RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy5913
(341 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 = 103 bits (258), Expect = 4e-28
Identities = 25/69 (36%), Positives = 35/69 (50%)
Query: 7 RRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66
+R+N ++ T L + H NPYP++ K LA +T++QVS WF N R R KK
Sbjct: 4 KRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNI 63
Query: 67 KMTWEPRNR 75
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 = 97.5 bits (243), Expect = 1e-25
Identities = 26/69 (37%), Positives = 41/69 (59%), Gaps = 2/69 (2%)
Query: 7 RRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66
R+ N E+ L+ W+ +H+ YP++ EK ML+ T ++L Q+S WF NARRR+ +
Sbjct: 10 RKGNLPAESVKILRDWMYKHRFKAYPSEEEKQMLSEKTNLSLLQISNWFINARRRILPD- 68
Query: 67 KMTWEPRNR 75
M + RN
Sbjct: 69 -MLQQRRND 76
>1du6_A PBX1, homeobox protein PBX1; homeodomain, gene regulation; NMR
{Mus musculus} SCOP: a.4.1.1
Length = 64
Score = 96.6 bits (241), Expect = 1e-25
Identities = 21/58 (36%), Positives = 31/58 (53%)
Query: 7 RRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64
++ ++ 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 = 96.8 bits (241), Expect = 2e-25
Identities = 25/76 (32%), Positives = 36/76 (47%)
Query: 7 RRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66
+R+N ++ T L + H NPYP++ K LA +T++QVS WF N R R KK
Sbjct: 4 KRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNI 63
Query: 67 KMTWEPRNRVEDEDNN 82
E N +
Sbjct: 64 GKFQEEANIYAAKTAV 79
>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 = 2e-25
Identities = 26/78 (33%), Positives = 38/78 (48%), Gaps = 9/78 (11%)
Query: 7 RRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE- 65
+E+ L+ WL EH+ N YP++ EK +L+ T ++ QV WF NARRRL +
Sbjct: 8 HSHMLPKESVQILRDWLYEHRYNAYPSEQEKALLSQQTHLSTLQVCNWFINARRRLLPDM 67
Query: 66 --------NKMTWEPRNR 75
N+ T R
Sbjct: 68 LRKDGKDPNQFTISRRGA 85
>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 = 95.2 bits (237), Expect = 5e-25
Identities = 24/60 (40%), Positives = 38/60 (63%)
Query: 7 RRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66
+R + T+ +++WL +H +PYPT+ EK +A T +TL QV+ WF NARRR+ +
Sbjct: 10 KRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRILQSG 69
>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 = 91.0 bits (226), Expect = 3e-23
Identities = 15/69 (21%), Positives = 25/69 (36%)
Query: 7 RRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66
R T+E L++W ++ +NPY L T ++ Q+ W A R + K
Sbjct: 5 RGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVAARRAKEKTIT 64
Query: 67 KMTWEPRNR 75
Sbjct: 65 IAPELADLL 73
>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 = 90.0 bits (224), Expect = 3e-23
Identities = 16/58 (27%), Positives = 27/58 (46%)
Query: 7 RRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64
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 = 1e-22
Identities = 22/58 (37%), Positives = 36/58 (62%)
Query: 8 RKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 65
+ T+ ++AWL +H +PYP++ +K LA T +T+ QV+ WF NARRR+ +
Sbjct: 2 SGIFPKVATNIMRAWLFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQP 59
>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 = 89.1 bits (221), Expect = 2e-22
Identities = 16/57 (28%), Positives = 27/57 (47%)
Query: 7 RRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLK 63
R T+E L++W ++ +NPY L T ++ Q+ W +N RR+ K
Sbjct: 30 RGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEK 86
>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 = 54.8 bits (132), Expect = 3e-10
Identities = 9/60 (15%), Positives = 25/60 (41%)
Query: 5 GARRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64
+ ++T + ++ +P E L +T + +++ WF++ R R ++
Sbjct: 2 AHHHHHHRKKTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQR 61
>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 = 54.9 bits (132), Expect = 3e-10
Identities = 17/68 (25%), Positives = 29/68 (42%), Gaps = 3/68 (4%)
Query: 7 RRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66
+ K E L++ +NP P E L TKMT ++ +WF+ R+++ E
Sbjct: 10 KYKERAPEQLRALESSF---AQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKVNAEE 66
Query: 67 KMTWEPRN 74
P +
Sbjct: 67 TKKSGPSS 74
>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 = 53.4 bits (128), Expect = 1e-09
Identities = 14/73 (19%), Positives = 30/73 (41%), Gaps = 3/73 (4%)
Query: 2 DINGARRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRR 61
D + K T+ L+ K+ +PT+ E L + TK++ ++ +WF+ R+
Sbjct: 11 DFAPQKFKEKTQGQVKILEDSFL---KSSFPTQAELDRLRVETKLSRREIDSWFSERRKL 67
Query: 62 LKKENKMTWEPRN 74
+ +
Sbjct: 68 RDSMEQAVLDSMG 80
>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 = 52.3 bits (125), Expect = 4e-09
Identities = 14/77 (18%), Positives = 25/77 (32%), Gaps = 3/77 (3%)
Query: 2 DINGARRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRR 61
D + K T E L+A + T E L TK+T ++ WF ++
Sbjct: 9 DFTPQKFKEKTAEQLRVLQASFL---NSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKS 65
Query: 62 LKKENKMTWEPRNRVED 78
+ + +
Sbjct: 66 KALKEEKMEIDESNAGS 82
>2dn0_A Zinc fingers and homeoboxes protein 3; triple homeobox 1 protein,
KIAA0395, TIX1, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 76
Score = 51.7 bits (124), Expect = 5e-09
Identities = 13/60 (21%), Positives = 25/60 (41%), Gaps = 3/60 (5%)
Query: 5 GARRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64
+ + E S LK +N +P + E L +T ++ +V WF++ R +
Sbjct: 9 SIYKNKKSHEQLSALKG---SFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCRN 65
>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 = 6e-07
Identities = 17/64 (26%), Positives = 25/64 (39%)
Query: 4 NGARRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLK 63
G +RK T A + K P P+ E LA ++ V WF N R++ K
Sbjct: 96 QGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKEK 155
Query: 64 KENK 67
+
Sbjct: 156 RMTP 159
>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 = 47.7 bits (113), Expect = 7e-07
Identities = 17/66 (25%), Positives = 29/66 (43%)
Query: 1 MDINGARRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARR 60
++ RRK T T+ A +N PT + ++A M + WF+N R+
Sbjct: 95 IEGLSRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQ 154
Query: 61 RLKKEN 66
+ K+ N
Sbjct: 155 KEKRIN 160
>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 = 15/66 (22%), Positives = 30/66 (45%), Gaps = 4/66 (6%)
Query: 5 GARRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64
G+ K T+E + LK++ + + + + L IT + ++ WF + R LK
Sbjct: 4 GSSGKRKTKEQLAILKSF---FLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKH 60
Query: 65 ENKMTW 70
++ W
Sbjct: 61 -GQLKW 65
>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 = 45.4 bits (107), Expect = 3e-06
Identities = 15/64 (23%), Positives = 27/64 (42%)
Query: 1 MDINGARRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARR 60
+ N +RK T + + A ++ P+ E + +A + V WF N R+
Sbjct: 81 VGANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQ 140
Query: 61 RLKK 64
R K+
Sbjct: 141 REKR 144
>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 = 42.5 bits (100), Expect = 8e-06
Identities = 10/61 (16%), Positives = 23/61 (37%), Gaps = 2/61 (3%)
Query: 7 RRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66
R + E L++++++ YP + L+ + + +F N R +K
Sbjct: 10 SRTKISLEALGILQSFIHD--VGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKHSG 67
Query: 67 K 67
Sbjct: 68 P 68
>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 = 41.8 bits (99), Expect = 9e-06
Identities = 13/57 (22%), Positives = 23/57 (40%), Gaps = 3/57 (5%)
Query: 7 RRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLK 63
+ + + + + L+ ++ EK +A +T QV WF N R R K
Sbjct: 8 GKSSISPQARAFLEE---VFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>2vi6_A Homeobox protein nanog; homeodomain, DNA-binding, transcription,
transcription facto developmental protein,
transcription regulation, NUC homeobox; 2.6A {Mus
musculus}
Length = 62
Score = 41.9 bits (99), Expect = 9e-06
Identities = 17/61 (27%), Positives = 30/61 (49%)
Query: 5 GARRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64
G ++K T + + L A + +K Y + + L+ I ++ QV TWF N R + K+
Sbjct: 1 GTKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKR 60
Query: 65 E 65
Sbjct: 61 W 61
>2d5v_A Hepatocyte nuclear factor 6; transcription factor,
transcription-DNA complex; 2.00A {Rattus norvegicus}
PDB: 1s7e_A
Length = 164
Score = 44.1 bits (103), Expect = 1e-05
Identities = 17/53 (32%), Positives = 25/53 (47%), Gaps = 3/53 (5%)
Query: 12 TRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64
T TL A E+ P+K +I ++ + L+ VS +F NARRR
Sbjct: 105 TDVQRRTLHAIFKEN---KRPSKELQITISQQLGLELSTVSNFFMNARRRSLD 154
>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 = 43.9 bits (103), Expect = 1e-05
Identities = 19/58 (32%), Positives = 26/58 (44%)
Query: 7 RRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64
+RK T T ++A +KNP PT E +A V WF+N R+ LK
Sbjct: 93 KRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEMAKELNYDREVVRVWFSNRRQTLKN 150
>2djn_A Homeobox protein DLX-5; structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 70
Score = 41.6 bits (98), Expect = 1e-05
Identities = 20/63 (31%), Positives = 28/63 (44%)
Query: 5 GARRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64
+ RK T ++ L A +K Y E+ LA +T TQV WF N R ++KK
Sbjct: 5 SSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKK 64
Query: 65 ENK 67
Sbjct: 65 SGP 67
>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 = 41.3 bits (97), Expect = 2e-05
Identities = 12/64 (18%), Positives = 26/64 (40%)
Query: 4 NGARRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLK 63
+ + R + + + Y + E+ LA + +++ QV TWF N R + +
Sbjct: 4 GSSGKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWR 63
Query: 64 KENK 67
+
Sbjct: 64 RSGP 67
>2l9r_A Homeobox protein NKX-3.1; structural genomics, northeast
structural genomics consortiu PSI-biology, protein
structure initiative; NMR {Homo sapiens}
Length = 69
Score = 41.2 bits (97), Expect = 2e-05
Identities = 15/63 (23%), Positives = 27/63 (42%)
Query: 5 GARRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64
G + + + + + + Y + E+ LA K+T TQV WF N R + K+
Sbjct: 2 GHHHHHHSHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKR 61
Query: 65 ENK 67
+
Sbjct: 62 KQL 64
>3a01_A Homeodomain-containing protein; homeodomain, protein-DNA complex,
DNA-binding, homeobox, NUC developmental protein; 2.70A
{Drosophila melanogaster}
Length = 93
Score = 41.8 bits (98), Expect = 2e-05
Identities = 20/67 (29%), Positives = 27/67 (40%)
Query: 5 GARRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64
R+K T T + K Y E+ LA KMT QV TWF N R + ++
Sbjct: 15 PKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRR 74
Query: 65 ENKMTWE 71
+ E
Sbjct: 75 QTAEERE 81
>1ftt_A TTF-1 HD, thyroid transcription factor 1 homeodomain; DNA binding
protein; NMR {Rattus norvegicus} SCOP: a.4.1.1
Length = 68
Score = 40.0 bits (94), Expect = 4e-05
Identities = 18/61 (29%), Positives = 30/61 (49%)
Query: 7 RRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66
RRK + + + K+ Y + E+ LA + +T TQV WF N R ++K++
Sbjct: 2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQA 61
Query: 67 K 67
K
Sbjct: 62 K 62
>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 = 40.9 bits (95), Expect = 5e-05
Identities = 14/64 (21%), Positives = 25/64 (39%), Gaps = 4/64 (6%)
Query: 7 RRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66
+ T E LK+ + +P+ E LA + + T + +WF + R K
Sbjct: 28 KICKKTPEQLHMLKS---AFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKN-G 83
Query: 67 KMTW 70
+ W
Sbjct: 84 NLKW 87
>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 = 42.0 bits (98), Expect = 5e-05
Identities = 13/66 (19%), Positives = 27/66 (40%)
Query: 1 MDINGARRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARR 60
+ AR++ T + K+P P+ + +A + V WF+N R+
Sbjct: 90 ETLVQARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQ 149
Query: 61 RLKKEN 66
+ K+ +
Sbjct: 150 KGKRSS 155
>3a03_A T-cell leukemia homeobox protein 2; homeodomain, developmental
protein, DNA-binding, N gene regulation; 1.54A {Homo
sapiens}
Length = 56
Score = 39.6 bits (93), Expect = 5e-05
Identities = 13/39 (33%), Positives = 20/39 (51%)
Query: 27 KKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 65
+ Y E+ LA +MT QV TWF N R + +++
Sbjct: 17 LRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ 55
>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 = 39.8 bits (93), Expect = 8e-05
Identities = 17/64 (26%), Positives = 27/64 (42%)
Query: 4 NGARRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLK 63
R++ T T L +K Y + ++I LA ++ QV TW+ N R + K
Sbjct: 14 AKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWK 73
Query: 64 KENK 67
K
Sbjct: 74 KSGP 77
>3rkq_A Homeobox protein NKX-2.5; helix-turn-helix, DNA binding, nucleus,
transcription-DNA CO; 1.70A {Homo sapiens}
Length = 58
Score = 38.8 bits (91), Expect = 8e-05
Identities = 19/58 (32%), Positives = 27/58 (46%), Gaps = 2/58 (3%)
Query: 6 ARRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLK 63
RRK + + + K+ Y + E+ LA + K+T TQV WF N RR K
Sbjct: 1 GRRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQN--RRYK 56
>1ig7_A Homeotic protein MSX-1; helix-turn-helix, transcription/DNA
complex; 2.20A {Mus musculus} SCOP: a.4.1.1
Length = 58
Score = 38.8 bits (91), Expect = 1e-04
Identities = 18/57 (31%), Positives = 28/57 (49%)
Query: 8 RKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64
RK T TT+ L A + ++ Y + E+ + +T TQV WF N R + K+
Sbjct: 1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57
>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 = 38.2 bits (89), Expect = 2e-04
Identities = 16/62 (25%), Positives = 24/62 (38%)
Query: 6 ARRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 65
R+ T T+S + + Y T L+ + QV WF N RRR K +
Sbjct: 1 GPRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQ 60
Query: 66 NK 67
+
Sbjct: 61 SD 62
>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 = 38.1 bits (89), Expect = 2e-04
Identities = 16/61 (26%), Positives = 26/61 (42%)
Query: 7 RRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66
R + TR T L+ + N YP E L+ + + + WF NAR++ +K
Sbjct: 7 GRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARKSG 66
Query: 67 K 67
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 = 38.6 bits (90), Expect = 2e-04
Identities = 15/63 (23%), Positives = 30/63 (47%)
Query: 5 GARRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64
++K T +++ L + ++ Y + + L+ I ++ QV TWF N R + K+
Sbjct: 20 VKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKR 79
Query: 65 ENK 67
K
Sbjct: 80 WQK 82
>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 = 2e-04
Identities = 14/86 (16%), Positives = 31/86 (36%), Gaps = 15/86 (17%)
Query: 4 NGARRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAI---------------ITKMTL 48
+ R + L + +N YP + ++ +A + ++T
Sbjct: 4 GSSGRGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTS 63
Query: 49 TQVSTWFANARRRLKKENKMTWEPRN 74
+V WFAN R+ +K+ + +
Sbjct: 64 LKVYNWFANRRKEIKRRANIAAILES 89
>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 = 37.8 bits (88), Expect = 3e-04
Identities = 16/63 (25%), Positives = 27/63 (42%)
Query: 5 GARRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64
+RK T + ++ Y + E+ LA + ++T TQV WF N R + K+
Sbjct: 7 NKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKR 66
Query: 65 ENK 67
Sbjct: 67 AQN 69
>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 = 37.7 bits (88), Expect = 3e-04
Identities = 10/64 (15%), Positives = 24/64 (37%)
Query: 4 NGARRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLK 63
+ ++ TR T L+ N P++ + +A + + + WF N + +
Sbjct: 4 GSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKER 63
Query: 64 KENK 67
+
Sbjct: 64 QSGP 67
>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 = 37.0 bits (86), Expect = 5e-04
Identities = 18/44 (40%), Positives = 24/44 (54%)
Query: 29 NPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKMTWEP 72
N Y T+ +I +A +T Q+ WF N R + KKENK EP
Sbjct: 24 NRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENKTKGEP 67
>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 = 40.8 bits (95), Expect = 7e-04
Identities = 47/296 (15%), Positives = 77/296 (26%), Gaps = 136/296 (45%)
Query: 154 RP---------HHFLHPAYHGLHHPHA-----RFQSS-PPPSHGPGA---TISPV----- 190
RP H L P A +F P P+ G A +P
Sbjct: 7 RPLTLSHGSLEHVLLVPT---ASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELVGK 63
Query: 191 -------NVNKPRIWSLADMAS-----------KENDIRS---SLPSS----VFSSGKMI 225
V ++ + + + NDI + L + + ++I
Sbjct: 64 FLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKELI 123
Query: 226 ------SPLAGRPHHLPHP------------------------NSY----RHDLYRLYGS 251
+A RP + Y R DLY+ Y
Sbjct: 124 KNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELR-DLYQTYHV 182
Query: 252 HLGAHPGSTEFLEQYQRHISSLSS-------------------NNANSSP----LSSV-- 286
+G + ++ +S L N +++P L S+
Sbjct: 183 LVG------DLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPI 236
Query: 287 -----GAVVAA--AAAASSGG-----------GSSTTPFGLAVTAGASSASSSGSS 324
G + A A G G++ GL VTA A + + S S
Sbjct: 237 SCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGL-VTAVAIAETDSWES 291
Score = 37.0 bits (85), Expect = 0.011
Identities = 43/304 (14%), Positives = 74/304 (24%), Gaps = 113/304 (37%)
Query: 112 GDRPPNHRLDLLDRPGGAVDTGSEWSESRPDSGPDSPECL------FERPHHFL-----H 160
D P +L+ + G V S P + L FE +L H
Sbjct: 50 ADDEPTTPAELVGKFLGYVS-----SLVEPSKVGQFDQVLNLCLTEFEN--CYLEGNDIH 102
Query: 161 PAYHGLHHP----------------HARFQS-SPPPSHGPGATISPVNVNKPRIWS---- 199
L AR + P A V ++ +
Sbjct: 103 ALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGG 162
Query: 200 ----------LADMASKENDIRSSLPSSVFSSGKMISPLAGRPHH--------------L 235
L D+ + + L + S + +S L L
Sbjct: 163 QGNTDDYFEELRDLYQTYHVLVGDL---IKFSAETLSELIRTTLDAEKVFTQGLNILEWL 219
Query: 236 PHPNSYRHDL--------------------YRLYGSHLGAHPGSTEFLEQYQRHISSLSS 275
+P++ D Y + LG PG + + ++ +
Sbjct: 220 ENPSN-TPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPG------ELRSYLKGATG 272
Query: 276 NNANSSPLSSVGAVVAAAAAASSGGGSS---------TTPF--GLAVTAGASSASSSGSS 324
+ +V A A A + S T F G+ + S S
Sbjct: 273 H---------SQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSI 323
Query: 325 VSES 328
+ +S
Sbjct: 324 LEDS 327
>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 = 37.1 bits (86), Expect = 8e-04
Identities = 15/39 (38%), Positives = 22/39 (56%)
Query: 29 NPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 67
N Y T+ +I +A +T Q+ WF N R +LKKE +
Sbjct: 42 NHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKEIQ 80
>2l7z_A Homeobox protein HOX-A13; gene regulation; NMR {Homo sapiens}
PDB: 2ld5_A*
Length = 73
Score = 36.4 bits (84), Expect = 0.001
Identities = 16/61 (26%), Positives = 29/61 (47%), Gaps = 3/61 (4%)
Query: 7 RRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66
+R T+ L+ E+ N + TK ++ ++ T ++ QV+ WF N R + KK
Sbjct: 10 KRVPYTKVQLKELE---REYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKVI 66
Query: 67 K 67
Sbjct: 67 N 67
>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 = 36.3 bits (84), Expect = 0.001
Identities = 13/61 (21%), Positives = 23/61 (37%)
Query: 7 RRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66
++ T T L+ ++ + PT+ +A + V WF N R R +K
Sbjct: 17 DKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERKSG 76
Query: 67 K 67
Sbjct: 77 P 77
>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 = 36.0 bits (83), Expect = 0.001
Identities = 11/39 (28%), Positives = 21/39 (53%)
Query: 29 NPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 67
N + TK ++ ++ T ++ Q++ WF N R + KK
Sbjct: 29 NKFITKDKRRKISAATSLSERQITIWFQNRRVKEKKSGP 67
>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 = 35.8 bits (83), Expect = 0.002
Identities = 15/62 (24%), Positives = 23/62 (37%)
Query: 7 RRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66
+ T L + NP P K L +T ++ + WF N R + KK +
Sbjct: 3 TTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRS 62
Query: 67 KM 68
M
Sbjct: 63 IM 64
>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 = 35.6 bits (82), Expect = 0.002
Identities = 15/39 (38%), Positives = 22/39 (56%)
Query: 29 NPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 67
N Y T+ + +A + +T QV WF N R ++KK NK
Sbjct: 35 NMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINK 73
>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 = 35.0 bits (81), Expect = 0.002
Identities = 14/58 (24%), Positives = 25/58 (43%), Gaps = 3/58 (5%)
Query: 8 RKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 65
R TR+ L+ E K Y ++ + LA + + + WF N R + K++
Sbjct: 5 RTAFTRDQLGRLE---KEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ 59
>2r5y_A Homeotic protein sex combs reduced; homeodomain; HET: DNA; 2.60A
{Drosophila melanogaster} PDB: 2r5z_A*
Length = 88
Score = 35.6 bits (82), Expect = 0.003
Identities = 15/39 (38%), Positives = 22/39 (56%)
Query: 29 NPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 67
N Y T+ +I +A +T Q+ WF N R + KKE+K
Sbjct: 50 NRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEHK 88
>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 = 34.2 bits (79), Expect = 0.004
Identities = 16/57 (28%), Positives = 26/57 (45%), Gaps = 3/57 (5%)
Query: 8 RKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64
R + E + LK E +N Y T+ + L+ + Q+ WF N R ++KK
Sbjct: 7 RTAFSSEQLARLK---REFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK 60
>2hi3_A Homeodomain-only protein; transcription; NMR {Mus musculus} SCOP:
a.4.1.1
Length = 73
Score = 34.7 bits (80), Expect = 0.004
Identities = 10/49 (20%), Positives = 19/49 (38%)
Query: 26 HKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKMTWEPRN 74
+K N +P ++A +T Q WF ++ + E R+
Sbjct: 22 NKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEGLPSECRS 70
>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 = 34.9 bits (80), Expect = 0.005
Identities = 18/63 (28%), Positives = 28/63 (44%)
Query: 5 GARRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64
G+ T TT L E N Y ++ ++ +A ++ TQV WF N R + KK
Sbjct: 32 GSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKK 91
Query: 65 ENK 67
+
Sbjct: 92 RER 94
>2h1k_A IPF-1, pancreatic and duodenal homeobox 1, homeodomain;
protein-DNA complex, transcription/DNA complex; 2.42A
{Mesocricetus auratus}
Length = 63
Score = 33.9 bits (78), Expect = 0.006
Identities = 13/42 (30%), Positives = 22/42 (52%)
Query: 25 EHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66
E N Y ++ ++ LA++ +T + WF N R + KKE
Sbjct: 21 EFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKEE 62
>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 = 33.8 bits (78), Expect = 0.007
Identities = 17/64 (26%), Positives = 32/64 (50%)
Query: 5 GARRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64
G++R+ T T+ L+ ++N YP + +A+ T +T +V WF N R + +K
Sbjct: 1 GSQRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK 60
Query: 65 ENKM 68
+
Sbjct: 61 REEF 64
>1lfb_A Liver transcription factor (LFB1); transcription regulation;
2.80A {Rattus norvegicus} SCOP: a.4.1.1 PDB: 2lfb_A
Length = 99
Score = 33.6 bits (76), Expect = 0.016
Identities = 14/83 (16%), Positives = 29/83 (34%), Gaps = 21/83 (25%)
Query: 7 RRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAII---------------------TK 45
R+N + ++ + +++ P+K E+ L
Sbjct: 9 GRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNL 68
Query: 46 MTLTQVSTWFANARRRLKKENKM 68
+T +V WFAN R+ +K+
Sbjct: 69 VTEVRVYNWFANRRKEEAFRHKL 91
>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 = 32.3 bits (74), Expect = 0.025
Identities = 16/62 (25%), Positives = 29/62 (46%)
Query: 8 RKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 67
R+ T T + ++ N + N YP LA + L ++ WF N R +LK+ ++
Sbjct: 2 RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHR 61
Query: 68 MT 69
+
Sbjct: 62 ES 63
>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 = 32.2 bits (72), Expect = 0.036
Identities = 14/67 (20%), Positives = 22/67 (32%), Gaps = 1/67 (1%)
Query: 8 RKNATRETTSTLK-AWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66
R + +TLK W N + + +A + V TW N RR+ +
Sbjct: 12 RTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIGNRRRKYRLMG 71
Query: 67 KMTWEPR 73
P
Sbjct: 72 IEVSGPS 78
>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB,
transcription factor, DNA-binding, DNA-directed RNA
polymerase; 4.30A {Saccharomyces cerevisiae}
Length = 197
Score = 33.5 bits (76), Expect = 0.059
Identities = 10/38 (26%), Positives = 10/38 (26%), Gaps = 15/38 (39%)
Query: 112 GDRPPNHRLDLLDRPG-------GAV------DTGSEW 136
PP G G V DT SEW
Sbjct: 28 KVYPPKIVER--FSEGDVVCALCGLVLSDKLVDTRSEW 63
>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 = 31.3 bits (71), Expect = 0.082
Identities = 13/62 (20%), Positives = 23/62 (37%)
Query: 7 RRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66
++ T L+ + N P + LA T +T + WF NAR + ++
Sbjct: 7 GKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNL 66
Query: 67 KM 68
Sbjct: 67 LR 68
>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 = 30.5 bits (69), Expect = 0.11
Identities = 7/41 (17%), Positives = 15/41 (36%)
Query: 27 KKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 67
YP + L+ ++ ++ WF + R + K
Sbjct: 29 SVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDKPSGP 69
>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 = 30.4 bits (69), Expect = 0.12
Identities = 16/61 (26%), Positives = 27/61 (44%)
Query: 7 RRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66
R++ T T L+A N ++ YP G + LA + +V WF N R + ++
Sbjct: 7 GRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRSG 66
Query: 67 K 67
Sbjct: 67 P 67
>2cue_A Paired box protein PAX6; homeobox domain, transcription factor,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
a.4.1.1
Length = 80
Score = 30.4 bits (69), Expect = 0.14
Identities = 16/69 (23%), Positives = 32/69 (46%)
Query: 7 RRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66
++N T T ++A E ++ YP + LA + ++ WF+N R + ++E
Sbjct: 7 GQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREE 66
Query: 67 KMTWEPRNR 75
K+ + R
Sbjct: 67 KLRNQRRQS 75
>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 = 31.8 bits (71), Expect = 0.18
Identities = 13/78 (16%), Positives = 26/78 (33%), Gaps = 21/78 (26%)
Query: 7 RRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAII---------------------TK 45
R+N + ++ + +++ P+K E+ L
Sbjct: 115 GRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNL 174
Query: 46 MTLTQVSTWFANARRRLK 63
+T +V WFAN R+
Sbjct: 175 VTEVRVYNWFANRRKEEA 192
>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 = 32.5 bits (73), Expect = 0.22
Identities = 40/295 (13%), Positives = 78/295 (26%), Gaps = 94/295 (31%)
Query: 12 TRETTSTLKAWLNEHKKNPYPTKGEKIM---LAIITKMTLTQVSTWFANARRRLKKENKM 68
E S L +L+ + P + L+II + ++
Sbjct: 300 PDEVKSLLLKYLD-CRPQDLPREVLTTNPRRLSIIAES----------------IRDGLA 342
Query: 69 TWEPRNRVEDEDNNNDDHSDGRKSA----DPKDHLDSKDSGTGSSEDGDRPPNHRLDLLD 124
TW+ V N D + +S+ +P ++ D + P L L+
Sbjct: 343 TWDNWKHV-----NCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPT-ILLSLI- 395
Query: 125 RPGGAVDTGSEWSESRPDSGPDSPE------CLFERPHHFLHPAYHGLHHPHARFQSSPP 178
W + + ++P + + +
Sbjct: 396 -----------WFDVIKSDVMVVVNKLHKYSLVEKQPKES----TISIPSIYLELKVKLE 440
Query: 179 PS---HGPGATISPVN-VNKPRIWSLADMASKENDIRSSLPSSVFSSGKMISPLAGRPHH 234
H +I V+ N P+ + D+ D S + HH
Sbjct: 441 NEYALH---RSI--VDHYNIPKTFDSDDLIPPYLD------------QYFYSHIG---HH 480
Query: 235 LPHPNSY-RHDLYR-LY-------------GSHLGAHPGSTEFLEQ---YQRHIS 271
L + R L+R ++ + A L+Q Y+ +I
Sbjct: 481 LKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYIC 535
Score = 32.5 bits (73), Expect = 0.22
Identities = 29/248 (11%), Positives = 59/248 (23%), Gaps = 73/248 (29%)
Query: 78 DEDNNNDDHS----------DGRKSADPKDHLDSKDSGTGSSEDGD-----RPPNHRLD- 121
D + + + D KD D S S E+ D +
Sbjct: 8 DFETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKS-ILSKEEIDHIIMSKDAVSGTLR 66
Query: 122 ----LLDRP--------GGAVDTGSEWSESR---PDSGPDSPECLFERPHHFLH------ 160
LL + + ++ S P ++ L+
Sbjct: 67 LFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVF 126
Query: 161 PAYH-GLHHPHARFQS-----SPPPS---HG-PGATISPVNVNKPRIWSLADMASKENDI 210
Y+ P+ + + P + G G+ K +A +
Sbjct: 127 AKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGS-------GK---TWVALDVCLSYKV 176
Query: 211 RSSLPSSVF--SSGKMISP------LAGRPHHLPHPNSYRHDLYRLYGSHLGAHPGSTEF 262
+ + +F + SP L + + + R D H
Sbjct: 177 QCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSD-------HSSNIKLRIHS 229
Query: 263 LEQYQRHI 270
++ R +
Sbjct: 230 IQAELRRL 237
>3cqd_A 6-phosphofructokinase isozyme 2; phosphofructokinases, PFK-2,
glycolysis, transferase; HET: ATP; 1.98A {Escherichia
coli} PDB: 3n1c_A*
Length = 309
Score = 32.1 bits (74), Expect = 0.23
Identities = 11/45 (24%), Positives = 19/45 (42%), Gaps = 3/45 (6%)
Query: 282 PLSSVGA---VVAAAAAASSGGGSSTTPFGLAVTAGASSASSSGS 323
S+VGA +V A + S V AG+++ + G+
Sbjct: 248 SQSTVGAGDSMVGAMTLKLAENASLEEMVRFGVAAGSAATLNQGT 292
>2e19_A Transcription factor 8; homeobox domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 64
Score = 29.2 bits (65), Expect = 0.33
Identities = 13/61 (21%), Positives = 22/61 (36%), Gaps = 3/61 (4%)
Query: 4 NGARRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLK 63
+G+ + + S LKA+ N P+ E +A + L V WF +
Sbjct: 3 SGSSGQPPLKNLLSLLKAYYA---LNAQPSAEELSKIADSVNLPLDVVKKWFEKMQAGQI 59
Query: 64 K 64
Sbjct: 60 S 60
>2abq_A Fructose 1-phosphate kinase; dimer, structural genomics, PSI,
protein structure initiative; 2.10A {Bacillus
halodurans} SCOP: c.72.1.1
Length = 306
Score = 31.3 bits (72), Expect = 0.36
Identities = 18/44 (40%), Positives = 22/44 (50%), Gaps = 3/44 (6%)
Query: 282 PLSSVGA---VVAAAAAASSGGGSSTTPFGLAVTAGASSASSSG 322
+SVGA VVA AA G S AV AG+++A S G
Sbjct: 241 VRNSVGAGDSVVAGFLAALQEGKSLEDAVPFAVAAGSATAFSDG 284
>3ie7_A LIN2199 protein; phosphofructokinases, transferase, glycero ION,
PSI-II, NYSGXRC, kinase, structural genomics, structure
initiative; HET: ATP; 1.60A {Listeria innocua} PDB:
3hic_A* 3jul_A* 3q1y_A
Length = 320
Score = 31.4 bits (72), Expect = 0.39
Identities = 11/45 (24%), Positives = 14/45 (31%), Gaps = 3/45 (6%)
Query: 284 SSVGA---VVAAAAAASSGGGSSTTPFGLAVTAGASSASSSGSSV 325
+ GA V A A + T +A AS SS
Sbjct: 247 NDTGAGDVFVGAFIAGLAMNMPITETLKVATGCSASKVMQQDSSS 291
>2jg5_A Fructose 1-phosphate kinase; 1-phosphofructokinase, transferase;
2.3A {Staphylococcus aureus}
Length = 306
Score = 31.3 bits (72), Expect = 0.44
Identities = 12/42 (28%), Positives = 18/42 (42%), Gaps = 3/42 (7%)
Query: 284 SSVGA---VVAAAAAASSGGGSSTTPFGLAVTAGASSASSSG 322
++VG+ VA A + G S F AV G ++A
Sbjct: 243 NTVGSGDSTVAGMVAGIASGLSIEKAFQQAVACGTATAFDED 284
>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 = 28.9 bits (65), Expect = 0.47
Identities = 13/62 (20%), Positives = 26/62 (41%)
Query: 7 RRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66
R+ T T + L K YP + +A+ + ++V WF N R + +++
Sbjct: 7 GRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQQ 66
Query: 67 KM 68
+
Sbjct: 67 QQ 68
>2f02_A Tagatose-6-phosphate kinase; LACC, structural genomics, PSI,
protein structure initiative YORK SGX research center
for structural genomics; HET: ATP; 1.90A {Enterococcus
faecalis} SCOP: c.72.1.1 PDB: 2awd_A*
Length = 323
Score = 30.6 bits (70), Expect = 0.60
Identities = 7/44 (15%), Positives = 15/44 (34%), Gaps = 3/44 (6%)
Query: 282 PLSSVGA---VVAAAAAASSGGGSSTTPFGLAVTAGASSASSSG 322
+ VG+ +A A + + + AG ++A
Sbjct: 249 AKNPVGSGDATIAGLAYGLAKDAPAAELLKWGMAAGMANAQERM 292
>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 = 28.0 bits (63), Expect = 0.62
Identities = 13/59 (22%), Positives = 26/59 (44%)
Query: 10 NATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKM 68
+ T+ L+ + YP + LA+ +T ++ WF N R + +K+ K+
Sbjct: 2 SHMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQEKV 60
>2jg1_A Tagatose-6-phosphate kinase; phosphoryl transfer, conformational
changes, transferase, lactose metabolism; HET: MSE ANP
TA6; 2.00A {Staphylococcus aureus} PDB: 2jgv_A* 2q5r_A*
Length = 330
Score = 30.2 bits (69), Expect = 0.79
Identities = 10/44 (22%), Positives = 16/44 (36%), Gaps = 3/44 (6%)
Query: 282 PLSSVGA---VVAAAAAASSGGGSSTTPFGLAVTAGASSASSSG 322
L+ VG+ VA +A + A T G +A +
Sbjct: 266 VLNPVGSGDSTVAGITSAILNHENDHDLLKKANTLGMLNAQEAQ 309
>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 = 28.7 bits (63), Expect = 1.00
Identities = 14/90 (15%), Positives = 30/90 (33%), Gaps = 21/90 (23%)
Query: 4 NGARRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAII-------------------- 43
+G+ +N + ++ + + + P+K E+ L
Sbjct: 3 SGSSGRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLG 62
Query: 44 -TKMTLTQVSTWFANARRRLKKENKMTWEP 72
+T +V WFAN R+ K+ +
Sbjct: 63 SNLVTEVRVYNWFANRRKEEAFRQKLAMDA 92
>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 = 28.1 bits (63), Expect = 1.00
Identities = 17/61 (27%), Positives = 30/61 (49%)
Query: 7 RRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66
+R++ T + S L ++ YP + LA T +T ++ WF N R RL+K++
Sbjct: 18 QRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQH 77
Query: 67 K 67
Sbjct: 78 T 78
>3dzy_A Retinoic acid receptor RXR-alpha; DNA-binding, HOST-virus
interaction, metal-binding, nucleus, receptor,
transcription, transcription regulation, zinc-FIN
activator; HET: DNA REA BRL; 3.10A {Homo sapiens} PDB:
3dzu_A* 3e00_A*
Length = 467
Score = 30.1 bits (67), Expect = 1.1
Identities = 16/134 (11%), Positives = 32/134 (23%), Gaps = 1/134 (0%)
Query: 155 PHHFLHPAYHGLHHPHARFQSSPPPSHGPGATISPVNVNKPRIWSLADMASKENDIRSSL 214
HH H + SS G G+ +P + S
Sbjct: 2 AHHHHHHVDDDDKMFSTQVNSSLTSPTGRGSMAAPSLHPSLGPGIGSPGQLHSPISTLSS 61
Query: 215 PSSVFSSGKMISPLAGRPHHLPHPNSYRHDLYRLYGSHLGAHPGSTEFLEQYQRHISSLS 274
P + + PH + P + + L + E + +
Sbjct: 62 PINGMGPPFSVISSPMGPHSMSVP-TTPTLGFSTGSPQLSSPMNPVSSSEDIKPPLGLNG 120
Query: 275 SNNANSSPLSSVGA 288
+ P ++ +
Sbjct: 121 VLKVPAHPSGNMAS 134
>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 = 27.7 bits (62), Expect = 1.3
Identities = 10/49 (20%), Positives = 19/49 (38%)
Query: 26 HKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKMTWEPRN 74
+K N +P ++A +T Q WF ++ + E R+
Sbjct: 21 NKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEGLPSECRS 69
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 29.0 bits (64), Expect = 1.5
Identities = 14/91 (15%), Positives = 28/91 (30%), Gaps = 20/91 (21%)
Query: 3 INGARRKNATRETTSTLKAWLNE-----HKKNPYPTKGEKIMLAIITKMTLTQVSTWFAN 57
I A R E+ ++ W E + + K+M + + W
Sbjct: 74 IAQADRLTQEPES---IRKWREEQRKRLQELD----AASKVMEQEWREKAKKDLEEWNQR 126
Query: 58 ARRRLKKENKMTWEPRNRVEDED---NNNDD 85
+++K NR+ D+ + D
Sbjct: 127 QSEQVEKNKI-----NNRIADKAFYQQPDAD 152
>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo,
protein-DNA, human disease; 3.20A {Homo sapiens}
Length = 221
Score = 29.2 bits (64), Expect = 1.5
Identities = 14/81 (17%), Positives = 26/81 (32%), Gaps = 21/81 (25%)
Query: 4 NGARRKNATRETTSTLKAWLNEHKKNPYPTKGEKIMLAII-------------------- 43
N R+N + ++ + + + P+K E+ L
Sbjct: 139 NKKMRRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLG 198
Query: 44 -TKMTLTQVSTWFANARRRLK 63
+T +V WFAN R+
Sbjct: 199 SNLVTEVRVYNWFANRRKEEA 219
>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP;
2.37A {Humulus lupulus}
Length = 339
Score = 29.5 bits (66), Expect = 1.6
Identities = 18/98 (18%), Positives = 33/98 (33%), Gaps = 25/98 (25%)
Query: 160 HPAYHGLHHPHARFQSSPPPSHGPGATISPVNVNKPRIWSLA--------DMASKENDIR 211
H +H + + ++P + ++ K ++ L ++ D+
Sbjct: 5 HHHHHHMDYASVAMAAAPTTTTTTNVSLRRQRHRKEKLLVLMGATGTGKSRLSI---DLA 61
Query: 212 SSLPSSVFSSGKM------------ISP--LAGRPHHL 235
+ P V +S KM IS G PHHL
Sbjct: 62 AHFPLEVINSDKMQVYKGLDITTNKISVPDRGGVPHHL 99
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 1752
Score = 29.7 bits (66), Expect = 1.7
Identities = 51/260 (19%), Positives = 77/260 (29%), Gaps = 16/260 (6%)
Query: 83 NDDHSDGRKSADPKDHLDSKDSGTGSSEDGDRPPNHRLDLLDRPGGAVDTGSEWSESRPD 142
+ D L GT +G P R ++D + +S
Sbjct: 1452 DQDMLMNYSLGTAVPTLAGSGMGTSQLPEGAGTPYERSPMVDSGFVGSPDAAAFSPLV-Q 1510
Query: 143 SGPDSPECLFERPHHFLHPAYHGLHHPHARFQSSPPPSHGPGAT------ISPVNVNKPR 196
G + E + Y G+ P S S G G T SP P
Sbjct: 1511 GGSEGREGFGDYGLLGAASPYKGVQSPGYTSPFSSAMSPGYGLTSPSYSPSSPGYSTSPA 1570
Query: 197 IWSLADMASKENDIRSSLPSSVFSSGKMISPLAGRPHHLPHPNSYRHDLYRLYGSHLGAH 256
+ S + S P+S S S P + SY Y ++
Sbjct: 1571 YMPSSPSYSPTSPSYS--PTSPSYSPTSPSYSPTSPSYSATSPSYSP-TSPSYSPTSPSY 1627
Query: 257 -PGSTEFL---EQYQRHISSLSSNNANSSPLSSVGAVVAAAAAASSGGGSSTTPFGLAVT 312
P S + Y S S + + SP S + + + + +S S T+P +
Sbjct: 1628 SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTS 1687
Query: 313 AGASSASS--SGSSVSESPG 330
S S S +S S SP
Sbjct: 1688 PSYSPTSPSYSPTSPSYSPT 1707
>2wsc_N PSAN, PSI-N, photosystem I-N subunit; photosynthesis, electron
transfer, membrane proteins, large complexes; HET: CL1
PQN BCR LMU LMG SUC UNL; 3.30A {Phaseolus vulgaris} PDB:
2wse_N* 2wsf_N*
Length = 170
Score = 28.9 bits (63), Expect = 1.8
Identities = 17/71 (23%), Positives = 31/71 (43%), Gaps = 1/71 (1%)
Query: 254 GAHPGSTEFLEQYQRHISSLSSNNANSSPLSSVGAVVAAAAAASSGGGSSTTPFGLAVTA 313
A G ++ L + S++S ++ L + A A + S G + LA T
Sbjct: 13 YARSGCSD-LNAKLTSMPSVASPQLSALKLPLIKAHQAKVTESKSDQGRRSALVYLAATL 71
Query: 314 GASSASSSGSS 324
++A++S SS
Sbjct: 72 FTAAAAASNSS 82
>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 = 4.3
Identities = 7/38 (18%), Positives = 13/38 (34%), Gaps = 1/38 (2%)
Query: 27 KKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64
+P + L+ + + WF RR +K
Sbjct: 21 AITKHPDEKRLEGLSKQLDWDVRSIQRWFRQ-RRNQEK 57
>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 = 27.2 bits (59), Expect = 5.1
Identities = 11/45 (24%), Positives = 16/45 (35%), Gaps = 22/45 (48%)
Query: 9 KNATRETTSTLKAWLNEHKKNPY-----PTKGEKIMLAIITKMTL 48
K A ++ ++LK Y P LAI K T+
Sbjct: 19 KQALKKLQASLK---------LYADDSAPA------LAI--KATM 46
Score = 26.5 bits (57), Expect = 9.2
Identities = 3/13 (23%), Positives = 5/13 (38%), Gaps = 5/13 (38%)
Query: 138 ESR-----PDSGP 145
++ DS P
Sbjct: 26 QASLKLYADDSAP 38
>2ajr_A Sugar kinase, PFKB family; TM0828, possible 1-phosphofructokinase
(EC 2.7.1.56), struct genomics, joint center for
structural genomics, JCSG; HET: MSE; 2.46A {Thermotoga
maritima} SCOP: c.72.1.1
Length = 331
Score = 28.0 bits (63), Expect = 5.3
Identities = 5/46 (10%), Positives = 11/46 (23%), Gaps = 4/46 (8%)
Query: 284 SSVGA---VVAA-AAAASSGGGSSTTPFGLAVTAGASSASSSGSSV 325
+GA VA G + + ++ +
Sbjct: 267 HLLGAGDAYVAGMVYYFIKHGANFLEMAKFGFASALAATRRKEKYM 312
>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 = 5.6
Identities = 9/51 (17%), Positives = 18/51 (35%), Gaps = 17/51 (33%)
Query: 19 LKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKMT 69
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 = 27.5 bits (62), Expect = 6.6
Identities = 12/51 (23%), Positives = 17/51 (33%), Gaps = 17/51 (33%)
Query: 19 LKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKMT 69
+LN++ GEKI I A RLK E ++
Sbjct: 372 FSLYLNQN-----VEIGEKIAQIAI------------DRASARLKTEKQIV 405
>2dby_A GTP-binding protein; GDP, structural genomics, NPPSFA, natio
project on protein structural and functional analyses;
HET: GDP; 1.76A {Thermus thermophilus} PDB: 2dwq_A
Length = 368
Score = 27.4 bits (62), Expect = 7.6
Identities = 10/40 (25%), Positives = 18/40 (45%), Gaps = 4/40 (10%)
Query: 183 PGATISP----VNVNKPRIWSLADMASKENDIRSSLPSSV 218
P ATI V + R+++L +K + +P+ V
Sbjct: 32 PFATIDKNVGVVPLEDERLYALQRTFAKGERVPPVVPTHV 71
>1g87_A Endocellulase 9G; endoglucanase, cellulose binding domain, (ALPH
6-helix barrel, beta barrel, hydrolase; 1.60A
{Clostridium cellulolyticum} SCOP: a.102.1.2 b.2.2.2
PDB: 1ga2_A* 1k72_A* 1kfg_A*
Length = 614
Score = 27.6 bits (61), Expect = 8.0
Identities = 23/116 (19%), Positives = 31/116 (26%), Gaps = 31/116 (26%)
Query: 231 RPHH----------LPHPNSYRHDLYRLYGSHLGAHPGSTEFLEQYQRHISSLSSN---- 276
PHH + P +RH +Y GA G + + Y I++ +N
Sbjct: 371 HPHHRTAHGSWTDQMTSPTYHRHTIY-------GALVGGPDNADGYTDEINNYVNNEIAC 423
Query: 277 --NANSSPLSSVGAVVAAAAAASSGGGSSTTPFGLAVTAGASSASSSGSSVSESPG 330
NA G A A GG F S P
Sbjct: 424 DYNA--------GFTGALAKMYKHSGGDPIPNFKAIEKITNDEVIIKAGLNSTGPN 471
>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 = 27.4 bits (60), Expect = 8.7
Identities = 42/237 (17%), Positives = 64/237 (27%), Gaps = 23/237 (9%)
Query: 100 DSKDSGTGSSEDGDRPPNHRLDLLDRPGGAVDTGSEWSESRPDSGPDSPECLFERPHHFL 159
+ K + +DG P L V +S D+ F
Sbjct: 1456 EQKITEIEDGQDGGVTPYSNESGLVNADLDVKDELMFSPLVDSGSNDAMAGGFTAYGG-- 1513
Query: 160 HPAYHGLHHPHARFQSSPPPSHGPGATISPVNVNKPRIWSLADMASKENDIRSSLPSSVF 219
Y P + P S G G + + P + S P+S
Sbjct: 1514 -ADYGEATSPFGAY-GEAPTSPGFGVSSPGFSPTSPTYSPTSPAYS---------PTSPS 1562
Query: 220 SSGKMISPLAGRPHHLPHPNSYRHDLYRLYGSHLGAHPGSTEFLE----------QYQRH 269
S S P + P SY + P S + Y
Sbjct: 1563 YSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPT 1622
Query: 270 ISSLSSNNANSSPLSSVGAVVAAAAAASSGGGSSTTPFGLAVTAGASSASSSGSSVS 326
S S + + SP S + + + + +S S T+P + S S S S S
Sbjct: 1623 SPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPSYSPTSPSYSPTS 1679
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
0.308 0.126 0.376
Gapped
Lambda K H
0.267 0.0770 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,255,730
Number of extensions: 311738
Number of successful extensions: 753
Number of sequences better than 10.0: 1
Number of HSP's gapped: 740
Number of HSP's successfully gapped: 106
Length of query: 341
Length of database: 6,701,793
Length adjustment: 94
Effective length of query: 247
Effective length of database: 4,077,219
Effective search space: 1007073093
Effective search space used: 1007073093
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 58 (26.0 bits)