Query 003242
Match_columns 837
No_of_seqs 405 out of 1812
Neff 7.8
Searched_HMMs 46136
Date Thu Mar 28 19:45:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/003242.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/003242hhsearch_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 2.5E-70 5.5E-75 645.5 46.1 472 268-761 72-623 (846)
2 cd06410 PB1_UP2 Uncharacterize 100.0 3.9E-32 8.5E-37 239.9 10.9 91 9-100 1-97 (97)
3 PF10551 MULE: MULE transposas 99.9 1.8E-21 4E-26 174.1 9.6 90 466-557 1-93 (93)
4 PF00872 Transposase_mut: Tran 99.8 1.1E-20 2.3E-25 211.5 3.2 239 367-654 112-366 (381)
5 PF03108 DBD_Tnp_Mut: MuDR fam 99.6 7.7E-16 1.7E-20 128.6 8.9 67 267-333 1-67 (67)
6 COG3328 Transposase and inacti 99.5 2.3E-13 5E-18 149.6 16.8 224 367-641 98-328 (379)
7 smart00666 PB1 PB1 domain. Pho 99.0 1.3E-09 2.8E-14 94.7 9.2 77 21-100 3-81 (81)
8 smart00575 ZnF_PMZ plant mutat 98.7 4.5E-09 9.8E-14 71.3 2.1 27 719-745 1-27 (28)
9 PF08731 AFT: Transcription fa 98.7 9.9E-08 2.1E-12 85.1 8.9 68 276-343 1-110 (111)
10 cd05992 PB1 The PB1 domain is 98.5 7.3E-07 1.6E-11 77.3 8.8 74 23-99 4-80 (81)
11 PF00564 PB1: PB1 domain; Int 98.4 8.5E-07 1.8E-11 77.5 7.6 77 23-101 5-83 (84)
12 cd06407 PB1_NLP A PB1 domain i 98.3 3.9E-06 8.5E-11 72.5 8.7 73 24-99 5-80 (82)
13 PF03101 FAR1: FAR1 DNA-bindin 98.3 1.7E-06 3.8E-11 76.8 6.8 59 284-343 1-88 (91)
14 PF04434 SWIM: SWIM zinc finge 97.8 9.7E-06 2.1E-10 60.2 2.5 30 714-743 10-39 (40)
15 cd06408 PB1_NoxR The PB1 domai 97.7 0.00011 2.3E-09 63.5 7.0 57 28-88 10-66 (86)
16 cd06398 PB1_Joka2 The PB1 doma 97.7 0.00028 6E-09 62.3 9.7 75 23-100 4-87 (91)
17 cd06405 PB1_Mekk2_3 The PB1 do 97.6 0.00038 8.3E-09 57.3 8.3 67 28-100 8-77 (79)
18 cd06406 PB1_P67 A PB1 domain i 97.5 0.00031 6.8E-09 59.6 7.2 65 23-91 6-70 (80)
19 cd06397 PB1_UP1 Uncharacterize 97.3 0.0011 2.4E-08 55.7 7.3 65 24-91 5-69 (82)
20 cd06404 PB1_aPKC PB1 domain is 97.1 0.0027 5.8E-08 54.1 8.6 60 27-88 7-67 (83)
21 cd06401 PB1_TFG The PB1 domain 97.1 0.0031 6.7E-08 53.6 8.6 69 28-99 8-80 (81)
22 cd06403 PB1_Par6 The PB1 domai 97.0 0.0063 1.4E-07 51.2 8.9 72 25-100 5-78 (80)
23 cd06402 PB1_p62 The PB1 domain 96.9 0.007 1.5E-07 52.7 8.8 68 30-100 15-85 (87)
24 cd06396 PB1_NBR1 The PB1 domai 96.8 0.004 8.6E-08 53.3 6.9 68 28-99 8-78 (81)
25 cd06411 PB1_p51 The PB1 domain 96.6 0.0077 1.7E-07 50.9 7.2 63 30-92 7-69 (78)
26 cd06409 PB1_MUG70 The MUG70 pr 95.8 0.057 1.2E-06 47.0 8.4 71 27-99 8-83 (86)
27 PF06782 UPF0236: Uncharacteri 94.7 0.47 1E-05 55.2 14.1 92 499-597 235-328 (470)
28 PF00098 zf-CCHC: Zinc knuckle 94.7 0.02 4.3E-07 34.6 1.5 18 818-835 1-18 (18)
29 PF13610 DDE_Tnp_IS240: DDE do 93.7 0.031 6.7E-07 53.8 1.5 81 459-543 1-81 (140)
30 PF01610 DDE_Tnp_ISL3: Transpo 93.1 0.16 3.4E-06 53.8 5.8 94 462-561 1-97 (249)
31 PF15288 zf-CCHC_6: Zinc knuck 92.7 0.051 1.1E-06 39.8 1.0 19 818-836 2-22 (40)
32 PF13696 zf-CCHC_2: Zinc knuck 90.0 0.19 4.1E-06 35.0 1.5 21 816-836 7-27 (32)
33 PRK14702 insertion element IS2 89.3 20 0.00042 38.4 17.2 145 353-532 10-164 (262)
34 COG3316 Transposase and inacti 89.1 3.6 7.9E-05 42.1 10.6 120 378-546 33-152 (215)
35 PF03106 WRKY: WRKY DNA -bindi 88.7 0.86 1.9E-05 37.0 4.7 39 305-343 21-59 (60)
36 PF04684 BAF1_ABF1: BAF1 / ABF 86.7 1.3 2.8E-05 49.7 6.2 58 270-327 22-80 (496)
37 cd06399 PB1_P40 The PB1 domain 85.6 2.7 5.8E-05 36.3 6.1 60 28-91 12-75 (92)
38 PF04500 FLYWCH: FLYWCH zinc f 84.9 1.6 3.6E-05 34.9 4.6 46 293-342 14-62 (62)
39 cd01799 Hoil1_N Ubiquitin-like 84.2 3.1 6.7E-05 35.4 6.1 38 27-65 10-47 (75)
40 PF00665 rve: Integrase core d 83.5 5.9 0.00013 36.2 8.3 76 458-534 5-81 (120)
41 cd01796 DDI1_N DNA damage indu 82.4 2.4 5.2E-05 35.6 4.7 38 28-65 8-45 (71)
42 PHA02517 putative transposase 82.1 14 0.00031 39.6 11.8 152 355-533 30-182 (277)
43 cd01807 GDX_N ubiquitin-like d 81.2 3.4 7.3E-05 34.9 5.2 42 24-65 5-46 (74)
44 cd01812 BAG1_N Ubiquitin-like 80.4 3.2 7E-05 34.4 4.8 41 24-65 5-45 (71)
45 PF11976 Rad60-SLD: Ubiquitin- 80.2 4.3 9.4E-05 33.8 5.5 41 24-64 5-46 (72)
46 cd01809 Scythe_N Ubiquitin-lik 79.3 4.5 9.7E-05 33.5 5.4 41 24-64 5-45 (72)
47 cd01794 DC_UbP_C dendritic cel 79.0 3.9 8.4E-05 34.3 4.8 43 23-65 2-44 (70)
48 PF03050 DDE_Tnp_IS66: Transpo 78.8 3.2 7E-05 44.5 5.5 133 368-562 19-156 (271)
49 cd01798 parkin_N amino-termina 78.7 4.3 9.3E-05 33.8 5.0 42 24-65 3-44 (70)
50 PF14560 Ubiquitin_2: Ubiquiti 78.5 4 8.7E-05 35.7 5.0 45 34-78 18-62 (87)
51 cd00196 UBQ Ubiquitin-like pro 77.4 5.3 0.00012 30.7 5.1 47 24-70 2-48 (69)
52 cd01803 Ubiquitin Ubiquitin. U 77.2 4.9 0.00011 33.7 5.0 41 24-64 5-45 (76)
53 smart00774 WRKY DNA binding do 76.2 3.6 7.8E-05 33.3 3.6 38 305-342 21-59 (59)
54 PF13565 HTH_32: Homeodomain-l 76.2 4.2 9.2E-05 34.3 4.4 41 355-395 34-76 (77)
55 PRK09409 IS2 transposase TnpB; 75.7 63 0.0014 35.3 14.4 143 355-532 51-203 (301)
56 PF04937 DUF659: Protein of un 75.4 42 0.00091 32.8 11.6 63 500-562 73-138 (153)
57 PTZ00044 ubiquitin; Provisiona 74.5 6.9 0.00015 33.0 5.2 42 24-65 5-46 (76)
58 smart00343 ZnF_C2HC zinc finge 73.9 1.6 3.5E-05 28.9 0.9 17 819-835 1-17 (26)
59 PF14392 zf-CCHC_4: Zinc knuck 72.8 1.4 2.9E-05 34.2 0.4 19 817-835 31-49 (49)
60 cd01800 SF3a120_C Ubiquitin-li 71.5 7.4 0.00016 33.0 4.7 39 27-65 5-43 (76)
61 cd01806 Nedd8 Nebb8-like ubiq 70.9 10 0.00022 31.7 5.5 42 24-65 5-46 (76)
62 PF11470 TUG-UBL1: GLUT4 regul 69.2 7.8 0.00017 32.0 4.1 39 27-65 4-42 (65)
63 cd01805 RAD23_N Ubiquitin-like 68.9 12 0.00026 31.5 5.5 42 24-65 5-48 (77)
64 cd01763 Sumo Small ubiquitin-r 68.4 10 0.00022 33.2 5.0 45 21-65 13-57 (87)
65 cd01769 UBL Ubiquitin-like dom 68.3 13 0.00027 30.2 5.4 41 25-65 3-43 (69)
66 cd01810 ISG15_repeat2 ISG15 ub 67.6 11 0.00024 31.7 4.9 42 24-65 3-44 (74)
67 COG5431 Uncharacterized metal- 67.0 9.8 0.00021 34.0 4.5 29 709-739 42-75 (117)
68 cd01789 Alp11_N Ubiquitin-like 66.3 13 0.00029 32.3 5.3 47 34-81 17-63 (84)
69 smart00213 UBQ Ubiquitin homol 66.0 14 0.0003 29.5 5.2 41 24-65 5-45 (64)
70 cd06395 PB1_Map2k5 PB1 domain 64.1 15 0.00032 31.3 4.8 49 38-89 21-69 (91)
71 cd01793 Fubi Fubi ubiquitin-li 62.5 17 0.00037 30.6 5.1 40 26-65 5-44 (74)
72 COG5179 TAF1 Transcription ini 60.6 5.2 0.00011 46.3 2.0 24 813-836 933-958 (968)
73 cd01813 UBP_N UBP ubiquitin pr 60.2 20 0.00044 30.3 5.1 37 28-64 8-44 (74)
74 cd01802 AN1_N ubiquitin-like d 59.6 19 0.00041 32.7 5.2 42 24-65 32-73 (103)
75 PF02178 AT_hook: AT hook moti 56.8 4.8 0.0001 22.3 0.5 9 798-806 2-10 (13)
76 cd01804 midnolin_N Ubiquitin-l 53.5 30 0.00064 29.5 5.2 41 25-65 7-47 (78)
77 PF00240 ubiquitin: Ubiquitin 51.7 35 0.00076 27.9 5.2 39 27-65 3-41 (69)
78 PF14847 Ras_bdg_2: Ras-bindin 51.4 47 0.001 30.3 6.3 80 24-103 5-89 (105)
79 smart00384 AT_hook DNA binding 44.1 13 0.00028 24.6 1.1 13 797-809 1-13 (26)
80 COG4279 Uncharacterized conser 42.8 11 0.00025 39.1 1.1 23 719-744 125-147 (266)
81 cd01797 NIRF_N amino-terminal 42.0 47 0.001 28.4 4.6 41 25-65 6-48 (78)
82 PRK09335 30S ribosomal protein 40.8 22 0.00047 31.5 2.3 27 794-825 2-28 (95)
83 cd01791 Ubl5 UBL5 ubiquitin-li 39.5 60 0.0013 27.4 4.8 38 28-65 10-47 (73)
84 PF13917 zf-CCHC_3: Zinc knuck 37.8 17 0.00037 27.3 1.0 19 817-835 4-22 (42)
85 cd01808 hPLIC_N Ubiquitin-like 36.5 70 0.0015 26.5 4.8 36 28-64 9-44 (71)
86 cd01792 ISG15_repeat1 ISG15 ub 36.1 62 0.0014 27.6 4.5 38 25-62 8-45 (80)
87 PLN00186 ribosomal protein S26 34.9 30 0.00065 31.4 2.3 27 794-825 2-28 (109)
88 PTZ00172 40S ribosomal protein 34.5 31 0.00066 31.3 2.3 27 794-825 2-28 (108)
89 PF12762 DDE_Tnp_IS1595: ISXO2 32.3 1.1E+02 0.0025 29.2 6.2 69 460-533 4-87 (151)
90 PHA00689 hypothetical protein 30.5 27 0.00059 26.7 1.1 14 814-827 14-27 (62)
91 PF14201 DUF4318: Domain of un 30.4 71 0.0015 27.2 3.7 29 275-303 13-41 (74)
92 PF13592 HTH_33: Winged helix- 29.8 59 0.0013 26.2 3.1 28 368-395 3-30 (60)
93 COG5082 AIR1 Arginine methyltr 29.2 28 0.00061 35.0 1.3 16 818-833 98-113 (190)
94 PF05741 zf-nanos: Nanos RNA b 28.9 21 0.00046 28.4 0.3 20 816-835 32-54 (55)
95 PF11543 UN_NPL4: Nuclear pore 27.5 62 0.0013 27.9 3.0 29 34-62 18-46 (80)
96 KOG3206 Alpha-tubulin folding 27.3 73 0.0016 32.4 3.8 61 36-101 19-80 (234)
97 cd01760 RBD Ubiquitin-like dom 26.9 1.2E+02 0.0025 25.7 4.4 36 29-64 9-44 (72)
98 PF08459 UvrC_HhH_N: UvrC Heli 26.6 1.7E+02 0.0037 28.7 6.2 64 461-542 32-101 (155)
99 PF02196 RBD: Raf-like Ras-bin 25.3 1.2E+02 0.0025 25.5 4.2 34 29-62 10-43 (71)
100 KOG3606 Cell polarity protein 25.2 87 0.0019 33.1 4.0 85 28-116 26-112 (358)
101 COG4715 Uncharacterized conser 25.1 1.6E+02 0.0034 34.7 6.4 44 702-747 50-99 (587)
102 smart00455 RBD Raf-like Ras-bi 24.4 1.4E+02 0.003 25.0 4.4 36 29-64 9-44 (70)
103 PF13276 HTH_21: HTH-like doma 23.5 1.3E+02 0.0028 23.9 4.1 41 356-396 6-47 (60)
104 PRK12286 rpmF 50S ribosomal pr 23.3 75 0.0016 25.5 2.5 34 794-827 4-37 (57)
105 KOG1769 Ubiquitin-like protein 22.8 1.7E+02 0.0037 26.3 4.8 38 27-64 28-65 (99)
106 PF01498 HTH_Tnp_Tc3_2: Transp 22.5 55 0.0012 27.2 1.7 36 360-396 4-39 (72)
107 KOG0010 Ubiquitin-like protein 21.2 3.6E+02 0.0078 31.3 8.2 41 24-65 20-60 (493)
108 COG5082 AIR1 Arginine methyltr 21.2 43 0.00094 33.7 0.9 19 816-834 59-77 (190)
109 PRK13907 rnhA ribonuclease H; 20.9 6.6E+02 0.014 23.1 10.0 77 461-540 3-81 (128)
110 PF04800 ETC_C1_NDUFA4: ETC co 20.7 1.3E+02 0.0028 27.3 3.7 29 272-304 51-79 (101)
111 cd01817 RGS12_RBD Ubiquitin do 20.1 2.8E+02 0.0062 23.5 5.4 32 29-60 9-40 (73)
No 1
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=100.00 E-value=2.5e-70 Score=645.50 Aligned_cols=472 Identities=16% Similarity=0.237 Sum_probs=375.4
Q ss_pred CCCCCCceeCCHHHHHHHHHHHHHhcceEEEEEeeCcc-------EEEEEec----------------------------
Q 003242 268 SITGVGQEFKSVIEFRDALQRFSIAHRFRYKFKKNETS-------RASGMCA---------------------------- 312 (837)
Q Consensus 268 ~~~~vG~~F~s~ee~~~ai~~yAi~~gf~~~~~ks~~~-------r~~~~C~---------------------------- 312 (837)
..+.+||+|+|.+|++.+|+.||...||.+|+.++.++ ..+++|+
T Consensus 72 ~~P~vGMeF~S~eeA~~FYn~YA~~~GFsVRi~~srrsk~~~~ii~r~fvCsreG~~~~~~~~~~~~~~~~~k~~~~~~~ 151 (846)
T PLN03097 72 LEPLSGMEFESHGEAYSFYQEYARSMGFNTAIQNSRRSKTSREFIDAKFACSRYGTKREYDKSFNRPRARQTKQDPENGT 151 (846)
T ss_pred ccCcCCCeECCHHHHHHHHHHHHhhcCceEEeeceeccCCCCcEEEEEEEEcCCCCCcccccccccccccccccCccccc
Confidence 45789999999999999999999999999998654322 2245564
Q ss_pred ------cCCCceEEEEEEeCCcceEEEEeecCCCccC--CCCCCCCCchhhhHHHHHHHhhcCCCCChhHHHHHHHHhcC
Q 003242 313 ------AEGCSWSFYASWVPSERVFKIKKMNETHTCG--ESSKTAHPTKNWLVSIIKDKLRESPHHKPKEISKSILRDFG 384 (837)
Q Consensus 313 ------~~gCpwri~as~~~~~~~~~I~~~~~~H~C~--~~~~~~~~~~~~ia~~~~~~l~~~~~~~~~~i~~~l~~~~g 384 (837)
++||+++|++++. ..+.|+|+.+..+|||+ +.......+++......+ .+....++ . .++.+.
T Consensus 152 ~rR~~tRtGC~A~m~Vk~~-~~gkW~V~~fv~eHNH~L~p~~~~~~~~r~~~~~~~~-~~~~~~~v-----~-~~~~d~- 222 (846)
T PLN03097 152 GRRSCAKTDCKASMHVKRR-PDGKWVIHSFVKEHNHELLPAQAVSEQTRKMYAAMAR-QFAEYKNV-----V-GLKNDS- 222 (846)
T ss_pred ccccccCCCCceEEEEEEc-CCCeEEEEEEecCCCCCCCCccccchhhhhhHHHHHh-hhhccccc-----c-ccchhh-
Confidence 3479999999875 44689999999999999 322211111111111000 00000000 0 000000
Q ss_pred cccchhhhHHHHHHHHHhhhCCHHHHHhchHHHHHHHHhhCCCcEEEEEecCCcceeEEEEEehhhHHHHHhcCCCeEEe
Q 003242 385 VTLNYSQVYRGIEGAREQLQGSYKEAYNQLPWFCDKLLEANPGSFIKLLIDNDKKFQRLFISFDASIHGFQNGCRPLLFL 464 (837)
Q Consensus 385 ~~~sy~~~~rak~~a~~~~~g~~~~sy~~L~~y~~~l~~~NPg~~~~v~~d~d~~f~~lF~a~~~si~~f~~~~~~vl~i 464 (837)
.++ .-+.|... +. ......|..||+++++.||+|+|++++|++++++++||+++.|+.+|.+ |+|||.|
T Consensus 223 --~~~--~~~~r~~~---~~---~gD~~~ll~yf~~~q~~nP~Ffy~~qlDe~~~l~niFWaD~~sr~~Y~~-FGDvV~f 291 (846)
T PLN03097 223 --KSS--FDKGRNLG---LE---AGDTKILLDFFTQMQNMNSNFFYAVDLGEDQRLKNLFWVDAKSRHDYGN-FSDVVSF 291 (846)
T ss_pred --cch--hhHHHhhh---cc---cchHHHHHHHHHHHHhhCCCceEEEEEccCCCeeeEEeccHHHHHHHHh-cCCEEEE
Confidence 001 11111111 11 1234679999999999999999999999999999999999999999999 9999999
Q ss_pred ecccccccccceEEEEEEecCCCCeEEEEEEEeccCChhHHHHHHHHHHHhhcCCCcEEEEecCchhHHHHHHHhcccCc
Q 003242 465 DSTSLRSKYHEILLTATALDGDDCIFPVAFAIVDTENDDSWNWFLEELRSAVSSSRSITFVSDKQKGLMESVLKIFENAH 544 (837)
Q Consensus 465 D~T~~~~~y~~~Ll~a~g~D~~~~~~plafalv~~E~~es~~wfL~~lk~~~~~~~p~~iisD~~~~l~~AI~~vfP~a~ 544 (837)
|+||++|+|++||+.++|+|+|+|++++|+||+.+|+.++|.|+|++|+++|++..|.+||||++.+|.+||++|||++.
T Consensus 292 DTTY~tN~y~~Pfa~FvGvNhH~qtvlfGcaLl~dEt~eSf~WLf~tfl~aM~gk~P~tIiTDqd~am~~AI~~VfP~t~ 371 (846)
T PLN03097 292 DTTYVRNKYKMPLALFVGVNQHYQFMLLGCALISDESAATYSWLMQTWLRAMGGQAPKVIITDQDKAMKSVISEVFPNAH 371 (846)
T ss_pred eceeeccccCcEEEEEEEecCCCCeEEEEEEEcccCchhhHHHHHHHHHHHhCCCCCceEEecCCHHHHHHHHHHCCCce
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeecHHHHHHHHHhhcCCCCCccccCchHHHHHHHHH-HHHHHHHHHHHHHHH-hhCchHHHHHhcc--ccccccccccc
Q 003242 545 HGYSIYHLLDNFMKNLKGPFHGEGKGSLPVNFLAAAC-AARLDSFRMSAEQVK-KVSSNAFDWMMQI--APEYWTNAAFK 620 (837)
Q Consensus 545 h~~C~~Hi~~N~~~~~~~~~~~e~~~~l~~~~~~~~~-a~t~~eFe~~~~~l~-~~~~~~~~~L~~~--~~~~Wa~a~f~ 620 (837)
|++|+|||++|+.++++..+.. .+.|...|..+++ +.+++||+..|..|. +++...++||..+ .|++|+++|++
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 9999999999999999876542 4579999999998 679999999999885 4668999999998 99999999999
Q ss_pred cCCcccc-cccchhhhHHHhhhhh--cCchHHHHHHHHHHHHHHHHhhhc-----------------ccccccccCcchH
Q 003242 621 GESYQHI-TFDVAESYANWIEEVW--ELPLIQKLERLLCKMTEMINNRRM-----------------NSSGWFTKLIPSR 680 (837)
Q Consensus 621 ~~~~~~~-TtN~~Es~N~~lk~~r--~lpi~~lle~ir~~l~~~~~~rr~-----------------~~~~~~~~~tp~~ 680 (837)
+.+++.| ||+++||+|++|+... ..+|..|++.+...+..+.....+ ...+.+..|||.+
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 9888766 7889999999998864 688888888876655443322111 0123478999999
Q ss_pred HHHHHHHHHhccceEEEEeC----CceEEEEc---CceeEe--e--cCCcccccCcccccCCccchHHHHHHhcCC--Cc
Q 003242 681 EQLVKDASRRAHYLKVLFSS----DTLFEVQG---DSTHVV--D--MNKRDCSCLVWKATGLPCHHAIAVFNSTGR--NV 747 (837)
Q Consensus 681 ~~kl~~~~~~a~~~~V~~~~----~~~feV~~---~~~~~V--~--l~~~~CSC~~~~~~GiPC~Halav~~~~~~--~~ 747 (837)
|++||+++..+..|.+.... ..+|.|.+ ...|.| | ..+.+|+|++|+..||||+|||.||...++ .|
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 25788865 345666 3 257899999999999999999999999998 49
Q ss_pred cccccccceecccc
Q 003242 748 YDYCSSYFTVDSYR 761 (837)
Q Consensus 748 ~~yv~~~yt~~~~~ 761 (837)
..||.++||.++-.
T Consensus 610 ~~YILkRWTKdAK~ 623 (846)
T PLN03097 610 SQYILKRWTKDAKS 623 (846)
T ss_pred hhhhhhhchhhhhh
Confidence 99999999977654
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=99.97 E-value=3.9e-32 Score=239.89 Aligned_cols=91 Identities=36% Similarity=0.686 Sum_probs=87.5
Q ss_pred EEecCCeeccCC-CCCeEeecCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEEecCCCC-CceEeecChHHHHHHH
Q 003242 9 ICQSGGEFVTKD-DGSLSYDGGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKYFLPGNK-QTLITICNDKDLKRMF 86 (837)
Q Consensus 9 ~~~~gg~~~~~~-~~~~~y~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~l~~~~-~~l~~~~~d~dl~~m~ 86 (837)
||||||+|+|++ ||+|+|+||+||+|+|+|+|||+||++||+++++++.+ ++||||||+|+ |+||||++||||.|||
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 799999999776 99999999999999999999999999999999998865 99999999999 9999999999999999
Q ss_pred hccC----CceeEEEEEe
Q 003242 87 DFHE----GSVTADVFVI 100 (837)
Q Consensus 87 ~~~~----~~~~~~v~~~ 100 (837)
++++ +++++|||++
T Consensus 80 ~e~~~~~~~~~rirvflf 97 (97)
T cd06410 80 EEYDRLSGGSARLRVFLF 97 (97)
T ss_pred HhhccccCCCceEEEEEC
Confidence 9999 9999999986
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=99.85 E-value=1.8e-21 Score=174.06 Aligned_cols=90 Identities=37% Similarity=0.695 Sum_probs=87.0
Q ss_pred cccccccccceEEE---EEEecCCCCeEEEEEEEeccCChhHHHHHHHHHHHhhcCCCcEEEEecCchhHHHHHHHhccc
Q 003242 466 STSLRSKYHEILLT---ATALDGDDCIFPVAFAIVDTENDDSWNWFLEELRSAVSSSRSITFVSDKQKGLMESVLKIFEN 542 (837)
Q Consensus 466 ~T~~~~~y~~~Ll~---a~g~D~~~~~~plafalv~~E~~es~~wfL~~lk~~~~~~~p~~iisD~~~~l~~AI~~vfP~ 542 (837)
|||++|+| ++++. ++|+|++|+.+|+||+++.+|+.++|.|||+.+++.++.. |.+||+|++.|+.+||+++||+
T Consensus 1 ~T~~tn~~-~~l~~~~~~~~~d~~~~~~~v~~~l~~~e~~~~~~~~l~~~~~~~~~~-p~~ii~D~~~~~~~Ai~~vfP~ 78 (93)
T PF10551_consen 1 GTYKTNKY-GPLLYLMIAVGIDGNGRGFPVAFALVSSESEESYEWFLEKLKEAMPQK-PKVIISDFDKALINAIKEVFPD 78 (93)
T ss_pred Cccccccc-cccceeceEEEEcCCCCEEEEEEEEEcCCChhhhHHHHHHhhhccccC-ceeeeccccHHHHHHHHHHCCC
Confidence 79999999 98886 9999999999999999999999999999999999999887 9999999999999999999999
Q ss_pred CceeecHHHHHHHHH
Q 003242 543 AHHGYSIYHLLDNFM 557 (837)
Q Consensus 543 a~h~~C~~Hi~~N~~ 557 (837)
+.|++|.||+.+|++
T Consensus 79 ~~~~~C~~H~~~n~k 93 (93)
T PF10551_consen 79 ARHQLCLFHILRNIK 93 (93)
T ss_pred ceEehhHHHHHHhhC
Confidence 999999999999985
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=99.80 E-value=1.1e-20 Score=211.54 Aligned_cols=239 Identities=21% Similarity=0.255 Sum_probs=185.9
Q ss_pred CCCCChhHHHHHHHHhcC-cccchhhhHHHHHHHHHhhhCCHHHHHhchHHHHHHHHhhCCCcEEEEEecCCcceeEEEE
Q 003242 367 SPHHKPKEISKSILRDFG-VTLNYSQVYRGIEGAREQLQGSYKEAYNQLPWFCDKLLEANPGSFIKLLIDNDKKFQRLFI 445 (837)
Q Consensus 367 ~~~~~~~~i~~~l~~~~g-~~~sy~~~~rak~~a~~~~~g~~~~sy~~L~~y~~~l~~~NPg~~~~v~~d~d~~f~~lF~ 445 (837)
-.|++.++|.+.++.-+| ..+|-+++.|..+...+.+ ..| +...
T Consensus 112 ~~G~Str~i~~~l~~l~g~~~~S~s~vSri~~~~~~~~-----------~~w----~~R~-------------------- 156 (381)
T PF00872_consen 112 LKGVSTRDIEEALEELYGEVAVSKSTVSRITKQLDEEV-----------EAW----RNRP-------------------- 156 (381)
T ss_pred ccccccccccchhhhhhcccccCchhhhhhhhhhhhhH-----------HHH----hhhc--------------------
Confidence 358899999999999999 7788888887655544322 111 1111
Q ss_pred EehhhHHHHHhcC-CCeEEeeccccccccc-----ceEEEEEEecCCCCeEEEEEEEeccCChhHHHHHHHHHHHhhcCC
Q 003242 446 SFDASIHGFQNGC-RPLLFLDSTSLRSKYH-----EILLTATALDGDDCIFPVAFAIVDTENDDSWNWFLEELRSAVSSS 519 (837)
Q Consensus 446 a~~~si~~f~~~~-~~vl~iD~T~~~~~y~-----~~Ll~a~g~D~~~~~~plafalv~~E~~es~~wfL~~lk~~~~~~ 519 (837)
.. +. -++|++||+|.+.+.+ ..+++++|+|.+|+..+||+.+...|+.++|.-||+.|++. |..
T Consensus 157 --------L~-~~~y~~l~iD~~~~kvr~~~~~~~~~~~v~iGi~~dG~r~vLg~~~~~~Es~~~W~~~l~~L~~R-Gl~ 226 (381)
T PF00872_consen 157 --------LE-SEPYPYLWIDGTYFKVREDGRVVKKAVYVAIGIDEDGRREVLGFWVGDRESAASWREFLQDLKER-GLK 226 (381)
T ss_pred --------cc-cccccceeeeeeecccccccccccchhhhhhhhhcccccceeeeecccCCccCEeeecchhhhhc-ccc
Confidence 00 13 4789999999987644 46799999999999999999999999999999999999988 555
Q ss_pred CcEEEEecCchhHHHHHHHhcccCceeecHHHHHHHHHhhcCCCCCccccCchHHHHHHHHHHHHHHHHHHHHHHH----
Q 003242 520 RSITFVSDKQKGLMESVLKIFENAHHGYSIYHLLDNFMKNLKGPFHGEGKGSLPVNFLAAACAARLDSFRMSAEQV---- 595 (837)
Q Consensus 520 ~p~~iisD~~~~l~~AI~~vfP~a~h~~C~~Hi~~N~~~~~~~~~~~e~~~~l~~~~~~~~~a~t~~eFe~~~~~l---- 595 (837)
.+..||+|+++||.+||+++||++.++.|.+|+++|+.+++.... ++.+...++.+..+.+.++....++++
T Consensus 227 ~~~lvv~Dg~~gl~~ai~~~fp~a~~QrC~vH~~RNv~~~v~~k~----~~~v~~~Lk~I~~a~~~e~a~~~l~~f~~~~ 302 (381)
T PF00872_consen 227 DILLVVSDGHKGLKEAIREVFPGAKWQRCVVHLMRNVLRKVPKKD----RKEVKADLKAIYQAPDKEEAREALEEFAEKW 302 (381)
T ss_pred ccceeeccccccccccccccccchhhhhheechhhhhcccccccc----chhhhhhccccccccccchhhhhhhhccccc
Confidence 699999999999999999999999999999999999999986643 445566666666666666666666555
Q ss_pred HhhCchHHHHHhccccccccccccccCCc-ccccccchhhhHHHhhhhh----cCchHHHHHHH
Q 003242 596 KKVSSNAFDWMMQIAPEYWTNAAFKGESY-QHITFDVAESYANWIEEVW----ELPLIQKLERL 654 (837)
Q Consensus 596 ~~~~~~~~~~L~~~~~~~Wa~a~f~~~~~-~~~TtN~~Es~N~~lk~~r----~lpi~~lle~i 654 (837)
...+|++.++|.+...+.|+..-|+...+ -..|||.+|++|+.||... ..|-.+.+..+
T Consensus 303 ~~kyp~~~~~l~~~~~~~~tf~~fP~~~~~~i~TTN~iEsln~~irrr~~~~~~Fp~~~s~lr~ 366 (381)
T PF00872_consen 303 EKKYPKAAKSLEENWDELLTFLDFPPEHRRSIRTTNAIESLNKEIRRRTKVVGIFPNEESALRL 366 (381)
T ss_pred ccccchhhhhhhhccccccceeeecchhccccchhhhccccccchhhhccccccCCCHHHHHHH
Confidence 45789999999998778888766775554 4569999999999997632 35544444333
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=99.64 E-value=7.7e-16 Score=128.63 Aligned_cols=67 Identities=33% Similarity=0.635 Sum_probs=65.0
Q ss_pred CCCCCCCceeCCHHHHHHHHHHHHHhcceEEEEEeeCccEEEEEeccCCCceEEEEEEeCCcceEEE
Q 003242 267 DSITGVGQEFKSVIEFRDALQRFSIAHRFRYKFKKNETSRASGMCAAEGCSWSFYASWVPSERVFKI 333 (837)
Q Consensus 267 ~~~~~vG~~F~s~ee~~~ai~~yAi~~gf~~~~~ks~~~r~~~~C~~~gCpwri~as~~~~~~~~~I 333 (837)
||.+.+||+|+|++||+.||..||++++|++++.+|+++|++++|...||||+|+|++.++++.|+|
T Consensus 1 n~~l~~G~~F~~~~e~k~av~~yai~~~~~~~v~ksd~~r~~~~C~~~~C~Wrv~as~~~~~~~~~I 67 (67)
T PF03108_consen 1 NPELEVGQTFPSKEEFKEAVREYAIKNGFEFKVKKSDKKRYRAKCKDKGCPWRVRASKRKRSDTFQI 67 (67)
T ss_pred CCccccCCEECCHHHHHHHHHHHHHhcCcEEEEeccCCEEEEEEEcCCCCCEEEEEEEcCCCCEEEC
Confidence 6789999999999999999999999999999999999999999999999999999999999999986
No 6
>COG3328 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=99.51 E-value=2.3e-13 Score=149.59 Aligned_cols=224 Identities=17% Similarity=0.162 Sum_probs=168.0
Q ss_pred CCCCChhHHHHHHHHhcCcccchhhhHHHHHHHHHhhhCCHHHHHhchHHHHHHHHhhCCCcEEEEEecCCcceeEEEEE
Q 003242 367 SPHHKPKEISKSILRDFGVTLNYSQVYRGIEGAREQLQGSYKEAYNQLPWFCDKLLEANPGSFIKLLIDNDKKFQRLFIS 446 (837)
Q Consensus 367 ~~~~~~~~i~~~l~~~~g~~~sy~~~~rak~~a~~~~~g~~~~sy~~L~~y~~~l~~~NPg~~~~v~~d~d~~f~~lF~a 446 (837)
..+++++++...+++.++..++-..+.+.-....+. +.+++.+-+
T Consensus 98 ~~gv~Tr~i~~~~~~~~~~~~s~~~iS~~~~~~~e~---------------v~~~~~r~l-------------------- 142 (379)
T COG3328 98 AKGVTTREIEALLEELYGHKVSPSVISVVTDRLDEK---------------VKAWQNRPL-------------------- 142 (379)
T ss_pred HcCCcHHHHHHHHHHhhCcccCHHHhhhHHHHHHHH---------------HHHHHhccc--------------------
Confidence 468999999999999988866665555543333322 222222211
Q ss_pred ehhhHHHHHhcCCCeEEeeccccccc--ccceEEEEEEecCCCCeEEEEEEEeccCChhHHHHHHHHHHHhhcCCCcEEE
Q 003242 447 FDASIHGFQNGCRPLLFLDSTSLRSK--YHEILLTATALDGDDCIFPVAFAIVDTENDDSWNWFLEELRSAVSSSRSITF 524 (837)
Q Consensus 447 ~~~si~~f~~~~~~vl~iD~T~~~~~--y~~~Ll~a~g~D~~~~~~plafalv~~E~~es~~wfL~~lk~~~~~~~p~~i 524 (837)
+..+++++|++|++-+ -+..+++|+|++.+|+...+++.+.+.|+ ..|.-||..|+.. |-.....+
T Consensus 143 ----------~~~~~v~~D~~~~k~r~v~~~~~~ia~Gv~~eG~reilg~~~~~~e~-~~w~~~l~~l~~r-gl~~v~l~ 210 (379)
T COG3328 143 ----------GDYPYVYLDAKYVKVRSVRNKAVYIAIGVTEEGRREILGIWVGVRES-KFWLSFLLDLKNR-GLSDVLLV 210 (379)
T ss_pred ----------cCceEEEEecceeehhhhhhheeeeeeccCcccchhhhceeeecccc-hhHHHHHHHHHhc-cccceeEE
Confidence 2678999999999977 45689999999999999999999999999 9999999888887 33445667
Q ss_pred EecCchhHHHHHHHhcccCceeecHHHHHHHHHhhcCCCCCccccCchHHHHHHHHHHHHHHH----HHHHHHHHHhhCc
Q 003242 525 VSDKQKGLMESVLKIFENAHHGYSIYHLLDNFMKNLKGPFHGEGKGSLPVNFLAAACAARLDS----FRMSAEQVKKVSS 600 (837)
Q Consensus 525 isD~~~~l~~AI~~vfP~a~h~~C~~Hi~~N~~~~~~~~~~~e~~~~l~~~~~~~~~a~t~~e----Fe~~~~~l~~~~~ 600 (837)
++|+.+|+.+||.++||.+.++.|..|+.+|+..+...+. ++.+...+....-+.+.++ |+...+.+...+|
T Consensus 211 v~Dg~~gl~~aI~~v~p~a~~Q~C~vH~~Rnll~~v~~k~----~d~i~~~~~~I~~a~~~e~~~~~~~~~~~~w~~~yP 286 (379)
T COG3328 211 VVDGLKGLPEAISAVFPQAAVQRCIVHLVRNLLDKVPRKD----QDAVLSDLRSIYIAPDAEEALLALLAFSELWGKRYP 286 (379)
T ss_pred ecchhhhhHHHHHHhccHhhhhhhhhHHHhhhhhhhhhhh----hHHHHhhhhhhhccCCcHHHHHHHHHHHHhhhhhcc
Confidence 7799999999999999999999999999999999976542 3344444444444444444 4444455566789
Q ss_pred hHHHHHhccccccccccccc-cCCcccccccchhhhHHHhhh
Q 003242 601 NAFDWMMQIAPEYWTNAAFK-GESYQHITFDVAESYANWIEE 641 (837)
Q Consensus 601 ~~~~~L~~~~~~~Wa~a~f~-~~~~~~~TtN~~Es~N~~lk~ 641 (837)
....|+.+..-+.|...-|+ ..+--..|||..|++|+.++.
T Consensus 287 ~i~~~~~~~~~~~~~F~~fp~~~r~~i~ttN~IE~~n~~ir~ 328 (379)
T COG3328 287 AILKSWRNALEELLPFFAFPSEIRKIIYTTNAIESLNKLIRR 328 (379)
T ss_pred hHHHHHHHHHHHhcccccCcHHHHhHhhcchHHHHHHHHHHH
Confidence 99999998866666554444 444567799999999997753
No 7
>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=99.02 E-value=1.3e-09 Score=94.68 Aligned_cols=77 Identities=26% Similarity=0.489 Sum_probs=66.9
Q ss_pred CCCeEeecCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEEecCCCCCceEeecChHHHHHHHhccCCc--eeEEEE
Q 003242 21 DGSLSYDGGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKYFLPGNKQTLITICNDKDLKRMFDFHEGS--VTADVF 98 (837)
Q Consensus 21 ~~~~~y~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~l~~~~~~l~~~~~d~dl~~m~~~~~~~--~~~~v~ 98 (837)
..+++| ||++|.+.|++++||+||+++|++.|++..+.++|||+ .++.-+|++++|+||..|+++...+ ..++|+
T Consensus 3 ~vK~~~-~~~~~~~~~~~~~s~~dL~~~i~~~~~~~~~~~~l~Y~--Dedgd~v~l~sd~Dl~~a~~~~~~~~~~~l~l~ 79 (81)
T smart00666 3 DVKLRY-GGETRRLSVPRDISFEDLRSKVAKRFGLDNQSFTLKYQ--DEDGDLVSLTSDEDLEEAIEEYDSLGSKKLRLH 79 (81)
T ss_pred cEEEEE-CCEEEEEEECCCCCHHHHHHHHHHHhCCCCCCeEEEEE--CCCCCEEEecCHHHHHHHHHHHHHcCCceEEEE
Confidence 357888 99999999999999999999999999987779999998 5554599999999999999988752 567777
Q ss_pred Ee
Q 003242 99 VI 100 (837)
Q Consensus 99 ~~ 100 (837)
+.
T Consensus 80 v~ 81 (81)
T smart00666 80 VF 81 (81)
T ss_pred eC
Confidence 63
No 8
>smart00575 ZnF_PMZ plant mutator transposase zinc finger.
Probab=98.74 E-value=4.5e-09 Score=71.26 Aligned_cols=27 Identities=37% Similarity=0.872 Sum_probs=25.1
Q ss_pred cccccCcccccCCccchHHHHHHhcCC
Q 003242 719 RDCSCLVWKATGLPCHHAIAVFNSTGR 745 (837)
Q Consensus 719 ~~CSC~~~~~~GiPC~Halav~~~~~~ 745 (837)
.+|||++|+..||||+|+|+|+...++
T Consensus 1 ~~CsC~~~~~~gipC~H~i~v~~~~~~ 27 (28)
T smart00575 1 KTCSCRKFQLSGIPCRHALAAAIHIGL 27 (28)
T ss_pred CcccCCCcccCCccHHHHHHHHHHhCC
Confidence 479999999999999999999998875
No 9
>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=98.67 E-value=9.9e-08 Score=85.13 Aligned_cols=68 Identities=13% Similarity=0.292 Sum_probs=64.9
Q ss_pred eCCHHHHHHHHHHHHHhcceEEEEEeeCccEEEEEecc------------------------------------------
Q 003242 276 FKSVIEFRDALQRFSIAHRFRYKFKKNETSRASGMCAA------------------------------------------ 313 (837)
Q Consensus 276 F~s~ee~~~ai~~yAi~~gf~~~~~ks~~~r~~~~C~~------------------------------------------ 313 (837)
|.+++|++.+|+.++...|+++.+.+||.+.+.++|..
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 CCCceEEEEEEeCCcceEEEEeecCCCccC
Q 003242 314 EGCSWSFYASWVPSERVFKIKKMNETHTCG 343 (837)
Q Consensus 314 ~gCpwri~as~~~~~~~~~I~~~~~~H~C~ 343 (837)
.+|||+|+|+.....+.|.|..+++.|+|+
T Consensus 81 ~~CPFriRA~yS~k~k~W~lvvvnn~HnH~ 110 (111)
T PF08731_consen 81 NTCPFRIRANYSKKNKKWTLVVVNNEHNHP 110 (111)
T ss_pred cCCCeEEEEEEEecCCeEEEEEecCCcCCC
Confidence 489999999999999999999999999996
No 10
>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=98.46 E-value=7.3e-07 Score=77.32 Aligned_cols=74 Identities=32% Similarity=0.549 Sum_probs=58.7
Q ss_pred CeEeecCceEEEEeC-CCCChHHHHHHHHHHhCCCCcceEEEEecCCCCCceEeecChHHHHHHHhccC--CceeEEEEE
Q 003242 23 SLSYDGGEANAVAIN-PETHFGDLKLKLAELLNLEYKSLSVKYFLPGNKQTLITICNDKDLKRMFDFHE--GSVTADVFV 99 (837)
Q Consensus 23 ~~~y~gg~~~~~~v~-~~~~~~~~~~~~~~~~~~~~~~~~~~y~l~~~~~~l~~~~~d~dl~~m~~~~~--~~~~~~v~~ 99 (837)
+++|.| +++.+.++ +++||.+|.++|++.|++....+.++| ..++..+|+|++|+||+.|++... +...++|++
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-EIRRFVVVSRSISFEDLRSKIAEKFGLDAVSFKLKY--PDEDGDLVTISSDEDLEEAIEEARRSGSKKLRLFV 80 (81)
T ss_pred EEEecC-CCEEEEEecCCCCHHHHHHHHHHHhCCCCCcEEEEe--eCCCCCEEEeCCHHHHHHHHHHHhhcCCccEEEEe
Confidence 567775 56666666 999999999999999997755666666 456668999999999999999887 355677765
No 11
>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=98.40 E-value=8.5e-07 Score=77.50 Aligned_cols=77 Identities=27% Similarity=0.477 Sum_probs=64.2
Q ss_pred CeEeecCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEEecCCCCCceEeecChHHHHHHHhccC--CceeEEEEEe
Q 003242 23 SLSYDGGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKYFLPGNKQTLITICNDKDLKRMFDFHE--GSVTADVFVI 100 (837)
Q Consensus 23 ~~~y~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~l~~~~~~l~~~~~d~dl~~m~~~~~--~~~~~~v~~~ 100 (837)
+++|.|+..+++.+++++||.+|.++|.+.|++....+.++|. .++.-+|+|++|+||..|++... +...++++|.
T Consensus 5 K~~~~~~~~~~~~~~~~~s~~~L~~~i~~~~~~~~~~~~l~Y~--D~dgD~V~i~sd~Dl~~a~~~~~~~~~~~lrl~v~ 82 (84)
T PF00564_consen 5 KVRYGGDIRRIISLPSDVSFDDLRSKIREKFGLLDEDFQLKYK--DEDGDLVTISSDEDLQEAIEQAKESGSKTLRLFVQ 82 (84)
T ss_dssp EEEETTEEEEEEEECSTSHHHHHHHHHHHHHTTSTSSEEEEEE--ETTSSEEEESSHHHHHHHHHHHHHCTTSCEEEEEE
T ss_pred EEEECCeeEEEEEcCCCCCHHHHHHHHHHHhCCCCccEEEEee--CCCCCEEEeCCHHHHHHHHHHHHhcCCCcEEEEEE
Confidence 5677777777799999999999999999999987678999995 45568999999999999999764 2347888875
Q ss_pred c
Q 003242 101 G 101 (837)
Q Consensus 101 ~ 101 (837)
.
T Consensus 83 ~ 83 (84)
T PF00564_consen 83 D 83 (84)
T ss_dssp E
T ss_pred e
Confidence 3
No 12
>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=98.28 E-value=3.9e-06 Score=72.55 Aligned_cols=73 Identities=26% Similarity=0.461 Sum_probs=60.1
Q ss_pred eEeecCceEEEEeCCCCChHHHHHHHHHHhCCCC-cceEEEEecCCCCCceEeecChHHHHHHHhccC--CceeEEEEE
Q 003242 24 LSYDGGEANAVAINPETHFGDLKLKLAELLNLEY-KSLSVKYFLPGNKQTLITICNDKDLKRMFDFHE--GSVTADVFV 99 (837)
Q Consensus 24 ~~y~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~-~~~~~~y~l~~~~~~l~~~~~d~dl~~m~~~~~--~~~~~~v~~ 99 (837)
..| ||+++.+.++.+++|.+|.+++++.|+++. +.++|||. -.| .-.++|+||+||+.-++.+. +..++++||
T Consensus 5 ~~~-~~d~~r~~l~~~~~~~~L~~~i~~r~~~~~~~~f~LkY~-Dde-gd~v~ltsd~DL~eai~i~~~~~~~~v~l~v 80 (82)
T cd06407 5 ATY-GEEKIRFRLPPSWGFTELKQEIAKRFKLDDMSAFDLKYL-DDD-EEWVLLTCDADLEECIDVYRSSGSHTIRLLV 80 (82)
T ss_pred EEe-CCeEEEEEcCCCCCHHHHHHHHHHHhCCCCCCeeEEEEE-CCC-CCeEEeecHHHHHHHHHHHHHCCCCeEEEEe
Confidence 344 889999999999999999999999999875 68999993 333 77899999999998766432 356788776
No 13
>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=98.28 E-value=1.7e-06 Score=76.77 Aligned_cols=59 Identities=15% Similarity=0.308 Sum_probs=52.2
Q ss_pred HHHHHHHHhcceEEEEEeeCcc-------EEEEEecc----------------------CCCceEEEEEEeCCcceEEEE
Q 003242 284 DALQRFSIAHRFRYKFKKNETS-------RASGMCAA----------------------EGCSWSFYASWVPSERVFKIK 334 (837)
Q Consensus 284 ~ai~~yAi~~gf~~~~~ks~~~-------r~~~~C~~----------------------~gCpwri~as~~~~~~~~~I~ 334 (837)
++|+.||..+||.++..++.+. ++.+.|.. +||||+|.+.+.+ ++.|.|.
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 4789999999999999876543 78899974 6999999999988 7899999
Q ss_pred eecCCCccC
Q 003242 335 KMNETHTCG 343 (837)
Q Consensus 335 ~~~~~H~C~ 343 (837)
.+..+|||+
T Consensus 80 ~~~~~HNH~ 88 (91)
T PF03101_consen 80 SFVLEHNHP 88 (91)
T ss_pred ECcCCcCCC
Confidence 999999997
No 14
>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=97.85 E-value=9.7e-06 Score=60.21 Aligned_cols=30 Identities=33% Similarity=0.754 Sum_probs=27.4
Q ss_pred eecCCcccccCcccccCCccchHHHHHHhc
Q 003242 714 VDMNKRDCSCLVWKATGLPCHHAIAVFNST 743 (837)
Q Consensus 714 V~l~~~~CSC~~~~~~GiPC~Halav~~~~ 743 (837)
+++...+|||..|+..|.||+|++|++...
T Consensus 10 ~~~~~~~CsC~~~~~~~~~CkHi~av~~~~ 39 (40)
T PF04434_consen 10 VSIEQASCSCPYFQFRGGPCKHIVAVLLAL 39 (40)
T ss_pred ccccccEeeCCCccccCCcchhHHHHHHhh
Confidence 667889999999999999999999998764
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=97.71 E-value=0.00011 Score=63.54 Aligned_cols=57 Identities=23% Similarity=0.405 Sum_probs=51.5
Q ss_pred cCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEEecCCCCCceEeecChHHHHHHHhc
Q 003242 28 GGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKYFLPGNKQTLITICNDKDLKRMFDF 88 (837)
Q Consensus 28 gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~l~~~~~~l~~~~~d~dl~~m~~~ 88 (837)
+|++++|.|+.+++|+||..||.++|++. +.+++||.=. ...++|++++||+.-+..
T Consensus 10 ~~Dv~~i~v~~~i~f~dL~~kIrdkf~~~-~~~~iKykDE---GD~iti~sq~DLd~Ai~~ 66 (86)
T cd06408 10 QDDTRYIMIGPDTGFADFEDKIRDKFGFK-RRLKIKMKDD---GDMITMGDQDDLDMAIDT 66 (86)
T ss_pred cCcEEEEEcCCCCCHHHHHHHHHHHhCCC-CceEEEEEcC---CCCccccCHHHHHHHHHH
Confidence 78899999999999999999999999986 6999999655 578999999999988763
No 16
>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=97.70 E-value=0.00028 Score=62.32 Aligned_cols=75 Identities=21% Similarity=0.388 Sum_probs=61.0
Q ss_pred CeEeecCceEEEEeCC-----CCChHHHHHHHHHHhCCCC-cceEEEEecCCCCCceEeecChHHHHHHHhcc---CCce
Q 003242 23 SLSYDGGEANAVAINP-----ETHFGDLKLKLAELLNLEY-KSLSVKYFLPGNKQTLITICNDKDLKRMFDFH---EGSV 93 (837)
Q Consensus 23 ~~~y~gg~~~~~~v~~-----~~~~~~~~~~~~~~~~~~~-~~~~~~y~l~~~~~~l~~~~~d~dl~~m~~~~---~~~~ 93 (837)
++.| ||++|-+.++. +++|.+|..|+.+.|+++. ..+.|+|. .++--+|++++|+||+.-++.. ....
T Consensus 4 Kv~y-~~~~rRf~l~~~~~~~d~~~~~L~~kI~~~f~l~~~~~~~l~Y~--Dedgd~V~l~~D~DL~~a~~~~~~~~~~~ 80 (91)
T cd06398 4 KVKY-GGTLRRFTFPVAENQLDLNMDGLREKVEELFSLSPDADLSLTYT--DEDGDVVTLVDDNDLTDAIQYFCSGSRLN 80 (91)
T ss_pred EEEe-CCEEEEEEeccccccCCCCHHHHHHHHHHHhCCCCCCcEEEEEE--CCCCCEEEEccHHHHHHHHHHHhccCCCc
Confidence 3456 88999999995 7999999999999999987 58999993 4468899999999999888865 1234
Q ss_pred eEEEEEe
Q 003242 94 TADVFVI 100 (837)
Q Consensus 94 ~~~v~~~ 100 (837)
++||+|.
T Consensus 81 ~lrl~v~ 87 (91)
T cd06398 81 PLRIDVT 87 (91)
T ss_pred eEEEEEE
Confidence 6777764
No 17
>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=97.60 E-value=0.00038 Score=57.28 Aligned_cols=67 Identities=19% Similarity=0.374 Sum_probs=55.8
Q ss_pred cCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEEecCCCCCceEeecChHHHHHHHhccCC---ceeEEEEEe
Q 003242 28 GGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKYFLPGNKQTLITICNDKDLKRMFDFHEG---SVTADVFVI 100 (837)
Q Consensus 28 gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~l~~~~~~l~~~~~d~dl~~m~~~~~~---~~~~~v~~~ 100 (837)
-||.|||-++|-+.|.|+.+|+.+.|| ..+.+.|+... -||++.|-+||++-+|-.+. -..+||.+.
T Consensus 8 ~gEKRIi~f~RPvkf~dl~~kv~~afG---q~mdl~ytn~e---L~iPl~~Q~DLDkAie~ld~s~~~ksLRilL~ 77 (79)
T cd06405 8 NGEKRIIQFPRPVKFKDLQQKVTTAFG---QPMDLHYTNNE---LLIPLKNQEDLDRAIELLDRSPHMKSLRILLS 77 (79)
T ss_pred cCceEEEecCCCccHHHHHHHHHHHhC---CeeeEEEeccc---EEEeccCHHHHHHHHHHHccCccccceeEeEe
Confidence 379999999999999999999999998 78889997544 99999999999998874443 334666554
No 18
>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=97.53 E-value=0.00031 Score=59.62 Aligned_cols=65 Identities=11% Similarity=0.257 Sum_probs=55.1
Q ss_pred CeEeecCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEEecCCCCCceEeecChHHHHHHHhccCC
Q 003242 23 SLSYDGGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKYFLPGNKQTLITICNDKDLKRMFDFHEG 91 (837)
Q Consensus 23 ~~~y~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~l~~~~~~l~~~~~d~dl~~m~~~~~~ 91 (837)
++.|.+ |-+|.|+++++|++|..||++.+++..+.++|.|.=+.. .-++.+ +|+||+-++...-+
T Consensus 6 KV~f~~--tIaIrvp~~~~y~~L~~ki~~kLkl~~e~i~LsYkde~s-~~~v~l-~d~dle~aws~~~~ 70 (80)
T cd06406 6 KVHFKY--TVAIQVARGLSYATLLQKISSKLELPAEHITLSYKSEAS-GEDVIL-SDTNMEDVWSQAKD 70 (80)
T ss_pred EEEEEE--EEEEEcCCCCCHHHHHHHHHHHhCCCchhcEEEeccCCC-CCccCc-ChHHHHHHHHhhcC
Confidence 578887 999999999999999999999999988899999954322 456777 89999999987655
No 19
>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=97.27 E-value=0.0011 Score=55.72 Aligned_cols=65 Identities=23% Similarity=0.395 Sum_probs=54.7
Q ss_pred eEeecCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEEecCCCCCceEeecChHHHHHHHhccCC
Q 003242 24 LSYDGGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKYFLPGNKQTLITICNDKDLKRMFDFHEG 91 (837)
Q Consensus 24 ~~y~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~l~~~~~~l~~~~~d~dl~~m~~~~~~ 91 (837)
+.| ||+||=++.++.-+|.+|.+||...|+++..++.++|. .||.-+|++++|+||+..+.....
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 344 56667777999999999999999999999888999994 335579999999999999886655
No 20
>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=97.15 E-value=0.0027 Score=54.14 Aligned_cols=60 Identities=15% Similarity=0.350 Sum_probs=50.8
Q ss_pred ecCceEEEEeCCCCChHHHHHHHHHHhCCCCc-ceEEEEecCCCCCceEeecChHHHHHHHhc
Q 003242 27 DGGEANAVAINPETHFGDLKLKLAELLNLEYK-SLSVKYFLPGNKQTLITICNDKDLKRMFDF 88 (837)
Q Consensus 27 ~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~-~~~~~y~l~~~~~~l~~~~~d~dl~~m~~~ 88 (837)
-+|+-.++.++.++||.+|.+|+.++|.+..+ ++++||- .|+--++++++|++|+.-+..
T Consensus 7 y~gdi~it~~d~~~s~e~L~~~v~~~c~~~~~q~ft~kw~--DEEGDp~tiSS~~EL~EA~rl 67 (83)
T cd06404 7 YNGDIMITSIDPSISLEELCNEVRDMCRFHNDQPFTLKWI--DEEGDPCTISSQMELEEAFRL 67 (83)
T ss_pred ecCcEEEEEcCCCcCHHHHHHHHHHHhCCCCCCcEEEEEE--CCCCCceeecCHHHHHHHHHH
Confidence 47899999999999999999999999987764 8999993 333447999999999977653
No 21
>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=97.12 E-value=0.0031 Score=53.59 Aligned_cols=69 Identities=22% Similarity=0.392 Sum_probs=55.5
Q ss_pred cCceEEEEeCCC-CChHHHHHHHHHHhCCCC---cceEEEEecCCCCCceEeecChHHHHHHHhccCCceeEEEEE
Q 003242 28 GGEANAVAINPE-THFGDLKLKLAELLNLEY---KSLSVKYFLPGNKQTLITICNDKDLKRMFDFHEGSVTADVFV 99 (837)
Q Consensus 28 gg~~~~~~v~~~-~~~~~~~~~~~~~~~~~~---~~~~~~y~l~~~~~~l~~~~~d~dl~~m~~~~~~~~~~~v~~ 99 (837)
||+.|.+.++.. ++|.||+..+...|+... .++.+||. .++..||+|++++||.--+...+ .-+++||+
T Consensus 8 g~DiR~~~~~~~~~t~~~L~~~v~~~F~~~~~~~~~flIKYk--D~dGDlVTIts~~dL~~A~~~~~-~~~l~~~~ 80 (81)
T cd06401 8 GDDIRRIPIHNEDITYDELLLMMQRVFRGKLGSSDDVLIKYK--DEDGDLITIFDSSDLSFAIQCSR-ILKLTLFV 80 (81)
T ss_pred CCeEEEEeccCccccHHHHHHHHHHHhccccCCcccEEEEEE--CCCCCEEEeccHHHHHHHHhcCc-ceEEEEec
Confidence 999999999985 899999999999997443 48999994 44467999999999987765553 55666654
No 22
>cd06403 PB1_Par6 The PB1 domain is an essential part of Par6 protein which in complex with Par3 and aPKC proteins is crucial for establishment of apical-basal polarity of animal cells. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants. The
Probab=96.95 E-value=0.0063 Score=51.21 Aligned_cols=72 Identities=18% Similarity=0.262 Sum_probs=62.7
Q ss_pred EeecCceEEEEeCCC--CChHHHHHHHHHHhCCCCcceEEEEecCCCCCceEeecChHHHHHHHhccCCceeEEEEEe
Q 003242 25 SYDGGEANAVAINPE--THFGDLKLKLAELLNLEYKSLSVKYFLPGNKQTLITICNDKDLKRMFDFHEGSVTADVFVI 100 (837)
Q Consensus 25 ~y~gg~~~~~~v~~~--~~~~~~~~~~~~~~~~~~~~~~~~y~l~~~~~~l~~~~~d~dl~~m~~~~~~~~~~~v~~~ 100 (837)
++-|+|.|=.+++|+ -||.||-+.|..+..+...+++++|+=| +--|++|+||+.+..-++-. -.-+||||-
T Consensus 5 SkfdaEfRRFsl~r~~~~~f~ef~~ll~~lH~l~~~~f~i~Y~D~--~gDLLPInNDdNf~kAlssa--~plLRl~iq 78 (80)
T cd06403 5 SKFDAEFRRFSLDRNKPGKFEDFYKLLEHLHHIPNVDFLIGYTDP--HGDLLPINNDDNFLKALSSA--NPLLRIFIQ 78 (80)
T ss_pred cccCCeEEEEEeccccCcCHHHHHHHHHHHhCCCCCcEEEEEeCC--CCCEecccCcHHHHHHHHcC--CCceEEEEE
Confidence 355899999999998 8999999999999998888999999988 56699999999999999844 346888874
No 23
>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=96.85 E-value=0.007 Score=52.70 Aligned_cols=68 Identities=19% Similarity=0.279 Sum_probs=53.7
Q ss_pred ceEEEEeCC--CCChHHHHHHHHHHh-CCCCcceEEEEecCCCCCceEeecChHHHHHHHhccCCceeEEEEEe
Q 003242 30 EANAVAINP--ETHFGDLKLKLAELL-NLEYKSLSVKYFLPGNKQTLITICNDKDLKRMFDFHEGSVTADVFVI 100 (837)
Q Consensus 30 ~~~~~~v~~--~~~~~~~~~~~~~~~-~~~~~~~~~~y~l~~~~~~l~~~~~d~dl~~m~~~~~~~~~~~v~~~ 100 (837)
|-|-.+++. ++||.+|..++.++| ++....+++||. .++--||+|++|++|..-+...+ -..+||||-
T Consensus 15 EIRRf~l~~~~~~s~~~L~~~V~~~f~~l~~~~ftlky~--DeeGDlvtIssdeEL~~A~~~~~-~~~~RlyI~ 85 (87)
T cd06402 15 EIRRFAIDEDVSTSYEYLVEKVAAVFPSLRGKNFQLFWK--DEEGDLVAFSSDEELVMALGSLN-DDTFRIYIK 85 (87)
T ss_pred ceEEEEecCCCCcCHHHHHHHHHHHccccCCCcEEEEEE--CCCCCEEeecCHHHHHHHHHcCC-CCcEEEEEE
Confidence 445666644 469999999999999 444568999994 44466999999999999999875 357999874
No 24
>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=96.83 E-value=0.004 Score=53.32 Aligned_cols=68 Identities=10% Similarity=0.255 Sum_probs=54.5
Q ss_pred cCceEEEEeCC--CCChHHHHHHHHHHhCCCCcceEEEEecCCCCCceEeecChHHHHHHHhccCCc-eeEEEEE
Q 003242 28 GGEANAVAINP--ETHFGDLKLKLAELLNLEYKSLSVKYFLPGNKQTLITICNDKDLKRMFDFHEGS-VTADVFV 99 (837)
Q Consensus 28 gg~~~~~~v~~--~~~~~~~~~~~~~~~~~~~~~~~~~y~l~~~~~~l~~~~~d~dl~~m~~~~~~~-~~~~v~~ 99 (837)
||++..+.++. +++|.+|.+.+.+.|+++ .+++|| |- |+.--++|+||.||+.-++-...+ ..++++|
T Consensus 8 ~~d~~rf~~~~~~~~~~~~L~~ev~~rf~l~--~f~lKY-lD-de~e~v~lssd~eLeE~~rl~~~~~~~l~~~v 78 (81)
T cd06396 8 NGESQSFLVSDSENTTWASVEAMVKVSFGLN--DIQIKY-VD-EENEEVSVNSQGEYEEALKSAVRQGNLLQMNV 78 (81)
T ss_pred CCeEEEEEecCCCCCCHHHHHHHHHHHhCCC--cceeEE-Ec-CCCCEEEEEchhhHHHHHHHHHhCCCEEEEEE
Confidence 78999999999 889999999999999988 899999 43 335578899999999777644332 2455554
No 25
>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=96.65 E-value=0.0077 Score=50.94 Aligned_cols=63 Identities=16% Similarity=0.228 Sum_probs=57.1
Q ss_pred ceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEEecCCCCCceEeecChHHHHHHHhccCCc
Q 003242 30 EANAVAINPETHFGDLKLKLAELLNLEYKSLSVKYFLPGNKQTLITICNDKDLKRMFDFHEGS 92 (837)
Q Consensus 30 ~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~l~~~~~~l~~~~~d~dl~~m~~~~~~~ 92 (837)
=|-+|.|+|+.+|++|..+|++.|.+..+..+|.|.-|+++.-|+.++.+|||+.+...-.+.
T Consensus 7 fTVai~v~~g~~y~~L~~~ls~kL~l~~~~~~LSY~~~~~~~~~v~l~~e~~me~aW~~v~~~ 69 (78)
T cd06411 7 FTVALRAPRGADVSSLRALLSQALPQQAQRGQLSYRAPGEDGHWVPISGEESLQRAWQDVADG 69 (78)
T ss_pred EEEEEEccCCCCHHHHHHHHHHHhcCChhhcEEEecCCCCCccEeecCcchHHHHHHHhccCC
Confidence 377899999999999999999999999999999999888887899999999999998866543
No 26
>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=95.78 E-value=0.057 Score=47.01 Aligned_cols=71 Identities=15% Similarity=0.296 Sum_probs=57.6
Q ss_pred ecCceEEEEeCCCCChHHHHHHHHHHhCCCC---cceEEEEecCCCCCceEeecChHHHHHHHhc--cCCceeEEEEE
Q 003242 27 DGGEANAVAINPETHFGDLKLKLAELLNLEY---KSLSVKYFLPGNKQTLITICNDKDLKRMFDF--HEGSVTADVFV 99 (837)
Q Consensus 27 ~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~---~~~~~~y~l~~~~~~l~~~~~d~dl~~m~~~--~~~~~~~~v~~ 99 (837)
-.|+++=+.+..+.++.+|++.+++.+|++. +.+.|+| |-.| .-.|++++|.||..-++. ..+..+++++|
T Consensus 8 ~~GrvhRf~~~~s~~~~~L~~~I~~Rl~~d~~~~~~~~L~Y-lDDE-gD~VllT~D~DL~e~v~iar~~g~~~v~L~v 83 (86)
T cd06409 8 PKGRVHRFRLRPSESLEELRTLISQRLGDDDFETHLYALSY-VDDE-GDIVLITSDSDLVAAVLVARSAGLKKLDLHL 83 (86)
T ss_pred CCCCEEEEEecCCCCHHHHHHHHHHHhCCccccCCcccEEE-EcCC-CCEEEEeccchHHHHHHHHHHcCCCEEEEEE
Confidence 3789999999999999999999999999987 5889999 4333 557899999999988774 34556677765
No 27
>PF06782 UPF0236: Uncharacterised protein family (UPF0236); InterPro: IPR009620 This is a group of proteins of unknown function.
Probab=94.68 E-value=0.47 Score=55.19 Aligned_cols=92 Identities=13% Similarity=0.152 Sum_probs=71.3
Q ss_pred cCChhHHHHHHHHHHHhhcCCC--cEEEEecCchhHHHHHHHhcccCceeecHHHHHHHHHhhcCCCCCccccCchHHHH
Q 003242 499 TENDDSWNWFLEELRSAVSSSR--SITFVSDKQKGLMESVLKIFENAHHGYSIYHLLDNFMKNLKGPFHGEGKGSLPVNF 576 (837)
Q Consensus 499 ~E~~es~~wfL~~lk~~~~~~~--p~~iisD~~~~l~~AI~~vfP~a~h~~C~~Hi~~N~~~~~~~~~~~e~~~~l~~~~ 576 (837)
..+.+-|.-+++.+-+...... -+++.+|+...+.+++. .||++.|.+..+|+.+.+.+.++.. ..+...+
T Consensus 235 ~~~~~~~~~v~~~i~~~Y~~~~~~~iiingDGa~WIk~~~~-~~~~~~~~LD~FHl~k~i~~~~~~~------~~~~~~~ 307 (470)
T PF06782_consen 235 ESAEEFWEEVLDYIYNHYDLDKTTKIIINGDGASWIKEGAE-FFPKAEYFLDRFHLNKKIKQALSHD------PELKEKI 307 (470)
T ss_pred cchHHHHHHHHHHHHHhcCcccceEEEEeCCCcHHHHHHHH-hhcCceEEecHHHHHHHHHHHhhhC------hHHHHHH
Confidence 5567889988888877754332 46788899999988776 9999999999999999999988642 1355666
Q ss_pred HHHHHHHHHHHHHHHHHHHHh
Q 003242 577 LAAACAARLDSFRMSAEQVKK 597 (837)
Q Consensus 577 ~~~~~a~t~~eFe~~~~~l~~ 597 (837)
+++.+.....+++..++.+..
T Consensus 308 ~~al~~~d~~~l~~~L~~~~~ 328 (470)
T PF06782_consen 308 RKALKKGDKKKLETVLDTAES 328 (470)
T ss_pred HHHHHhcCHHHHHHHHHHHHH
Confidence 677777777777777777654
No 28
>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=94.65 E-value=0.02 Score=34.59 Aligned_cols=18 Identities=28% Similarity=0.648 Sum_probs=16.3
Q ss_pred EeCCCCCCCCcCcCCCCC
Q 003242 818 VTCTKCKGIGHNKLSCKE 835 (837)
Q Consensus 818 ~~Cs~C~~~GHNk~tC~~ 835 (837)
++|-+|++.||-.+.||+
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 29
>PF13610 DDE_Tnp_IS240: DDE domain
Probab=93.70 E-value=0.031 Score=53.83 Aligned_cols=81 Identities=14% Similarity=0.136 Sum_probs=68.2
Q ss_pred CCeEEeecccccccccceEEEEEEecCCCCeEEEEEEEeccCChhHHHHHHHHHHHhhcCCCcEEEEecCchhHHHHHHH
Q 003242 459 RPLLFLDSTSLRSKYHEILLTATALDGDDCIFPVAFAIVDTENDDSWNWFLEELRSAVSSSRSITFVSDKQKGLMESVLK 538 (837)
Q Consensus 459 ~~vl~iD~T~~~~~y~~~Ll~a~g~D~~~~~~plafalv~~E~~es~~wfL~~lk~~~~~~~p~~iisD~~~~l~~AI~~ 538 (837)
++.+.+|-||.+-+-+ ..+...++|.+|+ .|.+-|...-+...=..||..+++..+ ..|..|+||+.++...|+++
T Consensus 1 ~~~w~~DEt~iki~G~-~~yl~~aiD~~~~--~l~~~ls~~Rd~~aA~~Fl~~~l~~~~-~~p~~ivtDk~~aY~~A~~~ 76 (140)
T PF13610_consen 1 GDSWHVDETYIKIKGK-WHYLWRAIDAEGN--ILDFYLSKRRDTAAAKRFLKRALKRHR-GEPRVIVTDKLPAYPAAIKE 76 (140)
T ss_pred CCEEEEeeEEEEECCE-EEEEEEeeccccc--chhhhhhhhcccccceeeccccceeec-cccceeecccCCccchhhhh
Confidence 3678999999985533 3455788999999 888999988888888999988888765 67899999999999999999
Q ss_pred hcccC
Q 003242 539 IFENA 543 (837)
Q Consensus 539 vfP~a 543 (837)
+++.-
T Consensus 77 l~~~~ 81 (140)
T PF13610_consen 77 LNPEG 81 (140)
T ss_pred ccccc
Confidence 99973
No 30
>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=93.05 E-value=0.16 Score=53.82 Aligned_cols=94 Identities=15% Similarity=0.176 Sum_probs=68.3
Q ss_pred EEeecccccccccceEEEEEEecC--CCCeEEEEEEEeccCChhHHHHHHHHH-HHhhcCCCcEEEEecCchhHHHHHHH
Q 003242 462 LFLDSTSLRSKYHEILLTATALDG--DDCIFPVAFAIVDTENDDSWNWFLEEL-RSAVSSSRSITFVSDKQKGLMESVLK 538 (837)
Q Consensus 462 l~iD~T~~~~~y~~~Ll~a~g~D~--~~~~~plafalv~~E~~es~~wfL~~l-k~~~~~~~p~~iisD~~~~l~~AI~~ 538 (837)
|+||=+.....++. +..+.+|. +++. -+.++++=+.++..-||..+ -.. ......+|++|...+..+||++
T Consensus 1 lgiDE~~~~~g~~~--y~t~~~d~~~~~~~---il~i~~~r~~~~l~~~~~~~~~~~-~~~~v~~V~~Dm~~~y~~~~~~ 74 (249)
T PF01610_consen 1 LGIDEFAFRKGHRS--YVTVVVDLDTDTGR---ILDILPGRDKETLKDFFRSLYPEE-ERKNVKVVSMDMSPPYRSAIRE 74 (249)
T ss_pred CeEeeeeeecCCcc--eeEEEEECccCCce---EEEEcCCccHHHHHHHHHHhCccc-cccceEEEEcCCCccccccccc
Confidence 45666665543332 33344444 3322 24588888899998888876 333 3356789999999999999999
Q ss_pred hcccCceeecHHHHHHHHHhhcC
Q 003242 539 IFENAHHGYSIYHLLDNFMKNLK 561 (837)
Q Consensus 539 vfP~a~h~~C~~Hi~~N~~~~~~ 561 (837)
.||+|.+..-.|||++++.+.+.
T Consensus 75 ~~P~A~iv~DrFHvvk~~~~al~ 97 (249)
T PF01610_consen 75 YFPNAQIVADRFHVVKLANRALD 97 (249)
T ss_pred cccccccccccchhhhhhhhcch
Confidence 99999999999999999887653
No 31
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=92.74 E-value=0.051 Score=39.77 Aligned_cols=19 Identities=32% Similarity=0.800 Sum_probs=16.6
Q ss_pred EeCCCCCCCCcCc--CCCCCC
Q 003242 818 VTCTKCKGIGHNK--LSCKET 836 (837)
Q Consensus 818 ~~Cs~C~~~GHNk--~tC~~~ 836 (837)
++|++|++.||.+ ++||.-
T Consensus 2 ~kC~~CG~~GH~~t~k~CP~~ 22 (40)
T PF15288_consen 2 VKCKNCGAFGHMRTNKRCPMY 22 (40)
T ss_pred ccccccccccccccCccCCCC
Confidence 5899999999998 789863
No 32
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=89.97 E-value=0.19 Score=35.03 Aligned_cols=21 Identities=24% Similarity=0.559 Sum_probs=18.7
Q ss_pred ceEeCCCCCCCCcCcCCCCCC
Q 003242 816 RTVTCTKCKGIGHNKLSCKET 836 (837)
Q Consensus 816 r~~~Cs~C~~~GHNk~tC~~~ 836 (837)
..+.|.+|++.||..+.||..
T Consensus 7 ~~Y~C~~C~~~GH~i~dCP~~ 27 (32)
T PF13696_consen 7 PGYVCHRCGQKGHWIQDCPTN 27 (32)
T ss_pred CCCEeecCCCCCccHhHCCCC
Confidence 358999999999999999974
No 33
>PRK14702 insertion element IS2 transposase InsD; Provisional
Probab=89.30 E-value=20 Score=38.42 Aligned_cols=145 Identities=17% Similarity=0.103 Sum_probs=88.3
Q ss_pred hhhhHHHHHHHhhcCCCCChhHHHHHHHHh---cCc-ccchhhhHHHHHHH-HHhhhCCHHHHHhchHHHHHHHHhhCCC
Q 003242 353 KNWLVSIIKDKLRESPHHKPKEISKSILRD---FGV-TLNYSQVYRGIEGA-REQLQGSYKEAYNQLPWFCDKLLEANPG 427 (837)
Q Consensus 353 ~~~ia~~~~~~l~~~~~~~~~~i~~~l~~~---~g~-~~sy~~~~rak~~a-~~~~~g~~~~sy~~L~~y~~~l~~~NPg 427 (837)
...+...|.+.+..++.+..+.|...|+++ .|+ .++..+++|....+ +.... +...+.
T Consensus 10 ~~~l~~~I~~~~~~~~~yG~rri~~~L~~~~~~~g~~~v~~krV~rlmr~~gL~~~~-----------------r~~~~~ 72 (262)
T PRK14702 10 DTDVLLRIHHVIGELPTYGYRRVWALLRRQAELDGMPAINAKRVYRLMRQNALLLER-----------------KPAVPP 72 (262)
T ss_pred hHHHHHHHHHHHHhCcccChHHHHHHHHhhhcccCccccCHHHHHHHHHHhCCcccc-----------------CCCCCC
Confidence 344556677776777889999999998875 377 48998888864332 11000 000000
Q ss_pred cEEEEEecCCcceeEEEEEehhhHHHHHhcCCCeEEeecccccccccceEEEEEEecCCCCeEEEEEEEecc-CChhHHH
Q 003242 428 SFIKLLIDNDKKFQRLFISFDASIHGFQNGCRPLLFLDSTSLRSKYHEILLTATALDGDDCIFPVAFAIVDT-ENDDSWN 506 (837)
Q Consensus 428 ~~~~v~~d~d~~f~~lF~a~~~si~~f~~~~~~vl~iD~T~~~~~y~~~Ll~a~g~D~~~~~~plafalv~~-E~~es~~ 506 (837)
+. . +.... |. ...-..++..|-||.....++.++.++-+|.... .+||+++... .+.+.-.
T Consensus 73 ~~------~-~~~~~-~~---------~~~pn~~W~~DiT~~~~~~g~~~Yl~~viD~~sR-~ivg~~is~~~~~~~~v~ 134 (262)
T PRK14702 73 SK------R-AHTGR-VA---------VKESNQRWCSDGFEFCCDNGERLRVTFALDCCDR-EALHWAVTTGGFNSETVQ 134 (262)
T ss_pred CC------c-CCCCc-cc---------cCCCCCEEEeeeEEEEecCCcEEEEEEEEecccc-eeeeEEeccCcCCHHHHH
Confidence 00 0 00000 10 1113468999999987654556888888887665 6889999874 5666666
Q ss_pred HHHHHHHHhh-c---CCCcEEEEecCchhH
Q 003242 507 WFLEELRSAV-S---SSRSITFVSDKQKGL 532 (837)
Q Consensus 507 wfL~~lk~~~-~---~~~p~~iisD~~~~l 532 (837)
-+|+...+.. + ...|.+|.||+...-
T Consensus 135 ~~l~~A~~~~~~~~~~~~~~iihSD~Gsqy 164 (262)
T PRK14702 135 DVMLGAVERRFGNDLPSSPVEWLTDNGSCY 164 (262)
T ss_pred HHHHHHHHHHhcccCCCCCeEEEcCCCccc
Confidence 6666544442 2 235788999987653
No 34
>COG3316 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=89.12 E-value=3.6 Score=42.11 Aligned_cols=120 Identities=17% Similarity=0.207 Sum_probs=83.4
Q ss_pred HHHHhcCcccchhhhHHHHHHHHHhhhCCHHHHHhchHHHHHHHHhhCCCcEEEEEecCCcceeEEEEEehhhHHHHHhc
Q 003242 378 SILRDFGVTLNYSQVYRGIEGAREQLQGSYKEAYNQLPWFCDKLLEANPGSFIKLLIDNDKKFQRLFISFDASIHGFQNG 457 (837)
Q Consensus 378 ~l~~~~g~~~sy~~~~rak~~a~~~~~g~~~~sy~~L~~y~~~l~~~NPg~~~~v~~d~d~~f~~lF~a~~~si~~f~~~ 457 (837)
.+..+.|+.+.+.++.|.-++.- |.+.+.+.+.++.
T Consensus 33 e~l~~rgi~v~h~Ti~rwv~k~~--------------~~~~~~~~~r~~~------------------------------ 68 (215)
T COG3316 33 EMLAERGIEVDHETIHRWVQKYG--------------PLLARRLKRRKRK------------------------------ 68 (215)
T ss_pred HHHHHcCcchhHHHHHHHHHHHh--------------HHHHHHhhhhccc------------------------------
Confidence 35567899999988887644432 2344555555543
Q ss_pred CCCeEEeecccccccccceEEEEEEecCCCCeEEEEEEEeccCChhHHHHHHHHHHHhhcCCCcEEEEecCchhHHHHHH
Q 003242 458 CRPLLFLDSTSLRSKYHEILLTATALDGDDCIFPVAFAIVDTENDDSWNWFLEELRSAVSSSRSITFVSDKQKGLMESVL 537 (837)
Q Consensus 458 ~~~vl~iD~T~~~~~y~~~Ll~a~g~D~~~~~~plafalv~~E~~es~~wfL~~lk~~~~~~~p~~iisD~~~~l~~AI~ 537 (837)
-++++-+|-||.+.+-++. +.-.++|.+| .++-+-|...-+...=.-||..+++.- ..|.+|+||+.+....|+.
T Consensus 69 ~~~~w~vDEt~ikv~gkw~-ylyrAid~~g--~~Ld~~L~~rRn~~aAk~Fl~kllk~~--g~p~v~vtDka~s~~~A~~ 143 (215)
T COG3316 69 AGDSWRVDETYIKVNGKWH-YLYRAIDADG--LTLDVWLSKRRNALAAKAFLKKLLKKH--GEPRVFVTDKAPSYTAALR 143 (215)
T ss_pred cccceeeeeeEEeeccEee-ehhhhhccCC--CeEEEEEEcccCcHHHHHHHHHHHHhc--CCCceEEecCccchHHHHH
Confidence 3567788888887543332 2234566665 456777777777777777888777775 6789999999999999999
Q ss_pred HhcccCcee
Q 003242 538 KIFENAHHG 546 (837)
Q Consensus 538 ~vfP~a~h~ 546 (837)
++-+.+.|+
T Consensus 144 ~l~~~~ehr 152 (215)
T COG3316 144 KLGSEVEHR 152 (215)
T ss_pred hcCcchhee
Confidence 998865554
No 35
>PF03106 WRKY: WRKY DNA -binding domain; InterPro: IPR003657 The WRKY domain is a 60 amino acid region that is defined by the conserved amino acid sequence WRKYGQK at its N-terminal end, together with a novel zinc-finger- like motif. The WRKY domain is found in one or two copies in a superfamily of plant transcription factors involved in the regulation of various physiological programs that are unique to plants, including pathogen defence, senescence, trichome development and the biosynthesis of secondary metabolites. The WRKY domain binds specifically to the DNA sequence motif (T)(T)TGAC(C/T), which is known as the W box. The invariant TGAC core of the W box is essential for function and WRKY binding []. Some proteins known to contain a WRKY domain include Arabidopsis thaliana ZAP1 (Zinc-dependent Activator Protein-1) and AtWRKY44/TTG2, a protein involved in trichome development and anthocyanin pigmentation; and wild oat ABF1-2, two proteins involved in the gibberelic acid-induced expression of the alpha-Amy2 gene. Structural studies indicate that this domain is a four-stranded beta-sheet with a zinc binding pocket, forming a novel zinc and DNA binding structure []. The WRKYGQK residues correspond to the most N-terminal beta-strand, which enables extensive hydrophobic interactions, contributing to the structural stability of the beta-sheet.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2AYD_A 1WJ2_A 2LEX_A.
Probab=88.71 E-value=0.86 Score=37.01 Aligned_cols=39 Identities=15% Similarity=0.195 Sum_probs=31.9
Q ss_pred cEEEEEeccCCCceEEEEEEeCCcceEEEEeecCCCccC
Q 003242 305 SRASGMCAAEGCSWSFYASWVPSERVFKIKKMNETHTCG 343 (837)
Q Consensus 305 ~r~~~~C~~~gCpwri~as~~~~~~~~~I~~~~~~H~C~ 343 (837)
-|..++|+..+|+++-...+..++....+.++.++|||.
T Consensus 21 pRsYYrCt~~~C~akK~Vqr~~~d~~~~~vtY~G~H~h~ 59 (60)
T PF03106_consen 21 PRSYYRCTHPGCPAKKQVQRSADDPNIVIVTYEGEHNHP 59 (60)
T ss_dssp EEEEEEEECTTEEEEEEEEEETTCCCEEEEEEES--SS-
T ss_pred eeEeeeccccChhheeeEEEecCCCCEEEEEEeeeeCCC
Confidence 466799999999999999988877788889999999996
No 36
>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=86.72 E-value=1.3 Score=49.69 Aligned_cols=58 Identities=10% Similarity=0.335 Sum_probs=50.9
Q ss_pred CCCCceeCCHHHHHHHHHHHHHhcceEEEEEeeC-ccEEEEEeccCCCceEEEEEEeCC
Q 003242 270 TGVGQEFKSVIEFRDALQRFSIAHRFRYKFKKNE-TSRASGMCAAEGCSWSFYASWVPS 327 (837)
Q Consensus 270 ~~vG~~F~s~ee~~~ai~~yAi~~gf~~~~~ks~-~~r~~~~C~~~gCpwri~as~~~~ 327 (837)
..-+..|+++++-+.+|+.|-...++.|..+.|- .+.|++.|....|||+|..+....
T Consensus 22 ~~~~~~f~tl~~wy~v~ndyefq~rcpiilknsh~nkhftfachlk~c~fkillsy~g~ 80 (496)
T PF04684_consen 22 SAQARKFPTLEAWYNVINDYEFQSRCPIILKNSHRNKHFTFACHLKNCPFKILLSYCGN 80 (496)
T ss_pred cccccCCCcHHHHHHHHhhhhhhhcCceeecccccccceEEEeeccCCCceeeeeeccc
Confidence 3457789999999999999999999999998775 467999999999999999987654
No 37
>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=85.62 E-value=2.7 Score=36.31 Aligned_cols=60 Identities=17% Similarity=0.224 Sum_probs=49.4
Q ss_pred cCceEEEEeCCCC----ChHHHHHHHHHHhCCCCcceEEEEecCCCCCceEeecChHHHHHHHhccCC
Q 003242 28 GGEANAVAINPET----HFGDLKLKLAELLNLEYKSLSVKYFLPGNKQTLITICNDKDLKRMFDFHEG 91 (837)
Q Consensus 28 gg~~~~~~v~~~~----~~~~~~~~~~~~~~~~~~~~~~~y~l~~~~~~l~~~~~d~dl~~m~~~~~~ 91 (837)
|-.+|=|.|..++ +|.||...+...|+ .+.+.|-|+=+..| ||-|-+|||+.=|++...+
T Consensus 12 ~~~~rdi~vee~l~~~P~~kdLl~lmr~~f~--~~dIaLNYrD~EGD--LIRllddeDv~LMV~~~r~ 75 (92)
T cd06399 12 ISTIRDIAVEEDLSSTPLLKDLLELTRREFQ--REDIALNYRDAEGD--LIRLLSDEDVALMVRQSRG 75 (92)
T ss_pred CccccceEeecccccCccHHHHHHHHHHHhc--hhheeeeeecCCCC--EEEEcchhhHHHHHHHHhc
Confidence 4567778877775 79999999999997 56899999855544 9999999999999997754
No 38
>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=84.91 E-value=1.6 Score=34.95 Aligned_cols=46 Identities=20% Similarity=0.429 Sum_probs=25.1
Q ss_pred cceEEEEEeeCccEEEEEeccC---CCceEEEEEEeCCcceEEEEeecCCCcc
Q 003242 293 HRFRYKFKKNETSRASGMCAAE---GCSWSFYASWVPSERVFKIKKMNETHTC 342 (837)
Q Consensus 293 ~gf~~~~~ks~~~r~~~~C~~~---gCpwri~as~~~~~~~~~I~~~~~~H~C 342 (837)
.|+.|...+.........|..- +|+++|... .+ ...|.....+|||
T Consensus 14 ~Gy~y~~~~~~~~~~~WrC~~~~~~~C~a~~~~~--~~--~~~~~~~~~~HnH 62 (62)
T PF04500_consen 14 DGYRYYFNKRNDGKTYWRCSRRRSHGCRARLITD--AG--DGRVVRTNGEHNH 62 (62)
T ss_dssp TTEEEEEEEE-SS-EEEEEGGGTTS----EEEEE------TTEEEE-S---SS
T ss_pred CCeEEECcCCCCCcEEEEeCCCCCCCCeEEEEEE--CC--CCEEEECCCccCC
Confidence 5788888777788899999853 899999987 22 2345555688987
No 39
>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=84.21 E-value=3.1 Score=35.42 Aligned_cols=38 Identities=11% Similarity=-0.006 Sum_probs=35.1
Q ss_pred ecCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEEe
Q 003242 27 DGGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKYF 65 (837)
Q Consensus 27 ~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~ 65 (837)
.+|.|..|.|+.++|-.+++.||.+..|++++...| |.
T Consensus 10 ~~~~t~~l~v~~~~TV~~lK~kI~~~~gip~~~QrL-~~ 47 (75)
T cd01799 10 SHTVTIWLTVRPDMTVAQLKDKVFLDYGFPPAVQRW-VI 47 (75)
T ss_pred cCCCeEEEEECCCCcHHHHHHHHHHHHCcCHHHEEE-Ec
Confidence 478999999999999999999999999999998888 64
No 40
>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=83.54 E-value=5.9 Score=36.16 Aligned_cols=76 Identities=12% Similarity=0.046 Sum_probs=57.6
Q ss_pred CCCeEEeeccccc-ccccceEEEEEEecCCCCeEEEEEEEeccCChhHHHHHHHHHHHhhcCCCcEEEEecCchhHHH
Q 003242 458 CRPLLFLDSTSLR-SKYHEILLTATALDGDDCIFPVAFAIVDTENDDSWNWFLEELRSAVSSSRSITFVSDKQKGLME 534 (837)
Q Consensus 458 ~~~vl~iD~T~~~-~~y~~~Ll~a~g~D~~~~~~plafalv~~E~~es~~wfL~~lk~~~~~~~p~~iisD~~~~l~~ 534 (837)
-...+.+|.++.. ...++.....+.+|..-. +.+++.+-..++.+.+..+|+......+...|.+|++|+..+..+
T Consensus 5 p~~~~~~D~~~~~~~~~~~~~~~~~~iD~~S~-~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~p~~i~tD~g~~f~~ 81 (120)
T PF00665_consen 5 PGERWQIDFTPMPIPDKGGRVYLLVFIDDYSR-FIYAFPVSSKETAEAALRALKRAIEKRGGRPPRVIRTDNGSEFTS 81 (120)
T ss_dssp TTTEEEEEEEEETGGCTT-CEEEEEEEETTTT-EEEEEEESSSSHHHHHHHHHHHHHHHHS-SE-SEEEEESCHHHHS
T ss_pred CCCEEEEeeEEEecCCCCccEEEEEEEECCCC-cEEEEEeecccccccccccccccccccccccceeccccccccccc
Confidence 3568999999666 345558888889997665 455777777788888888888877777766699999999998864
No 41
>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=82.42 E-value=2.4 Score=35.57 Aligned_cols=38 Identities=8% Similarity=0.151 Sum_probs=36.0
Q ss_pred cCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEEe
Q 003242 28 GGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKYF 65 (837)
Q Consensus 28 gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~ 65 (837)
||++..+.|+.++|..+|+.+|++..|++.+...|-|.
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 89999999999999999999999999999988888885
No 42
>PHA02517 putative transposase OrfB; Reviewed
Probab=82.13 E-value=14 Score=39.61 Aligned_cols=152 Identities=17% Similarity=0.115 Sum_probs=86.6
Q ss_pred hhHHHHHHHhhc-CCCCChhHHHHHHHHhcCcccchhhhHHHHHHHHHhhhCCHHHHHhchHHHHHHHHhhCCCcEEEEE
Q 003242 355 WLVSIIKDKLRE-SPHHKPKEISKSILRDFGVTLNYSQVYRGIEGAREQLQGSYKEAYNQLPWFCDKLLEANPGSFIKLL 433 (837)
Q Consensus 355 ~ia~~~~~~l~~-~~~~~~~~i~~~l~~~~g~~~sy~~~~rak~~a~~~~~g~~~~sy~~L~~y~~~l~~~NPg~~~~v~ 433 (837)
.+.+.+.+++.. .+.+..+.|...|+++ |+.++.++++|....+ |-.... . ..-.....+-. .
T Consensus 30 ~l~~~I~~i~~~~~~~~G~r~I~~~L~~~-g~~vs~~tV~Rim~~~-----gl~~~~-~------~k~~~~~~~~~---~ 93 (277)
T PHA02517 30 WLKSEILRVYDENHQVYGVRKVWRQLNRE-GIRVARCTVGRLMKEL-----GLAGVL-R------GKKVRTTISRK---A 93 (277)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHHHhc-CcccCHHHHHHHHHHc-----CCceEe-c------CCCcCCCCCCC---C
Confidence 455666666654 5788999999988765 9999999999864332 110000 0 00000000000 0
Q ss_pred ecCCcceeEEEEEehhhHHHHHhcCCCeEEeecccccccccceEEEEEEecCCCCeEEEEEEEeccCChhHHHHHHHHHH
Q 003242 434 IDNDKKFQRLFISFDASIHGFQNGCRPLLFLDSTSLRSKYHEILLTATALDGDDCIFPVAFAIVDTENDDSWNWFLEELR 513 (837)
Q Consensus 434 ~d~d~~f~~lF~a~~~si~~f~~~~~~vl~iD~T~~~~~y~~~Ll~a~g~D~~~~~~plafalv~~E~~es~~wfL~~lk 513 (837)
....+.+.+-|-+. .-..++..|.||..... +..+.++.+|...+ +++|+.+...++.+...-+|+...
T Consensus 94 ~~~~n~~~r~f~~~---------~pn~~w~~D~t~~~~~~-g~~yl~~iiD~~sr-~i~~~~~~~~~~~~~~~~~l~~a~ 162 (277)
T PHA02517 94 VAAPDRVNRQFVAT---------RPNQLWVADFTYVSTWQ-GWVYVAFIIDVFAR-RIVGWRVSSSMDTDFVLDALEQAL 162 (277)
T ss_pred CCCCCcccCCCCCC---------CCCCeEEeceeEEEeCC-CCEEEEEecccCCC-eeeecccCCCCChHHHHHHHHHHH
Confidence 00011122222111 13568999999986543 45667777776554 567888888888886665555555
Q ss_pred HhhcCCCcEEEEecCchhHH
Q 003242 514 SAVSSSRSITFVSDKQKGLM 533 (837)
Q Consensus 514 ~~~~~~~p~~iisD~~~~l~ 533 (837)
...+...+..|.||+.....
T Consensus 163 ~~~~~~~~~i~~sD~G~~y~ 182 (277)
T PHA02517 163 WARGRPGGLIHHSDKGSQYV 182 (277)
T ss_pred HhcCCCcCcEeecccccccc
Confidence 55444344677899987653
No 43
>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=81.17 E-value=3.4 Score=34.86 Aligned_cols=42 Identities=14% Similarity=0.199 Sum_probs=38.1
Q ss_pred eEeecCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEEe
Q 003242 24 LSYDGGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKYF 65 (837)
Q Consensus 24 ~~y~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~ 65 (837)
++..+|++..+.|+.+.|-.+|+++|++..|++.+...|-|.
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 467789999999999999999999999999999988888774
No 44
>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=80.44 E-value=3.2 Score=34.41 Aligned_cols=41 Identities=29% Similarity=0.513 Sum_probs=37.1
Q ss_pred eEeecCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEEe
Q 003242 24 LSYDGGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKYF 65 (837)
Q Consensus 24 ~~y~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~ 65 (837)
++| ||++.-+.|+.+.+-.+|+++|++..|++.+...|.|.
T Consensus 5 vk~-~g~~~~i~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~ 45 (71)
T cd01812 5 VKH-GGESHDLSISSQATFGDLKKMLAPVTGVEPRDQKLIFK 45 (71)
T ss_pred EEE-CCEEEEEEECCCCcHHHHHHHHHHhhCCChHHeEEeeC
Confidence 566 49999999999999999999999999999988888875
No 45
>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=80.17 E-value=4.3 Score=33.84 Aligned_cols=41 Identities=17% Similarity=0.263 Sum_probs=38.1
Q ss_pred eEeecCceEEEEeCCCCChHHHHHHHHHHhCCCC-cceEEEE
Q 003242 24 LSYDGGEANAVAINPETHFGDLKLKLAELLNLEY-KSLSVKY 64 (837)
Q Consensus 24 ~~y~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~-~~~~~~y 64 (837)
|+-.+|+.--+.|.++.+++.|+.+.++..|++. +.+.|.|
T Consensus 5 v~~~~~~~~~~~v~~~~~~~~l~~~~~~~~~i~~~~~~~l~f 46 (72)
T PF11976_consen 5 VRSQDGKEIKFKVKPTTTVSKLIEKYCEKKGIPPEESIRLIF 46 (72)
T ss_dssp EEETTSEEEEEEEETTSCCHHHHHHHHHHHTTTT-TTEEEEE
T ss_pred EEeCCCCEEEEEECCCCcHHHHHHHHHHhhCCCccceEEEEE
Confidence 5677899999999999999999999999999999 8899888
No 46
>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=79.29 E-value=4.5 Score=33.54 Aligned_cols=41 Identities=20% Similarity=0.262 Sum_probs=37.4
Q ss_pred eEeecCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEE
Q 003242 24 LSYDGGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKY 64 (837)
Q Consensus 24 ~~y~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y 64 (837)
++...|++..+.|+.+.+-.+|+++|++..|++.+...|-|
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 45678899999999999999999999999999988888888
No 47
>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=79.03 E-value=3.9 Score=34.29 Aligned_cols=43 Identities=12% Similarity=0.172 Sum_probs=39.1
Q ss_pred CeEeecCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEEe
Q 003242 23 SLSYDGGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKYF 65 (837)
Q Consensus 23 ~~~y~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~ 65 (837)
+++..+|++..+.|+.+.|-.+++++|.+..|++.....|-|.
T Consensus 2 ~vk~~~G~~~~l~v~~~~TV~~lK~~I~~~~gi~~~~q~Li~~ 44 (70)
T cd01794 2 KVRLSTGKDVKLSVSSKDTVGQLKKQLQAAEGVDPCCQRWFFS 44 (70)
T ss_pred eEEcCCCCEEEEEECCcChHHHHHHHHHHHhCCCHHHeEEEEC
Confidence 4678899999999999999999999999999999888888774
No 48
>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=78.81 E-value=3.2 Score=44.46 Aligned_cols=133 Identities=21% Similarity=0.230 Sum_probs=81.6
Q ss_pred CCCChhHHHHHHHHhcCcccchhhhHHHHHHHHHhhhCCHHHHHhchHHHHHHHHhhCCCcEEEEEecCCcceeEEEEEe
Q 003242 368 PHHKPKEISKSILRDFGVTLNYSQVYRGIEGAREQLQGSYKEAYNQLPWFCDKLLEANPGSFIKLLIDNDKKFQRLFISF 447 (837)
Q Consensus 368 ~~~~~~~i~~~l~~~~g~~~sy~~~~rak~~a~~~~~g~~~~sy~~L~~y~~~l~~~NPg~~~~v~~d~d~~f~~lF~a~ 447 (837)
-.++-..+.+.+.+. |+.+|...+.+.....-+.+.. .|. .+.+.
T Consensus 19 ~~lp~~r~~~~~~~~-G~~is~~ti~~~~~~~~~~l~~----~~~-------~l~~~----------------------- 63 (271)
T PF03050_consen 19 YHLPLYRIQQMLEDL-GITISRGTIANWIKRVAEALKP----LYE-------ALKEE----------------------- 63 (271)
T ss_pred CCCCHHHHhhhhhcc-ceeeccchhHhHhhhhhhhhhh----hhh-------hhhhh-----------------------
Confidence 445556666666666 9999999888775554433221 122 11111
Q ss_pred hhhHHHHHhcCCCeEEeeccccc----ccccc-eEEEEEEecCCCCeEEEEEEEeccCChhHHHHHHHHHHHhhcCCCcE
Q 003242 448 DASIHGFQNGCRPLLFLDSTSLR----SKYHE-ILLTATALDGDDCIFPVAFAIVDTENDDSWNWFLEELRSAVSSSRSI 522 (837)
Q Consensus 448 ~~si~~f~~~~~~vl~iD~T~~~----~~y~~-~Ll~a~g~D~~~~~~plafalv~~E~~es~~wfL~~lk~~~~~~~p~ 522 (837)
.. -.+++.+|-|..+ ++.+. -+-++++-+ .+.|.+.++=+.+...-+|.. -.-
T Consensus 64 -------~~-~~~~~~~DET~~~vl~~~~g~~~~~Wv~~~~~------~v~f~~~~sR~~~~~~~~L~~--------~~G 121 (271)
T PF03050_consen 64 -------LR-SSPVVHADETGWRVLDKGKGKKGYLWVFVSPE------VVLFFYAPSRSSKVIKEFLGD--------FSG 121 (271)
T ss_pred -------cc-ccceeccCCceEEEeccccccceEEEeeeccc------eeeeeecccccccchhhhhcc--------cce
Confidence 11 3578888888777 44332 233333322 555666666555555555433 224
Q ss_pred EEEecCchhHHHHHHHhcccCceeecHHHHHHHHHhhcCC
Q 003242 523 TFVSDKQKGLMESVLKIFENAHHGYSIYHLLDNFMKNLKG 562 (837)
Q Consensus 523 ~iisD~~~~l~~AI~~vfP~a~h~~C~~Hi~~N~~~~~~~ 562 (837)
+++||+-.+-.. +..+.|+.|+.|+.|.+.+-...
T Consensus 122 ilvsD~y~~Y~~-----~~~~~hq~C~AH~~R~~~~~~~~ 156 (271)
T PF03050_consen 122 ILVSDGYSAYNK-----LAGITHQLCWAHLRRDFQDAAES 156 (271)
T ss_pred eeeccccccccc-----ccccccccccccccccccccccc
Confidence 899999988754 33889999999999999887654
No 49
>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=78.66 E-value=4.3 Score=33.77 Aligned_cols=42 Identities=21% Similarity=0.317 Sum_probs=38.2
Q ss_pred eEeecCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEEe
Q 003242 24 LSYDGGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKYF 65 (837)
Q Consensus 24 ~~y~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~ 65 (837)
++..+|++..+.|+.+.|..+++++|++..|++.+...|-|.
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 456789999999999999999999999999999998888775
No 50
>PF14560 Ubiquitin_2: Ubiquitin-like domain; PDB: 1WJN_A 2KJ6_A 2KJR_A 1V6E_A 1T0Y_A.
Probab=78.51 E-value=4 Score=35.66 Aligned_cols=45 Identities=11% Similarity=0.151 Sum_probs=34.5
Q ss_pred EEeCCCCChHHHHHHHHHHhCCCCcceEEEEecCCCCCceEeecC
Q 003242 34 VAINPETHFGDLKLKLAELLNLEYKSLSVKYFLPGNKQTLITICN 78 (837)
Q Consensus 34 ~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~l~~~~~~l~~~~~ 78 (837)
+.++.+|+.+||+.||...+|++++.+.|.|.=..++..+..+.+
T Consensus 18 kr~~~~~Tv~eLK~kl~~~~Gi~~~~m~L~l~~~~~~~~~~~~~d 62 (87)
T PF14560_consen 18 KRFPKSITVSELKQKLEKLTGIPPSDMRLQLKSDKDDSKIEELDD 62 (87)
T ss_dssp EEEETTSBHHHHHHHHHHHHTS-TTTEEEEEE-TSSSSEEEESSG
T ss_pred EEcCCCCCHHHHHHHHHHHhCCCcccEEEEEEecCCCccccccCC
Confidence 679999999999999999999999999998842233355555533
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=77.45 E-value=5.3 Score=30.73 Aligned_cols=47 Identities=21% Similarity=0.145 Sum_probs=39.0
Q ss_pred eEeecCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEEecCCCC
Q 003242 24 LSYDGGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKYFLPGNK 70 (837)
Q Consensus 24 ~~y~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~l~~~~ 70 (837)
+.+.||.+..+.++.+++..+|++++++.++...+.+.|-|.-+..+
T Consensus 2 v~~~~~~~~~~~~~~~~tv~~l~~~i~~~~~~~~~~~~l~~~~~~~~ 48 (69)
T cd00196 2 VKLNDGKTVELLVPSGTTVADLKEKLAKKLGLPPEQQRLLVNGKILP 48 (69)
T ss_pred eEecCCCEEEEEcCCCCcHHHHHHHHHHHHCcChHHeEEEECCeECC
Confidence 34558999999999999999999999999998888888877654433
No 52
>cd01803 Ubiquitin Ubiquitin. Ubiquitin (includes Ubq/RPL40e and Ubq/RPS27a fusions as well as homopolymeric multiubiquitin protein chains)
Probab=77.25 E-value=4.9 Score=33.73 Aligned_cols=41 Identities=10% Similarity=0.225 Sum_probs=37.2
Q ss_pred eEeecCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEE
Q 003242 24 LSYDGGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKY 64 (837)
Q Consensus 24 ~~y~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y 64 (837)
++..+|++..+.|+.+.|-.+|+.+|++..+++.+.+.|.|
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 45667999999999999999999999999999988888887
No 53
>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=76.20 E-value=3.6 Score=33.26 Aligned_cols=38 Identities=16% Similarity=0.174 Sum_probs=30.4
Q ss_pred cEEEEEecc-CCCceEEEEEEeCCcceEEEEeecCCCcc
Q 003242 305 SRASGMCAA-EGCSWSFYASWVPSERVFKIKKMNETHTC 342 (837)
Q Consensus 305 ~r~~~~C~~-~gCpwri~as~~~~~~~~~I~~~~~~H~C 342 (837)
-|...+|+. .||+++=.+.+..++....+.++.++|||
T Consensus 21 pRsYYrCt~~~~C~a~K~Vq~~~~d~~~~~vtY~g~H~h 59 (59)
T smart00774 21 PRSYYRCTYSQGCPAKKQVQRSDDDPSVVEVTYEGEHTH 59 (59)
T ss_pred cceEEeccccCCCCCcccEEEECCCCCEEEEEEeeEeCC
Confidence 356689998 89999877777765556677789999998
No 54
>PF13565 HTH_32: Homeodomain-like domain
Probab=76.16 E-value=4.2 Score=34.33 Aligned_cols=41 Identities=29% Similarity=0.469 Sum_probs=34.5
Q ss_pred hhHHHHHHHhhcCCCCChhHHHHHHHHhcCccc--chhhhHHH
Q 003242 355 WLVSIIKDKLRESPHHKPKEISKSILRDFGVTL--NYSQVYRG 395 (837)
Q Consensus 355 ~ia~~~~~~l~~~~~~~~~~i~~~l~~~~g~~~--sy~~~~ra 395 (837)
.+...+.+.+..+|.+++.+|...|.+++|+.+ |++++||.
T Consensus 34 e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~~~S~~tv~R~ 76 (77)
T PF13565_consen 34 EQRERIIALIEEHPRWTPREIAEYLEEEFGISVRVSRSTVYRI 76 (77)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCCccHhHHHHh
Confidence 344567777788899999999999999999876 99999974
No 55
>PRK09409 IS2 transposase TnpB; Reviewed
Probab=75.73 E-value=63 Score=35.31 Aligned_cols=143 Identities=17% Similarity=0.111 Sum_probs=86.7
Q ss_pred hhHHHHHHHhhcCCCCChhHHHHHHHHhc---Cc-ccchhhhHHHHHHH-HHhhhCCHHHHHhchHHHHHHHHhhCCCcE
Q 003242 355 WLVSIIKDKLRESPHHKPKEISKSILRDF---GV-TLNYSQVYRGIEGA-REQLQGSYKEAYNQLPWFCDKLLEANPGSF 429 (837)
Q Consensus 355 ~ia~~~~~~l~~~~~~~~~~i~~~l~~~~---g~-~~sy~~~~rak~~a-~~~~~g~~~~sy~~L~~y~~~l~~~NPg~~ 429 (837)
.+...|.++....+.+..+.|...|+++. |+ .++..+++|..+.+ +.... ....+.+.
T Consensus 51 ~l~~~I~~i~~~~~~yG~Rri~~~L~~~g~~~g~~~v~~k~V~RlMr~~Gl~~~~-----------------~~~~~~~~ 113 (301)
T PRK09409 51 DVLLRIHHVIGELPTYGYRRVWALLRRQAELDGMPAINAKRVYRIMRQNALLLER-----------------KPAVPPSK 113 (301)
T ss_pred HHHHHHHHHHHhCccCCHHHHHHHHHhhhcccCccccCHHHHHHHHHHcCCcccc-----------------cCCCCCCC
Confidence 45556676666678899999999887752 66 58888888764332 10000 00000000
Q ss_pred EEEEecCCcceeEEEEEehhhHHHHHhcCCCeEEeecccccccccceEEEEEEecCCCCeEEEEEEEecc-CChhHHHHH
Q 003242 430 IKLLIDNDKKFQRLFISFDASIHGFQNGCRPLLFLDSTSLRSKYHEILLTATALDGDDCIFPVAFAIVDT-ENDDSWNWF 508 (837)
Q Consensus 430 ~~v~~d~d~~f~~lF~a~~~si~~f~~~~~~vl~iD~T~~~~~y~~~Ll~a~g~D~~~~~~plafalv~~-E~~es~~wf 508 (837)
...... |. ...-..++..|-||....-++.++.++-+|.... .+||+++... .+.+.-.-+
T Consensus 114 -------~~~~~~-~~---------~~~pN~~W~tDiT~~~~~~g~~~Yl~~ViD~~sR-~ivg~~~s~~~~~~~~v~~~ 175 (301)
T PRK09409 114 -------RAHTGR-VA---------VKESNQRWCSDGFEFCCDNGERLRVTFALDCCDR-EALHWAVTTGGFNSETVQDV 175 (301)
T ss_pred -------CCCCCC-cC---------CCCCCCEEEeeeEEEEeCCCCEEEEEEEeecccc-eEEEEEeccCCCCHHHHHHH
Confidence 000000 10 1114569999999986554556888888887776 6889999876 576666666
Q ss_pred HHHHHHh-hc---CCCcEEEEecCchhH
Q 003242 509 LEELRSA-VS---SSRSITFVSDKQKGL 532 (837)
Q Consensus 509 L~~lk~~-~~---~~~p~~iisD~~~~l 532 (837)
|+..... .+ ...|.+|-||+....
T Consensus 176 l~~a~~~~~~~~~~~~~~iihSDrGsqy 203 (301)
T PRK09409 176 MLGAVERRFGNDLPSSPVEWLTDNGSCY 203 (301)
T ss_pred HHHHHHHHhccCCCCCCcEEecCCCccc
Confidence 6644333 33 224678899987653
No 56
>PF04937 DUF659: Protein of unknown function (DUF 659); InterPro: IPR007021 These are transposase-like proteins with no known function.
Probab=75.39 E-value=42 Score=32.80 Aligned_cols=63 Identities=10% Similarity=0.175 Sum_probs=50.4
Q ss_pred CChhHHHHHHHHHHHhhcCCCcEEEEecCchhHHHHHH---HhcccCceeecHHHHHHHHHhhcCC
Q 003242 500 ENDDSWNWFLEELRSAVSSSRSITFVSDKQKGLMESVL---KIFENAHHGYSIYHLLDNFMKNLKG 562 (837)
Q Consensus 500 E~~es~~wfL~~lk~~~~~~~p~~iisD~~~~l~~AI~---~vfP~a~h~~C~~Hi~~N~~~~~~~ 562 (837)
.+.+...-+|+...+.+|..+..-||||....+.+|-+ +-+|.....-|.-|-+.-+.+.+..
T Consensus 73 ~~a~~l~~ll~~vIeeVG~~nVvqVVTDn~~~~~~a~~~L~~k~p~ifw~~CaaH~inLmledi~k 138 (153)
T PF04937_consen 73 KTAEYLFELLDEVIEEVGEENVVQVVTDNASNMKKAGKLLMEKYPHIFWTPCAAHCINLMLEDIGK 138 (153)
T ss_pred ccHHHHHHHHHHHHHHhhhhhhhHHhccCchhHHHHHHHHHhcCCCEEEechHHHHHHHHHHHHhc
Confidence 46667777777777778877878899999999888854 4489999999999998888877653
No 57
>PTZ00044 ubiquitin; Provisional
Probab=74.47 E-value=6.9 Score=32.99 Aligned_cols=42 Identities=17% Similarity=0.340 Sum_probs=37.9
Q ss_pred eEeecCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEEe
Q 003242 24 LSYDGGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKYF 65 (837)
Q Consensus 24 ~~y~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~ 65 (837)
++-..|++..+.|+.+.|=.+++++|++..|++.+...|-|.
T Consensus 5 vk~~~G~~~~l~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~ 46 (76)
T PTZ00044 5 IKTLTGKKQSFNFEPDNTVQQVKMALQEKEGIDVKQIRLIYS 46 (76)
T ss_pred EEeCCCCEEEEEECCCCcHHHHHHHHHHHHCCCHHHeEEEEC
Confidence 355689999999999999999999999999999998888884
No 58
>smart00343 ZnF_C2HC zinc finger.
Probab=73.89 E-value=1.6 Score=28.85 Aligned_cols=17 Identities=29% Similarity=0.724 Sum_probs=15.3
Q ss_pred eCCCCCCCCcCcCCCCC
Q 003242 819 TCTKCKGIGHNKLSCKE 835 (837)
Q Consensus 819 ~Cs~C~~~GHNk~tC~~ 835 (837)
.|.+|++.||..+.|+.
T Consensus 1 ~C~~CG~~GH~~~~C~~ 17 (26)
T smart00343 1 KCYNCGKEGHIARDCPK 17 (26)
T ss_pred CCccCCCCCcchhhCCc
Confidence 48999999999999983
No 59
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=72.81 E-value=1.4 Score=34.23 Aligned_cols=19 Identities=32% Similarity=0.761 Sum_probs=17.1
Q ss_pred eEeCCCCCCCCcCcCCCCC
Q 003242 817 TVTCTKCKGIGHNKLSCKE 835 (837)
Q Consensus 817 ~~~Cs~C~~~GHNk~tC~~ 835 (837)
...|.+|+..||..+.||.
T Consensus 31 p~~C~~C~~~gH~~~~C~k 49 (49)
T PF14392_consen 31 PRFCFHCGRIGHSDKECPK 49 (49)
T ss_pred ChhhcCCCCcCcCHhHcCC
Confidence 5689999999999999983
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=71.46 E-value=7.4 Score=33.03 Aligned_cols=39 Identities=15% Similarity=0.158 Sum_probs=36.3
Q ss_pred ecCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEEe
Q 003242 27 DGGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKYF 65 (837)
Q Consensus 27 ~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~ 65 (837)
.+|++..+.|+.++|-.+|+++|.+..+++.+...|.|.
T Consensus 5 l~g~~~~l~v~~~~TV~~lK~~i~~~~gip~~~q~L~~~ 43 (76)
T cd01800 5 LNGQMLNFTLQLSDPVSVLKVKIHEETGMPAGKQKLQYE 43 (76)
T ss_pred cCCeEEEEEECCCCcHHHHHHHHHHHHCCCHHHEEEEEC
Confidence 479999999999999999999999999999998888885
No 61
>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=70.94 E-value=10 Score=31.72 Aligned_cols=42 Identities=14% Similarity=0.203 Sum_probs=36.9
Q ss_pred eEeecCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEEe
Q 003242 24 LSYDGGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKYF 65 (837)
Q Consensus 24 ~~y~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~ 65 (837)
++-.+|++..+.|+.+.+-++|+.+|++..+++.+.+.|-|.
T Consensus 5 v~~~~g~~~~~~v~~~~tv~~lK~~i~~~~g~~~~~qrL~~~ 46 (76)
T cd01806 5 VKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYS 46 (76)
T ss_pred EEeCCCCEEEEEECCCCCHHHHHHHHhHhhCCChhhEEEEEC
Confidence 344578888899999999999999999999999998888874
No 62
>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=69.16 E-value=7.8 Score=32.02 Aligned_cols=39 Identities=15% Similarity=0.124 Sum_probs=27.7
Q ss_pred ecCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEEe
Q 003242 27 DGGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKYF 65 (837)
Q Consensus 27 ~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~ 65 (837)
-+|++.-|.|.++++..+...+.|+.++++.+...|+|+
T Consensus 4 ~~~rr~~vkvtp~~~l~~VL~eac~k~~l~~~~~~L~h~ 42 (65)
T PF11470_consen 4 YNFRRFKVKVTPNTTLNQVLEEACKKFGLDPSSYDLKHN 42 (65)
T ss_dssp TTS-EEEE---TTSBHHHHHHHHHHHTT--GGG-EEEET
T ss_pred cCCcEEEEEECCCCCHHHHHHHHHHHcCCCccceEEEEC
Confidence 367888899999999999999999999999986666663
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=68.86 E-value=12 Score=31.55 Aligned_cols=42 Identities=14% Similarity=0.195 Sum_probs=37.1
Q ss_pred eEeecCceEEEEeCCCCChHHHHHHHHHHhCC--CCcceEEEEe
Q 003242 24 LSYDGGEANAVAINPETHFGDLKLKLAELLNL--EYKSLSVKYF 65 (837)
Q Consensus 24 ~~y~gg~~~~~~v~~~~~~~~~~~~~~~~~~~--~~~~~~~~y~ 65 (837)
++..+|++..+.|+.+.|-.+|+.+|++..++ +.+...|-|.
T Consensus 5 vk~~~g~~~~l~v~~~~TV~~lK~~i~~~~~i~~~~~~q~L~~~ 48 (77)
T cd01805 5 FKTLKQQTFPIEVDPDDTVAELKEKIEEEKGCDYPPEQQKLIYS 48 (77)
T ss_pred EEeCCCCEEEEEECCCCcHHHHHHHHHHhhCCCCChhHeEEEEC
Confidence 56789999999999999999999999999998 7777777763
No 64
>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=68.41 E-value=10 Score=33.20 Aligned_cols=45 Identities=13% Similarity=0.090 Sum_probs=40.3
Q ss_pred CCCeEeecCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEEe
Q 003242 21 DGSLSYDGGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKYF 65 (837)
Q Consensus 21 ~~~~~y~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~ 65 (837)
.-.++..-|.+..+.|.++.+++.++.++++..|++.+.+.|-|.
T Consensus 13 ~I~v~~~~g~~~~~~v~~~~~l~~l~~~y~~~~gi~~~~~rf~f~ 57 (87)
T cd01763 13 NLKVKGQDGNEVFFKIKRSTPLKKLMEAYCQRQGLSMNSVRFLFD 57 (87)
T ss_pred EEEEECCCCCEEEEEEcCCCHHHHHHHHHHHHhCCCccceEEEEC
Confidence 345677789999999999999999999999999999999999984
No 65
>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=68.31 E-value=13 Score=30.23 Aligned_cols=41 Identities=17% Similarity=0.249 Sum_probs=35.6
Q ss_pred EeecCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEEe
Q 003242 25 SYDGGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKYF 65 (837)
Q Consensus 25 ~y~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~ 65 (837)
+..+|.+..+.++.+++..+|+.+|++.++++.+.+.|.|.
T Consensus 3 ~~~~~~~~~~~~~~~~ti~~lK~~i~~~~~~~~~~~~l~~~ 43 (69)
T cd01769 3 KTLTGKTFELEVSPDDTVAELKAKIAAKEGVPPEQQRLIYA 43 (69)
T ss_pred EccCCCEEEEEECCCChHHHHHHHHHHHHCcChHHEEEEEC
Confidence 44567788889999999999999999999999888888774
No 66
>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=67.59 E-value=11 Score=31.71 Aligned_cols=42 Identities=10% Similarity=0.188 Sum_probs=37.5
Q ss_pred eEeecCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEEe
Q 003242 24 LSYDGGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKYF 65 (837)
Q Consensus 24 ~~y~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~ 65 (837)
++...|++..+.|+.+.|-.+++++|++..|++.+...|-|.
T Consensus 3 vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~gi~~~~q~L~~~ 44 (74)
T cd01810 3 VRNDKGRSSIYEVQLTQTVATLKQQVSQRERVQADQFWLSFE 44 (74)
T ss_pred EECCCCCEEEEEECCcChHHHHHHHHHHHhCCCHHHeEEEEC
Confidence 466789999999999999999999999999998888888763
No 67
>COG5431 Uncharacterized metal-binding protein [Function unknown]
Probab=66.98 E-value=9.8 Score=34.02 Aligned_cols=29 Identities=28% Similarity=0.632 Sum_probs=22.0
Q ss_pred CceeEeecCCcccccCccc----ccC-CccchHHHH
Q 003242 709 DSTHVVDMNKRDCSCLVWK----ATG-LPCHHAIAV 739 (837)
Q Consensus 709 ~~~~~V~l~~~~CSC~~~~----~~G-iPC~Halav 739 (837)
++-|+++.+ -|||..|- +.| -||.|++.+
T Consensus 42 ~rdYIl~~g--fCSCp~~~~svvl~Gk~~C~Hi~gl 75 (117)
T COG5431 42 ERDYILEGG--FCSCPDFLGSVVLKGKSPCAHIIGL 75 (117)
T ss_pred ccceEEEcC--cccCHHHHhHhhhcCcccchhhhhe
Confidence 456888877 89999886 333 579999874
No 68
>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=66.27 E-value=13 Score=32.27 Aligned_cols=47 Identities=17% Similarity=0.280 Sum_probs=34.6
Q ss_pred EEeCCCCChHHHHHHHHHHhCCCCcceEEEEecCCCCCceEeecChHH
Q 003242 34 VAINPETHFGDLKLKLAELLNLEYKSLSVKYFLPGNKQTLITICNDKD 81 (837)
Q Consensus 34 ~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~l~~~~~~l~~~~~d~d 81 (837)
..++.+|+.++|+.||...+|++++.+.|.|. .+++..+..+.+|+.
T Consensus 17 kr~~~~~Tv~~lK~kl~~~~G~~~~~mrL~l~-~~~~~~~~~l~~d~~ 63 (84)
T cd01789 17 KKYSRGLTIAELKKKLELVVGTPASSMRLQLF-DGDDKLVSKLDDDDA 63 (84)
T ss_pred EecCCCCcHHHHHHHHHHHHCCCccceEEEEE-cCCCCeEeecCCCcc
Confidence 44899999999999999999999999999763 333333333444443
No 69
>smart00213 UBQ Ubiquitin homologues. Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression
Probab=66.05 E-value=14 Score=29.45 Aligned_cols=41 Identities=20% Similarity=0.283 Sum_probs=34.3
Q ss_pred eEeecCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEEe
Q 003242 24 LSYDGGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKYF 65 (837)
Q Consensus 24 ~~y~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~ 65 (837)
++..+ .+..+.|+.+.+-.+|+.+|++.++++.+.+.|.|.
T Consensus 5 vk~~~-~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~~~L~~~ 45 (64)
T smart00213 5 VKTLD-GTITLEVKPSDTVSELKEKIAELTGIPVEQQRLIYK 45 (64)
T ss_pred EEECC-ceEEEEECCCCcHHHHHHHHHHHHCCCHHHEEEEEC
Confidence 34455 577899999999999999999999998887777764
No 70
>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=64.13 E-value=15 Score=31.29 Aligned_cols=49 Identities=22% Similarity=0.426 Sum_probs=39.0
Q ss_pred CCCChHHHHHHHHHHhCCCCcceEEEEecCCCCCceEeecChHHHHHHHhcc
Q 003242 38 PETHFGDLKLKLAELLNLEYKSLSVKYFLPGNKQTLITICNDKDLKRMFDFH 89 (837)
Q Consensus 38 ~~~~~~~~~~~~~~~~~~~~~~~~~~y~l~~~~~~l~~~~~d~dl~~m~~~~ 89 (837)
..++|.|+..-|...+. +...-.|.| ..|+--=|+|.+||.|+.|+...
T Consensus 21 ~~L~F~DvL~~I~~vlp-~aT~tAFeY--EDE~gDRITVRSDeEm~AMlsyy 69 (91)
T cd06395 21 PQLLFRDVLDVIGQVLP-EATTTAFEY--EDEDGDRITVRSDEEMKAMLSYY 69 (91)
T ss_pred ccccHHHHHHHHHHhcc-cccccceee--ccccCCeeEecchHHHHHHHHHH
Confidence 56899999999999995 223456777 56666679999999999999844
No 71
>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=62.53 E-value=17 Score=30.57 Aligned_cols=40 Identities=10% Similarity=0.194 Sum_probs=36.2
Q ss_pred eecCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEEe
Q 003242 26 YDGGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKYF 65 (837)
Q Consensus 26 y~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~ 65 (837)
-.|+++..+.|+.+.+-.+++.+|++..|++.+...|-|.
T Consensus 5 vk~~~~~~l~v~~~~tV~~lK~~i~~~~gip~~~q~Li~~ 44 (74)
T cd01793 5 VRAQNTHTLEVTGQETVSDIKAHVAGLEGIDVEDQVLLLA 44 (74)
T ss_pred EECCCEEEEEECCcCcHHHHHHHHHhhhCCCHHHEEEEEC
Confidence 3467899999999999999999999999999998888885
No 72
>COG5179 TAF1 Transcription initiation factor TFIID, subunit TAF1 [Transcription]
Probab=60.62 E-value=5.2 Score=46.34 Aligned_cols=24 Identities=33% Similarity=0.681 Sum_probs=18.6
Q ss_pred CccceEeCCCCCCCCcCc--CCCCCC
Q 003242 813 IEHRTVTCTKCKGIGHNK--LSCKET 836 (837)
Q Consensus 813 ~~kr~~~Cs~C~~~GHNk--~tC~~~ 836 (837)
+...+++|++|||.||=+ +.||.-
T Consensus 933 RK~Ttr~C~nCGQvGHmkTNK~CP~f 958 (968)
T COG5179 933 RKNTTRTCGNCGQVGHMKTNKACPKF 958 (968)
T ss_pred CCCcceecccccccccccccccCccc
Confidence 334689999999999966 468853
No 73
>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=60.19 E-value=20 Score=30.31 Aligned_cols=37 Identities=22% Similarity=0.163 Sum_probs=34.8
Q ss_pred cCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEE
Q 003242 28 GGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKY 64 (837)
Q Consensus 28 gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y 64 (837)
+|++.-+.|+.+.+..+|+++|++..+++++..+|=|
T Consensus 8 ~g~~~~v~v~~~~Tv~~lK~~i~~~tgvp~~~QKLi~ 44 (74)
T cd01813 8 GGQEYSVTTLSEDTVLDLKQFIKTLTGVLPERQKLLG 44 (74)
T ss_pred CCEEEEEEECCCCCHHHHHHHHHHHHCCCHHHEEEEe
Confidence 6788889999999999999999999999999999988
No 74
>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=59.57 E-value=19 Score=32.69 Aligned_cols=42 Identities=12% Similarity=0.129 Sum_probs=38.2
Q ss_pred eEeecCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEEe
Q 003242 24 LSYDGGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKYF 65 (837)
Q Consensus 24 ~~y~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~ 65 (837)
++-.+|++..+.|+.+.|=.+|+++|++..|++.+...|-|.
T Consensus 32 Vk~l~G~~~~leV~~~~TV~~lK~kI~~~~gip~~~QrLi~~ 73 (103)
T cd01802 32 IETLTGTCFELRVSPFETVISVKAKIQRLEGIPVAQQHLIWN 73 (103)
T ss_pred EEcCCCCEEEEEeCCCCcHHHHHHHHHHHhCCChHHEEEEEC
Confidence 356689999999999999999999999999999988899885
No 75
>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=56.79 E-value=4.8 Score=22.29 Aligned_cols=9 Identities=22% Similarity=0.243 Sum_probs=3.4
Q ss_pred CCCCCCccc
Q 003242 798 RTPTTHQKR 806 (837)
Q Consensus 798 r~~GRPKk~ 806 (837)
|++|||++.
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 76
>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=53.54 E-value=30 Score=29.52 Aligned_cols=41 Identities=15% Similarity=0.240 Sum_probs=34.9
Q ss_pred EeecCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEEe
Q 003242 25 SYDGGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKYF 65 (837)
Q Consensus 25 ~y~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~ 65 (837)
+-..|++..+.|+.+.|-.||+.+|++..++..+...|-|.
T Consensus 7 k~~~G~~~~l~v~~~~TV~~LK~~I~~~~~~~~~~qrL~~~ 47 (78)
T cd01804 7 HSTTGTRFDLSVPPDETVEGLKKRISQRLKVPKERLALLHR 47 (78)
T ss_pred EECCCCEEEEEECCcCHHHHHHHHHHHHhCCChHHEEEEEC
Confidence 34468889999999999999999999999988877777664
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=51.74 E-value=35 Score=27.90 Aligned_cols=39 Identities=23% Similarity=0.359 Sum_probs=36.0
Q ss_pred ecCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEEe
Q 003242 27 DGGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKYF 65 (837)
Q Consensus 27 ~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~ 65 (837)
..|.+.-+.|+.+.+-.+|+.+|++..+++++.+.|-|.
T Consensus 3 ~~g~~~~~~v~~~~tV~~lK~~i~~~~~~~~~~~~L~~~ 41 (69)
T PF00240_consen 3 LSGKTFTLEVDPDDTVADLKQKIAEETGIPPEQQRLIYN 41 (69)
T ss_dssp TTSEEEEEEEETTSBHHHHHHHHHHHHTSTGGGEEEEET
T ss_pred CCCcEEEEEECCCCCHHHhhhhcccccccccccceeeee
Confidence 468899999999999999999999999999999988883
No 78
>PF14847 Ras_bdg_2: Ras-binding domain of Byr2; PDB: 1I35_A 1K8R_B.
Probab=51.37 E-value=47 Score=30.30 Aligned_cols=80 Identities=11% Similarity=0.172 Sum_probs=50.4
Q ss_pred eEeecCceEEEEeCCCCChHHHHHHHHHHhCCCCcce-EEEEecCC-C-CCceEeecChHHHHHHHhccCCceeEEEEE-
Q 003242 24 LSYDGGEANAVAINPETHFGDLKLKLAELLNLEYKSL-SVKYFLPG-N-KQTLITICNDKDLKRMFDFHEGSVTADVFV- 99 (837)
Q Consensus 24 ~~y~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~-~~~y~l~~-~-~~~l~~~~~d~dl~~m~~~~~~~~~~~v~~- 99 (837)
.-+.+|.||.|-|..=-+-.|.+.|+.++||+....- =--|.|-+ + ++.-+-.=+|.+|..+....+...+-|+.+
T Consensus 5 ~I~~dG~tk~VNV~~c~~a~eI~~rvLKKfg~~~~~~~~~~~v~d~~~~~~~~~~~LsD~EL~~IC~s~~r~er~Rlilr 84 (105)
T PF14847_consen 5 FILEDGSTKTVNVSGCFNAQEIKRRVLKKFGLPEHPRNYCFYVLDGESPDPSNCRPLSDVELVTICHSPDRPERNRLILR 84 (105)
T ss_dssp EEETTTEEEEEE--S--HHHHHHHHHHHHHTSS--CCCEEEEEE-S-----SSEEEE-SSHHHHHHHTT--SSS--EEE-
T ss_pred EECCCCcEEEEEECCCCCHHHHHHHHHHHcCCccccccceEEEecccccccccceECcHHHHHHHHcCCCCccccceEEE
Confidence 4578999999999999999999999999999876211 12344444 2 244444456788999999999999999999
Q ss_pred -eccC
Q 003242 100 -IGTS 103 (837)
Q Consensus 100 -~~~~ 103 (837)
++..
T Consensus 85 k~~~~ 89 (105)
T PF14847_consen 85 KVHKG 89 (105)
T ss_dssp -EESS
T ss_pred ecCCC
Confidence 6655
No 79
>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=44.12 E-value=13 Score=24.62 Aligned_cols=13 Identities=15% Similarity=0.207 Sum_probs=9.6
Q ss_pred CCCCCCCcccccc
Q 003242 797 TRTPTTHQKRRRK 809 (837)
Q Consensus 797 ~r~~GRPKk~R~~ 809 (837)
.|++|||+|....
T Consensus 1 kRkRGRPrK~~~~ 13 (26)
T smart00384 1 KRKRGRPRKAPKD 13 (26)
T ss_pred CCCCCCCCCCCCc
Confidence 3689999887643
No 80
>COG4279 Uncharacterized conserved protein [Function unknown]
Probab=42.80 E-value=11 Score=39.13 Aligned_cols=23 Identities=39% Similarity=0.810 Sum_probs=19.3
Q ss_pred cccccCcccccCCccchHHHHHHhcC
Q 003242 719 RDCSCLVWKATGLPCHHAIAVFNSTG 744 (837)
Q Consensus 719 ~~CSC~~~~~~GiPC~Halav~~~~~ 744 (837)
..|||..|. .||.|+-||....+
T Consensus 125 ~dCSCPD~a---nPCKHi~AvyY~la 147 (266)
T COG4279 125 TDCSCPDYA---NPCKHIAAVYYLLA 147 (266)
T ss_pred cccCCCCcc---cchHHHHHHHHHHH
Confidence 479999887 69999999987654
No 81
>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=41.96 E-value=47 Score=28.36 Aligned_cols=41 Identities=24% Similarity=0.337 Sum_probs=34.4
Q ss_pred EeecCce-EEE-EeCCCCChHHHHHHHHHHhCCCCcceEEEEe
Q 003242 25 SYDGGEA-NAV-AINPETHFGDLKLKLAELLNLEYKSLSVKYF 65 (837)
Q Consensus 25 ~y~gg~~-~~~-~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~ 65 (837)
+-..|++ ..+ .|+.+.|-++|+++|++..|++.+...|-|.
T Consensus 6 k~~~G~~~~~l~~v~~~~TV~~lK~~i~~~~gi~~~~QrLi~~ 48 (78)
T cd01797 6 RTMDGKETRTVDSLSRLTKVEELREKIQELFNVEPECQRLFYR 48 (78)
T ss_pred EcCCCCEEEEeeccCCcCcHHHHHHHHHHHhCCCHHHeEEEeC
Confidence 4456776 457 4899999999999999999999998889885
No 82
>PRK09335 30S ribosomal protein S26e; Provisional
Probab=40.82 E-value=22 Score=31.50 Aligned_cols=27 Identities=15% Similarity=0.363 Sum_probs=18.3
Q ss_pred CCCCCCCCCCcccccccCCCccceEeCCCCCC
Q 003242 794 PSSTRTPTTHQKRRRKILGIEHRTVTCTKCKG 825 (837)
Q Consensus 794 P~~~r~~GRPKk~R~~~~~~~kr~~~Cs~C~~ 825 (837)
|.++|..||-|+.|- ..+.++|++|+.
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 456677787776542 224689999986
No 83
>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=39.50 E-value=60 Score=27.39 Aligned_cols=38 Identities=26% Similarity=0.348 Sum_probs=34.7
Q ss_pred cCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEEe
Q 003242 28 GGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKYF 65 (837)
Q Consensus 28 gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~ 65 (837)
.|.+..+.|+.+.|-.||+.+|++..+++++...|-|.
T Consensus 10 ~Gk~~~~~v~~~~TV~~LK~~I~~~~~~~~~~qrLi~~ 47 (73)
T cd01791 10 LGKKVRVKCNPDDTIGDLKKLIAAQTGTRPEKIVLKKW 47 (73)
T ss_pred CCCEEEEEeCCCCcHHHHHHHHHHHhCCChHHEEEEeC
Confidence 47888889999999999999999999999998888886
No 84
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=37.80 E-value=17 Score=27.29 Aligned_cols=19 Identities=37% Similarity=0.809 Sum_probs=16.8
Q ss_pred eEeCCCCCCCCcCcCCCCC
Q 003242 817 TVTCTKCKGIGHNKLSCKE 835 (837)
Q Consensus 817 ~~~Cs~C~~~GHNk~tC~~ 835 (837)
...|.+|++.||-..-||+
T Consensus 4 ~~~CqkC~~~GH~tyeC~~ 22 (42)
T PF13917_consen 4 RVRCQKCGQKGHWTYECPN 22 (42)
T ss_pred CCcCcccCCCCcchhhCCC
Confidence 3589999999999999993
No 85
>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=36.46 E-value=70 Score=26.48 Aligned_cols=36 Identities=11% Similarity=0.254 Sum_probs=31.2
Q ss_pred cCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEE
Q 003242 28 GGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKY 64 (837)
Q Consensus 28 gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y 64 (837)
.|.+ .+.|+.+.|=.+|+.++++..++..+...+-|
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 4554 78999999999999999999998888888776
No 86
>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=36.09 E-value=62 Score=27.59 Aligned_cols=38 Identities=16% Similarity=0.232 Sum_probs=33.3
Q ss_pred EeecCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEE
Q 003242 25 SYDGGEANAVAINPETHFGDLKLKLAELLNLEYKSLSV 62 (837)
Q Consensus 25 ~y~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~ 62 (837)
+-.+|++-.+.|+.+.|=.||+.++++..+++.+...|
T Consensus 8 k~~~G~~~~~~v~~~~TV~~lK~~I~~~~~i~~~~qrL 45 (80)
T cd01792 8 KMLGGNEFLVSLRDSMTVSELKQQIAQKIGVPAFQQRL 45 (80)
T ss_pred EeCCCCEEEEEcCCCCcHHHHHHHHHHHhCCCHHHEEE
Confidence 44568898899999999999999999999988887776
No 87
>PLN00186 ribosomal protein S26; Provisional
Probab=34.90 E-value=30 Score=31.38 Aligned_cols=27 Identities=15% Similarity=0.437 Sum_probs=18.1
Q ss_pred CCCCCCCCCCcccccccCCCccceEeCCCCCC
Q 003242 794 PSSTRTPTTHQKRRRKILGIEHRTVTCTKCKG 825 (837)
Q Consensus 794 P~~~r~~GRPKk~R~~~~~~~kr~~~Cs~C~~ 825 (837)
|.++|..||-|+.|- .-+.++|++|+.
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 456667777775542 224689999986
No 88
>PTZ00172 40S ribosomal protein S26; Provisional
Probab=34.46 E-value=31 Score=31.29 Aligned_cols=27 Identities=22% Similarity=0.463 Sum_probs=18.3
Q ss_pred CCCCCCCCCCcccccccCCCccceEeCCCCCC
Q 003242 794 PSSTRTPTTHQKRRRKILGIEHRTVTCTKCKG 825 (837)
Q Consensus 794 P~~~r~~GRPKk~R~~~~~~~kr~~~Cs~C~~ 825 (837)
|.++|..||-|+.|- .-+.++|.+|+.
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 456677787776542 235689999986
No 89
>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=32.31 E-value=1.1e+02 Score=29.23 Aligned_cols=69 Identities=12% Similarity=0.116 Sum_probs=41.5
Q ss_pred CeEEeecccccccc--------------cceEEEEEEecCC-CCeEEEEEEEeccCChhHHHHHHHHHHHhhcCCCcEEE
Q 003242 460 PLLFLDSTSLRSKY--------------HEILLTATALDGD-DCIFPVAFAIVDTENDDSWNWFLEELRSAVSSSRSITF 524 (837)
Q Consensus 460 ~vl~iD~T~~~~~y--------------~~~Ll~a~g~D~~-~~~~plafalv~~E~~es~~wfL~~lk~~~~~~~p~~i 524 (837)
.+|-+|-||..++- .....++++++-+ +..--+...++.+.+.++..-+++.... +..+|
T Consensus 4 G~VEiDEty~~~~~~~~~~~~~~~gr~~~~k~~V~~~ver~~~~~~~~~~~~v~~~~~~tl~~~i~~~i~-----~gs~i 78 (151)
T PF12762_consen 4 GIVEIDETYFGGRKNKKPRRKGKRGRGSKNKVPVFGAVERNDGGTGRVFMFVVPDRSAETLKPIIQEHIE-----PGSTI 78 (151)
T ss_pred CEEEeCcCEECCcccccccCCCCCCCcCCCCcEEEEEEeecccCCceEEEEeecccccchhHHHHHHhhh-----cccee
Confidence 36777777775332 2234445555544 4344444556677888887776654332 34679
Q ss_pred EecCchhHH
Q 003242 525 VSDKQKGLM 533 (837)
Q Consensus 525 isD~~~~l~ 533 (837)
+||+.++-.
T Consensus 79 ~TD~~~aY~ 87 (151)
T PF12762_consen 79 ITDGWRAYN 87 (151)
T ss_pred eecchhhcC
Confidence 999988764
No 90
>PHA00689 hypothetical protein
Probab=30.54 E-value=27 Score=26.69 Aligned_cols=14 Identities=50% Similarity=1.030 Sum_probs=11.3
Q ss_pred ccceEeCCCCCCCC
Q 003242 814 EHRTVTCTKCKGIG 827 (837)
Q Consensus 814 ~kr~~~Cs~C~~~G 827 (837)
..|..+|.+|++.|
T Consensus 14 epravtckrcgktg 27 (62)
T PHA00689 14 EPRAVTCKRCGKTG 27 (62)
T ss_pred CcceeehhhccccC
Confidence 35788999999876
No 91
>PF14201 DUF4318: Domain of unknown function (DUF4318)
Probab=30.45 E-value=71 Score=27.19 Aligned_cols=29 Identities=17% Similarity=0.372 Sum_probs=25.6
Q ss_pred eeCCHHHHHHHHHHHHHhcceEEEEEeeC
Q 003242 275 EFKSVIEFRDALQRFSIAHRFRYKFKKNE 303 (837)
Q Consensus 275 ~F~s~ee~~~ai~~yAi~~gf~~~~~ks~ 303 (837)
.|+|.+++..+|..|+.+++-.+.+.+.+
T Consensus 13 ~yPs~e~i~~aIE~YC~~~~~~l~Fisr~ 41 (74)
T PF14201_consen 13 KYPSKEEICEAIEKYCIKNGESLEFISRD 41 (74)
T ss_pred CCCCHHHHHHHHHHHHHHcCCceEEEecC
Confidence 48999999999999999999999886543
No 92
>PF13592 HTH_33: Winged helix-turn helix
Probab=29.76 E-value=59 Score=26.18 Aligned_cols=28 Identities=39% Similarity=0.447 Sum_probs=24.1
Q ss_pred CCCChhHHHHHHHHhcCcccchhhhHHH
Q 003242 368 PHHKPKEISKSILRDFGVTLNYSQVYRG 395 (837)
Q Consensus 368 ~~~~~~~i~~~l~~~~g~~~sy~~~~ra 395 (837)
..++.++|...|.++||+.++.+.+|+.
T Consensus 3 ~~wt~~~i~~~I~~~fgv~ys~~~v~~l 30 (60)
T PF13592_consen 3 GRWTLKEIAAYIEEEFGVKYSPSGVYRL 30 (60)
T ss_pred CcccHHHHHHHHHHHHCCEEcHHHHHHH
Confidence 3467889999999999999999888875
No 93
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=29.19 E-value=28 Score=35.00 Aligned_cols=16 Identities=31% Similarity=0.777 Sum_probs=13.5
Q ss_pred EeCCCCCCCCcCcCCC
Q 003242 818 VTCTKCKGIGHNKLSC 833 (837)
Q Consensus 818 ~~Cs~C~~~GHNk~tC 833 (837)
..|.+|++.||-++-|
T Consensus 98 ~~C~~Cg~~GH~~~dC 113 (190)
T COG5082 98 KKCYNCGETGHLSRDC 113 (190)
T ss_pred cccccccccCcccccc
Confidence 5788888888888888
No 94
>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=28.90 E-value=21 Score=28.41 Aligned_cols=20 Identities=30% Similarity=0.710 Sum_probs=8.8
Q ss_pred ceEeCCCCCCCC---cCcCCCCC
Q 003242 816 RTVTCTKCKGIG---HNKLSCKE 835 (837)
Q Consensus 816 r~~~Cs~C~~~G---HNk~tC~~ 835 (837)
|.+.|..|+..| |..+=||.
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 568999999876 88888885
No 95
>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=27.50 E-value=62 Score=27.89 Aligned_cols=29 Identities=31% Similarity=0.527 Sum_probs=19.8
Q ss_pred EEeCCCCChHHHHHHHHHHhCCCCcceEE
Q 003242 34 VAINPETHFGDLKLKLAELLNLEYKSLSV 62 (837)
Q Consensus 34 ~~v~~~~~~~~~~~~~~~~~~~~~~~~~~ 62 (837)
|.|+.+-++++|..||.+.++++..++++
T Consensus 18 ie~~~~~t~~~L~~kI~~~l~~~~~~~~L 46 (80)
T PF11543_consen 18 IEVSPSSTLSDLKEKISEQLSIPDSSQSL 46 (80)
T ss_dssp EEE-TTSBHHHHHHHHHHHS---TTT---
T ss_pred EEcCCcccHHHHHHHHHHHcCCCCcceEE
Confidence 47899999999999999999988766554
No 96
>KOG3206 consensus Alpha-tubulin folding cofactor B [Posttranslational modification, protein turnover, chaperones]
Probab=27.31 E-value=73 Score=32.38 Aligned_cols=61 Identities=16% Similarity=0.245 Sum_probs=44.8
Q ss_pred eCCCCChHHHHHHHHHHhCCCCcceEEEEecCCCCCceEeecChHHHH-HHHhccCCceeEEEEEec
Q 003242 36 INPETHFGDLKLKLAELLNLEYKSLSVKYFLPGNKQTLITICNDKDLK-RMFDFHEGSVTADVFVIG 101 (837)
Q Consensus 36 v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~l~~~~~~l~~~~~d~dl~-~m~~~~~~~~~~~v~~~~ 101 (837)
.+++||..+|+.||.-.+|...++ ++-||-..+|.+++.-+++|-. +-+.-.+ -+||-|+-
T Consensus 19 ~~~~ltl~q~K~KLe~~~G~~~~~--M~l~l~~~~d~~~~~lsn~d~~lg~~~~~D---g~rihviD 80 (234)
T KOG3206|consen 19 LSNSLTLAQFKDKLELLTGTEAES--MELELYDGDDKKVSALSNEDADLGFYKVED---GLRIHVID 80 (234)
T ss_pred cCCcCcHHHHHhhhhhhhCCCccc--eEEEEEcCCCceeeeccCCcccccccCCCC---ceEEEEEe
Confidence 478999999999999999988775 5557878878888887777643 4333333 36666555
No 97
>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=26.91 E-value=1.2e+02 Score=25.73 Aligned_cols=36 Identities=19% Similarity=0.240 Sum_probs=31.4
Q ss_pred CceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEE
Q 003242 29 GEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKY 64 (837)
Q Consensus 29 g~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y 64 (837)
|.+-.+.|..++|-.|..+++|++-|+++..+.+.-
T Consensus 9 g~~t~V~vrpg~ti~d~L~~~c~kr~l~~~~~~v~~ 44 (72)
T cd01760 9 GQRTVVPVRPGMSVRDVLAKACKKRGLNPECCDVFL 44 (72)
T ss_pred CCeEEEEECCCCCHHHHHHHHHHHcCCCHHHEEEEE
Confidence 677889999999999999999999999987665544
No 98
>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=26.63 E-value=1.7e+02 Score=28.65 Aligned_cols=64 Identities=17% Similarity=0.314 Sum_probs=42.3
Q ss_pred eEEeecccccccccceEEEEEEecCCCCeEEEEEEEeccCChhHHHHHHHHHHHhhcC------CCcEEEEecCchhHHH
Q 003242 461 LLFLDSTSLRSKYHEILLTATALDGDDCIFPVAFAIVDTENDDSWNWFLEELRSAVSS------SRSITFVSDKQKGLME 534 (837)
Q Consensus 461 vl~iD~T~~~~~y~~~Ll~a~g~D~~~~~~plafalv~~E~~es~~wfL~~lk~~~~~------~~p~~iisD~~~~l~~ 534 (837)
|+|.||-+.++.|+- |-+-..+..+.|.-+-+.+.+.+.. .-|-.|+.|+.++-.+
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 566777777777664 2233334558888888888888754 2488999999999999
Q ss_pred HHHHhccc
Q 003242 535 SVLKIFEN 542 (837)
Q Consensus 535 AI~~vfP~ 542 (837)
|+.+++-.
T Consensus 94 aa~~~l~~ 101 (155)
T PF08459_consen 94 AAKEVLKE 101 (155)
T ss_dssp HHHHHHHC
T ss_pred HHHHHHHH
Confidence 99888653
No 99
>PF02196 RBD: Raf-like Ras-binding domain; InterPro: IPR003116 This is the Ras-binding domain found in proteins related to Ras. It is found in association with the PE-bind and pkinase domains.; GO: 0005057 receptor signaling protein activity, 0007165 signal transduction; PDB: 1RFA_A 1C1Y_B 3KUD_B 1GUA_B 3KUC_B 2L05_A 3NY5_D 1RRB_A 1WFY_A 1WXM_A.
Probab=25.29 E-value=1.2e+02 Score=25.52 Aligned_cols=34 Identities=21% Similarity=0.251 Sum_probs=26.5
Q ss_pred CceEEEEeCCCCChHHHHHHHHHHhCCCCcceEE
Q 003242 29 GEANAVAINPETHFGDLKLKLAELLNLEYKSLSV 62 (837)
Q Consensus 29 g~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~ 62 (837)
|.+=.+.|..++|-.|+.++++++.|++...+.+
T Consensus 10 ~q~t~V~vrpg~ti~d~L~~~~~kr~L~~~~~~V 43 (71)
T PF02196_consen 10 GQRTVVQVRPGMTIRDALSKACKKRGLNPECCDV 43 (71)
T ss_dssp TEEEEEEE-TTSBHHHHHHHHHHTTT--CCCEEE
T ss_pred CCEEEEEEcCCCCHHHHHHHHHHHcCCCHHHEEE
Confidence 5677889999999999999999999999875433
No 100
>KOG3606 consensus Cell polarity protein PAR6 [Signal transduction mechanisms]
Probab=25.22 E-value=87 Score=33.14 Aligned_cols=85 Identities=14% Similarity=0.216 Sum_probs=64.5
Q ss_pred cCceEEEEeCCC--CChHHHHHHHHHHhCCCCcceEEEEecCCCCCceEeecChHHHHHHHhccCCceeEEEEEeccCCC
Q 003242 28 GGEANAVAINPE--THFGDLKLKLAELLNLEYKSLSVKYFLPGNKQTLITICNDKDLKRMFDFHEGSVTADVFVIGTSGF 105 (837)
Q Consensus 28 gg~~~~~~v~~~--~~~~~~~~~~~~~~~~~~~~~~~~y~l~~~~~~l~~~~~d~dl~~m~~~~~~~~~~~v~~~~~~~~ 105 (837)
|-|-|=.+++|+ -+|.||-+-+...-.|..-.+++-|.=+. --|.+|.||+-|.+-++.-. .-+||||-.+.+.
T Consensus 26 daEfRRfsl~r~~~~~f~~F~~Lv~~~H~i~nvdvllgY~d~h--gDLLPinNDDn~~ka~~sa~--PlLR~~iQkr~ea 101 (358)
T KOG3606|consen 26 DAEFRRFSLPRHSASSFDEFYSLVEHLHHIPNVDVLLGYADTH--GDLLPINNDDNLHKALSSAR--PLLRLLIQKREEA 101 (358)
T ss_pred cchhheecccccCcccHHHHHHHHHHHhcCCCceEEEEEecCC--CceecccCchhHHHHhhccC--chhhhhhhhhhhh
Confidence 455666777776 49999998888887888778999997666 45999999999999988654 3599999888766
Q ss_pred cccchhhhccc
Q 003242 106 DREAFAIETGR 116 (837)
Q Consensus 106 ~~~~~~~~~~~ 116 (837)
|.+-++...+.
T Consensus 102 ~~~~~~fgt~s 112 (358)
T KOG3606|consen 102 DEEKYGFGTDS 112 (358)
T ss_pred hhhccCccccc
Confidence 65544444443
No 101
>COG4715 Uncharacterized conserved protein [Function unknown]
Probab=25.08 E-value=1.6e+02 Score=34.70 Aligned_cols=44 Identities=23% Similarity=0.362 Sum_probs=30.1
Q ss_pred ceEEEEcCcee--Eeec----CCcccccCcccccCCccchHHHHHHhcCCCc
Q 003242 702 TLFEVQGDSTH--VVDM----NKRDCSCLVWKATGLPCHHAIAVFNSTGRNV 747 (837)
Q Consensus 702 ~~feV~~~~~~--~V~l----~~~~CSC~~~~~~GiPC~Halav~~~~~~~~ 747 (837)
-..+|.+.+.| .|.+ -+..|||.. ...| =|.|++||+...-..|
T Consensus 50 v~A~V~Gs~~y~v~vtL~~~~~ss~CTCP~-~~~g-aCKH~VAvvl~~~~~p 99 (587)
T COG4715 50 VRAVVEGSRRYRVRVTLEGGALSSICTCPY-GGSG-ACKHVVAVVLEYLDDP 99 (587)
T ss_pred EEEEEeccceeeEEEEeecCCcCceeeCCC-CCCc-chHHHHHHHHHHhhcc
Confidence 35667776654 4455 457899997 5555 4999999988765443
No 102
>smart00455 RBD Raf-like Ras-binding domain.
Probab=24.40 E-value=1.4e+02 Score=25.03 Aligned_cols=36 Identities=17% Similarity=0.180 Sum_probs=30.8
Q ss_pred CceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEE
Q 003242 29 GEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKY 64 (837)
Q Consensus 29 g~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y 64 (837)
|.+-.+.|..+++-.|...+++++.|++...+.+.-
T Consensus 9 ~~~~~V~vrpg~tl~e~L~~~~~kr~l~~~~~~v~~ 44 (70)
T smart00455 9 NQRTVVKVRPGKTVRDALAKALKKRGLNPECCVVRL 44 (70)
T ss_pred CCEEEEEECCCCCHHHHHHHHHHHcCCCHHHEEEEE
Confidence 567788999999999999999999999887665543
No 103
>PF13276 HTH_21: HTH-like domain
Probab=23.55 E-value=1.3e+02 Score=23.94 Aligned_cols=41 Identities=27% Similarity=0.383 Sum_probs=33.6
Q ss_pred hHHHHHHHhhcC-CCCChhHHHHHHHHhcCcccchhhhHHHH
Q 003242 356 LVSIIKDKLRES-PHHKPKEISKSILRDFGVTLNYSQVYRGI 396 (837)
Q Consensus 356 ia~~~~~~l~~~-~~~~~~~i~~~l~~~~g~~~sy~~~~rak 396 (837)
+...+++.+..+ +.+..+.|...|.+++|+.+|..+++|..
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 555677776654 78899999999999999999999998864
No 104
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=23.30 E-value=75 Score=25.55 Aligned_cols=34 Identities=21% Similarity=0.344 Sum_probs=20.5
Q ss_pred CCCCCCCCCCcccccccCCCccceEeCCCCCCCC
Q 003242 794 PSSTRTPTTHQKRRRKILGIEHRTVTCTKCKGIG 827 (837)
Q Consensus 794 P~~~r~~GRPKk~R~~~~~~~kr~~~Cs~C~~~G 827 (837)
|..+.++.|..++|............|+.||..-
T Consensus 4 PKrk~S~srr~~RRsh~~l~~~~l~~C~~CG~~~ 37 (57)
T PRK12286 4 PKRKTSKSRKRKRRAHFKLKAPGLVECPNCGEPK 37 (57)
T ss_pred CcCcCChhhcchhcccccccCCcceECCCCCCcc
Confidence 4445556666666655443444567899998753
No 105
>KOG1769 consensus Ubiquitin-like proteins [Posttranslational modification, protein turnover, chaperones]
Probab=22.80 E-value=1.7e+02 Score=26.27 Aligned_cols=38 Identities=21% Similarity=0.241 Sum_probs=34.7
Q ss_pred ecCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEE
Q 003242 27 DGGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKY 64 (837)
Q Consensus 27 ~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y 64 (837)
.+|.+...-|.|+..+.-||+--|+.-|++.+++.|-|
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 46788899999999999999999999999999888877
No 106
>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=22.52 E-value=55 Score=27.16 Aligned_cols=36 Identities=22% Similarity=0.473 Sum_probs=16.1
Q ss_pred HHHHhhcCCCCChhHHHHHHHHhcCcccchhhhHHHH
Q 003242 360 IKDKLRESPHHKPKEISKSILRDFGVTLNYSQVYRGI 396 (837)
Q Consensus 360 ~~~~l~~~~~~~~~~i~~~l~~~~g~~~sy~~~~rak 396 (837)
|...++.+|..+..+|...+.+. |..+|..+++|.-
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 44566788999999999999888 9999999998864
No 107
>KOG0010 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones; General function prediction only]
Probab=21.22 E-value=3.6e+02 Score=31.31 Aligned_cols=41 Identities=15% Similarity=0.139 Sum_probs=35.6
Q ss_pred eEeecCceEEEEeCCCCChHHHHHHHHHHhCCCCcceEEEEe
Q 003242 24 LSYDGGEANAVAINPETHFGDLKLKLAELLNLEYKSLSVKYF 65 (837)
Q Consensus 24 ~~y~gg~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~y~ 65 (837)
+++.++ ...+.|+++.|-.+|+.+|+..|++..+..+|-|-
T Consensus 20 Vkt~~d-k~~~~V~~~ssV~qlKE~I~~~f~a~~dqlvLIfa 60 (493)
T KOG0010|consen 20 VKTPKD-KYEVNVASDSSVLQLKELIAQRFGAPPDQLVLIYA 60 (493)
T ss_pred EecCCc-ceeEecccchHHHHHHHHHHHhcCCChhHeeeeec
Confidence 445555 77899999999999999999999999998888884
No 108
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=21.18 E-value=43 Score=33.68 Aligned_cols=19 Identities=26% Similarity=0.655 Sum_probs=17.0
Q ss_pred ceEeCCCCCCCCcCcCCCC
Q 003242 816 RTVTCTKCKGIGHNKLSCK 834 (837)
Q Consensus 816 r~~~Cs~C~~~GHNk~tC~ 834 (837)
....|-+|++.||-++-||
T Consensus 59 ~~~~C~nCg~~GH~~~DCP 77 (190)
T COG5082 59 ENPVCFNCGQNGHLRRDCP 77 (190)
T ss_pred cccccchhcccCcccccCC
Confidence 3568999999999999999
No 109
>PRK13907 rnhA ribonuclease H; Provisional
Probab=20.87 E-value=6.6e+02 Score=23.07 Aligned_cols=77 Identities=10% Similarity=0.112 Sum_probs=45.7
Q ss_pred eEEeecccccccccceEEEEEEecCCCCeEEEEE-EEeccCChhHHHHHHHHHHHhhcCC-CcEEEEecCchhHHHHHHH
Q 003242 461 LLFLDSTSLRSKYHEILLTATALDGDDCIFPVAF-AIVDTENDDSWNWFLEELRSAVSSS-RSITFVSDKQKGLMESVLK 538 (837)
Q Consensus 461 vl~iD~T~~~~~y~~~Ll~a~g~D~~~~~~plaf-alv~~E~~es~~wfL~~lk~~~~~~-~p~~iisD~~~~l~~AI~~ 538 (837)
.|.+||.+..+.-.+-.-.++ .|..+... +.+ .-..+.+..-|.-++..|+.+.... .++.|-||. +.+.+++..
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 378899998764332222222 45555432 332 2234556677888888888876433 567778886 566677766
Q ss_pred hc
Q 003242 539 IF 540 (837)
Q Consensus 539 vf 540 (837)
.+
T Consensus 80 ~~ 81 (128)
T PRK13907 80 EY 81 (128)
T ss_pred HH
Confidence 55
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=20.68 E-value=1.3e+02 Score=27.30 Aligned_cols=29 Identities=14% Similarity=0.266 Sum_probs=22.1
Q ss_pred CCceeCCHHHHHHHHHHHHHhcceEEEEEeeCc
Q 003242 272 VGQEFKSVIEFRDALQRFSIAHRFRYKFKKNET 304 (837)
Q Consensus 272 vG~~F~s~ee~~~ai~~yAi~~gf~~~~~ks~~ 304 (837)
+.+.|+|+|++. .||.++|..|.+.....
T Consensus 51 v~l~F~skE~Ai----~yaer~G~~Y~V~~p~~ 79 (101)
T PF04800_consen 51 VRLKFDSKEDAI----AYAERNGWDYEVEEPKK 79 (101)
T ss_dssp CEEEESSHHHHH----HHHHHCT-EEEEE-STT
T ss_pred eEeeeCCHHHHH----HHHHHcCCeEEEeCCCC
Confidence 889999998765 68999999998865443
No 111
>cd01817 RGS12_RBD Ubiquitin domain of RGS12 and RGS14. RGS12 (regulator of G signalling 12), and RGS14, are members of a family of GTPase-activating proteins (GAP's) specific for the G-alpha subunit, which act as key inhibitors of G-protein-mediated cell responses in eukaryotes. Their domain architecture includes tandem RBD domains as well as PDZ , PTB, and RGS, and GoLoco domains.
Probab=20.09 E-value=2.8e+02 Score=23.53 Aligned_cols=32 Identities=25% Similarity=0.413 Sum_probs=27.9
Q ss_pred CceEEEEeCCCCChHHHHHHHHHHhCCCCcce
Q 003242 29 GEANAVAINPETHFGDLKLKLAELLNLEYKSL 60 (837)
Q Consensus 29 g~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~ 60 (837)
|.+-++.+..++|-.|..+|++++-|+.....
T Consensus 9 g~~T~V~vrpG~ti~d~L~kllekRgl~~~~~ 40 (73)
T cd01817 9 GSTTVVPTRPGESIRDLLSGLCEKRGINYAAV 40 (73)
T ss_pred CCeEEEEecCCCCHHHHHHHHHHHcCCChhHE
Confidence 56778999999999999999999999887544
Done!