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= psy1901
(205 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 131 bits (330), Expect = 2e-31, Method: Compositional matrix adjust.
Identities = 62/75 (82%), Positives = 68/75 (90%)
Query: 19 DESDTESEPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEAR 78
D SD ESEPGI LKRKQRRSRTTF+ QL+ELERAF+RTQYPD+YTREELAQ+T LTEAR
Sbjct: 2 DISDCESEPGIALKRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEAR 61
Query: 79 VQVWFSNRRARLRKQ 93
+QVWF NRRARLRKQ
Sbjct: 62 IQVWFQNRRARLRKQ 76
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 105 bits (263), Expect = 1e-23, Method: Compositional matrix adjust.
Identities = 51/59 (86%), Positives = 55/59 (93%)
Query: 35 QRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93
QRRSRTTFT +QLEELERAF+RT YPD+YTREELAQ+ KLTEARVQVWFSNRRAR RKQ
Sbjct: 2 QRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRARWRKQ 60
>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 = 97.4 bits (241), Expect = 5e-21, Method: Compositional matrix adjust.
Identities = 48/62 (77%), Positives = 52/62 (83%)
Query: 32 KRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLR 91
KRKQRR RTTFT QLEELE+AF RT YPDV+TREELA K LTEAR+QVWF NRRA+ R
Sbjct: 3 KRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWR 62
Query: 92 KQ 93
KQ
Sbjct: 63 KQ 64
>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4490c
Length = 75
Score = 90.9 bits (224), Expect = 5e-19, Method: Compositional matrix adjust.
Identities = 44/62 (70%), Positives = 52/62 (83%)
Query: 32 KRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLR 91
K K+RR+RTTFT QLEELE+ FQ+T YPDVY RE+LA +T LTEARVQVWF NRRA+ R
Sbjct: 6 KGKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWR 65
Query: 92 KQ 93
K+
Sbjct: 66 KR 67
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 89.0 bits (219), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 43/57 (75%), Positives = 47/57 (82%)
Query: 37 RSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93
R RTTFT QLEELE+AF RT YPDV+TREELA K LTEAR+QVWF NRRA+ RKQ
Sbjct: 1 RYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQ 57
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 86.3 bits (212), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 41/56 (73%), Positives = 45/56 (80%)
Query: 38 SRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93
S TFT QLEELE+AF RT YPDV+TREELA K LTEAR+QVWF NRRA+ RKQ
Sbjct: 2 SHMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQ 57
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 78.2 bits (191), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 35/57 (61%), Positives = 46/57 (80%)
Query: 37 RSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93
R+RT+FT +Q+E LE+ F+RT YPDV+ RE LA K L EAR+QVWFSNRRA+ R++
Sbjct: 9 RNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRRE 65
>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 = 77.4 bits (189), Expect = 6e-15, Method: Compositional matrix adjust.
Identities = 39/59 (66%), Positives = 46/59 (77%)
Query: 35 QRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93
QRR RT FT QL+ELE FQR +YPD+ TREE+A T LTEARV+VWF NRRA+ RK+
Sbjct: 3 QRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR 61
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 77.0 bits (188), Expect = 6e-15, Method: Compositional matrix adjust.
Identities = 39/59 (66%), Positives = 45/59 (76%)
Query: 35 QRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93
QRR RT FT QL+ELE FQR YPD+ TREE+A T LTEARV+VWF NRRA+ RK+
Sbjct: 3 QRRQRTHFTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR 61
>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Otx2
Length = 80
Score = 75.1 bits (183), Expect = 3e-14, Method: Compositional matrix adjust.
Identities = 34/56 (60%), Positives = 42/56 (75%)
Query: 36 RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLR 91
RR RTTFT QL+ LE F +T+YPD++ REE+A K L E+RVQVWF NRRA+ R
Sbjct: 8 RRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCR 63
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 73.6 bits (179), Expect = 7e-14, Method: Compositional matrix adjust.
Identities = 35/57 (61%), Positives = 43/57 (75%)
Query: 36 RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
RR RT FT +QLE LE FQ T+YPDV TRE+LA+K L E +V+VWF NRRA+ R+
Sbjct: 8 RRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRR 64
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant
R31lE42L
Length = 67
Score = 61.2 bits (147), Expect = 4e-10, Method: Composition-based stats.
Identities = 29/64 (45%), Positives = 39/64 (60%)
Query: 36 RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLN 95
RR RT FT +Q+E LE F+ YP + E+LAQK L R+Q+WF NRRA+L++
Sbjct: 2 RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHR 61
Query: 96 SQQL 99
Q
Sbjct: 62 ESQF 65
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor
Gbx1 From Homo Sapiens
Length = 71
Score = 57.4 bits (137), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 26/56 (46%), Positives = 37/56 (66%)
Query: 34 KQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRAR 89
K RR RT FT +QL ELE+ F +Y + R ++A KL+E +V++WF NRRA+
Sbjct: 6 KSRRRRTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRAK 61
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 55.5 bits (132), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 24/57 (42%), Positives = 39/57 (68%)
Query: 36 RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
R+ RT ++ QL L+R FQ+TQY + R ELA LT+ +V++WF N+R++++K
Sbjct: 8 RKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKK 64
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 50.8 bits (120), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 25/57 (43%), Positives = 36/57 (63%)
Query: 36 RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
R+ RT FT QL LER F++ QY + R E + LTE +V++WF NRRA+ ++
Sbjct: 1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57
>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX
Protein Lhx9
Length = 80
Score = 50.8 bits (120), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 26/63 (41%), Positives = 37/63 (58%)
Query: 36 RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLN 95
+R RT+F QL ++ F PD ++LAQKT LT+ +QVWF N RA+ R+ L
Sbjct: 8 KRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNLL 67
Query: 96 SQQ 98
Q+
Sbjct: 68 RQE 70
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Barh-Like 1
Length = 80
Score = 50.1 bits (118), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 28/67 (41%), Positives = 41/67 (61%), Gaps = 1/67 (1%)
Query: 26 EPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSN 85
EPG K K RRSRT FT QL LE+ F++ +Y R +LA+ L++ +V+ W+ N
Sbjct: 9 EPGTKAK-KGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQN 67
Query: 86 RRARLRK 92
RR + +K
Sbjct: 68 RRMKWKK 74
>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 = 49.3 bits (116), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 25/60 (41%), Positives = 40/60 (66%)
Query: 34 KQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93
K+++ RT+FT Q+ ELE+ F + +Y R LA+ K+T+A+V+ WF NRR + R+Q
Sbjct: 16 KRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQ 75
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 48.9 bits (115), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 24/62 (38%), Positives = 37/62 (59%)
Query: 35 QRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQL 94
+RR R T+T Q ELE+ F Y R E+A LTE ++++WF NRR +L+K++
Sbjct: 20 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKEI 79
Query: 95 NS 96
+
Sbjct: 80 QA 81
>pdb|2KT0|A Chain A, Solution Structure Of Human Stem Cell Transcription
Factor Nanog Homeodomain Fragment
Length = 84
Score = 48.1 bits (113), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 43/75 (57%), Gaps = 2/75 (2%)
Query: 15 PSSGDESDTESEPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKL 74
P+S + S + E +P+K+ +++RT F+ QL L FQR +Y + +EL+ L
Sbjct: 4 PTSAENSVAKKEDKVPVKK--QKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNL 61
Query: 75 TEARVQVWFSNRRAR 89
+ +V+ WF N+R +
Sbjct: 62 SYKQVKTWFQNQRMK 76
>pdb|1ZQ3|P Chain P, Nmr Solution Structure Of The Bicoid Homeodomain Bound
To The Consensus Dna Binding Site Taatcc
Length = 68
Score = 47.8 bits (112), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 24/54 (44%), Positives = 34/54 (62%)
Query: 36 RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRAR 89
RR+RTTFT Q+ ELE+ F + +Y +L+ K L A+V++WF NRR R
Sbjct: 3 RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRR 56
>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 = 47.4 bits (111), Expect = 5e-06, Method: Composition-based stats.
Identities = 21/58 (36%), Positives = 39/58 (67%)
Query: 35 QRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
++R RT F+ +QL L+R F +Y R++L+ + L EA++++WF N+RA+++K
Sbjct: 3 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK 60
>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 = 47.0 bits (110), Expect = 8e-06, Method: Composition-based stats.
Identities = 21/58 (36%), Positives = 39/58 (67%)
Query: 35 QRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
++R RT F+ +QL L+R F +Y R++L+ + L EA++++WF N+RA+++K
Sbjct: 3 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 60
>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 = 46.6 bits (109), Expect = 9e-06, Method: Composition-based stats.
Identities = 24/58 (41%), Positives = 35/58 (60%)
Query: 36 RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93
+R+RT +T QL ELE+ F +Y R ELA LTE +++WF NRR + +K+
Sbjct: 4 KRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKE 61
>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 = 46.6 bits (109), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 26/58 (44%), Positives = 35/58 (60%)
Query: 36 RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93
RR RT FT DQL LE+ F + Y R ELA + L E+ ++VWF NRR + ++Q
Sbjct: 2 RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ 59
>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 = 46.2 bits (108), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 26/70 (37%), Positives = 41/70 (58%), Gaps = 2/70 (2%)
Query: 28 GIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRR 87
G+P K+++RR FT Q ELER F++ +Y RE LA +LT +V++WF N R
Sbjct: 4 GLPNKKRKRR--VLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHR 61
Query: 88 ARLRKQLNSQ 97
+ ++ N +
Sbjct: 62 YKTKRAQNEK 71
>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 = 46.2 bits (108), Expect = 1e-05, Method: Composition-based stats.
Identities = 21/56 (37%), Positives = 38/56 (67%)
Query: 37 RSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
R RT F+ +QL L+R F +Y R++L+ + L EA++++WF+N+RA+++K
Sbjct: 1 RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANKRAKIKK 56
>pdb|1ZTR|A Chain A, Solution Structure Of Engrailed Homeodomain L16a Mutant
Length = 61
Score = 46.2 bits (108), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 38/58 (65%)
Query: 35 QRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
++R RT F+ +QL +R F +Y R++L+ + L EA++++WF N+RA++R+
Sbjct: 3 EKRPRTAFSSEQLARAKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIRR 60
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
Length = 60
Score = 46.2 bits (108), Expect = 1e-05, Method: Composition-based stats.
Identities = 21/58 (36%), Positives = 39/58 (67%)
Query: 35 QRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
++R RT F+ +QL L+R F +Y R++L+ + L EA++++WF N+RA+++K
Sbjct: 1 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 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 = 46.2 bits (108), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 22/58 (37%), Positives = 37/58 (63%)
Query: 35 QRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
++R RT F+ +QL L+R F +Y R++L+ + L EA+V+ WF N RA+++K
Sbjct: 4 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMRAKIKK 61
>pdb|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain
Length = 56
Score = 45.8 bits (107), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 23/54 (42%), Positives = 35/54 (64%)
Query: 40 TTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93
T+F+ Q+ ELER F R +Y R LA+ ++T+A+V+ WF NRR + R+Q
Sbjct: 2 TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ 55
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 45.8 bits (107), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/55 (41%), Positives = 33/55 (60%)
Query: 39 RTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93
RT FT QL ELE+ F +Y R E+A +L E +V++WF NRR + +K+
Sbjct: 38 RTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKR 92
>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 = 45.4 bits (106), Expect = 2e-05, Method: Composition-based stats.
Identities = 21/58 (36%), Positives = 38/58 (65%)
Query: 35 QRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
++R RT F+ +QL L+R F +Y R++L+ + L EA++++WF N RA+++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 = 45.4 bits (106), Expect = 2e-05, Method: Composition-based stats.
Identities = 21/58 (36%), Positives = 38/58 (65%)
Query: 35 QRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
++R RT F+ +QL L+R F +Y R++L+ + L EA++++WF N RA+++K
Sbjct: 1 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAKIKK 58
>pdb|1QRY|A Chain A, Homeobox Protein Vnd (Ventral Nervous System Defective
Protein)
Length = 80
Score = 45.1 bits (105), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 25/70 (35%), Positives = 40/70 (57%), Gaps = 2/70 (2%)
Query: 28 GIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRR 87
G+P K+++RR FT Q ELER F++ +Y RE L +LT +V++WF N R
Sbjct: 7 GLPNKKRKRR--VLFTKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVKIWFQNHR 64
Query: 88 ARLRKQLNSQ 97
+ ++ N +
Sbjct: 65 YKTKRAQNEK 74
>pdb|1FTT|A Chain A, Thyroid Transcription Factor 1 Homeodomain (Rattus
Norvegicus)
Length = 68
Score = 45.1 bits (105), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 22/58 (37%), Positives = 35/58 (60%)
Query: 36 RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93
R+ R F+ Q+ ELER F++ +Y RE LA LT +V++WF N R ++++Q
Sbjct: 3 RKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQ 60
>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 = 3e-05, Method: Compositional matrix adjust.
Identities = 22/53 (41%), Positives = 34/53 (64%)
Query: 35 QRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRR 87
+R+ R F+ Q+ ELER F++ +Y R++LA KLT +V++WF NRR
Sbjct: 2 RRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRR 54
>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 = 44.7 bits (104), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 25/53 (47%), Positives = 34/53 (64%), Gaps = 1/53 (1%)
Query: 46 QLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARL-RKQLNSQ 97
Q+ ELER F +Y R LA+ KLTE +V++WF NRR + RKQL+S+
Sbjct: 15 QVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQLSSE 67
>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 = 44.3 bits (103), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 22/58 (37%), Positives = 35/58 (60%)
Query: 36 RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93
+R RT++T Q ELE+ F +Y R E+A LTE ++++WF NRR + +K+
Sbjct: 29 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 86
>pdb|1ENH|A Chain A, Structural Studies Of The Engrailed Homeodomain
Length = 54
Score = 43.5 bits (101), Expect = 7e-05, Method: Composition-based stats.
Identities = 20/54 (37%), Positives = 35/54 (64%)
Query: 37 RSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARL 90
R RT F+ +QL L+R F +Y R++L+ + L EA++++WF N+RA++
Sbjct: 1 RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKI 54
>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 = 43.1 bits (100), Expect = 1e-04, Method: Composition-based stats.
Identities = 22/59 (37%), Positives = 35/59 (59%)
Query: 35 QRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93
++R R T+T Q ELE+ F +Y R E+A LTE ++++WF NRR + +K+
Sbjct: 2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 60
>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 = 21/60 (35%), Positives = 35/60 (58%)
Query: 36 RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLN 95
R+ R +T QL+ELER + ++ R ++ T L+E +V +WF NRR + +K +N
Sbjct: 2 RKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKVIN 61
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 43.1 bits (100), Expect = 1e-04, Method: Composition-based stats.
Identities = 22/57 (38%), Positives = 33/57 (57%)
Query: 36 RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
R+ R +T Q ELE+ F Y R E+A+ LTE +V++WF NRR +++K
Sbjct: 2 RKKRCPYTKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMKK 58
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 43.1 bits (100), Expect = 1e-04, Method: Composition-based stats.
Identities = 22/60 (36%), Positives = 36/60 (60%)
Query: 34 KQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93
+++R R T+T Q ELE+ F +Y R E+A LTE ++++WF NRR + +K+
Sbjct: 2 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 61
>pdb|2E1O|A Chain A, Solution Structure Of Rsgi Ruh-028, A Homeobox Domain
From Human Cdna
Length = 70
Score = 42.7 bits (99), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 21/51 (41%), Positives = 33/51 (64%)
Query: 42 FTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
F+ DQ ELE+ F+ +Y R+ LA+ +L+E +V+ WF NRRA+ R+
Sbjct: 14 FSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR 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 = 42.7 bits (99), Expect = 1e-04, Method: Composition-based stats.
Identities = 22/59 (37%), Positives = 35/59 (59%)
Query: 35 QRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93
++R R T+T Q ELE+ F +Y R E+A LTE ++++WF NRR + +K+
Sbjct: 2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 60
>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound
To Dna
Length = 77
Score = 42.7 bits (99), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/60 (38%), Positives = 34/60 (56%)
Query: 33 RKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
R R+ R +T Q ELE+ F Y R E+A+ LTE +V++WF NRR +++K
Sbjct: 11 RSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKK 70
>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain
Length = 73
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 35/60 (58%)
Query: 36 RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLN 95
R+ R +T QL+ELER + ++ R ++ T L+E +V +WF NRR + +K +N
Sbjct: 8 RKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKVIN 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 = 6e-04, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 33/57 (57%)
Query: 36 RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
R+ R ++ QL ELER + ++ R +++ T L+E ++ +WF NRR + +K
Sbjct: 8 RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK 64
>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 = 40.0 bits (92), Expect = 8e-04, Method: Composition-based stats.
Identities = 19/60 (31%), Positives = 30/60 (50%)
Query: 34 KQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93
K R RT QL L + PD +E+L + T L+ ++VWF N+R + +K+
Sbjct: 2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKR 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 = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 17/40 (42%), Positives = 27/40 (67%)
Query: 50 LERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRAR 89
LE+ F+R Q + +EE+A+K +T +V+VWF N+R R
Sbjct: 380 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMR 419
>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 = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 34/57 (59%)
Query: 36 RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
+R+R T+T Q ELE+ F +Y R ++A L+E ++++WF NRR + +K
Sbjct: 4 KRTRQTYTRYQTLELEKEFHFNRYITRRRRIDIANALSLSERQIKIWFQNRRMKSKK 60
>pdb|1B72|B Chain B, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 87
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 31/66 (46%), Gaps = 3/66 (4%)
Query: 36 RRSRTTFTGDQLEELERAF---QRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
RR R F E L F YP +EELA+K +T ++V WF N+R R +K
Sbjct: 2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 61
Query: 93 QLNSQQ 98
+ Q
Sbjct: 62 NIGKFQ 67
>pdb|2DA3|A Chain A, Solution Structure Of The Third Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 80
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/59 (38%), Positives = 32/59 (54%)
Query: 34 KQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
+ +R RTT T +QLE L + + P + +A + L + VQVWF N RAR RK
Sbjct: 16 RDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERK 74
>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 = 38.9 bits (89), Expect = 0.002, Method: Composition-based stats.
Identities = 20/53 (37%), Positives = 31/53 (58%)
Query: 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93
T+T Q ELE+ F +Y R E+A LTE ++++WF NRR + +K+
Sbjct: 2 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 54
>pdb|1LFU|P Chain P, Nmr Solution Stucture Of The Extended Pbx Homeodomain
Bound To Dna
Length = 82
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 32/66 (48%), Gaps = 3/66 (4%)
Query: 36 RRSRTTFTGDQLEELERAF---QRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
RR R F E L F YP +EELA+K+ +T ++V WF N+R R +K
Sbjct: 3 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKSGITVSQVSNWFGNKRIRYKK 62
Query: 93 QLNSQQ 98
+ Q
Sbjct: 63 NIGKFQ 68
>pdb|1PUF|B Chain B, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound
To Dna
Length = 73
Score = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 31/66 (46%), Gaps = 3/66 (4%)
Query: 36 RRSRTTFTGDQLEELERAFQR---TQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
RR R F E L F YP +EELA+K +T ++V WF N+R R +K
Sbjct: 2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 61
Query: 93 QLNSQQ 98
+ Q
Sbjct: 62 NIGKFQ 67
>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 = 37.0 bits (84), Expect = 0.007, Method: Composition-based stats.
Identities = 20/62 (32%), Positives = 34/62 (54%)
Query: 33 RKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
R++RR+ + + L E + YP +EELA+K +T ++V WF N+R R +K
Sbjct: 2 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCGITVSQVSNWFGNKRIRYKK 61
Query: 93 QL 94
+
Sbjct: 62 NI 63
>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 = 36.6 bits (83), Expect = 0.009, Method: Composition-based stats.
Identities = 19/58 (32%), Positives = 34/58 (58%)
Query: 32 KRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRAR 89
K K + +++ + LE+ F+R Q + +EE+A+K +T +V+VWF N+R R
Sbjct: 2 KEKSPKGKSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMR 59
>pdb|1AKH|A Chain A, Mat A1ALPHA2DNA TERNARY COMPLEX
Length = 61
Score = 36.6 bits (83), Expect = 0.010, Method: Composition-based stats.
Identities = 19/58 (32%), Positives = 33/58 (56%)
Query: 32 KRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRAR 89
K K + +++ + LE F+R Q + +EE+A+K +T +V+VWF N+R R
Sbjct: 2 KEKSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMR 59
>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 = 36.6 bits (83), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 39/78 (50%), Gaps = 2/78 (2%)
Query: 14 RPSSGDESDTESEPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTK 73
R G ++ E G P K+++RR T+FT +E L F++ P E A++
Sbjct: 74 RNQEGQQNLXEFVGGEPSKKRKRR--TSFTPQAIEALNAYFEKNPLPTGQEITEXAKELN 131
Query: 74 LTEARVQVWFSNRRARLR 91
V+VWFSNRR L+
Sbjct: 132 YDREVVRVWFSNRRQTLK 149
>pdb|1E3O|C Chain C, Crystal Structure Of Oct-1 Pou Dimer Bound To More
Length = 160
Score = 36.2 bits (82), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 34/63 (53%)
Query: 27 PGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNR 86
PGI ++R+ RT+ + LE++F Q P +A++ + + ++VWFSNR
Sbjct: 93 PGIEGLSRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNR 152
Query: 87 RAR 89
R +
Sbjct: 153 RQK 155
>pdb|2DN0|A Chain A, Solution Structure Of The Second Homeobox Domain Of
Human Zinc Fingers And Homeoboxes Protein 3
Length = 76
Score = 35.8 bits (81), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 26/47 (55%)
Query: 45 DQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLR 91
+QL L+ +F R Q+P E L + T L+ V+ WFS+RR R
Sbjct: 18 EQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCR 64
>pdb|1LE8|A Chain A, Crystal Structure Of The Mata1MATALPHA2-3a Heterodimer
Bound To Dna Complex
Length = 53
Score = 35.4 bits (80), Expect = 0.022, Method: Composition-based stats.
Identities = 17/40 (42%), Positives = 27/40 (67%)
Query: 50 LERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRAR 89
LE+ F+R Q + +EE+A+K +T +V+VWF N+R R
Sbjct: 12 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMR 51
>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 = 35.4 bits (80), Expect = 0.024, Method: Composition-based stats.
Identities = 17/58 (29%), Positives = 34/58 (58%)
Query: 35 QRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
+++ RT F+ QL L+ FQ+ +Y + +EL+ L+ +V+ WF N+R + ++
Sbjct: 3 KQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKR 60
>pdb|1UHS|A Chain A, Solution Structure Of Mouse Homeodomain-Only Protein Hop
Length = 72
Score = 35.0 bits (79), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 21/53 (39%), Positives = 29/53 (54%), Gaps = 1/53 (1%)
Query: 41 TFTGDQLEELERAFQRT-QYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
T T DQ+E LE F + ++PD T +A + LTE + Q WF R A R+
Sbjct: 7 TMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRR 59
>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 = 34.7 bits (78), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 33/63 (52%)
Query: 27 PGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNR 86
PGI ++R+ RT+ + LE++F Q P +A + + + ++VWFSNR
Sbjct: 92 PGIEGLSRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFSNR 151
Query: 87 RAR 89
R +
Sbjct: 152 RQK 154
>pdb|2CUF|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Hypothetical Protein Flj21616
Length = 95
Score = 34.3 bits (77), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 32/70 (45%), Gaps = 15/70 (21%)
Query: 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKT---------------KLTEARVQVWFSN 85
T+ + L +E F QYPD REE+A ++T +V WF+N
Sbjct: 13 TWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFAN 72
Query: 86 RRARLRKQLN 95
RR ++++ N
Sbjct: 73 RRKEIKRRAN 82
>pdb|2P81|A Chain A, Engrailed Homeodomain Helix-Turn-Helix Motif
Length = 44
Score = 34.3 bits (77), Expect = 0.050, Method: Composition-based stats.
Identities = 14/42 (33%), Positives = 28/42 (66%)
Query: 51 ERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
+R F +Y R++L+ + L EA++++WF N+RA+++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 = 33.9 bits (76), Expect = 0.059, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 36/69 (52%), Gaps = 1/69 (1%)
Query: 27 PGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNR 86
PGI ++R+ RT+ + LE++F Q P +A + + + ++VWF NR
Sbjct: 96 PGIEGLSERRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNR 155
Query: 87 RARLRKQLN 95
R + K++N
Sbjct: 156 RQK-EKRIN 163
>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 = 33.5 bits (75), Expect = 0.079, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 32/63 (50%)
Query: 27 PGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNR 86
PGI ++R+ RT+ + LE++F Q P +A + + + ++VWF NR
Sbjct: 95 PGIEGLSRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNR 154
Query: 87 RAR 89
R +
Sbjct: 155 RQK 157
>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 = 33.5 bits (75), Expect = 0.090, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 26/45 (57%)
Query: 43 TGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRR 87
T +QL L+ AF RTQ+P ++LA+++ L + WF + R
Sbjct: 33 TPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTR 77
>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 = 33.5 bits (75), Expect = 0.092, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 32/63 (50%)
Query: 27 PGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNR 86
PGI ++R+ RT+ + LE++F Q P +A + + + ++VWF NR
Sbjct: 88 PGIEGLSRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNR 147
Query: 87 RAR 89
R +
Sbjct: 148 RQK 150
>pdb|3NAU|A Chain A, Crystal Structure Of Zhx2 Hd2 (Zinc-Fingers And
Homeoboxes Protein 2, Homeodomain 2)
pdb|3NAU|B Chain B, Crystal Structure Of Zhx2 Hd2 (Zinc-Fingers And
Homeoboxes Protein 2, Homeodomain 2)
Length = 66
Score = 33.5 bits (75), Expect = 0.093, Method: Composition-based stats.
Identities = 15/50 (30%), Positives = 29/50 (58%)
Query: 43 TGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
T +Q+ L+ +F ++Q+PD L + T L + ++ WFS+ R R ++
Sbjct: 12 TKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQR 61
>pdb|2HI3|A Chain A, Solution Structure Of The Homeodomain-Only Protein Hop
Length = 73
Score = 33.1 bits (74), Expect = 0.097, Method: Compositional matrix adjust.
Identities = 20/51 (39%), Positives = 28/51 (54%), Gaps = 1/51 (1%)
Query: 43 TGDQLEELERAFQRT-QYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
T DQ+E LE F + ++PD T +A + LTE + Q WF R A R+
Sbjct: 10 TEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRR 60
>pdb|2LY9|A Chain A, Solution Nmr Structure Of Homeobox 2 Domain From Human
Zhx1 Repressor, Northeast Structural Genomics Consortium
(Nesg) Target Hr7907f
Length = 74
Score = 33.1 bits (74), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 34/65 (52%)
Query: 39 RTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQQ 98
R T +QL EL+ ++ + Q+P L + T LT+ ++ WFS+ R R ++Q
Sbjct: 10 RAKKTKEQLAELKVSYLKNQFPHDSEIIRLMKITGLTKGEIKKWFSDTRYNQRNSKSNQC 69
Query: 99 LNAFN 103
L+ N
Sbjct: 70 LHLNN 74
>pdb|4EGC|A Chain A, Crystal Structure Of Mbp-fused Human Six1 Bound To Human
Eya2 Eya Domain
Length = 559
Score = 33.1 bits (74), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 24/70 (34%), Positives = 33/70 (47%), Gaps = 9/70 (12%)
Query: 31 LKRKQRRSRTTFTGDQ----LEELERAFQR-----TQYPDVYTREELAQKTKLTEARVQV 81
++RK RT + G++ +E R R YP + ELA+ T LT +V
Sbjct: 481 VRRKFPLPRTIWDGEETSYCFKEKSRGVLREWYAHNPYPSPREKRELAEATGLTTTQVSN 540
Query: 82 WFSNRRARLR 91
WF NRR R R
Sbjct: 541 WFKNRRQRDR 550
>pdb|1DU6|A Chain A, Solution Structure Of The Truncated Pbx Homeodomain
Length = 64
Score = 32.7 bits (73), Expect = 0.13, Method: Composition-based stats.
Identities = 15/34 (44%), Positives = 22/34 (64%)
Query: 59 YPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
YP +EELA+K +T ++V WF N+R R +K
Sbjct: 30 YPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 63
>pdb|2DA1|A Chain A, Solution Structure Of The First Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 32.0 bits (71), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 25/50 (50%)
Query: 36 RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSN 85
+R RT T DQL L + F P +E+A K+ L + ++ WF N
Sbjct: 8 KRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRN 57
>pdb|1AU7|A Chain A, Pit-1 MutantDNA COMPLEX
pdb|1AU7|B Chain B, Pit-1 MutantDNA COMPLEX
Length = 146
Score = 32.0 bits (71), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 29/56 (51%)
Query: 34 KQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRAR 89
++R+ RTT + + LER F P +A++ L + V+VWF NRR R
Sbjct: 86 RKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQR 141
>pdb|1POG|A Chain A, Solution Structure Of The Oct-1 Pou-Homeo Domain
Determined By Nmr And Restrained Molecular Dynamics
Length = 67
Score = 32.0 bits (71), Expect = 0.26, Method: Composition-based stats.
Identities = 15/59 (25%), Positives = 31/59 (52%)
Query: 34 KQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
++R+ RT+ + LE++F Q P +A + + + ++VWF NRR + ++
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 = 32.0 bits (71), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 29/61 (47%)
Query: 29 IPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRA 88
I + ++R+ RT+ LE F + P + LA +L + V+VWF NRR
Sbjct: 93 IAAQGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQ 152
Query: 89 R 89
+
Sbjct: 153 K 153
>pdb|2DA2|A Chain A, Solution Structure Of The Second Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 31.2 bits (69), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 24/53 (45%)
Query: 40 TTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
T FT QL L+ F YP E+L+ L + VWF N R + RK
Sbjct: 12 TRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARK 64
>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 = 30.8 bits (68), Expect = 0.53, Method: Composition-based stats.
Identities = 15/58 (25%), Positives = 31/58 (53%)
Query: 35 QRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92
+R+ RT+ + LE++F Q P +A++ + + ++VWF NRR + ++
Sbjct: 1 RRKKRTSIETNVRFALEKSFLANQKPTSEEILLIAEQLHMEKEVIRVWFCNRRQKEKR 58
>pdb|2DMP|A Chain A, Solution Structure Of The Third Homeobox Domain Of Zinc
Fingers And Homeoboxes Protein 2
Length = 89
Score = 30.4 bits (67), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 31/58 (53%), Gaps = 1/58 (1%)
Query: 43 TGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQQLN 100
T Q++ LE +F ++ +P + L +TKL+ + WFS RR +LR + L+
Sbjct: 21 TQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERR-KLRDSMEQAVLD 77
>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 = 0.89, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 29/54 (53%), Gaps = 4/54 (7%)
Query: 45 DQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQQ 98
+QL LE +F + P + L +TK+T + WFS R RK++N+++
Sbjct: 17 EQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSER----RKKVNAEE 66
>pdb|1OCP|A Chain A, Solution Structure Of Oct3 Pou-Homeodomain
Length = 67
Score = 30.0 bits (66), Expect = 1.0, Method: Composition-based stats.
Identities = 17/62 (27%), Positives = 30/62 (48%)
Query: 31 LKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARL 90
L + ++R RT+ LE F + P + +A + L + V+VWF NRR +
Sbjct: 4 LVQARKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKG 63
Query: 91 RK 92
++
Sbjct: 64 KR 65
>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 = 29.6 bits (65), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 14/32 (43%), Positives = 19/32 (59%)
Query: 59 YPDVYTREELAQKTKLTEARVQVWFSNRRARL 90
YP +++LAQ T LT +V WF N R R+
Sbjct: 25 YPSEEQKKQLAQDTGLTILQVNNWFINARRRI 56
>pdb|1MNM|C Chain C, Yeast Matalpha2MCM1DNA TERNARY TRANSCRIPTION COMPLEX
Crystal Structure
pdb|1MNM|D Chain D, Yeast Matalpha2MCM1DNA TERNARY TRANSCRIPTION COMPLEX
Crystal Structure
Length = 87
Score = 27.7 bits (60), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 25/51 (49%), Gaps = 3/51 (5%)
Query: 42 FTGDQLEELERAFQRTQ---YPDVYTREELAQKTKLTEARVQVWFSNRRAR 89
FT + + LE F + Y D E L + T L+ +++ W SNRR +
Sbjct: 34 FTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRK 84
>pdb|1X2N|A Chain A, Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Pknox1
Length = 73
Score = 27.7 bits (60), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 19/32 (59%)
Query: 59 YPDVYTREELAQKTKLTEARVQVWFSNRRARL 90
YP ++++A +T LT +V WF N R R+
Sbjct: 34 YPTEDEKKQIAAQTNLTLLQVNNWFINARRRI 65
>pdb|2DMN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Tgif2lx
Length = 83
Score = 27.7 bits (60), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 23/42 (54%)
Query: 59 YPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQQLN 100
YP ++ L++KT L+ ++ WF N R R+ + Q+ N
Sbjct: 34 YPSEEEKQMLSEKTNLSLLQISNWFINARRRILPDMLQQRRN 75
>pdb|3L1P|A Chain A, Pou Protein:dna Complex
pdb|3L1P|B Chain B, Pou Protein:dna Complex
Length = 155
Score = 27.7 bits (60), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 28/55 (50%)
Query: 35 QRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRAR 89
++R RT+ LE F ++ P + +A + L + V+VWFSNRR +
Sbjct: 96 RKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQK 150
>pdb|2H8R|A Chain A, Hepatocyte Nuclear Factor 1b Bound To Dna: Mody5 Gene
Product
pdb|2H8R|B Chain B, Hepatocyte Nuclear Factor 1b Bound To Dna: Mody5 Gene
Product
Length = 221
Score = 27.3 bits (59), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 24/94 (25%), Positives = 38/94 (40%), Gaps = 26/94 (27%)
Query: 15 PSSGDESDTESEPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTK- 73
P D++ +E P +K RR+R + + L +A+ R + P RE L ++
Sbjct: 127 PGQSDDACSE-----PTNKKMRRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNR 181
Query: 74 --------------------LTEARVQVWFSNRR 87
+TE RV WF+NRR
Sbjct: 182 AECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRR 215
>pdb|2CQX|A Chain A, Solution Structure Of Rsgi Ruh-034, A Homeodomain From
Mouse Cdna
Length = 72
Score = 27.3 bits (59), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 23/39 (58%), Gaps = 1/39 (2%)
Query: 50 LERAF-QRTQYPDVYTREELAQKTKLTEARVQVWFSNRR 87
LE+ F T+YPD + L+++ + ++Q WF +RR
Sbjct: 23 LEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRR 61
>pdb|1APL|C Chain C, Crystal Structure Of A Mat-Alpha2 Homeodomain-Operator
Complex Suggests A General Model For Homeodomain-Dna
Interactions
pdb|1APL|D Chain D, Crystal Structure Of A Mat-Alpha2 Homeodomain-Operator
Complex Suggests A General Model For Homeodomain-Dna
Interactions
pdb|1YRN|B Chain B, Crystal Structure Of The Mata1MATALPHA2 HOMEODOMAIN
Heterodimer Bound To Dna
pdb|1AKH|B Chain B, Mat A1ALPHA2DNA TERNARY COMPLEX
Length = 83
Score = 27.3 bits (59), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 25/51 (49%), Gaps = 3/51 (5%)
Query: 42 FTGDQLEELERAFQRTQ---YPDVYTREELAQKTKLTEARVQVWFSNRRAR 89
FT + + LE F + Y D E L + T L+ +++ W SNRR +
Sbjct: 9 FTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRK 59
>pdb|1WH5|A Chain A, Solution Structure Of Homeobox Domain Of
Arabidopsisthaliana Zinc Finger Homeobox Family Protein
Length = 80
Score = 26.9 bits (58), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 26/55 (47%), Gaps = 4/55 (7%)
Query: 35 QRRSRTTFTGDQLEEL----ERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSN 85
++R RT FT +Q E + ER R Q D + Q+T + ++VW N
Sbjct: 17 RKRHRTKFTAEQKERMLALAERIGWRIQRQDDEVIQRFCQETGVPRQVLKVWLHN 71
>pdb|1G8I|A Chain A, Crystal Structure Of Human Frequenin (Neuronal Calcium
Sensor 1)
pdb|1G8I|B Chain B, Crystal Structure Of Human Frequenin (Neuronal Calcium
Sensor 1)
pdb|2LCP|A Chain A, Nmr Structure Of Calcium Loaded, Un-Myristoylated Human
Ncs-1
Length = 190
Score = 26.6 bits (57), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 22/46 (47%), Gaps = 4/46 (8%)
Query: 66 EELAQKTKLTEARVQVWFSNRRARLRKQLNSQQLNAFNSMSLHHQY 111
EEL +KT TE VQ W+ K S QL+A ++ Q+
Sbjct: 14 EELTRKTYFTEKEVQQWYKG----FIKDCPSGQLDAAGFQKIYKQF 55
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
0.311 0.122 0.371
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,030,733
Number of Sequences: 62578
Number of extensions: 205042
Number of successful extensions: 459
Number of sequences better than 100.0: 104
Number of HSP's better than 100.0 without gapping: 93
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 363
Number of HSP's gapped (non-prelim): 105
length of query: 205
length of database: 14,973,337
effective HSP length: 94
effective length of query: 111
effective length of database: 9,091,005
effective search space: 1009101555
effective search space used: 1009101555
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 49 (23.5 bits)