Query psy3140
Match_columns 138
No_of_seqs 109 out of 152
Neff 4.8
Searched_HMMs 46136
Date Fri Aug 16 17:29:05 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3140.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3140hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF06487 SAP18: Sin3 associate 100.0 4E-63 8.6E-68 369.5 11.3 119 13-131 1-120 (120)
2 KOG3391|consensus 100.0 1.9E-61 4.1E-66 367.9 10.7 137 1-137 1-141 (151)
3 PF11976 Rad60-SLD: Ubiquitin- 85.3 1 2.2E-05 29.2 2.9 61 49-131 12-72 (72)
4 cd01763 Sumo Small ubiquitin-r 85.2 2.6 5.7E-05 29.0 5.0 62 49-133 23-84 (87)
5 PF00240 ubiquitin: Ubiquitin 84.8 2.6 5.7E-05 26.9 4.6 62 49-133 7-68 (69)
6 PF13881 Rad60-SLD_2: Ubiquiti 75.4 6.6 0.00014 28.8 4.6 52 57-126 23-76 (111)
7 PF11543 UN_NPL4: Nuclear pore 73.0 8.4 0.00018 26.6 4.4 74 23-129 4-77 (80)
8 cd01805 RAD23_N Ubiquitin-like 72.5 3.7 8.1E-05 26.8 2.4 65 48-134 11-76 (77)
9 TIGR01687 moaD_arch MoaD famil 71.8 15 0.00032 24.8 5.4 19 56-74 23-41 (88)
10 cd01807 GDX_N ubiquitin-like d 71.5 3.8 8.2E-05 27.0 2.3 61 49-134 12-74 (74)
11 cd01803 Ubiquitin Ubiquitin. U 69.9 21 0.00045 22.8 5.6 61 49-134 12-74 (76)
12 PF08845 SymE_toxin: Toxin Sym 69.1 4 8.6E-05 26.8 1.9 21 113-133 30-50 (57)
13 cd01764 Urm1 Urm1-like ubuitin 65.0 23 0.00051 25.0 5.4 24 52-75 23-46 (94)
14 cd01792 ISG15_repeat1 ISG15 ub 55.4 55 0.0012 21.8 5.7 63 49-132 14-76 (80)
15 cd01800 SF3a120_C Ubiquitin-li 51.7 16 0.00035 24.2 2.5 57 56-135 16-72 (76)
16 cd01797 NIRF_N amino-terminal 51.7 14 0.00029 25.1 2.2 55 56-133 21-75 (78)
17 PF12078 DUF3557: Domain of un 49.6 46 0.001 24.2 5.0 41 44-85 112-152 (154)
18 cd01806 Nedd8 Nebb8-like ubiq 49.3 18 0.00038 23.2 2.4 56 56-134 19-74 (76)
19 PF01157 Ribosomal_L21e: Ribos 48.3 11 0.00023 27.6 1.3 15 119-133 31-45 (99)
20 PRK13605 endoribonuclease SymE 45.9 16 0.00035 27.5 2.0 21 113-133 44-64 (113)
21 cd01810 ISG15_repeat2 ISG15 ub 44.5 25 0.00055 23.0 2.6 56 56-134 17-72 (74)
22 cd01793 Fubi Fubi ubiquitin-li 41.7 31 0.00067 22.6 2.7 59 52-135 13-73 (74)
23 PF14732 UAE_UbL: Ubiquitin/SU 40.8 44 0.00096 23.2 3.5 19 112-130 49-67 (87)
24 PRK04306 50S ribosomal protein 39.7 22 0.00047 26.0 1.8 15 120-134 34-48 (98)
25 cd01796 DDI1_N DNA damage indu 38.6 26 0.00056 23.0 1.9 56 52-129 14-69 (71)
26 cd01799 Hoil1_N Ubiquitin-like 37.1 34 0.00074 23.0 2.4 61 49-132 14-75 (75)
27 PTZ00044 ubiquitin; Provisiona 36.5 39 0.00084 21.9 2.5 59 53-134 16-74 (76)
28 cd01795 USP48_C USP ubiquitin- 35.4 1.8E+02 0.0039 21.7 6.1 66 48-135 15-80 (107)
29 cd01808 hPLIC_N Ubiquitin-like 35.4 33 0.00071 22.2 2.0 58 51-131 13-70 (71)
30 PLN02560 enoyl-CoA reductase 33.0 1.2E+02 0.0027 25.9 5.6 58 55-130 21-81 (308)
31 PF09866 DUF2093: Uncharacteri 32.0 40 0.00086 21.2 1.9 11 122-132 3-13 (42)
32 cd01802 AN1_N ubiquitin-like d 31.9 64 0.0014 23.0 3.3 64 48-134 38-101 (103)
33 PF10490 CENP-F_C_Rb_bdg: Rb-b 31.5 27 0.00058 22.6 1.1 14 15-28 27-40 (49)
34 cd01767 UBX UBX (ubiquitin reg 31.0 1.6E+02 0.0034 19.3 5.4 49 56-123 21-69 (77)
35 PF08817 YukD: WXG100 protein 30.5 33 0.00071 23.0 1.5 57 56-129 21-78 (79)
36 cd01772 SAKS1_UBX SAKS1-like U 30.5 1.7E+02 0.0037 19.6 6.1 67 44-129 10-77 (79)
37 cd01815 BMSC_UbP_N Ubiquitin-l 28.6 47 0.001 22.9 2.0 58 53-131 16-74 (75)
38 PF12327 FtsZ_C: FtsZ family, 28.3 2.1E+02 0.0046 19.9 5.4 37 50-87 41-77 (95)
39 PF10302 DUF2407: DUF2407 ubiq 27.5 1.2E+02 0.0026 21.6 4.0 42 42-87 8-50 (97)
40 cd04910 ACT_AK-Ectoine_1 ACT d 27.4 61 0.0013 22.0 2.4 31 45-75 37-68 (71)
41 PF08529 NusA_N: NusA N-termin 27.0 98 0.0021 22.5 3.6 77 57-134 14-97 (122)
42 TIGR00601 rad23 UV excision re 26.9 1.9E+02 0.0042 25.5 6.0 64 50-135 13-78 (378)
43 PF07405 DUF1506: Protein of u 26.8 24 0.00052 26.9 0.3 18 113-130 82-99 (127)
44 PF08620 RPAP1_C: RPAP1-like, 26.8 31 0.00068 23.8 0.8 19 57-75 38-56 (73)
45 PTZ00189 60S ribosomal protein 26.5 46 0.00099 26.4 1.8 14 120-133 33-46 (160)
46 KOG3141|consensus 26.1 42 0.00091 29.2 1.6 20 112-131 154-173 (310)
47 cd05992 PB1 The PB1 domain is 24.7 1.4E+02 0.003 19.3 3.7 32 56-92 19-50 (81)
48 cd01814 NTGP5 Ubiquitin-like N 24.6 62 0.0013 24.3 2.1 57 56-128 24-80 (113)
49 cd01804 midnolin_N Ubiquitin-l 24.4 1.2E+02 0.0026 20.2 3.3 57 55-135 19-75 (78)
50 PF03110 SBP: SBP domain; Int 23.8 32 0.0007 24.1 0.5 17 27-43 41-57 (79)
51 cd01770 p47_UBX p47-like ubiqu 23.7 1.8E+02 0.0039 19.7 4.2 49 56-123 23-71 (79)
52 PLN00190 60S ribosomal protein 23.7 55 0.0012 25.9 1.8 14 120-133 33-46 (158)
53 cd01788 ElonginB Ubiquitin-lik 23.4 60 0.0013 24.6 1.8 12 110-121 51-62 (119)
54 PF04967 HTH_10: HTH DNA bindi 22.9 64 0.0014 20.8 1.7 15 53-67 18-33 (53)
55 cd01812 BAG1_N Ubiquitin-like 22.8 98 0.0021 19.4 2.6 56 50-130 12-69 (71)
56 COG2139 RPL21A Ribosomal prote 21.8 67 0.0014 23.6 1.8 15 120-134 32-46 (98)
57 cd01809 Scythe_N Ubiquitin-lik 21.7 81 0.0018 19.8 2.0 56 53-131 16-71 (72)
58 PF08731 AFT: Transcription fa 21.6 78 0.0017 23.7 2.1 21 12-32 73-93 (111)
59 PF01233 NMT: Myristoyl-CoA:pr 21.5 92 0.002 24.7 2.7 37 38-78 10-55 (162)
60 cd05693 S1_Rrp5_repeat_hs1_sc1 21.1 78 0.0017 22.3 2.0 17 119-135 65-81 (100)
61 COG0234 GroS Co-chaperonin Gro 20.7 1.7E+02 0.0037 21.3 3.7 42 85-129 25-67 (96)
62 PF13511 DUF4124: Domain of un 20.4 44 0.00096 20.9 0.6 9 50-58 13-21 (60)
63 PF15276 PP1_bind: Protein pho 20.2 45 0.00098 22.7 0.6 19 30-48 6-24 (64)
64 PF00789 UBX: UBX domain; Int 20.2 2.6E+02 0.0057 18.2 4.6 68 44-129 12-80 (82)
No 1
>PF06487 SAP18: Sin3 associated polypeptide p18 (SAP18); InterPro: IPR010516 This family consists of several eukaryotic Sin3 associated polypeptide p18 (SAP18) sequences. SAP18 is known to be a component of the Sin3-containing complex, which is responsible for the repression of transcription via the modification of histone polypeptides []. SAP18 is also present in the ASAP complex which is thought to be involved in the regulation of splicing during the execution of programmed cell death [].; PDB: 2HDE_A 4A90_A 4A6Q_A 4A8X_C.
Probab=100.00 E-value=4e-63 Score=369.49 Aligned_cols=119 Identities=56% Similarity=1.038 Sum_probs=97.9
Q ss_pred CCCCCccCCCccEEEEeecCCCCCCCCCCCC-CCCCCceeeeecCCCCHHHHHHHHHhhCccccCCCcEEEEEEEecCCC
Q psy3140 13 EKTVDREKTCPLLLRVFTNFGKHNNVSDFHN-GFPPNQLQIYTWMDATLRELTNLIREVNPEAQQRGTCFYFTLLTPERG 91 (138)
Q Consensus 13 ~~~idRektcPfLLRvF~~~g~~h~~~eF~~-~~P~~ElqIYtW~d~TLrEL~~Llk~~~p~~r~~gtr~~F~~VypD~~ 91 (138)
+++|||||||||||||||++|+||+++||+. ++|+||||||||||||||||++|||+++|++|++||+|+|++||||.+
T Consensus 1 ~~~idRektcPfLLRvF~~~g~~h~~~dF~~~~~P~~elqIYtW~d~TLrEL~~Lik~~~~~~r~~~tr~~F~~VypD~~ 80 (120)
T PF06487_consen 1 PKPIDREKTCPFLLRVFYRNGRHHRLDDFSRGSLPRNELQIYTWMDATLRELADLIKDVNPPARRRGTRLSFRLVYPDTR 80 (120)
T ss_dssp -----CCCS--EEEEEEESSSS---GGGCGCCS-TTTEEEEEE-TT-BHHHHHHHHHHH-HHHHSTT-EEEEEEEEECTT
T ss_pred CCCcccCCCCCeEEEEEEecCCCCCHHHccCCCCCcCeeEEEEcccCCHHHHHHHHHHhCcccCCCCCEEEEEEEeecCC
Confidence 3689999999999999999999999999998 899999999999999999999999999999999999999999999999
Q ss_pred CCCeeeeecceeeeCCCCCCcccccccCCCCCCcEEEEEe
Q psy3140 92 TSRFHVRDIGQTICGQKGPDDNKTLQQCRFIIGDYMDVKI 131 (138)
Q Consensus 92 ~~r~~~rdlGsv~~g~~~~dd~kTL~~~rF~iGDyidvaI 131 (138)
+++|.+||||+|++|.++.|++|||++++|+|||||||||
T Consensus 81 ~~r~~~kdlGsv~~g~~~~d~~kTL~~~~F~iGDyidvaI 120 (120)
T PF06487_consen 81 SGRYVSKDLGSVVSGRKGPDDNKTLADLRFVIGDYIDVAI 120 (120)
T ss_dssp TTCEEEEEEEEEETTB--TTTTSBCGGGT--TT-EEEEEE
T ss_pred CCceeeecCCeEECCCCCCCcccCHhhCCcccCCEEEEeC
Confidence 9999999999999999999999999999999999999998
No 2
>KOG3391|consensus
Probab=100.00 E-value=1.9e-61 Score=367.91 Aligned_cols=137 Identities=54% Similarity=0.937 Sum_probs=130.9
Q ss_pred CCceeeeeecc--CCCCCCccCCCccEEEEeec-CCCCCCCCCCCC-CCCCCceeeeecCCCCHHHHHHHHHhhCccccC
Q psy3140 1 MTAIESFVTSI--DEKTVDREKTCPLLLRVFTN-FGKHNNVSDFHN-GFPPNQLQIYTWMDATLRELTNLIREVNPEAQQ 76 (138)
Q Consensus 1 ~~~~~~~~~~~--~~~~idRektcPfLLRvF~~-~g~~h~~~eF~~-~~P~~ElqIYtW~d~TLrEL~~Llk~~~p~~r~ 76 (138)
||..+++++++ ..++||||||||||||||++ +|+||.++||+. ++|++||||||||||||+||+.||||++|++|+
T Consensus 1 Mav~~~vsq~~~~~~~piDrektCPlLlrVf~~~~g~hH~~def~~g~vPs~elQiYtW~datL~ELtsLvkevnpeaR~ 80 (151)
T KOG3391|consen 1 MAVGSSVSQEPELSKKPIDREKTCPLLLRVFTQFNGRHHVMDEFEDGNVPSSELQIYTWMDATLRELTSLVKEVNPEARK 80 (151)
T ss_pred CCccccccccCcccCCcccccccCcceeeeeeecCCCCcchhhhhcCCCCchheeEeehhhhhHHHHHHHHHHcCHHHhc
Confidence 88888888873 33599999999999999998 899999999999 999999999999999999999999999999999
Q ss_pred CCcEEEEEEEecCCCCCCeeeeecceeeeCCCCCCcccccccCCCCCCcEEEEEeeCCCCC
Q psy3140 77 RGTCFYFTLLTPERGTSRFHVRDIGQTICGQKGPDDNKTLQQCRFIIGDYMDVKILTPKRN 137 (138)
Q Consensus 77 ~gtr~~F~~VypD~~~~r~~~rdlGsv~~g~~~~dd~kTL~~~rF~iGDyidvaI~pP~~~ 137 (138)
+||.|+||+||||.++++|.+||+|++++|+++.||+|||++++|+|||||||||.||++.
T Consensus 81 kgt~f~fa~Vf~d~~~~~y~~RevG~t~~g~Kg~ddnktL~~~kf~iGD~lDVaI~~p~~~ 141 (151)
T KOG3391|consen 81 KGTSFDFAVVFPDKKSPRYIVREVGTTCLGRKGIDDNKTLQQTKFEIGDYLDVAITPPNRR 141 (151)
T ss_pred cCceEEEEEEeccCCCCCceeeeecccccCcccCCccchhhhCCccccceEEEEecCcccC
Confidence 9999999999999999999999999999999999999999999999999999999999875
No 3
>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=85.28 E-value=1 Score=29.25 Aligned_cols=61 Identities=21% Similarity=0.229 Sum_probs=40.8
Q ss_pred ceeeeecCCCCHHHHHHHHHhhCccccCCCcEEEEEEEecCCCCCCeeeeecceeeeCCCCCCcccccccCCCCCCcEEE
Q psy3140 49 QLQIYTWMDATLRELTNLIREVNPEAQQRGTCFYFTLLTPERGTSRFHVRDIGQTICGQKGPDDNKTLQQCRFIIGDYMD 128 (138)
Q Consensus 49 ElqIYtW~d~TLrEL~~Llk~~~p~~r~~gtr~~F~~VypD~~~~r~~~rdlGsv~~g~~~~dd~kTL~~~rF~iGDyid 128 (138)
++++...++.|++.|.....+...-.... .|+++| | |.. -++++|+++++..-||.|+
T Consensus 12 ~~~~~v~~~~~~~~l~~~~~~~~~i~~~~----~~~l~f-d-----------G~~------L~~~~T~~~~~ied~d~Id 69 (72)
T PF11976_consen 12 EIKFKVKPTTTVSKLIEKYCEKKGIPPEE----SIRLIF-D-----------GKR------LDPNDTPEDLGIEDGDTID 69 (72)
T ss_dssp EEEEEEETTSCCHHHHHHHHHHHTTTT-T----TEEEEE-T-----------TEE------E-TTSCHHHHT-STTEEEE
T ss_pred EEEEEECCCCcHHHHHHHHHHhhCCCccc----eEEEEE-C-----------CEE------cCCCCCHHHCCCCCCCEEE
Confidence 68888899999999998887754322212 233443 1 111 1467999999999999999
Q ss_pred EEe
Q psy3140 129 VKI 131 (138)
Q Consensus 129 vaI 131 (138)
|.|
T Consensus 70 v~I 72 (72)
T PF11976_consen 70 VII 72 (72)
T ss_dssp EE-
T ss_pred EEC
Confidence 986
No 4
>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=85.15 E-value=2.6 Score=28.97 Aligned_cols=62 Identities=15% Similarity=0.103 Sum_probs=43.7
Q ss_pred ceeeeecCCCCHHHHHHHHHhhCccccCCCcEEEEEEEecCCCCCCeeeeecceeeeCCCCCCcccccccCCCCCCcEEE
Q psy3140 49 QLQIYTWMDATLRELTNLIREVNPEAQQRGTCFYFTLLTPERGTSRFHVRDIGQTICGQKGPDDNKTLQQCRFIIGDYMD 128 (138)
Q Consensus 49 ElqIYtW~d~TLrEL~~Llk~~~p~~r~~gtr~~F~~VypD~~~~r~~~rdlGsv~~g~~~~dd~kTL~~~rF~iGDyid 128 (138)
++.+-.=++.||+.|...+.+..--.. . .++++|-.. - -+++.|+++++.+-||.|+
T Consensus 23 ~~~~~v~~~~~l~~l~~~y~~~~gi~~-~----~~rf~f~G~------------~------L~~~~T~~~l~m~d~d~I~ 79 (87)
T cd01763 23 EVFFKIKRSTPLKKLMEAYCQRQGLSM-N----SVRFLFDGQ------------R------IRDNQTPDDLGMEDGDEIE 79 (87)
T ss_pred EEEEEEcCCCHHHHHHHHHHHHhCCCc-c----ceEEEECCe------------E------CCCCCCHHHcCCCCCCEEE
Confidence 456666689999999998887653222 2 455565211 0 1467899999999999999
Q ss_pred EEeeC
Q psy3140 129 VKILT 133 (138)
Q Consensus 129 vaI~p 133 (138)
+.+..
T Consensus 80 v~l~l 84 (87)
T cd01763 80 VMLEQ 84 (87)
T ss_pred EEEec
Confidence 98753
No 5
>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=84.82 E-value=2.6 Score=26.91 Aligned_cols=62 Identities=21% Similarity=0.190 Sum_probs=44.9
Q ss_pred ceeeeecCCCCHHHHHHHHHhhCccccCCCcEEEEEEEecCCCCCCeeeeecceeeeCCCCCCcccccccCCCCCCcEEE
Q psy3140 49 QLQIYTWMDATLRELTNLIREVNPEAQQRGTCFYFTLLTPERGTSRFHVRDIGQTICGQKGPDDNKTLQQCRFIIGDYMD 128 (138)
Q Consensus 49 ElqIYtW~d~TLrEL~~Llk~~~p~~r~~gtr~~F~~VypD~~~~r~~~rdlGsv~~g~~~~dd~kTL~~~rF~iGDyid 128 (138)
.+.+-...+.|+.+|=..|.+...-.. . ..+++|. | .. -+|++||.++++..|+.|.
T Consensus 7 ~~~~~v~~~~tV~~lK~~i~~~~~~~~-~----~~~L~~~----G--------~~------L~d~~tL~~~~i~~~~~I~ 63 (69)
T PF00240_consen 7 TFTLEVDPDDTVADLKQKIAEETGIPP-E----QQRLIYN----G--------KE------LDDDKTLSDYGIKDGSTIH 63 (69)
T ss_dssp EEEEEEETTSBHHHHHHHHHHHHTSTG-G----GEEEEET----T--------EE------ESTTSBTGGGTTSTTEEEE
T ss_pred EEEEEECCCCCHHHhhhhccccccccc-c----cceeeee----e--------ec------ccCcCcHHHcCCCCCCEEE
Confidence 577888899999999999988554211 1 1344441 1 11 1589999999999999999
Q ss_pred EEeeC
Q psy3140 129 VKILT 133 (138)
Q Consensus 129 vaI~p 133 (138)
+.+.|
T Consensus 64 l~~k~ 68 (69)
T PF00240_consen 64 LVIKP 68 (69)
T ss_dssp EEESS
T ss_pred EEEec
Confidence 98765
No 6
>PF13881 Rad60-SLD_2: Ubiquitin-2 like Rad60 SUMO-like; PDB: 1SE9_A 1WGH_A 2GOW_A.
Probab=75.37 E-value=6.6 Score=28.84 Aligned_cols=52 Identities=29% Similarity=0.399 Sum_probs=33.8
Q ss_pred CCCHHHHHHHHHhhCcccc--CCCcEEEEEEEecCCCCCCeeeeecceeeeCCCCCCcccccccCCCCCCcE
Q psy3140 57 DATLRELTNLIREVNPEAQ--QRGTCFYFTLLTPERGTSRFHVRDIGQTICGQKGPDDNKTLQQCRFIIGDY 126 (138)
Q Consensus 57 d~TLrEL~~Llk~~~p~~r--~~gtr~~F~~VypD~~~~r~~~rdlGsv~~g~~~~dd~kTL~~~rF~iGDy 126 (138)
+.|..+|-.+|.+.-|+.- .+-+-=..|+|| .||+ -+|++||.+++|..|+-
T Consensus 23 ~~TV~~lKe~i~~~WP~d~~~~p~s~~~lRLI~----~Gri--------------L~d~~tL~~~~~~~~~~ 76 (111)
T PF13881_consen 23 STTVADLKERIWAEWPEDWEERPKSPSDLRLIY----AGRI--------------LEDNKTLSDCRLPSGET 76 (111)
T ss_dssp TSBHHHHHHHHHHSSSTTSSSTT-SGGGEEEEE----TTEE--------------E-SSSBTGGGT--TTSE
T ss_pred cChHHHHHHHHHHHCccccccCCCChhhEEEEe----CCee--------------cCCcCcHHHhCCCCCCC
Confidence 7899999999998877631 222333356665 2332 25899999999999995
No 7
>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=72.95 E-value=8.4 Score=26.56 Aligned_cols=74 Identities=23% Similarity=0.305 Sum_probs=37.9
Q ss_pred ccEEEEeecCCCCCCCCCCCCCCCCCceeeeecCCCCHHHHHHHHHhhCccccCCCcEEEEEEEecCCCCCCeeeeecce
Q psy3140 23 PLLLRVFTNFGKHNNVSDFHNGFPPNQLQIYTWMDATLRELTNLIREVNPEAQQRGTCFYFTLLTPERGTSRFHVRDIGQ 102 (138)
Q Consensus 23 PfLLRvF~~~g~~h~~~eF~~~~P~~ElqIYtW~d~TLrEL~~Llk~~~p~~r~~gtr~~F~~VypD~~~~r~~~rdlGs 102 (138)
..+|||..+.|-+ + ++ +=+++|+.+|-..|.+..+-... +| .+|-|... ..++
T Consensus 4 ~milRvrS~dG~~-R------------ie--~~~~~t~~~L~~kI~~~l~~~~~-----~~-~L~~~~~~----~~~l-- 56 (80)
T PF11543_consen 4 SMILRVRSKDGMK-R------------IE--VSPSSTLSDLKEKISEQLSIPDS-----SQ-SLSKDRNN----KEEL-- 56 (80)
T ss_dssp --EEEEE-SSEEE-E------------EE--E-TTSBHHHHHHHHHHHS---TT-----T----BSSGGG----GGCS--
T ss_pred cEEEEEECCCCCE-E------------EE--cCCcccHHHHHHHHHHHcCCCCc-----ce-EEEecCCC----Cccc--
Confidence 4689999988842 1 22 22689999999999998865432 22 23444211 1111
Q ss_pred eeeCCCCCCcccccccCCCCCCcEEEE
Q psy3140 103 TICGQKGPDDNKTLQQCRFIIGDYMDV 129 (138)
Q Consensus 103 v~~g~~~~dd~kTL~~~rF~iGDyidv 129 (138)
..++++||+++++.=||.|-+
T Consensus 57 ------~s~~~~tl~~lglkHGdmlyL 77 (80)
T PF11543_consen 57 ------KSSDSKTLSSLGLKHGDMLYL 77 (80)
T ss_dssp ------SS-TT-CCCCT---TT-EEE-
T ss_pred ------ccCCcCCHHHcCCCCccEEEE
Confidence 124689999999999999854
No 8
>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=72.52 E-value=3.7 Score=26.82 Aligned_cols=65 Identities=23% Similarity=0.265 Sum_probs=43.8
Q ss_pred CceeeeecCCCCHHHHHHHHHhhCccc-cCCCcEEEEEEEecCCCCCCeeeeecceeeeCCCCCCcccccccCCCCCCcE
Q psy3140 48 NQLQIYTWMDATLRELTNLIREVNPEA-QQRGTCFYFTLLTPERGTSRFHVRDIGQTICGQKGPDDNKTLQQCRFIIGDY 126 (138)
Q Consensus 48 ~ElqIYtW~d~TLrEL~~Llk~~~p~~-r~~gtr~~F~~VypD~~~~r~~~rdlGsv~~g~~~~dd~kTL~~~rF~iGDy 126 (138)
+.+.+....+.|..||=..|.+...-. +.. ..+++|. |.+ -+|++||++++..-||.
T Consensus 11 ~~~~l~v~~~~TV~~lK~~i~~~~~i~~~~~----~q~L~~~------------G~~------L~d~~~L~~~~i~~~~~ 68 (77)
T cd01805 11 QTFPIEVDPDDTVAELKEKIEEEKGCDYPPE----QQKLIYS------------GKI------LKDDTTLEEYKIDEKDF 68 (77)
T ss_pred CEEEEEECCCCcHHHHHHHHHHhhCCCCChh----HeEEEEC------------CEE------ccCCCCHHHcCCCCCCE
Confidence 346677778899999999998754210 001 1233331 111 14679999999999999
Q ss_pred EEEEeeCC
Q psy3140 127 MDVKILTP 134 (138)
Q Consensus 127 idvaI~pP 134 (138)
|-|.+..|
T Consensus 69 i~~~~~~~ 76 (77)
T cd01805 69 VVVMVSKP 76 (77)
T ss_pred EEEEEecC
Confidence 99999876
No 9
>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=71.80 E-value=15 Score=24.78 Aligned_cols=19 Identities=21% Similarity=0.246 Sum_probs=16.9
Q ss_pred CCCCHHHHHHHHHhhCccc
Q psy3140 56 MDATLRELTNLIREVNPEA 74 (138)
Q Consensus 56 ~d~TLrEL~~Llk~~~p~~ 74 (138)
..+|++||...|.+.+|..
T Consensus 23 ~~~tv~~l~~~l~~~~p~~ 41 (88)
T TIGR01687 23 EGKTVGDLLNELMARYPKE 41 (88)
T ss_pred CCCCHHHHHHHHHHHCcHH
Confidence 5899999999999999863
No 10
>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=71.51 E-value=3.8 Score=26.98 Aligned_cols=61 Identities=20% Similarity=0.246 Sum_probs=43.4
Q ss_pred ceeeeecCCCCHHHHHHHHHhhC--ccccCCCcEEEEEEEecCCCCCCeeeeecceeeeCCCCCCcccccccCCCCCCcE
Q psy3140 49 QLQIYTWMDATLRELTNLIREVN--PEAQQRGTCFYFTLLTPERGTSRFHVRDIGQTICGQKGPDDNKTLQQCRFIIGDY 126 (138)
Q Consensus 49 ElqIYtW~d~TLrEL~~Llk~~~--p~~r~~gtr~~F~~VypD~~~~r~~~rdlGsv~~g~~~~dd~kTL~~~rF~iGDy 126 (138)
.+.+-...+.|..+|=..|.+.. |.. ..+++| .|+. -+|++||.+++.+.|+.
T Consensus 12 ~~~l~v~~~~tV~~lK~~i~~~~gi~~~-------~q~L~~-----------------~G~~-L~d~~~L~~~~i~~~~~ 66 (74)
T cd01807 12 ECSLQVSEKESVSTLKKLVSEHLNVPEE-------QQRLLF-----------------KGKA-LADDKRLSDYSIGPNAK 66 (74)
T ss_pred EEEEEECCCCcHHHHHHHHHHHHCCCHH-------HeEEEE-----------------CCEE-CCCCCCHHHCCCCCCCE
Confidence 34556678999999999997653 221 134444 1221 24679999999999999
Q ss_pred EEEEeeCC
Q psy3140 127 MDVKILTP 134 (138)
Q Consensus 127 idvaI~pP 134 (138)
|.+.+.||
T Consensus 67 l~l~~~~~ 74 (74)
T cd01807 67 LNLVVRPP 74 (74)
T ss_pred EEEEEcCC
Confidence 99999887
No 11
>cd01803 Ubiquitin Ubiquitin. Ubiquitin (includes Ubq/RPL40e and Ubq/RPS27a fusions as well as homopolymeric multiubiquitin protein chains)
Probab=69.92 E-value=21 Score=22.84 Aligned_cols=61 Identities=13% Similarity=0.196 Sum_probs=43.4
Q ss_pred ceeeeecCCCCHHHHHHHHHhhC--ccccCCCcEEEEEEEecCCCCCCeeeeecceeeeCCCCCCcccccccCCCCCCcE
Q psy3140 49 QLQIYTWMDATLRELTNLIREVN--PEAQQRGTCFYFTLLTPERGTSRFHVRDIGQTICGQKGPDDNKTLQQCRFIIGDY 126 (138)
Q Consensus 49 ElqIYtW~d~TLrEL~~Llk~~~--p~~r~~gtr~~F~~VypD~~~~r~~~rdlGsv~~g~~~~dd~kTL~~~rF~iGDy 126 (138)
.+.+....+.|+.||-..|.+.. |..+ .+++|. | .. -+|++||.+++.+.|+-
T Consensus 12 ~~~~~v~~~~tV~~lK~~i~~~~g~~~~~-------q~L~~~----g--------~~------L~d~~~L~~~~i~~~~~ 66 (76)
T cd01803 12 TITLEVEPSDTIENVKAKIQDKEGIPPDQ-------QRLIFA----G--------KQ------LEDGRTLSDYNIQKEST 66 (76)
T ss_pred EEEEEECCcCcHHHHHHHHHHHhCCCHHH-------eEEEEC----C--------EE------CCCCCcHHHcCCCCCCE
Confidence 45677778999999999998754 2211 244441 1 11 24678999999999999
Q ss_pred EEEEeeCC
Q psy3140 127 MDVKILTP 134 (138)
Q Consensus 127 idvaI~pP 134 (138)
|.+.+.+.
T Consensus 67 i~l~~~~~ 74 (76)
T cd01803 67 LHLVLRLR 74 (76)
T ss_pred EEEEEEcc
Confidence 99998754
No 12
>PF08845 SymE_toxin: Toxin SymE, type I toxin-antitoxin system; InterPro: IPR014944 This entry represents a SOS-induced gene whose product shows homology to the antitoxin MazE (SymE), the coding region contains a cis-encoded antisense RNA. The small antisense RNA and the gene have the all the hallmarks of a toxin-antitoxin module. The synthesis of the SymE is tightly repressed at multiple levels; at the transcriptional level by the LexA repressor, at the level of mRNA stability and translation by the SymR RNA and at the level of protein stability by the Lon protease. SymE co-purifies with ribosomes and overproduction of the protein leads to cell growth inhibition, decreased protein synthesis and increased RNA degradation. These properties are shared with several RNA endonuclease toxins of toxin-antitoxin modules. It seems probable that the SymE protein represents an evolutionary derivative of a toxin containing the AbrB fold, whose representatives are typically antitoxins. The SymE promoted cleavage of RNA cleavage may be important for the recycling of RNAs damaged under SOS-inducing conditions []. ; GO: 0003723 RNA binding, 0016788 hydrolase activity, acting on ester bonds, 0016070 RNA metabolic process, 0005737 cytoplasm
Probab=69.05 E-value=4 Score=26.84 Aligned_cols=21 Identities=33% Similarity=0.632 Sum_probs=18.8
Q ss_pred ccccccCCCCCCcEEEEEeeC
Q psy3140 113 NKTLQQCRFIIGDYMDVKILT 133 (138)
Q Consensus 113 ~kTL~~~rF~iGDyidvaI~p 133 (138)
.+-|+++.|.+||-|.|.+.+
T Consensus 30 G~WL~~aGF~~G~~v~V~v~~ 50 (57)
T PF08845_consen 30 GKWLEEAGFTIGDPVKVRVMP 50 (57)
T ss_pred hhhhHHhCCCCCCEEEEEEEC
Confidence 578999999999999998865
No 13
>cd01764 Urm1 Urm1-like ubuitin domain. Urm1 (Ubiquitin-Related Modifier1) The Urm1 fold, like those of two closely related proteins MoaD (molybdopterin synthase) and ThiS (sulfur carrier protein), is similar to that of ubiquitin although there is little or no sequence similarity. The C-terminal glycines of Urm1 are conjugated to an E1-like protein Uba4 as part of a novel conjugation system in yeast. The Urm1 fold is found only in eukaryotes.
Probab=64.96 E-value=23 Score=24.97 Aligned_cols=24 Identities=13% Similarity=0.055 Sum_probs=18.9
Q ss_pred eeecCCCCHHHHHHHHHhhCcccc
Q psy3140 52 IYTWMDATLRELTNLIREVNPEAQ 75 (138)
Q Consensus 52 IYtW~d~TLrEL~~Llk~~~p~~r 75 (138)
+=.|..+|++||...|++.+|..+
T Consensus 23 ~~~~~~~tV~dll~~L~~~~~~~~ 46 (94)
T cd01764 23 LDGEKPVTVGDLLDYVASNLLEER 46 (94)
T ss_pred ccCCCCCcHHHHHHHHHHhCchhh
Confidence 334467999999999999997643
No 14
>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=55.36 E-value=55 Score=21.79 Aligned_cols=63 Identities=13% Similarity=0.017 Sum_probs=40.5
Q ss_pred ceeeeecCCCCHHHHHHHHHhhCccccCCCcEEEEEEEecCCCCCCeeeeecceeeeCCCCCCcccccccCCCCCCcEEE
Q psy3140 49 QLQIYTWMDATLRELTNLIREVNPEAQQRGTCFYFTLLTPERGTSRFHVRDIGQTICGQKGPDDNKTLQQCRFIIGDYMD 128 (138)
Q Consensus 49 ElqIYtW~d~TLrEL~~Llk~~~p~~r~~gtr~~F~~VypD~~~~r~~~rdlGsv~~g~~~~dd~kTL~~~rF~iGDyid 128 (138)
.+-+-...++|..||=..|.+... .. ..+..+..+| + |+ --+|++||++++...|+.|.
T Consensus 14 ~~~~~v~~~~TV~~lK~~I~~~~~-i~--~~~qrL~~~~----~-------------G~-~L~D~~tL~~~gi~~gs~l~ 72 (80)
T cd01792 14 EFLVSLRDSMTVSELKQQIAQKIG-VP--AFQQRLAHLD----S-------------RE-VLQDGVPLVSQGLGPGSTVL 72 (80)
T ss_pred EEEEEcCCCCcHHHHHHHHHHHhC-CC--HHHEEEEecc----C-------------CC-CCCCCCCHHHcCCCCCCEEE
Confidence 344455678999999999987652 11 1222222233 1 11 12467899999999999999
Q ss_pred EEee
Q psy3140 129 VKIL 132 (138)
Q Consensus 129 vaI~ 132 (138)
+.+.
T Consensus 73 l~~~ 76 (80)
T cd01792 73 LVVQ 76 (80)
T ss_pred EEEE
Confidence 8876
No 15
>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=51.73 E-value=16 Score=24.22 Aligned_cols=57 Identities=12% Similarity=0.067 Sum_probs=37.3
Q ss_pred CCCCHHHHHHHHHhhCccccCCCcEEEEEEEecCCCCCCeeeeecceeeeCCCCCCcccccccCCCCCCcEEEEEeeCCC
Q psy3140 56 MDATLRELTNLIREVNPEAQQRGTCFYFTLLTPERGTSRFHVRDIGQTICGQKGPDDNKTLQQCRFIIGDYMDVKILTPK 135 (138)
Q Consensus 56 ~d~TLrEL~~Llk~~~p~~r~~gtr~~F~~VypD~~~~r~~~rdlGsv~~g~~~~dd~kTL~~~rF~iGDyidvaI~pP~ 135 (138)
.+.|+.+|=..|.+..- .+... .+++|-. . --+|++||.+++...|+.|.+.+.++.
T Consensus 16 ~~~TV~~lK~~i~~~~g-ip~~~----q~L~~~G------------~------~L~d~~tL~~~~i~~g~~l~v~~~~~g 72 (76)
T cd01800 16 LSDPVSVLKVKIHEETG-MPAGK----QKLQYEG------------I------FIKDSNSLAYYNLANGTIIHLQLKERG 72 (76)
T ss_pred CCCcHHHHHHHHHHHHC-CCHHH----EEEEECC------------E------EcCCCCcHHHcCCCCCCEEEEEEecCC
Confidence 57788888888866431 11111 2344421 1 124679999999999999999887654
No 16
>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=51.68 E-value=14 Score=25.07 Aligned_cols=55 Identities=16% Similarity=0.163 Sum_probs=37.9
Q ss_pred CCCCHHHHHHHHHhhCccccCCCcEEEEEEEecCCCCCCeeeeecceeeeCCCCCCcccccccCCCCCCcEEEEEeeC
Q psy3140 56 MDATLRELTNLIREVNPEAQQRGTCFYFTLLTPERGTSRFHVRDIGQTICGQKGPDDNKTLQQCRFIIGDYMDVKILT 133 (138)
Q Consensus 56 ~d~TLrEL~~Llk~~~p~~r~~gtr~~F~~VypD~~~~r~~~rdlGsv~~g~~~~dd~kTL~~~rF~iGDyidvaI~p 133 (138)
.+.|..||=..|.+... .+. =..+++| +|+. -+|+.||++++++.|+.|.+.+.+
T Consensus 21 ~~~TV~~lK~~i~~~~g-i~~----~~QrLi~----~Gk~--------------L~D~~tL~~y~i~~~~~i~l~~~~ 75 (78)
T cd01797 21 RLTKVEELREKIQELFN-VEP----ECQRLFY----RGKQ--------------MEDGHTLFDYNVGLNDIIQLLVRQ 75 (78)
T ss_pred CcCcHHHHHHHHHHHhC-CCH----HHeEEEe----CCEE--------------CCCCCCHHHcCCCCCCEEEEEEec
Confidence 57899999888877431 111 1235555 1211 267899999999999999998865
No 17
>PF12078 DUF3557: Domain of unknown function (DUF3557); InterPro: IPR021942 This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is about 150 amino acids in length.
Probab=49.58 E-value=46 Score=24.22 Aligned_cols=41 Identities=17% Similarity=0.336 Sum_probs=31.9
Q ss_pred CCCCCceeeeecCCCCHHHHHHHHHhhCccccCCCcEEEEEE
Q psy3140 44 GFPPNQLQIYTWMDATLRELTNLIREVNPEAQQRGTCFYFTL 85 (138)
Q Consensus 44 ~~P~~ElqIYtW~d~TLrEL~~Llk~~~p~~r~~gtr~~F~~ 85 (138)
+++..++++- ...-+..++..+|+.=....|..||+|+|.+
T Consensus 112 ~l~n~~v~~~-~~~~~~~~~~~li~~W~~~~r~IGt~~sf~~ 152 (154)
T PF12078_consen 112 KLRNKRVHLK-NDEFSWDDFLRLIENWIENGRPIGTCFSFGI 152 (154)
T ss_pred hCCCCEEEEE-ecCCCHHHHHHHHHHHHhcCCCCcEEEEEEE
Confidence 3443455555 5778889999999998888899999999974
No 18
>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=49.33 E-value=18 Score=23.19 Aligned_cols=56 Identities=11% Similarity=0.174 Sum_probs=37.7
Q ss_pred CCCCHHHHHHHHHhhCccccCCCcEEEEEEEecCCCCCCeeeeecceeeeCCCCCCcccccccCCCCCCcEEEEEeeCC
Q psy3140 56 MDATLRELTNLIREVNPEAQQRGTCFYFTLLTPERGTSRFHVRDIGQTICGQKGPDDNKTLQQCRFIIGDYMDVKILTP 134 (138)
Q Consensus 56 ~d~TLrEL~~Llk~~~p~~r~~gtr~~F~~VypD~~~~r~~~rdlGsv~~g~~~~dd~kTL~~~rF~iGDyidvaI~pP 134 (138)
.+.|+.||-..|.+.. ..+.. ..+++|. |+ . -+|++||++++.+.|+-|.+.+..+
T Consensus 19 ~~~tv~~lK~~i~~~~-g~~~~----~qrL~~~----g~--------~------L~d~~tl~~~~i~~g~~i~l~~~~~ 74 (76)
T cd01806 19 PTDKVERIKERVEEKE-GIPPQ----QQRLIYS----GK--------Q------MNDDKTAADYKLEGGSVLHLVLALR 74 (76)
T ss_pred CCCCHHHHHHHHhHhh-CCChh----hEEEEEC----Ce--------E------ccCCCCHHHcCCCCCCEEEEEEEcc
Confidence 6789999999887653 11111 2444542 11 1 1367999999999999999988643
No 19
>PF01157 Ribosomal_L21e: Ribosomal protein L21e; InterPro: IPR001147 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 [, ]. L21E family contains proteins from a number of eukaryotic and archaebacterial organisms which include; mammalian L2, Entamoeba histolytica L21, Caenorhabditis elegans L21 (C14B9.7), Saccharomyces cerevisiae (Baker's yeast) L21E (URP1) and Haloarcula marismortui HL31.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZR_U 1S1I_Q 3O58_T 3IZS_U 3O5H_T 1Q82_R 1KQS_P 3CCJ_Q 3CCQ_Q 1VQ5_Q ....
Probab=48.27 E-value=11 Score=27.59 Aligned_cols=15 Identities=33% Similarity=0.578 Sum_probs=6.6
Q ss_pred CCCCCCcEEEEEeeC
Q psy3140 119 CRFIIGDYMDVKILT 133 (138)
Q Consensus 119 ~rF~iGDyidvaI~p 133 (138)
..|.+||++||-|.|
T Consensus 31 ~~yk~GD~V~I~id~ 45 (99)
T PF01157_consen 31 QEYKVGDKVDIKIDP 45 (99)
T ss_dssp ----TT-EEEE---T
T ss_pred HHccCCCEEEEEecC
Confidence 469999999999876
No 20
>PRK13605 endoribonuclease SymE; Provisional
Probab=45.94 E-value=16 Score=27.45 Aligned_cols=21 Identities=24% Similarity=0.503 Sum_probs=18.1
Q ss_pred ccccccCCCCCCcEEEEEeeC
Q psy3140 113 NKTLQQCRFIIGDYMDVKILT 133 (138)
Q Consensus 113 ~kTL~~~rF~iGDyidvaI~p 133 (138)
.+=|++++|.+|+-|.|.+.+
T Consensus 44 G~WLeeAGF~tG~~V~V~V~~ 64 (113)
T PRK13605 44 GQWLEAAGFATGTAVDVRVME 64 (113)
T ss_pred chhHHhhCCCCCCeEEEEEeC
Confidence 467999999999999998764
No 21
>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=44.53 E-value=25 Score=23.00 Aligned_cols=56 Identities=16% Similarity=0.155 Sum_probs=35.9
Q ss_pred CCCCHHHHHHHHHhhCccccCCCcEEEEEEEecCCCCCCeeeeecceeeeCCCCCCcccccccCCCCCCcEEEEEeeCC
Q psy3140 56 MDATLRELTNLIREVNPEAQQRGTCFYFTLLTPERGTSRFHVRDIGQTICGQKGPDDNKTLQQCRFIIGDYMDVKILTP 134 (138)
Q Consensus 56 ~d~TLrEL~~Llk~~~p~~r~~gtr~~F~~VypD~~~~r~~~rdlGsv~~g~~~~dd~kTL~~~rF~iGDyidvaI~pP 134 (138)
.+.|.++|=..|.+..- .+.. .++++| .|+.- +|++||.+++++.|+.|.+.....
T Consensus 17 ~~~tV~~lK~~I~~~~g-i~~~----~q~L~~-----------------~G~~L-~D~~tL~~~~i~~~~tl~l~~~l~ 72 (74)
T cd01810 17 LTQTVATLKQQVSQRER-VQAD----QFWLSF-----------------EGRPM-EDEHPLGEYGLKPGCTVFMNLRLR 72 (74)
T ss_pred CcChHHHHHHHHHHHhC-CCHH----HeEEEE-----------------CCEEC-CCCCCHHHcCCCCCCEEEEEEEcc
Confidence 56799999888866431 1111 123333 12222 366999999999999999987643
No 22
>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=41.68 E-value=31 Score=22.57 Aligned_cols=59 Identities=17% Similarity=0.101 Sum_probs=39.4
Q ss_pred eeecCCCCHHHHHHHHHhhC--ccccCCCcEEEEEEEecCCCCCCeeeeecceeeeCCCCCCcccccccCCCCCCcEEEE
Q psy3140 52 IYTWMDATLRELTNLIREVN--PEAQQRGTCFYFTLLTPERGTSRFHVRDIGQTICGQKGPDDNKTLQQCRFIIGDYMDV 129 (138)
Q Consensus 52 IYtW~d~TLrEL~~Llk~~~--p~~r~~gtr~~F~~VypD~~~~r~~~rdlGsv~~g~~~~dd~kTL~~~rF~iGDyidv 129 (138)
+-...+.|..+|-..|.+.. |.. ..+++| .|+. -+|++||.+++.+.|.-|.+
T Consensus 13 l~v~~~~tV~~lK~~i~~~~gip~~-------~q~Li~-----------------~Gk~-L~D~~tL~~~~i~~~~tl~l 67 (74)
T cd01793 13 LEVTGQETVSDIKAHVAGLEGIDVE-------DQVLLL-----------------AGVP-LEDDATLGQCGVEELCTLEV 67 (74)
T ss_pred EEECCcCcHHHHHHHHHhhhCCCHH-------HEEEEE-----------------CCeE-CCCCCCHHHcCCCCCCEEEE
Confidence 34456789999998887642 221 123343 1221 25779999999999999999
Q ss_pred EeeCCC
Q psy3140 130 KILTPK 135 (138)
Q Consensus 130 aI~pP~ 135 (138)
.+-++.
T Consensus 68 ~~~l~G 73 (74)
T cd01793 68 AGRLLG 73 (74)
T ss_pred EEecCC
Confidence 876653
No 23
>PF14732 UAE_UbL: Ubiquitin/SUMO-activating enzyme ubiquitin-like domain; PDB: 1Y8Q_B 1Y8R_E 3KYD_B 3KYC_B.
Probab=40.83 E-value=44 Score=23.24 Aligned_cols=19 Identities=21% Similarity=0.286 Sum_probs=13.6
Q ss_pred cccccccCCCCCCcEEEEE
Q psy3140 112 DNKTLQQCRFIIGDYMDVK 130 (138)
Q Consensus 112 d~kTL~~~rF~iGDyidva 130 (138)
-.|+|+++++.-|-+|.|-
T Consensus 49 l~k~L~elgi~~gs~L~v~ 67 (87)
T PF14732_consen 49 LPKKLSELGIVNGSILTVD 67 (87)
T ss_dssp TTSBGGGGT--TT-EEEEE
T ss_pred ccCChhHcCCCCCCEEEEE
Confidence 4799999999999988763
No 24
>PRK04306 50S ribosomal protein L21e; Reviewed
Probab=39.73 E-value=22 Score=25.99 Aligned_cols=15 Identities=27% Similarity=0.337 Sum_probs=12.8
Q ss_pred CCCCCcEEEEEeeCC
Q psy3140 120 RFIIGDYMDVKILTP 134 (138)
Q Consensus 120 rF~iGDyidvaI~pP 134 (138)
.|.+||++|+-|.|-
T Consensus 34 ~y~~Gd~V~I~~d~s 48 (98)
T PRK04306 34 EFEEGDKVHIVIDPS 48 (98)
T ss_pred hccCCCEEEEEecCc
Confidence 499999999998763
No 25
>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=38.63 E-value=26 Score=23.00 Aligned_cols=56 Identities=16% Similarity=0.121 Sum_probs=35.3
Q ss_pred eeecCCCCHHHHHHHHHhhCccccCCCcEEEEEEEecCCCCCCeeeeecceeeeCCCCCCcccccccCCCCCCcEEEE
Q psy3140 52 IYTWMDATLRELTNLIREVNPEAQQRGTCFYFTLLTPERGTSRFHVRDIGQTICGQKGPDDNKTLQQCRFIIGDYMDV 129 (138)
Q Consensus 52 IYtW~d~TLrEL~~Llk~~~p~~r~~gtr~~F~~VypD~~~~r~~~rdlGsv~~g~~~~dd~kTL~~~rF~iGDyidv 129 (138)
+-.=+++|..+|=..|.+..- .+.- ..+++| .|+.-.|+.+||++++++-||.|-+
T Consensus 14 l~v~~~~TV~~lK~~I~~~~g-ip~~----~q~Li~-----------------~Gk~L~D~~~~L~~~gi~~~~~l~l 69 (71)
T cd01796 14 LDVDPDLELENFKALCEAESG-IPAS----QQQLIY-----------------NGRELVDNKRLLALYGVKDGDLVVL 69 (71)
T ss_pred EEECCcCCHHHHHHHHHHHhC-CCHH----HeEEEE-----------------CCeEccCCcccHHHcCCCCCCEEEE
Confidence 333467899999988876531 1111 133443 2222345668999999999998865
No 26
>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=37.06 E-value=34 Score=23.04 Aligned_cols=61 Identities=20% Similarity=0.091 Sum_probs=39.8
Q ss_pred ceeeeecCCCCHHHHHHHHHhhCccccCCCcEEEEEEEecCCCCCCeeeeecceeeeCCCCCCcccccccCCCC-CCcEE
Q psy3140 49 QLQIYTWMDATLRELTNLIREVNPEAQQRGTCFYFTLLTPERGTSRFHVRDIGQTICGQKGPDDNKTLQQCRFI-IGDYM 127 (138)
Q Consensus 49 ElqIYtW~d~TLrEL~~Llk~~~p~~r~~gtr~~F~~VypD~~~~r~~~rdlGsv~~g~~~~dd~kTL~~~rF~-iGDyi 127 (138)
.+.|...++.|+.+|=..|.+..-- +...- ++ | .|+.-.||.+||++++.+ .||.+
T Consensus 14 t~~l~v~~~~TV~~lK~kI~~~~gi-p~~~Q----rL-~-----------------~G~~L~dD~~tL~~ygi~~~g~~~ 70 (75)
T cd01799 14 TIWLTVRPDMTVAQLKDKVFLDYGF-PPAVQ----RW-V-----------------IGQRLARDQETLYSHGIRTNGDSA 70 (75)
T ss_pred eEEEEECCCCcHHHHHHHHHHHHCc-CHHHE----EE-E-----------------cCCeeCCCcCCHHHcCCCCCCCEE
Confidence 3566778899999998888654311 11111 22 2 122234688999999999 88998
Q ss_pred EEEee
Q psy3140 128 DVKIL 132 (138)
Q Consensus 128 dvaI~ 132 (138)
-+-|+
T Consensus 71 ~l~~~ 75 (75)
T cd01799 71 FLYIL 75 (75)
T ss_pred EEEeC
Confidence 88763
No 27
>PTZ00044 ubiquitin; Provisional
Probab=36.53 E-value=39 Score=21.86 Aligned_cols=59 Identities=12% Similarity=0.163 Sum_probs=39.3
Q ss_pred eecCCCCHHHHHHHHHhhCccccCCCcEEEEEEEecCCCCCCeeeeecceeeeCCCCCCcccccccCCCCCCcEEEEEee
Q psy3140 53 YTWMDATLRELTNLIREVNPEAQQRGTCFYFTLLTPERGTSRFHVRDIGQTICGQKGPDDNKTLQQCRFIIGDYMDVKIL 132 (138)
Q Consensus 53 YtW~d~TLrEL~~Llk~~~p~~r~~gtr~~F~~VypD~~~~r~~~rdlGsv~~g~~~~dd~kTL~~~rF~iGDyidvaI~ 132 (138)
-.=.+.|+.+|-..|.+..- .+.. ..+++|.. +- -+|++||++++.+.|+.|.+.+.
T Consensus 16 ~v~~~~tv~~lK~~i~~~~g-i~~~----~q~L~~~g----~~--------------L~d~~~l~~~~i~~~~~i~l~~~ 72 (76)
T PTZ00044 16 NFEPDNTVQQVKMALQEKEG-IDVK----QIRLIYSG----KQ--------------MSDDLKLSDYKVVPGSTIHMVLQ 72 (76)
T ss_pred EECCCCcHHHHHHHHHHHHC-CCHH----HeEEEECC----EE--------------ccCCCcHHHcCCCCCCEEEEEEE
Confidence 33367889999998877542 1111 13444421 11 25789999999999999999887
Q ss_pred CC
Q psy3140 133 TP 134 (138)
Q Consensus 133 pP 134 (138)
++
T Consensus 73 ~~ 74 (76)
T PTZ00044 73 LR 74 (76)
T ss_pred cc
Confidence 54
No 28
>cd01795 USP48_C USP ubiquitin-specific protease. The USP (ubiquitin-specific protease) family is one of at least seven deubiquitylating enzyme (DUB) families capable of deconjugating ubiquitin and ubiquitin-like adducts. While the USP's have a conserved catalytic core domain, they differ in their domain architectures. This subfamily, which includes USP31, and USP48, has a carboxy-terminal ubiquitin-like domain in addition to a DUSP (domain of ubiquitin-specific proteases) domain,
Probab=35.38 E-value=1.8e+02 Score=21.71 Aligned_cols=66 Identities=24% Similarity=0.165 Sum_probs=47.2
Q ss_pred CceeeeecCCCCHHHHHHHHHhhCccccCCCcEEEEEEEecCCCCCCeeeeecceeeeCCCCCCcccccccCCCCCCcEE
Q psy3140 48 NQLQIYTWMDATLRELTNLIREVNPEAQQRGTCFYFTLLTPERGTSRFHVRDIGQTICGQKGPDDNKTLQQCRFIIGDYM 127 (138)
Q Consensus 48 ~ElqIYtW~d~TLrEL~~Llk~~~p~~r~~gtr~~F~~VypD~~~~r~~~rdlGsv~~g~~~~dd~kTL~~~rF~iGDyi 127 (138)
.|..+=.=.++|+.||-.+|.+..--+ |+...- +-+ |+.-.||.+||+++....|-.|
T Consensus 15 ~~~~L~V~~~~TVg~LK~lImQ~f~V~-------------P~dQkL---~~d------G~~L~DDsrTLssyGv~sgSvl 72 (107)
T cd01795 15 GEKALLVSANQTLKELKIQIMHAFSVA-------------PFDQNL---SID------GKILSDDCATLGTLGVIPESVI 72 (107)
T ss_pred CCceEEeCccccHHHHHHHHHHHhcCC-------------ccccee---eec------CceeccCCccHHhcCCCCCCEE
Confidence 366666778999999999998866432 122111 111 3345689999999999999999
Q ss_pred EEEeeCCC
Q psy3140 128 DVKILTPK 135 (138)
Q Consensus 128 dvaI~pP~ 135 (138)
.+-|.-|-
T Consensus 73 ~LlideP~ 80 (107)
T cd01795 73 LLKADEPI 80 (107)
T ss_pred EEEecCCc
Confidence 99887663
No 29
>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=35.36 E-value=33 Score=22.22 Aligned_cols=58 Identities=17% Similarity=0.153 Sum_probs=38.8
Q ss_pred eeeecCCCCHHHHHHHHHhhCccccCCCcEEEEEEEecCCCCCCeeeeecceeeeCCCCCCcccccccCCCCCCcEEEEE
Q psy3140 51 QIYTWMDATLRELTNLIREVNPEAQQRGTCFYFTLLTPERGTSRFHVRDIGQTICGQKGPDDNKTLQQCRFIIGDYMDVK 130 (138)
Q Consensus 51 qIYtW~d~TLrEL~~Llk~~~p~~r~~gtr~~F~~VypD~~~~r~~~rdlGsv~~g~~~~dd~kTL~~~rF~iGDyidva 130 (138)
.|-...++|..||=..|.+...- .+-.++++|. | +. -+|++||++++...|+.|.+.
T Consensus 13 ~l~v~~~~TV~~lK~~I~~~~~i-----~~~~~~Li~~----G-------------k~-L~d~~tL~~~~i~~~stl~l~ 69 (71)
T cd01808 13 EIEIAEDASVKDFKEAVSKKFKA-----NQEQLVLIFA----G-------------KI-LKDTDTLTQHNIKDGLTVHLV 69 (71)
T ss_pred EEEECCCChHHHHHHHHHHHhCC-----CHHHEEEEEC----C-------------eE-cCCCCcHHHcCCCCCCEEEEE
Confidence 34456889999999999776531 1122344541 1 11 246789999999999998876
Q ss_pred e
Q psy3140 131 I 131 (138)
Q Consensus 131 I 131 (138)
+
T Consensus 70 ~ 70 (71)
T cd01808 70 I 70 (71)
T ss_pred E
Confidence 4
No 30
>PLN02560 enoyl-CoA reductase
Probab=33.03 E-value=1.2e+02 Score=25.87 Aligned_cols=58 Identities=22% Similarity=0.186 Sum_probs=35.8
Q ss_pred cCCCCHHHHHHHHHhhCcc---ccCCCcEEEEEEEecCCCCCCeeeeecceeeeCCCCCCcccccccCCCCCCcEEEEE
Q psy3140 55 WMDATLRELTNLIREVNPE---AQQRGTCFYFTLLTPERGTSRFHVRDIGQTICGQKGPDDNKTLQQCRFIIGDYMDVK 130 (138)
Q Consensus 55 W~d~TLrEL~~Llk~~~p~---~r~~gtr~~F~~VypD~~~~r~~~rdlGsv~~g~~~~dd~kTL~~~rF~iGDyidva 130 (138)
=.|+|+.||-..|.+.++- .|. |+.+++..+. .-|.+ -+|++||+|.+...|+-|-+-
T Consensus 21 ~~~aTV~dLK~~Isk~~~~~~~~Rq-------RL~~~~~~gk-----~~g~~------L~d~ktL~d~gv~~gstLy~k 81 (308)
T PLN02560 21 PDSATVADLKKAIHKRKKKYYPSRQ-------RLTLPLPPGK-----TRPTV------LDDSKSLKDYGLGDGGTVVFK 81 (308)
T ss_pred CCCCcHHHHHHHHHHHcCCCChhhe-------EEEEecCCCC-----cCccc------cCCCCCHHhcCCCCCceEEEE
Confidence 4679999999999887643 222 4444432110 01111 257789999999888866553
No 31
>PF09866 DUF2093: Uncharacterized protein conserved in bacteria (DUF2093); InterPro: IPR018661 This family of various hypothetical prokaryotic proteins has no known function.
Probab=31.95 E-value=40 Score=21.22 Aligned_cols=11 Identities=9% Similarity=0.320 Sum_probs=9.9
Q ss_pred CCCcEEEEEee
Q psy3140 122 IIGDYMDVKIL 132 (138)
Q Consensus 122 ~iGDyidvaI~ 132 (138)
.+|+|+-|||.
T Consensus 3 ~pG~~V~CAVT 13 (42)
T PF09866_consen 3 SPGSFVRCAVT 13 (42)
T ss_pred cCCCEEEEEee
Confidence 58999999997
No 32
>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=31.86 E-value=64 Score=23.03 Aligned_cols=64 Identities=9% Similarity=0.036 Sum_probs=43.3
Q ss_pred CceeeeecCCCCHHHHHHHHHhhCccccCCCcEEEEEEEecCCCCCCeeeeecceeeeCCCCCCcccccccCCCCCCcEE
Q psy3140 48 NQLQIYTWMDATLRELTNLIREVNPEAQQRGTCFYFTLLTPERGTSRFHVRDIGQTICGQKGPDDNKTLQQCRFIIGDYM 127 (138)
Q Consensus 48 ~ElqIYtW~d~TLrEL~~Llk~~~p~~r~~gtr~~F~~VypD~~~~r~~~rdlGsv~~g~~~~dd~kTL~~~rF~iGDyi 127 (138)
..+.|..=.+.|..+|=..|.+..- .+. -.++++| + |+. -+|++||++++...|+-|
T Consensus 38 ~~~~leV~~~~TV~~lK~kI~~~~g-ip~----~~QrLi~----~-------------Gk~-L~D~~tL~dy~I~~~stL 94 (103)
T cd01802 38 TCFELRVSPFETVISVKAKIQRLEG-IPV----AQQHLIW----N-------------NME-LEDEYCLNDYNISEGCTL 94 (103)
T ss_pred CEEEEEeCCCCcHHHHHHHHHHHhC-CCh----HHEEEEE----C-------------CEE-CCCCCcHHHcCCCCCCEE
Confidence 3466667788999999999976531 111 1234444 1 111 357799999999999999
Q ss_pred EEEeeCC
Q psy3140 128 DVKILTP 134 (138)
Q Consensus 128 dvaI~pP 134 (138)
.+++..+
T Consensus 95 ~l~~~l~ 101 (103)
T cd01802 95 KLVLAMR 101 (103)
T ss_pred EEEEecC
Confidence 9988754
No 33
>PF10490 CENP-F_C_Rb_bdg: Rb-binding domain of kinetochore protein Cenp-F/LEK1; InterPro: IPR018302 This entry represents the Rb protein-binding domain from the centromere protein Cenp-F. Cenp-F is a centromeric kinetochore, microtubule-binding protein consisting of two 1,600-amino acid-long coils, that is involved in chromosome segregation during mitosis and is essential for the full functioning of the mitotic checkpoint pathway [, ]. Cenp-F interacts with retinoblastoma protein (RB), CENP-E and BUBR1. This domain is at the very C terminus of the C-terminal coiled-coil region, and binds to the Rb family of tumour suppressors [].
Probab=31.47 E-value=27 Score=22.60 Aligned_cols=14 Identities=36% Similarity=0.579 Sum_probs=11.2
Q ss_pred CCCccCCCccEEEE
Q psy3140 15 TVDREKTCPLLLRV 28 (138)
Q Consensus 15 ~idRektcPfLLRv 28 (138)
.|--.|+|||+||=
T Consensus 27 DIPtgk~sPyilRR 40 (49)
T PF10490_consen 27 DIPTGKTSPYILRR 40 (49)
T ss_pred cCCCCCCCceEEEe
Confidence 36667999999984
No 34
>cd01767 UBX UBX (ubiquitin regulatory X) domain. The UBX (ubiquitin regulatory X) domain has a beta-grasp fold that is structurally quite similar to ubiquitin although UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins. Most UBX-containing proteins including p47, FAF1, and SAKS1 (Y33K) also contain a UBA (ubiquitin-associated) domain and are thought to serve as adaptor molecules that shuttle proteins to the proteasome for degradation.
Probab=30.98 E-value=1.6e+02 Score=19.32 Aligned_cols=49 Identities=18% Similarity=0.274 Sum_probs=32.6
Q ss_pred CCCCHHHHHHHHHhhCccccCCCcEEEEEEEecCCCCCCeeeeecceeeeCCCCCCcccccccCCCCC
Q psy3140 56 MDATLRELTNLIREVNPEAQQRGTCFYFTLLTPERGTSRFHVRDIGQTICGQKGPDDNKTLQQCRFII 123 (138)
Q Consensus 56 ~d~TLrEL~~Llk~~~p~~r~~gtr~~F~~VypD~~~~r~~~rdlGsv~~g~~~~dd~kTL~~~rF~i 123 (138)
.+.||++|-+-|.....+ +..|.+..-||-+. | ...|.++||.++++..
T Consensus 21 ~~~tl~~l~~fv~~~~~~----~~~f~L~t~~Pr~~---~------------~~~~~~~TL~e~gL~~ 69 (77)
T cd01767 21 STHKLSDVRDFVESNGPP----AEPFTLMTSFPRRV---L------------TDLDYELTLQEAGLVN 69 (77)
T ss_pred CCCCHHHHHHHHHHcCCC----CCCEEEEeCCCCcc---C------------CCCCccCcHHHcCCcc
Confidence 588999999999876544 34455555555321 1 1125789999999984
No 35
>PF08817 YukD: WXG100 protein secretion system (Wss), protein YukD; InterPro: IPR014921 YukD is a bacterial protein that adopts a ubiquitin-like fold []. Ubiquitin covalently binds to protein and flags them for protein degradation, however conjugation assays have indicated that YukD lacks the capacity for covalent bond formation with other proteins []. ; PDB: 2BPS_B.
Probab=30.55 E-value=33 Score=22.95 Aligned_cols=57 Identities=19% Similarity=0.146 Sum_probs=28.7
Q ss_pred CCCCHHHHHHHHHhhCccc-cCCCcEEEEEEEecCCCCCCeeeeecceeeeCCCCCCcccccccCCCCCCcEEEE
Q psy3140 56 MDATLRELTNLIREVNPEA-QQRGTCFYFTLLTPERGTSRFHVRDIGQTICGQKGPDDNKTLQQCRFIIGDYMDV 129 (138)
Q Consensus 56 ~d~TLrEL~~Llk~~~p~~-r~~gtr~~F~~VypD~~~~r~~~rdlGsv~~g~~~~dd~kTL~~~rF~iGDyidv 129 (138)
-+.|++||...|-+..... ......+.+++. . .-|.. -++++||++++...||.|.+
T Consensus 21 ~~vpv~~li~~l~~~~~~~~~~~~~~~~~~L~-~----------~~g~~------L~~~~tL~~~gV~dGd~L~L 78 (79)
T PF08817_consen 21 ADVPVAELIPELVELLGLPGDDPPGHGQWVLA-R----------AGGRP------LDPDQTLADAGVRDGDVLVL 78 (79)
T ss_dssp TTSBTTHHHHHHHHHS---S---TT-E-EEEG------------GGTEE------EETTSBCGGGT--TT-EEEE
T ss_pred CCCcHHHHHHHHHHHhCCccCCCCCcceEEEE-e----------cCCcc------cCCcCcHhHcCCCCCCEEEe
Confidence 3568888888887766431 111111122222 0 12222 25789999999999998864
No 36
>cd01772 SAKS1_UBX SAKS1-like UBX domain. SAKS1 (SAPK-substrate-1), also known as Y33K, is a widely expressed protein containing N-terminal UBA (ubiquitin-associated) and C-terminal UBX (ubiqiutin-like) domains that was identified as a substrate of stress-activated protein kinases (SAPKs). SAKS1 is related evolutionarily to two other UBA/UBX-containing proteins, p47 and Faf1. The UBA and UBX domains of SAKS1 bind ubiquitin tetramers and valosin-containing protein (VCP), respectively suggesting a role for SAKS1 as an adaptor that directs VCP to polyubiquitinated proteins facilitating its destruction by the proteasome. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.
Probab=30.46 E-value=1.7e+02 Score=19.58 Aligned_cols=67 Identities=15% Similarity=0.105 Sum_probs=39.2
Q ss_pred CCCCCc-eeeeecCCCCHHHHHHHHHhhCccccCCCcEEEEEEEecCCCCCCeeeeecceeeeCCCCCCcccccccCCCC
Q psy3140 44 GFPPNQ-LQIYTWMDATLRELTNLIREVNPEAQQRGTCFYFTLLTPERGTSRFHVRDIGQTICGQKGPDDNKTLQQCRFI 122 (138)
Q Consensus 44 ~~P~~E-lqIYtW~d~TLrEL~~Llk~~~p~~r~~gtr~~F~~VypD~~~~r~~~rdlGsv~~g~~~~dd~kTL~~~rF~ 122 (138)
++|..+ ++-.==.+.||++|-.-|...... +..|.+..-||- |.++ ..|.++||.++++.
T Consensus 10 Rlp~G~~~~~~F~~~~tl~~v~~fV~~~~~~----~~~f~L~t~fPr--------k~~~-------~~d~~~TL~elgL~ 70 (79)
T cd01772 10 RLLDGTTLKQTFKAREQLAAVRLFVELNTGN----GGPFTLMTPFPR--------KVFT-------EDDMEKPLQELGLV 70 (79)
T ss_pred ECCCCCEEEEEeCCCChHHHHHHHHHHcCCC----CCCEEEEeCCCC--------eECC-------cccccCCHHHCCCC
Confidence 456544 333333479999999999765432 133444443443 2221 12457999999998
Q ss_pred CCcEEEE
Q psy3140 123 IGDYMDV 129 (138)
Q Consensus 123 iGDyidv 129 (138)
+-..|-|
T Consensus 71 Psa~L~v 77 (79)
T cd01772 71 PSAVLIV 77 (79)
T ss_pred CceEEEE
Confidence 8665543
No 37
>cd01815 BMSC_UbP_N Ubiquitin-like domain of BMSC-UbP. BMSC_UbP (bone marrow stromal cell-derived ubiquitin-like protein) has an N-terminal ubiquitin-like (UBQ) domain and a C-terminal ubiquitin-associated (UBA) domain, a domain architecture similar to those of the UBIN, Chap1, and ubiquilin proteins. This CD represents the N-terminal ubiquitin-like domain.
Probab=28.60 E-value=47 Score=22.94 Aligned_cols=58 Identities=17% Similarity=0.153 Sum_probs=38.4
Q ss_pred eecCCCCHHHHHHHHHhhCcc-ccCCCcEEEEEEEecCCCCCCeeeeecceeeeCCCCCCcccccccCCCCCCcEEEEEe
Q psy3140 53 YTWMDATLRELTNLIREVNPE-AQQRGTCFYFTLLTPERGTSRFHVRDIGQTICGQKGPDDNKTLQQCRFIIGDYMDVKI 131 (138)
Q Consensus 53 YtW~d~TLrEL~~Llk~~~p~-~r~~gtr~~F~~VypD~~~~r~~~rdlGsv~~g~~~~dd~kTL~~~rF~iGDyidvaI 131 (138)
-.--+.|..||=..|.+..++ .... =.+++||-- +- -+|++||.+++.+.|+.|-+-+
T Consensus 16 ~~~~~~TV~~LK~kI~~~~~egi~~~---dqQrLIy~G-----------------Ki-L~D~~TL~dygI~~gstlhLv~ 74 (75)
T cd01815 16 VSPGGYQVSTLKQLIAAQLPDSLPDP---ELIDLIHCG-----------------RK-LKDDQTLDFYGIQSGSTIHILR 74 (75)
T ss_pred cCCccCcHHHHHHHHHHhhccCCCCh---HHeEEEeCC-----------------cC-CCCCCcHHHcCCCCCCEEEEEe
Confidence 334578999999999887532 1000 124566522 11 3577999999999999997754
No 38
>PF12327 FtsZ_C: FtsZ family, C-terminal domain; InterPro: IPR024757 The FtsZ family of proteins are involved in polymer formation. FtsZ is the polymer-forming protein of bacterial cell division. It is part of a ring in the middle of the dividing cell that is required for constriction of cell membrane and cell envelope to yield two daughter cells. FtsZ is a GTPase, like tubulin []. FtsZ can polymerise into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria and archaea []. This entry represents a domain of FtsZ. In most FtsZ proteins is found in the C terminus, except in some alphaproteobacteria proteins where there is an extension C-terminal domain TIGR03483 from TIGRFAMs.; PDB: 2RHO_B 2RHJ_A 2VXY_A 2RHL_B 2RHH_A 2VAM_A 1W5F_B 2R75_1 2R6R_1 1RQ7_A ....
Probab=28.25 E-value=2.1e+02 Score=19.95 Aligned_cols=37 Identities=14% Similarity=0.146 Sum_probs=27.1
Q ss_pred eeeeecCCCCHHHHHHHHHhhCccccCCCcEEEEEEEe
Q psy3140 50 LQIYTWMDATLRELTNLIREVNPEAQQRGTCFYFTLLT 87 (138)
Q Consensus 50 lqIYtW~d~TLrEL~~Llk~~~p~~r~~gtr~~F~~Vy 87 (138)
++|..++|.||.|+...+........ ..+...|-..+
T Consensus 41 vni~~~~d~~l~ev~~~~~~i~~~~~-~~a~ii~G~~i 77 (95)
T PF12327_consen 41 VNITGGPDLSLSEVNEAMEIIREKAD-PDANIIWGASI 77 (95)
T ss_dssp EEEEE-TTS-HHHHHHHHHHHHHHSS-TTSEEEEEEEE
T ss_pred EEEEcCCCCCHHHHHHHHHHHHHHhh-cCceEEEEEEE
Confidence 78999999999999888876655443 66777777776
No 39
>PF10302 DUF2407: DUF2407 ubiquitin-like domain; InterPro: IPR019413 This entry represents a family of proteins of unknown function found in fungi. They contain a characteristic GFDRL sequence motif.
Probab=27.46 E-value=1.2e+02 Score=21.64 Aligned_cols=42 Identities=31% Similarity=0.374 Sum_probs=29.2
Q ss_pred CCCCCCCceeeeecCCCCHHHHHHHHHhhCc-cccCCCcEEEEEEEe
Q psy3140 42 HNGFPPNQLQIYTWMDATLRELTNLIREVNP-EAQQRGTCFYFTLLT 87 (138)
Q Consensus 42 ~~~~P~~ElqIYtW~d~TLrEL~~Llk~~~p-~~r~~gtr~~F~~Vy 87 (138)
+.++|.-+|.|-.-.++|..+|-.+|++..| +...+. .|+||
T Consensus 8 s~sipDl~L~I~~~~~~Tv~~LK~lIR~~~p~~~s~~r----LRlI~ 50 (97)
T PF10302_consen 8 SDSIPDLPLDIPSPNTTTVAWLKQLIRERLPPEPSRRR----LRLIY 50 (97)
T ss_pred CCCCCCceeecCCCCcccHHHHHHHHHhhcCCCCcccc----EEeee
Confidence 3356644566777788999999999999994 443343 34555
No 40
>cd04910 ACT_AK-Ectoine_1 ACT domains located C-terminal to the catalytic domain of the aspartokinase of the ectoine (1,4,5,6-tetrahydro-2-methyl pyrimidine-4-carboxylate) biosynthetic pathway. This CD includes the first of two ACT domains located C-terminal to the catalytic domain of the aspartokinase of the ectoine (1,4,5,6-tetrahydro-2-methyl pyrimidine-4-carboxylate) biosynthetic pathway found in Methylomicrobium alcaliphilum, Vibrio cholerae, and various other halotolerant or halophilic bacteria. Bacteria exposed to hyperosmotic stress accumulate organic solutes called 'compatible solutes' of which ectoine, a heterocyclic amino acid, is one. Apart from its osmotic function, ectoine also exhibits a protective effect on proteins, nucleic acids and membranes against a variety of stress factors. de novo synthesis of ectoine starts with the phosphorylation of L-aspartate and shares its first two enzymatic steps with the biosynthesis of amino acids of the aspartate family: aspartokinase
Probab=27.45 E-value=61 Score=22.04 Aligned_cols=31 Identities=23% Similarity=0.257 Sum_probs=27.0
Q ss_pred CCCCceeeeecCCC-CHHHHHHHHHhhCcccc
Q psy3140 45 FPPNQLQIYTWMDA-TLRELTNLIREVNPEAQ 75 (138)
Q Consensus 45 ~P~~ElqIYtW~d~-TLrEL~~Llk~~~p~~r 75 (138)
...|++-+|-|-+. +++.+...|++.+|++.
T Consensus 37 ~nANtit~yl~~~~k~~~r~~~~Le~~~p~a~ 68 (71)
T cd04910 37 TNANTITHYLAGSLKTIKRLTEDLENRFPNAE 68 (71)
T ss_pred cCCCeEEEEEEcCHHHHHHHHHHHHHhCccCc
Confidence 44589999999996 99999999999999763
No 41
>PF08529 NusA_N: NusA N-terminal domain; InterPro: IPR013735 This entry represents the N-terminal RNA polymerase-binding domain of bacterial transcription factors such as NusA (N-utilising substance A). NusA is involved in transcriptional pausing, termination and anti-termination. NusA from Thermotoga maritima contains an N-terminal domain and three RNA-binding domains (one S1 domain and two KH domains). The N-terminal domain consists of a bifurcated coiled beta-sheet within an alpha/beta(3)/alpha/beta/alpha fold, which can be divided into two subdomains: a globular head and a helical body. The globular head subdomain may interact with RNA polymerase, while the helical body displays a similar structure to that of the helical domain in sigma70 [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0031554 regulation of transcription termination, DNA-dependent; PDB: 1K0R_B 1HH2_P 1L2F_A 2KWP_A.
Probab=26.96 E-value=98 Score=22.52 Aligned_cols=77 Identities=14% Similarity=0.175 Sum_probs=39.2
Q ss_pred CCCHHHHHHHHHhhCccc--cCCCcEEEEEEEecCCCCCCeeeeecceeeeCCCCCCcccccccC-----CCCCCcEEEE
Q psy3140 57 DATLRELTNLIREVNPEA--QQRGTCFYFTLLTPERGTSRFHVRDIGQTICGQKGPDDNKTLQQC-----RFIIGDYMDV 129 (138)
Q Consensus 57 d~TLrEL~~Llk~~~p~~--r~~gtr~~F~~VypD~~~~r~~~rdlGsv~~g~~~~dd~kTL~~~-----rF~iGDyidv 129 (138)
+-+...|...|+++.-.+ +.-|.--.+++.+ |...|.+.+--.-.|+.....+.-..+|.++ +.++||++..
T Consensus 14 ~i~~e~v~~ale~al~~a~kK~~~~~~~~~v~i-d~~~g~i~v~~~~~VV~d~~d~~~eI~l~eAk~~~~~~~vGD~i~~ 92 (122)
T PF08529_consen 14 GIDKEVVIEALEEALIKAYKKKYGPEANIRVEI-DEDTGEIKVYRKKEVVEDVEDPDTEISLSEAKKIDPNAEVGDEIEE 92 (122)
T ss_dssp TB-HHHHHHHHHHHHHHHHHCCTTSSSSEEEEE-ETTTTEEEEEEEEEEETT-S-TTTEEEHHHHHCCCTT--TTCEEEE
T ss_pred CcCHHHHHHHHHHHHHHHHHHhhCCCCCEEEEE-ECCCCeEEEEEEeeecCCccCccceeeHHHHHhhCCCCccCCEEEe
Confidence 344556777777766554 2223444455554 4445556555555566553333334455443 5699999999
Q ss_pred EeeCC
Q psy3140 130 KILTP 134 (138)
Q Consensus 130 aI~pP 134 (138)
-|.|-
T Consensus 93 ~i~~~ 97 (122)
T PF08529_consen 93 EIDPE 97 (122)
T ss_dssp E---T
T ss_pred cCChh
Confidence 88553
No 42
>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=26.88 E-value=1.9e+02 Score=25.49 Aligned_cols=64 Identities=23% Similarity=0.289 Sum_probs=42.2
Q ss_pred eeeeecCCCCHHHHHHHHHhhCc--cccCCCcEEEEEEEecCCCCCCeeeeecceeeeCCCCCCcccccccCCCCCCcEE
Q psy3140 50 LQIYTWMDATLRELTNLIREVNP--EAQQRGTCFYFTLLTPERGTSRFHVRDIGQTICGQKGPDDNKTLQQCRFIIGDYM 127 (138)
Q Consensus 50 lqIYtW~d~TLrEL~~Llk~~~p--~~r~~gtr~~F~~VypD~~~~r~~~rdlGsv~~g~~~~dd~kTL~~~rF~iGDyi 127 (138)
+.|=.-.+.|+.+|=..|.+..- .... =..++||- |.+ -+|++||.+++...||+|
T Consensus 13 ~~IeV~~~~TV~dLK~kI~~~~g~~~ip~----~~QkLIy~------------Gki------L~Dd~tL~dy~I~e~~~I 70 (378)
T TIGR00601 13 FKIDMEPDETVKELKEKIEAEQGKDAYPV----AQQKLIYS------------GKI------LSDDKTVREYKIKEKDFV 70 (378)
T ss_pred EEEEeCCcChHHHHHHHHHHhhCCCCCCh----hHeEEEEC------------CEE------CCCCCcHHHcCCCCCCEE
Confidence 34444578899999999877532 0111 11455552 222 246789999999999999
Q ss_pred EEEeeCCC
Q psy3140 128 DVKILTPK 135 (138)
Q Consensus 128 dvaI~pP~ 135 (138)
.|-+..|.
T Consensus 71 vvmv~k~k 78 (378)
T TIGR00601 71 VVMVSKPK 78 (378)
T ss_pred EEEeccCC
Confidence 99887654
No 43
>PF07405 DUF1506: Protein of unknown function (DUF1506); InterPro: IPR010875 This entry represents proteins found primarily in Borrelia species. Their function is unknown.
Probab=26.82 E-value=24 Score=26.93 Aligned_cols=18 Identities=22% Similarity=0.274 Sum_probs=15.6
Q ss_pred ccccccCCCCCCcEEEEE
Q psy3140 113 NKTLQQCRFIIGDYMDVK 130 (138)
Q Consensus 113 ~kTL~~~rF~iGDyidva 130 (138)
--|+++++|..||-|+++
T Consensus 82 lYT~~~l~fE~~DrIsi~ 99 (127)
T PF07405_consen 82 LYTYQNLNFELKDRISIS 99 (127)
T ss_pred eeehhhccchhhceeehh
Confidence 459999999999998864
No 44
>PF08620 RPAP1_C: RPAP1-like, C-terminal; InterPro: IPR013929 Inhibition of RNA polymerase II-associated protein 1 (RPAP1) synthesis in Saccharomyces cerevisiae (Baker's yeast) results in changes in global gene expression that are similar to those caused by the loss of the RNAPII subunit Rpb11 []. This entry represents the C-terminal region that contains the motif GLHHH. This region is conserved from yeast to humans.
Probab=26.79 E-value=31 Score=23.77 Aligned_cols=19 Identities=32% Similarity=0.427 Sum_probs=16.4
Q ss_pred CCCHHHHHHHHHhhCcccc
Q psy3140 57 DATLRELTNLIREVNPEAQ 75 (138)
Q Consensus 57 d~TLrEL~~Llk~~~p~~r 75 (138)
--||.||..|.+..+|.-|
T Consensus 38 GYTi~El~~L~RSsv~~QR 56 (73)
T PF08620_consen 38 GYTIQELFHLSRSSVPSQR 56 (73)
T ss_pred CcCHHHHHHHHhcCcHHHH
Confidence 4589999999999998855
No 45
>PTZ00189 60S ribosomal protein L21; Provisional
Probab=26.54 E-value=46 Score=26.38 Aligned_cols=14 Identities=36% Similarity=0.838 Sum_probs=12.2
Q ss_pred CCCCCcEEEEEeeC
Q psy3140 120 RFIIGDYMDVKILT 133 (138)
Q Consensus 120 rF~iGDyidvaI~p 133 (138)
.|.+|||+|+-|.|
T Consensus 33 ~yk~GD~VdIk~d~ 46 (160)
T PTZ00189 33 TFKVGDYVDIVVDS 46 (160)
T ss_pred HccCCCEEEEEecC
Confidence 39999999998865
No 46
>KOG3141|consensus
Probab=26.07 E-value=42 Score=29.17 Aligned_cols=20 Identities=30% Similarity=0.375 Sum_probs=16.7
Q ss_pred cccccccCCCCCCcEEEEEe
Q psy3140 112 DNKTLQQCRFIIGDYMDVKI 131 (138)
Q Consensus 112 d~kTL~~~rF~iGDyidvaI 131 (138)
....|..-.|.+|||+||+=
T Consensus 154 pGt~l~~~hFk~GqyVDV~g 173 (310)
T KOG3141|consen 154 PGTPLFARHFKPGQYVDVTG 173 (310)
T ss_pred CCcccchhhcCCCceEEEEe
Confidence 45678888999999999973
No 47
>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=24.73 E-value=1.4e+02 Score=19.26 Aligned_cols=32 Identities=19% Similarity=0.205 Sum_probs=26.4
Q ss_pred CCCCHHHHHHHHHhhCccccCCCcEEEEEEEecCCCC
Q psy3140 56 MDATLRELTNLIREVNPEAQQRGTCFYFTLLTPERGT 92 (138)
Q Consensus 56 ~d~TLrEL~~Llk~~~p~~r~~gtr~~F~~VypD~~~ 92 (138)
.++|+.+|...|.+..+... ..|.+-|.|..+
T Consensus 19 ~~~s~~~L~~~i~~~~~~~~-----~~~~l~y~D~e~ 50 (81)
T cd05992 19 RSISFEDLRSKIAEKFGLDA-----VSFKLKYPDEDG 50 (81)
T ss_pred CCCCHHHHHHHHHHHhCCCC-----CcEEEEeeCCCC
Confidence 68999999999999998754 677888888643
No 48
>cd01814 NTGP5 Ubiquitin-like NTGP5 and ATGP4. NTGP5 and ATGP4 are plant-specific isoprenylated GTP-binding proteins with a single fold that resembles ubiquitin. The function of these proteins is unknown.
Probab=24.61 E-value=62 Score=24.27 Aligned_cols=57 Identities=19% Similarity=0.275 Sum_probs=34.6
Q ss_pred CCCCHHHHHHHHHhhCccccCCCcEEEEEEEecCCCCCCeeeeecceeeeCCCCCCcccccccCCCCCCcEEE
Q psy3140 56 MDATLRELTNLIREVNPEAQQRGTCFYFTLLTPERGTSRFHVRDIGQTICGQKGPDDNKTLQQCRFIIGDYMD 128 (138)
Q Consensus 56 ~d~TLrEL~~Llk~~~p~~r~~gtr~~F~~VypD~~~~r~~~rdlGsv~~g~~~~dd~kTL~~~rF~iGDyid 128 (138)
++.|..+|-..|.+..|..+ .|. -|...++=-+++|+- -+|++||++++.-.||.+.
T Consensus 24 ~sdTV~~lKekI~~~~p~~k-e~~--------------P~~~~~qKLIysGKi-LeD~~TL~d~~~p~g~~~~ 80 (113)
T cd01814 24 AATTVDFLKERVVSQWPKDK-EVG--------------PKTVNEVKLISAGKI-LENSKTVGECRSPVGDIAG 80 (113)
T ss_pred hhhHHHHHHHHHHHhccccc-ccC--------------CCCHHHeEEEeCCee-cCCCCcHHHhCCcccccCC
Confidence 67899999999988887521 111 111122222333332 2477999999977777655
No 49
>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=24.37 E-value=1.2e+02 Score=20.18 Aligned_cols=57 Identities=16% Similarity=0.060 Sum_probs=36.5
Q ss_pred cCCCCHHHHHHHHHhhCccccCCCcEEEEEEEecCCCCCCeeeeecceeeeCCCCCCcccccccCCCCCCcEEEEEeeCC
Q psy3140 55 WMDATLRELTNLIREVNPEAQQRGTCFYFTLLTPERGTSRFHVRDIGQTICGQKGPDDNKTLQQCRFIIGDYMDVKILTP 134 (138)
Q Consensus 55 W~d~TLrEL~~Llk~~~p~~r~~gtr~~F~~VypD~~~~r~~~rdlGsv~~g~~~~dd~kTL~~~rF~iGDyidvaI~pP 134 (138)
=.++|..||=..|.+... ... -..+++|. |+.- +|+ ||.+++...|+.|.+....+
T Consensus 19 ~~~~TV~~LK~~I~~~~~-~~~----~~qrL~~~-----------------Gk~L-~d~-~L~~~gi~~~~~i~l~~~~~ 74 (78)
T cd01804 19 PPDETVEGLKKRISQRLK-VPK----ERLALLHR-----------------ETRL-SSG-KLQDLGLGDGSKLTLVPTVE 74 (78)
T ss_pred CCcCHHHHHHHHHHHHhC-CCh----HHEEEEEC-----------------CcCC-CCC-cHHHcCCCCCCEEEEEeecc
Confidence 357899999999976541 111 12233432 1112 344 89999999999999887665
Q ss_pred C
Q psy3140 135 K 135 (138)
Q Consensus 135 ~ 135 (138)
.
T Consensus 75 ~ 75 (78)
T cd01804 75 A 75 (78)
T ss_pred c
Confidence 3
No 50
>PF03110 SBP: SBP domain; InterPro: IPR004333 The SBP plant protein domain is a sequence specific DNA-binding domain []. Proteins with this domain probably function as transcription factors involved in the control of early flower development. The domain contains 10 conserved cysteine and histidine residues that probably are zinc ligands.; GO: 0003677 DNA binding, 0005634 nucleus; PDB: 1UL4_A 1WJ0_A 1UL5_A.
Probab=23.81 E-value=32 Score=24.08 Aligned_cols=17 Identities=24% Similarity=0.548 Sum_probs=11.8
Q ss_pred EEeecCCCCCCCCCCCC
Q psy3140 27 RVFTNFGKHNNVSDFHN 43 (138)
Q Consensus 27 RvF~~~g~~h~~~eF~~ 43 (138)
|..-+=|+||.++||+.
T Consensus 41 RFCQQC~rfh~l~eFdg 57 (79)
T PF03110_consen 41 RFCQQCGRFHPLSEFDG 57 (79)
T ss_dssp EE-TTTSSEEETTCB-S
T ss_pred HHHHHHHcCCCHHHHcc
Confidence 43345599999999996
No 51
>cd01770 p47_UBX p47-like ubiquitin domain. p47_UBX p47 is an adaptor molecule of the cytosolic AAA ATPase p97. The principal role of the p97-p47 complex is to regulate membrane fusion events. Mono-ubiquitin recognition by p47 is crucial for p97-p47-mediated Golgi membrane fusion events. p47 has carboxy-terminal SEP and UBX domains. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.
Probab=23.69 E-value=1.8e+02 Score=19.66 Aligned_cols=49 Identities=16% Similarity=0.356 Sum_probs=32.4
Q ss_pred CCCCHHHHHHHHHhhCccccCCCcEEEEEEEecCCCCCCeeeeecceeeeCCCCCCcccccccCCCCC
Q psy3140 56 MDATLRELTNLIREVNPEAQQRGTCFYFTLLTPERGTSRFHVRDIGQTICGQKGPDDNKTLQQCRFII 123 (138)
Q Consensus 56 ~d~TLrEL~~Llk~~~p~~r~~gtr~~F~~VypD~~~~r~~~rdlGsv~~g~~~~dd~kTL~~~rF~i 123 (138)
.+.|+++|-.-|+...|+.. +..|....-||- |++ .++++||.|+++..
T Consensus 23 ~~~tv~~l~~~v~~~~~~~~--~~~f~L~t~fP~--------k~l---------~~~~~Tl~eagL~~ 71 (79)
T cd01770 23 SSHRVSDVRDFIVNARPEFA--ARPFTLMTAFPV--------KEL---------SDESLTLKEANLLN 71 (79)
T ss_pred CCCcHHHHHHHHHHhCCCCC--CCCEEEecCCCC--------ccc---------CCCCCcHHHCCCcC
Confidence 57899999999998766532 344444444553 222 24588999999874
No 52
>PLN00190 60S ribosomal protein L21; Provisional
Probab=23.67 E-value=55 Score=25.88 Aligned_cols=14 Identities=43% Similarity=0.916 Sum_probs=12.1
Q ss_pred CCCCCcEEEEEeeC
Q psy3140 120 RFIIGDYMDVKILT 133 (138)
Q Consensus 120 rF~iGDyidvaI~p 133 (138)
.|.+||++|+-|.|
T Consensus 33 ~yk~GD~VdIk~~~ 46 (158)
T PLN00190 33 TFKVGDYVDIKVNG 46 (158)
T ss_pred HhcCCCEEEEEecC
Confidence 38999999998865
No 53
>cd01788 ElonginB Ubiquitin-like domain of Elongin B. Elongin B is part of an E3 ubiquitin ligase complex called VEC that activates ubiquitylation by the E2 ubiquitin-conjugating enzyme Ubc5. VEC is composed of von Hippel-Lindau tumor suppressor protein (pVHL), elongin C, cullin 2, NEDD8, and Rbx1. ElonginB binds elonginC to form the elonginBC complex which is a positive regulator of RNA polymerase II elongation factor Elongin A. The BC complex then binds VHL (von Hippel-Lindau) tumour suppressor protein to form a VCB ternary complex. Elongin B has a ubiquitin-llike domain.
Probab=23.43 E-value=60 Score=24.64 Aligned_cols=12 Identities=58% Similarity=0.960 Sum_probs=10.5
Q ss_pred CCcccccccCCC
Q psy3140 110 PDDNKTLQQCRF 121 (138)
Q Consensus 110 ~dd~kTL~~~rF 121 (138)
-||+|||+|++|
T Consensus 51 LeD~kTL~d~g~ 62 (119)
T cd01788 51 LDDGKTLGDCGF 62 (119)
T ss_pred ecccccHHHcCc
Confidence 378999999999
No 54
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=22.88 E-value=64 Score=20.78 Aligned_cols=15 Identities=27% Similarity=0.335 Sum_probs=12.3
Q ss_pred eecC-CCCHHHHHHHH
Q psy3140 53 YTWM-DATLRELTNLI 67 (138)
Q Consensus 53 YtW~-d~TLrEL~~Ll 67 (138)
|.|+ ++||.||+..+
T Consensus 18 fd~PR~~tl~elA~~l 33 (53)
T PF04967_consen 18 FDVPRRITLEELAEEL 33 (53)
T ss_pred CCCCCcCCHHHHHHHh
Confidence 5554 89999999887
No 55
>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=22.82 E-value=98 Score=19.44 Aligned_cols=56 Identities=18% Similarity=0.218 Sum_probs=37.2
Q ss_pred eeeeecCCCCHHHHHHHHHhhC--ccccCCCcEEEEEEEecCCCCCCeeeeecceeeeCCCCCCcccccccCCCCCCcEE
Q psy3140 50 LQIYTWMDATLRELTNLIREVN--PEAQQRGTCFYFTLLTPERGTSRFHVRDIGQTICGQKGPDDNKTLQQCRFIIGDYM 127 (138)
Q Consensus 50 lqIYtW~d~TLrEL~~Llk~~~--p~~r~~gtr~~F~~VypD~~~~r~~~rdlGsv~~g~~~~dd~kTL~~~rF~iGDyi 127 (138)
..+-...++|+.||=..|.+.. |..+ .+++|- | +. -+|++||.+++...|+-|
T Consensus 12 ~~i~v~~~~tv~~lK~~i~~~~gi~~~~-------q~L~~~----g----~~----------l~d~~~L~~~~i~~g~~l 66 (71)
T cd01812 12 HDLSISSQATFGDLKKMLAPVTGVEPRD-------QKLIFK----G----KE----------RDDAETLDMSGVKDGSKV 66 (71)
T ss_pred EEEEECCCCcHHHHHHHHHHhhCCChHH-------eEEeeC----C----cc----------cCccCcHHHcCCCCCCEE
Confidence 3445668899999999997753 2211 334432 1 11 146799999999999988
Q ss_pred EEE
Q psy3140 128 DVK 130 (138)
Q Consensus 128 dva 130 (138)
.+.
T Consensus 67 ~v~ 69 (71)
T cd01812 67 MLL 69 (71)
T ss_pred EEe
Confidence 764
No 56
>COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis]
Probab=21.76 E-value=67 Score=23.61 Aligned_cols=15 Identities=20% Similarity=0.485 Sum_probs=13.0
Q ss_pred CCCCCcEEEEEeeCC
Q psy3140 120 RFIIGDYMDVKILTP 134 (138)
Q Consensus 120 rF~iGDyidvaI~pP 134 (138)
.|.+||.+++-|-|-
T Consensus 32 ey~~Gd~V~I~IdpS 46 (98)
T COG2139 32 EYKVGDKVHIDIDPS 46 (98)
T ss_pred hccCCCEEEEEeCcc
Confidence 589999999999873
No 57
>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=21.72 E-value=81 Score=19.76 Aligned_cols=56 Identities=16% Similarity=0.109 Sum_probs=35.5
Q ss_pred eecCCCCHHHHHHHHHhhCccccCCCcEEEEEEEecCCCCCCeeeeecceeeeCCCCCCcccccccCCCCCCcEEEEEe
Q psy3140 53 YTWMDATLRELTNLIREVNPEAQQRGTCFYFTLLTPERGTSRFHVRDIGQTICGQKGPDDNKTLQQCRFIIGDYMDVKI 131 (138)
Q Consensus 53 YtW~d~TLrEL~~Llk~~~p~~r~~gtr~~F~~VypD~~~~r~~~rdlGsv~~g~~~~dd~kTL~~~rF~iGDyidvaI 131 (138)
-.=.+.|+.+|-..|.+...- +.. ..+++|. | .. -+|++||++++...|+.|.+..
T Consensus 16 ~v~~~~tv~~lK~~i~~~~gi-~~~----~q~L~~~----g--------~~------L~d~~~L~~~~i~~~~~l~l~~ 71 (72)
T cd01809 16 TVEEEITVLDLKEKIAEEVGI-PVE----QQRLIYS----G--------RV------LKDDETLSEYKVEDGHTIHLVK 71 (72)
T ss_pred EECCCCcHHHHHHHHHHHHCc-CHH----HeEEEEC----C--------EE------CCCcCcHHHCCCCCCCEEEEEe
Confidence 333578999999888775421 111 1344441 1 11 2467899999999999887753
No 58
>PF08731 AFT: Transcription factor AFT; InterPro: IPR014842 AFT (activator of iron transcription) is an iron regulated transcriptional activator that regulates the expression of genes involved in iron homeostasis. This entry includes the paralogous pair of transcription factors AFT1 and AFT2.
Probab=21.59 E-value=78 Score=23.68 Aligned_cols=21 Identities=29% Similarity=0.540 Sum_probs=17.2
Q ss_pred CCCCCCccCCCccEEEEeecC
Q psy3140 12 DEKTVDREKTCPLLLRVFTNF 32 (138)
Q Consensus 12 ~~~~idRektcPfLLRvF~~~ 32 (138)
....+.|.-+|||=+|-.|..
T Consensus 73 ~k~t~srk~~CPFriRA~yS~ 93 (111)
T PF08731_consen 73 KKRTKSRKNTCPFRIRANYSK 93 (111)
T ss_pred CCcccccccCCCeEEEEEEEe
Confidence 356788999999999998763
No 59
>PF01233 NMT: Myristoyl-CoA:protein N-myristoyltransferase, N-terminal domain; InterPro: IPR022676 Myristoyl-CoA:protein N-myristoyltransferase (2.3.1.97 from EC) (Nmt) [] is the enzyme responsible for transferring a myristate group on the N-terminal glycine of a number of cellular eukaryotics and viral proteins. Nmt is a monomeric protein of about 50 to 60kDa whose sequence appears to be well conserved. The N and C-terminal domains of NMT are structurally similar, each adopting an acyl-CoA N-acyltransferase-like fold. This entry represents the N-terminal region. ; GO: 0004379 glycylpeptide N-tetradecanoyltransferase activity; PDB: 2P6G_B 2P6F_F 2P6E_A 1IIC_A 1IID_A 2NMT_A 4A33_A 3H5Z_A 4A2Z_A 2WSA_A ....
Probab=21.50 E-value=92 Score=24.71 Aligned_cols=37 Identities=24% Similarity=0.477 Sum_probs=22.9
Q ss_pred CCCCCC---CCCCCceeeeecCCCCH------HHHHHHHHhhCccccCCC
Q psy3140 38 VSDFHN---GFPPNQLQIYTWMDATL------RELTNLIREVNPEAQQRG 78 (138)
Q Consensus 38 ~~eF~~---~~P~~ElqIYtW~d~TL------rEL~~Llk~~~p~~r~~g 78 (138)
+++..+ .+|.. |.|.++.| +||-+||.+.+-+--...
T Consensus 10 ~~~v~~ep~~LP~g----F~W~~~dl~d~~~l~ely~lL~~nYVEDdd~~ 55 (162)
T PF01233_consen 10 VDEVRQEPYPLPDG----FEWSTLDLNDDEELKELYELLNENYVEDDDNM 55 (162)
T ss_dssp GGGS-SS----STT----EEEEE--TTSHHHHHHHHHHHHHHSSBTTTSS
T ss_pred HHHcCCCCCCCCCC----CEEEecCCCCHHHHHHHHHHHHhcCccCCcce
Confidence 344444 57754 89988765 999999999997753333
No 60
>cd05693 S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 1 (hs1) and S. cerevisiae S1 repeat 1 (sc1). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=21.06 E-value=78 Score=22.33 Aligned_cols=17 Identities=18% Similarity=0.383 Sum_probs=13.7
Q ss_pred CCCCCCcEEEEEeeCCC
Q psy3140 119 CRFIIGDYMDVKILTPK 135 (138)
Q Consensus 119 ~rF~iGDyidvaI~pP~ 135 (138)
-.|.+||.+-|.|+--+
T Consensus 65 ~~f~vGd~V~~kVi~~d 81 (100)
T cd05693 65 DLFSVGQLVRCKVVSLD 81 (100)
T ss_pred HhccCCCEEEEEEEEcc
Confidence 36999999999997443
No 61
>COG0234 GroS Co-chaperonin GroES (HSP10) [Posttranslational modification, protein turnover, chaperones]
Probab=20.72 E-value=1.7e+02 Score=21.34 Aligned_cols=42 Identities=19% Similarity=0.350 Sum_probs=29.2
Q ss_pred EEecCCCCCCeeeeecceeee-CCCCCCcccccccCCCCCCcEEEE
Q psy3140 85 LLTPERGTSRFHVRDIGQTIC-GQKGPDDNKTLQQCRFIIGDYMDV 129 (138)
Q Consensus 85 ~VypD~~~~r~~~rdlGsv~~-g~~~~dd~kTL~~~rF~iGDyidv 129 (138)
+|-||+... -.+-|.|+. |.++.+++.++..+.+..||-+-.
T Consensus 25 Ivlpdsake---K~~~g~VvAVG~G~~~~~g~~~~~~VkvGD~Vlf 67 (96)
T COG0234 25 IVLPDSAKE---KPQEGEVVAVGPGRRDENGELVPLDVKVGDRVLF 67 (96)
T ss_pred EEecCcccc---CCcceEEEEEccceecCCCCEeccccccCCEEEE
Confidence 455775321 224788876 555667778999999999998754
No 62
>PF13511 DUF4124: Domain of unknown function (DUF4124)
Probab=20.36 E-value=44 Score=20.88 Aligned_cols=9 Identities=33% Similarity=1.184 Sum_probs=6.7
Q ss_pred eeeeecCCC
Q psy3140 50 LQIYTWMDA 58 (138)
Q Consensus 50 lqIYtW~d~ 58 (138)
-+||.|.|.
T Consensus 13 a~vYk~~D~ 21 (60)
T PF13511_consen 13 AEVYKWVDE 21 (60)
T ss_pred ccEEEEECC
Confidence 478888874
No 63
>PF15276 PP1_bind: Protein phosphatase 1 binding
Probab=20.21 E-value=45 Score=22.71 Aligned_cols=19 Identities=37% Similarity=0.765 Sum_probs=16.0
Q ss_pred ecCCCCCCCCCCCCCCCCC
Q psy3140 30 TNFGKHNNVSDFHNGFPPN 48 (138)
Q Consensus 30 ~~~g~~h~~~eF~~~~P~~ 48 (138)
+..|.|-+++-|+.++|+|
T Consensus 6 VsFG~~LSPElFD~~LPpn 24 (64)
T PF15276_consen 6 VSFGEHLSPELFDKSLPPN 24 (64)
T ss_pred eccCCCCCHHHhcccCCCC
Confidence 4678999999999988875
No 64
>PF00789 UBX: UBX domain; InterPro: IPR001012 The UBX domain is found in ubiquitin-regulatory proteins, which are members of the ubiquitination pathway, as well as a number of other proteins including FAF-1 (FAS-associated factor 1), the human Rep-8 reproduction protein and several hypothetical proteins from yeast. The function of the UBX domain is not known although the fragment of avian FAF-1 containing the UBX domain causes apoptosis of transfected cells.; GO: 0005515 protein binding; PDB: 3QX1_A 1H8C_A 3QCA_B 3QQ8_B 3QC8_B 3R3M_A 3QWZ_B 1S3S_H 1JRU_A 1I42_A ....
Probab=20.20 E-value=2.6e+02 Score=18.18 Aligned_cols=68 Identities=21% Similarity=0.285 Sum_probs=41.7
Q ss_pred CCCCC-ceeeeecCCCCHHHHHHHHHhhCccccCCCcEEEEEEEecCCCCCCeeeeecceeeeCCCCCCcccccccCCCC
Q psy3140 44 GFPPN-QLQIYTWMDATLRELTNLIREVNPEAQQRGTCFYFTLLTPERGTSRFHVRDIGQTICGQKGPDDNKTLQQCRFI 122 (138)
Q Consensus 44 ~~P~~-ElqIYtW~d~TLrEL~~Llk~~~p~~r~~gtr~~F~~VypD~~~~r~~~rdlGsv~~g~~~~dd~kTL~~~rF~ 122 (138)
.+|.. .+|-.==.+.||++|-+.|.......... .|.+..-||- +++. .++++||+|++..
T Consensus 12 RlpdG~~l~~~F~~~~tl~~l~~~v~~~~~~~~~~--~f~L~~~~Pr--------~~l~--------~~~~~tl~e~~l~ 73 (82)
T PF00789_consen 12 RLPDGSRLQRRFPKSDTLQDLYDFVESQLFSPEES--DFELITAFPR--------RELT--------DEDSKTLEEAGLL 73 (82)
T ss_dssp EETTSTEEEEEEETTSBHHHHHHHHHHHHHCTTTS--SEEEEESSST--------EECC--------STTTSBTCCCTTS
T ss_pred ECCCCCEEEEEECCcchHHHHHHHHHHhcCCCCCc--cEEEEeCCCC--------cCCC--------ccccccHHHhcCC
Confidence 34542 35555558999999999998765443211 3444444551 1121 1236999999998
Q ss_pred CCcEEEE
Q psy3140 123 IGDYMDV 129 (138)
Q Consensus 123 iGDyidv 129 (138)
++--|-|
T Consensus 74 p~~~l~v 80 (82)
T PF00789_consen 74 PSATLIV 80 (82)
T ss_dssp SCEEEEE
T ss_pred CCeEEEE
Confidence 8876655
Done!