Query 030532
Match_columns 175
No_of_seqs 166 out of 636
Neff 3.2
Searched_HMMs 46136
Date Fri Mar 29 15:09:38 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030532.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030532hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0226 RNA-binding proteins [ 99.9 2E-22 4.3E-27 175.7 7.9 108 67-174 117-226 (290)
2 TIGR01661 ELAV_HUD_SF ELAV/HuD 98.4 4.4E-07 9.5E-12 76.2 5.7 40 135-174 266-305 (352)
3 KOG0148 Apoptosis-promoting RN 98.4 2.4E-07 5.3E-12 82.6 4.0 62 113-174 34-98 (321)
4 PF00076 RRM_1: RNA recognitio 98.4 4.1E-07 9E-12 58.8 3.7 33 141-173 1-33 (70)
5 PLN03134 glycine-rich RNA-bind 98.3 1E-06 2.2E-11 69.1 4.5 39 136-174 32-70 (144)
6 COG0724 RNA-binding proteins ( 98.2 3.2E-06 6.9E-11 63.2 5.9 37 138-174 115-151 (306)
7 TIGR01659 sex-lethal sex-letha 98.1 2.8E-06 6.2E-11 75.3 4.8 39 136-174 105-143 (346)
8 TIGR01648 hnRNP-R-Q heterogene 98.1 7.3E-06 1.6E-10 77.9 6.7 47 124-174 48-94 (578)
9 TIGR01659 sex-lethal sex-letha 97.9 1.3E-05 2.8E-10 71.2 4.3 38 137-174 192-229 (346)
10 smart00362 RRM_2 RNA recogniti 97.8 4.1E-05 9E-10 47.7 4.0 34 140-173 1-34 (72)
11 TIGR01628 PABP-1234 polyadenyl 97.8 3.4E-05 7.4E-10 70.0 4.9 38 137-174 284-321 (562)
12 PF14259 RRM_6: RNA recognitio 97.7 3.2E-05 6.9E-10 51.2 3.5 33 141-173 1-33 (70)
13 TIGR01645 half-pint poly-U bin 97.7 3.8E-05 8.3E-10 73.6 4.9 38 137-174 203-240 (612)
14 TIGR01622 SF-CC1 splicing fact 97.7 5.5E-05 1.2E-09 66.3 5.3 39 136-174 87-125 (457)
15 TIGR01645 half-pint poly-U bin 97.7 4.4E-05 9.5E-10 73.2 4.4 38 137-174 106-143 (612)
16 TIGR01649 hnRNP-L_PTB hnRNP-L/ 97.6 5.9E-05 1.3E-09 68.3 4.8 37 137-173 274-311 (481)
17 TIGR01642 U2AF_lg U2 snRNP aux 97.6 7E-05 1.5E-09 66.3 4.7 37 138-174 295-331 (509)
18 TIGR01628 PABP-1234 polyadenyl 97.6 8.9E-05 1.9E-09 67.4 4.8 38 137-174 87-124 (562)
19 KOG0226 RNA-binding proteins [ 97.5 2.6E-05 5.6E-10 69.2 0.7 61 113-173 71-134 (290)
20 TIGR01622 SF-CC1 splicing fact 97.5 0.00012 2.6E-09 64.1 4.8 38 137-174 185-222 (457)
21 KOG0145 RNA-binding protein EL 97.5 0.00012 2.6E-09 65.9 4.6 43 133-175 273-315 (360)
22 cd00590 RRM RRM (RNA recogniti 97.5 0.00022 4.8E-09 44.6 4.1 35 140-174 1-35 (74)
23 TIGR01648 hnRNP-R-Q heterogene 97.4 0.00018 3.9E-09 68.5 4.8 37 138-174 233-271 (578)
24 KOG0126 Predicted RNA-binding 97.3 3.8E-05 8.2E-10 65.8 -0.5 38 137-174 34-71 (219)
25 TIGR01661 ELAV_HUD_SF ELAV/HuD 97.3 0.0003 6.4E-09 59.2 4.3 38 137-174 88-125 (352)
26 TIGR01649 hnRNP-L_PTB hnRNP-L/ 97.2 0.00034 7.4E-09 63.5 4.3 36 138-173 96-131 (481)
27 smart00360 RRM RNA recognition 97.1 0.00058 1.3E-08 42.1 3.3 32 143-174 1-32 (71)
28 KOG0113 U1 small nuclear ribon 97.1 0.00092 2E-08 60.6 5.3 35 140-174 103-137 (335)
29 KOG0148 Apoptosis-promoting RN 97.0 0.00063 1.4E-08 61.2 4.0 41 134-174 160-200 (321)
30 KOG0127 Nucleolar protein fibr 97.0 0.00077 1.7E-08 65.2 4.6 42 133-174 287-328 (678)
31 KOG0125 Ataxin 2-binding prote 97.0 0.00086 1.9E-08 61.4 4.2 44 130-173 88-131 (376)
32 KOG0117 Heterogeneous nuclear 96.8 0.0009 1.9E-08 63.2 3.2 51 124-174 234-295 (506)
33 KOG0121 Nuclear cap-binding pr 96.8 0.00086 1.9E-08 55.1 2.7 35 136-170 34-68 (153)
34 KOG0123 Polyadenylate-binding 96.8 0.0012 2.7E-08 59.4 3.6 34 141-174 79-112 (369)
35 KOG0144 RNA-binding protein CU 96.7 0.001 2.3E-08 62.7 3.0 39 136-174 32-70 (510)
36 KOG0114 Predicted RNA-binding 96.5 0.0025 5.5E-08 50.9 3.5 32 140-171 20-51 (124)
37 KOG0144 RNA-binding protein CU 96.4 0.0013 2.8E-08 62.2 1.0 39 136-174 122-160 (510)
38 KOG0109 RNA-binding protein LA 96.3 0.0025 5.4E-08 57.9 2.6 39 136-174 76-114 (346)
39 KOG4205 RNA-binding protein mu 96.2 0.0072 1.6E-07 54.0 4.6 57 112-175 78-134 (311)
40 KOG0131 Splicing factor 3b, su 96.1 0.0029 6.3E-08 54.2 1.8 37 137-173 95-132 (203)
41 KOG0151 Predicted splicing reg 96.1 0.0065 1.4E-07 60.4 4.2 43 132-174 168-210 (877)
42 KOG0122 Translation initiation 96.0 0.011 2.4E-07 52.4 5.1 38 137-174 188-225 (270)
43 TIGR01642 U2AF_lg U2 snRNP aux 95.8 0.011 2.4E-07 52.6 4.3 27 136-162 173-199 (509)
44 KOG1457 RNA binding protein (c 95.7 0.0073 1.6E-07 53.5 2.4 33 138-170 210-242 (284)
45 KOG0117 Heterogeneous nuclear 95.6 0.017 3.6E-07 54.9 4.7 37 138-174 83-119 (506)
46 KOG4661 Hsp27-ERE-TATA-binding 95.2 0.013 2.9E-07 57.6 2.6 36 138-173 405-440 (940)
47 KOG0116 RasGAP SH3 binding pro 95.1 0.017 3.7E-07 53.6 3.0 32 140-171 290-321 (419)
48 KOG0153 Predicted RNA-binding 95.0 0.027 5.9E-07 52.0 3.9 40 133-172 220-262 (377)
49 KOG0132 RNA polymerase II C-te 94.8 0.022 4.7E-07 57.1 3.1 33 140-172 423-455 (894)
50 KOG0533 RRM motif-containing p 94.8 0.033 7.2E-07 48.5 3.8 41 134-174 79-119 (243)
51 KOG0146 RNA-binding protein ET 94.6 0.029 6.3E-07 51.1 3.1 39 136-174 283-321 (371)
52 KOG0124 Polypyrimidine tract-b 94.3 0.019 4.1E-07 54.1 1.4 37 138-174 113-149 (544)
53 KOG0415 Predicted peptidyl pro 94.1 0.038 8.1E-07 51.8 2.8 42 133-174 234-275 (479)
54 KOG0147 Transcriptional coacti 93.9 0.028 6.2E-07 54.0 1.6 37 138-174 277-314 (549)
55 KOG0129 Predicted RNA-binding 93.1 0.058 1.3E-06 51.7 2.3 27 139-165 260-286 (520)
56 KOG0124 Polypyrimidine tract-b 92.6 0.12 2.7E-06 48.8 3.6 38 138-175 210-247 (544)
57 KOG0130 RNA-binding protein RB 91.8 0.15 3.4E-06 42.5 3.0 36 139-174 73-108 (170)
58 KOG0145 RNA-binding protein EL 91.7 0.19 4.2E-06 45.7 3.6 39 136-174 39-77 (360)
59 KOG4660 Protein Mei2, essentia 91.1 0.16 3.5E-06 49.0 2.7 38 132-169 69-106 (549)
60 KOG0123 Polyadenylate-binding 90.9 0.2 4.4E-06 45.3 3.0 38 137-174 269-306 (369)
61 KOG1548 Transcription elongati 90.7 0.62 1.3E-05 43.3 6.0 30 137-166 133-162 (382)
62 KOG1855 Predicted RNA-binding 89.1 0.77 1.7E-05 43.8 5.3 59 114-172 204-265 (484)
63 KOG0129 Predicted RNA-binding 85.2 0.91 2E-05 43.8 3.5 37 138-174 370-407 (520)
64 KOG4210 Nuclear localization s 83.4 0.83 1.8E-05 40.2 2.3 37 137-173 184-220 (285)
65 KOG0127 Nucleolar protein fibr 83.3 1.3 2.9E-05 43.5 3.8 36 137-172 116-151 (678)
66 KOG0115 RNA-binding protein p5 82.4 1 2.2E-05 40.4 2.5 37 138-174 31-67 (275)
67 PF13893 RRM_5: RNA recognitio 81.6 1.2 2.7E-05 28.5 2.0 19 155-173 1-19 (56)
68 KOG4849 mRNA cleavage factor I 80.7 2.1 4.5E-05 40.6 3.9 29 135-163 77-105 (498)
69 KOG0110 RNA-binding protein (R 80.6 1.4 3E-05 44.0 2.9 33 136-168 383-415 (725)
70 KOG4206 Spliceosomal protein s 79.2 2.3 5E-05 37.1 3.5 36 136-171 144-179 (221)
71 KOG1190 Polypyrimidine tract-b 76.7 1.8 3.8E-05 41.4 2.2 31 137-167 149-179 (492)
72 smart00361 RRM_1 RNA recogniti 76.6 2.3 5E-05 28.8 2.3 23 152-174 2-29 (70)
73 KOG4209 Splicing factor RNPS1, 76.4 1.6 3.5E-05 37.4 1.8 38 137-174 100-137 (231)
74 KOG0110 RNA-binding protein (R 76.0 2 4.3E-05 42.9 2.5 35 138-172 515-549 (725)
75 KOG1190 Polypyrimidine tract-b 73.1 3.2 6.8E-05 39.8 2.9 32 139-170 29-60 (492)
76 KOG1457 RNA binding protein (c 71.6 4.3 9.4E-05 36.4 3.3 30 140-169 36-65 (284)
77 KOG4212 RNA-binding protein hn 59.4 6.7 0.00014 38.2 2.2 35 136-170 534-568 (608)
78 PF08777 RRM_3: RNA binding mo 58.9 8.7 0.00019 29.0 2.4 27 141-167 4-30 (105)
79 KOG0120 Splicing factor U2AF, 57.2 7.5 0.00016 37.5 2.2 38 137-174 288-325 (500)
80 KOG4212 RNA-binding protein hn 56.7 18 0.00039 35.3 4.6 37 138-174 44-81 (608)
81 KOG0147 Transcriptional coacti 55.8 5 0.00011 39.1 0.8 37 138-174 179-215 (549)
82 KOG0112 Large RNA-binding prot 52.0 6.5 0.00014 40.6 0.9 34 137-170 371-404 (975)
83 KOG3152 TBP-binding protein, a 41.1 32 0.0007 31.2 3.4 31 138-168 74-104 (278)
84 KOG4676 Splicing factor, argin 35.8 10 0.00022 36.3 -0.5 30 141-170 154-183 (479)
85 PF12631 GTPase_Cys_C: Catalyt 34.4 31 0.00067 24.1 1.9 15 148-162 58-72 (73)
86 KOG4454 RNA binding protein (R 34.3 14 0.00031 33.0 0.2 43 132-174 74-120 (267)
87 COG0724 RNA-binding proteins ( 28.7 76 0.0016 23.7 3.2 36 136-171 223-258 (306)
88 COG0030 KsgA Dimethyladenosine 28.3 90 0.0019 27.6 4.1 35 138-172 95-129 (259)
89 KOG0128 RNA-binding protein SA 28.3 34 0.00073 35.3 1.6 36 138-173 736-771 (881)
90 COG5175 MOT2 Transcriptional r 26.2 67 0.0014 30.7 3.1 28 141-168 117-150 (480)
91 smart00650 rADc Ribosomal RNA 25.8 1.3E+02 0.0029 23.2 4.3 35 138-172 77-111 (169)
92 PF15063 TC1: Thyroid cancer p 25.5 16 0.00035 27.6 -0.8 32 143-174 30-64 (79)
93 PTZ00338 dimethyladenosine tra 24.7 83 0.0018 27.6 3.3 34 138-171 101-134 (294)
94 cd00027 BRCT Breast Cancer Sup 24.4 1.6E+02 0.0036 17.6 3.8 27 139-165 2-28 (72)
95 cd03517 Link_domain_CSPGs_modu 23.9 79 0.0017 24.2 2.6 29 67-96 9-38 (95)
96 PRK00274 ksgA 16S ribosomal RN 23.2 94 0.002 26.4 3.2 33 139-171 106-138 (272)
97 PF00398 RrnaAD: Ribosomal RNA 22.4 54 0.0012 27.6 1.6 30 137-166 96-127 (262)
98 PF02358 Trehalose_PPase: Treh 20.9 62 0.0013 26.4 1.6 24 136-162 183-206 (235)
99 PF08862 DUF1829: Domain of un 20.8 1.2E+02 0.0025 22.3 2.9 38 125-163 41-79 (88)
No 1
>KOG0226 consensus RNA-binding proteins [General function prediction only]
Probab=99.87 E-value=2e-22 Score=175.66 Aligned_cols=108 Identities=51% Similarity=0.752 Sum_probs=98.9
Q ss_pred CCcCCchhhHHHHHHhhhccCCCCHHHHHHHHHHhhcchhhhhhhcCCCcc--ccccCCCcccCCCCCCCCCCCceeeec
Q 030532 67 APVYSLPQYHQAQQLFQRDAQTITPEALESVKAALASSDIEHKAETKKKSI--PRKAAGQTWEDPTLAEWPENDYRLFCG 144 (175)
Q Consensus 67 ~~~y~~~~~~qa~~~~q~~~~~~~peal~~v~aa~as~~~~~~~~~k~k~~--~R~a~G~~WeDptL~Ew~~ndfrIFVG 144 (175)
+.+|...+...+.++++++.+.|.+++++.+++..+.....+..++||... +|.++|++||||+|.||+.+|||||||
T Consensus 117 ~~~f~~~p~L~ktk~v~~~p~~~~~~~~~~~k~s~a~~k~~~~~~~Kki~~~~VR~a~gtswedPsl~ew~~~DfRIfcg 196 (290)
T KOG0226|consen 117 PVVFSEYPSLVKTKLVRDRPQPIRPEAFESFKASDALLKAETEKEKKKIGKPPVRLAAGTSWEDPSLAEWDEDDFRIFCG 196 (290)
T ss_pred hhhhccchhhhhhhhhhcCCCccCcccccCcchhhhhhhhccccccccccCcceeeccccccCCcccccCccccceeecc
Confidence 778888888889999999999999999999999988888777766555444 699999999999999999999999999
Q ss_pred CCCCCCCHHHHHHHhhcCCCcceeEEeecC
Q 030532 145 DLGNEVNDDVLSKAFSRFPSFNMAKVSFCF 174 (175)
Q Consensus 145 NLs~dVTDe~L~~aFskYGSV~~AKVV~D~ 174 (175)
||++||+|+.|.++|.+|.++.++|||.|-
T Consensus 197 dlgNevnd~vl~raf~Kfpsf~~akviRdk 226 (290)
T KOG0226|consen 197 DLGNEVNDDVLARAFKKFPSFQKAKVIRDK 226 (290)
T ss_pred cccccccHHHHHHHHHhccchhhccccccc
Confidence 999999999999999999999999999984
No 2
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor. These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
Probab=98.41 E-value=4.4e-07 Score=76.17 Aligned_cols=40 Identities=20% Similarity=0.328 Sum_probs=36.6
Q ss_pred CCCCceeeecCCCCCCCHHHHHHHhhcCCCcceeEEeecC
Q 030532 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVSFCF 174 (175)
Q Consensus 135 ~~ndfrIFVGNLs~dVTDe~L~~aFskYGSV~~AKVV~D~ 174 (175)
+...++||||||++++++++|+++|++||.|.+++|+.|.
T Consensus 266 ~~~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~ 305 (352)
T TIGR01661 266 DGAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDL 305 (352)
T ss_pred CCCCcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcC
Confidence 3445689999999999999999999999999999999985
No 3
>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]
Probab=98.39 E-value=2.4e-07 Score=82.60 Aligned_cols=62 Identities=23% Similarity=0.368 Sum_probs=48.4
Q ss_pred CCCccccccCCCcccCCCC---CCCCCCCceeeecCCCCCCCHHHHHHHhhcCCCcceeEEeecC
Q 030532 113 KKKSIPRKAAGQTWEDPTL---AEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVSFCF 174 (175)
Q Consensus 113 k~k~~~R~a~G~~WeDptL---~Ew~~ndfrIFVGNLs~dVTDe~L~~aFskYGSV~~AKVV~D~ 174 (175)
++.+++++.=+-.|....- ..-...||.+|||||+.+++-++|+++|.+||+|++||||+|+
T Consensus 34 ~~~k~i~~e~~v~wa~~p~nQsk~t~~~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~ 98 (321)
T KOG0148|consen 34 TKTKVIFDELKVNWATAPGNQSKPTSNQHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDM 98 (321)
T ss_pred ccceeehhhhccccccCcccCCCCccccceeEEehhcchhcchHHHHHHhccccccccceEeecc
Confidence 4456677766666643221 1112349999999999999999999999999999999999997
No 4
>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=98.37 E-value=4.1e-07 Score=58.78 Aligned_cols=33 Identities=30% Similarity=0.482 Sum_probs=31.6
Q ss_pred eeecCCCCCCCHHHHHHHhhcCCCcceeEEeec
Q 030532 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVSFC 173 (175)
Q Consensus 141 IFVGNLs~dVTDe~L~~aFskYGSV~~AKVV~D 173 (175)
||||||+.++|+++|+++|++||.|..++|+.|
T Consensus 1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~ 33 (70)
T PF00076_consen 1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRN 33 (70)
T ss_dssp EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEE
T ss_pred cEEcCCCCcCCHHHHHHHHHHhhhccccccccc
Confidence 799999999999999999999999999999875
No 5
>PLN03134 glycine-rich RNA-binding protein 4; Provisional
Probab=98.28 E-value=1e-06 Score=69.09 Aligned_cols=39 Identities=31% Similarity=0.306 Sum_probs=36.0
Q ss_pred CCCceeeecCCCCCCCHHHHHHHhhcCCCcceeEEeecC
Q 030532 136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVSFCF 174 (175)
Q Consensus 136 ~ndfrIFVGNLs~dVTDe~L~~aFskYGSV~~AKVV~D~ 174 (175)
....+||||||++++||++|+++|++||.|.+++|++|.
T Consensus 32 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~ 70 (144)
T PLN03134 32 LMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDR 70 (144)
T ss_pred CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecC
Confidence 345689999999999999999999999999999999885
No 6
>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]
Probab=98.21 E-value=3.2e-06 Score=63.15 Aligned_cols=37 Identities=22% Similarity=0.389 Sum_probs=35.3
Q ss_pred CceeeecCCCCCCCHHHHHHHhhcCCCcceeEEeecC
Q 030532 138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVSFCF 174 (175)
Q Consensus 138 dfrIFVGNLs~dVTDe~L~~aFskYGSV~~AKVV~D~ 174 (175)
.++||||||++++|+++|.++|.+||.+..++|+.|.
T Consensus 115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~ 151 (306)
T COG0724 115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDR 151 (306)
T ss_pred CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeecc
Confidence 6999999999999999999999999999999999884
No 7
>TIGR01659 sex-lethal sex-lethal family splicing factor. This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).
Probab=98.13 E-value=2.8e-06 Score=75.32 Aligned_cols=39 Identities=15% Similarity=0.241 Sum_probs=36.6
Q ss_pred CCCceeeecCCCCCCCHHHHHHHhhcCCCcceeEEeecC
Q 030532 136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVSFCF 174 (175)
Q Consensus 136 ~ndfrIFVGNLs~dVTDe~L~~aFskYGSV~~AKVV~D~ 174 (175)
....+||||||++++||++|+++|+.||.|.+++|+.|.
T Consensus 105 ~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~ 143 (346)
T TIGR01659 105 NSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDY 143 (346)
T ss_pred CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecC
Confidence 467899999999999999999999999999999999884
No 8
>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family. Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.
Probab=98.08 E-value=7.3e-06 Score=77.86 Aligned_cols=47 Identities=17% Similarity=0.405 Sum_probs=40.1
Q ss_pred CcccCCCCCCCCCCCceeeecCCCCCCCHHHHHHHhhcCCCcceeEEeecC
Q 030532 124 QTWEDPTLAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVSFCF 174 (175)
Q Consensus 124 ~~WeDptL~Ew~~ndfrIFVGNLs~dVTDe~L~~aFskYGSV~~AKVV~D~ 174 (175)
..|+... +....+||||||+.+++|++|+++|++||.|.++||++|.
T Consensus 48 ~~~~~~~----p~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D~ 94 (578)
T TIGR01648 48 PGWSGVQ----PGRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDF 94 (578)
T ss_pred CcccCCC----CCCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEECC
Confidence 4575433 3356899999999999999999999999999999999985
No 9
>TIGR01659 sex-lethal sex-lethal family splicing factor. This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).
Probab=97.89 E-value=1.3e-05 Score=71.21 Aligned_cols=38 Identities=18% Similarity=0.311 Sum_probs=35.5
Q ss_pred CCceeeecCCCCCCCHHHHHHHhhcCCCcceeEEeecC
Q 030532 137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVSFCF 174 (175)
Q Consensus 137 ndfrIFVGNLs~dVTDe~L~~aFskYGSV~~AKVV~D~ 174 (175)
.+.+|||+||+.++||++|+++|++||.|..++|+.|.
T Consensus 192 ~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~ 229 (346)
T TIGR01659 192 KDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDK 229 (346)
T ss_pred ccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecC
Confidence 46789999999999999999999999999999999884
No 10
>smart00362 RRM_2 RNA recognition motif.
Probab=97.77 E-value=4.1e-05 Score=47.67 Aligned_cols=34 Identities=29% Similarity=0.518 Sum_probs=31.7
Q ss_pred eeeecCCCCCCCHHHHHHHhhcCCCcceeEEeec
Q 030532 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVSFC 173 (175)
Q Consensus 140 rIFVGNLs~dVTDe~L~~aFskYGSV~~AKVV~D 173 (175)
+|||+||+.++++++|.++|.+||.|...+++.+
T Consensus 1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~ 34 (72)
T smart00362 1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKD 34 (72)
T ss_pred CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecC
Confidence 5899999999999999999999999999888765
No 11
>TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.
Probab=97.75 E-value=3.4e-05 Score=70.05 Aligned_cols=38 Identities=26% Similarity=0.350 Sum_probs=35.3
Q ss_pred CCceeeecCCCCCCCHHHHHHHhhcCCCcceeEEeecC
Q 030532 137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVSFCF 174 (175)
Q Consensus 137 ndfrIFVGNLs~dVTDe~L~~aFskYGSV~~AKVV~D~ 174 (175)
...+||||||+.++||++|+++|++||.|.+++|+.|.
T Consensus 284 ~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d~ 321 (562)
T TIGR01628 284 QGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDE 321 (562)
T ss_pred CCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEECC
Confidence 45679999999999999999999999999999999884
No 12
>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=97.75 E-value=3.2e-05 Score=51.16 Aligned_cols=33 Identities=18% Similarity=0.329 Sum_probs=29.0
Q ss_pred eeecCCCCCCCHHHHHHHhhcCCCcceeEEeec
Q 030532 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVSFC 173 (175)
Q Consensus 141 IFVGNLs~dVTDe~L~~aFskYGSV~~AKVV~D 173 (175)
|||+||++++++++|+++|+.||.|...+++.+
T Consensus 1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~ 33 (70)
T PF14259_consen 1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKN 33 (70)
T ss_dssp EEEESSTTT--HHHHHHHCTTSSBEEEEEEEES
T ss_pred CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEee
Confidence 799999999999999999999999999888775
No 13
>TIGR01645 half-pint poly-U binding splicing factor, half-pint family. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.
Probab=97.72 E-value=3.8e-05 Score=73.63 Aligned_cols=38 Identities=8% Similarity=0.215 Sum_probs=35.6
Q ss_pred CCceeeecCCCCCCCHHHHHHHhhcCCCcceeEEeecC
Q 030532 137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVSFCF 174 (175)
Q Consensus 137 ndfrIFVGNLs~dVTDe~L~~aFskYGSV~~AKVV~D~ 174 (175)
...+||||||+.++++++|+++|++||.|.+++|+.|.
T Consensus 203 ~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~ 240 (612)
T TIGR01645 203 KFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAP 240 (612)
T ss_pred ccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecC
Confidence 45799999999999999999999999999999999885
No 14
>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=97.71 E-value=5.5e-05 Score=66.27 Aligned_cols=39 Identities=15% Similarity=0.106 Sum_probs=35.8
Q ss_pred CCCceeeecCCCCCCCHHHHHHHhhcCCCcceeEEeecC
Q 030532 136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVSFCF 174 (175)
Q Consensus 136 ~ndfrIFVGNLs~dVTDe~L~~aFskYGSV~~AKVV~D~ 174 (175)
....+||||||+.++++++|.++|++||.|..++|+.|.
T Consensus 87 ~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~ 125 (457)
T TIGR01622 87 RDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDR 125 (457)
T ss_pred cCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecC
Confidence 346689999999999999999999999999999999873
No 15
>TIGR01645 half-pint poly-U binding splicing factor, half-pint family. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.
Probab=97.67 E-value=4.4e-05 Score=73.23 Aligned_cols=38 Identities=21% Similarity=0.409 Sum_probs=35.4
Q ss_pred CCceeeecCCCCCCCHHHHHHHhhcCCCcceeEEeecC
Q 030532 137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVSFCF 174 (175)
Q Consensus 137 ndfrIFVGNLs~dVTDe~L~~aFskYGSV~~AKVV~D~ 174 (175)
...+||||||+++++|++|+++|++||.|.+++|++|.
T Consensus 106 ~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~ 143 (612)
T TIGR01645 106 IMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDP 143 (612)
T ss_pred CCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecC
Confidence 34689999999999999999999999999999999984
No 16
>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family. Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).
Probab=97.65 E-value=5.9e-05 Score=68.34 Aligned_cols=37 Identities=22% Similarity=0.174 Sum_probs=34.2
Q ss_pred CCceeeecCCCC-CCCHHHHHHHhhcCCCcceeEEeec
Q 030532 137 NDYRLFCGDLGN-EVNDDVLSKAFSRFPSFNMAKVSFC 173 (175)
Q Consensus 137 ndfrIFVGNLs~-dVTDe~L~~aFskYGSV~~AKVV~D 173 (175)
....||||||++ .+|+++|+++|+.||.|.++||+.|
T Consensus 274 ~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~ 311 (481)
T TIGR01649 274 PGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKN 311 (481)
T ss_pred CCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeC
Confidence 456899999998 6999999999999999999999876
No 17
>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor. Members of this subfamily are found in plants, metazoa and fungi.
Probab=97.62 E-value=7e-05 Score=66.33 Aligned_cols=37 Identities=14% Similarity=0.260 Sum_probs=34.6
Q ss_pred CceeeecCCCCCCCHHHHHHHhhcCCCcceeEEeecC
Q 030532 138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVSFCF 174 (175)
Q Consensus 138 dfrIFVGNLs~dVTDe~L~~aFskYGSV~~AKVV~D~ 174 (175)
..+||||||++.+|+++|.++|+.||.|..++|+.|.
T Consensus 295 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~ 331 (509)
T TIGR01642 295 KDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDI 331 (509)
T ss_pred CCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecC
Confidence 4689999999999999999999999999999999874
No 18
>TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.
Probab=97.57 E-value=8.9e-05 Score=67.38 Aligned_cols=38 Identities=24% Similarity=0.301 Sum_probs=35.0
Q ss_pred CCceeeecCCCCCCCHHHHHHHhhcCCCcceeEEeecC
Q 030532 137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVSFCF 174 (175)
Q Consensus 137 ndfrIFVGNLs~dVTDe~L~~aFskYGSV~~AKVV~D~ 174 (175)
...+|||+||+.++|+++|+++|++||.|.+++|++|.
T Consensus 87 ~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~~ 124 (562)
T TIGR01628 87 GVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDE 124 (562)
T ss_pred CCCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeecC
Confidence 34579999999999999999999999999999999874
No 19
>KOG0226 consensus RNA-binding proteins [General function prediction only]
Probab=97.53 E-value=2.6e-05 Score=69.22 Aligned_cols=61 Identities=33% Similarity=0.483 Sum_probs=55.3
Q ss_pred CCCccccccCCCcccCCCCCCCCCCCceeeecCCCCCCCHHH-H--HHHhhcCCCcceeEEeec
Q 030532 113 KKKSIPRKAAGQTWEDPTLAEWPENDYRLFCGDLGNEVNDDV-L--SKAFSRFPSFNMAKVSFC 173 (175)
Q Consensus 113 k~k~~~R~a~G~~WeDptL~Ew~~ndfrIFVGNLs~dVTDe~-L--~~aFskYGSV~~AKVV~D 173 (175)
-+-++.|+.++..|+||++++|++++|+.|+|+++.+|.++- | ..+|+.|.++.+-+++.|
T Consensus 71 v~tav~~~s~~a~~~~Pt~l~~~P~vf~p~~~~~g~~v~pep~lp~~~~f~~~p~L~ktk~v~~ 134 (290)
T KOG0226|consen 71 VKTAVGRKSAPAVWADPTLLAPAPAVFRPFQSNAGATVNPEPPLPLPVVFSEYPSLVKTKLVRD 134 (290)
T ss_pred hhhhccccccccccCCCccCCCCcccccccccccccccCCCCCCcchhhhccchhhhhhhhhhc
Confidence 346679999999999999999999999999999999999987 5 899999999988888765
No 20
>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=97.52 E-value=0.00012 Score=64.13 Aligned_cols=38 Identities=18% Similarity=0.301 Sum_probs=35.2
Q ss_pred CCceeeecCCCCCCCHHHHHHHhhcCCCcceeEEeecC
Q 030532 137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVSFCF 174 (175)
Q Consensus 137 ndfrIFVGNLs~dVTDe~L~~aFskYGSV~~AKVV~D~ 174 (175)
+..+||||||+.++|+++|.++|+.||.|..++|+.|.
T Consensus 185 ~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~ 222 (457)
T TIGR01622 185 NFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDP 222 (457)
T ss_pred CCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcC
Confidence 46789999999999999999999999999999998774
No 21
>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]
Probab=97.50 E-value=0.00012 Score=65.88 Aligned_cols=43 Identities=23% Similarity=0.370 Sum_probs=39.0
Q ss_pred CCCCCCceeeecCCCCCCCHHHHHHHhhcCCCcceeEEeecCC
Q 030532 133 EWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVSFCFT 175 (175)
Q Consensus 133 Ew~~ndfrIFVGNLs~dVTDe~L~~aFskYGSV~~AKVV~D~~ 175 (175)
-.+..-+.|||=||+.|.+|..|.++|+.||.|..+|||.|+|
T Consensus 273 ~~~~~g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~t 315 (360)
T KOG0145|consen 273 GGPGGGWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFT 315 (360)
T ss_pred CCCCCeeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCC
Confidence 3345567899999999999999999999999999999999986
No 22
>cd00590 RRM RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
Probab=97.45 E-value=0.00022 Score=44.58 Aligned_cols=35 Identities=26% Similarity=0.441 Sum_probs=32.0
Q ss_pred eeeecCCCCCCCHHHHHHHhhcCCCcceeEEeecC
Q 030532 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVSFCF 174 (175)
Q Consensus 140 rIFVGNLs~dVTDe~L~~aFskYGSV~~AKVV~D~ 174 (175)
+|||+||+.++++++|.+.|..||.+...++..+.
T Consensus 1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~ 35 (74)
T cd00590 1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDK 35 (74)
T ss_pred CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCC
Confidence 58999999999999999999999999998887753
No 23
>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family. Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.
Probab=97.41 E-value=0.00018 Score=68.54 Aligned_cols=37 Identities=19% Similarity=0.299 Sum_probs=34.0
Q ss_pred CceeeecCCCCCCCHHHHHHHhhcC--CCcceeEEeecC
Q 030532 138 DYRLFCGDLGNEVNDDVLSKAFSRF--PSFNMAKVSFCF 174 (175)
Q Consensus 138 dfrIFVGNLs~dVTDe~L~~aFskY--GSV~~AKVV~D~ 174 (175)
..+||||||++++||++|+++|++| |.|.+++++.|+
T Consensus 233 ~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~rgf 271 (578)
T TIGR01648 233 VKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIRDY 271 (578)
T ss_pred ccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEeecCe
Confidence 3569999999999999999999999 999999998774
No 24
>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=97.34 E-value=3.8e-05 Score=65.84 Aligned_cols=38 Identities=13% Similarity=0.155 Sum_probs=34.9
Q ss_pred CCceeeecCCCCCCCHHHHHHHhhcCCCcceeEEeecC
Q 030532 137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVSFCF 174 (175)
Q Consensus 137 ndfrIFVGNLs~dVTDe~L~~aFskYGSV~~AKVV~D~ 174 (175)
+..=||||||+++.||.+|.-+|++||.++++.+|.|-
T Consensus 34 dsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk 71 (219)
T KOG0126|consen 34 DSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDK 71 (219)
T ss_pred cceEEEECCCcccccCCcEEEEeeccCceEEEEEEecC
Confidence 44569999999999999999999999999999999984
No 25
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor. These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
Probab=97.29 E-value=0.0003 Score=59.22 Aligned_cols=38 Identities=16% Similarity=0.211 Sum_probs=34.9
Q ss_pred CCceeeecCCCCCCCHHHHHHHhhcCCCcceeEEeecC
Q 030532 137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVSFCF 174 (175)
Q Consensus 137 ndfrIFVGNLs~dVTDe~L~~aFskYGSV~~AKVV~D~ 174 (175)
...+||||||+.++++++|+++|++||.|..++|+.|.
T Consensus 88 ~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~ 125 (352)
T TIGR01661 88 KGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDN 125 (352)
T ss_pred ccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecC
Confidence 45689999999999999999999999999999998874
No 26
>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family. Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).
Probab=97.23 E-value=0.00034 Score=63.46 Aligned_cols=36 Identities=14% Similarity=0.044 Sum_probs=33.4
Q ss_pred CceeeecCCCCCCCHHHHHHHhhcCCCcceeEEeec
Q 030532 138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVSFC 173 (175)
Q Consensus 138 dfrIFVGNLs~dVTDe~L~~aFskYGSV~~AKVV~D 173 (175)
-.+|||+||.+.+|+++|+++|+.||.|.+++|+.|
T Consensus 96 ~~~v~v~nl~~~vt~~~L~~~F~~~G~V~~v~i~~~ 131 (481)
T TIGR01649 96 VLRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTK 131 (481)
T ss_pred eEEEEEcCCCCCCCHHHHHHHHhccCCEEEEEEEec
Confidence 358999999999999999999999999999998766
No 27
>smart00360 RRM RNA recognition motif.
Probab=97.13 E-value=0.00058 Score=42.15 Aligned_cols=32 Identities=22% Similarity=0.376 Sum_probs=29.2
Q ss_pred ecCCCCCCCHHHHHHHhhcCCCcceeEEeecC
Q 030532 143 CGDLGNEVNDDVLSKAFSRFPSFNMAKVSFCF 174 (175)
Q Consensus 143 VGNLs~dVTDe~L~~aFskYGSV~~AKVV~D~ 174 (175)
|+||+.++++++|+++|+.||.|..++|..+.
T Consensus 1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~ 32 (71)
T smart00360 1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDK 32 (71)
T ss_pred CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCC
Confidence 68999999999999999999999999887753
No 28
>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]
Probab=97.06 E-value=0.00092 Score=60.56 Aligned_cols=35 Identities=14% Similarity=0.311 Sum_probs=33.6
Q ss_pred eeeecCCCCCCCHHHHHHHhhcCCCcceeEEeecC
Q 030532 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVSFCF 174 (175)
Q Consensus 140 rIFVGNLs~dVTDe~L~~aFskYGSV~~AKVV~D~ 174 (175)
+||||-|+++++|..|.+.|++||.|.+.+||.|.
T Consensus 103 TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~ 137 (335)
T KOG0113|consen 103 TLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDK 137 (335)
T ss_pred eeeeeeccccccHHHHHHHHHhcCcceeEEEeeec
Confidence 69999999999999999999999999999999983
No 29
>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]
Probab=97.05 E-value=0.00063 Score=61.19 Aligned_cols=41 Identities=15% Similarity=0.345 Sum_probs=37.5
Q ss_pred CCCCCceeeecCCCCCCCHHHHHHHhhcCCCcceeEEeecC
Q 030532 134 WPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVSFCF 174 (175)
Q Consensus 134 w~~ndfrIFVGNLs~dVTDe~L~~aFskYGSV~~AKVV~D~ 174 (175)
-++++.++||||++.-.||++|++.|+.||.|.++||-.|.
T Consensus 160 ssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~q 200 (321)
T KOG0148|consen 160 SSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKDQ 200 (321)
T ss_pred CCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEeccc
Confidence 35678899999999999999999999999999999998774
No 30
>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]
Probab=97.02 E-value=0.00077 Score=65.16 Aligned_cols=42 Identities=19% Similarity=0.218 Sum_probs=37.6
Q ss_pred CCCCCCceeeecCCCCCCCHHHHHHHhhcCCCcceeEEeecC
Q 030532 133 EWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVSFCF 174 (175)
Q Consensus 133 Ew~~ndfrIFVGNLs~dVTDe~L~~aFskYGSV~~AKVV~D~ 174 (175)
|.......+||-||++|+|+++|...|++||+|..|+||.|.
T Consensus 287 en~~~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k 328 (678)
T KOG0127|consen 287 ENITEGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDK 328 (678)
T ss_pred ccccccceEEEecCCccccHHHHHHHHHhhccceeEEEEecc
Confidence 334456899999999999999999999999999999999885
No 31
>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]
Probab=96.97 E-value=0.00086 Score=61.44 Aligned_cols=44 Identities=18% Similarity=0.218 Sum_probs=39.0
Q ss_pred CCCCCCCCCceeeecCCCCCCCHHHHHHHhhcCCCcceeEEeec
Q 030532 130 TLAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVSFC 173 (175)
Q Consensus 130 tL~Ew~~ndfrIFVGNLs~dVTDe~L~~aFskYGSV~~AKVV~D 173 (175)
+-.+-...+-||+|.|+++.-.|.||+.+|.+||-|.++.||++
T Consensus 88 t~s~s~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfN 131 (376)
T KOG0125|consen 88 TNSSSKDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFN 131 (376)
T ss_pred CcCCCCCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEec
Confidence 33445567889999999999999999999999999999999986
No 32
>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]
Probab=96.82 E-value=0.0009 Score=63.21 Aligned_cols=51 Identities=20% Similarity=0.477 Sum_probs=41.3
Q ss_pred CcccCCCCCCCC-------CCCc----eeeecCCCCCCCHHHHHHHhhcCCCcceeEEeecC
Q 030532 124 QTWEDPTLAEWP-------ENDY----RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVSFCF 174 (175)
Q Consensus 124 ~~WeDptL~Ew~-------~ndf----rIFVGNLs~dVTDe~L~~aFskYGSV~~AKVV~D~ 174 (175)
+.|......+|- ++.+ -|||-||..+||+|.|.++|++||.|.++|.+.|+
T Consensus 234 klwgn~~tVdWAep~~e~ded~ms~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rDY 295 (506)
T KOG0117|consen 234 KLWGNAITVDWAEPEEEPDEDTMSKVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRDY 295 (506)
T ss_pred eecCCcceeeccCcccCCChhhhhheeeeeeeccchhhhHHHHHHHHHhccceEEeecccce
Confidence 566555556662 2233 29999999999999999999999999999999885
No 33
>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]
Probab=96.82 E-value=0.00086 Score=55.07 Aligned_cols=35 Identities=11% Similarity=0.277 Sum_probs=31.0
Q ss_pred CCCceeeecCCCCCCCHHHHHHHhhcCCCcceeEE
Q 030532 136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKV 170 (175)
Q Consensus 136 ~ndfrIFVGNLs~dVTDe~L~~aFskYGSV~~AKV 170 (175)
.....||||||++-++||.+.++|++.|.|.....
T Consensus 34 r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiM 68 (153)
T KOG0121|consen 34 RKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIM 68 (153)
T ss_pred hhcceEEEeeeeeeecHHHHHHHHHhccchheeEe
Confidence 45678999999999999999999999999987543
No 34
>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]
Probab=96.77 E-value=0.0012 Score=59.41 Aligned_cols=34 Identities=24% Similarity=0.350 Sum_probs=33.2
Q ss_pred eeecCCCCCCCHHHHHHHhhcCCCcceeEEeecC
Q 030532 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVSFCF 174 (175)
Q Consensus 141 IFVGNLs~dVTDe~L~~aFskYGSV~~AKVV~D~ 174 (175)
|||-||+.++|+..|.++|+.||.|.++||++|.
T Consensus 79 ~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~ 112 (369)
T KOG0123|consen 79 VFIKNLDESIDNKSLYDTFSEFGNILSCKVATDE 112 (369)
T ss_pred eeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcC
Confidence 9999999999999999999999999999999985
No 35
>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]
Probab=96.73 E-value=0.001 Score=62.71 Aligned_cols=39 Identities=13% Similarity=0.238 Sum_probs=36.6
Q ss_pred CCCceeeecCCCCCCCHHHHHHHhhcCCCcceeEEeecC
Q 030532 136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVSFCF 174 (175)
Q Consensus 136 ~ndfrIFVGNLs~dVTDe~L~~aFskYGSV~~AKVV~D~ 174 (175)
.+-.++|||-++...+|.+|+++|++||.|.++.|+.|-
T Consensus 32 ~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk 70 (510)
T KOG0144|consen 32 GSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDK 70 (510)
T ss_pred chhhhheeccCCccccHHHHHHHHHHhCceeEEEeeccc
Confidence 567799999999999999999999999999999999984
No 36
>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=96.54 E-value=0.0025 Score=50.86 Aligned_cols=32 Identities=9% Similarity=0.347 Sum_probs=29.7
Q ss_pred eeeecCCCCCCCHHHHHHHhhcCCCcceeEEe
Q 030532 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVS 171 (175)
Q Consensus 140 rIFVGNLs~dVTDe~L~~aFskYGSV~~AKVV 171 (175)
=|||-||++++|.|+..++|.+||.|...||=
T Consensus 20 iLyirNLp~~ITseemydlFGkyg~IrQIRiG 51 (124)
T KOG0114|consen 20 ILYIRNLPFKITSEEMYDLFGKYGTIRQIRIG 51 (124)
T ss_pred eEEEecCCccccHHHHHHHhhcccceEEEEec
Confidence 48999999999999999999999999988863
No 37
>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]
Probab=96.37 E-value=0.0013 Score=62.16 Aligned_cols=39 Identities=21% Similarity=0.316 Sum_probs=36.5
Q ss_pred CCCceeeecCCCCCCCHHHHHHHhhcCCCcceeEEeecC
Q 030532 136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVSFCF 174 (175)
Q Consensus 136 ~ndfrIFVGNLs~dVTDe~L~~aFskYGSV~~AKVV~D~ 174 (175)
..|.+||||-|+..+||.+++++|++||-|.++.|.+|.
T Consensus 122 ~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~ 160 (510)
T KOG0144|consen 122 VEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDP 160 (510)
T ss_pred ccchhhhhhhccccccHHHHHHHHHhhCccchhhheecc
Confidence 458999999999999999999999999999999999874
No 38
>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]
Probab=96.32 E-value=0.0025 Score=57.88 Aligned_cols=39 Identities=10% Similarity=0.280 Sum_probs=36.1
Q ss_pred CCCceeeecCCCCCCCHHHHHHHhhcCCCcceeEEeecC
Q 030532 136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVSFCF 174 (175)
Q Consensus 136 ~ndfrIFVGNLs~dVTDe~L~~aFskYGSV~~AKVV~D~ 174 (175)
....+||||||++..+.++|++.|.+||.|.+++|+.|.
T Consensus 76 k~stkl~vgNis~tctn~ElRa~fe~ygpviecdivkdy 114 (346)
T KOG0109|consen 76 KASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVKDY 114 (346)
T ss_pred CCccccccCCCCccccCHHHhhhhcccCCceeeeeecce
Confidence 456789999999999999999999999999999999885
No 39
>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]
Probab=96.15 E-value=0.0072 Score=54.02 Aligned_cols=57 Identities=14% Similarity=0.275 Sum_probs=43.2
Q ss_pred cCCCccccccCCCcccCCCCCCCCCCCceeeecCCCCCCCHHHHHHHhhcCCCcceeEEeecCC
Q 030532 112 TKKKSIPRKAAGQTWEDPTLAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVSFCFT 175 (175)
Q Consensus 112 ~k~k~~~R~a~G~~WeDptL~Ew~~ndfrIFVGNLs~dVTDe~L~~aFskYGSV~~AKVV~D~~ 175 (175)
-.++++-|+.....=.- ..-..||||.|+.++++++|++.|.+||-|..+-+++|.+
T Consensus 78 e~k~av~r~~~~~~~~~-------~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~ 134 (311)
T KOG4205|consen 78 EPKRAVSREDQTKVGRH-------LRTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKT 134 (311)
T ss_pred cceeccCcccccccccc-------cceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeeccc
Confidence 34455566544433221 1566899999999999999999999999998998988863
No 40
>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]
Probab=96.11 E-value=0.0029 Score=54.15 Aligned_cols=37 Identities=30% Similarity=0.415 Sum_probs=31.9
Q ss_pred CCceeeecCCCCCCCHHHHHHHhhcCCCcce-eEEeec
Q 030532 137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNM-AKVSFC 173 (175)
Q Consensus 137 ndfrIFVGNLs~dVTDe~L~~aFskYGSV~~-AKVV~D 173 (175)
...+||||||..+|+|..|.++|+.||-|.+ -+|+.|
T Consensus 95 vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd 132 (203)
T KOG0131|consen 95 VGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRD 132 (203)
T ss_pred ccccccccccCcchhHHHHHHHHHhccccccCCccccc
Confidence 4489999999999999999999999999875 355555
No 41
>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]
Probab=96.07 E-value=0.0065 Score=60.37 Aligned_cols=43 Identities=21% Similarity=0.421 Sum_probs=38.9
Q ss_pred CCCCCCCceeeecCCCCCCCHHHHHHHhhcCCCcceeEEeecC
Q 030532 132 AEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVSFCF 174 (175)
Q Consensus 132 ~Ew~~ndfrIFVGNLs~dVTDe~L~~aFskYGSV~~AKVV~D~ 174 (175)
.+-|+...++|||||+..|+++.|...|.+||-|.++||+|-.
T Consensus 168 DdgDP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpR 210 (877)
T KOG0151|consen 168 DDGDPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPR 210 (877)
T ss_pred CCCCCcccceeeecCCccccHHHHHHHhcccCcccceeeeccc
Confidence 4447788899999999999999999999999999999999854
No 42
>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]
Probab=96.04 E-value=0.011 Score=52.44 Aligned_cols=38 Identities=13% Similarity=0.208 Sum_probs=35.4
Q ss_pred CCceeeecCCCCCCCHHHHHHHhhcCCCcceeEEeecC
Q 030532 137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVSFCF 174 (175)
Q Consensus 137 ndfrIFVGNLs~dVTDe~L~~aFskYGSV~~AKVV~D~ 174 (175)
++..|-|.||+.+++|++|+++|.+||.|.++-|++|.
T Consensus 188 D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK 225 (270)
T KOG0122|consen 188 DEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDK 225 (270)
T ss_pred ccceeEEecCccccChhHHHHHhhccCccceeEEEEcc
Confidence 56679999999999999999999999999999999885
No 43
>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor. Members of this subfamily are found in plants, metazoa and fungi.
Probab=95.83 E-value=0.011 Score=52.56 Aligned_cols=27 Identities=19% Similarity=0.438 Sum_probs=24.0
Q ss_pred CCCceeeecCCCCCCCHHHHHHHhhcC
Q 030532 136 ENDYRLFCGDLGNEVNDDVLSKAFSRF 162 (175)
Q Consensus 136 ~ndfrIFVGNLs~dVTDe~L~~aFskY 162 (175)
...-+||||||++++|+++|.++|..|
T Consensus 173 ~~~r~lyVgnLp~~~t~~~l~~~F~~~ 199 (509)
T TIGR01642 173 RQARRLYVGGIPPEFVEEAVVDFFNDL 199 (509)
T ss_pred ccccEEEEeCCCCCCCHHHHHHHHHHH
Confidence 445689999999999999999999865
No 44
>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]
Probab=95.65 E-value=0.0073 Score=53.55 Aligned_cols=33 Identities=33% Similarity=0.668 Sum_probs=29.9
Q ss_pred CceeeecCCCCCCCHHHHHHHhhcCCCcceeEE
Q 030532 138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKV 170 (175)
Q Consensus 138 dfrIFVGNLs~dVTDe~L~~aFskYGSV~~AKV 170 (175)
--.|||.||+.++|||+|+.+|++|.++...||
T Consensus 210 cstlfianl~~~~~ed~l~~~~~~~~gf~~l~~ 242 (284)
T KOG1457|consen 210 CSTLFIANLGPNCTEDELKQLLSRYPGFHILKI 242 (284)
T ss_pred hhhHhhhccCCCCCHHHHHHHHHhCCCceEEEE
Confidence 346999999999999999999999999987775
No 45
>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]
Probab=95.60 E-value=0.017 Score=54.92 Aligned_cols=37 Identities=16% Similarity=0.277 Sum_probs=34.6
Q ss_pred CceeeecCCCCCCCHHHHHHHhhcCCCcceeEEeecC
Q 030532 138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVSFCF 174 (175)
Q Consensus 138 dfrIFVGNLs~dVTDe~L~~aFskYGSV~~AKVV~D~ 174 (175)
-.-||||.|+.|+.||+|.-+|++-|.|-+.|+|+|.
T Consensus 83 G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~ 119 (506)
T KOG0117|consen 83 GCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDP 119 (506)
T ss_pred CceEEecCCCccccchhhHHHHHhccceeeEEEeecc
Confidence 3469999999999999999999999999999999993
No 46
>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]
Probab=95.17 E-value=0.013 Score=57.64 Aligned_cols=36 Identities=22% Similarity=0.248 Sum_probs=33.7
Q ss_pred CceeeecCCCCCCCHHHHHHHhhcCCCcceeEEeec
Q 030532 138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVSFC 173 (175)
Q Consensus 138 dfrIFVGNLs~dVTDe~L~~aFskYGSV~~AKVV~D 173 (175)
--+|||.+|+.-+...+|..+|++||-|+.||||++
T Consensus 405 gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTN 440 (940)
T KOG4661|consen 405 GRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTN 440 (940)
T ss_pred ccceeeeccccchhhhHHHHHHHHhcceeceeeeec
Confidence 346999999999999999999999999999999986
No 47
>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]
Probab=95.10 E-value=0.017 Score=53.63 Aligned_cols=32 Identities=16% Similarity=0.358 Sum_probs=29.2
Q ss_pred eeeecCCCCCCCHHHHHHHhhcCCCcceeEEe
Q 030532 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVS 171 (175)
Q Consensus 140 rIFVGNLs~dVTDe~L~~aFskYGSV~~AKVV 171 (175)
.|||+||+.++++++|.++|..||.|...+|-
T Consensus 290 ~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~ 321 (419)
T KOG0116|consen 290 GIFVKNLPPDATPAELEEVFKQFGPIKEGGIQ 321 (419)
T ss_pred ceEeecCCCCCCHHHHHHHHhhcccccccceE
Confidence 39999999999999999999999999876654
No 48
>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=94.97 E-value=0.027 Score=51.97 Aligned_cols=40 Identities=20% Similarity=0.344 Sum_probs=33.9
Q ss_pred CCCCCCc---eeeecCCCCCCCHHHHHHHhhcCCCcceeEEee
Q 030532 133 EWPENDY---RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVSF 172 (175)
Q Consensus 133 Ew~~ndf---rIFVGNLs~dVTDe~L~~aFskYGSV~~AKVV~ 172 (175)
+|++.|- .||||+|..+++|.+|++-|.+||++...+|+.
T Consensus 220 lepPeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~ 262 (377)
T KOG0153|consen 220 LEPPEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILP 262 (377)
T ss_pred cCCCcccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeec
Confidence 4555544 599999999999999999999999999877653
No 49
>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]
Probab=94.82 E-value=0.022 Score=57.05 Aligned_cols=33 Identities=18% Similarity=0.336 Sum_probs=30.7
Q ss_pred eeeecCCCCCCCHHHHHHHhhcCCCcceeEEee
Q 030532 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVSF 172 (175)
Q Consensus 140 rIFVGNLs~dVTDe~L~~aFskYGSV~~AKVV~ 172 (175)
+||||.|+..|++.+|..+|+.||+|.++++|-
T Consensus 423 TLwvG~i~k~v~e~dL~~~feefGeiqSi~li~ 455 (894)
T KOG0132|consen 423 TLWVGGIPKNVTEQDLANLFEEFGEIQSIILIP 455 (894)
T ss_pred eeeeccccchhhHHHHHHHHHhcccceeEeecc
Confidence 499999999999999999999999999988764
No 50
>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]
Probab=94.79 E-value=0.033 Score=48.46 Aligned_cols=41 Identities=17% Similarity=0.180 Sum_probs=35.0
Q ss_pred CCCCCceeeecCCCCCCCHHHHHHHhhcCCCcceeEEeecC
Q 030532 134 WPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVSFCF 174 (175)
Q Consensus 134 w~~ndfrIFVGNLs~dVTDe~L~~aFskYGSV~~AKVV~D~ 174 (175)
.+....+|.|.||+..|++++|.++|..||.+..+-|=+|.
T Consensus 79 ~~~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~ 119 (243)
T KOG0533|consen 79 NETRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDR 119 (243)
T ss_pred cCCCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCC
Confidence 44556789999999999999999999999988887776654
No 51
>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]
Probab=94.62 E-value=0.029 Score=51.07 Aligned_cols=39 Identities=28% Similarity=0.222 Sum_probs=36.9
Q ss_pred CCCceeeecCCCCCCCHHHHHHHhhcCCCcceeEEeecC
Q 030532 136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVSFCF 174 (175)
Q Consensus 136 ~ndfrIFVGNLs~dVTDe~L~~aFskYGSV~~AKVV~D~ 174 (175)
++-.+|||=.|+.|..|.+|..+|-.||.|.++||.+|.
T Consensus 283 PeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDR 321 (371)
T KOG0146|consen 283 PEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDR 321 (371)
T ss_pred CCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehh
Confidence 467899999999999999999999999999999999985
No 52
>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]
Probab=94.35 E-value=0.019 Score=54.09 Aligned_cols=37 Identities=22% Similarity=0.445 Sum_probs=34.7
Q ss_pred CceeeecCCCCCCCHHHHHHHhhcCCCcceeEEeecC
Q 030532 138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVSFCF 174 (175)
Q Consensus 138 dfrIFVGNLs~dVTDe~L~~aFskYGSV~~AKVV~D~ 174 (175)
-.|+|||.++++..||.|+.+|..||.|++...-||+
T Consensus 113 McRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp 149 (544)
T KOG0124|consen 113 MCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDP 149 (544)
T ss_pred hHheeeeeeEEEechHHHHhhccCCCCcceeeccccc
Confidence 3589999999999999999999999999999998886
No 53
>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=94.12 E-value=0.038 Score=51.84 Aligned_cols=42 Identities=24% Similarity=0.203 Sum_probs=38.1
Q ss_pred CCCCCCceeeecCCCCCCCHHHHHHHhhcCCCcceeEEeecC
Q 030532 133 EWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVSFCF 174 (175)
Q Consensus 133 Ew~~ndfrIFVGNLs~dVTDe~L~~aFskYGSV~~AKVV~D~ 174 (175)
+--+.+.-|||--|.+-+||++|.-+|++||.|.++.||.|.
T Consensus 234 d~~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ 275 (479)
T KOG0415|consen 234 DVKPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDR 275 (479)
T ss_pred ccCCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecc
Confidence 334677789999999999999999999999999999999985
No 54
>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]
Probab=93.92 E-value=0.028 Score=54.01 Aligned_cols=37 Identities=22% Similarity=0.395 Sum_probs=34.2
Q ss_pred Cce-eeecCCCCCCCHHHHHHHhhcCCCcceeEEeecC
Q 030532 138 DYR-LFCGDLGNEVNDDVLSKAFSRFPSFNMAKVSFCF 174 (175)
Q Consensus 138 dfr-IFVGNLs~dVTDe~L~~aFskYGSV~~AKVV~D~ 174 (175)
.|+ ||||||.++.+|++|+.+|+.||.|..+.+.+|.
T Consensus 277 p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~ 314 (549)
T KOG0147|consen 277 PMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDS 314 (549)
T ss_pred chhhhhhcccccCchHHHHhhhccCcccceeeeecccc
Confidence 455 9999999999999999999999999999998884
No 55
>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]
Probab=93.12 E-value=0.058 Score=51.69 Aligned_cols=27 Identities=22% Similarity=0.537 Sum_probs=25.4
Q ss_pred ceeeecCCCCCCCHHHHHHHhhcCCCc
Q 030532 139 YRLFCGDLGNEVNDDVLSKAFSRFPSF 165 (175)
Q Consensus 139 frIFVGNLs~dVTDe~L~~aFskYGSV 165 (175)
.+||||+|+++++|+.|.+.|..||+|
T Consensus 260 ~KVFvGGlp~dise~~i~~~F~~FGs~ 286 (520)
T KOG0129|consen 260 RKVFVGGLPWDITEAQINASFGQFGSV 286 (520)
T ss_pred cceeecCCCccccHHHHHhhcccccce
Confidence 469999999999999999999999995
No 56
>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]
Probab=92.58 E-value=0.12 Score=48.82 Aligned_cols=38 Identities=11% Similarity=0.230 Sum_probs=35.4
Q ss_pred CceeeecCCCCCCCHHHHHHHhhcCCCcceeEEeecCC
Q 030532 138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVSFCFT 175 (175)
Q Consensus 138 dfrIFVGNLs~dVTDe~L~~aFskYGSV~~AKVV~D~~ 175 (175)
-+||||.....|.+|++|..+|+-||.|.++++..+.|
T Consensus 210 fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt 247 (544)
T KOG0124|consen 210 FNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPT 247 (544)
T ss_pred hheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCC
Confidence 46899999999999999999999999999999988765
No 57
>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]
Probab=91.85 E-value=0.15 Score=42.52 Aligned_cols=36 Identities=8% Similarity=0.283 Sum_probs=32.9
Q ss_pred ceeeecCCCCCCCHHHHHHHhhcCCCcceeEEeecC
Q 030532 139 YRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVSFCF 174 (175)
Q Consensus 139 frIFVGNLs~dVTDe~L~~aFskYGSV~~AKVV~D~ 174 (175)
+-|||-++..+.||+++.+.|..||.|...++-.|.
T Consensus 73 wIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDR 108 (170)
T KOG0130|consen 73 WIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDR 108 (170)
T ss_pred EEEEEeccCcchhHHHHHHHHhhcccccceeecccc
Confidence 459999999999999999999999999998887764
No 58
>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]
Probab=91.70 E-value=0.19 Score=45.74 Aligned_cols=39 Identities=18% Similarity=0.178 Sum_probs=36.2
Q ss_pred CCCceeeecCCCCCCCHHHHHHHhhcCCCcceeEEeecC
Q 030532 136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVSFCF 174 (175)
Q Consensus 136 ~ndfrIFVGNLs~dVTDe~L~~aFskYGSV~~AKVV~D~ 174 (175)
+...+|.|.-|+..+|+|+|+.+|+.-|+|.++|+|+|-
T Consensus 39 ~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDK 77 (360)
T KOG0145|consen 39 ESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDK 77 (360)
T ss_pred cccceeeeeecccccCHHHHHHHhhcccceeeeeeeecc
Confidence 456789999999999999999999999999999999984
No 59
>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]
Probab=91.11 E-value=0.16 Score=49.05 Aligned_cols=38 Identities=21% Similarity=0.262 Sum_probs=33.0
Q ss_pred CCCCCCCceeeecCCCCCCCHHHHHHHhhcCCCcceeE
Q 030532 132 AEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAK 169 (175)
Q Consensus 132 ~Ew~~ndfrIFVGNLs~dVTDe~L~~aFskYGSV~~AK 169 (175)
.|.+-+.-.|+|=||+..|++++|+.+|+.||+|+..+
T Consensus 69 ~~~~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir 106 (549)
T KOG4660|consen 69 SEKDMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIR 106 (549)
T ss_pred CcccCccceEEEEecCCcCCHHHHHHHHHhhcchhhhh
Confidence 34556777899999999999999999999999998744
No 60
>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]
Probab=90.87 E-value=0.2 Score=45.33 Aligned_cols=38 Identities=29% Similarity=0.386 Sum_probs=34.8
Q ss_pred CCceeeecCCCCCCCHHHHHHHhhcCCCcceeEEeecC
Q 030532 137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVSFCF 174 (175)
Q Consensus 137 ndfrIFVGNLs~dVTDe~L~~aFskYGSV~~AKVV~D~ 174 (175)
..-+|||-||+..++++.|.+.|+.||.|.+++|+.|.
T Consensus 269 ~~~nl~vknld~~~~~e~L~~~f~~~GeI~s~kv~~~~ 306 (369)
T KOG0123|consen 269 QGANLYVKNLDETLSDEKLRKIFSSFGEITSAKVMVDE 306 (369)
T ss_pred cccccccccCccccchhHHHHHHhcccceeeEEEEecc
Confidence 45579999999999999999999999999999999874
No 61
>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]
Probab=90.71 E-value=0.62 Score=43.34 Aligned_cols=30 Identities=10% Similarity=0.184 Sum_probs=27.5
Q ss_pred CCceeeecCCCCCCCHHHHHHHhhcCCCcc
Q 030532 137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFN 166 (175)
Q Consensus 137 ndfrIFVGNLs~dVTDe~L~~aFskYGSV~ 166 (175)
-+.+|||.||+.|+|.++..++|+++|-|.
T Consensus 133 ~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~ 162 (382)
T KOG1548|consen 133 VNTSVYVSGLPLDITVDEFAEVMSKCGIIM 162 (382)
T ss_pred cCceEEecCCCCcccHHHHHHHHHhcceEe
Confidence 467899999999999999999999999874
No 62
>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]
Probab=89.09 E-value=0.77 Score=43.81 Aligned_cols=59 Identities=17% Similarity=0.183 Sum_probs=45.9
Q ss_pred CCccccccCCCcccCCCCCCCCCCC---ceeeecCCCCCCCHHHHHHHhhcCCCcceeEEee
Q 030532 114 KKSIPRKAAGQTWEDPTLAEWPEND---YRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVSF 172 (175)
Q Consensus 114 ~k~~~R~a~G~~WeDptL~Ew~~nd---frIFVGNLs~dVTDe~L~~aFskYGSV~~AKVV~ 172 (175)
.|.++-+.+-|+=.-..|.|.+..+ ..|-+=||+.|-.-+.|.++|+.+|+|..+||+.
T Consensus 204 ~kL~vseDgkKVrRisPlp~~~~eel~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIck 265 (484)
T KOG1855|consen 204 SKLEVSEDGKKVRRISPLPEFDEEELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICK 265 (484)
T ss_pred ceEEEccCCceeeecCCCCCccccccccceEEEecCCcchHHHHHHHHhhcccceeeeeecC
Confidence 3444555555555566777776654 4688999999999999999999999999999874
No 63
>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]
Probab=85.21 E-value=0.91 Score=43.79 Aligned_cols=37 Identities=14% Similarity=0.153 Sum_probs=33.2
Q ss_pred CceeeecCCCCCCCHHHHHHHhh-cCCCcceeEEeecC
Q 030532 138 DYRLFCGDLGNEVNDDVLSKAFS-RFPSFNMAKVSFCF 174 (175)
Q Consensus 138 dfrIFVGNLs~dVTDe~L~~aFs-kYGSV~~AKVV~D~ 174 (175)
.-+||||+|+..++.++|..+|+ -||.|.=|-|=+|+
T Consensus 370 rrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~ 407 (520)
T KOG0129|consen 370 RRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDP 407 (520)
T ss_pred cceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCc
Confidence 45699999999999999999998 99999988887773
No 64
>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]
Probab=83.39 E-value=0.83 Score=40.17 Aligned_cols=37 Identities=19% Similarity=0.275 Sum_probs=31.3
Q ss_pred CCceeeecCCCCCCCHHHHHHHhhcCCCcceeEEeec
Q 030532 137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVSFC 173 (175)
Q Consensus 137 ndfrIFVGNLs~dVTDe~L~~aFskYGSV~~AKVV~D 173 (175)
.+.-+|||||++++++++|.+.|..+|.+...++..+
T Consensus 184 s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~ 220 (285)
T KOG4210|consen 184 SDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTD 220 (285)
T ss_pred cccceeecccccccchHHHhhhccCcCcceeeccCCC
Confidence 3444559999999999999999999999998887655
No 65
>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]
Probab=83.33 E-value=1.3 Score=43.55 Aligned_cols=36 Identities=19% Similarity=0.237 Sum_probs=32.9
Q ss_pred CCceeeecCCCCCCCHHHHHHHhhcCCCcceeEEee
Q 030532 137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVSF 172 (175)
Q Consensus 137 ndfrIFVGNLs~dVTDe~L~~aFskYGSV~~AKVV~ 172 (175)
...||.|-||+|.+.+++|..+|+.||-|..+.|..
T Consensus 116 ~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~ 151 (678)
T KOG0127|consen 116 PKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPR 151 (678)
T ss_pred ccceEEeecCCcccCcHHHHHHHhhcceEEEEEccc
Confidence 367999999999999999999999999999987754
No 66
>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]
Probab=82.38 E-value=1 Score=40.38 Aligned_cols=37 Identities=24% Similarity=0.322 Sum_probs=34.4
Q ss_pred CceeeecCCCCCCCHHHHHHHhhcCCCcceeEEeecC
Q 030532 138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVSFCF 174 (175)
Q Consensus 138 dfrIFVGNLs~dVTDe~L~~aFskYGSV~~AKVV~D~ 174 (175)
|..|+|-||..-|+-|+|...|++||.+.++-|+.|.
T Consensus 31 ~a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~ 67 (275)
T KOG0115|consen 31 HAELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDD 67 (275)
T ss_pred cceEEEEecchhhhhHHHHHhhhhcCccchheeeecc
Confidence 4779999999999999999999999999999888885
No 67
>PF13893 RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); PDB: 2PE8_A 2PEH_A 2D9O_A 1A9N_D 2DIT_A 3S6E_A 2LQ5_A 1SJQ_A 2AD9_A 1X4D_A ....
Probab=81.62 E-value=1.2 Score=28.47 Aligned_cols=19 Identities=32% Similarity=0.312 Sum_probs=15.1
Q ss_pred HHHHhhcCCCcceeEEeec
Q 030532 155 LSKAFSRFPSFNMAKVSFC 173 (175)
Q Consensus 155 L~~aFskYGSV~~AKVV~D 173 (175)
|.++|++||.|.+.++..+
T Consensus 1 L~~~f~~fG~V~~i~~~~~ 19 (56)
T PF13893_consen 1 LYKLFSKFGEVKKIKIFKK 19 (56)
T ss_dssp HHHHHTTTS-EEEEEEETT
T ss_pred ChHHhCCcccEEEEEEEeC
Confidence 7899999999999887643
No 68
>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]
Probab=80.67 E-value=2.1 Score=40.59 Aligned_cols=29 Identities=24% Similarity=0.214 Sum_probs=23.8
Q ss_pred CCCCceeeecCCCCCCCHHHHHHHhhcCC
Q 030532 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFP 163 (175)
Q Consensus 135 ~~ndfrIFVGNLs~dVTDe~L~~aFskYG 163 (175)
....+.+|||||.|-+||++|.++....|
T Consensus 77 ~Grk~~~YvGNL~W~TTD~DL~~A~~S~G 105 (498)
T KOG4849|consen 77 EGRKYCCYVGNLLWYTTDADLLKALQSTG 105 (498)
T ss_pred cCceEEEEecceeEEeccHHHHHHHHhhh
Confidence 34678899999999999999988875433
No 69
>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=80.56 E-value=1.4 Score=44.04 Aligned_cols=33 Identities=21% Similarity=0.322 Sum_probs=30.1
Q ss_pred CCCceeeecCCCCCCCHHHHHHHhhcCCCccee
Q 030532 136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMA 168 (175)
Q Consensus 136 ~ndfrIFVGNLs~dVTDe~L~~aFskYGSV~~A 168 (175)
..+.-|+||||+.++.+++|..+|..||.|.+.
T Consensus 383 rs~~vil~kNlpa~t~~~elt~~F~~fG~i~rv 415 (725)
T KOG0110|consen 383 RSDTVILVKNLPAGTLSEELTEAFLRFGEIGRV 415 (725)
T ss_pred hhcceeeeccCccccccHHHHHHhhccccccee
Confidence 457889999999999999999999999999864
No 70
>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]
Probab=79.22 E-value=2.3 Score=37.08 Aligned_cols=36 Identities=25% Similarity=0.509 Sum_probs=32.3
Q ss_pred CCCceeeecCCCCCCCHHHHHHHhhcCCCcceeEEe
Q 030532 136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVS 171 (175)
Q Consensus 136 ~ndfrIFVGNLs~dVTDe~L~~aFskYGSV~~AKVV 171 (175)
+.+.-+|+-||+.+++.++|..+|.+|+++..+|.+
T Consensus 144 ppn~ilf~~niP~es~~e~l~~lf~qf~g~keir~i 179 (221)
T KOG4206|consen 144 PPNNILFLTNIPSESESEMLSDLFEQFPGFKEIRLI 179 (221)
T ss_pred CCceEEEEecCCcchhHHHHHHHHhhCcccceeEec
Confidence 456679999999999999999999999999988765
No 71
>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]
Probab=76.65 E-value=1.8 Score=41.44 Aligned_cols=31 Identities=26% Similarity=0.223 Sum_probs=28.6
Q ss_pred CCceeeecCCCCCCCHHHHHHHhhcCCCcce
Q 030532 137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNM 167 (175)
Q Consensus 137 ndfrIFVGNLs~dVTDe~L~~aFskYGSV~~ 167 (175)
.=.|++++|+-+.|+=|.|..+|++||-|.+
T Consensus 149 ~vLr~iie~m~ypVslDVLHqvFS~fG~VlK 179 (492)
T KOG1190|consen 149 PVLRTIIENMFYPVSLDVLHQVFSKFGFVLK 179 (492)
T ss_pred eeEEEEeccceeeeEHHHHHHHHhhcceeEE
Confidence 4569999999999999999999999999876
No 72
>smart00361 RRM_1 RNA recognition motif.
Probab=76.62 E-value=2.3 Score=28.79 Aligned_cols=23 Identities=17% Similarity=0.254 Sum_probs=19.6
Q ss_pred HHHHHHHhh----cCCCcceeE-EeecC
Q 030532 152 DDVLSKAFS----RFPSFNMAK-VSFCF 174 (175)
Q Consensus 152 De~L~~aFs----kYGSV~~AK-VV~D~ 174 (175)
+++|.+.|+ +||.|.++. |++|.
T Consensus 2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~ 29 (70)
T smart00361 2 DEDFEREFSEEEEYFGEVGKINKIYIDN 29 (70)
T ss_pred chhHHHHHHHHHHhcCCeeEEEEEEeCC
Confidence 688999998 999999985 77764
No 73
>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]
Probab=76.42 E-value=1.6 Score=37.43 Aligned_cols=38 Identities=13% Similarity=0.085 Sum_probs=33.7
Q ss_pred CCceeeecCCCCCCCHHHHHHHhhcCCCcceeEEeecC
Q 030532 137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVSFCF 174 (175)
Q Consensus 137 ndfrIFVGNLs~dVTDe~L~~aFskYGSV~~AKVV~D~ 174 (175)
+.-.+||||+.+.+|.+.+..-|+.||.+....|.+|.
T Consensus 100 d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~ 137 (231)
T KOG4209|consen 100 DAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDK 137 (231)
T ss_pred CCceEEEeccccccccchhhheeeccCCccceeeeccc
Confidence 45579999999999999999999999999888887774
No 74
>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=75.97 E-value=2 Score=42.95 Aligned_cols=35 Identities=20% Similarity=0.256 Sum_probs=31.1
Q ss_pred CceeeecCCCCCCCHHHHHHHhhcCCCcceeEEee
Q 030532 138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVSF 172 (175)
Q Consensus 138 dfrIFVGNLs~dVTDe~L~~aFskYGSV~~AKVV~ 172 (175)
+.+|||-||.+++|.+.|...|.++|.|.++.|..
T Consensus 515 ~t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~k 549 (725)
T KOG0110|consen 515 ETKLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISK 549 (725)
T ss_pred chhhhhhcCCcccchhHHHHHHHhcCeEEEEEEec
Confidence 34499999999999999999999999999987653
No 75
>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]
Probab=73.14 E-value=3.2 Score=39.78 Aligned_cols=32 Identities=16% Similarity=0.025 Sum_probs=28.2
Q ss_pred ceeeecCCCCCCCHHHHHHHhhcCCCcceeEE
Q 030532 139 YRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKV 170 (175)
Q Consensus 139 frIFVGNLs~dVTDe~L~~aFskYGSV~~AKV 170 (175)
--|-++||++|++|++|..++..||.|+..+.
T Consensus 29 kV~HlRnlp~e~tE~elI~Lg~pFG~vtn~~~ 60 (492)
T KOG1190|consen 29 KVVHLRNLPWEVTEEELISLGLPFGKVTNLLM 60 (492)
T ss_pred ceeEeccCCccccHHHHHHhcccccceeeeee
Confidence 34779999999999999999999999987654
No 76
>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]
Probab=71.57 E-value=4.3 Score=36.43 Aligned_cols=30 Identities=27% Similarity=0.460 Sum_probs=25.8
Q ss_pred eeeecCCCCCCCHHHHHHHhhcCCCcceeE
Q 030532 140 RLFCGDLGNEVNDDVLSKAFSRFPSFNMAK 169 (175)
Q Consensus 140 rIFVGNLs~dVTDe~L~~aFskYGSV~~AK 169 (175)
.|||.+|+.||.--+|..+|..|.+...+.
T Consensus 36 TLFVSGLP~DvKpREiynLFR~f~GYEgsl 65 (284)
T KOG1457|consen 36 TLFVSGLPNDVKPREIYNLFRRFHGYEGSL 65 (284)
T ss_pred eeeeccCCcccCHHHHHHHhccCCCcccee
Confidence 599999999999999999999887665443
No 77
>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]
Probab=59.35 E-value=6.7 Score=38.20 Aligned_cols=35 Identities=11% Similarity=0.182 Sum_probs=31.1
Q ss_pred CCCceeeecCCCCCCCHHHHHHHhhcCCCcceeEE
Q 030532 136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKV 170 (175)
Q Consensus 136 ~ndfrIFVGNLs~dVTDe~L~~aFskYGSV~~AKV 170 (175)
+.-.+|||-||+++.|=.+|++-|..||.|.-|.|
T Consensus 534 rKa~qIiirNlP~dfTWqmlrDKfre~G~v~yadi 568 (608)
T KOG4212|consen 534 RKACQIIIRNLPFDFTWQMLRDKFREIGHVLYADI 568 (608)
T ss_pred ccccEEEEecCCccccHHHHHHHHHhccceehhhh
Confidence 44567999999999999999999999999987765
No 78
>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=58.86 E-value=8.7 Score=29.01 Aligned_cols=27 Identities=26% Similarity=0.423 Sum_probs=16.7
Q ss_pred eeecCCCCCCCHHHHHHHhhcCCCcce
Q 030532 141 LFCGDLGNEVNDDVLSKAFSRFPSFNM 167 (175)
Q Consensus 141 IFVGNLs~dVTDe~L~~aFskYGSV~~ 167 (175)
|++-++..+++.++|.++|+.||.|.=
T Consensus 4 l~~~g~~~~~~re~iK~~f~~~g~V~y 30 (105)
T PF08777_consen 4 LKFSGLGEPTSREDIKEAFSQFGEVAY 30 (105)
T ss_dssp EEEEE--SS--HHHHHHHT-SS--EEE
T ss_pred EEEecCCCCcCHHHHHHHHHhcCCcce
Confidence 566679999999999999999998753
No 79
>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]
Probab=57.18 E-value=7.5 Score=37.45 Aligned_cols=38 Identities=13% Similarity=0.238 Sum_probs=33.3
Q ss_pred CCceeeecCCCCCCCHHHHHHHhhcCCCcceeEEeecC
Q 030532 137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVSFCF 174 (175)
Q Consensus 137 ndfrIFVGNLs~dVTDe~L~~aFskYGSV~~AKVV~D~ 174 (175)
...+||||+|+.-.+++.+.++-..||.+..-+.+.|.
T Consensus 288 ~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~ 325 (500)
T KOG0120|consen 288 SPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDS 325 (500)
T ss_pred ccchhhhccCcCccCHHHHHHHHHhcccchhheeeccc
Confidence 45689999999999999999999999999888887763
No 80
>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]
Probab=56.67 E-value=18 Score=35.35 Aligned_cols=37 Identities=11% Similarity=0.114 Sum_probs=32.2
Q ss_pred CceeeecCCCCCCCHHHHHHHhh-cCCCcceeEEeecC
Q 030532 138 DYRLFCGDLGNEVNDDVLSKAFS-RFPSFNMAKVSFCF 174 (175)
Q Consensus 138 dfrIFVGNLs~dVTDe~L~~aFs-kYGSV~~AKVV~D~ 174 (175)
+-.+||-|+++|+.=.+|+++|. +-|+|.-+.+.+|-
T Consensus 44 ~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~ 81 (608)
T KOG4212|consen 44 DRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDE 81 (608)
T ss_pred cceEEEecCcchhhhHhHHHHHHHhcCceEeeeeeccc
Confidence 33499999999999999999995 88999888887773
No 81
>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]
Probab=55.82 E-value=5 Score=39.11 Aligned_cols=37 Identities=16% Similarity=0.121 Sum_probs=34.4
Q ss_pred CceeeecCCCCCCCHHHHHHHhhcCCCcceeEEeecC
Q 030532 138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVSFCF 174 (175)
Q Consensus 138 dfrIFVGNLs~dVTDe~L~~aFskYGSV~~AKVV~D~ 174 (175)
.-.+||--|+..++.-+|.++|+..|-|..+++|.|.
T Consensus 179 ~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr 215 (549)
T KOG0147|consen 179 QRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDR 215 (549)
T ss_pred HHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccc
Confidence 3459999999999999999999999999999999985
No 82
>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=52.04 E-value=6.5 Score=40.59 Aligned_cols=34 Identities=18% Similarity=0.359 Sum_probs=29.3
Q ss_pred CCceeeecCCCCCCCHHHHHHHhhcCCCcceeEE
Q 030532 137 NDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKV 170 (175)
Q Consensus 137 ndfrIFVGNLs~dVTDe~L~~aFskYGSV~~AKV 170 (175)
..-.||+|||...+++.+|+.+|..||-|.++.|
T Consensus 371 atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDi 404 (975)
T KOG0112|consen 371 ATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDI 404 (975)
T ss_pred hhhhhhhcCcccchhhhhhhhhhhhhcccccccc
Confidence 3446999999999999999999999998876553
No 83
>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]
Probab=41.10 E-value=32 Score=31.17 Aligned_cols=31 Identities=6% Similarity=0.113 Sum_probs=27.6
Q ss_pred CceeeecCCCCCCCHHHHHHHhhcCCCccee
Q 030532 138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFNMA 168 (175)
Q Consensus 138 dfrIFVGNLs~dVTDe~L~~aFskYGSV~~A 168 (175)
.-=||+++++...+-.-|+++|+.||.|-++
T Consensus 74 ~GVvylS~IPp~m~~~rlReil~~yGeVGRv 104 (278)
T KOG3152|consen 74 TGVVYLSNIPPYMDPVRLREILSQYGEVGRV 104 (278)
T ss_pred ceEEEeccCCCccCHHHHHHHHHhccccceE
Confidence 3459999999999999999999999998554
No 84
>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]
Probab=35.81 E-value=10 Score=36.32 Aligned_cols=30 Identities=13% Similarity=-0.041 Sum_probs=27.7
Q ss_pred eeecCCCCCCCHHHHHHHhhcCCCcceeEE
Q 030532 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAKV 170 (175)
Q Consensus 141 IFVGNLs~dVTDe~L~~aFskYGSV~~AKV 170 (175)
|+|++|..++...++.+.|.+||+|.-+++
T Consensus 154 ~~v~sl~~~~~l~e~~e~f~r~Gev~ya~~ 183 (479)
T KOG4676|consen 154 REVQSLISAAILPESGESFERKGEVSYAHT 183 (479)
T ss_pred hhhhcchhhhcchhhhhhhhhcchhhhhhh
Confidence 999999999999999999999999977654
No 85
>PF12631 GTPase_Cys_C: Catalytic cysteine-containing C-terminus of GTPase, MnmE; PDB: 1XZQ_A 1XZP_A 2GJ8_D 3GEH_A 3GEI_B 3GEE_A.
Probab=34.41 E-value=31 Score=24.13 Aligned_cols=15 Identities=40% Similarity=0.764 Sum_probs=11.0
Q ss_pred CCCCHHHHHHHhhcC
Q 030532 148 NEVNDDVLSKAFSRF 162 (175)
Q Consensus 148 ~dVTDe~L~~aFskY 162 (175)
..++|+.|.++|++|
T Consensus 58 ~~~~ediLd~IFs~F 72 (73)
T PF12631_consen 58 EVVTEDILDNIFSNF 72 (73)
T ss_dssp SS--HHHHHHHHCTS
T ss_pred CCChHHHHHHHHHhh
Confidence 467789999999987
No 86
>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]
Probab=34.30 E-value=14 Score=33.03 Aligned_cols=43 Identities=23% Similarity=0.362 Sum_probs=37.2
Q ss_pred CCCCCCCceeeecC----CCCCCCHHHHHHHhhcCCCcceeEEeecC
Q 030532 132 AEWPENDYRLFCGD----LGNEVNDDVLSKAFSRFPSFNMAKVSFCF 174 (175)
Q Consensus 132 ~Ew~~ndfrIFVGN----Ls~dVTDe~L~~aFskYGSV~~AKVV~D~ 174 (175)
++-++....+++|+ |.-.++++.|...|+.=+.+..+|+-+|+
T Consensus 74 l~~~e~q~~~r~G~shapld~r~~~ei~~~v~s~a~p~~~~R~~~~~ 120 (267)
T KOG4454|consen 74 LEEDEEQRTLRCGNSHAPLDERVTEEILYEVFSQAGPIEGVRIPTDN 120 (267)
T ss_pred hccchhhcccccCCCcchhhhhcchhhheeeecccCCCCCccccccc
Confidence 33446788999999 99999999999999999999999887765
No 87
>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]
Probab=28.70 E-value=76 Score=23.67 Aligned_cols=36 Identities=19% Similarity=0.306 Sum_probs=30.5
Q ss_pred CCCceeeecCCCCCCCHHHHHHHhhcCCCcceeEEe
Q 030532 136 ENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVS 171 (175)
Q Consensus 136 ~ndfrIFVGNLs~dVTDe~L~~aFskYGSV~~AKVV 171 (175)
...-.++++++...++++.+...|..+|.+..+.+.
T Consensus 223 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 258 (306)
T COG0724 223 EKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLP 258 (306)
T ss_pred cccceeeccccccccchhHHHHhccccccceeeecc
Confidence 345579999999999999999999999998666544
No 88
>COG0030 KsgA Dimethyladenosine transferase (rRNA methylation) [Translation, ribosomal structure and biogenesis]
Probab=28.30 E-value=90 Score=27.58 Aligned_cols=35 Identities=9% Similarity=-0.005 Sum_probs=27.3
Q ss_pred CceeeecCCCCCCCHHHHHHHhhcCCCcceeEEee
Q 030532 138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVSF 172 (175)
Q Consensus 138 dfrIFVGNLs~dVTDe~L~~aFskYGSV~~AKVV~ 172 (175)
.....||||++.++...|.+++..-..+..+-+++
T Consensus 95 ~~~~vVaNlPY~Isspii~kll~~~~~~~~~v~M~ 129 (259)
T COG0030 95 QPYKVVANLPYNISSPILFKLLEEKFIIQDMVLMV 129 (259)
T ss_pred CCCEEEEcCCCcccHHHHHHHHhccCccceEEEEe
Confidence 56778999999999999999998655555554443
No 89
>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]
Probab=28.29 E-value=34 Score=35.35 Aligned_cols=36 Identities=6% Similarity=-0.056 Sum_probs=32.5
Q ss_pred CceeeecCCCCCCCHHHHHHHhhcCCCcceeEEeec
Q 030532 138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVSFC 173 (175)
Q Consensus 138 dfrIFVGNLs~dVTDe~L~~aFskYGSV~~AKVV~D 173 (175)
.+.+||.|+++..|++.|+.+|+..|.+.+.++++.
T Consensus 736 K~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~ 771 (881)
T KOG0128|consen 736 KISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTV 771 (881)
T ss_pred hhhhheeCCCCCCchHHHHhhccccCCccccchhhh
Confidence 557999999999999999999999999999877654
No 90
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=26.17 E-value=67 Score=30.71 Aligned_cols=28 Identities=14% Similarity=0.329 Sum_probs=23.4
Q ss_pred eeecCCCCCCCHHH----H--HHHhhcCCCccee
Q 030532 141 LFCGDLGNEVNDDV----L--SKAFSRFPSFNMA 168 (175)
Q Consensus 141 IFVGNLs~dVTDe~----L--~~aFskYGSV~~A 168 (175)
+||-+|+..|-+|+ | .+.|.+||.|.+.
T Consensus 117 vYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KI 150 (480)
T COG5175 117 VYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKI 150 (480)
T ss_pred eEEecCCCCCCcccccccccchhhhhhccceeEE
Confidence 79999999999877 2 4689999998764
No 91
>smart00650 rADc Ribosomal RNA adenine dimethylases.
Probab=25.85 E-value=1.3e+02 Score=23.17 Aligned_cols=35 Identities=20% Similarity=0.262 Sum_probs=25.5
Q ss_pred CceeeecCCCCCCCHHHHHHHhhcCCCcceeEEee
Q 030532 138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVSF 172 (175)
Q Consensus 138 dfrIFVGNLs~dVTDe~L~~aFskYGSV~~AKVV~ 172 (175)
.+-+.+||+++..+.+.|.+++........+-+++
T Consensus 77 ~~d~vi~n~Py~~~~~~i~~~l~~~~~~~~~~l~~ 111 (169)
T smart00650 77 QPYKVVGNLPYNISTPILFKLLEEPPAFRDAVLMV 111 (169)
T ss_pred CCCEEEECCCcccHHHHHHHHHhcCCCcceEEEEE
Confidence 46688999999999999999987433334444443
No 92
>PF15063 TC1: Thyroid cancer protein 1
Probab=25.52 E-value=16 Score=27.58 Aligned_cols=32 Identities=19% Similarity=0.234 Sum_probs=25.7
Q ss_pred ecCCCCCCCHHHHHHHhhcCCCcc---eeEEeecC
Q 030532 143 CGDLGNEVNDDVLSKAFSRFPSFN---MAKVSFCF 174 (175)
Q Consensus 143 VGNLs~dVTDe~L~~aFskYGSV~---~AKVV~D~ 174 (175)
++|+=.+|+.+.|.++|.+=|... +|++|+.+
T Consensus 30 saNIFe~vn~~qlqrLF~~sGD~kAEeRA~iI~~~ 64 (79)
T PF15063_consen 30 SANIFENVNLDQLQRLFQKSGDKKAEERARIIWEC 64 (79)
T ss_pred hhhhhhccCHHHHHHHHHHccchhHHHHHHHHHhh
Confidence 677778899999999999888764 57777654
No 93
>PTZ00338 dimethyladenosine transferase-like protein; Provisional
Probab=24.70 E-value=83 Score=27.61 Aligned_cols=34 Identities=12% Similarity=0.259 Sum_probs=25.8
Q ss_pred CceeeecCCCCCCCHHHHHHHhhcCCCcceeEEe
Q 030532 138 DYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVS 171 (175)
Q Consensus 138 dfrIFVGNLs~dVTDe~L~~aFskYGSV~~AKVV 171 (175)
.+.+.|+||++.++...|.++.+.-..+..+-+|
T Consensus 101 ~~d~VvaNlPY~Istpil~~ll~~~~~~~~~vlm 134 (294)
T PTZ00338 101 YFDVCVANVPYQISSPLVFKLLAHRPLFRCAVLM 134 (294)
T ss_pred ccCEEEecCCcccCcHHHHHHHhcCCCCceeeee
Confidence 4568899999999999999998654445555444
No 94
>cd00027 BRCT Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks.
Probab=24.43 E-value=1.6e+02 Score=17.61 Aligned_cols=27 Identities=7% Similarity=-0.026 Sum_probs=19.8
Q ss_pred ceeeecCCCCCCCHHHHHHHhhcCCCc
Q 030532 139 YRLFCGDLGNEVNDDVLSKAFSRFPSF 165 (175)
Q Consensus 139 frIFVGNLs~dVTDe~L~~aFskYGSV 165 (175)
+++++.+.....+.+.|.++...+|+-
T Consensus 2 ~~~~i~g~~~~~~~~~l~~~i~~~Gg~ 28 (72)
T cd00027 2 LTFVITGDLPSEERDELKELIEKLGGK 28 (72)
T ss_pred CEEEEEecCCCcCHHHHHHHHHHcCCE
Confidence 455665555478889999999888773
No 95
>cd03517 Link_domain_CSPGs_modules_1_3 Link_domain_CSPGs_modules_1_3; this extracellular link domain is found in the first and third link modules of the chondroitin sulfate proteoglycan core protein (CSPG) aggrecan. In addition, it is found in the first link module of three other CSPGs: versican, neurocan, and brevican. The link domain is a hyaluronan (HA)-binding domain. CSPGs are characterized by an N-terminal globular domain (G1 domain) containing two contiguous link modules (modules 1 and 2). Both link modules of the G1 domain of aggrecan are involved in interaction with HA. In addition, aggrecan contains a second globular domain (G2) which contains link modules 3 and 4. G2 appears to lack HA-binding activity. In cartilage, aggrecan forms cartilage link protein stabilized aggregates with HA. These aggregates contribute to the tissue's load bearing properties. Aggregates having other CSPGs substituting for aggrecan may contribute to the structural integrity of many different tissues.
Probab=23.94 E-value=79 Score=24.21 Aligned_cols=29 Identities=31% Similarity=0.425 Sum_probs=21.9
Q ss_pred CCcCCchhhHHHHHHhhhccCCC-CHHHHHH
Q 030532 67 APVYSLPQYHQAQQLFQRDAQTI-TPEALES 96 (175)
Q Consensus 67 ~~~y~~~~~~qa~~~~q~~~~~~-~peal~~ 96 (175)
.|.|.+ ..++|+++.+..+-+| +++-|..
T Consensus 9 ~grY~l-~f~eA~~aC~~~ga~lAs~~QL~~ 38 (95)
T cd03517 9 TARYAL-TFPRAQRACLDISAQIATPEQLLA 38 (95)
T ss_pred CCceeE-CHHHHHHHHHHcCCEeCCHHHHHH
Confidence 599998 6777999998555555 8887764
No 96
>PRK00274 ksgA 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed
Probab=23.21 E-value=94 Score=26.37 Aligned_cols=33 Identities=9% Similarity=-0.002 Sum_probs=24.5
Q ss_pred ceeeecCCCCCCCHHHHHHHhhcCCCcceeEEe
Q 030532 139 YRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKVS 171 (175)
Q Consensus 139 frIFVGNLs~dVTDe~L~~aFskYGSV~~AKVV 171 (175)
.-.+||||++.++.+.|.++...-..+..+-++
T Consensus 106 ~~~vv~NlPY~iss~ii~~~l~~~~~~~~~~l~ 138 (272)
T PRK00274 106 PLKVVANLPYNITTPLLFHLLEERDPIRDMVVM 138 (272)
T ss_pred cceEEEeCCccchHHHHHHHHhcCCCCCeeEEE
Confidence 367899999999999999998643335555443
No 97
>PF00398 RrnaAD: Ribosomal RNA adenine dimethylase; InterPro: IPR001737 This family of proteins include rRNA adenine dimethylases (e.g. KsgA) and the Erythromycin resistance methylases (Erm). The bacterial enzyme KsgA catalyses the transfer of a total of four methyl groups from S-adenosyl-l-methionine (S-AdoMet) to two adjacent adenosine bases in 16S rRNA. This enzyme and the resulting modified adenosine bases appear to be conserved in all species of eubacteria, eukaryotes, and archaea, and in eukaryotic organelles. Bacterial resistance to the aminoglycoside antibiotic kasugamycin involves inactivation of KsgA and resulting loss of the dimethylations, with modest consequences to the overall fitness of the organism. In contrast, the yeast ortholog, Dim1, is essential. In Saccharomyces cerevisiae (Baker's yeast), and presumably in other eukaryotes, the enzyme performs a vital role in pre-rRNA processing in addition to its methylating activity. The best conserved region in these enzymes is located in the N-terminal section and corresponds to a region that is probably involved in S-adenosyl methionine (SAM) binding domain. The crystal structure of KsgA from Escherichia coli has been solved to a resolution of 2.1A. It bears a strong similarity to the crystal structure of ErmC' from Bacillus stearothermophilus and a lesser similarity to the yeast mitochondrial transcription factor, sc-mtTFB []. The Erm family of RNA methyltransferases, which methylate a single adenosine base in 23S rRNA confer resistance to the MLS-B group of antibiotics. Despite their sequence similarity, the two enzyme families have strikingly different levels of regulation that remain to be elucidated. Other orthologs, of this family include the yeast and Homo sapiens (Human) mitochondrial transcription factors (MTF1 and h-mtTFB respectively), which are nuclear encoded []. Human-mtTFB is able to stimulate transcription in vitro independently of its S-adenosylmethionine binding and rRNA methyltransferase activity [].; GO: 0000179 rRNA (adenine-N6,N6-)-dimethyltransferase activity, 0008649 rRNA methyltransferase activity, 0000154 rRNA modification; PDB: 3FTF_A 3R9X_B 3FTE_A 3FTC_A 3FTD_A 3GRY_A 3FYC_A 3GRU_A 3FYD_A 3GRV_A ....
Probab=22.36 E-value=54 Score=27.58 Aligned_cols=30 Identities=27% Similarity=0.439 Sum_probs=24.4
Q ss_pred CCceeeecCCCCCCCHHHHHHHhh--cCCCcc
Q 030532 137 NDYRLFCGDLGNEVNDDVLSKAFS--RFPSFN 166 (175)
Q Consensus 137 ndfrIFVGNLs~dVTDe~L~~aFs--kYGSV~ 166 (175)
+.--++||||++.++...|.+++. .||-+.
T Consensus 96 ~~~~~vv~NlPy~is~~il~~ll~~~~~g~~~ 127 (262)
T PF00398_consen 96 NQPLLVVGNLPYNISSPILRKLLELYRFGRVR 127 (262)
T ss_dssp SSEEEEEEEETGTGHHHHHHHHHHHGGGCEEE
T ss_pred CCceEEEEEecccchHHHHHHHhhcccccccc
Confidence 456689999999999999999996 565543
No 98
>PF02358 Trehalose_PPase: Trehalose-phosphatase; InterPro: IPR003337 Trehalose-phosphatases 3.1.3.12 from EC catalyse the de-phosphorylation of trehalose-6-phosphate to trehalose and orthophosphate. Trehalose is a common disaccharide of bacteria, fungi and invertebrates that appears to play a major role in desiccation tolerance. A pathway for trehalose biosynthesis may also exist in plants []. The trehalose-phosphatase signature is found in the C terminus of trehalose-6-phosphate synthase 2.4.1.15 from EC adjacent to the trehalose-6-phosphate synthase domain (see IPR001830 from INTERPRO). It would appear that the two equivalent genes in the Escherichia coli otsBA operon: otsA, the trehalose-6-phosphate synthase and otsB, trehalose-phosphatase (this family) have undergone gene fusion in most eukaryotes [].; GO: 0003824 catalytic activity, 0005992 trehalose biosynthetic process; PDB: 1U02_A.
Probab=20.89 E-value=62 Score=26.38 Aligned_cols=24 Identities=25% Similarity=0.534 Sum_probs=17.3
Q ss_pred CCCceeeecCCCCCCCHHHHHHHhhcC
Q 030532 136 ENDYRLFCGDLGNEVNDDVLSKAFSRF 162 (175)
Q Consensus 136 ~ndfrIFVGNLs~dVTDe~L~~aFskY 162 (175)
..++-||+|| |+|||+..+.+...
T Consensus 183 ~~~~~l~~GD---D~tDE~~f~~~~~~ 206 (235)
T PF02358_consen 183 KPDFVLYIGD---DRTDEDAFRALREL 206 (235)
T ss_dssp ----EEEEES---SHHHHHHHHTTTTS
T ss_pred ccceeEEecC---CCCCHHHHHHHHhc
Confidence 4689999999 88899988888765
No 99
>PF08862 DUF1829: Domain of unknown function DUF1829; InterPro: IPR014961 This short protein is usually associated with IPR014960 from INTERPRO.
Probab=20.81 E-value=1.2e+02 Score=22.35 Aligned_cols=38 Identities=13% Similarity=0.391 Sum_probs=25.7
Q ss_pred cccCCC-CCCCCCCCceeeecCCCCCCCHHHHHHHhhcCC
Q 030532 125 TWEDPT-LAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFP 163 (175)
Q Consensus 125 ~WeDpt-L~Ew~~ndfrIFVGNLs~dVTDe~L~~aFskYG 163 (175)
.|+|-. ...-....+.+++-|...++++ .+..+|..|+
T Consensus 41 ~w~D~~~~~~~~~~~~~ii~ND~e~~i~~-~~~~a~~~y~ 79 (88)
T PF08862_consen 41 AWEDTKKRNRKSNSKFYIILNDSEKPISE-DIINALEQYN 79 (88)
T ss_pred HHhhhhhhccCCCceEEEEECCCCCccCH-HHHHHHHHCC
Confidence 466652 2223456888999888888876 5667888776
Done!