Query psy9172
Match_columns 80
No_of_seqs 120 out of 130
Neff 3.4
Searched_HMMs 46136
Date Fri Aug 16 20:42:31 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy9172.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/9172hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1190|consensus 99.8 4E-19 8.6E-24 144.6 5.3 69 2-74 113-191 (492)
2 KOG1456|consensus 98.9 1.9E-09 4.1E-14 88.3 4.0 42 20-62 113-154 (494)
3 TIGR01649 hnRNP-L_PTB hnRNP-L/ 97.6 5.5E-05 1.2E-09 60.0 3.8 38 24-62 91-128 (481)
4 KOG1190|consensus 96.6 0.002 4.4E-08 53.7 3.3 35 28-63 297-331 (492)
5 PF00076 RRM_1: RNA recognitio 90.9 0.29 6.3E-06 27.3 2.6 32 32-64 1-32 (70)
6 TIGR01661 ELAV_HUD_SF ELAV/HuD 88.7 0.48 1E-05 34.9 3.0 40 32-72 272-313 (352)
7 PLN03134 glycine-rich RNA-bind 86.8 0.92 2E-05 31.2 3.3 34 31-65 36-69 (144)
8 TIGR01628 PABP-1234 polyadenyl 84.1 1.5 3.2E-05 35.1 3.8 62 3-65 52-123 (562)
9 smart00362 RRM_2 RNA recogniti 82.9 1.6 3.4E-05 23.3 2.5 28 32-60 2-29 (72)
10 KOG4207|consensus 81.2 1.1 2.4E-05 35.1 2.0 38 28-68 12-49 (256)
11 PF13893 RRM_5: RNA recognitio 80.8 0.96 2.1E-05 25.4 1.2 13 46-59 1-13 (56)
12 TIGR01649 hnRNP-L_PTB hnRNP-L/ 77.0 2.6 5.5E-05 33.7 2.9 37 25-64 273-310 (481)
13 KOG0123|consensus 76.2 5.1 0.00011 31.9 4.4 67 4-72 48-118 (369)
14 TIGR01645 half-pint poly-U bin 71.5 4.4 9.5E-05 34.8 3.2 42 28-72 106-151 (612)
15 PLN03213 repressor of silencin 71.1 4.7 0.0001 35.3 3.3 42 28-72 9-50 (759)
16 PLN03121 nucleic acid binding 70.9 4.3 9.2E-05 31.5 2.7 35 30-65 6-40 (243)
17 TIGR01661 ELAV_HUD_SF ELAV/HuD 70.7 5.5 0.00012 29.3 3.2 32 30-62 4-35 (352)
18 TIGR01628 PABP-1234 polyadenyl 70.6 4.8 0.0001 32.3 3.0 34 31-65 287-320 (562)
19 KOG0415|consensus 69.1 9.3 0.0002 32.2 4.5 41 20-64 232-273 (479)
20 TIGR01622 SF-CC1 splicing fact 66.2 6.9 0.00015 30.2 3.0 30 30-60 187-216 (457)
21 cd00590 RRM RRM (RNA recogniti 65.9 6.7 0.00015 20.9 2.2 31 32-63 2-32 (74)
22 KOG0131|consensus 65.4 3.1 6.7E-05 31.8 0.9 35 33-68 100-134 (203)
23 TIGR01642 U2AF_lg U2 snRNP aux 64.1 7.9 0.00017 30.2 3.0 31 31-62 297-327 (509)
24 TIGR01659 sex-lethal sex-letha 63.8 8 0.00017 30.4 3.0 32 31-63 195-226 (346)
25 TIGR01645 half-pint poly-U bin 63.3 7.9 0.00017 33.3 3.1 35 29-64 204-238 (612)
26 PLN03120 nucleic acid binding 62.6 9.3 0.0002 29.8 3.2 39 31-72 6-45 (260)
27 TIGR01659 sex-lethal sex-letha 60.7 11 0.00024 29.7 3.3 33 29-62 107-139 (346)
28 COG0724 RNA-binding proteins ( 59.8 13 0.00028 24.2 3.0 34 30-64 116-149 (306)
29 KOG0127|consensus 57.9 9.5 0.00021 33.5 2.7 40 30-72 118-160 (678)
30 smart00360 RRM RNA recognition 57.3 8.5 0.00019 20.2 1.6 28 35-63 2-29 (71)
31 PF14259 RRM_6: RNA recognitio 51.9 22 0.00047 20.1 2.8 31 32-63 1-31 (70)
32 KOG0110|consensus 51.8 20 0.00043 32.0 3.6 66 4-70 571-653 (725)
33 KOG0125|consensus 49.2 17 0.00037 30.0 2.8 47 26-73 93-139 (376)
34 TIGR01622 SF-CC1 splicing fact 47.6 23 0.0005 27.3 3.1 31 31-62 91-121 (457)
35 KOG0148|consensus 46.3 18 0.00039 29.3 2.4 43 29-72 62-106 (321)
36 PF08777 RRM_3: RNA binding mo 45.7 20 0.00043 23.7 2.2 27 31-58 3-29 (105)
37 KOG0114|consensus 42.3 17 0.00037 25.9 1.5 31 25-58 16-46 (124)
38 KOG0145|consensus 40.0 52 0.0011 26.9 4.1 50 22-72 271-322 (360)
39 TIGR01642 U2AF_lg U2 snRNP aux 39.3 22 0.00048 27.7 1.9 34 26-62 408-451 (509)
40 PF12631 GTPase_Cys_C: Catalyt 39.2 15 0.00033 22.5 0.8 14 41-55 60-73 (73)
41 TIGR01648 hnRNP-R-Q heterogene 38.9 32 0.00068 29.4 2.9 42 30-72 59-101 (578)
42 KOG0115|consensus 34.5 26 0.00056 27.9 1.6 35 32-67 34-68 (275)
43 TIGR01648 hnRNP-R-Q heterogene 33.1 41 0.00089 28.7 2.7 33 29-62 233-267 (578)
44 KOG0147|consensus 31.2 19 0.00042 31.0 0.5 37 28-67 277-313 (549)
45 KOG0127|consensus 30.6 48 0.001 29.3 2.7 26 32-58 295-320 (678)
46 KOG0124|consensus 29.7 38 0.00082 28.9 1.9 38 29-69 113-150 (544)
47 PF08675 RNA_bind: RNA binding 28.7 29 0.00063 23.4 0.9 15 44-59 23-37 (87)
48 KOG0121|consensus 27.9 53 0.0011 24.2 2.2 35 32-69 39-73 (153)
49 KOG4206|consensus 26.3 92 0.002 24.0 3.4 43 25-71 7-53 (221)
50 TIGR00691 spoT_relA (p)ppGpp s 23.7 43 0.00094 28.8 1.3 45 29-77 237-283 (683)
51 KOG0117|consensus 22.1 68 0.0015 27.6 2.1 36 27-63 257-292 (506)
52 KOG0123|consensus 22.0 63 0.0014 25.8 1.8 32 39-72 8-39 (369)
53 COG0779 Uncharacterized protei 21.4 75 0.0016 22.8 2.0 27 24-51 33-59 (153)
54 KOG0533|consensus 20.7 82 0.0018 24.2 2.2 41 25-68 79-119 (243)
55 KOG4660|consensus 20.4 61 0.0013 28.1 1.5 26 32-58 78-103 (549)
No 1
>KOG1190|consensus
Probab=99.76 E-value=4e-19 Score=144.65 Aligned_cols=69 Identities=39% Similarity=0.621 Sum_probs=61.3
Q ss_pred ChHHHHHHHHHhhhhhcC----------CCCCCCCCcEEEEEEecccceeehhhhhhhhcccccceeeeceeeccccccC
Q psy9172 2 NSASAQAALQAAQALTGQ----------TDTQGGPNTVLRVIIEHMLYPITLDVLYQFDNYKFGHAFSTSLAMPRDELAG 71 (80)
Q Consensus 2 n~~~aqaALqa~n~v~~~----------~~~~~~pn~VLrviIeN~~YPVTldVLhqiFs~~fG~Vlrq~~a~~~~~~~~ 71 (80)
||.+++++++++++++.. ...+++||+|||+|||||+||||+|||||||| +||+|+ ++++|.|.+|
T Consensus 113 ~q~r~~~vy~~~s~~q~~~~~~s~~~~~~G~~~~~n~vLr~iie~m~ypVslDVLHqvFS-~fG~Vl---KIiTF~Knn~ 188 (492)
T KOG1190|consen 113 NQIRGQAVYQAVSSVQEIVLPLSASAVVVGNEDGPNPVLRTIIENMFYPVSLDVLHQVFS-KFGFVL---KIITFTKNNG 188 (492)
T ss_pred hhhhhhhHHhhhhcccccccccccccccccccCCCceeEEEEeccceeeeEHHHHHHHHh-hcceeE---EEEEEecccc
Confidence 567999999999876553 13677999999999999999999999999999 999999 8999999999
Q ss_pred ccc
Q psy9172 72 FRS 74 (80)
Q Consensus 72 ~~~ 74 (80)
|.-
T Consensus 189 FQA 191 (492)
T KOG1190|consen 189 FQA 191 (492)
T ss_pred hhh
Confidence 963
No 2
>KOG1456|consensus
Probab=98.86 E-value=1.9e-09 Score=88.31 Aligned_cols=42 Identities=38% Similarity=0.556 Sum_probs=38.6
Q ss_pred CCCCCCCCcEEEEEEecccceeehhhhhhhhcccccceeeece
Q psy9172 20 TDTQGGPNTVLRVIIEHMLYPITLDVLYQFDNYKFGHAFSTSL 62 (80)
Q Consensus 20 ~~~~~~pn~VLrviIeN~~YPVTldVLhqiFs~~fG~Vlrq~~ 62 (80)
+.....||+||+++|.|++||||+||||+|+. +.|.|+|-.+
T Consensus 113 g~es~~pN~VLl~TIlNp~YpItvDVly~Icn-p~GkVlRIvI 154 (494)
T KOG1456|consen 113 GDESATPNKVLLFTILNPQYPITVDVLYTICN-PQGKVLRIVI 154 (494)
T ss_pred CCCCCCCCeEEEEEeecCccccchhhhhhhcC-CCCceEEEEE
Confidence 56778999999999999999999999999999 9999998654
No 3
>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=97.64 E-value=5.5e-05 Score=60.00 Aligned_cols=38 Identities=55% Similarity=0.928 Sum_probs=34.7
Q ss_pred CCCCcEEEEEEecccceeehhhhhhhhcccccceeeece
Q psy9172 24 GGPNTVLRVIIEHMLYPITLDVLYQFDNYKFGHAFSTSL 62 (80)
Q Consensus 24 ~~pn~VLrviIeN~~YPVTldVLhqiFs~~fG~Vlrq~~ 62 (80)
.+++.+|+|.|.|+-|+||.|.|+++|+ +||.|.|-++
T Consensus 91 ~~~~~~~~v~v~nl~~~vt~~~L~~~F~-~~G~V~~v~i 128 (481)
T TIGR01649 91 AGPNKVLRVIVENPMYPITLDVLYQIFN-PYGKVLRIVT 128 (481)
T ss_pred CCCCceEEEEEcCCCCCCCHHHHHHHHh-ccCCEEEEEE
Confidence 3578999999999999999999999999 9999987655
No 4
>KOG1190|consensus
Probab=96.58 E-value=0.002 Score=53.65 Aligned_cols=35 Identities=17% Similarity=0.249 Sum_probs=28.9
Q ss_pred cEEEEEEecccceeehhhhhhhhcccccceeeecee
Q psy9172 28 TVLRVIIEHMLYPITLDVLYQFDNYKFGHAFSTSLA 63 (80)
Q Consensus 28 ~VLrviIeN~~YPVTldVLhqiFs~~fG~Vlrq~~a 63 (80)
++++..++++-|-||.|+||++|+ .||.|+|=|+-
T Consensus 297 n~vllvsnln~~~VT~d~LftlFg-vYGdVqRVkil 331 (492)
T KOG1190|consen 297 NVVLLVSNLNEEAVTPDVLFTLFG-VYGDVQRVKIL 331 (492)
T ss_pred ceEEEEecCchhccchhHHHHHHh-hhcceEEEEee
Confidence 455556677779999999999999 99999886653
No 5
>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=90.88 E-value=0.29 Score=27.35 Aligned_cols=32 Identities=19% Similarity=0.246 Sum_probs=26.8
Q ss_pred EEEecccceeehhhhhhhhcccccceeeeceee
Q psy9172 32 VIIEHMLYPITLDVLYQFDNYKFGHAFSTSLAM 64 (80)
Q Consensus 32 viIeN~~YPVTldVLhqiFs~~fG~Vlrq~~a~ 64 (80)
|.|.|+-.-+|-+-|.+.|+ +||.|..-.+..
T Consensus 1 l~v~nlp~~~t~~~l~~~f~-~~g~i~~~~~~~ 32 (70)
T PF00076_consen 1 LYVGNLPPDVTEEELRDFFS-QFGKIESIKVMR 32 (70)
T ss_dssp EEEESETTTSSHHHHHHHHH-TTSTEEEEEEEE
T ss_pred cEEcCCCCcCCHHHHHHHHH-Hhhhcccccccc
Confidence 56889988999999999999 999996555444
No 6
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor. These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
Probab=88.69 E-value=0.48 Score=34.90 Aligned_cols=40 Identities=15% Similarity=0.294 Sum_probs=31.6
Q ss_pred EEEecccceeehhhhhhhhcccccceeeeceeec--cccccCc
Q psy9172 32 VIIEHMLYPITLDVLYQFDNYKFGHAFSTSLAMP--RDELAGF 72 (80)
Q Consensus 32 viIeN~~YPVTldVLhqiFs~~fG~Vlrq~~a~~--~~~~~~~ 72 (80)
|.|.|+-+.+|-+-|..+|+ +||.|.+-++..- ...+-||
T Consensus 272 lfV~NL~~~~~e~~L~~~F~-~fG~v~~v~i~~d~~t~~skG~ 313 (352)
T TIGR01661 272 IFVYNLSPDTDETVLWQLFG-PFGAVQNVKIIRDLTTNQCKGY 313 (352)
T ss_pred EEEeCCCCCCCHHHHHHHHH-hCCCeEEEEEeEcCCCCCccce
Confidence 77999999999999999999 9999987655432 2345554
No 7
>PLN03134 glycine-rich RNA-binding protein 4; Provisional
Probab=86.77 E-value=0.92 Score=31.20 Aligned_cols=34 Identities=12% Similarity=0.183 Sum_probs=29.1
Q ss_pred EEEEecccceeehhhhhhhhcccccceeeeceeec
Q psy9172 31 RVIIEHMLYPITLDVLYQFDNYKFGHAFSTSLAMP 65 (80)
Q Consensus 31 rviIeN~~YPVTldVLhqiFs~~fG~Vlrq~~a~~ 65 (80)
+|-|.|+-+-+|-+-|-.+|+ +||.|.+-.+.+.
T Consensus 36 ~lfVgnL~~~~te~~L~~~F~-~~G~I~~v~i~~d 69 (144)
T PLN03134 36 KLFIGGLSWGTDDASLRDAFA-HFGDVVDAKVIVD 69 (144)
T ss_pred EEEEeCCCCCCCHHHHHHHHh-cCCCeEEEEEEec
Confidence 577889999999999999999 9999987665543
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=84.11 E-value=1.5 Score=35.13 Aligned_cols=62 Identities=19% Similarity=0.205 Sum_probs=40.8
Q ss_pred hHHHHHHHHHhhhhhcCC----------CCCCCCCcEEEEEEecccceeehhhhhhhhcccccceeeeceeec
Q psy9172 3 SASAQAALQAAQALTGQT----------DTQGGPNTVLRVIIEHMLYPITLDVLYQFDNYKFGHAFSTSLAMP 65 (80)
Q Consensus 3 ~~~aqaALqa~n~v~~~~----------~~~~~pn~VLrviIeN~~YPVTldVLhqiFs~~fG~Vlrq~~a~~ 65 (80)
...|+.||+..+-....+ +.....+..-.|.|.|+-+-+|-+-|+.+|+ +||.|..-++...
T Consensus 52 ~~~A~~Al~~ln~~~i~gk~i~i~~s~~~~~~~~~~~~~vfV~nLp~~~~~~~L~~~F~-~~G~i~~~~i~~~ 123 (562)
T TIGR01628 52 PADAERALETMNFKRLGGKPIRIMWSQRDPSLRRSGVGNIFVKNLDKSVDNKALFDTFS-KFGNILSCKVATD 123 (562)
T ss_pred HHHHHHHHHHhCCCEECCeeEEeecccccccccccCCCceEEcCCCccCCHHHHHHHHH-hcCCcceeEeeec
Confidence 347788888776321110 0011112233478999999999999999999 9999987665543
No 9
>smart00362 RRM_2 RNA recognition motif.
Probab=82.88 E-value=1.6 Score=23.35 Aligned_cols=28 Identities=21% Similarity=0.249 Sum_probs=24.0
Q ss_pred EEEecccceeehhhhhhhhcccccceeee
Q psy9172 32 VIIEHMLYPITLDVLYQFDNYKFGHAFST 60 (80)
Q Consensus 32 viIeN~~YPVTldVLhqiFs~~fG~Vlrq 60 (80)
|.|.|+-..++-+-|...|+ +||.|.+-
T Consensus 2 v~i~~l~~~~~~~~l~~~~~-~~g~v~~~ 29 (72)
T smart00362 2 LFVGNLPPDVTEEDLKELFS-KFGPIESV 29 (72)
T ss_pred EEEcCCCCcCCHHHHHHHHH-hcCCEEEE
Confidence 67888877889999999999 99998653
No 10
>KOG4207|consensus
Probab=81.16 E-value=1.1 Score=35.06 Aligned_cols=38 Identities=21% Similarity=0.433 Sum_probs=33.0
Q ss_pred cEEEEEEecccceeehhhhhhhhcccccceeeeceeecccc
Q psy9172 28 TVLRVIIEHMLYPITLDVLYQFDNYKFGHAFSTSLAMPRDE 68 (80)
Q Consensus 28 ~VLrviIeN~~YPVTldVLhqiFs~~fG~Vlrq~~a~~~~~ 68 (80)
-+.-+-|+|+.|--|-|-|.-+|. |||.| -.+-+|+|.
T Consensus 12 gm~SLkVdNLTyRTspd~LrrvFe-kYG~v--gDVyIPrdr 49 (256)
T KOG4207|consen 12 GMTSLKVDNLTYRTSPDDLRRVFE-KYGRV--GDVYIPRDR 49 (256)
T ss_pred cceeEEecceeccCCHHHHHHHHH-HhCcc--cceeccccc
Confidence 356788999999999999999999 99999 467788875
No 11
>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=80.79 E-value=0.96 Score=25.38 Aligned_cols=13 Identities=38% Similarity=0.662 Sum_probs=10.2
Q ss_pred hhhhhcccccceee
Q psy9172 46 LYQFDNYKFGHAFS 59 (80)
Q Consensus 46 LhqiFs~~fG~Vlr 59 (80)
|+..|+ +||.|.+
T Consensus 1 L~~~f~-~fG~V~~ 13 (56)
T PF13893_consen 1 LYKLFS-KFGEVKK 13 (56)
T ss_dssp HHHHHT-TTS-EEE
T ss_pred ChHHhC-CcccEEE
Confidence 688999 9999953
No 12
>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family. Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).
Probab=76.99 E-value=2.6 Score=33.74 Aligned_cols=37 Identities=19% Similarity=0.397 Sum_probs=28.5
Q ss_pred CCCcEEEEEEecccc-eeehhhhhhhhcccccceeeeceee
Q psy9172 25 GPNTVLRVIIEHMLY-PITLDVLYQFDNYKFGHAFSTSLAM 64 (80)
Q Consensus 25 ~pn~VLrviIeN~~Y-PVTldVLhqiFs~~fG~Vlrq~~a~ 64 (80)
+|+++| .|-|+-+ .||-|.|+.+|+ +||.|.+=++.+
T Consensus 273 ~~~~~l--~v~nL~~~~vt~~~L~~lF~-~yG~V~~vki~~ 310 (481)
T TIGR01649 273 GPGSVL--MVSGLHQEKVNCDRLFNLFC-VYGNVERVKFMK 310 (481)
T ss_pred CCCCEE--EEeCCCCCCCCHHHHHHHHH-hcCCeEEEEEEe
Confidence 355554 4678875 699999999999 999998655544
No 13
>KOG0123|consensus
Probab=76.20 E-value=5.1 Score=31.92 Aligned_cols=67 Identities=22% Similarity=0.263 Sum_probs=48.6
Q ss_pred HHHHHHHHHhhhhhcCCC----CCCCCCcEEEEEEecccceeehhhhhhhhcccccceeeeceeeccccccCc
Q psy9172 4 ASAQAALQAAQALTGQTD----TQGGPNTVLRVIIEHMLYPITLDVLYQFDNYKFGHAFSTSLAMPRDELAGF 72 (80)
Q Consensus 4 ~~aqaALqa~n~v~~~~~----~~~~pn~VLrviIeN~~YPVTldVLhqiFs~~fG~Vlrq~~a~~~~~~~~~ 72 (80)
+.|..|+++.|-...-|. +.....+=+ +-|-|+---|+-+.||-.|+ .||.|+.=++++.-+-+-||
T Consensus 48 ~da~~A~~~~n~~~~~~~~~rim~s~rd~~~-~~i~nl~~~~~~~~~~d~f~-~~g~ilS~kv~~~~~g~kg~ 118 (369)
T KOG0123|consen 48 ADAERALDTMNFDVLKGKPIRIMWSQRDPSL-VFIKNLDESIDNKSLYDTFS-EFGNILSCKVATDENGSKGY 118 (369)
T ss_pred HHHHHHHHHcCCcccCCcEEEeehhccCCce-eeecCCCcccCcHHHHHHHH-hhcCeeEEEEEEcCCCceee
Confidence 478899999884322221 111111112 88999988899999999999 99999999999887776665
No 14
>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=71.45 E-value=4.4 Score=34.79 Aligned_cols=42 Identities=24% Similarity=0.392 Sum_probs=33.1
Q ss_pred cEEEEEEecccceeehhhhhhhhcccccceeeeceeeccc----cccCc
Q psy9172 28 TVLRVIIEHMLYPITLDVLYQFDNYKFGHAFSTSLAMPRD----ELAGF 72 (80)
Q Consensus 28 ~VLrviIeN~~YPVTldVLhqiFs~~fG~Vlrq~~a~~~~----~~~~~ 72 (80)
..-+|-|.|+-|-+|-|-|+.+|+ +||.|.+ +-+++| ++-||
T Consensus 106 ~~~rLfVGnLp~~~tEe~Lr~lF~-~fG~I~s--V~I~~D~~TgkskGf 151 (612)
T TIGR01645 106 IMCRVYVGSISFELREDTIRRAFD-PFGPIKS--INMSWDPATGKHKGF 151 (612)
T ss_pred CCCEEEEcCCCCCCCHHHHHHHHH-ccCCEEE--EEEeecCCCCCcCCe
Confidence 344799999999999999999999 9999975 444444 45554
No 15
>PLN03213 repressor of silencing 3; Provisional
Probab=71.14 E-value=4.7 Score=35.35 Aligned_cols=42 Identities=14% Similarity=0.143 Sum_probs=35.0
Q ss_pred cEEEEEEecccceeehhhhhhhhcccccceeeeceeeccccccCc
Q psy9172 28 TVLRVIIEHMLYPITLDVLYQFDNYKFGHAFSTSLAMPRDELAGF 72 (80)
Q Consensus 28 ~VLrviIeN~~YPVTldVLhqiFs~~fG~Vlrq~~a~~~~~~~~~ 72 (80)
.-.||-|-|+-|-||=|=|..+|+ .||.|.+=.+. +.+--||
T Consensus 9 ~gMRIYVGNLSydVTEDDLravFS-eFGsVkdVEIp--RETGRGF 50 (759)
T PLN03213 9 GGVRLHVGGLGESVGRDDLLKIFS-PMGTVDAVEFV--RTKGRSF 50 (759)
T ss_pred cceEEEEeCCCCCCCHHHHHHHHH-hcCCeeEEEEe--cccCCce
Confidence 358999999999999999999999 99999876665 4443555
No 16
>PLN03121 nucleic acid binding protein; Provisional
Probab=70.93 E-value=4.3 Score=31.51 Aligned_cols=35 Identities=11% Similarity=0.101 Sum_probs=29.3
Q ss_pred EEEEEecccceeehhhhhhhhcccccceeeeceeec
Q psy9172 30 LRVIIEHMLYPITLDVLYQFDNYKFGHAFSTSLAMP 65 (80)
Q Consensus 30 LrviIeN~~YPVTldVLhqiFs~~fG~Vlrq~~a~~ 65 (80)
--|.|.|+-+-+|-+-|+..|+ .||.|..=.+...
T Consensus 6 ~TV~V~NLS~~tTE~dLrefFS-~~G~I~~V~I~~D 40 (243)
T PLN03121 6 YTAEVTNLSPKATEKDVYDFFS-HCGAIEHVEIIRS 40 (243)
T ss_pred eEEEEecCCCCCCHHHHHHHHH-hcCCeEEEEEecC
Confidence 4578999999999999999999 9999976554433
No 17
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor. These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
Probab=70.74 E-value=5.5 Score=29.32 Aligned_cols=32 Identities=16% Similarity=0.190 Sum_probs=27.3
Q ss_pred EEEEEecccceeehhhhhhhhcccccceeeece
Q psy9172 30 LRVIIEHMLYPITLDVLYQFDNYKFGHAFSTSL 62 (80)
Q Consensus 30 LrviIeN~~YPVTldVLhqiFs~~fG~Vlrq~~ 62 (80)
..|-|.|+=+-+|-+=|..+|+ +||.|.+=++
T Consensus 4 ~~l~V~nLp~~~~e~~l~~~F~-~~G~i~~v~i 35 (352)
T TIGR01661 4 TNLIVNYLPQTMTQEEIRSLFT-SIGEIESCKL 35 (352)
T ss_pred cEEEEeCCCCCCCHHHHHHHHH-ccCCEEEEEE
Confidence 3578999989999999999999 9999965444
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=70.59 E-value=4.8 Score=32.26 Aligned_cols=34 Identities=12% Similarity=0.182 Sum_probs=29.0
Q ss_pred EEEEecccceeehhhhhhhhcccccceeeeceeec
Q psy9172 31 RVIIEHMLYPITLDVLYQFDNYKFGHAFSTSLAMP 65 (80)
Q Consensus 31 rviIeN~~YPVTldVLhqiFs~~fG~Vlrq~~a~~ 65 (80)
.|-|.|+-+-+|-|-|..+|+ +||.|..-++...
T Consensus 287 ~l~V~nl~~~~~~~~L~~~F~-~~G~i~~~~i~~d 320 (562)
T TIGR01628 287 NLYVKNLDDTVTDEKLRELFS-ECGEITSAKVMLD 320 (562)
T ss_pred EEEEeCCCCccCHHHHHHHHH-hcCCeEEEEEEEC
Confidence 477899999999999999999 9999976665554
No 19
>KOG0415|consensus
Probab=69.15 E-value=9.3 Score=32.19 Aligned_cols=41 Identities=27% Similarity=0.288 Sum_probs=30.4
Q ss_pred CCCCCCCCcEEEEEEecccceeehh-hhhhhhcccccceeeeceee
Q psy9172 20 TDTQGGPNTVLRVIIEHMLYPITLD-VLYQFDNYKFGHAFSTSLAM 64 (80)
Q Consensus 20 ~~~~~~pn~VLrviIeN~~YPVTld-VLhqiFs~~fG~Vlrq~~a~ 64 (80)
-+...+|-+||-|-=-| |||.| =|+-||| +||.|..--++.
T Consensus 232 dAd~~PPeNVLFVCKLN---PVTtDeDLeiIFS-rFG~i~sceVIR 273 (479)
T KOG0415|consen 232 DADVKPPENVLFVCKLN---PVTTDEDLEIIFS-RFGKIVSCEVIR 273 (479)
T ss_pred ccccCCCcceEEEEecC---CcccccchhhHHh-hcccceeeeEEe
Confidence 34566888899877655 56665 6999999 999997655544
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=66.17 E-value=6.9 Score=30.15 Aligned_cols=30 Identities=23% Similarity=0.341 Sum_probs=26.5
Q ss_pred EEEEEecccceeehhhhhhhhcccccceeee
Q psy9172 30 LRVIIEHMLYPITLDVLYQFDNYKFGHAFST 60 (80)
Q Consensus 30 LrviIeN~~YPVTldVLhqiFs~~fG~Vlrq 60 (80)
-.|-|.|+-+-+|-+-|.++|+ +||.|..=
T Consensus 187 ~~l~v~nl~~~~te~~l~~~f~-~~G~i~~v 216 (457)
T TIGR01622 187 LKLYVGNLHFNITEQELRQIFE-PFGDIEDV 216 (457)
T ss_pred CEEEEcCCCCCCCHHHHHHHHH-hcCCeEEE
Confidence 4678999999999999999999 99999643
No 21
>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=65.88 E-value=6.7 Score=20.89 Aligned_cols=31 Identities=19% Similarity=0.285 Sum_probs=25.6
Q ss_pred EEEecccceeehhhhhhhhcccccceeeecee
Q psy9172 32 VIIEHMLYPITLDVLYQFDNYKFGHAFSTSLA 63 (80)
Q Consensus 32 viIeN~~YPVTldVLhqiFs~~fG~Vlrq~~a 63 (80)
|.|.|+-+.++-+-|-++|. .||.+.+-.+.
T Consensus 2 i~i~~l~~~~~~~~i~~~~~-~~g~i~~~~~~ 32 (74)
T cd00590 2 LFVGNLPPDVTEEDLRELFS-KFGKVESVRIV 32 (74)
T ss_pred EEEeCCCCccCHHHHHHHHH-hcCCEEEEEEe
Confidence 67888888899999999999 99999654433
No 22
>KOG0131|consensus
Probab=65.38 E-value=3.1 Score=31.79 Aligned_cols=35 Identities=17% Similarity=0.241 Sum_probs=29.9
Q ss_pred EEecccceeehhhhhhhhcccccceeeeceeecccc
Q psy9172 33 IIEHMLYPITLDVLYQFDNYKFGHAFSTSLAMPRDE 68 (80)
Q Consensus 33 iIeN~~YPVTldVLhqiFs~~fG~Vlrq~~a~~~~~ 68 (80)
-|-||=..|.=+.||.+|| +||.+.+.-.+|+.+.
T Consensus 100 fvgNLd~~vDe~~L~dtFs-afG~l~~~P~i~rd~~ 134 (203)
T KOG0131|consen 100 FVGNLDPEVDEKLLYDTFS-AFGVLISPPKIMRDPD 134 (203)
T ss_pred cccccCcchhHHHHHHHHH-hccccccCCccccccc
Confidence 3889888899999999999 9999998777777653
No 23
>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor. Members of this subfamily are found in plants, metazoa and fungi.
Probab=64.10 E-value=7.9 Score=30.17 Aligned_cols=31 Identities=19% Similarity=0.278 Sum_probs=27.0
Q ss_pred EEEEecccceeehhhhhhhhcccccceeeece
Q psy9172 31 RVIIEHMLYPITLDVLYQFDNYKFGHAFSTSL 62 (80)
Q Consensus 31 rviIeN~~YPVTldVLhqiFs~~fG~Vlrq~~ 62 (80)
+|.|.|+-+-+|-+-|..+|+ .||.|..-.+
T Consensus 297 ~l~v~nlp~~~~~~~l~~~f~-~~G~i~~~~~ 327 (509)
T TIGR01642 297 RIYIGNLPLYLGEDQIKELLE-SFGDLKAFNL 327 (509)
T ss_pred EEEEeCCCCCCCHHHHHHHHH-hcCCeeEEEE
Confidence 678999999999999999999 9999865443
No 24
>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=63.78 E-value=8 Score=30.39 Aligned_cols=32 Identities=19% Similarity=0.276 Sum_probs=27.1
Q ss_pred EEEEecccceeehhhhhhhhcccccceeeecee
Q psy9172 31 RVIIEHMLYPITLDVLYQFDNYKFGHAFSTSLA 63 (80)
Q Consensus 31 rviIeN~~YPVTldVLhqiFs~~fG~Vlrq~~a 63 (80)
.|.|.|+=+-+|-|-|-++|+ +||.|.+-++.
T Consensus 195 ~lfV~nLp~~vtee~L~~~F~-~fG~V~~v~i~ 226 (346)
T TIGR01659 195 NLYVTNLPRTITDDQLDTIFG-KYGQIVQKNIL 226 (346)
T ss_pred eeEEeCCCCcccHHHHHHHHH-hcCCEEEEEEe
Confidence 478899999999999999999 99999654443
No 25
>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=63.34 E-value=7.9 Score=33.29 Aligned_cols=35 Identities=14% Similarity=0.158 Sum_probs=29.4
Q ss_pred EEEEEEecccceeehhhhhhhhcccccceeeeceee
Q psy9172 29 VLRVIIEHMLYPITLDVLYQFDNYKFGHAFSTSLAM 64 (80)
Q Consensus 29 VLrviIeN~~YPVTldVLhqiFs~~fG~Vlrq~~a~ 64 (80)
.-+|-|.|+-+-++-|-|.++|+ +||.|.+=++..
T Consensus 204 ~~rLfVgnLp~~vteedLk~lFs-~FG~I~svrl~~ 238 (612)
T TIGR01645 204 FNRIYVASVHPDLSETDIKSVFE-AFGEIVKCQLAR 238 (612)
T ss_pred cceEEeecCCCCCCHHHHHHHHh-hcCCeeEEEEEe
Confidence 34789999999999999999999 999997555443
No 26
>PLN03120 nucleic acid binding protein; Provisional
Probab=62.64 E-value=9.3 Score=29.79 Aligned_cols=39 Identities=10% Similarity=0.048 Sum_probs=31.2
Q ss_pred EEEEecccceeehhhhhhhhcccccceeeeceeecccc-ccCc
Q psy9172 31 RVIIEHMLYPITLDVLYQFDNYKFGHAFSTSLAMPRDE-LAGF 72 (80)
Q Consensus 31 rviIeN~~YPVTldVLhqiFs~~fG~Vlrq~~a~~~~~-~~~~ 72 (80)
.|-|.|+-|-+|-+-|+..|+ .||.|.+-.+ ++++ ..||
T Consensus 6 tVfVgNLs~~tTE~dLrefFS-~~G~I~~V~I--~~d~~~~Gf 45 (260)
T PLN03120 6 TVKVSNVSLKATERDIKEFFS-FSGDIEYVEM--QSENERSQI 45 (260)
T ss_pred EEEEeCCCCCCCHHHHHHHHH-hcCCeEEEEE--eecCCCCCE
Confidence 578999999999999999999 9999976554 4443 3454
No 27
>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=60.70 E-value=11 Score=29.66 Aligned_cols=33 Identities=15% Similarity=0.163 Sum_probs=28.0
Q ss_pred EEEEEEecccceeehhhhhhhhcccccceeeece
Q psy9172 29 VLRVIIEHMLYPITLDVLYQFDNYKFGHAFSTSL 62 (80)
Q Consensus 29 VLrviIeN~~YPVTldVLhqiFs~~fG~Vlrq~~ 62 (80)
=-.|.|.|+=+.+|-+-|+.+|+ .||.|.+-++
T Consensus 107 ~~~LfVgnLp~~~te~~L~~lF~-~~G~V~~v~i 139 (346)
T TIGR01659 107 GTNLIVNYLPQDMTDRELYALFR-TIGPINTCRI 139 (346)
T ss_pred CcEEEEeCCCCCCCHHHHHHHHH-hcCCEEEEEE
Confidence 34688999999999999999999 9999864444
No 28
>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]
Probab=59.84 E-value=13 Score=24.15 Aligned_cols=34 Identities=21% Similarity=0.296 Sum_probs=29.0
Q ss_pred EEEEEecccceeehhhhhhhhcccccceeeeceee
Q psy9172 30 LRVIIEHMLYPITLDVLYQFDNYKFGHAFSTSLAM 64 (80)
Q Consensus 30 LrviIeN~~YPVTldVLhqiFs~~fG~Vlrq~~a~ 64 (80)
-.|-|.|+-+-+|=|-|...|. +||.|.+=.+..
T Consensus 116 ~~l~v~nL~~~~~~~~l~~~F~-~~g~~~~~~~~~ 149 (306)
T COG0724 116 NTLFVGNLPYDVTEEDLRELFK-KFGPVKRVRLVR 149 (306)
T ss_pred ceEEEeCCCCCCCHHHHHHHHH-hcCceeEEEeee
Confidence 6788999999999999999999 999996544444
No 29
>KOG0127|consensus
Probab=57.89 E-value=9.5 Score=33.50 Aligned_cols=40 Identities=28% Similarity=0.548 Sum_probs=31.5
Q ss_pred EEEEEecccceeehhhhhhhhcccccceeeeceeeccc---cccCc
Q psy9172 30 LRVIIEHMLYPITLDVLYQFDNYKFGHAFSTSLAMPRD---ELAGF 72 (80)
Q Consensus 30 LrviIeN~~YPVTldVLhqiFs~~fG~Vlrq~~a~~~~---~~~~~ 72 (80)
-|+||.||=+-..-+-|-.+|| .||+|+- +-+|+. ++.||
T Consensus 118 ~rLIIRNLPf~~k~~dLk~vFs-~~G~V~E--i~IP~k~dgklcGF 160 (678)
T KOG0127|consen 118 WRLIIRNLPFKCKKPDLKNVFS-NFGKVVE--IVIPRKKDGKLCGF 160 (678)
T ss_pred ceEEeecCCcccCcHHHHHHHh-hcceEEE--EEcccCCCCCccce
Confidence 4799999999999999999999 9999974 444543 34455
No 30
>smart00360 RRM RNA recognition motif.
Probab=57.27 E-value=8.5 Score=20.20 Aligned_cols=28 Identities=25% Similarity=0.261 Sum_probs=20.9
Q ss_pred ecccceeehhhhhhhhcccccceeeecee
Q psy9172 35 EHMLYPITLDVLYQFDNYKFGHAFSTSLA 63 (80)
Q Consensus 35 eN~~YPVTldVLhqiFs~~fG~Vlrq~~a 63 (80)
.|+-..++-+-|.+.|+ +||.|.+-.+.
T Consensus 2 ~~l~~~~~~~~l~~~f~-~~g~v~~~~i~ 29 (71)
T smart00360 2 GNLPPDVTEEELRELFS-KFGKIESVRLV 29 (71)
T ss_pred CCCCcccCHHHHHHHHH-hhCCEeEEEEE
Confidence 35555678889999999 99988654443
No 31
>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=51.94 E-value=22 Score=20.10 Aligned_cols=31 Identities=26% Similarity=0.277 Sum_probs=23.2
Q ss_pred EEEecccceeehhhhhhhhcccccceeeecee
Q psy9172 32 VIIEHMLYPITLDVLYQFDNYKFGHAFSTSLA 63 (80)
Q Consensus 32 viIeN~~YPVTldVLhqiFs~~fG~Vlrq~~a 63 (80)
|.|.|+=+-+|.+-|-..|+ +||.|.+=.+.
T Consensus 1 v~i~nlp~~~~~~~l~~~f~-~~g~v~~v~~~ 31 (70)
T PF14259_consen 1 VYISNLPPSTTEEDLRNFFS-RFGPVEKVRLI 31 (70)
T ss_dssp EEEESSTTT--HHHHHHHCT-TSSBEEEEEEE
T ss_pred CEEeCCCCCCCHHHHHHHHH-hcCCcceEEEE
Confidence 56889888899999999999 99998543333
No 32
>KOG0110|consensus
Probab=51.75 E-value=20 Score=31.96 Aligned_cols=66 Identities=23% Similarity=0.273 Sum_probs=45.2
Q ss_pred HHHHHHHHHhh-hh-hcC---------------CCCCCCCCcEEEEEEecccceeehhhhhhhhcccccceeeeceeecc
Q psy9172 4 ASAQAALQAAQ-AL-TGQ---------------TDTQGGPNTVLRVIIEHMLYPITLDVLYQFDNYKFGHAFSTSLAMPR 66 (80)
Q Consensus 4 ~~aqaALqa~n-~v-~~~---------------~~~~~~pn~VLrviIeN~~YPVTldVLhqiFs~~fG~Vlrq~~a~~~ 66 (80)
..|++|++++| .+ +|. |..-....+.--|+|-|+=|.-|.-=+.++|+ +||.+..=.+-.-+
T Consensus 571 e~A~~a~k~lqgtvldGH~l~lk~S~~k~~~~~gK~~~~kk~~tKIlVRNipFeAt~rEVr~LF~-aFGqlksvRlPKK~ 649 (725)
T KOG0110|consen 571 ESAQAALKALQGTVLDGHKLELKISENKPASTVGKKKSKKKKGTKILVRNIPFEATKREVRKLFT-AFGQLKSVRLPKKI 649 (725)
T ss_pred HHHHHHHHHhcCceecCceEEEEeccCccccccccccccccccceeeeeccchHHHHHHHHHHHh-cccceeeeccchhh
Confidence 37899999987 22 221 11112223456799999999999999999999 99999654444445
Q ss_pred cccc
Q psy9172 67 DELA 70 (80)
Q Consensus 67 ~~~~ 70 (80)
++.+
T Consensus 650 ~k~a 653 (725)
T KOG0110|consen 650 GKGA 653 (725)
T ss_pred cchh
Confidence 5555
No 33
>KOG0125|consensus
Probab=49.17 E-value=17 Score=30.02 Aligned_cols=47 Identities=17% Similarity=0.277 Sum_probs=36.1
Q ss_pred CCcEEEEEEecccceeehhhhhhhhcccccceeeeceeeccccccCcc
Q psy9172 26 PNTVLRVIIEHMLYPITLDVLYQFDNYKFGHAFSTSLAMPRDELAGFR 73 (80)
Q Consensus 26 pn~VLrviIeN~~YPVTldVLhqiFs~~fG~Vlrq~~a~~~~~~~~~~ 73 (80)
++.==|+.|.|+=|--.=-=|-+.|. +||.|+.=.|+.--.-|-||-
T Consensus 93 ~~~pkRLhVSNIPFrFRdpDL~aMF~-kfG~VldVEIIfNERGSKGFG 139 (376)
T KOG0125|consen 93 KDTPKRLHVSNIPFRFRDPDLRAMFE-KFGKVLDVEIIFNERGSKGFG 139 (376)
T ss_pred CCCCceeEeecCCccccCccHHHHHH-hhCceeeEEEEeccCCCCccc
Confidence 33445899999976666667889999 999999777776666677774
No 34
>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=47.61 E-value=23 Score=27.28 Aligned_cols=31 Identities=19% Similarity=0.251 Sum_probs=26.5
Q ss_pred EEEEecccceeehhhhhhhhcccccceeeece
Q psy9172 31 RVIIEHMLYPITLDVLYQFDNYKFGHAFSTSL 62 (80)
Q Consensus 31 rviIeN~~YPVTldVLhqiFs~~fG~Vlrq~~ 62 (80)
.|-|.|+-+-+|-+-|...|+ +||.|..-.+
T Consensus 91 ~l~V~nlp~~~~~~~l~~~F~-~~G~v~~v~i 121 (457)
T TIGR01622 91 TVFVLQLALKARERDLYEFFS-KVGKVRDVQC 121 (457)
T ss_pred EEEEeCCCCCCCHHHHHHHHH-hcCCeeEEEE
Confidence 578999999999999999999 9998854333
No 35
>KOG0148|consensus
Probab=46.35 E-value=18 Score=29.31 Aligned_cols=43 Identities=16% Similarity=0.236 Sum_probs=35.5
Q ss_pred EEEEEEecccceeehhhhhhhhcccccceeeecee--eccccccCc
Q psy9172 29 VLRVIIEHMLYPITLDVLYQFDNYKFGHAFSTSLA--MPRDELAGF 72 (80)
Q Consensus 29 VLrviIeN~~YPVTldVLhqiFs~~fG~Vlrq~~a--~~~~~~~~~ 72 (80)
=.+|.|+.+.-.|+.+-|...|. |||.|.--+++ |-+.||-||
T Consensus 62 hfhvfvgdls~eI~~e~lr~aF~-pFGevS~akvirD~~T~KsKGY 106 (321)
T KOG0148|consen 62 HFHVFVGDLSPEIDNEKLREAFA-PFGEVSDAKVIRDMNTGKSKGY 106 (321)
T ss_pred ceeEEehhcchhcchHHHHHHhc-cccccccceEeecccCCcccce
Confidence 45588999989999999999999 99999877766 456677765
No 36
>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=45.66 E-value=20 Score=23.68 Aligned_cols=27 Identities=11% Similarity=0.109 Sum_probs=15.9
Q ss_pred EEEEecccceeehhhhhhhhccccccee
Q psy9172 31 RVIIEHMLYPITLDVLYQFDNYKFGHAF 58 (80)
Q Consensus 31 rviIeN~~YPVTldVLhqiFs~~fG~Vl 58 (80)
.+.|+++-=|++-+.|+..|+ .||.|.
T Consensus 3 il~~~g~~~~~~re~iK~~f~-~~g~V~ 29 (105)
T PF08777_consen 3 ILKFSGLGEPTSREDIKEAFS-QFGEVA 29 (105)
T ss_dssp EEEEEE--SS--HHHHHHHT--SS--EE
T ss_pred EEEEecCCCCcCHHHHHHHHH-hcCCcc
Confidence 345666667899999999999 999774
No 37
>KOG0114|consensus
Probab=42.29 E-value=17 Score=25.95 Aligned_cols=31 Identities=26% Similarity=0.454 Sum_probs=25.9
Q ss_pred CCCcEEEEEEecccceeehhhhhhhhccccccee
Q psy9172 25 GPNTVLRVIIEHMLYPITLDVLYQFDNYKFGHAF 58 (80)
Q Consensus 25 ~pn~VLrviIeN~~YPVTldVLhqiFs~~fG~Vl 58 (80)
.-|.||- |-|+=|-||-|=.+.+|. +||.|-
T Consensus 16 evnriLy--irNLp~~ITseemydlFG-kyg~Ir 46 (124)
T KOG0114|consen 16 EVNRILY--IRNLPFKITSEEMYDLFG-KYGTIR 46 (124)
T ss_pred hhheeEE--EecCCccccHHHHHHHhh-cccceE
Confidence 3355554 789999999999999999 999984
No 38
>KOG0145|consensus
Probab=40.04 E-value=52 Score=26.92 Aligned_cols=50 Identities=18% Similarity=0.303 Sum_probs=36.8
Q ss_pred CCCCCCcEEEEEEecccceeehhhhhhhhcccccceeeeceeecc--ccccCc
Q psy9172 22 TQGGPNTVLRVIIEHMLYPITLDVLYQFDNYKFGHAFSTSLAMPR--DELAGF 72 (80)
Q Consensus 22 ~~~~pn~VLrviIeN~~YPVTldVLhqiFs~~fG~Vlrq~~a~~~--~~~~~~ 72 (80)
.++++..=--|-|-|+--.-.-.+|.|.|+ +||-|..-|+...+ +|--||
T Consensus 271 lp~~~~~g~ciFvYNLspd~de~~LWQlFg-pFGAv~nVKvirD~ttnkCKGf 322 (360)
T KOG0145|consen 271 LPGGPGGGWCIFVYNLSPDADESILWQLFG-PFGAVTNVKVIRDFTTNKCKGF 322 (360)
T ss_pred cCCCCCCeeEEEEEecCCCchHhHHHHHhC-cccceeeEEEEecCCcccccce
Confidence 345555566677888866666779999999 99999888887755 355554
No 39
>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor. Members of this subfamily are found in plants, metazoa and fungi.
Probab=39.30 E-value=22 Score=27.72 Aligned_cols=34 Identities=12% Similarity=0.240 Sum_probs=23.2
Q ss_pred CCcEEEEEEecccce----------eehhhhhhhhcccccceeeece
Q psy9172 26 PNTVLRVIIEHMLYP----------ITLDVLYQFDNYKFGHAFSTSL 62 (80)
Q Consensus 26 pn~VLrviIeN~~YP----------VTldVLhqiFs~~fG~Vlrq~~ 62 (80)
|+.||. +.||+++ -+++-|.+.|+ +||.|..=++
T Consensus 408 ~s~v~~--l~N~~~~~~l~~d~~~~~~~edl~~~f~-~~G~v~~v~i 451 (509)
T TIGR01642 408 PTKVVQ--LTNLVTGDDLMDDEEYEEIYEDVKTEFS-KYGPLINIVI 451 (509)
T ss_pred CceEEE--eccCCchhHhcCcchHHHHHHHHHHHHH-hcCCeeEEEe
Confidence 455544 5677644 34567899999 9999985443
No 40
>PF12631 GTPase_Cys_C: Catalytic cysteine-containing C-terminus of GTPase, MnmE; PDB: 1XZQ_A 1XZP_A 2GJ8_D 3GEH_A 3GEI_B 3GEE_A.
Probab=39.17 E-value=15 Score=22.48 Aligned_cols=14 Identities=29% Similarity=0.375 Sum_probs=10.0
Q ss_pred eehhhhhhhhccccc
Q psy9172 41 ITLDVLYQFDNYKFG 55 (80)
Q Consensus 41 VTldVLhqiFs~~fG 55 (80)
.+-|+|..||| +|.
T Consensus 60 ~~ediLd~IFs-~FC 73 (73)
T PF12631_consen 60 VTEDILDNIFS-NFC 73 (73)
T ss_dssp --HHHHHHHHC-TS-
T ss_pred ChHHHHHHHHH-hhC
Confidence 45699999999 883
No 41
>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=38.87 E-value=32 Score=29.41 Aligned_cols=42 Identities=19% Similarity=0.234 Sum_probs=32.9
Q ss_pred EEEEEecccceeehhhhhhhhcccccceeeeceeeccc-cccCc
Q psy9172 30 LRVIIEHMLYPITLDVLYQFDNYKFGHAFSTSLAMPRD-ELAGF 72 (80)
Q Consensus 30 LrviIeN~~YPVTldVLhqiFs~~fG~Vlrq~~a~~~~-~~~~~ 72 (80)
-.|-|-|+-+-+|-|-|..+|+ +||.|..-++.+... ++.||
T Consensus 59 ~~lFVgnLp~~~tEd~L~~~F~-~~G~I~~vrl~~D~sG~sRGf 101 (578)
T TIGR01648 59 CEVFVGKIPRDLYEDELVPLFE-KAGPIYELRLMMDFSGQNRGY 101 (578)
T ss_pred CEEEeCCCCCCCCHHHHHHHHH-hhCCEEEEEEEECCCCCccce
Confidence 4678889999999999999999 999998766666522 34444
No 42
>KOG0115|consensus
Probab=34.47 E-value=26 Score=27.93 Aligned_cols=35 Identities=14% Similarity=0.155 Sum_probs=28.9
Q ss_pred EEEecccceeehhhhhhhhcccccceeeeceeeccc
Q psy9172 32 VIIEHMLYPITLDVLYQFDNYKFGHAFSTSLAMPRD 67 (80)
Q Consensus 32 viIeN~~YPVTldVLhqiFs~~fG~Vlrq~~a~~~~ 67 (80)
++|.|+.-=++.|.|++.|+ .||.+.|-++.+.-+
T Consensus 34 l~V~nl~~~~sndll~~~f~-~fg~~e~av~~vD~r 68 (275)
T KOG0115|consen 34 LYVVNLMQGASNDLLEQAFR-RFGPIERAVAKVDDR 68 (275)
T ss_pred EEEEecchhhhhHHHHHhhh-hcCccchheeeeccc
Confidence 46778877799999999999 999999877766443
No 43
>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=33.06 E-value=41 Score=28.74 Aligned_cols=33 Identities=12% Similarity=0.184 Sum_probs=28.0
Q ss_pred EEEEEEecccceeehhhhhhhhcccc--cceeeece
Q psy9172 29 VLRVIIEHMLYPITLDVLYQFDNYKF--GHAFSTSL 62 (80)
Q Consensus 29 VLrviIeN~~YPVTldVLhqiFs~~f--G~Vlrq~~ 62 (80)
+-.|-|-|+-+.+|-|-|.+.|+ +| |.|.|-++
T Consensus 233 ~k~LfVgNL~~~~tee~L~~~F~-~f~~G~I~rV~~ 267 (578)
T TIGR01648 233 VKILYVRNLMTTTTEEIIEKSFS-EFKPGKVERVKK 267 (578)
T ss_pred ccEEEEeCCCCCCCHHHHHHHHH-hcCCCceEEEEe
Confidence 34577889999999999999999 99 99986543
No 44
>KOG0147|consensus
Probab=31.18 E-value=19 Score=31.04 Aligned_cols=37 Identities=22% Similarity=0.399 Sum_probs=30.4
Q ss_pred cEEEEEEecccceeehhhhhhhhcccccceeeeceeeccc
Q psy9172 28 TVLRVIIEHMLYPITLDVLYQFDNYKFGHAFSTSLAMPRD 67 (80)
Q Consensus 28 ~VLrviIeN~~YPVTldVLhqiFs~~fG~Vlrq~~a~~~~ 67 (80)
|..++-|.|+.+=||=|.|-.||. +||.|. .+-.+.|
T Consensus 277 p~~rl~vgnLHfNite~~lr~ife-pfg~Ie--~v~l~~d 313 (549)
T KOG0147|consen 277 PMRRLYVGNLHFNITEDMLRGIFE-PFGKIE--NVQLTKD 313 (549)
T ss_pred chhhhhhcccccCchHHHHhhhcc-Ccccce--eeeeccc
Confidence 456688999999999999999999 999995 4444444
No 45
>KOG0127|consensus
Probab=30.59 E-value=48 Score=29.32 Aligned_cols=26 Identities=23% Similarity=0.358 Sum_probs=24.6
Q ss_pred EEEecccceeehhhhhhhhccccccee
Q psy9172 32 VIIEHMLYPITLDVLYQFDNYKFGHAF 58 (80)
Q Consensus 32 viIeN~~YPVTldVLhqiFs~~fG~Vl 58 (80)
|-|.|+-|..|=+-|.+-|+ +||.|.
T Consensus 295 VFvRNL~fD~tEEel~~~fs-kFG~v~ 320 (678)
T KOG0127|consen 295 VFVRNLPFDTTEEELKEHFS-KFGEVK 320 (678)
T ss_pred EEEecCCccccHHHHHHHHH-hhccce
Confidence 67899999999999999999 999996
No 46
>KOG0124|consensus
Probab=29.70 E-value=38 Score=28.92 Aligned_cols=38 Identities=21% Similarity=0.314 Sum_probs=33.1
Q ss_pred EEEEEEecccceeehhhhhhhhcccccceeeeceeeccccc
Q psy9172 29 VLRVIIEHMLYPITLDVLYQFDNYKFGHAFSTSLAMPRDEL 69 (80)
Q Consensus 29 VLrviIeN~~YPVTldVLhqiFs~~fG~Vlrq~~a~~~~~~ 69 (80)
+-||-|-.+.|.+.-|.+.+.|. +||-+. ++-|+.|..
T Consensus 113 McRvYVGSIsfEl~EDtiR~AF~-PFGPIK--SInMSWDp~ 150 (544)
T KOG0124|consen 113 MCRVYVGSISFELREDTIRRAFD-PFGPIK--SINMSWDPA 150 (544)
T ss_pred hHheeeeeeEEEechHHHHhhcc-CCCCcc--eeecccccc
Confidence 55888889999999999999999 999995 788887744
No 47
>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN). ; GO: 0003723 RNA binding, 0004535 poly(A)-specific ribonuclease activity, 0046872 metal ion binding, 0006402 mRNA catabolic process, 0005634 nucleus, 0005737 cytoplasm; PDB: 3CTR_A 2ROK_A 3D45_B 1WHV_A.
Probab=28.74 E-value=29 Score=23.38 Aligned_cols=15 Identities=27% Similarity=0.596 Sum_probs=11.9
Q ss_pred hhhhhhhcccccceee
Q psy9172 44 DVLYQFDNYKFGHAFS 59 (80)
Q Consensus 44 dVLhqiFs~~fG~Vlr 59 (80)
.=|.++|+ +||.|.-
T Consensus 23 ~DI~qlFs-pfG~I~V 37 (87)
T PF08675_consen 23 SDIYQLFS-PFGQIYV 37 (87)
T ss_dssp HHHHHHCC-CCCCEEE
T ss_pred hhHHHHhc-cCCcEEE
Confidence 34678999 9999973
No 48
>KOG0121|consensus
Probab=27.89 E-value=53 Score=24.20 Aligned_cols=35 Identities=20% Similarity=0.332 Sum_probs=30.3
Q ss_pred EEEecccceeehhhhhhhhcccccceeeeceeeccccc
Q psy9172 32 VIIEHMLYPITLDVLYQFDNYKFGHAFSTSLAMPRDEL 69 (80)
Q Consensus 32 viIeN~~YPVTldVLhqiFs~~fG~Vlrq~~a~~~~~~ 69 (80)
|-|.|+-|=.|=|-+|..|| +-|.|.| ++|-+|+-
T Consensus 39 vyVgNlSfyttEEqiyELFs-~cG~irr--iiMGLdr~ 73 (153)
T KOG0121|consen 39 VYVGNLSFYTTEEQIYELFS-KCGDIRR--IIMGLDRF 73 (153)
T ss_pred EEEeeeeeeecHHHHHHHHH-hccchhe--eEeccccC
Confidence 56899999999999999999 9999964 78877763
No 49
>KOG4206|consensus
Probab=26.34 E-value=92 Score=24.01 Aligned_cols=43 Identities=23% Similarity=0.360 Sum_probs=30.2
Q ss_pred CCCcEEEEEEecccceeehhhhhh----hhcccccceeeeceeeccccccC
Q psy9172 25 GPNTVLRVIIEHMLYPITLDVLYQ----FDNYKFGHAFSTSLAMPRDELAG 71 (80)
Q Consensus 25 ~pn~VLrviIeN~~YPVTldVLhq----iFs~~fG~Vlrq~~a~~~~~~~~ 71 (80)
.||. -+-|-|+.=+|..|-|-. +|| .||+|+ ..++.-+-|+-|
T Consensus 7 ~pn~--TlYInnLnekI~~~elkrsL~~LFs-qfG~il-dI~a~kt~KmRG 53 (221)
T KOG4206|consen 7 NPNG--TLYINNLNEKIKKDELKRSLYLLFS-QFGKIL-DISAFKTPKMRG 53 (221)
T ss_pred CCCc--eEeehhccccccHHHHHHHHHHHHH-hhCCeE-EEEecCCCCccC
Confidence 5665 567889988899887654 999 999997 344444444443
No 50
>TIGR00691 spoT_relA (p)ppGpp synthetase, RelA/SpoT family. (p)ppGpp is a regulatory metabolite of the stringent response, but appears also to be involved in antibiotic biosynthesis in some species.
Probab=23.72 E-value=43 Score=28.78 Aligned_cols=45 Identities=24% Similarity=0.454 Sum_probs=30.0
Q ss_pred EEEEEEeccc--ceeehhhhhhhhcccccceeeeceeeccccccCcccccc
Q psy9172 29 VLRVIIEHML--YPITLDVLYQFDNYKFGHAFSTSLAMPRDELAGFRSEAT 77 (80)
Q Consensus 29 VLrviIeN~~--YPVTldVLhqiFs~~fG~Vlrq~~a~~~~~~~~~~~~~~ 77 (80)
=+||++.... |-+ ++++|+.|. +--.=.|.-+|.| |.-||+|--|
T Consensus 237 ~~RIi~~~~~dcy~v-lg~ih~~~~-p~~~~~kDyIa~P--K~nGYqSlHt 283 (683)
T TIGR00691 237 AIRIIVKSELDCYRV-LGIIHLLFK-PIPGRFKDYIASP--KENGYQSLHT 283 (683)
T ss_pred eEEEEECCHHHHHHH-HHHHHhcCC-CCcccccccccCC--CCCCcceeEE
Confidence 3678887655 544 899999998 5433335555554 6779988543
No 51
>KOG0117|consensus
Probab=22.11 E-value=68 Score=27.59 Aligned_cols=36 Identities=17% Similarity=0.239 Sum_probs=31.5
Q ss_pred CcEEEEEEecccceeehhhhhhhhcccccceeeecee
Q psy9172 27 NTVLRVIIEHMLYPITLDVLYQFDNYKFGHAFSTSLA 63 (80)
Q Consensus 27 n~VLrviIeN~~YPVTldVLhqiFs~~fG~Vlrq~~a 63 (80)
+.|=-+-|.|+.=-+|-|.|-..|+ .||.|.|=|+.
T Consensus 257 s~VKvLYVRNL~~~tTeE~lk~~F~-~~G~veRVkk~ 292 (506)
T KOG0117|consen 257 SKVKVLYVRNLMESTTEETLKKLFN-EFGKVERVKKP 292 (506)
T ss_pred hheeeeeeeccchhhhHHHHHHHHH-hccceEEeecc
Confidence 4566667899999999999999999 99999998776
No 52
>KOG0123|consensus
Probab=22.00 E-value=63 Score=25.79 Aligned_cols=32 Identities=16% Similarity=0.180 Sum_probs=28.0
Q ss_pred ceeehhhhhhhhcccccceeeeceeeccccccCc
Q psy9172 39 YPITLDVLYQFDNYKFGHAFSTSLAMPRDELAGF 72 (80)
Q Consensus 39 YPVTldVLhqiFs~~fG~Vlrq~~a~~~~~~~~~ 72 (80)
+-||-..|..+|+ ++|.|.+-.+.+.. -|.||
T Consensus 8 ~~v~e~~l~~~f~-~~~~v~s~rvc~d~-tslgy 39 (369)
T KOG0123|consen 8 PDVTEAMLFDKFS-PAGPVLSIRVCRDA-TSLGY 39 (369)
T ss_pred CcCChHHHHHHhc-ccCCceeEEEeecC-Cccce
Confidence 6789999999999 99999999998877 47775
No 53
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.42 E-value=75 Score=22.85 Aligned_cols=27 Identities=30% Similarity=0.400 Sum_probs=21.5
Q ss_pred CCCCcEEEEEEecccceeehhhhhhhhc
Q psy9172 24 GGPNTVLRVIIEHMLYPITLDVLYQFDN 51 (80)
Q Consensus 24 ~~pn~VLrviIeN~~YPVTldVLhqiFs 51 (80)
.++..+|||.|++. -.||+|-.-.+..
T Consensus 33 ~~~~~~lrI~id~~-g~v~lddC~~vSr 59 (153)
T COG0779 33 EGRDSVLRIYIDKE-GGVTLDDCADVSR 59 (153)
T ss_pred cCCCcEEEEEeCCC-CCCCHHHHHHHHH
Confidence 45668999999999 8999997655443
No 54
>KOG0533|consensus
Probab=20.73 E-value=82 Score=24.24 Aligned_cols=41 Identities=17% Similarity=0.249 Sum_probs=32.3
Q ss_pred CCCcEEEEEEecccceeehhhhhhhhcccccceeeeceeecccc
Q psy9172 25 GPNTVLRVIIEHMLYPITLDVLYQFDNYKFGHAFSTSLAMPRDE 68 (80)
Q Consensus 25 ~pn~VLrviIeN~~YPVTldVLhqiFs~~fG~Vlrq~~a~~~~~ 68 (80)
..+.--+|.|+|+-|-|+=+=|-+.|. .||.+ ...++-+++
T Consensus 79 ~~~~~~~v~v~NL~~~V~~~Dl~eLF~-~~~~~--~r~~vhy~~ 119 (243)
T KOG0533|consen 79 NETRSTKVNVSNLPYGVIDADLKELFA-EFGEL--KRVAVHYDR 119 (243)
T ss_pred cCCCcceeeeecCCcCcchHHHHHHHH-Hhccc--eEEeeccCC
Confidence 344456799999999999999999999 99944 556666655
No 55
>KOG4660|consensus
Probab=20.39 E-value=61 Score=28.11 Aligned_cols=26 Identities=12% Similarity=0.268 Sum_probs=22.3
Q ss_pred EEEecccceeehhhhhhhhccccccee
Q psy9172 32 VIIEHMLYPITLDVLYQFDNYKFGHAF 58 (80)
Q Consensus 32 viIeN~~YPVTldVLhqiFs~~fG~Vl 58 (80)
+.|.|+=--|+-|-||.+|+ .||.|.
T Consensus 78 L~v~nl~~~Vsn~~L~~~f~-~yGeir 103 (549)
T KOG4660|consen 78 LVVFNLPRSVSNDTLLRIFG-AYGEIR 103 (549)
T ss_pred EEEEecCCcCCHHHHHHHHH-hhcchh
Confidence 45677767799999999999 999995
Done!