Query 009405
Match_columns 535
No_of_seqs 20 out of 22
Neff 2.6
Searched_HMMs 46136
Date Thu Mar 28 12:43:13 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009405.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009405hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00076 RRM_1: RNA recognitio 98.7 3E-08 6.4E-13 73.6 5.6 69 373-447 1-69 (70)
2 PLN03134 glycine-rich RNA-bind 98.2 5.6E-06 1.2E-10 74.5 8.4 96 358-458 22-117 (144)
3 smart00362 RRM_2 RNA recogniti 98.0 3.2E-05 6.9E-10 55.4 7.6 70 373-449 2-71 (72)
4 cd00590 RRM RRM (RNA recogniti 97.9 7.1E-05 1.5E-09 53.9 7.7 72 373-450 2-73 (74)
5 TIGR01659 sex-lethal sex-letha 97.8 9.2E-05 2E-09 75.4 8.8 108 368-484 105-214 (346)
6 TIGR01661 ELAV_HUD_SF ELAV/HuD 97.7 0.00016 3.5E-09 70.0 8.4 82 368-454 267-348 (352)
7 smart00360 RRM RNA recognition 97.7 0.00022 4.8E-09 50.7 6.9 70 375-449 1-70 (71)
8 TIGR01628 PABP-1234 polyadenyl 97.6 0.00015 3.2E-09 75.9 8.2 81 367-453 282-362 (562)
9 TIGR01661 ELAV_HUD_SF ELAV/HuD 97.6 0.00022 4.9E-09 69.0 8.2 94 370-468 3-98 (352)
10 TIGR01642 U2AF_lg U2 snRNP aux 97.6 0.00023 5.1E-09 72.6 8.1 82 365-451 170-256 (509)
11 TIGR01642 U2AF_lg U2 snRNP aux 97.4 0.00068 1.5E-08 69.3 8.9 82 367-453 292-373 (509)
12 PF14259 RRM_6: RNA recognitio 97.4 0.00028 6E-09 53.7 4.5 69 373-447 1-69 (70)
13 TIGR01659 sex-lethal sex-letha 97.2 0.00099 2.2E-08 68.1 8.3 81 370-453 193-273 (346)
14 TIGR01628 PABP-1234 polyadenyl 97.2 0.00073 1.6E-08 70.8 7.4 74 372-450 2-75 (562)
15 TIGR01622 SF-CC1 splicing fact 97.2 0.00092 2E-08 67.6 7.7 79 365-449 84-162 (457)
16 TIGR01648 hnRNP-R-Q heterogene 97.2 0.0013 2.8E-08 71.8 9.3 107 367-482 55-161 (578)
17 TIGR01648 hnRNP-R-Q heterogene 97.2 0.00097 2.1E-08 72.8 8.1 77 368-457 231-309 (578)
18 TIGR01622 SF-CC1 splicing fact 97.1 0.0011 2.4E-08 66.9 7.4 79 370-453 186-264 (457)
19 TIGR01645 half-pint poly-U bin 97.1 0.0014 3.1E-08 72.1 8.1 82 368-454 202-283 (612)
20 smart00361 RRM_1 RNA recogniti 97.1 0.0012 2.6E-08 51.9 5.4 45 403-450 26-70 (70)
21 TIGR01649 hnRNP-L_PTB hnRNP-L/ 97.0 0.0014 3.1E-08 68.4 7.2 74 371-453 3-76 (481)
22 PLN03120 nucleic acid binding 97.0 0.0034 7.3E-08 63.2 8.6 76 369-453 3-78 (260)
23 TIGR01645 half-pint poly-U bin 96.9 0.0024 5.2E-08 70.3 8.0 83 363-450 100-182 (612)
24 TIGR01649 hnRNP-L_PTB hnRNP-L/ 96.9 0.0028 6.1E-08 66.3 7.9 76 367-452 272-348 (481)
25 COG0724 RNA-binding proteins ( 96.8 0.007 1.5E-07 52.3 8.0 80 370-454 115-194 (306)
26 KOG0533 RRM motif-containing p 96.6 0.005 1.1E-07 61.3 6.8 75 367-447 79-154 (243)
27 KOG0131 Splicing factor 3b, su 96.3 0.0074 1.6E-07 59.0 5.6 95 368-469 7-106 (203)
28 KOG0117 Heterogeneous nuclear 96.3 0.018 3.8E-07 62.2 8.8 107 368-482 81-187 (506)
29 PLN03121 nucleic acid binding 96.1 0.019 4.1E-07 57.6 7.8 76 368-452 3-78 (243)
30 PF13893 RRM_5: RNA recognitio 96.0 0.012 2.5E-07 44.0 4.4 34 414-450 21-54 (56)
31 KOG0110 RNA-binding protein (R 95.7 0.029 6.2E-07 63.0 7.7 118 373-499 518-653 (725)
32 KOG0148 Apoptosis-promoting RN 95.4 0.051 1.1E-06 56.0 7.6 88 355-456 149-239 (321)
33 KOG0123 Polyadenylate-binding 95.2 0.038 8.3E-07 57.4 6.1 72 373-452 79-150 (369)
34 KOG0123 Polyadenylate-binding 94.6 0.05 1.1E-06 56.6 5.1 89 358-452 257-346 (369)
35 PLN03213 repressor of silencin 93.9 0.24 5.2E-06 54.7 8.7 79 368-455 8-88 (759)
36 KOG0107 Alternative splicing f 93.5 0.15 3.2E-06 50.0 5.7 76 369-453 9-93 (195)
37 KOG0114 Predicted RNA-binding 93.1 0.31 6.7E-06 44.8 6.8 74 367-448 15-88 (124)
38 KOG1548 Transcription elongati 92.0 0.26 5.6E-06 52.2 5.5 78 370-453 265-350 (382)
39 KOG0127 Nucleolar protein fibr 91.7 0.51 1.1E-05 52.6 7.6 89 363-454 285-377 (678)
40 PF04059 RRM_2: RNA recognitio 91.6 0.6 1.3E-05 41.0 6.5 69 371-439 2-70 (97)
41 KOG0131 Splicing factor 3b, su 91.2 0.36 7.7E-06 47.6 5.2 88 370-469 96-187 (203)
42 KOG0148 Apoptosis-promoting RN 91.2 0.41 9E-06 49.6 5.9 83 396-486 87-187 (321)
43 KOG4209 Splicing factor RNPS1, 90.6 0.37 8E-06 47.6 4.7 82 369-459 100-184 (231)
44 KOG0108 mRNA cleavage and poly 90.3 0.51 1.1E-05 50.7 5.8 76 371-451 19-94 (435)
45 KOG4212 RNA-binding protein hn 89.4 0.9 1.9E-05 49.8 6.8 72 371-449 45-118 (608)
46 KOG0153 Predicted RNA-binding 89.2 0.58 1.3E-05 49.6 5.1 70 369-448 227-296 (377)
47 PF11608 Limkain-b1: Limkain b 88.7 1.5 3.3E-05 38.8 6.5 71 371-451 3-73 (90)
48 KOG4207 Predicted splicing fac 88.5 1.6 3.4E-05 44.2 7.3 86 367-457 10-98 (256)
49 KOG0121 Nuclear cap-binding pr 88.3 1.8 3.9E-05 41.2 7.1 94 348-450 16-111 (153)
50 KOG0117 Heterogeneous nuclear 85.4 1.8 3.9E-05 47.4 6.2 80 366-459 255-335 (506)
51 PF08777 RRM_3: RNA binding mo 83.9 1.6 3.6E-05 38.1 4.3 60 370-437 1-60 (105)
52 KOG4206 Spliceosomal protein s 82.3 3 6.5E-05 41.9 5.9 64 372-437 11-75 (221)
53 KOG0122 Translation initiation 82.0 2.9 6.2E-05 43.0 5.7 63 372-437 191-254 (270)
54 PF03467 Smg4_UPF3: Smg-4/UPF3 81.0 0.97 2.1E-05 42.7 1.9 71 367-437 4-78 (176)
55 KOG0120 Splicing factor U2AF, 80.8 4.2 9.1E-05 44.9 6.9 65 384-452 416-489 (500)
56 KOG0147 Transcriptional coacti 78.2 1.2 2.6E-05 49.4 1.8 98 351-452 403-525 (549)
57 KOG0127 Nucleolar protein fibr 77.8 7.6 0.00016 43.9 7.7 79 372-456 119-197 (678)
58 COG5175 MOT2 Transcriptional r 77.0 4.6 0.0001 43.4 5.6 81 369-453 113-201 (480)
59 KOG0130 RNA-binding protein RB 75.1 4.6 0.0001 38.9 4.6 73 369-448 71-145 (170)
60 KOG0149 Predicted RNA-binding 74.5 5.5 0.00012 40.6 5.2 94 389-487 28-132 (247)
61 KOG0124 Polypyrimidine tract-b 69.2 6.9 0.00015 42.5 4.7 70 371-448 114-186 (544)
62 PF08075 NOPS: NOPS (NUC059) d 68.9 1.4 3E-05 35.7 -0.3 20 485-504 33-52 (52)
63 KOG0111 Cyclophilin-type pepti 65.5 15 0.00032 37.9 5.9 83 369-459 9-94 (298)
64 KOG0144 RNA-binding protein CU 64.6 11 0.00023 41.6 5.1 86 373-462 127-213 (510)
65 KOG0110 RNA-binding protein (R 62.3 6.7 0.00015 44.9 3.2 74 370-448 613-686 (725)
66 KOG0105 Alternative splicing f 61.6 11 0.00024 38.0 4.2 61 370-435 6-66 (241)
67 PF02617 ClpS: ATP-dependent C 60.1 1.8 3.9E-05 35.8 -1.2 74 373-451 9-82 (82)
68 KOG4211 Splicing factor hnRNP- 59.1 17 0.00036 40.5 5.4 67 369-437 102-168 (510)
69 KOG2202 U2 snRNP splicing fact 59.0 5.7 0.00012 40.8 1.8 46 411-459 107-152 (260)
70 KOG4208 Nucleolar RNA-binding 53.4 27 0.00059 35.2 5.4 83 367-453 46-128 (214)
71 KOG4206 Spliceosomal protein s 50.0 30 0.00065 35.0 5.1 63 367-438 143-207 (221)
72 KOG0106 Alternative splicing f 48.9 8.5 0.00019 38.4 1.2 78 359-449 88-165 (216)
73 KOG0106 Alternative splicing f 48.5 30 0.00065 34.7 4.8 59 371-439 2-60 (216)
74 KOG0144 RNA-binding protein CU 47.2 30 0.00065 38.4 4.9 75 339-439 23-101 (510)
75 KOG0147 Transcriptional coacti 43.9 62 0.0013 36.6 6.8 117 373-494 281-407 (549)
76 PF14605 Nup35_RRM_2: Nup53/35 40.3 48 0.001 25.8 3.9 45 382-431 9-53 (53)
77 KOG0145 RNA-binding protein EL 40.2 99 0.0021 32.8 7.2 77 369-453 277-356 (360)
78 PRK00033 clpS ATP-dependent Cl 38.7 37 0.0008 30.3 3.4 68 373-451 30-97 (100)
79 KOG0120 Splicing factor U2AF, 38.3 35 0.00077 38.0 3.9 77 369-452 288-366 (500)
80 KOG0145 RNA-binding protein EL 37.2 57 0.0012 34.6 5.0 65 370-436 127-191 (360)
81 KOG4211 Splicing factor hnRNP- 33.0 83 0.0018 35.3 5.6 61 369-434 9-69 (510)
82 PF12133 Sars6: Open reading f 28.8 32 0.00069 28.7 1.3 38 2-39 1-49 (62)
83 KOG4660 Protein Mei2, essentia 24.3 1.3E+02 0.0028 34.2 5.3 64 366-437 72-135 (549)
84 PRK04326 methionine synthase; 24.2 95 0.0021 31.2 4.0 69 362-438 245-319 (330)
85 PF09673 TrbC_Ftype: Type-F co 22.3 3.8E+02 0.0083 23.8 6.9 92 360-471 14-107 (113)
86 PF13041 PPR_2: PPR repeat fam 21.9 66 0.0014 23.5 1.8 31 492-522 1-31 (50)
No 1
>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=98.70 E-value=3e-08 Score=73.60 Aligned_cols=69 Identities=28% Similarity=0.375 Sum_probs=62.9
Q ss_pred EEEecCCCCCCchhHHHHHHHHhhccceeeeccCCCCCCCCCceeEEEeechHHHHHHHhhhccceeeeeCCcee
Q 009405 373 VVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPL 447 (535)
Q Consensus 373 VlLqNLDPs~tS~eVEDli~~afke~C~AKmI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~egCL~ls~GRPL 447 (535)
|||.||+|.+|..||.+++.+ ++.-+.+++++. .+....|.|||.|.+.+.|+.|+..|++..+ +||+|
T Consensus 1 l~v~nlp~~~t~~~l~~~f~~-~g~i~~~~~~~~--~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~---~~~~i 69 (70)
T PF00076_consen 1 LYVGNLPPDVTEEELRDFFSQ-FGKIESIKVMRN--SSGKSKGYAFVEFESEEDAEKALEELNGKKI---NGRKI 69 (70)
T ss_dssp EEEESETTTSSHHHHHHHHHT-TSTEEEEEEEEE--TTSSEEEEEEEEESSHHHHHHHHHHHTTEEE---TTEEE
T ss_pred cEEcCCCCcCCHHHHHHHHHH-hhhccccccccc--ccccccceEEEEEcCHHHHHHHHHHcCCCEE---CccCc
Confidence 799999999999999999999 677788888887 6688899999999999999999999999766 88886
No 2
>PLN03134 glycine-rich RNA-binding protein 4; Provisional
Probab=98.21 E-value=5.6e-06 Score=74.46 Aligned_cols=96 Identities=18% Similarity=0.158 Sum_probs=73.3
Q ss_pred ChHHHHHhhhhcccEEEEecCCCCCCchhHHHHHHHHhhccceeeeccCCCCCCCCCceeEEEeechHHHHHHHhhhccc
Q 009405 358 PWEERIRVAHEHGTLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEG 437 (535)
Q Consensus 358 PWeerl~~A~E~GrlVlLqNLDPs~tS~eVEDli~~afke~C~AKmI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~eg 437 (535)
|-....-.+-.-++-||+.||++..|..||.+++.+ |..-..+++ +....+..+-|.|||.|.+.++|+.||..|+..
T Consensus 22 ~~~~~~~~~~~~~~~lfVgnL~~~~te~~L~~~F~~-~G~I~~v~i-~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~ 99 (144)
T PLN03134 22 PVTSMLGSLRLMSTKLFIGGLSWGTDDASLRDAFAH-FGDVVDAKV-IVDRETGRSRGFGFVNFNDEGAATAAISEMDGK 99 (144)
T ss_pred ccccccccccCCCCEEEEeCCCCCCCHHHHHHHHhc-CCCeEEEEE-EecCCCCCcceEEEEEECCHHHHHHHHHHcCCC
Confidence 444444445567889999999999999999999876 444444444 334445667899999999999999999999977
Q ss_pred eeeeeCCceeeeccCCcCCCC
Q 009405 438 CLLLSNGRPLLGSIGTPCFTG 458 (535)
Q Consensus 438 CL~ls~GRPL~~S~g~~~~p~ 458 (535)
-| +||+|.........+.
T Consensus 100 ~i---~Gr~l~V~~a~~~~~~ 117 (144)
T PLN03134 100 EL---NGRHIRVNPANDRPSA 117 (144)
T ss_pred EE---CCEEEEEEeCCcCCCC
Confidence 55 9999998877654443
No 3
>smart00362 RRM_2 RNA recognition motif.
Probab=98.02 E-value=3.2e-05 Score=55.45 Aligned_cols=70 Identities=30% Similarity=0.357 Sum_probs=55.6
Q ss_pred EEEecCCCCCCchhHHHHHHHHhhccceeeeccCCCCCCCCCceeEEEeechHHHHHHHhhhccceeeeeCCceeee
Q 009405 373 VVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPLLG 449 (535)
Q Consensus 373 VlLqNLDPs~tS~eVEDli~~afke~C~AKmI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~egCL~ls~GRPL~~ 449 (535)
|+|.||.+.++..||.+++.. ++.-...+++... ..+.|.|||.|.+.++|+.|+..++..= + +|+++..
T Consensus 2 v~i~~l~~~~~~~~l~~~~~~-~g~v~~~~~~~~~---~~~~~~~~v~f~~~~~a~~a~~~~~~~~--~-~~~~i~v 71 (72)
T smart00362 2 LFVGNLPPDVTEEDLKELFSK-FGPIESVKIPKDT---GKSKGFAFVEFESEEDAEKAIEALNGTK--L-GGRPLRV 71 (72)
T ss_pred EEEcCCCCcCCHHHHHHHHHh-cCCEEEEEEecCC---CCCCceEEEEeCCHHHHHHHHHHhCCcE--E-CCEEEee
Confidence 789999999999999998875 3344455555444 5678999999999999999999999742 3 7888753
No 4
>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=97.90 E-value=7.1e-05 Score=53.90 Aligned_cols=72 Identities=26% Similarity=0.300 Sum_probs=58.0
Q ss_pred EEEecCCCCCCchhHHHHHHHHhhccceeeeccCCCCCCCCCceeEEEeechHHHHHHHhhhccceeeeeCCceeeec
Q 009405 373 VVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPLLGS 450 (535)
Q Consensus 373 VlLqNLDPs~tS~eVEDli~~afke~C~AKmI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~egCL~ls~GRPL~~S 450 (535)
|+|.||++..+.+||.+++... ..-+...|...... ...|.|||-|.|.++|..|+..++..-+ +|+++..+
T Consensus 2 i~i~~l~~~~~~~~i~~~~~~~-g~i~~~~~~~~~~~--~~~~~~~v~f~s~~~a~~a~~~~~~~~~---~~~~~~v~ 73 (74)
T cd00590 2 LFVGNLPPDVTEEDLRELFSKF-GKVESVRIVRDKDT--KSKGFAFVEFEDEEDAEKALEALNGKEL---GGRPLRVE 73 (74)
T ss_pred EEEeCCCCccCHHHHHHHHHhc-CCEEEEEEeeCCCC--CcceEEEEEECCHHHHHHHHHHhCCCeE---CCeEEEEe
Confidence 7899999999999999999874 55566666654333 4589999999999999999999988753 78887643
No 5
>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=97.77 E-value=9.2e-05 Score=75.44 Aligned_cols=108 Identities=15% Similarity=0.158 Sum_probs=79.2
Q ss_pred hcccEEEEecCCCCCCchhHHHHHHHHhhccceeeeccCCCCCCCCCceeEEEeechHHHHHHHhhhccceeeeeCCcee
Q 009405 368 EHGTLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPL 447 (535)
Q Consensus 368 E~GrlVlLqNLDPs~tS~eVEDli~~afke~C~AKmI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~egCL~ls~GRPL 447 (535)
..+|.|++.||.+..|..||.+++... .+-..++++. ...+..+-|.|||-|.+.+.|+.||..|+..-| .||||
T Consensus 105 ~~~~~LfVgnLp~~~te~~L~~lF~~~-G~V~~v~i~~-d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l---~gr~i 179 (346)
T TIGR01659 105 NSGTNLIVNYLPQDMTDRELYALFRTI-GPINTCRIMR-DYKTGYSFGYAFVDFGSEADSQRAIKNLNGITV---RNKRL 179 (346)
T ss_pred CCCcEEEEeCCCCCCCHHHHHHHHHhc-CCEEEEEEEe-cCCCCccCcEEEEEEccHHHHHHHHHHcCCCcc---CCcee
Confidence 367999999999999999999999874 4455666653 333456679999999999999999999998655 89999
Q ss_pred eeccCCcCC--CCCCCccccceehhhHHHHHHHHHHhhh
Q 009405 448 LGSIGTPCF--TGKQSKFVGHLALDKLKFQMQREMREAV 484 (535)
Q Consensus 448 ~~S~g~~~~--p~k~s~f~GHl~i~k~r~q~qrEmr~AV 484 (535)
..+...+.. ......|+|.|.-+- ..+++|+..
T Consensus 180 ~V~~a~p~~~~~~~~~lfV~nLp~~v----tee~L~~~F 214 (346)
T TIGR01659 180 KVSYARPGGESIKDTNLYVTNLPRTI----TDDQLDTIF 214 (346)
T ss_pred eeecccccccccccceeEEeCCCCcc----cHHHHHHHH
Confidence 987765432 223345777665442 335555544
No 6
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor. These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
Probab=97.67 E-value=0.00016 Score=70.00 Aligned_cols=82 Identities=24% Similarity=0.232 Sum_probs=67.4
Q ss_pred hcccEEEEecCCCCCCchhHHHHHHHHhhccceeeeccCCCCCCCCCceeEEEeechHHHHHHHhhhccceeeeeCCcee
Q 009405 368 EHGTLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPL 447 (535)
Q Consensus 368 E~GrlVlLqNLDPs~tS~eVEDli~~afke~C~AKmI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~egCL~ls~GRPL 447 (535)
..|..|++.||.+..+..+|.+++.. |+.--.++++. ...+...-|.|||-|.+.+.|..||..|+...| +||+|
T Consensus 267 ~~~~~lfV~NL~~~~~e~~L~~~F~~-fG~v~~v~i~~-d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~---~gr~i 341 (352)
T TIGR01661 267 GAGYCIFVYNLSPDTDETVLWQLFGP-FGAVQNVKIIR-DLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTL---GNRVL 341 (352)
T ss_pred CCCcEEEEeCCCCCCCHHHHHHHHHh-CCCeEEEEEeE-cCCCCCccceEEEEECCHHHHHHHHHHhCCCEE---CCeEE
Confidence 56778999999999999998888864 55555677653 444567789999999999999999999999876 99999
Q ss_pred eeccCCc
Q 009405 448 LGSIGTP 454 (535)
Q Consensus 448 ~~S~g~~ 454 (535)
.-++.+.
T Consensus 342 ~V~~~~~ 348 (352)
T TIGR01661 342 QVSFKTN 348 (352)
T ss_pred EEEEccC
Confidence 8776654
No 7
>smart00360 RRM RNA recognition motif.
Probab=97.66 E-value=0.00022 Score=50.72 Aligned_cols=70 Identities=29% Similarity=0.356 Sum_probs=52.3
Q ss_pred EecCCCCCCchhHHHHHHHHhhccceeeeccCCCCCCCCCceeEEEeechHHHHHHHhhhccceeeeeCCceeee
Q 009405 375 LENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPLLG 449 (535)
Q Consensus 375 LqNLDPs~tS~eVEDli~~afke~C~AKmI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~egCL~ls~GRPL~~ 449 (535)
|.||++.++..||.+++.. ++.-...++++. .....+.|.|||.|.|.+.|+.|+..|+. +. + +|++|..
T Consensus 1 i~~l~~~~~~~~l~~~f~~-~g~v~~~~i~~~-~~~~~~~~~a~v~f~~~~~a~~a~~~~~~-~~-~-~~~~~~v 70 (71)
T smart00360 1 VGNLPPDVTEEELRELFSK-FGKIESVRLVRD-KDTGKSKGFAFVEFESEEDAEKALEALNG-KE-L-DGRPLKV 70 (71)
T ss_pred CCCCCcccCHHHHHHHHHh-hCCEeEEEEEeC-CCCCCCCceEEEEeCCHHHHHHHHHHcCC-Ce-e-CCcEEEe
Confidence 5789999999999998875 333334444443 33567789999999999999999999994 33 2 7888753
No 8
>TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.
Probab=97.64 E-value=0.00015 Score=75.89 Aligned_cols=81 Identities=27% Similarity=0.342 Sum_probs=68.2
Q ss_pred hhcccEEEEecCCCCCCchhHHHHHHHHhhccceeeeccCCCCCCCCCceeEEEeechHHHHHHHhhhccceeeeeCCce
Q 009405 367 HEHGTLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRP 446 (535)
Q Consensus 367 ~E~GrlVlLqNLDPs~tS~eVEDli~~afke~C~AKmI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~egCL~ls~GRP 446 (535)
..+++-||+.||++..|..+|.+++.. |++-+.++++.. ......|.|||.|.|.+.|..||..|+..-+ +|||
T Consensus 282 ~~~~~~l~V~nl~~~~~~~~L~~~F~~-~G~i~~~~i~~d--~~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~---~gk~ 355 (562)
T TIGR01628 282 KAQGVNLYVKNLDDTVTDEKLRELFSE-CGEITSAKVMLD--EKGVSRGFGFVCFSNPEEANRAVTEMHGRML---GGKP 355 (562)
T ss_pred ccCCCEEEEeCCCCccCHHHHHHHHHh-cCCeEEEEEEEC--CCCCcCCeEEEEeCCHHHHHHHHHHhcCCee---CCce
Confidence 446788999999999999999998875 677778887766 3466789999999999999999999999644 9999
Q ss_pred eeeccCC
Q 009405 447 LLGSIGT 453 (535)
Q Consensus 447 L~~S~g~ 453 (535)
|+...+.
T Consensus 356 l~V~~a~ 362 (562)
T TIGR01628 356 LYVALAQ 362 (562)
T ss_pred eEEEecc
Confidence 9876654
No 9
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor. These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
Probab=97.59 E-value=0.00022 Score=69.03 Aligned_cols=94 Identities=21% Similarity=0.231 Sum_probs=72.0
Q ss_pred ccEEEEecCCCCCCchhHHHHHHHHhhccceeeeccCCCCCCCCCceeEEEeechHHHHHHHhhhccceeeeeCCceeee
Q 009405 370 GTLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPLLG 449 (535)
Q Consensus 370 GrlVlLqNLDPs~tS~eVEDli~~afke~C~AKmI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~egCL~ls~GRPL~~ 449 (535)
-+-|++.||.+.+|-.||++++.. |++-..++++.- ..+..+-|.|||-|.+.+.|+.||..|+...| .||+|.-
T Consensus 3 ~~~l~V~nLp~~~~e~~l~~~F~~-~G~i~~v~i~~d-~~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~l---~g~~i~v 77 (352)
T TIGR01661 3 KTNLIVNYLPQTMTQEEIRSLFTS-IGEIESCKLVRD-KVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRL---QNKTIKV 77 (352)
T ss_pred CcEEEEeCCCCCCCHHHHHHHHHc-cCCEEEEEEEEc-CCCCccceEEEEEECcHHHHHHHHhhcccEEE---CCeeEEE
Confidence 467999999999999999999988 556666776542 33466789999999999999999999999766 8999987
Q ss_pred ccCCcCCC--CCCCcccccee
Q 009405 450 SIGTPCFT--GKQSKFVGHLA 468 (535)
Q Consensus 450 S~g~~~~p--~k~s~f~GHl~ 468 (535)
..+.|... ....-|+|+|.
T Consensus 78 ~~a~~~~~~~~~~~l~v~~l~ 98 (352)
T TIGR01661 78 SYARPSSDSIKGANLYVSGLP 98 (352)
T ss_pred EeecccccccccceEEECCcc
Confidence 66655432 22345555553
No 10
>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor. Members of this subfamily are found in plants, metazoa and fungi.
Probab=97.55 E-value=0.00023 Score=72.57 Aligned_cols=82 Identities=16% Similarity=0.142 Sum_probs=62.2
Q ss_pred hhhhcccEEEEecCCCCCCchhHHHHHHHHhhccceee-----eccCCCCCCCCCceeEEEeechHHHHHHHhhhcccee
Q 009405 365 VAHEHGTLVVLENLDPSYTSTVVEDLVWHAFKENCSAK-----MIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCL 439 (535)
Q Consensus 365 ~A~E~GrlVlLqNLDPs~tS~eVEDli~~afke~C~AK-----mI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~egCL 439 (535)
.+..+.|-||+.||++..|..||.+++.+.|...+-.. .|...-+ ...-|.|||.|.|.+.|..|| .|++--
T Consensus 170 ~~~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~-~~~kg~afVeF~~~e~A~~Al-~l~g~~- 246 (509)
T TIGR01642 170 QATRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNI-NKEKNFAFLEFRTVEEATFAM-ALDSII- 246 (509)
T ss_pred cCCccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEE-CCCCCEEEEEeCCHHHHhhhh-cCCCeE-
Confidence 56777899999999999999999999998766543221 2222222 456789999999999999999 588753
Q ss_pred eeeCCceeeecc
Q 009405 440 LLSNGRPLLGSI 451 (535)
Q Consensus 440 ~ls~GRPL~~S~ 451 (535)
+ +|+||.-..
T Consensus 247 -~-~g~~l~v~r 256 (509)
T TIGR01642 247 -Y-SNVFLKIRR 256 (509)
T ss_pred -e-eCceeEecC
Confidence 3 789987543
No 11
>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor. Members of this subfamily are found in plants, metazoa and fungi.
Probab=97.39 E-value=0.00068 Score=69.28 Aligned_cols=82 Identities=13% Similarity=0.143 Sum_probs=66.2
Q ss_pred hhcccEEEEecCCCCCCchhHHHHHHHHhhccceeeeccCCCCCCCCCceeEEEeechHHHHHHHhhhccceeeeeCCce
Q 009405 367 HEHGTLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRP 446 (535)
Q Consensus 367 ~E~GrlVlLqNLDPs~tS~eVEDli~~afke~C~AKmI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~egCL~ls~GRP 446 (535)
.+.++-|||.||.+..|..+|.+++.. |+.-..++++ ....+..+.|.|||.|.+.++|+.||..|+.-.| +|++
T Consensus 292 ~~~~~~l~v~nlp~~~~~~~l~~~f~~-~G~i~~~~~~-~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~---~~~~ 366 (509)
T TIGR01642 292 LDSKDRIYIGNLPLYLGEDQIKELLES-FGDLKAFNLI-KDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDT---GDNK 366 (509)
T ss_pred CCCCCEEEEeCCCCCCCHHHHHHHHHh-cCCeeEEEEE-ecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEE---CCeE
Confidence 456789999999999999999999876 4544444444 3344577889999999999999999999998866 8999
Q ss_pred eeeccCC
Q 009405 447 LLGSIGT 453 (535)
Q Consensus 447 L~~S~g~ 453 (535)
|....+.
T Consensus 367 l~v~~a~ 373 (509)
T TIGR01642 367 LHVQRAC 373 (509)
T ss_pred EEEEECc
Confidence 9876653
No 12
>PF14259 RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....
Probab=97.37 E-value=0.00028 Score=53.74 Aligned_cols=69 Identities=25% Similarity=0.274 Sum_probs=48.4
Q ss_pred EEEecCCCCCCchhHHHHHHHHhhccceeeeccCCCCCCCCCceeEEEeechHHHHHHHhhhccceeeeeCCcee
Q 009405 373 VVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPL 447 (535)
Q Consensus 373 VlLqNLDPs~tS~eVEDli~~afke~C~AKmI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~egCL~ls~GRPL 447 (535)
|+|.||.|+.+.+||.+++.... .-=..+|+.... ....|.|||-|.|.+.|..|+..++.-.+ +||.|
T Consensus 1 v~i~nlp~~~~~~~l~~~f~~~g-~v~~v~~~~~~~--~~~~~~a~v~f~~~~~a~~al~~~~~~~~---~g~~l 69 (70)
T PF14259_consen 1 VYISNLPPSTTEEDLRNFFSRFG-PVEKVRLIKNKD--GQSRGFAFVEFSSEEDAKRALELLNGKEI---DGRKL 69 (70)
T ss_dssp EEEESSTTT--HHHHHHHCTTSS-BEEEEEEEESTT--SSEEEEEEEEESSHHHHHHHHHHHTTEEE---TTEEE
T ss_pred CEEeCCCCCCCHHHHHHHHHhcC-CcceEEEEeeec--cccCCEEEEEeCCHHHHHHHHHHCCCcEE---CCEEc
Confidence 78999999988877777655432 112344443322 34579999999999999999999985544 88876
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=97.24 E-value=0.00099 Score=68.07 Aligned_cols=81 Identities=19% Similarity=0.267 Sum_probs=59.5
Q ss_pred ccEEEEecCCCCCCchhHHHHHHHHhhccceeeeccCCCCCCCCCceeEEEeechHHHHHHHhhhccceeeeeCCceeee
Q 009405 370 GTLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPLLG 449 (535)
Q Consensus 370 GrlVlLqNLDPs~tS~eVEDli~~afke~C~AKmI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~egCL~ls~GRPL~~ 449 (535)
.+-|+|.||++..|..||.+++.. |.+-..++++ +...+.-.-|.|||.|.+.+.|+.||..|+...+ --.++||..
T Consensus 193 ~~~lfV~nLp~~vtee~L~~~F~~-fG~V~~v~i~-~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~-~g~~~~l~V 269 (346)
T TIGR01659 193 DTNLYVTNLPRTITDDQLDTIFGK-YGQIVQKNIL-RDKLTGTPRGVAFVRFNKREEAQEAISALNNVIP-EGGSQPLTV 269 (346)
T ss_pred cceeEEeCCCCcccHHHHHHHHHh-cCCEEEEEEe-ecCCCCccceEEEEEECCHHHHHHHHHHhCCCcc-CCCceeEEE
Confidence 456999999999999999988854 3444455554 3333344458999999999999999999998755 213478876
Q ss_pred ccCC
Q 009405 450 SIGT 453 (535)
Q Consensus 450 S~g~ 453 (535)
..+.
T Consensus 270 ~~a~ 273 (346)
T TIGR01659 270 RLAE 273 (346)
T ss_pred EECC
Confidence 5443
No 14
>TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.
Probab=97.24 E-value=0.00073 Score=70.78 Aligned_cols=74 Identities=20% Similarity=0.213 Sum_probs=59.2
Q ss_pred EEEEecCCCCCCchhHHHHHHHHhhccceeeeccCCCCCCCCCceeEEEeechHHHHHHHhhhccceeeeeCCceeeec
Q 009405 372 LVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPLLGS 450 (535)
Q Consensus 372 lVlLqNLDPs~tS~eVEDli~~afke~C~AKmI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~egCL~ls~GRPL~~S 450 (535)
-||+.||+++.|.++|.+++.... + +.--.|.+...+....|.|||.|.+.+.|+.||..|+...+ +|||+.-.
T Consensus 2 sl~VgnLp~~vte~~L~~~F~~~G-~-v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i---~gk~i~i~ 75 (562)
T TIGR01628 2 SLYVGDLDPDVTEAKLYDLFKPFG-P-VLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRL---GGKPIRIM 75 (562)
T ss_pred eEEEeCCCCCCCHHHHHHHHHhcC-C-EEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEE---CCeeEEee
Confidence 389999999999999998876654 2 33333445555567789999999999999999999999877 89998754
No 15
>TIGR01622 SF-CC1 splicing factor, CC1-like family. A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.
Probab=97.22 E-value=0.00092 Score=67.57 Aligned_cols=79 Identities=16% Similarity=0.118 Sum_probs=62.6
Q ss_pred hhhhcccEEEEecCCCCCCchhHHHHHHHHhhccceeeeccCCCCCCCCCceeEEEeechHHHHHHHhhhccceeeeeCC
Q 009405 365 VAHEHGTLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNG 444 (535)
Q Consensus 365 ~A~E~GrlVlLqNLDPs~tS~eVEDli~~afke~C~AKmI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~egCL~ls~G 444 (535)
.+....+-||+.||.+..+..||.+++.+.. +--.+++| ....+...-|.|||-|.+.+.|+.||. |+..-+ .|
T Consensus 84 ~~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G-~v~~v~i~-~d~~~~~skg~afVeF~~~e~A~~Al~-l~g~~~---~g 157 (457)
T TIGR01622 84 EAERDDRTVFVLQLALKARERDLYEFFSKVG-KVRDVQCI-KDRNSRRSKGVAYVEFYDVESVIKALA-LTGQML---LG 157 (457)
T ss_pred ccccCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeeEEEEe-ecCCCCCcceEEEEEECCHHHHHHHHH-hCCCEE---CC
Confidence 4556688999999999999999999987744 43445554 344556778999999999999999996 777655 79
Q ss_pred ceeee
Q 009405 445 RPLLG 449 (535)
Q Consensus 445 RPL~~ 449 (535)
+||..
T Consensus 158 ~~i~v 162 (457)
T TIGR01622 158 RPIIV 162 (457)
T ss_pred eeeEE
Confidence 99874
No 16
>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family. Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.
Probab=97.21 E-value=0.0013 Score=71.81 Aligned_cols=107 Identities=20% Similarity=0.207 Sum_probs=80.4
Q ss_pred hhcccEEEEecCCCCCCchhHHHHHHHHhhccceeeeccCCCCCCCCCceeEEEeechHHHHHHHhhhccceeeeeCCce
Q 009405 367 HEHGTLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRP 446 (535)
Q Consensus 367 ~E~GrlVlLqNLDPs~tS~eVEDli~~afke~C~AKmI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~egCL~ls~GRP 446 (535)
-+.|+-|++.||.++.+.+||.+++.. |..-.+++++-. ++..+-|.|||.|.+.+.|+.||..|+...+ .+||.
T Consensus 55 p~~~~~lFVgnLp~~~tEd~L~~~F~~-~G~I~~vrl~~D--~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i--~~Gr~ 129 (578)
T TIGR01648 55 PGRGCEVFVGKIPRDLYEDELVPLFEK-AGPIYELRLMMD--FSGQNRGYAFVTFCGKEEAKEAVKLLNNYEI--RPGRL 129 (578)
T ss_pred CCCCCEEEeCCCCCCCCHHHHHHHHHh-hCCEEEEEEEEC--CCCCccceEEEEeCCHHHHHHHHHHcCCCee--cCCcc
Confidence 457899999999999999999999877 455566676554 7788999999999999999999999998866 47887
Q ss_pred eeeccCCcCCCCCCCccccceehhhHHHHHHHHHHh
Q 009405 447 LLGSIGTPCFTGKQSKFVGHLALDKLKFQMQREMRE 482 (535)
Q Consensus 447 L~~S~g~~~~p~k~s~f~GHl~i~k~r~q~qrEmr~ 482 (535)
|...... ..+..|+|-|.-+.-+.+..+++.+
T Consensus 130 l~V~~S~----~~~rLFVgNLP~~~TeeeL~eeFsk 161 (578)
T TIGR01648 130 LGVCISV----DNCRLFVGGIPKNKKREEILEEFSK 161 (578)
T ss_pred ccccccc----cCceeEeecCCcchhhHHHHHHhhc
Confidence 6433221 2466777776655544444455554
No 17
>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family. Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.
Probab=97.20 E-value=0.00097 Score=72.81 Aligned_cols=77 Identities=22% Similarity=0.254 Sum_probs=63.1
Q ss_pred hcccEEEEecCCCCCCchhHHHHHHHHh--hccceeeeccCCCCCCCCCceeEEEeechHHHHHHHhhhccceeeeeCCc
Q 009405 368 EHGTLVVLENLDPSYTSTVVEDLVWHAF--KENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGR 445 (535)
Q Consensus 368 E~GrlVlLqNLDPs~tS~eVEDli~~af--ke~C~AKmI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~egCL~ls~GR 445 (535)
...+.|++.||+++.+..+|++++-+ | .+-+.++++ .|.|||.|.+++.|+.||..|+..-| +||
T Consensus 231 ~~~k~LfVgNL~~~~tee~L~~~F~~-f~~G~I~rV~~~---------rgfAFVeF~s~e~A~kAi~~lnG~~i---~Gr 297 (578)
T TIGR01648 231 AKVKILYVRNLMTTTTEEIIEKSFSE-FKPGKVERVKKI---------RDYAFVHFEDREDAVKAMDELNGKEL---EGS 297 (578)
T ss_pred ccccEEEEeCCCCCCCHHHHHHHHHh-cCCCceEEEEee---------cCeEEEEeCCHHHHHHHHHHhCCCEE---CCE
Confidence 34689999999999999888888765 4 444444443 46899999999999999999999866 999
Q ss_pred eeeeccCCcCCC
Q 009405 446 PLLGSIGTPCFT 457 (535)
Q Consensus 446 PL~~S~g~~~~p 457 (535)
+|..+.+.|...
T Consensus 298 ~I~V~~Akp~~~ 309 (578)
T TIGR01648 298 EIEVTLAKPVDK 309 (578)
T ss_pred EEEEEEccCCCc
Confidence 999998877543
No 18
>TIGR01622 SF-CC1 splicing factor, CC1-like family. A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.
Probab=97.15 E-value=0.0011 Score=66.94 Aligned_cols=79 Identities=18% Similarity=0.149 Sum_probs=62.9
Q ss_pred ccEEEEecCCCCCCchhHHHHHHHHhhccceeeeccCCCCCCCCCceeEEEeechHHHHHHHhhhccceeeeeCCceeee
Q 009405 370 GTLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPLLG 449 (535)
Q Consensus 370 GrlVlLqNLDPs~tS~eVEDli~~afke~C~AKmI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~egCL~ls~GRPL~~ 449 (535)
.+-|||.||.+.+|..+|.+++.. |+.-...+++ +........|.|||.|.+.+.|..|+..|+...| +||||..
T Consensus 186 ~~~l~v~nl~~~~te~~l~~~f~~-~G~i~~v~~~-~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i---~g~~i~v 260 (457)
T TIGR01622 186 FLKLYVGNLHFNITEQELRQIFEP-FGDIEDVQLH-RDPETGRSKGFGFIQFHDAEEAKEALEVMNGFEL---AGRPIKV 260 (457)
T ss_pred CCEEEEcCCCCCCCHHHHHHHHHh-cCCeEEEEEE-EcCCCCccceEEEEEECCHHHHHHHHHhcCCcEE---CCEEEEE
Confidence 578999999999999999988854 4444444443 3444456779999999999999999999998544 8999998
Q ss_pred ccCC
Q 009405 450 SIGT 453 (535)
Q Consensus 450 S~g~ 453 (535)
+.+.
T Consensus 261 ~~a~ 264 (457)
T TIGR01622 261 GYAQ 264 (457)
T ss_pred EEcc
Confidence 8865
No 19
>TIGR01645 half-pint poly-U binding splicing factor, half-pint family. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.
Probab=97.10 E-value=0.0014 Score=72.08 Aligned_cols=82 Identities=12% Similarity=0.135 Sum_probs=69.6
Q ss_pred hcccEEEEecCCCCCCchhHHHHHHHHhhccceeeeccCCCCCCCCCceeEEEeechHHHHHHHhhhccceeeeeCCcee
Q 009405 368 EHGTLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPL 447 (535)
Q Consensus 368 E~GrlVlLqNLDPs~tS~eVEDli~~afke~C~AKmI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~egCL~ls~GRPL 447 (535)
...+.||+.||+|.++.+||.+++. .|++-..++++.... ...+-|.|||.|.+.+.|+.||..||.--| +||+|
T Consensus 202 ~~~~rLfVgnLp~~vteedLk~lFs-~FG~I~svrl~~D~~-tgksKGfGFVeFe~~e~A~kAI~amNg~el---gGr~L 276 (612)
T TIGR01645 202 KKFNRIYVASVHPDLSETDIKSVFE-AFGEIVKCQLARAPT-GRGHKGYGFIEYNNLQSQSEAIASMNLFDL---GGQYL 276 (612)
T ss_pred cccceEEeecCCCCCCHHHHHHHHh-hcCCeeEEEEEecCC-CCCcCCeEEEEECCHHHHHHHHHHhCCCee---CCeEE
Confidence 3456899999999999999999997 588888888775443 477889999999999999999999998766 99999
Q ss_pred eeccCCc
Q 009405 448 LGSIGTP 454 (535)
Q Consensus 448 ~~S~g~~ 454 (535)
--.+..+
T Consensus 277 rV~kAi~ 283 (612)
T TIGR01645 277 RVGKCVT 283 (612)
T ss_pred EEEecCC
Confidence 8776653
No 20
>smart00361 RRM_1 RNA recognition motif.
Probab=97.07 E-value=0.0012 Score=51.94 Aligned_cols=45 Identities=20% Similarity=0.385 Sum_probs=36.6
Q ss_pred eccCCCCCCCCCceeEEEeechHHHHHHHhhhccceeeeeCCceeeec
Q 009405 403 MIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPLLGS 450 (535)
Q Consensus 403 mI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~egCL~ls~GRPL~~S 450 (535)
++++.+.....-|.|||-|.+.+.|..|+..|+..-+ +||+|.++
T Consensus 26 ~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~---~gr~l~~~ 70 (70)
T smart00361 26 YIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYF---DGRTVKAE 70 (70)
T ss_pred EeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEE---CCEEEEeC
Confidence 4555443244569999999999999999999999855 99999875
No 21
>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family. Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).
Probab=97.04 E-value=0.0014 Score=68.37 Aligned_cols=74 Identities=20% Similarity=0.227 Sum_probs=59.5
Q ss_pred cEEEEecCCCCCCchhHHHHHHHHhhccceeeeccCCCCCCCCCceeEEEeechHHHHHHHhhhccceeeeeCCceeeec
Q 009405 371 TLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPLLGS 450 (535)
Q Consensus 371 rlVlLqNLDPs~tS~eVEDli~~afke~C~AKmI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~egCL~ls~GRPL~~S 450 (535)
++|++.||++..+..||.+++.. |+.-..++|++ .-|+|||-|.+.+.|+.||..++..-..+ +||||.-.
T Consensus 3 ~vv~V~nLp~~~te~~L~~~f~~-fG~V~~v~i~~-------~k~~afVef~~~e~A~~Ai~~~~~~~~~l-~g~~l~v~ 73 (481)
T TIGR01649 3 PVVHVRNLPQDVVEADLVEALIP-FGPVSYVMMLP-------GKRQALVEFEDEESAKACVNFATSVPIYI-RGQPAFFN 73 (481)
T ss_pred cEEEEcCCCCCCCHHHHHHHHHh-cCCeeEEEEEC-------CCCEEEEEeCchHHHHHHHHHhhcCCceE-cCeEEEEE
Confidence 78999999999999999999876 56666677774 34899999999999999999874322333 99999876
Q ss_pred cCC
Q 009405 451 IGT 453 (535)
Q Consensus 451 ~g~ 453 (535)
...
T Consensus 74 ~s~ 76 (481)
T TIGR01649 74 YST 76 (481)
T ss_pred ecC
Confidence 543
No 22
>PLN03120 nucleic acid binding protein; Provisional
Probab=96.95 E-value=0.0034 Score=63.17 Aligned_cols=76 Identities=13% Similarity=0.082 Sum_probs=60.7
Q ss_pred cccEEEEecCCCCCCchhHHHHHHHHhhccceeeeccCCCCCCCCCceeEEEeechHHHHHHHhhhccceeeeeCCceee
Q 009405 369 HGTLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPLL 448 (535)
Q Consensus 369 ~GrlVlLqNLDPs~tS~eVEDli~~afke~C~AKmI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~egCL~ls~GRPL~ 448 (535)
.++-||+.||+|+-|..||.|++-. +++-+.++|+.. ....|.|||.|.+.++|+.|| .|+..-| +||+|.
T Consensus 3 ~~rtVfVgNLs~~tTE~dLrefFS~-~G~I~~V~I~~d----~~~~GfAFVtF~d~eaAe~Al-lLnG~~l---~gr~V~ 73 (260)
T PLN03120 3 QVRTVKVSNVSLKATERDIKEFFSF-SGDIEYVEMQSE----NERSQIAYVTFKDPQGAETAL-LLSGATI---VDQSVT 73 (260)
T ss_pred CCCEEEEeCCCCCCCHHHHHHHHHh-cCCeEEEEEeec----CCCCCEEEEEeCcHHHHHHHH-HhcCCee---CCceEE
Confidence 3678999999999999999999866 455566666532 235799999999999999999 4885544 899998
Q ss_pred eccCC
Q 009405 449 GSIGT 453 (535)
Q Consensus 449 ~S~g~ 453 (535)
-+...
T Consensus 74 Vt~a~ 78 (260)
T PLN03120 74 ITPAE 78 (260)
T ss_pred EEecc
Confidence 77764
No 23
>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=96.93 E-value=0.0024 Score=70.33 Aligned_cols=83 Identities=17% Similarity=0.128 Sum_probs=65.6
Q ss_pred HHhhhhcccEEEEecCCCCCCchhHHHHHHHHhhccceeeeccCCCCCCCCCceeEEEeechHHHHHHHhhhccceeeee
Q 009405 363 IRVAHEHGTLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLS 442 (535)
Q Consensus 363 l~~A~E~GrlVlLqNLDPs~tS~eVEDli~~afke~C~AKmI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~egCL~ls 442 (535)
-..|....+.||+.||.+..+..+|.+++.. |++--.++| .....+..+.|.|||-|.+.++|+.||..||..-|
T Consensus 100 r~~a~~~~~rLfVGnLp~~~tEe~Lr~lF~~-fG~I~sV~I-~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i--- 174 (612)
T TIGR01645 100 RQQALAIMCRVYVGSISFELREDTIRRAFDP-FGPIKSINM-SWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQML--- 174 (612)
T ss_pred HhhhhcCCCEEEEcCCCCCCCHHHHHHHHHc-cCCEEEEEE-eecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEE---
Confidence 3456667789999999999999999998876 444334444 34555678899999999999999999999987533
Q ss_pred CCceeeec
Q 009405 443 NGRPLLGS 450 (535)
Q Consensus 443 ~GRPL~~S 450 (535)
+||+|.-.
T Consensus 175 ~GR~IkV~ 182 (612)
T TIGR01645 175 GGRNIKVG 182 (612)
T ss_pred ecceeeec
Confidence 89998654
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=96.90 E-value=0.0028 Score=66.26 Aligned_cols=76 Identities=16% Similarity=0.180 Sum_probs=62.9
Q ss_pred hhcccEEEEecCCC-CCCchhHHHHHHHHhhccceeeeccCCCCCCCCCceeEEEeechHHHHHHHhhhccceeeeeCCc
Q 009405 367 HEHGTLVVLENLDP-SYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGR 445 (535)
Q Consensus 367 ~E~GrlVlLqNLDP-s~tS~eVEDli~~afke~C~AKmI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~egCL~ls~GR 445 (535)
...+++||+.||++ ..|.++|.+|+-. ++.-..++++.. ..|.|||-|.+.+.|+.||..|+...| +||
T Consensus 272 ~~~~~~l~v~nL~~~~vt~~~L~~lF~~-yG~V~~vki~~~------~~g~afV~f~~~~~A~~Ai~~lng~~l---~g~ 341 (481)
T TIGR01649 272 GGPGSVLMVSGLHQEKVNCDRLFNLFCV-YGNVERVKFMKN------KKETALIEMADPYQAQLALTHLNGVKL---FGK 341 (481)
T ss_pred CCCCCEEEEeCCCCCCCCHHHHHHHHHh-cCCeEEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEE---CCc
Confidence 45789999999999 5899999998875 445446666542 259999999999999999999999877 899
Q ss_pred eeeeccC
Q 009405 446 PLLGSIG 452 (535)
Q Consensus 446 PL~~S~g 452 (535)
||..+..
T Consensus 342 ~l~v~~s 348 (481)
T TIGR01649 342 PLRVCPS 348 (481)
T ss_pred eEEEEEc
Confidence 9988765
No 25
>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]
Probab=96.77 E-value=0.007 Score=52.28 Aligned_cols=80 Identities=24% Similarity=0.240 Sum_probs=64.4
Q ss_pred ccEEEEecCCCCCCchhHHHHHHHHhhccceeeeccCCCCCCCCCceeEEEeechHHHHHHHhhhccceeeeeCCceeee
Q 009405 370 GTLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPLLG 449 (535)
Q Consensus 370 GrlVlLqNLDPs~tS~eVEDli~~afke~C~AKmI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~egCL~ls~GRPL~~ 449 (535)
.+-|++.||.+.+|..||.+++-+...- ..++ |+.........|.|||.|.+.+.|..|+..++..-| .||||.-
T Consensus 115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~-~~~~-~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~---~~~~~~v 189 (306)
T COG0724 115 NNTLFVGNLPYDVTEEDLRELFKKFGPV-KRVR-LVRDRETGKSRGFAFVEFESEESAEKAIEELNGKEL---EGRPLRV 189 (306)
T ss_pred CceEEEeCCCCCCCHHHHHHHHHhcCce-eEEE-eeeccccCccCceEEEEecCHHHHHHHHHHcCCCeE---CCceeEe
Confidence 6899999999999999999998875443 2222 333335578889999999999999999999997755 8999997
Q ss_pred ccCCc
Q 009405 450 SIGTP 454 (535)
Q Consensus 450 S~g~~ 454 (535)
....+
T Consensus 190 ~~~~~ 194 (306)
T COG0724 190 QKAQP 194 (306)
T ss_pred ecccc
Confidence 77554
No 26
>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]
Probab=96.60 E-value=0.005 Score=61.30 Aligned_cols=75 Identities=25% Similarity=0.256 Sum_probs=58.6
Q ss_pred hhcc-cEEEEecCCCCCCchhHHHHHHHHhhccceeeeccCCCCCCCCCceeEEEeechHHHHHHHhhhccceeeeeCCc
Q 009405 367 HEHG-TLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGR 445 (535)
Q Consensus 367 ~E~G-rlVlLqNLDPs~tS~eVEDli~~afke~C~AKmI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~egCL~ls~GR 445 (535)
++.| +.|++.||++.++.+||++|+.+-. .|. +.+=|.--+.+-.|.|-|+|..++-|+.||.+++.. .| +||
T Consensus 79 ~~~~~~~v~v~NL~~~V~~~Dl~eLF~~~~--~~~-r~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~gv--~l-dG~ 152 (243)
T KOG0533|consen 79 NETRSTKVNVSNLPYGVIDADLKELFAEFG--ELK-RVAVHYDRAGRSLGTADVSFNRRDDAERAVKKYNGV--AL-DGR 152 (243)
T ss_pred cCCCcceeeeecCCcCcchHHHHHHHHHhc--cce-EEeeccCCCCCCCccceeeecchHhHHHHHHHhcCc--cc-CCc
Confidence 4455 7899999999999999999988744 333 333333334666799999999999999999999994 34 898
Q ss_pred ee
Q 009405 446 PL 447 (535)
Q Consensus 446 PL 447 (535)
|+
T Consensus 153 ~m 154 (243)
T KOG0533|consen 153 PM 154 (243)
T ss_pred ee
Confidence 83
No 27
>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]
Probab=96.26 E-value=0.0074 Score=58.95 Aligned_cols=95 Identities=23% Similarity=0.332 Sum_probs=71.0
Q ss_pred hcccEEEEecCCCCCCchhHHHHHHHHhhc--cceeeeccCCCCCCCCCceeEEEeechHHHHHHHhhhccceeeeeCCc
Q 009405 368 EHGTLVVLENLDPSYTSTVVEDLVWHAFKE--NCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGR 445 (535)
Q Consensus 368 E~GrlVlLqNLDPs~tS~eVEDli~~afke--~C~AKmI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~egCL~ls~GR 445 (535)
.|+.-||+.|||+-.+- .|+|.-|-+ .+---.||+.-+.+-|.|.||+.|.|.|-||-||.=|+--=| .||
T Consensus 7 nqd~tiyvgnld~kvs~----~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkL---Ygr 79 (203)
T KOG0131|consen 7 NQDATLYVGNLDEKVSE----ELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKL---YGR 79 (203)
T ss_pred CCCceEEEecCCHHHHH----HHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHh---cCc
Confidence 46677999999998774 455554443 244468999999999999999999999999999999994333 999
Q ss_pred eeeeccCC---cCCCCCCCccccceeh
Q 009405 446 PLLGSIGT---PCFTGKQSKFVGHLAL 469 (535)
Q Consensus 446 PL~~S~g~---~~~p~k~s~f~GHl~i 469 (535)
||.-.+.. -..+..-..|+|-|.-
T Consensus 80 pIrv~kas~~~~nl~vganlfvgNLd~ 106 (203)
T KOG0131|consen 80 PIRVNKASAHQKNLDVGANLFVGNLDP 106 (203)
T ss_pred eeEEEecccccccccccccccccccCc
Confidence 99877766 2223334456666544
No 28
>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]
Probab=96.25 E-value=0.018 Score=62.17 Aligned_cols=107 Identities=19% Similarity=0.206 Sum_probs=86.7
Q ss_pred hcccEEEEecCCCCCCchhHHHHHHHHhhccceeeeccCCCCCCCCCceeEEEeechHHHHHHHhhhccceeeeeCCcee
Q 009405 368 EHGTLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPL 447 (535)
Q Consensus 368 E~GrlVlLqNLDPs~tS~eVEDli~~afke~C~AKmI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~egCL~ls~GRPL 447 (535)
.+|.=|++.-+--....+|+-.|+-.+. +--+.|+ =..+||.-|-|+|||-|.||++|..||..||.-=+ ..||+|
T Consensus 81 ~~G~EVfvGkIPrD~~EdeLvplfEkiG-~I~elRL-MmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Ei--r~GK~i 156 (506)
T KOG0117|consen 81 PRGCEVFVGKIPRDVFEDELVPLFEKIG-KIYELRL-MMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEI--RPGKLL 156 (506)
T ss_pred CCCceEEecCCCccccchhhHHHHHhcc-ceeeEEE-eecccCCCCcceEEEEeecHHHHHHHHHHhhCccc--cCCCEe
Confidence 9999999999999999999999887654 4556664 36789999999999999999999999999999866 789988
Q ss_pred eeccCCcCCCCCCCccccceehhhHHHHHHHHHHh
Q 009405 448 LGSIGTPCFTGKQSKFVGHLALDKLKFQMQREMRE 482 (535)
Q Consensus 448 ~~S~g~~~~p~k~s~f~GHl~i~k~r~q~qrEmr~ 482 (535)
-|+. --.+++.|+|-+-=++.|..-.+||++
T Consensus 157 gvc~----Svan~RLFiG~IPK~k~keeIlee~~k 187 (506)
T KOG0117|consen 157 GVCV----SVANCRLFIGNIPKTKKKEEILEEMKK 187 (506)
T ss_pred EEEE----eeecceeEeccCCccccHHHHHHHHHh
Confidence 6543 345789999987766655444455554
No 29
>PLN03121 nucleic acid binding protein; Provisional
Probab=96.12 E-value=0.019 Score=57.56 Aligned_cols=76 Identities=21% Similarity=0.172 Sum_probs=59.6
Q ss_pred hcccEEEEecCCCCCCchhHHHHHHHHhhccceeeeccCCCCCCCCCceeEEEeechHHHHHHHhhhccceeeeeCCcee
Q 009405 368 EHGTLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPL 447 (535)
Q Consensus 368 E~GrlVlLqNLDPs~tS~eVEDli~~afke~C~AKmI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~egCL~ls~GRPL 447 (535)
..|..|++.||.|+-|..||.|++-+.. +--..+||.. .-..|-|||.|+..++|+.|+ .|+..-| .++|+
T Consensus 3 ~~g~TV~V~NLS~~tTE~dLrefFS~~G-~I~~V~I~~D----~et~gfAfVtF~d~~aaetAl-lLnGa~l---~d~~I 73 (243)
T PLN03121 3 PGGYTAEVTNLSPKATEKDVYDFFSHCG-AIEHVEIIRS----GEYACTAYVTFKDAYALETAV-LLSGATI---VDQRV 73 (243)
T ss_pred CCceEEEEecCCCCCCHHHHHHHHHhcC-CeEEEEEecC----CCcceEEEEEECCHHHHHHHH-hcCCCee---CCceE
Confidence 4689999999999999999999999844 3334446644 223479999999999999999 6777755 78888
Q ss_pred eeccC
Q 009405 448 LGSIG 452 (535)
Q Consensus 448 ~~S~g 452 (535)
.-+..
T Consensus 74 ~It~~ 78 (243)
T PLN03121 74 CITRW 78 (243)
T ss_pred EEEeC
Confidence 76654
No 30
>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=96.02 E-value=0.012 Score=43.98 Aligned_cols=34 Identities=38% Similarity=0.483 Sum_probs=30.8
Q ss_pred CceeEEEeechHHHHHHHhhhccceeeeeCCceeeec
Q 009405 414 FGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPLLGS 450 (535)
Q Consensus 414 ~G~AfvIFkTkeAAdsai~KL~egCL~ls~GRPL~~S 450 (535)
.|.|||-|.+.++|+.|+..|+...+ +||||..+
T Consensus 21 ~~~a~V~f~~~~~A~~a~~~l~~~~~---~g~~l~V~ 54 (56)
T PF13893_consen 21 RGFAFVEFASVEDAQKAIEQLNGRQF---NGRPLKVS 54 (56)
T ss_dssp TTEEEEEESSHHHHHHHHHHHTTSEE---TTEEEEEE
T ss_pred CCEEEEEECCHHHHHHHHHHhCCCEE---CCcEEEEE
Confidence 59999999999999999999998765 99999754
No 31
>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=95.71 E-value=0.029 Score=62.96 Aligned_cols=118 Identities=20% Similarity=0.218 Sum_probs=93.4
Q ss_pred EEEecCCCCCCchhHHHHHHHHhhccceeeeccCCCCCC-----CCCceeEEEeechHHHHHHHhhhccceeeeeCCcee
Q 009405 373 VVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFAS-----PYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPL 447 (535)
Q Consensus 373 VlLqNLDPs~tS~eVEDli~~afke~C~AKmI~~~~~ss-----pn~G~AfvIFkTkeAAdsai~KL~egCL~ls~GRPL 447 (535)
+|++||.-.=|-.++++...... ..++|..+.--+ +-.|.+||-|.+.+-|..|+..|+..-| +|++|
T Consensus 518 lfvkNlnf~Tt~e~l~~~F~k~G----~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvl---dGH~l 590 (725)
T KOG0110|consen 518 LFVKNLNFDTTLEDLEDLFSKQG----TVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVL---DGHKL 590 (725)
T ss_pred hhhhcCCcccchhHHHHHHHhcC----eEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCcee---cCceE
Confidence 99999999999999999998822 333443333323 4569999999999999999999998855 99999
Q ss_pred eeccCC--------cCCCCCCCccccceehhhHHHHHH-HHHHhhhccc----cCCCCCcchhhc
Q 009405 448 LGSIGT--------PCFTGKQSKFVGHLALDKLKFQMQ-REMREAVSTS----HCSQPNSLEYDM 499 (535)
Q Consensus 448 ~~S~g~--------~~~p~k~s~f~GHl~i~k~r~q~q-rEmr~AVSTS----HcSQPNtIEYdm 499 (535)
.+++-. ...|.+.. .+-|=+-++..|++ ||.|+--++. -|.=|+-+-|.|
T Consensus 591 ~lk~S~~k~~~~~gK~~~~kk~--~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a 653 (725)
T KOG0110|consen 591 ELKISENKPASTVGKKKSKKKK--GTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGA 653 (725)
T ss_pred EEEeccCccccccccccccccc--cceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchh
Confidence 988765 33333333 56788889999888 9999999888 488899988888
No 32
>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]
Probab=95.38 E-value=0.051 Score=56.02 Aligned_cols=88 Identities=24% Similarity=0.327 Sum_probs=72.4
Q ss_pred cCCChHHHHHhhhhcccEEEEecCCCCCCchhHHHHHHHHhh---ccceeeeccCCCCCCCCCceeEEEeechHHHHHHH
Q 009405 355 KELPWEERIRVAHEHGTLVVLENLDPSYTSTVVEDLVWHAFK---ENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVV 431 (535)
Q Consensus 355 K~lPWeerl~~A~E~GrlVlLqNLDPs~tS~eVEDli~~afk---e~C~AKmI~~~~~sspn~G~AfvIFkTkeAAdsai 431 (535)
+++-+||-.--+--.++-||..|+-+.+| ||+||+.|- .--|.|+. +--|+|||-|-|+|||..||
T Consensus 149 ~~ltfdeV~NQssp~NtsVY~G~I~~~lt----e~~mr~~Fs~fG~I~EVRvF-------k~qGYaFVrF~tkEaAahAI 217 (321)
T KOG0148|consen 149 KPLTFDEVYNQSSPDNTSVYVGNIASGLT----EDLMRQTFSPFGPIQEVRVF-------KDQGYAFVRFETKEAAAHAI 217 (321)
T ss_pred CCccHHHHhccCCCCCceEEeCCcCcccc----HHHHHHhcccCCcceEEEEe-------cccceEEEEecchhhHHHHH
Confidence 34789998888888999999999999777 567787663 34555554 45688999999999999999
Q ss_pred hhhccceeeeeCCceeeeccCCcCC
Q 009405 432 TKLEEGCLLLSNGRPLLGSIGTPCF 456 (535)
Q Consensus 432 ~KL~egCL~ls~GRPL~~S~g~~~~ 456 (535)
-.+|..=+ +|.++-|+-|.-..
T Consensus 218 v~mNntei---~G~~VkCsWGKe~~ 239 (321)
T KOG0148|consen 218 VQMNNTEI---GGQLVRCSWGKEGD 239 (321)
T ss_pred HHhcCcee---CceEEEEeccccCC
Confidence 99999977 99999999985443
No 33
>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]
Probab=95.16 E-value=0.038 Score=57.40 Aligned_cols=72 Identities=28% Similarity=0.296 Sum_probs=57.7
Q ss_pred EEEecCCCCCCchhHHHHHHHHhhccceeeeccCCCCCCCCCceeEEEeechHHHHHHHhhhccceeeeeCCceeeeccC
Q 009405 373 VVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPLLGSIG 452 (535)
Q Consensus 373 VlLqNLDPs~tS~eVEDli~~afke~C~AKmI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~egCL~ls~GRPL~~S~g 452 (535)
|+|.||||+.+-.++.|+.- .|++...+|..-..-- --|. ||-|-+.++|..||.+||...| +|.++++...
T Consensus 79 ~~i~nl~~~~~~~~~~d~f~-~~g~ilS~kv~~~~~g---~kg~-FV~f~~e~~a~~ai~~~ng~ll---~~kki~vg~~ 150 (369)
T KOG0123|consen 79 VFIKNLDESIDNKSLYDTFS-EFGNILSCKVATDENG---SKGY-FVQFESEESAKKAIEKLNGMLL---NGKKIYVGLF 150 (369)
T ss_pred eeecCCCcccCcHHHHHHHH-hhcCeeEEEEEEcCCC---ceee-EEEeCCHHHHHHHHHHhcCccc---CCCeeEEeec
Confidence 99999999999999999875 4556555554433322 4567 9999999999999999999976 9999997544
No 34
>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]
Probab=94.56 E-value=0.05 Score=56.55 Aligned_cols=89 Identities=22% Similarity=0.316 Sum_probs=72.7
Q ss_pred ChHHHHHhh-hhcccEEEEecCCCCCCchhHHHHHHHHhhccceeeeccCCCCCCCCCceeEEEeechHHHHHHHhhhcc
Q 009405 358 PWEERIRVA-HEHGTLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEE 436 (535)
Q Consensus 358 PWeerl~~A-~E~GrlVlLqNLDPs~tS~eVEDli~~afke~C~AKmI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~e 436 (535)
-|.++.++- ..++.-||++|||...+..++.++. ..+++-|.++++--.. ++.-|.+||.|.+.+.|..|+..+++
T Consensus 257 ~~~~~~~~~~~~~~~nl~vknld~~~~~e~L~~~f-~~~GeI~s~kv~~~~~--g~skG~gfV~fs~~eeA~~A~~~~n~ 333 (369)
T KOG0123|consen 257 FEQEFAKRSVSLQGANLYVKNLDETLSDEKLRKIF-SSFGEITSAKVMVDEN--GKSKGFGFVEFSSPEEAKKAMTEMNG 333 (369)
T ss_pred hHhhhhhccccccccccccccCccccchhHHHHHH-hcccceeeEEEEeccC--CCccceEEEEcCCHHHHHHHHHhhCh
Confidence 445555555 6678899999999999988888765 4688888888876543 68899999999999999999999999
Q ss_pred ceeeeeCCceeeeccC
Q 009405 437 GCLLLSNGRPLLGSIG 452 (535)
Q Consensus 437 gCL~ls~GRPL~~S~g 452 (535)
..+ +|+|++-..+
T Consensus 334 ~~i---~~k~l~vav~ 346 (369)
T KOG0123|consen 334 RLI---GGKPLYVAVA 346 (369)
T ss_pred hhh---cCCchhhhHH
Confidence 966 9999884443
No 35
>PLN03213 repressor of silencing 3; Provisional
Probab=93.91 E-value=0.24 Score=54.74 Aligned_cols=79 Identities=9% Similarity=0.040 Sum_probs=62.7
Q ss_pred hcccEEEEecCCCCCCchhHHHHHHHHhhccceeeeccCCCCCCCCCceeEEEeech--HHHHHHHhhhccceeeeeCCc
Q 009405 368 EHGTLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTR--EVAELVVTKLEEGCLLLSNGR 445 (535)
Q Consensus 368 E~GrlVlLqNLDPs~tS~eVEDli~~afke~C~AKmI~~~~~sspn~G~AfvIFkTk--eAAdsai~KL~egCL~ls~GR 445 (535)
..|..||+.||.+..|.+|++.++- .|++--.+.+| +.+. -|-|||-|.+. +.++.||+.||..=. .||
T Consensus 8 ~~gMRIYVGNLSydVTEDDLravFS-eFGsVkdVEIp-RETG----RGFAFVEMssdddaEeeKAISaLNGAEW---KGR 78 (759)
T PLN03213 8 GGGVRLHVGGLGESVGRDDLLKIFS-PMGTVDAVEFV-RTKG----RSFAYIDFSPSSTNSLTKLFSTYNGCVW---KGG 78 (759)
T ss_pred CcceEEEEeCCCCCCCHHHHHHHHH-hcCCeeEEEEe-cccC----CceEEEEecCCcHHHHHHHHHHhcCCee---cCc
Confidence 3568899999999999999998864 45555556666 5543 79999999998 679999999998855 799
Q ss_pred eeeeccCCcC
Q 009405 446 PLLGSIGTPC 455 (535)
Q Consensus 446 PL~~S~g~~~ 455 (535)
.|.--++.|.
T Consensus 79 ~LKVNKAKP~ 88 (759)
T PLN03213 79 RLRLEKAKEH 88 (759)
T ss_pred eeEEeeccHH
Confidence 9986666553
No 36
>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]
Probab=93.50 E-value=0.15 Score=49.99 Aligned_cols=76 Identities=28% Similarity=0.186 Sum_probs=56.9
Q ss_pred cccEEEEecCCCCCCchhHHHHHHHHh--hccceeeeccCCCCCCCCCceeEEEeechHHHHHHHhhhccce-------e
Q 009405 369 HGTLVVLENLDPSYTSTVVEDLVWHAF--KENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGC-------L 439 (535)
Q Consensus 369 ~GrlVlLqNLDPs~tS~eVEDli~~af--ke~C~AKmI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~egC-------L 439 (535)
.++-||+.||.+.-+..|+|.++..-. .---.|+++ .|.|||.|...--|+-|+.-||..= |
T Consensus 9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnP---------PGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rV 79 (195)
T KOG0107|consen 9 GNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNP---------PGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRV 79 (195)
T ss_pred CCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecC---------CCceEEeccCcccHHHHHhhcCCccccCceEEE
Confidence 478999999999999999999887632 223344422 4789999999999999999999754 3
Q ss_pred eeeCCceeeeccCC
Q 009405 440 LLSNGRPLLGSIGT 453 (535)
Q Consensus 440 ~ls~GRPL~~S~g~ 453 (535)
=|+.|+|==+-.|.
T Consensus 80 E~S~G~~r~~r~gg 93 (195)
T KOG0107|consen 80 ELSTGRPRGSRRGG 93 (195)
T ss_pred EeecCCccccccCC
Confidence 45677776444344
No 37
>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=93.13 E-value=0.31 Score=44.83 Aligned_cols=74 Identities=20% Similarity=0.177 Sum_probs=56.9
Q ss_pred hhcccEEEEecCCCCCCchhHHHHHHHHhhccceeeeccCCCCCCCCCceeEEEeechHHHHHHHhhhccceeeeeCCce
Q 009405 367 HEHGTLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRP 446 (535)
Q Consensus 367 ~E~GrlVlLqNLDPs~tS~eVEDli~~afke~C~AKmI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~egCL~ls~GRP 446 (535)
-|-.|++||.||-...|++|+=||+ ++--+.+-|-.--- ----|.|||+|-.-.-|..|++.|..=-+ .||+
T Consensus 15 pevnriLyirNLp~~ITseemydlF----Gkyg~IrQIRiG~~-k~TrGTAFVVYedi~dAk~A~dhlsg~n~---~~ry 86 (124)
T KOG0114|consen 15 PEVNRILYIRNLPFKITSEEMYDLF----GKYGTIRQIRIGNT-KETRGTAFVVYEDIFDAKKACDHLSGYNV---DNRY 86 (124)
T ss_pred hhhheeEEEecCCccccHHHHHHHh----hcccceEEEEecCc-cCcCceEEEEehHhhhHHHHHHHhccccc---CCce
Confidence 4678999999999999999988875 44333333322111 22358999999999999999999988755 8999
Q ss_pred ee
Q 009405 447 LL 448 (535)
Q Consensus 447 L~ 448 (535)
|+
T Consensus 87 l~ 88 (124)
T KOG0114|consen 87 LV 88 (124)
T ss_pred EE
Confidence 98
No 38
>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]
Probab=91.99 E-value=0.26 Score=52.16 Aligned_cols=78 Identities=26% Similarity=0.382 Sum_probs=61.9
Q ss_pred ccEEEEecCCCCCCchhHH---HHHHH---Hhhccceee--eccCCCCCCCCCceeEEEeechHHHHHHHhhhccceeee
Q 009405 370 GTLVVLENLDPSYTSTVVE---DLVWH---AFKENCSAK--MIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLL 441 (535)
Q Consensus 370 GrlVlLqNLDPs~tS~eVE---Dli~~---afke~C~AK--mI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~egCL~l 441 (535)
.+.|.|.|+ ||+.+.+ |||+. -+.|.|+.- +=.-.-|+.+.-|-|.|-|++.++|+.+|.-|+++-+
T Consensus 265 ~~tVi~kn~---Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~d~hPdGvvtV~f~n~eeA~~ciq~m~GR~f-- 339 (382)
T KOG1548|consen 265 DRTVILKNM---FTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVYDRHPDGVVTVSFRNNEEADQCIQTMDGRWF-- 339 (382)
T ss_pred CcEEEeeec---CCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEeccCCCceeEEEeCChHHHHHHHHHhcCeee--
Confidence 468889998 8888877 66665 477777642 2223456778889999999999999999999999976
Q ss_pred eCCceeeeccCC
Q 009405 442 SNGRPLLGSIGT 453 (535)
Q Consensus 442 s~GRPL~~S~g~ 453 (535)
+||-|.|+.-.
T Consensus 340 -dgRql~A~i~D 350 (382)
T KOG1548|consen 340 -DGRQLTASIWD 350 (382)
T ss_pred -cceEEEEEEeC
Confidence 99999998643
No 39
>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]
Probab=91.74 E-value=0.51 Score=52.60 Aligned_cols=89 Identities=26% Similarity=0.301 Sum_probs=70.8
Q ss_pred HHhhhhcccEEEEecCCCCCCchhHHHHHHHHhhccceeeeccCCCCCCCCCceeEEEeechHHHHHHHhhh----ccce
Q 009405 363 IRVAHEHGTLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKL----EEGC 438 (535)
Q Consensus 363 l~~A~E~GrlVlLqNLDPs~tS~eVEDli~~afke~C~AKmI~~~~~sspn~G~AfvIFkTkeAAdsai~KL----~egC 438 (535)
++.-+-.|..|+|.||-..-|-.+|-..+.+ |++---|++.-+... ..--|.|||-|+|..||-.+|.-- +.|-
T Consensus 285 ~~en~~~~~tVFvRNL~fD~tEEel~~~fsk-FG~v~ya~iV~~k~T-~~skGtAFv~Fkt~~~~~~ci~~Aspa~e~g~ 362 (678)
T KOG0127|consen 285 TRENITEGKTVFVRNLPFDTTEEELKEHFSK-FGEVKYAIIVKDKDT-GHSKGTAFVKFKTQIAAQNCIEAASPASEDGS 362 (678)
T ss_pred ccccccccceEEEecCCccccHHHHHHHHHh-hccceeEEEEeccCC-CCcccceEEEeccHHHHHHHHHhcCccCCCce
Confidence 4556678999999999988888888777654 777777777766655 667799999999999999999988 6665
Q ss_pred eeeeCCceeeeccCCc
Q 009405 439 LLLSNGRPLLGSIGTP 454 (535)
Q Consensus 439 L~ls~GRPL~~S~g~~ 454 (535)
++| +||-|-.+.+++
T Consensus 363 ~ll-~GR~Lkv~~Av~ 377 (678)
T KOG0127|consen 363 VLL-DGRLLKVTLAVT 377 (678)
T ss_pred EEE-eccEEeeeeccc
Confidence 767 999998655543
No 40
>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=91.65 E-value=0.6 Score=40.99 Aligned_cols=69 Identities=19% Similarity=0.212 Sum_probs=59.8
Q ss_pred cEEEEecCCCCCCchhHHHHHHHHhhccceeeeccCCCCCCCCCceeEEEeechHHHHHHHhhhcccee
Q 009405 371 TLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCL 439 (535)
Q Consensus 371 rlVlLqNLDPs~tS~eVEDli~~afke~C~AKmI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~egCL 439 (535)
|-|-|.|+-..||..++.++|...++-.-+=--.|...-..-|-|+|||=|.+.++|..+....+...+
T Consensus 2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w 70 (97)
T PF04059_consen 2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKW 70 (97)
T ss_pred eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCcc
Confidence 568899999999999999999988776666667787777888999999999999999999998875544
No 41
>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]
Probab=91.25 E-value=0.36 Score=47.64 Aligned_cols=88 Identities=22% Similarity=0.307 Sum_probs=57.7
Q ss_pred ccEEEEecCCCCCCchhHHHHHHHHhhccceeeeccCCCCCCCCC----ceeEEEeechHHHHHHHhhhccceeeeeCCc
Q 009405 370 GTLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYF----GQSFVIFKTREVAELVVTKLEEGCLLLSNGR 445 (535)
Q Consensus 370 GrlVlLqNLDPs~tS~eVEDli~~afke~C~AKmI~~~~~sspn~----G~AfvIFkTkeAAdsai~KL~egCL~ls~GR 445 (535)
|.-+.++||||.. + |.++|+.|.-- -.-+-++..+-+|++ |-+|+-|.+.||+|.||..++.-.+ .+|
T Consensus 96 ganlfvgNLd~~v--D--e~~L~dtFsaf-G~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l---~nr 167 (203)
T KOG0131|consen 96 GANLFVGNLDPEV--D--EKLLYDTFSAF-GVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYL---CNR 167 (203)
T ss_pred cccccccccCcch--h--HHHHHHHHHhc-cccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchh---cCC
Confidence 3456699999933 2 35677744321 111122333445553 3799999999999999999999976 999
Q ss_pred eeeeccCCcCCCCCCCccccceeh
Q 009405 446 PLLGSIGTPCFTGKQSKFVGHLAL 469 (535)
Q Consensus 446 PL~~S~g~~~~p~k~s~f~GHl~i 469 (535)
|++-+.+--.+-+. -+|.+=
T Consensus 168 ~itv~ya~k~~~kg----~~~g~~ 187 (203)
T KOG0131|consen 168 PITVSYAFKKDTKG----ERHGTA 187 (203)
T ss_pred ceEEEEEEecCCCc----ccCCCH
Confidence 99977665444333 455553
No 42
>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]
Probab=91.24 E-value=0.41 Score=49.59 Aligned_cols=83 Identities=25% Similarity=0.304 Sum_probs=54.5
Q ss_pred hccceeeeccCCCCCCCCCceeEEEeechHHHHHHHhhhccceeeeeCCceeeeccCC------------------cCCC
Q 009405 396 KENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPLLGSIGT------------------PCFT 457 (535)
Q Consensus 396 ke~C~AKmI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~egCL~ls~GRPL~~S~g~------------------~~~p 457 (535)
.|--+||+|--... .---|++||-|..|+-||.||..|+.--| ++|-+----++ -.-|
T Consensus 87 GevS~akvirD~~T-~KsKGYgFVSf~~k~dAEnAI~~MnGqWl---G~R~IRTNWATRKp~e~n~~~ltfdeV~NQssp 162 (321)
T KOG0148|consen 87 GEVSDAKVIRDMNT-GKSKGYGFVSFPNKEDAENAIQQMNGQWL---GRRTIRTNWATRKPSEMNGKPLTFDEVYNQSSP 162 (321)
T ss_pred cccccceEeecccC-CcccceeEEeccchHHHHHHHHHhCCeee---ccceeeccccccCccccCCCCccHHHHhccCCC
Confidence 34667888764443 45567999999999999999999999988 88765321111 1234
Q ss_pred CCCCccccceehhhHHHHHHHHHHhhhcc
Q 009405 458 GKQSKFVGHLALDKLKFQMQREMREAVST 486 (535)
Q Consensus 458 ~k~s~f~GHl~i~k~r~q~qrEmr~AVST 486 (535)
.-++-|.|-+.-- -..++||+..|+
T Consensus 163 ~NtsVY~G~I~~~----lte~~mr~~Fs~ 187 (321)
T KOG0148|consen 163 DNTSVYVGNIASG----LTEDLMRQTFSP 187 (321)
T ss_pred CCceEEeCCcCcc----ccHHHHHHhccc
Confidence 4566667766541 123567766554
No 43
>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]
Probab=90.61 E-value=0.37 Score=47.56 Aligned_cols=82 Identities=22% Similarity=0.276 Sum_probs=70.4
Q ss_pred cccEEEEecCCCCCCchhHHHHHHHHhhccceee---eccCCCCCCCCCceeEEEeechHHHHHHHhhhccceeeeeCCc
Q 009405 369 HGTLVVLENLDPSYTSTVVEDLVWHAFKENCSAK---MIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGR 445 (535)
Q Consensus 369 ~GrlVlLqNLDPs~tS~eVEDli~~afke~C~AK---mI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~egCL~ls~GR 445 (535)
.-+.|++.|+|..-|..++|..+ +.|-.- .|+..-|....-|.||+-|...++++.++. ||++-| .||
T Consensus 100 d~~sv~v~nvd~~~t~~~~e~hf-----~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i---~~~ 170 (231)
T KOG4209|consen 100 DAPSVWVGNVDFLVTLTKIELHF-----ESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEI---PGP 170 (231)
T ss_pred CCceEEEeccccccccchhhhee-----eccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCccc---ccc
Confidence 45789999999999999977665 578777 799999988889999999999999999999 999977 899
Q ss_pred eeeeccCCcCCCCC
Q 009405 446 PLLGSIGTPCFTGK 459 (535)
Q Consensus 446 PL~~S~g~~~~p~k 459 (535)
++.-+..-.-.|+.
T Consensus 171 ~i~vt~~r~~~pg~ 184 (231)
T KOG4209|consen 171 AIEVTLKRTNVPGM 184 (231)
T ss_pred cceeeeeeeecCCc
Confidence 98877765556665
No 44
>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]
Probab=90.32 E-value=0.51 Score=50.72 Aligned_cols=76 Identities=18% Similarity=0.134 Sum_probs=59.1
Q ss_pred cEEEEecCCCCCCchhHHHHHHHHhhccceeeeccCCCCCCCCCceeEEEeechHHHHHHHhhhccceeeeeCCceeeec
Q 009405 371 TLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPLLGS 450 (535)
Q Consensus 371 rlVlLqNLDPs~tS~eVEDli~~afke~C~AKmI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~egCL~ls~GRPL~~S 450 (535)
+.|++.|+.++++.++|.+|+-.++.- ..-|++-...- +--.|.+|+-|++-+-|.+||+.||+.=+ +||+|-..
T Consensus 19 ~~v~vgnip~~~se~~l~~~~~~~g~v-~s~~~v~D~~t-G~~~G~~f~~~~~~~~~~~a~~~lNg~~~---~gr~l~v~ 93 (435)
T KOG0108|consen 19 SSVFVGNIPYEGSEEQLLSIFSGVGPV-LSFRLVYDRET-GKPKGFGFCEFTDEETAERAIRNLNGAEF---NGRKLRVN 93 (435)
T ss_pred cceEecCCCCcccHHHHHHHHhccCcc-ceeeecccccC-CCcCceeeEecCchhhHHHHHHhcCCccc---CCceEEee
Confidence 889999999999999999998765432 23333332222 44457999999999999999999999877 99997654
Q ss_pred c
Q 009405 451 I 451 (535)
Q Consensus 451 ~ 451 (535)
.
T Consensus 94 ~ 94 (435)
T KOG0108|consen 94 Y 94 (435)
T ss_pred c
Confidence 3
No 45
>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]
Probab=89.42 E-value=0.9 Score=49.82 Aligned_cols=72 Identities=25% Similarity=0.245 Sum_probs=59.3
Q ss_pred cEEEEecCCCCCCchhHHHHHHHHhhc--cceeeeccCCCCCCCCCceeEEEeechHHHHHHHhhhccceeeeeCCceee
Q 009405 371 TLVVLENLDPSYTSTVVEDLVWHAFKE--NCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPLL 448 (535)
Q Consensus 371 rlVlLqNLDPs~tS~eVEDli~~afke--~C~AKmI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~egCL~ls~GRPL~ 448 (535)
|-|+|.|+-+.|.=-|+.||++.-..| -|+--|=. +.---|-|.|.|++.|-+.-|+.+|+.--| +||||+
T Consensus 45 R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~----~GK~rGcavVEFk~~E~~qKa~E~lnk~~~---~GR~l~ 117 (608)
T KOG4212|consen 45 RSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDE----SGKARGCAVVEFKDPENVQKALEKLNKYEV---NGRELV 117 (608)
T ss_pred ceEEEecCcchhhhHhHHHHHHHhcCceEeeeeeccc----CCCcCCceEEEeeCHHHHHHHHHHhhhccc---cCceEE
Confidence 559999999999999999999997776 44443321 234457899999999999999999999877 999998
Q ss_pred e
Q 009405 449 G 449 (535)
Q Consensus 449 ~ 449 (535)
.
T Consensus 118 v 118 (608)
T KOG4212|consen 118 V 118 (608)
T ss_pred E
Confidence 3
No 46
>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=89.23 E-value=0.58 Score=49.61 Aligned_cols=70 Identities=24% Similarity=0.214 Sum_probs=53.1
Q ss_pred cccEEEEecCCCCCCchhHHHHHHHHhhccceeeeccCCCCCCCCCceeEEEeechHHHHHHHhhhccceeeeeCCceee
Q 009405 369 HGTLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPLL 448 (535)
Q Consensus 369 ~GrlVlLqNLDPs~tS~eVEDli~~afke~C~AKmI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~egCL~ls~GRPL~ 448 (535)
-=+.+||.+|-++.+-.||-|-..+-...+|.+ ..|+-|=|||-|.||+||+.|.-++-.- ++.+|+-|.
T Consensus 227 ~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~--------~~~~~~CAFv~ftTR~aAE~Aae~~~n~--lvI~G~Rl~ 296 (377)
T KOG0153|consen 227 SIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIR--------ILPRKGCAFVTFTTREAAEKAAEKSFNK--LVINGFRLK 296 (377)
T ss_pred ceeEEEecccccchhHHHHHHHHhhcCCeeeEE--------eecccccceeeehhhHHHHHHHHhhcce--eeecceEEE
Confidence 335799999999888877777766655555543 2567778999999999999999999884 445775554
No 47
>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=88.72 E-value=1.5 Score=38.78 Aligned_cols=71 Identities=20% Similarity=0.350 Sum_probs=43.4
Q ss_pred cEEEEecCCCCCCchhHHHHHHHHhhccceeeeccCCCCCCCCCceeEEEeechHHHHHHHhhhccceeeeeCCceeeec
Q 009405 371 TLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPLLGS 450 (535)
Q Consensus 371 rlVlLqNLDPs~tS~eVEDli~~afke~C~AKmI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~egCL~ls~GRPL~~S 450 (535)
+++|+-||--.-.+.-|--=+++ |-++|--|++..+ .|.|.+-|.|.++|++|..+|+.--+ .|+-+.-+
T Consensus 3 s~L~V~NLP~~~d~~~I~~RL~q-LsdNCGGkVl~v~------~~tAilrF~~~~~A~RA~KRmegEdV---fG~kI~v~ 72 (90)
T PF11608_consen 3 SLLYVSNLPTNKDPSSIKNRLRQ-LSDNCGGKVLSVS------GGTAILRFPNQEFAERAQKRMEGEDV---FGNKISVS 72 (90)
T ss_dssp EEEEEES--TTS-HHHHHHHHHH-HHHTTT--EEE--------TT-EEEEESSHHHHHHHHHHHTT--S---SSS--EEE
T ss_pred cEEEEecCCCCCCHHHHHHHHHH-HhhccCCEEEEEe------CCEEEEEeCCHHHHHHHHHhhccccc---ccceEEEE
Confidence 68899999554444433333332 3469999999885 38999999999999999999987633 67766544
Q ss_pred c
Q 009405 451 I 451 (535)
Q Consensus 451 ~ 451 (535)
+
T Consensus 73 ~ 73 (90)
T PF11608_consen 73 F 73 (90)
T ss_dssp S
T ss_pred E
Confidence 3
No 48
>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]
Probab=88.54 E-value=1.6 Score=44.21 Aligned_cols=86 Identities=22% Similarity=0.268 Sum_probs=68.4
Q ss_pred hhcccEEEEecCCCCCCchhHHHHHHHHhhccceeeeccCCCCCCCCCceeEEEeechHHHHHHHhhhccceeeeeCCce
Q 009405 367 HEHGTLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRP 446 (535)
Q Consensus 367 ~E~GrlVlLqNLDPs~tS~eVEDli~~afke~C~AKmI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~egCL~ls~GRP 446 (535)
++.=+-+.+.||...-|++++--++..-. .+---.||+..|+----|-|||-|.-+.-|+-|+..|+...| +||-
T Consensus 10 v~gm~SLkVdNLTyRTspd~LrrvFekYG--~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~l---dgRe 84 (256)
T KOG4207|consen 10 VEGMTSLKVDNLTYRTSPDDLRRVFEKYG--RVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVL---DGRE 84 (256)
T ss_pred cccceeEEecceeccCCHHHHHHHHHHhC--cccceecccccccccccceeEEEeeecchHHHHHHhhcceee---ccce
Confidence 44556688999999999888765543321 233457999999999999999999999999999999999955 9999
Q ss_pred e---eeccCCcCCC
Q 009405 447 L---LGSIGTPCFT 457 (535)
Q Consensus 447 L---~~S~g~~~~p 457 (535)
| +|--|-+.++
T Consensus 85 lrVq~arygr~~d~ 98 (256)
T KOG4207|consen 85 LRVQMARYGRPSDL 98 (256)
T ss_pred eeehhhhcCCCccc
Confidence 9 7777777554
No 49
>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]
Probab=88.25 E-value=1.8 Score=41.19 Aligned_cols=94 Identities=22% Similarity=0.241 Sum_probs=67.8
Q ss_pred ccccccccCCChHHHHHhhhhcccEEEEecCCCCCCchhHHHHHHHHhhccceeeec--cCCCCCCCCCceeEEEeechH
Q 009405 348 LDRSKWFKELPWEERIRVAHEHGTLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMI--PRVAFASPYFGQSFVIFKTRE 425 (535)
Q Consensus 348 ~drskWFK~lPWeerl~~A~E~GrlVlLqNLDPs~tS~eVEDli~~afke~C~AKmI--~~~~~sspn~G~AfvIFkTke 425 (535)
+-+-+-|++ =+++--.|..+-.-||+.||--.-| |+-||.-|-.-=+.|-| -..-|.-.-+|-|||+|-+++
T Consensus 16 ~Yr~~~f~g--t~~e~~~a~r~S~tvyVgNlSfytt----EEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~ 89 (153)
T KOG0121|consen 16 AYRDRRFRG--TDEEQLEALRKSCTVYVGNLSFYTT----EEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRD 89 (153)
T ss_pred HHHHHHhcC--chHHHHHHHhhcceEEEeeeeeeec----HHHHHHHHHhccchheeEeccccCCcCccceEEEEEecch
Confidence 345555665 2344456778888999999976555 44566655543344433 345566677999999999999
Q ss_pred HHHHHHhhhccceeeeeCCceeeec
Q 009405 426 VAELVVTKLEEGCLLLSNGRPLLGS 450 (535)
Q Consensus 426 AAdsai~KL~egCL~ls~GRPL~~S 450 (535)
-|+.|+.-|+..-| +.||+-.-
T Consensus 90 dA~~AlryisgtrL---ddr~ir~D 111 (153)
T KOG0121|consen 90 DAEDALRYISGTRL---DDRPIRID 111 (153)
T ss_pred hHHHHHHHhccCcc---cccceeee
Confidence 99999999999977 99998743
No 50
>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]
Probab=85.36 E-value=1.8 Score=47.40 Aligned_cols=80 Identities=23% Similarity=0.259 Sum_probs=62.9
Q ss_pred hhhcccEEEEecCCCCCCchhHHHHHHHHhhccceeee-ccCCCCCCCCCceeEEEeechHHHHHHHhhhccceeeeeCC
Q 009405 366 AHEHGTLVVLENLDPSYTSTVVEDLVWHAFKENCSAKM-IPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNG 444 (535)
Q Consensus 366 A~E~GrlVlLqNLDPs~tS~eVEDli~~afke~C~AKm-I~~~~~sspn~G~AfvIFkTkeAAdsai~KL~egCL~ls~G 444 (535)
+.++=.++|+.||-.+-|-.-|+.++.+- .|--|+ +++. +|||=|-.|+.|-.||..+|.-|| +|
T Consensus 255 ~ms~VKvLYVRNL~~~tTeE~lk~~F~~~---G~veRVkk~rD--------YaFVHf~eR~davkAm~~~ngkel---dG 320 (506)
T KOG0117|consen 255 TMSKVKVLYVRNLMESTTEETLKKLFNEF---GKVERVKKPRD--------YAFVHFAEREDAVKAMKETNGKEL---DG 320 (506)
T ss_pred hhhheeeeeeeccchhhhHHHHHHHHHhc---cceEEeecccc--------eeEEeecchHHHHHHHHHhcCcee---cC
Confidence 45567799999999998877676666654 222222 2222 799999999999999999999999 99
Q ss_pred ceeeeccCCcCCCCC
Q 009405 445 RPLLGSIGTPCFTGK 459 (535)
Q Consensus 445 RPL~~S~g~~~~p~k 459 (535)
-||=++-+.|.+-++
T Consensus 321 ~~iEvtLAKP~~k~k 335 (506)
T KOG0117|consen 321 SPIEVTLAKPVDKKK 335 (506)
T ss_pred ceEEEEecCChhhhc
Confidence 999999998876555
No 51
>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=83.87 E-value=1.6 Score=38.12 Aligned_cols=60 Identities=25% Similarity=0.329 Sum_probs=34.4
Q ss_pred ccEEEEecCCCCCCchhHHHHHHHHhhccceeeeccCCCCCCCCCceeEEEeechHHHHHHHhhhccc
Q 009405 370 GTLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEG 437 (535)
Q Consensus 370 GrlVlLqNLDPs~tS~eVEDli~~afke~C~AKmI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~eg 437 (535)
|.||.+.++++..+-.+ |..+|++-+..+.|- | .+-...|||=|.+.++|..|+.++.+.
T Consensus 1 G~il~~~g~~~~~~re~----iK~~f~~~g~V~yVD---~-~~G~~~g~VRf~~~~~A~~a~~~~~~~ 60 (105)
T PF08777_consen 1 GCILKFSGLGEPTSRED----IKEAFSQFGEVAYVD---F-SRGDTEGYVRFKTPEAAQKALEKLKEA 60 (105)
T ss_dssp --EEEEEE--SS--HHH----HHHHT-SS--EEEEE------TT-SEEEEEESS---HHHHHHHHHHT
T ss_pred CeEEEEecCCCCcCHHH----HHHHHHhcCCcceEE---e-cCCCCEEEEEECCcchHHHHHHHHHhc
Confidence 77899999988877433 455666666444442 3 234449999999999999999999988
No 52
>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]
Probab=82.32 E-value=3 Score=41.86 Aligned_cols=64 Identities=23% Similarity=0.356 Sum_probs=47.1
Q ss_pred EEEEecCCCCCCchhHHHHHHHHhhccceeeeccCCCC-CCCCCceeEEEeechHHHHHHHhhhccc
Q 009405 372 LVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAF-ASPYFGQSFVIFKTREVAELVVTKLEEG 437 (535)
Q Consensus 372 lVlLqNLDPs~tS~eVEDli~~afke~C~AKmI~~~~~-sspn~G~AfvIFkTkeAAdsai~KL~eg 437 (535)
-+||.||.---.-+|+-..+..-|..-= +++...++ .-+..|+|||+|+..++|-.|++.|+.=
T Consensus 11 TlYInnLnekI~~~elkrsL~~LFsqfG--~ildI~a~kt~KmRGQA~VvFk~~~~As~A~r~l~gf 75 (221)
T KOG4206|consen 11 TLYINNLNEKIKKDELKRSLYLLFSQFG--KILDISAFKTPKMRGQAFVVFKETEAASAALRALQGF 75 (221)
T ss_pred eEeehhccccccHHHHHHHHHHHHHhhC--CeEEEEecCCCCccCceEEEecChhHHHHHHHHhcCC
Confidence 6899999988888888776666555422 22333344 2456899999999999999999988653
No 53
>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]
Probab=82.04 E-value=2.9 Score=43.00 Aligned_cols=63 Identities=19% Similarity=0.140 Sum_probs=49.3
Q ss_pred EEEEecCCCCCCchhHHHHHHH-HhhccceeeeccCCCCCCCCCceeEEEeechHHHHHHHhhhccc
Q 009405 372 LVVLENLDPSYTSTVVEDLVWH-AFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEG 437 (535)
Q Consensus 372 lVlLqNLDPs~tS~eVEDli~~-afke~C~AKmI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~eg 437 (535)
-|.+-||--.-+-.|++||++- +.--+|-.-+ .--+..--|-|||-|.+++-|..||..||.-
T Consensus 191 tvRvtNLsed~~E~dL~eLf~~fg~i~rvylar---dK~TG~~kGFAFVtF~sRddA~rAI~~LnG~ 254 (270)
T KOG0122|consen 191 TVRVTNLSEDMREDDLEELFRPFGPITRVYLAR---DKETGLSKGFAFVTFESRDDAARAIADLNGY 254 (270)
T ss_pred eeEEecCccccChhHHHHHhhccCccceeEEEE---ccccCcccceEEEEEecHHHHHHHHHHccCc
Confidence 4889999999999999999987 4444443322 2223445678999999999999999999874
No 54
>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=81.05 E-value=0.97 Score=42.71 Aligned_cols=71 Identities=17% Similarity=0.258 Sum_probs=47.9
Q ss_pred hhcccEEEEecCCCCCCchhHHHHHHHHhhcc---cee-eeccCCCCCCCCCceeEEEeechHHHHHHHhhhccc
Q 009405 367 HEHGTLVVLENLDPSYTSTVVEDLVWHAFKEN---CSA-KMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEG 437 (535)
Q Consensus 367 ~E~GrlVlLqNLDPs~tS~eVEDli~~afke~---C~A-KmI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~eg 437 (535)
..+|+=|.|.+|-|++|-.+..+.|..++.+. .-. =..+..+|-.+.+.+||+.|.+.+....++..+++-
T Consensus 4 ~~~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~ 78 (176)
T PF03467_consen 4 EKEGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGH 78 (176)
T ss_dssp -----EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTE
T ss_pred cccCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCc
Confidence 34567799999999999998887666556655 111 136677888888999999999999999999998774
No 55
>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]
Probab=80.83 E-value=4.2 Score=44.85 Aligned_cols=65 Identities=22% Similarity=0.315 Sum_probs=49.9
Q ss_pred chhHHHHHHHHhhccc------eeeeccCC---CCCCCCCceeEEEeechHHHHHHHhhhccceeeeeCCceeeeccC
Q 009405 384 STVVEDLVWHAFKENC------SAKMIPRV---AFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPLLGSIG 452 (535)
Q Consensus 384 S~eVEDli~~afke~C------~AKmI~~~---~~sspn~G~AfvIFkTkeAAdsai~KL~egCL~ls~GRPL~~S~g 452 (535)
-.|+|||+- .++..| .--+||++ .+.-|-+|+-||.|.+.+++..|+..|.+.-. +||-+++|.-
T Consensus 416 d~EyeeIlE-dvr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF---~nRtVvtsYy 489 (500)
T KOG0120|consen 416 DEEYEEILE-DVRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKF---ANRTVVASYY 489 (500)
T ss_pred hHHHHHHHH-HHHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCcee---CCcEEEEEec
Confidence 345556654 556655 34578888 44556778999999999999999999998855 9999998754
No 56
>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]
Probab=78.16 E-value=1.2 Score=49.38 Aligned_cols=98 Identities=16% Similarity=0.227 Sum_probs=68.4
Q ss_pred cccccCCChHHHHHhhhhcccEEEEecCCCC------------------CCchhHH-----HHHHHHhhccceee-eccC
Q 009405 351 SKWFKELPWEERIRVAHEHGTLVVLENLDPS------------------YTSTVVE-----DLVWHAFKENCSAK-MIPR 406 (535)
Q Consensus 351 skWFK~lPWeerl~~A~E~GrlVlLqNLDPs------------------~tS~eVE-----Dli~~afke~C~AK-mI~~ 406 (535)
+.|-+.+---+.+..|...+-++-++|++|. |.+++.. .=|++-..|.|.+. -|.|
T Consensus 403 s~~~~~l~~~~~~~~~~~~~~~~~~~~~~p~~~~p~~~i~t~C~lL~nMFdpstete~n~d~eI~edV~Eec~k~g~v~h 482 (549)
T KOG0147|consen 403 STAISALLLLAKLASAAQFNGVVRVRSVDPADASPAFDIPTQCLLLSNMFDPSTETEPNWDQEIREDVIEECGKHGKVCH 482 (549)
T ss_pred chhhhHHHhccccchHHhhcCCcCccccCccccccccCCccHHHHHhhcCCcccccCcchhhHHHHHHHHHHHhcCCeeE
Confidence 4455555555556666666666667888888 6666544 22334445556332 1334
Q ss_pred CCCCCCCC-ceeEEEeechHHHHHHHhhhccceeeeeCCceeeeccC
Q 009405 407 VAFASPYF-GQSFVIFKTREVAELVVTKLEEGCLLLSNGRPLLGSIG 452 (535)
Q Consensus 407 ~~~sspn~-G~AfvIFkTkeAAdsai~KL~egCL~ls~GRPL~~S~g 452 (535)
..+ ++|+ |.-||-|.+.++|..|+.-|...-+ +||=++|++-
T Consensus 483 i~v-d~ns~g~VYvrc~s~~~A~~a~~alhgrWF---~gr~Ita~~~ 525 (549)
T KOG0147|consen 483 IFV-DKNSAGCVYVRCPSAEAAGTAVKALHGRWF---AGRMITAKYL 525 (549)
T ss_pred EEE-ccCCCceEEEecCcHHHHHHHHHHHhhhhh---ccceeEEEEe
Confidence 444 7788 9999999999999999999999977 9999988765
No 57
>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]
Probab=77.84 E-value=7.6 Score=43.86 Aligned_cols=79 Identities=19% Similarity=0.259 Sum_probs=63.0
Q ss_pred EEEEecCCCCCCchhHHHHHHHHhhccceeeeccCCCCCCCCCceeEEEeechHHHHHHHhhhccceeeeeCCceeeecc
Q 009405 372 LVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPLLGSI 451 (535)
Q Consensus 372 lVlLqNLDPs~tS~eVEDli~~afke~C~AKmI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~egCL~ls~GRPL~~S~ 451 (535)
.+.|.||--+-...|++-++-. |+--.++ .|| .-++.--+|-|||-|+-+..|+.||..+|.--+ +|||+-.-.
T Consensus 119 rLIIRNLPf~~k~~dLk~vFs~-~G~V~Ei-~IP-~k~dgklcGFaFV~fk~~~dA~~Al~~~N~~~i---~gR~VAVDW 192 (678)
T KOG0127|consen 119 RLIIRNLPFKCKKPDLKNVFSN-FGKVVEI-VIP-RKKDGKLCGFAFVQFKEKKDAEKALEFFNGNKI---DGRPVAVDW 192 (678)
T ss_pred eEEeecCCcccCcHHHHHHHhh-cceEEEE-Ecc-cCCCCCccceEEEEEeeHHHHHHHHHhccCcee---cCceeEEee
Confidence 4678999989888888876644 4444454 466 667788899999999999999999999999855 999998666
Q ss_pred CCcCC
Q 009405 452 GTPCF 456 (535)
Q Consensus 452 g~~~~ 456 (535)
+++.+
T Consensus 193 AV~Kd 197 (678)
T KOG0127|consen 193 AVDKD 197 (678)
T ss_pred ecccc
Confidence 66554
No 58
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=77.01 E-value=4.6 Score=43.41 Aligned_cols=81 Identities=20% Similarity=0.337 Sum_probs=58.2
Q ss_pred cccEEEEecCCCCCCchhHHHHH-HH-Hhhc--cceeeeccCCCCCCCCCc--ee--EEEeechHHHHHHHhhhccceee
Q 009405 369 HGTLVVLENLDPSYTSTVVEDLV-WH-AFKE--NCSAKMIPRVAFASPYFG--QS--FVIFKTREVAELVVTKLEEGCLL 440 (535)
Q Consensus 369 ~GrlVlLqNLDPs~tS~eVEDli-~~-afke--~C~AKmI~~~~~sspn~G--~A--fvIFkTkeAAdsai~KL~egCL~ 440 (535)
|..|||+--+.|-|.-.||...+ ++ -|++ .-..-.|++-+- +.|+. -| |+-|.|+|-|.++|..+++..+
T Consensus 113 QKNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~-s~nst~~h~gvYITy~~kedAarcIa~vDgs~~- 190 (480)
T COG5175 113 QKNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTS-SLNSTASHAGVYITYSTKEDAARCIAEVDGSLL- 190 (480)
T ss_pred ecceeEEecCCCCCCcccccccccchhhhhhccceeEEEeccccc-ccccccccceEEEEecchHHHHHHHHHhccccc-
Confidence 45689999999999999977433 33 4554 122223444432 33332 24 9999999999999999999965
Q ss_pred eeCCceeeeccCC
Q 009405 441 LSNGRPLLGSIGT 453 (535)
Q Consensus 441 ls~GRPL~~S~g~ 453 (535)
+||-|-|+-|+
T Consensus 191 --DGr~lkatYGT 201 (480)
T COG5175 191 --DGRVLKATYGT 201 (480)
T ss_pred --cCceEeeecCc
Confidence 99999999876
No 59
>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]
Probab=75.12 E-value=4.6 Score=38.86 Aligned_cols=73 Identities=16% Similarity=0.163 Sum_probs=57.1
Q ss_pred cccEEEEecCCCCCCchhHHHHHHHHhhccceee--eccCCCCCCCCCceeEEEeechHHHHHHHhhhccceeeeeCCce
Q 009405 369 HGTLVVLENLDPSYTSTVVEDLVWHAFKENCSAK--MIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRP 446 (535)
Q Consensus 369 ~GrlVlLqNLDPs~tS~eVEDli~~afke~C~AK--mI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~egCL~ls~GRP 446 (535)
+|-+|++-++-+--|..||+|.+-+ --+.| +.+..--+.+--|+|+|.|-|.+-|..||..||..-|| |.+
T Consensus 71 EGwIi~VtgvHeEatEedi~d~F~d----yGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll---~q~ 143 (170)
T KOG0130|consen 71 EGWIIFVTGVHEEATEEDIHDKFAD----YGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELL---GQN 143 (170)
T ss_pred eeEEEEEeccCcchhHHHHHHHHhh----cccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhh---CCc
Confidence 5889999999999998888876544 33334 34555666778899999999999999999999988773 455
Q ss_pred ee
Q 009405 447 LL 448 (535)
Q Consensus 447 L~ 448 (535)
+-
T Consensus 144 v~ 145 (170)
T KOG0130|consen 144 VS 145 (170)
T ss_pred ee
Confidence 54
No 60
>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]
Probab=74.53 E-value=5.5 Score=40.63 Aligned_cols=94 Identities=19% Similarity=0.124 Sum_probs=59.9
Q ss_pred HHHHH--HhhccceeeeccCCCCCCCCCceeEEEeechHHHHHHHhhhccceeeeeCCceee---eccCCc---CCCCCC
Q 009405 389 DLVWH--AFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPLL---GSIGTP---CFTGKQ 460 (535)
Q Consensus 389 Dli~~--afke~C~AKmI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~egCL~ls~GRPL~---~S~g~~---~~p~k~ 460 (535)
+|.++ -|+|-.+|.+|--.. +..--|..||-|+-.|||.+|...-+-- -|||--= |+.|.- ..|.-+
T Consensus 28 ~l~~yFeqfGeI~eavvitd~~-t~rskGyGfVTf~d~~aa~rAc~dp~pi----IdGR~aNcnlA~lg~~pR~~~~~~~ 102 (247)
T KOG0149|consen 28 TLRRYFEQFGEIVEAVVITDKN-TGRSKGYGFVTFRDAEAATRACKDPNPI----IDGRKANCNLASLGGKPRPVPPSQP 102 (247)
T ss_pred HHHHHHHHhCceEEEEEEeccC-CccccceeeEEeecHHHHHHHhcCCCCc----ccccccccchhhhcCccCCCCCCCc
Confidence 45554 799999999996544 4777789999999999999998776653 3777743 344322 334445
Q ss_pred CccccceehhhHHH---HHHHHHHhhhccc
Q 009405 461 SKFVGHLALDKLKF---QMQREMREAVSTS 487 (535)
Q Consensus 461 s~f~GHl~i~k~r~---q~qrEmr~AVSTS 487 (535)
.-..||+-..-..| -.|+.++--+.+|
T Consensus 103 ~~~~g~~~~~~~~~~~~~~q~~~~~~~~~s 132 (247)
T KOG0149|consen 103 QQAPGGQQNRPTGMLRALPQQTFGIPPHYS 132 (247)
T ss_pred ccccccccCCcccccccccccccCCCCccc
Confidence 55566655443333 2334555444444
No 61
>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]
Probab=69.22 E-value=6.9 Score=42.53 Aligned_cols=70 Identities=24% Similarity=0.288 Sum_probs=55.2
Q ss_pred cEEEEecCCCCCCchhH-HHHHHHHhhccceeeeccC--CCCCCCCCceeEEEeechHHHHHHHhhhccceeeeeCCcee
Q 009405 371 TLVVLENLDPSYTSTVV-EDLVWHAFKENCSAKMIPR--VAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPL 447 (535)
Q Consensus 371 rlVlLqNLDPs~tS~eV-EDli~~afke~C~AKmI~~--~~~sspn~G~AfvIFkTkeAAdsai~KL~egCL~ls~GRPL 447 (535)
-.||...+ |.|+ ||.||+||------|-|+- .+...-|-|-|||.|.-.|||.-|+..||+..| +||-+
T Consensus 114 cRvYVGSI-----sfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~ml---GGRNi 185 (544)
T KOG0124|consen 114 CRVYVGSI-----SFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQML---GGRNI 185 (544)
T ss_pred Hheeeeee-----EEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccc---cCccc
Confidence 35676654 3344 6999999987766677764 355567889999999999999999999999955 99987
Q ss_pred e
Q 009405 448 L 448 (535)
Q Consensus 448 ~ 448 (535)
.
T Consensus 186 K 186 (544)
T KOG0124|consen 186 K 186 (544)
T ss_pred c
Confidence 6
No 62
>PF08075 NOPS: NOPS (NUC059) domain; InterPro: IPR012975 This domain is found C-terminal to 1 or 2 IPR000504 from INTERPRO domains [] in NONA and PSP1 proteins.; PDB: 3SDE_B.
Probab=68.87 E-value=1.4 Score=35.68 Aligned_cols=20 Identities=25% Similarity=0.737 Sum_probs=15.0
Q ss_pred ccccCCCCCcchhhcccchh
Q 009405 485 STSHCSQPNSLEYDMAIEWS 504 (535)
Q Consensus 485 STSHcSQPNtIEYdmA~eW~ 504 (535)
.--|-+||||.||++|+-|.
T Consensus 33 ~~PRFA~pgsfE~eyg~RWK 52 (52)
T PF08075_consen 33 QGPRFAQPGSFEFEYGMRWK 52 (52)
T ss_dssp S-SEE--TTSHHHHHHHHHH
T ss_pred cCCCcCCCCCcchhhccccC
Confidence 35688999999999999993
No 63
>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=65.53 E-value=15 Score=37.93 Aligned_cols=83 Identities=23% Similarity=0.226 Sum_probs=63.1
Q ss_pred cccEEEEecCCCCCCchhHHHHHHH-Hhhccce--eeeccCCCCCCCCCceeEEEeechHHHHHHHhhhccceeeeeCCc
Q 009405 369 HGTLVVLENLDPSYTSTVVEDLVWH-AFKENCS--AKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGR 445 (535)
Q Consensus 369 ~GrlVlLqNLDPs~tS~eVEDli~~-afke~C~--AKmI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~egCL~ls~GR 445 (535)
+.|.+|...| .+||-+-|-| ||=---+ +--||..--+--|-|-+||.|--+|-|..||..||++=| .||
T Consensus 9 ~KrtlYVGGl-----adeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL---~Gr 80 (298)
T KOG0111|consen 9 QKRTLYVGGL-----ADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESEL---FGR 80 (298)
T ss_pred cceeEEeccc-----hHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhh---cce
Confidence 4577788776 4677766666 6544222 333566666788999999999999999999999999988 899
Q ss_pred eeeeccCCcCCCCC
Q 009405 446 PLLGSIGTPCFTGK 459 (535)
Q Consensus 446 PL~~S~g~~~~p~k 459 (535)
-+.--.+.|.-.+.
T Consensus 81 tirVN~AkP~kike 94 (298)
T KOG0111|consen 81 TIRVNLAKPEKIKE 94 (298)
T ss_pred eEEEeecCCccccC
Confidence 99877777766555
No 64
>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]
Probab=64.57 E-value=11 Score=41.62 Aligned_cols=86 Identities=20% Similarity=0.229 Sum_probs=63.9
Q ss_pred EEEecCCCCCCchhHHHHHHH-HhhccceeeeccCCCCCCCCCceeEEEeechHHHHHHHhhhccceeeeeCCceeeecc
Q 009405 373 VVLENLDPSYTSTVVEDLVWH-AFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPLLGSI 451 (535)
Q Consensus 373 VlLqNLDPs~tS~eVEDli~~-afke~C~AKmI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~egCL~ls~GRPL~~S~ 451 (535)
+++.=|.-.-|..||++|+-. +-=|.|- |=+.++ ..--|-|||-|.|||-|-.||..|+..--|=--.-|||--+
T Consensus 127 LFvg~lsK~~te~evr~iFs~fG~Ied~~---ilrd~~-~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVkF 202 (510)
T KOG0144|consen 127 LFVGMLSKQCTENEVREIFSRFGHIEDCY---ILRDPD-GLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVKF 202 (510)
T ss_pred hhhhhccccccHHHHHHHHHhhCccchhh---heeccc-ccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEEe
Confidence 355557777788899888766 4445553 344454 55679999999999999999999997766655568999888
Q ss_pred CCcCCCCCCCc
Q 009405 452 GTPCFTGKQSK 462 (535)
Q Consensus 452 g~~~~p~k~s~ 462 (535)
+++.-|+....
T Consensus 203 ADtqkdk~~~~ 213 (510)
T KOG0144|consen 203 ADTQKDKDGKR 213 (510)
T ss_pred cccCCCchHHH
Confidence 88877766443
No 65
>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=62.32 E-value=6.7 Score=44.94 Aligned_cols=74 Identities=27% Similarity=0.285 Sum_probs=59.9
Q ss_pred ccEEEEecCCCCCCchhHHHHHHHHhhccceeeeccCCCCCCCCCceeEEEeechHHHHHHHhhhccceeeeeCCceee
Q 009405 370 GTLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPLL 448 (535)
Q Consensus 370 GrlVlLqNLDPs~tS~eVEDli~~afke~C~AKmI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~egCL~ls~GRPL~ 448 (535)
||=++++|+--.-|.-||+.|.- +|++--+.++-..... .-|.|-|||-|-|+.-|..|+.-|-++-| .||-||
T Consensus 613 ~tKIlVRNipFeAt~rEVr~LF~-aFGqlksvRlPKK~~k-~a~rGF~Fv~f~t~~ea~nA~~al~STHl---yGRrLV 686 (725)
T KOG0110|consen 613 GTKILVRNIPFEATKREVRKLFT-AFGQLKSVRLPKKIGK-GAHRGFGFVDFLTPREAKNAFDALGSTHL---YGRRLV 686 (725)
T ss_pred cceeeeeccchHHHHHHHHHHHh-cccceeeeccchhhcc-hhhccceeeeccCcHHHHHHHHhhcccce---echhhh
Confidence 89999999999999999998874 6655555555444333 66789999999999999999999998877 688776
No 66
>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]
Probab=61.59 E-value=11 Score=37.97 Aligned_cols=61 Identities=16% Similarity=0.057 Sum_probs=45.0
Q ss_pred ccEEEEecCCCCCCchhHHHHHHHHhhccceeeeccCCCCCCCCCceeEEEeechHHHHHHHhhhc
Q 009405 370 GTLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLE 435 (535)
Q Consensus 370 GrlVlLqNLDPs~tS~eVEDli~~afke~C~AKmI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~ 435 (535)
-+.+|..||-|..-.-|||||+..-.+-.-.-.-+++-+ .+.|||.|...--||-||---+
T Consensus 6 ~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~g~-----ppfafVeFEd~RDAeDAiygRd 66 (241)
T KOG0105|consen 6 SRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRPGP-----PPFAFVEFEDPRDAEDAIYGRD 66 (241)
T ss_pred cceEEecCCCcchhhccHHHHHhhhcceEEEEeccCCCC-----CCeeEEEecCccchhhhhhccc
Confidence 467899999999999999999988544322222222211 3569999999999999998766
No 67
>PF02617 ClpS: ATP-dependent Clp protease adaptor protein ClpS; InterPro: IPR003769 In the bacterial cytosol, ATP-dependent protein degradation is performed by several different chaperone-protease pairs, including ClpAP. ClpS directly influences the ClpAP machine by binding to the N-terminal domain of the chaperone ClpA. The degradation of ClpAP substrates, both SsrA-tagged proteins and ClpA itself, is specifically inhibited by ClpS. ClpS modifies ClpA substrate specificity, potentially redirecting degradation by ClpAP toward aggregated proteins []. ClpS is a small alpha/beta protein that consists of three alpha-helices connected to three antiparallel beta-strands []. The protein has a globular shape, with a curved layer of three antiparallel alpha-helices over a twisted antiparallel beta-sheet. Dimerization of ClpS may occur through its N-terminal domain. This short extended N-terminal region in ClpS is followed by the central seven-residue beta-strand, which is flanked by two other beta-strands in a small beta-sheet. ; GO: 0030163 protein catabolic process; PDB: 3O2O_B 1MBU_D 3O2B_C 2WA9_D 3O1F_A 2W9R_A 1MG9_A 1MBX_C 2WA8_C 1R6O_D ....
Probab=60.12 E-value=1.8 Score=35.81 Aligned_cols=74 Identities=32% Similarity=0.373 Sum_probs=47.4
Q ss_pred EEEecCCCCCCchhHHHHHHHHhhccceeeeccCCCCCCCCCceeEEEeechHHHHHHHhhhccceeeeeCCceeeecc
Q 009405 373 VVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPLLGSI 451 (535)
Q Consensus 373 VlLqNLDPs~tS~eVEDli~~afke~C~AKmI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~egCL~ls~GRPL~~S~ 451 (535)
|+|=| |+--+=..|.+.++++| .|+-.....-+..--..|+|.|...+++.|+....+|...= =..|.||.+++
T Consensus 9 vvL~N-De~ht~~~Vi~~L~~~~--~~s~~~A~~~a~~v~~~G~avv~~~~~e~ae~~~~~l~~~g--~~~~~PL~~ti 82 (82)
T PF02617_consen 9 VVLWN-DEVHTFEQVIDVLRRVF--GCSEEQARQIAMEVHREGRAVVGTGSREEAEEYAEKLQRAG--RDSGHPLRATI 82 (82)
T ss_dssp EEEE---SSSBHHHHHHHHHHHC-----HHHHHHHHHHHHHHSEEEEEEEEHHHHHHHHHHHHHHH--HHTT---EEEE
T ss_pred EEEEc-CCCCCHHHHHHHHHHHH--CCCHHHHHHHHHHHhHcCCEeeeeCCHHHHHHHHHHHHHHh--hccCCCeEEeC
Confidence 34444 55556677889999988 45544443334444467999999999999999999998763 13688998763
No 68
>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]
Probab=59.11 E-value=17 Score=40.52 Aligned_cols=67 Identities=21% Similarity=0.225 Sum_probs=48.0
Q ss_pred cccEEEEecCCCCCCchhHHHHHHHHhhccceeeeccCCCCCCCCCceeEEEeechHHHHHHHhhhccc
Q 009405 369 HGTLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEG 437 (535)
Q Consensus 369 ~GrlVlLqNLDPs~tS~eVEDli~~afke~C~AKmI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~eg 437 (535)
---||.|.-|--+-|..||.|.+- .=+-++.-+.=..-+-.+-+|.|||-|-|.+.|+.|+.+..+-
T Consensus 102 ~d~vVRLRGLPfscte~dI~~FFa--GL~Iv~~gi~l~~d~rgR~tGEAfVqF~sqe~ae~Al~rhre~ 168 (510)
T KOG4211|consen 102 NDGVVRLRGLPFSCTEEDIVEFFA--GLEIVPDGILLPMDQRGRPTGEAFVQFESQESAEIALGRHREN 168 (510)
T ss_pred CCceEEecCCCccCcHHHHHHHhc--CCcccccceeeeccCCCCcccceEEEecCHHHHHHHHHHHHHh
Confidence 446999999999999999997541 1122222111222344678999999999999999999876654
No 69
>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]
Probab=59.05 E-value=5.7 Score=40.80 Aligned_cols=46 Identities=24% Similarity=0.394 Sum_probs=40.1
Q ss_pred CCCCceeEEEeechHHHHHHHhhhccceeeeeCCceeeeccCCcCCCCC
Q 009405 411 SPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPLLGSIGTPCFTGK 459 (535)
Q Consensus 411 spn~G~AfvIFkTkeAAdsai~KL~egCL~ls~GRPL~~S~g~~~~p~k 459 (535)
+---|-+||-|+.-|.|+.|+.-||..-. +|||++|=..-.++|.-
T Consensus 107 ~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~---~G~pi~ae~~pvT~~re 152 (260)
T KOG2202|consen 107 DHLVGNVYVKFRSEEDAEAALEDLNNRWY---NGRPIHAELSPVTDFRE 152 (260)
T ss_pred hhhhhhhhhhcccHHHHHHHHHHHcCccc---cCCcceeeecCcCchhh
Confidence 34458999999999999999999999977 99999988887777754
No 70
>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]
Probab=53.40 E-value=27 Score=35.22 Aligned_cols=83 Identities=16% Similarity=0.151 Sum_probs=60.5
Q ss_pred hhcccEEEEecCCCCCCchhHHHHHHHHhhccceeeeccCCCCCCCCCceeEEEeechHHHHHHHhhhccceeeeeCCce
Q 009405 367 HEHGTLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRP 446 (535)
Q Consensus 367 ~E~GrlVlLqNLDPs~tS~eVEDli~~afke~C~AKmI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~egCL~ls~GRP 446 (535)
.+.-.++|+..+--.|.-.++.-..++.++ .+.-.-..|.--..-.-|+|||-|-+.+.|..|-.-||.=+| .|+=
T Consensus 46 ~~~~g~~~~~~~p~g~~e~~~~~~~~q~~g-~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl---~e~l 121 (214)
T KOG4208|consen 46 QEIEGVVYVDHIPHGFFETEILNYFRQFGG-TVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLL---MEHL 121 (214)
T ss_pred cCCccceeecccccchhHHHHhhhhhhcCC-eeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhh---hhhe
Confidence 344467788777777777777777776553 333333445555566678999999999999999999999866 7888
Q ss_pred eeeccCC
Q 009405 447 LLGSIGT 453 (535)
Q Consensus 447 L~~S~g~ 453 (535)
|.|..=-
T Consensus 122 L~c~vmp 128 (214)
T KOG4208|consen 122 LECHVMP 128 (214)
T ss_pred eeeEEeC
Confidence 8877543
No 71
>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]
Probab=50.02 E-value=30 Score=35.02 Aligned_cols=63 Identities=25% Similarity=0.335 Sum_probs=52.9
Q ss_pred hhcccEEEEecCCCCCCchhHHHHHHH--HhhccceeeeccCCCCCCCCCceeEEEeechHHHHHHHhhhccce
Q 009405 367 HEHGTLVVLENLDPSYTSTVVEDLVWH--AFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGC 438 (535)
Q Consensus 367 ~E~GrlVlLqNLDPs~tS~eVEDli~~--afke~C~AKmI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~egC 438 (535)
.-...+++++|+...-++...++|..+ ||+| +|||+. -.|.|||-|.+.-.|..|..-|+..-
T Consensus 143 ~ppn~ilf~~niP~es~~e~l~~lf~qf~g~ke---ir~i~~------~~~iAfve~~~d~~a~~a~~~lq~~~ 207 (221)
T KOG4206|consen 143 APPNNILFLTNIPSESESEMLSDLFEQFPGFKE---IRLIPP------RSGIAFVEFLSDRQASAAQQALQGFK 207 (221)
T ss_pred CCCceEEEEecCCcchhHHHHHHHHhhCcccce---eEeccC------CCceeEEecchhhhhHHHhhhhccce
Confidence 445678999999999999999999988 7775 788874 35799999999999999998887653
No 72
>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]
Probab=48.88 E-value=8.5 Score=38.42 Aligned_cols=78 Identities=22% Similarity=0.194 Sum_probs=65.0
Q ss_pred hHHHHHhhhhcccEEEEecCCCCCCchhHHHHHHHHhhccceeeeccCCCCCCCCCceeEEEeechHHHHHHHhhhccce
Q 009405 359 WEERIRVAHEHGTLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGC 438 (535)
Q Consensus 359 Weerl~~A~E~GrlVlLqNLDPs~tS~eVEDli~~afke~C~AKmI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~egC 438 (535)
|.-..+.--.-..++.++|+---+.--|+.|.+..+.+. ++..-..+.|||-|.+.+-|-.|+++|++.=
T Consensus 88 ~~~~~~~p~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~----------~~~~~~~~~~~v~Fs~~~da~ra~~~l~~~~ 157 (216)
T KOG0106|consen 88 DSRRYRPPSRTHFRLIVRNLSLRVSWQDLKDHFRPAGEV----------TYVDARRNFAFVEFSEQEDAKRALEKLDGKK 157 (216)
T ss_pred hhhccCCcccccceeeeccchhhhhHHHHhhhhcccCCC----------chhhhhccccceeehhhhhhhhcchhccchh
Confidence 777788878889999999998888778888998887665 2222267899999999999999999999986
Q ss_pred eeeeCCceeee
Q 009405 439 LLLSNGRPLLG 449 (535)
Q Consensus 439 L~ls~GRPL~~ 449 (535)
+ +|++|..
T Consensus 158 ~---~~~~l~~ 165 (216)
T KOG0106|consen 158 L---NGRRISV 165 (216)
T ss_pred h---cCceeee
Confidence 6 8888886
No 73
>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]
Probab=48.51 E-value=30 Score=34.70 Aligned_cols=59 Identities=25% Similarity=0.134 Sum_probs=47.8
Q ss_pred cEEEEecCCCCCCchhHHHHHHHHhhccceeeeccCCCCCCCCCceeEEEeechHHHHHHHhhhcccee
Q 009405 371 TLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCL 439 (535)
Q Consensus 371 rlVlLqNLDPs~tS~eVEDli~~afke~C~AKmI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~egCL 439 (535)
.-||+.+|.+.-.-.|||.+.|.=++.. .|.| .+|.+||+|...-.||-||..|+.-=|
T Consensus 2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~-d~~m---------k~gf~fv~fed~rda~Dav~~l~~~~l 60 (216)
T KOG0106|consen 2 PRVYIGRLPYRARERDVERFFKGYGKIP-DADM---------KNGFGFVEFEDPRDADDAVHDLDGKEL 60 (216)
T ss_pred CceeecccCCccchhHHHHHHhhccccc-ccee---------ecccceeccCchhhhhcccchhcCcee
Confidence 3589999999999999999998766542 2222 467779999999999999999987655
No 74
>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]
Probab=47.19 E-value=30 Score=38.39 Aligned_cols=75 Identities=20% Similarity=0.124 Sum_probs=48.2
Q ss_pred ccccccCCCccccccccCC---Ch-HHHHHhhhhcccEEEEecCCCCCCchhHHHHHHHHhhccceeeeccCCCCCCCCC
Q 009405 339 IVEVTRRPSLDRSKWFKEL---PW-EERIRVAHEHGTLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYF 414 (535)
Q Consensus 339 i~evt~rP~~drskWFK~l---PW-eerl~~A~E~GrlVlLqNLDPs~tS~eVEDli~~afke~C~AKmI~~~~~sspn~ 414 (535)
...-|.-|+.|--|-|.+. -| |+.||+-.|+=-.||== .|.++-...---
T Consensus 23 ~~~~~d~~d~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~ei--------------------------nl~kDk~t~~s~ 76 (510)
T KOG0144|consen 23 SLDHTDNPDGSAVKLFVGQIPRTASEKDLRELFEKYGNVYEI--------------------------NLIKDKSTGQSK 76 (510)
T ss_pred CCCCCCCCCchhhhheeccCCccccHHHHHHHHHHhCceeEE--------------------------EeecccccCccc
Confidence 3344555666677777643 34 34455555554444322 234444455667
Q ss_pred ceeEEEeechHHHHHHHhhhcccee
Q 009405 415 GQSFVIFKTREVAELVVTKLEEGCL 439 (535)
Q Consensus 415 G~AfvIFkTkeAAdsai~KL~egCL 439 (535)
|-|||.|.|+|+||+||.-|-+--.
T Consensus 77 gcCFv~~~trk~a~~a~~Alhn~kt 101 (510)
T KOG0144|consen 77 GCCFVKYYTRKEADEAINALHNQKT 101 (510)
T ss_pred ceEEEEeccHHHHHHHHHHhhcccc
Confidence 9999999999999999998876544
No 75
>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]
Probab=43.88 E-value=62 Score=36.60 Aligned_cols=117 Identities=21% Similarity=0.201 Sum_probs=79.2
Q ss_pred EEEecCCCCCCchhHHHHHHHHhhccceeeeccCCCCCCCCCceeEEEeechHHHHHHHhhhccceeeeeCCceeeeccC
Q 009405 373 VVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPLLGSIG 452 (535)
Q Consensus 373 VlLqNLDPs~tS~eVEDli~~afke~C~AKmI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~egCL~ls~GRPL~~S~g 452 (535)
+|..||-+-.+.+.+-.|.. .|. ..+.-+.+...-.+...|..|+-|.-++-|..|+-+||. |-| .||++.-+-+
T Consensus 281 l~vgnLHfNite~~lr~ife-pfg-~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lng--fel-AGr~ikV~~v 355 (549)
T KOG0147|consen 281 LYVGNLHFNITEDMLRGIFE-PFG-KIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNG--FEL-AGRLIKVSVV 355 (549)
T ss_pred hhhcccccCchHHHHhhhcc-Ccc-cceeeeeccccccccccCcceEEEecHHHHHHHHHHhcc--cee-cCceEEEEEe
Confidence 78999998888666554332 121 455666666665688999999999999999999999999 555 9999875544
Q ss_pred CcCCCCC---CCccc------cceeh-hhHHHHHHHHHHhhhccccCCCCCc
Q 009405 453 TPCFTGK---QSKFV------GHLAL-DKLKFQMQREMREAVSTSHCSQPNS 494 (535)
Q Consensus 453 ~~~~p~k---~s~f~------GHl~i-~k~r~q~qrEmr~AVSTSHcSQPNt 494 (535)
+-.+-.+ +..|- +-|.+ +-.|.|.|+..-.+.-++-||-+|+
T Consensus 356 ~~r~~~~~a~~~~~d~D~~d~~gl~~~~~g~~Ql~~kla~~~~~~~~s~~~~ 407 (549)
T KOG0147|consen 356 TERVDTKEAAVTQFDFDEDDRQGLSLGSGGRNQLMAKLAEGKGRSLPSTAIS 407 (549)
T ss_pred eeecccccccccccccchhhccccccccccHHHHHHHHhccCCccccchhhh
Confidence 3222222 11111 11111 2336788888888888888887775
No 76
>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif
Probab=40.28 E-value=48 Score=25.84 Aligned_cols=45 Identities=16% Similarity=0.157 Sum_probs=29.2
Q ss_pred CCchhHHHHHHHHhhccceeeeccCCCCCCCCCceeEEEeechHHHHHHH
Q 009405 382 YTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVV 431 (535)
Q Consensus 382 ~tS~eVEDli~~afke~C~AKmI~~~~~sspn~G~AfvIFkTkeAAdsai 431 (535)
|...+.++++. -|..-++-..|.-+ +..-.+|+.|.++.+|+.|+
T Consensus 9 f~~~~~~~vl~-~F~~fGeI~~~~~~----~~~~~~~l~y~~~~~ae~Al 53 (53)
T PF14605_consen 9 FPPDLAEEVLE-HFASFGEIVDIYVP----ESTNWMYLKYKSRKDAEKAL 53 (53)
T ss_pred ECchHHHHHHH-HHHhcCCEEEEEcC----CCCcEEEEEECCHHHHHhhC
Confidence 44555555555 45554444444433 44557999999999999985
No 77
>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]
Probab=40.25 E-value=99 Score=32.84 Aligned_cols=77 Identities=25% Similarity=0.333 Sum_probs=60.6
Q ss_pred cccEEEEecCCCCCCchhHHHHHHHHhhc---cceeeeccCCCCCCCCCceeEEEeechHHHHHHHhhhccceeeeeCCc
Q 009405 369 HGTLVVLENLDPSYTSTVVEDLVWHAFKE---NCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGR 445 (535)
Q Consensus 369 ~GrlVlLqNLDPs~tS~eVEDli~~afke---~C~AKmI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~egCL~ls~GR 445 (535)
.|--+++=||-|.- =|-++||-|.. -..+|+|--.+. +---|.+||-...-+-|..||..||.--| ++|
T Consensus 277 ~g~ciFvYNLspd~----de~~LWQlFgpFGAv~nVKvirD~tt-nkCKGfgFVtMtNYdEAamAi~sLNGy~l---g~r 348 (360)
T KOG0145|consen 277 GGWCIFVYNLSPDA----DESILWQLFGPFGAVTNVKVIRDFTT-NKCKGFGFVTMTNYDEAAMAIASLNGYRL---GDR 348 (360)
T ss_pred CeeEEEEEecCCCc----hHhHHHHHhCcccceeeEEEEecCCc-ccccceeEEEecchHHHHHHHHHhcCccc---cce
Confidence 35568888987743 36799997765 566788755443 77789999999999999999999999987 899
Q ss_pred eeeeccCC
Q 009405 446 PLLGSIGT 453 (535)
Q Consensus 446 PL~~S~g~ 453 (535)
-|--|+.+
T Consensus 349 vLQVsFKt 356 (360)
T KOG0145|consen 349 VLQVSFKT 356 (360)
T ss_pred EEEEEEec
Confidence 88776643
No 78
>PRK00033 clpS ATP-dependent Clp protease adaptor protein ClpS; Reviewed
Probab=38.66 E-value=37 Score=30.28 Aligned_cols=68 Identities=25% Similarity=0.260 Sum_probs=47.4
Q ss_pred EEEecCCCCCCchhHHHHHHHHhhccceeeeccCCCCCCCCCceeEEEeechHHHHHHHhhhccceeeeeCCceeeecc
Q 009405 373 VVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRPLLGSI 451 (535)
Q Consensus 373 VlLqNLDPs~tS~eVEDli~~afke~C~AKmI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~egCL~ls~GRPL~~S~ 451 (535)
|+|-| |+==|=+-|-+++...| .++..-...-..--=+.|+|.|...++|-|+.-..+| .|.||.|+.
T Consensus 30 ViL~N-Dd~ntmd~Vv~vL~~vf--~~s~~~A~~iml~vH~~G~avv~~~~~e~AE~~~~~l--------~~~~L~~~i 97 (100)
T PRK00033 30 VLLHN-DDYTPMEFVVYVLQKFF--GYDRERATQIMLEVHNEGKAVVGVCTREVAETKVEQV--------HQHGLLCTM 97 (100)
T ss_pred EEEEc-CCCCCHHHHHHHHHHHH--CCCHHHHHHHHHHHhcCCcEEEEEEcHHHHHHHHHHH--------HcCCCeEEE
Confidence 55555 33233344667888888 4444444444444568899999999999999999999 677888764
No 79
>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]
Probab=38.27 E-value=35 Score=37.96 Aligned_cols=77 Identities=16% Similarity=0.097 Sum_probs=56.3
Q ss_pred cccEEEEecCCCCCCchhHHHHHHHHhhccceeeeccCCCCC--CCCCceeEEEeechHHHHHHHhhhccceeeeeCCce
Q 009405 369 HGTLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFA--SPYFGQSFVIFKTREVAELVVTKLEEGCLLLSNGRP 446 (535)
Q Consensus 369 ~GrlVlLqNLDPs~tS~eVEDli~~afke~C~AKmI~~~~~s--spn~G~AfvIFkTkeAAdsai~KL~egCL~ls~GRP 446 (535)
..-=+++.||-.-++.+.|-+||-. -|.-++-....=+ .-+.|.||..|..-...|.|+.-||.-|| ++.+
T Consensus 288 ~~~ki~v~~lp~~l~~~q~~Ell~~----fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~l---gd~~ 360 (500)
T KOG0120|consen 288 SPNKIFVGGLPLYLTEDQVKELLDS----FGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQL---GDKK 360 (500)
T ss_pred ccchhhhccCcCccCHHHHHHHHHh----cccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhh---cCce
Confidence 3444677888888888888777654 3333333322221 35678999999999999999999999999 8899
Q ss_pred eeeccC
Q 009405 447 LLGSIG 452 (535)
Q Consensus 447 L~~S~g 452 (535)
||...+
T Consensus 361 lvvq~A 366 (500)
T KOG0120|consen 361 LVVQRA 366 (500)
T ss_pred eEeehh
Confidence 986554
No 80
>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]
Probab=37.20 E-value=57 Score=34.56 Aligned_cols=65 Identities=17% Similarity=0.234 Sum_probs=50.2
Q ss_pred ccEEEEecCCCCCCchhHHHHHHHHhhccceeeeccCCCCCCCCCceeEEEeechHHHHHHHhhhcc
Q 009405 370 GTLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEE 436 (535)
Q Consensus 370 GrlVlLqNLDPs~tS~eVEDli~~afke~C~AKmI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~e 436 (535)
|.=+|+..|--+.|--|+|+|+.+ |+.--+.|+..- .....--|-+|+-|..|+-||+||.-||.
T Consensus 127 ~aNLYvSGlPktMtqkelE~iFs~-fGrIItSRiL~d-qvtg~srGVgFiRFDKr~EAe~AIk~lNG 191 (360)
T KOG0145|consen 127 DANLYVSGLPKTMTQKELEQIFSP-FGRIITSRILVD-QVTGLSRGVGFIRFDKRIEAEEAIKGLNG 191 (360)
T ss_pred ccceEEecCCccchHHHHHHHHHH-hhhhhhhhhhhh-cccceecceeEEEecchhHHHHHHHhccC
Confidence 446899999999999999999887 333344444432 23355667899999999999999999875
No 81
>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]
Probab=32.95 E-value=83 Score=35.33 Aligned_cols=61 Identities=23% Similarity=0.205 Sum_probs=43.8
Q ss_pred cccEEEEecCCCCCCchhHHHHHHHHhhccceeeeccCCCCCCCCCceeEEEeechHHHHHHHhhh
Q 009405 369 HGTLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKL 434 (535)
Q Consensus 369 ~GrlVlLqNLDPs~tS~eVEDli~~afke~C~AKmI~~~~~sspn~G~AfvIFkTkeAAdsai~KL 434 (535)
.+-+|.|+-|-=+-|-.||.|.+ ..|+..=.-.+-.....+|.|||.|.+.|-++.|+.|=
T Consensus 9 ~~~~vr~rGLPwsat~~ei~~Ff-----~~~~I~~~~~~r~~Gr~sGeA~Ve~~seedv~~Alkkd 69 (510)
T KOG4211|consen 9 TAFEVRLRGLPWSATEKEILDFF-----SNCGIENLEIPRRNGRPSGEAYVEFTSEEDVEKALKKD 69 (510)
T ss_pred cceEEEecCCCccccHHHHHHHH-----hcCceeEEEEeccCCCcCcceEEEeechHHHHHHHHhh
Confidence 34466777777777777777654 45554433344445789999999999999999999764
No 82
>PF12133 Sars6: Open reading frame 6 from SARS coronavirus; InterPro: IPR022736 This entry represents small proteins, typically between 42 to 63 amino acids in length, which are uncharacterised.
Probab=28.85 E-value=32 Score=28.73 Aligned_cols=38 Identities=29% Similarity=0.472 Sum_probs=29.2
Q ss_pred chhhHHHHHHHHHHHHhhcccccch-----------hhhhhhccCcccc
Q 009405 2 MLHFVLFVSLYLYLFLPLLSSFNVA-----------VKFIFNRQGYQNS 39 (535)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~ie-----------VKfifN~~~~Q~s 39 (535)
|+|.|-|-.-..-+.+-++.+||++ ||-+||++...+-
T Consensus 1 mf~lv~fqvtiae~li~im~sf~~a~~~~~i~i~s~~~~l~~~l~k~~y 49 (62)
T PF12133_consen 1 MFHLVDFQVTIAEILIIIMRSFRIAIWNIQIIISSIVRQLFNPLDKKNY 49 (62)
T ss_pred CceeehhHhhHHHHHHHHHHHHHHHHHhHHhHHHHHHHHHhcccccccc
Confidence 7888888777667777778899887 5778999875443
No 83
>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]
Probab=24.27 E-value=1.3e+02 Score=34.16 Aligned_cols=64 Identities=28% Similarity=0.319 Sum_probs=48.2
Q ss_pred hhhcccEEEEecCCCCCCchhHHHHHHHHhhccceeeeccCCCCCCCCCceeEEEeechHHHHHHHhhhccc
Q 009405 366 AHEHGTLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEG 437 (535)
Q Consensus 366 A~E~GrlVlLqNLDPs~tS~eVEDli~~afke~C~AKmI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~eg 437 (535)
-.-+|+||++ |||++.+-+++..|+ .+++|-=+.+|-++ +-|..||-|=----|+.|+..|+..
T Consensus 72 ~~~~~~L~v~-nl~~~Vsn~~L~~~f-~~yGeir~ir~t~~------~~~~~~v~FyDvR~A~~Alk~l~~~ 135 (549)
T KOG4660|consen 72 DMNQGTLVVF-NLPRSVSNDTLLRIF-GAYGEIREIRETPN------KRGIVFVEFYDVRDAERALKALNRR 135 (549)
T ss_pred cCccceEEEE-ecCCcCCHHHHHHHH-Hhhcchhhhhcccc------cCceEEEEEeehHhHHHHHHHHHHH
Confidence 3468888876 899999999998776 35666544444332 4689999998888889999888764
No 84
>PRK04326 methionine synthase; Provisional
Probab=24.16 E-value=95 Score=31.18 Aligned_cols=69 Identities=12% Similarity=0.195 Sum_probs=47.3
Q ss_pred HHHhhhhc--ccEEEEecCCCCC----CchhHHHHHHHHhhccceeeeccCCCCCCCCCceeEEEeechHHHHHHHhhhc
Q 009405 362 RIRVAHEH--GTLVVLENLDPSY----TSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLE 435 (535)
Q Consensus 362 rl~~A~E~--GrlVlLqNLDPs~----tS~eVEDli~~afke~C~AKmI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~ 435 (535)
.|..+.+. |..+.+.|+|+.. +.++|.+.++.+++ .+.+. --+-+|.||=+++ +.+.|...+.-|-
T Consensus 245 ~l~~~~~~~~~~~l~~Gvv~~~~~~~~~~e~v~~~v~~~~~-~~~~~----~~~lsp~Cgl~~~---~~~~a~~kl~~l~ 316 (330)
T PRK04326 245 LLDLLKEYGFDKELGLGVIDVHSARVESVEEIKEAIKKGLE-YVPPE----KLYINPDCGLKLL---PREIAYQKLVNMV 316 (330)
T ss_pred hHHHhhccCCCCeEEeEEEeCCCCCCCCHHHHHHHHHHHHH-hCChh----hEEECCCCCCCcC---CHHHHHHHHHHHH
Confidence 44445555 8899999999966 56778888888888 33321 2344788886643 6777777777666
Q ss_pred cce
Q 009405 436 EGC 438 (535)
Q Consensus 436 egC 438 (535)
+++
T Consensus 317 ~~a 319 (330)
T PRK04326 317 KAT 319 (330)
T ss_pred HHH
Confidence 554
No 85
>PF09673 TrbC_Ftype: Type-F conjugative transfer system pilin assembly protein; InterPro: IPR019106 This entry represents TrbC, a protein that is an essential component of the F-type conjugative pilus assembly system (aka type 4 secretion system) for the transfer of plasmid DNA [, ]. The N-terminal portion of these proteins is heterogeneous.
Probab=22.35 E-value=3.8e+02 Score=23.76 Aligned_cols=92 Identities=12% Similarity=0.134 Sum_probs=65.1
Q ss_pred HHHHHhhhhcccEEEEecCCCCCCchhHHHHHHHHhhccc--eeeeccCCCCCCCCCceeEEEeechHHHHHHHhhhccc
Q 009405 360 EERIRVAHEHGTLVVLENLDPSYTSTVVEDLVWHAFKENC--SAKMIPRVAFASPYFGQSFVIFKTREVAELVVTKLEEG 437 (535)
Q Consensus 360 eerl~~A~E~GrlVlLqNLDPs~tS~eVEDli~~afke~C--~AKmI~~~~~sspn~G~AfvIFkTkeAAdsai~KL~eg 437 (535)
..-++.|...|-.+.|.-+-+. .--+-...+.+.+++.+ ..=.|.+..|.-++.-+.=++
T Consensus 14 ~~l~~~a~~~~~~~V~RG~~~g-~~~~t~~~~~~l~~~~~~~~~v~IdP~~F~~y~I~~VPa~----------------- 75 (113)
T PF09673_consen 14 RNLLKQAERAGVVVVFRGFPDG-SFKPTAKAIQELLRKDDPCPGVQIDPRLFRQYNITAVPAF----------------- 75 (113)
T ss_pred HHHHHHHHhCCcEEEEECCCCC-CHHHHHHHHHHHhhccCCCcceeEChhHHhhCCceEcCEE-----------------
Confidence 3456788888999999999888 44444455566666654 457899999987777654332
Q ss_pred eeeeeCCceeeeccCCcCCCCCCCccccceehhh
Q 009405 438 CLLLSNGRPLLGSIGTPCFTGKQSKFVGHLALDK 471 (535)
Q Consensus 438 CL~ls~GRPL~~S~g~~~~p~k~s~f~GHl~i~k 471 (535)
++..+++..|.-..+|.|..--..+|+++++.
T Consensus 76 --V~~~~~~~~~~~~~~~~~~~~~~~~Gdvsl~~ 107 (113)
T PF09673_consen 76 --VVVKDRVCVCLSCGCCSPEDYDVVYGDVSLDY 107 (113)
T ss_pred --EEEcCcccccccCCcCCCCcceEEEccccHHH
Confidence 22233666667777888888888999999874
No 86
>PF13041 PPR_2: PPR repeat family
Probab=21.92 E-value=66 Score=23.47 Aligned_cols=31 Identities=19% Similarity=0.268 Sum_probs=28.0
Q ss_pred CCcchhhcccchhhhHHHHHHHHHHHHHHHH
Q 009405 492 PNSLEYDMAIEWSLLQERLDCAWKKLYEQQE 522 (535)
Q Consensus 492 PNtIEYdmA~eW~Llqek~~~~w~~L~k~~~ 522 (535)
||++-|...|.++.-+.+.+.+|+.+.+-+.
T Consensus 1 P~~~~yn~li~~~~~~~~~~~a~~l~~~M~~ 31 (50)
T PF13041_consen 1 PDVVTYNTLISGYCKAGKFEEALKLFKEMKK 31 (50)
T ss_pred CchHHHHHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 8999999999999999999999999876553
Done!