Query psy5391
Match_columns 157
No_of_seqs 120 out of 255
Neff 3.8
Searched_HMMs 46136
Date Sat Aug 17 01:24:26 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5391.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5391hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4089|consensus 99.9 1.4E-24 3.1E-29 174.5 5.7 98 1-100 1-103 (165)
2 PF00276 Ribosomal_L23: Riboso 99.7 6.8E-17 1.5E-21 117.7 8.1 65 35-108 19-83 (91)
3 PRK05738 rplW 50S ribosomal pr 99.6 4E-16 8.8E-21 114.4 7.6 65 36-109 20-84 (92)
4 CHL00030 rpl23 ribosomal prote 99.6 3.9E-15 8.6E-20 110.1 7.5 67 33-108 16-82 (93)
5 COG0089 RplW Ribosomal protein 99.5 1.7E-14 3.6E-19 107.4 7.6 68 35-110 20-87 (94)
6 PRK12280 rplW 50S ribosomal pr 99.5 1.4E-13 3E-18 110.5 7.4 63 34-101 20-82 (158)
7 TIGR03636 L23_arch archaeal ri 99.4 4.9E-13 1.1E-17 96.0 7.0 51 36-108 14-64 (77)
8 PRK14548 50S ribosomal protein 99.4 7.5E-13 1.6E-17 96.4 7.0 51 36-108 21-71 (84)
9 PTZ00191 60S ribosomal protein 99.2 4.1E-11 8.9E-16 95.3 7.6 49 35-101 81-129 (145)
10 KOG1751|consensus 98.4 3E-07 6.4E-12 74.2 4.4 46 34-79 92-137 (157)
11 cd01769 UBL Ubiquitin-like dom 68.7 13 0.00027 23.6 4.3 38 36-74 7-44 (69)
12 cd01798 parkin_N amino-termina 68.4 15 0.00032 24.4 4.7 44 34-78 6-49 (70)
13 PTZ00044 ubiquitin; Provisiona 67.6 16 0.00034 24.4 4.7 42 34-76 8-49 (76)
14 PF14560 Ubiquitin_2: Ubiquiti 67.1 19 0.00041 25.1 5.2 39 34-72 11-49 (87)
15 cd01789 Alp11_N Ubiquitin-like 67.0 16 0.00034 25.8 4.8 40 36-75 12-51 (84)
16 cd01806 Nedd8 Nebb8-like ubiq 62.6 30 0.00064 22.7 5.3 39 36-75 10-48 (76)
17 cd01803 Ubiquitin Ubiquitin. U 57.8 31 0.00068 22.6 4.7 35 36-70 10-44 (76)
18 PRK01178 rps24e 30S ribosomal 57.7 36 0.00078 25.6 5.5 43 25-67 5-51 (99)
19 smart00213 UBQ Ubiquitin homol 56.4 17 0.00036 22.7 3.1 34 37-70 10-43 (64)
20 cd01796 DDI1_N DNA damage indu 54.6 18 0.00038 24.5 3.2 41 35-76 8-48 (71)
21 cd01812 BAG1_N Ubiquitin-like 51.1 21 0.00046 23.2 3.1 35 36-70 9-43 (71)
22 cd01800 SF3a120_C Ubiquitin-li 50.7 36 0.00077 23.2 4.2 41 33-74 4-44 (76)
23 cd01805 RAD23_N Ubiquitin-like 47.2 50 0.0011 21.9 4.4 36 35-70 9-46 (77)
24 COG0084 TatD Mg-dependent DNas 46.2 13 0.00029 31.8 1.8 30 107-138 155-184 (256)
25 cd01809 Scythe_N Ubiquitin-lik 45.5 39 0.00085 21.9 3.7 40 35-75 9-48 (72)
26 PF00240 ubiquitin: Ubiquitin 44.3 36 0.00079 22.0 3.3 41 36-77 5-45 (69)
27 PF00076 RRM_1: RNA recognitio 44.0 53 0.0011 20.3 4.0 19 43-62 6-24 (70)
28 cd01802 AN1_N ubiquitin-like d 43.5 77 0.0017 23.4 5.3 44 34-78 35-78 (103)
29 PF09358 UBA_e1_C: Ubiquitin-a 42.3 38 0.00082 26.0 3.6 30 40-69 36-65 (125)
30 cd01807 GDX_N ubiquitin-like d 41.5 56 0.0012 21.9 4.0 43 35-78 9-51 (74)
31 COG1478 GTP and metal dependen 41.1 53 0.0011 28.9 4.7 84 40-124 122-208 (257)
32 cd01793 Fubi Fubi ubiquitin-li 40.6 38 0.00083 22.8 3.1 41 37-78 9-49 (74)
33 cd01794 DC_UbP_C dendritic cel 36.6 47 0.001 22.6 3.0 43 35-78 7-49 (70)
34 cd01810 ISG15_repeat2 ISG15 ub 36.3 94 0.002 20.8 4.5 41 34-75 6-46 (74)
35 smart00362 RRM_2 RNA recogniti 35.9 66 0.0014 19.1 3.4 27 42-70 6-32 (72)
36 PF03780 Asp23: Asp23 family; 35.4 70 0.0015 22.6 3.9 24 49-72 82-105 (108)
37 cd01799 Hoil1_N Ubiquitin-like 35.2 68 0.0015 22.3 3.7 39 35-75 11-49 (75)
38 cd01808 hPLIC_N Ubiquitin-like 31.8 86 0.0019 20.8 3.7 36 39-75 12-47 (71)
39 PTZ00156 60S ribosomal protein 31.7 53 0.0012 27.2 3.1 49 17-65 120-171 (172)
40 PF08766 DEK_C: DEK C terminal 29.4 41 0.0009 21.9 1.7 20 46-65 20-39 (54)
41 PF08671 SinI: Anti-repressor 29.4 40 0.00087 20.4 1.5 14 45-58 15-28 (30)
42 COG2004 RPS24A Ribosomal prote 29.3 1.4E+02 0.0031 23.0 4.9 42 29-70 10-55 (107)
43 cd00196 UBQ Ubiquitin-like pro 28.8 1.1E+02 0.0024 16.9 3.5 36 36-71 7-42 (69)
44 cd01792 ISG15_repeat1 ISG15 ub 27.7 1.6E+02 0.0034 20.2 4.5 35 36-70 12-46 (80)
45 PF12426 DUF3674: RNA dependen 27.5 41 0.00088 22.1 1.4 16 49-64 3-18 (41)
46 PF01282 Ribosomal_S24e: Ribos 27.1 43 0.00093 24.1 1.6 23 45-67 11-33 (84)
47 PF13356 DUF4102: Domain of un 26.8 46 0.00099 23.3 1.7 27 123-149 22-60 (89)
48 PF08777 RRM_3: RNA binding mo 26.3 65 0.0014 23.8 2.5 27 39-67 4-31 (105)
49 PF14259 RRM_6: RNA recognitio 25.7 51 0.0011 21.0 1.7 26 43-70 6-31 (70)
50 PTZ00071 40S ribosomal protein 24.8 2.4E+02 0.0053 22.4 5.6 32 31-62 16-51 (132)
51 COG2139 RPL21A Ribosomal prote 24.5 1.1E+02 0.0023 23.5 3.4 48 104-152 18-75 (98)
52 PF02192 PI3K_p85B: PI3-kinase 22.9 1.1E+02 0.0023 22.1 3.0 21 39-59 2-22 (78)
53 COG3978 Acetolactate synthase 22.6 1.8E+02 0.004 21.7 4.2 36 35-70 43-78 (86)
54 PRK04219 rpl5p 50S ribosomal p 22.5 1.1E+02 0.0024 25.3 3.4 48 18-65 126-176 (177)
55 PF13592 HTH_33: Winged helix- 21.4 1E+02 0.0022 20.3 2.5 37 48-87 6-42 (60)
56 PF10057 DUF2294: Uncharacteri 21.0 1.4E+02 0.0031 22.2 3.5 25 48-72 76-100 (118)
57 PF10281 Ish1: Putative stress 20.7 83 0.0018 19.1 1.8 19 47-66 4-22 (38)
No 1
>KOG4089|consensus
Probab=99.90 E-value=1.4e-24 Score=174.54 Aligned_cols=98 Identities=36% Similarity=0.695 Sum_probs=84.9
Q ss_pred CC-CccccceecCCCceeEeecCcEEEEeeCCCCCCCcEEEEEecCCCCHHHHHHHHHHHhCceeeEEEeeeecC----c
Q psy5391 1 MS-SRWYPIYQKGNPQLRIFLPNFWMKLVRSKEPLPPNVVEFHVPLAMTNHDIKNYLEKIYNVTVKHVESTLENA----T 75 (157)
Q Consensus 1 ms-~r~ypl~~~G~~q~rIFLPnf~~~LvR~~~~l~pN~vtF~Vp~~mTK~DIK~YLEkiYnVkV~~VnT~I~~g----k 75 (157)
|+ +|+||+|+.|+||++||||||||.|+||...++|++++|+||++|||+||++||+++||++|.+|+|.+.+| +
T Consensus 1 m~s~~~y~~~k~gn~q~rVf~Pn~~~~l~rp~~~q~p~~~~FrVp~~m~k~DvR~YL~~iY~l~v~~vrtrl~~Gk~~~~ 80 (165)
T KOG4089|consen 1 MGSRRGYRLYKFGNPQLRVFFPNFWINLVRPLVTQPPKIVKFRVPMSMNKFDVRDYLTHIYDLPVVDVRTRLQHGKDYKK 80 (165)
T ss_pred CcccceeeeeecCCcceeEecchhHHhhhcccccCCCceEEEEcchhhccccHHHHHHHhcCCceeeeeeeeeechhhhc
Confidence 55 779999999999999999999999999998899999999999999999999999999999999999999999 4
Q ss_pred ceeccccccceecccCCCceeeeee
Q psy5391 76 SMAEWVSWLAFQMTLQPTRTVSTSL 100 (157)
Q Consensus 76 ~KR~~~~~~R~~~~kqP~~k~a~~~ 100 (157)
.++..++- ..|.+.=+++.|.+.
T Consensus 81 ~k~r~~~~--k~i~kdmd~p~~Yv~ 103 (165)
T KOG4089|consen 81 TKKRLQSP--KRIKKDMDEPVAYVE 103 (165)
T ss_pred ceeccccc--ceeecccccceeeec
Confidence 44444443 334444478888883
No 2
>PF00276 Ribosomal_L23: Ribosomal protein L23; InterPro: IPR013025 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 [, ]. This domain is found in both eukaryotic L25 and prokaryotic and eukaryotic L23 proteins.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3DF4_T 3DF2_T 4A1E_R 4A1A_R 4A1C_R 4A17_R 2HGU_W 2HGQ_W 1N88_A 2HGJ_W ....
Probab=99.70 E-value=6.8e-17 Score=117.68 Aligned_cols=65 Identities=26% Similarity=0.287 Sum_probs=55.3
Q ss_pred CCcEEEEEecCCCCHHHHHHHHHHHhCceeeEEEeeeecCcceeccccccceecccCCCceeeeeeeecccccc
Q psy5391 35 PPNVVEFHVPLAMTNHDIKNYLEKIYNVTVKHVESTLENATSMAEWVSWLAFQMTLQPTRTVSTSLFESYLSSG 108 (157)
Q Consensus 35 ~pN~vtF~Vp~~mTK~DIK~YLEkiYnVkV~~VnT~I~~gk~KR~~~~~~R~~~~kqP~~k~a~~~~~~~l~~~ 108 (157)
.+|+++|+||++|||.|||+|||++|||+|.+|||++.+|+.+| .+.+. -+.++||+|+| +|..|
T Consensus 19 ~~n~~tF~V~~~atK~~Ik~aie~iy~V~V~~Vnt~~~~gk~kR-~g~~~----g~~~~~KKaiV----tL~~~ 83 (91)
T PF00276_consen 19 NPNQYTFEVDPRATKTEIKEAIEKIYGVKVKKVNTMNYPGKKKR-KGKFV----GKTKDYKKAIV----TLKEG 83 (91)
T ss_dssp HSSEEEEEETTTSTHHHHHHHHHHHHTSEEEEEEEEEETSEEEE-SSSCE----EEE-EEEEEEE----EESTT
T ss_pred cCCEEEEEEeCCCCHHHHHHHHHhhcCCCeeEEEEeEeCCCceE-eCCcc----ccCCCcEEEEE----EeCCC
Confidence 56999999999999999999999999999999999999999888 33332 35699999999 55554
No 3
>PRK05738 rplW 50S ribosomal protein L23; Reviewed
Probab=99.65 E-value=4e-16 Score=114.36 Aligned_cols=65 Identities=20% Similarity=0.201 Sum_probs=57.0
Q ss_pred CcEEEEEecCCCCHHHHHHHHHHHhCceeeEEEeeeecCcceeccccccceecccCCCceeeeeeeecccccch
Q psy5391 36 PNVVEFHVPLAMTNHDIKNYLEKIYNVTVKHVESTLENATSMAEWVSWLAFQMTLQPTRTVSTSLFESYLSSGI 109 (157)
Q Consensus 36 pN~vtF~Vp~~mTK~DIK~YLEkiYnVkV~~VnT~I~~gk~KR~~~~~~R~~~~kqP~~k~a~~~~~~~l~~~~ 109 (157)
+|+++|.|+++|||.|||+|+|++|||+|.+|||++.+|+.||..+ ..-+.++||+|+| +|.+|.
T Consensus 20 ~n~~~F~V~~~a~K~eIK~aie~lf~VkV~~VnT~~~~gk~kr~~~-----~~g~~~~~KKA~V----tL~~g~ 84 (92)
T PRK05738 20 QNKYVFEVAPDATKPEIKAAVEKLFGVKVESVNTLNVKGKTKRFGR-----RIGKRSDWKKAIV----TLAEGQ 84 (92)
T ss_pred CCEEEEEECCCCCHHHHHHHHHHHcCCceeEEEEEEeCCceeeecc-----cccccCCcEEEEE----EcCCCC
Confidence 7999999999999999999999999999999999999999987743 2446699999999 555553
No 4
>CHL00030 rpl23 ribosomal protein L23
Probab=99.59 E-value=3.9e-15 Score=110.06 Aligned_cols=67 Identities=22% Similarity=0.171 Sum_probs=57.2
Q ss_pred CCCCcEEEEEecCCCCHHHHHHHHHHHhCceeeEEEeeeecCcceeccccccceecccCCCceeeeeeeecccccc
Q psy5391 33 PLPPNVVEFHVPLAMTNHDIKNYLEKIYNVTVKHVESTLENATSMAEWVSWLAFQMTLQPTRTVSTSLFESYLSSG 108 (157)
Q Consensus 33 ~l~pN~vtF~Vp~~mTK~DIK~YLEkiYnVkV~~VnT~I~~gk~KR~~~~~~R~~~~kqP~~k~a~~~~~~~l~~~ 108 (157)
.+..|+++|.|++++||.|||+++|++|||+|.+|||++.+|+.||.. ++ .-..|++|+|+| +|.+|
T Consensus 16 l~e~n~y~F~V~~~anK~eIK~avE~lf~VkV~~VNt~~~~~k~kr~~-~~----~G~~~~~KKAiV----tL~~g 82 (93)
T CHL00030 16 LLEKNQYTFDVDSGSTKTEIKHWIELFFGVKVIAVNSHRLPRKKRRMG-PI----MGHKMHYKRMII----TLQPG 82 (93)
T ss_pred hhHCCEEEEEECCCCCHHHHHHHHHHHhCCeEEEEEEEEcCCCccccC-Cc----ccccCCcEEEEE----EcCCc
Confidence 346799999999999999999999999999999999999999988753 22 245699999999 55554
No 5
>COG0089 RplW Ribosomal protein L23 [Translation, ribosomal structure and biogenesis]
Probab=99.55 E-value=1.7e-14 Score=107.42 Aligned_cols=68 Identities=21% Similarity=0.223 Sum_probs=58.9
Q ss_pred CCcEEEEEecCCCCHHHHHHHHHHHhCceeeEEEeeeecCcceeccccccceecccCCCceeeeeeeecccccchh
Q psy5391 35 PPNVVEFHVPLAMTNHDIKNYLEKIYNVTVKHVESTLENATSMAEWVSWLAFQMTLQPTRTVSTSLFESYLSSGII 110 (157)
Q Consensus 35 ~pN~vtF~Vp~~mTK~DIK~YLEkiYnVkV~~VnT~I~~gk~KR~~~~~~R~~~~kqP~~k~a~~~~~~~l~~~~~ 110 (157)
..|+++|.|++++||.|||+++|++|||+|.+|||++++|+.||...+ .+-..+++++|+| ++..|..
T Consensus 20 ~~nk~vF~V~~~AtK~~IK~AvE~lF~VkV~kVNTl~~k~k~KR~~~k----~~G~~~~~kka~V----~l~~G~~ 87 (94)
T COG0089 20 KENKYVFIVDPDATKPEIKAAVEELFGVKVEKVNTLNTKGKTKRAGVK----RIGLRKDYKKAYV----TLKEGQS 87 (94)
T ss_pred hCCEEEEEECCCCCHHHHHHHHHHHhCCeEEEEEEEEeCCcceEEecc----ccccCcccceeEE----EccCCCE
Confidence 459999999999999999999999999999999999999999998654 2335689999999 5555553
No 6
>PRK12280 rplW 50S ribosomal protein L23; Reviewed
Probab=99.46 E-value=1.4e-13 Score=110.48 Aligned_cols=63 Identities=17% Similarity=0.146 Sum_probs=54.9
Q ss_pred CCCcEEEEEecCCCCHHHHHHHHHHHhCceeeEEEeeeecCcceeccccccceecccCCCceeeeeee
Q psy5391 34 LPPNVVEFHVPLAMTNHDIKNYLEKIYNVTVKHVESTLENATSMAEWVSWLAFQMTLQPTRTVSTSLF 101 (157)
Q Consensus 34 l~pN~vtF~Vp~~mTK~DIK~YLEkiYnVkV~~VnT~I~~gk~KR~~~~~~R~~~~kqP~~k~a~~~~ 101 (157)
++.|+++|.|+++|||.|||+++|.+|||+|.+|||++..|+.+|.+ ++ .-..++|++|+|++
T Consensus 20 ~e~N~ytF~V~~~anK~eIK~AVE~iF~VkV~~VNT~~~~~K~KR~g-~~----~G~~~~~KKAiVtL 82 (158)
T PRK12280 20 MSKNVYTFKVDRRANKIEIKKAVEFIFKVKVLKVNIFNVDKKPKRLG-RF----PGFTNSYKKAYVTL 82 (158)
T ss_pred hhCCEEEEEECCCCCHHHHHHHHHHHhCCceEEEEeEecCCcccccC-Cc----ccccCCcEEEEEEC
Confidence 46699999999999999999999999999999999999999988763 22 34569999999944
No 7
>TIGR03636 L23_arch archaeal ribosomal protein L23. This model describes the archaeal ribosomal protein L23P and rigorously excludes the bacterial counterpart L23. In order to capture every known instance of archaeal L23P, the trusted cutoff is set lower than a few of the highest scoring eukaryotic cytosolic ribosomal counterparts.
Probab=99.42 E-value=4.9e-13 Score=95.96 Aligned_cols=51 Identities=25% Similarity=0.332 Sum_probs=46.4
Q ss_pred CcEEEEEecCCCCHHHHHHHHHHHhCceeeEEEeeeecCcceeccccccceecccCCCceeeeeeeecccccc
Q psy5391 36 PNVVEFHVPLAMTNHDIKNYLEKIYNVTVKHVESTLENATSMAEWVSWLAFQMTLQPTRTVSTSLFESYLSSG 108 (157)
Q Consensus 36 pN~vtF~Vp~~mTK~DIK~YLEkiYnVkV~~VnT~I~~gk~KR~~~~~~R~~~~kqP~~k~a~~~~~~~l~~~ 108 (157)
.|+++|.|++++||.|||+++|++|||+|.+|||++.+ +.+|+|+| +|..|
T Consensus 14 ~n~y~F~V~~~anK~eIK~avE~lf~VkV~~Vnt~~~~------------------~~~KKA~V----tL~~g 64 (77)
T TIGR03636 14 ENKLTFIVDRKATKGDIKRAVEKLFDVKVEKVNTLITP------------------RGEKKAYV----KLAEE 64 (77)
T ss_pred CCEEEEEECCCCCHHHHHHHHHHHhCCceEEEEeEEcC------------------CCceEEEE----EECCC
Confidence 48999999999999999999999999999999999876 47999999 55555
No 8
>PRK14548 50S ribosomal protein L23P; Provisional
Probab=99.40 E-value=7.5e-13 Score=96.44 Aligned_cols=51 Identities=24% Similarity=0.321 Sum_probs=46.6
Q ss_pred CcEEEEEecCCCCHHHHHHHHHHHhCceeeEEEeeeecCcceeccccccceecccCCCceeeeeeeecccccc
Q psy5391 36 PNVVEFHVPLAMTNHDIKNYLEKIYNVTVKHVESTLENATSMAEWVSWLAFQMTLQPTRTVSTSLFESYLSSG 108 (157)
Q Consensus 36 pN~vtF~Vp~~mTK~DIK~YLEkiYnVkV~~VnT~I~~gk~KR~~~~~~R~~~~kqP~~k~a~~~~~~~l~~~ 108 (157)
.|+++|.|++++||.|||+++|++|||+|.+|||++.+ +++|||+| +|+.|
T Consensus 21 ~n~y~F~V~~~anK~eIK~AvE~lf~VkV~~VnT~~~~------------------~~~KKA~V----~L~~g 71 (84)
T PRK14548 21 ENKLTFIVDRRATKPDIKRAVEELFDVKVEKVNTLITP------------------KGEKKAYV----KLAEE 71 (84)
T ss_pred CCEEEEEECCCCCHHHHHHHHHHHhCCceEEEEeEEcC------------------CCcEEEEE----EeCCC
Confidence 59999999999999999999999999999999999886 47999999 56555
No 9
>PTZ00191 60S ribosomal protein L23a; Provisional
Probab=99.21 E-value=4.1e-11 Score=95.27 Aligned_cols=49 Identities=22% Similarity=0.273 Sum_probs=44.5
Q ss_pred CCcEEEEEecCCCCHHHHHHHHHHHhCceeeEEEeeeecCcceeccccccceecccCCCceeeeeee
Q psy5391 35 PPNVVEFHVPLAMTNHDIKNYLEKIYNVTVKHVESTLENATSMAEWVSWLAFQMTLQPTRTVSTSLF 101 (157)
Q Consensus 35 ~pN~vtF~Vp~~mTK~DIK~YLEkiYnVkV~~VnT~I~~gk~KR~~~~~~R~~~~kqP~~k~a~~~~ 101 (157)
..|+++|.|++++||.|||+++|++|||+|.+|||+|.++ .+|+|+|+|
T Consensus 81 ~~N~yvF~Vd~kAnK~qIK~AVEklf~VkV~kVNTli~p~------------------g~KKA~V~L 129 (145)
T PTZ00191 81 DNNTLVFIVDQRANKTQIKKAVEKLYDVKVVKVNTLITPD------------------GLKKAYIRL 129 (145)
T ss_pred hCCEEEEEEcCCCCHHHHHHHHHHHhCCeeEEEEeEEcCC------------------CceEEEEEE
Confidence 3599999999999999999999999999999999999877 578888843
No 10
>KOG1751|consensus
Probab=98.40 E-value=3e-07 Score=74.25 Aligned_cols=46 Identities=22% Similarity=0.320 Sum_probs=41.9
Q ss_pred CCCcEEEEEecCCCCHHHHHHHHHHHhCceeeEEEeeeecCcceec
Q psy5391 34 LPPNVVEFHVPLAMTNHDIKNYLEKIYNVTVKHVESTLENATSMAE 79 (157)
Q Consensus 34 l~pN~vtF~Vp~~mTK~DIK~YLEkiYnVkV~~VnT~I~~gk~KR~ 79 (157)
-+.|+++|.|+..+||++||+++.++|+++|.+|||+|.+.+.|+-
T Consensus 92 ednNtlvf~vd~kankhqiKqAVkkLyd~dvakvntli~p~g~kka 137 (157)
T KOG1751|consen 92 EDNNTLVFIVDSKANKHQIKQAVKKLYDTDVAKVNTLIRPDGEKKA 137 (157)
T ss_pred hhCceeEEEEecccchHHHHHHHHHHhccchhhheeeecCCCceeE
Confidence 4679999999999999999999999999999999999977776654
No 11
>cd01769 UBL Ubiquitin-like domain of UBL. UBLs function by remodeling the surface of their target proteins, changing their target's half-life, enzymatic activity, protein-protein interactions, subcellular localization or other properties. At least 10 different ubiquitin-like modifications exist in mammals, and attachment of different ubls to a target leads to different biological consequences. Ubl-conjugation cascades are initiated by activating enzymes, which also coordinate the ubls with their downstream pathways.
Probab=68.75 E-value=13 Score=23.56 Aligned_cols=38 Identities=13% Similarity=0.077 Sum_probs=31.8
Q ss_pred CcEEEEEecCCCCHHHHHHHHHHHhCceeeEEEeeeecC
Q psy5391 36 PNVVEFHVPLAMTNHDIKNYLEKIYNVTVKHVESTLENA 74 (157)
Q Consensus 36 pN~vtF~Vp~~mTK~DIK~YLEkiYnVkV~~VnT~I~~g 74 (157)
...+.|.++.++|=.|+|+.+++.+|++..+.+- +..|
T Consensus 7 ~~~~~~~~~~~~ti~~lK~~i~~~~~~~~~~~~l-~~~g 44 (69)
T cd01769 7 GKTFELEVSPDDTVAELKAKIAAKEGVPPEQQRL-IYAG 44 (69)
T ss_pred CCEEEEEECCCChHHHHHHHHHHHHCcChHHEEE-EECC
Confidence 4567899999999999999999999999888765 3444
No 12
>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=68.41 E-value=15 Score=24.42 Aligned_cols=44 Identities=9% Similarity=0.065 Sum_probs=36.3
Q ss_pred CCCcEEEEEecCCCCHHHHHHHHHHHhCceeeEEEeeeecCccee
Q psy5391 34 LPPNVVEFHVPLAMTNHDIKNYLEKIYNVTVKHVESTLENATSMA 78 (157)
Q Consensus 34 l~pN~vtF~Vp~~mTK~DIK~YLEkiYnVkV~~VnT~I~~gk~KR 78 (157)
+....+++.|++++|=.|+|+.++...|+++...+- +..|+.-.
T Consensus 6 ~~g~~~~~~v~~~~tV~~lK~~i~~~~gi~~~~q~L-i~~G~~L~ 49 (70)
T cd01798 6 NTGHTFPVEVDPDTDIKQLKEVVAKRQGVPPDQLRV-IFAGKELR 49 (70)
T ss_pred CCCCEEEEEECCCChHHHHHHHHHHHHCCCHHHeEE-EECCeECC
Confidence 355678999999999999999999999999988755 46666543
No 13
>PTZ00044 ubiquitin; Provisional
Probab=67.64 E-value=16 Score=24.42 Aligned_cols=42 Identities=17% Similarity=0.167 Sum_probs=36.0
Q ss_pred CCCcEEEEEecCCCCHHHHHHHHHHHhCceeeEEEeeeecCcc
Q psy5391 34 LPPNVVEFHVPLAMTNHDIKNYLEKIYNVTVKHVESTLENATS 76 (157)
Q Consensus 34 l~pN~vtF~Vp~~mTK~DIK~YLEkiYnVkV~~VnT~I~~gk~ 76 (157)
+.-+..++.|+++.|=.|||..++...|++....+-. ..|+.
T Consensus 8 ~~G~~~~l~v~~~~tv~~lK~~i~~~~gi~~~~q~L~-~~g~~ 49 (76)
T PTZ00044 8 LTGKKQSFNFEPDNTVQQVKMALQEKEGIDVKQIRLI-YSGKQ 49 (76)
T ss_pred CCCCEEEEEECCCCcHHHHHHHHHHHHCCCHHHeEEE-ECCEE
Confidence 4556889999999999999999999999999887776 55654
No 14
>PF14560 Ubiquitin_2: Ubiquitin-like domain; PDB: 1WJN_A 2KJ6_A 2KJR_A 1V6E_A 1T0Y_A.
Probab=67.07 E-value=19 Score=25.14 Aligned_cols=39 Identities=23% Similarity=0.313 Sum_probs=33.8
Q ss_pred CCCcEEEEEecCCCCHHHHHHHHHHHhCceeeEEEeeee
Q psy5391 34 LPPNVVEFHVPLAMTNHDIKNYLEKIYNVTVKHVESTLE 72 (157)
Q Consensus 34 l~pN~vtF~Vp~~mTK~DIK~YLEkiYnVkV~~VnT~I~ 72 (157)
.....+.-++|+++|=.|+|.-||.++|++...-+-...
T Consensus 11 ~~~~~~ekr~~~~~Tv~eLK~kl~~~~Gi~~~~m~L~l~ 49 (87)
T PF14560_consen 11 SKQRSVEKRFPKSITVSELKQKLEKLTGIPPSDMRLQLK 49 (87)
T ss_dssp SSSSEEEEEEETTSBHHHHHHHHHHHHTS-TTTEEEEEE
T ss_pred CCCeeEEEEcCCCCCHHHHHHHHHHHhCCCcccEEEEEE
Confidence 334788899999999999999999999999999888875
No 15
>cd01789 Alp11_N Ubiquitin-like domain of Alp11 tubulin-folding cofactor B. Alp11, also known as tubulin-folding cofactor B, is one of at least three proteins required for the proper folding of tubulins prior to their incorporation into microtubules. These cofactors are necessary for the biogenesis of microtubules and for cell viability. Alp11 has three domains including an N-terminal ubiquitin-like domain (represented by this CD) which executes the essential function, a central coiled-coil domain necessary for maintenance of cellular alpha-tubulin levels, and a C-terminal CLIP-170 domain is required for efficient binding to alpha-tubulin.
Probab=66.96 E-value=16 Score=25.81 Aligned_cols=40 Identities=15% Similarity=0.125 Sum_probs=34.7
Q ss_pred CcEEEEEecCCCCHHHHHHHHHHHhCceeeEEEeeeecCc
Q psy5391 36 PNVVEFHVPLAMTNHDIKNYLEKIYNVTVKHVESTLENAT 75 (157)
Q Consensus 36 pN~vtF~Vp~~mTK~DIK~YLEkiYnVkV~~VnT~I~~gk 75 (157)
.....-++|+++|=.++|+-||.++|+++..-+-.+..++
T Consensus 12 ~~~~ekr~~~~~Tv~~lK~kl~~~~G~~~~~mrL~l~~~~ 51 (84)
T cd01789 12 SFSFEKKYSRGLTIAELKKKLELVVGTPASSMRLQLFDGD 51 (84)
T ss_pred ceeeeEecCCCCcHHHHHHHHHHHHCCCccceEEEEEcCC
Confidence 4456778999999999999999999999999988776655
No 16
>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=62.64 E-value=30 Score=22.68 Aligned_cols=39 Identities=10% Similarity=0.078 Sum_probs=33.1
Q ss_pred CcEEEEEecCCCCHHHHHHHHHHHhCceeeEEEeeeecCc
Q psy5391 36 PNVVEFHVPLAMTNHDIKNYLEKIYNVTVKHVESTLENAT 75 (157)
Q Consensus 36 pN~vtF~Vp~~mTK~DIK~YLEkiYnVkV~~VnT~I~~gk 75 (157)
-..+.+.|+++.|=.|+|+.++...|+++...+-. ..|+
T Consensus 10 g~~~~~~v~~~~tv~~lK~~i~~~~g~~~~~qrL~-~~g~ 48 (76)
T cd01806 10 GKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLI-YSGK 48 (76)
T ss_pred CCEEEEEECCCCCHHHHHHHHhHhhCCChhhEEEE-ECCe
Confidence 45578999999999999999999999999987776 4444
No 17
>cd01803 Ubiquitin Ubiquitin. Ubiquitin (includes Ubq/RPL40e and Ubq/RPS27a fusions as well as homopolymeric multiubiquitin protein chains)
Probab=57.76 E-value=31 Score=22.58 Aligned_cols=35 Identities=9% Similarity=0.092 Sum_probs=30.5
Q ss_pred CcEEEEEecCCCCHHHHHHHHHHHhCceeeEEEee
Q psy5391 36 PNVVEFHVPLAMTNHDIKNYLEKIYNVTVKHVEST 70 (157)
Q Consensus 36 pN~vtF~Vp~~mTK~DIK~YLEkiYnVkV~~VnT~ 70 (157)
.....+.|++++|=.|+|+.+++..|+++...+-.
T Consensus 10 g~~~~~~v~~~~tV~~lK~~i~~~~g~~~~~q~L~ 44 (76)
T cd01803 10 GKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLI 44 (76)
T ss_pred CCEEEEEECCcCcHHHHHHHHHHHhCCCHHHeEEE
Confidence 45578999999999999999999999998876655
No 18
>PRK01178 rps24e 30S ribosomal protein S24e; Reviewed
Probab=57.68 E-value=36 Score=25.61 Aligned_cols=43 Identities=16% Similarity=0.217 Sum_probs=32.6
Q ss_pred EEEeeCCCCCCCcEEEEEec----CCCCHHHHHHHHHHHhCceeeEE
Q psy5391 25 MKLVRSKEPLPPNVVEFHVP----LAMTNHDIKNYLEKIYNVTVKHV 67 (157)
Q Consensus 25 ~~LvR~~~~l~pN~vtF~Vp----~~mTK~DIK~YLEkiYnVkV~~V 67 (157)
|.--+.++.|.-.++.|.|- ..-+|.||++-|.++||.+...|
T Consensus 5 I~~~~~N~LL~Rke~~~~v~h~g~~tpsr~eirekLa~~~~~~~~~v 51 (99)
T PRK01178 5 IISDKENPLLGRREIKFEVYHEGSATPSRKDVRKKLAAMLNADKELV 51 (99)
T ss_pred EEEeeecCCcCcEEEEEEEEeCCCCCCCHHHHHHHHHHHHCcCCCEE
Confidence 33344557788889999885 35699999999999999765443
No 19
>smart00213 UBQ Ubiquitin homologues. Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression
Probab=56.38 E-value=17 Score=22.70 Aligned_cols=34 Identities=12% Similarity=0.222 Sum_probs=29.8
Q ss_pred cEEEEEecCCCCHHHHHHHHHHHhCceeeEEEee
Q psy5391 37 NVVEFHVPLAMTNHDIKNYLEKIYNVTVKHVEST 70 (157)
Q Consensus 37 N~vtF~Vp~~mTK~DIK~YLEkiYnVkV~~VnT~ 70 (157)
....+.|++++|=.++|+.+++.+|++....+-.
T Consensus 10 ~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~~~L~ 43 (64)
T smart00213 10 GTITLEVKPSDTVSELKEKIAELTGIPVEQQRLI 43 (64)
T ss_pred ceEEEEECCCCcHHHHHHHHHHHHCCCHHHEEEE
Confidence 4788999999999999999999999988766554
No 20
>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=54.64 E-value=18 Score=24.52 Aligned_cols=41 Identities=10% Similarity=0.116 Sum_probs=33.8
Q ss_pred CCcEEEEEecCCCCHHHHHHHHHHHhCceeeEEEeeeecCcc
Q psy5391 35 PPNVVEFHVPLAMTNHDIKNYLEKIYNVTVKHVESTLENATS 76 (157)
Q Consensus 35 ~pN~vtF~Vp~~mTK~DIK~YLEkiYnVkV~~VnT~I~~gk~ 76 (157)
..+.....|++++|=.|+|+.++...|+++..-+- +..|+.
T Consensus 8 ~g~~~~l~v~~~~TV~~lK~~I~~~~gip~~~q~L-i~~Gk~ 48 (71)
T cd01796 8 SETTFSLDVDPDLELENFKALCEAESGIPASQQQL-IYNGRE 48 (71)
T ss_pred CCCEEEEEECCcCCHHHHHHHHHHHhCCCHHHeEE-EECCeE
Confidence 34568899999999999999999999999987654 455653
No 21
>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=51.14 E-value=21 Score=23.22 Aligned_cols=35 Identities=14% Similarity=0.166 Sum_probs=30.1
Q ss_pred CcEEEEEecCCCCHHHHHHHHHHHhCceeeEEEee
Q psy5391 36 PNVVEFHVPLAMTNHDIKNYLEKIYNVTVKHVEST 70 (157)
Q Consensus 36 pN~vtF~Vp~~mTK~DIK~YLEkiYnVkV~~VnT~ 70 (157)
.....+.|+.++|=.|+|+.+++..|++..+-+-.
T Consensus 9 g~~~~i~v~~~~tv~~lK~~i~~~~gi~~~~q~L~ 43 (71)
T cd01812 9 GESHDLSISSQATFGDLKKMLAPVTGVEPRDQKLI 43 (71)
T ss_pred CEEEEEEECCCCcHHHHHHHHHHhhCCChHHeEEe
Confidence 34577899999999999999999999998876654
No 22
>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=50.69 E-value=36 Score=23.18 Aligned_cols=41 Identities=10% Similarity=0.088 Sum_probs=33.8
Q ss_pred CCCCcEEEEEecCCCCHHHHHHHHHHHhCceeeEEEeeeecC
Q psy5391 33 PLPPNVVEFHVPLAMTNHDIKNYLEKIYNVTVKHVESTLENA 74 (157)
Q Consensus 33 ~l~pN~vtF~Vp~~mTK~DIK~YLEkiYnVkV~~VnT~I~~g 74 (157)
.+.-..+++.|++.+|=.|+|+.|+...|+++..-+-. ..|
T Consensus 4 ~l~g~~~~l~v~~~~TV~~lK~~i~~~~gip~~~q~L~-~~G 44 (76)
T cd01800 4 KLNGQMLNFTLQLSDPVSVLKVKIHEETGMPAGKQKLQ-YEG 44 (76)
T ss_pred ccCCeEEEEEECCCCcHHHHHHHHHHHHCCCHHHEEEE-ECC
Confidence 45567889999999999999999999999998776543 444
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=47.20 E-value=50 Score=21.92 Aligned_cols=36 Identities=11% Similarity=0.057 Sum_probs=30.6
Q ss_pred CCcEEEEEecCCCCHHHHHHHHHHHhCc--eeeEEEee
Q psy5391 35 PPNVVEFHVPLAMTNHDIKNYLEKIYNV--TVKHVEST 70 (157)
Q Consensus 35 ~pN~vtF~Vp~~mTK~DIK~YLEkiYnV--kV~~VnT~ 70 (157)
..+..++.|+.+.|=.|+|+.++...|+ ++...+-.
T Consensus 9 ~g~~~~l~v~~~~TV~~lK~~i~~~~~i~~~~~~q~L~ 46 (77)
T cd01805 9 KQQTFPIEVDPDDTVAELKEKIEEEKGCDYPPEQQKLI 46 (77)
T ss_pred CCCEEEEEECCCCcHHHHHHHHHHhhCCCCChhHeEEE
Confidence 4467899999999999999999999998 77666554
No 24
>COG0084 TatD Mg-dependent DNase [DNA replication, recombination, and repair]
Probab=46.15 E-value=13 Score=31.82 Aligned_cols=30 Identities=30% Similarity=0.298 Sum_probs=27.5
Q ss_pred cchhhHHHHHhHhhhhccccceeeCCceecce
Q psy5391 107 SGIITSAKRLMKCIKLQNGLFIKINPIGTKDL 138 (157)
Q Consensus 107 ~~~~~~~k~~~~~~~~~~~~~~~~np~~tk~~ 138 (157)
|.++-|+..+.+++++ |.||++++++|-+|
T Consensus 155 HcFsGs~e~a~~~~d~--G~yisisG~itfk~ 184 (256)
T COG0084 155 HCFSGSAEEARKLLDL--GFYISISGIVTFKN 184 (256)
T ss_pred EccCCCHHHHHHHHHc--CeEEEECceeecCC
Confidence 7788889999999998 89999999999888
No 25
>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=45.54 E-value=39 Score=21.86 Aligned_cols=40 Identities=15% Similarity=0.167 Sum_probs=33.0
Q ss_pred CCcEEEEEecCCCCHHHHHHHHHHHhCceeeEEEeeeecCc
Q psy5391 35 PPNVVEFHVPLAMTNHDIKNYLEKIYNVTVKHVESTLENAT 75 (157)
Q Consensus 35 ~pN~vtF~Vp~~mTK~DIK~YLEkiYnVkV~~VnT~I~~gk 75 (157)
.-...+|.|+++.|=.|+|+.+++..|+++...+-. ..|+
T Consensus 9 ~g~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~-~~g~ 48 (72)
T cd01809 9 DSQTHTFTVEEEITVLDLKEKIAEEVGIPVEQQRLI-YSGR 48 (72)
T ss_pred CCCEEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEE-ECCE
Confidence 346789999999999999999999999988876655 4444
No 26
>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=44.31 E-value=36 Score=22.04 Aligned_cols=41 Identities=12% Similarity=0.100 Sum_probs=35.2
Q ss_pred CcEEEEEecCCCCHHHHHHHHHHHhCceeeEEEeeeecCcce
Q psy5391 36 PNVVEFHVPLAMTNHDIKNYLEKIYNVTVKHVESTLENATSM 77 (157)
Q Consensus 36 pN~vtF~Vp~~mTK~DIK~YLEkiYnVkV~~VnT~I~~gk~K 77 (157)
...+.+.|+.+.|=.|+|+.+++..|+++...+-. ..|+.-
T Consensus 5 g~~~~~~v~~~~tV~~lK~~i~~~~~~~~~~~~L~-~~G~~L 45 (69)
T PF00240_consen 5 GKTFTLEVDPDDTVADLKQKIAEETGIPPEQQRLI-YNGKEL 45 (69)
T ss_dssp SEEEEEEEETTSBHHHHHHHHHHHHTSTGGGEEEE-ETTEEE
T ss_pred CcEEEEEECCCCCHHHhhhhcccccccccccceee-eeeecc
Confidence 34789999999999999999999999999998765 566644
No 27
>PF00076 RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); InterPro: IPR000504 Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [, , ]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [, ]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [, , ]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition []. The motif also appears in a few single stranded DNA binding proteins. The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases []. The RRM is reviewed in a number of publications [, , ].; GO: 0003676 nucleic acid binding; PDB: 2RNE_A 2DGO_A 2DO4_A 1YTY_B 2VOO_B 2VOP_A 2VON_B 1ZH5_B 2VOD_A 1S79_A ....
Probab=43.95 E-value=53 Score=20.29 Aligned_cols=19 Identities=11% Similarity=0.618 Sum_probs=16.7
Q ss_pred ecCCCCHHHHHHHHHHHhCc
Q psy5391 43 VPLAMTNHDIKNYLEKIYNV 62 (157)
Q Consensus 43 Vp~~mTK~DIK~YLEkiYnV 62 (157)
+|.++|..||++++++ ||-
T Consensus 6 lp~~~t~~~l~~~f~~-~g~ 24 (70)
T PF00076_consen 6 LPPDVTEEELRDFFSQ-FGK 24 (70)
T ss_dssp ETTTSSHHHHHHHHHT-TST
T ss_pred CCCcCCHHHHHHHHHH-hhh
Confidence 6899999999999999 553
No 28
>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=43.54 E-value=77 Score=23.35 Aligned_cols=44 Identities=16% Similarity=0.194 Sum_probs=35.7
Q ss_pred CCCcEEEEEecCCCCHHHHHHHHHHHhCceeeEEEeeeecCccee
Q psy5391 34 LPPNVVEFHVPLAMTNHDIKNYLEKIYNVTVKHVESTLENATSMA 78 (157)
Q Consensus 34 l~pN~vtF~Vp~~mTK~DIK~YLEkiYnVkV~~VnT~I~~gk~KR 78 (157)
+....+++.|++.+|=.|||+.++..+|+++..-+- +..|+.=.
T Consensus 35 l~G~~~~leV~~~~TV~~lK~kI~~~~gip~~~QrL-i~~Gk~L~ 78 (103)
T cd01802 35 LTGTCFELRVSPFETVISVKAKIQRLEGIPVAQQHL-IWNNMELE 78 (103)
T ss_pred CCCCEEEEEeCCCCcHHHHHHHHHHHhCCChHHEEE-EECCEECC
Confidence 456679999999999999999999999999877554 46666433
No 29
>PF09358 UBA_e1_C: Ubiquitin-activating enzyme e1 C-terminal domain; InterPro: IPR018965 This presumed domain found at the C terminus of Ubiquitin-activating enzyme e1 proteins is functionally uncharacterised. ; PDB: 3CMM_A.
Probab=42.33 E-value=38 Score=25.96 Aligned_cols=30 Identities=20% Similarity=0.386 Sum_probs=23.1
Q ss_pred EEEecCCCCHHHHHHHHHHHhCceeeEEEe
Q psy5391 40 EFHVPLAMTNHDIKNYLEKIYNVTVKHVES 69 (157)
Q Consensus 40 tF~Vp~~mTK~DIK~YLEkiYnVkV~~VnT 69 (157)
.|.|+-++|=.|+-+|+++-||++|..|.-
T Consensus 36 r~~v~~~~Tl~~li~~~~~~~~lev~ml~~ 65 (125)
T PF09358_consen 36 RIEVNGDMTLQELIDYFKEKYGLEVTMLSQ 65 (125)
T ss_dssp EEEEES--BHHHHHHHHHHTTS-EEEEEEE
T ss_pred EEEEcCCCCHHHHHHHHHHHhCceEEEEEe
Confidence 466777999999999999999999988753
No 30
>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=41.48 E-value=56 Score=21.89 Aligned_cols=43 Identities=12% Similarity=0.100 Sum_probs=35.4
Q ss_pred CCcEEEEEecCCCCHHHHHHHHHHHhCceeeEEEeeeecCccee
Q psy5391 35 PPNVVEFHVPLAMTNHDIKNYLEKIYNVTVKHVESTLENATSMA 78 (157)
Q Consensus 35 ~pN~vtF~Vp~~mTK~DIK~YLEkiYnVkV~~VnT~I~~gk~KR 78 (157)
.-+..++.|+.++|=.|+|+-++...|++....+-. ..|+.-.
T Consensus 9 ~G~~~~l~v~~~~tV~~lK~~i~~~~gi~~~~q~L~-~~G~~L~ 51 (74)
T cd01807 9 QGRECSLQVSEKESVSTLKKLVSEHLNVPEEQQRLL-FKGKALA 51 (74)
T ss_pred CCCEEEEEECCCCcHHHHHHHHHHHHCCCHHHeEEE-ECCEECC
Confidence 345788999999999999999999999999887664 6666443
No 31
>COG1478 GTP and metal dependent enzyme involved F420 coenzyme biosynthesis (catalyzes addition of two l-glutamates to F420 precursor) [Coenzyme transport and metabolism]
Probab=41.12 E-value=53 Score=28.93 Aligned_cols=84 Identities=12% Similarity=0.060 Sum_probs=65.1
Q ss_pred EEEecCCCCHHHHHHHHHHHhCceeeEEEeeeecCcceeccccccceecccC---CCceeeeeeeecccccchhhHHHHH
Q psy5391 40 EFHVPLAMTNHDIKNYLEKIYNVTVKHVESTLENATSMAEWVSWLAFQMTLQ---PTRTVSTSLFESYLSSGIITSAKRL 116 (157)
Q Consensus 40 tF~Vp~~mTK~DIK~YLEkiYnVkV~~VnT~I~~gk~KR~~~~~~R~~~~kq---P~~k~a~~~~~~~l~~~~~~~~k~~ 116 (157)
-.=.+++.+-..|+++|++.||++|-=|=|. ++|+--|+...-+..++..= =||.+..=+|+.+|.-....-+-+|
T Consensus 122 llP~dPd~Sa~~i~~~L~~~~g~~vgVIItD-t~grp~R~G~~gvAiG~~G~~pl~d~~G~~D~yGr~L~~T~~avaDeL 200 (257)
T COG1478 122 LLPKDPDASAETIRERLRELLGVKVGVIITD-THGRPFRRGQTGVAIGISGLSPLRDYRGERDLYGRELKVTEEAVADEL 200 (257)
T ss_pred eCCCChHHHHHHHHHHHHHHhCCceEEEEeC-CCCCccccCcceEEEeeccCchHHhhcCCcccCCCeeeeeHHHHHHHH
Confidence 4556888999999999999999998777776 66766666555444333322 3488888999999999999999999
Q ss_pred hHhhhhcc
Q psy5391 117 MKCIKLQN 124 (157)
Q Consensus 117 ~~~~~~~~ 124 (157)
..|-+|--
T Consensus 201 AaaA~LvM 208 (257)
T COG1478 201 AAAANLVM 208 (257)
T ss_pred HHHHHHhc
Confidence 99988843
No 32
>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=40.62 E-value=38 Score=22.78 Aligned_cols=41 Identities=20% Similarity=0.156 Sum_probs=34.2
Q ss_pred cEEEEEecCCCCHHHHHHHHHHHhCceeeEEEeeeecCccee
Q psy5391 37 NVVEFHVPLAMTNHDIKNYLEKIYNVTVKHVESTLENATSMA 78 (157)
Q Consensus 37 N~vtF~Vp~~mTK~DIK~YLEkiYnVkV~~VnT~I~~gk~KR 78 (157)
+..++.|+++.|=.|+|+.++...|+++...+- +..|+.=.
T Consensus 9 ~~~~l~v~~~~tV~~lK~~i~~~~gip~~~q~L-i~~Gk~L~ 49 (74)
T cd01793 9 NTHTLEVTGQETVSDIKAHVAGLEGIDVEDQVL-LLAGVPLE 49 (74)
T ss_pred CEEEEEECCcCcHHHHHHHHHhhhCCCHHHEEE-EECCeECC
Confidence 578999999999999999999999999988754 46666433
No 33
>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=36.59 E-value=47 Score=22.62 Aligned_cols=43 Identities=14% Similarity=0.019 Sum_probs=35.2
Q ss_pred CCcEEEEEecCCCCHHHHHHHHHHHhCceeeEEEeeeecCccee
Q psy5391 35 PPNVVEFHVPLAMTNHDIKNYLEKIYNVTVKHVESTLENATSMA 78 (157)
Q Consensus 35 ~pN~vtF~Vp~~mTK~DIK~YLEkiYnVkV~~VnT~I~~gk~KR 78 (157)
.-....+.|++++|=.|||+.++...|++....+- +..|+.=.
T Consensus 7 ~G~~~~l~v~~~~TV~~lK~~I~~~~gi~~~~q~L-i~~G~~L~ 49 (70)
T cd01794 7 TGKDVKLSVSSKDTVGQLKKQLQAAEGVDPCCQRW-FFSGKLLT 49 (70)
T ss_pred CCCEEEEEECCcChHHHHHHHHHHHhCCCHHHeEE-EECCeECC
Confidence 44678899999999999999999999999987654 46666433
No 34
>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=36.35 E-value=94 Score=20.83 Aligned_cols=41 Identities=12% Similarity=-0.006 Sum_probs=33.0
Q ss_pred CCCcEEEEEecCCCCHHHHHHHHHHHhCceeeEEEeeeecCc
Q psy5391 34 LPPNVVEFHVPLAMTNHDIKNYLEKIYNVTVKHVESTLENAT 75 (157)
Q Consensus 34 l~pN~vtF~Vp~~mTK~DIK~YLEkiYnVkV~~VnT~I~~gk 75 (157)
+.....++.|++++|=.|+|+.++...|+++..-+- +..|+
T Consensus 6 ~~g~~~~l~v~~~~tV~~lK~~I~~~~gi~~~~q~L-~~~G~ 46 (74)
T cd01810 6 DKGRSSIYEVQLTQTVATLKQQVSQRERVQADQFWL-SFEGR 46 (74)
T ss_pred CCCCEEEEEECCcChHHHHHHHHHHHhCCCHHHeEE-EECCE
Confidence 445678899999999999999999999998876654 34444
No 35
>smart00362 RRM_2 RNA recognition motif.
Probab=35.90 E-value=66 Score=19.06 Aligned_cols=27 Identities=22% Similarity=0.532 Sum_probs=19.2
Q ss_pred EecCCCCHHHHHHHHHHHhCceeeEEEee
Q psy5391 42 HVPLAMTNHDIKNYLEKIYNVTVKHVEST 70 (157)
Q Consensus 42 ~Vp~~mTK~DIK~YLEkiYnVkV~~VnT~ 70 (157)
.+|.+++..||+++++. || +|..+...
T Consensus 6 ~l~~~~~~~~l~~~~~~-~g-~v~~~~~~ 32 (72)
T smart00362 6 NLPPDVTEEDLKELFSK-FG-PIESVKIP 32 (72)
T ss_pred CCCCcCCHHHHHHHHHh-cC-CEEEEEEe
Confidence 35788999999999985 55 44455443
No 36
>PF03780 Asp23: Asp23 family; InterPro: IPR005531 This entry represents the alkaline shock protein 23 family. These small proteins are involved in alkaline pH tolerance of Staphylococcus aureus [,].
Probab=35.40 E-value=70 Score=22.60 Aligned_cols=24 Identities=21% Similarity=0.411 Sum_probs=21.5
Q ss_pred HHHHHHHHHHHhCceeeEEEeeee
Q psy5391 49 NHDIKNYLEKIYNVTVKHVESTLE 72 (157)
Q Consensus 49 K~DIK~YLEkiYnVkV~~VnT~I~ 72 (157)
...|+++||++-|++|.+|+-.+.
T Consensus 82 q~~V~~~v~~~tg~~v~~V~V~V~ 105 (108)
T PF03780_consen 82 QEKVKEAVEEMTGIEVSEVNVHVE 105 (108)
T ss_pred HHHHHHHHHHHHCCeeEEEEEEEE
Confidence 678999999999999999998764
No 37
>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=35.19 E-value=68 Score=22.26 Aligned_cols=39 Identities=13% Similarity=-0.035 Sum_probs=32.7
Q ss_pred CCcEEEEEecCCCCHHHHHHHHHHHhCceeeEEEeeeecCc
Q psy5391 35 PPNVVEFHVPLAMTNHDIKNYLEKIYNVTVKHVESTLENAT 75 (157)
Q Consensus 35 ~pN~vtF~Vp~~mTK~DIK~YLEkiYnVkV~~VnT~I~~gk 75 (157)
..-++++.|++++|=.+||+-|+...|++...-+- ..|+
T Consensus 11 ~~~t~~l~v~~~~TV~~lK~kI~~~~gip~~~QrL--~~G~ 49 (75)
T cd01799 11 HTVTIWLTVRPDMTVAQLKDKVFLDYGFPPAVQRW--VIGQ 49 (75)
T ss_pred CCCeEEEEECCCCcHHHHHHHHHHHHCcCHHHEEE--EcCC
Confidence 34578899999999999999999999999987665 4454
No 38
>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=31.82 E-value=86 Score=20.79 Aligned_cols=36 Identities=11% Similarity=0.166 Sum_probs=29.2
Q ss_pred EEEEecCCCCHHHHHHHHHHHhCceeeEEEeeeecCc
Q psy5391 39 VEFHVPLAMTNHDIKNYLEKIYNVTVKHVESTLENAT 75 (157)
Q Consensus 39 vtF~Vp~~mTK~DIK~YLEkiYnVkV~~VnT~I~~gk 75 (157)
.++.|++++|=.|+|+.+++.+|++....+- +..|+
T Consensus 12 ~~l~v~~~~TV~~lK~~I~~~~~i~~~~~~L-i~~Gk 47 (71)
T cd01808 12 EEIEIAEDASVKDFKEAVSKKFKANQEQLVL-IFAGK 47 (71)
T ss_pred EEEEECCCChHHHHHHHHHHHhCCCHHHEEE-EECCe
Confidence 4899999999999999999999987766653 34444
No 39
>PTZ00156 60S ribosomal protein L11; Provisional
Probab=31.66 E-value=53 Score=27.18 Aligned_cols=49 Identities=12% Similarity=0.171 Sum_probs=36.5
Q ss_pred eEeecCcEEEEeeCCCC-CCCcEEEEEecC--CCCHHHHHHHHHHHhCceee
Q psy5391 17 RIFLPNFWMKLVRSKEP-LPPNVVEFHVPL--AMTNHDIKNYLEKIYNVTVK 65 (157)
Q Consensus 17 rIFLPnf~~~LvR~~~~-l~pN~vtF~Vp~--~mTK~DIK~YLEkiYnVkV~ 65 (157)
.+|==|+.+.|-|||-. ......+.+||. ..||.|-.+++++-|||.|.
T Consensus 120 ~i~GmdI~ivl~rpG~rv~~R~~~~~~i~~~hrv~~eea~~~~~~~~~v~v~ 171 (172)
T PTZ00156 120 GIYGMDFYVVLGRPGFRVARRKRKQSKVGKSHRVTKEEAMKWFKTTFDGIIL 171 (172)
T ss_pred CcccCceEEEEeCCcceeeecccccccCCCCceeCHHHHHHHHHhhcCEEEc
Confidence 35555888999999822 233455566664 46999999999999999985
No 40
>PF08766 DEK_C: DEK C terminal domain; InterPro: IPR014876 DEK is a chromatin associated protein that is linked with cancers and autoimmune disease. This domain is found at the C-terminal of DEK and is of clinical importance since it can reverse the characteristic abnormal DNA-mutagen sensitivity in fibroblasts from ataxia-telangiectasia (A-T) patients []. The structure of this domain shows it to be homologous to the E2F/DP transcription factor family []. This domain is also found in chitin synthase proteins like Q8TF96 from SWISSPROT, and in protein phosphatases such as Q6NN85 from SWISSPROT. ; PDB: 1Q1V_A.
Probab=29.45 E-value=41 Score=21.87 Aligned_cols=20 Identities=20% Similarity=0.488 Sum_probs=13.6
Q ss_pred CCCHHHHHHHHHHHhCceee
Q psy5391 46 AMTNHDIKNYLEKIYNVTVK 65 (157)
Q Consensus 46 ~mTK~DIK~YLEkiYnVkV~ 65 (157)
.+|..+|+..||+-||++..
T Consensus 20 ~vT~k~vr~~Le~~~~~dL~ 39 (54)
T PF08766_consen 20 TVTKKQVREQLEERFGVDLS 39 (54)
T ss_dssp G--HHHHHHHHHHH-SS--S
T ss_pred HhhHHHHHHHHHHHHCCCcH
Confidence 46899999999999999865
No 41
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=29.44 E-value=40 Score=20.44 Aligned_cols=14 Identities=21% Similarity=0.562 Sum_probs=10.0
Q ss_pred CCCCHHHHHHHHHH
Q psy5391 45 LAMTNHDIKNYLEK 58 (157)
Q Consensus 45 ~~mTK~DIK~YLEk 58 (157)
.-+||.|||+||+-
T Consensus 15 ~Gls~eeir~FL~~ 28 (30)
T PF08671_consen 15 SGLSKEEIREFLEF 28 (30)
T ss_dssp TT--HHHHHHHHHH
T ss_pred cCCCHHHHHHHHHh
Confidence 35799999999974
No 42
>COG2004 RPS24A Ribosomal protein S24E [Translation, ribosomal structure and biogenesis]
Probab=29.32 E-value=1.4e+02 Score=22.97 Aligned_cols=42 Identities=14% Similarity=0.172 Sum_probs=33.3
Q ss_pred eCCCCCCCcEEEEEec----CCCCHHHHHHHHHHHhCceeeEEEee
Q psy5391 29 RSKEPLPPNVVEFHVP----LAMTNHDIKNYLEKIYNVTVKHVEST 70 (157)
Q Consensus 29 R~~~~l~pN~vtF~Vp----~~mTK~DIK~YLEkiYnVkV~~VnT~ 70 (157)
+.++.|.--.+.|.|. +.-||.|||+-|.++||++-..|-..
T Consensus 10 r~NpLL~RkEi~~~v~h~g~~TPSr~evrekla~~l~~d~e~VvV~ 55 (107)
T COG2004 10 RDNPLLKRKEIVFVVYHEGSPTPSRKEVREKLAAMLGADKELVVVD 55 (107)
T ss_pred ccCccccceEEEEEEEeCCCCCCCHHHHHHHHHHHHCCCcceEEEE
Confidence 5567778888888885 45599999999999999987766443
No 43
>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=28.83 E-value=1.1e+02 Score=16.95 Aligned_cols=36 Identities=25% Similarity=0.274 Sum_probs=29.3
Q ss_pred CcEEEEEecCCCCHHHHHHHHHHHhCceeeEEEeee
Q psy5391 36 PNVVEFHVPLAMTNHDIKNYLEKIYNVTVKHVESTL 71 (157)
Q Consensus 36 pN~vtF~Vp~~mTK~DIK~YLEkiYnVkV~~VnT~I 71 (157)
....++.++..+|=.|+++++.+.+|+....+.-..
T Consensus 7 ~~~~~~~~~~~~tv~~l~~~i~~~~~~~~~~~~l~~ 42 (69)
T cd00196 7 GKTVELLVPSGTTVADLKEKLAKKLGLPPEQQRLLV 42 (69)
T ss_pred CCEEEEEcCCCCcHHHHHHHHHHHHCcChHHeEEEE
Confidence 456788888999999999999999997666666553
No 44
>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=27.71 E-value=1.6e+02 Score=20.16 Aligned_cols=35 Identities=14% Similarity=0.082 Sum_probs=29.2
Q ss_pred CcEEEEEecCCCCHHHHHHHHHHHhCceeeEEEee
Q psy5391 36 PNVVEFHVPLAMTNHDIKNYLEKIYNVTVKHVEST 70 (157)
Q Consensus 36 pN~vtF~Vp~~mTK~DIK~YLEkiYnVkV~~VnT~ 70 (157)
...+.+.|++++|=.|+|+.+++..++++..-+-.
T Consensus 12 G~~~~~~v~~~~TV~~lK~~I~~~~~i~~~~qrL~ 46 (80)
T cd01792 12 GNEFLVSLRDSMTVSELKQQIAQKIGVPAFQQRLA 46 (80)
T ss_pred CCEEEEEcCCCCcHHHHHHHHHHHhCCCHHHEEEE
Confidence 35577899999999999999999999887766553
No 45
>PF12426 DUF3674: RNA dependent RNA polymerase; InterPro: IPR024378 This domain is found in the RNA-directed RNA polymerase. It is located towards the N terminus and is approximately 40 amino acids in length. There is a conserved MFNLKF sequence motif. There are two completely conserved residues (E and P) that may be functionally important.
Probab=27.49 E-value=41 Score=22.07 Aligned_cols=16 Identities=19% Similarity=0.470 Sum_probs=14.0
Q ss_pred HHHHHHHHHHHhCcee
Q psy5391 49 NHDIKNYLEKIYNVTV 64 (157)
Q Consensus 49 K~DIK~YLEkiYnVkV 64 (157)
|.|=|.+||.+||+|-
T Consensus 3 k~eER~aLEAMFNLKF 18 (41)
T PF12426_consen 3 KTEERSALEAMFNLKF 18 (41)
T ss_pred chhHHHHHHHHhceee
Confidence 6788999999999974
No 46
>PF01282 Ribosomal_S24e: Ribosomal protein S24e; InterPro: IPR001976 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 [, ]. This family contains the S24e ribosomal proteins from eukaryotes and archaebacteria. These proteins have 101 to 148 amino acids.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2V94_B 1YWX_A 2G1D_A 3IZ6_U 1XN9_A 2XZM_P 2XZN_P 3U5G_Y 3J16_D 3IZB_U ....
Probab=27.14 E-value=43 Score=24.13 Aligned_cols=23 Identities=17% Similarity=0.287 Sum_probs=17.5
Q ss_pred CCCCHHHHHHHHHHHhCceeeEE
Q psy5391 45 LAMTNHDIKNYLEKIYNVTVKHV 67 (157)
Q Consensus 45 ~~mTK~DIK~YLEkiYnVkV~~V 67 (157)
..-+|.||++-|.++||++...|
T Consensus 11 ~Tpsr~ei~~klA~~~~~~~~~i 33 (84)
T PF01282_consen 11 PTPSRKEIREKLAAMLNVDPDLI 33 (84)
T ss_dssp SS--HHHHHHHHHHHHTSTGCCE
T ss_pred CCCCHHHHHHHHHHHhCCCCCeE
Confidence 45689999999999999975543
No 47
>PF13356 DUF4102: Domain of unknown function (DUF4102); PDB: 3JU0_A 3RMP_A 3JTZ_A 2KJ8_A.
Probab=26.78 E-value=46 Score=23.26 Aligned_cols=27 Identities=37% Similarity=0.754 Sum_probs=17.2
Q ss_pred ccccceeeCCceec------------ceeEeeeecceee
Q psy5391 123 QNGLFIKINPIGTK------------DLLVLGVWGALSL 149 (157)
Q Consensus 123 ~~~~~~~~np~~tk------------~~~~~~~~~~~~~ 149 (157)
..||++.|+|.|+| ..+.+|.+.+++|
T Consensus 22 ~~GL~l~v~~~G~kt~~~r~~~~gk~~~~~lG~~p~~sl 60 (89)
T PF13356_consen 22 VPGLYLRVTPSGSKTFYFRYRINGKRRRITLGRYPELSL 60 (89)
T ss_dssp STTEEEEE-TTS-EEEEEEEEETTEEEEEEEEECTTS-H
T ss_pred CCCcEEEEEeCCCeEEEEEEEecceEEEeccCCCccCCH
Confidence 46999999999876 4556666666554
No 48
>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation. It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.
Probab=26.30 E-value=65 Score=23.84 Aligned_cols=27 Identities=22% Similarity=0.408 Sum_probs=16.0
Q ss_pred EEEE-ecCCCCHHHHHHHHHHHhCceeeEE
Q psy5391 39 VEFH-VPLAMTNHDIKNYLEKIYNVTVKHV 67 (157)
Q Consensus 39 vtF~-Vp~~mTK~DIK~YLEkiYnVkV~~V 67 (157)
+.|. ++...|+.|||+.+.. |+ +|..|
T Consensus 4 l~~~g~~~~~~re~iK~~f~~-~g-~V~yV 31 (105)
T PF08777_consen 4 LKFSGLGEPTSREDIKEAFSQ-FG-EVAYV 31 (105)
T ss_dssp EEEEE--SS--HHHHHHHT-S-S---EEEE
T ss_pred EEEecCCCCcCHHHHHHHHHh-cC-CcceE
Confidence 5677 8889999999999998 66 55554
No 49
>PF14259 RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....
Probab=25.70 E-value=51 Score=20.98 Aligned_cols=26 Identities=23% Similarity=0.554 Sum_probs=19.3
Q ss_pred ecCCCCHHHHHHHHHHHhCceeeEEEee
Q psy5391 43 VPLAMTNHDIKNYLEKIYNVTVKHVEST 70 (157)
Q Consensus 43 Vp~~mTK~DIK~YLEkiYnVkV~~VnT~ 70 (157)
+|.++|..||++.++.. | +|..|...
T Consensus 6 lp~~~~~~~l~~~f~~~-g-~v~~v~~~ 31 (70)
T PF14259_consen 6 LPPSTTEEDLRNFFSRF-G-PVEKVRLI 31 (70)
T ss_dssp STTT--HHHHHHHCTTS-S-BEEEEEEE
T ss_pred CCCCCCHHHHHHHHHhc-C-CcceEEEE
Confidence 68899999999999885 5 57777666
No 50
>PTZ00071 40S ribosomal protein S24; Provisional
Probab=24.79 E-value=2.4e+02 Score=22.40 Aligned_cols=32 Identities=28% Similarity=0.293 Sum_probs=26.8
Q ss_pred CCCCCCcEEEEEec----CCCCHHHHHHHHHHHhCc
Q psy5391 31 KEPLPPNVVEFHVP----LAMTNHDIKNYLEKIYNV 62 (157)
Q Consensus 31 ~~~l~pN~vtF~Vp----~~mTK~DIK~YLEkiYnV 62 (157)
++.|.-.++.|.|- ..-+|.||++-|.++|+|
T Consensus 16 NpLL~RkE~~~~v~Hpg~~TpSr~eirekLA~~~~v 51 (132)
T PTZ00071 16 NPLLNRKQFVVEVLHPGKGTVSKKDIKEKLAKQYKV 51 (132)
T ss_pred ccCcCcEEEEEEEEeCCCCCCCHHHHHHHHHHHhCC
Confidence 46778888888885 356999999999999994
No 51
>COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis]
Probab=24.47 E-value=1.1e+02 Score=23.45 Aligned_cols=48 Identities=25% Similarity=0.299 Sum_probs=37.7
Q ss_pred ccccchhhHHHHHhHhhhhccccceeeCCceec----------ceeEeeeecceeeeee
Q psy5391 104 YLSSGIITSAKRLMKCIKLQNGLFIKINPIGTK----------DLLVLGVWGALSLVKT 152 (157)
Q Consensus 104 ~l~~~~~~~~k~~~~~~~~~~~~~~~~np~~tk----------~~~~~~~~~~~~~~~~ 152 (157)
..|+|.+. +-+.+..++.-+-.-|.|||..-| --.++|++|+.-.|..
T Consensus 18 ~RerG~~p-lsr~l~ey~~Gd~V~I~IdpSv~kGmPh~rf~G~TG~Vvg~~g~ay~V~v 75 (98)
T COG2139 18 PRERGLSP-LSRYLQEYKVGDKVHIDIDPSVHKGMPHPRFQGKTGTVVGVRGRAYKVEV 75 (98)
T ss_pred ccccCCcc-hhhHHhhccCCCEEEEEeCcccccCCCCccccCcceEEEeccCCEEEEEE
Confidence 56667666 666778889888899999998865 3578999998887754
No 52
>PF02192 PI3K_p85B: PI3-kinase family, p85-binding domain; InterPro: IPR003113 This is the region of the p110 phosphatidylinositol 3-kinase (PI3-Kinase) that binds the p85 subunit.; GO: 0046934 phosphatidylinositol-4,5-bisphosphate 3-kinase activity, 0007165 signal transduction, 0005942 phosphatidylinositol 3-kinase complex; PDB: 3HIZ_A 3HHM_A 2RD0_A 4A55_A 2Y3A_A 2V1Y_A.
Probab=22.87 E-value=1.1e+02 Score=22.10 Aligned_cols=21 Identities=24% Similarity=0.183 Sum_probs=18.1
Q ss_pred EEEEecCCCCHHHHHHHHHHH
Q psy5391 39 VEFHVPLAMTNHDIKNYLEKI 59 (157)
Q Consensus 39 vtF~Vp~~mTK~DIK~YLEki 59 (157)
+++.|+.++|=.|||+.|++.
T Consensus 2 i~l~~~~~~Tl~~iK~~lw~~ 22 (78)
T PF02192_consen 2 IPLRVSRDATLSEIKEELWEE 22 (78)
T ss_dssp EEEEEETT-BHHHHHHHHHHH
T ss_pred eEEEccCcCcHHHHHHHHHHH
Confidence 789999999999999999864
No 53
>COG3978 Acetolactate synthase (isozyme II), small (regulatory) subunit [Function unknown]
Probab=22.60 E-value=1.8e+02 Score=21.73 Aligned_cols=36 Identities=19% Similarity=0.268 Sum_probs=30.1
Q ss_pred CCcEEEEEecCCCCHHHHHHHHHHHhCceeeEEEee
Q psy5391 35 PPNVVEFHVPLAMTNHDIKNYLEKIYNVTVKHVEST 70 (157)
Q Consensus 35 ~pN~vtF~Vp~~mTK~DIK~YLEkiYnVkV~~VnT~ 70 (157)
..-.+.|.|+-+=+=.-+.+-|||+|+|.-.+|.-.
T Consensus 43 ~~~nie~tV~s~R~~~lL~~QLeKl~Dv~~V~i~~~ 78 (86)
T COG3978 43 GNANIELTVDSDRSVDLLTSQLEKLYDVAHVEITQS 78 (86)
T ss_pred ccceEEEEEcCCCChHHHHHHHHHHccceeEEEeeh
Confidence 445689999999999999999999999987776543
No 54
>PRK04219 rpl5p 50S ribosomal protein L5P; Reviewed
Probab=22.50 E-value=1.1e+02 Score=25.33 Aligned_cols=48 Identities=21% Similarity=0.256 Sum_probs=34.3
Q ss_pred EeecCcEEEEeeCCCC-CCCcEEEEEecC--CCCHHHHHHHHHHHhCceee
Q psy5391 18 IFLPNFWMKLVRSKEP-LPPNVVEFHVPL--AMTNHDIKNYLEKIYNVTVK 65 (157)
Q Consensus 18 IFLPnf~~~LvR~~~~-l~pN~vtF~Vp~--~mTK~DIK~YLEkiYnVkV~ 65 (157)
+|==|+.+.+-|||-. ......+.+|+. ..||.|-.++++.-|||.|.
T Consensus 126 i~GmdI~ivt~rpg~rv~~r~~~~~~i~~~~~~~~~e~~~~~~~~~~~~~~ 176 (177)
T PRK04219 126 IFGMDVCVTLERPGYRVARRRRKRRKIPSRHRVTKEEAIEFLEENFGVEVV 176 (177)
T ss_pred cccccEEEEEcCCccchhhhhhccccCCCCceeCHHHHHHHHHHhcCeEEe
Confidence 3333566777777722 334555666764 46999999999999999985
No 55
>PF13592 HTH_33: Winged helix-turn helix
Probab=21.45 E-value=1e+02 Score=20.25 Aligned_cols=37 Identities=16% Similarity=0.143 Sum_probs=24.3
Q ss_pred CHHHHHHHHHHHhCceeeEEEeeeecCcceecccccccee
Q psy5391 48 TNHDIKNYLEKIYNVTVKHVESTLENATSMAEWVSWLAFQ 87 (157)
Q Consensus 48 TK~DIK~YLEkiYnVkV~~VnT~I~~gk~KR~~~~~~R~~ 87 (157)
|=.+|.++|++-|||.+ +..++-. =.+|.+.+|-++.
T Consensus 6 t~~~i~~~I~~~fgv~y-s~~~v~~--lL~r~G~s~~kp~ 42 (60)
T PF13592_consen 6 TLKEIAAYIEEEFGVKY-SPSGVYR--LLKRLGFSYQKPR 42 (60)
T ss_pred cHHHHHHHHHHHHCCEE-cHHHHHH--HHHHcCCccccCC
Confidence 56799999999999998 5554411 1344555554443
No 56
>PF10057 DUF2294: Uncharacterized conserved protein (DUF2294); InterPro: IPR018745 This domain of unknown function is found in a family of hypothetical bacterial proteins with no known function. It is also found at the C terminus of proteins provisionally annotated as response regulators.
Probab=21.04 E-value=1.4e+02 Score=22.22 Aligned_cols=25 Identities=24% Similarity=0.368 Sum_probs=22.2
Q ss_pred CHHHHHHHHHHHhCceeeEEEeeee
Q psy5391 48 TNHDIKNYLEKIYNVTVKHVESTLE 72 (157)
Q Consensus 48 TK~DIK~YLEkiYnVkV~~VnT~I~ 72 (157)
-+.++++++|.+-|++|.+.-+.+.
T Consensus 76 ~~~~l~~~ie~i~g~~V~~l~~D~~ 100 (118)
T PF10057_consen 76 LKPELKEMIEEILGVKVISLFSDIS 100 (118)
T ss_pred HHHHHHHHHHHHhCCeeEEEEEEcc
Confidence 4889999999999999999888754
No 57
>PF10281 Ish1: Putative stress-responsive nuclear envelope protein; InterPro: IPR018803 This group of proteins, found primarily in fungi, consists of putative stress-responsive nuclear envelope protein Ish1 and homologues [].
Probab=20.74 E-value=83 Score=19.11 Aligned_cols=19 Identities=21% Similarity=0.497 Sum_probs=14.9
Q ss_pred CCHHHHHHHHHHHhCceeeE
Q psy5391 47 MTNHDIKNYLEKIYNVTVKH 66 (157)
Q Consensus 47 mTK~DIK~YLEkiYnVkV~~ 66 (157)
-|-.|+++||++ +||++..
T Consensus 4 Ws~~~L~~wL~~-~gi~~~~ 22 (38)
T PF10281_consen 4 WSDSDLKSWLKS-HGIPVPK 22 (38)
T ss_pred CCHHHHHHHHHH-cCCCCCC
Confidence 366899999998 8887653
Done!