Query 028639
Match_columns 206
No_of_seqs 121 out of 187
Neff 4.3
Searched_HMMs 29240
Date Tue Mar 26 00:39:36 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028639.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/028639hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 3h0g_D DNA-directed RNA polyme 100.0 1.8E-37 6.3E-42 249.5 9.0 110 91-203 4-113 (135)
2 2c35_A Human RPB4, DNA-directe 100.0 4.2E-33 1.4E-37 227.5 11.4 113 88-203 18-130 (152)
3 3hou_D DNA-directed RNA polyme 100.0 4.3E-29 1.5E-33 214.5 10.6 114 90-203 17-200 (221)
4 1go3_F DNA-directed RNA polyme 99.9 5.7E-25 1.9E-29 170.5 8.5 90 102-202 2-91 (107)
5 1y14_A B32, RPB4, DNA-directed 99.9 1.4E-24 4.8E-29 183.2 8.8 66 138-203 101-166 (187)
6 4ayb_F DNA-directed RNA polyme 99.8 1.8E-22 6.1E-27 157.6 -2.3 86 109-204 8-93 (113)
7 3ayh_A DNA-directed RNA polyme 99.5 7.6E-15 2.6E-19 117.4 4.6 97 108-204 13-118 (136)
8 2ckz_A DNA-directed RNA polyme 99.3 5.7E-13 1.9E-17 109.8 3.0 96 109-204 7-144 (161)
9 3k4g_A DNA-directed RNA polyme 27.2 63 0.0022 23.6 3.7 38 137-175 32-69 (86)
10 1jw2_A Hemolysin expression mo 25.8 42 0.0014 24.1 2.5 33 147-180 8-40 (72)
11 1yse_A DNA-binding protein SAT 23.5 52 0.0018 26.4 2.9 55 140-194 4-59 (141)
12 2czy_A Paired amphipathic heli 23.2 1.9E+02 0.0065 20.1 5.5 53 113-173 2-56 (77)
13 3kev_A Galieria sulfuraria DCU 22.0 28 0.00095 29.0 1.0 59 144-204 26-90 (199)
14 1g1e_B SIN3A; four-helix bundl 20.4 1.6E+02 0.0056 21.1 4.8 39 109-155 4-42 (89)
No 1
>3h0g_D DNA-directed RNA polymerase II subunit RPB4; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}
Probab=100.00 E-value=1.8e-37 Score=249.47 Aligned_cols=110 Identities=23% Similarity=0.292 Sum_probs=100.2
Q ss_pred cccccCccccccCcccccccccccHHHHHHHHHHHHHHHhhhcCCCCCCchHHHHHHHHHHHhcCCCCCHHHHHHHHHHH
Q 028639 91 VVKEALPLELRVEQELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSL 170 (206)
Q Consensus 91 ~~~eEdaaeLkLG~eF~ena~cLslsEV~lILe~~~e~~~~~s~d~~~~~s~vf~KTleYv~rFSkfkn~Esv~aVRelL 170 (206)
+++||||++|+||+||+ |++|||||||++||+.++++++. ...+..+++.+|+||++|+++|+||++++++.+||++|
T Consensus 4 ~~~ee~a~~L~lg~eF~-~a~~Ls~sEv~~lL~~~~~~r~~-~~~~~~~~~~v~~kTl~Yl~~Fsk~~~~e~~~~v~~lL 81 (135)
T 3h0g_D 4 AIFEEDAAQLKLGPEFE-NEDMLTVSEAKILIETVLAQRAR-ETNGEIPMTDVMKKTVAYFNVFARFKTAEATYACERIL 81 (135)
T ss_dssp --CCCCCTTTCSCHHHH-HSCBCCHHHHHHHHHHHHHHHHT-TCCSCCCCTTHHHHHHHHHHTTCTTCSHHHHHHHHHHC
T ss_pred hHHHHhHHhhCCCHhhc-CcccccHHHHHHHHHHHHHHHHh-cccCCcchhHHHHHHHHHHHHccCCCCHHHHHHHHHHH
Confidence 67999999999999998 99999999999999999887642 12345678899999999999999999999999999999
Q ss_pred HhCCCCcchhhhhhccCCCCHHHHHHhhccccc
Q 028639 171 SEHGVTDGEICVIANICPETVEEAYAIVPSLKV 203 (206)
Q Consensus 171 ~~~gL~kFEIAqLaNLcPeTaEEAKALIPSL~~ 203 (206)
.. +||+||+|||+||||+|+||||+|||||++
T Consensus 82 ~~-~L~~fEia~L~NL~P~t~dEak~LIpsL~~ 113 (135)
T 3h0g_D 82 GN-RFHKFERAQLGTLCCEDAEEARTLIPSLAN 113 (135)
T ss_dssp CC-CSCHHHHHHHHHHCCCCHHHHHHHCGGGTT
T ss_pred Hh-cCCHHHHHHHccCCCCCHHHHHHHHHHhcc
Confidence 99 999999999999999999999999999985
No 2
>2c35_A Human RPB4, DNA-directed RNA polymerase II 16 kDa polypeptide; transcription, nucleotidyltransferase; 2.70A {Homo sapiens} SCOP: a.60.8.2
Probab=100.00 E-value=4.2e-33 Score=227.51 Aligned_cols=113 Identities=28% Similarity=0.380 Sum_probs=100.5
Q ss_pred CcccccccCccccccCcccccccccccHHHHHHHHHHHHHHHhhhcCCCCCCchHHHHHHHHHHHhcCCCCCHHHHHHHH
Q 028639 88 KVSVVKEALPLELRVEQELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLF 167 (206)
Q Consensus 88 k~~~~~eEdaaeLkLG~eF~ena~cLslsEV~lILe~~~e~~~~~s~d~~~~~s~vf~KTleYv~rFSkfkn~Esv~aVR 167 (206)
+..+.+||||++|+||++|. |++|||||||++||+++++++. ..++..+++++|++||+|+++|++|++++++++|+
T Consensus 18 ~~~~~~ee~a~~l~~gkef~-~~~~Lt~sEV~~lL~~~~~~~~--~~~~~~els~v~~kTl~Yl~~F~k~k~~e~~~~l~ 94 (152)
T 2c35_A 18 PRAGDVEEDASQLIFPKEFE-TAETLLNSEVHMLLEHRKQQNE--SAEDEQELSEVFMKTLNYTARFSRFKNRETIASVR 94 (152)
T ss_dssp ------CCBGGGTBCCSSSS-SCEECCHHHHHHHHHHHHHHHH--SSCSSCCCCHHHHHHHHHHHHTCSCCSHHHHHHHH
T ss_pred CCCCCccccHHHHhcchhhc-ccccccHHHHHHHHHHHHHhhc--ccccccchHHHHHHHHHHHHHccCCCCHHHHHHHH
Confidence 55677999999999999998 9999999999999999987653 34566788999999999999999999999999999
Q ss_pred HHHHhCCCCcchhhhhhccCCCCHHHHHHhhccccc
Q 028639 168 QSLSEHGVTDGEICVIANICPETVEEAYAIVPSLKV 203 (206)
Q Consensus 168 elL~~~gL~kFEIAqLaNLcPeTaEEAKALIPSL~~ 203 (206)
++|..++||+||+|+|+||||+|+||||+|||||+.
T Consensus 95 e~L~~~~L~~~E~a~L~NL~P~t~dEar~lipsl~~ 130 (152)
T 2c35_A 95 SLLLQKKLHKFELACLANLCPETAEESKALIPSLEG 130 (152)
T ss_dssp HHHHTSSCCHHHHHHHHHHCCSSHHHHHHHCGGGTT
T ss_pred HHHHhcCCCHHHHHHhccCCCCCHHHHHHHHHhhcc
Confidence 999999999999999999999999999999999974
No 3
>3hou_D DNA-directed RNA polymerase II subunit RPB4; RNA polymerase II, metal-binding, transcription bubble; HET: BRU; 3.20A {Saccharomyces cerevisiae} PDB: 1nt9_D 1y1w_D 1y1y_D 1y77_D* 2b63_D* 2b8k_D 2ja5_D* 2ja6_D* 2ja7_D* 2ja8_D* 2r7z_D 2r92_D 2r93_D 1y1v_D* 3fki_D 3h3v_E 2vum_D* 3hov_D* 3how_D* 3hox_D* ...
Probab=99.96 E-value=4.3e-29 Score=214.52 Aligned_cols=114 Identities=22% Similarity=0.268 Sum_probs=95.9
Q ss_pred ccccccCccccccCcccc----------cccccccHHHHHHHHHHHHH-HHhh--hc-----------------------
Q 028639 90 SVVKEALPLELRVEQELP----------KNAKCLMDCEAAHILEGIQE-QMAL--LS----------------------- 133 (206)
Q Consensus 90 ~~~~eEdaaeLkLG~eF~----------ena~cLslsEV~lILe~~~e-~~~~--~s----------------------- 133 (206)
-.++||+|+.|+||+||+ +...+|++||+++|+..... +++. .+
T Consensus 17 ~~~~eenaa~l~lg~efql~q~~~~g~~~~lialnlsearl~i~~al~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 96 (221)
T 3hou_D 17 KVEEEENAATLQLGQEFQLKQINHQGEEEELIALNLSEARLVIKEALVERRRAFKRSQKKHKKKHLKHENANDETTAVED 96 (221)
T ss_dssp CCCCCCCCSSSCCCGGGCSEEECTTSCEEECCBCCTTHHHHHHHHHHHHHHHHHHHTTCC--------------------
T ss_pred cccchhhhHHhhcCcccceeecccCCchhHhHhhhhHHHHHHHHHHHHHHHHHhhccccccccccccccccccccccccc
Confidence 357999999999999999 56779999999999965422 2110 00
Q ss_pred ------------CCC----------------------CCCchHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCCcch
Q 028639 134 ------------ADP----------------------TIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDGE 179 (206)
Q Consensus 134 ------------~d~----------------------~~~~s~vf~KTleYv~rFSkfkn~Esv~aVRelL~~~gL~kFE 179 (206)
.+. ....+.||+|||+||++|+||++++++.+||++|..++||+||
T Consensus 97 ~~~~~~~~~~~~~~~~~~~~~~~e~e~~~~~~~~~~~~g~~seVf~KTLdYl~rFSKfkn~EAv~aVrELL~~~gLheFE 176 (221)
T 3hou_D 97 EDDDLDEDDVNADDDDFMHSETREKELESIDVLLEQTTGGNNKDLKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFE 176 (221)
T ss_dssp ---------------------CTHHHHHHHHHHHHHHSCSCCHHHHHHHHHHHHSCSCCCHHHHHHHHHHHTTSCCCHHH
T ss_pred ccccccccccccccchhhhccchHHHHHHHHHHHhhcCCCccHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHhcCCChHH
Confidence 000 1145789999999999999999999999999999999999999
Q ss_pred hhhhhccCCCCHHHHHHhhccccc
Q 028639 180 ICVIANICPETVEEAYAIVPSLKV 203 (206)
Q Consensus 180 IAqLaNLcPeTaEEAKALIPSL~~ 203 (206)
+|+||||||+|+||||+|||||..
T Consensus 177 iAqLANLcPeTaDEARALIPSL~~ 200 (221)
T 3hou_D 177 VAQLGSLACDTADEAKTLIPSLNN 200 (221)
T ss_dssp HHHHHHSCCCSHHHHHHHCTTCTT
T ss_pred hheecccCCCCHHHHHHHHHhhcc
Confidence 999999999999999999999984
No 4
>1go3_F DNA-directed RNA polymerase subunit F; transferase, transferase, transcription; 1.75A {Methanococcus jannaschii} SCOP: a.60.8.2
Probab=99.91 E-value=5.7e-25 Score=170.46 Aligned_cols=90 Identities=19% Similarity=0.266 Sum_probs=79.9
Q ss_pred cCcccccccccccHHHHHHHHHHHHHHHhhhcCCCCCCchHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCCcchhh
Q 028639 102 VEQELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEIC 181 (206)
Q Consensus 102 LG~eF~ena~cLslsEV~lILe~~~e~~~~~s~d~~~~~s~vf~KTleYv~rFSkfkn~Esv~aVRelL~~~gL~kFEIA 181 (206)
+|.+|. +.+|||+|||+.||+++.+. .++++++++|++|+++|+|| +++.+.++++.|.+.+||+||+|
T Consensus 2 i~kei~-~~~~lt~sEa~~iL~~~~~~---------~e~s~~~~ktl~y~~kFsk~-~~e~a~~l~e~L~~~~l~e~~a~ 70 (107)
T 1go3_F 2 IGKKIL-GERYVTVSEAAEIMYNRAQI---------GELSYEQGCALDYLQKFAKL-DKEEAKKLVEELISLGIDEKTAV 70 (107)
T ss_dssp CSSEEE-EEEEECHHHHHHHHHHHHHH---------SCCCHHHHHHHHHHHHHCCS-CHHHHHHHHHHHHHTTCCHHHHH
T ss_pred chHHHh-cccccCHHHHHHHHHHHHhc---------ccccHHHHHHHHHHHHHhCC-CHHHHHHHHHHHHhCCCCHHHHH
Confidence 456787 99999999999999987653 35779999999999999999 57777777777778889999999
Q ss_pred hhhccCCCCHHHHHHhhcccc
Q 028639 182 VIANICPETVEEAYAIVPSLK 202 (206)
Q Consensus 182 qLaNLcPeTaEEAKALIPSL~ 202 (206)
+|+||||+|+||||+||||+.
T Consensus 71 ~I~nl~P~t~dElraii~~~~ 91 (107)
T 1go3_F 71 KIADILPEDLDDLRAIYYKRE 91 (107)
T ss_dssp HHHHHCCCSHHHHHHHSTTSC
T ss_pred HHHHhCCCCHHHHHHHHhccc
Confidence 999999999999999999985
No 5
>1y14_A B32, RPB4, DNA-directed RNA polymerase II 32 kDa polypeptide; transferase; 2.30A {Saccharomyces cerevisiae} SCOP: a.60.8.2
Probab=99.91 E-value=1.4e-24 Score=183.21 Aligned_cols=66 Identities=21% Similarity=0.341 Sum_probs=63.7
Q ss_pred CCchHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCCcchhhhhhccCCCCHHHHHHhhccccc
Q 028639 138 IKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICVIANICPETVEEAYAIVPSLKV 203 (206)
Q Consensus 138 ~~~s~vf~KTleYv~rFSkfkn~Esv~aVRelL~~~gL~kFEIAqLaNLcPeTaEEAKALIPSL~~ 203 (206)
.+++++|.+||+|+++|++|++++++++||++|..++||+||+|+|+||||+|+||||+|||||..
T Consensus 101 ~~ls~v~~KTLeYl~rFsk~kn~Esa~elre~L~~~kL~efE~aqLaNL~PeTadEaraLIpSle~ 166 (187)
T 1y14_A 101 GGNNKDLKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNN 166 (187)
T ss_dssp CSCCHHHHHHHHHHHHHCSCCSHHHHHHHHHHHHTTTCCHHHHHHHHHSCCSSHHHHHHHSGGGTT
T ss_pred ccccHHHHHHHHHHHHccCCCCHHHHHHHHHHHHhcCCCHHHHHHcCcCCCCCHHHHHHHHHhhcc
Confidence 478899999999999999999999999999999999999999999999999999999999999984
No 6
>4ayb_F DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_F 2y0s_F 2waq_F 4b1o_F 4b1p_U 2pmz_F 3hkz_F
Probab=99.82 E-value=1.8e-22 Score=157.60 Aligned_cols=86 Identities=15% Similarity=0.163 Sum_probs=74.2
Q ss_pred ccccccHHHHHHHHHHHHHHHhhhcCCCCCCchHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCCcchhhhhhccCC
Q 028639 109 NAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICVIANICP 188 (206)
Q Consensus 109 na~cLslsEV~lILe~~~e~~~~~s~d~~~~~s~vf~KTleYv~rFSkfkn~Esv~aVRelL~~~gL~kFEIAqLaNLcP 188 (206)
+.+.++++||+.||..+ .+..+.++++++||+|+++|+|| +++.+.++++.|...++|+||+|+|+||||
T Consensus 8 ~e~~it~~eakeiL~~~---------~~~~~~s~~~~ktl~y~~~Fsk~-~~e~a~~l~e~L~~~~l~~~~~a~IanL~P 77 (113)
T 4ayb_F 8 EEHYIPYSVAKKLLSDV---------IKSGSSSNLLQRTYDYLNSVEKC-DAESAQKVVEELSSIISREDVRAVLASICP 77 (113)
T ss_dssp EEEEECTTGGGGTTTTT---------SSSSCCCTTHHHHHHHTTTTCSS-CHHHHHHHHHHHHTTCCCHHHHHHHHHHCC
T ss_pred cccccCHHHHHHHHHHH---------HhcccccHHHHHHHHHHHHHcCC-CHHHHHHHHHHHHHcCCCHHHHHHHHHcCC
Confidence 44679999999999643 23345678999999999999999 567777788888888999999999999999
Q ss_pred CCHHHHHHhhcccccc
Q 028639 189 ETVEEAYAIVPSLKVW 204 (206)
Q Consensus 189 eTaEEAKALIPSL~~~ 204 (206)
+|+||||+||||+.++
T Consensus 78 ~~~dElrali~s~e~~ 93 (113)
T 4ayb_F 78 ITPDEVRSILIMDSNR 93 (113)
T ss_dssp CSSCCCCTTTTTTCCC
T ss_pred CCHHHHHHHHHhhccC
Confidence 9999999999999875
No 7
>3ayh_A DNA-directed RNA polymerase III subunit RPC9; transcription; 2.19A {Schizosaccharomyces pombe}
Probab=99.51 E-value=7.6e-15 Score=117.37 Aligned_cols=97 Identities=18% Similarity=0.160 Sum_probs=80.4
Q ss_pred cccccccHHHHHHHHHHHHHHHhhh--cCC-----CCCCchHHHHHHHHHHHhc--CCCCCHHHHHHHHHHHHhCCCCcc
Q 028639 108 KNAKCLMDCEAAHILEGIQEQMALL--SAD-----PTIKIPVSFDKGLLYAKTH--SHFTNPQAVKGLFQSLSEHGVTDG 178 (206)
Q Consensus 108 ena~cLslsEV~lILe~~~e~~~~~--s~d-----~~~~~s~vf~KTleYv~rF--Skfkn~Esv~aVRelL~~~gL~kF 178 (206)
.++.+|||.||..+|+++..+.... ... ...+.+.++.+|++|+++| +.+.+++++.++++.|..++|+++
T Consensus 13 ~~~a~LsN~EVl~~L~~~~~~~~~~~~~~~~~~~~~~~~l~ti~~e~l~YL~~~p~~~~q~~e~i~~l~~~L~~~~Ltk~ 92 (136)
T 3ayh_A 13 ARDAYLTNAEVFFHLKEMENEQNARTQERGAAQALVCENLRTIQFEILKYLSSQGNCEGLTKERFLDCIAIFNEFELTKA 92 (136)
T ss_dssp EEEEEECHHHHHHHHHHHHHHHHHHHHHHGGGGCCCCHHHHHHHHHHHHHHHTTTCCTTCCHHHHHHHHHTTTTTCCCHH
T ss_pred cccccccHHHHHHHHHHHHhhhcccccccCCccccccchHHHHHHHHHHHHHhCCCccccCHHHHHHHHHHHHhcCCCHH
Confidence 4678999999999999887643210 111 1245778999999999999 445689999999999999999999
Q ss_pred hhhhhhccCCCCHHHHHHhhcccccc
Q 028639 179 EICVIANICPETVEEAYAIVPSLKVW 204 (206)
Q Consensus 179 EIAqLaNLcPeTaEEAKALIPSL~~~ 204 (206)
|+.||+||||.|+.|+++||+..+..
T Consensus 93 E~LqivNl~P~t~vel~~iIEe~e~R 118 (136)
T 3ayh_A 93 EILVILNNKPSSVPELYACIEGIEER 118 (136)
T ss_dssp HHHHHHHHCCCSHHHHHHHSTTHHHH
T ss_pred HHHHHhccCCCCHHHHHHHHHhcccC
Confidence 99999999999999999999998744
No 8
>2ckz_A DNA-directed RNA polymerase III 18 KD polypeptide; multiprotein complex, nucleotidyltransferase, nuclear protein, hypothetical protein; 3.2A {Saccharomyces cerevisiae}
Probab=99.31 E-value=5.7e-13 Score=109.77 Aligned_cols=96 Identities=15% Similarity=0.155 Sum_probs=32.1
Q ss_pred ccccccHHHHHHHHHHHHHHHhh---------------hcCC--CCCCchHHHHHHHHHHHhcCC---------------
Q 028639 109 NAKCLMDCEAAHILEGIQEQMAL---------------LSAD--PTIKIPVSFDKGLLYAKTHSH--------------- 156 (206)
Q Consensus 109 na~cLslsEV~lILe~~~e~~~~---------------~s~d--~~~~~s~vf~KTleYv~rFSk--------------- 156 (206)
+..+|||.||..+|..+..+... .... +..+++.|+..|++|+.++++
T Consensus 7 ~~a~LSN~EVl~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~ti~~e~~~YL~~~p~~~~~~~~~~~~~~~~ 86 (161)
T 2ckz_A 7 RNAFLSDYEVLKFLTDLEKKHLWDQKSLAALKKSRSKGKQNRPYNHPELQGITRNVVNYLSINKNFINQEDEGEERESSG 86 (161)
T ss_dssp EEEEECHHHHHHHHHHHHHHTTCSHHHHHCC----------CCCCCHHHHHHHHHHHHHHTC------------------
T ss_pred hhhhhhHHHHHHHHHHhhhhccccccchhhhhcccccccccCCCCCccHHHHHHHHHHHHHhCCcccccccccccccccc
Confidence 56799999999999988765310 0011 113466799999999999998
Q ss_pred ----------CCCHHHHHHHHHHHHhCCCCcchhhhhhccCCCCHHHHHHhhcccccc
Q 028639 157 ----------FTNPQAVKGLFQSLSEHGVTDGEICVIANICPETVEEAYAIVPSLKVW 204 (206)
Q Consensus 157 ----------fkn~Esv~aVRelL~~~gL~kFEIAqLaNLcPeTaEEAKALIPSL~~~ 204 (206)
+.+++++..+.+.|..++|+++|+.||+||||.++.|+++||+.++..
T Consensus 87 ~~~~~~~~~~~~~~e~i~~l~~~L~~~~Ltk~E~lqivNl~P~s~vel~~iIEe~e~R 144 (161)
T 2ckz_A 87 AKDAEKSGISKMSDESFAELMTKLNSFKLFKAEKLQIVNQLPANMVHLYSIVEECDAR 144 (161)
T ss_dssp ----------------------------------------------------------
T ss_pred ccccccccccccCHHHHHHHHHHHHhcCCCHHHHHHHhccCCCCHHHHHHHHHhcccC
Confidence 355788888888888999999999999999999999999999988754
No 9
>3k4g_A DNA-directed RNA polymerase subunit alpha; bacterial transcription regulation, DNA-directed RNA polymer nucleotidyltransferase; HET: MLY; 2.05A {Escherichia coli k-12} SCOP: a.60.3.1 PDB: 3n4m_B* 1lb2_B* 3n97_B* 1xs9_D
Probab=27.18 E-value=63 Score=23.59 Aligned_cols=38 Identities=8% Similarity=0.066 Sum_probs=32.5
Q ss_pred CCCchHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCC
Q 028639 137 TIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGV 175 (206)
Q Consensus 137 ~~~~s~vf~KTleYv~rFSkfkn~Esv~aVRelL~~~gL 175 (206)
-..+.+++.+|-+.+-++-.|. +.++.+|++.|..+||
T Consensus 32 I~Tv~dL~~~se~dLlki~n~G-~KSl~EI~~~L~~~GL 69 (86)
T 3k4g_A 32 IHYIGDLVQRTEVELLXTPNLG-XXSLTEIXDVLASRGL 69 (86)
T ss_dssp CCBHHHHHHSCHHHHHTSTTCC-HHHHHHHHHHHHTTTC
T ss_pred CCcHHHHHhCCHHHHhhccccC-cccHHHHHHHHHHcCC
Confidence 3456788999999999998886 8999999999999887
No 10
>1jw2_A Hemolysin expression modulating protein HHA; structural genomics, protein structure initiative, OCSP, NESG, PSI; NMR {Escherichia coli} SCOP: a.23.5.1 PDB: 2jvp_A 2k5s_A
Probab=25.82 E-value=42 Score=24.14 Aligned_cols=33 Identities=9% Similarity=0.110 Sum_probs=25.5
Q ss_pred HHHHHHhcCCCCCHHHHHHHHHHHHhCCCCcchh
Q 028639 147 GLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEI 180 (206)
Q Consensus 147 TleYv~rFSkfkn~Esv~aVRelL~~~gL~kFEI 180 (206)
..+|+-+|-|+.+.++.+.|-+-+.- .|++-|+
T Consensus 8 k~d~L~k~Rrc~s~eTLEkv~e~~~y-~Lt~~el 40 (72)
T 1jw2_A 8 KTDYLMRLRRCQTIDTLERVIEKNKY-ELSDNEL 40 (72)
T ss_dssp HHHHHHHHHTSSCHHHHHHHHHHHHH-HSCHHHH
T ss_pred HHHHHHHHHhcCcHHHHHHHHHHhhc-cCCHHHH
Confidence 38999999999999999998776542 3655443
No 11
>1yse_A DNA-binding protein SATB1; all helical, DNA-binding domain, T-cell development; NMR {Homo sapiens} SCOP: a.35.1.7
Probab=23.52 E-value=52 Score=26.36 Aligned_cols=55 Identities=13% Similarity=0.106 Sum_probs=31.0
Q ss_pred chHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCCcchhhh-hhccCCCCHHHH
Q 028639 140 IPVSFDKGLLYAKTHSHFTNPQAVKGLFQSLSEHGVTDGEICV-IANICPETVEEA 194 (206)
Q Consensus 140 ~s~vf~KTleYv~rFSkfkn~Esv~aVRelL~~~gL~kFEIAq-LaNLcPeTaEEA 194 (206)
++..+.|-++|+.....--+.+-+..|++.|+++.+.+-=.|. +.|++..+.-|.
T Consensus 4 ~~~~~nkp~~~~~t~~~~vt~~I~~~Ik~eLk~~~IsQ~~FA~~VL~rsQGtLS~L 59 (141)
T 1yse_A 4 VSRSMNKPLEQQVSTNTEVSSEIYQWVRDELKRAGISQAVFARVAFNRTQGLLSEI 59 (141)
T ss_dssp ---------------CCSCCTHHHHHHHHHHHHHTCCHHHHHHHHCCSCTTHHHHH
T ss_pred HHHHhcCCccccccccccchHHHHHHHHHHHHHcCCCHHHHHHHHHHhhhhhHHHH
Confidence 3467899999999877766789999999999998888855444 788887775553
No 12
>2czy_A Paired amphipathic helix protein SIN3B; SIN3, PAH1, transcriptional repressor, gene regulation; NMR {Mus musculus}
Probab=23.21 E-value=1.9e+02 Score=20.11 Aligned_cols=53 Identities=17% Similarity=0.265 Sum_probs=39.9
Q ss_pred ccHHHHHHHHHHHHHHHhhhcCCCCCCchHHHHHHHHHHHhcC--CCCCHHHHHHHHHHHHhC
Q 028639 113 LMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHS--HFTNPQAVKGLFQSLSEH 173 (206)
Q Consensus 113 LslsEV~lILe~~~e~~~~~s~d~~~~~s~vf~KTleYv~rFS--kfkn~Esv~aVRelL~~~ 173 (206)
|+..+|...|++++++.+ ..+.++..-++-++.|- +...++.+..|..++..+
T Consensus 2 l~~~dA~~yl~~VK~~F~--------~~p~~Y~~FL~im~~~k~~~~~~~~v~~rv~~Lf~~h 56 (77)
T 2czy_A 2 VHVEDALTYLDQVKIRFG--------SDPATYNGFLEIMKEFKSQSIDTPGVIRRVSQLFHEH 56 (77)
T ss_dssp CSHHHHHHHHHHHHHHTT--------TCHHHHHHHHHHHHHHHTTCSCHHHHHHHHHHHTTTC
T ss_pred CCHHHHHHHHHHHHHHHc--------cChHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCC
Confidence 678899999999988752 12588999888888875 344467777788887754
No 13
>3kev_A Galieria sulfuraria DCUN1 domain-containing prote; cullin, neddylation, DCN-1, center for eukaryotic structural genomics, PSI; HET: CSO MSE; 1.30A {Galdieria sulphuraria}
Probab=22.02 E-value=28 Score=28.99 Aligned_cols=59 Identities=17% Similarity=0.082 Sum_probs=38.0
Q ss_pred HHHHHHHHHhcCCCCCHHHHHHH--HHHHHh---CCCCcchhhh-hhccCCCCHHHHHHhhcccccc
Q 028639 144 FDKGLLYAKTHSHFTNPQAVKGL--FQSLSE---HGVTDGEICV-IANICPETVEEAYAIVPSLKVW 204 (206)
Q Consensus 144 f~KTleYv~rFSkfkn~Esv~aV--RelL~~---~gL~kFEIAq-LaNLcPeTaEEAKALIPSL~~~ 204 (206)
..-+..|++.-.-= |+.+..+ --.|.. ..++..|-.. +.+|.+.|++..|+.||.|..-
T Consensus 26 ~dG~~~~~~DLgv~--ped~~~LvLaw~l~a~~~g~ftr~ef~~G~~~l~~dsi~~lk~~l~~l~~~ 90 (199)
T 3kev_A 26 AEGLQRLFEDIQVD--PSDVVTLVLAWKLKASSTCEFSEKEFVEGLANLQVDSLEKLKRKLSSLRKE 90 (199)
T ss_dssp HHHHHHHHHHTTCC--TTSHHHHHHHHHTTCCSTTCEEHHHHHHHHHHTTCCSHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCC--hhhHHHHHHHHHcCCCccCcccHHHHHHHHHHhCCCCHHHHHHHHHHHHHH
Confidence 57777888765543 4444432 222322 2355556433 7789999999999999998653
No 14
>1g1e_B SIN3A; four-helix bundle, protein-peptide complex, transcription; NMR {Mus musculus} SCOP: a.59.1.1 PDB: 1s5q_B 1s5r_B 2l9s_B
Probab=20.37 E-value=1.6e+02 Score=21.08 Aligned_cols=39 Identities=15% Similarity=0.080 Sum_probs=28.7
Q ss_pred ccccccHHHHHHHHHHHHHHHhhhcCCCCCCchHHHHHHHHHHHhcC
Q 028639 109 NAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHS 155 (206)
Q Consensus 109 na~cLslsEV~lILe~~~e~~~~~s~d~~~~~s~vf~KTleYv~rFS 155 (206)
+...++..+|...|++++.+.+ ..+++++.-|+-++.|-
T Consensus 4 ~~~~~~~~~A~~YvnkVK~rF~--------~~p~~Y~~FL~IL~~y~ 42 (89)
T 1g1e_B 4 NNQPVEFNHAINYVNKIKNRFQ--------GQPDIYKAFLEILHTYQ 42 (89)
T ss_dssp CCCTHHHHHHHHHHHHHHHHTT--------TCHHHHHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHHHHHHc--------cChHHHHHHHHHHHHHH
Confidence 5677888899999998887642 13577887777777773
Done!