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= psy9614
(103 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 = 75.5 bits (184), Expect = 8e-15, Method: Compositional matrix adjust.
Identities = 37/56 (66%), Positives = 47/56 (83%), Gaps = 1/56 (1%)
Query: 8 PGSANKPRKIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQV 63
PG A K RK RRSRTTF+ QL +LERAF++TQYPD++TRE+LA R +L+EAR+QV
Sbjct: 10 PGIALK-RKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQV 64
>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 = 73.2 bits (178), Expect = 4e-14, Method: Compositional matrix adjust.
Identities = 35/64 (54%), Positives = 47/64 (73%)
Query: 15 RKIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSDSQIPTLGS 74
RK RR RTTFT++QL +LE+AF +T YPDVFTRE+LA ++ L+EAR+QV ++
Sbjct: 4 RKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRK 63
Query: 75 NEKV 78
EKV
Sbjct: 64 QEKV 67
>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4490c
Length = 75
Score = 72.0 bits (175), Expect = 8e-14, Method: Compositional matrix adjust.
Identities = 35/53 (66%), Positives = 43/53 (81%), Gaps = 1/53 (1%)
Query: 11 ANKPRKIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQV 63
+NK +K RR+RTTFT+YQL +LE+ F KT YPDV+ RE LA R DL+EARVQV
Sbjct: 4 SNKGKK-RRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQV 55
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 70.1 bits (170), Expect = 3e-13, Method: Compositional matrix adjust.
Identities = 32/46 (69%), Positives = 39/46 (84%)
Query: 18 RRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQV 63
RRSRTTFT QL +LERAF++T YPD++TRE+LA R L+EARVQV
Sbjct: 3 RRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQV 48
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 67.0 bits (162), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 29/45 (64%), Positives = 39/45 (86%)
Query: 19 RSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQV 63
R RTTFT++QL +LE+AF +T YPDVFTRE+LA ++ L+EAR+QV
Sbjct: 1 RYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQV 45
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 65.1 bits (157), Expect = 8e-12, Method: Compositional matrix adjust.
Identities = 30/59 (50%), Positives = 42/59 (71%)
Query: 20 SRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSDSQIPTLGSNEKV 78
S TFT++QL +LE+AF +T YPDVFTRE+LA ++ L+EAR+QV ++ EKV
Sbjct: 2 SHMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQEKV 60
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 61.2 bits (147), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 26/45 (57%), Positives = 36/45 (80%)
Query: 19 RSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQV 63
R+RT+FT Q+ LE+ F++T YPDVF RE LA+++DL EAR+QV
Sbjct: 9 RNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQV 53
>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Otx2
Length = 80
Score = 57.8 bits (138), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 27/46 (58%), Positives = 35/46 (76%)
Query: 18 RRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQV 63
RR RTTFT QL LE F KT+YPD+F RE++A +++L E+RVQV
Sbjct: 8 RRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQV 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 = 50.8 bits (120), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 24/46 (52%), Positives = 34/46 (73%)
Query: 18 RRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQV 63
RR RT FT+ QL +LE F + +YPD+ TRE++A +L+EARV+V
Sbjct: 4 RRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRV 49
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 50.8 bits (120), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 24/46 (52%), Positives = 33/46 (71%)
Query: 18 RRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQV 63
RR RT FT+ QL +LE F + YPD+ TRE++A +L+EARV+V
Sbjct: 4 RRQRTHFTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRV 49
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 50.4 bits (119), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 25/46 (54%), Positives = 31/46 (67%)
Query: 18 RRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQV 63
RR RT FT QL LE F +T+YPDV TRE LA ++ L E +V+V
Sbjct: 8 RRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEV 53
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Barh-Like 1
Length = 80
Score = 43.9 bits (102), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 26/55 (47%), Positives = 34/55 (61%), Gaps = 2/55 (3%)
Query: 8 PGSANKPRKIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQ 62
PG+ K +K RRSRT FT QL LE+ F+K +Y R DLA L LS+ +V+
Sbjct: 10 PGT--KAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVK 62
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 41.6 bits (96), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/59 (37%), Positives = 37/59 (62%), Gaps = 3/59 (5%)
Query: 18 RRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQV---NSDSQIPTLG 73
R+ RT ++++QL L+R F KTQY + R +LA+ L L++ +V++ N S+I G
Sbjct: 8 RKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKKSG 66
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant
R31lE42L
Length = 67
Score = 40.4 bits (93), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/46 (43%), Positives = 26/46 (56%)
Query: 18 RRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQV 63
RR RT FT Q+ LE F YP + EDLA +L+L R+Q+
Sbjct: 2 RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQI 47
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 39.3 bits (90), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 20/46 (43%), Positives = 29/46 (63%)
Query: 18 RRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQV 63
R+ RT FTT QL LER F + QY + R + +S L L+E +V++
Sbjct: 1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKI 46
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor
Gbx1 From Homo Sapiens
Length = 71
Score = 38.5 bits (88), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 22/57 (38%), Positives = 31/57 (54%), Gaps = 5/57 (8%)
Query: 7 PPGSANKPRKIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQV 63
PG K RR RT FT+ QL +LE+ F +Y + R +A L LSE +V++
Sbjct: 2 APGG-----KSRRRRTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKI 53
>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 = 35.4 bits (80), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 20/47 (42%), Positives = 30/47 (63%)
Query: 17 IRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQV 63
+RR RT FT QL +LE+ F K Y R +LA++L+L E+ ++V
Sbjct: 1 VRRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKV 47
>pdb|1ZQ3|P Chain P, Nmr Solution Structure Of The Bicoid Homeodomain Bound
To The Consensus Dna Binding Site Taatcc
Length = 68
Score = 34.7 bits (78), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 31/46 (67%)
Query: 18 RRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQV 63
RR+RTTFT+ Q+ +LE+ F + +Y DL+++L L A+V++
Sbjct: 3 RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKI 48
>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 = 34.7 bits (78), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 29/50 (58%)
Query: 14 PRKIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQV 63
P K R+ R FT Q ++LER F + +Y RE LAS + L+ +V++
Sbjct: 6 PNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKI 55
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 34.3 bits (77), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 17/43 (39%), Positives = 28/43 (65%)
Query: 21 RTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQV 63
RT FTT QL +LE+ F +Y R ++A+ L+L+E +V++
Sbjct: 38 RTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKI 80
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 33.1 bits (74), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 31/62 (50%), Gaps = 2/62 (3%)
Query: 2 FFYFFPPGSANKPRKIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARV 61
F+ + N R RR R T+T YQ +LE+ F Y R ++A L L+E ++
Sbjct: 7 FYPWMAIAGTNGLR--RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQI 64
Query: 62 QV 63
++
Sbjct: 65 KI 66
>pdb|1QRY|A Chain A, Homeobox Protein Vnd (Ventral Nervous System Defective
Protein)
Length = 80
Score = 32.7 bits (73), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 28/50 (56%)
Query: 14 PRKIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQV 63
P K R+ R FT Q ++LER F + +Y RE L S + L+ +V++
Sbjct: 9 PNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVKI 58
>pdb|1FTT|A Chain A, Thyroid Transcription Factor 1 Homeodomain (Rattus
Norvegicus)
Length = 68
Score = 32.7 bits (73), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 28/46 (60%)
Query: 18 RRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQV 63
R+ R F+ Q+++LER F + +Y RE LAS + L+ +V++
Sbjct: 3 RKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKI 48
>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 = 32.3 bits (72), Expect = 0.075, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 29/46 (63%)
Query: 18 RRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQV 63
+R+R T+T YQ +LE+ F +Y R D+A+ L LSE ++++
Sbjct: 4 KRTRQTYTRYQTLELEKEFHFNRYITRRRRIDIANALSLSERQIKI 49
>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 = 32.0 bits (71), Expect = 0.084, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 30/49 (61%)
Query: 14 PRKIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQ 62
P K ++ RT+FT Q+ +LE+ F K +Y R LA L +++A+V+
Sbjct: 14 PPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVK 62
>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 = 32.0 bits (71), Expect = 0.099, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 28/46 (60%)
Query: 18 RRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQV 63
R+ R F+ Q+++LER F + +Y R+ LAS L L+ +V++
Sbjct: 3 RKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKI 48
>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 = 30.4 bits (67), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 28/46 (60%)
Query: 18 RRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQV 63
+R RT++T YQ +LE+ F +Y R ++A L L+E ++++
Sbjct: 29 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKI 74
>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 = 29.6 bits (65), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 28/46 (60%)
Query: 18 RRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQV 63
+R+RT +T QL +LE+ F +Y R +LA L+L+E +++
Sbjct: 4 KRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKI 49
>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 = 29.6 bits (65), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 38/78 (48%)
Query: 15 RKIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSDSQIPTLGS 74
+K+RR+R + L +A+D+ + P RE L + +E + S S+ LGS
Sbjct: 140 KKMRRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGS 199
Query: 75 NEKVQIVVTSDFTSKCAE 92
N ++ V + F ++ E
Sbjct: 200 NLVTEVRVYNWFANRRKE 217
>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 = 29.6 bits (65), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 27/46 (58%)
Query: 18 RRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQV 63
+R R T+T YQ +LE+ F +Y R ++A L L+E ++++
Sbjct: 3 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKI 48
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 28.9 bits (63), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 27/46 (58%)
Query: 18 RRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQV 63
+R R T+T YQ +LE+ F +Y R ++A L L+E ++++
Sbjct: 4 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKI 49
>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 = 28.9 bits (63), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 27/46 (58%)
Query: 18 RRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQV 63
+R R T+T YQ +LE+ F +Y R ++A L L+E ++++
Sbjct: 3 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKI 48
>pdb|1IC8|A Chain A, Hepatocyte Nuclear Factor 1a Bound To Dna : Mody3 Gene
Product
pdb|1IC8|B Chain B, Hepatocyte Nuclear Factor 1a Bound To Dna : Mody3 Gene
Product
Length = 194
Score = 28.1 bits (61), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 23/86 (26%), Positives = 39/86 (45%)
Query: 7 PPGSANKPRKIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSD 66
P G +K RR+R + L +A+++ + P RE L + +E + S
Sbjct: 105 PTGDELPTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSP 164
Query: 67 SQIPTLGSNEKVQIVVTSDFTSKCAE 92
SQ LGSN ++ V + F ++ E
Sbjct: 165 SQAQGLGSNLVTEVRVYNWFANRRKE 190
>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 = 27.3 bits (59), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 14/45 (31%), Positives = 18/45 (40%)
Query: 19 RSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQV 63
R RT QLH L + PD +E L LS ++V
Sbjct: 5 RVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRV 49
>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 = 26.9 bits (58), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 19/34 (55%), Gaps = 5/34 (14%)
Query: 28 QLHQLERAFDKTQYP-----DVFTREDLASRLDL 56
QLH L+ AF +TQ+P D +E +R D+
Sbjct: 36 QLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDI 69
>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 = 26.9 bits (58), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 26/44 (59%)
Query: 18 RRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARV 61
++ RT F+ QL L+ F K +Y + ++L+S L+LS +V
Sbjct: 4 QKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQV 47
>pdb|2DA2|A Chain A, Solution Structure Of The Second Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 26.6 bits (57), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 19/35 (54%)
Query: 22 TTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDL 56
T FT YQL L+ FD YP E L++ L+L
Sbjct: 12 TRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNL 46
>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX
Protein Lhx9
Length = 80
Score = 26.6 bits (57), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 14/46 (30%), Positives = 24/46 (52%)
Query: 18 RRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQV 63
+R RT+F +QL ++ F PD + LA + L++ +QV
Sbjct: 8 KRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQV 53
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 26.2 bits (56), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 26/46 (56%)
Query: 18 RRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQV 63
R+ R +T YQ +LE+ F Y R ++A L+L+E +V++
Sbjct: 2 RKKRCPYTKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKI 47
>pdb|2CUF|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Hypothetical Protein Flj21616
Length = 95
Score = 26.2 bits (56), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 11/30 (36%), Positives = 18/30 (60%)
Query: 23 TFTTYQLHQLERAFDKTQYPDVFTREDLAS 52
T+ L +E F++ QYPD RE++A+
Sbjct: 13 TWRKECLAVMESYFNENQYPDEAKREEIAN 42
>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 = 25.8 bits (55), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 13/41 (31%), Positives = 24/41 (58%)
Query: 23 TFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQV 63
T+T YQ +LE+ F +Y R ++A L L+E ++++
Sbjct: 2 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKI 42
>pdb|3CGH|A Chain A, Crystal Structure Of A Susd Homolog (Bt_3984) From
Bacteroides Thetaiotaomicron Vpi-5482 At 1.70 A
Resolution
Length = 516
Score = 25.8 bits (55), Expect = 6.6, Method: Composition-based stats.
Identities = 17/63 (26%), Positives = 27/63 (42%), Gaps = 3/63 (4%)
Query: 30 HQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSD---SQIPTLGSNEKVQIVVTSDF 86
H++ AF Y + ++A+ D E D + I TL N Q+V T+D+
Sbjct: 123 HRVTDAFGPIPYSQIGANGEIATPYDSQEVTYNTFFDELNAAIATLNENSNEQLVPTADY 182
Query: 87 TSK 89
K
Sbjct: 183 IYK 185
>pdb|2LD5|A Chain A, Solution Nmr-Derived Complex Structure Of Hoxa13 Dna
Binding Domain Bound To Dna
Length = 67
Score = 25.4 bits (54), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 13/46 (28%), Positives = 25/46 (54%)
Query: 18 RRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQV 63
R+ R +T QL +LER + ++ R +++ +LSE +V +
Sbjct: 2 RKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTI 47
>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain
Length = 73
Score = 25.4 bits (54), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 13/46 (28%), Positives = 25/46 (54%)
Query: 18 RRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQV 63
R+ R +T QL +LER + ++ R +++ +LSE +V +
Sbjct: 8 RKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTI 53
>pdb|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain
Length = 56
Score = 25.0 bits (53), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 25/41 (60%)
Query: 22 TTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQ 62
T+F+ Q+ +LER F + +Y R LA L +++A+V+
Sbjct: 2 TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVK 42
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
0.318 0.129 0.363
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,713,934
Number of Sequences: 62578
Number of extensions: 83764
Number of successful extensions: 185
Number of sequences better than 100.0: 50
Number of HSP's better than 100.0 without gapping: 48
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 137
Number of HSP's gapped (non-prelim): 50
length of query: 103
length of database: 14,973,337
effective HSP length: 68
effective length of query: 35
effective length of database: 10,718,033
effective search space: 375131155
effective search space used: 375131155
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 45 (21.9 bits)