Query 045565
Match_columns 83
No_of_seqs 107 out of 153
Neff 3.0
Searched_HMMs 46136
Date Fri Mar 29 03:21:48 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045565.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045565hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd06410 PB1_UP2 Uncharacterize 99.9 3.5E-25 7.5E-30 148.3 5.7 47 37-83 1-47 (97)
2 smart00666 PB1 PB1 domain. Pho 97.8 3.2E-05 7E-10 47.4 4.3 33 50-83 3-35 (81)
3 cd06408 PB1_NoxR The PB1 domai 96.6 0.0033 7.1E-08 42.1 4.0 28 56-83 9-36 (86)
4 PF00564 PB1: PB1 domain; Int 96.6 0.0021 4.6E-08 39.2 2.8 32 52-83 5-36 (84)
5 cd05992 PB1 The PB1 domain is 96.2 0.0095 2.1E-07 36.1 4.1 31 52-83 4-35 (81)
6 cd06405 PB1_Mekk2_3 The PB1 do 96.2 0.0065 1.4E-07 40.8 3.4 27 57-83 8-34 (79)
7 cd06407 PB1_NLP A PB1 domain i 95.2 0.038 8.2E-07 35.9 4.0 28 56-83 7-34 (82)
8 cd06404 PB1_aPKC PB1 domain is 94.1 0.085 1.8E-06 35.4 3.7 29 55-83 6-34 (83)
9 cd06398 PB1_Joka2 The PB1 doma 92.6 0.23 5.1E-06 32.9 4.0 29 53-82 5-38 (91)
10 cd06406 PB1_P67 A PB1 domain i 91.7 0.31 6.7E-06 32.4 3.7 28 52-81 6-33 (80)
11 cd06397 PB1_UP1 Uncharacterize 91.5 0.27 5.8E-06 33.2 3.3 26 57-82 8-33 (82)
12 cd06401 PB1_TFG The PB1 domain 91.1 0.39 8.4E-06 32.1 3.7 26 57-82 8-34 (81)
13 cd00196 UBQ Ubiquitin-like pro 90.2 0.99 2.1E-05 22.8 4.1 30 54-83 3-32 (69)
14 cd06396 PB1_NBR1 The PB1 domai 89.7 0.63 1.4E-05 30.8 3.9 28 56-83 7-36 (81)
15 cd01794 DC_UbP_C dendritic cel 87.5 1.3 2.7E-05 27.4 3.9 32 52-83 2-33 (70)
16 cd01807 GDX_N ubiquitin-like d 86.4 2 4.4E-05 25.9 4.4 31 53-83 5-35 (74)
17 cd01803 Ubiquitin Ubiquitin. U 86.3 1.9 4.1E-05 25.4 4.1 31 53-83 5-35 (76)
18 cd01812 BAG1_N Ubiquitin-like 86.1 1.8 3.9E-05 25.3 3.9 30 53-83 5-34 (71)
19 cd01809 Scythe_N Ubiquitin-lik 85.1 2.8 6.2E-05 24.4 4.4 31 53-83 5-35 (72)
20 PTZ00044 ubiquitin; Provisiona 83.3 3.4 7.3E-05 24.7 4.3 31 53-83 5-35 (76)
21 cd01796 DDI1_N DNA damage indu 83.0 2.7 5.9E-05 25.6 3.8 27 57-83 8-34 (71)
22 cd01799 Hoil1_N Ubiquitin-like 80.7 3.5 7.5E-05 25.9 3.8 28 56-83 10-37 (75)
23 cd01805 RAD23_N Ubiquitin-like 79.5 5.4 0.00012 23.8 4.3 31 53-83 5-35 (77)
24 cd01806 Nedd8 Nebb8-like ubiq 78.1 6.5 0.00014 23.0 4.3 30 54-83 6-35 (76)
25 cd01810 ISG15_repeat2 ISG15 ub 78.1 5.1 0.00011 24.2 3.9 31 53-83 3-33 (74)
26 PF11976 Rad60-SLD: Ubiquitin- 77.4 5 0.00011 23.7 3.6 31 53-83 5-35 (72)
27 cd01800 SF3a120_C Ubiquitin-li 74.2 6.7 0.00015 24.0 3.7 28 56-83 5-32 (76)
28 cd01798 parkin_N amino-termina 74.0 8.6 0.00019 22.8 4.1 31 53-83 3-33 (70)
29 PF14560 Ubiquitin_2: Ubiquiti 73.7 4.4 9.5E-05 25.3 2.8 21 63-83 18-38 (87)
30 cd01769 UBL Ubiquitin-like dom 73.7 9.3 0.0002 21.5 4.0 30 54-83 3-32 (69)
31 smart00213 UBQ Ubiquitin homol 73.2 11 0.00023 21.0 4.1 30 53-83 5-34 (64)
32 PF14107 DUF4280: Domain of un 69.6 2.9 6.4E-05 27.2 1.4 16 31-46 87-102 (108)
33 cd01802 AN1_N ubiquitin-like d 61.9 19 0.0004 23.9 4.1 31 53-83 32-62 (103)
34 cd01804 midnolin_N Ubiquitin-l 59.9 21 0.00047 22.0 3.9 28 55-82 8-35 (78)
35 cd06411 PB1_p51 The PB1 domain 58.6 15 0.00032 24.4 3.1 23 60-82 8-30 (78)
36 cd01789 Alp11_N Ubiquitin-like 57.2 14 0.0003 23.4 2.7 21 63-83 17-37 (84)
37 TIGR03831 YgiT_finger YgiT-typ 53.8 7.1 0.00015 21.2 0.9 27 37-66 3-31 (46)
38 cd01813 UBP_N UBP ubiquitin pr 52.8 31 0.00068 21.3 3.8 27 57-83 8-34 (74)
39 cd06403 PB1_Par6 The PB1 domai 51.9 26 0.00055 23.6 3.5 27 55-81 6-34 (80)
40 cd01792 ISG15_repeat1 ISG15 ub 51.1 39 0.00084 20.7 4.0 30 54-83 8-37 (80)
41 PF00240 ubiquitin: Ubiquitin 48.3 43 0.00093 19.3 3.7 28 56-83 3-30 (69)
42 cd01763 Sumo Small ubiquitin-r 46.5 39 0.00083 21.3 3.6 31 53-83 16-46 (87)
43 PHA00008 J DNA packaging prote 45.3 12 0.00026 20.6 0.9 9 52-60 16-24 (26)
44 cd01768 RA RA (Ras-associating 43.8 54 0.0012 19.9 3.8 28 56-83 10-37 (87)
45 PF09740 DUF2043: Uncharacteri 43.8 11 0.00023 26.5 0.7 21 32-52 84-104 (110)
46 cd01808 hPLIC_N Ubiquitin-like 43.2 57 0.0012 19.3 3.8 26 57-83 9-34 (71)
47 cd01793 Fubi Fubi ubiquitin-li 43.1 73 0.0016 19.1 4.3 27 57-83 7-33 (74)
48 cd00754 MoaD Ubiquitin domain 42.0 38 0.00082 20.0 2.9 26 56-81 13-38 (80)
49 cd06552 ASCH_yqfb_like ASC-1 h 42.0 27 0.00058 21.9 2.3 51 32-83 15-69 (100)
50 PF11543 UN_NPL4: Nuclear pore 40.9 32 0.0007 21.9 2.6 21 63-83 18-38 (80)
51 KOG0695 Serine/threonine prote 40.4 38 0.00083 29.4 3.6 28 55-82 21-48 (593)
52 cd04894 ACT_ACR-like_1 ACT dom 40.3 68 0.0015 21.2 4.0 39 40-82 24-68 (69)
53 cd06402 PB1_p62 The PB1 domain 36.8 56 0.0012 21.8 3.3 24 59-82 15-40 (87)
54 smart00314 RA Ras association 36.2 84 0.0018 19.2 3.9 27 56-82 13-39 (90)
55 PF13889 Chromosome_seg: Chrom 35.2 56 0.0012 20.5 2.9 29 33-71 8-36 (56)
56 TIGR00165 S18 ribosomal protei 34.2 15 0.00033 23.6 0.3 16 35-51 28-43 (70)
57 PF04663 Phenol_monoox: Phenol 34.1 31 0.00067 22.4 1.7 31 49-79 9-46 (67)
58 smart00295 B41 Band 4.1 homolo 33.8 81 0.0018 21.2 3.8 32 52-83 7-38 (207)
59 PF09379 FERM_N: FERM N-termin 33.3 67 0.0015 19.0 3.0 26 57-82 5-30 (80)
60 PRK06437 hypothetical protein; 33.1 71 0.0015 19.5 3.1 26 53-78 5-30 (67)
61 PF11784 DUF3320: Protein of u 32.1 13 0.00028 22.1 -0.3 23 61-83 19-41 (52)
62 PF12436 USP7_ICP0_bdg: ICP0-b 31.8 47 0.001 24.9 2.6 32 48-83 78-109 (249)
63 cd01797 NIRF_N amino-terminal 31.1 1.1E+02 0.0023 19.1 3.8 30 54-83 6-37 (78)
64 PF04726 Microvir_J: Microviru 30.4 24 0.00053 19.1 0.6 9 51-59 14-22 (24)
65 TIGR03649 ergot_EASG ergot alk 30.0 73 0.0016 22.7 3.2 43 41-83 154-214 (285)
66 cd01791 Ubl5 UBL5 ubiquitin-li 30.0 1.1E+02 0.0025 18.9 3.7 25 58-82 11-35 (73)
67 CHL00077 rps18 ribosomal prote 29.8 20 0.00043 24.2 0.3 16 35-51 38-53 (86)
68 PF00763 THF_DHG_CYH: Tetrahyd 29.1 82 0.0018 21.0 3.2 27 56-82 57-83 (117)
69 COG0424 Maf Nucleotide-binding 28.8 40 0.00088 25.4 1.8 15 37-51 73-87 (193)
70 PF00614 PLDc: Phospholipase D 28.4 35 0.00076 18.3 1.0 11 49-59 12-22 (28)
71 cd02168 NMNAT_Nudix Nicotinami 28.3 6.7 0.00014 28.3 -2.4 16 39-55 3-18 (181)
72 PRK01153 nicotinamide-nucleoti 26.4 7.3 0.00016 27.9 -2.4 17 39-56 4-20 (174)
73 TIGR00601 rad23 UV excision re 25.2 1.2E+02 0.0026 24.7 4.0 31 53-83 5-35 (378)
74 PF09992 DUF2233: Predicted pe 24.6 1.9E+02 0.0042 19.5 4.4 42 40-81 74-128 (170)
75 PF05678 VQ: VQ motif; InterP 24.4 54 0.0012 18.2 1.4 20 59-79 4-23 (31)
76 KOG1722 60s ribosomal protein 24.1 1.3E+02 0.0029 22.5 3.7 38 37-77 5-57 (155)
77 PF07929 PRiA4_ORF3: Plasmid p 23.6 1.1E+02 0.0025 21.2 3.2 24 60-83 19-42 (179)
78 COG2075 RPL24A Ribosomal prote 23.6 2.1E+02 0.0045 18.6 4.2 41 37-79 5-59 (66)
79 PF02519 Auxin_inducible: Auxi 23.1 92 0.002 20.8 2.5 36 48-83 37-76 (100)
80 PF00788 RA: Ras association ( 23.0 1.8E+02 0.0038 17.3 3.8 25 59-83 17-41 (93)
81 PF07045 DUF1330: Protein of u 22.7 79 0.0017 18.8 2.0 19 38-57 16-34 (65)
82 PF08856 DUF1826: Protein of u 22.3 49 0.0011 24.5 1.2 17 32-48 112-131 (196)
83 COG5470 Uncharacterized conser 22.3 87 0.0019 21.7 2.3 27 38-66 30-59 (96)
84 PRK13600 putative ribosomal pr 22.0 1.5E+02 0.0032 19.5 3.3 24 58-82 28-51 (84)
85 PF14832 Tautomerase_3: Putati 21.9 1.2E+02 0.0026 21.4 3.0 28 53-80 50-84 (136)
86 PF01084 Ribosomal_S18: Riboso 21.8 11 0.00023 23.0 -2.0 15 35-50 17-31 (54)
87 TIGR01687 moaD_arch MoaD famil 21.5 1.4E+02 0.0031 18.2 3.0 25 56-81 13-37 (88)
88 PRK02240 GTP cyclohydrolase II 21.3 1.6E+02 0.0034 23.3 3.9 31 49-80 177-210 (254)
89 PRK13793 nicotinamide-nucleoti 20.7 11 0.00024 28.2 -2.5 17 39-56 8-24 (196)
90 cd04870 ACT_PSP_1 CT domains f 20.7 1.5E+02 0.0032 17.6 2.9 21 62-82 44-64 (75)
91 KOG1513 Nuclear helicase MOP-3 20.6 1.1E+02 0.0024 29.2 3.3 25 59-83 1102-1126(1300)
92 PF13186 SPASM: Iron-sulfur cl 20.4 1.6E+02 0.0034 16.1 2.8 27 33-59 5-31 (64)
93 cd06257 DnaJ DnaJ domain or J- 20.4 64 0.0014 17.6 1.2 22 61-82 4-25 (55)
94 PF14847 Ras_bdg_2: Ras-bindin 20.3 1.2E+02 0.0025 20.7 2.6 30 54-83 6-35 (105)
95 PF01357 Pollen_allerg_1: Poll 20.2 75 0.0016 20.1 1.6 15 52-66 17-31 (82)
No 1
>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=99.91 E-value=3.5e-25 Score=148.30 Aligned_cols=47 Identities=66% Similarity=1.184 Sum_probs=46.0
Q ss_pred EeecCCEeeeCCCCCCeEEecCceeEEEEcCCCChHHHHHHHHhhhC
Q 045565 37 MCSFGGKILPRPHDNQLRYVGGDTRIVAVHRSSTFSTLLTKLSKLAG 83 (83)
Q Consensus 37 lCSyGGrIlPRp~Dg~LrYvGGeTRIisV~R~isf~eL~~Kls~l~G 83 (83)
||||||+|+|||+||||+|+|||||||+|+|++||+||++||+++|+
T Consensus 1 ~cs~GG~i~pr~~dg~l~Y~GG~tr~i~V~r~~s~~el~~kl~~~~~ 47 (97)
T cd06410 1 LCSYGGRILPRPPDGQLRYVGGETRIVSVDRSISFKELVSKLSELFG 47 (97)
T ss_pred CcccCCEEeCcCCCCCEEEcCCceEEEEEcCCCCHHHHHHHHHHHhC
Confidence 79999999999999999999999999999999999999999999985
No 2
>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=97.84 E-value=3.2e-05 Score=47.43 Aligned_cols=33 Identities=45% Similarity=0.739 Sum_probs=29.6
Q ss_pred CCCeEEecCceeEEEEcCCCChHHHHHHHHhhhC
Q 045565 50 DNQLRYVGGDTRIVAVHRSSTFSTLLTKLSKLAG 83 (83)
Q Consensus 50 Dg~LrYvGGeTRIisV~R~isf~eL~~Kls~l~G 83 (83)
..|++| ||++|.+.|+++++|.+|.+++.+.++
T Consensus 3 ~vK~~~-~~~~~~~~~~~~~s~~dL~~~i~~~~~ 35 (81)
T smart00666 3 DVKLRY-GGETRRLSVPRDISFEDLRSKVAKRFG 35 (81)
T ss_pred cEEEEE-CCEEEEEEECCCCCHHHHHHHHHHHhC
Confidence 357888 999999999999999999999998764
No 3
>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=96.64 E-value=0.0033 Score=42.12 Aligned_cols=28 Identities=21% Similarity=0.362 Sum_probs=26.3
Q ss_pred ecCceeEEEEcCCCChHHHHHHHHhhhC
Q 045565 56 VGGDTRIVAVHRSSTFSTLLTKLSKLAG 83 (83)
Q Consensus 56 vGGeTRIisV~R~isf~eL~~Kls~l~G 83 (83)
.+||+|+|.|+.+|+|++|..|+.+.||
T Consensus 9 ~~~Dv~~i~v~~~i~f~dL~~kIrdkf~ 36 (86)
T cd06408 9 AQDDTRYIMIGPDTGFADFEDKIRDKFG 36 (86)
T ss_pred ecCcEEEEEcCCCCCHHHHHHHHHHHhC
Confidence 3899999999999999999999999986
No 4
>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=96.62 E-value=0.0021 Score=39.16 Aligned_cols=32 Identities=28% Similarity=0.517 Sum_probs=25.9
Q ss_pred CeEEecCceeEEEEcCCCChHHHHHHHHhhhC
Q 045565 52 QLRYVGGDTRIVAVHRSSTFSTLLTKLSKLAG 83 (83)
Q Consensus 52 ~LrYvGGeTRIisV~R~isf~eL~~Kls~l~G 83 (83)
|++|-|+..|++.++++++|.+|..++++.+|
T Consensus 5 K~~~~~~~~~~~~~~~~~s~~~L~~~i~~~~~ 36 (84)
T PF00564_consen 5 KVRYGGDIRRIISLPSDVSFDDLRSKIREKFG 36 (84)
T ss_dssp EEEETTEEEEEEEECSTSHHHHHHHHHHHHHT
T ss_pred EEEECCeeEEEEEcCCCCCHHHHHHHHHHHhC
Confidence 45665555555999999999999999998875
No 5
>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=96.24 E-value=0.0095 Score=36.06 Aligned_cols=31 Identities=32% Similarity=0.546 Sum_probs=25.1
Q ss_pred CeEEecCceeEEEEc-CCCChHHHHHHHHhhhC
Q 045565 52 QLRYVGGDTRIVAVH-RSSTFSTLLTKLSKLAG 83 (83)
Q Consensus 52 ~LrYvGGeTRIisV~-R~isf~eL~~Kls~l~G 83 (83)
|++|- |++|.+.++ ++++|.+|.+++.+.++
T Consensus 4 K~~~~-~~~~~~~~~~~~~s~~~L~~~i~~~~~ 35 (81)
T cd05992 4 KVKYG-GEIRRFVVVSRSISFEDLRSKIAEKFG 35 (81)
T ss_pred EEEec-CCCEEEEEecCCCCHHHHHHHHHHHhC
Confidence 45555 677777887 99999999999998764
No 6
>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=96.18 E-value=0.0065 Score=40.84 Aligned_cols=27 Identities=30% Similarity=0.541 Sum_probs=25.6
Q ss_pred cCceeEEEEcCCCChHHHHHHHHhhhC
Q 045565 57 GGDTRIVAVHRSSTFSTLLTKLSKLAG 83 (83)
Q Consensus 57 GGeTRIisV~R~isf~eL~~Kls~l~G 83 (83)
-||.|||.++|.+.|.||.+|....||
T Consensus 8 ~gEKRIi~f~RPvkf~dl~~kv~~afG 34 (79)
T cd06405 8 NGEKRIIQFPRPVKFKDLQQKVTTAFG 34 (79)
T ss_pred cCceEEEecCCCccHHHHHHHHHHHhC
Confidence 489999999999999999999999887
No 7
>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=95.18 E-value=0.038 Score=35.90 Aligned_cols=28 Identities=18% Similarity=0.154 Sum_probs=25.9
Q ss_pred ecCceeEEEEcCCCChHHHHHHHHhhhC
Q 045565 56 VGGDTRIVAVHRSSTFSTLLTKLSKLAG 83 (83)
Q Consensus 56 vGGeTRIisV~R~isf~eL~~Kls~l~G 83 (83)
.|||++.+.++.+++|.+|.+++++.|+
T Consensus 7 ~~~d~~r~~l~~~~~~~~L~~~i~~r~~ 34 (82)
T cd06407 7 YGEEKIRFRLPPSWGFTELKQEIAKRFK 34 (82)
T ss_pred eCCeEEEEEcCCCCCHHHHHHHHHHHhC
Confidence 4899999999999999999999998874
No 8
>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=94.10 E-value=0.085 Score=35.45 Aligned_cols=29 Identities=17% Similarity=0.305 Sum_probs=26.5
Q ss_pred EecCceeEEEEcCCCChHHHHHHHHhhhC
Q 045565 55 YVGGDTRIVAVHRSSTFSTLLTKLSKLAG 83 (83)
Q Consensus 55 YvGGeTRIisV~R~isf~eL~~Kls~l~G 83 (83)
+.+|+-+|..++.+++|.+|.+|+.++|.
T Consensus 6 ~y~gdi~it~~d~~~s~e~L~~~v~~~c~ 34 (83)
T cd06404 6 AYNGDIMITSIDPSISLEELCNEVRDMCR 34 (83)
T ss_pred EecCcEEEEEcCCCcCHHHHHHHHHHHhC
Confidence 45889999999999999999999999983
No 9
>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=92.58 E-value=0.23 Score=32.88 Aligned_cols=29 Identities=24% Similarity=0.391 Sum_probs=25.1
Q ss_pred eEEecCceeEEEEcC-----CCChHHHHHHHHhhh
Q 045565 53 LRYVGGDTRIVAVHR-----SSTFSTLLTKLSKLA 82 (83)
Q Consensus 53 LrYvGGeTRIisV~R-----~isf~eL~~Kls~l~ 82 (83)
..| ||++|-+.++- +++|.+|..|+.++.
T Consensus 5 v~y-~~~~rRf~l~~~~~~~d~~~~~L~~kI~~~f 38 (91)
T cd06398 5 VKY-GGTLRRFTFPVAENQLDLNMDGLREKVEELF 38 (91)
T ss_pred EEe-CCEEEEEEeccccccCCCCHHHHHHHHHHHh
Confidence 445 89999999994 799999999999875
No 10
>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=91.71 E-value=0.31 Score=32.41 Aligned_cols=28 Identities=29% Similarity=0.428 Sum_probs=24.4
Q ss_pred CeEEecCceeEEEEcCCCChHHHHHHHHhh
Q 045565 52 QLRYVGGDTRIVAVHRSSTFSTLLTKLSKL 81 (83)
Q Consensus 52 ~LrYvGGeTRIisV~R~isf~eL~~Kls~l 81 (83)
|++|-+ |-.|.|+++++|++|..|+++-
T Consensus 6 KV~f~~--tIaIrvp~~~~y~~L~~ki~~k 33 (80)
T cd06406 6 KVHFKY--TVAIQVARGLSYATLLQKISSK 33 (80)
T ss_pred EEEEEE--EEEEEcCCCCCHHHHHHHHHHH
Confidence 466776 9999999999999999999874
No 11
>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=91.54 E-value=0.27 Score=33.21 Aligned_cols=26 Identities=35% Similarity=0.429 Sum_probs=23.1
Q ss_pred cCceeEEEEcCCCChHHHHHHHHhhh
Q 045565 57 GGDTRIVAVHRSSTFSTLLTKLSKLA 82 (83)
Q Consensus 57 GGeTRIisV~R~isf~eL~~Kls~l~ 82 (83)
+|+||=+++++..+|.+|.+||..|.
T Consensus 8 ~g~~RRf~~~~~pt~~~L~~kl~~Lf 33 (82)
T cd06397 8 LGDTRRIVFPDIPTWEALASKLENLY 33 (82)
T ss_pred CCceEEEecCCCccHHHHHHHHHHHh
Confidence 67788888999999999999999875
No 12
>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=91.07 E-value=0.39 Score=32.13 Aligned_cols=26 Identities=27% Similarity=0.553 Sum_probs=22.8
Q ss_pred cCceeEEEEcC-CCChHHHHHHHHhhh
Q 045565 57 GGDTRIVAVHR-SSTFSTLLTKLSKLA 82 (83)
Q Consensus 57 GGeTRIisV~R-~isf~eL~~Kls~l~ 82 (83)
|||.|.+.++. +++|.+|+..+.+++
T Consensus 8 g~DiR~~~~~~~~~t~~~L~~~v~~~F 34 (81)
T cd06401 8 GDDIRRIPIHNEDITYDELLLMMQRVF 34 (81)
T ss_pred CCeEEEEeccCccccHHHHHHHHHHHh
Confidence 99999999997 589999999987553
No 13
>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=90.22 E-value=0.99 Score=22.79 Aligned_cols=30 Identities=30% Similarity=0.339 Sum_probs=25.5
Q ss_pred EEecCceeEEEEcCCCChHHHHHHHHhhhC
Q 045565 54 RYVGGDTRIVAVHRSSTFSTLLTKLSKLAG 83 (83)
Q Consensus 54 rYvGGeTRIisV~R~isf~eL~~Kls~l~G 83 (83)
++-+|.+..+.++.+.+..+|.+++.+..|
T Consensus 3 ~~~~~~~~~~~~~~~~tv~~l~~~i~~~~~ 32 (69)
T cd00196 3 KLNDGKTVELLVPSGTTVADLKEKLAKKLG 32 (69)
T ss_pred EecCCCEEEEEcCCCCcHHHHHHHHHHHHC
Confidence 444899999999999999999999987643
No 14
>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=89.75 E-value=0.63 Score=30.85 Aligned_cols=28 Identities=14% Similarity=0.279 Sum_probs=25.5
Q ss_pred ecCceeEEEEcC--CCChHHHHHHHHhhhC
Q 045565 56 VGGDTRIVAVHR--SSTFSTLLTKLSKLAG 83 (83)
Q Consensus 56 vGGeTRIisV~R--~isf~eL~~Kls~l~G 83 (83)
.|||+..+.++. +++|.+|.+.+.+.|+
T Consensus 7 y~~d~~rf~~~~~~~~~~~~L~~ev~~rf~ 36 (81)
T cd06396 7 YNGESQSFLVSDSENTTWASVEAMVKVSFG 36 (81)
T ss_pred ECCeEEEEEecCCCCCCHHHHHHHHHHHhC
Confidence 489999999999 8899999999999885
No 15
>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=87.46 E-value=1.3 Score=27.38 Aligned_cols=32 Identities=22% Similarity=0.325 Sum_probs=28.6
Q ss_pred CeEEecCceeEEEEcCCCChHHHHHHHHhhhC
Q 045565 52 QLRYVGGDTRIVAVHRSSTFSTLLTKLSKLAG 83 (83)
Q Consensus 52 ~LrYvGGeTRIisV~R~isf~eL~~Kls~l~G 83 (83)
|++..+|+|..+.|+.+.+..+|.+++++..|
T Consensus 2 ~vk~~~G~~~~l~v~~~~TV~~lK~~I~~~~g 33 (70)
T cd01794 2 KVRLSTGKDVKLSVSSKDTVGQLKKQLQAAEG 33 (70)
T ss_pred eEEcCCCCEEEEEECCcChHHHHHHHHHHHhC
Confidence 46788999999999999999999999988654
No 16
>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=86.35 E-value=2 Score=25.95 Aligned_cols=31 Identities=19% Similarity=0.235 Sum_probs=27.4
Q ss_pred eEEecCceeEEEEcCCCChHHHHHHHHhhhC
Q 045565 53 LRYVGGDTRIVAVHRSSTFSTLLTKLSKLAG 83 (83)
Q Consensus 53 LrYvGGeTRIisV~R~isf~eL~~Kls~l~G 83 (83)
.+..+|++..+.|+.+.+..+|.+++++..|
T Consensus 5 vk~~~G~~~~l~v~~~~tV~~lK~~i~~~~g 35 (74)
T cd01807 5 VKLLQGRECSLQVSEKESVSTLKKLVSEHLN 35 (74)
T ss_pred EEeCCCCEEEEEECCCCcHHHHHHHHHHHHC
Confidence 4677899999999999999999999988654
No 17
>cd01803 Ubiquitin Ubiquitin. Ubiquitin (includes Ubq/RPL40e and Ubq/RPS27a fusions as well as homopolymeric multiubiquitin protein chains)
Probab=86.30 E-value=1.9 Score=25.37 Aligned_cols=31 Identities=23% Similarity=0.356 Sum_probs=26.7
Q ss_pred eEEecCceeEEEEcCCCChHHHHHHHHhhhC
Q 045565 53 LRYVGGDTRIVAVHRSSTFSTLLTKLSKLAG 83 (83)
Q Consensus 53 LrYvGGeTRIisV~R~isf~eL~~Kls~l~G 83 (83)
++..+|++..+.|+.+.+..+|.+++++..|
T Consensus 5 v~~~~g~~~~~~v~~~~tV~~lK~~i~~~~g 35 (76)
T cd01803 5 VKTLTGKTITLEVEPSDTIENVKAKIQDKEG 35 (76)
T ss_pred EEcCCCCEEEEEECCcCcHHHHHHHHHHHhC
Confidence 4556788999999999999999999998764
No 18
>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=86.12 E-value=1.8 Score=25.33 Aligned_cols=30 Identities=23% Similarity=0.527 Sum_probs=26.2
Q ss_pred eEEecCceeEEEEcCCCChHHHHHHHHhhhC
Q 045565 53 LRYVGGDTRIVAVHRSSTFSTLLTKLSKLAG 83 (83)
Q Consensus 53 LrYvGGeTRIisV~R~isf~eL~~Kls~l~G 83 (83)
++| +|++.-+.|+.+.+..+|.+++++.+|
T Consensus 5 vk~-~g~~~~i~v~~~~tv~~lK~~i~~~~g 34 (71)
T cd01812 5 VKH-GGESHDLSISSQATFGDLKKMLAPVTG 34 (71)
T ss_pred EEE-CCEEEEEEECCCCcHHHHHHHHHHhhC
Confidence 466 488888999999999999999998865
No 19
>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=85.06 E-value=2.8 Score=24.36 Aligned_cols=31 Identities=19% Similarity=0.282 Sum_probs=26.9
Q ss_pred eEEecCceeEEEEcCCCChHHHHHHHHhhhC
Q 045565 53 LRYVGGDTRIVAVHRSSTFSTLLTKLSKLAG 83 (83)
Q Consensus 53 LrYvGGeTRIisV~R~isf~eL~~Kls~l~G 83 (83)
.+...|++..+.|+.+.+..+|.+++++..|
T Consensus 5 vk~~~g~~~~~~v~~~~tv~~lK~~i~~~~g 35 (72)
T cd01809 5 VKTLDSQTHTFTVEEEITVLDLKEKIAEEVG 35 (72)
T ss_pred EEeCCCCEEEEEECCCCcHHHHHHHHHHHHC
Confidence 4566788999999999999999999988765
No 20
>PTZ00044 ubiquitin; Provisional
Probab=83.29 E-value=3.4 Score=24.70 Aligned_cols=31 Identities=13% Similarity=0.253 Sum_probs=27.0
Q ss_pred eEEecCceeEEEEcCCCChHHHHHHHHhhhC
Q 045565 53 LRYVGGDTRIVAVHRSSTFSTLLTKLSKLAG 83 (83)
Q Consensus 53 LrYvGGeTRIisV~R~isf~eL~~Kls~l~G 83 (83)
+|-..|+|..+.|+.+.+-.+|.+++++..|
T Consensus 5 vk~~~G~~~~l~v~~~~tv~~lK~~i~~~~g 35 (76)
T PTZ00044 5 IKTLTGKKQSFNFEPDNTVQQVKMALQEKEG 35 (76)
T ss_pred EEeCCCCEEEEEECCCCcHHHHHHHHHHHHC
Confidence 3556899999999999999999999998765
No 21
>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=83.00 E-value=2.7 Score=25.58 Aligned_cols=27 Identities=11% Similarity=0.053 Sum_probs=25.1
Q ss_pred cCceeEEEEcCCCChHHHHHHHHhhhC
Q 045565 57 GGDTRIVAVHRSSTFSTLLTKLSKLAG 83 (83)
Q Consensus 57 GGeTRIisV~R~isf~eL~~Kls~l~G 83 (83)
+|+|..|-|+.+.+..+|.+++++..|
T Consensus 8 ~g~~~~l~v~~~~TV~~lK~~I~~~~g 34 (71)
T cd01796 8 SETTFSLDVDPDLELENFKALCEAESG 34 (71)
T ss_pred CCCEEEEEECCcCCHHHHHHHHHHHhC
Confidence 899999999999999999999998765
No 22
>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=80.73 E-value=3.5 Score=25.92 Aligned_cols=28 Identities=21% Similarity=0.033 Sum_probs=25.2
Q ss_pred ecCceeEEEEcCCCChHHHHHHHHhhhC
Q 045565 56 VGGDTRIVAVHRSSTFSTLLTKLSKLAG 83 (83)
Q Consensus 56 vGGeTRIisV~R~isf~eL~~Kls~l~G 83 (83)
.+|.|..|.|+.+.+..+|.+|+.+..|
T Consensus 10 ~~~~t~~l~v~~~~TV~~lK~kI~~~~g 37 (75)
T cd01799 10 SHTVTIWLTVRPDMTVAQLKDKVFLDYG 37 (75)
T ss_pred cCCCeEEEEECCCCcHHHHHHHHHHHHC
Confidence 3688999999999999999999998765
No 23
>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=79.55 E-value=5.4 Score=23.75 Aligned_cols=31 Identities=19% Similarity=0.252 Sum_probs=27.3
Q ss_pred eEEecCceeEEEEcCCCChHHHHHHHHhhhC
Q 045565 53 LRYVGGDTRIVAVHRSSTFSTLLTKLSKLAG 83 (83)
Q Consensus 53 LrYvGGeTRIisV~R~isf~eL~~Kls~l~G 83 (83)
++..+|++..+.|+.+.+..+|.+++.+..|
T Consensus 5 vk~~~g~~~~l~v~~~~TV~~lK~~i~~~~~ 35 (77)
T cd01805 5 FKTLKQQTFPIEVDPDDTVAELKEKIEEEKG 35 (77)
T ss_pred EEeCCCCEEEEEECCCCcHHHHHHHHHHhhC
Confidence 5778999999999999999999999987654
No 24
>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=78.13 E-value=6.5 Score=23.03 Aligned_cols=30 Identities=7% Similarity=0.246 Sum_probs=25.2
Q ss_pred EEecCceeEEEEcCCCChHHHHHHHHhhhC
Q 045565 54 RYVGGDTRIVAVHRSSTFSTLLTKLSKLAG 83 (83)
Q Consensus 54 rYvGGeTRIisV~R~isf~eL~~Kls~l~G 83 (83)
+-.+|++-.+.|+.+.+..+|.+++.+..|
T Consensus 6 ~~~~g~~~~~~v~~~~tv~~lK~~i~~~~g 35 (76)
T cd01806 6 KTLTGKEIEIDIEPTDKVERIKERVEEKEG 35 (76)
T ss_pred EeCCCCEEEEEECCCCCHHHHHHHHhHhhC
Confidence 445688888999999999999999988654
No 25
>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=78.10 E-value=5.1 Score=24.24 Aligned_cols=31 Identities=26% Similarity=0.298 Sum_probs=26.9
Q ss_pred eEEecCceeEEEEcCCCChHHHHHHHHhhhC
Q 045565 53 LRYVGGDTRIVAVHRSSTFSTLLTKLSKLAG 83 (83)
Q Consensus 53 LrYvGGeTRIisV~R~isf~eL~~Kls~l~G 83 (83)
.|...|+|..+.|+.+.+..+|.+++++..|
T Consensus 3 vk~~~g~~~~l~v~~~~tV~~lK~~I~~~~g 33 (74)
T cd01810 3 VRNDKGRSSIYEVQLTQTVATLKQQVSQRER 33 (74)
T ss_pred EECCCCCEEEEEECCcChHHHHHHHHHHHhC
Confidence 4567899999999999999999999987654
No 26
>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=77.37 E-value=5 Score=23.68 Aligned_cols=31 Identities=26% Similarity=0.342 Sum_probs=26.5
Q ss_pred eEEecCceeEEEEcCCCChHHHHHHHHhhhC
Q 045565 53 LRYVGGDTRIVAVHRSSTFSTLLTKLSKLAG 83 (83)
Q Consensus 53 LrYvGGeTRIisV~R~isf~eL~~Kls~l~G 83 (83)
|+-.+|++--+.|.++.+|+.|+.+.++..|
T Consensus 5 v~~~~~~~~~~~v~~~~~~~~l~~~~~~~~~ 35 (72)
T PF11976_consen 5 VRSQDGKEIKFKVKPTTTVSKLIEKYCEKKG 35 (72)
T ss_dssp EEETTSEEEEEEEETTSCCHHHHHHHHHHHT
T ss_pred EEeCCCCEEEEEECCCCcHHHHHHHHHHhhC
Confidence 5667788888999999999999999987654
No 27
>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=74.24 E-value=6.7 Score=23.96 Aligned_cols=28 Identities=21% Similarity=0.287 Sum_probs=25.0
Q ss_pred ecCceeEEEEcCCCChHHHHHHHHhhhC
Q 045565 56 VGGDTRIVAVHRSSTFSTLLTKLSKLAG 83 (83)
Q Consensus 56 vGGeTRIisV~R~isf~eL~~Kls~l~G 83 (83)
.+|+|..|.|+.+.+..+|.+++.+..|
T Consensus 5 l~g~~~~l~v~~~~TV~~lK~~i~~~~g 32 (76)
T cd01800 5 LNGQMLNFTLQLSDPVSVLKVKIHEETG 32 (76)
T ss_pred cCCeEEEEEECCCCcHHHHHHHHHHHHC
Confidence 4789999999999999999999988754
No 28
>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=74.05 E-value=8.6 Score=22.84 Aligned_cols=31 Identities=26% Similarity=0.268 Sum_probs=26.9
Q ss_pred eEEecCceeEEEEcCCCChHHHHHHHHhhhC
Q 045565 53 LRYVGGDTRIVAVHRSSTFSTLLTKLSKLAG 83 (83)
Q Consensus 53 LrYvGGeTRIisV~R~isf~eL~~Kls~l~G 83 (83)
.+...|++..+.|+.+.+..+|.+++++..|
T Consensus 3 vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~g 33 (70)
T cd01798 3 VRTNTGHTFPVEVDPDTDIKQLKEVVAKRQG 33 (70)
T ss_pred EEcCCCCEEEEEECCCChHHHHHHHHHHHHC
Confidence 3567899999999999999999999987654
No 29
>PF14560 Ubiquitin_2: Ubiquitin-like domain; PDB: 1WJN_A 2KJ6_A 2KJR_A 1V6E_A 1T0Y_A.
Probab=73.72 E-value=4.4 Score=25.35 Aligned_cols=21 Identities=43% Similarity=0.449 Sum_probs=19.5
Q ss_pred EEEcCCCChHHHHHHHHhhhC
Q 045565 63 VAVHRSSTFSTLLTKLSKLAG 83 (83)
Q Consensus 63 isV~R~isf~eL~~Kls~l~G 83 (83)
+.++.++++.||..||..++|
T Consensus 18 kr~~~~~Tv~eLK~kl~~~~G 38 (87)
T PF14560_consen 18 KRFPKSITVSELKQKLEKLTG 38 (87)
T ss_dssp EEEETTSBHHHHHHHHHHHHT
T ss_pred EEcCCCCCHHHHHHHHHHHhC
Confidence 578999999999999999987
No 30
>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=73.65 E-value=9.3 Score=21.47 Aligned_cols=30 Identities=23% Similarity=0.308 Sum_probs=24.6
Q ss_pred EEecCceeEEEEcCCCChHHHHHHHHhhhC
Q 045565 54 RYVGGDTRIVAVHRSSTFSTLLTKLSKLAG 83 (83)
Q Consensus 54 rYvGGeTRIisV~R~isf~eL~~Kls~l~G 83 (83)
+...|.+-.+.++.+.+..+|.+++++.+|
T Consensus 3 ~~~~~~~~~~~~~~~~ti~~lK~~i~~~~~ 32 (69)
T cd01769 3 KTLTGKTFELEVSPDDTVAELKAKIAAKEG 32 (69)
T ss_pred EccCCCEEEEEECCCChHHHHHHHHHHHHC
Confidence 445677777899999999999999998765
No 31
>smart00213 UBQ Ubiquitin homologues. Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression
Probab=73.22 E-value=11 Score=20.97 Aligned_cols=30 Identities=30% Similarity=0.420 Sum_probs=24.2
Q ss_pred eEEecCceeEEEEcCCCChHHHHHHHHhhhC
Q 045565 53 LRYVGGDTRIVAVHRSSTFSTLLTKLSKLAG 83 (83)
Q Consensus 53 LrYvGGeTRIisV~R~isf~eL~~Kls~l~G 83 (83)
++..+ .+.-+.|+.+.+..+|.+++.+..|
T Consensus 5 vk~~~-~~~~~~v~~~~tv~~lk~~i~~~~~ 34 (64)
T smart00213 5 VKTLD-GTITLEVKPSDTVSELKEKIAELTG 34 (64)
T ss_pred EEECC-ceEEEEECCCCcHHHHHHHHHHHHC
Confidence 34555 5777899999999999999988764
No 32
>PF14107 DUF4280: Domain of unknown function (DUF4280)
Probab=69.58 E-value=2.9 Score=27.20 Aligned_cols=16 Identities=25% Similarity=0.615 Sum_probs=12.9
Q ss_pred CCeEEEEeecCCEeee
Q 045565 31 LTRVRFMCSFGGKILP 46 (83)
Q Consensus 31 ~~kvKllCSyGGrIlP 46 (83)
..+=+++|.|||.|-.
T Consensus 87 ~~~S~~~C~~gG~I~i 102 (108)
T PF14107_consen 87 TEDSKLTCAYGGIISI 102 (108)
T ss_pred ccCeEEeccCCCEEEE
Confidence 3467899999999865
No 33
>cd01802 AN1_N ubiquitin-like domain of AN1. AN1 (also known as ANUBL1 and RSD-7) is ubiquitin-like protein with a testis-specific expression in rats that has an N-terminal ubiquitin-like domain and a C-terminal zinc-binding domain. Unlike ubiquitin polyproteins and most ubiquitin fusion proteins, the N-terminal ubiquitin-like domain of An1 does not undergo proteolytic processing. The function of AN1 is unknown.
Probab=61.91 E-value=19 Score=23.91 Aligned_cols=31 Identities=19% Similarity=0.273 Sum_probs=27.0
Q ss_pred eEEecCceeEEEEcCCCChHHHHHHHHhhhC
Q 045565 53 LRYVGGDTRIVAVHRSSTFSTLLTKLSKLAG 83 (83)
Q Consensus 53 LrYvGGeTRIisV~R~isf~eL~~Kls~l~G 83 (83)
++-.+|++..|-|+.+.+-.+|.+++++.-|
T Consensus 32 Vk~l~G~~~~leV~~~~TV~~lK~kI~~~~g 62 (103)
T cd01802 32 IETLTGTCFELRVSPFETVISVKAKIQRLEG 62 (103)
T ss_pred EEcCCCCEEEEEeCCCCcHHHHHHHHHHHhC
Confidence 4667899999999999999999999987643
No 34
>cd01804 midnolin_N Ubiquitin-like domain of midnolin. midnolin_N Midnolin (midbrain nucleolar protein) is expressed in the nucleolus and is thought to regulate genes involved in neurogenesis. Midnolin contains an amino-terminal ubiquitin-like domain.
Probab=59.85 E-value=21 Score=22.00 Aligned_cols=28 Identities=18% Similarity=0.132 Sum_probs=23.7
Q ss_pred EecCceeEEEEcCCCChHHHHHHHHhhh
Q 045565 55 YVGGDTRIVAVHRSSTFSTLLTKLSKLA 82 (83)
Q Consensus 55 YvGGeTRIisV~R~isf~eL~~Kls~l~ 82 (83)
-..|.+..|.|+.+.+..+|.+++++..
T Consensus 8 ~~~G~~~~l~v~~~~TV~~LK~~I~~~~ 35 (78)
T cd01804 8 STTGTRFDLSVPPDETVEGLKKRISQRL 35 (78)
T ss_pred ECCCCEEEEEECCcCHHHHHHHHHHHHh
Confidence 3457778899999999999999998754
No 35
>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=58.61 E-value=15 Score=24.42 Aligned_cols=23 Identities=26% Similarity=0.226 Sum_probs=20.4
Q ss_pred eeEEEEcCCCChHHHHHHHHhhh
Q 045565 60 TRIVAVHRSSTFSTLLTKLSKLA 82 (83)
Q Consensus 60 TRIisV~R~isf~eL~~Kls~l~ 82 (83)
|-.|.|+|.++|++|..++++-.
T Consensus 8 TVai~v~~g~~y~~L~~~ls~kL 30 (78)
T cd06411 8 TVALRAPRGADVSSLRALLSQAL 30 (78)
T ss_pred EEEEEccCCCCHHHHHHHHHHHh
Confidence 77899999999999999998753
No 36
>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=57.15 E-value=14 Score=23.40 Aligned_cols=21 Identities=29% Similarity=0.317 Sum_probs=18.9
Q ss_pred EEEcCCCChHHHHHHHHhhhC
Q 045565 63 VAVHRSSTFSTLLTKLSKLAG 83 (83)
Q Consensus 63 isV~R~isf~eL~~Kls~l~G 83 (83)
..++.+++.++|..||..++|
T Consensus 17 kr~~~~~Tv~~lK~kl~~~~G 37 (84)
T cd01789 17 KKYSRGLTIAELKKKLELVVG 37 (84)
T ss_pred EecCCCCcHHHHHHHHHHHHC
Confidence 458999999999999999887
No 37
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=53.77 E-value=7.1 Score=21.16 Aligned_cols=27 Identities=30% Similarity=0.701 Sum_probs=18.8
Q ss_pred EeecCCEeeeCCC-CCCeEEecCceeEE-EEc
Q 045565 37 MCSFGGKILPRPH-DNQLRYVGGDTRIV-AVH 66 (83)
Q Consensus 37 lCSyGGrIlPRp~-Dg~LrYvGGeTRIi-sV~ 66 (83)
+| ||.-+.+-. +-.+.| ||+..+| .|+
T Consensus 3 ~C--~~~~~~~~~~~~~~~~-~~~~~~i~~vp 31 (46)
T TIGR03831 3 IC--GGEELEGKTTTETYEY-GGELIVIENVP 31 (46)
T ss_pred CC--CCceecceEEEEEEEe-CCEEEEEeCCC
Confidence 46 677777665 667888 8888777 444
No 38
>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=52.80 E-value=31 Score=21.30 Aligned_cols=27 Identities=26% Similarity=0.326 Sum_probs=23.9
Q ss_pred cCceeEEEEcCCCChHHHHHHHHhhhC
Q 045565 57 GGDTRIVAVHRSSTFSTLLTKLSKLAG 83 (83)
Q Consensus 57 GGeTRIisV~R~isf~eL~~Kls~l~G 83 (83)
+|++.-|.|+.+.+..+|.++|.++.|
T Consensus 8 ~g~~~~v~v~~~~Tv~~lK~~i~~~tg 34 (74)
T cd01813 8 GGQEYSVTTLSEDTVLDLKQFIKTLTG 34 (74)
T ss_pred CCEEEEEEECCCCCHHHHHHHHHHHHC
Confidence 678888999999999999999998754
No 39
>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=51.90 E-value=26 Score=23.58 Aligned_cols=27 Identities=19% Similarity=0.333 Sum_probs=23.8
Q ss_pred EecCceeEEEEcCC--CChHHHHHHHHhh
Q 045565 55 YVGGDTRIVAVHRS--STFSTLLTKLSKL 81 (83)
Q Consensus 55 YvGGeTRIisV~R~--isf~eL~~Kls~l 81 (83)
+.++|+|=.+++|+ .+|.|+.+.+..+
T Consensus 6 kfdaEfRRFsl~r~~~~~f~ef~~ll~~l 34 (80)
T cd06403 6 KFDAEFRRFSLDRNKPGKFEDFYKLLEHL 34 (80)
T ss_pred ccCCeEEEEEeccccCcCHHHHHHHHHHH
Confidence 46899999999998 8999999888765
No 40
>cd01792 ISG15_repeat1 ISG15 ubiquitin-like protein, first repeat of 2. ISG15 is a ubiquitin-like protein containing two ubiquitin homology domains that becomes conjugated to a variety of proteins when cells are treated with type I interferon or lipopolysaccharide. Although ISG15 has properties similar to those of other ubiquitin-like molecules, it is a unique member of the ubiquitin-like superfamily, whose expression and conjugation to target proteins are tightly regulated by specific signaling pathways, indicating it may have specialized functions in the immune system.
Probab=51.10 E-value=39 Score=20.73 Aligned_cols=30 Identities=27% Similarity=0.488 Sum_probs=24.9
Q ss_pred EEecCceeEEEEcCCCChHHHHHHHHhhhC
Q 045565 54 RYVGGDTRIVAVHRSSTFSTLLTKLSKLAG 83 (83)
Q Consensus 54 rYvGGeTRIisV~R~isf~eL~~Kls~l~G 83 (83)
+-..|++-.+.|+.+.+-.+|..++++..|
T Consensus 8 k~~~G~~~~~~v~~~~TV~~lK~~I~~~~~ 37 (80)
T cd01792 8 KMLGGNEFLVSLRDSMTVSELKQQIAQKIG 37 (80)
T ss_pred EeCCCCEEEEEcCCCCcHHHHHHHHHHHhC
Confidence 445688888899999999999999987654
No 41
>PF00240 ubiquitin: Ubiquitin family; InterPro: IPR000626 Ubiquitinylation is an ATP-dependent process that involves the action of at least three enzymes: a ubiquitin-activating enzyme (E1, IPR000011 from INTERPRO), a ubiquitin-conjugating enzyme (E2, IPR000608 from INTERPRO), and a ubiquitin ligase (E3, IPR000569 from INTERPRO, IPR003613 from INTERPRO), which work sequentially in a cascade. There are many different E3 ligases, which are responsible for the type of ubiquitin chain formed, the specificity of the target protein, and the regulation of the ubiquitinylation process []. Ubiquitinylation is an important regulatory tool that controls the concentration of key signalling proteins, such as those involved in cell cycle control, as well as removing misfolded, damaged or mutant proteins that could be harmful to the cell. Several ubiquitin-like molecules have been discovered, such as Ufm1 (IPR005375 from INTERPRO), SUMO1 (IPR003653 from INTERPRO), NEDD8, Rad23 (IPR004806 from INTERPRO), Elongin B and Parkin (IPR003977 from INTERPRO), the latter being involved in Parkinson's disease []. Ubiquitin is a protein of 76 amino acid residues, found in all eukaryotic cells and whose sequence is extremely well conserved from protozoan to vertebrates. Ubiquitin acts through its post-translational attachment (ubiquitinylation) to other proteins, where these modifications alter the function, location or trafficking of the protein, or targets it for destruction by the 26S proteasome []. The terminal glycine in the C-terminal 4-residue tail of ubiquitin can form an isopeptide bond with a lysine residue in the target protein, or with a lysine in another ubiquitin molecule to form a ubiquitin chain that attaches itself to a target protein. Ubiquitin has seven lysine residues, any one of which can be used to link ubiquitin molecules together, resulting in different structures that alter the target protein in different ways. It appears that Lys(11)-, Lys(29) and Lys(48)-linked poly-ubiquitin chains target the protein to the proteasome for degradation, while mono-ubiquitinylated and Lys(6)- or Lys(63)-linked poly-ubiquitin chains signal reversible modifications in protein activity, location or trafficking []. For example, Lys(63)-linked poly-ubiquitinylation is known to be involved in DNA damage tolerance, inflammatory response, protein trafficking and signal transduction through kinase activation []. In addition, the length of the ubiquitin chain alters the fate of the target protein. Regulatory proteins such as transcription factors and histones are frequent targets of ubquitinylation [].; GO: 0005515 protein binding; PDB: 2DZI_A 2XEW_E 3NOB_E 2KWU_B 2Y5B_F 3PHD_G 2KWV_B 2KOX_A 2XK5_B 3NHE_B ....
Probab=48.27 E-value=43 Score=19.29 Aligned_cols=28 Identities=25% Similarity=0.382 Sum_probs=24.6
Q ss_pred ecCceeEEEEcCCCChHHHHHHHHhhhC
Q 045565 56 VGGDTRIVAVHRSSTFSTLLTKLSKLAG 83 (83)
Q Consensus 56 vGGeTRIisV~R~isf~eL~~Kls~l~G 83 (83)
..|.+-.+.|+.+.+..+|..++++..|
T Consensus 3 ~~g~~~~~~v~~~~tV~~lK~~i~~~~~ 30 (69)
T PF00240_consen 3 LSGKTFTLEVDPDDTVADLKQKIAEETG 30 (69)
T ss_dssp TTSEEEEEEEETTSBHHHHHHHHHHHHT
T ss_pred CCCcEEEEEECCCCCHHHhhhhcccccc
Confidence 4688889999999999999999998754
No 42
>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=46.47 E-value=39 Score=21.26 Aligned_cols=31 Identities=16% Similarity=0.356 Sum_probs=25.1
Q ss_pred eEEecCceeEEEEcCCCChHHHHHHHHhhhC
Q 045565 53 LRYVGGDTRIVAVHRSSTFSTLLTKLSKLAG 83 (83)
Q Consensus 53 LrYvGGeTRIisV~R~isf~eL~~Kls~l~G 83 (83)
++..-|.+..+.|.++.++..|+.+.++.-|
T Consensus 16 v~~~~g~~~~~~v~~~~~l~~l~~~y~~~~g 46 (87)
T cd01763 16 VKGQDGNEVFFKIKRSTPLKKLMEAYCQRQG 46 (87)
T ss_pred EECCCCCEEEEEEcCCCHHHHHHHHHHHHhC
Confidence 3445677888999999999999999887543
No 43
>PHA00008 J DNA packaging protein
Probab=45.27 E-value=12 Score=20.62 Aligned_cols=9 Identities=56% Similarity=1.047 Sum_probs=7.4
Q ss_pred CeEEecCce
Q 045565 52 QLRYVGGDT 60 (83)
Q Consensus 52 ~LrYvGGeT 60 (83)
.|.||||..
T Consensus 16 RLWYVGGtQ 24 (26)
T PHA00008 16 RLWYVGGTQ 24 (26)
T ss_pred EEEEeccEE
Confidence 599999963
No 44
>cd01768 RA RA (Ras-associating) ubiquitin domain. The RA (Ras-associating) domain is structurally similar to ubiquitin and is present in one or two copies in a number of signalling molecules that bind and regulate a small GTPase called Ras or the Ras-related GTPases, Ral and Rap. RA-containing proteins include RalGDS, AF6, RIN1, RASSF1, SNX27, CYR1, STE50, and phospholipase C epsilon.
Probab=43.81 E-value=54 Score=19.94 Aligned_cols=28 Identities=25% Similarity=0.421 Sum_probs=24.1
Q ss_pred ecCceeEEEEcCCCChHHHHHHHHhhhC
Q 045565 56 VGGDTRIVAVHRSSTFSTLLTKLSKLAG 83 (83)
Q Consensus 56 vGGeTRIisV~R~isf~eL~~Kls~l~G 83 (83)
.+|..+.|.|+++.+-++++..+.+-+|
T Consensus 10 ~~~~~kti~V~~~~t~~~Vi~~~l~k~~ 37 (87)
T cd01768 10 SGGTYKTLRVSKDTTAQDVIQQLLKKFG 37 (87)
T ss_pred CCccEEEEEECCCCCHHHHHHHHHHHhC
Confidence 4788899999999999999998877543
No 45
>PF09740 DUF2043: Uncharacterized conserved protein (DUF2043); InterPro: IPR018610 This entry consists of uncharacterised proteins of unknown function. They contain three conserved cysteines and a {CP}{y/l}{HG} motif.
Probab=43.77 E-value=11 Score=26.50 Aligned_cols=21 Identities=43% Similarity=0.817 Sum_probs=16.8
Q ss_pred CeEEEEeecCCEeeeCCCCCC
Q 045565 32 TRVRFMCSFGGKILPRPHDNQ 52 (83)
Q Consensus 32 ~kvKllCSyGGrIlPRp~Dg~ 52 (83)
-+-++-|=|-|+|+||-..|.
T Consensus 84 RrD~~kCPfHG~IIpRD~~G~ 104 (110)
T PF09740_consen 84 RRDRKKCPFHGKIIPRDDEGN 104 (110)
T ss_pred ccCcccCCCCCcccCCCCCCC
Confidence 356778999999999976654
No 46
>cd01808 hPLIC_N Ubiquitin-like domain of hPLIC-1 and hPLIC2. hPLIC-1 and hPLIC-2 (human homologs of the yeast ubiquitin-like Dsk2 protein) are type2 UBL's (ubiquitin-like) proteins that are thought to serve as adaptors that link the ubiquitination machinery to the proteasome. The hPLIC's have an N-terminal UBL domain that binds the S5a subunit of the proteasome and a C-terminal UBA (ubiquitin-associated) domain that binds a ubiquitylated protein.
Probab=43.18 E-value=57 Score=19.33 Aligned_cols=26 Identities=8% Similarity=0.091 Sum_probs=21.4
Q ss_pred cCceeEEEEcCCCChHHHHHHHHhhhC
Q 045565 57 GGDTRIVAVHRSSTFSTLLTKLSKLAG 83 (83)
Q Consensus 57 GGeTRIisV~R~isf~eL~~Kls~l~G 83 (83)
.|.+ .|.|+.+.+-.+|.+++++..|
T Consensus 9 ~g~~-~l~v~~~~TV~~lK~~I~~~~~ 34 (71)
T cd01808 9 KDKE-EIEIAEDASVKDFKEAVSKKFK 34 (71)
T ss_pred CCCE-EEEECCCChHHHHHHHHHHHhC
Confidence 4554 7899999999999999987654
No 47
>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=43.06 E-value=73 Score=19.08 Aligned_cols=27 Identities=22% Similarity=0.342 Sum_probs=23.1
Q ss_pred cCceeEEEEcCCCChHHHHHHHHhhhC
Q 045565 57 GGDTRIVAVHRSSTFSTLLTKLSKLAG 83 (83)
Q Consensus 57 GGeTRIisV~R~isf~eL~~Kls~l~G 83 (83)
+++|..+.|+.+.+..+|.+++++.-|
T Consensus 7 ~~~~~~l~v~~~~tV~~lK~~i~~~~g 33 (74)
T cd01793 7 AQNTHTLEVTGQETVSDIKAHVAGLEG 33 (74)
T ss_pred CCCEEEEEECCcCcHHHHHHHHHhhhC
Confidence 457889999999999999999987643
No 48
>cd00754 MoaD Ubiquitin domain of MoaD-like proteins. MoaD family. Members of this family are involved in biosynthesis of the molybdenum cofactor (Moco), an essential cofactor of a diverse group of redox enzymes. Moco biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and eukaryotes. Moco contains a tricyclic pyranopterin, termed molybdopterin (MPT), that contains the cis-dithiolene group responsible for molybdenum ligation. This dithiolene group is generated by MPT synthase, the second major step in Moco biosynthesis. MPT synthase consists of a large (MoeE) and small (MoaD) subunit. The small subunit is inserted into the lare subunit to form the active site. The small subunit, which is structurally similar to ubiquitin, contains a C-terminal thiocarboxylated glycine residue that serves as a sulfur donor for the synthesis of the MPT dithiolene group.
Probab=42.01 E-value=38 Score=20.02 Aligned_cols=26 Identities=23% Similarity=0.314 Sum_probs=20.4
Q ss_pred ecCceeEEEEcCCCChHHHHHHHHhh
Q 045565 56 VGGDTRIVAVHRSSTFSTLLTKLSKL 81 (83)
Q Consensus 56 vGGeTRIisV~R~isf~eL~~Kls~l 81 (83)
+|-+..-+.++.+++..||+++|.+.
T Consensus 13 ~g~~~~~~~~~~~~tv~~ll~~l~~~ 38 (80)
T cd00754 13 AGKDEEELELPEGATVGELLDALEAR 38 (80)
T ss_pred hCCceEEEECCCCCcHHHHHHHHHHH
Confidence 35555667888899999999999764
No 49
>cd06552 ASCH_yqfb_like ASC-1 homology domain, subfamily similar to Escherichia coli Yqfb. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation.
Probab=41.99 E-value=27 Score=21.95 Aligned_cols=51 Identities=20% Similarity=0.200 Sum_probs=32.5
Q ss_pred CeEEEEeecCCEeeeCCCCCCeEEe----cCceeEEEEcCCCChHHHHHHHHhhhC
Q 045565 32 TRVRFMCSFGGKILPRPHDNQLRYV----GGDTRIVAVHRSSTFSTLLTKLSKLAG 83 (83)
Q Consensus 32 ~kvKllCSyGGrIlPRp~Dg~LrYv----GGeTRIisV~R~isf~eL~~Kls~l~G 83 (83)
++-..=|+.+.+-.|.|.|--.-|. -|..+|.+|.+ ++|.+|-...++.+|
T Consensus 15 G~Kt~t~R~~~~~~~~~Gd~~~~~~~~~~~~~~~v~~V~~-~~~~~l~~~~A~~eG 69 (100)
T cd06552 15 GKKTATIRDGGESHLKPGDVVEVHTGERIFGEAEITSVEE-KTLGELTDEDARQEG 69 (100)
T ss_pred CCCEEEEeCCCccCCCCCCEEEEEECCEEEEEEEEEEEEE-EEhhhCCHHHHHhcC
Confidence 3334445554555566665544443 46778888877 888888887777665
No 50
>PF11543 UN_NPL4: Nuclear pore localisation protein NPL4; InterPro: IPR024682 Npl4, along with Ufd1, forms the heterodimer adaptor complex UN, which is involved in the recruitment of p97, an AAA ATPase, for tasks involving the ubiquitin pathway. Npl4 has a N-terminal ubiquitin-like domain which has within its structure a beta-grasp fold with a helical insert []. This entry represents the ubiquitin-like domain.; PDB: 2PJH_A 1WF9_A.
Probab=40.95 E-value=32 Score=21.95 Aligned_cols=21 Identities=38% Similarity=0.403 Sum_probs=16.6
Q ss_pred EEEcCCCChHHHHHHHHhhhC
Q 045565 63 VAVHRSSTFSTLLTKLSKLAG 83 (83)
Q Consensus 63 isV~R~isf~eL~~Kls~l~G 83 (83)
|.|+.+.++.+|.+|+.+.++
T Consensus 18 ie~~~~~t~~~L~~kI~~~l~ 38 (80)
T PF11543_consen 18 IEVSPSSTLSDLKEKISEQLS 38 (80)
T ss_dssp EEE-TTSBHHHHHHHHHHHS-
T ss_pred EEcCCcccHHHHHHHHHHHcC
Confidence 378999999999999998653
No 51
>KOG0695 consensus Serine/threonine protein kinase [Signal transduction mechanisms]
Probab=40.38 E-value=38 Score=29.35 Aligned_cols=28 Identities=29% Similarity=0.477 Sum_probs=23.5
Q ss_pred EecCceeEEEEcCCCChHHHHHHHHhhh
Q 045565 55 YVGGDTRIVAVHRSSTFSTLLTKLSKLA 82 (83)
Q Consensus 55 YvGGeTRIisV~R~isf~eL~~Kls~l~ 82 (83)
|.+|+.-|..++..++|.+|.+.+..+|
T Consensus 21 ~y~g~i~i~~~~p~~~~e~~~~~vrd~c 48 (593)
T KOG0695|consen 21 HYGGDIFITSVDPATTFEELCEEVRDMC 48 (593)
T ss_pred eecCcEEEEeccCcccHHHHHHHHHHHH
Confidence 4455556889999999999999999888
No 52
>cd04894 ACT_ACR-like_1 ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). This CD includes the N-terminal ACT domain of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) have been described, however, the ACR-like sequences in this CD are distinct from those characterized. This CD includes the Oryza sativa ACR-like protein (Os05g0113000) encoded on chromosome 5 and the Arabidopsis thaliana predicted gene product, At2g39570. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=40.31 E-value=68 Score=21.17 Aligned_cols=39 Identities=23% Similarity=0.316 Sum_probs=27.5
Q ss_pred cCCEeeeC--CCCCCeEEecCceeEEEEcCC----CChHHHHHHHHhhh
Q 045565 40 FGGKILPR--PHDNQLRYVGGDTRIVAVHRS----STFSTLLTKLSKLA 82 (83)
Q Consensus 40 yGGrIlPR--p~Dg~LrYvGGeTRIisV~R~----isf~eL~~Kls~l~ 82 (83)
||=.|.-- ..||+-+||= .-.|+|. +.|.-|..+|.++|
T Consensus 24 fGl~i~rgd~sTDGkWCyiv----~wVv~~~~~~~~rW~lLK~RL~~~C 68 (69)
T cd04894 24 FGLNITRGDDSTDGRWCYIV----FWVVPRPPSIKVRWDLLKNRLMSAC 68 (69)
T ss_pred hceEEEecccccCCcEEEEE----EEEecCCCCCcccHHHHHHHHHhcC
Confidence 44444432 5899999972 2234665 78999999999987
No 53
>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=36.83 E-value=56 Score=21.75 Aligned_cols=24 Identities=17% Similarity=0.398 Sum_probs=20.0
Q ss_pred ceeEEEEcCC--CChHHHHHHHHhhh
Q 045565 59 DTRIVAVHRS--STFSTLLTKLSKLA 82 (83)
Q Consensus 59 eTRIisV~R~--isf~eL~~Kls~l~ 82 (83)
|-|-+++++. ++|.+|..++.++|
T Consensus 15 EIRRf~l~~~~~~s~~~L~~~V~~~f 40 (87)
T cd06402 15 EIRRFAIDEDVSTSYEYLVEKVAAVF 40 (87)
T ss_pred ceEEEEecCCCCcCHHHHHHHHHHHc
Confidence 6688888555 69999999999987
No 54
>smart00314 RA Ras association (RalGDS/AF-6) domain. RasGTP effectors (in cases of AF6, canoe and RalGDS); putative RasGTP effectors in other cases. Kalhammer et al. have shown that not all RA domains bind RasGTP. Predicted structure similar to that determined, and that of the RasGTP-binding domain of Raf kinase. Predicted RA domains in PLC210 and nore1 found to bind RasGTP. Included outliers (Grb7, Grb14, adenylyl cyclases etc.)
Probab=36.22 E-value=84 Score=19.24 Aligned_cols=27 Identities=19% Similarity=0.272 Sum_probs=23.2
Q ss_pred ecCceeEEEEcCCCChHHHHHHHHhhh
Q 045565 56 VGGDTRIVAVHRSSTFSTLLTKLSKLA 82 (83)
Q Consensus 56 vGGeTRIisV~R~isf~eL~~Kls~l~ 82 (83)
.++..+.|.|.++.+-+|++..+.+-.
T Consensus 13 ~~~~~kti~v~~~tTa~~Vi~~~l~k~ 39 (90)
T smart00314 13 PGGTYKTLRVSSRTTARDVIQQLLEKF 39 (90)
T ss_pred CCCcEEEEEECCCCCHHHHHHHHHHHh
Confidence 367799999999999999999887654
No 55
>PF13889 Chromosome_seg: Chromosome segregation during meiosis
Probab=35.19 E-value=56 Score=20.52 Aligned_cols=29 Identities=34% Similarity=0.666 Sum_probs=22.1
Q ss_pred eEEEEeecCCEeeeCCCCCCeEEecCceeEEEEcCCCCh
Q 045565 33 RVRFMCSFGGKILPRPHDNQLRYVGGDTRIVAVHRSSTF 71 (83)
Q Consensus 33 kvKllCSyGGrIlPRp~Dg~LrYvGGeTRIisV~R~isf 71 (83)
.++|+|+-.||| |.=++-|||-..|....
T Consensus 8 HLrf~~~~~gr~----------YLh~dIRvvF~~r~~d~ 36 (56)
T PF13889_consen 8 HLRFCCPRSGRF----------YLHTDIRVVFARRSPDS 36 (56)
T ss_pred EEEEecCCCCcE----------EEECCeEEEEeccCCCC
Confidence 479999988887 77778888877776543
No 56
>TIGR00165 S18 ribosomal protein S18. This ribosomal small subunit protein is found in all eubacteria so far, as well as in chloroplasts. YER050C from Saccharomyces cerevisiae and a related protein from Caenorhabditis elegans appear to be homologous and may represent mitochondrial forms. The trusted cutoff is set high enough that these two candidate S18 proteins are not categorized automatically.
Probab=34.23 E-value=15 Score=23.64 Aligned_cols=16 Identities=44% Similarity=0.810 Sum_probs=11.6
Q ss_pred EEEeecCCEeeeCCCCC
Q 045565 35 RFMCSFGGKILPRPHDN 51 (83)
Q Consensus 35 KllCSyGGrIlPRp~Dg 51 (83)
+|+.. .|+|+||.-.|
T Consensus 28 ~Fis~-~GkIlpRriTg 43 (70)
T TIGR00165 28 KFISE-RGKILPRRITG 43 (70)
T ss_pred HhcCC-CCeEcCCccCC
Confidence 45554 59999997665
No 57
>PF04663 Phenol_monoox: Phenol hydroxylase conserved region; InterPro: IPR006756 Under aerobic conditions, phenol is usually hydroxylated to catechol and degraded via the meta or ortho pathways. Two types of phenol hydroxylase are known: one is a multi-component enzyme the other is a single-component monooxygenase. This signature is found in both types of enzymes [, ].; PDB: 3U52_F 2INN_F 2INP_E.
Probab=34.14 E-value=31 Score=22.39 Aligned_cols=31 Identities=29% Similarity=0.503 Sum_probs=22.5
Q ss_pred CCCCeEEecCcee-------EEEEcCCCChHHHHHHHH
Q 045565 49 HDNQLRYVGGDTR-------IVAVHRSSTFSTLLTKLS 79 (83)
Q Consensus 49 ~Dg~LrYvGGeTR-------IisV~R~isf~eL~~Kls 79 (83)
++++|=|||=|-+ -+-|+.+.+|.+|+++.-
T Consensus 9 ~g~qLlYigWd~HllFcap~~~plpP~mpFg~l~~~vl 46 (67)
T PF04663_consen 9 HGNQLLYIGWDDHLLFCAPFAFPLPPDMPFGALVEQVL 46 (67)
T ss_dssp TT-EEEEEE-TT-TTS-S-EEEEE-TTSBHHHHHHHTH
T ss_pred CCceEEEEEecCCeeeecceeecCCCCCcHHHHHHHhh
Confidence 5678899998865 578999999999998754
No 58
>smart00295 B41 Band 4.1 homologues. Also known as ezrin/radixin/moesin (ERM) protein domains. Present in myosins, ezrin, radixin, moesin, protein tyrosine phosphatases. Plasma membrane-binding domain. These proteins play structural and regulatory roles in the assembly and stabilization of specialized plasmamembrane domains. Some PDZ domain containing proteins bind one or more of this family. Now includes JAKs.
Probab=33.80 E-value=81 Score=21.18 Aligned_cols=32 Identities=25% Similarity=0.326 Sum_probs=27.4
Q ss_pred CeEEecCceeEEEEcCCCChHHHHHHHHhhhC
Q 045565 52 QLRYVGGDTRIVAVHRSSTFSTLLTKLSKLAG 83 (83)
Q Consensus 52 ~LrYvGGeTRIisV~R~isf~eL~~Kls~l~G 83 (83)
++...+|.++-+.|+.+++-.|++..+.+.+|
T Consensus 7 ~V~l~dg~~~~~~~~~~~t~~ev~~~v~~~~~ 38 (207)
T smart00295 7 KVYLLDGTTLEFEVDSSTTAEELLETVCRKLG 38 (207)
T ss_pred EEEecCCCEEEEEECCCCCHHHHHHHHHHHhC
Confidence 34566788999999999999999999988765
No 59
>PF09379 FERM_N: FERM N-terminal domain ; InterPro: IPR018979 This domain is the N-terminal ubiquitin-like structural domain of the FERM domain. The FERM domain (F for 4.1 protein, E for ezrin, R for radixin and M for moesin) is a widespread protein module involved in localising proteins to the plasma membrane []. FERM domains are found in a number of cytoskeletal-associated proteins that associate with various proteins at the interface between the plasma membrane and the cytoskeleton. The FERM domain is located at the N terminus of the majority of FERM-containing proteins [, ], which includes: Band 4.1, which links the spectrin-actin cytoskeleton of erythrocytes to the plasma membrane. Ezrin, a component of the undercoat of the microvilli plasma membrane. Moesin, which is probably involved in binding major cytoskeletal structures to the plasma membrane. Radixin, which is involved in the binding of the barbed end of actin filaments to the plasma membrane in the undercoat of the cell- to-cell adherens junction. Talin, a cytoskeletal protein concentrated in regions of cell-substratum contact and, in lymphocytes, of cell-cell contacts. Filopodin, a slime mold protein that binds actin and which is involved in the control of cell motility and chemotaxis. Merlin (or schwannomin). Protein NBL4. Unconventional myosins X, VIIa and XV, which are mutated in congenital deafness. Focal-adhesion kinases (FAKs), cytoplasmic protein tyrosine kinases involved in signalling through integrins. Janus tyrosine kinases (JAKs), cytoplasmic tyrosine kinases that are non-covalently associated with the cytoplasmic tails of receptors for cytokines or polypeptidic hormones. Non-receptor tyrosine-protein kinase TYK2. Protein-tyrosine phosphatases PTPN3 and PTPN4, enzyme that appear to act at junctions between the membrane and the cytoskeleton. Protein-tyrosine phosphatases PTPN14 and PTP-D1, PTP-RL10 and PTP2E. Caenorhabditis elegans protein phosphatase ptp-1. Ezrin, moesin, and radixin are highly related proteins (ERM protein family), but the other proteins in which the FERM domain is found do not share any region of similarity outside of this domain. ERM proteins are made of three domains, the FERM domain, a central helical domain and a C-terminal tail domain, which binds F-actin. The amino-acid sequence of the FERM domain is highly conserved among ERM proteins and is responsible for membrane association by direct binding to the cytoplasmic domain or tail of integral membrane proteins. ERM proteins are regulated by an intramolecular association of the FERM and C-terminal tail domains that masks their binding sites for other molecules. For cytoskeleton-membrane cross-linking, the dormant molecules becomes activated and the FERM domain attaches to the membrane by binding specific membrane proteins, while the last 34 residues of the tail bind actin filaments. Aside from binding to membranes, the activated FERM domain of ERM proteins can also bind the guanine nucleotide dissociation inhibitor of Rho GTPase (RhoDGI), which suggests that in addition to functioning as a cross-linker, ERM proteins may influence Rho signalling pathways. The crystal structure of the FERM domain reveals that it is composed of three structural modules (F1, F2, and F3) that together form a compact clover-shaped structure []. The FERM domain has also been called the amino-terminal domain, the 30kDa domain, 4.1N30, the membrane-cytoskeletal-linking domain, the ERM-like domain, the ezrin-like domain of the band 4.1 superfamily, the conserved N-terminal region, and the membrane attachment domain [].; PDB: 1EF1_B 1SGH_A 1E5W_A 2KC2_A 2KMA_A 3IVF_A 1H4R_B 3U8Z_A 1ISN_A 3BIN_A ....
Probab=33.33 E-value=67 Score=18.99 Aligned_cols=26 Identities=23% Similarity=0.282 Sum_probs=22.2
Q ss_pred cCceeEEEEcCCCChHHHHHHHHhhh
Q 045565 57 GGDTRIVAVHRSSTFSTLLTKLSKLA 82 (83)
Q Consensus 57 GGeTRIisV~R~isf~eL~~Kls~l~ 82 (83)
-|.++.+.|+++.+-.+|..++.+..
T Consensus 5 D~~~~~~~v~~~~t~~~l~~~v~~~l 30 (80)
T PF09379_consen 5 DGTTKTFEVDPKTTGQDLLEQVCDKL 30 (80)
T ss_dssp SEEEEEEEEETTSBHHHHHHHHHHHH
T ss_pred CCCcEEEEEcCCCcHHHHHHHHHHHc
Confidence 46789999999999999999887654
No 60
>PRK06437 hypothetical protein; Provisional
Probab=33.13 E-value=71 Score=19.48 Aligned_cols=26 Identities=15% Similarity=0.356 Sum_probs=22.1
Q ss_pred eEEecCceeEEEEcCCCChHHHHHHH
Q 045565 53 LRYVGGDTRIVAVHRSSTFSTLLTKL 78 (83)
Q Consensus 53 LrYvGGeTRIisV~R~isf~eL~~Kl 78 (83)
.+-.|+.++-+.++.+.+.++|++.|
T Consensus 5 ~~v~g~~~~~~~i~~~~tv~dLL~~L 30 (67)
T PRK06437 5 IRVKGHINKTIEIDHELTVNDIIKDL 30 (67)
T ss_pred EEecCCcceEEEcCCCCcHHHHHHHc
Confidence 44558899999999999999999876
No 61
>PF11784 DUF3320: Protein of unknown function (DUF3320); InterPro: IPR021754 This family is conserved in Proteobacteria and Chlorobi families. Many members are annotated as being putative DNA helicase-related proteins.
Probab=32.09 E-value=13 Score=22.13 Aligned_cols=23 Identities=22% Similarity=0.294 Sum_probs=19.1
Q ss_pred eEEEEcCCCChHHHHHHHHhhhC
Q 045565 61 RIVAVHRSSTFSTLLTKLSKLAG 83 (83)
Q Consensus 61 RIisV~R~isf~eL~~Kls~l~G 83 (83)
.||.+.-.|+..+|.+|+.+.+|
T Consensus 19 ~Iv~~EgPI~~~~L~~Ri~~a~G 41 (52)
T PF11784_consen 19 QIVEVEGPIHEDELARRIARAWG 41 (52)
T ss_pred HHHHHcCCccHHHHHHHHHHHcC
Confidence 35666778999999999999887
No 62
>PF12436 USP7_ICP0_bdg: ICP0-binding domain of Ubiquitin-specific protease 7; InterPro: IPR024729 This domain is found in eukaryotes, and is approximately 40 amino acids in length. It is found in proteins of the peptidase C19 family, which contains contains ubiquitinyl hydrolases like ubiquitin-specific protease 7 (USP7). USP7 regulates the turnover of p53 [].; PDB: 2KVR_A 2YLM_A.
Probab=31.85 E-value=47 Score=24.87 Aligned_cols=32 Identities=34% Similarity=0.614 Sum_probs=26.1
Q ss_pred CCCCCeEEecCceeEEEEcCCCChHHHHHHHHhhhC
Q 045565 48 PHDNQLRYVGGDTRIVAVHRSSTFSTLLTKLSKLAG 83 (83)
Q Consensus 48 p~Dg~LrYvGGeTRIisV~R~isf~eL~~Kls~l~G 83 (83)
|...+|+|+|- +.|+++.+.++|...+.+++|
T Consensus 78 p~~q~L~~iGh----~~v~~~~~v~~l~~~i~~~~g 109 (249)
T PF12436_consen 78 PETQTLRYIGH----VYVPKNDKVSELVPLINERAG 109 (249)
T ss_dssp TTTTEEEEEEE----EEEETT-BGGGTHHHHHHHHT
T ss_pred CCCCEEEEEeE----EEECCCCCHHHHHHHHHHHcC
Confidence 46778999994 567999999999999998876
No 63
>cd01797 NIRF_N amino-terminal ubiquitin-like domain of Np95 and NIRF. NIRF_N This CD represents the amino-terminal ubiquitin-like domain of a family of nuclear proteins that includes Np95 and NIRF (Np95/ICBP90-like RING finger) protein. Both Np95 and NIRF have a domain architecture consisting of a ubiquitin-like domain, a PHD finger, a YDG/SRA domain, Rb-binding motifs and a RING finger domain. Both Np95 and NIRF are ubiquitin ligases that ubiquitinate PCNP (PEST-containing nuclear proteins). While Np95 is capable of binding histones, NIRF is involved in cell cycle regulation.
Probab=31.06 E-value=1.1e+02 Score=19.06 Aligned_cols=30 Identities=27% Similarity=0.400 Sum_probs=22.7
Q ss_pred EEecCce-eEEE-EcCCCChHHHHHHHHhhhC
Q 045565 54 RYVGGDT-RIVA-VHRSSTFSTLLTKLSKLAG 83 (83)
Q Consensus 54 rYvGGeT-RIis-V~R~isf~eL~~Kls~l~G 83 (83)
+-..|.+ .-+. |+.+.+..+|.+++++..|
T Consensus 6 k~~~G~~~~~l~~v~~~~TV~~lK~~i~~~~g 37 (78)
T cd01797 6 RTMDGKETRTVDSLSRLTKVEELREKIQELFN 37 (78)
T ss_pred EcCCCCEEEEeeccCCcCcHHHHHHHHHHHhC
Confidence 4456776 3464 7889999999999988654
No 64
>PF04726 Microvir_J: Microvirus J protein; InterPro: IPR006815 This small protein is involved in DNA packaging, interacting with DNA via its hydrophobic C terminus. In bacteriophage phi-X174, J is present in 60 copies, and forms an S-shaped polypeptide chain without any secondary structure. It is thought to interact with DNA through simple charge interactions [].; GO: 0003677 DNA binding, 0019073 viral DNA genome packaging, 0019028 viral capsid; PDB: 1M06_J 1GFF_3 1RB8_J 2BPA_3.
Probab=30.37 E-value=24 Score=19.08 Aligned_cols=9 Identities=56% Similarity=1.036 Sum_probs=3.3
Q ss_pred CCeEEecCc
Q 045565 51 NQLRYVGGD 59 (83)
Q Consensus 51 g~LrYvGGe 59 (83)
-.|.||||.
T Consensus 14 arlwyvgg~ 22 (24)
T PF04726_consen 14 ARLWYVGGT 22 (24)
T ss_dssp S----SSS-
T ss_pred eEEEEecce
Confidence 369999995
No 65
>TIGR03649 ergot_EASG ergot alkaloid biosynthesis protein, AFUA_2G17970 family. This family consists of fungal proteins of unknown function associated with secondary metabolite biosynthesis, such as of the ergot alkaloids such as ergovaline. Nomenclature differs because gene order differs - this is EasG in Neotyphodium lolii but is designated ergot alkaloid biosynthetic protein A in several other fungi.
Probab=30.01 E-value=73 Score=22.69 Aligned_cols=43 Identities=21% Similarity=0.304 Sum_probs=30.4
Q ss_pred CCEeeeCCCCCCeEEe------------------cCceeEEEEcCCCChHHHHHHHHhhhC
Q 045565 41 GGKILPRPHDNQLRYV------------------GGDTRIVAVHRSSTFSTLLTKLSKLAG 83 (83)
Q Consensus 41 GGrIlPRp~Dg~LrYv------------------GGeTRIisV~R~isf~eL~~Kls~l~G 83 (83)
+|+|..-..|+++.|| .|.+.++.-+..+|+.|+.+.+++..|
T Consensus 154 ~~~~~~~~g~~~~~~v~~~Dva~~~~~~l~~~~~~~~~~~l~g~~~~s~~eia~~l~~~~g 214 (285)
T TIGR03649 154 ENKIYSATGDGKIPFVSADDIARVAYRALTDKVAPNTDYVVLGPELLTYDDVAEILSRVLG 214 (285)
T ss_pred CCeEEecCCCCccCcccHHHHHHHHHHHhcCCCcCCCeEEeeCCccCCHHHHHHHHHHHhC
Confidence 3555544456666654 245566777889999999999998876
No 66
>cd01791 Ubl5 UBL5 ubiquitin-like modifier. UBL5 (also known as HUB1) is a ubiquitin-like modifier that is both widely expressed and highly phylogenetically conserved. At the C-terminal end of the ubiquitin-like fold of UBL5 is a di-tyrosine motif followed by a single variable residue instead of the characteristic di-glycine found in all other ubiquitin-like modifiers. ULB5 interacts with a cyclin-like kinase called CLK4 but not with other cyclin-like kinase family members.
Probab=30.00 E-value=1.1e+02 Score=18.87 Aligned_cols=25 Identities=16% Similarity=0.181 Sum_probs=21.5
Q ss_pred CceeEEEEcCCCChHHHHHHHHhhh
Q 045565 58 GDTRIVAVHRSSTFSTLLTKLSKLA 82 (83)
Q Consensus 58 GeTRIisV~R~isf~eL~~Kls~l~ 82 (83)
|.+..+.|+.+.+..+|.+++++..
T Consensus 11 Gk~~~~~v~~~~TV~~LK~~I~~~~ 35 (73)
T cd01791 11 GKKVRVKCNPDDTIGDLKKLIAAQT 35 (73)
T ss_pred CCEEEEEeCCCCcHHHHHHHHHHHh
Confidence 6777789999999999999998754
No 67
>CHL00077 rps18 ribosomal protein S18
Probab=29.78 E-value=20 Score=24.22 Aligned_cols=16 Identities=44% Similarity=0.704 Sum_probs=12.4
Q ss_pred EEEeecCCEeeeCCCCC
Q 045565 35 RFMCSFGGKILPRPHDN 51 (83)
Q Consensus 35 KllCSyGGrIlPRp~Dg 51 (83)
+|++. .|+|+||--.|
T Consensus 38 ~Fis~-~GkIlpRriTG 53 (86)
T CHL00077 38 RFISE-QGKILSRRVTR 53 (86)
T ss_pred HhcCC-CCeEcCcccCC
Confidence 46665 89999997665
No 68
>PF00763 THF_DHG_CYH: Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; InterPro: IPR020630 Enzymes that participate in the transfer of one-carbon units require the coenzyme tetrahydrofolate (THF). Various reactions generate one-carbon derivatives of THF, which can be interconverted between different oxidation states by methylene-THF dehydrogenase (1.5.1.5 from EC), methenyl-THF cyclohydrolase (3.5.4.9 from EC) and formyl-THF synthetase (6.3.4.3 from EC) [, ]. The dehydrogenase and cyclohydrolase activities are expressed by a variety of multifunctional enzymes, including the tri-functional eukaryotic C1-tetrahydrofolate synthase []; a bifunctional eukaryotic mitochondrial protein; and the bifunctional Escherichia coli folD protein [, ]. Methylene-tetrahydrofolate dehydrogenase and methenyltetrahydrofolate cyclo-hydrolase share an overlapping active site [], and as such are usually located together in proteins, acting in tandem on the carbon-nitrogen bonds of substrates other than peptide bonds. This entry represents the N-terminal catalytic domain of these enzymes. ; GO: 0003824 catalytic activity, 0004488 methylenetetrahydrofolate dehydrogenase (NADP+) activity, 0009396 folic acid-containing compound biosynthetic process, 0055114 oxidation-reduction process; PDB: 2C2X_B 2C2Y_A 1EDZ_A 1EE9_A 4A26_B 3NGL_C 3NGX_A 1B0A_A 1DIA_A 1A4I_B ....
Probab=29.11 E-value=82 Score=21.00 Aligned_cols=27 Identities=19% Similarity=0.297 Sum_probs=22.2
Q ss_pred ecCceeEEEEcCCCChHHHHHHHHhhh
Q 045565 56 VGGDTRIVAVHRSSTFSTLLTKLSKLA 82 (83)
Q Consensus 56 vGGeTRIisV~R~isf~eL~~Kls~l~ 82 (83)
+|-+++++.++.+++-.+|.+.+.++.
T Consensus 57 ~Gi~~~~~~l~~~~~~~el~~~i~~lN 83 (117)
T PF00763_consen 57 LGIEFELIELPEDISEEELLELIEKLN 83 (117)
T ss_dssp HT-EEEEEEE-TTSSHHHHHHHHHHHH
T ss_pred cCCceEEEECCCCcCHHHHHHHHHHHh
Confidence 488999999999999999999988763
No 69
>COG0424 Maf Nucleotide-binding protein implicated in inhibition of septum formation [Cell division and chromosome partitioning]
Probab=28.79 E-value=40 Score=25.35 Aligned_cols=15 Identities=33% Similarity=0.775 Sum_probs=13.2
Q ss_pred EeecCCEeeeCCCCC
Q 045565 37 MCSFGGKILPRPHDN 51 (83)
Q Consensus 37 lCSyGGrIlPRp~Dg 51 (83)
+|..||||++.|.|-
T Consensus 73 vv~ldgrilgKP~~~ 87 (193)
T COG0424 73 VVVLDGRILGKPKDE 87 (193)
T ss_pred EEEECCEEecCCCCH
Confidence 678999999999884
No 70
>PF00614 PLDc: Phospholipase D Active site motif; InterPro: IPR001736 Phosphatidylcholine-hydrolysing phospholipase D (PLD) isoforms are activated by ADP-ribosylation factors (ARFs). PLD produces phosphatidic acid from phosphatidylcholine, which may be essential for the formation of certain types of transport vesicles or may be constitutive vesicular transport to signal transduction pathways. PC-hydrolysing PLD is a homologue of cardiolipin synthase, phosphatidylserine synthase, bacterial PLDs, and viral proteins. Each of these appears to possess a domain duplication which is apparent by the presence of two motifs containing well-conserved histidine, lysine, and/or asparagine residues which may contribute to the active site aspartic acid. An Escherichia coli endonuclease (nuc) and similar proteins appear to be PLD homologues but possess only one of these motifs [, , , ].; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 3HSI_C.
Probab=28.37 E-value=35 Score=18.27 Aligned_cols=11 Identities=36% Similarity=0.878 Sum_probs=7.9
Q ss_pred CCCCeEEecCc
Q 045565 49 HDNQLRYVGGD 59 (83)
Q Consensus 49 ~Dg~LrYvGGe 59 (83)
-|+++.||||-
T Consensus 12 vD~~~a~vGg~ 22 (28)
T PF00614_consen 12 VDDRVAFVGGA 22 (28)
T ss_dssp ETTTEEEEE--
T ss_pred EcCCEEEECce
Confidence 58889999984
No 71
>cd02168 NMNAT_Nudix Nicotinamide/nicotinate mononucleotide adenylyltransferase of bifunctional proteins, also containing a Nudix hydrolase domain. N-terminal NMNAT (Nicotinamide/nicotinate mononucleotide adenylyltransferase) domain of a novel bifunctional enzyme endowed with NMN adenylyltransferase and Nudix hydrolase activities. This domain is highly homologous to the archeal NMN adenyltransferase that catalyzes NAD synthesis from NMN and ATP. NMNAT is an essential enzyme in the biosynthesis of NAD(+) and NADP(+). Nicotinamide-nucleotide adenylyltransferase synthesizes NAD via the salvage pathway, while nicotinate-nucleotide adenylyltransferase synthesizes the immediate precursor of NAD via the de novo pathway. The C-terminal domain of this enzyme shares homology with the archaeal ADP-ribose pyrophosphatase, a member of the 'Nudix' hydrolase family.
Probab=28.30 E-value=6.7 Score=28.28 Aligned_cols=16 Identities=25% Similarity=0.505 Sum_probs=13.2
Q ss_pred ecCCEeeeCCCCCCeEE
Q 045565 39 SFGGKILPRPHDNQLRY 55 (83)
Q Consensus 39 SyGGrIlPRp~Dg~LrY 55 (83)
=|||++.| +|.|.|..
T Consensus 3 l~~GrF~P-~H~GHl~~ 18 (181)
T cd02168 3 VYIGRFQP-FHNGHLAV 18 (181)
T ss_pred EEeeccCC-CCHHHHHH
Confidence 48999999 89988754
No 72
>PRK01153 nicotinamide-nucleotide adenylyltransferase; Provisional
Probab=26.43 E-value=7.3 Score=27.90 Aligned_cols=17 Identities=29% Similarity=0.538 Sum_probs=13.6
Q ss_pred ecCCEeeeCCCCCCeEEe
Q 045565 39 SFGGKILPRPHDNQLRYV 56 (83)
Q Consensus 39 SyGGrIlPRp~Dg~LrYv 56 (83)
=|||++.| +|.|.|.++
T Consensus 4 l~~G~F~P-~H~GHl~~i 20 (174)
T PRK01153 4 LFIGRFQP-FHKGHLEVI 20 (174)
T ss_pred EEeeccCC-CCHHHHHHH
Confidence 48999999 888877554
No 73
>TIGR00601 rad23 UV excision repair protein Rad23. All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=25.18 E-value=1.2e+02 Score=24.75 Aligned_cols=31 Identities=13% Similarity=0.182 Sum_probs=26.9
Q ss_pred eEEecCceeEEEEcCCCChHHHHHHHHhhhC
Q 045565 53 LRYVGGDTRIVAVHRSSTFSTLLTKLSKLAG 83 (83)
Q Consensus 53 LrYvGGeTRIisV~R~isf~eL~~Kls~l~G 83 (83)
++...|++..|.|+.+.+..+|.+|+.+..|
T Consensus 5 VKtl~g~~~~IeV~~~~TV~dLK~kI~~~~g 35 (378)
T TIGR00601 5 FKTLQQQKFKIDMEPDETVKELKEKIEAEQG 35 (378)
T ss_pred EEeCCCCEEEEEeCCcChHHHHHHHHHHhhC
Confidence 5667899999999999999999999987653
No 74
>PF09992 DUF2233: Predicted periplasmic protein (DUF2233); InterPro: IPR018711 This entry contains proteins that catalyze the second step in the formation of the mannose 6-phosphate targeting signal on lysosomal enzyme oligosaccharides, this is achieved by removing GlcNAc residues from GlcNAc-alpha-P-mannose moieties, which are formed in the first step.; PDB: 3OHG_A.
Probab=24.60 E-value=1.9e+02 Score=19.47 Aligned_cols=42 Identities=26% Similarity=0.380 Sum_probs=22.9
Q ss_pred cCCEeeeCCCCCC--------eEE-ecCceeEEEEc----CCCChHHHHHHHHhh
Q 045565 40 FGGKILPRPHDNQ--------LRY-VGGDTRIVAVH----RSSTFSTLLTKLSKL 81 (83)
Q Consensus 40 yGGrIlPRp~Dg~--------LrY-vGGeTRIisV~----R~isf~eL~~Kls~l 81 (83)
.+|++.+...+.+ +-| -.|+--++.|+ ..+++.||.+-|.+|
T Consensus 74 ~nG~~~~~~~~~~~~~~~RtaiG~~~~g~l~l~~vdg~~~~g~tl~ela~~l~~l 128 (170)
T PF09992_consen 74 KNGKIVPNFSDEGWGRHPRTAIGVTADGKLLLIVVDGRQSAGMTLDELAQLLKSL 128 (170)
T ss_dssp ETTEE----TTSGGSSB-EEEEEE-TTSEEEEEEE----S--B-HHHHHHHHHHH
T ss_pred ECCEEccCcccCccccCCEEEEEEeCCCcEEEEEEcCCcCCCCCHHHHHHHHHHc
Confidence 5888887766653 223 24555666777 689999999877664
No 75
>PF05678 VQ: VQ motif; InterPro: IPR008889 This short motif is found in a variety of plant proteins. These proteins vary greatly in length and are mostly composed of low complexity regions. They all conserve a short motif FXhVQChTG, where X is any amino acid and h is a hydrophobic amino acid. The function of this motif is uncertain, however one protein in this family has been found to bind the SigA sigma factor Q9LDH1 from SWISSPROT. It would seem plausible that this motif is needed for this activity and that this whole family might be involved in modulating plastid sigma factors.
Probab=24.43 E-value=54 Score=18.17 Aligned_cols=20 Identities=20% Similarity=0.471 Sum_probs=15.0
Q ss_pred ceeEEEEcCCCChHHHHHHHH
Q 045565 59 DTRIVAVHRSSTFSTLLTKLS 79 (83)
Q Consensus 59 eTRIisV~R~isf~eL~~Kls 79 (83)
.|++|.++.+ .|.+|+++|.
T Consensus 4 ~p~vi~~d~~-~Fr~lVQ~LT 23 (31)
T PF05678_consen 4 PPTVIHTDPS-NFRALVQRLT 23 (31)
T ss_pred CCEEEEeCHH-HHHHHHHHhH
Confidence 3667776654 8999999985
No 76
>KOG1722 consensus 60s ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=24.06 E-value=1.3e+02 Score=22.49 Aligned_cols=38 Identities=37% Similarity=0.734 Sum_probs=27.0
Q ss_pred EeecCC-EeeeCCCCCCeEEecCceeEEEE--------------cCCCChHHHHHH
Q 045565 37 MCSFGG-KILPRPHDNQLRYVGGDTRIVAV--------------HRSSTFSTLLTK 77 (83)
Q Consensus 37 lCSyGG-rIlPRp~Dg~LrYvGGeTRIisV--------------~R~isf~eL~~K 77 (83)
+|||-| +|.| . .--+||-||..|..+ ||.|.|.-|-.+
T Consensus 5 lCsFSG~KIyP--G-~G~r~vR~D~Kvf~Fln~Kc~~~f~~rrnPr~l~WTvLyR~ 57 (155)
T KOG1722|consen 5 LCSFSGYKIYP--G-HGRRFVRGDGKVFRFLNSKCESLFLQRRNPRRLAWTVLYRK 57 (155)
T ss_pred EeeccCceecC--C-CceeEEecCCeeeeehhhhhHHHHHhccChhhhhHHHHHHH
Confidence 799977 6777 2 236788898888754 455777777654
No 77
>PF07929 PRiA4_ORF3: Plasmid pRiA4b ORF-3-like protein; InterPro: IPR012912 Members of this family are similar to the protein product of ORF-3 (Q44206 from SWISSPROT) found on plasmid pRiA4 in the bacterium Agrobacterium rhizogenes. This plasmid is responsible for tumourigenesis at wound sites of plants infected by this bacterium, but the ORF-3 product does not seem to be involved in the pathogenetic process []. Other proteins found in this family are annotated as being putative TnpR resolvases (Q9LCU7 from SWISSPROT, Q50439 from SWISSPROT), but no further evidence was found to back this. Moreover, another member of this family is described as a probable lexA repressor (Q7UEI4 from SWISSPROT) and in fact carries a LexA DNA binding domain (IPR006199 from INTERPRO), but no references were found to expand on this. ; PDB: 2I1S_A.
Probab=23.64 E-value=1.1e+02 Score=21.24 Aligned_cols=24 Identities=21% Similarity=0.195 Sum_probs=18.7
Q ss_pred eeEEEEcCCCChHHHHHHHHhhhC
Q 045565 60 TRIVAVHRSSTFSTLLTKLSKLAG 83 (83)
Q Consensus 60 TRIisV~R~isf~eL~~Kls~l~G 83 (83)
.|-|.|+-+++|.+|-.-+-...|
T Consensus 19 wRri~Vp~~~tl~~Lh~~Iq~afg 42 (179)
T PF07929_consen 19 WRRIEVPADITLADLHEVIQAAFG 42 (179)
T ss_dssp EEEEEEETT-BHHHHHHHHHHHTT
T ss_pred EEEEEECCCCCHHHHHHHHHHHhC
Confidence 688999999999999877665543
No 78
>COG2075 RPL24A Ribosomal protein L24E [Translation, ribosomal structure and biogenesis]
Probab=23.63 E-value=2.1e+02 Score=18.63 Aligned_cols=41 Identities=27% Similarity=0.549 Sum_probs=28.8
Q ss_pred EeecCCEeeeCCCCCCeEEecCceeEEE--------------EcCCCChHHHHHHHH
Q 045565 37 MCSFGGKILPRPHDNQLRYVGGDTRIVA--------------VHRSSTFSTLLTKLS 79 (83)
Q Consensus 37 lCSyGGrIlPRp~Dg~LrYvGGeTRIis--------------V~R~isf~eL~~Kls 79 (83)
.|||=|+.++ |..| +=||=+|-+|+- .||.+.|...-.++.
T Consensus 5 ~CsFcG~~I~-PGtG-~m~Vr~Dg~v~~FcssKc~k~~~~~rnPRk~~WT~~~~~~~ 59 (66)
T COG2075 5 VCSFCGKKIE-PGTG-IMYVRNDGKVLRFCSSKCEKLFKLGRNPRKLKWTKKYRKMH 59 (66)
T ss_pred EecCcCCccC-CCce-EEEEecCCeEEEEechhHHHHHHccCCCccchhHHHHHHHH
Confidence 5999887766 3444 558999998885 467777777666553
No 79
>PF02519 Auxin_inducible: Auxin responsive protein; InterPro: IPR003676 This family consists of the protein products of a gene cluster that encodes a group of auxin-regulated RNAs (small auxin up RNAs, SAURs) []. Proteins from this ARG7 auxin responsive genes family have no identified functional role [].
Probab=23.14 E-value=92 Score=20.83 Aligned_cols=36 Identities=31% Similarity=0.422 Sum_probs=25.8
Q ss_pred CCCCCeEEecCceeEEEEcCC----CChHHHHHHHHhhhC
Q 045565 48 PHDNQLRYVGGDTRIVAVHRS----STFSTLLTKLSKLAG 83 (83)
Q Consensus 48 p~Dg~LrYvGGeTRIisV~R~----isf~eL~~Kls~l~G 83 (83)
|...--=|||-+.|-..|+-. --|.+|+.+-.+-+|
T Consensus 37 p~G~~~VyVG~~~~Rfvvp~~~L~hp~f~~LL~~aeeEfG 76 (100)
T PF02519_consen 37 PKGHFAVYVGEERRRFVVPVSYLNHPLFQELLEQAEEEFG 76 (100)
T ss_pred CCCeEEEEeCccceEEEechHHcCchhHHHHHHHHhhhcC
Confidence 444456799998988888865 468888877766443
No 80
>PF00788 RA: Ras association (RalGDS/AF-6) domain; InterPro: IPR000159 Proteins with this domain are mostly RasGTP effectors and include guanine-nucleotide releasing factor in mammals []. This factor stimulates the dissociation of GDP from the Ras-related RALA and RALB GTPases, which allows GTP binding and activation of the GTPases. It interacts and acts as an effector molecule for R-ras, K-Ras and Rap []. The domain is also present in a number of other proteins among them the sexual differentiation protein in yeast that is essential for mating and meiosis and yeast adenylate cyclase. These proteins contain repeated leucine-rich (LRR) segments.; GO: 0007165 signal transduction; PDB: 3EC8_A 2C5L_D 2BYF_A 2CS4_A 3KH0_A 2B3A_A 1RAX_A 2RGF_A 1WGR_A 1WXA_A ....
Probab=22.99 E-value=1.8e+02 Score=17.25 Aligned_cols=25 Identities=16% Similarity=0.171 Sum_probs=21.6
Q ss_pred ceeEEEEcCCCChHHHHHHHHhhhC
Q 045565 59 DTRIVAVHRSSTFSTLLTKLSKLAG 83 (83)
Q Consensus 59 eTRIisV~R~isf~eL~~Kls~l~G 83 (83)
.++.|.|+.+.+-.|++..+.+-+|
T Consensus 17 ~~k~i~v~~~tTa~evi~~~l~k~~ 41 (93)
T PF00788_consen 17 TYKTIKVSSSTTAREVIEMALEKFG 41 (93)
T ss_dssp SEEEEEEETTSBHHHHHHHHHHHTT
T ss_pred cEEEEEECCCCCHHHHHHHHHHHhC
Confidence 4899999999999999998877553
No 81
>PF07045 DUF1330: Protein of unknown function (DUF1330); InterPro: IPR010753 This family consists of several hypothetical bacterial proteins of around 90 residues in length. The function of this family is unknown.; PDB: 2FIU_B 3HHL_A 3DCA_D 3LO3_I.
Probab=22.74 E-value=79 Score=18.83 Aligned_cols=19 Identities=26% Similarity=0.518 Sum_probs=11.0
Q ss_pred eecCCEeeeCCCCCCeEEec
Q 045565 38 CSFGGKILPRPHDNQLRYVG 57 (83)
Q Consensus 38 CSyGGrIlPRp~Dg~LrYvG 57 (83)
=.|||+++-| .+.....-|
T Consensus 16 ~~~GG~~l~~-~~~~~~leG 34 (65)
T PF07045_consen 16 EKYGGRVLAR-GGEPEVLEG 34 (65)
T ss_dssp HHTT-EEEEE-CEEEEEEES
T ss_pred HHcCCEEEEE-CCceeEEec
Confidence 3589999998 223344444
No 82
>PF08856 DUF1826: Protein of unknown function (DUF1826); InterPro: IPR014955 These proteins are functionally uncharacterised.
Probab=22.34 E-value=49 Score=24.48 Aligned_cols=17 Identities=29% Similarity=0.876 Sum_probs=12.5
Q ss_pred CeEEEEeecCC---EeeeCC
Q 045565 32 TRVRFMCSFGG---KILPRP 48 (83)
Q Consensus 32 ~kvKllCSyGG---rIlPRp 48 (83)
--+||+|.|.| ..++..
T Consensus 112 vp~RLlcTY~G~GTewl~~~ 131 (196)
T PF08856_consen 112 VPLRLLCTYRGPGTEWLPND 131 (196)
T ss_pred cceEEEEEEecCCcEEccCc
Confidence 35899999988 455554
No 83
>COG5470 Uncharacterized conserved protein [Function unknown]
Probab=22.27 E-value=87 Score=21.68 Aligned_cols=27 Identities=30% Similarity=0.375 Sum_probs=16.9
Q ss_pred eecCCEeeeCCCCCCeEEec--Cc-eeEEEEc
Q 045565 38 CSFGGKILPRPHDNQLRYVG--GD-TRIVAVH 66 (83)
Q Consensus 38 CSyGGrIlPRp~Dg~LrYvG--Ge-TRIisV~ 66 (83)
=.||||.|-|-.+- .=.= .. ||+|.|.
T Consensus 30 ~~~Ggr~LvRGG~v--~~lEG~w~ptr~vviE 59 (96)
T COG5470 30 EKFGGRYLVRGGEV--ETLEGEWRPTRNVVIE 59 (96)
T ss_pred HHhCCeeEeeCCCe--eeccCCCCcccEEEEE
Confidence 35999999975432 2222 44 7787763
No 84
>PRK13600 putative ribosomal protein L7Ae-like; Provisional
Probab=21.95 E-value=1.5e+02 Score=19.51 Aligned_cols=24 Identities=8% Similarity=0.122 Sum_probs=20.9
Q ss_pred CceeEEEEcCCCChHHHHHHHHhhh
Q 045565 58 GDTRIVAVHRSSTFSTLLTKLSKLA 82 (83)
Q Consensus 58 GeTRIisV~R~isf~eL~~Kls~l~ 82 (83)
|+.+.|-|.++++ ..++.+|-.+|
T Consensus 28 g~~~~v~iA~Da~-~~vv~~l~~lc 51 (84)
T PRK13600 28 DQVTSLIIAEDVE-VYLMTRVLSQI 51 (84)
T ss_pred CCceEEEEeCCCC-HHHHHHHHHHH
Confidence 8889999999999 66888888887
No 85
>PF14832 Tautomerase_3: Putative oxalocrotonate tautomerase enzyme; PDB: 3C6V_C 3N4D_I 3N4G_C 3N4H_A 2FLZ_C 3MF8_A 3MF7_A 2FLT_A.
Probab=21.94 E-value=1.2e+02 Score=21.37 Aligned_cols=28 Identities=25% Similarity=0.312 Sum_probs=18.2
Q ss_pred eEEecCcee-------EEEEcCCCChHHHHHHHHh
Q 045565 53 LRYVGGDTR-------IVAVHRSSTFSTLLTKLSK 80 (83)
Q Consensus 53 LrYvGGeTR-------IisV~R~isf~eL~~Kls~ 80 (83)
--||||+.+ |-.+-|++.-.|..+++.+
T Consensus 50 ~~fvGG~~~~~fvrI~i~hiaR~~~~~e~~~~~~~ 84 (136)
T PF14832_consen 50 DFFVGGKPRDNFVRIVIDHIARTGPDDEQRRRLLD 84 (136)
T ss_dssp SEEETTEE-SSCEEEEEEEEEEST-SHHHHHHHHH
T ss_pred CeEECCcCcCceEEEEEEEEeecCCCHHHHHHHHH
Confidence 689999977 3344577777777766654
No 86
>PF01084 Ribosomal_S18: Ribosomal protein S18; InterPro: IPR001648 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Evidence suggests that, in prokaryotes, the peptidyl transferase reaction is performed by the large subunit 23S rRNA, whereas proteins probably have a greater role in eukaryotic ribosomes. Most of the proteins lie close to, or on the surface of, the 30S subunit, arranged peripherally around the rRNA []. The small subunit ribosomal proteins can be categorised as primary binding proteins, which bind directly and independently to 16S rRNA; secondary binding proteins, which display no specific affinity for 16S rRNA, but its assembly is contingent upon the presence of one or more primary binding proteins; and tertiary binding proteins, which require the presence of one or more secondary binding proteins and sometimes other tertiary binding proteins. The small ribosomal subunit protein S18 is known to be involved in binding the aminoacyl-tRNA complex in Escherichia coli [], and appears to be situated at the tRNA A-site. Experimental evidence has revealed that S18 is well exposed on the surface of the E. coli ribosome, and is a secondary rRNA binding protein []. S18 belongs to a family of ribosomal proteins [] that includes: eubacterial S18; metazoan mitochondrial S18, algal and plant chloroplast S18; and cyanelle S18.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2UXD_R 3I8G_U 3UZ7_U 1N33_R 2XSY_R 3V24_R 3OGY_R 2XUY_R 2XFZ_R 3UXT_R ....
Probab=21.77 E-value=11 Score=23.02 Aligned_cols=15 Identities=47% Similarity=0.831 Sum_probs=10.4
Q ss_pred EEEeecCCEeeeCCCC
Q 045565 35 RFMCSFGGKILPRPHD 50 (83)
Q Consensus 35 KllCSyGGrIlPRp~D 50 (83)
+|+.. .|+|+||--.
T Consensus 17 ~Fi~~-~GkIl~rr~T 31 (54)
T PF01084_consen 17 QFISP-TGKILPRRIT 31 (54)
T ss_dssp CGBTT-SSSBSTHHHH
T ss_pred HHcCc-ccceehhhhc
Confidence 35555 8999998533
No 87
>TIGR01687 moaD_arch MoaD family protein, archaeal. Members of this family appear to be archaeal versions of MoaD, subunit 1 of molybdopterin converting factor. This model has been split from the bacterial/eukaryotic equivalog model TIGR01682 because the presence of two members of this family in a substantial number of archaeal species suggests that roles might not be interchangeable.
Probab=21.50 E-value=1.4e+02 Score=18.19 Aligned_cols=25 Identities=20% Similarity=0.335 Sum_probs=18.7
Q ss_pred ecCceeEEEEcCCCChHHHHHHHHhh
Q 045565 56 VGGDTRIVAVHRSSTFSTLLTKLSKL 81 (83)
Q Consensus 56 vGGeTRIisV~R~isf~eL~~Kls~l 81 (83)
+|..+..|.++ ..+..||++.|.+.
T Consensus 13 ~g~~~~~v~~~-~~tv~~l~~~l~~~ 37 (88)
T TIGR01687 13 TGKKSEEIEIE-GKTVGDLLNELMAR 37 (88)
T ss_pred hCCceEEEEeC-CCCHHHHHHHHHHH
Confidence 34445566777 89999999999764
No 88
>PRK02240 GTP cyclohydrolase III; Provisional
Probab=21.29 E-value=1.6e+02 Score=23.31 Aligned_cols=31 Identities=26% Similarity=0.390 Sum_probs=21.6
Q ss_pred CCCCeEEecCceeEEEEcCCC---ChHHHHHHHHh
Q 045565 49 HDNQLRYVGGDTRIVAVHRSS---TFSTLLTKLSK 80 (83)
Q Consensus 49 ~Dg~LrYvGGeTRIisV~R~i---sf~eL~~Kls~ 80 (83)
+++-.-|+|||+-| +|-.++ +|.+.+..+.+
T Consensus 177 ~g~l~ff~GGDN~~-~~~~~l~~~~~~~~i~~i~~ 210 (254)
T PRK02240 177 HDALSFFVGGDNFM-APCPGLSEGDFLDAIEHVRE 210 (254)
T ss_pred cCcEEEEecCceEE-EECCCCCHHHHHHHHHHHhh
Confidence 55667899999854 555667 67777666543
No 89
>PRK13793 nicotinamide-nucleotide adenylyltransferase; Provisional
Probab=20.69 E-value=11 Score=28.25 Aligned_cols=17 Identities=24% Similarity=0.440 Sum_probs=13.9
Q ss_pred ecCCEeeeCCCCCCeEEe
Q 045565 39 SFGGKILPRPHDNQLRYV 56 (83)
Q Consensus 39 SyGGrIlPRp~Dg~LrYv 56 (83)
=|.||++| .|-|.|.++
T Consensus 8 v~iGRFQP-fH~GHl~~I 24 (196)
T PRK13793 8 VFIGRFQP-FHLAHMQTI 24 (196)
T ss_pred EEEecCCC-CcHHHHHHH
Confidence 38899999 788888765
No 90
>cd04870 ACT_PSP_1 CT domains found N-terminal of phosphoserine phosphatase (PSP, SerB). The ACT_PSP_1 CD includes the first of the two ACT domains found N-terminal of phosphoserine phosphatase (PSP, SerB). PSPs belong to the L-2-haloacid dehalogenase-like protein superfamily. PSP is involved in serine metabolism; serine is synthesized from phosphoglycerate through sequential reactions catalyzed by 3-phosphoglycerate dehydrogenase (SerA), 3-phosphoserine aminotransferase (SerC), and SerB. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=20.67 E-value=1.5e+02 Score=17.65 Aligned_cols=21 Identities=29% Similarity=0.264 Sum_probs=17.8
Q ss_pred EEEEcCCCChHHHHHHHHhhh
Q 045565 62 IVAVHRSSTFSTLLTKLSKLA 82 (83)
Q Consensus 62 IisV~R~isf~eL~~Kls~l~ 82 (83)
.+.++.+.++.+|.+.|.++|
T Consensus 44 ~v~~p~~~~~~~l~~~l~~l~ 64 (75)
T cd04870 44 LVQIPDSADSEALLKDLLFKA 64 (75)
T ss_pred EEEcCCCCCHHHHHHHHHHHH
Confidence 667788889999999998876
No 91
>KOG1513 consensus Nuclear helicase MOP-3/SNO (DEAD-box superfamily) [Transcription; Signal transduction mechanisms]
Probab=20.60 E-value=1.1e+02 Score=29.16 Aligned_cols=25 Identities=20% Similarity=0.473 Sum_probs=21.4
Q ss_pred ceeEEEEcCCCChHHHHHHHHhhhC
Q 045565 59 DTRIVAVHRSSTFSTLLTKLSKLAG 83 (83)
Q Consensus 59 eTRIisV~R~isf~eL~~Kls~l~G 83 (83)
|-.-|+|+|.++|.|-++|-.++.|
T Consensus 1102 ElhtIsVERGmsWEeA~~k~~elt~ 1126 (1300)
T KOG1513|consen 1102 ELHTISVERGMSWEEAFAKYKELTG 1126 (1300)
T ss_pred EEEEEEeccCccHHHHHHHHHhhcC
Confidence 4567999999999999999888764
No 92
>PF13186 SPASM: Iron-sulfur cluster-binding domain
Probab=20.41 E-value=1.6e+02 Score=16.13 Aligned_cols=27 Identities=19% Similarity=0.273 Sum_probs=20.7
Q ss_pred eEEEEeecCCEeeeCCCCCCeEEecCc
Q 045565 33 RVRFMCSFGGKILPRPHDNQLRYVGGD 59 (83)
Q Consensus 33 kvKllCSyGGrIlPRp~Dg~LrYvGGe 59 (83)
.-.|.-...|.|.|.+.+..-.|.-|.
T Consensus 5 ~~~~~I~~dG~v~pC~~~~~~~~~~Gn 31 (64)
T PF13186_consen 5 WNSLYIDPDGDVYPCCHDYDPEFKIGN 31 (64)
T ss_pred CeEEEEeeCccEEeCCCCCCCCeEEee
Confidence 345667789999999888766776665
No 93
>cd06257 DnaJ DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification.
Probab=20.38 E-value=64 Score=17.56 Aligned_cols=22 Identities=23% Similarity=0.243 Sum_probs=16.4
Q ss_pred eEEEEcCCCChHHHHHHHHhhh
Q 045565 61 RIVAVHRSSTFSTLLTKLSKLA 82 (83)
Q Consensus 61 RIisV~R~isf~eL~~Kls~l~ 82 (83)
.|+.|+++.+..++.++..+|+
T Consensus 4 ~vLgl~~~~~~~~ik~~y~~l~ 25 (55)
T cd06257 4 DILGVPPDASDEEIKKAYRKLA 25 (55)
T ss_pred HHcCCCCCCCHHHHHHHHHHHH
Confidence 4677888999998887766553
No 94
>PF14847 Ras_bdg_2: Ras-binding domain of Byr2; PDB: 1I35_A 1K8R_B.
Probab=20.27 E-value=1.2e+02 Score=20.70 Aligned_cols=30 Identities=20% Similarity=0.187 Sum_probs=21.6
Q ss_pred EEecCceeEEEEcCCCChHHHHHHHHhhhC
Q 045565 54 RYVGGDTRIVAVHRSSTFSTLLTKLSKLAG 83 (83)
Q Consensus 54 rYvGGeTRIisV~R~isf~eL~~Kls~l~G 83 (83)
-+-+|.||.|-|..=-+-.|++.|.-+-.|
T Consensus 6 I~~dG~tk~VNV~~c~~a~eI~~rvLKKfg 35 (105)
T PF14847_consen 6 ILEDGSTKTVNVSGCFNAQEIKRRVLKKFG 35 (105)
T ss_dssp EETTTEEEEEE--S--HHHHHHHHHHHHHT
T ss_pred ECCCCcEEEEEECCCCCHHHHHHHHHHHcC
Confidence 466899999999999999999988876554
No 95
>PF01357 Pollen_allerg_1: Pollen allergen; InterPro: IPR007117 Expansins are unusual proteins that mediate cell wall extension in plants []. They are believed to act as a sort of chemical grease, allowing polymers to slide past one another by disrupting non-covalent hydrogen bonds that hold many wall polymers to one another. This process is not degradative and hence does not weaken the wall, which could otherwise rupture under internal pressure during growth. Sequence comparisons indicate at least four distinct expansin cDNAs in rice and at least six in Arabidopsis. The proteins are highly conserved in size and sequence (75-95% amino acid sequence similarity between any pairwise comparison), and phylogenetic trees indicate that this multigene family formed before the evolutionary divergence of monocotyledons and dicotyledons []. Sequence and motif analyses show no similarities to known functional domains that might account for expansin action on wall extension. It is thought that several highly-conserved tryptophans may function in expansin binding to cellulose, or other glycans. The high conservation of the family indicates that the mechanism by which expansins promote wall extensin tolerates little variation in protein structure. Grass pollens, such as pollen from timothy grass, represent a major cause of type I allergy []. Interestingly, expansins share a high degree of sequence similarity with the Lol p I family of allergens. This entry represents the C-terminal domain.; PDB: 2VXQ_A 1WHP_A 1BMW_A 1WHO_A 2HCZ_X 2JNZ_A 3FT9_A 3FT1_C 1N10_B.
Probab=20.18 E-value=75 Score=20.12 Aligned_cols=15 Identities=47% Similarity=0.665 Sum_probs=11.3
Q ss_pred CeEEecCceeEEEEc
Q 045565 52 QLRYVGGDTRIVAVH 66 (83)
Q Consensus 52 ~LrYvGGeTRIisV~ 66 (83)
.+.|+||..-|.+|.
T Consensus 17 ~v~n~gG~gdi~~Ve 31 (82)
T PF01357_consen 17 LVKNVGGDGDIKAVE 31 (82)
T ss_dssp EEEECCTTS-EEEEE
T ss_pred EEEEcCCCccEEEEE
Confidence 368999999888874
Done!