Query 003524
Match_columns 813
No_of_seqs 524 out of 3413
Neff 6.3
Searched_HMMs 29240
Date Tue Mar 26 18:23:36 2013
Command hhsearch -i /local_scratch/syshi/lefta3m/003524.a3m -d /local_scratch/syshi/pdb70.hhm -v 0 -o /local_scratch/syshi/H1_1572-1576//hhsearch_pdb/003524hhsearch_pdb
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 3smz_A Protein raver-1, ribonu 1.0 1 1 266.7 23.0 238 69-316 22-273 (284)
2 2ghp_A U4/U6 snRNA-associated 1.0 1 1 260.4 22.2 231 69-308 41-292 (292)
3 4f02_A Polyadenylate-binding p 1.0 1 1 236.6 17.4 166 144-311 12-185 (213)
4 3smz_A Protein raver-1, ribonu 1.0 1 1 227.8 20.4 150 145-306 20-174 (284)
5 3pgw_A U1-A; protein-RNA compl 1.0 1 1 225.5 21.5 79 230-308 7-91 (282)
6 2ghp_A U4/U6 snRNA-associated 1.0 1 1 221.7 19.2 153 142-306 36-196 (292)
7 2adc_A Polypyrimidine tract-bi 1.0 1 1 221.4 21.7 165 143-307 30-228 (229)
8 2qfj_A FBP-interacting repress 1.0 1 1 218.3 19.0 164 145-308 26-206 (216)
9 1fje_B Nucleolin RBD12, protei 1.0 1 1 216.1 13.2 162 144-308 10-175 (175)
10 3tyt_A Heterogeneous nuclear r 1.0 1 1 215.3 19.1 160 145-304 2-204 (205)
No 1
>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E
Probab=1.00 E-value=1 Score=266.75 Aligned_cols=238 Identities=16% Similarity=0.245 Sum_probs=201.8
Q ss_pred CCCCCCCCCCCCCCCHHHHHHHCCCCCEEEECCCCCCCCCCEEEEEECCHHHHC----CCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 672122368888980656776227996256214899986438999937965322----2478635899975578899999
Q 003524 69 MDDFDLRGLPSSLEDLEDYDIFGSGGGMELEGEPQESLSMSMSKISISDSASGN----GLLHYSVPNGAGTVAGEHPYGE 144 (813)
Q Consensus 69 ~~e~~ir~Lf~~~geie~~diF~~~Ggi~l~~D~~tg~skG~afV~f~d~~~A~----~~~~~~~~n~~~kv~g~~~~~~ 144 (813)
...++|++||..+++.++.++|..+| +.-+.. ++++|||||+|.+.+.|. .+.+..+.+..+.+...
T Consensus 22 ~~~l~V~nLp~~~te~~l~~~F~~~G-i~~~~~---~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~~----- 92 (284)
T 3smz_A 22 RRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFV---DKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQ----- 92 (284)
T ss_dssp CCEEEEECCCTTCCHHHHHHHTTTSC-EEEEEE---ETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC-----
T ss_pred CCEEEEECCCCCCCHHHHHHHHHHCC-CEEEEE---ECCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEEEC-----
T ss_conf 97799959998899999999998749-779999---667877999967899999999970798558827999843-----
Q ss_pred CCCCEEEECCCCCCCCHHHHHHHHHHCCCEEEEEE-----CCCCCEEEEEEECCHHHHHHHHHHHCCCCCCCCEEEEEEC
Q ss_conf 99978998189999989999999751399899995-----8874309999982398999999980377555411346415
Q 003524 145 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS 219 (813)
Q Consensus 145 ~~srtLfVgNLp~~vteeeLr~lFs~fG~I~~v~~-----tgkskGfaFV~F~d~e~A~~Ai~~Lng~~l~gr~L~V~~a 219 (813)
.+.++|||+|||+++++++|+++|++||.|..+++ +++++|||||+|.+.++|.+|+..|++..+.|++|.|.++
T Consensus 93 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a 172 (284)
T 3smz_A 93 PTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWT 172 (284)
T ss_dssp CCSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred CCCCEEEECCCCCCCCHHHHHHHHHHCCCEEEEEEEEECCCCCCCEEEEEEECCHHHHHHHHHHHCCCEECCCEEEEEEC
T ss_conf 89988999089974789999999986398468999750899954449999989999999999980897768947999988
Q ss_pred CCCCCCCCCCCCCCEEEEECCCCCC-CHHHHHHHHCCCCCEEEEEE----CCCCCCEEEEEECCHHHHHHHHHHHCCCCC
Q ss_conf 7989999876775302652259999-97799987614697589985----799762899997699999999998199822
Q 003524 220 IPKDNPSDKDLNQGTLVVFNLDPSV-SNEDLRQIFGAYGEVKEIRE----TPHKRHHKFIEFYDVRAAEAALKSLNRSDI 294 (813)
Q Consensus 220 ~pk~~~~~~~~~~~tL~V~NLp~~v-teeeL~~iFs~fG~I~~vri----t~~srG~aFVeF~d~~~A~~Ai~~LnG~~i 294 (813)
.++.... ......+|||+|||.++ ++++|+++|+.||.|..+++ ++.++|+|||+|.+.++|.+|+..|||..+
T Consensus 173 ~~~~~~~-~~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~ 251 (284)
T 3smz_A 173 DAGQLTP-ALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSL 251 (284)
T ss_dssp CGGGCCT-TTTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECSSCCEEEEEEEECSSHHHHHHHHHHHTTCEE
T ss_pred CCCCCCC-CCCCCCEEEEECCCCCCCCHHHHHHHHHCCCCEEEEEEEECCCCCCCCEEEEEECCHHHHHHHHHHHCCCCC
T ss_conf 8888985-447864799846996537999999985178876999987789998563799985898999999999679860
Q ss_pred CCCEEEEEECCCCCCCCHHHHC
Q ss_conf 8926899734897310023121
Q 003524 295 AGKRIKLEPSRPGGARRNLMLQ 316 (813)
Q Consensus 295 ~Gk~I~V~~a~~~~~r~~~~~q 316 (813)
.|++|+|.|+.++..++..+.+
T Consensus 252 ~g~~l~v~~a~~~~~~~~~~~~ 273 (284)
T 3smz_A 252 GGSHLRVSFCAPGPPGRSMLAA 273 (284)
T ss_dssp TTEECEEEECCSSSCHHHHHHH
T ss_pred CCEEEEEEEECCCCCCCCHHHH
T ss_conf 9848999981579866212333
No 2
>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A
Probab=1.00 E-value=1 Score=260.36 Aligned_cols=231 Identities=18% Similarity=0.276 Sum_probs=194.8
Q ss_pred CCCCCCCCCCCCCCCHHHHHHHCCCCCEE---EECCCCCCCCCCEEEEEECCHHHHCCCC---CCCCCCCCCCCCCCCCC
Q ss_conf 67212236888898065677622799625---6214899986438999937965322247---86358999755788999
Q 003524 69 MDDFDLRGLPSSLEDLEDYDIFGSGGGME---LEGEPQESLSMSMSKISISDSASGNGLL---HYSVPNGAGTVAGEHPY 142 (813)
Q Consensus 69 ~~e~~ir~Lf~~~geie~~diF~~~Ggi~---l~~D~~tg~skG~afV~f~d~~~A~~~~---~~~~~n~~~kv~g~~~~ 142 (813)
...++|++|+..+.+.++.++|..+|.+. +..|... ++|||||+|.+.+.|.... +..+.+..+.+..
T Consensus 41 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~--~~g~afV~f~~~~~A~~A~~~~~~~~~g~~i~v~~---- 114 (292)
T 2ghp_A 41 LTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKK--NFRFARIEFARYDGALAAITKTHKVVGQNEIIVSH---- 114 (292)
T ss_dssp -CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTS--SSEEEEEEESSHHHHHHHHTTTTCEETTEECEEEE----
T ss_pred CCEEEEECCCCCCCHHHHHHHHHHCCCEEEEEEEECCCC--CCEEEEEEECCHHHHHHHHHHCCCEECCCEEEEEE----
T ss_conf 778999089988999999999986498489999987999--95799999777999999997189586994799998----
Q ss_pred CCCCCCEEEECCCCCCCCHHHHHHHHHHCC-CEEEEEE----CCCCCEEEEEEECCHHHHHHHHHHHCCCCCCCCEEEEE
Q ss_conf 999997899818999998999999975139-9899995----88743099999823989999999803775554113464
Q 003524 143 GEHPSRTLFVRNINSNVEDSELRALFEQYG-DIRTLYT----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIH 217 (813)
Q Consensus 143 ~~~~srtLfVgNLp~~vteeeLr~lFs~fG-~I~~v~~----tgkskGfaFV~F~d~e~A~~Ai~~Lng~~l~gr~L~V~ 217 (813)
...++|||+|||+++++++|+++|++|| +|..+++ .++++|||||+|.+.++|.+|+..|++..+.|++|.|.
T Consensus 115 --~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~ 192 (292)
T 2ghp_A 115 --LTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTK 192 (292)
T ss_dssp --CCSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred --CCCCEEEEECCCCCCCHHHHHHHHHHHCCCEEEEEEEECCCCCCCEEEEEEECCHHHHHHHHHHHCCCEECCCEEEEE
T ss_conf --899889997999989999999999984997289998767999835299999788999999999828977499079999
Q ss_pred ECCCCCCCCC---CCCCCCEEEEECCCCC-CCHHHHHHHHCCCCCEEEEEEC------CCCCCEEEEEECCHHHHHHHHH
Q ss_conf 1579899998---7677530265225999-9977999876146975899857------9976289999769999999999
Q 003524 218 FSIPKDNPSD---KDLNQGTLVVFNLDPS-VSNEDLRQIFGAYGEVKEIRET------PHKRHHKFIEFYDVRAAEAALK 287 (813)
Q Consensus 218 ~a~pk~~~~~---~~~~~~tL~V~NLp~~-vteeeL~~iFs~fG~I~~vrit------~~srG~aFVeF~d~~~A~~Ai~ 287 (813)
++.++..... ......+|||+|||.+ +++++|+++|+.||.|..+++. +.++|+|||+|.+.++|.+|+
T Consensus 193 ~a~~~~~~~~~~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~- 271 (292)
T 2ghp_A 193 VSNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL- 271 (292)
T ss_dssp ECCCC---------CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-
T ss_pred ECCCCCCCCCCCCCCCCCCEEEEECCCCCCCCHHHHHHHHHCCCCEEEEEEEECCCCCCCCCEEEEEEECCHHHHHHHH-
T ss_conf 8887754332435677775699977992208999999998545874699997457767887559999968999999999-
Q ss_pred HHCCCCCCCCEEEEEECCCCC
Q ss_conf 819982289268997348973
Q 003524 288 SLNRSDIAGKRIKLEPSRPGG 308 (813)
Q Consensus 288 ~LnG~~i~Gk~I~V~~a~~~~ 308 (813)
.|||..+.|+.|+|.|+.++.
T Consensus 272 ~l~g~~~~g~~i~V~~a~~k~ 292 (292)
T 2ghp_A 272 QMNRSLLGNREISVSLADKKP 292 (292)
T ss_dssp GGTTEEETTEEEEEEECCCCC
T ss_pred HHCCCEECCCEEEEEEECCCC
T ss_conf 746978899689999835799
No 3
>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*
Probab=1.00 E-value=1 Score=236.56 Aligned_cols=166 Identities=19% Similarity=0.346 Sum_probs=148.4
Q ss_pred CCCCCEEEECCCCCCCCHHHHHHHHHHCCCEEEEEE-----CCCCCEEEEEEECCHHHHHHHHHHHCCCCCCCCEEEEEE
Q ss_conf 999978998189999989999999751399899995-----887430999998239899999998037755541134641
Q 003524 144 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF 218 (813)
Q Consensus 144 ~~~srtLfVgNLp~~vteeeLr~lFs~fG~I~~v~~-----tgkskGfaFV~F~d~e~A~~Ai~~Lng~~l~gr~L~V~~ 218 (813)
..|.++|||+|||++++|++|+++|++||+|..|++ +++++|||||+|.+.++|++|+..+++..+.++.|++.+
T Consensus 12 ~~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~ 91 (213)
T 4f02_A 12 SYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMW 91 (213)
T ss_dssp ---CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred CCCCCEEEEECCCCCCCHHHHHHHHHHHCCEEEEEEECCCCCCCCCCCCCCEECCHHHHHHHHHHHHHHHCCCCCCCCCC
T ss_conf 99975899939998787999999998619879998731468887566461000899999999998402102783320023
Q ss_pred CCCCCCCCCCCCCCCEEEEECCCCCCCHHHHHHHHCCCCCEEEEEE---CCCCCCEEEEEECCHHHHHHHHHHHCCCCCC
Q ss_conf 5798999987677530265225999997799987614697589985---7997628999976999999999981998228
Q 003524 219 SIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE---TPHKRHHKFIEFYDVRAAEAALKSLNRSDIA 295 (813)
Q Consensus 219 a~pk~~~~~~~~~~~tL~V~NLp~~vteeeL~~iFs~fG~I~~vri---t~~srG~aFVeF~d~~~A~~Ai~~LnG~~i~ 295 (813)
+..... .......+|||+|||.++++++|+++|+.||.|..+++ .+.++|+|||+|.+.++|++|++.|||..|.
T Consensus 92 ~~~~~~--~~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~ 169 (213)
T 4f02_A 92 SQRDPS--LRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLN 169 (213)
T ss_dssp CCCCTH--HHHHCTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESSHHHHHHHHHHHTTCEET
T ss_pred CCCCCC--CCCCCCCCCEECCCCCCCHHHHHHHHHHHCCCEEEEEEECCCCCCCEEEEEEECCHHHHHHHHHHHCCCEEC
T ss_conf 332110--101345553477764442799999998566996799763258988428999868899999999981999889
Q ss_pred CCEEEEEECCCCCCCC
Q ss_conf 9268997348973100
Q 003524 296 GKRIKLEPSRPGGARR 311 (813)
Q Consensus 296 Gk~I~V~~a~~~~~r~ 311 (813)
|++|+|++++++..+.
T Consensus 170 g~~i~V~~a~~~~~~~ 185 (213)
T 4f02_A 170 DRKVFVGRFKSRKERE 185 (213)
T ss_dssp TEECEEEECCCHHHHH
T ss_pred CEEEEEEECCCCCCCC
T ss_conf 9888999757876651
No 4
>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E
Probab=1.00 E-value=1 Score=227.82 Aligned_cols=150 Identities=19% Similarity=0.368 Sum_probs=138.1
Q ss_pred CCCCEEEECCCCCCCCHHHHHHHHHHCCCEEEEEECCCCCEEEEEEECCHHHHHHHHHHHCCCCCCCCEEEEEECCCCCC
Q ss_conf 99978998189999989999999751399899995887430999998239899999998037755541134641579899
Q 003524 145 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKDN 224 (813)
Q Consensus 145 ~~srtLfVgNLp~~vteeeLr~lFs~fG~I~~v~~tgkskGfaFV~F~d~e~A~~Ai~~Lng~~l~gr~L~V~~a~pk~~ 224 (813)
.++++|||+|||+++++++|+++|++|| |..+.+ ++++|||||+|.+.++|++|+..|++..+.|++|.|.++.
T Consensus 20 ~~~~~l~V~nLp~~~te~~l~~~F~~~G-i~~~~~-~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~~~---- 93 (284)
T 3smz_A 20 RNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFV-DKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQP---- 93 (284)
T ss_dssp HCCCEEEEECCCTTCCHHHHHHHTTTSC-EEEEEE-ETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC----
T ss_pred CCCCEEEEECCCCCCCHHHHHHHHHHCC-CEEEEE-ECCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEEECC----
T ss_conf 8997799959998899999999998749-779999-6678779999678999999999707985588279998438----
Q ss_pred CCCCCCCCCEEEEECCCCCCCHHHHHHHHCCCCCEEEEEE-----CCCCCCEEEEEECCHHHHHHHHHHHCCCCCCCCEE
Q ss_conf 9987677530265225999997799987614697589985-----79976289999769999999999819982289268
Q 003524 225 PSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRI 299 (813)
Q Consensus 225 ~~~~~~~~~tL~V~NLp~~vteeeL~~iFs~fG~I~~vri-----t~~srG~aFVeF~d~~~A~~Ai~~LnG~~i~Gk~I 299 (813)
...+|||+|||.++++++|+++|+.||.|..+++ ++.++|+|||+|.+.++|.+|+..|+|..+.|+.|
T Consensus 94 ------~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i 167 (284)
T 3smz_A 94 ------TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTL 167 (284)
T ss_dssp ------CSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred ------CCCEEEECCCCCCCCHHHHHHHHHHCCCEEEEEEEEECCCCCCCEEEEEEECCHHHHHHHHHHHCCCEECCCEE
T ss_conf ------99889990899747899999999863984689997508999544499999899999999999808977689479
Q ss_pred EEEECCC
Q ss_conf 9973489
Q 003524 300 KLEPSRP 306 (813)
Q Consensus 300 ~V~~a~~ 306 (813)
.|.++.+
T Consensus 168 ~v~~a~~ 174 (284)
T 3smz_A 168 YVHWTDA 174 (284)
T ss_dssp EEEECCG
T ss_pred EEEECCC
T ss_conf 9998888
No 5
>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A
Probab=1.00 E-value=1 Score=225.51 Aligned_cols=79 Identities=22% Similarity=0.425 Sum_probs=66.0
Q ss_pred CCCCEEEEECCCCCCCHHHHH----HHHCCCCCEEEEEE--CCCCCCEEEEEECCHHHHHHHHHHHCCCCCCCCEEEEEE
Q ss_conf 775302652259999977999----87614697589985--799762899997699999999998199822892689973
Q 003524 230 LNQGTLVVFNLDPSVSNEDLR----QIFGAYGEVKEIRE--TPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRIKLEP 303 (813)
Q Consensus 230 ~~~~tL~V~NLp~~vteeeL~----~iFs~fG~I~~vri--t~~srG~aFVeF~d~~~A~~Ai~~LnG~~i~Gk~I~V~~ 303 (813)
...++|||+|||.++++++|+ ++|+.||.|.+|++ ++.++|+|||+|.+.++|.+|++.|||..+.|+.|+|.|
T Consensus 7 ~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~ 86 (282)
T 3pgw_A 7 RPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQY 86 (282)
T ss_pred CCCCEEEEECCCCCCCHHHHHHHHHHHHHCCCCEEEEEECCCCCCCEEEEEEECCHHHHHHHHHHHCCCEECCCEEEEEE
T ss_conf 99877999599988899999999999973369768999767998462899997999999999999669861796799998
Q ss_pred CCCCC
Q ss_conf 48973
Q 003524 304 SRPGG 308 (813)
Q Consensus 304 a~~~~ 308 (813)
++...
T Consensus 87 a~~~~ 91 (282)
T 3pgw_A 87 AKTDS 91 (282)
T ss_pred ECCCC
T ss_conf 32685
No 6
>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A
Probab=1.00 E-value=1 Score=221.69 Aligned_cols=153 Identities=19% Similarity=0.272 Sum_probs=138.2
Q ss_pred CCCCCCCEEEECCCCCCCCHHHHHHHHHHCCCEEEEEE---CCCCCEEEEEEECCHHHHHHHHHHHCCCCCCCCEEEEEE
Q ss_conf 99999978998189999989999999751399899995---887430999998239899999998037755541134641
Q 003524 142 YGEHPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT---ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHF 218 (813)
Q Consensus 142 ~~~~~srtLfVgNLp~~vteeeLr~lFs~fG~I~~v~~---tgkskGfaFV~F~d~e~A~~Ai~~Lng~~l~gr~L~V~~ 218 (813)
..+.+.++|||+|||+++++++|+.+|+.||+|..|++ ...++|||||+|.+.++|++|+. +++..+.|++|.|.+
T Consensus 36 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~g~afV~f~~~~~A~~A~~-~~~~~~~g~~i~v~~ 114 (292)
T 2ghp_A 36 TRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSH 114 (292)
T ss_dssp ------CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSSSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEE
T ss_pred CCCCCCCEEEEECCCCCCCHHHHHHHHHHCCCEEEEEEEECCCCCCEEEEEEECCHHHHHHHHH-HCCCEECCCEEEEEE
T ss_conf 5688877899908998899999999998649848999998799995799999777999999997-189586994799998
Q ss_pred CCCCCCCCCCCCCCCEEEEECCCCCCCHHHHHHHHCCCC-CEEEEEEC----CCCCCEEEEEECCHHHHHHHHHHHCCCC
Q ss_conf 579899998767753026522599999779998761469-75899857----9976289999769999999999819982
Q 003524 219 SIPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYG-EVKEIRET----PHKRHHKFIEFYDVRAAEAALKSLNRSD 293 (813)
Q Consensus 219 a~pk~~~~~~~~~~~tL~V~NLp~~vteeeL~~iFs~fG-~I~~vrit----~~srG~aFVeF~d~~~A~~Ai~~LnG~~ 293 (813)
+. ..+|||+|||.++++++|+++|+.|| .|..+++. +.++|+|||+|.+.++|.+|+..|||..
T Consensus 115 ~~-----------~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~ 183 (292)
T 2ghp_A 115 LT-----------ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLK 183 (292)
T ss_dssp CC-----------SCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCE
T ss_pred CC-----------CCEEEEECCCCCCCHHHHHHHHHHHCCCEEEEEEEECCCCCCCEEEEEEECCHHHHHHHHHHHCCCE
T ss_conf 89-----------9889997999989999999999984997289998767999835299999788999999999828977
Q ss_pred CCCCEEEEEECCC
Q ss_conf 2892689973489
Q 003524 294 IAGKRIKLEPSRP 306 (813)
Q Consensus 294 i~Gk~I~V~~a~~ 306 (813)
+.|+.|.|.++.+
T Consensus 184 ~~g~~l~v~~a~~ 196 (292)
T 2ghp_A 184 IEGYTLVTKVSNP 196 (292)
T ss_dssp ETTEECEEEECCC
T ss_pred ECCCEEEEEECCC
T ss_conf 4990799998887
No 7
>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A
Probab=1.00 E-value=1 Score=221.37 Aligned_cols=165 Identities=25% Similarity=0.354 Sum_probs=147.5
Q ss_pred CCCCCCEEEECCCCC-CCCHHHHHHHHHHCCCEEEEEECCCCCEEEEEEECCHHHHHHHHHHHCCCCCCCCEEEEEECCC
Q ss_conf 999997899818999-9989999999751399899995887430999998239899999998037755541134641579
Q 003524 143 GEHPSRTLFVRNINS-NVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIP 221 (813)
Q Consensus 143 ~~~~srtLfVgNLp~-~vteeeLr~lFs~fG~I~~v~~tgkskGfaFV~F~d~e~A~~Ai~~Lng~~l~gr~L~V~~a~p 221 (813)
...++++|||+|||+ ++++++|+++|++||+|..+++....+|||||+|.+.++|++|++.|++..+.|++|.|.++.+
T Consensus 30 ~~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~ 109 (229)
T 2adc_A 30 AGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKH 109 (229)
T ss_dssp GCCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTTSCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSC
T ss_pred CCCCCCEEEEECCCCCCCCHHHHHHHHHHCCCEEEEEEEECCCCEEEEEECCHHHHHHHHHHHCCCEECCEEEEEEEECC
T ss_conf 99997889994888143999999999982798689999978998799997999999999998689727885789998068
Q ss_pred CCCCCCC-------------------------------CCCCCEEEEECCCCCCCHHHHHHHHCCCC-CEEEEEECCCCC
Q ss_conf 8999987-------------------------------67753026522599999779998761469-758998579976
Q 003524 222 KDNPSDK-------------------------------DLNQGTLVVFNLDPSVSNEDLRQIFGAYG-EVKEIRETPHKR 269 (813)
Q Consensus 222 k~~~~~~-------------------------------~~~~~tL~V~NLp~~vteeeL~~iFs~fG-~I~~vrit~~sr 269 (813)
+.....+ .....+|||+|||.++++++|+++|++|| .|..+++.+..+
T Consensus 110 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~ 189 (229)
T 2adc_A 110 QNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDR 189 (229)
T ss_dssp CCCCCCCSSSSTTTTEEECTTCSSCCCCSTTSGGGTTCCCSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSSST
T ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCHHHHHHHHHHCCCCEEEEEEEECCC
T ss_conf 65457666665543013445684002487322344567899777999699965899999999987599705899997898
Q ss_pred CEEEEEECCHHHHHHHHHHHCCCCCC-CCEEEEEECCCC
Q ss_conf 28999976999999999981998228-926899734897
Q 003524 270 HHKFIEFYDVRAAEAALKSLNRSDIA-GKRIKLEPSRPG 307 (813)
Q Consensus 270 G~aFVeF~d~~~A~~Ai~~LnG~~i~-Gk~I~V~~a~~~ 307 (813)
|+|||+|.+.++|.+|+..|||..+. |+.|+|+|++++
T Consensus 190 g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~~~ 228 (229)
T 2adc_A 190 KMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST 228 (229)
T ss_dssp TCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSSC
T ss_pred CEEEEEECCHHHHHHHHHHHCCCCCCCCCEEEEEEECCC
T ss_conf 689999798999999999977876589986999983588
No 8
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Probab=1.00 E-value=1 Score=218.26 Aligned_cols=164 Identities=20% Similarity=0.383 Sum_probs=145.8
Q ss_pred CCCCEEEECCCCCCCCHHHHHHHHHHCCCEEEEEE-----CCCCCEEEEEEECCHHHHHHHHHHHCCCCCCCCEEEEEEC
Q ss_conf 99978998189999989999999751399899995-----8874309999982398999999980377555411346415
Q 003524 145 HPSRTLFVRNINSNVEDSELRALFEQYGDIRTLYT-----ACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS 219 (813)
Q Consensus 145 ~~srtLfVgNLp~~vteeeLr~lFs~fG~I~~v~~-----tgkskGfaFV~F~d~e~A~~Ai~~Lng~~l~gr~L~V~~a 219 (813)
.++++|||+|||+++++++|+++|++||+|..+++ +++++|||||+|.+.++|++|+..|++..+.++.|.|.++
T Consensus 26 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~ 105 (216)
T 2qfj_A 26 AIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRP 105 (216)
T ss_dssp HHHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECC
T ss_pred CCCCEEEEECCCCCCCHHHHHHHHHHCCCEEEEEEEECCCCCCCCCEEEEEECCHHHHHHHHHHCCCCEECCEEEEEECC
T ss_conf 76877999789998999999999985799789998665888863766999968999999999874677269916898568
Q ss_pred CCCCCCC-------CCCCCCCEEEEECCCCCCCHHHHHHHHCCCCCEEEEEE-----CCCCCCEEEEEECCHHHHHHHHH
Q ss_conf 7989999-------87677530265225999997799987614697589985-----79976289999769999999999
Q 003524 220 IPKDNPS-------DKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRE-----TPHKRHHKFIEFYDVRAAEAALK 287 (813)
Q Consensus 220 ~pk~~~~-------~~~~~~~tL~V~NLp~~vteeeL~~iFs~fG~I~~vri-----t~~srG~aFVeF~d~~~A~~Ai~ 287 (813)
....... .......+|||+|||.++++++|+++|++||.|..+++ ++.++|+|||+|.+.++|.+|+.
T Consensus 106 ~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~ 185 (216)
T 2qfj_A 106 SNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVS 185 (216)
T ss_dssp SCCGGGHHHHHHHHHHHTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHCCCCCCCEEEEECCCCCCCHHHHHHHHHCCCCEEEEEEEECCCCCCCCCEEEEEECCHHHHHHHHH
T ss_conf 88431010234330026787579993789758899999997436986689987358899757569999668999999999
Q ss_pred HHCCCCCCCCEEEEEECCCCC
Q ss_conf 819982289268997348973
Q 003524 288 SLNRSDIAGKRIKLEPSRPGG 308 (813)
Q Consensus 288 ~LnG~~i~Gk~I~V~~a~~~~ 308 (813)
.|||..+.|+.|+|.|+.++.
T Consensus 186 ~l~g~~~~g~~i~V~~a~~~~ 206 (216)
T 2qfj_A 186 SMNLFDLGGQYLRVGKAVTPP 206 (216)
T ss_dssp HHTTCBCSSSBCEEEECSSCS
T ss_pred HCCCCEECCCEEEEEEECCCC
T ss_conf 736877289589999812799
No 9
>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A
Probab=1.00 E-value=1 Score=216.07 Aligned_cols=162 Identities=19% Similarity=0.274 Sum_probs=144.6
Q ss_pred CCCCCEEEECCCCCCCCHHHHHHHHHHCCCEEE----EEECCCCCEEEEEEECCHHHHHHHHHHHCCCCCCCCEEEEEEC
Q ss_conf 999978998189999989999999751399899----9958874309999982398999999980377555411346415
Q 003524 144 EHPSRTLFVRNINSNVEDSELRALFEQYGDIRT----LYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFS 219 (813)
Q Consensus 144 ~~~srtLfVgNLp~~vteeeLr~lFs~fG~I~~----v~~tgkskGfaFV~F~d~e~A~~Ai~~Lng~~l~gr~L~V~~a 219 (813)
..+.++|||+|||+++++++|+++|++||.+.. -..+++++|||||+|.+.++|++|++ |++..+.|++|.|.++
T Consensus 10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~v~~~ 88 (175)
T 1fje_B 10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKP 88 (175)
T ss_dssp CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECC
T ss_pred CCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCEEEEEECCCCCCCCEEEEEECCHHHHHHHHH-CCCCEECCEEEEEECC
T ss_conf 899747999689987798999999998577330799988889634189999789999999986-4897867768998637
Q ss_pred CCCCCCCCCCCCCCEEEEECCCCCCCHHHHHHHHCCCCCEEEEEECCCCCCEEEEEECCHHHHHHHHHHHCCCCCCCCEE
Q ss_conf 79899998767753026522599999779998761469758998579976289999769999999999819982289268
Q 003524 220 IPKDNPSDKDLNQGTLVVFNLDPSVSNEDLRQIFGAYGEVKEIRETPHKRHHKFIEFYDVRAAEAALKSLNRSDIAGKRI 299 (813)
Q Consensus 220 ~pk~~~~~~~~~~~tL~V~NLp~~vteeeL~~iFs~fG~I~~vrit~~srG~aFVeF~d~~~A~~Ai~~LnG~~i~Gk~I 299 (813)
.++... ......+|||+|||.++++++|+++|++||.|..+..++.++|+|||+|.+.++|.+|+..|||..+.|+.|
T Consensus 89 ~~~~~~--~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i 166 (175)
T 1fje_B 89 KGRDSK--KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSV 166 (175)
T ss_dssp CCSSCS--TTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEECSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEE
T ss_pred CCCCCC--CCCCCCEEEEECCCCCCCHHHHHHHHHHCCEEEEECCCCCCCEEEEEEECCHHHHHHHHHHHCCCEECCEEE
T ss_conf 776544--556577899969998899999999998657699806899876689999778999999999847988888489
Q ss_pred EEEECCCCC
Q ss_conf 997348973
Q 003524 300 KLEPSRPGG 308 (813)
Q Consensus 300 ~V~~a~~~~ 308 (813)
+|+|++++.
T Consensus 167 ~v~~a~~k~ 175 (175)
T 1fje_B 167 SLYYTGEKG 175 (175)
T ss_dssp EEEECSSCC
T ss_pred EEEECCCCC
T ss_conf 999657899
No 10
>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A
Probab=1.00 E-value=1 Score=215.29 Aligned_cols=160 Identities=18% Similarity=0.225 Sum_probs=137.8
Q ss_pred CCCCEEEECCCC-CCCCHHHHHHHHHHCCCEEEEEECCCCCEEEEEEECCHHHHHHHHHHHCCCCCCCCEEEEEECCCCC
Q ss_conf 999789981899-9998999999975139989999588743099999823989999999803775554113464157989
Q 003524 145 HPSRTLFVRNIN-SNVEDSELRALFEQYGDIRTLYTACKHRGFVMISYYDIRAARTAMRALQNKPLRRRKLDIHFSIPKD 223 (813)
Q Consensus 145 ~~srtLfVgNLp-~~vteeeLr~lFs~fG~I~~v~~tgkskGfaFV~F~d~e~A~~Ai~~Lng~~l~gr~L~V~~a~pk~ 223 (813)
.++++|||+||| .++++++|+++|++||+|.++++....+|||||+|.+.++|++|++.|+|..+.|++|.|.++..+.
T Consensus 2 ~~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s~~~~ 81 (205)
T 3tyt_A 2 ADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQPA 81 (205)
T ss_dssp CCCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTTSTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSCSC
T ss_pred CCCCEEEEECCCCCCCCHHHHHHHHHHCCCEEEEEEECCCCCEEEEEECCHHHHHHHHHHHCCCEECCCEEEEEECCCCC
T ss_conf 98888999489801199999999998359858999950899889999898999999999868997789658999815876
Q ss_pred CCCC---------------------C------------CCCCCEEEEECCCCCCCHHHHHHHHCCCCCE--EEEEECC--
Q ss_conf 9998---------------------7------------6775302652259999977999876146975--8998579--
Q 003524 224 NPSD---------------------K------------DLNQGTLVVFNLDPSVSNEDLRQIFGAYGEV--KEIRETP-- 266 (813)
Q Consensus 224 ~~~~---------------------~------------~~~~~tL~V~NLp~~vteeeL~~iFs~fG~I--~~vrit~-- 266 (813)
.... + .....+|||+|||+++++++|+++|++||.| ..+++..
T Consensus 82 ~~p~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~ 161 (205)
T 3tyt_A 82 IMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGK 161 (205)
T ss_dssp CCCCSCCBCTTSCBSEEECTTCTTCSCSSHHHHTTSCCCCCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCC
T ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCHHHHHHHHHHCCCCCEEEEEEECCC
T ss_conf 57876556666784433467775446467543333556898546777379987899999999986498241799997389
Q ss_pred -CCCCEEEEEECCHHHHHHHHHHHCCCCCCCC----EEEEEEC
Q ss_conf -9762899997699999999998199822892----6899734
Q 003524 267 -HKRHHKFIEFYDVRAAEAALKSLNRSDIAGK----RIKLEPS 304 (813)
Q Consensus 267 -~srG~aFVeF~d~~~A~~Ai~~LnG~~i~Gk----~I~V~~a 304 (813)
.++|+|||+|.+.++|.+||..|||.++.|+ ++.|+++
T Consensus 162 ~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~~vk~~ 204 (205)
T 3tyt_A 162 SERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLKLC 204 (205)
T ss_dssp SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCEECEEE
T ss_pred CCCCEEEEEEECCHHHHHHHHHHHCCCCCCCCCCCCCEEEEEC
T ss_conf 9876079999699999999999867888269888764499950
Done!