Query 037095
Match_columns 334
No_of_seqs 270 out of 1333
Neff 5.8
Searched_HMMs 46136
Date Fri Mar 29 08:36:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/037095.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/037095hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0116 RasGAP SH3 binding pro 100.0 9.6E-56 2.1E-60 438.5 26.2 317 1-333 1-325 (419)
2 KOG2104 Nuclear transport fact 100.0 7.4E-34 1.6E-38 234.8 11.1 118 12-134 5-123 (126)
3 cd00780 NTF2 Nuclear transport 100.0 5.7E-33 1.2E-37 231.8 15.1 118 12-134 1-119 (119)
4 PF02136 NTF2: Nuclear transpo 99.9 1.9E-27 4.2E-32 196.0 13.0 113 16-132 1-118 (118)
5 KOG4353 RNA export factor NXT1 99.9 1.2E-23 2.6E-28 176.5 6.8 116 12-134 11-136 (139)
6 cd00531 NTF2_like Nuclear tran 98.7 4.6E-07 1E-11 71.8 12.7 115 18-132 2-123 (124)
7 PF10429 Mtr2: Nuclear pore RN 98.4 4.5E-07 9.7E-12 80.2 5.8 98 15-119 5-109 (166)
8 KOG3763 mRNA export factor TAP 98.1 1.3E-05 2.9E-10 82.5 9.8 124 11-136 335-499 (585)
9 PF00076 RRM_1: RNA recognitio 98.0 5.5E-06 1.2E-10 60.8 4.1 32 299-330 1-32 (70)
10 PLN03134 glycine-rich RNA-bind 98.0 8E-06 1.7E-10 71.0 4.9 37 295-331 33-69 (144)
11 KOG0127 Nucleolar protein fibr 97.9 8.5E-06 1.8E-10 83.4 4.5 41 290-330 286-326 (678)
12 KOG0114 Predicted RNA-binding 97.9 1.2E-05 2.7E-10 66.6 3.6 33 296-328 18-50 (124)
13 TIGR01661 ELAV_HUD_SF ELAV/HuD 97.9 3.1E-05 6.7E-10 74.9 6.8 38 294-331 267-304 (352)
14 PF14259 RRM_6: RNA recognitio 97.7 5.1E-05 1.1E-09 56.5 3.9 31 299-329 1-31 (70)
15 TIGR01659 sex-lethal sex-letha 97.6 7E-05 1.5E-09 74.0 5.6 40 291-330 102-141 (346)
16 PF15008 DUF4518: Domain of un 97.5 0.00074 1.6E-08 64.3 10.2 124 11-134 125-260 (262)
17 smart00362 RRM_2 RNA recogniti 97.5 0.00015 3.2E-09 52.0 3.9 32 298-329 1-32 (72)
18 KOG0121 Nuclear cap-binding pr 97.4 0.00011 2.3E-09 63.2 2.4 31 295-325 35-65 (153)
19 COG0724 RNA-binding proteins ( 97.3 0.00022 4.7E-09 63.4 4.3 35 296-330 115-149 (306)
20 TIGR01659 sex-lethal sex-letha 97.2 0.00028 6.1E-09 69.8 4.3 35 296-330 193-227 (346)
21 cd00590 RRM RRM (RNA recogniti 97.2 0.00049 1.1E-08 49.5 3.8 32 298-329 1-32 (74)
22 PF13474 SnoaL_3: SnoaL-like d 97.1 0.0083 1.8E-07 48.2 10.8 110 18-131 2-117 (121)
23 TIGR01622 SF-CC1 splicing fact 97.1 0.00055 1.2E-08 68.9 4.6 38 293-330 86-123 (457)
24 TIGR01642 U2AF_lg U2 snRNP aux 97.1 0.00057 1.2E-08 69.6 4.7 36 295-330 294-329 (509)
25 TIGR01645 half-pint poly-U bin 97.1 0.00061 1.3E-08 72.0 4.9 36 295-330 106-141 (612)
26 TIGR02246 conserved hypothetic 97.0 0.023 4.9E-07 46.3 12.7 112 15-131 4-124 (128)
27 TIGR01648 hnRNP-R-Q heterogene 97.0 0.00076 1.6E-08 70.9 4.7 36 295-330 57-92 (578)
28 TIGR01628 PABP-1234 polyadenyl 96.9 0.00089 1.9E-08 69.5 4.6 38 294-331 283-320 (562)
29 TIGR01645 half-pint poly-U bin 96.8 0.0012 2.5E-08 69.9 4.4 35 295-329 203-237 (612)
30 TIGR01649 hnRNP-L_PTB hnRNP-L/ 96.8 0.0015 3.3E-08 66.9 5.0 37 294-330 273-310 (481)
31 TIGR01622 SF-CC1 splicing fact 96.7 0.0016 3.4E-08 65.6 4.4 34 296-329 186-219 (457)
32 KOG0113 U1 small nuclear ribon 96.6 0.0017 3.6E-08 62.7 3.5 35 295-329 100-134 (335)
33 PF14534 DUF4440: Domain of un 96.6 0.038 8.1E-07 43.0 10.5 101 19-125 3-107 (107)
34 TIGR01648 hnRNP-R-Q heterogene 96.5 0.0025 5.5E-08 67.0 4.4 33 296-328 233-267 (578)
35 TIGR01661 ELAV_HUD_SF ELAV/HuD 96.5 0.0031 6.7E-08 61.0 4.6 37 295-331 88-124 (352)
36 smart00360 RRM RNA recognition 96.4 0.0028 6E-08 45.0 2.7 30 301-330 1-30 (71)
37 KOG0126 Predicted RNA-binding 96.3 0.00093 2E-08 60.6 -0.5 37 295-332 34-70 (219)
38 TIGR01649 hnRNP-L_PTB hnRNP-L/ 96.2 0.0052 1.1E-07 63.1 4.8 36 295-330 393-428 (481)
39 KOG0117 Heterogeneous nuclear 96.2 0.0028 6E-08 64.1 2.5 32 297-328 260-291 (506)
40 KOG0148 Apoptosis-promoting RN 96.2 0.0045 9.7E-08 59.2 3.7 35 295-329 163-197 (321)
41 TIGR01628 PABP-1234 polyadenyl 96.1 0.0061 1.3E-07 63.3 4.5 35 295-329 177-211 (562)
42 KOG0125 Ataxin 2-binding prote 95.8 0.01 2.2E-07 58.1 4.0 36 296-331 96-131 (376)
43 TIGR01642 U2AF_lg U2 snRNP aux 95.6 0.014 3E-07 59.5 4.4 27 294-320 173-199 (509)
44 KOG0122 Translation initiation 95.4 0.017 3.7E-07 54.6 3.9 36 295-330 188-223 (270)
45 KOG0533 RRM motif-containing p 95.3 0.017 3.6E-07 54.8 3.6 35 295-329 82-116 (243)
46 PF12680 SnoaL_2: SnoaL-like d 95.3 0.093 2E-06 40.0 7.3 72 21-100 1-75 (102)
47 KOG0145 RNA-binding protein EL 94.9 0.012 2.6E-07 56.1 1.7 36 295-330 126-161 (360)
48 PF12893 Lumazine_bd_2: Putati 94.6 0.72 1.6E-05 37.8 11.3 105 17-131 6-116 (116)
49 KOG0127 Nucleolar protein fibr 94.5 0.027 5.8E-07 58.5 3.0 33 296-328 117-149 (678)
50 KOG0110 RNA-binding protein (R 94.4 0.022 4.9E-07 60.4 2.1 37 295-331 612-648 (725)
51 KOG0144 RNA-binding protein CU 94.3 0.037 8.1E-07 56.0 3.3 35 294-328 32-66 (510)
52 KOG0144 RNA-binding protein CU 94.1 0.018 4E-07 58.1 0.8 35 295-329 123-157 (510)
53 KOG1548 Transcription elongati 94.1 0.042 9E-07 54.2 3.2 32 295-326 133-164 (382)
54 KOG0123 Polyadenylate-binding 93.4 0.065 1.4E-06 53.7 3.4 36 298-333 78-113 (369)
55 KOG0153 Predicted RNA-binding 93.2 0.083 1.8E-06 52.2 3.6 37 295-331 227-263 (377)
56 cd00781 ketosteroid_isomerase 92.7 0.99 2.1E-05 36.5 8.8 52 18-72 6-58 (122)
57 KOG4212 RNA-binding protein hn 92.6 0.085 1.8E-06 53.6 2.8 34 295-328 535-568 (608)
58 KOG4661 Hsp27-ERE-TATA-binding 92.4 0.22 4.7E-06 52.2 5.5 36 295-330 404-439 (940)
59 KOG0130 RNA-binding protein RB 92.4 0.11 2.5E-06 45.3 2.9 37 294-330 70-106 (170)
60 KOG0415 Predicted peptidyl pro 92.3 0.091 2E-06 52.2 2.5 37 297-334 240-276 (479)
61 KOG0145 RNA-binding protein EL 92.3 0.14 3E-06 49.1 3.6 36 294-329 276-311 (360)
62 KOG0148 Apoptosis-promoting RN 92.0 0.11 2.5E-06 49.8 2.7 33 297-329 63-95 (321)
63 KOG0109 RNA-binding protein LA 91.9 0.082 1.8E-06 51.2 1.7 34 296-329 78-111 (346)
64 KOG4205 RNA-binding protein mu 91.7 0.15 3.3E-06 50.0 3.3 34 295-328 96-129 (311)
65 KOG0129 Predicted RNA-binding 91.6 0.13 2.7E-06 53.2 2.7 32 296-327 259-290 (520)
66 KOG0151 Predicted splicing reg 91.6 0.26 5.6E-06 52.8 5.0 36 293-328 171-206 (877)
67 PF08332 CaMKII_AD: Calcium/ca 91.4 3.5 7.6E-05 35.4 11.0 111 14-127 3-121 (128)
68 KOG0132 RNA polymerase II C-te 90.2 0.21 4.6E-06 53.8 2.9 32 296-327 421-452 (894)
69 KOG0131 Splicing factor 3b, su 90.0 0.18 3.8E-06 46.0 1.8 31 295-325 95-125 (203)
70 KOG0146 RNA-binding protein ET 89.6 0.35 7.5E-06 46.6 3.5 40 292-331 281-320 (371)
71 KOG0124 Polypyrimidine tract-b 89.3 0.15 3.3E-06 50.8 1.0 32 295-326 112-143 (544)
72 KOG0110 RNA-binding protein (R 89.1 0.24 5.3E-06 52.8 2.3 35 296-330 515-549 (725)
73 KOG0117 Heterogeneous nuclear 88.9 0.34 7.3E-06 49.5 3.0 35 295-329 82-116 (506)
74 KOG4660 Protein Mei2, essentia 88.3 0.4 8.7E-06 49.9 3.2 30 296-325 75-104 (549)
75 KOG1190 Polypyrimidine tract-b 88.0 0.43 9.3E-06 48.3 3.1 32 295-326 27-58 (492)
76 KOG0147 Transcriptional coacti 87.3 0.29 6.2E-06 50.9 1.5 37 296-332 278-314 (549)
77 KOG0123 Polyadenylate-binding 86.8 0.53 1.2E-05 47.2 3.1 37 294-330 268-304 (369)
78 TIGR02096 conserved hypothetic 83.4 17 0.00038 29.3 10.2 60 20-82 3-65 (129)
79 PF13577 SnoaL_4: SnoaL-like d 82.8 11 0.00025 30.0 8.8 68 16-85 8-78 (127)
80 KOG0115 RNA-binding protein p5 79.6 1.5 3.3E-05 41.9 2.8 34 297-330 32-65 (275)
81 KOG1457 RNA binding protein (c 79.3 1.2 2.6E-05 42.0 1.9 32 297-328 211-242 (284)
82 KOG1855 Predicted RNA-binding 78.9 2 4.4E-05 43.8 3.5 37 292-328 227-263 (484)
83 PF08777 RRM_3: RNA binding mo 78.7 2.1 4.5E-05 35.3 3.0 32 296-327 1-32 (105)
84 KOG0124 Polypyrimidine tract-b 78.2 2.2 4.8E-05 42.8 3.5 33 296-328 210-242 (544)
85 KOG3152 TBP-binding protein, a 73.2 3.4 7.4E-05 39.6 3.2 34 296-329 74-107 (278)
86 KOG1457 RNA binding protein (c 73.0 3.3 7.1E-05 39.2 3.0 28 295-322 33-60 (284)
87 KOG0129 Predicted RNA-binding 72.3 3.7 8.1E-05 42.7 3.5 36 295-330 369-405 (520)
88 COG4875 Uncharacterized protei 72.0 66 0.0014 27.9 11.5 111 10-128 33-147 (156)
89 KOG4209 Splicing factor RNPS1, 70.6 2.5 5.3E-05 39.8 1.7 34 293-326 98-131 (231)
90 KOG4210 Nuclear localization s 70.5 3 6.5E-05 40.4 2.3 32 297-328 185-217 (285)
91 PF13893 RRM_5: RNA recognitio 69.9 3.4 7.3E-05 29.2 1.9 16 313-328 1-16 (56)
92 KOG4211 Splicing factor hnRNP- 67.7 5 0.00011 41.6 3.3 32 296-328 103-134 (510)
93 KOG4849 mRNA cleavage factor I 60.5 4.9 0.00011 40.2 1.6 28 294-321 78-105 (498)
94 KOG1995 Conserved Zn-finger pr 55.9 8 0.00017 38.6 2.2 31 296-326 66-96 (351)
95 KOG0128 RNA-binding protein SA 55.0 6.5 0.00014 43.2 1.6 32 296-327 736-767 (881)
96 PF07366 SnoaL: SnoaL-like pol 54.8 1.1E+02 0.0024 24.6 8.8 60 22-85 5-67 (126)
97 PF12870 Lumazine_bd: Lumazine 54.7 58 0.0013 25.2 6.7 45 77-126 67-111 (111)
98 KOG0112 Large RNA-binding prot 52.0 6 0.00013 43.8 0.7 42 292-333 368-409 (975)
99 KOG0120 Splicing factor U2AF, 51.0 9.1 0.0002 40.0 1.8 34 295-328 288-321 (500)
100 smart00361 RRM_1 RNA recogniti 49.3 14 0.00031 27.4 2.3 18 310-327 2-23 (70)
101 TIGR02960 SigX5 RNA polymerase 43.7 1.7E+02 0.0037 27.9 9.3 51 17-70 206-257 (324)
102 PRK08241 RNA polymerase factor 43.6 1.3E+02 0.0028 29.0 8.6 55 13-70 212-267 (339)
103 smart00593 RUN domain involved 42.9 27 0.00058 25.8 2.9 44 19-71 12-55 (64)
104 COG5073 VID24 Vacuolar import 41.3 13 0.00029 35.4 1.2 74 20-104 53-126 (272)
105 KOG0147 Transcriptional coacti 40.6 5.6 0.00012 41.7 -1.5 38 292-329 175-212 (549)
106 KOG4208 Nucleolar RNA-binding 38.6 32 0.00068 32.1 3.1 39 296-334 49-87 (214)
107 PF12642 TpcC: Conjugative tra 37.9 2.9E+02 0.0063 25.1 9.5 88 15-126 140-231 (232)
108 PF02759 RUN: RUN domain; Int 37.4 21 0.00045 29.4 1.7 50 12-70 64-122 (133)
109 PF14605 Nup35_RRM_2: Nup53/35 37.2 32 0.00069 24.7 2.4 31 298-329 3-33 (53)
110 KOG4212 RNA-binding protein hn 36.5 34 0.00073 35.5 3.2 32 296-327 44-76 (608)
111 COG4319 Ketosteroid isomerase 35.7 2.4E+02 0.0053 24.6 8.0 94 30-129 26-128 (137)
112 KOG4307 RNA binding protein RB 35.0 36 0.00079 37.1 3.3 35 298-333 869-903 (944)
113 PRK09636 RNA polymerase sigma 35.0 1.4E+02 0.0031 28.3 7.2 54 17-71 173-231 (293)
114 PF08863 YolD: YolD-like prote 32.0 1.1E+02 0.0023 23.6 4.9 84 31-130 4-90 (92)
115 PF08675 RNA_bind: RNA binding 30.9 50 0.0011 26.7 2.8 27 297-324 10-36 (87)
116 KOG1365 RNA-binding protein Fu 30.7 31 0.00068 35.1 1.9 32 297-328 281-313 (508)
117 KOG4206 Spliceosomal protein s 30.6 45 0.00098 31.4 2.8 31 297-327 147-177 (221)
118 KOG3266 Predicted glycine clea 29.0 94 0.002 27.9 4.4 84 1-103 1-86 (172)
119 PF05172 Nup35_RRM: Nup53/35/4 28.0 55 0.0012 26.9 2.6 32 295-327 5-36 (100)
120 COG0724 RNA-binding proteins ( 27.8 53 0.0011 28.7 2.7 33 295-327 224-256 (306)
121 KOG1190 Polypyrimidine tract-b 25.8 52 0.0011 33.8 2.5 28 297-324 151-178 (492)
122 KOG1365 RNA-binding protein Fu 25.0 60 0.0013 33.2 2.7 29 296-324 161-189 (508)
123 PF11411 DNA_ligase_IV: DNA li 24.3 54 0.0012 22.2 1.6 17 306-322 19-35 (36)
124 KOG0106 Alternative splicing f 24.2 45 0.00099 31.2 1.7 28 296-323 99-126 (216)
125 PF00398 RrnaAD: Ribosomal RNA 24.2 41 0.00088 31.7 1.4 29 296-324 97-127 (262)
126 cd00027 BRCT Breast Cancer Sup 23.6 1.1E+02 0.0024 20.9 3.3 29 296-324 1-29 (72)
127 COG0030 KsgA Dimethyladenosine 23.0 87 0.0019 30.1 3.4 28 296-323 95-122 (259)
128 PF05629 Nanovirus_C8: Nanovir 22.4 2.1E+02 0.0046 24.9 5.2 45 92-136 50-104 (153)
129 PF11608 Limkain-b1: Limkain b 21.8 1E+02 0.0022 25.0 3.0 24 298-321 4-31 (90)
130 PF07858 LEH: Limonene-1,2-epo 21.0 5.2E+02 0.011 22.0 9.1 64 12-82 2-68 (125)
131 PF04059 RRM_2: RNA recognitio 20.8 1.1E+02 0.0023 25.0 3.1 24 297-320 2-25 (97)
132 KOG4410 5-formyltetrahydrofola 20.1 1.1E+02 0.0024 30.1 3.4 26 297-322 331-356 (396)
133 KOG0128 RNA-binding protein SA 20.1 10 0.00022 41.8 -3.9 35 295-329 666-700 (881)
No 1
>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]
Probab=100.00 E-value=9.6e-56 Score=438.51 Aligned_cols=317 Identities=40% Similarity=0.602 Sum_probs=204.7
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHHHHhcCcchhcccccCCCceeccCCCCcccccccHHHHHHHHhcCCCccceEEEE
Q 037095 1 MAQQADSSSALSPQVVGNAFVEQYYCILHQNPDVVHRFYQESSMVSRPDQSGSMTSVTTIKEINDMIVSLDYQNYNVQIF 80 (334)
Q Consensus 1 ma~~~~~~~~~~a~~VG~~FV~qYY~~L~~~p~~L~~fY~~~S~l~~~g~~g~~~~~~G~~~I~~~i~sL~~~~~~~~I~ 80 (334)
|++++.....++++.||++||+|||++|++.|+.||+||.+.|.|+|.|.+|+|..++|.++|+++|++|+|..|+++|.
T Consensus 1 ~~~~~~~~~~~~~~~vg~~Fv~qYY~~L~~~P~~lhrfY~~~S~ltr~~~dg~m~s~t~~~~I~~~i~sld~~~~s~eI~ 80 (419)
T KOG0116|consen 1 MDAQAMLSPVPTPQLVGNEFVRQYYNVLQNSPSKLHRFYMDDSVLTRPGLDGKMVSVTGLEAIHEKIMSLDYEVCSVEIS 80 (419)
T ss_pred CCccccccCCCCHHHHHHHHHHHHHHHHhhChHHHHHHhhccceeeccCCCCceEEEecHHHhhhheeecCCCceeEEEE
Confidence 44455334479999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEEEeCCCCEEEEEEEEEEeCCCCcceeEEEEEEEEeCCeEEEEccEEEeecCCCCCCCCCCccccccCCCCCCCCCC
Q 037095 81 SADAQASYDNGLTVLVTGCLIGKDNVRRKFTQSFFLAPQDKGYFVLNDILRYVDEIDDKDGSAGLTINDVDENAPAAPLT 160 (334)
Q Consensus 81 tvD~Q~s~~ggvlI~VtG~v~~~d~~~r~FsQtF~Lap~~~~Y~V~NDiFR~vd~~~~~~~~~~~~~~~~~~~~~~~~~~ 160 (334)
++|+|.|+++||+|+|+|.|++++..+|+|+|||||+|++++|||+||||||+|+.... +. .... +.
T Consensus 81 tvdsQ~S~~~GvvI~VtG~lt~~~~~rRkF~QtFfLapq~~~yfVlNDiFRfvde~~~~--e~-~~~~-vp--------- 147 (419)
T KOG0116|consen 81 TVDSQASLEKGVVIMVTGYLTNKDGPRRKFSQTFFLAPQEKGYFVLNDIFRFVDEEFEP--EA-NTDE-VP--------- 147 (419)
T ss_pred EEehhhhccCCeEEEEEEEEEeCCCcceEEEEEEEEeecCCceEEEechhhhccccccc--cc-cccc-CC---------
Confidence 99999999999999999999999999999999999999999999999999999966411 11 0000 00
Q ss_pred CCCCCCCCCCCccc-ccCCCCCccccCCcccCCCCCCCccccccc-cccCCCCCCCCc-CCCCCCCCCCCCCcccCCCcc
Q 037095 161 PDPEPTQVPNNTVL-NHVNPVNEDAKSSNEASHPLDNGQVLVAEK-AVAADPPVVASQ-NDARPAKEPAASKNEEEAPKK 237 (334)
Q Consensus 161 ~e~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~p~~~~~~~v~e~-~~~~e~~~~~~~-~~~~~~~~~~~~~~~~e~pKk 237 (334)
++-..+.....+. ..+....+.. .+....+..+++..+.++ ....|...+... .+.......++..+++++||+
T Consensus 148 -~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~V~~~~~~~~~~~~~~~~~ee~v~~~~~~~~p~~~~~~~~~~ 224 (419)
T KOG0116|consen 148 -EANPAVVVSVEKASQLVEAVVESE--PEPEPEPKAEDEVEVPEEATVEDEAKEKTKEELVIQQTVSEAPAAPQGDAPKK 224 (419)
T ss_pred -CCCcceeecccccccccccccccC--CCCcccccccCceeccccccccccccccCchhhcccccccCCCccccccccch
Confidence 0000000000000 0000000000 000000000010000000 000000000001 111111111222338999999
Q ss_pred hhHHHHhhhccCCCCCccccCCCCCccccCCccCCCCCCCCCCCC--CC---ccccCccccCCcceEEEeCCCCCCCHHH
Q 037095 238 SFASVVHDLNKSKAPFNVIMRAPSLKTVESSRATAAPKVAAPPSS--NS---SLERNNDHAAKGHSIFVGNLPDSATVDQ 312 (334)
Q Consensus 238 SYASIv~v~k~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~---~~~~~~~~e~~~~~iyV~nLp~~~t~~~ 312 (334)
|||||+++++.+..+..+...+....+.+.|...+.+...+.+++ .. ...++.+....+.+|||+|||+++++++
T Consensus 225 s~asv~~~~~~~~~~~~~~~~p~~~~~~~~p~~~~~~~~~s~~~~p~~~~~~~n~~~~~~~~~~~~i~V~nlP~da~~~~ 304 (419)
T KOG0116|consen 225 SFASVVKVLKKSAAVQQSKGSPPQIQPQQQPSTKPQAERQSKPPSPVRESKSGNSNNQEPRADGLGIFVKNLPPDATPAE 304 (419)
T ss_pred hhhhhhhhcccccccceeccCCCccccccCCccCcchhhccCCCCccccccccccCCcceeecccceEeecCCCCCCHHH
Confidence 999999999998877322111111111111111111011111111 11 1135555666778899999999999999
Q ss_pred HHHHhhcCCceeeceEEeeec
Q 037095 313 LKLIFEQFGPVKPDGIQVRSQ 333 (334)
Q Consensus 313 l~~~F~~fG~v~~~~i~vRs~ 333 (334)
|+++|++||+|+.+||+||++
T Consensus 305 l~~~Fk~FG~Ik~~~I~vr~~ 325 (419)
T KOG0116|consen 305 LEEVFKQFGPIKEGGIQVRSP 325 (419)
T ss_pred HHHHHhhcccccccceEEecc
Confidence 999999999999999999983
No 2
>KOG2104 consensus Nuclear transport factor 2 [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=7.4e-34 Score=234.75 Aligned_cols=118 Identities=29% Similarity=0.493 Sum_probs=113.7
Q ss_pred CHHHHHHHHHHHHHHHHhcCcchhcccccCCCceeccCCCCcccccccHHHHHHHHhcCCCccceEEEEEEEEEEeCCCC
Q 037095 12 SPQVVGNAFVEQYYCILHQNPDVVHRFYQESSMVSRPDQSGSMTSVTTIKEINDMIVSLDYQNYNVQIFSADAQASYDNG 91 (334)
Q Consensus 12 ~a~~VG~~FV~qYY~~L~~~p~~L~~fY~~~S~l~~~g~~g~~~~~~G~~~I~~~i~sL~~~~~~~~I~tvD~Q~s~~gg 91 (334)
.++.||.+|+++||.+||.+|..|..||.+.|+|+|+|. .++|.++|.+||.||||.+|++.|+++||||+++||
T Consensus 5 ~~e~v~~~FvqhYY~~FD~dR~ql~~lY~~~S~LTfEGq-----q~qG~~~IveKl~sLpFqkiqh~IttvD~QPt~~g~ 79 (126)
T KOG2104|consen 5 VYEAVAKAFVQHYYSLFDNDRSQLGALYIDTSMLTFEGQ-----QIQGKDAIVEKLTSLPFQKIQHSITTVDSQPTPDGG 79 (126)
T ss_pred cHHHHHHHHHHHHHHHhcCchhHhhhhhcccceeeEcch-----hhcchHHHHHHHhcCChhhhhceeeecccccCCCCc
Confidence 578999999999999999999999999999999999998 799999999999999999999999999999999999
Q ss_pred EEEEEEEEEEeCCCCcceeEEEEEEEEeC-CeEEEEccEEEeec
Q 037095 92 LTVLVTGCLIGKDNVRRKFTQSFFLAPQD-KGYFVLNDILRYVD 134 (334)
Q Consensus 92 vlI~VtG~v~~~d~~~r~FsQtF~Lap~~-~~Y~V~NDiFR~vd 134 (334)
|||+|+|.|+.++++..+|+|+|+|.|+. ++|||.|||||+--
T Consensus 80 ilv~V~G~Lk~dEd~~~~FsQvF~L~~n~~~~~~v~ndiFRLn~ 123 (126)
T KOG2104|consen 80 ILVMVVGQLKLDEDPILRFSQVFLLKPNIQGSYYVFNDIFRLNL 123 (126)
T ss_pred EEEEEeeeeeeccCCccceeeEEEEeEcCCCCEEEEeeeEEEec
Confidence 99999999999999999999999999984 78999999999853
No 3
>cd00780 NTF2 Nuclear transport factor 2 (NTF2) domain plays an important role in the trafficking of macromolecules, ions and small molecules between the cytoplasm and nucleus. This bi-directional transport of macromolecules across the nuclear envelope requires many soluble factors that includes GDP-binding protein Ran (RanGDP). RanGDP is required for both import and export of proteins and poly(A) RNA. RanGDP also has been implicated in cell cycle control, specifically in mitotic spindle assembly. In interphase cells, RanGDP is predominately nuclear and thought to be GTP bound, but it is also present in the cytoplasm, probably in the GDP-bound state. NTF2 mediates the nuclear import of RanGDP. NTF2 binds to both RanGDP and FxFG repeat-containing nucleoporins.
Probab=100.00 E-value=5.7e-33 Score=231.76 Aligned_cols=118 Identities=44% Similarity=0.718 Sum_probs=113.3
Q ss_pred CHHHHHHHHHHHHHHHHhcCcchhcccccCCCceeccC-CCCcccccccHHHHHHHHhcCCCccceEEEEEEEEEEeCCC
Q 037095 12 SPQVVGNAFVEQYYCILHQNPDVVHRFYQESSMVSRPD-QSGSMTSVTTIKEINDMIVSLDYQNYNVQIFSADAQASYDN 90 (334)
Q Consensus 12 ~a~~VG~~FV~qYY~~L~~~p~~L~~fY~~~S~l~~~g-~~g~~~~~~G~~~I~~~i~sL~~~~~~~~I~tvD~Q~s~~g 90 (334)
++++||+.||++||++|+++|+.|++||+++|+|+|.| . .+.|.++|.++|++||+..++++|.++|||++.++
T Consensus 1 ~~~~v~~~Fv~~YY~~l~~~~~~L~~fY~~~s~~~~~~~~-----~~~g~~~I~~~l~~lp~~~~~~~i~~~d~q~~~~~ 75 (119)
T cd00780 1 SAEDVAKAFVQQYYSIFDNNREGLHRLYGDTSMLSREGMK-----QVTGRDAIVEKLSSLPFQKTKHKITTVDSQPTPSG 75 (119)
T ss_pred CHHHHHHHHHHHHHHHHhcCHHHHHhhcCCCcEEEECCce-----EecCHHHHHHHHHhCCCcceEEEEEEEeeeEcCCC
Confidence 46899999999999999999999999999999999999 5 78899999999999998778999999999999999
Q ss_pred CEEEEEEEEEEeCCCCcceeEEEEEEEEeCCeEEEEccEEEeec
Q 037095 91 GLTVLVTGCLIGKDNVRRKFTQSFFLAPQDKGYFVLNDILRYVD 134 (334)
Q Consensus 91 gvlI~VtG~v~~~d~~~r~FsQtF~Lap~~~~Y~V~NDiFR~vd 134 (334)
++||+|+|.|+.+++..|+|+|+|+|++++++|+|+||+|||+|
T Consensus 76 ~ili~V~G~~~~~~~~~~~F~q~F~L~~~~~~~~I~nD~fr~~~ 119 (119)
T cd00780 76 GVIVMVTGSLKLDEQPPRKFSQTFVLAPQNGGYFVLNDIFRFVD 119 (119)
T ss_pred CEEEEEEEEEEECCCCceeEeEEEEEEecCCeEEEEeeEEEecC
Confidence 99999999999999899999999999999999999999999986
No 4
>PF02136 NTF2: Nuclear transport factor 2 (NTF2) domain; InterPro: IPR002075 Nuclear transport factor 2 (NTF2) is a homodimer which stimulates efficient nuclear import of a cargo protein. NTF2 binds to both RanGDP and FxFG repeat-containing nucleoporins. NTF2 folds into a cone with a deep hydrophobic cavity, the opening of which is surrounded by several negatively charged residues. RanGDP binds to NTF2 by inserting a conserved phenylalanine residue into the hydrophobic pocket of NTF2 and making electrostatic interactions with the conserved negatively charged residues that surround the cavity []. This entry represent the main structural domain of NTF2 and related domains which are found in other nuclear import proteins.; GO: 0006810 transport, 0005622 intracellular; PDB: 3UJM_B 1JKG_B 1JN5_B 1M98_A 3MG1_A 3MG2_A 3MG3_B 2Z76_A 2Z7A_D 2Z77_A ....
Probab=99.95 E-value=1.9e-27 Score=196.03 Aligned_cols=113 Identities=35% Similarity=0.635 Sum_probs=105.6
Q ss_pred HHHHHHHHHHHHHhc-Ccchhcccc-cCCCceeccCCCCcccccccHHHHHHHHhcCCCccceEEEEEEEEE--EeCCCC
Q 037095 16 VGNAFVEQYYCILHQ-NPDVVHRFY-QESSMVSRPDQSGSMTSVTTIKEINDMIVSLDYQNYNVQIFSADAQ--ASYDNG 91 (334)
Q Consensus 16 VG~~FV~qYY~~L~~-~p~~L~~fY-~~~S~l~~~g~~g~~~~~~G~~~I~~~i~sL~~~~~~~~I~tvD~Q--~s~~gg 91 (334)
||+.||++||++|+. +|+.|++|| .+.|.++|.|. ..+.|.++|.++|.+|+.+.++++|.++||| ++.+++
T Consensus 1 v~~~Fv~~Yy~~~d~~~~~~L~~~Y~~~~s~~~~~~~----~~~~G~~~I~~~~~~l~~~~~~~~i~~~d~qp~~~~~~~ 76 (118)
T PF02136_consen 1 VANSFVQQYYQLFDSGDREGLHKLYHDDASFLTWNGN----RPVVGREAIQEFFQSLPATGVQHRITSVDCQPSPSSDGS 76 (118)
T ss_dssp HHHHHHHHHHHHHHHTHGGGGGGGEEEEEEEEEETTE----CEEESHHHHHHHHHHHTTSSEEEEEEEEEEEEEEECCSE
T ss_pred CHHHHHHHHHHHHccCCHHHHHHHHcCCCeeecCCCc----hhhhhHHHHHHHHhcCCCcccEEEecccccccccccCCc
Confidence 799999999999999 999999999 78888999886 2688999999999999998889999999999 568999
Q ss_pred EEEEEEEEEEeCCCC-cceeEEEEEEEEeCCeEEEEccEEEe
Q 037095 92 LTVLVTGCLIGKDNV-RRKFTQSFFLAPQDKGYFVLNDILRY 132 (334)
Q Consensus 92 vlI~VtG~v~~~d~~-~r~FsQtF~Lap~~~~Y~V~NDiFR~ 132 (334)
|+|+|+|.++.++.. .|+|+|+|+|.+.+++|+|.||||||
T Consensus 77 i~i~v~G~~~~~~~~~~~~F~q~FvL~~~~~~~~I~nd~~r~ 118 (118)
T PF02136_consen 77 ILITVTGQFKEDDNPNPRRFSQTFVLVPQNNGYFIANDIFRF 118 (118)
T ss_dssp EEEEEEEEEEETTSEEEEEEEEEEEEEEETTEEEEEEEEEEE
T ss_pred EEEEEEeEEEecCCCcccEEEEEEEEEEcCCEEEEEeeEEEC
Confidence 999999999999875 69999999999999999999999998
No 5
>KOG4353 consensus RNA export factor NXT1 [RNA processing and modification]
Probab=99.89 E-value=1.2e-23 Score=176.50 Aligned_cols=116 Identities=24% Similarity=0.399 Sum_probs=107.5
Q ss_pred CHHHHHHHHHHHHHHHHhcCcchhcccccCCCceeccCCCCcccccccHHHHHHHHhcCCCccceEEEEEEEEEEeCC--
Q 037095 12 SPQVVGNAFVEQYYCILHQNPDVVHRFYQESSMVSRPDQSGSMTSVTTIKEINDMIVSLDYQNYNVQIFSADAQASYD-- 89 (334)
Q Consensus 12 ~a~~VG~~FV~qYY~~L~~~p~~L~~fY~~~S~l~~~g~~g~~~~~~G~~~I~~~i~sL~~~~~~~~I~tvD~Q~s~~-- 89 (334)
++...+.+||+.||..|+++|..|.+||.++|.+.|+|+ .++|.+.|.+++..||.+ ++.|.++||||.++
T Consensus 11 s~cr~A~eFv~~YY~smD~rR~~i~rlY~~~atlvWNGn-----~v~g~esls~ff~~LPsS--~~qi~~lD~Qpv~dqa 83 (139)
T KOG4353|consen 11 SACRAAEEFVNVYYSSMDKRRRGIGRLYLDNATLVWNGN-----PVSGTESLSEFFNMLPSS--EFQINDLDCQPVHDQA 83 (139)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhHHHhhccceEEEcCC-----cchhHHHHHHHHHhCCCc--cccccccccccchhhc
Confidence 345678999999999999999999999999999999998 899999999999999987 89999999999864
Q ss_pred ----CCEEEEEEEEEEeCCCCcceeEEEEEEEEeCCeEE----EEccEEEeec
Q 037095 90 ----NGLTVLVTGCLIGKDNVRRKFTQSFFLAPQDKGYF----VLNDILRYVD 134 (334)
Q Consensus 90 ----ggvlI~VtG~v~~~d~~~r~FsQtF~Lap~~~~Y~----V~NDiFR~vd 134 (334)
-+|||+|+|.++++++..|.|.|||+|..++..|- |.+|+|||.|
T Consensus 84 t~~q~~vLvvvsGtVkFdG~k~r~F~qt~ll~~e~~~~k~~~~v~Sd~fr~~d 136 (139)
T KOG4353|consen 84 TGSQTTVLVVVSGTVKFDGNKQRVFNQTFLLTAEDPPFKTVWKVASDCFRFQD 136 (139)
T ss_pred ccccceEEEEEeeeEEEcCCccccccceeEEeecCCccchhhhhhhhhhhhhh
Confidence 36999999999999999999999999999987666 9999999987
No 6
>cd00531 NTF2_like Nuclear transport factor 2 (NTF2-like) superfamily. This family includes members of the NTF2 family, Delta-5-3-ketosteroid isomerases, Scytalone Dehydratases, and the beta subunit of Ring hydroxylating dioxygenases. This family is a classic example of divergent evolution wherein the proteins have many common structural details but diverge greatly in their function. For example, nuclear transport factor 2 (NTF2) mediates the nuclear import of RanGDP and binds to both RanGDP and FxFG repeat-containing nucleoporins while Ketosteroid isomerases catalyze the isomerization of delta-5-3-ketosteroid to delta-4-3-ketosteroid, by intramolecular transfer of the C4-beta proton to the C6-beta position. While the function of the beta sub-unit of the Ring hydroxylating dioxygenases is not known, Scytalone Dehydratases catalyzes two reactions in the biosynthetic pathway that produces fungal melanin. Members of the NTF2-like superfamily are widely distributed among bacteria, archaea
Probab=98.69 E-value=4.6e-07 Score=71.79 Aligned_cols=115 Identities=22% Similarity=0.301 Sum_probs=91.1
Q ss_pred HHHHHHHHHHHh-cCcchhcccccCCCceeccCCCCcccccccHHHHHHHHhcCCC--ccceEEEEEEEEEEeCC-CCEE
Q 037095 18 NAFVEQYYCILH-QNPDVVHRFYQESSMVSRPDQSGSMTSVTTIKEINDMIVSLDY--QNYNVQIFSADAQASYD-NGLT 93 (334)
Q Consensus 18 ~~FV~qYY~~L~-~~p~~L~~fY~~~S~l~~~g~~g~~~~~~G~~~I~~~i~sL~~--~~~~~~I~tvD~Q~s~~-ggvl 93 (334)
..|+.+||..|+ .+++.|..||.+++.+.+.+.++......|.++|.+.+..+.. ...+|-+.+++++...+ .+..
T Consensus 2 ~~l~~~y~~~ld~~~~~~l~~~~~~d~~~~~~~~~~~~~~~~g~~~i~~~~~~~~~~~~~~~h~~~~~~~~~~~~~~~~~ 81 (124)
T cd00531 2 EQFLYRYARLLDAGDREWLALLYADDAYFEPPGGDGLIYPDDGREAIEDRVRRLPFGPSRTRHLVSNVDVQPGDDGEGVV 81 (124)
T ss_pred HHHHHHHHHHhCCchHHHHHhhCcCcEEEEEccCCEEEEcCChHHHHHHHHHhcCCCCCceEEEEEeEEEEeCCCCEEEE
Confidence 579999999999 6788999999999999987642122356799999999998863 33455568888887654 3466
Q ss_pred EEEEEEEEeCC---CCcceeEEEEEEEEeCCeEEEEccEEEe
Q 037095 94 VLVTGCLIGKD---NVRRKFTQSFFLAPQDKGYFVLNDILRY 132 (334)
Q Consensus 94 I~VtG~v~~~d---~~~r~FsQtF~Lap~~~~Y~V~NDiFR~ 132 (334)
+.+.|.+...+ ...+.|.+.|.+...+++|.|.+..++|
T Consensus 82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~w~i~~~~~~~ 123 (124)
T cd00531 82 VSVFGVLRTRGDGEQDVFAGGQTFVLRPQGGGGKIANRRFRL 123 (124)
T ss_pred EEEEEEEEEccCCceeEEEEEEEEEEEEeCCEEEEEEEEEec
Confidence 77778887765 3457899999999999999999999987
No 7
>PF10429 Mtr2: Nuclear pore RNA shuttling protein Mtr2; InterPro: IPR019488 Mtr2 is a monomeric, dual-action, RNA-shuttle protein found in yeasts. Transport across the nuclear-cytoplasmic membrane is via the macro-molecular membrane-spanning nuclear pore complex, NPC. The pore is lined by a subset of NPC members called nucleoporins that present FG (Phe-Gly) receptors, characteristically GLFG and FXFG motifs, for shuttling RNAs and proteins. RNA cargo is bound to soluble transport proteins (nuclear export factors) such as Mex67 in yeasts, and TAP in metazoa, which pass along the pore by binding to successive FG receptors. Mtr2 when bound to Mex67 maximises this FG-binding. Mtr2 also acts independently of Mex67 in transporting the large ribosomal RNA subunit through the pore []. ; PDB: 1Q40_A 1Q42_A 1OF5_B.
Probab=98.40 E-value=4.5e-07 Score=80.16 Aligned_cols=98 Identities=11% Similarity=0.076 Sum_probs=77.8
Q ss_pred HHHHHHHHHHHHHHh-----cCcchhcccccCCCceeccCCCCcccccccHHHHHHHHhcCC-CccceEEEEEEEEEEeC
Q 037095 15 VVGNAFVEQYYCILH-----QNPDVVHRFYQESSMVSRPDQSGSMTSVTTIKEINDMIVSLD-YQNYNVQIFSADAQASY 88 (334)
Q Consensus 15 ~VG~~FV~qYY~~L~-----~~p~~L~~fY~~~S~l~~~g~~g~~~~~~G~~~I~~~i~sL~-~~~~~~~I~tvD~Q~s~ 88 (334)
++.+-||+.||..|| +..+.|-.||..+|.+.|+|. .+.+..+-.++|.+++ .+ +|++.++||+.++
T Consensus 5 q~~E~FvKk~la~LD~~~~~~l~~~l~~F~~~~~~II~Ng~-----Pi~~~~~F~~~w~~~pv~T--qH~L~s~D~H~IP 77 (166)
T PF10429_consen 5 QIIETFVKKILAHLDEQDPPNLNSFLTQFLPPNCKIIWNGT-----PIAQPTAFQQTWQQQPVQT--QHQLTSFDCHVIP 77 (166)
T ss_dssp CCHHHHHHHHHHHHCT-SS--HHHHHTTCECCEEEEEETTE-----EES-HHHHHHHHHCCS--E--EEEEEEEEEEEET
T ss_pred hhHHHHHHHHHHHhcCcchHHHHHHhHhhcCCCcEEEECCc-----cCCCHHHHHHHHHhCccce--eeeeeeeeeeEeC
Confidence 456889999999999 334688899999999999998 8889999999999999 55 9999999999997
Q ss_pred C-CCEEEEEEEEEEeCCCCcceeEEEEEEEEe
Q 037095 89 D-NGLTVLVTGCLIGKDNVRRKFTQSFFLAPQ 119 (334)
Q Consensus 89 ~-ggvlI~VtG~v~~~d~~~r~FsQtF~Lap~ 119 (334)
+ |++++.|+|.|.+++..+-+--|+..|.+.
T Consensus 78 Gsgt~i~N~n~KVRFDEsGrdk~G~~a~l~~~ 109 (166)
T PF10429_consen 78 GSGTFIINVNCKVRFDESGRDKLGEDADLPQP 109 (166)
T ss_dssp TTTEEEEEEEEEEEEB-SSB-TTS-B--TTS-
T ss_pred CCCeEEEeeeEEEEecCCCCCCCCCceeeccc
Confidence 5 679999999999987666566777776553
No 8
>KOG3763 consensus mRNA export factor TAP/MEX67 [RNA processing and modification]
Probab=98.11 E-value=1.3e-05 Score=82.54 Aligned_cols=124 Identities=20% Similarity=0.235 Sum_probs=93.0
Q ss_pred CCHHHHHHHHHHHHHHHHhcC-cchhcccccCCCceecc-----CC--CC-----------------------ccccccc
Q 037095 11 LSPQVVGNAFVEQYYCILHQN-PDVVHRFYQESSMVSRP-----DQ--SG-----------------------SMTSVTT 59 (334)
Q Consensus 11 ~~a~~VG~~FV~qYY~~L~~~-p~~L~~fY~~~S~l~~~-----g~--~g-----------------------~~~~~~G 59 (334)
....++..+|+++||.+++.+ +..+...|+++|+++.. +. +. ......|
T Consensus 335 ~~l~~LV~~Fl~~y~~~yD~~d~q~~~~~y~dns~FSlsi~~~~~~s~~~~~~~~~Y~k~SRNi~~l~~~~~r~srl~~g 414 (585)
T KOG3763|consen 335 EELKQLVLQFLQQYYKIYDNNDGQLLLYAYHDNSTFSLTINFLPVPSHPDPSSLGKYFKDSRNILKLKDPYLRASRLKHG 414 (585)
T ss_pred hHHHHHHHHHHHHHHHhhcCchhhhHHhhcCccceeEEEecccCCCCCCchHHHHHHHhhcchhhhhcCHHHHHHhhhcc
Confidence 457789999999999999965 45888888899988642 11 10 0135678
Q ss_pred HHHHHHHHhcCCCccceEEEEEEEEEEe--CCCCEEEEEEEEEEeCCC----Ccce---eEEEEEEEEeCC-eEEEEccE
Q 037095 60 IKEINDMIVSLDYQNYNVQIFSADAQAS--YDNGLTVLVTGCLIGKDN----VRRK---FTQSFFLAPQDK-GYFVLNDI 129 (334)
Q Consensus 60 ~~~I~~~i~sL~~~~~~~~I~tvD~Q~s--~~ggvlI~VtG~v~~~d~----~~r~---FsQtF~Lap~~~-~Y~V~NDi 129 (334)
..+|...|..||.+ +|...++-.--+ ...++.+.|.|.+.-.++ ..+. |+.||++.|.++ +-.|.||.
T Consensus 415 ~~~Iv~aLs~LPkT--~Hdl~s~vvDv~~~~~~~l~ftv~G~f~d~~g~~~~s~~~~~~FtRtfvv~P~~ns~l~iv~d~ 492 (585)
T KOG3763|consen 415 ACDIVVALSALPKT--QHDLDSFVVDVWYQTGNLLGFTVAGVFRDGEGQNSPSNRALLGFTRTFVVTPRENSGLAIVNDQ 492 (585)
T ss_pred chHHHHHHHhCccc--hhhhhhhheeeeecccceEEEEEEEEeecCCccCCcccccccccceEEEEeeCCCCceEEEece
Confidence 88999999999976 777765322222 256799999999875442 2245 999999999875 99999999
Q ss_pred EEeecCC
Q 037095 130 LRYVDEI 136 (334)
Q Consensus 130 FR~vd~~ 136 (334)
+-.....
T Consensus 493 Lfi~~~s 499 (585)
T KOG3763|consen 493 LFIASAS 499 (585)
T ss_pred eEEeecc
Confidence 9887754
No 9
>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=98.03 E-value=5.5e-06 Score=60.83 Aligned_cols=32 Identities=34% Similarity=0.674 Sum_probs=29.3
Q ss_pred EEEeCCCCCCCHHHHHHHhhcCCceeeceEEe
Q 037095 299 IFVGNLPDSATVDQLKLIFEQFGPVKPDGIQV 330 (334)
Q Consensus 299 iyV~nLp~~~t~~~l~~~F~~fG~v~~~~i~v 330 (334)
|||+|||+++|+++|+++|++||.|....|..
T Consensus 1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~ 32 (70)
T PF00076_consen 1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMR 32 (70)
T ss_dssp EEEESETTTSSHHHHHHHHHTTSTEEEEEEEE
T ss_pred cEEcCCCCcCCHHHHHHHHHHhhhcccccccc
Confidence 79999999999999999999999997776655
No 10
>PLN03134 glycine-rich RNA-binding protein 4; Provisional
Probab=97.99 E-value=8e-06 Score=71.00 Aligned_cols=37 Identities=24% Similarity=0.387 Sum_probs=33.9
Q ss_pred CcceEEEeCCCCCCCHHHHHHHhhcCCceeeceEEee
Q 037095 295 KGHSIFVGNLPDSATVDQLKLIFEQFGPVKPDGIQVR 331 (334)
Q Consensus 295 ~~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~i~vR 331 (334)
.+++|||+|||+++|+++|+++|++||.|+...|...
T Consensus 33 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d 69 (144)
T PLN03134 33 MSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVD 69 (144)
T ss_pred CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEec
Confidence 4678999999999999999999999999999888754
No 11
>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]
Probab=97.93 E-value=8.5e-06 Score=83.38 Aligned_cols=41 Identities=37% Similarity=0.545 Sum_probs=37.2
Q ss_pred ccccCCcceEEEeCCCCCCCHHHHHHHhhcCCceeeceEEe
Q 037095 290 NDHAAKGHSIFVGNLPDSATVDQLKLIFEQFGPVKPDGIQV 330 (334)
Q Consensus 290 ~~~e~~~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~i~v 330 (334)
.++...|.+||||||||++|+++|.++|++||.|+.+.|.+
T Consensus 286 ~en~~~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~ 326 (678)
T KOG0127|consen 286 RENITEGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVK 326 (678)
T ss_pred cccccccceEEEecCCccccHHHHHHHHHhhccceeEEEEe
Confidence 45556789999999999999999999999999999998875
No 12
>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=97.86 E-value=1.2e-05 Score=66.56 Aligned_cols=33 Identities=21% Similarity=0.497 Sum_probs=29.8
Q ss_pred cceEEEeCCCCCCCHHHHHHHhhcCCceeeceE
Q 037095 296 GHSIFVGNLPDSATVDQLKLIFEQFGPVKPDGI 328 (334)
Q Consensus 296 ~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~i 328 (334)
..-||||||||++|.+++-++|++||+|+.-+|
T Consensus 18 nriLyirNLp~~ITseemydlFGkyg~IrQIRi 50 (124)
T KOG0114|consen 18 NRILYIRNLPFKITSEEMYDLFGKYGTIRQIRI 50 (124)
T ss_pred heeEEEecCCccccHHHHHHHhhcccceEEEEe
Confidence 457999999999999999999999999996554
No 13
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor. These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
Probab=97.85 E-value=3.1e-05 Score=74.93 Aligned_cols=38 Identities=32% Similarity=0.366 Sum_probs=34.5
Q ss_pred CCcceEEEeCCCCCCCHHHHHHHhhcCCceeeceEEee
Q 037095 294 AKGHSIFVGNLPDSATVDQLKLIFEQFGPVKPDGIQVR 331 (334)
Q Consensus 294 ~~~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~i~vR 331 (334)
..+.+|||+|||+++++++|+++|++||.|...+|...
T Consensus 267 ~~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d 304 (352)
T TIGR01661 267 GAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRD 304 (352)
T ss_pred CCCcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEc
Confidence 45779999999999999999999999999999988653
No 14
>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=97.66 E-value=5.1e-05 Score=56.51 Aligned_cols=31 Identities=35% Similarity=0.742 Sum_probs=25.7
Q ss_pred EEEeCCCCCCCHHHHHHHhhcCCceeeceEE
Q 037095 299 IFVGNLPDSATVDQLKLIFEQFGPVKPDGIQ 329 (334)
Q Consensus 299 iyV~nLp~~~t~~~l~~~F~~fG~v~~~~i~ 329 (334)
|||+|||+++++++|+++|+.||.|....+.
T Consensus 1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~ 31 (70)
T PF14259_consen 1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLI 31 (70)
T ss_dssp EEEESSTTT--HHHHHHHCTTSSBEEEEEEE
T ss_pred CEEeCCCCCCCHHHHHHHHHhcCCcceEEEE
Confidence 7999999999999999999999998755543
No 15
>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=97.64 E-value=7e-05 Score=74.05 Aligned_cols=40 Identities=28% Similarity=0.480 Sum_probs=35.8
Q ss_pred cccCCcceEEEeCCCCCCCHHHHHHHhhcCCceeeceEEe
Q 037095 291 DHAAKGHSIFVGNLPDSATVDQLKLIFEQFGPVKPDGIQV 330 (334)
Q Consensus 291 ~~e~~~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~i~v 330 (334)
.+...+++|||+|||+++|+++|+++|++||.|+...|..
T Consensus 102 ~~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~ 141 (346)
T TIGR01659 102 DTNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMR 141 (346)
T ss_pred CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEe
Confidence 3455688999999999999999999999999999998864
No 16
>PF15008 DUF4518: Domain of unknown function (DUF4518)
Probab=97.50 E-value=0.00074 Score=64.34 Aligned_cols=124 Identities=15% Similarity=0.168 Sum_probs=90.8
Q ss_pred CCHHHHHHHHHHHHHHHHhc--CcchhcccccCCCc-eeccCCCCccc-ccccHHHHHHHHhcCCCccce---EEEEE--
Q 037095 11 LSPQVVGNAFVEQYYCILHQ--NPDVVHRFYQESSM-VSRPDQSGSMT-SVTTIKEINDMIVSLDYQNYN---VQIFS-- 81 (334)
Q Consensus 11 ~~a~~VG~~FV~qYY~~L~~--~p~~L~~fY~~~S~-l~~~g~~g~~~-~~~G~~~I~~~i~sL~~~~~~---~~I~t-- 81 (334)
.+.+.+|..|.+|||.+|+. +-=..--|+.|.++ |.....++... .+.|.+.+..+|.+|.....- -.+.+
T Consensus 125 ~~~~~L~~~F~~WFf~llNs~~~~wgpqhFW~Da~L~~~~~~~~~~~e~~~~Ga~~vs~~Llsl~~e~~l~fnPNl~~~G 204 (262)
T PF15008_consen 125 YPIHLLAEEFCEWFFELLNSPQDDWGPQHFWPDAKLKLYYSTSEQNVEEYCEGAEEVSLRLLSLVKEERLFFNPNLDSDG 204 (262)
T ss_pred CCHHHHHHHHHHHHHHHhcccccccChhhccCCCeEEEEEEcCCCceeEEecCHHHHHHHHHHHhhcccEEECCCCCCCC
Confidence 46789999999999999998 44466778888773 43333333333 448999999999999644211 11233
Q ss_pred EEEEEeCCCCEEEEEEEEEEeCCCCcceeEEEEEEEEe---CCeEEEEccEEEeec
Q 037095 82 ADAQASYDNGLTVLVTGCLIGKDNVRRKFTQSFFLAPQ---DKGYFVLNDILRYVD 134 (334)
Q Consensus 82 vD~Q~s~~ggvlI~VtG~v~~~d~~~r~FsQtF~Lap~---~~~Y~V~NDiFR~vd 134 (334)
+.|-.+..|.|+|.|.|++-.++.--=-|-|.|=|... +|.|-|.+=-+|+..
T Consensus 205 ~k~~~~phGlV~V~v~GTvH~~~~ClGiFEq~FGLiRdP~~~N~WKiK~~~l~i~~ 260 (262)
T PF15008_consen 205 VKGRISPHGLVLVAVCGTVHRDNTCLGIFEQIFGLIRDPFAENNWKIKFVNLRIRG 260 (262)
T ss_pred cceEEcCCCcEEEEEeeeEecCCceEeehhhhhhcccCccccCceeEEEEEEEEEe
Confidence 66777788999999999997765444579999999875 378999887777764
No 17
>smart00362 RRM_2 RNA recognition motif.
Probab=97.46 E-value=0.00015 Score=52.01 Aligned_cols=32 Identities=44% Similarity=0.858 Sum_probs=29.1
Q ss_pred eEEEeCCCCCCCHHHHHHHhhcCCceeeceEE
Q 037095 298 SIFVGNLPDSATVDQLKLIFEQFGPVKPDGIQ 329 (334)
Q Consensus 298 ~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~i~ 329 (334)
+|||+|||.+++.++|+++|++||.|....+.
T Consensus 1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~ 32 (72)
T smart00362 1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIP 32 (72)
T ss_pred CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEe
Confidence 58999999999999999999999999876554
No 18
>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]
Probab=97.36 E-value=0.00011 Score=63.15 Aligned_cols=31 Identities=29% Similarity=0.536 Sum_probs=28.9
Q ss_pred CcceEEEeCCCCCCCHHHHHHHhhcCCceee
Q 037095 295 KGHSIFVGNLPDSATVDQLKLIFEQFGPVKP 325 (334)
Q Consensus 295 ~~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~ 325 (334)
.+.+||||||++-++|++|-++|++.|+|+.
T Consensus 35 ~S~tvyVgNlSfyttEEqiyELFs~cG~irr 65 (153)
T KOG0121|consen 35 KSCTVYVGNLSFYTTEEQIYELFSKCGDIRR 65 (153)
T ss_pred hcceEEEeeeeeeecHHHHHHHHHhccchhe
Confidence 4678999999999999999999999999985
No 19
>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]
Probab=97.33 E-value=0.00022 Score=63.42 Aligned_cols=35 Identities=40% Similarity=0.752 Sum_probs=31.6
Q ss_pred cceEEEeCCCCCCCHHHHHHHhhcCCceeeceEEe
Q 037095 296 GHSIFVGNLPDSATVDQLKLIFEQFGPVKPDGIQV 330 (334)
Q Consensus 296 ~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~i~v 330 (334)
..+|||+|||+++|+++|+++|++||.|....|..
T Consensus 115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~ 149 (306)
T COG0724 115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVR 149 (306)
T ss_pred CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeee
Confidence 68999999999999999999999999997666654
No 20
>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=97.24 E-value=0.00028 Score=69.78 Aligned_cols=35 Identities=34% Similarity=0.597 Sum_probs=32.0
Q ss_pred cceEEEeCCCCCCCHHHHHHHhhcCCceeeceEEe
Q 037095 296 GHSIFVGNLPDSATVDQLKLIFEQFGPVKPDGIQV 330 (334)
Q Consensus 296 ~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~i~v 330 (334)
.++|||+|||+++|+++|+++|++||.|+...|..
T Consensus 193 ~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~ 227 (346)
T TIGR01659 193 DTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILR 227 (346)
T ss_pred cceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEee
Confidence 46899999999999999999999999999888764
No 21
>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=97.16 E-value=0.00049 Score=49.54 Aligned_cols=32 Identities=41% Similarity=0.758 Sum_probs=28.5
Q ss_pred eEEEeCCCCCCCHHHHHHHhhcCCceeeceEE
Q 037095 298 SIFVGNLPDSATVDQLKLIFEQFGPVKPDGIQ 329 (334)
Q Consensus 298 ~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~i~ 329 (334)
+|||+|||+.+++++|+++|+.||.|....+.
T Consensus 1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~ 32 (74)
T cd00590 1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIV 32 (74)
T ss_pred CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEe
Confidence 58999999999999999999999999765544
No 22
>PF13474 SnoaL_3: SnoaL-like domain; PDB: 2GXF_A 3KSP_A 3KE7_A 3BB9_E 3CNX_A 3F7S_A 3GWR_B.
Probab=97.09 E-value=0.0083 Score=48.19 Aligned_cols=110 Identities=8% Similarity=0.134 Sum_probs=78.1
Q ss_pred HHHHHHHHHHHhc-CcchhcccccCCCceeccCCCCcccccccHHHHHHHHhc-CC-CccceEEEEEEEEEEeCCCCEEE
Q 037095 18 NAFVEQYYCILHQ-NPDVVHRFYQESSMVSRPDQSGSMTSVTTIKEINDMIVS-LD-YQNYNVQIFSADAQASYDNGLTV 94 (334)
Q Consensus 18 ~~FV~qYY~~L~~-~p~~L~~fY~~~S~l~~~g~~g~~~~~~G~~~I~~~i~s-L~-~~~~~~~I~tvD~Q~s~~ggvlI 94 (334)
.+++++|+..+.. +-+.+..+|.++..+...+.+ ....|.++|.+++.. +. +..+.+++..+.++. .++.+++
T Consensus 2 ~~~~~~~~~a~~~~D~~~~~~~~~~d~~~~~~~~~---~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~v~~-~~~~a~~ 77 (121)
T PF13474_consen 2 EALLEEWIEAFERGDIDALLSLFSDDFVFFGTGPG---EIWRGREAIRAYFERDFESFRPISIEFEDVQVSV-SGDVAVV 77 (121)
T ss_dssp HHHHHHHHHHHHCT-HHHHHHHEEEEEEEEETTSS---SEEESHHHHHHHHHHHHHTHSEEEEEEEEEEEEE-ETTEEEE
T ss_pred HHHHHHHHHHHHhCCHHHHHHhhCCCEEEEcCCCC---ceECCHHHHHHHHHHHhhhCceEEEEEEEEEEEE-CCCEEEE
Confidence 4688999999884 568999999988877665432 146799999888875 22 245677777777765 3455666
Q ss_pred EEEEEEEeC--CC-CcceeEEEEEEEEeCCeEEEEccEEE
Q 037095 95 LVTGCLIGK--DN-VRRKFTQSFFLAPQDKGYFVLNDILR 131 (334)
Q Consensus 95 ~VtG~v~~~--d~-~~r~FsQtF~Lap~~~~Y~V~NDiFR 131 (334)
...+.++.. +. ....+..||+|...+++|.|...-+.
T Consensus 78 ~~~~~~~~~~~~~~~~~~~r~t~v~~k~~~~Wki~h~H~S 117 (121)
T PF13474_consen 78 TGEFRLRFRNDGEEIEMRGRATFVFRKEDGGWKIVHIHWS 117 (121)
T ss_dssp EEEEEEEEECTTCEEEEEEEEEEEEEEETTEEEEEEEEEE
T ss_pred EEEEEEEEecCCccceeeEEEEEEEEEECCEEEEEEEEec
Confidence 666666542 22 24678899999999999999876654
No 23
>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=97.08 E-value=0.00055 Score=68.85 Aligned_cols=38 Identities=21% Similarity=0.220 Sum_probs=33.8
Q ss_pred cCCcceEEEeCCCCCCCHHHHHHHhhcCCceeeceEEe
Q 037095 293 AAKGHSIFVGNLPDSATVDQLKLIFEQFGPVKPDGIQV 330 (334)
Q Consensus 293 e~~~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~i~v 330 (334)
+.+..+|||+|||+++++++|+++|++||.|....|..
T Consensus 86 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~ 123 (457)
T TIGR01622 86 ERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIK 123 (457)
T ss_pred ccCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEee
Confidence 34578999999999999999999999999999877753
No 24
>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor. Members of this subfamily are found in plants, metazoa and fungi.
Probab=97.08 E-value=0.00057 Score=69.65 Aligned_cols=36 Identities=33% Similarity=0.517 Sum_probs=32.8
Q ss_pred CcceEEEeCCCCCCCHHHHHHHhhcCCceeeceEEe
Q 037095 295 KGHSIFVGNLPDSATVDQLKLIFEQFGPVKPDGIQV 330 (334)
Q Consensus 295 ~~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~i~v 330 (334)
...+|||+|||+++|+++|+++|++||.|+...|..
T Consensus 294 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~ 329 (509)
T TIGR01642 294 SKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIK 329 (509)
T ss_pred CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEe
Confidence 467999999999999999999999999999887754
No 25
>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=97.07 E-value=0.00061 Score=71.97 Aligned_cols=36 Identities=22% Similarity=0.454 Sum_probs=33.2
Q ss_pred CcceEEEeCCCCCCCHHHHHHHhhcCCceeeceEEe
Q 037095 295 KGHSIFVGNLPDSATVDQLKLIFEQFGPVKPDGIQV 330 (334)
Q Consensus 295 ~~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~i~v 330 (334)
..++||||||||++++++|+++|++||.|++..|..
T Consensus 106 ~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~ 141 (612)
T TIGR01645 106 IMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSW 141 (612)
T ss_pred CCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEee
Confidence 467999999999999999999999999999988765
No 26
>TIGR02246 conserved hypothetical protein. This family consists of uncharacterized proteins found in a number of genera and species, including Streptomyces, Xanthomonas, Oceanobacillus iheyensis, Caulobacter crescentus CB15, and Xylella fastidiosa. The function is unknown.
Probab=97.00 E-value=0.023 Score=46.28 Aligned_cols=112 Identities=12% Similarity=0.098 Sum_probs=71.3
Q ss_pred HHHHHHHHHHHHHHhc-CcchhcccccCCCcee-ccCCCCcccccccHHHHHHHHhcC-C--CccceEEEEEEEEEEeCC
Q 037095 15 VVGNAFVEQYYCILHQ-NPDVVHRFYQESSMVS-RPDQSGSMTSVTTIKEINDMIVSL-D--YQNYNVQIFSADAQASYD 89 (334)
Q Consensus 15 ~VG~~FV~qYY~~L~~-~p~~L~~fY~~~S~l~-~~g~~g~~~~~~G~~~I~~~i~sL-~--~~~~~~~I~tvD~Q~s~~ 89 (334)
+--++.+..|+..+++ +++.|..+|.+++.+. ..|. ...|.++|.+.+..+ . ....++.+.....+-..+
T Consensus 4 ~~i~~l~~~~~~a~~~~D~~~~~~~~~~Da~~~~~~g~-----~~~G~~~i~~~~~~~~~~~~~~~~~~~~~~~i~~~~~ 78 (128)
T TIGR02246 4 RAIRALVATWEAAWAAGDAEGFADLFTPDGVFVTVPGQ-----VWKGREAIAAAHEAFLAGPYKGTRVTIDVIEVRFLGP 78 (128)
T ss_pred HHHHHHHHHHHHHHHcCCHHHHHHhhCCCceEECCCCC-----eecCHHHHHHHHHHHhcccCCCcEEEeeeEEEEecCC
Confidence 3446788999999995 8889999999999876 4443 578999999988753 1 122245555555443333
Q ss_pred CCEEEEEEEEEEeCCCC--cc--eeEEEEEEEEeCCeEEEEccEEE
Q 037095 90 NGLTVLVTGCLIGKDNV--RR--KFTQSFFLAPQDKGYFVLNDILR 131 (334)
Q Consensus 90 ggvlI~VtG~v~~~d~~--~r--~FsQtF~Lap~~~~Y~V~NDiFR 131 (334)
+..++.....+...++. .. ...-+|++...+++|.|..|-+.
T Consensus 79 ~~A~~~~~~~~~~~~~~~~~~~~~~~~t~~~~~~~g~W~I~~~h~s 124 (128)
T TIGR02246 79 DLAIVHAIQTITAPGKGRARPDAAVRLTFVAVKRDGRWLLAADHNT 124 (128)
T ss_pred CEEEEEEEEEEEcCCCCCCCCCcceEEEEEEEeeCCeEEEEeccCC
Confidence 43333333333333321 11 23446667778889999988654
No 27
>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=96.98 E-value=0.00076 Score=70.92 Aligned_cols=36 Identities=31% Similarity=0.619 Sum_probs=32.7
Q ss_pred CcceEEEeCCCCCCCHHHHHHHhhcCCceeeceEEe
Q 037095 295 KGHSIFVGNLPDSATVDQLKLIFEQFGPVKPDGIQV 330 (334)
Q Consensus 295 ~~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~i~v 330 (334)
.+++|||+|||+++++++|+++|++||.|...+|..
T Consensus 57 ~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~ 92 (578)
T TIGR01648 57 RGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMM 92 (578)
T ss_pred CCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEE
Confidence 468999999999999999999999999999877643
No 28
>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=96.93 E-value=0.00089 Score=69.53 Aligned_cols=38 Identities=26% Similarity=0.558 Sum_probs=34.2
Q ss_pred CCcceEEEeCCCCCCCHHHHHHHhhcCCceeeceEEee
Q 037095 294 AKGHSIFVGNLPDSATVDQLKLIFEQFGPVKPDGIQVR 331 (334)
Q Consensus 294 ~~~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~i~vR 331 (334)
..+.+|||+||++++|+++|+++|++||.|+...|...
T Consensus 283 ~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d 320 (562)
T TIGR01628 283 AQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLD 320 (562)
T ss_pred cCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEEC
Confidence 35678999999999999999999999999998887654
No 29
>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=96.82 E-value=0.0012 Score=69.89 Aligned_cols=35 Identities=23% Similarity=0.405 Sum_probs=32.2
Q ss_pred CcceEEEeCCCCCCCHHHHHHHhhcCCceeeceEE
Q 037095 295 KGHSIFVGNLPDSATVDQLKLIFEQFGPVKPDGIQ 329 (334)
Q Consensus 295 ~~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~i~ 329 (334)
..++|||+|||+++++++|+++|++||.|+...|.
T Consensus 203 ~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~ 237 (612)
T TIGR01645 203 KFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLA 237 (612)
T ss_pred ccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEE
Confidence 34799999999999999999999999999988875
No 30
>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=96.79 E-value=0.0015 Score=66.93 Aligned_cols=37 Identities=22% Similarity=0.329 Sum_probs=33.0
Q ss_pred CCcceEEEeCCCC-CCCHHHHHHHhhcCCceeeceEEe
Q 037095 294 AKGHSIFVGNLPD-SATVDQLKLIFEQFGPVKPDGIQV 330 (334)
Q Consensus 294 ~~~~~iyV~nLp~-~~t~~~l~~~F~~fG~v~~~~i~v 330 (334)
..+.+|||+|||+ ++|+++|+++|++||.|....|..
T Consensus 273 ~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~ 310 (481)
T TIGR01649 273 GPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMK 310 (481)
T ss_pred CCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEe
Confidence 3578999999998 699999999999999999887754
No 31
>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=96.73 E-value=0.0016 Score=65.63 Aligned_cols=34 Identities=32% Similarity=0.515 Sum_probs=31.3
Q ss_pred cceEEEeCCCCCCCHHHHHHHhhcCCceeeceEE
Q 037095 296 GHSIFVGNLPDSATVDQLKLIFEQFGPVKPDGIQ 329 (334)
Q Consensus 296 ~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~i~ 329 (334)
..+|||+|||+++|+++|+++|++||.|....|.
T Consensus 186 ~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~ 219 (457)
T TIGR01622 186 FLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLH 219 (457)
T ss_pred CCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEE
Confidence 5789999999999999999999999999887664
No 32
>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]
Probab=96.62 E-value=0.0017 Score=62.71 Aligned_cols=35 Identities=26% Similarity=0.473 Sum_probs=32.0
Q ss_pred CcceEEEeCCCCCCCHHHHHHHhhcCCceeeceEE
Q 037095 295 KGHSIFVGNLPDSATVDQLKLIFEQFGPVKPDGIQ 329 (334)
Q Consensus 295 ~~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~i~ 329 (334)
.=.+|||+.|+|+++|..|+++|.+||+|+.-+++
T Consensus 100 Py~TLFv~RLnydT~EskLrreF~~YG~IkrirlV 134 (335)
T KOG0113|consen 100 PYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLV 134 (335)
T ss_pred ccceeeeeeccccccHHHHHHHHHhcCcceeEEEe
Confidence 45799999999999999999999999999987763
No 33
>PF14534 DUF4440: Domain of unknown function (DUF4440); PDB: 3HX8_A 3SOY_A 3ROB_B 3GZR_A 3B7C_A 3CU3_A 3FSD_A 2R4I_C 1TP6_A.
Probab=96.56 E-value=0.038 Score=42.99 Aligned_cols=101 Identities=12% Similarity=0.062 Sum_probs=68.5
Q ss_pred HHHHHHHHHHh-cCcchhcccccCCCceeccCCCCcccccccHHHHHHHHhcCCCccceEEEEEEEEEEeCCCCEEEEEE
Q 037095 19 AFVEQYYCILH-QNPDVVHRFYQESSMVSRPDQSGSMTSVTTIKEINDMIVSLDYQNYNVQIFSADAQASYDNGLTVLVT 97 (334)
Q Consensus 19 ~FV~qYY~~L~-~~p~~L~~fY~~~S~l~~~g~~g~~~~~~G~~~I~~~i~sL~~~~~~~~I~tvD~Q~s~~ggvlI~Vt 97 (334)
+..++|...+. .+.+.|.++|+++..+...+. ...|.+++.+.+..-.......++.....+.. ++..++...
T Consensus 3 a~~~~~~~A~~~~D~~~~~~~~~~d~~~~~~~g-----~~~~~~~~l~~~~~~~~~~~~~~~~~~~v~~~-gd~a~~~~~ 76 (107)
T PF14534_consen 3 ALEEQYEDAFNAGDIDALASLYADDFVFVGPGG-----TILGKEAILAAFKSGFARFSSIKFEDVEVRVL-GDTAVVRGR 76 (107)
T ss_dssp HHHHHHHHHHHTTHHHHHHTTEEEEEEEEETTS-----EEEEHHHHHHHHHHHCEEEEEEEEEEEEEEEE-TTEEEEEEE
T ss_pred HHHHHHHHHHHhCCHHHHHhhhCCCEEEECCCC-----CEeCHHHHHHHHhhccCCCceEEEEEEEEEEE-CCEEEEEEE
Confidence 56788888877 458899999999988876654 34589999899887433333556666666666 454545555
Q ss_pred EEEEeCCCC---cceeEEEEEEEEeCCeEEE
Q 037095 98 GCLIGKDNV---RRKFTQSFFLAPQDKGYFV 125 (334)
Q Consensus 98 G~v~~~d~~---~r~FsQtF~Lap~~~~Y~V 125 (334)
..++...+. ...+..+.++..++++|.|
T Consensus 77 ~~~~~~~~g~~~~~~~~~~~v~~k~~g~W~i 107 (107)
T PF14534_consen 77 WTFTWRGDGEPVTIRGRFTSVWKKQDGKWRI 107 (107)
T ss_dssp EEEEETTTTEEEEEEEEEEEEEEEETTEEEE
T ss_pred EEEEEecCCceEEEEEEEEEEEEEeCCEEEC
Confidence 555544321 2456667777777888875
No 34
>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=96.52 E-value=0.0025 Score=67.04 Aligned_cols=33 Identities=24% Similarity=0.348 Sum_probs=30.2
Q ss_pred cceEEEeCCCCCCCHHHHHHHhhcC--CceeeceE
Q 037095 296 GHSIFVGNLPDSATVDQLKLIFEQF--GPVKPDGI 328 (334)
Q Consensus 296 ~~~iyV~nLp~~~t~~~l~~~F~~f--G~v~~~~i 328 (334)
..+|||+||++++|+++|+++|++| |.|+...+
T Consensus 233 ~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~ 267 (578)
T TIGR01648 233 VKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKK 267 (578)
T ss_pred ccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEe
Confidence 4689999999999999999999999 99997654
No 35
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor. These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
Probab=96.49 E-value=0.0031 Score=61.03 Aligned_cols=37 Identities=32% Similarity=0.606 Sum_probs=32.9
Q ss_pred CcceEEEeCCCCCCCHHHHHHHhhcCCceeeceEEee
Q 037095 295 KGHSIFVGNLPDSATVDQLKLIFEQFGPVKPDGIQVR 331 (334)
Q Consensus 295 ~~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~i~vR 331 (334)
.+.+|||+|||+++++++|+++|++||.|....|...
T Consensus 88 ~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~ 124 (352)
T TIGR01661 88 KGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSD 124 (352)
T ss_pred ccceEEECCccccCCHHHHHHHHhccCCEEEEEEEec
Confidence 3568999999999999999999999999998777553
No 36
>smart00360 RRM RNA recognition motif.
Probab=96.38 E-value=0.0028 Score=44.98 Aligned_cols=30 Identities=33% Similarity=0.654 Sum_probs=26.7
Q ss_pred EeCCCCCCCHHHHHHHhhcCCceeeceEEe
Q 037095 301 VGNLPDSATVDQLKLIFEQFGPVKPDGIQV 330 (334)
Q Consensus 301 V~nLp~~~t~~~l~~~F~~fG~v~~~~i~v 330 (334)
|+|||+.+++++|+++|++||.|....|.-
T Consensus 1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~ 30 (71)
T smart00360 1 VGNLPPDVTEEELRELFSKFGKIESVRLVR 30 (71)
T ss_pred CCCCCcccCHHHHHHHHHhhCCEeEEEEEe
Confidence 689999999999999999999998766643
No 37
>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=96.26 E-value=0.00093 Score=60.55 Aligned_cols=37 Identities=24% Similarity=0.489 Sum_probs=31.3
Q ss_pred CcceEEEeCCCCCCCHHHHHHHhhcCCceeeceEEeee
Q 037095 295 KGHSIFVGNLPDSATVDQLKLIFEQFGPVKPDGIQVRS 332 (334)
Q Consensus 295 ~~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~i~vRs 332 (334)
++.-||||||||+.||.||--+|++||.|.+.- -||-
T Consensus 34 dsA~Iyiggl~~~LtEgDil~VFSqyGe~vdin-LiRD 70 (219)
T KOG0126|consen 34 DSAYIYIGGLPYELTEGDILCVFSQYGEIVDIN-LIRD 70 (219)
T ss_pred cceEEEECCCcccccCCcEEEEeeccCceEEEE-EEec
Confidence 456799999999999999999999999998653 3443
No 38
>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=96.24 E-value=0.0052 Score=63.08 Aligned_cols=36 Identities=22% Similarity=0.373 Sum_probs=29.7
Q ss_pred CcceEEEeCCCCCCCHHHHHHHhhcCCceeeceEEe
Q 037095 295 KGHSIFVGNLPDSATVDQLKLIFEQFGPVKPDGIQV 330 (334)
Q Consensus 295 ~~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~i~v 330 (334)
.+.+|||+|||+++|+++|+++|++||.+....|.+
T Consensus 393 ps~~L~v~NLp~~~tee~L~~lF~~~G~~~i~~ik~ 428 (481)
T TIGR01649 393 PSATLHLSNIPLSVSEEDLKELFAENGVHKVKKFKF 428 (481)
T ss_pred CCcEEEEecCCCCCCHHHHHHHHHhcCCccceEEEE
Confidence 467899999999999999999999999843333433
No 39
>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]
Probab=96.21 E-value=0.0028 Score=64.07 Aligned_cols=32 Identities=34% Similarity=0.544 Sum_probs=29.1
Q ss_pred ceEEEeCCCCCCCHHHHHHHhhcCCceeeceE
Q 037095 297 HSIFVGNLPDSATVDQLKLIFEQFGPVKPDGI 328 (334)
Q Consensus 297 ~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~i 328 (334)
+-||||||+-++|+|.|+++|++||.|..+..
T Consensus 260 KvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk 291 (506)
T KOG0117|consen 260 KVLYVRNLMESTTEETLKKLFNEFGKVERVKK 291 (506)
T ss_pred eeeeeeccchhhhHHHHHHHHHhccceEEeec
Confidence 45999999999999999999999999987653
No 40
>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]
Probab=96.20 E-value=0.0045 Score=59.20 Aligned_cols=35 Identities=29% Similarity=0.605 Sum_probs=32.8
Q ss_pred CcceEEEeCCCCCCCHHHHHHHhhcCCceeeceEE
Q 037095 295 KGHSIFVGNLPDSATVDQLKLIFEQFGPVKPDGIQ 329 (334)
Q Consensus 295 ~~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~i~ 329 (334)
+.++|||||++.-+||++|+..|+.||+|...||.
T Consensus 163 ~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvF 197 (321)
T KOG0148|consen 163 DNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVF 197 (321)
T ss_pred CCceEEeCCcCccccHHHHHHhcccCCcceEEEEe
Confidence 56899999999999999999999999999998874
No 41
>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=96.09 E-value=0.0061 Score=63.35 Aligned_cols=35 Identities=29% Similarity=0.539 Sum_probs=31.4
Q ss_pred CcceEEEeCCCCCCCHHHHHHHhhcCCceeeceEE
Q 037095 295 KGHSIFVGNLPDSATVDQLKLIFEQFGPVKPDGIQ 329 (334)
Q Consensus 295 ~~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~i~ 329 (334)
..++|||+|||+++|+++|+++|++||.|....|.
T Consensus 177 ~~~~l~V~nl~~~~tee~L~~~F~~fG~i~~~~i~ 211 (562)
T TIGR01628 177 KFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVM 211 (562)
T ss_pred CCCeEEEeCCCCcCCHHHHHHHHHhcCCEEEEEEE
Confidence 35689999999999999999999999999876654
No 42
>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]
Probab=95.75 E-value=0.01 Score=58.10 Aligned_cols=36 Identities=28% Similarity=0.391 Sum_probs=33.6
Q ss_pred cceEEEeCCCCCCCHHHHHHHhhcCCceeeceEEee
Q 037095 296 GHSIFVGNLPDSATVDQLKLIFEQFGPVKPDGIQVR 331 (334)
Q Consensus 296 ~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~i~vR 331 (334)
-.+|+|.|+||.-.+-||+.+|.+||.|.++-|+.-
T Consensus 96 pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfN 131 (376)
T KOG0125|consen 96 PKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFN 131 (376)
T ss_pred CceeEeecCCccccCccHHHHHHhhCceeeEEEEec
Confidence 479999999999999999999999999999999763
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=95.56 E-value=0.014 Score=59.55 Aligned_cols=27 Identities=15% Similarity=0.448 Sum_probs=24.8
Q ss_pred CCcceEEEeCCCCCCCHHHHHHHhhcC
Q 037095 294 AKGHSIFVGNLPDSATVDQLKLIFEQF 320 (334)
Q Consensus 294 ~~~~~iyV~nLp~~~t~~~l~~~F~~f 320 (334)
....+|||||||+++|+++|+++|++|
T Consensus 173 ~~~r~lyVgnLp~~~t~~~l~~~F~~~ 199 (509)
T TIGR01642 173 RQARRLYVGGIPPEFVEEAVVDFFNDL 199 (509)
T ss_pred ccccEEEEeCCCCCCCHHHHHHHHHHH
Confidence 356799999999999999999999986
No 44
>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]
Probab=95.35 E-value=0.017 Score=54.56 Aligned_cols=36 Identities=25% Similarity=0.431 Sum_probs=32.7
Q ss_pred CcceEEEeCCCCCCCHHHHHHHhhcCCceeeceEEe
Q 037095 295 KGHSIFVGNLPDSATVDQLKLIFEQFGPVKPDGIQV 330 (334)
Q Consensus 295 ~~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~i~v 330 (334)
+..+|-|.|||-++++++|+++|.+||.|....|+.
T Consensus 188 D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylar 223 (270)
T KOG0122|consen 188 DEATVRVTNLSEDMREDDLEELFRPFGPITRVYLAR 223 (270)
T ss_pred ccceeEEecCccccChhHHHHHhhccCccceeEEEE
Confidence 457999999999999999999999999999887753
No 45
>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]
Probab=95.27 E-value=0.017 Score=54.76 Aligned_cols=35 Identities=29% Similarity=0.495 Sum_probs=30.7
Q ss_pred CcceEEEeCCCCCCCHHHHHHHhhcCCceeeceEE
Q 037095 295 KGHSIFVGNLPDSATVDQLKLIFEQFGPVKPDGIQ 329 (334)
Q Consensus 295 ~~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~i~ 329 (334)
..+.|+|.||||.++++||+++|..||.++.+-|.
T Consensus 82 ~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vh 116 (243)
T KOG0533|consen 82 RSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVH 116 (243)
T ss_pred CcceeeeecCCcCcchHHHHHHHHHhccceEEeec
Confidence 34789999999999999999999999988766553
No 46
>PF12680 SnoaL_2: SnoaL-like domain; PDB: 3F40_A 3RGA_A 3G8Z_A 3DMC_A 3FH1_A 1TUH_A 3F14_A 3ER7_A 1Z1S_A 3F7X_A ....
Probab=95.26 E-value=0.093 Score=40.05 Aligned_cols=72 Identities=10% Similarity=0.206 Sum_probs=49.7
Q ss_pred HHHHHHHHhc-CcchhcccccCCCceeccCCCCcccccccHHHHHHHHhcCC--CccceEEEEEEEEEEeCCCCEEEEEE
Q 037095 21 VEQYYCILHQ-NPDVVHRFYQESSMVSRPDQSGSMTSVTTIKEINDMIVSLD--YQNYNVQIFSADAQASYDNGLTVLVT 97 (334)
Q Consensus 21 V~qYY~~L~~-~p~~L~~fY~~~S~l~~~g~~g~~~~~~G~~~I~~~i~sL~--~~~~~~~I~tvD~Q~s~~ggvlI~Vt 97 (334)
|+.||..+++ +.+.|..||+++..+..++. ...|.++|.+.+..+- +...+++|..+ ...++.+++...
T Consensus 1 V~~~~~a~~~~d~~~i~~~~~~d~~~~~~~~-----~~~g~~~~~~~~~~~~~~~~~~~~~~~~~---~~~gd~v~~~~~ 72 (102)
T PF12680_consen 1 VRRFFEAWNAGDLDAIAALFAPDAVFHDPGG-----TLRGREAIREFFEEFFESFPDIRFEIHDI---FADGDRVVVEWT 72 (102)
T ss_dssp HHHHHHHHHTTHHHHHHHTEEEEEEEEETTS-----EEESHHHHHHHHHHHHHHEEEEEEEEEEE---EEETTEEEEEEE
T ss_pred CHHHHHHHHcCCHHHHHHHcCCCEEEEeCCC-----cccCHHHHHHHHHHHHhcCCceEEEEEEE---EEcCCEEEEEEE
Confidence 6899999984 56899999999999887743 4889999999888763 34344555444 122344444444
Q ss_pred EEE
Q 037095 98 GCL 100 (334)
Q Consensus 98 G~v 100 (334)
+..
T Consensus 73 ~~~ 75 (102)
T PF12680_consen 73 VTG 75 (102)
T ss_dssp EEE
T ss_pred EEE
Confidence 443
No 47
>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]
Probab=94.94 E-value=0.012 Score=56.08 Aligned_cols=36 Identities=33% Similarity=0.605 Sum_probs=32.9
Q ss_pred CcceEEEeCCCCCCCHHHHHHHhhcCCceeeceEEe
Q 037095 295 KGHSIFVGNLPDSATVDQLKLIFEQFGPVKPDGIQV 330 (334)
Q Consensus 295 ~~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~i~v 330 (334)
.+.+|||.+||-+.|..||+.+|++||+|...||-|
T Consensus 126 k~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~ 161 (360)
T KOG0145|consen 126 KDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILV 161 (360)
T ss_pred cccceEEecCCccchHHHHHHHHHHhhhhhhhhhhh
Confidence 467999999999999999999999999998888754
No 48
>PF12893 Lumazine_bd_2: Putative lumazine-binding; PDB: 3BLZ_C 3DUK_F 3FKA_C.
Probab=94.60 E-value=0.72 Score=37.81 Aligned_cols=105 Identities=17% Similarity=0.200 Sum_probs=71.6
Q ss_pred HHHHHHHHHHHHh-cCcchhcccccCCCceeccCCCCcccccccHHHHHHHHhc-----CCCccceEEEEEEEEEEeCCC
Q 037095 17 GNAFVEQYYCILH-QNPDVVHRFYQESSMVSRPDQSGSMTSVTTIKEINDMIVS-----LDYQNYNVQIFSADAQASYDN 90 (334)
Q Consensus 17 G~~FV~qYY~~L~-~~p~~L~~fY~~~S~l~~~g~~g~~~~~~G~~~I~~~i~s-----L~~~~~~~~I~tvD~Q~s~~g 90 (334)
-.+-|+.|+..|+ .+...|.+.+++++.|...+. |.. ...+.++-.+.+.+ -....+..+|.++|.. ++
T Consensus 6 I~~~v~~Y~dg~~~gD~~~l~~~f~~~a~~~~~~~-~~~-~~~~~~~~~~~~~~~~~p~~~~~~~~~~i~~i~i~---g~ 80 (116)
T PF12893_consen 6 IEATVQDYFDGLYNGDSEKLRSAFHPDARLQGVRK-GKL-RTMPIEEFIARVKSRVSPKPPGQERKESILSIDID---GD 80 (116)
T ss_dssp HHHHHHHHHHHHHHT-HHHHGGGEEEEEEEEEEET-TEE-EEEETHHHHHHHHHC---H-SSTT-EEEEEEEEEE---TT
T ss_pred HHHHHHHHHHHHHhcCHHHHHHhhCCCcEEEEEcC-Cce-EEeCHHHHHHHHHhhccccCCCCCceeEEEEEEEE---CC
Confidence 3456888999988 577899999999998766542 332 23345555555554 2344678888888866 34
Q ss_pred CEEEEEEEEEEeCCCCcceeEEEEEEEEeCCeEEEEccEEE
Q 037095 91 GLTVLVTGCLIGKDNVRRKFTQSFFLAPQDKGYFVLNDILR 131 (334)
Q Consensus 91 gvlI~VtG~v~~~d~~~r~FsQtF~Lap~~~~Y~V~NDiFR 131 (334)
.-++.|.-.+. .+.|.-.|.|...+++|-|.|=+|+
T Consensus 81 ~A~a~v~~~~~-----~~~~~d~~~L~K~dg~WkIv~k~~~ 116 (116)
T PF12893_consen 81 VASAKVEYEFP-----GFWFVDYFTLVKTDGGWKIVSKVYH 116 (116)
T ss_dssp EEEEEEEEEEE-----TEEEEEEEEEEEETTEEEEEEEEEE
T ss_pred EEEEEEEEEEC-----CCceEEEEEEEEECCEEEEEEEecC
Confidence 44455544433 3389999999999999999998875
No 49
>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]
Probab=94.54 E-value=0.027 Score=58.47 Aligned_cols=33 Identities=30% Similarity=0.407 Sum_probs=30.1
Q ss_pred cceEEEeCCCCCCCHHHHHHHhhcCCceeeceE
Q 037095 296 GHSIFVGNLPDSATVDQLKLIFEQFGPVKPDGI 328 (334)
Q Consensus 296 ~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~i 328 (334)
--+|-||||||.+.+.+|+.+|++||.|...-|
T Consensus 117 k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~I 149 (678)
T KOG0127|consen 117 KWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVI 149 (678)
T ss_pred cceEEeecCCcccCcHHHHHHHhhcceEEEEEc
Confidence 458999999999999999999999999987655
No 50
>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=94.38 E-value=0.022 Score=60.38 Aligned_cols=37 Identities=32% Similarity=0.567 Sum_probs=34.0
Q ss_pred CcceEEEeCCCCCCCHHHHHHHhhcCCceeeceEEee
Q 037095 295 KGHSIFVGNLPDSATVDQLKLIFEQFGPVKPDGIQVR 331 (334)
Q Consensus 295 ~~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~i~vR 331 (334)
.++.|.||||||.++-.+++.+|..||.|++.||=.+
T Consensus 612 ~~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK 648 (725)
T KOG0110|consen 612 KGTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKK 648 (725)
T ss_pred ccceeeeeccchHHHHHHHHHHHhcccceeeeccchh
Confidence 3789999999999999999999999999999988544
No 51
>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]
Probab=94.27 E-value=0.037 Score=55.96 Aligned_cols=35 Identities=29% Similarity=0.615 Sum_probs=31.1
Q ss_pred CCcceEEEeCCCCCCCHHHHHHHhhcCCceeeceE
Q 037095 294 AKGHSIFVGNLPDSATVDQLKLIFEQFGPVKPDGI 328 (334)
Q Consensus 294 ~~~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~i 328 (334)
.+.-++|||-+|..++|.||+++|++||.|-..-|
T Consensus 32 ~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl 66 (510)
T KOG0144|consen 32 GSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINL 66 (510)
T ss_pred chhhhheeccCCccccHHHHHHHHHHhCceeEEEe
Confidence 45678999999999999999999999999986544
No 52
>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]
Probab=94.11 E-value=0.018 Score=58.12 Aligned_cols=35 Identities=29% Similarity=0.520 Sum_probs=32.2
Q ss_pred CcceEEEeCCCCCCCHHHHHHHhhcCCceeeceEE
Q 037095 295 KGHSIFVGNLPDSATVDQLKLIFEQFGPVKPDGIQ 329 (334)
Q Consensus 295 ~~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~i~ 329 (334)
+..+||||-|+-.+||.+++++|++||.|++..|-
T Consensus 123 ~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~il 157 (510)
T KOG0144|consen 123 EERKLFVGMLSKQCTENEVREIFSRFGHIEDCYIL 157 (510)
T ss_pred cchhhhhhhccccccHHHHHHHHHhhCccchhhhe
Confidence 45799999999999999999999999999988764
No 53
>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]
Probab=94.10 E-value=0.042 Score=54.20 Aligned_cols=32 Identities=28% Similarity=0.485 Sum_probs=29.1
Q ss_pred CcceEEEeCCCCCCCHHHHHHHhhcCCceeec
Q 037095 295 KGHSIFVGNLPDSATVDQLKLIFEQFGPVKPD 326 (334)
Q Consensus 295 ~~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~ 326 (334)
-.++|||.|||.++|.+++.++|++||-|.++
T Consensus 133 ~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d 164 (382)
T KOG1548|consen 133 VNTSVYVSGLPLDITVDEFAEVMSKCGIIMRD 164 (382)
T ss_pred cCceEEecCCCCcccHHHHHHHHHhcceEecc
Confidence 35689999999999999999999999988765
No 54
>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]
Probab=93.45 E-value=0.065 Score=53.65 Aligned_cols=36 Identities=22% Similarity=0.364 Sum_probs=33.6
Q ss_pred eEEEeCCCCCCCHHHHHHHhhcCCceeeceEEeeec
Q 037095 298 SIFVGNLPDSATVDQLKLIFEQFGPVKPDGIQVRSQ 333 (334)
Q Consensus 298 ~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~i~vRs~ 333 (334)
.|||+||+-+++..+|.+.|+.||.|.+..|..+.+
T Consensus 78 ~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~ 113 (369)
T KOG0123|consen 78 LVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDEN 113 (369)
T ss_pred eeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCC
Confidence 399999999999999999999999999999988753
No 55
>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=93.21 E-value=0.083 Score=52.15 Aligned_cols=37 Identities=22% Similarity=0.421 Sum_probs=33.7
Q ss_pred CcceEEEeCCCCCCCHHHHHHHhhcCCceeeceEEee
Q 037095 295 KGHSIFVGNLPDSATVDQLKLIFEQFGPVKPDGIQVR 331 (334)
Q Consensus 295 ~~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~i~vR 331 (334)
...+||||||--.+++.+|+++|-+||.|+.-.|.-|
T Consensus 227 ~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~ 263 (377)
T KOG0153|consen 227 SIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR 263 (377)
T ss_pred ceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc
Confidence 4679999999889999999999999999999888765
No 56
>cd00781 ketosteroid_isomerase ketosteroid isomerase: Many biological reactions proceed by enzymatic cleavage of a C-H bond adjacent to carbonyl or a carboxyl group, leading to an enol or a enolate intermediate that is subsequently re-protonated at the same or an adjacent carbon. Ketosteroid isomerases are important members of this class of enzymes which are the most proficient of all enzymes known and have served as a paradigm for enzymatic enolizations since its discovery in 1954. This CD includes members of this class that calalyze the isomerization of various beta,gamma-unsaturated isomers at nearly a diffusion-controlled rate. These enzymes are widely distributed in bacteria.
Probab=92.67 E-value=0.99 Score=36.54 Aligned_cols=52 Identities=15% Similarity=0.210 Sum_probs=41.8
Q ss_pred HHHHHHHHHHHh-cCcchhcccccCCCceeccCCCCcccccccHHHHHHHHhcCCC
Q 037095 18 NAFVEQYYCILH-QNPDVVHRFYQESSMVSRPDQSGSMTSVTTIKEINDMIVSLDY 72 (334)
Q Consensus 18 ~~FV~qYY~~L~-~~p~~L~~fY~~~S~l~~~g~~g~~~~~~G~~~I~~~i~sL~~ 72 (334)
+..|+.||..++ .+.+.|..+|.++..+.++... ..+.|.++|.+.+..+..
T Consensus 6 ~~~v~~~~~a~~~~D~~~~~~l~aed~~~~~p~~~---~~~~G~~~i~~~~~~~~~ 58 (122)
T cd00781 6 KAAVQRYVEAVNAGDPEGIVALFADDATVEDPVGS---PPRSGRAAIAAFYAQSLG 58 (122)
T ss_pred HHHHHHHHHHHHCCCHHHHHHHcCCCeEEeCCCCC---CCccCHHHHHHHHHHHhc
Confidence 567899999988 4788999999999999765321 258899999999988753
No 57
>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]
Probab=92.64 E-value=0.085 Score=53.61 Aligned_cols=34 Identities=32% Similarity=0.362 Sum_probs=31.3
Q ss_pred CcceEEEeCCCCCCCHHHHHHHhhcCCceeeceE
Q 037095 295 KGHSIFVGNLPDSATVDQLKLIFEQFGPVKPDGI 328 (334)
Q Consensus 295 ~~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~i 328 (334)
..+.|||||||++.|=..|++-|..||.|+.+-|
T Consensus 535 Ka~qIiirNlP~dfTWqmlrDKfre~G~v~yadi 568 (608)
T KOG4212|consen 535 KACQIIIRNLPFDFTWQMLRDKFREIGHVLYADI 568 (608)
T ss_pred cccEEEEecCCccccHHHHHHHHHhccceehhhh
Confidence 4578999999999999999999999999998776
No 58
>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]
Probab=92.41 E-value=0.22 Score=52.21 Aligned_cols=36 Identities=22% Similarity=0.478 Sum_probs=32.9
Q ss_pred CcceEEEeCCCCCCCHHHHHHHhhcCCceeeceEEe
Q 037095 295 KGHSIFVGNLPDSATVDQLKLIFEQFGPVKPDGIQV 330 (334)
Q Consensus 295 ~~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~i~v 330 (334)
-|.+++|.+|+..+..-||+++|++||.|.-+.|+-
T Consensus 404 ~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVT 439 (940)
T KOG4661|consen 404 LGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVT 439 (940)
T ss_pred cccceeeeccccchhhhHHHHHHHHhcceeceeeee
Confidence 467899999999999999999999999999888764
No 59
>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]
Probab=92.40 E-value=0.11 Score=45.28 Aligned_cols=37 Identities=24% Similarity=0.461 Sum_probs=33.7
Q ss_pred CCcceEEEeCCCCCCCHHHHHHHhhcCCceeeceEEe
Q 037095 294 AKGHSIFVGNLPDSATVDQLKLIFEQFGPVKPDGIQV 330 (334)
Q Consensus 294 ~~~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~i~v 330 (334)
++|.-|||.++--.+|++++.+.|..||.||.-.+.+
T Consensus 70 VEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNL 106 (170)
T KOG0130|consen 70 VEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNL 106 (170)
T ss_pred eeeEEEEEeccCcchhHHHHHHHHhhcccccceeecc
Confidence 5789999999999999999999999999999876654
No 60
>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=92.34 E-value=0.091 Score=52.16 Aligned_cols=37 Identities=30% Similarity=0.586 Sum_probs=32.5
Q ss_pred ceEEEeCCCCCCCHHHHHHHhhcCCceeeceEEeeecC
Q 037095 297 HSIFVGNLPDSATVDQLKLIFEQFGPVKPDGIQVRSQK 334 (334)
Q Consensus 297 ~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~i~vRs~k 334 (334)
.-|||+.|..-+|++||+-+|+.||.|++.-| ||-+|
T Consensus 240 NVLFVCKLNPVTtDeDLeiIFSrFG~i~sceV-IRD~k 276 (479)
T KOG0415|consen 240 NVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEV-IRDRK 276 (479)
T ss_pred ceEEEEecCCcccccchhhHHhhcccceeeeE-Eeccc
Confidence 36999999999999999999999999998775 56554
No 61
>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]
Probab=92.33 E-value=0.14 Score=49.10 Aligned_cols=36 Identities=33% Similarity=0.410 Sum_probs=33.5
Q ss_pred CCcceEEEeCCCCCCCHHHHHHHhhcCCceeeceEE
Q 037095 294 AKGHSIFVGNLPDSATVDQLKLIFEQFGPVKPDGIQ 329 (334)
Q Consensus 294 ~~~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~i~ 329 (334)
..|..|||=||..+++|.-|-.+|+.||.|..+.|.
T Consensus 276 ~~g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvi 311 (360)
T KOG0145|consen 276 GGGWCIFVYNLSPDADESILWQLFGPFGAVTNVKVI 311 (360)
T ss_pred CCeeEEEEEecCCCchHhHHHHHhCcccceeeEEEE
Confidence 458999999999999999999999999999998874
No 62
>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]
Probab=91.97 E-value=0.11 Score=49.81 Aligned_cols=33 Identities=27% Similarity=0.533 Sum_probs=31.2
Q ss_pred ceEEEeCCCCCCCHHHHHHHhhcCCceeeceEE
Q 037095 297 HSIFVGNLPDSATVDQLKLIFEQFGPVKPDGIQ 329 (334)
Q Consensus 297 ~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~i~ 329 (334)
.-+||+.|...++-++|++.|.+||+|.+++|+
T Consensus 63 fhvfvgdls~eI~~e~lr~aF~pFGevS~akvi 95 (321)
T KOG0148|consen 63 FHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVI 95 (321)
T ss_pred eeEEehhcchhcchHHHHHHhccccccccceEe
Confidence 469999999999999999999999999999984
No 63
>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]
Probab=91.92 E-value=0.082 Score=51.24 Aligned_cols=34 Identities=32% Similarity=0.580 Sum_probs=31.1
Q ss_pred cceEEEeCCCCCCCHHHHHHHhhcCCceeeceEE
Q 037095 296 GHSIFVGNLPDSATVDQLKLIFEQFGPVKPDGIQ 329 (334)
Q Consensus 296 ~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~i~ 329 (334)
.++|+||||...++-.+|++.|.+||+|...-|.
T Consensus 78 stkl~vgNis~tctn~ElRa~fe~ygpviecdiv 111 (346)
T KOG0109|consen 78 STKLHVGNISPTCTNQELRAKFEKYGPVIECDIV 111 (346)
T ss_pred ccccccCCCCccccCHHHhhhhcccCCceeeeee
Confidence 5789999999999999999999999999877663
No 64
>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]
Probab=91.72 E-value=0.15 Score=49.99 Aligned_cols=34 Identities=44% Similarity=0.655 Sum_probs=30.1
Q ss_pred CcceEEEeCCCCCCCHHHHHHHhhcCCceeeceE
Q 037095 295 KGHSIFVGNLPDSATVDQLKLIFEQFGPVKPDGI 328 (334)
Q Consensus 295 ~~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~i 328 (334)
..+.|||++||.++++++|++.|.+||.|....|
T Consensus 96 ~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~ 129 (311)
T KOG4205|consen 96 RTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVI 129 (311)
T ss_pred ceeEEEecCcCCCCchHHHhhhhhccceeEeeEE
Confidence 3569999999999999999999999998776554
No 65
>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]
Probab=91.61 E-value=0.13 Score=53.16 Aligned_cols=32 Identities=44% Similarity=0.622 Sum_probs=29.2
Q ss_pred cceEEEeCCCCCCCHHHHHHHhhcCCceeece
Q 037095 296 GHSIFVGNLPDSATVDQLKLIFEQFGPVKPDG 327 (334)
Q Consensus 296 ~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~ 327 (334)
...||||+|||+++|++|...|..||.++-++
T Consensus 259 S~KVFvGGlp~dise~~i~~~F~~FGs~~VdW 290 (520)
T KOG0129|consen 259 SRKVFVGGLPWDITEAQINASFGQFGSVKVDW 290 (520)
T ss_pred ccceeecCCCccccHHHHHhhcccccceEeec
Confidence 45799999999999999999999999998654
No 66
>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]
Probab=91.59 E-value=0.26 Score=52.80 Aligned_cols=36 Identities=31% Similarity=0.509 Sum_probs=32.6
Q ss_pred cCCcceEEEeCCCCCCCHHHHHHHhhcCCceeeceE
Q 037095 293 AAKGHSIFVGNLPDSATVDQLKLIFEQFGPVKPDGI 328 (334)
Q Consensus 293 e~~~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~i 328 (334)
+...+++||+||+..+++.+|-..|+.||+|...+|
T Consensus 171 DP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKi 206 (877)
T KOG0151|consen 171 DPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKI 206 (877)
T ss_pred CCcccceeeecCCccccHHHHHHHhcccCcccceee
Confidence 345678999999999999999999999999988776
No 67
>PF08332 CaMKII_AD: Calcium/calmodulin dependent protein kinase II Association; InterPro: IPR013543 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. This domain is found at the C terminus of the Calcium/calmodulin dependent protein kinases II (CaMKII). These proteins also have a Ser/Thr protein kinase domain (IPR000719 from INTERPRO) at their N terminus []. The function of the CaMKII association domain is the assembly of the single proteins into large (8 to 14 subunits) multimers [] and is a prominent kinase in the central nervous system that may function in long-term potentiation and neurotransmitter release. ; GO: 0004683 calmodulin-dependent protein kinase activity, 0005516 calmodulin binding, 0006468 protein phosphorylation; PDB: 2W2C_F 3H51_B 3SOA_A 2UX0_A 1HKX_M 2F86_B.
Probab=91.37 E-value=3.5 Score=35.38 Aligned_cols=111 Identities=12% Similarity=0.064 Sum_probs=71.4
Q ss_pred HHHHHHHHHHHHHHHhcCcchhcccccCC-CceeccCCCCcccccccHHHHHHHHhcC-C--CccceEEEEEEEEEEeCC
Q 037095 14 QVVGNAFVEQYYCILHQNPDVVHRFYQES-SMVSRPDQSGSMTSVTTIKEINDMIVSL-D--YQNYNVQIFSADAQASYD 89 (334)
Q Consensus 14 ~~VG~~FV~qYY~~L~~~p~~L~~fY~~~-S~l~~~g~~g~~~~~~G~~~I~~~i~sL-~--~~~~~~~I~tvD~Q~s~~ 89 (334)
++|...|-++==.+-..+++.+.++|+++ ++|...-. | ..+.|++.|...|..+ . ..+.+..|..-..|-..+
T Consensus 3 ~eI~~l~~~w~~ai~tgD~~~~~~ly~~d~av~~Pt~s-~--~~~~g~~~~~~YF~~~l~~~~~~~~~tI~~p~V~~lg~ 79 (128)
T PF08332_consen 3 QEIAALFDRWNDAIQTGDPETYAKLYAPDVAVFEPTVS-N--QLREGLEFHKFYFDHFLAKKPQGVNTTILNPHVRLLGD 79 (128)
T ss_dssp HHHHHHHHHHHHHHHHT-HHHHHHHEEEEEEEEEGGGT-T--SEEESCHHHHHHHHHTGTTTSSCEEEEEEEEEEEEEST
T ss_pred HHHHHHHHHHHHHHHcCCHHHHhhhcCCCeeEeccccC-C--ceecChHHHHHHHhcccccCCCceeeEecCCeEEEcCC
Confidence 56666665554444557999999999999 88876533 1 2678999999888743 2 233345566666666555
Q ss_pred CCEEEEEEEEEEeCC--CCc--ceeEEEEEEEEeCCeEEEEc
Q 037095 90 NGLTVLVTGCLIGKD--NVR--RKFTQSFFLAPQDKGYFVLN 127 (334)
Q Consensus 90 ggvlI~VtG~v~~~d--~~~--r~FsQtF~Lap~~~~Y~V~N 127 (334)
+..++.=+=.++..| +.+ ..--.||+-...+++|.|++
T Consensus 80 ~~Ai~~gvy~f~~~d~~G~~~~~~areT~v~~~~~g~W~ivh 121 (128)
T PF08332_consen 80 NAAIDAGVYTFQFVDKDGVPRTVQARETRVWQKRDGKWKIVH 121 (128)
T ss_dssp TEEEEEEEEEEEEESTTSSEEEEEEEEEEEEEEETTEEEEEE
T ss_pred CEEEEeeEEEEEeecCCCCeeeEEEeEEEEEEEeCCeEEEEE
Confidence 555444444444433 333 24467888889999998875
No 68
>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]
Probab=90.19 E-value=0.21 Score=53.81 Aligned_cols=32 Identities=28% Similarity=0.616 Sum_probs=29.4
Q ss_pred cceEEEeCCCCCCCHHHHHHHhhcCCceeece
Q 037095 296 GHSIFVGNLPDSATVDQLKLIFEQFGPVKPDG 327 (334)
Q Consensus 296 ~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~ 327 (334)
+++||||.|+.++++.||.++|+.||.|.+.-
T Consensus 421 SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~ 452 (894)
T KOG0132|consen 421 SRTLWVGGIPKNVTEQDLANLFEEFGEIQSII 452 (894)
T ss_pred eeeeeeccccchhhHHHHHHHHHhcccceeEe
Confidence 56899999999999999999999999998754
No 69
>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]
Probab=89.99 E-value=0.18 Score=45.99 Aligned_cols=31 Identities=32% Similarity=0.482 Sum_probs=28.6
Q ss_pred CcceEEEeCCCCCCCHHHHHHHhhcCCceee
Q 037095 295 KGHSIFVGNLPDSATVDQLKLIFEQFGPVKP 325 (334)
Q Consensus 295 ~~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~ 325 (334)
-|.+||||||-..+++..|-..|+.||.|..
T Consensus 95 vganlfvgNLd~~vDe~~L~dtFsafG~l~~ 125 (203)
T KOG0131|consen 95 VGANLFVGNLDPEVDEKLLYDTFSAFGVLIS 125 (203)
T ss_pred ccccccccccCcchhHHHHHHHHHhcccccc
Confidence 3589999999999999999999999999865
No 70
>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]
Probab=89.59 E-value=0.35 Score=46.60 Aligned_cols=40 Identities=23% Similarity=0.416 Sum_probs=36.8
Q ss_pred ccCCcceEEEeCCCCCCCHHHHHHHhhcCCceeeceEEee
Q 037095 292 HAAKGHSIFVGNLPDSATVDQLKLIFEQFGPVKPDGIQVR 331 (334)
Q Consensus 292 ~e~~~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~i~vR 331 (334)
+..+|++|||=.||-.-.+.+|...|-.||.|.++.|.|-
T Consensus 281 eGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvD 320 (371)
T KOG0146|consen 281 EGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVD 320 (371)
T ss_pred cCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeeh
Confidence 3457999999999999999999999999999999999873
No 71
>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]
Probab=89.27 E-value=0.15 Score=50.76 Aligned_cols=32 Identities=25% Similarity=0.505 Sum_probs=29.5
Q ss_pred CcceEEEeCCCCCCCHHHHHHHhhcCCceeec
Q 037095 295 KGHSIFVGNLPDSATVDQLKLIFEQFGPVKPD 326 (334)
Q Consensus 295 ~~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~ 326 (334)
-.++||||.+.|...|+.||..|..||+||+-
T Consensus 112 iMcRvYVGSIsfEl~EDtiR~AF~PFGPIKSI 143 (544)
T KOG0124|consen 112 IMCRVYVGSISFELREDTIRRAFDPFGPIKSI 143 (544)
T ss_pred HhHheeeeeeEEEechHHHHhhccCCCCccee
Confidence 35789999999999999999999999999963
No 72
>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=89.06 E-value=0.24 Score=52.82 Aligned_cols=35 Identities=29% Similarity=0.372 Sum_probs=31.3
Q ss_pred cceEEEeCCCCCCCHHHHHHHhhcCCceeeceEEe
Q 037095 296 GHSIFVGNLPDSATVDQLKLIFEQFGPVKPDGIQV 330 (334)
Q Consensus 296 ~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~i~v 330 (334)
.++|||+||+|++|.++|+.+|.+.|.|....|--
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 34499999999999999999999999999887754
No 73
>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]
Probab=88.89 E-value=0.34 Score=49.45 Aligned_cols=35 Identities=29% Similarity=0.584 Sum_probs=32.5
Q ss_pred CcceEEEeCCCCCCCHHHHHHHhhcCCceeeceEE
Q 037095 295 KGHSIFVGNLPDSATVDQLKLIFEQFGPVKPDGIQ 329 (334)
Q Consensus 295 ~~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~i~ 329 (334)
.|+-||||.||.++.|++|.-+|.+-|.|-..|+-
T Consensus 82 ~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLM 116 (506)
T KOG0117|consen 82 RGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLM 116 (506)
T ss_pred CCceEEecCCCccccchhhHHHHHhccceeeEEEe
Confidence 68999999999999999999999999999987753
No 74
>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]
Probab=88.33 E-value=0.4 Score=49.91 Aligned_cols=30 Identities=33% Similarity=0.532 Sum_probs=28.5
Q ss_pred cceEEEeCCCCCCCHHHHHHHhhcCCceee
Q 037095 296 GHSIFVGNLPDSATVDQLKLIFEQFGPVKP 325 (334)
Q Consensus 296 ~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~ 325 (334)
..+|+|-|||.+++.++|+++|+.||+|+.
T Consensus 75 ~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ 104 (549)
T KOG4660|consen 75 QGTLVVFNLPRSVSNDTLLRIFGAYGEIRE 104 (549)
T ss_pred cceEEEEecCCcCCHHHHHHHHHhhcchhh
Confidence 468999999999999999999999999996
No 75
>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]
Probab=87.98 E-value=0.43 Score=48.27 Aligned_cols=32 Identities=25% Similarity=0.259 Sum_probs=28.9
Q ss_pred CcceEEEeCCCCCCCHHHHHHHhhcCCceeec
Q 037095 295 KGHSIFVGNLPDSATVDQLKLIFEQFGPVKPD 326 (334)
Q Consensus 295 ~~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~ 326 (334)
.+.-|-+|||||+++|+||-+++..||.|..-
T Consensus 27 pSkV~HlRnlp~e~tE~elI~Lg~pFG~vtn~ 58 (492)
T KOG1190|consen 27 PSKVVHLRNLPWEVTEEELISLGLPFGKVTNL 58 (492)
T ss_pred CcceeEeccCCccccHHHHHHhcccccceeee
Confidence 45679999999999999999999999999864
No 76
>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]
Probab=87.31 E-value=0.29 Score=50.90 Aligned_cols=37 Identities=35% Similarity=0.484 Sum_probs=32.5
Q ss_pred cceEEEeCCCCCCCHHHHHHHhhcCCceeeceEEeee
Q 037095 296 GHSIFVGNLPDSATVDQLKLIFEQFGPVKPDGIQVRS 332 (334)
Q Consensus 296 ~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~i~vRs 332 (334)
..++|||||=++.|+++|+.+|+.||.|...-...++
T Consensus 278 ~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~ 314 (549)
T KOG0147|consen 278 MRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDS 314 (549)
T ss_pred hhhhhhcccccCchHHHHhhhccCcccceeeeecccc
Confidence 3459999999999999999999999999987776654
No 77
>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]
Probab=86.82 E-value=0.53 Score=47.19 Aligned_cols=37 Identities=27% Similarity=0.603 Sum_probs=34.0
Q ss_pred CCcceEEEeCCCCCCCHHHHHHHhhcCCceeeceEEe
Q 037095 294 AKGHSIFVGNLPDSATVDQLKLIFEQFGPVKPDGIQV 330 (334)
Q Consensus 294 ~~~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~i~v 330 (334)
..+.+|||.||.-.++.+.|++.|+.||.|....|++
T Consensus 268 ~~~~nl~vknld~~~~~e~L~~~f~~~GeI~s~kv~~ 304 (369)
T KOG0123|consen 268 LQGANLYVKNLDETLSDEKLRKIFSSFGEITSAKVMV 304 (369)
T ss_pred ccccccccccCccccchhHHHHHHhcccceeeEEEEe
Confidence 4567999999999999999999999999999988776
No 78
>TIGR02096 conserved hypothetical protein, steroid delta-isomerase-related. This family of proteins about 135 amino acids in length largely restricted to the Proteobacteria. This family and a delta5-3-ketosteroid isomerase from Pseudomonas testosteroni appear homologous, especially toward their respective N-termini. Members, therefore, probably are enzymes.
Probab=83.43 E-value=17 Score=29.27 Aligned_cols=60 Identities=7% Similarity=0.205 Sum_probs=41.7
Q ss_pred HHHHHHHHHhc-CcchhcccccCCCceeccCCCCcccccccHHHHHHHHhcCC--CccceEEEEEE
Q 037095 20 FVEQYYCILHQ-NPDVVHRFYQESSMVSRPDQSGSMTSVTTIKEINDMIVSLD--YQNYNVQIFSA 82 (334)
Q Consensus 20 FV~qYY~~L~~-~p~~L~~fY~~~S~l~~~g~~g~~~~~~G~~~I~~~i~sL~--~~~~~~~I~tv 82 (334)
-++.||+.+++ +.+.|..||+++..+..++.. ....|.++|.+.+..+- +.+++++|..+
T Consensus 3 iv~~~~~a~~~~d~~~~~~~~~~d~~~~~~~~~---~~~~G~~~~~~~~~~~~~~~~~~~~~i~~~ 65 (129)
T TIGR02096 3 LAQHWIEAFNRGDMDAVLALLAEDVLYDDNQGG---RVLGGKAQLARFLAPYRTAFPDLLVDVVVC 65 (129)
T ss_pred HHHHHHHHHHCCCHHHHHHhcCCCeEEEcCCCC---cEeccHHHHHHHHHHHHHhCchhhceeEEE
Confidence 47889999885 778999999999887765431 14567999988776542 23445555533
No 79
>PF13577 SnoaL_4: SnoaL-like domain; PDB: 3S5C_B 3EJV_A 2RFR_A 3B8L_F 2CHC_A 3A76_A 3EF8_B.
Probab=82.78 E-value=11 Score=30.05 Aligned_cols=68 Identities=7% Similarity=0.105 Sum_probs=48.0
Q ss_pred HHHHHHHHHHHHHh-cCcchhcccccCCCceeccCCCCcccccccHHHHHHHHhcC--CCccceEEEEEEEEE
Q 037095 16 VGNAFVEQYYCILH-QNPDVVHRFYQESSMVSRPDQSGSMTSVTTIKEINDMIVSL--DYQNYNVQIFSADAQ 85 (334)
Q Consensus 16 VG~~FV~qYY~~L~-~~p~~L~~fY~~~S~l~~~g~~g~~~~~~G~~~I~~~i~sL--~~~~~~~~I~tvD~Q 85 (334)
--..++..|...++ .+.+.+..+|.+++.+.+.+.. ...+.|.++|.+.+... ....+.|.+......
T Consensus 8 ~I~~l~~~~~~~~D~~~~~~~~~lft~d~~~~~~~~~--~~~~~G~~~i~~~~~~~~~~~~~~~H~~~~~~v~ 78 (127)
T PF13577_consen 8 AIRDLIARYARALDTGDWEEWADLFTEDAVFDFPGFG--FGRYRGRDAIRAFLRARFDGFAATRHMVTNPVVD 78 (127)
T ss_dssp HHHHHHHHHHHHHHTT-HHHHHTTEEEEEEEEETTTC--EEEEESHHHHHHHHHHHHHHEEEEEEEEEEEEEE
T ss_pred HHHHHHHHHHHHhhCCCHHHHHhccCCcEEEEEeCcc--ccccCCHHHHHHHHHHhcccccceeEEccceEEE
Confidence 34577888888888 4678999999999998887520 22688999999998875 222445665554444
No 80
>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]
Probab=79.60 E-value=1.5 Score=41.87 Aligned_cols=34 Identities=32% Similarity=0.547 Sum_probs=31.0
Q ss_pred ceEEEeCCCCCCCHHHHHHHhhcCCceeeceEEe
Q 037095 297 HSIFVGNLPDSATVDQLKLIFEQFGPVKPDGIQV 330 (334)
Q Consensus 297 ~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~i~v 330 (334)
..|||.||+.-++-+.|++.|+.||+|..+=|.|
T Consensus 32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~v 65 (275)
T KOG0115|consen 32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKV 65 (275)
T ss_pred ceEEEEecchhhhhHHHHHhhhhcCccchheeee
Confidence 4799999999999999999999999998876655
No 81
>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]
Probab=79.32 E-value=1.2 Score=42.03 Aligned_cols=32 Identities=25% Similarity=0.414 Sum_probs=26.7
Q ss_pred ceEEEeCCCCCCCHHHHHHHhhcCCceeeceE
Q 037095 297 HSIFVGNLPDSATVDQLKLIFEQFGPVKPDGI 328 (334)
Q Consensus 297 ~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~i 328 (334)
.+|||.||.-++||++|+.+|+.|--...-+|
T Consensus 211 stlfianl~~~~~ed~l~~~~~~~~gf~~l~~ 242 (284)
T KOG1457|consen 211 STLFIANLGPNCTEDELKQLLSRYPGFHILKI 242 (284)
T ss_pred hhHhhhccCCCCCHHHHHHHHHhCCCceEEEE
Confidence 46999999999999999999999965544333
No 82
>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]
Probab=78.91 E-value=2 Score=43.76 Aligned_cols=37 Identities=27% Similarity=0.403 Sum_probs=33.6
Q ss_pred ccCCcceEEEeCCCCCCCHHHHHHHhhcCCceeeceE
Q 037095 292 HAAKGHSIFVGNLPDSATVDQLKLIFEQFGPVKPDGI 328 (334)
Q Consensus 292 ~e~~~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~i 328 (334)
+|-.+..|-+.|||.+-.-+-|.++|+.||.|+..+|
T Consensus 227 eel~srtivaenLP~Dh~~enl~kiFg~~G~IksIRI 263 (484)
T KOG1855|consen 227 EELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRI 263 (484)
T ss_pred cccccceEEEecCCcchHHHHHHHHhhcccceeeeee
Confidence 3446889999999999999999999999999998877
No 83
>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=78.66 E-value=2.1 Score=35.34 Aligned_cols=32 Identities=25% Similarity=0.372 Sum_probs=20.6
Q ss_pred cceEEEeCCCCCCCHHHHHHHhhcCCceeece
Q 037095 296 GHSIFVGNLPDSATVDQLKLIFEQFGPVKPDG 327 (334)
Q Consensus 296 ~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~ 327 (334)
|.-|+|.++.-.++-++|+++|++||.|...-
T Consensus 1 G~il~~~g~~~~~~re~iK~~f~~~g~V~yVD 32 (105)
T PF08777_consen 1 GCILKFSGLGEPTSREDIKEAFSQFGEVAYVD 32 (105)
T ss_dssp --EEEEEE--SS--HHHHHHHT-SS--EEEEE
T ss_pred CeEEEEecCCCCcCHHHHHHHHHhcCCcceEE
Confidence 46789999999999999999999999998654
No 84
>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]
Probab=78.21 E-value=2.2 Score=42.83 Aligned_cols=33 Identities=21% Similarity=0.399 Sum_probs=30.0
Q ss_pred cceEEEeCCCCCCCHHHHHHHhhcCCceeeceE
Q 037095 296 GHSIFVGNLPDSATVDQLKLIFEQFGPVKPDGI 328 (334)
Q Consensus 296 ~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~i 328 (334)
-.+|||..+-.+.+++||+.+|..||+|+...+
T Consensus 210 fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~L 242 (544)
T KOG0124|consen 210 FNRIYVASVHPDLSETDIKSVFEAFGEIVKCQL 242 (544)
T ss_pred hheEEeeecCCCccHHHHHHHHHhhcceeeEEe
Confidence 358999999999999999999999999987654
No 85
>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]
Probab=73.20 E-value=3.4 Score=39.59 Aligned_cols=34 Identities=24% Similarity=0.380 Sum_probs=29.8
Q ss_pred cceEEEeCCCCCCCHHHHHHHhhcCCceeeceEE
Q 037095 296 GHSIFVGNLPDSATVDQLKLIFEQFGPVKPDGIQ 329 (334)
Q Consensus 296 ~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~i~ 329 (334)
..-||++|+|......-|+++|++||.|-...+|
T Consensus 74 ~GVvylS~IPp~m~~~rlReil~~yGeVGRvylq 107 (278)
T KOG3152|consen 74 TGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQ 107 (278)
T ss_pred ceEEEeccCCCccCHHHHHHHHHhccccceEEec
Confidence 3579999999999999999999999999765544
No 86
>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]
Probab=72.98 E-value=3.3 Score=39.16 Aligned_cols=28 Identities=21% Similarity=0.476 Sum_probs=25.1
Q ss_pred CcceEEEeCCCCCCCHHHHHHHhhcCCc
Q 037095 295 KGHSIFVGNLPDSATVDQLKLIFEQFGP 322 (334)
Q Consensus 295 ~~~~iyV~nLp~~~t~~~l~~~F~~fG~ 322 (334)
...+|||.+||.++...+|..+|..|--
T Consensus 33 ~VRTLFVSGLP~DvKpREiynLFR~f~G 60 (284)
T KOG1457|consen 33 AVRTLFVSGLPNDVKPREIYNLFRRFHG 60 (284)
T ss_pred ccceeeeccCCcccCHHHHHHHhccCCC
Confidence 4579999999999999999999998843
No 87
>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]
Probab=72.34 E-value=3.7 Score=42.67 Aligned_cols=36 Identities=39% Similarity=0.660 Sum_probs=33.0
Q ss_pred CcceEEEeCCCCCCCHHHHHHHhh-cCCceeeceEEe
Q 037095 295 KGHSIFVGNLPDSATVDQLKLIFE-QFGPVKPDGIQV 330 (334)
Q Consensus 295 ~~~~iyV~nLp~~~t~~~l~~~F~-~fG~v~~~~i~v 330 (334)
.-.+||||+||--++.++|..+|. -||-|..+||-+
T Consensus 369 prrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDt 405 (520)
T KOG0129|consen 369 PRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDT 405 (520)
T ss_pred ccceEEecCCCCcchHHHHHHHHHHhcCceEEEEecc
Confidence 357899999999999999999998 899999999854
No 88
>COG4875 Uncharacterized protein conserved in bacteria with a cystatin-like fold [Function unknown]
Probab=72.00 E-value=66 Score=27.91 Aligned_cols=111 Identities=14% Similarity=0.163 Sum_probs=66.2
Q ss_pred CCCHHHHHHHHHHHHHHHHhcCcchhcccccCCCceeccCCCCcccccccHHHHHHHHhcC----CCccceEEEEEEEEE
Q 037095 10 ALSPQVVGNAFVEQYYCILHQNPDVVHRFYQESSMVSRPDQSGSMTSVTTIKEINDMIVSL----DYQNYNVQIFSADAQ 85 (334)
Q Consensus 10 ~~~a~~VG~~FV~qYY~~L~~~p~~L~~fY~~~S~l~~~g~~g~~~~~~G~~~I~~~i~sL----~~~~~~~~I~tvD~Q 85 (334)
-++-++|+.-|=+|-=.++..+|..+...|.+++.|.-.-.+ +.-.++.+|.+.+..+ |...+..+.-++-|-
T Consensus 33 ~~t~~~vAaLFdrWN~~L~TGdP~kV~anyApDaVLLPT~Sn---~vR~s~~ei~DYF~~FLk~KPqG~IdsR~i~~gcN 109 (156)
T COG4875 33 NVTEREVAALFDRWNAALTTGDPNKVAANYAPDAVLLPTMSN---QVRSSRSEILDYFSHFLKLKPQGYIDSRKITLGCN 109 (156)
T ss_pred CccHHHHHHHHHHHHhhhhcCChHHHHhhcCCceEeeccccc---ccccCHHHHHHHHHHHhccCCcceecceeEEeccc
Confidence 467788999998888888889999999999999987543221 1334677887766643 221111111112233
Q ss_pred EeCCCCEEEEEEEEEEeCCCCcceeEEEEEEEEeCCeEEEEcc
Q 037095 86 ASYDNGLTVLVTGCLIGKDNVRRKFTQSFFLAPQDKGYFVLND 128 (334)
Q Consensus 86 ~s~~ggvlI~VtG~v~~~d~~~r~FsQtF~Lap~~~~Y~V~ND 128 (334)
.-.+-|..- +++.|+..-.=--+|.-..+++.|.|.|.
T Consensus 110 ~AlD~GtYT-----F~f~DGs~v~ARYtftY~w~~g~WlI~~H 147 (156)
T COG4875 110 NALDAGTYT-----FIFTDGSNVQARYTFTYSWIDGTWLIVNH 147 (156)
T ss_pred cccccceEE-----EEEcCCcceeEEEEEEEEecCCeEEEEec
Confidence 223333222 22334322112236778889999999875
No 89
>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]
Probab=70.59 E-value=2.5 Score=39.83 Aligned_cols=34 Identities=26% Similarity=0.432 Sum_probs=30.5
Q ss_pred cCCcceEEEeCCCCCCCHHHHHHHhhcCCceeec
Q 037095 293 AAKGHSIFVGNLPDSATVDQLKLIFEQFGPVKPD 326 (334)
Q Consensus 293 e~~~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~ 326 (334)
+.+..++||+|+-|.+|.++++.+|+.||.|+..
T Consensus 98 ~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ 131 (231)
T KOG4209|consen 98 EVDAPSVWVGNVDFLVTLTKIELHFESCGGINRV 131 (231)
T ss_pred ccCCceEEEeccccccccchhhheeeccCCccce
Confidence 4567899999999999999999999999999643
No 90
>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]
Probab=70.46 E-value=3 Score=40.43 Aligned_cols=32 Identities=38% Similarity=0.449 Sum_probs=28.4
Q ss_pred ceEE-EeCCCCCCCHHHHHHHhhcCCceeeceE
Q 037095 297 HSIF-VGNLPDSATVDQLKLIFEQFGPVKPDGI 328 (334)
Q Consensus 297 ~~iy-V~nLp~~~t~~~l~~~F~~fG~v~~~~i 328 (334)
.+|| |+||+++++.++|..+|..+|.|...++
T Consensus 185 ~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~ 217 (285)
T KOG4210|consen 185 DTIFFVGELDFSLTRDDLKEHFVSSGEITSVRL 217 (285)
T ss_pred ccceeecccccccchHHHhhhccCcCcceeecc
Confidence 4566 9999999999999999999999987664
No 91
>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=69.93 E-value=3.4 Score=29.17 Aligned_cols=16 Identities=44% Similarity=0.615 Sum_probs=12.8
Q ss_pred HHHHhhcCCceeeceE
Q 037095 313 LKLIFEQFGPVKPDGI 328 (334)
Q Consensus 313 l~~~F~~fG~v~~~~i 328 (334)
|.++|++||.|+...+
T Consensus 1 L~~~f~~fG~V~~i~~ 16 (56)
T PF13893_consen 1 LYKLFSKFGEVKKIKI 16 (56)
T ss_dssp HHHHHTTTS-EEEEEE
T ss_pred ChHHhCCcccEEEEEE
Confidence 7899999999987665
No 92
>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]
Probab=67.68 E-value=5 Score=41.56 Aligned_cols=32 Identities=28% Similarity=0.458 Sum_probs=27.8
Q ss_pred cceEEEeCCCCCCCHHHHHHHhhcCCceeeceE
Q 037095 296 GHSIFVGNLPDSATVDQLKLIFEQFGPVKPDGI 328 (334)
Q Consensus 296 ~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~i 328 (334)
..-|-+|+|||.+|++||.++|+-- .|.++||
T Consensus 103 d~vVRLRGLPfscte~dI~~FFaGL-~Iv~~gi 134 (510)
T KOG4211|consen 103 DGVVRLRGLPFSCTEEDIVEFFAGL-EIVPDGI 134 (510)
T ss_pred CceEEecCCCccCcHHHHHHHhcCC-cccccce
Confidence 4579999999999999999999987 6666676
No 93
>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]
Probab=60.54 E-value=4.9 Score=40.22 Aligned_cols=28 Identities=25% Similarity=0.246 Sum_probs=23.2
Q ss_pred CCcceEEEeCCCCCCCHHHHHHHhhcCC
Q 037095 294 AKGHSIFVGNLPDSATVDQLKLIFEQFG 321 (334)
Q Consensus 294 ~~~~~iyV~nLp~~~t~~~l~~~F~~fG 321 (334)
..-+.+|||||-|-+|++||-+....-|
T Consensus 78 Grk~~~YvGNL~W~TTD~DL~~A~~S~G 105 (498)
T KOG4849|consen 78 GRKYCCYVGNLLWYTTDADLLKALQSTG 105 (498)
T ss_pred CceEEEEecceeEEeccHHHHHHHHhhh
Confidence 3457899999999999999988776554
No 94
>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]
Probab=55.88 E-value=8 Score=38.56 Aligned_cols=31 Identities=32% Similarity=0.420 Sum_probs=28.6
Q ss_pred cceEEEeCCCCCCCHHHHHHHhhcCCceeec
Q 037095 296 GHSIFVGNLPDSATVDQLKLIFEQFGPVKPD 326 (334)
Q Consensus 296 ~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~ 326 (334)
.-+|||=+||-++++.+|.++|.++|.|+..
T Consensus 66 ~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrn 96 (351)
T KOG1995|consen 66 NETIFVWGCPDSVCENDNADFFLQCGVIKRN 96 (351)
T ss_pred cccceeeccCccchHHHHHHHHhhcceeccC
Confidence 4589999999999999999999999999865
No 95
>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]
Probab=55.04 E-value=6.5 Score=43.22 Aligned_cols=32 Identities=22% Similarity=0.210 Sum_probs=29.8
Q ss_pred cceEEEeCCCCCCCHHHHHHHhhcCCceeece
Q 037095 296 GHSIFVGNLPDSATVDQLKLIFEQFGPVKPDG 327 (334)
Q Consensus 296 ~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~ 327 (334)
-+++||+|+|+..|.++|+.+|+++|.+++-+
T Consensus 736 K~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~ 767 (881)
T KOG0128|consen 736 KISVAISGPPFQGTKEELKSLASKTGNVTSLR 767 (881)
T ss_pred hhhhheeCCCCCCchHHHHhhccccCCccccc
Confidence 46899999999999999999999999999875
No 96
>PF07366 SnoaL: SnoaL-like polyketide cyclase; InterPro: IPR009959 This domain is found in SnoaL [] a polyketide cyclase involved in nogalamycin biosynthesis. This domain was formerly known as DUF1486. It adopts a distorted alpha-beta barrel fold []. Structural data together with site-directed mutagenesis experiments have shown that SnoaL has a different mechanism to that of the classical aldolase for catalysing intramolecular aldol condensation [].; PDB: 2GEY_C 3F9S_A 2GEX_A 3EHC_B 2F99_D 2F98_D 1SJW_A 3K0Z_B.
Probab=54.84 E-value=1.1e+02 Score=24.60 Aligned_cols=60 Identities=10% Similarity=0.217 Sum_probs=39.2
Q ss_pred HHHHHHHhc-CcchhcccccCCCceeccCCCCcccccccHHHHHHHHhcC--CCccceEEEEEEEEE
Q 037095 22 EQYYCILHQ-NPDVVHRFYQESSMVSRPDQSGSMTSVTTIKEINDMIVSL--DYQNYNVQIFSADAQ 85 (334)
Q Consensus 22 ~qYY~~L~~-~p~~L~~fY~~~S~l~~~g~~g~~~~~~G~~~I~~~i~sL--~~~~~~~~I~tvD~Q 85 (334)
+.|+..+++ +.+.+..||+++..+...+.. ...|.+++.+.+..+ -|-+.+++|..+=+.
T Consensus 5 ~~~~~~~n~~d~~~~~~~~~~d~~~~~~~~~----~~~G~~~~~~~~~~~~~afPD~~~~i~~~~~~ 67 (126)
T PF07366_consen 5 RFYEEVWNRGDLDALDELVAPDVVFHDPGPG----PPVGREGFKEFLKELRAAFPDLRFEIEDVVAE 67 (126)
T ss_dssp HHHHHHHHTT-GCHHHGTEEEEEEEEGCTTT----EEEHHHHHHHHHHHHHHHSTTTEEEEEEEEEE
T ss_pred HHHHHHHhCCCHHHHHHhcCCCEEEEecCCC----CCCCHHHHHHHHHHHHHHCCCCEEEEEEEEEE
Confidence 344455564 678999999999988776541 566777777666654 133557777665443
No 97
>PF12870 Lumazine_bd: Lumazine-binding domain; InterPro: IPR024267 This entry represents a lumazine-binding domain found in a family of putative lipoproteins from bacteria. Lumazine is a fluorescent accessory protein having 6,7-dimethyl-8-(1'-D-ribityl) lumazine (DMRL) as its authentic chromophore; it modulates the emission of bacterial luciferase to shorter wavelengths with increasing luminous strength.; PDB: 3K7C_C.
Probab=54.73 E-value=58 Score=25.24 Aligned_cols=45 Identities=20% Similarity=0.165 Sum_probs=25.5
Q ss_pred EEEEEEEEEEeCCCCEEEEEEEEEEeCCCCcceeEEEEEEEEeCCeEEEE
Q 037095 77 VQIFSADAQASYDNGLTVLVTGCLIGKDNVRRKFTQSFFLAPQDKGYFVL 126 (334)
Q Consensus 77 ~~I~tvD~Q~s~~ggvlI~VtG~v~~~d~~~r~FsQtF~Lap~~~~Y~V~ 126 (334)
+++..+.-... + =...|+..+..+++.... .+|.|...++.|.|.
T Consensus 67 ~~~~~v~~~~~-g--~~A~V~v~~~~~~g~~~~--~~~~lvk~dg~Wkv~ 111 (111)
T PF12870_consen 67 IKIVEVEENTI-G--DTATVTVKITYKDGKEKT--FTVPLVKEDGKWKVC 111 (111)
T ss_dssp EEEEEEEEEEE-S--SEEEEEEEEEETTS-EEE--EEEEEEEETTEEEE-
T ss_pred eEEEEEEEecc-C--CEEEEEEEEEECCCCeeE--EEEEEEEECCEEEeC
Confidence 44444443333 3 334455556666655544 467888899999983
No 98
>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=52.00 E-value=6 Score=43.78 Aligned_cols=42 Identities=21% Similarity=0.370 Sum_probs=36.3
Q ss_pred ccCCcceEEEeCCCCCCCHHHHHHHhhcCCceeeceEEeeec
Q 037095 292 HAAKGHSIFVGNLPDSATVDQLKLIFEQFGPVKPDGIQVRSQ 333 (334)
Q Consensus 292 ~e~~~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~i~vRs~ 333 (334)
+.....+||+|||...+++.+|+..|..||.|....|-.+..
T Consensus 368 D~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~ 409 (975)
T KOG0112|consen 368 DFRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHI 409 (975)
T ss_pred chhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCCC
Confidence 334456899999999999999999999999999998877654
No 99
>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]
Probab=50.99 E-value=9.1 Score=40.04 Aligned_cols=34 Identities=41% Similarity=0.661 Sum_probs=30.3
Q ss_pred CcceEEEeCCCCCCCHHHHHHHhhcCCceeeceE
Q 037095 295 KGHSIFVGNLPDSATVDQLKLIFEQFGPVKPDGI 328 (334)
Q Consensus 295 ~~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~i 328 (334)
...+|||+|||+..++.++.|+-..||.++.-..
T Consensus 288 ~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~l 321 (500)
T KOG0120|consen 288 SPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRL 321 (500)
T ss_pred ccchhhhccCcCccCHHHHHHHHHhcccchhhee
Confidence 4579999999999999999999999999986543
No 100
>smart00361 RRM_1 RNA recognition motif.
Probab=49.34 E-value=14 Score=27.41 Aligned_cols=18 Identities=22% Similarity=0.296 Sum_probs=16.0
Q ss_pred HHHHHHHhh----cCCceeece
Q 037095 310 VDQLKLIFE----QFGPVKPDG 327 (334)
Q Consensus 310 ~~~l~~~F~----~fG~v~~~~ 327 (334)
+++|+++|+ +||.|....
T Consensus 2 ~~~l~~~~~~~~~~fG~v~~v~ 23 (70)
T smart00361 2 DEDFEREFSEEEEYFGEVGKIN 23 (70)
T ss_pred chhHHHHHHHHHHhcCCeeEEE
Confidence 578999999 999999886
No 101
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=43.74 E-value=1.7e+02 Score=27.88 Aligned_cols=51 Identities=14% Similarity=0.211 Sum_probs=42.1
Q ss_pred HHHHHHHHHHHHh-cCcchhcccccCCCceeccCCCCcccccccHHHHHHHHhcC
Q 037095 17 GNAFVEQYYCILH-QNPDVVHRFYQESSMVSRPDQSGSMTSVTTIKEINDMIVSL 70 (334)
Q Consensus 17 G~~FV~qYY~~L~-~~p~~L~~fY~~~S~l~~~g~~g~~~~~~G~~~I~~~i~sL 70 (334)
...-|++||..+. .+.+.|..++.++..+..+.. ...+.|.+.|..++..+
T Consensus 206 ~~~~v~~~~~a~~~gD~~~l~~Lla~Dv~~~~p~~---~~~~~G~~~v~~~~~~~ 257 (324)
T TIGR02960 206 EQDLLERYIAAFESYDLDALTALLHEDAIWEMPPY---TLWYQGRPAIVGFIHTV 257 (324)
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHhcCCeEEEcCCC---CcceeCHHHHHHHHHHh
Confidence 4677999999999 567899999999998886632 12688999999999887
No 102
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=43.64 E-value=1.3e+02 Score=29.03 Aligned_cols=55 Identities=13% Similarity=0.129 Sum_probs=43.6
Q ss_pred HHHHHHHHHHHHHHHHhc-CcchhcccccCCCceeccCCCCcccccccHHHHHHHHhcC
Q 037095 13 PQVVGNAFVEQYYCILHQ-NPDVVHRFYQESSMVSRPDQSGSMTSVTTIKEINDMIVSL 70 (334)
Q Consensus 13 a~~VG~~FV~qYY~~L~~-~p~~L~~fY~~~S~l~~~g~~g~~~~~~G~~~I~~~i~sL 70 (334)
....-...|+.||..|.. +.+.|..++.++..+..+.. ...+.|.++|..+|..+
T Consensus 212 ~~~~~~~~v~~~~~A~~~gD~~~l~~lla~Dv~~~~p~~---~~~~~G~~~v~~~~~~~ 267 (339)
T PRK08241 212 DDPEERALLARYVAAFEAYDVDALVALLTEDATWSMPPF---PLWYRGRDAIAAFLAGQ 267 (339)
T ss_pred CChHHHHHHHHHHHHHhcCCHHHHHHHhcCCEEEEcCCC---CCcccCHHHHHHHHHhh
Confidence 345566779999999984 67899999999998877643 12488999999999886
No 103
>smart00593 RUN domain involved in Ras-like GTPase signaling.
Probab=42.93 E-value=27 Score=25.80 Aligned_cols=44 Identities=11% Similarity=0.447 Sum_probs=32.9
Q ss_pred HHHHHHHHHHhcCcchhcccccCCCceeccCCCCcccccccHHHHHHHHhcCC
Q 037095 19 AFVEQYYCILHQNPDVVHRFYQESSMVSRPDQSGSMTSVTTIKEINDMIVSLD 71 (334)
Q Consensus 19 ~FV~qYY~~L~~~p~~L~~fY~~~S~l~~~g~~g~~~~~~G~~~I~~~i~sL~ 71 (334)
.-+.+|.+.|..+.+.+.+||.+.|.|.-.+ +...+...+.+|.
T Consensus 12 ~~L~~~l~~l~~~~~~~~~~Y~~~A~l~~~~---------~~~~l~~~L~~L~ 55 (64)
T smart00593 12 KLLSSWLNLLLSDEELLSKYYEPWAFLRDPE---------EGEQLLGLLVGLS 55 (64)
T ss_pred hHHHHHHHHHHhChHHHHHhCCCCceeeChh---------HHHHHHHHHhCcc
Confidence 3467889899989999999999999886533 3455666666653
No 104
>COG5073 VID24 Vacuolar import and degradation protein [Intracellular trafficking and secretion]
Probab=41.33 E-value=13 Score=35.35 Aligned_cols=74 Identities=23% Similarity=0.210 Sum_probs=56.1
Q ss_pred HHHHHHHHHhcCcchhcccccCCCceeccCCCCcccccccHHHHHHHHhcCCCccceEEEEEEEEEEeCCCCEEEEEEEE
Q 037095 20 FVEQYYCILHQNPDVVHRFYQESSMVSRPDQSGSMTSVTTIKEINDMIVSLDYQNYNVQIFSADAQASYDNGLTVLVTGC 99 (334)
Q Consensus 20 FV~qYY~~L~~~p~~L~~fY~~~S~l~~~g~~g~~~~~~G~~~I~~~i~sL~~~~~~~~I~tvD~Q~s~~ggvlI~VtG~ 99 (334)
-|..||.+-++++..+..-|...+-+.|+|. .+.|.+ |...+.-.+.+.|.+||-+. -++.-|=+++|.
T Consensus 53 ~ve~~~~~~~kn~~~~~~s~~~~~~~Lr~G~-----qF~G~Q-----is~~~~~~v~v~i~~Vdl~~-kd~~sl~~l~G~ 121 (272)
T COG5073 53 KVETYYMIRHKNKRRLFSSYTRRSGFLRNGA-----QFGGVQ-----ISGYPPLTVEVNIDTVDLPK-KDDYSLPHLCGT 121 (272)
T ss_pred eEeecceecccCceEeeeeccchhhhccCcc-----ccccEe-----ccCCcceEEEEEEEEEeccc-cccccccceeeE
Confidence 4667888888888899999988888888887 677776 34444445678899999887 444344889999
Q ss_pred EEeCC
Q 037095 100 LIGKD 104 (334)
Q Consensus 100 v~~~d 104 (334)
+.+..
T Consensus 122 l~i~~ 126 (272)
T COG5073 122 LNIQN 126 (272)
T ss_pred EEEec
Confidence 98765
No 105
>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]
Probab=40.60 E-value=5.6 Score=41.66 Aligned_cols=38 Identities=18% Similarity=0.260 Sum_probs=34.3
Q ss_pred ccCCcceEEEeCCCCCCCHHHHHHHhhcCCceeeceEE
Q 037095 292 HAAKGHSIFVGNLPDSATVDQLKLIFEQFGPVKPDGIQ 329 (334)
Q Consensus 292 ~e~~~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~i~ 329 (334)
+|-+..++|+--|+..+++.+|+++|+.+|.|.+++|+
T Consensus 175 eERd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI 212 (549)
T KOG0147|consen 175 EERDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRII 212 (549)
T ss_pred hHHhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEee
Confidence 45567789999999999999999999999999999986
No 106
>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]
Probab=38.64 E-value=32 Score=32.13 Aligned_cols=39 Identities=18% Similarity=0.284 Sum_probs=29.5
Q ss_pred cceEEEeCCCCCCCHHHHHHHhhcCCceeeceEEeeecC
Q 037095 296 GHSIFVGNLPDSATVDQLKLIFEQFGPVKPDGIQVRSQK 334 (334)
Q Consensus 296 ~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~i~vRs~k 334 (334)
..-+||+.+|.-.-+.++...|++||........=||+|
T Consensus 49 ~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkr 87 (214)
T KOG4208|consen 49 EGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKR 87 (214)
T ss_pred ccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccc
Confidence 346999999999999999999999954333333346654
No 107
>PF12642 TpcC: Conjugative transposon protein TcpC; InterPro: IPR024735 This family of bacterial proteins are annotated as conjugative transposon protein TcpC. The transfer clostridial plasmid (tcp) locus is part of some conjugative antibiotic resistance and virulence plasmids. TcpC was one of five genes whose products had low-level sequence identity to Tn916 proteins, having similarity to ORF13 homologues from Tn916, Tn5397, and CW459tet [].; PDB: 3UB1_A.
Probab=37.94 E-value=2.9e+02 Score=25.10 Aligned_cols=88 Identities=16% Similarity=0.229 Sum_probs=44.8
Q ss_pred HHHHHHHHHHHHHHhcCc-chhcccccCCCceeccCCCCcccccccHHHHHHHHhcCCCccceEEEEEEEEEEeCCCCEE
Q 037095 15 VVGNAFVEQYYCILHQNP-DVVHRFYQESSMVSRPDQSGSMTSVTTIKEINDMIVSLDYQNYNVQIFSADAQASYDNGLT 93 (334)
Q Consensus 15 ~VG~~FV~qYY~~L~~~p-~~L~~fY~~~S~l~~~g~~g~~~~~~G~~~I~~~i~sL~~~~~~~~I~tvD~Q~s~~ggvl 93 (334)
.-...|+..|+..+-..- +.|.+|-.+.+.+...|. . ++ -.+|..+-.-...++ ..
T Consensus 140 ~~i~~fl~~Ff~aY~t~~~~~L~~y~~~~~~~~l~~~----------------~----~~--~~~v~~~~~~~~~~~-~~ 196 (232)
T PF12642_consen 140 KPIEEFLEQFFKAYLTGNQGDLSYYMKPGAIIGLNGA----------------P----YK--FVKVDDIKVYKTKDK-GR 196 (232)
T ss_dssp HHHHHHHHHHHHHHHHS-HHHHHTTB-TT-----------------------------SE--EEEEEEEEEEEEETT-EE
T ss_pred HHHHHHHHHHHHHHHcCCHHHHHHHhcCCcccccCCC----------------c----eE--EEeeeeEEeecCCCC-cE
Confidence 456789999999986544 888888777765522222 0 11 234444444333333 33
Q ss_pred EEEEEEEEeCCCC-cceeEEEEEEE--EeCCeEEEE
Q 037095 94 VLVTGCLIGKDNV-RRKFTQSFFLA--PQDKGYFVL 126 (334)
Q Consensus 94 I~VtG~v~~~d~~-~r~FsQtF~La--p~~~~Y~V~ 126 (334)
+.|. .+++.+.. ....+|+|-|. ..+++|+|.
T Consensus 197 ~~v~-tVt~~~~~t~~~~~~~y~LtL~~~~~~w~V~ 231 (232)
T PF12642_consen 197 VVVQ-TVTFKDPGTKATLTQQYTLTLTKRGGRWYVT 231 (232)
T ss_dssp EEE---EEEEEEETTEEEEEEEEEEEEEETTEEEEE
T ss_pred EEEE-EEEEEECCCCcEEEEEEEEEEEEcCCEEEEe
Confidence 3333 44444422 34566666664 557899985
No 108
>PF02759 RUN: RUN domain; InterPro: IPR004012 This domain is present in several proteins that are linked to the functions of GTPases in the Rap and Rab families. They could therefore play important roles in multiple Ras-like GTPase signalling pathways.; PDB: 3CWZ_B 2CXF_A 2DWK_A 2DWG_A 2CXL_A.
Probab=37.35 E-value=21 Score=29.38 Aligned_cols=50 Identities=14% Similarity=0.405 Sum_probs=34.5
Q ss_pred CHHHHHHHHHH---------HHHHHHhcCcchhcccccCCCceeccCCCCcccccccHHHHHHHHhcC
Q 037095 12 SPQVVGNAFVE---------QYYCILHQNPDVVHRFYQESSMVSRPDQSGSMTSVTTIKEINDMIVSL 70 (334)
Q Consensus 12 ~a~~VG~~FV~---------qYY~~L~~~p~~L~~fY~~~S~l~~~g~~g~~~~~~G~~~I~~~i~sL 70 (334)
+...-++.||+ +|...|..+++.|.+||.+.|.|...+. .+.|...|..|
T Consensus 64 ~~~gk~ra~Ir~aLn~~~L~~~l~~l~~~~~~l~~~Y~~~A~l~~~~~---------~~~l~~~L~~L 122 (133)
T PF02759_consen 64 SSDGKFRAWIRLALNEKCLSSWLQLLLSDPKLLRKYYEPWAFLRDPEL---------REQLLSLLSGL 122 (133)
T ss_dssp --HHHHHHHHHHHHHCT-HHHHHHHHCTTHHHHCCCB-TTSCTTSHHH---------HHHHHHHHGGG
T ss_pred hHHHHHHHHHHHHHHHChHHHHHHHHHhcchHHcCccCCcceeeCcch---------HHHHHHHHhhh
Confidence 34666777764 5788888999999999999998866543 34555555554
No 109
>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif
Probab=37.23 E-value=32 Score=24.71 Aligned_cols=31 Identities=19% Similarity=0.282 Sum_probs=20.8
Q ss_pred eEEEeCCCCCCCHHHHHHHhhcCCceeeceEE
Q 037095 298 SIFVGNLPDSATVDQLKLIFEQFGPVKPDGIQ 329 (334)
Q Consensus 298 ~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~i~ 329 (334)
.|=|.+-+.+.. +.+...|++||+|..-.+-
T Consensus 3 wI~V~Gf~~~~~-~~vl~~F~~fGeI~~~~~~ 33 (53)
T PF14605_consen 3 WISVSGFPPDLA-EEVLEHFASFGEIVDIYVP 33 (53)
T ss_pred EEEEEeECchHH-HHHHHHHHhcCCEEEEEcC
Confidence 455666665544 4566699999999875443
No 110
>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]
Probab=36.54 E-value=34 Score=35.47 Aligned_cols=32 Identities=25% Similarity=0.373 Sum_probs=27.2
Q ss_pred cceEEEeCCCCCCCHHHHHHHhh-cCCceeece
Q 037095 296 GHSIFVGNLPDSATVDQLKLIFE-QFGPVKPDG 327 (334)
Q Consensus 296 ~~~iyV~nLp~~~t~~~l~~~F~-~fG~v~~~~ 327 (334)
-.++||.|+||++.=.+|+++|+ +-|.|..+-
T Consensus 44 ~R~vfItNIpyd~rWqdLKdLvrekvGev~yve 76 (608)
T KOG4212|consen 44 DRSVFITNIPYDYRWQDLKDLVREKVGEVEYVE 76 (608)
T ss_pred cceEEEecCcchhhhHhHHHHHHHhcCceEeee
Confidence 35699999999999999999995 678887553
No 111
>COG4319 Ketosteroid isomerase homolog [Function unknown]
Probab=35.67 E-value=2.4e+02 Score=24.61 Aligned_cols=94 Identities=15% Similarity=0.181 Sum_probs=59.0
Q ss_pred cCcchhcccccCCCceecc-CCCCcccccccHHHHHHHHhcCC-CccceEEEEEEEEEEeCCCCEEEEEEEEEEeCC---
Q 037095 30 QNPDVVHRFYQESSMVSRP-DQSGSMTSVTTIKEINDMIVSLD-YQNYNVQIFSADAQASYDNGLTVLVTGCLIGKD--- 104 (334)
Q Consensus 30 ~~p~~L~~fY~~~S~l~~~-g~~g~~~~~~G~~~I~~~i~sL~-~~~~~~~I~tvD~Q~s~~ggvlI~VtG~v~~~d--- 104 (334)
.+-+.|..||.++..+.=. +. ...|.++|.+.+...- ........+..+-|-.- .|=+..++|.+.++.
T Consensus 26 ~D~~av~~~YtdDav~f~~~~~-----~~~Gk~~i~k~~~~~~~~~~~~~~f~~~el~v~~-~GD~a~~~~~~~~~~~~~ 99 (137)
T COG4319 26 KDADAVADFYTDDAVVFPPPGL-----QRKGKAAIRKAFEGIFAMGIGPLKFTLEELQVHE-SGDVAFVTALLLLTGTKK 99 (137)
T ss_pred ccHHHHHHhcCCceEEecCCCC-----cccCHHHHHHHHHHHHHhccCCCcceeeeeeeec-cCCEEEEEEeeeeeccCC
Confidence 4567899999999976544 44 6779999999887541 11113444455555322 333455666655432
Q ss_pred -CCc--ceeEEEEEEEEeCC-eEEEEccE
Q 037095 105 -NVR--RKFTQSFFLAPQDK-GYFVLNDI 129 (334)
Q Consensus 105 -~~~--r~FsQtF~Lap~~~-~Y~V~NDi 129 (334)
+.. ..---|.++.++.+ +|.|.-|-
T Consensus 100 dg~~~~~~~Rat~v~rK~~dg~Wk~~~dh 128 (137)
T COG4319 100 DGPPADLAGRATYVFRKEADGGWKLAHDH 128 (137)
T ss_pred CCcchhheeeeEEEEEEcCCCCEEEEEec
Confidence 221 34556888888875 99998884
No 112
>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]
Probab=35.03 E-value=36 Score=37.12 Aligned_cols=35 Identities=20% Similarity=0.498 Sum_probs=31.2
Q ss_pred eEEEeCCCCCCCHHHHHHHhhcCCceeeceEEeeec
Q 037095 298 SIFVGNLPDSATVDQLKLIFEQFGPVKPDGIQVRSQ 333 (334)
Q Consensus 298 ~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~i~vRs~ 333 (334)
-|-++|.|++++-+||-++|..| .+.++-|.+|-+
T Consensus 869 V~~~~n~Pf~v~l~dI~~FF~dY-~~~p~sI~~r~n 903 (944)
T KOG4307|consen 869 VLSCNNFPFDVTLEDIVEFFNDY-EPDPNSIRIRRN 903 (944)
T ss_pred EEEecCCCccccHHHHHHHhccc-ccCCCceeEeec
Confidence 68899999999999999999999 777788888754
No 113
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=35.02 E-value=1.4e+02 Score=28.26 Aligned_cols=54 Identities=13% Similarity=0.346 Sum_probs=43.2
Q ss_pred HHHHHHHHHHHHhc-CcchhcccccCCCceeccCCCCc----ccccccHHHHHHHHhcCC
Q 037095 17 GNAFVEQYYCILHQ-NPDVVHRFYQESSMVSRPDQSGS----MTSVTTIKEINDMIVSLD 71 (334)
Q Consensus 17 G~~FV~qYY~~L~~-~p~~L~~fY~~~S~l~~~g~~g~----~~~~~G~~~I~~~i~sL~ 71 (334)
....|+.|+..|.. +.+.|..+|.++..+.-.|. |. ...+.|.+.|..+|..+-
T Consensus 173 ~~~~v~~f~~A~~~gD~~~l~~Lla~Dv~~~~dgg-g~~~~~~~~~~G~~~v~~~l~~~~ 231 (293)
T PRK09636 173 GAELVEAFFAALASGDLDALVALLAPDVVLHADGG-GKVPTALRPIYGADKVARFFLGLA 231 (293)
T ss_pred HHHHHHHHHHHHHhCCHHHHHHHHhhCeEEEecCC-CccCCCCccccCHHHHHHHHHHHh
Confidence 46789999999984 77899999999999886654 33 246789999999987663
No 114
>PF08863 YolD: YolD-like protein; InterPro: IPR014962 These proteins are functionally uncharacterised. However it has been predicted that these proteins are functionally equivalent to the UmuD subunit of polymerase V from Gram-negative bacteria [].
Probab=31.98 E-value=1.1e+02 Score=23.63 Aligned_cols=84 Identities=20% Similarity=0.347 Sum_probs=51.2
Q ss_pred CcchhcccccCCCceeccCCCCcccccccHHHHHHHHhc-CCCccceEEEEEEEEEEeCCCCEEEEEEEEEEeCCCCcce
Q 037095 31 NPDVVHRFYQESSMVSRPDQSGSMTSVTTIKEINDMIVS-LDYQNYNVQIFSADAQASYDNGLTVLVTGCLIGKDNVRRK 109 (334)
Q Consensus 31 ~p~~L~~fY~~~S~l~~~g~~g~~~~~~G~~~I~~~i~s-L~~~~~~~~I~tvD~Q~s~~ggvlI~VtG~v~~~d~~~r~ 109 (334)
+.+.|.+++.+.....++.- .-.-.++|+.+|+. +.. +..+.|+.++ +|-...++|.+..-|.
T Consensus 4 H~e~L~~~~~e~~k~~kp~L-----de~~leei~~~l~~a~~~-~~~v~ity~~------~g~~~~~~G~I~~id~---- 67 (92)
T PF08863_consen 4 HKEALRELIKEQNKVEKPEL-----DEQQLEEINEKLSEAYQE-NQPVTITYYE------DGYYQSVTGTIHKIDE---- 67 (92)
T ss_pred HHHHHHHHHHHhcccCCCCC-----cHHHHHHHHHHHHHHhcC-CCEEEEEEEE------CCeeEEEEEEEEEEcC----
Confidence 34556666666666655533 12347888888874 443 4567777766 8899999999986553
Q ss_pred eEEEEEEEEe-CC-eEEEEccEE
Q 037095 110 FTQSFFLAPQ-DK-GYFVLNDIL 130 (334)
Q Consensus 110 FsQtF~Lap~-~~-~Y~V~NDiF 130 (334)
..+.+.|.-. ++ .+.=++||+
T Consensus 68 ~~~~l~~~~~~~~~~~I~~~~I~ 90 (92)
T PF08863_consen 68 INRTLKLKDEDGETEKIPFDDII 90 (92)
T ss_pred CCCEEEEEeCCCCEEEEEhhhEE
Confidence 2355566552 22 344444544
No 115
>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN). ; GO: 0003723 RNA binding, 0004535 poly(A)-specific ribonuclease activity, 0046872 metal ion binding, 0006402 mRNA catabolic process, 0005634 nucleus, 0005737 cytoplasm; PDB: 3CTR_A 2ROK_A 3D45_B 1WHV_A.
Probab=30.91 E-value=50 Score=26.65 Aligned_cols=27 Identities=19% Similarity=0.471 Sum_probs=19.5
Q ss_pred ceEEEeCCCCCCCHHHHHHHhhcCCcee
Q 037095 297 HSIFVGNLPDSATVDQLKLIFEQFGPVK 324 (334)
Q Consensus 297 ~~iyV~nLp~~~t~~~l~~~F~~fG~v~ 324 (334)
+-.||. .|-...-.||.++|+.||.|.
T Consensus 10 HVFhlt-FPkeWK~~DI~qlFspfG~I~ 36 (87)
T PF08675_consen 10 HVFHLT-FPKEWKTSDIYQLFSPFGQIY 36 (87)
T ss_dssp CEEEEE---TT--HHHHHHHCCCCCCEE
T ss_pred eEEEEe-CchHhhhhhHHHHhccCCcEE
Confidence 445666 999999999999999999985
No 116
>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]
Probab=30.74 E-value=31 Score=35.12 Aligned_cols=32 Identities=22% Similarity=0.444 Sum_probs=26.2
Q ss_pred ceEEEeCCCCCCCHHHHHHHhhcCCc-eeeceE
Q 037095 297 HSIFVGNLPDSATVDQLKLIFEQFGP-VKPDGI 328 (334)
Q Consensus 297 ~~iyV~nLp~~~t~~~l~~~F~~fG~-v~~~~i 328 (334)
-.|-+|+|||.++.++|-.+|+.|-. |+.-||
T Consensus 281 dcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gV 313 (508)
T KOG1365|consen 281 DCVRLRGLPYEATVEDILDFLGDFATDIRFQGV 313 (508)
T ss_pred CeeEecCCChhhhHHHHHHHHHHHhhhccccee
Confidence 37999999999999999999999864 444343
No 117
>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]
Probab=30.56 E-value=45 Score=31.36 Aligned_cols=31 Identities=29% Similarity=0.479 Sum_probs=27.7
Q ss_pred ceEEEeCCCCCCCHHHHHHHhhcCCceeece
Q 037095 297 HSIFVGNLPDSATVDQLKLIFEQFGPVKPDG 327 (334)
Q Consensus 297 ~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~ 327 (334)
..+|+-|||-.++.+.|..+|.+|+-.+..+
T Consensus 147 ~ilf~~niP~es~~e~l~~lf~qf~g~keir 177 (221)
T KOG4206|consen 147 NILFLTNIPSESESEMLSDLFEQFPGFKEIR 177 (221)
T ss_pred eEEEEecCCcchhHHHHHHHHhhCcccceeE
Confidence 4799999999999999999999998877554
No 118
>KOG3266 consensus Predicted glycine cleavage system H protein [Amino acid transport and metabolism]
Probab=28.95 E-value=94 Score=27.87 Aligned_cols=84 Identities=14% Similarity=0.023 Sum_probs=46.2
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHHHHhcCcchhcccccCCCc--eeccCCCCcccccccHHHHHHHHhcCCCccceEE
Q 037095 1 MAQQADSSSALSPQVVGNAFVEQYYCILHQNPDVVHRFYQESSM--VSRPDQSGSMTSVTTIKEINDMIVSLDYQNYNVQ 78 (334)
Q Consensus 1 ma~~~~~~~~~~a~~VG~~FV~qYY~~L~~~p~~L~~fY~~~S~--l~~~g~~g~~~~~~G~~~I~~~i~sL~~~~~~~~ 78 (334)
||+-.....+-.+..|-+.|.++||..|..+-.+=.-+|+.++. ++.... -|.-...--
T Consensus 1 ~at~~~~~~~~~pS~vdr~ftr~y~~d~kg~~~D~~i~~HsnricvI~la~~-------------------hp~l~~g~~ 61 (172)
T KOG3266|consen 1 MATEIGMAEPSYPSVVDRYFTRYYKEDFKGSGYDHCIYQHSNRICVITLAPS-------------------HPALQSGKT 61 (172)
T ss_pred CCccccccCCCChhhhhhhhhhhhhhhccCCCCCceEEecCCceEEEEecCC-------------------Cchhhcccc
Confidence 56554322345677888999999999888765444444444442 121111 111111223
Q ss_pred EEEEEEEEeCCCCEEEEEEEEEEeC
Q 037095 79 IFSADAQASYDNGLTVLVTGCLIGK 103 (334)
Q Consensus 79 I~tvD~Q~s~~ggvlI~VtG~v~~~ 103 (334)
|.++++|-+-.+...-.|+|..+.+
T Consensus 62 i~sv~~~ign~dRsqnkVSGK~Kkg 86 (172)
T KOG3266|consen 62 IKSVTFQIGNCDRSQNKVSGKGKKG 86 (172)
T ss_pred eeeeecccccchhhhheeccccccc
Confidence 6677777663455666778776543
No 119
>PF05172 Nup35_RRM: Nup53/35/40-type RNA recognition motif; InterPro: IPR007846 The MPPN (Mitotic PhosphoProtein N end) family is uncharacterised however it probably plays a role in the cell cycle because the family includes mitotic phosphoproteins O13026 from SWISSPROT []. This family also includes Q05166 from SWISSPROT a suppressor of thermosensitive mutations in the DNA polymerase delta gene, Pol III []. The conserved central region appears to be distantly related to the RNA-binding region RNP-1 (RNA recognition motif, IPR000504 from INTERPRO), suggesting an RNA binding function for this protein.; PDB: 1WWH_C 3P3D_A.
Probab=27.96 E-value=55 Score=26.87 Aligned_cols=32 Identities=22% Similarity=0.240 Sum_probs=22.3
Q ss_pred CcceEEEeCCCCCCCHHHHHHHhhcCCceeece
Q 037095 295 KGHSIFVGNLPDSATVDQLKLIFEQFGPVKPDG 327 (334)
Q Consensus 295 ~~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~ 327 (334)
....|-|=+-|-. ....+-++|++||.|....
T Consensus 5 ~~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~ 36 (100)
T PF05172_consen 5 SETWVTVFGFPPS-ASNQVLRHFSSFGTILEHF 36 (100)
T ss_dssp GCCEEEEE---GG-GHHHHHHHHHCCS-EECEE
T ss_pred CCeEEEEEccCHH-HHHHHHHHHHhcceEEEee
Confidence 4567888898888 6677888999999998764
No 120
>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]
Probab=27.85 E-value=53 Score=28.67 Aligned_cols=33 Identities=27% Similarity=0.527 Sum_probs=29.5
Q ss_pred CcceEEEeCCCCCCCHHHHHHHhhcCCceeece
Q 037095 295 KGHSIFVGNLPDSATVDQLKLIFEQFGPVKPDG 327 (334)
Q Consensus 295 ~~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~ 327 (334)
.+..+|++|+++.++..++...|..+|.+....
T Consensus 224 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 256 (306)
T COG0724 224 KSDNLYVGNLPLKTAEEELADLFKSRGDIVRAS 256 (306)
T ss_pred ccceeeccccccccchhHHHHhccccccceeee
Confidence 567899999999999999999999999995443
No 121
>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]
Probab=25.82 E-value=52 Score=33.83 Aligned_cols=28 Identities=25% Similarity=0.400 Sum_probs=26.4
Q ss_pred ceEEEeCCCCCCCHHHHHHHhhcCCcee
Q 037095 297 HSIFVGNLPDSATVDQLKLIFEQFGPVK 324 (334)
Q Consensus 297 ~~iyV~nLp~~~t~~~l~~~F~~fG~v~ 324 (334)
-++.|+|+-|-+|-+-|-.+|++||.|.
T Consensus 151 Lr~iie~m~ypVslDVLHqvFS~fG~Vl 178 (492)
T KOG1190|consen 151 LRTIIENMFYPVSLDVLHQVFSKFGFVL 178 (492)
T ss_pred EEEEeccceeeeEHHHHHHHHhhcceeE
Confidence 5799999999999999999999999985
No 122
>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]
Probab=25.00 E-value=60 Score=33.15 Aligned_cols=29 Identities=24% Similarity=0.177 Sum_probs=24.1
Q ss_pred cceEEEeCCCCCCCHHHHHHHhhcCCcee
Q 037095 296 GHSIFVGNLPDSATVDQLKLIFEQFGPVK 324 (334)
Q Consensus 296 ~~~iyV~nLp~~~t~~~l~~~F~~fG~v~ 324 (334)
.--|-.|+|||++++.|+.++|..--.|+
T Consensus 161 qvivRmRGLPfdat~~dVv~FF~~~cpv~ 189 (508)
T KOG1365|consen 161 QVIVRMRGLPFDATALDVVEFFGPPCPVT 189 (508)
T ss_pred ceEEEecCCCCCcchHHHHHhcCCCCccc
Confidence 34788999999999999999997555554
No 123
>PF11411 DNA_ligase_IV: DNA ligase IV; InterPro: IPR021536 DNA ligase IV along with Xrcc4 functions in DNA non-homologous end joining. This process is required to mend double-strand breaks. Upon ligase binding to an Xrcc4 dimer, the helical tails unwind leading to a flat interaction surface []. ; GO: 0003910 DNA ligase (ATP) activity; PDB: 3II6_Y 2E2W_A 1IK9_C.
Probab=24.32 E-value=54 Score=22.24 Aligned_cols=17 Identities=29% Similarity=0.391 Sum_probs=10.4
Q ss_pred CCCCHHHHHHHhhcCCc
Q 037095 306 DSATVDQLKLIFEQFGP 322 (334)
Q Consensus 306 ~~~t~~~l~~~F~~fG~ 322 (334)
-++++++|++.|.+.+.
T Consensus 19 ~Dtd~~~Lk~vF~~i~~ 35 (36)
T PF11411_consen 19 VDTDEDQLKEVFNRIKK 35 (36)
T ss_dssp S---HHHHHHHHHCS--
T ss_pred ccCCHHHHHHHHHHhcc
Confidence 36899999999987653
No 124
>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]
Probab=24.23 E-value=45 Score=31.23 Aligned_cols=28 Identities=29% Similarity=0.296 Sum_probs=26.8
Q ss_pred cceEEEeCCCCCCCHHHHHHHhhcCCce
Q 037095 296 GHSIFVGNLPDSATVDQLKLIFEQFGPV 323 (334)
Q Consensus 296 ~~~iyV~nLp~~~t~~~l~~~F~~fG~v 323 (334)
.+++.|.||+..+...+|.+.|.+||.+
T Consensus 99 ~~r~~~~~~~~r~~~qdl~d~~~~~g~~ 126 (216)
T KOG0106|consen 99 HFRLIVRNLSLRVSWQDLKDHFRPAGEV 126 (216)
T ss_pred cceeeeccchhhhhHHHHhhhhcccCCC
Confidence 5789999999999999999999999999
No 125
>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=24.23 E-value=41 Score=31.65 Aligned_cols=29 Identities=34% Similarity=0.605 Sum_probs=24.0
Q ss_pred cceEEEeCCCCCCCHHHHHHHhh--cCCcee
Q 037095 296 GHSIFVGNLPDSATVDQLKLIFE--QFGPVK 324 (334)
Q Consensus 296 ~~~iyV~nLp~~~t~~~l~~~F~--~fG~v~ 324 (334)
..-+.|+||||+.+..-|..++. .||.+.
T Consensus 97 ~~~~vv~NlPy~is~~il~~ll~~~~~g~~~ 127 (262)
T PF00398_consen 97 QPLLVVGNLPYNISSPILRKLLELYRFGRVR 127 (262)
T ss_dssp SEEEEEEEETGTGHHHHHHHHHHHGGGCEEE
T ss_pred CceEEEEEecccchHHHHHHHhhcccccccc
Confidence 45799999999999999999987 566543
No 126
>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=23.64 E-value=1.1e+02 Score=20.89 Aligned_cols=29 Identities=24% Similarity=0.302 Sum_probs=24.3
Q ss_pred cceEEEeCCCCCCCHHHHHHHhhcCCcee
Q 037095 296 GHSIFVGNLPDSATVDQLKLIFEQFGPVK 324 (334)
Q Consensus 296 ~~~iyV~nLp~~~t~~~l~~~F~~fG~v~ 324 (334)
++.+|+.+.....+.++|+++...+|--.
T Consensus 1 ~~~~~i~g~~~~~~~~~l~~~i~~~Gg~v 29 (72)
T cd00027 1 GLTFVITGDLPSEERDELKELIEKLGGKV 29 (72)
T ss_pred CCEEEEEecCCCcCHHHHHHHHHHcCCEE
Confidence 46788888877899999999999998643
No 127
>COG0030 KsgA Dimethyladenosine transferase (rRNA methylation) [Translation, ribosomal structure and biogenesis]
Probab=23.03 E-value=87 Score=30.10 Aligned_cols=28 Identities=21% Similarity=0.112 Sum_probs=23.2
Q ss_pred cceEEEeCCCCCCCHHHHHHHhhcCCce
Q 037095 296 GHSIFVGNLPDSATVDQLKLIFEQFGPV 323 (334)
Q Consensus 296 ~~~iyV~nLp~~~t~~~l~~~F~~fG~v 323 (334)
....-|+||||++|..=|..+++..-.+
T Consensus 95 ~~~~vVaNlPY~Isspii~kll~~~~~~ 122 (259)
T COG0030 95 QPYKVVANLPYNISSPILFKLLEEKFII 122 (259)
T ss_pred CCCEEEEcCCCcccHHHHHHHHhccCcc
Confidence 3467899999999999999999866544
No 128
>PF05629 Nanovirus_C8: Nanovirus component 8 (C8) protein; InterPro: IPR008706 This family consists of a group of 17.4 kDa nanovirus proteins which are highly related to the Faba bean necrotic yellows virus component 8 protein whose function is unknown [].
Probab=22.45 E-value=2.1e+02 Score=24.88 Aligned_cols=45 Identities=22% Similarity=0.242 Sum_probs=31.7
Q ss_pred EEEEEEEEEEeCCCCcceeEEEEEEEEeC----------CeEEEEccEEEeecCC
Q 037095 92 LTVLVTGCLIGKDNVRRKFTQSFFLAPQD----------KGYFVLNDILRYVDEI 136 (334)
Q Consensus 92 vlI~VtG~v~~~d~~~r~FsQtF~Lap~~----------~~Y~V~NDiFR~vd~~ 136 (334)
+.|..+|.+...+...|.|.|.=++.-.+ +||.-+||..-|-.+.
T Consensus 50 ~~v~FnGSF~G~NRNVRG~l~vsm~~DDG~~RPi~~vP~GGY~YHnDy~Y~eG~~ 104 (153)
T PF05629_consen 50 CSVSFNGSFYGSNRNVRGQLQVSMRQDDGVMRPIGYVPIGGYLYHNDYGYYEGQK 104 (153)
T ss_pred EEEEecceeecCCcceeeEEEEEEEcCCCeeeeEEEEeecceEEeccceEEeccc
Confidence 33455677776666678888877765432 6899999998887654
No 129
>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes. Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.
Probab=21.75 E-value=1e+02 Score=25.01 Aligned_cols=24 Identities=21% Similarity=0.522 Sum_probs=16.5
Q ss_pred eEEEeCCCCCCCHHHH----HHHhhcCC
Q 037095 298 SIFVGNLPDSATVDQL----KLIFEQFG 321 (334)
Q Consensus 298 ~iyV~nLp~~~t~~~l----~~~F~~fG 321 (334)
-|||.|||.+.+...+ +.++..+|
T Consensus 4 ~L~V~NLP~~~d~~~I~~RL~qLsdNCG 31 (90)
T PF11608_consen 4 LLYVSNLPTNKDPSSIKNRLRQLSDNCG 31 (90)
T ss_dssp EEEEES--TTS-HHHHHHHHHHHHHTTT
T ss_pred EEEEecCCCCCCHHHHHHHHHHHhhccC
Confidence 5899999999998875 55666776
No 130
>PF07858 LEH: Limonene-1,2-epoxide hydrolase catalytic domain; InterPro: IPR013100 Epoxide hydrolases catalyse the hydrolysis of epoxides to corresponding diols, which is important in detoxification, synthesis of signal molecules, or metabolism. Limonene-1,2- epoxide hydrolase (LEH) differs from many other epoxide hydrolases in its structure and its novel one-step catalytic mechanism. Its main fold consists of a six-stranded mixed beta-sheet, with three N-terminal alpha helices packed to one side to create a pocket that extends into the protein core. A fourth helix lies in such a way that it acts as a rim to this pocket. Although mainly lined by hydrophobic residues, this pocket features a cluster of polar groups that lie at its deepest point and constitute the enzymes active site []. ; PDB: 2BNG_C 1NWW_A 1NU3_B.
Probab=20.98 E-value=5.2e+02 Score=21.96 Aligned_cols=64 Identities=9% Similarity=0.265 Sum_probs=36.0
Q ss_pred CHHHHHHHHHHHHHHHHhcC-cchhcccccCCCceeccCCCCcccccccHHHHHHHHhcC--CCccceEEEEEE
Q 037095 12 SPQVVGNAFVEQYYCILHQN-PDVVHRFYQESSMVSRPDQSGSMTSVTTIKEINDMIVSL--DYQNYNVQIFSA 82 (334)
Q Consensus 12 ~a~~VG~~FV~qYY~~L~~~-p~~L~~fY~~~S~l~~~g~~g~~~~~~G~~~I~~~i~sL--~~~~~~~~I~tv 82 (334)
++.++...|++-+. ..+ ...+..|..+.....-.+- -++.|.++|.+.|..+ ++..+.++|..+
T Consensus 2 ~~~~vV~~F~~a~~---~~D~~~a~~~~~~~d~vy~Nvpl----p~i~G~~~~~~~l~~~~~~~~~~e~~i~~i 68 (125)
T PF07858_consen 2 TPEEVVRAFLAALE---DRDVDAALASLFDDDAVYHNVPL----PPIRGRDAIRAFLRGFLDSLSGFEFDIHRI 68 (125)
T ss_dssp HHHHHHHHHHHHHH---HT-HHHHHHHCEECC-EEEETTT----EEEESHHHHHHHHHCCHCCCEEEEEEEEEE
T ss_pred ChHHHHHHHHHHHH---cCCHHHHHHHhcCCCcEEEeCCC----CCcccHHHHHHHHHHHhcccceeEEEEEEE
Confidence 35566677776553 122 2345555555544443332 2788999999999987 344344444443
No 131
>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2. It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).
Probab=20.82 E-value=1.1e+02 Score=25.04 Aligned_cols=24 Identities=21% Similarity=0.495 Sum_probs=21.2
Q ss_pred ceEEEeCCCCCCCHHHHHHHhhcC
Q 037095 297 HSIFVGNLPDSATVDQLKLIFEQF 320 (334)
Q Consensus 297 ~~iyV~nLp~~~t~~~l~~~F~~f 320 (334)
++|=+||+|-..|.++|.+++...
T Consensus 2 TTvMirNIPn~~t~~~L~~~l~~~ 25 (97)
T PF04059_consen 2 TTVMIRNIPNKYTQEMLIQILDEH 25 (97)
T ss_pred eeEEEecCCCCCCHHHHHHHHHHh
Confidence 578999999999999999998654
No 132
>KOG4410 consensus 5-formyltetrahydrofolate cyclo-ligase [Coenzyme transport and metabolism]
Probab=20.15 E-value=1.1e+02 Score=30.13 Aligned_cols=26 Identities=23% Similarity=0.169 Sum_probs=23.2
Q ss_pred ceEEEeCCCCCCCHHHHHHHhhcCCc
Q 037095 297 HSIFVGNLPDSATVDQLKLIFEQFGP 322 (334)
Q Consensus 297 ~~iyV~nLp~~~t~~~l~~~F~~fG~ 322 (334)
+.||++|||.++...||+....+-|-
T Consensus 331 ~di~~~nl~rd~rv~dlk~~lr~~~~ 356 (396)
T KOG4410|consen 331 TDIKLTNLSRDIRVKDLKSELRKREC 356 (396)
T ss_pred cceeeccCccccchHHHHHHHHhcCC
Confidence 56999999999999999999887764
No 133
>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]
Probab=20.10 E-value=10 Score=41.78 Aligned_cols=35 Identities=26% Similarity=0.285 Sum_probs=31.4
Q ss_pred CcceEEEeCCCCCCCHHHHHHHhhcCCceeeceEE
Q 037095 295 KGHSIFVGNLPDSATVDQLKLIFEQFGPVKPDGIQ 329 (334)
Q Consensus 295 ~~~~iyV~nLp~~~t~~~l~~~F~~fG~v~~~~i~ 329 (334)
+..++||+||++...+++|...|..||.+....|.
T Consensus 666 ~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~ 700 (881)
T KOG0128|consen 666 DLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIV 700 (881)
T ss_pred HHHHHHHhhcchhhcCchhhhhcCccchhhhHHHH
Confidence 34689999999999999999999999999887765
Done!