Query 039468
Match_columns 1282
No_of_seqs 418 out of 1820
Neff 6.1
Searched_HMMs 46136
Date Fri Mar 29 09:58:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/039468.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/039468hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03097 FHY3 Protein FAR-RED 100.0 4.1E-65 8.9E-70 634.5 46.1 476 708-1206 72-624 (846)
2 cd06410 PB1_UP2 Uncharacterize 99.8 7.1E-20 1.5E-24 174.8 11.3 90 534-624 1-96 (97)
3 PF10551 MULE: MULE transposas 99.8 9.2E-20 2E-24 173.0 8.2 90 909-1000 1-93 (93)
4 PF00872 Transposase_mut: Tran 99.8 1.2E-19 2.5E-24 214.6 4.6 226 810-1084 112-349 (381)
5 PF03108 DBD_Tnp_Mut: MuDR fam 99.6 1.4E-14 3E-19 130.1 9.2 67 707-773 1-67 (67)
6 COG3328 Transposase and inacti 99.4 3.9E-12 8.4E-17 148.9 16.3 224 810-1084 98-328 (379)
7 smart00575 ZnF_PMZ plant mutat 98.5 6.9E-08 1.5E-12 72.0 2.0 27 1163-1189 1-27 (28)
8 PF08731 AFT: Transcription fa 98.4 1.6E-06 3.4E-11 84.3 9.2 69 716-784 1-111 (111)
9 smart00666 PB1 PB1 domain. Pho 98.2 1.4E-05 2.9E-10 74.4 10.3 75 547-624 4-80 (81)
10 PF03101 FAR1: FAR1 DNA-bindin 98.1 5.4E-06 1.2E-10 78.7 6.6 61 724-785 1-90 (91)
11 PF04434 SWIM: SWIM zinc finge 97.7 3.1E-05 6.6E-10 62.6 3.1 30 1158-1187 10-39 (40)
12 cd05992 PB1 The PB1 domain is 97.5 0.00074 1.6E-08 62.6 10.1 74 548-624 4-80 (81)
13 PF00564 PB1: PB1 domain; Int 97.3 0.0017 3.6E-08 60.6 9.7 77 548-626 5-83 (84)
14 cd06407 PB1_NLP A PB1 domain i 97.0 0.0043 9.2E-08 58.4 9.6 71 553-625 8-81 (82)
15 cd06408 PB1_NoxR The PB1 domai 96.4 0.011 2.5E-07 55.8 7.4 61 549-614 7-67 (86)
16 cd06406 PB1_P67 A PB1 domain i 95.8 0.029 6.3E-07 52.3 7.1 66 548-617 6-71 (80)
17 cd06396 PB1_NBR1 The PB1 domai 95.8 0.063 1.4E-06 50.3 9.2 69 553-625 8-79 (81)
18 cd06398 PB1_Joka2 The PB1 doma 94.7 0.35 7.6E-06 46.6 10.8 75 549-626 5-88 (91)
19 cd06404 PB1_aPKC PB1 domain is 94.1 0.37 8E-06 45.3 9.3 65 551-617 6-71 (83)
20 cd06402 PB1_p62 The PB1 domain 94.0 0.37 8.1E-06 46.0 9.2 69 555-626 15-86 (87)
21 PF04684 BAF1_ABF1: BAF1 / ABF 93.5 0.55 1.2E-05 56.3 11.5 53 712-764 24-77 (496)
22 cd06403 PB1_Par6 The PB1 domai 93.2 0.66 1.4E-05 43.2 9.1 73 549-625 4-78 (80)
23 PF06782 UPF0236: Uncharacteri 92.8 3.6 7.9E-05 51.0 17.9 130 942-1084 235-377 (470)
24 PF15288 zf-CCHC_6: Zinc knuck 92.1 0.074 1.6E-06 43.1 1.3 19 1263-1281 2-22 (40)
25 cd06397 PB1_UP1 Uncharacterize 91.2 1 2.2E-05 42.1 7.8 62 553-616 8-69 (82)
26 cd06409 PB1_MUG70 The MUG70 pr 91.2 1.1 2.4E-05 42.8 8.3 71 553-625 9-84 (86)
27 PF00098 zf-CCHC: Zinc knuckle 90.7 0.17 3.6E-06 34.3 1.7 18 1263-1280 1-18 (18)
28 PF01610 DDE_Tnp_ISL3: Transpo 90.3 0.35 7.6E-06 54.3 5.0 94 905-1004 1-97 (249)
29 PF03050 DDE_Tnp_IS66: Transpo 90.1 0.74 1.6E-05 52.6 7.5 147 795-1005 5-156 (271)
30 cd06401 PB1_TFG The PB1 domain 89.6 2.1 4.5E-05 40.3 8.5 68 553-623 8-79 (81)
31 cd06405 PB1_Mekk2_3 The PB1 do 88.6 2.6 5.7E-05 38.8 8.1 67 553-625 8-77 (79)
32 cd06411 PB1_p51 The PB1 domain 88.2 1.8 3.8E-05 40.5 6.9 63 555-617 7-69 (78)
33 PF13610 DDE_Tnp_IS240: DDE do 88.1 0.14 3.1E-06 52.8 -0.2 80 903-986 2-81 (140)
34 PRK14702 insertion element IS2 86.8 42 0.0009 38.6 18.8 145 795-974 9-163 (262)
35 PF03106 WRKY: WRKY DNA -bindi 85.7 2.1 4.6E-05 38.1 5.9 44 740-783 15-59 (60)
36 PHA02517 putative transposase 84.7 5.8 0.00013 45.3 10.6 151 797-976 29-182 (277)
37 PF13696 zf-CCHC_2: Zinc knuck 77.7 1.4 2.9E-05 34.4 1.5 20 1261-1280 7-26 (32)
38 KOG3069 Peroxisomal NUDIX hydr 71.7 3.4 7.3E-05 46.1 3.2 45 476-526 32-76 (246)
39 PF04500 FLYWCH: FLYWCH zinc f 71.1 6 0.00013 34.2 4.1 46 733-782 14-62 (62)
40 PF13565 HTH_32: Homeodomain-l 70.8 7 0.00015 35.7 4.7 41 798-838 34-76 (77)
41 COG3316 Transposase and inacti 70.5 27 0.00058 38.9 9.8 120 821-989 33-152 (215)
42 cd01799 Hoil1_N Ubiquitin-like 70.3 9.4 0.0002 35.4 5.4 65 552-624 10-74 (75)
43 PF00665 rve: Integrase core d 68.7 30 0.00065 33.7 9.0 76 901-977 5-81 (120)
44 COG5179 TAF1 Transcription ini 67.2 3 6.6E-05 51.5 1.9 25 1258-1282 933-959 (968)
45 smart00774 WRKY DNA binding do 64.1 9.7 0.00021 33.9 3.9 38 745-782 21-59 (59)
46 PF14560 Ubiquitin_2: Ubiquiti 54.9 33 0.00072 32.4 6.2 48 556-603 15-62 (87)
47 smart00343 ZnF_C2HC zinc finge 52.7 6.8 0.00015 28.7 0.9 17 1264-1280 1-17 (26)
48 PF14392 zf-CCHC_4: Zinc knuck 52.6 5.7 0.00012 33.8 0.6 19 1262-1280 31-49 (49)
49 PRK09409 IS2 transposase TnpB; 50.2 2E+02 0.0044 33.7 13.0 143 798-975 51-203 (301)
50 cd01812 BAG1_N Ubiquitin-like 48.9 31 0.00068 30.8 4.8 41 549-590 5-45 (71)
51 cd00196 UBQ Ubiquitin-like pro 48.5 35 0.00075 27.7 4.8 43 549-591 2-44 (69)
52 PF11976 Rad60-SLD: Ubiquitin- 42.9 59 0.0013 29.2 5.7 42 549-590 5-47 (72)
53 cd01807 GDX_N ubiquitin-like d 42.2 46 0.001 30.3 4.9 42 549-590 5-46 (74)
54 cd06395 PB1_Map2k5 PB1 domain 42.0 53 0.0011 31.0 5.0 58 555-615 11-70 (91)
55 cd01796 DDI1_N DNA damage indu 40.7 43 0.00093 30.5 4.4 38 553-590 8-45 (71)
56 cd01809 Scythe_N Ubiquitin-lik 38.3 64 0.0014 28.7 5.1 40 550-589 6-45 (72)
57 cd01803 Ubiquitin Ubiquitin. U 38.2 55 0.0012 29.5 4.8 40 550-589 6-45 (76)
58 cd06399 PB1_P40 The PB1 domain 36.9 1.1E+02 0.0024 29.5 6.3 60 553-616 12-75 (92)
59 cd01798 parkin_N amino-termina 35.9 63 0.0014 29.1 4.7 41 550-590 4-44 (70)
60 PF04937 DUF659: Protein of un 34.5 1.2E+02 0.0027 32.1 7.2 63 943-1005 73-138 (153)
61 cd01794 DC_UbP_C dendritic cel 33.5 70 0.0015 29.2 4.6 42 548-589 2-43 (70)
62 cd01806 Nedd8 Nebb8-like ubiq 33.2 94 0.002 28.0 5.4 38 552-589 8-45 (76)
63 KOG0695 Serine/threonine prote 33.1 2.1E+02 0.0045 34.1 9.1 67 551-619 21-88 (593)
64 COG4066 Uncharacterized protei 32.9 32 0.00069 36.0 2.4 39 347-394 117-155 (165)
65 cd01800 SF3a120_C Ubiquitin-li 32.0 67 0.0015 29.6 4.3 38 553-590 6-43 (76)
66 PTZ00044 ubiquitin; Provisiona 31.9 85 0.0018 28.5 4.9 39 551-589 7-45 (76)
67 PF11470 TUG-UBL1: GLUT4 regul 31.1 67 0.0015 29.3 3.9 37 553-589 5-41 (65)
68 PF02178 AT_hook: AT hook moti 29.8 23 0.0005 22.3 0.5 9 1243-1251 2-10 (13)
69 COG5431 Uncharacterized metal- 28.9 30 0.00065 34.1 1.4 44 1153-1198 42-90 (117)
70 cd01805 RAD23_N Ubiquitin-like 28.0 1.3E+02 0.0028 27.3 5.5 41 549-589 5-47 (77)
71 cd01793 Fubi Fubi ubiquitin-li 27.6 1.2E+02 0.0026 27.6 5.2 40 551-590 5-44 (74)
72 smart00213 UBQ Ubiquitin homol 27.5 1.2E+02 0.0025 26.0 4.9 35 555-589 10-44 (64)
73 cd01769 UBL Ubiquitin-like dom 26.9 1.3E+02 0.0029 26.1 5.2 39 551-589 4-42 (69)
74 cd01789 Alp11_N Ubiquitin-like 26.8 1.5E+02 0.0033 28.0 5.7 33 558-590 16-48 (84)
75 PF12762 DDE_Tnp_IS1595: ISXO2 26.5 2.4E+02 0.0053 29.0 7.8 69 904-977 5-88 (151)
76 cd01763 Sumo Small ubiquitin-r 24.8 1.5E+02 0.0031 28.2 5.3 41 550-590 17-57 (87)
77 smart00384 AT_hook DNA binding 24.7 43 0.00093 25.1 1.2 12 1242-1253 1-12 (26)
78 PF13592 HTH_33: Winged helix- 24.3 84 0.0018 27.8 3.3 30 811-840 3-32 (60)
79 PF14201 DUF4318: Domain of un 24.2 99 0.0021 29.0 3.8 30 715-744 13-42 (74)
80 COG4279 Uncharacterized conser 24.0 36 0.00079 38.6 1.1 23 1163-1188 125-147 (266)
81 PF00240 ubiquitin: Ubiquitin 23.4 1.4E+02 0.003 26.5 4.6 37 553-589 4-40 (69)
82 PF04800 ETC_C1_NDUFA4: ETC co 23.3 1.2E+02 0.0025 30.2 4.3 31 712-746 51-81 (101)
83 PF08985 DUF1888: Domain of un 22.4 33 0.00071 34.8 0.4 77 279-372 8-97 (124)
84 cd01813 UBP_N UBP ubiquitin pr 21.9 1.3E+02 0.0029 27.7 4.2 38 553-590 8-45 (74)
85 cd01612 APG12_C Ubiquitin-like 20.8 4E+02 0.0087 25.6 7.3 61 558-623 19-79 (87)
86 cd01810 ISG15_repeat2 ISG15 ub 20.3 1.8E+02 0.0038 26.6 4.7 40 550-589 4-43 (74)
87 PRK09335 30S ribosomal protein 20.0 79 0.0017 30.9 2.3 27 1239-1270 2-28 (95)
88 PF13276 HTH_21: HTH-like doma 20.0 1.6E+02 0.0034 25.7 4.2 42 799-840 6-48 (60)
No 1
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=100.00 E-value=4.1e-65 Score=634.50 Aligned_cols=476 Identities=16% Similarity=0.215 Sum_probs=378.2
Q ss_pred CCCCCCcEECCHHHHHHHHHHHHHHcCceEEEeecCCe-------EEEEeee----------------------------
Q 039468 708 CITGVHQRFNNVHDFRDALYKYSVAHGFTYCFKKNEGL-------RVTAKCK---------------------------- 752 (1282)
Q Consensus 708 ~il~VGm~F~S~eEfk~AI~~YAi~~gF~~rvkKSdk~-------Rv~~~C~---------------------------- 752 (1282)
..+.+||+|.|.+|++++|+.||...||.+|+.++.++ ..+++|+
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 45789999999999999999999999999988544321 2245664
Q ss_pred ------cCCCceEEEEEEeCCCCeEEEEeecCCCcCCCCCCCCccchhhhhhHHHHHHHHhhcCCCCChhhHHHHHHHhc
Q 039468 753 ------AEGCPWRIHASRVPTTQLFQIKTMNGMHTCKAGPDPTTRSKASRKLLASIVKEKLLEAPKCKPKEIAEEIRRDF 826 (1282)
Q Consensus 753 ------~~GCpWrI~As~~~~s~~w~Ik~~~~eHnC~~~~~~~~hr~aSsr~IA~~ik~~ir~~p~~~p~~I~~~l~~~~ 826 (1282)
++||+++|.+.+. ..+.|+|+.+..+|||++.+..... ..+++......+ .+....++. .++.+.
T Consensus 152 ~rR~~tRtGC~A~m~Vk~~-~~gkW~V~~fv~eHNH~L~p~~~~~-~~~r~~~~~~~~-~~~~~~~v~------~~~~d~ 222 (846)
T PLN03097 152 GRRSCAKTDCKASMHVKRR-PDGKWVIHSFVKEHNHELLPAQAVS-EQTRKMYAAMAR-QFAEYKNVV------GLKNDS 222 (846)
T ss_pred ccccccCCCCceEEEEEEc-CCCeEEEEEEecCCCCCCCCccccc-hhhhhhHHHHHh-hhhcccccc------ccchhh
Confidence 3479999999875 4468999999999999998654211 111111111100 010000000 000000
Q ss_pred CcccChHhHHHhhHhhhccCCCChhhhhhcHHHHHHHHHhhCCCcEEEEccccCccceeeeecchhhHHHHHhcCCCeee
Q 039468 827 GIELGYVKAWRALENARGESQVSYKDSYNQLPWLVDKILETNPGSVVTLSTREDLSFHHLFVALHASLYGFQNGCRPLIF 906 (1282)
Q Consensus 827 G~~iSy~q~~Rak~ka~e~i~G~~~esy~~L~~yl~~l~e~NPGs~~~v~~ded~~F~rlF~a~~~si~gf~~gcrpVI~ 906 (1282)
.....+.|.+.+ -.| ..+.|..|++++++.||+|+|++++|++++++++|||++.++..|.+ |+|||.
T Consensus 223 -----~~~~~~~r~~~~--~~g----D~~~ll~yf~~~q~~nP~Ffy~~qlDe~~~l~niFWaD~~sr~~Y~~-FGDvV~ 290 (846)
T PLN03097 223 -----KSSFDKGRNLGL--EAG----DTKILLDFFTQMQNMNSNFFYAVDLGEDQRLKNLFWVDAKSRHDYGN-FSDVVS 290 (846)
T ss_pred -----cchhhHHHhhhc--ccc----hHHHHHHHHHHHHhhCCCceEEEEEccCCCeeeEEeccHHHHHHHHh-cCCEEE
Confidence 001111122211 123 34679999999999999999999999999999999999999999998 999999
Q ss_pred ecccccccccCcceeeeeeecCCCCeEEEEEEEeccCCchhHHHHHHHHHHhhcCCceEEEEecCcchHHHHHHHHhhcc
Q 039468 907 LDSFPIKSKYQSSLLTATALDGNDEIFPVAFGVVDAVSDDNWHWFLLQLKSALSTCQSITFVTDRLGQLRASILSVFENS 986 (1282)
Q Consensus 907 iD~TyltnkY~g~Ll~avGvD~n~~~~pvAfAvV~~Et~esw~WfLe~Lk~~m~~~~p~vIISD~~~gL~~AI~eVFP~a 986 (1282)
+|+||++|+|++||+.++|+|+|+|++++|+||+.+|+.++|.|+|++|+++|++..|.+||||++.+|.+||++|||++
T Consensus 291 fDTTY~tN~y~~Pfa~FvGvNhH~qtvlfGcaLl~dEt~eSf~WLf~tfl~aM~gk~P~tIiTDqd~am~~AI~~VfP~t 370 (846)
T PLN03097 291 FDTTYVRNKYKMPLALFVGVNQHYQFMLLGCALISDESAATYSWLMQTWLRAMGGQAPKVIITDQDKAMKSVISEVFPNA 370 (846)
T ss_pred EeceeeccccCcEEEEEEEecCCCCeEEEEEEEcccCchhhHHHHHHHHHHHhCCCCCceEEecCCHHHHHHHHHHCCCc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ceeccchhhhHHHHhhccCCccHHHHHHHHHHHHHHhhcc-cHHHHHHHHHHHh-hcchhhhHHHhhc--Ccchhhhhhc
Q 039468 987 YYCYCLHHLTEELKRDLKGSYTEEVVSVIVAHLYDAAQAG-TLDEFSKFIDSIK-SVSSEAFDWILRS--EPENWANALF 1062 (1282)
Q Consensus 987 ~H~~C~~HI~~N~~k~lk~~~~~e~k~~~~~~f~~~a~A~-t~eeFe~~~e~L~-~~~pea~~wL~~~--~~ekWa~Ayf 1062 (1282)
.|++|+|||++|+.+++...+.. .+.|...|..|++.+ +++||+..|.+|. +++.+..+||..+ .|++||++|+
T Consensus 371 ~Hr~C~wHI~~~~~e~L~~~~~~--~~~f~~~f~~cv~~s~t~eEFE~~W~~mi~ky~L~~n~WL~~LY~~RekWapaY~ 448 (846)
T PLN03097 371 HHCFFLWHILGKVSENLGQVIKQ--HENFMAKFEKCIYRSWTEEEFGKRWWKILDRFELKEDEWMQSLYEDRKQWVPTYM 448 (846)
T ss_pred eehhhHHHHHHHHHHHhhHHhhh--hhHHHHHHHHHHhCCCCHHHHHHHHHHHHHhhcccccHHHHHHHHhHhhhhHHHh
Confidence 99999999999999999765432 357888999988765 9999999998876 6678899999998 9999999999
Q ss_pred cCCCc-CcCCcchhhhHHHHHcc--CCCCChhhHHHHHHHHHHHHHHHhh-----------------hhhhhhhccCChh
Q 039468 1063 KGSRH-NQMTSHIAESFYCWVGE--LPELPIVQIISTICRKIMELMYSRR-----------------MDSNQWLTKLTPS 1122 (1282)
Q Consensus 1063 ~g~r~-g~mTTN~sESfNa~LK~--~R~lpI~~lle~Ir~klm~~~~~rr-----------------~~s~k~~~~lTP~ 1122 (1282)
++.++ ++.||+++||+|+.+++ .+..+|..|++.+-.-+..+..+.. ...++++..|||.
T Consensus 449 k~~F~agm~sTqRSES~Ns~fk~yv~~~tsL~~Fv~qye~~l~~~~ekE~~aD~~s~~~~P~l~t~~piEkQAs~iYT~~ 528 (846)
T PLN03097 449 RDAFLAGMSTVQRSESINAFFDKYVHKKTTVQEFVKQYETILQDRYEEEAKADSDTWNKQPALKSPSPLEKSVSGVYTHA 528 (846)
T ss_pred cccccCCcccccccccHHHHHHHHhCcCCCHHHHHHHHHHHHHHHHHHHHHhhhhcccCCcccccccHHHHHHHHHhHHH
Confidence 98887 56677899999999998 6888899888765443332221111 1134568999999
Q ss_pred HHHHHHHHHHhccceEEEE----ecCceEEEEee--CeeEEe--cc--ceeeeeccCccccCccchhHHHHHhhhCC--C
Q 039468 1123 LEDKLQNEMLKTHSLQVLL----GLGSSFEVRGL--GTFNVV--NI--DVWDCNCRGWQLNGFPCVHAAAVLQHVGR--N 1190 (1282)
Q Consensus 1123 i~kkLqeei~ka~~~~V~~----~~~~~FeV~~~--~~~~vV--dl--~~~tCSCr~wq~~GIPC~HaLAVl~~~g~--~ 1190 (1282)
+|++||+|+..+..|.+.. +...+|.|.+. ...|.| |. ...+|+|++|+..||||+|||.||...++ .
T Consensus 529 iF~kFQ~El~~~~~~~~~~~~~dg~~~~y~V~~~~~~~~~~V~~d~~~~~v~CsC~kFE~~GILCrHaLkVL~~~~v~~I 608 (846)
T PLN03097 529 VFKKFQVEVLGAVACHPKMESQDETSITFRVQDFEKNQDFTVTWNQTKLEVSCICRLFEYKGYLCRHALVVLQMCQLSAI 608 (846)
T ss_pred HHHHHHHHHHHhhheEEeeeccCCceEEEEEEEecCCCcEEEEEecCCCeEEeeccCeecCccchhhHHHHHhhcCcccC
Confidence 9999999999999888763 23357888764 345666 32 57899999999999999999999999997 6
Q ss_pred ccccccccccHHHHhc
Q 039468 1191 LPDYCSKFYTTEAFRL 1206 (1282)
Q Consensus 1191 p~dyI~~~yt~eayr~ 1206 (1282)
|+.||.++||+++-+.
T Consensus 609 P~~YILkRWTKdAK~~ 624 (846)
T PLN03097 609 PSQYILKRWTKDAKSR 624 (846)
T ss_pred chhhhhhhchhhhhhc
Confidence 8999999999987643
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=99.81 E-value=7.1e-20 Score=174.81 Aligned_cols=90 Identities=30% Similarity=0.652 Sum_probs=83.5
Q ss_pred EEEeCCeEe-eCCCCcEEEeCCceeEEEEcCCCChHHHHHHHHHhcCCCCCceEEEEEecCCC-CceEEeechHHHHHHH
Q 039468 534 ICQSGGKFT-TANDGSLVYSGGDAHALSVNKESSFDELKLEMAEMWKYDPNSMIVKYFLPNNN-KTLITISGDKDIRRLI 611 (1282)
Q Consensus 534 ~c~~GG~~~-~~~dG~~~Y~GG~t~~i~Vdr~iSf~ef~~kL~e~~~~~~~~~~lky~LP~~~-~~Li~v~dD~Dl~~M~ 611 (1282)
+|||||+|+ +.+||+++|+||+|+++.|++++||+||+++|+++++++.+ +.+||+||+++ +.|++|++|+||.+|+
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 599999999 45699999999999999999999999999999999998755 89999999997 4599999999999999
Q ss_pred Hhhc----CcCeEEEEE
Q 039468 612 DFHE----DSGTVDVYV 624 (1282)
Q Consensus 612 e~~~----~~~~v~IYv 624 (1282)
++++ ...+++||+
T Consensus 80 ~e~~~~~~~~~rirvfl 96 (97)
T cd06410 80 EEYDRLSGGSARLRVFL 96 (97)
T ss_pred HhhccccCCCceEEEEE
Confidence 9999 888888886
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=99.80 E-value=9.2e-20 Score=172.96 Aligned_cols=90 Identities=33% Similarity=0.557 Sum_probs=87.0
Q ss_pred ccccccccCcceee---eeeecCCCCeEEEEEEEeccCCchhHHHHHHHHHHhhcCCceEEEEecCcchHHHHHHHHhhc
Q 039468 909 SFPIKSKYQSSLLT---ATALDGNDEIFPVAFGVVDAVSDDNWHWFLLQLKSALSTCQSITFVTDRLGQLRASILSVFEN 985 (1282)
Q Consensus 909 ~TyltnkY~g~Ll~---avGvD~n~~~~pvAfAvV~~Et~esw~WfLe~Lk~~m~~~~p~vIISD~~~gL~~AI~eVFP~ 985 (1282)
|||++|+| ++++. ++|+|++++.+|+||+++++|+.++|.|||+.|++.+... |.+||||+++|+.+||+++||+
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 69999999 98886 9999999999999999999999999999999999999887 9999999999999999999999
Q ss_pred cceeccchhhhHHHH
Q 039468 986 SYYCYCLHHLTEELK 1000 (1282)
Q Consensus 986 a~H~~C~~HI~~N~~ 1000 (1282)
+.|++|.||+.+|++
T Consensus 79 ~~~~~C~~H~~~n~k 93 (93)
T PF10551_consen 79 ARHQLCLFHILRNIK 93 (93)
T ss_pred ceEehhHHHHHHhhC
Confidence 999999999999984
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=99.77 E-value=1.2e-19 Score=214.65 Aligned_cols=226 Identities=18% Similarity=0.197 Sum_probs=181.1
Q ss_pred CCCCChhhHHHHHHHhcC-cccChHhHHHhhHhhhccCCCChhhhhhcHHHHHHHHHhhCCCcEEEEccccCccceeeee
Q 039468 810 APKCKPKEIAEEIRRDFG-IELGYVKAWRALENARGESQVSYKDSYNQLPWLVDKILETNPGSVVTLSTREDLSFHHLFV 888 (1282)
Q Consensus 810 ~p~~~p~~I~~~l~~~~G-~~iSy~q~~Rak~ka~e~i~G~~~esy~~L~~yl~~l~e~NPGs~~~v~~ded~~F~rlF~ 888 (1282)
-.+++.++|.+.++.-+| ..+|.+++.|..+...+.+ ..|. ... +
T Consensus 112 ~~G~Str~i~~~l~~l~g~~~~S~s~vSri~~~~~~~~-----------~~w~----~R~--------------L----- 157 (381)
T PF00872_consen 112 LKGVSTRDIEEALEELYGEVAVSKSTVSRITKQLDEEV-----------EAWR----NRP--------------L----- 157 (381)
T ss_pred ccccccccccchhhhhhcccccCchhhhhhhhhhhhhH-----------HHHh----hhc--------------c-----
Confidence 457899999999999999 7899999988665543311 1111 111 0
Q ss_pred cchhhHHHHHhcC-CCeeeecccccccccC-----cceeeeeeecCCCCeEEEEEEEeccCCchhHHHHHHHHHHhhcCC
Q 039468 889 ALHASLYGFQNGC-RPLIFLDSFPIKSKYQ-----SSLLTATALDGNDEIFPVAFGVVDAVSDDNWHWFLLQLKSALSTC 962 (1282)
Q Consensus 889 a~~~si~gf~~gc-rpVI~iD~TyltnkY~-----g~Ll~avGvD~n~~~~pvAfAvV~~Et~esw~WfLe~Lk~~m~~~ 962 (1282)
.+. -++|+||++|.+-+.+ ..+++|+|+|.+|+..+||+.+.+.|+.++|.-||+.|++. |..
T Consensus 158 ----------~~~~y~~l~iD~~~~kvr~~~~~~~~~~~v~iGi~~dG~r~vLg~~~~~~Es~~~W~~~l~~L~~R-Gl~ 226 (381)
T PF00872_consen 158 ----------ESEPYPYLWIDGTYFKVREDGRVVKKAVYVAIGIDEDGRREVLGFWVGDRESAASWREFLQDLKER-GLK 226 (381)
T ss_pred ----------ccccccceeeeeeecccccccccccchhhhhhhhhcccccceeeeecccCCccCEeeecchhhhhc-ccc
Confidence 013 3789999999997644 46899999999999999999999999999999999999988 555
Q ss_pred ceEEEEecCcchHHHHHHHHhhccceeccchhhhHHHHhhccCCccHHHHHHHHHHHHHHhhcccHHHHHHHHHHH----
Q 039468 963 QSITFVTDRLGQLRASILSVFENSYYCYCLHHLTEELKRDLKGSYTEEVVSVIVAHLYDAAQAGTLDEFSKFIDSI---- 1038 (1282)
Q Consensus 963 ~p~vIISD~~~gL~~AI~eVFP~a~H~~C~~HI~~N~~k~lk~~~~~e~k~~~~~~f~~~a~A~t~eeFe~~~e~L---- 1038 (1282)
.+..||+|+++||.+||+++||++.++.|.+|+++|+.++++.+.. +.+...++.+..+.+.+++...++++
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 DILLVVSDGHKGLKEAIREVFPGAKWQRCVVHLMRNVLRKVPKKDR----KEVKADLKAIYQAPDKEEAREALEEFAEKW 302 (381)
T ss_pred ccceeeccccccccccccccccchhhhhheechhhhhccccccccc----hhhhhhccccccccccchhhhhhhhccccc
Confidence 6899999999999999999999999999999999999999976544 35556666666677766666666665
Q ss_pred hhcchhhhHHHhhcCcchhhhhhccCCC-cCcCCcchhhhHHHHHcc
Q 039468 1039 KSVSSEAFDWILRSEPENWANALFKGSR-HNQMTSHIAESFYCWVGE 1084 (1282)
Q Consensus 1039 ~~~~pea~~wL~~~~~ekWa~Ayf~g~r-~g~mTTN~sESfNa~LK~ 1084 (1282)
...+|++.++|.+...+.|+..-|+... --+.|||.+||+|+.||+
T Consensus 303 ~~kyp~~~~~l~~~~~~~~tf~~fP~~~~~~i~TTN~iEsln~~irr 349 (381)
T PF00872_consen 303 EKKYPKAAKSLEENWDELLTFLDFPPEHRRSIRTTNAIESLNKEIRR 349 (381)
T ss_pred ccccchhhhhhhhccccccceeeecchhccccchhhhccccccchhh
Confidence 4568999999998877777766566443 467899999999999987
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=99.55 E-value=1.4e-14 Score=130.09 Aligned_cols=67 Identities=39% Similarity=0.759 Sum_probs=64.9
Q ss_pred CCCCCCCcEECCHHHHHHHHHHHHHHcCceEEEeecCCeEEEEeeecCCCceEEEEEEeCCCCeEEE
Q 039468 707 NCITGVHQRFNNVHDFRDALYKYSVAHGFTYCFKKNEGLRVTAKCKAEGCPWRIHASRVPTTQLFQI 773 (1282)
Q Consensus 707 n~il~VGm~F~S~eEfk~AI~~YAi~~gF~~rvkKSdk~Rv~~~C~~~GCpWrI~As~~~~s~~w~I 773 (1282)
||.|.+||+|+|++||++||..||++++|++++.+|+++|++++|...||||+|+|++.++++.|+|
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 5789999999999999999999999999999999999999999999999999999999999999986
No 6
>COG3328 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=99.39 E-value=3.9e-12 Score=148.93 Aligned_cols=224 Identities=17% Similarity=0.142 Sum_probs=171.7
Q ss_pred CCCCChhhHHHHHHHhcCcccChHhHHHhhHhhhccCCCChhhhhhcHHHHHHHHHhhCCCcEEEEccccCccceeeeec
Q 039468 810 APKCKPKEIAEEIRRDFGIELGYVKAWRALENARGESQVSYKDSYNQLPWLVDKILETNPGSVVTLSTREDLSFHHLFVA 889 (1282)
Q Consensus 810 ~p~~~p~~I~~~l~~~~G~~iSy~q~~Rak~ka~e~i~G~~~esy~~L~~yl~~l~e~NPGs~~~v~~ded~~F~rlF~a 889 (1282)
..++++++|...+++.++..++...+.+.-...++ .+..++..-
T Consensus 98 ~~gv~Tr~i~~~~~~~~~~~~s~~~iS~~~~~~~e---------------~v~~~~~r~--------------------- 141 (379)
T COG3328 98 AKGVTTREIEALLEELYGHKVSPSVISVVTDRLDE---------------KVKAWQNRP--------------------- 141 (379)
T ss_pred HcCCcHHHHHHHHHHhhCcccCHHHhhhHHHHHHH---------------HHHHHHhcc---------------------
Confidence 45789999999999998887777776654443332 222222221
Q ss_pred chhhHHHHHhcCCCeeeecccccccc--cCcceeeeeeecCCCCeEEEEEEEeccCCchhHHHHHHHHHHhhcCCceEEE
Q 039468 890 LHASLYGFQNGCRPLIFLDSFPIKSK--YQSSLLTATALDGNDEIFPVAFGVVDAVSDDNWHWFLLQLKSALSTCQSITF 967 (1282)
Q Consensus 890 ~~~si~gf~~gcrpVI~iD~Tyltnk--Y~g~Ll~avGvD~n~~~~pvAfAvV~~Et~esw~WfLe~Lk~~m~~~~p~vI 967 (1282)
. +..+++++|++|++-+ -+..+++|+|++.+|+...+++-+-+.|+ ..|.-||..|+.. +......+
T Consensus 142 --------l-~~~~~v~~D~~~~k~r~v~~~~~~ia~Gv~~eG~reilg~~~~~~e~-~~w~~~l~~l~~r-gl~~v~l~ 210 (379)
T COG3328 142 --------L-GDYPYVYLDAKYVKVRSVRNKAVYIAIGVTEEGRREILGIWVGVRES-KFWLSFLLDLKNR-GLSDVLLV 210 (379)
T ss_pred --------c-cCceEEEEecceeehhhhhhheeeeeeccCcccchhhhceeeecccc-hhHHHHHHHHHhc-cccceeEE
Confidence 0 2568999999999977 45689999999999999999999999999 9999899889888 33345667
Q ss_pred EecCcchHHHHHHHHhhccceeccchhhhHHHHhhccCCccHHHHHHHHHHHHHHhhcccHHHHHHHHHH----Hhhcch
Q 039468 968 VTDRLGQLRASILSVFENSYYCYCLHHLTEELKRDLKGSYTEEVVSVIVAHLYDAAQAGTLDEFSKFIDS----IKSVSS 1043 (1282)
Q Consensus 968 ISD~~~gL~~AI~eVFP~a~H~~C~~HI~~N~~k~lk~~~~~e~k~~~~~~f~~~a~A~t~eeFe~~~e~----L~~~~p 1043 (1282)
++|+.+|+.+||.++||.+.++.|..|+.+|+.++...+ .++.+...+..+..+.+.++....+.. +...+|
T Consensus 211 v~Dg~~gl~~aI~~v~p~a~~Q~C~vH~~Rnll~~v~~k----~~d~i~~~~~~I~~a~~~e~~~~~~~~~~~~w~~~yP 286 (379)
T COG3328 211 VVDGLKGLPEAISAVFPQAAVQRCIVHLVRNLLDKVPRK----DQDAVLSDLRSIYIAPDAEEALLALLAFSELWGKRYP 286 (379)
T ss_pred ecchhhhhHHHHHHhccHhhhhhhhhHHHhhhhhhhhhh----hhHHHHhhhhhhhccCCcHHHHHHHHHHHHhhhhhcc
Confidence 779999999999999999999999999999999998654 344566666666666666666665555 445678
Q ss_pred hhhHHHhhcCcchhhhhhcc-CCCcCcCCcchhhhHHHHHcc
Q 039468 1044 EAFDWILRSEPENWANALFK-GSRHNQMTSHIAESFYCWVGE 1084 (1282)
Q Consensus 1044 ea~~wL~~~~~ekWa~Ayf~-g~r~g~mTTN~sESfNa~LK~ 1084 (1282)
...+++.+..-+.|...-|+ ..+--+.|||..|++|+.++.
T Consensus 287 ~i~~~~~~~~~~~~~F~~fp~~~r~~i~ttN~IE~~n~~ir~ 328 (379)
T COG3328 287 AILKSWRNALEELLPFFAFPSEIRKIIYTTNAIESLNKLIRR 328 (379)
T ss_pred hHHHHHHHHHHHhcccccCcHHHHhHhhcchHHHHHHHHHHH
Confidence 88888888766666544444 344578899999999998875
No 7
>smart00575 ZnF_PMZ plant mutator transposase zinc finger.
Probab=98.47 E-value=6.9e-08 Score=72.01 Aligned_cols=27 Identities=48% Similarity=0.987 Sum_probs=25.1
Q ss_pred eeeeccCccccCccchhHHHHHhhhCC
Q 039468 1163 WDCNCRGWQLNGFPCVHAAAVLQHVGR 1189 (1282)
Q Consensus 1163 ~tCSCr~wq~~GIPC~HaLAVl~~~g~ 1189 (1282)
++|||++||..||||+|+|+|+...++
T Consensus 1 ~~CsC~~~~~~gipC~H~i~v~~~~~~ 27 (28)
T smart00575 1 KTCSCRKFQLSGIPCRHALAAAIHIGL 27 (28)
T ss_pred CcccCCCcccCCccHHHHHHHHHHhCC
Confidence 479999999999999999999998875
No 8
>PF08731 AFT: Transcription factor AFT; InterPro: IPR014842 AFT (activator of iron transcription) is an iron regulated transcriptional activator that regulates the expression of genes involved in iron homeostasis. This entry includes the paralogous pair of transcription factors AFT1 and AFT2.
Probab=98.37 E-value=1.6e-06 Score=84.31 Aligned_cols=69 Identities=20% Similarity=0.438 Sum_probs=65.4
Q ss_pred ECCHHHHHHHHHHHHHHcCceEEEeecCCeEEEEeeec------------------------------------------
Q 039468 716 FNNVHDFRDALYKYSVAHGFTYCFKKNEGLRVTAKCKA------------------------------------------ 753 (1282)
Q Consensus 716 F~S~eEfk~AI~~YAi~~gF~~rvkKSdk~Rv~~~C~~------------------------------------------ 753 (1282)
|.+++|++.+|++++...||++...||+.+.+.++|..
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 CCCceEEEEEEeCCCCeEEEEeecCCCcCCC
Q 039468 754 EGCPWRIHASRVPTTQLFQIKTMNGMHTCKA 784 (1282)
Q Consensus 754 ~GCpWrI~As~~~~s~~w~Ik~~~~eHnC~~ 784 (1282)
..|||+|+|....+.+.|.|+.+++.|+|++
T Consensus 81 ~~CPFriRA~yS~k~k~W~lvvvnn~HnH~l 111 (111)
T PF08731_consen 81 NTCPFRIRANYSKKNKKWTLVVVNNEHNHPL 111 (111)
T ss_pred cCCCeEEEEEEEecCCeEEEEEecCCcCCCC
Confidence 3799999999999999999999999999975
No 9
>smart00666 PB1 PB1 domain. Phox and Bem1p domain, present in many eukaryotic cytoplasmic signalling proteins. The domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate.
Probab=98.16 E-value=1.4e-05 Score=74.40 Aligned_cols=75 Identities=27% Similarity=0.514 Sum_probs=65.0
Q ss_pred CcEEEeCCceeEEEEcCCCChHHHHHHHHHhcCCCCCceEEEEEecCCCCceEEeechHHHHHHHHhhcCc--CeEEEEE
Q 039468 547 GSLVYSGGDAHALSVNKESSFDELKLEMAEMWKYDPNSMIVKYFLPNNNKTLITISGDKDIRRLIDFHEDS--GTVDVYV 624 (1282)
Q Consensus 547 G~~~Y~GG~t~~i~Vdr~iSf~ef~~kL~e~~~~~~~~~~lky~LP~~~~~Li~v~dD~Dl~~M~e~~~~~--~~v~IYv 624 (1282)
.++.| ||+++.+.|++++||.+|.++|.+.|+...+.+.++|. .+...+++|.+|+|+..|++++... ..+.|++
T Consensus 4 vK~~~-~~~~~~~~~~~~~s~~dL~~~i~~~~~~~~~~~~l~Y~--Dedgd~v~l~sd~Dl~~a~~~~~~~~~~~l~l~v 80 (81)
T smart00666 4 VKLRY-GGETRRLSVPRDISFEDLRSKVAKRFGLDNQSFTLKYQ--DEDGDLVSLTSDEDLEEAIEEYDSLGSKKLRLHV 80 (81)
T ss_pred EEEEE-CCEEEEEEECCCCCHHHHHHHHHHHhCCCCCCeEEEEE--CCCCCEEEecCHHHHHHHHHHHHHcCCceEEEEe
Confidence 35677 89999999999999999999999999987778999999 4456699999999999999998763 5577765
No 10
>PF03101 FAR1: FAR1 DNA-binding domain; InterPro: IPR004330 Phytochrome A is the primary photoreceptor for mediating various far-red light-induced responses in higher plants. It has been found that the proteins governing this response, which include FAR-RED ELONGATED HYPOCOTYL3 (FHY3) and FAR-RED-IMPAIRED RESPONSE1 (FAR1), are a pair of homologous proteins sharing significant sequence homology to mutator-like transposases. These proteins appear to be novel transcription factors, which are essential for activating the expression of FHY1 and FHL (for FHY1-like) and related genes, whose products are required for light-induced phytochrome A nuclear accumulation and subsequent light responses in plants. The FRS (FAR1 Related Sequences) family of proteins share a similar domain structure to mutator-like transposases, including an N-terminal C2H2 zinc finger domain, a central putative core transposase domain, and a C-terminal SWIM motif (named after SWI2/SNF and MuDR transposases). It seems plausible that the FRS family represent transcription factors derived from mutator-like transposases [, ]. This entry represents a domain found in FAR1 and FRS proteins. It contains a WRKY like fold and is therefore most likely a zinc binding DNA-binding domain.
Probab=98.11 E-value=5.4e-06 Score=78.69 Aligned_cols=61 Identities=25% Similarity=0.356 Sum_probs=53.4
Q ss_pred HHHHHHHHHcCceEEEeecCCe-------EEEEeeec----------------------CCCceEEEEEEeCCCCeEEEE
Q 039468 724 DALYKYSVAHGFTYCFKKNEGL-------RVTAKCKA----------------------EGCPWRIHASRVPTTQLFQIK 774 (1282)
Q Consensus 724 ~AI~~YAi~~gF~~rvkKSdk~-------Rv~~~C~~----------------------~GCpWrI~As~~~~s~~w~Ik 774 (1282)
++++.||..+||.++..++.+. ++.++|.. +||||+|.+.+.. ++.|.|+
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 4789999999999999766543 78899974 6999999999888 7899999
Q ss_pred eecCCCcCCCC
Q 039468 775 TMNGMHTCKAG 785 (1282)
Q Consensus 775 ~~~~eHnC~~~ 785 (1282)
.+..+|||++.
T Consensus 80 ~~~~~HNH~L~ 90 (91)
T PF03101_consen 80 SFVLEHNHPLC 90 (91)
T ss_pred ECcCCcCCCCC
Confidence 99999999975
No 11
>PF04434 SWIM: SWIM zinc finger; InterPro: IPR007527 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the SWIM (SWI2/SNF2 and MuDR) zinc-binding domain, which is found in a variety of prokaryotic and eukaryotic proteins, such as mitogen-activated protein kinase kinase kinase 1 (or MEKK1). It is also found in the related protein MEX (MEKK1-related protein X), a testis-expressed protein that acts as an E3 ubiquitin ligase through the action of E2 ubiquitin-conjugating enzymes in the proteasome degradation pathway; the SWIM domain is critical for MEX ubiquitination []. SWIM domains are also found in the homologous recombination protein Sws1 [], as well as in several hypothetical proteins. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=97.68 E-value=3.1e-05 Score=62.60 Aligned_cols=30 Identities=40% Similarity=0.748 Sum_probs=27.5
Q ss_pred eccceeeeeccCccccCccchhHHHHHhhh
Q 039468 1158 VNIDVWDCNCRGWQLNGFPCVHAAAVLQHV 1187 (1282)
Q Consensus 1158 Vdl~~~tCSCr~wq~~GIPC~HaLAVl~~~ 1187 (1282)
+++...+|||..|+..|.||+|++|++...
T Consensus 10 ~~~~~~~CsC~~~~~~~~~CkHi~av~~~~ 39 (40)
T PF04434_consen 10 VSIEQASCSCPYFQFRGGPCKHIVAVLLAL 39 (40)
T ss_pred ccccccEeeCCCccccCCcchhHHHHHHhh
Confidence 677889999999999999999999998765
No 12
>cd05992 PB1 The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as a noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants.
Probab=97.50 E-value=0.00074 Score=62.61 Aligned_cols=74 Identities=28% Similarity=0.478 Sum_probs=58.5
Q ss_pred cEEEeCCceeEEEEc-CCCChHHHHHHHHHhcCCCCCceEEEEEecCCCCceEEeechHHHHHHHHhhcC--cCeEEEEE
Q 039468 548 SLVYSGGDAHALSVN-KESSFDELKLEMAEMWKYDPNSMIVKYFLPNNNKTLITISGDKDIRRLIDFHED--SGTVDVYV 624 (1282)
Q Consensus 548 ~~~Y~GG~t~~i~Vd-r~iSf~ef~~kL~e~~~~~~~~~~lky~LP~~~~~Li~v~dD~Dl~~M~e~~~~--~~~v~IYv 624 (1282)
+++|. |+.+.+.+. +++||.+|.++|.+.++.....+.++|.- +...+++|++|+|+..|++.+.. .+.+.|++
T Consensus 4 K~~~~-~~~~~~~~~~~~~s~~~L~~~i~~~~~~~~~~~~l~y~D--~e~d~v~l~sd~Dl~~a~~~~~~~~~~~l~l~v 80 (81)
T cd05992 4 KVKYG-GEIRRFVVVSRSISFEDLRSKIAEKFGLDAVSFKLKYPD--EDGDLVTISSDEDLEEAIEEARRSGSKKLRLFV 80 (81)
T ss_pred EEEec-CCCEEEEEecCCCCHHHHHHHHHHHhCCCCCcEEEEeeC--CCCCEEEeCCHHHHHHHHHHHhhcCCccEEEEe
Confidence 45566 556777777 88999999999999999865566666665 44489999999999999999874 56677765
No 13
>PF00564 PB1: PB1 domain; InterPro: IPR000270 The Phox and Bem1p domain, is present in many eukaryotic cytoplasmic signalling proteins. The domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate.; GO: 0005515 protein binding; PDB: 1IPG_A 1IP9_A 2KFK_A 1WMH_A 1VD2_A 1WI0_A 1OEY_C 1PQS_A 1Q1O_A 1TZ1_A ....
Probab=97.27 E-value=0.0017 Score=60.63 Aligned_cols=77 Identities=26% Similarity=0.427 Sum_probs=62.0
Q ss_pred cEEEeCCceeEEEEcCCCChHHHHHHHHHhcCCCCCceEEEEEecCCCCceEEeechHHHHHHHHhhcC--cCeEEEEEe
Q 039468 548 SLVYSGGDAHALSVNKESSFDELKLEMAEMWKYDPNSMIVKYFLPNNNKTLITISGDKDIRRLIDFHED--SGTVDVYVM 625 (1282)
Q Consensus 548 ~~~Y~GG~t~~i~Vdr~iSf~ef~~kL~e~~~~~~~~~~lky~LP~~~~~Li~v~dD~Dl~~M~e~~~~--~~~v~IYve 625 (1282)
++.|.|+..+.+.+.+++||.+|..+|.+.|+.....+.++|.=. ...+++|++|+||..|++.+.. .+.+.|+|.
T Consensus 5 K~~~~~~~~~~~~~~~~~s~~~L~~~i~~~~~~~~~~~~l~Y~D~--dgD~V~i~sd~Dl~~a~~~~~~~~~~~lrl~v~ 82 (84)
T PF00564_consen 5 KVRYGGDIRRIISLPSDVSFDDLRSKIREKFGLLDEDFQLKYKDE--DGDLVTISSDEDLQEAIEQAKESGSKTLRLFVQ 82 (84)
T ss_dssp EEEETTEEEEEEEECSTSHHHHHHHHHHHHHTTSTSSEEEEEEET--TSSEEEESSHHHHHHHHHHHHHCTTSCEEEEEE
T ss_pred EEEECCeeEEEEEcCCCCCHHHHHHHHHHHhCCCCccEEEEeeCC--CCCEEEeCCHHHHHHHHHHHHhcCCCcEEEEEE
Confidence 345555444458999999999999999999998767888999743 3489999999999999998764 357888886
Q ss_pred e
Q 039468 626 V 626 (1282)
Q Consensus 626 ~ 626 (1282)
.
T Consensus 83 ~ 83 (84)
T PF00564_consen 83 D 83 (84)
T ss_dssp E
T ss_pred e
Confidence 4
No 14
>cd06407 PB1_NLP A PB1 domain is present in NIN like proteins (NLP), a key enzyme in a process of establishment of symbiosis betweeen legumes and nitrogen fixing bacteria (Rhizobium). The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes like osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-inte
Probab=97.03 E-value=0.0043 Score=58.41 Aligned_cols=71 Identities=25% Similarity=0.400 Sum_probs=60.3
Q ss_pred CCceeEEEEcCCCChHHHHHHHHHhcCCCC-CceEEEEEecCCCCceEEeechHHHHHHHHhhcC--cCeEEEEEe
Q 039468 553 GGDAHALSVNKESSFDELKLEMAEMWKYDP-NSMIVKYFLPNNNKTLITISGDKDIRRLIDFHED--SGTVDVYVM 625 (1282)
Q Consensus 553 GG~t~~i~Vdr~iSf~ef~~kL~e~~~~~~-~~~~lky~LP~~~~~Li~v~dD~Dl~~M~e~~~~--~~~v~IYve 625 (1282)
||+...+.+..+++|.+|.++|.+.|++.. +.+.++|.=.. ...++|++|.||+.-++.+.. ...+.++|-
T Consensus 8 ~~d~~r~~l~~~~~~~~L~~~i~~r~~~~~~~~f~LkY~Dde--gd~v~ltsd~DL~eai~i~~~~~~~~v~l~v~ 81 (82)
T cd06407 8 GEEKIRFRLPPSWGFTELKQEIAKRFKLDDMSAFDLKYLDDD--EEWVLLTCDADLEECIDVYRSSGSHTIRLLVH 81 (82)
T ss_pred CCeEEEEEcCCCCCHHHHHHHHHHHhCCCCCCeeEEEEECCC--CCeEEeecHHHHHHHHHHHHHCCCCeEEEEee
Confidence 778999999999999999999999999965 67899998443 679999999999999998665 455888763
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=96.38 E-value=0.011 Score=55.80 Aligned_cols=61 Identities=13% Similarity=0.285 Sum_probs=52.6
Q ss_pred EEEeCCceeEEEEcCCCChHHHHHHHHHhcCCCCCceEEEEEecCCCCceEEeechHHHHHHHHhh
Q 039468 549 LVYSGGDAHALSVNKESSFDELKLEMAEMWKYDPNSMIVKYFLPNNNKTLITISGDKDIRRLIDFH 614 (1282)
Q Consensus 549 ~~Y~GG~t~~i~Vdr~iSf~ef~~kL~e~~~~~~~~~~lky~LP~~~~~Li~v~dD~Dl~~M~e~~ 614 (1282)
++| +|+++.+.|+.+++|.+|.++|.++|++. +.++++|.=. ...++|+++.||+.-+.-.
T Consensus 7 v~~-~~Dv~~i~v~~~i~f~dL~~kIrdkf~~~-~~~~iKykDE---GD~iti~sq~DLd~Ai~~a 67 (86)
T cd06408 7 VHA-QDDTRYIMIGPDTGFADFEDKIRDKFGFK-RRLKIKMKDD---GDMITMGDQDDLDMAIDTA 67 (86)
T ss_pred EEe-cCcEEEEEcCCCCCHHHHHHHHHHHhCCC-CceEEEEEcC---CCCccccCHHHHHHHHHHH
Confidence 344 56799999999999999999999999996 6789999866 4789999999999988754
No 16
>cd06406 PB1_P67 A PB1 domain is present in p67 proteins which forms a signaling complex with p40, a crucial step for activation of NADPH oxidase during phagocytosis. PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes . A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants. The p67 proteins contain
Probab=95.82 E-value=0.029 Score=52.30 Aligned_cols=66 Identities=11% Similarity=0.201 Sum_probs=54.3
Q ss_pred cEEEeCCceeEEEEcCCCChHHHHHHHHHhcCCCCCceEEEEEecCCCCceEEeechHHHHHHHHhhcCc
Q 039468 548 SLVYSGGDAHALSVNKESSFDELKLEMAEMWKYDPNSMIVKYFLPNNNKTLITISGDKDIRRLIDFHEDS 617 (1282)
Q Consensus 548 ~~~Y~GG~t~~i~Vdr~iSf~ef~~kL~e~~~~~~~~~~lky~LP~~~~~Li~v~dD~Dl~~M~e~~~~~ 617 (1282)
+++|.+ +-.|.|..+++|.+|.++|++++++..+.+++.|.-... ..++.+ +|+|++.+.+...++
T Consensus 6 KV~f~~--tIaIrvp~~~~y~~L~~ki~~kLkl~~e~i~LsYkde~s-~~~v~l-~d~dle~aws~~~~~ 71 (80)
T cd06406 6 KVHFKY--TVAIQVARGLSYATLLQKISSKLELPAEHITLSYKSEAS-GEDVIL-SDTNMEDVWSQAKDG 71 (80)
T ss_pred EEEEEE--EEEEEcCCCCCHHHHHHHHHHHhCCCchhcEEEeccCCC-CCccCc-ChHHHHHHHHhhcCC
Confidence 578887 999999999999999999999999977778888875432 335566 899999999977554
No 17
>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=95.79 E-value=0.063 Score=50.35 Aligned_cols=69 Identities=9% Similarity=0.321 Sum_probs=57.3
Q ss_pred CCceeEEEEcC--CCChHHHHHHHHHhcCCCCCceEEEEEecCCCCceEEeechHHHHHHHHhhcCcCe-EEEEEe
Q 039468 553 GGDAHALSVNK--ESSFDELKLEMAEMWKYDPNSMIVKYFLPNNNKTLITISGDKDIRRLIDFHEDSGT-VDVYVM 625 (1282)
Q Consensus 553 GG~t~~i~Vdr--~iSf~ef~~kL~e~~~~~~~~~~lky~LP~~~~~Li~v~dD~Dl~~M~e~~~~~~~-v~IYve 625 (1282)
||++..+.++. +++|.+|..++...|++. .+.+||. .+....+.|++|.||+.-++.+.+.++ +.|.|.
T Consensus 8 ~~d~~rf~~~~~~~~~~~~L~~ev~~rf~l~--~f~lKYl--Dde~e~v~lssd~eLeE~~rl~~~~~~~l~~~v~ 79 (81)
T cd06396 8 NGESQSFLVSDSENTTWASVEAMVKVSFGLN--DIQIKYV--DEENEEVSVNSQGEYEEALKSAVRQGNLLQMNVY 79 (81)
T ss_pred CCeEEEEEecCCCCCCHHHHHHHHHHHhCCC--cceeEEE--cCCCCEEEEEchhhHHHHHHHHHhCCCEEEEEEe
Confidence 57788888988 799999999999999998 6888887 334579999999999999998777655 666653
No 18
>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=94.68 E-value=0.35 Score=46.59 Aligned_cols=75 Identities=19% Similarity=0.423 Sum_probs=57.5
Q ss_pred EEEeCCceeEEEEcC-----CCChHHHHHHHHHhcCCCC-CceEEEEEecCCCCceEEeechHHHHHHHHhh-c--CcCe
Q 039468 549 LVYSGGDAHALSVNK-----ESSFDELKLEMAEMWKYDP-NSMIVKYFLPNNNKTLITISGDKDIRRLIDFH-E--DSGT 619 (1282)
Q Consensus 549 ~~Y~GG~t~~i~Vdr-----~iSf~ef~~kL~e~~~~~~-~~~~lky~LP~~~~~Li~v~dD~Dl~~M~e~~-~--~~~~ 619 (1282)
+.| ||+.+.+.++. +++|.+|..+|.+.|++.. .++.++|.=. ...+++|.+|.||..-++.. . ....
T Consensus 5 v~y-~~~~rRf~l~~~~~~~d~~~~~L~~kI~~~f~l~~~~~~~l~Y~De--dgd~V~l~~D~DL~~a~~~~~~~~~~~~ 81 (91)
T cd06398 5 VKY-GGTLRRFTFPVAENQLDLNMDGLREKVEELFSLSPDADLSLTYTDE--DGDVVTLVDDNDLTDAIQYFCSGSRLNP 81 (91)
T ss_pred EEe-CCEEEEEEeccccccCCCCHHHHHHHHHHHhCCCCCCcEEEEEECC--CCCEEEEccHHHHHHHHHHHhccCCCce
Confidence 445 66777777774 7999999999999999965 5778877632 55699999999999988874 2 2345
Q ss_pred EEEEEee
Q 039468 620 VDVYVMV 626 (1282)
Q Consensus 620 v~IYve~ 626 (1282)
+.|+|..
T Consensus 82 lrl~v~~ 88 (91)
T cd06398 82 LRIDVTV 88 (91)
T ss_pred EEEEEEE
Confidence 7777765
No 19
>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=94.14 E-value=0.37 Score=45.34 Aligned_cols=65 Identities=20% Similarity=0.279 Sum_probs=53.3
Q ss_pred EeCCceeEEEEcCCCChHHHHHHHHHhcCCCC-CceEEEEEecCCCCceEEeechHHHHHHHHhhcCc
Q 039468 551 YSGGDAHALSVNKESSFDELKLEMAEMWKYDP-NSMIVKYFLPNNNKTLITISGDKDIRRLIDFHEDS 617 (1282)
Q Consensus 551 Y~GG~t~~i~Vdr~iSf~ef~~kL~e~~~~~~-~~~~lky~LP~~~~~Li~v~dD~Dl~~M~e~~~~~ 617 (1282)
.-+|+..+..++..+||++|.+++.++|.... ..++|||.=. .-.++.+++|.+|+.-+..+...
T Consensus 6 ~y~gdi~it~~d~~~s~e~L~~~v~~~c~~~~~q~ft~kw~DE--EGDp~tiSS~~EL~EA~rl~~~n 71 (83)
T cd06404 6 AYNGDIMITSIDPSISLEELCNEVRDMCRFHNDQPFTLKWIDE--EGDPCTISSQMELEEAFRLYELN 71 (83)
T ss_pred EecCcEEEEEcCCCcCHHHHHHHHHHHhCCCCCCcEEEEEECC--CCCceeecCHHHHHHHHHHHHhc
Confidence 34678888999999999999999999998855 4688998743 33589999999999988875443
No 20
>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=94.00 E-value=0.37 Score=45.95 Aligned_cols=69 Identities=12% Similarity=0.276 Sum_probs=55.4
Q ss_pred ceeEEEEcCC--CChHHHHHHHHHhcC-CCCCceEEEEEecCCCCceEEeechHHHHHHHHhhcCcCeEEEEEee
Q 039468 555 DAHALSVNKE--SSFDELKLEMAEMWK-YDPNSMIVKYFLPNNNKTLITISGDKDIRRLIDFHEDSGTVDVYVMV 626 (1282)
Q Consensus 555 ~t~~i~Vdr~--iSf~ef~~kL~e~~~-~~~~~~~lky~LP~~~~~Li~v~dD~Dl~~M~e~~~~~~~v~IYve~ 626 (1282)
+.|.+.++.. +||.+|.+++.+.|. +....+.|+|.=. .-.|++|++|++|..-++... .+.+.|||..
T Consensus 15 EIRRf~l~~~~~~s~~~L~~~V~~~f~~l~~~~ftlky~De--eGDlvtIssdeEL~~A~~~~~-~~~~RlyI~~ 86 (87)
T cd06402 15 EIRRFAIDEDVSTSYEYLVEKVAAVFPSLRGKNFQLFWKDE--EGDLVAFSSDEELVMALGSLN-DDTFRIYIKE 86 (87)
T ss_pred ceEEEEecCCCCcCHHHHHHHHHHHccccCCCcEEEEEECC--CCCEEeecCHHHHHHHHHcCC-CCcEEEEEEe
Confidence 5666777775 799999999999984 4456788888733 346999999999999998876 6789999853
No 21
>PF04684 BAF1_ABF1: BAF1 / ABF1 chromatin reorganising factor; InterPro: IPR006774 ABF1 is a sequence-specific DNA binding protein involved in transcription activation, gene silencing and initiation of DNA replication. ABF1 is known to remodel chromatin, and it is proposed that it mediates its effects on transcription and gene expression by modifying local chromatin architecture []. These functions require a conserved stretch of 20 amino acids in the C-terminal region of ABF1 (amino acids 639 to 662 Saccharomyces cerevisiae (P14164 from SWISSPROT)) []. The N-terminal two thirds of the protein are necessary for DNA binding, and the N terminus (amino acids 9 to 91 in S. cerevisiae) is thought to contain a novel zinc-finger motif which may stabilise the protein structure [].; GO: 0003677 DNA binding, 0006338 chromatin remodeling, 0005634 nucleus
Probab=93.50 E-value=0.55 Score=56.35 Aligned_cols=53 Identities=17% Similarity=0.416 Sum_probs=47.6
Q ss_pred CCcEECCHHHHHHHHHHHHHHcCceEEEeecC-CeEEEEeeecCCCceEEEEEE
Q 039468 712 VHQRFNNVHDFRDALYKYSVAHGFTYCFKKNE-GLRVTAKCKAEGCPWRIHASR 764 (1282)
Q Consensus 712 VGm~F~S~eEfk~AI~~YAi~~gF~~rvkKSd-k~Rv~~~C~~~GCpWrI~As~ 764 (1282)
-+..|++.++-+++|..|-.+.+..|..+.|- .+.+++.|....|||+|..+.
T Consensus 24 ~~~~f~tl~~wy~v~ndyefq~rcpiilknsh~nkhftfachlk~c~fkillsy 77 (496)
T PF04684_consen 24 QARKFPTLEAWYNVINDYEFQSRCPIILKNSHRNKHFTFACHLKNCPFKILLSY 77 (496)
T ss_pred cccCCCcHHHHHHHHhhhhhhhcCceeecccccccceEEEeeccCCCceeeeee
Confidence 35679999999999999999999999987775 478999999999999998875
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=93.24 E-value=0.66 Score=43.21 Aligned_cols=73 Identities=10% Similarity=0.274 Sum_probs=61.1
Q ss_pred EEEeCCceeEEEEcCC--CChHHHHHHHHHhcCCCCCceEEEEEecCCCCceEEeechHHHHHHHHhhcCcCeEEEEEe
Q 039468 549 LVYSGGDAHALSVNKE--SSFDELKLEMAEMWKYDPNSMIVKYFLPNNNKTLITISGDKDIRRLIDFHEDSGTVDVYVM 625 (1282)
Q Consensus 549 ~~Y~GG~t~~i~Vdr~--iSf~ef~~kL~e~~~~~~~~~~lky~LP~~~~~Li~v~dD~Dl~~M~e~~~~~~~v~IYve 625 (1282)
.++-+++.+-+.++++ -||.||-+.|....++...++.+.|.=| ...|++|+||+.+.+-++-. --.+.|+|.
T Consensus 4 KSkfdaEfRRFsl~r~~~~~f~ef~~ll~~lH~l~~~~f~i~Y~D~--~gDLLPInNDdNf~kAlssa--~plLRl~iq 78 (80)
T cd06403 4 KSKFDAEFRRFSLDRNKPGKFEDFYKLLEHLHHIPNVDFLIGYTDP--HGDLLPINNDDNFLKALSSA--NPLLRIFIQ 78 (80)
T ss_pred ecccCCeEEEEEeccccCcCHHHHHHHHHHHhCCCCCcEEEEEeCC--CCCEecccCcHHHHHHHHcC--CCceEEEEE
Confidence 3567899999999997 8999999999888888778899999988 56799999999999988833 334777765
No 23
>PF06782 UPF0236: Uncharacterised protein family (UPF0236); InterPro: IPR009620 This is a group of proteins of unknown function.
Probab=92.81 E-value=3.6 Score=51.05 Aligned_cols=130 Identities=15% Similarity=0.215 Sum_probs=87.1
Q ss_pred cCCchhHHHHHHHHHHhhcCC--ceEEEEecCcchHHHHHHHHhhccceeccchhhhHHHHhhccCCccHHHHHHHHHHH
Q 039468 942 AVSDDNWHWFLLQLKSALSTC--QSITFVTDRLGQLRASILSVFENSYYCYCLHHLTEELKRDLKGSYTEEVVSVIVAHL 1019 (1282)
Q Consensus 942 ~Et~esw~WfLe~Lk~~m~~~--~p~vIISD~~~gL~~AI~eVFP~a~H~~C~~HI~~N~~k~lk~~~~~e~k~~~~~~f 1019 (1282)
..+.+-|.-+++.+-+..... .-+++.+|+...+.+++. .||++.|.+..+|+.+.+.+.++.. . .+...+
T Consensus 235 ~~~~~~~~~v~~~i~~~Y~~~~~~~iiingDGa~WIk~~~~-~~~~~~~~LD~FHl~k~i~~~~~~~--~----~~~~~~ 307 (470)
T PF06782_consen 235 ESAEEFWEEVLDYIYNHYDLDKTTKIIINGDGASWIKEGAE-FFPKAEYFLDRFHLNKKIKQALSHD--P----ELKEKI 307 (470)
T ss_pred cchHHHHHHHHHHHHHhcCcccceEEEEeCCCcHHHHHHHH-hhcCceEEecHHHHHHHHHHHhhhC--h----HHHHHH
Confidence 455678988888887776533 357788999999988775 9999999999999999999988643 1 244545
Q ss_pred HHHhhcccHHHHHHHHHHHhhcc---------hhhhHHHhhcCcchhhhh--hccCCCcCcCCcchhhhHHHHHcc
Q 039468 1020 YDAAQAGTLDEFSKFIDSIKSVS---------SEAFDWILRSEPENWANA--LFKGSRHNQMTSHIAESFYCWVGE 1084 (1282)
Q Consensus 1020 ~~~a~A~t~eeFe~~~e~L~~~~---------pea~~wL~~~~~ekWa~A--yf~g~r~g~mTTN~sESfNa~LK~ 1084 (1282)
+++.+.....+++..++.+.... .++..||..+ |... |- .+-+.......|+.+..+..
T Consensus 308 ~~al~~~d~~~l~~~L~~~~~~~~~~~~~~~i~~~~~Yl~~n----~~~i~~y~--~~~~~~g~g~ee~~~~~~s~ 377 (470)
T PF06782_consen 308 RKALKKGDKKKLETVLDTAESCAKDEEERKKIRKLRKYLLNN----WDGIKPYR--EREGLRGIGAEESVSHVLSY 377 (470)
T ss_pred HHHHHhcCHHHHHHHHHHHHHhhhchHHHHHHHHHHHHHHHC----HHHhhhhh--hccCCCccchhhhhhhHHHH
Confidence 56666667777777777665422 1345555554 4321 21 11233344457777777643
No 24
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=92.13 E-value=0.074 Score=43.11 Aligned_cols=19 Identities=42% Similarity=1.074 Sum_probs=17.4
Q ss_pred eeccccCcCCCCc--CCCCCC
Q 039468 1263 LHCSKCKGAGHNR--KTCHVY 1281 (1282)
Q Consensus 1263 ~~CSrCk~~GHNk--rTCp~~ 1281 (1282)
++|++|++.||.+ ++||++
T Consensus 2 ~kC~~CG~~GH~~t~k~CP~~ 22 (40)
T PF15288_consen 2 VKCKNCGAFGHMRTNKRCPMY 22 (40)
T ss_pred ccccccccccccccCccCCCC
Confidence 6999999999998 889986
No 25
>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=91.23 E-value=1 Score=42.07 Aligned_cols=62 Identities=15% Similarity=0.304 Sum_probs=52.4
Q ss_pred CCceeEEEEcCCCChHHHHHHHHHhcCCCCCceEEEEEecCCCCceEEeechHHHHHHHHhhcC
Q 039468 553 GGDAHALSVNKESSFDELKLEMAEMWKYDPNSMIVKYFLPNNNKTLITISGDKDIRRLIDFHED 616 (1282)
Q Consensus 553 GG~t~~i~Vdr~iSf~ef~~kL~e~~~~~~~~~~lky~LP~~~~~Li~v~dD~Dl~~M~e~~~~ 616 (1282)
||.+|-+..+.+-+|.+|.+||...|++....+.+.|.=. +...|+|++|.||+..+.....
T Consensus 8 ~g~~RRf~~~~~pt~~~L~~kl~~Lf~lp~~~~~vtYiDe--D~D~ITlssd~eL~d~~~~~~~ 69 (82)
T cd06397 8 LGDTRRIVFPDIPTWEALASKLENLYNLPEIKVGVTYIDN--DNDEITLSSNKELQDFYRLSHR 69 (82)
T ss_pred CCceEEEecCCCccHHHHHHHHHHHhCCChhHeEEEEEcC--CCCEEEecchHHHHHHHHhccc
Confidence 5677777888899999999999999999877888888743 5579999999999998886544
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=91.18 E-value=1.1 Score=42.76 Aligned_cols=71 Identities=15% Similarity=0.290 Sum_probs=56.8
Q ss_pred CCceeEEEEcCCCChHHHHHHHHHhcCCCC---CceEEEEEecCCCCceEEeechHHHHHHHHhhcCc--CeEEEEEe
Q 039468 553 GGDAHALSVNKESSFDELKLEMAEMWKYDP---NSMIVKYFLPNNNKTLITISGDKDIRRLIDFHEDS--GTVDVYVM 625 (1282)
Q Consensus 553 GG~t~~i~Vdr~iSf~ef~~kL~e~~~~~~---~~~~lky~LP~~~~~Li~v~dD~Dl~~M~e~~~~~--~~v~IYve 625 (1282)
.|+++-+.+...+++.+|++.|...+|.+. ..+.++|.= +....++|++|.||..-++++... ..+.++|.
T Consensus 9 ~GrvhRf~~~~s~~~~~L~~~I~~Rl~~d~~~~~~~~L~YlD--DEgD~VllT~D~DL~e~v~iar~~g~~~v~L~v~ 84 (86)
T cd06409 9 KGRVHRFRLRPSESLEELRTLISQRLGDDDFETHLYALSYVD--DEGDIVLITSDSDLVAAVLVARSAGLKKLDLHLH 84 (86)
T ss_pred CCCEEEEEecCCCCHHHHHHHHHHHhCCccccCCcccEEEEc--CCCCEEEEeccchHHHHHHHHHHcCCCEEEEEEe
Confidence 688889999989999999999999999875 456667662 234589999999999999986544 45888774
No 27
>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=90.75 E-value=0.17 Score=34.26 Aligned_cols=18 Identities=28% Similarity=0.711 Sum_probs=16.4
Q ss_pred eeccccCcCCCCcCCCCC
Q 039468 1263 LHCSKCKGAGHNRKTCHV 1280 (1282)
Q Consensus 1263 ~~CSrCk~~GHNkrTCp~ 1280 (1282)
++|-+|++.||..+.||.
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 479999999999999985
No 28
>PF01610 DDE_Tnp_ISL3: Transposase; InterPro: IPR002560 Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element. Transposases have been grouped into various families [, , ]. This family includes the IS204 [], IS1001 [], IS1096 [] and IS1165 [] transposases. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=90.25 E-value=0.35 Score=54.28 Aligned_cols=94 Identities=15% Similarity=0.173 Sum_probs=68.8
Q ss_pred eeecccccccccCcceeeeeeecC--CCCeEEEEEEEeccCCchhHHHHHHHH-HHhhcCCceEEEEecCcchHHHHHHH
Q 039468 905 IFLDSFPIKSKYQSSLLTATALDG--NDEIFPVAFGVVDAVSDDNWHWFLLQL-KSALSTCQSITFVTDRLGQLRASILS 981 (1282)
Q Consensus 905 I~iD~TyltnkY~g~Ll~avGvD~--n~~~~pvAfAvV~~Et~esw~WfLe~L-k~~m~~~~p~vIISD~~~gL~~AI~e 981 (1282)
|+||=+.....+.. +..+-+|. +.+. -+.++++-+.++..-||+.+ -.. ......+|++|...+..+||++
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 45666655543332 33344444 3332 24588888889988888877 333 3346789999999999999999
Q ss_pred HhhccceeccchhhhHHHHhhcc
Q 039468 982 VFENSYYCYCLHHLTEELKRDLK 1004 (1282)
Q Consensus 982 VFP~a~H~~C~~HI~~N~~k~lk 1004 (1282)
.||+|.+..-.|||++++.+.+.
T Consensus 75 ~~P~A~iv~DrFHvvk~~~~al~ 97 (249)
T PF01610_consen 75 YFPNAQIVADRFHVVKLANRALD 97 (249)
T ss_pred cccccccccccchhhhhhhhcch
Confidence 99999999999999999888654
No 29
>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=90.11 E-value=0.74 Score=52.57 Aligned_cols=147 Identities=17% Similarity=0.135 Sum_probs=87.8
Q ss_pred hhhhHHHHHHHHhhcCCCCChhhHHHHHHHhcCcccChHhHHHhhHhhhccCCCChhhhhhcHHHHHHHHHhhCCCcEEE
Q 039468 795 SRKLLASIVKEKLLEAPKCKPKEIAEEIRRDFGIELGYVKAWRALENARGESQVSYKDSYNQLPWLVDKILETNPGSVVT 874 (1282)
Q Consensus 795 Ssr~IA~~ik~~ir~~p~~~p~~I~~~l~~~~G~~iSy~q~~Rak~ka~e~i~G~~~esy~~L~~yl~~l~e~NPGs~~~ 874 (1282)
+.+++|-.+.... .-.++...|.+.+.+. |+.+|.+.+.+...++.+.+.. ..+.|++.-
T Consensus 5 g~~~~a~i~~l~~--~~~lp~~r~~~~~~~~-G~~is~~ti~~~~~~~~~~l~~-----------~~~~l~~~~------ 64 (271)
T PF03050_consen 5 GPSLLALIAYLKY--VYHLPLYRIQQMLEDL-GITISRGTIANWIKRVAEALKP-----------LYEALKEEL------ 64 (271)
T ss_pred CHHHHHHHHHHHh--cCCCCHHHHhhhhhcc-ceeeccchhHhHhhhhhhhhhh-----------hhhhhhhhc------
Confidence 3445554443332 2345566667777666 9999999888776555432211 111121111
Q ss_pred EccccCccceeeeecchhhHHHHHhcCCCeeeecccccc----cccC-cceeeeeeecCCCCeEEEEEEEeccCCchhHH
Q 039468 875 LSTREDLSFHHLFVALHASLYGFQNGCRPLIFLDSFPIK----SKYQ-SSLLTATALDGNDEIFPVAFGVVDAVSDDNWH 949 (1282)
Q Consensus 875 v~~ded~~F~rlF~a~~~si~gf~~gcrpVI~iD~Tylt----nkY~-g~Ll~avGvD~n~~~~pvAfAvV~~Et~esw~ 949 (1282)
. -.+|+.+|-|..+ ++.+ +-+-++++-+ .+.|.+.++-+.+...
T Consensus 65 -----------------------~--~~~~~~~DET~~~vl~~~~g~~~~~Wv~~~~~------~v~f~~~~sR~~~~~~ 113 (271)
T PF03050_consen 65 -----------------------R--SSPVVHADETGWRVLDKGKGKKGYLWVFVSPE------VVLFFYAPSRSSKVIK 113 (271)
T ss_pred -----------------------c--ccceeccCCceEEEeccccccceEEEeeeccc------eeeeeecccccccchh
Confidence 1 2477888888776 4333 2333333333 5566666666666555
Q ss_pred HHHHHHHHhhcCCceEEEEecCcchHHHHHHHHhhccceeccchhhhHHHHhhccC
Q 039468 950 WFLLQLKSALSTCQSITFVTDRLGQLRASILSVFENSYYCYCLHHLTEELKRDLKG 1005 (1282)
Q Consensus 950 WfLe~Lk~~m~~~~p~vIISD~~~gL~~AI~eVFP~a~H~~C~~HI~~N~~k~lk~ 1005 (1282)
-+|.. . .-+++||+-.+-.. +....|+.|..|+.+.|.+-...
T Consensus 114 ~~L~~-------~-~GilvsD~y~~Y~~-----~~~~~hq~C~AH~~R~~~~~~~~ 156 (271)
T PF03050_consen 114 EFLGD-------F-SGILVSDGYSAYNK-----LAGITHQLCWAHLRRDFQDAAES 156 (271)
T ss_pred hhhcc-------c-ceeeeccccccccc-----ccccccccccccccccccccccc
Confidence 55443 1 24899999998654 23889999999999999887654
No 30
>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=89.64 E-value=2.1 Score=40.34 Aligned_cols=68 Identities=24% Similarity=0.417 Sum_probs=52.7
Q ss_pred CCceeEEEEcCC-CChHHHHHHHHHhcCCC---CCceEEEEEecCCCCceEEeechHHHHHHHHhhcCcCeEEEE
Q 039468 553 GGDAHALSVNKE-SSFDELKLEMAEMWKYD---PNSMIVKYFLPNNNKTLITISGDKDIRRLIDFHEDSGTVDVY 623 (1282)
Q Consensus 553 GG~t~~i~Vdr~-iSf~ef~~kL~e~~~~~---~~~~~lky~LP~~~~~Li~v~dD~Dl~~M~e~~~~~~~v~IY 623 (1282)
||+.|.+.+..+ ++|.+|++.+...|+.. ..++.+||.=+. ..|++|.++.||.--+... +.-.+.|+
T Consensus 8 g~DiR~~~~~~~~~t~~~L~~~v~~~F~~~~~~~~~flIKYkD~d--GDlVTIts~~dL~~A~~~~-~~~~l~~~ 79 (81)
T cd06401 8 GDDIRRIPIHNEDITYDELLLMMQRVFRGKLGSSDDVLIKYKDED--GDLITIFDSSDLSFAIQCS-RILKLTLF 79 (81)
T ss_pred CCeEEEEeccCccccHHHHHHHHHHHhccccCCcccEEEEEECCC--CCEEEeccHHHHHHHHhcC-cceEEEEe
Confidence 899999999985 89999999999888753 357889997543 3699999999998776654 33344444
No 31
>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=88.60 E-value=2.6 Score=38.85 Aligned_cols=67 Identities=16% Similarity=0.379 Sum_probs=54.2
Q ss_pred CCceeEEEEcCCCChHHHHHHHHHhcCCCCCceEEEEEecCCCCceEEeechHHHHHHHHhhcCc---CeEEEEEe
Q 039468 553 GGDAHALSVNKESSFDELKLEMAEMWKYDPNSMIVKYFLPNNNKTLITISGDKDIRRLIDFHEDS---GTVDVYVM 625 (1282)
Q Consensus 553 GG~t~~i~Vdr~iSf~ef~~kL~e~~~~~~~~~~lky~LP~~~~~Li~v~dD~Dl~~M~e~~~~~---~~v~IYve 625 (1282)
-|+.+++.+.|-+.|.|+..|+.+.||. ++-++|... .-+++|.+.+||++-++..+.+ +.+.|++.
T Consensus 8 ~gEKRIi~f~RPvkf~dl~~kv~~afGq---~mdl~ytn~---eL~iPl~~Q~DLDkAie~ld~s~~~ksLRilL~ 77 (79)
T cd06405 8 NGEKRIIQFPRPVKFKDLQQKVTTAFGQ---PMDLHYTNN---ELLIPLKNQEDLDRAIELLDRSPHMKSLRILLS 77 (79)
T ss_pred cCceEEEecCCCccHHHHHHHHHHHhCC---eeeEEEecc---cEEEeccCHHHHHHHHHHHccCccccceeEeEe
Confidence 4789999999999999999999999885 477888743 3789999999999988865543 44666654
No 32
>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=88.17 E-value=1.8 Score=40.54 Aligned_cols=63 Identities=16% Similarity=0.239 Sum_probs=56.0
Q ss_pred ceeEEEEcCCCChHHHHHHHHHhcCCCCCceEEEEEecCCCCceEEeechHHHHHHHHhhcCc
Q 039468 555 DAHALSVNKESSFDELKLEMAEMWKYDPNSMIVKYFLPNNNKTLITISGDKDIRRLIDFHEDS 617 (1282)
Q Consensus 555 ~t~~i~Vdr~iSf~ef~~kL~e~~~~~~~~~~lky~LP~~~~~Li~v~dD~Dl~~M~e~~~~~ 617 (1282)
-|-.|.|.+..+|++|..+|+++|..-.+..++.|.-|.....+++|+.|+|++.+-....++
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 467889999999999999999999998888999999998887899999999999988865443
No 33
>PF13610 DDE_Tnp_IS240: DDE domain
Probab=88.07 E-value=0.14 Score=52.84 Aligned_cols=80 Identities=19% Similarity=0.101 Sum_probs=67.0
Q ss_pred CeeeecccccccccCcceeeeeeecCCCCeEEEEEEEeccCCchhHHHHHHHHHHhhcCCceEEEEecCcchHHHHHHHH
Q 039468 903 PLIFLDSFPIKSKYQSSLLTATALDGNDEIFPVAFGVVDAVSDDNWHWFLLQLKSALSTCQSITFVTDRLGQLRASILSV 982 (1282)
Q Consensus 903 pVI~iD~TyltnkY~g~Ll~avGvD~n~~~~pvAfAvV~~Et~esw~WfLe~Lk~~m~~~~p~vIISD~~~gL~~AI~eV 982 (1282)
+.+.+|-||.+-+=+ ..+...++|.+++ .|.+-|...-+...=..||..+.+... ..|..|+||+.++...|++++
T Consensus 2 ~~w~~DEt~iki~G~-~~yl~~aiD~~~~--~l~~~ls~~Rd~~aA~~Fl~~~l~~~~-~~p~~ivtDk~~aY~~A~~~l 77 (140)
T PF13610_consen 2 DSWHVDETYIKIKGK-WHYLWRAIDAEGN--ILDFYLSKRRDTAAAKRFLKRALKRHR-GEPRVIVTDKLPAYPAAIKEL 77 (140)
T ss_pred CEEEEeeEEEEECCE-EEEEEEeeccccc--chhhhhhhhcccccceeeccccceeec-cccceeecccCCccchhhhhc
Confidence 578899999884422 3455788999999 888999888888888889888887765 579999999999999999999
Q ss_pred hhcc
Q 039468 983 FENS 986 (1282)
Q Consensus 983 FP~a 986 (1282)
++..
T Consensus 78 ~~~~ 81 (140)
T PF13610_consen 78 NPEG 81 (140)
T ss_pred cccc
Confidence 9874
No 34
>PRK14702 insertion element IS2 transposase InsD; Provisional
Probab=86.84 E-value=42 Score=38.56 Aligned_cols=145 Identities=13% Similarity=0.115 Sum_probs=88.0
Q ss_pred hhhhHHHHHHHHhhcCCCCChhhHHHHHHHh---cCc-ccChHhHHHhhHhh-hccCCCChhhhhhcHHHHHHHHHhhCC
Q 039468 795 SRKLLASIVKEKLLEAPKCKPKEIAEEIRRD---FGI-ELGYVKAWRALENA-RGESQVSYKDSYNQLPWLVDKILETNP 869 (1282)
Q Consensus 795 Ssr~IA~~ik~~ir~~p~~~p~~I~~~l~~~---~G~-~iSy~q~~Rak~ka-~e~i~G~~~esy~~L~~yl~~l~e~NP 869 (1282)
....+...|++.+...+.+..+.|...|+++ .|+ .++..+++|....+ +....... .+
T Consensus 9 ~~~~l~~~I~~~~~~~~~yG~rri~~~L~~~~~~~g~~~v~~krV~rlmr~~gL~~~~r~~-----------------~~ 71 (262)
T PRK14702 9 DDTDVLLRIHHVIGELPTYGYRRVWALLRRQAELDGMPAINAKRVYRLMRQNALLLERKPA-----------------VP 71 (262)
T ss_pred chHHHHHHHHHHHHhCcccChHHHHHHHHhhhcccCccccCHHHHHHHHHHhCCccccCCC-----------------CC
Confidence 3445666777777778889999999999876 377 58999999875432 21100000 00
Q ss_pred CcEEEEccccCccceeeeecchhhHHHHHhcCCCeeeecccccccccCcceeeeeeecCCCCeEEEEEEEecc-CCchhH
Q 039468 870 GSVVTLSTREDLSFHHLFVALHASLYGFQNGCRPLIFLDSFPIKSKYQSSLLTATALDGNDEIFPVAFGVVDA-VSDDNW 948 (1282)
Q Consensus 870 Gs~~~v~~ded~~F~rlF~a~~~si~gf~~gcrpVI~iD~TyltnkY~g~Ll~avGvD~n~~~~pvAfAvV~~-Et~esw 948 (1282)
.+. ...... |. ...-..++..|-||.....++.++.++-+|...+ .+||+++... .+.+.-
T Consensus 72 ~~~-------~~~~~~-~~---------~~~pn~~W~~DiT~~~~~~g~~~Yl~~viD~~sR-~ivg~~is~~~~~~~~v 133 (262)
T PRK14702 72 PSK-------RAHTGR-VA---------VKESNQRWCSDGFEFCCDNGERLRVTFALDCCDR-EALHWAVTTGGFNSETV 133 (262)
T ss_pred CCC-------cCCCCc-cc---------cCCCCCEEEeeeEEEEecCCcEEEEEEEEecccc-eeeeEEeccCcCCHHHH
Confidence 000 000000 10 1113468889999877554446888888887666 7789999874 565555
Q ss_pred HHHHHHHHHh-hc---CCceEEEEecCcch
Q 039468 949 HWFLLQLKSA-LS---TCQSITFVTDRLGQ 974 (1282)
Q Consensus 949 ~WfLe~Lk~~-m~---~~~p~vIISD~~~g 974 (1282)
.-+|+...+. .+ ...|.+|.||+...
T Consensus 134 ~~~l~~A~~~~~~~~~~~~~~iihSD~Gsq 163 (262)
T PRK14702 134 QDVMLGAVERRFGNDLPSSPVEWLTDNGSC 163 (262)
T ss_pred HHHHHHHHHHHhcccCCCCCeEEEcCCCcc
Confidence 5555544333 22 23578899999874
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=85.72 E-value=2.1 Score=38.09 Aligned_cols=44 Identities=25% Similarity=0.359 Sum_probs=34.8
Q ss_pred eecC-CeEEEEeeecCCCceEEEEEEeCCCCeEEEEeecCCCcCC
Q 039468 740 KKNE-GLRVTAKCKAEGCPWRIHASRVPTTQLFQIKTMNGMHTCK 783 (1282)
Q Consensus 740 kKSd-k~Rv~~~C~~~GCpWrI~As~~~~s~~w~Ik~~~~eHnC~ 783 (1282)
++++ -.|..++|+..+||++-...+..++....++++..+|||+
T Consensus 15 i~g~~~pRsYYrCt~~~C~akK~Vqr~~~d~~~~~vtY~G~H~h~ 59 (60)
T PF03106_consen 15 IKGSPYPRSYYRCTHPGCPAKKQVQRSADDPNIVIVTYEGEHNHP 59 (60)
T ss_dssp ETTTTCEEEEEEEECTTEEEEEEEEEETTCCCEEEEEEES--SS-
T ss_pred cCCCceeeEeeeccccChhheeeEEEecCCCCEEEEEEeeeeCCC
Confidence 4444 3577899999999999999888877889999999999996
No 36
>PHA02517 putative transposase OrfB; Reviewed
Probab=84.72 E-value=5.8 Score=45.34 Aligned_cols=151 Identities=15% Similarity=0.023 Sum_probs=87.1
Q ss_pred hhHHHHHHHHhhc-CCCCChhhHHHHHHHhcCcccChHhHHHhhHhh-hccC-CCChhhhhhcHHHHHHHHHhhCCCcEE
Q 039468 797 KLLASIVKEKLLE-APKCKPKEIAEEIRRDFGIELGYVKAWRALENA-RGES-QVSYKDSYNQLPWLVDKILETNPGSVV 873 (1282)
Q Consensus 797 r~IA~~ik~~ir~-~p~~~p~~I~~~l~~~~G~~iSy~q~~Rak~ka-~e~i-~G~~~esy~~L~~yl~~l~e~NPGs~~ 873 (1282)
..+.+.+.+++.. .+.+..+.|...|+++ |+.+|.++++|..+.. +... ..... +. ......
T Consensus 29 ~~l~~~I~~i~~~~~~~~G~r~I~~~L~~~-g~~vs~~tV~Rim~~~gl~~~~~~k~~--~~---------~~~~~~--- 93 (277)
T PHA02517 29 DWLKSEILRVYDENHQVYGVRKVWRQLNRE-GIRVARCTVGRLMKELGLAGVLRGKKV--RT---------TISRKA--- 93 (277)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHHHhc-CcccCHHHHHHHHHHcCCceEecCCCc--CC---------CCCCCC---
Confidence 3466667777655 5789999999998765 9999999999865432 1100 00000 00 000000
Q ss_pred EEccccCccceeeeecchhhHHHHHhcCCCeeeecccccccccCcceeeeeeecCCCCeEEEEEEEeccCCchhHHHHHH
Q 039468 874 TLSTREDLSFHHLFVALHASLYGFQNGCRPLIFLDSFPIKSKYQSSLLTATALDGNDEIFPVAFGVVDAVSDDNWHWFLL 953 (1282)
Q Consensus 874 ~v~~ded~~F~rlF~a~~~si~gf~~gcrpVI~iD~TyltnkY~g~Ll~avGvD~n~~~~pvAfAvV~~Et~esw~WfLe 953 (1282)
....+.+.+-|-+. .-..++..|-|+..... +..+.++.+|...+ +++|+.+...++.+...-+|+
T Consensus 94 ---~~~~n~~~r~f~~~---------~pn~~w~~D~t~~~~~~-g~~yl~~iiD~~sr-~i~~~~~~~~~~~~~~~~~l~ 159 (277)
T PHA02517 94 ---VAAPDRVNRQFVAT---------RPNQLWVADFTYVSTWQ-GWVYVAFIIDVFAR-RIVGWRVSSSMDTDFVLDALE 159 (277)
T ss_pred ---CCCCCcccCCCCCC---------CCCCeEEeceeEEEeCC-CCEEEEEecccCCC-eeeecccCCCCChHHHHHHHH
Confidence 00011222222111 13468999999986543 55667777776555 567788887777775544444
Q ss_pred HHHHhhcCCceEEEEecCcchHH
Q 039468 954 QLKSALSTCQSITFVTDRLGQLR 976 (1282)
Q Consensus 954 ~Lk~~m~~~~p~vIISD~~~gL~ 976 (1282)
.+....+...+.+|.||+.....
T Consensus 160 ~a~~~~~~~~~~i~~sD~G~~y~ 182 (277)
T PHA02517 160 QALWARGRPGGLIHHSDKGSQYV 182 (277)
T ss_pred HHHHhcCCCcCcEeecccccccc
Confidence 44444343334677899988754
No 37
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=77.74 E-value=1.4 Score=34.37 Aligned_cols=20 Identities=25% Similarity=0.630 Sum_probs=18.1
Q ss_pred ceeeccccCcCCCCcCCCCC
Q 039468 1261 RELHCSKCKGAGHNRKTCHV 1280 (1282)
Q Consensus 1261 r~~~CSrCk~~GHNkrTCp~ 1280 (1282)
..+.|.+|++.||..+.||.
T Consensus 7 ~~Y~C~~C~~~GH~i~dCP~ 26 (32)
T PF13696_consen 7 PGYVCHRCGQKGHWIQDCPT 26 (32)
T ss_pred CCCEeecCCCCCccHhHCCC
Confidence 34899999999999999996
No 38
>KOG3069 consensus Peroxisomal NUDIX hydrolase [Replication, recombination and repair]
Probab=71.69 E-value=3.4 Score=46.10 Aligned_cols=45 Identities=16% Similarity=0.148 Sum_probs=36.2
Q ss_pred ccccchhcccccceEEeeecccCCCCceEeecccccccccccccccccccc
Q 039468 476 AEKENLYEVGKIAGIAICEARTSPQGQSVLIPDVYSHLVRGSDIGTGCEAM 526 (1282)
Q Consensus 476 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~m 526 (1282)
+-|..-.+..+-++|+||++-+--++.+|||++ |+.++.|++..|
T Consensus 32 ~~~~~~~~~~~~~aVlI~L~~~~~~~l~vLltk------RSr~LrshsGev 76 (246)
T KOG3069|consen 32 SKSETHDFPNRKAAVLIPLVQVGSGELSVLLTK------RSRTLRSHSGEV 76 (246)
T ss_pred hhcccccCCCCCccEEEEEEEcCCCceEEEEEe------ccccccccCCce
Confidence 334444457788999999999977789999999 999999998443
No 39
>PF04500 FLYWCH: FLYWCH zinc finger domain; InterPro: IPR007588 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a potential FLYWCH Zn-finger domain found in a number of eukaryotic proteins. FLYWCH is a C2H2-type zinc finger characterised by five conserved hydrophobic residues, containing the conserved sequence motif: F/Y-X(n)-L-X(n)-F/Y-X(n)-WXCX(6-12)CX(17-22)HXH where X indicates any amino acid. This domain was first characterised in Drosophila Modifier of mdg4 proteins, Mod(mgd4), putative chromatin modulators involved in higher order chromatin domains. Mod(mdg4) proteins share a common N-terminal BTB/POZ domain, but differ in their C-terminal region, most containing C-terminal FLYWCH zinc finger motifs []. The FLYWCH domain in Mod(mdg4) proteins has a putative role in protein-protein interactions; for example, Mod(mdg4)-67.2 interacts with DNA-binding protein Su(Hw) via its FLYWCH domain. FLYWCH domains have been described in other proteins as well, including suppressor of killer of prune, Su(Kpn), which contains 4 terminal FLYWCH zinc finger motifs in a tandem array and a C-terminal glutathione SH-transferase (GST) domain []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2RPR_A.
Probab=71.05 E-value=6 Score=34.25 Aligned_cols=46 Identities=24% Similarity=0.465 Sum_probs=25.4
Q ss_pred cCceEEEeecCCeEEEEeeecC---CCceEEEEEEeCCCCeEEEEeecCCCcC
Q 039468 733 HGFTYCFKKNEGLRVTAKCKAE---GCPWRIHASRVPTTQLFQIKTMNGMHTC 782 (1282)
Q Consensus 733 ~gF~~rvkKSdk~Rv~~~C~~~---GCpWrI~As~~~~s~~w~Ik~~~~eHnC 782 (1282)
.|+.|.+.+.........|... +|+++|... .+ .-.|.....+|||
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 5788888777788899999863 899999997 22 2345555578887
No 40
>PF13565 HTH_32: Homeodomain-like domain
Probab=70.75 E-value=7 Score=35.68 Aligned_cols=41 Identities=27% Similarity=0.463 Sum_probs=34.9
Q ss_pred hHHHHHHHHhhcCCCCChhhHHHHHHHhcCccc--ChHhHHHh
Q 039468 798 LLASIVKEKLLEAPKCKPKEIAEEIRRDFGIEL--GYVKAWRA 838 (1282)
Q Consensus 798 ~IA~~ik~~ir~~p~~~p~~I~~~l~~~~G~~i--Sy~q~~Ra 838 (1282)
.+.+.+.+.+..+|.+++.+|+..|.+++|+.+ |.+.+||.
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 344667777888999999999999999999876 99999874
No 41
>COG3316 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=70.48 E-value=27 Score=38.93 Aligned_cols=120 Identities=17% Similarity=0.092 Sum_probs=80.8
Q ss_pred HHHHhcCcccChHhHHHhhHhhhccCCCChhhhhhcHHHHHHHHHhhCCCcEEEEccccCccceeeeecchhhHHHHHhc
Q 039468 821 EIRRDFGIELGYVKAWRALENARGESQVSYKDSYNQLPWLVDKILETNPGSVVTLSTREDLSFHHLFVALHASLYGFQNG 900 (1282)
Q Consensus 821 ~l~~~~G~~iSy~q~~Rak~ka~e~i~G~~~esy~~L~~yl~~l~e~NPGs~~~v~~ded~~F~rlF~a~~~si~gf~~g 900 (1282)
.+..+.|+.+.+..+.|.-++.- |.+.+.+++.++.
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 34567799999998887654321 3344555555433
Q ss_pred CCCeeeecccccccccCcceeeeeeecCCCCeEEEEEEEeccCCchhHHHHHHHHHHhhcCCceEEEEecCcchHHHHHH
Q 039468 901 CRPLIFLDSFPIKSKYQSSLLTATALDGNDEIFPVAFGVVDAVSDDNWHWFLLQLKSALSTCQSITFVTDRLGQLRASIL 980 (1282)
Q Consensus 901 crpVI~iD~TyltnkY~g~Ll~avGvD~n~~~~pvAfAvV~~Et~esw~WfLe~Lk~~m~~~~p~vIISD~~~gL~~AI~ 980 (1282)
-++++.+|-||.+-+-+. ...--++|.+|+ ++-+-+...-+...=.-||..+++.- ..|.+|+||+.+....|+.
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 AGDSWRVDETYIKVNGKW-HYLYRAIDADGL--TLDVWLSKRRNALAAKAFLKKLLKKH--GEPRVFVTDKAPSYTAALR 143 (215)
T ss_pred cccceeeeeeEEeeccEe-eehhhhhccCCC--eEEEEEEcccCcHHHHHHHHHHHHhc--CCCceEEecCccchHHHHH
Confidence 245777888888743322 223345566644 56667777777766677777766665 5789999999999999999
Q ss_pred HHhhcccee
Q 039468 981 SVFENSYYC 989 (1282)
Q Consensus 981 eVFP~a~H~ 989 (1282)
++-+...|+
T Consensus 144 ~l~~~~ehr 152 (215)
T COG3316 144 KLGSEVEHR 152 (215)
T ss_pred hcCcchhee
Confidence 998866554
No 42
>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=70.32 E-value=9.4 Score=35.43 Aligned_cols=65 Identities=12% Similarity=0.148 Sum_probs=44.7
Q ss_pred eCCceeEEEEcCCCChHHHHHHHHHhcCCCCCceEEEEEecCCCCceEEeechHHHHHHHHhhcCcCeEEEEE
Q 039468 552 SGGDAHALSVNKESSFDELKLEMAEMWKYDPNSMIVKYFLPNNNKTLITISGDKDIRRLIDFHEDSGTVDVYV 624 (1282)
Q Consensus 552 ~GG~t~~i~Vdr~iSf~ef~~kL~e~~~~~~~~~~lky~LP~~~~~Li~v~dD~Dl~~M~e~~~~~~~v~IYv 624 (1282)
.+|.+..+.|+.++|..+++.+|.+..|+..++.++ |. +.. +.+|.....-...-..+.++.+|+
T Consensus 10 ~~~~t~~l~v~~~~TV~~lK~kI~~~~gip~~~QrL-~~--G~~-----L~dD~~tL~~ygi~~~g~~~~l~~ 74 (75)
T cd01799 10 SHTVTIWLTVRPDMTVAQLKDKVFLDYGFPPAVQRW-VI--GQR-----LARDQETLYSHGIRTNGDSAFLYI 74 (75)
T ss_pred cCCCeEEEEECCCCcHHHHHHHHHHHHCcCHHHEEE-Ec--CCe-----eCCCcCCHHHcCCCCCCCEEEEEe
Confidence 367888899999999999999999999998888877 53 221 343433222222233446677775
No 43
>PF00665 rve: Integrase core domain; InterPro: IPR001584 Integrase comprises three domains capable of folding independently and whose three-dimensional structures are known. However, the manner in which the N-terminal, catalytic, and C-terminal domains interact in the holoenzyme remains obscure. Numerous studies indicate that the enzyme functions as a multimer, minimally a dimer. The integrase proteins from Human immunodeficiency virus 1 (HIV-1) and Avian sarcoma virus (ASV) have been studied most carefully with respect to the structural basis of catalysis. Although the active site of ASV integrase does not undergo significant conformational changes on binding the required metal cofactor, that of HIV-1 does. This active site-mediated conformational change in HIV-1 reorganises the catalytic core and C-terminal domains and appears to promote an interaction that is favourable for catalysis []. Retroviral integrase is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. The presence of retrovirus integrase-related gene sequences in eukaryotes is known. Bacterial transposases involved in the transposition of the insertion sequence also belong to this group. HIV integrase catalyses the incorporation of virally derived DNA into the human genome. This unique step in the virus life cycle provides a variety of points for intervention and hence is an attractive target for the development of new therapeutics for the treatment of AIDS []. Substrate recognition by the retroviral integrase enzyme is critical for retroviral integration. To catalyse this recombination event, integrase must recognise and act on two types of substrates, viral DNA and host DNA, yet the necessary interactions exhibit markedly different degrees of specificity [].; GO: 0015074 DNA integration; PDB: 3AO3_A 3OVN_A 3AO5_A 3AO4_A 3AO1_A 1C6V_D 3HPG_A 3HPH_A 3OYD_A 3OYF_B ....
Probab=68.67 E-value=30 Score=33.67 Aligned_cols=76 Identities=13% Similarity=0.040 Sum_probs=56.0
Q ss_pred CCCeeeecccccc-cccCcceeeeeeecCCCCeEEEEEEEeccCCchhHHHHHHHHHHhhcCCceEEEEecCcchHHH
Q 039468 901 CRPLIFLDSFPIK-SKYQSSLLTATALDGNDEIFPVAFGVVDAVSDDNWHWFLLQLKSALSTCQSITFVTDRLGQLRA 977 (1282)
Q Consensus 901 crpVI~iD~Tylt-nkY~g~Ll~avGvD~n~~~~pvAfAvV~~Et~esw~WfLe~Lk~~m~~~~p~vIISD~~~gL~~ 977 (1282)
-..++.+|.++.. ...++.....+.+|..-+ +.+++.+-..++.+.+.-+|+......+...|.+|+||+.++..+
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 3467889998666 344558888889997665 455777777778888888888777776665599999999998874
No 44
>COG5179 TAF1 Transcription initiation factor TFIID, subunit TAF1 [Transcription]
Probab=67.19 E-value=3 Score=51.48 Aligned_cols=25 Identities=28% Similarity=0.748 Sum_probs=20.2
Q ss_pred CCCceeeccccCcCCCCc--CCCCCCC
Q 039468 1258 RPKRELHCSKCKGAGHNR--KTCHVYA 1282 (1282)
Q Consensus 1258 ~~Kr~~~CSrCk~~GHNk--rTCp~~~ 1282 (1282)
++..+++|++|+|.||-| +.||+|+
T Consensus 933 RK~Ttr~C~nCGQvGHmkTNK~CP~f~ 959 (968)
T COG5179 933 RKNTTRTCGNCGQVGHMKTNKACPKFS 959 (968)
T ss_pred CCCcceecccccccccccccccCcccc
Confidence 344678999999999966 5799885
No 45
>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=64.14 E-value=9.7 Score=33.93 Aligned_cols=38 Identities=26% Similarity=0.398 Sum_probs=31.5
Q ss_pred eEEEEeeec-CCCceEEEEEEeCCCCeEEEEeecCCCcC
Q 039468 745 LRVTAKCKA-EGCPWRIHASRVPTTQLFQIKTMNGMHTC 782 (1282)
Q Consensus 745 ~Rv~~~C~~-~GCpWrI~As~~~~s~~w~Ik~~~~eHnC 782 (1282)
.|..++|+. .||+++=...+..++....++++..+|||
T Consensus 21 pRsYYrCt~~~~C~a~K~Vq~~~~d~~~~~vtY~g~H~h 59 (59)
T smart00774 21 PRSYYRCTYSQGCPAKKQVQRSDDDPSVVEVTYEGEHTH 59 (59)
T ss_pred cceEEeccccCCCCCcccEEEECCCCCEEEEEEeeEeCC
Confidence 466789998 89999877777766667788999999998
No 46
>PF14560 Ubiquitin_2: Ubiquitin-like domain; PDB: 1WJN_A 2KJ6_A 2KJR_A 1V6E_A 1T0Y_A.
Probab=54.94 E-value=33 Score=32.41 Aligned_cols=48 Identities=13% Similarity=0.195 Sum_probs=35.7
Q ss_pred eeEEEEcCCCChHHHHHHHHHhcCCCCCceEEEEEecCCCCceEEeec
Q 039468 556 AHALSVNKESSFDELKLEMAEMWKYDPNSMIVKYFLPNNNKTLITISG 603 (1282)
Q Consensus 556 t~~i~Vdr~iSf~ef~~kL~e~~~~~~~~~~lky~LP~~~~~Li~v~d 603 (1282)
.....++.+|+..||+.+|...+|+.+..+++.+.-..+...+..+.+
T Consensus 15 ~~ekr~~~~~Tv~eLK~kl~~~~Gi~~~~m~L~l~~~~~~~~~~~~~d 62 (87)
T PF14560_consen 15 SVEKRFPKSITVSELKQKLEKLTGIPPSDMRLQLKSDKDDSKIEELDD 62 (87)
T ss_dssp EEEEEEETTSBHHHHHHHHHHHHTS-TTTEEEEEE-TSSSSEEEESSG
T ss_pred eEEEEcCCCCCHHHHHHHHHHHhCCCcccEEEEEEecCCCccccccCC
Confidence 455789999999999999999999999999997753344444444433
No 47
>smart00343 ZnF_C2HC zinc finger.
Probab=52.74 E-value=6.8 Score=28.67 Aligned_cols=17 Identities=29% Similarity=0.802 Sum_probs=15.3
Q ss_pred eccccCcCCCCcCCCCC
Q 039468 1264 HCSKCKGAGHNRKTCHV 1280 (1282)
Q Consensus 1264 ~CSrCk~~GHNkrTCp~ 1280 (1282)
.|.+|++.||..+.||.
T Consensus 1 ~C~~CG~~GH~~~~C~~ 17 (26)
T smart00343 1 KCYNCGKEGHIARDCPK 17 (26)
T ss_pred CCccCCCCCcchhhCCc
Confidence 48999999999999983
No 48
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=52.60 E-value=5.7 Score=33.79 Aligned_cols=19 Identities=32% Similarity=0.704 Sum_probs=17.2
Q ss_pred eeeccccCcCCCCcCCCCC
Q 039468 1262 ELHCSKCKGAGHNRKTCHV 1280 (1282)
Q Consensus 1262 ~~~CSrCk~~GHNkrTCp~ 1280 (1282)
...|+.|+..||+.+.||.
T Consensus 31 p~~C~~C~~~gH~~~~C~k 49 (49)
T PF14392_consen 31 PRFCFHCGRIGHSDKECPK 49 (49)
T ss_pred ChhhcCCCCcCcCHhHcCC
Confidence 4689999999999999984
No 49
>PRK09409 IS2 transposase TnpB; Reviewed
Probab=50.17 E-value=2e+02 Score=33.73 Aligned_cols=143 Identities=13% Similarity=0.141 Sum_probs=87.6
Q ss_pred hHHHHHHHHhhcCCCCChhhHHHHHHHhc---Cc-ccChHhHHHhhHhh-hccCCCChhhhhhcHHHHHHHHHhhCCCcE
Q 039468 798 LLASIVKEKLLEAPKCKPKEIAEEIRRDF---GI-ELGYVKAWRALENA-RGESQVSYKDSYNQLPWLVDKILETNPGSV 872 (1282)
Q Consensus 798 ~IA~~ik~~ir~~p~~~p~~I~~~l~~~~---G~-~iSy~q~~Rak~ka-~e~i~G~~~esy~~L~~yl~~l~e~NPGs~ 872 (1282)
.+.+.|++++...+.+..+.|...|+++. |+ .++..+++|..+.+ +...... ..+.+.
T Consensus 51 ~l~~~I~~i~~~~~~yG~Rri~~~L~~~g~~~g~~~v~~k~V~RlMr~~Gl~~~~~~-----------------~~~~~~ 113 (301)
T PRK09409 51 DVLLRIHHVIGELPTYGYRRVWALLRRQAELDGMPAINAKRVYRIMRQNALLLERKP-----------------AVPPSK 113 (301)
T ss_pred HHHHHHHHHHHhCccCCHHHHHHHHHhhhcccCccccCHHHHHHHHHHcCCcccccC-----------------CCCCCC
Confidence 45556666667778899999999998763 66 58999998865432 2110000 000000
Q ss_pred EEEccccCccceeeeecchhhHHHHHhcCCCeeeecccccccccCcceeeeeeecCCCCeEEEEEEEecc-CCchhHHHH
Q 039468 873 VTLSTREDLSFHHLFVALHASLYGFQNGCRPLIFLDSFPIKSKYQSSLLTATALDGNDEIFPVAFGVVDA-VSDDNWHWF 951 (1282)
Q Consensus 873 ~~v~~ded~~F~rlF~a~~~si~gf~~gcrpVI~iD~TyltnkY~g~Ll~avGvD~n~~~~pvAfAvV~~-Et~esw~Wf 951 (1282)
..+... |. ...-..++..|-||....-++.++.++-+|...+ .+||+++... .+.+.-.-+
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 000001 10 1123468999999976554556788888888776 6889999875 566665556
Q ss_pred HHH-HHHhhc---CCceEEEEecCcchH
Q 039468 952 LLQ-LKSALS---TCQSITFVTDRLGQL 975 (1282)
Q Consensus 952 Le~-Lk~~m~---~~~p~vIISD~~~gL 975 (1282)
|+. +....+ ...+.+|.||+....
T Consensus 176 l~~a~~~~~~~~~~~~~~iihSDrGsqy 203 (301)
T PRK09409 176 MLGAVERRFGNDLPSSPVEWLTDNGSCY 203 (301)
T ss_pred HHHHHHHHhccCCCCCCcEEecCCCccc
Confidence 654 444333 224778999998753
No 50
>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=48.86 E-value=31 Score=30.79 Aligned_cols=41 Identities=24% Similarity=0.474 Sum_probs=34.6
Q ss_pred EEEeCCceeEEEEcCCCChHHHHHHHHHhcCCCCCceEEEEE
Q 039468 549 LVYSGGDAHALSVNKESSFDELKLEMAEMWKYDPNSMIVKYF 590 (1282)
Q Consensus 549 ~~Y~GG~t~~i~Vdr~iSf~ef~~kL~e~~~~~~~~~~lky~ 590 (1282)
+.+ +|++..+.|+.+.|..+|+.+|.+.+++..+..++.|-
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 455 48888899999999999999999999998877777654
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=48.46 E-value=35 Score=27.71 Aligned_cols=43 Identities=16% Similarity=0.161 Sum_probs=35.0
Q ss_pred EEEeCCceeEEEEcCCCChHHHHHHHHHhcCCCCCceEEEEEe
Q 039468 549 LVYSGGDAHALSVNKESSFDELKLEMAEMWKYDPNSMIVKYFL 591 (1282)
Q Consensus 549 ~~Y~GG~t~~i~Vdr~iSf~ef~~kL~e~~~~~~~~~~lky~L 591 (1282)
+.+.+|....+.+..+.|..+++.+|.+.++...+.+.+.+-.
T Consensus 2 v~~~~~~~~~~~~~~~~tv~~l~~~i~~~~~~~~~~~~l~~~~ 44 (69)
T cd00196 2 VKLNDGKTVELLVPSGTTVADLKEKLAKKLGLPPEQQRLLVNG 44 (69)
T ss_pred eEecCCCEEEEEcCCCCcHHHHHHHHHHHHCcChHHeEEEECC
Confidence 3455888999999999999999999999998776666665544
No 52
>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=42.95 E-value=59 Score=29.24 Aligned_cols=42 Identities=14% Similarity=0.169 Sum_probs=35.5
Q ss_pred EEEeCCceeEEEEcCCCChHHHHHHHHHhcCCCC-CceEEEEE
Q 039468 549 LVYSGGDAHALSVNKESSFDELKLEMAEMWKYDP-NSMIVKYF 590 (1282)
Q Consensus 549 ~~Y~GG~t~~i~Vdr~iSf~ef~~kL~e~~~~~~-~~~~lky~ 590 (1282)
+.-.+|+...+.|.++.++..|+.+.++..+++. ++++|.|-
T Consensus 5 v~~~~~~~~~~~v~~~~~~~~l~~~~~~~~~i~~~~~~~l~fd 47 (72)
T PF11976_consen 5 VRSQDGKEIKFKVKPTTTVSKLIEKYCEKKGIPPEESIRLIFD 47 (72)
T ss_dssp EEETTSEEEEEEEETTSCCHHHHHHHHHHHTTTT-TTEEEEET
T ss_pred EEeCCCCEEEEEECCCCcHHHHHHHHHHhhCCCccceEEEEEC
Confidence 4456778888999999999999999999999987 77776663
No 53
>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=42.20 E-value=46 Score=30.35 Aligned_cols=42 Identities=17% Similarity=0.170 Sum_probs=35.6
Q ss_pred EEEeCCceeEEEEcCCCChHHHHHHHHHhcCCCCCceEEEEE
Q 039468 549 LVYSGGDAHALSVNKESSFDELKLEMAEMWKYDPNSMIVKYF 590 (1282)
Q Consensus 549 ~~Y~GG~t~~i~Vdr~iSf~ef~~kL~e~~~~~~~~~~lky~ 590 (1282)
++..+|++..+.|+.+.|..+|+.+|.+..|+..++.++-|.
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 455678888999999999999999999999998777777554
No 54
>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=41.97 E-value=53 Score=31.03 Aligned_cols=58 Identities=12% Similarity=0.278 Sum_probs=41.1
Q ss_pred ceeEEEEcC--CCChHHHHHHHHHhcCCCCCceEEEEEecCCCCceEEeechHHHHHHHHhhc
Q 039468 555 DAHALSVNK--ESSFDELKLEMAEMWKYDPNSMIVKYFLPNNNKTLITISGDKDIRRLIDFHE 615 (1282)
Q Consensus 555 ~t~~i~Vdr--~iSf~ef~~kL~e~~~~~~~~~~lky~LP~~~~~Li~v~dD~Dl~~M~e~~~ 615 (1282)
..--+.|+. .++|.++++-|.+.+.-. ....|.| ..+...-|.|.+|+.++.|++.+.
T Consensus 11 g~vDw~V~~~~~L~F~DvL~~I~~vlp~a-T~tAFeY--EDE~gDRITVRSDeEm~AMlsyy~ 70 (91)
T cd06395 11 GAVDWTVQSGPQLLFRDVLDVIGQVLPEA-TTTAFEY--EDEDGDRITVRSDEEMKAMLSYYC 70 (91)
T ss_pred CcccccccCcccccHHHHHHHHHHhcccc-cccceee--ccccCCeeEecchHHHHHHHHHHH
Confidence 344466775 499999999999865422 2234444 344566899999999999999754
No 55
>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=40.66 E-value=43 Score=30.52 Aligned_cols=38 Identities=11% Similarity=0.112 Sum_probs=33.8
Q ss_pred CCceeEEEEcCCCChHHHHHHHHHhcCCCCCceEEEEE
Q 039468 553 GGDAHALSVNKESSFDELKLEMAEMWKYDPNSMIVKYF 590 (1282)
Q Consensus 553 GG~t~~i~Vdr~iSf~ef~~kL~e~~~~~~~~~~lky~ 590 (1282)
+|++..+.|+.+.|..+|+.+|.+..|+..++.++.|-
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 88999999999999999999999999998777777654
No 56
>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=38.30 E-value=64 Score=28.74 Aligned_cols=40 Identities=20% Similarity=0.205 Sum_probs=34.5
Q ss_pred EEeCCceeEEEEcCCCChHHHHHHHHHhcCCCCCceEEEE
Q 039468 550 VYSGGDAHALSVNKESSFDELKLEMAEMWKYDPNSMIVKY 589 (1282)
Q Consensus 550 ~Y~GG~t~~i~Vdr~iSf~ef~~kL~e~~~~~~~~~~lky 589 (1282)
....|++..+.|+.+.+..+|..+|.+.+|+..+..++.|
T Consensus 6 k~~~g~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~ 45 (72)
T cd01809 6 KTLDSQTHTFTVEEEITVLDLKEKIAEEVGIPVEQQRLIY 45 (72)
T ss_pred EeCCCCEEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEEE
Confidence 4456788889999999999999999999999877777776
No 57
>cd01803 Ubiquitin Ubiquitin. Ubiquitin (includes Ubq/RPL40e and Ubq/RPS27a fusions as well as homopolymeric multiubiquitin protein chains)
Probab=38.20 E-value=55 Score=29.50 Aligned_cols=40 Identities=13% Similarity=0.228 Sum_probs=34.0
Q ss_pred EEeCCceeEEEEcCCCChHHHHHHHHHhcCCCCCceEEEE
Q 039468 550 VYSGGDAHALSVNKESSFDELKLEMAEMWKYDPNSMIVKY 589 (1282)
Q Consensus 550 ~Y~GG~t~~i~Vdr~iSf~ef~~kL~e~~~~~~~~~~lky 589 (1282)
...+|++..+.|+.+.|-.+|+.+|.+.+++..+..++.|
T Consensus 6 ~~~~g~~~~~~v~~~~tV~~lK~~i~~~~g~~~~~q~L~~ 45 (76)
T cd01803 6 KTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIF 45 (76)
T ss_pred EcCCCCEEEEEECCcCcHHHHHHHHHHHhCCCHHHeEEEE
Confidence 3446788889999999999999999999999877777765
No 58
>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=36.89 E-value=1.1e+02 Score=29.54 Aligned_cols=60 Identities=12% Similarity=0.217 Sum_probs=45.9
Q ss_pred CCceeEEEEcCC----CChHHHHHHHHHhcCCCCCceEEEEEecCCCCceEEeechHHHHHHHHhhcC
Q 039468 553 GGDAHALSVNKE----SSFDELKLEMAEMWKYDPNSMIVKYFLPNNNKTLITISGDKDIRRLIDFHED 616 (1282)
Q Consensus 553 GG~t~~i~Vdr~----iSf~ef~~kL~e~~~~~~~~~~lky~LP~~~~~Li~v~dD~Dl~~M~e~~~~ 616 (1282)
|-.++-+.|..+ =+|.+|+..++..|+- +.+.+-|.=+.. .||.|-||+|+.-|++....
T Consensus 12 ~~~~rdi~vee~l~~~P~~kdLl~lmr~~f~~--~dIaLNYrD~EG--DLIRllddeDv~LMV~~~r~ 75 (92)
T cd06399 12 ISTIRDIAVEEDLSSTPLLKDLLELTRREFQR--EDIALNYRDAEG--DLIRLLSDEDVALMVRQSRG 75 (92)
T ss_pred CccccceEeecccccCccHHHHHHHHHHHhch--hheeeeeecCCC--CEEEEcchhhHHHHHHHHhc
Confidence 455666777765 4799999999998764 457788875433 59999999999999997643
No 59
>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=35.86 E-value=63 Score=29.07 Aligned_cols=41 Identities=17% Similarity=0.274 Sum_probs=35.0
Q ss_pred EEeCCceeEEEEcCCCChHHHHHHHHHhcCCCCCceEEEEE
Q 039468 550 VYSGGDAHALSVNKESSFDELKLEMAEMWKYDPNSMIVKYF 590 (1282)
Q Consensus 550 ~Y~GG~t~~i~Vdr~iSf~ef~~kL~e~~~~~~~~~~lky~ 590 (1282)
...+|++..+.|+.+.|..++++.|.+..|+..++.++.|-
T Consensus 4 k~~~g~~~~~~v~~~~tV~~lK~~i~~~~gi~~~~q~Li~~ 44 (70)
T cd01798 4 RTNTGHTFPVEVDPDTDIKQLKEVVAKRQGVPPDQLRVIFA 44 (70)
T ss_pred EcCCCCEEEEEECCCChHHHHHHHHHHHHCCCHHHeEEEEC
Confidence 34578889999999999999999999999998877777554
No 60
>PF04937 DUF659: Protein of unknown function (DUF 659); InterPro: IPR007021 These are transposase-like proteins with no known function.
Probab=34.48 E-value=1.2e+02 Score=32.07 Aligned_cols=63 Identities=11% Similarity=0.201 Sum_probs=47.7
Q ss_pred CCchhHHHHHHHHHHhhcCCceEEEEecCcchHHHHHH---HHhhccceeccchhhhHHHHhhccC
Q 039468 943 VSDDNWHWFLLQLKSALSTCQSITFVTDRLGQLRASIL---SVFENSYYCYCLHHLTEELKRDLKG 1005 (1282)
Q Consensus 943 Et~esw~WfLe~Lk~~m~~~~p~vIISD~~~gL~~AI~---eVFP~a~H~~C~~HI~~N~~k~lk~ 1005 (1282)
.+.+...-+|+...+.+|..+-+-||||....+.+|-+ +-+|.-...-|..|-+.-+.+.+.+
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 45556666666666667777777899999999888844 4578888889999998888777654
No 61
>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=33.46 E-value=70 Score=29.20 Aligned_cols=42 Identities=21% Similarity=0.238 Sum_probs=35.9
Q ss_pred cEEEeCCceeEEEEcCCCChHHHHHHHHHhcCCCCCceEEEE
Q 039468 548 SLVYSGGDAHALSVNKESSFDELKLEMAEMWKYDPNSMIVKY 589 (1282)
Q Consensus 548 ~~~Y~GG~t~~i~Vdr~iSf~ef~~kL~e~~~~~~~~~~lky 589 (1282)
++...+|++..+.|+.+.|-.+++.+|.+..|+...+.++-|
T Consensus 2 ~vk~~~G~~~~l~v~~~~TV~~lK~~I~~~~gi~~~~q~Li~ 43 (70)
T cd01794 2 KVRLSTGKDVKLSVSSKDTVGQLKKQLQAAEGVDPCCQRWFF 43 (70)
T ss_pred eEEcCCCCEEEEEECCcChHHHHHHHHHHHhCCCHHHeEEEE
Confidence 356678999999999999999999999999998777766654
No 62
>cd01806 Nedd8 Nebb8-like ubiquitin protein. Nedd8 (also known as Rub1) has a single conserved ubiquitin-like domain that is part of a protein modification pathway similar to that of ubiquitin. Nedd8 modifies a family of molecular scaffold proteins called cullins that are responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis.
Probab=33.18 E-value=94 Score=28.00 Aligned_cols=38 Identities=13% Similarity=0.224 Sum_probs=32.7
Q ss_pred eCCceeEEEEcCCCChHHHHHHHHHhcCCCCCceEEEE
Q 039468 552 SGGDAHALSVNKESSFDELKLEMAEMWKYDPNSMIVKY 589 (1282)
Q Consensus 552 ~GG~t~~i~Vdr~iSf~ef~~kL~e~~~~~~~~~~lky 589 (1282)
.+|++..+.|+.+.|..+|+.+|.+..++..+..++.|
T Consensus 8 ~~g~~~~~~v~~~~tv~~lK~~i~~~~g~~~~~qrL~~ 45 (76)
T cd01806 8 LTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIY 45 (76)
T ss_pred CCCCEEEEEECCCCCHHHHHHHHhHhhCCChhhEEEEE
Confidence 46777788999999999999999999999887777765
No 63
>KOG0695 consensus Serine/threonine protein kinase [Signal transduction mechanisms]
Probab=33.08 E-value=2.1e+02 Score=34.10 Aligned_cols=67 Identities=19% Similarity=0.333 Sum_probs=50.3
Q ss_pred EeCCceeEEEEcCCCChHHHHHHHHHhcCCC-CCceEEEEEecCCCCceEEeechHHHHHHHHhhcCcCe
Q 039468 551 YSGGDAHALSVNKESSFDELKLEMAEMWKYD-PNSMIVKYFLPNNNKTLITISGDKDIRRLIDFHEDSGT 619 (1282)
Q Consensus 551 Y~GG~t~~i~Vdr~iSf~ef~~kL~e~~~~~-~~~~~lky~LP~~~~~Li~v~dD~Dl~~M~e~~~~~~~ 619 (1282)
|-+|+.-+.+++..++|++|...+.+++... .+.+++||.-. .-.+++|++.-.|..-+.+......
T Consensus 21 ~y~g~i~i~~~~p~~~~e~~~~~vrd~c~~h~~q~~t~kwide--egdp~tv~sqmeleea~r~~~~~~d 88 (593)
T KOG0695|consen 21 HYGGDIFITSVDPATTFEELCEEVRDMCRLHQQQPLTLKWIDE--EGDPCTVSSQMELEEAFRLARQCRD 88 (593)
T ss_pred eecCcEEEEeccCcccHHHHHHHHHHHHHHhhcCCceeEeecC--CCCcceechhhhHHHHHHHHHhccc
Confidence 4455555667888899999999999999874 45578888743 3457888999899888887665544
No 64
>COG4066 Uncharacterized protein conserved in archaea [Function unknown]
Probab=32.88 E-value=32 Score=36.02 Aligned_cols=39 Identities=28% Similarity=0.549 Sum_probs=31.8
Q ss_pred CCCCccccCCCceeeccCCCCCCcccceeeecCCCcccccCCcccCCC
Q 039468 347 NCPPYHITPHNKKIYRNDTANFPYGAYHYYCAPGNAQHLEQPVDTCDP 394 (1282)
Q Consensus 347 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 394 (1282)
+=||+-+||.|-+|-|.|.. |||-=- -+.+.+|.+.|+=
T Consensus 117 lHPpgt~FPGgfkVrkkgnv--------yYCPVK-dkq~n~pgslC~f 155 (165)
T COG4066 117 LHPPGTTFPGGFKVRKKGNV--------YYCPVK-DKQLNQPGSLCEF 155 (165)
T ss_pred CCCCCCcCCCceEEEeeCCE--------Eecccc-ccccCCCcchhhe
Confidence 45999999999999998864 788554 5668899999973
No 65
>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=32.02 E-value=67 Score=29.57 Aligned_cols=38 Identities=13% Similarity=0.191 Sum_probs=34.0
Q ss_pred CCceeEEEEcCCCChHHHHHHHHHhcCCCCCceEEEEE
Q 039468 553 GGDAHALSVNKESSFDELKLEMAEMWKYDPNSMIVKYF 590 (1282)
Q Consensus 553 GG~t~~i~Vdr~iSf~ef~~kL~e~~~~~~~~~~lky~ 590 (1282)
+|++..+.|+.+.|..+|+.+|.+..++..++.++.|.
T Consensus 6 ~g~~~~l~v~~~~TV~~lK~~i~~~~gip~~~q~L~~~ 43 (76)
T cd01800 6 NGQMLNFTLQLSDPVSVLKVKIHEETGMPAGKQKLQYE 43 (76)
T ss_pred CCeEEEEEECCCCcHHHHHHHHHHHHCCCHHHEEEEEC
Confidence 68889999999999999999999999998888777764
No 66
>PTZ00044 ubiquitin; Provisional
Probab=31.94 E-value=85 Score=28.52 Aligned_cols=39 Identities=13% Similarity=0.284 Sum_probs=34.2
Q ss_pred EeCCceeEEEEcCCCChHHHHHHHHHhcCCCCCceEEEE
Q 039468 551 YSGGDAHALSVNKESSFDELKLEMAEMWKYDPNSMIVKY 589 (1282)
Q Consensus 551 Y~GG~t~~i~Vdr~iSf~ef~~kL~e~~~~~~~~~~lky 589 (1282)
-..|++..+.|+.+.|-.+|+.+|.+..|+..++.++.|
T Consensus 7 ~~~G~~~~l~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~ 45 (76)
T PTZ00044 7 TLTGKKQSFNFEPDNTVQQVKMALQEKEGIDVKQIRLIY 45 (76)
T ss_pred eCCCCEEEEEECCCCcHHHHHHHHHHHHCCCHHHeEEEE
Confidence 346888999999999999999999999999888877776
No 67
>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=31.06 E-value=67 Score=29.26 Aligned_cols=37 Identities=16% Similarity=0.232 Sum_probs=25.4
Q ss_pred CCceeEEEEcCCCChHHHHHHHHHhcCCCCCceEEEE
Q 039468 553 GGDAHALSVNKESSFDELKLEMAEMWKYDPNSMIVKY 589 (1282)
Q Consensus 553 GG~t~~i~Vdr~iSf~ef~~kL~e~~~~~~~~~~lky 589 (1282)
+|+...+.|..+.++.+++++.|.+++++.++..++|
T Consensus 5 ~~rr~~vkvtp~~~l~~VL~eac~k~~l~~~~~~L~h 41 (65)
T PF11470_consen 5 NFRRFKVKVTPNTTLNQVLEEACKKFGLDPSSYDLKH 41 (65)
T ss_dssp TS-EEEE---TTSBHHHHHHHHHHHTT--GGG-EEEE
T ss_pred CCcEEEEEECCCCCHHHHHHHHHHHcCCCccceEEEE
Confidence 5778889999999999999999999999877555444
No 68
>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=29.81 E-value=23 Score=22.35 Aligned_cols=9 Identities=33% Similarity=0.604 Sum_probs=3.5
Q ss_pred CCCCCCCCc
Q 039468 1243 PLTGPPKKR 1251 (1282)
Q Consensus 1243 R~~GRPKKk 1251 (1282)
|++|||+|.
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 69
>COG5431 Uncharacterized metal-binding protein [Function unknown]
Probab=28.94 E-value=30 Score=34.10 Aligned_cols=44 Identities=18% Similarity=0.323 Sum_probs=27.6
Q ss_pred CeeEEeccceeeeeccCcc----c-cCccchhHHHHHhhhCCCcccccccc
Q 039468 1153 GTFNVVNIDVWDCNCRGWQ----L-NGFPCVHAAAVLQHVGRNLPDYCSKF 1198 (1282)
Q Consensus 1153 ~~~~vVdl~~~tCSCr~wq----~-~GIPC~HaLAVl~~~g~~p~dyI~~~ 1198 (1282)
++.|+++.+ -|||..+- . -.-||.|++++=...-..-.++|+-+
T Consensus 42 ~rdYIl~~g--fCSCp~~~~svvl~Gk~~C~Hi~glk~A~~~gk~~~I~~y 90 (117)
T COG5431 42 ERDYILEGG--FCSCPDFLGSVVLKGKSPCAHIIGLKVAKITGKYDYIDAY 90 (117)
T ss_pred ccceEEEcC--cccCHHHHhHhhhcCcccchhhhheeeeeecCcEEEEEEe
Confidence 567888887 89998876 2 23579999886333222233444433
No 70
>cd01805 RAD23_N Ubiquitin-like domain of RAD23. RAD23 belongs to a family of adaptor molecules having affinity for both the proteasome and ubiquitinylated proteins and thought to shuttle these ubiquitinylated proteins to the proteasome for destruction. RAD23 interacts with ubiquitin through its C-terminal ubiquitin-associated domains (UBA) and with the proteasome through its N-terminal ubiquitin-like domain (UBL).
Probab=28.03 E-value=1.3e+02 Score=27.32 Aligned_cols=41 Identities=17% Similarity=0.238 Sum_probs=34.1
Q ss_pred EEEeCCceeEEEEcCCCChHHHHHHHHHhcCC--CCCceEEEE
Q 039468 549 LVYSGGDAHALSVNKESSFDELKLEMAEMWKY--DPNSMIVKY 589 (1282)
Q Consensus 549 ~~Y~GG~t~~i~Vdr~iSf~ef~~kL~e~~~~--~~~~~~lky 589 (1282)
+...+|++..+.|+.+.|-.+|..+|.+..++ ..+..++-|
T Consensus 5 vk~~~g~~~~l~v~~~~TV~~lK~~i~~~~~i~~~~~~q~L~~ 47 (77)
T cd01805 5 FKTLKQQTFPIEVDPDDTVAELKEKIEEEKGCDYPPEQQKLIY 47 (77)
T ss_pred EEeCCCCEEEEEECCCCcHHHHHHHHHHhhCCCCChhHeEEEE
Confidence 45567888999999999999999999999988 666666655
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=27.61 E-value=1.2e+02 Score=27.61 Aligned_cols=40 Identities=15% Similarity=0.253 Sum_probs=33.7
Q ss_pred EeCCceeEEEEcCCCChHHHHHHHHHhcCCCCCceEEEEE
Q 039468 551 YSGGDAHALSVNKESSFDELKLEMAEMWKYDPNSMIVKYF 590 (1282)
Q Consensus 551 Y~GG~t~~i~Vdr~iSf~ef~~kL~e~~~~~~~~~~lky~ 590 (1282)
-.++++..+.|+.+.|-.+++.+|.+..|+..++.++.|.
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 3456788899999999999999999999998777777664
No 72
>smart00213 UBQ Ubiquitin homologues. Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression
Probab=27.55 E-value=1.2e+02 Score=26.05 Aligned_cols=35 Identities=23% Similarity=0.265 Sum_probs=29.4
Q ss_pred ceeEEEEcCCCChHHHHHHHHHhcCCCCCceEEEE
Q 039468 555 DAHALSVNKESSFDELKLEMAEMWKYDPNSMIVKY 589 (1282)
Q Consensus 555 ~t~~i~Vdr~iSf~ef~~kL~e~~~~~~~~~~lky 589 (1282)
.+..+.|+.+.+..+|+.+|.+.+++..+..++.|
T Consensus 10 ~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~~~L~~ 44 (64)
T smart00213 10 GTITLEVKPSDTVSELKEKIAELTGIPVEQQRLIY 44 (64)
T ss_pred ceEEEEECCCCcHHHHHHHHHHHHCCCHHHEEEEE
Confidence 46678899999999999999999999777666654
No 73
>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=26.88 E-value=1.3e+02 Score=26.05 Aligned_cols=39 Identities=23% Similarity=0.299 Sum_probs=32.3
Q ss_pred EeCCceeEEEEcCCCChHHHHHHHHHhcCCCCCceEEEE
Q 039468 551 YSGGDAHALSVNKESSFDELKLEMAEMWKYDPNSMIVKY 589 (1282)
Q Consensus 551 Y~GG~t~~i~Vdr~iSf~ef~~kL~e~~~~~~~~~~lky 589 (1282)
..+|.+..+.++.+.+..+|+.+|.+.+++..+.+++.|
T Consensus 4 ~~~~~~~~~~~~~~~ti~~lK~~i~~~~~~~~~~~~l~~ 42 (69)
T cd01769 4 TLTGKTFELEVSPDDTVAELKAKIAAKEGVPPEQQRLIY 42 (69)
T ss_pred ccCCCEEEEEECCCChHHHHHHHHHHHHCcChHHEEEEE
Confidence 345777778899999999999999999998877777744
No 74
>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=26.84 E-value=1.5e+02 Score=28.01 Aligned_cols=33 Identities=18% Similarity=0.210 Sum_probs=28.3
Q ss_pred EEEEcCCCChHHHHHHHHHhcCCCCCceEEEEE
Q 039468 558 ALSVNKESSFDELKLEMAEMWKYDPNSMIVKYF 590 (1282)
Q Consensus 558 ~i~Vdr~iSf~ef~~kL~e~~~~~~~~~~lky~ 590 (1282)
...++.+|+..+|+++|..++|+.+..+++.++
T Consensus 16 ekr~~~~~Tv~~lK~kl~~~~G~~~~~mrL~l~ 48 (84)
T cd01789 16 EKKYSRGLTIAELKKKLELVVGTPASSMRLQLF 48 (84)
T ss_pred eEecCCCCcHHHHHHHHHHHHCCCccceEEEEE
Confidence 355888899999999999999999888888653
No 75
>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=26.46 E-value=2.4e+02 Score=29.04 Aligned_cols=69 Identities=14% Similarity=0.088 Sum_probs=41.7
Q ss_pred eeeeccccccccc--------------CcceeeeeeecCC-CCeEEEEEEEeccCCchhHHHHHHHHHHhhcCCceEEEE
Q 039468 904 LIFLDSFPIKSKY--------------QSSLLTATALDGN-DEIFPVAFGVVDAVSDDNWHWFLLQLKSALSTCQSITFV 968 (1282)
Q Consensus 904 VI~iD~TyltnkY--------------~g~Ll~avGvD~n-~~~~pvAfAvV~~Et~esw~WfLe~Lk~~m~~~~p~vII 968 (1282)
+|-||-||+.++- .....++++++-+ ++.--+...++.+.+.++..=+++...+ +..+|+
T Consensus 5 ~VEiDEty~~~~~~~~~~~~~~~gr~~~~k~~V~~~ver~~~~~~~~~~~~v~~~~~~tl~~~i~~~i~-----~gs~i~ 79 (151)
T PF12762_consen 5 IVEIDETYFGGRKNKKPRRKGKRGRGSKNKVPVFGAVERNDGGTGRVFMFVVPDRSAETLKPIIQEHIE-----PGSTII 79 (151)
T ss_pred EEEeCcCEECCcccccccCCCCCCCcCCCCcEEEEEEeecccCCceEEEEeecccccchhHHHHHHhhh-----ccceee
Confidence 5667777665332 2234455555554 4444455556677888877666544332 356799
Q ss_pred ecCcchHHH
Q 039468 969 TDRLGQLRA 977 (1282)
Q Consensus 969 SD~~~gL~~ 977 (1282)
||..++-..
T Consensus 80 TD~~~aY~~ 88 (151)
T PF12762_consen 80 TDGWRAYNG 88 (151)
T ss_pred ecchhhcCc
Confidence 999988643
No 76
>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=24.83 E-value=1.5e+02 Score=28.22 Aligned_cols=41 Identities=10% Similarity=0.098 Sum_probs=34.7
Q ss_pred EEeCCceeEEEEcCCCChHHHHHHHHHhcCCCCCceEEEEE
Q 039468 550 VYSGGDAHALSVNKESSFDELKLEMAEMWKYDPNSMIVKYF 590 (1282)
Q Consensus 550 ~Y~GG~t~~i~Vdr~iSf~ef~~kL~e~~~~~~~~~~lky~ 590 (1282)
...-|.+..+.|.++.++..++.+++++.|+..++.+|.|-
T Consensus 17 ~~~~g~~~~~~v~~~~~l~~l~~~y~~~~gi~~~~~rf~f~ 57 (87)
T cd01763 17 KGQDGNEVFFKIKRSTPLKKLMEAYCQRQGLSMNSVRFLFD 57 (87)
T ss_pred ECCCCCEEEEEEcCCCHHHHHHHHHHHHhCCCccceEEEEC
Confidence 44457778889999999999999999999998888777774
No 77
>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=24.69 E-value=43 Score=25.05 Aligned_cols=12 Identities=25% Similarity=0.288 Sum_probs=9.4
Q ss_pred CCCCCCCCCccc
Q 039468 1242 LPLTGPPKKRRI 1253 (1282)
Q Consensus 1242 rR~~GRPKKkRi 1253 (1282)
.|++|||+|...
T Consensus 1 kRkRGRPrK~~~ 12 (26)
T smart00384 1 KRKRGRPRKAPK 12 (26)
T ss_pred CCCCCCCCCCCC
Confidence 478999998754
No 78
>PF13592 HTH_33: Winged helix-turn helix
Probab=24.31 E-value=84 Score=27.76 Aligned_cols=30 Identities=30% Similarity=0.466 Sum_probs=25.9
Q ss_pred CCCChhhHHHHHHHhcCcccChHhHHHhhH
Q 039468 811 PKCKPKEIAEEIRRDFGIELGYVKAWRALE 840 (1282)
Q Consensus 811 p~~~p~~I~~~l~~~~G~~iSy~q~~Rak~ 840 (1282)
..++.++|+..|.++||+.+|.+.+++.-.
T Consensus 3 ~~wt~~~i~~~I~~~fgv~ys~~~v~~lL~ 32 (60)
T PF13592_consen 3 GRWTLKEIAAYIEEEFGVKYSPSGVYRLLK 32 (60)
T ss_pred CcccHHHHHHHHHHHHCCEEcHHHHHHHHH
Confidence 457889999999999999999999988644
No 79
>PF14201 DUF4318: Domain of unknown function (DUF4318)
Probab=24.19 E-value=99 Score=28.98 Aligned_cols=30 Identities=17% Similarity=0.404 Sum_probs=26.7
Q ss_pred EECCHHHHHHHHHHHHHHcCceEEEeecCC
Q 039468 715 RFNNVHDFRDALYKYSVAHGFTYCFKKNEG 744 (1282)
Q Consensus 715 ~F~S~eEfk~AI~~YAi~~gF~~rvkKSdk 744 (1282)
.+||.+++-.||.+|+.+++-.+++.+.++
T Consensus 13 ~yPs~e~i~~aIE~YC~~~~~~l~Fisr~~ 42 (74)
T PF14201_consen 13 KYPSKEEICEAIEKYCIKNGESLEFISRDK 42 (74)
T ss_pred CCCCHHHHHHHHHHHHHHcCCceEEEecCC
Confidence 589999999999999999999999976554
No 80
>COG4279 Uncharacterized conserved protein [Function unknown]
Probab=23.99 E-value=36 Score=38.56 Aligned_cols=23 Identities=39% Similarity=0.791 Sum_probs=19.5
Q ss_pred eeeeccCccccCccchhHHHHHhhhC
Q 039468 1163 WDCNCRGWQLNGFPCVHAAAVLQHVG 1188 (1282)
Q Consensus 1163 ~tCSCr~wq~~GIPC~HaLAVl~~~g 1188 (1282)
..|||..+. .||.|+-||....+
T Consensus 125 ~dCSCPD~a---nPCKHi~AvyY~la 147 (266)
T COG4279 125 TDCSCPDYA---NPCKHIAAVYYLLA 147 (266)
T ss_pred cccCCCCcc---cchHHHHHHHHHHH
Confidence 479999876 59999999987765
No 81
>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=23.45 E-value=1.4e+02 Score=26.48 Aligned_cols=37 Identities=24% Similarity=0.407 Sum_probs=33.1
Q ss_pred CCceeEEEEcCCCChHHHHHHHHHhcCCCCCceEEEE
Q 039468 553 GGDAHALSVNKESSFDELKLEMAEMWKYDPNSMIVKY 589 (1282)
Q Consensus 553 GG~t~~i~Vdr~iSf~ef~~kL~e~~~~~~~~~~lky 589 (1282)
.|++..+.|+.+.+..+|..+|.+..++......+.|
T Consensus 4 ~g~~~~~~v~~~~tV~~lK~~i~~~~~~~~~~~~L~~ 40 (69)
T PF00240_consen 4 SGKTFTLEVDPDDTVADLKQKIAEETGIPPEQQRLIY 40 (69)
T ss_dssp TSEEEEEEEETTSBHHHHHHHHHHHHTSTGGGEEEEE
T ss_pred CCcEEEEEECCCCCHHHhhhhcccccccccccceeee
Confidence 5778889999999999999999999999888877766
No 82
>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=23.30 E-value=1.2e+02 Score=30.16 Aligned_cols=31 Identities=19% Similarity=0.413 Sum_probs=22.0
Q ss_pred CCcEECCHHHHHHHHHHHHHHcCceEEEeecCCeE
Q 039468 712 VHQRFNNVHDFRDALYKYSVAHGFTYCFKKNEGLR 746 (1282)
Q Consensus 712 VGm~F~S~eEfk~AI~~YAi~~gF~~rvkKSdk~R 746 (1282)
+.+.|+|+|++. .||.++|..|.+......+
T Consensus 51 v~l~F~skE~Ai----~yaer~G~~Y~V~~p~~r~ 81 (101)
T PF04800_consen 51 VRLKFDSKEDAI----AYAERNGWDYEVEEPKKRK 81 (101)
T ss_dssp CEEEESSHHHHH----HHHHHCT-EEEEE-STT--
T ss_pred eEeeeCCHHHHH----HHHHHcCCeEEEeCCCCCc
Confidence 788999998764 6899999999986554433
No 83
>PF08985 DUF1888: Domain of unknown function (DUF1888); InterPro: IPR015078 This entry represents a family of hypothetical bacterial proteins.; PDB: 3NJG_A 3NJF_A 3NJH_D 3N55_A 3NJN_B 3NJI_B 3NJJ_A 3NJL_A 3NJM_A 3NJK_A ....
Probab=22.38 E-value=33 Score=34.80 Aligned_cols=77 Identities=29% Similarity=0.480 Sum_probs=39.8
Q ss_pred CCCcEEEEEEEEeeCCCCCceEEEEeccccccCCCCCCCCccc----cccceeeeeeeCCCCC--------CCcCCCCCC
Q 039468 279 SPNFKVRLTLDVKQGGGPNSQFYLIDMGSCWKNDGSPCNGDVF----TDVTRYSEMIINPRTP--------AWCSPTAQK 346 (1282)
Q Consensus 279 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~--------~~~~~~~~~ 346 (1282)
.+.|+|.++|+ + |-|. |-.- .++|+||+|+|+ +.+ .|+ ++..|. ..-.| .+
T Consensus 8 ~~~~~V~V~l~--n-~ep~--F~Yt------~~~G~~~~G~v~Vt~~~ti-tY~---L~d~T~kgl~F~Ga~f~tp--fD 70 (124)
T PF08985_consen 8 VQFIQVNVTLE--N-GEPV--FSYT------DASGEPCTGDVTVTEATTI-TYT---LDDQTGKGLKFVGAGFTTP--FD 70 (124)
T ss_dssp EEEEEEEEEEE--T-TEEE--EEEE-------TTSBEE-S-EEESSSEEE-EEE---EEE-SSS--EEEEEEESST--TS
T ss_pred ceEEEEEEEeC--C-CCcE--EEEE------cCCCCCccCCEEEeccceE-EEE---eccccCCCcEEEccEeccc--cc
Confidence 35689999998 3 3333 4322 466999999985 111 232 244442 11122 22
Q ss_pred CCC-CccccCCCceeeccCCCCCCccc
Q 039468 347 NCP-PYHITPHNKKIYRNDTANFPYGA 372 (1282)
Q Consensus 347 ~~~-~~~~~~~~~~~~~~~~~~~~~~~ 372 (1282)
++= -+-+..||..|.=.|+.+=|=.+
T Consensus 71 ~~id~v~iS~dG~~i~lvD~D~~~Gtt 97 (124)
T PF08985_consen 71 NIIDSVTISDDGQLIQLVDTDENPGTT 97 (124)
T ss_dssp SSS-EEEE-TTSSEEEEEESS-S-EEE
T ss_pred cceeEEEEcCCCeEEEEEEcCCCCCeE
Confidence 222 34578899999888888765444
No 84
>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=21.90 E-value=1.3e+02 Score=27.72 Aligned_cols=38 Identities=16% Similarity=0.156 Sum_probs=33.7
Q ss_pred CCceeEEEEcCCCChHHHHHHHHHhcCCCCCceEEEEE
Q 039468 553 GGDAHALSVNKESSFDELKLEMAEMWKYDPNSMIVKYF 590 (1282)
Q Consensus 553 GG~t~~i~Vdr~iSf~ef~~kL~e~~~~~~~~~~lky~ 590 (1282)
+|.+.-+.|+.+-+..+|.++|.+.+++.+++.++-|.
T Consensus 8 ~g~~~~v~v~~~~Tv~~lK~~i~~~tgvp~~~QKLi~~ 45 (74)
T cd01813 8 GGQEYSVTTLSEDTVLDLKQFIKTLTGVLPERQKLLGL 45 (74)
T ss_pred CCEEEEEEECCCCCHHHHHHHHHHHHCCCHHHEEEEee
Confidence 56677789999999999999999999999888999883
No 85
>cd01612 APG12_C Ubiquitin-like domain of APG12. APG12_C The carboxy-terminal ubiquitin-like domain of APG12. Autophagy is a process in which cytoplasmic components are delivered to the lysosome/vacuole for degradation. Autophagy requires a ubiquitin-like protein conjugation system, in which APG12 is covalently bound to APG5.
Probab=20.84 E-value=4e+02 Score=25.63 Aligned_cols=61 Identities=18% Similarity=0.274 Sum_probs=44.0
Q ss_pred EEEEcCCCChHHHHHHHHHhcCCCCCceEEEEEecCCCCceEEeechHHHHHHHHhhcCcCeEEEE
Q 039468 558 ALSVNKESSFDELKLEMAEMWKYDPNSMIVKYFLPNNNKTLITISGDKDIRRLIDFHEDSGTVDVY 623 (1282)
Q Consensus 558 ~i~Vdr~iSf~ef~~kL~e~~~~~~~~~~lky~LP~~~~~Li~v~dD~Dl~~M~e~~~~~~~v~IY 623 (1282)
..-|+++.++.+|+..|+..+++++++..+-|. |+ . ...+.|+-+...-+++++.+.++|.
T Consensus 19 kflv~~~~tv~~~~~~lrk~L~l~~~~slflyv---nn-~-f~p~~d~~~g~LY~~~~~dGfLyi~ 79 (87)
T cd01612 19 VFKISATQSFQAVIDFLRKRLKLKASDSLFLYI---NN-S-FAPSPDENVGNLYRCFGTNGELIVS 79 (87)
T ss_pred EEEeCCCCCHHHHHHHHHHHhCCCccCeEEEEE---CC-c-cCCCchhHHHHHHHhcCCCCEEEEE
Confidence 456899999999999999999998777666555 22 1 1234678888888888655655443
No 86
>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=20.32 E-value=1.8e+02 Score=26.56 Aligned_cols=40 Identities=10% Similarity=0.199 Sum_probs=33.6
Q ss_pred EEeCCceeEEEEcCCCChHHHHHHHHHhcCCCCCceEEEE
Q 039468 550 VYSGGDAHALSVNKESSFDELKLEMAEMWKYDPNSMIVKY 589 (1282)
Q Consensus 550 ~Y~GG~t~~i~Vdr~iSf~ef~~kL~e~~~~~~~~~~lky 589 (1282)
....|++..+.|+.+.|..+++.+|.+..|+...+.++.|
T Consensus 4 k~~~g~~~~l~v~~~~tV~~lK~~I~~~~gi~~~~q~L~~ 43 (74)
T cd01810 4 RNDKGRSSIYEVQLTQTVATLKQQVSQRERVQADQFWLSF 43 (74)
T ss_pred ECCCCCEEEEEECCcChHHHHHHHHHHHhCCCHHHeEEEE
Confidence 4456888899999999999999999999998777766654
No 87
>PRK09335 30S ribosomal protein S26e; Provisional
Probab=20.04 E-value=79 Score=30.90 Aligned_cols=27 Identities=19% Similarity=0.279 Sum_probs=18.8
Q ss_pred CCCCCCCCCCCCcccCCCCCCCceeeccccCc
Q 039468 1239 PPLLPLTGPPKKRRIRWRGRPKRELHCSKCKG 1270 (1282)
Q Consensus 1239 P~~rR~~GRPKKkRi~s~~~~Kr~~~CSrCk~ 1270 (1282)
|..||..||-|+.|- .-+.++|++|+.
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 456777888876652 234589999986
No 88
>PF13276 HTH_21: HTH-like domain
Probab=20.02 E-value=1.6e+02 Score=25.73 Aligned_cols=42 Identities=29% Similarity=0.447 Sum_probs=34.7
Q ss_pred HHHHHHHHhhcC-CCCChhhHHHHHHHhcCcccChHhHHHhhH
Q 039468 799 LASIVKEKLLEA-PKCKPKEIAEEIRRDFGIELGYVKAWRALE 840 (1282)
Q Consensus 799 IA~~ik~~ir~~-p~~~p~~I~~~l~~~~G~~iSy~q~~Rak~ 840 (1282)
+.+.+++.+..+ +.+..+.|...|++++|+.+|..+++|...
T Consensus 6 l~~~I~~i~~~~~~~yG~rri~~~L~~~~~~~v~~krV~RlM~ 48 (60)
T PF13276_consen 6 LRELIKEIFKESKPTYGYRRIWAELRREGGIRVSRKRVRRLMR 48 (60)
T ss_pred HHHHHHHHHHHcCCCeehhHHHHHHhccCcccccHHHHHHHHH
Confidence 455677776655 789999999999999999999999998754
Done!