BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= psy4325
(306 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2JTN|A Chain A, Nmr Solution Structure Of A Ldb1-Lid:lhx3-Lim Complex
Length = 182
Score = 198 bits (504), Expect = 3e-51, Method: Compositional matrix adjust.
Identities = 88/123 (71%), Positives = 102/123 (82%)
Query: 69 SIPKCGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCFARNGLLFCKEDFFKRF 128
IP C GC ILDRFILK L+R WH++CLKC +C PLAE+CF+R ++CK+DFFKRF
Sbjct: 59 EIPMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERCFSRGESVYCKDDFFKRF 118
Query: 129 GTKCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDYE 188
GTKCA C++GIPPTQVVRRAQD VYHL+CFACV+C RQL TGDEFYLMED +LVCK DYE
Sbjct: 119 GTKCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYE 178
Query: 189 AAK 191
AK
Sbjct: 179 TAK 181
>pdb|2RGT|A Chain A, Crystal Structure Of Lhx3 Lim Domains 1 And 2 With The
Binding Domain Of Isl1
pdb|2RGT|B Chain B, Crystal Structure Of Lhx3 Lim Domains 1 And 2 With The
Binding Domain Of Isl1
Length = 169
Score = 197 bits (502), Expect = 4e-51, Method: Compositional matrix adjust.
Identities = 88/122 (72%), Positives = 102/122 (83%)
Query: 70 IPKCGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCFARNGLLFCKEDFFKRFG 129
IP C GC ILDRFILK L+R WH++CLKC +C PLAE+CF+R ++CK+DFFKRFG
Sbjct: 6 IPMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERCFSRGESVYCKDDFFKRFG 65
Query: 130 TKCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDYEA 189
TKCA C++GIPPTQVVRRAQD VYHL+CFACV+C RQL TGDEFYLMED +LVCK DYE
Sbjct: 66 TKCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYET 125
Query: 190 AK 191
AK
Sbjct: 126 AK 127
>pdb|3MMK|A Chain A, The Structural Basis For Partial Redundancy In A Class Of
Transcription Factors, The Lim-Homeodomain Proteins, In
Neural Cell Type Specification
pdb|3MMK|B Chain B, The Structural Basis For Partial Redundancy In A Class Of
Transcription Factors, The Lim-Homeodomain Proteins, In
Neural Cell Type Specification
Length = 169
Score = 193 bits (491), Expect = 9e-50, Method: Compositional matrix adjust.
Identities = 85/125 (68%), Positives = 102/125 (81%)
Query: 67 IASIPKCGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCFARNGLLFCKEDFFK 126
+ IP+C GC ILD+FILKVL+R WH+ CLKC +C LA++CF+R G ++CKEDFFK
Sbjct: 3 MQQIPQCAGCNQHILDKFILKVLDRHWHSSCLKCADCQMQLADRCFSRAGSVYCKEDFFK 62
Query: 127 RFGTKCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPD 186
RFGTKC C+ GIPPTQVVR+AQD VYHL+CFAC++C RQL TGDEFYLMED +LVCK D
Sbjct: 63 RFGTKCTACQQGIPPTQVVRKAQDFVYHLHCFACIICNRQLATGDEFYLMEDGRLVCKED 122
Query: 187 YEAAK 191
YE AK
Sbjct: 123 YETAK 127
>pdb|2DFY|X Chain X, Crystal Structure Of A Cyclized Protein Fusion Of Lmo4 Lim
Domains 1 And 2 With The Lim Interacting Domain Of Ldb1
pdb|2DFY|C Chain C, Crystal Structure Of A Cyclized Protein Fusion Of Lmo4 Lim
Domains 1 And 2 With The Lim Interacting Domain Of Ldb1
Length = 195
Score = 102 bits (253), Expect = 3e-22, Method: Compositional matrix adjust.
Identities = 49/127 (38%), Positives = 72/127 (56%), Gaps = 6/127 (4%)
Query: 69 SIPKCGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAE---KCFARNGLLFCKEDFF 125
S +C GCG I DRF+L ++ WH+RCLKC C A L + + ++G++ C+ D+
Sbjct: 2 SWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYI 61
Query: 126 KRFGTK--CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVC 183
+ FG C+ C IP +++V RAQ VYHL CF C C +L GD F+ + + L C
Sbjct: 62 RLFGNSGACSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNRLVPGDRFHYI-NGSLFC 120
Query: 184 KPDYEAA 190
+ D A
Sbjct: 121 EHDRPTA 127
Score = 29.3 bits (64), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 26/67 (38%), Gaps = 1/67 (1%)
Query: 131 KCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDYEAA 190
+CAGC G + + A D +H C C C QL + ++C+ DY
Sbjct: 5 RCAGCG-GKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRL 63
Query: 191 KAKDGNC 197
G C
Sbjct: 64 FGNSGAC 70
>pdb|1RUT|X Chain X, Complex Of Lmo4 Lim Domains 1 And 2 With The Ldb1 Lid
Domain
Length = 188
Score = 102 bits (253), Expect = 4e-22, Method: Compositional matrix adjust.
Identities = 49/127 (38%), Positives = 72/127 (56%), Gaps = 6/127 (4%)
Query: 69 SIPKCGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAE---KCFARNGLLFCKEDFF 125
S +C GCG I DRF+L ++ WH+RCLKC C A L + + ++G++ C+ D+
Sbjct: 4 SWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYI 63
Query: 126 KRFGTK--CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVC 183
+ FG C+ C IP +++V RAQ VYHL CF C C +L GD F+ + + L C
Sbjct: 64 RLFGNSGACSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNRLVPGDRFHYI-NGSLFC 122
Query: 184 KPDYEAA 190
+ D A
Sbjct: 123 EHDRPTA 129
Score = 29.3 bits (64), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 26/67 (38%), Gaps = 1/67 (1%)
Query: 131 KCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDYEAA 190
+CAGC G + + A D +H C C C QL + ++C+ DY
Sbjct: 7 RCAGCG-GKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRL 65
Query: 191 KAKDGNC 197
G C
Sbjct: 66 FGNSGAC 72
>pdb|2XJY|A Chain A, Crystal Structure Of The Lmo2:ldb1-Lid Complex, P21
Crystal Form
pdb|2XJZ|A Chain A, Crystal Structure Of The Lmo2:ldb1-Lid Complex, C2 Crystal
Form
pdb|2XJZ|B Chain B, Crystal Structure Of The Lmo2:ldb1-Lid Complex, C2 Crystal
Form
pdb|2XJZ|C Chain C, Crystal Structure Of The Lmo2:ldb1-Lid Complex, C2 Crystal
Form
pdb|2XJZ|D Chain D, Crystal Structure Of The Lmo2:ldb1-Lid Complex, C2 Crystal
Form
pdb|2XJZ|E Chain E, Crystal Structure Of The Lmo2:ldb1-Lid Complex, C2 Crystal
Form
Length = 131
Score = 86.3 bits (212), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 48/129 (37%), Positives = 68/129 (52%), Gaps = 7/129 (5%)
Query: 69 SIPKCGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAE---KCFARNGLLFCKEDFF 125
S+ CGGC I DR+ LK +++ WH CL C CG L E + + + G C+ D+
Sbjct: 1 SLLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYL 60
Query: 126 KRFGTK--CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVC 183
+ FG CA C+ I ++ R +D VYHL CF C C + GD YL+ + +VC
Sbjct: 61 RLFGQDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCVGDR-YLLINSDIVC 119
Query: 184 KPD-YEAAK 191
+ D YE K
Sbjct: 120 EQDIYEWTK 128
>pdb|2DA3|A Chain A, Solution Structure Of The Third Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 80
Score = 63.2 bits (152), Expect = 2e-10, Method: Composition-based stats.
Identities = 30/66 (45%), Positives = 41/66 (62%)
Query: 202 QPNKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKR 261
Q +KR RTTIT +QLE L Y P R + + ++ + GL RVVQVWFQN RA+E++
Sbjct: 15 QRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERK 74
Query: 262 LKKDAG 267
+G
Sbjct: 75 SGPSSG 80
>pdb|2L4Z|A Chain A, Nmr Structure Of Fusion Of Ctip (641-685) To Lmo4-Lim1
(18-82)
Length = 123
Score = 62.8 bits (151), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 24/61 (39%), Positives = 38/61 (62%), Gaps = 3/61 (4%)
Query: 72 KCGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAE---KCFARNGLLFCKEDFFKRF 128
+C GCG I DRF+L ++ WH+RCLKC C A L + + ++G++ C+ D+ + F
Sbjct: 63 RCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLF 122
Query: 129 G 129
G
Sbjct: 123 G 123
Score = 28.5 bits (62), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 24/57 (42%), Gaps = 1/57 (1%)
Query: 131 KCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDY 187
+CAGC G + + A D +H C C C QL + ++C+ DY
Sbjct: 63 RCAGCG-GKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDY 118
>pdb|1M3V|A Chain A, Flin4: Fusion Of The Lim Binding Domain Of Ldb1 And The N-
Terminal Lim Domain Of Lmo4
Length = 122
Score = 60.1 bits (144), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 24/63 (38%), Positives = 38/63 (60%), Gaps = 3/63 (4%)
Query: 69 SIPKCGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAE---KCFARNGLLFCKEDFF 125
S +C GCG I DRF+L ++ WH+RCLKC C A L + + ++G++ C+ D+
Sbjct: 4 SWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYI 63
Query: 126 KRF 128
+ F
Sbjct: 64 RLF 66
Score = 28.5 bits (62), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 24/57 (42%), Gaps = 1/57 (1%)
Query: 131 KCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDY 187
+CAGC G + + A D +H C C C QL + ++C+ DY
Sbjct: 7 RCAGCG-GKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDY 62
>pdb|1BW5|A Chain A, The Nmr Solution Structure Of The Homeodomain Of The Rat
Insulin Gene Enhancer Protein Isl-1, 50 Structures
Length = 66
Score = 58.2 bits (139), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 27/56 (48%), Positives = 39/56 (69%)
Query: 206 RPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKR 261
R RT + KQL TL+ Y +P+P ++EQL + TGL RV++VWFQN+R K+K+
Sbjct: 5 RVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKK 60
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant R31lE42L
Length = 67
Score = 56.2 bits (134), Expect = 2e-08, Method: Composition-based stats.
Identities = 24/62 (38%), Positives = 38/62 (61%)
Query: 205 KRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKK 264
+RPRT T Q+E L+ + + P + E L+Q L++ +Q+WFQNRRAK KR +
Sbjct: 2 RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHR 61
Query: 265 DA 266
++
Sbjct: 62 ES 63
>pdb|1FJL|A Chain A, Homeodomain From The Drosophila Paired Protein Bound To A
Dna Oligonucleotide
pdb|1FJL|B Chain B, Homeodomain From The Drosophila Paired Protein Bound To A
Dna Oligonucleotide
pdb|1FJL|C Chain C, Homeodomain From The Drosophila Paired Protein Bound To A
Dna Oligonucleotide
Length = 81
Score = 54.7 bits (130), Expect = 6e-08, Method: Composition-based stats.
Identities = 25/57 (43%), Positives = 38/57 (66%)
Query: 205 KRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKR 261
+R RTT +A QL+ L+ A+ + P + RE+L+Q T L +QVWFQNRRA+ ++
Sbjct: 19 RRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRK 75
>pdb|3A01|B Chain B, Crystal Structure Of Aristaless And Clawless Homeodomains
Bo
pdb|3A01|F Chain F, Crystal Structure Of Aristaless And Clawless Homeodomains
Bo
Length = 67
Score = 54.3 bits (129), Expect = 8e-08, Method: Composition-based stats.
Identities = 27/60 (45%), Positives = 39/60 (65%)
Query: 205 KRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKK 264
+R RTT T+ QLE L+ A++ + P RE+L+ GL +QVWFQNRRAK ++ +K
Sbjct: 7 RRYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQEK 66
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 53.5 bits (127), Expect = 1e-07, Method: Composition-based stats.
Identities = 26/57 (45%), Positives = 37/57 (64%)
Query: 205 KRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKR 261
+R RTT TA+QLE L+ A+ + P + RE+L+Q L VQVWF NRRA+ ++
Sbjct: 3 RRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRARWRK 59
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 53.1 bits (126), Expect = 2e-07, Method: Composition-based stats.
Identities = 26/56 (46%), Positives = 36/56 (64%)
Query: 206 RPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKR 261
R RTT T+ QLE L+ A++ + P RE+L+ GL +QVWFQNRRAK ++
Sbjct: 1 RYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRK 56
>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX
Protein Lhx9
Length = 80
Score = 53.1 bits (126), Expect = 2e-07, Method: Composition-based stats.
Identities = 29/65 (44%), Positives = 40/65 (61%), Gaps = 2/65 (3%)
Query: 205 KRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKR--L 262
KR RT+ QL T+K + + P +QL+Q TGL RV+QVWFQN RAK +R L
Sbjct: 8 KRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNLL 67
Query: 263 KKDAG 267
+++ G
Sbjct: 68 RQENG 72
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
Length = 60
Score = 52.4 bits (124), Expect = 3e-07, Method: Composition-based stats.
Identities = 24/57 (42%), Positives = 37/57 (64%)
Query: 205 KRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKR 261
KRPRT +++QL LK +N + R+QLS + GL+ +++WFQN+RAK K+
Sbjct: 2 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 58
>pdb|1HDD|C Chain C, Crystal Structure Of An Engrailed Homeodomain-Dna Complex
At 2.8 Angstroms Resolution: A Framework For
Understanding Homeodomain-Dna Interactions
pdb|1HDD|D Chain D, Crystal Structure Of An Engrailed Homeodomain-Dna Complex
At 2.8 Angstroms Resolution: A Framework For
Understanding Homeodomain-Dna Interactions
pdb|2JWT|A Chain A, Solution Structure Of Engrailed Homeodomain Wt
Length = 61
Score = 52.4 bits (124), Expect = 3e-07, Method: Composition-based stats.
Identities = 24/57 (42%), Positives = 37/57 (64%)
Query: 205 KRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKR 261
KRPRT +++QL LK +N + R+QLS + GL+ +++WFQN+RAK K+
Sbjct: 4 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 60
>pdb|1P7J|A Chain A, Crystal Structure Of Engrailed Homeodomain Mutant K52e
pdb|1P7J|B Chain B, Crystal Structure Of Engrailed Homeodomain Mutant K52e
pdb|1P7J|C Chain C, Crystal Structure Of Engrailed Homeodomain Mutant K52e
pdb|1P7J|D Chain D, Crystal Structure Of Engrailed Homeodomain Mutant K52e
Length = 59
Score = 52.0 bits (123), Expect = 5e-07, Method: Composition-based stats.
Identities = 24/57 (42%), Positives = 36/57 (63%)
Query: 205 KRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKR 261
KRPRT +++QL LK +N + R+QLS + GL+ +++WFQN RAK K+
Sbjct: 2 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNERAKIKK 58
>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4490c
Length = 75
Score = 51.6 bits (122), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 27/54 (50%), Positives = 34/54 (62%)
Query: 205 KRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAK 258
+R RTT T+ QLE L+ + + P + REQL+ T L VQVWFQNRRAK
Sbjct: 10 RRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAK 63
>pdb|1P7I|A Chain A, Crystal Structure Of Engrailed Homeodomain Mutant K52a
pdb|1P7I|B Chain B, Crystal Structure Of Engrailed Homeodomain Mutant K52a
pdb|1P7I|C Chain C, Crystal Structure Of Engrailed Homeodomain Mutant K52a
pdb|1P7I|D Chain D, Crystal Structure Of Engrailed Homeodomain Mutant K52a
Length = 59
Score = 51.2 bits (121), Expect = 7e-07, Method: Composition-based stats.
Identities = 24/57 (42%), Positives = 36/57 (63%)
Query: 205 KRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKR 261
KRPRT +++QL LK +N + R+QLS + GL+ +++WFQN RAK K+
Sbjct: 2 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAKIKK 58
>pdb|2HDD|A Chain A, Engrailed Homeodomain Q50k Variant Dna Complex
pdb|2HDD|B Chain B, Engrailed Homeodomain Q50k Variant Dna Complex
Length = 61
Score = 50.8 bits (120), Expect = 1e-06, Method: Composition-based stats.
Identities = 23/57 (40%), Positives = 37/57 (64%)
Query: 205 KRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKR 261
KRPRT +++QL LK +N + R+QLS + GL+ +++WF+N+RAK K+
Sbjct: 4 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK 60
>pdb|1ZTR|A Chain A, Solution Structure Of Engrailed Homeodomain L16a Mutant
Length = 61
Score = 50.4 bits (119), Expect = 1e-06, Method: Composition-based stats.
Identities = 25/62 (40%), Positives = 39/62 (62%), Gaps = 2/62 (3%)
Query: 200 GDQPNKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKE 259
GD+ KRPRT +++QL K +N + R+QLS + GL+ +++WFQN+RAK
Sbjct: 1 GDE--KRPRTAFSSEQLARAKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKI 58
Query: 260 KR 261
+R
Sbjct: 59 RR 60
>pdb|1ENH|A Chain A, Structural Studies Of The Engrailed Homeodomain
Length = 54
Score = 50.1 bits (118), Expect = 2e-06, Method: Composition-based stats.
Identities = 22/53 (41%), Positives = 34/53 (64%)
Query: 206 RPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAK 258
RPRT +++QL LK +N + R+QLS + GL+ +++WFQN+RAK
Sbjct: 1 RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 53
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 50.1 bits (118), Expect = 2e-06, Method: Composition-based stats.
Identities = 24/55 (43%), Positives = 35/55 (63%)
Query: 210 TITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKK 264
T T+ QLE L+ A++ + P RE+L+ GL +QVWFQNRRAK ++ +K
Sbjct: 5 TFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQEK 59
>pdb|2LXD|A Chain A, Backbone 1h, 13c, And 15n Chemical Shift Assignments For
Lmo2(Lim2)- Ldb1(Lid)
Length = 125
Score = 49.3 bits (116), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/71 (36%), Positives = 38/71 (53%), Gaps = 4/71 (5%)
Query: 124 FFKRFGTK--CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKL 181
+ + FG CA C+ I ++ R +D VYHL CF C C + + GD YL+ + +
Sbjct: 3 YLRLFGQDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFSVGDR-YLLINSDI 61
Query: 182 VCKPD-YEAAK 191
VC+ D YE K
Sbjct: 62 VCEQDIYEWTK 72
>pdb|2L6Y|B Chain B, Haddock Model Of Gata1nf:lmo2lim2-Ldb1lid
pdb|2L6Z|C Chain C, Haddock Model Of Gata1nf:lmo2lim2-Ldb1lid With Fog
Length = 96
Score = 48.9 bits (115), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 26/71 (36%), Positives = 38/71 (53%), Gaps = 4/71 (5%)
Query: 124 FFKRFGTK--CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKL 181
+ + FG CA C+ I ++ R +D VYHL CF C C + + GD YL+ + +
Sbjct: 1 YLRLFGQDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFSVGDR-YLLINSDI 59
Query: 182 VCKPD-YEAAK 191
VC+ D YE K
Sbjct: 60 VCEQDIYEWTK 70
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 48.9 bits (115), Expect = 4e-06, Method: Composition-based stats.
Identities = 25/63 (39%), Positives = 36/63 (57%)
Query: 205 KRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKK 264
+R RT T +QLE L+ + + P REQL++ L V+VWF+NRRAK +R
Sbjct: 8 RRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRSGP 67
Query: 265 DAG 267
+G
Sbjct: 68 SSG 70
>pdb|1DU0|A Chain A, Engrailed Homeodomain Q50a Variant Dna Complex
pdb|1DU0|B Chain B, Engrailed Homeodomain Q50a Variant Dna Complex
Length = 57
Score = 48.5 bits (114), Expect = 4e-06, Method: Composition-based stats.
Identities = 22/56 (39%), Positives = 35/56 (62%)
Query: 206 RPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKR 261
RPRT +++QL LK +N + R+QLS + GL+ +++WF N+RAK K+
Sbjct: 1 RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANKRAKIKK 56
>pdb|1J2O|A Chain A, Structure Of Flin2, A Complex Containing The N-Terminal
Lim Domain Of Lmo2 And Ldb1-Lid
Length = 114
Score = 47.8 bits (112), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 33/62 (53%), Gaps = 3/62 (4%)
Query: 68 ASIPKCGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAE---KCFARNGLLFCKEDF 124
S+ CGGC I DR+ LK +++ WH CL C CG L E + + + G C+ D+
Sbjct: 1 GSLLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDY 60
Query: 125 FK 126
+
Sbjct: 61 LR 62
>pdb|2HOS|A Chain A, Phage-selected Homeodomain Bound To Unmodified Dna
pdb|2HOS|B Chain B, Phage-selected Homeodomain Bound To Unmodified Dna
pdb|2HOT|A Chain A, Phage Selected Homeodomain Bound To Modified Dna
pdb|2HOT|B Chain B, Phage Selected Homeodomain Bound To Modified Dna
Length = 63
Score = 47.8 bits (112), Expect = 8e-06, Method: Composition-based stats.
Identities = 24/57 (42%), Positives = 35/57 (61%)
Query: 205 KRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKR 261
KRPRT +++QL LK +N + R+QLS + GL+ V+ WF+N RAK K+
Sbjct: 5 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMRAKIKK 61
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 47.0 bits (110), Expect = 1e-05, Method: Composition-based stats.
Identities = 25/68 (36%), Positives = 38/68 (55%)
Query: 205 KRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKK 264
+R RT+ T +Q+E L+ + + P RE+L+ L +QVWF NRRAK +R +K
Sbjct: 8 QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEK 67
Query: 265 DAGRTRWS 272
+ R S
Sbjct: 68 LRNQRRQS 75
>pdb|2DJ7|A Chain A, Solution Structure Of 3rd Lim Domain Of Actin-Binding Lim
Protein 3
Length = 80
Score = 46.2 bits (108), Expect = 2e-05, Method: Composition-based stats.
Identities = 18/58 (31%), Positives = 31/58 (53%)
Query: 73 CGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCFARNGLLFCKEDFFKRFGT 130
C GC + I L L++ WH C KC C L + +++G+ +C+ D+ +FG+
Sbjct: 18 CAGCKEEIKHGQSLLALDKQWHVSCFKCQTCSVILTGEYISKDGVPYCESDYHAQFGS 75
Score = 33.1 bits (74), Expect = 0.19, Method: Composition-based stats.
Identities = 23/63 (36%), Positives = 34/63 (53%), Gaps = 4/63 (6%)
Query: 127 RFGTKCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPD 186
R + CAGC+ I Q + A D +H++CF C C+ L TG+ Y+ +D C+ D
Sbjct: 13 RGPSHCAGCKEEIKHGQSLL-ALDKQWHVSCFKCQTCSVIL-TGE--YISKDGVPYCESD 68
Query: 187 YEA 189
Y A
Sbjct: 69 YHA 71
>pdb|2DA1|A Chain A, Solution Structure Of The First Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 45.8 bits (107), Expect = 3e-05, Method: Composition-based stats.
Identities = 20/63 (31%), Positives = 37/63 (58%)
Query: 205 KRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKK 264
KRPRT IT QL L+ ++ + P+ ++++ +GL +V++ WF+N KE++
Sbjct: 8 KRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKERQSGP 67
Query: 265 DAG 267
+G
Sbjct: 68 SSG 70
>pdb|3L1P|A Chain A, Pou Protein:dna Complex
pdb|3L1P|B Chain B, Pou Protein:dna Complex
Length = 155
Score = 45.1 bits (105), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 24/60 (40%), Positives = 34/60 (56%)
Query: 202 QPNKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKR 261
Q KR RT+I + +L+ + SPKP+ ++ GL+ VV+VWF NRR K KR
Sbjct: 94 QARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGKR 153
>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain
Length = 73
Score = 45.1 bits (105), Expect = 5e-05, Method: Composition-based stats.
Identities = 22/58 (37%), Positives = 33/58 (56%)
Query: 205 KRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRL 262
++ R T QL+ L+ Y T+ + R ++S T L R V +WFQNRR KEK++
Sbjct: 8 RKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKV 65
>pdb|2XQN|T Chain T, Complex Of The 2nd And 3rd Lim Domains Of Tes With The
Evh1 Domain Of Mena And The N-Terminal Domain Of
Actin-Like Protein Arp7a
Length = 126
Score = 45.1 bits (105), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 30/110 (27%), Positives = 47/110 (42%), Gaps = 4/110 (3%)
Query: 71 PKCGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCFAR-NGLLFCKEDFFKRFG 129
P+C GC +LI + + WH + C +C + LA + + N CK + K
Sbjct: 4 PRCAGCDELIFSNEYTQAENQNWHLKHFCCFDCDSILAGEIYVMVNDKPVCKPCYVKNHA 63
Query: 130 TKCAGCEMGIPPTQVVRRAQDLVYHLN--CFACVMCARQLNTGDEFYLME 177
C GC I P + +H + CF C C++ L G +F +E
Sbjct: 64 VVCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCL-IGQKFMPVE 112
Score = 31.6 bits (70), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 30/57 (52%), Gaps = 3/57 (5%)
Query: 131 KCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDY 187
+CAGC+ I + + A++ +HL F C C L E Y+M + K VCKP Y
Sbjct: 5 RCAGCDELIFSNEYTQ-AENQNWHLKHFCCFDCDSIL--AGEIYVMVNDKPVCKPCY 58
>pdb|2LD5|A Chain A, Solution Nmr-Derived Complex Structure Of Hoxa13 Dna
Binding Domain Bound To Dna
Length = 67
Score = 44.7 bits (104), Expect = 6e-05, Method: Composition-based stats.
Identities = 22/58 (37%), Positives = 33/58 (56%)
Query: 205 KRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRL 262
++ R T QL+ L+ Y T+ + R ++S T L R V +WFQNRR KEK++
Sbjct: 2 RKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKV 59
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 44.7 bits (104), Expect = 6e-05, Method: Composition-based stats.
Identities = 21/57 (36%), Positives = 35/57 (61%)
Query: 205 KRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKR 261
+R RT T++QL+ L+ + + P RE+++ T L V+VWF+NRRAK ++
Sbjct: 4 RRQRTHFTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK 60
>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Otx2
Length = 80
Score = 44.7 bits (104), Expect = 6e-05, Method: Composition-based stats.
Identities = 22/54 (40%), Positives = 32/54 (59%)
Query: 205 KRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAK 258
+R RTT T QL+ L+ + + P +RE+++ L VQVWF+NRRAK
Sbjct: 8 RRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAK 61
>pdb|2L7F|P Chain P, Solution Structure Of The Pitx2 Homeodomain
pdb|2LKX|A Chain A, Nmr Structure Of The Homeodomain Of Pitx2 In Complex With
A Taatcc Dna Binding Site
Length = 68
Score = 44.7 bits (104), Expect = 7e-05, Method: Composition-based stats.
Identities = 21/57 (36%), Positives = 35/57 (61%)
Query: 205 KRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKR 261
+R RT T++QL+ L+ + + P RE+++ T L V+VWF+NRRAK ++
Sbjct: 4 RRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK 60
>pdb|1OCP|A Chain A, Solution Structure Of Oct3 Pou-Homeodomain
Length = 67
Score = 44.3 bits (103), Expect = 1e-04, Method: Composition-based stats.
Identities = 23/60 (38%), Positives = 33/60 (55%)
Query: 202 QPNKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKR 261
Q KR RT+I + +L+ + PKP+ ++ GL+ VV+VWF NRR K KR
Sbjct: 6 QARKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKR 65
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 43.1 bits (100), Expect = 2e-04, Method: Composition-based stats.
Identities = 22/58 (37%), Positives = 30/58 (51%)
Query: 205 KRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRL 262
++PRT T QL L+ + + R + S L V++WFQNRRAK KRL
Sbjct: 1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKRL 58
>pdb|2XSD|C Chain C, Crystal Structure Of The Dimeric Oct-6 (Pou3f1) Pou Domain
Bound To Palindromic More Dna
Length = 164
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/63 (38%), Positives = 34/63 (53%)
Query: 205 KRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKK 264
++ RT+I L+ + PKP+ H L+ L+ VV+VWF NRR KEKR+
Sbjct: 100 RKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKEKRMTP 159
Query: 265 DAG 267
AG
Sbjct: 160 AAG 162
>pdb|1AU7|A Chain A, Pit-1 MutantDNA COMPLEX
pdb|1AU7|B Chain B, Pit-1 MutantDNA COMPLEX
Length = 146
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 39/66 (59%)
Query: 198 LDGDQPNKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRA 257
+ ++ ++ RTTI+ + L+ + KP+ +++++ L+ VV+VWF NRR
Sbjct: 81 VGANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQ 140
Query: 258 KEKRLK 263
+EKR+K
Sbjct: 141 REKRVK 146
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor Gbx1
From Homo Sapiens
Length = 71
Score = 42.7 bits (99), Expect = 2e-04, Method: Composition-based stats.
Identities = 22/60 (36%), Positives = 35/60 (58%)
Query: 204 NKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLK 263
++R RT T++QL L+ ++ + R Q++ L V++WFQNRRAK KR+K
Sbjct: 7 SRRRRTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRAKWKRIK 66
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 42.4 bits (98), Expect = 3e-04, Method: Composition-based stats.
Identities = 19/60 (31%), Positives = 36/60 (60%)
Query: 208 RTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKKDAG 267
RT T +QL L+ ++ + +R R +++ L+ V++WFQNRR K+K+ +++ G
Sbjct: 38 RTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKREREGG 97
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 42.0 bits (97), Expect = 4e-04, Method: Composition-based stats.
Identities = 20/63 (31%), Positives = 35/63 (55%)
Query: 205 KRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKK 264
++PRT ++ QL L+ + + A R +L+ GL V++WFQN+R+K K+
Sbjct: 8 RKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKKSGP 67
Query: 265 DAG 267
+G
Sbjct: 68 SSG 70
>pdb|1X6A|A Chain A, Solution Structures Of The Second Lim Domain Of Human Lim-
Kinase 2 (limk2)
Length = 81
Score = 41.2 bits (95), Expect = 7e-04, Method: Composition-based stats.
Identities = 20/62 (32%), Positives = 33/62 (53%), Gaps = 2/62 (3%)
Query: 122 EDFFKRFGTKCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKL 181
+D++ +FG C GC + + +V A + YH CFAC+ C + GD + L++ L
Sbjct: 8 KDYWGKFGEFCHGCSLLMTGPFMV--AGEFKYHPECFACMSCKVIIEDGDAYALVQHATL 65
Query: 182 VC 183
C
Sbjct: 66 YC 67
>pdb|2CRA|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeo
Box B13
Length = 70
Score = 40.8 bits (94), Expect = 0.001, Method: Composition-based stats.
Identities = 20/63 (31%), Positives = 32/63 (50%)
Query: 205 KRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKK 264
++ R + QL L+ Y + + R ++S T L R + +WFQNRR KEK+
Sbjct: 8 RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKKSGP 67
Query: 265 DAG 267
+G
Sbjct: 68 SSG 70
>pdb|1X3H|A Chain A, Solution Structure Of The Lim Domain Of Human Leupaxin
Length = 80
Score = 40.8 bits (94), Expect = 0.001, Method: Composition-based stats.
Identities = 19/61 (31%), Positives = 30/61 (49%), Gaps = 2/61 (3%)
Query: 71 PKCGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCFAR-NGLLFCKEDFFKRFG 129
PKCGGC +L+ + L ++ WH C C +C + F +G FC+ + R G
Sbjct: 16 PKCGGCNRPVLENY-LSAMDTVWHPECFVCGDCFTSFSTGSFFELDGRPFCELHYHHRRG 74
Query: 130 T 130
+
Sbjct: 75 S 75
Score = 38.1 bits (87), Expect = 0.005, Method: Composition-based stats.
Identities = 23/66 (34%), Positives = 29/66 (43%), Gaps = 4/66 (6%)
Query: 122 EDFFKRFGTKCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKL 181
+DF F KC GC P + A D V+H CF C C +TG F L D +
Sbjct: 8 KDFLAMFSPKCGGCNR--PVLENYLSAMDTVWHPECFVCGDCFTSFSTGSFFEL--DGRP 63
Query: 182 VCKPDY 187
C+ Y
Sbjct: 64 FCELHY 69
>pdb|1CXX|A Chain A, Mutant R122a Of Quail Cysteine And Glycine-Rich Protein,
Nmr, Minimized Structure
Length = 113
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 28/61 (45%), Gaps = 1/61 (1%)
Query: 72 KCGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCFA-RNGLLFCKEDFFKRFGT 130
KC CGD + + + WH C +C +CG L + G ++CK + K FG
Sbjct: 38 KCSACGDSVYAAEKVIGAGKPWHKNCFRCAKCGKSLESTTLTEKEGEIYCKGCYAKNFGP 97
Query: 131 K 131
K
Sbjct: 98 K 98
>pdb|2H1K|A Chain A, Crystal Structure Of The Pdx1 Homeodomain In Complex With
Dna
pdb|2H1K|B Chain B, Crystal Structure Of The Pdx1 Homeodomain In Complex With
Dna
Length = 63
Score = 39.7 bits (91), Expect = 0.002, Method: Composition-based stats.
Identities = 22/58 (37%), Positives = 32/58 (55%)
Query: 204 NKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKR 261
NKR RT T QL L+ + + +R R +L+ L R +++WFQNRR K K+
Sbjct: 3 NKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKK 60
>pdb|2DA2|A Chain A, Solution Structure Of The Second Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 38.5 bits (88), Expect = 0.004, Method: Composition-based stats.
Identities = 21/59 (35%), Positives = 29/59 (49%)
Query: 209 TTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKKDAG 267
T T QL L+ ++ + P EQLS L RV+ VWFQN R K ++ +G
Sbjct: 12 TRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARKSGPSSG 70
>pdb|1IBI|A Chain A, Quail Cysteine And Glycine-Rich Protein, Nmr, 15 Minimized
Model Structures
pdb|1QLI|A Chain A, Quail Cysteine And Glycine-Rich Protein, Nmr, Minimized
Average Structure
Length = 113
Score = 38.5 bits (88), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 28/61 (45%), Gaps = 1/61 (1%)
Query: 72 KCGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCFA-RNGLLFCKEDFFKRFGT 130
KC CGD + + + WH C +C +CG L + G ++CK + K FG
Sbjct: 38 KCSRCGDSVYAAEKVIGAGKPWHKNCFRCAKCGKSLESTTLTEKEGEIYCKGCYAKNFGP 97
Query: 131 K 131
K
Sbjct: 98 K 98
>pdb|2CUP|A Chain A, Solution Structure Of The Skeletal Muscle Lim-Protein 1
Length = 101
Score = 38.5 bits (88), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 33/70 (47%), Gaps = 1/70 (1%)
Query: 91 RTWHARCLKCHECGAPLAEKCF-ARNGLLFCKEDFFKRFGTKCAGCEMGIPPTQVVRRAQ 149
R WH C +C +C PLA + F A++ + C + + KC GC I +
Sbjct: 27 RFWHDTCFRCAKCLHPLANETFVAKDNKILCNKCTTREDSPKCKGCFKAIVAGDQNVEYK 86
Query: 150 DLVYHLNCFA 159
V+H +CF+
Sbjct: 87 GTVWHKDCFS 96
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 38.1 bits (87), Expect = 0.006, Method: Composition-based stats.
Identities = 19/57 (33%), Positives = 31/57 (54%)
Query: 205 KRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKR 261
+R R T T Q L+ ++T+ R R +++ L R +++WFQNRR K K+
Sbjct: 21 RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKK 77
>pdb|1G47|A Chain A, 1st Lim Domain Of Pinch Protein
Length = 77
Score = 38.1 bits (87), Expect = 0.006, Method: Composition-based stats.
Identities = 19/57 (33%), Positives = 28/57 (49%), Gaps = 2/57 (3%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDYE 188
C C+ G P + + + +YH CF C C +Q G FY E RK C+ D++
Sbjct: 14 CERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEG-LFYEFEGRKY-CEHDFQ 68
>pdb|1E3O|C Chain C, Crystal Structure Of Oct-1 Pou Dimer Bound To More
Length = 160
Score = 38.1 bits (87), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 35/65 (53%)
Query: 198 LDGDQPNKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRA 257
++G ++ RT+I L+ ++ + KP +++ ++ V++VWF NRR
Sbjct: 95 IEGLSRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQ 154
Query: 258 KEKRL 262
KEKR+
Sbjct: 155 KEKRI 159
>pdb|2R5Y|A Chain A, Structure Of ScrEXD COMPLEX BOUND TO A CONSENSUS HOX-Exd
Site
pdb|2R5Z|A Chain A, Structure Of ScrEXD COMPLEX BOUND TO A DNA SEQUENCE
Derived From The Fkh Gene
Length = 88
Score = 38.1 bits (87), Expect = 0.007, Method: Composition-based stats.
Identities = 20/67 (29%), Positives = 35/67 (52%)
Query: 198 LDGDQPNKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRA 257
++ + KR RT+ T Q L+ ++ + R R +++ L R +++WFQNRR
Sbjct: 22 VNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRM 81
Query: 258 KEKRLKK 264
K K+ K
Sbjct: 82 KWKKEHK 88
>pdb|3F6Q|B Chain B, Crystal Structure Of Integrin-Linked Kinase Ankyrin Repeat
Domain In Complex With Pinch1 Lim1 Domain
Length = 72
Score = 37.7 bits (86), Expect = 0.008, Method: Composition-based stats.
Identities = 19/57 (33%), Positives = 28/57 (49%), Gaps = 2/57 (3%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDYE 188
C C+ G P + + + +YH CF C C +Q G FY E RK C+ D++
Sbjct: 14 CERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEG-LFYEFEGRKY-CEHDFQ 68
>pdb|1HF0|A Chain A, Crystal Structure Of The Dna-Binding Domain Of Oct-1 Bound
To Dna As A Dimer
pdb|1HF0|B Chain B, Crystal Structure Of The Dna-Binding Domain Of Oct-1 Bound
To Dna As A Dimer
pdb|1GT0|C Chain C, Crystal Structure Of A PouHMGDNA TERNARY COMPLEX
Length = 159
Score = 37.4 bits (85), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 34/65 (52%)
Query: 198 LDGDQPNKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRA 257
++G ++ RT+I L+ ++ + KP ++ ++ V++VWF NRR
Sbjct: 94 IEGLSRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFSNRRQ 153
Query: 258 KEKRL 262
KEKR+
Sbjct: 154 KEKRI 158
>pdb|1AHD|P Chain P, Determination Of The Nmr Solution Structure Of An
Antennapedia Homeodomain-Dna Complex
pdb|2HOA|A Chain A, Structure Determination Of The Antp(C39->s) Homeodomain
From Nuclear Magnetic Resonance Data In Solution Using A
Novel Strategy For The Structure Calculation With The
Programs Diana, Caliba, Habas And Glomsa
Length = 68
Score = 37.4 bits (85), Expect = 0.010, Method: Composition-based stats.
Identities = 21/63 (33%), Positives = 32/63 (50%)
Query: 205 KRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKK 264
KR R T T Q L+ ++ + R R +++ L R +++WFQNRR K K+ K
Sbjct: 3 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENK 62
Query: 265 DAG 267
G
Sbjct: 63 TKG 65
>pdb|3D1N|I Chain I, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|J Chain J, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|K Chain K, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|L Chain L, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|M Chain M, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|N Chain N, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|O Chain O, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|P Chain P, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
Length = 151
Score = 37.4 bits (85), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 32/59 (54%), Gaps = 2/59 (3%)
Query: 200 GDQPNKRP--RTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRR 256
G +P+K+ RT+ T + +E L + +P P + +++ D VV+VWF NRR
Sbjct: 87 GGEPSKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEXAKELNYDREVVRVWFSNRR 145
>pdb|2D8X|A Chain A, Solution Structure Of The Second Lim Domain Of
Particularly Interesting New Cys-His Protein (Pinch)
Length = 70
Score = 37.0 bits (84), Expect = 0.012, Method: Composition-based stats.
Identities = 15/44 (34%), Positives = 24/44 (54%), Gaps = 1/44 (2%)
Query: 73 CGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCFARNG 116
C CG+ I+ R ++K + +WH C +C C LA+ F +N
Sbjct: 8 CHQCGEFIIGR-VIKAMNNSWHPECFRCDLCQEVLADIGFVKNA 50
>pdb|1POG|A Chain A, Solution Structure Of The Oct-1 Pou-Homeo Domain
Determined By Nmr And Restrained Molecular Dynamics
Length = 67
Score = 37.0 bits (84), Expect = 0.015, Method: Composition-based stats.
Identities = 17/58 (29%), Positives = 31/58 (53%)
Query: 205 KRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRL 262
++ RT+I L+ ++ + KP ++ ++ V++VWF NRR KEKR+
Sbjct: 8 RKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKRI 65
>pdb|1FTZ|A Chain A, Nuclear Magnetic Resonance Solution Structure Of The Fushi
Tarazu Homeodomain From Drosophila And Comparison With
The Antennapedia Homeodomain
Length = 70
Score = 36.6 bits (83), Expect = 0.018, Method: Composition-based stats.
Identities = 19/58 (32%), Positives = 30/58 (51%)
Query: 204 NKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKR 261
+KR R T T Q L+ ++ + R R ++ L R +++WFQNRR K K+
Sbjct: 3 SKRTRQTYTRYQTLELEKEFHFNRYITRRRRIDIANALSLSERQIKIWFQNRRMKSKK 60
>pdb|2DLO|A Chain A, Solution Structure Of The Second Lim Domain Of Human
Thyroid Receptor-Interacting Protein 6
Length = 81
Score = 36.6 bits (83), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 33/66 (50%), Gaps = 3/66 (4%)
Query: 67 IASIPKCGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCFARNGL--LFCKEDF 124
+A++ KC C ILDR IL+ + + +H C C C L F + + C EDF
Sbjct: 12 VATLEKCATCSQPILDR-ILRAMGKAYHPGCFTCVVCHRGLDGIPFTVDATSQIHCIEDF 70
Query: 125 FKRFGT 130
++F +
Sbjct: 71 HRKFAS 76
Score = 33.1 bits (74), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 27/58 (46%), Gaps = 3/58 (5%)
Query: 131 KCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDYE 188
KCA C P + RA YH CF CV+C R L+ G F + ++ C D+
Sbjct: 17 KCATCSQ--PILDRILRAMGKAYHPGCFTCVVCHRGLD-GIPFTVDATSQIHCIEDFH 71
>pdb|2P81|A Chain A, Engrailed Homeodomain Helix-Turn-Helix Motif
Length = 44
Score = 36.2 bits (82), Expect = 0.022, Method: Composition-based stats.
Identities = 16/42 (38%), Positives = 26/42 (61%)
Query: 220 KMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKR 261
K +N + R+QLS + GL+ +++WFQN+RAK K+
Sbjct: 2 KREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 43
>pdb|1O4X|A Chain A, Ternary Complex Of The Dna Binding Domains Of The Oct1 And
Sox2 Transcription Factors With A 19mer Oligonucleotide
From The Hoxb1 Regulatory Element
Length = 167
Score = 36.2 bits (82), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 34/65 (52%)
Query: 198 LDGDQPNKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRA 257
++G ++ RT+I L+ ++ + KP ++ ++ V++VWF NRR
Sbjct: 98 IEGLSERRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQ 157
Query: 258 KEKRL 262
KEKR+
Sbjct: 158 KEKRI 162
>pdb|1HOM|A Chain A, Determination Of The Three-Dimensional Structure Of The
Antennapedia Homeodomain From Drosophila In Solution By
1h Nuclear Magnetic Resonance Spectroscopy
Length = 68
Score = 36.2 bits (82), Expect = 0.023, Method: Composition-based stats.
Identities = 21/63 (33%), Positives = 32/63 (50%)
Query: 205 KRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKK 264
KR R T T Q L+ ++ + R R +++ L R +++WFQNRR K K+ K
Sbjct: 3 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 62
Query: 265 DAG 267
G
Sbjct: 63 TKG 65
>pdb|1B8T|A Chain A, Solution Structure Of The Chicken Crp1
Length = 192
Score = 36.2 bits (82), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 28/57 (49%), Gaps = 1/57 (1%)
Query: 76 CGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCFA-RNGLLFCKEDFFKRFGTK 131
CG + + ++WH C +C +CG L A ++G ++CK + K FG K
Sbjct: 121 CGQAVYAAEKVIGAGKSWHKSCFRCAKCGKSLESTTLADKDGEIYCKGCYAKNFGPK 177
Score = 28.5 bits (62), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 27/52 (51%), Gaps = 7/52 (13%)
Query: 129 GTKCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNT------GDEFY 174
G KC C+ + + V+ + +H +CF C++C + L++ GDE Y
Sbjct: 7 GKKCGVCQKAVYFAEEVQ-CEGSSFHKSCFLCMVCKKNLDSTTVAVHGDEIY 57
>pdb|1OCT|C Chain C, Crystal Structure Of The Oct-1 Pou Domain Bound To An
Octamer Site: Dna Recognition With Tethered Dna-Binding
Modules
Length = 156
Score = 36.2 bits (82), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 34/65 (52%)
Query: 198 LDGDQPNKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRA 257
++G ++ RT+I L+ ++ + KP ++ ++ V++VWF NRR
Sbjct: 90 IEGLSRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQ 149
Query: 258 KEKRL 262
KEKR+
Sbjct: 150 KEKRI 154
>pdb|1CTL|A Chain A, Structure Of The Carboxy-Terminal Lim Domain From The
Cysteine Rich Protein Crp
Length = 85
Score = 36.2 bits (82), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 28/57 (49%), Gaps = 1/57 (1%)
Query: 76 CGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCFA-RNGLLFCKEDFFKRFGTK 131
CG + + ++WH C +C +CG L A ++G ++CK + K FG K
Sbjct: 14 CGQAVYAAEKVIGAGKSWHKSCFRCAKCGKSLESTTLADKDGEIYCKGCYAKNFGPK 70
>pdb|1CQT|A Chain A, Crystal Structure Of A Ternary Complex Containing An Oca-B
Peptide, The Oct-1 Pou Domain, And An Octamer Element
pdb|1CQT|B Chain B, Crystal Structure Of A Ternary Complex Containing An Oca-B
Peptide, The Oct-1 Pou Domain, And An Octamer Element
Length = 163
Score = 35.8 bits (81), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 34/65 (52%)
Query: 198 LDGDQPNKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRA 257
++G ++ RT+I L+ ++ + KP ++ ++ V++VWF NRR
Sbjct: 97 IEGLSRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQ 156
Query: 258 KEKRL 262
KEKR+
Sbjct: 157 KEKRI 161
>pdb|2KBX|B Chain B, Solution Structure Of Ilk-Pinch Complex
Length = 70
Score = 35.8 bits (81), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 28/57 (49%), Gaps = 2/57 (3%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDYE 188
C C+ G P + + + +YH CF C C +Q G FY E RK C+ D++
Sbjct: 10 CERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGL-FYEFEGRK-YCEHDFQ 64
>pdb|1NYP|A Chain A, 4th Lim Domain Of Pinch Protein
pdb|1U5S|B Chain B, Nmr Structure Of The Complex Between Nck-2 Sh3 Domain And
Pinch-1 Lim4 Domain
Length = 66
Score = 35.8 bits (81), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 30/62 (48%), Gaps = 2/62 (3%)
Query: 69 SIPKCGGCGDLILDRFILKVLERTWHARCLKCHECGAP-LAEKCFARNGLLFCKEDFFKR 127
+P CG C I R ++ + + WH C +C P L + + R GL +C+ + +
Sbjct: 4 GVPICGACRRPIEGR-VVNAMGKQWHVEHFVCAKCEKPFLGHRHYERKGLAYCETHYNQL 62
Query: 128 FG 129
FG
Sbjct: 63 FG 64
>pdb|3K2A|A Chain A, Crystal Structure Of The Homeobox Domain Of Human Homeobox
Protein Meis2
pdb|3K2A|B Chain B, Crystal Structure Of The Homeobox Domain Of Human Homeobox
Protein Meis2
Length = 67
Score = 35.8 bits (81), Expect = 0.031, Method: Composition-based stats.
Identities = 15/34 (44%), Positives = 21/34 (61%)
Query: 225 TSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAK 258
T P P+ ++QL+QDTGL + V WF N R +
Sbjct: 22 THPYPSEEQKKQLAQDTGLTILQVNNWFINARRR 55
>pdb|1HDP|A Chain A, Solution Structure Of A Pou-Specific Homeodomain: 3d-Nmr
Studies Of Human B-Cell Transcription Factor Oct-2
Length = 63
Score = 35.8 bits (81), Expect = 0.034, Method: Composition-based stats.
Identities = 17/58 (29%), Positives = 32/58 (55%)
Query: 205 KRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRL 262
++ RT+I L+ ++ + KP +++ ++ V++VWF NRR KEKR+
Sbjct: 2 RKKRTSIETNVRFALEKSFLANQKPTSEEILLIAEQLHMEKEVIRVWFCNRRQKEKRI 59
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 35.4 bits (80), Expect = 0.035, Method: Composition-based stats.
Identities = 19/57 (33%), Positives = 30/57 (52%)
Query: 205 KRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKR 261
KR R T T Q L+ ++ + R R +++ L R +++WFQNRR K K+
Sbjct: 4 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKK 60
>pdb|2KT0|A Chain A, Solution Structure Of Human Stem Cell Transcription Factor
Nanog Homeodomain Fragment
Length = 84
Score = 35.4 bits (80), Expect = 0.039, Method: Composition-based stats.
Identities = 18/61 (29%), Positives = 31/61 (50%)
Query: 205 KRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKK 264
++ RT ++ QL L + + ++LS L + V+ WFQN+R K KR +K
Sbjct: 23 QKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRWQK 82
Query: 265 D 265
+
Sbjct: 83 N 83
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Barh-Like 1
Length = 80
Score = 35.4 bits (80), Expect = 0.041, Method: Composition-based stats.
Identities = 20/63 (31%), Positives = 30/63 (47%)
Query: 205 KRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKK 264
+R RT T QL L+ + + R L++ GL V+ W+QNRR K K+
Sbjct: 18 RRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKKSGP 77
Query: 265 DAG 267
+G
Sbjct: 78 SSG 80
>pdb|3IXE|B Chain B, Structural Basis Of Competition Between Pinch1 And Pinch2
For Binding To The Ankyrin Repeat Domain Of
Integrin-Linked Kinase
Length = 72
Score = 35.0 bits (79), Expect = 0.048, Method: Composition-based stats.
Identities = 18/57 (31%), Positives = 27/57 (47%), Gaps = 2/57 (3%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDYE 188
C C+ P + + + +YH +CF C C R G FY E RK C+ D++
Sbjct: 14 CQRCQARFSPAERIVNSNGELYHEHCFVCAQCFRPFPEG-LFYEFEGRKY-CEHDFQ 68
>pdb|1LFU|P Chain P, Nmr Solution Stucture Of The Extended Pbx Homeodomain
Bound To Dna
Length = 82
Score = 35.0 bits (79), Expect = 0.052, Method: Composition-based stats.
Identities = 18/67 (26%), Positives = 35/67 (52%), Gaps = 6/67 (8%)
Query: 205 KRPRTTITAKQLETLK---MAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKR 261
+R R + E L ++ ++P P+ +E+L++ +G+ + V WF N+R R
Sbjct: 3 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKSGITVSQVSNWFGNKRI---R 59
Query: 262 LKKDAGR 268
KK+ G+
Sbjct: 60 YKKNIGK 66
>pdb|1JGG|A Chain A, Even-Skipped Homeodomain Complexed To At-Rich Dna
pdb|1JGG|B Chain B, Even-Skipped Homeodomain Complexed To At-Rich Dna
Length = 60
Score = 35.0 bits (79), Expect = 0.058, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 30/57 (52%)
Query: 205 KRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKR 261
+R RT T QL L+ + +R R +L+ L ++VWFQNRR K+KR
Sbjct: 2 RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKR 58
>pdb|1S7E|A Chain A, Solution Structure Of Hnf-6
Length = 147
Score = 34.3 bits (77), Expect = 0.094, Method: Compositional matrix adjust.
Identities = 25/85 (29%), Positives = 39/85 (45%), Gaps = 5/85 (5%)
Query: 172 EFYLMEDRKLVCKPDYEAAKAKDGNCLDGDQPNKRPRTTITAKQLETLKMAYNTSPKPAR 231
EF M +L E KD G+ P K+PR T Q TL + + +P++
Sbjct: 68 EFQRMSALRLAACKRKEQEHGKD----RGNTP-KKPRLVFTDVQRRTLHAIFKENKRPSK 122
Query: 232 HVREQLSQDTGLDMRVVQVWFQNRR 256
++ +SQ GL++ V +F N R
Sbjct: 123 ELQITISQQLGLELSTVSNFFMNAR 147
>pdb|2D8Y|A Chain A, Solution Structure Of The Lim Domain Of Epithelial Protein
Lost In Neoplasm
Length = 91
Score = 33.9 bits (76), Expect = 0.11, Method: Composition-based stats.
Identities = 19/69 (27%), Positives = 32/69 (46%), Gaps = 3/69 (4%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDYEAAK 191
C C+ + P + + Q V+H++CF C C +L+ G Y ++ CKP +
Sbjct: 18 CVECQKTVYPMERLLANQQ-VFHISCFRCSYCNNKLSLGT--YASLHGRIYCKPHFNQLF 74
Query: 192 AKDGNCLDG 200
GN +G
Sbjct: 75 KSKGNYDEG 83
>pdb|2DN0|A Chain A, Solution Structure Of The Second Homeobox Domain Of Human
Zinc Fingers And Homeoboxes Protein 3
Length = 76
Score = 33.9 bits (76), Expect = 0.11, Method: Composition-based stats.
Identities = 18/50 (36%), Positives = 28/50 (56%)
Query: 214 KQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLK 263
+QL LK ++ + P + E L++ TGL R V+ WF +RR + LK
Sbjct: 18 EQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCRNLK 67
>pdb|1B72|B Chain B, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 87
Score = 33.9 bits (76), Expect = 0.12, Method: Composition-based stats.
Identities = 18/67 (26%), Positives = 34/67 (50%), Gaps = 6/67 (8%)
Query: 205 KRPRTTITAKQLETLK---MAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKR 261
+R R + E L ++ ++P P+ +E+L++ G+ + V WF N+R R
Sbjct: 2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRI---R 58
Query: 262 LKKDAGR 268
KK+ G+
Sbjct: 59 YKKNIGK 65
>pdb|2D5V|A Chain A, Crystal Structure Of Hnf-6alpha Dna-Binding Domain In
Complex With The Ttr Promoter
pdb|2D5V|B Chain B, Crystal Structure Of Hnf-6alpha Dna-Binding Domain In
Complex With The Ttr Promoter
Length = 164
Score = 33.9 bits (76), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 25/87 (28%), Positives = 40/87 (45%), Gaps = 5/87 (5%)
Query: 172 EFYLMEDRKLVCKPDYEAAKAKDGNCLDGDQPNKRPRTTITAKQLETLKMAYNTSPKPAR 231
EF M +L E KD G+ P K+PR T Q TL + + +P++
Sbjct: 70 EFQRMSALRLAACKRKEQEHGKD----RGNTP-KKPRLVFTDVQRRTLHAIFKENKRPSK 124
Query: 232 HVREQLSQDTGLDMRVVQVWFQNRRAK 258
++ +SQ GL++ V +F N R +
Sbjct: 125 ELQITISQQLGLELSTVSNFFMNARRR 151
>pdb|3RKQ|A Chain A, Nkx2.5 Homeodomain Dimer Bound To Anf-242 Dna
pdb|3RKQ|B Chain B, Nkx2.5 Homeodomain Dimer Bound To Anf-242 Dna
Length = 58
Score = 33.9 bits (76), Expect = 0.13, Method: Composition-based stats.
Identities = 17/56 (30%), Positives = 28/56 (50%)
Query: 205 KRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEK 260
++PR + Q+ L+ + + R+QL+ L V++WFQNRR K K
Sbjct: 3 RKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58
>pdb|1ZQ3|P Chain P, Nmr Solution Structure Of The Bicoid Homeodomain Bound To
The Consensus Dna Binding Site Taatcc
Length = 68
Score = 33.5 bits (75), Expect = 0.13, Method: Composition-based stats.
Identities = 21/61 (34%), Positives = 31/61 (50%), Gaps = 10/61 (16%)
Query: 205 KRPRTTITAKQLETLKM-----AYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKE 259
+R RTT T+ Q+ L+ Y T+P+ A LS L V++WF+NRR +
Sbjct: 3 RRTRTTFTSSQIAELEQHFLQGRYLTAPRLA-----DLSAKLALGTAQVKIWFKNRRRRH 57
Query: 260 K 260
K
Sbjct: 58 K 58
>pdb|4EGC|A Chain A, Crystal Structure Of Mbp-fused Human Six1 Bound To Human
Eya2 Eya Domain
Length = 559
Score = 33.5 bits (75), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 25/43 (58%)
Query: 218 TLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEK 260
L+ Y +P P+ + +L++ TGL V WF+NRR +++
Sbjct: 508 VLREWYAHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDR 550
>pdb|1PUF|B Chain B, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 73
Score = 33.5 bits (75), Expect = 0.16, Method: Composition-based stats.
Identities = 18/67 (26%), Positives = 34/67 (50%), Gaps = 6/67 (8%)
Query: 205 KRPRTTITAKQLETLK---MAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKR 261
+R R + E L ++ ++P P+ +E+L++ G+ + V WF N+R R
Sbjct: 2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRI---R 58
Query: 262 LKKDAGR 268
KK+ G+
Sbjct: 59 YKKNIGK 65
>pdb|2E1O|A Chain A, Solution Structure Of Rsgi Ruh-028, A Homeobox Domain From
Human Cdna
Length = 70
Score = 33.1 bits (74), Expect = 0.20, Method: Composition-based stats.
Identities = 21/54 (38%), Positives = 31/54 (57%), Gaps = 7/54 (12%)
Query: 214 KQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKKDAG 267
K+ ET K Y + P+ R++L++ L R V+ WFQNRRAK +R +G
Sbjct: 24 KKFETQK--YLSPPE-----RKRLAKMLQLSERQVKTWFQNRRAKWRRSGPSSG 70
>pdb|1SAN|A Chain A, The Des(1-6)antennapedia Homeodomain: Comparison Of The
Nmr Solution Structure And The Dna Binding Affinity With
The Intact Antennapedia Homeodomain
Length = 62
Score = 33.1 bits (74), Expect = 0.21, Method: Composition-based stats.
Identities = 18/58 (31%), Positives = 29/58 (50%)
Query: 210 TITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKKDAG 267
T T Q L+ ++ + R R +++ L R +++WFQNRR K K+ K G
Sbjct: 2 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENKTKG 59
>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 77
Score = 33.1 bits (74), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 24/39 (61%)
Query: 230 ARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKKDAGR 268
R R ++++ L R V++WFQNRR K K++ KD +
Sbjct: 39 TRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINKDRAK 77
>pdb|1X61|A Chain A, Solution Structure Of The First Lim Domain Of Thyroid
Receptor Interacting Protein 6 (Trip6)
Length = 72
Score = 32.7 bits (73), Expect = 0.27, Method: Composition-based stats.
Identities = 18/42 (42%), Positives = 23/42 (54%), Gaps = 2/42 (4%)
Query: 148 AQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDYEA 189
A D V+H+ CF C C QL G FY +E R+ C+ Y A
Sbjct: 24 ALDRVFHVGCFVCSTCRAQLR-GQHFYAVE-RRAYCEGCYVA 63
>pdb|1B8I|B Chain B, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
pdb|2R5Y|B Chain B, Structure Of ScrEXD COMPLEX BOUND TO A CONSENSUS HOX-Exd
Site
pdb|2R5Z|B Chain B, Structure Of ScrEXD COMPLEX BOUND TO A DNA SEQUENCE
Derived From The Fkh Gene
Length = 63
Score = 32.7 bits (73), Expect = 0.27, Method: Composition-based stats.
Identities = 15/60 (25%), Positives = 32/60 (53%), Gaps = 3/60 (5%)
Query: 205 KRPRTTITAKQLETLK---MAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKR 261
+R R + + E L ++ ++P P+ +E+L++ G+ + V WF N+R + K+
Sbjct: 2 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCGITVSQVSNWFGNKRIRYKK 61
>pdb|3NAR|A Chain A, Crystal Structure Of Zhx1 Hd4 (Zinc-Fingers And Homeoboxes
Protein 1, Homeodomain 4)
pdb|3NAR|B Chain B, Crystal Structure Of Zhx1 Hd4 (Zinc-Fingers And Homeoboxes
Protein 1, Homeodomain 4)
Length = 96
Score = 32.3 bits (72), Expect = 0.32, Method: Composition-based stats.
Identities = 18/66 (27%), Positives = 33/66 (50%), Gaps = 5/66 (7%)
Query: 212 TAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKKDAGRTRW 271
T +QL LK A+ + P+ ++L++++GL + WF + R K G +W
Sbjct: 33 TPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKN-----GNLKW 87
Query: 272 SQYFRS 277
Y++S
Sbjct: 88 YYYYQS 93
>pdb|1QRY|A Chain A, Homeobox Protein Vnd (Ventral Nervous System Defective
Protein)
Length = 80
Score = 32.3 bits (72), Expect = 0.34, Method: Composition-based stats.
Identities = 22/75 (29%), Positives = 33/75 (44%), Gaps = 2/75 (2%)
Query: 195 GNCLDGDQPNKRP--RTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWF 252
G+ + PNK+ R T Q L+ + + RE L+ L V++WF
Sbjct: 1 GSHMSDGLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVKIWF 60
Query: 253 QNRRAKEKRLKKDAG 267
QN R K KR + + G
Sbjct: 61 QNHRYKTKRAQNEKG 75
>pdb|1DU6|A Chain A, Solution Structure Of The Truncated Pbx Homeodomain
Length = 64
Score = 32.3 bits (72), Expect = 0.34, Method: Composition-based stats.
Identities = 11/37 (29%), Positives = 23/37 (62%)
Query: 225 TSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKR 261
++P P+ +E+L++ G+ + V WF N+R + K+
Sbjct: 27 SNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 63
>pdb|2EHE|A Chain A, Solution Structure Of The First Lim Domain From Human Four
And A Half Lim Domains Protein 3
Length = 82
Score = 32.3 bits (72), Expect = 0.37, Method: Composition-based stats.
Identities = 20/63 (31%), Positives = 28/63 (44%), Gaps = 2/63 (3%)
Query: 128 FGTKCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDY 187
F CA C+ I +D +H CF C C R L DE + +D +L+C Y
Sbjct: 14 FANTCAECQQLIGHDSRELFYEDRHFHEGCFRCCRCQRSL--ADEPFTCQDSELLCNDCY 71
Query: 188 EAA 190
+A
Sbjct: 72 CSA 74
>pdb|1NK2|P Chain P, VndNK-2 HomeodomainDNA COMPLEX, NMR, 20 STRUCTURES
pdb|1NK3|P Chain P, VndNK-2 HomeodomainDNA COMPLEX, NMR, MINIMIZED AVERAGE
Structure
pdb|1VND|A Chain A, VndNK-2 Protein (Homeodomain), Nmr
Length = 77
Score = 32.0 bits (71), Expect = 0.40, Method: Composition-based stats.
Identities = 21/67 (31%), Positives = 30/67 (44%), Gaps = 2/67 (2%)
Query: 203 PNKRP--RTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEK 260
PNK+ R T Q L+ + + RE L+ L V++WFQN R K K
Sbjct: 6 PNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTK 65
Query: 261 RLKKDAG 267
R + + G
Sbjct: 66 RAQNEKG 72
>pdb|2CUR|A Chain A, Solution Structure Of Skeletal Muscle Lim-Protein 1
Length = 69
Score = 31.6 bits (70), Expect = 0.65, Method: Composition-based stats.
Identities = 16/48 (33%), Positives = 24/48 (50%), Gaps = 3/48 (6%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDR 179
C C I + QD +H +CF CV C+++L G F +ED+
Sbjct: 8 CVKCNKAITSGGITY--QDQPWHADCFVCVTCSKKL-AGQRFTAVEDQ 52
>pdb|1FTT|A Chain A, Thyroid Transcription Factor 1 Homeodomain (Rattus
Norvegicus)
Length = 68
Score = 31.2 bits (69), Expect = 0.75, Method: Composition-based stats.
Identities = 18/61 (29%), Positives = 28/61 (45%)
Query: 205 KRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKK 264
++ R + Q+ L+ + + RE L+ L V++WFQN R K KR K
Sbjct: 3 RKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAK 62
Query: 265 D 265
D
Sbjct: 63 D 63
>pdb|1V6G|A Chain A, Solution Structure Of The Lim Domain Of The Human Actin
Binding Lim Protein 2
Length = 81
Score = 31.2 bits (69), Expect = 0.79, Method: Composition-based stats.
Identities = 16/49 (32%), Positives = 23/49 (46%), Gaps = 2/49 (4%)
Query: 123 DFFKRFGTKCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGD 171
D+ + +GT+C C+ I V A YH +CF C +C GD
Sbjct: 9 DYQRLYGTRCFSCDQFIEGEVV--SALGKTYHPDCFVCAVCRLPFPPGD 55
>pdb|2L9R|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Homeobox
Protein Nkx-3.1 From Homo Sapiens, Northeast Structural
Genomics Consortium Target Hr6470a
Length = 69
Score = 31.2 bits (69), Expect = 0.85, Method: Composition-based stats.
Identities = 13/28 (46%), Positives = 18/28 (64%)
Query: 234 REQLSQDTGLDMRVVQVWFQNRRAKEKR 261
R L+++ L V++WFQNRR K KR
Sbjct: 34 RAHLAKNLKLTETQVKIWFQNRRYKTKR 61
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 30.8 bits (68), Expect = 0.89, Method: Composition-based stats.
Identities = 17/58 (29%), Positives = 30/58 (51%)
Query: 205 KRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRL 262
++ R T Q L+ + + R R ++++ L R V++WFQNRR K K++
Sbjct: 2 RKKRCPYTKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMKKM 59
>pdb|3A01|A Chain A, Crystal Structure Of Aristaless And Clawless Homeodomains
Bo
pdb|3A01|E Chain E, Crystal Structure Of Aristaless And Clawless Homeodomains
Bo
Length = 93
Score = 30.8 bits (68), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 26/71 (36%), Positives = 35/71 (49%), Gaps = 6/71 (8%)
Query: 195 GNCLDGDQPNKR--PRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQV-- 250
G+ P KR PRT+ T Q+ L+ ++ A R L++ GL M QV
Sbjct: 6 GHPYQNRTPPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALAR--GLKMTDAQVKT 63
Query: 251 WFQNRRAKEKR 261
WFQNRR K +R
Sbjct: 64 WFQNRRTKWRR 74
>pdb|1X2M|A Chain A, Solution Structure Of The Homeobox Domain Of Mouse Lag1
Longevity Assurance Homolog 6
Length = 64
Score = 30.0 bits (66), Expect = 1.5, Method: Composition-based stats.
Identities = 17/45 (37%), Positives = 23/45 (51%), Gaps = 2/45 (4%)
Query: 216 LETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEK 260
LE + A P R E LS+ D+R +Q WF+ RR +EK
Sbjct: 15 LEKVFTAITKHPDEKR--LEGLSKQLDWDVRSIQRWFRQRRNQEK 57
>pdb|2DA5|A Chain A, Solution Structure Of The Second Homeobox Domain Of Zinc
Fingers And Homeoboxes Protein 3 (Triple Homeobox 1
Protein)
Length = 75
Score = 30.0 bits (66), Expect = 1.6, Method: Composition-based stats.
Identities = 13/45 (28%), Positives = 23/45 (51%)
Query: 214 KQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAK 258
+QL L+ ++ +P P ++L +T + R + WF RR K
Sbjct: 17 EQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKK 61
>pdb|1X63|A Chain A, Solution Structure Of The Second Lim Domain Of Skeletal
Muscle Lim Protein 1
Length = 82
Score = 29.6 bits (65), Expect = 2.0, Method: Composition-based stats.
Identities = 16/48 (33%), Positives = 21/48 (43%)
Query: 131 KCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMED 178
KC GC I + V+H +CF C C + + TG F ED
Sbjct: 17 KCKGCFKAIVAGDQNVEYKGTVWHKDCFTCSNCKQVIGTGSFFPKGED 64
>pdb|1WIG|A Chain A, Solution Structure Of Rsgi Ruh-019, A Lim Domain Of Actin
Binding Lim Protein 2 (kiaa1808 Protein) From Human Cdna
Length = 73
Score = 29.3 bits (64), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 17/44 (38%), Positives = 21/44 (47%), Gaps = 2/44 (4%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYL 175
C CE I T V A + YH +C CV C + G+E YL
Sbjct: 8 CDSCEKYI--TGRVLEAGEKHYHPSCALCVRCGQMFAEGEEMYL 49
>pdb|2VI6|A Chain A, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|B Chain B, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|C Chain C, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|D Chain D, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|E Chain E, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|F Chain F, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|G Chain G, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|H Chain H, Crystal Structure Of The Nanog Homeodomain
Length = 62
Score = 29.3 bits (64), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 28/59 (47%)
Query: 203 PNKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKR 261
++ RT + QL LK + + ++LS L + V+ WFQN+R K KR
Sbjct: 2 TKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKR 60
>pdb|1WH5|A Chain A, Solution Structure Of Homeobox Domain Of
Arabidopsisthaliana Zinc Finger Homeobox Family Protein
Length = 80
Score = 29.3 bits (64), Expect = 2.9, Method: Composition-based stats.
Identities = 19/56 (33%), Positives = 30/56 (53%), Gaps = 4/56 (7%)
Query: 205 KRPRTTITAKQLE-TLKMAYNTSPKPARH---VREQLSQDTGLDMRVVQVWFQNRR 256
KR RT TA+Q E L +A + R V ++ Q+TG+ +V++VW N +
Sbjct: 18 KRHRTKFTAEQKERMLALAERIGWRIQRQDDEVIQRFCQETGVPRQVLKVWLHNNK 73
>pdb|1IML|A Chain A, Cysteine Rich Intestinal Protein, Nmr, 48 Structures
Length = 76
Score = 29.3 bits (64), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 27/63 (42%), Gaps = 2/63 (3%)
Query: 71 PKCGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCFARN-GLLFCKEDFFKR-F 128
PKC C + + L + WH CLKC +CG L A + G +C + F
Sbjct: 1 PKCPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMF 60
Query: 129 GTK 131
G K
Sbjct: 61 GPK 63
>pdb|1X4K|A Chain A, Solution Structure Of Lim Domain In Lim-Protein 3
Length = 72
Score = 28.9 bits (63), Expect = 3.6, Method: Composition-based stats.
Identities = 9/21 (42%), Positives = 11/21 (52%)
Query: 92 TWHARCLKCHECGAPLAEKCF 112
+WH C CH C P+ K F
Sbjct: 28 SWHETCFICHRCQQPIGTKSF 48
>pdb|1WYH|A Chain A, Solution Structure Of The Lim Domain From Human Skeletal
Muscle Lim-Protein 2
Length = 72
Score = 28.1 bits (61), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 13/46 (28%), Positives = 21/46 (45%), Gaps = 1/46 (2%)
Query: 86 LKVLERTWHARCLKCHECGAPLAEKCFARN-GLLFCKEDFFKRFGT 130
L+ +TWH C C C PL + F + G +C + +F +
Sbjct: 22 LEYGGQTWHEHCFLCSGCEQPLGSRSFVPDKGAHYCVPCYENKFAS 67
>pdb|2O13|A Chain A, Solution Structure Of The C-Terminal Lim Domain Of MlpCRP3
Length = 58
Score = 27.7 bits (60), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 26/58 (44%), Gaps = 1/58 (1%)
Query: 72 KCGGCGDLILDRFILKVLERTWHARCLKCHECGAPL-AEKCFARNGLLFCKEDFFKRF 128
KC CG + + + WH C +C CG L + ++G L+CK + K F
Sbjct: 1 KCPRCGKSVYAAEKVMGGGKPWHKTCFRCAICGKSLESTNVTDKDGELYCKVCYAKNF 58
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.323 0.137 0.435
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,254,015
Number of Sequences: 62578
Number of extensions: 371273
Number of successful extensions: 1019
Number of sequences better than 100.0: 130
Number of HSP's better than 100.0 without gapping: 109
Number of HSP's successfully gapped in prelim test: 21
Number of HSP's that attempted gapping in prelim test: 873
Number of HSP's gapped (non-prelim): 151
length of query: 306
length of database: 14,973,337
effective HSP length: 98
effective length of query: 208
effective length of database: 8,840,693
effective search space: 1838864144
effective search space used: 1838864144
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 51 (24.3 bits)