RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy5541
(301 letters)
>1b72_B Protein (PBX1); homeodomain, DNA, complex, DNA-binding protein,
protein/DNA complex; HET: DNA; 2.35A {Homo sapiens}
SCOP: a.4.1.1 PDB: 1lfu_P
Length = 87
Score = 125 bits (315), Expect = 1e-36
Identities = 72/85 (84%), Positives = 78/85 (91%)
Query: 108 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYK 167
ARRKRRNF+KQA+EILNEYFYSHLSNPYPSEEAKEELA+KC IT+SQVSNWFGNKRIRYK
Sbjct: 1 ARRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYK 60
Query: 168 KNIGKAQEEANLYAAKKAAGASPYS 192
KNIGK QEEAN+YAAK A A+ S
Sbjct: 61 KNIGKFQEEANIYAAKTAVTATNVS 85
>1puf_B PRE-B-cell leukemia transcription factor-1; homeodomian,
protein-DNA complex, HOX hexapeptide, TALE homeodomain,
homeodomain interaction; 1.90A {Homo sapiens} SCOP:
a.4.1.1 PDB: 1b8i_B* 2r5y_B* 2r5z_B*
Length = 73
Score = 120 bits (303), Expect = 6e-35
Identities = 66/73 (90%), Positives = 71/73 (97%)
Query: 108 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYK 167
ARRKRRNF+KQA+EILNEYFYSHLSNPYPSEEAKEELA+KC IT+SQVSNWFGNKRIRYK
Sbjct: 1 ARRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYK 60
Query: 168 KNIGKAQEEANLY 180
KNIGK QEEAN+Y
Sbjct: 61 KNIGKFQEEANIY 73
>1du6_A PBX1, homeobox protein PBX1; homeodomain, gene regulation; NMR {Mus
musculus} SCOP: a.4.1.1
Length = 64
Score = 108 bits (272), Expect = 2e-30
Identities = 50/62 (80%), Positives = 56/62 (90%)
Query: 108 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYK 167
+ R+ +KQA+EILNEYFYSHLSNPYPSEEAKEELA+KC IT+SQVSNWFGNKRIRYK
Sbjct: 3 GHIEGRHMNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYK 62
Query: 168 KN 169
KN
Sbjct: 63 KN 64
>3k2a_A Homeobox protein MEIS2; homeobox domain, DNA-binding,
transcription, nucleus, phosphoprotein, DNA bindi
protein; 1.95A {Homo sapiens}
Length = 67
Score = 93.9 bits (234), Expect = 6e-25
Identities = 25/66 (37%), Positives = 39/66 (59%)
Query: 112 RRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKNIG 171
F K A+ I+ + + HL++PYPSEE K++LA+ +T+ QV+NWF N R R + +
Sbjct: 2 SGIFPKVATNIMRAWLFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQPMI 61
Query: 172 KAQEEA 177
A
Sbjct: 62 DQSNRA 67
>2dmn_A Homeobox protein TGIF2LX; TGFB-induced factor 2-like protein,
X-linked TGF(beta) induced transcription factor 2-like
protein, TGIF-like on the X; NMR {Homo sapiens}
Length = 83
Score = 93.7 bits (233), Expect = 1e-24
Identities = 23/68 (33%), Positives = 41/68 (60%)
Query: 107 DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRY 166
++++ N ++ +IL ++ Y H YPSEE K+ L+ K N++L Q+SNWF N R R
Sbjct: 6 SGKKRKGNLPAESVKILRDWMYKHRFKAYPSEEEKQMLSEKTNLSLLQISNWFINARRRI 65
Query: 167 KKNIGKAQ 174
++ + +
Sbjct: 66 LPDMLQQR 73
>1x2n_A Homeobox protein pknox1; homeobox domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} SCOP: a.4.1.1
Length = 73
Score = 92.8 bits (231), Expect = 2e-24
Identities = 22/63 (34%), Positives = 40/63 (63%)
Query: 107 DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRY 166
+ KR K A+ ++ + + H+ +PYP+E+ K+++A + N+TL QV+NWF N R R
Sbjct: 6 SGKNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRI 65
Query: 167 KKN 169
++
Sbjct: 66 LQS 68
>2lk2_A Homeobox protein TGIF1; NESG, structural genomics, northeast
structural genomics CON PSI-biology, transcription; NMR
{Homo sapiens}
Length = 89
Score = 92.6 bits (230), Expect = 4e-24
Identities = 22/84 (26%), Positives = 40/84 (47%), Gaps = 1/84 (1%)
Query: 108 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYK 167
K++ +IL ++ Y H N YPSE+ K L+++ +++ QV NWF N R R
Sbjct: 5 HHHHSHMLPKESVQILRDWLYEHRYNAYPSEQEKALLSQQTHLSTLQVCNWFINARRRLL 64
Query: 168 KN-IGKAQEEANLYAAKKAAGASP 190
+ + K ++ N + +
Sbjct: 65 PDMLRKDGKDPNQFTISRRGAKIS 88
>1k61_A Mating-type protein alpha-2; protein-DNA complex, homeodomain,
hoogsteen base PAIR, transcription/DNA complex; HET:
5IU; 2.10A {Synthetic} SCOP: a.4.1.1
Length = 60
Score = 89.7 bits (223), Expect = 2e-23
Identities = 16/58 (27%), Positives = 30/58 (51%)
Query: 111 KRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
+ F+K+ IL +F ++ NPY + E L + +++ Q+ NW N+R + K
Sbjct: 1 RGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT 58
>1mnm_C Protein (MAT alpha-2 transcriptional repressor); transcription
regulation, transcriptional repression, DNA- binding
protein; HET: DNA; 2.25A {Saccharomyces cerevisiae}
SCOP: a.4.1.1
Length = 87
Score = 89.9 bits (223), Expect = 4e-23
Identities = 16/59 (27%), Positives = 30/59 (50%)
Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYK 167
+ F+K+ IL +F ++ NPY + E L + +++ Q+ NW N+R + K
Sbjct: 28 PYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEK 86
>1le8_B Mating-type protein alpha-2; matalpha2, isothermal titration
calorimetry, protein-DNA complex, transcription/DNA
complex; 2.30A {Saccharomyces cerevisiae} SCOP: a.4.1.1
PDB: 1akh_B* 1apl_C* 1yrn_B*
Length = 83
Score = 88.7 bits (220), Expect = 9e-23
Identities = 21/79 (26%), Positives = 38/79 (48%), Gaps = 1/79 (1%)
Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
+ F+K+ IL +F ++ NPY + E L + +++ Q+ NW +R +K
Sbjct: 3 PYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVAARR-AKEK 61
Query: 169 NIGKAQEEANLYAAKKAAG 187
I A E A+L + + A
Sbjct: 62 TITIAPELADLLSGEPLAK 80
>2cuf_A FLJ21616 protein; homeobox domain, hepatocyte transcription factor,
structural genomics, loop insertion, NPPSFA; NMR {Homo
sapiens} SCOP: a.4.1.1
Length = 95
Score = 65.4 bits (159), Expect = 7e-14
Identities = 23/85 (27%), Positives = 34/85 (40%), Gaps = 18/85 (21%)
Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCN---------------ITLS 153
R R + K+ ++ YF N YP E +EE+A CN +T
Sbjct: 8 RGSRFTWRKECLAVMESYFNE---NQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSL 64
Query: 154 QVSNWFGNKRIRYKKNIGKAQEEAN 178
+V NWF N+R K+ A +
Sbjct: 65 KVYNWFANRRKEIKRRANIAAILES 89
>2dn0_A Zinc fingers and homeoboxes protein 3; triple homeobox 1 protein,
KIAA0395, TIX1, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 76
Score = 57.8 bits (140), Expect = 2e-11
Identities = 13/68 (19%), Positives = 24/68 (35%), Gaps = 3/68 (4%)
Query: 107 DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRY 166
A + S + L F N +P + E L + ++ +V WF ++R
Sbjct: 7 GASIYKNKKSHEQLSALKGSF---CRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHC 63
Query: 167 KKNIGKAQ 174
+ G
Sbjct: 64 RNLKGSRS 71
>3nau_A Zinc fingers and homeoboxes protein 2; ZHX2, corepressor,
homeodomain, domain swapping, structural oxford protein
production facility, OPPF; 2.70A {Homo sapiens}
Length = 66
Score = 57.5 bits (139), Expect = 2e-11
Identities = 13/64 (20%), Positives = 24/64 (37%), Gaps = 3/64 (4%)
Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
R +K+ L F L + +P + L + S++ WF + R R ++
Sbjct: 5 HHHHRKKTKEQIAHLKASF---LQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQR 61
Query: 169 NIGK 172
I
Sbjct: 62 GIVH 65
>1wi3_A DNA-binding protein SATB2; homeodomain, helix-turn-helix, riken
structural genomics/proteomics initiative, RSGI,
structural genomics; NMR {Homo sapiens} SCOP: a.4.1.1
Length = 71
Score = 57.1 bits (138), Expect = 3e-11
Identities = 16/61 (26%), Positives = 27/61 (44%), Gaps = 2/61 (3%)
Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
R R S +A IL + H YP +EA L+ + ++ + +F N+R K
Sbjct: 8 PRSRTKISLEALGILQSFI--HDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKH 65
Query: 169 N 169
+
Sbjct: 66 S 66
>1akh_A Protein (mating-type protein A-1); complex (TWO DNA-binding
proteins/DNA), complex, DNA- binding protein, DNA; HET:
DNA; 2.50A {Saccharomyces cerevisiae} SCOP: a.4.1.1 PDB:
1f43_A 1yrn_A*
Length = 61
Score = 54.5 bits (132), Expect = 2e-10
Identities = 23/60 (38%), Positives = 32/60 (53%), Gaps = 3/60 (5%)
Query: 108 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYK 167
+ + + + S QA L E F + + KEE+A+KC IT QV WF NKR+R K
Sbjct: 5 SPKGKSSISPQARAFLEEVFRRK---QSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 60.3 bits (145), Expect = 2e-10
Identities = 35/176 (19%), Positives = 57/176 (32%), Gaps = 46/176 (26%)
Query: 16 LLHAIEHSDYRAKLAQIRTIYQQELEKYEQACSEF------TTHVMNLLREQSRTRPITP 69
L IE S + + E K S F T +++L+
Sbjct: 355 LTTIIESS--------LNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDV-----IK 401
Query: 70 KEIERMVQIIHRKFSSIQMQLKQST-------------CEAVMILRSRFLDARRKRRNFS 116
++ +V +H+ S ++ Q K+ST E L +D + F
Sbjct: 402 SDVMVVVNKLHKY-SLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFD 460
Query: 117 KQ--ASEILNEYFYS----HLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRY 166
L++YFYS HL N E + L R + + K IR+
Sbjct: 461 SDDLIPPYLDQYFYSHIGHHLKNIEHPE--RMTLFRMVFLDF----RFLEQK-IRH 509
Score = 45.2 bits (106), Expect = 2e-05
Identities = 48/339 (14%), Positives = 98/339 (28%), Gaps = 103/339 (30%)
Query: 24 DYRAKLAQIRTIYQQ---ELEKYEQACSEFTTHVMNLLREQSRTRPITPKEIERMVQIIH 80
+Y+ ++ I+T +Q Y + R + + + R
Sbjct: 90 NYKFLMSPIKTEQRQPSMMTRMYIEQRD----------RLYNDNQVFAKYNVSR-----L 134
Query: 81 RKFSSIQ---MQLKQS-------------TCEAVMILRSRFLDARRKRR----NFSKQAS 120
+ + ++ ++L+ + T A+ + S + + + N S
Sbjct: 135 QPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNS 194
Query: 121 -----EILNEYFY----------SHLSN-PYPSEEAKEELAR--------KCNITLSQVS 156
E+L + Y H SN + EL R C + L V
Sbjct: 195 PETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQ 254
Query: 157 NW-----FGNK-RI----RYKKNIGKAQEEANLYAAKKAAGASPYSMGASTPMMSPAPDS 206
N F +I R+K+ AA + S+ + ++P +
Sbjct: 255 NAKAWNAFNLSCKILLTTRFKQVT----------DFLSAATTTHISLDHHSMTLTP-DEV 303
Query: 207 VG-YSKEANLYAAK---KAAGASPY--SM-GASTPMMSPAPDSVGYSSMEDRMHNTNMLP 259
K + + +P S+ + + + N + L
Sbjct: 304 KSLLLKYLDCRPQDLPREVLTTNPRRLSIIAE---SIRDGLATWDNW----KHVNCDKLT 356
Query: 260 NYIEGANDINT-DPQGPRK--QDISDILQQILNITDQSL 295
IE + +N +P RK +S + +I L
Sbjct: 357 TIIE--SSLNVLEPAEYRKMFDRLS-VFPPSAHIPTILL 392
Score = 31.7 bits (71), Expect = 0.33
Identities = 14/64 (21%), Positives = 21/64 (32%), Gaps = 17/64 (26%)
Query: 237 SPAPDSVGYSSMEDRMHNTN-MLPNYIEGANDINTDPQGPRKQDISDILQQILNITDQSL 295
P+ + Y DR++N N + Y R Q L+Q L L
Sbjct: 104 QPSMMTRMYIEQRDRLYNDNQVFAKY-----------NVSRLQPYLK-LRQAL----LEL 147
Query: 296 DEAQ 299
A+
Sbjct: 148 RPAK 151
Score = 29.4 bits (65), Expect = 1.9
Identities = 7/50 (14%), Positives = 22/50 (44%), Gaps = 10/50 (20%)
Query: 249 EDRMHNTNMLPNYIEG-ANDINTDPQGPRKQDISDILQQILNITDQSLDE 297
E + ++L + + ++ + +D+ D+ + IL + + +D
Sbjct: 13 EHQYQYKDILSVFEDAFVDNFDC-------KDVQDMPKSIL--SKEEIDH 53
>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo,
protein-DNA, human disease; 3.20A {Homo sapiens}
Length = 221
Score = 55.8 bits (133), Expect = 2e-09
Identities = 26/161 (16%), Positives = 50/161 (31%), Gaps = 34/161 (21%)
Query: 28 KLAQIRTIYQQELEKYEQACSEFTTHVMNLLREQSRTRPITPKEIERMVQIIHRKFSSIQ 87
K + +Y + K + +F V QS ++++ +
Sbjct: 72 KTQKRAALYTWYVRKQREILRQFNQTV------QSSGNMTDKSSQDQLLFLFPEFSQQSH 125
Query: 88 MQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARK 147
+ + + RR R + + +IL + + PS+E +E L +
Sbjct: 126 GPGQSDDACSEPTNKKM----RRNRFKWGPASQQILYQAY---DRQKNPSKEEREALVEE 178
Query: 148 CN---------------------ITLSQVSNWFGNKRIRYK 167
CN +T +V NWF N+R
Sbjct: 179 CNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRRKEEA 219
>3d1n_I POU domain, class 6, transcription factor 1; protein-DNA complex,
helix-turn-helix (HTH), DNA-binding, homeobox, nucleus,
transcription regulation; 2.51A {Homo sapiens}
Length = 151
Score = 54.3 bits (130), Expect = 2e-09
Identities = 26/102 (25%), Positives = 50/102 (49%), Gaps = 3/102 (2%)
Query: 67 ITPKEIERMVQIIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEY 126
ITPK +++ ++ + + +++ ++ + + R++R +F+ QA E LN Y
Sbjct: 52 ITPKSAQKLKPVLEKWLNEAELRNQEGQQNLMEFVGGEPSKKRKRRTSFTPQAIEALNAY 111
Query: 127 FYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
F NP P+ + E+A++ N V WF N+R K
Sbjct: 112 F---EKNPLPTGQEITEMAKELNYDREVVRVWFSNRRQTLKN 150
>2da5_A Zinc fingers and homeoboxes protein 3; homeobox domain, three
helices with the DNA binding helix- turn-helix motif,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 75
Score = 51.4 bits (123), Expect = 4e-09
Identities = 13/71 (18%), Positives = 27/71 (38%), Gaps = 3/71 (4%)
Query: 108 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYK 167
K + + + L F NP P +E + L + +T ++ +WF +R +
Sbjct: 7 GPTKYKERAPEQLRALESSF---AQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKVN 63
Query: 168 KNIGKAQEEAN 178
K ++
Sbjct: 64 AEETKKSGPSS 74
>1lfb_A Liver transcription factor (LFB1); transcription regulation; 2.80A
{Rattus norvegicus} SCOP: a.4.1.1 PDB: 2lfb_A
Length = 99
Score = 52.1 bits (124), Expect = 5e-09
Identities = 19/81 (23%), Positives = 30/81 (37%), Gaps = 24/81 (29%)
Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCN------------------- 149
RR R + + +IL + + PS+E +E L +CN
Sbjct: 10 RRNRFKWGPASQQILFQAYER---QKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGS 66
Query: 150 --ITLSQVSNWFGNKRIRYKK 168
+T +V NWF N+R
Sbjct: 67 NLVTEVRVYNWFANRRKEEAF 87
>1ic8_A Hepatocyte nuclear factor 1-alpha; transcription regulation,
DNA-binding, POU domain, diabetes, disease mutation,
MODY3, transcription/DNA comple; 2.60A {Homo sapiens}
SCOP: a.4.1.1 a.35.1.1
Length = 194
Score = 53.7 bits (128), Expect = 7e-09
Identities = 19/80 (23%), Positives = 30/80 (37%), Gaps = 24/80 (30%)
Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCN------------------- 149
RR R + + +IL + + PS+E +E L +CN
Sbjct: 116 RRNRFKWGPASQQILFQAY---ERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGS 172
Query: 150 --ITLSQVSNWFGNKRIRYK 167
+T +V NWF N+R
Sbjct: 173 NLVTEVRVYNWFANRRKEEA 192
>2hi3_A Homeodomain-only protein; transcription; NMR {Mus musculus} SCOP:
a.4.1.1
Length = 73
Score = 50.1 bits (120), Expect = 1e-08
Identities = 13/72 (18%), Positives = 29/72 (40%), Gaps = 2/72 (2%)
Query: 108 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYK 167
+ + ++ EIL F + N +P +A + +T Q WF + ++
Sbjct: 2 SAQTVSGPTEDQVEILEYNF--NKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWR 59
Query: 168 KNIGKAQEEANL 179
++ G E ++
Sbjct: 60 RSEGLPSECRSV 71
>2d5v_A Hepatocyte nuclear factor 6; transcription factor,
transcription-DNA complex; 2.00A {Rattus norvegicus}
PDB: 1s7e_A
Length = 164
Score = 52.6 bits (125), Expect = 1e-08
Identities = 24/146 (16%), Positives = 55/146 (37%), Gaps = 19/146 (13%)
Query: 37 QQELEKYEQACSEFTTHVMNLLR--------------EQSRTRPITPKEIERMVQIIHRK 82
EL++Y + F V+ + + R + + + + ++
Sbjct: 14 TTELKRYSIPQAIFAQRVLCRSQGTLSDLLRNPKPWSKLKSGRETFRRMWKWLQEPEFQR 73
Query: 83 FSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKE 142
S++++ + + R ++ R F+ L+ F + PS+E +
Sbjct: 74 MSALRLAACKRKEQEHGKDRGN--TPKKPRLVFTDVQRRTLHAIFKEN---KRPSKELQI 128
Query: 143 ELARKCNITLSQVSNWFGNKRIRYKK 168
++++ + LS VSN+F N R R
Sbjct: 129 TISQQLGLELSTVSNFFMNARRRSLD 154
>2da2_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three
helices with the DNA binding helix- turn-helix motif,
structural genomics; NMR {Homo sapiens}
Length = 70
Score = 50.1 bits (120), Expect = 1e-08
Identities = 16/61 (26%), Positives = 30/61 (49%), Gaps = 3/61 (4%)
Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
R R F+ +L ++F + N YP ++ E+L+ N+ + WF N R + +K
Sbjct: 8 RSSRTRFTDYQLRVLQDFFDA---NAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARK 64
Query: 169 N 169
+
Sbjct: 65 S 65
>2da1_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three
helices with the DNA binding helix- turn-helix motif,
structural genomics; NMR {Homo sapiens}
Length = 70
Score = 49.3 bits (118), Expect = 2e-08
Identities = 16/61 (26%), Positives = 29/61 (47%), Gaps = 3/61 (4%)
Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
+R R + +L +YF N PSEE +E+A K + + +WF N + ++
Sbjct: 8 KRPRTRITDDQLRVLRQYF---DINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKERQ 64
Query: 169 N 169
+
Sbjct: 65 S 65
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 53.9 bits (129), Expect = 3e-08
Identities = 61/385 (15%), Positives = 120/385 (31%), Gaps = 120/385 (31%)
Query: 12 TLR--ILLH-AIEHS----------------DYRAKLAQIRTIYQQELEKYEQA--CSEF 50
+ R L H ++EH + L + + + E A +F
Sbjct: 5 STRPLTLSHGSLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELVGKF 64
Query: 51 TTHVMNLLR--EQSRTRPITP---KEIERMVQI-----IHRKFSSIQMQLKQSTCEAVMI 100
+V +L+ + + + E E IH + + + + + +
Sbjct: 65 LGYVSSLVEPSKVGQFDQVLNLCLTEFEN--CYLEGNDIHALAAKLLQENDTTLVKTKEL 122
Query: 101 LRSRFLDARR-KRRNFSKQASEIL---------------------NEYF---------YS 129
+++ ++ AR +R F K+++ L ++YF Y
Sbjct: 123 IKN-YITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYH 181
Query: 130 HLSNPYPSEEAK--EELAR---KCNITLSQ---VSNWFGNKRIRYKKN-----------I 170
L A+ EL R +Q + W N K+ I
Sbjct: 182 VLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLI 241
Query: 171 GKAQEEANLYAAKKAAGASPYSM-----GAST---PMMSPAPDSVGYSKEANLYAAKKAA 222
G Q A+ K G +P + GA+ +++ + S E+ + +KA
Sbjct: 242 GVIQ-LAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAI 300
Query: 223 GASPYSMGA----STPMMSPAPDSVGYSSMEDRMHNTNMLPNY---IEGANDINTDPQGP 275
+ +G + P S P S +ED + N +P+ I
Sbjct: 301 TVL-FFIGVRCYEAYPNTSLPP-----SILEDSLENNEGVPSPMLSISNL---------T 345
Query: 276 RKQDISDILQQILNITDQSLDEAQA 300
++Q +Q +N T+ L +
Sbjct: 346 QEQ-----VQDYVNKTNSHLPAGKQ 365
Score = 48.5 bits (115), Expect = 2e-06
Identities = 50/300 (16%), Positives = 101/300 (33%), Gaps = 82/300 (27%)
Query: 24 DYRAKLAQIRTIYQQELEKYEQACSEFTTHVMNLLREQSRTRPITPKEIERMVQIIHRKF 83
D + ++ + + + F+ +++++ P + IH F
Sbjct: 1634 DLYKTSKAAQDVWN-RADNHFKDTYGFS--ILDIVINN-------PVNL-----TIH--F 1676
Query: 84 SSIQMQ-LKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKE 142
+ + ++++ + MI + +D + K K+ +E Y + K
Sbjct: 1677 GGEKGKRIRENY--SAMIFET-IVDGKLKTEKIFKEINEHSTSYTFRS---E------KG 1724
Query: 143 ELARKCN----ITLSQVSNWFGNKRIRYKKNIGKAQEEANL-------YAAKKAAGASPY 191
L+ +TL + + + + ++ K G +A YAA A+ A
Sbjct: 1725 LLSATQFTQPALTLMEKAAF---EDLKSK---GLIPADATFAGHSLGEYAA-LASLA--- 1774
Query: 192 SMGASTPMMSPAPDSV------G-YSKEANLYAAKKAAGASPYSMGASTP-MMSPAPDSV 243
MS V G + A + G S Y M A P ++ +
Sbjct: 1775 --DV----MSIE-SLVEVVFYRGMTMQVA---VPRDELGRSNYGMIAINPGRVAASFSQE 1824
Query: 244 GYSSMEDRM-HNTNMLPNYIEGANDINTDPQ-----GPRKQDISDILQQILN-ITDQSLD 296
+ +R+ T L +E N N + Q G + + D + +LN I Q +D
Sbjct: 1825 ALQYVVERVGKRTGWL---VEIVNY-NVENQQYVAAG-DLRAL-DTVTNVLNFIKLQKID 1878
>1e3o_C Octamer-binding transcription factor 1; transcription factor, POU
domain, dimer, DNA binding; 1.9A {Homo sapiens} SCOP:
a.4.1.1 a.35.1.1 PDB: 1gt0_C 1hf0_A* 1cqt_A* 1o4x_A
1oct_C* 1pou_A 1pog_A 1hdp_A
Length = 160
Score = 50.3 bits (120), Expect = 7e-08
Identities = 15/60 (25%), Positives = 27/60 (45%), Gaps = 3/60 (5%)
Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
R+KR + L + F + N P+ E +A + N+ + WF N+R + K+
Sbjct: 102 RKKRTSIETNIRVALEKSF---MENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKR 158
>1au7_A Protein PIT-1, GHF-1; complex (DNA-binding protein/DNA), pituitary,
CPHD, POU domain, transcription factor,
transcription/DNA complex; HET: DNA; 2.30A {Rattus
norvegicus} SCOP: a.4.1.1 a.35.1.1
Length = 146
Score = 49.6 bits (118), Expect = 1e-07
Identities = 20/102 (19%), Positives = 39/102 (38%), Gaps = 8/102 (7%)
Query: 67 ITPKEIERMVQIIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEY 126
++ K ++ I+ + + + R R ++R S A + L +
Sbjct: 51 LSFKNACKLKAILSKWLEEAEQVGALYNEKVGANERKR-----KRRTTISIAAKDALERH 105
Query: 127 FYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
F + PS + +A + N+ V WF N+R R K+
Sbjct: 106 F---GEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKR 144
>1bw5_A ISL-1HD, insulin gene enhancer protein ISL-1; DNA-binding protein,
homeodomain, LIM domain; NMR {Rattus norvegicus} SCOP:
a.4.1.1
Length = 66
Score = 47.0 bits (112), Expect = 1e-07
Identities = 16/66 (24%), Positives = 27/66 (40%), Gaps = 3/66 (4%)
Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
R R +++ L + + NP P KE+L ++ + WF NKR + KK
Sbjct: 4 TRVRTVLNEKQLHTLRTCYAA---NPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKK 60
Query: 169 NIGKAQ 174
+
Sbjct: 61 RSIMMK 66
>3l1p_A POU domain, class 5, transcription factor 1; POU, transcription
factor DNA complex, pore, stem cells; HET: DNA; 2.80A
{Mus musculus} PDB: 1ocp_A
Length = 155
Score = 49.0 bits (116), Expect = 2e-07
Identities = 16/63 (25%), Positives = 28/63 (44%), Gaps = 3/63 (4%)
Query: 107 DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRY 166
+RKR + + L F L +P PS + +A + + V WF N+R +
Sbjct: 95 ARKRKRTSIENRVRWSLETMF---LKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKG 151
Query: 167 KKN 169
K++
Sbjct: 152 KRS 154
>2da3_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three
helices with the DNA binding helix- turn-helix motif,
structural genomics; NMR {Homo sapiens}
Length = 80
Score = 46.7 bits (111), Expect = 2e-07
Identities = 15/61 (24%), Positives = 29/61 (47%), Gaps = 3/61 (4%)
Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
+R R + + EIL + + L + P+ + + +A + + V WF N R R +K
Sbjct: 18 KRLRTTITPEQLEILYQKY---LLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERK 74
Query: 169 N 169
+
Sbjct: 75 S 75
>2cqx_A LAG1 longevity assurance homolog 5; homeodomain, DNA binding
domain, transcription, structural genomics, NPPSFA; NMR
{Mus musculus} SCOP: a.4.1.1
Length = 72
Score = 46.7 bits (111), Expect = 2e-07
Identities = 12/67 (17%), Positives = 31/67 (46%), Gaps = 3/67 (4%)
Query: 103 SRFLDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNK 162
+ N + ++ L + F S YP E+ + L+++ + ++ ++ WF ++
Sbjct: 4 GSSGGIKDSPVN-KVEPNDTLEKVFVSV--TKYPDEKRLKGLSKQLDWSVRKIQCWFRHR 60
Query: 163 RIRYKKN 169
R + K +
Sbjct: 61 RNQDKPS 67
>2k40_A Homeobox expressed in ES cells 1; thermostable homeodomain variant,
DNA binding protein, developmental protein, disease
mutation, DNA-binding; NMR {Homo sapiens}
Length = 67
Score = 45.8 bits (109), Expect = 4e-07
Identities = 22/66 (33%), Positives = 37/66 (56%), Gaps = 3/66 (4%)
Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
RR R F++ E+L F N YP + E+LA+K N+ L ++ WF N+R + K+
Sbjct: 2 RRPRTAFTQNQIEVLENVFRV---NCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKR 58
Query: 169 NIGKAQ 174
+ ++Q
Sbjct: 59 SHRESQ 64
>2xsd_C POU domain, class 3, transcription factor 1; transcription-DNA
complex, SOX; 2.05A {Mus musculus}
Length = 164
Score = 47.7 bits (113), Expect = 5e-07
Identities = 17/60 (28%), Positives = 24/60 (40%), Gaps = 3/60 (5%)
Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
R+KR + L +F L P PS LA + V WF N+R + K+
Sbjct: 100 RKKRTSIEVGVKGALESHF---LKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKEKR 156
>2l7z_A Homeobox protein HOX-A13; gene regulation; NMR {Homo sapiens} PDB:
2ld5_A*
Length = 73
Score = 45.2 bits (107), Expect = 6e-07
Identities = 22/76 (28%), Positives = 42/76 (55%), Gaps = 5/76 (6%)
Query: 103 SRFLDARRKRRNFSK-QASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGN 161
S L+ R+KR ++K Q E+ EY N + +++ + ++ N++ QV+ WF N
Sbjct: 2 SHMLEGRKKRVPYTKVQLKELEREYAT----NKFITKDKRRRISATTNLSERQVTIWFQN 57
Query: 162 KRIRYKKNIGKAQEEA 177
+R++ KK I K + +
Sbjct: 58 RRVKEKKVINKLKTTS 73
>3nar_A ZHX1, zinc fingers and homeoboxes protein 1; corepressor,
homeodomain, structural genomics, oxford production
facility, OPPF, transcription; 2.60A {Homo sapiens}
Length = 96
Score = 45.9 bits (108), Expect = 7e-07
Identities = 13/61 (21%), Positives = 28/61 (45%), Gaps = 3/61 (4%)
Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
K + + +L F + +PS E ++LA++ + + + +WFG+ R +K
Sbjct: 26 TGKICKKTPEQLHMLKSAF---VRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKN 82
Query: 169 N 169
Sbjct: 83 G 83
>2dmp_A Zinc fingers and homeoboxes protein 2; homeobox domain, three
helices with the DNA binding helix- turn-helix motif,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 89
Score = 45.4 bits (107), Expect = 8e-07
Identities = 12/80 (15%), Positives = 34/80 (42%), Gaps = 3/80 (3%)
Query: 108 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYK 167
A +K + ++ +IL + F L + +P++ + L + ++ ++ +WF +R
Sbjct: 13 APQKFKEKTQGQVKILEDSF---LKSSFPTQAELDRLRVETKLSRREIDSWFSERRKLRD 69
Query: 168 KNIGKAQEEANLYAAKKAAG 187
+ + ++G
Sbjct: 70 SMEQAVLDSMGSGKSGPSSG 89
>2ecb_A Zinc fingers and homeoboxes protein 1; homeobox domain,
transcription factor, structural genomics, NPPSFA; NMR
{Homo sapiens} SCOP: a.4.1.1
Length = 89
Score = 45.0 bits (106), Expect = 1e-06
Identities = 16/86 (18%), Positives = 36/86 (41%), Gaps = 7/86 (8%)
Query: 105 FLDARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRI 164
F + K + + + +L F L++ ++E L + +T ++ WF K
Sbjct: 10 FTPQKFKEK--TAEQLRVLQASF---LNSSVLTDEELNRLRAQTKLTRREIDAWFTEK-- 62
Query: 165 RYKKNIGKAQEEANLYAAKKAAGASP 190
+ K + + + E + A ++G S
Sbjct: 63 KKSKALKEEKMEIDESNAGSSSGPSS 88
>2ecc_A Homeobox and leucine zipper protein homez; homeobox domain,
transcription factor, leucine zipper- containing factor,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
a.4.1.1
Length = 76
Score = 44.2 bits (104), Expect = 2e-06
Identities = 12/60 (20%), Positives = 24/60 (40%), Gaps = 3/60 (5%)
Query: 110 RKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKN 169
+ +K+ IL +F L + E ++L + + ++ WFG+ R K
Sbjct: 5 SSGKRKTKEQLAILKSFF---LQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHG 61
>1yz8_P Pituitary homeobox 2; DNA binding protein, transcription/DNA
complex; NMR {Homo sapiens} SCOP: a.4.1.1 PDB: 2l7f_P
2lkx_A* 2l7m_P
Length = 68
Score = 43.8 bits (104), Expect = 2e-06
Identities = 21/61 (34%), Positives = 34/61 (55%), Gaps = 3/61 (4%)
Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
RR+R +F+ Q + L F N YP +EE+A N+T ++V WF N+R +++K
Sbjct: 4 RRQRTHFTSQQLQQLEATF---QRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK 60
Query: 169 N 169
Sbjct: 61 R 61
>2dms_A Homeobox protein OTX2; homeobox domain, three helices with the DNA
binding helix- turn-helix motif, structural genomics,
NPPSFA; NMR {Mus musculus}
Length = 80
Score = 43.9 bits (104), Expect = 2e-06
Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 3/61 (4%)
Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
RR+R F++ ++L F YP +EE+A K N+ S+V WF N+R + ++
Sbjct: 8 RRERTTFTRAQLDVLEALF---AKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQ 64
Query: 169 N 169
Sbjct: 65 Q 65
>2dmq_A LIM/homeobox protein LHX9; homeobox domain, three helices with the
DNA binding helix- turn-helix motif, structural
genomics, NPPSFA; NMR {Homo sapiens}
Length = 80
Score = 44.0 bits (104), Expect = 2e-06
Identities = 16/66 (24%), Positives = 32/66 (48%), Gaps = 3/66 (4%)
Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
+R R +F + YF N P + ++LA+K +T + WF N R ++++
Sbjct: 8 KRMRTSFKHHQLRTMKSYFAI---NHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRR 64
Query: 169 NIGKAQ 174
N+ + +
Sbjct: 65 NLLRQE 70
>2dmu_A Homeobox protein goosecoid; homeobox domain, three helices with the
DNA binding helix- turn-helix motif, structural
genomics, NPPSFA; NMR {Homo sapiens}
Length = 70
Score = 42.7 bits (101), Expect = 4e-06
Identities = 19/62 (30%), Positives = 33/62 (53%), Gaps = 5/62 (8%)
Query: 109 RRKRRNFSKQASEILNEYF-YSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYK 167
RR R F+ + E L F + YP +E+LARK ++ +V WF N+R +++
Sbjct: 8 RRHRTIFTDEQLEALENLFQETK----YPDVGTREQLARKVHLREEKVEVWFKNRRAKWR 63
Query: 168 KN 169
++
Sbjct: 64 RS 65
>1uhs_A HOP, homeodomain only protein; structural genomics, cardiac
development, riken structural genomics/proteomics
initiative, RSGI, transcription; NMR {Mus musculus}
SCOP: a.4.1.1
Length = 72
Score = 42.8 bits (101), Expect = 4e-06
Identities = 11/62 (17%), Positives = 23/62 (37%), Gaps = 2/62 (3%)
Query: 108 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYK 167
++ EIL F + N +P +A + +T Q WF + ++
Sbjct: 1 GSEGAATMTEDQVEILEYNF--NKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWR 58
Query: 168 KN 169
++
Sbjct: 59 RS 60
>2cra_A Homeobox protein HOX-B13; DNA-binding, transcription regulation,
helix-turn-helix, structural genomics, NPPSFA; NMR {Homo
sapiens} SCOP: a.4.1.1
Length = 70
Score = 42.1 bits (99), Expect = 8e-06
Identities = 18/67 (26%), Positives = 37/67 (55%), Gaps = 5/67 (7%)
Query: 103 SRFLDARRKRRNFSK-QASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGN 161
S R+KR +SK Q E+ EY N + +++ + +++ +++ Q++ WF N
Sbjct: 2 SSGSSGRKKRIPYSKGQLRELEREYAA----NKFITKDKRRKISAATSLSERQITIWFQN 57
Query: 162 KRIRYKK 168
+R++ KK
Sbjct: 58 RRVKEKK 64
>1fjl_A Paired protein; DNA-binding protein, paired BOX, transcription
regulation; HET: DNA; 2.00A {Drosophila melanogaster}
SCOP: a.4.1.1 PDB: 3a01_B
Length = 81
Score = 42.4 bits (100), Expect = 9e-06
Identities = 21/60 (35%), Positives = 31/60 (51%), Gaps = 3/60 (5%)
Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
RR R FS + L F YP +EELA++ N+T +++ WF N+R R +K
Sbjct: 19 RRSRTTFSASQLDELERAF---ERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRK 75
>2cue_A Paired box protein PAX6; homeobox domain, transcription factor,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
a.4.1.1
Length = 80
Score = 41.6 bits (98), Expect = 1e-05
Identities = 18/62 (29%), Positives = 36/62 (58%), Gaps = 5/62 (8%)
Query: 109 RRKRRNFSKQASEILNEYF-YSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYK 167
+R R +F+++ E L + F +H YP A+E LA K ++ +++ WF N+R +++
Sbjct: 8 QRNRTSFTQEQIEALEKEFERTH----YPDVFARERLAAKIDLPEARIQVWFSNRRAKWR 63
Query: 168 KN 169
+
Sbjct: 64 RE 65
>1puf_A HOX-1.7, homeobox protein HOX-A9; homeodomian, protein-DNA complex,
HOX hexapeptide, TALE homeodomain, homeodomain
interaction; 1.90A {Mus musculus} SCOP: a.4.1.1 PDB:
1san_A
Length = 77
Score = 41.8 bits (98), Expect = 1e-05
Identities = 22/63 (34%), Positives = 36/63 (57%), Gaps = 5/63 (7%)
Query: 107 DARRKRRNFSK-QASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIR 165
R+KR ++K Q E+ E+ + N Y + + + E+AR N+T QV WF N+R++
Sbjct: 12 STRKKRCPYTKHQTLELEKEFLF----NMYLTRDRRYEVARLLNLTERQVKIWFQNRRMK 67
Query: 166 YKK 168
KK
Sbjct: 68 MKK 70
>2da6_A Hepatocyte nuclear factor 1-beta; homeobox domain, three helices
with the DNA binding helix- turn-helix motif, structural
genomics, NPPSFA; NMR {Homo sapiens}
Length = 102
Score = 41.8 bits (97), Expect = 2e-05
Identities = 18/77 (23%), Positives = 30/77 (38%), Gaps = 24/77 (31%)
Query: 108 ARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCN------------------ 149
+ R R + + +IL + + PS+E +E L +CN
Sbjct: 6 SGRNRFKWGPASQQILYQAYDR---QKNPSKEEREALVEECNRAECLQRGVSPSKAHGLG 62
Query: 150 ---ITLSQVSNWFGNKR 163
+T +V NWF N+R
Sbjct: 63 SNLVTEVRVYNWFANRR 79
>2hdd_A Protein (engrailed homeodomain Q50K); DNA binding, complex (DNA
binding protein/DNA), transcription/DNA complex; HET:
DNA; 1.90A {Drosophila melanogaster} SCOP: a.4.1.1 PDB:
1hdd_C* 2jwt_A 3hdd_A 1p7j_A* 1p7i_A* 2hos_A 2hot_A
1du0_A* 1ztr_A 1enh_A 2p81_A
Length = 61
Score = 40.0 bits (94), Expect = 4e-05
Identities = 18/65 (27%), Positives = 35/65 (53%), Gaps = 5/65 (7%)
Query: 106 LDARRKRRNFS-KQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRI 164
+ +R R FS +Q + + E+ N Y +E +++L+ + + +Q+ WF NKR
Sbjct: 1 MAEKRPRTAFSSEQLARLKREFNE----NRYLTERRRQQLSSELGLNEAQIKIWFKNKRA 56
Query: 165 RYKKN 169
+ KK+
Sbjct: 57 KIKKS 61
>1x2m_A LAG1 longevity assurance homolog 6; homeobox domain, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Mus musculus} SCOP:
a.4.1.1
Length = 64
Score = 39.8 bits (93), Expect = 5e-05
Identities = 11/53 (20%), Positives = 25/53 (47%), Gaps = 2/53 (3%)
Query: 111 KRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKR 163
+ + Q + IL E ++ +P E+ E L+++ + + + WF +R
Sbjct: 3 SGSSGTAQPNAIL-EKVFTA-ITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRR 53
>1ftt_A TTF-1 HD, thyroid transcription factor 1 homeodomain; DNA binding
protein; NMR {Rattus norvegicus} SCOP: a.4.1.1
Length = 68
Score = 38.5 bits (90), Expect = 1e-04
Identities = 22/69 (31%), Positives = 30/69 (43%), Gaps = 4/69 (5%)
Query: 109 RRKRRN-FSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYK 167
RRKRR FS+ L F Y S +E LA ++T +QV WF N R + K
Sbjct: 2 RRKRRVLFSQAQVYELERRF---KQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMK 58
Query: 168 KNIGKAQEE 176
+ +
Sbjct: 59 RQAKDKAAQ 67
>1b72_A Protein (homeobox protein HOX-B1); homeodomain, DNA, complex,
DNA-binding protein, protein/DNA complex; HET: DNA;
2.35A {Homo sapiens} SCOP: a.4.1.1
Length = 97
Score = 38.7 bits (90), Expect = 2e-04
Identities = 21/82 (25%), Positives = 40/82 (48%), Gaps = 5/82 (6%)
Query: 88 MQLKQSTCEAVMILRSRFLDARRKRRNF-SKQASEILNEYFYSHLSNPYPSEEAKEELAR 146
M++K++ + + R NF ++Q +E+ E+ + N Y S + E+A
Sbjct: 14 MKVKRNPPKTAKVSEPGLGSPSGLRTNFTTRQLTELEKEFHF----NKYLSRARRVEIAA 69
Query: 147 KCNITLSQVSNWFGNKRIRYKK 168
+ +QV WF N+R++ KK
Sbjct: 70 TLELNETQVKIWFQNRRMKQKK 91
>1zq3_P PRD-4, homeotic bicoid protein; protein-DNA complex, double helix,
helix-turn-helix; NMR {Drosophila melanogaster} SCOP:
a.4.1.1
Length = 68
Score = 37.8 bits (88), Expect = 2e-04
Identities = 17/70 (24%), Positives = 33/70 (47%), Gaps = 5/70 (7%)
Query: 109 RRKRRNFSK-QASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYK 167
RR R F+ Q +E+ + Y + +L+ K + +QV WF N+R R+K
Sbjct: 3 RRTRTTFTSSQIAELEQHFLQ----GRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHK 58
Query: 168 KNIGKAQEEA 177
+ ++++
Sbjct: 59 IQSDQHKDQS 68
>1ahd_P Antennapedia protein mutant; DNA binding protein/DNA; HET: DNA; NMR
{Drosophila melanogaster} SCOP: a.4.1.1 PDB: 2hoa_A
1hom_A 1ftz_A
Length = 68
Score = 37.8 bits (88), Expect = 2e-04
Identities = 17/61 (27%), Positives = 35/61 (57%), Gaps = 5/61 (8%)
Query: 109 RRKRRNFSK-QASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYK 167
+R R+ +++ Q E+ E+ + N Y + + E+A ++T Q+ WF N+R+++K
Sbjct: 3 KRGRQTYTRYQTLELEKEFHF----NRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWK 58
Query: 168 K 168
K
Sbjct: 59 K 59
>3rkq_A Homeobox protein NKX-2.5; helix-turn-helix, DNA binding, nucleus,
transcription-DNA CO; 1.70A {Homo sapiens}
Length = 58
Score = 37.6 bits (88), Expect = 2e-04
Identities = 20/61 (32%), Positives = 28/61 (45%), Gaps = 4/61 (6%)
Query: 108 ARRKRRN-FSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRY 166
RRK R FS+ L F Y S +++LA +T +QV WF N+R +
Sbjct: 1 GRRKPRVLFSQAQVYELERRF---KQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKS 57
Query: 167 K 167
K
Sbjct: 58 K 58
>2da4_A Hypothetical protein DKFZP686K21156; homeobox domain, three helices
with the DNA binding helix- turn-helix motif, structural
genomics, NPPSFA; NMR {Homo sapiens}
Length = 80
Score = 38.0 bits (87), Expect = 3e-04
Identities = 16/62 (25%), Positives = 30/62 (48%), Gaps = 1/62 (1%)
Query: 108 ARRKRRNFSKQASEILNEYFYSHLSN-PYPSEEAKEELARKCNITLSQVSNWFGNKRIRY 166
A + R FS + L +Y+ + +++ E E +A + N+ V W GN+R +Y
Sbjct: 8 ALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIGNRRRKY 67
Query: 167 KK 168
+
Sbjct: 68 RL 69
>3a02_A Homeobox protein aristaless; homeodomain, developmental protein,
DNA-binding, N gene regulation; 1.00A {Drosophila
melanogaster} PDB: 3lnq_A 3cmy_A
Length = 60
Score = 37.2 bits (87), Expect = 3e-04
Identities = 17/58 (29%), Positives = 28/58 (48%), Gaps = 3/58 (5%)
Query: 112 RRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKN 169
F+ E L + F YP +EELA K +T +++ WF N+R +++K
Sbjct: 3 HMTFTSFQLEELEKAFSR---THYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQ 57
>1ig7_A Homeotic protein MSX-1; helix-turn-helix, transcription/DNA
complex; 2.20A {Mus musculus} SCOP: a.4.1.1
Length = 58
Score = 36.8 bits (86), Expect = 4e-04
Identities = 16/60 (26%), Positives = 26/60 (43%), Gaps = 3/60 (5%)
Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
R+ R F+ L F Y S + E + ++T +QV WF N+R + K+
Sbjct: 1 RKPRTPFTTAQLLALERKFRQ---KQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57
>2djn_A Homeobox protein DLX-5; structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 70
Score = 37.4 bits (87), Expect = 4e-04
Identities = 19/60 (31%), Positives = 26/60 (43%), Gaps = 3/60 (5%)
Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
R+ R +S L F Y + + ELA +T +QV WF NKR + KK
Sbjct: 8 RKPRTIYSSFQLAALQRRFQK---TQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKK 64
>1jgg_A Segmentation protein EVEN-skipped; homeodomain, protein-DNA
complex, transcription/DNA complex; 2.00A {Drosophila
melanogaster} SCOP: a.4.1.1
Length = 60
Score = 36.6 bits (85), Expect = 5e-04
Identities = 18/61 (29%), Positives = 31/61 (50%), Gaps = 5/61 (8%)
Query: 109 RRKRRNFSK-QASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYK 167
RR R F++ Q + E++ Y S + ELA + N+ S + WF N+R++ K
Sbjct: 2 RRYRTAFTRDQLGRLEKEFYK----ENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDK 57
Query: 168 K 168
+
Sbjct: 58 R 58
>2h1k_A IPF-1, pancreatic and duodenal homeobox 1, homeodomain; protein-DNA
complex, transcription/DNA complex; 2.42A {Mesocricetus
auratus}
Length = 63
Score = 36.6 bits (85), Expect = 6e-04
Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 5/63 (7%)
Query: 107 DARRKRRNFSK-QASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIR 165
+R R +++ Q E+ E+ + N Y S + ELA N+T + WF N+R++
Sbjct: 2 SNKRTRTAYTRAQLLELEKEFLF----NKYISRPRRVELAVMLNLTERHIKIWFQNRRMK 57
Query: 166 YKK 168
+KK
Sbjct: 58 WKK 60
>2vi6_A Homeobox protein nanog; homeodomain, DNA-binding, transcription,
transcription facto developmental protein, transcription
regulation, NUC homeobox; 2.6A {Mus musculus}
Length = 62
Score = 36.5 bits (85), Expect = 7e-04
Identities = 17/60 (28%), Positives = 30/60 (50%), Gaps = 3/60 (5%)
Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
++ R FS+ L + F Y S + +EL+ N++ QV WF N+R++ K+
Sbjct: 4 QKMRTVFSQAQLCALKDRFQK---QKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKR 60
>2e1o_A Homeobox protein PRH; DNA binding protein, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} SCOP: a.4.1.1
Length = 70
Score = 36.2 bits (84), Expect = 0.001
Identities = 14/63 (22%), Positives = 29/63 (46%), Gaps = 5/63 (7%)
Query: 107 DARRKRRNFSK-QASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIR 165
+ + FS Q E+ ++ Y S ++ LA+ ++ QV WF N+R +
Sbjct: 6 SGKGGQVRFSNDQTIELEKKFET----QKYLSPPERKRLAKMLQLSERQVKTWFQNRRAK 61
Query: 166 YKK 168
+++
Sbjct: 62 WRR 64
>2r5y_A Homeotic protein sex combs reduced; homeodomain; HET: DNA; 2.60A
{Drosophila melanogaster} PDB: 2r5z_A*
Length = 88
Score = 36.8 bits (85), Expect = 0.001
Identities = 17/63 (26%), Positives = 37/63 (58%), Gaps = 5/63 (7%)
Query: 107 DARRKRRNFSK-QASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIR 165
+ +R+R ++++ Q E+ E+ + N Y + + E+A ++T Q+ WF N+R++
Sbjct: 27 ETKRQRTSYTRYQTLELEKEFHF----NRYLTRRRRIEIAHALSLTERQIKIWFQNRRMK 82
Query: 166 YKK 168
+KK
Sbjct: 83 WKK 85
>1nk2_P Homeobox protein VND; homeodomain, DNA-binding protein, embryonic
development, complex (homeodomain/DNA); HET: DNA; NMR
{Drosophila melanogaster} SCOP: a.4.1.1 PDB: 1nk3_P*
1vnd_A 1qry_A
Length = 77
Score = 36.3 bits (84), Expect = 0.001
Identities = 20/70 (28%), Positives = 31/70 (44%), Gaps = 3/70 (4%)
Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
R++R F+K + L F Y S +E LA +T +QV WF N R + K+
Sbjct: 10 RKRRVLFTKAQTYELERRF---RQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKR 66
Query: 169 NIGKAQEEAN 178
+ E +
Sbjct: 67 AQNEKGYEGH 76
>1b8i_A Ultrabithorax, protein (ultrabithorax homeotic protein IV); DNA
binding, homeodomain, homeotic proteins, development,
specificity; HET: DNA; 2.40A {Drosophila melanogaster}
SCOP: a.4.1.1 PDB: 9ant_A*
Length = 81
Score = 36.3 bits (84), Expect = 0.001
Identities = 18/63 (28%), Positives = 33/63 (52%), Gaps = 5/63 (7%)
Query: 107 DARRKRRNFSK-QASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIR 165
RR R+ +++ Q E+ E+ N Y + + E+A ++T Q+ WF N+R++
Sbjct: 19 LRRRGRQTYTRYQTLELEKEFHT----NHYLTRRRRIEMAHALSLTERQIKIWFQNRRMK 74
Query: 166 YKK 168
KK
Sbjct: 75 LKK 77
>2kt0_A Nanog, homeobox protein nanog; homeodomain, structural genomics,
protein structure initiative, PSI, center for eukaryotic
structural genomics; NMR {Homo sapiens}
Length = 84
Score = 36.3 bits (84), Expect = 0.001
Identities = 18/60 (30%), Positives = 31/60 (51%), Gaps = 3/60 (5%)
Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
++ R FS +LN+ F Y S + +EL+ N++ QV WF N+R++ K+
Sbjct: 23 QKTRTVFSSTQLCVLNDRFQR---QKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKR 79
>3a01_A Homeodomain-containing protein; homeodomain, protein-DNA complex,
DNA-binding, homeobox, NUC developmental protein; 2.70A
{Drosophila melanogaster}
Length = 93
Score = 35.6 bits (82), Expect = 0.002
Identities = 19/76 (25%), Positives = 36/76 (47%), Gaps = 4/76 (5%)
Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
++ R +F++ L + F Y + + LAR +T +QV WF N+R ++++
Sbjct: 18 KKPRTSFTRIQVAELEKRF---HKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRR 74
Query: 169 NIGKAQEEANLYAAKK 184
+ EA AA +
Sbjct: 75 Q-TAEEREAERQAANR 89
>2dmt_A Homeobox protein BARH-like 1; homeobox domain, three helices with
the DNA binding helix- turn-helix motif, structural
genomics, NPPSFA; NMR {Homo sapiens}
Length = 80
Score = 34.8 bits (80), Expect = 0.004
Identities = 17/60 (28%), Positives = 29/60 (48%), Gaps = 3/60 (5%)
Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
RR R F++ L + F Y S + +LA ++ QV W+ N+R+++KK
Sbjct: 18 RRSRTVFTELQLMGLEKRFEK---QKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKK 74
>2l9r_A Homeobox protein NKX-3.1; structural genomics, northeast structural
genomics consortiu PSI-biology, protein structure
initiative; NMR {Homo sapiens}
Length = 69
Score = 34.3 bits (79), Expect = 0.004
Identities = 15/60 (25%), Positives = 23/60 (38%), Gaps = 3/60 (5%)
Query: 109 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
+ S L F Y S + LA+ +T +QV WF N+R + K+
Sbjct: 5 HHHHSHMSHTQVIELERKFSH---QKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKR 61
>3a03_A T-cell leukemia homeobox protein 2; homeodomain, developmental
protein, DNA-binding, N gene regulation; 1.54A {Homo
sapiens}
Length = 56
Score = 32.7 bits (75), Expect = 0.014
Identities = 10/37 (27%), Positives = 20/37 (54%)
Query: 132 SNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
Y + + LA+ +T +QV WF N+R ++++
Sbjct: 18 RQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRR 54
>2e19_A Transcription factor 8; homeobox domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 64
Score = 31.2 bits (70), Expect = 0.053
Identities = 13/52 (25%), Positives = 19/52 (36%), Gaps = 3/52 (5%)
Query: 117 KQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKK 168
K +L Y+ N PS E ++A N+ L V WF +
Sbjct: 12 KNLLSLLKAYY---ALNAQPSAEELSKIADSVNLPLDVVKKWFEKMQAGQIS 60
>3bd1_A CRO protein; transcription factor, helix-turn-helix, prophage,
structural evolution, transcription; 1.40A {Xylella
fastidiosa}
Length = 79
Score = 30.7 bits (69), Expect = 0.094
Identities = 7/22 (31%), Positives = 10/22 (45%)
Query: 143 ELARKCNITLSQVSNWFGNKRI 164
LA + S +SNW R+
Sbjct: 16 ALAASLGVRQSAISNWRARGRV 37
>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription,
mRNA, multiprotein complex; HET: UTP; 2.30A
{Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A
1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A*
1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A*
1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ...
Length = 1733
Score = 33.1 bits (75), Expect = 0.13
Identities = 15/69 (21%), Positives = 21/69 (30%)
Query: 180 YAAKKAAGASPYSMGASTPMMSPAPDSVGYSKEANLYAAKKAAGASPYSMGASTPMMSPA 239
K SP S M+ + G + + A G +P S G +
Sbjct: 1484 LDVKDELMFSPLVDSGSNDAMAGGFTAYGGADYGEATSPFGAYGEAPTSPGFGVSSPGFS 1543
Query: 240 PDSVGYSSM 248
P S YS
Sbjct: 1544 PTSPTYSPT 1552
Score = 32.0 bits (72), Expect = 0.31
Identities = 22/75 (29%), Positives = 29/75 (38%), Gaps = 3/75 (4%)
Query: 187 GASPYSMGASTPMMSPAPDSVGYSKEANLYAAKKAAGASPYSMGASTPMMSPAPDSVGYS 246
SP S S S +P S YS + Y+ + SP S S S +P S YS
Sbjct: 1562 SYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPT-SPSYSPTSPSYSPTSPSYSPTSPSYS 1620
Query: 247 SMEDRMHNTNMLPNY 261
T+ P+Y
Sbjct: 1621 PTSPSYSPTS--PSY 1633
Score = 31.6 bits (71), Expect = 0.38
Identities = 17/83 (20%), Positives = 27/83 (32%), Gaps = 10/83 (12%)
Query: 187 GASPYSMGASTPMMSPAPDSVGYSKEANLYAAKKAAGASPYSMGASTPMMSPAPDSVGYS 246
GA + AP S G+ + + SP S S + +P S YS
Sbjct: 1513 GADYGEATSPFGAYGEAPTSPGFGVSSPGF--------SPTSPTYSPTSPAYSPTSPSYS 1564
Query: 247 SMEDRMHNTNMLPNYIEGANDIN 269
T+ P+Y + +
Sbjct: 1565 PTSPSYSPTS--PSYSPTSPSYS 1585
Score = 28.5 bits (63), Expect = 3.8
Identities = 14/82 (17%), Positives = 21/82 (25%), Gaps = 7/82 (8%)
Query: 185 AAGASPYSMGASTPMMSPAPDSVGYSKEANLYAAKKAAGASPYSMGASTPMMSP-----A 239
+ + M SP DS A + A A + +P
Sbjct: 1477 SGLVNADLDVKDELMFSPLVDSGSNDAMAGGFTAYGGADYGEATSPFGAYGEAPTSPGFG 1536
Query: 240 PDSVGYSSMEDRMHNTNMLPNY 261
S G+S + P Y
Sbjct: 1537 VSSPGFSPTSPTY--SPTSPAY 1556
Score = 28.1 bits (62), Expect = 4.2
Identities = 19/67 (28%), Positives = 24/67 (35%), Gaps = 6/67 (8%)
Query: 187 GASPYSMGASTPMMSPAPDSVGYSKEANLYAAKKAA------GASPYSMGASTPMMSPAP 240
SP S S S +P S YS + Y+ + SP S S S +P
Sbjct: 1576 SYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSP 1635
Query: 241 DSVGYSS 247
S YS
Sbjct: 1636 TSPSYSP 1642
>2da7_A Zinc finger homeobox protein 1B; homeobox domain, three helices
with the DNA binding helix- turn-helix motif, structural
genomics, NPPSFA; NMR {Homo sapiens}
Length = 71
Score = 30.1 bits (67), Expect = 0.13
Identities = 10/59 (16%), Positives = 21/59 (35%), Gaps = 3/59 (5%)
Query: 111 KRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRYKKN 169
N K +L Y+ N P+ + +++ + V WF +++ N
Sbjct: 8 SPINPYKDHMSVLKAYY---AMNMEPNSDELLKISIAVGLPQEFVKEWFEQRKVYQYSN 63
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 30.7 bits (68), Expect = 0.34
Identities = 9/31 (29%), Positives = 14/31 (45%), Gaps = 5/31 (16%)
Query: 167 KKNIGKAQEEANLYAAKKAAGASP-YSMGAS 196
K+ + K Q LYA A P ++ A+
Sbjct: 19 KQALKKLQASLKLYADDSA----PALAIKAT 45
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 1752
Score = 31.2 bits (70), Expect = 0.44
Identities = 19/67 (28%), Positives = 26/67 (38%), Gaps = 7/67 (10%)
Query: 187 GASPYSMGASTPMMSP--APDSVGYSKEANLYAAKKAAGASPYSMGASTPMMSPA----- 239
ASPY S SP + S GY + Y+ ++ + S+P SP
Sbjct: 1527 AASPYKGVQSPGYTSPFSSAMSPGYGLTSPSYSPSSPGYSTSPAYMPSSPSYSPTSPSYS 1586
Query: 240 PDSVGYS 246
P S YS
Sbjct: 1587 PTSPSYS 1593
Score = 30.0 bits (67), Expect = 1.1
Identities = 15/81 (18%), Positives = 18/81 (22%), Gaps = 13/81 (16%)
Query: 187 GASPYSMGASTP----------MMSPAPDSVGYSKEANLYAAKKAAGASPYSMGASTPMM 236
+PY SP G ASPY S
Sbjct: 1482 AGTPYERSPMVDSGFVGSPDAAAFSPLVQG-GSEGREGFGDYGLLGAASPYKGVQSPGYT 1540
Query: 237 SP--APDSVGYSSMEDRMHNT 255
SP + S GY +
Sbjct: 1541 SPFSSAMSPGYGLTSPSYSPS 1561
Score = 27.7 bits (61), Expect = 5.6
Identities = 22/73 (30%), Positives = 29/73 (39%), Gaps = 3/73 (4%)
Query: 189 SPYSMGASTPMMSPAPDSVGYSKEANLYAAKKAAGASPYSMGASTPMMSPAPDSVGYSSM 248
SP S S S +P S YS + Y+ + SP S S S +P S YS
Sbjct: 1635 SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPT-SPSYSPTSPSYSPTSPSYSPTSPSYSPT 1693
Query: 249 EDRMHNTNMLPNY 261
T+ P+Y
Sbjct: 1694 SPSYSPTS--PSY 1704
>3go9_A Insulinase family protease; IDP00573, structural genomics, for
structural genomics of infectious diseases, csgid, HYDR;
HET: MSE; 1.62A {Yersinia pestis}
Length = 492
Score = 29.8 bits (67), Expect = 1.2
Identities = 19/154 (12%), Positives = 40/154 (25%), Gaps = 30/154 (19%)
Query: 60 EQSRTRPITPKEIERMVQIIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQA 119
R ++ E + ++ + + S L A R +
Sbjct: 353 AALRANGLSQAEFDALMTQKNDQLSK--------------------LFATYARTDTDILM 392
Query: 120 SEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVS----NWFGNKRIRY-----KKNI 170
S+ L S + + P + K A +TL++++ +
Sbjct: 393 SQRLR-SQQSGVVDIAPEQYQKLRQAFLSGLTLAELNRELKQQLSQDTTLVLMQPKGEPE 451
Query: 171 GKAQEEANLYAAKKAAGASPYSMGASTPMMSPAP 204
+ +Y A A + AP
Sbjct: 452 VNVKALQEIYNGIMAPQTVAEEEVAPAEAVETAP 485
>1mh3_A Maltose binding-A1 homeodomain protein chimera; MATA1, binding
cooperativity, maltose binding protein, MBP, sugar
binding, DNA binding protein; 2.10A {Escherichia coli}
SCOP: a.4.1.1 c.94.1.1 PDB: 1mh4_A 1le8_A
Length = 421
Score = 29.4 bits (66), Expect = 1.5
Identities = 19/61 (31%), Positives = 27/61 (44%), Gaps = 2/61 (3%)
Query: 107 DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCNITLSQVSNWFGNKRIRY 166
A+ + E + + + KEE+A+KC IT QV WF NKR+R
Sbjct: 363 AAQTAAAAAISPQARAFLEQVF--RRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRS 420
Query: 167 K 167
K
Sbjct: 421 K 421
>1twf_B DNA-directed RNA polymerase II 140 kDa polypeptid; transcription,
mRNA, multiprotein complex; HET: UTP; 2.30A
{Saccharomyces cerevisiae} SCOP: e.29.1.1 PDB: 1i3q_B
1i6h_B 1k83_B* 1nik_B 1nt9_B 1pqv_B 1r5u_B 1r9s_B*
1r9t_B* 1sfo_B* 1twa_B* 1twc_B* 1i50_B* 1twg_B* 1twh_B*
1wcm_B 1y1v_B 1y1w_B 1y1y_B 1y77_B* ...
Length = 1224
Score = 29.1 bits (65), Expect = 2.1
Identities = 25/116 (21%), Positives = 38/116 (32%), Gaps = 23/116 (19%)
Query: 70 KEIERMVQIIHRKFSSIQMQ--LKQSTCEAVMILRS----RFLDARRKRRNFSKQ----- 118
EI ++ I + QM LK + +I F+ R K+
Sbjct: 295 GEI---LEHICYDVNDWQMLEMLKPCVEDGFVIQDRETALDFIGRRGTALGIKKEKRIQY 351
Query: 119 ASEILNEYFYSHLSNPYPSEEAKEE-LARKCNITLSQVSNW--------FGNKRIR 165
A +IL + F H++ E K L N L + FG KR+
Sbjct: 352 AKDILQKEFLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLD 407
>3h0g_B DNA-directed RNA polymerase II subunit RPB2; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 1210
Score = 28.7 bits (64), Expect = 3.1
Identities = 20/116 (17%), Positives = 42/116 (36%), Gaps = 23/116 (19%)
Query: 70 KEIERMVQIIHRKFSSIQMQ--LKQSTCEAVMILRSR----FLDARRKRRNFSKQ----- 118
++I ++ I + QM +K EA +I ++ R +++
Sbjct: 281 RDI---LEHICYDPNDFQMLEMMKPCIEEAFVIQDKDIALDYIGKRGSTTGVTREKRLRY 337
Query: 119 ASEILNEYFYSHLSNPYPSEEAKE----ELARK---CNITLSQVSNW--FGNKRIR 165
A +IL + H++ E K + + C + + + FG KR+
Sbjct: 338 AHDILQKELLPHITTMEGFETRKAFFLGYMIHRMLLCALERREPDDRDHFGKKRLD 393
>1x57_A Endothelial differentiation-related factor 1; HMBF1alpha,
helix-turn-helix, structural genomics, NPPSFA; NMR {Homo
sapiens} SCOP: a.35.1.12
Length = 91
Score = 26.7 bits (59), Expect = 3.2
Identities = 4/17 (23%), Positives = 10/17 (58%)
Query: 142 EELARKCNITLSQVSNW 158
++LA K N ++++
Sbjct: 30 KDLATKINEKPQVIADY 46
>4ayb_B DNA-directed RNA polymerase; transferase, multi-subunit,
transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_B
2y0s_B 2waq_B 4b1o_B 4b1p_R 2pmz_B 3hkz_B
Length = 1131
Score = 28.3 bits (63), Expect = 3.5
Identities = 22/110 (20%), Positives = 38/110 (34%), Gaps = 21/110 (19%)
Query: 67 ITPKEIERMVQIIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQASEILNEY 126
EI+ + + SSI +A+ + SR +KR N ++A +I+++Y
Sbjct: 246 SLDPEIQNELFPSLEQASSIANVD-----DALDFIGSRV-AIGQKRENRIEKAQQIIDKY 299
Query: 127 FYSHLSNPYPSEEAKEEL----ARKCNITLSQVSNW--------FGNKRI 164
F HL K K + + NKR+
Sbjct: 300 FLPHLGTSADDRRKKAYYLAYAISKV---IELYLGRREPDDKDHYANKRL 346
>3bdn_A Lambda repressor; repressor, allostery; HET: DNA; 3.91A
{Enterobacteria phage lambda}
Length = 236
Score = 27.6 bits (61), Expect = 4.6
Identities = 7/34 (20%), Positives = 10/34 (29%)
Query: 142 EELARKCNITLSQVSNWFGNKRIRYKKNIGKAQE 175
E +A K + S V F N +
Sbjct: 34 ESVADKMGMGQSGVGALFNGINALNAYNAALLAK 67
>1r69_A Repressor protein CI; gene regulating protein; 2.00A {Phage 434}
SCOP: a.35.1.2 PDB: 1pra_A 1per_L 1rpe_L* 2or1_L* 1r63_A
2r63_A 1sq8_A
Length = 69
Score = 25.7 bits (57), Expect = 4.7
Identities = 5/17 (29%), Positives = 7/17 (41%)
Query: 142 EELARKCNITLSQVSNW 158
ELA+K T +
Sbjct: 18 AELAQKVGTTQQSIEQL 34
>2r1j_L Repressor protein C2; protein-DNA complex, helix-turn-helix,
DNA-binding, transcription, transcription regulation;
1.53A {Enterobacteria phage P22} SCOP: a.35.1.2 PDB:
3jxb_C 3jxc_L 3jxd_L
Length = 68
Score = 25.6 bits (57), Expect = 5.3
Identities = 3/17 (17%), Positives = 7/17 (41%)
Query: 142 EELARKCNITLSQVSNW 158
L + ++ +S W
Sbjct: 22 AALGKMVGVSNVAISQW 38
>1ecm_A Endo-oxabicyclic transition state analogue; P-protein, chorismate
mutase domain, chorismate mutase; HET: TSA; 2.20A
{Escherichia coli} SCOP: a.130.1.1
Length = 109
Score = 26.1 bits (58), Expect = 5.9
Identities = 13/68 (19%), Positives = 23/68 (33%), Gaps = 10/68 (14%)
Query: 26 RAKLAQIRTIYQQELEKYEQACSEFTTHVMNLLREQSRTRPITPKEIERMVQIIHRKFSS 85
+AKL R + + E+ ++ L + + I R+ Q+I
Sbjct: 37 KAKLLSHRPVRDIDRER----------DLLERLITLGKAHHLDAHYITRLFQLIIEDSVL 86
Query: 86 IQMQLKQS 93
Q L Q
Sbjct: 87 TQQALLQQ 94
>3omt_A Uncharacterized protein; structural genomics, PSI-2, protein
structure initiative, MI center for structural genomics,
MCSG; 1.65A {Cytophaga hutchinsonii}
Length = 73
Score = 25.7 bits (57), Expect = 6.1
Identities = 5/22 (22%), Positives = 7/22 (31%)
Query: 142 EELARKCNITLSQVSNWFGNKR 163
L + + VS W N
Sbjct: 25 LWLTETLDKNKTTVSKWCTNDV 46
>1u4q_A Spectrin alpha chain, brain; alpha spectrin, three repeats of
spectrin, alpha-helical linker region, 3-helix
coiled-coil, structural protein; 2.50A {Gallus gallus}
SCOP: a.7.1.1 a.7.1.1 a.7.1.1
Length = 322
Score = 27.2 bits (60), Expect = 6.6
Identities = 13/94 (13%), Positives = 33/94 (35%), Gaps = 15/94 (15%)
Query: 37 QQELEKYEQACSEFTTH------VMNLLREQSRTRPITPKEIERMVQIIHRKFSSIQMQL 90
Q +K+++ +E H V++ ++ S I +EI++ + + ++
Sbjct: 145 QNLRKKHKRLEAELAAHEPAIQGVLDTGKKLSDDNTIGKEEIQQRLAQFVDHWKELKQLA 204
Query: 91 KQSTCEAVMILRSRFLDARRKRRNFSKQASEILN 124
R + L+ + + F E
Sbjct: 205 AA---------RGQRLEESLEYQQFVANVEEEEA 229
>3bs3_A Putative DNA-binding protein; XRE-family, structural genomics,
PSI-2, protein structure initiative; HET: MSE; 1.65A
{Bacteroides fragilis}
Length = 76
Score = 25.3 bits (56), Expect = 7.1
Identities = 6/22 (27%), Positives = 10/22 (45%)
Query: 142 EELARKCNITLSQVSNWFGNKR 163
LA + + + +S W NK
Sbjct: 27 RWLAEQMGKSENTISRWCSNKS 48
>1adr_A P22 C2 repressor; transcription regulation; NMR {Enterobacteria
phage P22} SCOP: a.35.1.2
Length = 76
Score = 25.3 bits (56), Expect = 7.3
Identities = 3/17 (17%), Positives = 7/17 (41%)
Query: 142 EELARKCNITLSQVSNW 158
L + ++ +S W
Sbjct: 22 AALGKMVGVSNVAISQW 38
>2p5t_A Putative transcriptional regulator PEZA; postsegregational killing
system, phosphoryltransferase, HEL helix motif,
transcription regulator; 3.20A {Streptococcus
pneumoniae}
Length = 158
Score = 26.4 bits (58), Expect = 8.0
Identities = 5/17 (29%), Positives = 9/17 (52%)
Query: 142 EELARKCNITLSQVSNW 158
E AR I+ + +S +
Sbjct: 18 LEFARIVGISRNSLSRY 34
>2om6_A Probable phosphoserine phosphatase; rossmann fold, B-hairpin,
four-helix bundle, structural GENO NPPSFA; 2.20A
{Pyrococcus horikoshii}
Length = 235
Score = 26.7 bits (59), Expect = 8.2
Identities = 9/104 (8%), Positives = 34/104 (32%), Gaps = 6/104 (5%)
Query: 58 LREQSRTRPITPKEIERMVQIIHRKFSSIQMQLKQSTCEAVMILRSRFLDARRKRRNFSK 117
+ ++ + K++ V + + ++ Q + + + + +A +
Sbjct: 26 SHQLAKISGLHIKDVANAVIEVRNEIKKMRAQASEDPRK----VLTGSQEALAGKLKVDV 81
Query: 118 QASEILNEYFYSHLSNPYPSEEAKEELA--RKCNITLSQVSNWF 159
+ + ++ E KE L ++ + + + N
Sbjct: 82 ELVKRATARAILNVDESLVLEGTKEALQFVKERGLKTAVIGNVM 125
>1uqw_A Putative binding protein YLIB; Zn binding protein, transport,
lipoprotein, bacterial targets at IGS-CNRS, france,
BIGS, structural genomics; 2.72A {Escherichia coli}
SCOP: c.94.1.1
Length = 509
Score = 27.3 bits (61), Expect = 8.3
Identities = 15/53 (28%), Positives = 22/53 (41%), Gaps = 11/53 (20%)
Query: 194 GASTPMMSPAPDSVGYSKEANLYA-----AK---KAAGASPYSMGASTPMMSP 238
G +TP P S+ Y++ + A+ K AG Y G ST + S
Sbjct: 302 GYATPATGVVPPSIAYAQSYKPWPYDPVKARELLKEAG---YPNGFSTTLWSS 351
>3t76_A VANU, transcriptional regulator vanug; structural genomics, center
for structural genomics of infec diseases, csgid; HET:
MSE; 1.12A {Enterococcus faecalis} PDB: 3t75_A* 3tyr_A*
3tys_A*
Length = 88
Score = 25.5 bits (56), Expect = 8.9
Identities = 5/27 (18%), Positives = 10/27 (37%)
Query: 141 KEELARKCNITLSQVSNWFGNKRIRYK 167
K EL ++ S + N+ +
Sbjct: 40 KGELREAVGVSKSTFAKLGKNENVSLT 66
>3op9_A PLI0006 protein; structural genomics, PSI-2, protein structure
initiative, MI center for structural genomics, MCSG,
transcription regulat; HET: MSE; 1.90A {Listeria
innocua}
Length = 114
Score = 25.9 bits (57), Expect = 9.0
Identities = 3/23 (13%), Positives = 9/23 (39%)
Query: 142 EELARKCNITLSQVSNWFGNKRI 164
++A N+ V+ + +
Sbjct: 26 HQIAELLNVQTRTVAYYMSGETK 48
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.315 0.127 0.354
Gapped
Lambda K H
0.267 0.0620 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,429,674
Number of extensions: 256062
Number of successful extensions: 876
Number of sequences better than 10.0: 1
Number of HSP's gapped: 830
Number of HSP's successfully gapped: 127
Length of query: 301
Length of database: 6,701,793
Length adjustment: 93
Effective length of query: 208
Effective length of database: 4,105,140
Effective search space: 853869120
Effective search space used: 853869120
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 57 (26.0 bits)