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= 003075
(850 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 52.0 bits (123), Expect = 1e-06, Method: Composition-based stats.
Identities = 19/53 (35%), Positives = 36/53 (67%), Gaps = 4/53 (7%)
Query: 27 EQVEALERVYSECPKPSSLRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQR 79
+Q+ L Y+ P+P +L ++QL+ ++ + P+ I+VWFQN+RC++K+R
Sbjct: 13 KQLHTLRTCYAANPRPDALMKEQLVE----MTGLSPRVIRVWFQNKRCKDKKR 61
>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4490c
Length = 75
Score = 43.9 bits (102), Expect = 4e-04, Method: Composition-based stats.
Identities = 19/63 (30%), Positives = 38/63 (60%), Gaps = 4/63 (6%)
Query: 24 YTPEQVEALERVYSECPKPSSLRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQRKEAS 83
+T Q+E LE+V+ + P R+QL + +++ +++VWFQNRR + ++R+
Sbjct: 16 FTSYQLEELEKVFQKTHYPDVYAREQL----AMRTDLTEARVQVWFQNRRAKWRKRERFG 71
Query: 84 RLQ 86
++Q
Sbjct: 72 QMQ 74
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 43.1 bits (100), Expect = 6e-04, Method: Composition-based stats.
Identities = 20/60 (33%), Positives = 37/60 (61%), Gaps = 4/60 (6%)
Query: 24 YTPEQVEALERVYSECPKPSSLRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQRKEAS 83
+T EQ+EALE ++ E P R+QL R+ ++ ++++VWF+NRR + ++ +S
Sbjct: 14 FTDEQLEALENLFQETKYPDVGTREQLARKV----HLREEKVEVWFKNRRAKWRRSGPSS 69
>pdb|1AU7|A Chain A, Pit-1 MutantDNA COMPLEX
pdb|1AU7|B Chain B, Pit-1 MutantDNA COMPLEX
Length = 146
Score = 42.7 bits (99), Expect = 0.001, Method: Composition-based stats.
Identities = 24/51 (47%), Positives = 34/51 (66%), Gaps = 4/51 (7%)
Query: 30 EALERVYSECPKPSSLRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQRK 80
+ALER + E KPSS Q+++R L N+E + ++VWF NRR REK+ K
Sbjct: 100 DALERHFGEHSKPSS---QEIMRMAEEL-NLEKEVVRVWFCNRRQREKRVK 146
>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain
Length = 73
Score = 42.4 bits (98), Expect = 0.001, Method: Composition-based stats.
Identities = 24/70 (34%), Positives = 39/70 (55%), Gaps = 6/70 (8%)
Query: 20 KYVRYTPEQVEALERVYSECPKPSSLRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQR 79
K V YT Q++ LER Y+ + +R R +N+ +Q+ +WFQNRR +EK
Sbjct: 10 KRVPYTKVQLKELEREYATNKFITKDKR----RRISATTNLSERQVTIWFQNRRVKEK-- 63
Query: 80 KEASRLQTVN 89
K ++L+T +
Sbjct: 64 KVINKLKTTS 73
>pdb|2LD5|A Chain A, Solution Nmr-Derived Complex Structure Of Hoxa13 Dna
Binding Domain Bound To Dna
Length = 67
Score = 42.4 bits (98), Expect = 0.001, Method: Composition-based stats.
Identities = 24/70 (34%), Positives = 39/70 (55%), Gaps = 6/70 (8%)
Query: 20 KYVRYTPEQVEALERVYSECPKPSSLRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQR 79
K V YT Q++ LER Y+ + +R R +N+ +Q+ +WFQNRR +EK
Sbjct: 4 KRVPYTKVQLKELEREYATNKFITKDKR----RRISATTNLSERQVTIWFQNRRVKEK-- 57
Query: 80 KEASRLQTVN 89
K ++L+T +
Sbjct: 58 KVINKLKTTS 67
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
Length = 60
Score = 39.3 bits (90), Expect = 0.009, Method: Composition-based stats.
Identities = 20/55 (36%), Positives = 32/55 (58%), Gaps = 4/55 (7%)
Query: 24 YTPEQVEALERVYSECPKPSSLRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 78
++ EQ+ L+R ++E + RRQQL E + QIK+WFQN+R + K+
Sbjct: 8 FSSEQLARLKREFNENRYLTERRRQQLSSEL----GLNEAQIKIWFQNKRAKIKK 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 = 39.3 bits (90), Expect = 0.009, Method: Composition-based stats.
Identities = 20/55 (36%), Positives = 32/55 (58%), Gaps = 4/55 (7%)
Query: 24 YTPEQVEALERVYSECPKPSSLRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 78
++ EQ+ L+R ++E + RRQQL E + QIK+WFQN+R + K+
Sbjct: 10 FSSEQLARLKREFNENRYLTERRRQQLSSEL----GLNEAQIKIWFQNKRAKIKK 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 = 38.5 bits (88), Expect = 0.014, Method: Composition-based stats.
Identities = 17/56 (30%), Positives = 32/56 (57%), Gaps = 4/56 (7%)
Query: 24 YTPEQVEALERVYSECPKPSSLRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQR 79
++ Q++ LER + P R++L + +N+ +I+VWFQNRR R +++
Sbjct: 25 FSASQLDELERAFERTQYPDIYTREELAQR----TNLTEARIQVWFQNRRARLRKQ 76
>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 = 38.1 bits (87), Expect = 0.019, Method: Composition-based stats.
Identities = 20/55 (36%), Positives = 31/55 (56%), Gaps = 4/55 (7%)
Query: 24 YTPEQVEALERVYSECPKPSSLRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 78
++ EQ+ L+R ++E + RRQQL E + QIK+WFQN R + K+
Sbjct: 8 FSSEQLARLKREFNENRYLTERRRQQLSSEL----GLNEAQIKIWFQNERAKIKK 58
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 38.1 bits (87), Expect = 0.020, Method: Composition-based stats.
Identities = 16/58 (27%), Positives = 33/58 (56%), Gaps = 4/58 (6%)
Query: 24 YTPEQVEALERVYSECPKPSSLRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQRKE 81
+T +Q++ LE + P R+ E + +N+ +++VWF+NRR + ++R+E
Sbjct: 10 FTSQQLQELEATFQRNHYPDMSTRE----EIAVWTNLTEARVRVWFKNRRAKWRKREE 63
>pdb|2CRA|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeo
Box B13
Length = 70
Score = 38.1 bits (87), Expect = 0.020, Method: Composition-based stats.
Identities = 20/64 (31%), Positives = 35/64 (54%), Gaps = 4/64 (6%)
Query: 20 KYVRYTPEQVEALERVYSECPKPSSLRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQR 79
K + Y+ Q+ LER Y+ + +R R+ +++ +QI +WFQNRR +EK+
Sbjct: 10 KRIPYSKGQLRELEREYAANKFITKDKR----RKISAATSLSERQITIWFQNRRVKEKKS 65
Query: 80 KEAS 83
+S
Sbjct: 66 GPSS 69
>pdb|1ENH|A Chain A, Structural Studies Of The Engrailed Homeodomain
Length = 54
Score = 38.1 bits (87), Expect = 0.021, Method: Composition-based stats.
Identities = 19/52 (36%), Positives = 30/52 (57%), Gaps = 4/52 (7%)
Query: 24 YTPEQVEALERVYSECPKPSSLRRQQLIRECPILSNIEPKQIKVWFQNRRCR 75
++ EQ+ L+R ++E + RRQQL E + QIK+WFQN+R +
Sbjct: 6 FSSEQLARLKREFNENRYLTERRRQQLSSEL----GLNEAQIKIWFQNKRAK 53
>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 = 38.1 bits (87), Expect = 0.022, Method: Composition-based stats.
Identities = 16/58 (27%), Positives = 33/58 (56%), Gaps = 4/58 (6%)
Query: 24 YTPEQVEALERVYSECPKPSSLRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQRKE 81
+T +Q++ LE + P R+ E + +N+ +++VWF+NRR + ++R+E
Sbjct: 10 FTSQQLQELEATFQRNRYPDMSTRE----EIAVWTNLTEARVRVWFKNRRAKWRKREE 63
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 38.1 bits (87), Expect = 0.023, Method: Composition-based stats.
Identities = 17/61 (27%), Positives = 35/61 (57%), Gaps = 4/61 (6%)
Query: 21 YVRYTPEQVEALERVYSECPKPSSLRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQRK 80
++ +T Q+E LE+ +S P R++L + + +I+VWFQNRR + ++++
Sbjct: 3 HMTFTSFQLEELEKAFSRTHYPDVFTREELAMKI----GLTEARIQVWFQNRRAKWRKQE 58
Query: 81 E 81
+
Sbjct: 59 K 59
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 37.7 bits (86), Expect = 0.027, Method: Composition-based stats.
Identities = 17/56 (30%), Positives = 31/56 (55%), Gaps = 4/56 (7%)
Query: 24 YTPEQVEALERVYSECPKPSSLRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQR 79
+T EQ+E LER + P R++L + + + +++VWF NRR R +++
Sbjct: 9 FTAEQLEELERAFERTHYPDIYTREELAQR----AKLTEARVQVWFSNRRARWRKQ 60
>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 = 37.7 bits (86), Expect = 0.029, Method: Composition-based stats.
Identities = 20/55 (36%), Positives = 31/55 (56%), Gaps = 4/55 (7%)
Query: 24 YTPEQVEALERVYSECPKPSSLRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 78
++ EQ+ L+R ++E + RRQQL E + QIK+WFQN R + K+
Sbjct: 8 FSSEQLARLKREFNENRYLTERRRQQLSSEL----GLNEAQIKIWFQNARAKIKK 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 = 37.7 bits (86), Expect = 0.029, Method: Composition-based stats.
Identities = 19/55 (34%), Positives = 32/55 (58%), Gaps = 4/55 (7%)
Query: 24 YTPEQVEALERVYSECPKPSSLRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 78
++ EQ+ L+R ++E + RRQQL E + QIK+WF+N+R + K+
Sbjct: 10 FSSEQLARLKREFNENRYLTERRRQQLSSEL----GLNEAQIKIWFKNKRAKIKK 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 = 37.4 bits (85), Expect = 0.038, Method: Composition-based stats.
Identities = 17/58 (29%), Positives = 33/58 (56%), Gaps = 4/58 (6%)
Query: 24 YTPEQVEALERVYSECPKPSSLRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQRKE 81
+T Q+E LE+ +S P R++L + + +I+VWFQNRR + +++++
Sbjct: 13 FTSFQLEELEKAFSRTHYPDVFTREELAMKI----GLTEARIQVWFQNRRAKWRKQEK 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 = 37.0 bits (84), Expect = 0.041, Method: Composition-based stats.
Identities = 20/58 (34%), Positives = 31/58 (53%), Gaps = 4/58 (6%)
Query: 28 QVEALERVYSECPKPSSLRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQRKEASRL 85
QV LER +S S+ R L + + Q+K+WFQNRR + K+++ +S L
Sbjct: 15 QVIELERKFSHQKYLSAPERAHLAKNLKLTET----QVKIWFQNRRYKTKRKQLSSEL 68
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 37.0 bits (84), Expect = 0.043, Method: Composition-based stats.
Identities = 17/57 (29%), Positives = 32/57 (56%), Gaps = 4/57 (7%)
Query: 24 YTPEQVEALERVYSECPKPSSLRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQRK 80
+T Q+E LE+ +S P R++L + + +I+VWFQNRR + ++++
Sbjct: 6 FTSFQLEELEKAFSRTHYPDVFTREELAMKI----GLTEARIQVWFQNRRAKWRKQE 58
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor
Gbx1 From Homo Sapiens
Length = 71
Score = 37.0 bits (84), Expect = 0.046, Method: Composition-based stats.
Identities = 22/57 (38%), Positives = 32/57 (56%), Gaps = 4/57 (7%)
Query: 24 YTPEQVEALERVYSECPKPSSLRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQRK 80
+T EQ+ LE+ + C K SL + I LS + Q+K+WFQNRR + K+ K
Sbjct: 14 FTSEQLLELEKEF-HCKKYLSLTERSQIAHALKLSEV---QVKIWFQNRRAKWKRIK 66
>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 = 36.6 bits (83), Expect = 0.057, Method: Composition-based stats.
Identities = 19/55 (34%), Positives = 31/55 (56%), Gaps = 4/55 (7%)
Query: 24 YTPEQVEALERVYSECPKPSSLRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 78
++ EQ+ L+R ++E + RRQQL E + QIK+WF N+R + K+
Sbjct: 6 FSSEQLARLKREFNENRYLTERRRQQLSSEL----GLNEAQIKIWFANKRAKIKK 56
>pdb|1FTT|A Chain A, Thyroid Transcription Factor 1 Homeodomain (Rattus
Norvegicus)
Length = 68
Score = 36.6 bits (83), Expect = 0.058, Method: Composition-based stats.
Identities = 20/71 (28%), Positives = 36/71 (50%), Gaps = 4/71 (5%)
Query: 16 MDSTKYVRYTPEQVEALERVYSECPKPSSLRRQQLIRECPILSNIEPKQIKVWFQNRRCR 75
M + V ++ QV LER + + S+ R+ L + ++ P Q+K+WFQN R +
Sbjct: 1 MRRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLAS----MIHLTPTQVKIWFQNHRYK 56
Query: 76 EKQRKEASRLQ 86
K++ + Q
Sbjct: 57 MKRQAKDKAAQ 67
>pdb|1QRY|A Chain A, Homeobox Protein Vnd (Ventral Nervous System Defective
Protein)
Length = 80
Score = 35.8 bits (81), Expect = 0.096, Method: Composition-based stats.
Identities = 19/59 (32%), Positives = 30/59 (50%), Gaps = 4/59 (6%)
Query: 20 KYVRYTPEQVEALERVYSECPKPSSLRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 78
+ V +T Q LER + + S+ R+ L L + P Q+K+WFQN R + K+
Sbjct: 15 RRVLFTKAQTYELERRFRQQRYLSAPEREHLTS----LIRLTPTQVKIWFQNHRYKTKR 69
>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound
To Dna
Length = 77
Score = 35.8 bits (81), Expect = 0.097, Method: Composition-based stats.
Identities = 25/74 (33%), Positives = 37/74 (50%), Gaps = 6/74 (8%)
Query: 7 NKEFANKQIMDSTKYVR--YTPEQVEALERVYSECPKPSSLRRQQLIRECPILSNIEPKQ 64
N AN ST+ R YT Q LE+ + + RR ++ R L N+ +Q
Sbjct: 1 NNPAANWLHARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVAR----LLNLTERQ 56
Query: 65 IKVWFQNRRCREKQ 78
+K+WFQNRR + K+
Sbjct: 57 VKIWFQNRRMKMKK 70
>pdb|1ZTR|A Chain A, Solution Structure Of Engrailed Homeodomain L16a Mutant
Length = 61
Score = 35.8 bits (81), Expect = 0.11, Method: Composition-based stats.
Identities = 18/52 (34%), Positives = 29/52 (55%), Gaps = 4/52 (7%)
Query: 24 YTPEQVEALERVYSECPKPSSLRRQQLIRECPILSNIEPKQIKVWFQNRRCR 75
++ EQ+ +R ++E + RRQQL E + QIK+WFQN+R +
Sbjct: 10 FSSEQLARAKREFNENRYLTERRRQQLSSEL----GLNEAQIKIWFQNKRAK 57
>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 = 35.4 bits (80), Expect = 0.13, Method: Composition-based stats.
Identities = 22/66 (33%), Positives = 35/66 (53%), Gaps = 6/66 (9%)
Query: 18 STKYVR--YTPEQVEALERVYSECPKPSSLRRQQLIRECPILSNIEPKQIKVWFQNRRCR 75
S K R YT Q+ LE+ + S RR +L ++ N+ + IK+WFQNRR +
Sbjct: 2 SNKRTRTAYTRAQLLELEKEFLFNKYISRPRRVEL----AVMLNLTERHIKIWFQNRRMK 57
Query: 76 EKQRKE 81
K+ ++
Sbjct: 58 WKKEED 63
>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 = 35.4 bits (80), Expect = 0.13, Method: Composition-based stats.
Identities = 19/59 (32%), Positives = 30/59 (50%), Gaps = 4/59 (6%)
Query: 20 KYVRYTPEQVEALERVYSECPKPSSLRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 78
+ V +T Q LER + + S+ R+ L L + P Q+K+WFQN R + K+
Sbjct: 12 RRVLFTKAQTYELERRFRQQRYLSAPEREHLAS----LIRLTPTQVKIWFQNHRYKTKR 66
>pdb|1E3O|C Chain C, Crystal Structure Of Oct-1 Pou Dimer Bound To More
Length = 160
Score = 35.4 bits (80), Expect = 0.13, Method: Composition-based stats.
Identities = 21/52 (40%), Positives = 30/52 (57%), Gaps = 12/52 (23%)
Query: 31 ALERVYSECPKPSS----LRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 78
ALE+ + E KP+S L +QL N+E + I+VWF NRR +EK+
Sbjct: 115 ALEKSFMENQKPTSEDITLIAEQL--------NMEKEVIRVWFSNRRQKEKR 158
>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 = 0.16, Method: Composition-based stats.
Identities = 19/57 (33%), Positives = 33/57 (57%), Gaps = 4/57 (7%)
Query: 24 YTPEQVEALERVYSECPKPSSLRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQRK 80
+T +Q+ LE+ + + S RR +L + N+ IKVWFQNRR ++K+++
Sbjct: 8 FTRDQLGRLEKEFYKENYVSRPRRCELAAQL----NLPESTIKVWFQNRRMKDKRQR 60
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant
R31lE42L
Length = 67
Score = 35.0 bits (79), Expect = 0.16, Method: Composition-based stats.
Identities = 19/62 (30%), Positives = 32/62 (51%), Gaps = 4/62 (6%)
Query: 24 YTPEQVEALERVYSECPKPSSLRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQRKEAS 83
+T Q+E LE V+ P + L ++ N+E +I++WFQNRR + K+ S
Sbjct: 8 FTQNQIEVLENVFRVNCYPGIDILEDLAQKL----NLELDRIQIWFQNRRAKLKRSHRES 63
Query: 84 RL 85
+
Sbjct: 64 QF 65
>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 = 35.0 bits (79), Expect = 0.18, Method: Composition-based stats.
Identities = 16/53 (30%), Positives = 30/53 (56%), Gaps = 4/53 (7%)
Query: 25 TPEQVEALERVYSECPKPSSLRRQQLIRECPILSNIEPKQIKVWFQNRRCREK 77
+P+ LE+V+ +S ++++ ++C I P Q++VWF N+R R K
Sbjct: 13 SPQARAFLEQVFRRKQSLNSKEKEEVAKKC----GITPLQVRVWFINKRMRSK 61
>pdb|1LE8|A Chain A, Crystal Structure Of The Mata1MATALPHA2-3a Heterodimer
Bound To Dna Complex
Length = 53
Score = 35.0 bits (79), Expect = 0.19, Method: Composition-based stats.
Identities = 16/53 (30%), Positives = 30/53 (56%), Gaps = 4/53 (7%)
Query: 25 TPEQVEALERVYSECPKPSSLRRQQLIRECPILSNIEPKQIKVWFQNRRCREK 77
+P+ LE+V+ +S ++++ ++C I P Q++VWF N+R R K
Sbjct: 5 SPQARAFLEQVFRRKQSLNSKEKEEVAKKC----GITPLQVRVWFINKRMRSK 53
>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 = 34.7 bits (78), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 30/53 (56%), Gaps = 4/53 (7%)
Query: 25 TPEQVEALERVYSECPKPSSLRRQQLIRECPILSNIEPKQIKVWFQNRRCREK 77
+P+ LE+V+ +S ++++ ++C I P Q++VWF N+R R K
Sbjct: 373 SPQARAFLEQVFRRKQSLNSKEKEEVAKKC----GITPLQVRVWFINKRMRSK 421
>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 = 34.7 bits (78), Expect = 0.21, Method: Composition-based stats.
Identities = 20/56 (35%), Positives = 29/56 (51%), Gaps = 4/56 (7%)
Query: 22 VRYTPEQVEALERVYSECPKPSSLRRQQLIRECPILSNIEPKQIKVWFQNRRCREK 77
V ++ QV LER + + S+ R QL + S Q+K+WFQNRR + K
Sbjct: 7 VLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTST----QVKIWFQNRRYKSK 58
>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 = 0.21, Method: Composition-based stats.
Identities = 18/48 (37%), Positives = 28/48 (58%), Gaps = 4/48 (8%)
Query: 31 ALERVYSECPKPSSLRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 78
ALE+ + E KP+S + + N+E + I+VWF NRR +EK+
Sbjct: 114 ALEKSFLENQKPTSEEITMIADQL----NMEKEVIRVWFSNRRQKEKR 157
>pdb|1AKH|A Chain A, Mat A1ALPHA2DNA TERNARY COMPLEX
Length = 61
Score = 34.7 bits (78), Expect = 0.24, Method: Composition-based stats.
Identities = 16/53 (30%), Positives = 29/53 (54%), Gaps = 4/53 (7%)
Query: 25 TPEQVEALERVYSECPKPSSLRRQQLIRECPILSNIEPKQIKVWFQNRRCREK 77
+P+ LE V+ +S ++++ ++C I P Q++VWF N+R R K
Sbjct: 13 SPQARAFLEEVFRRKQSLNSKEKEEVAKKC----GITPLQVRVWFINKRMRSK 61
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 34.3 bits (77), Expect = 0.30, Method: Composition-based stats.
Identities = 17/57 (29%), Positives = 30/57 (52%), Gaps = 4/57 (7%)
Query: 24 YTPEQVEALERVYSECPKPSSLRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQRK 80
+T Q+ LE+ + S RR ++ + Q+K+WFQNRR ++K+R+
Sbjct: 41 FTTRQLTELEKEFHFNKYLSRARRVEIAATL----ELNETQVKIWFQNRRMKQKKRE 93
>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 = 34.3 bits (77), Expect = 0.31, Method: Composition-based stats.
Identities = 17/50 (34%), Positives = 27/50 (54%), Gaps = 4/50 (8%)
Query: 24 YTPEQVEALERVYSECPKPSSLRRQQLIRECPILSNIEPKQIKVWFQNRR 73
+TP+ +EAL + + P P+ Q I E N + + ++VWF NRR
Sbjct: 100 FTPQAIEALNAYFEKNPLPTG----QEITEXAKELNYDREVVRVWFSNRR 145
>pdb|2DA3|A Chain A, Solution Structure Of The Third Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 80
Score = 34.3 bits (77), Expect = 0.34, Method: Composition-based stats.
Identities = 18/59 (30%), Positives = 30/59 (50%), Gaps = 4/59 (6%)
Query: 25 TPEQVEALERVYSECPKPSSLRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQRKEAS 83
TPEQ+E L + Y P+ + E ++ + ++VWFQN R RE++ +S
Sbjct: 25 TPEQLEILYQKYLLDSNPTRKMLDHIAHEV----GLKKRVVQVWFQNTRARERKSGPSS 79
>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 = 0.46, Method: Composition-based stats.
Identities = 18/48 (37%), Positives = 28/48 (58%), Gaps = 4/48 (8%)
Query: 31 ALERVYSECPKPSSLRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 78
ALE+ + E KP+S + + N+E + I+VWF NRR +EK+
Sbjct: 110 ALEKSFLENQKPTSEEITMIADQL----NMEKEVIRVWFCNRRQKEKR 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 = 33.5 bits (75), Expect = 0.48, Method: Composition-based stats.
Identities = 18/48 (37%), Positives = 28/48 (58%), Gaps = 4/48 (8%)
Query: 31 ALERVYSECPKPSSLRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 78
ALE+ + E KP+S + + N+E + I+VWF NRR +EK+
Sbjct: 21 ALEKSFLENQKPTSEEITMIADQL----NMEKEVIRVWFCNRRQKEKR 64
>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 = 0.49, Method: Composition-based stats.
Identities = 18/48 (37%), Positives = 28/48 (58%), Gaps = 4/48 (8%)
Query: 31 ALERVYSECPKPSSLRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 78
ALE+ + E KP+S + + N+E + I+VWF NRR +EK+
Sbjct: 117 ALEKSFLENQKPTSEEITMIADQL----NMEKEVIRVWFCNRRQKEKR 160
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 33.5 bits (75), Expect = 0.53, Method: Composition-based stats.
Identities = 18/55 (32%), Positives = 30/55 (54%), Gaps = 4/55 (7%)
Query: 24 YTPEQVEALERVYSECPKPSSLRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 78
YT Q LE+ + + RR ++ R + N+ +Q+K+WFQNRR + K+
Sbjct: 8 YTKYQTLELEKEFLFNMYLTRDRRYEVAR----VLNLTERQVKIWFQNRRMKMKK 58
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 33.5 bits (75), Expect = 0.54, Method: Composition-based stats.
Identities = 23/59 (38%), Positives = 31/59 (52%), Gaps = 4/59 (6%)
Query: 24 YTPEQVEALERVYSECPKPSSLRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQRKEA 82
YT Q LE+ E L R++ I LS E +QIK+WFQNRR + K+ +A
Sbjct: 27 YTRYQTLELEK---EFHTNHYLTRRRRIEMAHALSLTE-RQIKIWFQNRRMKLKKEIQA 81
>pdb|2P81|A Chain A, Engrailed Homeodomain Helix-Turn-Helix Motif
Length = 44
Score = 33.5 bits (75), Expect = 0.54, Method: Composition-based stats.
Identities = 17/46 (36%), Positives = 26/46 (56%), Gaps = 4/46 (8%)
Query: 33 ERVYSECPKPSSLRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 78
+R ++E + RRQQL E + QIK+WFQN+R + K+
Sbjct: 2 KREFNENRYLTERRRQQLSSEL----GLNEAQIKIWFQNKRAKIKK 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 = 33.5 bits (75), Expect = 0.56, Method: Composition-based stats.
Identities = 18/48 (37%), Positives = 28/48 (58%), Gaps = 4/48 (8%)
Query: 31 ALERVYSECPKPSSLRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 78
ALE+ + E KP+S + + N+E + I+VWF NRR +EK+
Sbjct: 118 ALEKSFLENQKPTSEEITMIADQL----NMEKEVIRVWFCNRRQKEKR 161
>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 = 0.59, Method: Composition-based stats.
Identities = 17/62 (27%), Positives = 33/62 (53%), Gaps = 4/62 (6%)
Query: 22 VRYTPEQVEALERVYSECPKPSSLRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQRKE 81
VR++ +Q LE+ + S R++L + + + +Q+K WFQNRR + ++
Sbjct: 12 VRFSNDQTIELEKKFETQKYLSPPERKRLAK----MLQLSERQVKTWFQNRRAKWRRSGP 67
Query: 82 AS 83
+S
Sbjct: 68 SS 69
>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 = 33.1 bits (74), Expect = 0.62, Method: Composition-based stats.
Identities = 18/55 (32%), Positives = 30/55 (54%), Gaps = 4/55 (7%)
Query: 24 YTPEQVEALERVYSECPKPSSLRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 78
++ EQ+ L+R ++E + RRQQL E + Q+K WF+N R + K+
Sbjct: 11 FSSEQLARLKREFNENRYLTERRRQQLSSEL----GLNEAQVKGWFKNMRAKIKK 61
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 33.1 bits (74), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 29/52 (55%), Gaps = 4/52 (7%)
Query: 24 YTPEQVEALERVYSECPKPSSLRRQQLIRECPILSNIEPKQIKVWFQNRRCR 75
+T EQ+EALE+ + P R++L + ++ +I+VWF NRR +
Sbjct: 14 FTQEQIEALEKEFERTHYPDVFARERLAAKI----DLPEARIQVWFSNRRAK 61
>pdb|2XSD|C Chain C, Crystal Structure Of The Dimeric Oct-6 (Pou3f1) Pou Domain
Bound To Palindromic More Dna
Length = 164
Score = 32.3 bits (72), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 27/48 (56%), Gaps = 4/48 (8%)
Query: 31 ALERVYSECPKPSSLRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 78
ALE + +CPKPS+ L +E + ++VWF NRR +EK+
Sbjct: 113 ALESHFLKCPKPSAHEITGLADSL----QLEKEVVRVWFCNRRQKEKR 156
>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 = 32.3 bits (72), Expect = 1.1, Method: Composition-based stats.
Identities = 23/71 (32%), Positives = 33/71 (46%), Gaps = 13/71 (18%)
Query: 24 YTPEQVEALERVYSECPKPSSLRRQQLIRECPILSNIEPKQIKVWFQNRRC--------- 74
+T QV LE+ + + +S R L R + Q+K WFQNRR
Sbjct: 24 FTRIQVAELEKRFHKQKYLASAERAALARGLKMTD----AQVKTWFQNRRTKWRRQTAEE 79
Query: 75 REKQRKEASRL 85
RE +R+ A+RL
Sbjct: 80 REAERQAANRL 90
>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 = 32.3 bits (72), Expect = 1.1, Method: Composition-based stats.
Identities = 11/17 (64%), Positives = 15/17 (88%)
Query: 63 KQIKVWFQNRRCREKQR 79
+QIK+WFQNRR + K+R
Sbjct: 1 RQIKIWFQNRRMKWKKR 17
>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 = 32.3 bits (72), Expect = 1.2, Method: Composition-based stats.
Identities = 22/60 (36%), Positives = 30/60 (50%), Gaps = 7/60 (11%)
Query: 19 TKYVRYTPEQVEALERVYSECPKPSSLRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 78
T Y RY ++E E L R++ I LS E +QIK+WFQNRR + K+
Sbjct: 33 TSYTRYQTLELE------KEFHFNRYLTRRRRIEIAHALSLTE-RQIKIWFQNRRMKWKK 85
>pdb|1OCP|A Chain A, Solution Structure Of Oct3 Pou-Homeodomain
Length = 67
Score = 32.0 bits (71), Expect = 1.6, Method: Composition-based stats.
Identities = 18/48 (37%), Positives = 28/48 (58%), Gaps = 4/48 (8%)
Query: 31 ALERVYSECPKPSSLRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 78
+LE ++ +CPKPS QQ+ L +E ++VWF NRR + K+
Sbjct: 22 SLETMFLKCPKPS---LQQITHIANQLG-LEKDVVRVWFCNRRQKGKR 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 = 31.6 bits (70), Expect = 1.8, Method: Composition-based stats.
Identities = 10/22 (45%), Positives = 17/22 (77%)
Query: 59 NIEPKQIKVWFQNRRCREKQRK 80
++ +QIK+WFQNRR + K+ +
Sbjct: 41 SLSERQIKIWFQNRRMKSKKDR 62
>pdb|2KT0|A Chain A, Solution Structure Of Human Stem Cell Transcription
Factor Nanog Homeodomain Fragment
Length = 84
Score = 31.6 bits (70), Expect = 1.9, Method: Composition-based stats.
Identities = 12/30 (40%), Positives = 20/30 (66%)
Query: 49 QLIRECPILSNIEPKQIKVWFQNRRCREKQ 78
Q ++E + N+ KQ+K WFQN+R + K+
Sbjct: 50 QQMQELSNILNLSYKQVKTWFQNQRMKSKR 79
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 31.6 bits (70), Expect = 2.0, Method: Composition-based stats.
Identities = 17/55 (30%), Positives = 28/55 (50%), Gaps = 4/55 (7%)
Query: 24 YTPEQVEALERVYSECPKPSSLRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 78
+T Q+ ALER + + S R + ++ Q+K+WFQNRR + K+
Sbjct: 7 FTTAQLLALERKFRQKQYLSIAERAEFSSSL----SLTETQVKIWFQNRRAKAKR 57
>pdb|3S9G|A Chain A, Structure Of Human Hexim1 (Delta Stammer) Coiled Coil
Domain
pdb|3S9G|B Chain B, Structure Of Human Hexim1 (Delta Stammer) Coiled Coil
Domain
Length = 104
Score = 31.2 bits (69), Expect = 2.3, Method: Composition-based stats.
Identities = 24/94 (25%), Positives = 45/94 (47%), Gaps = 16/94 (17%)
Query: 30 EALERVYSECPKPSSLRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQRKEASRLQTVN 89
E ER ++E + ++ +Q+LI+E + + + + E +RL+ +
Sbjct: 17 ETYERYHTESLQ--NMSKQELIKE--------------YLELEKSLSRMEDENNRLRLES 60
Query: 90 RKLSAMNKLLMEENDRLQKQVSHLVYENGYMRQQ 123
++L A + L E DRL+ + L+ EN RQQ
Sbjct: 61 KRLDARVRELELELDRLRAENLQLLTENELHRQQ 94
>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 = 31.2 bits (69), Expect = 2.4, Method: Composition-based stats.
Identities = 16/37 (43%), Positives = 23/37 (62%), Gaps = 1/37 (2%)
Query: 45 LRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQRKE 81
L R++ I LS E +QIK+WFQNRR + K+ +
Sbjct: 21 LTRRRRIEIAHALSLTE-RQIKIWFQNRRMKWKKENK 56
>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 = 31.2 bits (69), Expect = 2.4, Method: Composition-based stats.
Identities = 16/37 (43%), Positives = 23/37 (62%), Gaps = 1/37 (2%)
Query: 45 LRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQRKE 81
L R++ I LS E +QIK+WFQNRR + K+ +
Sbjct: 27 LTRRRRIEIAHALSLTE-RQIKIWFQNRRMKWKKENK 62
>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 = 31.2 bits (69), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 27/57 (47%), Gaps = 4/57 (7%)
Query: 19 TKYVRYTPEQVEALERVYSECPKPSSLRRQQLIRECPILSNIEPKQIKVWFQNRRCR 75
TKY PEQ+ ALE +++ P P +L E + ++I WF RR +
Sbjct: 9 TKYKERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTR----REIDSWFSERRKK 61
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 31.2 bits (69), Expect = 2.8, Method: Composition-based stats.
Identities = 16/34 (47%), Positives = 22/34 (64%), Gaps = 1/34 (2%)
Query: 45 LRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 78
L R++ I LS E +QIK+WFQNRR + K+
Sbjct: 28 LTRRRRIEIAHALSLTE-RQIKIWFQNRRMKWKK 60
>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Otx2
Length = 80
Score = 30.4 bits (67), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 30/54 (55%), Gaps = 6/54 (11%)
Query: 24 YTPEQVEALERVYSECPKPSSLRRQQLIRECPILSNIEPKQIKVWFQNRR--CR 75
+T Q++ LE ++++ P R+ E + N+ +++VWF+NRR CR
Sbjct: 14 FTRAQLDVLEALFAKTRYPDIFMRE----EVALKINLPESRVQVWFKNRRAKCR 63
>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 = 30.4 bits (67), Expect = 4.3, Method: Composition-based stats.
Identities = 12/30 (40%), Positives = 20/30 (66%)
Query: 49 QLIRECPILSNIEPKQIKVWFQNRRCREKQ 78
Q ++E + N+ KQ+K WFQN+R + K+
Sbjct: 31 QQMQELSSILNLSYKQVKTWFQNQRMKCKR 60
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
0.320 0.133 0.400
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 24,020,958
Number of Sequences: 62578
Number of extensions: 944992
Number of successful extensions: 2195
Number of sequences better than 100.0: 67
Number of HSP's better than 100.0 without gapping: 19
Number of HSP's successfully gapped in prelim test: 48
Number of HSP's that attempted gapping in prelim test: 2156
Number of HSP's gapped (non-prelim): 67
length of query: 850
length of database: 14,973,337
effective HSP length: 107
effective length of query: 743
effective length of database: 8,277,491
effective search space: 6150175813
effective search space used: 6150175813
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: 56 (26.2 bits)