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= psy2704
(256 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 118 bits (295), Expect = 3e-27, Method: Compositional matrix adjust.
Identities = 54/65 (83%), Positives = 62/65 (95%)
Query: 111 KRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWR 170
KRKQRRYRTTF++FQLEELE+AF +THYPDVF REELA++I LTEAR+QVWFQNRRAKWR
Sbjct: 3 KRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWR 62
Query: 171 KQEKL 175
KQEK+
Sbjct: 63 KQEKV 67
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 107 bits (267), Expect = 7e-24, Method: Compositional matrix adjust.
Identities = 48/58 (82%), Positives = 55/58 (94%)
Query: 116 RYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE 173
RYRTTF++FQLEELE+AF +THYPDVF REELA++I LTEAR+QVWFQNRRAKWRKQE
Sbjct: 1 RYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQE 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 = 106 bits (265), Expect = 1e-23, Method: Compositional matrix adjust.
Identities = 48/66 (72%), Positives = 58/66 (87%)
Query: 110 GKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKW 169
K K+RR RTTF+++QLEELE+ F KTHYPDV+ RE+LA+R DLTEARVQVWFQNRRAKW
Sbjct: 5 NKGKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKW 64
Query: 170 RKQEKL 175
RK+E+
Sbjct: 65 RKRERF 70
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 102 bits (253), Expect = 3e-22, Method: Compositional matrix adjust.
Identities = 45/56 (80%), Positives = 53/56 (94%)
Query: 120 TFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKL 175
TF++FQLEELE+AF +THYPDVF REELA++I LTEAR+QVWFQNRRAKWRKQEK+
Sbjct: 5 TFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQEKV 60
>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 = 99.8 bits (247), Expect = 1e-21, Method: Compositional matrix adjust.
Identities = 48/67 (71%), Positives = 55/67 (82%)
Query: 111 KRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWR 170
KRKQRR RTTFS QL+ELERAF +T YPD++ REELA R +LTEAR+QVWFQNRRA+ R
Sbjct: 15 KRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLR 74
Query: 171 KQEKLVS 177
KQ VS
Sbjct: 75 KQHTSVS 81
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 96.7 bits (239), Expect = 1e-20, Method: Composition-based stats.
Identities = 45/59 (76%), Positives = 50/59 (84%)
Query: 114 QRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ 172
QRR RTTF+ QLEELERAF +THYPD++ REELA R LTEARVQVWF NRRA+WRKQ
Sbjct: 2 QRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRARWRKQ 60
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 92.0 bits (227), Expect = 3e-19, Method: Compositional matrix adjust.
Identities = 41/66 (62%), Positives = 53/66 (80%)
Query: 116 RYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKL 175
R RT+F+ Q+E LE+ F +THYPDVF RE LA +IDL EAR+QVWF NRRAKWR++EKL
Sbjct: 9 RNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKL 68
Query: 176 VSKQPQ 181
+++ Q
Sbjct: 69 RNQRRQ 74
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 82.8 bits (203), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 38/63 (60%), Positives = 51/63 (80%)
Query: 114 QRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE 173
QRR RT F++ QL+ELE F + HYPD+ REE+A+ +LTEARV+VWF+NRRAKWRK+E
Sbjct: 3 QRRQRTHFTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE 62
Query: 174 KLV 176
+ +
Sbjct: 63 EFI 65
>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Otx2
Length = 80
Score = 79.7 bits (195), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 37/56 (66%), Positives = 45/56 (80%)
Query: 115 RRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWR 170
RR RTTF+ QL+ LE F KT YPD+F REE+AL+I+L E+RVQVWF+NRRAK R
Sbjct: 8 RRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCR 63
>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 = 79.3 bits (194), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 37/63 (58%), Positives = 50/63 (79%)
Query: 114 QRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE 173
QRR RT F++ QL+ELE F + YPD+ REE+A+ +LTEARV+VWF+NRRAKWRK+E
Sbjct: 3 QRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE 62
Query: 174 KLV 176
+ +
Sbjct: 63 EFI 65
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 75.9 bits (185), Expect = 2e-14, Method: Composition-based stats.
Identities = 33/57 (57%), Positives = 44/57 (77%)
Query: 115 RRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
RR+RT F++ QLE LE F +T YPDV RE+LA ++ L E +V+VWF+NRRAKWR+
Sbjct: 8 RRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRR 64
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor Gbx1
From Homo Sapiens
Length = 71
Score = 64.3 bits (155), Expect = 7e-11, Method: Composition-based stats.
Identities = 28/59 (47%), Positives = 41/59 (69%)
Query: 113 KQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
K RR RT F++ QL ELE+ FH Y + R ++A + L+E +V++WFQNRRAKW++
Sbjct: 6 KSRRRRTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRAKWKR 64
>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 = 59.7 bits (143), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 28/60 (46%), Positives = 41/60 (68%)
Query: 113 KQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ 172
K+++ RT+F+ Q+ ELE+ FHK Y R LA + +T+A+V+ WFQNRR KWR+Q
Sbjct: 16 KRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQ 75
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 58.9 bits (141), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 27/57 (47%), Positives = 40/57 (70%)
Query: 115 RRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
R+ RT +S+FQL L+R F KT Y + R ELA + LT+ +V++WFQN+R+K +K
Sbjct: 8 RKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKK 64
>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 = 58.9 bits (141), Expect = 3e-09, Method: Composition-based stats.
Identities = 26/61 (42%), Positives = 40/61 (65%)
Query: 114 QRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE 173
++R R T++ +Q ELE+ FH Y R E+A + LTE ++++WFQNRR KW+K+
Sbjct: 2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEN 61
Query: 174 K 174
K
Sbjct: 62 K 62
>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 = 58.5 bits (140), Expect = 4e-09, Method: Composition-based stats.
Identities = 27/59 (45%), Positives = 39/59 (66%)
Query: 115 RRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE 173
+R RT ++ QL ELE+ F Y R ELA+ ++LTE +++WFQNRR KW+K+E
Sbjct: 4 KRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKEE 62
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 58.5 bits (140), Expect = 4e-09, Method: Composition-based stats.
Identities = 26/59 (44%), Positives = 39/59 (66%)
Query: 114 QRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ 172
+RR R T++ +Q ELE+ FH HY R E+A + LTE ++++WFQNRR K +K+
Sbjct: 20 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKE 78
>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 = 58.2 bits (139), Expect = 4e-09, Method: Composition-based stats.
Identities = 26/61 (42%), Positives = 40/61 (65%)
Query: 114 QRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE 173
++R R T++ +Q ELE+ FH Y R E+A + LTE ++++WFQNRR KW+K+
Sbjct: 2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 61
Query: 174 K 174
K
Sbjct: 62 K 62
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 57.8 bits (138), Expect = 6e-09, Method: Composition-based stats.
Identities = 25/60 (41%), Positives = 40/60 (66%)
Query: 113 KQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ 172
+++R R T++ +Q ELE+ FH Y R E+A + LTE ++++WFQNRR KW+K+
Sbjct: 2 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 61
>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 = 56.2 bits (134), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 26/60 (43%), Positives = 40/60 (66%)
Query: 115 RRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK 174
+R RT+++ +Q ELE+ FH Y R E+A + LTE ++++WFQNRR KW+K+ K
Sbjct: 29 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEHK 88
>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 = 54.7 bits (130), Expect = 5e-08, Method: Composition-based stats.
Identities = 24/55 (43%), Positives = 36/55 (65%)
Query: 120 TFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK 174
T++ +Q ELE+ FH Y R E+A + LTE ++++WFQNRR KW+K+ K
Sbjct: 2 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENK 56
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant R31lE42L
Length = 67
Score = 53.9 bits (128), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 26/60 (43%), Positives = 38/60 (63%)
Query: 115 RRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK 174
RR RT F+ Q+E LE F YP + E+LA +++L R+Q+WFQNRRAK ++ +
Sbjct: 2 RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHR 61
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Barh-Like 1
Length = 80
Score = 53.9 bits (128), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 26/60 (43%), Positives = 37/60 (61%)
Query: 112 RKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
+K RR RT F+ QL LE+ F K Y R +LA + L++ +V+ W+QNRR KW+K
Sbjct: 15 KKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKK 74
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 53.5 bits (127), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 26/57 (45%), Positives = 37/57 (64%)
Query: 118 RTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK 174
RT F+ QL ELE+ FH Y R E+A ++L E +V++WFQNRR K +K+E+
Sbjct: 38 RTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRER 94
>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 = 52.4 bits (124), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 28/58 (48%), Positives = 40/58 (68%)
Query: 115 RRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ 172
RRYRT F+ QL LE+ F+K +Y R ELA +++L E+ ++VWFQNRR K ++Q
Sbjct: 2 RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ 59
>pdb|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain
Length = 56
Score = 52.0 bits (123), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 26/54 (48%), Positives = 35/54 (64%)
Query: 119 TTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ 172
T+FS Q+ ELER F + Y R LA + +T+A+V+ WFQNRR KWR+Q
Sbjct: 2 TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ 55
>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 = 50.4 bits (119), Expect = 9e-07, Method: Composition-based stats.
Identities = 23/58 (39%), Positives = 40/58 (68%)
Query: 114 QRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
++R RT FS+ QL L+R F++ Y R++L+ + L EA++++WF+N+RAK +K
Sbjct: 3 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK 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 = 23/58 (39%), Positives = 39/58 (67%)
Query: 114 QRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
++R RT FS+ QL +R F++ Y R++L+ + L EA++++WFQN+RAK R+
Sbjct: 3 EKRPRTAFSSEQLARAKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIRR 60
>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX
Protein Lhx9
Length = 80
Score = 50.1 bits (118), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 24/57 (42%), Positives = 36/57 (63%)
Query: 115 RRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
+R RT+F + QL ++ F H PD ++LA + LT+ +QVWFQN RAK+R+
Sbjct: 8 KRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRR 64
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 25/54 (46%), Positives = 34/54 (62%)
Query: 115 RRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAK 168
R+ RT F+ QL LER F + Y + R E + + LTE +V++WFQNRRAK
Sbjct: 1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAK 54
>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 = 49.3 bits (116), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 24/58 (41%), Positives = 40/58 (68%)
Query: 114 QRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
++R RT FS+ QL L+R F++ Y R++L+ + L EA++++WFQN+RAK +K
Sbjct: 3 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 60
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
Length = 60
Score = 48.9 bits (115), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 24/58 (41%), Positives = 40/58 (68%)
Query: 114 QRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
++R RT FS+ QL L+R F++ Y R++L+ + L EA++++WFQN+RAK +K
Sbjct: 1 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 58
>pdb|2E1O|A Chain A, Solution Structure Of Rsgi Ruh-028, A Homeobox Domain From
Human Cdna
Length = 70
Score = 48.5 bits (114), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 25/51 (49%), Positives = 32/51 (62%)
Query: 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
FSN Q ELE+ F Y R+ LA + L+E +V+ WFQNRRAKWR+
Sbjct: 14 FSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR 64
>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 = 47.8 bits (112), Expect = 5e-06, Method: Composition-based stats.
Identities = 23/56 (41%), Positives = 37/56 (66%)
Query: 116 RYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
R RT FS+ QL L+R F++ Y R++L+ + L EA++++WF N+RAK +K
Sbjct: 1 RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANKRAKIKK 56
>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 = 47.8 bits (112), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 24/58 (41%), Positives = 39/58 (67%)
Query: 114 QRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
++R RT FS+ QL L+R F++ Y R++L+ + L EA++++WFQN RAK +K
Sbjct: 1 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNERAKIKK 58
>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 = 47.4 bits (111), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 24/58 (41%), Positives = 39/58 (67%)
Query: 114 QRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
++R RT FS+ QL L+R F++ Y R++L+ + L EA++++WFQN RAK +K
Sbjct: 1 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAKIKK 58
>pdb|1ENH|A Chain A, Structural Studies Of The Engrailed Homeodomain
Length = 54
Score = 47.4 bits (111), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 22/51 (43%), Positives = 35/51 (68%)
Query: 118 RTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAK 168
RT FS+ QL L+R F++ Y R++L+ + L EA++++WFQN+RAK
Sbjct: 3 RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 53
>pdb|1FTT|A Chain A, Thyroid Transcription Factor 1 Homeodomain (Rattus
Norvegicus)
Length = 68
Score = 46.6 bits (109), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 27/61 (44%), Positives = 36/61 (59%)
Query: 114 QRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE 173
+R+ R FS Q+ ELER F + Y RE LA I LT +V++WFQN R K ++Q
Sbjct: 2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQA 61
Query: 174 K 174
K
Sbjct: 62 K 62
>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 77
Score = 46.6 bits (109), Expect = 1e-05, Method: Composition-based stats.
Identities = 25/63 (39%), Positives = 36/63 (57%)
Query: 112 RKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
R R+ R ++ Q ELE+ F Y R E+A ++LTE +V++WFQNRR K +K
Sbjct: 11 RSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKK 70
Query: 172 QEK 174
K
Sbjct: 71 INK 73
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 45.4 bits (106), Expect = 3e-05, Method: Composition-based stats.
Identities = 23/57 (40%), Positives = 35/57 (61%)
Query: 115 RRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
R+ R ++ +Q ELE+ F Y R E+A ++LTE +V++WFQNRR K +K
Sbjct: 2 RKKRCPYTKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMKK 58
>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 = 45.4 bits (106), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 24/58 (41%), Positives = 38/58 (65%)
Query: 114 QRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
++R RT FS+ QL L+R F++ Y R++L+ + L EA+V+ WF+N RAK +K
Sbjct: 4 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMRAKIKK 61
>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 = 45.1 bits (105), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 24/63 (38%), Positives = 38/63 (60%)
Query: 115 RRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK 174
+R R T++ +Q ELE+ FH Y R ++A + L+E ++++WFQNRR K +K
Sbjct: 4 KRTRQTYTRYQTLELEKEFHFNRYITRRRRIDIANALSLSERQIKIWFQNRRMKSKKDRT 63
Query: 175 LVS 177
L S
Sbjct: 64 LDS 66
>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 = 44.7 bits (104), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 24/55 (43%), Positives = 34/55 (61%)
Query: 114 QRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAK 168
+R+ R FS Q+ ELER F + Y R++LA + LT +V++WFQNRR K
Sbjct: 2 RRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYK 56
>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 = 43.9 bits (102), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 25/56 (44%), Positives = 32/56 (57%)
Query: 113 KQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAK 168
K+R+ R F+ Q ELER F + Y RE LA I LT +V++WFQN R K
Sbjct: 8 KKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYK 63
>pdb|2LD5|A Chain A, Solution Nmr-Derived Complex Structure Of Hoxa13 Dna
Binding Domain Bound To Dna
Length = 67
Score = 43.1 bits (100), Expect = 1e-04, Method: Composition-based stats.
Identities = 20/57 (35%), Positives = 33/57 (57%)
Query: 115 RRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
R+ R ++ QL+ELER + + R ++ +L+E +V +WFQNRR K +K
Sbjct: 2 RKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKK 58
>pdb|2CRA|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeo
Box B13
Length = 70
Score = 42.7 bits (99), Expect = 2e-04, Method: Composition-based stats.
Identities = 20/57 (35%), Positives = 32/57 (56%)
Query: 115 RRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
R+ R +S QL ELER + + R +++ L+E ++ +WFQNRR K +K
Sbjct: 8 RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK 64
>pdb|1QRY|A Chain A, Homeobox Protein Vnd (Ventral Nervous System Defective
Protein)
Length = 80
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/56 (42%), Positives = 31/56 (55%)
Query: 113 KQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAK 168
K+R+ R F+ Q ELER F + Y RE L I LT +V++WFQN R K
Sbjct: 11 KKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVKIWFQNHRYK 66
>pdb|1ZQ3|P Chain P, Nmr Solution Structure Of The Bicoid Homeodomain Bound To
The Consensus Dna Binding Site Taatcc
Length = 68
Score = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/68 (35%), Positives = 42/68 (61%), Gaps = 4/68 (5%)
Query: 115 RRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK 174
RR RTTF++ Q+ ELE+ F + Y +L+ ++ L A+V++WF+NR R++ K
Sbjct: 3 RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNR----RRRHK 58
Query: 175 LVSKQPQE 182
+ S Q ++
Sbjct: 59 IQSDQHKD 66
>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 = 41.2 bits (95), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 21/49 (42%), Positives = 30/49 (61%)
Query: 125 QLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE 173
Q+ ELER F Y R LA + LTE +V++WFQNRR K ++++
Sbjct: 15 QVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQ 63
>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain
Length = 73
Score = 40.8 bits (94), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 33/57 (57%)
Query: 115 RRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
R+ R ++ QL+ELER + + R ++ +L+E +V +WFQNRR K +K
Sbjct: 8 RKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKK 64
>pdb|1UHS|A Chain A, Solution Structure Of Mouse Homeodomain-Only Protein Hop
Length = 72
Score = 38.9 bits (89), Expect = 0.002, Method: Composition-based stats.
Identities = 23/60 (38%), Positives = 34/60 (56%), Gaps = 1/60 (1%)
Query: 120 TFSNFQLEELERAFHKTH-YPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKLVSK 178
T + Q+E LE F+K + +PD +A LTE + Q WF+ R A+WR+ E L S+
Sbjct: 7 TMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEGLPSE 66
>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 = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 30/60 (50%)
Query: 113 KQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ 172
K R RT + QL L + PD +E+L L+ ++VWFQN+R K +K+
Sbjct: 2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKR 61
>pdb|2P81|A Chain A, Engrailed Homeodomain Helix-Turn-Helix Motif
Length = 44
Score = 38.5 bits (88), Expect = 0.003, Method: Composition-based stats.
Identities = 16/42 (38%), Positives = 29/42 (69%)
Query: 130 ERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
+R F++ Y R++L+ + L EA++++WFQN+RAK +K
Sbjct: 2 KREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 43
>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 = 38.1 bits (87), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 20/54 (37%), Positives = 32/54 (59%)
Query: 115 RRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAK 168
++ RT FS QL L+ F K Y + +EL+ ++L+ +V+ WFQN+R K
Sbjct: 4 QKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMK 57
>pdb|2KT0|A Chain A, Solution Structure Of Human Stem Cell Transcription Factor
Nanog Homeodomain Fragment
Length = 84
Score = 37.4 bits (85), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 37/62 (59%), Gaps = 3/62 (4%)
Query: 113 KQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAK---W 169
K+++ RT FS+ QL L F + Y + +EL+ ++L+ +V+ WFQN+R K W
Sbjct: 21 KKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRW 80
Query: 170 RK 171
+K
Sbjct: 81 QK 82
>pdb|2HI3|A Chain A, Solution Structure Of The Homeodomain-Only Protein Hop
Length = 73
Score = 37.0 bits (84), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 22/55 (40%), Positives = 32/55 (58%), Gaps = 1/55 (1%)
Query: 125 QLEELERAFHKTH-YPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKLVSK 178
Q+E LE F+K + +PD +A LTE + Q WF+ R A+WR+ E L S+
Sbjct: 13 QVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEGLPSE 67
>pdb|2DA3|A Chain A, Solution Structure Of The Third Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 80
Score = 36.6 bits (83), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 22/59 (37%), Positives = 32/59 (54%)
Query: 113 KQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
+ +R RTT + QLE L + + P + +A + L + VQVWFQN RA+ RK
Sbjct: 16 RDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERK 74
>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 = 35.8 bits (81), Expect = 0.023, Method: Composition-based stats.
Identities = 21/60 (35%), Positives = 31/60 (51%), Gaps = 3/60 (5%)
Query: 115 RRYRTTFSNFQLEELERAFHK---THYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
RR R FS E L F+ YP +EELA + +T ++V WF N+R +++K
Sbjct: 2 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCGITVSQVSNWFGNKRIRYKK 61
>pdb|1PUF|B Chain B, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 73
Score = 35.4 bits (80), Expect = 0.032, Method: Composition-based stats.
Identities = 21/61 (34%), Positives = 33/61 (54%), Gaps = 5/61 (8%)
Query: 115 RRYRTTFSNFQLEELERAFHKTH----YPDVFFREELALRIDLTEARVQVWFQNRRAKWR 170
RR R F N Q E+ + +H YP +EELA + +T ++V WF N+R +++
Sbjct: 2 RRKRRNF-NKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYK 60
Query: 171 K 171
K
Sbjct: 61 K 61
>pdb|1LFU|P Chain P, Nmr Solution Stucture Of The Extended Pbx Homeodomain
Bound To Dna
Length = 82
Score = 35.0 bits (79), Expect = 0.044, Method: Composition-based stats.
Identities = 21/61 (34%), Positives = 33/61 (54%), Gaps = 5/61 (8%)
Query: 115 RRYRTTFSNFQLEELERAFHKTH----YPDVFFREELALRIDLTEARVQVWFQNRRAKWR 170
RR R F N Q E+ + +H YP +EELA + +T ++V WF N+R +++
Sbjct: 3 RRKRRNF-NKQATEILNEYFYSHLSNPYPSEEAKEELAKKSGITVSQVSNWFGNKRIRYK 61
Query: 171 K 171
K
Sbjct: 62 K 62
>pdb|2DA2|A Chain A, Solution Structure Of The Second Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 34.7 bits (78), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 20/53 (37%), Positives = 29/53 (54%)
Query: 119 TTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
T F+++QL L+ F YP E+L+ ++L + VWFQN R K RK
Sbjct: 12 TRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARK 64
>pdb|1B72|B Chain B, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 87
Score = 34.3 bits (77), Expect = 0.066, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 33/61 (54%), Gaps = 5/61 (8%)
Query: 115 RRYRTTFSNFQLEELERAFHKTH----YPDVFFREELALRIDLTEARVQVWFQNRRAKWR 170
RR R F N Q E+ + +H YP +EELA + +T ++V WF N+R +++
Sbjct: 2 RRKRRNF-NKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYK 60
Query: 171 K 171
K
Sbjct: 61 K 61
>pdb|1DU6|A Chain A, Solution Structure Of The Truncated Pbx Homeodomain
Length = 64
Score = 32.7 bits (73), Expect = 0.21, Method: Composition-based stats.
Identities = 17/53 (32%), Positives = 29/53 (54%), Gaps = 4/53 (7%)
Query: 123 NFQLEELERAFHKTH----YPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
N Q E+ + +H YP +EELA + +T ++V WF N+R +++K
Sbjct: 11 NKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 63
>pdb|2NZZ|A Chain A, Nmr Structure Analysis Of The Penetratin Conjugated Gas
(374-394) Peptide
pdb|2O00|A Chain A, Nmr Structure Analysis Of The Penetratin Conjugated Gas
(374-394) Peptide
Length = 37
Score = 32.0 bits (71), Expect = 0.35, Method: Composition-based stats.
Identities = 9/16 (56%), Positives = 15/16 (93%)
Query: 157 RVQVWFQNRRAKWRKQ 172
++++WFQNRR KW+K+
Sbjct: 2 QIKIWFQNRRMKWKKR 17
>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 = 30.8 bits (68), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 27/54 (50%)
Query: 113 KQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRR 166
K+R+ RT+F+ +E L F K P E A ++ V+VWF NRR
Sbjct: 92 KKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEXAKELNYDREVVRVWFSNRR 145
>pdb|1KZ0|A Chain A, Solution Structure Of The Third Helix Of Antennapedia
Homeodomain
Length = 16
Score = 30.8 bits (68), Expect = 0.83, Method: Composition-based stats.
Identities = 9/15 (60%), Positives = 14/15 (93%)
Query: 157 RVQVWFQNRRAKWRK 171
++++WFQNRR KW+K
Sbjct: 2 QIKIWFQNRRMKWKK 16
>pdb|1OMQ|A Chain A, Structure Of Penetratin In Bicellar Solution
Length = 16
Score = 30.8 bits (68), Expect = 0.83, Method: Composition-based stats.
Identities = 9/15 (60%), Positives = 14/15 (93%)
Query: 157 RVQVWFQNRRAKWRK 171
++++WFQNRR KW+K
Sbjct: 2 QIKIWFQNRRMKWKK 16
>pdb|1AU7|A Chain A, Pit-1 MutantDNA COMPLEX
pdb|1AU7|B Chain B, Pit-1 MutantDNA COMPLEX
Length = 146
Score = 30.0 bits (66), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 30/56 (53%)
Query: 113 KQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAK 168
++R+ RTT S + LER F + P +A ++L + V+VWF NRR +
Sbjct: 86 RKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQR 141
>pdb|3L1P|A Chain A, Pou Protein:dna Complex
pdb|3L1P|B Chain B, Pou Protein:dna Complex
Length = 155
Score = 30.0 bits (66), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 31/58 (53%)
Query: 114 QRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
++R RT+ N LE F K+ P + +A ++ L + V+VWF NRR K ++
Sbjct: 96 RKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGKR 153
>pdb|1POG|A Chain A, Solution Structure Of The Oct-1 Pou-Homeo Domain
Determined By Nmr And Restrained Molecular Dynamics
Length = 67
Score = 29.6 bits (65), Expect = 1.7, Method: Composition-based stats.
Identities = 15/59 (25%), Positives = 32/59 (54%)
Query: 113 KQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
++R+ RT+ LE++F + P +A ++++ + ++VWF NRR K ++
Sbjct: 6 RRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKR 64
>pdb|2XSD|C Chain C, Crystal Structure Of The Dimeric Oct-6 (Pou3f1) Pou Domain
Bound To Palindromic More Dna
Length = 164
Score = 29.3 bits (64), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 28/59 (47%)
Query: 113 KQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171
++R+ RT+ LE F K P LA + L + V+VWF NRR K ++
Sbjct: 98 RKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKEKR 156
>pdb|2CQX|A Chain A, Solution Structure Of Rsgi Ruh-034, A Homeodomain From
Mouse Cdna
Length = 72
Score = 29.3 bits (64), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 25/41 (60%), Gaps = 1/41 (2%)
Query: 127 EELERAF-HKTHYPDVFFREELALRIDLTEARVQVWFQNRR 166
+ LE+ F T YPD + L+ ++D + ++Q WF++RR
Sbjct: 21 DTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRR 61
>pdb|1MH3|A Chain A, Maltose Binding-A1 Homeodomain Protein Chimera, Crystal
Form I
pdb|1MH4|A Chain A, Maltose Binding-A1 Homeodomain Protein Chimera, Crystal
Form Ii
Length = 421
Score = 28.9 bits (63), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 13/40 (32%), Positives = 24/40 (60%)
Query: 129 LERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAK 168
LE+ F + + +EE+A + +T +V+VWF N+R +
Sbjct: 380 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMR 419
>pdb|1YRN|A Chain A, Crystal Structure Of The Mata1MATALPHA2 HOMEODOMAIN
Heterodimer Bound To Dna
pdb|1F43|A Chain A, Solution Structure Of The Mata1 Homeodomain
Length = 61
Score = 28.9 bits (63), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 23/38 (60%)
Query: 129 LERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRR 166
LE+ F + + +EE+A + +T +V+VWF N+R
Sbjct: 20 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKR 57
>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 = 28.5 bits (62), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 14/46 (30%), Positives = 22/46 (47%)
Query: 125 QLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWR 170
QL L+ AF +T +P ++LA L + WF + R W+
Sbjct: 36 QLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWK 81
>pdb|1OCP|A Chain A, Solution Structure Of Oct3 Pou-Homeodomain
Length = 67
Score = 28.5 bits (62), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 28/55 (50%)
Query: 114 QRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAK 168
++R RT+ N LE F K P + +A ++ L + V+VWF NRR K
Sbjct: 8 RKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQK 62
>pdb|1AKH|A Chain A, Mat A1ALPHA2DNA TERNARY COMPLEX
Length = 61
Score = 28.5 bits (62), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 22/38 (57%)
Query: 129 LERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRR 166
LE F + + +EE+A + +T +V+VWF N+R
Sbjct: 20 LEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKR 57
>pdb|1LE8|A Chain A, Crystal Structure Of The Mata1MATALPHA2-3a Heterodimer
Bound To Dna Complex
Length = 53
Score = 28.5 bits (62), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 13/40 (32%), Positives = 24/40 (60%)
Query: 129 LERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAK 168
LE+ F + + +EE+A + +T +V+VWF N+R +
Sbjct: 12 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMR 51
>pdb|4EGC|A Chain A, Crystal Structure Of Mbp-fused Human Six1 Bound To Human
Eya2 Eya Domain
Length = 559
Score = 28.5 bits (62), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 19/36 (52%)
Query: 138 YPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE 173
YP + ELA LT +V WF+NRR + R E
Sbjct: 518 YPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAE 553
>pdb|1E3O|C Chain C, Crystal Structure Of Oct-1 Pou Dimer Bound To More
Length = 160
Score = 28.5 bits (62), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 17/65 (26%), Positives = 35/65 (53%), Gaps = 6/65 (9%)
Query: 110 GKRKQRRYRTTFSNFQLEELERAFHKTHYP---DVFFREELALRIDLTEARVQVWFQNRR 166
G ++R+ RT+ LE++F + P D+ +A ++++ + ++VWF NRR
Sbjct: 97 GLSRRRKKRTSIETNIRVALEKSFMENQKPTSEDITL---IAEQLNMEKEVIRVWFSNRR 153
Query: 167 AKWRK 171
K ++
Sbjct: 154 QKEKR 158
>pdb|2EKS|B Chain B, Crystal Structure Of Humanized Hyhel-10 Fv-Hen Lysozyme
Complex
Length = 113
Score = 27.7 bits (60), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 18/29 (62%)
Query: 225 GMEWGGFMSYQGASTPQPQKESSDIISTD 253
G+EW G++SY G++ P +S IS D
Sbjct: 44 GLEWIGYVSYSGSTYYNPSLKSRVTISVD 72
>pdb|2DN0|A Chain A, Solution Structure Of The Second Homeobox Domain Of Human
Zinc Fingers And Homeoboxes Protein 3
Length = 76
Score = 27.7 bits (60), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 25/54 (46%)
Query: 117 YRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWR 170
Y+ S+ QL L+ +F + +P E L L+ V+ WF +RR R
Sbjct: 11 YKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCR 64
>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 = 27.7 bits (60), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 16/62 (25%), Positives = 33/62 (53%)
Query: 110 GKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKW 169
G ++R+ RT+ LE++F + P +A ++++ + ++VWF NRR K
Sbjct: 96 GLSRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFSNRRQKE 155
Query: 170 RK 171
++
Sbjct: 156 KR 157
>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 = 27.3 bits (59), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 16/62 (25%), Positives = 33/62 (53%)
Query: 110 GKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKW 169
G ++R+ RT+ LE++F + P +A ++++ + ++VWF NRR K
Sbjct: 100 GLSERRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKE 159
Query: 170 RK 171
++
Sbjct: 160 KR 161
>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 = 27.3 bits (59), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 16/62 (25%), Positives = 33/62 (53%)
Query: 110 GKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKW 169
G ++R+ RT+ LE++F + P +A ++++ + ++VWF NRR K
Sbjct: 99 GLSRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKE 158
Query: 170 RK 171
++
Sbjct: 159 KR 160
>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 = 26.9 bits (58), Expect = 9.6, Method: Compositional matrix adjust.
Identities = 16/62 (25%), Positives = 33/62 (53%)
Query: 110 GKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKW 169
G ++R+ RT+ LE++F + P +A ++++ + ++VWF NRR K
Sbjct: 92 GLSRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKE 151
Query: 170 RK 171
++
Sbjct: 152 KR 153
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
0.319 0.134 0.404
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,365,745
Number of Sequences: 62578
Number of extensions: 212736
Number of successful extensions: 598
Number of sequences better than 100.0: 90
Number of HSP's better than 100.0 without gapping: 87
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 510
Number of HSP's gapped (non-prelim): 90
length of query: 256
length of database: 14,973,337
effective HSP length: 97
effective length of query: 159
effective length of database: 8,903,271
effective search space: 1415620089
effective search space used: 1415620089
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)