Query 000632
Match_columns 1381
No_of_seqs 99 out of 101
Neff 3.4
Searched_HMMs 29240
Date Tue Mar 26 17:38:23 2013
Command hhsearch -i /local_scratch/syshi/lefta3m/000632.a3m -d /local_scratch/syshi/pdb70.hhm -v 0 -o /local_scratch/syshi/H1_403-407//hhsearch_pdb/000632hhsearch_pdb
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 1wjt_A Transcription elongatio 1.0 1 1 98.2 2.5 58 148-205 30-90 (103)
2 1pqv_S STP-alpha, transcriptio 1.0 1 1 93.4 7.0 61 148-208 20-83 (309)
3 2xpp_A IWS1, ECU08_0440; trans 1.0 1 1 59.4 6.6 123 71-204 8-141 (145)
4 3nfq_A Transcription factor IW 1.0 1 1 57.6 5.1 97 95-202 54-154 (170)
5 3tpo_A Importin subunit alpha- 1.0 1 1 29.1 4.5 25 103-127 105-129 (529)
6 3ul1_B Importin subunit alpha- 1.0 1 1 27.1 4.9 20 107-126 133-152 (510)
7 2b4j_C PC4 and SFRS1 interacti 1.0 1 1 26.2 4.2 58 148-205 26-88 (98)
8 1z9e_A PC4 and SFRS1 interacti 1.0 1 1 26.0 3.4 57 148-204 26-87 (127)
9 4b8j_A Importin subunit alpha- 1.0 1 1 20.0 4.8 109 69-194 72-184 (528)
10 3clj_A Protein NRD1; CTD-inter 1.0 1 1 16.8 5.7 74 115-205 58-137 (157)
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=98.18 Aligned_cols=58 Identities=26% Similarity=0.430 Sum_probs=55.1
Q ss_pred HHHHHHHHHHHHCCCCCHHHHHHCCC--CCCCCCCC-CCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 31489999975118762544621373--01012467-889999999998999788655433
Q 000632 148 EEFPLVSLRALDKLPVNLHALQMGNM--FVNHLRTH-KNLEIQKKARSLVDTWKKRVEAEM 205 (1381)
Q Consensus 148 ee~ll~LLrAL~kLPIdle~Lkst~I--tVn~LRkh-kn~EIqk~Ak~LvdsWKk~V~aE~ 205 (1381)
++.++++|+.|+++||++++|++|+| +||.||+| .|.+|+++|+.||+.||+.|+.++
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=93.45 Aligned_cols=61 Identities=20% Similarity=0.373 Sum_probs=57.2
Q ss_pred HHHHHHHHHHH-HCCCCCHHHHHHCCC--CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 31489999975-118762544621373--01012467889999999998999788655433204
Q 000632 148 EEFPLVSLRAL-DKLPVNLHALQMGNM--FVNHLRTHKNLEIQKKARSLVDTWKKRVEAEMNAK 208 (1381)
Q Consensus 148 ee~ll~LLrAL-~kLPIdle~Lkst~I--tVn~LRkhkn~EIqk~Ak~LvdsWKk~V~aE~~aK 208 (1381)
++.++++|+.| +.+||++++|++|+| +||.||+|++.+|+++|+.||+.||+.|..+...+
T Consensus 20 ~~~~l~~L~~L~~~~~it~~~L~~T~IG~~Vn~lrkh~~~~v~~~Ak~Li~~WK~~v~~~~~~~ 83 (309)
T 1pqv_S 20 DAAVLEILHVLDKEFVPTEKLLRETKVGVEVNKFKKSTNVEISKLVKKMISSWKDAINKNKRSR 83 (309)
T ss_pred HHHHHHHHHHHHHCCCCCHHHHHHCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf 8999999999876389889999748756999988738978999999999999999877750577
No 3
>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=59.38 Aligned_cols=123 Identities=14% Similarity=0.132 Sum_probs=90.9
Q ss_pred HHHHHHHHHHCCCCCC-------CCCCCCCHHHHHHHHHHCCCHHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCCCCCCC
Q ss_conf 6589999974358423-------432311025778888730450245466450680439999999841655899999999
Q 000632 71 EGVEKFIQLMVPDRNE-------RKIDLVCRSMLAGVVAAADKFDCLSKFVQVKGLHVFDEWLQEVHKGKIGDGSNPKDG 143 (1381)
Q Consensus 71 e~V~kLV~LM~~~~~~-------kk~~l~~R~~la~vIaaTes~DcL~~FVql~GL~vLd~WLqea~kGk~g~~~~p~~~ 143 (1381)
+.+..|+.-|..--.. ++-.+.-.-||-.|.+.-.+.+.-..|+..+-|.+|..||.-.-. |+-|
T Consensus 8 ~~~~~l~~~M~~Aa~~D~~a~~~~~PA~~KlklL~~V~~~l~k~~l~~~~ld~giL~~l~~WL~PLpD-----gsLP--- 79 (145)
T 2xpp_A 8 EISRSLKKRMQDILKKDNANNLEGRPATGKIENVEEISDILMSKALQESLLDEGILDEIKGWLEPLPD-----KSMP--- 79 (145)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHTSCCCHHHHHHHHHHHHHTCTTTHHHHHHTTHHHHHHHHHSCCTT-----SCCC---
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHCCCCC-----CCCC---
T ss_conf 99999999999999999998776985889996599999997348999999885779999998182999-----9999---
Q ss_pred CCHHHHHHHHHHHHHHCCCCCHHHHHHCCC--CCCCCCCC--CCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 930131489999975118762544621373--01012467--88999999999899978865543
Q 000632 144 DKAIEEFPLVSLRALDKLPVNLHALQMGNM--FVNHLRTH--KNLEIQKKARSLVDTWKKRVEAE 204 (1381)
Q Consensus 144 dk~vee~ll~LLrAL~kLPIdle~Lkst~I--tVn~LRkh--kn~EIqk~Ak~LvdsWKk~V~aE 204 (1381)
--..-..||++|..|||+.++|+.++| .|.-|.+| +..+++++|+.||+.|..-|-..
T Consensus 80 ---~~~Ir~~lL~~L~~lPI~~e~Lk~SglGkvv~~l~k~~~et~~nk~la~~Li~~WsRpi~~~ 141 (145)
T 2xpp_A 80 ---NIKIRKRLLDVLKTMKIHKEHLVTSGVGKIVYFYSINPKESKEVRASAKALVQKWTNEVFKP 141 (145)
T ss_dssp ---CHHHHHHHHHHHHTSCCCHHHHHHHCHHHHHHHHHHCTTSCHHHHHHHHHHHHHHHHHHTC-
T ss_pred ---CHHHHHHHHHHHHHCCCCHHHHHCCCCCCCHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHCC
T ss_conf ---78999999999997899999830389780115565499537899999999999987877377
No 4
>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=57.58 Aligned_cols=97 Identities=23% Similarity=0.369 Sum_probs=78.7
Q ss_pred HHHHHHHHHCCCHHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHCCC-
Q ss_conf 5778888730450245466450680439999999841655899999999930131489999975118762544621373-
Q 000632 95 SMLAGVVAAADKFDCLSKFVQVKGLHVFDEWLQEVHKGKIGDGSNPKDGDKAIEEFPLVSLRALDKLPVNLHALQMGNM- 173 (1381)
Q Consensus 95 ~~la~vIaaTes~DcL~~FVql~GL~vLd~WLqea~kGk~g~~~~p~~~dk~vee~ll~LLrAL~kLPIdle~Lkst~I- 173 (1381)
.||-.|+..-.+.+.-..|+..+.|.+|..||.-.-. |+-| -...-.+||++|.+|||+.++|+.++|
T Consensus 54 kmL~~V~~~L~k~~L~~~~ld~giL~~l~~WLePLpD-----gSLP------~~~Ir~~lL~~L~~lPI~~e~Lk~SglG 122 (170)
T 3nfq_A 54 KLLPKVVSVLSKANLADTILDNNLLQSVRIWLEPLPD-----GSLP------SFEIQKSLFAALNDLPVKTEHLKESGLG 122 (170)
T ss_dssp HHHHHHHHHHTCGGGHHHHHHTTHHHHHHHHHSCCTT-----SCCC------CHHHHHHHHHHHHTSCCCHHHHHHHSHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHCCCCC-----CCCC------CHHHHHHHHHHHHHCCCCHHHHHHCCCC
T ss_conf 5189999998278899999874659999998275889-----9998------5799999999999789999997627978
Q ss_pred -CCCCCCCCC--CHHHHHHHHHHHHHHHHHHH
Q ss_conf -010124678--89999999998999788655
Q 000632 174 -FVNHLRTHK--NLEIQKKARSLVDTWKKRVE 202 (1381)
Q Consensus 174 -tVn~LRkhk--n~EIqk~Ak~LvdsWKk~V~ 202 (1381)
.|.-|.+|+ ..+++++|+.||+.|..-|-
T Consensus 123 kvV~~l~k~~~et~~nkrla~~Li~~WsRpI~ 154 (170)
T 3nfq_A 123 RVVIFYTKSKRVEAQLARLAEKLIAEWTRPII 154 (170)
T ss_dssp HHHHHHHHCTTSCHHHHHHHHHHHHHHTCCCC
T ss_pred CEEEEHHCCCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf 23200115985367899999999999889985
No 5
>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=29.08 Aligned_cols=25 Identities=12% Similarity=0.204 Sum_probs=15.1
Q ss_pred HCCCHHHHHHHHHCCCHHHHHHHHH
Q ss_conf 3045024546645068043999999
Q 000632 103 AADKFDCLSKFVQVKGLHVFDEWLQ 127 (1381)
Q Consensus 103 aTes~DcL~~FVql~GL~vLd~WLq 127 (1381)
..+.....+.+|+.++++.|=+.|+
T Consensus 105 s~~~~~~i~~ii~~G~ip~Lv~lL~ 129 (529)
T 3tpo_A 105 SREKQPPIDNIIRAGLIPKFVSFLG 129 (529)
T ss_dssp TSSSCCCHHHHHHTTHHHHHHHHHT
T ss_pred CCCCCCHHHHHHHCCCHHHHHHHHC
T ss_conf 2789844999998889999999876
No 6
>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=27.13 Aligned_cols=20 Identities=15% Similarity=0.084 Sum_probs=8.5
Q ss_pred HHHHHHHHHCCCHHHHHHHH
Q ss_conf 02454664506804399999
Q 000632 107 FDCLSKFVQVKGLHVFDEWL 126 (1381)
Q Consensus 107 ~DcL~~FVql~GL~vLd~WL 126 (1381)
.+.-...++.++++.|-.-|
T Consensus 133 ~e~~~~vv~~GaIp~Lv~lL 152 (510)
T 3ul1_B 133 SEQTKAVVDGGAIPAFISLL 152 (510)
T ss_dssp HHHHHHHHHTTHHHHHHHHT
T ss_pred HHHHHHHHHCCCHHHHHHHH
T ss_conf 99999999788799999988
No 7
>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=26.19 Aligned_cols=58 Identities=19% Similarity=0.182 Sum_probs=50.3
Q ss_pred HHHHHHHHHHHHCCCCCHHHHHHCCC---CCCCCCC-CCCHHHHHHHHHHHHHHHHHHH-HHH
Q ss_conf 31489999975118762544621373---0101246-7889999999998999788655-433
Q 000632 148 EEFPLVSLRALDKLPVNLHALQMGNM---FVNHLRT-HKNLEIQKKARSLVDTWKKRVE-AEM 205 (1381)
Q Consensus 148 ee~ll~LLrAL~kLPIdle~Lkst~I---tVn~LRk-hkn~EIqk~Ak~LvdsWKk~V~-aE~ 205 (1381)
-.-++++|.-|.+|+++.-.|+.+-- |+.+||. ..+..|+++|..++++.|.++. +|-
T Consensus 26 v~kcl~~L~~l~~l~~T~~mL~rnpe~V~t~kklRry~g~q~Ir~kA~~iY~kfK~~f~~~eg 88 (98)
T 2b4j_C 26 VNRCIEALDELASLQVTMQQAQKHTEMITTLKKIRRFKVSQVIMEKSTMLYNKFKNMFLVGEG 88 (98)
T ss_dssp HHHHHHHHHHHHTCCCCHHHHHTTHHHHHHHHHHTTCTTCHHHHHHHHHHHHHHHHC------
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf 999999999870243349988239099999999999833099999999999999999746888
No 8
>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=25.95 Aligned_cols=57 Identities=19% Similarity=0.206 Sum_probs=50.0
Q ss_pred HHHHHHHHHHHHCCCCCHHHHHHCCC---CCCCCCC-CCCHHHHHHHHHHHHHHHHHHH-HH
Q ss_conf 31489999975118762544621373---0101246-7889999999998999788655-43
Q 000632 148 EEFPLVSLRALDKLPVNLHALQMGNM---FVNHLRT-HKNLEIQKKARSLVDTWKKRVE-AE 204 (1381)
Q Consensus 148 ee~ll~LLrAL~kLPIdle~Lkst~I---tVn~LRk-hkn~EIqk~Ak~LvdsWKk~V~-aE 204 (1381)
-.-++.+|.-|..|+|+.-.|+.+-- |+..||. ..|..|+++|..|+++.|.++. +|
T Consensus 26 v~kCl~~Leel~~l~vT~~mL~Rnpe~V~TlkklRrY~gnq~Ir~kA~~iY~kFK~lf~~ge 87 (127)
T 1z9e_A 26 VNRCIEALDELASLQVTMQQAQKHTEMITTLKKIRRFKVSQVIMEKSTMLYNKFKNMFLVGE 87 (127)
T ss_dssp HHHHHHHHHHHHHSCCCHHHHGGGHHHHHHHHHHTTCTTCSSHHHHHHHHHHHHHHHHHC--
T ss_pred HHHHHHHHHHHCCCCCCHHHHHHCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCC
T ss_conf 99999999987124234998823809999999999972549999999999999999984689
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=20.01 Aligned_cols=109 Identities=13% Similarity=0.118 Sum_probs=51.8
Q ss_pred CHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHCCCHHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCHHH
Q ss_conf 83658999997435842343231102577888873045024546645068043999999984165589999999993013
Q 000632 69 DFEGVEKFIQLMVPDRNERKIDLVCRSMLAGVVAAADKFDCLSKFVQVKGLHVFDEWLQEVHKGKIGDGSNPKDGDKAIE 148 (1381)
Q Consensus 69 ~~e~V~kLV~LM~~~~~~kk~~l~~R~~la~vIaaTes~DcL~~FVql~GL~vLd~WLqea~kGk~g~~~~p~~~dk~ve 148 (1381)
..+.++.|+.+++.+..+ +.+.. +..+.-++..+..+....+++.++++.|-+.|+... +..+-
T Consensus 72 ~~~~l~~lv~~L~s~~~~--~~~~A-~~~L~~l~s~~~~~~~~~~~~~g~v~~Lv~lL~~~~-------------~~~v~ 135 (528)
T 4b8j_A 72 KLESLPAMIGGVYSDDNN--LQLEA-TTQFRKLLSIERSPPIEEVIQSGVVPRFVQFLTRED-------------FPQLQ 135 (528)
T ss_dssp ---CHHHHHHHHTSSCHH--HHHHH-HHHHHHHHTCSSSCCHHHHHHTTCHHHHHHHHTCTT-------------CHHHH
T ss_pred HHHHHHHHHHHHCCCCHH--HHHHH-HHHHHHHHCCCCCCHHHHHHHCCCHHHHHHHHCCCC-------------CHHHH
T ss_conf 677899999987699999--99999-999999814777962999998887999999847899-------------78999
Q ss_pred HHHHHHHHHHHCC-CCCHHHHHHCCC---CCCCCCCCCCHHHHHHHHHHH
Q ss_conf 1489999975118-762544621373---010124678899999999989
Q 000632 149 EFPLVSLRALDKL-PVNLHALQMGNM---FVNHLRTHKNLEIQKKARSLV 194 (1381)
Q Consensus 149 e~ll~LLrAL~kL-PIdle~Lkst~I---tVn~LRkhkn~EIqk~Ak~Lv 194 (1381)
..++..|..|..- +-....+...++ .+..| .+.+.+|+..|-..+
T Consensus 136 ~~A~~~L~~l~~~~~~~~~~~~~~g~i~~L~~lL-~~~~~~v~~~a~~aL 184 (528)
T 4b8j_A 136 FEAAWALTNIASGTSENTKVVIDHGAVPIFVKLL-GSSSDDVREQAVWAL 184 (528)
T ss_dssp HHHHHHHHHHHTSCHHHHHHHHHTTHHHHHHHHT-TCSCHHHHHHHHHHH
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHCCCHHHHHHHH-CCCCHHHHHHHHHHH
T ss_conf 9999999999679988799999688678999885-699999999999999
No 10
>3clj_A Protein NRD1; CTD-interacting domain, nucleus, phosphoprotein, RNA polymer binding protein, RNA binding protein; 2.10A {Saccharomyces cerevisiae}
Probab=1.00 E-value=1 Score=16.80 Aligned_cols=74 Identities=15% Similarity=0.303 Sum_probs=41.2
Q ss_pred HCCCHHHHHH----HHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHCCCCCCCCCCCCCHHHHHHH
Q ss_conf 5068043999----999984165589999999993013148999997511876254462137301012467889999999
Q 000632 115 QVKGLHVFDE----WLQEVHKGKIGDGSNPKDGDKAIEEFPLVSLRALDKLPVNLHALQMGNMFVNHLRTHKNLEIQKKA 190 (1381)
Q Consensus 115 ql~GL~vLd~----WLqea~kGk~g~~~~p~~~dk~vee~ll~LLrAL~kLPIdle~Lkst~ItVn~LRkhkn~EIqk~A 190 (1381)
+|.||-|+|. |+.++++ .|+. .+.+-..+.-.+-+ +.. .++. +++.+-...+++.+.+-
T Consensus 58 KL~~LYVvDSIvR~~~~~~~k--~g~~-----~~a~~gt~a~~v~~-~~e---~i~~------l~~~~~~~~~~~~k~Ki 120 (157)
T 3clj_A 58 KLGSLYIIDSIGRAYLDETRS--NSNS-----SSNKPGTCAHAINT-LGE---VIQE------LLSDAIAKSNQDHKEKI 120 (157)
T ss_dssp HHHHHHHHHHHHHHHHHHHHT--CCC---------STTSHHHHHHH-HHH---HHHH------HHHHHHHHSCHHHHHHH
T ss_pred EEEEEEEHHHHHHHHHHHHHH--CCCC-----CCCCCCCHHHHHHH-HHH---HHHH------HHHHHHHCCCHHHHHHH
T ss_conf 100231228999999999875--2776-----67888617899999-999---9999------99999974999899999
Q ss_pred HHHHHHHHHH--HHHHH
Q ss_conf 9989997886--55433
Q 000632 191 RSLVDTWKKR--VEAEM 205 (1381)
Q Consensus 191 k~LvdsWKk~--V~aE~ 205 (1381)
+.|++-|.+. ...|+
T Consensus 121 ~klldiW~k~~~Fp~e~ 137 (157)
T 3clj_A 121 RMLLDIWDRSGLFQKSY 137 (157)
T ss_dssp HHHHHHHHHHTTTTTSC
T ss_pred HHHHHHHCCCCCCCHHH
T ss_conf 99999970679899899
Done!