Query 030915
Match_columns 169
No_of_seqs 138 out of 1123
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 06:30:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030915.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030915hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 CHL00030 rpl23 ribosomal prote 99.9 3.6E-28 7.8E-33 180.3 8.1 87 14-102 2-91 (93)
2 PRK05738 rplW 50S ribosomal pr 99.9 7.4E-28 1.6E-32 177.8 8.0 86 14-101 2-91 (92)
3 PRK12280 rplW 50S ribosomal pr 99.9 5E-27 1.1E-31 188.6 8.6 97 11-109 2-101 (158)
4 PF00276 Ribosomal_L23: Riboso 99.9 2.5E-27 5.3E-32 174.2 4.7 86 13-100 1-90 (91)
5 COG0089 RplW Ribosomal protein 99.9 8.8E-26 1.9E-30 168.0 6.9 88 12-101 1-93 (94)
6 PRK14548 50S ribosomal protein 99.8 4.4E-21 9.5E-26 140.1 6.8 69 13-94 2-74 (84)
7 TIGR03636 L23_arch archaeal ri 99.8 3E-20 6.5E-25 133.7 6.7 63 19-94 1-67 (77)
8 KOG4089 Predicted mitochondria 99.8 5E-20 1.1E-24 148.4 7.2 103 1-103 1-120 (165)
9 PTZ00191 60S ribosomal protein 99.8 1.4E-19 3.1E-24 143.7 5.8 73 10-95 60-137 (145)
10 KOG1751 60s ribosomal protein 99.4 2.6E-13 5.7E-18 109.2 5.1 72 9-94 70-147 (157)
11 KOG4089 Predicted mitochondria 92.5 0.0046 9.9E-08 50.6 -5.2 93 12-107 12-105 (165)
12 PTZ00044 ubiquitin; Provisiona 71.9 9.1 0.0002 25.9 4.4 40 27-67 9-48 (76)
13 cd01769 UBL Ubiquitin-like dom 70.7 12 0.00026 24.0 4.5 38 28-66 7-44 (69)
14 cd01798 parkin_N amino-termina 68.6 12 0.00025 25.2 4.3 40 27-67 7-46 (70)
15 cd01799 Hoil1_N Ubiquitin-like 68.5 12 0.00027 26.1 4.5 45 21-67 5-49 (75)
16 PF14560 Ubiquitin_2: Ubiquiti 65.6 13 0.00028 26.2 4.2 36 29-64 14-49 (87)
17 cd01806 Nedd8 Nebb8-like ubiq 65.4 19 0.0004 24.0 4.8 38 29-67 11-48 (76)
18 PF00240 ubiquitin: Ubiquitin 64.8 12 0.00025 24.7 3.6 39 28-67 5-43 (69)
19 cd01789 Alp11_N Ubiquitin-like 63.2 25 0.00053 25.0 5.3 37 31-67 15-51 (84)
20 cd01803 Ubiquitin Ubiquitin. U 61.8 18 0.00039 24.0 4.2 38 29-67 11-48 (76)
21 smart00213 UBQ Ubiquitin homol 60.6 19 0.0004 22.8 3.9 34 29-62 10-43 (64)
22 cd01809 Scythe_N Ubiquitin-lik 59.2 24 0.00051 23.2 4.4 39 28-67 10-48 (72)
23 cd01796 DDI1_N DNA damage indu 57.6 21 0.00045 24.3 4.0 39 28-67 9-47 (71)
24 cd01807 GDX_N ubiquitin-like d 54.7 29 0.00063 23.5 4.3 39 28-67 10-48 (74)
25 cd01805 RAD23_N Ubiquitin-like 52.8 33 0.00072 23.0 4.3 40 27-67 9-50 (77)
26 cd01812 BAG1_N Ubiquitin-like 52.7 25 0.00055 23.1 3.7 34 29-62 10-43 (71)
27 cd01800 SF3a120_C Ubiquitin-li 49.7 40 0.00088 23.1 4.4 39 28-67 7-45 (76)
28 cd01813 UBP_N UBP ubiquitin pr 48.5 38 0.00082 23.4 4.1 35 29-63 10-44 (74)
29 PF03780 Asp23: Asp23 family; 47.5 28 0.00062 24.9 3.5 24 41-64 82-105 (108)
30 PRK01178 rps24e 30S ribosomal 47.2 34 0.00074 25.7 4.0 34 29-62 17-54 (99)
31 cd01802 AN1_N ubiquitin-like d 45.9 45 0.00098 24.7 4.4 39 28-67 37-75 (103)
32 cd01794 DC_UbP_C dendritic cel 45.3 50 0.0011 22.6 4.3 39 28-67 8-46 (70)
33 cd01793 Fubi Fubi ubiquitin-li 44.4 43 0.00093 22.7 3.9 38 29-67 9-46 (74)
34 PF14259 RRM_6: RNA recognitio 42.3 32 0.00069 22.2 2.9 43 34-90 5-48 (70)
35 cd01810 ISG15_repeat2 ISG15 ub 40.2 69 0.0015 21.7 4.4 39 28-67 8-46 (74)
36 cd04929 ACT_TPH ACT domain of 35.1 39 0.00085 23.6 2.5 25 29-53 41-65 (74)
37 cd01792 ISG15_repeat1 ISG15 ub 34.9 83 0.0018 21.7 4.2 39 29-67 13-52 (80)
38 PF08777 RRM_3: RNA binding mo 31.8 86 0.0019 23.3 4.0 45 31-93 4-49 (105)
39 cd01808 hPLIC_N Ubiquitin-like 31.6 83 0.0018 21.0 3.6 36 31-67 12-47 (71)
40 PF10411 DsbC_N: Disulfide bon 30.7 29 0.00062 23.0 1.2 23 44-66 1-24 (57)
41 PF01282 Ribosomal_S24e: Ribos 30.4 53 0.0012 23.7 2.6 25 37-61 11-35 (84)
42 PF09581 Spore_III_AF: Stage I 28.0 1.7E+02 0.0038 23.0 5.5 45 41-92 89-133 (188)
43 cd01791 Ubl5 UBL5 ubiquitin-li 27.7 1.5E+02 0.0033 20.4 4.5 38 29-67 12-49 (73)
44 TIGR01622 SF-CC1 splicing fact 27.5 2.1E+02 0.0046 25.4 6.5 33 29-63 91-123 (457)
45 PF00076 RRM_1: RNA recognitio 27.3 1.4E+02 0.0029 18.6 4.0 46 32-91 3-49 (70)
46 KOG3424 40S ribosomal protein 27.1 1E+02 0.0022 24.5 3.8 25 38-62 34-58 (132)
47 cd01804 midnolin_N Ubiquitin-l 25.8 1.6E+02 0.0034 20.3 4.3 38 29-67 12-49 (78)
48 COG1035 FrhB Coenzyme F420-red 22.8 1.7E+02 0.0037 26.5 5.0 45 35-95 182-227 (332)
49 PF12426 DUF3674: RNA dependen 22.6 52 0.0011 21.3 1.2 16 41-56 3-18 (41)
50 TIGR02830 spore_III_AG stage I 22.0 1E+02 0.0022 25.7 3.2 24 40-63 161-184 (186)
51 COG2004 RPS24A Ribosomal prote 21.9 2.2E+02 0.0049 21.8 4.8 34 29-62 18-55 (107)
52 PF08766 DEK_C: DEK C terminal 21.6 81 0.0018 20.5 2.0 20 38-57 20-39 (54)
53 cd04931 ACT_PAH ACT domain of 21.5 75 0.0016 23.1 2.0 25 28-52 54-79 (90)
54 cd01790 Herp_N Homocysteine-re 20.7 2.1E+02 0.0045 20.5 4.2 41 27-67 10-53 (79)
55 PLN03134 glycine-rich RNA-bind 20.3 3.3E+02 0.0072 21.0 5.6 51 29-93 36-88 (144)
56 TIGR01661 ELAV_HUD_SF ELAV/HuD 20.2 2.8E+02 0.0061 23.5 5.6 34 29-64 5-38 (352)
No 1
>CHL00030 rpl23 ribosomal protein L23
Probab=99.95 E-value=3.6e-28 Score=180.28 Aligned_cols=87 Identities=22% Similarity=0.327 Sum_probs=82.4
Q ss_pred CcceeecCCCCcccC---CeEEEEeCCCCCHHHHHHHHHHHhCCceeEEEeeecCCcccccCCcccCCCCceEEEEEcCC
Q 030915 14 NLPIKLLMPNTFQNI---TEIALKTIPSASKIEIKRVLESLYGFEVDKVRTLNMEGKKKKRGGLLIAKPDYKKAYVTLKN 90 (169)
Q Consensus 14 ni~ikpv~tEK~~~~---n~~~F~V~~~atK~eIK~alekiY~VkV~kVnT~~~~GK~kR~~~~~gk~~~~KKAyVtL~~ 90 (169)
+++++|++|||++.+ |+|+|.|+++|||.|||+|||.+|||+|.+|||++.+|+.+|.+++.|++++||||||||++
T Consensus 2 ~iI~~PivTEKs~~l~e~n~y~F~V~~~anK~eIK~avE~lf~VkV~~VNt~~~~~k~kr~~~~~G~~~~~KKAiVtL~~ 81 (93)
T CHL00030 2 DGIKYPVFTDKSIRLLEKNQYTFDVDSGSTKTEIKHWIELFFGVKVIAVNSHRLPRKKRRMGPIMGHKMHYKRMIITLQP 81 (93)
T ss_pred ceeccceeCHHHHHhhHCCEEEEEECCCCCHHHHHHHHHHHhCCeEEEEEEEEcCCCccccCCcccccCCcEEEEEEcCC
Confidence 578999999999864 99999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCccCCCCCccc
Q 030915 91 PLSLSEDLFPIR 102 (169)
Q Consensus 91 g~~i~PdlF~~k 102 (169)
|++|+ +|+..
T Consensus 82 g~~I~--~~~~~ 91 (93)
T CHL00030 82 GYSIP--LFREK 91 (93)
T ss_pred cCEec--ccccc
Confidence 99998 88653
No 2
>PRK05738 rplW 50S ribosomal protein L23; Reviewed
Probab=99.95 E-value=7.4e-28 Score=177.76 Aligned_cols=86 Identities=30% Similarity=0.453 Sum_probs=81.9
Q ss_pred CcceeecCCCCccc----CCeEEEEeCCCCCHHHHHHHHHHHhCCceeEEEeeecCCcccccCCcccCCCCceEEEEEcC
Q 030915 14 NLPIKLLMPNTFQN----ITEIALKTIPSASKIEIKRVLESLYGFEVDKVRTLNMEGKKKKRGGLLIAKPDYKKAYVTLK 89 (169)
Q Consensus 14 ni~ikpv~tEK~~~----~n~~~F~V~~~atK~eIK~alekiY~VkV~kVnT~~~~GK~kR~~~~~gk~~~~KKAyVtL~ 89 (169)
+++++|++|||++. .|+|+|.|+++|||+|||+|||++|||+|.+|||++++|+.+|.++..|++++||||||+|.
T Consensus 2 ~ii~~P~~TEKs~~~~e~~n~~~F~V~~~a~K~eIK~aie~lf~VkV~~VnT~~~~gk~kr~~~~~g~~~~~KKA~VtL~ 81 (92)
T PRK05738 2 DVIKRPVITEKSTLLMEKQNKYVFEVAPDATKPEIKAAVEKLFGVKVESVNTLNVKGKTKRFGRRIGKRSDWKKAIVTLA 81 (92)
T ss_pred ccccccccCHHHHHhHHhCCEEEEEECCCCCHHHHHHHHHHHcCCceeEEEEEEeCCceeeecccccccCCcEEEEEEcC
Confidence 58999999999985 59999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCccCCCCCcc
Q 030915 90 NPLSLSEDLFPI 101 (169)
Q Consensus 90 ~g~~i~PdlF~~ 101 (169)
+|++|+ +|+.
T Consensus 82 ~g~~i~--~~~~ 91 (92)
T PRK05738 82 EGQKID--FFGG 91 (92)
T ss_pred CCCEEe--cccC
Confidence 999999 8864
No 3
>PRK12280 rplW 50S ribosomal protein L23; Reviewed
Probab=99.94 E-value=5e-27 Score=188.56 Aligned_cols=97 Identities=31% Similarity=0.430 Sum_probs=89.0
Q ss_pred ecCCcceeecCCCCcccC---CeEEEEeCCCCCHHHHHHHHHHHhCCceeEEEeeecCCcccccCCcccCCCCceEEEEE
Q 030915 11 HFTNLPIKLLMPNTFQNI---TEIALKTIPSASKIEIKRVLESLYGFEVDKVRTLNMEGKKKKRGGLLIAKPDYKKAYVT 87 (169)
Q Consensus 11 flpni~ikpv~tEK~~~~---n~~~F~V~~~atK~eIK~alekiY~VkV~kVnT~~~~GK~kR~~~~~gk~~~~KKAyVt 87 (169)
.+.++|++|++||+++.+ |+|+|.|+++|||+|||+|||.||||+|.+|||+|++|+.+|.|++.|++++||||||+
T Consensus 2 d~~~iIk~PviTEKs~~l~e~N~ytF~V~~~anK~eIK~AVE~iF~VkV~~VNT~~~~~K~KR~g~~~G~~~~~KKAiVt 81 (158)
T PRK12280 2 NINEVIKKPILTEKSYSLMSKNVYTFKVDRRANKIEIKKAVEFIFKVKVLKVNIFNVDKKPKRLGRFPGFTNSYKKAYVT 81 (158)
T ss_pred ChHhhhhccccCHHHHhhhhCCEEEEEECCCCCHHHHHHHHHHHhCCceEEEEeEecCCcccccCCcccccCCcEEEEEE
Confidence 466899999999999853 99999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCccCCCCCccccchHHHH
Q 030915 88 LKNPLSLSEDLFPIRVIQDEKE 109 (169)
Q Consensus 88 L~~g~~i~PdlF~~k~~~~~~~ 109 (169)
|.+|++|+ ||+....+++.+
T Consensus 82 L~~g~~I~--~f~~~~~~~~~~ 101 (158)
T PRK12280 82 LAEGYSIN--LFPEESEKEQKE 101 (158)
T ss_pred CCCCCEee--ccCCcchhcchh
Confidence 99999999 998876444444
No 4
>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=99.94 E-value=2.5e-27 Score=174.19 Aligned_cols=86 Identities=36% Similarity=0.537 Sum_probs=77.8
Q ss_pred CCcceeecCCCCccc----CCeEEEEeCCCCCHHHHHHHHHHHhCCceeEEEeeecCCcccccCCcccCCCCceEEEEEc
Q 030915 13 TNLPIKLLMPNTFQN----ITEIALKTIPSASKIEIKRVLESLYGFEVDKVRTLNMEGKKKKRGGLLIAKPDYKKAYVTL 88 (169)
Q Consensus 13 pni~ikpv~tEK~~~----~n~~~F~V~~~atK~eIK~alekiY~VkV~kVnT~~~~GK~kR~~~~~gk~~~~KKAyVtL 88 (169)
.+++++|++|||++. +|+|+|.|+++|||+|||+|||++|||+|.+|||++++||.+|.|...|++++||||||+|
T Consensus 1 ~~ii~~p~iTeKs~~~~~~~n~~tF~V~~~atK~~Ik~aie~iy~V~V~~Vnt~~~~gk~kR~g~~~g~~~~~KKaiVtL 80 (91)
T PF00276_consen 1 YDIIKKPVITEKSMKLLENPNQYTFEVDPRATKTEIKEAIEKIYGVKVKKVNTMNYPGKKKRKGKFVGKTKDYKKAIVTL 80 (91)
T ss_dssp TTTEEEE--SHHHHHHHHHSSEEEEEETTTSTHHHHHHHHHHHHTSEEEEEEEEEETSEEEESSSCEEEE-EEEEEEEEE
T ss_pred CCEeecceecHhHHHhhhcCCEEEEEEeCCCCHHHHHHHHHhhcCCCeeEEEEeEeCCCceEeCCccccCCCcEEEEEEe
Confidence 478999999999764 5999999999999999999999999999999999999999999988889999999999999
Q ss_pred CCCCccCCCCCc
Q 030915 89 KNPLSLSEDLFP 100 (169)
Q Consensus 89 ~~g~~i~PdlF~ 100 (169)
.+|+.|+ +|+
T Consensus 81 ~~~~~i~--~~~ 90 (91)
T PF00276_consen 81 KEGDKIP--LFE 90 (91)
T ss_dssp STTSCHH--HHH
T ss_pred CCCCccc--ccc
Confidence 9999988 664
No 5
>COG0089 RplW Ribosomal protein L23 [Translation, ribosomal structure and biogenesis]
Probab=99.92 E-value=8.8e-26 Score=167.95 Aligned_cols=88 Identities=35% Similarity=0.467 Sum_probs=82.2
Q ss_pred cCCcceeecCCCCccc----CCeEEEEeCCCCCHHHHHHHHHHHhCCceeEEEeeecCCcccccCC-cccCCCCceEEEE
Q 030915 12 FTNLPIKLLMPNTFQN----ITEIALKTIPSASKIEIKRVLESLYGFEVDKVRTLNMEGKKKKRGG-LLIAKPDYKKAYV 86 (169)
Q Consensus 12 lpni~ikpv~tEK~~~----~n~~~F~V~~~atK~eIK~alekiY~VkV~kVnT~~~~GK~kR~~~-~~gk~~~~KKAyV 86 (169)
+.++|++|++|||++. .|+|+|.|+++|||+|||.|||.||||+|.+|||+|.+|+.||.+. +.|++++||+|||
T Consensus 1 ~~dvI~~PvvTEKa~~l~~~~nk~vF~V~~~AtK~~IK~AvE~lF~VkV~kVNTl~~k~k~KR~~~k~~G~~~~~kka~V 80 (94)
T COG0089 1 LYDVIKSPVVTEKAMLLMEKENKYVFIVDPDATKPEIKAAVEELFGVKVEKVNTLNTKGKTKRAGVKRIGLRKDYKKAYV 80 (94)
T ss_pred CcchhhcceecHHHHHhHhhCCEEEEEECCCCCHHHHHHHHHHHhCCeEEEEEEEEeCCcceEEeccccccCcccceeEE
Confidence 3578999999999985 3999999999999999999999999999999999999999999987 8999999999999
Q ss_pred EcCCCCccCCCCCcc
Q 030915 87 TLKNPLSLSEDLFPI 101 (169)
Q Consensus 87 tL~~g~~i~PdlF~~ 101 (169)
+|..|++|+ +|..
T Consensus 81 ~l~~G~~i~--~~~~ 93 (94)
T COG0089 81 TLKEGQSID--FFGG 93 (94)
T ss_pred EccCCCEEe--eccc
Confidence 999999988 7653
No 6
>PRK14548 50S ribosomal protein L23P; Provisional
Probab=99.84 E-value=4.4e-21 Score=140.12 Aligned_cols=69 Identities=29% Similarity=0.329 Sum_probs=63.7
Q ss_pred CCcceeecCCCCccc----CCeEEEEeCCCCCHHHHHHHHHHHhCCceeEEEeeecCCcccccCCcccCCCCceEEEEEc
Q 030915 13 TNLPIKLLMPNTFQN----ITEIALKTIPSASKIEIKRVLESLYGFEVDKVRTLNMEGKKKKRGGLLIAKPDYKKAYVTL 88 (169)
Q Consensus 13 pni~ikpv~tEK~~~----~n~~~F~V~~~atK~eIK~alekiY~VkV~kVnT~~~~GK~kR~~~~~gk~~~~KKAyVtL 88 (169)
.+++++|++|||++. .|+|+|.|+++|||.|||+|||++|||+|.+|||++.++ +||||||+|
T Consensus 2 ~~iI~~PviTEK~~~~~e~~n~y~F~V~~~anK~eIK~AvE~lf~VkV~~VnT~~~~~-------------~~KKA~V~L 68 (84)
T PRK14548 2 YSIIKYPLVTEKAMNLIEKENKLTFIVDRRATKPDIKRAVEELFDVKVEKVNTLITPK-------------GEKKAYVKL 68 (84)
T ss_pred ccchhccccCHHHHHHHHhCCEEEEEECCCCCHHHHHHHHHHHhCCceEEEEeEEcCC-------------CcEEEEEEe
Confidence 368999999999985 399999999999999999999999999999999999974 699999999
Q ss_pred CCCCcc
Q 030915 89 KNPLSL 94 (169)
Q Consensus 89 ~~g~~i 94 (169)
.+|++.
T Consensus 69 ~~g~~A 74 (84)
T PRK14548 69 AEEYDA 74 (84)
T ss_pred CCCCcH
Confidence 999874
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=99.81 E-value=3e-20 Score=133.74 Aligned_cols=63 Identities=32% Similarity=0.382 Sum_probs=58.3
Q ss_pred ecCCCCccc----CCeEEEEeCCCCCHHHHHHHHHHHhCCceeEEEeeecCCcccccCCcccCCCCceEEEEEcCCCCcc
Q 030915 19 LLMPNTFQN----ITEIALKTIPSASKIEIKRVLESLYGFEVDKVRTLNMEGKKKKRGGLLIAKPDYKKAYVTLKNPLSL 94 (169)
Q Consensus 19 pv~tEK~~~----~n~~~F~V~~~atK~eIK~alekiY~VkV~kVnT~~~~GK~kR~~~~~gk~~~~KKAyVtL~~g~~i 94 (169)
|++|||++. .|+|+|.|+++|||+|||+|||++|||+|.+|||++.++ +||||||+|.+|++.
T Consensus 1 P~iTEKs~~~~e~~n~y~F~V~~~anK~eIK~avE~lf~VkV~~Vnt~~~~~-------------~~KKA~VtL~~g~~a 67 (77)
T TIGR03636 1 PLVTEKAMNLIEKENKLTFIVDRKATKGDIKRAVEKLFDVKVEKVNTLITPR-------------GEKKAYVKLAEEYAA 67 (77)
T ss_pred CcccHHHHHHHHhCCEEEEEECCCCCHHHHHHHHHHHhCCceEEEEeEEcCC-------------CceEEEEEECCCCcH
Confidence 788999875 389999999999999999999999999999999999875 799999999999864
No 8
>KOG4089 consensus Predicted mitochondrial ribosomal protein L23 [Translation, ribosomal structure and biogenesis]
Probab=99.81 E-value=5e-20 Score=148.40 Aligned_cols=103 Identities=32% Similarity=0.364 Sum_probs=89.2
Q ss_pred CCccCCcc---------eeecCCcceeecCCCCcccCCeEEEEeCCCCCHHHHHHHHHHHhCCceeEEEeeecCC----c
Q 030915 1 MGSRLGTR---------VVHFTNLPIKLLMPNTFQNITEIALKTIPSASKIEIKRVLESLYGFEVDKVRTLNMEG----K 67 (169)
Q Consensus 1 ~~~r~g~r---------~Iflpni~ikpv~tEK~~~~n~~~F~V~~~atK~eIK~alekiY~VkV~kVnT~~~~G----K 67 (169)
|+|++|+| .|||||++|.++.|-..+++++++|.|++.+||.||++||+.|||++|.+|+|.++.| +
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 77777766 5888999999999888888999999999999999999999999999999999999999 4
Q ss_pred ccccCC---cccCCCCceEEEEEcCCCCccC-CCCCcccc
Q 030915 68 KKKRGG---LLIAKPDYKKAYVTLKNPLSLS-EDLFPIRV 103 (169)
Q Consensus 68 ~kR~~~---~~gk~~~~KKAyVtL~~g~~i~-PdlF~~k~ 103 (169)
.+.+-. .+.+..+++-|||.++.++++. ||+|+++.
T Consensus 81 ~k~r~~~~k~i~kdmd~p~~Yv~~pr~~~~~~Pd~~eek~ 120 (165)
T KOG4089|consen 81 TKKRLQSPKRIKKDMDEPVAYVEEPRGSKFSFPDFFEEKD 120 (165)
T ss_pred ceecccccceeecccccceeeecCCCCccccCCccchhhh
Confidence 444322 2334559999999999999999 99999887
No 9
>PTZ00191 60S ribosomal protein L23a; Provisional
Probab=99.78 E-value=1.4e-19 Score=143.75 Aligned_cols=73 Identities=26% Similarity=0.299 Sum_probs=66.4
Q ss_pred eecCCcceeecCCCCccc----CCeEEEEeCCCCCHHHHHHHHHHHhCCceeEEEeeecCCcccccCCcccCCCCceEEE
Q 030915 10 VHFTNLPIKLLMPNTFQN----ITEIALKTIPSASKIEIKRVLESLYGFEVDKVRTLNMEGKKKKRGGLLIAKPDYKKAY 85 (169)
Q Consensus 10 Iflpni~ikpv~tEK~~~----~n~~~F~V~~~atK~eIK~alekiY~VkV~kVnT~~~~GK~kR~~~~~gk~~~~KKAy 85 (169)
....++|.+|+.||+++. .|+|+|.|+++|||.|||+|||++|||+|.+|||+|.++ +|||||
T Consensus 60 md~~~IIk~Pl~TEKa~~~~E~~N~yvF~Vd~kAnK~qIK~AVEklf~VkV~kVNTli~p~-------------g~KKA~ 126 (145)
T PTZ00191 60 LDKYSIIKYPLTTEKAMKKIEDNNTLVFIVDQRANKTQIKKAVEKLYDVKVVKVNTLITPD-------------GLKKAY 126 (145)
T ss_pred CchhhhhhcccccHHHHHHHhhCCEEEEEEcCCCCHHHHHHHHHHHhCCeeEEEEeEEcCC-------------CceEEE
Confidence 344678999999999985 499999999999999999999999999999999999988 589999
Q ss_pred EEcCCCCc-cC
Q 030915 86 VTLKNPLS-LS 95 (169)
Q Consensus 86 VtL~~g~~-i~ 95 (169)
|+|.+|++ |+
T Consensus 127 V~L~~~~~aid 137 (145)
T PTZ00191 127 IRLSPDVDALD 137 (145)
T ss_pred EEECCCCcHHH
Confidence 99999997 54
No 10
>KOG1751 consensus 60s ribosomal protein L23 [Translation, ribosomal structure and biogenesis]
Probab=99.40 E-value=2.6e-13 Score=109.18 Aligned_cols=72 Identities=26% Similarity=0.288 Sum_probs=62.0
Q ss_pred eeecCCc-ceeecCCCCccc----CCeEEEEeCCCCCHHHHHHHHHHHhCCceeEEEeeecC-CcccccCCcccCCCCce
Q 030915 9 VVHFTNL-PIKLLMPNTFQN----ITEIALKTIPSASKIEIKRVLESLYGFEVDKVRTLNME-GKKKKRGGLLIAKPDYK 82 (169)
Q Consensus 9 ~Iflpni-~ikpv~tEK~~~----~n~~~F~V~~~atK~eIK~alekiY~VkV~kVnT~~~~-GK~kR~~~~~gk~~~~K 82 (169)
....+++ |..|+.||+++- .|+++|.|+..+||+|||++|.+||+++|.+|||+|.+ |. |
T Consensus 70 kld~y~~iik~plTtEsamKk~ednNtlvf~vd~kankhqiKqAVkkLyd~dvakvntli~p~g~--------------k 135 (157)
T KOG1751|consen 70 KLDHYAIIIKFPLTTESAMKKIEDNNTLVFIVDSKANKHQIKQAVKKLYDTDVAKVNTLIRPDGE--------------K 135 (157)
T ss_pred cchhhhhHhccccchhhhhcchhhCceeEEEEecccchHHHHHHHHHHhccchhhheeeecCCCc--------------e
Confidence 3444455 788889999874 59999999999999999999999999999999999865 54 8
Q ss_pred EEEEEcCCCCcc
Q 030915 83 KAYVTLKNPLSL 94 (169)
Q Consensus 83 KAyVtL~~g~~i 94 (169)
||||.|.++++.
T Consensus 136 kayv~la~dyda 147 (157)
T KOG1751|consen 136 KAYVRLAPDYDA 147 (157)
T ss_pred eEEEecCCchhH
Confidence 999999998864
No 11
>KOG4089 consensus Predicted mitochondrial ribosomal protein L23 [Translation, ribosomal structure and biogenesis]
Probab=92.50 E-value=0.0046 Score=50.57 Aligned_cols=93 Identities=25% Similarity=0.315 Sum_probs=70.3
Q ss_pred cCCcceeecCCCCcccCCeEEEEeCCCCCHHHHHHHHHHHhCCceeEEEeeecCCcccccCCcccCCCCceEEEEEcCCC
Q 030915 12 FTNLPIKLLMPNTFQNITEIALKTIPSASKIEIKRVLESLYGFEVDKVRTLNMEGKKKKRGGLLIAKPDYKKAYVTLKNP 91 (169)
Q Consensus 12 lpni~ikpv~tEK~~~~n~~~F~V~~~atK~eIK~alekiY~VkV~kVnT~~~~GK~kR~~~~~gk~~~~KKAyVtL~~g 91 (169)
+.|..++.++|...+.+-.- - ...+.+..+....+.+++++|.+++|+|+.++....+.......+++++++++..+
T Consensus 12 ~gn~q~rVf~Pn~~~~l~rp-~--~~q~p~~~~FrVp~~m~k~DvR~YL~~iY~l~v~~vrtrl~~Gk~~~~~k~r~~~~ 88 (165)
T KOG4089|consen 12 FGNPQLRVFFPNFWINLVRP-L--VTQPPKIVKFRVPMSMNKFDVRDYLTHIYDLPVVDVRTRLQHGKDYKKTKKRLQSP 88 (165)
T ss_pred cCCcceeEecchhHHhhhcc-c--ccCCCceEEEEcchhhccccHHHHHHHhcCCceeeeeeeeeechhhhcceeccccc
Confidence 45667788888887765331 1 11257788889999999999999999999999887777777777799999999998
Q ss_pred CccCCC-CCccccchHH
Q 030915 92 LSLSED-LFPIRVIQDE 107 (169)
Q Consensus 92 ~~i~Pd-lF~~k~~~~~ 107 (169)
..|..| .++-.-+++.
T Consensus 89 k~i~kdmd~p~~Yv~~p 105 (165)
T KOG4089|consen 89 KRIKKDMDEPVAYVEEP 105 (165)
T ss_pred ceeecccccceeeecCC
Confidence 888844 6665544433
No 12
>PTZ00044 ubiquitin; Provisional
Probab=71.85 E-value=9.1 Score=25.86 Aligned_cols=40 Identities=20% Similarity=0.355 Sum_probs=35.2
Q ss_pred cCCeEEEEeCCCCCHHHHHHHHHHHhCCceeEEEeeecCCc
Q 030915 27 NITEIALKTIPSASKIEIKRVLESLYGFEVDKVRTLNMEGK 67 (169)
Q Consensus 27 ~~n~~~F~V~~~atK~eIK~alekiY~VkV~kVnT~~~~GK 67 (169)
.-+++++.|++..|=.+||+.|+...|+++...+.. +.|+
T Consensus 9 ~G~~~~l~v~~~~tv~~lK~~i~~~~gi~~~~q~L~-~~g~ 48 (76)
T PTZ00044 9 TGKKQSFNFEPDNTVQQVKMALQEKEGIDVKQIRLI-YSGK 48 (76)
T ss_pred CCCEEEEEECCCCcHHHHHHHHHHHHCCCHHHeEEE-ECCE
Confidence 346789999999999999999999999999888877 6675
No 13
>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=70.70 E-value=12 Score=24.04 Aligned_cols=38 Identities=18% Similarity=0.240 Sum_probs=32.2
Q ss_pred CCeEEEEeCCCCCHHHHHHHHHHHhCCceeEEEeeecCC
Q 030915 28 ITEIALKTIPSASKIEIKRVLESLYGFEVDKVRTLNMEG 66 (169)
Q Consensus 28 ~n~~~F~V~~~atK~eIK~alekiY~VkV~kVnT~~~~G 66 (169)
...+.|.+++.+|=.++|+.|+..+++++..+.. ...|
T Consensus 7 ~~~~~~~~~~~~ti~~lK~~i~~~~~~~~~~~~l-~~~g 44 (69)
T cd01769 7 GKTFELEVSPDDTVAELKAKIAAKEGVPPEQQRL-IYAG 44 (69)
T ss_pred CCEEEEEECCCChHHHHHHHHHHHHCcChHHEEE-EECC
Confidence 4667899999999999999999999999988766 4444
No 14
>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=68.62 E-value=12 Score=25.19 Aligned_cols=40 Identities=20% Similarity=0.304 Sum_probs=34.3
Q ss_pred cCCeEEEEeCCCCCHHHHHHHHHHHhCCceeEEEeeecCCc
Q 030915 27 NITEIALKTIPSASKIEIKRVLESLYGFEVDKVRTLNMEGK 67 (169)
Q Consensus 27 ~~n~~~F~V~~~atK~eIK~alekiY~VkV~kVnT~~~~GK 67 (169)
.-.++++.|++..|=.+||+.|+...|+++..... ++.|+
T Consensus 7 ~g~~~~~~v~~~~tV~~lK~~i~~~~gi~~~~q~L-i~~G~ 46 (70)
T cd01798 7 TGHTFPVEVDPDTDIKQLKEVVAKRQGVPPDQLRV-IFAGK 46 (70)
T ss_pred CCCEEEEEECCCChHHHHHHHHHHHHCCCHHHeEE-EECCe
Confidence 34678899999999999999999999999987655 57775
No 15
>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=68.51 E-value=12 Score=26.13 Aligned_cols=45 Identities=20% Similarity=0.237 Sum_probs=37.8
Q ss_pred CCCCcccCCeEEEEeCCCCCHHHHHHHHHHHhCCceeEEEeeecCCc
Q 030915 21 MPNTFQNITEIALKTIPSASKIEIKRVLESLYGFEVDKVRTLNMEGK 67 (169)
Q Consensus 21 ~tEK~~~~n~~~F~V~~~atK~eIK~alekiY~VkV~kVnT~~~~GK 67 (169)
+-.+.....++++.|++.+|=.+||+.|+..+|+++..-+. +.|+
T Consensus 5 ~~~~~~~~~t~~l~v~~~~TV~~lK~kI~~~~gip~~~QrL--~~G~ 49 (75)
T cd01799 5 VEDAQSHTVTIWLTVRPDMTVAQLKDKVFLDYGFPPAVQRW--VIGQ 49 (75)
T ss_pred EeccccCCCeEEEEECCCCcHHHHHHHHHHHHCcCHHHEEE--EcCC
Confidence 44556667889999999999999999999999999987766 6664
No 16
>PF14560 Ubiquitin_2: Ubiquitin-like domain; PDB: 1WJN_A 2KJ6_A 2KJR_A 1V6E_A 1T0Y_A.
Probab=65.64 E-value=13 Score=26.21 Aligned_cols=36 Identities=22% Similarity=0.207 Sum_probs=31.5
Q ss_pred CeEEEEeCCCCCHHHHHHHHHHHhCCceeEEEeeec
Q 030915 29 TEIALKTIPSASKIEIKRVLESLYGFEVDKVRTLNM 64 (169)
Q Consensus 29 n~~~F~V~~~atK~eIK~alekiY~VkV~kVnT~~~ 64 (169)
..+.-++++.+|=.|+|.-|+.++|+++...+....
T Consensus 14 ~~~ekr~~~~~Tv~eLK~kl~~~~Gi~~~~m~L~l~ 49 (87)
T PF14560_consen 14 RSVEKRFPKSITVSELKQKLEKLTGIPPSDMRLQLK 49 (87)
T ss_dssp SEEEEEEETTSBHHHHHHHHHHHHTS-TTTEEEEEE
T ss_pred eeEEEEcCCCCCHHHHHHHHHHHhCCCcccEEEEEE
Confidence 467788999999999999999999999999888765
No 17
>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=65.39 E-value=19 Score=23.96 Aligned_cols=38 Identities=26% Similarity=0.363 Sum_probs=33.2
Q ss_pred CeEEEEeCCCCCHHHHHHHHHHHhCCceeEEEeeecCCc
Q 030915 29 TEIALKTIPSASKIEIKRVLESLYGFEVDKVRTLNMEGK 67 (169)
Q Consensus 29 n~~~F~V~~~atK~eIK~alekiY~VkV~kVnT~~~~GK 67 (169)
..+.+.|++..|=.+||+.|+..+|+++...+.. +.|+
T Consensus 11 ~~~~~~v~~~~tv~~lK~~i~~~~g~~~~~qrL~-~~g~ 48 (76)
T cd01806 11 KEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLI-YSGK 48 (76)
T ss_pred CEEEEEECCCCCHHHHHHHHhHhhCCChhhEEEE-ECCe
Confidence 4577899999999999999999999999987776 6664
No 18
>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=64.83 E-value=12 Score=24.72 Aligned_cols=39 Identities=18% Similarity=0.316 Sum_probs=33.7
Q ss_pred CCeEEEEeCCCCCHHHHHHHHHHHhCCceeEEEeeecCCc
Q 030915 28 ITEIALKTIPSASKIEIKRVLESLYGFEVDKVRTLNMEGK 67 (169)
Q Consensus 28 ~n~~~F~V~~~atK~eIK~alekiY~VkV~kVnT~~~~GK 67 (169)
-..+.+.|++..|=.++|+.|+...++++...+.+ +.|+
T Consensus 5 g~~~~~~v~~~~tV~~lK~~i~~~~~~~~~~~~L~-~~G~ 43 (69)
T PF00240_consen 5 GKTFTLEVDPDDTVADLKQKIAEETGIPPEQQRLI-YNGK 43 (69)
T ss_dssp SEEEEEEEETTSBHHHHHHHHHHHHTSTGGGEEEE-ETTE
T ss_pred CcEEEEEECCCCCHHHhhhhcccccccccccceee-eeee
Confidence 35789999999999999999999999999888765 4554
No 19
>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=63.21 E-value=25 Score=24.95 Aligned_cols=37 Identities=22% Similarity=0.258 Sum_probs=32.7
Q ss_pred EEEEeCCCCCHHHHHHHHHHHhCCceeEEEeeecCCc
Q 030915 31 IALKTIPSASKIEIKRVLESLYGFEVDKVRTLNMEGK 67 (169)
Q Consensus 31 ~~F~V~~~atK~eIK~alekiY~VkV~kVnT~~~~GK 67 (169)
..-++++.+|=.++|+-|+.++|+++...+...+.++
T Consensus 15 ~ekr~~~~~Tv~~lK~kl~~~~G~~~~~mrL~l~~~~ 51 (84)
T cd01789 15 FEKKYSRGLTIAELKKKLELVVGTPASSMRLQLFDGD 51 (84)
T ss_pred eeEecCCCCcHHHHHHHHHHHHCCCccceEEEEEcCC
Confidence 4556999999999999999999999999999777765
No 20
>cd01803 Ubiquitin Ubiquitin. Ubiquitin (includes Ubq/RPL40e and Ubq/RPS27a fusions as well as homopolymeric multiubiquitin protein chains)
Probab=61.76 E-value=18 Score=24.01 Aligned_cols=38 Identities=26% Similarity=0.405 Sum_probs=32.7
Q ss_pred CeEEEEeCCCCCHHHHHHHHHHHhCCceeEEEeeecCCc
Q 030915 29 TEIALKTIPSASKIEIKRVLESLYGFEVDKVRTLNMEGK 67 (169)
Q Consensus 29 n~~~F~V~~~atK~eIK~alekiY~VkV~kVnT~~~~GK 67 (169)
..+.+.|++..|=.+||+.|+...++++...+.. +.|+
T Consensus 11 ~~~~~~v~~~~tV~~lK~~i~~~~g~~~~~q~L~-~~g~ 48 (76)
T cd01803 11 KTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLI-FAGK 48 (76)
T ss_pred CEEEEEECCcCcHHHHHHHHHHHhCCCHHHeEEE-ECCE
Confidence 4678999999999999999999999999887766 5564
No 21
>smart00213 UBQ Ubiquitin homologues. Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression
Probab=60.56 E-value=19 Score=22.77 Aligned_cols=34 Identities=29% Similarity=0.460 Sum_probs=29.9
Q ss_pred CeEEEEeCCCCCHHHHHHHHHHHhCCceeEEEee
Q 030915 29 TEIALKTIPSASKIEIKRVLESLYGFEVDKVRTL 62 (169)
Q Consensus 29 n~~~F~V~~~atK~eIK~alekiY~VkV~kVnT~ 62 (169)
..+.+.|++.+|=.++|+.|+..+++++...+.+
T Consensus 10 ~~~~~~v~~~~tv~~lk~~i~~~~~~~~~~~~L~ 43 (64)
T smart00213 10 GTITLEVKPSDTVSELKEKIAELTGIPVEQQRLI 43 (64)
T ss_pred ceEEEEECCCCcHHHHHHHHHHHHCCCHHHEEEE
Confidence 4688999999999999999999999998776654
No 22
>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=59.18 E-value=24 Score=23.18 Aligned_cols=39 Identities=13% Similarity=0.280 Sum_probs=33.0
Q ss_pred CCeEEEEeCCCCCHHHHHHHHHHHhCCceeEEEeeecCCc
Q 030915 28 ITEIALKTIPSASKIEIKRVLESLYGFEVDKVRTLNMEGK 67 (169)
Q Consensus 28 ~n~~~F~V~~~atK~eIK~alekiY~VkV~kVnT~~~~GK 67 (169)
-.+++|.|++..|=.++|+.|+..+|+++...+.. +.|+
T Consensus 10 g~~~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~-~~g~ 48 (72)
T cd01809 10 SQTHTFTVEEEITVLDLKEKIAEEVGIPVEQQRLI-YSGR 48 (72)
T ss_pred CCEEEEEECCCCcHHHHHHHHHHHHCcCHHHeEEE-ECCE
Confidence 36789999999999999999999999998877665 4554
No 23
>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=57.62 E-value=21 Score=24.33 Aligned_cols=39 Identities=18% Similarity=0.213 Sum_probs=33.1
Q ss_pred CCeEEEEeCCCCCHHHHHHHHHHHhCCceeEEEeeecCCc
Q 030915 28 ITEIALKTIPSASKIEIKRVLESLYGFEVDKVRTLNMEGK 67 (169)
Q Consensus 28 ~n~~~F~V~~~atK~eIK~alekiY~VkV~kVnT~~~~GK 67 (169)
.+++++.|++.+|=.++|+.|+..+|+++...+. ++.|+
T Consensus 9 g~~~~l~v~~~~TV~~lK~~I~~~~gip~~~q~L-i~~Gk 47 (71)
T cd01796 9 ETTFSLDVDPDLELENFKALCEAESGIPASQQQL-IYNGR 47 (71)
T ss_pred CCEEEEEECCcCCHHHHHHHHHHHhCCCHHHeEE-EECCe
Confidence 4668899999999999999999999999977644 46675
No 24
>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=54.69 E-value=29 Score=23.48 Aligned_cols=39 Identities=21% Similarity=0.279 Sum_probs=33.8
Q ss_pred CCeEEEEeCCCCCHHHHHHHHHHHhCCceeEEEeeecCCc
Q 030915 28 ITEIALKTIPSASKIEIKRVLESLYGFEVDKVRTLNMEGK 67 (169)
Q Consensus 28 ~n~~~F~V~~~atK~eIK~alekiY~VkV~kVnT~~~~GK 67 (169)
-+.+++.|++..|=.++|+.|+...|+++...+.. +.|+
T Consensus 10 G~~~~l~v~~~~tV~~lK~~i~~~~gi~~~~q~L~-~~G~ 48 (74)
T cd01807 10 GRECSLQVSEKESVSTLKKLVSEHLNVPEEQQRLL-FKGK 48 (74)
T ss_pred CCEEEEEECCCCcHHHHHHHHHHHHCCCHHHeEEE-ECCE
Confidence 46688999999999999999999999999887664 6775
No 25
>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=52.78 E-value=33 Score=23.03 Aligned_cols=40 Identities=18% Similarity=0.312 Sum_probs=32.8
Q ss_pred cCCeEEEEeCCCCCHHHHHHHHHHHhCC--ceeEEEeeecCCc
Q 030915 27 NITEIALKTIPSASKIEIKRVLESLYGF--EVDKVRTLNMEGK 67 (169)
Q Consensus 27 ~~n~~~F~V~~~atK~eIK~alekiY~V--kV~kVnT~~~~GK 67 (169)
..+++++.|++..|=.++|+.|+..+|+ ++...... +.|+
T Consensus 9 ~g~~~~l~v~~~~TV~~lK~~i~~~~~i~~~~~~q~L~-~~G~ 50 (77)
T cd01805 9 KQQTFPIEVDPDDTVAELKEKIEEEKGCDYPPEQQKLI-YSGK 50 (77)
T ss_pred CCCEEEEEECCCCcHHHHHHHHHHhhCCCCChhHeEEE-ECCE
Confidence 3467899999999999999999999999 87776654 4454
No 26
>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=52.73 E-value=25 Score=23.12 Aligned_cols=34 Identities=18% Similarity=0.244 Sum_probs=30.1
Q ss_pred CeEEEEeCCCCCHHHHHHHHHHHhCCceeEEEee
Q 030915 29 TEIALKTIPSASKIEIKRVLESLYGFEVDKVRTL 62 (169)
Q Consensus 29 n~~~F~V~~~atK~eIK~alekiY~VkV~kVnT~ 62 (169)
..+.+.|++.+|=.++|+.|+...|+++...+..
T Consensus 10 ~~~~i~v~~~~tv~~lK~~i~~~~gi~~~~q~L~ 43 (71)
T cd01812 10 ESHDLSISSQATFGDLKKMLAPVTGVEPRDQKLI 43 (71)
T ss_pred EEEEEEECCCCcHHHHHHHHHHhhCCChHHeEEe
Confidence 4577889999999999999999999999877665
No 27
>cd01800 SF3a120_C Ubiquitin-like domain of Mammalian splicing factor SF3a_120. SF3a120_C Mammalian splicing factor SF3a consists of three subunits of 60, 66, and 120 kDa and functions early during pre-mRNA splicing by converting the U2 snRNP to its active form. The 120kDa subunit (SF3a120) has a carboxy-terminal ubiquitin-like domain and two SWAP (suppressor-of-white-apricot) domains, referred to collectively as the SURP module, at its amino-terminus.
Probab=49.71 E-value=40 Score=23.06 Aligned_cols=39 Identities=15% Similarity=0.069 Sum_probs=33.0
Q ss_pred CCeEEEEeCCCCCHHHHHHHHHHHhCCceeEEEeeecCCc
Q 030915 28 ITEIALKTIPSASKIEIKRVLESLYGFEVDKVRTLNMEGK 67 (169)
Q Consensus 28 ~n~~~F~V~~~atK~eIK~alekiY~VkV~kVnT~~~~GK 67 (169)
-.++++.|++.+|=.++|+.|+...|+++.....+ +.|+
T Consensus 7 g~~~~l~v~~~~TV~~lK~~i~~~~gip~~~q~L~-~~G~ 45 (76)
T cd01800 7 GQMLNFTLQLSDPVSVLKVKIHEETGMPAGKQKLQ-YEGI 45 (76)
T ss_pred CeEEEEEECCCCcHHHHHHHHHHHHCCCHHHEEEE-ECCE
Confidence 36788999999999999999999999999876554 5563
No 28
>cd01813 UBP_N UBP ubiquitin processing protease. The UBP (ubiquitin processing protease) domain (also referred to as USP which stands for "ubiquitin-specific protease") is present at in a large family of cysteine proteases that specifically cleave ubiquitin conjugates. This family includes Rpn11, UBP6 (USP14), USP7 (HAUSP). This domain is closely related to the amino-terminal ubiquitin-like domain of BAG1 (Bcl2-associated anthanogene1) protein and is found only in eukaryotes.
Probab=48.48 E-value=38 Score=23.45 Aligned_cols=35 Identities=17% Similarity=0.418 Sum_probs=31.8
Q ss_pred CeEEEEeCCCCCHHHHHHHHHHHhCCceeEEEeee
Q 030915 29 TEIALKTIPSASKIEIKRVLESLYGFEVDKVRTLN 63 (169)
Q Consensus 29 n~~~F~V~~~atK~eIK~alekiY~VkV~kVnT~~ 63 (169)
.+|.+.|++.+|=.++|+.|+...||++..-..+-
T Consensus 10 ~~~~v~v~~~~Tv~~lK~~i~~~tgvp~~~QKLi~ 44 (74)
T cd01813 10 QEYSVTTLSEDTVLDLKQFIKTLTGVLPERQKLLG 44 (74)
T ss_pred EEEEEEECCCCCHHHHHHHHHHHHCCCHHHEEEEe
Confidence 56788999999999999999999999999888875
No 29
>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=47.54 E-value=28 Score=24.94 Aligned_cols=24 Identities=25% Similarity=0.379 Sum_probs=21.4
Q ss_pred HHHHHHHHHHHhCCceeEEEeeec
Q 030915 41 KIEIKRVLESLYGFEVDKVRTLNM 64 (169)
Q Consensus 41 K~eIK~alekiY~VkV~kVnT~~~ 64 (169)
...|+++|+.+-|++|.+||..+.
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 678999999999999999998753
No 30
>PRK01178 rps24e 30S ribosomal protein S24e; Reviewed
Probab=47.18 E-value=34 Score=25.73 Aligned_cols=34 Identities=15% Similarity=0.302 Sum_probs=25.8
Q ss_pred CeEEEEeC----CCCCHHHHHHHHHHHhCCceeEEEee
Q 030915 29 TEIALKTI----PSASKIEIKRVLESLYGFEVDKVRTL 62 (169)
Q Consensus 29 n~~~F~V~----~~atK~eIK~alekiY~VkV~kVnT~ 62 (169)
.++.|.|. +..+|.||++.|.++|+.+..-|=..
T Consensus 17 ke~~~~v~h~g~~tpsr~eirekLa~~~~~~~~~vvv~ 54 (99)
T PRK01178 17 REIKFEVYHEGSATPSRKDVRKKLAAMLNADKELVVVR 54 (99)
T ss_pred EEEEEEEEeCCCCCCCHHHHHHHHHHHHCcCCCEEEEE
Confidence 66777653 45699999999999999776555443
No 31
>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=45.90 E-value=45 Score=24.73 Aligned_cols=39 Identities=21% Similarity=0.215 Sum_probs=33.3
Q ss_pred CCeEEEEeCCCCCHHHHHHHHHHHhCCceeEEEeeecCCc
Q 030915 28 ITEIALKTIPSASKIEIKRVLESLYGFEVDKVRTLNMEGK 67 (169)
Q Consensus 28 ~n~~~F~V~~~atK~eIK~alekiY~VkV~kVnT~~~~GK 67 (169)
..++++.|++.+|=.+||+.|+..+|+++...+. ++.|+
T Consensus 37 G~~~~leV~~~~TV~~lK~kI~~~~gip~~~QrL-i~~Gk 75 (103)
T cd01802 37 GTCFELRVSPFETVISVKAKIQRLEGIPVAQQHL-IWNNM 75 (103)
T ss_pred CCEEEEEeCCCCcHHHHHHHHHHHhCCChHHEEE-EECCE
Confidence 3678999999999999999999999999977554 56775
No 32
>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=45.30 E-value=50 Score=22.58 Aligned_cols=39 Identities=18% Similarity=0.176 Sum_probs=33.5
Q ss_pred CCeEEEEeCCCCCHHHHHHHHHHHhCCceeEEEeeecCCc
Q 030915 28 ITEIALKTIPSASKIEIKRVLESLYGFEVDKVRTLNMEGK 67 (169)
Q Consensus 28 ~n~~~F~V~~~atK~eIK~alekiY~VkV~kVnT~~~~GK 67 (169)
-.+.++.|++.+|=.+||+.|+...|+++...+. ++.|+
T Consensus 8 G~~~~l~v~~~~TV~~lK~~I~~~~gi~~~~q~L-i~~G~ 46 (70)
T cd01794 8 GKDVKLSVSSKDTVGQLKKQLQAAEGVDPCCQRW-FFSGK 46 (70)
T ss_pred CCEEEEEECCcChHHHHHHHHHHHhCCCHHHeEE-EECCe
Confidence 4678899999999999999999999999987654 57775
No 33
>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=44.37 E-value=43 Score=22.70 Aligned_cols=38 Identities=18% Similarity=0.244 Sum_probs=33.0
Q ss_pred CeEEEEeCCCCCHHHHHHHHHHHhCCceeEEEeeecCCc
Q 030915 29 TEIALKTIPSASKIEIKRVLESLYGFEVDKVRTLNMEGK 67 (169)
Q Consensus 29 n~~~F~V~~~atK~eIK~alekiY~VkV~kVnT~~~~GK 67 (169)
++.++.|++..|=.++|+.|+...|+++...+. ++.|+
T Consensus 9 ~~~~l~v~~~~tV~~lK~~i~~~~gip~~~q~L-i~~Gk 46 (74)
T cd01793 9 NTHTLEVTGQETVSDIKAHVAGLEGIDVEDQVL-LLAGV 46 (74)
T ss_pred CEEEEEECCcCcHHHHHHHHHhhhCCCHHHEEE-EECCe
Confidence 578999999999999999999999999988754 56675
No 34
>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=42.34 E-value=32 Score=22.20 Aligned_cols=43 Identities=23% Similarity=0.460 Sum_probs=29.9
Q ss_pred EeCCCCCHHHHHHHHHHHhCCceeEEEeeecC-CcccccCCcccCCCCceEEEEEcCC
Q 030915 34 KTIPSASKIEIKRVLESLYGFEVDKVRTLNME-GKKKKRGGLLIAKPDYKKAYVTLKN 90 (169)
Q Consensus 34 ~V~~~atK~eIK~alekiY~VkV~kVnT~~~~-GK~kR~~~~~gk~~~~KKAyVtL~~ 90 (169)
.+++.+|..||++.++.. | +|..|.....+ | .....|||++..
T Consensus 5 nlp~~~~~~~l~~~f~~~-g-~v~~v~~~~~~~~------------~~~~~a~v~f~~ 48 (70)
T PF14259_consen 5 NLPPSTTEEDLRNFFSRF-G-PVEKVRLIKNKDG------------QSRGFAFVEFSS 48 (70)
T ss_dssp SSTTT--HHHHHHHCTTS-S-BEEEEEEEESTTS------------SEEEEEEEEESS
T ss_pred CCCCCCCHHHHHHHHHhc-C-CcceEEEEeeecc------------ccCCEEEEEeCC
Confidence 478899999999999885 5 58888777432 2 234689999973
No 35
>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=40.24 E-value=69 Score=21.66 Aligned_cols=39 Identities=10% Similarity=0.114 Sum_probs=32.8
Q ss_pred CCeEEEEeCCCCCHHHHHHHHHHHhCCceeEEEeeecCCc
Q 030915 28 ITEIALKTIPSASKIEIKRVLESLYGFEVDKVRTLNMEGK 67 (169)
Q Consensus 28 ~n~~~F~V~~~atK~eIK~alekiY~VkV~kVnT~~~~GK 67 (169)
-.++++.|++.+|=.+||+.|+...|+++..-.. ++.|+
T Consensus 8 g~~~~l~v~~~~tV~~lK~~I~~~~gi~~~~q~L-~~~G~ 46 (74)
T cd01810 8 GRSSIYEVQLTQTVATLKQQVSQRERVQADQFWL-SFEGR 46 (74)
T ss_pred CCEEEEEECCcChHHHHHHHHHHHhCCCHHHeEE-EECCE
Confidence 3668899999999999999999999998877655 46665
No 36
>cd04929 ACT_TPH ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. TPH catalyses the hydroxylation of L-Trp to 5-hydroxytryptophan, the rate limiting step in the biosynthesis of 5-hydroxytryptamine (serotonin) and the first reaction in the synthesis of melatonin. Very little is known about the role of the ACT domain in TPH, which appears to be regulated by phosphorylation but not by its substrate or cofactor. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=35.11 E-value=39 Score=23.57 Aligned_cols=25 Identities=8% Similarity=0.098 Sum_probs=22.0
Q ss_pred CeEEEEeCCCCCHHHHHHHHHHHhC
Q 030915 29 TEIALKTIPSASKIEIKRVLESLYG 53 (169)
Q Consensus 29 n~~~F~V~~~atK~eIK~alekiY~ 53 (169)
..|.|.|+.+.+..+|+++|+.+=.
T Consensus 41 ~~y~F~id~e~~~~~i~~~l~~l~~ 65 (74)
T cd04929 41 SEFEIFVDCECDQRRLDELVQLLKR 65 (74)
T ss_pred ceEEEEEEEEcCHHHHHHHHHHHHH
Confidence 6799999999999999999998743
No 37
>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=34.86 E-value=83 Score=21.69 Aligned_cols=39 Identities=15% Similarity=0.080 Sum_probs=31.8
Q ss_pred CeEEEEeCCCCCHHHHHHHHHHHhCCceeEEEee-ecCCc
Q 030915 29 TEIALKTIPSASKIEIKRVLESLYGFEVDKVRTL-NMEGK 67 (169)
Q Consensus 29 n~~~F~V~~~atK~eIK~alekiY~VkV~kVnT~-~~~GK 67 (169)
.++++.|++.+|=.|+|+.|+..+++++..-+.. +..|+
T Consensus 13 ~~~~~~v~~~~TV~~lK~~I~~~~~i~~~~qrL~~~~~G~ 52 (80)
T cd01792 13 NEFLVSLRDSMTVSELKQQIAQKIGVPAFQQRLAHLDSRE 52 (80)
T ss_pred CEEEEEcCCCCcHHHHHHHHHHHhCCCHHHEEEEeccCCC
Confidence 5577789999999999999999999988777664 34553
No 38
>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=31.79 E-value=86 Score=23.29 Aligned_cols=45 Identities=27% Similarity=0.459 Sum_probs=24.2
Q ss_pred EEEE-eCCCCCHHHHHHHHHHHhCCceeEEEeeecCCcccccCCcccCCCCceEEEEEcCCCCc
Q 030915 31 IALK-TIPSASKIEIKRVLESLYGFEVDKVRTLNMEGKKKKRGGLLIAKPDYKKAYVTLKNPLS 93 (169)
Q Consensus 31 ~~F~-V~~~atK~eIK~alekiY~VkV~kVnT~~~~GK~kR~~~~~gk~~~~KKAyVtL~~g~~ 93 (169)
+.|. ++..+++.+||..|.. |+ +|.-|-- ..|- +.+||.+.....
T Consensus 4 l~~~g~~~~~~re~iK~~f~~-~g-~V~yVD~--~~G~--------------~~g~VRf~~~~~ 49 (105)
T PF08777_consen 4 LKFSGLGEPTSREDIKEAFSQ-FG-EVAYVDF--SRGD--------------TEGYVRFKTPEA 49 (105)
T ss_dssp EEEEE--SS--HHHHHHHT-S-S---EEEEE----TT---------------SEEEEEESS---
T ss_pred EEEecCCCCcCHHHHHHHHHh-cC-CcceEEe--cCCC--------------CEEEEEECCcch
Confidence 5666 8889999999999998 55 5544332 2343 789999987754
No 39
>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=31.64 E-value=83 Score=21.01 Aligned_cols=36 Identities=14% Similarity=0.192 Sum_probs=30.1
Q ss_pred EEEEeCCCCCHHHHHHHHHHHhCCceeEEEeeecCCc
Q 030915 31 IALKTIPSASKIEIKRVLESLYGFEVDKVRTLNMEGK 67 (169)
Q Consensus 31 ~~F~V~~~atK~eIK~alekiY~VkV~kVnT~~~~GK 67 (169)
.++.|++.+|=.++|+.|+..+|++....+. ++.|+
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 4789999999999999999999988877654 55664
No 40
>PF10411 DsbC_N: Disulfide bond isomerase protein N-terminus; InterPro: IPR018950 This is the N-terminal domain of the disulphide bond isomerase DsbC. The whole molecule is V-shaped, where each arm is a DsbC monomer of two domains linked by a hinge; and the N-termini of each monomer join to form the dimer interface at the base of the V, so are vital for dimerisation []. DsbC is required for disulphide bond formation and functions as a disulphide bond isomerase during oxidative protein-folding in bacterial periplasm. It also has chaperone activity []. ; PDB: 1EEJ_B 2IYJ_A 1TJD_A 1JZD_B 1JZO_A 1G0T_B 1T3B_A.
Probab=30.75 E-value=29 Score=23.04 Aligned_cols=23 Identities=30% Similarity=0.622 Sum_probs=17.8
Q ss_pred HHHHHHHHh-CCceeEEEeeecCC
Q 030915 44 IKRVLESLY-GFEVDKVRTLNMEG 66 (169)
Q Consensus 44 IK~alekiY-~VkV~kVnT~~~~G 66 (169)
|+++|++++ +++|.+|.-.-.+|
T Consensus 1 i~~~l~~~~p~~~v~~v~~spi~G 24 (57)
T PF10411_consen 1 IKQALKKAFPGLKVESVSPSPIPG 24 (57)
T ss_dssp CHHHHHCT--T-TCEEEEE-SSTT
T ss_pred ChhHHHhhcCCCceeEEEcCCCCC
Confidence 578999999 99999999988777
No 41
>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=30.43 E-value=53 Score=23.70 Aligned_cols=25 Identities=24% Similarity=0.457 Sum_probs=18.9
Q ss_pred CCCCHHHHHHHHHHHhCCceeEEEe
Q 030915 37 PSASKIEIKRVLESLYGFEVDKVRT 61 (169)
Q Consensus 37 ~~atK~eIK~alekiY~VkV~kVnT 61 (169)
+-.+|.||++.|.++||++..-|=.
T Consensus 11 ~Tpsr~ei~~klA~~~~~~~~~ivv 35 (84)
T PF01282_consen 11 PTPSRKEIREKLAAMLNVDPDLIVV 35 (84)
T ss_dssp SS--HHHHHHHHHHHHTSTGCCEEE
T ss_pred CCCCHHHHHHHHHHHhCCCCCeEEE
Confidence 4568999999999999998765544
No 42
>PF09581 Spore_III_AF: Stage III sporulation protein AF (Spore_III_AF); InterPro: IPR014245 This family represents the stage III sporulation protein AF (SpoIIIAF) of the bacterial endospore formation program, which exists in some but not all members of the Firmicutes (formerly called low-GC Gram-positives). The C-terminal region of these proteins is poorly conserved.
Probab=28.04 E-value=1.7e+02 Score=23.05 Aligned_cols=45 Identities=33% Similarity=0.319 Sum_probs=33.3
Q ss_pred HHHHHHHHHHHhCCceeEEEeeecCCcccccCCcccCCCCceEEEEEcCCCC
Q 030915 41 KIEIKRVLESLYGFEVDKVRTLNMEGKKKKRGGLLIAKPDYKKAYVTLKNPL 92 (169)
Q Consensus 41 K~eIK~alekiY~VkV~kVnT~~~~GK~kR~~~~~gk~~~~KKAyVtL~~g~ 92 (169)
+.+|+.-++..||+.+.+|......+.... .. .-++..|+|.++.
T Consensus 89 ~~~i~~~l~~~~g~~~~~V~v~~~~~~~~~-----~~--~I~~I~v~l~~~~ 133 (188)
T PF09581_consen 89 EKQIKALLEDKYGVEVVKVEVEIDEDEESP-----DF--EIKEIKVTLSEEE 133 (188)
T ss_pred HHHHHHHHhhhcCCceEEEEEEEEcCCCcc-----cc--ceeEEEEEEcCCC
Confidence 567888899899999999999876553100 01 5688999998854
No 43
>cd01791 Ubl5 UBL5 ubiquitin-like modifier. UBL5 (also known as HUB1) is a ubiquitin-like modifier that is both widely expressed and highly phylogenetically conserved. At the C-terminal end of the ubiquitin-like fold of UBL5 is a di-tyrosine motif followed by a single variable residue instead of the characteristic di-glycine found in all other ubiquitin-like modifiers. ULB5 interacts with a cyclin-like kinase called CLK4 but not with other cyclin-like kinase family members.
Probab=27.74 E-value=1.5e+02 Score=20.42 Aligned_cols=38 Identities=13% Similarity=0.167 Sum_probs=32.2
Q ss_pred CeEEEEeCCCCCHHHHHHHHHHHhCCceeEEEeeecCCc
Q 030915 29 TEIALKTIPSASKIEIKRVLESLYGFEVDKVRTLNMEGK 67 (169)
Q Consensus 29 n~~~F~V~~~atK~eIK~alekiY~VkV~kVnT~~~~GK 67 (169)
..+...|++++|=.|+|+.|+.-+|+++...+.. +.|+
T Consensus 12 k~~~~~v~~~~TV~~LK~~I~~~~~~~~~~qrLi-~~Gk 49 (73)
T cd01791 12 KKVRVKCNPDDTIGDLKKLIAAQTGTRPEKIVLK-KWYT 49 (73)
T ss_pred CEEEEEeCCCCcHHHHHHHHHHHhCCChHHEEEE-eCCc
Confidence 5567799999999999999999999999988875 4463
No 44
>TIGR01622 SF-CC1 splicing factor, CC1-like family. A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.
Probab=27.48 E-value=2.1e+02 Score=25.42 Aligned_cols=33 Identities=18% Similarity=0.288 Sum_probs=28.0
Q ss_pred CeEEEEeCCCCCHHHHHHHHHHHhCCceeEEEeee
Q 030915 29 TEIALKTIPSASKIEIKRVLESLYGFEVDKVRTLN 63 (169)
Q Consensus 29 n~~~F~V~~~atK~eIK~alekiY~VkV~kVnT~~ 63 (169)
..|+-.++..+|..+|++.|++ || +|..|..+.
T Consensus 91 ~l~V~nlp~~~~~~~l~~~F~~-~G-~v~~v~i~~ 123 (457)
T TIGR01622 91 TVFVLQLALKARERDLYEFFSK-VG-KVRDVQCIK 123 (457)
T ss_pred EEEEeCCCCCCCHHHHHHHHHh-cC-CeeEEEEee
Confidence 4567778999999999999988 67 888998874
No 45
>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=27.25 E-value=1.4e+02 Score=18.59 Aligned_cols=46 Identities=15% Similarity=0.347 Sum_probs=29.9
Q ss_pred EEEeCCCCCHHHHHHHHHHHhCCceeEEEeee-cCCcccccCCcccCCCCceEEEEEcCCC
Q 030915 32 ALKTIPSASKIEIKRVLESLYGFEVDKVRTLN-MEGKKKKRGGLLIAKPDYKKAYVTLKNP 91 (169)
Q Consensus 32 ~F~V~~~atK~eIK~alekiY~VkV~kVnT~~-~~GK~kR~~~~~gk~~~~KKAyVtL~~g 91 (169)
+=.+++++|..||+++++. ||.- ..+.... ..++ ...-|||++...
T Consensus 3 v~nlp~~~t~~~l~~~f~~-~g~i-~~~~~~~~~~~~------------~~~~a~V~F~~~ 49 (70)
T PF00076_consen 3 VGNLPPDVTEEELRDFFSQ-FGKI-ESIKVMRNSSGK------------SKGYAFVEFESE 49 (70)
T ss_dssp EESETTTSSHHHHHHHHHT-TSTE-EEEEEEEETTSS------------EEEEEEEEESSH
T ss_pred EcCCCCcCCHHHHHHHHHH-hhhc-cccccccccccc------------ccceEEEEEcCH
Confidence 3347899999999999999 5432 4555443 2232 124778877643
No 46
>KOG3424 consensus 40S ribosomal protein S24 [Translation, ribosomal structure and biogenesis]
Probab=27.12 E-value=1e+02 Score=24.50 Aligned_cols=25 Identities=32% Similarity=0.412 Sum_probs=21.7
Q ss_pred CCCHHHHHHHHHHHhCCceeEEEee
Q 030915 38 SASKIEIKRVLESLYGFEVDKVRTL 62 (169)
Q Consensus 38 ~atK~eIK~alekiY~VkV~kVnT~ 62 (169)
..+|.||++-|.++|.++...|-..
T Consensus 34 ~vsK~EirEKla~mYkt~~d~V~vf 58 (132)
T KOG3424|consen 34 NVSKTEIREKLAKMYKTTPDAVFVF 58 (132)
T ss_pred CCCHHHHHHHHHHHhcCCcceEEEE
Confidence 6699999999999999987777665
No 47
>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=25.81 E-value=1.6e+02 Score=20.28 Aligned_cols=38 Identities=13% Similarity=0.192 Sum_probs=31.3
Q ss_pred CeEEEEeCCCCCHHHHHHHHHHHhCCceeEEEeeecCCc
Q 030915 29 TEIALKTIPSASKIEIKRVLESLYGFEVDKVRTLNMEGK 67 (169)
Q Consensus 29 n~~~F~V~~~atK~eIK~alekiY~VkV~kVnT~~~~GK 67 (169)
....+.|++.+|=.|+|+.|+.-.++++...+.. +.|+
T Consensus 12 ~~~~l~v~~~~TV~~LK~~I~~~~~~~~~~qrL~-~~Gk 49 (78)
T cd01804 12 TRFDLSVPPDETVEGLKKRISQRLKVPKERLALL-HRET 49 (78)
T ss_pred CEEEEEECCcCHHHHHHHHHHHHhCCChHHEEEE-ECCc
Confidence 4578999999999999999999999988766553 5564
No 48
>COG1035 FrhB Coenzyme F420-reducing hydrogenase, beta subunit [Energy production and conversion]
Probab=22.83 E-value=1.7e+02 Score=26.47 Aligned_cols=45 Identities=24% Similarity=0.331 Sum_probs=35.5
Q ss_pred eCCCCCHHHHHHHHHHHhCCceeEEEeeec-CCcccccCCcccCCCCceEEEEEcCCCCccC
Q 030915 35 TIPSASKIEIKRVLESLYGFEVDKVRTLNM-EGKKKKRGGLLIAKPDYKKAYVTLKNPLSLS 95 (169)
Q Consensus 35 V~~~atK~eIK~alekiY~VkV~kVnT~~~-~GK~kR~~~~~gk~~~~KKAyVtL~~g~~i~ 95 (169)
+-.+.+-..+++.|+..|+|++.+|.-+.. +| |..|+|..|..+.
T Consensus 182 C~e~f~y~~l~~~l~e~~gvd~~dV~k~di~kG----------------k~~v~~~dG~~~~ 227 (332)
T COG1035 182 CMENFSYEGLKKFLEEDLGVDPEDVEKMDIRKG----------------KFVVELKDGEVKE 227 (332)
T ss_pred cCCCcCHHHHHHHHHHHhCCCHHHeEEEEeeCc----------------eEEEEecCCcEEE
Confidence 455667777999999999999999999854 67 6777777775554
No 49
>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=22.56 E-value=52 Score=21.31 Aligned_cols=16 Identities=25% Similarity=0.551 Sum_probs=13.8
Q ss_pred HHHHHHHHHHHhCCce
Q 030915 41 KIEIKRVLESLYGFEV 56 (169)
Q Consensus 41 K~eIK~alekiY~VkV 56 (169)
|.|=+.+||.+||++-
T Consensus 3 k~eER~aLEAMFNLKF 18 (41)
T PF12426_consen 3 KTEERSALEAMFNLKF 18 (41)
T ss_pred chhHHHHHHHHhceee
Confidence 6788999999999874
No 50
>TIGR02830 spore_III_AG stage III sporulation protein AG. CC A comparative genome analysis of all sequenced genomes of shows a number of proteins conserved strictly among the endospore-forming subset of the Firmicutes. This protein, a member of this panel, is found in a spore formation operon and is designated stage III sporulation protein AG.
Probab=22.00 E-value=1e+02 Score=25.66 Aligned_cols=24 Identities=21% Similarity=0.241 Sum_probs=21.1
Q ss_pred CHHHHHHHHHHHhCCceeEEEeee
Q 030915 40 SKIEIKRVLESLYGFEVDKVRTLN 63 (169)
Q Consensus 40 tK~eIK~alekiY~VkV~kVnT~~ 63 (169)
-|.+|-+|+..+|||+..+|+.+-
T Consensus 161 Vk~~I~~AV~~ll~v~~hkI~V~~ 184 (186)
T TIGR02830 161 IKYRIVEAVSRVLDVPAHKVSVLP 184 (186)
T ss_pred HHHHHHHHHHHHhCCCcceEEEEe
Confidence 578888999999999999998863
No 51
>COG2004 RPS24A Ribosomal protein S24E [Translation, ribosomal structure and biogenesis]
Probab=21.89 E-value=2.2e+02 Score=21.85 Aligned_cols=34 Identities=24% Similarity=0.383 Sum_probs=27.8
Q ss_pred CeEEEEeC----CCCCHHHHHHHHHHHhCCceeEEEee
Q 030915 29 TEIALKTI----PSASKIEIKRVLESLYGFEVDKVRTL 62 (169)
Q Consensus 29 n~~~F~V~----~~atK~eIK~alekiY~VkV~kVnT~ 62 (169)
.++.|.|. +-.++.||++.|..+||++..-|-..
T Consensus 18 kEi~~~v~h~g~~TPSr~evrekla~~l~~d~e~VvV~ 55 (107)
T COG2004 18 KEIVFVVYHEGSPTPSRKEVREKLAAMLGADKELVVVD 55 (107)
T ss_pred eEEEEEEEeCCCCCCCHHHHHHHHHHHHCCCcceEEEE
Confidence 66777664 45699999999999999998877665
No 52
>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=21.64 E-value=81 Score=20.50 Aligned_cols=20 Identities=20% Similarity=0.551 Sum_probs=13.2
Q ss_pred CCCHHHHHHHHHHHhCCcee
Q 030915 38 SASKIEIKRVLESLYGFEVD 57 (169)
Q Consensus 38 ~atK~eIK~alekiY~VkV~ 57 (169)
.+|..+|++.|+.-||++..
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 35889999999999999864
No 53
>cd04931 ACT_PAH ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, phenylalanine hydroxylases (PAH). ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, phenylalanine hydroxylases (PAH). PAH catalyzes the hydroxylation of L-Phe to L-Tyr, the first step in the catabolic degradation of L-Phe. In PAH, an autoregulatory sequence, N-terminal of the ACT domain, extends across the catalytic domain active site and regulates the enzyme by intrasteric regulation. It appears that the activation by L-Phe induces a conformational change that converts the enzyme to a high-affinity and high-activity state. Modulation of activity is achieved through inhibition by BH4 and activation by phosphorylation of serine residues of the autoregulatory region. The molecular basis for the cooperative activation process is not fully understood yet. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=21.48 E-value=75 Score=23.09 Aligned_cols=25 Identities=12% Similarity=0.068 Sum_probs=19.9
Q ss_pred CCeEEEEeCCCCC-HHHHHHHHHHHh
Q 030915 28 ITEIALKTIPSAS-KIEIKRVLESLY 52 (169)
Q Consensus 28 ~n~~~F~V~~~at-K~eIK~alekiY 52 (169)
..+|.|.|+.+.. ...++++|+.+-
T Consensus 54 ~~~Y~FfVDieg~~~~~~~~~l~~L~ 79 (90)
T cd04931 54 KDEYEFFINLDKKSAPALDPIIKSLR 79 (90)
T ss_pred CceEEEEEEEEcCCCHHHHHHHHHHH
Confidence 3679999998886 778888888764
No 54
>cd01790 Herp_N Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain protein. Herp (Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain protein) , is an integral membrane protein that is induced by the endoplasmic reticulum (ER) stress response pathway and is involved in improving the balance of folding capacity and protein loads in the ER. Herp has an N-terminal ubiquitin-like domain that is involved in Herp degradation, but is not necessary for its enhancement of amyloid beta-protein generation.
Probab=20.74 E-value=2.1e+02 Score=20.51 Aligned_cols=41 Identities=20% Similarity=0.141 Sum_probs=29.3
Q ss_pred cCCeEEEEe--CCCCCHHHHHHHHHHHhC-CceeEEEeeecCCc
Q 030915 27 NITEIALKT--IPSASKIEIKRVLESLYG-FEVDKVRTLNMEGK 67 (169)
Q Consensus 27 ~~n~~~F~V--~~~atK~eIK~alekiY~-VkV~kVnT~~~~GK 67 (169)
+..+..|.| ++.+|=.|+|+.|+.-++ .....=.-+|+.||
T Consensus 10 ~~~~~~~~ve~~~~~TV~~lK~~i~~~~~~~~~~~~QrLIy~GK 53 (79)
T cd01790 10 NQKYEDQTVSCFLNWTVGELKTHLSRVYPSKPLEQDQRLIYSGK 53 (79)
T ss_pred CCCeEEEEEecCCcChHHHHHHHHHHhcCCCCChhHeEEEEcCe
Confidence 335556666 899999999999999885 33223345688886
No 55
>PLN03134 glycine-rich RNA-binding protein 4; Provisional
Probab=20.27 E-value=3.3e+02 Score=21.03 Aligned_cols=51 Identities=8% Similarity=0.152 Sum_probs=35.4
Q ss_pred CeEEEEeCCCCCHHHHHHHHHHHhCCceeEEEeeecC--CcccccCCcccCCCCceEEEEEcCCCCc
Q 030915 29 TEIALKTIPSASKIEIKRVLESLYGFEVDKVRTLNME--GKKKKRGGLLIAKPDYKKAYVTLKNPLS 93 (169)
Q Consensus 29 n~~~F~V~~~atK~eIK~alekiY~VkV~kVnT~~~~--GK~kR~~~~~gk~~~~KKAyVtL~~g~~ 93 (169)
..|+=.++..+|..+|++.+++ || +|.+|....-. |+ .---|||++...+.
T Consensus 36 ~lfVgnL~~~~te~~L~~~F~~-~G-~I~~v~i~~d~~tg~------------~kGfaFV~F~~~e~ 88 (144)
T PLN03134 36 KLFIGGLSWGTDDASLRDAFAH-FG-DVVDAKVIVDRETGR------------SRGFGFVNFNDEGA 88 (144)
T ss_pred EEEEeCCCCCCCHHHHHHHHhc-CC-CeEEEEEEecCCCCC------------cceEEEEEECCHHH
Confidence 4456668999999999999998 67 77787776432 22 11368888775443
No 56
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor. These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
Probab=20.21 E-value=2.8e+02 Score=23.49 Aligned_cols=34 Identities=18% Similarity=0.253 Sum_probs=28.3
Q ss_pred CeEEEEeCCCCCHHHHHHHHHHHhCCceeEEEeeec
Q 030915 29 TEIALKTIPSASKIEIKRVLESLYGFEVDKVRTLNM 64 (169)
Q Consensus 29 n~~~F~V~~~atK~eIK~alekiY~VkV~kVnT~~~ 64 (169)
+.++=..+.++|..||++.++. || +|..|.++.-
T Consensus 5 ~l~V~nLp~~~~e~~l~~~F~~-~G-~i~~v~i~~d 38 (352)
T TIGR01661 5 NLIVNYLPQTMTQEEIRSLFTS-IG-EIESCKLVRD 38 (352)
T ss_pred EEEEeCCCCCCCHHHHHHHHHc-cC-CEEEEEEEEc
Confidence 4455567889999999999999 78 8999999864
Done!