Conserved Domains in CDD Database
Conserved Domains in CDD Database Detected by RPS-BLAST
Original result of RPS-BLAST against CDD database part I
Original result of RPS-BLASTagainst CDD database part II
Identity Alignment graph Length
Definition
E-value Target 100
integration host factor, beta subunit [Candidatus Liber
PRK00199 94
PRK00199, ihfB, integration host factor subunit beta; R
3e-31 TIGR00988 94
TIGR00988, hip, integration host factor, beta subunit
1e-24 smart00411 90
smart00411, BHL, bacterial (prokaryotic) histone like d
4e-22 COG0776 94
COG0776, HimA, Bacterial nucleoid DNA-binding protein [
6e-20 cd00591 87
cd00591, HU_IHF, Integration host factor (IHF) and HU a
7e-19 PRK10664 90
PRK10664, PRK10664, transcriptional regulator HU subuni
2e-10 PRK00285 99
PRK00285, ihfA, integration host factor subunit alpha;
1e-09 TIGR00987 96
TIGR00987, himA, integration host factor, alpha subunit
2e-08 PRK10753 90
PRK10753, PRK10753, transcriptional regulator HU subuni
3e-06 pfam00216 90
pfam00216, Bac_DNA_binding, Bacterial DNA-binding prote
4e-22
>gnl|CDD|178925 PRK00199, ihfB, integration host factor subunit beta; Reviewed
Back Show alignment and domain information
Score = 128 bits (324), Expect = 3e-31
Identities = 47/91 (51%), Positives = 62/91 (68%)
Query: 1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARL 60
M KS LI +A +NP L+ +DVE V +LEEM+ ALA G R+EIRGFGSFS+ R R+
Sbjct: 1 MTKSELIERLAARNPHLSAKDVENAVKEILEEMSDALARGDRIEIRGFGSFSLHYRPPRV 60
Query: 61 ARAPLAQKVISVEEKMVPFFRAGKNLKERLN 91
R P + + +EEK VP F+ GK L+ER+N
Sbjct: 61 GRNPKTGEKVELEEKYVPHFKPGKELRERVN 91
>gnl|CDD|130061 TIGR00988, hip, integration host factor, beta subunit
Back Show alignment and domain information
Score = 106 bits (267), Expect = 1e-24
Identities = 43/94 (45%), Positives = 55/94 (58%)
Query: 1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARL 60
M KS LI IA + L +DVE V +LE M ALA G R+EIRGFGSFS+ RA R
Sbjct: 1 MTKSELIERIATQQSHLPAKDVEDAVKTMLEHMASALAQGDRIEIRGFGSFSLHYRAPRT 60
Query: 61 ARAPLAQKVISVEEKMVPFFRAGKNLKERLNSPD 94
R P + ++ K VP F+ GK L++R N +
Sbjct: 61 GRNPKTGDSVELDGKYVPHFKPGKELRDRANIYE 94
This protein forms a site-specific DNA-binding heterodimer with the homologous integration host factor alpha subunit. It is closely related to the DNA-binding protein HU. Length = 94
>gnl|CDD|128689 smart00411, BHL, bacterial (prokaryotic) histone like domain
Back Show alignment and domain information
Score = 98.4 bits (246), Expect = 4e-22
Identities = 41/91 (45%), Positives = 57/91 (62%), Gaps = 1/91 (1%)
Query: 1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARL 60
M KS LI IA+K L+ +D + V+ LE +T+AL G +VE+RGFG+F VR+R AR
Sbjct: 1 MTKSELIDAIAEKA-GLSKKDAKAAVDAFLEIITEALKKGEKVELRGFGTFEVRERKARE 59
Query: 61 ARAPLAQKVISVEEKMVPFFRAGKNLKERLN 91
R P + I + K VP F+ GK LK+ +N
Sbjct: 60 GRNPKTGEEIEIPAKKVPKFKPGKALKDAVN 90
>gnl|CDD|31119 COG0776, HimA, Bacterial nucleoid DNA-binding protein [DNA replication, recombination, and repair]
Back Show alignment and domain information
Score = 91.0 bits (226), Expect = 6e-20
Identities = 46/93 (49%), Positives = 61/93 (65%), Gaps = 1/93 (1%)
Query: 1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARL 60
M KS LI IA+K L+ +D E+ V+ LEE+T+ALA G RVE+RGFG+F VR+RAAR
Sbjct: 2 MTKSELIDAIAEKA-GLSKKDAEEAVDAFLEEITEALAKGERVELRGFGTFEVRERAART 60
Query: 61 ARAPLAQKVISVEEKMVPFFRAGKNLKERLNSP 93
R P + I + K VP F+ GK LK+ +N
Sbjct: 61 GRNPKTGEEIKIPAKKVPKFKPGKALKDAVNGA 93
>gnl|CDD|29683 cd00591, HU_IHF, Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and higher-order nucleoprotein complex assembly
Back Show alignment and domain information
Score = 87.4 bits (217), Expect = 7e-19
Identities = 39/87 (44%), Positives = 54/87 (62%), Gaps = 1/87 (1%)
Query: 3 KSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARLAR 62
KS LI IA+K L+ +D E V+ L+ +T+ALA G +VE+ GFG+F VR+RAAR R
Sbjct: 2 KSELIEAIAEKT-GLSKKDAEAAVDAFLDVITEALAKGEKVELPGFGTFEVRERAARTGR 60
Query: 63 APLAQKVISVEEKMVPFFRAGKNLKER 89
P + I + K V F+ GK LK+
Sbjct: 61 NPKTGEEIKIPAKKVVKFKPGKALKDA 87
The dimer subunits associate to form a compact globular core from which two beta ribbon arms (one from each subunit) protrude. The beta arms track and bind the DNA minor groove. Despite sequence and structural similarity, IHF and HU can be distinguished by their different DNA substrate preferences.. Length = 87
>gnl|CDD|170612 PRK10664, PRK10664, transcriptional regulator HU subunit beta; Provisional
Back Show alignment and domain information
Score = 59.3 bits (143), Expect = 2e-10
Identities = 34/91 (37%), Positives = 53/91 (58%), Gaps = 1/91 (1%)
Query: 1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARL 60
M KS LI IA ++ + ++ ++ +T++L G V + GFG+F+V++RAAR
Sbjct: 1 MNKSQLIDKIAA-GADISKAAAGRALDAIIASVTESLKEGDDVALVGFGTFAVKERAART 59
Query: 61 ARAPLAQKVISVEEKMVPFFRAGKNLKERLN 91
R P K I++ VP FRAGK LK+ +N
Sbjct: 60 GRNPQTGKEITIAAAKVPSFRAGKALKDAVN 90
>gnl|CDD|178961 PRK00285, ihfA, integration host factor subunit alpha; Reviewed
Back Show alignment and domain information
Score = 57.2 bits (139), Expect = 1e-09
Identities = 24/75 (32%), Positives = 43/75 (57%)
Query: 17 LNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARLARAPLAQKVISVEEKM 76
L+ ++ +++V + EE+ AL NG +V++ GFG+F +R + R R P + I + +
Sbjct: 18 LSKREAKELVELFFEEIRDALENGEQVKLSGFGNFQLRDKNQRPGRNPKTGEEIPISARR 77
Query: 77 VPFFRAGKNLKERLN 91
V FR + LK R+
Sbjct: 78 VVTFRPSQKLKSRVE 92
>gnl|CDD|130060 TIGR00987, himA, integration host factor, alpha subunit
Back Show alignment and domain information
Score = 53.0 bits (127), Expect = 2e-08
Identities = 25/74 (33%), Positives = 45/74 (60%)
Query: 17 LNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARLARAPLAQKVISVEEKM 76
L+ ++ +++V + EE+ +AL NG +V++ GFG+F +R + R R P + I + +
Sbjct: 17 LSKREAKELVELFFEEIRRALENGEQVKLSGFGNFDLRDKNQRPGRNPKTGEEIPITARR 76
Query: 77 VPFFRAGKNLKERL 90
V FR G+ LK R+
Sbjct: 77 VVTFRPGQKLKSRV 90
This protein forms a site-specific DNA-binding heterodimer with the integration host factor beta subunit. It is closely related to the DNA-binding protein HU. Length = 96
>gnl|CDD|138142 PRK10753, PRK10753, transcriptional regulator HU subunit alpha; Provisional
Back Show alignment and domain information
Score = 45.5 bits (107), Expect = 3e-06
Identities = 32/88 (36%), Positives = 46/88 (52%), Gaps = 1/88 (1%)
Query: 1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARL 60
M K+ LI IA K +L+ + + L +T++L G V++ GFG+F V RA R
Sbjct: 1 MNKTQLIDVIADK-AELSKTQAKAALESTLAAITESLKEGDAVQLVGFGTFKVNHRAERT 59
Query: 61 ARAPLAQKVISVEEKMVPFFRAGKNLKE 88
R P K I + VP F +GK LK+
Sbjct: 60 GRNPQTGKEIKIAAANVPAFVSGKALKD 87
>gnl|CDD|143973 pfam00216, Bac_DNA_binding, Bacterial DNA-binding protein
Back Show alignment and domain information
Score = 98.0 bits (245), Expect = 4e-22
Identities = 41/91 (45%), Positives = 56/91 (61%), Gaps = 1/91 (1%)
Query: 1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARL 60
M K LI IA+K L+ +D E IV+ L+ +T+AL G +VE+RGFG+F VR+R AR
Sbjct: 1 MTKKELIKAIAEKTG-LSKKDAEAIVDAFLDVITEALKKGEKVELRGFGTFEVRERKART 59
Query: 61 ARAPLAQKVISVEEKMVPFFRAGKNLKERLN 91
R P + I + K V F+ GK LKE +N
Sbjct: 60 GRNPKTGEEIKIPAKKVVKFKPGKELKEAVN 90
Conserved Domains in CDD Database Detected by HHsearch
Original result of HHsearch against CDD database
Identity Alignment graph Length
Definition
Probability Target
100
integration host factor, beta subunit [Candidatus Liber
PRK00199 91
ihfB integration host factor subunit beta; Reviewed
99.94 PRK10664 90
transcriptional regulator HU subunit beta; Provisional
99.94 PRK00285 100
ihfA integration host factor subunit alpha; Reviewed
99.94 PRK10753 90
transcriptional regulator HU subunit alpha; Provisional
99.94 COG0776 94
HimA Bacterial nucleoid DNA-binding protein [DNA replic
99.94 smart00411 90
BHL bacterial (prokaryotic) histone like domain.
99.93 TIGR00988 94
hip integration host factor, beta subunit; InterPro: IP
99.92 pfam00216 90
Bac_DNA_binding Bacterial DNA-binding protein.
99.92 cd00591 87
HU_IHF Integration host factor (IHF) and HU are small h
99.89 TIGR00987 96
himA integration host factor, alpha subunit; InterPro:
99.82 TIGR01201 198
HU_rel DNA-binding protein, putative; InterPro: IPR0059
97.9 pfam08006 181
DUF1700 Protein of unknown function (DUF1700). This fam
92.36
>PRK00199 ihfB integration host factor subunit beta; Reviewed
Back Show alignment and domain information
Probab=99.94 E-value=6.3e-27 Score=192.62 Aligned_cols=91 Identities=49% Similarity=0.819 Sum_probs=89.7
Q ss_pred CCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEEECCCCCCEECCCCCCEEEECCCCEEEE
Q ss_conf 98899999999973899989999999999999999986498512034578886214654102588988899468734676
Q gi|254780748|r 1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARLARAPLAQKVISVEEKMVPFF 80 (100)
Q Consensus 1 MtK~eli~~ia~~~~~ls~~~~~~~vd~~~~~i~~~L~~~~~V~i~gfGtF~~~~~~~r~~rNP~Tge~i~i~~~~~v~F 80 (100)
T Consensus 1 M~K~eli~~ia~~~~~l~~~~~~~iv~~~~~~i~~~l~~g~~V~i~gFGtF~~~~r~~R~gRNP~Tge~i~I~~k~~v~F 80 (91)
T PRK00199 1 MTKSELIERLATRQPHLPAKDVEDAVKTMLEEMADALAQGDRIEIRGFGSFSLHYRPPRVGRNPKTGEKVEVEGKYVPHF 80 (91)
T ss_pred CCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCEEEECCEEEEEEEEECCCCCCCCCCCCEEEECCCCCEEE
T ss_conf 97899999999876998999999999999999999997699299634589999985672450849999899659765787
Q ss_pred CCCHHHHHHHC
Q ss_conf 26989999707
Q gi|254780748|r 81 RAGKNLKERLN 91 (100)
Q Consensus 81 k~sk~lk~~iN 91 (100)
T Consensus 81 kpsk~Lk~~lN 91 (91)
T PRK00199 81 KPGKELRDRVN 91 (91)
T ss_pred CCCHHHHHHHC
T ss_conf 78989998519
>PRK10664 transcriptional regulator HU subunit beta; Provisional
Back Show alignment and domain information
Probab=99.94 E-value=1.3e-26 Score=190.52 Aligned_cols=90 Identities=38% Similarity=0.627 Sum_probs=88.8
Q ss_pred CCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEEECCCCCCEECCCCCCEEEECCCCEEEE
Q ss_conf 98899999999973899989999999999999999986498512034578886214654102588988899468734676
Q gi|254780748|r 1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARLARAPLAQKVISVEEKMVPFF 80 (100)
Q Consensus 1 MtK~eli~~ia~~~~~ls~~~~~~~vd~~~~~i~~~L~~~~~V~i~gfGtF~~~~~~~r~~rNP~Tge~i~i~~~~~v~F 80 (100)
T Consensus 1 M~K~eLi~~ia~~~-~ltk~~a~~~v~~~~~~i~~~l~~g~~V~l~gFGtF~v~~r~aR~grNP~Tge~i~Ipa~~v~~F 79 (90)
T PRK10664 1 MNKSQLIDKIAAGA-DISKAAAGRALDAIIASVTESLKEGDDVALVGFGTFAVKERAARTGRNPQTGKEITIAAAKVPSF 79 (90)
T ss_pred CCHHHHHHHHHHHC-CCCHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEEEEEEEEECCCCCCCCCCCCEEEECCCCCEEE
T ss_conf 97899999999870-99999999999999999999997799399800589999876672560919998898658654777
Q ss_pred CCCHHHHHHHC
Q ss_conf 26989999707
Q gi|254780748|r 81 RAGKNLKERLN 91 (100)
Q Consensus 81 k~sk~lk~~iN 91 (100)
T Consensus 80 k~sk~LK~~vN 90 (90)
T PRK10664 80 RAGKALKDAVN 90 (90)
T ss_pred CCCHHHHHHHC
T ss_conf 47989998539
>PRK00285 ihfA integration host factor subunit alpha; Reviewed
Back Show alignment and domain information
Probab=99.94 E-value=3.3e-26 Score=188.01 Aligned_cols=95 Identities=31% Similarity=0.576 Sum_probs=92.1
Q ss_pred CCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEEECCCCCCEECCCCCCEEEECCCCEEEE
Q ss_conf 98899999999973899989999999999999999986498512034578886214654102588988899468734676
Q gi|254780748|r 1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARLARAPLAQKVISVEEKMVPFF 80 (100)
Q Consensus 1 MtK~eli~~ia~~~~~ls~~~~~~~vd~~~~~i~~~L~~~~~V~i~gfGtF~~~~~~~r~~rNP~Tge~i~i~~~~~v~F 80 (100)
T Consensus 4 MtK~eli~~ia~~~-g~s~~~a~~~v~~~~~~i~~~L~~g~~V~i~gFGtF~v~~r~~R~grNP~Tge~i~Ip~r~~v~F 82 (100)
T PRK00285 4 LTKAELAELLFDKV-GLSKREAKELVELFFEEIRDALENGEQVKLSGFGNFQLRDKNQRPGRNPKTGEEIPITARRVVTF 82 (100)
T ss_pred CCHHHHHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEEEEEEEEECCCCCCCCCCCCEEEECCCCCEEE
T ss_conf 27999999999986-95999999999999999999997699288722389999850661452849998899758765787
Q ss_pred CCCHHHHHHHCCCCCC
Q ss_conf 2698999970786100
Q gi|254780748|r 81 RAGKNLKERLNSPDST 96 (100)
Q Consensus 81 k~sk~lk~~iN~~~~~ 96 (100)
T Consensus 83 kpsk~LK~~Vn~~~~~ 98 (100)
T PRK00285 83 RAGQKLKSRVENAHPK 98 (100)
T ss_pred ECCHHHHHHHHCCCCC
T ss_conf 1599999998460634
>PRK10753 transcriptional regulator HU subunit alpha; Provisional
Back Show alignment and domain information
Probab=99.94 E-value=4.9e-26 Score=186.94 Aligned_cols=90 Identities=36% Similarity=0.570 Sum_probs=88.0
Q ss_pred CCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEEECCCCCCEECCCCCCEEEECCCCEEEE
Q ss_conf 98899999999973899989999999999999999986498512034578886214654102588988899468734676
Q gi|254780748|r 1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARLARAPLAQKVISVEEKMVPFF 80 (100)
Q Consensus 1 MtK~eli~~ia~~~~~ls~~~~~~~vd~~~~~i~~~L~~~~~V~i~gfGtF~~~~~~~r~~rNP~Tge~i~i~~~~~v~F 80 (100)
T Consensus 1 MnK~eLi~~ia~~~-~~sk~~~~~~v~~~~~~i~~~L~~g~~V~l~GFGtF~v~~r~aR~grNP~TGe~i~Ipa~~v~~F 79 (90)
T PRK10753 1 MNKTQLIDVIADKA-ELSKTQAKAALESTLAAITESLKEGDAVQLVGFGTFKVNHRAERTGRNPQTGKEIKIAAANVPAF 79 (90)
T ss_pred CCHHHHHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHCCCCEEEECEEEEEEEEECCCCCCCCCCCCEEEECCCCCEEE
T ss_conf 97899999999873-98999999999999999999997699199803289999865781350819999898758764677
Q ss_pred CCCHHHHHHHC
Q ss_conf 26989999707
Q gi|254780748|r 81 RAGKNLKERLN 91 (100)
Q Consensus 81 k~sk~lk~~iN 91 (100)
T Consensus 80 kp~k~LK~~vk 90 (90)
T PRK10753 80 VSGKALKDAVK 90 (90)
T ss_pred CCCHHHHHHHC
T ss_conf 26989998639
>COG0776 HimA Bacterial nucleoid DNA-binding protein [DNA replication, recombination, and repair]
Back Show alignment and domain information
Probab=99.94 E-value=3.8e-26 Score=187.65 Aligned_cols=92 Identities=50% Similarity=0.767 Sum_probs=90.0
Q ss_pred CCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEEECCCCCCEECCCCCCEEEECCCCEEEE
Q ss_conf 98899999999973899989999999999999999986498512034578886214654102588988899468734676
Q gi|254780748|r 1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARLARAPLAQKVISVEEKMVPFF 80 (100)
Q Consensus 1 MtK~eli~~ia~~~~~ls~~~~~~~vd~~~~~i~~~L~~~~~V~i~gfGtF~~~~~~~r~~rNP~Tge~i~i~~~~~v~F 80 (100)
T Consensus 2 mtKseli~~ia~~~-~l~k~~a~~~v~~~~~~i~~aL~~G~~V~l~gFG~F~v~~R~aR~GRNPkTGe~i~I~a~~vp~F 80 (94)
T COG0776 2 MTKSELIDAIAEKA-GLSKKDAEEAVDAFLEEITEALAKGERVELRGFGTFEVRERAARTGRNPKTGEEIKIPAKKVPKF 80 (94)
T ss_pred CCHHHHHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEEEEEEECCCCCCCCCCCCCCEEEECCCCCCCC
T ss_conf 87899999999970-98799999999999999999997699489830046676202787787999998686357523355
Q ss_pred CCCHHHHHHHCCC
Q ss_conf 2698999970786
Q gi|254780748|r 81 RAGKNLKERLNSP 93 (100)
Q Consensus 81 k~sk~lk~~iN~~ 93 (100)
T Consensus 81 k~gK~LK~~vn~~ 93 (94)
T COG0776 81 KPGKALKDAVNGA 93 (94)
T ss_pred CCCHHHHHHHHCC
T ss_conf 8768999988334
>smart00411 BHL bacterial (prokaryotic) histone like domain
Back Show alignment and domain information
Probab=99.93 E-value=4.8e-25 Score=180.67 Aligned_cols=90 Identities=46% Similarity=0.710 Sum_probs=88.8
Q ss_pred CCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEEECCCCCCEECCCCCCEEEECCCCEEEE
Q ss_conf 98899999999973899989999999999999999986498512034578886214654102588988899468734676
Q gi|254780748|r 1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARLARAPLAQKVISVEEKMVPFF 80 (100)
Q Consensus 1 MtK~eli~~ia~~~~~ls~~~~~~~vd~~~~~i~~~L~~~~~V~i~gfGtF~~~~~~~r~~rNP~Tge~i~i~~~~~v~F 80 (100)
T Consensus 1 MtK~eli~~ia~~~-~~s~~~~~~~v~~~~~~i~~~L~~~~~v~i~~fG~F~~~~~~~R~grNP~Tge~i~i~~~~~v~F 79 (90)
T smart00411 1 MTKSELIDAIAEKA-GLSKKDAKAAVDAFLEIITEALKKGEKVELRGFGTFEVRERKAREGRNPKTGEEIEIPAKKVPKF 79 (90)
T ss_pred CCHHHHHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHCCCEEEECEEEEEEEEEECCEEEECCCCCCEEEECCCCCEEE
T ss_conf 97899999999986-96999999999999999999996799399340499999970661347879998899758765798
Q ss_pred CCCHHHHHHHC
Q ss_conf 26989999707
Q gi|254780748|r 81 RAGKNLKERLN 91 (100)
Q Consensus 81 k~sk~lk~~iN 91 (100)
T Consensus 80 k~sk~lk~~iN 90 (90)
T smart00411 80 KPGKALKDAVN 90 (90)
T ss_pred CCCHHHHHHHC
T ss_conf 06989998639
>TIGR00988 hip integration host factor, beta subunit; InterPro: IPR005685 Integration host factor (IHF) is a heterodimeric protein consisting of alpha (IPR005684 from INTERPRO) and beta subunits
Back Show alignment and domain information
Probab=99.92 E-value=9.1e-26 Score=185.25 Aligned_cols=94 Identities=49% Similarity=0.771 Sum_probs=92.1
Q ss_pred CCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEEECCCCCCEECCCCCCEEEECCCCEEEE
Q ss_conf 98899999999973899989999999999999999986498512034578886214654102588988899468734676
Q gi|254780748|r 1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARLARAPLAQKVISVEEKMVPFF 80 (100)
Q Consensus 1 MtK~eli~~ia~~~~~ls~~~~~~~vd~~~~~i~~~L~~~~~V~i~gfGtF~~~~~~~r~~rNP~Tge~i~i~~~~~v~F 80 (100)
T Consensus 1 M~kSELI~~i~~~~~~l~~k~VE~~v~~~lE~~~~alA~GdRiE~RGFGsFSl~~R~~R~GRNPkTG~~V~ld~K~VP~F 80 (94)
T TIGR00988 1 MTKSELIERIATEQSHLFAKDVEKAVKTMLEEMIEALARGDRIEIRGFGSFSLHYRAPRTGRNPKTGESVALDGKYVPHF 80 (94)
T ss_pred CCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCEEECCCCCCCCCCCCCCCEEEECCCCCCCC
T ss_conf 93378889987407875533389999999999999860798467601442000005788898899887665478042840
Q ss_pred CCCHHHHHHHCCCC
Q ss_conf 26989999707861
Q gi|254780748|r 81 RAGKNLKERLNSPD 94 (100)
Q Consensus 81 k~sk~lk~~iN~~~ 94 (100)
T Consensus 81 K~GK~LRDR~N~~e 94 (94)
T TIGR00988 81 KPGKELRDRLNEGE 94 (94)
T ss_pred CCCCCHHCCCCCCC
T ss_conf 48630110047889
IHF binds the minor groove of DNA in a sequence-specific manner to induce a large bend. This bending stabilises distinct DNA conformations that are required during several bacterial processes, such as recombination, transposition, replication and transcription .; GO: 0003677 DNA binding, 0005694 chromosome.
>pfam00216 Bac_DNA_binding Bacterial DNA-binding protein
Back Show alignment and domain information
Probab=99.92 E-value=1.2e-24 Score=178.09 Aligned_cols=90 Identities=46% Similarity=0.705 Sum_probs=88.6
Q ss_pred CCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEEECCCCCCEECCCCCCEEEECCCCEEEE
Q ss_conf 98899999999973899989999999999999999986498512034578886214654102588988899468734676
Q gi|254780748|r 1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARLARAPLAQKVISVEEKMVPFF 80 (100)
Q Consensus 1 MtK~eli~~ia~~~~~ls~~~~~~~vd~~~~~i~~~L~~~~~V~i~gfGtF~~~~~~~r~~rNP~Tge~i~i~~~~~v~F 80 (100)
T Consensus 1 mtK~~li~~ia~~~-~ls~~~~~~~v~~~~~~i~~~L~~~~~v~i~gfG~F~~~~~~~r~~rNP~Tge~i~i~~~~~v~F 79 (90)
T pfam00216 1 MTKKELIKAIAEKT-GLSKKDAEAIVDAFLDVITEALKKGEKVELRGFGTFEVRERKARTGRNPKTGEEIKIPAKKVVKF 79 (90)
T ss_pred CCHHHHHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHCCCEEEECCEEEEEEEEECCEEEECCCCCCEEEECCCCCEEE
T ss_conf 97899999999864-96999999999999999999996799498554589999960565428869997899759765898
Q ss_pred CCCHHHHHHHC
Q ss_conf 26989999707
Q gi|254780748|r 81 RAGKNLKERLN 91 (100)
Q Consensus 81 k~sk~lk~~iN 91 (100)
T Consensus 80 k~sk~lk~~iN 90 (90)
T pfam00216 80 KPGKELKEAVN 90 (90)
T ss_pred ECCHHHHHHHC
T ss_conf 06989998639
>cd00591 HU_IHF Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and higher-order nucleoprotein complex assembly
Back Show alignment and domain information
Probab=99.89 E-value=6.7e-23 Score=167.07 Aligned_cols=87 Identities=45% Similarity=0.674 Sum_probs=84.8
Q ss_pred CHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEEECCCCCCEECCCCCCEEEECCCCEEEEC
Q ss_conf 88999999999738999899999999999999999864985120345788862146541025889888994687346762
Q gi|254780748|r 2 IKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARLARAPLAQKVISVEEKMVPFFR 81 (100)
Q Consensus 2 tK~eli~~ia~~~~~ls~~~~~~~vd~~~~~i~~~L~~~~~V~i~gfGtF~~~~~~~r~~rNP~Tge~i~i~~~~~v~Fk 81 (100)
T Consensus 1 TK~dLi~~ia~~~-~~s~~~~~~~v~~~~~~i~~~L~~~~~V~i~~fG~F~~~~~~~r~grNP~Tge~i~i~~~~~v~Fk 79 (87)
T cd00591 1 TKSELIEAIAEKT-GLSKKDAEAAVDAFLDVITEALAKGEKVELPGFGTFEVRERAARTGRNPKTGEEIKIPAKKVVKFK 79 (87)
T ss_pred CHHHHHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHCCCEEEECCCEEEEEEEECCEEEECCCCCCEEEECCCCCEEEC
T ss_conf 9899999999986-969999999999999999999977996996360799999825624488899988997597667975
Q ss_pred CCHHHHHH
Q ss_conf 69899997
Q gi|254780748|r 82 AGKNLKER 89 (100)
Q Consensus 82 ~sk~lk~~ 89 (100)
T Consensus 80 ~sk~lK~~ 87 (87)
T cd00591 80 PGKALKDA 87 (87)
T ss_pred CCHHHCCC
T ss_conf 08787179
The dimer subunits associate to form a compact globular core from which two beta ribbon arms (one from each subunit) protrude. The beta arms track and bind the DNA minor groove. Despite sequence and structural similarity, IHF and HU can be distinguished by their different DNA substrate preferences.
>TIGR00987 himA integration host factor, alpha subunit; InterPro: IPR005684 Integration host factor (IHF) is a heterodimeric protein consisting of alpha and beta (IPR005685 from INTERPRO) subunits
Back Show alignment and domain information
Probab=99.82 E-value=2.3e-20 Score=150.93 Aligned_cols=94 Identities=29% Similarity=0.586 Sum_probs=90.4
Q ss_pred CCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEEECCCCCCEECCCCCCEEEECCCCEEEE
Q ss_conf 98899999999973899989999999999999999986498512034578886214654102588988899468734676
Q gi|254780748|r 1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARLARAPLAQKVISVEEKMVPFF 80 (100)
Q Consensus 1 MtK~eli~~ia~~~~~ls~~~~~~~vd~~~~~i~~~L~~~~~V~i~gfGtF~~~~~~~r~~rNP~Tge~i~i~~~~~v~F 80 (100)
T Consensus 2 LT~~~~sE~~f~~~-GLs~~ea~~LVE~~~~~~~~AL~~gE~VKlS~FG~F~~RDK~~R~GRNPKTGEeiPI~~RRV~~F 80 (96)
T TIGR00987 2 LTKAELSEALFREL-GLSKREAKELVELFLEEIRDALERGEQVKLSGFGNFDLRDKTQRPGRNPKTGEEIPITARRVVTF 80 (96)
T ss_pred CCHHHHHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEE
T ss_conf 50557889999982-88855778999999999999986388465303655210107778765579988788677413532
Q ss_pred CCCHHHHHHHCCCCC
Q ss_conf 269899997078610
Q gi|254780748|r 81 RAGKNLKERLNSPDS 95 (100)
Q Consensus 81 k~sk~lk~~iN~~~~ 95 (100)
T Consensus 81 RP~~~lK~RV~~~~~ 95 (96)
T TIGR00987 81 RPGQKLKDRVEERNA 95 (96)
T ss_pred CCCHHHHHHHHHHCC
T ss_conf 764568899875158
IHF binds the minor groove of DNA in a sequence-specific manner to induce a large bend. This bending stabilises distinct DNA conformations that are required during several bacterial processes, such as recombination, transposition, replication and transcription .; GO: 0003677 DNA binding, 0005694 chromosome.
>TIGR01201 HU_rel DNA-binding protein, putative; InterPro: IPR005902 This family of proteins is related to, but longer than, DNA-binding protein HU
Back Show alignment and domain information
Probab=97.90 E-value=3.8e-05 Score=54.40 Aligned_cols=79 Identities=23% Similarity=0.292 Sum_probs=65.8
Q ss_pred CHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEEECCCCCCEECCCCCC---EEEECC--CC
Q ss_conf 8899999999973899989999999999999999986498512034578886214654102588988---899468--73
Q gi|254780748|r 2 IKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARLARAPLAQK---VISVEE--KM 76 (100)
Q Consensus 2 tK~eli~~ia~~~~~ls~~~~~~~vd~~~~~i~~~L~~~~~V~i~gfGtF~~~~~~~r~~rNP~Tge---~i~i~~--~~ 76 (100)
T Consensus 35 ~~~~~~~~ia~~S-~~s~GDV~~i~~~L~~~l~~eL~~G~~v~lg~~G~FR~~~-~~kg-~~ve~~eGGt~v~~~~~~~~ 111 (198)
T TIGR01201 35 DFEEIAELIAEES-SLSPGDVKGILDRLAYVLRRELASGKTVRLGEIGTFRLSA-TAKG-SGVEEAEGGTEVSAEQVKKA 111 (198)
T ss_pred CHHHHHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHCCCCEEEECCCEEEEEEE-EECC-CCCCCCCCCCCCCHHHHCCC
T ss_conf 3789999986764-6885689999999999999971379869874732589986-1032-43646677821167652122
Q ss_pred EEEECCC
Q ss_conf 4676269
Q gi|254780748|r 77 VPFFRAG 83 (100)
Q Consensus 77 ~v~Fk~s 83 (100)
T Consensus 112 rv~F~p~ 118 (198)
T TIGR01201 112 RVLFTPE 118 (198)
T ss_pred CEEECCC
T ss_conf 2154223
It contains a distinctive domain architecture when compared to HU and related histone-like DNA-binding. Members include, so far, a protein from Bacteroides fragilis and ten from Porphyromonas gingivalis (Bacteroides gingivalis). Both species are oral pathogens. .
>pfam08006 DUF1700 Protein of unknown function (DUF1700)
Back Show alignment and domain information
Probab=92.36 E-value=0.42 Score=28.72 Aligned_cols=50 Identities=18% Similarity=0.228 Sum_probs=42.0
Q ss_pred CCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCC--CCEEEEE
Q ss_conf 9889999999997389998999999999999999998649851--2034578
Q gi|254780748|r 1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRV--EIRGFGS 50 (100)
Q Consensus 1 MtK~eli~~ia~~~~~ls~~~~~~~vd~~~~~i~~~L~~~~~V--~i~gfGt 50 (100)
T Consensus 1 M~k~efL~~L~~~L~~lp~~e~~~il~~y~e~f~~~~~~G~se~ei~~~LG~ 52 (181)
T pfam08006 1 MNKIEFLNELESSLKKLPEEERKDILYDYEEHFYEGEEEGKSEEEIIKELGN 52 (181)
T ss_pred CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCC
T ss_conf 9899999999998865999999999999999999876689999999988299
This family contains many hypothetical bacterial proteins and two putative membrane proteins.
Homologous Domains in SCOP and MMDB Database
Homologous Domains in SCOP70 (Version1.75) Database Detected by RPS-BLAST
Original result of RPS-BLAST against SCOP70(version1.75) database
Identity Alignment graph Length
Definition
E-value Target 100
integration host factor, beta subunit [Candidatus Liber
d1owfb_ 94
a.55.1.1 (B:) Integration host factor beta subunit (IHF
3e-19 d1p71a_ 94
a.55.1.1 (A:) HU protein {Anabaena sp. [TaxId: 1167]} L
8e-17 d1huua_ 90
a.55.1.1 (A:) HU protein {Bacillus stearothermophilus [
1e-16 d1mula_ 90
a.55.1.1 (A:) HU protein {Escherichia coli [TaxId: 562]
3e-16 d1owfa_ 96
a.55.1.1 (A:) Integration host factor alpha subunit (IH
3e-16 d2o97b1 90
a.55.1.1 (B:1-90) HU protein {Escherichia coli, beta-is
5e-16 d1b8za_ 90
a.55.1.1 (A:) HU protein {Thermotoga maritima [TaxId: 2
2e-15 d1exea_ 99
a.55.1.1 (A:) Transcription factor 1, TF1 {Bacteriophag
3e-15
>d1owfb_ a.55.1.1 (B:) Integration host factor beta subunit (IHFB) {Escherichia coli [TaxId: 562]} Length = 94
Back Hide information, alignment and structure
class: All alpha proteins
fold: IHF-like DNA-binding proteins
superfamily: IHF-like DNA-binding proteins
family: Prokaryotic DNA-bending protein
domain: Integration host factor beta subunit (IHFB)
species: Escherichia coli [TaxId: 562]
Score = 87.2 bits (216), Expect = 3e-19
Identities = 39/91 (42%), Positives = 51/91 (56%)
Query: 1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARL 60
M KS LI +A + + + VE V +LE M LA G R+ IRGFGSFS+ RA R
Sbjct: 1 MTKSELIERLATQQSHIPAKTVEDAVKEMLEHMASTLAQGERIAIRGFGSFSLHYRAPRT 60
Query: 61 ARAPLAQKVISVEEKMVPFFRAGKNLKERLN 91
R P + +E K VP F+ GK L++R N
Sbjct: 61 GRNPKTGDKVELEGKYVPHFKPGKELRDRAN 91
>d1p71a_ a.55.1.1 (A:) HU protein {Anabaena sp. [TaxId: 1167]} Length = 94
Back Show information, alignment and structure
class: All alpha proteins
fold: IHF-like DNA-binding proteins
superfamily: IHF-like DNA-binding proteins
family: Prokaryotic DNA-bending protein
domain: HU protein
species: Anabaena sp. [TaxId: 1167]
Score = 79.5 bits (196), Expect = 8e-17
Identities = 29/95 (30%), Positives = 52/95 (54%), Gaps = 1/95 (1%)
Query: 1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARL 60
M K L+ +A+K + + + ++ LE + +A+++G +V + GFGSF R+R AR
Sbjct: 1 MNKGELVDAVAEKA-SVTKKQADAVLTAALETIIEAVSSGDKVTLVGFGSFESRERKARE 59
Query: 61 ARAPLAQKVISVEEKMVPFFRAGKNLKERLNSPDS 95
R P + + + VP F AGK +E++ P +
Sbjct: 60 GRNPKTNEKMEIPATRVPAFSAGKLFREKVAPPKA 94
>d1huua_ a.55.1.1 (A:) HU protein {Bacillus stearothermophilus [TaxId: 1422]} Length = 90
Back Show information, alignment and structure
class: All alpha proteins
fold: IHF-like DNA-binding proteins
superfamily: IHF-like DNA-binding proteins
family: Prokaryotic DNA-bending protein
domain: HU protein
species: Bacillus stearothermophilus [TaxId: 1422]
Score = 79.1 bits (195), Expect = 1e-16
Identities = 33/90 (36%), Positives = 55/90 (61%), Gaps = 1/90 (1%)
Query: 1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARL 60
M K+ LI +A+ + L+ +D K V+ + + +T+AL G +V++ GFG+F VR+RAAR
Sbjct: 1 MNKTELINAVAETS-GLSKKDATKAVDAVFDSITEALRKGDKVQLIGFGNFEVRERAARK 59
Query: 61 ARAPLAQKVISVEEKMVPFFRAGKNLKERL 90
R P + + + VP F+ GK LK+ +
Sbjct: 60 GRNPQTGEEMEIPASKVPAFKPGKALKDAV 89
>d1mula_ a.55.1.1 (A:) HU protein {Escherichia coli [TaxId: 562]} Length = 90
Back Show information, alignment and structure
class: All alpha proteins
fold: IHF-like DNA-binding proteins
superfamily: IHF-like DNA-binding proteins
family: Prokaryotic DNA-bending protein
domain: HU protein
species: Escherichia coli [TaxId: 562]
Score = 77.5 bits (191), Expect = 3e-16
Identities = 32/90 (35%), Positives = 48/90 (53%), Gaps = 1/90 (1%)
Query: 1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARL 60
M K+ LI IA+K +L+ + + L +T++L G V++ GFG+F V RA R
Sbjct: 1 MNKTQLIDVIAEK-AELSKTQAKAALESTLAAITESLKEGDAVQLVGFGTFKVNHRAERT 59
Query: 61 ARAPLAQKVISVEEKMVPFFRAGKNLKERL 90
R P K I + VP F +GK LK+ +
Sbjct: 60 GRNPQTGKEIKIAAANVPAFVSGKALKDAV 89
>d1owfa_ a.55.1.1 (A:) Integration host factor alpha subunit (IHFA) {Escherichia coli [TaxId: 562]} Length = 96
Back Show information, alignment and structure
class: All alpha proteins
fold: IHF-like DNA-binding proteins
superfamily: IHF-like DNA-binding proteins
family: Prokaryotic DNA-bending protein
domain: Integration host factor alpha subunit (IHFA)
species: Escherichia coli [TaxId: 562]
Score = 77.6 bits (191), Expect = 3e-16
Identities = 28/92 (30%), Positives = 52/92 (56%), Gaps = 1/92 (1%)
Query: 1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARL 60
+ K+ + + K L+ +D +++V + EE+ +AL NG +V++ GFG+F +R + R
Sbjct: 2 LTKAEMSEYLFDKL-GLSKRDAKELVELFFEEIRRALENGEQVKLSGFGNFDLRDKNQRP 60
Query: 61 ARAPLAQKVISVEEKMVPFFRAGKNLKERLNS 92
R P + I + + V FR G+ LK R+ +
Sbjct: 61 GRNPKTGEDIPITARRVVTFRPGQKLKSRVEN 92
>d2o97b1 a.55.1.1 (B:1-90) HU protein {Escherichia coli, beta-isoform [TaxId: 562]} Length = 90
Back Show information, alignment and structure
class: All alpha proteins
fold: IHF-like DNA-binding proteins
superfamily: IHF-like DNA-binding proteins
family: Prokaryotic DNA-bending protein
domain: HU protein
species: Escherichia coli, beta-isoform [TaxId: 562]
Score = 76.8 bits (189), Expect = 5e-16
Identities = 34/91 (37%), Positives = 53/91 (58%), Gaps = 1/91 (1%)
Query: 1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARL 60
M KS LI IA ++ + ++ ++ +T++L G V + GFG+F+V++RAAR
Sbjct: 1 MNKSQLIDKIAAG-ADISKAAAGRALDAIIASVTESLKEGDDVALVGFGTFAVKERAART 59
Query: 61 ARAPLAQKVISVEEKMVPFFRAGKNLKERLN 91
R P K I++ VP FRAGK LK+ +N
Sbjct: 60 GRNPQTGKEITIAAAKVPSFRAGKALKDAVN 90
>d1b8za_ a.55.1.1 (A:) HU protein {Thermotoga maritima [TaxId: 2336]} Length = 90
Back Show information, alignment and structure
class: All alpha proteins
fold: IHF-like DNA-binding proteins
superfamily: IHF-like DNA-binding proteins
family: Prokaryotic DNA-bending protein
domain: HU protein
species: Thermotoga maritima [TaxId: 2336]
Score = 74.8 bits (184), Expect = 2e-15
Identities = 42/90 (46%), Positives = 59/90 (65%), Gaps = 1/90 (1%)
Query: 1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARL 60
M K LI +AKK +DV+ I++ +LE +T+ALA G +V+I GFGSF VRK AAR
Sbjct: 1 MNKKELIDRVAKKA-GAKKKDVKLILDTILETITEALAKGEKVQIVGFGSFEVRKAAARK 59
Query: 61 ARAPLAQKVISVEEKMVPFFRAGKNLKERL 90
P +K I++ E+ VP F+ GK LKE++
Sbjct: 60 GVNPQTRKPITIPERKVPKFKPGKALKEKV 89
>d1exea_ a.55.1.1 (A:) Transcription factor 1, TF1 {Bacteriophage SPO1 [TaxId: 10685]} Length = 99
Back Show information, alignment and structure
class: All alpha proteins
fold: IHF-like DNA-binding proteins
superfamily: IHF-like DNA-binding proteins
family: Prokaryotic DNA-bending protein
domain: Transcription factor 1, TF1
species: Bacteriophage SPO1 [TaxId: 10685]
Score = 74.1 bits (182), Expect = 3e-15
Identities = 23/91 (25%), Positives = 43/91 (47%), Gaps = 1/91 (1%)
Query: 1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARL 60
M K+ LI IA+ L V K++ + +T+ +A G +V++ GF + R AR
Sbjct: 1 MNKTELIKAIAQD-TGLTQVSVSKMLASFEKIITETVAKGDKVQLTGFLNIKPVARQARK 59
Query: 61 ARAPLAQKVISVEEKMVPFFRAGKNLKERLN 91
P Q+ + + + + G++LK+
Sbjct: 60 GFNPQTQEALEIAPSVGVSVKPGESLKKAAE 90
Homologous Domains in SCOP70 (Version 1.75) Database Detected by HHsearch
Original result of HHsearch against SCOP70(version1.75) database
Identity Alignment graph Length
Definition
Probability Target 100
integration host factor, beta subunit [Candidatus Liber
d1p71a_ 94
HU protein {Anabaena sp. [TaxId: 1167]}
99.93 d1owfb_ 94
Integration host factor beta subunit (IHFB) {Escherichi
99.93 d1owfa_ 96
Integration host factor alpha subunit (IHFA) {Escherich
99.93 d2o97b1 90
HU protein {Escherichia coli, beta-isoform [TaxId: 562]
99.92 d1mula_ 90
HU protein {Escherichia coli [TaxId: 562]}
99.91 d1exea_ 99
Transcription factor 1, TF1 {Bacteriophage SPO1 [TaxId:
99.91 d1b8za_ 90
HU protein {Thermotoga maritima [TaxId: 2336]}
99.91 d1huua_ 90
HU protein {Bacillus stearothermophilus [TaxId: 1422]}
99.9
>d1p71a_ a.55.1.1 (A:) HU protein {Anabaena sp. [TaxId: 1167]}
Back Hide information, alignment and structure
class: All alpha proteins
fold: IHF-like DNA-binding proteins
superfamily: IHF-like DNA-binding proteins
family: Prokaryotic DNA-bending protein
domain: HU protein
species: Anabaena sp. [TaxId: 1167]
Probab=99.93 E-value=1.9e-26 Score=186.66 Aligned_cols=94 Identities=31% Similarity=0.592 Sum_probs=91.8
Q ss_pred CCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEEECCCCCCEECCCCCCEEEECCCCEEEE
Q ss_conf 98899999999973899989999999999999999986498512034578886214654102588988899468734676
Q gi|254780748|r 1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARLARAPLAQKVISVEEKMVPFF 80 (100)
Q Consensus 1 MtK~eli~~ia~~~~~ls~~~~~~~vd~~~~~i~~~L~~~~~V~i~gfGtF~~~~~~~r~~rNP~Tge~i~i~~~~~v~F 80 (100)
|||+|||+.||+++ ++++++++.++|+|++.|.++|..|++|+|+|||+|+++.+++|.||||+|||.+.||++++|+|
T Consensus 1 M~K~eli~~ia~~~-~ls~~~~~~~v~~~~~~i~~~L~~~~~V~l~~fG~F~~~~~~~R~grNP~Tge~i~ip~k~~v~F 79 (94)
T d1p71a_ 1 MNKGELVDAVAEKA-SVTKKQADAVLTAALETIIEAVSSGDKVTLVGFGSFESRERKAREGRNPKTNEKMEIPATRVPAF 79 (94)
T ss_dssp CBHHHHHHHHHHHH-TCCHHHHHHHHHHHHHHHHHHHHTTCCEEETTTEEEEEEEECCEEEECTTTCCEEEECCEEEEEE
T ss_pred CCHHHHHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHCCCEEEEECEEEEEEEECCCCEEECCCCCCEEEECCCCEEEE
T ss_conf 97899999999855-96999999999999999999984599799934378988823663048899998898628720899
Q ss_pred CCCHHHHHHHCCCCC
Q ss_conf 269899997078610
Q gi|254780748|r 81 RAGKNLKERLNSPDS 95 (100)
Q Consensus 81 k~sk~lk~~iN~~~~ 95 (100)
+||+.|++.||++.+
T Consensus 80 k~sk~Lk~~vN~~ka 94 (94)
T d1p71a_ 80 SAGKLFREKVAPPKA 94 (94)
T ss_dssp EECHHHHHHHSCCCC
T ss_pred ECCHHHHHHHCCCCC
T ss_conf 559999997677899
>d1owfb_ a.55.1.1 (B:) Integration host factor beta subunit (IHFB) {Escherichia coli [TaxId: 562]}
Back Show information, alignment and structure
class: All alpha proteins
fold: IHF-like DNA-binding proteins
superfamily: IHF-like DNA-binding proteins
family: Prokaryotic DNA-bending protein
domain: Integration host factor beta subunit (IHFB)
species: Escherichia coli [TaxId: 562]
Probab=99.93 E-value=2.2e-26 Score=186.22 Aligned_cols=93 Identities=42% Similarity=0.669 Sum_probs=90.8
Q ss_pred CCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEEECCCCCCEECCCCCCEEEECCCCEEEE
Q ss_conf 98899999999973899989999999999999999986498512034578886214654102588988899468734676
Q gi|254780748|r 1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARLARAPLAQKVISVEEKMVPFF 80 (100)
Q Consensus 1 MtK~eli~~ia~~~~~ls~~~~~~~vd~~~~~i~~~L~~~~~V~i~gfGtF~~~~~~~r~~rNP~Tge~i~i~~~~~v~F 80 (100)
|||+|||+.||.+++++++++++.++|+|++.|.++|.+|++|+|+|||+|+++.+++|.||||+|||.+.||++++|+|
T Consensus 1 MtK~eli~~ia~~~~~ls~~~~~~~v~~~~~~i~~~L~~~~~V~l~gfG~F~~~~~~~R~grNP~Tge~i~ip~k~~v~F 80 (94)
T d1owfb_ 1 MTKSELIERLATQQSHIPAKTVEDAVKEMLEHMASTLAQGERIAIRGFGSFSLHYRAPRTGRNPKTGDKVELEGKYVPHF 80 (94)
T ss_dssp CBHHHHHHHHHHHCTTSCHHHHHHHHHHHHHHHHHHHHTTCCEEETTTEEEEEEEECCEEEECTTTCCEEEECCEEEEEE
T ss_pred CCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCEEEECCEEEEEEEECCCCCCCCCCCCCEEEECCCCCEEE
T ss_conf 97899999999867999899999999999999999987699287336037887602664315889999898638630898
Q ss_pred CCCHHHHHHHCCC
Q ss_conf 2698999970786
Q gi|254780748|r 81 RAGKNLKERLNSP 93 (100)
Q Consensus 81 k~sk~lk~~iN~~ 93 (100)
+||+.|+++||..
T Consensus 81 k~sk~lk~~vN~~ 93 (94)
T d1owfb_ 81 KPGKELRDRANIY 93 (94)
T ss_dssp EECHHHHHHHCCC
T ss_pred ECCHHHHHHHCCC
T ss_conf 1699999987539
>d1owfa_ a.55.1.1 (A:) Integration host factor alpha subunit (IHFA) {Escherichia coli [TaxId: 562]}
Back Show information, alignment and structure
class: All alpha proteins
fold: IHF-like DNA-binding proteins
superfamily: IHF-like DNA-binding proteins
family: Prokaryotic DNA-bending protein
domain: Integration host factor alpha subunit (IHFA)
species: Escherichia coli [TaxId: 562]
Probab=99.93 E-value=7.1e-26 Score=183.05 Aligned_cols=94 Identities=30% Similarity=0.569 Sum_probs=91.8
Q ss_pred CCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEEECCCCCCEECCCCCCEEEECCCCEEEE
Q ss_conf 98899999999973899989999999999999999986498512034578886214654102588988899468734676
Q gi|254780748|r 1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARLARAPLAQKVISVEEKMVPFF 80 (100)
Q Consensus 1 MtK~eli~~ia~~~~~ls~~~~~~~vd~~~~~i~~~L~~~~~V~i~gfGtF~~~~~~~r~~rNP~Tge~i~i~~~~~v~F 80 (100)
|||+|||+.||+++ ++++++++.++|+|++.|.++|.+|++|+|+|||+|+++.+++|.||||+|||.++||++++|+|
T Consensus 2 mTK~eli~~ia~~~-~lsk~~~~~~~~~~~~~i~~~L~~g~~V~l~gfGtF~~~~~~~r~~rNP~Tge~i~ip~~~~v~F 80 (96)
T d1owfa_ 2 LTKAEMSEYLFDKL-GLSKRDAKELVELFFEEIRRALENGEQVKLSGFGNFDLRDKNQRPGRNPKTGEDIPITARRVVTF 80 (96)
T ss_dssp BCHHHHHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHTTCCEEETTTEEEEEEEECCEEEECSSSCCEEEECCEEEEEE
T ss_pred CCHHHHHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHCCCEEEECCEEEEEEEECCCCCEECCCCCCEEEECCCCEEEE
T ss_conf 78899999999985-98999999999999999999985699799667778999960660126889998898548613899
Q ss_pred CCCHHHHHHHCCCCC
Q ss_conf 269899997078610
Q gi|254780748|r 81 RAGKNLKERLNSPDS 95 (100)
Q Consensus 81 k~sk~lk~~iN~~~~ 95 (100)
+||+.|++.||+..+
T Consensus 81 k~sk~lk~~vn~~~~ 95 (96)
T d1owfa_ 81 RPGQKLKSRVENASP 95 (96)
T ss_dssp EECHHHHHHHHTCCC
T ss_pred EECHHHHHHHHCCCC
T ss_conf 729999999835499
>d2o97b1 a.55.1.1 (B:1-90) HU protein {Escherichia coli, beta-isoform [TaxId: 562]}
Back Show information, alignment and structure
class: All alpha proteins
fold: IHF-like DNA-binding proteins
superfamily: IHF-like DNA-binding proteins
family: Prokaryotic DNA-bending protein
domain: HU protein
species: Escherichia coli, beta-isoform [TaxId: 562]
Probab=99.92 E-value=5.5e-26 Score=183.74 Aligned_cols=90 Identities=38% Similarity=0.627 Sum_probs=88.5
Q ss_pred CCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEEECCCCCCEECCCCCCEEEECCCCEEEE
Q ss_conf 98899999999973899989999999999999999986498512034578886214654102588988899468734676
Q gi|254780748|r 1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARLARAPLAQKVISVEEKMVPFF 80 (100)
Q Consensus 1 MtK~eli~~ia~~~~~ls~~~~~~~vd~~~~~i~~~L~~~~~V~i~gfGtF~~~~~~~r~~rNP~Tge~i~i~~~~~v~F 80 (100)
|||+|||+.||+++ ++++++++.++|.|+++|.++|.+|++|+|+|||+|+++.+++|.||||+|||.+.||++++|+|
T Consensus 1 M~K~eLi~~ia~~~-~l~~~~~~~~v~~~~~~i~~~L~~~~~v~l~~fG~F~~~~~~~r~~rNP~Tge~i~ip~k~~v~F 79 (90)
T d2o97b1 1 MNKSQLIDKIAAGA-DISKAAAGRALDAIIASVTESLKEGDDVALVGFGTFAVKERAARTGRNPQTGKEITIAAAKVPSF 79 (90)
T ss_dssp CBHHHHHHHHHHTT-C-CHHHHHHHHHHHHHHHHHHHHTTCCEEETTTEEEEEECCC------------------CEEEE
T ss_pred CCHHHHHHHHHHCC-CCCHHHHHHHHHHHHHHHHHHHHCCCEEECCCEEEEEEEEECCCEEECCCCCCEEEECCCCEEEE
T ss_conf 97899999999720-98999999999999999999997398173242279999850464008899997899528722899
Q ss_pred CCCHHHHHHHC
Q ss_conf 26989999707
Q gi|254780748|r 81 RAGKNLKERLN 91 (100)
Q Consensus 81 k~sk~lk~~iN 91 (100)
+||+.|++.||
T Consensus 80 kpsk~lk~~lN 90 (90)
T d2o97b1 80 RAGKALKDAVN 90 (90)
T ss_dssp EECHHHHHHCC
T ss_pred ECCHHHHHHHC
T ss_conf 54999997539
>d1mula_ a.55.1.1 (A:) HU protein {Escherichia coli [TaxId: 562]}
Back Show information, alignment and structure
class: All alpha proteins
fold: IHF-like DNA-binding proteins
superfamily: IHF-like DNA-binding proteins
family: Prokaryotic DNA-bending protein
domain: HU protein
species: Escherichia coli [TaxId: 562]
Probab=99.91 E-value=5e-25 Score=177.67 Aligned_cols=90 Identities=36% Similarity=0.573 Sum_probs=87.9
Q ss_pred CCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEEECCCCCCEECCCCCCEEEECCCCEEEE
Q ss_conf 98899999999973899989999999999999999986498512034578886214654102588988899468734676
Q gi|254780748|r 1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARLARAPLAQKVISVEEKMVPFF 80 (100)
Q Consensus 1 MtK~eli~~ia~~~~~ls~~~~~~~vd~~~~~i~~~L~~~~~V~i~gfGtF~~~~~~~r~~rNP~Tge~i~i~~~~~v~F 80 (100)
|||+|||+.||+++ ++++++++.++|+|++.|.++|..|++|+|+|||+|+++.+++|.||||+|||.++||++++|+|
T Consensus 1 M~K~eli~~ia~~~-~ltk~~~~~~v~~~~~~i~~~L~~~~~v~l~gfG~F~~~~~~~R~grNP~Tge~i~ip~k~~v~F 79 (90)
T d1mula_ 1 MNKTQLIDVIAEKA-ELSKTQAKAALESTLAAITESLKEGDAVQLVGFGTFKVNHRAERTGRNPQTGKEIKIAAANVPAF 79 (90)
T ss_dssp CCHHHHHHHHHHHT-TCCHHHHHHHHHHHHHHHHHHHHTTCCEEETTTEEEEEEEECC--------------CCEEEEEE
T ss_pred CCHHHHHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHHCCCCEECCCEEEEEEECCCEEEECCCCCCEEEECCCCCEEE
T ss_conf 97899999999704-96999999999999999999997299728657248999853761118889998899648641799
Q ss_pred CCCHHHHHHHC
Q ss_conf 26989999707
Q gi|254780748|r 81 RAGKNLKERLN 91 (100)
Q Consensus 81 k~sk~lk~~iN 91 (100)
+||+.|+++|.
T Consensus 80 kpsk~LK~~vk 90 (90)
T d1mula_ 80 VSGKALKDAVK 90 (90)
T ss_dssp EECHHHHHHHC
T ss_pred EECHHHHHHHC
T ss_conf 72899998629
>d1exea_ a.55.1.1 (A:) Transcription factor 1, TF1 {Bacteriophage SPO1 [TaxId: 10685]}
Back Show information, alignment and structure
class: All alpha proteins
fold: IHF-like DNA-binding proteins
superfamily: IHF-like DNA-binding proteins
family: Prokaryotic DNA-bending protein
domain: Transcription factor 1, TF1
species: Bacteriophage SPO1 [TaxId: 10685]
Probab=99.91 E-value=6.1e-26 Score=183.44 Aligned_cols=93 Identities=25% Similarity=0.365 Sum_probs=90.6
Q ss_pred CCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEEECCCCCCEECCCCCCEEEECCCCEEEE
Q ss_conf 98899999999973899989999999999999999986498512034578886214654102588988899468734676
Q gi|254780748|r 1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARLARAPLAQKVISVEEKMVPFF 80 (100)
Q Consensus 1 MtK~eli~~ia~~~~~ls~~~~~~~vd~~~~~i~~~L~~~~~V~i~gfGtF~~~~~~~r~~rNP~Tge~i~i~~~~~v~F 80 (100)
|||+|||+.||+++ ++++++++.++|+|++.|.++|.+|++|+|+|||+|+++.+++|.||||+|||.+.||++++|+|
T Consensus 1 M~K~eli~~ia~~~-~ls~~~~~~~~~~~~~~i~~~L~~g~~V~l~gfG~F~~~~r~~r~grNP~Tge~i~ip~~~~v~F 79 (99)
T d1exea_ 1 MNKTELIKAIAQDT-GLTQVSVSKMLASFEKIITETVAKGDKVQLTGFLNIKPVARQARKGFNPQTQEALEIAPSVGVSV 79 (99)
T ss_dssp CCTTHHHHHHHHHH-CSCCTTHHHHHHHHHHHHHHHHHHTCCCCBTTTBCCCCCCCCCCCCCCSSSSSCCCCCCCCCCCC
T ss_pred CCHHHHHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEEEEEEEECCCCCCCCCCCCCEEEECCCCCEEE
T ss_conf 97899999999852-98999999999999999999984599378753468999704663317869999898648653788
Q ss_pred CCCHHHHHHHCCCC
Q ss_conf 26989999707861
Q gi|254780748|r 81 RAGKNLKERLNSPD 94 (100)
Q Consensus 81 k~sk~lk~~iN~~~ 94 (100)
+||+.||+.||+..
T Consensus 80 k~sk~LK~~vn~~~ 93 (99)
T d1exea_ 80 KPGESLKKAAEGLK 93 (99)
T ss_dssp CCCHHHHHHHHHHT
T ss_pred ECCHHHHHHHCCCC
T ss_conf 44989999882996
>d1b8za_ a.55.1.1 (A:) HU protein {Thermotoga maritima [TaxId: 2336]}
Back Show information, alignment and structure
class: All alpha proteins
fold: IHF-like DNA-binding proteins
superfamily: IHF-like DNA-binding proteins
family: Prokaryotic DNA-bending protein
domain: HU protein
species: Thermotoga maritima [TaxId: 2336]
Probab=99.91 E-value=6.4e-25 Score=177.00 Aligned_cols=90 Identities=47% Similarity=0.707 Sum_probs=88.0
Q ss_pred CCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEEECCCCCCEECCCCCCEEEECCCCEEEE
Q ss_conf 98899999999973899989999999999999999986498512034578886214654102588988899468734676
Q gi|254780748|r 1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARLARAPLAQKVISVEEKMVPFF 80 (100)
Q Consensus 1 MtK~eli~~ia~~~~~ls~~~~~~~vd~~~~~i~~~L~~~~~V~i~gfGtF~~~~~~~r~~rNP~Tge~i~i~~~~~v~F 80 (100)
|||+|||+.||+++ ++++++++.++|+|++.|.++|.+|++|+|+|||+|+++.+++|.||||+|||.++||++++|+|
T Consensus 1 MnK~eli~~ia~~~-~~s~~~~~~~~~~~~~~i~~~L~~~~~v~l~gfG~F~~~~~~~r~~rNP~Tge~i~ip~k~~v~F 79 (90)
T d1b8za_ 1 MNKKELIDRVAKKA-GAKKKDVKLILDTILETITEALAKGEKVQIVGFGSFEVRKAAARKGVNPQTRKPITIPERKVPKF 79 (90)
T ss_dssp CCHHHHHHHHHHHH-TCCHHHHHHHHHHHHHHHHHHHHTTCCEEETTTEEEEC-----------------------CCEE
T ss_pred CCHHHHHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHHCCCCEECCEEEEEEECCCCEEEECCCCCCEEEECCCCEEEE
T ss_conf 97899999999864-98999999999999999999997288756267447887513655557899998898538630899
Q ss_pred CCCHHHHHHHC
Q ss_conf 26989999707
Q gi|254780748|r 81 RAGKNLKERLN 91 (100)
Q Consensus 81 k~sk~lk~~iN 91 (100)
+||+.|+++|.
T Consensus 80 k~sk~lk~~vk 90 (90)
T d1b8za_ 80 KPGKALKEKVK 90 (90)
T ss_dssp EECHHHHHHHC
T ss_pred EECHHHHHHHC
T ss_conf 65899998629
>d1huua_ a.55.1.1 (A:) HU protein {Bacillus stearothermophilus [TaxId: 1422]}
Back Show information, alignment and structure
class: All alpha proteins
fold: IHF-like DNA-binding proteins
superfamily: IHF-like DNA-binding proteins
family: Prokaryotic DNA-bending protein
domain: HU protein
species: Bacillus stearothermophilus [TaxId: 1422]
Probab=99.90 E-value=9.6e-25 Score=175.86 Aligned_cols=90 Identities=37% Similarity=0.655 Sum_probs=88.0
Q ss_pred CCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEEECCCCCCEECCCCCCEEEECCCCEEEE
Q ss_conf 98899999999973899989999999999999999986498512034578886214654102588988899468734676
Q gi|254780748|r 1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARLARAPLAQKVISVEEKMVPFF 80 (100)
Q Consensus 1 MtK~eli~~ia~~~~~ls~~~~~~~vd~~~~~i~~~L~~~~~V~i~gfGtF~~~~~~~r~~rNP~Tge~i~i~~~~~v~F 80 (100)
|||+|||+.||+++ ++++++++.++|.|+++|.++|.+|++|+|+|||+|+++.+++|.||||+|||.+.|||+++|+|
T Consensus 1 MtK~dli~~ia~~~-~~~~~~~~~~~~~~~~~i~~~L~~~~~v~i~~fG~F~~~~~~~r~~rNP~Tge~i~ip~k~~v~F 79 (90)
T d1huua_ 1 MNKTELINAVAETS-GLSKKDATKAVDAVFDSITEALRKGDKVQLIGFGNFEVRERAARKGRNPQTGEEMEIPASKVPAF 79 (90)
T ss_dssp CCHHHHHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHTTCCEEETTTEEEEEEEECCB----------TTBCCEEEEEE
T ss_pred CCHHHHHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHCCCCEEEECEEEEEEEECCCEEEECCCCCCEEEECCCCEEEE
T ss_conf 97899999999864-98999999999999999999985399647604579999971662108889998899538731899
Q ss_pred CCCHHHHHHHC
Q ss_conf 26989999707
Q gi|254780748|r 81 RAGKNLKERLN 91 (100)
Q Consensus 81 k~sk~lk~~iN 91 (100)
+||+.||++|.
T Consensus 80 k~sk~lK~~ik 90 (90)
T d1huua_ 80 KPGKALKDAVK 90 (90)
T ss_dssp EECHHHHHHHC
T ss_pred EECHHHHHHHC
T ss_conf 62889998639
Homologous Domains in MMDB70 Database Detected by RPS-BLAST
Original result of RPS-BLAST against MMDB70 database
Identity Alignment graph Length
Definition
E-value Target
100
integration host factor, beta subunit [Candidatus
1owf_B_ 94
(B:) IHF-beta, integration HOST factor beta-subuni
2e-19 1p71_A_ 94
(A:) DNA-binding protein HU; protein-DNA complex,
9e-18 2o97_B_ 90
(B:) NS1, HU-1, DNA-binding protein HU-beta; heter
2e-17 1b8z_A_ 90
(A:) Protein (histonelike protein HU); thermostabl
4e-17 3c4i_A_ 99
(A:) DNA-binding protein HU homolog; dimerization
8e-17 1exe_A_ 99
(A:) Transcription factor 1; beta ribbon ARMS, DNA
1e-16 1hue_A_ 90
(A:) HU protein; DNA-binding; NMR {Geobacillus ste
2e-16 1mul_A_ 90
(A:) NS2, HU-2, DNA binding protein HU-alpha; hist
2e-16 2iie_A_ 204
(A:) Integration HOST factor; DNA kinking, bending
7e-10 2iie_A_ 204
(A:) Integration HOST factor; DNA kinking, bending
2e-07 1owf_A_42-99 58
(A:42-99) IHF-alpha, integration HOST factor alpha
9e-13 2np2_A_53-108 56
(A:53-108) HBB; protein-DNA complex, DNA-binding p
7e-12
>1owf_B (B:) IHF-beta, integration HOST factor beta-subunit; protein-DNA recognition, indirect readout, DNA bending, minor groove; 1.95A {Escherichia coli}Length = 94
Back Hide alignment and structure
Score = 89.1 bits (221), Expect = 2e-19
Identities = 39/92 (42%), Positives = 51/92 (55%)
Query: 1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARL 60
M KS LI +A + + + VE V +LE M LA G R+ IRGFGSFS+ RA R
Sbjct: 1 MTKSELIERLATQQSHIPAKTVEDAVKEMLEHMASTLAQGERIAIRGFGSFSLHYRAPRT 60
Query: 61 ARAPLAQKVISVEEKMVPFFRAGKNLKERLNS 92
R P + +E K VP F+ GK L++R N
Sbjct: 61 GRNPKTGDKVELEGKYVPHFKPGKELRDRANI 92
>1p71_A (A:) DNA-binding protein HU; protein-DNA complex, DNA bending, DNA binding protein/DNA complex; 1.90A {Anabaena SP}Length = 94
Back Show alignment and structure
Score = 83.3 bits (206), Expect = 9e-18
Identities = 29/95 (30%), Positives = 52/95 (54%), Gaps = 1/95 (1%)
Query: 1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARL 60
M K L+ +A+K + + + ++ LE + +A+++G +V + GFGSF R+R AR
Sbjct: 1 MNKGELVDAVAEK-ASVTKKQADAVLTAALETIIEAVSSGDKVTLVGFGSFESRERKARE 59
Query: 61 ARAPLAQKVISVEEKMVPFFRAGKNLKERLNSPDS 95
R P + + + VP F AGK +E++ P +
Sbjct: 60 GRNPKTNEKMEIPATRVPAFSAGKLFREKVAPPKA 94
>2o97_B (B:) NS1, HU-1, DNA-binding protein HU-beta; heterodimer, DNA structure, DNA supercoiling, E. coli; 2.45A {Escherichia coli}Length = 90
Back Show alignment and structure
Score = 82.6 bits (204), Expect = 2e-17
Identities = 34/91 (37%), Positives = 53/91 (58%), Gaps = 1/91 (1%)
Query: 1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARL 60
M KS LI IA ++ + ++ ++ +T++L G V + GFG+F+V++RAAR
Sbjct: 1 MNKSQLIDKIAAG-ADISKAAAGRALDAIIASVTESLKEGDDVALVGFGTFAVKERAART 59
Query: 61 ARAPLAQKVISVEEKMVPFFRAGKNLKERLN 91
R P K I++ VP FRAGK LK+ +N
Sbjct: 60 GRNPQTGKEITIAAAKVPSFRAGKALKDAVN 90
>1b8z_A (A:) Protein (histonelike protein HU); thermostable DNA binding protein; 1.60A {Thermotoga maritima}Length = 90
Back Show alignment and structure
Score = 81.4 bits (201), Expect = 4e-17
Identities = 42/91 (46%), Positives = 59/91 (64%), Gaps = 1/91 (1%)
Query: 1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARL 60
M K LI +AKK +DV+ I++ +LE +T+ALA G +V+I GFGSF VRK AAR
Sbjct: 1 MNKKELIDRVAKK-AGAKKKDVKLILDTILETITEALAKGEKVQIVGFGSFEVRKAAARK 59
Query: 61 ARAPLAQKVISVEEKMVPFFRAGKNLKERLN 91
P +K I++ E+ VP F+ GK LKE++
Sbjct: 60 GVNPQTRKPITIPERKVPKFKPGKALKEKVK 90
>3c4i_A (A:) DNA-binding protein HU homolog; dimerization by four helix bundle interaction, DNA condensation; 2.04A {Mycobacterium tuberculosis}Length = 99
Back Show alignment and structure
Score = 80.3 bits (198), Expect = 8e-17
Identities = 29/91 (31%), Positives = 47/91 (51%), Gaps = 1/91 (1%)
Query: 1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARL 60
M K+ LI + +K + + V +++ + +A+ G V I GFG F R+RAAR+
Sbjct: 1 MNKAELIDVLTQKL-GSDRRQATAAVENVVDTIVRAVHKGDSVTITGFGVFEQRRRAARV 59
Query: 61 ARAPLAQKVISVEEKMVPFFRAGKNLKERLN 91
AR P + + V+ VP FR G K ++
Sbjct: 60 ARNPRTGETVKVKPTSVPAFRPGAQFKAVVS 90
>1exe_A (A:) Transcription factor 1; beta ribbon ARMS, DNA-binding, DNA-bending protein; NMR {Bacillus phage SPO1}Length = 99
Back Show alignment and structure
Score = 79.5 bits (196), Expect = 1e-16
Identities = 23/92 (25%), Positives = 43/92 (46%), Gaps = 1/92 (1%)
Query: 1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARL 60
M K+ LI IA+ L V K++ + +T+ +A G +V++ GF + R AR
Sbjct: 1 MNKTELIKAIAQDT-GLTQVSVSKMLASFEKIITETVAKGDKVQLTGFLNIKPVARQARK 59
Query: 61 ARAPLAQKVISVEEKMVPFFRAGKNLKERLNS 92
P Q+ + + + + G++LK+
Sbjct: 60 GFNPQTQEALEIAPSVGVSVKPGESLKKAAEG 91
>1hue_A (A:) HU protein; DNA-binding; NMR {Geobacillus stearothermophilus}Length = 90
Back Show alignment and structure
Score = 79.5 bits (196), Expect = 2e-16
Identities = 33/90 (36%), Positives = 55/90 (61%), Gaps = 1/90 (1%)
Query: 1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARL 60
M K+ LI +A+ + L+ +D K V+ + + +T+AL G +V++ GFG+F VR+RAAR
Sbjct: 1 MNKTELINAVAETS-GLSKKDATKAVDAVFDSITEALRKGDKVQLIGFGNFEVRERAARK 59
Query: 61 ARAPLAQKVISVEEKMVPFFRAGKNLKERL 90
R P + + + VP F+ GK LK+ +
Sbjct: 60 GRNPQTGEEMEIPASKVPAFKPGKALKDAV 89
>1mul_A (A:) NS2, HU-2, DNA binding protein HU-alpha; histone-like; HET: DNA; 2.30A {Escherichia coli}Length = 90
Back Show alignment and structure
Score = 79.5 bits (196), Expect = 2e-16
Identities = 32/90 (35%), Positives = 48/90 (53%), Gaps = 1/90 (1%)
Query: 1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARL 60
M K+ LI IA+K +L+ + + L +T++L G V++ GFG+F V RA R
Sbjct: 1 MNKTQLIDVIAEK-AELSKTQAKAALESTLAAITESLKEGDAVQLVGFGTFKVNHRAERT 59
Query: 61 ARAPLAQKVISVEEKMVPFFRAGKNLKERL 90
R P K I + VP F +GK LK+ +
Sbjct: 60 GRNPQTGKEIKIAAANVPAFVSGKALKDAV 89
>2iie_A (A:) Integration HOST factor; DNA kinking, bending, U-turn, intercalation, divalent, metal, recombination/DNA complex; HET: DNA; 2.41A {Escherichia coli} PDB: 2iif_A*Length = 204
Back Show alignment and structure
Score = 57.4 bits (138), Expect = 7e-10
Identities = 24/81 (29%), Positives = 45/81 (55%), Gaps = 1/81 (1%)
Query: 1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARL 60
+ K+ + + K L+ +D +++V + EE+ +AL NG +V++ GFG+F +R + R
Sbjct: 47 LTKAEMSEYLFDKL-GLSKRDAKELVELFFEEIRRALENGEQVKLSGFGNFDLRDKNQRP 105
Query: 61 ARAPLAQKVISVEEKMVPFFR 81
R P + I + + V FR
Sbjct: 106 GRNPKTGEDIPITARRVVTFR 126
>2iie_A (A:) Integration HOST factor; DNA kinking, bending, U-turn, intercalation, divalent, metal, recombination/DNA complex; HET: DNA; 2.41A {Escherichia coli} PDB: 2iif_A*Length = 204
Back Show alignment and structure
Score = 49.3 bits (117), Expect = 2e-07
Identities = 29/81 (35%), Positives = 40/81 (49%)
Query: 12 KKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARLARAPLAQKVIS 71
+ P + V L+ + G R+EIRGFGSFS+ RA R R P +
Sbjct: 113 EDIPITARRVVTFRPGQKLKSRVENAGGGERIEIRGFGSFSLHYRAPRTGRNPKTGDKVE 172
Query: 72 VEEKMVPFFRAGKNLKERLNS 92
+E K VP F+ GK L++R N
Sbjct: 173 LEGKYVPHFKPGKELRDRANI 193
>1owf_A (A:42-99) IHF-alpha, integration HOST factor alpha-subunit; protein-DNA recognition, indirect readout, DNA bending, minor groove; 1.95A {Escherichia coli}Length = 58
Back Show alignment and structure
Score = 67.0 bits (164), Expect = 9e-13
Identities = 17/54 (31%), Positives = 29/54 (53%)
Query: 42 RVEIRGFGSFSVRKRAARLARAPLAQKVISVEEKMVPFFRAGKNLKERLNSPDS 95
+V++ GFG+F +R + R R P + I + + V FR G+ LK R+ +
Sbjct: 2 QVKLSGFGNFDLRDKNQRPGRNPKTGEDIPITARRVVTFRPGQKLKSRVENASP 55
>2np2_A (A:53-108) HBB; protein-DNA complex, DNA-binding protein, DNA-bending protein, dnabii family, HU/IHF family, DNA binding protein/DNA complex; 3.02A {Borrelia burgdorferi}Length = 56
Back Show alignment and structure
Score = 63.9 bits (156), Expect = 7e-12
Identities = 24/54 (44%), Positives = 32/54 (59%), Gaps = 1/54 (1%)
Query: 42 RVEIRGFGSFSVRKRAARL-ARAPLAQKVISVEEKMVPFFRAGKNLKERLNSPD 94
+E R FG+F VRKR RL AR P + + V + V +FR GK+LKER+
Sbjct: 2 VIEFRSFGTFEVRKRKGRLNARNPQTGEYVKVLDHHVAYFRPGKDLKERVWGIK 55
Homologous Domains in MMDB70 Database Detected by HHsearch
Original result of HHsearch against MMDB70 database
Identity Alignment graph Length
Definition
Probability Target 100
integration host factor, beta subunit [Candidatus Liber
1p71_A_ 94
DNA-binding protein HU; protein-DNA complex, DNA b
99.92 1owf_B_ 94
IHF-beta, integration HOST factor beta-subunit; pr
99.92 3c4i_A_ 99
DNA-binding protein HU homolog; dimerization by fo
99.91 2o97_B_ 90
NS1, HU-1, DNA-binding protein HU-beta; heterodime
99.91 1mul_A_ 90
NS2, HU-2, DNA binding protein HU-alpha; histone-l
99.9 1b8z_A_ 90
Protein (histonelike protein HU); thermostable DNA
99.9 1hue_A_ 90
HU protein; DNA-binding; NMR {Geobacillus stearoth
99.88 1exe_A_ 99
Transcription factor 1; beta ribbon ARMS, DNA-bind
99.88 2iie_A_ 204
Integration HOST factor; DNA kinking, bending, U-t
99.87 2iie_A_ 204
Integration HOST factor; DNA kinking, bending, U-t
99.67 1owf_A_42-99 58
IHF-alpha, integration HOST factor alpha-subunit;
99.54 2np2_A_53-108 56
HBB; protein-DNA complex, DNA-binding protein, DNA
99.5
>1p71_A (A:) DNA-binding protein HU; protein-DNA complex, DNA bending, DNA binding protein/DNA complex; 1.90A {Anabaena SP}
Back Hide alignment and structure
Probab=99.92 E-value=6.6e-25 Score=179.38 Aligned_cols=94 Identities=31% Similarity=0.592 Sum_probs=91.5
Q ss_pred CCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEEECCCCCCEECCCCCCEEEECCCCEEEE
Q ss_conf 98899999999973899989999999999999999986498512034578886214654102588988899468734676
Q gi|254780748|r 1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARLARAPLAQKVISVEEKMVPFF 80 (100)
Q Consensus 1 MtK~eli~~ia~~~~~ls~~~~~~~vd~~~~~i~~~L~~~~~V~i~gfGtF~~~~~~~r~~rNP~Tge~i~i~~~~~v~F 80 (100)
|||+|||+.||+++ ++++++++.++|+|++.|.++|.+|+.|+|+|||+|+++.+++|.|+||+|||.+.||++++|+|
T Consensus 1 MtK~eli~~ia~~~-~ls~~~v~~~i~~~~~~i~~~L~~~~~V~l~~fG~F~v~~~~~r~~~Np~Tge~i~i~~~~~v~F 79 (94)
T 1p71_A 1 MNKGELVDAVAEKA-SVTKKQADAVLTAALETIIEAVSSGDKVTLVGFGSFESRERKAREGRNPKTNEKMEIPATRVPAF 79 (94)
T ss_dssp CBHHHHHHHHHHHH-TCCHHHHHHHHHHHHHHHHHHHHTTCCEEETTTEEEEEEEECCEEEECTTTCCEEEECCEEEEEE
T ss_pred CCHHHHHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHCCCCCEECCEEEEEEEEECCCEEECCCCCCEEEECCCCCEEE
T ss_conf 98899999999845-97999999999999999999986488605035269999983672328979997899648740899
Q ss_pred CCCHHHHHHHCCCCC
Q ss_conf 269899997078610
Q gi|254780748|r 81 RAGKNLKERLNSPDS 95 (100)
Q Consensus 81 k~sk~lk~~iN~~~~ 95 (100)
+||+.|+++||+..+
T Consensus 80 kpsk~lk~~in~~~a 94 (94)
T 1p71_A 80 SAGKLFREKVAPPKA 94 (94)
T ss_dssp EECHHHHHHHSCCCC
T ss_pred ECCHHHHHHHCCCCC
T ss_conf 549899997577899
>1owf_B (B:) IHF-beta, integration HOST factor beta-subunit; protein-DNA recognition, indirect readout, DNA bending, minor groove; 1.95A {Escherichia coli}
Back Show alignment and structure
Probab=99.92 E-value=8.2e-25 Score=178.77 Aligned_cols=93 Identities=42% Similarity=0.669 Sum_probs=91.2
Q ss_pred CCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEEECCCCCCEECCCCCCEEEECCCCEEEE
Q ss_conf 98899999999973899989999999999999999986498512034578886214654102588988899468734676
Q gi|254780748|r 1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARLARAPLAQKVISVEEKMVPFF 80 (100)
Q Consensus 1 MtK~eli~~ia~~~~~ls~~~~~~~vd~~~~~i~~~L~~~~~V~i~gfGtF~~~~~~~r~~rNP~Tge~i~i~~~~~v~F 80 (100)
|||+|||+.||++++++++++++.++|+|++.|.++|.+|++|+|+|||+|+++.+++|.++||+|||.+.||++++|+|
T Consensus 1 MtK~eli~~ia~~~~~~sk~~~~~~v~~~~~~i~~~L~~~~~V~l~gfG~F~~~~r~~r~~~nP~Tge~~~ip~k~~v~F 80 (94)
T 1owf_B 1 MTKSELIERLATQQSHIPAKTVEDAVKEMLEHMASTLAQGERIAIRGFGSFSLHYRAPRTGRNPKTGDKVELEGKYVPHF 80 (94)
T ss_dssp CBHHHHHHHHHHHCTTSCHHHHHHHHHHHHHHHHHHHHTTCCEEETTTEEEEEEEECCEEEECTTTCCEEEECCEEEEEE
T ss_pred CCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCEEEECCCEEEEEEEECCCCCCCCCCCCEEEECCCCCEEE
T ss_conf 97899999999876999999999999999999999997699599657379999860683333849999898648631898
Q ss_pred CCCHHHHHHHCCC
Q ss_conf 2698999970786
Q gi|254780748|r 81 RAGKNLKERLNSP 93 (100)
Q Consensus 81 k~sk~lk~~iN~~ 93 (100)
+||+.|++.||+.
T Consensus 81 kpsk~lk~~vn~~ 93 (94)
T 1owf_B 81 KPGKELRDRANIY 93 (94)
T ss_dssp EECHHHHHHHCCC
T ss_pred ECCHHHHHHHCCC
T ss_conf 1698999987559
>3c4i_A (A:) DNA-binding protein HU homolog; dimerization by four helix bundle interaction, DNA condensation; 2.04A {Mycobacterium tuberculosis}
Back Show alignment and structure
Probab=99.91 E-value=6.7e-24 Score=172.98 Aligned_cols=97 Identities=30% Similarity=0.507 Sum_probs=93.3
Q ss_pred CCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEEECCCCCCEECCCCCCEEEECCCCEEEE
Q ss_conf 98899999999973899989999999999999999986498512034578886214654102588988899468734676
Q gi|254780748|r 1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARLARAPLAQKVISVEEKMVPFF 80 (100)
Q Consensus 1 MtK~eli~~ia~~~~~ls~~~~~~~vd~~~~~i~~~L~~~~~V~i~gfGtF~~~~~~~r~~rNP~Tge~i~i~~~~~v~F 80 (100)
|||+|||..||+++ ++|+.++..++|+|++.|.++|.+|+.|+|+|||+|+++.+++|.++||+|||.+.+|++++|+|
T Consensus 1 Mtk~eli~~ia~~~-~~s~~~v~~~i~~~~~~i~~~L~~g~~V~l~~fG~F~~~~~~~r~~~np~T~e~i~i~~k~~v~F 79 (99)
T 3c4i_A 1 MNKAELIDVLTQKL-GSDRRQATAAVENVVDTIVRAVHKGDSVTITGFGVFEQRRRAARVARNPRTGETVKVKPTSVPAF 79 (99)
T ss_dssp CBHHHHHHHHHHHH-TCCHHHHHHHHHHHHHHHHHHHHTTCCEEETTTEEEEEEEECSEEEECTTTCCEEEECCEEEEEE
T ss_pred CCHHHHHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHCCCCEECCCEEEEEEEEECCEEEECCCCCCEEEECCCCEEEE
T ss_conf 97899999999874-98999999999999999999996499613155689999875681106859998898638722899
Q ss_pred CCCHHHHHHHCCCCCCCC
Q ss_conf 269899997078610012
Q gi|254780748|r 81 RAGKNLKERLNSPDSTLS 98 (100)
Q Consensus 81 k~sk~lk~~iN~~~~~~~ 98 (100)
+||+.|++.||.......
T Consensus 80 kpsk~Lk~~in~~~~~~~ 97 (99)
T 3c4i_A 80 RPGAQFKAVVSGAQRLPA 97 (99)
T ss_dssp EECHHHHHHHHTSSCCCC
T ss_pred ECCHHHHHHHCCCCCCCC
T ss_conf 629899998666668999
>2o97_B (B:) NS1, HU-1, DNA-binding protein HU-beta; heterodimer, DNA structure, DNA supercoiling, E. coli; 2.45A {Escherichia coli}
Back Show alignment and structure
Probab=99.91 E-value=3.7e-24 Score=174.64 Aligned_cols=90 Identities=38% Similarity=0.627 Sum_probs=88.7
Q ss_pred CCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEEECCCCCCEECCCCCCEEEECCCCEEEE
Q ss_conf 98899999999973899989999999999999999986498512034578886214654102588988899468734676
Q gi|254780748|r 1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARLARAPLAQKVISVEEKMVPFF 80 (100)
Q Consensus 1 MtK~eli~~ia~~~~~ls~~~~~~~vd~~~~~i~~~L~~~~~V~i~gfGtF~~~~~~~r~~rNP~Tge~i~i~~~~~v~F 80 (100)
|||+|||+.||+++ ++++++++.++|+|++.|.++|.+|++|+|+|||+|+++.+++|.++||+|||.+.+|++++|+|
T Consensus 1 Mtk~eli~~ia~~~-~~t~~~v~~~v~~~~~~i~~~L~~~~~V~l~~fG~F~v~~~~~r~~~np~tge~~~i~~k~~v~F 79 (90)
T 2o97_B 1 MNKSQLIDKIAAGA-DISKAAAGRALDAIIASVTESLKEGDDVALVGFGTFAVKERAARTGRNPQTGKEITIAAAKVPSF 79 (90)
T ss_dssp CBHHHHHHHHHHTT-C-CHHHHHHHHHHHHHHHHHHHHTTCCEEETTTEEEEEECCC------------------CEEEE
T ss_pred CCHHHHHHHHHHCC-CCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEECCCEEECCCCCCEEEECCCCEEEE
T ss_conf 97899999999720-99999999999999999999998076444550589999840564028899997899538622899
Q ss_pred CCCHHHHHHHC
Q ss_conf 26989999707
Q gi|254780748|r 81 RAGKNLKERLN 91 (100)
Q Consensus 81 k~sk~lk~~iN 91 (100)
+||+.|++.||
T Consensus 80 kp~k~lk~~iN 90 (90)
T 2o97_B 80 RAGKALKDAVN 90 (90)
T ss_dssp EECHHHHHHCC
T ss_pred ECCHHHHHHHC
T ss_conf 63989997629
>1mul_A (A:) NS2, HU-2, DNA binding protein HU-alpha; histone-like; HET: DNA; 2.30A {Escherichia coli}
Back Show alignment and structure
Probab=99.90 E-value=5.1e-24 Score=173.76 Aligned_cols=90 Identities=36% Similarity=0.573 Sum_probs=87.9
Q ss_pred CCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEEECCCCCCEECCCCCCEEEECCCCEEEE
Q ss_conf 98899999999973899989999999999999999986498512034578886214654102588988899468734676
Q gi|254780748|r 1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARLARAPLAQKVISVEEKMVPFF 80 (100)
Q Consensus 1 MtK~eli~~ia~~~~~ls~~~~~~~vd~~~~~i~~~L~~~~~V~i~gfGtF~~~~~~~r~~rNP~Tge~i~i~~~~~v~F 80 (100)
|||+|||+.||+++ ++++++++.++|+|++.|.++|.+|+.|.|+|||+|+++.+++|.++||+|||.+.||++++|+|
T Consensus 1 Mtk~eli~~ia~~~-~~s~~~v~~~v~~~~~~i~~~L~~~~~v~l~~fG~F~v~~r~~r~~~Np~Tge~i~ip~k~~v~F 79 (90)
T 1mul_A 1 MNKTQLIDVIAEKA-ELSKTQAKAALESTLAAITESLKEGDAVQLVGFGTFKVNHRAERTGRNPQTGKEIKIAAANVPAF 79 (90)
T ss_dssp CCHHHHHHHHHHHT-TCCHHHHHHHHHHHHHHHHHHHHTTCCEEETTTEEEEEEEECC--------------CCEEEEEE
T ss_pred CCHHHHHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEEEECCCEEEECCCCCCEEEECCCCCEEE
T ss_conf 97899999999704-96999999999999999999997199877203699999862884308939997899748740899
Q ss_pred CCCHHHHHHHC
Q ss_conf 26989999707
Q gi|254780748|r 81 RAGKNLKERLN 91 (100)
Q Consensus 81 k~sk~lk~~iN 91 (100)
+||+.|+++|.
T Consensus 80 rp~k~lk~~i~ 90 (90)
T 1mul_A 80 VSGKALKDAVK 90 (90)
T ss_dssp EECHHHHHHHC
T ss_pred ECCHHHHHHHC
T ss_conf 72989998639
>1b8z_A (A:) Protein (histonelike protein HU); thermostable DNA binding protein; 1.60A {Thermotoga maritima}
Back Show alignment and structure
Probab=99.90 E-value=4.2e-24 Score=174.30 Aligned_cols=90 Identities=47% Similarity=0.707 Sum_probs=88.8
Q ss_pred CCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEEECCCCCCEECCCCCCEEEECCCCEEEE
Q ss_conf 98899999999973899989999999999999999986498512034578886214654102588988899468734676
Q gi|254780748|r 1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARLARAPLAQKVISVEEKMVPFF 80 (100)
Q Consensus 1 MtK~eli~~ia~~~~~ls~~~~~~~vd~~~~~i~~~L~~~~~V~i~gfGtF~~~~~~~r~~rNP~Tge~i~i~~~~~v~F 80 (100)
|||+|||+.|++++ ++++++++.++|+|++.|.++|.+|++|+|+|||+|+++.+++|.++||+|||.+.+|++++|+|
T Consensus 1 Mtk~eli~~ia~~~-~~s~~~~~~~v~~~~~~i~~~L~~~~~V~l~~fG~F~v~~~~~r~~~np~tge~i~i~~k~~v~F 79 (90)
T 1b8z_A 1 MNKKELIDRVAKKA-GAKKKDVKLILDTILETITEALAKGEKVQIVGFGSFEVRKAAARKGVNPQTRKPITIPERKVPKF 79 (90)
T ss_dssp CCHHHHHHHHHHHH-TCCHHHHHHHHHHHHHHHHHHHHTTCCEEETTTEEEEC-----------------------CCEE
T ss_pred CCHHHHHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHHCCCCEECCEEEEEEECCCCEEEECCCCCCEEEECCCCEEEE
T ss_conf 97899999999854-98999999999999999999987288637466578988613544445799998898638721899
Q ss_pred CCCHHHHHHHC
Q ss_conf 26989999707
Q gi|254780748|r 81 RAGKNLKERLN 91 (100)
Q Consensus 81 k~sk~lk~~iN 91 (100)
+||+.|++.||
T Consensus 80 k~sk~Lk~~in 90 (90)
T 1b8z_A 80 KPGKALKEKVK 90 (90)
T ss_dssp EECHHHHHHHC
T ss_pred EECHHHHHHHC
T ss_conf 73899998639
>1hue_A (A:) HU protein; DNA-binding; NMR {Geobacillus stearothermophilus}
Back Show alignment and structure
Probab=99.88 E-value=6e-23 Score=166.93 Aligned_cols=90 Identities=37% Similarity=0.655 Sum_probs=88.0
Q ss_pred CCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEEECCCCCCEECCCCCCEEEECCCCEEEE
Q ss_conf 98899999999973899989999999999999999986498512034578886214654102588988899468734676
Q gi|254780748|r 1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARLARAPLAQKVISVEEKMVPFF 80 (100)
Q Consensus 1 MtK~eli~~ia~~~~~ls~~~~~~~vd~~~~~i~~~L~~~~~V~i~gfGtF~~~~~~~r~~rNP~Tge~i~i~~~~~v~F 80 (100)
|||+|||..|++++ ++++++++.++|+|++.|.++|.+|++|+|+|||+|+++.+++|.++||+|||.+.+||+++|+|
T Consensus 1 Mtk~~li~~i~~~~-~~s~~~v~~~i~~~~~~i~~~L~~~~~v~l~~fG~F~v~~~~~r~~~Np~Tge~~~i~~k~~vkF 79 (90)
T 1hue_A 1 MNKTELINAVAETS-GLSKKDATKAVDAVFDSITEALRKGDKVQLIGFGNFEVRERAARKGRNPQTGEEMEIPASKVPAF 79 (90)
T ss_dssp CBSHHHHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHHTCCCCBTTTBEECCCCCCCCEEECSSSSSEEECCCCCCCCE
T ss_pred CCHHHHHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHCCCEEEEECCEEEEEEEECCCCCCCCCCCCEEEECCCCEEEE
T ss_conf 97899999999854-98999999999999999999996598288402439999861684455839998899548741898
Q ss_pred CCCHHHHHHHC
Q ss_conf 26989999707
Q gi|254780748|r 81 RAGKNLKERLN 91 (100)
Q Consensus 81 k~sk~lk~~iN 91 (100)
+||+.|+++|.
T Consensus 80 r~sk~lk~~ik 90 (90)
T 1hue_A 80 KPGKALKDAVK 90 (90)
T ss_dssp ECTTHHHHHTC
T ss_pred ECCHHHHHHHC
T ss_conf 13989998639
>1exe_A (A:) Transcription factor 1; beta ribbon ARMS, DNA-binding, DNA-bending protein; NMR {Bacillus phage SPO1}
Back Show alignment and structure
Probab=99.88 E-value=7.6e-24 Score=172.63 Aligned_cols=94 Identities=24% Similarity=0.354 Sum_probs=91.2
Q ss_pred CCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEEECCCCCCEECCCCCCEEEECCCCEEEE
Q ss_conf 98899999999973899989999999999999999986498512034578886214654102588988899468734676
Q gi|254780748|r 1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARLARAPLAQKVISVEEKMVPFF 80 (100)
Q Consensus 1 MtK~eli~~ia~~~~~ls~~~~~~~vd~~~~~i~~~L~~~~~V~i~gfGtF~~~~~~~r~~rNP~Tge~i~i~~~~~v~F 80 (100)
|||+|||+.||+++ ++++++++.++|+|+++|.++|.+|+.|+|+|||+|+++.+++|.++||+|||.+.||++++|+|
T Consensus 1 Mtk~eli~~ia~~~-~~s~~~v~~~i~~~~~~i~~~L~~g~~V~l~gfG~F~v~~~~~r~~~np~Tge~i~i~~k~~v~F 79 (99)
T 1exe_A 1 MNKTELIKAIAQDT-GLTQVSVSKMLASFEKIITETVAKGDKVQLTGFLNIKPVARQARKGFNPQTQEALEIAPSVGVSV 79 (99)
T ss_dssp CCTTHHHHHHHHHH-CSCCTTHHHHHHHHHHHHHHHHHHTCCCCBTTTBCCCCCCCCCCCCCCSSSSSCCCCCCCCCCCC
T ss_pred CCHHHHHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHCCCEEEECCCEEEEEEEECCCCCCCCCCCCEEEECCCCCEEE
T ss_conf 98899999999986-96999999999999999999996899599736789998755573447899998898428534799
Q ss_pred CCCHHHHHHHCCCCC
Q ss_conf 269899997078610
Q gi|254780748|r 81 RAGKNLKERLNSPDS 95 (100)
Q Consensus 81 k~sk~lk~~iN~~~~ 95 (100)
+||+.|+++||....
T Consensus 80 kpsk~LK~~in~~~~ 94 (99)
T 1exe_A 80 KPGESLKKAAEGLKY 94 (99)
T ss_dssp CCCHHHHHHHHHHTH
T ss_pred ECCHHHHHHHCCCCH
T ss_conf 349899998828985
>2iie_A (A:) Integration HOST factor; DNA kinking, bending, U-turn, intercalation, divalent, metal, recombination/DNA complex; HET: DNA; 2.41A {Escherichia coli} PDB: 2iif_A*
Back Show alignment and structure
Probab=99.87 E-value=1.4e-22 Score=164.58 Aligned_cols=92 Identities=30% Similarity=0.578 Sum_probs=75.1
Q ss_pred CCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEEECCCCCCEECCCCCCEEEECCCCEEEE
Q ss_conf 98899999999973899989999999999999999986498512034578886214654102588988899468734676
Q gi|254780748|r 1 MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARLARAPLAQKVISVEEKMVPFF 80 (100)
Q Consensus 1 MtK~eli~~ia~~~~~ls~~~~~~~vd~~~~~i~~~L~~~~~V~i~gfGtF~~~~~~~r~~rNP~Tge~i~i~~~~~v~F 80 (100)
|||+|||+.||+++ ++++++++.++|+|++.|.++|.+|+.|.|+|||+|+++.+++|.++||+|||.+.+|++++|+|
T Consensus 47 MtK~eLi~~ia~~~-glskk~a~~ii~~~~~~I~e~L~~g~~V~l~gfGtF~v~~r~~R~~rNP~Tge~i~i~~kk~vkF 125 (204)
T 2iie_A 47 LTKAEMSEYLFDKL-GLSKRDAKELVELFFEEIRRALENGEQVKLSGFGNFDLRDKNQRPGRNPKTGEDIPITARRVVTF 125 (204)
T ss_dssp BCHHHHHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHTTCEEEETTTEEEEEEEECCBCCBCTTTCCBCCBCCEEEEEE
T ss_pred CCHHHHHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEEEEEEEEECCCCCCCCCCCCEEEECCCCCEEE
T ss_conf 35999999999986-97999999999999999999996699256511589999876471123889998898648651799
Q ss_pred CCCHHHHHHHCCC
Q ss_conf 2698999970786
Q gi|254780748|r 81 RAGKNLKERLNSP 93 (100)
Q Consensus 81 k~sk~lk~~iN~~ 93 (100)
+||+.|+..+|..
T Consensus 126 k~~k~LK~iveaL 138 (204)
T 2iie_A 126 RPGQKLKSRVENA 138 (204)
T ss_dssp EECHHHHHHHHHH
T ss_pred EECHHHHHHHHCC
T ss_conf 9547999886413
>2iie_A (A:) Integration HOST factor; DNA kinking, bending, U-turn, intercalation, divalent, metal, recombination/DNA complex; HET: DNA; 2.41A {Escherichia coli} PDB: 2iif_A*
Back Show alignment and structure
Probab=99.67 E-value=8.3e-17 Score=127.97 Aligned_cols=71 Identities=38% Similarity=0.630 Sum_probs=67.2
Q ss_pred HHHHHHHHHHHHHCCCCCCCEEEEEEEEECCCCCCEECCCCCCEEEECCCCEEEECCCHHHHHHHCCCCCC
Q ss_conf 99999999999864985120345788862146541025889888994687346762698999970786100
Q gi|254780748|r 26 VNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARLARAPLAQKVISVEEKMVPFFRAGKNLKERLNSPDST 96 (100)
Q Consensus 26 vd~~~~~i~~~L~~~~~V~i~gfGtF~~~~~~~r~~rNP~Tge~i~i~~~~~v~Fk~sk~lk~~iN~~~~~ 96 (100)
.+.+++.+.++|..++.|+|+|||+|+++.+++|.||||+|||.|.||++++|+|+||+.|+++||+....
T Consensus 127 ~~k~LK~iveaL~~ge~V~i~~fG~F~~~~r~~R~grNP~Tge~i~Ipa~~~~~Fk~~k~lk~~vn~~~~~ 197 (204)
T 2iie_A 127 PGQKLKSRVENAGGGERIEIRGFGSFSLHYRAPRTGRNPKTGDKVELEGKYVPHFKPGKELRDRANIYGGS 197 (204)
T ss_dssp ECHHHHHHHHHHCCCCCEEETTTEEEEEEEECCEEEECTTTCCEEEECCEEEEEEEECHHHHHHHCSSCCS
T ss_pred ECHHHHHHHHCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCCCEEEECCCCCEEECCCHHHHHHHCCCCCC
T ss_conf 54799988641344654222656889987406735619299998886597536878788999987579998
>1owf_A (A:42-99) IHF-alpha, integration HOST factor alpha-subunit; protein-DNA recognition, indirect readout, DNA bending, minor groove; 1.95A {Escherichia coli}
Back Show alignment and structure
Probab=99.54 E-value=4.2e-15 Score=117.17 Aligned_cols=56 Identities=30% Similarity=0.608 Sum_probs=53.4
Q ss_pred CCCCCEEEEEEEEECCCCCCEECCCCCCEEEECCCCEEEECCCHHHHHHHCCCCCC
Q ss_conf 85120345788862146541025889888994687346762698999970786100
Q gi|254780748|r 41 GRVEIRGFGSFSVRKRAARLARAPLAQKVISVEEKMVPFFRAGKNLKERLNSPDST 96 (100)
Q Consensus 41 ~~V~i~gfGtF~~~~~~~r~~rNP~Tge~i~i~~~~~v~Fk~sk~lk~~iN~~~~~ 96 (100)
++|.|+|||+|+++.+++|.|+||+|||.|.||++++|+|+||+.|+++||+....
T Consensus 1 ekV~l~gfGtF~~~~r~~R~grNP~Tge~i~I~ak~~v~Fk~sk~Lk~~vn~~~~~ 56 (58)
T 1owf_A 1 EQVKLSGFGNFDLRDKNQRPGRNPKTGEDIPITARRVVTFRPGQKLKSRVENASPK 56 (58)
T ss_dssp CCEEETTTEEEEEEEECCEEEECSSSCCEEEECCEEEEEEEECHHHHHHHHTCCCC
T ss_pred CEEEECCEEEEEEEEECCCCCCCCCCCCEEEECCCCEEEEEECHHHHHHHHCCCCC
T ss_conf 97995113799998766821258899988995387228997499999998078968
>2np2_A (A:53-108) HBB; protein-DNA complex, DNA-binding protein, DNA-bending protein, dnabii family, HU/IHF family, DNA binding protein/DNA complex; 3.02A {Borrelia burgdorferi}
Back Show alignment and structure
Probab=99.50 E-value=7.4e-15 Score=115.59 Aligned_cols=54 Identities=43% Similarity=0.706 Sum_probs=51.5
Q ss_pred CCCCCEEEEEEEEECCCCC-CEECCCCCCEEEECCCCEEEECCCHHHHHHHCCCC
Q ss_conf 8512034578886214654-10258898889946873467626989999707861
Q gi|254780748|r 41 GRVEIRGFGSFSVRKRAAR-LARAPLAQKVISVEEKMVPFFRAGKNLKERLNSPD 94 (100)
Q Consensus 41 ~~V~i~gfGtF~~~~~~~r-~~rNP~Tge~i~i~~~~~v~Fk~sk~lk~~iN~~~ 94 (100)
++|.|+|||+|+++.+++| .||||+|||.|.||++++|+|+||+.|+++||+..
T Consensus 1 d~V~l~gFGtF~~~~r~~R~~grNP~Tge~i~I~a~~v~~Fk~~k~lk~~vn~~~ 55 (56)
T 2np2_A 1 NVIEFRSFGTFEVRKRKGRLNARNPQTGEYVKVLDHHVAYFRPGKDLKERVWGIK 55 (56)
T ss_dssp CEEEETTTEEEEEEEECCBSSCBCTTTCCBCCBCCEEEEEEEECHHHHHHHHSCC
T ss_pred CEEEEEEEEEEEEEEECCCCCCCCCCCCCEEEECCCCCEEECCCHHHHHHHHCCC
T ss_conf 9699844689999730476555388999889853875678748989999970679