78 IITDGWRAYN 87 (151)
T ss_pred eeecchhhcC
Confidence 8999988764
No 103
>PF13877 RPAP3_C: Potential Monad-binding region of RPAP3
Probab=25.24 E-value=65 Score=27.81 Aligned_cols=34 Identities=21% Similarity=0.236 Sum_probs=27.8
Q ss_pred CCHHHHHHHHHHHHhccHHHHHHHHhccCCCccc
Q 003638 554 PTPEEFERSIESIKSISLEAYNWILQSEYLNWAN 587 (806)
Q Consensus 554 ~t~~eF~~~~~~l~~~~~~~~~~l~~~~~~~W~~ 587 (806)
.|..+|++.|..+.......++||....++....
T Consensus 5 ~~~~eF~~~w~~~~~~~~~~~~yL~~i~p~~l~~ 38 (94)
T PF13877_consen 5 KNSYEFERDWRRLKKDPEERYEYLKSIPPDSLPK 38 (94)
T ss_pred CCHHHHHHHHHHHcCCHHHHHHHHHhCChHHHHH
Confidence 4678999999999877778999999987766554
No 104
>KOG3389 consensus NADH:ubiquinone oxidoreductase, NDUFS4/18 kDa subunit [Energy production and conversion]
Probab=25.10 E-value=58 Score=30.20 Aligned_cols=28 Identities=14% Similarity=0.422 Sum_probs=21.8
Q ss_pred cCc--ccCCHHHHHHHHHHHHHHcCeEEEEeecC
Q 003638 240 VGQ--RFSSVHEFRELLRKYAIAHQFAFKYKKND 271 (806)
Q Consensus 240 vG~--~F~s~ee~~~a~~~yAi~~gf~~~~~ks~ 271 (806)
||| .|.++|+++ .||-++|.+|.+.+-.
T Consensus 125 vgm~L~F~tkEdA~----sFaEkngW~ydveep~ 154 (178)
T KOG3389|consen 125 VGMALAFDTKEDAK----SFAEKNGWDYDVEEPN 154 (178)
T ss_pred cceeeeeccHHHHH----HHHHHcCCcccccCCC
Confidence 565 799998875 5788999999887544
No 105
>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=24.86 E-value=1.5e+02 Score=23.88 Aligned_cols=36 Identities=22% Similarity=0.481 Sum_probs=30.6
Q ss_pred cCceEEEEecCCCChHHHHHHHHHHcCCCCccEEEEE
Q 003638 69 GGDAHAIDVDEQMKFNDFKTEVAEMFNCSFNAILLKY 105 (806)
Q Consensus 69 Gg~~~~i~v~~~~s~~e~~~~l~~~~~~~~~~~~~~y 105 (806)
.|.. .|.|+.+.|-.+|+.++.+..++.....++-|
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 69999999999999999999998888888877
No 106
>cd01768 RA RA (Ras-associating) ubiquitin domain. The RA (Ras-associating) domain is structurally similar to ubiquitin and is present in one or two copies in a number of signalling molecules that bind and regulate a small GTPase called Ras or the Ras-related GTPases, Ral and Rap. RA-containing proteins include RalGDS, AF6, RIN1, RASSF1, SNX27, CYR1, STE50, and phospholipase C epsilon.
Probab=24.85 E-value=4.1e+02 Score=22.18 Aligned_cols=31 Identities=16% Similarity=0.275 Sum_probs=28.0
Q ss_pred ecCceEEEEecCCCChHHHHHHHHHHcCCCC
Q 003638 68 KGGDAHAIDVDEQMKFNDFKTEVAEMFNCSF 98 (806)
Q Consensus 68 ~Gg~~~~i~v~~~~s~~e~~~~l~~~~~~~~ 98 (806)
.||..+.|.|++++|=.|++..+.++++++.
T Consensus 10 ~~~~~kti~V~~~~t~~~Vi~~~l~k~~l~~ 40 (87)
T cd01768 10 SGGTYKTLRVSKDTTAQDVIQQLLKKFGLDD 40 (87)
T ss_pred CCccEEEEEECCCCCHHHHHHHHHHHhCCcC
Confidence 4677899999999999999999999999873
No 107
>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=24.73 E-value=1.4e+02 Score=24.92 Aligned_cols=38 Identities=16% Similarity=0.320 Sum_probs=32.2
Q ss_pred EecCceEEEEecCCCChHHHHHHHHHHcCCCCccEEEE
Q 003638 67 YKGGDAHAIDVDEQMKFNDFKTEVAEMFNCSFNAILLK 104 (806)
Q Consensus 67 Y~Gg~~~~i~v~~~~s~~e~~~~l~~~~~~~~~~~~~~ 104 (806)
-.+|.+-.+.|+.+.|-.||+.++.+..++.....+|-
T Consensus 9 ~~~G~~~~~~v~~~~TV~~lK~~I~~~~~i~~~~qrL~ 46 (80)
T cd01792 9 MLGGNEFLVSLRDSMTVSELKQQIAQKIGVPAFQQRLA 46 (80)
T ss_pred eCCCCEEEEEcCCCCcHHHHHHHHHHHhCCCHHHEEEE
Confidence 34577777899999999999999999999888888774
No 108
>PF00788 RA: Ras association (RalGDS/AF-6) domain; InterPro: IPR000159 Proteins with this domain are mostly RasGTP effectors and include guanine-nucleotide releasing factor in mammals []. This factor stimulates the dissociation of GDP from the Ras-related RALA and RALB GTPases, which allows GTP binding and activation of the GTPases. It interacts and acts as an effector molecule for R-ras, K-Ras and Rap []. The domain is also present in a number of other proteins among them the sexual differentiation protein in yeast that is essential for mating and meiosis and yeast adenylate cyclase. These proteins contain repeated leucine-rich (LRR) segments.; GO: 0007165 signal transduction; PDB: 3EC8_A 2C5L_D 2BYF_A 2CS4_A 3KH0_A 2B3A_A 1RAX_A 2RGF_A 1WGR_A 1WXA_A ....
Probab=22.72 E-value=4.6e+02 Score=21.92 Aligned_cols=69 Identities=9% Similarity=-0.025 Sum_probs=45.7
Q ss_pred eEEEEecCCCChHHHHHHHHHHcCC--CCccEEEEEEcCCCCceeEEEeChHHHHHHHHhcCCC-CeEEEEEE
Q 003638 72 AHAIDVDEQMKFNDFKTEVAEMFNC--SFNAILLKYFLPGNKKTLITISNDKDLQRMIKFNGDS-ATTDVFVI 141 (806)
Q Consensus 72 ~~~i~v~~~~s~~e~~~~l~~~~~~--~~~~~~~~y~l~~~~~~l~~~~~D~dl~~M~~~~~~~-~~v~iyv~ 141 (806)
.+.|.|+.++|=.|++..+.+++++ ++..+.|--.+ .....-..|.+|+-...+....... ....+++.
T Consensus 18 ~k~i~v~~~tTa~evi~~~l~k~~l~~~~~~y~L~~~~-~~~~~er~L~~~E~pl~i~~~~~~~~~~~~f~lr 89 (93)
T PF00788_consen 18 YKTIKVSSSTTAREVIEMALEKFGLAEDPSDYCLVEVE-ESGGEERPLDDDECPLQIQLQWPKDSQNSRFVLR 89 (93)
T ss_dssp EEEEEEETTSBHHHHHHHHHHHTTTSSSGGGEEEEEEE-CTTTEEEEETTTSBHHHHHHTTSSGTTTEEEEEE
T ss_pred EEEEEECCCCCHHHHHHHHHHHhCCCCCCCCEEEEEEE-cCCCEEEEcCCCCchHHHHHhCccccCceEEEEE
Confidence 7889999999999999999999998 33466664111 2233444677777666655544333 34556654
No 109
>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=21.91 E-value=1e+02 Score=23.99 Aligned_cols=39 Identities=10% Similarity=0.287 Sum_probs=21.2
Q ss_pred CCCCCCCCCccCCCCC-CCCCceEeCCCCCCCCCCcCcCC
Q 003638 765 TRRPPGRPTTKKIGTQ-DVMKRQLQCSKCKGLGHNKSTCK 803 (806)
Q Consensus 765 ~~r~~GRPkkkR~~~~-~~~k~~~~Cs~C~~~GHn~~tC~ 803 (806)
.+..+-|.+++|.... ........|+.|++.-..=+-|+
T Consensus 4 rk~Sksr~~~RRah~~kl~~p~l~~C~~cG~~~~~H~vc~ 43 (55)
T TIGR01031 4 RKTSKSRKRKRRSHDAKLTAPTLVVCPNCGEFKLPHRVCP 43 (55)
T ss_pred CcCCcccccchhcCcccccCCcceECCCCCCcccCeeECC
Confidence 3334445555554422 23345678999996554444444
No 110
>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=21.63 E-value=1.2e+02 Score=26.89 Aligned_cols=31 Identities=16% Similarity=0.305 Sum_probs=22.5
Q ss_pred ccCcccCCHHHHHHHHHHHHHHcCeEEEEeecCce
Q 003638 239 GVGQRFSSVHEFRELLRKYAIAHQFAFKYKKNDSH 273 (806)
Q Consensus 239 ~vG~~F~s~ee~~~a~~~yAi~~gf~~~~~ks~~~ 273 (806)
.+.+.|+|+|++. .||.++|..|.+......
T Consensus 50 ~v~l~F~skE~Ai----~yaer~G~~Y~V~~p~~r 80 (101)
T PF04800_consen 50 SVRLKFDSKEDAI----AYAERNGWDYEVEEPKKR 80 (101)
T ss_dssp -CEEEESSHHHHH----HHHHHCT-EEEEE-STT-
T ss_pred eeEeeeCCHHHHH----HHHHHcCCeEEEeCCCCC
Confidence 3788999999875 589999999998765443
No 111
>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=21.15 E-value=3.3e+02 Score=26.17 Aligned_cols=65 Identities=23% Similarity=0.356 Sum_probs=42.4
Q ss_pred eEEeccccccccccceEEEEeeecCCCCeeeEEEEEecCCCchhHHHHHHHHHHHccCC-----CCCeEEEecCchhHHH
Q 003638 431 LLFLDSVPLKSKYQGTLLAATAADGDDGVFPVAFAVVDAETNDDWHWFLLQLKSALSTA-----TCPITFVADKQKGLRE 505 (806)
Q Consensus 431 vi~lD~T~~~~~y~~~ll~a~g~d~~~~~~plafa~v~~E~~esw~wfl~~lk~~~~~~-----~~p~~iisD~~~~l~~ 505 (806)
|++.|+-+.++.|+- |-+-+.+..+.|.-.-+.+...+... ..|..|+.|+-++-.+
T Consensus 32 Vvf~~G~~~k~~YR~------------------f~i~~~~~~dDy~~M~Evl~RR~~~~~~~~~~lPDLilIDGG~gQl~ 93 (155)
T PF08459_consen 32 VVFENGKPDKSEYRR------------------FNIKTVDGGDDYAAMREVLTRRFKRLKEEKEPLPDLILIDGGKGQLN 93 (155)
T ss_dssp EEEETTEE-GGG-EE------------------EEEE--STT-HHHHHHHHHHHHHCCCHHHT----SEEEESSSHHHHH
T ss_pred EEEECCccChhhCce------------------EecCCCCCCcHHHHHHHHHHHHHhcccccCCCCCCEEEEcCCHHHHH
Confidence 666777777777763 33444455688888888887776543 2589999999999999
Q ss_pred HHHhhccc
Q 003638 506 SIAEIFKG 513 (806)
Q Consensus 506 Ai~~vfP~ 513 (806)
|+.+++-.
T Consensus 94 aa~~~l~~ 101 (155)
T PF08459_consen 94 AAKEVLKE 101 (155)
T ss_dssp HHHHHHHC
T ss_pred HHHHHHHH
Confidence 98887643
No 112
>PF13551 HTH_29: Winged helix-turn helix
Probab=20.99 E-value=1.6e+02 Score=25.74 Aligned_cols=38 Identities=18% Similarity=0.289 Sum_probs=30.1
Q ss_pred HHHHHHhcCC-----CCChHHHHHHH-HHHhCccccHHHHHHHH
Q 003638 329 IIKEKLKVFP-----NYKPKDIVNDI-KQEYGIQLNYFQAWRGK 366 (806)
Q Consensus 329 ~i~~~i~~~~-----~~~~~~I~~~l-~~~~g~~~s~~~~~rak 366 (806)
.+.+.+..+| .+++..|...+ .+.+|+.+|.+.+++.-
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 4555666666 47889999876 89999999999999864
No 113
>cd01760 RBD Ubiquitin-like domain of RBD-like S/T kinases. The ras-binding domain (RBD) of the serine/threonine kinase raf is structurally quite similar to the beta-grasp fold of ubiquitin. A raf-like RBD is also present in RGS12 and other members of a family of GTPase activating proteins and TIAM1, a guanine nucleotide exchange protein.
Probab=20.55 E-value=2.6e+02 Score=23.04 Aligned_cols=37 Identities=11% Similarity=0.092 Sum_probs=30.6
Q ss_pred CceEEEEecCCCChHHHHHHHHHHcCCCCccEEEEEE
Q 003638 70 GDAHAIDVDEQMKFNDFKTEVAEMFNCSFNAILLKYF 106 (806)
Q Consensus 70 g~~~~i~v~~~~s~~e~~~~l~~~~~~~~~~~~~~y~ 106 (806)
|+.-.+.|..++|..|++.+++++-|+++....+...
T Consensus 9 g~~t~V~vrpg~ti~d~L~~~c~kr~l~~~~~~v~~~ 45 (72)
T cd01760 9 GQRTVVPVRPGMSVRDVLAKACKKRGLNPECCDVFLL 45 (72)
T ss_pred CCeEEEEECCCCCHHHHHHHHHHHcCCCHHHEEEEEe
Confidence 4556789999999999999999999998876666554
No 114
>KOG0695 consensus Serine/threonine protein kinase [Signal transduction mechanisms]
Probab=20.43 E-value=2.6e+02 Score=30.15 Aligned_cols=65 Identities=22% Similarity=0.366 Sum_probs=46.9
Q ss_pred EecCceEEEEecCCCChHHHHHHHHHHcCCCCc-cEEEEEEcCCCCceeEEEeChHHHHHHHHhcCCC
Q 003638 67 YKGGDAHAIDVDEQMKFNDFKTEVAEMFNCSFN-AILLKYFLPGNKKTLITISNDKDLQRMIKFNGDS 133 (806)
Q Consensus 67 Y~Gg~~~~i~v~~~~s~~e~~~~l~~~~~~~~~-~~~~~y~l~~~~~~l~~~~~D~dl~~M~~~~~~~ 133 (806)
|-||+.-+..++..++|.+|-..+.+++.+... .+++||- .+.-.+++|++--.|+.-+.+....
T Consensus 21 ~y~g~i~i~~~~p~~~~e~~~~~vrd~c~~h~~q~~t~kwi--deegdp~tv~sqmeleea~r~~~~~ 86 (593)
T KOG0695|consen 21 HYGGDIFITSVDPATTFEELCEEVRDMCRLHQQQPLTLKWI--DEEGDPCTVSSQMELEEAFRLARQC 86 (593)
T ss_pred eecCcEEEEeccCcccHHHHHHHHHHHHHHhhcCCceeEee--cCCCCcceechhhhHHHHHHHHHhc
Confidence 445666677888899999999999998755544 7788884 4444567777777777666655544
Done!