Query 006819
Match_columns 630
No_of_seqs 97 out of 116
Neff 3.7
Searched_HMMs 29240
Date Mon Mar 25 09:49:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/006819.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/006819hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 2wvr_C DNA replication factor 100.0 6.1E-67 2.1E-71 567.2 11.6 360 74-629 164-539 (546)
2 1wlq_C CDT1 protein; coiled-co 100.0 2.6E-46 8.8E-51 363.7 13.7 172 73-262 9-194 (201)
3 2zxx_C DNA replication factor 100.0 2.3E-39 8E-44 313.3 13.7 173 72-262 4-190 (197)
4 3a4c_A DNA replication factor 100.0 2E-28 6.9E-33 217.5 10.5 98 530-628 2-99 (106)
5 4h62_K Mediator of RNA polymer 39.9 15 0.00053 27.2 2.1 17 580-596 15-31 (40)
6 1nha_A TFIIF-alpha, transcript 33.3 62 0.0021 28.0 5.1 60 548-614 22-81 (82)
7 1b8z_A Protein (histonelike pr 31.0 39 0.0013 28.0 3.6 38 562-601 1-38 (90)
8 1owf_B IHF-beta, integration H 29.7 52 0.0018 27.5 4.2 39 562-601 1-39 (94)
9 1mul_A NS2, HU-2, DNA binding 26.8 55 0.0019 27.1 3.8 38 562-601 1-38 (90)
10 1p71_A DNA-binding protein HU; 26.6 52 0.0018 27.6 3.6 38 562-601 1-38 (94)
11 1i27_A Transcription factor II 25.0 66 0.0023 27.2 3.9 60 548-614 13-72 (73)
12 2l5g_B Putative uncharacterize 23.7 34 0.0012 26.2 1.7 29 562-593 2-30 (42)
13 2o97_B NS1, HU-1, DNA-binding 23.6 72 0.0025 26.5 3.9 38 562-601 1-38 (90)
14 1owf_A IHF-alpha, integration 22.5 68 0.0023 27.2 3.6 39 561-601 2-40 (99)
15 2krc_A DNA-directed RNA polyme 22.2 65 0.0022 28.3 3.4 43 117-159 15-59 (99)
16 2iie_A Integration HOST factor 21.9 2.9E+02 0.0098 26.6 8.3 57 543-601 28-84 (204)
17 2np2_A HBB; protein-DNA comple 21.1 86 0.0029 27.0 4.0 43 558-601 5-51 (108)
No 1
>2wvr_C DNA replication factor CDT1; DNA replication license, DNA replication inhibitor, phosphoprotein, UBL conjugation, DNA-binding, polymorphism; HET: DNA; 3.30A {Homo sapiens} PDB: 2klo_A*
Probab=100.00 E-value=6.1e-67 Score=567.16 Aligned_cols=360 Identities=23% Similarity=0.364 Sum_probs=139.8
Q ss_pred chhHHhhhhhcccCCCCCCCCCCCCCCCCCCchhHHHHHHHHhhHHHHHHHHHhcCCCCchhchhHHHHHHhhcccccch
Q 006819 74 KDQIESAGKQISASPSVKSSVNPAGSGSPKLPAKYMQLAECFDSLDAVIRLLKLKCSSPTFTSICPKIECLTDRRFSLGH 153 (630)
Q Consensus 74 ~~~~~~~~r~~~~~ps~~~~~~~~~~~~L~LP~KYr~LaElFr~mDTvvsML~nRkE~~TF~Klk~~VE~MtrRrF~~~H 153 (630)
....++|+||.++... +.+++.||+||+.|+++|++||||++||++|++++||.|||++||+|++|+|++.|
T Consensus 164 ~~~~Pay~Rf~~l~~~--------~~~~l~LP~ky~~L~elF~alDtvlslL~~R~~~~tf~kI~~~Ve~mtkrrFt~~h 235 (546)
T 2wvr_C 164 GEKAPAYQRFHALAQP--------GLPGLVLPYKYQVLAEMFRSMDTIVGMLHNRSETPTFAKVQRGVQDMMRRRFEERN 235 (546)
T ss_dssp ---CCHHHHTHHHHCC--------SSSCCCCCHHHHHHHHHHHHHHHHHHHHHHTTCCCBHHHHHHHHHHHHSSCCCHHH
T ss_pred cccCcHHHHHHHhccC--------CCccccCcHHHHHHHHHHHHHHHHHHHHHhccCCccHHHHHHHHHHHHcCCccHHH
Confidence 4477889999998875 55789999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhhhccccEEEEEEEec-cCCCCCCCCCeeEEEeecccccCC---CCCccchhhHHHHHHHHHHHHHHHhCCCC---
Q 006819 154 LAQLKFILPEVIQIKKVLTF-DEKTSCMKPDLHVTVNADAIECDG---KSKCNSKNLNLRTVFRARLMDFLKDHPEG--- 226 (630)
Q Consensus 154 LAQIK~IyPeAy~~~qek~~-d~~S~~~k~d~qLtL~p~~~E~~~---~~~s~S~lLeRRrvF~~~Lld~vK~HHe~--- 226 (630)
||||+||||+||.|+|++.. .++++|++++|||+|.|++.++.+ ..++.+.+++||++||++|++||++||++
T Consensus 236 LaQI~~I~PeaY~l~~~k~~~~f~s~~k~~dyqL~I~P~l~~e~~~~~~~~s~s~l~~Rr~~Fr~rL~~~Vk~hHe~fL~ 315 (546)
T 2wvr_C 236 VGQIKTVYPASYRFRQERSVPTFKDGTRRSDYQLTIEPLLEQEADGAAPQLTASRLLQRRQIFSQKLVEHVKEHHKAFLA 315 (546)
T ss_dssp HHHHHHHCGGGEEEEEC---------------CEEEEECCCCCTTCCSSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred HHHHHHhccchhhhhhhhccccccccccCCCceEEEecCCccccccccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 99999999999999999765 558899999999999997765322 34677889999999999999999999998
Q ss_pred -----CCCCCCCCCC---CCCCCchhhhhhhhcccCCCCCCCCCCchhhhhcccCCCccccccccccccCCccccccccC
Q 006819 227 -----DEIPEETLPE---PFNRSRSDLQLNMVKKSTSLTPADSPTDASVEQQQVSSPTCQNSKLLNIVKAPSISMVTGTS 298 (630)
Q Consensus 227 -----~dIPEa~LPe---pFN~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~~~~~~~p~~~~~~~~~ 298 (630)
++||++.|++ .||.+.++ +|.|+.+| +
T Consensus 316 sL~pp~~Ip~e~L~rwhp~Fdle~vp----------dI~pa~LP----------q------------------------- 350 (546)
T 2wvr_C 316 SLSPAMVVPEDQLTRWHPRFNVDEVP----------DIEPAALP----------Q------------------------- 350 (546)
T ss_dssp TTTTSCCCCGGGCCSCCTTCCSTTSC----------CCCCCCCC----------C-------------------------
T ss_pred hcCCcccCchhhccccCCCCCccccC----------CccccccC----------C-------------------------
Confidence 7999999999 56666655 67777777 1
Q ss_pred CCCcccccchhhccccc-ccccchhhhhhHHHHhhhhhccCCcccCCCCCCCCchhhhcccchhhhhhhhhhhhhhhccc
Q 006819 299 ASASDNQQPIVASHFSS-RRHFSQKFVNSLAEKKKAERISSGVSIEPSTTPALEPCLRKISSIEETCSTAAISAVELSSK 377 (630)
Q Consensus 299 ~~~~~e~~~~~~shl~~-rr~fSqK~~~t~~Ek~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~e~~~~~l~~~p~~~~~~ 377 (630)
++..+..++++..|.. +.+||++ +|+ + +. .|+.
T Consensus 351 -pP~~~k~sSa~evL~~arslls~~-----mek--a--------------------ls----------~la~-------- 384 (546)
T 2wvr_C 351 -PPATEKLTTAQEVLARARNLISPR-----MEK--A--------------------LS----------QLAL-------- 384 (546)
T ss_dssp -CCC----------------------------------------------------------------------------
T ss_pred -CccccCCCcHHHHHHhcccccChh-----hHh--H--------------------HH----------HHHh--------
Confidence 2233333456666666 7788876 555 2 22 2221
Q ss_pred cccccccccccCCCCCCCCCCCCCCCccccCCCCCCCccCcccccCCCCCCccCCCccccccCCCCCCCCCcccCCCCcc
Q 006819 378 STSKENCLTYCASPTRLSQSCPPVTPVKEIDPMESKVSYPIKVDSEQSTPAKLVSTPARLMIGTPALHQPKRCYMTPENV 457 (630)
Q Consensus 378 ~~~k~~~~~~~~~~~~~~q~~~~~tp~~~i~~~~s~~~~~~~~~~~~stP~k~~stp~~lma~TPa~~~PkR~l~~~~~~ 457 (630)
+ . +++ ++|.. + ...|.+.+++. +|
T Consensus 385 ---k------------~--------------a~~-------------~Sp~~--s-~~~lp~~~~~t-~~---------- 408 (546)
T 2wvr_C 385 ---R------------S--------------AAP-------------SSPGS--P-RPALPATPPAT-PP---------- 408 (546)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred ---c------------c--------------cCC-------------CCCCC--C-CccccCCCCCC-Cc----------
Confidence 0 0 000 00000 0 01111111110 00
Q ss_pred cCCCCCCcCCCCCCccccccccCCCcccchhhhccccccccCCCccccCCchhHHHHHHHHHHHHHHhhCchhHHHHHHH
Q 006819 458 SASSPNKLTRRPPHSRTLKSLKFDTPVKNATVEHKLNEDISVDGDVLDILPENLIQSIREKERKFMEERDPAISQAKWRR 537 (630)
Q Consensus 458 s~~~~~k~arrp~~~r~L~~~~F~sp~k~~~~~~~~~~~~s~d~~~l~~vpesLl~sIrekE~~~~~~q~t~~~~~~~r~ 537 (630)
+.. ...|+|+|++||++||+||+.+.+++++..+++++|+
T Consensus 409 --------~~~--------------------------------~s~lKGvs~sLLERIRaKEa~kk~e~~t~~p~~~~r~ 448 (546)
T 2wvr_C 409 --------AAS--------------------------------PSALKGVSQDLLERIRAKEAQKQLAQMTRCPEQEQRL 448 (546)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred --------ccC--------------------------------cchhccCCHHHHHHHHHHHHHHHHHhhccCHhHHHHH
Confidence 000 1223589999999999999999999999999999999
Q ss_pred HHhhchhHHHHHHHHHHHhhccccccHHHHHHHHHhhccccCChhHHHHHHHHHHHhcccchhhcccCCCCeEEEeccCC
Q 006819 538 QMIASLPKLFNMIHFLFQSIKRSVITKEELIHKIISSHLQITDRREVEEQMNLMLELVPEWISEKLSSCGDLLVCINKMT 617 (630)
Q Consensus 538 ~~ia~LP~L~~iir~IF~S~krs~ITKEELvhKIias~~~I~d~gEvEEqL~LLeeLvPDWIS~k~i~sGD~~~ki~K~~ 617 (630)
+++++||+||||||+||+++++++|||++||++|++||..+++++|||+||+||++|+||||+.+.++ |++|||||+.+
T Consensus 449 ~~lsrLP~la~iL~~lF~s~kks~l~m~~lv~kI~~S~~~~ls~~EiEe~L~LL~el~PeWisi~~i~-g~~~lklnk~~ 527 (546)
T 2wvr_C 449 QRLERLPELARVLRSVFVSERKPALSMEVACARMVGSCCTIMSPGEMEKHLLLLSELLPDWLSLHRIR-TDTYVKLDKAA 527 (546)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred HHHHhhHHHHHHHHHHHHhcCCCceEHHHHHHHHHhhccccCCHHHHHHHHHHHHHhChHhheeeeeC-CceEEEeeccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999776 89999999999
Q ss_pred ChHHHHHHhhhc
Q 006819 618 CPESIRARLEES 629 (630)
Q Consensus 618 dl~sVraRL~e~ 629 (630)
|+++||+||+++
T Consensus 528 Dl~~Vr~rL~~~ 539 (546)
T 2wvr_C 528 DLAHITARLAHQ 539 (546)
T ss_dssp ------------
T ss_pred CHHHHHHHHHHH
Confidence 999999999975
No 2
>1wlq_C CDT1 protein; coiled-coil; 2.80A {Mus musculus} PDB: 2zxx_C*
Probab=100.00 E-value=2.6e-46 Score=363.67 Aligned_cols=172 Identities=22% Similarity=0.340 Sum_probs=159.0
Q ss_pred CchhHHhhhhhcccCCCCCCCCCCCCCCCCCCchhHHHHHHHHhhHHHHHHHHHhcCCCCchhchhHHHHHHhhcccccc
Q 006819 73 PKDQIESAGKQISASPSVKSSVNPAGSGSPKLPAKYMQLAECFDSLDAVIRLLKLKCSSPTFTSICPKIECLTDRRFSLG 152 (630)
Q Consensus 73 ~~~~~~~~~r~~~~~ps~~~~~~~~~~~~L~LP~KYr~LaElFr~mDTvvsML~nRkE~~TF~Klk~~VE~MtrRrF~~~ 152 (630)
-....++|+|+-++..+ +.++|+||+||+.|+|||+|||||++||+||+++|||+|||++||+|+||+|+++
T Consensus 9 ~~~~~pay~r~~~l~~~--------~~~~l~LP~kY~~L~e~F~~ldtv~~ml~~R~~~~Tf~~ik~~VE~~trr~F~~~ 80 (201)
T 1wlq_C 9 CVEKAPAYQRFHALAQP--------GLPGLVLPYKYQVLVEMFHSMDTIVSMLHNRSETVTFAKVKQGVQEMMRKRFEER 80 (201)
T ss_dssp ---CCCHHHHTHHHHCC--------SSSSCCCCHHHHHHHHHHHHHHHHHHHHHHTTCCCBHHHHHHHHHHHHTSCCCHH
T ss_pred CcccccHHHHHHHHhcC--------CCCCCcCCHHHHHHHHHHHHHHHHHHHHHcCCccccHHHHHHHHHHHhcCCcCHH
Confidence 34567899999999886 6778999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhhhhccccEEEEEEEe-ccCCCCCCCCCeeEEEeecccccCC--CCCccchhhHHHHHHHHHHHHHHHhCCCC---
Q 006819 153 HLAQLKFILPEVIQIKKVLT-FDEKTSCMKPDLHVTVNADAIECDG--KSKCNSKNLNLRTVFRARLMDFLKDHPEG--- 226 (630)
Q Consensus 153 HLAQIK~IyPeAy~~~qek~-~d~~S~~~k~d~qLtL~p~~~E~~~--~~~s~S~lLeRRrvF~~~Lld~vK~HHe~--- 226 (630)
||||||||||+||.|+|+++ ++++++|+..+|||+|.|++.+..+ +.++++.+++||++||++|+++||+||++
T Consensus 81 hLaQIk~IyPeay~l~~~k~~~~f~s~~k~~~yqL~i~Pnv~~~~~~~~~ls~s~l~~Rr~~F~~~Ll~~Vk~~H~~FL~ 160 (201)
T 1wlq_C 81 NVGQIKTVYPMSYRFRQECNVPTFKDSIKRSDYQLTIEPLLGQEAGGATQLTATCLLQRRQVFRQNLVERVKEQHKVFLA 160 (201)
T ss_dssp HHHHHHHHCTTSEEEEEEECCSSCCSCCCGGGEEEEEEECSSCC--CCSSCCHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHhccCceEEEeeecccccccccccCcceEEEecccccccCCCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999997 7889999999999999999886442 57889999999999999999999999998
Q ss_pred -----CCCCCCCCCC---CCCCCchhhhhhhhcccCCCCCCCCC
Q 006819 227 -----DEIPEETLPE---PFNRSRSDLQLNMVKKSTSLTPADSP 262 (630)
Q Consensus 227 -----~dIPEa~LPe---pFN~~~~~~~~~~~~~~~~~~~~~~~ 262 (630)
+.||++.|++ .||.+.++ +|.+++||
T Consensus 161 sl~~pi~i~~d~l~RWHP~F~ld~vp----------~I~~a~LP 194 (201)
T 1wlq_C 161 SLNPPMAVPDDQLTRWHPRFNVDEVP----------DIEPAELP 194 (201)
T ss_dssp TSSSCCCCCTTTCCSCCTTCCGGGSC----------CCCCCCCC
T ss_pred hCCCCCcCChhhccccCCCCCcccCC----------CCCcCCCC
Confidence 7899999999 99999999 99999999
No 3
>2zxx_C DNA replication factor CDT1; coiled-coil, cell cycle, coiled coil, DNA replication inhibitor, phosphoprotein, DNA-binding, nucleus, proto-oncogene; HET: DNA; 2.80A {Mus musculus}
Probab=100.00 E-value=2.3e-39 Score=313.25 Aligned_cols=173 Identities=22% Similarity=0.355 Sum_probs=155.0
Q ss_pred CCchhHHhhhhhcccCCCCCCCCCCCCCCCCCCchhHHHHHHHHhhHHHHHHHHHhcCCCCchhchhHHHHHHhhccccc
Q 006819 72 PPKDQIESAGKQISASPSVKSSVNPAGSGSPKLPAKYMQLAECFDSLDAVIRLLKLKCSSPTFTSICPKIECLTDRRFSL 151 (630)
Q Consensus 72 ~~~~~~~~~~r~~~~~ps~~~~~~~~~~~~L~LP~KYr~LaElFr~mDTvvsML~nRkE~~TF~Klk~~VE~MtrRrF~~ 151 (630)
+.....++|+|+-++..+ +.++|.||+||+.|+++|++||||++||++|++++||.+||++||.|++|+|++
T Consensus 4 ~~~~~~pay~r~~~l~~~--------~~~~l~LP~ky~~L~~~F~~ld~v~~~l~~R~~~~tf~~lk~~Ve~~~~r~f~~ 75 (197)
T 2zxx_C 4 PCVEKAPAYQRFHALAQP--------GLPGLVLPYKYQVLVEMFRSMDTIVSMLHNRSETVTFAKVKQGVQEMMRKRFEE 75 (197)
T ss_dssp ----CCCHHHHTTGGGCC--------SSCSCCCCHHHHHHHHHHHHHHHHHHHHHHTTCCCBHHHHHHHHHHHHSSCCCH
T ss_pred CCccCCchHHHHHHhccC--------CCCCCCCCHHHHHHHHHHHHHHHHHHHHHhcCccccHHHHHHHHHHHHcCCCCH
Confidence 445667899999988875 566899999999999999999999999999999999999999999999999999
Q ss_pred chhhhhhhhccccEEEEEEEe-ccCCCCCCCCCeeEEEeecccccCC--CCCccchhhHHHHHHHHHHHHHHHhCCCC--
Q 006819 152 GHLAQLKFILPEVIQIKKVLT-FDEKTSCMKPDLHVTVNADAIECDG--KSKCNSKNLNLRTVFRARLMDFLKDHPEG-- 226 (630)
Q Consensus 152 ~HLAQIK~IyPeAy~~~qek~-~d~~S~~~k~d~qLtL~p~~~E~~~--~~~s~S~lLeRRrvF~~~Lld~vK~HHe~-- 226 (630)
.||||||||||+||.|+|++. ++.++++++.+|||+|.|++.+..+ +.++++.+++||++||++|+++||.||+.
T Consensus 76 ~~LaqI~~l~P~a~~~~~~~~~~~~~~~~~~~~yqL~i~p~~~~~~~~~~~~s~~~l~~R~~~Fr~~Ll~~Vk~~H~~fL 155 (197)
T 2zxx_C 76 RNVGQIKTVYPTSYRFRQECNVPTFKDSIKRSDYQLTIEPLLGQEAGGATQLTATCLLQRRQVFRQNLVERVKEQHKVFL 155 (197)
T ss_dssp HHHHHHHHHCGGGEEEEEEECCSSCCSCCCGGGEEEEEEECSSCC--CCSSCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHhccCeeEEEEEecccccCCccccccceEEEeecCccccccCCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999995 5669999999999999999887543 45678889999999999999999999998
Q ss_pred ------CCCCCCCCCC---CCCCCchhhhhhhhcccCCCCCCCCC
Q 006819 227 ------DEIPEETLPE---PFNRSRSDLQLNMVKKSTSLTPADSP 262 (630)
Q Consensus 227 ------~dIPEa~LPe---pFN~~~~~~~~~~~~~~~~~~~~~~~ 262 (630)
+.||.+.|.+ .||.+.++ +|.||.||
T Consensus 156 ~~l~~~~~~~~~~l~rWHP~F~le~vp----------dI~~a~LP 190 (197)
T 2zxx_C 156 ASLNPPMAVPDDQLTRWHPRFNVDEVP----------DIEPAELP 190 (197)
T ss_dssp TTSSSCCCCCGGGCCSCCTTCCGGGSC----------CCCCCCCC
T ss_pred HhcCCCCcCchhhccccCCCCCcccCC----------CCCcccCC
Confidence 5689999998 99988888 89999999
No 4
>3a4c_A DNA replication factor CDT1; alpha-beta structure, cell cycle, DNA- binding, nucleus, phosphoprotein, proto-oncogene, UBL conjugation; HET: DNA; 1.89A {Mus musculus} PDB: 2rqq_A*
Probab=99.95 E-value=2e-28 Score=217.52 Aligned_cols=98 Identities=24% Similarity=0.396 Sum_probs=95.5
Q ss_pred hHHHHHHHHHhhchhHHHHHHHHHHHhhccccccHHHHHHHHHhhccccCChhHHHHHHHHHHHhcccchhhcccCCCCe
Q 006819 530 ISQAKWRRQMIASLPKLFNMIHFLFQSIKRSVITKEELIHKIISSHLQITDRREVEEQMNLMLELVPEWISEKLSSCGDL 609 (630)
Q Consensus 530 ~~~~~~r~~~ia~LP~L~~iir~IF~S~krs~ITKEELvhKIias~~~I~d~gEvEEqL~LLeeLvPDWIS~k~i~sGD~ 609 (630)
.++|++|.+++++||+|||+||+||+++||++||||++|+||+.||+.++++||||+||+||.+|+||||+.|.++ ++.
T Consensus 2 ~p~qeke~~~~srLPelArilR~vFvaEkK~vl~~e~~~~ki~~Syr~~ls~~EmE~hl~lL~ellPdWls~~~vR-~~~ 80 (106)
T 3a4c_A 2 CPEQELRLQRLERLPELARVLRNVFVSERKPALTMEVVCARMVDSCQTALSPGEMEKHLVLLAELLPDWLSLHRIR-TDT 80 (106)
T ss_dssp CHHHHHHHHHHHHHHHHHHHHHHHHHTCSSSEEEHHHHHHHHHHTSCCSCCHHHHHHHHHHHHHHCTTTEEEEEET-TEE
T ss_pred CHHHHHHHHHHHhhHHHHHHHHHHHHhcccCCccHHHHHHHHHhhhhccCCHHHHHHHHHHHHHhCcchheeeeee-ccc
Confidence 5789999999999999999999999999999999999999999999999999999999999999999999999999 699
Q ss_pred EEEeccCCChHHHHHHhhh
Q 006819 610 LVCINKMTCPESIRARLEE 628 (630)
Q Consensus 610 ~~ki~K~~dl~sVraRL~e 628 (630)
|+||+|..|++.|.+||+.
T Consensus 81 ylKl~k~~dl~~i~~rLe~ 99 (106)
T 3a4c_A 81 YVKLDKAVDLAGLTARLAH 99 (106)
T ss_dssp EEEECTTSCHHHHHHHHHH
T ss_pred eeeeehhhhHHHHHHHHHH
Confidence 9999999999999999974
No 5
>4h62_K Mediator of RNA polymerase II transcription subun; mediator complex, nucleus; HET: MES; 3.00A {Saccharomyces cerevisiae}
Probab=39.91 E-value=15 Score=27.20 Aligned_cols=17 Identities=29% Similarity=0.612 Sum_probs=14.4
Q ss_pred ChhHHHHHHHHHHHhcc
Q 006819 580 DRREVEEQMNLMLELVP 596 (630)
Q Consensus 580 d~gEvEEqL~LLeeLvP 596 (630)
|+..|||||.||.-++-
T Consensus 15 dtekmeeqldllsaild 31 (40)
T 4h62_K 15 DTEKMEEQLDLLSAILD 31 (40)
T ss_pred cHHHHHHHHHHHHHHcC
Confidence 67899999999987763
No 6
>1nha_A TFIIF-alpha, transcription initiation factor IIF, alpha subunit; transcription factor, human general transcription factor TFIIF, RAP74; NMR {Homo sapiens} SCOP: a.4.5.30 PDB: 1onv_A
Probab=33.27 E-value=62 Score=27.96 Aligned_cols=60 Identities=15% Similarity=0.328 Sum_probs=46.1
Q ss_pred HHHHHHHHhhccccccHHHHHHHHHhhccccCChhHHHHHHHHHHHhcccchhhcccCCCCeEEEec
Q 006819 548 NMIHFLFQSIKRSVITKEELIHKIISSHLQITDRREVEEQMNLMLELVPEWISEKLSSCGDLLVCIN 614 (630)
Q Consensus 548 ~iir~IF~S~krs~ITKEELvhKIias~~~I~d~gEvEEqL~LLeeLvPDWIS~k~i~sGD~~~ki~ 614 (630)
+-||.++. |-+||=+||++|+-..+...-....++.--+||-.|-|+- +.+. |..|+.|.
T Consensus 22 e~VRryL~---rkPmTT~dLl~KFK~r~~~~~~~e~v~~~a~ILKki~p~q---k~~~-g~~y~~Lk 81 (82)
T 1nha_A 22 DAVRRYLT---RKPMTTKDLLKKFQTKKTGLSSEQTVNVLAQILKRLNPER---KMIN-DKMHFSLK 81 (82)
T ss_dssp HHHHHHHH---HSCBCHHHHHHHTTSSCCSSCHHHHHHHHHHHHHHHCCEE---EEET-TEEEEECC
T ss_pred HHHHHHHH---hCCccHHHHHHHHHHhcccCCCHHHHHHHHHHHHHcCHHh---hccC-CceEEEec
Confidence 44566664 7899999999999777766666666777778999999987 5555 78887764
No 7
>1b8z_A Protein (histonelike protein HU); thermostable DNA binding protein; 1.60A {Thermotoga maritima} SCOP: a.55.1.1 PDB: 1riy_A
Probab=30.95 E-value=39 Score=27.98 Aligned_cols=38 Identities=21% Similarity=0.452 Sum_probs=32.2
Q ss_pred ccHHHHHHHHHhhccccCChhHHHHHHHHHHHhcccchhh
Q 006819 562 ITKEELIHKIISSHLQITDRREVEEQMNLMLELVPEWISE 601 (630)
Q Consensus 562 ITKEELvhKIias~~~I~d~gEvEEqL~LLeeLvPDWIS~ 601 (630)
|||.||+..|-. ...+ +.+++++-|..|.+.+-++|..
T Consensus 1 mtk~eli~~ia~-~~~l-s~~~~~~~l~~~~~~i~~~L~~ 38 (90)
T 1b8z_A 1 MNKKELIDRVAK-KAGA-KKKDVKLILDTILETITEALAK 38 (90)
T ss_dssp CCHHHHHHHHHH-HHTC-CHHHHHHHHHHHHHHHHHHHHT
T ss_pred CCHHHHHHHHHH-HhCc-CHHHHHHHHHHHHHHHHHHHhC
Confidence 799999999854 4444 8999999999999999999876
No 8
>1owf_B IHF-beta, integration HOST factor beta-subunit; protein-DNA recognition, indirect readout, DNA bending, minor groove; 1.95A {Escherichia coli} SCOP: a.55.1.1 PDB: 1ouz_B 2ht0_B 1ihf_B 1owg_B
Probab=29.74 E-value=52 Score=27.50 Aligned_cols=39 Identities=28% Similarity=0.477 Sum_probs=32.4
Q ss_pred ccHHHHHHHHHhhccccCChhHHHHHHHHHHHhcccchhh
Q 006819 562 ITKEELIHKIISSHLQITDRREVEEQMNLMLELVPEWISE 601 (630)
Q Consensus 562 ITKEELvhKIias~~~I~d~gEvEEqL~LLeeLvPDWIS~ 601 (630)
|||.||+..|...+..+ +.+++++-|..|.+.+-+.|..
T Consensus 1 Mtk~eli~~ia~~~~~l-s~~~~~~~l~~~~~~i~~~L~~ 39 (94)
T 1owf_B 1 MTKSELIERLATQQSHI-PAKTVEDAVKEMLEHMASTLAQ 39 (94)
T ss_dssp CBHHHHHHHHHHHCTTS-CHHHHHHHHHHHHHHHHHHHHT
T ss_pred CCHHHHHHHHHHhcCCC-CHHHHHHHHHHHHHHHHHHHhC
Confidence 79999999996664444 7899999999999998888765
No 9
>1mul_A NS2, HU-2, DNA binding protein HU-alpha; histone-like; HET: DNA; 2.30A {Escherichia coli} SCOP: a.55.1.1 PDB: 2o97_A
Probab=26.80 E-value=55 Score=27.11 Aligned_cols=38 Identities=18% Similarity=0.364 Sum_probs=31.7
Q ss_pred ccHHHHHHHHHhhccccCChhHHHHHHHHHHHhcccchhh
Q 006819 562 ITKEELIHKIISSHLQITDRREVEEQMNLMLELVPEWISE 601 (630)
Q Consensus 562 ITKEELvhKIias~~~I~d~gEvEEqL~LLeeLvPDWIS~ 601 (630)
|||.||+..|.. ...+ +.+++++-|..|.+.+-++|..
T Consensus 1 m~k~eli~~ia~-~~~l-s~~~~~~~l~~~~~~i~~~L~~ 38 (90)
T 1mul_A 1 MNKTQLIDVIAE-KAEL-SKTQAKAALESTLAAITESLKE 38 (90)
T ss_dssp CCHHHHHHHHHH-HTTC-CHHHHHHHHHHHHHHHHHHHHT
T ss_pred CCHHHHHHHHHH-HhCC-CHHHHHHHHHHHHHHHHHHHhC
Confidence 799999999855 4444 8999999999999998888765
No 10
>1p71_A DNA-binding protein HU; protein-DNA complex, DNA bending, DNA binding protein-DN; 1.90A {Anabaena SP} SCOP: a.55.1.1 PDB: 1p51_A 1p78_A
Probab=26.55 E-value=52 Score=27.56 Aligned_cols=38 Identities=18% Similarity=0.378 Sum_probs=31.9
Q ss_pred ccHHHHHHHHHhhccccCChhHHHHHHHHHHHhcccchhh
Q 006819 562 ITKEELIHKIISSHLQITDRREVEEQMNLMLELVPEWISE 601 (630)
Q Consensus 562 ITKEELvhKIias~~~I~d~gEvEEqL~LLeeLvPDWIS~ 601 (630)
|||.||+..|-.. ..+ +.+++++-|..|.+.+-++|..
T Consensus 1 M~k~eli~~ia~~-~~l-s~~~~~~~l~~~~~~i~~~L~~ 38 (94)
T 1p71_A 1 MNKGELVDAVAEK-ASV-TKKQADAVLTAALETIIEAVSS 38 (94)
T ss_dssp CBHHHHHHHHHHH-HTC-CHHHHHHHHHHHHHHHHHHHHT
T ss_pred CCHHHHHHHHHHH-hCC-CHHHHHHHHHHHHHHHHHHHhC
Confidence 7999999998654 444 8999999999999999888865
No 11
>1i27_A Transcription factor IIF; general transcription factor, RAP74, RAP30, TFIIF, RNA polymerase II, winged-helix domain; 1.02A {Homo sapiens} SCOP: a.4.5.30 PDB: 1j2x_A 2k7l_A*
Probab=25.03 E-value=66 Score=27.21 Aligned_cols=60 Identities=15% Similarity=0.328 Sum_probs=46.7
Q ss_pred HHHHHHHHhhccccccHHHHHHHHHhhccccCChhHHHHHHHHHHHhcccchhhcccCCCCeEEEec
Q 006819 548 NMIHFLFQSIKRSVITKEELIHKIISSHLQITDRREVEEQMNLMLELVPEWISEKLSSCGDLLVCIN 614 (630)
Q Consensus 548 ~iir~IF~S~krs~ITKEELvhKIias~~~I~d~gEvEEqL~LLeeLvPDWIS~k~i~sGD~~~ki~ 614 (630)
+-||.++. |-+||=+||++|+-..+.+.-....++---+||-.|-|+- +.+. |..|+.|.
T Consensus 13 e~VrryL~---rkPmTt~dLl~KFK~r~~~~~~~e~v~~~a~ILkki~p~q---~~~~-g~~y~~Lk 72 (73)
T 1i27_A 13 DAVRRYLT---RKPMTTKDLLKKFQTKKTGLSSEQTVNVLAQILKRLNPER---KMIN-DKMHFSLK 72 (73)
T ss_dssp HHHHHHHH---HSCBCHHHHHHTSCHHHHCCCHHHHHHHHHHHHHHHCCEE---EEET-TEEEEESC
T ss_pred HHHHHHHH---cCCccHHHHHHHHHHhcccCCCHHHHHHHHHHHHHcCHHh---hccC-CceEEEec
Confidence 44566664 8899999999999888766666677777788999999987 5566 67787664
No 12
>2l5g_B Putative uncharacterized protein NCOR2, G protein pathway suppressor 2; GPS2, SMRT, TBL1, CO-repressor, transcription regulator; NMR {Homo sapiens}
Probab=23.72 E-value=34 Score=26.24 Aligned_cols=29 Identities=31% Similarity=0.444 Sum_probs=22.3
Q ss_pred ccHHHHHHHHHhhccccCChhHHHHHHHHHHH
Q 006819 562 ITKEELIHKIISSHLQITDRREVEEQMNLMLE 593 (630)
Q Consensus 562 ITKEELvhKIias~~~I~d~gEvEEqL~LLee 593 (630)
+||+||+.+|=-=+.+| .-+|++|.-|..
T Consensus 2 ~tk~~l~qkI~kVdrEI---~Kte~kI~~lqk 30 (42)
T 2l5g_B 2 LSKEELIQNMDRVDREI---TMVEQQISKLKK 30 (42)
T ss_dssp CSSSHHHHHHHHHHHHH---HHHHHHHHHHHH
T ss_pred CcHHHHHHHHHHHHHHH---HHHHHHHHHHHH
Confidence 69999999997777777 666777766543
No 13
>2o97_B NS1, HU-1, DNA-binding protein HU-beta; heterodimer, DNA structure, DNA supercoiling, E DNA binding protein; 2.45A {Escherichia coli} SCOP: a.55.1.1
Probab=23.56 E-value=72 Score=26.48 Aligned_cols=38 Identities=24% Similarity=0.402 Sum_probs=31.2
Q ss_pred ccHHHHHHHHHhhccccCChhHHHHHHHHHHHhcccchhh
Q 006819 562 ITKEELIHKIISSHLQITDRREVEEQMNLMLELVPEWISE 601 (630)
Q Consensus 562 ITKEELvhKIias~~~I~d~gEvEEqL~LLeeLvPDWIS~ 601 (630)
|||.||+..|-. ...+ +.+++++-|..|.+.+-+.|..
T Consensus 1 m~k~eli~~ia~-~~~l-s~~~~~~~l~~~~~~i~~~L~~ 38 (90)
T 2o97_B 1 MNKSQLIDKIAA-GADI-SKAAAGRALDAIIASVTESLKE 38 (90)
T ss_dssp CBHHHHHHHHHH-TTC--CHHHHHHHHHHHHHHHHHHHHT
T ss_pred CCHHHHHHHHHH-HhCC-CHHHHHHHHHHHHHHHHHHHHC
Confidence 799999999854 4444 8999999999999998888765
No 14
>1owf_A IHF-alpha, integration HOST factor alpha-subunit; protein-DNA recognition, indirect readout, DNA bending, minor groove; 1.95A {Escherichia coli} SCOP: a.55.1.1 PDB: 1ihf_A 1ouz_A 1owg_A 2ht0_A
Probab=22.48 E-value=68 Score=27.15 Aligned_cols=39 Identities=21% Similarity=0.423 Sum_probs=32.7
Q ss_pred cccHHHHHHHHHhhccccCChhHHHHHHHHHHHhcccchhh
Q 006819 561 VITKEELIHKIISSHLQITDRREVEEQMNLMLELVPEWISE 601 (630)
Q Consensus 561 ~ITKEELvhKIias~~~I~d~gEvEEqL~LLeeLvPDWIS~ 601 (630)
.|||.||+..|-.. ..+ +.+++++-|..|.+.+-++|..
T Consensus 2 ~m~k~eli~~ia~~-~~l-s~~~~~~vl~~~~~~i~~~L~~ 40 (99)
T 1owf_A 2 ALTKAEMSEYLFDK-LGL-SKRDAKELVELFFEEIRRALEN 40 (99)
T ss_dssp CBCHHHHHHHHHHH-HCC-CHHHHHHHHHHHHHHHHHHHHT
T ss_pred CcCHHHHHHHHHHH-hCC-CHHHHHHHHHHHHHHHHHHHhC
Confidence 48999999998654 444 8999999999999999888865
No 15
>2krc_A DNA-directed RNA polymerase subunit delta; delta subunit, GRAM-positive bacteria, nucleotidyltransferase, transcription, transferase; NMR {Bacillus subtilis}
Probab=22.16 E-value=65 Score=28.28 Aligned_cols=43 Identities=14% Similarity=0.139 Sum_probs=35.9
Q ss_pred hHHHHHHHHHhcCCCCchhchhHHHHHHhhccccc--chhhhhhh
Q 006819 117 SLDAVIRLLKLKCSSPTFTSICPKIECLTDRRFSL--GHLAQLKF 159 (630)
Q Consensus 117 ~mDTvvsML~nRkE~~TF~Klk~~VE~MtrRrF~~--~HLAQIK~ 159 (630)
-+|.+..+|..+++..+|..|=..|+.+.+...+. .-+||+-+
T Consensus 15 miDvAy~iL~~~~~~~~F~dL~~eV~~~~~~s~ee~~~~iaqfYT 59 (99)
T 2krc_A 15 LVEIAHELFEEHKKPVPFQELLNEIASLLGVKKEELGDRIAQFYT 59 (99)
T ss_dssp HHHHHHHHHHHHCSCEEHHHHHHHHHHHHTSCGGGGTHHHHHHHH
T ss_pred HHHHHHHHHHHcCCcccHHHHHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 36889999999999999999999999998776654 55666655
No 16
>2iie_A Integration HOST factor; DNA kinking, bending, U-turn, intercalation, divalent, metal, recombination/DNA complex; HET: DNA; 2.41A {Escherichia coli} PDB: 2iif_A*
Probab=21.93 E-value=2.9e+02 Score=26.58 Aligned_cols=57 Identities=14% Similarity=0.279 Sum_probs=43.0
Q ss_pred hhHHHHHHHHHHHhhccccccHHHHHHHHHhhccccCChhHHHHHHHHHHHhcccchhh
Q 006819 543 LPKLFNMIHFLFQSIKRSVITKEELIHKIISSHLQITDRREVEEQMNLMLELVPEWISE 601 (630)
Q Consensus 543 LP~L~~iir~IF~S~krs~ITKEELvhKIias~~~I~d~gEvEEqL~LLeeLvPDWIS~ 601 (630)
+-.+++.|..-........|||.||+..|-. ...+ +.+++++-|..|.+.+-++|..
T Consensus 28 Ve~~l~~i~~~L~~~~~~~Mtk~eLi~~ia~-~~~l-sk~da~~vl~~l~~~i~~~L~~ 84 (204)
T 2iie_A 28 VKEMLEHMASTLAQGGSGGLTKAEMSEYLFD-KLGL-SKRDAKELVELFFEEIRRALEN 84 (204)
T ss_dssp HHHHHHHHHHHHHTCCSSSBCHHHHHHHHHH-HHCC-CHHHHHHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHhhcccCCcCHHHHHHHHHH-HcCC-CHHHHHHHHHHHHHHHHHHHhC
Confidence 4455666665554455667999999999854 4444 8999999999999998888765
No 17
>2np2_A HBB; protein-DNA complex, DNA-binding protein, DNA-bending protein, dnabii family, HU/IHF family, DNA binding protein/DNA complex; 3.02A {Borrelia burgdorferi}
Probab=21.08 E-value=86 Score=27.05 Aligned_cols=43 Identities=14% Similarity=0.393 Sum_probs=34.2
Q ss_pred ccccccHHHHHHHHHh----hccccCChhHHHHHHHHHHHhcccchhh
Q 006819 558 KRSVITKEELIHKIIS----SHLQITDRREVEEQMNLMLELVPEWISE 601 (630)
Q Consensus 558 krs~ITKEELvhKIia----s~~~I~d~gEvEEqL~LLeeLvPDWIS~ 601 (630)
++..|||.||+..|.. ....+ +.+++++-|..|.+.+-+.|..
T Consensus 5 ~~~~mtk~eLi~~ia~~~~~~~~~l-sk~~~~~vl~~~~~~i~~~L~~ 51 (108)
T 2np2_A 5 RRPKVTKSDIVDQIALNIKNNNLKL-EKKYIRLVIDAFFEELKSNLCS 51 (108)
T ss_dssp -CCEEEHHHHHHHHHHHHHHTTCCC-CHHHHHHHHHHHHHHHHHHHHT
T ss_pred ccCCcCHHHHHHHHHhhhhhhhcCC-CHHHHHHHHHHHHHHHHHHHHC
Confidence 4567999999999862 45544 7899999999999998888765
Done!