Query 001593
Match_columns 1048
No_of_seqs 157 out of 190
Neff 2.2
Searched_HMMs 46136
Date Fri Mar 29 04:40:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001593.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/001593hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0921 Dosage compensation co 96.4 0.017 3.8E-07 70.0 10.6 11 748-758 1231-1241(1282)
2 PLN03134 glycine-rich RNA-bind 96.4 0.0031 6.6E-08 60.7 3.6 42 657-698 41-84 (144)
3 KOG3973 Uncharacterized conser 96.2 0.019 4.1E-07 64.0 9.2 17 770-787 443-459 (465)
4 KOG3262 H/ACA small nucleolar 95.3 0.036 7.9E-07 57.7 6.3 21 759-780 193-213 (215)
5 TIGR01659 sex-lethal sex-letha 95.1 0.029 6.2E-07 61.2 5.1 43 656-698 199-243 (346)
6 KOG3973 Uncharacterized conser 94.9 0.11 2.4E-06 58.2 9.1 17 770-787 438-454 (465)
7 KOG3262 H/ACA small nucleolar 94.4 0.086 1.9E-06 55.1 6.2 41 726-768 171-212 (215)
8 PTZ00146 fibrillarin; Provisio 92.8 0.23 4.9E-06 54.1 6.5 6 849-854 110-115 (293)
9 TIGR01661 ELAV_HUD_SF ELAV/HuD 92.7 0.03 6.5E-07 58.0 -0.2 41 658-698 277-319 (352)
10 KOG4210 Nuclear localization s 86.1 0.3 6.6E-06 52.5 1.0 41 658-698 193-235 (285)
11 KOG0122 Translation initiation 86.0 0.2 4.4E-06 54.1 -0.4 41 658-698 197-239 (270)
12 TIGR01659 sex-lethal sex-letha 85.2 0.25 5.3E-06 54.2 -0.2 41 658-698 115-157 (346)
13 TIGR01661 ELAV_HUD_SF ELAV/HuD 84.9 0.23 5.1E-06 51.5 -0.5 42 657-698 10-53 (352)
14 PLN03213 repressor of silencin 83.6 0.32 7E-06 56.6 -0.2 37 658-698 18-56 (759)
15 KOG0116 RasGAP SH3 binding pro 82.6 1.5 3.3E-05 50.0 4.5 40 658-698 296-338 (419)
16 COG0724 RNA-binding proteins ( 80.8 0.52 1.1E-05 43.6 0.1 41 658-698 123-165 (306)
17 TIGR01645 half-pint poly-U bin 79.5 0.62 1.3E-05 55.1 0.1 42 657-698 114-157 (612)
18 TIGR01628 PABP-1234 polyadenyl 78.5 0.56 1.2E-05 52.7 -0.5 42 657-698 7-50 (562)
19 PLN03120 nucleic acid binding 77.3 0.69 1.5E-05 50.0 -0.3 39 657-698 11-51 (260)
20 TIGR01622 SF-CC1 splicing fact 75.6 0.84 1.8E-05 49.6 -0.2 42 657-698 96-139 (457)
21 KOG0108 mRNA cleavage and poly 75.6 1.1 2.4E-05 51.2 0.7 42 657-698 25-68 (435)
22 TIGR01645 half-pint poly-U bin 75.4 0.93 2E-05 53.7 0.1 43 656-698 210-254 (612)
23 KOG0113 U1 small nuclear ribon 73.3 0.98 2.1E-05 50.1 -0.4 42 657-698 108-151 (335)
24 PLN03121 nucleic acid binding 68.9 1.5 3.2E-05 47.3 -0.2 39 657-698 12-52 (243)
25 TIGR01648 hnRNP-R-Q heterogene 68.1 5.2 0.00011 47.4 3.9 34 657-698 240-277 (578)
26 smart00360 RRM RNA recognition 67.6 1.5 3.2E-05 33.2 -0.4 41 658-698 4-46 (71)
27 TIGR01622 SF-CC1 splicing fact 66.1 1.7 3.7E-05 47.2 -0.4 42 657-698 193-236 (457)
28 KOG4207 Predicted splicing fac 64.8 2 4.2E-05 46.2 -0.3 41 658-698 21-63 (256)
29 TIGR01648 hnRNP-R-Q heterogene 61.7 2.4 5.3E-05 50.0 -0.3 41 657-698 65-107 (578)
30 TIGR01642 U2AF_lg U2 snRNP aux 61.5 2.2 4.9E-05 46.9 -0.6 42 657-698 302-345 (509)
31 KOG0126 Predicted RNA-binding 55.7 5.9 0.00013 42.1 1.3 37 658-694 43-81 (219)
32 KOG0149 Predicted RNA-binding 52.0 4.4 9.5E-05 44.0 -0.3 42 658-699 20-63 (247)
33 PF14259 RRM_6: RNA recognitio 48.4 2.7 5.8E-05 34.3 -2.0 40 658-698 6-47 (70)
34 TIGR01628 PABP-1234 polyadenyl 47.7 5.8 0.00013 44.9 -0.2 40 658-698 293-334 (562)
35 KOG0147 Transcriptional coacti 46.1 9.2 0.0002 45.3 1.1 42 657-698 285-328 (549)
36 KOG0127 Nucleolar protein fibr 39.5 9.9 0.00022 45.4 0.0 42 657-698 299-342 (678)
37 PF00076 RRM_1: RNA recognitio 37.9 3.2 6.9E-05 32.9 -3.0 40 658-698 6-47 (70)
38 KOG4209 Splicing factor RNPS1, 35.8 17 0.00037 38.6 1.1 43 656-698 107-151 (231)
39 smart00361 RRM_1 RNA recogniti 35.3 11 0.00024 31.8 -0.3 28 671-698 15-45 (70)
40 KOG0116 RasGAP SH3 binding pro 30.3 84 0.0018 36.5 5.4 9 689-697 309-317 (419)
41 smart00362 RRM_2 RNA recogniti 25.4 24 0.00052 26.8 0.1 39 658-698 7-47 (72)
42 cd00590 RRM RRM (RNA recogniti 25.2 20 0.00042 27.5 -0.5 40 658-698 7-48 (74)
43 KOG0124 Polypyrimidine tract-b 24.9 24 0.00052 40.8 -0.0 41 657-697 120-162 (544)
44 KOG4205 RNA-binding protein mu 21.0 48 0.001 37.0 1.3 42 657-698 13-56 (311)
45 PF06273 eIF-4B: Plant specifi 20.9 4.2E+02 0.009 32.0 8.6 9 678-686 91-99 (492)
46 KOG0145 RNA-binding protein EL 20.8 38 0.00082 37.9 0.5 40 658-697 286-327 (360)
47 KOG1999 RNA polymerase II tran 20.7 1.3E+03 0.028 30.4 13.0 128 279-424 726-868 (1024)
No 1
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=96.38 E-value=0.017 Score=70.04 Aligned_cols=11 Identities=45% Similarity=0.948 Sum_probs=4.9
Q ss_pred CCCCCCCCCCC
Q 001593 748 DREGFGGRGGS 758 (1048)
Q Consensus 748 dRGGFgGRGgG 758 (1048)
.||||++-++|
T Consensus 1231 srgGfrnnggG 1241 (1282)
T KOG0921|consen 1231 SRGGFRNNGGG 1241 (1282)
T ss_pred cCCccccCCCC
Confidence 34455444433
No 2
>PLN03134 glycine-rich RNA-binding protein 4; Provisional
Probab=96.36 E-value=0.0031 Score=60.69 Aligned_cols=42 Identities=10% Similarity=-0.044 Sum_probs=39.4
Q ss_pred CCCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCC
Q 001593 657 SGSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRS 698 (1048)
Q Consensus 657 SLSFDANEDSVWe--se~GSwnSVRIPTDpESG~~KGFGYv~~~ 698 (1048)
-|+++++|+.|.+ ++||.|..|+|+.|++|+..|+|+||.+.
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 5889999999999 89999999999999999999999998875
No 3
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=96.24 E-value=0.019 Score=64.03 Aligned_cols=17 Identities=59% Similarity=1.109 Sum_probs=7.4
Q ss_pred CCCCCCCCCCCCCCCCCC
Q 001593 770 DRGGFGGRGRGRRDQGGG 787 (1048)
Q Consensus 770 ~RGGFggRgr~~r~~~gg 787 (1048)
+|+| ++|+|++.+.+|+
T Consensus 443 gr~g-ggrgrgggggrg~ 459 (465)
T KOG3973|consen 443 GRDG-GGRGRGGGGGRGG 459 (465)
T ss_pred CCCC-CCCCCCCCCCCcc
Confidence 3443 4444444444444
No 4
>KOG3262 consensus H/ACA small nucleolar RNP component GAR1 [Translation, ribosomal structure and biogenesis]
Probab=95.29 E-value=0.036 Score=57.70 Aligned_cols=21 Identities=71% Similarity=1.434 Sum_probs=10.3
Q ss_pred CCCCCCCCCCCCCCCCCCCCCC
Q 001593 759 DRGGFGGRGSSDRGGFGGRGRG 780 (1048)
Q Consensus 759 ~RGGfrGRGrG~RGGFggRgr~ 780 (1048)
.|++|++|+ +.+++|++|+|.
T Consensus 193 ~rGG~~~Rg-g~ggg~rgrgR~ 213 (215)
T KOG3262|consen 193 SRGGFRGRG-GHGGGFRGRGRG 213 (215)
T ss_pred CCCCccccC-CCCCCCCCCCCC
Confidence 344454433 235566666654
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=95.06 E-value=0.029 Score=61.21 Aligned_cols=43 Identities=5% Similarity=-0.124 Sum_probs=39.7
Q ss_pred CCCCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCC
Q 001593 656 NSGSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRS 698 (1048)
Q Consensus 656 nSLSFDANEDSVWe--se~GSwnSVRIPTDpESG~~KGFGYv~~~ 698 (1048)
.-|+++++++.|.+ ++||.|..|+|+.|.+|+.+|+|+||++.
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 99999999999999999999999999874
No 6
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=94.92 E-value=0.11 Score=58.21 Aligned_cols=17 Identities=59% Similarity=1.179 Sum_probs=10.2
Q ss_pred CCCCCCCCCCCCCCCCCC
Q 001593 770 DRGGFGGRGRGRRDQGGG 787 (1048)
Q Consensus 770 ~RGGFggRgr~~r~~~gg 787 (1048)
+|+| ++|+.++|++.||
T Consensus 438 gr~g-ggr~gggrgrggg 454 (465)
T KOG3973|consen 438 GRDG-GGRDGGGRGRGGG 454 (465)
T ss_pred CCCC-CCCCCCCCCCCCC
Confidence 4555 5666666666655
No 7
>KOG3262 consensus H/ACA small nucleolar RNP component GAR1 [Translation, ribosomal structure and biogenesis]
Probab=94.35 E-value=0.086 Score=55.06 Aligned_cols=41 Identities=59% Similarity=1.144 Sum_probs=20.5
Q ss_pred CCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 001593 726 DRGGFGGRGR-TNRGGYGGRGRFDREGFGGRGGSDRGGFGGRGS 768 (1048)
Q Consensus 726 ~RGGFgGrgg-G~RGGfGGrGrGdRGGFgGRGgG~RGGfrGRGr 768 (1048)
.|++|++|++ ++|++|.++ .+.|++|.+|+ +.+++|++|+|
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 5566665532 233444444 24556655433 24556666554
No 8
>PTZ00146 fibrillarin; Provisional
Probab=92.84 E-value=0.23 Score=54.07 Aligned_cols=6 Identities=33% Similarity=0.894 Sum_probs=2.7
Q ss_pred CcCCCC
Q 001593 849 WNNSNT 854 (1048)
Q Consensus 849 Wn~s~~ 854 (1048)
||--+|
T Consensus 110 w~p~rS 115 (293)
T PTZ00146 110 WNPFRS 115 (293)
T ss_pred eCCccc
Confidence 444443
No 9
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor. These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
Probab=92.72 E-value=0.03 Score=57.98 Aligned_cols=41 Identities=15% Similarity=0.059 Sum_probs=39.0
Q ss_pred CCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCC
Q 001593 658 GSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRS 698 (1048)
Q Consensus 658 LSFDANEDSVWe--se~GSwnSVRIPTDpESG~~KGFGYv~~~ 698 (1048)
|+++++++.|++ +.||.|.+|+|+.|+.|+..|+||||.+.
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 99999999999999999999999998874
No 10
>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]
Probab=86.13 E-value=0.3 Score=52.51 Aligned_cols=41 Identities=15% Similarity=-0.053 Sum_probs=37.0
Q ss_pred CCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCC
Q 001593 658 GSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRS 698 (1048)
Q Consensus 658 LSFDANEDSVWe--se~GSwnSVRIPTDpESG~~KGFGYv~~~ 698 (1048)
|+|++++|.|.. ..|+.|..||+|++++|+..|+|+|+...
T Consensus 193 ~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~ 235 (285)
T KOG4210|consen 193 LDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFS 235 (285)
T ss_pred cccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhh
Confidence 788999999875 77789999999999999999999998764
No 11
>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]
Probab=86.03 E-value=0.2 Score=54.08 Aligned_cols=41 Identities=12% Similarity=0.031 Sum_probs=38.0
Q ss_pred CCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCC
Q 001593 658 GSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRS 698 (1048)
Q Consensus 658 LSFDANEDSVWe--se~GSwnSVRIPTDpESG~~KGFGYv~~~ 698 (1048)
||-|++|+.|.+ ..+|-|.+|+|--|.+||..|||+||.+.
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 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=85.20 E-value=0.25 Score=54.16 Aligned_cols=41 Identities=7% Similarity=0.049 Sum_probs=38.5
Q ss_pred CCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCC
Q 001593 658 GSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRS 698 (1048)
Q Consensus 658 LSFDANEDSVWe--se~GSwnSVRIPTDpESG~~KGFGYv~~~ 698 (1048)
|+.+++++.|.+ ++|+.|++|+|..|+.|+..|+|+||++.
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 88999999999999999999999998863
No 13
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor. These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
Probab=84.92 E-value=0.23 Score=51.52 Aligned_cols=42 Identities=10% Similarity=-0.065 Sum_probs=39.2
Q ss_pred CCCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCC
Q 001593 657 SGSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRS 698 (1048)
Q Consensus 657 SLSFDANEDSVWe--se~GSwnSVRIPTDpESG~~KGFGYv~~~ 698 (1048)
-|+++++|+.|.+ ++||.|..|+|..|..++..++|+||.+.
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 99999999999999999999999999864
No 14
>PLN03213 repressor of silencing 3; Provisional
Probab=83.55 E-value=0.32 Score=56.63 Aligned_cols=37 Identities=5% Similarity=0.003 Sum_probs=34.7
Q ss_pred CCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCC
Q 001593 658 GSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRS 698 (1048)
Q Consensus 658 LSFDANEDSVWe--se~GSwnSVRIPTDpESG~~KGFGYv~~~ 698 (1048)
|+|+++++.|.. .+||.|.+|.|| +||| |+|+||...
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 8998 999998865
No 15
>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]
Probab=82.60 E-value=1.5 Score=50.02 Aligned_cols=40 Identities=13% Similarity=-0.053 Sum_probs=30.8
Q ss_pred CCCCCccccccc--cccCCceeeecCCCC-CCCCCCCCCCCCCC
Q 001593 658 GSDDANQESSWG--KKQGNWNSGSRDGHQ-ESSWGKKSDWNSRS 698 (1048)
Q Consensus 658 LSFDANEDSVWe--se~GSwnSVRIPTDp-ESG~~KGFGYv~~~ 698 (1048)
|++||+++.|-+ +.+|.|..++|+.-- .-..+ .|+|+++.
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 89998653
No 16
>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]
Probab=80.77 E-value=0.52 Score=43.56 Aligned_cols=41 Identities=15% Similarity=-0.005 Sum_probs=38.4
Q ss_pred CCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCC
Q 001593 658 GSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRS 698 (1048)
Q Consensus 658 LSFDANEDSVWe--se~GSwnSVRIPTDpESG~~KGFGYv~~~ 698 (1048)
|+++++++.|.+ .+++.|..|+|+.|+.++..++|+|+.+.
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 99999999999999999999999998874
No 17
>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=79.47 E-value=0.62 Score=55.12 Aligned_cols=42 Identities=12% Similarity=-0.074 Sum_probs=39.5
Q ss_pred CCCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCC
Q 001593 657 SGSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRS 698 (1048)
Q Consensus 657 SLSFDANEDSVWe--se~GSwnSVRIPTDpESG~~KGFGYv~~~ 698 (1048)
.|+++++++.|.+ .+||.|.+|+|+.|+.|+..|+|+||.+.
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 88999999999999999999999999875
No 18
>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=78.46 E-value=0.56 Score=52.74 Aligned_cols=42 Identities=10% Similarity=-0.066 Sum_probs=39.2
Q ss_pred CCCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCC
Q 001593 657 SGSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRS 698 (1048)
Q Consensus 657 SLSFDANEDSVWe--se~GSwnSVRIPTDpESG~~KGFGYv~~~ 698 (1048)
.|+++++|+.|.+ ++||.|.+|+|..|..|+..++|+||.+.
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 99999999999999999999999998874
No 19
>PLN03120 nucleic acid binding protein; Provisional
Probab=77.34 E-value=0.69 Score=50.01 Aligned_cols=39 Identities=10% Similarity=-0.002 Sum_probs=35.3
Q ss_pred CCCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCC
Q 001593 657 SGSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRS 698 (1048)
Q Consensus 657 SLSFDANEDSVWe--se~GSwnSVRIPTDpESG~~KGFGYv~~~ 698 (1048)
-|+++++|+.|++ +.||.|..|+||.|+++ ++|+||.+.
T Consensus 11 NLs~~tTE~dLrefFS~~G~I~~V~I~~d~~~---~GfAFVtF~ 51 (260)
T PLN03120 11 NVSLKATERDIKEFFSFSGDIEYVEMQSENER---SQIAYVTFK 51 (260)
T ss_pred CCCCCCCHHHHHHHHHhcCCeEEEEEeecCCC---CCEEEEEeC
Confidence 3889999999999 99999999999999874 789999875
No 20
>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=75.62 E-value=0.84 Score=49.56 Aligned_cols=42 Identities=12% Similarity=-0.009 Sum_probs=39.0
Q ss_pred CCCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCC
Q 001593 657 SGSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRS 698 (1048)
Q Consensus 657 SLSFDANEDSVWe--se~GSwnSVRIPTDpESG~~KGFGYv~~~ 698 (1048)
-|+++++++.|.+ ++||.|..|+|+.|+.|+..|+|+||.+.
T Consensus 96 nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~ 139 (457)
T TIGR01622 96 QLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFY 139 (457)
T ss_pred CCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEC
Confidence 4788999999999 88999999999999999999999999975
No 21
>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]
Probab=75.59 E-value=1.1 Score=51.24 Aligned_cols=42 Identities=12% Similarity=-0.088 Sum_probs=38.6
Q ss_pred CCCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCC
Q 001593 657 SGSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRS 698 (1048)
Q Consensus 657 SLSFDANEDSVWe--se~GSwnSVRIPTDpESG~~KGFGYv~~~ 698 (1048)
.++|+++|+.|-. +++|.|.++|+-.|+|||.+|+|+|++.-
T Consensus 25 nip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~ 68 (435)
T KOG0108|consen 25 NIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFT 68 (435)
T ss_pred CCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecC
Confidence 3789999999999 88899999999999999999999998864
No 22
>TIGR01645 half-pint poly-U binding splicing factor, half-pint family. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.
Probab=75.36 E-value=0.93 Score=53.71 Aligned_cols=43 Identities=9% Similarity=-0.075 Sum_probs=39.7
Q ss_pred CCCCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCC
Q 001593 656 NSGSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRS 698 (1048)
Q Consensus 656 nSLSFDANEDSVWe--se~GSwnSVRIPTDpESG~~KGFGYv~~~ 698 (1048)
-.|+++++++.|.+ +.||.|.+|+|+.|++++..|+|+|+.+.
T Consensus 210 gnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe 254 (612)
T TIGR01645 210 ASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYN 254 (612)
T ss_pred ecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEEC
Confidence 35889999999998 88999999999999999999999999875
No 23
>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]
Probab=73.31 E-value=0.98 Score=50.14 Aligned_cols=42 Identities=10% Similarity=-0.065 Sum_probs=38.8
Q ss_pred CCCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCC
Q 001593 657 SGSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRS 698 (1048)
Q Consensus 657 SLSFDANEDSVWe--se~GSwnSVRIPTDpESG~~KGFGYv~~~ 698 (1048)
-|+++++|+.|.+ ..||.|..|+|-.|..||-+|+|+||+..
T Consensus 108 RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye 151 (335)
T KOG0113|consen 108 RLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYE 151 (335)
T ss_pred eccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEec
Confidence 4788999999999 89999999999999999999999998853
No 24
>PLN03121 nucleic acid binding protein; Provisional
Probab=68.93 E-value=1.5 Score=47.27 Aligned_cols=39 Identities=10% Similarity=0.003 Sum_probs=34.9
Q ss_pred CCCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCC
Q 001593 657 SGSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRS 698 (1048)
Q Consensus 657 SLSFDANEDSVWe--se~GSwnSVRIPTDpESG~~KGFGYv~~~ 698 (1048)
-||+.++|..|++ +.||.|..|+|+.|.++ ++|+||.+.
T Consensus 12 NLS~~tTE~dLrefFS~~G~I~~V~I~~D~et---~gfAfVtF~ 52 (243)
T PLN03121 12 NLSPKATEKDVYDFFSHCGAIEHVEIIRSGEY---ACTAYVTFK 52 (243)
T ss_pred cCCCCCCHHHHHHHHHhcCCeEEEEEecCCCc---ceEEEEEEC
Confidence 3899999999999 99999999999999776 479999875
No 25
>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=68.11 E-value=5.2 Score=47.35 Aligned_cols=34 Identities=6% Similarity=-0.079 Sum_probs=28.8
Q ss_pred CCCCCCccccccc--ccc--CCceeeecCCCCCCCCCCCCCCCCCC
Q 001593 657 SGSDDANQESSWG--KKQ--GNWNSGSRDGHQESSWGKKSDWNSRS 698 (1048)
Q Consensus 657 SLSFDANEDSVWe--se~--GSwnSVRIPTDpESG~~KGFGYv~~~ 698 (1048)
.|+++++++.|.+ ++| |.|.+|+++ ++|+||.+.
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 469998864
No 26
>smart00360 RRM RNA recognition motif.
Probab=67.58 E-value=1.5 Score=33.24 Aligned_cols=41 Identities=15% Similarity=0.022 Sum_probs=35.7
Q ss_pred CCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCC
Q 001593 658 GSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRS 698 (1048)
Q Consensus 658 LSFDANEDSVWe--se~GSwnSVRIPTDpESG~~KGFGYv~~~ 698 (1048)
|+..++++.|.. ..+|.|..|.++.++.++.+++++|+...
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 88899999999999999999999998764
No 27
>TIGR01622 SF-CC1 splicing factor, CC1-like family. A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.
Probab=66.09 E-value=1.7 Score=47.23 Aligned_cols=42 Identities=7% Similarity=-0.040 Sum_probs=38.8
Q ss_pred CCCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCC
Q 001593 657 SGSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRS 698 (1048)
Q Consensus 657 SLSFDANEDSVWe--se~GSwnSVRIPTDpESG~~KGFGYv~~~ 698 (1048)
.|+++++++.|.+ +.||.|..|+|+.+++++..|+|+||.+.
T Consensus 193 nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~ 236 (457)
T TIGR01622 193 NLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFH 236 (457)
T ss_pred CCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEEC
Confidence 4788999999999 88999999999999999999999998875
No 28
>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]
Probab=64.78 E-value=2 Score=46.22 Aligned_cols=41 Identities=5% Similarity=-0.103 Sum_probs=37.8
Q ss_pred CCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCC
Q 001593 658 GSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRS 698 (1048)
Q Consensus 658 LSFDANEDSVWe--se~GSwnSVRIPTDpESG~~KGFGYv~~~ 698 (1048)
|.|-++.|+|.. ++||.|.-|.||-|+-|.+.++|+||-+.
T Consensus 21 LTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~ 63 (256)
T KOG4207|consen 21 LTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFH 63 (256)
T ss_pred eeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEee
Confidence 677888899998 99999999999999999999999998764
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=61.75 E-value=2.4 Score=49.98 Aligned_cols=41 Identities=10% Similarity=-0.113 Sum_probs=37.6
Q ss_pred CCCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCC
Q 001593 657 SGSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRS 698 (1048)
Q Consensus 657 SLSFDANEDSVWe--se~GSwnSVRIPTDpESG~~KGFGYv~~~ 698 (1048)
-|+++++|+.|.+ +++|.|..|+|+.| .++..++|+||.+.
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 89999999999999 89999999998864
No 30
>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor. Members of this subfamily are found in plants, metazoa and fungi.
Probab=61.49 E-value=2.2 Score=46.89 Aligned_cols=42 Identities=5% Similarity=-0.113 Sum_probs=38.8
Q ss_pred CCCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCC
Q 001593 657 SGSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRS 698 (1048)
Q Consensus 657 SLSFDANEDSVWe--se~GSwnSVRIPTDpESG~~KGFGYv~~~ 698 (1048)
-|+++++++.|.+ +.||.|..|.|..+++|+..|+|+||.+.
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 88999999999999999999999998874
No 31
>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=55.67 E-value=5.9 Score=42.08 Aligned_cols=37 Identities=5% Similarity=-0.088 Sum_probs=35.4
Q ss_pred CCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCC
Q 001593 658 GSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDW 694 (1048)
Q Consensus 658 LSFDANEDSVWe--se~GSwnSVRIPTDpESG~~KGFGY 694 (1048)
|+|+++|..|=. ++||+|+.|-|--|-+||-.|||+|
T Consensus 43 l~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaF 81 (219)
T KOG0126|consen 43 LPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAF 81 (219)
T ss_pred CcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEE
Confidence 899999999888 9999999999999999999999988
No 32
>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]
Probab=52.01 E-value=4.4 Score=43.96 Aligned_cols=42 Identities=7% Similarity=0.005 Sum_probs=37.5
Q ss_pred CCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCCC
Q 001593 658 GSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRSE 699 (1048)
Q Consensus 658 LSFDANEDSVWe--se~GSwnSVRIPTDpESG~~KGFGYv~~~~ 699 (1048)
|.+.+..++++. +++|+|+-+-+=||.+|++.|+||||++.+
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 566777888888 999999999999999999999999999753
No 33
>PF14259 RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....
Probab=48.37 E-value=2.7 Score=34.28 Aligned_cols=40 Identities=8% Similarity=-0.033 Sum_probs=33.7
Q ss_pred CCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCC
Q 001593 658 GSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRS 698 (1048)
Q Consensus 658 LSFDANEDSVWe--se~GSwnSVRIPTDpESG~~KGFGYv~~~ 698 (1048)
|+++++++.|.+ ..++.|..|++..+++ +..++++|+...
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 999999998753
No 34
>TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.
Probab=47.67 E-value=5.8 Score=44.91 Aligned_cols=40 Identities=15% Similarity=0.017 Sum_probs=36.6
Q ss_pred CCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCC
Q 001593 658 GSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRS 698 (1048)
Q Consensus 658 LSFDANEDSVWe--se~GSwnSVRIPTDpESG~~KGFGYv~~~ 698 (1048)
|+.+++++.|.+ ++||.|.+|+|..| +++..|+|+||.+.
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 88999999998875
No 35
>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]
Probab=46.05 E-value=9.2 Score=45.31 Aligned_cols=42 Identities=10% Similarity=0.011 Sum_probs=38.9
Q ss_pred CCCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCC
Q 001593 657 SGSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRS 698 (1048)
Q Consensus 657 SLSFDANEDSVWe--se~GSwnSVRIPTDpESG~~KGFGYv~~~ 698 (1048)
+|=|+.+++.+.. +.+|.|.-|-|+-|.|||..|+|+|+++.
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
>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]
Probab=39.45 E-value=9.9 Score=45.41 Aligned_cols=42 Identities=12% Similarity=0.018 Sum_probs=39.4
Q ss_pred CCCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCC
Q 001593 657 SGSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRS 698 (1048)
Q Consensus 657 SLSFDANEDSVWe--se~GSwnSVRIPTDpESG~~KGFGYv~~~ 698 (1048)
-|+||++|+.|-+ .++|.|..++|--|+.|+.+||-+|+.+.
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 37
>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=37.91 E-value=3.2 Score=32.88 Aligned_cols=40 Identities=15% Similarity=-0.004 Sum_probs=35.3
Q ss_pred CCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCC
Q 001593 658 GSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRS 698 (1048)
Q Consensus 658 LSFDANEDSVWe--se~GSwnSVRIPTDpESG~~KGFGYv~~~ 698 (1048)
|+.+++++.|.. +++|.|..+.+..+ .++..++++|+.+.
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 88999999999988 78899999998754
No 38
>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]
Probab=35.79 E-value=17 Score=38.61 Aligned_cols=43 Identities=9% Similarity=-0.179 Sum_probs=35.7
Q ss_pred CCCCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCC
Q 001593 656 NSGSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRS 698 (1048)
Q Consensus 656 nSLSFDANEDSVWe--se~GSwnSVRIPTDpESG~~KGFGYv~~~ 698 (1048)
..+-|.++-..+-. +.|+.|+.|-||+|..++.+|+|+|+++.
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 89999999999999999999999999875
No 39
>smart00361 RRM_1 RNA recognition motif.
Probab=35.33 E-value=11 Score=31.83 Aligned_cols=28 Identities=4% Similarity=-0.171 Sum_probs=22.3
Q ss_pred ccCCceeee-cCCCCCC--CCCCCCCCCCCC
Q 001593 671 KQGNWNSGS-RDGHQES--SWGKKSDWNSRS 698 (1048)
Q Consensus 671 e~GSwnSVR-IPTDpES--G~~KGFGYv~~~ 698 (1048)
++|.|.+|. |+-++++ +..++|+||...
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 899999998764
No 40
>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]
Probab=30.27 E-value=84 Score=36.51 Aligned_cols=9 Identities=11% Similarity=-0.385 Sum_probs=4.0
Q ss_pred CCCCCCCCC
Q 001593 689 GKKSDWNSR 697 (1048)
Q Consensus 689 ~KGFGYv~~ 697 (1048)
.|.|+=+..
T Consensus 309 Fk~FG~Ik~ 317 (419)
T KOG0116|consen 309 FKQFGPIKE 317 (419)
T ss_pred Hhhcccccc
Confidence 444544443
No 41
>smart00362 RRM_2 RNA recognition motif.
Probab=25.43 E-value=24 Score=26.84 Aligned_cols=39 Identities=15% Similarity=-0.035 Sum_probs=31.9
Q ss_pred CCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCC
Q 001593 658 GSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRS 698 (1048)
Q Consensus 658 LSFDANEDSVWe--se~GSwnSVRIPTDpESG~~KGFGYv~~~ 698 (1048)
|+..++++.|.+ .++|.|..+++..++ +.+++++|+...
T Consensus 7 l~~~~~~~~l~~~~~~~g~v~~~~~~~~~--~~~~~~~~v~f~ 47 (72)
T smart00362 7 LPPDVTEEDLKELFSKFGPIESVKIPKDT--GKSKGFAFVEFE 47 (72)
T ss_pred CCCcCCHHHHHHHHHhcCCEEEEEEecCC--CCCCceEEEEeC
Confidence 566778888888 888999999999887 678889987754
No 42
>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=25.17 E-value=20 Score=27.46 Aligned_cols=40 Identities=15% Similarity=0.014 Sum_probs=32.9
Q ss_pred CCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCC
Q 001593 658 GSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRS 698 (1048)
Q Consensus 658 LSFDANEDSVWe--se~GSwnSVRIPTDpESG~~KGFGYv~~~ 698 (1048)
|+.+++++.|.+ ..++.|..+.++.++.+ .+++++|+...
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 78889987653
No 43
>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]
Probab=24.88 E-value=24 Score=40.81 Aligned_cols=41 Identities=12% Similarity=-0.078 Sum_probs=38.3
Q ss_pred CCCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCC
Q 001593 657 SGSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSR 697 (1048)
Q Consensus 657 SLSFDANEDSVWe--se~GSwnSVRIPTDpESG~~KGFGYv~~ 697 (1048)
|+||..-||+|+. -.+|-|.||..-=||-|+--|+|+|++-
T Consensus 120 SIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEY 162 (544)
T KOG0124|consen 120 SISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEY 162 (544)
T ss_pred eeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEE
Confidence 7899999999999 7889999999999999999999999764
No 44
>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]
Probab=20.96 E-value=48 Score=36.99 Aligned_cols=42 Identities=10% Similarity=-0.025 Sum_probs=38.3
Q ss_pred CCCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCCC
Q 001593 657 SGSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSRS 698 (1048)
Q Consensus 657 SLSFDANEDSVWe--se~GSwnSVRIPTDpESG~~KGFGYv~~~ 698 (1048)
.||++++|+.|.+ .++|+|.-+-+-.|+.|++.++|+++++.
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 88899999999999999999999998764
No 45
>PF06273 eIF-4B: Plant specific eukaryotic initiation factor 4B; InterPro: IPR010433 This family consists of several plant specific eukaryotic initiation factor 4B proteins.
Probab=20.88 E-value=4.2e+02 Score=31.96 Aligned_cols=9 Identities=0% Similarity=-0.363 Sum_probs=6.2
Q ss_pred eecCCCCCC
Q 001593 678 GSRDGHQES 686 (1048)
Q Consensus 678 VRIPTDpES 686 (1048)
|.|||.|-.
T Consensus 91 m~LPTGPRe 99 (492)
T PF06273_consen 91 MMLPTGPRE 99 (492)
T ss_pred eecCCCCCC
Confidence 468887764
No 46
>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]
Probab=20.79 E-value=38 Score=37.93 Aligned_cols=40 Identities=15% Similarity=0.033 Sum_probs=37.0
Q ss_pred CCCCCccccccc--cccCCceeeecCCCCCCCCCCCCCCCCC
Q 001593 658 GSDDANQESSWG--KKQGNWNSGSRDGHQESSWGKKSDWNSR 697 (1048)
Q Consensus 658 LSFDANEDSVWe--se~GSwnSVRIPTDpESG~~KGFGYv~~ 697 (1048)
|+-|++|..+|. ..+|-|+.|.|-.|..|-.-|+|+||+-
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 47
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=20.71 E-value=1.3e+03 Score=30.36 Aligned_cols=128 Identities=23% Similarity=0.437 Sum_probs=69.4
Q ss_pred cCcCCCCCCCCCCCCCCCCCcCCCCCCCCccCCcccccccCCCCCCCCCCCCCccc-cCCCCCCCc----ccCCCCCccc
Q 001593 279 MGKQDGGSSWGKQDGGSSLGKQDGGSSWGKQDGRSSLAKQDGGSSWGKQDRGSSWG-KQDEGSSWS----KRDGGSSWGK 353 (1048)
Q Consensus 279 ~~~~~ggs~w~~~~gg~g~~~~~ggssw~~k~g~~~~a~~~g~~~W~~~~~g~Swg-~~d~~~sW~----k~d~~~sW~~ 353 (1048)
+++......|...+++..+ +|. .+-.-.|...|+..+.|++|. ..+++..|. ..+..+.--.
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 5666666666665555444 343 233344556666666777776 556666665 2111111111
Q ss_pred cCCCCcccccCCCCCCCccCCCCCccc-----cCCCC-CccccCCCCCCCccCCCCCcCcCC--CCCCCCcC--CCCCCC
Q 001593 354 QDGGSSLAKQDGGSSWGKQDGGSSLGK-----QDGGS-SWSKQDGGSSWGKQDGGSSWGKQD--GGSSWGKQ--DGGSSW 423 (1048)
Q Consensus 354 ~Dg~~s~~~~DGgssWgk~d~~~s~~~-----~DGgs-SW~kkd~g~sw~k~dGgsSWgkkd--G~ssWgk~--dgGSsW 423 (1048)
.||..+.+ +...|... .+.+-+. .+|.. +|.+.... +|...-.++.|++.. +.++|+++ +.+|.|
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 001593 424 S 424 (1048)
Q Consensus 424 s 424 (1048)
.
T Consensus 868 ~ 868 (1024)
T KOG1999|consen 868 G 868 (1024)
T ss_pred c
Confidence 7
Done!