RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy10105
(197 letters)
>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 = 101 bits (253), Expect = 1e-28
Identities = 25/69 (36%), Positives = 36/69 (52%)
Query: 68 RRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127
+R+N +++T L + H NPYP++ K LA +T++QVS WF N R R KK
Sbjct: 4 KRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNI 63
Query: 128 KMTWEPKNK 136
E N
Sbjct: 64 GKFQEEANI 72
>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 = 99.8 bits (249), Expect = 6e-28
Identities = 26/76 (34%), Positives = 41/76 (53%), Gaps = 2/76 (2%)
Query: 68 RRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127
R+ N ES L+ W+ +H+ YP++ EK ML+ T ++L Q+S WF NARRR+ +
Sbjct: 10 RKGNLPAESVKILRDWMYKHRFKAYPSEEEKQMLSEKTNLSLLQISNWFINARRRILPD- 68
Query: 128 KMTWEPKNKTDDDDDA 143
M + +N
Sbjct: 69 -MLQQRRNDPSGPSSG 83
>1du6_A PBX1, homeobox protein PBX1; homeodomain, gene regulation; NMR {Mus
musculus} SCOP: a.4.1.1
Length = 64
Score = 98.2 bits (245), Expect = 1e-27
Identities = 21/58 (36%), Positives = 32/58 (55%)
Query: 68 RRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 125
++ +++T L + H NPYP++ K LA +T++QVS WF N R R KK
Sbjct: 6 EGRHMNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 63
>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 = 98.3 bits (245), Expect = 2e-27
Identities = 25/76 (32%), Positives = 36/76 (47%)
Query: 68 RRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127
+R+N +++T L + H NPYP++ K LA +T++QVS WF N R R KK
Sbjct: 4 KRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNI 63
Query: 128 KMTWEPKNKTDDDDDA 143
E N
Sbjct: 64 GKFQEEANIYAAKTAV 79
>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 = 97.5 bits (243), Expect = 3e-27
Identities = 24/60 (40%), Positives = 38/60 (63%)
Query: 68 RRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127
+R + +T +++WL +H +PYPT+ EK +A T +TL QV+ WF NARRR+ +
Sbjct: 10 KRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRILQSG 69
>2lk2_A Homeobox protein TGIF1; NESG, structural genomics, northeast
structural genomics CON PSI-biology, transcription; NMR
{Homo sapiens}
Length = 89
Score = 96.8 bits (241), Expect = 8e-27
Identities = 30/82 (36%), Positives = 42/82 (51%), Gaps = 2/82 (2%)
Query: 68 RRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE- 126
+ES L+ WL EH+ N YP++ EK +L+ T ++ QV WF NARRRL +
Sbjct: 8 HSHMLPKESVQILRDWLYEHRYNAYPSEQEKALLSQQTHLSTLQVCNWFINARRRLLPDM 67
Query: 127 -NKMTWEPKNKTDDDDDAIISD 147
K +P T A IS+
Sbjct: 68 LRKDGKDPNQFTISRRGAKISE 89
>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 = 91.8 bits (228), Expect = 7e-25
Identities = 15/73 (20%), Positives = 28/73 (38%)
Query: 68 RRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127
R T+E+ L++W ++ +NPY L T ++ Q+ W A R + K
Sbjct: 5 RGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVAARRAKEKTIT 64
Query: 128 KMTWEPKNKTDDD 140
+ +
Sbjct: 65 IAPELADLLSGEP 77
>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 = 90.3 bits (224), Expect = 3e-24
Identities = 16/57 (28%), Positives = 28/57 (49%)
Query: 68 RRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLK 124
R T+E+ L++W ++ +NPY L T ++ Q+ W +N RR+ K
Sbjct: 30 RGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEK 86
>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 = 88.9 bits (221), Expect = 5e-24
Identities = 16/58 (27%), Positives = 28/58 (48%)
Query: 68 RRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 125
R T+E+ L++W ++ +NPY L T ++ Q+ W +N RR+ K
Sbjct: 1 RGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT 58
>3k2a_A Homeobox protein MEIS2; homeobox domain, DNA-binding,
transcription, nucleus, phosphoprotein, DNA bindi
protein; 1.95A {Homo sapiens}
Length = 67
Score = 88.5 bits (220), Expect = 8e-24
Identities = 22/58 (37%), Positives = 36/58 (62%)
Query: 69 RKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 126
+ +T ++AWL +H +PYP++ +K LA T +T+ QV+ WF NARRR+ +
Sbjct: 2 SGIFPKVATNIMRAWLFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQP 59
>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 = 54.5 bits (131), Expect = 1e-10
Identities = 17/68 (25%), Positives = 29/68 (42%), Gaps = 3/68 (4%)
Query: 68 RRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127
+ K E L++ +NP P E L TKMT ++ +WF+ R+++ E
Sbjct: 10 KYKERAPEQLRALESSF---AQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKVNAEE 66
Query: 128 KMTWEPKN 135
P +
Sbjct: 67 TKKSGPSS 74
>2dn0_A Zinc fingers and homeoboxes protein 3; triple homeobox 1 protein,
KIAA0395, TIX1, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 76
Score = 54.0 bits (130), Expect = 2e-10
Identities = 12/58 (20%), Positives = 25/58 (43%), Gaps = 3/58 (5%)
Query: 68 RRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 125
+ + E + LK +N +P + E L +T ++ +V WF++ R +
Sbjct: 11 YKNKKSHEQLSALKG---SFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCRN 65
>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 = 54.2 bits (130), Expect = 2e-10
Identities = 13/78 (16%), Positives = 30/78 (38%), Gaps = 3/78 (3%)
Query: 66 AARRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 125
+ K T+ L+ K+ +PT+ E L + TK++ ++ +WF+ R+
Sbjct: 14 PQKFKEKTQGQVKILEDSFL---KSSFPTQAELDRLRVETKLSRREIDSWFSERRKLRDS 70
Query: 126 ENKMTWEPKNKTDDDDDA 143
+ + +
Sbjct: 71 MEQAVLDSMGSGKSGPSS 88
>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 = 52.9 bits (127), Expect = 4e-10
Identities = 9/61 (14%), Positives = 27/61 (44%)
Query: 65 LAARRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLK 124
+A + +++ + ++ +P E L +T + +++ WF++ R R +
Sbjct: 1 MAHHHHHHRKKTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQ 60
Query: 125 K 125
+
Sbjct: 61 R 61
>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 = 52.7 bits (126), Expect = 7e-10
Identities = 13/76 (17%), Positives = 25/76 (32%), Gaps = 3/76 (3%)
Query: 68 RRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127
+ K T E L+A + T E L TK+T ++ WF ++ +
Sbjct: 14 KFKEKTAEQLRVLQASFL---NSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKE 70
Query: 128 KMTWEPKNKTDDDDDA 143
+ ++
Sbjct: 71 EKMEIDESNAGSSSGP 86
>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 = 45.3 bits (107), Expect = 2e-06
Identities = 17/95 (17%), Positives = 31/95 (32%), Gaps = 3/95 (3%)
Query: 33 PALQSRRQLCGIDKQVIQVSNLTAVRYGAGYDLAARRKNATRESTATLKAWLNEHKKNPY 92
L D + S L + +R + L+ +N
Sbjct: 69 KWLNDAEANLSSDSSLSSPSALNSPGIEGLSRRRKKRTSIETNIRVALEKSFM---ENQK 125
Query: 93 PTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127
PT + ++A M + WF+N R++ K+ N
Sbjct: 126 PTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKRIN 160
>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 = 43.3 bits (102), Expect = 2e-06
Identities = 10/61 (16%), Positives = 24/61 (39%), Gaps = 2/61 (3%)
Query: 68 RRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127
R + E+ L++++++ YP + L+ + + +F N R +K
Sbjct: 10 SRTKISLEALGILQSFIHD--VGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKHSG 67
Query: 128 K 128
Sbjct: 68 P 68
>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 = 43.1 bits (101), Expect = 2e-06
Identities = 14/61 (22%), Positives = 26/61 (42%), Gaps = 3/61 (4%)
Query: 67 ARRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 126
+ K T+E A LK++ + + + + L IT + ++ WF + R LK
Sbjct: 5 SSGKRKTKEQLAILKSF---FLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHG 61
Query: 127 N 127
Sbjct: 62 Q 62
>2xsd_C POU domain, class 3, transcription factor 1; transcription-DNA
complex, SOX; 2.05A {Mus musculus}
Length = 164
Score = 45.0 bits (106), Expect = 2e-06
Identities = 14/61 (22%), Positives = 24/61 (39%), Gaps = 3/61 (4%)
Query: 68 RRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127
+R + L++ K P P+ E LA ++ V WF N R++ K+
Sbjct: 102 KRTSIEVGVKGALESHFL---KCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKEKRMT 158
Query: 128 K 128
Sbjct: 159 P 159
>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 = 45.6 bits (107), Expect = 4e-06
Identities = 26/221 (11%), Positives = 60/221 (27%), Gaps = 74/221 (33%)
Query: 1 MAYTSPETKTLRPELQLFTQVPIQVNISSTKVPALQSRRQLCGIDKQVIQVSNLTAVRYG 60
M T E L + ++ +P R++ + + + +
Sbjct: 296 MTLTPDEV------KSLLLKY---LDCRPQDLP-----REVLTTNPRRLSI--------- 332
Query: 61 AGYDLAARRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANAR 120
+A R+ AT W + +K+ I + +L + A R
Sbjct: 333 ----IAES----IRDGLATWDNWKH--------VNCDKLTTII--ESSLNVLEP--AEYR 372
Query: 121 RRLKK-----EN--------KMTWEPKNKTDDDDDAIISDCDEK---DKD---------D 155
+ + + + W + D +++ + +K
Sbjct: 373 KMFDRLSVFPPSAHIPTILLSLIWF--DVIKSDVMVVVNKLHKYSLVEKQPKESTISIPS 430
Query: 156 LMMDE----EKMKQHHRMVKGHFPHMYVTKYETLPPTNLQG 192
+ ++ E HR + H+ + L P L
Sbjct: 431 IYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQ 471
>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 = 41.7 bits (97), Expect = 9e-06
Identities = 14/70 (20%), Positives = 27/70 (38%), Gaps = 4/70 (5%)
Query: 68 RRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127
+ T E LK+ + +P+ E LA + + T + +WF + R K
Sbjct: 28 KICKKTPEQLHMLKS---AFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKN-G 83
Query: 128 KMTWEPKNKT 137
+ W ++
Sbjct: 84 NLKWYYYYQS 93
>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 = 41.9 bits (98), Expect = 2e-05
Identities = 13/58 (22%), Positives = 24/58 (41%), Gaps = 3/58 (5%)
Query: 68 RRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 125
RR + + L+ ++ P+ E + +A + V WF N R+R K+
Sbjct: 90 RRTTISIAAKDALERHFG---EHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKR 144
>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 = 41.6 bits (97), Expect = 3e-05
Identities = 20/60 (33%), Positives = 26/60 (43%), Gaps = 2/60 (3%)
Query: 68 RRKNATRES-TATLKAWLNEH-KKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 125
+K R S T LN + +KNP PT E +A V WF+N R+ LK
Sbjct: 91 SKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEMAKELNYDREVVRVWFSNRRQTLKN 150
>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 = 38.9 bits (90), Expect = 1e-04
Identities = 14/83 (16%), Positives = 31/83 (37%), Gaps = 15/83 (18%)
Query: 68 RRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAI---------------ITKMTLTQV 112
R + L + +N YP + ++ +A + ++T +V
Sbjct: 7 GRGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKV 66
Query: 113 STWFANARRRLKKENKMTWEPKN 135
WFAN R+ +K+ + ++
Sbjct: 67 YNWFANRRKEIKRRANIAAILES 89
>2djn_A Homeobox protein DLX-5; structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 70
Score = 37.8 bits (88), Expect = 1e-04
Identities = 22/67 (32%), Positives = 30/67 (44%)
Query: 62 GYDLAARRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARR 121
G ++ RK T S+ L A +K Y E+ LA +T TQV WF N R
Sbjct: 1 GSSGSSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRS 60
Query: 122 RLKKENK 128
++KK
Sbjct: 61 KIKKSGP 67
>2d5v_A Hepatocyte nuclear factor 6; transcription factor,
transcription-DNA complex; 2.00A {Rattus norvegicus}
PDB: 1s7e_A
Length = 164
Score = 39.5 bits (91), Expect = 2e-04
Identities = 17/53 (32%), Positives = 25/53 (47%), Gaps = 3/53 (5%)
Query: 73 TRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 125
T TL A E+ P+K +I ++ + L+ VS +F NARRR
Sbjct: 105 TDVQRRTLHAIFKEN---KRPSKELQITISQQLGLELSTVSNFFMNARRRSLD 154
>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 = 39.3 bits (91), Expect = 2e-04
Identities = 12/60 (20%), Positives = 25/60 (41%)
Query: 68 RRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127
R++ T + K+P P+ + +A + V WF+N R++ K+ +
Sbjct: 96 RKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGKRSS 155
>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 = 37.4 bits (87), Expect = 2e-04
Identities = 14/67 (20%), Positives = 28/67 (41%)
Query: 62 GYDLAARRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARR 121
G ++ + R S + + Y + E+ LA + +++ QV TWF N R
Sbjct: 1 GSSGSSGKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRA 60
Query: 122 RLKKENK 128
+ ++
Sbjct: 61 KWRRSGP 67
>3a01_A Homeodomain-containing protein; homeodomain, protein-DNA complex,
DNA-binding, homeobox, NUC developmental protein; 2.70A
{Drosophila melanogaster}
Length = 93
Score = 37.9 bits (88), Expect = 2e-04
Identities = 19/69 (27%), Positives = 29/69 (42%)
Query: 68 RRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127
R+K T + + K Y E+ LA KMT QV TWF N R + +++
Sbjct: 17 RKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQT 76
Query: 128 KMTWEPKNK 136
E + +
Sbjct: 77 AEEREAERQ 85
>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 = 36.8 bits (86), Expect = 3e-04
Identities = 14/57 (24%), Positives = 24/57 (42%), Gaps = 3/57 (5%)
Query: 68 RRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLK 124
+ + + ++ A L+ ++ EK +A +T QV WF N R R K
Sbjct: 8 GKSSISPQARAFLEE---VFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>2l9r_A Homeobox protein NKX-3.1; structural genomics, northeast structural
genomics consortiu PSI-biology, protein structure
initiative; NMR {Homo sapiens}
Length = 69
Score = 36.6 bits (85), Expect = 4e-04
Identities = 15/64 (23%), Positives = 26/64 (40%)
Query: 65 LAARRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLK 124
+ + + S + + Y + E+ LA K+T TQV WF N R + K
Sbjct: 1 MGHHHHHHSHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTK 60
Query: 125 KENK 128
++
Sbjct: 61 RKQL 64
>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 = 36.6 bits (85), Expect = 5e-04
Identities = 9/60 (15%), Positives = 23/60 (38%), Gaps = 3/60 (5%)
Query: 69 RKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 128
R T + L+ + + N P++ + +A + + + WF N + ++
Sbjct: 11 RTRITDDQLRVLRQYFD---INNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKERQSGP 67
>2vi6_A Homeobox protein nanog; homeodomain, DNA-binding, transcription,
transcription facto developmental protein, transcription
regulation, NUC homeobox; 2.6A {Mus musculus}
Length = 62
Score = 35.7 bits (83), Expect = 8e-04
Identities = 18/61 (29%), Positives = 29/61 (47%)
Query: 66 AARRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 125
++K T S A L A + +K Y + + L+ I ++ QV TWF N R + K+
Sbjct: 1 GTKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKR 60
Query: 126 E 126
Sbjct: 61 W 61
>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 = 35.8 bits (83), Expect = 8e-04
Identities = 15/61 (24%), Positives = 26/61 (42%)
Query: 68 RRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127
R + TR + L+ + N YP E L+ + + + WF NAR++ +K
Sbjct: 7 GRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARKSG 66
Query: 128 K 128
Sbjct: 67 P 67
>2kt0_A Nanog, homeobox protein nanog; homeodomain, structural genomics,
protein structure initiative, PSI, center for eukaryotic
structural genomics; NMR {Homo sapiens}
Length = 84
Score = 35.9 bits (83), Expect = 0.001
Identities = 16/61 (26%), Positives = 29/61 (47%)
Query: 68 RRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127
++K T S+ L + ++ Y + + L+ I ++ QV TWF N R + K+
Sbjct: 22 KQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRWQ 81
Query: 128 K 128
K
Sbjct: 82 K 82
>1ftt_A TTF-1 HD, thyroid transcription factor 1 homeodomain; DNA binding
protein; NMR {Rattus norvegicus} SCOP: a.4.1.1
Length = 68
Score = 35.4 bits (82), Expect = 0.001
Identities = 20/61 (32%), Positives = 30/61 (49%)
Query: 68 RRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127
RRK S A + K+ Y + E+ LA + +T TQV WF N R ++K++
Sbjct: 2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQA 61
Query: 128 K 128
K
Sbjct: 62 K 62
>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 = 35.5 bits (82), Expect = 0.001
Identities = 16/61 (26%), Positives = 27/61 (44%)
Query: 68 RRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127
R++ T + L +K Y + ++I LA ++ QV TW+ N R + KK
Sbjct: 17 GRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKKSG 76
Query: 128 K 128
Sbjct: 77 P 77
>3a03_A T-cell leukemia homeobox protein 2; homeodomain, developmental
protein, DNA-binding, N gene regulation; 1.54A {Homo
sapiens}
Length = 56
Score = 34.6 bits (80), Expect = 0.001
Identities = 13/39 (33%), Positives = 20/39 (51%)
Query: 88 KKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 126
+ Y E+ LA +MT QV TWF N R + +++
Sbjct: 17 LRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ 55
>3rkq_A Homeobox protein NKX-2.5; helix-turn-helix, DNA binding, nucleus,
transcription-DNA CO; 1.70A {Homo sapiens}
Length = 58
Score = 34.5 bits (80), Expect = 0.002
Identities = 21/58 (36%), Positives = 27/58 (46%), Gaps = 2/58 (3%)
Query: 67 ARRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLK 124
RRK S A + K+ Y + E+ LA + K+T TQV WF N RR K
Sbjct: 1 GRRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQN--RRYK 56
>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 = 35.1 bits (81), Expect = 0.002
Identities = 16/61 (26%), Positives = 27/61 (44%)
Query: 68 RRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127
+RK + A ++ Y + E+ LA + ++T TQV WF N R + K+
Sbjct: 9 KRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQ 68
Query: 128 K 128
Sbjct: 69 N 69
>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 = 34.7 bits (80), Expect = 0.002
Identities = 16/60 (26%), Positives = 22/60 (36%), Gaps = 3/60 (5%)
Query: 69 RKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 128
R T A L+ + Y T L+ + QV WF N RRR K ++
Sbjct: 6 RTTFTSSQIAELE---QHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSD 62
>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 = 35.2 bits (81), Expect = 0.002
Identities = 14/60 (23%), Positives = 19/60 (31%), Gaps = 3/60 (5%)
Query: 69 RKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 128
R T E L + PT+ +A + V WF N R R +K
Sbjct: 21 RTTITPEQLEILYQKYL---LDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERKSGP 77
>1ig7_A Homeotic protein MSX-1; helix-turn-helix, transcription/DNA
complex; 2.20A {Mus musculus} SCOP: a.4.1.1
Length = 58
Score = 34.1 bits (79), Expect = 0.002
Identities = 18/57 (31%), Positives = 28/57 (49%)
Query: 69 RKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 125
RK T +TA L A + ++ Y + E+ + +T TQV WF N R + K+
Sbjct: 1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57
>2hi3_A Homeodomain-only protein; transcription; NMR {Mus musculus} SCOP:
a.4.1.1
Length = 73
Score = 33.6 bits (77), Expect = 0.005
Identities = 11/52 (21%), Positives = 21/52 (40%)
Query: 87 HKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKMTWEPKNKTD 138
+K N +P ++A +T Q WF ++ + E ++ TD
Sbjct: 22 NKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEGLPSECRSVTD 73
>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 = 33.6 bits (77), Expect = 0.005
Identities = 15/39 (38%), Positives = 22/39 (56%)
Query: 90 NPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 128
N Y T+ +I +A +T Q+ WF N R +LKKE +
Sbjct: 42 NHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKEIQ 80
>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 = 33.2 bits (76), Expect = 0.007
Identities = 18/44 (40%), Positives = 24/44 (54%)
Query: 90 NPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKMTWEP 133
N Y T+ +I +A +T Q+ WF N R + KKENK EP
Sbjct: 24 NRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENKTKGEP 67
>2r5y_A Homeotic protein sex combs reduced; homeodomain; HET: DNA; 2.60A
{Drosophila melanogaster} PDB: 2r5z_A*
Length = 88
Score = 33.3 bits (76), Expect = 0.009
Identities = 23/79 (29%), Positives = 36/79 (45%), Gaps = 3/79 (3%)
Query: 50 QVSNLTAVRYGAGYDLAARRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTL 109
+ +L A + +R + TR T L+ E N Y T+ +I +A +T
Sbjct: 13 KRVHLGTSTVNANGETKRQRTSYTRYQTLELE---KEFHFNRYLTRRRRIEIAHALSLTE 69
Query: 110 TQVSTWFANARRRLKKENK 128
Q+ WF N R + KKE+K
Sbjct: 70 RQIKIWFQNRRMKWKKEHK 88
>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 = 32.9 bits (75), Expect = 0.010
Identities = 14/60 (23%), Positives = 28/60 (46%), Gaps = 3/60 (5%)
Query: 69 RKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 128
R ++ L+ E+ N + TK ++ ++ T ++ Q++ WF N R + KK
Sbjct: 11 RIPYSKGQLRELE---REYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKKSGP 67
>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 = 32.5 bits (74), Expect = 0.013
Identities = 15/39 (38%), Positives = 22/39 (56%)
Query: 90 NPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 128
N Y T+ + +A + +T QV WF N R ++KK NK
Sbjct: 35 NMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINK 73
>2l7z_A Homeobox protein HOX-A13; gene regulation; NMR {Homo sapiens} PDB:
2ld5_A*
Length = 73
Score = 32.1 bits (73), Expect = 0.018
Identities = 16/61 (26%), Positives = 29/61 (47%), Gaps = 3/61 (4%)
Query: 68 RRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127
+R T+ L+ E+ N + TK ++ ++ T ++ QV+ WF N R + KK
Sbjct: 10 KRVPYTKVQLKELE---REYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKVI 66
Query: 128 K 128
Sbjct: 67 N 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 = 32.6 bits (74), Expect = 0.021
Identities = 13/43 (30%), Positives = 22/43 (51%)
Query: 86 EHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 128
E N Y ++ ++ +A ++ TQV WF N R + KK +
Sbjct: 52 EFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRER 94
>1lfb_A Liver transcription factor (LFB1); transcription regulation; 2.80A
{Rattus norvegicus} SCOP: a.4.1.1 PDB: 2lfb_A
Length = 99
Score = 32.5 bits (73), Expect = 0.023
Identities = 15/83 (18%), Positives = 29/83 (34%), Gaps = 21/83 (25%)
Query: 68 RRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAII---------------------TK 106
R+N + A+ + +++ P+K E+ L
Sbjct: 9 GRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNL 68
Query: 107 MTLTQVSTWFANARRRLKKENKM 129
+T +V WFAN R+ +K+
Sbjct: 69 VTEVRVYNWFANRRKEEAFRHKL 91
>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 = 31.2 bits (71), Expect = 0.033
Identities = 14/58 (24%), Positives = 25/58 (43%), Gaps = 3/58 (5%)
Query: 69 RKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 126
R TR+ L+ E K Y ++ + LA + + + WF N R + K++
Sbjct: 5 RTAFTRDQLGRLE---KEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ 59
>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 = 30.8 bits (70), Expect = 0.038
Identities = 17/57 (29%), Positives = 26/57 (45%), Gaps = 3/57 (5%)
Query: 69 RKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 125
R + E A LK E +N Y T+ + L+ + Q+ WF N R ++KK
Sbjct: 7 RTAFSSEQLARLK---REFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK 60
>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 = 31.2 bits (71), Expect = 0.038
Identities = 15/62 (24%), Positives = 24/62 (38%)
Query: 68 RRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127
+ T + L + NP P K L +T ++ + WF N R + KK +
Sbjct: 3 TTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRS 62
Query: 128 KM 129
M
Sbjct: 63 IM 64
>2h1k_A IPF-1, pancreatic and duodenal homeobox 1, homeodomain; protein-DNA
complex, transcription/DNA complex; 2.42A {Mesocricetus
auratus}
Length = 63
Score = 30.8 bits (70), Expect = 0.046
Identities = 13/42 (30%), Positives = 22/42 (52%)
Query: 86 EHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127
E N Y ++ ++ LA++ +T + WF N R + KKE
Sbjct: 21 EFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKEE 62
>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 = 31.1 bits (69), Expect = 0.046
Identities = 15/67 (22%), Positives = 22/67 (32%), Gaps = 1/67 (1%)
Query: 69 RKNATRESTATLK-AWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127
R + ATLK W N + + +A + V TW N RR+ +
Sbjct: 12 RTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIGNRRRKYRLMG 71
Query: 128 KMTWEPK 134
P
Sbjct: 72 IEVSGPS 78
>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 = 32.7 bits (74), Expect = 0.077
Identities = 32/231 (13%), Positives = 68/231 (29%), Gaps = 102/231 (44%)
Query: 4 TSPETKTLRPELQLFTQVPIQVNISSTKVPALQSRRQLCGIDKQVIQVSNLTAVRYGAGY 63
+P P+ +PI S P + VIQ+++ G+
Sbjct: 220 ENPSN---TPDKDYLLSIPI-----S--CPLIG-----------VIQLAHYVVTAKLLGF 258
Query: 64 ---DLAARRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTW---FA 117
+L + K AT + ++ A+ + + +W F
Sbjct: 259 TPGELRSYLKGAT--------------------GHSQGLVTAVA----IAETDSWESFFV 294
Query: 118 NARRRLKKENKMTW--------------EPKNKTDDDDDAIISDCDEKDKDD--LM---- 157
+ R+ + + + P +I+ D E ++ M
Sbjct: 295 SVRKAITV---LFFIGVRCYEAYPNTSLPP---------SILEDSLENNEGVPSPMLSIS 342
Query: 158 -MDEEKMKQHHRMVKGHFP---HMYVTKYETL-----------PPTNLQGL 193
+ +E+++ + H P + ++ L PP +L GL
Sbjct: 343 NLTQEQVQDYVNKTNSHLPAGKQVEIS----LVNGAKNLVVSGPPQSLYGL 389
>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 = 30.2 bits (68), Expect = 0.079
Identities = 7/41 (17%), Positives = 15/41 (36%)
Query: 88 KKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 128
YP + L+ ++ ++ WF + R + K
Sbjct: 29 SVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDKPSGP 69
>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 = 30.6 bits (68), Expect = 0.095
Identities = 14/87 (16%), Positives = 27/87 (31%), Gaps = 21/87 (24%)
Query: 68 RRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAII---------------------TK 106
+N + A+ + + + P+K E+ L
Sbjct: 6 SGRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNL 65
Query: 107 MTLTQVSTWFANARRRLKKENKMTWEP 133
+T +V WFAN R+ K+ +
Sbjct: 66 VTEVRVYNWFANRRKEEAFRQKLAMDA 92
>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 = 31.4 bits (70), Expect = 0.11
Identities = 14/78 (17%), Positives = 26/78 (33%), Gaps = 21/78 (26%)
Query: 68 RRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAII---------------------TK 106
R+N + A+ + +++ P+K E+ L
Sbjct: 115 GRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNL 174
Query: 107 MTLTQVSTWFANARRRLK 124
+T +V WFAN R+
Sbjct: 175 VTEVRVYNWFANRRKEEA 192
>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 = 29.7 bits (67), Expect = 0.15
Identities = 14/68 (20%), Positives = 26/68 (38%)
Query: 62 GYDLAARRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARR 121
G ++ ++ T L+ + N P + LA T +T + WF NAR
Sbjct: 1 GSSGSSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARA 60
Query: 122 RLKKENKM 129
+ ++
Sbjct: 61 KFRRNLLR 68
>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 = 29.2 bits (66), Expect = 0.19
Identities = 15/62 (24%), Positives = 28/62 (45%)
Query: 69 RKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 128
R+ T + ++ N + N YP LA + L ++ WF N R +LK+ ++
Sbjct: 2 RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHR 61
Query: 129 MT 130
+
Sbjct: 62 ES 63
>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 = 28.8 bits (65), Expect = 0.21
Identities = 15/62 (24%), Positives = 30/62 (48%)
Query: 68 RRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127
+R+ T ++ L+ ++N YP + +A+ T +T +V WF N R + +K
Sbjct: 3 QRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE 62
Query: 128 KM 129
+
Sbjct: 63 EF 64
>2cue_A Paired box protein PAX6; homeobox domain, transcription factor,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
a.4.1.1
Length = 80
Score = 28.9 bits (65), Expect = 0.31
Identities = 14/70 (20%), Positives = 32/70 (45%)
Query: 68 RRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127
++N T + ++A E ++ YP + LA + ++ WF+N R + ++E
Sbjct: 7 GQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREE 66
Query: 128 KMTWEPKNKT 137
K+ + +
Sbjct: 67 KLRNQRRQSG 76
>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo,
protein-DNA, human disease; 3.20A {Homo sapiens}
Length = 221
Score = 29.6 bits (65), Expect = 0.49
Identities = 14/78 (17%), Positives = 25/78 (32%), Gaps = 21/78 (26%)
Query: 68 RRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAII---------------------TK 106
R+N + A+ + + + P+K E+ L
Sbjct: 142 MRRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNL 201
Query: 107 MTLTQVSTWFANARRRLK 124
+T +V WFAN R+
Sbjct: 202 VTEVRVYNWFANRRKEEA 219
>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 = 28.1 bits (63), Expect = 0.50
Identities = 15/61 (24%), Positives = 27/61 (44%)
Query: 68 RRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127
R++ T + L+A N ++ YP G + LA + +V WF N R + ++
Sbjct: 7 GRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRSG 66
Query: 128 K 128
Sbjct: 67 P 67
>2e19_A Transcription factor 8; homeobox domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 64
Score = 27.7 bits (61), Expect = 0.58
Identities = 11/60 (18%), Positives = 20/60 (33%), Gaps = 3/60 (5%)
Query: 66 AARRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 125
+ + + + LKA+ N P+ E +A + L V WF +
Sbjct: 4 GSSGQPPLKNLLSLLKAYYA---LNAQPSAEELSKIADSVNLPLDVVKKWFEKMQAGQIS 60
>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 = 27.3 bits (61), Expect = 0.80
Identities = 11/52 (21%), Positives = 21/52 (40%)
Query: 87 HKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKMTWEPKNKTD 138
+K N +P ++A +T Q WF ++ + E ++ TD
Sbjct: 21 NKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEGLPSECRSVTD 72
>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 = 27.4 bits (61), Expect = 0.87
Identities = 13/62 (20%), Positives = 26/62 (41%)
Query: 68 RRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127
R+ T + A L K YP + +A+ + ++V WF N R + +++
Sbjct: 7 GRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQQ 66
Query: 128 KM 129
+
Sbjct: 67 QQ 68
>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 = 27.1 bits (59), Expect = 0.99
Identities = 11/63 (17%), Positives = 23/63 (36%), Gaps = 3/63 (4%)
Query: 66 AARRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 125
+ N ++ + LKA+ N P E + ++I + V WF +
Sbjct: 6 SGSPINPYKDHMSVLKAYY---AMNMEPNSDELLKISIAVGLPQEFVKEWFEQRKVYQYS 62
Query: 126 ENK 128
++
Sbjct: 63 NSR 65
>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 = 26.4 bits (59), Expect = 1.6
Identities = 11/42 (26%), Positives = 21/42 (50%)
Query: 88 KKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKM 129
+ YP + LA+ +T ++ WF N R + +K+ K+
Sbjct: 19 SRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQEKV 60
>1r79_A Diacylglycerol kinase, delta; C1 domain, cystein-rich zinc binding
domain, structural genomics, riken structural
genomics/proteomics initiative; NMR {Homo sapiens} SCOP:
g.49.1.1
Length = 84
Score = 26.5 bits (58), Expect = 2.0
Identities = 5/26 (19%), Positives = 13/26 (50%)
Query: 150 EKDKDDLMMDEEKMKQHHRMVKGHFP 175
D++ D + + H+ ++G+ P
Sbjct: 11 ASIGKDIIEDADGIAMPHQWLEGNLP 36
>1s16_A Topoisomerase IV subunit B; two-domain protein complexed with
ADPNP; HET: ANP; 2.10A {Escherichia coli} SCOP: d.14.1.3
d.122.1.2
Length = 390
Score = 27.8 bits (63), Expect = 2.2
Identities = 9/51 (17%), Positives = 18/51 (35%), Gaps = 17/51 (33%)
Query: 80 LKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKMT 130
WLN++ E + I ++A+RR++ K+
Sbjct: 354 FILWLNQN-----VQAAELLAEMAI------------SSAQRRMRAAKKVV 387
>3lnu_A Topoisomerase IV subunit B; PARE, ATP-binding, nucleotide-BI
topoisomerase; 2.20A {Xanthomonas oryzae PV} PDB:
3lps_A*
Length = 408
Score = 27.9 bits (63), Expect = 2.3
Identities = 12/51 (23%), Positives = 17/51 (33%), Gaps = 17/51 (33%)
Query: 80 LKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKMT 130
+LN++ GEKI I A RLK E ++
Sbjct: 372 FSLYLNQN-----VEIGEKIAQIAI------------DRASARLKTEKQIV 405
>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 = 25.9 bits (57), Expect = 2.8
Identities = 7/38 (18%), Positives = 13/38 (34%), Gaps = 1/38 (2%)
Query: 88 KKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 125
+P + L+ + + WF RR +K
Sbjct: 21 AITKHPDEKRLEGLSKQLDWDVRSIQRWFRQ-RRNQEK 57
>2dnu_A RUH-061, SH3 multiple domains 1; RSGI, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 71
Score = 25.7 bits (57), Expect = 3.0
Identities = 5/19 (26%), Positives = 10/19 (52%)
Query: 171 KGHFPHMYVTKYETLPPTN 189
+G P Y+ K + P++
Sbjct: 52 EGWAPASYLKKAKDSGPSS 70
>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 = 26.2 bits (58), Expect = 3.1
Identities = 17/61 (27%), Positives = 30/61 (49%)
Query: 68 RRKNATRESTATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 127
+R++ T S + L ++ YP + LA T +T ++ WF N R RL+K++
Sbjct: 18 QRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQH 77
Query: 128 K 128
Sbjct: 78 T 78
>1u5s_A Cytoplasmic protein NCK2; protein-protein complex, beta barrel,
beta sheet, zinc finger, metal binding protein; NMR
{Homo sapiens} SCOP: b.34.2.1 PDB: 2fry_A
Length = 71
Score = 25.3 bits (56), Expect = 4.7
Identities = 5/18 (27%), Positives = 6/18 (33%)
Query: 172 GHFPHMYVTKYETLPPTN 189
G P YV P +
Sbjct: 54 GLVPKNYVVVLSDGPALH 71
>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 = 26.5 bits (57), Expect = 4.9
Identities = 8/29 (27%), Positives = 11/29 (37%), Gaps = 9/29 (31%)
Query: 7 ETKTLRPELQLFTQVPIQVNISSTKVPAL 35
K L+ L+L+ S PAL
Sbjct: 21 ALKKLQASLKLYA--D-----DSA--PAL 40
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 0.129 0.377
Gapped
Lambda K H
0.267 0.0479 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,944,950
Number of extensions: 163114
Number of successful extensions: 451
Number of sequences better than 10.0: 1
Number of HSP's gapped: 447
Number of HSP's successfully gapped: 90
Length of query: 197
Length of database: 6,701,793
Length adjustment: 89
Effective length of query: 108
Effective length of database: 4,216,824
Effective search space: 455416992
Effective search space used: 455416992
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: 55 (25.6 bits)