RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy8148
(390 letters)
>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 = 63.1 bits (154), Expect = 3e-13
Identities = 15/55 (27%), Positives = 27/55 (49%), Gaps = 3/55 (5%)
Query: 271 FKERSRNALKECYDKNR---YPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTP 322
F + + L+ + KN Y + L + T L+ Q+ NW NRR++++T
Sbjct: 5 FTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKTI 59
Score = 61.2 bits (149), Expect = 2e-12
Identities = 14/52 (26%), Positives = 25/52 (48%), Gaps = 3/52 (5%)
Query: 329 RSRNALKECYDKNR---YPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTP 377
+ L+ + KN Y + L + T L+ Q+ NW NRR++++T
Sbjct: 8 ENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKTI 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 = 64.1 bits (156), Expect = 3e-13
Identities = 15/54 (27%), Positives = 27/54 (50%), Gaps = 3/54 (5%)
Query: 271 FKERSRNALKECYDKNR---YPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRT 321
F + + L+ + KN Y + L + T L+ Q+ NW NRR++++T
Sbjct: 34 FTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT 87
Score = 61.8 bits (150), Expect = 2e-12
Identities = 14/51 (27%), Positives = 25/51 (49%), Gaps = 3/51 (5%)
Query: 329 RSRNALKECYDKNR---YPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRT 376
+ L+ + KN Y + L + T L+ Q+ NW NRR++++T
Sbjct: 37 ENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT 87
>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 = 62.1 bits (151), Expect = 1e-12
Identities = 14/59 (23%), Positives = 25/59 (42%), Gaps = 3/59 (5%)
Query: 271 FKERSRNALKECYDKNR---YPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRS 326
F + + L+ + KN Y + L + T L+ Q+ NW RR +++T
Sbjct: 9 FTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVAARRAKEKTITIAP 67
Score = 60.6 bits (147), Expect = 4e-12
Identities = 15/66 (22%), Positives = 27/66 (40%), Gaps = 6/66 (9%)
Query: 321 TPQQRSIQRSRNA---LKECYDKNR---YPNPDEKRQLSEITGLTLTQVSNWFKNRRQRD 374
T R + ++ L+ + KN Y + L + T L+ Q+ NW RR ++
Sbjct: 1 TKPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVAARRAKE 60
Query: 375 RTPQQR 380
+T
Sbjct: 61 KTITIA 66
>2dn0_A Zinc fingers and homeoboxes protein 3; triple homeobox 1 protein,
KIAA0395, TIX1, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 76
Score = 60.9 bits (148), Expect = 2e-12
Identities = 17/70 (24%), Positives = 33/70 (47%), Gaps = 7/70 (10%)
Query: 313 KNRRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQ 372
+ + ++ +Q S LK + +N++P E L+++TGL+ +V WF +RR
Sbjct: 9 SIYKNK-KSHEQLSA------LKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRY 61
Query: 373 RDRTPQQRAK 382
R +
Sbjct: 62 HCRNLKGSRS 71
Score = 57.8 bits (140), Expect = 3e-11
Identities = 16/48 (33%), Positives = 27/48 (56%)
Query: 278 ALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQR 325
ALK + +N++P E L+++TGL+ +V WF +RR R +
Sbjct: 22 ALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCRNLKGS 69
>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 = 61.1 bits (148), Expect = 2e-12
Identities = 14/72 (19%), Positives = 31/72 (43%), Gaps = 6/72 (8%)
Query: 312 FKNRRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
+ ++R P+Q L+ + +N P +E +L T +T ++ +WF RR
Sbjct: 6 SGPTKYKERAPEQLRA------LESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERR 59
Query: 372 QRDRTPQQRAKN 383
++ + +
Sbjct: 60 KKVNAEETKKSG 71
Score = 57.2 bits (138), Expect = 6e-11
Identities = 15/59 (25%), Positives = 30/59 (50%), Gaps = 3/59 (5%)
Query: 271 FKERSRN---ALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRS 326
+KER+ AL+ + +N P +E +L T +T ++ +WF RR++ + +
Sbjct: 11 YKERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKVNAEETKK 69
>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 = 60.8 bits (148), Expect = 2e-12
Identities = 21/74 (28%), Positives = 38/74 (51%), Gaps = 8/74 (10%)
Query: 315 RRQRDRTPQQRSIQRSRNALKECYDKNR---YPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
RR+R +Q + L E + + YP+ + K +L++ G+T++QVSNWF N+R
Sbjct: 2 RRKRRNFNKQ-----ATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKR 56
Query: 372 QRDRTPQQRAKNRT 385
R + + +
Sbjct: 57 IRYKKNIGKFQEEA 70
Score = 59.7 bits (145), Expect = 6e-12
Identities = 18/63 (28%), Positives = 36/63 (57%), Gaps = 3/63 (4%)
Query: 271 FKERSRNALKECYDKNR---YPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRSI 327
F +++ L E + + YP+ + K +L++ G+T++QVSNWF N+R R + +
Sbjct: 8 FNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKFQ 67
Query: 328 QRS 330
+ +
Sbjct: 68 EEA 70
>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 = 60.2 bits (146), Expect = 7e-12
Identities = 18/65 (27%), Positives = 36/65 (55%), Gaps = 3/65 (4%)
Query: 271 FKERSRNALKECYDKNR---YPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRSI 327
F +++ L E + + YP+ + K +L++ G+T++QVSNWF N+R R + +
Sbjct: 8 FNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKFQ 67
Query: 328 QRSRN 332
+ +
Sbjct: 68 EEANI 72
Score = 60.2 bits (146), Expect = 7e-12
Identities = 21/73 (28%), Positives = 38/73 (52%), Gaps = 8/73 (10%)
Query: 315 RRQRDRTPQQRSIQRSRNALKECYDKNR---YPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
RR+R +Q + L E + + YP+ + K +L++ G+T++QVSNWF N+R
Sbjct: 2 RRKRRNFNKQ-----ATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKR 56
Query: 372 QRDRTPQQRAKNR 384
R + + +
Sbjct: 57 IRYKKNIGKFQEE 69
>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 = 59.3 bits (144), Expect = 9e-12
Identities = 21/72 (29%), Positives = 35/72 (48%), Gaps = 8/72 (11%)
Query: 313 KNRRQRDRTPQQRSIQRSRNALKECYDKNR---YPNPDEKRQLSEITGLTLTQVSNWFKN 369
+ +R P+ + N ++ ++ YP DEK+Q++ T LTL QV+NWF N
Sbjct: 6 SGKNKRGVLPKH-----ATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFIN 60
Query: 370 RRQRDRTPQQRA 381
R+R +
Sbjct: 61 ARRRILQSGPSS 72
Score = 58.2 bits (141), Expect = 3e-11
Identities = 19/42 (45%), Positives = 25/42 (59%)
Query: 285 KNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRS 326
+ YP DEK+Q++ T LTL QV+NWF N R+R S
Sbjct: 31 GHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRILQSGPSS 72
>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 = 58.5 bits (141), Expect = 3e-11
Identities = 17/79 (21%), Positives = 36/79 (45%), Gaps = 6/79 (7%)
Query: 312 FKNRRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
F ++ +++T Q I L++ + K+ +P E +L T L+ ++ +WF RR
Sbjct: 12 FAPQKFKEKTQGQVKI------LEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERR 65
Query: 372 QRDRTPQQRAKNRTFDPYS 390
+ + +Q + S
Sbjct: 66 KLRDSMEQAVLDSMGSGKS 84
Score = 53.8 bits (129), Expect = 1e-09
Identities = 15/63 (23%), Positives = 32/63 (50%), Gaps = 3/63 (4%)
Query: 271 FKERSR---NALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRSI 327
FKE+++ L++ + K+ +P E +L T L+ ++ +WF RR+ + +Q +
Sbjct: 17 FKEKTQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERRKLRDSMEQAVL 76
Query: 328 QRS 330
Sbjct: 77 DSM 79
>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 = 57.8 bits (140), Expect = 4e-11
Identities = 21/75 (28%), Positives = 37/75 (49%), Gaps = 8/75 (10%)
Query: 313 KNRRQRDRTPQQRSIQRSRNALKE---CYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKN 369
++++ P + S L++ + YP+ +EK+ LSE T L+L Q+SNWF N
Sbjct: 6 SGKKRKGNLPAE-----SVKILRDWMYKHRFKAYPSEEEKQMLSEKTNLSLLQISNWFIN 60
Query: 370 RRQRDRTPQQRAKNR 384
R+R + +
Sbjct: 61 ARRRILPDMLQQRRN 75
Score = 57.5 bits (139), Expect = 5e-11
Identities = 18/49 (36%), Positives = 27/49 (55%)
Query: 285 KNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRSIQRSRNA 333
YP+ +EK+ LSE T L+L Q+SNWF N R+R + + +
Sbjct: 31 FKAYPSEEEKQMLSEKTNLSLLQISNWFINARRRILPDMLQQRRNDPSG 79
>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 = 58.1 bits (140), Expect = 4e-11
Identities = 11/73 (15%), Positives = 32/73 (43%), Gaps = 6/73 (8%)
Query: 312 FKNRRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
F ++ +++T +Q + L+ + + +E +L T LT ++ WF ++
Sbjct: 10 FTPQKFKEKTAEQLRV------LQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKK 63
Query: 372 QRDRTPQQRAKNR 384
+ +++ +
Sbjct: 64 KSKALKEEKMEID 76
Score = 55.0 bits (132), Expect = 4e-10
Identities = 13/66 (19%), Positives = 28/66 (42%), Gaps = 3/66 (4%)
Query: 271 FKERSRN---ALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRSI 327
FKE++ L+ + + +E +L T LT ++ WF +++ +++
Sbjct: 15 FKEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEEKME 74
Query: 328 QRSRNA 333
NA
Sbjct: 75 IDESNA 80
>3k2a_A Homeobox protein MEIS2; homeobox domain, DNA-binding,
transcription, nucleus, phosphoprotein, DNA bindi
protein; 1.95A {Homo sapiens}
Length = 67
Score = 57.0 bits (138), Expect = 6e-11
Identities = 20/45 (44%), Positives = 30/45 (66%)
Query: 340 KNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRAKNR 384
+ YP+ ++K+QL++ TGLT+ QV+NWF N R+R P NR
Sbjct: 22 THPYPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQPMIDQSNR 66
Score = 55.0 bits (133), Expect = 2e-10
Identities = 19/46 (41%), Positives = 30/46 (65%)
Query: 285 KNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRSIQRS 330
+ YP+ ++K+QL++ TGLT+ QV+NWF N R+R P R+
Sbjct: 22 THPYPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQPMIDQSNRA 67
>2lk2_A Homeobox protein TGIF1; NESG, structural genomics, northeast
structural genomics CON PSI-biology, transcription; NMR
{Homo sapiens}
Length = 89
Score = 57.1 bits (138), Expect = 9e-11
Identities = 19/49 (38%), Positives = 24/49 (48%)
Query: 285 KNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRSIQRSRNA 333
N YP+ EK LS+ T L+ QV NWF N R+R R + N
Sbjct: 29 YNAYPSEQEKALLSQQTHLSTLQVCNWFINARRRLLPDMLRKDGKDPNQ 77
Score = 56.3 bits (136), Expect = 2e-10
Identities = 21/77 (27%), Positives = 32/77 (41%), Gaps = 8/77 (10%)
Query: 312 FKNRRQRDRTPQQRSIQRSRNALKECYDKNR---YPNPDEKRQLSEITGLTLTQVSNWFK 368
+ P+ S L++ ++R YP+ EK LS+ T L+ QV NWF
Sbjct: 3 HHHHHHSHMLPK-----ESVQILRDWLYEHRYNAYPSEQEKALLSQQTHLSTLQVCNWFI 57
Query: 369 NRRQRDRTPQQRAKNRT 385
N R+R R +
Sbjct: 58 NARRRLLPDMLRKDGKD 74
>2d5v_A Hepatocyte nuclear factor 6; transcription factor,
transcription-DNA complex; 2.00A {Rattus norvegicus}
PDB: 1s7e_A
Length = 164
Score = 58.0 bits (139), Expect = 3e-10
Identities = 19/115 (16%), Positives = 43/115 (37%), Gaps = 6/115 (5%)
Query: 211 ESHNFDSKYHAELQQLWMRGHYKEHAKIRGRDLGAVDKYRIRKKFPLPKTIWDGEETVYC 270
+ + + ++ + +R ++ + + PK +
Sbjct: 50 SKLKSGRETFRRMWKWLQEPEFQRMSALRLAACKRKEQEHGKDRGNTPK------KPRLV 103
Query: 271 FKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQR 325
F + R L + +N+ P+ + + +S+ GL L+ VSN+F N R+R
Sbjct: 104 FTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNARRRSLDKWLE 158
Score = 54.9 bits (131), Expect = 3e-09
Identities = 20/95 (21%), Positives = 38/95 (40%)
Query: 286 NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRSIQRSRNALKECYDKNRYPN 345
P+ +R + + K+R + P+ R L + +N+ P+
Sbjct: 64 KWLQEPEFQRMSALRLAACKRKEQEHGKDRGNTPKKPRLVFTDVQRRTLHAIFKENKRPS 123
Query: 346 PDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQR 380
+ + +S+ GL L+ VSN+F N R+R
Sbjct: 124 KELQITISQQLGLELSTVSNFFMNARRRSLDKWLE 158
>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 = 16/61 (26%), Positives = 32/61 (52%), Gaps = 6/61 (9%)
Query: 315 RRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRD 374
R +T +Q + LK + ++++P+ E +L E+TGL +++ WF + R R
Sbjct: 6 HHHRKKTKEQIAH------LKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRC 59
Query: 375 R 375
+
Sbjct: 60 Q 60
Score = 52.5 bits (126), Expect = 2e-09
Identities = 13/44 (29%), Positives = 26/44 (59%)
Query: 277 NALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 320
LK + ++++P+ E +L E+TGL +++ WF + R R +
Sbjct: 17 AHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQ 60
>1du6_A PBX1, homeobox protein PBX1; homeodomain, gene regulation; NMR {Mus
musculus} SCOP: a.4.1.1
Length = 64
Score = 54.6 bits (132), Expect = 4e-10
Identities = 18/64 (28%), Positives = 32/64 (50%), Gaps = 8/64 (12%)
Query: 313 KNRRQRDRTPQQRSIQRSRNALKECYDKNR---YPNPDEKRQLSEITGLTLTQVSNWFKN 369
+ +Q + L E + + YP+ + K +L++ G+T++QVSNWF N
Sbjct: 2 SGHIEGRHMNKQ-----ATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGN 56
Query: 370 RRQR 373
+R R
Sbjct: 57 KRIR 60
Score = 53.9 bits (130), Expect = 5e-10
Identities = 17/51 (33%), Positives = 31/51 (60%), Gaps = 3/51 (5%)
Query: 271 FKERSRNALKECYDKNR---YPNPDEKRQLSEITGLTLTQVSNWFKNRRQR 318
+++ L E + + YP+ + K +L++ G+T++QVSNWF N+R R
Sbjct: 10 MNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIR 60
>2xsd_C POU domain, class 3, transcription factor 1; transcription-DNA
complex, SOX; 2.05A {Mus musculus}
Length = 164
Score = 53.1 bits (127), Expect = 1e-08
Identities = 17/76 (22%), Positives = 32/76 (42%), Gaps = 7/76 (9%)
Query: 307 QVSNWFKNRRQRDR-TPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSN 365
+++ + R++R + AL+ + K P+ E L++ L V
Sbjct: 92 KIAAQGRKRKKRTSIEVGVK------GALESHFLKCPKPSAHEITGLADSLQLEKEVVRV 145
Query: 366 WFKNRRQRDRTPQQRA 381
WF NRRQ+++ A
Sbjct: 146 WFCNRRQKEKRMTPAA 161
Score = 50.4 bits (120), Expect = 9e-08
Identities = 14/57 (24%), Positives = 25/57 (43%)
Query: 270 CFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRS 326
+ + AL+ + K P+ E L++ L V WF NRRQ+++ +
Sbjct: 105 SIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKEKRMTPAA 161
>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 = 50.4 bits (121), Expect = 1e-08
Identities = 15/64 (23%), Positives = 34/64 (53%), Gaps = 7/64 (10%)
Query: 313 KNRRQRDR-TPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
+R R R T Q + L++ +D N P+ ++ +++++ +GL + +WF+N
Sbjct: 6 SGKRPRTRITDDQLRV------LRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTL 59
Query: 372 QRDR 375
++R
Sbjct: 60 FKER 63
Score = 49.3 bits (118), Expect = 3e-08
Identities = 11/56 (19%), Positives = 29/56 (51%)
Query: 271 FKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRS 326
+ L++ +D N P+ ++ +++++ +GL + +WF+N ++R S
Sbjct: 14 ITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKERQSGPSS 69
>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 = 52.3 bits (125), Expect = 2e-08
Identities = 17/64 (26%), Positives = 36/64 (56%), Gaps = 3/64 (4%)
Query: 312 FKNRRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
+RR++ RT + +I R AL++ + +N+ P ++ ++E + + WF NRR
Sbjct: 97 GLSRRRKKRTSIETNI---RVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRR 153
Query: 372 QRDR 375
Q+++
Sbjct: 154 QKEK 157
Score = 49.6 bits (118), Expect = 2e-07
Identities = 12/51 (23%), Positives = 27/51 (52%)
Query: 270 CFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 320
+ R AL++ + +N+ P ++ ++E + + WF NRRQ+++
Sbjct: 107 SIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEK 157
>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 = 49.6 bits (118), Expect = 3e-08
Identities = 14/66 (21%), Positives = 32/66 (48%), Gaps = 6/66 (9%)
Query: 315 RRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRD 374
+ +T +Q +I LK + + ++ ++ ++L +ITGL ++ WF + R
Sbjct: 5 SSGKRKTKEQLAI------LKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYAL 58
Query: 375 RTPQQR 380
+ Q +
Sbjct: 59 KHGQLK 64
Score = 46.2 bits (109), Expect = 4e-07
Identities = 11/55 (20%), Positives = 28/55 (50%)
Query: 279 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRSIQRSRNA 333
LK + + ++ ++ ++L +ITGL ++ WF + R + Q + + + +
Sbjct: 18 LKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQLKWFRDNASG 72
>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 = 51.1 bits (122), Expect = 3e-08
Identities = 18/78 (23%), Positives = 37/78 (47%), Gaps = 5/78 (6%)
Query: 298 SEITGLTLTQVSNWFKNRRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITG 357
++ L +V + R++R +++AL+ + ++ P+ E +++E
Sbjct: 71 EQVGALYNEKVGANERKRKRRTTISIA-----AKDALERHFGEHSKPSSQEIMRMAEELN 125
Query: 358 LTLTQVSNWFKNRRQRDR 375
L V WF NRRQR++
Sbjct: 126 LEKEVVRVWFCNRRQREK 143
Score = 50.8 bits (121), Expect = 5e-08
Identities = 14/51 (27%), Positives = 27/51 (52%)
Query: 270 CFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 320
+++AL+ + ++ P+ E +++E L V WF NRRQR++
Sbjct: 93 TISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREK 143
>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 = 49.4 bits (117), Expect = 6e-08
Identities = 15/70 (21%), Positives = 34/70 (48%), Gaps = 6/70 (8%)
Query: 311 WFKNRRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNR 370
+ +TP+Q + LK + + ++P+P+E +L++ +GL T + +WF +
Sbjct: 23 SGSTGKICKKTPEQLHM------LKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDT 76
Query: 371 RQRDRTPQQR 380
R + +
Sbjct: 77 RYAWKNGNLK 86
Score = 45.9 bits (108), Expect = 9e-07
Identities = 14/78 (17%), Positives = 33/78 (42%)
Query: 256 PLPKTIWDGEETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNR 315
P + + LK + + ++P+P+E +L++ +GL T + +WF +
Sbjct: 17 QGPAPKSGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDT 76
Query: 316 RQRDRTPQQRSIQRSRNA 333
R + + ++A
Sbjct: 77 RYAWKNGNLKWYYYYQSA 94
>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 = 48.6 bits (116), Expect = 6e-08
Identities = 17/64 (26%), Positives = 27/64 (42%), Gaps = 7/64 (10%)
Query: 313 KNRRQRDR-TPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
+++R R TP+Q L + Y + P ++ GL V WF+N R
Sbjct: 16 RDKRLRTTITPEQL------EILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTR 69
Query: 372 QRDR 375
R+R
Sbjct: 70 ARER 73
Score = 47.1 bits (112), Expect = 2e-07
Identities = 13/56 (23%), Positives = 19/56 (33%)
Query: 271 FKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRS 326
L + Y + P ++ GL V WF+N R R+R S
Sbjct: 24 ITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERKSGPSS 79
>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 = 6e-08
Identities = 71/456 (15%), Positives = 134/456 (29%), Gaps = 183/456 (40%)
Query: 8 MSFTPEQIDCLCEAMQQSGDFD---KLAM------FLW---------SLPPQE--AIRGQ 47
+ + ++ + G FD L + +L L + +
Sbjct: 65 LGYVSSLVEP-----SKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKT 119
Query: 48 ESVLRA--RAVVAYKR-------HAFHE--------LYAILESHNF-----DSKYHAELQ 85
+ +++ A + KR A L AI F Y EL+
Sbjct: 120 KELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAI-----FGGQGNTDDYFEELR 174
Query: 86 QLWMRGHYKEHAKIRGRDLGYSSDDSSPVLYE--TNAHDFNKHY---------LEIQQKA 134
L+ Y DL S+ L E D K + LE
Sbjct: 175 DLY--QTYHVLVG----DL---IKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNT 225
Query: 135 --QEYLNMKKLNPNMSFTP----EQIDCLCEAMQQSGDFDKLAMFLWSLPPQE---AIRG 185
++YL L+ +S P Q+ + G P E ++G
Sbjct: 226 PDKDYL----LSIPISC-PLIGVIQLAHYVVTAKLLG-----------FTPGELRSYLKG 269
Query: 186 QESVLRARAVVAYKRHAFHELYAILESHNFDSKYHAELQQL----WMRGHYKEHAKIRGR 241
+ ++ +V A AI E+ +++S + + + + +
Sbjct: 270 --ATGHSQGLVT----AV----AIAETDSWESFFVSVRKAITVLFF-------------- 305
Query: 242 DLGAVDKYRIRKKFP---LPKTIWDGEETVYCFKERSRNALKECYDKNR-YPNPDEKRQL 297
+G R + +P LP +I L++ + N P+P L
Sbjct: 306 -IG----VRCYEAYPNTSLPPSI-----------------LEDSLENNEGVPSP----ML 339
Query: 298 SEITGLTLTQVSNWFKNRRQRDRTPQQRSIQRS-RNALKECYDKNRYPNPDEKRQLSEIT 356
S I+ LT QV ++ + P + ++ S N + L ++
Sbjct: 340 S-ISNLTQEQVQDYV--NKTNSHLPAGKQVEISLVNG---------------AKNLV-VS 380
Query: 357 G--LTLTQVSNWFKNRRQRDRTPQQRAKNRTFDPYS 390
G +L ++ + + Q R P+S
Sbjct: 381 GPPQSLYGLNLTLRKAKAPSGLDQSRI------PFS 410
Score = 41.2 bits (96), Expect = 6e-04
Identities = 41/253 (16%), Positives = 79/253 (31%), Gaps = 73/253 (28%)
Query: 173 FLWSLP-PQEAIRGQE---SV--LRAR--AVVAYKRH-----AFHE-LYAILESHNFDSK 218
F LP P E + + L + V+ F + L L F++
Sbjct: 37 FNKILPEPTEGFAADDEPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTE--FENC 94
Query: 219 Y------HAELQQLWMRGHYKEHAKIRGRDLGAVDKY---RIRKKFPLPKT--------I 261
Y HA +L +E+ + + Y RI K P K +
Sbjct: 95 YLEGNDIHALAAKL-----LQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAV 149
Query: 262 WDGEETVY-----------CFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSN 310
+G + F+E L++ Y Y L + + TL+++
Sbjct: 150 GEGNAQLVAIFGGQGNTDDYFEE-----LRDLYQ--TYH--VLVGDLIKFSAETLSELI- 199
Query: 311 WFKNRRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEIT----GLTLTQVSNW 366
R ++ + N L+ + + P+ D L I + + Q++++
Sbjct: 200 -------RTTLDAEKVFTQGLNILEWLENPSNTPDKD---YLLSIPISCPLIGVIQLAHY 249
Query: 367 FKNRRQRDRTPQQ 379
+ TP +
Sbjct: 250 VVTAKLLGFTPGE 262
Score = 36.6 bits (84), Expect = 0.015
Identities = 48/307 (15%), Positives = 91/307 (29%), Gaps = 112/307 (36%)
Query: 68 YAILESHNFDSKYHAELQQLWMRGHYKEHAKIRGRDL-GYSSDD--SSPVLYETNAHDFN 124
+ +L S + A QL ++ KI G+++DD ++P E F
Sbjct: 18 HVLLVPTA--SFFIAS--QLQ-----EQFNKILPEPTEGFAADDEPTTPA--ELVGK-F- 64
Query: 125 KHYLEIQQKAQEYLNMKKLNPNMSFTPEQIDCLCEAMQQSGDFD---KLAM------FLW 175
+ + ++ + G FD L + +L
Sbjct: 65 ----------------------LGYVSSLVEP-----SKVGQFDQVLNLCLTEFENCYLE 97
Query: 176 ---------SLPPQE--AIRGQESVLRA--RAVVAYKR-------HAFHE--------LY 207
L + + + +++ A + KR A L
Sbjct: 98 GNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLV 157
Query: 208 AILESHNF-----DSKYHAELQQLWMRGHYKEHAKIRGRDLGAVDKYRIRKKF-PLPKTI 261
AI F Y EL+ L+ Y DL + + L +T
Sbjct: 158 AI-----FGGQGNTDDYFEELRDLY--QTYHVLVG----DL--IK--FSAETLSELIRTT 202
Query: 262 WDGEETVYCFKERSRNALKECYDKNRYPNPDEKRQLSEIT----GLTLTQVSNWFKNRRQ 317
D E V+ + N L+ + + P+ D L I + + Q++++ +
Sbjct: 203 LD-AEKVF---TQGLNILEWLENPSNTPDKD---YLLSIPISCPLIGVIQLAHYVVTAKL 255
Query: 318 RDRTPQQ 324
TP +
Sbjct: 256 LGFTPGE 262
Score = 33.9 bits (77), Expect = 0.11
Identities = 32/193 (16%), Positives = 65/193 (33%), Gaps = 49/193 (25%)
Query: 25 SGDFDKL--------AMFLWSLPPQEAIRGQESVLRARAVVA------YKRHAFHELYAI 70
+ L A+ L E ++ + ++ A A A Y A L ++
Sbjct: 1720 RSEKGLLSATQFTQPALTLMEKAAFEDLK-SKGLIPADATFAGHSLGEYA--A---LASL 1773
Query: 71 LESHNFDSKYHAELQQLWMRGHYKEHAKIRGRDLGYSSDDSSPVLYETNAHDFNKHYLE- 129
+ + +S E+ ++ RG + A R +LG S+ + A F++ L+
Sbjct: 1774 ADVMSIESL--VEV--VFYRGMTMQVAVPRD-ELGRSNYGMIAINPGRVAASFSQEALQY 1828
Query: 130 ----IQQKAQEYL---NMKKLN-PNM----SFTPEQIDCLCEAMQQSG----DFDKLAMF 173
+ ++ + N N N + +D + + D +L
Sbjct: 1829 VVERVGKRTGWLVEIVN---YNVENQQYVAAGDLRALDTVTNVLNFIKLQKIDIIELQK- 1884
Query: 174 LWSLPPQEAIRGQ 186
SL +E + G
Sbjct: 1885 --SLSLEE-VEGH 1894
Score = 31.9 bits (72), Expect = 0.41
Identities = 15/108 (13%), Positives = 28/108 (25%), Gaps = 49/108 (45%)
Query: 240 GRDLGAVDKYRIRKKFPLPKTIWD----------------------GEETVYCFKERSRN 277
G DL K + +W+ T++ E+ +
Sbjct: 1632 GMDL--------YKTSKAAQDVWNRADNHFKDTYGFSILDIVINNPVNLTIHFGGEKGK- 1682
Query: 278 ALKECYDKNRY-PNPDEKRQ-----------LSEIT--G----LTLTQ 307
++E Y + D K + + T L+ TQ
Sbjct: 1683 RIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQ 1730
>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 = 47.4 bits (113), Expect = 1e-07
Identities = 23/68 (33%), Positives = 31/68 (45%), Gaps = 7/68 (10%)
Query: 309 SNWFKNRRQRDR-TPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWF 367
S+ R R R T Q L++ +D N YP DE QLS + L + WF
Sbjct: 2 SSGSSGRSSRTRFTDYQL------RVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWF 55
Query: 368 KNRRQRDR 375
+N RQ+ R
Sbjct: 56 QNARQKAR 63
Score = 43.9 bits (104), Expect = 3e-06
Identities = 19/56 (33%), Positives = 27/56 (48%)
Query: 271 FKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRS 326
F + L++ +D N YP DE QLS + L + WF+N RQ+ R S
Sbjct: 14 FTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARKSGPSS 69
>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 = 46.8 bits (112), Expect = 2e-07
Identities = 18/62 (29%), Positives = 33/62 (53%), Gaps = 7/62 (11%)
Query: 313 KNRRQRDR-TPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
K+ + + +PQ R+ L+E + + + N EK ++++ G+T QV WF N+R
Sbjct: 4 KSPKGKSSISPQARAF------LEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKR 57
Query: 372 QR 373
R
Sbjct: 58 MR 59
Score = 43.7 bits (104), Expect = 2e-06
Identities = 14/42 (33%), Positives = 24/42 (57%)
Query: 277 NALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQR 318
L+E + + + N EK ++++ G+T QV WF N+R R
Sbjct: 18 AFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMR 59
>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 = 49.3 bits (117), Expect = 2e-07
Identities = 17/85 (20%), Positives = 35/85 (41%), Gaps = 3/85 (3%)
Query: 292 DEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQ 351
+E ++ L + +++++ RT ++ AL ++KN P E +
Sbjct: 69 NEAELRNQEGQQNLMEFVGGEPSKKRKRRTSFT---PQAIEALNAYFEKNPLPTGQEITE 125
Query: 352 LSEITGLTLTQVSNWFKNRRQRDRT 376
+++ V WF NRRQ +
Sbjct: 126 MAKELNYDREVVRVWFSNRRQTLKN 150
Score = 48.1 bits (114), Expect = 5e-07
Identities = 14/52 (26%), Positives = 23/52 (44%)
Query: 270 CFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRT 321
F ++ AL ++KN P E ++++ V WF NRRQ +
Sbjct: 99 SFTPQAIEALNAYFEKNPLPTGQEITEMAKELNYDREVVRVWFSNRRQTLKN 150
>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 = 47.1 bits (112), Expect = 2e-07
Identities = 14/68 (20%), Positives = 26/68 (38%), Gaps = 6/68 (8%)
Query: 309 SNWFKNRRQRDR-TPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWF 367
S+ R R + + + I +S D YP+ + LS L + +F
Sbjct: 2 SSGSSGPRSRTKISLEALGILQSFIH-----DVGLYPDQEAIHTLSAQLDLPKHTIIKFF 56
Query: 368 KNRRQRDR 375
+N+R +
Sbjct: 57 QNQRYHVK 64
Score = 42.5 bits (100), Expect = 7e-06
Identities = 9/37 (24%), Positives = 16/37 (43%)
Query: 284 DKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 320
D YP+ + LS L + +F+N+R +
Sbjct: 28 DVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVK 64
>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 = 45.0 bits (107), Expect = 8e-07
Identities = 22/71 (30%), Positives = 33/71 (46%), Gaps = 7/71 (9%)
Query: 313 KNRRQRDR-TPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
K R R +Q + L+ CY N P+ K QL E+TGL+ + WF+N+R
Sbjct: 2 KTTRVRTVLNEKQL------HTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKR 55
Query: 372 QRDRTPQQRAK 382
+D+ K
Sbjct: 56 CKDKKRSIMMK 66
Score = 45.0 bits (107), Expect = 9e-07
Identities = 18/58 (31%), Positives = 32/58 (55%), Gaps = 1/58 (1%)
Query: 271 FKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRSIQ 328
E+ + L+ CY N P+ K QL E+TGL+ + WF+N+R +D+ + ++
Sbjct: 10 LNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKK-RSIMMK 66
>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 = 49.5 bits (117), Expect = 1e-06
Identities = 42/241 (17%), Positives = 78/241 (32%), Gaps = 61/241 (25%)
Query: 136 EYLNMKKLNPNMSFTPEQIDCLCEA-MQQSGDFDKLAMF-------------LWSLPPQE 181
+++N KL + + ++ L A ++ FD+L++F +W +
Sbjct: 348 KHVNCDKLTTIIESS---LNVLEPAEYRKM--FDRLSVFPPSAHIPTILLSLIWFDVIKS 402
Query: 182 AIRGQESVLRARAVVAYKRHAFHELYAILESHNFDSKYHAE-LQQLWMRGHYKEHAKIRG 240
+ + L ++V ++ +I + + K E L H I
Sbjct: 403 DVMVVVNKLHKYSLV--EKQPKESTISIPSIY-LELKVKLENEYAL--------HRSI-- 449
Query: 241 RDLGAVDKYRIRKKFP---LPKTIWDGEETVYCFKERSRNALKECYDKNRYPNPDEKRQL 297
VD Y I K F L D Y + + LK E+ L
Sbjct: 450 -----VDHYNIPKTFDSDDLIPPYLDQ----YFYSHIGHH-LKNI-------EHPERMTL 492
Query: 298 SEITGLTLTQVSNWFKNRRQRDRTPQQRSIQRSRNALK--ECYDKNRYPN-PDEKRQLSE 354
+ L + + + + D T S N L+ + Y N P +R ++
Sbjct: 493 FRMVFLDF----RFLEQKIRHDSTAWNAS-GSILNTLQQLKFYKPYICDNDPKYERLVNA 547
Query: 355 I 355
I
Sbjct: 548 I 548
Score = 43.7 bits (102), Expect = 9e-05
Identities = 42/270 (15%), Positives = 83/270 (30%), Gaps = 86/270 (31%)
Query: 15 IDCLCEA-MQQSGDFDKLAMF-------------LWSLPPQEAIRGQESVLRARAVVAYK 60
++ L A ++ FD+L++F +W + + + L ++V +
Sbjct: 363 LNVLEPAEYRKM--FDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLV--E 418
Query: 61 RHAFHELYAILESHNFDSKYHAE-LQQLWMRGHYKEHAKIRGRD---LGYSSDDSSPVLY 116
+ +I + + K E L H I + SDD P
Sbjct: 419 KQPKESTISIPSIY-LELKVKLENEYAL--------HRSIVDHYNIPKTFDSDDLIPPYL 469
Query: 117 ETNAHDFNKHYLEIQQKAQEYLNMKKLNPNMSFTPEQIDCLCEAMQQSGDFDKLAMFLWS 176
+ + H+L+ + + + + F DF FL
Sbjct: 470 DQYFYSHIGHHLKNIEHPERMTLFRMV-----FL---------------DFR----FL-- 503
Query: 177 LPPQEAIRGQESVLRARAVVA--------YKRH------AFHEL-YAIL------ESHNF 215
++ IR + A + YK + + L AIL E +
Sbjct: 504 ---EQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLPKIEENLI 560
Query: 216 DSKYHAELQQLWM----RGHYKEHAKIRGR 241
SK + +L ++ + ++E K R
Sbjct: 561 CSK-YTDLLRIALMAEDEAIFEEAHKQVQR 589
Score = 31.7 bits (71), Expect = 0.50
Identities = 42/282 (14%), Positives = 79/282 (28%), Gaps = 66/282 (23%)
Query: 92 HYKEHAKIRGRDLGYSSDDSSPVLYETNAHDFN-KHYLEIQQKAQEYLNMKKLNPNMSFT 150
H+ H + Y D V + +F+ K ++ + +
Sbjct: 2 HHHHHMDFETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSI--------------LS 47
Query: 151 PEQIDCLCEAMQQSGDFDKLAMFLWSLPPQEAIRGQESVLRARAVVAYKRHAFHELYAIL 210
E+ID + W+L + QE + ++ F E +L
Sbjct: 48 KEEID---HIIMSKDAVSGTLRLFWTL-----LSKQEEM--------VQK--FVE--EVL 87
Query: 211 ESHNFD---SKYHAELQQLWM-RGHYKEHAKIRGRDLGAVDKY---RIRKKFPLPKTIWD 263
N+ S E +Q M Y E D KY R++ L + + +
Sbjct: 88 RI-NYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLE 146
Query: 264 GEE----TVY----CFKERSRNALKECYD---KNRYPNP---------DEKRQLSEITGL 303
+ K + AL C + + + + E+
Sbjct: 147 LRPAKNVLIDGVLGSGK--TWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQK 204
Query: 304 TLTQVSNWFKNRRQRDRTPQQRSIQRSRNALKECYDKNRYPN 345
L Q+ + +R + R I + L+ Y N
Sbjct: 205 LLYQIDPNWTSRSDHSSNIKLR-IHSIQAELRRLLKSKPYEN 245
Score = 31.0 bits (69), Expect = 0.80
Identities = 51/420 (12%), Positives = 108/420 (25%), Gaps = 157/420 (37%)
Query: 80 YHAELQQLWMRGHYK------EHAKIRGRDLGYSSDDSSPVLYETNA---------HDFN 124
+H + + + YK E A + D D +L + +
Sbjct: 5 HHMDFETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSIL--SKEEIDHIIMSKDAVS 62
Query: 125 KHY-----LEIQQK--AQEYLNMKKLNPNMSFTPEQIDCLCEAMQQSGD----------- 166
L +Q+ Q+++ + L N F I E Q S
Sbjct: 63 GTLRLFWTLLSKQEEMVQKFVE-EVLRINYKFLMSPIKT--EQRQPSMMTRMYIEQRDRL 119
Query: 167 ------FDKLAMFLWSLPPQEAIR--------------------GQESVLRARAVVAYKR 200
F K + L P +R G+ + + ++YK
Sbjct: 120 YNDNQVFAK--YNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGK-TWVALDVCLSYKV 176
Query: 201 HAF----------------HELYAILES--HNFDSKYHAELQQLWMRGHYKEHAKIRGRD 242
+ +L+ + D + + R + + K+R
Sbjct: 177 QCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTS-------RSDHSSNIKLRIHS 229
Query: 243 LGAVDKYRIRKKF---PLPKT------IWDGEETVYCFKERSR-----------NALKEC 282
+ + +R+ P + + + F + + L
Sbjct: 230 I----QAELRRLLKSKPYENCLLVLLNVQN-AKAWNAFNLSCKILLTTRFKQVTDFLSAA 284
Query: 283 YDKNRYPN-------PDEKRQL-------------SEITG---LTLTQVS-------NWF 312
+ + PDE + L E+ L+ ++ +
Sbjct: 285 TTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATW 344
Query: 313 KNRRQRDRTPQQRSIQRSRNALKECYDKNRYPN----PDEKRQLSEITGLTLTQVSNWFK 368
N + + I+ S N L+ + + P + I + L+ + WF
Sbjct: 345 DNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPS----AHIPTILLSLI--WFD 398
>2e19_A Transcription factor 8; homeobox domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 64
Score = 44.3 bits (104), Expect = 1e-06
Identities = 13/58 (22%), Positives = 26/58 (44%)
Query: 321 TPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQ 378
+ Q ++ + LK Y N P+ +E ++++ L L V WF+ + + Q
Sbjct: 5 SSGQPPLKNLLSLLKAYYALNAQPSAEELSKIADSVNLPLDVVKKWFEKMQAGQISVQ 62
Score = 40.4 bits (94), Expect = 4e-05
Identities = 15/58 (25%), Positives = 26/58 (44%), Gaps = 5/58 (8%)
Query: 273 ERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRSIQRS 330
+ + LK Y N P+ +E ++++ L L V WF+ + Q S+Q S
Sbjct: 12 KNLLSLLKAYYALNAQPSAEELSKIADSVNLPLDVVKKWFEKMQAG-----QISVQSS 64
>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 = 46.6 bits (110), Expect = 2e-06
Identities = 14/51 (27%), Positives = 25/51 (49%)
Query: 270 CFKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 320
+ R R +L+ + K+ P+ + ++ GL V WF NRRQ+ +
Sbjct: 102 SIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGK 152
Score = 45.1 bits (106), Expect = 5e-06
Identities = 15/80 (18%), Positives = 31/80 (38%), Gaps = 8/80 (10%)
Query: 304 TLTQVSNWFKNRRQRDRTPQQRSIQRSR--------NALKECYDKNRYPNPDEKRQLSEI 355
+ + N + ++ +R R +L+ + K+ P+ + ++
Sbjct: 73 WVEEADNNENLQEISKSETLVQARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQ 132
Query: 356 TGLTLTQVSNWFKNRRQRDR 375
GL V WF NRRQ+ +
Sbjct: 133 LGLEKDVVRVWFSNRRQKGK 152
>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 = 45.0 bits (106), Expect = 2e-06
Identities = 15/87 (17%), Positives = 35/87 (40%), Gaps = 22/87 (25%)
Query: 313 KNRRQRDR-TPQQRSIQRSRNALKECYDKNRYPNPDEKRQL---------------SEIT 356
R R + ++ ++ +++N+YP+ ++ ++ S++
Sbjct: 6 SGRGSRFTWRKECLAV------MESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLE 59
Query: 357 GLTLTQVSNWFKNRRQRDRTPQQRAKN 383
+T +V NWF NRR+ + A
Sbjct: 60 RVTSLKVYNWFANRRKEIKRRANIAAI 86
Score = 41.5 bits (97), Expect = 3e-05
Identities = 12/65 (18%), Positives = 32/65 (49%), Gaps = 15/65 (23%)
Query: 271 FKERSRNALKECYDKNRYPNPDEKRQL---------------SEITGLTLTQVSNWFKNR 315
+++ ++ +++N+YP+ ++ ++ S++ +T +V NWF NR
Sbjct: 14 WRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANR 73
Query: 316 RQRDR 320
R+ +
Sbjct: 74 RKEIK 78
>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 = 43.2 bits (102), Expect = 4e-06
Identities = 10/43 (23%), Positives = 25/43 (58%), Gaps = 1/43 (2%)
Query: 279 LKECYDK-NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 320
L++ + +YP+ + LS+ ++ ++ WF++RR +D+
Sbjct: 23 LEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDK 65
Score = 43.2 bits (102), Expect = 4e-06
Identities = 10/43 (23%), Positives = 25/43 (58%), Gaps = 1/43 (2%)
Query: 334 LKECYDK-NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 375
L++ + +YP+ + LS+ ++ ++ WF++RR +D+
Sbjct: 23 LEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDK 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 = 40.9 bits (96), Expect = 4e-05
Identities = 20/76 (26%), Positives = 33/76 (43%), Gaps = 9/76 (11%)
Query: 313 KNRRQRDRT---PQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKN 369
+ +R RT Q +K + N P+ + +QL++ TGLT + WF+N
Sbjct: 4 GSSGKRMRTSFKHHQL------RTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQN 57
Query: 370 RRQRDRTPQQRAKNRT 385
R + R R +N
Sbjct: 58 ARAKFRRNLLRQENGG 73
Score = 39.4 bits (92), Expect = 1e-04
Identities = 17/63 (26%), Positives = 28/63 (44%)
Query: 271 FKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRSIQRS 330
FK +K + N P+ + +QL++ TGLT + WF+N R + R R
Sbjct: 14 FKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNLLRQENGG 73
Query: 331 RNA 333
+
Sbjct: 74 VSG 76
>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 = 40.5 bits (94), Expect = 4e-05
Identities = 15/56 (26%), Positives = 22/56 (39%)
Query: 321 TPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRT 376
+ + LK Y N PN DE ++S GL V WF+ R+ +
Sbjct: 7 GSPINPYKDHMSVLKAYYAMNMEPNSDELLKISIAVGLPQEFVKEWFEQRKVYQYS 62
Score = 38.2 bits (88), Expect = 3e-04
Identities = 15/43 (34%), Positives = 20/43 (46%)
Query: 279 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRT 321
LK Y N PN DE ++S GL V WF+ R+ +
Sbjct: 20 LKAYYAMNMEPNSDELLKISIAVGLPQEFVKEWFEQRKVYQYS 62
>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 = 37.9 bits (88), Expect = 3e-04
Identities = 7/36 (19%), Positives = 17/36 (47%)
Query: 285 KNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 320
++P+ LS+ + + WF+ RR +++
Sbjct: 22 ITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEK 57
Score = 37.9 bits (88), Expect = 3e-04
Identities = 7/36 (19%), Positives = 17/36 (47%)
Query: 340 KNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 375
++P+ LS+ + + WF+ RR +++
Sbjct: 22 ITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEK 57
>2hi3_A Homeodomain-only protein; transcription; NMR {Mus musculus} SCOP:
a.4.1.1
Length = 73
Score = 37.0 bits (86), Expect = 7e-04
Identities = 12/44 (27%), Positives = 19/44 (43%)
Query: 286 NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRSIQR 329
N++P+P ++ GLT Q WFK R R + +
Sbjct: 25 NKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEGLPSEC 68
Score = 36.3 bits (84), Expect = 0.001
Identities = 12/44 (27%), Positives = 18/44 (40%)
Query: 341 NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRAKNR 384
N++P+P ++ GLT Q WFK R R +
Sbjct: 25 NKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEGLPSEC 68
>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 = 37.0 bits (86), Expect = 7e-04
Identities = 23/79 (29%), Positives = 37/79 (46%), Gaps = 7/79 (8%)
Query: 313 KNRRQRDR-TPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
RR+R T Q + L+ + K RYP+ + +++ L ++V WFKNRR
Sbjct: 6 SGRRERTTFTRAQL------DVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRR 59
Query: 372 QRDRTPQQRAKNRTFDPYS 390
+ R QQ+ +N S
Sbjct: 60 AKCRQQQQQQQNGGQSGPS 78
Score = 35.5 bits (82), Expect = 0.003
Identities = 17/63 (26%), Positives = 31/63 (49%)
Query: 271 FKERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRSIQRS 330
F + L+ + K RYP+ + +++ L ++V WFKNRR + R QQ+
Sbjct: 14 FTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQQQQQQNGG 73
Query: 331 RNA 333
++
Sbjct: 74 QSG 76
>3a03_A T-cell leukemia homeobox protein 2; homeodomain, developmental
protein, DNA-binding, N gene regulation; 1.54A {Homo
sapiens}
Length = 56
Score = 36.5 bits (85), Expect = 8e-04
Identities = 12/38 (31%), Positives = 21/38 (55%)
Query: 279 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 316
L+ + + +Y E+ L++ +T QV WF+NRR
Sbjct: 12 LERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRR 49
Score = 36.5 bits (85), Expect = 8e-04
Identities = 12/38 (31%), Positives = 21/38 (55%)
Query: 334 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
L+ + + +Y E+ L++ +T QV WF+NRR
Sbjct: 12 LERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRR 49
>3rkq_A Homeobox protein NKX-2.5; helix-turn-helix, DNA binding, nucleus,
transcription-DNA CO; 1.70A {Homo sapiens}
Length = 58
Score = 36.1 bits (84), Expect = 0.001
Identities = 16/39 (41%), Positives = 24/39 (61%)
Query: 278 ALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 316
L+ + + RY + E+ QL+ + LT TQV WF+NRR
Sbjct: 16 ELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRR 54
Score = 36.1 bits (84), Expect = 0.001
Identities = 16/39 (41%), Positives = 24/39 (61%)
Query: 333 ALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
L+ + + RY + E+ QL+ + LT TQV WF+NRR
Sbjct: 16 ELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRR 54
>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 = 36.1 bits (84), Expect = 0.001
Identities = 15/52 (28%), Positives = 24/52 (46%), Gaps = 1/52 (1%)
Query: 277 NALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRSIQ 328
L+ + N YP D L++ L L ++ WF+NRR + + R Q
Sbjct: 14 EVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKR-SHRESQ 64
Score = 36.1 bits (84), Expect = 0.001
Identities = 19/70 (27%), Positives = 28/70 (40%), Gaps = 8/70 (11%)
Query: 315 RRQRDR-TPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQR 373
RR R T Q L+ + N YP D L++ L L ++ WF+NRR +
Sbjct: 2 RRPRTAFTQNQI------EVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAK 55
Query: 374 DRTPQQRAKN 383
+ R
Sbjct: 56 LKR-SHRESQ 64
>1ftt_A TTF-1 HD, thyroid transcription factor 1 homeodomain; DNA binding
protein; NMR {Rattus norvegicus} SCOP: a.4.1.1
Length = 68
Score = 35.0 bits (81), Expect = 0.003
Identities = 13/39 (33%), Positives = 22/39 (56%)
Query: 278 ALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 316
L+ + + +Y + E+ L+ + LT TQV WF+N R
Sbjct: 16 ELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHR 54
Score = 35.0 bits (81), Expect = 0.003
Identities = 13/39 (33%), Positives = 22/39 (56%)
Query: 333 ALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
L+ + + +Y + E+ L+ + LT TQV WF+N R
Sbjct: 16 ELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHR 54
>2vi6_A Homeobox protein nanog; homeodomain, DNA-binding, transcription,
transcription facto developmental protein, transcription
regulation, NUC homeobox; 2.6A {Mus musculus}
Length = 62
Score = 35.0 bits (81), Expect = 0.003
Identities = 15/39 (38%), Positives = 25/39 (64%)
Query: 278 ALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 316
ALK+ + K +Y + + ++LS I L+ QV WF+N+R
Sbjct: 17 ALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQR 55
Score = 35.0 bits (81), Expect = 0.003
Identities = 15/39 (38%), Positives = 25/39 (64%)
Query: 333 ALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
ALK+ + K +Y + + ++LS I L+ QV WF+N+R
Sbjct: 17 ALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQR 55
>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 = 35.0 bits (81), Expect = 0.003
Identities = 23/64 (35%), Positives = 33/64 (51%), Gaps = 7/64 (10%)
Query: 313 KNRRQRDR-TPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
RRQR T QQ L+ + +NRYP+ + +++ T LT +V WFKNRR
Sbjct: 2 SQRRQRTHFTSQQL------QQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRR 55
Query: 372 QRDR 375
+ R
Sbjct: 56 AKWR 59
Score = 33.1 bits (76), Expect = 0.016
Identities = 17/53 (32%), Positives = 29/53 (54%), Gaps = 1/53 (1%)
Query: 277 NALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRSIQR 329
L+ + +NRYP+ + +++ T LT +V WFKNRR + R ++ I
Sbjct: 16 QQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK-REEFIVT 67
>1ig7_A Homeotic protein MSX-1; helix-turn-helix, transcription/DNA
complex; 2.20A {Mus musculus} SCOP: a.4.1.1
Length = 58
Score = 34.5 bits (80), Expect = 0.003
Identities = 15/39 (38%), Positives = 23/39 (58%)
Query: 278 ALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 316
AL+ + + +Y + E+ + S LT TQV WF+NRR
Sbjct: 14 ALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRR 52
Score = 34.5 bits (80), Expect = 0.003
Identities = 15/39 (38%), Positives = 23/39 (58%)
Query: 333 ALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
AL+ + + +Y + E+ + S LT TQV WF+NRR
Sbjct: 14 ALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRR 52
>2kt0_A Nanog, homeobox protein nanog; homeodomain, structural genomics,
protein structure initiative, PSI, center for eukaryotic
structural genomics; NMR {Homo sapiens}
Length = 84
Score = 35.6 bits (82), Expect = 0.003
Identities = 15/66 (22%), Positives = 29/66 (43%), Gaps = 8/66 (12%)
Query: 314 NRRQRDRTPQQRSIQRSRNA--------LKECYDKNRYPNPDEKRQLSEITGLTLTQVSN 365
N + Q++R L + + + +Y + + ++LS I L+ QV
Sbjct: 9 NSVAKKEDKVPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKT 68
Query: 366 WFKNRR 371
WF+N+R
Sbjct: 69 WFQNQR 74
Score = 34.8 bits (80), Expect = 0.005
Identities = 12/39 (30%), Positives = 23/39 (58%)
Query: 278 ALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 316
L + + + +Y + + ++LS I L+ QV WF+N+R
Sbjct: 36 VLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQR 74
>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 = 37.2 bits (85), Expect = 0.004
Identities = 20/85 (23%), Positives = 33/85 (38%), Gaps = 28/85 (32%)
Query: 313 KNRRQRDR-TPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEI---------------- 355
K RR R + P + I L + Y++ + P+ +E+ L E
Sbjct: 114 KGRRNRFKWGPASQQI------LFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQA 167
Query: 356 -----TGLTLTQVSNWFKNRRQRDR 375
+T +V NWF NRR+ +
Sbjct: 168 QGLGSNLVTEVRVYNWFANRRKEEA 192
Score = 35.6 bits (81), Expect = 0.012
Identities = 15/71 (21%), Positives = 28/71 (39%), Gaps = 21/71 (29%)
Query: 271 FKERSRNALKECYDKNRYPNPDEKRQLSEI---------------------TGLTLTQVS 309
+ S+ L + Y++ + P+ +E+ L E +T +V
Sbjct: 122 WGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVY 181
Query: 310 NWFKNRRQRDR 320
NWF NRR+ +
Sbjct: 182 NWFANRRKEEA 192
>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 = 34.6 bits (80), Expect = 0.005
Identities = 20/64 (31%), Positives = 30/64 (46%), Gaps = 7/64 (10%)
Query: 313 KNRRQRDR-TPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
RR R T +Q AL+ + + +YP+ + QL+ L +V WFKNRR
Sbjct: 6 SGRRHRTIFTDEQL------EALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRR 59
Query: 372 QRDR 375
+ R
Sbjct: 60 AKWR 63
Score = 32.7 bits (75), Expect = 0.024
Identities = 16/50 (32%), Positives = 25/50 (50%)
Query: 277 NALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRS 326
AL+ + + +YP+ + QL+ L +V WFKNRR + R S
Sbjct: 20 EALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRSGPSS 69
>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 = 34.7 bits (80), Expect = 0.005
Identities = 14/39 (35%), Positives = 22/39 (56%)
Query: 278 ALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 316
L+ + + RY + E+ L+ + LT TQV WF+N R
Sbjct: 23 ELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHR 61
Score = 34.7 bits (80), Expect = 0.005
Identities = 14/39 (35%), Positives = 22/39 (56%)
Query: 333 ALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
L+ + + RY + E+ L+ + LT TQV WF+N R
Sbjct: 23 ELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHR 61
>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 = 33.9 bits (78), Expect = 0.012
Identities = 19/64 (29%), Positives = 34/64 (53%), Gaps = 7/64 (10%)
Query: 313 KNRRQRDR-TPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
K RR R + Q + L+ +++ +YP+ + +L++ T LT ++ WF+NRR
Sbjct: 17 KQRRSRTTFSASQL------DELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRR 70
Query: 372 QRDR 375
R R
Sbjct: 71 ARLR 74
Score = 31.2 bits (71), Expect = 0.092
Identities = 14/44 (31%), Positives = 28/44 (63%)
Query: 277 NALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 320
+ L+ +++ +YP+ + +L++ T LT ++ WF+NRR R R
Sbjct: 31 DELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLR 74
>3a01_A Homeodomain-containing protein; homeodomain, protein-DNA complex,
DNA-binding, homeobox, NUC developmental protein; 2.70A
{Drosophila melanogaster}
Length = 93
Score = 34.1 bits (78), Expect = 0.013
Identities = 15/51 (29%), Positives = 23/51 (45%)
Query: 283 YDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRSIQRSRNA 333
+ K +Y E+ L+ +T QV WF+NRR + R + R A
Sbjct: 36 FHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQTAEEREAERQA 86
Score = 33.3 bits (76), Expect = 0.025
Identities = 12/34 (35%), Positives = 18/34 (52%)
Query: 338 YDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
+ K +Y E+ L+ +T QV WF+NRR
Sbjct: 36 FHKQKYLASAERAALARGLKMTDAQVKTWFQNRR 69
>2l9r_A Homeobox protein NKX-3.1; structural genomics, northeast structural
genomics consortiu PSI-biology, protein structure
initiative; NMR {Homo sapiens}
Length = 69
Score = 33.1 bits (76), Expect = 0.016
Identities = 13/34 (38%), Positives = 20/34 (58%)
Query: 283 YDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 316
+ +Y + E+ L++ LT TQV WF+NRR
Sbjct: 23 FSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRR 56
Score = 33.1 bits (76), Expect = 0.016
Identities = 13/34 (38%), Positives = 20/34 (58%)
Query: 338 YDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
+ +Y + E+ L++ LT TQV WF+NRR
Sbjct: 23 FSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRR 56
>3bdn_A Lambda repressor; repressor, allostery; HET: DNA; 3.91A
{Enterobacteria phage lambda}
Length = 236
Score = 35.7 bits (82), Expect = 0.018
Identities = 10/62 (16%), Positives = 24/62 (38%), Gaps = 3/62 (4%)
Query: 314 NRRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQR 373
+ +++ T +Q R LK Y+K + + +++ G+ + V F
Sbjct: 1 STKKKPLTQEQLEDAR---RLKAIYEKKKNELGLSQESVADKMGMGQSGVGALFNGINAL 57
Query: 374 DR 375
+
Sbjct: 58 NA 59
Score = 31.1 bits (70), Expect = 0.54
Identities = 7/42 (16%), Positives = 16/42 (38%)
Query: 279 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 320
LK Y+K + + +++ G+ + V F +
Sbjct: 18 LKAIYEKKKNELGLSQESVADKMGMGQSGVGALFNGINALNA 59
>2djn_A Homeobox protein DLX-5; structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 70
Score = 32.8 bits (75), Expect = 0.019
Identities = 16/39 (41%), Positives = 24/39 (61%)
Query: 278 ALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 316
AL+ + K +Y E+ +L+ GLT TQV WF+N+R
Sbjct: 21 ALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKR 59
Score = 32.8 bits (75), Expect = 0.019
Identities = 16/39 (41%), Positives = 24/39 (61%)
Query: 333 ALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
AL+ + K +Y E+ +L+ GLT TQV WF+N+R
Sbjct: 21 ALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKR 59
>2l7z_A Homeobox protein HOX-A13; gene regulation; NMR {Homo sapiens} PDB:
2ld5_A*
Length = 73
Score = 32.9 bits (75), Expect = 0.022
Identities = 14/45 (31%), Positives = 28/45 (62%)
Query: 341 NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRAKNRT 385
N++ D++R++S T L+ QV+ WF+NRR +++ + K +
Sbjct: 29 NKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKVINKLKTTS 73
Score = 31.0 bits (70), Expect = 0.091
Identities = 14/45 (31%), Positives = 27/45 (60%)
Query: 286 NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRSIQRS 330
N++ D++R++S T L+ QV+ WF+NRR +++ + S
Sbjct: 29 NKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKVINKLKTTS 73
>1lfb_A Liver transcription factor (LFB1); transcription regulation; 2.80A
{Rattus norvegicus} SCOP: a.4.1.1 PDB: 2lfb_A
Length = 99
Score = 33.3 bits (75), Expect = 0.027
Identities = 21/93 (22%), Positives = 36/93 (38%), Gaps = 28/93 (30%)
Query: 313 KNRRQRDR-TPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEI---------------- 355
K RR R + P + I L + Y++ + P+ +E+ L E
Sbjct: 8 KGRRNRFKWGPASQQI------LFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQA 61
Query: 356 -----TGLTLTQVSNWFKNRRQRDRTPQQRAKN 383
+T +V NWF NRR+ + + A +
Sbjct: 62 QGLGSNLVTEVRVYNWFANRRKEEAFRHKLAMD 94
Score = 32.1 bits (72), Expect = 0.064
Identities = 15/71 (21%), Positives = 28/71 (39%), Gaps = 21/71 (29%)
Query: 271 FKERSRNALKECYDKNRYPNPDEKRQLSEI---------------------TGLTLTQVS 309
+ S+ L + Y++ + P+ +E+ L E +T +V
Sbjct: 16 WGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVY 75
Query: 310 NWFKNRRQRDR 320
NWF NRR+ +
Sbjct: 76 NWFANRRKEEA 86
>2cue_A Paired box protein PAX6; homeobox domain, transcription factor,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
a.4.1.1
Length = 80
Score = 32.8 bits (75), Expect = 0.027
Identities = 17/72 (23%), Positives = 35/72 (48%), Gaps = 8/72 (11%)
Query: 313 KNRRQRDR-TPQQRSIQRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
+R R T +Q AL++ +++ YP+ + +L+ L ++ WF NRR
Sbjct: 6 SGQRNRTSFTQEQI------EALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRR 59
Query: 372 QRDRTPQQRAKN 383
+ R +++ +N
Sbjct: 60 AKWRR-EEKLRN 70
Score = 31.2 bits (71), Expect = 0.081
Identities = 14/57 (24%), Positives = 30/57 (52%)
Query: 277 NALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRSIQRSRNA 333
AL++ +++ YP+ + +L+ L ++ WF NRR + R ++ QR ++
Sbjct: 20 EALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKLRNQRRQSG 76
>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo,
protein-DNA, human disease; 3.20A {Homo sapiens}
Length = 221
Score = 34.2 bits (77), Expect = 0.048
Identities = 24/111 (21%), Positives = 39/111 (35%), Gaps = 30/111 (27%)
Query: 289 PNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRT---PQQRSIQRSRNALKECYDKNRYPN 345
E Q S G + S + +R+R P + I L + YD+ + P+
Sbjct: 115 FLFPEFSQQSHGPGQSDDACSEPTNKKMRRNRFKWGPASQQI------LYQAYDRQKNPS 168
Query: 346 PDEKRQLSEI---------------------TGLTLTQVSNWFKNRRQRDR 375
+E+ L E +T +V NWF NRR+ +
Sbjct: 169 KEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRRKEEA 219
Score = 34.2 bits (77), Expect = 0.050
Identities = 16/71 (22%), Positives = 28/71 (39%), Gaps = 21/71 (29%)
Query: 271 FKERSRNALKECYDKNRYPNPDEKRQLSEI---------------------TGLTLTQVS 309
+ S+ L + YD+ + P+ +E+ L E +T +V
Sbjct: 149 WGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVY 208
Query: 310 NWFKNRRQRDR 320
NWF NRR+ +
Sbjct: 209 NWFANRRKEEA 219
>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 = 32.0 bits (73), Expect = 0.048
Identities = 14/55 (25%), Positives = 24/55 (43%), Gaps = 1/55 (1%)
Query: 277 NALKECYDK-NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRSIQRS 330
L+ ++K N++P+P ++ GLT Q WFK R R + +
Sbjct: 14 EILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEGLPSECR 68
Score = 31.6 bits (72), Expect = 0.053
Identities = 14/45 (31%), Positives = 22/45 (48%), Gaps = 1/45 (2%)
Query: 332 NALKECYDK-NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 375
L+ ++K N++P+P ++ GLT Q WFK R R
Sbjct: 14 EILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWR 58
>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 = 31.4 bits (72), Expect = 0.050
Identities = 13/44 (29%), Positives = 25/44 (56%)
Query: 277 NALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 320
L++ + + YP+ + +L+ GLT ++ WF+NRR + R
Sbjct: 12 EELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWR 55
Score = 31.4 bits (72), Expect = 0.050
Identities = 13/44 (29%), Positives = 25/44 (56%)
Query: 332 NALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 375
L++ + + YP+ + +L+ GLT ++ WF+NRR + R
Sbjct: 12 EELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWR 55
>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 = 31.2 bits (71), Expect = 0.069
Identities = 12/31 (38%), Positives = 22/31 (70%)
Query: 286 NRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 316
+Y +P E+++L+++ L+ QV WF+NRR
Sbjct: 29 QKYLSPPERKRLAKMLQLSERQVKTWFQNRR 59
Score = 31.2 bits (71), Expect = 0.069
Identities = 12/31 (38%), Positives = 22/31 (70%)
Query: 341 NRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
+Y +P E+++L+++ L+ QV WF+NRR
Sbjct: 29 QKYLSPPERKRLAKMLQLSERQVKTWFQNRR 59
>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 = 31.3 bits (71), Expect = 0.088
Identities = 12/34 (35%), Positives = 22/34 (64%)
Query: 283 YDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 316
++K +Y + ++ L+E GL+ QV W++NRR
Sbjct: 36 FEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRR 69
Score = 31.3 bits (71), Expect = 0.088
Identities = 12/34 (35%), Positives = 22/34 (64%)
Query: 338 YDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
++K +Y + ++ L+E GL+ QV W++NRR
Sbjct: 36 FEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRR 69
>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 = 31.8 bits (71), Expect = 0.17
Identities = 12/38 (31%), Positives = 16/38 (42%), Gaps = 11/38 (28%)
Query: 83 ELQQLWMRGHYKEHAKIRGRDLGYSSDDSSPVLYETNA 120
E Q L K K++ L +DDS+P L A
Sbjct: 18 EKQAL------K---KLQAS-LKLYADDSAPAL-AIKA 44
Score = 27.2 bits (59), Expect = 5.4
Identities = 5/31 (16%), Positives = 15/31 (48%), Gaps = 7/31 (22%)
Query: 323 QQRSIQRSRNALKECYDKNRYPNPDEKRQLS 353
+++++++ + +LK Y D L+
Sbjct: 18 EKQALKKLQASLK------LYA-DDSAPALA 41
>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 = 30.2 bits (68), Expect = 0.19
Identities = 13/41 (31%), Positives = 26/41 (63%)
Query: 286 NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRS 326
N++ D++R++S T L+ Q++ WF+NRR +++ S
Sbjct: 29 NKFITKDKRRKISAATSLSERQITIWFQNRRVKEKKSGPSS 69
Score = 29.4 bits (66), Expect = 0.31
Identities = 12/31 (38%), Positives = 22/31 (70%)
Query: 341 NRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
N++ D++R++S T L+ Q++ WF+NRR
Sbjct: 29 NKFITKDKRRKISAATSLSERQITIWFQNRR 59
>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 = 29.7 bits (67), Expect = 0.25
Identities = 15/45 (33%), Positives = 21/45 (46%)
Query: 341 NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRAKNRT 385
RY LS L QV WFKNRR+R + + K+++
Sbjct: 24 GRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSDQHKDQS 68
Score = 28.9 bits (65), Expect = 0.44
Identities = 15/45 (33%), Positives = 19/45 (42%)
Query: 286 NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRSIQRS 330
RY LS L QV WFKNRR+R + + +S
Sbjct: 24 GRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSDQHKDQS 68
>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 = 29.5 bits (65), Expect = 0.33
Identities = 10/66 (15%), Positives = 22/66 (33%), Gaps = 4/66 (6%)
Query: 314 NRRQRDRTPQQRSIQRSRNALKECYDKN----RYPNPDEKRQLSEITGLTLTQVSNWFKN 369
+ + + R LK+ +D ++ ++ + V W N
Sbjct: 3 SGSSGALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIGN 62
Query: 370 RRQRDR 375
RR++ R
Sbjct: 63 RRRKYR 68
Score = 28.8 bits (63), Expect = 0.79
Identities = 11/54 (20%), Positives = 21/54 (38%), Gaps = 4/54 (7%)
Query: 271 FKERSRNALKECYDKN----RYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 320
F +R LK+ +D ++ ++ + V W NRR++ R
Sbjct: 15 FSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIGNRRRKYR 68
>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 = 29.8 bits (66), Expect = 0.44
Identities = 17/78 (21%), Positives = 32/78 (41%), Gaps = 21/78 (26%)
Query: 271 FKERSRNALKECYDKNRYPNPDEKRQLSEI---------------------TGLTLTQVS 309
+ S+ L + YD+ + P+ +E+ L E +T +V
Sbjct: 13 WGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVY 72
Query: 310 NWFKNRRQRDRTPQQRSI 327
NWF NRR+ + Q+ ++
Sbjct: 73 NWFANRRKEEAFRQKLAM 90
Score = 29.1 bits (64), Expect = 0.86
Identities = 18/75 (24%), Positives = 31/75 (41%), Gaps = 21/75 (28%)
Query: 330 SRNALKECYDKNRYPNPDEKRQLSEI---------------------TGLTLTQVSNWFK 368
S+ L + YD+ + P+ +E+ L E +T +V NWF
Sbjct: 17 SQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFA 76
Query: 369 NRRQRDRTPQQRAKN 383
NRR+ + Q+ A +
Sbjct: 77 NRRKEEAFRQKLAMD 91
>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 = 28.4 bits (64), Expect = 0.52
Identities = 16/38 (42%), Positives = 23/38 (60%)
Query: 279 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 316
LK +++NRY ++QLS GL Q+ WFKN+R
Sbjct: 18 LKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKR 55
Score = 28.4 bits (64), Expect = 0.52
Identities = 16/38 (42%), Positives = 23/38 (60%)
Query: 334 LKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
LK +++NRY ++QLS GL Q+ WFKN+R
Sbjct: 18 LKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKR 55
>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 = 28.7 bits (64), Expect = 0.74
Identities = 12/43 (27%), Positives = 22/43 (51%)
Query: 286 NRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRSIQ 328
N Y D + +++ + LT QV WF+NRR + + + +
Sbjct: 35 NMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINKDRAK 77
Score = 27.9 bits (62), Expect = 1.4
Identities = 12/31 (38%), Positives = 18/31 (58%)
Query: 341 NRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
N Y D + +++ + LT QV WF+NRR
Sbjct: 35 NMYLTRDRRYEVARLLNLTERQVKIWFQNRR 65
>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 = 30.2 bits (68), Expect = 1.3
Identities = 14/49 (28%), Positives = 28/49 (57%)
Query: 272 KERSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 320
++R L++ + + + N EK ++++ G+T QV WF N+R R +
Sbjct: 373 SPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 421
Score = 29.8 bits (67), Expect = 1.7
Identities = 14/48 (29%), Positives = 28/48 (58%)
Query: 328 QRSRNALKECYDKNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 375
++R L++ + + + N EK ++++ G+T QV WF N+R R +
Sbjct: 374 PQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 421
>2ii2_A Alpha-11 giardin; helix-turn-helix, metal binding protein; 1.10A
{Giardia intestinalis} PDB: 2iic_A
Length = 310
Score = 29.4 bits (66), Expect = 1.7
Identities = 8/96 (8%), Positives = 22/96 (22%), Gaps = 20/96 (20%)
Query: 25 SGDFDKLAMFLWSLPPQ-------EAIRG--QESVL------RARAVVAYKRHAFHELYA 69
+G ++ + W +A++ + A+ E
Sbjct: 62 NGPYEDVMALGWDCNISARVNVIKKAMKNVNDFRAIHDVVLIATPDERLKLAQAYKEKTG 121
Query: 70 I-----LESHNFDSKYHAELQQLWMRGHYKEHAKIR 100
+ + L L +R + +
Sbjct: 122 NDLLQDFVDQIPLTSAASYLCHLAIRENRTPRGSVA 157
Score = 29.4 bits (66), Expect = 1.7
Identities = 8/96 (8%), Positives = 22/96 (22%), Gaps = 20/96 (20%)
Query: 164 SGDFDKLAMFLWSLPPQ-------EAIRG--QESVL------RARAVVAYKRHAFHELYA 208
+G ++ + W +A++ + A+ E
Sbjct: 62 NGPYEDVMALGWDCNISARVNVIKKAMKNVNDFRAIHDVVLIATPDERLKLAQAYKEKTG 121
Query: 209 I-----LESHNFDSKYHAELQQLWMRGHYKEHAKIR 239
+ + L L +R + +
Sbjct: 122 NDLLQDFVDQIPLTSAASYLCHLAIRENRTPRGSVA 157
>1sig_A Sigma70, RNA polymerase primary sigma factor; RNA polymerase sigma
factor, transcription regulation; 2.60A {Escherichia
coli} SCOP: a.177.1.1
Length = 339
Score = 29.1 bits (65), Expect = 2.8
Identities = 18/118 (15%), Positives = 35/118 (29%), Gaps = 23/118 (19%)
Query: 124 NKHYLEIQQKAQEYLNMKKLNPNMSFTPEQIDCLCEAMQQSGDFDKLAMFLWSLPPQEAI 183
+ E K E +L P Q D L +M+ + +
Sbjct: 133 HATAQEEILKLSEVFKQFRLVPK------QFDYLVNSMRVM---------------MDRV 171
Query: 184 RGQESVLRARAVVAYK--RHAFHELYAILESHNFDSKYHAELQQLWMRGHYKEHAKIR 239
R QE ++ V K + F L+ E+ + + + W + ++
Sbjct: 172 RTQERLIMKLCVEQCKMPKKNFITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVH 229
>2h1k_A IPF-1, pancreatic and duodenal homeobox 1, homeodomain; protein-DNA
complex, transcription/DNA complex; 2.42A {Mesocricetus
auratus}
Length = 63
Score = 26.2 bits (58), Expect = 3.6
Identities = 10/31 (32%), Positives = 18/31 (58%)
Query: 286 NRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 316
N+Y + + +L+ + LT + WF+NRR
Sbjct: 25 NKYISRPRRVELAVMLNLTERHIKIWFQNRR 55
Score = 26.2 bits (58), Expect = 3.6
Identities = 10/31 (32%), Positives = 18/31 (58%)
Query: 341 NRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
N+Y + + +L+ + LT + WF+NRR
Sbjct: 25 NKYISRPRRVELAVMLNLTERHIKIWFQNRR 55
>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 = 26.2 bits (58), Expect = 3.8
Identities = 10/36 (27%), Positives = 19/36 (52%)
Query: 285 KNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 320
K Y + + +L+ L + + WF+NRR +D+
Sbjct: 22 KENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDK 57
Score = 26.2 bits (58), Expect = 3.8
Identities = 10/36 (27%), Positives = 19/36 (52%)
Query: 340 KNRYPNPDEKRQLSEITGLTLTQVSNWFKNRRQRDR 375
K Y + + +L+ L + + WF+NRR +D+
Sbjct: 22 KENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDK 57
>3a4u_B Multiple coagulation factor deficiency protein 2; lectin, ergic,
ER, golgi, transport, disulfide bond, endopla reticulum,
ER-golgi transport; 1.84A {Homo sapiens} PDB: 2vrg_A
3lcp_C
Length = 143
Score = 27.2 bits (60), Expect = 5.0
Identities = 9/84 (10%), Positives = 26/84 (30%), Gaps = 4/84 (4%)
Query: 90 RGHYKEHAKIRGRDLGYSSDDSSPVLYETNAHDFNKH----YLEIQQKAQEYLNMKKLNP 145
+ H EH + L+ HD++ + LE+ +
Sbjct: 46 QEHIMEHLEGVINKPEAEMSPQELQLHYFKMHDYDGNNLLDGLELSTAITHVHKEEGSEQ 105
Query: 146 NMSFTPEQIDCLCEAMQQSGDFDK 169
+ +++ + + + + D +
Sbjct: 106 APLMSEDELINIIDGVLRDDDKNN 129
>2r5y_A Homeotic protein sex combs reduced; homeodomain; HET: DNA; 2.60A
{Drosophila melanogaster} PDB: 2r5z_A*
Length = 88
Score = 26.4 bits (58), Expect = 5.3
Identities = 11/31 (35%), Positives = 17/31 (54%)
Query: 286 NRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 316
NRY + +++ LT Q+ WF+NRR
Sbjct: 50 NRYLTRRRRIEIAHALSLTERQIKIWFQNRR 80
Score = 26.4 bits (58), Expect = 5.3
Identities = 11/31 (35%), Positives = 17/31 (54%)
Query: 341 NRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
NRY + +++ LT Q+ WF+NRR
Sbjct: 50 NRYLTRRRRIEIAHALSLTERQIKIWFQNRR 80
>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 = 26.8 bits (59), Expect = 5.3
Identities = 11/31 (35%), Positives = 18/31 (58%)
Query: 286 NRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 316
N+Y + + +++ L TQV WF+NRR
Sbjct: 56 NKYLSRARRVEIAATLELNETQVKIWFQNRR 86
Score = 26.8 bits (59), Expect = 5.3
Identities = 11/31 (35%), Positives = 18/31 (58%)
Query: 341 NRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
N+Y + + +++ L TQV WF+NRR
Sbjct: 56 NKYLSRARRVEIAATLELNETQVKIWFQNRR 86
>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 = 25.8 bits (57), Expect = 5.7
Identities = 11/31 (35%), Positives = 17/31 (54%)
Query: 286 NRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 316
NRY + +++ LT Q+ WF+NRR
Sbjct: 24 NRYLTRRRRIEIAHALSLTERQIKIWFQNRR 54
Score = 25.8 bits (57), Expect = 5.7
Identities = 11/31 (35%), Positives = 17/31 (54%)
Query: 341 NRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
NRY + +++ LT Q+ WF+NRR
Sbjct: 24 NRYLTRRRRIEIAHALSLTERQIKIWFQNRR 54
>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 = 26.3 bits (58), Expect = 5.7
Identities = 10/31 (32%), Positives = 16/31 (51%)
Query: 286 NRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 316
N Y + +++ LT Q+ WF+NRR
Sbjct: 42 NHYLTRRRRIEMAHALSLTERQIKIWFQNRR 72
Score = 26.3 bits (58), Expect = 5.7
Identities = 10/31 (32%), Positives = 16/31 (51%)
Query: 341 NRYPNPDEKRQLSEITGLTLTQVSNWFKNRR 371
N Y + +++ LT Q+ WF+NRR
Sbjct: 42 NHYLTRRRRIEMAHALSLTERQIKIWFQNRR 72
>3qho_A Endoglucanase, 458AA long hypothetical endo-1,4-beta-glucanase;
cellulase, catalytic domain, hydrolase; HET: CTT; 1.65A
{Pyrococcus horikoshii} PDB: 3axx_A* 2zum_A 2zun_A*
3qhm_A* 3qhn_A*
Length = 458
Score = 27.9 bits (61), Expect = 5.8
Identities = 21/192 (10%), Positives = 50/192 (26%), Gaps = 23/192 (11%)
Query: 65 HELYAILESHNFDSKYHAEL-------QQLWMRG------HYKEHAKIRGRDL-----GY 106
++ +L+ H + L ++ ++ + ++ + G DL
Sbjct: 146 LGIFVLLDYHRIGCTHIEPLWYTEDFSEEDFINTWIEVAKRFGKYWNVIGADLKNEPHSV 205
Query: 107 SSDDSSPVLYETNAHDFNKHYLEIQQKAQEYLN-MKKLNPNMSFTPEQIDCLCEAMQQSG 165
+S ++ + A+ + K+ P+ E ++
Sbjct: 206 TSPPAAYTDGTGATWGMGNPATDWNLAAERIGKAILKVAPHWLIFVEGTQF---TNPKTD 262
Query: 166 DFDKLAMFLWSLPPQEAIRGQESVLRARAVVAYKRHAFHELYAILESHNFDSKYHAELQQ 225
K W A++ L +V Y H F + L
Sbjct: 263 SSYKWGYNAWWGGNLMAVKDYPVNLPRNKLV-YSPHVFGPDVYNQPYFGPAKGFPDNLPD 321
Query: 226 LWMRGHYKEHAK 237
+W +
Sbjct: 322 IWYHHFGYVKLE 333
>3iyd_F RNA polymerase sigma factor RPOD; transcription, initiation, class
I, activator, RNA polymeras holoenzyme, sigma70, open
complex, CAP, CRP; HET: DNA CMP; 19.80A {Escherichia
coli k-12}
Length = 613
Score = 27.7 bits (61), Expect = 7.9
Identities = 26/179 (14%), Positives = 54/179 (30%), Gaps = 29/179 (16%)
Query: 115 LYETNAHDFNKHYLEIQQKAQEYLNMKKLNPNMSFTPEQIDCLCEAMQQSGDFDKLAMFL 174
Y +E L + ++ P+Q D L +M+ D
Sbjct: 227 QYVVTRDTIKAKGRSHATAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDR------- 279
Query: 175 WSLPPQEAIRGQESVLRARAVVAYK--RHAFHELYAILESHNFDSKYHAELQQLWMRGHY 232
+R QE ++ V K + F L+ E+ + + + W +
Sbjct: 280 --------VRTQERLIMKLCVEQCKMPKKNFITLFTGNETSDTWFNAAIAMNKPWSEKLH 331
Query: 233 KEHAKIRG-----RDLGAVDKYRIRKKFPLPKTIWDGEETVYCFKERSRNALKECYDKN 286
++ + + I + + + + GE ++R A KE + N
Sbjct: 332 DVSEEVHRALQKLQQIEEETGLTIEQVKDINRRMSIGE-------AKARRAKKEMVEAN 383
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 27.0 bits (59), Expect = 7.9
Identities = 13/95 (13%), Positives = 24/95 (25%), Gaps = 33/95 (34%)
Query: 291 PDEKRQLSEITGLTLTQVSNWFKNRRQRDRTPQQRSIQRSRNALKECYDKNRYPNPDEKR 350
D Q E + W R ++ + Q+ D K
Sbjct: 77 ADRLTQEPE-------SIRKW---REEQRKRLQEL-------------DAA------SKV 107
Query: 351 QLSEITGLTLTQVSNWFKNRR-QRDRTPQQRAKNR 384
E + W + + Q ++ + NR
Sbjct: 108 MEQEWREKAKKDLEEWNQRQSEQVEKN---KINNR 139
>3oa2_A WBPB; oxidoreductase, sugar biosynthesis, dehydrogenase; HET: NAD;
1.50A {Pseudomonas aeruginosa}
Length = 318
Score = 27.2 bits (60), Expect = 10.0
Identities = 13/89 (14%), Positives = 23/89 (25%), Gaps = 11/89 (12%)
Query: 40 PQEAIRGQESVLRARAVVAY---KRH--AFHELYAILESHNFDSKYHAELQQLWMRGHYK 94
P+ + + RH A L + KY +L + RG++
Sbjct: 110 PEMLDQLAVIERETDKRLYNILQLRHHQAIIALKDKVAREKSPHKYEVDLTYITSRGNWY 169
Query: 95 EHAKIRGRDLGYSSDDSSPVLYETNAHDF 123
+ S V H +
Sbjct: 170 LKSWKGDP------RKSFGVATNIGVHFY 192
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
0.319 0.133 0.406
Gapped
Lambda K H
0.267 0.0504 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 6,146,074
Number of extensions: 367062
Number of successful extensions: 1191
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1177
Number of HSP's successfully gapped: 191
Length of query: 390
Length of database: 6,701,793
Length adjustment: 95
Effective length of query: 295
Effective length of database: 4,049,298
Effective search space: 1194542910
Effective search space used: 1194542910
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 58 (26.7 bits)