Query 001496
Match_columns 1066
No_of_seqs 157 out of 190
Neff 2.2
Searched_HMMs 46136
Date Fri Mar 29 02:17:02 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001496.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/001496hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03134 glycine-rich RNA-bind 96.7 0.0014 3.1E-08 63.0 3.6 42 675-716 41-84 (144)
2 KOG0921 Dosage compensation co 96.5 0.011 2.5E-07 71.6 9.8 11 766-776 1231-1241(1282)
3 TIGR01659 sex-lethal sex-letha 95.5 0.018 4E-07 62.8 5.5 43 674-716 199-243 (346)
4 KOG3973 Uncharacterized conser 95.5 0.054 1.2E-06 60.7 8.8 11 693-703 294-304 (465)
5 KOG3262 H/ACA small nucleolar 94.8 0.06 1.3E-06 56.2 6.3 21 777-798 193-213 (215)
6 TIGR01661 ELAV_HUD_SF ELAV/HuD 94.0 0.014 3E-07 60.5 -0.2 41 676-716 277-319 (352)
7 KOG3262 H/ACA small nucleolar 93.0 0.2 4.4E-06 52.5 6.2 41 744-786 171-212 (215)
8 PTZ00146 fibrillarin; Provisio 92.3 0.29 6.3E-06 53.3 6.5 6 867-872 110-115 (293)
9 KOG0122 Translation initiation 88.7 0.11 2.5E-06 56.0 -0.4 41 676-716 197-239 (270)
10 KOG4210 Nuclear localization s 88.7 0.17 3.8E-06 54.4 1.0 41 676-716 193-235 (285)
11 TIGR01661 ELAV_HUD_SF ELAV/HuD 88.4 0.12 2.6E-06 53.7 -0.5 42 675-716 10-53 (352)
12 TIGR01659 sex-lethal sex-letha 88.3 0.13 2.9E-06 56.3 -0.2 41 676-716 115-157 (346)
13 PLN03213 repressor of silencin 87.3 0.17 3.6E-06 58.9 -0.2 37 676-716 18-56 (759)
14 COG0724 RNA-binding proteins ( 85.3 0.27 5.9E-06 45.5 0.1 41 676-716 123-165 (306)
15 TIGR01645 half-pint poly-U bin 84.3 0.32 6.9E-06 57.5 0.1 42 675-716 114-157 (612)
16 KOG0116 RasGAP SH3 binding pro 84.1 1.2 2.6E-05 50.9 4.5 40 676-716 296-338 (419)
17 TIGR01628 PABP-1234 polyadenyl 83.2 0.31 6.7E-06 54.8 -0.5 42 675-716 7-50 (562)
18 PLN03120 nucleic acid binding 83.1 0.36 7.8E-06 52.1 -0.1 40 675-717 11-52 (260)
19 KOG0108 mRNA cleavage and poly 82.7 0.52 1.1E-05 53.9 0.9 43 675-717 25-69 (435)
20 TIGR01645 half-pint poly-U bin 81.8 0.47 1E-05 56.2 0.2 44 674-717 210-255 (612)
21 TIGR01622 SF-CC1 splicing fact 81.7 0.44 9.5E-06 51.7 -0.1 43 675-717 96-140 (457)
22 KOG0113 U1 small nuclear ribon 78.0 0.61 1.3E-05 51.8 -0.4 42 675-716 108-151 (335)
23 PLN03121 nucleic acid binding 76.9 0.74 1.6E-05 49.6 -0.2 40 675-717 12-53 (243)
24 smart00360 RRM RNA recognition 75.7 0.75 1.6E-05 34.9 -0.4 41 676-716 4-46 (71)
25 TIGR01622 SF-CC1 splicing fact 73.5 0.96 2.1E-05 49.2 -0.4 43 675-717 193-237 (457)
26 TIGR01648 hnRNP-R-Q heterogene 73.3 3.5 7.5E-05 48.8 4.0 34 675-716 240-277 (578)
27 KOG4207 Predicted splicing fac 73.0 1 2.3E-05 48.3 -0.3 41 676-716 21-63 (256)
28 TIGR01642 U2AF_lg U2 snRNP aux 70.2 1.3 2.8E-05 48.8 -0.3 42 675-716 302-345 (509)
29 TIGR01648 hnRNP-R-Q heterogene 70.2 1.3 2.9E-05 52.1 -0.2 41 675-716 65-107 (578)
30 KOG0126 Predicted RNA-binding 62.1 4 8.6E-05 43.4 1.4 37 676-712 43-81 (219)
31 KOG0149 Predicted RNA-binding 61.3 2.5 5.4E-05 45.8 -0.3 42 676-717 20-63 (247)
32 PF14259 RRM_6: RNA recognitio 59.3 1.4 3E-05 36.0 -2.0 40 676-716 6-47 (70)
33 TIGR01628 PABP-1234 polyadenyl 59.1 3.1 6.6E-05 47.1 -0.1 40 676-716 293-334 (562)
34 smart00361 RRM_1 RNA recogniti 52.2 4.5 9.8E-05 34.3 -0.1 28 689-716 15-45 (70)
35 KOG0147 Transcriptional coacti 50.9 7 0.00015 46.3 1.1 42 675-716 285-328 (549)
36 PF00076 RRM_1: RNA recognitio 50.4 1.6 3.4E-05 34.7 -3.0 40 676-716 6-47 (70)
37 KOG4209 Splicing factor RNPS1, 46.4 9.6 0.00021 40.5 1.2 43 674-716 107-151 (231)
38 KOG0127 Nucleolar protein fibr 44.4 7.5 0.00016 46.4 0.1 42 675-716 299-342 (678)
39 cd00590 RRM RRM (RNA recogniti 35.9 10 0.00022 29.1 -0.4 40 676-716 7-48 (74)
40 smart00362 RRM_2 RNA recogniti 35.5 12 0.00026 28.5 -0.0 39 676-716 7-47 (72)
41 KOG0124 Polypyrimidine tract-b 34.7 13 0.00028 42.9 -0.0 41 675-715 120-162 (544)
42 PF06273 eIF-4B: Plant specifi 30.9 2.1E+02 0.0046 34.3 8.7 9 696-704 91-99 (492)
43 KOG4205 RNA-binding protein mu 29.4 27 0.00058 39.0 1.3 42 675-716 13-56 (311)
44 KOG0116 RasGAP SH3 binding pro 29.3 90 0.0019 36.4 5.4 9 707-715 309-317 (419)
45 KOG0145 RNA-binding protein EL 27.7 23 0.00051 39.5 0.5 40 676-715 286-327 (360)
46 KOG0148 Apoptosis-promoting RN 26.2 23 0.00051 39.6 0.2 41 676-716 70-112 (321)
47 KOG0121 Nuclear cap-binding pr 25.7 15 0.00033 37.5 -1.2 42 675-716 43-86 (153)
48 KOG1999 RNA polymerase II tran 22.8 1.1E+03 0.024 31.0 13.0 128 297-442 726-868 (1024)
49 KOG0127 Nucleolar protein fibr 20.4 52 0.0011 39.8 1.5 43 674-716 11-55 (678)
No 1
>PLN03134 glycine-rich RNA-binding protein 4; Provisional
Probab=96.69 E-value=0.0014 Score=63.05 Aligned_cols=42 Identities=10% Similarity=-0.044 Sum_probs=39.6
Q ss_pred CCCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCC
Q 001496 675 SGSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRS 716 (1066)
Q Consensus 675 SLSFDANEDSVWe--se~GSw~SVRIPTDpESG~pKGFGYV~~~ 716 (1066)
-|+++++|+.|.+ ++||.|..|+|+.|++|+..|+|+||++.
T Consensus 41 nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~ 84 (144)
T PLN03134 41 GLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFN 84 (144)
T ss_pred CCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEEC
Confidence 4889999999999 89999999999999999999999999875
No 2
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=96.47 E-value=0.011 Score=71.61 Aligned_cols=11 Identities=45% Similarity=0.948 Sum_probs=4.8
Q ss_pred CCCCCCCCCCC
Q 001496 766 DREGFGGRGGS 776 (1066)
Q Consensus 766 ~RGGFGGRGgG 776 (1066)
.||||++-++|
T Consensus 1231 srgGfrnnggG 1241 (1282)
T KOG0921|consen 1231 SRGGFRNNGGG 1241 (1282)
T ss_pred cCCccccCCCC
Confidence 34455443333
No 3
>TIGR01659 sex-lethal sex-lethal family splicing factor. This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).
Probab=95.54 E-value=0.018 Score=62.75 Aligned_cols=43 Identities=5% Similarity=-0.124 Sum_probs=39.9
Q ss_pred CCCCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCC
Q 001496 674 NSGSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRS 716 (1066)
Q Consensus 674 nSLSFDANEDSVWe--se~GSw~SVRIPTDpESG~pKGFGYV~~~ 716 (1066)
.-|+++++++.|.+ ++||.|..|+|+.|.+|+.+|+|+||++.
T Consensus 199 ~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~ 243 (346)
T TIGR01659 199 TNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFN 243 (346)
T ss_pred eCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEEC
Confidence 45889999999999 99999999999999999999999999975
No 4
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=95.49 E-value=0.054 Score=60.68 Aligned_cols=11 Identities=9% Similarity=-0.163 Sum_probs=4.9
Q ss_pred ceeeecCCCCC
Q 001496 693 WNSGSRDGHQE 703 (1066)
Q Consensus 693 w~SVRIPTDpE 703 (1066)
|..+.|-.-|+
T Consensus 294 i~k~~igrvPD 304 (465)
T KOG3973|consen 294 IHKLSIGRVPD 304 (465)
T ss_pred hcccccccCCC
Confidence 44444444443
No 5
>KOG3262 consensus H/ACA small nucleolar RNP component GAR1 [Translation, ribosomal structure and biogenesis]
Probab=94.81 E-value=0.06 Score=56.24 Aligned_cols=21 Identities=71% Similarity=1.434 Sum_probs=11.2
Q ss_pred CCCCCCCCCCCCCCCCCCCCCC
Q 001496 777 DRGGFGGRGSSDRGGFGGRGRG 798 (1066)
Q Consensus 777 dRGGfrGrGrg~RGGFgGrgrg 798 (1066)
.|++|++|+ +.|++|++|+|.
T Consensus 193 ~rGG~~~Rg-g~ggg~rgrgR~ 213 (215)
T KOG3262|consen 193 SRGGFRGRG-GHGGGFRGRGRG 213 (215)
T ss_pred CCCCccccC-CCCCCCCCCCCC
Confidence 345554432 236667666665
No 6
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor. These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
Probab=94.01 E-value=0.014 Score=60.46 Aligned_cols=41 Identities=15% Similarity=0.059 Sum_probs=39.1
Q ss_pred CCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCC
Q 001496 676 GSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRS 716 (1066)
Q Consensus 676 LSFDANEDSVWe--se~GSw~SVRIPTDpESG~pKGFGYV~~~ 716 (1066)
|+++++++.|++ +.||.|.+|+|+.|+.|+..||||||.+.
T Consensus 277 L~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~ 319 (352)
T TIGR01661 277 LSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMT 319 (352)
T ss_pred CCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEEC
Confidence 889999999999 99999999999999999999999999875
No 7
>KOG3262 consensus H/ACA small nucleolar RNP component GAR1 [Translation, ribosomal structure and biogenesis]
Probab=93.02 E-value=0.2 Score=52.46 Aligned_cols=41 Identities=59% Similarity=1.144 Sum_probs=19.1
Q ss_pred CCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 001496 744 DRGGFGGRGR-TNRGGYGGRGRFDREGFGGRGGSDRGGFGGRGS 786 (1066)
Q Consensus 744 ~RGGFgGrgg-~dRGGfgGrg~G~RGGFGGRGgGdRGGfrGrGr 786 (1066)
.|++|++|++ .+|++|.++ .+.|++|.+|+ +.+++|++|+|
T Consensus 171 ~rGg~~grGrgg~~Gg~rgg-gg~rGG~~~Rg-g~ggg~rgrgR 212 (215)
T KOG3262|consen 171 GRGGFGGRGRGGGGGGFRGG-GGSRGGFRGRG-GHGGGFRGRGR 212 (215)
T ss_pred CcCCCCCCCCCCCCCcccCC-CCCCCCccccC-CCCCCCCCCCC
Confidence 5556655532 223444443 24455554432 24555655543
No 8
>PTZ00146 fibrillarin; Provisional
Probab=92.30 E-value=0.29 Score=53.32 Aligned_cols=6 Identities=33% Similarity=0.894 Sum_probs=2.7
Q ss_pred CcCCCC
Q 001496 867 WNNSNT 872 (1066)
Q Consensus 867 Wn~s~~ 872 (1066)
||--+|
T Consensus 110 w~p~rS 115 (293)
T PTZ00146 110 WNPFRS 115 (293)
T ss_pred eCCccc
Confidence 444443
No 9
>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]
Probab=88.72 E-value=0.11 Score=55.97 Aligned_cols=41 Identities=12% Similarity=0.031 Sum_probs=38.1
Q ss_pred CCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCC
Q 001496 676 GSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRS 716 (1066)
Q Consensus 676 LSFDANEDSVWe--se~GSw~SVRIPTDpESG~pKGFGYV~~~ 716 (1066)
||-|++|+.|.+ ..+|-|.+|+|--|++||..|||+||.+.
T Consensus 197 Lsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~ 239 (270)
T KOG0122|consen 197 LSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFE 239 (270)
T ss_pred CccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEe
Confidence 778999999988 78899999999999999999999999875
No 10
>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]
Probab=88.70 E-value=0.17 Score=54.37 Aligned_cols=41 Identities=15% Similarity=-0.053 Sum_probs=37.2
Q ss_pred CCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCC
Q 001496 676 GSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRS 716 (1066)
Q Consensus 676 LSFDANEDSVWe--se~GSw~SVRIPTDpESG~pKGFGYV~~~ 716 (1066)
|+|++++|.|.. ..|+.|..||+|++++|+..|+|+|+.+.
T Consensus 193 ~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~ 235 (285)
T KOG4210|consen 193 LDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFS 235 (285)
T ss_pred cccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhh
Confidence 778999999875 77789999999999999999999998874
No 11
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor. These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
Probab=88.38 E-value=0.12 Score=53.75 Aligned_cols=42 Identities=10% Similarity=-0.065 Sum_probs=39.4
Q ss_pred CCCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCC
Q 001496 675 SGSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRS 716 (1066)
Q Consensus 675 SLSFDANEDSVWe--se~GSw~SVRIPTDpESG~pKGFGYV~~~ 716 (1066)
-|+++++|+.|.+ ++||.|..|+|..|+.++..++|+||.+.
T Consensus 10 nLp~~~~e~~l~~~F~~~G~i~~v~i~~d~~~g~s~g~afV~f~ 53 (352)
T TIGR01661 10 YLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYV 53 (352)
T ss_pred CCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEEC
Confidence 3889999999999 99999999999999999999999999974
No 12
>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=88.31 E-value=0.13 Score=56.27 Aligned_cols=41 Identities=7% Similarity=0.049 Sum_probs=38.7
Q ss_pred CCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCC
Q 001496 676 GSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRS 716 (1066)
Q Consensus 676 LSFDANEDSVWe--se~GSw~SVRIPTDpESG~pKGFGYV~~~ 716 (1066)
|+.+++++.|.+ ++|+.|++|+|..|+.|+..|+|+||++.
T Consensus 115 Lp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~ 157 (346)
T TIGR01659 115 LPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFG 157 (346)
T ss_pred CCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEc
Confidence 889999999999 88999999999999999999999999863
No 13
>PLN03213 repressor of silencing 3; Provisional
Probab=87.30 E-value=0.17 Score=58.92 Aligned_cols=37 Identities=5% Similarity=0.003 Sum_probs=34.8
Q ss_pred CCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCC
Q 001496 676 GSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRS 716 (1066)
Q Consensus 676 LSFDANEDSVWe--se~GSw~SVRIPTDpESG~pKGFGYV~~~ 716 (1066)
|+|+++++.|.. .+||.|.+|.|| +||| |+|+||...
T Consensus 18 LSydVTEDDLravFSeFGsVkdVEIp--RETG--RGFAFVEMs 56 (759)
T PLN03213 18 LGESVGRDDLLKIFSPMGTVDAVEFV--RTKG--RSFAYIDFS 56 (759)
T ss_pred CCCCCCHHHHHHHHHhcCCeeEEEEe--cccC--CceEEEEec
Confidence 899999999999 999999999999 9998 999999874
No 14
>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]
Probab=85.26 E-value=0.27 Score=45.45 Aligned_cols=41 Identities=15% Similarity=-0.005 Sum_probs=38.5
Q ss_pred CCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCC
Q 001496 676 GSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRS 716 (1066)
Q Consensus 676 LSFDANEDSVWe--se~GSw~SVRIPTDpESG~pKGFGYV~~~ 716 (1066)
|+++++++.|.+ .+++.|..|+|+.|+.++..++|+||.+.
T Consensus 123 L~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~ 165 (306)
T COG0724 123 LPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFE 165 (306)
T ss_pred CCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEec
Confidence 678999999999 99999999999999999999999999874
No 15
>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=84.25 E-value=0.32 Score=57.53 Aligned_cols=42 Identities=12% Similarity=-0.074 Sum_probs=39.6
Q ss_pred CCCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCC
Q 001496 675 SGSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRS 716 (1066)
Q Consensus 675 SLSFDANEDSVWe--se~GSw~SVRIPTDpESG~pKGFGYV~~~ 716 (1066)
.|+++++++.|.+ .+||.|.+|+|+.|+.|+..|||+||++.
T Consensus 114 nLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~ 157 (612)
T TIGR01645 114 SISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYE 157 (612)
T ss_pred CCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeC
Confidence 3899999999999 88999999999999999999999999975
No 16
>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]
Probab=84.14 E-value=1.2 Score=50.87 Aligned_cols=40 Identities=13% Similarity=-0.053 Sum_probs=31.2
Q ss_pred CCCCCccccccc--cccCCceeeecCCCC-CCCCCCCCCCCCCC
Q 001496 676 GSDDANQESSWG--KKQGNWNSGSRDGHQ-ESSWGKKSDWNSRS 716 (1066)
Q Consensus 676 LSFDANEDSVWe--se~GSw~SVRIPTDp-ESG~pKGFGYV~~~ 716 (1066)
|++||+++.|-+ +.+|.|...+|+.-- .-..+ .||||++.
T Consensus 296 lP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~-~fgFV~f~ 338 (419)
T KOG0116|consen 296 LPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNP-CFGFVEFE 338 (419)
T ss_pred CCCCCCHHHHHHHHhhcccccccceEEeccCCCcC-ceEEEEEe
Confidence 889999999999 999999999887532 22233 89998764
No 17
>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=83.24 E-value=0.31 Score=54.84 Aligned_cols=42 Identities=10% Similarity=-0.066 Sum_probs=39.4
Q ss_pred CCCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCC
Q 001496 675 SGSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRS 716 (1066)
Q Consensus 675 SLSFDANEDSVWe--se~GSw~SVRIPTDpESG~pKGFGYV~~~ 716 (1066)
.|+++++|+.|.+ ++||.|.+|+|..|..|+..++|+||.+.
T Consensus 7 nLp~~vte~~L~~~F~~~G~v~~v~v~~d~~t~~s~G~afV~F~ 50 (562)
T TIGR01628 7 DLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQ 50 (562)
T ss_pred CCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEEC
Confidence 4889999999999 99999999999999999999999999975
No 18
>PLN03120 nucleic acid binding protein; Provisional
Probab=83.09 E-value=0.36 Score=52.15 Aligned_cols=40 Identities=10% Similarity=0.014 Sum_probs=35.8
Q ss_pred CCCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCCC
Q 001496 675 SGSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRSE 717 (1066)
Q Consensus 675 SLSFDANEDSVWe--se~GSw~SVRIPTDpESG~pKGFGYV~~~e 717 (1066)
-|+++++|+.|++ +.||.|..|+||.|++ .++|+||++.+
T Consensus 11 NLs~~tTE~dLrefFS~~G~I~~V~I~~d~~---~~GfAFVtF~d 52 (260)
T PLN03120 11 NVSLKATERDIKEFFSFSGDIEYVEMQSENE---RSQIAYVTFKD 52 (260)
T ss_pred CCCCCCCHHHHHHHHHhcCCeEEEEEeecCC---CCCEEEEEeCc
Confidence 3889999999999 9999999999999987 47999999853
No 19
>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]
Probab=82.69 E-value=0.52 Score=53.87 Aligned_cols=43 Identities=12% Similarity=-0.065 Sum_probs=39.3
Q ss_pred CCCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCCC
Q 001496 675 SGSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRSE 717 (1066)
Q Consensus 675 SLSFDANEDSVWe--se~GSw~SVRIPTDpESG~pKGFGYV~~~e 717 (1066)
.++|+++|+.|-. +++|.|.++|+-.|+|||.+|||+|+++-+
T Consensus 25 nip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~ 69 (435)
T KOG0108|consen 25 NIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTD 69 (435)
T ss_pred CCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCc
Confidence 3789999999999 888999999999999999999999988753
No 20
>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=81.81 E-value=0.47 Score=56.15 Aligned_cols=44 Identities=9% Similarity=-0.067 Sum_probs=40.2
Q ss_pred CCCCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCCC
Q 001496 674 NSGSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRSE 717 (1066)
Q Consensus 674 nSLSFDANEDSVWe--se~GSw~SVRIPTDpESG~pKGFGYV~~~e 717 (1066)
-.|+++++++.|.+ +.||.|.+|+|+.|++++..|||+||.+..
T Consensus 210 gnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~ 255 (612)
T TIGR01645 210 ASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNN 255 (612)
T ss_pred ecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECC
Confidence 35889999999998 889999999999999999999999999864
No 21
>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=81.73 E-value=0.44 Score=51.75 Aligned_cols=43 Identities=12% Similarity=0.012 Sum_probs=39.5
Q ss_pred CCCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCCC
Q 001496 675 SGSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRSE 717 (1066)
Q Consensus 675 SLSFDANEDSVWe--se~GSw~SVRIPTDpESG~pKGFGYV~~~e 717 (1066)
-|+++++++.|.+ ++||.|..|+|+.|+.|+..|+|+||++..
T Consensus 96 nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~ 140 (457)
T TIGR01622 96 QLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYD 140 (457)
T ss_pred CCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECC
Confidence 4788999999999 889999999999999999999999999853
No 22
>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]
Probab=77.97 E-value=0.61 Score=51.75 Aligned_cols=42 Identities=10% Similarity=-0.065 Sum_probs=38.9
Q ss_pred CCCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCC
Q 001496 675 SGSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRS 716 (1066)
Q Consensus 675 SLSFDANEDSVWe--se~GSw~SVRIPTDpESG~pKGFGYV~~~ 716 (1066)
-|+++++|+.|.+ ..||.|..|+|-.|..||-+|||+||+..
T Consensus 108 RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye 151 (335)
T KOG0113|consen 108 RLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYE 151 (335)
T ss_pred eccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEec
Confidence 4788999999999 89999999999999999999999998854
No 23
>PLN03121 nucleic acid binding protein; Provisional
Probab=76.90 E-value=0.74 Score=49.56 Aligned_cols=40 Identities=10% Similarity=0.025 Sum_probs=35.5
Q ss_pred CCCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCCC
Q 001496 675 SGSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRSE 717 (1066)
Q Consensus 675 SLSFDANEDSVWe--se~GSw~SVRIPTDpESG~pKGFGYV~~~e 717 (1066)
-||+.++|..|++ +.||.|..|+|+.|.++ ++|+||++.+
T Consensus 12 NLS~~tTE~dLrefFS~~G~I~~V~I~~D~et---~gfAfVtF~d 53 (243)
T PLN03121 12 NLSPKATEKDVYDFFSHCGAIEHVEIIRSGEY---ACTAYVTFKD 53 (243)
T ss_pred cCCCCCCHHHHHHHHHhcCCeEEEEEecCCCc---ceEEEEEECC
Confidence 3899999999999 99999999999999766 4799999863
No 24
>smart00360 RRM RNA recognition motif.
Probab=75.73 E-value=0.75 Score=34.91 Aligned_cols=41 Identities=15% Similarity=0.022 Sum_probs=36.1
Q ss_pred CCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCC
Q 001496 676 GSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRS 716 (1066)
Q Consensus 676 LSFDANEDSVWe--se~GSw~SVRIPTDpESG~pKGFGYV~~~ 716 (1066)
|+..++++.|.. ..+|.|..|.++.++.++.+++++|+.+.
T Consensus 4 l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~ 46 (71)
T smart00360 4 LPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFE 46 (71)
T ss_pred CCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeC
Confidence 566788888888 88899999999999999999999998864
No 25
>TIGR01622 SF-CC1 splicing factor, CC1-like family. A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.
Probab=73.46 E-value=0.96 Score=49.20 Aligned_cols=43 Identities=7% Similarity=-0.018 Sum_probs=39.3
Q ss_pred CCCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCCC
Q 001496 675 SGSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRSE 717 (1066)
Q Consensus 675 SLSFDANEDSVWe--se~GSw~SVRIPTDpESG~pKGFGYV~~~e 717 (1066)
.|+++++++.|.+ +.||.|..|+|+.+++++..|+|+||.+..
T Consensus 193 nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~ 237 (457)
T TIGR01622 193 NLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHD 237 (457)
T ss_pred CCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECC
Confidence 4788999999999 889999999999999999999999998753
No 26
>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=73.26 E-value=3.5 Score=48.82 Aligned_cols=34 Identities=6% Similarity=-0.079 Sum_probs=29.1
Q ss_pred CCCCCCccccccc--ccc--CCceeeecCCCCCCCCCCCCCCCCCC
Q 001496 675 SGSDDANQESSWG--KKQ--GNWNSGSRDGHQESSWGKKSDWNSRS 716 (1066)
Q Consensus 675 SLSFDANEDSVWe--se~--GSw~SVRIPTDpESG~pKGFGYV~~~ 716 (1066)
.|+++++++.|.+ ++| |+|+.|+++ ++|+||.+.
T Consensus 240 NL~~~~tee~L~~~F~~f~~G~I~rV~~~--------rgfAFVeF~ 277 (578)
T TIGR01648 240 NLMTTTTEEIIEKSFSEFKPGKVERVKKI--------RDYAFVHFE 277 (578)
T ss_pred CCCCCCCHHHHHHHHHhcCCCceEEEEee--------cCeEEEEeC
Confidence 3888999999999 888 999999875 569999874
No 27
>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]
Probab=72.99 E-value=1 Score=48.26 Aligned_cols=41 Identities=5% Similarity=-0.103 Sum_probs=38.0
Q ss_pred CCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCC
Q 001496 676 GSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRS 716 (1066)
Q Consensus 676 LSFDANEDSVWe--se~GSw~SVRIPTDpESG~pKGFGYV~~~ 716 (1066)
|.|-++.|+|.. ++||.|.-|.||-|+-|.+.++|+||-+.
T Consensus 21 LTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~ 63 (256)
T KOG4207|consen 21 LTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFH 63 (256)
T ss_pred eeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEee
Confidence 677888899998 99999999999999999999999999875
No 28
>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor. Members of this subfamily are found in plants, metazoa and fungi.
Probab=70.24 E-value=1.3 Score=48.79 Aligned_cols=42 Identities=5% Similarity=-0.113 Sum_probs=39.0
Q ss_pred CCCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCC
Q 001496 675 SGSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRS 716 (1066)
Q Consensus 675 SLSFDANEDSVWe--se~GSw~SVRIPTDpESG~pKGFGYV~~~ 716 (1066)
-|+++++++.|.+ +.||.|..|.|..+++|+..|+|+||.+.
T Consensus 302 nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~ 345 (509)
T TIGR01642 302 NLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYK 345 (509)
T ss_pred CCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEEC
Confidence 3889999999999 88999999999999999999999999875
No 29
>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family. Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.
Probab=70.15 E-value=1.3 Score=52.12 Aligned_cols=41 Identities=10% Similarity=-0.113 Sum_probs=37.8
Q ss_pred CCCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCC
Q 001496 675 SGSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRS 716 (1066)
Q Consensus 675 SLSFDANEDSVWe--se~GSw~SVRIPTDpESG~pKGFGYV~~~ 716 (1066)
-|+++++|+.|.+ +++|.|..|+|+.| .++..|+|+||.+.
T Consensus 65 nLp~~~tEd~L~~~F~~~G~I~~vrl~~D-~sG~sRGfaFV~F~ 107 (578)
T TIGR01648 65 KIPRDLYEDELVPLFEKAGPIYELRLMMD-FSGQNRGYAFVTFC 107 (578)
T ss_pred CCCCCCCHHHHHHHHHhhCCEEEEEEEEC-CCCCccceEEEEeC
Confidence 4888999999999 88999999999999 89999999998864
No 30
>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=62.07 E-value=4 Score=43.37 Aligned_cols=37 Identities=5% Similarity=-0.088 Sum_probs=35.4
Q ss_pred CCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCC
Q 001496 676 GSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDW 712 (1066)
Q Consensus 676 LSFDANEDSVWe--se~GSw~SVRIPTDpESG~pKGFGY 712 (1066)
|+|+++|..|=. ++||+|+.|-|--|-+||-.|||+|
T Consensus 43 l~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaF 81 (219)
T KOG0126|consen 43 LPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAF 81 (219)
T ss_pred CcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEE
Confidence 889999999888 9999999999999999999999998
No 31
>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]
Probab=61.28 E-value=2.5 Score=45.81 Aligned_cols=42 Identities=7% Similarity=0.005 Sum_probs=37.6
Q ss_pred CCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCCC
Q 001496 676 GSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRSE 717 (1066)
Q Consensus 676 LSFDANEDSVWe--se~GSw~SVRIPTDpESG~pKGFGYV~~~e 717 (1066)
|.+.+..++++. +++|+|+-+-+=||.+|++.||||||++-|
T Consensus 20 L~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d 63 (247)
T KOG0149|consen 20 LAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRD 63 (247)
T ss_pred cccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeec
Confidence 566778888888 999999999999999999999999999854
No 32
>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=59.27 E-value=1.4 Score=35.96 Aligned_cols=40 Identities=8% Similarity=-0.033 Sum_probs=34.1
Q ss_pred CCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCC
Q 001496 676 GSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRS 716 (1066)
Q Consensus 676 LSFDANEDSVWe--se~GSw~SVRIPTDpESG~pKGFGYV~~~ 716 (1066)
|+++++++.|.+ ..++.|..|++..+++ +.+++++|+.+.
T Consensus 6 lp~~~~~~~l~~~f~~~g~v~~v~~~~~~~-~~~~~~a~v~f~ 47 (70)
T PF14259_consen 6 LPPSTTEEDLRNFFSRFGPVEKVRLIKNKD-GQSRGFAFVEFS 47 (70)
T ss_dssp STTT--HHHHHHHCTTSSBEEEEEEEESTT-SSEEEEEEEEES
T ss_pred CCCCCCHHHHHHHHHhcCCcceEEEEeeec-cccCCEEEEEeC
Confidence 778899999999 8889999999999988 999999998864
No 33
>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=59.08 E-value=3.1 Score=47.13 Aligned_cols=40 Identities=15% Similarity=0.017 Sum_probs=36.8
Q ss_pred CCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCC
Q 001496 676 GSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRS 716 (1066)
Q Consensus 676 LSFDANEDSVWe--se~GSw~SVRIPTDpESG~pKGFGYV~~~ 716 (1066)
|+.+++++.|.+ ++||.|.+|+|..| +++..|+|+||.+.
T Consensus 293 l~~~~~~~~L~~~F~~~G~i~~~~i~~d-~~g~~~g~gfV~f~ 334 (562)
T TIGR01628 293 LDDTVTDEKLRELFSECGEITSAKVMLD-EKGVSRGFGFVCFS 334 (562)
T ss_pred CCCccCHHHHHHHHHhcCCeEEEEEEEC-CCCCcCCeEEEEeC
Confidence 678999999999 99999999999999 88999999999875
No 34
>smart00361 RRM_1 RNA recognition motif.
Probab=52.18 E-value=4.5 Score=34.25 Aligned_cols=28 Identities=4% Similarity=-0.171 Sum_probs=22.8
Q ss_pred ccCCceeee-cCCCCCC--CCCCCCCCCCCC
Q 001496 689 KQGNWNSGS-RDGHQES--SWGKKSDWNSRS 716 (1066)
Q Consensus 689 e~GSw~SVR-IPTDpES--G~pKGFGYV~~~ 716 (1066)
++|.|.+|. |+-++++ +.+|+|+||.+.
T Consensus 15 ~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~ 45 (70)
T smart00361 15 YFGEVGKINKIYIDNVGYENHKRGNVYITFE 45 (70)
T ss_pred hcCCeeEEEEEEeCCCCCCCCCcEEEEEEEC
Confidence 778999884 6666666 999999999875
No 35
>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]
Probab=50.94 E-value=7 Score=46.32 Aligned_cols=42 Identities=10% Similarity=0.011 Sum_probs=38.9
Q ss_pred CCCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCC
Q 001496 675 SGSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRS 716 (1066)
Q Consensus 675 SLSFDANEDSVWe--se~GSw~SVRIPTDpESG~pKGFGYV~~~ 716 (1066)
+|=|+.+++.+.. +.+|.|.-|-|+-|.|||+.|+|||+++.
T Consensus 285 nLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~ 328 (549)
T KOG0147|consen 285 NLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFV 328 (549)
T ss_pred ccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEe
Confidence 4789999999999 88899999999999999999999998864
No 36
>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=50.40 E-value=1.6 Score=34.68 Aligned_cols=40 Identities=15% Similarity=-0.004 Sum_probs=35.7
Q ss_pred CCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCC
Q 001496 676 GSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRS 716 (1066)
Q Consensus 676 LSFDANEDSVWe--se~GSw~SVRIPTDpESG~pKGFGYV~~~ 716 (1066)
|+.+++++.|.. +++|.|..+.+..+ .++..++|+||.+.
T Consensus 6 lp~~~t~~~l~~~f~~~g~i~~~~~~~~-~~~~~~~~a~V~F~ 47 (70)
T PF00076_consen 6 LPPDVTEEELRDFFSQFGKIESIKVMRN-SSGKSKGYAFVEFE 47 (70)
T ss_dssp ETTTSSHHHHHHHHHTTSTEEEEEEEEE-TTSSEEEEEEEEES
T ss_pred CCCcCCHHHHHHHHHHhhhccccccccc-ccccccceEEEEEc
Confidence 678999999999 88999999999998 78899999998864
No 37
>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]
Probab=46.36 E-value=9.6 Score=40.49 Aligned_cols=43 Identities=9% Similarity=-0.179 Sum_probs=35.8
Q ss_pred CCCCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCC
Q 001496 674 NSGSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRS 716 (1066)
Q Consensus 674 nSLSFDANEDSVWe--se~GSw~SVRIPTDpESG~pKGFGYV~~~ 716 (1066)
..+-|.++-..+-. +.|+.|+.|-||+|..++.+|+|+|+++.
T Consensus 107 ~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~ 151 (231)
T KOG4209|consen 107 GNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFS 151 (231)
T ss_pred eccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecc
Confidence 34566666666555 89999999999999999999999999975
No 38
>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]
Probab=44.41 E-value=7.5 Score=46.41 Aligned_cols=42 Identities=12% Similarity=0.018 Sum_probs=39.4
Q ss_pred CCCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCC
Q 001496 675 SGSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRS 716 (1066)
Q Consensus 675 SLSFDANEDSVWe--se~GSw~SVRIPTDpESG~pKGFGYV~~~ 716 (1066)
-|+||++|+.|-+ .++|+|..++|--|+.|+.+||-+||.+-
T Consensus 299 NL~fD~tEEel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fk 342 (678)
T KOG0127|consen 299 NLPFDTTEEELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFK 342 (678)
T ss_pred cCCccccHHHHHHHHHhhccceeEEEEeccCCCCcccceEEEec
Confidence 3899999999999 89999999999999999999999998874
No 39
>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=35.87 E-value=10 Score=29.12 Aligned_cols=40 Identities=15% Similarity=0.014 Sum_probs=33.5
Q ss_pred CCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCC
Q 001496 676 GSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRS 716 (1066)
Q Consensus 676 LSFDANEDSVWe--se~GSw~SVRIPTDpESG~pKGFGYV~~~ 716 (1066)
|+.+++++.|.+ ..++.|..+.++.++.+ .+++++|+.+.
T Consensus 7 l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~-~~~~~~~v~f~ 48 (74)
T cd00590 7 LPPDVTEEDLRELFSKFGKVESVRIVRDKDT-KSKGFAFVEFE 48 (74)
T ss_pred CCCccCHHHHHHHHHhcCCEEEEEEeeCCCC-CcceEEEEEEC
Confidence 566788888888 77899999999998887 88999998753
No 40
>smart00362 RRM_2 RNA recognition motif.
Probab=35.47 E-value=12 Score=28.50 Aligned_cols=39 Identities=15% Similarity=-0.035 Sum_probs=32.5
Q ss_pred CCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCC
Q 001496 676 GSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRS 716 (1066)
Q Consensus 676 LSFDANEDSVWe--se~GSw~SVRIPTDpESG~pKGFGYV~~~ 716 (1066)
|+.+++++.|.+ .++|.|..+++..++ +.+++++|+.+.
T Consensus 7 l~~~~~~~~l~~~~~~~g~v~~~~~~~~~--~~~~~~~~v~f~ 47 (72)
T smart00362 7 LPPDVTEEDLKELFSKFGPIESVKIPKDT--GKSKGFAFVEFE 47 (72)
T ss_pred CCCcCCHHHHHHHHHhcCCEEEEEEecCC--CCCCceEEEEeC
Confidence 566788888888 888999999999887 678899998764
No 41
>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]
Probab=34.68 E-value=13 Score=42.91 Aligned_cols=41 Identities=12% Similarity=-0.078 Sum_probs=38.4
Q ss_pred CCCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCC
Q 001496 675 SGSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSR 715 (1066)
Q Consensus 675 SLSFDANEDSVWe--se~GSw~SVRIPTDpESG~pKGFGYV~~ 715 (1066)
|+||..-||+|+. -.+|-|.||..-=||-|+--|+|+||+-
T Consensus 120 SIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEY 162 (544)
T KOG0124|consen 120 SISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEY 162 (544)
T ss_pred eeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEE
Confidence 7899999999999 7889999999999999999999999774
No 42
>PF06273 eIF-4B: Plant specific eukaryotic initiation factor 4B; InterPro: IPR010433 This family consists of several plant specific eukaryotic initiation factor 4B proteins.
Probab=30.88 E-value=2.1e+02 Score=34.28 Aligned_cols=9 Identities=0% Similarity=-0.363 Sum_probs=5.9
Q ss_pred eecCCCCCC
Q 001496 696 GSRDGHQES 704 (1066)
Q Consensus 696 VRIPTDpES 704 (1066)
+.|||.|-.
T Consensus 91 m~LPTGPRe 99 (492)
T PF06273_consen 91 MMLPTGPRE 99 (492)
T ss_pred eecCCCCCC
Confidence 467877654
No 43
>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]
Probab=29.41 E-value=27 Score=38.95 Aligned_cols=42 Identities=10% Similarity=-0.025 Sum_probs=38.6
Q ss_pred CCCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCC
Q 001496 675 SGSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRS 716 (1066)
Q Consensus 675 SLSFDANEDSVWe--se~GSw~SVRIPTDpESG~pKGFGYV~~~ 716 (1066)
.||++++|+.|.+ .++++|.-+-+--||.|++.++|++|++.
T Consensus 13 gisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~ 56 (311)
T KOG4205|consen 13 GLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFA 56 (311)
T ss_pred CcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecC
Confidence 4789999999999 88899999999999999999999998864
No 44
>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]
Probab=29.30 E-value=90 Score=36.37 Aligned_cols=9 Identities=11% Similarity=-0.385 Sum_probs=4.5
Q ss_pred CCCCCCCCC
Q 001496 707 GKKSDWNSR 715 (1066)
Q Consensus 707 pKGFGYV~~ 715 (1066)
.|.||=+..
T Consensus 309 Fk~FG~Ik~ 317 (419)
T KOG0116|consen 309 FKQFGPIKE 317 (419)
T ss_pred Hhhcccccc
Confidence 455554444
No 45
>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]
Probab=27.70 E-value=23 Score=39.54 Aligned_cols=40 Identities=15% Similarity=0.033 Sum_probs=37.1
Q ss_pred CCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCC
Q 001496 676 GSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSR 715 (1066)
Q Consensus 676 LSFDANEDSVWe--se~GSw~SVRIPTDpESG~pKGFGYV~~ 715 (1066)
|+-|++|..+|. ..+|-|+.|.+-.|..|-.-|||+||+-
T Consensus 286 Lspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtM 327 (360)
T KOG0145|consen 286 LSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTM 327 (360)
T ss_pred cCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEe
Confidence 677999999999 8899999999999999999999999874
No 46
>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]
Probab=26.24 E-value=23 Score=39.64 Aligned_cols=41 Identities=12% Similarity=-0.015 Sum_probs=36.4
Q ss_pred CCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCC
Q 001496 676 GSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRS 716 (1066)
Q Consensus 676 LSFDANEDSVWe--se~GSw~SVRIPTDpESG~pKGFGYV~~~ 716 (1066)
||-+++-+.|++ ..+|+|..+||-.|+.|+-.||||||++.
T Consensus 70 ls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~ 112 (321)
T KOG0148|consen 70 LSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFP 112 (321)
T ss_pred cchhcchHHHHHHhccccccccceEeecccCCcccceeEEecc
Confidence 555777788888 88899999999999999999999999975
No 47
>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]
Probab=25.70 E-value=15 Score=37.53 Aligned_cols=42 Identities=10% Similarity=-0.185 Sum_probs=38.9
Q ss_pred CCCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCC
Q 001496 675 SGSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRS 716 (1066)
Q Consensus 675 SLSFDANEDSVWe--se~GSw~SVRIPTDpESG~pKGFGYV~~~ 716 (1066)
-|||.++|+.||| ++||.|..|-.--|+.+=.|=||.||..+
T Consensus 43 NlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy 86 (153)
T KOG0121|consen 43 NLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYY 86 (153)
T ss_pred eeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEe
Confidence 4899999999999 99999999999999999999999998864
No 48
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=22.75 E-value=1.1e+03 Score=30.95 Aligned_cols=128 Identities=23% Similarity=0.437 Sum_probs=69.0
Q ss_pred cCcCCCCCCCCCCCCCCCCCcCCCCCCCCccCCcccccccCCCCCCCCCCCCCccc-cCCCCCCCc----ccCCCCCccc
Q 001496 297 MGKQDGGSSWGKQDGGSSLGKQDGGSSWGKQDGRSSLAKQDGGSSWGKQDRGSSWG-KQDEGSSWS----KRDGGSSWGK 371 (1066)
Q Consensus 297 ~~~~~ggs~w~~~~gg~g~~~~~ggssw~~k~g~~~~a~~~g~~~W~~~~~g~Swg-~~d~~~sW~----k~d~~~sW~~ 371 (1066)
+++......|...+++..+ +|. .+-.-.|...|+..+.|++|. ..+++..|. ..+..+.--.
T Consensus 726 vd~~~~~~v~~~~~~g~~~-------sYg------~~~~~~g~~~~~~~~~Gs~tp~~~s~tpl~~~s~tp~~~~~~Tp~ 792 (1024)
T KOG1999|consen 726 VDRLKRKIVGSTRDGGETS-------SYG------ERTPGYGRVTPARYGMGSSTPMYGSNTPLWGGSRTPARDGGATPS 792 (1024)
T ss_pred echhhceEEeeccCCCCcc-------ccc------cccccccccCccccCCCCcCccCCCCCCCCCcccCccccCCCCcC
Confidence 5665566666665555444 333 233344555666666677776 556666665 2211111111
Q ss_pred cCCCCcccccCCCCCCCccCCCCCccc-----cCCCC-CccccCCCCCCCccCCCCCcCcCC--CCCCCCcC--CCCCCC
Q 001496 372 QDGGSSLAKQDGGSSWGKQDGGSSLGK-----QDGGS-SWSKQDGGSSWGKQDGGSSWGKQD--GGSSWGKQ--DGGSSW 441 (1066)
Q Consensus 372 ~Dg~~s~~~~DGgssWgk~d~~~s~~~-----~DGgs-SW~kkd~g~sw~k~dGgsSWgkkd--G~ssWgk~--dgGSsW 441 (1066)
.||..+.+ +...|... .+.+-+. .+|.. +|.+.... +|...-.++.|++.. +.++|+++ +.+|.|
T Consensus 793 ~dG~rTP~---r~~aW~~~-~~~tPa~~~~~~~~g~~g~~g~sp~~-~~~a~Tpg~~~~~~~~~~~~~~~g~~~~~gsa~ 867 (1024)
T KOG1999|consen 793 HDGSRTPA---RGRAWNPY-NGKTPARNFDNREPGFEGSGGRSPQG-YYSAPTPGSNWGSTGGGGAPAWPGTPNGNGSAW 867 (1024)
T ss_pred CCCCcCCC---CCCCcCCC-CCCCCccccCCcccCCCCCCCCCCCC-CcCCCCCCCCCCcCCCCCCcCCCCCCCCCcccc
Confidence 25555555 45566666 3333333 22222 34333211 155677778888865 57889998 788999
Q ss_pred C
Q 001496 442 S 442 (1066)
Q Consensus 442 s 442 (1066)
.
T Consensus 868 ~ 868 (1024)
T KOG1999|consen 868 G 868 (1024)
T ss_pred c
Confidence 7
No 49
>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]
Probab=20.35 E-value=52 Score=39.84 Aligned_cols=43 Identities=9% Similarity=-0.113 Sum_probs=39.0
Q ss_pred CCCCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCC
Q 001496 674 NSGSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRS 716 (1066)
Q Consensus 674 nSLSFDANEDSVWe--se~GSw~SVRIPTDpESG~pKGFGYV~~~ 716 (1066)
..|+|++..+.+-+ +.+|-|..+.+-|++.+...+||+||++.
T Consensus 11 ~~lp~~~~~~qL~e~FS~vGPik~~~vVt~~gs~~~RGfgfVtFa 55 (678)
T KOG0127|consen 11 SRLPFSSTGEQLEEFFSYVGPIKHAVVVTNKGSSEKRGFGFVTFA 55 (678)
T ss_pred ecCCCccchhHHHHhhhcccCcceeEEecCCCcccccCccceeee
Confidence 36899999999988 88899999999999999999999999874
Done!