Query 000530
Match_columns 1440
No_of_seqs 166 out of 324
Neff 3.4
Searched_HMMs 29240
Date Tue Mar 26 15:55:07 2013
Command hhsearch -i /local_scratch/syshi/lefta3m/000530.a3m -d /local_scratch/syshi/pdb70.hhm -v 0 -o /local_scratch/syshi/H1_305-308//hhsearch_pdb/000530hhsearch_pdb
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 1wjt_A Transcription elongatio 1.0 1 1 113.9 1.7 60 172-231 30-90 (103)
2 1pqv_S STP-alpha, transcriptio 1.0 1 1 112.1 7.0 65 171-235 19-84 (309)
3 3nfq_A Transcription factor IW 1.0 1 1 67.3 4.4 98 119-227 54-153 (170)
4 2xpp_A IWS1, ECU08_0440; trans 1.0 1 1 67.3 4.8 122 95-227 8-138 (145)
5 1z9e_A PC4 and SFRS1 interacti 1.0 1 1 30.8 2.0 58 171-228 25-84 (127)
6 2b4j_C PC4 and SFRS1 interacti 1.0 1 1 30.5 3.6 58 171-228 25-84 (98)
7 3tpo_A Importin subunit alpha- 1.0 1 1 21.8 5.8 24 127-150 105-128 (529)
8 3ul1_B Importin subunit alpha- 1.0 1 1 21.3 4.7 54 94-150 99-152 (510)
9 4b8j_A Importin subunit alpha- 1.0 1 1 19.5 2.6 112 93-221 72-185 (528)
10 4db6_A Armadillo repeat protei 1.0 1 1 15.0 4.0 52 94-150 53-105 (210)
No 1
>1wjt_A Transcription elongation factor S-II protein 3; four-helix bundle, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: a.48.3.1
Probab=1.00 E-value=1 Score=113.90 Aligned_cols=60 Identities=30% Similarity=0.493 Sum_probs=56.2
Q ss_pred HHHHHHHHHHHCCCCCCHHHHHHCCCCCCCCCCCCC-CCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 899999999831899858765205887422334588-888999999999999999899975
Q 000530 172 EEFLLILLRALDKLPVNLNALQMCNIGKSVNHLRTH-KNVEIQKKARSLVDTWKKRVEAEM 231 (1440)
Q Consensus 172 ee~lLeLLraLkkLPITveiLksT~IGKtVNkLRKH-~neEI~kLAk~LVkkWKkiVe~Ek 231 (1440)
.+.++++|+.|+.++||+++|++|+||++||+|||| .+++|+.+|+.||++||++|+.+.
T Consensus 30 ~~~~l~~L~~L~~~~iT~e~L~~T~IGk~Vn~LrKh~~~~~V~~lAk~Lv~~WK~~v~~~~ 90 (103)
T 1wjt_A 30 TEGALDLLKKLNSCQMSIQLLQTTRIGVAVNGVRKHCSDKEVVSLAKVLIKNWKRLLDSPR 90 (103)
T ss_dssp CSSHHHHHHHHHTSCCCHHHHHHTCHHHHHHHHHHHCCCSHHHHHHHHHHHHHHHHTCCSC
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHC
T ss_conf 9999999999857899899998765649999988469958999999999999999988741
No 2
>1pqv_S STP-alpha, transcription elongation factor S-II, DNA; mRNA cleavage, proofreading, BACKTRACKING, gene expression, multiprotein complex; 3.80A {Saccharomyces cerevisiae} SCOP: i.8.1.1 PDB: 1eo0_A
Probab=1.00 E-value=1 Score=112.11 Aligned_cols=65 Identities=23% Similarity=0.449 Sum_probs=60.1
Q ss_pred HHHHHHHHHHHH-CCCCCCHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf 289999999983-18998587652058874223345888889999999999999998999750399
Q 000530 171 VEEFLLILLRAL-DKLPVNLNALQMCNIGKSVNHLRTHKNVEIQKKARSLVDTWKKRVEAEMDARP 235 (1440)
Q Consensus 171 ~ee~lLeLLraL-kkLPITveiLksT~IGKtVNkLRKH~neEI~kLAk~LVkkWKkiVe~Ek~~kp 235 (1440)
..+.+|++|+.| +.++||+++|++|+||++||+||||.+++|+.+|+.||++||++|.++...+.
T Consensus 19 ~~~~~l~~L~~L~~~~~it~~~L~~T~IG~~Vn~lrkh~~~~v~~~Ak~Li~~WK~~v~~~~~~~~ 84 (309)
T 1pqv_S 19 NDAAVLEILHVLDKEFVPTEKLLRETKVGVEVNKFKKSTNVEISKLVKKMISSWKDAINKNKRSRQ 84 (309)
T ss_pred CHHHHHHHHHHHHHCCCCCHHHHHHCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf 989999999998763898899997487569999887389789999999999999998777505776
No 3
>3nfq_A Transcription factor IWS1; SPN1, RNA polymerase II; 1.85A {Saccharomyces cerevisiae} PDB: 3o8z_A 3oak_A
Probab=1.00 E-value=1 Score=67.35 Aligned_cols=98 Identities=24% Similarity=0.397 Sum_probs=82.1
Q ss_pred HHHHHHHHHCCHHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCHHHHHHCCCC
Q ss_conf 67999998238035788998760835478999998513668999999999972899999999831899858765205887
Q 000530 119 SLLAGVVAATDKFDCLNWFVQLRGLLVFDEWLQEVHKGKIGDAGSPRDGDKSVEEFLLILLRALDKLPVNLNALQMCNIG 198 (1440)
Q Consensus 119 ~~l~~Vi~~T~~qd~L~rFvql~Gl~vL~eWLqEa~Kgk~Gd~~sP~~~dks~ee~lLeLLraLkkLPITveiLksT~IG 198 (1440)
-++-.|.....+.+....|+..+.|.++..||.-+- |+.-| .-..--.+|+.|..+||+.++|+.++||
T Consensus 54 kmL~~V~~~L~k~~L~~~~ld~giL~~l~~WLePLp-----DgSLP------~~~Ir~~lL~~L~~lPI~~e~Lk~SglG 122 (170)
T 3nfq_A 54 KLLPKVVSVLSKANLADTILDNNLLQSVRIWLEPLP-----DGSLP------SFEIQKSLFAALNDLPVKTEHLKESGLG 122 (170)
T ss_dssp HHHHHHHHHHTCGGGHHHHHHTTHHHHHHHHHSCCT-----TSCCC------CHHHHHHHHHHHHTSCCCHHHHHHHSHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHCCCC-----CCCCC------CHHHHHHHHHHHHHCCCCHHHHHHCCCC
T ss_conf 518999999827889999987465999999827588-----99998------5799999999999789999997627978
Q ss_pred CCCCCCCCCC--CHHHHHHHHHHHHHHHHHH
Q ss_conf 4223345888--8899999999999999989
Q 000530 199 KSVNHLRTHK--NVEIQKKARSLVDTWKKRV 227 (1440)
Q Consensus 199 KtVNkLRKH~--neEI~kLAk~LVkkWKkiV 227 (1440)
+.|.-|.+|+ ..+++++|..||.+|-..|
T Consensus 123 kvV~~l~k~~~et~~nkrla~~Li~~WsRpI 153 (170)
T 3nfq_A 123 RVVIFYTKSKRVEAQLARLAEKLIAEWTRPI 153 (170)
T ss_dssp HHHHHHHHCTTSCHHHHHHHHHHHHHHTCCC
T ss_pred CEEEEHHCCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf 2320011598536789999999999988998
No 4
>2xpp_A IWS1, ECU08_0440; transcription, elongation, histone chaperone, RNA polymerase mRNA export; 1.74A {Encephalitozoon cuniculi} PDB: 2xpo_A 2xpn_A 2xpl_A
Probab=1.00 E-value=1 Score=67.35 Aligned_cols=122 Identities=16% Similarity=0.177 Sum_probs=92.1
Q ss_pred HHHHHHHHHHCCCCCC-C------CCCCCHHHHHHHHHHHCCHHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf 7799999972245321-2------11101036799999823803578899876083547899999851366899999999
Q 000530 95 DGVEKLVQLMVPERND-K------KIDLVCRSLLAGVVAATDKFDCLNWFVQLRGLLVFDEWLQEVHKGKIGDAGSPRDG 167 (1440)
Q Consensus 95 e~V~klV~LM~~~~~~-k------ki~La~R~~l~~Vi~~T~~qd~L~rFvql~Gl~vL~eWLqEa~Kgk~Gd~~sP~~~ 167 (1440)
+.+..|+..|...-.+ . +--+.-.-++-.|.....+.+....|+..+-+.++..||.-+- |+.-|
T Consensus 8 ~~~~~l~~~M~~Aa~~D~~a~~~~~PA~~KlklL~~V~~~l~k~~l~~~~ld~giL~~l~~WL~PLp-----DgsLP--- 79 (145)
T 2xpp_A 8 EISRSLKKRMQDILKKDNANNLEGRPATGKIENVEEISDILMSKALQESLLDEGILDEIKGWLEPLP-----DKSMP--- 79 (145)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHTSCCCHHHHHHHHHHHHHTCTTTHHHHHHTTHHHHHHHHHSCCT-----TSCCC---
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHCCCC-----CCCCC---
T ss_conf 9999999999999999999877698588999659999999734899999988577999999818299-----99999---
Q ss_pred CCCHHHHHHHHHHHHCCCCCCHHHHHHCCCCCCCCCCCCCC--CHHHHHHHHHHHHHHHHHH
Q ss_conf 99728999999998318998587652058874223345888--8899999999999999989
Q 000530 168 DKSVEEFLLILLRALDKLPVNLNALQMCNIGKSVNHLRTHK--NVEIQKKARSLVDTWKKRV 227 (1440)
Q Consensus 168 dks~ee~lLeLLraLkkLPITveiLksT~IGKtVNkLRKH~--neEI~kLAk~LVkkWKkiV 227 (1440)
.-..--.+|+.|..+||+.++|+.++||+.|..|.+|+ ..+++++|+.||.+|...|
T Consensus 80 ---~~~Ir~~lL~~L~~lPI~~e~Lk~SglGkvv~~l~k~~~et~~nk~la~~Li~~WsRpi 138 (145)
T 2xpp_A 80 ---NIKIRKRLLDVLKTMKIHKEHLVTSGVGKIVYFYSINPKESKEVRASAKALVQKWTNEV 138 (145)
T ss_dssp ---CHHHHHHHHHHHHTSCCCHHHHHHHCHHHHHHHHHHCTTSCHHHHHHHHHHHHHHHHHH
T ss_pred ---CHHHHHHHHHHHHHCCCCHHHHHCCCCCCCHHHHHCCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf ---78999999999997899999830389780115565499537899999999999987877
No 5
>1z9e_A PC4 and SFRS1 interacting protein 2; heat repeat-like, ledgf, protein binding/transcription complex; NMR {Homo sapiens} SCOP: a.48.4.1
Probab=1.00 E-value=1 Score=30.77 Aligned_cols=58 Identities=17% Similarity=0.177 Sum_probs=51.6
Q ss_pred HHHHHHHHHHHHCCCCCCHHHHH-HCCCCCCCCCCCCC-CCHHHHHHHHHHHHHHHHHHH
Q ss_conf 28999999998318998587652-05887422334588-888999999999999999899
Q 000530 171 VEEFLLILLRALDKLPVNLNALQ-MCNIGKSVNHLRTH-KNVEIQKKARSLVDTWKKRVE 228 (1440)
Q Consensus 171 ~ee~lLeLLraLkkLPITveiLk-sT~IGKtVNkLRKH-~neEI~kLAk~LVkkWKkiVe 228 (1440)
.-..||++|..|+.+++|--+|+ .+.|=-++.+||++ .|..|++.|..|+.+.|.++.
T Consensus 25 Dv~kCl~~Leel~~l~vT~~mL~Rnpe~V~TlkklRrY~gnq~Ir~kA~~iY~kFK~lf~ 84 (127)
T 1z9e_A 25 DVNRCIEALDELASLQVTMQQAQKHTEMITTLKKIRRFKVSQVIMEKSTMLYNKFKNMFL 84 (127)
T ss_dssp CHHHHHHHHHHHHHSCCCHHHHGGGHHHHHHHHHHTTCTTCSSHHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHCCCCCCHHHHHHCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHH
T ss_conf 899999999987124234998823809999999999972549999999999999999984
No 6
>2b4j_C PC4 and SFRS1 interacting protein; HIV, integration, transcription, viral protein, recombinatio; 2.02A {Homo sapiens} SCOP: a.48.4.1 PDB: 3f9k_C 3hpg_G 3u88_C* 3hph_E
Probab=1.00 E-value=1 Score=30.50 Aligned_cols=58 Identities=17% Similarity=0.177 Sum_probs=51.5
Q ss_pred HHHHHHHHHHHHCCCCCCHHHHH-HCCCCCCCCCCCCC-CCHHHHHHHHHHHHHHHHHHH
Q ss_conf 28999999998318998587652-05887422334588-888999999999999999899
Q 000530 171 VEEFLLILLRALDKLPVNLNALQ-MCNIGKSVNHLRTH-KNVEIQKKARSLVDTWKKRVE 228 (1440)
Q Consensus 171 ~ee~lLeLLraLkkLPITveiLk-sT~IGKtVNkLRKH-~neEI~kLAk~LVkkWKkiVe 228 (1440)
.-..|+++|..|+.+++|.-+|+ ...+=-++.+||++ .+..|++.|..|+.+.|.++.
T Consensus 25 Dv~kcl~~L~~l~~l~~T~~mL~rnpe~V~t~kklRry~g~q~Ir~kA~~iY~kfK~~f~ 84 (98)
T 2b4j_C 25 DVNRCIEALDELASLQVTMQQAQKHTEMITTLKKIRRFKVSQVIMEKSTMLYNKFKNMFL 84 (98)
T ss_dssp CHHHHHHHHHHHHTCCCCHHHHHTTHHHHHHHHHHTTCTTCHHHHHHHHHHHHHHHHC--
T ss_pred CHHHHHHHHHHHHCCCCCHHHHHHCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHH
T ss_conf 899999999987024334998823909999999999983309999999999999999974
No 7
>3tpo_A Importin subunit alpha-2; nuclear import, protein transport; 2.10A {Mus musculus} PDB: 1qgk_B 1qgr_B
Probab=1.00 E-value=1 Score=21.84 Aligned_cols=24 Identities=13% Similarity=0.162 Sum_probs=14.4
Q ss_pred HCCHHHHHHHHHHHCCHHHHHHHH
Q ss_conf 238035788998760835478999
Q 000530 127 ATDKFDCLNWFVQLRGLLVFDEWL 150 (1440)
Q Consensus 127 ~T~~qd~L~rFvql~Gl~vL~eWL 150 (1440)
..+....+..+++.++++.|-..|
T Consensus 105 s~~~~~~i~~ii~~G~ip~Lv~lL 128 (529)
T 3tpo_A 105 SREKQPPIDNIIRAGLIPKFVSFL 128 (529)
T ss_dssp TSSSCCCHHHHHHTTHHHHHHHHH
T ss_pred CCCCCCHHHHHHHCCCHHHHHHHH
T ss_conf 278984499999888999999987
No 8
>3ul1_B Importin subunit alpha-2; arm repeat, armadillo repeat, nuclear transport, nuclear LOC signal binding, importin beta binding; 1.90A {Mus musculus} PDB: 3ukx_B 3uky_B 3ukz_B 3ukw_B 3ul0_B 3oqs_A 3rz9_A 3rzx_A 3uvu_A 1q1s_C 1q1t_C 3knd_A 1ejy_I 1iq1_C 1ejl_I 1pjn_B 1pjm_B 3q5u_A 3fey_C 3fex_C ...
Probab=1.00 E-value=1 Score=21.30 Aligned_cols=54 Identities=13% Similarity=0.068 Sum_probs=22.6
Q ss_pred HHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHCCHHHHHHHHHHHCCHHHHHHHH
Q ss_conf 577999999722453212111010367999998238035788998760835478999
Q 000530 94 YDGVEKLVQLMVPERNDKKIDLVCRSLLAGVVAATDKFDCLNWFVQLRGLLVFDEWL 150 (1440)
Q Consensus 94 ~e~V~klV~LM~~~~~~kki~La~R~~l~~Vi~~T~~qd~L~rFvql~Gl~vL~eWL 150 (1440)
.-.|+.||++++...+. .+...- +..+.-|+ +...+....+++.++++.|-..|
T Consensus 99 ~G~ip~LV~lL~~~~~~-~lq~~A-a~aL~nia-s~~~e~~~~vv~~GaIp~Lv~lL 152 (510)
T 3ul1_B 99 AGLIPKFVSFLGKTDCS-PIQFES-AWALTNIA-SGTSEQTKAVVDGGAIPAFISLL 152 (510)
T ss_dssp TTHHHHHHHHTTCTTCH-HHHHHH-HHHHHHHH-TSCHHHHHHHHHTTHHHHHHHHT
T ss_pred CCCHHHHHHHHCCCCCH-HHHHHH-HHHHHHHH-CCCHHHHHHHHHCCCHHHHHHHH
T ss_conf 88889999987789989-999999-99999996-49999999999788799999988
No 9
>4b8j_A Importin subunit alpha-1A; transport protein, nuclear localization signal; 2.00A {Oryza sativa japonica group} PDB: 4b8o_A 2yns_A 4b8p_A
Probab=1.00 E-value=1 Score=19.55 Aligned_cols=112 Identities=8% Similarity=0.040 Sum_probs=50.7
Q ss_pred CHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHCCHHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCHH
Q ss_conf 45779999997224532121110103679999982380357889987608354789999985136689999999999728
Q 000530 93 DYDGVEKLVQLMVPERNDKKIDLVCRSLLAGVVAATDKFDCLNWFVQLRGLLVFDEWLQEVHKGKIGDAGSPRDGDKSVE 172 (1440)
Q Consensus 93 ~~e~V~klV~LM~~~~~~kki~La~R~~l~~Vi~~T~~qd~L~rFvql~Gl~vL~eWLqEa~Kgk~Gd~~sP~~~dks~e 172 (1440)
..+.++.||.++.... . .+.+.. +..+.-+......+....+++.++++.|-+.|+.-. +...-
T Consensus 72 ~~~~l~~lv~~L~s~~-~-~~~~~A-~~~L~~l~s~~~~~~~~~~~~~g~v~~Lv~lL~~~~-------------~~~v~ 135 (528)
T 4b8j_A 72 KLESLPAMIGGVYSDD-N-NLQLEA-TTQFRKLLSIERSPPIEEVIQSGVVPRFVQFLTRED-------------FPQLQ 135 (528)
T ss_dssp ---CHHHHHHHHTSSC-H-HHHHHH-HHHHHHHHTCSSSCCHHHHHHTTCHHHHHHHHTCTT-------------CHHHH
T ss_pred HHHHHHHHHHHHCCCC-H-HHHHHH-HHHHHHHHCCCCCCHHHHHHHCCCHHHHHHHHCCCC-------------CHHHH
T ss_conf 6778999999876999-9-999999-999999814777962999998887999999847899-------------78999
Q ss_pred HHHHHHHHHHCCC-CCCHHHHHH-CCCCCCCCCCCCCCCHHHHHHHHHHHH
Q ss_conf 9999999983189-985876520-588742233458888899999999999
Q 000530 173 EFLLILLRALDKL-PVNLNALQM-CNIGKSVNHLRTHKNVEIQKKARSLVD 221 (1440)
Q Consensus 173 e~lLeLLraLkkL-PITveiLks-T~IGKtVNkLRKH~neEI~kLAk~LVk 221 (1440)
...+.+|..|... +-....+.. .-|...+.-|+. .+.+|+..|...+.
T Consensus 136 ~~A~~~L~~l~~~~~~~~~~~~~~g~i~~L~~lL~~-~~~~v~~~a~~aL~ 185 (528)
T 4b8j_A 136 FEAAWALTNIASGTSENTKVVIDHGAVPIFVKLLGS-SSDDVREQAVWALG 185 (528)
T ss_dssp HHHHHHHHHHHTSCHHHHHHHHHTTHHHHHHHHTTC-SCHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHCCCHHHHHHHHCC-CCHHHHHHHHHHHH
T ss_conf 999999999967998879999968867899988569-99999999999999
No 10
>4db6_A Armadillo repeat protein; solenoid repeat, armadillo repeat motif, de novo protein; 1.80A {Synthetic construct} PDB: 4db9_A 4dba_A
Probab=1.00 E-value=1 Score=15.04 Aligned_cols=52 Identities=13% Similarity=0.183 Sum_probs=25.8
Q ss_pred HHHHHHHHHHHCCCCCCCCCCCCHHH-HHHHHHHHCCHHHHHHHHHHHCCHHHHHHHH
Q ss_conf 57799999972245321211101036-7999998238035788998760835478999
Q 000530 94 YDGVEKLVQLMVPERNDKKIDLVCRS-LLAGVVAATDKFDCLNWFVQLRGLLVFDEWL 150 (1440)
Q Consensus 94 ~e~V~klV~LM~~~~~~kki~La~R~-~l~~Vi~~T~~qd~L~rFvql~Gl~vL~eWL 150 (1440)
..+++.|++++.... .. +...+ ..+.-| +....+....+++.++++.|-..|
T Consensus 53 ~g~i~~L~~lL~~~~--~~--v~~~a~~~L~~l-~~~~~~~~~~i~~~g~i~~L~~lL 105 (210)
T 4db6_A 53 AGALPALVQLLSSPN--EQ--ILQEALWALSNI-ASGGNEQIQAVIDAGALPALVQLL 105 (210)
T ss_dssp TTHHHHHHHHTTCSC--HH--HHHHHHHHHHHH-TTSCHHHHHHHHHTTCHHHHHHHT
T ss_pred CCCHHHHHHHHCCCC--HH--HHHHHHHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 487799999986998--87--999999999998-569928999999888888999998
Done!