Query 024281
Match_columns 269
No_of_seqs 302 out of 1790
Neff 6.8
Searched_HMMs 46136
Date Fri Mar 29 03:25:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024281.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024281hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0107 Alternative splicing f 99.8 3.2E-18 7E-23 143.6 12.2 44 2-45 46-89 (195)
2 KOG4207 Predicted splicing fac 99.3 7.3E-11 1.6E-15 101.9 14.8 40 2-41 54-93 (256)
3 KOG0109 RNA-binding protein LA 99.0 1.9E-10 4.1E-15 103.7 4.7 70 1-79 110-179 (346)
4 KOG0109 RNA-binding protein LA 99.0 8E-10 1.7E-14 99.7 5.6 42 1-42 34-75 (346)
5 PLN03134 glycine-rich RNA-bind 98.5 2.9E-07 6.3E-12 76.3 7.7 42 2-43 75-116 (144)
6 PF13893 RRM_5: RNA recognitio 98.4 5.8E-07 1.2E-11 62.0 5.9 35 4-38 22-56 (56)
7 smart00361 RRM_1 RNA recogniti 98.4 4.1E-07 9E-12 65.9 4.7 34 2-35 36-69 (70)
8 KOG0105 Alternative splicing f 98.4 8.1E-07 1.8E-11 76.0 6.0 38 4-41 46-83 (241)
9 KOG0111 Cyclophilin-type pepti 98.2 8.3E-07 1.8E-11 77.7 3.1 39 3-41 52-90 (298)
10 KOG0113 U1 small nuclear ribon 98.1 2.8E-05 6.1E-10 70.8 10.7 40 2-41 142-181 (335)
11 KOG0125 Ataxin 2-binding prote 98.0 4.7E-06 1E-10 76.6 4.0 39 2-40 135-173 (376)
12 PF00076 RRM_1: RNA recognitio 98.0 1E-05 2.2E-10 57.0 4.1 33 2-34 38-70 (70)
13 KOG0106 Alternative splicing f 97.9 5.1E-06 1.1E-10 73.1 2.7 42 1-42 33-74 (216)
14 TIGR01659 sex-lethal sex-letha 97.9 1.2E-05 2.7E-10 75.7 4.8 39 2-40 148-186 (346)
15 TIGR01661 ELAV_HUD_SF ELAV/HuD 97.9 1.4E-05 3.1E-10 74.2 4.8 40 2-41 44-83 (352)
16 KOG0130 RNA-binding protein RB 97.9 1.1E-05 2.4E-10 65.9 3.1 40 2-41 113-152 (170)
17 TIGR01648 hnRNP-R-Q heterogene 97.8 2.8E-05 6.1E-10 77.7 5.7 42 2-43 268-309 (578)
18 KOG0121 Nuclear cap-binding pr 97.8 3E-05 6.6E-10 62.8 4.3 39 3-41 78-116 (153)
19 smart00360 RRM RNA recognition 97.8 4.5E-05 9.8E-10 52.5 4.6 34 3-36 38-71 (71)
20 KOG0127 Nucleolar protein fibr 97.7 3E-05 6.6E-10 75.6 4.7 39 4-42 159-197 (678)
21 KOG0148 Apoptosis-promoting RN 97.7 3E-05 6.5E-10 69.9 4.1 41 2-42 103-143 (321)
22 TIGR01645 half-pint poly-U bin 97.7 6.9E-05 1.5E-09 75.3 5.9 41 2-42 245-285 (612)
23 smart00362 RRM_2 RNA recogniti 97.6 8.6E-05 1.9E-09 51.3 4.5 34 3-36 39-72 (72)
24 KOG0415 Predicted peptidyl pro 97.6 3.1E-05 6.7E-10 72.1 2.8 40 4-43 282-321 (479)
25 TIGR01642 U2AF_lg U2 snRNP aux 97.6 0.0001 2.2E-09 72.1 6.0 40 2-41 336-375 (509)
26 KOG0131 Splicing factor 3b, su 97.6 5E-05 1.1E-09 64.9 3.1 38 2-39 50-87 (203)
27 TIGR01622 SF-CC1 splicing fact 97.6 9.3E-05 2E-09 71.5 5.2 37 3-39 228-264 (457)
28 TIGR01659 sex-lethal sex-letha 97.6 0.00011 2.4E-09 69.3 5.5 39 3-41 235-275 (346)
29 TIGR01649 hnRNP-L_PTB hnRNP-L/ 97.5 0.00013 2.7E-09 71.7 5.7 39 2-40 312-350 (481)
30 PLN03213 repressor of silencin 97.5 9.8E-05 2.1E-09 71.4 4.8 37 3-39 48-86 (759)
31 COG5082 AIR1 Arginine methyltr 97.5 4.8E-05 1E-09 65.4 2.4 40 60-99 60-114 (190)
32 cd00590 RRM RRM (RNA recogniti 97.5 0.00019 4.2E-09 49.7 5.2 35 3-37 40-74 (74)
33 PF14259 RRM_6: RNA recognitio 97.5 0.00014 3E-09 51.8 4.1 32 3-34 39-70 (70)
34 TIGR01628 PABP-1234 polyadenyl 97.4 0.00021 4.6E-09 71.1 5.6 39 2-40 325-363 (562)
35 COG0724 RNA-binding proteins ( 97.4 0.00024 5.1E-09 61.3 5.1 38 2-39 156-193 (306)
36 KOG4208 Nucleolar RNA-binding 97.4 0.00017 3.7E-09 62.7 3.9 39 2-40 91-129 (214)
37 PLN03120 nucleic acid binding 97.4 0.00029 6.2E-09 63.7 5.3 38 2-40 42-79 (260)
38 TIGR01645 half-pint poly-U bin 97.3 0.00021 4.7E-09 71.8 4.8 38 2-39 148-185 (612)
39 KOG0108 mRNA cleavage and poly 97.3 0.0002 4.4E-09 69.3 4.4 41 2-42 59-99 (435)
40 PTZ00368 universal minicircle 97.3 0.00016 3.5E-09 59.9 3.0 42 60-101 77-122 (148)
41 PTZ00368 universal minicircle 97.3 0.00023 4.9E-09 59.0 3.6 42 60-101 27-71 (148)
42 KOG0110 RNA-binding protein (R 97.2 0.00039 8.4E-09 69.7 5.2 40 2-41 559-598 (725)
43 PF00098 zf-CCHC: Zinc knuckle 97.2 0.00022 4.9E-09 38.4 1.9 17 62-78 2-18 (18)
44 KOG0117 Heterogeneous nuclear 97.2 0.00045 9.8E-09 66.1 4.8 40 3-42 293-332 (506)
45 KOG0145 RNA-binding protein EL 97.2 0.00038 8.1E-09 62.7 4.0 39 4-42 84-122 (360)
46 TIGR01628 PABP-1234 polyadenyl 97.2 0.00049 1.1E-08 68.5 5.1 37 3-39 42-78 (562)
47 KOG0147 Transcriptional coacti 97.1 0.00058 1.3E-08 66.7 4.7 38 2-39 319-356 (549)
48 KOG0117 Heterogeneous nuclear 97.1 0.00076 1.6E-08 64.6 5.0 40 2-41 124-164 (506)
49 TIGR01622 SF-CC1 splicing fact 97.0 0.0008 1.7E-08 65.0 5.2 38 2-40 130-167 (457)
50 TIGR01642 U2AF_lg U2 snRNP aux 97.0 0.00054 1.2E-08 67.0 4.0 35 3-38 223-257 (509)
51 TIGR01649 hnRNP-L_PTB hnRNP-L/ 97.0 0.00091 2E-08 65.6 5.3 37 4-40 135-173 (481)
52 TIGR01661 ELAV_HUD_SF ELAV/HuD 96.9 0.0014 3E-08 60.9 5.4 39 2-40 130-170 (352)
53 KOG0126 Predicted RNA-binding 96.9 0.00022 4.8E-09 61.1 -0.0 39 2-40 76-114 (219)
54 KOG0114 Predicted RNA-binding 96.9 0.0014 3.1E-08 51.4 4.4 37 3-39 57-93 (124)
55 KOG0148 Apoptosis-promoting RN 96.9 0.0015 3.2E-08 59.2 4.9 39 3-41 200-238 (321)
56 KOG0124 Polypyrimidine tract-b 96.8 0.00082 1.8E-08 63.0 3.2 35 3-37 155-189 (544)
57 COG5082 AIR1 Arginine methyltr 96.8 0.00073 1.6E-08 58.2 2.6 42 61-102 98-140 (190)
58 KOG4400 E3 ubiquitin ligase in 96.7 0.00093 2E-08 60.5 2.7 42 61-103 144-185 (261)
59 TIGR01648 hnRNP-R-Q heterogene 96.7 0.0014 3.1E-08 65.7 3.9 37 2-38 98-135 (578)
60 KOG0106 Alternative splicing f 96.6 0.0023 5.1E-08 56.4 4.4 34 2-35 132-165 (216)
61 PLN03121 nucleic acid binding 96.5 0.0038 8.3E-08 55.8 4.8 36 3-39 44-79 (243)
62 PF00098 zf-CCHC: Zinc knuckle 96.5 0.0019 4.1E-08 34.8 1.7 17 84-100 2-18 (18)
63 KOG0123 Polyadenylate-binding 96.4 0.0035 7.7E-08 59.7 4.5 39 4-42 38-76 (369)
64 KOG0110 RNA-binding protein (R 96.2 0.0047 1E-07 62.2 4.1 39 3-41 9-47 (725)
65 KOG0127 Nucleolar protein fibr 96.2 0.0035 7.6E-08 61.6 3.0 42 2-43 46-87 (678)
66 KOG1457 RNA binding protein (c 96.2 0.0078 1.7E-07 53.3 4.8 40 4-43 78-120 (284)
67 KOG0123 Polyadenylate-binding 96.1 0.0064 1.4E-07 57.9 4.5 37 2-39 115-151 (369)
68 KOG0119 Splicing factor 1/bran 96.0 0.0026 5.7E-08 61.7 1.2 95 5-101 206-304 (554)
69 PF11608 Limkain-b1: Limkain b 96.0 0.011 2.4E-07 44.7 4.2 38 2-39 38-75 (90)
70 KOG4212 RNA-binding protein hn 95.8 0.01 2.2E-07 57.0 4.1 39 2-40 85-123 (608)
71 KOG0144 RNA-binding protein CU 95.7 0.012 2.7E-07 56.4 4.4 41 1-41 163-206 (510)
72 KOG0131 Splicing factor 3b, su 95.7 0.015 3.3E-07 49.9 4.5 40 2-41 138-177 (203)
73 KOG0107 Alternative splicing f 95.7 0.061 1.3E-06 46.0 7.9 33 8-42 49-81 (195)
74 KOG4661 Hsp27-ERE-TATA-binding 95.4 0.022 4.8E-07 56.4 5.0 41 3-43 447-487 (940)
75 KOG4209 Splicing factor RNPS1, 95.3 0.018 3.9E-07 51.5 3.7 39 2-41 142-180 (231)
76 KOG0149 Predicted RNA-binding 95.1 0.014 3E-07 51.9 2.3 38 2-40 53-90 (247)
77 KOG0145 RNA-binding protein EL 95.0 0.03 6.5E-07 50.7 4.2 40 1-40 167-208 (360)
78 KOG0226 RNA-binding proteins [ 94.8 0.018 3.8E-07 51.9 2.3 37 2-38 231-267 (290)
79 KOG4400 E3 ubiquitin ligase in 94.6 0.026 5.6E-07 51.1 2.8 19 83-101 144-162 (261)
80 KOG0124 Polypyrimidine tract-b 94.5 0.025 5.4E-07 53.3 2.6 38 3-40 252-289 (544)
81 PF13696 zf-CCHC_2: Zinc knuck 94.5 0.029 6.2E-07 34.7 2.0 22 58-79 6-27 (32)
82 KOG4206 Spliceosomal protein s 94.2 0.049 1.1E-06 48.1 3.5 41 2-42 51-91 (221)
83 KOG0147 Transcriptional coacti 94.0 0.057 1.2E-06 53.2 4.0 36 4-39 491-526 (549)
84 KOG4207 Predicted splicing fac 93.6 1.5 3.2E-05 38.8 11.4 23 6-28 61-85 (256)
85 KOG0116 RasGAP SH3 binding pro 93.4 0.18 3.8E-06 48.9 6.1 40 4-44 331-370 (419)
86 PF03880 DbpA: DbpA RNA bindin 93.3 0.097 2.1E-06 38.2 3.3 36 2-38 39-74 (74)
87 PF04059 RRM_2: RNA recognitio 93.3 0.13 2.9E-06 39.8 4.2 38 3-40 45-86 (97)
88 KOG1548 Transcription elongati 93.2 0.15 3.3E-06 47.8 5.1 40 2-41 313-352 (382)
89 KOG0132 RNA polymerase II C-te 92.6 0.16 3.4E-06 52.2 4.5 40 2-41 456-495 (894)
90 KOG2202 U2 snRNP splicing fact 92.5 0.083 1.8E-06 47.6 2.3 38 3-40 110-147 (260)
91 PF13917 zf-CCHC_3: Zinc knuck 92.4 0.075 1.6E-06 34.9 1.4 19 60-78 4-22 (42)
92 KOG2314 Translation initiation 90.8 0.2 4.4E-06 49.7 3.1 35 3-37 105-140 (698)
93 KOG0153 Predicted RNA-binding 90.1 0.35 7.7E-06 45.4 3.9 39 2-40 263-302 (377)
94 KOG4660 Protein Mei2, essentia 90.0 0.16 3.4E-06 50.2 1.6 33 2-34 111-143 (549)
95 KOG1995 Conserved Zn-finger pr 89.7 0.19 4.1E-06 47.2 1.8 40 2-41 115-154 (351)
96 PF13696 zf-CCHC_2: Zinc knuck 89.5 0.29 6.3E-06 30.2 2.0 21 81-101 7-27 (32)
97 KOG0120 Splicing factor U2AF, 89.4 0.19 4.2E-06 49.6 1.7 41 2-42 330-370 (500)
98 KOG0105 Alternative splicing f 89.4 0.97 2.1E-05 39.2 5.7 28 2-29 149-176 (241)
99 KOG4454 RNA binding protein (R 89.3 0.2 4.4E-06 44.4 1.6 37 5-41 51-87 (267)
100 smart00343 ZnF_C2HC zinc finge 89.2 0.2 4.4E-06 29.0 1.1 16 62-77 1-16 (26)
101 KOG0533 RRM motif-containing p 89.1 0.6 1.3E-05 42.1 4.5 38 3-40 124-161 (243)
102 PF14787 zf-CCHC_5: GAG-polypr 88.9 0.26 5.5E-06 31.2 1.4 19 61-79 3-21 (36)
103 KOG1456 Heterogeneous nuclear 88.3 0.57 1.2E-05 44.6 3.9 37 5-41 161-199 (494)
104 KOG1190 Polypyrimidine tract-b 85.9 1.2 2.5E-05 43.0 4.6 39 2-40 334-372 (492)
105 KOG0144 RNA-binding protein CU 84.7 1.1 2.5E-05 43.3 3.9 40 2-41 75-117 (510)
106 COG5175 MOT2 Transcriptional r 84.7 1.2 2.5E-05 42.0 3.9 33 7-39 169-201 (480)
107 KOG1456 Heterogeneous nuclear 84.1 1.7 3.6E-05 41.5 4.7 39 2-40 324-362 (494)
108 PF11767 SET_assoc: Histone ly 83.8 1.5 3.3E-05 31.5 3.4 30 7-36 37-66 (66)
109 KOG0146 RNA-binding protein ET 83.2 1.6 3.4E-05 40.0 4.0 39 2-40 59-100 (371)
110 KOG1548 Transcription elongati 83.2 1.2 2.7E-05 41.9 3.4 42 2-43 182-223 (382)
111 PF08952 DUF1866: Domain of un 82.5 2.3 5.1E-05 35.4 4.5 33 6-39 73-105 (146)
112 PF13917 zf-CCHC_3: Zinc knuck 80.8 0.84 1.8E-05 29.9 1.1 19 82-100 4-22 (42)
113 COG5222 Uncharacterized conser 80.6 0.97 2.1E-05 41.8 1.8 24 56-79 172-195 (427)
114 PF14392 zf-CCHC_4: Zinc knuck 80.4 1.7 3.8E-05 29.1 2.5 17 61-77 32-48 (49)
115 PF08206 OB_RNB: Ribonuclease 77.9 1.2 2.6E-05 30.9 1.2 37 2-39 7-44 (58)
116 KOG4211 Splicing factor hnRNP- 73.6 3.5 7.6E-05 40.5 3.5 37 2-39 48-84 (510)
117 KOG2193 IGF-II mRNA-binding pr 71.8 2.5 5.4E-05 41.0 2.0 39 1-39 35-74 (584)
118 PF15288 zf-CCHC_6: Zinc knuck 71.3 2.5 5.5E-05 27.4 1.3 19 61-79 2-22 (40)
119 COG5222 Uncharacterized conser 70.3 2.2 4.7E-05 39.6 1.2 21 81-101 175-195 (427)
120 PF04847 Calcipressin: Calcipr 69.9 5.5 0.00012 34.4 3.6 36 6-41 34-71 (184)
121 KOG4205 RNA-binding protein mu 67.3 2.1 4.6E-05 40.0 0.5 38 2-40 47-84 (311)
122 PF14787 zf-CCHC_5: GAG-polypr 65.9 3.6 7.7E-05 26.1 1.2 20 83-102 3-22 (36)
123 KOG4205 RNA-binding protein mu 65.6 3.5 7.5E-05 38.6 1.6 38 2-40 138-175 (311)
124 PF08777 RRM_3: RNA binding mo 65.4 5.1 0.00011 31.3 2.3 35 5-39 39-78 (105)
125 PF05172 Nup35_RRM: Nup53/35/4 64.6 16 0.00035 28.4 4.9 35 3-38 54-89 (100)
126 KOG4211 Splicing factor hnRNP- 63.0 5.8 0.00013 39.0 2.6 34 3-37 145-178 (510)
127 KOG2068 MOT2 transcription fac 62.4 2 4.2E-05 40.3 -0.7 34 6-39 128-161 (327)
128 KOG3116 Predicted C3H1-type Zn 59.2 2.2 4.7E-05 35.7 -0.9 20 60-79 27-46 (177)
129 KOG4660 Protein Mei2, essentia 58.4 9.3 0.0002 38.1 3.1 25 3-27 431-455 (549)
130 KOG4212 RNA-binding protein hn 56.0 20 0.00043 35.2 4.8 40 2-41 255-294 (608)
131 KOG4307 RNA binding protein RB 55.3 11 0.00024 38.9 3.1 34 4-38 41-74 (944)
132 KOG2318 Uncharacterized conser 54.2 16 0.00034 36.9 3.9 35 4-38 269-305 (650)
133 PF14392 zf-CCHC_4: Zinc knuck 54.0 5.5 0.00012 26.6 0.6 19 81-99 30-48 (49)
134 KOG4676 Splicing factor, argin 53.0 11 0.00023 36.4 2.4 33 5-38 54-86 (479)
135 PF12353 eIF3g: Eukaryotic tra 51.5 20 0.00044 29.1 3.6 52 28-80 72-125 (128)
136 PRK11634 ATP-dependent RNA hel 51.5 31 0.00067 35.3 5.7 36 3-39 526-561 (629)
137 KOG1365 RNA-binding protein Fu 50.7 6.8 0.00015 37.6 0.8 37 3-39 324-360 (508)
138 PF14605 Nup35_RRM_2: Nup53/35 46.2 20 0.00042 24.3 2.3 18 3-20 36-53 (53)
139 KOG2416 Acinus (induces apopto 45.8 25 0.00054 35.7 3.9 36 4-39 482-520 (718)
140 KOG0120 Splicing factor U2AF, 42.8 14 0.00031 36.7 1.7 34 2-36 222-255 (500)
141 KOG4019 Calcineurin-mediated s 41.8 43 0.00093 29.0 4.2 39 4-42 52-91 (193)
142 PF03439 Spt5-NGN: Early trans 39.9 35 0.00076 25.3 3.1 26 2-27 43-68 (84)
143 PF07576 BRAP2: BRCA1-associat 38.6 40 0.00087 26.6 3.4 24 6-29 57-80 (110)
144 KOG4210 Nuclear localization s 38.4 20 0.00043 33.1 1.8 41 2-43 226-266 (285)
145 KOG2591 c-Mpl binding protein, 37.8 15 0.00033 36.9 1.0 28 7-34 216-245 (684)
146 PF02714 DUF221: Domain of unk 37.3 36 0.00078 31.2 3.4 32 6-39 1-32 (325)
147 KOG1365 RNA-binding protein Fu 36.0 32 0.00069 33.2 2.8 20 3-22 206-225 (508)
148 PF03467 Smg4_UPF3: Smg-4/UPF3 35.7 60 0.0013 27.6 4.3 35 5-39 57-96 (176)
149 PF11823 DUF3343: Protein of u 33.4 50 0.0011 23.6 2.9 29 4-32 2-30 (73)
150 KOG2044 5'-3' exonuclease HKE1 32.1 17 0.00037 38.0 0.4 20 60-79 260-279 (931)
151 PRK08559 nusG transcription an 31.1 45 0.00099 27.6 2.7 24 3-26 46-69 (153)
152 PF10309 DUF2414: Protein of u 30.3 58 0.0013 23.1 2.7 18 6-23 45-62 (62)
153 KOG0314 Predicted E3 ubiquitin 29.7 62 0.0013 31.9 3.7 41 61-101 134-177 (448)
154 TIGR02381 cspD cold shock doma 28.9 77 0.0017 22.5 3.3 38 2-40 12-55 (68)
155 COG1278 CspC Cold shock protei 27.7 25 0.00054 25.4 0.5 39 2-40 12-55 (67)
156 COG5638 Uncharacterized conser 27.2 68 0.0015 31.3 3.4 29 4-32 259-287 (622)
157 PRK15463 cold shock-like prote 27.1 76 0.0017 22.8 3.0 39 2-40 15-58 (70)
158 PRK12380 hydrogenase nickel in 25.1 1.2E+02 0.0025 23.9 4.0 30 12-41 40-70 (113)
159 TIGR00100 hypA hydrogenase nic 24.8 1.3E+02 0.0029 23.6 4.3 57 11-92 39-96 (115)
160 TIGR00405 L26e_arch ribosomal 23.8 71 0.0015 25.9 2.6 24 3-26 38-61 (145)
161 KOG2187 tRNA uracil-5-methyltr 21.3 49 0.0011 33.2 1.3 37 3-39 63-99 (534)
162 KOG0119 Splicing factor 1/bran 21.2 48 0.001 33.0 1.2 20 61-80 286-305 (554)
163 COG5179 TAF1 Transcription ini 20.6 59 0.0013 33.5 1.7 24 55-78 932-957 (968)
No 1
>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]
Probab=99.77 E-value=3.2e-18 Score=143.56 Aligned_cols=44 Identities=59% Similarity=0.964 Sum_probs=41.2
Q ss_pred CCCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEecCCCCCC
Q 024281 2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGP 45 (269)
Q Consensus 2 krGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~~~~rg~ 45 (269)
+.|||||||+++.||++||..|||.+|+|.+|+||+..+.++++
T Consensus 46 PPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G~~r~~ 89 (195)
T KOG0107|consen 46 PPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTGRPRGS 89 (195)
T ss_pred CCCceEEeccCcccHHHHHhhcCCccccCceEEEEeecCCcccc
Confidence 56999999999999999999999999999999999999888743
No 2
>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]
Probab=99.31 E-value=7.3e-11 Score=101.92 Aligned_cols=40 Identities=48% Similarity=0.766 Sum_probs=37.6
Q ss_pred CCCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEecCC
Q 024281 2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG 41 (269)
Q Consensus 2 krGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~~~ 41 (269)
.+|||||-|.+..||++||++|||.+|+|+.|.|++|+-.
T Consensus 54 sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~aryg 93 (256)
T KOG4207|consen 54 SRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQMARYG 93 (256)
T ss_pred ccceeEEEeeecchHHHHHHhhcceeeccceeeehhhhcC
Confidence 4799999999999999999999999999999999999743
No 3
>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]
Probab=99.04 E-value=1.9e-10 Score=103.71 Aligned_cols=70 Identities=30% Similarity=0.729 Sum_probs=58.2
Q ss_pred CCCCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEecCCCCCCCCCCCCCCCCCCCCCCCcccCCCCCCCCCcccCC
Q 024281 1 MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGGSREYLGRGPPPGSGRCFNCGIDGHWARDCKAG 79 (269)
Q Consensus 1 lkrGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~~~~rg~g~~r~~~~R~~~~~~~rc~~cG~~GH~ardC~~~ 79 (269)
|-|+|+||.|+..+||.+||..||+++|.|++|.|.+....-+...++. -+-.||.||..|||.++||..
T Consensus 110 ivkdy~fvh~d~~eda~~air~l~~~~~~gk~m~vq~stsrlrtapgmg---------Dq~~cyrcGkeghwskEcP~~ 179 (346)
T KOG0109|consen 110 IVKDYAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLSTSRLRTAPGMG---------DQSGCYRCGKEGHWSKECPVD 179 (346)
T ss_pred eecceeEEEEeeccchHHHHhcccccccccceeeeeeeccccccCCCCC---------CHHHheeccccccccccCCcc
Confidence 3579999999999999999999999999999999999987655333332 234799999999999999964
No 4
>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]
Probab=98.96 E-value=8e-10 Score=99.69 Aligned_cols=42 Identities=29% Similarity=0.503 Sum_probs=38.7
Q ss_pred CCCCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEecCCC
Q 024281 1 MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP 42 (269)
Q Consensus 1 lkrGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~~~~ 42 (269)
|-|+||||.+++...|++||.+|+|.+|+|..|.||.++...
T Consensus 34 IvKNYgFVHiEdktaaedairNLhgYtLhg~nInVeaSksKs 75 (346)
T KOG0109|consen 34 IVKNYGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSKS 75 (346)
T ss_pred eecccceEEeecccccHHHHhhcccceecceEEEEEeccccC
Confidence 347899999999999999999999999999999999998763
No 5
>PLN03134 glycine-rich RNA-binding protein 4; Provisional
Probab=98.54 E-value=2.9e-07 Score=76.31 Aligned_cols=42 Identities=33% Similarity=0.589 Sum_probs=38.5
Q ss_pred CCCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEecCCCC
Q 024281 2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPR 43 (269)
Q Consensus 2 krGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~~~~r 43 (269)
.+|||||+|.+.++|+.||+.||+.+|+|+.|.|+++.....
T Consensus 75 ~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~a~~~~~ 116 (144)
T PLN03134 75 SRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPANDRPS 116 (144)
T ss_pred cceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEeCCcCCC
Confidence 379999999999999999999999999999999999976543
No 6
>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=98.43 E-value=5.8e-07 Score=61.97 Aligned_cols=35 Identities=46% Similarity=0.727 Sum_probs=34.1
Q ss_pred CeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEe
Q 024281 4 DFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA 38 (269)
Q Consensus 4 GfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a 38 (269)
++|||+|.+.++|+.|+..|+|..|+|+.|.|+|+
T Consensus 22 ~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a 56 (56)
T PF13893_consen 22 GFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA 56 (56)
T ss_dssp TEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred CEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence 89999999999999999999999999999999986
No 7
>smart00361 RRM_1 RNA recognition motif.
Probab=98.40 E-value=4.1e-07 Score=65.89 Aligned_cols=34 Identities=35% Similarity=0.541 Sum_probs=32.3
Q ss_pred CCCeEEEEECCHHHHHHHHHHhCCCeecCceEEE
Q 024281 2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIV 35 (269)
Q Consensus 2 krGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~V 35 (269)
.+|||||+|.+.++|.+||..|||..|+|+.|.+
T Consensus 36 ~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~ 69 (70)
T smart00361 36 KRGNVYITFERSEDAARAIVDLNGRYFDGRTVKA 69 (70)
T ss_pred CcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEe
Confidence 4799999999999999999999999999999876
No 8
>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]
Probab=98.35 E-value=8.1e-07 Score=75.97 Aligned_cols=38 Identities=66% Similarity=1.110 Sum_probs=36.5
Q ss_pred CeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEecCC
Q 024281 4 DFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG 41 (269)
Q Consensus 4 GfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~~~ 41 (269)
.||||+|+++.||++||+.-||..++|.+|+|||+.+.
T Consensus 46 pfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfprgg 83 (241)
T KOG0105|consen 46 PFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPRGG 83 (241)
T ss_pred CeeEEEecCccchhhhhhcccccccCcceEEEEeccCC
Confidence 59999999999999999999999999999999999865
No 9
>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=98.21 E-value=8.3e-07 Score=77.71 Aligned_cols=39 Identities=36% Similarity=0.547 Sum_probs=37.3
Q ss_pred CCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEecCC
Q 024281 3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG 41 (269)
Q Consensus 3 rGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~~~ 41 (269)
+|||||+|+..|||..||++||+.+|.|+.|+|.+|+..
T Consensus 52 RgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~AkP~ 90 (298)
T KOG0111|consen 52 RGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLAKPE 90 (298)
T ss_pred cceeEEEeeccchhHHHhhcCchhhhcceeEEEeecCCc
Confidence 699999999999999999999999999999999999854
No 10
>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]
Probab=98.10 E-value=2.8e-05 Score=70.82 Aligned_cols=40 Identities=35% Similarity=0.709 Sum_probs=37.6
Q ss_pred CCCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEecCC
Q 024281 2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG 41 (269)
Q Consensus 2 krGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~~~ 41 (269)
.+|||||+|+++.||..|+++.+|++|+|++|.|.+..+.
T Consensus 142 skGYAFIeye~erdm~~AYK~adG~~Idgrri~VDvERgR 181 (335)
T KOG0113|consen 142 SKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDVERGR 181 (335)
T ss_pred ccceEEEEeccHHHHHHHHHhccCceecCcEEEEEecccc
Confidence 4799999999999999999999999999999999998754
No 11
>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]
Probab=98.01 E-value=4.7e-06 Score=76.65 Aligned_cols=39 Identities=41% Similarity=0.662 Sum_probs=36.8
Q ss_pred CCCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEecC
Q 024281 2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG 40 (269)
Q Consensus 2 krGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~~ 40 (269)
.||||||+|++.+||+.|-.+|+|+.|+|++|.|..+..
T Consensus 135 SKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~ATa 173 (376)
T KOG0125|consen 135 SKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNATA 173 (376)
T ss_pred CCccceEEecChhhHHHHHHHhhcceeeceEEEEeccch
Confidence 489999999999999999999999999999999998864
No 12
>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=97.95 E-value=1e-05 Score=57.00 Aligned_cols=33 Identities=39% Similarity=0.743 Sum_probs=30.7
Q ss_pred CCCeEEEEECCHHHHHHHHHHhCCCeecCceEE
Q 024281 2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRII 34 (269)
Q Consensus 2 krGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~ 34 (269)
.+|||||+|.+.++|+.||+.|+|..|.|..|+
T Consensus 38 ~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir 70 (70)
T PF00076_consen 38 SKGYAFVEFESEEDAEKALEELNGKKINGRKIR 70 (70)
T ss_dssp EEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred ccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence 368999999999999999999999999999875
No 13
>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]
Probab=97.94 E-value=5.1e-06 Score=73.11 Aligned_cols=42 Identities=57% Similarity=0.964 Sum_probs=39.3
Q ss_pred CCCCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEecCCC
Q 024281 1 MKRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP 42 (269)
Q Consensus 1 lkrGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~~~~ 42 (269)
|++|||||+|++..||++||..||+.+|.|.++.|+++.+..
T Consensus 33 mk~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~~ 74 (216)
T KOG0106|consen 33 MKNGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGKR 74 (216)
T ss_pred eecccceeccCchhhhhcccchhcCceecceeeeeecccccc
Confidence 689999999999999999999999999999999999998643
No 14
>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=97.90 E-value=1.2e-05 Score=75.73 Aligned_cols=39 Identities=36% Similarity=0.554 Sum_probs=36.5
Q ss_pred CCCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEecC
Q 024281 2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG 40 (269)
Q Consensus 2 krGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~~ 40 (269)
.+|||||+|.+.++|+.||+.|+|++|.++.|.|.++..
T Consensus 148 srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~~a~p 186 (346)
T TIGR01659 148 SFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSYARP 186 (346)
T ss_pred cCcEEEEEEccHHHHHHHHHHcCCCccCCceeeeecccc
Confidence 469999999999999999999999999999999999864
No 15
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor. These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
Probab=97.88 E-value=1.4e-05 Score=74.24 Aligned_cols=40 Identities=35% Similarity=0.581 Sum_probs=37.0
Q ss_pred CCCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEecCC
Q 024281 2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG 41 (269)
Q Consensus 2 krGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~~~ 41 (269)
.+|||||+|.+.+||+.||+.|||.+|.|+.|.|+++...
T Consensus 44 s~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~i~v~~a~~~ 83 (352)
T TIGR01661 44 SLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYARPS 83 (352)
T ss_pred cceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEeeccc
Confidence 3689999999999999999999999999999999998743
No 16
>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]
Probab=97.85 E-value=1.1e-05 Score=65.85 Aligned_cols=40 Identities=25% Similarity=0.439 Sum_probs=37.2
Q ss_pred CCCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEecCC
Q 024281 2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG 41 (269)
Q Consensus 2 krGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~~~ 41 (269)
.+|||+|+|+..++|+.||++|||.+|.|..|.|.|+-..
T Consensus 113 ~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~Fv~ 152 (170)
T KOG0130|consen 113 VKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDWCFVK 152 (170)
T ss_pred ccceeeeehHhHHHHHHHHHhccchhhhCCceeEEEEEec
Confidence 4799999999999999999999999999999999998644
No 17
>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family. Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.
Probab=97.80 E-value=2.8e-05 Score=77.72 Aligned_cols=42 Identities=43% Similarity=0.652 Sum_probs=38.5
Q ss_pred CCCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEecCCCC
Q 024281 2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPR 43 (269)
Q Consensus 2 krGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~~~~r 43 (269)
.++||||+|++.++|+.||++|||.+|+|+.|.|.|++....
T Consensus 268 ~rgfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~~Akp~~~ 309 (578)
T TIGR01648 268 IRDYAFVHFEDREDAVKAMDELNGKELEGSEIEVTLAKPVDK 309 (578)
T ss_pred ecCeEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEccCCCc
Confidence 468999999999999999999999999999999999986543
No 18
>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]
Probab=97.77 E-value=3e-05 Score=62.81 Aligned_cols=39 Identities=31% Similarity=0.511 Sum_probs=36.5
Q ss_pred CCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEecCC
Q 024281 3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG 41 (269)
Q Consensus 3 rGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~~~ 41 (269)
-||+||+|...+||++||..|+|+.|+.+.|.|.|.-+-
T Consensus 78 CGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~D~GF 116 (153)
T KOG0121|consen 78 CGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDWDAGF 116 (153)
T ss_pred cceEEEEEecchhHHHHHHHhccCcccccceeeeccccc
Confidence 489999999999999999999999999999999998753
No 19
>smart00360 RRM RNA recognition motif.
Probab=97.76 E-value=4.5e-05 Score=52.46 Aligned_cols=34 Identities=44% Similarity=0.782 Sum_probs=31.7
Q ss_pred CCeEEEEECCHHHHHHHHHHhCCCeecCceEEEE
Q 024281 3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVE 36 (269)
Q Consensus 3 rGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve 36 (269)
+|||||+|.+.++|+.|+..|++..|.|..|.|+
T Consensus 38 ~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v~ 71 (71)
T smart00360 38 KGFAFVEFESEEDAEKALEALNGKELDGRPLKVK 71 (71)
T ss_pred CceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEeC
Confidence 5899999999999999999999999999998873
No 20
>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]
Probab=97.75 E-value=3e-05 Score=75.56 Aligned_cols=39 Identities=36% Similarity=0.647 Sum_probs=37.2
Q ss_pred CeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEecCCC
Q 024281 4 DFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP 42 (269)
Q Consensus 4 GfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~~~~ 42 (269)
|||||+|.+..||+.||+.|||.+|+|+.|.|.||....
T Consensus 159 GFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~Kd 197 (678)
T KOG0127|consen 159 GFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVDKD 197 (678)
T ss_pred ceEEEEEeeHHHHHHHHHhccCceecCceeEEeeecccc
Confidence 999999999999999999999999999999999998654
No 21
>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]
Probab=97.73 E-value=3e-05 Score=69.88 Aligned_cols=41 Identities=27% Similarity=0.511 Sum_probs=38.5
Q ss_pred CCCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEecCCC
Q 024281 2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP 42 (269)
Q Consensus 2 krGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~~~~ 42 (269)
.||||||.|...+|||.||..|+|.+|.++.|+-.||.-.+
T Consensus 103 sKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWATRKp 143 (321)
T KOG0148|consen 103 SKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWATRKP 143 (321)
T ss_pred ccceeEEeccchHHHHHHHHHhCCeeeccceeeccccccCc
Confidence 48999999999999999999999999999999999998655
No 22
>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=97.66 E-value=6.9e-05 Score=75.31 Aligned_cols=41 Identities=22% Similarity=0.386 Sum_probs=38.0
Q ss_pred CCCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEecCCC
Q 024281 2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP 42 (269)
Q Consensus 2 krGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~~~~ 42 (269)
.+|||||+|++.++|..||..||+++|+|+.|+|.++...+
T Consensus 245 sKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kAi~pP 285 (612)
T TIGR01645 245 HKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVTPP 285 (612)
T ss_pred cCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEecCCCc
Confidence 47999999999999999999999999999999999988543
No 23
>smart00362 RRM_2 RNA recognition motif.
Probab=97.64 E-value=8.6e-05 Score=51.29 Aligned_cols=34 Identities=44% Similarity=0.706 Sum_probs=31.6
Q ss_pred CCeEEEEECCHHHHHHHHHHhCCCeecCceEEEE
Q 024281 3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVE 36 (269)
Q Consensus 3 rGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve 36 (269)
.|||||+|.+.++|+.|+..|++..|.|..|.|.
T Consensus 39 ~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~ 72 (72)
T smart00362 39 KGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE 72 (72)
T ss_pred CceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence 5899999999999999999999999999998773
No 24
>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=97.64 E-value=3.1e-05 Score=72.09 Aligned_cols=40 Identities=25% Similarity=0.594 Sum_probs=37.6
Q ss_pred CeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEecCCCC
Q 024281 4 DFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPR 43 (269)
Q Consensus 4 GfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~~~~r 43 (269)
.||||+|++.++|++|+++||+..|+.++|.|.|.+.+.+
T Consensus 282 qyaFiEFen~escE~AyFKMdNvLIDDrRIHVDFSQSVsk 321 (479)
T KOG0415|consen 282 QYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDFSQSVSK 321 (479)
T ss_pred heeeeeecchhhHHHHHhhhcceeeccceEEeehhhhhhh
Confidence 3999999999999999999999999999999999987755
No 25
>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor. Members of this subfamily are found in plants, metazoa and fungi.
Probab=97.59 E-value=0.0001 Score=72.13 Aligned_cols=40 Identities=35% Similarity=0.570 Sum_probs=37.3
Q ss_pred CCCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEecCC
Q 024281 2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG 41 (269)
Q Consensus 2 krGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~~~ 41 (269)
.+|||||+|.+.++|+.||..|+|..|.|..|.|.++...
T Consensus 336 ~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~~~ 375 (509)
T TIGR01642 336 SKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACVG 375 (509)
T ss_pred cCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECccC
Confidence 4799999999999999999999999999999999998754
No 26
>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]
Probab=97.58 E-value=5e-05 Score=64.90 Aligned_cols=38 Identities=34% Similarity=0.373 Sum_probs=36.0
Q ss_pred CCCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEec
Q 024281 2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR 39 (269)
Q Consensus 2 krGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~ 39 (269)
-+|||||||.+.+||+.||+-|++..|.|+.|+|..+.
T Consensus 50 ~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~kas 87 (203)
T KOG0131|consen 50 HQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKAS 87 (203)
T ss_pred ccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEecc
Confidence 47999999999999999999999999999999998876
No 27
>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=97.56 E-value=9.3e-05 Score=71.46 Aligned_cols=37 Identities=32% Similarity=0.652 Sum_probs=35.7
Q ss_pred CCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEec
Q 024281 3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR 39 (269)
Q Consensus 3 rGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~ 39 (269)
+|||||+|.+.++|+.||..|+|.+|.|+.|.|.|+.
T Consensus 228 ~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~ 264 (457)
T TIGR01622 228 KGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQ 264 (457)
T ss_pred ceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEcc
Confidence 6899999999999999999999999999999999976
No 28
>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=97.56 E-value=0.00011 Score=69.35 Aligned_cols=39 Identities=31% Similarity=0.443 Sum_probs=34.9
Q ss_pred CCeEEEEECCHHHHHHHHHHhCCCeecC--ceEEEEEecCC
Q 024281 3 RDFAFVEFSDPRDADDARYSLNGRDVDG--SRIIVEFARGG 41 (269)
Q Consensus 3 rGfgfVeF~~~~dA~~Ai~~ldG~~l~G--r~I~Ve~a~~~ 41 (269)
+|||||+|.+.++|++||++|+++.|++ ..|.|.++...
T Consensus 235 kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~~a~~~ 275 (346)
T TIGR01659 235 RGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRLAEEH 275 (346)
T ss_pred ceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEECCcc
Confidence 5899999999999999999999999987 57888888754
No 29
>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family. Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).
Probab=97.53 E-value=0.00013 Score=71.67 Aligned_cols=39 Identities=31% Similarity=0.384 Sum_probs=36.7
Q ss_pred CCCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEecC
Q 024281 2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG 40 (269)
Q Consensus 2 krGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~~ 40 (269)
++|||||+|.+.++|+.||.+|+|..|.|+.|.|.+++.
T Consensus 312 ~~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s~~ 350 (481)
T TIGR01649 312 KKETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPSKQ 350 (481)
T ss_pred CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEccc
Confidence 479999999999999999999999999999999999864
No 30
>PLN03213 repressor of silencing 3; Provisional
Probab=97.53 E-value=9.8e-05 Score=71.42 Aligned_cols=37 Identities=30% Similarity=0.471 Sum_probs=34.9
Q ss_pred CCeEEEEECCH--HHHHHHHHHhCCCeecCceEEEEEec
Q 024281 3 RDFAFVEFSDP--RDADDARYSLNGRDVDGSRIIVEFAR 39 (269)
Q Consensus 3 rGfgfVeF~~~--~dA~~Ai~~ldG~~l~Gr~I~Ve~a~ 39 (269)
+|||||+|... .++++||..|||.+++|+.|+|+.|+
T Consensus 48 RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNKAK 86 (759)
T PLN03213 48 RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEKAK 86 (759)
T ss_pred CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEeecc
Confidence 69999999987 67999999999999999999999987
No 31
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=97.53 E-value=4.8e-05 Score=65.43 Aligned_cols=40 Identities=53% Similarity=1.252 Sum_probs=34.1
Q ss_pred CCCcccCCCCCCCCCcccC---------C------CCCcccccCCCCCcccccCC
Q 024281 60 SGRCFNCGIDGHWARDCKA---------G------DWKNKCYRCGERGHIERNCQ 99 (269)
Q Consensus 60 ~~rc~~cG~~GH~ardC~~---------~------~~k~~CyrCG~~Gh~~r~c~ 99 (269)
...||+||+.||+.+|||. . .+...||.||+.||+..+|.
T Consensus 60 ~~~C~nCg~~GH~~~DCP~~iC~~C~~~~H~s~~C~~~~~C~~Cg~~GH~~~dC~ 114 (190)
T COG5082 60 NPVCFNCGQNGHLRRDCPHSICYNCSWDGHRSNHCPKPKKCYNCGETGHLSRDCN 114 (190)
T ss_pred ccccchhcccCcccccCChhHhhhcCCCCcccccCCcccccccccccCccccccC
Confidence 4589999999999999991 1 24568999999999999995
No 32
>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=97.53 E-value=0.00019 Score=49.74 Aligned_cols=35 Identities=49% Similarity=0.843 Sum_probs=32.9
Q ss_pred CCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEE
Q 024281 3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEF 37 (269)
Q Consensus 3 rGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~ 37 (269)
.|+|||+|.+.++|..|++.|++..|+|..|.|.+
T Consensus 40 ~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~ 74 (74)
T cd00590 40 KGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF 74 (74)
T ss_pred ceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence 68999999999999999999999999999998864
No 33
>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=97.49 E-value=0.00014 Score=51.76 Aligned_cols=32 Identities=50% Similarity=0.808 Sum_probs=30.0
Q ss_pred CCeEEEEECCHHHHHHHHHHhCCCeecCceEE
Q 024281 3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRII 34 (269)
Q Consensus 3 rGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~ 34 (269)
+|||||+|.+.++|+.|+..+++.+|+|+.|.
T Consensus 39 ~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~ 70 (70)
T PF14259_consen 39 RGFAFVEFSSEEDAKRALELLNGKEIDGRKLR 70 (70)
T ss_dssp EEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred CCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence 58999999999999999999999999999874
No 34
>TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.
Probab=97.41 E-value=0.00021 Score=71.08 Aligned_cols=39 Identities=36% Similarity=0.644 Sum_probs=36.9
Q ss_pred CCCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEecC
Q 024281 2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG 40 (269)
Q Consensus 2 krGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~~ 40 (269)
.+|||||+|.+.++|+.||.+|+|..|.|+.|.|.++..
T Consensus 325 ~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~a~~ 363 (562)
T TIGR01628 325 SRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQR 363 (562)
T ss_pred cCCeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEeccC
Confidence 479999999999999999999999999999999999874
No 35
>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]
Probab=97.40 E-value=0.00024 Score=61.29 Aligned_cols=38 Identities=39% Similarity=0.662 Sum_probs=36.3
Q ss_pred CCCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEec
Q 024281 2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR 39 (269)
Q Consensus 2 krGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~ 39 (269)
.+|||||+|.+.++|..||+.|+|..|+|+.|.|.++.
T Consensus 156 ~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~ 193 (306)
T COG0724 156 SRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQ 193 (306)
T ss_pred cCceEEEEecCHHHHHHHHHHcCCCeECCceeEeeccc
Confidence 47999999999999999999999999999999999975
No 36
>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]
Probab=97.37 E-value=0.00017 Score=62.66 Aligned_cols=39 Identities=21% Similarity=0.198 Sum_probs=35.5
Q ss_pred CCCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEecC
Q 024281 2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG 40 (269)
Q Consensus 2 krGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~~ 40 (269)
.+|||||+|++.+.|+-|-+.||++.|.+..|.+.+...
T Consensus 91 SKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~vmpp 129 (214)
T KOG4208|consen 91 SKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECHVMPP 129 (214)
T ss_pred cCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeEEeCc
Confidence 379999999999999999999999999999998887653
No 37
>PLN03120 nucleic acid binding protein; Provisional
Probab=97.36 E-value=0.00029 Score=63.72 Aligned_cols=38 Identities=26% Similarity=0.485 Sum_probs=35.0
Q ss_pred CCCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEecC
Q 024281 2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG 40 (269)
Q Consensus 2 krGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~~ 40 (269)
.+|||||+|.+.++|+.|| .|+|..|.|+.|.|.++..
T Consensus 42 ~~GfAFVtF~d~eaAe~Al-lLnG~~l~gr~V~Vt~a~~ 79 (260)
T PLN03120 42 RSQIAYVTFKDPQGAETAL-LLSGATIVDQSVTITPAED 79 (260)
T ss_pred CCCEEEEEeCcHHHHHHHH-HhcCCeeCCceEEEEeccC
Confidence 3689999999999999999 5999999999999999863
No 38
>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=97.35 E-value=0.00021 Score=71.81 Aligned_cols=38 Identities=34% Similarity=0.489 Sum_probs=35.5
Q ss_pred CCCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEec
Q 024281 2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR 39 (269)
Q Consensus 2 krGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~ 39 (269)
.+|||||+|.+.++|+.||.+|||..|+|+.|.|.+..
T Consensus 148 skGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp~ 185 (612)
T TIGR01645 148 HKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPS 185 (612)
T ss_pred cCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeecccc
Confidence 47999999999999999999999999999999998654
No 39
>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]
Probab=97.34 E-value=0.0002 Score=69.28 Aligned_cols=41 Identities=32% Similarity=0.618 Sum_probs=38.1
Q ss_pred CCCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEecCCC
Q 024281 2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP 42 (269)
Q Consensus 2 krGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~~~~ 42 (269)
.+||||++|.+.++|+.||..|+|.+|.|+.|+|.|+....
T Consensus 59 ~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~~~~ 99 (435)
T KOG0108|consen 59 PKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYASNRK 99 (435)
T ss_pred cCceeeEecCchhhHHHHHHhcCCcccCCceEEeecccccc
Confidence 47999999999999999999999999999999999987543
No 40
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=97.32 E-value=0.00016 Score=59.91 Aligned_cols=42 Identities=43% Similarity=1.115 Sum_probs=28.3
Q ss_pred CCCcccCCCCCCCCCcccCCC----CCcccccCCCCCcccccCCCC
Q 024281 60 SGRCFNCGIDGHWARDCKAGD----WKNKCYRCGERGHIERNCQNS 101 (269)
Q Consensus 60 ~~rc~~cG~~GH~ardC~~~~----~k~~CyrCG~~Gh~~r~c~~~ 101 (269)
...||+|+..+|++.+|+... ....||.|++.+|++.+|+..
T Consensus 77 ~~~C~~Cg~~GH~~~~C~~~~~~~~~~~~C~~Cg~~gH~~~~C~~~ 122 (148)
T PTZ00368 77 PRSCYNCGQTGHISRECPNRAKGGAARRACYNCGGEGHISRDCPNA 122 (148)
T ss_pred CcccCcCCCCCcccccCCCcccccccchhhcccCcCCcchhcCCCc
Confidence 346777777777777777632 134677777777777777763
No 41
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=97.29 E-value=0.00023 Score=59.04 Aligned_cols=42 Identities=36% Similarity=1.065 Sum_probs=32.3
Q ss_pred CCCcccCCCCCCCCCcccCCC---CCcccccCCCCCcccccCCCC
Q 024281 60 SGRCFNCGIDGHWARDCKAGD---WKNKCYRCGERGHIERNCQNS 101 (269)
Q Consensus 60 ~~rc~~cG~~GH~ardC~~~~---~k~~CyrCG~~Gh~~r~c~~~ 101 (269)
...||+|+..||++.+|+... ....||.|+..+|++.+|++.
T Consensus 27 ~~~C~~Cg~~GH~~~~Cp~~~~~~~~~~C~~Cg~~GH~~~~Cp~~ 71 (148)
T PTZ00368 27 ARPCYKCGEPGHLSRECPSAPGGRGERSCYNCGKTGHLSRECPEA 71 (148)
T ss_pred CccCccCCCCCcCcccCcCCCCCCCCcccCCCCCcCcCcccCCCc
Confidence 467888888888888887654 345688888888888888764
No 42
>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=97.24 E-value=0.00039 Score=69.70 Aligned_cols=40 Identities=30% Similarity=0.567 Sum_probs=37.1
Q ss_pred CCCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEecCC
Q 024281 2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG 41 (269)
Q Consensus 2 krGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~~~ 41 (269)
..|||||+|.+.++|..||.+|+|+.|+|..|.|.++...
T Consensus 559 SmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~~k 598 (725)
T KOG0110|consen 559 SMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISENK 598 (725)
T ss_pred ccceeEEEecCHHHHHHHHHHhcCceecCceEEEEeccCc
Confidence 4599999999999999999999999999999999998833
No 43
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=97.23 E-value=0.00022 Score=38.39 Aligned_cols=17 Identities=65% Similarity=1.425 Sum_probs=12.5
Q ss_pred CcccCCCCCCCCCcccC
Q 024281 62 RCFNCGIDGHWARDCKA 78 (269)
Q Consensus 62 rc~~cG~~GH~ardC~~ 78 (269)
.||+||..||++.+|+.
T Consensus 2 ~C~~C~~~GH~~~~Cp~ 18 (18)
T PF00098_consen 2 KCFNCGEPGHIARDCPK 18 (18)
T ss_dssp BCTTTSCSSSCGCTSSS
T ss_pred cCcCCCCcCcccccCcc
Confidence 57777777777777763
No 44
>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]
Probab=97.19 E-value=0.00045 Score=66.11 Aligned_cols=40 Identities=43% Similarity=0.638 Sum_probs=37.6
Q ss_pred CCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEecCCC
Q 024281 3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP 42 (269)
Q Consensus 3 rGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~~~~ 42 (269)
+.||||.|.+.+||-+|++.|||++|+|..|-|.+|+...
T Consensus 293 rDYaFVHf~eR~davkAm~~~ngkeldG~~iEvtLAKP~~ 332 (506)
T KOG0117|consen 293 RDYAFVHFAEREDAVKAMKETNGKELDGSPIEVTLAKPVD 332 (506)
T ss_pred cceeEEeecchHHHHHHHHHhcCceecCceEEEEecCChh
Confidence 5799999999999999999999999999999999998654
No 45
>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]
Probab=97.18 E-value=0.00038 Score=62.68 Aligned_cols=39 Identities=33% Similarity=0.627 Sum_probs=36.7
Q ss_pred CeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEecCCC
Q 024281 4 DFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP 42 (269)
Q Consensus 4 GfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~~~~ 42 (269)
|||||.|.+++||++||..|||..|..+.|+|.+|+...
T Consensus 84 GYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSyARPSs 122 (360)
T KOG0145|consen 84 GYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSYARPSS 122 (360)
T ss_pred ccceeeecChHHHHHHHhhhcceeeccceEEEEeccCCh
Confidence 899999999999999999999999999999999998543
No 46
>TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.
Probab=97.16 E-value=0.00049 Score=68.47 Aligned_cols=37 Identities=24% Similarity=0.525 Sum_probs=35.2
Q ss_pred CCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEec
Q 024281 3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR 39 (269)
Q Consensus 3 rGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~ 39 (269)
+|||||+|.+.+||+.||+.|++..|.|+.|.|.|+.
T Consensus 42 ~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s~ 78 (562)
T TIGR01628 42 LGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQ 78 (562)
T ss_pred ceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeeccc
Confidence 5899999999999999999999999999999999875
No 47
>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]
Probab=97.10 E-value=0.00058 Score=66.75 Aligned_cols=38 Identities=32% Similarity=0.514 Sum_probs=35.6
Q ss_pred CCCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEec
Q 024281 2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR 39 (269)
Q Consensus 2 krGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~ 39 (269)
.+|||||+|.+.++|..|+..|||.+|.|+.|+|....
T Consensus 319 skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~ 356 (549)
T KOG0147|consen 319 SKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVT 356 (549)
T ss_pred ccCcceEEEecHHHHHHHHHHhccceecCceEEEEEee
Confidence 58999999999999999999999999999999998765
No 48
>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]
Probab=97.07 E-value=0.00076 Score=64.61 Aligned_cols=40 Identities=28% Similarity=0.434 Sum_probs=35.9
Q ss_pred CCCeEEEEECCHHHHHHHHHHhCCCee-cCceEEEEEecCC
Q 024281 2 KRDFAFVEFSDPRDADDARYSLNGRDV-DGSRIIVEFARGG 41 (269)
Q Consensus 2 krGfgfVeF~~~~dA~~Ai~~ldG~~l-~Gr~I~Ve~a~~~ 41 (269)
-+|||||+|-+.++|+.||+.||+.+| .|+.|.|......
T Consensus 124 nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc~Svan 164 (506)
T KOG0117|consen 124 NRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVCVSVAN 164 (506)
T ss_pred CcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEEEeeec
Confidence 479999999999999999999999999 5999999887643
No 49
>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=97.05 E-value=0.0008 Score=64.99 Aligned_cols=38 Identities=32% Similarity=0.447 Sum_probs=34.6
Q ss_pred CCCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEecC
Q 024281 2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG 40 (269)
Q Consensus 2 krGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~~ 40 (269)
.+|||||+|.+.++|+.|| .|+|..|.|..|.|.++..
T Consensus 130 skg~afVeF~~~e~A~~Al-~l~g~~~~g~~i~v~~~~~ 167 (457)
T TIGR01622 130 SKGVAYVEFYDVESVIKAL-ALTGQMLLGRPIIVQSSQA 167 (457)
T ss_pred cceEEEEEECCHHHHHHHH-HhCCCEECCeeeEEeecch
Confidence 4799999999999999999 5999999999999988754
No 50
>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor. Members of this subfamily are found in plants, metazoa and fungi.
Probab=97.04 E-value=0.00054 Score=66.99 Aligned_cols=35 Identities=23% Similarity=0.304 Sum_probs=32.2
Q ss_pred CCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEe
Q 024281 3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA 38 (269)
Q Consensus 3 rGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a 38 (269)
+|||||+|.+.++|..|| +|||+.|.|..|.|...
T Consensus 223 kg~afVeF~~~e~A~~Al-~l~g~~~~g~~l~v~r~ 257 (509)
T TIGR01642 223 KNFAFLEFRTVEEATFAM-ALDSIIYSNVFLKIRRP 257 (509)
T ss_pred CCEEEEEeCCHHHHhhhh-cCCCeEeeCceeEecCc
Confidence 689999999999999999 69999999999988644
No 51
>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family. Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).
Probab=97.01 E-value=0.00091 Score=65.65 Aligned_cols=37 Identities=32% Similarity=0.486 Sum_probs=33.7
Q ss_pred CeEEEEECCHHHHHHHHHHhCCCeecC--ceEEEEEecC
Q 024281 4 DFAFVEFSDPRDADDARYSLNGRDVDG--SRIIVEFARG 40 (269)
Q Consensus 4 GfgfVeF~~~~dA~~Ai~~ldG~~l~G--r~I~Ve~a~~ 40 (269)
|+|||+|.+.++|+.||.+|||.+|.+ ..|.|+|++.
T Consensus 135 ~~afVef~~~~~A~~A~~~Lng~~i~~~~~~l~v~~sk~ 173 (481)
T TIGR01649 135 FQALVEFESVNSAQHAKAALNGADIYNGCCTLKIEYAKP 173 (481)
T ss_pred eEEEEEECCHHHHHHHHHHhcCCcccCCceEEEEEEecC
Confidence 589999999999999999999999975 4899999874
No 52
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor. These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
Probab=96.91 E-value=0.0014 Score=60.91 Aligned_cols=39 Identities=33% Similarity=0.570 Sum_probs=33.9
Q ss_pred CCCeEEEEECCHHHHHHHHHHhCCCeecC--ceEEEEEecC
Q 024281 2 KRDFAFVEFSDPRDADDARYSLNGRDVDG--SRIIVEFARG 40 (269)
Q Consensus 2 krGfgfVeF~~~~dA~~Ai~~ldG~~l~G--r~I~Ve~a~~ 40 (269)
.+|||||+|.+.++|+.||..|+|..+.| ..|.|.++..
T Consensus 130 ~~g~~fv~f~~~~~A~~ai~~l~g~~~~g~~~~i~v~~a~~ 170 (352)
T TIGR01661 130 SKGVGFIRFDKRDEADRAIKTLNGTTPSGCTEPITVKFANN 170 (352)
T ss_pred cCcEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEECCC
Confidence 36899999999999999999999999987 4677777753
No 53
>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=96.91 E-value=0.00022 Score=61.07 Aligned_cols=39 Identities=31% Similarity=0.429 Sum_probs=36.3
Q ss_pred CCCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEecC
Q 024281 2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG 40 (269)
Q Consensus 2 krGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~~ 40 (269)
.+||||+.|++.....-||++|||+.|.|+.|+|.+...
T Consensus 76 SKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv~~ 114 (219)
T KOG0126|consen 76 SKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHVSN 114 (219)
T ss_pred ccceEEEEecCccceEEEEeccCCceecceeEEeeeccc
Confidence 479999999999999999999999999999999998754
No 54
>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=96.90 E-value=0.0014 Score=51.44 Aligned_cols=37 Identities=35% Similarity=0.472 Sum_probs=34.6
Q ss_pred CCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEec
Q 024281 3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR 39 (269)
Q Consensus 3 rGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~ 39 (269)
+|-|||.|++..||..|+++|.|..++++-+.|-+-+
T Consensus 57 rGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq 93 (124)
T KOG0114|consen 57 RGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQ 93 (124)
T ss_pred CceEEEEehHhhhHHHHHHHhcccccCCceEEEEecC
Confidence 6899999999999999999999999999999988765
No 55
>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]
Probab=96.87 E-value=0.0015 Score=59.21 Aligned_cols=39 Identities=23% Similarity=0.505 Sum_probs=36.7
Q ss_pred CCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEecCC
Q 024281 3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG 41 (269)
Q Consensus 3 rGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~~~ 41 (269)
+||+||-|+..|.|..||..||+++|.|..++..|-+..
T Consensus 200 qGYaFVrF~tkEaAahAIv~mNntei~G~~VkCsWGKe~ 238 (321)
T KOG0148|consen 200 QGYAFVRFETKEAAAHAIVQMNNTEIGGQLVRCSWGKEG 238 (321)
T ss_pred cceEEEEecchhhHHHHHHHhcCceeCceEEEEeccccC
Confidence 699999999999999999999999999999999998754
No 56
>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]
Probab=96.84 E-value=0.00082 Score=63.04 Aligned_cols=35 Identities=37% Similarity=0.524 Sum_probs=33.5
Q ss_pred CCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEE
Q 024281 3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEF 37 (269)
Q Consensus 3 rGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~ 37 (269)
||||||||+-+|.|.-|++.|||.+|.|+.|+|..
T Consensus 155 KgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgr 189 (544)
T KOG0124|consen 155 KGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGR 189 (544)
T ss_pred cceEEEEEeCcHHHHHHHHHhccccccCccccccC
Confidence 79999999999999999999999999999999974
No 57
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=96.83 E-value=0.00073 Score=58.21 Aligned_cols=42 Identities=33% Similarity=0.910 Sum_probs=37.0
Q ss_pred CCcccCCCCCCCCCcc-cCCCCCcccccCCCCCcccccCCCCC
Q 024281 61 GRCFNCGIDGHWARDC-KAGDWKNKCYRCGERGHIERNCQNSP 102 (269)
Q Consensus 61 ~rc~~cG~~GH~ardC-~~~~~k~~CyrCG~~Gh~~r~c~~~~ 102 (269)
..||+||..||++.+| |....+..|+.|...+|+..+|+..-
T Consensus 98 ~~C~~Cg~~GH~~~dC~P~~~~~~~C~~C~s~~H~s~~Cp~~~ 140 (190)
T COG5082 98 KKCYNCGETGHLSRDCNPSKDQQKSCFDCNSTRHSSEDCPSIW 140 (190)
T ss_pred cccccccccCccccccCcccccCcceeccCCCccccccCcccc
Confidence 6899999999999999 66666778999999999999998743
No 58
>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=96.74 E-value=0.00093 Score=60.50 Aligned_cols=42 Identities=38% Similarity=1.028 Sum_probs=35.0
Q ss_pred CCcccCCCCCCCCCcccCCCCCcccccCCCCCcccccCCCCCC
Q 024281 61 GRCFNCGIDGHWARDCKAGDWKNKCYRCGERGHIERNCQNSPK 103 (269)
Q Consensus 61 ~rc~~cG~~GH~ardC~~~~~k~~CyrCG~~Gh~~r~c~~~~r 103 (269)
..||+||..|||..+|+.. ....||.|+..+|+..+|+....
T Consensus 144 ~~Cy~Cg~~GH~s~~C~~~-~~~~c~~c~~~~h~~~~C~~~~~ 185 (261)
T KOG4400|consen 144 AKCYSCGEQGHISDDCPEN-KGGTCFRCGKVGHGSRDCPSKQK 185 (261)
T ss_pred CccCCCCcCCcchhhCCCC-CCCccccCCCcceecccCCcccc
Confidence 4599999999999999966 45689999999999999987543
No 59
>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=96.71 E-value=0.0014 Score=65.67 Aligned_cols=37 Identities=30% Similarity=0.468 Sum_probs=31.4
Q ss_pred CCCeEEEEECCHHHHHHHHHHhCCCeec-CceEEEEEe
Q 024281 2 KRDFAFVEFSDPRDADDARYSLNGRDVD-GSRIIVEFA 38 (269)
Q Consensus 2 krGfgfVeF~~~~dA~~Ai~~ldG~~l~-Gr~I~Ve~a 38 (269)
.+|||||+|.+.++|+.||+.||+.+|. |+.|.|.++
T Consensus 98 sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~S 135 (578)
T TIGR01648 98 NRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCIS 135 (578)
T ss_pred ccceEEEEeCCHHHHHHHHHHcCCCeecCCcccccccc
Confidence 4799999999999999999999999885 666655543
No 60
>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]
Probab=96.64 E-value=0.0023 Score=56.44 Aligned_cols=34 Identities=50% Similarity=0.850 Sum_probs=32.5
Q ss_pred CCCeEEEEECCHHHHHHHHHHhCCCeecCceEEE
Q 024281 2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIV 35 (269)
Q Consensus 2 krGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~V 35 (269)
..+|+||+|.+.+||..||..|+|.+|.++.|.|
T Consensus 132 ~~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~ 165 (216)
T KOG0106|consen 132 RRNFAFVEFSEQEDAKRALEKLDGKKLNGRRISV 165 (216)
T ss_pred hccccceeehhhhhhhhcchhccchhhcCceeee
Confidence 4689999999999999999999999999999999
No 61
>PLN03121 nucleic acid binding protein; Provisional
Probab=96.50 E-value=0.0038 Score=55.85 Aligned_cols=36 Identities=22% Similarity=0.260 Sum_probs=33.0
Q ss_pred CCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEec
Q 024281 3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR 39 (269)
Q Consensus 3 rGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~ 39 (269)
.+||||+|.++++|+.|| .|+|..|.+..|.|....
T Consensus 44 ~gfAfVtF~d~~aaetAl-lLnGa~l~d~~I~It~~~ 79 (243)
T PLN03121 44 ACTAYVTFKDAYALETAV-LLSGATIVDQRVCITRWG 79 (243)
T ss_pred ceEEEEEECCHHHHHHHH-hcCCCeeCCceEEEEeCc
Confidence 479999999999999999 899999999999988754
No 62
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=96.48 E-value=0.0019 Score=34.75 Aligned_cols=17 Identities=59% Similarity=1.497 Sum_probs=15.7
Q ss_pred ccccCCCCCcccccCCC
Q 024281 84 KCYRCGERGHIERNCQN 100 (269)
Q Consensus 84 ~CyrCG~~Gh~~r~c~~ 100 (269)
.||.|++.||++.+|++
T Consensus 2 ~C~~C~~~GH~~~~Cp~ 18 (18)
T PF00098_consen 2 KCFNCGEPGHIARDCPK 18 (18)
T ss_dssp BCTTTSCSSSCGCTSSS
T ss_pred cCcCCCCcCcccccCcc
Confidence 69999999999999974
No 63
>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]
Probab=96.43 E-value=0.0035 Score=59.70 Aligned_cols=39 Identities=28% Similarity=0.534 Sum_probs=36.5
Q ss_pred CeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEecCCC
Q 024281 4 DFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP 42 (269)
Q Consensus 4 GfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~~~~ 42 (269)
|||||.|.++.||+.||+.||...|.|+.|+|-|....+
T Consensus 38 gy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~rd~ 76 (369)
T KOG0123|consen 38 GYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQRDP 76 (369)
T ss_pred ceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhccCC
Confidence 799999999999999999999999999999999987543
No 64
>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=96.20 E-value=0.0047 Score=62.16 Aligned_cols=39 Identities=33% Similarity=0.497 Sum_probs=36.6
Q ss_pred CCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEecCC
Q 024281 3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG 41 (269)
Q Consensus 3 rGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~~~ 41 (269)
++||||.|.+.++|++||.++|++.|+-.+|.|+++...
T Consensus 9 R~F~FiGf~~eeeA~~Ai~~fn~s~i~ts~i~Ve~~~~~ 47 (725)
T KOG0110|consen 9 RRFGFIGFKSEEEAQKAIKYFNKSFINTSRITVEFCKSF 47 (725)
T ss_pred eeeeEeeeccHHHHHHHHHHhhccccccceEEEEehhhc
Confidence 579999999999999999999999999999999998743
No 65
>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]
Probab=96.18 E-value=0.0035 Score=61.55 Aligned_cols=42 Identities=29% Similarity=0.401 Sum_probs=38.9
Q ss_pred CCCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEecCCCC
Q 024281 2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPR 43 (269)
Q Consensus 2 krGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~~~~r 43 (269)
.+|||||.|.=.+|++.||..+.+..|.|+.|.|.+|.-..+
T Consensus 46 ~RGfgfVtFam~ED~qrA~~e~~~~kf~Gr~l~v~~A~~R~r 87 (678)
T KOG0127|consen 46 KRGFGFVTFAMEEDVQRALAETEQSKFEGRILNVDPAKKRAR 87 (678)
T ss_pred ccCccceeeehHhHHHHHHHHhhcCcccceeccccccccccc
Confidence 579999999999999999999999999999999999986544
No 66
>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]
Probab=96.16 E-value=0.0078 Score=53.27 Aligned_cols=40 Identities=33% Similarity=0.465 Sum_probs=36.3
Q ss_pred CeEEEEECCHHHHHHHHHHhCCCeec---CceEEEEEecCCCC
Q 024281 4 DFAFVEFSDPRDADDARYSLNGRDVD---GSRIIVEFARGGPR 43 (269)
Q Consensus 4 GfgfVeF~~~~dA~~Ai~~ldG~~l~---Gr~I~Ve~a~~~~r 43 (269)
-||||.|.+..+|.+|+.+|||..|+ +..|+||+|+...+
T Consensus 78 pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLhiElAKSNtK 120 (284)
T KOG1457|consen 78 PVAFATFTSHQFALAAMNALNGVRFDPETGSTLHIELAKSNTK 120 (284)
T ss_pred ceEEEEecchHHHHHHHHHhcCeeeccccCceeEeeehhcCcc
Confidence 48999999999999999999999996 77899999997654
No 67
>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]
Probab=96.14 E-value=0.0064 Score=57.95 Aligned_cols=37 Identities=30% Similarity=0.515 Sum_probs=34.1
Q ss_pred CCCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEec
Q 024281 2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR 39 (269)
Q Consensus 2 krGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~ 39 (269)
.+|| ||+|++++.|..||++|||..|.|..|.|..+.
T Consensus 115 ~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~ 151 (369)
T KOG0123|consen 115 SKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFE 151 (369)
T ss_pred ceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeecc
Confidence 3689 999999999999999999999999999997665
No 68
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=96.01 E-value=0.0026 Score=61.69 Aligned_cols=95 Identities=20% Similarity=0.326 Sum_probs=58.7
Q ss_pred eEEEEECCHHHHHHHHHHhCCCeecCceEEEEEecCCCCCCCCCC--CCCCCCCCCCCCCcccCCCCCCCCCcccCC--C
Q 024281 5 FAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRGPGGSR--EYLGRGPPPGSGRCFNCGIDGHWARDCKAG--D 80 (269)
Q Consensus 5 fgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~~~~rg~g~~r--~~~~R~~~~~~~rc~~cG~~GH~ardC~~~--~ 80 (269)
+++|+=+++|.+++||+.+....... |.|-.....-+...-.. .-.+-..-.....|.+||..+|-..+|+.. .
T Consensus 206 H~~Isadt~eki~~Ai~vienli~~a--v~~~e~~n~l~~~Qlrela~lNgt~r~~d~~~c~~cg~~~H~q~~cp~r~~~ 283 (554)
T KOG0119|consen 206 HCLISADTQEKIKKAIAVIENLIQSA--VSVPEGQNDLKRLQLRELARLNGTLRDDDNRACRNCGSTGHKQYDCPGRIPN 283 (554)
T ss_pred eEEEecchHHHHHHHHHHHHHHHHhh--ccCccccccccHHHHHHHHHhCCCCCccccccccccCCCccccccCCccccc
Confidence 78999999999999997776533221 11111110000000000 000001111225899999999999999976 2
Q ss_pred CCcccccCCCCCcccccCCCC
Q 024281 81 WKNKCYRCGERGHIERNCQNS 101 (269)
Q Consensus 81 ~k~~CyrCG~~Gh~~r~c~~~ 101 (269)
+..+|+.|+..||+..+|+..
T Consensus 284 ~~n~c~~cg~~gH~~~dc~~~ 304 (554)
T KOG0119|consen 284 TTNVCKICGPLGHISIDCKVN 304 (554)
T ss_pred ccccccccCCcccccccCCCc
Confidence 456999999999999999875
No 69
>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=95.99 E-value=0.011 Score=44.71 Aligned_cols=38 Identities=29% Similarity=0.455 Sum_probs=29.7
Q ss_pred CCCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEec
Q 024281 2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR 39 (269)
Q Consensus 2 krGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~ 39 (269)
..+-|+|-|.+.+.|+.|.+.|+|.++.|..|.|.|..
T Consensus 38 ~~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~~~ 75 (90)
T PF11608_consen 38 SGGTAILRFPNQEFAERAQKRMEGEDVFGNKISVSFSP 75 (90)
T ss_dssp -TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEESS-
T ss_pred eCCEEEEEeCCHHHHHHHHHhhcccccccceEEEEEcC
Confidence 35789999999999999999999999999999999975
No 70
>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]
Probab=95.78 E-value=0.01 Score=57.04 Aligned_cols=39 Identities=33% Similarity=0.524 Sum_probs=36.0
Q ss_pred CCCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEecC
Q 024281 2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG 40 (269)
Q Consensus 2 krGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~~ 40 (269)
.+|.|+|||.++|.+++|+++|+-.+|.|+.|.|.....
T Consensus 85 ~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd~d 123 (608)
T KOG4212|consen 85 ARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKEDHD 123 (608)
T ss_pred cCCceEEEeeCHHHHHHHHHHhhhccccCceEEEeccCc
Confidence 478999999999999999999999999999999987654
No 71
>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]
Probab=95.73 E-value=0.012 Score=56.35 Aligned_cols=41 Identities=37% Similarity=0.545 Sum_probs=34.8
Q ss_pred CCCCeEEEEECCHHHHHHHHHHhCCC-eecCc--eEEEEEecCC
Q 024281 1 MKRDFAFVEFSDPRDADDARYSLNGR-DVDGS--RIIVEFARGG 41 (269)
Q Consensus 1 lkrGfgfVeF~~~~dA~~Ai~~ldG~-~l~Gr--~I~Ve~a~~~ 41 (269)
+.+|+|||.|.+.+-|..||++|||+ .+.|. .|.|.||...
T Consensus 163 ~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVkFADtq 206 (510)
T KOG0144|consen 163 LSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVKFADTQ 206 (510)
T ss_pred cccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEEecccC
Confidence 46899999999999999999999996 45554 7999998643
No 72
>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]
Probab=95.72 E-value=0.015 Score=49.91 Aligned_cols=40 Identities=25% Similarity=0.387 Sum_probs=37.2
Q ss_pred CCCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEecCC
Q 024281 2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG 41 (269)
Q Consensus 2 krGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~~~ 41 (269)
.+|||||.|...+.++.||..|+|..|..+.|.|.++...
T Consensus 138 ~~~~g~i~~~sfeasd~ai~s~ngq~l~nr~itv~ya~k~ 177 (203)
T KOG0131|consen 138 PKGFGFINYASFEASDAAIGSMNGQYLCNRPITVSYAFKK 177 (203)
T ss_pred CCCCeEEechhHHHHHHHHHHhccchhcCCceEEEEEEec
Confidence 4689999999999999999999999999999999999744
No 73
>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]
Probab=95.67 E-value=0.061 Score=46.02 Aligned_cols=33 Identities=24% Similarity=0.214 Sum_probs=26.6
Q ss_pred EEECCHHHHHHHHHHhCCCeecCceEEEEEecCCC
Q 024281 8 VEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP 42 (269)
Q Consensus 8 VeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~~~~ 42 (269)
+.|.+++|..+|.+++.. |+|+.|.-..+....
T Consensus 49 fAFVEFed~RDA~DAvr~--LDG~~~cG~r~rVE~ 81 (195)
T KOG0107|consen 49 FAFVEFEDPRDAEDAVRY--LDGKDICGSRIRVEL 81 (195)
T ss_pred ceEEeccCcccHHHHHhh--cCCccccCceEEEEe
Confidence 478999999999999977 999998776555443
No 74
>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]
Probab=95.42 E-value=0.022 Score=56.39 Aligned_cols=41 Identities=29% Similarity=0.429 Sum_probs=37.8
Q ss_pred CCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEecCCCC
Q 024281 3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPR 43 (269)
Q Consensus 3 rGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~~~~r 43 (269)
+-||||+|.+..+|..+|.+|+-++|.|+.|.|+.++..+.
T Consensus 447 RCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEkaKNEp~ 487 (940)
T KOG4661|consen 447 RCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKAKNEPG 487 (940)
T ss_pred ceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeecccCcc
Confidence 45999999999999999999999999999999999986554
No 75
>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]
Probab=95.30 E-value=0.018 Score=51.47 Aligned_cols=39 Identities=33% Similarity=0.556 Sum_probs=36.2
Q ss_pred CCCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEecCC
Q 024281 2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG 41 (269)
Q Consensus 2 krGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~~~ 41 (269)
.+||+||+|.+.+.++.||. |||.+|.|..|.|.+.+..
T Consensus 142 ~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt~~r~~ 180 (231)
T KOG4209|consen 142 PKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVTLKRTN 180 (231)
T ss_pred cceeEEEecccHhhhHHHhh-cCCcccccccceeeeeeee
Confidence 47899999999999999998 9999999999999998755
No 76
>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]
Probab=95.09 E-value=0.014 Score=51.91 Aligned_cols=38 Identities=26% Similarity=0.365 Sum_probs=32.6
Q ss_pred CCCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEecC
Q 024281 2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG 40 (269)
Q Consensus 2 krGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~~ 40 (269)
.||||||+|.|.+.|..|++..+- .|+|++..+.+|.-
T Consensus 53 skGyGfVTf~d~~aa~rAc~dp~p-iIdGR~aNcnlA~l 90 (247)
T KOG0149|consen 53 SKGYGFVTFRDAEAATRACKDPNP-IIDGRKANCNLASL 90 (247)
T ss_pred ccceeeEEeecHHHHHHHhcCCCC-cccccccccchhhh
Confidence 589999999999999999987765 58999988887753
No 77
>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]
Probab=95.00 E-value=0.03 Score=50.70 Aligned_cols=40 Identities=33% Similarity=0.595 Sum_probs=35.4
Q ss_pred CCCCeEEEEECCHHHHHHHHHHhCCCeecCc--eEEEEEecC
Q 024281 1 MKRDFAFVEFSDPRDADDARYSLNGRDVDGS--RIIVEFARG 40 (269)
Q Consensus 1 lkrGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr--~I~Ve~a~~ 40 (269)
+.+|.|||-|....+|+.||+.|||..--|. .|.|.|+..
T Consensus 167 ~srGVgFiRFDKr~EAe~AIk~lNG~~P~g~tepItVKFann 208 (360)
T KOG0145|consen 167 LSRGVGFIRFDKRIEAEEAIKGLNGQKPSGCTEPITVKFANN 208 (360)
T ss_pred eecceeEEEecchhHHHHHHHhccCCCCCCCCCCeEEEecCC
Confidence 4689999999999999999999999887664 799999864
No 78
>KOG0226 consensus RNA-binding proteins [General function prediction only]
Probab=94.85 E-value=0.018 Score=51.88 Aligned_cols=37 Identities=30% Similarity=0.486 Sum_probs=33.0
Q ss_pred CCCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEe
Q 024281 2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA 38 (269)
Q Consensus 2 krGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a 38 (269)
.+|||||.|.+..|+..|+..|||..+.-+.|.+.-.
T Consensus 231 SkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRkS 267 (290)
T KOG0226|consen 231 SKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRKS 267 (290)
T ss_pred cccceeeeecCHHHHHHHHHhhcccccccchhHhhhh
Confidence 4799999999999999999999999999888876543
No 79
>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=94.59 E-value=0.026 Score=51.08 Aligned_cols=19 Identities=53% Similarity=1.349 Sum_probs=16.2
Q ss_pred cccccCCCCCcccccCCCC
Q 024281 83 NKCYRCGERGHIERNCQNS 101 (269)
Q Consensus 83 ~~CyrCG~~Gh~~r~c~~~ 101 (269)
..||.||+.||+..+|++.
T Consensus 144 ~~Cy~Cg~~GH~s~~C~~~ 162 (261)
T KOG4400|consen 144 AKCYSCGEQGHISDDCPEN 162 (261)
T ss_pred CccCCCCcCCcchhhCCCC
Confidence 3599999999999999965
No 80
>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]
Probab=94.54 E-value=0.025 Score=53.34 Aligned_cols=38 Identities=21% Similarity=0.358 Sum_probs=35.1
Q ss_pred CCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEecC
Q 024281 3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG 40 (269)
Q Consensus 3 rGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~~ 40 (269)
+|||||||.+.....+||..||-+.|.|..|+|-.+..
T Consensus 252 kGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk~vT 289 (544)
T KOG0124|consen 252 KGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVT 289 (544)
T ss_pred cceeeEEeccccchHHHhhhcchhhcccceEecccccC
Confidence 79999999999999999999999999999999976653
No 81
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=94.52 E-value=0.029 Score=34.67 Aligned_cols=22 Identities=41% Similarity=1.103 Sum_probs=15.5
Q ss_pred CCCCCcccCCCCCCCCCcccCC
Q 024281 58 PGSGRCFNCGIDGHWARDCKAG 79 (269)
Q Consensus 58 ~~~~rc~~cG~~GH~ardC~~~ 79 (269)
.....|+.|+..|||..+||..
T Consensus 6 P~~Y~C~~C~~~GH~i~dCP~~ 27 (32)
T PF13696_consen 6 PPGYVCHRCGQKGHWIQDCPTN 27 (32)
T ss_pred CCCCEeecCCCCCccHhHCCCC
Confidence 3456777777777777777764
No 82
>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]
Probab=94.18 E-value=0.049 Score=48.10 Aligned_cols=41 Identities=27% Similarity=0.410 Sum_probs=37.7
Q ss_pred CCCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEecCCC
Q 024281 2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP 42 (269)
Q Consensus 2 krGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~~~~ 42 (269)
.+|-|||.|.+.+.|-.|+.+|+|.-|.|+.|+|.+|+...
T Consensus 51 mRGQA~VvFk~~~~As~A~r~l~gfpFygK~mriqyA~s~s 91 (221)
T KOG4206|consen 51 MRGQAFVVFKETEAASAALRALQGFPFYGKPMRIQYAKSDS 91 (221)
T ss_pred ccCceEEEecChhHHHHHHHHhcCCcccCchhheecccCcc
Confidence 36889999999999999999999999999999999998653
No 83
>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]
Probab=94.02 E-value=0.057 Score=53.18 Aligned_cols=36 Identities=22% Similarity=0.318 Sum_probs=34.3
Q ss_pred CeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEec
Q 024281 4 DFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR 39 (269)
Q Consensus 4 GfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~ 39 (269)
|+.||-|++.++|..|+.+|+|.+|.|+.|...|..
T Consensus 491 g~VYvrc~s~~~A~~a~~alhgrWF~gr~Ita~~~~ 526 (549)
T KOG0147|consen 491 GCVYVRCPSAEAAGTAVKALHGRWFAGRMITAKYLP 526 (549)
T ss_pred ceEEEecCcHHHHHHHHHHHhhhhhccceeEEEEee
Confidence 899999999999999999999999999999998875
No 84
>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]
Probab=93.58 E-value=1.5 Score=38.76 Aligned_cols=23 Identities=39% Similarity=0.538 Sum_probs=18.0
Q ss_pred EEEEECCHHHHHHHHHH--hCCCee
Q 024281 6 AFVEFSDPRDADDARYS--LNGRDV 28 (269)
Q Consensus 6 gfVeF~~~~dA~~Ai~~--ldG~~l 28 (269)
-|-.-.+++||.+||+. |||.+|
T Consensus 61 rf~~k~daedA~damDG~~ldgRel 85 (256)
T KOG4207|consen 61 RFHDKRDAEDALDAMDGAVLDGREL 85 (256)
T ss_pred EeeecchHHHHHHhhcceeecccee
Confidence 36667788888888865 888888
No 85
>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]
Probab=93.38 E-value=0.18 Score=48.92 Aligned_cols=40 Identities=33% Similarity=0.482 Sum_probs=34.5
Q ss_pred CeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEecCCCCC
Q 024281 4 DFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPRG 44 (269)
Q Consensus 4 GfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~~~~rg 44 (269)
+||||+|++...++.||.+- -..|.+++|.|+..+....+
T Consensus 331 ~fgFV~f~~~~~~~~~i~As-p~~ig~~kl~Veek~~~~~g 370 (419)
T KOG0116|consen 331 CFGFVEFENAAAVQNAIEAS-PLEIGGRKLNVEEKRPGFRG 370 (419)
T ss_pred ceEEEEEeecchhhhhhhcC-ccccCCeeEEEEeccccccc
Confidence 79999999999999999776 77889999999998765443
No 86
>PF03880 DbpA: DbpA RNA binding domain ; InterPro: IPR005580 This RNA binding domain is found at the C terminus of a number of DEAD helicase proteins [].; PDB: 2G0C_A 3MOJ_B.
Probab=93.34 E-value=0.097 Score=38.21 Aligned_cols=36 Identities=33% Similarity=0.555 Sum_probs=22.1
Q ss_pred CCCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEe
Q 024281 2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA 38 (269)
Q Consensus 2 krGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a 38 (269)
...|+||+.... .|+++|.+|++..+.|+.|.|+.|
T Consensus 39 ~~~~S~vev~~~-~a~~v~~~l~~~~~~gk~v~ve~A 74 (74)
T PF03880_consen 39 FDNFSFVEVPEE-VAEKVLEALNGKKIKGKKVRVERA 74 (74)
T ss_dssp -SS-EEEEE-TT--HHHHHHHHTT--SSS----EEE-
T ss_pred eeeEEEEEECHH-HHHHHHHHhcCCCCCCeeEEEEEC
Confidence 456899998654 799999999999999999999875
No 87
>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=93.27 E-value=0.13 Score=39.82 Aligned_cols=38 Identities=26% Similarity=0.389 Sum_probs=31.4
Q ss_pred CCeEEEEECCHHHHHHHHHHhCCCeec----CceEEEEEecC
Q 024281 3 RDFAFVEFSDPRDADDARYSLNGRDVD----GSRIIVEFARG 40 (269)
Q Consensus 3 rGfgfVeF~~~~dA~~Ai~~ldG~~l~----Gr~I~Ve~a~~ 40 (269)
.|||||.|.++++|..-++.++|..+. .+...|.+|+-
T Consensus 45 ~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~Kvc~i~yAri 86 (97)
T PF04059_consen 45 LGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKKVCEISYARI 86 (97)
T ss_pred eEEEEEEcCCHHHHHHHHHHHcCCccccCCCCcEEEEehhHh
Confidence 489999999999999999999998775 44566666653
No 88
>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]
Probab=93.20 E-value=0.15 Score=47.79 Aligned_cols=40 Identities=23% Similarity=0.391 Sum_probs=35.6
Q ss_pred CCCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEecCC
Q 024281 2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG 41 (269)
Q Consensus 2 krGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~~~ 41 (269)
..|.+.|.|.+.++|+.||..|+|..|+|+.|..++--+.
T Consensus 313 PdGvvtV~f~n~eeA~~ciq~m~GR~fdgRql~A~i~DG~ 352 (382)
T KOG1548|consen 313 PDGVVTVSFRNNEEADQCIQTMDGRWFDGRQLTASIWDGK 352 (382)
T ss_pred CCceeEEEeCChHHHHHHHHHhcCeeecceEEEEEEeCCc
Confidence 4588999999999999999999999999999988876543
No 89
>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]
Probab=92.55 E-value=0.16 Score=52.17 Aligned_cols=40 Identities=28% Similarity=0.404 Sum_probs=37.1
Q ss_pred CCCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEecCC
Q 024281 2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG 41 (269)
Q Consensus 2 krGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~~~ 41 (269)
.+|.|||.|....||++||.+|....|.++.|+|.|+.+.
T Consensus 456 ~R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g~ 495 (894)
T KOG0132|consen 456 PRGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVGK 495 (894)
T ss_pred CCceeEEEEeehhHHHHHHHHHhcccccceeeEEeeeccC
Confidence 4689999999999999999999999999999999999753
No 90
>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]
Probab=92.49 E-value=0.083 Score=47.58 Aligned_cols=38 Identities=29% Similarity=0.337 Sum_probs=34.7
Q ss_pred CCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEecC
Q 024281 3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG 40 (269)
Q Consensus 3 rGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~~ 40 (269)
.|-++|.|...++|+.|+..||+.+|.|+.|..++...
T Consensus 110 ~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~pv 147 (260)
T KOG2202|consen 110 VGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSPV 147 (260)
T ss_pred hhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecCc
Confidence 35689999999999999999999999999999998764
No 91
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=92.36 E-value=0.075 Score=34.91 Aligned_cols=19 Identities=42% Similarity=1.165 Sum_probs=14.3
Q ss_pred CCCcccCCCCCCCCCcccC
Q 024281 60 SGRCFNCGIDGHWARDCKA 78 (269)
Q Consensus 60 ~~rc~~cG~~GH~ardC~~ 78 (269)
...|.+|+..|||..+|+.
T Consensus 4 ~~~CqkC~~~GH~tyeC~~ 22 (42)
T PF13917_consen 4 RVRCQKCGQKGHWTYECPN 22 (42)
T ss_pred CCcCcccCCCCcchhhCCC
Confidence 3568888888888888774
No 92
>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]
Probab=90.79 E-value=0.2 Score=49.71 Aligned_cols=35 Identities=37% Similarity=0.657 Sum_probs=29.7
Q ss_pred CCeEEEEECCHHHHHHHHHHhCCCeecCc-eEEEEE
Q 024281 3 RDFAFVEFSDPRDADDARYSLNGRDVDGS-RIIVEF 37 (269)
Q Consensus 3 rGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr-~I~Ve~ 37 (269)
+||.|++|.+..+|+.||+.|||..|+-. ++.|..
T Consensus 105 kG~lf~E~~~~~~A~~aVK~l~G~~ldknHtf~v~~ 140 (698)
T KOG2314|consen 105 KGYLFVEYASMRDAKKAVKSLNGKRLDKNHTFFVRL 140 (698)
T ss_pred eeEEEEEecChhhHHHHHHhcccceecccceEEeeh
Confidence 69999999999999999999999988754 455543
No 93
>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=90.12 E-value=0.35 Score=45.39 Aligned_cols=39 Identities=26% Similarity=0.475 Sum_probs=33.3
Q ss_pred CCCeEEEEECCHHHHHHHHHH-hCCCeecCceEEEEEecC
Q 024281 2 KRDFAFVEFSDPRDADDARYS-LNGRDVDGSRIIVEFARG 40 (269)
Q Consensus 2 krGfgfVeF~~~~dA~~Ai~~-ldG~~l~Gr~I~Ve~a~~ 40 (269)
.++.|||+|...+.|+.|..+ ++-..|+|.+|.|.|..+
T Consensus 263 ~~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~Wg~~ 302 (377)
T KOG0153|consen 263 RKGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKWGRP 302 (377)
T ss_pred ccccceeeehhhHHHHHHHHhhcceeeecceEEEEEeCCC
Confidence 356899999999999998866 555678999999999887
No 94
>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]
Probab=90.00 E-value=0.16 Score=50.24 Aligned_cols=33 Identities=52% Similarity=0.756 Sum_probs=31.3
Q ss_pred CCCeEEEEECCHHHHHHHHHHhCCCeecCceEE
Q 024281 2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRII 34 (269)
Q Consensus 2 krGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~ 34 (269)
++|..||+|.|..+|+.|+++|++.+|.|+.|.
T Consensus 111 ~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k 143 (549)
T KOG4660|consen 111 KRGIVFVEFYDVRDAERALKALNRREIAGKRIK 143 (549)
T ss_pred cCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence 578999999999999999999999999999987
No 95
>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]
Probab=89.66 E-value=0.19 Score=47.23 Aligned_cols=40 Identities=30% Similarity=0.362 Sum_probs=36.7
Q ss_pred CCCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEecCC
Q 024281 2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG 41 (269)
Q Consensus 2 krGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~~~ 41 (269)
.||.|.|.|++...|+.||..+++..|.+..|.|.+|...
T Consensus 115 ~KGeatvS~~D~~~akaai~~~agkdf~gn~ikvs~a~~r 154 (351)
T KOG1995|consen 115 PKGEATVSYEDPPAAKAAIEWFAGKDFCGNTIKVSLAERR 154 (351)
T ss_pred cCCceeeeecChhhhhhhhhhhccccccCCCchhhhhhhc
Confidence 4789999999999999999999999999999999888643
No 96
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=89.52 E-value=0.29 Score=30.23 Aligned_cols=21 Identities=33% Similarity=0.822 Sum_probs=18.6
Q ss_pred CCcccccCCCCCcccccCCCC
Q 024281 81 WKNKCYRCGERGHIERNCQNS 101 (269)
Q Consensus 81 ~k~~CyrCG~~Gh~~r~c~~~ 101 (269)
....|+.|+..||+..+|+..
T Consensus 7 ~~Y~C~~C~~~GH~i~dCP~~ 27 (32)
T PF13696_consen 7 PGYVCHRCGQKGHWIQDCPTN 27 (32)
T ss_pred CCCEeecCCCCCccHhHCCCC
Confidence 357899999999999999974
No 97
>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]
Probab=89.37 E-value=0.19 Score=49.55 Aligned_cols=41 Identities=34% Similarity=0.582 Sum_probs=37.6
Q ss_pred CCCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEecCCC
Q 024281 2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGP 42 (269)
Q Consensus 2 krGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~~~~ 42 (269)
-+||||.+|.++...+.||.+|||..|.+..|.|..|....
T Consensus 330 skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~~g~ 370 (500)
T KOG0120|consen 330 SKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAIVGA 370 (500)
T ss_pred ccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhhccc
Confidence 47999999999999999999999999999999999987543
No 98
>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]
Probab=89.36 E-value=0.97 Score=39.25 Aligned_cols=28 Identities=18% Similarity=0.254 Sum_probs=25.3
Q ss_pred CCCeEEEEECCHHHHHHHHHHhCCCeec
Q 024281 2 KRDFAFVEFSDPRDADDARYSLNGRDVD 29 (269)
Q Consensus 2 krGfgfVeF~~~~dA~~Ai~~ldG~~l~ 29 (269)
+-|+|+|+|...+||+.||.+|+.+.+.
T Consensus 149 rDg~GvV~~~r~eDMkYAvr~ld~~~~~ 176 (241)
T KOG0105|consen 149 RDGVGVVEYLRKEDMKYAVRKLDDQKFR 176 (241)
T ss_pred cccceeeeeeehhhHHHHHHhhcccccc
Confidence 4589999999999999999999998774
No 99
>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]
Probab=89.25 E-value=0.2 Score=44.38 Aligned_cols=37 Identities=24% Similarity=0.313 Sum_probs=34.0
Q ss_pred eEEEEECCHHHHHHHHHHhCCCeecCceEEEEEecCC
Q 024281 5 FAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG 41 (269)
Q Consensus 5 fgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~~~ 41 (269)
||||+|+++.....|+.-|||..|.+..|.|.+-.+.
T Consensus 51 Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r~G~ 87 (267)
T KOG4454|consen 51 FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLRCGN 87 (267)
T ss_pred eeeeecccccchhhhhhhcccchhccchhhcccccCC
Confidence 9999999999999999999999999999988876654
No 100
>smart00343 ZnF_C2HC zinc finger.
Probab=89.20 E-value=0.2 Score=28.97 Aligned_cols=16 Identities=63% Similarity=1.566 Sum_probs=12.6
Q ss_pred CcccCCCCCCCCCccc
Q 024281 62 RCFNCGIDGHWARDCK 77 (269)
Q Consensus 62 rc~~cG~~GH~ardC~ 77 (269)
.|+.||..+|++.+|+
T Consensus 1 ~C~~CG~~GH~~~~C~ 16 (26)
T smart00343 1 KCYNCGKEGHIARDCP 16 (26)
T ss_pred CCccCCCCCcchhhCC
Confidence 4788888888888876
No 101
>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]
Probab=89.08 E-value=0.6 Score=42.11 Aligned_cols=38 Identities=29% Similarity=0.344 Sum_probs=34.5
Q ss_pred CCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEecC
Q 024281 3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG 40 (269)
Q Consensus 3 rGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~~ 40 (269)
.|.|-|.|...+||+.||+.++|+.|+|..|.|+....
T Consensus 124 ~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i~~ 161 (243)
T KOG0533|consen 124 LGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEIISS 161 (243)
T ss_pred CccceeeecchHhHHHHHHHhcCcccCCceeeeEEecC
Confidence 47899999999999999999999999999999987653
No 102
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=88.86 E-value=0.26 Score=31.18 Aligned_cols=19 Identities=42% Similarity=1.097 Sum_probs=11.6
Q ss_pred CCcccCCCCCCCCCcccCC
Q 024281 61 GRCFNCGIDGHWARDCKAG 79 (269)
Q Consensus 61 ~rc~~cG~~GH~ardC~~~ 79 (269)
..|++|++..||+.+|...
T Consensus 3 ~~CprC~kg~Hwa~~C~sk 21 (36)
T PF14787_consen 3 GLCPRCGKGFHWASECRSK 21 (36)
T ss_dssp -C-TTTSSSCS-TTT---T
T ss_pred ccCcccCCCcchhhhhhhh
Confidence 4799999999999999864
No 103
>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]
Probab=88.32 E-value=0.57 Score=44.59 Aligned_cols=37 Identities=32% Similarity=0.479 Sum_probs=32.2
Q ss_pred eEEEEECCHHHHHHHHHHhCCCeecC--ceEEEEEecCC
Q 024281 5 FAFVEFSDPRDADDARYSLNGRDVDG--SRIIVEFARGG 41 (269)
Q Consensus 5 fgfVeF~~~~dA~~Ai~~ldG~~l~G--r~I~Ve~a~~~ 41 (269)
-|+|||+..+-|+.|..+|||.+|.- ..|+||+|+..
T Consensus 161 QAmVEFdsv~~AqrAk~alNGADIYsGCCTLKIeyAkP~ 199 (494)
T KOG1456|consen 161 QAMVEFDSVEVAQRAKAALNGADIYSGCCTLKIEYAKPT 199 (494)
T ss_pred eeEEeechhHHHHHHHhhcccccccccceeEEEEecCcc
Confidence 38999999999999999999998853 48999999853
No 104
>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]
Probab=85.90 E-value=1.2 Score=42.97 Aligned_cols=39 Identities=28% Similarity=0.447 Sum_probs=35.5
Q ss_pred CCCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEecC
Q 024281 2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG 40 (269)
Q Consensus 2 krGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~~ 40 (269)
|+--|+|+|.|...|+-|+.+|+|..|.|+.|+|.+.+-
T Consensus 334 kkd~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SKH 372 (492)
T KOG1190|consen 334 KKDNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSKH 372 (492)
T ss_pred CCcceeeeecchhHHHHHHHHhhcceecCceEEEeeccC
Confidence 345699999999999999999999999999999999873
No 105
>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]
Probab=84.71 E-value=1.1 Score=43.29 Aligned_cols=40 Identities=25% Similarity=0.523 Sum_probs=31.9
Q ss_pred CCCeEEEEECCHHHHHHHHHHhCCC-eecCc--eEEEEEecCC
Q 024281 2 KRDFAFVEFSDPRDADDARYSLNGR-DVDGS--RIIVEFARGG 41 (269)
Q Consensus 2 krGfgfVeF~~~~dA~~Ai~~ldG~-~l~Gr--~I~Ve~a~~~ 41 (269)
.+|++||.|...+||.+||.+|+.. .|-|- .|.|.+|.+.
T Consensus 75 s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqvk~Ad~E 117 (510)
T KOG0144|consen 75 SKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQVKYADGE 117 (510)
T ss_pred ccceEEEEeccHHHHHHHHHHhhcccccCCCCcceeecccchh
Confidence 4799999999999999999999985 45454 5667776544
No 106
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=84.66 E-value=1.2 Score=42.02 Aligned_cols=33 Identities=18% Similarity=0.417 Sum_probs=30.4
Q ss_pred EEEECCHHHHHHHHHHhCCCeecCceEEEEEec
Q 024281 7 FVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR 39 (269)
Q Consensus 7 fVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~ 39 (269)
||+|...+||+.||..+||..++|+.|+..+..
T Consensus 169 YITy~~kedAarcIa~vDgs~~DGr~lkatYGT 201 (480)
T COG5175 169 YITYSTKEDAARCIAEVDGSLLDGRVLKATYGT 201 (480)
T ss_pred EEEecchHHHHHHHHHhccccccCceEeeecCc
Confidence 999999999999999999999999998877643
No 107
>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]
Probab=84.10 E-value=1.7 Score=41.49 Aligned_cols=39 Identities=26% Similarity=0.278 Sum_probs=35.9
Q ss_pred CCCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEecC
Q 024281 2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG 40 (269)
Q Consensus 2 krGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~~ 40 (269)
|-|-|+||+-+....+.||.+|++..|-|.+|.|.+.+.
T Consensus 324 k~gtamVemgd~~aver~v~hLnn~~lfG~kl~v~~SkQ 362 (494)
T KOG1456|consen 324 KPGTAMVEMGDAYAVERAVTHLNNIPLFGGKLNVCVSKQ 362 (494)
T ss_pred ccceeEEEcCcHHHHHHHHHHhccCccccceEEEeeccc
Confidence 568899999999999999999999999999999988764
No 108
>PF11767 SET_assoc: Histone lysine methyltransferase SET associated; InterPro: IPR024636 The SET domain is a protein-protein interaction domain found in protein lysine methyltransferase enzymes. This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].
Probab=83.83 E-value=1.5 Score=31.55 Aligned_cols=30 Identities=20% Similarity=0.346 Sum_probs=27.0
Q ss_pred EEEECCHHHHHHHHHHhCCCeecCceEEEE
Q 024281 7 FVEFSDPRDADDARYSLNGRDVDGSRIIVE 36 (269)
Q Consensus 7 fVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve 36 (269)
||.|.+..+|+.++...||+.|...+|.++
T Consensus 37 YIvF~~~~Ea~rC~~~~~~~~~f~y~m~M~ 66 (66)
T PF11767_consen 37 YIVFNDSKEAERCFRAEDGTLFFTYRMQME 66 (66)
T ss_pred EEEECChHHHHHHHHhcCCCEEEEEEEEeC
Confidence 799999999999999999999988877653
No 109
>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]
Probab=83.20 E-value=1.6 Score=40.01 Aligned_cols=39 Identities=33% Similarity=0.589 Sum_probs=32.0
Q ss_pred CCCeEEEEECCHHHHHHHHHHhCCCe-ecCc--eEEEEEecC
Q 024281 2 KRDFAFVEFSDPRDADDARYSLNGRD-VDGS--RIIVEFARG 40 (269)
Q Consensus 2 krGfgfVeF~~~~dA~~Ai~~ldG~~-l~Gr--~I~Ve~a~~ 40 (269)
.||.|||.|....||..||..|+|.. +-|. -|.|.|+-.
T Consensus 59 sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLVVK~ADT 100 (371)
T KOG0146|consen 59 SKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVVKFADT 100 (371)
T ss_pred CCCceEEEeccchHHHHHHHHhcccccCCCCccceEEEeccc
Confidence 47999999999999999999999964 4343 577888754
No 110
>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]
Probab=83.17 E-value=1.2 Score=41.88 Aligned_cols=42 Identities=17% Similarity=0.148 Sum_probs=38.1
Q ss_pred CCCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEecCCCC
Q 024281 2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPR 43 (269)
Q Consensus 2 krGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~~~~r 43 (269)
.+|-|+|.|--.+.++-||..||+..|.|..|+|+.|+-..+
T Consensus 182 lKGDaLc~y~K~ESVeLA~~ilDe~~~rg~~~rVerAkfq~K 223 (382)
T KOG1548|consen 182 LKGDALCCYIKRESVELAIKILDEDELRGKKLRVERAKFQMK 223 (382)
T ss_pred ccCceEEEeecccHHHHHHHHhCcccccCcEEEEehhhhhhc
Confidence 368899999999999999999999999999999999986544
No 111
>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function. ; PDB: 1UFW_A 2DNR_A.
Probab=82.49 E-value=2.3 Score=35.38 Aligned_cols=33 Identities=30% Similarity=0.479 Sum_probs=28.4
Q ss_pred EEEEECCHHHHHHHHHHhCCCeecCceEEEEEec
Q 024281 6 AFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR 39 (269)
Q Consensus 6 gfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~ 39 (269)
=+|+|.+.+.|..|+ .|+|.+|.|..|.|....
T Consensus 73 mwVTF~dg~sALaal-s~dg~~v~g~~l~i~LKt 105 (146)
T PF08952_consen 73 MWVTFRDGQSALAAL-SLDGIQVNGRTLKIRLKT 105 (146)
T ss_dssp EEEEESSCHHHHHHH-HGCCSEETTEEEEEEE--
T ss_pred EEEEECccHHHHHHH-ccCCcEECCEEEEEEeCC
Confidence 479999999999988 899999999999998754
No 112
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=80.84 E-value=0.84 Score=29.95 Aligned_cols=19 Identities=37% Similarity=1.106 Sum_probs=17.2
Q ss_pred CcccccCCCCCcccccCCC
Q 024281 82 KNKCYRCGERGHIERNCQN 100 (269)
Q Consensus 82 k~~CyrCG~~Gh~~r~c~~ 100 (269)
...|.+|++.|||.+.|++
T Consensus 4 ~~~CqkC~~~GH~tyeC~~ 22 (42)
T PF13917_consen 4 RVRCQKCGQKGHWTYECPN 22 (42)
T ss_pred CCcCcccCCCCcchhhCCC
Confidence 4579999999999999995
No 113
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=80.65 E-value=0.97 Score=41.84 Aligned_cols=24 Identities=42% Similarity=1.259 Sum_probs=14.8
Q ss_pred CCCCCCCcccCCCCCCCCCcccCC
Q 024281 56 PPPGSGRCFNCGIDGHWARDCKAG 79 (269)
Q Consensus 56 ~~~~~~rc~~cG~~GH~ardC~~~ 79 (269)
++.....||.||..|||-.+|+..
T Consensus 172 ppPpgY~CyRCGqkgHwIqnCpTN 195 (427)
T COG5222 172 PPPPGYVCYRCGQKGHWIQNCPTN 195 (427)
T ss_pred CCCCceeEEecCCCCchhhcCCCC
Confidence 334445677777777777777643
No 114
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=80.36 E-value=1.7 Score=29.08 Aligned_cols=17 Identities=41% Similarity=1.032 Sum_probs=13.2
Q ss_pred CCcccCCCCCCCCCccc
Q 024281 61 GRCFNCGIDGHWARDCK 77 (269)
Q Consensus 61 ~rc~~cG~~GH~ardC~ 77 (269)
.-|++||..||...+|+
T Consensus 32 ~~C~~C~~~gH~~~~C~ 48 (49)
T PF14392_consen 32 RFCFHCGRIGHSDKECP 48 (49)
T ss_pred hhhcCCCCcCcCHhHcC
Confidence 35888888888887776
No 115
>PF08206 OB_RNB: Ribonuclease B OB domain; InterPro: IPR013223 This domain includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies.; PDB: 2ID0_D 2IX1_A 2IX0_A.
Probab=77.92 E-value=1.2 Score=30.89 Aligned_cols=37 Identities=30% Similarity=0.469 Sum_probs=21.8
Q ss_pred CCCeEEEEECC-HHHHHHHHHHhCCCeecCceEEEEEec
Q 024281 2 KRDFAFVEFSD-PRDADDARYSLNGRDVDGSRIIVEFAR 39 (269)
Q Consensus 2 krGfgfVeF~~-~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~ 39 (269)
++|||||...+ .+|.--.-..|++. |+|-.+.|....
T Consensus 7 ~~GfGFv~~~~~~~DifIp~~~l~~A-~~gD~V~v~i~~ 44 (58)
T PF08206_consen 7 PKGFGFVIPDDGGEDIFIPPRNLNGA-MDGDKVLVRITP 44 (58)
T ss_dssp SSS-EEEEECT-TEEEEE-HHHHTTS--TT-EEEEEEEE
T ss_pred cCCCEEEEECCCCCCEEECHHHHCCC-CCCCEEEEEEec
Confidence 68999999998 44443344556554 556666776665
No 116
>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]
Probab=73.56 E-value=3.5 Score=40.51 Aligned_cols=37 Identities=24% Similarity=0.211 Sum_probs=28.4
Q ss_pred CCCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEec
Q 024281 2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR 39 (269)
Q Consensus 2 krGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~ 39 (269)
..|.|||||...+|++.|++ +|-..|..+-|.|..+.
T Consensus 48 ~sGeA~Ve~~seedv~~Alk-kdR~~mg~RYIEVf~~~ 84 (510)
T KOG4211|consen 48 PSGEAYVEFTSEEDVEKALK-KDRESMGHRYIEVFTAG 84 (510)
T ss_pred cCcceEEEeechHHHHHHHH-hhHHHhCCceEEEEccC
Confidence 35899999999999999994 45555666677776653
No 117
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=71.83 E-value=2.5 Score=40.95 Aligned_cols=39 Identities=33% Similarity=0.531 Sum_probs=35.1
Q ss_pred CCCCeEEEEECCHHHHHHHHHHhCCC-eecCceEEEEEec
Q 024281 1 MKRDFAFVEFSDPRDADDARYSLNGR-DVDGSRIIVEFAR 39 (269)
Q Consensus 1 lkrGfgfVeF~~~~dA~~Ai~~ldG~-~l~Gr~I~Ve~a~ 39 (269)
|+.||+||.+.+..-|.+||+.|+|. +|.|+++.|+...
T Consensus 35 ~k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv 74 (584)
T KOG2193|consen 35 VKSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSV 74 (584)
T ss_pred eecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchh
Confidence 57899999999999999999999994 7889999888765
No 118
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=71.31 E-value=2.5 Score=27.41 Aligned_cols=19 Identities=37% Similarity=0.768 Sum_probs=15.1
Q ss_pred CCcccCCCCCCCC--CcccCC
Q 024281 61 GRCFNCGIDGHWA--RDCKAG 79 (269)
Q Consensus 61 ~rc~~cG~~GH~a--rdC~~~ 79 (269)
.+|.+||..||+. +.||..
T Consensus 2 ~kC~~CG~~GH~~t~k~CP~~ 22 (40)
T PF15288_consen 2 VKCKNCGAFGHMRTNKRCPMY 22 (40)
T ss_pred ccccccccccccccCccCCCC
Confidence 5799999999986 667754
No 119
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=70.26 E-value=2.2 Score=39.59 Aligned_cols=21 Identities=43% Similarity=1.005 Sum_probs=18.3
Q ss_pred CCcccccCCCCCcccccCCCC
Q 024281 81 WKNKCYRCGERGHIERNCQNS 101 (269)
Q Consensus 81 ~k~~CyrCG~~Gh~~r~c~~~ 101 (269)
....||+||..|||...|+..
T Consensus 175 pgY~CyRCGqkgHwIqnCpTN 195 (427)
T COG5222 175 PGYVCYRCGQKGHWIQNCPTN 195 (427)
T ss_pred CceeEEecCCCCchhhcCCCC
Confidence 356899999999999999864
No 120
>PF04847 Calcipressin: Calcipressin; InterPro: IPR006931 Calcipressin 1 negatively regulates calcineurin (IPR015757 from INTERPRO) by direct binding and is essential for the survival of T helper type 1 cells. Calcipressin 1 is a phosphoprotein that increases its capacity to inhibit calcineurin when phosphorylated at the FLISPP motif, and this phosphorylation also controls the half-life of calcipressin 1 by accelerating its degradation []. Calcineurin is a calcium-responsive enzyme that dephosphorylates the nuclear factor of activated T cells (NFAT). In so doing it promotes its nuclear translocation and uniquely links calcium signalling to transcriptional regulation []. Calcipressins are a family of proteins derived from three genes. Calcipressin 1 is also known as modulatory calcineurin-interacting protein 1 (MCIP1), Adapt78 and Down syndrome critical region 1 (DSCR1). Calcipressin 2 is variously known as MCIP2, ZAKI-4 and DSCR1-like 1. Calcipressin 3 is also called MCIP3 and DSCR1-like 2 []. DSCR1 (Adapt78) is associated with successful adaptation to oxidative stress and calcium stress as well as with diseases like Alzheimer's and Down syndrome. The DSCR1 (Adapt78) isoform 1 protein, calcipressin 1, inhibits calcineurin and protects against acute calcium-mediated stress damage, including transient oxidative stress []. Calcipressin 1 is encoded by DSCR1, a gene on human chromosome 21. Calcipressin 1 isoform 1 has an N-terminal coding region, which generates a new polypeptide of 252 amino acids. Endogenous calcipressin 1 exists as a complex together with the calcineurin A and B heterodimer []. ; GO: 0019722 calcium-mediated signaling; PDB: 1WEY_A.
Probab=69.94 E-value=5.5 Score=34.40 Aligned_cols=36 Identities=33% Similarity=0.493 Sum_probs=28.1
Q ss_pred EEEEECCHHHHHHHHHHhC--CCeecCceEEEEEecCC
Q 024281 6 AFVEFSDPRDADDARYSLN--GRDVDGSRIIVEFARGG 41 (269)
Q Consensus 6 gfVeF~~~~dA~~Ai~~ld--G~~l~Gr~I~Ve~a~~~ 41 (269)
.+|.|.+.++|..|...|+ +..|.|..|+|.|+...
T Consensus 34 i~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~~ 71 (184)
T PF04847_consen 34 IRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQPT 71 (184)
T ss_dssp EEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----S
T ss_pred EEEEeCCHHHHHHHHHHhcccccccCCCceEEEEcccc
Confidence 5899999999999999999 99999999999998643
No 121
>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]
Probab=67.28 E-value=2.1 Score=39.96 Aligned_cols=38 Identities=26% Similarity=0.432 Sum_probs=27.7
Q ss_pred CCCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEecC
Q 024281 2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG 40 (269)
Q Consensus 2 krGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~~ 40 (269)
++||+||+|++.+....+|. ..-..|+|+.|-+..|..
T Consensus 47 srgFgfv~f~~~~~v~~vl~-~~~h~~dgr~ve~k~av~ 84 (311)
T KOG4205|consen 47 SRGFGFVTFATPEGVDAVLN-ARTHKLDGRSVEPKRAVS 84 (311)
T ss_pred cccccceecCCCcchheeec-ccccccCCccccceeccC
Confidence 46999999998887777763 334467888877766654
No 122
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=65.93 E-value=3.6 Score=26.06 Aligned_cols=20 Identities=30% Similarity=0.725 Sum_probs=12.4
Q ss_pred cccccCCCCCcccccCCCCC
Q 024281 83 NKCYRCGERGHIERNCQNSP 102 (269)
Q Consensus 83 ~~CyrCG~~Gh~~r~c~~~~ 102 (269)
..|.+|++..|++.+|....
T Consensus 3 ~~CprC~kg~Hwa~~C~sk~ 22 (36)
T PF14787_consen 3 GLCPRCGKGFHWASECRSKT 22 (36)
T ss_dssp -C-TTTSSSCS-TTT---TC
T ss_pred ccCcccCCCcchhhhhhhhh
Confidence 57999999999999998643
No 123
>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]
Probab=65.62 E-value=3.5 Score=38.56 Aligned_cols=38 Identities=26% Similarity=0.387 Sum_probs=29.7
Q ss_pred CCCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEecC
Q 024281 2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARG 40 (269)
Q Consensus 2 krGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~~ 40 (269)
.+|||||.|.+.+.++.++ .+.-.+|+|+.+.|..|..
T Consensus 138 ~rgFgfv~~~~e~sVdkv~-~~~f~~~~gk~vevkrA~p 175 (311)
T KOG4205|consen 138 PRGFGFVTFDSEDSVDKVT-LQKFHDFNGKKVEVKRAIP 175 (311)
T ss_pred cccceeeEeccccccceec-ccceeeecCceeeEeeccc
Confidence 5799999998877777665 4556788998888877763
No 124
>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=65.37 E-value=5.1 Score=31.26 Aligned_cols=35 Identities=23% Similarity=0.415 Sum_probs=21.6
Q ss_pred eEEEEECCHHHHHHHHHHhCCC-----eecCceEEEEEec
Q 024281 5 FAFVEFSDPRDADDARYSLNGR-----DVDGSRIIVEFAR 39 (269)
Q Consensus 5 fgfVeF~~~~dA~~Ai~~ldG~-----~l~Gr~I~Ve~a~ 39 (269)
.|||-|.+.++|+.|+.+|... .|.+..+.++...
T Consensus 39 ~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~vLe 78 (105)
T PF08777_consen 39 EGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLEVLE 78 (105)
T ss_dssp EEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE---
T ss_pred EEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEEECC
Confidence 6999999999999999876443 5666666666543
No 125
>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=64.55 E-value=16 Score=28.39 Aligned_cols=35 Identities=23% Similarity=0.405 Sum_probs=27.5
Q ss_pred CCeEEEEECCHHHHHHHHHHhCCCeecCceEE-EEEe
Q 024281 3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRII-VEFA 38 (269)
Q Consensus 3 rGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~-Ve~a 38 (269)
.++-.|.|.+..+|.+|| ..||..|.|..|. |.+.
T Consensus 54 ~NWi~I~Y~~~~~A~rAL-~~NG~i~~g~~mvGV~~~ 89 (100)
T PF05172_consen 54 GNWIHITYDNPLSAQRAL-QKNGTIFSGSLMVGVKPC 89 (100)
T ss_dssp TTEEEEEESSHHHHHHHH-TTTTEEETTCEEEEEEE-
T ss_pred CCEEEEECCCHHHHHHHH-HhCCeEEcCcEEEEEEEc
Confidence 357789999999999999 7799999887554 4443
No 126
>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]
Probab=63.04 E-value=5.8 Score=39.05 Aligned_cols=34 Identities=24% Similarity=0.132 Sum_probs=24.4
Q ss_pred CCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEE
Q 024281 3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEF 37 (269)
Q Consensus 3 rGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~ 37 (269)
-|.|||+|++.++|+.||.+- -..|.-+-|.|..
T Consensus 145 tGEAfVqF~sqe~ae~Al~rh-re~iGhRYIEvF~ 178 (510)
T KOG4211|consen 145 TGEAFVQFESQESAEIALGRH-RENIGHRYIEVFR 178 (510)
T ss_pred ccceEEEecCHHHHHHHHHHH-HHhhccceEEeeh
Confidence 478999999999999998442 3345555565544
No 127
>KOG2068 consensus MOT2 transcription factor [Transcription]
Probab=62.37 E-value=2 Score=40.28 Aligned_cols=34 Identities=18% Similarity=0.382 Sum_probs=29.6
Q ss_pred EEEEECCHHHHHHHHHHhCCCeecCceEEEEEec
Q 024281 6 AFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR 39 (269)
Q Consensus 6 gfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~ 39 (269)
++|+|+..+||+.||...+|+.++|+.|...+..
T Consensus 128 ~yITy~~~eda~rci~~v~g~~~dg~~lka~~gt 161 (327)
T KOG2068|consen 128 VYITYEEEEDADRCIDDVDGFVDDGRALKASLGT 161 (327)
T ss_pred ccccccchHhhhhHHHHhhhHHhhhhhhHHhhCC
Confidence 6899999999999999999999999986655543
No 128
>KOG3116 consensus Predicted C3H1-type Zn-finger protein [General function prediction only]
Probab=59.23 E-value=2.2 Score=35.66 Aligned_cols=20 Identities=45% Similarity=1.059 Sum_probs=17.4
Q ss_pred CCCcccCCCCCCCCCcccCC
Q 024281 60 SGRCFNCGIDGHWARDCKAG 79 (269)
Q Consensus 60 ~~rc~~cG~~GH~ardC~~~ 79 (269)
..+|-.|.+.|||.++|.+.
T Consensus 27 ~~rCQKClq~GHWtYECk~k 46 (177)
T KOG3116|consen 27 SARCQKCLQAGHWTYECKNK 46 (177)
T ss_pred chhHHHHHhhccceeeecCc
Confidence 35899999999999999874
No 129
>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]
Probab=58.43 E-value=9.3 Score=38.13 Aligned_cols=25 Identities=20% Similarity=0.448 Sum_probs=23.0
Q ss_pred CCeEEEEECCHHHHHHHHHHhCCCe
Q 024281 3 RDFAFVEFSDPRDADDARYSLNGRD 27 (269)
Q Consensus 3 rGfgfVeF~~~~dA~~Ai~~ldG~~ 27 (269)
-|||||.|.+++++..++++++|+.
T Consensus 431 vGYAFINm~sp~ai~~F~kAFnGk~ 455 (549)
T KOG4660|consen 431 VGYAFINMTSPEAIIRFYKAFNGKK 455 (549)
T ss_pred cceeEEeecCHHHHHHHHHHHcCCc
Confidence 3899999999999999999999964
No 130
>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]
Probab=56.05 E-value=20 Score=35.18 Aligned_cols=40 Identities=28% Similarity=0.395 Sum_probs=33.8
Q ss_pred CCCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEecCC
Q 024281 2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGG 41 (269)
Q Consensus 2 krGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~~~ 41 (269)
.+||++|+|..+.+|-+||..|++..+..+.+.|.....-
T Consensus 255 s~G~~vi~y~hpveavqaIsml~~~g~~~~~~~~Rl~~~~ 294 (608)
T KOG4212|consen 255 SRGFAVIEYDHPVEAVQAISMLDRQGLFDRRMTVRLDRIP 294 (608)
T ss_pred cCCeeEEEecchHHHHHHHHhhccCCCccccceeeccccc
Confidence 4689999999999999999999988777787777765543
No 131
>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]
Probab=55.35 E-value=11 Score=38.90 Aligned_cols=34 Identities=24% Similarity=0.263 Sum_probs=27.9
Q ss_pred CeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEe
Q 024281 4 DFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA 38 (269)
Q Consensus 4 GfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a 38 (269)
|.|||.|.+-|||.-|+- .|+.+|.|..+++-+.
T Consensus 41 GeaFI~FsTDeDARlaM~-kdr~~i~g~~VrLlLS 74 (944)
T KOG4307|consen 41 GEAFIGFSTDEDARLAMT-KDRLMIHGAEVRLLLS 74 (944)
T ss_pred cceEEEecccchhhhhhh-hcccceecceEEEEec
Confidence 689999999999999984 4667788887777654
No 132
>KOG2318 consensus Uncharacterized conserved protein [Function unknown]
Probab=54.16 E-value=16 Score=36.89 Aligned_cols=35 Identities=20% Similarity=0.300 Sum_probs=28.5
Q ss_pred CeEEEEECCHHHHHHHHHHhCCCeecCc--eEEEEEe
Q 024281 4 DFAFVEFSDPRDADDARYSLNGRDVDGS--RIIVEFA 38 (269)
Q Consensus 4 GfgfVeF~~~~dA~~Ai~~ldG~~l~Gr--~I~Ve~a 38 (269)
=||+|+|.+.+.|...+..+||++|.-. .|-+.|.
T Consensus 269 YyAVvecDsi~tA~~vYe~CDG~EfEsS~~~~DLRFI 305 (650)
T KOG2318|consen 269 YYAVVECDSIETAKAVYEECDGIEFESSANKLDLRFI 305 (650)
T ss_pred EEEEEEecCchHHHHHHHhcCcceeccccceeeeeec
Confidence 3899999999999999999999999754 4444443
No 133
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=53.99 E-value=5.5 Score=26.59 Aligned_cols=19 Identities=32% Similarity=1.006 Sum_probs=17.2
Q ss_pred CCcccccCCCCCcccccCC
Q 024281 81 WKNKCYRCGERGHIERNCQ 99 (269)
Q Consensus 81 ~k~~CyrCG~~Gh~~r~c~ 99 (269)
....|+.||..||...+|+
T Consensus 30 lp~~C~~C~~~gH~~~~C~ 48 (49)
T PF14392_consen 30 LPRFCFHCGRIGHSDKECP 48 (49)
T ss_pred cChhhcCCCCcCcCHhHcC
Confidence 5678999999999999997
No 134
>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]
Probab=52.99 E-value=11 Score=36.43 Aligned_cols=33 Identities=21% Similarity=0.242 Sum_probs=25.6
Q ss_pred eEEEEECCHHHHHHHHHHhCCCeecCceEEEEEe
Q 024281 5 FAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFA 38 (269)
Q Consensus 5 fgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a 38 (269)
.+||.|.+...+..|. +|..+.|-++.|.|..+
T Consensus 54 tcyVkf~d~~sv~vaQ-hLtntvfvdraliv~p~ 86 (479)
T KOG4676|consen 54 TCYVKFLDSQSVTVAQ-HLTNTVFVDRALIVRPY 86 (479)
T ss_pred eEEEeccCCcceeHHh-hhccceeeeeeEEEEec
Confidence 6899999988887775 77777777777766543
No 135
>PF12353 eIF3g: Eukaryotic translation initiation factor 3 subunit G ; InterPro: IPR024675 At least eleven different protein factors are involved in initiation of protein synthesis in eukaryotes. Binding of initiator tRNA and mRNA to the 40S subunit requires the presence of the translation initiation factors eIF-2 and eIF-3, with eIF-3 being particularly important for 80S ribosome dissociation and mRNA binding []. eIF-3 is the most complex translation inititation factor, consisting of about 13 putative subunits and having a molecular weight of between 550 - 700 kDa in mammalian cells. Subunits are designated eIF-3a - eIF-3m; the large number of subunits means that the interactions between the individual subunits that make up the eIF-3 complex are complex and varied. Subunit G is required for eIF3 integrity. This entry represents a domain of approximately 130 amino acids in length found at the N terminus of eukaryotic translation initiation factor 3 subunit G. This domain is commonly found in association with the RNA recognition domain PF00076 from PFAM.
Probab=51.54 E-value=20 Score=29.06 Aligned_cols=52 Identities=21% Similarity=0.388 Sum_probs=30.4
Q ss_pred ecCceEEEEEecCCCCCCCCCCCC--CCCCCCCCCCCcccCCCCCCCCCcccCCC
Q 024281 28 VDGSRIIVEFARGGPRGPGGSREY--LGRGPPPGSGRCFNCGIDGHWARDCKAGD 80 (269)
Q Consensus 28 l~Gr~I~Ve~a~~~~rg~g~~r~~--~~R~~~~~~~rc~~cG~~GH~ardC~~~~ 80 (269)
.-+..|.+++.............. ...........|..|+ ..||...||.-+
T Consensus 72 ~~~EeI~l~~~~~~~~~~~~~~~~~~~~~~~~~~~v~CR~Ck-GdH~T~~CPyKd 125 (128)
T PF12353_consen 72 QVGEEIFLELSRNWESEEEEEEEEEAKKKKKGKSKVKCRICK-GDHWTSKCPYKD 125 (128)
T ss_pred cccceEEEEecCCccccccccccchhhhcccCCceEEeCCCC-CCcccccCCccc
Confidence 346678887766432211111100 2233344567899997 889999999753
No 136
>PRK11634 ATP-dependent RNA helicase DeaD; Provisional
Probab=51.50 E-value=31 Score=35.32 Aligned_cols=36 Identities=3% Similarity=0.057 Sum_probs=30.3
Q ss_pred CCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEec
Q 024281 3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR 39 (269)
Q Consensus 3 rGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~ 39 (269)
..|.||+... ..|+..+.+|.+..+.|+.|.|+.+.
T Consensus 526 ~~~s~v~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~ 561 (629)
T PRK11634 526 ASHSTIELPK-GMPGEVLQHFTRTRILNKPMNMQLLG 561 (629)
T ss_pred CCceEEEcCh-hhHHHHHHHhccccccCCceEEEECC
Confidence 4688998854 45888889999999999999999875
No 137
>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]
Probab=50.68 E-value=6.8 Score=37.61 Aligned_cols=37 Identities=16% Similarity=0.104 Sum_probs=31.3
Q ss_pred CCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEec
Q 024281 3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR 39 (269)
Q Consensus 3 rGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~ 39 (269)
-|.|||+|.+.++|..|..+.+.+.++.+.|.|.-+.
T Consensus 324 SGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvfp~S 360 (508)
T KOG1365|consen 324 SGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVFPCS 360 (508)
T ss_pred ChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEeecc
Confidence 4789999999999999998888887888888776543
No 138
>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif
Probab=46.22 E-value=20 Score=24.34 Aligned_cols=18 Identities=17% Similarity=0.575 Sum_probs=16.1
Q ss_pred CCeEEEEECCHHHHHHHH
Q 024281 3 RDFAFVEFSDPRDADDAR 20 (269)
Q Consensus 3 rGfgfVeF~~~~dA~~Ai 20 (269)
..+.||.|.+..+|+.||
T Consensus 36 ~~~~~l~y~~~~~ae~Al 53 (53)
T PF14605_consen 36 TNWMYLKYKSRKDAEKAL 53 (53)
T ss_pred CcEEEEEECCHHHHHhhC
Confidence 568999999999999985
No 139
>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]
Probab=45.76 E-value=25 Score=35.67 Aligned_cols=36 Identities=22% Similarity=0.453 Sum_probs=31.4
Q ss_pred CeEEEEECCHHHHHHHHHHhCCCee---cCceEEEEEec
Q 024281 4 DFAFVEFSDPRDADDARYSLNGRDV---DGSRIIVEFAR 39 (269)
Q Consensus 4 GfgfVeF~~~~dA~~Ai~~ldG~~l---~Gr~I~Ve~a~ 39 (269)
-.+||.|...++|...+.+|+|... +.+.|.|+|+.
T Consensus 482 ShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L~adf~~ 520 (718)
T KOG2416|consen 482 SHCYVSYSSVEEAAATREALHNVQWPPSNPKHLIADFVR 520 (718)
T ss_pred cceeEecccHHHHHHHHHHHhccccCCCCCceeEeeecc
Confidence 4699999999999999999999755 67789898876
No 140
>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]
Probab=42.84 E-value=14 Score=36.69 Aligned_cols=34 Identities=29% Similarity=0.612 Sum_probs=28.5
Q ss_pred CCCeEEEEECCHHHHHHHHHHhCCCeecCceEEEE
Q 024281 2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVE 36 (269)
Q Consensus 2 krGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve 36 (269)
-++|+||+|...++|..|+ .+++..|.|..+++.
T Consensus 222 ~~nfa~ie~~s~~~at~~~-~~~~~~f~g~~~~~~ 255 (500)
T KOG0120|consen 222 EKNFAFIEFRSISEATEAM-ALDGIIFEGRPLKIR 255 (500)
T ss_pred cccceeEEecCCCchhhhh-cccchhhCCCCceec
Confidence 4679999999999999997 788888888876654
No 141
>KOG4019 consensus Calcineurin-mediated signaling pathway inhibitor DSCR1 [Signal transduction mechanisms; General function prediction only]
Probab=41.79 E-value=43 Score=29.01 Aligned_cols=39 Identities=31% Similarity=0.511 Sum_probs=33.8
Q ss_pred CeEEEEECCHHHHHHHHHHhCCCeecCc-eEEEEEecCCC
Q 024281 4 DFAFVEFSDPRDADDARYSLNGRDVDGS-RIIVEFARGGP 42 (269)
Q Consensus 4 GfgfVeF~~~~dA~~Ai~~ldG~~l~Gr-~I~Ve~a~~~~ 42 (269)
++.-|.|.+++.|++|..+++++.|.|. .+...|++..-
T Consensus 52 rrvRi~f~~p~~a~~a~i~~~~~~f~~~~~~k~yfaQ~~~ 91 (193)
T KOG4019|consen 52 RRVRINFSNPEAAADARIKLHSTSFNGKNELKLYFAQPGH 91 (193)
T ss_pred ceeEEeccChhHHHHHHHHhhhcccCCCceEEEEEccCCC
Confidence 3556889999999999999999999999 88888987543
No 142
>PF03439 Spt5-NGN: Early transcription elongation factor of RNA pol II, NGN section; InterPro: IPR005100 Spt5p and prokaryotic NusG are shown to contain a novel 'NGN' domain. The combined NGN and KOW motif regions of Spt5 form the binding domain with Spt4 []. Spt5 complexes with Spt4 as a 1:1 heterodimer snf this Spt5-Spt4 complex regulates early transcription elongation by RNA polymerase II and has an imputed role in pre-mRNA processing via its physical association with mRNA capping enzymes. The Schizosaccharomyces pombe core Spt5-Spt4 complex is a heterodimer bearing a trypsin-resistant Spt4-binding domain within the Spt5 subunit []. ; PDB: 3H7H_B 3QQC_D 3P8B_B 2EXU_A.
Probab=39.95 E-value=35 Score=25.30 Aligned_cols=26 Identities=15% Similarity=0.253 Sum_probs=21.6
Q ss_pred CCCeEEEEECCHHHHHHHHHHhCCCe
Q 024281 2 KRDFAFVEFSDPRDADDARYSLNGRD 27 (269)
Q Consensus 2 krGfgfVeF~~~~dA~~Ai~~ldG~~ 27 (269)
-+||-|||=....++.+|+..+-+..
T Consensus 43 lkGyIyVEA~~~~~V~~ai~gi~~i~ 68 (84)
T PF03439_consen 43 LKGYIYVEAERESDVKEAIRGIRHIR 68 (84)
T ss_dssp STSEEEEEESSHHHHHHHHTT-TTEE
T ss_pred CceEEEEEeCCHHHHHHHHhccccee
Confidence 37999999999999999998887743
No 143
>PF07576 BRAP2: BRCA1-associated protein 2; InterPro: IPR011422 These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localisation signals (NLSs) in vitro and in yeast two-hybrid screening []. These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.
Probab=38.64 E-value=40 Score=26.60 Aligned_cols=24 Identities=25% Similarity=0.535 Sum_probs=22.0
Q ss_pred EEEEECCHHHHHHHHHHhCCCeec
Q 024281 6 AFVEFSDPRDADDARYSLNGRDVD 29 (269)
Q Consensus 6 gfVeF~~~~dA~~Ai~~ldG~~l~ 29 (269)
++|.|.+.++|+.-+..+||+.|+
T Consensus 57 VLikF~~~~~Ad~Fy~~fNGk~Fn 80 (110)
T PF07576_consen 57 VLIKFRDQESADEFYEEFNGKPFN 80 (110)
T ss_pred EEEEECCHHHHHHHHHHhCCCccC
Confidence 678999999999999999998775
No 144
>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]
Probab=38.40 E-value=20 Score=33.06 Aligned_cols=41 Identities=24% Similarity=0.409 Sum_probs=35.0
Q ss_pred CCCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEecCCCC
Q 024281 2 KRDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFARGGPR 43 (269)
Q Consensus 2 krGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~~~~r 43 (269)
.+|||||+|....++..|+.. +...+.+..|.|++....+.
T Consensus 226 ~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~ 266 (285)
T KOG4210|consen 226 SKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLEEDEPRPK 266 (285)
T ss_pred hhhhhhhhhhhchhHHHHhhc-ccCcccCcccccccCCCCcc
Confidence 468999999999999999877 78889999999999876554
No 145
>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]
Probab=37.76 E-value=15 Score=36.89 Aligned_cols=28 Identities=25% Similarity=0.476 Sum_probs=21.0
Q ss_pred EEEECCHHHHHHHHHHhCC--CeecCceEE
Q 024281 7 FVEFSDPRDADDARYSLNG--RDVDGSRII 34 (269)
Q Consensus 7 fVeF~~~~dA~~Ai~~ldG--~~l~Gr~I~ 34 (269)
||+|+...||+.|++.|-- ++|.|+.|.
T Consensus 216 yITfesd~DAQqAykylreevk~fqgKpIm 245 (684)
T KOG2591|consen 216 YITFESDTDAQQAYKYLREEVKTFQGKPIM 245 (684)
T ss_pred EEEeecchhHHHHHHHHHHHHHhhcCcchh
Confidence 8999999999999977654 345555443
No 146
>PF02714 DUF221: Domain of unknown function DUF221; InterPro: IPR003864 This domain is found in a family of hypothetical transmembrane proteins none of which have any known function, the aligned region is at 538 residues at maximum length.; GO: 0016020 membrane
Probab=37.30 E-value=36 Score=31.20 Aligned_cols=32 Identities=28% Similarity=0.210 Sum_probs=24.2
Q ss_pred EEEEECCHHHHHHHHHHhCCCeecCceEEEEEec
Q 024281 6 AFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR 39 (269)
Q Consensus 6 gfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~ 39 (269)
|||+|.+..+|+.|++.+.... ...+.|+.|-
T Consensus 1 aFVtF~~~~~a~~~~q~~~~~~--~~~~~v~~AP 32 (325)
T PF02714_consen 1 AFVTFNSQKSAQIALQLLLSKR--PNSWRVSPAP 32 (325)
T ss_pred CEEEECCHHHHHHHHHHHhcCC--CCCceEeeCC
Confidence 7999999999999998766643 3455666654
No 147
>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]
Probab=36.00 E-value=32 Score=33.24 Aligned_cols=20 Identities=35% Similarity=0.205 Sum_probs=17.8
Q ss_pred CCeEEEEECCHHHHHHHHHH
Q 024281 3 RDFAFVEFSDPRDADDARYS 22 (269)
Q Consensus 3 rGfgfVeF~~~~dA~~Ai~~ 22 (269)
-|-|||.|.++++|+.||.+
T Consensus 206 TGdAFvlfa~ee~aq~aL~k 225 (508)
T KOG1365|consen 206 TGDAFVLFACEEDAQFALRK 225 (508)
T ss_pred ccceEEEecCHHHHHHHHHH
Confidence 37899999999999999955
No 148
>PF03467 Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120 Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons. Three 'up-frameshift' proteins, UPF1, UPF2 and UPF3, are essential for this process in organisms ranging from yeast, human to plants []. Exon junction complexes (EJCs) are deposited ~24 nucleotides upstream of exon-exon junctions after splicing. Translation causes displacement of the EJCs, however, premature translation termination upstream of one or more EJCs triggers the recruitment of UPF1, UPF2 and UPF3 and activates the NMD pathway [, ]. This family contains UPF3. The crystal structure of the complex between human UPF2 and UPF3b, which are, respectively, a MIF4G (middle portion of eIF4G) domain and an RNP domain (ribonucleoprotein-type RNA-binding domain) has been determined to 1.95A. The protein-protein interface is mediated by highly conserved charged residues in UPF2 and UPF3b and involves the beta-sheet surface of the UPF3b ribonucleoprotein (RNP) domain, which is generally used by these domains to bind nucleic acids. In UPF3b the RNP domain does not bind RNA, whereas the UPF2 construct and the complex do. It is clear that some RNP domains have evolved for specific protein-protein interactions rather than as nucleic acid binding modules [].; PDB: 1UW4_A 2L08_A.
Probab=35.67 E-value=60 Score=27.63 Aligned_cols=35 Identities=31% Similarity=0.497 Sum_probs=27.0
Q ss_pred eEEEEECCHHHHHHHHHHhCCCeecCc-----eEEEEEec
Q 024281 5 FAFVEFSDPRDADDARYSLNGRDVDGS-----RIIVEFAR 39 (269)
Q Consensus 5 fgfVeF~~~~dA~~Ai~~ldG~~l~Gr-----~I~Ve~a~ 39 (269)
-|||.|.+.+++..-++.++|..|.+. ...|++|-
T Consensus 57 RaYi~F~~~~~~~~F~~~~~g~~F~D~kg~~~~~~VE~Ap 96 (176)
T PF03467_consen 57 RAYINFKNPEDLLEFRDRFDGHVFVDSKGNEYPAVVEFAP 96 (176)
T ss_dssp EEEEEESSCHHHHHHHHHCTTEEEE-TTS-EEEEEEEE-S
T ss_pred EEEEEeCCHHHHHHHHHhcCCcEEECCCCCCcceeEEEcc
Confidence 489999999999999999999777433 45567664
No 149
>PF11823 DUF3343: Protein of unknown function (DUF3343); InterPro: IPR021778 This family of proteins are functionally uncharacterised. This protein is found in bacteria and archaea. Proteins in this family are typically between 78 to 102 amino acids in length.
Probab=33.42 E-value=50 Score=23.60 Aligned_cols=29 Identities=17% Similarity=0.243 Sum_probs=23.1
Q ss_pred CeEEEEECCHHHHHHHHHHhCCCeecCce
Q 024281 4 DFAFVEFSDPRDADDARYSLNGRDVDGSR 32 (269)
Q Consensus 4 GfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~ 32 (269)
.+.+|.|.+..+|-.|.+.|....|..+.
T Consensus 2 ~~~~i~F~st~~a~~~ek~lk~~gi~~~l 30 (73)
T PF11823_consen 2 KYYLITFPSTHDAMKAEKLLKKNGIPVRL 30 (73)
T ss_pred ceEEEEECCHHHHHHHHHHHHHCCCcEEE
Confidence 47899999999999999888776554443
No 150
>KOG2044 consensus 5'-3' exonuclease HKE1/RAT1 [Replication, recombination and repair; RNA processing and modification]
Probab=32.14 E-value=17 Score=38.02 Aligned_cols=20 Identities=50% Similarity=1.099 Sum_probs=17.4
Q ss_pred CCCcccCCCCCCCCCcccCC
Q 024281 60 SGRCFNCGIDGHWARDCKAG 79 (269)
Q Consensus 60 ~~rc~~cG~~GH~ardC~~~ 79 (269)
...||.||..||.+.+|...
T Consensus 260 ~~~C~~cgq~gh~~~dc~g~ 279 (931)
T KOG2044|consen 260 PRRCFLCGQTGHEAKDCEGK 279 (931)
T ss_pred cccchhhcccCCcHhhcCCc
Confidence 34799999999999999965
No 151
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=31.09 E-value=45 Score=27.59 Aligned_cols=24 Identities=13% Similarity=0.225 Sum_probs=21.3
Q ss_pred CCeEEEEECCHHHHHHHHHHhCCC
Q 024281 3 RDFAFVEFSDPRDADDARYSLNGR 26 (269)
Q Consensus 3 rGfgfVeF~~~~dA~~Ai~~ldG~ 26 (269)
.||-||+....+++..+|..+.+.
T Consensus 46 pGYVfVe~~~~~~~~~~i~~v~~v 69 (153)
T PRK08559 46 KGYVLVEAESKGAVEEAIRGIPHV 69 (153)
T ss_pred CcEEEEEEEChHHHHHHHhcCCCE
Confidence 699999999889999999888773
No 152
>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function.
Probab=30.32 E-value=58 Score=23.11 Aligned_cols=18 Identities=33% Similarity=0.309 Sum_probs=15.7
Q ss_pred EEEEECCHHHHHHHHHHh
Q 024281 6 AFVEFSDPRDADDARYSL 23 (269)
Q Consensus 6 gfVeF~~~~dA~~Ai~~l 23 (269)
+-|.|.+.+.|..||.+|
T Consensus 45 cNvvf~d~~~A~~AL~~L 62 (62)
T PF10309_consen 45 CNVVFKDEETAARALVAL 62 (62)
T ss_pred EEEEECCHHHHHHHHHcC
Confidence 568899999999999876
No 153
>KOG0314 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=29.72 E-value=62 Score=31.86 Aligned_cols=41 Identities=24% Similarity=0.630 Sum_probs=29.5
Q ss_pred CCcccCCCCCCCCCcccCC---CCCcccccCCCCCcccccCCCC
Q 024281 61 GRCFNCGIDGHWARDCKAG---DWKNKCYRCGERGHIERNCQNS 101 (269)
Q Consensus 61 ~rc~~cG~~GH~ardC~~~---~~k~~CyrCG~~Gh~~r~c~~~ 101 (269)
..|..|-..+||-..|... .....|++|+..|||.+.|+..
T Consensus 134 ~~~~~~~~~~~~iq~~~~~g~Pppsy~c~rc~~~g~wikacptv 177 (448)
T KOG0314|consen 134 YVCHRCNSPGHFIQHCSTNGSPPPSYKCVKCPTPGPWIKACPTV 177 (448)
T ss_pred ceeeecccCccccccccccCCCCCCcceecCCCCCccceecccc
Confidence 3455566666766666533 2457899999999999999864
No 154
>TIGR02381 cspD cold shock domain protein CspD. This model represents what appears to be a phylogenetically distinct clade, containing E. coli CspD and related proteobacterial proteins within the larger family of cold shock domain proteins described by pfam model pfam00313. The gene symbol cspD may have been used idependently for other subfamilies of cold shock domain proteins, such as for B. subtilis CspD. These proteins typically are shorter than 70 amino acids. In E. coli, CspD is a stress response protein induced in stationary phase. This homodimer binds single-stranded DNA and appears to inhibit DNA replication.
Probab=28.92 E-value=77 Score=22.48 Aligned_cols=38 Identities=21% Similarity=0.341 Sum_probs=21.7
Q ss_pred CCCeEEEEECC-HHHH---HHHHHHhCC-C-eecCceEEEEEecC
Q 024281 2 KRDFAFVEFSD-PRDA---DDARYSLNG-R-DVDGSRIIVEFARG 40 (269)
Q Consensus 2 krGfgfVeF~~-~~dA---~~Ai~~ldG-~-~l~Gr~I~Ve~a~~ 40 (269)
.+|||||+-.+ .+|+ ..||.. +| . ...|..|..+...+
T Consensus 12 ~kGfGFI~~~~g~~dvfvH~s~~~~-~g~~~l~~G~~V~f~~~~~ 55 (68)
T TIGR02381 12 AKGFGFICPEGVDGDIFAHYSTIQM-DGYRTLKAGQKVQFEVVQG 55 (68)
T ss_pred CCCeEEEecCCCCccEEEEHHHhhh-cCCCCCCCCCEEEEEEEEC
Confidence 48999999876 3443 234432 23 2 23566666655553
No 155
>COG1278 CspC Cold shock proteins [Transcription]
Probab=27.74 E-value=25 Score=25.43 Aligned_cols=39 Identities=23% Similarity=0.366 Sum_probs=22.1
Q ss_pred CCCeEEEEECCH-HHHH---HHHHHhCCCe-ecCceEEEEEecC
Q 024281 2 KRDFAFVEFSDP-RDAD---DARYSLNGRD-VDGSRIIVEFARG 40 (269)
Q Consensus 2 krGfgfVeF~~~-~dA~---~Ai~~ldG~~-l~Gr~I~Ve~a~~ 40 (269)
.+|||||+-++- .|+- .||....-.. ..|.++..+...+
T Consensus 12 ~KGfGFI~p~~G~~DvFVH~Sai~~~g~~~L~eGQ~V~f~~~~g 55 (67)
T COG1278 12 TKGFGFITPEDGGKDVFVHISAIQRAGFRTLREGQKVEFEVEQG 55 (67)
T ss_pred CCcceEcCCCCCCcCEEEEeeeeccCCCcccCCCCEEEEEEecC
Confidence 479999998776 4542 3442222122 3576665555554
No 156
>COG5638 Uncharacterized conserved protein [Function unknown]
Probab=27.17 E-value=68 Score=31.33 Aligned_cols=29 Identities=21% Similarity=0.297 Sum_probs=25.5
Q ss_pred CeEEEEECCHHHHHHHHHHhCCCeecCce
Q 024281 4 DFAFVEFSDPRDADDARYSLNGRDVDGSR 32 (269)
Q Consensus 4 GfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~ 32 (269)
-||+|+|.+.+.+...+.++||+++....
T Consensus 259 YyAvvec~d~~tsK~iY~~CDG~Eye~sa 287 (622)
T COG5638 259 YYAVVECEDIETSKNIYSACDGVEYENSA 287 (622)
T ss_pred EEEEEEeccchhhHHHHhccCcccccccc
Confidence 38999999999999999999999886543
No 157
>PRK15463 cold shock-like protein CspF; Provisional
Probab=27.14 E-value=76 Score=22.79 Aligned_cols=39 Identities=21% Similarity=0.124 Sum_probs=21.9
Q ss_pred CCCeEEEEECCH-HHH---HHHHHHhCC-CeecCceEEEEEecC
Q 024281 2 KRDFAFVEFSDP-RDA---DDARYSLNG-RDVDGSRIIVEFARG 40 (269)
Q Consensus 2 krGfgfVeF~~~-~dA---~~Ai~~ldG-~~l~Gr~I~Ve~a~~ 40 (269)
.+|||||+-.+- +|+ ..||..... ....|..|..+...+
T Consensus 15 ~kGfGFI~~~~g~~DvFvH~sal~~~g~~~l~~G~~V~f~v~~~ 58 (70)
T PRK15463 15 KSGKGLITPSDGRKDVQVHISALNLRDAEELTTGLRVEFCRING 58 (70)
T ss_pred CCceEEEecCCCCccEEEEehhhhhcCCCCCCCCCEEEEEEEEC
Confidence 489999988763 343 244433222 233576766665553
No 158
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=25.06 E-value=1.2e+02 Score=23.90 Aligned_cols=30 Identities=7% Similarity=0.107 Sum_probs=20.6
Q ss_pred CHHHHHHHHHHh-CCCeecCceEEEEEecCC
Q 024281 12 DPRDADDARYSL-NGRDVDGSRIIVEFARGG 41 (269)
Q Consensus 12 ~~~dA~~Ai~~l-dG~~l~Gr~I~Ve~a~~~ 41 (269)
.++.++.|++.| .|+.+.|..|.|++....
T Consensus 40 ~pe~L~f~f~~~~~~T~~egA~L~I~~vp~~ 70 (113)
T PRK12380 40 EESAVRFSFEIVCHGTVAQGCDLHIVYKPAQ 70 (113)
T ss_pred CHHHHHHHHHHHhCCCccCCCEEEEEeeCcE
Confidence 455556666553 478889999998887643
No 159
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=24.81 E-value=1.3e+02 Score=23.62 Aligned_cols=57 Identities=16% Similarity=0.204 Sum_probs=34.5
Q ss_pred CCHHHHHHHHHHh-CCCeecCceEEEEEecCCCCCCCCCCCCCCCCCCCCCCCcccCCCCCCCCCcccCCCCCcccccCC
Q 024281 11 SDPRDADDARYSL-NGRDVDGSRIIVEFARGGPRGPGGSREYLGRGPPPGSGRCFNCGIDGHWARDCKAGDWKNKCYRCG 89 (269)
Q Consensus 11 ~~~~dA~~Ai~~l-dG~~l~Gr~I~Ve~a~~~~rg~g~~r~~~~R~~~~~~~rc~~cG~~GH~ardC~~~~~k~~CyrCG 89 (269)
.+++.++.|++.+ .|+.+.|..|.|++.... ..|..||....... ....|-.||
T Consensus 39 V~p~~L~faf~~~~~~t~~ega~L~I~~~p~~-------------------~~C~~Cg~~~~~~~------~~~~CP~Cg 93 (115)
T TIGR00100 39 VNPSQLQFAFEVVREGTVAEGAKLNIEDEPVE-------------------CECEDCSEEVSPEI------DLYRCPKCH 93 (115)
T ss_pred cCHHHHHHHHHHHhCCCccCCCEEEEEeeCcE-------------------EEcccCCCEEecCC------cCccCcCCc
Confidence 3555566666553 467788888888876543 46888885443210 123577777
Q ss_pred CCC
Q 024281 90 ERG 92 (269)
Q Consensus 90 ~~G 92 (269)
...
T Consensus 94 s~~ 96 (115)
T TIGR00100 94 GIM 96 (115)
T ss_pred CCC
Confidence 643
No 160
>TIGR00405 L26e_arch ribosomal protein L24p/L26e, archaeal. This protein contains a KOW domain, shared by bacterial NusG and the L24p/L26e family of ribosomal proteins. Although called archaeal NusG in several publications, it is the only close homolog of eukaryotic L26e in archaeal genomes, shares an operon with L11 in many genomes, and has been sequenced from purified ribosomes. It is here designated as a ribosomal protein for these reasons.
Probab=23.82 E-value=71 Score=25.88 Aligned_cols=24 Identities=13% Similarity=0.169 Sum_probs=20.9
Q ss_pred CCeEEEEECCHHHHHHHHHHhCCC
Q 024281 3 RDFAFVEFSDPRDADDARYSLNGR 26 (269)
Q Consensus 3 rGfgfVeF~~~~dA~~Ai~~ldG~ 26 (269)
.||-||++....+...+|..+.|.
T Consensus 38 pGYvFV~~~~~~~~~~~i~~~~gv 61 (145)
T TIGR00405 38 KGYILVEAETKIDMRNPIIGVPHV 61 (145)
T ss_pred CcEEEEEEECcHHHHHHHhCCCCE
Confidence 689999999888889999888883
No 161
>KOG2187 consensus tRNA uracil-5-methyltransferase and related tRNA-modifying enzymes [Translation, ribosomal structure and biogenesis]
Probab=21.32 E-value=49 Score=33.16 Aligned_cols=37 Identities=27% Similarity=0.424 Sum_probs=32.6
Q ss_pred CCeEEEEECCHHHHHHHHHHhCCCeecCceEEEEEec
Q 024281 3 RDFAFVEFSDPRDADDARYSLNGRDVDGSRIIVEFAR 39 (269)
Q Consensus 3 rGfgfVeF~~~~dA~~Ai~~ldG~~l~Gr~I~Ve~a~ 39 (269)
..|+++.|+...++..|+..++|....+..+.|..+.
T Consensus 63 ~~~~~~~~et~~~~~ka~~~v~g~~~k~~~~~~~~~~ 99 (534)
T KOG2187|consen 63 PKYAYVTFETPSDAGKAINLVDGLLYKGFILRVQLGA 99 (534)
T ss_pred CCceEEEEeccchhhhHHHHHhhhhhhcchhhhhhcc
Confidence 4689999999999999999999998888888777665
No 162
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=21.22 E-value=48 Score=32.97 Aligned_cols=20 Identities=45% Similarity=0.823 Sum_probs=18.1
Q ss_pred CCcccCCCCCCCCCcccCCC
Q 024281 61 GRCFNCGIDGHWARDCKAGD 80 (269)
Q Consensus 61 ~rc~~cG~~GH~ardC~~~~ 80 (269)
..|+.||..||+..+|...+
T Consensus 286 n~c~~cg~~gH~~~dc~~~~ 305 (554)
T KOG0119|consen 286 NVCKICGPLGHISIDCKVND 305 (554)
T ss_pred ccccccCCcccccccCCCcc
Confidence 48999999999999999873
No 163
>COG5179 TAF1 Transcription initiation factor TFIID, subunit TAF1 [Transcription]
Probab=20.58 E-value=59 Score=33.47 Aligned_cols=24 Identities=33% Similarity=0.707 Sum_probs=17.6
Q ss_pred CCCCCCCCcccCCCCCCCC--CcccC
Q 024281 55 GPPPGSGRCFNCGIDGHWA--RDCKA 78 (269)
Q Consensus 55 ~~~~~~~rc~~cG~~GH~a--rdC~~ 78 (269)
|.......|-+||+.|||. .-||.
T Consensus 932 GRK~Ttr~C~nCGQvGHmkTNK~CP~ 957 (968)
T COG5179 932 GRKNTTRTCGNCGQVGHMKTNKACPK 957 (968)
T ss_pred CCCCcceecccccccccccccccCcc
Confidence 3455678999999999985 34553
Done!