Query 008981
Match_columns 547
No_of_seqs 233 out of 632
Neff 4.0
Searched_HMMs 46136
Date Thu Mar 28 18:57:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008981.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008981hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd08037 LARP_1 La RNA-binding 100.0 1.1E-30 2.4E-35 217.2 4.4 72 398-469 2-73 (73)
2 cd08038 LARP_2 La RNA-binding 100.0 1.6E-30 3.4E-35 216.3 4.7 72 398-469 2-73 (73)
3 cd08034 LARP_1_2 La RNA-bindin 100.0 5.2E-30 1.1E-34 213.1 4.8 73 397-469 1-73 (73)
4 cd08036 LARP_5 La RNA-binding 100.0 3.5E-30 7.5E-35 214.8 3.4 71 398-468 2-74 (75)
5 cd08035 LARP_4 La RNA-binding 100.0 6.2E-30 1.3E-34 213.6 4.6 71 398-468 2-74 (75)
6 cd08032 LARP_7 La RNA-binding 99.9 1E-28 2.2E-33 209.5 5.8 76 394-469 3-82 (82)
7 KOG1855 Predicted RNA-binding 99.9 1.2E-28 2.5E-33 257.2 7.1 150 394-543 138-302 (484)
8 cd08033 LARP_6 La RNA-binding 99.9 1.5E-28 3.3E-33 206.2 5.0 72 398-469 2-77 (77)
9 smart00715 LA Domain in the RN 99.9 2.4E-28 5.3E-33 206.1 5.5 76 395-470 2-80 (80)
10 cd08031 LARP_4_5_like La RNA-b 99.9 2.1E-28 4.6E-33 204.5 4.6 71 398-468 2-74 (75)
11 cd08028 LARP_3 La RNA-binding 99.9 5.1E-28 1.1E-32 205.2 5.5 76 394-469 2-82 (82)
12 cd08029 LA_like_fungal La-moti 99.9 1.8E-27 4E-32 199.2 4.5 71 398-469 2-76 (76)
13 cd07323 LAM LA motif RNA-bindi 99.9 5.5E-27 1.2E-31 195.5 4.9 72 398-469 2-75 (75)
14 cd08030 LA_like_plant La-motif 99.9 4.8E-27 1E-31 202.4 4.3 73 397-469 2-90 (90)
15 PF05383 La: La domain; Inter 99.9 5E-24 1.1E-28 171.5 2.9 58 400-457 1-61 (61)
16 KOG2591 c-Mpl binding protein, 99.8 2.8E-21 6.1E-26 206.9 7.5 135 394-545 94-230 (684)
17 KOG2590 RNA-binding protein LA 99.8 5.3E-19 1.2E-23 188.1 22.1 75 398-477 302-377 (448)
18 KOG4213 RNA-binding protein La 99.7 1.1E-18 2.5E-23 166.5 4.1 142 394-545 11-168 (205)
19 COG5193 LHP1 La protein, small 99.4 3.8E-14 8.3E-19 148.4 2.6 83 397-479 271-377 (438)
20 COG5193 LHP1 La protein, small 99.4 2.2E-13 4.7E-18 142.9 2.6 144 400-545 75-244 (438)
21 TIGR01659 sex-lethal sex-letha 97.4 0.00015 3.3E-09 76.2 4.5 96 445-545 157-253 (346)
22 PF14259 RRM_6: RNA recognitio 96.7 0.00064 1.4E-08 53.6 1.3 55 488-545 3-57 (70)
23 PF00076 RRM_1: RNA recognitio 96.6 0.00069 1.5E-08 52.3 0.7 53 489-545 4-57 (70)
24 TIGR01622 SF-CC1 splicing fact 96.3 0.0035 7.6E-08 66.3 3.7 64 480-545 86-149 (457)
25 PLN03134 glycine-rich RNA-bind 96.2 0.0028 6.1E-08 58.8 2.3 59 486-546 37-95 (144)
26 KOG4211 Splicing factor hnRNP- 96.0 0.0044 9.5E-08 67.9 3.2 60 483-547 10-69 (510)
27 TIGR01645 half-pint poly-U bin 95.9 0.013 2.9E-07 66.2 6.4 98 445-545 157-264 (612)
28 TIGR01628 PABP-1234 polyadenyl 95.9 0.011 2.4E-07 64.8 5.3 96 445-545 50-147 (562)
29 TIGR01648 hnRNP-R-Q heterogene 95.8 0.01 2.2E-07 66.7 5.0 72 472-546 46-118 (578)
30 TIGR01661 ELAV_HUD_SF ELAV/HuD 95.7 0.016 3.5E-07 58.9 5.6 96 446-545 54-149 (352)
31 smart00362 RRM_2 RNA recogniti 95.7 0.0065 1.4E-07 45.5 2.1 55 487-545 3-57 (72)
32 TIGR01659 sex-lethal sex-letha 95.7 0.0058 1.2E-07 64.5 2.2 59 485-545 109-167 (346)
33 KOG2590 RNA-binding protein LA 95.4 0.0029 6.3E-08 69.0 -1.2 90 388-477 89-183 (448)
34 smart00360 RRM RNA recognition 95.3 0.0095 2.1E-07 44.3 1.7 53 490-545 3-56 (71)
35 TIGR01648 hnRNP-R-Q heterogene 95.1 0.025 5.4E-07 63.7 5.1 91 446-544 108-199 (578)
36 TIGR01628 PABP-1234 polyadenyl 95.0 0.031 6.7E-07 61.3 5.4 97 446-545 138-237 (562)
37 TIGR01661 ELAV_HUD_SF ELAV/HuD 95.0 0.015 3.2E-07 59.2 2.5 57 486-545 6-63 (352)
38 TIGR01642 U2AF_lg U2 snRNP aux 94.9 0.04 8.7E-07 59.1 5.6 58 485-545 297-355 (509)
39 PLN03120 nucleic acid binding 94.6 0.021 4.5E-07 58.7 2.6 59 484-547 5-63 (260)
40 cd00590 RRM RRM (RNA recogniti 94.6 0.019 4E-07 43.2 1.7 55 488-545 4-58 (74)
41 KOG0121 Nuclear cap-binding pr 94.3 0.032 7E-07 52.6 2.7 82 436-545 15-96 (153)
42 TIGR01649 hnRNP-L_PTB hnRNP-L/ 93.7 0.11 2.3E-06 56.7 5.9 60 484-545 395-454 (481)
43 KOG0122 Translation initiation 93.4 0.048 1E-06 55.8 2.4 59 484-545 190-249 (270)
44 KOG0123 Polyadenylate-binding 93.1 0.087 1.9E-06 56.3 3.8 89 445-545 45-133 (369)
45 TIGR01642 U2AF_lg U2 snRNP aux 92.5 0.1 2.2E-06 56.1 3.4 63 483-545 175-241 (509)
46 KOG0117 Heterogeneous nuclear 92.1 0.2 4.3E-06 55.0 5.0 95 448-546 45-144 (506)
47 TIGR01649 hnRNP-L_PTB hnRNP-L/ 91.9 0.18 3.8E-06 55.0 4.4 55 485-545 98-152 (481)
48 COG0724 RNA-binding proteins ( 91.9 0.11 2.4E-06 47.6 2.5 60 484-545 116-175 (306)
49 KOG0145 RNA-binding protein EL 91.7 0.13 2.7E-06 53.5 2.7 96 446-545 92-187 (360)
50 PLN03121 nucleic acid binding 91.3 0.14 3E-06 52.3 2.6 58 484-546 6-63 (243)
51 smart00361 RRM_1 RNA recogniti 91.1 0.077 1.7E-06 42.9 0.5 47 498-545 3-55 (70)
52 PF13893 RRM_5: RNA recognitio 91.1 0.043 9.2E-07 42.1 -1.0 39 500-545 1-39 (56)
53 KOG4205 RNA-binding protein mu 91.0 0.33 7.2E-06 51.1 5.1 127 402-546 21-158 (311)
54 TIGR01622 SF-CC1 splicing fact 90.7 0.16 3.4E-06 54.0 2.5 59 484-545 187-246 (457)
55 KOG4211 Splicing factor hnRNP- 90.6 0.63 1.4E-05 51.7 6.9 122 405-546 28-164 (510)
56 TIGR01645 half-pint poly-U bin 90.5 0.17 3.7E-06 57.6 2.7 58 486-545 110-167 (612)
57 PF09421 FRQ: Frequency clock 89.7 0.28 6.1E-06 58.1 3.6 48 423-470 473-523 (989)
58 KOG4849 mRNA cleavage factor I 89.3 10 0.00022 41.3 14.3 45 321-367 280-325 (498)
59 KOG0114 Predicted RNA-binding 88.7 0.39 8.4E-06 44.2 3.0 59 478-544 15-74 (124)
60 PRK00819 RNA 2'-phosphotransfe 88.3 0.57 1.2E-05 45.8 4.1 50 422-471 27-78 (179)
61 PF01885 PTS_2-RNA: RNA 2'-pho 88.0 0.53 1.2E-05 46.0 3.8 50 422-471 26-82 (186)
62 KOG0108 mRNA cleavage and poly 84.6 0.6 1.3E-05 51.3 2.3 59 485-545 20-78 (435)
63 KOG0107 Alternative splicing f 81.3 0.96 2.1E-05 44.8 2.1 49 486-543 13-63 (195)
64 KOG2278 RNA:NAD 2'-phosphotran 80.6 1.3 2.9E-05 43.7 2.8 41 419-459 25-65 (207)
65 KOG1365 RNA-binding protein Fu 79.3 2.5 5.4E-05 46.2 4.5 61 486-546 164-225 (508)
66 KOG4207 Predicted splicing fac 77.2 1.7 3.8E-05 44.1 2.5 59 484-545 14-73 (256)
67 KOG0921 Dosage compensation co 73.6 27 0.00058 42.4 11.0 11 260-270 1225-1235(1282)
68 KOG0106 Alternative splicing f 71.5 3.2 6.9E-05 42.0 2.8 48 488-545 104-151 (216)
69 KOG4307 RNA binding protein RB 70.6 4 8.6E-05 47.5 3.5 57 484-543 868-925 (944)
70 KOG0113 U1 small nuclear ribon 70.5 2.8 6E-05 44.5 2.2 60 484-546 102-162 (335)
71 PLN03213 repressor of silencin 70.3 2.8 6.1E-05 47.1 2.2 53 486-544 13-67 (759)
72 KOG0149 Predicted RNA-binding 68.3 4.2 9E-05 41.8 2.8 55 489-545 18-72 (247)
73 KOG0130 RNA-binding protein RB 68.1 2.7 5.9E-05 40.3 1.4 55 489-545 78-132 (170)
74 KOG0127 Nucleolar protein fibr 66.8 3.9 8.5E-05 46.4 2.5 60 484-545 293-352 (678)
75 KOG0144 RNA-binding protein CU 66.2 2.5 5.5E-05 46.7 0.8 130 398-545 49-183 (510)
76 KOG0110 RNA-binding protein (R 64.9 4.7 0.0001 46.8 2.6 56 488-545 618-673 (725)
77 KOG0148 Apoptosis-promoting RN 64.2 3.6 7.7E-05 43.3 1.4 52 485-544 166-217 (321)
78 KOG1924 RhoA GTPase effector D 63.4 37 0.0008 40.6 9.3 18 425-443 676-693 (1102)
79 KOG4660 Protein Mei2, essentia 62.4 3.9 8.5E-05 46.2 1.5 58 481-545 73-130 (549)
80 KOG0127 Nucleolar protein fibr 60.0 5.9 0.00013 45.1 2.3 59 485-545 7-65 (678)
81 PF14605 Nup35_RRM_2: Nup53/35 56.5 9.8 0.00021 30.0 2.4 49 485-544 5-53 (53)
82 KOG4212 RNA-binding protein hn 56.2 7.4 0.00016 43.4 2.2 63 481-545 42-104 (608)
83 KOG0116 RasGAP SH3 binding pro 54.9 8.5 0.00019 42.4 2.5 58 486-546 291-349 (419)
84 KOG0110 RNA-binding protein (R 54.8 5.8 0.00013 46.0 1.2 58 487-546 519-579 (725)
85 KOG0148 Apoptosis-promoting RN 54.3 10 0.00023 40.0 2.9 61 483-546 62-123 (321)
86 KOG0144 RNA-binding protein CU 52.1 8.9 0.00019 42.6 2.0 52 490-544 41-93 (510)
87 KOG0123 Polyadenylate-binding 50.6 10 0.00022 40.9 2.2 58 485-545 272-329 (369)
88 COG1859 KptA RNA:NAD 2'-phosph 47.7 19 0.00041 36.6 3.4 52 423-474 54-107 (211)
89 PF08777 RRM_3: RNA binding mo 46.7 8.4 0.00018 34.4 0.7 49 489-545 7-55 (105)
90 KOG4208 Nucleolar RNA-binding 45.3 22 0.00048 36.1 3.4 49 491-542 57-107 (214)
91 KOG4205 RNA-binding protein mu 44.1 18 0.00039 38.4 2.8 55 490-546 13-67 (311)
92 KOG0153 Predicted RNA-binding 42.3 20 0.00044 38.9 2.8 62 475-544 220-281 (377)
93 KOG0117 Heterogeneous nuclear 41.6 37 0.0008 38.1 4.7 87 446-540 134-221 (506)
94 KOG1548 Transcription elongati 41.2 23 0.0005 38.5 3.0 64 476-539 126-195 (382)
95 KOG0125 Ataxin 2-binding prote 40.6 17 0.00036 39.3 1.9 53 486-543 99-152 (376)
96 PTZ00315 2'-phosphotransferase 39.3 22 0.00048 40.8 2.7 49 422-470 399-455 (582)
97 KOG2253 U1 snRNP complex, subu 36.3 22 0.00047 41.3 2.0 51 413-465 51-101 (668)
98 KOG0131 Splicing factor 3b, su 36.3 19 0.00042 36.1 1.5 57 485-543 11-67 (203)
99 KOG0147 Transcriptional coacti 36.0 18 0.00039 41.1 1.3 58 487-546 282-339 (549)
100 KOG0146 RNA-binding protein ET 35.4 21 0.00045 37.9 1.6 50 493-545 29-78 (371)
101 PRK02001 hypothetical protein; 35.2 7.7 0.00017 37.1 -1.4 77 395-477 9-89 (152)
102 PF04963 Sigma54_CBD: Sigma-54 34.7 19 0.00041 35.2 1.1 40 393-432 14-54 (194)
103 KOG0145 RNA-binding protein EL 34.0 27 0.00058 36.9 2.1 53 490-545 48-101 (360)
104 PF05172 Nup35_RRM: Nup53/35/4 32.3 25 0.00055 31.5 1.4 59 486-547 9-74 (100)
105 KOG0147 Transcriptional coacti 31.9 12 0.00026 42.4 -0.8 55 483-540 179-234 (549)
106 KOG0120 Splicing factor U2AF, 31.4 30 0.00066 39.1 2.1 24 522-545 449-472 (500)
107 KOG1365 RNA-binding protein Fu 30.7 24 0.00053 38.9 1.2 55 489-543 286-340 (508)
108 KOG3973 Uncharacterized conser 30.3 1.9E+02 0.0042 31.9 7.7 9 218-226 384-392 (465)
109 KOG0105 Alternative splicing f 28.9 40 0.00086 34.2 2.3 55 486-545 9-63 (241)
110 KOG0111 Cyclophilin-type pepti 28.6 31 0.00066 35.8 1.4 60 483-544 10-69 (298)
111 KOG4209 Splicing factor RNPS1, 28.4 49 0.0011 33.7 2.9 51 493-545 111-161 (231)
112 KOG0533 RRM motif-containing p 28.1 39 0.00085 34.9 2.1 59 484-546 84-143 (243)
113 PRK12469 RNA polymerase factor 24.3 30 0.00064 38.9 0.5 67 394-461 123-192 (481)
114 TIGR02395 rpoN_sigma RNA polym 22.0 36 0.00078 37.5 0.6 59 393-456 75-136 (429)
115 PRK14642 hypothetical protein; 20.5 23 0.00051 35.5 -1.1 79 394-477 4-99 (197)
116 PRK05932 RNA polymerase factor 20.2 42 0.00091 37.3 0.7 60 393-457 100-162 (455)
No 1
>cd08037 LARP_1 La RNA-binding domain of La-related protein 1. This domain is found in vertebrate La-related protein 1 (LARP1). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.
Probab=99.96 E-value=1.1e-30 Score=217.22 Aligned_cols=72 Identities=50% Similarity=0.858 Sum_probs=70.8
Q ss_pred HHHHHhhhhhcCcCcccccchhhhccCCCCcEEehhhccchhhhhcccCHHHHHHHHhcCCcEEEcCCeEee
Q 008981 398 AMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVKNLTSNIQLILDSLRTSTVVEVQDDRVRR 469 (547)
Q Consensus 398 ~~I~kQVEYYFSDeNL~kD~FLr~~Md~qG~VPLs~IasFnRVK~Lt~d~~lI~eALr~S~~LEVsgdKVRR 469 (547)
++|++||||||||+||++|.|||++|++||||||++|++|||||+||.|+++|++||+.|++|||+++||||
T Consensus 2 ~~I~~QvEyYFSd~NL~~D~fLr~~md~dG~Vpi~~ia~F~rmk~Lt~d~~~I~~Al~~S~~vev~~~~~r~ 73 (73)
T cd08037 2 DYIKRQIEYYFSVDNLERDFFLRRKMDEDGFLPVTLIASFHRVQALTTDISLIIKALKDSKVVEIIDMKIRR 73 (73)
T ss_pred hHHHHHHHHhccHhhhccCHHHHHHhccCCCEeHHHHhcchHHHHhcCCHHHHHHHHHcCCeEEEecchhcC
Confidence 689999999999999999999999999999999999999999999999999999999999999999999997
No 2
>cd08038 LARP_2 La RNA-binding domain of La-related protein 2. This domain is found in vertebrate La-related protein 2 (LARP2). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.
Probab=99.96 E-value=1.6e-30 Score=216.28 Aligned_cols=72 Identities=51% Similarity=0.862 Sum_probs=70.9
Q ss_pred HHHHHhhhhhcCcCcccccchhhhccCCCCcEEehhhccchhhhhcccCHHHHHHHHhcCCcEEEcCCeEee
Q 008981 398 AMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVKNLTSNIQLILDSLRTSTVVEVQDDRVRR 469 (547)
Q Consensus 398 ~~I~kQVEYYFSDeNL~kD~FLr~~Md~qG~VPLs~IasFnRVK~Lt~d~~lI~eALr~S~~LEVsgdKVRR 469 (547)
++|++||||||||+||++|.|||++|++||||||++|++|||||+|+.|+++|++||+.|+.|||++++|||
T Consensus 2 e~I~~QvEfYFSd~NL~~D~fLr~~m~~~G~Vpl~~ia~F~rmk~lt~d~~~I~~Al~~S~~ve~~~~~~r~ 73 (73)
T cd08038 2 EYIKRQIEYYFSTENLERDFFLRRKMDLQGFLPISLIAGFYRVQALTTNVDLILEALKDSTEVEIVDQKIRR 73 (73)
T ss_pred hHHHhhHHhhcchhhhccCHHHHHHhCCCCCEeHHHHhcchHHHHhcCCHHHHHHHHHcCCeEEEeCCcccC
Confidence 689999999999999999999999999999999999999999999999999999999999999999999996
No 3
>cd08034 LARP_1_2 La RNA-binding domain proteins similar to La-related proteins 1 and 2. This domain is found in proteins similar to vertebrate La-related proteins 1 and 2 (LARP1, LARP2). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.
Probab=99.96 E-value=5.2e-30 Score=213.13 Aligned_cols=73 Identities=52% Similarity=0.850 Sum_probs=71.1
Q ss_pred HHHHHHhhhhhcCcCcccccchhhhccCCCCcEEehhhccchhhhhcccCHHHHHHHHhcCCcEEEcCCeEee
Q 008981 397 AAMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVKNLTSNIQLILDSLRTSTVVEVQDDRVRR 469 (547)
Q Consensus 397 ~~~I~kQVEYYFSDeNL~kD~FLr~~Md~qG~VPLs~IasFnRVK~Lt~d~~lI~eALr~S~~LEVsgdKVRR 469 (547)
+++|++||||||||+||++|.|||++|+.+|||||++|++|+|||+|+.|+++|++||+.|+.|||+++||||
T Consensus 1 ~~~i~~QvEfYFSd~NL~~D~fLr~~m~~~G~Vpl~~i~~F~rmk~l~~d~~~i~~Al~~S~~lev~e~kvR~ 73 (73)
T cd08034 1 KEYIKKQIEYYFSVDNLEKDFFLRRKMDPEGYLPIALIASFHRVQALTTDVNLILEALKDSTVVELVDEKVRC 73 (73)
T ss_pred ChHHHhhHHhhcCHhhhccCHHHHHHcCCCCCEeHHHHhccHHHHHHcCCHHHHHHHHHcCCeEEEecCeecC
Confidence 3689999999999999999999999999999999999999999999999999999999999999999999996
No 4
>cd08036 LARP_5 La RNA-binding domain of La-related protein 5. This domain is found in vertebrate La-related protein 5 (LARP5). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.
Probab=99.96 E-value=3.5e-30 Score=214.75 Aligned_cols=71 Identities=34% Similarity=0.677 Sum_probs=68.3
Q ss_pred HHHHHhhhhhcCcCcccccchhhhccCCCCcEEehhhccchhhhhcccCHHHHHHHHhcCCcEEEcC--CeEe
Q 008981 398 AMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVKNLTSNIQLILDSLRTSTVVEVQD--DRVR 468 (547)
Q Consensus 398 ~~I~kQVEYYFSDeNL~kD~FLr~~Md~qG~VPLs~IasFnRVK~Lt~d~~lI~eALr~S~~LEVsg--dKVR 468 (547)
+.|++||||||||+||++|.|||++||+||||||++||+|+|||+||+|+++|++||++|++|||++ +|||
T Consensus 2 e~i~kQvEyYFS~~NL~~D~fLr~~md~~g~Vpi~~ia~F~rik~Lt~D~~lI~~aL~~S~~vevse~g~kVR 74 (75)
T cd08036 2 ELLKKTLEFCLSRENLASDMYLISQMDSDQYVPIMTVANLDHIKKLSTDVDLIVDVLRSLPLVQVDEKGEKVR 74 (75)
T ss_pred hhhhcceeeeechhhccccHHHHHHhccCCCEehHHHhccHHHHHhcCCHHHHHHHHhhCCeEEECCCCCccC
Confidence 6799999999999999999999999999999999999999999999999999999999999999975 5777
No 5
>cd08035 LARP_4 La RNA-binding domain of La-related protein 4. This domain is found in vertebrate La-related protein 4 (LARP4), also known as c-MPL binding protein. La-type domains often co-occur with RNA-recognition motifs (RRMs). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.
Probab=99.96 E-value=6.2e-30 Score=213.64 Aligned_cols=71 Identities=42% Similarity=0.709 Sum_probs=68.4
Q ss_pred HHHHHhhhhhcCcCcccccchhhhccCCCCcEEehhhccchhhhhcccCHHHHHHHHhcCCcEEEcC--CeEe
Q 008981 398 AMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVKNLTSNIQLILDSLRTSTVVEVQD--DRVR 468 (547)
Q Consensus 398 ~~I~kQVEYYFSDeNL~kD~FLr~~Md~qG~VPLs~IasFnRVK~Lt~d~~lI~eALr~S~~LEVsg--dKVR 468 (547)
++|++||||||||+||++|.||+++||+||||||++|++|||||+||.|+++|++||+.|++|||++ +|||
T Consensus 2 e~i~~QvEyYFSd~NL~~D~fL~~~md~~G~Vpi~~iasF~rik~lt~d~~~I~~AL~~S~~levsedg~kVR 74 (75)
T cd08035 2 ECLKKQLEFCFSRENLSKDLYLISQMDSDQFVPIWTVANMEGIKKLTTDMDLILDVLRSSPMVQVDETGEKVR 74 (75)
T ss_pred hHHHhhHHhhcCHhhcccCHHHHHhhCcCCCEehHHHhccHHHHHhcCCHHHHHHHHHcCCeEEEcCCCCccC
Confidence 6899999999999999999999999999999999999999999999999999999999999999975 5777
No 6
>cd08032 LARP_7 La RNA-binding domain of La-related protein 7. LARP7 is a component of the 7SK snRNP, a key factor in the regulation of RNA polymerase II transcription. 7SK functionality is dependent on the presence of LARP7, which is thought to stabilize the 7SK RNA by interacting with its 3' end. The release of 7SK RNA from P-TEFb/HEXIM/7SK complexes activates the cyclin-dependent kinase P-TEFb, which in turn phosphorylates the C-terminal domain of RNA pol II and mediates a transition into productive transcription elongation.
Probab=99.95 E-value=1e-28 Score=209.53 Aligned_cols=76 Identities=39% Similarity=0.722 Sum_probs=72.3
Q ss_pred HHHHHHHHHhhhhhcCcCcccccchhhhccC--CCCcEEehhhccchhhhhcccCHHHHHHHHhcCCcEEEcC--CeEee
Q 008981 394 PSLAAMLIHQIDYYFSDANLVKDEFLKSNMD--DQGWVPITLIASFPRVKNLTSNIQLILDSLRTSTVVEVQD--DRVRR 469 (547)
Q Consensus 394 ~~L~~~I~kQVEYYFSDeNL~kD~FLr~~Md--~qG~VPLs~IasFnRVK~Lt~d~~lI~eALr~S~~LEVsg--dKVRR 469 (547)
.+|.++|++||||||||+||++|.||+++|+ .||||||++|++|||||+||.|+++|++||+.|+.|||++ ++|||
T Consensus 3 ~~l~~~I~~QvEfYFSd~NL~~D~fL~~~~~~~~dG~Vpl~~i~~F~rmk~lt~d~~~i~~Al~~S~~lev~ed~~~VRR 82 (82)
T cd08032 3 KQLLADIAKQVDFWFGDVNLHKDRFLREQIEKSRDGYIDISLLVSFNKMKKLTTDGKLIARALKNSSVVELNLEGTRIRR 82 (82)
T ss_pred HHHHHHHHHHHHhhcchhhcccCHHHHHHhcCCCCCCEeHHHHhcchHHHHHcCCHHHHHHHHhcCCEEEEcCCCCccCC
Confidence 4788999999999999999999999999996 7999999999999999999999999999999999999996 47886
No 7
>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]
Probab=99.95 E-value=1.2e-28 Score=257.17 Aligned_cols=150 Identities=31% Similarity=0.439 Sum_probs=131.5
Q ss_pred HHHHHHHHHhhhhhcCcCcccccchhhhcc--CCCCcEEehhhccchhhhhcccCHHHHHHHHhcCCcEEEcCC--eEee
Q 008981 394 PSLAAMLIHQIDYYFSDANLVKDEFLKSNM--DDQGWVPITLIASFPRVKNLTSNIQLILDSLRTSTVVEVQDD--RVRR 469 (547)
Q Consensus 394 ~~L~~~I~kQVEYYFSDeNL~kD~FLr~~M--d~qG~VPLs~IasFnRVK~Lt~d~~lI~eALr~S~~LEVsgd--KVRR 469 (547)
++|..+|++||||||||+||.+|.||.++| |++|||||++|++|||||+||.|+.+|.+|||.|.+|||++| ||||
T Consensus 138 edl~~kIv~QVEyyFSDenL~~d~fLlkhvrrnkeGyVpv~~vaSFKKvK~LTrd~~~va~ALr~S~kL~vseDgkKVrR 217 (484)
T KOG1855|consen 138 EDLAAKIVDQVEYYFSDENLLKDAFLLKHVRRNKEGYVPVKLVASFKKVKALTRDWKLVADALRKSSKLEVSEDGKKVRR 217 (484)
T ss_pred HHHHHHHHHHhheeeccccccchHHHHHHHhcCCCCceeeehhhhHHHHHHHhhhhHHHHHHHhhcceEEEccCCceeee
Confidence 689999999999999999999999999999 699999999999999999999999999999999999999865 8999
Q ss_pred CCcccccCCCCCCceeeeecCCCCCCChhhhhhhccccccccccc--c----cccccC-CCcc----cCCcccEEcCChh
Q 008981 470 RNEWMKWIATPGRISTESGLSSPAGSSVDVLAPSFQNITVKEGAV--N----QRSLTG-NANC----HCEDAPGIHSSEG 538 (547)
Q Consensus 470 r~~w~kwvp~~~r~~tV~g~~~p~~~T~d~L~~~F~~~gle~~~~--~----~~s~R~-~~k~----f~GsvfVEFsSeE 538 (547)
..++..+.-++.+.++|.+.+++.+.++++|+++|.++|...+++ + ....|. .++. .++-+||||...|
T Consensus 218 isPlp~~~~eel~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~ 297 (484)
T KOG1855|consen 218 ISPLPEFDEEELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVE 297 (484)
T ss_pred cCCCCCccccccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhH
Confidence 999998887778999999999999999999999999999644443 1 112232 1222 3788999999999
Q ss_pred hhhcC
Q 008981 539 EATEE 543 (547)
Q Consensus 539 eAkk~ 543 (547)
.|.|+
T Consensus 298 ~A~KA 302 (484)
T KOG1855|consen 298 AARKA 302 (484)
T ss_pred HHHHH
Confidence 99876
No 8
>cd08033 LARP_6 La RNA-binding domain of La-related protein 6. This domain is found in animal and plant proteins related to the La autoantigen. A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.
Probab=99.95 E-value=1.5e-28 Score=206.24 Aligned_cols=72 Identities=46% Similarity=0.833 Sum_probs=68.9
Q ss_pred HHHHHhhhhhcCcCcccccchhhhcc--CCCCcEEehhhccchhhhhcccCHHHHHHHHhcCCcEEEcCC--eEee
Q 008981 398 AMLIHQIDYYFSDANLVKDEFLKSNM--DDQGWVPITLIASFPRVKNLTSNIQLILDSLRTSTVVEVQDD--RVRR 469 (547)
Q Consensus 398 ~~I~kQVEYYFSDeNL~kD~FLr~~M--d~qG~VPLs~IasFnRVK~Lt~d~~lI~eALr~S~~LEVsgd--KVRR 469 (547)
++|++||||||||+||++|.||+++| |+||||||++|++|+|||+|+.|+++|++||+.|+.|||++| +|||
T Consensus 2 ~~i~~QvEfYFSd~NL~~D~fL~~~~~~~~dG~Vpl~~i~~F~rmk~l~~d~~~I~~Al~~S~~lev~~d~~~VRR 77 (77)
T cd08033 2 QKIVKQVEYYFSDENLLKDAFLLKHVRRNKEGYVPIKLIASFKKVKALTRDWRVVAAALRRSSKLVVSEDGKKVRR 77 (77)
T ss_pred hHHHhHHHhhcCHhhhccCHHHHHHhccCCCCcEehHHHhcchHHHHHcCCHHHHHHHHHhCCeEEEcCCCCccCC
Confidence 58999999999999999999999999 789999999999999999999999999999999999999965 7886
No 9
>smart00715 LA Domain in the RNA-binding Lupus La protein; unknown function.
Probab=99.95 E-value=2.4e-28 Score=206.09 Aligned_cols=76 Identities=51% Similarity=0.917 Sum_probs=72.5
Q ss_pred HHHHHHHHhhhhhcCcCcccccchhhhccCC-CCcEEehhhccchhhhhcccCHHHHHHHHhcCCcEEEcCC--eEeeC
Q 008981 395 SLAAMLIHQIDYYFSDANLVKDEFLKSNMDD-QGWVPITLIASFPRVKNLTSNIQLILDSLRTSTVVEVQDD--RVRRR 470 (547)
Q Consensus 395 ~L~~~I~kQVEYYFSDeNL~kD~FLr~~Md~-qG~VPLs~IasFnRVK~Lt~d~~lI~eALr~S~~LEVsgd--KVRRr 470 (547)
+++++|++||||||||+||++|.||+++|+. +|||||++|++|+|||+|+.|.++|++||+.|..|||++| +|||+
T Consensus 2 ~~~~~i~~QvEfYFSd~NL~~D~fLr~~~~~~~g~Vpl~~i~~F~r~k~l~~d~~~i~~Al~~S~~lel~~d~~~VRR~ 80 (80)
T smart00715 2 ELKQKIKKQVEYYFSDENLPRDKFLRKKMDKNDGYVPISTIASFKRVKSLTTDVNLIVEALRSSPKLEVSEDGLKVRRR 80 (80)
T ss_pred hHHHHHHHHHHHHcCHhhhhhCHHHHHHhccCCCCEEhHHHhCchhHHHHcCCHHHHHHHHHhCCeEEEcCCCCeeCcC
Confidence 6889999999999999999999999999987 9999999999999999999999999999999999999965 78874
No 10
>cd08031 LARP_4_5_like La RNA-binding domain of proteins similar to La-related proteins 4 and 5. This domain is found in proteins similar to La-related proteins 4 and 5 (LARP4, LARP5). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.
Probab=99.95 E-value=2.1e-28 Score=204.47 Aligned_cols=71 Identities=45% Similarity=0.793 Sum_probs=68.2
Q ss_pred HHHHHhhhhhcCcCcccccchhhhccCCCCcEEehhhccchhhhhcccCHHHHHHHHhcCCcEEEcCC--eEe
Q 008981 398 AMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVKNLTSNIQLILDSLRTSTVVEVQDD--RVR 468 (547)
Q Consensus 398 ~~I~kQVEYYFSDeNL~kD~FLr~~Md~qG~VPLs~IasFnRVK~Lt~d~~lI~eALr~S~~LEVsgd--KVR 468 (547)
++|++||||||||+||++|.||+++|++||||||++|++|+|||+|+.|.++|++||+.|+.|||++| +||
T Consensus 2 ~~i~~QvEfYFSd~NL~~D~fL~~~m~~dG~Vpl~~i~~F~rmk~lt~d~~~i~~Al~~S~~lev~ed~~~VR 74 (75)
T cd08031 2 ELLKRQLEYYFSRENLANDAYLLSQMDSDQYVPIWTIANFNKIKKLTTDIDLIVEALRESPNVQVDEKGEKVR 74 (75)
T ss_pred hHHHHHHHHHcCHhhhccCHHHHHHhCCCCCEEHHHHhCchhHHHHcCCHHHHHHHHHhCCeEEEcCCCCccC
Confidence 68999999999999999999999999999999999999999999999999999999999999999965 566
No 11
>cd08028 LARP_3 La RNA-binding domain of La-related protein 3. This domain is found at the N-terminus of the La autoantigen and similar proteins, and co-occurs with an RNA-recognition motif (RRM). Together these domains function to bind primary transcripts of RNA polymerase III at their 3' terminus and protect them from exonucleolytic degradation. Binding is specific for the 3'-terminal UUU-OH motif. The La autoantigen is also called Lupus La protein, LARP3, or Sjoegren syndrome type B antigen (SS-B).
Probab=99.94 E-value=5.1e-28 Score=205.23 Aligned_cols=76 Identities=42% Similarity=0.857 Sum_probs=71.9
Q ss_pred HHHHHHHHHhhhhhcCcCcccccchhhhccC-CCCcEEehhhccchhhhhcccCHHHHHHHHhcCC--cEEEcCC--eEe
Q 008981 394 PSLAAMLIHQIDYYFSDANLVKDEFLKSNMD-DQGWVPITLIASFPRVKNLTSNIQLILDSLRTST--VVEVQDD--RVR 468 (547)
Q Consensus 394 ~~L~~~I~kQVEYYFSDeNL~kD~FLr~~Md-~qG~VPLs~IasFnRVK~Lt~d~~lI~eALr~S~--~LEVsgd--KVR 468 (547)
++|+.+|++||||||||+||++|.|||++|+ .||||||++|++|+|||+|+.|.++|++||+.|+ +|||++| +||
T Consensus 2 ~~l~~~I~~QvEfYFSd~NL~~D~fLr~~m~~~~G~Vpl~~i~~F~rmk~l~~d~~~i~~Al~~S~~~~lev~~d~~~VR 81 (82)
T cd08028 2 DDLEKKIIRQIEYYFGDFNLPRDKFLKEQIKEDDGWVPMEVMLKFNRLKSLSSDPEVIAKALKKSKSGLIEVSEDKTKIR 81 (82)
T ss_pred hHHHHHHHHHHHhhcCHhhhccCHHHHHHHhccCCCEEhHHHhCChhHHHhcCCHHHHHHHHHhCCCCEEEEcCCCCccC
Confidence 4689999999999999999999999999997 5999999999999999999999999999999999 9999965 687
Q ss_pred e
Q 008981 469 R 469 (547)
Q Consensus 469 R 469 (547)
|
T Consensus 82 R 82 (82)
T cd08028 82 R 82 (82)
T ss_pred C
Confidence 6
No 12
>cd08029 LA_like_fungal La-motif domain of fungal proteins similar to the La autoantigen. This domain is found in fungal proteins related to the La autoantigen. A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.
Probab=99.94 E-value=1.8e-27 Score=199.19 Aligned_cols=71 Identities=41% Similarity=0.778 Sum_probs=66.9
Q ss_pred HHHHHhhhhhcCcCcccccchhhhcc--CCCCcEEehhhccchhhhhcccCHHHHHHHHhcCCcEEEcCC--eEee
Q 008981 398 AMLIHQIDYYFSDANLVKDEFLKSNM--DDQGWVPITLIASFPRVKNLTSNIQLILDSLRTSTVVEVQDD--RVRR 469 (547)
Q Consensus 398 ~~I~kQVEYYFSDeNL~kD~FLr~~M--d~qG~VPLs~IasFnRVK~Lt~d~~lI~eALr~S~~LEVsgd--KVRR 469 (547)
++|++||||||||+||++|.|||++| +.||||||++|++|+|||+|+.+ ++|++||+.|+.|||++| +|||
T Consensus 2 ~~I~~QvEfYFSd~NL~~D~fLr~~~~~~~~G~Vpl~~i~~F~rmk~l~~~-~~i~~Al~~S~~lev~~d~~~VRR 76 (76)
T cd08029 2 EEIRKQVEFYFSDSNLPTDKFLWTLTGGSNNGWVPIKTIASFKRMRRFQPL-EAVVEALRESELLEVSEDGENVRR 76 (76)
T ss_pred hHHHhhHHhhcCHhhhccCHHHHHHhccCCCCcEehHHHhCchHHHHcCCH-HHHHHHHHhCCeEEEeCCCCcccC
Confidence 58999999999999999999999999 69999999999999999999965 999999999999999965 7887
No 13
>cd07323 LAM LA motif RNA-binding domain. This domain is found at the N-terminus of La RNA-binding proteins as well as in other related proteins. Typically, the domain co-occurs with an RNA-recognition motif (RRM), and together these domains function to bind primary transcripts of RNA polymerase III in the La autoantigen (Lupus La protein, LARP3, or Sjoegren syndrome type B antigen, SS-B). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.
Probab=99.93 E-value=5.5e-27 Score=195.45 Aligned_cols=72 Identities=60% Similarity=1.051 Sum_probs=69.1
Q ss_pred HHHHHhhhhhcCcCcccccchhhhccCCCCcEEehhhccchhhhhcccCHHHHHHHHhcCCcEEEcCC--eEee
Q 008981 398 AMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVKNLTSNIQLILDSLRTSTVVEVQDD--RVRR 469 (547)
Q Consensus 398 ~~I~kQVEYYFSDeNL~kD~FLr~~Md~qG~VPLs~IasFnRVK~Lt~d~~lI~eALr~S~~LEVsgd--KVRR 469 (547)
++|++||||||||+||++|.||+++|+++|||||++|++|+|||+|+.|.++|++||+.|..|||+++ +|||
T Consensus 2 ~~i~~QvEfYFSd~NL~~D~fL~~~~~~~g~Vpl~~i~~F~r~k~l~~~~~~i~~Al~~s~~lel~~~~~~Vrr 75 (75)
T cd07323 2 EKIKKQVEYYFSDENLCKDRFLRSLMDDDGWVPLSLLASFNRVKKLTTDVELILEALRDSSVVEVSEDGTKVRR 75 (75)
T ss_pred hHHHhhhHhccCHhhhCcCHHHHHhcCCCCCEEHHHHhCchHHHHHcCCHHHHHHHHHhCCeEEEeCCCCccCC
Confidence 57999999999999999999999999999999999999999999999999999999999999999974 6876
No 14
>cd08030 LA_like_plant La-motif domain of plant proteins similar to the La autoantigen. This domain is found in plant proteins related to the La autoantigen. A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.
Probab=99.93 E-value=4.8e-27 Score=202.40 Aligned_cols=73 Identities=40% Similarity=0.772 Sum_probs=68.0
Q ss_pred HHHHHHhhhhhcCcCcccccchhhhcc--CCCCcEEehhhccchhhhhccc------------CHHHHHHHHhcCCcEEE
Q 008981 397 AAMLIHQIDYYFSDANLVKDEFLKSNM--DDQGWVPITLIASFPRVKNLTS------------NIQLILDSLRTSTVVEV 462 (547)
Q Consensus 397 ~~~I~kQVEYYFSDeNL~kD~FLr~~M--d~qG~VPLs~IasFnRVK~Lt~------------d~~lI~eALr~S~~LEV 462 (547)
+++|++||||||||+||++|+||+++| ++||||||++|++|||||+|+. |+++|++||+.|++|||
T Consensus 2 ~~~i~~QvEfYFSd~NL~~D~fL~~~~~~~~dG~V~i~~i~~F~rmk~l~~~~~~~~~~~~~~~~~~I~~ALk~S~~lev 81 (90)
T cd08030 2 KEKVLRQVEFYFSDSNLPRDDFLLEEVEEDPDGMVSLALICSFSRMRSLLGLGGGKPEDVPEDTLKAVAEALRTSTLLKV 81 (90)
T ss_pred hHHHHHHHHcccchhhcccCHHHHHHhccCCCCCEehHHHhcChHHHHHhhcccccccccchhHHHHHHHHHccCCEEEE
Confidence 579999999999999999999999999 7899999999999999999985 37899999999999999
Q ss_pred cCC--eEee
Q 008981 463 QDD--RVRR 469 (547)
Q Consensus 463 sgd--KVRR 469 (547)
++| +|||
T Consensus 82 seD~~~VRR 90 (90)
T cd08030 82 SEDGKRVGR 90 (90)
T ss_pred cCCCCccCC
Confidence 976 6776
No 15
>PF05383 La: La domain; InterPro: IPR006630 Human Ro ribonucleoproteins (RNPs) are composed of one of the four small Y RNAs and at least two proteins, Ro60 and La. The La protein is a 47 kDa polypeptide that frequently acts as an autoantigen in systemic lupus erythematosus and Sjogren's syndrome []. In the nucleus, La acts as a RNA polymerase III (RNAP III) transcription factor, while in the cytoplasm, La acts as a translation factor []. In the nucleus, La binds to the 3'UTR of nascent RNAP III transcripts to assist in folding and maturation []. In the cytoplasm, La recognises specific classes of mRNAs that contain a 5'-terminal oligopyrimidine (5'TOP) motif known to control protein synthesis []. The specific recognition is mediated by the N-terminal domain of La, which comprises a La motif and a RNA recognition motif (RRM). The La motif adopts an alpha/beta fold that comprises a winged-helix motif []. Homologous La domain-containing proteins have been identified in a wide range of organisms except Archaea, bacteria and viruses [].; PDB: 1S29_A 1YTY_B 2VOO_B 1S7A_A 2VOP_A 2VON_B 1ZH5_B 2VOD_A 2CQK_A.
Probab=99.88 E-value=5e-24 Score=171.51 Aligned_cols=58 Identities=55% Similarity=1.016 Sum_probs=53.3
Q ss_pred HHHhhhhhcCcCcccccchhhhccCC--CCcEEehhhccchhhhhcc-cCHHHHHHHHhcC
Q 008981 400 LIHQIDYYFSDANLVKDEFLKSNMDD--QGWVPITLIASFPRVKNLT-SNIQLILDSLRTS 457 (547)
Q Consensus 400 I~kQVEYYFSDeNL~kD~FLr~~Md~--qG~VPLs~IasFnRVK~Lt-~d~~lI~eALr~S 457 (547)
|++||||||||+||++|+||+++|+. ||||||++|++|+|||+|+ .|+++|++||++|
T Consensus 1 I~~QvEfYFSd~NL~~D~fL~~~~~~~~~g~Vpi~~i~~F~r~k~l~~~~~~~I~~al~~S 61 (61)
T PF05383_consen 1 IKKQVEFYFSDENLPRDKFLRSQMDSNPDGWVPISTILSFNRMKALTNTDIELIVDALRDS 61 (61)
T ss_dssp HHHHHHHHTSHHHHCC-HHHHHHHCTTTTTBEEHHHHTTSHHHHHH--S-HHHHHHHHHTS
T ss_pred ChhHHHHhcCHHHhCcCHHHHHHHHhcCCCcEeHHHHHchHHHHHHhcCCHHHHHHHHHcC
Confidence 78999999999999999999999986 9999999999999999999 8999999999987
No 16
>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]
Probab=99.83 E-value=2.8e-21 Score=206.88 Aligned_cols=135 Identities=29% Similarity=0.459 Sum_probs=107.3
Q ss_pred HHHHHHHHHhhhhhcCcCcccccchhhhccCCCCcEEehhhccchhhhhcccCHHHHHHHHhcCCcEEEcC--CeEeeCC
Q 008981 394 PSLAAMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVKNLTSNIQLILDSLRTSTVVEVQD--DRVRRRN 471 (547)
Q Consensus 394 ~~L~~~I~kQVEYYFSDeNL~kD~FLr~~Md~qG~VPLs~IasFnRVK~Lt~d~~lI~eALr~S~~LEVsg--dKVRRr~ 471 (547)
.+|++.|++|||||||.+||..|.||+.+||+|.||||.+||.|..|++||+|++||+|+||+|..||||+ +|||-.
T Consensus 94 ~~~kq~lk~qlEy~fSreNlssD~YL~sQMDSDqyVPI~tva~~~~i~klttDvdLI~Evlresp~VqvDekgekVrp~- 172 (684)
T KOG2591|consen 94 RDLKQLLKKQLEYYFSRENLSSDRYLISQMDSDQYVPINTVANFPEIMKLTTDVDLIVEVLRESPNVQVDEKGEKVRPN- 172 (684)
T ss_pred hhHHHHHHHHHHHhhccccccchhhhhhhcccccccchhhhccchhhhhhccchHHHHHHHhcCCCceeccCccccccC-
Confidence 39999999999999999999999999999999999999999999999999999999999999999999995 577732
Q ss_pred cccccCCCCCCceeeeecCCCCCCChhhhhhhcccccccccccccccccCCCcccCCcccEEcCChhhhhcCCC
Q 008981 472 EWMKWIATPGRISTESGLSSPAGSSVDVLAPSFQNITVKEGAVNQRSLTGNANCHCEDAPGIHSSEGEATEEPN 545 (547)
Q Consensus 472 ~w~kwvp~~~r~~tV~g~~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R~~~k~f~GsvfVEFsSeEeAkk~~~ 545 (547)
-.|++++..+. ++..-+|+++.+|..-.+... +++ +=.+...-||.|.+++||+++.|
T Consensus 173 --------~kRcIvilREI-pettp~e~Vk~lf~~encPk~----isc---efa~N~nWyITfesd~DAQqAyk 230 (684)
T KOG2591|consen 173 --------HKRCIVILREI-PETTPIEVVKALFKGENCPKV----ISC---EFAHNDNWYITFESDTDAQQAYK 230 (684)
T ss_pred --------cceeEEEEeec-CCCChHHHHHHHhccCCCCCc----eee---eeeecCceEEEeecchhHHHHHH
Confidence 22444445543 566667778887776432111 111 12234567999999999998753
No 17
>KOG2590 consensus RNA-binding protein LARP/SRO9 and related La domain proteins [Posttranslational modification, protein turnover, chaperones; Translation, ribosomal structure and biogenesis]
Probab=99.83 E-value=5.3e-19 Score=188.12 Aligned_cols=75 Identities=41% Similarity=0.753 Sum_probs=68.8
Q ss_pred HHHHHhhhhhcCcCcccccchhhhccCCCCcEEehhhccchhhhhcccCHHHHHHHHhcCCcEEEcCCeEee-CCccccc
Q 008981 398 AMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVKNLTSNIQLILDSLRTSTVVEVQDDRVRR-RNEWMKW 476 (547)
Q Consensus 398 ~~I~kQVEYYFSDeNL~kD~FLr~~Md~qG~VPLs~IasFnRVK~Lt~d~~lI~eALr~S~~LEVsgdKVRR-r~~w~kw 476 (547)
+.|.+|||||||.||||+|.||+++| |+|.||++|+||..|+.|+++|++||+.+.+||+.+|.+|| +..|-.|
T Consensus 302 ~~~~~~ie~~FSeE~~~~d~~n~~k~-----~~l~~ia~F~r~ad~s~d~nli~~alr~s~ive~~~d~~~r~~~~~g~~ 376 (448)
T KOG2590|consen 302 AFIQEPIEFYFSEENLQRDRFNREKF-----VPLRVIAKFKRVADLSSDINLILAALRNSLIVEETGDLERRGGDRWGNH 376 (448)
T ss_pred cccccccccccchHHHhhhhhhhccc-----chhhhhhhhhhhhhcccCHHHHHHHHhhhhhhhccchhhhcccccccce
Confidence 57899999999999999999999865 66999999999999999999999999999999999888887 6677777
Q ss_pred C
Q 008981 477 I 477 (547)
Q Consensus 477 v 477 (547)
+
T Consensus 377 ~ 377 (448)
T KOG2590|consen 377 V 377 (448)
T ss_pred e
Confidence 6
No 18
>KOG4213 consensus RNA-binding protein La [RNA processing and modification]
Probab=99.73 E-value=1.1e-18 Score=166.52 Aligned_cols=142 Identities=25% Similarity=0.422 Sum_probs=109.3
Q ss_pred HHHHHHHHHhhhhhcCcCcccccchhhhcc--CCCCcEEehhhccchhhhhcccCHHHHHHHHhcCC--cEEEcCCe--E
Q 008981 394 PSLAAMLIHQIDYYFSDANLVKDEFLKSNM--DDQGWVPITLIASFPRVKNLTSNIQLILDSLRTST--VVEVQDDR--V 467 (547)
Q Consensus 394 ~~L~~~I~kQVEYYFSDeNL~kD~FLr~~M--d~qG~VPLs~IasFnRVK~Lt~d~~lI~eALr~S~--~LEVsgdK--V 467 (547)
.+|.++|..||||||.|-||.||.|||.+| ..+|||||.++..|+|+..|++|++.|++||+.|. ++||++|+ +
T Consensus 11 a~lE~kii~qleyy~Gd~nl~rdkfl~eqi~k~~~gwvpi~i~i~FnRla~lttD~~~Iv~al~ksk~~l~eisedk~k~ 90 (205)
T KOG4213|consen 11 AALEAKIIHQLEYYFGDLNLPRDKFLREQIHKLDDGWVPIEIMIKFNRLASLTTDFNVIVEALSKSKAELMEISEDKTKI 90 (205)
T ss_pred hHHHHhhhhhhhhhhcccCchHHHHHHHHhhhhccCCccchhhhhhhhhhhccccHHHHHHHHhhCHHhhhhhhhchhhh
Confidence 478889999999999999999999999999 48999999999999999999999999999999984 89999874 6
Q ss_pred eeCCcccccCCCC-------CCceeeeecCCCCCCChhhhhhhccccccccccccccccc-CCC--cccCCcccEEcCCh
Q 008981 468 RRRNEWMKWIATP-------GRISTESGLSSPAGSSVDVLAPSFQNITVKEGAVNQRSLT-GNA--NCHCEDAPGIHSSE 537 (547)
Q Consensus 468 RRr~~w~kwvp~~-------~r~~tV~g~~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R-~~~--k~f~GsvfVEFsSe 537 (547)
||. ..+-+|+- ...++|+.- +.+..+++|..|-..-+. ....| ... .-|+|++||.|.+.
T Consensus 91 rr~--~skplpEvt~e~~~~~~~r~v~~K--~td~ql~~l~qw~~~k~~------nv~mr~~~~k~~~fkGsvkv~f~tk 160 (205)
T KOG4213|consen 91 RRS--PSKPLPEVTDEYKEGIKERTVYKK--ITDDQLDDLNQWASGKGH------NVKMRRHGNKAHPFKGSVKVTFQTK 160 (205)
T ss_pred hcC--cCCCCccccHHHHHHHHHhhhhcc--CCHHHHHHHHHHhcccce------EeeccccCCCCCCCCCceEEEeecH
Confidence 654 23333332 233444443 567778888887762221 11223 223 48999999999999
Q ss_pred hhhhcCCC
Q 008981 538 GEATEEPN 545 (547)
Q Consensus 538 EeAkk~~~ 545 (547)
|.|+.-++
T Consensus 161 ~qa~a~~~ 168 (205)
T KOG4213|consen 161 EQAFANDD 168 (205)
T ss_pred HHHHhhhh
Confidence 99987443
No 19
>COG5193 LHP1 La protein, small RNA-binding pol III transcript stabilizing protein and related La-motif-containing proteins involved in translation [Posttranslational modification, protein turnover, chaperones / Translation, ribosomal structure and biogenesis]
Probab=99.43 E-value=3.8e-14 Score=148.42 Aligned_cols=83 Identities=30% Similarity=0.637 Sum_probs=70.7
Q ss_pred HHHHHHhhhhhcCcCcccccchhhhccCCCCcEEehhhccchhhhhcccCHHHHHHHHhcC-----------------C-
Q 008981 397 AAMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVKNLTSNIQLILDSLRTS-----------------T- 458 (547)
Q Consensus 397 ~~~I~kQVEYYFSDeNL~kD~FLr~~Md~qG~VPLs~IasFnRVK~Lt~d~~lI~eALr~S-----------------~- 458 (547)
...|+.|||||||.+|||.|.|||++|+++||||+++|..|.|.+.+..|.++|+.|||.+ .
T Consensus 271 I~a~k~QiEyYFseenl~~d~~lrkk~~kaGf~plsfi~kf~Rn~Sf~gd~nLilaa~ke~v~n~a~~~~~~~~~~~~d~ 350 (438)
T COG5193 271 IMAKKEQIEYYFSEENLKSDEFLRKKFKKAGFIPLSFIGKFYRNLSFGGDKNLILAAMKEVVQNKATNHLEIALGSIEDA 350 (438)
T ss_pred hhhHHhhhHhhhhHHhhhhhhHHHhhhhhcccccHhhhhhhhhccccCCchhhhHHHHHHHhhhhhhhhhhhhhhccchh
Confidence 3467779999999999999999999999999999999999999999999999999999987 1
Q ss_pred -cEEEc----C-CeEeeCCcccccCCC
Q 008981 459 -VVEVQ----D-DRVRRRNEWMKWIAT 479 (547)
Q Consensus 459 -~LEVs----g-dKVRRr~~w~kwvp~ 479 (547)
..+.+ + ..++|++.|..|+++
T Consensus 351 ~~~~~k~~sp~~~~f~rkk~wSewl~e 377 (438)
T COG5193 351 QKNEAKDFSPGKKYFIRKKEWSEWLME 377 (438)
T ss_pred hhccccccCcchhhhhhhhhhhhhhcc
Confidence 11111 1 247888899999965
No 20
>COG5193 LHP1 La protein, small RNA-binding pol III transcript stabilizing protein and related La-motif-containing proteins involved in translation [Posttranslational modification, protein turnover, chaperones / Translation, ribosomal structure and biogenesis]
Probab=99.36 E-value=2.2e-13 Score=142.85 Aligned_cols=144 Identities=26% Similarity=0.305 Sum_probs=107.7
Q ss_pred HHHhhhhhcC-----cCcccccchhhhcc----CCCCcEEehhhccchhhhhcccCHHHHHHHHhcC---CcEEEcC--C
Q 008981 400 LIHQIDYYFS-----DANLVKDEFLKSNM----DDQGWVPITLIASFPRVKNLTSNIQLILDSLRTS---TVVEVQD--D 465 (547)
Q Consensus 400 I~kQVEYYFS-----DeNL~kD~FLr~~M----d~qG~VPLs~IasFnRVK~Lt~d~~lI~eALr~S---~~LEVsg--d 465 (547)
+.+|+||||| |.|+.+|+||+..- ..+|||||..|++|+|||.++..+..|..||++| .++||+. .
T Consensus 75 ~l~qvE~~fS~s~~~d~n~~~dk~~ktta~Kn~~~~kwVpIkt~~tfn~~k~~gs~~~~v~~a~rks~~~rv~e~Sssgs 154 (438)
T COG5193 75 TLKQVEFYFSGSKDTDSNFPKDKFLKTTAPKNKKRDKWVPIKTIATFNRMKNSGSPVSAVSGALRKSLDARVLEVSSSGS 154 (438)
T ss_pred cccceeEEeeccccccccccchhhhccccccccCCCCceeeeeeeeeccccccCCchhhhhhhhhcCcccceeeeccccc
Confidence 8899999999 99999999999875 2599999999999999999999999999999999 7999984 4
Q ss_pred eEeeCCcccccCCC--CC--CceeeeecCCCCCC------ChhhhhhhcccccccccccccccccC-C-CcccCCcccEE
Q 008981 466 RVRRRNEWMKWIAT--PG--RISTESGLSSPAGS------SVDVLAPSFQNITVKEGAVNQRSLTG-N-ANCHCEDAPGI 533 (547)
Q Consensus 466 KVRRr~~w~kwvp~--~~--r~~tV~g~~~p~~~------T~d~L~~~F~~~gle~~~~~~~s~R~-~-~k~f~GsvfVE 533 (547)
++||++......-. +. |..++.+++..... +.++|..+|-.-++... ..+..|. - .+.|.|+||+|
T Consensus 155 n~~r~~k~~s~n~~s~~~~qr~~y~n~fG~e~~~~a~~~e~~~d~~~~~p~h~h~~~--~~i~~rrd~~nkn~~gSv~~e 232 (438)
T COG5193 155 NKNRTEKLISNNNKSTSQMQRDVYQNGFGKEDVNNASRPEQQEDLEIQFPPHYHAPP--SQIRNRRDWLNKNFRGSVFVE 232 (438)
T ss_pred cccccchhhhhhhhhhhhHhhhHHhhcCCcccccccccchhhhhHHhhCCCcccCCh--hhccchhhhhhccccCccccc
Confidence 66666543332211 22 23334444433222 25689999988543221 2223343 2 78999999999
Q ss_pred cCChhhhhcCCC
Q 008981 534 HSSEGEATEEPN 545 (547)
Q Consensus 534 FsSeEeAkk~~~ 545 (547)
|+..++|+..++
T Consensus 233 fk~~~~~q~~nn 244 (438)
T COG5193 233 FKYFREAQRFNN 244 (438)
T ss_pred ccChHHHHHHhc
Confidence 999999998885
No 21
>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=97.39 E-value=0.00015 Score=76.19 Aligned_cols=96 Identities=13% Similarity=-0.015 Sum_probs=63.8
Q ss_pred cCHHHHHHHHhcCCcEEEcCCeEeeCCcccccCCCCCCceeeeecCCCCCCChhhhhhhccccccccccccccccc-CCC
Q 008981 445 SNIQLILDSLRTSTVVEVQDDRVRRRNEWMKWIATPGRISTESGLSSPAGSSVDVLAPSFQNITVKEGAVNQRSLT-GNA 523 (547)
Q Consensus 445 ~d~~lI~eALr~S~~LEVsgdKVRRr~~w~kwvp~~~r~~tV~g~~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R-~~~ 523 (547)
.|.+...+||+...-++|.+.+|+-. |.+.-.+......+...+++...|.++|+++|.+++.... .+ -++ ..+
T Consensus 157 ~~~e~A~~Ai~~LnG~~l~gr~i~V~--~a~p~~~~~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~-v~--i~~d~~t 231 (346)
T TIGR01659 157 GSEADSQRAIKNLNGITVRNKRLKVS--YARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQ-KN--ILRDKLT 231 (346)
T ss_pred ccHHHHHHHHHHcCCCccCCceeeee--cccccccccccceeEEeCCCCcccHHHHHHHHHhcCCEEE-EE--EeecCCC
Confidence 36777888888777777777666532 2221111222334556678999999999999999983211 11 122 234
Q ss_pred cccCCcccEEcCChhhhhcCCC
Q 008981 524 NCHCEDAPGIHSSEGEATEEPN 545 (547)
Q Consensus 524 k~f~GsvfVEFsSeEeAkk~~~ 545 (547)
...+|.+||||.+.|+|+++++
T Consensus 232 g~~kG~aFV~F~~~e~A~~Ai~ 253 (346)
T TIGR01659 232 GTPRGVAFVRFNKREEAQEAIS 253 (346)
T ss_pred CccceEEEEEECCHHHHHHHHH
Confidence 5567999999999999999875
No 22
>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=96.73 E-value=0.00064 Score=53.61 Aligned_cols=55 Identities=16% Similarity=0.021 Sum_probs=39.1
Q ss_pred ecCCCCCCChhhhhhhcccccccccccccccccCCCcccCCcccEEcCChhhhhcCCC
Q 008981 488 GLSSPAGSSVDVLAPSFQNITVKEGAVNQRSLTGNANCHCEDAPGIHSSEGEATEEPN 545 (547)
Q Consensus 488 g~~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R~~~k~f~GsvfVEFsSeEeAkk~~~ 545 (547)
..++|...|.++|.++|..++.. .++.-.+.....+++.+||||.|+|+|+++++
T Consensus 3 i~nlp~~~~~~~l~~~f~~~g~v---~~v~~~~~~~~~~~~~a~v~f~~~~~a~~al~ 57 (70)
T PF14259_consen 3 ISNLPPSTTEEDLRNFFSRFGPV---EKVRLIKNKDGQSRGFAFVEFSSEEDAKRALE 57 (70)
T ss_dssp EESSTTT--HHHHHHHCTTSSBE---EEEEEEESTTSSEEEEEEEEESSHHHHHHHHH
T ss_pred EeCCCCCCCHHHHHHHHHhcCCc---ceEEEEeeeccccCCEEEEEeCCHHHHHHHHH
Confidence 34678889999999999999742 11111122236889999999999999999875
No 23
>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=96.61 E-value=0.00069 Score=52.30 Aligned_cols=53 Identities=15% Similarity=0.030 Sum_probs=42.4
Q ss_pred cCCCCCCChhhhhhhccccccccccccccccc-CCCcccCCcccEEcCChhhhhcCCC
Q 008981 489 LSSPAGSSVDVLAPSFQNITVKEGAVNQRSLT-GNANCHCEDAPGIHSSEGEATEEPN 545 (547)
Q Consensus 489 ~~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R-~~~k~f~GsvfVEFsSeEeAkk~~~ 545 (547)
.+++...|.++|.++|+.+|...... +. ...+.+++.+||+|.++|+|+++++
T Consensus 4 ~nlp~~~t~~~l~~~f~~~g~i~~~~----~~~~~~~~~~~~a~V~F~~~~~a~~a~~ 57 (70)
T PF00076_consen 4 GNLPPDVTEEELRDFFSQFGKIESIK----VMRNSSGKSKGYAFVEFESEEDAEKALE 57 (70)
T ss_dssp ESETTTSSHHHHHHHHHTTSTEEEEE----EEEETTSSEEEEEEEEESSHHHHHHHHH
T ss_pred cCCCCcCCHHHHHHHHHHhhhccccc----ccccccccccceEEEEEcCHHHHHHHHH
Confidence 46789999999999999998542221 22 2678889999999999999999875
No 24
>TIGR01622 SF-CC1 splicing factor, CC1-like family. A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.
Probab=96.25 E-value=0.0035 Score=66.31 Aligned_cols=64 Identities=11% Similarity=-0.162 Sum_probs=47.1
Q ss_pred CCCceeeeecCCCCCCChhhhhhhcccccccccccccccccCCCcccCCcccEEcCChhhhhcCCC
Q 008981 480 PGRISTESGLSSPAGSSVDVLAPSFQNITVKEGAVNQRSLTGNANCHCEDAPGIHSSEGEATEEPN 545 (547)
Q Consensus 480 ~~r~~tV~g~~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R~~~k~f~GsvfVEFsSeEeAkk~~~ 545 (547)
+...++|...+++...|.++|.++|.++|.. ...... ........+|.+||||.++|+|+++|.
T Consensus 86 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v-~~v~i~-~d~~~~~skg~afVeF~~~e~A~~Al~ 149 (457)
T TIGR01622 86 ERDDRTVFVLQLALKARERDLYEFFSKVGKV-RDVQCI-KDRNSRRSKGVAYVEFYDVESVIKALA 149 (457)
T ss_pred ccCCcEEEEeCCCCCCCHHHHHHHHHhcCCe-eEEEEe-ecCCCCCcceEEEEEECCHHHHHHHHH
Confidence 3345567777889999999999999999831 111111 113356679999999999999999875
No 25
>PLN03134 glycine-rich RNA-binding protein 4; Provisional
Probab=96.20 E-value=0.0028 Score=58.85 Aligned_cols=59 Identities=14% Similarity=-0.071 Sum_probs=43.2
Q ss_pred eeecCCCCCCChhhhhhhcccccccccccccccccCCCcccCCcccEEcCChhhhhcCCCC
Q 008981 486 ESGLSSPAGSSVDVLAPSFQNITVKEGAVNQRSLTGNANCHCEDAPGIHSSEGEATEEPNQ 546 (547)
Q Consensus 486 V~g~~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R~~~k~f~GsvfVEFsSeEeAkk~~~~ 546 (547)
+..-+++...|.++|+++|++++-..... ..........+|.+||+|.++|+|++++++
T Consensus 37 lfVgnL~~~~te~~L~~~F~~~G~I~~v~--i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~ 95 (144)
T PLN03134 37 LFIGGLSWGTDDASLRDAFAHFGDVVDAK--VIVDRETGRSRGFGFVNFNDEGAATAAISE 95 (144)
T ss_pred EEEeCCCCCCCHHHHHHHHhcCCCeEEEE--EEecCCCCCcceEEEEEECCHHHHHHHHHH
Confidence 44446788999999999999997311111 111234567899999999999999998853
No 26
>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]
Probab=96.03 E-value=0.0044 Score=67.92 Aligned_cols=60 Identities=10% Similarity=0.021 Sum_probs=48.7
Q ss_pred ceeeeecCCCCCCChhhhhhhcccccccccccccccccCCCcccCCcccEEcCChhhhhcCCCCC
Q 008981 483 ISTESGLSSPAGSSVDVLAPSFQNITVKEGAVNQRSLTGNANCHCEDAPGIHSSEGEATEEPNQN 547 (547)
Q Consensus 483 ~~tV~g~~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R~~~k~f~GsvfVEFsSeEeAkk~~~~~ 547 (547)
..+|..-++|-..|.++|..||.+++|+..+.. ...-...|.|+|||.+|||++++||.+
T Consensus 10 ~~~vr~rGLPwsat~~ei~~Ff~~~~I~~~~~~-----r~~Gr~sGeA~Ve~~seedv~~Alkkd 69 (510)
T KOG4211|consen 10 AFEVRLRGLPWSATEKEILDFFSNCGIENLEIP-----RRNGRPSGEAYVEFTSEEDVEKALKKD 69 (510)
T ss_pred ceEEEecCCCccccHHHHHHHHhcCceeEEEEe-----ccCCCcCcceEEEeechHHHHHHHHhh
Confidence 345666678999999999999999999876552 223556899999999999999999853
No 27
>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=95.90 E-value=0.013 Score=66.19 Aligned_cols=98 Identities=7% Similarity=-0.092 Sum_probs=64.5
Q ss_pred cCHHHHHHHHhcCCcEEEcCCeEe--eCCccc------ccCCC-CCCceeeeecCCCCCCChhhhhhhcccccccccccc
Q 008981 445 SNIQLILDSLRTSTVVEVQDDRVR--RRNEWM------KWIAT-PGRISTESGLSSPAGSSVDVLAPSFQNITVKEGAVN 515 (547)
Q Consensus 445 ~d~~lI~eALr~S~~LEVsgdKVR--Rr~~w~------kwvp~-~~r~~tV~g~~~p~~~T~d~L~~~F~~~gle~~~~~ 515 (547)
.+.+....||+...-.+|.|.+|| +-..+. +++.. ......+...+++...+.++|.++|+.||-.....
T Consensus 157 ~s~e~A~~Ai~~lnG~~i~GR~IkV~rp~~~p~a~~~~~~~~~~~~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svr- 235 (612)
T TIGR01645 157 EVPEAAQLALEQMNGQMLGGRNIKVGRPSNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQ- 235 (612)
T ss_pred CcHHHHHHHHHhcCCeEEecceeeecccccccccccccccccccccccceEEeecCCCCCCHHHHHHHHhhcCCeeEEE-
Confidence 367888888888777888877544 322211 12211 11223455567889999999999999998421111
Q ss_pred ccccc-CCCcccCCcccEEcCChhhhhcCCC
Q 008981 516 QRSLT-GNANCHCEDAPGIHSSEGEATEEPN 545 (547)
Q Consensus 516 ~~s~R-~~~k~f~GsvfVEFsSeEeAkk~~~ 545 (547)
-.+ ......+|.+||+|.++|+|+++++
T Consensus 236 --l~~D~~tgksKGfGFVeFe~~e~A~kAI~ 264 (612)
T TIGR01645 236 --LARAPTGRGHKGYGFIEYNNLQSQSEAIA 264 (612)
T ss_pred --EEecCCCCCcCCeEEEEECCHHHHHHHHH
Confidence 112 2345689999999999999998864
No 28
>TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.
Probab=95.85 E-value=0.011 Score=64.76 Aligned_cols=96 Identities=10% Similarity=-0.036 Sum_probs=63.7
Q ss_pred cCHHHHHHHHhcCCcEEEcCCeEeeCCcccccCCCCC--CceeeeecCCCCCCChhhhhhhcccccccccccccccccCC
Q 008981 445 SNIQLILDSLRTSTVVEVQDDRVRRRNEWMKWIATPG--RISTESGLSSPAGSSVDVLAPSFQNITVKEGAVNQRSLTGN 522 (547)
Q Consensus 445 ~d~~lI~eALr~S~~LEVsgdKVRRr~~w~kwvp~~~--r~~tV~g~~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R~~ 522 (547)
.+.+....||.......|.+..||- .|.+..+... ....+...+++.+.+.++|.++|.++|...... -++..
T Consensus 50 ~~~~~A~~Al~~ln~~~i~gk~i~i--~~s~~~~~~~~~~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~---i~~~~ 124 (562)
T TIGR01628 50 QNPADAERALETMNFKRLGGKPIRI--MWSQRDPSLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCK---VATDE 124 (562)
T ss_pred CCHHHHHHHHHHhCCCEECCeeEEe--ecccccccccccCCCceEEcCCCccCCHHHHHHHHHhcCCcceeE---eeecC
Confidence 3677777888877777788776663 2332221111 122355567889999999999999998422211 11233
Q ss_pred CcccCCcccEEcCChhhhhcCCC
Q 008981 523 ANCHCEDAPGIHSSEGEATEEPN 545 (547)
Q Consensus 523 ~k~f~GsvfVEFsSeEeAkk~~~ 545 (547)
....+|.+||+|.++|+|++++.
T Consensus 125 ~g~skg~afV~F~~~e~A~~Ai~ 147 (562)
T TIGR01628 125 NGKSRGYGFVHFEKEESAKAAIQ 147 (562)
T ss_pred CCCcccEEEEEECCHHHHHHHHH
Confidence 44578999999999999998863
No 29
>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=95.83 E-value=0.01 Score=66.71 Aligned_cols=72 Identities=19% Similarity=0.073 Sum_probs=51.0
Q ss_pred cccccC-CCCCCceeeeecCCCCCCChhhhhhhcccccccccccccccccCCCcccCCcccEEcCChhhhhcCCCC
Q 008981 472 EWMKWI-ATPGRISTESGLSSPAGSSVDVLAPSFQNITVKEGAVNQRSLTGNANCHCEDAPGIHSSEGEATEEPNQ 546 (547)
Q Consensus 472 ~w~kwv-p~~~r~~tV~g~~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R~~~k~f~GsvfVEFsSeEeAkk~~~~ 546 (547)
+...|. ........+..-+++.+.+.++|.++|+++|..... .-++..+...+|.+||+|.++|+|+++|++
T Consensus 46 Pp~~~~~~~p~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~v---rl~~D~sG~sRGfaFV~F~~~e~A~~Ai~~ 118 (578)
T TIGR01648 46 PPPGWSGVQPGRGCEVFVGKIPRDLYEDELVPLFEKAGPIYEL---RLMMDFSGQNRGYAFVTFCGKEEAKEAVKL 118 (578)
T ss_pred CCCcccCCCCCCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEE---EEEECCCCCccceEEEEeCCHHHHHHHHHH
Confidence 444564 222233456666889999999999999999842211 122345677899999999999999998753
No 30
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor. These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
Probab=95.74 E-value=0.016 Score=58.94 Aligned_cols=96 Identities=6% Similarity=-0.092 Sum_probs=62.9
Q ss_pred CHHHHHHHHhcCCcEEEcCCeEeeCCcccccCCCCCCceeeeecCCCCCCChhhhhhhcccccccccccccccccCCCcc
Q 008981 446 NIQLILDSLRTSTVVEVQDDRVRRRNEWMKWIATPGRISTESGLSSPAGSSVDVLAPSFQNITVKEGAVNQRSLTGNANC 525 (547)
Q Consensus 446 d~~lI~eALr~S~~LEVsgdKVRRr~~w~kwvp~~~r~~tV~g~~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R~~~k~ 525 (547)
+.+....||+...-.++.+.+|+-. |.+-.........+...+++...+.++|.+.|+.+|-..... .........
T Consensus 54 ~~~~A~~Ai~~l~g~~l~g~~i~v~--~a~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~--~~~~~~~~~ 129 (352)
T TIGR01661 54 RPEDAEKAVNSLNGLRLQNKTIKVS--YARPSSDSIKGANLYVSGLPKTMTQHELESIFSPFGQIITSR--ILSDNVTGL 129 (352)
T ss_pred cHHHHHHHHhhcccEEECCeeEEEE--eecccccccccceEEECCccccCCHHHHHHHHhccCCEEEEE--EEecCCCCC
Confidence 5677778888777788887765532 111111112233455567899999999999999997321111 111122456
Q ss_pred cCCcccEEcCChhhhhcCCC
Q 008981 526 HCEDAPGIHSSEGEATEEPN 545 (547)
Q Consensus 526 f~GsvfVEFsSeEeAkk~~~ 545 (547)
.+|.+||+|.+.|+|+++++
T Consensus 130 ~~g~~fv~f~~~~~A~~ai~ 149 (352)
T TIGR01661 130 SKGVGFIRFDKRDEADRAIK 149 (352)
T ss_pred cCcEEEEEECCHHHHHHHHH
Confidence 78999999999999999874
No 31
>smart00362 RRM_2 RNA recognition motif.
Probab=95.73 E-value=0.0065 Score=45.50 Aligned_cols=55 Identities=15% Similarity=-0.010 Sum_probs=39.9
Q ss_pred eecCCCCCCChhhhhhhcccccccccccccccccCCCcccCCcccEEcCChhhhhcCCC
Q 008981 487 SGLSSPAGSSVDVLAPSFQNITVKEGAVNQRSLTGNANCHCEDAPGIHSSEGEATEEPN 545 (547)
Q Consensus 487 ~g~~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R~~~k~f~GsvfVEFsSeEeAkk~~~ 545 (547)
...+.+...+.++|.++|+.+|-... ..+..+.+...|.+||+|.+.++|+++++
T Consensus 3 ~i~~l~~~~~~~~l~~~~~~~g~v~~----~~~~~~~~~~~~~~~v~f~~~~~a~~a~~ 57 (72)
T smart00362 3 FVGNLPPDVTEEDLKELFSKFGPIES----VKIPKDTGKSKGFAFVEFESEEDAEKAIE 57 (72)
T ss_pred EEcCCCCcCCHHHHHHHHHhcCCEEE----EEEecCCCCCCceEEEEeCCHHHHHHHHH
Confidence 34456788899999999999983111 11222226678999999999999998764
No 32
>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=95.67 E-value=0.0058 Score=64.48 Aligned_cols=59 Identities=12% Similarity=-0.101 Sum_probs=43.2
Q ss_pred eeeecCCCCCCChhhhhhhcccccccccccccccccCCCcccCCcccEEcCChhhhhcCCC
Q 008981 485 TESGLSSPAGSSVDVLAPSFQNITVKEGAVNQRSLTGNANCHCEDAPGIHSSEGEATEEPN 545 (547)
Q Consensus 485 tV~g~~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R~~~k~f~GsvfVEFsSeEeAkk~~~ 545 (547)
++...+++.+.|.++|.++|++++...... +.....+...+|.+||||.++|+|+++++
T Consensus 109 ~LfVgnLp~~~te~~L~~lF~~~G~V~~v~--i~~d~~tg~srGyaFVeF~~~e~A~~Ai~ 167 (346)
T TIGR01659 109 NLIVNYLPQDMTDRELYALFRTIGPINTCR--IMRDYKTGYSFGYAFVDFGSEADSQRAIK 167 (346)
T ss_pred EEEEeCCCCCCCHHHHHHHHHhcCCEEEEE--EEecCCCCccCcEEEEEEccHHHHHHHHH
Confidence 345556889999999999999998421111 11113456678999999999999999875
No 33
>KOG2590 consensus RNA-binding protein LARP/SRO9 and related La domain proteins [Posttranslational modification, protein turnover, chaperones; Translation, ribosomal structure and biogenesis]
Probab=95.38 E-value=0.0029 Score=69.00 Aligned_cols=90 Identities=22% Similarity=0.289 Sum_probs=80.1
Q ss_pred CCCCCcHHHHHHHHH--hhhhhcCcCcccccchhhhccCCCC---cEEehhhccchhhhhcccCHHHHHHHHhcCCcEEE
Q 008981 388 LMPVPEPSLAAMLIH--QIDYYFSDANLVKDEFLKSNMDDQG---WVPITLIASFPRVKNLTSNIQLILDSLRTSTVVEV 462 (547)
Q Consensus 388 ~~P~~d~~L~~~I~k--QVEYYFSDeNL~kD~FLr~~Md~qG---~VPLs~IasFnRVK~Lt~d~~lI~eALr~S~~LEV 462 (547)
.++++...|++++.. +++|||+..++.+|.|++..|+..| +.+++.+..|.++..++++...++..++.|...+.
T Consensus 89 ~~~~ps~~l~e~~~~~k~~s~~~~~~~~~~~~~~~~k~~~t~~~~~~~~S~~~~s~~~~~~s~n~~~~~~~~~~sa~~~~ 168 (448)
T KOG2590|consen 89 VISVPSPPLKEYSKSDKKKSWPASKPFTPRDSFKGSKPTNTGNGTFLPISKISSSGPVSGGSANNSNIRGPLKGSASSNP 168 (448)
T ss_pred ccccccccccccccccccccCcccCCCCccccccCCCccccCCCccCCCccccccccccCcccccccccCcCCCCCcCCc
Confidence 344455566677765 9999999999999999999999888 99999999999999999999999999999888888
Q ss_pred cCCeEeeCCcccccC
Q 008981 463 QDDRVRRRNEWMKWI 477 (547)
Q Consensus 463 sgdKVRRr~~w~kwv 477 (547)
...++|++..-.+|.
T Consensus 169 ~~~~~~~~~~~qr~~ 183 (448)
T KOG2590|consen 169 VPNNSRAKPLNQRWP 183 (448)
T ss_pred CccccccccccccCC
Confidence 889999998888886
No 34
>smart00360 RRM RNA recognition motif.
Probab=95.30 E-value=0.0095 Score=44.30 Aligned_cols=53 Identities=13% Similarity=0.020 Sum_probs=38.5
Q ss_pred CCCCCCChhhhhhhcccccc-cccccccccccCCCcccCCcccEEcCChhhhhcCCC
Q 008981 490 SSPAGSSVDVLAPSFQNITV-KEGAVNQRSLTGNANCHCEDAPGIHSSEGEATEEPN 545 (547)
Q Consensus 490 ~~p~~~T~d~L~~~F~~~gl-e~~~~~~~s~R~~~k~f~GsvfVEFsSeEeAkk~~~ 545 (547)
+++...+.++|..+|+.+|- ..... .........+|.+||+|.+.|+|+++++
T Consensus 3 ~l~~~~~~~~l~~~f~~~g~v~~~~i---~~~~~~~~~~~~a~v~f~~~~~a~~a~~ 56 (71)
T smart00360 3 NLPPDVTEEELRELFSKFGKIESVRL---VRDKDTGKSKGFAFVEFESEEDAEKALE 56 (71)
T ss_pred CCCcccCHHHHHHHHHhhCCEeEEEE---EeCCCCCCCCceEEEEeCCHHHHHHHHH
Confidence 35677899999999999982 22111 1112246788999999999999998764
No 35
>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=95.14 E-value=0.025 Score=63.69 Aligned_cols=91 Identities=9% Similarity=-0.106 Sum_probs=56.0
Q ss_pred CHHHHHHHHhcCCcEEEcC-CeEeeCCcccccCCCCCCceeeeecCCCCCCChhhhhhhcccccccccccccccccCCCc
Q 008981 446 NIQLILDSLRTSTVVEVQD-DRVRRRNEWMKWIATPGRISTESGLSSPAGSSVDVLAPSFQNITVKEGAVNQRSLTGNAN 524 (547)
Q Consensus 446 d~~lI~eALr~S~~LEVsg-dKVRRr~~w~kwvp~~~r~~tV~g~~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R~~~k 524 (547)
+.+...+||+.....+|.. .+|..+ | ......+..-+++...|.++|.+.|.+++.......+.....++.
T Consensus 108 ~~e~A~~Ai~~lng~~i~~Gr~l~V~-----~---S~~~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~~~~kg 179 (578)
T TIGR01648 108 GKEEAKEAVKLLNNYEIRPGRLLGVC-----I---SVDNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKK 179 (578)
T ss_pred CHHHHHHHHHHcCCCeecCCcccccc-----c---cccCceeEeecCCcchhhHHHHHHhhcccCCceEEEEeccccccC
Confidence 5677777887766666643 222211 1 111223444567889999999999999853221111111113445
Q ss_pred ccCCcccEEcCChhhhhcCC
Q 008981 525 CHCEDAPGIHSSEGEATEEP 544 (547)
Q Consensus 525 ~f~GsvfVEFsSeEeAkk~~ 544 (547)
..+|.+||||.++|+|++++
T Consensus 180 KnRGFAFVeF~s~edAa~Ai 199 (578)
T TIGR01648 180 KNRGFAFVEYESHRAAAMAR 199 (578)
T ss_pred ccCceEEEEcCCHHHHHHHH
Confidence 67899999999999998764
No 36
>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=95.04 E-value=0.031 Score=61.29 Aligned_cols=97 Identities=10% Similarity=-0.033 Sum_probs=59.1
Q ss_pred CHHHHHHHHhcCCcEEEcCCeEeeCCccccc---CCCCCCceeeeecCCCCCCChhhhhhhcccccccccccccccccCC
Q 008981 446 NIQLILDSLRTSTVVEVQDDRVRRRNEWMKW---IATPGRISTESGLSSPAGSSVDVLAPSFQNITVKEGAVNQRSLTGN 522 (547)
Q Consensus 446 d~~lI~eALr~S~~LEVsgdKVRRr~~w~kw---vp~~~r~~tV~g~~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R~~ 522 (547)
+.+...+||+...-..+++.+|+-.....+. .........+...+++...|.++|.++|..+|..... .-.+..
T Consensus 138 ~~e~A~~Ai~~lng~~~~~~~i~v~~~~~~~~~~~~~~~~~~~l~V~nl~~~~tee~L~~~F~~fG~i~~~---~i~~~~ 214 (562)
T TIGR01628 138 KEESAKAAIQKVNGMLLNDKEVYVGRFIKKHEREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSA---AVMKDG 214 (562)
T ss_pred CHHHHHHHHHHhcccEecCceEEEeccccccccccccccCCCeEEEeCCCCcCCHHHHHHHHHhcCCEEEE---EEEECC
Confidence 4556666777666566666544321100000 0011122334555678899999999999999842221 112234
Q ss_pred CcccCCcccEEcCChhhhhcCCC
Q 008981 523 ANCHCEDAPGIHSSEGEATEEPN 545 (547)
Q Consensus 523 ~k~f~GsvfVEFsSeEeAkk~~~ 545 (547)
....+|.+||+|.+.|+|+++++
T Consensus 215 ~g~~~G~afV~F~~~e~A~~Av~ 237 (562)
T TIGR01628 215 SGRSRGFAFVNFEKHEDAAKAVE 237 (562)
T ss_pred CCCcccEEEEEECCHHHHHHHHH
Confidence 45678999999999999998764
No 37
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor. These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
Probab=94.98 E-value=0.015 Score=59.19 Aligned_cols=57 Identities=11% Similarity=-0.088 Sum_probs=42.7
Q ss_pred eeecCCCCCCChhhhhhhccccccccccccccccc-CCCcccCCcccEEcCChhhhhcCCC
Q 008981 486 ESGLSSPAGSSVDVLAPSFQNITVKEGAVNQRSLT-GNANCHCEDAPGIHSSEGEATEEPN 545 (547)
Q Consensus 486 V~g~~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R-~~~k~f~GsvfVEFsSeEeAkk~~~ 545 (547)
+..-+++...|.++|.++|..+|-..... -++ ..+...+|.+||||.++|||+++|+
T Consensus 6 l~V~nLp~~~~e~~l~~~F~~~G~i~~v~---i~~d~~~g~s~g~afV~f~~~~~A~~Ai~ 63 (352)
T TIGR01661 6 LIVNYLPQTMTQEEIRSLFTSIGEIESCK---LVRDKVTGQSLGYGFVNYVRPEDAEKAVN 63 (352)
T ss_pred EEEeCCCCCCCHHHHHHHHHccCCEEEEE---EEEcCCCCccceEEEEEECcHHHHHHHHh
Confidence 44456899999999999999998321111 122 2345688999999999999999875
No 38
>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor. Members of this subfamily are found in plants, metazoa and fungi.
Probab=94.89 E-value=0.04 Score=59.10 Aligned_cols=58 Identities=5% Similarity=-0.220 Sum_probs=43.1
Q ss_pred eeeecCCCCCCChhhhhhhccccccccccccccccc-CCCcccCCcccEEcCChhhhhcCCC
Q 008981 485 TESGLSSPAGSSVDVLAPSFQNITVKEGAVNQRSLT-GNANCHCEDAPGIHSSEGEATEEPN 545 (547)
Q Consensus 485 tV~g~~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R-~~~k~f~GsvfVEFsSeEeAkk~~~ 545 (547)
.+...+++...|.++|.++|+.||-.... .-++ ......+|.+||||.+.++|+++++
T Consensus 297 ~l~v~nlp~~~~~~~l~~~f~~~G~i~~~---~~~~~~~~g~~~g~afv~f~~~~~a~~A~~ 355 (509)
T TIGR01642 297 RIYIGNLPLYLGEDQIKELLESFGDLKAF---NLIKDIATGLSKGYAFCEYKDPSVTDVAIA 355 (509)
T ss_pred EEEEeCCCCCCCHHHHHHHHHhcCCeeEE---EEEecCCCCCcCeEEEEEECCHHHHHHHHH
Confidence 45555788999999999999999832211 1122 2356688999999999999998764
No 39
>PLN03120 nucleic acid binding protein; Provisional
Probab=94.64 E-value=0.021 Score=58.68 Aligned_cols=59 Identities=10% Similarity=-0.127 Sum_probs=42.9
Q ss_pred eeeeecCCCCCCChhhhhhhcccccccccccccccccCCCcccCCcccEEcCChhhhhcCCCCC
Q 008981 484 STESGLSSPAGSSVDVLAPSFQNITVKEGAVNQRSLTGNANCHCEDAPGIHSSEGEATEEPNQN 547 (547)
Q Consensus 484 ~tV~g~~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R~~~k~f~GsvfVEFsSeEeAkk~~~~~ 547 (547)
++|...+++...|.++|.+||..+|-..... +..+ +..+|.+||+|.++++|+++|.-|
T Consensus 5 rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~----I~~d-~~~~GfAFVtF~d~eaAe~AllLn 63 (260)
T PLN03120 5 RTVKVSNVSLKATERDIKEFFSFSGDIEYVE----MQSE-NERSQIAYVTFKDPQGAETALLLS 63 (260)
T ss_pred CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEE----Eeec-CCCCCEEEEEeCcHHHHHHHHHhc
Confidence 4566667888999999999999998321111 1111 225799999999999999988643
No 40
>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=94.62 E-value=0.019 Score=43.21 Aligned_cols=55 Identities=13% Similarity=-0.024 Sum_probs=39.3
Q ss_pred ecCCCCCCChhhhhhhcccccccccccccccccCCCcccCCcccEEcCChhhhhcCCC
Q 008981 488 GLSSPAGSSVDVLAPSFQNITVKEGAVNQRSLTGNANCHCEDAPGIHSSEGEATEEPN 545 (547)
Q Consensus 488 g~~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R~~~k~f~GsvfVEFsSeEeAkk~~~ 545 (547)
..+++...+.++|.++|+.++-. ....-.+......+|.++|+|.+.|+|+.+++
T Consensus 4 i~~l~~~~~~~~i~~~~~~~g~i---~~~~~~~~~~~~~~~~~~v~f~s~~~a~~a~~ 58 (74)
T cd00590 4 VGNLPPDVTEEDLRELFSKFGKV---ESVRIVRDKDTKSKGFAFVEFEDEEDAEKALE 58 (74)
T ss_pred EeCCCCccCHHHHHHHHHhcCCE---EEEEEeeCCCCCcceEEEEEECCHHHHHHHHH
Confidence 34577888999999999998621 11111122233678999999999999998875
No 41
>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]
Probab=94.26 E-value=0.032 Score=52.58 Aligned_cols=82 Identities=16% Similarity=0.061 Sum_probs=55.0
Q ss_pred cchhhhhcccCHHHHHHHHhcCCcEEEcCCeEeeCCcccccCCCCCCceeeeecCCCCCCChhhhhhhcccccccccccc
Q 008981 436 SFPRVKNLTSNIQLILDSLRTSTVVEVQDDRVRRRNEWMKWIATPGRISTESGLSSPAGSSVDVLAPSFQNITVKEGAVN 515 (547)
Q Consensus 436 sFnRVK~Lt~d~~lI~eALr~S~~LEVsgdKVRRr~~w~kwvp~~~r~~tV~g~~~p~~~T~d~L~~~F~~~gle~~~~~ 515 (547)
++-|.+.+..+-+.-++|||+|..|-|.. +-.-.|.+.|-|.|.++|-...++
T Consensus 15 s~Yr~~~f~gt~~e~~~a~r~S~tvyVgN--------------------------lSfyttEEqiyELFs~cG~irrii- 67 (153)
T KOG0121|consen 15 SAYRDRRFRGTDEEQLEALRKSCTVYVGN--------------------------LSFYTTEEQIYELFSKCGDIRRII- 67 (153)
T ss_pred hHHHHHHhcCchHHHHHHHhhcceEEEee--------------------------eeeeecHHHHHHHHHhccchheeE-
Confidence 45566666655566667777777665542 222345577788888887321111
Q ss_pred cccccCCCcccCCcccEEcCChhhhhcCCC
Q 008981 516 QRSLTGNANCHCEDAPGIHSSEGEATEEPN 545 (547)
Q Consensus 516 ~~s~R~~~k~f~GsvfVEFsSeEeAkk~~~ 545 (547)
--+-..++.+||.+||||-+-+||+.+|+
T Consensus 68 -MGLdr~kktpCGFCFVeyy~~~dA~~Alr 96 (153)
T KOG0121|consen 68 -MGLDRFKKTPCGFCFVEYYSRDDAEDALR 96 (153)
T ss_pred -eccccCCcCccceEEEEEecchhHHHHHH
Confidence 12346789999999999999999998875
No 42
>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=93.72 E-value=0.11 Score=56.67 Aligned_cols=60 Identities=17% Similarity=-0.038 Sum_probs=42.5
Q ss_pred eeeeecCCCCCCChhhhhhhcccccccccccccccccCCCcccCCcccEEcCChhhhhcCCC
Q 008981 484 STESGLSSPAGSSVDVLAPSFQNITVKEGAVNQRSLTGNANCHCEDAPGIHSSEGEATEEPN 545 (547)
Q Consensus 484 ~tV~g~~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R~~~k~f~GsvfVEFsSeEeAkk~~~ 545 (547)
.++...+++...|.++|+++|+.+|...... ..+-......++.+||||.++|+|.++|.
T Consensus 395 ~~L~v~NLp~~~tee~L~~lF~~~G~~~i~~--ik~~~~~~~~~~~gfVeF~~~e~A~~Al~ 454 (481)
T TIGR01649 395 ATLHLSNIPLSVSEEDLKELFAENGVHKVKK--FKFFPKDNERSKMGLLEWESVEDAVEALI 454 (481)
T ss_pred cEEEEecCCCCCCHHHHHHHHHhcCCccceE--EEEecCCCCcceeEEEEcCCHHHHHHHHH
Confidence 4566778889999999999999998411111 11111112247899999999999998874
No 43
>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]
Probab=93.43 E-value=0.048 Score=55.82 Aligned_cols=59 Identities=12% Similarity=-0.078 Sum_probs=46.8
Q ss_pred eeeeecCCCCCCChhhhhhhccccccccccccccccc-CCCcccCCcccEEcCChhhhhcCCC
Q 008981 484 STESGLSSPAGSSVDVLAPSFQNITVKEGAVNQRSLT-GNANCHCEDAPGIHSSEGEATEEPN 545 (547)
Q Consensus 484 ~tV~g~~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R-~~~k~f~GsvfVEFsSeEeAkk~~~ 545 (547)
.++...++.++.+.++|++.|.+||...... -.| .++-+++|++||.|.+.|||.++++
T Consensus 190 ~tvRvtNLsed~~E~dL~eLf~~fg~i~rvy---lardK~TG~~kGFAFVtF~sRddA~rAI~ 249 (270)
T KOG0122|consen 190 ATVRVTNLSEDMREDDLEELFRPFGPITRVY---LARDKETGLSKGFAFVTFESRDDAARAIA 249 (270)
T ss_pred ceeEEecCccccChhHHHHHhhccCccceeE---EEEccccCcccceEEEEEecHHHHHHHHH
Confidence 4577789999999999999999998422211 122 4578999999999999999998764
No 44
>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]
Probab=93.06 E-value=0.087 Score=56.34 Aligned_cols=89 Identities=11% Similarity=-0.031 Sum_probs=64.7
Q ss_pred cCHHHHHHHHhcCCcEEEcCCeEeeCCcccccCCCCCCceeeeecCCCCCCChhhhhhhcccccccccccccccccCCCc
Q 008981 445 SNIQLILDSLRTSTVVEVQDDRVRRRNEWMKWIATPGRISTESGLSSPAGSSVDVLAPSFQNITVKEGAVNQRSLTGNAN 524 (547)
Q Consensus 445 ~d~~lI~eALr~S~~LEVsgdKVRRr~~w~kwvp~~~r~~tV~g~~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R~~~k 524 (547)
.+.+....||..-..=.+.+..|| ..|..-.+.. +...++....+...|-.+|..||-..+. ++-++++
T Consensus 45 ~~~~da~~A~~~~n~~~~~~~~~r--im~s~rd~~~-----~~i~nl~~~~~~~~~~d~f~~~g~ilS~----kv~~~~~ 113 (369)
T KOG0123|consen 45 QQPADAERALDTMNFDVLKGKPIR--IMWSQRDPSL-----VFIKNLDESIDNKSLYDTFSEFGNILSC----KVATDEN 113 (369)
T ss_pred CCHHHHHHHHHHcCCcccCCcEEE--eehhccCCce-----eeecCCCcccCcHHHHHHHHhhcCeeEE----EEEEcCC
Confidence 367788888988887778888887 4555543332 5556788899999999999999832221 2224445
Q ss_pred ccCCcccEEcCChhhhhcCCC
Q 008981 525 CHCEDAPGIHSSEGEATEEPN 545 (547)
Q Consensus 525 ~f~GsvfVEFsSeEeAkk~~~ 545 (547)
--+|. ||+|.+||+|+++++
T Consensus 114 g~kg~-FV~f~~e~~a~~ai~ 133 (369)
T KOG0123|consen 114 GSKGY-FVQFESEESAKKAIE 133 (369)
T ss_pred Cceee-EEEeCCHHHHHHHHH
Confidence 57788 999999999999763
No 45
>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor. Members of this subfamily are found in plants, metazoa and fungi.
Probab=92.51 E-value=0.1 Score=56.09 Aligned_cols=63 Identities=14% Similarity=-0.014 Sum_probs=41.2
Q ss_pred ceeeeecCCCCCCChhhhhhhcccccccccccc---ccccc-CCCcccCCcccEEcCChhhhhcCCC
Q 008981 483 ISTESGLSSPAGSSVDVLAPSFQNITVKEGAVN---QRSLT-GNANCHCEDAPGIHSSEGEATEEPN 545 (547)
Q Consensus 483 ~~tV~g~~~p~~~T~d~L~~~F~~~gle~~~~~---~~s~R-~~~k~f~GsvfVEFsSeEeAkk~~~ 545 (547)
.++++.-+++...|.++|.++|..+........ ...+. ......+|.+||||.+.|+|+++|+
T Consensus 175 ~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~~~~kg~afVeF~~~e~A~~Al~ 241 (509)
T TIGR01642 175 ARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNINKEKNFAFLEFRTVEEATFAMA 241 (509)
T ss_pred ccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEECCCCCEEEEEeCCHHHHhhhhc
Confidence 445666678899999999999998632111000 00111 0112346899999999999999985
No 46
>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]
Probab=92.12 E-value=0.2 Score=55.04 Aligned_cols=95 Identities=20% Similarity=0.132 Sum_probs=59.9
Q ss_pred HHHHHHHhcCC--cEEEc-CCeEeeCCcccccC-CCCCCceeeeecCCCCCCChhhhhhhccccccccccccccccc-CC
Q 008981 448 QLILDSLRTST--VVEVQ-DDRVRRRNEWMKWI-ATPGRISTESGLSSPAGSSVDVLAPSFQNITVKEGAVNQRSLT-GN 522 (547)
Q Consensus 448 ~lI~eALr~S~--~LEVs-gdKVRRr~~w~kwv-p~~~r~~tV~g~~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R-~~ 522 (547)
+..+++|.+-+ .|+|. +++ +-.-+...|. +...+-..|..-.+|.+...|+|.-+|+++|. +....-++ ..
T Consensus 45 eaal~al~E~tgy~l~ve~gqr-k~ggPpP~weg~~p~~G~EVfvGkIPrD~~EdeLvplfEkiG~---I~elRLMmD~~ 120 (506)
T KOG0117|consen 45 EAALKALLERTGYTLVVENGQR-KYGGPPPGWEGPPPPRGCEVFVGKIPRDVFEDELVPLFEKIGK---IYELRLMMDPF 120 (506)
T ss_pred HHHHHHHHHhcCceEEEecccc-ccCCCCCcccCCCCCCCceEEecCCCccccchhhHHHHHhccc---eeeEEEeeccc
Confidence 33444444433 56664 331 1112344465 33344445555568999999999999999983 22211222 35
Q ss_pred CcccCCcccEEcCChhhhhcCCCC
Q 008981 523 ANCHCEDAPGIHSSEGEATEEPNQ 546 (547)
Q Consensus 523 ~k~f~GsvfVEFsSeEeAkk~~~~ 546 (547)
+-..+|-+||.|.+.|+|+++.++
T Consensus 121 sG~nRGYAFVtf~~Ke~Aq~Aik~ 144 (506)
T KOG0117|consen 121 SGDNRGYAFVTFCTKEEAQEAIKE 144 (506)
T ss_pred CCCCcceEEEEeecHHHHHHHHHH
Confidence 778899999999999999998653
No 47
>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=91.88 E-value=0.18 Score=55.04 Aligned_cols=55 Identities=18% Similarity=-0.005 Sum_probs=39.7
Q ss_pred eeeecCCCCCCChhhhhhhcccccccccccccccccCCCcccCCcccEEcCChhhhhcCCC
Q 008981 485 TESGLSSPAGSSVDVLAPSFQNITVKEGAVNQRSLTGNANCHCEDAPGIHSSEGEATEEPN 545 (547)
Q Consensus 485 tV~g~~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R~~~k~f~GsvfVEFsSeEeAkk~~~ 545 (547)
.|...++....|.+.|.++|..+|-...+. -.+.. ..+.+||||.+.|+|+++++
T Consensus 98 ~v~v~nl~~~vt~~~L~~~F~~~G~V~~v~---i~~~~---~~~~afVef~~~~~A~~A~~ 152 (481)
T TIGR01649 98 RVIVENPMYPITLDVLYQIFNPYGKVLRIV---TFTKN---NVFQALVEFESVNSAQHAKA 152 (481)
T ss_pred EEEEcCCCCCCCHHHHHHHHhccCCEEEEE---EEecC---CceEEEEEECCHHHHHHHHH
Confidence 455567778899999999999998422221 12221 23579999999999999864
No 48
>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]
Probab=91.87 E-value=0.11 Score=47.65 Aligned_cols=60 Identities=13% Similarity=-0.095 Sum_probs=45.9
Q ss_pred eeeeecCCCCCCChhhhhhhcccccccccccccccccCCCcccCCcccEEcCChhhhhcCCC
Q 008981 484 STESGLSSPAGSSVDVLAPSFQNITVKEGAVNQRSLTGNANCHCEDAPGIHSSEGEATEEPN 545 (547)
Q Consensus 484 ~tV~g~~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R~~~k~f~GsvfVEFsSeEeAkk~~~ 545 (547)
.++...+++...|.++|.++|..+|...... ..........+|.+||+|.++|+|++++.
T Consensus 116 ~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~--~~~d~~~~~~~g~~~v~f~~~~~~~~a~~ 175 (306)
T COG0724 116 NTLFVGNLPYDVTEEDLRELFKKFGPVKRVR--LVRDRETGKSRGFAFVEFESEESAEKAIE 175 (306)
T ss_pred ceEEEeCCCCCCCHHHHHHHHHhcCceeEEE--eeeccccCccCceEEEEecCHHHHHHHHH
Confidence 5566677889999999999999998531111 11112568899999999999999998764
No 49
>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]
Probab=91.66 E-value=0.13 Score=53.50 Aligned_cols=96 Identities=8% Similarity=-0.058 Sum_probs=60.2
Q ss_pred CHHHHHHHHhcCCcEEEcCCeEeeCCcccccCCCCCCceeeeecCCCCCCChhhhhhhcccccccccccccccccCCCcc
Q 008981 446 NIQLILDSLRTSTVVEVQDDRVRRRNEWMKWIATPGRISTESGLSSPAGSSVDVLAPSFQNITVKEGAVNQRSLTGNANC 525 (547)
Q Consensus 446 d~~lI~eALr~S~~LEVsgdKVRRr~~w~kwvp~~~r~~tV~g~~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R~~~k~ 525 (547)
|.+.-.+|+-...-|.++...|+- .+.+--.+.++--..+..++|...|+.+|+.+|..||.. +..++-+.....+
T Consensus 92 ~p~DAe~AintlNGLrLQ~KTIKV--SyARPSs~~Ik~aNLYvSGlPktMtqkelE~iFs~fGrI--ItSRiL~dqvtg~ 167 (360)
T KOG0145|consen 92 RPKDAEKAINTLNGLRLQNKTIKV--SYARPSSDSIKDANLYVSGLPKTMTQKELEQIFSPFGRI--ITSRILVDQVTGL 167 (360)
T ss_pred ChHHHHHHHhhhcceeeccceEEE--EeccCChhhhcccceEEecCCccchHHHHHHHHHHhhhh--hhhhhhhhcccce
Confidence 455556666666667777654431 111110111222223445689999999999999999842 2222222233577
Q ss_pred cCCcccEEcCChhhhhcCCC
Q 008981 526 HCEDAPGIHSSEGEATEEPN 545 (547)
Q Consensus 526 f~GsvfVEFsSeEeAkk~~~ 545 (547)
-+|..||+|.-.+||+++++
T Consensus 168 srGVgFiRFDKr~EAe~AIk 187 (360)
T KOG0145|consen 168 SRGVGFIRFDKRIEAEEAIK 187 (360)
T ss_pred ecceeEEEecchhHHHHHHH
Confidence 89999999999999998765
No 50
>PLN03121 nucleic acid binding protein; Provisional
Probab=91.28 E-value=0.14 Score=52.31 Aligned_cols=58 Identities=7% Similarity=-0.160 Sum_probs=42.6
Q ss_pred eeeeecCCCCCCChhhhhhhcccccccccccccccccCCCcccCCcccEEcCChhhhhcCCCC
Q 008981 484 STESGLSSPAGSSVDVLAPSFQNITVKEGAVNQRSLTGNANCHCEDAPGIHSSEGEATEEPNQ 546 (547)
Q Consensus 484 ~tV~g~~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R~~~k~f~GsvfVEFsSeEeAkk~~~~ 546 (547)
.+|...++....|.++|.+||..+|-..... -++. +...+.+||||.++++|+.+|.-
T Consensus 6 ~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~---I~~D--~et~gfAfVtF~d~~aaetAllL 63 (243)
T PLN03121 6 YTAEVTNLSPKATEKDVYDFFSHCGAIEHVE---IIRS--GEYACTAYVTFKDAYALETAVLL 63 (243)
T ss_pred eEEEEecCCCCCCHHHHHHHHHhcCCeEEEE---EecC--CCcceEEEEEECCHHHHHHHHhc
Confidence 4566778889999999999999998422211 1122 33457999999999999988753
No 51
>smart00361 RRM_1 RNA recognition motif.
Probab=91.15 E-value=0.077 Score=42.94 Aligned_cols=47 Identities=6% Similarity=-0.060 Sum_probs=29.5
Q ss_pred hhhhhhcc----cccccccccccccccCC--CcccCCcccEEcCChhhhhcCCC
Q 008981 498 DVLAPSFQ----NITVKEGAVNQRSLTGN--ANCHCEDAPGIHSSEGEATEEPN 545 (547)
Q Consensus 498 d~L~~~F~----~~gle~~~~~~~s~R~~--~k~f~GsvfVEFsSeEeAkk~~~ 545 (547)
++|.++|. .+|-.....++ .+... ...-+|.+||+|.++|||+++++
T Consensus 3 ~~l~~~~~~~~~~fG~v~~v~~v-~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~ 55 (70)
T smart00361 3 EDFEREFSEEEEYFGEVGKINKI-YIDNVGYENHKRGNVYITFERSEDAARAIV 55 (70)
T ss_pred hhHHHHHHHHHHhcCCeeEEEEE-EeCCCCCCCCCcEEEEEEECCHHHHHHHHH
Confidence 56777777 77632222101 11111 15567999999999999999875
No 52
>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=91.08 E-value=0.043 Score=42.08 Aligned_cols=39 Identities=13% Similarity=-0.077 Sum_probs=25.4
Q ss_pred hhhhcccccccccccccccccCCCcccCCcccEEcCChhhhhcCCC
Q 008981 500 LAPSFQNITVKEGAVNQRSLTGNANCHCEDAPGIHSSEGEATEEPN 545 (547)
Q Consensus 500 L~~~F~~~gle~~~~~~~s~R~~~k~f~GsvfVEFsSeEeAkk~~~ 545 (547)
|.+.|+++|-..... -. .++ .+.+||||.+.|+|+++++
T Consensus 1 L~~~f~~fG~V~~i~---~~-~~~---~~~a~V~f~~~~~A~~a~~ 39 (56)
T PF13893_consen 1 LYKLFSKFGEVKKIK---IF-KKK---RGFAFVEFASVEDAQKAIE 39 (56)
T ss_dssp HHHHHTTTS-EEEEE---EE-TTS---TTEEEEEESSHHHHHHHHH
T ss_pred ChHHhCCcccEEEEE---EE-eCC---CCEEEEEECCHHHHHHHHH
Confidence 456788887321111 11 111 7999999999999998764
No 53
>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]
Probab=90.96 E-value=0.33 Score=51.15 Aligned_cols=127 Identities=15% Similarity=0.069 Sum_probs=76.5
Q ss_pred HhhhhhcCcCcccccchhhhccC-----CCCcEEehhhccchhhhhcccCHHHHHHHHhcCCcEEEcCCe------EeeC
Q 008981 402 HQIDYYFSDANLVKDEFLKSNMD-----DQGWVPITLIASFPRVKNLTSNIQLILDSLRTSTVVEVQDDR------VRRR 470 (547)
Q Consensus 402 kQVEYYFSDeNL~kD~FLr~~Md-----~qG~VPLs~IasFnRVK~Lt~d~~lI~eALr~S~~LEVsgdK------VRRr 470 (547)
++|.+||+..-...|..+.+-+. .-|||..+.-....++.. .. .+.|++-+ |-|.
T Consensus 21 e~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~-------------~~-~h~~dgr~ve~k~av~r~ 86 (311)
T KOG4205|consen 21 ESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLN-------------AR-THKLDGRSVEPKRAVSRE 86 (311)
T ss_pred HHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeec-------------cc-ccccCCccccceeccCcc
Confidence 57788998888888888776552 355555543333333322 21 12222211 1111
Q ss_pred CcccccCCCCCCceeeeecCCCCCCChhhhhhhcccccccccccccccccCCCcccCCcccEEcCChhhhhcCCCC
Q 008981 471 NEWMKWIATPGRISTESGLSSPAGSSVDVLAPSFQNITVKEGAVNQRSLTGNANCHCEDAPGIHSSEGEATEEPNQ 546 (547)
Q Consensus 471 ~~w~kwvp~~~r~~tV~g~~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R~~~k~f~GsvfVEFsSeEeAkk~~~~ 546 (547)
.. .+- ....+...+..-+.+.+.+..+|.++|++++++ ..++..+..++...+|.-||.|.+||..++++.|
T Consensus 87 ~~-~~~-~~~~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v--~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~~ 158 (311)
T KOG4205|consen 87 DQ-TKV-GRHLRTKKIFVGGLPPDTTEEDFKDYFEQFGKV--ADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTLQ 158 (311)
T ss_pred cc-ccc-ccccceeEEEecCcCCCCchHHHhhhhhcccee--EeeEEeecccccccccceeeEeccccccceeccc
Confidence 10 000 000012223233678999999999999999942 2333445567888999999999999999999876
No 54
>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=90.72 E-value=0.16 Score=54.00 Aligned_cols=59 Identities=10% Similarity=-0.176 Sum_probs=43.3
Q ss_pred eeeeecCCCCCCChhhhhhhccccccccccccccccc-CCCcccCCcccEEcCChhhhhcCCC
Q 008981 484 STESGLSSPAGSSVDVLAPSFQNITVKEGAVNQRSLT-GNANCHCEDAPGIHSSEGEATEEPN 545 (547)
Q Consensus 484 ~tV~g~~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R-~~~k~f~GsvfVEFsSeEeAkk~~~ 545 (547)
.++...+++...|.++|.++|+.+|...... -++ ......+|.+||+|.+.|+|+++++
T Consensus 187 ~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~---~~~d~~~g~~~g~afV~f~~~e~A~~A~~ 246 (457)
T TIGR01622 187 LKLYVGNLHFNITEQELRQIFEPFGDIEDVQ---LHRDPETGRSKGFGFIQFHDAEEAKEALE 246 (457)
T ss_pred CEEEEcCCCCCCCHHHHHHHHHhcCCeEEEE---EEEcCCCCccceEEEEEECCHHHHHHHHH
Confidence 4456667889999999999999998421111 112 2234678999999999999998875
No 55
>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]
Probab=90.57 E-value=0.63 Score=51.66 Aligned_cols=122 Identities=12% Similarity=0.095 Sum_probs=73.9
Q ss_pred hhhcCcCcccccchhhhcc--CCCCcEEehhhccchhhhhcccCHHHHHHHHhc------CCcEEEc---CC---eEeeC
Q 008981 405 DYYFSDANLVKDEFLKSNM--DDQGWVPITLIASFPRVKNLTSNIQLILDSLRT------STVVEVQ---DD---RVRRR 470 (547)
Q Consensus 405 EYYFSDeNL~kD~FLr~~M--d~qG~VPLs~IasFnRVK~Lt~d~~lI~eALr~------S~~LEVs---gd---KVRRr 470 (547)
-=+|+|.++..=+|-|..= .-|-||.+ +..+.+..|||+ ..-|||= .+ .+=|+
T Consensus 28 ~~Ff~~~~I~~~~~~r~~Gr~sGeA~Ve~-------------~seedv~~AlkkdR~~mg~RYIEVf~~~~~e~d~~~~~ 94 (510)
T KOG4211|consen 28 LDFFSNCGIENLEIPRRNGRPSGEAYVEF-------------TSEEDVEKALKKDRESMGHRYIEVFTAGGAEADWVMRP 94 (510)
T ss_pred HHHHhcCceeEEEEeccCCCcCcceEEEe-------------echHHHHHHHHhhHHHhCCceEEEEccCCccccccccC
Confidence 3478888888722323211 13445543 246777778876 3468874 11 12122
Q ss_pred CcccccCCCC-CCceeeeecCCCCCCChhhhhhhcccccccccccccccccCCCcccCCcccEEcCChhhhhcCCCC
Q 008981 471 NEWMKWIATP-GRISTESGLSSPAGSSVDVLAPSFQNITVKEGAVNQRSLTGNANCHCEDAPGIHSSEGEATEEPNQ 546 (547)
Q Consensus 471 ~~w~kwvp~~-~r~~tV~g~~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R~~~k~f~GsvfVEFsSeEeAkk~~~~ 546 (547)
.. +.. ..-.+|.--++|-..|.++|.+||+.+-|....+- =+....-..+|-+||.|.|.|.|+++|+.
T Consensus 95 ~g-----~~s~~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~--l~~d~rgR~tGEAfVqF~sqe~ae~Al~r 164 (510)
T KOG4211|consen 95 GG-----PNSSANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGIL--LPMDQRGRPTGEAFVQFESQESAEIALGR 164 (510)
T ss_pred CC-----CCCCCCCceEEecCCCccCcHHHHHHHhcCCccccccee--eeccCCCCcccceEEEecCHHHHHHHHHH
Confidence 11 111 11233444578999999999999999976544220 11122334899999999999999999864
No 56
>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=90.51 E-value=0.17 Score=57.56 Aligned_cols=58 Identities=12% Similarity=-0.162 Sum_probs=42.7
Q ss_pred eeecCCCCCCChhhhhhhcccccccccccccccccCCCcccCCcccEEcCChhhhhcCCC
Q 008981 486 ESGLSSPAGSSVDVLAPSFQNITVKEGAVNQRSLTGNANCHCEDAPGIHSSEGEATEEPN 545 (547)
Q Consensus 486 V~g~~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R~~~k~f~GsvfVEFsSeEeAkk~~~ 545 (547)
+...+++...+.++|.++|..||-..... ..........+|.+||||.++|+|+++++
T Consensus 110 LfVGnLp~~~tEe~Lr~lF~~fG~I~sV~--I~~D~~TgkskGfAFVeF~s~e~A~~Ai~ 167 (612)
T TIGR01645 110 VYVGSISFELREDTIRRAFDPFGPIKSIN--MSWDPATGKHKGFAFVEYEVPEAAQLALE 167 (612)
T ss_pred EEEcCCCCCCCHHHHHHHHHccCCEEEEE--EeecCCCCCcCCeEEEEeCcHHHHHHHHH
Confidence 44446788999999999999998422211 11112345689999999999999999875
No 57
>PF09421 FRQ: Frequency clock protein; InterPro: IPR018554 The frequency clock protein, is the central component of the frq-based circadian negative feedback loop, regulates various aspects of the circadian clock in Neurospora crassa []. This protein has been shown to interact with itself via a coiled-coil [].
Probab=89.70 E-value=0.28 Score=58.10 Aligned_cols=48 Identities=19% Similarity=0.463 Sum_probs=42.4
Q ss_pred cCCCCcEEehhhccchhhhhcccCHHHHHHHHhc-CCcEEEc--CCeEeeC
Q 008981 423 MDDQGWVPITLIASFPRVKNLTSNIQLILDSLRT-STVVEVQ--DDRVRRR 470 (547)
Q Consensus 423 Md~qG~VPLs~IasFnRVK~Lt~d~~lI~eALr~-S~~LEVs--gdKVRRr 470 (547)
.|.+|||-|.|||+.-.|--|..+.+.|+.||.+ |+.|||+ |.|||=|
T Consensus 473 pDaeGWVYLNLL~NmAQLHiiNVTPdFVRsAV~E~StKfQLSpDGrKIRWR 523 (989)
T PF09421_consen 473 PDAEGWVYLNLLCNMAQLHIINVTPDFVRSAVSEKSTKFQLSPDGRKIRWR 523 (989)
T ss_pred cccccceehHHHHHHHHHHhhccCHHHHHHHHHhcccceeeCCCCCeeeec
Confidence 4899999999999999988888899999999885 8999997 5699954
No 58
>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]
Probab=89.31 E-value=10 Score=41.28 Aligned_cols=45 Identities=31% Similarity=0.512 Sum_probs=27.0
Q ss_pred CCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCcceecCCCCc
Q 008981 321 QPQRGPPRGF-VRPAPPNAAAFAPPQPMRPFPNPMGFPEFIYIPPMPV 367 (547)
Q Consensus 321 ~~q~~~pr~f-~RPppp~~~~f~~p~p~~p~~~p~~~p~~yy~P~~~~ 367 (547)
+||.+++.+| +||+..-++..|+++|+..-+.|+.-+ .|+|++..
T Consensus 280 qq~p~pp~~~ppRP~m~l~phl~gppPga~pPaph~Np--affpPP~~ 325 (498)
T KOG4849|consen 280 QQQPQPPMGQPPRPMMQLSPHLMGPPPGAGPPAPHNNP--AFFPPPQL 325 (498)
T ss_pred ccCCCCCCCCCCCcccccCcccCCCCCCCCCCCcccCc--ccCCCCCc
Confidence 4455556677 777777777788888765444443322 45655443
No 59
>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=88.71 E-value=0.39 Score=44.16 Aligned_cols=59 Identities=14% Similarity=0.030 Sum_probs=47.2
Q ss_pred CCCCCceeeeecCCCCCCChhhhhhhccccccccccccccccc-CCCcccCCcccEEcCChhhhhcCC
Q 008981 478 ATPGRISTESGLSSPAGSSVDVLAPSFQNITVKEGAVNQRSLT-GNANCHCEDAPGIHSSEGEATEEP 544 (547)
Q Consensus 478 p~~~r~~tV~g~~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R-~~~k~f~GsvfVEFsSeEeAkk~~ 544 (547)
++..|+.++. ++|...|-|+.-+.|+++|-.. .+| +.++..+|++||-+.+.+|||++.
T Consensus 15 pevnriLyir--NLp~~ITseemydlFGkyg~Ir------QIRiG~~k~TrGTAFVVYedi~dAk~A~ 74 (124)
T KOG0114|consen 15 PEVNRILYIR--NLPFKITSEEMYDLFGKYGTIR------QIRIGNTKETRGTAFVVYEDIFDAKKAC 74 (124)
T ss_pred hhhheeEEEe--cCCccccHHHHHHHhhcccceE------EEEecCccCcCceEEEEehHhhhHHHHH
Confidence 5555655554 5788999999999999998422 234 778999999999999999999874
No 60
>PRK00819 RNA 2'-phosphotransferase; Reviewed
Probab=88.27 E-value=0.57 Score=45.78 Aligned_cols=50 Identities=22% Similarity=0.399 Sum_probs=39.1
Q ss_pred ccCCCCcEEehhhccchhhhhcccCHHHHHHHHhcCCc--EEEcCCeEeeCC
Q 008981 422 NMDDQGWVPITLIASFPRVKNLTSNIQLILDSLRTSTV--VEVQDDRVRRRN 471 (547)
Q Consensus 422 ~Md~qG~VPLs~IasFnRVK~Lt~d~~lI~eALr~S~~--LEVsgdKVRRr~ 471 (547)
.||++|||+|+.|+...+.+...-+.+.|.+++++.++ .|+++++||-+.
T Consensus 27 ~ld~~G~v~v~~Ll~~~~~~~~~~t~~~l~~vV~~d~K~Rf~l~~~~IRA~q 78 (179)
T PRK00819 27 TLDEEGWVDIDALIEALAKAYKWVTRELLEAVVESDDKGRFEISGDRIRARQ 78 (179)
T ss_pred ccCCCCCEEHHHHHHHHHHccCCCCHHHHHHHHHcCCCcceEecCceEEecc
Confidence 37999999999999876654333468899999998764 677788999764
No 61
>PF01885 PTS_2-RNA: RNA 2'-phosphotransferase, Tpt1 / KptA family; InterPro: IPR002745 The final step of tRNA splicing in Saccharomyces cerevisiae (Baker's yeast) requires 2'-phosphotransferase (Tpt1) to transfer the 2'-phosphate from ligated tRNA to NAD, producing mature tRNA and ADP ribose-1' '-2' '-cyclic phosphate. Yeast and Mus musculus (Mouse) Tpt1 protein and bacterial KptA protein can catalyze the conversion of the generated intermediate to both product and the original substrate, these enzymes likely use the same reaction mechanism. Step 1 of this reaction is strikingly similar to the ADP-ribosylation of proteins catalyzed by a number of bacterial toxins. KptA, a functional Tpt1 protein homologue from Escherichia coli is strikingly similar to yeast Tpt1 in its kinetic parameters, although E. coli is not known to have a 2'-phosphorylated RNA substrate [,].; GO: 0016772 transferase activity, transferring phosphorus-containing groups, 0006388 tRNA splicing, via endonucleolytic cleavage and ligation; PDB: 1WFX_A.
Probab=88.04 E-value=0.53 Score=45.97 Aligned_cols=50 Identities=26% Similarity=0.353 Sum_probs=34.4
Q ss_pred ccCCCCcEEehhhccchhhhhcccCHHHHHHHHhcCCc--EEEc-----CCeEeeCC
Q 008981 422 NMDDQGWVPITLIASFPRVKNLTSNIQLILDSLRTSTV--VEVQ-----DDRVRRRN 471 (547)
Q Consensus 422 ~Md~qG~VPLs~IasFnRVK~Lt~d~~lI~eALr~S~~--LEVs-----gdKVRRr~ 471 (547)
.||++|||+|+.|+...+++.+.-+.+.|.++++..+. .|+. +.+||-+.
T Consensus 26 ~~d~~G~v~v~dLL~~~~~~~~~~t~~~i~~vV~~~~K~Rfel~~~~~~~~~IRA~q 82 (186)
T PF01885_consen 26 VMDPDGWVSVDDLLRALRFKGLWVTEEDIREVVETDDKQRFELRYEDPGGWRIRANQ 82 (186)
T ss_dssp ---TT--EEHHHHHHHHHHT-TT--HHHHHHHHHH-SS--EEEE-----TTEEEESS
T ss_pred ccCCCCCEeHHHHHHHHHHcCCCCCHHHHHHHHhhCCCCCeeEEcccccCceEEECC
Confidence 37899999999999999998777778999999988763 5666 67898763
No 62
>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]
Probab=84.58 E-value=0.6 Score=51.33 Aligned_cols=59 Identities=10% Similarity=-0.125 Sum_probs=45.0
Q ss_pred eeeecCCCCCCChhhhhhhcccccccccccccccccCCCcccCCcccEEcCChhhhhcCCC
Q 008981 485 TESGLSSPAGSSVDVLAPSFQNITVKEGAVNQRSLTGNANCHCEDAPGIHSSEGEATEEPN 545 (547)
Q Consensus 485 tV~g~~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R~~~k~f~GsvfVEFsSeEeAkk~~~ 545 (547)
.|..-+.+.+.+.+.|.++|..+|...+..- -....+..|+|.+|+||.++|+|+.+..
T Consensus 20 ~v~vgnip~~~se~~l~~~~~~~g~v~s~~~--v~D~~tG~~~G~~f~~~~~~~~~~~a~~ 78 (435)
T KOG0108|consen 20 SVFVGNIPYEGSEEQLLSIFSGVGPVLSFRL--VYDRETGKPKGFGFCEFTDEETAERAIR 78 (435)
T ss_pred ceEecCCCCcccHHHHHHHHhccCccceeee--cccccCCCcCceeeEecCchhhHHHHHH
Confidence 3444467899999999999999985333321 1115678999999999999999998754
No 63
>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]
Probab=81.27 E-value=0.96 Score=44.75 Aligned_cols=49 Identities=12% Similarity=-0.093 Sum_probs=37.4
Q ss_pred eeecCCCCCCChhhhhhhcccccccccccccccccC--CCcccCCcccEEcCChhhhhcC
Q 008981 486 ESGLSSPAGSSVDVLAPSFQNITVKEGAVNQRSLTG--NANCHCEDAPGIHSSEGEATEE 543 (547)
Q Consensus 486 V~g~~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R~--~~k~f~GsvfVEFsSeEeAkk~ 543 (547)
|+.-++....+..+|+..|..+|. ++. -....-|+|||||.+.-||+.+
T Consensus 13 VYVGnL~~~a~k~eLE~~F~~yG~---------lrsvWvArnPPGfAFVEFed~RDA~DA 63 (195)
T KOG0107|consen 13 VYVGNLGSRATKRELERAFSKYGP---------LRSVWVARNPPGFAFVEFEDPRDAEDA 63 (195)
T ss_pred EEeccCCCCcchHHHHHHHHhcCc---------ceeEEEeecCCCceEEeccCcccHHHH
Confidence 444467889999999999999983 221 1246789999999998877765
No 64
>KOG2278 consensus RNA:NAD 2'-phosphotransferase TPT1 [Translation, ribosomal structure and biogenesis]
Probab=80.64 E-value=1.3 Score=43.74 Aligned_cols=41 Identities=20% Similarity=0.372 Sum_probs=35.9
Q ss_pred hhhccCCCCcEEehhhccchhhhhcccCHHHHHHHHhcCCc
Q 008981 419 LKSNMDDQGWVPITLIASFPRVKNLTSNIQLILDSLRTSTV 459 (547)
Q Consensus 419 Lr~~Md~qG~VPLs~IasFnRVK~Lt~d~~lI~eALr~S~~ 459 (547)
++=+|+.||||+|..|++.++.|-+...+++|.++++.-++
T Consensus 25 ~~L~m~~dGfvpv~~lL~lnq~r~~~~t~ddi~riVk~ndK 65 (207)
T KOG2278|consen 25 LRLNMRGDGFVPVEDLLNLNQFRGANHTIDDIRRIVKRNDK 65 (207)
T ss_pred hcccccCCCceEHHHHhccchhcccCCcHHHHHHHHhcccc
Confidence 44567899999999999999999998889999999987653
No 65
>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]
Probab=79.30 E-value=2.5 Score=46.22 Aligned_cols=61 Identities=15% Similarity=0.003 Sum_probs=42.1
Q ss_pred eeecCCCCCCChhhhhhhcccc-cccccccccccccCCCcccCCcccEEcCChhhhhcCCCC
Q 008981 486 ESGLSSPAGSSVDVLAPSFQNI-TVKEGAVNQRSLTGNANCHCEDAPGIHSSEGEATEEPNQ 546 (547)
Q Consensus 486 V~g~~~p~~~T~d~L~~~F~~~-gle~~~~~~~s~R~~~k~f~GsvfVEFsSeEeAkk~~~~ 546 (547)
|.--++|-+.|-.++.+||..- -+.....++.=++.....-.|.+||-|.+||+|+++|..
T Consensus 164 vRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rpdgrpTGdAFvlfa~ee~aq~aL~k 225 (508)
T KOG1365|consen 164 VRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRPDGRPTGDAFVLFACEEDAQFALRK 225 (508)
T ss_pred EEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECCCCCcccceEEEecCHHHHHHHHHH
Confidence 3345788899999999999621 111111122334455677899999999999999998853
No 66
>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]
Probab=77.16 E-value=1.7 Score=44.09 Aligned_cols=59 Identities=10% Similarity=-0.075 Sum_probs=43.7
Q ss_pred eeeeecCCCCCCChhhhhhhcccccc-cccccccccccCCCcccCCcccEEcCChhhhhcCCC
Q 008981 484 STESGLSSPAGSSVDVLAPSFQNITV-KEGAVNQRSLTGNANCHCEDAPGIHSSEGEATEEPN 545 (547)
Q Consensus 484 ~tV~g~~~p~~~T~d~L~~~F~~~gl-e~~~~~~~s~R~~~k~f~GsvfVEFsSeEeAkk~~~ 545 (547)
..++..++-.-.|-|+|...|+++|- .++.+ .-..-++.-.|++||.|....||+++|.
T Consensus 14 ~SLkVdNLTyRTspd~LrrvFekYG~vgDVyI---Prdr~Tr~sRgFaFVrf~~k~daedA~d 73 (256)
T KOG4207|consen 14 TSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYI---PRDRYTRQSRGFAFVRFHDKRDAEDALD 73 (256)
T ss_pred eeEEecceeccCCHHHHHHHHHHhCcccceec---ccccccccccceeEEEeeecchHHHHHH
Confidence 34566667777889999999999983 33333 2224467889999999999988888763
No 67
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=73.55 E-value=27 Score=42.44 Aligned_cols=11 Identities=27% Similarity=0.673 Sum_probs=5.0
Q ss_pred CCCCCCCCCCc
Q 008981 260 SNWDARPVGGF 270 (547)
Q Consensus 260 ~~~~~~~~~gf 270 (547)
+++..-.+|||
T Consensus 1225 ~GyrGvsrgGf 1235 (1282)
T KOG0921|consen 1225 NGYRGVSRGGF 1235 (1282)
T ss_pred CCCccccCCcc
Confidence 34444444544
No 68
>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]
Probab=71.47 E-value=3.2 Score=41.99 Aligned_cols=48 Identities=13% Similarity=-0.080 Sum_probs=36.5
Q ss_pred ecCCCCCCChhhhhhhcccccccccccccccccCCCcccCCcccEEcCChhhhhcCCC
Q 008981 488 GLSSPAGSSVDVLAPSFQNITVKEGAVNQRSLTGNANCHCEDAPGIHSSEGEATEEPN 545 (547)
Q Consensus 488 g~~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R~~~k~f~GsvfVEFsSeEeAkk~~~ 545 (547)
...+.....+.+|...|...|.. . ....-.+..||||+++|+|+++|.
T Consensus 104 ~~~~~~r~~~qdl~d~~~~~g~~-~---------~~~~~~~~~~v~Fs~~~da~ra~~ 151 (216)
T KOG0106|consen 104 VRNLSLRVSWQDLKDHFRPAGEV-T---------YVDARRNFAFVEFSEQEDAKRALE 151 (216)
T ss_pred eccchhhhhHHHHhhhhcccCCC-c---------hhhhhccccceeehhhhhhhhcch
Confidence 34566777789999999999853 1 112256889999999999999874
No 69
>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]
Probab=70.56 E-value=4 Score=47.50 Aligned_cols=57 Identities=12% Similarity=0.095 Sum_probs=45.8
Q ss_pred eeeeecCCCCCCChhhhhhhccccccccccccccccc-CCCcccCCcccEEcCChhhhhcC
Q 008981 484 STESGLSSPAGSSVDVLAPSFQNITVKEGAVNQRSLT-GNANCHCEDAPGIHSSEGEATEE 543 (547)
Q Consensus 484 ~tV~g~~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R-~~~k~f~GsvfVEFsSeEeAkk~ 543 (547)
++++.-++|.+.|+++|.+||..+.+. -+.+.+| .++-+-.|.+-|-|.|.|||..+
T Consensus 868 ~V~~~~n~Pf~v~l~dI~~FF~dY~~~---p~sI~~r~nd~G~pTGe~mvAfes~~eAr~A 925 (944)
T KOG4307|consen 868 RVLSCNNFPFDVTLEDIVEFFNDYEPD---PNSIRIRRNDDGVPTGECMVAFESQEEARRA 925 (944)
T ss_pred eEEEecCCCccccHHHHHHHhcccccC---CCceeEeecCCCCcccceeEeecCHHHHHhh
Confidence 456777899999999999999999752 2222333 67889999999999999999875
No 70
>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]
Probab=70.47 E-value=2.8 Score=44.46 Aligned_cols=60 Identities=10% Similarity=-0.146 Sum_probs=42.3
Q ss_pred eeeeecCCCCCCChhhhhhhcccccccccccccccccC-CCcccCCcccEEcCChhhhhcCCCC
Q 008981 484 STESGLSSPAGSSVDVLAPSFQNITVKEGAVNQRSLTG-NANCHCEDAPGIHSSEGEATEEPNQ 546 (547)
Q Consensus 484 ~tV~g~~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R~-~~k~f~GsvfVEFsSeEeAkk~~~~ 546 (547)
.|+...-+.-+.+.+.|...|+.+|-...+. -|+. .+..-+|-+||||..|-|++.+-|+
T Consensus 102 ~TLFv~RLnydT~EskLrreF~~YG~Ikrir---lV~d~vTgkskGYAFIeye~erdm~~AYK~ 162 (335)
T KOG0113|consen 102 KTLFVARLNYDTSESKLRREFEKYGPIKRIR---LVRDKVTGKSKGYAFIEYEHERDMKAAYKD 162 (335)
T ss_pred ceeeeeeccccccHHHHHHHHHhcCcceeEE---EeeecccCCccceEEEEeccHHHHHHHHHh
Confidence 4433334567888999999999998422222 2332 3566799999999999999887653
No 71
>PLN03213 repressor of silencing 3; Provisional
Probab=70.30 E-value=2.8 Score=47.11 Aligned_cols=53 Identities=11% Similarity=-0.147 Sum_probs=36.9
Q ss_pred eeecCCCCCCChhhhhhhcccccccccccccccccCCCcccCCcccEEcCCh--hhhhcCC
Q 008981 486 ESGLSSPAGSSVDVLAPSFQNITVKEGAVNQRSLTGNANCHCEDAPGIHSSE--GEATEEP 544 (547)
Q Consensus 486 V~g~~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R~~~k~f~GsvfVEFsSe--EeAkk~~ 544 (547)
++.-++....|.++|.+.|..||-..... -+|.+. +|++||||.++ +++++++
T Consensus 13 IYVGNLSydVTEDDLravFSeFGsVkdVE---IpRETG---RGFAFVEMssdddaEeeKAI 67 (759)
T PLN03213 13 LHVGGLGESVGRDDLLKIFSPMGTVDAVE---FVRTKG---RSFAYIDFSPSSTNSLTKLF 67 (759)
T ss_pred EEEeCCCCCCCHHHHHHHHHhcCCeeEEE---EecccC---CceEEEEecCCcHHHHHHHH
Confidence 34446788999999999999998422211 124322 89999999987 5566554
No 72
>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]
Probab=68.31 E-value=4.2 Score=41.85 Aligned_cols=55 Identities=9% Similarity=-0.118 Sum_probs=42.3
Q ss_pred cCCCCCCChhhhhhhcccccccccccccccccCCCcccCCcccEEcCChhhhhcCCC
Q 008981 489 LSSPAGSSVDVLAPSFQNITVKEGAVNQRSLTGNANCHCEDAPGIHSSEGEATEEPN 545 (547)
Q Consensus 489 ~~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R~~~k~f~GsvfVEFsSeEeAkk~~~ 545 (547)
-+++-..+-|.|..+|+.|| |.++.+++ +......-+|--||.|.+-|.|..+.+
T Consensus 18 ggL~w~T~~~~l~~yFeqfG-eI~eavvi-td~~t~rskGyGfVTf~d~~aa~rAc~ 72 (247)
T KOG0149|consen 18 GGLAWETHKETLRRYFEQFG-EIVEAVVI-TDKNTGRSKGYGFVTFRDAEAATRACK 72 (247)
T ss_pred cCcccccchHHHHHHHHHhC-ceEEEEEE-eccCCccccceeeEEeecHHHHHHHhc
Confidence 35777888999999999998 33444332 234567779999999999999998865
No 73
>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]
Probab=68.11 E-value=2.7 Score=40.35 Aligned_cols=55 Identities=9% Similarity=-0.061 Sum_probs=41.4
Q ss_pred cCCCCCCChhhhhhhcccccccccccccccccCCCcccCCcccEEcCChhhhhcCCC
Q 008981 489 LSSPAGSSVDVLAPSFQNITVKEGAVNQRSLTGNANCHCEDAPGIHSSEGEATEEPN 545 (547)
Q Consensus 489 ~~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R~~~k~f~GsvfVEFsSeEeAkk~~~ 545 (547)
.+.....|.++|...|..+|-..++- .++..-+..-+|.+|||+.+.++|++++.
T Consensus 78 tgvHeEatEedi~d~F~dyGeiKNih--LNLDRRtGy~KGYaLvEYet~keAq~A~~ 132 (170)
T KOG0130|consen 78 TGVHEEATEEDIHDKFADYGEIKNIH--LNLDRRTGYVKGYALVEYETLKEAQAAID 132 (170)
T ss_pred eccCcchhHHHHHHHHhhccccccee--eccccccccccceeeeehHhHHHHHHHHH
Confidence 35678899999999999998422221 23334467889999999999999998754
No 74
>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]
Probab=66.80 E-value=3.9 Score=46.42 Aligned_cols=60 Identities=12% Similarity=-0.053 Sum_probs=46.5
Q ss_pred eeeeecCCCCCCChhhhhhhcccccccccccccccccCCCcccCCcccEEcCChhhhhcCCC
Q 008981 484 STESGLSSPAGSSVDVLAPSFQNITVKEGAVNQRSLTGNANCHCEDAPGIHSSEGEATEEPN 545 (547)
Q Consensus 484 ~tV~g~~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R~~~k~f~GsvfVEFsSeEeAkk~~~ 545 (547)
.+|..-+++.+.|.+.|.+.|..||-....+- =+-..+..-+|++||-|+++++|++.|.
T Consensus 293 ~tVFvRNL~fD~tEEel~~~fskFG~v~ya~i--V~~k~T~~skGtAFv~Fkt~~~~~~ci~ 352 (678)
T KOG0127|consen 293 KTVFVRNLPFDTTEEELKEHFSKFGEVKYAII--VKDKDTGHSKGTAFVKFKTQIAAQNCIE 352 (678)
T ss_pred ceEEEecCCccccHHHHHHHHHhhccceeEEE--EeccCCCCcccceEEEeccHHHHHHHHH
Confidence 56777789999999999999999984333221 1115678889999999999999987653
No 75
>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]
Probab=66.17 E-value=2.5 Score=46.69 Aligned_cols=130 Identities=13% Similarity=0.060 Sum_probs=75.6
Q ss_pred HHHHHhhhhhcC--cCcccccchhhhccCCCCcEEehhhccchhhhhcccCHHHHHHHHhcCCcEEEcC--CeEeeCCcc
Q 008981 398 AMLIHQIDYYFS--DANLVKDEFLKSNMDDQGWVPITLIASFPRVKNLTSNIQLILDSLRTSTVVEVQD--DRVRRRNEW 473 (547)
Q Consensus 398 ~~I~kQVEYYFS--DeNL~kD~FLr~~Md~qG~VPLs~IasFnRVK~Lt~d~~lI~eALr~S~~LEVsg--dKVRRr~~w 473 (547)
..|+.-.|=|=. .-||.||+--+ ...|+.-|. |...| |-...+.||.+-..|.=-- -+||-.+--
T Consensus 49 ~dlr~lFe~yg~V~einl~kDk~t~---~s~gcCFv~----~~trk----~a~~a~~Alhn~ktlpG~~~pvqvk~Ad~E 117 (510)
T KOG0144|consen 49 KDLRELFEKYGNVYEINLIKDKSTG---QSKGCCFVK----YYTRK----EADEAINALHNQKTLPGMHHPVQVKYADGE 117 (510)
T ss_pred HHHHHHHHHhCceeEEEeecccccC---cccceEEEE----eccHH----HHHHHHHHhhcccccCCCCcceeecccchh
Confidence 455556665643 35888886544 467876543 33333 3455566776654432110 122211100
Q ss_pred cccCCCCCCceeeeecCCCCCCChhhhhhhcccccc-cccccccccccCCCcccCCcccEEcCChhhhhcCCC
Q 008981 474 MKWIATPGRISTESGLSSPAGSSVDVLAPSFQNITV-KEGAVNQRSLTGNANCHCEDAPGIHSSEGEATEEPN 545 (547)
Q Consensus 474 ~kwvp~~~r~~tV~g~~~p~~~T~d~L~~~F~~~gl-e~~~~~~~s~R~~~k~f~GsvfVEFsSeEeAkk~~~ 545 (547)
..-+.++ +..+|- -+....|..+++++|..||. |+.. -+|+..+.-+|-+||.|++.|-|..++|
T Consensus 118 ~er~~~e-~KLFvg--~lsK~~te~evr~iFs~fG~Ied~~----ilrd~~~~sRGcaFV~fstke~A~~Aik 183 (510)
T KOG0144|consen 118 RERIVEE-RKLFVG--MLSKQCTENEVREIFSRFGHIEDCY----ILRDPDGLSRGCAFVKFSTKEMAVAAIK 183 (510)
T ss_pred hhccccc-hhhhhh--hccccccHHHHHHHHHhhCccchhh----heecccccccceeEEEEehHHHHHHHHH
Confidence 0000111 111222 24567889999999999985 3333 4888999999999999999998876554
No 76
>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=64.90 E-value=4.7 Score=46.79 Aligned_cols=56 Identities=9% Similarity=-0.098 Sum_probs=42.0
Q ss_pred ecCCCCCCChhhhhhhcccccccccccccccccCCCcccCCcccEEcCChhhhhcCCC
Q 008981 488 GLSSPAGSSVDVLAPSFQNITVKEGAVNQRSLTGNANCHCEDAPGIHSSEGEATEEPN 545 (547)
Q Consensus 488 g~~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R~~~k~f~GsvfVEFsSeEeAkk~~~ 545 (547)
.-+.+-..|+-+++.+|..||.-.. .....+..+..+.|.+||+|-|..||+.+++
T Consensus 618 VRNipFeAt~rEVr~LF~aFGqlks--vRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~ 673 (725)
T KOG0110|consen 618 VRNIPFEATKREVRKLFTAFGQLKS--VRLPKKIGKGAHRGFGFVDFLTPREAKNAFD 673 (725)
T ss_pred eeccchHHHHHHHHHHHhcccceee--eccchhhcchhhccceeeeccCcHHHHHHHH
Confidence 3467888999999999999984211 1122224567789999999999999998764
No 77
>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]
Probab=64.17 E-value=3.6 Score=43.30 Aligned_cols=52 Identities=10% Similarity=-0.073 Sum_probs=37.7
Q ss_pred eeeecCCCCCCChhhhhhhcccccccccccccccccCCCcccCCcccEEcCChhhhhcCC
Q 008981 485 TESGLSSPAGSSVDVLAPSFQNITVKEGAVNQRSLTGNANCHCEDAPGIHSSEGEATEEP 544 (547)
Q Consensus 485 tV~g~~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R~~~k~f~GsvfVEFsSeEeAkk~~ 544 (547)
+|+.-++....|.|.|+..|..||-. . -+|. =..+|.+||+|.+.|.|.+++
T Consensus 166 sVY~G~I~~~lte~~mr~~Fs~fG~I---~---EVRv--Fk~qGYaFVrF~tkEaAahAI 217 (321)
T KOG0148|consen 166 SVYVGNIASGLTEDLMRQTFSPFGPI---Q---EVRV--FKDQGYAFVRFETKEAAAHAI 217 (321)
T ss_pred eEEeCCcCccccHHHHHHhcccCCcc---e---EEEE--ecccceEEEEecchhhHHHHH
Confidence 45555666778999999999999831 1 1121 112689999999999998875
No 78
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=63.41 E-value=37 Score=40.60 Aligned_cols=18 Identities=22% Similarity=0.128 Sum_probs=7.8
Q ss_pred CCCcEEehhhccchhhhhc
Q 008981 425 DQGWVPITLIASFPRVKNL 443 (547)
Q Consensus 425 ~qG~VPLs~IasFnRVK~L 443 (547)
.+|-|.-+.+ .=|+++.|
T Consensus 676 ~e~~eekkt~-~kKk~kel 693 (1102)
T KOG1924|consen 676 QEGGEEKKTG-TKKKVKEL 693 (1102)
T ss_pred ccccccccch-hhhhhhhh
Confidence 3444544444 23444443
No 79
>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]
Probab=62.44 E-value=3.9 Score=46.16 Aligned_cols=58 Identities=12% Similarity=-0.032 Sum_probs=46.3
Q ss_pred CCceeeeecCCCCCCChhhhhhhcccccccccccccccccCCCcccCCcccEEcCChhhhhcCCC
Q 008981 481 GRISTESGLSSPAGSSVDVLAPSFQNITVKEGAVNQRSLTGNANCHCEDAPGIHSSEGEATEEPN 545 (547)
Q Consensus 481 ~r~~tV~g~~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R~~~k~f~GsvfVEFsSeEeAkk~~~ 545 (547)
...+++..++.+...+.++|..+|+.+|- ++. + ..+....|.+||||-+.-+|+.+||
T Consensus 73 ~~~~~L~v~nl~~~Vsn~~L~~~f~~yGe----ir~--i-r~t~~~~~~~~v~FyDvR~A~~Alk 130 (549)
T KOG4660|consen 73 MNQGTLVVFNLPRSVSNDTLLRIFGAYGE----IRE--I-RETPNKRGIVFVEFYDVRDAERALK 130 (549)
T ss_pred CccceEEEEecCCcCCHHHHHHHHHhhcc----hhh--h-hcccccCceEEEEEeehHhHHHHHH
Confidence 34567788889999999999999999982 211 1 3456667899999999999998876
No 80
>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]
Probab=60.00 E-value=5.9 Score=45.05 Aligned_cols=59 Identities=14% Similarity=-0.057 Sum_probs=43.3
Q ss_pred eeeecCCCCCCChhhhhhhcccccccccccccccccCCCcccCCcccEEcCChhhhhcCCC
Q 008981 485 TESGLSSPAGSSVDVLAPSFQNITVKEGAVNQRSLTGNANCHCEDAPGIHSSEGEATEEPN 545 (547)
Q Consensus 485 tV~g~~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R~~~k~f~GsvfVEFsSeEeAkk~~~ 545 (547)
|+....++...+.++|+++|..+|-..-...+ +-..+....|..||.|+=+||++.+|+
T Consensus 7 TlfV~~lp~~~~~~qL~e~FS~vGPik~~~vV--t~~gs~~~RGfgfVtFam~ED~qrA~~ 65 (678)
T KOG0127|consen 7 TLFVSRLPFSSTGEQLEEFFSYVGPIKHAVVV--TNKGSSEKRGFGFVTFAMEEDVQRALA 65 (678)
T ss_pred eEEEecCCCccchhHHHHhhhcccCcceeEEe--cCCCcccccCccceeeehHhHHHHHHH
Confidence 44445578899999999999999842221111 114567899999999999999998764
No 81
>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif
Probab=56.47 E-value=9.8 Score=30.03 Aligned_cols=49 Identities=12% Similarity=0.003 Sum_probs=31.6
Q ss_pred eeeecCCCCCCChhhhhhhcccccccccccccccccCCCcccCCcccEEcCChhhhhcCC
Q 008981 485 TESGLSSPAGSSVDVLAPSFQNITVKEGAVNQRSLTGNANCHCEDAPGIHSSEGEATEEP 544 (547)
Q Consensus 485 tV~g~~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R~~~k~f~GsvfVEFsSeEeAkk~~ 544 (547)
+|.|+ + ....+.+.++|..||-... ..+. .-.-.++|+|.++.+|+++|
T Consensus 5 ~V~Gf--~-~~~~~~vl~~F~~fGeI~~----~~~~----~~~~~~~l~y~~~~~ae~Al 53 (53)
T PF14605_consen 5 SVSGF--P-PDLAEEVLEHFASFGEIVD----IYVP----ESTNWMYLKYKSRKDAEKAL 53 (53)
T ss_pred EEEeE--C-chHHHHHHHHHHhcCCEEE----EEcC----CCCcEEEEEECCHHHHHhhC
Confidence 34554 3 3345667779999983111 1111 23567899999999999986
No 82
>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]
Probab=56.18 E-value=7.4 Score=43.37 Aligned_cols=63 Identities=10% Similarity=-0.125 Sum_probs=45.2
Q ss_pred CCceeeeecCCCCCCChhhhhhhcccccccccccccccccCCCcccCCcccEEcCChhhhhcCCC
Q 008981 481 GRISTESGLSSPAGSSVDVLAPSFQNITVKEGAVNQRSLTGNANCHCEDAPGIHSSEGEATEEPN 545 (547)
Q Consensus 481 ~r~~tV~g~~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R~~~k~f~GsvfVEFsSeEeAkk~~~ 545 (547)
.+-+.|...+.|.+....+|...|.... .+++.... +-..+-.-+|-+.|||+++|.+||++.
T Consensus 42 ~r~R~vfItNIpyd~rWqdLKdLvrekv-Gev~yveL-l~D~~GK~rGcavVEFk~~E~~qKa~E 104 (608)
T KOG4212|consen 42 ARDRSVFITNIPYDYRWQDLKDLVREKV-GEVEYVEL-LFDESGKARGCAVVEFKDPENVQKALE 104 (608)
T ss_pred cccceEEEecCcchhhhHhHHHHHHHhc-CceEeeee-ecccCCCcCCceEEEeeCHHHHHHHHH
Confidence 3556688888999999999999888763 23333111 123445567889999999999999763
No 83
>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]
Probab=54.88 E-value=8.5 Score=42.41 Aligned_cols=58 Identities=5% Similarity=-0.087 Sum_probs=42.4
Q ss_pred eeecCCCCCCChhhhhhhcccccccccccccccccC-CCcccCCcccEEcCChhhhhcCCCC
Q 008981 486 ESGLSSPAGSSVDVLAPSFQNITVKEGAVNQRSLTG-NANCHCEDAPGIHSSEGEATEEPNQ 546 (547)
Q Consensus 486 V~g~~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R~-~~k~f~GsvfVEFsSeEeAkk~~~~ 546 (547)
+...++|.+.+.+.|+++|..||.... ..+.+|. ..+.. ...||||.+-++++.+++-
T Consensus 291 i~V~nlP~da~~~~l~~~Fk~FG~Ik~--~~I~vr~~~~~~~-~fgFV~f~~~~~~~~~i~A 349 (419)
T KOG0116|consen 291 IFVKNLPPDATPAELEEVFKQFGPIKE--GGIQVRSPGGKNP-CFGFVEFENAAAVQNAIEA 349 (419)
T ss_pred eEeecCCCCCCHHHHHHHHhhcccccc--cceEEeccCCCcC-ceEEEEEeecchhhhhhhc
Confidence 556678999999999999999984221 2223332 33444 7889999999999988754
No 84
>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=54.85 E-value=5.8 Score=46.02 Aligned_cols=58 Identities=9% Similarity=-0.148 Sum_probs=41.4
Q ss_pred eecCCCCCCChhhhhhhcccccccccccccccccC---CCcccCCcccEEcCChhhhhcCCCC
Q 008981 487 SGLSSPAGSSVDVLAPSFQNITVKEGAVNQRSLTG---NANCHCEDAPGIHSSEGEATEEPNQ 546 (547)
Q Consensus 487 ~g~~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R~---~~k~f~GsvfVEFsSeEeAkk~~~~ 546 (547)
...+..-+.|.++|+..|...|.+.+.. ++.+. ++-+=.|.+||||.+.|+|+.+|++
T Consensus 519 fvkNlnf~Tt~e~l~~~F~k~G~VlS~~--I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~ 579 (725)
T KOG0110|consen 519 FVKNLNFDTTLEDLEDLFSKQGTVLSIE--ISKKKDPANKYLSMGFGFVEFAKPESAQAALKA 579 (725)
T ss_pred hhhcCCcccchhHHHHHHHhcCeEEEEE--EeccccccccccccceeEEEecCHHHHHHHHHH
Confidence 3346667888999999999988655542 12221 1333459999999999999998764
No 85
>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]
Probab=54.34 E-value=10 Score=39.95 Aligned_cols=61 Identities=8% Similarity=-0.098 Sum_probs=44.5
Q ss_pred ceeeeecCCCCCCChhhhhhhccccccccccccccccc-CCCcccCCcccEEcCChhhhhcCCCC
Q 008981 483 ISTESGLSSPAGSSVDVLAPSFQNITVKEGAVNQRSLT-GNANCHCEDAPGIHSSEGEATEEPNQ 546 (547)
Q Consensus 483 ~~tV~g~~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R-~~~k~f~GsvfVEFsSeEeAkk~~~~ 546 (547)
...|....+....+.+.|++-|.+|| |.++.+ -+| .++..-||-.||-|...|||+.++.|
T Consensus 62 hfhvfvgdls~eI~~e~lr~aF~pFG-evS~ak--virD~~T~KsKGYgFVSf~~k~dAEnAI~~ 123 (321)
T KOG0148|consen 62 HFHVFVGDLSPEIDNEKLREAFAPFG-EVSDAK--VIRDMNTGKSKGYGFVSFPNKEDAENAIQQ 123 (321)
T ss_pred ceeEEehhcchhcchHHHHHHhcccc-ccccce--EeecccCCcccceeEEeccchHHHHHHHHH
Confidence 33344445667788899999999998 334333 234 34666799999999999999988654
No 86
>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]
Probab=52.08 E-value=8.9 Score=42.61 Aligned_cols=52 Identities=13% Similarity=-0.054 Sum_probs=38.8
Q ss_pred CCCCCCChhhhhhhccccccccccccccccc-CCCcccCCcccEEcCChhhhhcCC
Q 008981 490 SSPAGSSVDVLAPSFQNITVKEGAVNQRSLT-GNANCHCEDAPGIHSSEGEATEEP 544 (547)
Q Consensus 490 ~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R-~~~k~f~GsvfVEFsSeEeAkk~~ 544 (547)
..|...|..+|++.|+++|....+ +-+| .....-+|-+||.|.+-|||.++.
T Consensus 41 qIprt~sE~dlr~lFe~yg~V~ei---nl~kDk~t~~s~gcCFv~~~trk~a~~a~ 93 (510)
T KOG0144|consen 41 QIPRTASEKDLRELFEKYGNVYEI---NLIKDKSTGQSKGCCFVKYYTRKEADEAI 93 (510)
T ss_pred cCCccccHHHHHHHHHHhCceeEE---EeecccccCcccceEEEEeccHHHHHHHH
Confidence 458889999999999999853222 2233 223467889999999999998764
No 87
>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]
Probab=50.61 E-value=10 Score=40.92 Aligned_cols=58 Identities=14% Similarity=-0.098 Sum_probs=42.9
Q ss_pred eeeecCCCCCCChhhhhhhcccccccccccccccccCCCcccCCcccEEcCChhhhhcCCC
Q 008981 485 TESGLSSPAGSSVDVLAPSFQNITVKEGAVNQRSLTGNANCHCEDAPGIHSSEGEATEEPN 545 (547)
Q Consensus 485 tV~g~~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R~~~k~f~GsvfVEFsSeEeAkk~~~ 545 (547)
.++..+.....+.+.|.+.|+.+|-..... -.......-+|..||+|++.|||++++.
T Consensus 272 nl~vknld~~~~~e~L~~~f~~~GeI~s~k---v~~~~~g~skG~gfV~fs~~eeA~~A~~ 329 (369)
T KOG0123|consen 272 NLYVKNLDETLSDEKLRKIFSSFGEITSAK---VMVDENGKSKGFGFVEFSSPEEAKKAMT 329 (369)
T ss_pred ccccccCccccchhHHHHHHhcccceeeEE---EEeccCCCccceEEEEcCCHHHHHHHHH
Confidence 344455677888999999999998422211 1224577889999999999999998764
No 88
>COG1859 KptA RNA:NAD 2'-phosphotransferase [Translation, ribosomal structure and biogenesis]
Probab=47.68 E-value=19 Score=36.55 Aligned_cols=52 Identities=21% Similarity=0.351 Sum_probs=40.1
Q ss_pred cCCCCcEEehhhccchhhhhcccCHHHHHHHHhcCCc--EEEcCCeEeeCCccc
Q 008981 423 MDDQGWVPITLIASFPRVKNLTSNIQLILDSLRTSTV--VEVQDDRVRRRNEWM 474 (547)
Q Consensus 423 Md~qG~VPLs~IasFnRVK~Lt~d~~lI~eALr~S~~--LEVsgdKVRRr~~w~ 474 (547)
||++||+.|+-|+.--|-+----|.++|..+++..++ .|+.+.+||-+.-+.
T Consensus 54 lD~~Gwa~i~~l~~~~~k~~~~~~~~~l~~iV~~d~K~Rf~l~~~~IRA~yGHS 107 (211)
T COG1859 54 LDEEGWADIDELLEGLRKAGRWLTRELLLAVVATDDKGRFELKEGKIRARYGHS 107 (211)
T ss_pred eccccchhHHHHHHHHHhhccCCCHHHHHHHHhcCCCceeEecccceeeccCcc
Confidence 6899999998887765543222368899988888765 788899999887665
No 89
>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=46.67 E-value=8.4 Score=34.40 Aligned_cols=49 Identities=10% Similarity=-0.044 Sum_probs=25.9
Q ss_pred cCCCCCCChhhhhhhcccccccccccccccccCCCcccCCcccEEcCChhhhhcCCC
Q 008981 489 LSSPAGSSVDVLAPSFQNITVKEGAVNQRSLTGNANCHCEDAPGIHSSEGEATEEPN 545 (547)
Q Consensus 489 ~~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R~~~k~f~GsvfVEFsSeEeAkk~~~ 545 (547)
.+...+.+.++|.+.|..++ .+.. +.- ..-....+|+|.+.|.|++++.
T Consensus 7 ~g~~~~~~re~iK~~f~~~g--~V~y-VD~-----~~G~~~g~VRf~~~~~A~~a~~ 55 (105)
T PF08777_consen 7 SGLGEPTSREDIKEAFSQFG--EVAY-VDF-----SRGDTEGYVRFKTPEAAQKALE 55 (105)
T ss_dssp EE--SS--HHHHHHHT-SS----EEE-EE-------TT-SEEEEEESS---HHHHHH
T ss_pred ecCCCCcCHHHHHHHHHhcC--Ccce-EEe-----cCCCCEEEEEECCcchHHHHHH
Confidence 33567788999999999997 1221 111 1234478999999999998764
No 90
>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]
Probab=45.28 E-value=22 Score=36.10 Aligned_cols=49 Identities=16% Similarity=-0.052 Sum_probs=30.0
Q ss_pred CCCCCChhhhhhhcccccccccccccccc-c-CCCcccCCcccEEcCChhhhhc
Q 008981 491 SPAGSSVDVLAPSFQNITVKEGAVNQRSL-T-GNANCHCEDAPGIHSSEGEATE 542 (547)
Q Consensus 491 ~p~~~T~d~L~~~F~~~gle~~~~~~~s~-R-~~~k~f~GsvfVEFsSeEeAkk 542 (547)
.+..+-.-.|..+|..++ ..+.+ ..+ | .-+..-+|.+||||.++|.|+=
T Consensus 57 ~p~g~~e~~~~~~~~q~~-g~v~r--~rlsRnkrTGNSKgYAFVEFEs~eVA~I 107 (214)
T KOG4208|consen 57 IPHGFFETEILNYFRQFG-GTVTR--FRLSRNKRTGNSKGYAFVEFESEEVAKI 107 (214)
T ss_pred cccchhHHHHhhhhhhcC-CeeEE--EEeecccccCCcCceEEEEeccHHHHHH
Confidence 345555566777777774 11111 111 1 2245668999999999999974
No 91
>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]
Probab=44.08 E-value=18 Score=38.45 Aligned_cols=55 Identities=5% Similarity=-0.143 Sum_probs=40.6
Q ss_pred CCCCCCChhhhhhhcccccccccccccccccCCCcccCCcccEEcCChhhhhcCCCC
Q 008981 490 SSPAGSSVDVLAPSFQNITVKEGAVNQRSLTGNANCHCEDAPGIHSSEGEATEEPNQ 546 (547)
Q Consensus 490 ~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R~~~k~f~GsvfVEFsSeEeAkk~~~~ 546 (547)
.+.-+.|.+.|.++|..++. .....+-..+ ....=.|..||+|.+.|...++|++
T Consensus 13 gisw~ttee~Lr~yf~~~Ge-v~d~~vm~d~-~t~rsrgFgfv~f~~~~~v~~vl~~ 67 (311)
T KOG4205|consen 13 GLSWETTEESLREYFSQFGE-VTDCVVMRDP-STGRSRGFGFVTFATPEGVDAVLNA 67 (311)
T ss_pred CcCccccHHHHHHHhcccCc-eeeEEEeccC-CCCCcccccceecCCCcchheeecc
Confidence 45667889999999999973 2222222222 2377789999999999999999876
No 92
>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=42.29 E-value=20 Score=38.87 Aligned_cols=62 Identities=8% Similarity=-0.237 Sum_probs=42.6
Q ss_pred ccCCCCCCceeeeecCCCCCCChhhhhhhcccccccccccccccccCCCcccCCcccEEcCChhhhhcCC
Q 008981 475 KWIATPGRISTESGLSSPAGSSVDVLAPSFQNITVKEGAVNQRSLTGNANCHCEDAPGIHSSEGEATEEP 544 (547)
Q Consensus 475 kwvp~~~r~~tV~g~~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R~~~k~f~GsvfVEFsSeEeAkk~~ 544 (547)
-|.|+++.+.+...-++....+..+|..+|..+|--+++. - ....+-|||+|.|-+.|+++.
T Consensus 220 lepPeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~------~--~~~~~CAFv~ftTR~aAE~Aa 281 (377)
T KOG0153|consen 220 LEPPEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIR------I--LPRKGCAFVTFTTREAAEKAA 281 (377)
T ss_pred cCCCcccceeEEEecccccchhHHHHHHHHhhcCCeeeEE------e--ecccccceeeehhhHHHHHHH
Confidence 4667776555554444445888899999999998322222 1 233457999999999998764
No 93
>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]
Probab=41.60 E-value=37 Score=38.09 Aligned_cols=87 Identities=9% Similarity=-0.049 Sum_probs=57.8
Q ss_pred CHHHHHHHHhcCCcEEEc-CCeEeeCCcccccCCCCCCceeeeecCCCCCCChhhhhhhcccccccccccccccccCCCc
Q 008981 446 NIQLILDSLRTSTVVEVQ-DDRVRRRNEWMKWIATPGRISTESGLSSPAGSSVDVLAPSFQNITVKEGAVNQRSLTGNAN 524 (547)
Q Consensus 446 d~~lI~eALr~S~~LEVs-gdKVRRr~~w~kwvp~~~r~~tV~g~~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R~~~k 524 (547)
.-++-.+|++....-||. |..|+......+ .+...| +.|...+.++|.+-|.+++-..+..-+-+.-+++.
T Consensus 134 ~Ke~Aq~Aik~lnn~Eir~GK~igvc~Svan-------~RLFiG-~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~ 205 (506)
T KOG0117|consen 134 TKEEAQEAIKELNNYEIRPGKLLGVCVSVAN-------CRLFIG-NIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKT 205 (506)
T ss_pred cHHHHHHHHHHhhCccccCCCEeEEEEeeec-------ceeEec-cCCccccHHHHHHHHHhhCCCeeEEEEecCccccc
Confidence 356667889988888876 455654432211 222334 56899999999999999963222222223346788
Q ss_pred ccCCcccEEcCChhhh
Q 008981 525 CHCEDAPGIHSSEGEA 540 (547)
Q Consensus 525 ~f~GsvfVEFsSeEeA 540 (547)
..+|++||||-+--.|
T Consensus 206 KNRGFaFveYe~H~~A 221 (506)
T KOG0117|consen 206 KNRGFAFVEYESHRAA 221 (506)
T ss_pred cccceEEEEeecchhH
Confidence 9999999999876554
No 94
>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]
Probab=41.20 E-value=23 Score=38.46 Aligned_cols=64 Identities=14% Similarity=0.075 Sum_probs=43.1
Q ss_pred cC-CCCCCceeeeecCCCCCCChhhhhhhccccccccccccccc-----ccCCCcccCCcccEEcCChhh
Q 008981 476 WI-ATPGRISTESGLSSPAGSSVDVLAPSFQNITVKEGAVNQRS-----LTGNANCHCEDAPGIHSSEGE 539 (547)
Q Consensus 476 wv-p~~~r~~tV~g~~~p~~~T~d~L~~~F~~~gle~~~~~~~s-----~R~~~k~f~GsvfVEFsSeEe 539 (547)
|. ++..+--.|+..++|.+.|++++.+.|.++|+.-....... -|.+...++|.+++-|.-+|.
T Consensus 126 ~~~~~~~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~G~lKGDaLc~y~K~ES 195 (382)
T KOG1548|consen 126 WFNPEPKVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQGKLKGDALCCYIKRES 195 (382)
T ss_pred ccCcccccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCCCCccCceEEEeecccH
Confidence 44 44443333667778999999999999999996333221111 225678899999988865443
No 95
>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]
Probab=40.59 E-value=17 Score=39.31 Aligned_cols=53 Identities=9% Similarity=-0.122 Sum_probs=40.0
Q ss_pred eeecCCCCCCChhhhhhhccccccc-ccccccccccCCCcccCCcccEEcCChhhhhcC
Q 008981 486 ESGLSSPAGSSVDVLAPSFQNITVK-EGAVNQRSLTGNANCHCEDAPGIHSSEGEATEE 543 (547)
Q Consensus 486 V~g~~~p~~~T~d~L~~~F~~~gle-~~~~~~~s~R~~~k~f~GsvfVEFsSeEeAkk~ 543 (547)
++.++.|-.+.--+|+.-|++||.. ++++- -+++--||+=||.|.+.+||+++
T Consensus 99 LhVSNIPFrFRdpDL~aMF~kfG~VldVEII-----fNERGSKGFGFVTmen~~dadRA 152 (376)
T KOG0125|consen 99 LHVSNIPFRFRDPDLRAMFEKFGKVLDVEII-----FNERGSKGFGFVTMENPADADRA 152 (376)
T ss_pred eEeecCCccccCccHHHHHHhhCceeeEEEE-----eccCCCCccceEEecChhhHHHH
Confidence 3455677888889999999999842 22221 45677789999999999999864
No 96
>PTZ00315 2'-phosphotransferase; Provisional
Probab=39.31 E-value=22 Score=40.82 Aligned_cols=49 Identities=18% Similarity=0.262 Sum_probs=37.9
Q ss_pred ccCCCCcEEehhhccchhhhhcccCHHHHHHHHhcCCc--EEEc-----C-CeEeeC
Q 008981 422 NMDDQGWVPITLIASFPRVKNLTSNIQLILDSLRTSTV--VEVQ-----D-DRVRRR 470 (547)
Q Consensus 422 ~Md~qG~VPLs~IasFnRVK~Lt~d~~lI~eALr~S~~--LEVs-----g-dKVRRr 470 (547)
.||++|||.|+.|+.-.+.+...-+.+.|.+++++.++ .|+. + .+||..
T Consensus 399 ~ld~~Gwv~vd~LL~~~~~~~~~~t~e~i~~VV~~ndK~RF~l~~~~~~~~~~IRA~ 455 (582)
T PTZ00315 399 PITSNGYVLLDDILRQPPMRNDPVSVQDVARVVRDSDKQRFKLAYGAADGRLYIRAN 455 (582)
T ss_pred CcCCCCCEEHHHHHHHHHhcCCCCCHHHHHHHHHcCCCCceEEeccCCCCceEEEec
Confidence 37899999999999888877655578999999998864 5554 2 258854
No 97
>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]
Probab=36.31 E-value=22 Score=41.33 Aligned_cols=51 Identities=29% Similarity=0.296 Sum_probs=33.2
Q ss_pred ccccchhhhccCCCCcEEehhhccchhhhhcccCHHHHHHHHhcCCcEEEcCC
Q 008981 413 LVKDEFLKSNMDDQGWVPITLIASFPRVKNLTSNIQLILDSLRTSTVVEVQDD 465 (547)
Q Consensus 413 L~kD~FLr~~Md~qG~VPLs~IasFnRVK~Lt~d~~lI~eALr~S~~LEVsgd 465 (547)
+|-+.|+++.+..-|||+...++.|..+--+ +...+..|++..+.+.++++
T Consensus 51 ~~s~~~~~~il~~~g~v~s~kr~~fgf~~f~--~~~~~~ra~r~~t~~~~~~~ 101 (668)
T KOG2253|consen 51 LVSQEFWKSILAKSGFVPSWKRDKFGFCEFL--KHIGDLRASRLLTELNIDDQ 101 (668)
T ss_pred hhhHHHHHHHHhhCCcchhhhhhhhcccchh--hHHHHHHHHHHhcccCCCcc
Confidence 4447788888888999988888776654332 24444556666566666554
No 98
>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]
Probab=36.25 E-value=19 Score=36.08 Aligned_cols=57 Identities=12% Similarity=-0.141 Sum_probs=36.9
Q ss_pred eeeecCCCCCCChhhhhhhcccccccccccccccccCCCcccCCcccEEcCChhhhhcC
Q 008981 485 TESGLSSPAGSSVDVLAPSFQNITVKEGAVNQRSLTGNANCHCEDAPGIHSSEGEATEE 543 (547)
Q Consensus 485 tV~g~~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R~~~k~f~GsvfVEFsSeEeAkk~ 543 (547)
++..-++....|..-|-|.|-..|-..... .-.. .....+.|.+|+||-+||||+=+
T Consensus 11 tiyvgnld~kvs~~~l~EL~iqagpVv~i~-iPkD-rv~~~~qGygF~Ef~~eedadYA 67 (203)
T KOG0131|consen 11 TLYVGNLDEKVSEELLYELFIQAGPVVNLH-IPKD-RVTQKHQGYGFAEFRTEEDADYA 67 (203)
T ss_pred eEEEecCCHHHHHHHHHHHHHhcCceeeee-cchh-hhcccccceeEEEEechhhhHHH
Confidence 444455667777777888887776322111 0011 22457899999999999999743
No 99
>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]
Probab=35.95 E-value=18 Score=41.08 Aligned_cols=58 Identities=10% Similarity=-0.083 Sum_probs=44.5
Q ss_pred eecCCCCCCChhhhhhhcccccccccccccccccCCCcccCCcccEEcCChhhhhcCCCC
Q 008981 487 SGLSSPAGSSVDVLAPSFQNITVKEGAVNQRSLTGNANCHCEDAPGIHSSEGEATEEPNQ 546 (547)
Q Consensus 487 ~g~~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R~~~k~f~GsvfVEFsSeEeAkk~~~~ 546 (547)
+.-++....|-++|..+|+.||..+++- ..+.......+|.-||+|...|+|+++|.|
T Consensus 282 ~vgnLHfNite~~lr~ifepfg~Ie~v~--l~~d~~tG~skgfGfi~f~~~~~ar~a~e~ 339 (549)
T KOG0147|consen 282 YVGNLHFNITEDMLRGIFEPFGKIENVQ--LTKDSETGRSKGFGFITFVNKEDARKALEQ 339 (549)
T ss_pred hhcccccCchHHHHhhhccCcccceeee--eccccccccccCcceEEEecHHHHHHHHHH
Confidence 4446788899999999999998533322 122244788999999999999999998654
No 100
>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]
Probab=35.44 E-value=21 Score=37.88 Aligned_cols=50 Identities=26% Similarity=0.084 Sum_probs=38.6
Q ss_pred CCCChhhhhhhcccccccccccccccccCCCcccCCcccEEcCChhhhhcCCC
Q 008981 493 AGSSVDVLAPSFQNITVKEGAVNQRSLTGNANCHCEDAPGIHSSEGEATEEPN 545 (547)
Q Consensus 493 ~~~T~d~L~~~F~~~gle~~~~~~~s~R~~~k~f~GsvfVEFsSeEeAkk~~~ 545 (547)
...+.|+++..|+.||..+... -+|+....-||-+||.|++.-||+.+++
T Consensus 29 kqq~e~dvrrlf~pfG~~~e~t---vlrg~dg~sKGCAFVKf~s~~eAqaAI~ 78 (371)
T KOG0146|consen 29 KQQSEDDVRRLFQPFGNIEECT---VLRGPDGNSKGCAFVKFSSHAEAQAAIN 78 (371)
T ss_pred ccccHHHHHHHhcccCCcceeE---EecCCCCCCCCceEEEeccchHHHHHHH
Confidence 4556799999999998533222 3677777789999999999999987653
No 101
>PRK02001 hypothetical protein; Validated
Probab=35.19 E-value=7.7 Score=37.14 Aligned_cols=77 Identities=18% Similarity=0.187 Sum_probs=57.2
Q ss_pred HHHHHHHHhhhhhcCcCcccccchhhhccCCCCcEEehhhccchhhhhcccCHHHHHHHHhcCCcEEEc----CCeEeeC
Q 008981 395 SLAAMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVKNLTSNIQLILDSLRTSTVVEVQ----DDRVRRR 470 (547)
Q Consensus 395 ~L~~~I~kQVEYYFSDeNL~kD~FLr~~Md~qG~VPLs~IasFnRVK~Lt~d~~lI~eALr~S~~LEVs----gdKVRRr 470 (547)
-+.+.+...+.|++=|-.+.+..+||=.+|.+|-|.|...+.|.|--. .++++....=.|||+ +..+++.
T Consensus 9 ~~~e~~~~~~g~eLvdv~~~~~~~lrV~ID~~~Gv~lddC~~vSr~is------~~LD~~d~~Y~LEVSSPGldRpL~~~ 82 (152)
T PRK02001 9 LLVEELLEGPELFLVDLTISPDNKIVVEIDGDEGVWIEDCVELSRAIE------HNLDREEEDFELEVGSAGLTSPLKVP 82 (152)
T ss_pred HHHHhhhhhcCcEEEEEEEEcCCEEEEEEECCCCCCHHHHHHHHHHHH------HHhcCCCCCeEEEEeCCCCCCcCCCH
Confidence 456778889999999999999888988889877799999888877432 223322345579998 3457777
Q ss_pred CcccccC
Q 008981 471 NEWMKWI 477 (547)
Q Consensus 471 ~~w~kwv 477 (547)
..|.+++
T Consensus 83 ~~f~r~~ 89 (152)
T PRK02001 83 RQYKKNI 89 (152)
T ss_pred HHHHHhC
Confidence 7788776
No 102
>PF04963 Sigma54_CBD: Sigma-54 factor, core binding domain; InterPro: IPR007046 This domain makes a direct interaction with the core RNA polymerase, to form an enhancer dependent holoenzyme []. The centre of this domain contains a very weak similarity to a helix-turn-helix motif, which may represent a DNA binding domain.; GO: 0003677 DNA binding, 0006352 transcription initiation, DNA-dependent; PDB: 2K9L_A 2K9M_A.
Probab=34.67 E-value=19 Score=35.20 Aligned_cols=40 Identities=28% Similarity=0.394 Sum_probs=24.4
Q ss_pred cHHHHHHHHHhhhhhcCcCc-ccccchhhhccCCCCcEEeh
Q 008981 393 EPSLAAMLIHQIDYYFSDAN-LVKDEFLKSNMDDQGWVPIT 432 (547)
Q Consensus 393 d~~L~~~I~kQVEYYFSDeN-L~kD~FLr~~Md~qG~VPLs 432 (547)
++.|.+.|..||...+-++. ..-=.||...+|++||+.+.
T Consensus 14 ~~sL~e~L~~Ql~~~~l~~~~~~ia~~lI~~LD~~GyL~~~ 54 (194)
T PF04963_consen 14 EESLYEHLLEQLNLSPLSEEEREIAEYLIDNLDDDGYLTES 54 (194)
T ss_dssp -----HHHHHHHHHH---TCCHHHHHHHCCCBTTTSTCSS-
T ss_pred ccCHHHHHHHHHcCcccCHHHHHHHHHHHHcCCCCCccCCC
Confidence 46899999999998754443 33357788888999998544
No 103
>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]
Probab=34.01 E-value=27 Score=36.94 Aligned_cols=53 Identities=15% Similarity=-0.006 Sum_probs=38.5
Q ss_pred CCCCCCChhhhhhhcccccccccccccccccC-CCcccCCcccEEcCChhhhhcCCC
Q 008981 490 SSPAGSSVDVLAPSFQNITVKEGAVNQRSLTG-NANCHCEDAPGIHSSEGEATEEPN 545 (547)
Q Consensus 490 ~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R~-~~k~f~GsvfVEFsSeEeAkk~~~ 545 (547)
-+|...|+|+|+..|..+|-.++-. -+|. -+..--|.-||.+-+++||+++.+
T Consensus 48 YLPQ~MTqdE~rSLF~SiGeiEScK---LvRDKitGqSLGYGFVNYv~p~DAe~Ain 101 (360)
T KOG0145|consen 48 YLPQNMTQDELRSLFGSIGEIESCK---LVRDKITGQSLGYGFVNYVRPKDAEKAIN 101 (360)
T ss_pred ecccccCHHHHHHHhhcccceeeee---eeeccccccccccceeeecChHHHHHHHh
Confidence 3688999999999999998433322 1232 133345778999999999999865
No 104
>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=32.31 E-value=25 Score=31.54 Aligned_cols=59 Identities=8% Similarity=-0.038 Sum_probs=33.7
Q ss_pred eeecCCCCCCChhhhhhhcccccccccccccccccC-------CCcccCCcccEEcCChhhhhcCCCCC
Q 008981 486 ESGLSSPAGSSVDVLAPSFQNITVKEGAVNQRSLTG-------NANCHCEDAPGIHSSEGEATEEPNQN 547 (547)
Q Consensus 486 V~g~~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R~-------~~k~f~GsvfVEFsSeEeAkk~~~~~ 547 (547)
|..++++.. ..+.+...|+++|-... ...-+|. ....-..=+-|+|.+..+|+++|+.|
T Consensus 9 VtVFGfp~~-~~~~Vl~~F~~~G~Ile--~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~~N 74 (100)
T PF05172_consen 9 VTVFGFPPS-ASNQVLRHFSSFGTILE--HFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQKN 74 (100)
T ss_dssp EEEE---GG-GHHHHHHHHHCCS-EEC--EEGGG----------E-CCTTEEEEEESSHHHHHHHHTTT
T ss_pred EEEEccCHH-HHHHHHHHHHhcceEEE--eecccccccccccccCCCCCCEEEEECCCHHHHHHHHHhC
Confidence 334445544 56778899999983111 1111221 11223445778999999999999987
No 105
>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]
Probab=31.85 E-value=12 Score=42.37 Aligned_cols=55 Identities=13% Similarity=-0.070 Sum_probs=38.5
Q ss_pred ceeeeecCCCCCCChhhhhhhccccccccccccccccc-CCCcccCCcccEEcCChhhh
Q 008981 483 ISTESGLSSPAGSSVDVLAPSFQNITVKEGAVNQRSLT-GNANCHCEDAPGIHSSEGEA 540 (547)
Q Consensus 483 ~~tV~g~~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R-~~~k~f~GsvfVEFsSeEeA 540 (547)
.++|..-.+....+--+|++||..+|.... +.-+. ..++..+|.++|||.+++--
T Consensus 179 ~Rtvf~~qla~r~~pRdL~efFs~~gkVrd---VriI~Dr~s~rskgi~Yvef~D~~sV 234 (549)
T KOG0147|consen 179 QRTVFCMQLARRNPPRDLEEFFSIVGKVRD---VRIIGDRNSRRSKGIAYVEFCDEQSV 234 (549)
T ss_pred HHHHHHHHHhhcCCchhHHHHHHhhcCcce---eEeeccccchhhcceeEEEEecccch
Confidence 456666566677788899999999984221 11111 45677999999999987653
No 106
>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]
Probab=31.39 E-value=30 Score=39.13 Aligned_cols=24 Identities=4% Similarity=-0.133 Sum_probs=19.9
Q ss_pred CCcccCCcccEEcCChhhhhcCCC
Q 008981 522 NANCHCEDAPGIHSSEGEATEEPN 545 (547)
Q Consensus 522 ~~k~f~GsvfVEFsSeEeAkk~~~ 545 (547)
....-+|-|||||.|.|++++++.
T Consensus 449 ~~~~G~GkVFVefas~ed~qrA~~ 472 (500)
T KOG0120|consen 449 NPVPGTGKVFVEFADTEDSQRAME 472 (500)
T ss_pred CcCCCcccEEEEecChHHHHHHHH
Confidence 345569999999999999998753
No 107
>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]
Probab=30.71 E-value=24 Score=38.93 Aligned_cols=55 Identities=7% Similarity=-0.033 Sum_probs=39.6
Q ss_pred cCCCCCCChhhhhhhcccccccccccccccccCCCcccCCcccEEcCChhhhhcC
Q 008981 489 LSSPAGSSVDVLAPSFQNITVKEGAVNQRSLTGNANCHCEDAPGIHSSEGEATEE 543 (547)
Q Consensus 489 ~~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R~~~k~f~GsvfVEFsSeEeAkk~ 543 (547)
-++|-..|+++|..||..|-.....-.+--+-..+....|.+||+|.++|+|..+
T Consensus 286 RGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N~qGrPSGeAFIqm~nae~a~aa 340 (508)
T KOG1365|consen 286 RGLPYEATVEDILDFLGDFATDIRFQGVHMVLNGQGRPSGEAFIQMRNAERARAA 340 (508)
T ss_pred cCCChhhhHHHHHHHHHHHhhhcccceeEEEEcCCCCcChhhhhhhhhhHHHHHH
Confidence 3678999999999999999532211101111145778899999999999998754
No 108
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=30.27 E-value=1.9e+02 Score=31.88 Aligned_cols=9 Identities=22% Similarity=0.231 Sum_probs=4.5
Q ss_pred CCCCCCCCC
Q 008981 218 PTQPPPPPP 226 (547)
Q Consensus 218 ~~~~~p~~~ 226 (547)
+-+|+.+++
T Consensus 384 yqqp~~~~~ 392 (465)
T KOG3973|consen 384 YQQPQQQQQ 392 (465)
T ss_pred CcCchhhhh
Confidence 445555555
No 109
>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]
Probab=28.87 E-value=40 Score=34.21 Aligned_cols=55 Identities=11% Similarity=-0.143 Sum_probs=37.3
Q ss_pred eeecCCCCCCChhhhhhhcccccccccccccccccCCCcccCCcccEEcCChhhhhcCCC
Q 008981 486 ESGLSSPAGSSVDVLAPSFQNITVKEGAVNQRSLTGNANCHCEDAPGIHSSEGEATEEPN 545 (547)
Q Consensus 486 V~g~~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R~~~k~f~GsvfVEFsSeEeAkk~~~ 545 (547)
++.-++|.+...-+|+..|-+++....+- | .+-...-..+||||.+.-||+.+++
T Consensus 9 iyvGNLP~diRekeieDlFyKyg~i~~ie----L-K~r~g~ppfafVeFEd~RDAeDAiy 63 (241)
T KOG0105|consen 9 IYVGNLPGDIREKEIEDLFYKYGRIREIE----L-KNRPGPPPFAFVEFEDPRDAEDAIY 63 (241)
T ss_pred EEecCCCcchhhccHHHHHhhhcceEEEE----e-ccCCCCCCeeEEEecCccchhhhhh
Confidence 34446788888888999999997422111 1 1123345689999999999987764
No 110
>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=28.60 E-value=31 Score=35.78 Aligned_cols=60 Identities=13% Similarity=-0.134 Sum_probs=42.3
Q ss_pred ceeeeecCCCCCCChhhhhhhcccccccccccccccccCCCcccCCcccEEcCChhhhhcCC
Q 008981 483 ISTESGLSSPAGSSVDVLAPSFQNITVKEGAVNQRSLTGNANCHCEDAPGIHSSEGEATEEP 544 (547)
Q Consensus 483 ~~tV~g~~~p~~~T~d~L~~~F~~~gle~~~~~~~s~R~~~k~f~GsvfVEFsSeEeAkk~~ 544 (547)
.++++.-++..+.|.--|.+-|=.||- ...-...+.-....++|..||||.--|||-.++
T Consensus 10 KrtlYVGGladeVtekvLhaAFIPFGD--I~dIqiPlDyesqkHRgFgFVefe~aEDAaaAi 69 (298)
T KOG0111|consen 10 KRTLYVGGLADEVTEKVLHAAFIPFGD--IKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAI 69 (298)
T ss_pred ceeEEeccchHHHHHHHHHhccccccc--hhhcccccchhcccccceeEEEeeccchhHHHh
Confidence 344444456777888889999988872 111123444567889999999999999997765
No 111
>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]
Probab=28.41 E-value=49 Score=33.69 Aligned_cols=51 Identities=10% Similarity=-0.192 Sum_probs=34.0
Q ss_pred CCCChhhhhhhcccccccccccccccccCCCcccCCcccEEcCChhhhhcCCC
Q 008981 493 AGSSVDVLAPSFQNITVKEGAVNQRSLTGNANCHCEDAPGIHSSEGEATEEPN 545 (547)
Q Consensus 493 ~~~T~d~L~~~F~~~gle~~~~~~~s~R~~~k~f~GsvfVEFsSeEeAkk~~~ 545 (547)
...|.+.++..|+.|+-...+. ..+.......+|.++|||.+.+.+.+.|+
T Consensus 111 ~~~t~~~~e~hf~~Cg~i~~~t--i~~d~~~~~~k~~~yvef~~~~~~~~ay~ 161 (231)
T KOG4209|consen 111 FLVTLTKIELHFESCGGINRVT--VPKDKFRGHPKGFAYVEFSSYELVEEAYK 161 (231)
T ss_pred cccccchhhheeeccCCcccee--eeccccCCCcceeEEEecccHhhhHHHhh
Confidence 3455566999999997422111 11112233378999999999999998876
No 112
>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]
Probab=28.07 E-value=39 Score=34.90 Aligned_cols=59 Identities=17% Similarity=0.083 Sum_probs=41.5
Q ss_pred eeeeecCCCCCCChhhhhhhccccc-ccccccccccccCCCcccCCcccEEcCChhhhhcCCCC
Q 008981 484 STESGLSSPAGSSVDVLAPSFQNIT-VKEGAVNQRSLTGNANCHCEDAPGIHSSEGEATEEPNQ 546 (547)
Q Consensus 484 ~tV~g~~~p~~~T~d~L~~~F~~~g-le~~~~~~~s~R~~~k~f~GsvfVEFsSeEeAkk~~~~ 546 (547)
..+...+++...+.++|++.|+.++ ++.+..+.+. .-.-.|++.|-|+--+||..+++|
T Consensus 84 ~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~----~G~s~Gta~v~~~r~~DA~~avk~ 143 (243)
T KOG0533|consen 84 TKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDR----AGRSLGTADVSFNRRDDAERAVKK 143 (243)
T ss_pred ceeeeecCCcCcchHHHHHHHHHhccceEEeeccCC----CCCCCccceeeecchHhHHHHHHH
Confidence 4466678899999999999999994 3333222111 122239999999999999887654
No 113
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=24.32 E-value=30 Score=38.90 Aligned_cols=67 Identities=19% Similarity=0.281 Sum_probs=43.1
Q ss_pred HHHHHHHHHhhhhhcCcCcc-cccchhhhccCCCCcE--EehhhccchhhhhcccCHHHHHHHHhcCCcEE
Q 008981 394 PSLAAMLIHQIDYYFSDANL-VKDEFLKSNMDDQGWV--PITLIASFPRVKNLTSNIQLILDSLRTSTVVE 461 (547)
Q Consensus 394 ~~L~~~I~kQVEYYFSDeNL-~kD~FLr~~Md~qG~V--PLs~IasFnRVK~Lt~d~~lI~eALr~S~~LE 461 (547)
+.|.+.|..||.+++-+..- .-=.||...+|++||+ ++..|+.-.. ..|..+.+.|.+||+.-..||
T Consensus 123 ~sL~~~L~~Ql~~~~~~~~~~~ia~~lI~~LD~~GyL~~~~~eia~~~~-~~l~~~~~~ve~vL~~iQ~le 192 (481)
T PRK12469 123 PTLHEHLHDALRLYFLTERDREIARTIIDALDDDGYLRQDLSELAEAAD-PELGLSEQELEVALRLVQSLD 192 (481)
T ss_pred CCHHHHHHHHHhccCCCHHHHHHHHHHHhhCCCCCCCCCCHHHHHhccc-cccCCCHHHHHHHHHHHhcCC
Confidence 47889999999998666643 2235888999999998 5555653311 123345666666665543333
No 114
>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., PubMed:15231786). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations
Probab=22.03 E-value=36 Score=37.48 Aligned_cols=59 Identities=20% Similarity=0.275 Sum_probs=38.7
Q ss_pred cHHHHHHHHHhhhhhcCc-CcccccchhhhccCCCCcEE--ehhhccchhhhhcccCHHHHHHHHhc
Q 008981 393 EPSLAAMLIHQIDYYFSD-ANLVKDEFLKSNMDDQGWVP--ITLIASFPRVKNLTSNIQLILDSLRT 456 (547)
Q Consensus 393 d~~L~~~I~kQVEYYFSD-eNL~kD~FLr~~Md~qG~VP--Ls~IasFnRVK~Lt~d~~lI~eALr~ 456 (547)
...|.+.|..||.+++-+ .-..-=.||...+|++||+. +..|+.- +..+.+.|.+||..
T Consensus 75 ~~sL~e~L~~Ql~~~~~~~~~~~ia~~iI~~LD~~GyL~~~~~eia~~-----l~~~~~~ve~~l~~ 136 (429)
T TIGR02395 75 TESLFEHLLEQLDLQLFTERDRKIALYIIDNLDEDGYLEIDLEEIADE-----LEVSEEEVEKVLEL 136 (429)
T ss_pred CCCHHHHHHHHHhccCCCHHHHHHHHHHHHhCCCCCCCCCCHHHHHHH-----cCCCHHHHHHHHHH
Confidence 458889999999998443 44444578889999999986 4445322 22345555555544
No 115
>PRK14642 hypothetical protein; Provisional
Probab=20.52 E-value=23 Score=35.47 Aligned_cols=79 Identities=11% Similarity=0.254 Sum_probs=57.1
Q ss_pred HHHHHHHHHhhhhhcCcCcccccchhhhccCC-------------CCcEEehhhccchhhhhcccCHHHHHHHHhcCCcE
Q 008981 394 PSLAAMLIHQIDYYFSDANLVKDEFLKSNMDD-------------QGWVPITLIASFPRVKNLTSNIQLILDSLRTSTVV 460 (547)
Q Consensus 394 ~~L~~~I~kQVEYYFSDeNL~kD~FLr~~Md~-------------qG~VPLs~IasFnRVK~Lt~d~~lI~eALr~S~~L 460 (547)
.+|.+.+...+.|++=|-.+.+..+||=.||. ++.|.|.....+.|--...-|.+.+ .-..|
T Consensus 4 ~~liepvv~~lG~eLvdve~~~~~~LrV~ID~~~~~~~~~~~~~~~~gVtidDC~~vSR~Is~~LDve~~-----~y~~L 78 (197)
T PRK14642 4 QQIVEQTVTGLGYDLVEIERSAGGLLRVTIDLPWVPPTEGAPVGPEQFVTVEDCEKVTRQLQFALEVDGV-----DYKRL 78 (197)
T ss_pred HHHHHHHHHHcCCEEEEEEEecCCEEEEEEecCccccccccccccCCCccHHHHHHHHHHHHHHhcccCc-----cccEE
Confidence 46778889999999999888888889888874 5789998888887754433232221 12269
Q ss_pred EEc----CCeEeeCCcccccC
Q 008981 461 EVQ----DDRVRRRNEWMKWI 477 (547)
Q Consensus 461 EVs----gdKVRRr~~w~kwv 477 (547)
||+ +.-+|+..+|.+++
T Consensus 79 EVSSPGldRPLk~~~df~rfi 99 (197)
T PRK14642 79 EVSSPGIDRPLRHEQDFERFA 99 (197)
T ss_pred EEeCCCCCCCCCCHHHHHHhC
Confidence 998 23577777888876
No 116
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=20.20 E-value=42 Score=37.30 Aligned_cols=60 Identities=20% Similarity=0.285 Sum_probs=38.9
Q ss_pred cHHHHHHHHHhhhhhcCcCc-ccccchhhhccCCCCcE--EehhhccchhhhhcccCHHHHHHHHhcC
Q 008981 393 EPSLAAMLIHQIDYYFSDAN-LVKDEFLKSNMDDQGWV--PITLIASFPRVKNLTSNIQLILDSLRTS 457 (547)
Q Consensus 393 d~~L~~~I~kQVEYYFSDeN-L~kD~FLr~~Md~qG~V--PLs~IasFnRVK~Lt~d~~lI~eALr~S 457 (547)
...|.+.|..||.+++-+.. ..-=.||...+|++||+ ++..|+.- |..+.+.|.+||+.-
T Consensus 100 ~~sL~e~L~~Ql~~~~l~~~~~~ia~~iI~~LD~~GyL~~~~~eia~~-----l~~~~~~v~~~l~~l 162 (455)
T PRK05932 100 TESLQDHLLEQIELTPFSETDRAIATYIIDALDDEGYLTEDLEEIAES-----LGVELDEVEAVLKRI 162 (455)
T ss_pred CCCHHHHHHHHHcccCCCHHHHHHHHHHHHhCCCCCCCCCCHHHHHHH-----cCCCHHHHHHHHHHH
Confidence 34788999999999854433 33346788889999998 44555432 223455555555543
Done!