Query psy16924
Match_columns 94
No_of_seqs 91 out of 93
Neff 2.4
Searched_HMMs 46136
Date Fri Aug 16 17:11:02 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16924.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16924hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0149|consensus 99.8 4.1E-21 8.9E-26 150.8 4.1 36 1-36 61-96 (247)
2 PF13893 RRM_5: RNA recognitio 80.8 0.63 1.4E-05 26.7 0.4 28 1-28 28-56 (56)
3 PF14259 RRM_6: RNA recognitio 76.0 0.67 1.5E-05 27.0 -0.5 23 1-23 46-69 (70)
4 PLN03134 glycine-rich RNA-bind 72.0 2.4 5.2E-05 29.8 1.5 28 2-29 84-112 (144)
5 smart00361 RRM_1 RNA recogniti 70.2 2.4 5.1E-05 25.7 1.0 24 2-25 45-69 (70)
6 KOG0125|consensus 68.7 2.3 4.9E-05 36.2 0.9 31 1-31 143-174 (376)
7 smart00360 RRM RNA recognition 67.9 3.8 8.3E-05 21.8 1.4 24 2-25 46-70 (71)
8 smart00362 RRM_2 RNA recogniti 61.8 4.7 0.0001 21.6 1.1 24 2-25 47-71 (72)
9 PF09722 DUF2384: Protein of u 56.4 6.5 0.00014 23.1 1.1 23 2-24 9-31 (54)
10 cd00590 RRM RRM (RNA recogniti 46.4 13 0.00029 19.9 1.2 25 2-26 48-73 (74)
11 TIGR01649 hnRNP-L_PTB hnRNP-L/ 38.9 19 0.00041 29.4 1.6 30 1-30 45-77 (481)
12 TIGR01642 U2AF_lg U2 snRNP aux 38.4 23 0.0005 28.0 1.9 34 2-35 345-379 (509)
13 TIGR01661 ELAV_HUD_SF ELAV/HuD 35.4 23 0.00051 26.4 1.5 27 2-28 319-346 (352)
14 PLN03120 nucleic acid binding 33.6 31 0.00068 27.7 2.0 29 1-29 50-78 (260)
15 TIGR01628 PABP-1234 polyadenyl 31.0 30 0.00064 28.3 1.5 29 2-30 334-363 (562)
16 TIGR01648 hnRNP-R-Q heterogene 25.2 41 0.00089 29.5 1.4 28 1-28 276-304 (578)
17 TIGR01649 hnRNP-L_PTB hnRNP-L/ 23.7 46 0.001 27.2 1.4 28 1-28 320-348 (481)
18 COG0278 Glutaredoxin-related p 21.4 38 0.00082 24.4 0.4 13 57-69 66-78 (105)
No 1
>KOG0149|consensus
Probab=99.82 E-value=4.1e-21 Score=150.80 Aligned_cols=36 Identities=75% Similarity=1.121 Sum_probs=34.6
Q ss_pred CCCHHHHHHHhcCCCCcccccccceeeeecCCccCC
Q psy16924 1 MGDRPAAERACKDPNPIIDGRKANVNLAILGAKPRG 36 (94)
Q Consensus 1 m~D~eaA~rAc~dpnPiIDGRrANcNLA~LGakPr~ 36 (94)
|+|+|||+|||+||||||||||||||||+||+|||.
T Consensus 61 f~d~~aa~rAc~dp~piIdGR~aNcnlA~lg~~pR~ 96 (247)
T KOG0149|consen 61 FRDAEAATRACKDPNPIIDGRKANCNLASLGGKPRP 96 (247)
T ss_pred eecHHHHHHHhcCCCCcccccccccchhhhcCccCC
Confidence 689999999999999999999999999999999984
No 2
>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=80.83 E-value=0.63 Score=26.67 Aligned_cols=28 Identities=25% Similarity=0.345 Sum_probs=20.8
Q ss_pred CCCHHHHHHHhcCCC-Ccccccccceeee
Q psy16924 1 MGDRPAAERACKDPN-PIIDGRKANVNLA 28 (94)
Q Consensus 1 m~D~eaA~rAc~dpn-PiIDGRrANcNLA 28 (94)
|.+.++|++|.+.-| -.++||+-+|..|
T Consensus 28 f~~~~~A~~a~~~l~~~~~~g~~l~V~~a 56 (56)
T PF13893_consen 28 FASVEDAQKAIEQLNGRQFNGRPLKVSYA 56 (56)
T ss_dssp ESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred ECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence 468899999998433 2379998887764
No 3
>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=76.02 E-value=0.67 Score=26.97 Aligned_cols=23 Identities=39% Similarity=0.417 Sum_probs=18.8
Q ss_pred CCCHHHHHHHhcCCC-Cccccccc
Q psy16924 1 MGDRPAAERACKDPN-PIIDGRKA 23 (94)
Q Consensus 1 m~D~eaA~rAc~dpn-PiIDGRrA 23 (94)
+.+.++|.+|++.-+ ..|+||+-
T Consensus 46 f~~~~~a~~al~~~~~~~~~g~~l 69 (70)
T PF14259_consen 46 FSSEEDAKRALELLNGKEIDGRKL 69 (70)
T ss_dssp ESSHHHHHHHHHHHTTEEETTEEE
T ss_pred eCCHHHHHHHHHHCCCcEECCEEc
Confidence 368899999999555 88999974
No 4
>PLN03134 glycine-rich RNA-binding protein 4; Provisional
Probab=72.04 E-value=2.4 Score=29.78 Aligned_cols=28 Identities=32% Similarity=0.353 Sum_probs=23.8
Q ss_pred CCHHHHHHHhcCCC-Ccccccccceeeee
Q psy16924 2 GDRPAAERACKDPN-PIIDGRKANVNLAI 29 (94)
Q Consensus 2 ~D~eaA~rAc~dpn-PiIDGRrANcNLA~ 29 (94)
.|.|+|++|++.-| ..|+||+-.|+.|.
T Consensus 84 ~~~e~A~~Al~~lng~~i~Gr~l~V~~a~ 112 (144)
T PLN03134 84 NDEGAATAAISEMDGKELNGRHIRVNPAN 112 (144)
T ss_pred CCHHHHHHHHHHcCCCEECCEEEEEEeCC
Confidence 68899999998655 56999999999874
No 5
>smart00361 RRM_1 RNA recognition motif.
Probab=70.23 E-value=2.4 Score=25.70 Aligned_cols=24 Identities=33% Similarity=0.371 Sum_probs=19.1
Q ss_pred CCHHHHHHHhcCCCC-cccccccce
Q psy16924 2 GDRPAAERACKDPNP-IIDGRKANV 25 (94)
Q Consensus 2 ~D~eaA~rAc~dpnP-iIDGRrANc 25 (94)
.+.++|.+|++.-|. .++||+-+|
T Consensus 45 ~~~~dA~~A~~~l~g~~~~gr~l~~ 69 (70)
T smart00361 45 ERSEDAARAIVDLNGRYFDGRTVKA 69 (70)
T ss_pred CCHHHHHHHHHHhCCCEECCEEEEe
Confidence 578999999998764 589987654
No 6
>KOG0125|consensus
Probab=68.70 E-value=2.3 Score=36.21 Aligned_cols=31 Identities=32% Similarity=0.468 Sum_probs=25.5
Q ss_pred CCCHHHHHHHhcCCC-CcccccccceeeeecC
Q psy16924 1 MGDRPAAERACKDPN-PIIDGRKANVNLAILG 31 (94)
Q Consensus 1 m~D~eaA~rAc~dpn-PiIDGRrANcNLA~LG 31 (94)
|..+++|+||=+.-+ -+|+|||.-||.|---
T Consensus 143 men~~dadRARa~LHgt~VEGRkIEVn~ATar 174 (376)
T KOG0125|consen 143 MENPADADRARAELHGTVVEGRKIEVNNATAR 174 (376)
T ss_pred ecChhhHHHHHHHhhcceeeceEEEEeccchh
Confidence 567788888888776 6799999999999653
No 7
>smart00360 RRM RNA recognition motif.
Probab=67.86 E-value=3.8 Score=21.82 Aligned_cols=24 Identities=33% Similarity=0.407 Sum_probs=18.4
Q ss_pred CCHHHHHHHhcCCC-Ccccccccce
Q psy16924 2 GDRPAAERACKDPN-PIIDGRKANV 25 (94)
Q Consensus 2 ~D~eaA~rAc~dpn-PiIDGRrANc 25 (94)
.|.++|.+|++.-+ ..++|++-.|
T Consensus 46 ~~~~~a~~a~~~~~~~~~~~~~~~v 70 (71)
T smart00360 46 ESEEDAEKALEALNGKELDGRPLKV 70 (71)
T ss_pred CCHHHHHHHHHHcCCCeeCCcEEEe
Confidence 57899999998554 7788887655
No 8
>smart00362 RRM_2 RNA recognition motif.
Probab=61.85 E-value=4.7 Score=21.60 Aligned_cols=24 Identities=29% Similarity=0.360 Sum_probs=18.0
Q ss_pred CCHHHHHHHhcCCC-Ccccccccce
Q psy16924 2 GDRPAAERACKDPN-PIIDGRKANV 25 (94)
Q Consensus 2 ~D~eaA~rAc~dpn-PiIDGRrANc 25 (94)
.|.++|++|++.-+ ..|+|++..+
T Consensus 47 ~~~~~a~~a~~~~~~~~~~~~~i~v 71 (72)
T smart00362 47 ESEEDAEKAIEALNGTKLGGRPLRV 71 (72)
T ss_pred CCHHHHHHHHHHhCCcEECCEEEee
Confidence 57889999998444 7788887543
No 9
>PF09722 DUF2384: Protein of unknown function (DUF2384); InterPro: IPR024467 This domain is found predominantly in proteobacterial proteins. Its function in unknown.
Probab=56.44 E-value=6.5 Score=23.14 Aligned_cols=23 Identities=39% Similarity=0.660 Sum_probs=19.4
Q ss_pred CCHHHHHHHhcCCCCcccccccc
Q psy16924 2 GDRPAAERACKDPNPIIDGRKAN 24 (94)
Q Consensus 2 ~D~eaA~rAc~dpnPiIDGRrAN 24 (94)
.|.+.|++=...|||..||+++-
T Consensus 9 gd~~~a~~Wl~~p~~~l~g~~Pl 31 (54)
T PF09722_consen 9 GDEDKARRWLRTPNPALGGRTPL 31 (54)
T ss_pred CCHHHHHHHHHChHHHhCCCCHH
Confidence 47788888899999999999863
No 10
>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=46.40 E-value=13 Score=19.91 Aligned_cols=25 Identities=32% Similarity=0.385 Sum_probs=18.4
Q ss_pred CCHHHHHHHhcCCCCc-cccccccee
Q psy16924 2 GDRPAAERACKDPNPI-IDGRKANVN 26 (94)
Q Consensus 2 ~D~eaA~rAc~dpnPi-IDGRrANcN 26 (94)
++.++|.+|++.-+.. ++|++..++
T Consensus 48 ~s~~~a~~a~~~~~~~~~~~~~~~v~ 73 (74)
T cd00590 48 EDEEDAEKALEALNGKELGGRPLRVE 73 (74)
T ss_pred CCHHHHHHHHHHhCCCeECCeEEEEe
Confidence 4678899999865544 888886654
No 11
>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=38.89 E-value=19 Score=29.40 Aligned_cols=30 Identities=23% Similarity=0.270 Sum_probs=24.4
Q ss_pred CCCHHHHHHHhcC--CCC-cccccccceeeeec
Q psy16924 1 MGDRPAAERACKD--PNP-IIDGRKANVNLAIL 30 (94)
Q Consensus 1 m~D~eaA~rAc~d--pnP-iIDGRrANcNLA~L 30 (94)
|.|.|+|++|++. -|+ .|+||+..++.+--
T Consensus 45 f~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~s~~ 77 (481)
T TIGR01649 45 FEDEESAKACVNFATSVPIYIRGQPAFFNYSTS 77 (481)
T ss_pred eCchHHHHHHHHHhhcCCceEcCeEEEEEecCC
Confidence 4689999999984 455 59999999998854
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=38.41 E-value=23 Score=28.03 Aligned_cols=34 Identities=24% Similarity=0.191 Sum_probs=28.4
Q ss_pred CCHHHHHHHhcCCC-CcccccccceeeeecCCccC
Q psy16924 2 GDRPAAERACKDPN-PIIDGRKANVNLAILGAKPR 35 (94)
Q Consensus 2 ~D~eaA~rAc~dpn-PiIDGRrANcNLA~LGakPr 35 (94)
.|.++|.+||+.-| -.|+|++-.|..|..|.++.
T Consensus 345 ~~~~~a~~A~~~l~g~~~~~~~l~v~~a~~~~~~~ 379 (509)
T TIGR01642 345 KDPSVTDVAIAALNGKDTGDNKLHVQRACVGANQA 379 (509)
T ss_pred CCHHHHHHHHHHcCCCEECCeEEEEEECccCCCCC
Confidence 57899999998766 45999999999999887653
No 13
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor. These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
Probab=35.44 E-value=23 Score=26.41 Aligned_cols=27 Identities=19% Similarity=0.107 Sum_probs=22.2
Q ss_pred CCHHHHHHHhcCCC-Ccccccccceeee
Q psy16924 2 GDRPAAERACKDPN-PIIDGRKANVNLA 28 (94)
Q Consensus 2 ~D~eaA~rAc~dpn-PiIDGRrANcNLA 28 (94)
.+.|+|++|++.-| -.|+||+-.|..+
T Consensus 319 ~~~~~A~~Ai~~lnG~~~~gr~i~V~~~ 346 (352)
T TIGR01661 319 TNYDEAAMAILSLNGYTLGNRVLQVSFK 346 (352)
T ss_pred CCHHHHHHHHHHhCCCEECCeEEEEEEc
Confidence 57899999999766 4499999888765
No 14
>PLN03120 nucleic acid binding protein; Provisional
Probab=33.56 E-value=31 Score=27.72 Aligned_cols=29 Identities=21% Similarity=0.118 Sum_probs=25.0
Q ss_pred CCCHHHHHHHhcCCCCcccccccceeeee
Q psy16924 1 MGDRPAAERACKDPNPIIDGRKANVNLAI 29 (94)
Q Consensus 1 m~D~eaA~rAc~dpnPiIDGRrANcNLA~ 29 (94)
+.|.++|+.|+.--+-.|+||+-+|+.+-
T Consensus 50 F~d~eaAe~AllLnG~~l~gr~V~Vt~a~ 78 (260)
T PLN03120 50 FKDPQGAETALLLSGATIVDQSVTITPAE 78 (260)
T ss_pred eCcHHHHHHHHHhcCCeeCCceEEEEecc
Confidence 46889999999855788999999999974
No 15
>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=31.04 E-value=30 Score=28.30 Aligned_cols=29 Identities=24% Similarity=0.337 Sum_probs=24.3
Q ss_pred CCHHHHHHHhcCCC-Ccccccccceeeeec
Q psy16924 2 GDRPAAERACKDPN-PIIDGRKANVNLAIL 30 (94)
Q Consensus 2 ~D~eaA~rAc~dpn-PiIDGRrANcNLA~L 30 (94)
.+.|+|++|++.-| -+|+||+-.|.+|--
T Consensus 334 ~~~~~A~~A~~~~~g~~~~gk~l~V~~a~~ 363 (562)
T TIGR01628 334 SNPEEANRAVTEMHGRMLGGKPLYVALAQR 363 (562)
T ss_pred CCHHHHHHHHHHhcCCeeCCceeEEEeccC
Confidence 57899999998665 779999999988763
No 16
>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family. Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.
Probab=25.25 E-value=41 Score=29.50 Aligned_cols=28 Identities=32% Similarity=0.465 Sum_probs=24.1
Q ss_pred CCCHHHHHHHhcCCC-Ccccccccceeee
Q psy16924 1 MGDRPAAERACKDPN-PIIDGRKANVNLA 28 (94)
Q Consensus 1 m~D~eaA~rAc~dpn-PiIDGRrANcNLA 28 (94)
+.+.|+|++|++.-| -.|+||+.+|.+|
T Consensus 276 F~s~e~A~kAi~~lnG~~i~Gr~I~V~~A 304 (578)
T TIGR01648 276 FEDREDAVKAMDELNGKELEGSEIEVTLA 304 (578)
T ss_pred eCCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence 468899999998665 5699999999998
No 17
>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=23.72 E-value=46 Score=27.22 Aligned_cols=28 Identities=25% Similarity=0.156 Sum_probs=23.7
Q ss_pred CCCHHHHHHHhcCCCC-cccccccceeee
Q psy16924 1 MGDRPAAERACKDPNP-IIDGRKANVNLA 28 (94)
Q Consensus 1 m~D~eaA~rAc~dpnP-iIDGRrANcNLA 28 (94)
|.|.++|++|++.-|- .|+||+-.|..+
T Consensus 320 f~~~~~A~~Ai~~lng~~l~g~~l~v~~s 348 (481)
T TIGR01649 320 MADPYQAQLALTHLNGVKLFGKPLRVCPS 348 (481)
T ss_pred ECCHHHHHHHHHHhCCCEECCceEEEEEc
Confidence 5789999999997764 589999999876
No 18
>COG0278 Glutaredoxin-related protein [Posttranslational modification, protein turnover, chaperones]
Probab=21.40 E-value=38 Score=24.43 Aligned_cols=13 Identities=46% Similarity=1.329 Sum_probs=11.1
Q ss_pred ccCCCchhheehc
Q psy16924 57 YTGWPSFLMIYVH 69 (94)
Q Consensus 57 ~~G~ps~~~~y~~ 69 (94)
|..||+.|++|+.
T Consensus 66 ~s~WPT~PQLyi~ 78 (105)
T COG0278 66 YSNWPTFPQLYVN 78 (105)
T ss_pred hcCCCCCceeeEC
Confidence 5579999999984
Done!