Query 044301
Match_columns 154
No_of_seqs 122 out of 318
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 13:17:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/044301.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/044301hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3152 TBP-binding protein, a 99.9 1.8E-28 3.9E-33 208.9 3.5 88 14-106 53-140 (278)
2 PF00076 RRM_1: RNA recognitio 98.3 3.5E-07 7.6E-12 58.4 1.9 33 38-70 1-33 (70)
3 PF14259 RRM_6: RNA recognitio 98.1 3.2E-06 7E-11 55.2 3.4 50 38-105 1-50 (70)
4 KOG4208 Nucleolar RNA-binding 98.1 2.8E-06 6E-11 71.4 3.6 57 32-105 46-103 (214)
5 smart00362 RRM_2 RNA recogniti 97.7 6.8E-05 1.5E-09 46.1 4.2 34 38-71 2-35 (72)
6 TIGR01661 ELAV_HUD_SF ELAV/HuD 97.5 9.8E-05 2.1E-09 61.2 3.6 37 35-71 3-39 (352)
7 cd00590 RRM RRM (RNA recogniti 97.5 0.0002 4.3E-09 44.3 4.0 52 37-106 1-52 (74)
8 PLN03134 glycine-rich RNA-bind 97.4 0.00015 3.3E-09 55.9 3.5 37 34-70 33-69 (144)
9 PLN03121 nucleic acid binding 97.1 0.00056 1.2E-08 58.5 4.2 34 37-70 7-40 (243)
10 PLN03120 nucleic acid binding 97.1 0.00054 1.2E-08 59.0 3.9 34 37-70 6-39 (260)
11 TIGR01661 ELAV_HUD_SF ELAV/HuD 97.1 0.00084 1.8E-08 55.7 4.6 35 37-71 271-305 (352)
12 TIGR01649 hnRNP-L_PTB hnRNP-L/ 96.8 0.0015 3.3E-08 58.4 4.5 34 36-69 3-36 (481)
13 TIGR01659 sex-lethal sex-letha 96.8 0.0014 3.1E-08 57.4 3.9 36 35-70 107-142 (346)
14 KOG0113 U1 small nuclear ribon 96.7 0.0016 3.4E-08 58.0 3.8 34 37-70 103-136 (335)
15 TIGR01628 PABP-1234 polyadenyl 96.7 0.0015 3.2E-08 58.7 3.6 35 37-71 2-36 (562)
16 TIGR01659 sex-lethal sex-letha 96.7 0.0016 3.5E-08 57.0 3.4 36 35-70 193-228 (346)
17 TIGR01622 SF-CC1 splicing fact 96.6 0.0023 4.9E-08 55.4 3.9 36 35-70 186-221 (457)
18 TIGR01645 half-pint poly-U bin 96.6 0.0018 3.9E-08 61.3 3.4 37 35-71 204-240 (612)
19 smart00360 RRM RNA recognition 96.5 0.0035 7.5E-08 38.1 3.4 31 40-70 1-31 (71)
20 COG0724 RNA-binding proteins ( 96.4 0.0064 1.4E-07 45.0 4.6 36 35-70 115-150 (306)
21 TIGR01645 half-pint poly-U bin 96.2 0.01 2.2E-07 56.4 6.2 38 33-70 105-142 (612)
22 TIGR01642 U2AF_lg U2 snRNP aux 96.2 0.0058 1.3E-07 53.5 4.3 36 35-70 295-330 (509)
23 TIGR01628 PABP-1234 polyadenyl 96.2 0.0059 1.3E-07 54.8 4.3 37 34-70 87-123 (562)
24 TIGR01649 hnRNP-L_PTB hnRNP-L/ 96.1 0.0067 1.5E-07 54.3 4.1 36 35-70 275-311 (481)
25 TIGR01622 SF-CC1 splicing fact 95.9 0.01 2.2E-07 51.5 4.4 35 36-70 90-124 (457)
26 KOG0122 Translation initiation 95.7 0.01 2.2E-07 51.6 3.6 38 35-72 189-226 (270)
27 TIGR01648 hnRNP-R-Q heterogene 95.0 0.031 6.6E-07 52.7 4.5 35 36-70 59-93 (578)
28 KOG0148 Apoptosis-promoting RN 94.6 0.034 7.3E-07 49.4 3.4 36 35-70 164-199 (321)
29 KOG0126 Predicted RNA-binding 94.4 0.0091 2E-07 50.5 -0.4 39 33-71 33-71 (219)
30 KOG0144 RNA-binding protein CU 94.3 0.044 9.5E-07 51.1 3.5 34 38-71 37-70 (510)
31 KOG0114 Predicted RNA-binding 93.3 0.11 2.4E-06 40.7 3.7 38 35-72 18-55 (124)
32 KOG0145 RNA-binding protein EL 93.0 0.063 1.4E-06 47.8 2.2 31 33-63 125-155 (360)
33 PLN03213 repressor of silencin 92.6 0.14 3E-06 49.1 4.0 34 37-70 12-45 (759)
34 TIGR01648 hnRNP-R-Q heterogene 92.1 0.18 4E-06 47.6 4.1 33 35-67 233-267 (578)
35 PF13893 RRM_5: RNA recognitio 91.8 0.14 3.1E-06 32.3 2.2 20 52-71 1-20 (56)
36 TIGR01642 U2AF_lg U2 snRNP aux 91.1 0.29 6.4E-06 42.9 4.1 24 37-60 177-200 (509)
37 KOG0124 Polypyrimidine tract-b 90.9 0.32 6.8E-06 45.2 4.2 63 35-114 210-272 (544)
38 KOG0121 Nuclear cap-binding pr 90.8 0.26 5.6E-06 39.9 3.2 40 31-70 32-71 (153)
39 KOG0116 RasGAP SH3 binding pro 90.0 0.39 8.4E-06 44.0 4.0 33 38-70 291-323 (419)
40 KOG0105 Alternative splicing f 89.8 0.31 6.8E-06 41.7 3.0 36 34-69 5-40 (241)
41 KOG0127 Nucleolar protein fibr 88.4 1 2.2E-05 43.5 5.6 39 35-73 5-43 (678)
42 KOG0125 Ataxin 2-binding prote 87.7 0.46 9.9E-06 43.2 2.8 37 33-69 94-130 (376)
43 KOG0107 Alternative splicing f 86.0 1 2.3E-05 37.8 3.9 34 37-70 12-45 (195)
44 KOG0144 RNA-binding protein CU 86.0 0.34 7.3E-06 45.4 1.0 35 38-72 127-161 (510)
45 KOG4206 Spliceosomal protein s 85.2 0.88 1.9E-05 38.9 3.1 34 35-68 9-46 (221)
46 KOG0533 RRM motif-containing p 84.8 0.99 2.1E-05 38.7 3.3 38 33-70 81-118 (243)
47 PF08777 RRM_3: RNA binding mo 84.7 1.1 2.4E-05 33.2 3.1 34 37-70 3-36 (105)
48 KOG0117 Heterogeneous nuclear 84.3 0.73 1.6E-05 43.3 2.4 33 35-67 259-291 (506)
49 KOG4205 RNA-binding protein mu 82.9 1.2 2.7E-05 39.3 3.2 35 37-71 99-133 (311)
50 KOG0117 Heterogeneous nuclear 81.9 1.6 3.4E-05 41.2 3.6 55 37-108 85-139 (506)
51 KOG0109 RNA-binding protein LA 80.7 1 2.2E-05 40.5 1.9 28 38-65 5-32 (346)
52 KOG0108 mRNA cleavage and poly 80.6 2.4 5.2E-05 39.1 4.3 35 36-70 19-53 (435)
53 KOG4207 Predicted splicing fac 79.5 0.95 2.1E-05 39.2 1.3 31 41-71 19-49 (256)
54 KOG0132 RNA polymerase II C-te 78.8 1.9 4.2E-05 42.9 3.2 36 35-70 421-456 (894)
55 KOG0149 Predicted RNA-binding 77.7 2.8 6.1E-05 36.4 3.6 37 37-73 14-50 (247)
56 PF14605 Nup35_RRM_2: Nup53/35 77.1 2.1 4.6E-05 28.1 2.1 32 38-70 4-35 (53)
57 KOG0130 RNA-binding protein RB 76.3 2.9 6.4E-05 34.3 3.1 34 37-70 74-107 (170)
58 KOG0110 RNA-binding protein (R 75.9 2.7 5.9E-05 41.2 3.3 33 33-65 383-415 (725)
59 KOG0127 Nucleolar protein fibr 74.3 3.2 6.9E-05 40.2 3.3 39 35-73 292-330 (678)
60 KOG4205 RNA-binding protein mu 73.7 3.8 8.2E-05 36.2 3.4 39 34-72 5-43 (311)
61 KOG1548 Transcription elongati 73.4 3 6.4E-05 38.2 2.7 28 37-64 136-163 (382)
62 PF15513 DUF4651: Domain of un 73.2 3.6 7.8E-05 29.0 2.5 24 50-73 9-32 (62)
63 KOG0147 Transcriptional coacti 71.9 2.1 4.6E-05 40.8 1.5 57 34-107 276-333 (549)
64 PF08675 RNA_bind: RNA binding 70.4 5.3 0.00012 29.9 3.0 35 33-68 7-41 (87)
65 KOG0123 Polyadenylate-binding 68.0 6.6 0.00014 35.1 3.7 41 32-72 267-307 (369)
66 KOG0131 Splicing factor 3b, su 65.8 4.4 9.5E-05 34.4 2.0 37 34-70 8-44 (203)
67 PF04940 BLUF: Sensors of blue 64.7 4.6 9.9E-05 29.3 1.7 22 37-58 4-25 (93)
68 KOG0148 Apoptosis-promoting RN 63.2 7.4 0.00016 34.9 3.0 56 36-108 63-118 (321)
69 KOG4660 Protein Mei2, essentia 62.5 7 0.00015 37.4 2.9 41 31-71 71-111 (549)
70 KOG0123 Polyadenylate-binding 61.6 9.2 0.0002 34.2 3.4 36 35-70 76-111 (369)
71 KOG0153 Predicted RNA-binding 61.3 9.2 0.0002 35.1 3.3 39 34-72 227-265 (377)
72 smart00361 RRM_1 RNA recogniti 58.1 10 0.00023 25.1 2.4 18 49-66 2-23 (70)
73 KOG0106 Alternative splicing f 51.4 14 0.0003 31.4 2.7 32 38-69 4-35 (216)
74 KOG0124 Polypyrimidine tract-b 48.8 11 0.00024 35.3 1.8 97 34-151 112-231 (544)
75 KOG0110 RNA-binding protein (R 45.8 13 0.00028 36.8 1.8 35 35-69 613-647 (725)
76 KOG0145 RNA-binding protein EL 45.2 23 0.00049 32.0 3.1 35 37-71 43-77 (360)
77 KOG4209 Splicing factor RNPS1, 40.9 28 0.0006 29.4 2.9 43 29-71 95-137 (231)
78 PF03721 UDPG_MGDP_dh_N: UDP-g 40.2 17 0.00037 29.0 1.4 34 35-68 114-148 (185)
79 KOG4676 Splicing factor, argin 38.5 28 0.0006 32.8 2.7 38 33-70 5-42 (479)
80 KOG0129 Predicted RNA-binding 38.0 23 0.0005 33.9 2.1 26 37-62 261-286 (520)
81 KOG0115 RNA-binding protein p5 37.4 28 0.0006 30.9 2.4 36 36-71 32-67 (275)
82 KOG0151 Predicted splicing reg 35.9 33 0.00072 34.5 2.9 34 35-68 174-207 (877)
83 PF04059 RRM_2: RNA recognitio 35.9 63 0.0014 24.0 3.8 33 37-69 3-37 (97)
84 cd01789 Alp11_N Ubiquitin-like 34.9 42 0.00092 23.5 2.7 27 42-68 18-46 (84)
85 cd00842 MPP_ASMase acid sphing 34.2 44 0.00095 27.5 3.0 27 35-61 214-248 (296)
86 cd00027 BRCT Breast Cancer Sup 33.7 60 0.0013 19.3 2.9 25 37-61 3-27 (72)
87 KOG0146 RNA-binding protein ET 33.5 28 0.00062 31.5 1.9 35 35-69 285-321 (371)
88 PRK06369 nac nascent polypepti 32.7 37 0.0008 26.4 2.2 27 44-70 2-34 (115)
89 COG1308 EGD2 Transcription fac 31.5 37 0.0008 26.8 2.1 18 43-60 2-19 (122)
90 KOG0111 Cyclophilin-type pepti 30.7 26 0.00056 31.0 1.2 56 34-106 9-64 (298)
91 KOG0415 Predicted peptidyl pro 28.7 87 0.0019 29.5 4.2 36 35-70 239-274 (479)
92 COG0106 HisA Phosphoribosylfor 28.6 71 0.0015 27.7 3.5 31 37-70 100-130 (241)
93 PF14581 SseB_C: SseB protein 27.2 15 0.00033 26.3 -0.7 22 49-70 21-42 (108)
94 PF12949 HeH: HeH/LEM domain; 25.3 45 0.00097 20.8 1.3 17 44-60 1-17 (35)
95 PF03467 Smg4_UPF3: Smg-4/UPF3 24.7 18 0.00038 29.1 -0.8 26 37-62 9-35 (176)
96 KOG3089 Predicted DEAD-box-con 23.4 89 0.0019 27.6 3.1 52 3-68 46-98 (271)
97 cd00080 HhH2_motif Helix-hairp 22.9 30 0.00065 24.0 0.1 33 37-70 21-53 (75)
98 PF11608 Limkain-b1: Limkain b 22.6 86 0.0019 23.7 2.5 22 37-58 4-25 (90)
99 PF06297 PET: PET Domain; Int 21.7 77 0.0017 24.1 2.2 24 38-61 19-42 (106)
100 PF00276 Ribosomal_L23: Riboso 21.3 70 0.0015 23.1 1.8 33 37-69 21-55 (91)
101 KOG0120 Splicing factor U2AF, 20.4 68 0.0015 30.5 2.0 35 37-71 291-325 (500)
102 PF04355 SmpA_OmlA: SmpA / Oml 20.2 70 0.0015 21.2 1.5 19 40-58 9-27 (71)
103 KOG4661 Hsp27-ERE-TATA-binding 20.0 70 0.0015 31.9 2.0 33 35-67 405-437 (940)
No 1
>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]
Probab=99.94 E-value=1.8e-28 Score=208.93 Aligned_cols=88 Identities=50% Similarity=0.796 Sum_probs=74.6
Q ss_pred hcccchhhhHHHHHHHhhcCCcceEEecCCCCCCCHHHHHHHHhccCccceEEeccCCCchhhhhhhhccccCCCCCCCc
Q 044301 14 SKHSKSKKKQRLLEEAAKADQRGICYLSRIPPHMDPVKLRQILSQYGEIQRIYLAPEDPSTRVLRKRENRKRDGGFQDQG 93 (154)
Q Consensus 14 ~k~~k~k~kk~l~k~~~k~~k~GVIYlSrIPp~M~p~klR~llsqfGeI~RIyL~pEd~~~~~~rk~~~rkK~gg~k~~~ 93 (154)
.+..+..+...+.+..++..++||||||+|||+|+|.+||+||++||+||||||+||+.+.++.|+ ++||+..++
T Consensus 53 ~~~l~~~k~~~~~~a~~kkrk~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~-----~~~~n~~~~ 127 (278)
T KOG3152|consen 53 EKELKEKKLTELSEAKAKKRKTGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARK-----RKGGNYKKL 127 (278)
T ss_pred hhhhhhhhhcccchhhhhhccceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHh-----hcCCCcccc
Confidence 333444555555556666679999999999999999999999999999999999999988776654 889999999
Q ss_pred ccccceeeeeccc
Q 044301 94 FSEGYKQKVQQES 106 (154)
Q Consensus 94 FtEGWVEf~~k~~ 106 (154)
|+||||||.+|..
T Consensus 128 y~EGWvEF~~Krv 140 (278)
T KOG3152|consen 128 YSEGWVEFISKRV 140 (278)
T ss_pred chhHHHHHHHHHH
Confidence 9999999999876
No 2
>PF00076 RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); InterPro: IPR000504 Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [, , ]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [, ]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [, , ]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition []. The motif also appears in a few single stranded DNA binding proteins. The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases []. The RRM is reviewed in a number of publications [, , ].; GO: 0003676 nucleic acid binding; PDB: 2RNE_A 2DGO_A 2DO4_A 1YTY_B 2VOO_B 2VOP_A 2VON_B 1ZH5_B 2VOD_A 1S79_A ....
Probab=98.29 E-value=3.5e-07 Score=58.36 Aligned_cols=33 Identities=30% Similarity=0.672 Sum_probs=31.8
Q ss_pred EEecCCCCCCCHHHHHHHHhccCccceEEeccC
Q 044301 38 CYLSRIPPHMDPVKLRQILSQYGEIQRIYLAPE 70 (154)
Q Consensus 38 IYlSrIPp~M~p~klR~llsqfGeI~RIyL~pE 70 (154)
|||+.||+.++...|+++|++||.|..+.+.+.
T Consensus 1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~ 33 (70)
T PF00076_consen 1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRN 33 (70)
T ss_dssp EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEE
T ss_pred cEEcCCCCcCCHHHHHHHHHHhhhccccccccc
Confidence 799999999999999999999999999999886
No 3
>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=98.09 E-value=3.2e-06 Score=55.17 Aligned_cols=50 Identities=22% Similarity=0.475 Sum_probs=39.6
Q ss_pred EEecCCCCCCCHHHHHHHHhccCccceEEeccCCCchhhhhhhhccccCCCCCCCcccccceeeeecc
Q 044301 38 CYLSRIPPHMDPVKLRQILSQYGEIQRIYLAPEDPSTRVLRKRENRKRDGGFQDQGFSEGYKQKVQQE 105 (154)
Q Consensus 38 IYlSrIPp~M~p~klR~llsqfGeI~RIyL~pEd~~~~~~rk~~~rkK~gg~k~~~FtEGWVEf~~k~ 105 (154)
|||+.||+.+++..|+.+|+.||.|.+|++..... ......+||+|-+.+
T Consensus 1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~------------------~~~~~~a~v~f~~~~ 50 (70)
T PF14259_consen 1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKD------------------GQSRGFAFVEFSSEE 50 (70)
T ss_dssp EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTT------------------SSEEEEEEEEESSHH
T ss_pred CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeec------------------cccCCEEEEEeCCHH
Confidence 79999999999999999999999999999987522 123456999997644
No 4
>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]
Probab=98.08 E-value=2.8e-06 Score=71.43 Aligned_cols=57 Identities=23% Similarity=0.451 Sum_probs=47.2
Q ss_pred cCCcceEEecCCCCCCCHHHHHHHHhcc-CccceEEeccCCCchhhhhhhhccccCCCCCCCcccccceeeeecc
Q 044301 32 ADQRGICYLSRIPPHMDPVKLRQILSQY-GEIQRIYLAPEDPSTRVLRKRENRKRDGGFQDQGFSEGYKQKVQQE 105 (154)
Q Consensus 32 ~~k~GVIYlSrIPp~M~p~klR~llsqf-GeI~RIyL~pEd~~~~~~rk~~~rkK~gg~k~~~FtEGWVEf~~k~ 105 (154)
....||+|+.|||.+++.+.+..+|.|| |.|.|++|++. +|+|.++.+.| |||-+.+
T Consensus 46 ~~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRn-------------krTGNSKgYAF----VEFEs~e 103 (214)
T KOG4208|consen 46 QEIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRN-------------KRTGNSKGYAF----VEFESEE 103 (214)
T ss_pred cCCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecc-------------cccCCcCceEE----EEeccHH
Confidence 3578999999999999999999999999 99999999876 26777776655 5666544
No 5
>smart00362 RRM_2 RNA recognition motif.
Probab=97.70 E-value=6.8e-05 Score=46.11 Aligned_cols=34 Identities=18% Similarity=0.628 Sum_probs=31.8
Q ss_pred EEecCCCCCCCHHHHHHHHhccCccceEEeccCC
Q 044301 38 CYLSRIPPHMDPVKLRQILSQYGEIQRIYLAPED 71 (154)
Q Consensus 38 IYlSrIPp~M~p~klR~llsqfGeI~RIyL~pEd 71 (154)
|||+.||+.++...|+++|++||.|.++++....
T Consensus 2 v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~ 35 (72)
T smart00362 2 LFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT 35 (72)
T ss_pred EEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC
Confidence 8999999999999999999999999999988763
No 6
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor. These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
Probab=97.48 E-value=9.8e-05 Score=61.25 Aligned_cols=37 Identities=19% Similarity=0.390 Sum_probs=34.1
Q ss_pred cceEEecCCCCCCCHHHHHHHHhccCccceEEeccCC
Q 044301 35 RGICYLSRIPPHMDPVKLRQILSQYGEIQRIYLAPED 71 (154)
Q Consensus 35 ~GVIYlSrIPp~M~p~klR~llsqfGeI~RIyL~pEd 71 (154)
+--||++.||+.++...|+++|++||+|.+|+|....
T Consensus 3 ~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~d~ 39 (352)
T TIGR01661 3 KTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDK 39 (352)
T ss_pred CcEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcC
Confidence 4469999999999999999999999999999998864
No 7
>cd00590 RRM RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
Probab=97.47 E-value=0.0002 Score=44.25 Aligned_cols=52 Identities=13% Similarity=0.447 Sum_probs=41.9
Q ss_pred eEEecCCCCCCCHHHHHHHHhccCccceEEeccCCCchhhhhhhhccccCCCCCCCcccccceeeeeccc
Q 044301 37 ICYLSRIPPHMDPVKLRQILSQYGEIQRIYLAPEDPSTRVLRKRENRKRDGGFQDQGFSEGYKQKVQQES 106 (154)
Q Consensus 37 VIYlSrIPp~M~p~klR~llsqfGeI~RIyL~pEd~~~~~~rk~~~rkK~gg~k~~~FtEGWVEf~~k~~ 106 (154)
.|||+.||+.++...|+++|++||.|.++++...... ....-+|++|-+.+.
T Consensus 1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~------------------~~~~~~~v~f~s~~~ 52 (74)
T cd00590 1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDT------------------KSKGFAFVEFEDEED 52 (74)
T ss_pred CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCC------------------CcceEEEEEECCHHH
Confidence 4899999999999999999999999999999876432 123347899876543
No 8
>PLN03134 glycine-rich RNA-binding protein 4; Provisional
Probab=97.40 E-value=0.00015 Score=55.91 Aligned_cols=37 Identities=11% Similarity=0.268 Sum_probs=33.9
Q ss_pred CcceEEecCCCCCCCHHHHHHHHhccCccceEEeccC
Q 044301 34 QRGICYLSRIPPHMDPVKLRQILSQYGEIQRIYLAPE 70 (154)
Q Consensus 34 k~GVIYlSrIPp~M~p~klR~llsqfGeI~RIyL~pE 70 (154)
..-.|||+.||..+++..|+++|++||.|.++.+...
T Consensus 33 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d 69 (144)
T PLN03134 33 MSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVD 69 (144)
T ss_pred CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEec
Confidence 3557999999999999999999999999999999764
No 9
>PLN03121 nucleic acid binding protein; Provisional
Probab=97.11 E-value=0.00056 Score=58.54 Aligned_cols=34 Identities=12% Similarity=0.307 Sum_probs=32.9
Q ss_pred eEEecCCCCCCCHHHHHHHHhccCccceEEeccC
Q 044301 37 ICYLSRIPPHMDPVKLRQILSQYGEIQRIYLAPE 70 (154)
Q Consensus 37 VIYlSrIPp~M~p~klR~llsqfGeI~RIyL~pE 70 (154)
.||++.|++..++..||.+||.||+|..|+|.+.
T Consensus 7 TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D 40 (243)
T PLN03121 7 TAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRS 40 (243)
T ss_pred EEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecC
Confidence 7999999999999999999999999999999976
No 10
>PLN03120 nucleic acid binding protein; Provisional
Probab=97.09 E-value=0.00054 Score=59.03 Aligned_cols=34 Identities=15% Similarity=0.284 Sum_probs=32.2
Q ss_pred eEEecCCCCCCCHHHHHHHHhccCccceEEeccC
Q 044301 37 ICYLSRIPPHMDPVKLRQILSQYGEIQRIYLAPE 70 (154)
Q Consensus 37 VIYlSrIPp~M~p~klR~llsqfGeI~RIyL~pE 70 (154)
-||++.||+..+...|+.+|+.||+|.+|.|...
T Consensus 6 tVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d 39 (260)
T PLN03120 6 TVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSE 39 (260)
T ss_pred EEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeec
Confidence 5899999999999999999999999999999765
No 11
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor. These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
Probab=97.05 E-value=0.00084 Score=55.75 Aligned_cols=35 Identities=17% Similarity=0.429 Sum_probs=33.0
Q ss_pred eEEecCCCCCCCHHHHHHHHhccCccceEEeccCC
Q 044301 37 ICYLSRIPPHMDPVKLRQILSQYGEIQRIYLAPED 71 (154)
Q Consensus 37 VIYlSrIPp~M~p~klR~llsqfGeI~RIyL~pEd 71 (154)
.|||++||+.++...|+++|++||.|.++.+....
T Consensus 271 ~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~ 305 (352)
T TIGR01661 271 CIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDL 305 (352)
T ss_pred EEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcC
Confidence 59999999999999999999999999999998753
No 12
>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family. Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).
Probab=96.81 E-value=0.0015 Score=58.36 Aligned_cols=34 Identities=15% Similarity=0.396 Sum_probs=32.0
Q ss_pred ceEEecCCCCCCCHHHHHHHHhccCccceEEecc
Q 044301 36 GICYLSRIPPHMDPVKLRQILSQYGEIQRIYLAP 69 (154)
Q Consensus 36 GVIYlSrIPp~M~p~klR~llsqfGeI~RIyL~p 69 (154)
=||||+.||..++...|+++|++||.|.+|.+.+
T Consensus 3 ~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~ 36 (481)
T TIGR01649 3 PVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLP 36 (481)
T ss_pred cEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEEC
Confidence 3899999999999999999999999999999874
No 13
>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=96.77 E-value=0.0014 Score=57.37 Aligned_cols=36 Identities=14% Similarity=0.230 Sum_probs=33.3
Q ss_pred cceEEecCCCCCCCHHHHHHHHhccCccceEEeccC
Q 044301 35 RGICYLSRIPPHMDPVKLRQILSQYGEIQRIYLAPE 70 (154)
Q Consensus 35 ~GVIYlSrIPp~M~p~klR~llsqfGeI~RIyL~pE 70 (154)
.-.|||+.||+.++...|+++|++||.|..+.|...
T Consensus 107 ~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d 142 (346)
T TIGR01659 107 GTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRD 142 (346)
T ss_pred CcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEec
Confidence 457999999999999999999999999999999764
No 14
>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]
Probab=96.72 E-value=0.0016 Score=57.97 Aligned_cols=34 Identities=29% Similarity=0.538 Sum_probs=32.6
Q ss_pred eEEecCCCCCCCHHHHHHHHhccCccceEEeccC
Q 044301 37 ICYLSRIPPHMDPVKLRQILSQYGEIQRIYLAPE 70 (154)
Q Consensus 37 VIYlSrIPp~M~p~klR~llsqfGeI~RIyL~pE 70 (154)
.+||++|+-..++.+|+..|+.||.|-||+|+..
T Consensus 103 TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d 136 (335)
T KOG0113|consen 103 TLFVARLNYDTSESKLRREFEKYGPIKRIRLVRD 136 (335)
T ss_pred eeeeeeccccccHHHHHHHHHhcCcceeEEEeee
Confidence 4899999999999999999999999999999986
No 15
>TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.
Probab=96.70 E-value=0.0015 Score=58.67 Aligned_cols=35 Identities=14% Similarity=0.450 Sum_probs=32.8
Q ss_pred eEEecCCCCCCCHHHHHHHHhccCccceEEeccCC
Q 044301 37 ICYLSRIPPHMDPVKLRQILSQYGEIQRIYLAPED 71 (154)
Q Consensus 37 VIYlSrIPp~M~p~klR~llsqfGeI~RIyL~pEd 71 (154)
-|||+.||+.++...|+++|++||+|..|++.+..
T Consensus 2 sl~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~ 36 (562)
T TIGR01628 2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDS 36 (562)
T ss_pred eEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecC
Confidence 48999999999999999999999999999998764
No 16
>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=96.65 E-value=0.0016 Score=57.02 Aligned_cols=36 Identities=19% Similarity=0.435 Sum_probs=32.9
Q ss_pred cceEEecCCCCCCCHHHHHHHHhccCccceEEeccC
Q 044301 35 RGICYLSRIPPHMDPVKLRQILSQYGEIQRIYLAPE 70 (154)
Q Consensus 35 ~GVIYlSrIPp~M~p~klR~llsqfGeI~RIyL~pE 70 (154)
.--|||+.||..++...|+++|++||+|.++.|.+.
T Consensus 193 ~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d 228 (346)
T TIGR01659 193 DTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRD 228 (346)
T ss_pred cceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeec
Confidence 346999999999999999999999999999999764
No 17
>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=96.61 E-value=0.0023 Score=55.43 Aligned_cols=36 Identities=22% Similarity=0.404 Sum_probs=33.5
Q ss_pred cceEEecCCCCCCCHHHHHHHHhccCccceEEeccC
Q 044301 35 RGICYLSRIPPHMDPVKLRQILSQYGEIQRIYLAPE 70 (154)
Q Consensus 35 ~GVIYlSrIPp~M~p~klR~llsqfGeI~RIyL~pE 70 (154)
.-.|||+.||+.++...|+++|++||.|..|.|...
T Consensus 186 ~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d 221 (457)
T TIGR01622 186 FLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRD 221 (457)
T ss_pred CCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEc
Confidence 367999999999999999999999999999999865
No 18
>TIGR01645 half-pint poly-U binding splicing factor, half-pint family. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.
Probab=96.59 E-value=0.0018 Score=61.34 Aligned_cols=37 Identities=19% Similarity=0.459 Sum_probs=34.1
Q ss_pred cceEEecCCCCCCCHHHHHHHHhccCccceEEeccCC
Q 044301 35 RGICYLSRIPPHMDPVKLRQILSQYGEIQRIYLAPED 71 (154)
Q Consensus 35 ~GVIYlSrIPp~M~p~klR~llsqfGeI~RIyL~pEd 71 (154)
...||++.||+.++...|+++|++||+|.+++|.+..
T Consensus 204 ~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~ 240 (612)
T TIGR01645 204 FNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAP 240 (612)
T ss_pred cceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecC
Confidence 3579999999999999999999999999999998753
No 19
>smart00360 RRM RNA recognition motif.
Probab=96.52 E-value=0.0035 Score=38.12 Aligned_cols=31 Identities=26% Similarity=0.708 Sum_probs=28.6
Q ss_pred ecCCCCCCCHHHHHHHHhccCccceEEeccC
Q 044301 40 LSRIPPHMDPVKLRQILSQYGEIQRIYLAPE 70 (154)
Q Consensus 40 lSrIPp~M~p~klR~llsqfGeI~RIyL~pE 70 (154)
|+.||..++...|+++|++||.|..+.+.+.
T Consensus 1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~ 31 (71)
T smart00360 1 VGNLPPDVTEEELRELFSKFGKIESVRLVRD 31 (71)
T ss_pred CCCCCcccCHHHHHHHHHhhCCEeEEEEEeC
Confidence 5789999999999999999999999988765
No 20
>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]
Probab=96.37 E-value=0.0064 Score=44.96 Aligned_cols=36 Identities=17% Similarity=0.539 Sum_probs=34.1
Q ss_pred cceEEecCCCCCCCHHHHHHHHhccCccceEEeccC
Q 044301 35 RGICYLSRIPPHMDPVKLRQILSQYGEIQRIYLAPE 70 (154)
Q Consensus 35 ~GVIYlSrIPp~M~p~klR~llsqfGeI~RIyL~pE 70 (154)
.-.|||+.||...+...|+.+|.+||.|.+|++...
T Consensus 115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d 150 (306)
T COG0724 115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRD 150 (306)
T ss_pred CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeec
Confidence 489999999999999999999999999999999876
No 21
>TIGR01645 half-pint poly-U binding splicing factor, half-pint family. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.
Probab=96.23 E-value=0.01 Score=56.40 Aligned_cols=38 Identities=16% Similarity=0.290 Sum_probs=35.0
Q ss_pred CCcceEEecCCCCCCCHHHHHHHHhccCccceEEeccC
Q 044301 33 DQRGICYLSRIPPHMDPVKLRQILSQYGEIQRIYLAPE 70 (154)
Q Consensus 33 ~k~GVIYlSrIPp~M~p~klR~llsqfGeI~RIyL~pE 70 (154)
....-||++.||..++...|+++|++||.|.+|++...
T Consensus 105 ~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D 142 (612)
T TIGR01645 105 AIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWD 142 (612)
T ss_pred cCCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeec
Confidence 45678999999999999999999999999999999774
No 22
>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor. Members of this subfamily are found in plants, metazoa and fungi.
Probab=96.23 E-value=0.0058 Score=53.53 Aligned_cols=36 Identities=14% Similarity=0.509 Sum_probs=33.0
Q ss_pred cceEEecCCCCCCCHHHHHHHHhccCccceEEeccC
Q 044301 35 RGICYLSRIPPHMDPVKLRQILSQYGEIQRIYLAPE 70 (154)
Q Consensus 35 ~GVIYlSrIPp~M~p~klR~llsqfGeI~RIyL~pE 70 (154)
+-.|||+.||..++...|+++|++||.|..+.|...
T Consensus 295 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~ 330 (509)
T TIGR01642 295 KDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKD 330 (509)
T ss_pred CCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEec
Confidence 457999999999999999999999999999998764
No 23
>TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.
Probab=96.19 E-value=0.0059 Score=54.83 Aligned_cols=37 Identities=19% Similarity=0.335 Sum_probs=33.6
Q ss_pred CcceEEecCCCCCCCHHHHHHHHhccCccceEEeccC
Q 044301 34 QRGICYLSRIPPHMDPVKLRQILSQYGEIQRIYLAPE 70 (154)
Q Consensus 34 k~GVIYlSrIPp~M~p~klR~llsqfGeI~RIyL~pE 70 (154)
..+.|||+.||+.++...|+.+|+.||.|..+.+...
T Consensus 87 ~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~ 123 (562)
T TIGR01628 87 GVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATD 123 (562)
T ss_pred CCCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeec
Confidence 3578999999999999999999999999999988654
No 24
>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family. Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).
Probab=96.10 E-value=0.0067 Score=54.32 Aligned_cols=36 Identities=14% Similarity=0.360 Sum_probs=32.8
Q ss_pred cceEEecCCCC-CCCHHHHHHHHhccCccceEEeccC
Q 044301 35 RGICYLSRIPP-HMDPVKLRQILSQYGEIQRIYLAPE 70 (154)
Q Consensus 35 ~GVIYlSrIPp-~M~p~klR~llsqfGeI~RIyL~pE 70 (154)
.-+|||+.||+ .+++..|+.||++||+|.+|.+...
T Consensus 275 ~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~ 311 (481)
T TIGR01649 275 GSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKN 311 (481)
T ss_pred CCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeC
Confidence 34999999998 6999999999999999999999764
No 25
>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=95.94 E-value=0.01 Score=51.46 Aligned_cols=35 Identities=9% Similarity=0.248 Sum_probs=32.7
Q ss_pred ceEEecCCCCCCCHHHHHHHHhccCccceEEeccC
Q 044301 36 GICYLSRIPPHMDPVKLRQILSQYGEIQRIYLAPE 70 (154)
Q Consensus 36 GVIYlSrIPp~M~p~klR~llsqfGeI~RIyL~pE 70 (154)
=.|||+.||..++...|+++|++||.|..|.|...
T Consensus 90 ~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d 124 (457)
T TIGR01622 90 RTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKD 124 (457)
T ss_pred cEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeec
Confidence 36999999999999999999999999999999764
No 26
>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]
Probab=95.74 E-value=0.01 Score=51.64 Aligned_cols=38 Identities=21% Similarity=0.490 Sum_probs=34.6
Q ss_pred cceEEecCCCCCCCHHHHHHHHhccCccceEEeccCCC
Q 044301 35 RGICYLSRIPPHMDPVKLRQILSQYGEIQRIYLAPEDP 72 (154)
Q Consensus 35 ~GVIYlSrIPp~M~p~klR~llsqfGeI~RIyL~pEd~ 72 (154)
.--|-|+.||-.|+...|+.||-.||.|.||||+....
T Consensus 189 ~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~ 226 (270)
T KOG0122|consen 189 EATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKE 226 (270)
T ss_pred cceeEEecCccccChhHHHHHhhccCccceeEEEEccc
Confidence 34599999999999999999999999999999998743
No 27
>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family. Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.
Probab=95.02 E-value=0.031 Score=52.73 Aligned_cols=35 Identities=17% Similarity=0.322 Sum_probs=32.5
Q ss_pred ceEEecCCCCCCCHHHHHHHHhccCccceEEeccC
Q 044301 36 GICYLSRIPPHMDPVKLRQILSQYGEIQRIYLAPE 70 (154)
Q Consensus 36 GVIYlSrIPp~M~p~klR~llsqfGeI~RIyL~pE 70 (154)
--|||++||+.++...|+++|++||.|-.+.|...
T Consensus 59 ~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D 93 (578)
T TIGR01648 59 CEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD 93 (578)
T ss_pred CEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEEC
Confidence 36999999999999999999999999999998765
No 28
>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]
Probab=94.60 E-value=0.034 Score=49.35 Aligned_cols=36 Identities=22% Similarity=0.400 Sum_probs=33.0
Q ss_pred cceEEecCCCCCCCHHHHHHHHhccCccceEEeccC
Q 044301 35 RGICYLSRIPPHMDPVKLRQILSQYGEIQRIYLAPE 70 (154)
Q Consensus 35 ~GVIYlSrIPp~M~p~klR~llsqfGeI~RIyL~pE 70 (154)
---||.+.|+++++...||+.||+||.|.-|++-+.
T Consensus 164 NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~ 199 (321)
T KOG0148|consen 164 NTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKD 199 (321)
T ss_pred CceEEeCCcCccccHHHHHHhcccCCcceEEEEecc
Confidence 356999999999999999999999999999988765
No 29
>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=94.44 E-value=0.0091 Score=50.48 Aligned_cols=39 Identities=26% Similarity=0.459 Sum_probs=36.1
Q ss_pred CCcceEEecCCCCCCCHHHHHHHHhccCccceEEeccCC
Q 044301 33 DQRGICYLSRIPPHMDPVKLRQILSQYGEIQRIYLAPED 71 (154)
Q Consensus 33 ~k~GVIYlSrIPp~M~p~klR~llsqfGeI~RIyL~pEd 71 (154)
....-|||+.||--+++..|--.|||||+|-.|-|.+..
T Consensus 33 kdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk 71 (219)
T KOG0126|consen 33 KDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDK 71 (219)
T ss_pred ccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecC
Confidence 457899999999999999999999999999999999873
No 30
>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]
Probab=94.26 E-value=0.044 Score=51.10 Aligned_cols=34 Identities=24% Similarity=0.571 Sum_probs=31.9
Q ss_pred EEecCCCCCCCHHHHHHHHhccCccceEEeccCC
Q 044301 38 CYLSRIPPHMDPVKLRQILSQYGEIQRIYLAPED 71 (154)
Q Consensus 38 IYlSrIPp~M~p~klR~llsqfGeI~RIyL~pEd 71 (154)
+|++.||..|++..||+||++||.|.-|-|-+..
T Consensus 37 lfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk 70 (510)
T KOG0144|consen 37 LFVGQIPRTASEKDLRELFEKYGNVYEINLIKDK 70 (510)
T ss_pred heeccCCccccHHHHHHHHHHhCceeEEEeeccc
Confidence 7999999999999999999999999999998753
No 31
>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=93.29 E-value=0.11 Score=40.74 Aligned_cols=38 Identities=18% Similarity=0.495 Sum_probs=34.8
Q ss_pred cceEEecCCCCCCCHHHHHHHHhccCccceEEeccCCC
Q 044301 35 RGICYLSRIPPHMDPVKLRQILSQYGEIQRIYLAPEDP 72 (154)
Q Consensus 35 ~GVIYlSrIPp~M~p~klR~llsqfGeI~RIyL~pEd~ 72 (154)
.-|+||-.+|-..+-.++..||..||.|-.|++--+..
T Consensus 18 nriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~ 55 (124)
T KOG0114|consen 18 NRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKE 55 (124)
T ss_pred heeEEEecCCccccHHHHHHHhhcccceEEEEecCccC
Confidence 56999999999999999999999999999999987643
No 32
>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]
Probab=93.01 E-value=0.063 Score=47.84 Aligned_cols=31 Identities=32% Similarity=0.504 Sum_probs=27.7
Q ss_pred CCcceEEecCCCCCCCHHHHHHHHhccCccc
Q 044301 33 DQRGICYLSRIPPHMDPVKLRQILSQYGEIQ 63 (154)
Q Consensus 33 ~k~GVIYlSrIPp~M~p~klR~llsqfGeI~ 63 (154)
-+-.-+|+|-||.-|+-..|.+||++||.|=
T Consensus 125 Ik~aNLYvSGlPktMtqkelE~iFs~fGrII 155 (360)
T KOG0145|consen 125 IKDANLYVSGLPKTMTQKELEQIFSPFGRII 155 (360)
T ss_pred hcccceEEecCCccchHHHHHHHHHHhhhhh
Confidence 3566799999999999999999999999863
No 33
>PLN03213 repressor of silencing 3; Provisional
Probab=92.63 E-value=0.14 Score=49.09 Aligned_cols=34 Identities=12% Similarity=0.164 Sum_probs=32.1
Q ss_pred eEEecCCCCCCCHHHHHHHHhccCccceEEeccC
Q 044301 37 ICYLSRIPPHMDPVKLRQILSQYGEIQRIYLAPE 70 (154)
Q Consensus 37 VIYlSrIPp~M~p~klR~llsqfGeI~RIyL~pE 70 (154)
=||++.|+...+...|+.+|++||.|.+++|.++
T Consensus 12 RIYVGNLSydVTEDDLravFSeFGsVkdVEIpRE 45 (759)
T PLN03213 12 RLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRT 45 (759)
T ss_pred EEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecc
Confidence 4999999999999999999999999999999844
No 34
>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family. Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.
Probab=92.06 E-value=0.18 Score=47.65 Aligned_cols=33 Identities=15% Similarity=0.348 Sum_probs=30.4
Q ss_pred cceEEecCCCCCCCHHHHHHHHhcc--CccceEEe
Q 044301 35 RGICYLSRIPPHMDPVKLRQILSQY--GEIQRIYL 67 (154)
Q Consensus 35 ~GVIYlSrIPp~M~p~klR~llsqf--GeI~RIyL 67 (154)
.-+|||+.||..+++..|+++|++| |+|.+|.+
T Consensus 233 ~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~ 267 (578)
T TIGR01648 233 VKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKK 267 (578)
T ss_pred ccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEe
Confidence 4579999999999999999999999 99999854
No 35
>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=91.78 E-value=0.14 Score=32.31 Aligned_cols=20 Identities=25% Similarity=0.639 Sum_probs=16.9
Q ss_pred HHHHHhccCccceEEeccCC
Q 044301 52 LRQILSQYGEIQRIYLAPED 71 (154)
Q Consensus 52 lR~llsqfGeI~RIyL~pEd 71 (154)
|+++|++||+|.+|.+.+..
T Consensus 1 L~~~f~~fG~V~~i~~~~~~ 20 (56)
T PF13893_consen 1 LYKLFSKFGEVKKIKIFKKK 20 (56)
T ss_dssp HHHHHTTTS-EEEEEEETTS
T ss_pred ChHHhCCcccEEEEEEEeCC
Confidence 68999999999999998763
No 36
>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor. Members of this subfamily are found in plants, metazoa and fungi.
Probab=91.11 E-value=0.29 Score=42.95 Aligned_cols=24 Identities=17% Similarity=0.315 Sum_probs=22.5
Q ss_pred eEEecCCCCCCCHHHHHHHHhccC
Q 044301 37 ICYLSRIPPHMDPVKLRQILSQYG 60 (154)
Q Consensus 37 VIYlSrIPp~M~p~klR~llsqfG 60 (154)
-|||+.||+.++...|+.+|++|+
T Consensus 177 ~lyVgnLp~~~t~~~l~~~F~~~~ 200 (509)
T TIGR01642 177 RLYVGGIPPEFVEEAVVDFFNDLM 200 (509)
T ss_pred EEEEeCCCCCCCHHHHHHHHHHHH
Confidence 499999999999999999999974
No 37
>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]
Probab=90.90 E-value=0.32 Score=45.24 Aligned_cols=63 Identities=19% Similarity=0.373 Sum_probs=47.4
Q ss_pred cceEEecCCCCCCCHHHHHHHHhccCccceEEeccCCCchhhhhhhhccccCCCCCCCcccccceeeeecccCCCCCCCC
Q 044301 35 RGICYLSRIPPHMDPVKLRQILSQYGEIQRIYLAPEDPSTRVLRKRENRKRDGGFQDQGFSEGYKQKVQQESQTHPELPG 114 (154)
Q Consensus 35 ~GVIYlSrIPp~M~p~klR~llsqfGeI~RIyL~pEd~~~~~~rk~~~rkK~gg~k~~~FtEGWVEf~~k~~g~~~e~~~ 114 (154)
=--||+++|.|.++.+.|+..|+.||+|-..-|.+.... + |++++ |+.||-++.+..++-++-
T Consensus 210 fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~-~------------~HkGy----GfiEy~n~qs~~eAiasM 272 (544)
T KOG0124|consen 210 FNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTG-R------------GHKGY----GFIEYNNLQSQSEAIASM 272 (544)
T ss_pred hheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCC-C------------Cccce----eeEEeccccchHHHhhhc
Confidence 345999999999999999999999999999888876322 1 23333 778888777666544443
No 38
>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]
Probab=90.80 E-value=0.26 Score=39.91 Aligned_cols=40 Identities=15% Similarity=0.335 Sum_probs=35.2
Q ss_pred hcCCcceEEecCCCCCCCHHHHHHHHhccCccceEEeccC
Q 044301 31 KADQRGICYLSRIPPHMDPVKLRQILSQYGEIQRIYLAPE 70 (154)
Q Consensus 31 k~~k~GVIYlSrIPp~M~p~klR~llsqfGeI~RIyL~pE 70 (154)
...+.-.||+|+|.=+-++.+|.+|||..|+|-||-+--.
T Consensus 32 a~r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLd 71 (153)
T KOG0121|consen 32 ALRKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLD 71 (153)
T ss_pred HHhhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccc
Confidence 3456788999999999999999999999999999977543
No 39
>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]
Probab=90.03 E-value=0.39 Score=44.00 Aligned_cols=33 Identities=21% Similarity=0.572 Sum_probs=31.3
Q ss_pred EEecCCCCCCCHHHHHHHHhccCccceEEeccC
Q 044301 38 CYLSRIPPHMDPVKLRQILSQYGEIQRIYLAPE 70 (154)
Q Consensus 38 IYlSrIPp~M~p~klR~llsqfGeI~RIyL~pE 70 (154)
||+..||+.-++..|.+.|.+||+|...+++.-
T Consensus 291 i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr 323 (419)
T KOG0116|consen 291 IFVKNLPPDATPAELEEVFKQFGPIKEGGIQVR 323 (419)
T ss_pred eEeecCCCCCCHHHHHHHHhhcccccccceEEe
Confidence 999999999999999999999999999988764
No 40
>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]
Probab=89.78 E-value=0.31 Score=41.68 Aligned_cols=36 Identities=19% Similarity=0.463 Sum_probs=32.9
Q ss_pred CcceEEecCCCCCCCHHHHHHHHhccCccceEEecc
Q 044301 34 QRGICYLSRIPPHMDPVKLRQILSQYGEIQRIYLAP 69 (154)
Q Consensus 34 k~GVIYlSrIPp~M~p~klR~llsqfGeI~RIyL~p 69 (154)
..+-||+++||+......|..||.+||.|.-|=|.-
T Consensus 5 ~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~ 40 (241)
T KOG0105|consen 5 NSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKN 40 (241)
T ss_pred ccceEEecCCCcchhhccHHHHHhhhcceEEEEecc
Confidence 467899999999999999999999999999998863
No 41
>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]
Probab=88.45 E-value=1 Score=43.53 Aligned_cols=39 Identities=21% Similarity=0.318 Sum_probs=35.3
Q ss_pred cceEEecCCCCCCCHHHHHHHHhccCccceEEeccCCCc
Q 044301 35 RGICYLSRIPPHMDPVKLRQILSQYGEIQRIYLAPEDPS 73 (154)
Q Consensus 35 ~GVIYlSrIPp~M~p~klR~llsqfGeI~RIyL~pEd~~ 73 (154)
+-.+|+|+||...+-.+|-.+||.+|.|.+-|+.-+..+
T Consensus 5 g~TlfV~~lp~~~~~~qL~e~FS~vGPik~~~vVt~~gs 43 (678)
T KOG0127|consen 5 GATLFVSRLPFSSTGEQLEEFFSYVGPIKHAVVVTNKGS 43 (678)
T ss_pred CceEEEecCCCccchhHHHHhhhcccCcceeEEecCCCc
Confidence 357999999999999999999999999999999987543
No 42
>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]
Probab=87.74 E-value=0.46 Score=43.19 Aligned_cols=37 Identities=19% Similarity=0.326 Sum_probs=32.3
Q ss_pred CCcceEEecCCCCCCCHHHHHHHHhccCccceEEecc
Q 044301 33 DQRGICYLSRIPPHMDPVKLRQILSQYGEIQRIYLAP 69 (154)
Q Consensus 33 ~k~GVIYlSrIPp~M~p~klR~llsqfGeI~RIyL~p 69 (154)
+-+=-+|+|.||=.|....||++|.+||.|-.|=+.=
T Consensus 94 ~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIf 130 (376)
T KOG0125|consen 94 DTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIF 130 (376)
T ss_pred CCCceeEeecCCccccCccHHHHHHhhCceeeEEEEe
Confidence 4566799999999999999999999999998876554
No 43
>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]
Probab=86.04 E-value=1 Score=37.84 Aligned_cols=34 Identities=18% Similarity=0.476 Sum_probs=32.2
Q ss_pred eEEecCCCCCCCHHHHHHHHhccCccceEEeccC
Q 044301 37 ICYLSRIPPHMDPVKLRQILSQYGEIQRIYLAPE 70 (154)
Q Consensus 37 VIYlSrIPp~M~p~klR~llsqfGeI~RIyL~pE 70 (154)
-||++.||...+...|-.+|+.||.|--|+++..
T Consensus 12 kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArn 45 (195)
T KOG0107|consen 12 KVYVGNLGSRATKRELERAFSKYGPLRSVWVARN 45 (195)
T ss_pred eEEeccCCCCcchHHHHHHHHhcCcceeEEEeec
Confidence 4999999999999999999999999999999874
No 44
>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]
Probab=85.95 E-value=0.34 Score=45.42 Aligned_cols=35 Identities=17% Similarity=0.473 Sum_probs=32.8
Q ss_pred EEecCCCCCCCHHHHHHHHhccCccceEEeccCCC
Q 044301 38 CYLSRIPPHMDPVKLRQILSQYGEIQRIYLAPEDP 72 (154)
Q Consensus 38 IYlSrIPp~M~p~klR~llsqfGeI~RIyL~pEd~ 72 (154)
+||+-|+..-++..||+||++||.|..+|+.+.+.
T Consensus 127 LFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~ 161 (510)
T KOG0144|consen 127 LFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPD 161 (510)
T ss_pred hhhhhccccccHHHHHHHHHhhCccchhhheeccc
Confidence 69999999999999999999999999999998654
No 45
>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]
Probab=85.21 E-value=0.88 Score=38.85 Aligned_cols=34 Identities=24% Similarity=0.499 Sum_probs=30.0
Q ss_pred cceEEecCCCCCCCHHHHHH----HHhccCccceEEec
Q 044301 35 RGICYLSRIPPHMDPVKLRQ----ILSQYGEIQRIYLA 68 (154)
Q Consensus 35 ~GVIYlSrIPp~M~p~klR~----llsqfGeI~RIyL~ 68 (154)
-|-|||.+|+-..+-..|+. ||||||+|-.|-.-
T Consensus 9 n~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~ 46 (221)
T KOG4206|consen 9 NGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAF 46 (221)
T ss_pred CceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEec
Confidence 35899999999999999998 99999999887654
No 46
>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]
Probab=84.80 E-value=0.99 Score=38.70 Aligned_cols=38 Identities=16% Similarity=0.408 Sum_probs=34.1
Q ss_pred CCcceEEecCCCCCCCHHHHHHHHhccCccceEEeccC
Q 044301 33 DQRGICYLSRIPPHMDPVKLRQILSQYGEIQRIYLAPE 70 (154)
Q Consensus 33 ~k~GVIYlSrIPp~M~p~klR~llsqfGeI~RIyL~pE 70 (154)
..+.-|||+.+|.+.....|++||.+||++.|+.|...
T Consensus 81 ~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~ 118 (243)
T KOG0533|consen 81 TRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYD 118 (243)
T ss_pred CCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccC
Confidence 34567999999999999999999999999999988875
No 47
>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=84.66 E-value=1.1 Score=33.22 Aligned_cols=34 Identities=18% Similarity=0.317 Sum_probs=22.1
Q ss_pred eEEecCCCCCCCHHHHHHHHhccCccceEEeccC
Q 044301 37 ICYLSRIPPHMDPVKLRQILSQYGEIQRIYLAPE 70 (154)
Q Consensus 37 VIYlSrIPp~M~p~klR~llsqfGeI~RIyL~pE 70 (154)
||+|+-++..++-..|+..|++||.|.-|-+++-
T Consensus 3 il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G 36 (105)
T PF08777_consen 3 ILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRG 36 (105)
T ss_dssp EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT
T ss_pred EEEEecCCCCcCHHHHHHHHHhcCCcceEEecCC
Confidence 7888889999999999999999999988877664
No 48
>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]
Probab=84.27 E-value=0.73 Score=43.30 Aligned_cols=33 Identities=12% Similarity=0.424 Sum_probs=30.3
Q ss_pred cceEEecCCCCCCCHHHHHHHHhccCccceEEe
Q 044301 35 RGICYLSRIPPHMDPVKLRQILSQYGEIQRIYL 67 (154)
Q Consensus 35 ~GVIYlSrIPp~M~p~klR~llsqfGeI~RIyL 67 (154)
==|+|+-+||--.+...|..+|++||.|.||--
T Consensus 259 VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk 291 (506)
T KOG0117|consen 259 VKVLYVRNLMESTTEETLKKLFNEFGKVERVKK 291 (506)
T ss_pred eeeeeeeccchhhhHHHHHHHHHhccceEEeec
Confidence 348999999999999999999999999999854
No 49
>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]
Probab=82.90 E-value=1.2 Score=39.25 Aligned_cols=35 Identities=11% Similarity=0.463 Sum_probs=31.4
Q ss_pred eEEecCCCCCCCHHHHHHHHhccCccceEEeccCC
Q 044301 37 ICYLSRIPPHMDPVKLRQILSQYGEIQRIYLAPED 71 (154)
Q Consensus 37 VIYlSrIPp~M~p~klR~llsqfGeI~RIyL~pEd 71 (154)
.|+++.||++.....+|++|.|||.|.++=+.-..
T Consensus 99 kiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~ 133 (311)
T KOG4205|consen 99 KIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDK 133 (311)
T ss_pred EEEecCcCCCCchHHHhhhhhccceeEeeEEeecc
Confidence 89999999999999999999999988887666543
No 50
>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]
Probab=81.87 E-value=1.6 Score=41.15 Aligned_cols=55 Identities=16% Similarity=0.263 Sum_probs=43.8
Q ss_pred eEEecCCCCCCCHHHHHHHHhccCccceEEeccCCCchhhhhhhhccccCCCCCCCcccccceeeeecccCC
Q 044301 37 ICYLSRIPPHMDPVKLRQILSQYGEIQRIYLAPEDPSTRVLRKRENRKRDGGFQDQGFSEGYKQKVQQESQT 108 (154)
Q Consensus 37 VIYlSrIPp~M~p~klR~llsqfGeI~RIyL~pEd~~~~~~rk~~~rkK~gg~k~~~FtEGWVEf~~k~~g~ 108 (154)
=|||+.||..+.+..|.-||..-|+|--++|.-+.. +|.|+.+.| |-|..|+.-+
T Consensus 85 EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~-------------sG~nRGYAF----Vtf~~Ke~Aq 139 (506)
T KOG0117|consen 85 EVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPF-------------SGDNRGYAF----VTFCTKEEAQ 139 (506)
T ss_pred eEEecCCCccccchhhHHHHHhccceeeEEEeeccc-------------CCCCcceEE----EEeecHHHHH
Confidence 599999999999999999999999999999998732 233555555 5677666533
No 51
>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]
Probab=80.66 E-value=1 Score=40.54 Aligned_cols=28 Identities=21% Similarity=0.578 Sum_probs=25.7
Q ss_pred EEecCCCCCCCHHHHHHHHhccCccceE
Q 044301 38 CYLSRIPPHMDPVKLRQILSQYGEIQRI 65 (154)
Q Consensus 38 IYlSrIPp~M~p~klR~llsqfGeI~RI 65 (154)
+||+.+|.--+..+||+||.+||.|.--
T Consensus 5 LFIGNLp~~~~~~elr~lFe~ygkVlEC 32 (346)
T KOG0109|consen 5 LFIGNLPREATEQELRSLFEQYGKVLEC 32 (346)
T ss_pred hhccCCCcccchHHHHHHHHhhCceEee
Confidence 6899999999999999999999998653
No 52
>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]
Probab=80.63 E-value=2.4 Score=39.12 Aligned_cols=35 Identities=20% Similarity=0.283 Sum_probs=33.0
Q ss_pred ceEEecCCCCCCCHHHHHHHHhccCccceEEeccC
Q 044301 36 GICYLSRIPPHMDPVKLRQILSQYGEIQRIYLAPE 70 (154)
Q Consensus 36 GVIYlSrIPp~M~p~klR~llsqfGeI~RIyL~pE 70 (154)
..||+++||.-++...|..+|+..|.|--+.|.-.
T Consensus 19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D 53 (435)
T KOG0108|consen 19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYD 53 (435)
T ss_pred cceEecCCCCcccHHHHHHHHhccCccceeeeccc
Confidence 78999999999999999999999999999999764
No 53
>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]
Probab=79.54 E-value=0.95 Score=39.23 Aligned_cols=31 Identities=19% Similarity=0.596 Sum_probs=25.6
Q ss_pred cCCCCCCCHHHHHHHHhccCccceEEeccCC
Q 044301 41 SRIPPHMDPVKLRQILSQYGEIQRIYLAPED 71 (154)
Q Consensus 41 SrIPp~M~p~klR~llsqfGeI~RIyL~pEd 71 (154)
-+|--.-+|..||.+|.+||.||-||+-.+.
T Consensus 19 dNLTyRTspd~LrrvFekYG~vgDVyIPrdr 49 (256)
T KOG4207|consen 19 DNLTYRTSPDDLRRVFEKYGRVGDVYIPRDR 49 (256)
T ss_pred cceeccCCHHHHHHHHHHhCcccceeccccc
Confidence 3455556899999999999999999997763
No 54
>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]
Probab=78.84 E-value=1.9 Score=42.95 Aligned_cols=36 Identities=28% Similarity=0.561 Sum_probs=32.5
Q ss_pred cceEEecCCCCCCCHHHHHHHHhccCccceEEeccC
Q 044301 35 RGICYLSRIPPHMDPVKLRQILSQYGEIQRIYLAPE 70 (154)
Q Consensus 35 ~GVIYlSrIPp~M~p~klR~llsqfGeI~RIyL~pE 70 (154)
.-.++|+.||..|+...|+++|..||+|.+|-|.+.
T Consensus 421 SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~ 456 (894)
T KOG0132|consen 421 SRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPP 456 (894)
T ss_pred eeeeeeccccchhhHHHHHHHHHhcccceeEeeccC
Confidence 345789999999999999999999999999988774
No 55
>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]
Probab=77.73 E-value=2.8 Score=36.44 Aligned_cols=37 Identities=16% Similarity=0.313 Sum_probs=32.1
Q ss_pred eEEecCCCCCCCHHHHHHHHhccCccceEEeccCCCc
Q 044301 37 ICYLSRIPPHMDPVKLRQILSQYGEIQRIYLAPEDPS 73 (154)
Q Consensus 37 VIYlSrIPp~M~p~klR~llsqfGeI~RIyL~pEd~~ 73 (154)
=||++-||=.-.-..||.+|+|||+|--.-+.-....
T Consensus 14 KifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t 50 (247)
T KOG0149|consen 14 KIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNT 50 (247)
T ss_pred EEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCC
Confidence 4899999999999999999999999988877766433
No 56
>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif
Probab=77.11 E-value=2.1 Score=28.07 Aligned_cols=32 Identities=25% Similarity=0.556 Sum_probs=23.5
Q ss_pred EEecCCCCCCCHHHHHHHHhccCccceEEeccC
Q 044301 38 CYLSRIPPHMDPVKLRQILSQYGEIQRIYLAPE 70 (154)
Q Consensus 38 IYlSrIPp~M~p~klR~llsqfGeI~RIyL~pE 70 (154)
|-++=.|+.+.. .++..|++||+|.++++.+.
T Consensus 4 I~V~Gf~~~~~~-~vl~~F~~fGeI~~~~~~~~ 35 (53)
T PF14605_consen 4 ISVSGFPPDLAE-EVLEHFASFGEIVDIYVPES 35 (53)
T ss_pred EEEEeECchHHH-HHHHHHHhcCCEEEEEcCCC
Confidence 445666777664 45567888999999999844
No 57
>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]
Probab=76.27 E-value=2.9 Score=34.32 Aligned_cols=34 Identities=21% Similarity=0.447 Sum_probs=32.2
Q ss_pred eEEecCCCCCCCHHHHHHHHhccCccceEEeccC
Q 044301 37 ICYLSRIPPHMDPVKLRQILSQYGEIQRIYLAPE 70 (154)
Q Consensus 37 VIYlSrIPp~M~p~klR~llsqfGeI~RIyL~pE 70 (154)
|||++.|.+--+...|-..|+.||+|..|+|.-.
T Consensus 74 Ii~VtgvHeEatEedi~d~F~dyGeiKNihLNLD 107 (170)
T KOG0130|consen 74 IIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLD 107 (170)
T ss_pred EEEEeccCcchhHHHHHHHHhhcccccceeeccc
Confidence 8999999999999999999999999999999764
No 58
>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=75.85 E-value=2.7 Score=41.22 Aligned_cols=33 Identities=18% Similarity=0.398 Sum_probs=30.5
Q ss_pred CCcceEEecCCCCCCCHHHHHHHHhccCccceE
Q 044301 33 DQRGICYLSRIPPHMDPVKLRQILSQYGEIQRI 65 (154)
Q Consensus 33 ~k~GVIYlSrIPp~M~p~klR~llsqfGeI~RI 65 (154)
.---||.+..||-+-.+..|..+|..||.|+||
T Consensus 383 rs~~vil~kNlpa~t~~~elt~~F~~fG~i~rv 415 (725)
T KOG0110|consen 383 RSDTVILVKNLPAGTLSEELTEAFLRFGEIGRV 415 (725)
T ss_pred hhcceeeeccCccccccHHHHHHhhccccccee
Confidence 335689999999999999999999999999999
No 59
>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]
Probab=74.32 E-value=3.2 Score=40.25 Aligned_cols=39 Identities=13% Similarity=0.380 Sum_probs=34.2
Q ss_pred cceEEecCCCCCCCHHHHHHHHhccCccceEEeccCCCc
Q 044301 35 RGICYLSRIPPHMDPVKLRQILSQYGEIQRIYLAPEDPS 73 (154)
Q Consensus 35 ~GVIYlSrIPp~M~p~klR~llsqfGeI~RIyL~pEd~~ 73 (154)
-=+|||-+||=.-+...|.+.|++||+|.-+.|.-...+
T Consensus 292 ~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k~T 330 (678)
T KOG0127|consen 292 GKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDKDT 330 (678)
T ss_pred cceEEEecCCccccHHHHHHHHHhhccceeEEEEeccCC
Confidence 368999999999999999999999999998888765433
No 60
>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]
Probab=73.67 E-value=3.8 Score=36.24 Aligned_cols=39 Identities=18% Similarity=0.365 Sum_probs=35.4
Q ss_pred CcceEEecCCCCCCCHHHHHHHHhccCccceEEeccCCC
Q 044301 34 QRGICYLSRIPPHMDPVKLRQILSQYGEIQRIYLAPEDP 72 (154)
Q Consensus 34 k~GVIYlSrIPp~M~p~klR~llsqfGeI~RIyL~pEd~ 72 (154)
..|=++|+-|+..-+...||.+|++||+|.-..+.....
T Consensus 5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~ 43 (311)
T KOG4205|consen 5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPS 43 (311)
T ss_pred CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCC
Confidence 467899999999999999999999999999999987643
No 61
>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]
Probab=73.37 E-value=3 Score=38.22 Aligned_cols=28 Identities=25% Similarity=0.481 Sum_probs=26.0
Q ss_pred eEEecCCCCCCCHHHHHHHHhccCccce
Q 044301 37 ICYLSRIPPHMDPVKLRQILSQYGEIQR 64 (154)
Q Consensus 37 VIYlSrIPp~M~p~klR~llsqfGeI~R 64 (154)
-||||.||...+...+-++|+.+|-|-|
T Consensus 136 ~VYVsgLP~DiT~dE~~~~~sKcGiI~~ 163 (382)
T KOG1548|consen 136 SVYVSGLPLDITVDEFAEVMSKCGIIMR 163 (382)
T ss_pred eEEecCCCCcccHHHHHHHHHhcceEec
Confidence 5999999999999999999999998754
No 62
>PF15513 DUF4651: Domain of unknown function (DUF4651)
Probab=73.18 E-value=3.6 Score=28.98 Aligned_cols=24 Identities=38% Similarity=0.722 Sum_probs=21.0
Q ss_pred HHHHHHHhccCccceEEeccCCCc
Q 044301 50 VKLRQILSQYGEIQRIYLAPEDPS 73 (154)
Q Consensus 50 ~klR~llsqfGeI~RIyL~pEd~~ 73 (154)
..||+.||+.|+|.=+|+.+-.+.
T Consensus 9 ~~iR~~fs~lG~I~vLYvn~~eS~ 32 (62)
T PF15513_consen 9 AEIRQFFSQLGEIAVLYVNPYESD 32 (62)
T ss_pred HHHHHHHHhcCcEEEEEEcccccC
Confidence 579999999999999999987543
No 63
>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]
Probab=71.89 E-value=2.1 Score=40.80 Aligned_cols=57 Identities=19% Similarity=0.327 Sum_probs=44.4
Q ss_pred Ccce-EEecCCCCCCCHHHHHHHHhccCccceEEeccCCCchhhhhhhhccccCCCCCCCcccccceeeeecccC
Q 044301 34 QRGI-CYLSRIPPHMDPVKLRQILSQYGEIQRIYLAPEDPSTRVLRKRENRKRDGGFQDQGFSEGYKQKVQQESQ 107 (154)
Q Consensus 34 k~GV-IYlSrIPp~M~p~klR~llsqfGeI~RIyL~pEd~~~~~~rk~~~rkK~gg~k~~~FtEGWVEf~~k~~g 107 (154)
-|.. +|.+.|...|+...||.+|..||.|.-|-|.......+ ++.. |.++|++++.-
T Consensus 276 ~p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~-------------skgf----Gfi~f~~~~~a 333 (549)
T KOG0147|consen 276 GPMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGR-------------SKGF----GFITFVNKEDA 333 (549)
T ss_pred cchhhhhhcccccCchHHHHhhhccCcccceeeeecccccccc-------------ccCc----ceEEEecHHHH
Confidence 4556 89999999999999999999999999999987643322 2222 66779987653
No 64
>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN). ; GO: 0003723 RNA binding, 0004535 poly(A)-specific ribonuclease activity, 0046872 metal ion binding, 0006402 mRNA catabolic process, 0005634 nucleus, 0005737 cytoplasm; PDB: 3CTR_A 2ROK_A 3D45_B 1WHV_A.
Probab=70.36 E-value=5.3 Score=29.87 Aligned_cols=35 Identities=17% Similarity=0.405 Sum_probs=25.2
Q ss_pred CCcceEEecCCCCCCCHHHHHHHHhccCccceEEec
Q 044301 33 DQRGICYLSRIPPHMDPVKLRQILSQYGEIQRIYLA 68 (154)
Q Consensus 33 ~k~GVIYlSrIPp~M~p~klR~llsqfGeI~RIyL~ 68 (154)
+.-.|.||+ .|+--.-..|.+||+.||.|.=-+|-
T Consensus 7 ~RdHVFhlt-FPkeWK~~DI~qlFspfG~I~VsWi~ 41 (87)
T PF08675_consen 7 SRDHVFHLT-FPKEWKTSDIYQLFSPFGQIYVSWIN 41 (87)
T ss_dssp SGCCEEEEE---TT--HHHHHHHCCCCCCEEEEEEC
T ss_pred CcceEEEEe-CchHhhhhhHHHHhccCCcEEEEEEc
Confidence 445788887 99999999999999999998655553
No 65
>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]
Probab=68.00 E-value=6.6 Score=35.08 Aligned_cols=41 Identities=24% Similarity=0.398 Sum_probs=36.9
Q ss_pred cCCcceEEecCCCCCCCHHHHHHHHhccCccceEEeccCCC
Q 044301 32 ADQRGICYLSRIPPHMDPVKLRQILSQYGEIQRIYLAPEDP 72 (154)
Q Consensus 32 ~~k~GVIYlSrIPp~M~p~klR~llsqfGeI~RIyL~pEd~ 72 (154)
...-..+|+..++.-++...|+.+|+.||+|..++|+-.+.
T Consensus 267 ~~~~~nl~vknld~~~~~e~L~~~f~~~GeI~s~kv~~~~~ 307 (369)
T KOG0123|consen 267 SLQGANLYVKNLDETLSDEKLRKIFSSFGEITSAKVMVDEN 307 (369)
T ss_pred cccccccccccCccccchhHHHHHHhcccceeeEEEEeccC
Confidence 34568899999999999999999999999999999998654
No 66
>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]
Probab=65.79 E-value=4.4 Score=34.37 Aligned_cols=37 Identities=14% Similarity=0.291 Sum_probs=33.0
Q ss_pred CcceEEecCCCCCCCHHHHHHHHhccCccceEEeccC
Q 044301 34 QRGICYLSRIPPHMDPVKLRQILSQYGEIQRIYLAPE 70 (154)
Q Consensus 34 k~GVIYlSrIPp~M~p~klR~llsqfGeI~RIyL~pE 70 (154)
.---||++.|++..+.+.|.+||-|-|.|-+||+-..
T Consensus 8 qd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkD 44 (203)
T KOG0131|consen 8 QDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKD 44 (203)
T ss_pred CCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchh
Confidence 3457999999999999999999999999999998543
No 67
>PF04940 BLUF: Sensors of blue-light using FAD; InterPro: IPR007024 An FAD-binding domain, BLUF, exemplified by the N terminus of the AppA protein, (Q53119 from SWISSPROT), from Rhodobacter sphaeroides, is present in various proteins, primarily from Bacteria. The BLUF domain is involved in sensing blue-light (and possibly redox) using FAD and is similar to the flavin-binding PAS domains and cryptochromes. The predicted secondary structure reveals that the BLUF domain is a novel FAD-binding fold [].; PDB: 2IYG_A 2IYI_B 1X0P_A 2HFN_G 3MZI_A 2HFO_E 3GFZ_A 3GG1_B 2KB2_A 3GFY_A ....
Probab=64.68 E-value=4.6 Score=29.25 Aligned_cols=22 Identities=27% Similarity=0.525 Sum_probs=18.7
Q ss_pred eEEecCCCCCCCHHHHHHHHhc
Q 044301 37 ICYLSRIPPHMDPVKLRQILSQ 58 (154)
Q Consensus 37 VIYlSrIPp~M~p~klR~llsq 58 (154)
+||+|++...|++..|.+||..
T Consensus 4 l~Y~S~~~~~~~~~~~~~Il~~ 25 (93)
T PF04940_consen 4 LIYVSTASEDLSPEDLADILRS 25 (93)
T ss_dssp EEEEEEE-TTS-HHHHHHHHHH
T ss_pred EEEEEccCCCCCHHHHHHHHHH
Confidence 7999999999999999999975
No 68
>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]
Probab=63.22 E-value=7.4 Score=34.92 Aligned_cols=56 Identities=16% Similarity=0.355 Sum_probs=43.0
Q ss_pred ceEEecCCCCCCCHHHHHHHHhccCccceEEeccCCCchhhhhhhhccccCCCCCCCcccccceeeeecccCC
Q 044301 36 GICYLSRIPPHMDPVKLRQILSQYGEIQRIYLAPEDPSTRVLRKRENRKRDGGFQDQGFSEGYKQKVQQESQT 108 (154)
Q Consensus 36 GVIYlSrIPp~M~p~klR~llsqfGeI~RIyL~pEd~~~~~~rk~~~rkK~gg~k~~~FtEGWVEf~~k~~g~ 108 (154)
=-|+++-+-+..+-.+||+-|.+||+|....+.+..... +++. | |.|-|.+|+.-+
T Consensus 63 fhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~-------------KsKG--Y--gFVSf~~k~dAE 118 (321)
T KOG0148|consen 63 FHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTG-------------KSKG--Y--GFVSFPNKEDAE 118 (321)
T ss_pred eeEEehhcchhcchHHHHHHhccccccccceEeecccCC-------------cccc--e--eEEeccchHHHH
Confidence 357889999999999999999999999999998864332 1222 2 778888877643
No 69
>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]
Probab=62.54 E-value=7 Score=37.43 Aligned_cols=41 Identities=27% Similarity=0.447 Sum_probs=35.7
Q ss_pred hcCCcceEEecCCCCCCCHHHHHHHHhccCccceEEeccCC
Q 044301 31 KADQRGICYLSRIPPHMDPVKLRQILSQYGEIQRIYLAPED 71 (154)
Q Consensus 31 k~~k~GVIYlSrIPp~M~p~klR~llsqfGeI~RIyL~pEd 71 (154)
+....|-+.|-.||+-.+.+.|+++|+.||+|--|.-.|..
T Consensus 71 ~~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~~~ 111 (549)
T KOG4660|consen 71 KDMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETPNK 111 (549)
T ss_pred ccCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhccccc
Confidence 34678999999999999999999999999999887766643
No 70
>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]
Probab=61.62 E-value=9.2 Score=34.20 Aligned_cols=36 Identities=17% Similarity=0.406 Sum_probs=33.1
Q ss_pred cceEEecCCCCCCCHHHHHHHHhccCccceEEeccC
Q 044301 35 RGICYLSRIPPHMDPVKLRQILSQYGEIQRIYLAPE 70 (154)
Q Consensus 35 ~GVIYlSrIPp~M~p~klR~llsqfGeI~RIyL~pE 70 (154)
+-.|||..+++.++-..|..+||.||+|-.+.|...
T Consensus 76 ~~~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~ 111 (369)
T KOG0123|consen 76 PSLVFIKNLDESIDNKSLYDTFSEFGNILSCKVATD 111 (369)
T ss_pred CceeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEc
Confidence 444999999999999999999999999999999875
No 71
>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=61.30 E-value=9.2 Score=35.09 Aligned_cols=39 Identities=23% Similarity=0.388 Sum_probs=34.9
Q ss_pred CcceEEecCCCCCCCHHHHHHHHhccCccceEEeccCCC
Q 044301 34 QRGICYLSRIPPHMDPVKLRQILSQYGEIQRIYLAPEDP 72 (154)
Q Consensus 34 k~GVIYlSrIPp~M~p~klR~llsqfGeI~RIyL~pEd~ 72 (154)
.--.+||+.+=+......||..|-|||+|--|.+.++..
T Consensus 227 ~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~~~ 265 (377)
T KOG0153|consen 227 SIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPRKG 265 (377)
T ss_pred ceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecccc
Confidence 345789999988999999999999999999999998754
No 72
>smart00361 RRM_1 RNA recognition motif.
Probab=58.13 E-value=10 Score=25.08 Aligned_cols=18 Identities=22% Similarity=0.451 Sum_probs=15.3
Q ss_pred HHHHHHHHh----ccCccceEE
Q 044301 49 PVKLRQILS----QYGEIQRIY 66 (154)
Q Consensus 49 p~klR~lls----qfGeI~RIy 66 (154)
...|+++|+ +||+|++|+
T Consensus 2 ~~~l~~~~~~~~~~fG~v~~v~ 23 (70)
T smart00361 2 DEDFEREFSEEEEYFGEVGKIN 23 (70)
T ss_pred chhHHHHHHHHHHhcCCeeEEE
Confidence 356888898 999999996
No 73
>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]
Probab=51.41 E-value=14 Score=31.35 Aligned_cols=32 Identities=19% Similarity=0.453 Sum_probs=28.7
Q ss_pred EEecCCCCCCCHHHHHHHHhccCccceEEecc
Q 044301 38 CYLSRIPPHMDPVKLRQILSQYGEIQRIYLAP 69 (154)
Q Consensus 38 IYlSrIPp~M~p~klR~llsqfGeI~RIyL~p 69 (154)
|||+++|..-....|.++|..||.|-.+-+..
T Consensus 4 v~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk~ 35 (216)
T KOG0106|consen 4 VYIGRLPYRARERDVERFFKGYGKIPDADMKN 35 (216)
T ss_pred eeecccCCccchhHHHHHHhhccccccceeec
Confidence 79999999999999999999999998775543
No 74
>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]
Probab=48.80 E-value=11 Score=35.35 Aligned_cols=97 Identities=26% Similarity=0.364 Sum_probs=63.3
Q ss_pred CcceEEecCCCCCCCHHHHHHHHhccCccceEEeccCCCchhhhhhhhccccCCCCCCCcccccce--------eeee-c
Q 044301 34 QRGICYLSRIPPHMDPVKLRQILSQYGEIQRIYLAPEDPSTRVLRKRENRKRDGGFQDQGFSEGYK--------QKVQ-Q 104 (154)
Q Consensus 34 k~GVIYlSrIPp~M~p~klR~llsqfGeI~RIyL~pEd~~~~~~rk~~~rkK~gg~k~~~FtEGWV--------Ef~~-k 104 (154)
..--||+++|-=-+.+.-||.-|..||.|..|-++=. +.. +.++...|+|==| |-.+ .
T Consensus 112 iMcRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWD-p~T------------~kHKgFAFVEYEvPEaAqLAlEqMNg~ 178 (544)
T KOG0124|consen 112 IMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWD-PAT------------GKHKGFAFVEYEVPEAAQLALEQMNGQ 178 (544)
T ss_pred HhHheeeeeeEEEechHHHHhhccCCCCcceeecccc-ccc------------ccccceEEEEEeCcHHHHHHHHHhccc
Confidence 4556999999999999999999999999999988753 322 2244555655322 1111 1
Q ss_pred ccCCCCCCCCCcccccccc--cCCCCCccccCC------------CCCCCccchhhhcccc
Q 044301 105 ESQTHPELPGSEQVTKVIR--HFPQKQPVTDNA------------APSKSRLSKDILAGVF 151 (154)
Q Consensus 105 ~~g~~~e~~~~~~~~~~~r--~~~q~kp~~~~~------------~~~k~~l~~d~la~vf 151 (154)
-.|+ +--||-| ++||-+||-|.- +.--|+||.+=|-+||
T Consensus 179 mlGG--------RNiKVgrPsNmpQAQpiID~vqeeAk~fnRiYVaSvHpDLSe~DiKSVF 231 (544)
T KOG0124|consen 179 MLGG--------RNIKVGRPSNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVF 231 (544)
T ss_pred cccC--------ccccccCCCCCcccchHHHHHHHHHHhhheEEeeecCCCccHHHHHHHH
Confidence 1122 1122222 578999986532 3446899998888887
No 75
>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=45.84 E-value=13 Score=36.77 Aligned_cols=35 Identities=14% Similarity=0.375 Sum_probs=31.3
Q ss_pred cceEEecCCCCCCCHHHHHHHHhccCccceEEecc
Q 044301 35 RGICYLSRIPPHMDPVKLRQILSQYGEIQRIYLAP 69 (154)
Q Consensus 35 ~GVIYlSrIPp~M~p~klR~llsqfGeI~RIyL~p 69 (154)
..=|.+-.||=..+--.||+||+.||.|--|+|--
T Consensus 613 ~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPK 647 (725)
T KOG0110|consen 613 GTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPK 647 (725)
T ss_pred cceeeeeccchHHHHHHHHHHHhcccceeeeccch
Confidence 56789999999999999999999999999888843
No 76
>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]
Probab=45.22 E-value=23 Score=32.04 Aligned_cols=35 Identities=23% Similarity=0.403 Sum_probs=31.0
Q ss_pred eEEecCCCCCCCHHHHHHHHhccCccceEEeccCC
Q 044301 37 ICYLSRIPPHMDPVKLRQILSQYGEIQRIYLAPED 71 (154)
Q Consensus 37 VIYlSrIPp~M~p~klR~llsqfGeI~RIyL~pEd 71 (154)
-+-+--+|-.|+...+|.||+--|+|....|.+.+
T Consensus 43 NLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDK 77 (360)
T KOG0145|consen 43 NLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDK 77 (360)
T ss_pred eeeeeecccccCHHHHHHHhhcccceeeeeeeecc
Confidence 35567789999999999999999999999998864
No 77
>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]
Probab=40.87 E-value=28 Score=29.39 Aligned_cols=43 Identities=12% Similarity=0.193 Sum_probs=37.3
Q ss_pred HhhcCCcceEEecCCCCCCCHHHHHHHHhccCccceEEeccCC
Q 044301 29 AAKADQRGICYLSRIPPHMDPVKLRQILSQYGEIQRIYLAPED 71 (154)
Q Consensus 29 ~~k~~k~GVIYlSrIPp~M~p~klR~llsqfGeI~RIyL~pEd 71 (154)
.++....=.||+|++=-.-+++++-..|+-||.|.||=+....
T Consensus 95 ~~~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~ 137 (231)
T KOG4209|consen 95 RQKEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDK 137 (231)
T ss_pred hhhccCCceEEEeccccccccchhhheeeccCCccceeeeccc
Confidence 3455667789999999999999999999999999999887763
No 78
>PF03721 UDPG_MGDP_dh_N: UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain; InterPro: IPR001732 The UDP-glucose/GDP-mannose dehydrogenases are a small group of enzymes which possesses the ability to catalyse the NAD-dependent 2-fold oxidation of an alcohol to an acid without the release of an aldehyde intermediate [, ]. The enzymes have a wide range of functions. In plants UDP-glucose dehydrogenase, 1.1.1.22 from EC, is an important enzyme in the synthesis of hemicellulose and pectin [], which are the components of newly formed cell walls; while in zebrafish UDP-glucose dehydrogenase is required for cardiac valve formation []. In Xanthomonas campestris, a plant pathogen, UDP-glucose dehydrogenase is required for virulence []. GDP-mannose dehydrogenase, 1.1.1.132 from EC, catalyses the formation of GDP-mannuronic acid, which is the monomeric unit from which the exopolysaccharide alginate is formed. Alginate is secreted by a number of bacteria, which include Pseudomonas aeruginosa and Azotobacter vinelandii. In P. aeruginosa, alginate is believed to play an important role in the bacteria's resistance to antibiotics and the host immune response [], while in A. vinelandii it is essential for the encystment process []. This entry represents the N-terminal NAD(+)-binding domain. Structural studies indicate that this domain forms an alpha-beta structure containing the six-stranded parallel beta sheet characteristic of the dinucleotide binding Rossman fold [, ].; GO: 0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor, 0051287 NAD binding, 0055114 oxidation-reduction process; PDB: 3OJO_A 3OJL_A 1MV8_B 1MUU_A 1MFZ_C 3GG2_D 1DLJ_A 1DLI_A 3G79_B 2Y0E_D ....
Probab=40.15 E-value=17 Score=29.00 Aligned_cols=34 Identities=24% Similarity=0.268 Sum_probs=27.0
Q ss_pred cceEEecCCCCCCCHHHHHHHHhccCcc-ceEEec
Q 044301 35 RGICYLSRIPPHMDPVKLRQILSQYGEI-QRIYLA 68 (154)
Q Consensus 35 ~GVIYlSrIPp~M~p~klR~llsqfGeI-~RIyL~ 68 (154)
.=||+=|++||+.+...++.+|.+++.. ..++|.
T Consensus 114 ~lvV~~STvppGtt~~~~~~ile~~~~~~~~f~la 148 (185)
T PF03721_consen 114 DLVVIESTVPPGTTEELLKPILEKRSGKKEDFHLA 148 (185)
T ss_dssp EEEEESSSSSTTHHHHHHHHHHHHHCCTTTCEEEE
T ss_pred ceEEEccEEEEeeehHhhhhhhhhhcccccCCeEE
Confidence 3568889999999999999999998854 334443
No 79
>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]
Probab=38.49 E-value=28 Score=32.83 Aligned_cols=38 Identities=18% Similarity=0.450 Sum_probs=35.7
Q ss_pred CCcceEEecCCCCCCCHHHHHHHHhccCccceEEeccC
Q 044301 33 DQRGICYLSRIPPHMDPVKLRQILSQYGEIQRIYLAPE 70 (154)
Q Consensus 33 ~k~GVIYlSrIPp~M~p~klR~llsqfGeI~RIyL~pE 70 (154)
...|||-+..|-|-.+-.+|+.||...|.|.-+.|.|.
T Consensus 5 ~~~~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~ 42 (479)
T KOG4676|consen 5 SSLGVIQVANISPSATKDQMQTLFGNLGKIPELRLYPN 42 (479)
T ss_pred CCCceeeecccCchhhHHHHHHHHhhccccccccccCC
Confidence 45789999999999999999999999999999999994
No 80
>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]
Probab=38.00 E-value=23 Score=33.86 Aligned_cols=26 Identities=12% Similarity=0.447 Sum_probs=24.0
Q ss_pred eEEecCCCCCCCHHHHHHHHhccCcc
Q 044301 37 ICYLSRIPPHMDPVKLRQILSQYGEI 62 (154)
Q Consensus 37 VIYlSrIPp~M~p~klR~llsqfGeI 62 (154)
=||+|-||+.|+...|-..|-+||.|
T Consensus 261 KVFvGGlp~dise~~i~~~F~~FGs~ 286 (520)
T KOG0129|consen 261 KVFVGGLPWDITEAQINASFGQFGSV 286 (520)
T ss_pred ceeecCCCccccHHHHHhhcccccce
Confidence 37999999999999999999999975
No 81
>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]
Probab=37.38 E-value=28 Score=30.86 Aligned_cols=36 Identities=19% Similarity=0.290 Sum_probs=32.4
Q ss_pred ceEEecCCCCCCCHHHHHHHHhccCccceEEeccCC
Q 044301 36 GICYLSRIPPHMDPVKLRQILSQYGEIQRIYLAPED 71 (154)
Q Consensus 36 GVIYlSrIPp~M~p~klR~llsqfGeI~RIyL~pEd 71 (154)
.++|+-.++++.+...+.+-|++||+|.|--....|
T Consensus 32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~ 67 (275)
T KOG0115|consen 32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDD 67 (275)
T ss_pred ceEEEEecchhhhhHHHHHhhhhcCccchheeeecc
Confidence 789999999999999999999999999987666654
No 82
>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]
Probab=35.92 E-value=33 Score=34.47 Aligned_cols=34 Identities=15% Similarity=0.370 Sum_probs=29.4
Q ss_pred cceEEecCCCCCCCHHHHHHHHhccCccceEEec
Q 044301 35 RGICYLSRIPPHMDPVKLRQILSQYGEIQRIYLA 68 (154)
Q Consensus 35 ~GVIYlSrIPp~M~p~klR~llsqfGeI~RIyL~ 68 (154)
+-.+|+++|+|-|+...|...|..||.|--|.+.
T Consensus 174 TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKim 207 (877)
T KOG0151|consen 174 TTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIM 207 (877)
T ss_pred ccceeeecCCccccHHHHHHHhcccCcccceeee
Confidence 4479999999999999999999999998665543
No 83
>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2. It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).
Probab=35.87 E-value=63 Score=24.01 Aligned_cols=33 Identities=27% Similarity=0.379 Sum_probs=27.9
Q ss_pred eEEecCCCCCCCHHHHHHHHhc--cCccceEEecc
Q 044301 37 ICYLSRIPPHMDPVKLRQILSQ--YGEIQRIYLAP 69 (154)
Q Consensus 37 VIYlSrIPp~M~p~klR~llsq--fGeI~RIyL~p 69 (154)
-|-|-.||+.++...|.++|.. .|..+=+||--
T Consensus 3 TvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPi 37 (97)
T PF04059_consen 3 TVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPI 37 (97)
T ss_pred eEEEecCCCCCCHHHHHHHHHHhccCcceEEEeee
Confidence 3678899999999999999988 67888888843
No 84
>cd01789 Alp11_N Ubiquitin-like domain of Alp11 tubulin-folding cofactor B. Alp11, also known as tubulin-folding cofactor B, is one of at least three proteins required for the proper folding of tubulins prior to their incorporation into microtubules. These cofactors are necessary for the biogenesis of microtubules and for cell viability. Alp11 has three domains including an N-terminal ubiquitin-like domain (represented by this CD) which executes the essential function, a central coiled-coil domain necessary for maintenance of cellular alpha-tubulin levels, and a C-terminal CLIP-170 domain is required for efficient binding to alpha-tubulin.
Probab=34.92 E-value=42 Score=23.53 Aligned_cols=27 Identities=15% Similarity=0.241 Sum_probs=22.0
Q ss_pred CCCCCCCHHHHHHHHhc-cCc-cceEEec
Q 044301 42 RIPPHMDPVKLRQILSQ-YGE-IQRIYLA 68 (154)
Q Consensus 42 rIPp~M~p~klR~llsq-fGe-I~RIyL~ 68 (154)
++|+.|+..+|++.|.. +|. ...+.|+
T Consensus 18 r~~~~~Tv~~lK~kl~~~~G~~~~~mrL~ 46 (84)
T cd01789 18 KYSRGLTIAELKKKLELVVGTPASSMRLQ 46 (84)
T ss_pred ecCCCCcHHHHHHHHHHHHCCCccceEEE
Confidence 59999999999999988 563 5666664
No 85
>cd00842 MPP_ASMase acid sphingomyelinase and related proteins, metallophosphatase domain. Acid sphingomyelinase (ASMase) is a ubiquitously expressed phosphodiesterase which hydrolyzes sphingomyelin in acid pH conditions to form ceramide, a bioactive second messenger, as part of the sphingomyelin signaling pathway. ASMase is localized at the noncytosolic leaflet of biomembranes (for example the luminal leaflet of endosomes, lysosomes and phagosomes, and the extracellular leaflet of plasma membranes). ASMase-deficient humans develop Niemann-Pick disease. This disease is characterized by lysosomal storage of sphingomyelin in all tissues. Although ASMase-deficient mice are resistant to stress-induced apoptosis, they have greater susceptibility to bacterial infection. The latter correlates with defective phagolysosomal fusion and antibacterial killing activity in ASMase-deficient macrophages. ASMase belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but
Probab=34.18 E-value=44 Score=27.52 Aligned_cols=27 Identities=22% Similarity=0.592 Sum_probs=21.5
Q ss_pred cceEEecCCCCCCCH--------HHHHHHHhccCc
Q 044301 35 RGICYLSRIPPHMDP--------VKLRQILSQYGE 61 (154)
Q Consensus 35 ~GVIYlSrIPp~M~p--------~klR~llsqfGe 61 (154)
.-|+-++||||+... ..+.+|+.+|..
T Consensus 214 ~~v~I~~HiPp~~~~~~~~~~~~~~~~~ii~~y~~ 248 (296)
T cd00842 214 EKVWIIGHIPPGVNSYDTLENWSERYLQIINRYSD 248 (296)
T ss_pred CeEEEEeccCCCCcccccchHHHHHHHHHHHHHHH
Confidence 347889999998753 568899999975
No 86
>cd00027 BRCT Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks.
Probab=33.73 E-value=60 Score=19.31 Aligned_cols=25 Identities=12% Similarity=0.291 Sum_probs=21.7
Q ss_pred eEEecCCCCCCCHHHHHHHHhccCc
Q 044301 37 ICYLSRIPPHMDPVKLRQILSQYGE 61 (154)
Q Consensus 37 VIYlSrIPp~M~p~klR~llsqfGe 61 (154)
.+||+..++......|.+++..+|-
T Consensus 3 ~~~i~g~~~~~~~~~l~~~i~~~Gg 27 (72)
T cd00027 3 TFVITGDLPSEERDELKELIEKLGG 27 (72)
T ss_pred EEEEEecCCCcCHHHHHHHHHHcCC
Confidence 4788888878999999999999985
No 87
>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]
Probab=33.45 E-value=28 Score=31.53 Aligned_cols=35 Identities=14% Similarity=0.428 Sum_probs=29.3
Q ss_pred cceEEecCCCCCCCHHHHHHHHhccCccc--eEEecc
Q 044301 35 RGICYLSRIPPHMDPVKLRQILSQYGEIQ--RIYLAP 69 (154)
Q Consensus 35 ~GVIYlSrIPp~M~p~klR~llsqfGeI~--RIyL~p 69 (154)
.-.+||=|+|--|..+.|-++|-.||.|- .||+-+
T Consensus 285 GCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDR 321 (371)
T KOG0146|consen 285 GCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDR 321 (371)
T ss_pred cceEEEEeCchhhccHHHHHHhccccceeeeeeeehh
Confidence 34789999999999999999999999884 455543
No 88
>PRK06369 nac nascent polypeptide-associated complex protein; Reviewed
Probab=32.66 E-value=37 Score=26.37 Aligned_cols=27 Identities=22% Similarity=0.477 Sum_probs=20.5
Q ss_pred CCCCCHHHHHHHHhccCc------cceEEeccC
Q 044301 44 PPHMDPVKLRQILSQYGE------IQRIYLAPE 70 (154)
Q Consensus 44 Pp~M~p~klR~llsqfGe------I~RIyL~pE 70 (154)
+.+|+|.++|++|.+.|- |.||-+...
T Consensus 2 ~~~~nprk~rkmmkkmGik~e~i~v~~V~Ir~~ 34 (115)
T PRK06369 2 MGGMNPRKMKQMMKQMGIDVEELDVEEVIIRLK 34 (115)
T ss_pred CCCCCHHHHHHHHHHcCCcchhcCeEEEEEEeC
Confidence 678999999999999992 345555443
No 89
>COG1308 EGD2 Transcription factor homologous to NACalpha-BTF3 [Transcription]
Probab=31.48 E-value=37 Score=26.79 Aligned_cols=18 Identities=44% Similarity=0.868 Sum_probs=17.0
Q ss_pred CCCCCCHHHHHHHHhccC
Q 044301 43 IPPHMDPVKLRQILSQYG 60 (154)
Q Consensus 43 IPp~M~p~klR~llsqfG 60 (154)
||-+|+|.+|++++.|.|
T Consensus 2 ~pg~mnpr~l~k~mkqmG 19 (122)
T COG1308 2 IPGGMNPRKLKKLMKQMG 19 (122)
T ss_pred CCCcCCHHHHHHHHHHhC
Confidence 688899999999999999
No 90
>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=30.75 E-value=26 Score=30.98 Aligned_cols=56 Identities=23% Similarity=0.456 Sum_probs=44.5
Q ss_pred CcceEEecCCCCCCCHHHHHHHHhccCccceEEeccCCCchhhhhhhhccccCCCCCCCcccccceeeeeccc
Q 044301 34 QRGICYLSRIPPHMDPVKLRQILSQYGEIQRIYLAPEDPSTRVLRKRENRKRDGGFQDQGFSEGYKQKVQQES 106 (154)
Q Consensus 34 k~GVIYlSrIPp~M~p~klR~llsqfGeI~RIyL~pEd~~~~~~rk~~~rkK~gg~k~~~FtEGWVEf~~k~~ 106 (154)
..-++|++-+-.-.+..-|...|-.||.|..|-+ |-|..+.++| .| |+|||...++
T Consensus 9 ~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqi-PlDyesqkHR--------------gF--gFVefe~aED 64 (298)
T KOG0111|consen 9 QKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQI-PLDYESQKHR--------------GF--GFVEFEEAED 64 (298)
T ss_pred cceeEEeccchHHHHHHHHHhccccccchhhccc-ccchhccccc--------------ce--eEEEeeccch
Confidence 3458999999999999999999999999999875 5566555433 12 7899987665
No 91
>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=28.73 E-value=87 Score=29.48 Aligned_cols=36 Identities=17% Similarity=0.402 Sum_probs=31.7
Q ss_pred cceEEecCCCCCCCHHHHHHHHhccCccceEEeccC
Q 044301 35 RGICYLSRIPPHMDPVKLRQILSQYGEIQRIYLAPE 70 (154)
Q Consensus 35 ~GVIYlSrIPp~M~p~klR~llsqfGeI~RIyL~pE 70 (154)
--|+|+.-|-|--+-..|--|||.||.|-..-+.+.
T Consensus 239 eNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD 274 (479)
T KOG0415|consen 239 ENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRD 274 (479)
T ss_pred cceEEEEecCCcccccchhhHHhhcccceeeeEEec
Confidence 479999999999999999999999999987766654
No 92
>COG0106 HisA Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase [Amino acid transport and metabolism]
Probab=28.63 E-value=71 Score=27.66 Aligned_cols=31 Identities=19% Similarity=0.406 Sum_probs=27.3
Q ss_pred eEEecCCCCCCCHHHHHHHHhccCccceEEeccC
Q 044301 37 ICYLSRIPPHMDPVKLRQILSQYGEIQRIYLAPE 70 (154)
Q Consensus 37 VIYlSrIPp~M~p~klR~llsqfGeI~RIyL~pE 70 (154)
.|-|++++ ..+|..+++++..|| +||.+.-.
T Consensus 100 rViiGt~a-v~~p~~v~~~~~~~g--~rivv~lD 130 (241)
T COG0106 100 RVIIGTAA-VKNPDLVKELCEEYG--DRIVVALD 130 (241)
T ss_pred EEEEecce-ecCHHHHHHHHHHcC--CcEEEEEE
Confidence 35678888 799999999999999 99999865
No 93
>PF14581 SseB_C: SseB protein C-terminal domain
Probab=27.24 E-value=15 Score=26.34 Aligned_cols=22 Identities=23% Similarity=0.270 Sum_probs=18.4
Q ss_pred HHHHHHHHhccCccceEEeccC
Q 044301 49 PVKLRQILSQYGEIQRIYLAPE 70 (154)
Q Consensus 49 p~klR~llsqfGeI~RIyL~pE 70 (154)
...|.++|++++.|.+.||.--
T Consensus 21 ~~aL~~~~~~~~~V~~Ayl~~~ 42 (108)
T PF14581_consen 21 LAALSEYFKQHKNVRAAYLALM 42 (108)
T ss_pred HHHHHHHHhhCccHHHhHHHHh
Confidence 3578899999999999999753
No 94
>PF12949 HeH: HeH/LEM domain; PDB: 2OUT_A.
Probab=25.31 E-value=45 Score=20.82 Aligned_cols=17 Identities=29% Similarity=0.632 Sum_probs=13.5
Q ss_pred CCCCCHHHHHHHHhccC
Q 044301 44 PPHMDPVKLRQILSQYG 60 (154)
Q Consensus 44 Pp~M~p~klR~llsqfG 60 (154)
|.-|+..+||.+|..+|
T Consensus 1 p~sltV~~Lk~iL~~~~ 17 (35)
T PF12949_consen 1 PKSLTVAQLKRILDEHG 17 (35)
T ss_dssp STT--SHHHHHHHHHHT
T ss_pred CCcCcHHHHHHHHHHcC
Confidence 56789999999999998
No 95
>PF03467 Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120 Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons. Three 'up-frameshift' proteins, UPF1, UPF2 and UPF3, are essential for this process in organisms ranging from yeast, human to plants []. Exon junction complexes (EJCs) are deposited ~24 nucleotides upstream of exon-exon junctions after splicing. Translation causes displacement of the EJCs, however, premature translation termination upstream of one or more EJCs triggers the recruitment of UPF1, UPF2 and UPF3 and activates the NMD pathway [, ]. This family contains UPF3. The crystal structure of the complex between human UPF2 and UPF3b, which are, respectively, a MIF4G (middle portion of eIF4G) domain and an RNP domain (ribonucleoprotein-type RNA-binding domain) has been determined to 1.95A. The protein-protein interface is mediated by highly conserved charged residues in UPF2 and UPF3b and involves the beta-sheet surface of the UPF3b ribonucleoprotein (RNP) domain, which is generally used by these domains to bind nucleic acids. In UPF3b the RNP domain does not bind RNA, whereas the UPF2 construct and the complex do. It is clear that some RNP domains have evolved for specific protein-protein interactions rather than as nucleic acid binding modules [].; PDB: 1UW4_A 2L08_A.
Probab=24.68 E-value=18 Score=29.07 Aligned_cols=26 Identities=15% Similarity=0.364 Sum_probs=19.4
Q ss_pred eEEecCCCCCCCHHHHHHHHhc-cCcc
Q 044301 37 ICYLSRIPPHMDPVKLRQILSQ-YGEI 62 (154)
Q Consensus 37 VIYlSrIPp~M~p~klR~llsq-fGeI 62 (154)
=|-|-||||.|+...+...++. +++-
T Consensus 9 KvVIR~LPP~LteeeF~~~i~~~l~~~ 35 (176)
T PF03467_consen 9 KVVIRRLPPNLTEEEFWEQISPWLPDE 35 (176)
T ss_dssp EEEEEEE-TTS-HHHHCCCCSS--SSE
T ss_pred eEEEeCCCCCCCHHHHHHHhhhhcccc
Confidence 4678999999999999998887 6654
No 96
>KOG3089 consensus Predicted DEAD-box-containing helicase [General function prediction only]
Probab=23.37 E-value=89 Score=27.63 Aligned_cols=52 Identities=38% Similarity=0.564 Sum_probs=30.0
Q ss_pred cchhhhhhhhhhcccchhhhHHHHHHHhhc-CCcceEEecCCCCCCCHHHHHHHHhccCccceEEec
Q 044301 3 EGKQEELNEKNSKHSKSKKKQRLLEEAAKA-DQRGICYLSRIPPHMDPVKLRQILSQYGEIQRIYLA 68 (154)
Q Consensus 3 ~g~q~e~~~~~~k~~k~k~kk~l~k~~~k~-~k~GVIYlSrIPp~M~p~klR~llsqfGeI~RIyL~ 68 (154)
||+.+|-++..++.++. ++++|.+..++. ...|- |..|-.||..| |..+|+-
T Consensus 46 dgKkeeRk~~~~k~rkR-kk~Kl~e~~~~~~~~i~s-----------Pe~l~~ll~~y--i~s~~~d 98 (271)
T KOG3089|consen 46 DGKKEERKENTTKTRKR-KKKKLTEVLAKSEPKIGS-----------PEDLQKLLKDY--ISSRRLD 98 (271)
T ss_pred hhhHHHhhhhhhhHHHH-HHHHHHHHHhccCCCCCC-----------hHHHHHHHHHH--HHhhcCc
Confidence 56667777777775533 444444443322 33332 88898888877 4444443
No 97
>cd00080 HhH2_motif Helix-hairpin-helix class 2 (Pol1 family) motif. HhH2 domains are found in Rad2 family of prokaryotic and eukaryotic replication and repair nucleases, i.e., DNA polymerase I, Taq DNA polymerase, DNA repair protein Rad2 endonuclease, flap endonuclease, exonuclease I and IX, 5'-3' exonuclease and also bacteriophage Rnase H. These nucleases degrade RNA-DNA or DNA-DNA duplexes, or both and play essential roles in DNA duplication, repair, and recombination.
Probab=22.87 E-value=30 Score=23.98 Aligned_cols=33 Identities=15% Similarity=0.404 Sum_probs=27.2
Q ss_pred eEEecCCCCCCCHHHHHHHHhccCccceEEeccC
Q 044301 37 ICYLSRIPPHMDPVKLRQILSQYGEIQRIYLAPE 70 (154)
Q Consensus 37 VIYlSrIPp~M~p~klR~llsqfGeI~RIyL~pE 70 (154)
.=|+..|| +|.+..-..++.+||.+..|+-..+
T Consensus 21 ~D~i~gv~-giG~k~A~~ll~~~~~~~~~~~~~~ 53 (75)
T cd00080 21 SDNIPGVP-GIGPKTALKLLKEYGSLENLLENLD 53 (75)
T ss_pred cccCCCCC-cccHHHHHHHHHHhCCHHHHHHHHH
Confidence 55677775 5999999999999999998886554
No 98
>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes. Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.
Probab=22.61 E-value=86 Score=23.68 Aligned_cols=22 Identities=32% Similarity=0.688 Sum_probs=16.4
Q ss_pred eEEecCCCCCCCHHHHHHHHhc
Q 044301 37 ICYLSRIPPHMDPVKLRQILSQ 58 (154)
Q Consensus 37 VIYlSrIPp~M~p~klR~llsq 58 (154)
.+|++.||..-.+..|+.-|.|
T Consensus 4 ~L~V~NLP~~~d~~~I~~RL~q 25 (90)
T PF11608_consen 4 LLYVSNLPTNKDPSSIKNRLRQ 25 (90)
T ss_dssp EEEEES--TTS-HHHHHHHHHH
T ss_pred EEEEecCCCCCCHHHHHHHHHH
Confidence 6899999999999988877775
No 99
>PF06297 PET: PET Domain; InterPro: IPR010442 The PET domain is a ~110 amino acid motif in the N-terminal part of LIM domain proteins. The domain was described in Drosophila proteins involved in cell differentiation and is named after Prickle, Espinas and Testin. PET domain proteins contain about three zinc-binding LIM domains (see PDOC00382 from INTERPRO, IPR001781 from INTERPRO) and are found among metazoans. The PET domain has been suggested to play a role in protein-protein interactions with proteins involved in planar polarity signalling or organisation of the cytoskeleton []. Some proteins known to contain a PET domain: Mammalian testin protein (Q9UGI8 from SWISSPROT), which may function as a tumour suppressor. Mammalian LIM domain only protein 6 (LMO6/Prickle3, O43900 from SWISSPROT). Fruit fly prickle (A1Z6W3 from SWISSPROT) and espinas (Q9U1I1 from SWISSPROT) proteins encoded by the tissue polarity gene prickle (pk), involved in the control of orientation of bristles and hairs. Mammalian prickle-like proteins 1 (Q96MT3 from SWISSPROT) and 2 (Q7Z3G6 from SWISSPROT). ; GO: 0008270 zinc ion binding
Probab=21.73 E-value=77 Score=24.15 Aligned_cols=24 Identities=25% Similarity=0.368 Sum_probs=20.3
Q ss_pred EEecCCCCCCCHHHHHHHHhccCc
Q 044301 38 CYLSRIPPHMDPVKLRQILSQYGE 61 (154)
Q Consensus 38 IYlSrIPp~M~p~klR~llsqfGe 61 (154)
+=..=+||++++..+..||+...+
T Consensus 19 ~~Y~WvPpgl~~~~v~~Ym~~LP~ 42 (106)
T PF06297_consen 19 EEYAWVPPGLSPELVEQYMSCLPE 42 (106)
T ss_pred ceeeecCCCCChHHHHHHHHhCCC
Confidence 344569999999999999999875
No 100
>PF00276 Ribosomal_L23: Ribosomal protein L23; InterPro: IPR013025 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This domain is found in both eukaryotic L25 and prokaryotic and eukaryotic L23 proteins.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3DF4_T 3DF2_T 4A1E_R 4A1A_R 4A1C_R 4A17_R 2HGU_W 2HGQ_W 1N88_A 2HGJ_W ....
Probab=21.30 E-value=70 Score=23.08 Aligned_cols=33 Identities=12% Similarity=0.425 Sum_probs=26.1
Q ss_pred eEEecCCCCCCCHHHHHHHHhc-cC-ccceEEecc
Q 044301 37 ICYLSRIPPHMDPVKLRQILSQ-YG-EIQRIYLAP 69 (154)
Q Consensus 37 VIYlSrIPp~M~p~klR~llsq-fG-eI~RIyL~p 69 (154)
-.|-..+|+.|+-..|+++|.+ || .|..|.-..
T Consensus 21 n~~tF~V~~~atK~~Ik~aie~iy~V~V~~Vnt~~ 55 (91)
T PF00276_consen 21 NQYTFEVDPRATKTEIKEAIEKIYGVKVKKVNTMN 55 (91)
T ss_dssp SEEEEEETTTSTHHHHHHHHHHHHTSEEEEEEEEE
T ss_pred CEEEEEEeCCCCHHHHHHHHHhhcCCCeeEEEEeE
Confidence 3789999999999999999999 77 344444443
No 101
>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]
Probab=20.42 E-value=68 Score=30.50 Aligned_cols=35 Identities=11% Similarity=0.424 Sum_probs=31.3
Q ss_pred eEEecCCCCCCCHHHHHHHHhccCccceEEeccCC
Q 044301 37 ICYLSRIPPHMDPVKLRQILSQYGEIQRIYLAPED 71 (154)
Q Consensus 37 VIYlSrIPp~M~p~klR~llsqfGeI~RIyL~pEd 71 (154)
=||+|-||-+++...++++++-||.+.-.-|....
T Consensus 291 ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~ 325 (500)
T KOG0120|consen 291 KIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDS 325 (500)
T ss_pred hhhhccCcCccCHHHHHHHHHhcccchhheeeccc
Confidence 48999999999999999999999999888887653
No 102
>PF04355 SmpA_OmlA: SmpA / OmlA family; InterPro: IPR007450 This is a bacterial outer membrane lipoprotein, possibly involved in maintaining the structural integrity of the cell envelope []. The lipid attachment site is a conserved N-terminal cysteine residue sometimes found adjacent to the OmpA domain (IPR006665 from INTERPRO).; GO: 0019867 outer membrane; PDB: 4DM5_C 2PXG_A 2YH9_B 2KXX_A 2KM7_A.
Probab=20.16 E-value=70 Score=21.21 Aligned_cols=19 Identities=32% Similarity=0.565 Sum_probs=16.1
Q ss_pred ecCCCCCCCHHHHHHHHhc
Q 044301 40 LSRIPPHMDPVKLRQILSQ 58 (154)
Q Consensus 40 lSrIPp~M~p~klR~llsq 58 (154)
|+.|-++|+..+++++|..
T Consensus 9 ~~~i~~GmTk~qV~~lLG~ 27 (71)
T PF04355_consen 9 LAQIKPGMTKDQVRALLGS 27 (71)
T ss_dssp HTTT-TTSBHHHHHHHHTS
T ss_pred HHhhcCCCCHHHHHHhcCC
Confidence 5688999999999999976
No 103
>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]
Probab=20.00 E-value=70 Score=31.90 Aligned_cols=33 Identities=15% Similarity=0.355 Sum_probs=27.0
Q ss_pred cceEEecCCCCCCCHHHHHHHHhccCccceEEe
Q 044301 35 RGICYLSRIPPHMDPVKLRQILSQYGEIQRIYL 67 (154)
Q Consensus 35 ~GVIYlSrIPp~M~p~klR~llsqfGeI~RIyL 67 (154)
.-.+++|-|.-.-..+.|+.|||+||.|--.-+
T Consensus 405 gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKV 437 (940)
T KOG4661|consen 405 GRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKV 437 (940)
T ss_pred ccceeeeccccchhhhHHHHHHHHhcceeceee
Confidence 346889999999999999999999998754433
Done!