Query 025931
Match_columns 246
No_of_seqs 147 out of 172
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 11:11:11 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025931.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025931hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03120 nucleic acid binding 100.0 2.3E-73 5.1E-78 514.1 18.5 224 1-227 36-259 (260)
2 PLN03121 nucleic acid binding 100.0 1.9E-66 4.2E-71 464.9 14.1 195 1-199 37-242 (243)
3 PLN03120 nucleic acid binding 95.5 0.014 3E-07 54.0 4.0 51 84-134 135-192 (260)
4 PLN03121 nucleic acid binding 94.5 0.045 9.8E-07 50.3 4.1 47 82-128 146-195 (243)
5 PF13893 RRM_5: RNA recognitio 93.7 0.095 2.1E-06 35.8 3.5 33 8-40 21-54 (56)
6 PF00076 RRM_1: RNA recognitio 93.1 0.12 2.6E-06 35.4 3.2 34 5-38 36-70 (70)
7 PLN03134 glycine-rich RNA-bind 91.3 0.24 5.2E-06 41.3 3.6 35 8-42 76-111 (144)
8 smart00362 RRM_2 RNA recogniti 89.4 0.58 1.3E-05 30.9 3.6 32 8-39 39-71 (72)
9 smart00360 RRM RNA recognition 89.1 0.63 1.4E-05 30.5 3.6 33 8-40 38-71 (71)
10 smart00361 RRM_1 RNA recogniti 86.6 0.76 1.7E-05 33.1 3.0 32 8-39 37-69 (70)
11 PF14259 RRM_6: RNA recognitio 84.8 1 2.2E-05 31.4 2.9 33 6-38 37-70 (70)
12 TIGR01642 U2AF_lg U2 snRNP aux 84.3 0.97 2.1E-05 43.3 3.4 38 9-46 224-261 (509)
13 TIGR01661 ELAV_HUD_SF ELAV/HuD 80.4 1.4 3E-05 39.9 2.7 34 9-42 46-80 (352)
14 TIGR01622 SF-CC1 splicing fact 77.8 5 0.00011 38.0 5.7 38 9-46 229-267 (457)
15 TIGR01648 hnRNP-R-Q heterogene 76.4 2.4 5.2E-05 43.3 3.3 33 10-42 271-304 (578)
16 TIGR01659 sex-lethal sex-letha 74.4 2.5 5.4E-05 40.2 2.7 34 9-42 150-184 (346)
17 TIGR01622 SF-CC1 splicing fact 73.2 4.3 9.3E-05 38.4 3.9 35 8-42 131-165 (457)
18 TIGR01642 U2AF_lg U2 snRNP aux 70.2 4.6 9.9E-05 38.7 3.4 35 8-42 337-372 (509)
19 KOG0107 Alternative splicing f 70.0 4.6 9.9E-05 36.3 3.1 33 9-41 48-81 (195)
20 PF01296 Galanin: Galanin; In 69.6 0.71 1.5E-05 29.7 -1.5 26 79-104 4-29 (29)
21 KOG4676 Splicing factor, argin 69.4 6.1 0.00013 39.3 4.1 45 4-48 48-92 (479)
22 cd00590 RRM RRM (RNA recogniti 69.1 6.3 0.00014 25.9 3.0 33 8-40 40-73 (74)
23 KOG4209 Splicing factor RNPS1, 66.4 4.6 9.9E-05 36.7 2.4 34 9-42 144-177 (231)
24 TIGR01628 PABP-1234 polyadenyl 64.7 5.9 0.00013 38.9 3.0 32 9-40 43-75 (562)
25 TIGR01649 hnRNP-L_PTB hnRNP-L/ 64.4 7 0.00015 38.2 3.5 35 8-42 313-348 (481)
26 PF08952 DUF1866: Domain of un 64.2 8.2 0.00018 33.2 3.4 33 10-42 72-104 (146)
27 TIGR01645 half-pint poly-U bin 52.2 11 0.00024 38.9 2.7 34 9-42 150-184 (612)
28 TIGR01659 sex-lethal sex-letha 48.3 25 0.00055 33.5 4.2 35 9-43 236-273 (346)
29 TIGR01649 hnRNP-L_PTB hnRNP-L/ 47.5 18 0.00039 35.4 3.2 33 10-42 40-75 (481)
30 PF05172 Nup35_RRM: Nup53/35/4 45.3 19 0.00041 28.8 2.5 34 9-42 55-89 (100)
31 COG0724 RNA-binding proteins ( 43.7 24 0.00052 28.5 2.9 37 7-43 156-193 (306)
32 TIGR01628 PABP-1234 polyadenyl 41.2 31 0.00068 33.9 3.8 34 9-42 327-361 (562)
33 PLN03213 repressor of silencin 36.5 41 0.00088 34.9 3.7 40 2-42 43-85 (759)
34 smart00071 Galanin Galanin. Ga 33.4 7.9 0.00017 31.4 -1.4 28 79-106 16-43 (103)
35 TIGR01645 half-pint poly-U bin 32.3 44 0.00095 34.8 3.3 34 9-42 247-281 (612)
36 KOG0147 Transcriptional coacti 31.7 42 0.00092 34.5 3.0 33 9-41 222-254 (549)
37 KOG4454 RNA binding protein (R 30.2 32 0.00069 32.2 1.7 37 6-42 47-84 (267)
38 KOG3430 Dynein light chain typ 30.1 75 0.0016 25.5 3.6 34 88-121 19-54 (90)
39 TIGR01661 ELAV_HUD_SF ELAV/HuD 29.5 62 0.0013 29.3 3.5 33 8-40 131-166 (352)
40 PF14605 Nup35_RRM_2: Nup53/35 29.0 38 0.00082 23.8 1.6 20 6-25 34-53 (53)
41 PF11985 DUF3486: Protein of u 27.8 3.8E+02 0.0083 22.8 10.3 21 73-93 30-54 (180)
42 PRK10163 DNA-binding transcrip 25.7 1.5E+02 0.0032 26.8 5.2 54 70-123 55-118 (271)
43 KOG0415 Predicted peptidyl pro 25.4 61 0.0013 32.3 2.8 36 5-40 278-314 (479)
44 PF08543 Phos_pyr_kin: Phospho 25.4 80 0.0017 28.0 3.4 26 71-97 202-227 (246)
45 KOG0123 Polyadenylate-binding 25.2 75 0.0016 30.7 3.4 35 8-42 115-150 (369)
46 KOG0149 Predicted RNA-binding 22.0 54 0.0012 30.6 1.7 31 10-40 56-86 (247)
47 PF11848 DUF3368: Domain of un 21.6 1.5E+02 0.0033 20.3 3.5 26 71-96 20-45 (48)
48 TIGR01648 hnRNP-R-Q heterogene 20.5 78 0.0017 32.7 2.6 32 9-40 100-133 (578)
No 1
>PLN03120 nucleic acid binding protein; Provisional
Probab=100.00 E-value=2.3e-73 Score=514.08 Aligned_cols=224 Identities=75% Similarity=1.004 Sum_probs=205.3
Q ss_pred CCCCCCCceEEEEEEeccchhhHHhhccCCeecCceEEEecCCCCCCCCCccccccccCCCCCCccchhhhHHHHHHHHH
Q 025931 1 MKSDNEWTQIAYVTFKDMQGAETAVLLSGATIVDLSVSISLAPDYQLPPAASALHETKNKTPNGAESALRKAEDVVSSML 80 (246)
Q Consensus 1 ~~~~~e~sqtA~VTFe~~~Aa~TALLLsGAtL~d~~V~It~~~~~~~~~~~~~~~~~e~~~qe~kp~a~~~a~~IvAemL 80 (246)
|.++.+..+.|||||+++.++++||||||++|+|+.|+|+++++|.+|+.......... .......+++++++||++||
T Consensus 36 I~~d~~~~GfAFVtF~d~eaAe~AllLnG~~l~gr~V~Vt~a~~~~~p~~~~~~~~~~~-~~~~~~~~~~~a~~vva~mL 114 (260)
T PLN03120 36 MQSENERSQIAYVTFKDPQGAETALLLSGATIVDQSVTITPAEDYQLPPEALAPLSSNS-PASGAESAVKKAEDVVSSML 114 (260)
T ss_pred EeecCCCCCEEEEEeCcHHHHHHHHHhcCCeeCCceEEEEeccCCCCCccccccccccc-CCCCccchhhHHHHHHHHHH
Confidence 34566677899999999999999999999999999999999999999877643321111 11111148999999999999
Q ss_pred hccccccHHHHHHHHHhhhhcCccHHHHHHHhhhhhhcCccccccccchhhhhhhhhhccccchhHhHHHHHHHHHHHHh
Q 025931 81 AKGFILGKDAVFKAKTFDEKHQFTSTASAKVASFDKKIGFSEKISVGTSVVSDRVREVDQKFQVSEKTKSAFVAAEQKVS 160 (246)
Q Consensus 81 AkGYvLgddAi~KAi~fDekHgiSs~f~a~v~slD~K~glTeKis~g~~~v~ekak~vDeky~VSektksa~~aaeq~~~ 160 (246)
||||+||||||+|||+||||||||++|+++|++||+||||||||+.|+++||+++|+||||||||+||++++.++||+++
T Consensus 115 AkGy~l~~dA~~kAk~fDekH~~ss~a~a~v~~~d~k~gltek~~~g~~~v~~~~k~vDeky~vs~kt~sa~~~~~~~~~ 194 (260)
T PLN03120 115 AKGFILGKDAVNKAKAFDEKHQLTSTASAKVASLDKKIGLSEKLSAGTAVVNEKVKEVDQKYQVSEKTKSALAAAEQKVS 194 (260)
T ss_pred hhhhhhhHHHHHHHHHHHHhhchHHHHHHHHHhhhhhcCcccccccchHHHHHHHHhhhhhhchhHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhhhcCcccccchhhhhhHHHHHHHHHhhhhhhHHHHhhhhHHHHhhhhcccccccccCCCCCC
Q 025931 161 SVGSAIMKNRYVFTGASWVAGAFNKVAQAAGEVGQKAKEKAGMAEEEQKRKMVDDFAQVHLAESPKT 227 (246)
Q Consensus 161 ~agsai~~n~Yvs~Ga~wvsga~~~vakaa~~~g~~~~ek~~~~~~~~~~~~~~~~~~~~~~~~~~~ 227 (246)
+||||||+||||++||+||||||+||||||.|+|+|++|||+++|+++ +++++|+++|+++||++
T Consensus 195 ~a~sai~~~~y~~~ga~w~~~a~~~~a~aa~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~ 259 (260)
T PLN03120 195 SAGSAIMKNRYVLTGASWVTGAFNKVAKAAEEVGQKTKEKVGAAEEEQ--QVVDAYANIHLSESPKA 259 (260)
T ss_pred HHHHHHhcCcccccchHHHHHHHHHHHHHHHHHhhhhHHHHhhhhhhc--ccccccceeecCCCCCC
Confidence 999999999999999999999999999999999999999999988887 99999999999999975
No 2
>PLN03121 nucleic acid binding protein; Provisional
Probab=100.00 E-value=1.9e-66 Score=464.91 Aligned_cols=195 Identities=42% Similarity=0.593 Sum_probs=177.0
Q ss_pred CCCCCCCceEEEEEEeccchhhHHhhccCCeecCceEEEecCCCCCCCCCcccccc----c-c-----CCCCCCcc-chh
Q 025931 1 MKSDNEWTQIAYVTFKDMQGAETAVLLSGATIVDLSVSISLAPDYQLPPAASALHE----T-K-----NKTPNGAE-SAL 69 (246)
Q Consensus 1 ~~~~~e~sqtA~VTFe~~~Aa~TALLLsGAtL~d~~V~It~~~~~~~~~~~~~~~~----~-e-----~~~qe~kp-~a~ 69 (246)
|+++++..+.|||+|+++++++|||||||++|+|++|+|+++++|++++.....+. + . ....-..| .++
T Consensus 37 I~~D~et~gfAfVtF~d~~aaetAllLnGa~l~d~~I~It~~~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~a~ 116 (243)
T PLN03121 37 IIRSGEYACTAYVTFKDAYALETAVLLSGATIVDQRVCITRWGQYEDEFDFWNRPSWDTEDISTHNYETNQFASTPGEAV 116 (243)
T ss_pred EecCCCcceEEEEEECCHHHHHHHHhcCCCeeCCceEEEEeCcccccCcccccCccccccccccccccccccCCCchhhH
Confidence 56788888999999999999999999999999999999999999999876422111 0 0 00111122 489
Q ss_pred hhHHHHHHHHHhccccccHHHHHHHHHhhhhcCccHHHHHHHhhhhhhcCccccccccchhhhhhhhhhccccchhHhHH
Q 025931 70 RKAEDVVSSMLAKGFILGKDAVFKAKTFDEKHQFTSTASAKVASFDKKIGFSEKISVGTSVVSDRVREVDQKFQVSEKTK 149 (246)
Q Consensus 70 ~~a~~IvAemLAkGYvLgddAi~KAi~fDekHgiSs~f~a~v~slD~K~glTeKis~g~~~v~ekak~vDeky~VSektk 149 (246)
++|++||++||||||+||+|||+|||+|||+||||++++++|.+||+|+||||||++|+ +++|+||||||||++||
T Consensus 117 ~~aq~Vv~tmLAkGyvLgkda~~KAkafDE~h~lss~a~a~v~~~d~~iglt~k~~~g~----~~vk~vDeky~vs~~tk 192 (243)
T PLN03121 117 TVAQEVVKTMLAKGYVLGKDALSKAKAFDESHQVSATAAAKVAELSKRIGLTDKIFAGM----EAVRSVDEKYHVSEFTK 192 (243)
T ss_pred HHHHHHHHHHHHhcchhhHHHHHHHHHHHHhcCccHhhhhhhhhhhhhccchhhhhhhH----HHHHhhhhhhhhHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999 88999999999999999
Q ss_pred HHHHHHHHHHhhhhhhhhcCcccccchhhhhhHHHHHHHHHhhhhhhHHH
Q 025931 150 SAFVAAEQKVSSVGSAIMKNRYVFTGASWVAGAFNKVAQAAGEVGQKAKE 199 (246)
Q Consensus 150 sa~~aaeq~~~~agsai~~n~Yvs~Ga~wvsga~~~vakaa~~~g~~~~e 199 (246)
||+.++||+++.|||+|||||||++||+||||||+||||||.|+|+++++
T Consensus 193 sA~~aa~~~~~~a~sai~~~~Y~~~Ga~w~sga~~~~akaa~~~g~~~~~ 242 (243)
T PLN03121 193 SAATATGRTAAAAANAVVNSSYFSKGALWVSDALTRAAKAAADLGAHGSN 242 (243)
T ss_pred HHHHHHHHHHHHhhhhhhhcchhhcchHHHHHHHHHHHHHHHHhhccccC
Confidence 99999999999999999999999999999999999999999999999976
No 3
>PLN03120 nucleic acid binding protein; Provisional
Probab=95.54 E-value=0.014 Score=54.01 Aligned_cols=51 Identities=25% Similarity=0.285 Sum_probs=41.4
Q ss_pred ccccHHHHHHHHHhhhhcCccHHHH-------HHHhhhhhhcCccccccccchhhhhh
Q 025931 84 FILGKDAVFKAKTFDEKHQFTSTAS-------AKVASFDKKIGFSEKISVGTSVVSDR 134 (246)
Q Consensus 84 YvLgddAi~KAi~fDekHgiSs~f~-------a~v~slD~K~glTeKis~g~~~v~ek 134 (246)
.-|+-.+..+...||+|.|||.++. .++.++|+|||+|||.....++..++
T Consensus 135 H~~ss~a~a~v~~~d~k~gltek~~~g~~~v~~~~k~vDeky~vs~kt~sa~~~~~~~ 192 (260)
T PLN03120 135 HQLTSTASAKVASLDKKIGLSEKLSAGTAVVNEKVKEVDQKYQVSEKTKSALAAAEQK 192 (260)
T ss_pred hchHHHHHHHHHhhhhhcCcccccccchHHHHHHHHhhhhhhchhHHHHHHHHHHHHH
Confidence 3456778889999999999999865 68999999999999877766554333
No 4
>PLN03121 nucleic acid binding protein; Provisional
Probab=94.48 E-value=0.045 Score=50.32 Aligned_cols=47 Identities=19% Similarity=0.165 Sum_probs=39.4
Q ss_pred ccccccHHHHHHHHHhhhhcCccHHHH---HHHhhhhhhcCccccccccc
Q 025931 82 KGFILGKDAVFKAKTFDEKHQFTSTAS---AKVASFDKKIGFSEKISVGT 128 (246)
Q Consensus 82 kGYvLgddAi~KAi~fDekHgiSs~f~---a~v~slD~K~glTeKis~g~ 128 (246)
.-+-|+-.|-.|.-+||+|.|||.++. .+|.++|+|||++|+-....
T Consensus 146 E~h~lss~a~a~v~~~d~~iglt~k~~~g~~~vk~vDeky~vs~~tksA~ 195 (243)
T PLN03121 146 ESHQVSATAAAKVAELSKRIGLTDKIFAGMEAVRSVDEKYHVSEFTKSAA 195 (243)
T ss_pred HhcCccHhhhhhhhhhhhhccchhhhhhhHHHHHhhhhhhhhHHHHHHHH
Confidence 345688899999999999999999995 67899999999997644433
No 5
>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=93.66 E-value=0.095 Score=35.82 Aligned_cols=33 Identities=24% Similarity=0.437 Sum_probs=30.7
Q ss_pred ceEEEEEEeccchhhHHhh-ccCCeecCceEEEe
Q 025931 8 TQIAYVTFKDMQGAETAVL-LSGATIVDLSVSIS 40 (246)
Q Consensus 8 sqtA~VTFe~~~Aa~TALL-LsGAtL~d~~V~It 40 (246)
...|+|+|.+...|+.|+- |||..+.|.+|.|.
T Consensus 21 ~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~ 54 (56)
T PF13893_consen 21 RGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVS 54 (56)
T ss_dssp TTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEE
T ss_pred CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence 4689999999999999996 99999999999985
No 6
>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=93.05 E-value=0.12 Score=35.37 Aligned_cols=34 Identities=26% Similarity=0.368 Sum_probs=30.2
Q ss_pred CCCceEEEEEEeccchhhHHhh-ccCCeecCceEE
Q 025931 5 NEWTQIAYVTFKDMQGAETAVL-LSGATIVDLSVS 38 (246)
Q Consensus 5 ~e~sqtA~VTFe~~~Aa~TALL-LsGAtL~d~~V~ 38 (246)
+.....|+|+|+++..++.|+- |+|-.|.|..|+
T Consensus 36 ~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir 70 (70)
T PF00076_consen 36 GKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR 70 (70)
T ss_dssp SSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred ccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence 3456789999999999999999 999999998874
No 7
>PLN03134 glycine-rich RNA-binding protein 4; Provisional
Probab=91.33 E-value=0.24 Score=41.26 Aligned_cols=35 Identities=20% Similarity=0.385 Sum_probs=31.8
Q ss_pred ceEEEEEEeccchhhHHhh-ccCCeecCceEEEecC
Q 025931 8 TQIAYVTFKDMQGAETAVL-LSGATIVDLSVSISLA 42 (246)
Q Consensus 8 sqtA~VTFe~~~Aa~TALL-LsGAtL~d~~V~It~~ 42 (246)
...|||+|+++.+++.||- |||..|.|..|.|..+
T Consensus 76 kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~a 111 (144)
T PLN03134 76 RGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPA 111 (144)
T ss_pred ceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEeC
Confidence 3579999999999999995 9999999999999755
No 8
>smart00362 RRM_2 RNA recognition motif.
Probab=89.39 E-value=0.58 Score=30.86 Aligned_cols=32 Identities=25% Similarity=0.448 Sum_probs=28.2
Q ss_pred ceEEEEEEeccchhhHHhh-ccCCeecCceEEE
Q 025931 8 TQIAYVTFKDMQGAETAVL-LSGATIVDLSVSI 39 (246)
Q Consensus 8 sqtA~VTFe~~~Aa~TALL-LsGAtL~d~~V~I 39 (246)
...++|+|.++..++.|+. |+|..+.|..|.|
T Consensus 39 ~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v 71 (72)
T smart00362 39 KGFAFVEFESEEDAEKAIEALNGTKLGGRPLRV 71 (72)
T ss_pred CceEEEEeCCHHHHHHHHHHhCCcEECCEEEee
Confidence 4689999999999999986 6779999988887
No 9
>smart00360 RRM RNA recognition motif.
Probab=89.09 E-value=0.63 Score=30.48 Aligned_cols=33 Identities=24% Similarity=0.433 Sum_probs=28.7
Q ss_pred ceEEEEEEeccchhhHHh-hccCCeecCceEEEe
Q 025931 8 TQIAYVTFKDMQGAETAV-LLSGATIVDLSVSIS 40 (246)
Q Consensus 8 sqtA~VTFe~~~Aa~TAL-LLsGAtL~d~~V~It 40 (246)
...|+|+|.+...++-|+ .|+|..+.|..|.|.
T Consensus 38 ~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v~ 71 (71)
T smart00360 38 KGFAFVEFESEEDAEKALEALNGKELDGRPLKVK 71 (71)
T ss_pred CceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEeC
Confidence 348999999999999998 678899999998873
No 10
>smart00361 RRM_1 RNA recognition motif.
Probab=86.60 E-value=0.76 Score=33.09 Aligned_cols=32 Identities=25% Similarity=0.381 Sum_probs=28.6
Q ss_pred ceEEEEEEeccchhhHHhh-ccCCeecCceEEE
Q 025931 8 TQIAYVTFKDMQGAETAVL-LSGATIVDLSVSI 39 (246)
Q Consensus 8 sqtA~VTFe~~~Aa~TALL-LsGAtL~d~~V~I 39 (246)
-..+||+|+++..+..|+- |+|..+.|..|.+
T Consensus 37 rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~ 69 (70)
T smart00361 37 RGNVYITFERSEDAARAIVDLNGRYFDGRTVKA 69 (70)
T ss_pred cEEEEEEECCHHHHHHHHHHhCCCEECCEEEEe
Confidence 3569999999999999987 8999999999876
No 11
>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=84.85 E-value=1 Score=31.41 Aligned_cols=33 Identities=21% Similarity=0.241 Sum_probs=28.2
Q ss_pred CCceEEEEEEeccchhhHHhhccC-CeecCceEE
Q 025931 6 EWTQIAYVTFKDMQGAETAVLLSG-ATIVDLSVS 38 (246)
Q Consensus 6 e~sqtA~VTFe~~~Aa~TALLLsG-AtL~d~~V~ 38 (246)
.....|+|+|.++..++.|+-+.+ -.|.|..|.
T Consensus 37 ~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~ 70 (70)
T PF14259_consen 37 QSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR 70 (70)
T ss_dssp SEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred ccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence 347899999999999999998888 778887764
No 12
>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor. Members of this subfamily are found in plants, metazoa and fungi.
Probab=84.29 E-value=0.97 Score=43.30 Aligned_cols=38 Identities=21% Similarity=0.372 Sum_probs=34.4
Q ss_pred eEEEEEEeccchhhHHhhccCCeecCceEEEecCCCCC
Q 025931 9 QIAYVTFKDMQGAETAVLLSGATIVDLSVSISLAPDYQ 46 (246)
Q Consensus 9 qtA~VTFe~~~Aa~TALLLsGAtL~d~~V~It~~~~~~ 46 (246)
..|||+|+++..|..||-|+|..|.|..|.|....+|.
T Consensus 224 g~afVeF~~~e~A~~Al~l~g~~~~g~~l~v~r~~~~~ 261 (509)
T TIGR01642 224 NFAFLEFRTVEEATFAMALDSIIYSNVFLKIRRPHDYI 261 (509)
T ss_pred CEEEEEeCCHHHHhhhhcCCCeEeeCceeEecCccccC
Confidence 47999999999999999999999999999998666665
No 13
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor. These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
Probab=80.38 E-value=1.4 Score=39.95 Aligned_cols=34 Identities=26% Similarity=0.432 Sum_probs=30.9
Q ss_pred eEEEEEEeccchhhHHh-hccCCeecCceEEEecC
Q 025931 9 QIAYVTFKDMQGAETAV-LLSGATIVDLSVSISLA 42 (246)
Q Consensus 9 qtA~VTFe~~~Aa~TAL-LLsGAtL~d~~V~It~~ 42 (246)
.-|||+|.++..++.|| .|||..|.|..|.|..+
T Consensus 46 g~afV~f~~~~~A~~Ai~~l~g~~l~g~~i~v~~a 80 (352)
T TIGR01661 46 GYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYA 80 (352)
T ss_pred eEEEEEECcHHHHHHHHhhcccEEECCeeEEEEee
Confidence 47999999999999999 69999999999999643
No 14
>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=77.80 E-value=5 Score=38.02 Aligned_cols=38 Identities=18% Similarity=0.453 Sum_probs=33.4
Q ss_pred eEEEEEEeccchhhHHh-hccCCeecCceEEEecCCCCC
Q 025931 9 QIAYVTFKDMQGAETAV-LLSGATIVDLSVSISLAPDYQ 46 (246)
Q Consensus 9 qtA~VTFe~~~Aa~TAL-LLsGAtL~d~~V~It~~~~~~ 46 (246)
..|+|+|.+...++-|| .|+|..|.|..|.|..+.++.
T Consensus 229 g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~~~~ 267 (457)
T TIGR01622 229 GFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQDST 267 (457)
T ss_pred eEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEccCCC
Confidence 47999999999999999 599999999999998765443
No 15
>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=76.36 E-value=2.4 Score=43.33 Aligned_cols=33 Identities=30% Similarity=0.485 Sum_probs=30.8
Q ss_pred EEEEEEeccchhhHHhh-ccCCeecCceEEEecC
Q 025931 10 IAYVTFKDMQGAETAVL-LSGATIVDLSVSISLA 42 (246)
Q Consensus 10 tA~VTFe~~~Aa~TALL-LsGAtL~d~~V~It~~ 42 (246)
-|+|+|++...|+.|+. |||..|.|+.|.|.-+
T Consensus 271 fAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~~A 304 (578)
T TIGR01648 271 YAFVHFEDREDAVKAMDELNGKELEGSEIEVTLA 304 (578)
T ss_pred eEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence 69999999999999997 9999999999999844
No 16
>TIGR01659 sex-lethal sex-lethal family splicing factor. This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).
Probab=74.44 E-value=2.5 Score=40.23 Aligned_cols=34 Identities=26% Similarity=0.417 Sum_probs=30.6
Q ss_pred eEEEEEEeccchhhHHh-hccCCeecCceEEEecC
Q 025931 9 QIAYVTFKDMQGAETAV-LLSGATIVDLSVSISLA 42 (246)
Q Consensus 9 qtA~VTFe~~~Aa~TAL-LLsGAtL~d~~V~It~~ 42 (246)
..|+|+|+++..++.|| -|+|..|.+..|.|..+
T Consensus 150 GyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~~a 184 (346)
T TIGR01659 150 GYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSYA 184 (346)
T ss_pred cEEEEEEccHHHHHHHHHHcCCCccCCceeeeecc
Confidence 36999999999999999 59999999999999743
No 17
>TIGR01622 SF-CC1 splicing factor, CC1-like family. A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.
Probab=73.22 E-value=4.3 Score=38.45 Aligned_cols=35 Identities=23% Similarity=0.451 Sum_probs=32.2
Q ss_pred ceEEEEEEeccchhhHHhhccCCeecCceEEEecC
Q 025931 8 TQIAYVTFKDMQGAETAVLLSGATIVDLSVSISLA 42 (246)
Q Consensus 8 sqtA~VTFe~~~Aa~TALLLsGAtL~d~~V~It~~ 42 (246)
...|||+|.++..++-||-|+|..|.|.+|.|...
T Consensus 131 kg~afVeF~~~e~A~~Al~l~g~~~~g~~i~v~~~ 165 (457)
T TIGR01622 131 KGVAYVEFYDVESVIKALALTGQMLLGRPIIVQSS 165 (457)
T ss_pred ceEEEEEECCHHHHHHHHHhCCCEECCeeeEEeec
Confidence 46899999999999999999999999999999753
No 18
>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor. Members of this subfamily are found in plants, metazoa and fungi.
Probab=70.16 E-value=4.6 Score=38.74 Aligned_cols=35 Identities=23% Similarity=0.335 Sum_probs=31.6
Q ss_pred ceEEEEEEeccchhhHHh-hccCCeecCceEEEecC
Q 025931 8 TQIAYVTFKDMQGAETAV-LLSGATIVDLSVSISLA 42 (246)
Q Consensus 8 sqtA~VTFe~~~Aa~TAL-LLsGAtL~d~~V~It~~ 42 (246)
...|+|+|+++..+.-|+ .|+|..|.|..|.|..+
T Consensus 337 ~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a 372 (509)
T TIGR01642 337 KGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRA 372 (509)
T ss_pred CeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEC
Confidence 457999999999999999 59999999999999755
No 19
>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]
Probab=69.96 E-value=4.6 Score=36.27 Aligned_cols=33 Identities=36% Similarity=0.580 Sum_probs=29.4
Q ss_pred eEEEEEEeccchhhHHh-hccCCeecCceEEEec
Q 025931 9 QIAYVTFKDMQGAETAV-LLSGATIVDLSVSISL 41 (246)
Q Consensus 9 qtA~VTFe~~~Aa~TAL-LLsGAtL~d~~V~It~ 41 (246)
-.|+|+|+|+--|+-|+ -|+|..|.|..|.|..
T Consensus 48 GfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~ 81 (195)
T KOG0107|consen 48 GFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVEL 81 (195)
T ss_pred CceEEeccCcccHHHHHhhcCCccccCceEEEEe
Confidence 46999999999888887 6999999999999973
No 20
>PF01296 Galanin: Galanin; InterPro: IPR008174 Galanin is a peptide hormone that controls various biological activities []. Galanin-like immuno-reactivity has been found in the central and peripheral nervous systems of mammals, with high concentrations demonstrated in discrete regions of the central nervous system, including the median eminence, hypothalamus, arcuate nucleus, septum, neuro-intermediate lobe of the pituitary, and the spinal cord. Its localisation within neurosecretory granules suggests that galanin may function as a neurotransmitter, and it has been shown to coexist with a variety of other peptide and amine neurotransmitters within individual neurons []. Although the precise physiological role of galanin is uncertain, it has a number of pharmacological properties: it stimulates food intake, when injected into the third ventricle of rats; it increases levels of plasma growth hormone and prolactin, and decreases dopamine levels in the median eminence []; and infusion into humans results in hyperglycemia and glucose intolerance, and inhibits pancreatic release of insulin, somatostatin and pancreatic peptide. Galanin also modulates smooth muscle contractility within the gastro-intestinal and genito-urinary tracts, all such activities suggesting that the hormone may play an important role in the nervous modulation of endocrine and smooth muscle function []. Galanin is a 29 amino acid peptide processed from a larger precursor protein. Except in human, galanin is C-terminally amidated. Its sequence is highly conserved and the first 14 residues are identical in all currently known sequences.; GO: 0005179 hormone activity, 0005576 extracellular region
Probab=69.56 E-value=0.71 Score=29.70 Aligned_cols=26 Identities=27% Similarity=0.657 Sum_probs=22.5
Q ss_pred HHhccccccHHHHHHHHHhhhhcCcc
Q 025931 79 MLAKGFILGKDAVFKAKTFDEKHQFT 104 (246)
Q Consensus 79 mLAkGYvLgddAi~KAi~fDekHgiS 104 (246)
+-..||.||..||.-=+.|-+||||.
T Consensus 4 lnsagyLlGPhaiD~HRSf~DK~Gla 29 (29)
T PF01296_consen 4 LNSAGYLLGPHAIDNHRSFGDKHGLA 29 (29)
T ss_pred ccccceEeccccccCccccccccCCC
Confidence 34579999999999999999999974
No 21
>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]
Probab=69.41 E-value=6.1 Score=39.35 Aligned_cols=45 Identities=24% Similarity=0.285 Sum_probs=39.7
Q ss_pred CCCCceEEEEEEeccchhhHHhhccCCeecCceEEEecCCCCCCC
Q 025931 4 DNEWTQIAYVTFKDMQGAETAVLLSGATIVDLSVSISLAPDYQLP 48 (246)
Q Consensus 4 ~~e~sqtA~VTFe~~~Aa~TALLLsGAtL~d~~V~It~~~~~~~~ 48 (246)
++..+.++||-|-|++-+..|-+|+++..+|-.+.|-|+.+...|
T Consensus 48 ~pv~sRtcyVkf~d~~sv~vaQhLtntvfvdraliv~p~~~~~~p 92 (479)
T KOG4676|consen 48 IPVISRTCYVKFLDSQSVTVAQHLTNTVFVDRALIVRPYGDEVIP 92 (479)
T ss_pred CcceeeeEEEeccCCcceeHHhhhccceeeeeeEEEEecCCCCCc
Confidence 456789999999999999999999999999999999888766544
No 22
>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=69.09 E-value=6.3 Score=25.88 Aligned_cols=33 Identities=27% Similarity=0.454 Sum_probs=27.3
Q ss_pred ceEEEEEEeccchhhHHhh-ccCCeecCceEEEe
Q 025931 8 TQIAYVTFKDMQGAETAVL-LSGATIVDLSVSIS 40 (246)
Q Consensus 8 sqtA~VTFe~~~Aa~TALL-LsGAtL~d~~V~It 40 (246)
...++|+|+++..+..|+. |++..+.|..|.|.
T Consensus 40 ~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~ 73 (74)
T cd00590 40 KGFAFVEFEDEEDAEKALEALNGKELGGRPLRVE 73 (74)
T ss_pred ceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEe
Confidence 5689999999999999997 45555888888874
No 23
>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]
Probab=66.42 E-value=4.6 Score=36.65 Aligned_cols=34 Identities=29% Similarity=0.449 Sum_probs=31.8
Q ss_pred eEEEEEEeccchhhHHhhccCCeecCceEEEecC
Q 025931 9 QIAYVTFKDMQGAETAVLLSGATIVDLSVSISLA 42 (246)
Q Consensus 9 qtA~VTFe~~~Aa~TALLLsGAtL~d~~V~It~~ 42 (246)
..|||.|.+..+.+.||.|+|..|.+..|.|+..
T Consensus 144 ~~~yvef~~~~~~~~ay~l~gs~i~~~~i~vt~~ 177 (231)
T KOG4209|consen 144 GFAYVEFSSYELVEEAYKLDGSEIPGPAIEVTLK 177 (231)
T ss_pred eeEEEecccHhhhHHHhhcCCcccccccceeeee
Confidence 4899999999999999999999999999999843
No 24
>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=64.66 E-value=5.9 Score=38.94 Aligned_cols=32 Identities=22% Similarity=0.300 Sum_probs=30.1
Q ss_pred eEEEEEEeccchhhHHh-hccCCeecCceEEEe
Q 025931 9 QIAYVTFKDMQGAETAV-LLSGATIVDLSVSIS 40 (246)
Q Consensus 9 qtA~VTFe~~~Aa~TAL-LLsGAtL~d~~V~It 40 (246)
..|||+|.++..|+-|| .|++..|.|..|.|.
T Consensus 43 G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~ 75 (562)
T TIGR01628 43 GYGYVNFQNPADAERALETMNFKRLGGKPIRIM 75 (562)
T ss_pred eEEEEEECCHHHHHHHHHHhCCCEECCeeEEee
Confidence 58999999999999999 799999999999996
No 25
>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=64.37 E-value=7 Score=38.18 Aligned_cols=35 Identities=17% Similarity=0.284 Sum_probs=31.6
Q ss_pred ceEEEEEEeccchhhHHhh-ccCCeecCceEEEecC
Q 025931 8 TQIAYVTFKDMQGAETAVL-LSGATIVDLSVSISLA 42 (246)
Q Consensus 8 sqtA~VTFe~~~Aa~TALL-LsGAtL~d~~V~It~~ 42 (246)
...|+|+|.++..|+.||- |+|..|.|..|.|...
T Consensus 313 ~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s 348 (481)
T TIGR01649 313 KETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPS 348 (481)
T ss_pred CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEc
Confidence 3589999999999999995 9999999999999743
No 26
>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function. ; PDB: 1UFW_A 2DNR_A.
Probab=64.23 E-value=8.2 Score=33.25 Aligned_cols=33 Identities=33% Similarity=0.455 Sum_probs=29.8
Q ss_pred EEEEEEeccchhhHHhhccCCeecCceEEEecC
Q 025931 10 IAYVTFKDMQGAETAVLLSGATIVDLSVSISLA 42 (246)
Q Consensus 10 tA~VTFe~~~Aa~TALLLsGAtL~d~~V~It~~ 42 (246)
.--|||.+-+.|=.||=|+|.+|.|..|+|..-
T Consensus 72 ~mwVTF~dg~sALaals~dg~~v~g~~l~i~LK 104 (146)
T PF08952_consen 72 TMWVTFRDGQSALAALSLDGIQVNGRTLKIRLK 104 (146)
T ss_dssp CEEEEESSCHHHHHHHHGCCSEETTEEEEEEE-
T ss_pred eEEEEECccHHHHHHHccCCcEECCEEEEEEeC
Confidence 457999999999999999999999999999843
No 27
>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=52.20 E-value=11 Score=38.94 Aligned_cols=34 Identities=15% Similarity=0.315 Sum_probs=30.7
Q ss_pred eEEEEEEeccchhhHHh-hccCCeecCceEEEecC
Q 025931 9 QIAYVTFKDMQGAETAV-LLSGATIVDLSVSISLA 42 (246)
Q Consensus 9 qtA~VTFe~~~Aa~TAL-LLsGAtL~d~~V~It~~ 42 (246)
.-|||+|+++.+++.|+ -|||..|.|..|.|...
T Consensus 150 GfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp 184 (612)
T TIGR01645 150 GFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRP 184 (612)
T ss_pred CeEEEEeCcHHHHHHHHHhcCCeEEecceeeeccc
Confidence 47999999999999999 49999999999999743
No 28
>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=48.26 E-value=25 Score=33.50 Aligned_cols=35 Identities=23% Similarity=0.373 Sum_probs=29.1
Q ss_pred eEEEEEEeccchhhHHhh-ccCCeecC--ceEEEecCC
Q 025931 9 QIAYVTFKDMQGAETAVL-LSGATIVD--LSVSISLAP 43 (246)
Q Consensus 9 qtA~VTFe~~~Aa~TALL-LsGAtL~d--~~V~It~~~ 43 (246)
..|+|+|++...|+.||- |||..|.+ ..|.|..+.
T Consensus 236 G~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~~a~ 273 (346)
T TIGR01659 236 GVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRLAE 273 (346)
T ss_pred eEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEECC
Confidence 489999999999999997 89998876 577776443
No 29
>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=47.54 E-value=18 Score=35.40 Aligned_cols=33 Identities=21% Similarity=0.161 Sum_probs=29.4
Q ss_pred EEEEEEeccchhhHHhh---ccCCeecCceEEEecC
Q 025931 10 IAYVTFKDMQGAETAVL---LSGATIVDLSVSISLA 42 (246)
Q Consensus 10 tA~VTFe~~~Aa~TALL---LsGAtL~d~~V~It~~ 42 (246)
.|+|+|+++..|+.|+= +++..|.|..|.|...
T Consensus 40 ~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~s 75 (481)
T TIGR01649 40 QALVEFEDEESAKACVNFATSVPIYIRGQPAFFNYS 75 (481)
T ss_pred EEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEec
Confidence 69999999999999994 6899999999999643
No 30
>PF05172 Nup35_RRM: Nup53/35/40-type RNA recognition motif; InterPro: IPR007846 The MPPN (Mitotic PhosphoProtein N end) family is uncharacterised however it probably plays a role in the cell cycle because the family includes mitotic phosphoproteins O13026 from SWISSPROT []. This family also includes Q05166 from SWISSPROT a suppressor of thermosensitive mutations in the DNA polymerase delta gene, Pol III []. The conserved central region appears to be distantly related to the RNA-binding region RNP-1 (RNA recognition motif, IPR000504 from INTERPRO), suggesting an RNA binding function for this protein.; PDB: 1WWH_C 3P3D_A.
Probab=45.32 E-value=19 Score=28.84 Aligned_cols=34 Identities=12% Similarity=0.154 Sum_probs=27.6
Q ss_pred eEEEEEEeccchhhHHhhccCCeecCceEE-EecC
Q 025931 9 QIAYVTFKDMQGAETAVLLSGATIVDLSVS-ISLA 42 (246)
Q Consensus 9 qtA~VTFe~~~Aa~TALLLsGAtL~d~~V~-It~~ 42 (246)
.=..|+|.++..|.-||.-||..|.|..+- |.+.
T Consensus 55 NWi~I~Y~~~~~A~rAL~~NG~i~~g~~mvGV~~~ 89 (100)
T PF05172_consen 55 NWIHITYDNPLSAQRALQKNGTIFSGSLMVGVKPC 89 (100)
T ss_dssp TEEEEEESSHHHHHHHHTTTTEEETTCEEEEEEE-
T ss_pred CEEEEECCCHHHHHHHHHhCCeEEcCcEEEEEEEc
Confidence 346899999999999999999999987554 5443
No 31
>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]
Probab=43.75 E-value=24 Score=28.55 Aligned_cols=37 Identities=19% Similarity=0.219 Sum_probs=31.2
Q ss_pred CceEEEEEEeccchhhHHhhccC-CeecCceEEEecCC
Q 025931 7 WTQIAYVTFKDMQGAETAVLLSG-ATIVDLSVSISLAP 43 (246)
Q Consensus 7 ~sqtA~VTFe~~~Aa~TALLLsG-AtL~d~~V~It~~~ 43 (246)
....|+|+|.++..+..|+...+ ..|.|..|.|....
T Consensus 156 ~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~ 193 (306)
T COG0724 156 SRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQ 193 (306)
T ss_pred cCceEEEEecCHHHHHHHHHHcCCCeECCceeEeeccc
Confidence 34689999999999999987655 99999999998753
No 32
>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=41.17 E-value=31 Score=33.95 Aligned_cols=34 Identities=24% Similarity=0.382 Sum_probs=30.9
Q ss_pred eEEEEEEeccchhhHHh-hccCCeecCceEEEecC
Q 025931 9 QIAYVTFKDMQGAETAV-LLSGATIVDLSVSISLA 42 (246)
Q Consensus 9 qtA~VTFe~~~Aa~TAL-LLsGAtL~d~~V~It~~ 42 (246)
..++|+|.++..+..|+ -|+|..|.|..|.|..+
T Consensus 327 g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~a 361 (562)
T TIGR01628 327 GFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALA 361 (562)
T ss_pred CeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEec
Confidence 57999999999999999 49999999999999754
No 33
>PLN03213 repressor of silencing 3; Provisional
Probab=36.49 E-value=41 Score=34.90 Aligned_cols=40 Identities=13% Similarity=0.160 Sum_probs=33.5
Q ss_pred CCCCCCceEEEEEEecc--chhhHHhh-ccCCeecCceEEEecC
Q 025931 2 KSDNEWTQIAYVTFKDM--QGAETAVL-LSGATIVDLSVSISLA 42 (246)
Q Consensus 2 ~~~~e~sqtA~VTFe~~--~Aa~TALL-LsGAtL~d~~V~It~~ 42 (246)
+|+.| -..|||+|..+ ..++.|+= |||+.+.|+.|.|..+
T Consensus 43 pRETG-RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNKA 85 (759)
T PLN03213 43 VRTKG-RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEKA 85 (759)
T ss_pred ecccC-CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEeec
Confidence 46667 57899999998 56778875 9999999999999755
No 34
>smart00071 Galanin Galanin. Galanin [1,2,3] is a neuropeptide that controls various biological activities: it regulates the release growth hormone, inhibits the release of insulin and somatostatin, contracts smooth muscle of the gastrointestinal and genitourinary tract and may be involved in the control of adrenal secretion
Probab=33.40 E-value=7.9 Score=31.40 Aligned_cols=28 Identities=29% Similarity=0.642 Sum_probs=23.9
Q ss_pred HHhccccccHHHHHHHHHhhhhcCccHH
Q 025931 79 MLAKGFILGKDAVFKAKTFDEKHQFTST 106 (246)
Q Consensus 79 mLAkGYvLgddAi~KAi~fDekHgiSs~ 106 (246)
+=..||.||..||.--+.|-+|||++.+
T Consensus 16 lnsagyllgp~aid~hrs~~dk~g~~gK 43 (103)
T smart00071 16 LNSAGYLLGPHAIDNHRSFHDKHGLTGK 43 (103)
T ss_pred eccCceeeCccccccccccccCCCcccc
Confidence 4457999999999999999999998764
No 35
>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=32.30 E-value=44 Score=34.75 Aligned_cols=34 Identities=6% Similarity=0.206 Sum_probs=31.0
Q ss_pred eEEEEEEeccchhhHHh-hccCCeecCceEEEecC
Q 025931 9 QIAYVTFKDMQGAETAV-LLSGATIVDLSVSISLA 42 (246)
Q Consensus 9 qtA~VTFe~~~Aa~TAL-LLsGAtL~d~~V~It~~ 42 (246)
..+||+|++.+.+.-|+ -|||-.|+|+.|.|..+
T Consensus 247 GfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kA 281 (612)
T TIGR01645 247 GYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKC 281 (612)
T ss_pred CeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEec
Confidence 47999999999999999 79999999999999744
No 36
>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]
Probab=31.66 E-value=42 Score=34.52 Aligned_cols=33 Identities=39% Similarity=0.579 Sum_probs=31.0
Q ss_pred eEEEEEEeccchhhHHhhccCCeecCceEEEec
Q 025931 9 QIAYVTFKDMQGAETAVLLSGATIVDLSVSISL 41 (246)
Q Consensus 9 qtA~VTFe~~~Aa~TALLLsGAtL~d~~V~It~ 41 (246)
-.+||.|-|++.+--|+-|+|..+.|.+|.|-+
T Consensus 222 gi~Yvef~D~~sVp~aiaLsGqrllg~pv~vq~ 254 (549)
T KOG0147|consen 222 GIAYVEFCDEQSVPLAIALSGQRLLGVPVIVQL 254 (549)
T ss_pred ceeEEEEecccchhhHhhhcCCcccCceeEecc
Confidence 479999999999999999999999999999953
No 37
>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]
Probab=30.17 E-value=32 Score=32.16 Aligned_cols=37 Identities=22% Similarity=0.250 Sum_probs=31.9
Q ss_pred CCceEEEEEEeccchhhHHh-hccCCeecCceEEEecC
Q 025931 6 EWTQIAYVTFKDMQGAETAV-LLSGATIVDLSVSISLA 42 (246)
Q Consensus 6 e~sqtA~VTFe~~~Aa~TAL-LLsGAtL~d~~V~It~~ 42 (246)
+..+.|||.|+++-.+--|. ||||--|-+..+.|++-
T Consensus 47 ~~~kFa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r 84 (267)
T KOG4454|consen 47 QEQKFAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLR 84 (267)
T ss_pred CCCceeeeecccccchhhhhhhcccchhccchhhcccc
Confidence 45567999999999998886 88999999999999843
No 38
>KOG3430 consensus Dynein light chain type 1 [Cytoskeleton]
Probab=30.06 E-value=75 Score=25.54 Aligned_cols=34 Identities=29% Similarity=0.343 Sum_probs=22.8
Q ss_pred HHHHHHHHHhhhhcC-ccHHHHHHHh-hhhhhcCcc
Q 025931 88 KDAVFKAKTFDEKHQ-FTSTASAKVA-SFDKKIGFS 121 (246)
Q Consensus 88 ddAi~KAi~fDekHg-iSs~f~a~v~-slD~K~glT 121 (246)
++||.-|++-=+++. +......+|+ +||+|||-+
T Consensus 19 ~~a~~~a~~al~~f~~~~k~iA~~iKkefDkkyG~~ 54 (90)
T KOG3430|consen 19 QEAIELARQALEKFNVIEKDIAAFIKKEFDKKYGPT 54 (90)
T ss_pred HHHHHHHHHHHHHcCCChHHHHHHHHHHHhhhcCCc
Confidence 356666666555666 6666666664 799999876
No 39
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor. These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
Probab=29.50 E-value=62 Score=29.33 Aligned_cols=33 Identities=18% Similarity=0.446 Sum_probs=27.4
Q ss_pred ceEEEEEEeccchhhHHh-hccCCeecCc--eEEEe
Q 025931 8 TQIAYVTFKDMQGAETAV-LLSGATIVDL--SVSIS 40 (246)
Q Consensus 8 sqtA~VTFe~~~Aa~TAL-LLsGAtL~d~--~V~It 40 (246)
...++|+|++...++-|+ .|+|..+.+. .|.|.
T Consensus 131 ~g~~fv~f~~~~~A~~ai~~l~g~~~~g~~~~i~v~ 166 (352)
T TIGR01661 131 KGVGFIRFDKRDEADRAIKTLNGTTPSGCTEPITVK 166 (352)
T ss_pred CcEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEE
Confidence 347999999999999999 7999998774 45554
No 40
>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif
Probab=29.04 E-value=38 Score=23.75 Aligned_cols=20 Identities=35% Similarity=0.496 Sum_probs=17.8
Q ss_pred CCceEEEEEEeccchhhHHh
Q 025931 6 EWTQIAYVTFKDMQGAETAV 25 (246)
Q Consensus 6 e~sqtA~VTFe~~~Aa~TAL 25 (246)
+..-.+||+|+++.+++.||
T Consensus 34 ~~~~~~~l~y~~~~~ae~Al 53 (53)
T PF14605_consen 34 ESTNWMYLKYKSRKDAEKAL 53 (53)
T ss_pred CCCcEEEEEECCHHHHHhhC
Confidence 45778999999999999997
No 41
>PF11985 DUF3486: Protein of unknown function (DUF3486); InterPro: IPR021874 This entry is represented by Bacteriophage Mu, Gp27. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=27.77 E-value=3.8e+02 Score=22.81 Aligned_cols=21 Identities=19% Similarity=0.526 Sum_probs=19.2
Q ss_pred HHHHHHHHhc----cccccHHHHHH
Q 025931 73 EDVVSSMLAK----GFILGKDAVFK 93 (246)
Q Consensus 73 ~~IvAemLAk----GYvLgddAi~K 93 (246)
.+|+++++.. ||.+|+.+|++
T Consensus 30 ~ei~~~~~~~~~~~g~~iSrSav~R 54 (180)
T PF11985_consen 30 YEILAEWLEELAEEGYDISRSAVHR 54 (180)
T ss_pred HHHHHHHHHhhhccCCCcCHHHHHH
Confidence 6899999999 99999999987
No 42
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=25.67 E-value=1.5e+02 Score=26.78 Aligned_cols=54 Identities=11% Similarity=0.111 Sum_probs=45.2
Q ss_pred hhHHHHHHHHHhcccc----------ccHHHHHHHHHhhhhcCccHHHHHHHhhhhhhcCcccc
Q 025931 70 RKAEDVVSSMLAKGFI----------LGKDAVFKAKTFDEKHQFTSTASAKVASFDKKIGFSEK 123 (246)
Q Consensus 70 ~~a~~IvAemLAkGYv----------LgddAi~KAi~fDekHgiSs~f~a~v~slD~K~glTeK 123 (246)
.++.+++.+|...||+ ||...+.-+..+-....+...+.-.+.+|-+++|.|=.
T Consensus 55 Stv~RlL~tL~~~G~l~~~~~~~~Y~lG~~l~~Lg~~~~~~~~l~~~a~p~l~~La~~~getv~ 118 (271)
T PRK10163 55 STTFRLLKVLQAADFVYQDSQLGWWHIGLGVFNVGAAYIHNRDVLSVAGPFMRRLMLLSGETVN 118 (271)
T ss_pred HHHHHHHHHHHHCCCEEEcCCCCeEEecHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHCCeEE
Confidence 5679999999999987 56667888888888888988888999999998887743
No 43
>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=25.45 E-value=61 Score=32.29 Aligned_cols=36 Identities=19% Similarity=0.389 Sum_probs=31.9
Q ss_pred CCCceEEEEEEeccchhhHHhh-ccCCeecCceEEEe
Q 025931 5 NEWTQIAYVTFKDMQGAETAVL-LSGATIVDLSVSIS 40 (246)
Q Consensus 5 ~e~sqtA~VTFe~~~Aa~TALL-LsGAtL~d~~V~It 40 (246)
++.-|-|+|.|++....+-|.. +.|..|+|..|+|.
T Consensus 278 gdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVD 314 (479)
T KOG0415|consen 278 GDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVD 314 (479)
T ss_pred cchhheeeeeecchhhHHHHHhhhcceeeccceEEee
Confidence 4566899999999999999975 78999999999995
No 44
>PF08543 Phos_pyr_kin: Phosphomethylpyrimidine kinase; InterPro: IPR013749 This enzyme 2.7.4.7 from EC is part of the Thiamine pyrophosphate (TPP) synthesis pathway, TPP is an essential cofactor for many enzymes []. ; PDB: 2DDW_B 2DDO_B 2DDM_A 3IBQ_A 3H74_A 3HYO_A 1UB0_A 1VI9_D 1TD2_B 2PHP_D ....
Probab=25.42 E-value=80 Score=27.97 Aligned_cols=26 Identities=42% Similarity=0.611 Sum_probs=22.5
Q ss_pred hHHHHHHHHHhccccccHHHHHHHHHh
Q 025931 71 KAEDVVSSMLAKGFILGKDAVFKAKTF 97 (246)
Q Consensus 71 ~a~~IvAemLAkGYvLgddAi~KAi~f 97 (246)
....+++.+|++||-| .+|+++|+.|
T Consensus 202 ~fss~laa~l~~g~~l-~~Av~~A~~~ 227 (246)
T PF08543_consen 202 LFSSALAAFLAKGYSL-EEAVEKAKNF 227 (246)
T ss_dssp HHHHHHHHHHHTTSSH-HHHHHHHHHH
T ss_pred HHHHHHHHHHHcCCCH-HHHHHHHHHH
Confidence 4578899999999999 8899999876
No 45
>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]
Probab=25.16 E-value=75 Score=30.73 Aligned_cols=35 Identities=20% Similarity=0.338 Sum_probs=30.5
Q ss_pred ceEEEEEEeccchhhHHh-hccCCeecCceEEEecC
Q 025931 8 TQIAYVTFKDMQGAETAV-LLSGATIVDLSVSISLA 42 (246)
Q Consensus 8 sqtA~VTFe~~~Aa~TAL-LLsGAtL~d~~V~It~~ 42 (246)
++..+|.|+++.+++.|+ +|||-.+.|..|-|-+.
T Consensus 115 ~kg~FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~ 150 (369)
T KOG0123|consen 115 SKGYFVQFESEESAKKAIEKLNGMLLNGKKIYVGLF 150 (369)
T ss_pred ceeeEEEeCCHHHHHHHHHHhcCcccCCCeeEEeec
Confidence 555699999999999998 88999999999999644
No 46
>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]
Probab=22.05 E-value=54 Score=30.63 Aligned_cols=31 Identities=23% Similarity=0.276 Sum_probs=28.1
Q ss_pred EEEEEEeccchhhHHhhccCCeecCceEEEe
Q 025931 10 IAYVTFKDMQGAETAVLLSGATIVDLSVSIS 40 (246)
Q Consensus 10 tA~VTFe~~~Aa~TALLLsGAtL~d~~V~It 40 (246)
-.+|||+|..++.-|+-=.+=.|+|...+.-
T Consensus 56 yGfVTf~d~~aa~rAc~dp~piIdGR~aNcn 86 (247)
T KOG0149|consen 56 YGFVTFRDAEAATRACKDPNPIIDGRKANCN 86 (247)
T ss_pred eeeEEeecHHHHHHHhcCCCCcccccccccc
Confidence 4699999999999999999999999988774
No 47
>PF11848 DUF3368: Domain of unknown function (DUF3368); InterPro: IPR021799 This domain is functionally uncharacterised. This domain is found in bacteria and archaea. This presumed domain is about 50 amino acids in length.
Probab=21.59 E-value=1.5e+02 Score=20.27 Aligned_cols=26 Identities=8% Similarity=0.216 Sum_probs=22.3
Q ss_pred hHHHHHHHHHhccccccHHHHHHHHH
Q 025931 71 KAEDVVSSMLAKGFILGKDAVFKAKT 96 (246)
Q Consensus 71 ~a~~IvAemLAkGYvLgddAi~KAi~ 96 (246)
.+...+..|..+||-+|++.++++..
T Consensus 20 ~~~~~l~~l~~~g~~is~~l~~~~L~ 45 (48)
T PF11848_consen 20 EVKPLLDRLQQAGFRISPKLIEEILR 45 (48)
T ss_pred hHHHHHHHHHHcCcccCHHHHHHHHH
Confidence 44678999999999999999998764
No 48
>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=20.50 E-value=78 Score=32.68 Aligned_cols=32 Identities=31% Similarity=0.366 Sum_probs=26.0
Q ss_pred eEEEEEEeccchhhHHh-hccCCeec-CceEEEe
Q 025931 9 QIAYVTFKDMQGAETAV-LLSGATIV-DLSVSIS 40 (246)
Q Consensus 9 qtA~VTFe~~~Aa~TAL-LLsGAtL~-d~~V~It 40 (246)
--|||+|.++..++-|| .|+|..|. +..|.|.
T Consensus 100 GfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~ 133 (578)
T TIGR01648 100 GYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVC 133 (578)
T ss_pred ceEEEEeCCHHHHHHHHHHcCCCeecCCcccccc
Confidence 47999999999999999 58999886 5555553
Done!