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= psy9529
(149 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4490c
Length = 75
Score = 94.4 bits (233), Expect = 2e-20, Method: Compositional matrix adjust.
Identities = 42/61 (68%), Positives = 51/61 (83%)
Query: 12 KRRRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRKK 71
K+RR+RT F S+QLEELE+ F +HYPDV+ RE LA+R DL E+RV VWFQNRRAKWRK+
Sbjct: 8 KKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRKR 67
Query: 72 E 72
E
Sbjct: 68 E 68
>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 = 90.9 bits (224), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 41/61 (67%), Positives = 51/61 (83%)
Query: 12 KRRRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRKK 71
K+RR RT F S+QLEELE+AF +HYPDVF RE LA+++ L E+R+ VWFQNRRAKWRK+
Sbjct: 5 KQRRYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQ 64
Query: 72 E 72
E
Sbjct: 65 E 65
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 87.4 bits (215), Expect = 3e-18, Method: Compositional matrix adjust.
Identities = 39/58 (67%), Positives = 48/58 (82%)
Query: 15 RSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRKKE 72
R RT F S+QLEELE+AF +HYPDVF RE LA+++ L E+R+ VWFQNRRAKWRK+E
Sbjct: 1 RYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQE 58
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 84.0 bits (206), Expect = 3e-17, Method: Compositional matrix adjust.
Identities = 37/57 (64%), Positives = 46/57 (80%)
Query: 16 SRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRKKE 72
S F S+QLEELE+AF +HYPDVF RE LA+++ L E+R+ VWFQNRRAKWRK+E
Sbjct: 2 SHMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQE 58
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 80.9 bits (198), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 38/58 (65%), Positives = 45/58 (77%)
Query: 14 RRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRKK 71
RRSRT F + QLEELERAF +HYPD++ RE LA R L E+RV VWF NRRA+WRK+
Sbjct: 3 RRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRARWRKQ 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 = 80.1 bits (196), Expect = 4e-16, Method: Compositional matrix adjust.
Identities = 39/66 (59%), Positives = 51/66 (77%), Gaps = 1/66 (1%)
Query: 9 LASKRRRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKW 68
L K+RRSRT F++ QL+ELERAF + YPD++ RE LA R +L E+R+ VWFQNRRA+
Sbjct: 14 LKRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARL 73
Query: 69 RKKEHT 74
R K+HT
Sbjct: 74 R-KQHT 78
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 77.4 bits (189), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 35/63 (55%), Positives = 47/63 (74%)
Query: 10 ASKRRRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWR 69
S +R+RT+F Q+E LE+ F +HYPDVF RE LA ++DL E+R+ VWF NRRAKWR
Sbjct: 4 GSSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWR 63
Query: 70 KKE 72
++E
Sbjct: 64 REE 66
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 73.2 bits (178), Expect = 5e-14, Method: Compositional matrix adjust.
Identities = 35/59 (59%), Positives = 45/59 (76%)
Query: 14 RRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRKKE 72
RR RT+F S QL+ELE F +HYPD+ RE +A+ +L E+RV VWF+NRRAKWRK+E
Sbjct: 4 RRQRTHFTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE 62
>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Otx2
Length = 80
Score = 72.4 bits (176), Expect = 9e-14, Method: Compositional matrix adjust.
Identities = 34/60 (56%), Positives = 42/60 (70%)
Query: 10 ASKRRRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWR 69
S RR RT F QL+ LE F + YPD+FMRE +AL+++L ESRV VWF+NRRAK R
Sbjct: 4 GSSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCR 63
>pdb|2L7F|P Chain P, Solution Structure Of The Pitx2 Homeodomain
pdb|2LKX|A Chain A, Nmr Structure Of The Homeodomain Of Pitx2 In Complex
With A Taatcc Dna Binding Site
Length = 68
Score = 69.7 bits (169), Expect = 6e-13, Method: Compositional matrix adjust.
Identities = 34/59 (57%), Positives = 44/59 (74%)
Query: 14 RRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRKKE 72
RR RT+F S QL+ELE F + YPD+ RE +A+ +L E+RV VWF+NRRAKWRK+E
Sbjct: 4 RRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE 62
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 65.9 bits (159), Expect = 8e-12, Method: Compositional matrix adjust.
Identities = 33/61 (54%), Positives = 40/61 (65%)
Query: 10 ASKRRRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWR 69
S RR RT F QLE LE F + YPDV RE LA ++ L+E +V VWF+NRRAKWR
Sbjct: 4 GSSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWR 63
Query: 70 K 70
+
Sbjct: 64 R 64
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor
Gbx1 From Homo Sapiens
Length = 71
Score = 55.5 bits (132), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 29/61 (47%), Positives = 36/61 (59%)
Query: 10 ASKRRRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWR 69
K RR RT F S QL ELE+ F Y + R +A L L E +V +WFQNRRAKW+
Sbjct: 4 GGKSRRRRTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRAKWK 63
Query: 70 K 70
+
Sbjct: 64 R 64
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant
R31lE42L
Length = 67
Score = 53.9 bits (128), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 26/57 (45%), Positives = 37/57 (64%)
Query: 14 RRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRK 70
RR RT F Q+E LE F + YP + + E LA +L+L+ R+ +WFQNRRAK ++
Sbjct: 2 RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKR 58
>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 = 52.8 bits (125), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 27/59 (45%), Positives = 38/59 (64%)
Query: 14 RRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRKKE 72
+R+RT + QL ELE+ FL + Y R LA+ L+L E + +WFQNRR KW+K+E
Sbjct: 4 KRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKEE 62
>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 = 52.0 bits (123), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 27/67 (40%), Positives = 38/67 (56%)
Query: 13 RRRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRKKE 72
R+R R + +Q ELE+ F + Y R +A L L E ++ +WFQNRR KW+K+
Sbjct: 2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEN 61
Query: 73 HTKKGPG 79
TK PG
Sbjct: 62 KTKGEPG 68
>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 = 51.2 bits (121), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 29/73 (39%), Positives = 42/73 (57%)
Query: 12 KRRRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRKK 71
KR++ RT+F Q+ ELE+ F Y R ALA L + +++V WFQNRR KWR++
Sbjct: 16 KRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQ 75
Query: 72 EHTKKGPGRPAHN 84
++ R A N
Sbjct: 76 TAEEREAERQAAN 88
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 51.2 bits (121), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 26/56 (46%), Positives = 36/56 (64%)
Query: 17 RTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRKKE 72
RTNF + QL ELE+ F + Y R +A L+L E++V +WFQNRR K +K+E
Sbjct: 38 RTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRE 93
>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 = 51.2 bits (121), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 27/67 (40%), Positives = 38/67 (56%)
Query: 13 RRRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRKKE 72
R+R R + +Q ELE+ F + Y R +A L L E ++ +WFQNRR KW+K+
Sbjct: 2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 61
Query: 73 HTKKGPG 79
TK PG
Sbjct: 62 KTKGEPG 68
>pdb|1QRY|A Chain A, Homeobox Protein Vnd (Ventral Nervous System Defective
Protein)
Length = 80
Score = 49.3 bits (116), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 28/78 (35%), Positives = 41/78 (52%)
Query: 4 NLSDDLASKRRRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQN 63
++SD L +K+R+ R F Q ELER F Y RE L + L ++V +WFQN
Sbjct: 3 HMSDGLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVKIWFQN 62
Query: 64 RRAKWRKKEHTKKGPGRP 81
R K ++ ++ K G P
Sbjct: 63 HRYKTKRAQNEKGYEGHP 80
>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 = 49.3 bits (116), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 29/76 (38%), Positives = 40/76 (52%)
Query: 6 SDDLASKRRRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRR 65
SD L +K+R+ R F Q ELER F Y RE LA + L ++V +WFQN R
Sbjct: 2 SDGLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHR 61
Query: 66 AKWRKKEHTKKGPGRP 81
K ++ ++ K G P
Sbjct: 62 YKTKRAQNEKGYEGHP 77
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 49.3 bits (116), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 24/61 (39%), Positives = 38/61 (62%)
Query: 10 ASKRRRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWR 69
S R+ RT ++S+QL L+R F + Y + R LA L L +++V +WFQN+R+K +
Sbjct: 4 GSSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIK 63
Query: 70 K 70
K
Sbjct: 64 K 64
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Barh-Like 1
Length = 80
Score = 48.1 bits (113), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 28/61 (45%), Positives = 33/61 (54%)
Query: 10 ASKRRRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWR 69
A K RRSRT F QL LE+ F Y R LA L L + +V W+QNRR KW+
Sbjct: 14 AKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWK 73
Query: 70 K 70
K
Sbjct: 74 K 74
>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 = 48.1 bits (113), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 27/71 (38%), Positives = 40/71 (56%), Gaps = 1/71 (1%)
Query: 3 GNLSDDLASKRRRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQ 62
G + + + +R RT++ +Q ELE+ F + Y R +A L L E ++ +WFQ
Sbjct: 18 GTSTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQ 77
Query: 63 NRRAKWRKKEH 73
NRR KW KKEH
Sbjct: 78 NRRMKW-KKEH 87
>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 = 47.0 bits (110), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 24/61 (39%), Positives = 34/61 (55%)
Query: 19 NFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRKKEHTKKGP 78
+ +Q ELE+ F + Y R +A L L E ++ +WFQNRR KW+K+ TK P
Sbjct: 2 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENKTKGEP 61
Query: 79 G 79
G
Sbjct: 62 G 62
>pdb|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain
Length = 56
Score = 46.6 bits (109), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 25/54 (46%), Positives = 34/54 (62%)
Query: 18 TNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRKK 71
T+F+ Q+ ELER FL Y R ALA L + +++V WFQNRR KWR++
Sbjct: 2 TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ 55
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 46.2 bits (108), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 24/58 (41%), Positives = 33/58 (56%)
Query: 13 RRRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRK 70
RRR R + +Q ELE+ F +HY R +A L L E ++ +WFQNRR K +K
Sbjct: 20 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKK 77
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 46.2 bits (108), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 24/54 (44%), Positives = 31/54 (57%)
Query: 14 RRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAK 67
R+ RT F + QL LER F Y + R + L L E++V +WFQNRRAK
Sbjct: 1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAK 54
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
Length = 60
Score = 45.1 bits (105), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 24/57 (42%), Positives = 36/57 (63%)
Query: 14 RRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRK 70
+R RT F+S QL L+R F + Y R+ L+ L L E+++ +WFQN+RAK +K
Sbjct: 2 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 58
>pdb|1HDD|C Chain C, Crystal Structure Of An Engrailed Homeodomain-Dna
Complex At 2.8 Angstroms Resolution: A Framework For
Understanding Homeodomain-Dna Interactions
pdb|1HDD|D Chain D, Crystal Structure Of An Engrailed Homeodomain-Dna
Complex At 2.8 Angstroms Resolution: A Framework For
Understanding Homeodomain-Dna Interactions
pdb|2JWT|A Chain A, Solution Structure Of Engrailed Homeodomain Wt
Length = 61
Score = 45.1 bits (105), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 24/57 (42%), Positives = 36/57 (63%)
Query: 14 RRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRK 70
+R RT F+S QL L+R F + Y R+ L+ L L E+++ +WFQN+RAK +K
Sbjct: 4 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 60
>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 = 44.3 bits (103), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 26/54 (48%), Positives = 31/54 (57%)
Query: 14 RRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAK 67
RR RT F QL LE+ F +Y R LA +L+L ES + VWFQNRR K
Sbjct: 2 RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMK 55
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 44.3 bits (103), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 23/58 (39%), Positives = 33/58 (56%)
Query: 13 RRRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRK 70
R+R R + +Q ELE+ F + Y R +A L L E ++ +WFQNRR KW+K
Sbjct: 3 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKK 60
>pdb|1P7J|A Chain A, Crystal Structure Of Engrailed Homeodomain Mutant K52e
pdb|1P7J|B Chain B, Crystal Structure Of Engrailed Homeodomain Mutant K52e
pdb|1P7J|C Chain C, Crystal Structure Of Engrailed Homeodomain Mutant K52e
pdb|1P7J|D Chain D, Crystal Structure Of Engrailed Homeodomain Mutant K52e
Length = 59
Score = 43.9 bits (102), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 24/57 (42%), Positives = 35/57 (61%)
Query: 14 RRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRK 70
+R RT F+S QL L+R F + Y R+ L+ L L E+++ +WFQN RAK +K
Sbjct: 2 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNERAKIKK 58
>pdb|1ZQ3|P Chain P, Nmr Solution Structure Of The Bicoid Homeodomain Bound
To The Consensus Dna Binding Site Taatcc
Length = 68
Score = 43.9 bits (102), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 22/52 (42%), Positives = 31/52 (59%)
Query: 14 RRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRR 65
RR+RT F S Q+ ELE+ FL Y L+ +L L ++V +WF+NRR
Sbjct: 3 RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRR 54
>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX
Protein Lhx9
Length = 80
Score = 43.9 bits (102), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 23/61 (37%), Positives = 34/61 (55%)
Query: 10 ASKRRRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWR 69
S +R RT+F QL ++ F +H PD + LA + L + + VWFQN RAK+R
Sbjct: 4 GSSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFR 63
Query: 70 K 70
+
Sbjct: 64 R 64
>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 = 43.1 bits (100), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 24/57 (42%), Positives = 35/57 (61%)
Query: 14 RRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRK 70
+R RT F+S QL L+R F + Y R+ L+ L L E+++ +WFQN RAK +K
Sbjct: 2 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAKIKK 58
>pdb|2E1O|A Chain A, Solution Structure Of Rsgi Ruh-028, A Homeobox Domain
From Human Cdna
Length = 70
Score = 43.1 bits (100), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 24/51 (47%), Positives = 30/51 (58%)
Query: 20 FNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRK 70
F++ Q ELE+ F Y R+ LA L L E +V WFQNRRAKWR+
Sbjct: 14 FSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR 64
>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 = 43.1 bits (100), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 23/57 (40%), Positives = 36/57 (63%)
Query: 14 RRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRK 70
+R RT F+S QL L+R F + Y R+ L+ L L E+++ +WF+N+RAK +K
Sbjct: 4 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK 60
>pdb|1ZTR|A Chain A, Solution Structure Of Engrailed Homeodomain L16a Mutant
Length = 61
Score = 42.7 bits (99), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 23/57 (40%), Positives = 35/57 (61%)
Query: 14 RRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRK 70
+R RT F+S QL +R F + Y R+ L+ L L E+++ +WFQN+RAK R+
Sbjct: 4 KRPRTAFSSEQLARAKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIRR 60
>pdb|1ENH|A Chain A, Structural Studies Of The Engrailed Homeodomain
Length = 54
Score = 42.7 bits (99), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 23/53 (43%), Positives = 33/53 (62%)
Query: 15 RSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAK 67
R RT F+S QL L+R F + Y R+ L+ L L E+++ +WFQN+RAK
Sbjct: 1 RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 53
>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 = 42.7 bits (99), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 24/55 (43%), Positives = 31/55 (56%)
Query: 13 RRRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAK 67
RR+ R F+ Q+ ELER F Y R+ LA L L ++V +WFQNRR K
Sbjct: 2 RRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYK 56
>pdb|2CRA|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeo
Box B13
Length = 70
Score = 42.4 bits (98), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 33/61 (54%)
Query: 10 ASKRRRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWR 69
S R+ R ++ QL ELER + A+ + R ++ L E ++ +WFQNRR K +
Sbjct: 4 GSSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEK 63
Query: 70 K 70
K
Sbjct: 64 K 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 = 42.4 bits (98), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/60 (38%), Positives = 30/60 (50%)
Query: 12 KRRRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRKK 71
K R RT N QL L + A+ PD M+E L L + VWFQN+R K +K+
Sbjct: 2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKR 61
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 42.0 bits (97), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/57 (40%), Positives = 33/57 (57%)
Query: 14 RRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRK 70
R+ R + +Q ELE+ FL + Y R +A L+L E +V +WFQNRR K +K
Sbjct: 2 RKKRCPYTKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMKK 58
>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 = 41.6 bits (96), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/56 (41%), Positives = 34/56 (60%)
Query: 15 RSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRK 70
R RT F+S QL L+R F + Y R+ L+ L L E+++ +WF N+RAK +K
Sbjct: 1 RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANKRAKIKK 56
>pdb|1FTT|A Chain A, Thyroid Transcription Factor 1 Homeodomain (Rattus
Norvegicus)
Length = 68
Score = 41.2 bits (95), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/59 (38%), Positives = 33/59 (55%)
Query: 13 RRRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRKK 71
RR+ R F+ Q+ ELER F Y RE LA + L ++V +WFQN R K +++
Sbjct: 2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQ 60
>pdb|2LD5|A Chain A, Solution Nmr-Derived Complex Structure Of Hoxa13 Dna
Binding Domain Bound To Dna
Length = 67
Score = 41.2 bits (95), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 32/57 (56%)
Query: 14 RRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRK 70
R+ R + QL+ELER + + + R ++ +L E +V +WFQNRR K +K
Sbjct: 2 RKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKK 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 = 40.8 bits (94), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 25/61 (40%), Positives = 35/61 (57%)
Query: 10 ASKRRRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWR 69
S +R RT F+S QL L+R F + Y R+ L+ L L E++V WF+N RAK +
Sbjct: 1 GSDEKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMRAKIK 60
Query: 70 K 70
K
Sbjct: 61 K 61
>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain
Length = 73
Score = 40.8 bits (94), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 32/57 (56%)
Query: 14 RRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRK 70
R+ R + QL+ELER + + + R ++ +L E +V +WFQNRR K +K
Sbjct: 8 RKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKK 64
>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 = 40.8 bits (94), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 22/49 (44%), Positives = 29/49 (59%)
Query: 24 QLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRKKE 72
Q+ ELER F Y R LA L L E++V +WFQNRR K ++K+
Sbjct: 15 QVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQ 63
>pdb|2DA3|A Chain A, Solution Structure Of The Third Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 80
Score = 39.7 bits (91), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 23/57 (40%), Positives = 31/57 (54%)
Query: 14 RRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRK 70
+R RT QLE L + +L P M + +A + LK+ V VWFQN RA+ RK
Sbjct: 18 KRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERK 74
>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound
To Dna
Length = 77
Score = 39.7 bits (91), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 23/57 (40%), Positives = 32/57 (56%)
Query: 14 RRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRK 70
R+ R + Q ELE+ FL + Y R +A L+L E +V +WFQNRR K +K
Sbjct: 14 RKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKK 70
>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 = 8e-04, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 33/65 (50%)
Query: 14 RRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRKKEH 73
+R+R + +Q ELE+ F + Y R +A L L E ++ +WFQNRR K +K
Sbjct: 4 KRTRQTYTRYQTLELEKEFHFNRYITRRRRIDIANALSLSERQIKIWFQNRRMKSKKDRT 63
Query: 74 TKKGP 78
P
Sbjct: 64 LDSSP 68
>pdb|1B72|B Chain B, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 87
Score = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/60 (36%), Positives = 33/60 (55%), Gaps = 3/60 (5%)
Query: 14 RRSRTNFNSWQLEELERAF---LASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRK 70
RR R NFN E L F L++ YP +E LA + + S+V+ WF N+R +++K
Sbjct: 2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 61
>pdb|1PUF|B Chain B, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound
To Dna
Length = 73
Score = 38.1 bits (87), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/60 (36%), Positives = 33/60 (55%), Gaps = 3/60 (5%)
Query: 14 RRSRTNFNSWQLEELERAF---LASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRK 70
RR R NFN E L F L++ YP +E LA + + S+V+ WF N+R +++K
Sbjct: 2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 61
>pdb|1LFU|P Chain P, Nmr Solution Stucture Of The Extended Pbx Homeodomain
Bound To Dna
Length = 82
Score = 37.4 bits (85), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/60 (36%), Positives = 33/60 (55%), Gaps = 3/60 (5%)
Query: 14 RRSRTNFNSWQLEELERAF---LASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRK 70
RR R NFN E L F L++ YP +E LA + + S+V+ WF N+R +++K
Sbjct: 3 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKSGITVSQVSNWFGNKRIRYKK 62
>pdb|2DA2|A Chain A, Solution Structure Of The Second Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 37.0 bits (84), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 22/53 (41%), Positives = 28/53 (52%)
Query: 18 TNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRK 70
T F +QL L+ F A+ YP E L+ L+L + VWFQN R K RK
Sbjct: 12 TRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARK 64
>pdb|2KT0|A Chain A, Solution Structure Of Human Stem Cell Transcription
Factor Nanog Homeodomain Fragment
Length = 84
Score = 36.6 bits (83), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 36/67 (53%), Gaps = 3/67 (4%)
Query: 7 DDLASKRRRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRA 66
D + K++++RT F+S QL L F Y + + L+ L+L +V WFQN+R
Sbjct: 16 DKVPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRM 75
Query: 67 K---WRK 70
K W+K
Sbjct: 76 KSKRWQK 82
>pdb|1B8I|B Chain B, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
pdb|2R5Y|B Chain B, Structure Of ScrEXD COMPLEX BOUND TO A CONSENSUS HOX-Exd
Site
pdb|2R5Z|B Chain B, Structure Of ScrEXD COMPLEX BOUND TO A DNA SEQUENCE
Derived From The Fkh Gene
Length = 63
Score = 35.4 bits (80), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 22/61 (36%), Positives = 33/61 (54%), Gaps = 5/61 (8%)
Query: 14 RRSRTNFNSWQLEELERAFLASH----YPDVFMREALALRLDLKESRVAVWFQNRRAKWR 69
RR R NF S Q E+ + SH YP +E LA + + S+V+ WF N+R +++
Sbjct: 2 RRKRRNF-SKQASEILNEYFYSHLSNPYPSEEAKEELARKCGITVSQVSNWFGNKRIRYK 60
Query: 70 K 70
K
Sbjct: 61 K 61
>pdb|3L1P|A Chain A, Pou Protein:dna Complex
pdb|3L1P|B Chain B, Pou Protein:dna Complex
Length = 155
Score = 35.4 bits (80), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 34/65 (52%)
Query: 6 SDDLASKRRRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRR 65
S+ L R+R RT+ + LE FL S P + +A +L L++ V VWF NRR
Sbjct: 89 SETLVQARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRR 148
Query: 66 AKWRK 70
K ++
Sbjct: 149 QKGKR 153
>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 = 0.018, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 33/57 (57%)
Query: 11 SKRRRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAK 67
S+RR+ RT+ + LE++FL + P +A +L++++ + VWF NRR K
Sbjct: 98 SRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFSNRRQK 154
>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 = 34.7 bits (78), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 33/57 (57%)
Query: 11 SKRRRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAK 67
S+RR+ RT+ + LE++FL + P +A +L++++ + VWF NRR K
Sbjct: 101 SRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQK 157
>pdb|1O4X|A Chain A, Ternary Complex Of The Dna Binding Domains Of The Oct1 And
Sox2 Transcription Factors With A 19mer Oligonucleotide
From The Hoxb1 Regulatory Element
Length = 167
Score = 34.3 bits (77), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 35/60 (58%)
Query: 11 SKRRRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRK 70
S+RR+ RT+ + LE++FL + P +A +L++++ + VWF NRR K ++
Sbjct: 102 SERRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKR 161
>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 = 34.3 bits (77), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 33/57 (57%)
Query: 11 SKRRRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAK 67
S+RR+ RT+ + LE++FL + P +A +L++++ + VWF NRR K
Sbjct: 94 SRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQK 150
>pdb|1E3O|C Chain C, Crystal Structure Of Oct-1 Pou Dimer Bound To More
Length = 160
Score = 33.9 bits (76), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 33/57 (57%)
Query: 11 SKRRRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAK 67
S+RR+ RT+ + LE++F+ + P +A +L++++ + VWF NRR K
Sbjct: 99 SRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQK 155
>pdb|2P81|A Chain A, Engrailed Homeodomain Helix-Turn-Helix Motif
Length = 44
Score = 33.5 bits (75), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 16/41 (39%), Positives = 25/41 (60%)
Query: 30 RAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRK 70
R F + Y R+ L+ L L E+++ +WFQN+RAK +K
Sbjct: 3 REFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 43
>pdb|1DU6|A Chain A, Solution Structure Of The Truncated Pbx Homeodomain
Length = 64
Score = 32.7 bits (73), Expect = 0.070, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 27/46 (58%)
Query: 25 LEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRK 70
L E + L++ YP +E LA + + S+V+ WF N+R +++K
Sbjct: 18 LNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 63
>pdb|1OCP|A Chain A, Solution Structure Of Oct3 Pou-Homeodomain
Length = 67
Score = 32.7 bits (73), Expect = 0.081, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 30/61 (49%)
Query: 7 DDLASKRRRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRA 66
+ L R+R RT+ + LE FL P + +A +L L++ V VWF NRR
Sbjct: 2 ETLVQARKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQ 61
Query: 67 K 67
K
Sbjct: 62 K 62
>pdb|1POG|A Chain A, Solution Structure Of The Oct-1 Pou-Homeo Domain
Determined By Nmr And Restrained Molecular Dynamics
Length = 67
Score = 32.3 bits (72), Expect = 0.090, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 32/56 (57%)
Query: 12 KRRRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAK 67
+RR+ RT+ + LE++FL + P +A +L++++ + VWF NRR K
Sbjct: 6 RRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQK 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 = 0.10, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 28/60 (46%)
Query: 11 SKRRRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRK 70
++R+ RT+ LE FL P LA L L++ V VWF NRR K ++
Sbjct: 97 GRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKEKR 156
>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 = 31.6 bits (70), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 31/55 (56%)
Query: 13 RRRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAK 67
RR+ RT+ + LE++FLA+ P +A +L +++ + VWF NRR K
Sbjct: 1 RRKKRTSIETNVRFALEKSFLANQKPTSEEILLIAEQLHMEKEVIRVWFCNRRQK 55
>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 = 31.2 bits (69), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 29/55 (52%)
Query: 13 RRRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAK 67
+++ RT F+ QL L+ F Y + + L+ L+L +V WFQN+R K
Sbjct: 3 KQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMK 57
>pdb|3D1N|I Chain I, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|J Chain J, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|K Chain K, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|L Chain L, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|M Chain M, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|N Chain N, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|O Chain O, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|P Chain P, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
Length = 151
Score = 30.4 bits (67), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 30/68 (44%), Gaps = 3/68 (4%)
Query: 1 GDGNLSDDLA---SKRRRSRTNFNSWQLEELERAFLASHYPDVFMREALALRLDLKESRV 57
G NL + + SK+R+ RT+F +E L F + P A L+ V
Sbjct: 78 GQQNLXEFVGGEPSKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEXAKELNYDREVV 137
Query: 58 AVWFQNRR 65
VWF NRR
Sbjct: 138 RVWFSNRR 145
>pdb|2HI3|A Chain A, Solution Structure Of The Homeodomain-Only Protein Hop
Length = 73
Score = 29.3 bits (64), Expect = 0.96, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 25/50 (50%), Gaps = 1/50 (2%)
Query: 24 QLEELERAF-LASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRKKE 72
Q+E LE F + +PD +A L E + WF+ R A+WR+ E
Sbjct: 13 QVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE 62
>pdb|1UHS|A Chain A, Solution Structure Of Mouse Homeodomain-Only Protein Hop
Length = 72
Score = 28.9 bits (63), Expect = 1.00, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 25/50 (50%), Gaps = 1/50 (2%)
Query: 24 QLEELERAF-LASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRKKE 72
Q+E LE F + +PD +A L E + WF+ R A+WR+ E
Sbjct: 12 QVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE 61
>pdb|2CQX|A Chain A, Solution Structure Of Rsgi Ruh-034, A Homeodomain From
Mouse Cdna
Length = 72
Score = 28.5 bits (62), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 13/41 (31%), Positives = 25/41 (60%), Gaps = 1/41 (2%)
Query: 26 EELERAFLA-SHYPDVFMREALALRLDLKESRVAVWFQNRR 65
+ LE+ F++ + YPD + L+ +LD ++ WF++RR
Sbjct: 21 DTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRR 61
>pdb|2DN0|A Chain A, Solution Structure Of The Second Homeobox Domain Of
Human Zinc Fingers And Homeoboxes Protein 3
Length = 76
Score = 28.1 bits (61), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 24/55 (43%)
Query: 24 QLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWRKKEHTKKGP 78
QL L+ +F + +P E L L V WF +RR R + ++ GP
Sbjct: 19 QLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCRNLKGSRSGP 73
>pdb|4H2H|A Chain A, Crystal Structure Of An Enolase (Mandalate Racemase
Subgroup, Target Efi-502101) From Pelagibaca Bermudensis
Htcc2601, With Bound Mg And L-4-Hydroxyproline Betaine
(Betonicine)
pdb|4H2H|B Chain B, Crystal Structure Of An Enolase (Mandalate Racemase
Subgroup, Target Efi-502101) From Pelagibaca Bermudensis
Htcc2601, With Bound Mg And L-4-Hydroxyproline Betaine
(Betonicine)
pdb|4H2H|C Chain C, Crystal Structure Of An Enolase (Mandalate Racemase
Subgroup, Target Efi-502101) From Pelagibaca Bermudensis
Htcc2601, With Bound Mg And L-4-Hydroxyproline Betaine
(Betonicine)
pdb|4H2H|D Chain D, Crystal Structure Of An Enolase (Mandalate Racemase
Subgroup, Target Efi-502101) From Pelagibaca Bermudensis
Htcc2601, With Bound Mg And L-4-Hydroxyproline Betaine
(Betonicine)
pdb|4H2H|E Chain E, Crystal Structure Of An Enolase (Mandalate Racemase
Subgroup, Target Efi-502101) From Pelagibaca Bermudensis
Htcc2601, With Bound Mg And L-4-Hydroxyproline Betaine
(Betonicine)
pdb|4H2H|F Chain F, Crystal Structure Of An Enolase (Mandalate Racemase
Subgroup, Target Efi-502101) From Pelagibaca Bermudensis
Htcc2601, With Bound Mg And L-4-Hydroxyproline Betaine
(Betonicine)
pdb|4H2H|G Chain G, Crystal Structure Of An Enolase (Mandalate Racemase
Subgroup, Target Efi-502101) From Pelagibaca Bermudensis
Htcc2601, With Bound Mg And L-4-Hydroxyproline Betaine
(Betonicine)
pdb|4H2H|H Chain H, Crystal Structure Of An Enolase (Mandalate Racemase
Subgroup, Target Efi-502101) From Pelagibaca Bermudensis
Htcc2601, With Bound Mg And L-4-Hydroxyproline Betaine
(Betonicine)
Length = 376
Score = 27.7 bits (60), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 9/34 (26%), Positives = 21/34 (61%)
Query: 114 KSLERQQRKLAAKGVTVDLETLKREWESQQASEL 147
+ R Q KL A+ + +D+E +++ WE+ + + +
Sbjct: 164 EGYSRLQVKLGARPIEIDIEAIRKVWEAVRGTGI 197
>pdb|2PMQ|A Chain A, Crystal Structure Of A Mandelate RacemaseMUCONATE
LACTONIZING ENZYME From Roseovarius Sp. Htcc2601
pdb|2PMQ|B Chain B, Crystal Structure Of A Mandelate RacemaseMUCONATE
LACTONIZING ENZYME From Roseovarius Sp. Htcc2601
Length = 377
Score = 27.3 bits (59), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 9/34 (26%), Positives = 21/34 (61%)
Query: 114 KSLERQQRKLAAKGVTVDLETLKREWESQQASEL 147
+ R Q KL A+ + +D+E +++ WE+ + + +
Sbjct: 157 EGYSRLQVKLGARPIEIDIEAIRKVWEAVRGTGI 190
>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 = 27.3 bits (59), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 13/46 (28%), Positives = 22/46 (47%)
Query: 24 QLEELERAFLASHYPDVFMREALALRLDLKESRVAVWFQNRRAKWR 69
QL L+ AF+ + +P + LA L + + WF + R W+
Sbjct: 36 QLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWK 81
>pdb|2INP|A Chain A, Structure Of The Phenol Hydroxylase-Regulatory Protein
Complex
pdb|2INP|B Chain B, Structure Of The Phenol Hydroxylase-Regulatory Protein
Complex
Length = 494
Score = 26.9 bits (58), Expect = 3.8, Method: Composition-based stats.
Identities = 10/24 (41%), Positives = 16/24 (66%)
Query: 18 TNFNSWQLEELERAFLASHYPDVF 41
TNF++W E+ E +++ YPD F
Sbjct: 341 TNFHTWIPEKEEMDWMSEKYPDTF 364
>pdb|3U52|A Chain A, X-Ray Crystal Structure Of Xenon-Pressurized Phenol
Hydroxylase From Pseudomonas Sp. Ox1
pdb|3U52|B Chain B, X-Ray Crystal Structure Of Xenon-Pressurized Phenol
Hydroxylase From Pseudomonas Sp. Ox1
Length = 511
Score = 26.9 bits (58), Expect = 3.8, Method: Composition-based stats.
Identities = 10/24 (41%), Positives = 16/24 (66%)
Query: 18 TNFNSWQLEELERAFLASHYPDVF 41
TNF++W E+ E +++ YPD F
Sbjct: 346 TNFHTWIPEKEEMDWMSEKYPDTF 369
>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 = 26.9 bits (58), Expect = 4.1, Method: Composition-based stats.
Identities = 9/16 (56%), Positives = 14/16 (87%)
Query: 56 RVAVWFQNRRAKWRKK 71
++ +WFQNRR KW+K+
Sbjct: 2 QIKIWFQNRRMKWKKR 17
>pdb|1Q3T|A Chain A, Solution Structure And Function Of An Essential Cmp Kinase
Of Streptococcus Pneumoniae
Length = 236
Score = 26.6 bits (57), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 12/23 (52%), Positives = 17/23 (73%)
Query: 117 ERQQRKLAAKGVTVDLETLKREW 139
ER+ ++ AKG+ DLETLK+E
Sbjct: 168 ERRYKENIAKGIETDLETLKKEI 190
>pdb|4IZG|A Chain A, Crystal Structure Of An Enolase (mandelate Racemase
Subgroup) From Paracococus Denitrificans Pd1222 (target
Nysgrc-012907) With Bound Cis-4oh-d-proline Betaine
(product)
pdb|4IZG|B Chain B, Crystal Structure Of An Enolase (mandelate Racemase
Subgroup) From Paracococus Denitrificans Pd1222 (target
Nysgrc-012907) With Bound Cis-4oh-d-proline Betaine
(product)
Length = 391
Score = 26.6 bits (57), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 9/27 (33%), Positives = 17/27 (62%)
Query: 114 KSLERQQRKLAAKGVTVDLETLKREWE 140
+ R Q K+ + V +D+ET+++ WE
Sbjct: 178 EGFPRLQIKIGGRPVEIDIETVRKVWE 204
>pdb|4E8G|A Chain A, Crystal Structure Of An Enolase (Mandelate Racemase
Subgroup) From Paracococus Denitrificans Pd1222 (Target
Nysgrc-012907) With Bound Mg
pdb|4E8G|B Chain B, Crystal Structure Of An Enolase (Mandelate Racemase
Subgroup) From Paracococus Denitrificans Pd1222 (Target
Nysgrc-012907) With Bound Mg
Length = 391
Score = 26.6 bits (57), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 9/27 (33%), Positives = 17/27 (62%)
Query: 114 KSLERQQRKLAAKGVTVDLETLKREWE 140
+ R Q K+ + V +D+ET+++ WE
Sbjct: 178 EGFPRLQIKIGGRPVEIDIETVRKVWE 204
>pdb|1AU7|A Chain A, Pit-1 MutantDNA COMPLEX
pdb|1AU7|B Chain B, Pit-1 MutantDNA COMPLEX
Length = 146
Score = 26.6 bits (57), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 29/56 (51%), Gaps = 4/56 (7%)
Query: 12 KRRRSRTNFNSWQLEELERAFLASHYPDV--FMREALALRLDLKESRVAVWFQNRR 65
++R+ RT + + LER F P MR +A L+L++ V VWF NRR
Sbjct: 86 RKRKRRTTISIAAKDALERHFGEHSKPSSQEIMR--MAEELNLEKEVVRVWFCNRR 139
>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 = 25.8 bits (55), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 26/57 (45%), Gaps = 4/57 (7%)
Query: 24 QLEELERAFLASHYPDVFMREALALRLDLKESR--VAVWFQNRRAKWRKKEHTKKGP 78
QL LE +F + P E LR + K +R + WF RR K +E K GP
Sbjct: 18 QLRALESSFAQNPLP--LDEELDRLRSETKMTRREIDSWFSERRKKVNAEETKKSGP 72
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
0.316 0.130 0.389
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,995,782
Number of Sequences: 62578
Number of extensions: 122610
Number of successful extensions: 296
Number of sequences better than 100.0: 93
Number of HSP's better than 100.0 without gapping: 91
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 205
Number of HSP's gapped (non-prelim): 93
length of query: 149
length of database: 14,973,337
effective HSP length: 90
effective length of query: 59
effective length of database: 9,341,317
effective search space: 551137703
effective search space used: 551137703
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 47 (22.7 bits)